Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate Dsui_2069 Dsui_2069 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= BRENDA::Q99NB1 (682 letters) >FitnessBrowser__PS:Dsui_2069 Length = 529 Score = 164 bits (415), Expect = 1e-44 Identities = 157/539 (29%), Positives = 240/539 (44%), Gaps = 41/539 (7%) Query: 116 PETIALI-WE---RDEPGTEVRITYRELLETTCRLANTLKRHGVHRGDRVAIYMPVSPLA 171 P+ ALI WE D P TY +L R A+ L GV +GD VA ++ +P Sbjct: 19 PDKPALIAWEGGDHDTPAQRRVWTYAQLNAEVNRHAHALLALGVQKGDVVAAFLYNTPAF 78 Query: 172 VAAMLACARIGAIHTVVFAGFSAESLAGRINDAKCKAVITFNQGLRGGRVVELKKIVDEA 231 V ++LA AR+GA+ + +A+ LA + D + K ++ +G ++V++A Sbjct: 79 VFSLLAAARVGAVFNPINYRLAAQELAFILEDGQAKVLLFEKEGC---------EVVEKA 129 Query: 232 VKSCPTVQHVLVAHRTDTKVPMGSLDIPLEQEMAKEAPVCTPESMSSEDMLFMLYTSGST 291 + H + A D+ L+Q + + P + D ++YTSG+T Sbjct: 130 REHGVPTAHWIYA---DSDAAPAFATARLDQLVRHQPATLPPVIVEENDNCILMYTSGTT 186 Query: 292 GTPKGLVHTQAGYLLYAAMTHKLVFDYQPGDVFGCVADIGWITGHSYVVYGP-LCNGATT 350 G PKG++HT L + AM H+ DV VA + T + + P L GAT Sbjct: 187 GRPKGVLHTHRSKLAHNAMMHQ-AMTLSREDVGLAVAPLNH-TAELHTSFLPRLQLGATQ 244 Query: 351 VLFESTPVYPDAGRYWETVQRLKINQFYGAPTAVRLLLKYGDAWVKKYDRSSLRTLGSVG 410 VL DAG W + K+ F+ APT V LLL + D V D SSLR + G Sbjct: 245 VLLRRF----DAGEAWRLTEVEKVTHFFAAPTMVTLLLHHPD--VASRDLSSLRLVEYGG 298 Query: 411 EPI-NHEAWEWLHKVVGDGRCTLVDTWWQTETGGICIAPRPSED----GAEILPGMAMRP 465 + H EW K VG G LV + TE G P E G+ LP + Sbjct: 299 ASMAPHLIREW-DKKVGAG---LVQIYGTTEMGPCMSVLYPHEQLSHAGSAGLPSLN--- 351 Query: 466 FFGIVPVLMDEKGNVLEGGDVSGALCISQAWPGMARTIYGDHQRFVDAYFRAYP-GYYFT 524 ++ + G+ + D++ + + + G + +A RA G+Y T Sbjct: 352 -HDLLVARVKADGSPSDPADLAAPDEVGEILV-RGPCMMGGYLNRPEANARALAFGWYHT 409 Query: 525 GDGAHRTEGGYYQITGRMDDVINISGHRLGTAEIEDAMADHPAVPETAVIGYPHDIKGEA 584 GD + GY I R+D +IN + E+EDA+ +HP V E AV+G P D G+ Sbjct: 410 GDLGSLDKEGYLWIRDRIDHMINSGAENVYPREVEDALVEHPGVLEVAVVGEPDDTWGQV 469 Query: 585 AFAFIVLKDNISDENMVVNELKLSVATKIAKYAVPDQILVVKRLPKTRSGKVMRRLLRK 643 A +V K + ++ L ++A Y P + ++ LPKT SGK+ + LLR+ Sbjct: 470 VAAHVVAKPGATLTQEALDHFLLE-GDRLAHYKRPRRYHFIEALPKTTSGKIQKHLLRQ 527 Lambda K H 0.320 0.136 0.421 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: 861 Number of extensions: 44 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: 2 Length of query: 682 Length of database: 529 Length adjustment: 37 Effective length of query: 645 Effective length of database: 492 Effective search space: 317340 Effective search space used: 317340 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 (21.8 bits) S2: 53 (25.0 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