Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO353_03060 AO353_03060 acetyl-CoA synthetase
Query= reanno::pseudo3_N2E3:AO353_03060 (651 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03060 Length = 651 Score = 1340 bits (3469), Expect = 0.0 Identities = 651/651 (100%), Positives = 651/651 (100%) Query: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF Sbjct: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF Sbjct: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL Sbjct: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300 Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA Sbjct: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360 Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA Sbjct: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420 Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD Sbjct: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480 Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600 Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 651 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA Sbjct: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHKTMNVA 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: 1791 Number of extensions: 63 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 AO353_03060 AO353_03060 (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.17868.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 1013.5 0.1 0 1013.3 0.1 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 AO353_03060 acetyl-CoA synthetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 AO353_03060 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1013.3 0.1 0 0 3 628 .. 20 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1013.3 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvd 64 + +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++ ++kWf+dg+lnvsync+d lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNCLD 83 5679*********************5.*************99887789***************** PP TIGR02188 65 rhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeavi 129 rh+++r d++aiiwegd++ e sr++tY+el+++vc++an+l+ + v++gd v+iY+pmipeav+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 84 RHLAERGDQIAIIWEGDDPAE-SRNITYRELHEQVCKFANALRGQDVHRGDVVTIYMPMIPEAVV 147 *******************96.******************************************* PP TIGR02188 130 amlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee. 193 amlac+RiGa+hsvvf+Gfs+eala Ri+d+++k+vitadeglR gk+i+lk++vd+al++ e+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 148 AMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGLRAGKKISLKANVDDALTNPETs 212 *************************************************************9998 PP TIGR02188 194 svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvl 258 s++kv+v+krtg +++ w++ rD+w+e+l++ a + c+p+++++e+ lfiLYtsGstGkPkGv+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 213 SIQKVIVCKRTGGNIK-WNQHRDIWYEDLMKV-AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQ 275 **************76.**************5.******************************** PP TIGR02188 259 httgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdas 323 httgGyll+aalt++ vfd+++++i+wCtaDvGWvtGh+YivygPLanGattllfegvp+ypd lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 276 HTTGGYLLYAALTHERVFDYRPGEIYWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDIT 340 ***************************************************************** PP TIGR02188 324 rfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGke 388 r++++i+k+kv+i+YtaPtaiRa+m++g+++v+ d sslr+lgsvGepinpeaweWyy++vG++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 341 RVAKIIDKHKVNILYTAPTAIRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQS 405 ***************************************************************** PP TIGR02188 389 kcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikk 453 +cpivdtwWqtetG++l++plpg a lkpgsa++P+fG+ +++vd+ g+ +e +e g Lvi + lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 406 RCPIVDTWWQTETGATLMSPLPG-AHGLKPGSAARPFFGVVPALVDNLGNIIEGVAE-GNLVILD 468 ***********************.6***************************98777.79***** PP TIGR02188 454 pwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeie 518 +wP+++rt+ygd++rfv+tYfk+++g+yftGDgarrd+dGy wi+GRvDdv+nvsGhr+gtaeie lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 469 SWPGQARTLYGDHDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIE 533 ***************************************************************** PP TIGR02188 519 salvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583 sa+v+h++vaeaavvgvp++ikg+ i+++v+l+ g+e++e +l+ elk++vrkeigpia+pd i+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 534 SAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSE-ALRLELKNWVRKEIGPIASPDVIQ 597 ***************************************9.5*********************** PP TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +++ lPktRsGkimRR+lrkia+ge + lgd+stl+dp vv++l++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03060 598 WAPGLPKTRSGKIMRRILRKIATGEyDGLGDISTLADPGVVQHLID 643 *************************9****************9975 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 12.30 // [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