Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate BPHYT_RS07000 BPHYT_RS07000 acetyl-CoA synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__BFirm:BPHYT_RS07000 Length = 660 Score = 1120 bits (2898), Expect = 0.0 Identities = 526/659 (79%), Positives = 595/659 (90%) Query: 1 MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60 MSAIESV+ E RVF P A+ AAI M+AY+AL EAE DYEGFW R ARE L W P Sbjct: 1 MSAIESVLHERRVFPPSAEAAAGAAISGMDAYRALAAEAESDYEGFWGRLARETLSWNTP 60 Query: 61 FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120 FTKVLD++NAPFY WFEDG++NASYN +DR+++ GN ++VAI+FEADDG+VT VTY++L Sbjct: 61 FTKVLDETNAPFYTWFEDGQINASYNSIDRHVEAGNGERVAIIFEADDGTVTNVTYQDLL 120 Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180 +V RFAN LK G++KGDRVVIYMPMS+EG+VAMQACAR+GATHSVVFGGFS+KSL ER Sbjct: 121 QRVSRFANALKKRGVKKGDRVVIYMPMSIEGIVAMQACARIGATHSVVFGGFSSKSLNER 180 Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240 LVDVGAVAL+T+DEQMRGGKALPLK IAD+ALA+GGCEAV +VIVY+RTGGKVAW EGRD Sbjct: 181 LVDVGAVALVTSDEQMRGGKALPLKNIADEALAMGGCEAVTSVIVYQRTGGKVAWNEGRD 240 Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300 WM +++ + D C E V AEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA T+KWTFD Sbjct: 241 LWMHELTQAESDQCAPEWVGAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAAQTLKWTFD 300 Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360 KP D+FWCTADIGW+TGH+YI YGPL G TQVVFEGVPTYPNAGRFWDMIA+HKVS+F Sbjct: 301 WKPSDVFWCTADIGWITGHSYITYGPLTLGGTQVVFEGVPTYPNAGRFWDMIAKHKVSLF 360 Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420 YTAPTAIRSLIKAA+AD+K+HPK YDLS+LR++GTVGEPINPEAW+WYY+N+G RCPIV Sbjct: 361 YTAPTAIRSLIKAADADQKVHPKSYDLSTLRIIGTVGEPINPEAWIWYYENVGGSRCPIV 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 GTMEIESALVSNPLVAEAAVVGRPD TGEA+CAFVVLKR+RP GEEAVK+A ELRNWVG Sbjct: 541 GTMEIESALVSNPLVAEAAVVGRPDATTGEAVCAFVVLKRARPEGEEAVKLANELRNWVG 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: 1590 Number of extensions: 70 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: 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 BPHYT_RS07000 BPHYT_RS07000 (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.3116.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-296 969.7 0.0 3.4e-296 969.5 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS07000 BPHYT_RS07000 acetyl-CoA synthet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS07000 BPHYT_RS07000 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 969.5 0.0 3.4e-296 3.4e-296 2 627 .. 27 657 .. 26 659 .. 0.97 Alignments for each domain: == domain 1 score: 969.5 bits; conditional E-value: 3.4e-296 TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 + +++y++l +ea++d+e fw++la+e+l+w +pf+kvlde+++p+++Wfedg++n+syn++drhve+ + lcl|FitnessBrowser__BFirm:BPHYT_RS07000 27 SGMDAYRALAAEAESDYEGFWGRLARETLSWNTPFTKVLDETNAPFYTWFEDGQINASYNSIDRHVEAgN 96 5789****************************************************************** PP TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGav 140 ++vaii+e+d+ + + ++tY++ll++v+r+an+lk+ Gvkkgdrv+iY+pm +e ++am+acaRiGa+ lcl|FitnessBrowser__BFirm:BPHYT_RS07000 97 GERVAIIFEADDGT--VTNVTYQDLLQRVSRFANALKKRGVKKGDRVVIYMPMSIEGIVAMQACARIGAT 164 ***********664..8***************************************************** PP TIGR02188 141 hsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeeva 209 hsvvf+Gfs+++l+eR+vd+ a ++t+de++Rggk+++lk+i+deal++ + +v +v+v++rtg +va lcl|FitnessBrowser__BFirm:BPHYT_RS07000 165 HSVVFGGFSSKSLNERLVDVGAVALVTSDEQMRGGKALPLKNIADEALAMGGCeAVTSVIVYQRTGGKVA 234 **************************************************99889*************77 PP TIGR02188 210 ewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik 279 w+egrD+w++el++ +s++c+pe++++e+plfiLYtsGstGkPkGv+h+tgGyll+aa t k++fd k lcl|FitnessBrowser__BFirm:BPHYT_RS07000 235 -WNEGRDLWMHELTQA-ESDQCAPEWVGAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAAQTLKWTFDWK 302 .**************5.***************************************************** PP TIGR02188 280 dedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmk 349 ++d+fwCtaD+GW+tGhsYi ygPL+ G t+++fegvptyp+a+rfw++i k+kv+ fYtaPtaiR+l+k lcl|FitnessBrowser__BFirm:BPHYT_RS07000 303 PSDVFWCTADIGWITGHSYITYGPLTLGGTQVVFEGVPTYPNAGRFWDMIAKHKVSLFYTAPTAIRSLIK 372 ********************************************************************** PP TIGR02188 350 lgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415 ++++ ++k++dls+lr++g+vGepinpeaw Wyye+vG ++cpivdtwWqtetGg++itplpg at+ lcl|FitnessBrowser__BFirm:BPHYT_RS07000 373 AADAdqkvHPKSYDLSTLRIIGTVGEPINPEAWIWYYENVGGSRCPIVDTWWQTETGGHMITPLPG-ATP 441 985422337899******************************************************.6** PP TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyft 483 l pgs+tlPl+Gi+a+vvde+g++v ++++ g+Lv+k+pwPsmlr ++gd++r+ ++Yf + g ly++ lcl|FitnessBrowser__BFirm:BPHYT_RS07000 442 LVPGSCTLPLPGIMAAVVDETGQDVPNGQG-GILVVKRPWPSMLRNVWGDPDRYKKSYFPEELGgkLYLA 510 ***************************999.8***************************9876567**** PP TIGR02188 484 GDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlke 552 GDga+rdkd Gy++i+GR+Ddv+nvsGhrlgt+eiesalvs++ vaeaavvg+pd ++gea++afvvlk+ lcl|FitnessBrowser__BFirm:BPHYT_RS07000 511 GDGAVRDKDtGYFTIMGRIDDVLNVSGHRLGTMEIESALVSNPLVAEAAVVGRPDATTGEAVCAFVVLKR 580 ********99************************************************************ PP TIGR02188 553 gveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledp 620 ++ e ee +l++el+++v keigpiakp++i++ e+lPktRsGkimRRllr++a+gee+++dvstle+p lcl|FitnessBrowser__BFirm:BPHYT_RS07000 581 ARPEGEEavKLANELRNWVGKEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEEITQDVSTLENP 650 99988887799*********************************************************** PP TIGR02188 621 svveelk 627 +++++l lcl|FitnessBrowser__BFirm:BPHYT_RS07000 651 AILDQLG 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 12.18 // [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