# 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_1685.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1685 [L=912] Description: # 1805010 # 1807745 # -1 # ID=1_1685;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.262 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-137 458.0 2.3 3.6e-137 457.3 1.3 1.8 2 DNA_pol_A DNA polymerase family A 9.1e-47 158.8 0.1 2.2e-46 157.6 0.1 1.6 1 5_3_exonuc_N 5'-3' exonuclease, N-terminal resolvase-like do 2.7e-23 82.3 2.6 7.2e-23 80.9 0.1 3.1 3 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold 1e-05 26.0 0.1 4.1e-05 24.0 0.1 2.1 1 HHH_5 Helix-hairpin-helix domain 0.0095 15.9 0.1 0.048 13.7 0.0 2.3 2 HHH_2 Helix-hairpin-helix motif ------ inclusion threshold ------ 0.01 16.2 1.4 0.99 9.8 0.1 3.8 4 YxiJ YxiJ-like protein Domain annotation for each model (and alignments): >> DNA_pol_A DNA polymerase family A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.7 0.0 0.39 1.1e+03 327 346 .. 489 508 .. 470 518 .. 0.83 2 ! 457.3 1.3 1.3e-140 3.6e-137 2 376 .] 533 909 .. 532 909 .. 0.97 Alignments for each domain: == domain 1 score: -1.7 bits; conditional E-value: 0.39 EEEETTEEEEEEECCCHHHH CS DNA_pol_A 327 llqvHDElvfevpeeeveev 346 +l + DEl + +++e+++++ 23726_FusoPortal_Gene_1685 489 ILAIYDELNYLLKKEDLYKI 508 7899************9987 PP == domain 2 score: 457.3 bits; conditional E-value: 1.3e-140 HHHHHHHHHHHHHHHHHHHHHHHHSS.C-STTTCCCCHHHHTCCCCS.TTSBETTSBTTTCCHHHHHTS..-CHHHHHHHHHH CS DNA_pol_A 2 eeleelseeleeeleeleeeiyelag.efnlnSpkqlaevLfeklklpekkktktgystdeevLeklak..hplaklileyre 81 ++++++s ele+el ++e+ iye ag efn+nSpkql+++Lf kl+lp++kktktgystd vLe+l++ +++a+l+l+yr+ 23726_FusoPortal_Gene_1685 533 QYFKNYSLELEKELLKVEKAIYEEAGeEFNINSPKQLGDILFVKLNLPSGKKTKTGYSTDVMVLEDLESygYNIARLLLDYRK 615 5789999*******************77***************************************94579*********** PP HHHHHHHTTTTGGGCCBTTTSEE--EEESSSSSSS--EEESS-GGGS-TTSCCHHHHHHTBCG-TTCCEEEEEEETTHHHHHH CS DNA_pol_A 82 lsklkstyvdallklinkktgrihtsfnqtvtatGrlsssepnlqnipirteegrriRkafvaeegghvlvsaDysqiELRil 164 l+klk+tyvd+l+ l++ +++rihtsfnq +tatGrlsssepnlqnip++t++g +iR+ f+a eg +vl+s+Dysq+ELR+l 23726_FusoPortal_Gene_1685 616 LNKLKTTYVDTLPLLVD-ENSRIHTSFNQIGTATGRLSSSEPNLQNIPVKTDDGIKIREGFIAGEG-KVLMSIDYSQVELRVL 696 ****************6.689*******************************************96.66************** PP HHHCT-HHHHHHHHTTH-HHHHHHHHHCTS-G.GGHHHHHHHHHHHHHHHHHTT--HHHHHHHHTSSHHHHHHHHHHHHHHSH CS DNA_pol_A 165 AhlsgdeklieafkegeDiHsktAsevfgvpv.eevtkeqRrkaKainfGiiYGmgakglaeqlgiseeeAkefiekyferyp 246 ++s+de+liea++e++D+H tA+++f+ p e+v++eqR+ aK inf+iiYG +++gla++l+i+ ++A+e+i+kyfe+yp 23726_FusoPortal_Gene_1685 697 TSMSKDENLIEAYREEKDLHDLTARRIFNLPDsETVSREQRTIAKIINFSIIYGKTPFGLAKELKIPVKDASEYIKKYFEQYP 779 ******************************99899************************************************ PP HHHHHHHHHHHHCCCESCCEETTCSEEEECTTT-CCHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE