hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file: /usr1/pfam-23.0/Pfam_fs
Sequence file: 160897962.fa
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Query sequence: gi|160897962|ref|YP_001563544.1|
Accession: [none]
Description: YD repeat-containing protein [Delftia acidovorans SPH-1]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RHS_repeat RHS Repeat 227.6 3.2e-65 12
RHS RHS protein 73.6 1e-22 2
PAAR_motif PAAR motif 9.6 0.12 2
Phe_hydrox_dim Phenol hydroxylase, C-terminal dimeri 5.7 0.24 1
CMD Carboxymuconolactone decarboxylase fa 7.4 0.33 1
Trp_leader2 Tryptophan operon leader peptide 4.0 0.75 1
Glyco_hydro_6 Glycosyl hydrolases family 6 3.0 1.2 1
Troponin Troponin 4.5 1.3 1
GalP_UDP_tr_C Galactose-1-phosphate uridyl transfer 3.9 1.5 1
MOSC MOSC domain 4.4 1.5 1
DUF883 Bacterial protein of unknown function 4.1 2.6 1
DUF2220 Uncharacterized protein conserved in 1.2 2.6 1
HrpA_pilin HrpA pilus formation protein 0.8 2.8 1
HIPIP High potential iron-sulfur protein 1.8 3.3 1
Amidohydro_2 Amidohydrolase 1.7 3.3 1
DUF2135 Uncharacterized protein conserved in 3.5 3.9 1
DUF1052 Protein of unknown function (DUF1052) 1.3 3.9 1
Lipocalin_2 Lipocalin-like domain 2.2 4 1
Glucodextran_N Glucodextranase, domain N -0.6 4.7 1
RNA_pol_Rpb2_3 RNA polymerase Rpb2, domain 3 2.9 4.8 1
DUF2505 Protein of unknown function (DUF2505) 1.3 5.1 1
DUF1612 Protein of unknown function (DUF1612) -2.0 5.1 1
DUF2063 Uncharacterized protein conserved in 2.3 5.2 1
HlyC RTX toxin acyltransferase family 1.2 5.7 1
DUF1630 Protein of unknown function (DUF1630) -0.8 6 1
MR_MLE_N Mandelate racemase / muconate lactoni 0.9 6.4 1
APH_6_hur Aminoglycoside/hydroxyurea antibiotic 1.4 6.5 1
FTZ Fushi tarazu (FTZ), N-terminal region -0.5 7.6 1
MdcG Phosphoribosyl-dephospho-CoA transfer -0.2 7.8 1
DUF2109 Predicted membrane protein (DUF2109) 1.7 8 1
CSF-1 Macrophage colony stimulating factor- -0.5 8.1 1
Amidase_5 Bacteriophage peptidoglycan hydrolase 0.6 8.2 1
DUF2117 Uncharacterized protein conserved in -0.0 9.1 1
DUF2084 Uncharacterized protein conserved in 1.0 9.1 1
TBP Transcription factor TFIID (or TATA-b 1.8 9.4 1
GSPII_N Bacterial type II secretion system pr -0.4 9.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
PAAR_motif 1/2 2 16 .. 11 25 .] 6.4 1
MOSC 1/1 14 50 .. 137 172 .] 4.4 1.5
PAAR_motif 2/2 18 30 .. 1 13 [. 3.2 8.3
Glyco_hydro_6 1/1 48 75 .. 1 29 [. 3.0 1.2
RNA_pol_Rpb2_3 1/1 86 97 .. 52 63 .. 2.9 4.8
FTZ 1/1 161 174 .. 298 311 .] -0.5 7.6
RHS_repeat 1/12 240 254 .. 25 44 .] 2.1 9.7
APH_6_hur 1/1 270 280 .. 261 271 .] 1.4 6.5
RHS_repeat 2/12 310 345 .. 1 42 [. 15.4 0.0016
Amidohydro_2 1/1 337 428 .. 1 61 [. 1.7 3.3
Amidase_5 1/1 346 359 .. 140 155 .] 0.6 8.2
RHS_repeat 3/12 429 466 .. 1 44 [] 26.1 1.5e-06
RHS_repeat 4/12 471 509 .. 1 44 [] 37.4 9e-10
RHS 1/2 492 506 .. 27 41 .] 5.0 0.73
CSF-1 1/1 516 534 .. 293 311 .] -0.5 8.1
RHS_repeat 5/12 542 579 .. 1 44 [] 31.5 4.2e-08
GSPII_N 1/1 583 595 .. 242 257 .] -0.4 9.8
