t/data/hmmsearch3_multi.out

   1 # hmmsearch :: search profile(s) against a sequence database
   2 # HMMER 3.0 (March 2010); http://hmmer.org/
   3 # Copyright (C) 2010 Howard Hughes Medical Institute.
   4 # Freely distributed under the GNU General Public License (GPLv3).
   5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   6 # query HMM file:                  Pfam-A.hmm
   7 # target sequence database:        test_seqs.seq_raw.txt
   8 # output directed to file:         hmmsearch.output.txt
   9 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  10
  11 Query:       1-cysPrx_C  [M=40]
  12 Accession:   PF10417.4
  13 Description: C-terminal domain of 1-Cys peroxiredoxin
  14 Scores for complete sequences (score includes all domains):
  15    --- full sequence ---   --- best 1 domain ---    -#dom-
  16     E-value  score  bias    E-value  score  bias    exp  N  Sequence Description
  17     ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  18
  19    [No hits detected that satisfy reporting thresholds]
  20
  21
  22 Domain annotation for each sequence (and alignments):
  23
  24    [No targets detected that satisfy reporting thresholds]
  25
  26
  27 Internal pipeline statistics summary:
  28 -------------------------------------
  29 Query model(s):                            1  (40 nodes)
  30 Target sequences:                          3  (2141 residues)
  31 Passed MSV filter:                         0  (0); expected 0.1 (0.02)
  32 Passed bias filter:                        0  (0); expected 0.1 (0.02)
  33 Passed Vit filter:                         0  (0); expected 0.0 (0.001)
  34 Passed Fwd filter:                         0  (0); expected 0.0 (1e-05)
  35 Initial search space (Z):                  3  [actual number of targets]
  36 Domain search space  (domZ):               0  [number of targets reported over threshold]
  37 # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
  38 # Mc/sec: 14.27
  39 //
  40 Query:       DUF4229  [M=69]
  41 Accession:   PF14012.1
  42 Description: Protein of unknown function (DUF4229)
  43 Scores for complete sequences (score includes all domains):
  44    --- full sequence ---   --- best 1 domain ---    -#dom-
  45     E-value  score  bias    E-value  score  bias    exp  N  Sequence             Description
  46     ------- ------ -----    ------- ------ -----   ---- --  --------             -----------
  47   ------ inclusion threshold ------
  48           3  -17.8  37.0      0.019    3.0   2.5    4.3  5  lcl|Protein_ID1.3|M3 complement(48376..51420)
  49
  50
  51 Domain annotation for each sequence (and alignments):
  52 >> lcl|Protein_ID1.3|M3  complement(48376..51420)
  53    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
  54  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
  55    1 ?   -4.3   1.7         1         3      34      40 ..     305     311 ..     277     337 .. 0.55
  56    2 ?    2.6   2.1    0.0084     0.025      12      50 ..     382     418 ..     374     422 .. 0.69
  57    3 ?   -1.1   0.6      0.12      0.36       4      36 ..     841     874 ..     841     882 .. 0.52
  58    4 ?    3.0   2.5    0.0064     0.019       7      59 ..     872     925 ..     870     929 .. 0.90
  59    5 ?   -0.7   0.9     0.087      0.26      31      50 ..     972     991 ..     937    1001 .. 0.56
  60
  61   Alignments for each domain:
  62   == domain 1    score: -4.3 bits;  conditional E-value: 1
  63                DUF4229  34 laallAl 40
  64                            la+l A+
  65   lcl|Protein_ID1.3|M3 305 LAILSAI 311
  66                            3333332 PP
  67
  68   == domain 2    score: 2.6 bits;  conditional E-value: 0.0084
  69                DUF4229  12 fvvllavlvllgvligllvplllaallAlvvalplSfll 50