CS DNA_pol_A 247 gvksyleetleeakekgyvetllgrrrylpeinsknaalrekaeraavNapiQGsAaDiiklamikieealkeeklkarlllq 329 +v+++ +e++e+ +e+gyv+tl+gr+ry++ i+skn++ +++aer+avN++iQG+Aa+++k +m+k+++ lk+++ + lllq 23726_FusoPortal_Gene_1685 780 RVTTFEKEVIEFGEEHGYVKTLFGRKRYISGIDSKNKTIKSQAERMAVNTVIQGTAAEVLKKVMVKVYDILKDKE-DIALLLQ 861 ***********************************************************************9986.899**** PP ETTEEEEEEECCCHHHHHHHHHHHHHHHHHS.SS--EEEEEEESSCCC CS DNA_pol_A 330 vHDElvfevpeeeveevaelvkeaMenavel.dvplkvevkvGknWge 376 vHDEl+fev+++ ve+ + ++ ++M+n+v+l dv+l++++++GknW+e 23726_FusoPortal_Gene_1685 862 VHDELIFEVEKNSVEKYSGILADIMKNTVQLeDVKLNININIGKNWAE 909 ******************************87**************86 PP >> 5_3_exonuc_N 5'-3' exonuclease, N-terminal resolvase-like domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 157.6 0.1 7.7e-50 2.2e-46 2 142 .. 4 148 .. 3 169 .. 0.88 Alignments for each domain: == domain 1 score: 157.6 bits; conditional E-value: 7.7e-50 5_3_exonuc_N 2 llLiDgsslifRayyallt.tsdgeptnavygflnmllklleeekpthlavvfDa.kkktfRhelypeYKanReetpeelkeq 82 +L+D s++++Ray+a ++ ++++ept+avygf+n+ll++++e+kp+++a++fD +++ R+e+y++YK+nR+++pe+l++q 23726_FusoPortal_Gene_1685 4 AVLLDVSAIMYRAYFANMNfRTKNEPTGAVYGFINTLLSIINEFKPDYMAAAFDVkRSSLKRTEIYSDYKSNRQSAPEDLIKQ 86 69**************744255779*********************99******6356678********************** PP 5_3_exonuc_N 83 lplikevlealgikvlevegyEADDvigtlakraeeeg..vvivsgDkDllQlvednvrvld 142 +p i+e+lea++i+ +++egyEADDv+g+lak+ ++++ v+iv+gDkDl Qlve+n++v 23726_FusoPortal_Gene_1685 87 IPRIEEALEAFNINRYKIEGYEADDVLGSLAKKLAKQDieVIIVTGDKDLSQLVEKNITVAL 148 *********************************6554446**************99999876 PP >> 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.8 0.1 1.7 4.7e+03 33 61 .. 82 121 .. 78 142 .. 0.55 2 ! 80.9 0.1 2.6e-26 7.2e-23 1 91 [. 173 268 .. 173 273 .. 0.93 3 ? -2.1 0.1 2.1 5.7e+03 57 76 .. 344 363 .. 305 371 .. 0.69 Alignments for each domain: == domain 1 score: -1.8 bits; conditional E-value: 1.7 5_3_exonuc 33 kLlkeygsleailenld....elke.......kklkekLe 61 L+k++ +e+ le+ + ++++ ++l++kL+ 23726_FusoPortal_Gene_1685 82 DLIKQIPRIEEALEAFNinryKIEGyeaddvlGSLAKKLA 121 5888888888888866422112222222222223333333 PP == domain 2 score: 80.9 bits; conditional E-value: 2.6e-26 5_3_exonuc 1 vkPeqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleailenldelke.....kklkekLeenkeearlskkLatikt 78 v Pe+i+dl +L+GD+sD ipGv +iGek+A ++ ++y+sle+i+en+d+lk+ ++l ++L ++k+ a++s++La+i t 23726_FusoPortal_Gene_1685 173 VVPEKIPDLFGLIGDKSDGIPGVTKIGEKKALSIFSQYDSLEKIYENIDNLKSidgigPSLIKNLINEKDIAFMSRELAKIFT 255 67***********************************************9888877888899********************* PP 5_3_exonuc 79 dvpleleledlkl 91 ++++++e + l++ 23726_FusoPortal_Gene_1685 256 NLDITVEEDGLQY 268 ***9998877765 PP == domain 3 score: -2.1 bits; conditional E-value: 2.1 5_3_exonuc 57 kekLeenkeearlskkLati 76 +++L+e+ke++ +kk+a i 23726_FusoPortal_Gene_1685 344 ENSLNEQKEYLTNYKKIASI 363 45667777777777776666 PP >> HHH_5 Helix-hairpin-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 24.0 0.1 1.5e-08 4.1e-05 7 54 .. 