RHS_repeat 6/12 584 620 .. 1 44 [] 19.3 0.00012
HrpA_pilin 1/1 603 624 .. 102 125 .. 0.8 2.8
RHS_repeat 7/12 637 673 .. 1 44 [] 24.5 4.1e-06
DUF1052 1/1 651 673 .. 136 158 .] 1.3 3.9
RHS_repeat 8/12 678 715 .. 1 44 [] 15.6 0.0014
DUF1612 1/1 723 731 .. 187 195 .. -2.0 5.1
RHS_repeat 9/12 723 769 .. 1 44 [] 12.9 0.0081
MR_MLE_N 1/1 749 765 .. 113 129 .] 0.9 6.4
DUF2084 1/1 778 791 .. 19 32 .. 1.0 9.1
DUF2505 1/1 812 825 .. 1 14 [. 1.3 5.1
DUF2109 1/1 818 828 .. 68 78 .] 1.7 8
HlyC 1/1 828 842 .. 1 15 [. 1.2 5.7
DUF2220 1/1 889 905 .. 1 19 [. 1.2 2.6
RHS_repeat 10/12 894 946 .. 1 44 [] 11.0 0.029
HIPIP 1/1 913 921 .. 1 9 [. 1.8 3.3
RHS_repeat 11/12 958 987 .. 1 29 [. 20.6 5.4e-05
Glucodextran_N 1/1 990 997 .. 1 8 [. -0.6 4.7
GalP_UDP_tr_C 1/1 994 1016 .. 199 221 .] 3.9 1.5
RHS_repeat 12/12 1074 1123 .. 1 44 [] 11.0 0.029
CMD 1/1 1079 1100 .. 28 51 .. 7.4 0.33
DUF883 1/1 1086 1118 .. 34 66 .. 4.1 2.6
Lipocalin_2 1/1 1127 1139 .. 144 156 .] 2.2 4
TBP 1/1 1148 1163 .. 28 44 .. 1.8 9.4
MdcG 1/1 1162 1189 .. 12 49 .. -0.2 7.8
DUF1630 1/1 1204 1220 .. 652 668 .] -0.8 6
DUF2063 1/1 1215 1233 .. 1 19 [. 2.3 5.2
Troponin 1/1 1247 1268 .. 40 62 .. 4.5 1.3
Trp_leader2 1/1 1256 1270 .. 1 16 [. 4.0 0.75
RHS 2/2 1269 1309 .. 1 41 [] 68.5 4e-21
DUF2135 1/1 1394 1404 .. 1 11 [. 3.5 3.9
Phe_hydrox_dim 1/1 1406 1428 .. 10 41 .. 5.7 0.24
DUF2117 1/1 1445 1468 .. 52 77 .. -0.0 9.1
Alignments of top-scoring domains:
PAAR_motif: domain 1 of 2, from 2 to 16: score 6.4, E = 1
*->nGkPAARlGDsvvCp<-*
+GkPAAR +Dsvv +
gi|1608979 2 SGKPAARITDSVVKG 16
MOSC: domain 1 of 1, from 14 to 50: score 4.4, E = 1.5
CS ...... HHHHHCCTSS-EEEEEEE-EEEETTSEEEE
*->rdgkgl..fgrnlaagkrGiyarVlrpGtirvGDevel<-*
++gk++++ ++l+ ++G+ + V +pG i+vG +v +
gi|1608979 14 VKGKIVtgSLTVLIGSQGGLACSV-CPGGITVGSPVNP 50
PAAR_motif: domain 2 of 2, from 18 to 30: score 3.2, E = 8.3
*->iieGspnvkvnGk<-*
i++Gs++v ++++
gi|1608979 18 IVTGSLTVLIGSQ 30
Glyco_hydro_6: domain 1 of 1, from 48 to 75: score 3.0, E = 1.2
CS --CCCHHHHHHHCGGCT-CCHHHHHHHCT
*->vnPksaaevwvaArnpgDgrlaaiaekVA<-*
vnP+ a+v A + +D++l+ +a VA
gi|1608979 48 VNPQLGAKVLLGA-QDLDFALPSAALPVA 75
RNA_pol_Rpb2_3: domain 1 of 1, from 86 to 97: score 2.9, E = 4.8
*->PErGqncGLvns<-*
PE+G++cGL+ +
gi|1608979 86 PEHGAACGLLGH 97
FTZ: domain 1 of 1, from 161 to 174: score -0.5, E = 7.6
*->aadFnWsHiEEtlA<-*
aa+ WsH+E +l
gi|1608979 161 AANPRWSHVEQALV 174
RHS_repeat: domain 1 of 12, from 240 to 254: score 2.1, E = 9.7
*->aagrltaltlttstdasGtt<-*
+agrl++l d+ G++
gi|1608979 240 PAGRLVSL-----SDGTGRR 254
APH_6_hur: domain 1 of 1, from 270 to 280: score 1.4, E = 6.5
*->glSaaWfiEDG<-*
gl+++W ++DG
gi|1608979 270 GLNGLWGADDG 280
RHS_repeat: domain 2 of 12, from 310 to 345: score 15.4, E = 0.0016
*->YDanGrLtavtdpsgpvgqt.YrYDaagrltaltlttstdasG<-*
Y+++G+L++v d +g+ + +++++D+ +r+ a+ + asG
gi|1608979 310 YSSAGDLITVHDRAGQLV-ReFEWDH-HRISAH-----RHASG 345
Amidohydro_2: domain 1 of 1, from 337 to 428: score 1.7, E = 3.3
CS EEBS--. ....... ... ..
