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:            hmm1/seq/C47A10.1
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Query:  C47A10.1  CE15714  locus:pgp-9 multidrug resistance protein (p-glycoprotein) (2 domains) status:Partially_confirmed TR:O45721 protein_id:

Scores for sequence family classification (score includes all domains):
Model          Description                              Score    E-value  N
--------       -----------                              -----    ------- ---
ABC_tran       ABC transporter                          448.3   6.7e-131   2
ABC_membrane   ABC transporter transmembrane region     396.0   3.7e-115   2
SKI            Shikimate kinase                          20.5     0.0001   2
AIG1           AIG1 family                               16.1     0.0029   2
PRK            Phosphoribulokinase / Uridine kinase f    11.2      0.037   2
MS_channel     Mechanosensitive ion channel               6.1        1.8   1
DUF258         Protein of unknown function, DUF258        5.3        1.6   1
DUF624         Protein of unknown function, DUF624        5.0        7.1   1
APS_kinase     Adenylylsulfate kinase                     4.9        2.4   2
GTP_EFTU_D2    Elongation factor Tu domain 2              4.6        8.8   2
gntR           Bacterial regulatory proteins, gntR fa     4.3        9.6   1
PNPase         Polyribonucleotide nucleotidyltransfer     4.2       0.98   1
HR1            Hr1 repeat                                 4.1        7.3   1
CoaE           Dephospho-CoA kinase                       3.7        4.5   1
AIRS_C         AIR synthase related protein, C-termin     3.6        4.7   2
Rad17          Rad17 cell cycle checkpoint protein        2.9        4.5   2
Topoisomer_I_N Eukaryotic DNA topoisomerase I, DNA bi     2.5        5.2   1
IKI3           IKI3 family                                2.5        2.2   1

Parsed for domains:
Model          Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------       ------- ----- -----    ----- -----      -----  -------
Topoisomer_I_N   1/1     100   112 ..   214   227 .]     2.5      5.2
IKI3             1/1     266   279 ..  1070  1083 .]     2.5      2.2
DUF624           1/1     281   301 ..    57    77 .]     5.0      7.1
GTP_EFTU_D2      1/2     302   322 ..     1    33 [.     4.5      9.7
ABC_membrane     1/2      46   336 ..     1   285 []   208.4  1.1e-58
MS_channel       1/1     320   354 ..     1    35 [.     6.1      1.8
GTP_EFTU_D2      2/2     400   415 ..    78    96 .]     0.1  1.6e+02
AIRS_C           1/2     409   423 ..     1    22 [.     2.0       14
AIG1             1/2     412   426 ..     1    15 [.     6.4      1.3
APS_kinase       1/2     410   427 ..     1    18 [.     1.1       32
PRK              1/2     413   431 ..     1    19 [.     6.0      1.1
Rad17            1/2     401   431 ..    35    68 ..     1.8      9.1
SKI              1/2     412   431 ..     1    20 [.     9.5     0.16
CoaE             1/1     412   432 ..     1    21 [.     3.7      4.5
ABC_tran         1/2     411   595 ..     1   199 []   226.7  1.7e-64
HR1              1/1     673   697 ..     1    25 [.     4.1      7.3
gntR             1/1     774   788 ..     1    15 [.     4.3      9.6
ABC_membrane     2/2     706   984 ..     1   285 []   195.9  6.4e-55
PNPase           1/1    1006  1016 ..    71    81 ..     4.2     0.98
AIRS_C           2/2    1056  1070 ..     1    22 [.     1.6       19
AIG1             2/2    1059  1073 ..     1    15 [.    10.2     0.11
SKI              2/2    1059  1074 ..     1    16 [.    12.7    0.019
DUF258           1/1    1063  1078 ..    33    48 ..     5.3      1.6
Rad17            2/2    1056  1078 ..    46    68 ..     6.8     0.35
PRK              2/2    1062  1079 ..     1    20 [.     6.6     0.75
APS_kinase       2/2    1057  1080 ..     1    24 [.     5.3      1.8
ABC_tran         2/2    1058  1244 ..     1   199 []   224.2  9.1e-64

Alignments of top-scoring domains:
Topoisomer_I_N: domain 1 of 1, from 100 to 112: score 2.5, E = 5.2
                   *->kENIngqvFKYVfL<-*
                      +E I++ + KYV+L
    C47A10.1   100    HEVIQNCL-KYVYL    112

