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:            hmm4/seq/T27E9.7
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Query:  T27E9.7  CE18971   ABC transporters (2 domains) status:Confirmed TR:Q9XTD9 protein_id:CAB04880.1

Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N
--------        -----------                             -----    ------- ---
ABC_tran        ABC transporter                         258.0    1.2e-73   2
Thymidylate_kin Thymidylate kinase                       11.6     0.0032   2
SKI             Shikimate kinase                          9.4       0.16   2
NB-ARC          NB-ARC domain                             6.9       0.43   1
SMC_N           RecF/RecN/SMC N terminal domain           6.6       0.68   2
AIG1            AIG1 family                               6.1        1.5   1
FlaG            FlaG protein                              5.2        6.4   1
NS3_envE        Nonstructural protein NS3/Small envel     4.0        5.4   1
HypB_UreG       HypB/UreG nucleotide-binding domain       4.0        6.8   1
SRP54           SRP54-type protein, GTPase domain         3.6        6.4   1
Rad17           Rad17 cell cycle checkpoint protein       3.5          3   1
tRNA_synt_1c_R1 Glutaminyl-tRNA synthetase, non-speci     1.3        9.2   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
SKI               1/2     112   123 ..     5    16 ..     3.1       10
SMC_N             1/2     112   127 ..    30    45 ..     5.5      1.4
Thymidylate_kin   1/2     114   130 ..     1    19 [.     6.9     0.14
NB-ARC            1/1     117   132 ..    51    66 ..     6.9     0.43
FlaG              1/1     185   205 ..    92   122 .]     5.2      6.4
ABC_tran          1/2     107   299 ..     1   199 []   127.6  8.8e-36
tRNA_synt_1c_R1   1/1     355   379 ..     1    25 [.     1.3      9.2
NS3_envE          1/1     379   399 ..    65    85 .]     4.0      5.4
SRP54             1/1     419   434 ..     1    16 [.     3.6      6.4
SMC_N             2/2     425   435 ..    29    39 ..     3.6      4.8
AIG1              1/1     422   436 ..     1    15 [.     6.1      1.5
SKI               2/2     422   437 ..     1    16 [.     7.3     0.65
Thymidylate_kin   2/2     426   441 ..     1    16 [.     4.7     0.86
HypB_UreG         1/1     421   442 ..     1    32 [.     4.0      6.8
Rad17             1/1     426   443 ..    53    70 ..     3.5        3
ABC_tran          2/2     421   587 ..     1   199 []   130.5  1.3e-36

Alignments of top-scoring domains:
SKI: domain 1 of 2, from 112 to 123: score 3.1, E = 10
                   *->LIGmmGaGKsTv<-*
                      LIG+ G+GKsT+
     T27E9.7   112    LIGLNGSGKSTI    123

SMC_N: domain 1 of 2, from 112 to 127: score 5.5, E = 1.4
                   *->IvGPNGSGKSNilDAI<-*
                      ++G NGSGKS i+ AI
     T27E9.7   112    LIGLNGSGKSTIIQAI    127

Thymidylate_kin: domain 1 of 2, from 114 to 130: score 6.9, E = 0.14
                   *->iEGiDGaGKTTqaelLker<-*
                        G++G+GK+T++++++ +
     T27E9.7   114    --GLNGSGKSTIIQAIYNK    130

NB-ARC: domain 1 of 1, from 117 to 132: score 6.9, E = 0.43
                   *->GvGKTTLAkqiyndes<-*
                      G+GK+T+ ++iyn+e+
     T27E9.7   117    GSGKSTIIQAIYNKEM    132

FlaG: domain 1 of 1, from 185 to 205: score 5.2, E = 6.4
                   *->EElLelakRlkevEqdatnlgsriGlLfDkr<-*
                      ++l+++++Rl+e+          +  L +k+
     T27E9.7   185    DKLMDVYERLDEM----------DASLAEKK    205

ABC_tran: domain 1 of 2, from 107 to 299: score 127.6, E = 8.8e-36
                   *->GevlalvGpNGaGKSTLLklisGllp..pteGtilldGardlsdlsk
                      G +++l+G NG+GKST++ +i+  +++ p++ + +l   r++  ++
     T27E9.7   107    GRRYGLIGLNGSGKSTIIQAIYNKEMpiPESVDMYLVS-REMPASE- 151

                   lkerlerlrknigvvfQdptlfpnpeltvreniafglrls..........
                       +  l++         +       +vr  + + ++++ +++++++++
     T27E9.7   152 ----KTALQA---------VVD---VDSVRKELEHLAEQLasqtdeesqd 185

                   .........lglskdeqrdrlkkagaeelLerlglgydhlldrrpgtLSG
                   +  +  ++ ++++   ++++     a e+L+ lg ++ +   ++++ +SG
     T27E9.7   186 klmdvyerlDEMDASLAEKK-----AAEILHGLGFTK-TMQMKKCKDFSG 229

                   GqkQRvaiARaLltkpklLlLDEPTagLDpasraqllellrelrqqggTv
                   G+++R+a+ARaL++kp +LlLDEPT++LD ++  +l+e l ++    +T+
     T27E9.7   230 GWRMRIALARALFLKPSVLLLDEPTNHLDLEACVWLEEELAQY---KRTL 276

                   llitHdldlldrlaDrilvledG<-*
                   l+++H++d++  +++ i+ l +
     T27E9.7   277 LVVSHSQDFMNGVCTNIIHLFQK    299

tRNA_synt_1c_R1: domain 1 of 1, from 355 to 379: score 1.3, E = 9.2
                   *->sakeeLlaLFsqiGLdekKAkETlk<-*
                      ++ke+  a+ ++ GL ek + ET+k
     T27E9.7   355    QSKEKTMAKMIAGGLAEKAVTETVK    379

NS3_envE: domain 1 of 1, from 379 to 399: score 4.0, E = 5.4
                   *->kqlYkyYneevkPPvLevDDv<-*
                      kq+Y +   e+ PPv+ v  v
     T27E9.7   379    KQFYFFDAGEIPPPVIMVQHV    399

SRP54: domain 1 of 1, from 419 to 434: score 3.6, E = 6.4
                   *->kkpnVillVGlqGsGK<-*
                         + i+lVG++G+GK
     T27E9.7   419    DLDTRIALVGPNGAGK    434

SMC_N: domain 2 of 2, from 425 to 435: score 3.6, E = 4.8
                   *->aIvGPNGSGKS<-*
                      a+vGPNG GKS
     T27E9.7   425    ALVGPNGAGKS    435

	[output cut off at A = 10 top alignments]


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