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# 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: multimodel.c.cm
# target sequence database: multiseqs.fa
# number of worker threads: 4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tRNA5 [CLEN=72]
Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- -------------- ------ ------ --- ----- ---- -----------
(1) ! 2.9e-21 71.5 0.0 mrum-tRNA.1 1 72 + cm no 0.50 -
(2) ! 2e-20 68.8 0.0 mrum-tRNA.2 1 73 + cm no 0.67 -
(3) ! 6.1e-19 64.1 0.0 mrum-tRNA.3 1 74 + cm no 0.59 -
(4) ! 2e-18 62.5 0.0 mrum-tRNA.4 1 75 + cm no 0.61 -
(5) ! 2.1e-18 62.4 0.0 AAGA01015927.1 229 302 + cm no 0.62 Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
(6) ! 3.6e-18 61.7 0.0 mrum-tRNA.5 1 74 + cm no 0.53 -
(7) ! 2.2e-17 59.2 0.0 mrum-tRNA.6 1 73 + cm no 0.51 -
(8) ! 2.2e-17 59.2 0.0 mrum-tRNA.7 1 75 + cm no 0.60 -
(9) ! 2.4e-17 59.1 0.0 mrum-tRNA.8 1 74 + cm no 0.59 -
(10) ! 2.7e-17 58.9 0.0 mrum-tRNA.9 1 110 + cm no 0.61 -
(11) ! 8.7e-17 57.3 0.0 mrum-tRNA.10 1 72 + cm no 0.42 -
(12) ! 1.4e-15 53.5 0.0 AAGA01015927.1 314 386 + cm no 0.59 Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
Hit alignments:
>> mrum-tRNA.1
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 2.9e-21 71.5 0.0 cm 1 72 [] 1 72 + [] 1.00 no 0.50
v v v v NC
(((((((,,<<<<_______>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgUGGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
G: G::AUAGC:CA+UGG AG:GCG:::G:CUG+CA :C:::AGGU : GGGUUCGAUUCCC :U::C :CA
mrum-tRNA.1 1 GGAGCUAUAGCUCAAUGGCAGAGCGUUUGGCUGACAUCCAAAAGGUUAUGGGUUCGAUUCCCUUUAGCCCCA 72
************************************************************************ PP
>> mrum-tRNA.2
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ! 2e-20 68.8 0.0 cm 1 72 [] 1 73 + [] 1.00 no 0.67
NC
(((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
G::::C UAGC:CAGU GG AG:GCGC:::CCU+ CAAG:::GAGG CC:GGGUUC A UCCC:G G::::CA
mrum-tRNA.2 1 GGGCCCGUAGCUCAGUuGGGAGAGCGCUGCCCUUGCAAGGCAGAGGCCCCGGGUUCAAAUCCCGGUGGGUCCA 73
************************************************************************* PP
>> mrum-tRNA.3
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(3) ! 6.1e-19 64.1 0.0 cm 1 72 [] 1 74 + [] 1.00 no 0.59
NC
(((((((,,<<<<___..____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU..GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
G::::CAUAGC::AG GGUA::GCGC :G:CU + AA:C: GA GUC::GGGUUCGA UCCC::UG::::CA
mrum-tRNA.3 1 GGGCCCAUAGCUUAGCcaGGUAGAGCGCUCGGCUCAUAACCGGGAUGUCAUGGGUUCGAAUCCCAUUGGGCCCA 74
************************************************************************** PP
>> mrum-tRNA.4
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(4) ! 2e-18 62.5 0.0 cm 1 72 [] 1 75 + [] 1.00 no 0.61
v v NC
(((((((,,<<<<___..___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU..GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
:::::::U+GC CAG GGU AG GCGC::G:CUG+ AA:C::GAGGUCC:GGGUUCGA UCCC:G:::::::A
mrum-tRNA.4 1 AGGCUAGUGGCACAGCcuGGUcAGCGCGCACGGCUGAUAACCGUGAGGUCCUGGGUUCGAAUCCCAGCUAGCCUA 75
***************999********************************************************* PP
>> AAGA01015927.1 Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(5) ! 2.1e-18 62.4 0.0 cm 1 72 [] 229 302 + .. 1.00 no 0.62
NC
(((((((,,<<<<___.___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