IKI3: domain 1 of 1, from 266 to 279: score 2.5, E = 2.2
                   *->kRYekALshLsecg<-*
                      kRYe+AL+h ++ g
    C47A10.1   266    KRYEDALEHGKKTG    279

DUF624: domain 1 of 1, from 281 to 301: score 5.0, E = 7.1
                   *->vkaNllGlfflligliLllnL<-*
                      +k+ l+G+ ++ ++ i+++ +
    C47A10.1   281    KKSFLIGAGLASFFVIIYASY    301

GTP_EFTU_D2: domain 1 of 2, from 302 to 322: score 4.5, E = 9.7
                   *->adVfkikytmDpyrrTSdGrGtVatgRvesGtl<-*
                      +++f + +             +V+ gR+esGt+
    C47A10.1   302    CLAFWVGT------------NFVYSGRLESGTV    322

ABC_membrane: domain 1 of 2, from 46 to 336: score 208.4, E = 1.1e-58
                   *->lliailllilagatalvtfplllgrlldsgfplsdgnddh.......
                      l  +i+++   g+  ++ +++++g + ++  +++ g ++ +++++ +
    C47A10.1    46    LAVGIIVSCATGVGLPL-MSIIMGNVSQN--FVTLGTIFLdpnstas 89

                   ..........arsslislailslfavfvliglllqgsfyllagerlgqrl
                   ++   + + +++     l ++ +++ +++ + +lq+s + ++ e+l+ r
    C47A10.1    90 ekaaaraefsHEVIQNCLKYV-YLGCGIFAAGFLQASCFMVICEKLSNRF 138

                   rkrlfrallrqilglfdsffdtnsvGeltsRltnDvekirdglgeklgll
                   r+++f++++rq++++ d     n++G+l ++l + +e++r+g+g+k+gl
    C47A10.1   139 RRQFFHSVMRQEIAWYDK----NTSGTLSNKLFDNLERVREGTGDKVGLA 184

                   fqslatvvgglivmfyyswkLtLillailpllillsavlakklrklsrke
                   fq +a+++gg++v+f+y w LtLi+++++p ++++ ++lak l ++  ke
    C47A10.1   185 FQMMAQFIGGFAVAFTYDWLLTLIMMSLSPFMMICGLFLAKLLATAATKE 234

                   qkayakagsvaeEslsgirTVkafgrEeyelerfdkaledaekagikkai
                   +k+ya ag +aeE+l+ irTV+af+++eye++r+++ale  +k+gikk +
    C47A10.1   235 AKQYAVAGGIAEEVLTSIRTVIAFNGQEYECKRYEDALEHGKKTGIKKSF 284

                   iagllfgitqlisylsyalalwfGgylvasvisgglsvgtlfaflslgnq
                   + g+  +  + i+y+sy la+w+G+ +   v sg l +gt+ +++  +++
    C47A10.1   285 LIGAGLASFFVIIYASYCLAFWVGTNF---VYSGRLESGTVLTVFFSVMM 331

                   ligpl<-*
                    +++l
    C47A10.1   332 GSMAL    336

MS_channel: domain 1 of 1, from 320 to 354: score 6.1, E = 1.8
                   *->kkilkyliivvgilivLsllGvnvsaLlAglGilG<-*
                      +++l++   v++  ++L++ G++++++ ++lG+++
    C47A10.1   320    GTVLTVFFSVMMGSMALGQAGQQFATIGTALGAAA    354

GTP_EFTU_D2: domain 2 of 2, from 400 to 415: score 0.1, E = 1.6e+02
                   *->ivagiglkdaaikrGdvla<-*
                      i++g+ l+    + G+++a
    C47A10.1   400    ILKGVSLDA---QPGQTVA    415

AIRS_C: domain 1 of 2, from 409 to 423: score 2.0, E = 14
                   *->kpGDvlillgstgkktgrsGlh<-*
                      +pG+ + l+gs       sG +
    C47A10.1   409    QPGQTVALVGS-------SGCG    423

AIG1: domain 1 of 2, from 412 to 426: score 6.4, E = 1.3
                   *->rnIVLVGRTGNGKSA<-*
                       ++ LVG +G+GKS+
    C47A10.1   412    QTVALVGSSGCGKST    426

APS_kinase: domain 1 of 2, from 410 to 427: score 1.1, E = 32
                   *->rGctvWfTGLSGsGKSTI<-*
                       G tv + G SG GKSTI
    C47A10.1   410    PGQTVALVGSSGCGKSTI    427

	[output cut off at A = 10 top alignments]


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