Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate Dsui_2925 Dsui_2925 propionate--CoA ligase
Query= curated2:O93730 (670 letters) >FitnessBrowser__PS:Dsui_2925 Length = 630 Score = 497 bits (1279), Expect = e-145 Identities = 266/637 (41%), Positives = 402/637 (63%), Gaps = 21/637 (3%) Query: 32 AYFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRH 91 +Y +FHR+++E ++FW A+ ++W KP+D+V D S PPF KWFVGG+ NL Y AVDRH Sbjct: 3 SYKEFHRRSIEQPDAFWSEQAQLIDWHKPFDQVCDYSRPPFAKWFVGGQTNLCYNAVDRH 62 Query: 92 VKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITL 151 KT + I E E Y ++ +L REV R+A + Q+ GVKKGD++ + Sbjct: 63 AKTRPNDNALIFISTETDVEKVY-------SFAELQREVERMA-AIYQSLGVKKGDRVLI 114 Query: 152 YLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVR 211 Y+PM+ E +LA RIGAI SVVF GF++ +LA RI+D++ +++++D R G+ V Sbjct: 115 YMPMIAEACFAILACARIGAIHSVVFGGFASGSLATRIDDAKPVLIVSSDAGMRGGKAVP 174 Query: 212 LKEVVDAALEKATGVESVIVLPRLGL-KDVPMTEGRDYWWNKLMQGIPPNAYIEPEPVES 270 K ++D A+ +A +++ GL K EGRD + L +A + VES Sbjct: 175 YKHLLDDAINQAEHKPGKVLMVDRGLDKAFNKVEGRDVDYAALRAQFM-DAQVPVTWVES 233 Query: 271 EHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSY 330 PS+ILYTSGTTGKPKG+ DTGG+AV + +++K ++ + + F+ T+DIGWV GHSY Sbjct: 234 SDPSYILYTSGTTGKPKGVQRDTGGYAVALASSIKHIYCGKPGETFFSTSDIGWVVGHSY 293 Query: 331 VVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKH 390 ++ GPL+ G ++YEG P P WW I+E+Y V + +++PTA R+ ++ + K+ Sbjct: 294 IIYGPLIGGMATIMYEGTPIRPDAGIWWQIVEKYKVNVMFSAPTAARVLKKHDPAFLHKY 353 Query: 391 DLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMK 450 DLS+L+ + GEP++ W ++G K+ +W TETG ++S G+ +K Sbjct: 354 DLSSLKHLFLAGEPLDQPTHEW---IMGELKLPVIDNYWQTETGWPMLSTVRGVEDTKIK 410 Query: 451 PGTNGPPLPGFEVDVVDENGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSRF 509 GT P+ G++V + E+G+ KG L + P PG L +WGD ER++ TY+S F Sbjct: 411 YGTPSFPVYGYDVRIFREDGSECDANEKGILGVVPPLPPGCLTTVWGDDERFVNTYFSLF 470 Query: 510 --PGMFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGV 567 P ++ + D+AIKD +GY ++LGR D+VI VAGHRLGT E+E A+ HPAVAE AVVGV Sbjct: 471 KEPLVYSSYDWAIKDDEGYHFILGRTDDVINVAGHRLGTREIEEAVQGHPAVAEVAVVGV 530 Query: 568 PDAIKGEVPIAFVVLKQG--VAPSD---ELRKELREHVRRTIGPIAEPAQIFFVTKLPKT 622 DA+KG++P+AF V+K +A + L KE+ + V T+G IA P +++F++ LPKT Sbjct: 531 NDALKGQLPVAFAVVKDASKIATPELVAALEKEVMKRVDETLGAIARPGRVYFISGLPKT 590 Query: 623 RSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRA 659 RSGK++RR ++A+A G GD+TT+ED T++E+ K A Sbjct: 591 RSGKLLRRSIQALAEGRDPGDLTTIEDPTALEQIKAA 627 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: 1224 Number of extensions: 68 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: 630 Length adjustment: 38 Effective length of query: 632 Effective length of database: 592 Effective search space: 374144 Effective search space used: 374144 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 17 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