Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF832 HP15_811 acetyl-CoA synthetase
Query= SwissProt::Q8ZKF6 (652 letters) >FitnessBrowser__Marino:GFF832 Length = 649 Score = 968 bits (2502), Expect = 0.0 Identities = 455/643 (70%), Positives = 535/643 (83%), Gaps = 1/643 (0%) Query: 1 MSQTHKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSF 60 M+ + + +A + L+N EQYE Y+QS+ DPDTFWGE GK L+WI PY KVKNT++ Sbjct: 1 MTGKQVYPVSPEVAKQALLNREQYEEMYRQSVEDPDTFWGEHGKRLEWIKPYTKVKNTTY 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRF 120 N+SIKW+EDG LN +ANCLDRHL++ GD+TAII+EGDD + S++++YRELH + +F Sbjct: 61 DYNNLSIKWFEDGQLNASANCLDRHLEKRGDQTAIIFEGDDPADSRNVTYRELHEETSKF 120 Query: 121 ANTLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSS 180 AN L LG+KKGDVV IYMPM+ E AVAMLACARIGA+HSV+FGGFSPEA+ RI++ S Sbjct: 121 ANVLKGLGVKKGDVVTIYMPMIVETAVAMLACARIGAIHSVVFGGFSPEALGARIVNGKS 180 Query: 181 RLVITADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTG-SDIDWQEGRDLWWRD 239 R V+TADEGVR GR IPLKKNVD ALKN + +VE V+V+ RTG S++ W E RD + D Sbjct: 181 RFVVTADEGVRGGRKIPLKKNVDAALKNEDAANVEKVVVVTRTGNSEVPWNEARDERYED 240 Query: 240 LIEKASPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGD 299 L++ AS + QPE MNAEDPLF+LYTSGSTG PKGVLHTTGGY+VYA+ T +YVFDYH GD Sbjct: 241 LMKSASADCQPEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYASMTHEYVFDYHEGD 300 Query: 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPT 359 +YWCTAD GWVTGHSY+LYGPLA GA T++FEGVPN+P +RM QVVDKH+VNILYTAPT Sbjct: 301 VYWCTADFGWVTGHSYILYGPLANGAITVLFEGVPNYPDSSRMGQVVDKHKVNILYTAPT 360 Query: 360 AIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETG 419 AIRALMAEG+ + GT R SL++LGSVGEPINPEAWEWY + IG KCP+VDTWWQTETG Sbjct: 361 AIRALMAEGESCMNGTTRESLKLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETG 420 Query: 420 GFMITPLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFG 479 G +I+PLPGAI+LK GSAT PFFGVQPALVDN+G+ EG TEGNLVI DSWPGQ RT++G Sbjct: 421 GILISPLPGAIDLKPGSATVPFFGVQPALVDNDGNILEGKTEGNLVILDSWPGQMRTIYG 480 Query: 480 DHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539 DHERF QTYFST+K MYF+GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H Sbjct: 481 DHERFAQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSH 540 Query: 540 PKIAEAAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599 K+AEAAVVG PH IKGQ IY YVTL HG+EPS EL E+ WVRKEIGP+A+PDV+ W Sbjct: 541 EKVAEAAVVGYPHDIKGQGIYVYVTLVHGQEPSDELKKELVQWVRKEIGPIASPDVIQWA 600 Query: 600 DSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLL 642 LPKTRSGKIMRRILRKIAA + LGDTSTLADPGVV+ L+ Sbjct: 601 PGLPKTRSGKIMRRILRKIAANEHDQLGDTSTLADPGVVDDLI 643 Lambda K H 0.317 0.135 0.423 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1485 Number of extensions: 64 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 652 Length of database: 649 Length adjustment: 38 Effective length of query: 614 Effective length of database: 611 Effective search space: 375154 Effective search space used: 375154 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate GFF832 HP15_811 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02188.hmm # target sequence database: /tmp/gapView.17992.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02188 [M=629] Accession: TIGR02188 Description: Ac_CoA_lig_AcsA: acetate--CoA ligase 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 1029.2 0.0 0 1029.0 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF832 HP15_811 acetyl-CoA synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF832 HP15_811 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1029.0 0.0 0 0 3 627 .. 