Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate H281DRAFT_04953 H281DRAFT_04953 acetyl-coenzyme A synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__Burk376:H281DRAFT_04953 Length = 660 Score = 1120 bits (2898), Expect = 0.0 Identities = 527/659 (79%), Positives = 593/659 (89%) Query: 1 MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60 MSAIESV+QE RVF P A+ A I M+AY AL EAERDYEGFW R ARE L W KP Sbjct: 1 MSAIESVLQERRVFPPSAEAAAGATISGMDAYHALTAEAERDYEGFWGRLARETLSWNKP 60 Query: 61 FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120 FTKVLD+S APFY WFEDG+LNASYN +DR+++ GN ++VAI+FEADDG+VT VTY++L Sbjct: 61 FTKVLDESKAPFYTWFEDGQLNASYNSIDRHVEAGNGERVAIIFEADDGTVTNVTYQDLL 120 Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180 +V RFAN LK G++KGDRVVIYMPMS+EG+VAMQACAR+GATHSVVFGGFS+KSL ER Sbjct: 121 QRVSRFANALKTRGVKKGDRVVIYMPMSIEGIVAMQACARIGATHSVVFGGFSSKSLNER 180 Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240 LVDVGAVAL+T+DEQMRGGKALPLK IAD+ALA+GGCEAV++VIVY+RTGGK+AW E RD Sbjct: 181 LVDVGAVALVTSDEQMRGGKALPLKNIADEALAMGGCEAVKSVIVYQRTGGKIAWNESRD 240 Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300 WM ++S + D C E V AEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA TMKWTFD Sbjct: 241 LWMHEISQAESDQCAPEWVGAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAAQTMKWTFD 300 Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360 K D+FWCTADIGW+TGH+YI YGPL G TQVVFEGVPTYPNAGRFWDMIA+HKV++F Sbjct: 301 WKSSDVFWCTADIGWITGHSYITYGPLTLGGTQVVFEGVPTYPNAGRFWDMIAKHKVTLF 360 Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420 YTAPTAIRSLIKAAEAD K+HPK YDLS+LR++GTVGEPINPEAW+WYY+N+G RCPIV Sbjct: 361 YTAPTAIRSLIKAAEADAKVHPKSYDLSTLRIIGTVGEPINPEAWVWYYENVGGGRCPIV 420 Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480 DT+WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAA+VDETG DVPNG GGILVVKRPW Sbjct: 421 DTWWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAVVDETGQDVPNGQGGILVVKRPW 480 Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 P+M+R +WGDP+R++KSYFPEELGGKLYLAGDG++RDKDTGYFTIMGRIDDVLNVSGHR+ Sbjct: 481 PSMLRNVWGDPDRYKKSYFPEELGGKLYLAGDGAVRDKDTGYFTIMGRIDDVLNVSGHRL 540 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 GTMEIESALVSNP+VAEAAVVGRPD TGEA+CAFVVLKR+RP GEEAVK+A ELRNWVG Sbjct: 541 GTMEIESALVSNPIVAEAAVVGRPDATTGEAVCAFVVLKRARPEGEEAVKLANELRNWVG 600 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659 KEIGPIAKPKDIRFG+NLPKTRSGKIMRRLLRSLAKGEEITQD STLENPAIL+QL ++ Sbjct: 601 KEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEEITQDVSTLENPAILDQLGES 659 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: 1583 Number of extensions: 67 Number of successful extensions: 2 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: 660 Length adjustment: 38 Effective length of query: 622 Effective length of database: 622 Effective search space: 386884 Effective search space used: 386884 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 H281DRAFT_04953 H281DRAFT_04953 (acetyl-coenzyme A 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.25735.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-297 972.1 0.0 6.4e-297 971.9 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04953 H281DRAFT_04953 acetyl-coenzyme Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04953 H281DRAFT_04953 acetyl-coenzyme A synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 971.9 0.0 6.4e-297 6.4e-297 2 627 .. 27 657 .. 26 659 .. 