*->iDaHaHl..........................pvpglay.rrl.dr
i aH H +++ ++ + ++ +++ + +++++++ ++++y ++++++
gi|1608979 337 ISAHRHAsgpwhryryesaqpgarviehsnqegLSYRFDYlAQPpGP 383
CS . -B-CC HHHHTT--SS--S-B-HHHHHHHHHH S--EE--B--
p.psdpg.rlpamvrrgydprdaspadllvlgaa.gvaravivaa<-*
+++ ++++r ++ +r +++ +++a l+ l+a++ ++++ +a
gi|1608979 384 DgQPRAAtRVSDSLDRIETYYFEGAAGLSRLIAHhKADGSRWLQA 428
Amidase_5: domain 1 of 1, from 346 to 359: score 0.6, E = 8.2
*->psYvYvwRlnggasqp<-*
p++ Y R+ ++++++
gi|1608979 346 PWHRY--RYESAQPGA 359
RHS_repeat: domain 3 of 12, from 429 to 466: score 26.1, E = 1.5e-06
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
YD+ GrL + tdp g+++ ++r D+ grl+ + ++G+
gi|1608979 429 YDSFGRLASRTDPLGRSV-HLRRDGQGRLIGV-----QLPDGRS 466
RHS_repeat: domain 4 of 12, from 471 to 509: score 37.4, E = 9e-10
*->YD.anGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-
+D+a+GrL++ td++g+++ Y+YDa+grlt++ t a+G t
gi|1608979 471 HDeATGRLLQSTDTAGATT-GYQYDAWGRLTQI-----TQADGST 509
*
gi|1608979 - -
RHS: domain 1 of 2, from 492 to 506: score 5.0, E = 0.73
*->rYdaWGnvleEevsq<-*
+YdaWG++++ +++
gi|1608979 492 QYDAWGRLTQITQAD 506
CSF-1: domain 1 of 1, from 516 to 534: score -0.5, E = 8.1
*->qpegSlltqdedrqeelPv<-*
+p ++lt+d++r++e+
gi|1608979 516 DPQEAPLTCDSPRRIEDAQ 534
RHS_repeat: domain 5 of 12, from 542 to 579: score 31.5, E = 4.2e-08
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
++++G+L++ td sg ++ +Y+YD +g l+ + ++a G +
gi|1608979 542 WSDAGQLLSYTDCSGHST-HYHYDRWGALIEV-----DNALGQR 579
GSPII_N: domain 1 of 1, from 583 to 595: score -0.4, E = 9.8
*->qpDeQGrrPlrfQGrL<-*
q+D+QGr+ ++ +L
gi|1608979 583 QRDGQGRI---VASEL 595
RHS_repeat: domain 6 of 12, from 584 to 620: score 19.3, E = 0.00012
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
D +Gr++a p+g+ +Y+YD+ag+lt++ d++ +
gi|1608979 584 RDGQGRIVASELPNGQIE-RYHYDSAGHLTRI------DPAQPA 620
HrpA_pilin: domain 1 of 1, from 603 to 624: score 0.8, E = 2.8
*->YmqDsAGkLtPWDPtPnanTttGs<-*
Y DsAG Lt DP a+T +s
gi|1608979 603 YHYDSAGHLTRIDPAQPAGT--SS 624
RHS_repeat: domain 7 of 12, from 637 to 673: score 24.5, E = 4.1e-06
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
YD GrL++ t +g ++ ++YD+agrl +l + +G
gi|1608979 637 YDLWGRLVQRT-HGGLTL-AFEYDSAGRLLRL-----VNENGSQ 673
DUF1052: domain 1 of 1, from 651 to 673: score 1.3, E = 3.9
*->ltlrFaRaAAaRlmaaelarlsv<-*
ltl+F A Rl++++ +++s
gi|1608979 651 LTLAFEYDSAGRLLRLVNENGSQ 673
