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# hmmscan :: search sequence(s) against a profile database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file: BA000019.orf8.fasta
# target HMM database: Pfam-A.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: BA000019.orf8 [L=348]
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
6.7e-11 41.3 0.0 1.5e-09 37.0 0.0 2.5 2 HTH_AraC Bacterial regulatory helix-turn-helix proteins, Ara
3.8e-12 38.2 11.9 5.9e-08 25.0 2.5 2.9 2 PKSI-KS_m3
0.023 13.9 0.0 0.54 9.5 0.0 2.3 2 DUF746 Domain of Unknown Function (DUF746)
Domain annotation for each model (and alignments):
>> HTH_AraC Bacterial regulatory helix-turn-helix proteins, AraC family
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 1.5 0.0 0.038 2.3e+02 10 36 .. 251 277 .. 242 278 .. 0.80
2 ! 37.0 0.0 2.6e-13 1.5e-09 8 41 .. 298 332 .. 295 333 .. 0.94
Alignments for each domain:
== domain 1 score: 1.5 bits; conditional E-value: 0.038
-HHHHHHHHTS-HHHHHHHHHHH---- CS
HTH_AraC 10 siadiAeevgfSpsyfsrlFkkytGvt 36
s+ +++++vg++ +++r F+ ++ t
BA000019.orf8 251 SLMELSRQVGLNDCTLKRGFRLVFDTT 277
66689999999999*******999877 PP
== domain 2 score: 37.0 bits; conditional E-value: 2.6e-13
.--HHHHHHHHTS.-HHHHHHHHHHH----HHHHH CS
HTH_AraC 8 nwsiadiAeevgf.SpsyfsrlFkkytGvtPsqyr 41
+++i++ A++vgf S+syf+++F+k++G++P++++
BA000019.orf8 298 EINISQAARRVGFsSRSYFATAFRKKFGINPKEFL 332
5789*****************************97 PP
>> PKSI-KS_m3
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 25.0 2.5 3.6e-09 5.9e-08 1 16 [] 538 553 .. 538 553 .. 0.99
2 ! 17.4 0.9 9e-07 1.5e-05 1 15 [. 1672 1686 .. 1672 1687 .. 0.96
Alignments for each domain:
== domain 1 score: 25.0 bits; conditional E-value: 3.6e-09
PKSI-KS_m3 1 GPSvtVDTACSSSLvA 16
GPSvtVDT CSSSLvA
AM746336.orf22 538 GPSVTVDTLCSSSLVA 553
9**************9 PP
== domain 2 score: 17.4 bits; conditional E-value: 9e-07
PKSI-KS_m3 1 GPSvtVDTACSSSLv 15
GP +++D ACSS Lv
AM746336.orf22 1672 GPNLVIDSACSSALV 1686
9*************9 PP
>> DUF746 Domain of Unknown Function (DUF746)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 9.5 0.0 9.1e-05 0.54 4 32 .. 240 268 .. 237 275 .. 0.85
2 ? 1.8 0.0 0.022 1.3e+02 13 28 .. 298 313 .. 293 319 .. 0.87
Alignments for each domain:
== domain 1 score: 9.5 bits; conditional E-value: 9.1e-05
DUF746 4 rllIrlLsqplslaeaadqlgtdegiiak 32
+ lIr L p sl+e+++q+g+ + ++
BA000019.orf8 240 EILIRNLENPPSLMELSRQVGLNDCTLKR 268
579******************98766655 PP
== domain 2 score: 1.8 bits; conditional E-value: 0.022
DUF746 13 plslaeaadqlgtdeg 28
++ + +aa+++g +++
BA000019.orf8 298 EINISQAARRVGFSSR 313
6899********9876 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (348 residues)
Target model(s): 11912 (2158902 nodes)
Passed MSV filter: 248 (0.0208193); expected 238.2 (0.02)
Passed bias filter: 220 (0.0184688); expected 238.2 (0.02)
Passed Vit filter: 19 (0.00159503); expected 11.9 (0.001)
Passed Fwd filter: 2 (0.000167898); expected 0.1 (1e-05)
Initial search space (Z): 11912 [actual number of targets]
Domain search space (domZ): 2 [number of targets reported over threshold]
# CPU time: 0.24u 0.15s 00:00:00.39 Elapsed: 00:00:00.27
# Mc/sec: 2782.58
//
Query: lcl|aorf_00010|P1 [L=132]
Description: IS481.original transposase
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
3.4e-40 130.0 0.4 3.8e-40 129.9 0.3 1.0 1 IS481.original.hmm
Domain annotation for each model (and alignments):
>> IS481.original.hmm
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 129.9 0.3 6.6e-42 3.8e-40 127 281 .. 7 130 .. 2 132 .] 0.97
Alignments for each domain:
== domain 1 score: 129.9 bits; conditional E-value: 6.6e-42
IS481.original.hmm 127 kRYErdhPgeLvhmDvkklgripdgGgvkighRwrgrtrgrgkrtnqsrnrglgkayvitaiDDhSRfayaeilsd 202
+++E++hP +L+++D++++g+i + G+ +y++t++D++S+ ++++++
lcl|aorf_00010|P1 7 GEIETAHPSYLGSQDTFYVGNITGAGR----------------------------IYQQTFVDTYSKWDSTKLYTT 54
579*******************88888............................********************* PP
IS481.original.hmm 203 ettttaadfllraaayfygkigeeiitrvlTDnGaayrskkrsakhdFqealaelGIkhilTrprsPqTNGKiERF 278
+t++taad l++ ++ f+ ++++i r lTD+ ++y+sk ++ d+ +la ++I+h++T++++PqTN ++ RF
lcl|aorf_00010|P1 55 KTPITAADLLNDRVLSFFA-EQGMGIIRLLTDRSTEYCSKA--ETQDYELCLALNDIEHTKTKVYHPQTNDICRRF 127
*******************.********************8..********************************* PP
IS481.original.hmm 279 hrT 281
h+
lcl|aorf_00010|P1 128 HKA 130
*95 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (132 residues)
Target model(s): 116 (57162 nodes)
Passed MSV filter: 4 (0.0344828); expected 2.3 (0.02)
Passed bias filter: 4 (0.0344828); expected 2.3 (0.02)
Passed Vit filter: 3 (0.0258621); expected 0.1 (0.001)
Passed Fwd filter: 1 (0.0172414); expected 0.0 (1e-05)
Initial search space (Z): 116 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.06u 0.00s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 117.90
//
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