Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_057507018.1 ABB28_RS02085 propionate--CoA ligase
Query= curated2:O93730 (670 letters) >NCBI__GCF_001431535.1:WP_057507018.1 Length = 626 Score = 490 bits (1261), Expect = e-143 Identities = 265/633 (41%), Positives = 391/633 (61%), Gaps = 18/633 (2%) Query: 33 YFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHV 92 Y + +R++++ E+FW A + W KP +VLD SNPPF +W+VGG NL Y AVDRH+ Sbjct: 3 YEETYRRSIDEPEAFWGEEANRIYWHKPPRQVLDYSNPPFRRWYVGGETNLCYNAVDRHL 62 Query: 93 KTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLY 152 R ++LA+ V + R++TY LYREVN A +LK+ V GD++ +Y Sbjct: 63 AE-RPDQLAL------VAVSTETGTTREITYRQLYREVNDFAAVLKR-LDVGHGDRVVIY 114 Query: 153 LPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRL 212 +P + E MLA RIGA+ SVVF GF+A LA RI+D++ +++I AD R G+++ Sbjct: 115 MPNMAEAVFAMLACARIGAVHSVVFGGFAAHNLALRIDDARPKLLIAADAGMRGGKLIPY 174 Query: 213 KEVVDAALEKATGVESVIVLPRLGLKDV-PMTEGRDYWWNKLMQGIPPNAYIEPEPVESE 271 K +VDAA +A +++ GL P GRD + L + + + +ES Sbjct: 175 KGMVDAACAEAQNPPPHVLIVSRGLDPAEPRQAGRDVDYATLRAEVG-EVDVPVQWLESS 233 Query: 272 HPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYV 331 PS++LYTSGTTGKPKG+ D GG+AV + +M+ VFD + + + T+D+GW GHSY Sbjct: 234 EPSYLLYTSGTTGKPKGVQRDVGGYAVAMAQSMQTVFDCQPGQVMFSTSDVGWAVGHSYN 293 Query: 332 VLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHD 391 V GPL+ G T ++YEG P P P WW++ E+Y V ++SPTAIR+ ++ ++ R+HD Sbjct: 294 VYGPLIGGCTSLLYEGLPTNPDPGIWWALCEQYNVRTLFSSPTAIRVLKKHDVDFIRRHD 353 Query: 392 LSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMKP 451 L L+ I GEP++ WA LG + +W TETG ++ PGL + P++ Sbjct: 354 LKALKYIFLAGEPLDEPTAHWANEALGKPII---DNYWQTETGWPALTLLPGLDMKPVRF 410 Query: 452 GTNGPPLPGFEVDVVDEN-GNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSRF 509 G+ G P G+ + V+DEN G PG KG LV+ P PG + +W D R++++Y+S F Sbjct: 411 GSPGFPNLGYRMKVIDENTGVEVAPGQKGVLVMTPPLPPGCMSTVWNDDARFLQSYFSHF 470 Query: 510 PGMFYAG-DYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGVP 568 + Y+ D+AI+D+DGY ++LGR D+VI VAGHRLGT E+E A+ HP VAE+AV+GV Sbjct: 471 KELLYSSLDWAIRDEDGYTFILGRTDDVINVAGHRLGTREIEEAISGHPRVAEAAVIGVK 530 Query: 569 DAIKGEVPIAFVVLKQGVAPSD--ELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGK 626 D +KG+VP+ FV LKQG+ D + E+ V ++G +A PA I V LPKTRSGK Sbjct: 531 DELKGQVPLVFVTLKQGLNGEDPAPVVAEMMAAVTASLGAVARPAHIHVVNALPKTRSGK 590 Query: 627 IMRRLLKAVATGAPLGDVTTLEDETSVEEAKRA 659 ++RR L+A+A GD++TL+D +++E +RA Sbjct: 591 LLRRSLQALAEQRDPGDLSTLDDPAALDEIRRA 623 Lambda K H 0.319 0.138 0.440 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: 1291 Number of extensions: 81 Number of successful extensions: 10 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: 670 Length of database: 626 Length adjustment: 38 Effective length of query: 632 Effective length of database: 588 Effective search space: 371616 Effective search space used: 371616 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