Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate SMc00261 SMc00261 acyl-CoA synthetase
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__Smeli:SMc00261 Length = 549 Score = 159 bits (402), Expect = 3e-43 Identities = 158/565 (27%), Positives = 248/565 (43%), Gaps = 48/565 (8%) Query: 8 PASSSPLTPLGFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIA-SLGIENGHV 66 P S+ + FL +AA D ++V+ + WS+ R +A ++ G+ G Sbjct: 12 PVSTRVMNLANFLSQAARRNPDEIALVHGDRRWRWSEMEARVDAMAYALVHEFGVRKGDR 71 Query: 67 VSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLIL 126 + V + N QM+E FA AGA+ N R ++ L S ++L+ Sbjct: 72 ILVHSANCNQMFESMFAAFRAGAVWVPTNFRQLPEEVAYLAESSGARLVIFQ-------- 123 Query: 127 EAIALFPKQAPVPRLVFMADESESGN-----SSELGKEFFCSYKDLIDRGDPDFKWVMPK 181 A F A R A + G+ SS +G++ Y ++ R + Sbjct: 124 ---AAFEAHAEACR----AAGEQIGSCIPIGSSRVGED----YDAIVARNLGRSVSPVAV 172 Query: 182 SEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDW--GVPKQPVYLWTLPMFHANG 239 DP YTSGTT PK V H + + + + D + + P+ H G Sbjct: 173 DRDDPCWYFYTSGTTGRPKAAVLTHGQMAFVINNHIGDLFPATTHRDRSIVVAPLSHGAG 232 Query: 240 WSYPWGMAAVGGTNICL--RKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSEPL-- 295 + A G T I L K D + ++++ V ++ P ++ +L P + Sbjct: 233 -IHQLCQVARGATTILLPSEKLDIPQFWALVEKWRVNNLFAVPTIVKLLIEDPSVDRYDH 291 Query: 296 KTTVQIMTAGAPPPSAVLFRT-ESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERA 354 + ++ AGAP A + E LG + +GL E G + ++ A Sbjct: 292 SSLRYVIYAGAPMYRADQKKALEKLGAVLVQYFGLGEVTGAIT--VLPPAFHSSEDGPDA 349 Query: 355 RLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMT 414 R+ + T MQ +I D A G+T GE+ + G +V GY ++PE AK+ Sbjct: 350 RIGTCGFERTGMQLQIQDEDGNEVPA----GAT-GEICVIGPAVFAGYYRNPEANAKAFR 404 Query: 415 ADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARP 474 +GWF TGD+G + G+L I R+ D+ ISGG N+ E+E L HPDI EAA+V P Sbjct: 405 -NGWFRTGDLGHVDAQGFLYITGRASDMYISGGSNVYPREIEEKLLMHPDISEAAIVGVP 463 Query: 475 DEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQK 534 D WGE A + G T + E+ K+ RY +PK +VF E+PK++ GK+ K Sbjct: 464 DPVWGEVGIAVCVARGGATVGAA--ALREWLDGKIARYKLPKKIVFWSEMPKSAYGKITK 521 Query: 535 FILRD--MARG---MGSATAGASRS 554 ++R+ RG +GSA G RS Sbjct: 522 KLIREELERRGELDIGSAGIGERRS 546 Lambda K H 0.319 0.135 0.412 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: 772 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 549 Length adjustment: 36 Effective length of query: 520 Effective length of database: 513 Effective search space: 266760 Effective search space used: 266760 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: 53 (25.0 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