# hmmsearch :: search profile(s) against a sequence 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 HMM file: Pfam-A.hmm
# target sequence database: test_seqs.seq_raw.txt
# output directed to file: hmmsearch.output.txt
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: 1-cysPrx_C [M=40]
Accession: PF10417.4
Description: C-terminal domain of 1-Cys peroxiredoxin
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
[No hits detected that satisfy reporting thresholds]
Domain annotation for each sequence (and alignments):
[No targets detected that satisfy reporting thresholds]
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (40 nodes)
Target sequences: 3 (2141 residues)
Passed MSV filter: 0 (0); expected 0.1 (0.02)
Passed bias filter: 0 (0); expected 0.1 (0.02)
Passed Vit filter: 0 (0); expected 0.0 (0.001)
Passed Fwd filter: 0 (0); expected 0.0 (1e-05)
Initial search space (Z): 3 [actual number of targets]
Domain search space (domZ): 0 [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 14.27
//
Query: DUF4229 [M=69]
Accession: PF14012.1
Description: Protein of unknown function (DUF4229)
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
------ inclusion threshold ------
3 -17.8 37.0 0.019 3.0 2.5 4.3 5 lcl|Protein_ID1.3|M3 complement(48376..51420)
Domain annotation for each sequence (and alignments):
>> lcl|Protein_ID1.3|M3 complement(48376..51420)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -4.3 1.7 1 3 34 40 .. 305 311 .. 277 337 .. 0.55
2 ? 2.6 2.1 0.0084 0.025 12 50 .. 382 418 .. 374 422 .. 0.69
3 ? -1.1 0.6 0.12 0.36 4 36 .. 841 874 .. 841 882 .. 0.52
4 ? 3.0 2.5 0.0064 0.019 7 59 .. 872 925 .. 870 929 .. 0.90
5 ? -0.7 0.9 0.087 0.26 31 50 .. 972 991 .. 937 1001 .. 0.56
Alignments for each domain:
== domain 1 score: -4.3 bits; conditional E-value: 1
DUF4229 34 laallAl 40
la+l A+
lcl|Protein_ID1.3|M3 305 LAILSAI 311
3333332 PP
== domain 2 score: 2.6 bits; conditional E-value: 0.0084
DUF4229 12 fvvllavlvllgvligllvplllaallAlvvalplSfll 50
+ v ++ l gv l +p+ a++++++ +++lS +
lcl|Protein_ID1.3|M3 382 VFVPMF--SLTGVPRYLFIPMAEAVIFGMLSSFVLSQTF 418
333333..34455555449*****************776 PP
== domain 3 score: -1.1 bits; conditional E-value: 0.12
DUF4229 4 YtalRlglfvvllav..lvllgvligllvplllaa 36
Y +l lgl++ + ++ lv+++ + +l+ p++++
lcl|Protein_ID1.3|M3 841 YRGLSLGLVASIILIyfLVVVNFESWLD-PFVIIT 874
5566688888777774344444444444.554443 PP
== domain 4 score: 3.0 bits; conditional E-value: 0.0064
DUF4229 7 lRlglfvvllavlvllgvligll.vplllaallAlvvalplSflllrklRrrat 59
+ +l ++l++++++l + + l vp l a++ + va + S+l+ + R+r++
lcl|Protein_ID1.3|M3 872 IITALPAALAGIVWMLYLTGTTLsVPALTGAIMCMGVATANSILVISFARERLA 925
56789999******9999999889*********************999999875 PP
== domain 5 score: -0.7 bits; conditional E-value: 0.087
DUF4229 31 plllaallAlvvalplSfll 50
pl a++ +l++a + +++
lcl|Protein_ID1.3|M3 972 PLGRAVIGGLLLATIATLIF 991
55555555555554444333 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (69 nodes)
Target sequences: 3 (2141 residues)
Passed MSV filter: 1 (0.333333); expected 0.1 (0.02)
Passed bias filter: 1 (0.333333); expected 0.1 (0.02)
Passed Vit filter: 1 (0.333333); expected 0.0 (0.001)
Passed Fwd filter: 1 (0.333333); expected 0.0 (1e-05)
Initial search space (Z): 3 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.41
//
Query: ACR_tran [M=1021]
