Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate AO353_19945 AO353_19945 acetyl-CoA synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19945 Length = 588 Score = 337 bits (863), Expect = 1e-96 Identities = 215/593 (36%), Positives = 308/593 (51%), Gaps = 28/593 (4%) Query: 47 DWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSK 106 +W+ Q + S+ ++ G LNLA +DRH + R + D Sbjct: 19 NWLDSVQAREGFSWQGEASALAGLPGGGLNLAYEAVDRHAEGKHRRHTALRILDRNGGRC 78 Query: 107 HISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGF 166 ISY L RFAN L LG+ G+ + + E + +L ++G V S +F F Sbjct: 79 DISYARLSLLSNRFANVLKTLGVVPGERLFVLCGRGLELYLGVLGGLKLGCVVSPLFCAF 138 Query: 167 SPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGK 226 PE + R+ +++TS+ L ++ A++ + +++HV++ GG Sbjct: 139 GPEPIETRLRLGEGSVLLTSET---------LYRHKVAAIRE-RLPALKHVLLYDEEGGN 188 Query: 227 IDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAA 286 EG L H L+ A+D + A+ P + +TSG+TG PKGVLH G L + Sbjct: 189 TTPVEGT-LSLHRLLANATDHFEIAHTTADSPALLHFTSGTTGTPKGVLHVHGAVLTHR- 246 Query: 287 LTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVV 346 +T KY D HP DIYWC+AD GWVTG SY + PL G T+++ EG R + + Sbjct: 247 VTGKYALDLHPDDIYWCSADPGWVTGTSYGIIAPLLLGVTSVV-EGREF--DAERWYRTL 303 Query: 347 DKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEK 406 +K QV + YTAPTAIR LM G + LR + SVGEP+NPEA W + +G Sbjct: 304 EKQQVTVWYTAPTAIRLLMKAGAELAHSHRFPCLRFIASVGEPLNPEAVWWGQEVLG--- 360 Query: 407 CPVVDTWWQTETGGFMITPLPGATELKAGSATRPFFGVQPALV----DNEGNPLEGATEG 462 P+ D WWQTETGG MI T +K GS +P GV+ A+V E + L G Sbjct: 361 LPIHDNWWQTETGGIMIANTVAMT-IKPGSMGKPLPGVEAAVVVRGAAGELDYLGDNEVG 419 Query: 463 SLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNV 522 L + WP RT G ER+ Q + + + Y SGD RRD DGYYW GR DDV+ Sbjct: 420 ELALKQPWPAMFRTYLGQEERYRQCFVAGW---YLSGDLVRRDADGYYWFIGRSDDVIKS 476 Query: 523 SGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNW 582 +GH +G E+ES+L+ HP +AEAAV+G P + G+ + +V+L G S L+ E+ Sbjct: 477 AGHLIGPFEVESSLMEHPAVAEAAVIGKPDPLLGETVKVFVSLKSGFTASQALHDELLGH 536 Query: 583 VRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADP 635 RK +G + P L + ++LP TRSGK+MRR+L+ G GDTS+L +P Sbjct: 537 GRKRLGAVVAPKELEFVEALPHTRSGKLMRRLLKARELGLPE--GDTSSLENP 587 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: 1113 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: 652 Length of database: 588 Length adjustment: 37 Effective length of query: 615 Effective length of database: 551 Effective search space: 338865 Effective search space used: 338865 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 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