Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate H281DRAFT_04471 H281DRAFT_04471 propionyl-CoA synthetase
Query= curated2:O93730 (670 letters) >FitnessBrowser__Burk376:H281DRAFT_04471 Length = 635 Score = 495 bits (1275), Expect = e-144 Identities = 266/641 (41%), Positives = 395/641 (61%), Gaps = 25/641 (3%) Query: 33 YFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHV 92 Y FHR+++EN E+FW A+ + W P+D VLD SNPPF +WFVGGR NL + AVDRH+ Sbjct: 4 YRDFHRRSIENPEAFWRDEARRIHWETPFDTVLDRSNPPFARWFVGGRTNLCHNAVDRHL 63 Query: 93 KTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLY 152 + + E E R+ TY +LY E+NR+A +++ + GVK+GD + LY Sbjct: 64 VDRAQQNALVYVSTETGIE-------RRYTYAELYAEINRMAAVMR-SLGVKRGDVVLLY 115 Query: 153 LPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRL 212 LPM+PE MLA R+GAI SVVF GF+A LA RI+D++ +++TAD R G+V+ Sbjct: 116 LPMIPEALFAMLACARLGAIHSVVFGGFAAPNLAARIDDAKPVLIVTADAGARGGKVIDY 175 Query: 213 KEVVDAALEKATGVESVIVL--PRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPVES 270 +VD A+ +AT + ++L +L + + T DY + ++ +A++ E +ES Sbjct: 176 TPLVDEAIARATHKTARVLLIDRQLAPERLNATYLVDY---EPLREQFFDAHVSCEWLES 232 Query: 271 EHPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSY 330 PS++LYTSGTTGKPKG+ D GG+AV + A+M+++F+ + D + +D+GWV GHSY Sbjct: 233 SEPSYVLYTSGTTGKPKGVQRDVGGYAVALAASMEYIFEGKAGDTMFTASDVGWVVGHSY 292 Query: 331 VVLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKH 390 +V PL+ G T V+YEG P P WW ++E++ + + +T+PTA+R+ + Sbjct: 293 IVYAPLIAGLTTVMYEGTPIRPDGGIWWRLVEQHKINLMFTAPTALRVLKKQDPALLESA 352 Query: 391 DLSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMK 450 DLS+LR + GEP++ W LG + +W TETG +++ G+ +P K Sbjct: 353 DLSSLRTLFLAGEPLDEPTASWITGALGKPVI---DNYWQTETGWPMLAIPRGVEALPTK 409 Query: 451 PGTNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSR 508 G+ G P GF + + +E G P PPG KG L + P PG + +WGD +R+I TYWS Sbjct: 410 LGSPGVPSAGFNLTLRNELTGEPCPPGEKGVLTLNYPLPPGCMSTVWGDDKRFISTYWSS 469 Query: 509 FPG--MFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVG 566 FP ++ D+ I+D+DGY+ +LGR D+VI VAGHRLGT E+E AL SH AVAE AVVG Sbjct: 470 FPDQQVYSTFDWGIQDEDGYVTILGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVG 529 Query: 567 VPDAIKGEVPIAFVVLKQGVAPSD-----ELRKELREHVRRTIGPIAEPAQIFFVTKLPK 621 V D +KG+ +AFVVL+ A +D +L EL V R +G IA P+++ V+ LPK Sbjct: 530 VADPLKGQAAMAFVVLRDAQAYADVDARTKLEAELTATVDRQLGAIARPSRVVIVSMLPK 589 Query: 622 TRSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYEE 662 TRSGK++RR + A+A G G++ T+ED ++++ + E Sbjct: 590 TRSGKLLRRAIAALAEGREPGELPTIEDPAALQQVREGLSE 630 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: 1274 Number of extensions: 77 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: 670 Length of database: 635 Length adjustment: 38 Effective length of query: 632 Effective length of database: 597 Effective search space: 377304 Effective search space used: 377304 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