Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 5209055 Shew_1533 acetyl-CoA synthetase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__PV4:5209055 Length = 650 Score = 984 bits (2544), Expect = 0.0 Identities = 461/644 (71%), Positives = 537/644 (83%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MS SLY V E+AA+ ++ YK MYQ+SVVNP+GFWRE +R+DW+KPFT VK+TSF Sbjct: 1 MSTQSLYKVPSEIAANAHINDEKYKKMYQESVVNPEGFWREHGQRIDWMKPFTKVKKTSF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 DDH++ I WF DGTLN S NCLDRHLA+ D++AIIWEGDD ++ R +TY ELH EVCKF Sbjct: 61 DDHNLSINWFYDGTLNASVNCLDRHLADNADKLAIIWEGDDAADQRTLTYGELHTEVCKF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANALR Q V RGDVVT+YMPM+PEA V MLAC RIGAIHSVVFGGFSP+++A R+ID KS Sbjct: 121 ANALRSQGVRRGDVVTVYMPMVPEAAVVMLACARIGAIHSVVFGGFSPDSIASRVIDGKS 180 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 KVVITADEGVR G+ IPLKAN+D+AL++P+ + ++KVIV +RT + W + RDI + L Sbjct: 181 KVVITADEGVRGGRTIPLKANIDEALSHPDVTCVEKVIVLERTGNPVNWVEGRDIKWASL 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 M+ A C +EMGAE+ LF+LYTSGSTG PKGV HTT GYL+YA++THE VFDYK GE+ Sbjct: 241 METASEHCVAEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKEGEI 300 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTADVGW+TGHSY+VYGPLANGAT L+ EG+PNYP R+ ++ID+HKV+ILYTAPT Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATILIHEGIPNYPTPARLGEMIDRHKVNILYTAPTL 360 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IRA+MA G +G DGSSLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG Sbjct: 361 IRALMAEGKEQFDGFDGSSLRIMGSVGEPINPEAWRWYHEVIGHENCPIVDTWWQTETGG 420 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LISPLPGAT KPGSATRPFFGV PALVDN+GN+I+GAAEGNLVILDSWPGQ RT+YGD Sbjct: 421 ILISPLPGATDTKPGSATRPFFGVQPALVDNMGNIIDGAAEGNLVILDSWPGQMRTVYGD 480 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 HDRF TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAH Sbjct: 481 HDRFALTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHE 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 VAEAAVVG PHDIKGQGIY YVTL G + SE LR EL+ WVRKEIG +A+PD+IQWA Sbjct: 541 HVAEAAVVGYPHDIKGQGIYAYVTLTKGTQESEELRQELRQWVRKEIGALATPDLIQWAG 600 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIET 644 GLPKTRSGKIMRR LRKIA E LGD STLADP V+ LIET Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIDTLIET 644 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: 1474 Number of extensions: 50 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: 650 Length adjustment: 38 Effective length of query: 613 Effective length of database: 612 Effective search space: 375156 Effective search space used: 375156 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 5209055 Shew_1533 (acetyl-CoA synthetase (RefSeq))
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.11462.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 1021.6 0.1 0 1021.4 0.1 1.0 1 lcl|FitnessBrowser__PV4:5209055 Shew_1533 acetyl-CoA synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209055 Shew_1533 acetyl-CoA synthetase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1021.4 0.1 0 0 3 628 .. 20 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1021.4 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaii 77 + e+yk++y+e++ +pe fw+++++ +++w+kpf+kv+++s+++ +++Wf dg+ln+s+nc+drh+++++dk+aii lcl|FitnessBrowser__PV4:5209055 20 NDEKYKKMYQESVVNPEGFWREHGQ-RIDWMKPFTKVKKTSFDDhnlSINWFYDGTLNASVNCLDRHLADNADKLAII 96 5689********************9.5*************99887789****************************** PP TIGR02188 78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealae 155 wegd++ d+r+ltY el++evc++an+l+++Gv++gd v++Y+pm+pea+++mlacaRiGa+hsvvf+Gfs++++a+ lcl|FitnessBrowser__PV4:5209055 97 WEGDDAA-DQRTLTYGELHTEVCKFANALRSQGVRRGDVVTVYMPMVPEAAVVMLACARIGAIHSVVFGGFSPDSIAS 173 ****998.6********************************************************************* PP TIGR02188 156 RivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaece 232 R++d ++k+vitadeg+Rgg++i+lk+++deal++ + vekv+v++rtg++v+ w+egrD++w +l+e+ as++c lcl|FitnessBrowser__PV4:5209055 174 RVIDGKSKVVITADEGVRGGRTIPLKANIDEALSHPDVtCVEKVIVLERTGNPVN-WVEGRDIKWASLMET-ASEHCV 249 ***********************************99989*************66.**************6.****** PP TIGR02188 233 pekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGatt 310 +e++++edplf+LYtsGstG+PkGvlhttgGyl++a++t++yvfd+k+++i+wCtaDvGW+tGhsY+vygPLanGat lcl|FitnessBrowser__PV4:5209055 250 AEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKEGEIYWCTADVGWITGHSYMVYGPLANGATI 327 ****************************************************************************** PP TIGR02188 311 llfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGke 388 l++eg+p+yp+++r+ e+i+++kv+i+YtaPt+iRalm++g+e+++ d sslr++gsvGepinpeaw+Wy+ev+G+e lcl|FitnessBrowser__PV4:5209055 328 LIHEGIPNYPTPARLGEMIDRHKVNILYTAPTLIRALMAEGKEQFDGFDGSSLRIMGSVGEPINPEAWRWYHEVIGHE 405 ****************************************************************************** PP TIGR02188 389 kcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygde 466 +cpivdtwWqtetGgili+plpg at++kpgsat+P+fG+++++vd+ g+ ++ +e g Lvi ++wP+++rt+ygd+ lcl|FitnessBrowser__PV4:5209055 406 NCPIVDTWWQTETGGILISPLPG-ATDTKPGSATRPFFGVQPALVDNMGNIIDGAAE-GNLVILDSWPGQMRTVYGDH 481 ***********************.6****************************8777.79****************** PP TIGR02188 467 erfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeai 544 +rf tYfk+++g+yftGDgarrd+dGy+wi+GRvDdvinvsGhrlgtae+esalv+he+vaeaavvg+p++ikg+ i lcl|FitnessBrowser__PV4:5209055 482 DRFALTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHEHVAEAAVVGYPHDIKGQGI 559 ****************************************************************************** PP TIGR02188 545 vafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledps 621 +a+v+l++g++e+e el++el+++vrkeig++a+pd i+++ lPktRsGkimRR+lrkia++e ++lgd stl+dp+ lcl|FitnessBrowser__PV4:5209055 560 YAYVTLTKGTQESE-ELRQELRQWVRKEIGALATPDLIQWAGGLPKTRSGKIMRRFLRKIAANEvTNLGDASTLADPA 636 ***********999.5************************************************************** PP TIGR02188 622 vveelke 628 v+++l+e lcl|FitnessBrowser__PV4:5209055 637 VIDTLIE 643 ***9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (650 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: 9.63 // [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