Motif confirmation by HMMer
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
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HMM file: /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file: hmm2/seq/DH11.3
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Query: DH11.3 CE24868 locus:pgp-11 multidrug resistance protein status:Partially_confirmed TR:Q19015 protein_id:CAA88940.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ABC_tran ABC transporter 427.5 1.2e-124 2
ABC_membrane ABC transporter transmembrane region 138.6 1.1e-37 2
SKI Shikimate kinase 15.6 0.0028 2
AIG1 AIG1 family 9.6 0.17 2
Cys-protease-3C 3C cysteine protease (picornain 3C) 5.7 0.33 1
PAPS_reduct Phosphoadenosine phosphosulfate reduc 5.5 4.1 1
Pox_P35 Poxvirus P35 protein 4.4 1.8 1
GTP_CDC Cell division protein 3.9 4.2 1
AAA ATPase family associated with various 2.8 8.5 1
RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2 2.7 7 1
Hanta_nucleocap Hantavirus nucleocapsid protein 1.7 4.9 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
PAPS_reduct 1/1 224 245 .. 1 22 [. 5.5 4.1
Hanta_nucleocap 1/1 241 254 .. 415 428 .] 1.7 4.9
ABC_membrane 1/2 75 357 .. 1 285 [] 109.5 6.6e-29
SKI 1/2 428 442 .. 1 15 [. 6.5 1.1
AIG1 1/2 428 442 .. 1 15 [. 6.5 1.2
Cys-protease-3C 1/1 458 479 .. 47 68 .. 5.7 0.33
ABC_tran 1/2 427 610 .. 1 199 [] 207.8 4.9e-59
Pox_P35 1/1 803 817 .. 327 341 .] 4.4 1.8
ABC_membrane 2/2 728 955 .. 47 285 .] 36.0 3.4e-08
AIG1 2/2 1028 1042 .. 1 15 [. 4.9 3.3
AAA 1/1 1029 1043 .. 1 15 [. 2.8 8.5
SKI 2/2 1028 1043 .. 1 16 [. 11.1 0.051
GTP_CDC 1/1 1018 1044 .. 1 21 [. 3.9 4.2
RNA_pol_Rpb2_2 1/1 1043 1064 .. 187 208 .. 2.7 7
ABC_tran 2/2 1027 1211 .. 1 199 [] 224.2 9.2e-64
Alignments of top-scoring domains:
PAPS_reduct: domain 1 of 1, from 224 to 245: score 5.5, E = 4.1
*->VllssfGkdssVllhLaskafp<-*
++++ G+ s+++lhL++k+++
DH11.3 224 FITFTMGPVSAFVLHLLTKVNE 245
Hanta_nucleocap: domain 1 of 1, from 241 to 254: score 1.7, E = 4.9
*->vKvKEisnqEpLKl<-*
+Kv E+sn E++ l
DH11.3 241 TKVNEVSNEELMSL 254
ABC_membrane: domain 1 of 2, from 75 to 357: score 109.5, E = 6.6e-29
*->lliailllilagatalvtfplllgrlldsgfplsdgnddh.arssli
++ a+++++l+g + +v l+ g ++d+ + + + +++ +l+
DH11.3 75 IITALICALLGGTIQPV-VLLIGGWITDL---YLTNGNTAgNDEFLY 117
slailslfavfvliglllqgsfyllagerlgqrlrkrlfrallrqilglf
s+ l + ++++++++l ++ +++ r ++r+ +++ l +l+++
DH11.3 118 SVLTLIYAGLGFGVIILVLALIQGVCIQRGTSRILDSIRKEFLGAVLRQD 167
dsffdtnsvGeltsRltnDvekirdglgeklgllfqslatvvgglivmfy
+++d++s+G++t l + +e i+dglg k +l++ +a++ + +i +
DH11.3 168 ANWLDKHSSGSITCQLNENIEVISDGLGNKCCMLVRGFAMFTSSIIACAF 217
yswkLtLillailpllillsavlakklrklsrkeqkayakagsvaeEsls
++w+Lt i++ + p+ +++ l+k +++ ++ a++ +++eEs+
