Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate SMc00774 SMc00774 acetoacetyl-CoA synthetase
Query= SwissProt::A0R5G1 (940 letters) >FitnessBrowser__Smeli:SMc00774 Length = 650 Score = 185 bits (469), Expect = 9e-51 Identities = 177/601 (29%), Positives = 270/601 (44%), Gaps = 61/601 (10%) Query: 355 AKWFVGGKINVAYNCVDRHVEAGNGDRVAIHWEGEPVGDARSITYAELKDEVCKAANALT 414 A++F ++N A N + + G+GD A+ + GE R +T+ EL+ V + AL Sbjct: 80 ARFFPEARLNFAENLLRK---TGSGD--ALIFRGEDKVSYR-LTWDELRALVSRLQQALR 133 Query: 415 DLGLVAGDRVAIYMPMIPEAIVAMLACARLGVMHSVVFAGFSASALRARIEDAEAKLVIT 474 G+ AGDRVA MP +PE I MLA A +G + S F + R KL I Sbjct: 134 AQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQIAPKLFIV 193 Query: 475 SDGQYRRGKAASLKEAVDEAVADQPSVKNVLVVRRTGIDVKWTDGRDLWWDETVEQAST- 533 DG + GK + V AVA V+V G TVE T Sbjct: 194 CDGYWYNGKRQDVDSKV-RAVAKSLGAPTVIVPYA---------GDSAALAPTVEGGVTL 243 Query: 534 -------EHIPAAFDS---EQPLFLLYTSGTTGKPKGIVHTSGGYLTQSSYTHWNVFDVK 583 + P F+ PL++L++SGTTG PK IVH++GG L Q H ++ Sbjct: 244 ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLR 303 Query: 584 PESDVYWCTADIGWVTGHTYIVYGPLSNGVTQVVYEGTPTSPTEHRHFEVIEKYGVTIYY 643 +++ T GW+ + ++ G L+ G T +Y+G+P P + F+ ++ Sbjct: 304 DGERLFYFTT-CGWMMWN-WLASG-LAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360 Query: 644 TAPTLIRTFMKLGHQIPASHDLSSLRLLGSVGEPINPEAWRWYREHIG--------GGKT 695 T+ I K G +HDLSSLRL+ S G P++PE + + E I G T Sbjct: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420 Query: 696 PIVDTWWQTETGAIMISPLPGVTAAKPGSAMTPLPGISAKIVDDEGNQLVPGADEAEHVT 755 IV + ++ +PL V G P G++ + +DEG + Sbjct: 421 DIVSCF-------VLGNPLKPVWR---GEIQGPGLGLAVDVWNDEGKPV-------RGEK 463 Query: 756 GYLVLDQPWPAMLRGIWGDPQ--RFKDTYWSRFAEQGWYFAGDGARYDSDGHIWVLGRID 813 G LV + +P+M W DP +++ Y+ RF + W GD A + G I + GR D Sbjct: 464 GELVCTRAFPSMPVMFWNDPDGAKYRAAYFDRF-DNVWCH-GDFAEWTPHGGIVIHGRSD 521 Query: 814 DVMNVSGHRISTAEVESALVGHAGVAEAAVVGASDDTTGQAICAFVILKASAHGGPENMI 873 +N G RI TAE+ + + VAEA +G D + FV L A E + Sbjct: 522 ATLNPGGVRIGTAEIYNQVEQMDEVAEALCIG-QDWEDDVRVVLFVRL-ARGVELTEALT 579 Query: 874 EELRAEVAREISPIAKPREIHIVPELPKTRSGKIMRRLLRDVAEGRELGDTSTLVDPSVF 933 E++ + SP P +I V ++P+T+SGKI+ +RDV GR + + L +P Sbjct: 580 REIKNRIRSGASPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEAL 639 Query: 934 E 934 + Sbjct: 640 D 640 Lambda K H 0.315 0.129 0.395 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: 1468 Number of extensions: 61 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 940 Length of database: 650 Length adjustment: 41 Effective length of query: 899 Effective length of database: 609 Effective search space: 547491 Effective search space used: 547491 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 (21.6 bits) S2: 55 (25.8 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