Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 408300 DVU0748 acetyl-CoA synthetase
Query= SwissProt::P31638 (660 letters) >MicrobesOnline__882:408300 Length = 648 Score = 591 bits (1523), Expect = e-173 Identities = 308/654 (47%), Positives = 420/654 (64%), Gaps = 14/654 (2%) Query: 2 SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61 + ++++++E RVF P + A + + +A ++A FW A EL W + + Sbjct: 6 ATLDALLREERVFRPLPRVVADAVVNPQDVARAR-EQAGTAPLAFWEEAAEEL-EWFRRW 63 Query: 62 TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121 VLD SNAPF +WF N +N LDR+++ N ++A+++E + G R TY +L+ Sbjct: 64 DGVLDDSNAPFMRWFPGALCNIVHNALDRHIETSNRHRLALIWEGEPGDSRRFTYFDLYR 123 Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181 +V R AN +++LG+ KGDRVVIYMP E V AM ACA++GA HS VFGGFSA+SL +R+ Sbjct: 124 EVNRLANAMRSLGVTKGDRVVIYMPPLPETVFAMLACAKIGAVHSTVFGGFSARSLCDRV 183 Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEA---VRNVIVYRRTGGKVAWTEG 238 D L+T D R G+ +PLK +ADDA+ EA + +V+V R + +G Sbjct: 184 EDARPTLLLTVDGFYRNGRVVPLKPVADDAVDALSPEARAGLHHVVVVHRAHLETPMRDG 243 Query: 239 RDRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWT 298 RD W D+ GQ E +SA PLFVLYTSG+TGKPKG+ HS GGY++ TM+W Sbjct: 244 RDIWYHDLVRGQSTEALTEVLSANDPLFVLYTSGTTGKPKGLVHSHGGYMVGVHRTMRWV 303 Query: 299 FDIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVS 358 FD++P D+FWCTA+ GW+TGH+Y YGPL AG T V++EG P YP AGR W M+ R V+ Sbjct: 304 FDVRPTDIFWCTAEPGWITGHSYGVYGPLMAGTTTVLYEGHPLYPEAGRLWSMVERWGVT 363 Query: 359 IFYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCP 418 I YT PT IR L++ ++P ++D+++LRLL TVGEPI+PE W+W+Y+ IG RCP Sbjct: 364 ILYTVPTVIRMLMRFG----PLYPARHDITTLRLLATVGEPISPETWVWFYRTIGRGRCP 419 Query: 419 IVDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKR 478 ++DT+WQTETG M++PLP + L PGS PLPG+ IVD G VP G GG+LVVK Sbjct: 420 VLDTWWQTETGMIMVSPLP-VSALKPGSVARPLPGVDVDIVDGEGAPVPPGRGGLLVVKN 478 Query: 479 PWPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGH 538 PWPAM ++GD E FR+ Y+ G Y GD + RD D GY I GR DDV+ ++GH Sbjct: 479 PWPAMACGVFGDDEAFRRLYWERFPG--WYCTGDVARRD-DDGYIWIQGRADDVILIAGH 535 Query: 539 RMGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNW 598 R+GT E+E+AL S+P VAE AV+G PD + GE AFVVL+ + E +AT L Sbjct: 536 RIGTAEMEAALASHPAVAECAVIGVPDRLKGEVGKAFVVLRDTEEAAAEEQALATSLVGH 595 Query: 599 VGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAI 652 V +E+GP+A +D+ F + LP+ RSGKIMRR+LRS G E T D STLE+ I Sbjct: 596 VRRELGPVAVIRDVVFREGLPRNRSGKIMRRILRSEEMGVE-TGDLSTLEDAYI 648 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: 1342 Number of extensions: 67 Number of successful extensions: 6 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: 648 Length adjustment: 38 Effective length of query: 622 Effective length of database: 610 Effective search space: 379420 Effective search space used: 379420 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 Aug 03 2021. The underlying query database was built on Aug 03 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