Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate BPHYT_RS13830 BPHYT_RS13830 acetyl-CoA synthetase
Query= curated2:O93730 (670 letters) >FitnessBrowser__BFirm:BPHYT_RS13830 Length = 634 Score = 479 bits (1233), Expect = e-139 Identities = 256/640 (40%), Positives = 386/640 (60%), Gaps = 21/640 (3%) Query: 32 AYFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRH 91 +Y FHR+++E+ E+FW A+ + W P+D VLD SNPPF +WFVGGR NL + AVDRH Sbjct: 3 SYRDFHRRSIEDPEAFWRDEARRIHWHTPFDTVLDRSNPPFARWFVGGRTNLCHNAVDRH 62 Query: 92 VKTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITL 151 + + + E E R+ TY +LY EVNR+A +++ + VK+GD + L Sbjct: 63 LAERAQQNALVYVSTETGIE-------RRYTYAELYGEVNRMAAVMR-SLDVKRGDVVLL 114 Query: 152 YLPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVR 211 YLPM+PE MLA R+GAI SVVF GF+A LA RI+D++ +++TAD R G+V+ Sbjct: 115 YLPMIPEALFAMLACARLGAIHSVVFGGFAAPNLAARIDDAKPVLIVTADAGARGGKVID 174 Query: 212 LKEVVDAALEKATGVESVIVLPRLGLKDVPMTEGRDYWWNKLMQGIPPNAYIEPEPVESE 271 ++D AL +A ++L L + + L + +A++ E +ES Sbjct: 175 YTPLMDEALARAQHKTPRVLLIDRQLAPERLNASYLVAYEPLREQFF-DAHVPCEWLESN 233 Query: 272 HPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYV 331 PS++LYTSGTTGKPKG+ D GG+AV + A+M+ +F + D+ + +D+GWV GHSY+ Sbjct: 234 EPSYVLYTSGTTGKPKGVQRDVGGYAVALAASMEHIFQGKAGDVMFTASDVGWVVGHSYI 293 Query: 332 VLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHD 391 V PL+ G T V+YEG P P WW ++ + + + +T+PTA+R+ + ++ D Sbjct: 294 VYAPLIAGLTTVMYEGTPIRPDGGIWWRLVAHHRINLMFTAPTALRVLKKQDPALLKQAD 353 Query: 392 LSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMKP 451 L++LR + GEP++ W L + +W TETG +++ G+ +P + Sbjct: 354 LTSLRALFLAGEPLDEPTAAWIAGALDKPVI---DNYWQTETGWPMLAIPRGVEALPTRL 410 Query: 452 GTNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSRF 509 G+ G P GF + + +E G P PPG KG L + P PG + +WGD +R++ TYWS Sbjct: 411 GSPGVPSAGFNLTLRNELTGEPCPPGEKGVLTLDYPLPPGCMSTVWGDDKRFVSTYWSSI 470 Query: 510 PG--MFYAGDYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGV 567 P ++ D+ ++D+DGY+ +LGR D+VI VAGHRLGT E+E AL SH AVAE AVVGV Sbjct: 471 PNQQVYSTFDWGVQDEDGYVTILGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVGV 530 Query: 568 PDAIKGEVPIAFVVLKQGVAPSD-----ELRKELREHVRRTIGPIAEPAQIFFVTKLPKT 622 D +KG+ +AFVVL+ A +D +L EL V R +G IA P+++ V LPKT Sbjct: 531 TDPLKGQAAMAFVVLRDAQAYADTKKRSKLDAELTATVDRQLGAIARPSRVVVVPMLPKT 590 Query: 623 RSGKIMRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYEE 662 RSGK++RR + A+A G GD+ T+ED ++++ + A ++ Sbjct: 591 RSGKLLRRAIAALAEGREPGDLPTIEDPAALQQVREALDD 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: 1262 Number of extensions: 79 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: 634 Length adjustment: 38 Effective length of query: 632 Effective length of database: 596 Effective search space: 376672 Effective search space used: 376672 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