20 643 .. 18 645 .. 0.98 Alignments for each domain: == domain 1 score: 1029.0 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 + e+y+e+y++++edp++fw++++k +lew+kp++kv++++ + ++kWfedg+ln+s+nc+drh+ekr d++a lcl|FitnessBrowser__Marino:GFF832 20 NREQYEEMYRQSVEDPDTFWGEHGK-RLEWIKPYTKVKNTTYDYnnlSIKWFEDGQLNASANCLDRHLEKRGDQTA 94 679**********************.5***********9986655579**************************** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151 ii+egd++ dsr++tY+el++e++++anvlk lGvkkgd v+iY+pmi+e+++amlacaRiGa+hsvvf+Gfs+e lcl|FitnessBrowser__Marino:GFF832 95 IIFEGDDPA-DSRNVTYRELHEETSKFANVLKGLGVKKGDVVTIYMPMIVETAVAMLACARIGAIHSVVFGGFSPE 169 ********9.5***************************************************************** PP TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelveke 226 al Riv+ ++++v+tadeg+Rgg++i+lkk+vd+al+++++ +vekv+vv rtg++ ++w+e rD +e+l+++ lcl|FitnessBrowser__Marino:GFF832 170 ALGARIVNGKSRFVVTADEGVRGGRKIPLKKNVDAALKNEDAaNVEKVVVVTRTGNSEVPWNEARDERYEDLMKS- 244 ***************************************9999*************99****************6. PP TIGR02188 227 asaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivyg 302 asa+c+pe++++edplf+LYtsGstG PkGvlhttgGy+++a++t++yvfd++++d++wCtaD GWvtGhsYi+yg lcl|FitnessBrowser__Marino:GFF832 245 ASADCQPEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYASMTHEYVFDYHEGDVYWCTADFGWVTGHSYILYG 320 **************************************************************************** PP TIGR02188 303 PLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaw 378 PLanGa t+lfegvp+ypd+sr+ +v++k+kv+i+YtaPtaiRalm++ge+ ++ + ++sl++lgsvGepinpeaw lcl|FitnessBrowser__Marino:GFF832 321 PLANGAITVLFEGVPNYPDSSRMGQVVDKHKVNILYTAPTAIRALMAEGESCMNGTTRESLKLLGSVGEPINPEAW 396 **************************************************************************** PP TIGR02188 379 eWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkp 454 eWy++v+G++kcpivdtwWqtetGgili+plpg a++lkpgsat+P+fG+++++vd++g+ +e ++e g Lvi ++ lcl|FitnessBrowser__Marino:GFF832 397 EWYHRVIGNSKCPIVDTWWQTETGGILISPLPG-AIDLKPGSATVPFFGVQPALVDNDGNILEGKTE-GNLVILDS 470 *********************************.6****************************8777.79****** PP TIGR02188 455 wPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaea 530 wP+++rtiygd+erf +tYf+++kg+yftGDgarrd+dGy+wi+GRvDdv+nvsGhrlgtae+esalvshe+vaea lcl|FitnessBrowser__Marino:GFF832 471 WPGQMRTIYGDHERFAQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHEKVAEA 546 **************************************************************************** PP TIGR02188 531 avvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiae 606 avvg+p++ikg+ i+++v+l +g+e+++e l+kel ++vrkeigpia+pd i++++ lPktRsGkimRR+lrkia+ lcl|FitnessBrowser__Marino:GFF832 547 AVVGYPHDIKGQGIYVYVTLVHGQEPSDE-LKKELVQWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAA 621 ****************************5.********************************************** PP TIGR02188 607 ge.ellgdvstledpsvveelk 627 +e ++lgd+stl+dp vv++l+ lcl|FitnessBrowser__Marino:GFF832 622 NEhDQLGDTSTLADPGVVDDLI 643 **9****************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (649 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 12.37 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory