Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_110205235.1 DNK54_RS01815 AMP-binding protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_003194585.1:WP_110205235.1 Length = 510 Score = 303 bits (777), Expect = 8e-87 Identities = 194/522 (37%), Positives = 270/522 (51%), Gaps = 44/522 (8%) Query: 27 FLERAGKYFKDKTAVVYRDSR-------YTYSTFYDNVMVQASALMRRGFSREDKLSFIS 79 F+ RA + D+ V+ + TY ++ A+ L G D+++ +S Sbjct: 10 FVNRAATVYGDRIGVIDEPDQPAPSLGSLTYREMHERAARMAARLDELGIGVGDRVAVVS 69 Query: 80 RNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQ 139 N L +FFGV G VLVP+NFRL P E+AYII HS ++ + VD +L EV + Sbjct: 70 HNSARLLTAFFGVAGYGRVLVPVNFRLRPDEVAYIIEHSGARVLYVDPELDEALAEVTAE 129 Query: 140 IKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTT 199 + + E+ P +E E +E + + YTSGTT Sbjct: 130 HRFVLGHDEELFAPEGAEPKAWE---------------------PDENATACINYTSGTT 168 Query: 200 GLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCL 259 PKGV HR ++NA+ L + V L TLPMFHA WG +A +G +V L Sbjct: 169 ARPKGVQITHRNIWVNAVTFALHVGLTDRDVILHTLPMFHANGWGMPFAATGLGIKHVVL 228 Query: 260 DKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMK--RNNLKFSNRVHMLVAGAAPAPAT 317 K+D I R V E VT MCAAP V ++ + + + +RV ++VAGA P T Sbjct: 229 RKIDGTEILRRVRDEGVTFMCAAPAVVASVLEAAQSWEGEIPGRDRVRIIVAGAPPPTKT 288 Query: 318 LKAMQ-EIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDV 376 + ++ E+G +YGLTET +I R EWD LP+EE+A R G P + Sbjct: 289 VARVETELGWEFIQIYGLTETSPLLTINRSRAEWDDLPVEERAGKLIRAGQPAI------ 342 Query: 377 FDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIE 436 G + D + GEV+ R + + GY++ PE+TA + GWFH+GD V+ DGY+ Sbjct: 343 ----GVTLATDPE--GEVLARSNVILEGYWQQPEETARALDGGWFHTGDGGVIGEDGYLT 396 Query: 437 IVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKL 496 I DR KD+I TGGE VSSI VE L P V VAV G P EKWGE + A + L G + Sbjct: 397 ISDRKKDVIITGGENVSSIEVEDALFSHPAVAEVAVIGVPSEKWGETIKALVVLAPGAQA 456 Query: 497 TEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537 TE ++I +CKERLA ++ P VEF + TATGK+QK+ LR Sbjct: 457 TEADLIGWCKERLAGYKAPTSVEFRDELARTATGKLQKFKLR 498 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: 679 Number of extensions: 32 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: 549 Length of database: 510 Length adjustment: 35 Effective length of query: 514 Effective length of database: 475 Effective search space: 244150 Effective search space used: 244150 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