Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_028989221.1 G579_RS0104490 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_000423825.1:WP_028989221.1 Length = 652 Score = 809 bits (2089), Expect = 0.0 Identities = 409/654 (62%), Positives = 488/654 (74%), Gaps = 10/654 (1%) Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63 +ES++ E RVF E FA QA + S E Y ALC AE D GFW AR+ L W KPFT+ Sbjct: 6 LESILTEARVFPVHEDFARQANLNS-EQYAALCRRAEEDPSGFWGDLARQELAWDKPFTQ 64 Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123 VLD S APFY+WF DGELN + NCLDR+L + +K A+++E +DG V TY +LH +V Sbjct: 65 VLDDSRAPFYRWFADGELNVAANCLDRHLSSPTRNKAALIWEGEDGEVRTFTYGQLHREV 124 Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183 RFAN LK LGI GDRV IYMPM E VAM ACARLGA HSVVFGGFSA++L++R+ D Sbjct: 125 SRFANVLKKLGITTGDRVAIYMPMVPEAAVAMLACARLGAIHSVVFGGFSAEALKDRIED 184 Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243 A LITAD R G+ + LK AD AL G +V V+V RRTG +V +GRD W Sbjct: 185 TQAKLLITADGGFRAGRVVHLKQHADQALMRDG-HSVDKVVVLRRTGQEVDMLDGRDLWW 243 Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303 ++ C A V+AEHPLFVLYTSGSTGKPKG+ HS+GGYLLW+ +TM+W FDIKP Sbjct: 244 HELMQDAEPQCPAVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFDIKP 303 Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363 +D++WCTADIGWVTGHTY YGPLA GAT ++FEGVPTYP+AGRFW MI RH VS+FYTA Sbjct: 304 EDVYWCTADIGWVTGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVFYTA 363 Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423 PTA+R+L+K E P +YDLSSLRLLGTVGEPINPEAWMWYY+ IG ERCP+VDT+ Sbjct: 364 PTAVRALMKLGEE----WPGKYDLSSLRLLGTVGEPINPEAWMWYYRVIGKERCPVVDTW 419 Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGN-GGILVVKRPWPA 482 WQTETGGH+I PLPG TPL PGSCT PLPGI IVDE G V GG LVVKRPWP Sbjct: 420 WQTETGGHLIAPLPGVTPLKPGSCTRPLPGIFPDIVDEEGDPVQGTEAGGYLVVKRPWPG 479 Query: 483 MIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGT 542 M+RT+WG+ R+ ++Y+ + + Y+AGD + RD D GY+ IMGRIDDVLNVSGHR+GT Sbjct: 480 MLRTVWGNDARYLETYW-AKFQNRYYVAGDSAHRDAD-GYYWIMGRIDDVLNVSGHRLGT 537 Query: 543 MEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKE 602 MEIESALVS+P VAEAAVVGRP ++ GEAI AFV+L++S ++ ++ LR V + Sbjct: 538 MEIESALVSHPAVAEAAVVGRPHEIKGEAITAFVILRQSH-VQDDRDRLTEALRQHVSEA 596 Query: 603 IGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656 IGPIAKP DIRF DNLPKTRSGKIMRRLLR++A+GEEITQDTSTLEN + QL Sbjct: 597 IGPIAKPDDIRFTDNLPKTRSGKIMRRLLRAIARGEEITQDTSTLENEETVRQL 650 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: 1406 Number of extensions: 78 Number of successful extensions: 9 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: 652 Length adjustment: 38 Effective length of query: 622 Effective length of database: 614 Effective search space: 381908 Effective search space used: 381908 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