Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Ac3H11_951 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_951 Length = 664 Score = 1038 bits (2684), Expect = 0.0 Identities = 495/659 (75%), Positives = 568/659 (86%), Gaps = 2/659 (0%) Query: 2 SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61 SAIESV+ E+RVF P + A + M Y ALC EA++D+EGFWAR ARE ++WTKPF Sbjct: 6 SAIESVLVENRVFPPSDAVVKAARVSGMAGYDALCAEADKDFEGFWARLARENVNWTKPF 65 Query: 62 TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121 + LD SNAPF+KWF+DGELNAS NCLDR++ +K AIVFEADDG+VTR+TY+EL Sbjct: 66 NRTLDTSNAPFFKWFDDGELNASANCLDRHIGTPTENKTAIVFEADDGTVTRITYKELLA 125 Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181 +V +FAN LKA G+ KGDRV+IYMPM++EGV+AMQACAR+GATHSVVFGGFSAK++QER+ Sbjct: 126 RVSQFANALKAHGVTKGDRVLIYMPMTIEGVIAMQACARIGATHSVVFGGFSAKAVQERI 185 Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDR 241 +D GAVA+ITA+ QMRGGK LPLKAI D+ALA+GGC+ +RNV VY+RT GRD+ Sbjct: 186 IDAGAVAVITANYQMRGGKELPLKAIIDEALAMGGCDTIRNVFVYQRTATACNMVAGRDK 245 Query: 242 WMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDI 301 ++ AGQ C PV AEHPLF+LYTSGSTGKPKGVQH+TGGYLLWA +TM WTFD+ Sbjct: 246 TFGEMLAGQSTECAPVPVGAEHPLFILYTSGSTGKPKGVQHATGGYLLWAKLTMDWTFDL 305 Query: 302 KPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFY 361 + DD+FWCTADIGW+TGHTY+AYGPLAAGATQ++FEGVPT+PNAGRFW MI +HK +IFY Sbjct: 306 RADDVFWCTADIGWITGHTYVAYGPLAAGATQIIFEGVPTFPNAGRFWQMIEKHKCTIFY 365 Query: 362 TAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVD 421 TAPTAIRSLIKAAE D +HP + DLSSLR+LG+VGEPINPEAWMWY+KN+G ERCPIVD Sbjct: 366 TAPTAIRSLIKAAEGDAAVHPARSDLSSLRILGSVGEPINPEAWMWYHKNVGGERCPIVD 425 Query: 422 TFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWP 481 TFWQTETGGH+ITPLPGATPLVPGSCTLPLPGI AAIVDE G+DV NG GGILV+K+PWP Sbjct: 426 TFWQTETGGHVITPLPGATPLVPGSCTLPLPGISAAIVDEMGNDVANGAGGILVIKKPWP 485 Query: 482 AMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMG 541 +MIRTIW DPERF+K+YFPEEL G YLAGDG++R D GYF I GRIDDVLNVSGHRMG Sbjct: 486 SMIRTIWNDPERFKKAYFPEELKG-YYLAGDGAVRSADRGYFRITGRIDDVLNVSGHRMG 544 Query: 542 TMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 TMEIESALVS LVAEAAVVGRPDD+TGEAICAFVVLKRSRPTGEEA +IA ELRNWV Sbjct: 545 TMEIESALVSKTDLVAEAAVVGRPDDVTGEAICAFVVLKRSRPTGEEAKQIANELRNWVA 604 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRS+AKGE ITQDTSTLENPAIL+QL +A Sbjct: 605 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEAITQDTSTLENPAILDQLAKA 663 Lambda K H 0.319 0.136 0.422 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: 1493 Number of extensions: 73 Number of successful extensions: 4 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: 660 Length of database: 664 Length adjustment: 38 Effective length of query: 622 Effective length of database: 626 Effective search space: 389372 Effective search space used: 389372 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 Ac3H11_951 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
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.5104.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-292 955.6 0.0 6.2e-292 955.4 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 Acetyl-coenzyme A synthetase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 Acetyl-coenzyme A synthetase (EC 6.2.1.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 955.4 0.0 6.2e-292 6.2e-292 4 628 .. 33 662 .. 30 663 .. 