Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF2136 PS417_10895 AMP-dependent synthetase
Query= BRENDA::A4YDT1 (564 letters) >FitnessBrowser__WCS417:GFF2136 Length = 566 Score = 373 bits (957), Expect = e-107 Identities = 223/544 (40%), Positives = 300/544 (55%), Gaps = 36/544 (6%) Query: 35 LRRFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLK 94 L FNW D F+ + G+ +W G E + S+ +L+ SN+V + LR G+ Sbjct: 31 LGEFNWALDYFDAM---AEGNPADALWIVEEDGSEQRYSFQQLAARSNQVANHLRALGVN 87 Query: 95 KGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRA 154 +GD V LM W LA K G V++P+ L +++ R R Sbjct: 88 RGDRVLLMLGNDVALWDTMLAAFKLGAVVIPATALLNPDDLRDRIE------------RG 135 Query: 155 SVMEEALGSLKVEKFL----------IDGKRETWNSLEDESSNAEPEDTRGE----DVII 200 V +G V KF + W + E + +G D ++ Sbjct: 136 QVRHVVVGEAHVHKFAGLAQGCSRICVGSAPAGWVAHNAAFEYPEQFEAQGRTLATDPML 195 Query: 201 NYFTSGTTGMPKRVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPL 260 YFTSGTT PK V+H+ SYPVG ++T +G++ DLHLN+S+ GWAK AWS F+P Sbjct: 196 LYFTSGTTSKPKMVLHSHQSYPVGHLSTMYWIGLQPGDLHLNISSPGWAKHAWSCLFAPW 255 Query: 261 LVGATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFE-RLRSVV 319 GA + I+ + L +E GVTS CAPPT WR I DL +R LR +V Sbjct: 256 NAGACIF-IHNVARFSAPALLSALERYGVTSLCAPPTVWRMLIQEDLASYRPRLSLRELV 314 Query: 320 SAGEPLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLL 379 AGEPLNPE+I+ + + L +RD +GQ+ETTA+VGN P +KPGSMG+P P Y + LL Sbjct: 315 GAGEPLNPEIIEQIQQAWGLPLRDGFGQSETTALVGNTPGQLLKPGSMGRPLPGYQVALL 374 Query: 380 DDEGKEITKPYEVGHITVKLNPRPIGLFLGYSDE-KKNMESFREGYYYTGDKAYFDEEGY 438 D +G P G + + L+ RP+GL L Y D +K E R+GYY TGD A D +GY Sbjct: 375 DPDGI----PGNEGEVALPLDVRPLGLMLCYEDSPEKTAEVMRDGYYRTGDTAQIDADGY 430 Query: 439 FYFVGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGY 498 FVGR DDV K SDYR+ PFE+ESAL+EHPAV E AVV PD +R + KA+++L Sbjct: 431 ITFVGRADDVFKASDYRISPFELESALIEHPAVMEVAVVPSPDPLRLAVPKAFLILAHDE 490 Query: 499 MPSKELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKGEVG 558 S LA+ I + L+PYK R IEFV ELPKTISGKIRRVELR+ E +R+ G Sbjct: 491 PGSAALAQHILAFAREHLAPYKRVRRIEFVTELPKTISGKIRRVELRQMEVLRRQGDTRG 550 Query: 559 QNEY 562 ++E+ Sbjct: 551 EHEH 554 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: 747 Number of extensions: 35 Number of successful extensions: 6 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: 566 Length adjustment: 36 Effective length of query: 528 Effective length of database: 530 Effective search space: 279840 Effective search space used: 279840 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