Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate GFF2847 PGA1_c28930 dihydrodipicolinate synthase DapA
Query= curated2:B1W1P9 (320 letters) >FitnessBrowser__Phaeo:GFF2847 Length = 290 Score = 101 bits (251), Expect = 2e-26 Identities = 88/273 (32%), Positives = 127/273 (46%), Gaps = 16/273 (5%) Query: 21 VTAFGPDGAVDLAVFRAHVRAGIDAGAAAVFACCGTGEFHALTPEEFRLAVGAAVEESAG 80 VT F +G +DL + V ID G+ A+ TGE LT EE + V+ +AG Sbjct: 10 VTPFS-NGELDLDTLKRLVEWHIDQGSTALVPVGTTGESPTLTHEEHETVIAEVVKIAAG 68 Query: 81 QVPVLAGAG-YGTALAVQYARAAEEAGADGLLAMPPYLVVADQQGLLHHYAALAAATGLE 139 +VPV+AGAG T ++ + A E GAD L + PY Q+GL+ H+ L + Sbjct: 69 RVPVIAGAGSNNTVEGKRFVQFAAEVGADAALVVTPYYNKPTQRGLIAHFTELHNCADIP 128 Query: 140 TIVYQ---RDNAVFTPETVVALARTPGVIGLKDGHGDLDLMQRIVSAVRTHRPGGDFLYF 196 ++Y R TP T+ LA+ +IG+KD GD+ + + ++ G DF+ Sbjct: 129 IVIYNIPGRSVIDMTPATMGELAKLERIIGVKDATGDIARVSQQRASC-----GADFIQL 183 Query: 197 NGLPTAELTGPAYRGIGVTLYSSAVFAFAPDIALAFYRALDSGDDALVDGLLDHFYRPLV 256 +G L A+ G+G ++ V AP + F A +GD AL D PL Sbjct: 184 SGEDATALGFNAHGGVGCISVTANV---APKLCAEFQAATLAGDYALALEYQDKL-MPLH 239 Query: 257 ELRAQGRGYAVSLVKAGVRLQGLDVGEVRTPLT 289 E G A + K G+ GL EVR PLT Sbjct: 240 EAIFIEPGLAGA--KYGLSKLGLCSEEVRLPLT 270 Lambda K H 0.322 0.138 0.405 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: 197 Number of extensions: 22 Number of successful extensions: 3 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: 320 Length of database: 290 Length adjustment: 27 Effective length of query: 293 Effective length of database: 263 Effective search space: 77059 Effective search space used: 77059 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 (21.9 bits) S2: 48 (23.1 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