G::::::UA:::CAGU GGU AG:::+CC:GCCUGUCA+GC:GG GGU :GGGUUCGA UCCC: ::::::C+
AAGA01015927.1 229 GGAGCGGUAGUUCAGUcGGUuAGAAUACCUGCCUGUCACGCAGGGGGUUGCGGGUUCGAGUCCCGUCCGUUCCG 302
************************************************************************** PP
>> mrum-tRNA.5
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(6) ! 3.6e-18 61.7 0.0 cm 1 72 [] 1 74 + [] 1.00 no 0.53
NC
(((((((,,<<<<___..____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU..GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
:CCG:C:UAGC:CA+U GG AG:GCG:::G:CUGU++A:C:::A GU :::GGUUC A UCC::::G:CGG:A
mrum-tRNA.5 1 CCCGACUUAGCUCAAUuuGGCAGAGCGUUGGACUGUAGAUCCAAAUGUUGCUGGUUCAAGUCCGGCAGUCGGGA 74
************************************************************************** PP
>> mrum-tRNA.6
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(7) ! 2.2e-17 59.2 0.0 cm 1 72 [] 1 73 + [] 1.00 no 0.51
NC
(((((((,,<<<<___.___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
GC::::AU+G G:A+U GG A:C C+:C:G:CU+UC+A:C:G: + C:GGGUUC A UCCC:GU::::GCA
mrum-tRNA.6 1 GCUUCUAUGGGGUAAUcGGCaAACCCAUCGGACUUUCGAUCCGAUAA-UCCGGGUUCAAAUCCCGGUAGAAGCA 73
***********************************************.9************************* PP
>> mrum-tRNA.7
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(8) ! 2.2e-17 59.2 0.0 cm 1 72 [] 1 75 + [] 0.99 no 0.60
NC
(((((((,,<<<<___..___.._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU..GGu..AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
GC::::AU+::G:AGU GG A:C:: :C:GCCU+UC+AGC:G:AG+ C :GGGUUCGA UCCC: U::::GCA
mrum-tRNA.7 1 GCUCCGAUGGUGUAGUccGGCcaAUCAUUUCGGCCUUUCGAGCCGAAGA-CUCGGGUUCGAAUCCCGGUCGGAGCA 75
********************9999*************************.************************** PP
>> mrum-tRNA.8
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(9) ! 2.4e-17 59.1 0.0 cm 1 72 [] 1 74 + [] 1.00 no 0.59
v v NC
(((((((,,<<<<___..___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU..GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
GC:G:::UAG:: AG GGU A ::C C:A:CCUG CA+G:U:GAG+ CC:GGGUUC A UCCC:G:::C:GCA
mrum-tRNA.8 1 GCGGUGUUAGUCCAGCcuGGUuAAGACUCUAGCCUGCCACGUUAGAGA-CCCGGGUUCAAAUCCCGGACGCCGCA 74
***************999******************************.************************** PP
>> mrum-tRNA.9
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(10) ! 2.7e-17 58.9 0.0 cm 1 72 [] 1 110 + [] 0.98 no 0.61
NC
(((((((,,<<<<___.___._>>>>,<<<<<___~~~~~~>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUg*[ 4]*gcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
GCCGG::U+GC:CAG GGU AG:GCGC::G:CU :C::GAG+UC::GGGUUCGA UCCC::::CCGGCA
mrum-tRNA.9 1 GCCGGGGUGGCUCAGCuGGUuAGAGCGCACGGCUC*[40]*CCGUGAGAUCGCGGGUUCGAAUCCCGCCCCCGGCA 110
********************************995...*..*********************************** PP
>> mrum-tRNA.10
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(11) ! 8.7e-17 57.3 0.0 cm 1 72 [] 1 72 + [] 1.00 no 0.42
v v NC
(((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
G:::::AUAG:::A+ GGUA:::C+ C G:CUGU AA:C G AG+ :G :GUUCGA UC: C:U:::::C+
mrum-tRNA.10 1 GGUUCUAUAGUUUAACaGGUAAAACAACUGGCUGUUAACCGGCAGA-UAGGAGUUCGAAUCUUCUUAGAACCG 72
**********************************************.9************************* PP
>> AAGA01015927.1 Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(12) ! 1.4e-15 53.5 0.0 cm 1 72 [] 314 386 + .. 1.00 no 0.59