195 240 .. 192 241 .. 0.94 Alignments for each domain: == domain 1 score: 24.0 bits; conditional E-value: 1.5e-08 STT--HHHHHHHHTTT--SHHHHHCS-HHHHHTSTTS-HHHHHHHHHH CS HHH_5 7 vsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriile 54 v +iG+k Al++ s+ ++s+e++ + +++ L +i GiG+ + +++i e 23726_FusoPortal_Gene_1685 195 VTKIGEKKALSIFSQ-YDSLEKIYE-NIDNLKSIDGIGPSLIKNLINE 240 889************.******999.6******************976 PP >> HHH_2 Helix-hairpin-helix motif # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.7 0.0 1.7e-05 0.048 7 46 .. 194 232 .. 191 239 .. 0.90 2 ? -3.2 0.0 3.3 9.1e+03 16 27 .. 247 258 .. 246 259 .. 0.88 Alignments for each domain: == domain 1 score: 13.7 bits; conditional E-value: 1.7e-05 HHH_2 7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGee 46 G+ ++Gek A + ++++sl+++ + ++++L ++d+iG+ 23726_FusoPortal_Gene_1685 194 GVTKIGEKKALSIFSQYDSLEKIYE-NIDNLKSIDGIGPS 232 77889******************87.79**********97 PP == domain 2 score: -3.2 bits; conditional E-value: 3.3 HHH_2 16 AklLakrFksld 27 +++Lak F +ld 23726_FusoPortal_Gene_1685 247 SRELAKIFTNLD 258 689******998 PP >> YxiJ YxiJ-like protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.0 0.0 3.4 9.6e+03 77 95 .. 205 223 .. 187 225 .. 0.75 2 ? 1.0 0.0 0.19 5.3e+02 14 40 .. 237 264 .. 231 286 .. 0.78 3 ? 0.7 0.0 0.25 6.9e+02 20 49 .. 453 486 .. 440 510 .. 0.74 4 ? 9.8 0.1 0.00036 0.99 59 94 .. 758 793 .. 745 803 .. 0.82 Alignments for each domain: == domain 1 score: -3.0 bits; conditional E-value: 3.4 YxiJ 77 elyPqykflekelekypll 95 + qy +lek+ e+ l 23726_FusoPortal_Gene_1685 205 SIFSQYDSLEKIYENIDNL 223 5788888888887776555 PP == domain 2 score: 1.0 bits; conditional E-value: 0.19 YxiJ 14 afPsediekleedlkkdftkddc.lsaD 40 ++di+++ ++l k ft++d+ +++D 23726_FusoPortal_Gene_1685 237 LINEKDIAFMSRELAKIFTNLDItVEED 264 55679***************99614455 PP == domain 3 score: 0.7 bits; conditional E-value: 0.25 YxiJ 20 iekle.edlkkdftkdd...clsaDfneyfmlia 49 +kle +d+k f k + + ++Df +y++ i+ 23726_FusoPortal_Gene_1685 453 YSKLEpKDFKTAFGKVNvelITAQDFSKYLSDIS 486 555543677888888777768899*****99887 PP == domain 4 score: 9.8 bits; conditional E-value: 0.00036 YxiJ 59 keqkipkkqikllkksFfelyPqykflekelekypl 94 ke kip k k +fe+yP++ ++eke+ ++ + 23726_FusoPortal_Gene_1685 758 KELKIPVKDASEYIKKYFEQYPRVTTFEKEVIEFGE 793 568999888877777899*************99976 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (912 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 691 (0.0413475); expected 334.2 (0.02) Passed bias filter: 360 (0.0215414); expected 334.2 (0.02) Passed Vit filter: 38 (0.00227382); expected 16.7 (0.001) Passed Fwd filter: 6 (0.000359023); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.44 # Mc/sec: 6025.48 // [ok]