Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_028989221.1 G579_RS0104490 acetate--CoA ligase
Query= BRENDA::Q9Z3R3 (650 letters) >NCBI__GCF_000423825.1:WP_028989221.1 Length = 652 Score = 205 bits (521), Expect = 6e-57 Identities = 175/593 (29%), Positives = 272/593 (45%), Gaps = 34/593 (5%) Query: 71 LVDGDRMLDARFFPEARLNFAENLLRK-----TGSGDALIFRGEDKVSYRLTWDELRALV 125 ++D R R+F + LN A N L + T + ALI+ GED T+ +L V Sbjct: 65 VLDDSRAPFYRWFADGELNVAANCLDRHLSSPTRNKAALIWEGEDGEVRTFTYGQLHREV 124 Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185 SR L+ GI GDRVA MP +PE MLA A +GAI S F + + DR Sbjct: 125 SRFANVLKKLGITTGDRVAIYMPMVPEAAVAMLACARLGAIHSVVFGGFSAEALKDRIED 184 Query: 186 IAPKLFIVCDGYWYNGK----RQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGGV 241 KL I DG + G+ +Q D + S+ V++ G + ++G Sbjct: 185 TQAKLLITADGGFRAGRVVHLKQHADQALMRDGHSVDK-VVVLRRTGQEVDM---LDGRD 240 Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301 + + HPL++L++SG+TG PK IVHS+GG LL R+ Sbjct: 241 LWWHELMQDAEPQCPAVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFD 300 Query: 302 LRDGERLFYFTTCGWMMWNWLA--SGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVF 359 ++ + + GW+ + A LAVGAT+ L++G P PD + +VF Sbjct: 301 IKPEDVYWCTADIGWVTGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVF 360 Query: 360 GTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKP------DVQL 413 T+ + A+ K G +DLSSLRL+ + G P++PE + + Y I D Sbjct: 361 YTAPTAVRALMKLGEEWPGKYDLSSLRLLGTVGEPINPEAWMWYYRVIGKERCPVVDTWW 420 Query: 414 ASISGGTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEK--GELVCTRA 471 + +GG +++ PLKP G P G+ D+ ++EG PV+G + G LV R Sbjct: 421 QTETGG-HLIAPLPGVTPLKP---GSCTRPLPGIFPDIVDEEGDPVQGTEAGGYLVVKRP 476 Query: 472 FPSMPVMFWNDPDGAKYRAAYFDRFDN-VWCHGDFAEWTPHGGIVIHGRSDATLNPGGVR 530 +P M W + A+Y Y+ +F N + GD A G I GR D LN G R Sbjct: 477 WPGMLRTVWG--NDARYLETYWAKFQNRYYVAGDSAHRDADGYYWIMGRIDDVLNVSGHR 534 Query: 531 IGTAEIYNQVEQMDEVAEALCIGQDWE---DDVRVVLFVRLARGVELTEALTREIKNRIR 587 +GT EI + + VAEA +G+ E + + + +R + + + LT ++ + Sbjct: 535 LGTMEIESALVSHPAVAEAAVVGRPHEIKGEAITAFVILRQSHVQDDRDRLTEALRQHVS 594 Query: 588 SGASPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPV-KNKEALANPEAL 639 P P I ++P+T+SGKI+ +R + G + ++ L N E + Sbjct: 595 EAIGPIAKPDDIRFTDNLPKTRSGKIMRRLLRAIARGEEITQDTSTLENEETV 647 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: 1243 Number of extensions: 85 Number of successful extensions: 6 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: 650 Length of database: 652 Length adjustment: 38 Effective length of query: 612 Effective length of database: 614 Effective search space: 375768 Effective search space used: 375768 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 Apr 09 2024. 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