{
"cells": [
{
"cell_type": "code",
"execution_count": 32,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"import nglview\n",
"import rna_pdb_tools.Seq as Seq\n",
"import rna_pdb_tools.BlastPDB\n",
"from rna_pdb_tools.BlastPDB import BlastPDB\n",
"reload(rna_pdb_tools.BlastPDB);\n",
"reload(Seq);\n"
]
},
{
"cell_type": "code",
"execution_count": 49,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"seq = Seq.Seq(\"GGGGCGCGGCGCUCAUUCCUGCGCAAGCAGGGCAAGGCCCAGUCCCGUGCAAGCCGGGACCGCCCC\")"
]
},
{
"cell_type": "code",
"execution_count": 50,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"GGGGCGCGGCGCUCAUUCCUGCGCAAGCAGGGCAAGGCCCAGUCCCGUGCAAGCCGGGACCGCCCC"
]
},
"execution_count": 50,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"seq"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Secondary structure prediction"
]
},
{
"cell_type": "code",
"execution_count": 51,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"((((((.((.(((...((((((....))))))...))))).((((((.......))))))))))))\n"
]
}
],
"source": [
"print seq.predict_ss()"
]
},
{
"cell_type": "code",
"execution_count": 52,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"GGGGCGCGGCGCUCAUUCCUGCGCAAGCAGGGCAAGGCCCAGUCCCGUGCAAGCCGGGACCGCCCC -3490 100\n",
"(((((((.((((........))))..)).((((...)))).((((((.......)))))).))))) -34.40\n",
"(((((((.((((........))))..)).((((...)))).((((((.(....))))))).))))) -34.40\n",
"((((((.((.(((...((((((....))))))...))))).(((((((....)).))))))))))) -33.90\n",
"((((((.((.(((...((((((....))))))...))))).((((((.......)))))))))))) -34.90\n",
"((((((.((.(((...((((((....))))))...))))).((((((.(....))))))))))))) -34.90\n",
"((((((.((.(((...((((((....))))))...))))).(((((((....).)))))))))))) -33.90\n",
"((((((.(((.((...((((((....))))))..)))))..((((((.......)))))))))))) -33.90\n",
"((((((.(((.((...((((((....))))))..)))))..((((((.(....))))))))))))) -33.90\n"
]
}
],
"source": [
"print seq.predict_ss(method='RNAsubopt')"
]
},
{
"cell_type": "code",
"execution_count": 53,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"((((((.((.(((...((((((....))))))...))))).((((((.......))))))))))))\n"
]
}
],
"source": [
"print seq.predict_ss(method='ipknot')"
]
},
{
"cell_type": "code",
"execution_count": 54,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"((((((.((.(((...((((((....))))))...))))).((((((.......)))))))))))) (g=1,th=0.5,e=-27.53)\n"
]
}
],
"source": [
"print seq.predict_ss(method='centroid_fold')"
]
},
{
"cell_type": "code",
"execution_count": 55,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"((((((....(((...((((((....))))))...)))...((((((.......))))))))))))\n",
"\n"
]
}
],
"source": [
"print seq.predict_ss(method='contextfold')"
]
},
{
"cell_type": "code",
"execution_count": 48,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"GCAGGGCAAGGCCCAGUCCCGUGCAAGCCGGGACCGCCCCGCAAGGGGCGCGGCGCUCAUUCCUGC\n",
"# cmscan :: search sequence(s) against a CM database\n",
"# INFERNAL 1.1.2 (July 2016)\n",
"# Copyright (C) 2016 Howard Hughes Medical Institute.\n",
"# Freely distributed under a BSD open source license.\n",
"# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n",
"# query sequence file: /tmp/ss.fa\n",
"# target CM database: Rfam.cm\n",
"# sequence reporting threshold: E-value <= 1\n",
"# number of worker threads: 4\n",
"# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n",
"\n",
"Query: test [L=65]\n",
"Hit scores:\n",
" rank E-value score bias modelname start end mdl trunc gc description\n",
" ---- --------- ------ ----- --------- ------ ------ --- ----- ---- -----------\n",
"\n",
" [No hits detected that satisfy reporting thresholds]\n",
"\n",
"\n",
"Hit alignments:\n",
"\n",
" [No hits detected that satisfy reporting thresholds]\n",
"\n",
"\n",
"Internal HMM-only pipeline statistics summary: (run for model(s) with zero basepairs)\n",
"--------------------------------------------------------------------------------------\n",
"Query sequence(s): 1 (130 residues searched)\n",
"Target model(s): 347 (40911 consensus positions)\n",
"Windows passing local HMM SSV filter: 5 (0.007205); expected (0.02)\n",
"Windows passing local HMM MSV bias filter: 3 (0.004323); expected (0.02)\n",
"Windows passing local HMM Viterbi filter: 0 (0); expected (0.001)\n",
"Windows passing local HMM Forward filter: 0 (0); expected (1e-05)\n",
"Total HMM hits reported: 0 (0)\n",
"\n",
"Internal CM pipeline statistics summary:\n",
"----------------------------------------\n",
"Query sequence(s): 1 (130 residues searched)\n",
"Query sequences re-searched for truncated hits: 1 (378.5 residues re-searched, avg per model)\n",
"Target model(s): 2126 (267652 consensus positions)\n",
"Windows passing local HMM SSV filter: 1136 (0.06392); expected (0.35)\n",
"Windows passing local HMM Viterbi filter: (off)\n",
"Windows passing local HMM Viterbi bias filter: (off)\n",
"Windows passing local HMM Forward filter: 570 (0.0328); expected (0.02)\n",
"Windows passing local HMM Forward bias filter: 451 (0.02601); expected (0.02)\n",
"Windows passing glocal HMM Forward filter: 138 (0.008112); expected (0.02)\n",
"Windows passing glocal HMM Forward bias filter: 122 (0.00715); expected (0.02)\n",
"Envelopes passing glocal HMM envelope defn filter: 118 (0.006324); expected (0.02)\n",
"Envelopes passing local CM CYK filter: 17 (0.0006004); expected (0.0001)\n",
"Total CM hits reported: 0 (0); includes 0 truncated hit(s)\n",
"\n",
"Total CM and HMM hits reported: 0\n",
"\n",
"# CPU time: 4.46u 0.47s 00:00:04.93 Elapsed: 00:00:02.36\n",
"//\n",
"[ok]\n",
"\n"
]
}
],
"source": [
"import rna_pdb_tools.RfamSearch as rf\n",
"#reload(rf)\n",
"\n",
"#seq = Seq.Seq(\"GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG\")\n",
"rs = rf.RfamSearch()\n",
"print rs.cmscan(seq)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# PDB Blast search"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"BLAST Search Results\n",
"\n",
"\n",
"BLASTN 2.2.18 [Mar-02-2008]\n",
"\n",
"\n",
"Reference:\n",
"Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, \n",
"Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), \n",
"\"Gapped BLAST and PSI-BLAST: a new generation of protein database search\n",
"programs\", Nucleic Acids Res. 25:3389-3402.\n",
"\n",
"Query= UNKNOWN_SEQUENCE\n",
" (65 letters)\n",
"\n",
"Database: pdb_nucleotide \n",
" 15,787 sequences; 2,694,141 total letters\n",
"\n",
"Searching..................................................done\n",
"\n",
"\n",
"\n",
"\n",
" Score E\n",
"Sequences producing significant alignments: (bits) Value\n",
"\n",
