Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Dsui_2187 Dsui_2187 acyl-CoA synthetase/AMP-acid ligase
Query= BRENDA::A4YDT1 (564 letters) >FitnessBrowser__PS:Dsui_2187 Length = 565 Score = 424 bits (1090), Expect = e-123 Identities = 233/534 (43%), Positives = 328/534 (61%), Gaps = 17/534 (3%) Query: 35 LRRFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLK 94 L FNW D F+ V +G+ +W G E K+S+ ++S SN+V + L+ G+K Sbjct: 33 LTEFNWALDHFD---VMAKGNDKPALWIVEEDGTEHKISFAQMSARSNQVANWLKAQGVK 89 Query: 95 KGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRA 154 +GD + +M W L IK G V++P+ T LT +++ R + +I + Sbjct: 90 RGDRILMMLGNEVPLWETMLGCIKLGAVLIPATTLLTPEDLRDRLDRGQVKHVIIGAAHT 149 Query: 155 SVMEEALGSLKVEKFLIDGKRETWNSLEDE---SSNAEPED-TRGEDVIINYFTSGTTGM 210 + G + + G+ W + +D S+ P+ T+ D ++ YFTSGTT Sbjct: 150 DKFTDLAGDYT--RICVGGEPAGWKAFKDSHTASAEYTPDAATKVSDPLLLYFTSGTTSK 207 Query: 211 PKRVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGIN 270 PK V+HT SYPVG ++T +G++ D+HLN+S+ GWAK AWS FF+P GA + N Sbjct: 208 PKLVLHTHQSYPVGHLSTMYWIGLQPGDIHLNISSPGWAKHAWSCFFAPWNAGACIFLYN 267 Query: 271 YEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFE-RLRSVVSAGEPLNPEV 329 Y + + L +E VT+ CAPPT WR I DL ++ ++R ++ AGEPLNPE+ Sbjct: 268 YS-RFSAKSMLNVLEKYQVTTMCAPPTVWRMMIQEDLAAYKGRLKIRELIGAGEPLNPEI 326 Query: 330 IKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKP 389 I+ ++ +N+TIRD +GQTETTA +GN P +KPGSMG+P P Y + L+D EG E + Sbjct: 327 IEQLQNAWNITIRDGFGQTETTAEIGNTPGQPLKPGSMGRPLPGYQVVLVDSEGNEAAE- 385 Query: 390 YEVGHITVKLNPRPIGLFLGYS-DEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDV 448 G I++KLNPRP+GL +GYS D +K E R+G Y+TGD A DE+GY +VGR DDV Sbjct: 386 ---GEISLKLNPRPLGLMVGYSGDAEKTAEVMRDGVYHTGDVATKDEDGYITYVGRADDV 442 Query: 449 IKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEI 508 K SDYR+ PFE+ES L+EHPAVAEAAVV PD VR + KAY++L+ G PSKELA++I Sbjct: 443 FKASDYRISPFELESVLIEHPAVAEAAVVPSPDPVRLAVPKAYVILRNGEKPSKELAKDI 502 Query: 509 REKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKGEVGQNEY 562 ++ L+PYK R +EF D LPKTISGKIRRVELR E ++R E G+ E+ Sbjct: 503 FAFLRANLAPYKRIRRLEFSD-LPKTISGKIRRVELRANEAKRRNANEKGEWEF 555 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: 791 Number of extensions: 39 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: 565 Length adjustment: 36 Effective length of query: 528 Effective length of database: 529 Effective search space: 279312 Effective search space used: 279312 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 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