Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011373080.1 SUDEN_RS07585 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_000012965.1:WP_011373080.1 Length = 651 Score = 718 bits (1853), Expect = 0.0 Identities = 359/650 (55%), Positives = 459/650 (70%), Gaps = 12/650 (1%) Query: 13 VFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAPF 72 VF P + F+ A I +M YQ L + A DYEGFW +A+E L W +PFT V+++SN PF Sbjct: 5 VFKPNKEFSKSARIKNMCEYQDLQEYALEDYEGFWGSYAKEKLEWMQPFTNVMNESNFPF 64 Query: 73 YKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLK- 131 KWFE G+LN S C+DR+L++ +K AI+FE D G +TY EL+ V +FAN LK Sbjct: 65 VKWFEGGKLNVSVQCIDRHLKS-RKNKAAIIFEGDRGDKQIITYLELYYNVNKFANLLKN 123 Query: 132 ALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALIT 191 ++KGDRV+IYMPM E AM ACAR+GA HS+VFGGFSA++L++R++D GA +IT Sbjct: 124 EFDVKKGDRVIIYMPMIPEAAYAMLACARIGAIHSIVFGGFSAEALKDRVIDAGAKVVIT 183 Query: 192 ADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQP 251 AD R K LK + D+AL G V+ V+V R G V W GRD ++ Q Sbjct: 184 ADGAYRKDKPYMLKPVVDEALR--GETPVKKVLVVERNGEDVTWVAGRDYSYNELIKHQS 241 Query: 252 DTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTA 311 CE E + +E PLF+LYTSGSTGKPKGVQH++ GY+LWA MTM+W FD+K +D +WCTA Sbjct: 242 GKCEPEVMDSEDPLFLLYTSGSTGKPKGVQHNSAGYILWAQMTMEWVFDVKENDTYWCTA 301 Query: 312 DIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLI 371 D+GW+TGHTYI YGPLA GAT ++FEGVPTYP+AGR W M+ +KV+ FYTAPTAIR L Sbjct: 302 DVGWITGHTYIVYGPLAMGATTIMFEGVPTYPDAGRPWKMVEEYKVNQFYTAPTAIRVLH 361 Query: 372 KAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGH 431 K E + P +YDLSSL++LGTVGEPI+P AW WYY+ IG +C IVDT+WQTETGGH Sbjct: 362 KTGENE----PAKYDLSSLKVLGTVGEPIDPPAWKWYYEAIGGSKCAIVDTYWQTETGGH 417 Query: 432 MITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDP 491 +++PLPGATP+ P T PLPGIMA I+DE G+ G G++ V RPWPAMIR +WGD Sbjct: 418 IVSPLPGATPIKPACATFPLPGIMAEILDENGNRAEVGEKGLMCVTRPWPAMIRGVWGDE 477 Query: 492 ERFRKSYFPE--ELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESAL 549 ERF KSYF + + G +Y GDG+I D+D GY TI GR DDV+NVSGHRMGT E+E+A+ Sbjct: 478 ERFVKSYFGDVKKDGKPVYFTGDGAIYDED-GYITITGRTDDVINVSGHRMGTAEVEAAI 536 Query: 550 VSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKP 609 +P VAE AVVG+P ++ GE I A++VLK +E ++ + + KEIG IA Sbjct: 537 KKHPNVAEVAVVGKPHEIKGEGIFAYIVLKSDSGIADEVEEVKA-INKVIQKEIGNIALC 595 Query: 610 KDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659 D+ F LPKTRSGKIMRR+LRS+AKGEEITQD STLE+P+I+ + A Sbjct: 596 DDVVFVVGLPKTRSGKIMRRILRSIAKGEEITQDISTLEDPSIVATIASA 645 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: 1312 Number of extensions: 74 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: 651 Length adjustment: 38 Effective length of query: 622 Effective length of database: 613 Effective search space: 381286 Effective search space used: 381286 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 Sep 24 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