"5J8B:1:A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5J4D:2:B,GB|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5J4C:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5J4B:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5J3C:1:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5J30:1:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5IMR:23:D|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5IMQ:7:D|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5IBB:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5IB8:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5IB7:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5HD1:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5HCR:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5HCQ:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5HCP:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5HAU:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5FDV:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5FDU:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5F8K:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5EL7:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5EL6:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5EL5:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5EL4:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5E81:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5E7K:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5DOY:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5DOX:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5DFE:4:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5D8B:51:VC,ZC|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5CZP:1:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5AA0:1:AA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"5A9Z:1:AA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4ZSN:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4ZER:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4Z8C:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4Z3S:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4YZV:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4YPB:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4Y4P:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4Y4O:1:1A,2A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4XEJ:51:A23S,B23S|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WZO:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WZD:24:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WU1:24:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WT1:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WSM:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WSD:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WRO:5:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WRA:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WR6:25:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WQY:1:AA,CA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WQU:1:AA,CA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WQR:26:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WQF:1:AA,CA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WQ1:25:14,1H|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4WPO:1:AA,CA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4W4G:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4W2I:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4W2H:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4W2G:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4W2F:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4W2E:1:A|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4W29:59:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9S:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9R:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9Q:1:AA,CA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9N:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9M:58:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9L:59:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9K:59:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9J:60:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9I:26:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9H:25:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9B:24:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V9A:24:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V97:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V95:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V90:35:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8X:36:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8U:36:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8Q:11:AA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8O:35:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8N:35:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8J:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8I:23:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8H:23:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8G:23:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8F:1:AA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8E:1:AA,CA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8D:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8C:1:AA,BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8B:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V8A:1:AA,BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V87:1:AA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V84:23:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V83:23:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V7P:25:BA,CA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V7M:27:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V7L:27:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V7K:57:AA,BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V7J:57:AA,BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V6G:24:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V6F:1:AA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V6F:55:DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V6A:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V67:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V63:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5S:36:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5R:36:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5Q:36:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5P:36:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5N:35:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5M:35:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5L:36:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5K:35:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5J:35:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5G:36:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5F:35:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V5E:35:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4Z:25:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4Y:24:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4X:24:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4T:26:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4S:27:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4R:27:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4P:2:AA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4J:1:w|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V4I:1:w|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4V42:25:BA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4TUE:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4TUD:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4TUC:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4TUB:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4TUA:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4P70:22:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4P6F:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4LT8:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4LSK:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4LNT:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4LFZ:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4LEL:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4L71:22:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"4L47:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"1VY7:26:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"1VY6:25:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"1VY5:26:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"1VY4:26:BA,DA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"1VVJ:25:RA,YA|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"1ML5:4:a|pdbid|entity|chain(s)|sequence 24 6.2 \n",