DH11.3 218 INWQLTFITFTMGPVSAFVLHLLTKVNEVSNEELMSLSAQSHAIIEESIL 267
girTVkafgrEeyelerfdkaledaekagikkaiiagllfgitqlisyls
++rTV++ +++ +++++ ++ +e+ +k + k ++ag+++g + +++y++
DH11.3 268 NVRTVQSCNGQNFMITKLNQVNEKIKKFYNKSTFWAGFFDGLALFVIYFI 317
yalalwfGg..ylvasvisgglsvgtlfaflslgnqligpl<-*
+ l fG++ y+ ++i+ + +v+ ++ ++ ++++++g l
DH11.3 318 TGISLFFGCrlYFN-QEIGKAGDVILIVNTICVTGYFLGLL 357
SKI: domain 1 of 2, from 428 to 442: score 6.5, E = 1.1
*->rnifLIGmmGaGKsT<-*
+++ L+G G+GKsT
DH11.3 428 QTVALVGTSGCGKST 442
AIG1: domain 1 of 2, from 428 to 442: score 6.5, E = 1.2
*->rnIVLVGRTGNGKSA<-*
++ LVG +G+GKS+
DH11.3 428 QTVALVGTSGCGKST 442
Cys-protease-3C: domain 1 of 1, from 458 to 479: score 5.7, E = 0.33
*->IlmngkeVeVLDAkeLeDkagt<-*
Il++gk + LDAk L + g+
DH11.3 458 ILIDGKNIDMLDAKSLRQQIGI 479
ABC_tran: domain 1 of 2, from 427 to 610: score 207.8, E = 4.9e-59
*->GevlalvGpNGaGKSTLLklisGllppteGtilldGardlsdlsklk
G+++alvG +G+GKST + l++ l++ eG+il+dG + ++ l+
DH11.3 427 GQTVALVGTSGCGKSTSIGLLTKLYRASEGEILIDG-KNIDMLD--- 469
erlerlrknigvvfQdptlfpnpeltvreniafglrlslglskdeqrdrl
+lr++ig v Q+p lf +t+ eni +g++ +++ +++++
DH11.3 470 --AKSLRQQIGIVQQEPKLF---DGTIMENIKLGRNV----DEETIKTAA 510
kkagaeelLerlglgydhlldrrpgtLSGGqkQRvaiARaLltkpklLlL
+ a+a ++e+l gy+++l+ + +LSGGqkQR++iARaL+t p +LlL
DH11.3 511 DIANASSFIEKLENGYETRLGPGGVQLSGGQKQRICIARALVTSPSILLL 560
DEPTagLDpasraqllellrelrqqggTvllitHdldlldrlaDrilvle
DE+T++LD +++ + ++l + + g+T+++i H+l ++ Dri+vl+
DH11.3 561 DEATSALDSHNEHIVNKALTKASE-GRTTIIIAHRLSS-LKSVDRIYVLD 608
dG<-*
+G
DH11.3 609 QG 610
Pox_P35: domain 1 of 1, from 803 to 817: score 4.4, E = 1.8
*->KLLWFLaGaLvTyIi<-*
++ WF+aG+ ++ ++
DH11.3 803 RFVWFIAGTIFSLLL 817
ABC_membrane: domain 2 of 2, from 728 to 955: score 36.0, E = 3.4e-08
*->slailslfavfvliglllqgsfyllagerlgqrlrkrlfrallrqil
s++i+ + ++f + +l+g++ + + + +++ + +l++ +
DH11.3 728 SYGIG-MSFAFKTLQMYLCGWLAN----EVMNEVKQEMLSEVLNKPI 769
glfdsffdtnsvGeltsRltnDvekirdglgeklgllfqslatvvggliv
+fd+ +++s + +sR+ + + ++ l +++ +++ +a + l++
DH11.3 770 PYFDN--PETSPSACVSRIISHAHNCYACLDHRAIRFVWFIAGTIFSLLL 817
mfyyswkLtLillailpllillsavlakklrklsrkeqkayakagsvaeE
+f + w L ++ l i+ ll ++s+ + + +++ + e++ ++k+g +a+E
DH11.3 818 AFPFVWELGVLGLGITILLTIFSLHFVSVAHRA-HSEKSVMDKSGEFAVE 866
slsgirTVkafgrEeyelerfdkaledaekagikkaiiagllfgitqlis
+++ ir +k ++ E y++++f ++l + e k +++++l+f+itq+ +
DH11.3 867 IVEHIRAIKLLAVEGYFENKFSEYLKTSEIYENKIGFVSSLNFAITQSYV 916
ylsyalalwfGgylvasvisgglsvgtlfaflslgnqligpl<-*
+++ l + +G+ l + g s+ ++f++++ + + +
DH11.3 917 FACDMLLFFVGTLL---IYHGRYSPDKVFLAFNGAQMSAWGV 955
AIG1: domain 2 of 2, from 1028 to 1042: score 4.9, E = 3.3
*->rnIVLVGRTGNGKSA<-*
I LVG +G+GKS+
DH11.3 1028 HSIALVGASGCGKST 1042
[output cut off at A = 10 top alignments]