Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Pf6N2E2_1143 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases
Query= BRENDA::A4YDT1 (564 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1143 Length = 557 Score = 252 bits (644), Expect = 2e-71 Identities = 182/516 (35%), Positives = 260/516 (50%), Gaps = 29/516 (5%) Query: 56 KTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGDVVYLMTKVHPMHWAVFLA 115 + AL W G +A +Y +L + R + LR G+ KGD V + V LA Sbjct: 46 RIALFWEG-RDGSDATWTYRDLQDNAARFANFLRAQGVGKGDKVAGLLPRTAELLIVVLA 104 Query: 116 VIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKF------ 169 + G V P T +++R +++D++ + E G + Sbjct: 105 TWRIGAVYQPLFTAFGPKAIEHRVGSSGARIVVTDAVNRPKLNEIAGCPTIVTVGGEKGQ 164 Query: 170 -LIDGKRETWNSLEDESSNAEPEDTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSIT- 227 ++ G W + + SS EP GED + FTSGTTG K A+S P+ +I Sbjct: 165 GIVRGDYSFWAEVANHSSQCEPLMLTGEDPFLLMFTSGTTGPAK-----ALSVPLKAIVA 219 Query: 228 ----TASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGE 283 T V +R D N++ GWA + PL +G + Y+G Sbjct: 220 FQSYTRDAVDLRPEDAFWNVADPGWAYGIYFGVTGPLAMGHPITF--YDGPFTLESTCRV 277 Query: 284 VENLGVTSFCAPPTAWRQFITLDLDQFRFE---RLRSVVSAGEPLNPEVIKIWKDKFNLT 340 + G+T+ PTA+R I +QF +LR V SAGEPLNPEVI+ + D N+ Sbjct: 278 INKYGITNLTGSPTAYRLLIAGG-EQFARSIKGKLRIVSSAGEPLNPEVIRWFADNLNVV 336 Query: 341 IRDFYGQTETTAMVGNFPFLK--VKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVK 398 I D YGQTE ++ N L+ V G+ G P + I +LD+ +E+ + G + V Sbjct: 337 IHDHYGQTELGMVLCNHHGLEHPVHLGAAGFASPGHRIVVLDENQRELGVG-QPGILAVD 395 Query: 399 LNPRPIGLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGP 458 + P+ F GY E ++F YY +GD + +G FVGR DDVI TS YRVGP Sbjct: 396 RSQSPMCWFAGY--EGAPTKAFVGDYYLSGDTVELNLDGSISFVGRSDDVITTSGYRVGP 453 Query: 459 FEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSP 518 F+VESAL+EHPAV EAAV+G PD R +LVKA++VL Y S ELAEE+R ++ L+ Sbjct: 454 FDVESALIEHPAVVEAAVIGKPDPERTELVKAFVVLSTQYRASPELAEELRLHVRKRLAA 513 Query: 519 YKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKK 554 + PR IEFV +LPKT SGK++R LR +E K ++ Sbjct: 514 HAYPREIEFVSDLPKTPSGKLQRFILRNQEIAKAQE 549 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: 679 Number of extensions: 33 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: 564 Length of database: 557 Length adjustment: 36 Effective length of query: 528 Effective length of database: 521 Effective search space: 275088 Effective search space used: 275088 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 Aug 03 2021. The underlying query database was built on Aug 03 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