t/data/cysprot1b.hmmsearch

   1 hmmsearch - search a sequence database with a profile HMM
   2 HMMER 2.2g (August 2001)
   3 Copyright (C) 1992-2001 HHMI/Washington University School of Medicine
   4 Freely distributed under the GNU General Public License (GPL)
   5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   6 HMM file:                   Peptidase_C1.hmm [Peptidase_C1]
   7 Sequence database:          cysprot1b.fa
   8 per-sequence score cutoff:  [none]
   9 per-domain score cutoff:    [none]
  10 per-sequence Eval cutoff:   <= 10
  11 per-domain Eval cutoff:     [none]
  12 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  13
  14 Query HMM:   Peptidase_C1
  15 Accession:   PF00112
  16 Description: Papain family cysteine protease
  17   [HMM has been calibrated; E-values are empirical estimates]
  18
  19 Scores for complete sequences (score includes all domains):
  20 Sequence   Description                                  Score    E-value  N
  21 --------   -----------                                  -----    ------- ---
  22 CATL_RAT                                                449.4     2e-135   1
  23 CATL_HUMAN                                              444.5   6.1e-134   1
  24 CATH_RAT                                                381.8   4.8e-115   1
  25 PAPA_CARPA                                              337.7     9e-102   1
  26
  27 Parsed for domains:
  28 Sequence   Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
  29 --------   ------- ----- -----    ----- -----      -----  -------
  30 CATL_RAT     1/1     114   332 ..     1   337 []   449.4   2e-135
  31 CATL_HUMAN   1/1     114   332 ..     1   337 []   444.5 6.1e-134
  32 CATH_RAT     1/1     114   330 ..     1   337 []   381.8 4.8e-115
  33 PAPA_CARPA   1/1     134   343 ..     1   337 []   337.7   9e-102
  34
  35 Alignments of top-scoring domains:
  36 CATL_RAT: domain 1 of 1, from 114 to 332: score 449.4, E = 2e-135
  37                    *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt
  38                       +P+++DWRe kg  VtpVK+QG qCGSCWAFSa g lEg+ ++kt
  39     CATL_RAT   114    IPKTVDWRE-KG-CVTPVKNQG-QCGSCWAFSASGCLEGQMFLKT-- 155
  40
  41                    kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke
  42                        gkl+sLSEQ+LvDC++ d gn+      GCnG Glmd Af+Yik+
  43     CATL_RAT   156 ----GKLISLSEQNLVDCSH-DQGNQ------GCNG-GLMDFAFQYIKE- 192
  44
  45                    qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt
  46                        NgGl++E++Y     PY+    +kd                   g+
  47     CATL_RAT   193 ----NGGLDSEESY-----PYE----AKD-------------------GS 210
  48
  49                    CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai
  50                    Cky+  + ++     a+++g++d+p++     E+al+ka+a++GP+sVa+
  51     CATL_RAT   211 CKYR-AEYAV-----ANDTGFVDIPQQ-----EKALMKAVATVGPISVAM 249
  52
  53                    dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY
  54                    das+ s    q+Y+sG       +Y+++    C+++   +LdH+Vl+VGY
  55     CATL_RAT   250 DASHPS---LQFYSSG-------IYYEP---NCSSK---DLDHGVLVVGY 283
  56
  57                    GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW
  58                    G e+                                      ++++ +YW
  59     CATL_RAT   284 GYEG-T------------------------------------DSNKDKYW 296
  60
  61                    IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-*
  62                    +VKNSWG++WG++GY++ia+++n    n+CG+a+ asypi
  63     CATL_RAT   297 LVKNSWGKEWGMDGYIKIAKDRN----NHCGLATAASYPI    332
  64
  65 CATL_HUMAN: domain 1 of 1, from 114 to 332: score 444.5, E = 6.1e-134
  66                    *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt
  67                       +P s+DWRe kg +VtpVK+QG qCGSCWAFSa+galEg+ ++kt
  68   CATL_HUMAN   114    APRSVDWRE-KG-YVTPVKNQG-QCGSCWAFSATGALEGQMFRKT-- 155
  69
  70                    kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke
  71                        g l+sLSEQ+LvDC+g + gn+      GCnG Glmd+Af+Y+++
  72   CATL_HUMAN   156 ----GRLISLSEQNLVDCSG-PQGNE------GCNG-GLMDYAFQYVQD- 192
  73
  74                    qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt
  75                        NgGl++E++Y     PY+    +++                    +
  76   CATL_HUMAN   193 ----NGGLDSEESY-----PYE----ATE-------------------ES 210
  77
  78                    CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai
  79                    Ckyn +k s+     a+++g++d+p +     E+al+ka+a++GP+sVai
  80   CATL_HUMAN   211 CKYN-PKYSV-----ANDTGFVDIPKQ-----EKALMKAVATVGPISVAI 249
  81
  82                    dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY
  83                    da++ s   F +Yk G       +Y ++   +C+++   + dH+Vl+VGY
  84   CATL_HUMAN   250 DAGHES---FLFYKEG-------IYFEP---DCSSE---DMDHGVLVVGY 283
  85
  86                    GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW
  87                    G e+                                      e+++ +YW
  88   CATL_HUMAN   284 GFES-T------------------------------------ESDNNKYW 296
  89
  90                    IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-*
  91                    +VKNSWG++WG+ GY+++a+++     n+CGIas asyp+
  92   CATL_HUMAN   297 LVKNSWGEEWGMGGYVKMAKDRR----NHCGIASAASYPT    332
  93
  94 CATH_RAT: domain 1 of 1, from 114 to 330: score 381.8, E = 4.8e-115
  95                    *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt
  96                        P s+DWR+ kg  V+pVK+QG  CGSCW FS++galE++ +i++
  97     CATH_RAT   114    YPSSMDWRK-KGNVVSPVKNQG-ACGSCWTFSTTGALESAVAIAS-- 156
  98
  99                    kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke
 100                        gk   L EQqLvDC   +++n+      GC+G Gl+++AfeYi++
 101     CATH_RAT   157 ----GKMMTLAEQQLVDCAQ-NFNNH------GCQG-GLPSQAFEYILY- 193
 102
 103                    qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt
 104                        N+G++ E++Y     PY     gk+                   g+
 105     CATH_RAT   194 ----NKGIMGEDSY-----PYI----GKN-------------------GQ 211
 106
 107                    CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai
 108                    Ck+n +++++     a++k+ ++++ n    dE+a+ +a+a + Pvs a+
 109     CATH_RAT   212 CKFN-PEKAV-----AFVKNVVNITLN----DEAAMVEAVALYNPVSFAF 251
 110
 111                    dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY
 112                    +++e    DF++YksG       vY++    +C +tp + ++HAVl+VGY
 113     CATH_RAT   252 EVTE----DFMMYKSG-------VYSSN---SCHKTP-DKVNHAVLAVGY 286
 114
 115                    GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW
 116                    G +n g                                          YW
 117     CATH_RAT   287 GEQN-GLL----------------------------------------YW 295
 118
 119                    IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-*
 120                    IVKNSWG++WG nGYf i+Rgkn     +CG+a +asypi
 121     CATH_RAT   296 IVKNSWGSNWGNNGYFLIERGKN-----MCGLAACASYPI    330
 122
 123 PAPA_CARPA: domain 1 of 1, from 134 to 343: score 337.7, E = 9e-102
 124                    *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt
 125                       +Pe +DWR+ kg aVtpVK+QG +CGSCWAFSav ++Eg+++i+t
 126   PAPA_CARPA   134    IPEYVDWRQ-KG-AVTPVKNQG-SCGSCWAFSAVVTIEGIIKIRT-- 175
 127
 128                    kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke
 129                        g+l  +SEQ+L+DCd+    ++      GCnG G+++ A++ + +
 130   PAPA_CARPA   176 ----GNLNEYSEQELLDCDR---RSY------GCNG-GYPWSALQLVAQ- 210
 131
 132                    qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt
 133                          G++    Y     PY+    g++
 134   PAPA_CARPA   211 -----YGIHYRNTY-----PYE----GVQ-------------------RY 227
 135
 136                    CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai
 137                    C+++ +k+ +    +ak +g ++v+++    +E al + +a+ +PvsV
 138   PAPA_CARPA   228 CRSR-EKGPY----AAKTDGVRQVQPY----NEGALLYSIAN-QPVSVVL 267
 139
 140                    dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY
 141                    +a +    DFqlY++G       ++++    +Cg+     +dHAV++VGY
 142   PAPA_CARPA   268 EAAGK---DFQLYRGG-------IFVG----PCGN----KVDHAVAAVGY 299
 143
 144                    GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW
 145                    G                                              +Y
 146   PAPA_CARPA   300 G---------------------------------------------PNYI 304
 147
 148                    IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-*
 149                    ++KNSWGt WGEnGY+ri+Rg+++s ++ CG+ ++  yp+
 150   PAPA_CARPA   305 LIKNSWGTGWGENGYIRIKRGTGNS-YGVCGLYTSSFYPV    343
 151
 152
 153 Histogram of all scores:
 154 score    obs    exp  (one = represents 1 sequences)
 155 -----    ---    ---
 156 > 337      4      -|====
 157
 158
 159 % Statistical details of theoretical EVD fit:
 160               mu =  -195.8384
 161           lambda =     0.1423
 162 chi-sq statistic =     0.0000
 163   P(chi-square)  =          0
 164
 165 Total sequences searched: 4
 166
 167 Whole sequence top hits:
 168 tophits_s report:
 169      Total hits:           4
 170      Satisfying E cutoff:  4
 171      Total memory:         16K
 172
 173 Domain top hits:
 174 tophits_s report:
 175      Total hits:           4
 176      Satisfying E cutoff:  4
 177      Total memory:         20K