Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 5209735 Shew_2188 long-chain-fatty-acid--CoA ligase (RefSeq)
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__PV4:5209735 Length = 557 Score = 146 bits (369), Expect = 2e-39 Identities = 145/553 (26%), Positives = 234/553 (42%), Gaps = 50/553 (9%) Query: 17 LGFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIAS-LGIENGHVVSVLAPNVP 75 + E + Y D + V + T+ + R A+ + + L ++ G V+++ PN+ Sbjct: 26 IDLFESSVAKYADQPAFVNMGATLTYRKLEERSRAFAAYLQNELKLQKGDRVAIMMPNLL 85 Query: 76 QMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQ 135 Q F + AG ++ VN R + L+ S +K I V + + + + P + Sbjct: 86 QYPIALFGILRAGMVVVNVNPLYTPRELKHQLNDSGAKAIVVVSNFANTLEQVVEQTPVK 145 Query: 136 ------------APVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSE 183 AP LV + + S + + +G ++V P + Sbjct: 146 SVILTGLGDLLSAPKRTLVNFVVKYIKKMVPKYHLPHAISMRQSLSKGRR-LQYVKPTIK 204 Query: 184 WDPM-ILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVY-------LWTLPMF 235 D + L YT GTT KG + H I V +L+ P+ + LP++ Sbjct: 205 GDDIAFLQYTGGTTGVSKGAMLTHGNI----VSNLLQADAAYSPLLADGKEFVVTALPLY 260 Query: 236 HANGWSYPWGMAAVGGTNICL--RKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSE 293 H + + G N L D +K+H T + G + N L ++ + Sbjct: 261 HIFALTVNCLLFLHKGANNLLITNPRDIPAFVSELKKHPFTALTGVNTLFNALVSSEEFK 320 Query: 294 PLKTTVQIMTAGAPPPSAVLFRTESLGFAVSH---GYGLTETAGLVVSCAWKKEWNHLPA 350 L + ++ G + G + GYGLTE + L+ C + E + Sbjct: 321 TLDFSNLKLSIGGGMAVQRAVADKWQGITKTRLLEGYGLTEASPLLTCCPYNLEGYN--- 377 Query: 351 TERARLKSRQGVG-TVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGT 409 +G V T + V D V G T GE+ +G VM GY + PE T Sbjct: 378 ---------GSIGFPVANTDMQVRDEEGN--VLPQGET-GELFAKGPQVMKGYWQRPEET 425 Query: 410 AKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAA 469 AK + DG+ TGD+G M G+ I DR KD+I+ G N+ EVE ++ HP +LE A Sbjct: 426 AKVIDKDGYLATGDIGYMDEQGFFFIVDRKKDMILVSGFNVFPNEVEEVVALHPKVLEVA 485 Query: 470 VVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTST 529 V P E GE FV K K TE++++++CR L Y +PK V F++ELPK++ Sbjct: 486 AVGVPHEVSGELVKVFVVPK---DKSLTEEQVIKHCRHHLTGYKIPKLVEFRDELPKSNV 542 Query: 530 GKVQKFILRDMAR 542 GK+ + LRD A+ Sbjct: 543 GKILRRELRDEAK 555 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: 694 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 556 Length of database: 557 Length adjustment: 36 Effective length of query: 520 Effective length of database: 521 Effective search space: 270920 Effective search space used: 270920 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