# hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: ASH1L.fa # target HMM database: /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm # output directed to file: ASH1L.PFam-27-A # per-seq hits tabular output: ASH1L-hmmscan.tblout # number of worker threads: 16 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|110349788|ref|NP_060959.2| [L=2964] Description: histone-lysine N-methyltransferase ASH1L [Homo sapiens] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-26 93.7 1.8 2.7e-25 89.5 0.1 3.9 2 SET SET domain 2.2e-18 66.1 0.1 6.1e-18 64.6 0.1 1.8 1 BAH BAH domain 3.1e-17 62.2 0.0 9.5e-17 60.7 0.0 1.9 1 Bromodomain Bromodomain 6.3e-07 28.9 13.5 6.3e-07 28.9 9.3 2.6 3 PHD PHD-finger Domain annotation for each model (and alignments): >> SET SET domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.1 0.1 0.27 1e+03 42 71 .. 1244 1281 .. 1165 1298 .. 0.70 2 ! 89.5 0.1 7.3e-29 2.7e-25 1 162 [] 2151 2256 .. 2151 2256 .. 0.93 Alignments for each domain: == domain 1 score: -0.1 bits; conditional E-value: 0.27 HHC.TTCCTCE........HHHHHHHHHHTHHHHHHH. CS xxxxxxxxxxx........xxxxxxxxxxxxxxxxxxx RF SET 42 kaleaasrala........akskrqkagksvrspaals 71 ++++++++ + +k+krqk++ +++ p++ + gi|110349788|ref|NP_060959.2| 1244 LKEKHKHKCKRrnhdylsyDKMKRQKRKRKKKYPQLRN 1281 22222222222556677778999999999999998865 PP == domain 2 score: 89.5 bits; conditional E-value: 7.3e-29 SEEEEESS-B-TTEEEEEECCEEEECCCCHH......HHHHHHHHHHC.TTCCTCEHHHHHHHHHHTHHHHHHH.TTT CS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF SET 1 GrGvrAtedIpkgefvceyvgelltddeaek....kpelerldlskaleaasralaakskrqkagksvrspaalsars 74 G+G+r++e++++g+f++ey ge+++ +e ++ + + + gi|110349788|ref|NP_060959.2| 2151 GWGIRTKEPLKAGQFIIEYLGEVVSEQEFRNrmieQ---------------YHNHS---------------------- 2191 9******************************76532...............33333...................... PP S.GGG..HHHHHHHHHHHHHH.EEETTSSCEEEEECEECCECCCGGGHEESSS.SEEEEEECSTTSSEEEEEESS-B- CS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF SET 75 galksalaasvdasesaaepkatedeyeeeeseyvidakllgnlarflNHSCdpNltvqavfvlrlprvaffAtrdIk 152 +++ + +s vid+ +gn arf+NHSCdpN++ q ++v++ +r++++A++d + gi|110349788|ref|NP_060959.2| 2192 -----------------------DHYCLNLDSGMVIDSYRMGNEARFINHSCDPNCEMQKWSVNGVYRIGLYALKDMP 2246 .......................68999************************************************** PP TTEEEEEEES CS xxxxxxxxxx RF SET 153 kGeEltidYg 162 +G+Elt+dY+ gi|110349788|ref|NP_060959.2| 2247 AGTELTYDYN 2256 *********7 PP >> BAH BAH domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 64.6 0.1 1.7e-21 6.1e-18 3 117 .. 2658 2791 .. 2656 2793 .. 0.95 Alignments for each domain: == domain 1 score: 64.6 bits; conditional E-value: 1.7e-21 EETTCEEEEEETT...................TTTEEEEEEEEEEEEETTTTCEEEEEEEEEECGGGS..TTCHHSTT CS BAH 3 yavGdfVyvddts...................tdepyqirrieelkenakneaeatvlvrwflrpeet..sllklrqk 59 ++ Gd+Vy+ +s ++ + i+rie+l++n+k+e ++++++ ++rp+et s + +++ gi|110349788|ref|NP_060959.2| 2658 LRQGDCVYLMRDSrrtpdghpvrqsyrllshiNRDKLDIFRIEKLWKNEKEE--RFAFGHHYFRPHEThhSPSRRFYH 2733 578*****************************9******************9..