Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF1013 PGA1_c10300 acetyl-coenzyme A synthetase AcsA
Query= BRENDA::A4YDT1 (564 letters) >FitnessBrowser__Phaeo:GFF1013 Length = 516 Score = 185 bits (469), Expect = 4e-51 Identities = 156/501 (31%), Positives = 240/501 (47%), Gaps = 41/501 (8%) Query: 63 DINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGDVVYLMTKVHPMHWAVFLAVIKGGFV 122 D+ TG + Y EL M + V L + ++ GD V ++ LA+ K G + Sbjct: 43 DLTTGARRDIRYGELRQMVDAVARDLMQR-VQPGDRVGVLLSQSVDCAVAHLAIWKIGAI 101 Query: 123 MVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLIDGKRETWNSLE 182 VP + R D +++D + LGSL + D ++ Sbjct: 102 SVPLFKLFQHDALASRIGDAGLELVLTDGGGTA----QLGSLAQPLLVAD----ILSAST 153 Query: 183 DESSNAEP-EDTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSITTASIVGVRESDLHL 241 +S + P +T E + +TSGTTG K +H + + + GV S HL Sbjct: 154 GQSDHLLPYAETTPETPAVLIYTSGTTGSAKGALHGH------RVLSGHLPGVAISHDHL 207 Query: 242 NLSATG-W--AKFAWSSFFSPLLVGATVVGINY-EGKLD--TRRYLGEVENLG-VTSFCA 294 W A +AW +L+ +G+ +LD T E+ G V + Sbjct: 208 GQPGDCLWTPADWAWIGGLFDVLMPGLALGVPVVAARLDKFTPEACAEIIRQGDVRNVFF 267 Query: 295 PPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDFYGQTE----T 350 PPTA R L + LRSV S GEPL E++ + +TI +FYGQTE Sbjct: 268 PPTALR---LLKAAGQGLDGLRSVASGGEPLGAEMLAWGQRHLGVTINEFYGQTECNMTV 324 Query: 351 TAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRPIGLFLGY 410 ++ V +FP V+PG +G+P P + +LDD G T + G + V+ + L + Sbjct: 325 SSCVADFP---VRPGCIGRPVPGCTVEVLDDTG---TPTKDEGDVAVRRGAASMMLEY-W 377 Query: 411 SDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESALLEHPA 470 + E F + TGD+ ++ + Y FVGR DDVI ++ YR+GP E+E L+ HPA Sbjct: 378 NRPDATAEKFHADWLITGDRGIWEGD-YLRFVGREDDVITSAGYRIGPAEIEDCLMTHPA 436 Query: 471 VAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPRIIEFVDE 530 VA VVG PD +R ++VKAY+VLK G+ PS+ ++++ +K+ L+ Y PR +EF+D Sbjct: 437 VATVGVVGKPDELRTEIVKAYVVLKPGHSPSE---SDLQDYVKSRLAKYSYPREVEFLDA 493 Query: 531 LPKTISGKIRRVELRKREEEK 551 LP T++GK+ R EL+ R K Sbjct: 494 LPMTVTGKVIRKELKARAAGK 514 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: 637 Number of extensions: 30 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: 516 Length adjustment: 35 Effective length of query: 529 Effective length of database: 481 Effective search space: 254449 Effective search space used: 254449 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 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