  70                            + v ++   l gv   l +p+  a++++++ +++lS  +
  71   lcl|Protein_ID1.3|M3 382 VFVPMF--SLTGVPRYLFIPMAEAVIFGMLSSFVLSQTF 418
  72                            333333..34455555449*****************776 PP
  73
  74   == domain 3    score: -1.1 bits;  conditional E-value: 0.12
  75                DUF4229   4 YtalRlglfvvllav..lvllgvligllvplllaa 36
  76                            Y +l lgl++ + ++  lv+++ + +l+ p++++
  77   lcl|Protein_ID1.3|M3 841 YRGLSLGLVASIILIyfLVVVNFESWLD-PFVIIT 874
  78                            5566688888777774344444444444.554443 PP
  79
  80   == domain 4    score: 3.0 bits;  conditional E-value: 0.0064
  81                DUF4229   7 lRlglfvvllavlvllgvligll.vplllaallAlvvalplSflllrklRrrat 59
  82                            +  +l ++l++++++l + +  l vp l  a++ + va + S+l+ +  R+r++
  83   lcl|Protein_ID1.3|M3 872 IITALPAALAGIVWMLYLTGTTLsVPALTGAIMCMGVATANSILVISFARERLA 925
  84                            56789999******9999999889*********************999999875 PP
  85
  86   == domain 5    score: -0.7 bits;  conditional E-value: 0.087
  87                DUF4229  31 plllaallAlvvalplSfll 50
  88                            pl  a++ +l++a +  +++
  89   lcl|Protein_ID1.3|M3 972 PLGRAVIGGLLLATIATLIF 991
  90                            55555555555554444333 PP
  91
  92
  93
  94 Internal pipeline statistics summary:
  95 -------------------------------------
  96 Query model(s):                            1  (69 nodes)
  97 Target sequences:                          3  (2141 residues)
  98 Passed MSV filter:                         1  (0.333333); expected 0.1 (0.02)
  99 Passed bias filter:                        1  (0.333333); expected 0.1 (0.02)
 100 Passed Vit filter:                         1  (0.333333); expected 0.0 (0.001)
 101 Passed Fwd filter:                         1  (0.333333); expected 0.0 (1e-05)
 102 Initial search space (Z):                  3  [actual number of targets]
 103 Domain search space  (domZ):               1  [number of targets reported over threshold]
 104 # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
 105 # Mc/sec: 16.41
 106 //
 107 Query:       ACR_tran  [M=1021]
 108 Accession:   PF00873.14
 109 Description: AcrB/AcrD/AcrF family
 110 Scores for complete sequences (score includes all domains):
 111    --- full sequence ---   --- best 1 domain ---    -#dom-
 112     E-value  score  bias    E-value  score  bias    exp  N  Sequence             Description
 113     ------- ------ -----    ------- ------ -----   ---- --  --------             -----------
 114    9.3e-189  616.9  10.5   1.2e-188  616.6   7.2    1.0  1  lcl|Protein_ID1.3|M3 complement(48376..51420)
 115
 116
 117 Domain annotation for each sequence (and alignments):
 118 >> lcl|Protein_ID1.3|M3  complement(48376..51420)
 119    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 120  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
 121    1 !  616.6   7.2  3.9e-189  1.2e-188      71    1021 .]      11    1000 ..       2    1000 .. 0.93
 122
 123   Alignments for each domain:
 124   == domain 1    score: 616.6 bits;  conditional E-value: 3.9e-189
 125                             S-TTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHHHHHHHHHGGGS-HHHHHH-EEEEEEECCECEEEEEEESSSTS-HHHHHHHH CS
 126               ACR_tran   71 gldglkyvsSqSseglssitvtFedgtdidiArqqvqnrlqeaknkLPeevqepgiskiktssseilvlavtskdgsltktdlrdla 157
 127                              ++ +++++SqS  g   + + F+ + di  A+ qv++  q + +++P ++++p i   +++  +il+la++sk   l++  + dl
 128   lcl|Protein_ID1.3|M3   11 TVNDIEHIESQSLFGYGIVKIFFQPDVDIRTANAQVTAISQTVLKQMPPGITPPLILNYNAATVPILQLALSSK--VLSEDRIFDLG 95
 129                             578899********************************************************************..*********** PP
 130
