# hmmscan :: search sequence(s) against a profile 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 sequence file: AA/23726_FusoPortal_Gene_1777.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1777 [L=365] Description: # 1899084 # 1900178 # 1 # ID=1_1777;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.245 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-19 68.1 10.8 5.8e-15 55.4 0.2 3.1 3 DNA_pol3_beta DNA polymerase III beta subunit, N-terminal 1.6e-16 60.5 0.1 7.3e-14 51.9 0.1 2.7 2 DNA_pol3_beta_2 DNA polymerase III beta subunit, central dom 2.4e-06 27.3 9.4 3.9e-06 26.6 2.0 3.2 3 DNA_pol3_beta_3 DNA polymerase III beta subunit, C-terminal ------ inclusion threshold ------ 0.12 12.6 2.1 0.22 11.7 0.1 2.2 2 Psb28 Psb28 protein Domain annotation for each model (and alignments): >> DNA_pol3_beta DNA polymerase III beta subunit, N-terminal domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 55.4 0.2 1.4e-18 5.8e-15 1 120 [. 1 113 [. 1 114 [. 0.92 2 ! 8.5 0.3 0.00048 2 9 112 .. 128 231 .. 123 239 .. 0.76 3 ! 10.2 0.9 0.00014 0.57 3 107 .. 251 353 .. 249 361 .. 0.85 Alignments for each domain: == domain 1 score: 55.4 bits; conditional E-value: 1.4e-18 -EEEEEHHHHHHHHHHHHTTTSSSTSSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEESEECEE-EEEEEEHHHHHHHHHHSS CS DNA_pol3_beta 1 mkftiereellkelekvakvisnRntlpiLsgvllevkdsqlsltgtDleisiestisaeseeeegkvlvparllldivkaLp 83 mkf+i+r++ ++ + + +++++ ++ p L+g+ +++k++q+ ++g + ei++ + e+e +eg+vl+++ lll+ +k L+ 23726_FusoPortal_Gene_1777 1 MKFSINRQKTIEIIGEYSNILKDNPVKPSLAGLFIQAKNNQVVFKGANTEIELIRYANCEIE-SEGQVLIKPALLLEYIKLLE 82 9*************************************************************.88****************** PP STSEEEEEEETTEEEEEEETTEEEEEE-BEGGGS--- CS DNA_pol3_beta 84 ndkkvkisvneqklliiksgssrfslstlsaeeypnl 120 ++++++ ++ +l + +++fs+ l+ + yp+l 23726_FusoPortal_Gene_1777 83 G-ENINFEKKDGYLIVN---NAEFSI--LDDNTYPEL 113 9.999999888887777...888875..677777765 PP == domain 2 score: 8.5 bits; conditional E-value: 0.00048 HHHHHHHHHHTTTSSSTSSGGG.GEEEEEEETTEEEEEEE-S..SEEEEEEEESEECEE-EEEEEEHH...HHHHHHHHSSST CS DNA_pol3_beta 9 ellkelekvakvisnRntlpiL.sgvllevkdsqlsltgtDl..eisiestisaeseeeegkvlvpar...llldivkaLpnd 85 ++ +lekv+ ++ + + L + +++ kd+ l l +tD+ i +++++++ ++ vlvp+ l+ i k L++ 23726_FusoPortal_Gene_1777 128 KFTMSLEKVKFLTNSSTSTDTLfNSIKMIFKDNVLELVSTDSfrLIYMKKELNNMIN---KDVLVPGDsiaVLYKIFKDLDE- 206 5677888888888887777766367****************7325888888888888...47****9723358899999988. PP SEEEEEEETTEEEEEEETTEEEEEE-B CS DNA_pol3_beta 86 kkvkisvneqklliiksgssrfslstl 112 + ++ +++kl ++ + f+ + l 23726_FusoPortal_Gene_1777 207 -EFSLAASDDKLIVT-WKDAYFTCKLL 231 .88888888888887.66677766555 PP == domain 3 score: 10.2 bits; conditional E-value: 0.00014 EEEEHHHHHHHHHHHHTTTSSSTSSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEESEECEE-EEEEEEHHHHHHHHHHSSST