RHS_repeat: domain 8 of 12, from 678 to 715: score 15.6, E = 0.0014
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
+Da++rL++ + + +Yr+Daag+l + td++ +
gi|1608979 678 WDALDRLVQEEGFDQRLQ-RYRWDAAGQLMEA-----TDGNAAQ 715
DUF1612: domain 1 of 1, from 723 to 731: score -2.0, E = 5.1
*->WDEdaRLsE<-*
WDE++RL+E
gi|1608979 723 WDEGGRLAE 731
RHS_repeat: domain 9 of 12, from 723 to 769: score 12.9, E = 0.0081
*->YDanGrLta....vtdpsgpvgq.tYrYDaagrltaltltts...td
+D+ GrL +++ + t p p+ +++Y++Daagrlta+ s +++
gi|1608979 723 WDEGGRLAErqlpAT-PHAPAQThRYEWDAAGRLTAA----SvwqHT 764
asGtt<-*
++ t+
gi|1608979 765 GENTA 769
MR_MLE_N: domain 1 of 1, from 749 to 765: score 0.9, E = 6.4
CS HHHHHHHTTSBHHHHTT
*->wDlkaKalnlPladLLG<-*
wD++++ +++++ G
gi|1608979 749 WDAAGRLTAASVWQHTG 765
DUF2084: domain 1 of 1, from 778 to 791: score 1.0, E = 9.1
*->rIeleRdenGkite<-*
rI+leRd+ G+it+
gi|1608979 778 RIALERDALGRITA 791
DUF2505: domain 1 of 1, from 812 to 825: score 1.3, E = 5.1
*->fdvsaeypatverV<-*
+++++++++t++r+
gi|1608979 812 IEYEHRIAHTLDRL 825
DUF2109: domain 1 of 1, from 818 to 828: score 1.7, E = 8
*->IAyTlaggeei<-*
IA+Tl++++ +
gi|1608979 818 IAHTLDRLGGR 828
HlyC: domain 1 of 1, from 828 to 842: score 1.2, E = 5.7
*->nktndFevLGnIAWL<-*
+ + LG+IAWL
gi|1608979 828 RQHSQLQGLGEIAWL 842
DUF2220: domain 1 of 1, from 889 to 905: score 1.2, E = 2.6
*->qvrrlWdshrgslLaallt<-*
qv+r+Wd L+al+t
gi|1608979 889 QVQRQWD--SLGRLTALGT 905
RHS_repeat: domain 10 of 12, from 894 to 946: score 11.0, E = 0.029
*->YDanGrLta..............vt.dpsgpvgq.tYrYDaagrlta
+D++GrLta ++++ + ++++ + + g+ + ++Y+YD++g+l+a
gi|1608979 894 WDSLGRLTAlgttglqalqptdaQAhALIGQILGrRYHYDSLGQLVA 940
ltlttstdasGtt<-*
+ a+ +
gi|1608979 941 I-----EQAG--A 946
HIPIP: domain 1 of 1, from 913 to 921: score 1.8, E = 3.3
CS TTSHHHHHT
*->ekdpqAqAL<-*
++d+qA+AL
gi|1608979 913 PTDAQAHAL 921
RHS_repeat: domain 11 of 12, from 958 to 987: score 20.6, E = 5.4e-05
*->YDanGrLtavtdpsgpvgq.tYrYDaagrl<-*
YD++GrL a td+ +p+++++++ D+ag++
gi|1608979 958 YDSAGRLRAATDSQHPQTTtRWQLDPAGNR 987
Glucodextran_N: domain 1 of 1, from 990 to 997: score -0.6, E = 4.7
CS -TTTT---
*->ApGaPGaa<-*
ApGaPGa+
gi|1608979 990 APGAPGAT 997
GalP_UDP_tr_C: domain 1 of 1, from 994 to 1016: score 3.9, E = 1.5
CS -..............SS-TTCCT
*->sgaDPktaLedNkmaevHyewal<-*
+ga +t +dN a+vH +w+
gi|1608979 994 PGATGQTNTQDNWAAQVHAHWRH 1016
RHS_repeat: domain 12 of 12, from 1074 to 1123: score 11.0, E = 0.029
*->YDanGrLtavtd.........psgpvgqtYrYDaagr....ltaltl