 131                             HHCTHHHHHTSTTEEEEEESS.--EEEEEEE-HHHHHCTT--HHHHHHHHHHHSSB-EEEECTT-SB-EEEE-SB---SCCHHCT-E CS
 132               ACR_tran  158 esnikdqlsrveGVgdvqliGgsekavriwldpqklaklgltltdvvsalkeqnvqvaaGqlegqqeelliraqgrlqsaediekii 244
 133                             ++ i++ql+ v G +    +Gg+ ++++i ldpq++++ +++++dv++al++qn   + G+ +  + e+++++++   +   ++++
 134   lcl|Protein_ID1.3|M3   96 QNFIRPQLATVRGSAVPSPYGGKVRQIQIDLDPQAMQSKRVSPDDVARALSQQNLVLSPGTEKIGSFEYNVKINDSPDEFTLLNNLP 182
 135                             *************************************************************************************** PP
 136
 137                             EEETTSEEEEHHHCEEEEEEESSSS-EEEETTCEEEEEEEEEETTSBHHHHHHHHHHHHHCCGGGSSTTEEEEEEEESHHHHHHHHH CS
 138               ACR_tran  245 vksqdgskvrlrDvAkvelgaeeeriaatlngkpavllavkklpganaievvkavkekleelketlPegveivvvydttefvrasie 331
 139                             +k+  g  + ++DvA+v +g   + ++++ +g   vl+++ k     ++++++  ke +++lketlP+++ ++vv d++ fv+++i+
 140   lcl|Protein_ID1.3|M3  183 IKNVGGVTIFIHDVAHVRDGFPPQINVVRDDGRRSVLMTILKNGATSTLDIIQGTKELIPKLKETLPNNLVLKVVGDQSIFVKSAIS 269
 141                             *************************************************************************************** PP
 142
 143                             HHHHHHHHHHHHHHHHHHHHHSSHCCCHHHHHHHHHHHHHHHHHHHHTT--EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS CS
 144               ACR_tran  332 eVvktlleaivLvvlvlflFLqnlratlipaiavPlsllgtfavlkalglsiNlltlfgLvlAiGlvvDdAiVvvEnverkleeege 418
 145                              Vv +  +a +L  ++++lFL+++r+t+i+ +++Pl++l ++++l++ g ++N++tl+gL+lA+G++vDdA Vv+En+  +le+ g+
 146   lcl|Protein_ID1.3|M3  270 GVVREGTIAGILTSVMILLFLGSWRSTIIISMSIPLAILSAIIFLSLTGNTLNVMTLGGLALAVGMLVDDATVVIENINHHLEM-GK 355
 147                             ************************************************************************************.** PP
 148
 149                             -HHHHHHHHHHHHCCHHHHHHHHHHHHCCGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCS----TT-CC...... CS
 150               ACR_tran  419 kpleaalksmkeiegalvaialvllavfvPilflgGveGklfrqfaltivlaillsvlvaltltPalcallLkarkeekek...... 499
 151                                +a++ ++++i  + + ++l++++vfvP+++l+Gv   lf ++a ++++ +l s +++ t++P ++  lLk + ++ ++
 152   lcl|Protein_ID1.3|M3  356 PTTKAIIDAARQIIQPALVSTLSICIVFVPMFSLTGVPRYLFIPMAEAVIFGMLSSFVLSQTFVPTVANKLLKYQTQHFKHehhtda 442
 153                             *************************************************************************8776544446799* PP
 154
 155                             ........................CHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHH.HHHHHCCS-BESS----TSEE CS
 156               ACR_tran  500 ........................gffrefnrlfdalerrYekllekvlrhravvllvalllvvg.slllfvripkeflPeedegvl 561
 157                                                     ++ + f++ f ++   Y+ +l++ l hr+  ++++l +v++ ++ lf+ ++k+f+Pe d g++
 158   lcl|Protein_ID1.3|M3  443 hrpehdpnfkvhrsvkasifqffiNIQQGFEKRFTKVRLVYRSILHFALDHRKKFITLFLGFVIVsCVTLFPLLGKNFFPEVDSGDM 529
 159                             *******************9655555578*************************999999887775899****************** PP
 160
 161                             EEEEE-STTC-HHHHHHHHHHHHHHHH...TTTTEEEEEEEESESSSS..E........CTTEEEEEEEE--CTTS-SCCCSHHHHH CS
 162               ACR_tran  562 vtsvqlppgvsleqtekvlkqvekilk...ekpevesvfavtGfafagdta........gqnsakvfisLkpekerkeeektveali 637
 163                              ++++++ g+ +e+t+k  + +e++++    ++e + ++   G + +g +         g++ +++ i+L ++      ++  ++ +
 164   lcl|Protein_ID1.3|M3  530 KIHIRVQVGTRIEETAKQFDLIENTIRrlvPQNELDTIVDNIGLSVSGINTaysstgtiGPQDGDILIHLNEN------HHPTKEYM 610
 165                             ************************8875446889999999999888774331111111134445555555444......45688999 PP
 166