CS DNA_pol3_beta 3 ftiereellkelekvakvisnRntlpiLsgvllevkdsqlsltgtDleisiestisaeseeeegkvlvparllldivkaLpnd 85 f +r+el+ +l+kv +v ++n + + + k +ql ++g + + +i++++++ + e+ k ++ +++ d + + +++ 23726_FusoPortal_Gene_1777 251 FEFNRDELNLALKKVISV--TKNSSDSKNVATFNFKGNQLLISGVSANAKINQKVNMIKTGEDLKLGMNCKYIKDFIDNVDKN 331 777899999999999887..6788888888899************************9999*****************99995 PP SEEEEEEETTEEEEEEETTEEE CS DNA_pol3_beta 86 kkvkisvneqklliiksgssrf 107 ++ + + + l +++g++++ 23726_FusoPortal_Gene_1777 332 IIIDATNSSSMLRFMEEGNENY 353 5555555557777888888776 PP >> DNA_pol3_beta_2 DNA polymerase III beta subunit, central domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 5.9 0.0 0.0032 14 4 101 .. 7 100 .. 4 112 .. 0.71 2 ! 51.9 0.1 1.8e-17 7.3e-14 6 116 .] 128 237 .. 124 237 .. 0.90 Alignments for each domain: == domain 1 score: 5.9 bits; conditional E-value: 0.0032 HHHHHHHHHHHGGGS-SSTTSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEEEEECCCCEEEEEEEHHHHHHHHHCCTSSSSE CS DNA_pol3_beta_2 4 qkelkelieqvafaasedetrpvLtGvrleieedklllaaTdghRlavrkleleeeeedeasvivPaktlaelaklledneeq 86 ++ +e+i + + + + ++p L G+ ++ +++++++ + +r ++e e+e +v++ l+e klle e+ 23726_FusoPortal_Gene_1777 7 RQKTIEIIGEYSNILKDNPVKPSLAGLFIQAKNNQVVFKGANTEIELIRYANCEIESE--GQVLIKPALLLEYIKLLEG--EN 85 55666777777777888999*****************987776544455555555555..4777777788888888887..77 PP EEEEEESSEEEEEET CS DNA_pol3_beta_2 87 vklalsegkirfevg 101 ++ ++g++ ++ + 23726_FusoPortal_Gene_1777 86 INFEKKDGYLIVNNA 100 777777777666554 PP == domain 2 score: 51.9 bits; conditional E-value: 1.8e-17 HHHHHHHHHGGGS-SS.TTSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEEEEECCCCEEEEEEEHHHHHHHHHCCTSSSSEE CS DNA_pol3_beta_2 6 elkelieqvafaased.etrpvLtGvrleieedklllaaTdghRlavrkleleeeeedeasvivPaktlaelaklledneeqv 87 ++ +e+v+f ++++ t + + +++ +++ l+l++Td++Rl +k el++ + ++v+vP ++a l k+ +d +e+ 23726_FusoPortal_Gene_1777 128 KFTMSLEKVKFLTNSStSTDTLFNSIKMIFKDNVLELVSTDSFRLIYMKKELNNMIN--KDVLVPGDSIAVLYKIFKDLDEEF 208 56677889999777651566777**********************999999988887..69********************** PP EEEEESSEEEEEETTEEEEEE-BSS---B CS DNA_pol3_beta_2 88 klalsegkirfevgnvrltsrlldgkfPd 116 +la s++k+ ++++++++t++ll +fPd 23726_FusoPortal_Gene_1777 209 SLAASDDKLIVTWKDAYFTCKLLSLSFPD 237 ****************************8 PP >> DNA_pol3_beta_3 DNA polymerase III beta subunit, C-terminal domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.0 0.2 0.082 3.4e+02 39 96 .. 35 90 .. 29 105 .. 0.68 2 ? 2.6 0.0 0.025 1.1e+02 28 52 .. 144 168 .. 116 178 .. 0.76 3 ! 26.6 2.0 9.3e-10 3.9e-06 6 120 .. 245 360 .. 243 361 .. 