Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_006748465.1 THITH_RS12445 acetate--CoA ligase
Query= BRENDA::Q9Z3R3 (650 letters) >NCBI__GCF_000227685.2:WP_006748465.1 Length = 652 Score = 201 bits (510), Expect = 1e-55 Identities = 163/575 (28%), Positives = 264/575 (45%), Gaps = 22/575 (3%) Query: 82 FFPEARLNFAENLLRK----TGSGDALIFRGEDKVSYRLTWDELRALVSRLQQALRAQGI 137 +F + R+N + N + + G A+IF GE+ + T+ +L V +L LRA G+ Sbjct: 75 WFTDGRMNVSYNCIDRHLDTRGDKPAIIFEGENGDTRTYTYRDLYHEVGKLANGLRASGV 134 Query: 138 GAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQIAPKLFIVCDGY 197 GDRV MP + E + M A A +GA+ S F + DR ++ I DG Sbjct: 135 RKGDRVVIYMPMIAEAVIAMQACARIGAVHSVVFGGFSADALRDRIDNSGAEVMITADGG 194 Query: 198 WYNGK---RQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGGVTLADFIAGFQAGP 254 G+ + K + ++ AG+ + T V D +A Q Sbjct: 195 TRGGRVVSLKKTADKALDICSGTVRKVIVCKRAGNEVNM--TEGRDVWWQDLVAD-QPVD 251 Query: 255 LVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLRDGERLFYFTTC 314 E + HPL++L++SG+TG PK I H++ G LL + + + L D + + Sbjct: 252 CEPEWVESEHPLFLLYTSGSTGKPKGIQHASAGYLLNTIITNEWVFDLHDEDIFWCTADV 311 Query: 315 GWMM-WNWLASG-LAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSAKYIDAVRKG 372 GW+ +++A G LAVGAT +Y+G P PDG + A VF T+ I A+ K Sbjct: 312 GWITGHSYVAYGPLAVGATQVVYEGVPTVPDGGRWWQMCQAHGVTVFYTAPTAIRALMKL 371 Query: 373 GFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPD-VQLASISGGTDIVSCFVLGNP 431 G +DLS LRL+ + G P++PE + + Y I + + T+ + + P Sbjct: 372 GDEIPAEYDLSKLRLLGTVGEPINPEAWMWYYRTIGGERCPIVDTWWQTETGAHMIAPLP 431 Query: 432 -LKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGE-LVCTRAFPSMPVMFWNDPDGAKYR 489 + + G P G+ DV N+EG+ + ++G LV + +PSM W D +Y+ Sbjct: 432 SVTTLTPGSCTRPLPGIVADVVNEEGESLGPDQGGFLVIKKPWPSMLRTVWQDDH--RYK 489 Query: 490 AAYFDRFD-NVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQMDEVAE 548 + Y+ +FD + GD A P G I GR D LN G R+GT EI + + + VAE Sbjct: 490 STYWPKFDGKYYLAGDSARRDPDGNFWIMGRIDDVLNVSGHRLGTMEIESALVAHEAVAE 549 Query: 549 ALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGAS----PRHVPAKIIAVAD 604 A +G+ + ++ + +G T A E+ +R S P P I Sbjct: 550 AAVVGRPHDVKGEAIVAFVILKGERPTGAAAEEMVKALREWVSEHIGPIAKPDDIRFADG 609 Query: 605 IPRTKSGKIVELAVRDVVHGRPVKNKEALANPEAL 639 +P+T+SGKI+ +R + G + + + EA+ Sbjct: 610 LPKTRSGKIMRRLLRSIAKGEEITSDTSTLENEAV 644 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: 1224 Number of extensions: 78 Number of successful extensions: 5 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: 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 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