# 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/Anolis_carolinensis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.00034 20.3 0.0 0.00058 19.6 0.0 1.3 1 tr|H9GCS8|H9GCS8_ANOCA PDX1 C-terminal inhibiting factor 1 O ------ inclusion threshold ------ 0.081 12.6 0.0 0.16 11.6 0.0 1.5 1 tr|G1KPE0|G1KPE0_ANOCA Ankyrin repeat and SOCS box containin 0.14 11.8 0.0 0.26 10.9 0.0 1.4 1 tr|R4GCJ8|R4GCJ8_ANOCA Uncharacterized protein OS=Anolis car Domain annotation for each sequence (and alignments): >> tr|H9GCS8|H9GCS8_ANOCA PDX1 C-terminal inhibiting factor 1 OS=Anolis carolinensis OX=28377 GN=PCIF1 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 19.6 0.0 9.4e-08 0.00058 1 32 [. 446 477 .. 446 492 .. 0.95 Alignments for each domain: == domain 1 score: 19.6 bits; conditional E-value: 9.4e-08 PCIF1_WW 1 kLkeLyesseeddekleaflsrvfalllrYda 32 kL Ly++s+ dd+++e fl rv++ll+rY+ tr|H9GCS8|H9GCS8_ANOCA 446 KLWLLYRYSCIDDSSFERFLPRVWCLLRRYQV 477 7899**************************95 PP >> tr|G1KPE0|G1KPE0_ANOCA Ankyrin repeat and SOCS box containing 4 OS=Anolis carolinensis OX=28377 GN=ASB4 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.6 0.0 2.6e-05 0.16 19 63 .. 331 375 .. 313 379 .. 0.89 Alignments for each domain: == domain 1 score: 11.6 bits; conditional E-value: 2.6e-05 PCIF1_WW 19 flsrvfalllrYdallgeaglqaalpeevfevLkkefgvsfecfA 63 ++++v +++ Y++++++++++aa+pe+vf++ k+ ++ fe++A tr|G1KPE0|G1KPE0_ANOCA 331 YPRAVEVIVNSYEHIKATTKWRAAIPEDVFQMHKDFYESLFEACA 375 6677889999********************************999 PP >> tr|R4GCJ8|R4GCJ8_ANOCA Uncharacterized protein OS=Anolis carolinensis OX=28377 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.9 0.0 4.2e-05 0.26 39 106 .. 370 437 .. 331 450 .. 0.80 Alignments for each domain: == domain 1 score: 10.9 bits; conditional E-value: 4.2e-05 PCIF1_WW 39 lqaalpeevfevLkkefg.vsfecfAsPlncyfeqycsafpdtDayFGsvGsffdfkpasgsfeanPPf 106 +++ l e+++ L ++g +++ fAsP n+++ +y + p ++ G++G+ f ++ + + ++PP tr|R4GCJ8|R4GCJ8_ANOCA 370 HEWKLDPEILDDLFLHWGrPTLDLFASPRNAQLPRYGARLPP-NSFPGCLGDAFLLDWSAEMLYLFPPI 437 55666667777666666646899***************9975.6888*****99888888888888873 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (172 nodes) Target sequences: 18528 (9796552 residues searched) Passed MSV filter: 549 (0.0296308); expected 370.6 (0.02) Passed bias filter: 424 (0.0228843); expected 370.6 (0.02) Passed Vit filter: 30 (0.00161917); expected 18.5 (0.001) Passed Fwd filter: 3 (0.000161917); expected 0.2 (1e-05) Initial search space (Z): 18528 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.07 # Mc/sec: 24071.53 // [ok]