Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011766145.1 AZO_RS12180 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_000061505.1:WP_011766145.1 Length = 654 Score = 1061 bits (2745), Expect = 0.0 Identities = 500/649 (77%), Positives = 571/649 (87%) Query: 9 QEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQS 68 Q+ R++NP E AA+ MEAY ALC EAE+DYEG+WAR+AREL+ W KPFT+VLD+S Sbjct: 5 QQVRIYNPSEEVVKNAAVSGMEAYWALCKEAEQDYEGYWARNARELIDWKKPFTQVLDES 64 Query: 69 NAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFAN 128 NAPF+KWF DG+LN SYNCLDRN++ G DKVA++FEAD G VTRVTY++L G+VC+FAN Sbjct: 65 NAPFFKWFADGQLNVSYNCLDRNVEKGLGDKVALIFEADSGEVTRVTYKDLLGRVCKFAN 124 Query: 129 GLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVA 188 L+A GI+KGDRVVIY+PMS+EGVVAMQACAR+GATHS+VFGGFSA++L++R+ D GAVA Sbjct: 125 ALRASGIKKGDRVVIYLPMSIEGVVAMQACARIGATHSIVFGGFSAQALRDRINDAGAVA 184 Query: 189 LITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSA 248 LIT+D Q RGGKALPLK IAD+AL+LGGCE ++NV V +RTG VA+ GRD W DV A Sbjct: 185 LITSDGQFRGGKALPLKPIADEALSLGGCETIKNVFVVKRTGADVAFVAGRDVWYHDVVA 244 Query: 249 GQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFW 308 Q D CE E V AEHPLF+LYTSGSTGKPKGVQHSTGGYLL A++TMK+TFDIKP D+FW Sbjct: 245 SQSDVCEPEWVDAEHPLFLLYTSGSTGKPKGVQHSTGGYLLHAILTMKYTFDIKPSDVFW 304 Query: 309 CTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIR 368 CTADIGWVTGHTYI YGPLA G+T++VFEGVPTYP+AGRFW MI HKV+IFYTAPTAIR Sbjct: 305 CTADIGWVTGHTYITYGPLACGSTEIVFEGVPTYPDAGRFWKMIQDHKVNIFYTAPTAIR 364 Query: 369 SLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTET 428 SLIKAA+ + +HPK YDLSSLR+LG+VGEPINP AW WYY+N+G RCPIVDTFWQTET Sbjct: 365 SLIKAADNNPTVHPKNYDLSSLRILGSVGEPINPAAWEWYYENVGGGRCPIVDTFWQTET 424 Query: 429 GGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIW 488 GGHMITPLPGATPLVPGSCTLP PGI AA+VDETG +VPNG GGILVVKRPWP+MIRTIW Sbjct: 425 GGHMITPLPGATPLVPGSCTLPFPGIQAAVVDETGTEVPNGQGGILVVKRPWPSMIRTIW 484 Query: 489 GDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESA 548 GDPERF+KSY+P++ GKLYLAGDG+IRDK+TGYFTI GRIDDVLNVSGHRMGTMEIESA Sbjct: 485 GDPERFKKSYYPDDFKGKLYLAGDGAIRDKETGYFTITGRIDDVLNVSGHRMGTMEIESA 544 Query: 549 LVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAK 608 LV++ VAEAAVVGRPDD+TGEAI AFVVLK +RPTGE A + EL+NWVG EIGPIAK Sbjct: 545 LVAHEKVAEAAVVGRPDDLTGEAIVAFVVLKGARPTGEAAAAVVKELQNWVGHEIGPIAK 604 Query: 609 PKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657 PKDIRFG+NLPKTRSGKIMRRLLR LAKGEEITQDTSTLENPAILEQLK Sbjct: 605 PKDIRFGENLPKTRSGKIMRRLLRQLAKGEEITQDTSTLENPAILEQLK 653 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: 1528 Number of extensions: 63 Number of successful extensions: 1 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: 654 Length adjustment: 38 Effective length of query: 622 Effective length of database: 616 Effective search space: 383152 Effective search space used: 383152 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 Jul 25 2024. The underlying query database was built on Jul 25 2024.
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