Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_043765768.1 U743_RS04305 long-chain-fatty-acid--CoA ligase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000733765.1:WP_043765768.1 Length = 513 Score = 247 bits (630), Expect = 9e-70 Identities = 159/518 (30%), Positives = 257/518 (49%), Gaps = 24/518 (4%) Query: 28 LERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLE 87 L RA + D TA V D R ++ D V A A+ G R D+++ +S N ++E Sbjct: 7 LRRAVQTRGDATATVCGDRRRSWREVADRVARLAGAVQALGVQRGDRVAILSLNSDRYIE 66 Query: 88 SFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKA--EII 145 + V +AG P+N R++P E+AY + S S+ + VD+ + L +++Q+ A ++I Sbjct: 67 YLYAVAWAGAAANPVNIRMAPGEIAYTLEDSGSRVLFVDDTFAPMLPALREQVSALEQVI 126 Query: 146 LLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGV 205 D + P ++ + L+ + P+P E + L+YT GTTG KGV Sbjct: 127 FCGDGELPEGTQG--------FEALI--AAHGPVPDADAGEEDLAGLFYTGGTTGKAKGV 176 Query: 206 MHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCLDKVDYP 265 M H N + + D ++VYL PMFH A ++A A G + + + D Sbjct: 177 MLSHDNVMHNMLNAIPILGYDASTVYLHAGPMFHLADMASTFAVTAAGGVHCVIPRFDIE 236 Query: 266 LIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPAT--LKAMQE 323 + ++++E+VTH PT+ L + S+ ML GA+P P L+AM+ Sbjct: 237 PLLEIMQREKVTHTMLVPTMINMLLASGRIQEFDLSSLRRMLY-GASPMPEAVLLRAMEA 295 Query: 324 IGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKP 383 + G T+ YG + A G+P S ++ + D +G Sbjct: 296 LP-----TTGFTQGYGQTEAAPLITFMPPEAHYAGSDKLASAGVPGYSVDVAIMDEDGTA 350 Query: 384 VPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKD 443 +P +GEV RG N+ GY+K E+TA + RDGW +GD + DG++ IVDR KD Sbjct: 351 LP--NGQVGEVCARGGNIMQGYWKRAEQTAATLRDGWLRTGDLGYMDDDGFVFIVDRAKD 408 Query: 444 LINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIK 503 +I +GGE V S+ VE + + P V+ AV G P E+WGE V A + + G TE+ +I+ Sbjct: 409 MIISGGENVFSVEVEGAIYQHPDVQETAVIGVPSERWGEAVHAVVVPKAGATPTEQAIIE 468 Query: 504 FCKERLAHFECPKIVEF--GPIPMTATGKMQKYVLRNE 539 C+ +A ++ P+ VE P+P++ GK+ K LR++ Sbjct: 469 HCRGVIADYKLPRSVEIRSEPLPVSGAGKILKTTLRDD 506 Lambda K H 0.319 0.136 0.411 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: 656 Number of extensions: 32 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: 549 Length of database: 513 Length adjustment: 35 Effective length of query: 514 Effective length of database: 478 Effective search space: 245692 Effective search space used: 245692 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: 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