Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_050655293.1 C1M55_RS02775 acetate--CoA ligase
Query= BRENDA::Q9Z3R3 (650 letters) >NCBI__GCF_002893965.1:WP_050655293.1 Length = 643 Score = 223 bits (567), Expect = 3e-62 Identities = 187/628 (29%), Positives = 292/628 (46%), Gaps = 37/628 (5%) Query: 36 ADYDAFHDWSVSERGAFWTAVWEHCKVIGESGEKALVDGDRMLDARFFPEARLNFAENLL 95 AD D W+ W W ++D A++F +LN A N + Sbjct: 33 ADTDRLAFWANQAERLHWHEKWTD-----------VLDWTDAPVAKWFVGGKLNVAYNCV 81 Query: 96 RK---TGSGD--ALIFRGEDKVSYRLTWDELRALVSRLQQALRAQGIGAGDRVAAMMPNM 150 + G+GD A+ F GE S LT+++L A VSR G+ AGDRVA MP + Sbjct: 82 DRHVLAGNGDRIAIHFEGEPGDSRDLTYNDLLAEVSRAANTFTDLGLVAGDRVAIYMPMI 141 Query: 151 PETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQIAPKLFIVCDGYWYNGKRQDVDSKV 210 PE I MLA A +G S F + R KL + DG W G + + V Sbjct: 142 PEAIVTMLACARLGLTHSVVFAGFSATALRSRIDDAQAKLVVTVDGQWRRGAAAPIKTAV 201 Query: 211 -RAVAKSLGAPTVIVPYAGDSAALAPTVEGGVTLADFIAGFQAGPLVFERLPFG--HPLY 267 +VA + V+V + + G L QA P E F HPL+ Sbjct: 202 DESVAGAESVQNVLVV---NRTGIDVDWTDGRDLWWHETVAQASP-EHEAQAFDAEHPLF 257 Query: 268 ILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLRDGERLFYFTT-CGWMMWN-WLASG 325 IL++SGTTG PK I+H++GG L Q H + G+ +++ T GW+ + ++ G Sbjct: 258 ILYTSGTTGKPKGIIHTSGGYLTQASYTHHNVFDHKAGQDVYWCTADIGWVTGHSYIVYG 317 Query: 326 -LAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSAKYIDAVRKGGFTPARTHDLSS 384 L+ G T +Y+G+P P+ + FD +++ T+ + K G HDLSS Sbjct: 318 PLSNGVTQVVYEGTPNSPNEHRHFDIIEKYGVSIYYTAPTLVRTFMKWGREIPDAHDLSS 377 Query: 385 LRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDIVSCFVLGNPLKPVWR---GEIQ 441 +RL+ S G P++PE + + E I + + + + ++ +PL + G Sbjct: 378 IRLLGSVGEPINPEAWRWFREVIGGN-KAPIVDTWWQTETGAIMISPLPGITATKPGSAM 436 Query: 442 GPGLGLAVDVWNDEGKPVR-GEKGELVCTRAFPSMPVMFWNDPDGAKYRAAYFDRF--DN 498 P G++ + +D+ KP+ G G LV +P+M W D D +YR Y+ R+ + Sbjct: 437 APLPGISAKIVDDDAKPLGPGGNGYLVLDEPWPAMLRGIWGDMD--RYRDTYWSRYAEEG 494 Query: 499 VWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQMDEVAEALCIGQ-DWE 557 + GD A++ G + + GR D +N G RI T+E+ + + VAEA +G D Sbjct: 495 WYFAGDGAKYDDDGALWVLGRVDDVMNVSGHRISTSEVESALVNHHGVAEAAVVGAADET 554 Query: 558 DDVRVVLFVRLARGVELT-EALTREIKNRIRSGASPRHVPAKIIAVADIPRTKSGKIVEL 616 +V FV L GVE T + L E+K ++ + SP P +I V ++P+T+SGKI+ Sbjct: 555 TGQGIVAFVILREGVENTGDVLIAELKAQVSTDISPIAKPRQITIVPELPKTRSGKIMRR 614 Query: 617 AVRDVVHGRPVKNKEALANPEALDLFAG 644 +RDV GR + + L +P+ D G Sbjct: 615 LLRDVAEGRDLGDTSTLVDPKVFDAIRG 642 Lambda K H 0.322 0.139 0.441 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: 1187 Number of extensions: 73 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 650 Length of database: 643 Length adjustment: 38 Effective length of query: 612 Effective length of database: 605 Effective search space: 370260 Effective search space used: 370260 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 (21.9 bits) S2: 54 (25.4 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