Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 3606823 Dshi_0253 AMP-dependent synthetase and ligase (RefSeq)
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__Dino:3606823 Length = 519 Score = 163 bits (412), Expect = 2e-44 Identities = 141/515 (27%), Positives = 225/515 (43%), Gaps = 53/515 (10%) Query: 41 TWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDA 100 T +Q R A + + GI G VV+++APN+P AGA + +N Sbjct: 45 TGAQLEGRIRACAGGLRARGIGPGDVVAIMAPNMPDYATAFHGAAFAGATVTTLNPTYTT 104 Query: 101 RTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESESGNSSELGKEF 160 + L S ++++ DL EA+ + V V M + G Sbjct: 105 EEAAHQLRDSGAQMLVTVPAFADLAAEAV----QGTGVTETVMMGTTGPGSLEALFGPPL 160 Query: 161 FCSYKDLIDRGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDW 220 + R D ++L Y+SGTT PKGV+ HR + + + Sbjct: 161 AAQVAVDLAR--------------DIVVLPYSSGTTGLPKGVMLSHRNLVVNVDQTAEII 206 Query: 221 GVPKQPVYLWTLPMFHANGWSYPWGM-AAVGGTNICLRKFDSEIIYDMIKRHGVTHMCGA 279 G+ Q V + LP FH G + + G + + +FD E + + H + A Sbjct: 207 GITVQDVTVGFLPFFHIYGMTVLMNCYLSRGAAVVTMPRFDLEQFLSLCQTHRPRQLYIA 266 Query: 280 PVVLNMLSNAPGSEPLKTT-VQIMTAGAPPPSAVLFRT--ESLGFAVSHGYGLTETAGLV 336 P V L+ P + + V+ + +GA P + LG + GYG+TE + + Sbjct: 267 PPVALALAKHPMVDDYDLSGVEFILSGAAPLGGDVAEAVGRRLGVEMVQGYGMTEMSPV- 325 Query: 337 VSCAWKKEWNHLPATERARLKSRQGVG-TVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRG 395 + ++P + VG T + +VDP TG + + GEV +RG Sbjct: 326 --SHFTPPGQNVPGS----------VGPTAPSAESRIVDPETG-----EDAAEGEVWVRG 368 Query: 396 GSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEV 455 +M GYL P+ TA+++T DGW TGD+G G L I DR K++I G ++ E+ Sbjct: 369 PQIMQGYLNRPDATAETVTRDGWLKTGDLGRFDEAGNLFITDRVKELIKVSGFQVAPAEL 428 Query: 456 ESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKP--TEKEIVEYCRSKLPRYM 513 E++L +HP I +AAV+ PD+ GE P AFV + P +E ++ + L Y Sbjct: 429 EAVLLTHPAITDAAVIGVPDDSAGERPMAFV-----VRSDPDLSEGAVIAHAAEHLAHYK 483 Query: 514 VPKTVVFKEELPKTSTGKVQKFILR-----DMARG 543 V F E +PK+++GK+ + +LR DMA G Sbjct: 484 RIARVAFVEAVPKSASGKILRRLLRAKVGEDMATG 518 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: 692 Number of extensions: 37 Number of successful extensions: 4 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: 519 Length adjustment: 35 Effective length of query: 521 Effective length of database: 484 Effective search space: 252164 Effective search space used: 252164 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: 52 (24.6 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