"\n",
"\n",
">5J8B:1:A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5J4D:2:B,GB|pdbid|entity|chain(s)|sequence\n",
" Length = 2880\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 561 gccccgcaaggg 572\n",
"\n",
"\n",
"\n",
"\n",
">5J4C:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5J4B:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5J3C:1:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5J30:1:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5IMR:23:D|pdbid|entity|chain(s)|sequence\n",
" Length = 2893\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">5IMQ:7:D|pdbid|entity|chain(s)|sequence\n",
" Length = 2893\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">5IBB:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5IB8:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5IB7:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5HD1:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5HCR:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5HCQ:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5HCP:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5HAU:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5FDV:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5FDU:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5F8K:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5EL7:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5EL6:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5EL5:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5EL4:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5E81:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5E7K:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">5DOY:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5DOX:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5DFE:4:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5D8B:51:VC,ZC|pdbid|entity|chain(s)|sequence\n",
" Length = 2893\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">5CZP:1:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">5AA0:1:AA|pdbid|entity|chain(s)|sequence\n",
" Length = 2889\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">5A9Z:1:AA|pdbid|entity|chain(s)|sequence\n",
" Length = 2889\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4ZSN:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4ZER:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4Z8C:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4Z3S:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4YZV:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4YPB:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4Y4P:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4Y4O:1:1A,2A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4XEJ:51:A23S,B23S|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4WZO:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WZD:24:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WU1:24:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WT1:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WSM:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WSD:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WRO:5:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WRA:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2918\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 566 gccccgcaaggg 577\n",
"\n",
"\n",
"\n",
"\n",
">4WR6:25:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WQY:1:AA,CA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4WQU:1:AA,CA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4WQR:26:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2917\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WQF:1:AA,CA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4WQ1:25:14,1H|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4WPO:1:AA,CA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4W4G:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4W2I:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4W2H:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4W2G:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4W2F:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4W2E:1:A|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4W29:59:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V9S:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V9R:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V9Q:1:AA,CA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V9N:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V9M:58:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V9L:59:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V9K:59:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V9J:60:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V9I:26:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V9H:25:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V9B:24:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V9A:24:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V97:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V95:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V90:35:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V8X:36:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2848\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 558 gccccgcaaggg 569\n",
"\n",
"\n",
"\n",
"\n",
">4V8U:36:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V8Q:11:AA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V8O:35:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V8N:35:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V8J:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V8I:23:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V8H:23:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2913\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 561 gccccgcaaggg 572\n",
"\n",
"\n",
"\n",
"\n",
">4V8G:23:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V8F:1:AA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V8E:1:AA,CA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V8D:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V8C:1:AA,BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V8B:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V8A:1:AA,BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V87:1:AA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V84:23:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V83:23:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V7P:25:BA,CA|pdbid|entity|chain(s)|sequence\n",
