# 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_1116.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1116 [L=300] Description: # 1223986 # 1224885 # 1 # ID=1_1116;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.276 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-33 115.8 0.1 2.9e-32 112.0 0.1 2.0 2 WYL WYL domain 5e-15 55.1 0.1 1.1e-14 54.0 0.1 1.6 1 HTH_11 HTH domain 5.8e-08 32.3 0.0 1.9e-07 30.6 0.0 1.9 2 HTH_DeoR DeoR-like helix-turn-helix domain 0.00034 20.8 0.0 0.00095 19.4 0.0 1.7 1 Rrf2 Transcriptional regulator 0.00081 19.8 0.8 0.0043 17.5 0.0 2.6 3 Mga Mga helix-turn-helix domain 0.0061 16.5 0.0 0.023 14.7 0.0 1.9 1 HTH_7 Helix-turn-helix domain of resolvase ------ inclusion threshold ------ 0.011 15.7 0.5 0.72 9.9 0.0 3.1 3 HTH_22 HTH domain 0.012 15.0 0.0 0.031 13.7 0.0 1.8 1 HTH_24 Winged helix-turn-helix DNA-binding 0.021 14.5 0.0 0.045 13.5 0.0 1.6 1 Phage_Nu1 Phage DNA packaging protein Nu1 0.027 14.3 0.0 0.067 13.0 0.0 1.6 1 TrmB Sugar-specific transcriptional regulator TrmB 0.058 13.4 0.1 0.42 10.6 0.0 2.4 2 SpoIIID Stage III sporulation protein D 0.075 13.6 0.0 0.21 12.2 0.0 1.7 1 RPA_C Replication protein A C terminal 0.17 11.0 0.1 0.21 10.7 0.1 1.2 1 Nha1_C Alkali metal cation/H+ antiporter Nha1 C terminus 0.2 11.5 1.0 1.2 9.0 0.4 2.6 2 PuR_N Bacterial purine repressor, N-terminal Domain annotation for each model (and alignments): >> WYL WYL domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 4.3 0.0 0.03 35 64 119 .. 81 135 .. 79 137 .. 0.91 2 ! 112.0 0.1 2.4e-35 2.9e-32 2 172 .] 130 294 .. 129 294 .. 0.87 Alignments for each domain: == domain 1 score: 4.3 bits; conditional E-value: 0.03 WYL 64 iselelldetfeppdfdlakylsksfgvfkspvevkvrfspeaarrvrerrfpdqk 119 +s l++ld+t + + dl ls f++++ + +++v f++ +++++ e+ f+d k 23726_FusoPortal_Gene_1116 81 MSALQVLDNTTKQYENDLLTKLSALFKIKS-TNWIEVDFNNWQNNQMYEKTFNDIK 135 7899*****9998899**************.**********999999999988765 PP == domain 2 score: 112.0 bits; conditional E-value: 2.4e-35 WYL 2 vletlaeAieerrrvefrYrspagegeertvePyglvlkngrwYLvaydekrdeirtfrldRiselelldetfeppdfdlaky 84 ++++++ i ++ +++f+Y +++++++ r+v+P++l kn+ wYL+a ++ r+++r f+l+Ri++le++ e+fe++ +d+ 23726_FusoPortal_Gene_1116 130 TFNDIKSSILNKYTISFSYFNSNEKETSRSVKPVRLLSKNQDWYLYALCLLRNDFRYFKLSRIKNLEIHTEKFEDNFDDI--I 210 578999***************766666**********************************************9776664..3 PP WYL 85 lsksfgvfkspvevkvrfspeaarrvrerrfpdqkieeedddgsvrvelpvesleellswllsfgdeveVlePaeLreevkee 167 l+k + ++++kv+f+ ++a rv + ++++ ie+ ++g + e+++ + l+s++lsfgd +eVleP+e+r ++k+ 23726_FusoPortal_Gene_1116 211 LKKEMSHNN-TIHIKVKFEHKVAFRVYD-EINNEIIED--AKGNLYTEMEIPNDYNLYSYILSFGDGAEVLEPKEIRMQIKKM 289 444445567.9********999999976.677776666..66666666666699***************************** PP WYL 168 aerll 172 + +++ 23726_FusoPortal_Gene_1116 290 ISKMA 294 *9996 PP >> HTH_11 HTH domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 54.0 0.1 8.9e-18 1.1e-14 1 53 [. 