# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: pfam_list/PCIF1_WW.hmm.txt # target sequence database: proteomes/Nematostella_vectensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PCIF1_WW [M=172] Accession: PF12237.8 Description: Phosphorylated CTD interacting factor 1 WW domain Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.0027 17.8 0.0 2.7 8.0 0.0 2.2 2 tr|A7SPD4|A7SPD4_NEMVE Predicted protein (Fragment) OS=Nemat ------ inclusion threshold ------ 0.064 13.3 0.0 0.076 13.1 0.0 1.1 1 tr|A7T0T6|A7T0T6_NEMVE Predicted protein OS=Nematostella vec Domain annotation for each sequence (and alignments): >> tr|A7SPD4|A7SPD4_NEMVE Predicted protein (Fragment) OS=Nematostella vectensis OX=45351 GN=v1g125955 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 7.7 0.0 0.00027 3.3 88 137 .. 7 60 .. 5 100 .. 0.73 2 ! 8.0 0.0 0.00022 2.7 88 137 .. 168 221 .. 158 261 .. 0.75 Alignments for each domain: == domain 1 score: 7.7 bits; conditional E-value: 0.00027 PCIF1_WW 88 GsffdfkpasgsfeanPPfveevleraaehieklLeaaeeese....pLsfvvv 137 Gs+ d + + sf +PP+ + ++a+ hi ++ ++++++ e +Ls v tr|A7SPD4|A7SPD4_NEMVE 7 GSIPDSSITASSFRGHPPYNGRLNNQAVGHIGAWAAEKAQKGEflqvDLSQVTW 60 8899999999***********************999988777622234444444 PP == domain 2 score: 8.0 bits; conditional E-value: 0.00022 PCIF1_WW 88 GsffdfkpasgsfeanPPfveevleraaehieklLeaaeeese....pLsfvvv 137 Gs+ d + + sf +PP+ + ++a+ hi ++ ++++++ e +Ls v tr|A7SPD4|A7SPD4_NEMVE 168 GSIPDSSITASSFRGHPPYNGRLNNQAVGHIGAWAAEKAQKGEflqvDLSQVTW 221 899999999************************999988777622234444444 PP >> tr|A7T0T6|A7T0T6_NEMVE Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g220590 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.1 0.0 6.2e-06 0.076 41 78 .. 46 84 .. 22 99 .. 0.84 Alignments for each domain: == domain 1 score: 13.1 bits; conditional E-value: 6.2e-06 PCIF1_WW 41 aalpeevfevLkkefg.vsfecfAsPlncyfeqycsafp 78 a ++vf++L+ ++g +++ fA+ n+++++++s+f+ tr|A7T0T6|A7T0T6_NEMVE 46 LARIAAVFRLLNIKWGpYTIDRFATHYNAQLSRFHSKFA 84 566689*********9889*******************4 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (172 nodes) Target sequences: 24428 (8257945 residues searched) Passed MSV filter: 591 (0.0241935); expected 488.6 (0.02) Passed bias filter: 452 (0.0185034); expected 488.6 (0.02) Passed Vit filter: 30 (0.0012281); expected 24.4 (0.001) Passed Fwd filter: 2 (8.18733e-05); expected 0.2 (1e-05) Initial search space (Z): 24428 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.12u 0.01s 00:00:00.13 Elapsed: 00:00:00.06 # Mc/sec: 23672.78 // [ok]