***************999****** PP TEEEEEEEEEEEEGGGEEEEEEEEEHHHHTTCHCHCHHTTTEEEEEEEEETTTTEEEE CS BAH 60 rEvfltreseilplaairgkcrVvllsdgeeaqnylpklddtFycslvydpeaktfla 117 +E+f + +ei+pl+a+ g c V++l ++++ +++ k++d++ c++ d++a f + gi|110349788|ref|NP_060959.2| 2734 NELFRVPLYEIIPLEAVVGTCCVLDLYTYCKGRPKGVKEQDVYICDYRLDKSAHLFYK 2791 ************************************66*************9987765 PP >> Bromodomain Bromodomain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 60.7 0.0 2.6e-20 9.5e-17 1 82 [. 2448 2531 .. 2448 2533 .. 0.91 Alignments for each domain: == domain 1 score: 60.7 bits; conditional E-value: 2.6e-20 HHHHHH..HBHTTTCGGGGCSTT-GCCSTTHHHH-SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTS CS Bromodomain 1 ceqile..dlqehklastFsapvdakeapdYydiikrPidLktIqkklasgkyqslaqfekdlelvfsNavkyneegs 76 c+ i++ d ++ la++ + +++k++ dYy++i+ P+dL tI+k + g+y+++++f +d+ vf Na ky++ +s gi|110349788|ref|NP_060959.2| 2448 CDGIISykDSSRQALAAPLLNLPPKKKNADYYEKISDPLDLITIEKQILTGYYKTVEAFDADMLKVFRNAEKYYGRKS 2525 6677764466666699************************************************************** PP HHHHHH CS Bromodomain 77 dvyeda 82 +v +d+ gi|110349788|ref|NP_060959.2| 2526 PVGRDV 2531 *98875 PP >> PHD PHD-finger # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.5 0.3 2.3 8.6e+03 22 43 .. 1534 1556 .. 1533 1557 .. 0.67 2 ? -3.8 0.8 2.8 1e+04 4 17 .. 2128 2141 .. 2127 2143 .. 0.86 3 ! 28.9 9.3 1.7e-10 6.3e-07 1 50 [. 2582 2625 .. 2582 2626 .. 0.91 Alignments for each domain: == domain 1 score: -3.5 bits; conditional E-value: 2.3 SEEETTTSTSSSSHHSHHSS.TB CS PHD 22 ewfHlkClglkleseekpeg.ew 43 + +H++C +l+ +++ + ++ +w gi|110349788|ref|NP_060959.2| 1534 HRCHMSCPHLSPSKSLINREeQW 1556 568****9988776555444455 PP == domain 2 score: -3.8 bits; conditional E-value: 2.8 TTSSTCTTSSEEEB CS PHD 4 vCgksdeegelvlC 17 +C++ + +e+v+C gi|110349788|ref|NP_060959.2| 2128 CCNQRIQRHEWVQC 2141 49999999*****9 PP == domain 3 score: 28.9 bits; conditional E-value: 1.7e-10 SBTTTSSTCTTSSEEEBSSSSSEEETTTSTSSSSHHSHHSSTBSSHHHHT CS PHD 1 rCkvCgksdeegelvlCdgCkewfHlkClglkleseekpegewlCeeCke 50 rC +Cg ++eg +++Cd+C w+H +C+g++ + + +++lCe+C++ gi|110349788|ref|NP_060959.2| 2582 RC-ICGLYKDEGLMIQCDKCMVWQHCDCMGVNSD---V--EHYLCEQCDP 2625 69.****************************976...3..25******97 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (2964 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 979 (0.0660104); expected 296.6 (0.02) Passed bias filter: 151 (0.0101814); expected 296.6 (0.02) Passed Vit filter: 29 (0.00195536); expected 14.8 (0.001) Passed Fwd filter: 5 (0.000337132); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 1.10u 0.24s 00:00:01.34 Elapsed: 00:00:00.33 # Mc/sec: 23445.53 //