5 56 .. 5 59 .. 0.92 Alignments for each domain: == domain 1 score: 54.0 bits; conditional E-value: 8.9e-18 HTH_11 1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrG 53 Rl+ il +le+ + + +++LA++++vS rt++rdI++L+++g+pI+ ++g+G 23726_FusoPortal_Gene_1116 5 RLFRILYYILEKGK-VRANQLADRFEVSVRTIYRDIDSLSSAGIPIYTTQGKG 56 8999****956555.*************************************6 PP >> HTH_DeoR DeoR-like helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 30.6 0.0 1.6e-10 1.9e-07 1 44 [. 5 49 .. 5 59 .. 0.90 2 ? -2.9 0.0 4.6 5.5e+03 19 47 .. 101 130 .. 99 133 .. 0.63 Alignments for each domain: == domain 1 score: 30.6 bits; conditional E-value: 1.6e-10 HTH_DeoR 1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgl.l 44 R+ il ++ ++gk++ ++l+++++vS Ti RD++ L+ +g+ + 23726_FusoPortal_Gene_1116 5 RLFRILYYILEKGKVRANQLADRFEVSVRTIYRDIDSLSSAGIpI 49 56679***********************************99844 PP == domain 2 score: -2.9 bits; conditional E-value: 4.6 HTH_DeoR 19 elvellgv.SeaTiRRDLneLeeqglltRt 47 +l++l+++ S++ i D+n+ ++ + ++t 23726_FusoPortal_Gene_1116 101 KLSALFKIkSTNWIEVDFNNWQNNQMYEKT 130 566666665555566678877777666655 PP >> Rrf2 Transcriptional regulator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 19.4 0.0 7.9e-07 0.00095 13 70 .. 9 64 .. 4 66 .. 0.88 Alignments for each domain: == domain 1 score: 19.4 bits; conditional E-value: 7.9e-07 HHHHHHCSTTCC.--HHHHHHHHTS-HHHHHHHHHHHHHTTS.EEEETTT.TCEEESS- CS Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkagl.vksvrGkgGGyrLakp 70 +l+y+ ++ + v+++++a+r+++s + + + + L+ ag+ + +++GkgGG+ +ak+ 23726_FusoPortal_Gene_1116 9 ILYYILEKGK---VRANQLADRFEVSVRTIYRDIDSLSSAGIpIYTTQGKGGGIEIAKD 64 5556555544...99**************************99*************997 PP >> Mga Mga helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.5 0.0 3.6e-06 0.0043 14 55 .. 2 43 .. 1 50 [. 0.92 2 ? -2.1 0.0 4.7 5.6e+03 37 49 .. 62 74 .. 58 89 .. 0.52 3 ? -2.2 0.1 4.9 5.9e+03 28 52 .. 129 154 .. 123 165 .. 0.57 Alignments for each domain: == domain 1 score: 17.5 bits; conditional E-value: 3.6e-06 HHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS Mga 14 keslkyqllkflfeeeevsieelaqelyiSestlkrkikeln 55 k++ +++l +++e+ +v +la+++ +S t++r+i+ l 23726_FusoPortal_Gene_1116 2 KDNRLFRILYYILEKGKVRANQLADRFEVSVRTIYRDIDSLS 43 67788*********************************9875 PP == domain 2 score: -2.1 bits; conditional E-value: 4.7 HHHCT--HHHHHH CS Mga 37 aqelyiSestlkr 49 a+ +++S+s l 23726_FusoPortal_Gene_1116 62 AKDYVLSKSLLSE 74 4555555554432 PP == domain 3 score: -2.2 bits; conditional E-value: 4.9 HSEEEHH.HHHHHCT--HHHHHHHHH CS Mga 28 eeevsie.elaqelyiSestlkrkik 52 + +++i+ ++ +++ iS s ++ k 23726_FusoPortal_Gene_1116 129 KTFNDIKsSILNKYTISFSYFNSNEK 154 44555541355666666666655555 PP >> HTH_7 Helix-turn-helix domain of resolvase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 14.7 0.0 1.9e-05 0.023 18 40 .. 