Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_013518028.1 ALIDE2_RS18585 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_000204645.1:WP_013518028.1 Length = 665 Score = 1069 bits (2764), Expect = 0.0 Identities = 508/660 (76%), Positives = 581/660 (88%), Gaps = 5/660 (0%) Query: 2 SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61 SAIESV+ E+RVF PPEG A I M Y+ALC EA++D+EGFWAR ARE L WT+PF Sbjct: 6 SAIESVLIENRVFPPPEGLVKTARISGMAGYEALCAEADKDFEGFWARLARENLQWTRPF 65 Query: 62 TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121 TK LD+SNAPFY+WF DGELNAS NCLDR++ K AI+FEADDG+VT+VTY+EL Sbjct: 66 TKTLDESNAPFYQWFADGELNASANCLDRHMGTPVESKTAIIFEADDGAVTKVTYKELLA 125 Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181 +V +FAN LKA G++KGDRV+IYMPM++EGVVAMQACAR+GATHSVVFGGFSAK++QER+ Sbjct: 126 RVAQFANALKAQGVKKGDRVLIYMPMTIEGVVAMQACARIGATHSVVFGGFSAKAVQERI 185 Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWT--EGR 239 +D GAVA+ITA+ Q+RGGK LPLKAI D+ +A+GGCE++++V+VY RT AW +GR Sbjct: 186 IDAGAVAVITANYQLRGGKELPLKAIVDEGIAMGGCESIKSVLVYERT--PTAWNRVDGR 243 Query: 240 DRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTF 299 D+ + AGQ C V AEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA +TM WTF Sbjct: 244 DKSFAEALAGQSTECVPVAVEAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAKLTMDWTF 303 Query: 300 DIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSI 359 D++PDD+FWCTADIGWVTGHTYIAYGPLAAG TQV+FEG+PTYPNAGRFW MI RHKVSI Sbjct: 304 DLRPDDVFWCTADIGWVTGHTYIAYGPLAAGGTQVMFEGIPTYPNAGRFWQMIERHKVSI 363 Query: 360 FYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPI 419 FYTAPTAIRSLIKAA++DEK+HPK +DLSSLR+LG+VGEPINPEAWMWYYKN+G ERCPI Sbjct: 364 FYTAPTAIRSLIKAADSDEKVHPKNWDLSSLRILGSVGEPINPEAWMWYYKNVGGERCPI 423 Query: 420 VDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRP 479 VDT+WQTE GGH+ITPLPGATPLVPGSCTLPLPGI AAIVDETG DVPNG+GG+LV+KRP Sbjct: 424 VDTWWQTENGGHLITPLPGATPLVPGSCTLPLPGIAAAIVDETGKDVPNGSGGMLVIKRP 483 Query: 480 WPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHR 539 WP+MIRTIW DPERF+KSYFPEE+GGK+YLAGDG++RD T YF + GRIDDVLNVSGHR Sbjct: 484 WPSMIRTIWNDPERFKKSYFPEEMGGKIYLAGDGAVRDAKTAYFRVTGRIDDVLNVSGHR 543 Query: 540 MGTMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNW 598 MGTMEIESALV+ + LVAEAAVVGRPDD+TGEAICAFVVLKR+RPTGEEA +IA ELRNW Sbjct: 544 MGTMEIESALVAKSDLVAEAAVVGRPDDLTGEAICAFVVLKRARPTGEEAKQIAAELRNW 603 Query: 599 VGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658 V KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGE ITQDTSTLENPAIL+QL Q Sbjct: 604 VAKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEAITQDTSTLENPAILDQLAQ 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: 1552 Number of extensions: 69 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: 665 Length adjustment: 38 Effective length of query: 622 Effective length of database: 627 Effective search space: 389994 Effective search space used: 389994 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