Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_066599219.1 V473_RS00565 long-chain fatty acid--CoA ligase
Query= metacyc::MONOMER-20124 (573 letters) >NCBI__GCF_001046645.1:WP_066599219.1 Length = 503 Score = 191 bits (485), Expect = 6e-53 Identities = 156/532 (29%), Positives = 255/532 (47%), Gaps = 42/532 (7%) Query: 48 LERSSKAYRDNTSLVYGSVRYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLPEIY 107 L S+ + D ++++ + R T+ + A+ L L I P VA N + Sbjct: 7 LFESASRHCDKLAIIFENRRLTYGALRLEVERAAAGLQA-LDIGPSKRVAVMLENGLDFV 65 Query: 108 ELHFAVPMAGGILCTLNARNDSAMVSTLLAHSEAKLIFVEPQLLETARAALDLLAQKDIK 167 ++A G + T++A + S +L S A L+ ++ +TA+AA D + + Sbjct: 66 VAYYATLATGASVVTVSALLTVSEASYVLKDSTADLLIGGGRVWDTAQAAADGAGLQAFQ 125 Query: 168 PPTLVLLTDSESFTSSSYDHYNHLLANGSDDFEIRRPKNEWDPISINYTSGTTARPKAVV 227 L +E T + P + D I YTSGTT +PK + Sbjct: 126 LADL-----AEGLT-----------------YICPTPPDGRDEAVIMYTSGTTGKPKGAI 163 Query: 228 YSHRGAYLNSIATVL--LHGMGTTSVYLWSVPMFHCNGW-CFPWGAAAQGATNICIRKVS 284 +H +N++ +V + + V L +P+FH +G C GAT + +R+ + Sbjct: 164 LTHDNLTMNALVSVGQGMFNLSPEDVVLCCIPLFHASGQSCLLNTGLLAGATVVIMRQFA 223 Query: 285 PKAIFDNIHLHKVTHFGAAPTVLNMIVNSPEGNLHTPLPHKVEVMTGGSPPPPKVIARME 344 +A+ D + L KVT F PT+ +++ N LPH ++GG+P P V+ +E Sbjct: 224 AQAVLDVMRLEKVTFFLGVPTMYVGLLSLVRPN-KAELPHWRVAVSGGAPIPVAVLEEVE 282 Query: 345 EMGFQVNHI--YGLTETCGPAANCVCKPEWDALQPEERYALKARQGLNHLAMEEMDVRDP 402 + F+V+ YGLTET A C +P+++ A+ Q +A E++ R Sbjct: 283 RL-FEVDIYEGYGLTETSPTA--CFNQPDFERRPGTIGKAIWGVQC--EVARIELEDR-- 335 Query: 403 VTMESVRADGATIGEVMFRGNTVMSGYFKDLKATEEAFEGGWFRSGDLGVKHEDGYIQLK 462 +E + AD +GE++ RG+ V +GY AT GWFR+GD+ K EDGY+++ Sbjct: 336 --IELLAAD--EVGELVVRGHNVFAGYLNQADATRACMVDGWFRTGDIATKDEDGYVRIV 391 Query: 463 DRKKDVVISGGENISTVEVETVLYSHEAVLEAAVVARPDKLWGETPCAFVTLKEGFDNDV 522 DRKKD++I GG N+ + E+E VL +H A+ AAVV RPD L+GE A V L + Sbjct: 392 DRKKDMIIRGGFNVYSREIEEVLSTHPAIALAAVVGRPDDLFGEEIVAVVQLHRDMAG-I 450 Query: 523 SADQIIKFCRDRLPHYMAPKTVVF-EELPKTSTGKIQKYILKEKAMAMGSLS 573 S+ ++++ + L Y P+ VF E +P +GKI K L E + + S Sbjct: 451 SSSDMVEWAKRHLAKYKYPREFVFVETIPLGPSGKILKRELAELVARLSTAS 502 Lambda K H 0.318 0.133 0.408 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: 633 Number of extensions: 44 Number of successful extensions: 4 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: 573 Length of database: 503 Length adjustment: 35 Effective length of query: 538 Effective length of database: 468 Effective search space: 251784 Effective search space used: 251784 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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