" Length = 2879\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V7M:27:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V7L:27:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V7K:57:AA,BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2848\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 558 gccccgcaaggg 569\n",
"\n",
"\n",
"\n",
"\n",
">4V7J:57:AA,BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2848\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 558 gccccgcaaggg 569\n",
"\n",
"\n",
"\n",
"\n",
">4V6G:24:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2898\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 560 gccccgcaaggg 571\n",
"\n",
"\n",
"\n",
"\n",
">4V6F:1:AA|pdbid|entity|chain(s)|sequence\n",
" Length = 2909\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 562 gccccgcaaggg 573\n",
"\n",
"\n",
"\n",
"\n",
">4V6F:55:DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2912\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V6A:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4V67:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2894\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V63:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2894\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V5S:36:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5R:36:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5Q:36:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5P:36:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5N:35:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5M:35:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5L:36:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5K:35:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2848\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 558 gccccgcaaggg 569\n",
"\n",
"\n",
"\n",
"\n",
">4V5J:35:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5G:36:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5F:35:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4V5E:35:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2901\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 558 gccccgcaaggg 569\n",
"\n",
"\n",
"\n",
"\n",
">4V4Z:25:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V4Y:24:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V4X:24:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V4T:26:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V4S:27:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V4R:27:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V4P:2:AA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V4J:1:w|pdbid|entity|chain(s)|sequence\n",
" Length = 2889\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V4I:1:w|pdbid|entity|chain(s)|sequence\n",
" Length = 2889\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4V42:25:BA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
">4TUE:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4TUD:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4TUC:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4TUB:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4TUA:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4P70:22:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4P6F:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">4LT8:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4LSK:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4LNT:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4LFZ:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4LEL:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4L71:22:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">4L47:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">1VY7:26:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">1VY6:25:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">1VY5:26:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">1VY4:26:BA,DA|pdbid|entity|chain(s)|sequence\n",
" Length = 2915\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 563 gccccgcaaggg 574\n",
"\n",
"\n",
"\n",
"\n",
">1VVJ:25:RA,YA|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 564 gccccgcaaggg 575\n",
"\n",
"\n",
"\n",
"\n",
">1ML5:4:a|pdbid|entity|chain(s)|sequence\n",
" Length = 2916\n",
"\n",
" Score = 24.3 bits (12), Expect = 6.2\n",
" Identities = 12/12 (100%)\n",
" Strand = Plus / Plus\n",
"\n",
" \n",
"Query: 36 gccccgcaaggg 47\n",
" ||||||||||||\n",
"Sbjct: 565 gccccgcaaggg 576\n",
"\n",
"\n",
"\n",
"\n",
" Database: pdb_nucleotide\n",
" Posted date: Oct 30, 2016 3:26 AM\n",
" Number of letters in database: 2,694,141\n",
" Number of sequences in database: 15,787\n",
" \n",
"Lambda K H\n",
" 1.37 0.711 1.31 \n",
"\n",
"Gapped\n",
"Lambda K H\n",
" 1.37 0.711 1.31 \n",
"\n",
"\n",
"Matrix: blastn matrix:1 -3\n",
"Gap Penalties: Existence: 5, Extension: 2\n",
"Number of Sequences: 15787\n",
"Number of Hits to DB: 2101\n",
"Number of extensions: 158\n",
"Number of successful extensions: 158\n",
"Number of sequences better than 10.0: 149\n",
"Number of HSP's gapped: 158\n",
"Number of HSP's successfully gapped: 149\n",
"Length of query: 65\n",
"Length of database: 2,694,141\n",
"Length adjustment: 14\n",
"Effective length of query: 51\n",
"Effective length of database: 2,473,123\n",
"Effective search space: 126129273\n",
"Effective search space used: 126129273\n",
"X1: 10 (19.8 bits)\n",
"X2: 15 (29.7 bits)\n",
"X3: 50 (99.1 bits)\n",
"S1: 10 (20.3 bits)\n",
"S2: 12 (24.3 bits)\n",
"\n",
"\n",
"\n"
]
}
],
"source": [
"p = BlastPDB(seq.seq)\n",
"p.search()\n",
"print p.result"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# 3D structure analysis"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"from rna_pdb_tools.pdb_parser_lib import RNAStructure\n",
"\n",
"fn = \"rna_pdb_tools/data/260c8ff6-f24e-4eff-9760-1831407fc770_ALL_thrs5.30A_clust01-000001_AA.pdb\"\n",
"\n",
"s = RNAStructure(fn)\n",
"print s.get_report()\n",
"print s.get_info_chains()\n",
"print s.get_head()\n",
"#print s.view() # image paste here :-)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"%%bash\n",
"cd rna_pdb_tools\n",
"./rna-pdb-tools.py --no_hr --get_seq data/260c8ff6-f24e-4eff-9760-1831407fc770_ALL_thrs5.30A_clust01-000001_AA.pdb"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# RNA 3D structure prediction"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# model using SimRNA\n",
"#res = SimRNA(ss,seq.get_ss())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"# fake import, should be \n",
"res = \"rna_pdb_tools/data/260c8ff6-f24e-4eff-9760-1831407fc770_ALL_thrs5.30A_clust01-000001_AA.pdb\"\n",
"# view\n",
"view = nglview.show_structure_file(res)\n",
"view.add_representation(repr_type='cartoon')\n",
"view"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# rna_pdb_tools --get_seq"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"%%bash\n",
"cd rna_pdb_tools\n",
"./rna-pdb-tools.py --no_hr --get_seq input/5k7c.pdb"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"%%bash\n",
"cd rna_pdb_tools\n",
"./rna-pdb-tools.py --no_hr --get_seq input/5k7c.pdb\n",
"./rna-pdb-tools.py --no_hr --get_seq input/tetraloop.pdb\n",
"./rna-pdb-tools.py --get_seq input/1xjr.pdb"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.12"
}
},
"nbformat": 4,
"nbformat_minor": 0
}