Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_090439307.1 BLS63_RS02720 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_900100495.1:WP_090439307.1 Length = 587 Score = 343 bits (881), Expect = 1e-98 Identities = 216/568 (38%), Positives = 300/568 (52%), Gaps = 28/568 (4%) Query: 72 DGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKK 131 D LNLA ++RH Q R + D ISY +L RFAN L LG++ Sbjct: 43 DDGLNLAYEAVERHAQGPHRRHVALRILDRNGGRCDISYAQLSSLTNRFANVLKGLGVEA 102 Query: 132 GDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVR 191 G+ + + E + +L + G V S +F F PE + R+ +++TS+ R Sbjct: 103 GERLFVLSGRGLELYLGVLGGLKNGCVVSPLFSAFGPEPIETRLRLGEGSVLLTSETLYR 162 Query: 192 AGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAE 251 R + + ALK HV+V GG +D G H L+ +A++ Sbjct: 163 --RKVAALRERLPALK--------HVLVYDENGGTVDAPPGTHSL-HRLLAEAAEDFSIA 211 Query: 252 EMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVT 311 A+ P + +TSG+TG PKG LH G L + +T KY D H DIYWC+AD GWVT Sbjct: 212 PTRADTPALLHFTSGTTGTPKGALHVHGAALTHL-VTGKYALDLHRDDIYWCSADPGWVT 270 Query: 312 GHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKA 371 G SY + PL G T ++ G + R +++K +V++ YTAPTAIR LM G + Sbjct: 271 GTSYGILAPLMLGVTCVVDSGEFD---AERWYAILEKQRVSVWYTAPTAIRLLMKAGPEL 327 Query: 372 IEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATE 431 + LR + SVGEP+NPEA W + +G P+ D WWQTETGG MI P A Sbjct: 328 AHRHNFPQLRFIASVGEPLNPEAVWWGKEVLG---LPIHDNWWQTETGGIMIANTP-AML 383 Query: 432 LKAGSATRPFFGVQPALV---DNEGNPLEGATE-GSLVITDSWPGQARTLFGDHERFEQT 487 +K GS +P GV+ A+V D+ G L G + G L + WP R G ER+ + Sbjct: 384 IKPGSMGKPLPGVEAAIVQRRDDGGLQLLGDEQLGELALKQPWPALFRGYLGQEERYRRC 443 Query: 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAV 547 + + Y SGD ARRD DGYYW GR DDV+ +GH +G E+ES L+ HP +AEAAV Sbjct: 444 FVGDW---YLSGDLARRDADGYYWFVGRSDDVIKSAGHLIGPFEVESVLMEHPAVAEAAV 500 Query: 548 VGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRS 607 +G+P + G+ + A+V+L G E S L+ E+ RK +G P L + SLP+TRS Sbjct: 501 IGMPDELLGETVKAFVSLKSGIEASEALHDELLGHARKRLGAAVAPKALAFLPSLPRTRS 560 Query: 608 GKIMRRILRKIAAGDTSNLGDTSTLADP 635 GK+MRR+L+ G GDTSTL +P Sbjct: 561 GKLMRRLLKARELGLPE--GDTSTLENP 586 Lambda K H 0.317 0.135 0.421 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: 1077 Number of extensions: 51 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: 652 Length of database: 587 Length adjustment: 37 Effective length of query: 615 Effective length of database: 550 Effective search space: 338250 Effective search space used: 338250 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: 53 (25.0 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