# 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
//
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