Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate Ac3H11_663 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_663 Length = 559 Score = 171 bits (432), Expect = 9e-47 Identities = 160/573 (27%), Positives = 242/573 (42%), Gaps = 69/573 (12%) Query: 6 PRPASSSPLTPL-GFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENG 64 P +S T L ++ A Y D + + T+ QT A+ + SLG+ G Sbjct: 15 PADIDTSQYTSLVALMDEAFKKYADRVAYSFMGKEVTYGQTDSLSSAFAAYLQSLGLVKG 74 Query: 65 HVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDL 124 V+++ PNVPQ AV AG ++ VN R + L S +K I + Sbjct: 75 DRVAIMMPNVPQYPVAVAAVLRAGFVVVNVNPLYTPRELEHQLKDSGAKAIVIIENFAAT 134 Query: 125 ILEAIALFPKQAPVPRLVFMADESESG------------NSSELGKEF----FCSYKDLI 168 + + IA PV +V A + G N ++ + + + Sbjct: 135 LEQCIA----HTPVKHVVLCAMGDQLGLLKGALVNYVVRNVKKMVPAYNLPGAVRFNQAV 190 Query: 169 DRGD------PDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGV 222 +G PD K D +L YT GTT KG V HR I + S W Sbjct: 191 AQGTRSTLKKPDIK------PDDIALLQYTGGTTGVSKGAVLLHRNILANVLQSEA-WNS 243 Query: 223 P--------KQPVYLWTLPMFHANGWSYPW--GMAAVGGTNICLRKFDSEIIYDMIKRHG 272 P +QP + LP++H ++ M G T + D + + +H Sbjct: 244 PVMSKVPAGEQPTAVCALPLYHIFAFTVNMMLSMRTGGKTILIPNPRDLPAVLKELSKHT 303 Query: 273 VTHMCGAPVVLNMLSNAPGSEPLK-TTVQIMTAGAPPPSAVLFRT--ESLGFAVSHGYGL 329 + N L+N P + +++ G + + E G + GYGL Sbjct: 304 FHSFPAVNTLFNGLANHPDFNTVNWKNLKVSVGGGMAVQGAVAKLWLEKTGCPICEGYGL 363 Query: 330 TETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLG 389 +ET+ SC N + ATE GT M+ D +T G Sbjct: 364 SETSPST-SC------NPVTATEYTGTIGVPIPGTYMKLIDDEGREITTLGEP------G 410 Query: 390 EVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGEN 449 E+ ++G VM GY + P+ TAK MT DG+F +GD+G+M G+ +I DR KD+++ G N Sbjct: 411 EIAIKGPQVMAGYWQRPDETAKVMTDDGYFKSGDIGIMDARGFFKIVDRKKDMVLVSGFN 470 Query: 450 LSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKP---TEKEIVEYCR 506 + EVE ++ S P +LE AVV PDE GE ++K + KK TE ++ E+CR Sbjct: 471 VYPNEVEEVVASCPGVLECAVVGVPDEKTGE------AVKLVIVKKDPALTEAQVKEFCR 524 Query: 507 SKLPRYMVPKTVVFKEELPKTSTGKVQKFILRD 539 +L Y PK + F+ ELPKT GK+ + LRD Sbjct: 525 RELTGYKQPKVIEFRTELPKTPVGKILRRELRD 557 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: 766 Number of extensions: 41 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: 559 Length adjustment: 36 Effective length of query: 520 Effective length of database: 523 Effective search space: 271960 Effective search space used: 271960 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