Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_011766904.1 AZO_RS15950 propionate--CoA ligase
Query= curated2:Q9RRL7 (649 letters) >NCBI__GCF_000061505.1:WP_011766904.1 Length = 630 Score = 498 bits (1281), Expect = e-145 Identities = 269/635 (42%), Positives = 400/635 (62%), Gaps = 26/635 (4%) Query: 33 AEYERRYRQSLDQPDDFWSEVAHDLHWMKDWDRVLDWQEP-HAQWFVGGQTNIAYNALDR 91 + Y+ +R+S+DQ D+FW+E A + W K +++ D+ +P +WF GG+TN+ YNA+DR Sbjct: 2 SNYKEFHRRSIDQRDEFWAEQAQLVDWHKPAEQICDFSKPPFVKWFKGGETNLCYNAVDR 61 Query: 92 NVQRGLGDKRAIIWEGEDGEVRTYTYAELLREVCKAANALEELGVVAGDRVTLYMPLIPE 151 + + D+ + E E + Y++AEL REV + A ++LGV GDRV +YMP+I E Sbjct: 62 HAAKRPDDRALVYISTETNEEKVYSFAELQREVERMAAIYQDLGVKRGDRVLIYMPMIAE 121 Query: 152 AAIAMLACARIGAVHSIVFGGFSVSALADRINNAQSKLLITADAGYRRGKPVTLKINADE 211 AA AMLACARIGA+HS+VFGGF+ +LA RI++A+ L++++DAG R GKPV K DE Sbjct: 122 AAFAMLACARIGAIHSVVFGGFAAGSLATRIDDAKPVLMVSSDAGMRNGKPVPYKHLVDE 181 Query: 212 AAKLAPC-LEHVLVVKRA---GIPLEWWTEGRDLWWHDVVDRQSD-QHEATALDSEHPLF 266 A KLA VL+V R G P E RD+ + ++ + D + T L+S P + Sbjct: 182 ACKLAEFPPAKVLIVDRGLDKGFPK---VESRDVDYAELRAKHIDAKVPVTWLESSEPSY 238 Query: 267 ILYTSGSTGAPKGVQHTTGGYMVGTYLTTQTVFDLRDDDIYWCTADIGWITGHSYSVYGP 326 ILYTSG+TG PKGVQ TGGY V + + +F + + T+DIGW+ GHSY +YGP Sbjct: 239 ILYTSGTTGKPKGVQRDTGGYTVALAASMKHIFTGGSGETMFSTSDIGWVVGHSYIIYGP 298 Query: 327 LLNGATVVMYEGAPNQPDWGRFWDIVQKHRVTILYTAPTAIRSFMQHGDEIPGRYDLASL 386 L+ G +MYEG P +PD G +W IV+K++V+++++APTA+R + +YDL+SL Sbjct: 299 LIAGMATIMYEGTPLRPDAGIWWQIVEKYKVSVMFSAPTAVRVLKKQDPAFLKKYDLSSL 358 Query: 387 RLLGSVGEPINPEAWMWYYRVIGGERCPVVDTWWQTETGSIMLTTLPGAFPS--KPGSAG 444 + L GEP++ + W +G PV+D +WQTETG ML + G S K GS Sbjct: 359 KHLFLAGEPLDETSHKWIMSELG---IPVIDNYWQTETGWPMLAIVRGVEDSKIKLGSPA 415 Query: 445 LPMFGVEPALMTRDGEEIGDDDGGLLVIKRPW-PSMLRTVYGDDERYRKSYWGEI--PHV 501 P++G + + DG E G ++ G++ I P P L TV+G DER+ +Y+ P V Sbjct: 416 FPVYGYDLRIFREDGSECGPNEKGIVGIVPPLPPGCLSTVWGQDERFVSTYFSLFTDPVV 475 Query: 502 YFAGDGARRDHDGYYTIVGRVDDVLNVSGHRLGTMEIESALVAHPDVSEAAVVGRPDPVK 561 Y + D +D +GY+TI+GR+DDV+NV+GHRLGT EIE A+ HP ++E AVVG D +K Sbjct: 476 YSSSDWGIKDENGYHTILGRMDDVINVAGHRLGTREIEEAVQTHPAIAEVAVVGVHDELK 535 Query: 562 GESVVAYVLLQDGHTADPAALRAHVSSEI--------GALARPDAIYIADALPKTRSGKI 613 G+ +A+ +++D T D A RA + E+ GA+ARP ++ + LPKTRSGK+ Sbjct: 536 GQMPMAFAVVKDASTVDTAEKRAALEKEVMKKVDESLGAIARPARVHFINGLPKTRSGKM 595 Query: 614 MRRFLRQLAAGQPVQGDTSTLEDPTVLERLQASPA 648 +RR ++ LA G+ GD +T++DPT L++++A+ A Sbjct: 596 LRRSIQALAEGRDA-GDLTTIDDPTTLDQIKAALA 629 Lambda K H 0.319 0.137 0.432 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: 1126 Number of extensions: 61 Number of successful extensions: 9 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: 649 Length of database: 630 Length adjustment: 38 Effective length of query: 611 Effective length of database: 592 Effective search space: 361712 Effective search space used: 361712 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: 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