Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate BPHYT_RS31920 BPHYT_RS31920 acetate--CoA ligase
Query= curated2:Q8KBY0 (659 letters) >FitnessBrowser__BFirm:BPHYT_RS31920 Length = 650 Score = 324 bits (830), Expect = 9e-93 Identities = 212/633 (33%), Positives = 319/633 (50%), Gaps = 38/633 (6%) Query: 39 MEQYEKLYADAAADPDKYWGDLAEQFHWFKKWDSVLEWNAPYA------------KWFNG 86 + Y++LYA + A+P +YW H W + W APY+ +WF G Sbjct: 30 LRDYDELYAYSIANPGEYW-------HRLMVWLGI-RWQAPYSAYVDLSDGKPFPQWFPG 81 Query: 87 GTTNIAYNCLDVHVGSWRKNKAAIIWEGEEGNERILTYGELHRQVSKFANVLKIAGIKPG 146 G N + + R + A+I E E G TY EL V FA L + + PG Sbjct: 82 GKLNWVDSIFECEADKERLQRIALIAEDESGRVTQRTYAELREDVQSFAAGLMTSKLGPG 141 Query: 147 DKVAIYMGMVPELVIAVLACARVGAVHNVIFAGFAAHAITERVNDSRAKIVICADGTRRR 206 D V + M E V+ LA + +GA+ +F+GF A AI R+ AK ++ G RR Sbjct: 142 DCVGLLMESSVESVVTYLALSYIGAIAVPLFSGFGADAIVARLQGCDAKGLVATAGFMRR 201 Query: 207 GSTINLKNIVDEAIINTPSVKNVIVLKVTGEEIHMHDG-MDHWWHDLMGLA----VDECE 261 G + ++ ++ +I PS++ ++V + G + +H G +D W+D++ +D Sbjct: 202 GKPVLTRDAIESSIPALPSLEVLVVKPMRGSQGSVHAGALD--WYDVLAAGRAEPLDHAV 259 Query: 262 PAQVDSEHPLFLLYTSGSTGKPKGILHTTAGYMVHAASSFKYVFDIKDEDIYFCTADIGW 321 PA+ ++ P ++YTSG+TGKPKG +HT G+ + A F++ D + AD+GW Sbjct: 260 PAEANT--PCMIVYTSGTTGKPKGTVHTHGGFPLKIAHDAAVYFNLGAGDRWLWPADMGW 317 Query: 322 ITGHTYIIYGPLLNGATVFMYEGAPNYPQWDRFWDIINRHKITILYTAPTAIRAFIRAGN 381 + G I G L GAT+ Y+GAPN P W R +I R+ +T +PT IR + A Sbjct: 318 VAG-PITIAGAFLRGATLVCYDGAPNCPDWSRLPQLIRRYAVTHFGASPTLIRT-LSAHE 375 Query: 382 EWVTKHDLSSLRLLGTVGEPINPEAWMWYHKYVGQEKCPIVDTWWQTETGGIMISPMPGA 441 + DLSS+RL T GE I+ E++ WY + + CP+++ +E G ++ + Sbjct: 376 SSIAPDDLSSVRLAITAGEVIDSESFRWYGE---RFACPVINFTGGSEVSGGLLGNVV-V 431 Query: 442 TPTKPGTATRPLPGIMVDVVRKDGTPCNANEGGYLVVKRPWPSMLRTIYGDNERYEKTYW 501 P PG PGI VDV DG E G L V P+ M R+ + + ERY TYW Sbjct: 432 KPIVPGGFNAIAPGIRVDVRGADGKQVR-GEVGELAVLEPFVGMTRSFWKNPERYLDTYW 490 Query: 502 SEFPGMYFTGDGARKDDDGYIWIMGRVDDVVNVSGHRLGTSEVESALVSHEAVAEAAVVS 561 P ++ GD A + DD + GR DD + ++G R+G SE+E +V VAEAA V Sbjct: 491 RNVPDVWIHGDLAIQFDDHAFVLCGRSDDTLKIAGKRVGPSEIEDVIVEIAEVAEAAAVG 550 Query: 562 RPDEIKGNALVAFVTLKDGYEGDAKLRDSLGKHVAKEIGAIAKPDEIRWAKGLPKTRSGK 621 D +KG LV FV + D R+ + V++ +G P ++ LPKTRSGK Sbjct: 551 ISDPVKGQRLVVFV-VADKERCTVAFREQIVDMVSRRLGKPFAPSQVYVVGELPKTRSGK 609 Query: 622 IMRRLLRELATSNEIKGDVTTLEDLGVIENLRE 654 IMRRL++ A + GD +LE+ IE +RE Sbjct: 610 IMRRLIKR-AYEGQPLGDTASLENPWAIEMIRE 641 Lambda K H 0.318 0.135 0.424 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: 1083 Number of extensions: 63 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: 659 Length of database: 650 Length adjustment: 38 Effective length of query: 621 Effective length of database: 612 Effective search space: 380052 Effective search space used: 380052 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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