Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_041099385.1 SUTH_RS11485 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_000828635.1:WP_041099385.1 Length = 660 Score = 1060 bits (2740), Expect = 0.0 Identities = 506/658 (76%), Positives = 569/658 (86%) Query: 1 MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60 MS+IES + E RVF P + +A I M AY+ALC EA++DY GFWAR ARE + W +P Sbjct: 1 MSSIESNVTETRVFPPADAVVKKATISGMAAYEALCKEADQDYAGFWARLAREHVSWKQP 60 Query: 61 FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120 FTK LD+S APFY+WF DG+LN SYNCLDRN++ G DKVAI+FEAD G V+++TY+EL Sbjct: 61 FTKSLDESKAPFYEWFADGKLNVSYNCLDRNIEAGLGDKVAIIFEADGGQVSKITYKELL 120 Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180 +V RFAN LKA GI+KGDRV+IYMPMSVEGVVAMQACAR+GA HSVVFGGFSAKS+QER Sbjct: 121 VRVARFANALKAQGIKKGDRVLIYMPMSVEGVVAMQACARIGAIHSVVFGGFSAKSVQER 180 Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240 + D GAVA+IT+DEQ RGGK +PLK DD +A+GGCE+++ VIV++RTGG GRD Sbjct: 181 IQDAGAVAVITSDEQCRGGKNIPLKPAVDDGIAMGGCESIKTVIVFKRTGGPCNMVAGRD 240 Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300 W ED +AGQ D CE E V AEHPLF+LYTSGSTGKPKGVQHS+GGYLL A++TMKWTFD Sbjct: 241 IWWEDATAGQSDVCEPEWVGAEHPLFLLYTSGSTGKPKGVQHSSGGYLLHAILTMKWTFD 300 Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360 IKPDD+FWCTADIGWVTGHTYI YGPLA GAT++VFEGVPTYP+AGRFW I +HKV+IF Sbjct: 301 IKPDDVFWCTADIGWVTGHTYITYGPLACGATEIVFEGVPTYPDAGRFWKTIEKHKVNIF 360 Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420 YTAPTAIRSLIKA E HPK +DLSSLR+LG+VGEPINPEAWMWYY N+G RCPIV Sbjct: 361 YTAPTAIRSLIKAGENAPTTHPKNFDLSSLRILGSVGEPINPEAWMWYYNNVGGARCPIV 420 Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480 DTFWQTETGGHMITPLPGATPLVPGSCTLP PGI AAIVDETG+DV G GG LVVK+PW Sbjct: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPFPGIAAAIVDETGNDVEWGKGGFLVVKKPW 480 Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 PAMIRTI+GDPER++KSYFP + GG LYLAGDG++RD TGYFTIMGRIDDVLNVSGHRM Sbjct: 481 PAMIRTIYGDPERYKKSYFPVDFGGNLYLAGDGAMRDAKTGYFTIMGRIDDVLNVSGHRM 540 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 GTMEIESALVSNPLVAEAAVVGRPDD+TGEAICAFVVLK++RPT EEA KIA ELRNWVG Sbjct: 541 GTMEIESALVSNPLVAEAAVVGRPDDLTGEAICAFVVLKQARPTAEEAKKIANELRNWVG 600 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658 KEIGPIAKPKDIRFG+NLPKTRSGKIMRRLLRSLAKGEEITQD STLENP IL+QLKQ Sbjct: 601 KEIGPIAKPKDIRFGENLPKTRSGKIMRRLLRSLAKGEEITQDVSTLENPGILDQLKQ 658 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: 1546 Number of extensions: 63 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 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