Accession: PF00873.14
Description: AcrB/AcrD/AcrF family
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
9.3e-189 616.9 10.5 1.2e-188 616.6 7.2 1.0 1 lcl|Protein_ID1.3|M3 complement(48376..51420)
Domain annotation for each sequence (and alignments):
>> lcl|Protein_ID1.3|M3 complement(48376..51420)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 616.6 7.2 3.9e-189 1.2e-188 71 1021 .] 11 1000 .. 2 1000 .. 0.93
Alignments for each domain:
== domain 1 score: 616.6 bits; conditional E-value: 3.9e-189
S-TTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHHHHHHHHHGGGS-HHHHHH-EEEEEEECCECEEEEEEESSSTS-HHHHHHHH CS
ACR_tran 71 gldglkyvsSqSseglssitvtFedgtdidiArqqvqnrlqeaknkLPeevqepgiskiktssseilvlavtskdgsltktdlrdla 157
++ +++++SqS g + + F+ + di A+ qv++ q + +++P ++++p i +++ +il+la++sk l++ + dl
lcl|Protein_ID1.3|M3 11 TVNDIEHIESQSLFGYGIVKIFFQPDVDIRTANAQVTAISQTVLKQMPPGITPPLILNYNAATVPILQLALSSK--VLSEDRIFDLG 95
578899********************************************************************..*********** PP
HHCTHHHHHTSTTEEEEEESS.--EEEEEEE-HHHHHCTT--HHHHHHHHHHHSSB-EEEECTT-SB-EEEE-SB---SCCHHCT-E CS
ACR_tran 158 esnikdqlsrveGVgdvqliGgsekavriwldpqklaklgltltdvvsalkeqnvqvaaGqlegqqeelliraqgrlqsaediekii 244
++ i++ql+ v G + +Gg+ ++++i ldpq++++ +++++dv++al++qn + G+ + + e+++++++ + ++++
lcl|Protein_ID1.3|M3 96 QNFIRPQLATVRGSAVPSPYGGKVRQIQIDLDPQAMQSKRVSPDDVARALSQQNLVLSPGTEKIGSFEYNVKINDSPDEFTLLNNLP 182
*************************************************************************************** PP
EEETTSEEEEHHHCEEEEEEESSSS-EEEETTCEEEEEEEEEETTSBHHHHHHHHHHHHHCCGGGSSTTEEEEEEEESHHHHHHHHH CS
ACR_tran 245 vksqdgskvrlrDvAkvelgaeeeriaatlngkpavllavkklpganaievvkavkekleelketlPegveivvvydttefvrasie 331
+k+ g + ++DvA+v +g + ++++ +g vl+++ k ++++++ ke +++lketlP+++ ++vv d++ fv+++i+
lcl|Protein_ID1.3|M3 183 IKNVGGVTIFIHDVAHVRDGFPPQINVVRDDGRRSVLMTILKNGATSTLDIIQGTKELIPKLKETLPNNLVLKVVGDQSIFVKSAIS 269
*************************************************************************************** PP
HHHHHHHHHHHHHHHHHHHHHSSHCCCHHHHHHHHHHHHHHHHHHHHTT--EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS CS
ACR_tran 332 eVvktlleaivLvvlvlflFLqnlratlipaiavPlsllgtfavlkalglsiNlltlfgLvlAiGlvvDdAiVvvEnverkleeege 418
Vv + +a +L ++++lFL+++r+t+i+ +++Pl++l ++++l++ g ++N++tl+gL+lA+G++vDdA Vv+En+ +le+ g+
lcl|Protein_ID1.3|M3 270 GVVREGTIAGILTSVMILLFLGSWRSTIIISMSIPLAILSAIIFLSLTGNTLNVMTLGGLALAVGMLVDDATVVIENINHHLEM-GK 355
************************************************************************************.** PP
-HHHHHHHHHHHHCCHHHHHHHHHHHHCCGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCS----TT-CC...... CS
ACR_tran 419 kpleaalksmkeiegalvaialvllavfvPilflgGveGklfrqfaltivlaillsvlvaltltPalcallLkarkeekek...... 499
+a++ ++++i + + ++l++++vfvP+++l+Gv lf ++a ++++ +l s +++ t++P ++ lLk + ++ ++
lcl|Protein_ID1.3|M3 356 PTTKAIIDAARQIIQPALVSTLSICIVFVPMFSLTGVPRYLFIPMAEAVIFGMLSSFVLSQTFVPTVANKLLKYQTQHFKHehhtda 442
*************************************************************************8776544446799* PP
........................CHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHH.HHHHHCCS-BESS----TSEE CS
ACR_tran 500 ........................gffrefnrlfdalerrYekllekvlrhravvllvalllvvg.slllfvripkeflPeedegvl 561
++ + f++ f ++ Y+ +l++ l hr+ ++++l +v++ ++ lf+ ++k+f+Pe d g++
lcl|Protein_ID1.3|M3 443 hrpehdpnfkvhrsvkasifqffiNIQQGFEKRFTKVRLVYRSILHFALDHRKKFITLFLGFVIVsCVTLFPLLGKNFFPEVDSGDM 529
