Align 4-hydroxybutyrate-CoA ligase (AMP-forming) (EC 6.2.1.40) (characterized)
to candidate H281DRAFT_01203 H281DRAFT_01203 acetyl-CoA synthetase
Query= BRENDA::A4YDT1 (564 letters) >FitnessBrowser__Burk376:H281DRAFT_01203 Length = 567 Score = 360 bits (923), Expect = e-103 Identities = 215/537 (40%), Positives = 306/537 (56%), Gaps = 20/537 (3%) Query: 35 LRRFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLK 94 L +FNW D F+ I TAL D E +LSY ++S S R+ + LR G+K Sbjct: 33 LEQFNWALDYFDVI--ARDNDNTALWIVDDPASEGLRLSYAQMSERSARMANFLRSVGVK 90 Query: 95 KGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRA 154 +GD V LM W V LA +K G +++P+ T L+ +++ R + ++ DS Sbjct: 91 RGDRVLLMLPNRVELWDVMLAAMKLGAIVLPATTQLSADDVRDRVQIGGANFVVVDSAEL 150 Query: 155 SVMEEALGSLKVEKFLIDGKRETWNSLE---DESSNAEPED-TRGEDVIINYFTSGTTGM 210 S + + + + + R W L D S P+ TR D ++ YFTSGTT Sbjct: 151 SKFDSL--DVPLTRLSVGTPRAGWTDLAAAYDASPQFTPDGVTRAADPLLLYFTSGTTSK 208 Query: 211 PKRVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGIN 270 PK V HT SYPVG ++T +G++ D+H N+S+ GWAK AWS FF+P A V N Sbjct: 209 PKLVEHTHQSYPVGHLSTMYWIGLQPGDIHWNISSPGWAKHAWSCFFAPWNAQACVFVFN 268 Query: 271 YEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVI 330 + + + L + VT+ CAPPT WR + L + +LR +V AGEPLNPE+I Sbjct: 269 F-ARFVPKDTLDVLVRFNVTTVCAPPTVWRMLVQEHLTDYPV-KLREIVGAGEPLNPEII 326 Query: 331 KIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPY 390 + K + +TIRD +GQTETT +GN P V GSMG+P P Y I LLD + + +T+ Sbjct: 327 ERVKHAWGITIRDGFGQTETTCQIGNSPGQPVVAGSMGRPLPGYRIELLDADDQPVTE-- 384 Query: 391 EVGHITVKLNP----RPIGLFLGYSD-EKKNMESFREGYYYTGDKAYFDEEGYFYFVGRG 445 G I + + P RP+GL GY++ E+ ++ R G+Y T D A E+GY+ +VGR Sbjct: 385 --GEIALPIGPDGKQRPLGLMTGYANSEQATAQAMRNGFYRTSDVALRREDGYYVYVGRA 442 Query: 446 DDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELA 505 DDV K+SDYR+ PFE+ES L+EH A+ EAAVV D +R + KA++ ++ GY ELA Sbjct: 443 DDVFKSSDYRLSPFELESVLIEHEAIGEAAVVPSADALRLSVPKAFVTVRHGYQAGPELA 502 Query: 506 EEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKGEVGQNEY 562 + + L+PYK R ++F ELPKTISGKIRRVELR+RE E++ + +EY Sbjct: 503 RAVFAFSREKLAPYKRIRRLQF-SELPKTISGKIRRVELRRREMERQAEPARLPDEY 558 Lambda K H 0.318 0.137 0.402 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: 758 Number of extensions: 38 Number of successful extensions: 7 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: 564 Length of database: 567 Length adjustment: 36 Effective length of query: 528 Effective length of database: 531 Effective search space: 280368 Effective search space used: 280368 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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