YD +++L+av+ ++ +++ ++ ++ ++ Y+YDa+gr+ ++ + +
gi|1608979 1074 YDGAHQLIAVRSsqiqgnaeqLRHHSR--YTYDALGRrlkqQVES-- 1116
ttstdasGtt<-*
d++ t+
gi|1608979 1117 ---ADGNPTR 1123
CMD: domain 1 of 1, from 1079 to 1100: score 7.4, E = 0.33
CS HHHHHHHHHHTT-HHHHHHHHHHH
*->ELialavsaanGCeyCieLdaHtr<-*
+Lia++ s+++G + +L++H r
gi|1608979 1079 QLIAVRSSQIQGNAE--QLRHHSR 1100
DUF883: domain 1 of 1, from 1086 to 1118: score 4.1, E = 2.6
*->eraesrLddaRerlsdaedaaverakaAadaad<-*
+++++ +++R++ + ++da+ +r k+ ++ ad
gi|1608979 1086 SQIQGNAEQLRHHSRYTYDALGRRLKQQVESAD 1118
Lipocalin_2: domain 1 of 1, from 1127 to 1139: score 2.2, E = 4
*->YGYDvskLiwvpq<-*
YG+D ++Li+++
gi|1608979 1127 YGWDGDRLIHTER 1139
TBP: domain 1 of 1, from 1148 to 1163: score 1.8, E = 9.4
CS S..TTEEEETTTCSSEE
*->lslpnveYePeqFpGli<-*
+ ++++ YeP++F +l+
gi|1608979 1148 H-IEHTIYEPGSFTPLV 1163
MdcG: domain 1 of 1, from 1162 to 1189: score -0.2, E = 7.8
*->LvwLspaawaaallacalpdaaappwvaawlrlaaglP<-*
Lv+Ls+ a + ++ +p+++ +++ aaglP
gi|1608979 1162 LVRLSTTA--------SGDPQNEPHLLVQAI--AAGLP 1189
DUF1630: domain 1 of 1, from 1204 to 1220: score -0.8, E = 6
*->eaiissLPdDLqqvLll<-*
++++s++P D+qq +
gi|1608979 1204 QTMLSAMPRDMQQDAAR 1220
DUF2063: domain 1 of 1, from 1215 to 1233: score 2.3, E = 5.2
*->QqaFaaalRdPeaapvPaG<-*
Qq+ a++lR+ + +P+G
gi|1608979 1215 QQDAARHLRHTLEHGLPPG 1233
Troponin: domain 1 of 1, from 1247 to 1268: score 4.5, E = 1.3
CS XXXXXXXXXXXXXXXXXXXXXXX
*->elegaeqqreLqElckElharid<-*
+l + + q++LqE++kE hari+
gi|1608979 1247 RLLSGM-QAKLQEQEKEQHARIA 1268
Trp_leader2: domain 1 of 1, from 1256 to 1270: score 4.0, E = 0.75
*->mLqEFnqnqKAKlAlh<-*
LqE + q A++A+h
gi|1608979 1256 -LQEQEKEQHARIAIH 1270
RHS: domain 2 of 2, from 1269 to 1309: score 68.5, E = 4e-21
*->vyYYHtDqiGtPLeLtdseGeivWqArYdaWGnvleEevsq<-*
+++YH+D++GtP +Ltd+ G+++W A+ d WGnvl+E ++q
gi|1608979 1269 IHHYHCDHLGTPMALTDQTGQVAWAAKLDPWGNVLQEYNPQ 1309
DUF2135: domain 1 of 1, from 1394 to 1404: score 3.5, E = 3.9
*->pvpGtYlVyVN<-*
p+ G+Y+V ++
gi|1608979 1394 PKSGVYQVGAH 1404
Phe_hydrox_dim: domain 1 of 1, from 1406 to 1428: score 5.7, E = 0.24
CS SBTTB-STT-............-GGGCTTS-T
*->gPSllvmkpeWrkaaaesdkilspqeLAtglv<-*
+PSl+v++++ kilsp++LA++++
gi|1608979 1406 NPSLIVDDKG---------KILSPSDLAKKIK 1428
DUF2117: domain 1 of 1, from 1445 to 1468: score -0.0, E = 9.1
*->NtkndrkaktiaekLSelLgLkiesp<-*
N +++ +++a+kL+++Lg k++ p
gi|1608979 1445 N--TGKGNDPYAKKLANELGAKVSAP 1468
//