Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate BPHYT_RS31695 BPHYT_RS31695 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__BFirm:BPHYT_RS31695 Length = 595 Score = 821 bits (2120), Expect = 0.0 Identities = 394/595 (66%), Positives = 478/595 (80%), Gaps = 1/595 (0%) Query: 1 MSDTPERR-LRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTP 59 MS +R+ LRS WFN+ + MTALY+ER+MNYG+T EEL+S RP+IGIAQTGSDL+P Sbjct: 1 MSKNRDRKSLRSRAWFNNSDNPAMTALYLERFMNYGLTLEELKSERPVIGIAQTGSDLSP 60 Query: 60 CNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPL 119 CNRHH+ELAQRVK GIRDAGGIP+EFPVHPI E RRPTA+LDRNLAYLGLVE L+GYP Sbjct: 61 CNRHHVELAQRVKDGIRDAGGIPIEFPVHPIQETVRRPTASLDRNLAYLGLVEALYGYPF 120 Query: 120 DGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAA 179 DGVVLTTGCDKTTPA LM AAT D+P+IVLSGGPML+ +KGE GSGT++WHAR+ +AA Sbjct: 121 DGVVLTTGCDKTTPAMLMGAATVDIPSIVLSGGPMLNAWYKGERAGSGTIIWHARSELAA 180 Query: 180 GEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAY 239 G +DY+ F+ ++PS+GHCN+MGTALSMN+LAE LGMSLPGC +IPAPYRERGQMAY Sbjct: 181 GRMDYDEFLSCVANSAPSIGHCNSMGTALSMNSLAEVLGMSLPGCGTIPAPYRERGQMAY 240 Query: 240 ATGKRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDD 299 TG++I +LV D+RPS ++TR+AFENAI VASA+GAS+NCPPH+ AIARH+GV+L + D Sbjct: 241 QTGRQIVQLVHDDVRPSSLLTREAFENAIVVASAIGASTNCPPHINAIARHIGVDLDIRD 300 Query: 300 WQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIV 359 W R+G D+PLLVNCMPAGKYLGE FHRAGGV +V+HEL KAG+LH D TVSG+T+ + Sbjct: 301 WDRLGYDIPLLVNCMPAGKYLGEEFHRAGGVAAVVHELLKAGKLHGDVQTVSGKTLAQCY 360 Query: 360 SSSLTSNADVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSF 419 S ++ADVI P+ +PLK AGF VL GN FDSA+MK SV+ + FR YL P +F Sbjct: 361 GDSPATDADVIRPYASPLKSEAGFAVLGGNLFDSAVMKTSVISDDFRHKYLENPADPGAF 420 Query: 420 EARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI 479 E RAIVFEGPEDYH RIDDPAL+IDE CIL IRG G VGYPG+AEVVNM PP+ LIK+G+ Sbjct: 421 EGRAIVFEGPEDYHDRIDDPALEIDENCILFIRGTGPVGYPGAAEVVNMIPPSELIKRGV 480 Query: 480 DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEM 539 LPC+GDGRQSGTSASPSILN SPE+A+GGGLA+LQT DR++ DL R ++L+ ++E+ Sbjct: 481 TLLPCVGDGRQSGTSASPSILNASPESAIGGGLAILQTGDRVRFDLTRRRADMLVPEDEL 540 Query: 540 ARRRLEWTPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGEPRHSH 594 RRR EW +QTPWQEL+R+ VGQL G CL+ + + RV G PR +H Sbjct: 541 DRRRREWKAYEFVNQTPWQELHRRYVGQLEDGACLDFSVKYQRVAEVHGVPRDNH 595 Lambda K H 0.319 0.135 0.407 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: 1091 Number of extensions: 43 Number of successful extensions: 1 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: 594 Length of database: 595 Length adjustment: 37 Effective length of query: 557 Effective length of database: 558 Effective search space: 310806 Effective search space used: 310806 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