Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_109940435.1 DLD82_RS07210 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_003173335.1:WP_109940435.1 Length = 630 Score = 546 bits (1408), Expect = e-160 Identities = 293/649 (45%), Positives = 416/649 (64%), Gaps = 21/649 (3%) Query: 1 MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60 M A E + + +V+ P + + A I Y L E E+D + FW R A +LL W K Sbjct: 1 MPAEEVLKPDQKVYYPDPSYQNSALIRD---YDELYREFEKDPDAFWRRIASDLL-WFKQ 56 Query: 61 FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120 + V + P WF + ELN +YNCL+R++ N +KVAI + ++G +TY +L+ Sbjct: 57 WDTVRTWDH-PHASWFTNAELNITYNCLERHVNNDRRNKVAIFWAGENGKERILTYYQLY 115 Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180 V R N LK+LG+RKGDRV IY+P E VV+M ACAR+GA H+VVF G+ AK+L ER Sbjct: 116 KDVMRMGNALKSLGVRKGDRVCIYLPGIPELVVSMLACARIGAVHTVVFAGYGAKALNER 175 Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240 + GA +ITAD +R G ++PLK I ++AL V VI+ R KV + + Sbjct: 176 ITGAGAKIVITADASVRRGGSIPLKPIVEEALI--HAPTVEKVIILRTQEPKVGLLDDFE 233 Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300 E++ + CE E V++E PLF+LYTSG+TG PKG+ H+ GGY++ A T K+ Sbjct: 234 LDYEELISQADRNCEPEHVNSEDPLFILYTSGTTGAPKGIVHTAGGYMVGAYYTTKYVLT 293 Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360 ++ +D++WCTAD GW+TGHTY YGPL G T + E P YP+AG +W +I + V+IF Sbjct: 294 LRENDVYWCTADPGWITGHTYGIYGPLLVGGTIFLTEYTPDYPDAGIWWKLIEEYGVTIF 353 Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420 YTAPTAIR ++ E ++YDLSSLRLLG+VGEP+NPEA+ W+YK+IG + CPI+ Sbjct: 354 YTAPTAIRMFMRMGEE----WSEKYDLSSLRLLGSVGEPLNPEAFEWFYKHIGKKNCPIL 409 Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480 DT+WQTETG HMIT + G P+ PG P+PG++A +V+E G VP G G L +K PW Sbjct: 410 DTWWQTETGMHMITTMVG-LPMKPGFAGKPIPGVVATVVNEEGDPVPPGTNGFLAIKEPW 468 Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 P+M++T++ + ER+R+ + + G Y + D ++ D+D GY ++GR DD++ V+GH + Sbjct: 469 PSMMKTVYQNDERYRQYWNFGKYG--YYSSNDIAMMDED-GYIMLLGRSDDIIIVAGHNV 525 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRS-RPTGEEAVKIATELRNWV 599 GT EIESALVS+ VAEAA +G+PD + G I AFV+L+ PT K+ +L+ V Sbjct: 526 GTAEIESALVSHSAVAEAAAIGKPDPLKGNIIKAFVILRNGVSPT----PKLIHDLKYHV 581 Query: 600 GKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLE 648 +GPI+ P ++ F DNLPKTRSGKIMRR+L++ G + D STL+ Sbjct: 582 RIMLGPISVPAELDFVDNLPKTRSGKIMRRVLKAQEMGID-PGDVSTLD 629 Lambda K H 0.319 0.136 0.422 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: 1240 Number of extensions: 70 Number of successful extensions: 7 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: 660 Length of database: 630 Length adjustment: 38 Effective length of query: 622 Effective length of database: 592 Effective search space: 368224 Effective search space used: 368224 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 (21.7 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