0.96 Alignments for each domain: == domain 1 score: 955.4 bits; conditional E-value: 6.2e-292 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrh 66 + y +l++ea +d e fwa+la+e+++w+kpf+++ld+s++p+ kWf+dgeln+s+nc+drh lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 33 MAGYDALCAEADKDFEGFWARLARENVNWTKPFNRTLDTSNAPFFKWFDDGELNASANCLDRH 95 67899********************************************************** PP TIGR02188 67 vek.rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeav 128 + + +++k+ai++e+d+ + + ++tY+ell++v+++an+lk++Gv kgdrv iY+pm++e v lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 96 IGTpTENKTAIVFEADDGT--VTRITYKELLARVSQFANALKAHGVTKGDRVLIYMPMTIEGV 156 ***9************664..89**************************************** PP TIGR02188 129 iamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealeka 191 iam+acaRiGa+hsvvf+Gfsa+a++eRi+da a vita+ ++Rggk ++lk+i+deal++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 157 IAMQACARIGATHSVVFGGFSAKAVQERIIDAGAVAVITANYQMRGGKELPLKAIIDEALAMG 219 **************************************************************9 PP TIGR02188 192 ee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGk 253 + ++++v v++rt + +++ grD+++ e+++ ++s+ec+p ++++e+plfiLYtsGstGk lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 220 GCdTIRNVFVYQRTATA-CNMVAGRDKTFGEMLA-GQSTECAPVPVGAEHPLFILYTSGSTGK 280 988**************.56**************.6*************************** PP TIGR02188 254 PkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegv 316 PkGv+h+tgGyll+a+lt+ ++fd++ +d+fwCtaD+GW+tGh+Y+ ygPLa+Gat+++fegv lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 281 PKGVQHATGGYLLWAKLTMDWTFDLRADDVFWCTADIGWITGHTYVAYGPLAAGATQIIFEGV 343 *************************************************************** PP TIGR02188 317 ptypdasrfweviekykvtifYtaPtaiRalmklg....eelvkkhdlsslrvlgsvGepinp 375 pt+p+a+rfw++iek+k tifYtaPtaiR+l+k++ ++++ dlsslr+lgsvGepinp lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 344 PTFPNAGRFWQMIEKHKCTIFYTAPTAIRSLIKAAegdaAVHPARSDLSSLRILGSVGEPINP 406 ********************************98733223467899***************** PP TIGR02188 376 eaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438 eaw+Wy+++vG e+cpivdt+WqtetGg++itplpg at+l pgs+tlPl+Gi+a++vde g+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 407 EAWMWYHKNVGGERCPIVDTFWQTETGGHVITPLPG-ATPLVPGSCTLPLPGISAAIVDEMGN 468 ************************************.6************************* PP TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfk.klkglyftGDgarrdkd.GyiwilG 499 +v ++++ g+LvikkpwPsm+rti++d+erf ++Yf +lkg+y++GDga+r +d Gy+ i+G lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 469 DVANGAG-GILVIKKPWPSMIRTIWNDPERFKKAYFPeELKGYYLAGDGAVRSADrGYFRITG 530 ****999.8***************************626889**********9988******* PP TIGR02188 500 RvDdvinvsGhrlgtaeiesalvshe.avaeaavvgvpdeikgeaivafvvlkegveedee.. 559 R+Ddv+nvsGhr+gt+eiesalvs++ vaeaavvg+pd+++geai+afvvlk+++ + ee lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 531 RIDDVLNVSGHRMGTMEIESALVSKTdLVAEAAVVGRPDDVTGEAICAFVVLKRSRPTGEEak 593 ***********************975269*************************998776666 PP TIGR02188 560 elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsv 622 ++++el+++v+keigpiakp++i++ ++lPktRsGkimRRllr+ia+ge +++d+stle+p++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 594 QIANELRNWVAKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEAITQDTSTLENPAI 656 9************************************************************** PP TIGR02188 623 veelke 628 +++l + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_951 657 LDQLAK 662 **9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (664 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 0.01s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 7.96 // [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