*******************9655555578*************************999999887775899****************** PP
EEEEE-STTC-HHHHHHHHHHHHHHHH...TTTTEEEEEEEESESSSS..E........CTTEEEEEEEE--CTTS-SCCCSHHHHH CS
ACR_tran 562 vtsvqlppgvsleqtekvlkqvekilk...ekpevesvfavtGfafagdta........gqnsakvfisLkpekerkeeektveali 637
++++++ g+ +e+t+k + +e++++ ++e + ++ G + +g + g++ +++ i+L ++ ++ ++ +
lcl|Protein_ID1.3|M3 530 KIHIRVQVGTRIEETAKQFDLIENTIRrlvPQNELDTIVDNIGLSVSGINTaysstgtiGPQDGDILIHLNEN------HHPTKEYM 610
************************8875446889999999999888774331111111134445555555444......45688999 PP
HHHHHHC.CTSTSSEEEEEE-SSSCCCSSSSSEEEEEEE.TSSSCHHHHHHHHHHHHHHHCCSTTEECEEESS-S-EEEEEEEE-HH CS
ACR_tran 638 erlrkel.ekikganvellapiqlreletlsgvrlelqvklfgddleaLseareqllaalkqlpeladvrseqqedepqlqvkidre 723
++lr+ l ++++g++ +++ p +++ + gv + ++ + g ++++ + ++++l+ ++++p++ad+r++q ++ pq++v+idr
lcl|Protein_ID1.3|M3 611 KKLRETLpRAFPGVS-FAFLPADITSQILNFGVPAPIDIRVDGPNHDNNLKFVRAILKDIRNVPGIADLRVQQATNYPQFNVDIDRS 696
999999945678887.7888999*999************************************************************ PP
HHHHCTB-HHHHHHHHHHHHT-..EEEEEEEETTE...EEEEEEEE-GGGSSSGGGGCC-EEEETTSE.EEECGGCEEEEEEEE-SE CS
ACR_tran 724 kaaalGvsiadinetlstalgg..syvndfieegr...vvkvvvqleedlrsspedlkklyvrnkkgk.mvplsavakieeekgpns 804
+a+++G++ di + l + l g +++ +f +++ + +v+q+++ + +s+ dl+++++++k++ m l+ + +ie+ ++ +
lcl|Protein_ID1.3|M3 697 QAKNYGLTEGDITNSLVATLAGtsQVAPTFWLNNKngvSYPIVIQMPQYKINSLADLANIPITTKESSsMQVLGGLGSIERDQSDSV 783
************8877666655434556776544422279***********************998764889*************** PP
EEEETTCEEEEEEEEESTTS...-HHHHHHHHHHCCTT..SSTTEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCTSSST CS
ACR_tran 805 ierenglrsveisgevaegd...slgeaeeavekiakqvklPagvgiewtglseqeqeagnsllllvalalllvflvLaalyeslsd 888
i+++n ++s+ i ++++ +d ++g++e+++++ +++ lP+gv+++ +g+ q ++ l+l ++++++l++++ + +es++d
lcl|Protein_ID1.3|M3 784 ISHYNIKPSFDIFASLQGRDlgsISGDIETIIQHHHQE--LPKGVSVKLQGQVPIMQDSYRGLSLGLVASIILIYFLVVVNFESWLD 868
****************8876222578999999999888..*********************************************** PP
CHHHHTTHHHHHHHHHHHHHHTT--BSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTBHHHHHHHHHHHHCHHHHHHHHHHHHH CS
ACR_tran 889 pllvlltvPlalvGallalllrglelsviaqvGlilliGlavkNailivefakelrekeglsleeAileaaklRLrPiLMTalaail 975
p+++++ +P al+G + l+l+g++lsv a+ G i+ +G+a N il+++fa+e + ++ +A+lea+ +R+rP+LMTa a+++
lcl|Protein_ID1.3|M3 869 PFVIITALPAALAGIVWMLYLTGTTLSVPALTGAIMCMGVATANSILVISFARERLA-IVKDSTQAALEAGYTRFRPVLMTASAMLI 954
*********************************************************.888899*********************** PP
CCHHHHTT-STTHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH CS
ACR_tran 976 GvlPLalstGaGselqqplgivvlGGlvtstvLtlllvPvlYvlva 1021
G++P+al+ G+G e plg +v+GGl+++t+ tl +vPv++ +v+
lcl|Protein_ID1.3|M3 955 GMIPMALGLGDGGEQNAPLGRAVIGGLLLATIATLIFVPVVFSVVH 1000
******************************************9997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1021 nodes)
Target sequences: 3 (2141 residues)
Passed MSV filter: 1 (0.333333); expected 0.1 (0.02)
Passed bias filter: 1 (0.333333); expected 0.1 (0.02)
Passed Vit filter: 1 (0.333333); expected 0.0 (0.001)
Passed Fwd filter: 1 (0.333333); expected 0.0 (1e-05)
Initial search space (Z): 3 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.17u 0.03s 00:00:00.20 Elapsed: 00:00:00.19
# Mc/sec: 11.27
//