Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_053544053.1 CDES_RS02115 long-chain fatty acid--CoA ligase
Query= metacyc::MONOMER-20125 (556 letters) >NCBI__GCF_001277995.1:WP_053544053.1 Length = 568 Score = 157 bits (398), Expect = 8e-43 Identities = 143/521 (27%), Positives = 239/521 (45%), Gaps = 41/521 (7%) Query: 39 SYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRL 98 S T+++ + A+ + +LG+ G V+++ PN PQ +AV GA + N Sbjct: 51 SQTYAELDKEVRRTAAGLRALGVRPGDRVAIILPNCPQHIAAFYAVLKLGATVIEHNPLY 110 Query: 99 DARTI--SILLHHSESKLIF------VDHLSRDLILEAIA---LFPKQAPVPRLVF---- 143 A + H + +++ V+ L + LE I + V RL Sbjct: 111 TAHELLEPFKDHGARVAIVWDKASPVVEKLRGETNLETIVSVNMINAMPTVQRLALKLPI 170 Query: 144 --MADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPM-ILNYTSGTTSSPK 200 + E+ + S F + G+ + P D + ++ YTSGTT +PK Sbjct: 171 PALRKSREALSGSAPNTVPFETLASAAMGGEGEDIVSEPSVTKDTVALILYTSGTTGTPK 230 Query: 201 GVVHCHRGIFIMTVDSLIDW--GVPKQPV-YLWTLPMFHANGWSYPWGMAA-VGGTNICL 256 G H +F + W G+ +P L LPMFHA G + ++ +GG + L Sbjct: 231 GAQLTHGNLFSNLLQGK-HWVPGLGDKPERMLAALPMFHAYGLTMVGTLSVFIGGEMVLL 289 Query: 257 RKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSE--PLKTTVQIMTAGAPPPSAVLF 314 ++I +++K+H T + G P + + +A E P+K + + + + Sbjct: 290 PTPRIDLIMNIMKKHTPTWLPGVPTLYEKIVDASDKEGIPIKGVRNAFSGASTLSTRTVE 349 Query: 315 RTES-LGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVV 373 R E+ G + GYGLTET+ ++V P ++ R + G+ T + + Sbjct: 350 RWENHTGGRLVEGYGLTETSPIIVGN---------PMSDH-RKQGYVGI-PFPDTIVRIA 398 Query: 374 DPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYL 433 +P DG GEV+++G V GYL E T S + W+ TGDVGVM DG++ Sbjct: 399 NPENLDETVPDGEE-GEVLVKGPQVFKGYLNQEEATKNSFHGE-WYRTGDVGVMEEDGFI 456 Query: 434 EIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLT 493 + R K+VII+GG N+ EVE ++ +HPD+ +AAVV P E E A ++L +G Sbjct: 457 RLVARIKEVIITGGFNVYPAEVEDVITAHPDVEDAAVVGIPREDGSENVVAAITLVEGAA 516 Query: 494 KKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQK 534 P + + ++ R L RY VP+T EE+P+ GK+++ Sbjct: 517 LDP--EGLKDFARENLTRYKVPRTFYHFEEMPRDQMGKIRR 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: 779 Number of extensions: 50 Number of successful extensions: 7 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: 568 Length adjustment: 36 Effective length of query: 520 Effective length of database: 532 Effective search space: 276640 Effective search space used: 276640 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