14 37 .. 12 38 .. 0.93 Alignments for each domain: == domain 1 score: 14.7 bits; conditional E-value: 1.9e-05 TTTT.--STTTSSSS---SSSS-- CS HTH_7 18 leeG.isiskIAkevnisRsTvYR 40 le+G ++++A+++ +s+ T+YR 23726_FusoPortal_Gene_1116 14 LEKGkVRANQLADRFEVSVRTIYR 37 68888999***************9 PP >> HTH_22 HTH domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.9 0.0 0.0006 0.72 44 62 .. 21 39 .. 16 40 .. 0.88 2 ? 2.4 0.1 0.13 1.5e+02 16 33 .. 68 85 .. 60 87 .. 0.80 3 ? -3.3 0.0 7.6 9.1e+03 39 50 .. 285 296 .. 284 296 .. 0.74 Alignments for each domain: == domain 1 score: 9.9 bits; conditional E-value: 0.0006 HTH_22 44 vekvAekLgiSraTvYryL 62 ++++A+++++S T+Yr + 23726_FusoPortal_Gene_1116 21 ANQLADRFEVSVRTIYRDI 39 5789*************98 PP == domain 2 score: 2.4 bits; conditional E-value: 0.13 HTH_22 16 pverltkeekieivraLd 33 + + l+ +ek++i++aL+ 23726_FusoPortal_Gene_1116 68 SKSLLSENEKKQIMSALQ 85 55689***********97 PP == domain 3 score: -3.3 bits; conditional E-value: 7.6 HTH_22 39 llkgavekvAek 50 ++k+ ++k Aek 23726_FusoPortal_Gene_1116 285 QIKKMISKMAEK 296 688888888875 PP >> HTH_24 Winged helix-turn-helix DNA-binding # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.7 0.0 2.6e-05 0.031 2 46 .. 3 47 .. 2 47 .. 0.89 Alignments for each domain: == domain 1 score: 13.7 bits; conditional E-value: 2.6e-05 HTH_24 2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46 d ++IL ++ ++++ ++LA+r +S+ t+ r ++ L ++G+ 23726_FusoPortal_Gene_1116 3 DNRLFRILYYILEKGKVRANQLADRFEVSVRTIYRDIDSLSSAGI 47 66779***************************9998888877775 PP >> Phage_Nu1 Phage DNA packaging protein Nu1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.5 0.0 3.7e-05 0.045 3 39 .. 19 59 .. 17 97 .. 0.82 Alignments for each domain: == domain 1 score: 13.5 bits; conditional E-value: 3.7e-05 Phage_Nu1 3 vnkaklaeifgvsvrtv....daWqsqGlPvvkgGGkGnea 39 v ++la+ f+vsvrt+ d+ s G+P+ + GkG+ + 23726_FusoPortal_Gene_1116 19 VRANQLADRFEVSVRTIyrdiDSLSSAGIPIYTTQGKGGGI 59 7789***********9644337899********99999754 PP >> TrmB Sugar-specific transcriptional regulator TrmB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.0 0.0 5.6e-05 0.067 13 51 .. 9 47 .. 7 56 .. 0.92 Alignments for each domain: == domain 1 score: 13.0 bits; conditional E-value: 5.6e-05 HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGl 51 + ++l++g+ +a+++a + +v+ ++Y+ + sL+++G+ 23726_FusoPortal_Gene_1116 9 ILYYILEKGKVRANQLADRFEVSVRTIYRDIDSLSSAGI 47 56789*******************************995 PP >> SpoIIID Stage III sporulation protein D # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.6 0.0 0.00035 0.42 6 40 .. 