Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_033100144.1 JG50_RS0105805 AMP-binding protein
Query= BRENDA::Q9Z3R3 (650 letters) >NCBI__GCF_000763315.1:WP_033100144.1 Length = 646 Score = 256 bits (655), Expect = 2e-72 Identities = 199/659 (30%), Positives = 315/659 (47%), Gaps = 46/659 (6%) Query: 5 RPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIG 64 +P+W P +E +E++ + F+ G F DYD F++ S+ FW +V+ Sbjct: 3 KPVWFPKQEQMEQTRLYRFMKRLG------FRDYDRFYEQSIKNIAWFWD------EVVN 50 Query: 65 ESGEKALVDGDRMLD-------ARFFPEARLNFAENLLRKTGSGDA------LIFRGEDK 111 + G + ++ ++LD R+F + ++N ++N L + A LI+ G+D Sbjct: 51 DLGLRWMMPYRQVLDMSDGIAWTRWFVDGKINISDNCLDRFVEEPAARHRLALIWEGDDG 110 Query: 112 VSYRLTWDELRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCS 171 + + T+ +L V+RL L+ G+ AGD VA MP + E + MLA A +GAI++ C Sbjct: 111 TTKKYTYRDLWLEVNRLACGLKKLGVAAGDCVAIYMPMIAENVIAMLAVARIGAIFTPCF 170 Query: 172 PDFGEQGVLDRFGQIAPKLFIVCDGYWYNGK----RQDVDSKVRAVAKSLGAP-TVIVPY 226 +G + V R K I DGY GK +++ D RA S V+V Sbjct: 171 SGYGAEAVATRIQGCQAKWLITADGYLRRGKVVAMKEEAD---RAADLSPSVEKVVVVSR 227 Query: 227 AGDSAALAPTVEGGVTLADFIAGFQA-GPLVFERLPFGHPLYILFSSGTTGVPKCIVHSA 285 G P + V A + P V + P I+++SGTTG PK VH Sbjct: 228 LGRDCPWNP--DRDVKWDQLTAEMKTLSPAVTDA---NDPFMIIYTSGTTGKPKGTVHVH 282 Query: 286 GGTLLQHLKEHRFHCGLRDGERLFYFTTCGWMMWNWLASG-LAVGATLCLYDGSPFCPDG 344 G L+ + + + G+ LF+ T GWMM W+ G L +G+T+ +++G+P P Sbjct: 283 SGFPLKAAFDAGYAFDVGPGDILFWVTDMGWMMGPWMVFGTLLLGSTMLVFEGTPDYPIP 342 Query: 345 NVLFDYAAAERFAVFGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVY 404 L++ G S I A+ K G + DLSSLR+ STG P +PE + +++ Sbjct: 343 GRLWELTEKHGVTHLGISPTLIRALMKHGTSWFSQRDLSSLRVFGSTGEPWNPEPWHWLF 402 Query: 405 EGIKPD-VQLASISGGTDIVSCFVLGNPL-KPVWRGEIQGPGLGLAVDVWNDEGKPVRGE 462 E + V + + SGGT+I S +LGN KP+ GP G+ +V++D+GK VRGE Sbjct: 403 EQVGGKRVPIFNYSGGTEI-SGGILGNHFFKPIVPCGFAGPLPGMDAEVFDDQGKTVRGE 461 Query: 463 KGELVCTRAFPSMPVMFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDA 522 GELV + + M FW D +Y Y+ R+ W HGD+ G I GRSD Sbjct: 462 VGELVLRQPWVGMTSGFWQ--DARRYEDTYWSRWPKTWLHGDWVIVDEGGQWFITGRSDD 519 Query: 523 TLNPGGVRIGTAEIYNQVEQMDEVAEALCIG-QDWEDDVRVVLFVRLARGVELTEALTRE 581 TL G R+G AE+ + + V EA IG D + V FV + E ++LT E Sbjct: 520 TLKIAGKRLGPAEMESVLVDHPSVIEAATIGVPDADKGESAVCFVVVRGDGEEVQSLTEE 579 Query: 582 IKNRIRSGASPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALD 640 + + P ++ V ++P+T++GKI+ +R G + +L N A++ Sbjct: 580 LVRFVGERMGKALKPKRVHIVDELPKTRNGKILRRVIRAAYLGENAGDLSSLENAHAVE 638 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: 1267 Number of extensions: 77 Number of successful extensions: 7 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: 646 Length adjustment: 38 Effective length of query: 612 Effective length of database: 608 Effective search space: 372096 Effective search space used: 372096 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