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)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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