Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF4246 PS417_21750 acetyl-CoA synthetase
Query= reanno::pseudo3_N2E3:AO353_03060 (651 letters) >FitnessBrowser__WCS417:GFF4246 Length = 651 Score = 1298 bits (3359), Expect = 0.0 Identities = 626/651 (96%), Positives = 637/651 (97%) Query: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF Sbjct: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQ AIIWEGDDP+ESR ITYRELHE+VCKF Sbjct: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQAAIIWEGDDPSESRTITYRELHEEVCKF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240 KVVITADEG+RAGKKI LKANVDDALTNPETSSIQKVIVCKRT GNIKWNQHRDIWYEDL Sbjct: 181 KVVITADEGIRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTNGNIKWNQHRDIWYEDL 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300 Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKI+DKHKVNILYTAPTA Sbjct: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTA 360 Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420 IRAMMA GTAA EGADGSSLRLLGSVGEPINPEAW+WYYKNVGQSRCPIVDTWWQTETG Sbjct: 361 IRAMMASGTAACEGADGSSLRLLGSVGEPINPEAWDWYYKNVGQSRCPIVDTWWQTETGG 420 Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480 +MSPLPGAH LKPGSAARPFFGVVPALVDNLGN+IEG AEGNLVILDSWPGQARTL+GD Sbjct: 421 NMMSPLPGAHALKPGSAARPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLFGD 480 Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 HDRFVDTYFKTFRGMYFTGDGARRD DGY+WITGRVDDVLNVSGHRMGTAEIESAMVAHP Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600 KVAEAAVVGVPHDIKGQGIYVYVTL GEEP+EALRLELKNWVRKEIGPIASPDVIQWAP Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNEALRLELKNWVRKEIGPIASPDVIQWAP 600 Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVV HLI+THKTMNVA Sbjct: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVAHLIETHKTMNVA 651 Lambda K H 0.319 0.136 0.425 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: 1751 Number of extensions: 56 Number of successful extensions: 1 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: 651 Length of database: 651 Length adjustment: 38 Effective length of query: 613 Effective length of database: 613 Effective search space: 375769 Effective search space used: 375769 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate GFF4246 PS417_21750 (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.24652.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 1018.4 0.1 0 1018.2 0.1 1.0 1 lcl|FitnessBrowser__WCS417:GFF4246 PS417_21750 acetyl-CoA synthetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4246 PS417_21750 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1018.2 0.1 0 0 3 628 .. 20 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1018.2 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkv 74 + +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++ ++kWf+dg+lnvsync+drh+++r d++ lcl|FitnessBrowser__WCS417:GFF4246 20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNCLDRHLAERGDQA 93 5679*********************5.*************99887789*************************** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfs 149 aiiwegd+++e sr++tY+el++evc++an+l+ + v++gd v+iY+pmipeav+amlac+RiGa+hsvvf+Gfs lcl|FitnessBrowser__WCS417:GFF4246 94 AIIWEGDDPSE-SRTITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFS 167 *********96.*************************************************************** PP TIGR02188 150 aealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelv 223 +eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al++ e+ s++kv+v+krt+ +++ w++ rD+w+e+l+ lcl|FitnessBrowser__WCS417:GFF4246 168 PEALAGRIIDCKSKVVITADEGIRAGKKIPLKANVDDALTNPETsSIQKVIVCKRTNGNIK-WNQHRDIWYEDLM 241 *****************************************9998**************76.************* PP TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298 + a + c+p+++++e+ lfiLYtsGstGkPkGv+httgGyll+aalt++ vfd+++++i+wCtaDvGWvtGh+Y lcl|FitnessBrowser__WCS417:GFF4246 242 KV-AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTADVGWVTGHTY 315 *5.************************************************************************ PP TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepi 373 ivygPLanGattllfegvp+ypd r++++++k+kv+i+YtaPtaiRa+m+ g+++ + d sslr+lgsvGepi lcl|FitnessBrowser__WCS417:GFF4246 316 IVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTAIRAMMASGTAACEGADGSSLRLLGSVGEPI 390 *************************************************************************** PP TIGR02188 374 npeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448 npeaw+Wyy++vG+++cpivdtwWqtetGg +++plpg a +lkpgsa++P+fG+ +++vd+ g+ +e +e g lcl|FitnessBrowser__WCS417:GFF4246 391 NPEAWDWYYKNVGQSRCPIVDTWWQTETGGNMMSPLPG-AHALKPGSAARPFFGVVPALVDNLGNLIEGAAE-GN 463 **************************************.6****************************8777.79 PP TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvs 523 Lvi ++wP+++rt++gd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGhr+gtaeiesa+v+ lcl|FitnessBrowser__WCS417:GFF4246 464 LVILDSWPGQARTLFGDHDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVA 538 *************************************************************************** PP TIGR02188 524 heavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimR 598 h++vaeaavvgvp++ikg+ i+++v+lk+g+e++e +l+ elk++vrkeigpia+pd i++++ lPktRsGkimR lcl|FitnessBrowser__WCS417:GFF4246 539 HPKVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNE-ALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMR 612 **********************************9.5************************************** PP TIGR02188 599 Rllrkiaege.ellgdvstledpsvveelke 628 R+lrkia+ge + lgd+stl+dp vv++l+e lcl|FitnessBrowser__WCS417:GFF4246 613 RILRKIATGEyDGLGDISTLADPGVVAHLIE 643 **********9****************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (651 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 7.41 // [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