Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate BPHYT_RS31695 BPHYT_RS31695 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__BFirm:BPHYT_RS31695 Length = 595 Score = 470 bits (1210), Expect = e-137 Identities = 256/571 (44%), Positives = 352/571 (61%), Gaps = 15/571 (2%) Query: 9 RKLRSQEWYGGTSRDV---IYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65 + LRS+ W+ + +Y ++ +L RPVIGI T SD++PCN H E Sbjct: 8 KSLRSRAWFNNSDNPAMTALYLERFMNYGLTLEELKSERPVIGIAQTGSDLSPCNRHHVE 67 Query: 66 LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125 LA++VK G+ +AGG P+E PV E RPTA + RNLA L + EA+ G P DG VL Sbjct: 68 LAQRVKDGIRDAGGIPIEFPVHPIQETVRRPTASLDRNLAYLGLVEALYGYPFDGVVLTT 127 Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185 GCDKTTP++LMGAA+ D+PSIV++GGPMLN +++GER GSGT +W + AG M E Sbjct: 128 GCDKTTPAMLMGAATVDIPSIVLSGGPMLNAWYKGERAGSGTIIWHARSELAAGRMDYDE 187 Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245 FL A+ + S G CN+MGTA +M S+AE LGM+L G IP R MA TGR+IV Sbjct: 188 FLSCVANSAPSIGHCNSMGTALSMNSLAEVLGMSLPGCGTIPAPYRERGQMAYQTGRQIV 247 Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305 Q+V DD++PS ++T++AFENAI +AIG STN H+ AIA +G+DL + DWDR G D Sbjct: 248 QLVHDDVRPSSLLTREAFENAIVVASAIGASTNCPPHINAIARHIGVDLDIRDWDRLGYD 307 Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365 +P +VN MP+GKYL EEF AGG+ V+ L +AG LH D TVSG+T+ D + Sbjct: 308 IPLLVNCMPAGKYLGEEFHRAGGVAAVVHELLKAGKLHGDVQTVSGKTLAQCYGDSPATD 367 Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAVV 414 DVI P L S G VL GNL AV+K S S +GRA+V Sbjct: 368 ADVIRPYASPLKSEAGFAVLGGNLF-DSAVMKTSVISDDFRHKYLENPADPGAFEGRAIV 426 Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474 FE +DY +I+D L+IDENCI+ ++ GP GYPG AEV NM P +++K+G+ + + Sbjct: 427 FEGPEDYHDRIDDPALEIDENCILFIRGTGPVGYPGAAEVVNMIPPSELIKRGVTLLPCV 486 Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAE 534 D R SGT+ +L+ SPE+A+GG LA+++ GD + D+ RR + + ++EL RR E Sbjct: 487 GDGRQSGTSASPSILNASPESAIGGGLAILQTGDRVRFDLTRRRADMLVPEDELDRRRRE 546 Query: 535 WQPNHDLPTSGYAFLHQQHVEGADTGADLDF 565 W+ + + + LH+++V + GA LDF Sbjct: 547 WKAYEFVNQTPWQELHRRYVGQLEDGACLDF 577 Lambda K H 0.318 0.135 0.408 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: 975 Number of extensions: 60 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: 579 Length of database: 595 Length adjustment: 37 Effective length of query: 542 Effective length of database: 558 Effective search space: 302436 Effective search space used: 302436 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 (21.7 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