Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate Dsui_3212 Dsui_3212 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= metacyc::MONOMER-20124 (573 letters) >FitnessBrowser__PS:Dsui_3212 Length = 555 Score = 124 bits (310), Expect = 1e-32 Identities = 144/554 (25%), Positives = 223/554 (40%), Gaps = 64/554 (11%) Query: 49 ERSSKAYRDNTSLVYGSVRYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLPEIYE 108 E+S YRD + + V T+ + A+ L L + G VA NL + Sbjct: 30 EQSCAQYRDRVAYINMGVGITYGELDRLSRDFAAYLQDVLKLPQGARVALMMPNLLQYPV 89 Query: 109 LHFAVPMAGGILCTLNARNDSAMVSTLLAHSEAKLIFVEPQLLETARAALDLLAQKDIKP 168 F AG ++ N + L S A+ I + T AL L+ +K Sbjct: 90 CMFGALRAGYVVVNCNPLYTHRELEHQLKDSGAEAIVIVENFAHTLEQALPLVP--GLKH 147 Query: 169 PTLVLLTDS--------------------ESFTSSSYDHYNHLLANGSDDFEIRRPKNEW 208 + L D ++ + + +A G Sbjct: 148 VIVTSLGDMLGALKGTVVNLVVRHVKKMVPAWKLPRHVKFKAAMARGKGATLRPVQVGHE 207 Query: 209 DPISINYTSGTTARPKAVVYSHRGAYLN-----SIATVLLHGMGTTSVYLWSVPMFHC-- 261 D + YT GTT K + HR N + LH + + ++P++H Sbjct: 208 DIAYLQYTGGTTGVAKGAMLLHRNIIANLQQAHAWIEPFLHK--DQQLIITALPLYHIFS 265 Query: 262 -NGWCFPWGAAAQGATNICIRKVSPKAI---FDNIHLHKVTHFGAAPTVLNMIVNSPEGN 317 C + GATN+ I +P+ I + +K T T+ N ++N+P+ Sbjct: 266 LTANCLTF--LKIGATNVLI--TNPRDIPGFVKELAQYKFTVITGVNTLFNALLNNPD-- 319 Query: 318 LHTPLPHK-VEVMTGGSPPPPKVIARM--EEMGFQVNHIYGLTETCGPAANCVCKPEWDA 374 L + GG K +A+ + G + YGLTET PAA Sbjct: 320 -FAKLDFSALRAALGGGMAVQKSVAQKWRQVTGKPLIEAYGLTET-SPAAT--------- 368 Query: 375 LQPEERYALKARQGLNHLAMEEMDVRDPVTMESVRADGATIGEVMFRGNTVMSGYFKDLK 434 + P + GL ++ E+ +RD + + GE+ RG VM GY+ Sbjct: 369 INPLDLGEFNGAIGLP-ISSTEIVIRDDLGNDLPVGQA---GEICIRGPQVMKGYWLRPD 424 Query: 435 ATEEAFEG-GWFRSGDLGVKHEDGYIQLKDRKKDVVISGGENISTVEVETVLYSHEAVLE 493 T F G+ R+GD+GV E G++++ DRKKD+++ G N+ EVE V+ H AV+E Sbjct: 425 ETATVFYADGFLRTGDVGVMDEKGFVRIVDRKKDMILVSGFNVYPNEVEAVVAMHPAVME 484 Query: 494 AAVVARPDKLWGETPCAFVTLKEGFDNDVSADQIIKFCRDRLPHYMAPKTVVF-EELPKT 552 A V P + GE FV LK D V+ +Q+I C++ L Y P V F ++LPKT Sbjct: 485 VAAVGVPSEHSGEAVKIFVVLK---DKSVTKEQLIAHCKENLTGYKVPHLVEFRDDLPKT 541 Query: 553 STGKIQKYILKEKA 566 + GKI + LKE A Sbjct: 542 NVGKILRRALKEAA 555 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: 638 Number of extensions: 28 Number of successful extensions: 5 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: 555 Length adjustment: 36 Effective length of query: 537 Effective length of database: 519 Effective search space: 278703 Effective search space used: 278703 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: 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