 167                             HHHHHHC.CTSTSSEEEEEE-SSSCCCSSSSSEEEEEEE.TSSSCHHHHHHHHHHHHHHHCCSTTEECEEESS-S-EEEEEEEE-HH CS
 168               ACR_tran  638 erlrkel.ekikganvellapiqlreletlsgvrlelqvklfgddleaLseareqllaalkqlpeladvrseqqedepqlqvkidre 723
 169                             ++lr+ l ++++g++ +++ p +++ +    gv + ++  + g ++++  + ++++l+ ++++p++ad+r++q ++ pq++v+idr
 170   lcl|Protein_ID1.3|M3  611 KKLRETLpRAFPGVS-FAFLPADITSQILNFGVPAPIDIRVDGPNHDNNLKFVRAILKDIRNVPGIADLRVQQATNYPQFNVDIDRS 696
 171                             999999945678887.7888999*999************************************************************ PP
 172
 173                             HHHHCTB-HHHHHHHHHHHHT-..EEEEEEEETTE...EEEEEEEE-GGGSSSGGGGCC-EEEETTSE.EEECGGCEEEEEEEE-SE CS
 174               ACR_tran  724 kaaalGvsiadinetlstalgg..syvndfieegr...vvkvvvqleedlrsspedlkklyvrnkkgk.mvplsavakieeekgpns 804
 175                             +a+++G++  di + l + l g  +++ +f  +++    + +v+q+++ + +s+ dl+++++++k++  m  l+ + +ie+ ++ +
 176   lcl|Protein_ID1.3|M3  697 QAKNYGLTEGDITNSLVATLAGtsQVAPTFWLNNKngvSYPIVIQMPQYKINSLADLANIPITTKESSsMQVLGGLGSIERDQSDSV 783
 177                             ************8877666655434556776544422279***********************998764889*************** PP
 178
 179                             EEEETTCEEEEEEEEESTTS...-HHHHHHHHHHCCTT..SSTTEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCTSSST CS
 180               ACR_tran  805 ierenglrsveisgevaegd...slgeaeeavekiakqvklPagvgiewtglseqeqeagnsllllvalalllvflvLaalyeslsd 888
 181                             i+++n ++s+ i ++++ +d   ++g++e+++++ +++  lP+gv+++ +g+    q ++  l+l ++++++l++++  + +es++d
 182   lcl|Protein_ID1.3|M3  784 ISHYNIKPSFDIFASLQGRDlgsISGDIETIIQHHHQE--LPKGVSVKLQGQVPIMQDSYRGLSLGLVASIILIYFLVVVNFESWLD 868
 183                             ****************8876222578999999999888..*********************************************** PP
 184
 185                             CHHHHTTHHHHHHHHHHHHHHTT--BSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTBHHHHHHHHHHHHCHHHHHHHHHHHHH CS
 186               ACR_tran  889 pllvlltvPlalvGallalllrglelsviaqvGlilliGlavkNailivefakelrekeglsleeAileaaklRLrPiLMTalaail 975
 187                             p+++++ +P al+G +  l+l+g++lsv a+ G i+ +G+a  N il+++fa+e  +   ++  +A+lea+ +R+rP+LMTa a+++
 188   lcl|Protein_ID1.3|M3  869 PFVIITALPAALAGIVWMLYLTGTTLSVPALTGAIMCMGVATANSILVISFARERLA-IVKDSTQAALEAGYTRFRPVLMTASAMLI 954
 189                             *********************************************************.888899*********************** PP
 190
 191                             CCHHHHTT-STTHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH CS
 192               ACR_tran  976 GvlPLalstGaGselqqplgivvlGGlvtstvLtlllvPvlYvlva 1021
 193                             G++P+al+ G+G e   plg +v+GGl+++t+ tl +vPv++ +v+
 194   lcl|Protein_ID1.3|M3  955 GMIPMALGLGDGGEQNAPLGRAVIGGLLLATIATLIFVPVVFSVVH 1000
 195                             ******************************************9997 PP
 196
 197
 198
 199 Internal pipeline statistics summary:
 200 -------------------------------------
 201 Query model(s):                            1  (1021 nodes)
 202 Target sequences:                          3  (2141 residues)
 203 Passed MSV filter:                         1  (0.333333); expected 0.1 (0.02)
 204 Passed bias filter:                        1  (0.333333); expected 0.1 (0.02)
 205 Passed Vit filter:                         1  (0.333333); expected 0.0 (0.001)
 206 Passed Fwd filter:                         1  (0.333333); expected 0.0 (1e-05)
 207 Initial search space (Z):                  3  [actual number of targets]
 208 Domain search space  (domZ):               1  [number of targets reported over threshold]
 209 # CPU time: 0.17u 0.03s 00:00:00.20 Elapsed: 00:00:00.19
 210 # Mc/sec: 11.27
 211 //