Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 8502070 DvMF_2783 acetate/CoA ligase (RefSeq)
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__Miya:8502070 Length = 651 Score = 585 bits (1507), Expect = e-171 Identities = 303/652 (46%), Positives = 423/652 (64%), Gaps = 17/652 (2%) Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63 I+++++E RVF P + A + + +A A D +G+W A EL W + + Sbjct: 8 IDALLREERVFRPLPQVVAGAVVNPQDVARARA-RAAADPDGYWEEAAEEL-EWFRRWDA 65 Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123 V D SNAPF++WF N +N LDR+++ G +++A+++E + G TY +L+ +V Sbjct: 66 VHDGSNAPFHRWFTGARCNIVHNALDRHIETGTKNRLALIWEGESGDTRSFTYYQLYREV 125 Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183 R AN L+ LG+ KGDRV+IYMP E V AM A A++GA HS VFGGFSA+SL++R+ D Sbjct: 126 NRLANALRGLGVGKGDRVIIYMPPLPETVFAMLAAAKIGAVHSTVFGGFSARSLRDRMED 185 Query: 184 VGAVALITADEQMRGGKALPLKAIADDALAL---GGCEAVRNVIVYRRTGGKVAWTEGRD 240 ++T D R G+ +PLK IAD+A+A VR+++V R + TEGRD Sbjct: 186 ARPAVIVTVDGFYRNGRVIPLKPIADEAVATLPPDLAAGVRHMVVVHRAHVETPMTEGRD 245 Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300 W D GQ E + + PLF+LYTSG+TGKPKG H+ GGY++ TM+W FD Sbjct: 246 IWYHDAVRGQHHEALTEIMDSTDPLFLLYTSGTTGKPKGHVHAHGGYMVGVHRTMRWVFD 305 Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360 +KP D+FWCTA+ GW+TGH+Y+ YGPL AG T V++EG P YP GR W M+ R ++I Sbjct: 306 VKPTDIFWCTAEPGWITGHSYVVYGPLMAGTTTVLYEGHPLYPEPGRVWSMVERLGITIL 365 Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420 YTAPT +R L++ H ++DL++LRLLGTVGEPI+PEAW+W+++++G RCP++ Sbjct: 366 YTAPTLVRMLMRHGAQ----HVARHDLTTLRLLGTVGEPISPEAWLWFHRHVGRGRCPVL 421 Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480 DT+WQTETG M++PLP + L PGS T PLPGI A +VDE G V G+GG+LV++RPW Sbjct: 422 DTWWQTETGMIMLSPLP-VSLLKPGSVTRPLPGIEADVVDEHGKPVGPGHGGLLVLQRPW 480 Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 PAM ++ D E +R+ Y+ G Y GD + RD+D GYF I GR DDVL ++GHR+ Sbjct: 481 PAMSCGVYNDDESYRRLYWERFPG--WYCTGDVARRDED-GYFWIQGRADDVLLIAGHRI 537 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRP---TGEEAVKIATELRN 597 GT E+E+AL S+ VAE AV+G PD + GE AFVVL P T A ++A EL Sbjct: 538 GTAEMEAALASHRSVAECAVIGVPDALRGEVAKAFVVLVDDHPPLGTMVNADELAAELVE 597 Query: 598 WVGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLEN 649 V +E+GP+A +++ F + LP+ RSGKIMRR+LRS G + T D STLE+ Sbjct: 598 HVRRELGPVAVIREVSFREGLPRNRSGKIMRRVLRSEELGRD-TGDLSTLED 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: 1349 Number of extensions: 74 Number of successful extensions: 8 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 17 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