Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate BPHYT_RS31695 BPHYT_RS31695 dihydroxy-acid dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__BFirm:BPHYT_RS31695 Length = 595 Score = 476 bits (1224), Expect = e-138 Identities = 265/594 (44%), Positives = 372/594 (62%), Gaps = 23/594 (3%) Query: 5 NQTKKPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEFDG-RPVIGICNTWSELTPCNA 61 N+ +K LRS+AWF D L+ N G+ +E RPVIGI T S+L+PCN Sbjct: 4 NRDRKSLRSRAWFNNSDNPAMTALYLERFMNYGLTLEELKSERPVIGIAQTGSDLSPCNR 63 Query: 62 HFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGV 121 H ELA+ VK G+ +AGG+P+EFPV + ET RPTA L RNLA + + E++ G P DGV Sbjct: 64 HHVELAQRVKDGIRDAGGIPIEFPVHPIQETVRRPTASLDRNLAYLGLVEALYGYPFDGV 123 Query: 122 ILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTM 181 +L GCDKTTPA+LMGAA+ ++P++ +SGGPMLN ++G+ GSGT +W E+ AG M Sbjct: 124 VLTTGCDKTTPAMLMGAATVDIPSIVLSGGPMLNAWYKGERAGSGTIIWHARSELAAGRM 183 Query: 182 TQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAG 241 +EF + S GHC +MGTA +M S+ E LGM LP IPA R +A+ G Sbjct: 184 DYDEFLSCVANSAPSIGHCNSMGTALSMNSLAEVLGMSLPGCGTIPAPYRERGQMAYQTG 243 Query: 242 RRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE- 300 R+IV +V +D+ +LTR+AFENAI +AIG STN H+ A+A+ IGV+L + DW+ Sbjct: 244 RQIVQLVHDDVRPSSLLTREAFENAIVVASAIGASTNCPPHINAIARHIGVDLDIRDWDR 303 Query: 301 LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNA 360 LG ++P LVN P+G+YL E+F+ AGG+ AV+ +L + G LH + TV+GKTL ++ Sbjct: 304 LGYDIPLLVNCMPAGKYLGEEFHRAGGVAAVVHELLKAGKLHGDVQTVSGKTLAQCYGDS 363 Query: 361 ANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHR------------ 408 D VI +A P K +AG AVL GNL + AV+K S + +H+ Sbjct: 364 PATDADVIRPYASPLKSEAGFAVLGGNLF-DSAVMKTSVISDD-FRHKYLENPADPGAFE 421 Query: 409 GRAVVFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGIT 468 GRA+VFE E+ H +IDD +L+IDE+CI+ ++G GP GYPG AEV NM P +++++G+T Sbjct: 422 GRAIVFEGPEDYHDRIDDPALEIDENCILFIRGTGPVGYPGAAEVVNMIPPSELIKRGVT 481 Query: 469 DMVRISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELA 528 + + DGR SGT+ +L+ SPE+A GG LA +QTGD + D+ RR + V ++EL Sbjct: 482 LLPCVGDGRQSGTSASPSILNASPESAIGGGLAILQTGDRVRFDLTRRRADMLVPEDELD 541 Query: 529 RRRAAWQAPE-APKRGYYKLYVEHVLQADQGADLDFLVGSSGAP----VPRDSH 577 RRR W+A E + + +L+ +V Q + GA LDF V VPRD+H Sbjct: 542 RRRREWKAYEFVNQTPWQELHRRYVGQLEDGACLDFSVKYQRVAEVHGVPRDNH 595 Lambda K H 0.318 0.135 0.401 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: 912 Number of extensions: 47 Number of successful extensions: 4 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: 577 Length of database: 595 Length adjustment: 37 Effective length of query: 540 Effective length of database: 558 Effective search space: 301320 Effective search space used: 301320 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