4 39 .. 2 45 .. 0.84 2 ? -1.3 0.0 1.9 2.2e+03 24 37 .. 60 73 .. 42 94 .. 0.76 Alignments for each domain: == domain 1 score: 10.6 bits; conditional E-value: 0.00035 SpoIIID 6 eRvleiakyiveska.tvRkaakvfgvskstvhkDv 40 +R +i +yi+e+ + + a f vs t+++D+ 23726_FusoPortal_Gene_1116 4 NRLFRILYYILEKGKvRANQLADRFEVSVRTIYRDI 39 689999*****9854156689**************8 PP == domain 2 score: -1.3 bits; conditional E-value: 1.9 SpoIIID 24 kaakvfgvskstvh 37 ++ak + +sks + 23726_FusoPortal_Gene_1116 60 EIAKDYVLSKSLLS 73 57899999998764 PP >> RPA_C Replication protein A C terminal # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.2 0.0 0.00017 0.21 68 101 .. 19 53 .. 15 55 .. 0.93 Alignments for each domain: == domain 1 score: 12.2 bits; conditional E-value: 0.00017 EEHHHHHHHSTSXHHHHHHHHHHHHHTTS.EEESS CS RPA_C 68 vhvdeiaqklrlsvndvkqavdeLsneGi.iYsTi 101 v ++++a ++++sv+++ + +d+Ls++Gi iY+T+ 23726_FusoPortal_Gene_1116 19 VRANQLADRFEVSVRTIYRDIDSLSSAGIpIYTTQ 53 66789***********************99****7 PP >> Nha1_C Alkali metal cation/H+ antiporter Nha1 C terminus # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.7 0.1 0.00017 0.21 147 184 .. 221 258 .. 119 265 .. 0.73 Alignments for each domain: == domain 1 score: 10.7 bits; conditional E-value: 0.00017 Nha1_C 147 rkeekkeeeeppvevYqEGdkiIiEdeeGevlevedkp 184 + + k e++ + vY+E ++ IiEd +G+ ++ + p 23726_FusoPortal_Gene_1116 221 IHIKVKFEHKVAFRVYDEINNEIIEDAKGNLYTEMEIP 258 34678899999*******************98655555 PP >> PuR_N Bacterial purine repressor, N-terminal # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.0 0.4 0.00099 1.2 2 66 .. 2 59 .. 1 62 [. 0.82 2 ? -0.7 0.0 1.1 1.3e+03 26 39 .. 61 74 .. 59 85 .. 0.85 Alignments for each domain: == domain 1 score: 9.0 bits; conditional E-value: 0.00099 PuR_N 2 RseRlvaitkiLlenPnklisltyfaerfeaAKSsiSeDlaiikealekeglGkletvaGaaGGv 66 + +Rl++i+ ++le+ + + +++a+rfe++ +i D++ ++ + g+ + t++G+ GG+ 23726_FusoPortal_Gene_1116 2 KDNRLFRILYYILEKGK--VRANQLADRFEVSVRTIYRDIDSLS----SAGI-PIYTTQGKGGGI 59 5789*********9865..8899*****************8655....4454.477888888887 PP == domain 2 score: -0.7 bits; conditional E-value: 1.1 PuR_N 26 faerfeaAKSsiSe 39 +a+++ +KS +Se 23726_FusoPortal_Gene_1116 61 IAKDYVLSKSLLSE 74 68899999**9999 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (300 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 1220 (0.0730014); expected 334.2 (0.02) Passed bias filter: 397 (0.0237554); expected 334.2 (0.02) Passed Vit filter: 57 (0.00341072); expected 16.7 (0.001) Passed Fwd filter: 14 (0.000837721); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 14 [number of targets reported over threshold] # CPU time: 0.27u 0.23s 00:00:00.50 Elapsed: 00:00:00.33 # Mc/sec: 2642.76 // [ok]