Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_043772607.1 U743_RS16760 long-chain-fatty-acid--CoA ligase
Query= metacyc::MONOMER-20125 (556 letters) >NCBI__GCF_000733765.1:WP_043772607.1 Length = 540 Score = 249 bits (636), Expect = 2e-70 Identities = 163/511 (31%), Positives = 275/511 (53%), Gaps = 23/511 (4%) Query: 36 DAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVN 95 D YT+ + R +A+++ + G++ G + LA N + +EL++A+ G++++ +N Sbjct: 36 DIHRYTYGEAAARARQMANALTAAGLKPGERAATLAWNGYRHFELYYAISGIGSVMHTIN 95 Query: 96 LRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESESGNSSE 155 RL ++ +++H+E +++F D ++ +AIA K V V M+D + E Sbjct: 96 PRLHPEQVAWIVNHAEDRILFFDATFAPIV-DAIA--DKCPTVQHWVAMSDPDKM---PE 149 Query: 156 LGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVD 215 L SY+D + +++W + E L YTSGTT +PKG+++ HR + + T Sbjct: 150 LKNVSATSYEDFMAGQPTEYEWPV-LDENTAACLCYTSGTTGNPKGILYSHRSLVLHTYG 208 Query: 216 SLID--WGVPKQPVYLWTLPMFHANGWSYPWGMAAVGGTNICLR--KFDSEIIYDMIKRH 271 + + +GV V L +PMFH N WS P+ + A+GG + K D E +Y++ + Sbjct: 209 ACLPDAFGVTAMDVVLPVVPMFHVNAWSLPY-VGALGGVKLVFPGPKLDGESLYELFESE 267 Query: 272 GVTHMCGAPVVLNMLSNAPGSEPLK-TTVQIMTAG--APPPSAVLFRTESLGFAVSHGYG 328 GVT G P V ++ L+ +T++ MT G A PP+ + + G + H +G Sbjct: 268 GVTISAGVPTVWQLVLQHLQKNKLQLSTLKRMTVGGSACPPALMETFEKEFGVRLEHAWG 327 Query: 329 LTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTL 388 +TE + L K + L E+ +++ +QG V ++ +VD G +DG + Sbjct: 328 MTEMSPLGTYNHLKAKHQKLSEDEQFQVRIKQG-RAVFGVEMKIVDE-NGKRQPQDGKST 385 Query: 389 GEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGE 448 G++ +RG ++ Y K E S DGWF TGDVG + PDGYL I DR+KDVI SGGE Sbjct: 386 GDLHVRGPWIIKQYFKKDE----SPLIDGWFPTGDVGHIDPDGYLTITDRTKDVIKSGGE 441 Query: 449 NLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSK 508 + S+++E+I SHP + AA +A E W E P V LK+G + T+++++++ K Sbjct: 442 WIGSIDLENIAMSHPAVATAACIAAKHEKWDERPLLLVQLKEG--QSATKEDLLKHYEGK 499 Query: 509 LPRYMVPKTVVFKEELPKTSTGKVQKFILRD 539 + ++ P ++F + LP +TGKVQK LRD Sbjct: 500 IAKWWTPDDILFVDGLPLGATGKVQKNKLRD 530 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: 769 Number of extensions: 52 Number of successful extensions: 8 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: 556 Length of database: 540 Length adjustment: 36 Effective length of query: 520 Effective length of database: 504 Effective search space: 262080 Effective search space used: 262080 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 24 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