Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO356_18695 AO356_18695 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 AO356_18695 acetyl-CoA synthetase Length = 651 Score = 1332 bits (3448), Expect = 0.0 Identities = 651/651 (100%), Positives = 651/651 (100%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF Sbjct: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF Sbjct: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL Sbjct: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA Sbjct: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG Sbjct: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD Sbjct: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP Sbjct: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA Sbjct: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651 Lambda K H 0.318 0.135 0.418 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: 1737 Number of extensions: 47 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate AO356_18695 AO356_18695 (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.5065.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 1021.5 0.2 0 1021.2 0.2 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 AO356_18695 acetyl-CoA synthetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 AO356_18695 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1021.2 0.2 0 0 3 628 .. 20 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1021.2 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsync 62 + +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++ ++kWf+dg+lnvsync lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNC 81 5679*********************5.*************99887789*************** PP TIGR02188 63 vdrhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmip 125 +drh+++r d++aiiwegd+++e sr++tY+el++evc++an+l+ + v++gd v+iY+pmip lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 82 LDRHLAERGDQIAIIWEGDDPSE-SRNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIP 143 *********************96.*************************************** PP TIGR02188 126 eaviamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdeal 188 eav+amlac+RiGa+hsvvf+Gfs+eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 144 EAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANVDDAL 206 *************************************************************** PP TIGR02188 189 ekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGs 250 ++ e+ s++kv+v+krt +++ w++ rD+w+e+l++ a + c+p+++++e+ lfiLYtsGs lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 207 TNPETsSIQKVIVCKRTAGNIK-WNQHRDIWYEDLMKV-AGTVCAPKEMGAEEALFILYTSGS 267 **9998**************76.**************5.************************ PP TIGR02188 251 tGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllf 313 tGkPkGv+htt+Gyll+aalt++ vfd+k+++++wCtaDvGWvtGhsYivygPLanGattllf lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 268 TGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTADVGWVTGHSYIVYGPLANGATTLLF 330 *************************************************************** PP TIGR02188 314 egvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpe 376 egvp+ypd r+++vi+k+kv+i+YtaPtaiRa+m+ g+++v+ d sslr+lgsvGepinpe lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 331 EGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPE 393 *************************************************************** PP TIGR02188 377 aweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439 aw+Wyy++vGke+cpivdtwWqtetGg+li+plpg at+lkpgsat+P+fG+ +++vd+ g+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 394 AWDWYYKNVGKERCPIVDTWWQTETGGVLISPLPG-ATALKPGSATRPFFGVVPALVDNLGNL 455 ***********************************.6************************** PP TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvD 502 +e +e g Lvi ++wP+++rt+ygd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvD lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 456 IEGAAE-GNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVD 517 **8777.79****************************************************** PP TIGR02188 503 dvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekel 565 dv+nvsGhr+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ el lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 518 DVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSE-ALRLEL 579 *****************************************************999.6***** PP TIGR02188 566 kklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627 k++vrkeigpia+pd i++++ lPktRsGkimRR+lrkia+ e + lgd+stl+dp vv++l+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 580 KNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEyDGLGDISTLADPGVVAHLI 642 *******************************************9****************998 PP TIGR02188 628 e 628 e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 643 E 643 6 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 9.15 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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