NC
(((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
tRNA5 1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
:::GGC:UAG :CA+U GGUAG: C+CC:G:CU +AA:C:GG GU : G:GUUCGA UC:C ::GCC:::+
AAGA01015927.1 314 AGGGGCGUAGUUCAAUuGGUAGAGCACCGGUCUCCAAAACCGGGUGUUGGGAGUUCGAGUCUCUCCGCCCCUG 386
************************************************************************* PP
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (72 consensus positions)
Target sequences: 13 (12958 residues searched)
Target sequences re-searched for truncated hits: 13 (5412 residues re-searched)
Windows passing local HMM SSV filter: 81 (0.3848); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 50 (0.2035); expected (0.02)
Windows passing local HMM Forward bias filter: 48 (0.195); expected (0.02)
Windows passing glocal HMM Forward filter: 42 (0.1794); expected (0.02)
Windows passing glocal HMM Forward bias filter: 42 (0.1794); expected (0.02)
Envelopes passing glocal HMM envelope defn filter: 43 (0.1724); expected (0.02)
Envelopes passing local CM CYK filter: 40 (0.1612); expected (0.0001)
Total CM hits reported: 12 (0.05003); includes 0 truncated hit(s)
# CPU time: 0.42u 0.01s 00:00:00.43 Elapsed: 00:00:00.44
//
Query: Cobalamin [CLEN=191]
Accession: RF00174
Description: Cobalamin riboswitch
Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- -------------- ------ ------ --- ----- ---- -----------
(1) ! 1.4e-08 30.0 0.0 AAFY01022046.1 934 832 - cm 5' 0.48 Metagenome sequence AGZO15064.g2, whole genome shotgun sequence
Hit alignments:
>> AAFY01022046.1 Metagenome sequence AGZO15064.g2, whole genome shotgun sequence
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 1.4e-08 30.0 0.0 cm 32 191 ~] 934 832 - ~. 0.92 5' 0.48
??? v v v v ???? NC
~~~~~~______>>>,,,,,(((,,,<.<<<<_______>>>>>,,<<<____>>>,<<<---<<<<~~~~~~>>>>---->>>,,,,)))]]]] CS
Cobalamin 1 <[31]*agugaaggguuAAaaGGGAAc.ccGGUGaaAaUCCgggGCuGcCCCCgCaACuGUAAgcGg*[61]*cCgcgAGcCaGGAGACCuGCCa 174
+G+ + AA: GGAA: : GGUG AAAUCC ::+C:G CCC C:ACUGUAA:C: :G:+AG+CAG A AC : C
AAFY01022046.1 934 <[ 0]*GUAGGCAAAAGGAAGAGGAAGgAUGGUGGAAAUCCUUCACGGGCCCGGCCACUGUAACCAG*[ 4]*UUGGAAGUCAG-AUACUCUUCU 849
......44455566666899******989************************************97...7..79*********.9********* PP
?? NC
]]::::::::::::::: CS
Cobalamin 175 ucaguuuuugaaucucc 191
++++ GAA+CU C
AAFY01022046.1 848 AUUAAGGCGGAAACUAC 832
***************** PP
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (191 consensus positions)
Target sequences: 13 (12958 residues searched)
Target sequences re-searched for truncated hits: 13 (10152 residues re-searched)
Windows passing local HMM SSV filter: 10 (0.207); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 2 (0.03116); expected (0.02)
Windows passing local HMM Forward bias filter: 2 (0.03116); expected (0.02)
Windows passing glocal HMM Forward filter: 1 (0.01558); expected (0.02)
Windows passing glocal HMM Forward bias filter: 1 (0.01558); expected (0.02)
Envelopes passing glocal HMM envelope defn filter: 1 (0.008784); expected (0.02)
Envelopes passing local CM CYK filter: 1 (0.005712); expected (0.0001)
Total CM hits reported: 1 (0.008914); includes 1 truncated hit(s)
# CPU time: 0.16u 0.01s 00:00:00.17 Elapsed: 00:00:00.17
//
[ok]
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