0.86 Alignments for each domain: == domain 1 score: 1.0 bits; conditional E-value: 0.082 EEEETTEEEEEEEETTTEEEEEEEE-CEE.CS-EEEEEEHHHHHHHHCCH-SSEEEEEE CS DNA_pol3_beta_3 39 LsleegqlklsaensevgeaeEevdvnye.GeeleiafNvsYlldalkaleteevelql 96 ++++++q+ +++ n+e++ +n e +e ++ + + ll+ +k le+e+++++ 23726_FusoPortal_Gene_1777 35 IQAKNNQVVFKGANTEIELIR---YANCEiESEGQVLIKPALLLEYIKLLEGENINFEK 90 566677777777777766543...23333355556678888899999999999998875 PP == domain 2 score: 2.6 bits; conditional E-value: 0.025 CCSSTTTGEEEEEEETTEEEEEEEE CS DNA_pol3_beta_3 28 lladeknrkvrLsleegqlklsaen 52 + d ++++++ +++++l+l +++ 23726_FusoPortal_Gene_1777 144 TSTDTLFNSIKMIFKDNVLELVSTD 168 445567899***********99876 PP == domain 3 score: 26.6 bits; conditional E-value: 9.3e-10 SS-SEEEEEEHHHHHHHHHHHCCCSS...TTTGEEEEEEETTEEEEEEEETTTEEEEEEEE-CEECS-EEEEEEHHHHHHHHC CS DNA_pol3_beta_3 6 kefkkkvtvdlkelkealkRvallad...eknrkvrLsleegqlklsaensevgeaeEevdvnyeGeeleiafNvsYlldalk 85 ++++k + +++el alk+v + + + +++ +++ +ql +s+ + ++ + +v+ +Ge+l++++N +Y+ d + 23726_FusoPortal_Gene_1777 245 TNHDKRFEFNRDELNLALKKVISVTKnssDSKNVATFNFKGNQLLISGVSA-NAKINQKVNMIKTGEDLKLGMNCKYIKDFID 326 5788999999999999999986665435467788899*******9987665.5678888999899****************** PP CH-SSEEEEEESTTTS-EEEEETTEESEEEEE--B CS DNA_pol3_beta_3 86 aleteevelqltdstkpvllsevedesvkyvilpm 120 +++ ++ + t+s++ + e ++e+ y+i+p+ 23726_FusoPortal_Gene_1777 327 NVDK-NIIIDATNSSSMLRFMEEGNENYIYLIMPV 360 **97.5779*************************7 PP >> Psb28 Psb28 protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.6 0.2 0.36 1.5e+03 26 57 .. 127 160 .. 122 185 .. 0.59 2 ? 11.7 0.1 5.2e-05 0.22 15 96 .. 266 347 .. 257 353 .. 0.83 Alignments for each domain: == domain 1 score: -0.6 bits; conditional E-value: 0.36 EEEEEEEES-HHHCTS..GCG..---EEEEETTE CS Psb28 26 gtavfiFeepkalekesstke..itglyliDeEG 57 + ++ e++k+l+++s++++ + + +i ++ 23726_FusoPortal_Gene_1777 127 VKFTMSLEKVKFLTNSSTSTDtlFNSIKMIFKDN 160 4567788888998888444443655555544333 PP == domain 2 score: 11.7 bits; conditional E-value: 5.2e-05 EEEEE-TTSSSEEEEEEEES-HHHCTS...GCG.---EEEEETTEEEEE--EEEEEETTEEEEEEEEEEE-SCHHHHHHHHHH CS Psb28 15 vrltrsrdgekgtavfiFeepkaleke.sstke.itglyliDeEGeistrevkakfvngkpealeatyelkseeewdRfmRFm 95 +++t++ + +k++a+f F+ ++l + s +++ +++ +i Ge +++k++++ ++++ + +++ +++ ++RFm 23726_FusoPortal_Gene_1777 266 ISVTKNSSDSKNVATFNFKGNQLLISGvSANAKiNQKVNMIKT-GEDLKLGMNCKYIKDFIDNVDKNIIIDATNS-SSMLRFM 346 899*******************999998888885677888865.555566899**********999998887665.5688999 PP H CS Psb28 96 e 96 e 23726_FusoPortal_Gene_1777 347 E 347 8 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (365 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 648 (0.0387745); expected 334.2 (0.02) Passed bias filter: 300 (0.0179512); expected 334.2 (0.02) Passed Vit filter: 23 (0.00137626); expected 16.7 (0.001) Passed Fwd filter: 4 (0.000239349); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.27u 0.24s 00:00:00.51 Elapsed: 00:00:00.32 # Mc/sec: 3315.83 // [ok]