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:            hmm3/seq/H06O01.2
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Query:  H06O01.2  CE11572   chromodomain-helicase-DNA-biniding protein status:Partially_confirmed TR:O17909 protein_id:CAB07481.1

Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N
--------        -----------                             -----    ------- ---
SNF2_N          SNF2 family N-terminal domain           410.2     2e-119   1
helicase_C      Helicase conserved C-terminal domain     83.2    3.7e-22   1
chromo          'chromo' (CHRromatin Organization MOd    78.0    1.9e-21   2
Peptidase_M16_C Peptidase M16 inactive domain             5.1          3   1
DUF89           Protein of unknown function DUF89         3.7        2.6   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
chromo            1/2     238   259 ..    29    50 .]    39.3  4.7e-10
chromo            2/2     307   354 ..     1    50 []    39.0  5.5e-10
DUF89             1/1     617   641 ..   401   425 .]     3.7      2.6
SNF2_N            1/1     408   689 ..     1   356 []   410.2   2e-119
helicase_C        1/1     751   825 ..     1    72 []    83.2  3.7e-22
Peptidase_M16_C   1/1     832   853 ..   177   197 .]     5.1        3

Alignments of top-scoring domains:
chromo: domain 1 of 2, from 238 to 259: score 39.3, E = 4.7e-10
                   *->eYlvKWkGysdseNTWEpeenI<-*
                      +++vKW+G+s+ +NTWE+e ++
    H06O01.2   238    QFFVKWTGWSHLHNTWESENSL    259

chromo: domain 2 of 2, from 307 to 354: score 39.0, E = 5.5e-10
                   *->eeeyvVEkdDPniIldhrvkke...dgaGkleYlvKWkGysdseNTW
                      ee++ VE+     + +h  ++++  dg    eYl+KW G+++s++TW
    H06O01.2   307    EEYKKVER-----VVAHQTSRDraaDGSMATEYLIKWSGLPYSDCTW 348

                   EpeenI<-*
                   E+e+ +
    H06O01.2   349 EDEKMV    354

DUF89: domain 1 of 1, from 617 to 641: score 3.7, E = 2.6
                   *->caLRtkKadVargLgvgvgdkllkk<-*
                      ++LR++K+dV   L++++++ l ++
    H06O01.2   617    FLLRRVKKDVEKSLPPKTEQILRVD    641

SNF2_N: domain 1 of 1, from 408 to 689: score 410.2, E = 2e-119
                   *->YQleGvnWLislyknlvkkendscglggILADEMGLGKTlQtIslla
                      YQleG+nW++  +++         g++ ILADEMGLGKT+Q+Islla
    H06O01.2   408    YQLEGLNWMVYAWCK---------GNSSILADEMGLGKTIQSISLLA 445

                   yllelkpkaekrigpfLvVcPlStldnWlnEfekWapddlnivvyygdgn
                    l + + +a    gp+LvV+PlSt+  W+ Ef +Wap ++n+vvy+gd
    H06O01.2   446 SLFHRYDLA----GPYLVVVPLSTMAAWQKEFAQWAP-EMNLVVYMGDVV 490

                   srdqirkdellrnflkdggr.lkydvlitsYeiirkNkLlkdkdeLkklg
                   srd+ir +e+    +  g +++k + ++t+Yei++k     dk++L++
    H06O01.2   491 SRDMIRQYEW----FVGGTKkMKINAILTTYEILLK-----DKAFLSS-- 529

                   inwdylilDEgHHrlKNedSklrkskalnklkhtrnRLlLTGTPlQNnLk
                   i+w  l +DE+ HrlKN +S l  +k l +++  +++Ll+TGTPlQN+Lk
    H06O01.2   530 IDWAALLVDEA-HRLKNDESLL--YKSLTQFR-FNHKLLITGTPLQNSLK 575

                   ElwsLlnFlmPgiFgsleeyindgksFdkwfnnpilegrdsavLadasla
                   Elw+Ll+F+mP +F+ +       ++F+  +n  ++ g
    H06O01.2   576 ELWALLHFIMPEKFDCW-------EEFETAHNESNHKG------------ 606

                   LrrkkdveeglkllnrLhkilkpflLRRlkkdveksLpppeKteyvlfck
                                + +Lhk l pflLRR+kkdveksLpp  Kte++l++
    H06O01.2   607 -------------ISALHKKLEPFLLRRVKKDVEKSLPP--KTEQILRVD 641

                   lsklQkelYkkflkgeskdvkaindserreggkeknegksrllnlimqLr
                   +++ Qk++Yk++l   +k++  + +     g+k+   ++ ++ nl m+L+
    H06O01.2   642 MTAHQKQFYKWIL---TKNYRELSK-----GVKG---SINGFVNLVMELK 680

                   KicNfHPyLf<-*
                   K+cN H  L
    H06O01.2   681 KCCN-HASLT    689

helicase_C: domain 1 of 1, from 751 to 825: score 83.2, E = 3.7e-22
                   *->gikvarlhGglsqeeReeilekFrngks...kvLvaTdvaarGiDip
                       ++  rl+G++ ++ R+++l+  ++  s++  +L++T+++++Gi++
    H06O01.2   751    RFPSQRLDGSMRADLRKQALDHYNAPGStdfAFLLSTRAGGLGINLA 797

                   dvnlVInydlpwnpesyiQRiGRaGRaG<-*
                    +++VI++d +wnp++++Q++ Ra+R+G
    H06O01.2   798 TADTVIIFDSDWNPQNDLQAMSRAHRIG    825

Peptidase_M16_C: domain 1 of 1, from 832 to 853: score 5.1, E = 3
                   *->leklaeeG.iteeeleraknql<-*
                      + +l+++G++ ee++erak+ l
    H06O01.2   832    IYRLVTKGsVEEEIVERAKRKL    853



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