Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_072790532.1 BUA36_RS28615 propionate--CoA ligase
Query= curated2:O93730 (670 letters) >NCBI__GCF_900143065.1:WP_072790532.1 Length = 622 Score = 484 bits (1246), Expect = e-141 Identities = 254/631 (40%), Positives = 394/631 (62%), Gaps = 18/631 (2%) Query: 33 YFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHV 92 Y +F+++++ E FW+ A ++W P+ +VLD + PPF +WFVGG NL + AVDR Sbjct: 3 YAEFYQRSIVTPEQFWQDEAALIDWNTPFTQVLDYAKPPFARWFVGGHTNLCHNAVDRWC 62 Query: 93 KTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLY 152 T I E E Y ++ +L EV R A M+ Q+ GV+KGD++ +Y Sbjct: 63 ATQGDQPALIAISTETNTERCY-------SFNELRAEVERWAAMM-QSLGVRKGDRVLIY 114 Query: 153 LPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRL 212 +PM+ E MLA RIGA+ SVVF GF+A++LA RI+D++ ++++AD R G+ + Sbjct: 115 MPMIAEAAFAMLACARIGAVHSVVFGGFAANSLASRIDDAKPVLIVSADAGSRNGKAIPY 174 Query: 213 KEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPVESEH 272 K ++D A+ ++ S ++L GL + M EGRD + L + A++ +ES Sbjct: 175 KPLLDEAIALSSAKPSRVLLVDRGLAPMAMVEGRDVDYAAL-RAAHLAAHVPVTWLESNE 233 Query: 273 PSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYVV 332 PS+ILYTSGTTGKPKG+ D GG+AV + A+MK+ F + + F+ T+DIGWV GHSY+V Sbjct: 234 PSYILYTSGTTGKPKGVQRDVGGYAVALAASMKYNFCGKAGETFFATSDIGWVVGHSYIV 293 Query: 333 LGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHDL 392 GPL+ G ++YEG P P P WWSI+E+Y VT +++PTAIR+ + E+ RK+D Sbjct: 294 YGPLIAGMATIMYEGLPICPDPGIWWSIVEKYKVTRMFSAPTAIRVLRKQAPEFMRKYDK 353 Query: 393 STLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMKPG 452 S+L+ ++ GEP++ W + V +W TETG ++S A G+ P + G Sbjct: 354 SSLKALYLAGEPLDETTSSW---IADELNVPIIDNYWQTETGWPILSIAKGIEDTPTRLG 410 Query: 453 TNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSRFP 510 + G + G++V +++E NG KG ++++ P PG + ++GD +R++ TYWS Sbjct: 411 SPGLAMYGYKVRLINEINGQECGANEKGVVMVEGPLPPGCMQTVYGDDQRFVDTYWSEHD 470 Query: 511 G--MFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGVP 568 G ++ D+ ++D DGY ++LGR D+VI VAGHRLGT E+E ++ SHP V+E AVVGV Sbjct: 471 GKMVYSTFDWGLRDADGYYFILGRTDDVINVAGHRLGTREIEESITSHPNVSEVAVVGVE 530 Query: 569 DAIKGEVPIAFVVLKQGVAPSDELRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKIM 628 D +KG+V +AF +LK A + E +++ V R +G +A PA+++FVT+LPKTRSGK++ Sbjct: 531 DKLKGQVAVAFAILKDANAATSE--QDVMSVVDRQLGAVARPARVYFVTQLPKTRSGKLL 588 Query: 629 RRLLKAVATGAPLGDVTTLEDETSVEEAKRA 659 RR ++A+ G GD+T +ED S+++ +RA Sbjct: 589 RRSIQAICEGRNPGDLTAIEDPASLQQIQRA 619 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: 1226 Number of extensions: 65 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: 670 Length of database: 622 Length adjustment: 38 Effective length of query: 632 Effective length of database: 584 Effective search space: 369088 Effective search space used: 369088 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