# cmsearch :: search CM(s) against a sequence database # INFERNAL 1.1.1 (July 2014) # Copyright (C) 2014 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query CM file: RF00174.cm # target sequence database: NC_000913.fna # CM configuration: glocal # number of worker threads: 16 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Cobalamin [CLEN=191] Accession: RF00174 Hit scores: rank E-value score bias sequence start end mdl trunc gc description ---- --------- ------ ----- ----------------------------- ------- ------- --- ----- ---- ----------- (1) ! 8.7e-16 98.2 0.0 gi|556503834|ref|NC_000913.3| 4163384 4163574 + cm no 0.54 Escherichia coli str. K-12 substr. MG1655, com ------ inclusion threshold ------ (2) ? 0.63 8.4 0.0 gi|556503834|ref|NC_000913.3| 4593356 4593565 + cm no 0.53 Escherichia coli str. K-12 substr. MG1655, com Hit alignments: >> gi|556503834|ref|NC_000913.3| Escherichia coli str. K-12 substr. MG1655, complete genome rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (1) ! 8.7e-16 98.2 0.0 cm 1 191 [] 4163384 4163574 + .. 0.98 no 0.54 v v NC :::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<< CS Cobalamin 1 uuaaauugaaacgaugauGGUuccccuuuaaagugaaggguuAAaaGGGAAcccGGUGaaAaUCCgggGCuG 72 U +A ++ + UG::GGU C : U : GUUAA AGGGAA:CC:GUG++AAUC:GG:GCUG gi|556503834|ref|NC_000913.3| 4163384 CUGUAGCAUCCACUUGCCGGU-CCUGU----------GAGUUAAUAGGGAAUCCAGUGCGAAUCUGGAGCUG 4163444 *********************.98888..........99********************************* PP v v v NC <____>>>,<<<---<<<<------<<<<<<-----......<<<-<<<<<<______>>>>>>--->>>>> CS Cobalamin 73 cCCCCgCaACuGUAAgcGgagagcaccccccAauAa......GCCACUggcccgcaagggccGGGAAGGCgg 138 C C CA+C:GUAAG:: AG+ ++:::::: + + G:CACU::C +++ G::GGGAAG:C:: gi|556503834|ref|NC_000913.3| 4163445 A-CGCGCAGCGGUAAGGAAAGGUGCGAUGAUUGCGUuaugcgGACACUGCC--AUUC--GGUGGGAAGUCAU 4163511 *.*********************************9***************..5555..************* PP v NC >>>>----------..........>>>>---->>>,,,,)))]]]]]]::::::::::::::: CS Cobalamin 139 ggggaaggaaugac..........cCgcgAGcCaGGAGACCuGCCaucaguuuuugaaucucc 191 :::: +A+U+ C ::C+AGCC:G+AGACCUGCC::C ++ U G AUCU gi|556503834|ref|NC_000913.3| 4163512 CAUCUCUUAGUAUCuuagauacccCUCCAAGCCCGAAGACCUGCCGGCCAACGUCGCAUCUGG 4163574 **********9998************************************************* PP >> gi|556503834|ref|NC_000913.3| Escherichia coli str. K-12 substr. MG1655, complete genome rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (2) ? 0.63 8.4 0.0 cm 1 191 [] 4593356 4593565 + .. 0.72 no 0.53 v v v v NC :::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<< CS Cobalamin 1 uuaaauugaaacgaugauGGUuccccuuuaaagugaaggguuAAaaGGGAAcccGGUGaaAaUCCgggGCuG 72 A AUU+A+++ :UGG :C +U ++ G G: +AA : GGAA: G C :+ G gi|556503834|ref|NC_000913.3| 4593356 GGAGAUUAAUCUUUACGUGGG-UCGUUGAUCGG---CUGACGAACCAGGAAGAUGU-------ACGCCAGUG 4593416 *********************.88877554444...5777779*********9996.......7999***** PP v v v vvvvvv vvv vvv NC <____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<_____.................... CS Cobalamin 73 cCCCCgCaACuGUAAgcGg.agagcaccccccAauAaGCCACUggcccgcaa.................... 123 CCCCCGC +C GU+A :: GCA ++ ++ A GCCA G+C G gi|556503834|ref|NC_000913.3| 4593417 CCCCCGCUGCGGUGACGCAa-CCGCAGAUGAUUAGU-GCCA---GACGG---aaugagugggugguaucaac 4593480 ***************88873.333333333333333.4544...33333...44566655444444444444 PP vvv vvvvvvvvv NC ........._>>>>>>--->>>>>>>>>----------.................................. CS Cobalamin 124 .........gggccGGGAAGGCggggggaaggaaugac.................................. 152 gi|556503834|ref|NC_000913.3| 4593481 aauaaaacc-----------------------------aguaaugaucggcgcaaaagaggcgcagaugaag 4593523 444444444.............................5666666666666666666666666777777777 PP v v v NC ..>>>>----.>>>,,,,)))]]]]]]::::::::::::::: CS Cobalamin 153 ..cCgcgAGc.CaGGAGACCuGCCaucaguuuuugaaucucc 191 :: +AG+ C GGA AC : CCA: + + + + AU gi|556503834|ref|NC_000913.3| 4593524 cuGGCAAAGUuCUGGAUACUGCCCACCGACGCAGUCAUGCGA 4593565 76788899966******************************* PP Internal CM pipeline statistics summary: ---------------------------------------- Query model(s): 1 (191 consensus positions) Target sequences: 1 (9283304 residues searched) Target sequences re-searched for truncated hits: 1 (1840 residues re-searched) Windows passing local HMM SSV filter: 7160 (0.4322); expected (0.35) Windows passing local HMM Viterbi filter: (off) Windows passing local HMM Viterbi bias filter: (off) Windows passing local HMM Forward filter: 171 (0.01188); expected (0.005) Windows passing local HMM Forward bias filter: 139 (0.0095); expected (0.005) Windows passing glocal HMM Forward filter: 76 (0.005795); expected (0.005) Windows passing glocal HMM Forward bias filter: 69 (0.005313); expected (0.005) Envelopes passing glocal HMM envelope defn filter: 70 (0.002021); expected (0.005) Envelopes passing glocal CM CYK filter: 2 (4.534e-05); expected (0.0001) Total CM hits reported: 2 (4.319e-05); includes 0 truncated hit(s) # CPU time: 11.74u 1.00s 00:00:12.74 Elapsed: 00:00:02.27 // [ok]