Align 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening) (EC 3.7.1.22) (characterized)
to candidate Pf1N1B4_4279 Epi-inositol hydrolase (EC 3.7.1.-)
Query= BRENDA::P42415 (637 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4279 Length = 643 Score = 691 bits (1784), Expect = 0.0 Identities = 352/639 (55%), Positives = 450/639 (70%), Gaps = 7/639 (1%) Query: 6 RLTTAQALIKFLNQQYIHVDGKEEPFVEGIFTIFGHGNVLGIGQALEQDAGHLKVYQGKN 65 RLT AQAL+KFL+ QYI VDG + FV GIFTIFGHGNVLG+GQALEQD+G L V+QG+N Sbjct: 5 RLTMAQALVKFLDNQYIEVDGVQSKFVAGIFTIFGHGNVLGLGQALEQDSGDLIVHQGRN 64 Query: 66 EQGMAHAAMAYSKQMLRRKIYAVSTSVGPGAANLVAAAGTALANNIPVLLIPADTFATRQ 125 EQGMAHAA+ ++KQ LRRKIYA S+SVGPGAAN++ AA TA AN IP+LL+P D +A RQ Sbjct: 65 EQGMAHAAIGFAKQHLRRKIYACSSSVGPGAANMLTAAATATANRIPLLLLPGDVYACRQ 124 Query: 126 PDPVLQQMEQEYSAAITTNDALKPVSRYWDRITRPEQLMSSLLRAFEVMTDPAKAGPATI 185 PDPVLQQ+EQ + +I+TNDA K VS+YWDRI RPEQLM++ + A V+TDPA+ G T+ Sbjct: 125 PDPVLQQIEQFHDLSISTNDAFKAVSKYWDRINRPEQLMTAAIHAMRVLTDPAETGAVTL 184 Query: 186 CISQDVEGEAYDFDESFFVKRVHYIDRMQPSERELQGAAELIKSSKKPVILVGGGAKYSG 245 + QDV+ EAYD+ + F KRVH I+R +E L A L K KP+I+ GGG KYSG Sbjct: 185 ALPQDVQAEAYDYPDYFLQKRVHRIERRPATEAMLGDAVALFKGKHKPLIICGGGVKYSG 244 Query: 246 ARDELVAISEAYNIPLVETQAGKSTVEADFANNLGGMGITGTLAANKAARQADLIIGIGT 305 A L A +E ++IP ETQAGKS V + N+GG+G TG LAAN A+ ADLIIG+GT Sbjct: 245 ANAALQAFAERFDIPFAETQAGKSAVVSSHPLNVGGIGETGCLAANLLAKDADLIIGVGT 304 Query: 306 RYTDFATSSKTAFDFDKAKFLNINVSRMQAYKLDAFQVVADAKVTLGKLHGLLEGYESEF 365 RY+DF T+SK+ F +FLN+N+S A KLD Q++ADAK L L +L Y S + Sbjct: 305 RYSDFTTASKSLFKHPDVQFLNLNISPCDALKLDGVQLLADAKTGLQALAEVLGDYRSSW 364 Query: 366 GTTIRELKDEWLAERERLSKVTFKREAFDPEIKNHFSQEVLNEYADALNTELPQTTALLT 425 G R+ K + E +R+ +V ++ + F PEI +H VL E+ + + L Q+ L Sbjct: 365 GDQPRQAKTQLDEEVDRIYQVEYQAKDFVPEINDHLDPAVLREFIELTGSCLTQSRVLGV 424 Query: 426 INETIPEDSVIICSAGSLPGDLQRLWHSNVPNTYHLEYGYSCMGYEVSGTLGLKLAHPDR 485 +NET+ +D+VI+ +AGSLPGDLQR W S NTYH+EYGYSCMGYEV+ LG+KLA P+R Sbjct: 425 LNETLADDAVIVAAAGSLPGDLQRSWRSKGVNTYHVEYGYSCMGYEVNAALGVKLAEPER 484 Query: 486 EVYSIVGDGSFLMLHSELITAIQYNKKINVLLFDNSGFGCINNLQMDHGSGSYYCEFRTD 545 EVY++VGDGS++MLHSEL T+IQ +KINV+L DN FGCINNLQM+HG S+ EFR Sbjct: 485 EVYALVGDGSYMMLHSELATSIQERRKINVVLLDNMTFGCINNLQMEHGMDSFGTEFRFR 544 Query: 546 -------DNQILNVDYAKVAEGYGAKTYRANTVEELKAALEDAKKQDVSTLIEMKVLPKT 598 D + VD+A A YG KTY+ NTVE+L+ AL DA+ Q VSTLI++KVLPKT Sbjct: 545 NPETGKLDGGFVPVDFAMSAAAYGCKTYKVNTVEQLQDALADARLQTVSTLIDIKVLPKT 604 Query: 599 MTDGYDSWWHVGVAEVSEQESVQKAYEAKEKKLESAKQY 637 M Y SWW VGVA+VS + ++L A+QY Sbjct: 605 MIHKYLSWWRVGVAQVSTSARTDAVAKTLNERLAKARQY 643 Lambda K H 0.316 0.132 0.375 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: 1001 Number of extensions: 29 Number of successful extensions: 2 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: 637 Length of database: 643 Length adjustment: 38 Effective length of query: 599 Effective length of database: 605 Effective search space: 362395 Effective search space used: 362395 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 54 (25.4 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