0.97 Alignments for each domain: == domain 1 score: 971.9 bits; conditional E-value: 6.4e-297 TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhv 67 + +++y++l++ea++d+e fw++la+e+l+w kpf+kvldes++p+++Wfedg+ln+syn++drhv lcl|FitnessBrowser__Burk376:H281DRAFT_04953 27 SGMDAYHALTAEAERDYEGFWGRLARETLSWNKPFTKVLDESKAPFYTWFEDGQLNASYNSIDRHV 92 57899************************************************************* PP TIGR02188 68 ek.rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviaml 132 e+ + ++vaii+e+d+ + + ++tY++ll++v+r+an+lk+ Gvkkgdrv+iY+pm +e ++am+ lcl|FitnessBrowser__Burk376:H281DRAFT_04953 93 EAgNGERVAIIFEADDGT--VTNVTYQDLLQRVSRFANALKTRGVKKGDRVVIYMPMSIEGIVAMQ 156 ***************664..8********************************************* PP TIGR02188 133 acaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svek 197 acaRiGa+hsvvf+Gfs+++l+eR+vd+ a ++t+de++Rggk+++lk+i+deal++ + +v++ lcl|FitnessBrowser__Burk376:H281DRAFT_04953 157 ACARIGATHSVVFGGFSSKSLNERLVDVGAVALVTSDEQMRGGKALPLKNIADEALAMGGCeAVKS 222 **********************************************************99889*** PP TIGR02188 198 vlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgG 263 v+v++rtg ++a w+e+rD+w++e+ + +s++c+pe++++e+plfiLYtsGstGkPkGv+h+tgG lcl|FitnessBrowser__Burk376:H281DRAFT_04953 223 VIVYQRTGGKIA-WNESRDLWMHEISQA-ESDQCAPEWVGAEHPLFILYTSGSTGKPKGVQHSTGG 286 **********77.*************95.************************************* PP TIGR02188 264 ylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfwevi 329 yll+aa t+k++fd k +d+fwCtaD+GW+tGhsYi ygPL+ G t+++fegvptyp+a+rfw++i lcl|FitnessBrowser__Burk376:H281DRAFT_04953 287 YLLWAAQTMKWTFDWKSSDVFWCTADIGWITGHSYITYGPLTLGGTQVVFEGVPTYPNAGRFWDMI 352 ****************************************************************** PP TIGR02188 330 ekykvtifYtaPtaiRalmklg....eelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcp 391 k+kvt fYtaPtaiR+l+k++ + ++k++dls+lr++g+vGepinpeaw Wyye+vG ++cp lcl|FitnessBrowser__Burk376:H281DRAFT_04953 353 AKHKVTLFYTAPTAIRSLIKAAeadaKVHPKSYDLSTLRIIGTVGEPINPEAWVWYYENVGGGRCP 418 *******************9983333457899********************************** PP TIGR02188 392 ivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPs 457 ivdtwWqtetGg++itplpg at+l pgs+tlPl+Gi+a+vvde+g++v ++++ g+Lv+k+pwPs lcl|FitnessBrowser__Burk376:H281DRAFT_04953 419 IVDTWWQTETGGHMITPLPG-ATPLVPGSCTLPLPGIMAAVVDETGQDVPNGQG-GILVVKRPWPS 482 ********************.6*****************************999.8********** PP TIGR02188 458 mlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesa 520 mlr ++gd++r+ ++Yf + g ly++GDga+rdkd Gy++i+GR+Ddv+nvsGhrlgt+eiesa lcl|FitnessBrowser__Burk376:H281DRAFT_04953 483 MLRNVWGDPDRYKKSYFPEELGgkLYLAGDGAVRDKDtGYFTIMGRIDDVLNVSGHRLGTMEIESA 548 *****************9876567************99**************************** PP TIGR02188 521 lvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeigpiakpdkilv 584 lvs++ vaeaavvg+pd ++gea++afvvlk+++ e ee +l++el+++v keigpiakp++i++ lcl|FitnessBrowser__Burk376:H281DRAFT_04953 549 LVSNPIVAEAAVVGRPDATTGEAVCAFVVLKRARPEGEEavKLANELRNWVGKEIGPIAKPKDIRF 614 ********************************99988887799*********************** PP TIGR02188 585 veelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627 e+lPktRsGkimRRllr++a+gee+++dvstle+p+++++l lcl|FitnessBrowser__Burk376:H281DRAFT_04953 615 GENLPKTRSGKIMRRLLRSLAKGEEITQDVSTLENPAILDQLG 657 ****************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (660 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: 8.27 // [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