Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate 3606718 Dshi_0149 dihydrodipicolinate synthase (RefSeq)
Query= curated2:B1W1P9 (320 letters) >FitnessBrowser__Dino:3606718 Length = 291 Score = 119 bits (299), Expect = 7e-32 Identities = 97/283 (34%), Positives = 136/283 (48%), Gaps = 26/283 (9%) Query: 27 DGAVDLAVFRAHVRAGIDAGAAAVFACCGTGEFHALTPEEFRLAVGAAVEESAGQVPVLA 86 DGAVD A A V I G+ + TGE L+ EE V +E +AG+VPV+A Sbjct: 15 DGAVDFATLEALVEWQIAEGSHGLVPVGTTGESPTLSHEEHEAVVAKVIEVAAGRVPVIA 74 Query: 87 GAGYG-TALAVQYARAAEEAGADGLLAMPPYLVVADQQGLLHHYAALAAATGLETIVYQ- 144 GAG T AV++ R A++AGADG L + PY Q G++ HY ALA A + ++Y Sbjct: 75 GAGSNNTVEAVRFVRHAKDAGADGALVVTPYYNKPTQGGMIAHYTALAEAADIPIVIYNI 134 Query: 145 --RDNAVFTPETVVALARTPGVIGLKDGHGDLDLMQRIVSAVRTHRPGGDFLYFNGLPTA 202 R TP T+ ALA P ++G+KD GDL + + A G +F+ +G Sbjct: 135 PGRSVVDMTPATMAALAALPTIVGVKDATGDLARVSQTRMAC-----GPEFIQLSGEDAT 189 Query: 203 ELTGPAYRGIGVTLYSSAVFAFAPDIALAFYRALDSGDD----ALVDGLLDHFYRPLVEL 258 L A+ G+G ++ V AP + F A +GD AL D L+ VE Sbjct: 190 ALGFNAHGGVGCISVTANV---APALCAQFQEATLAGDFATALALQDKLMPLHEAIFVEP 246 Query: 259 RAQGRGYAVSLVKAGVRLQGLDVGEVRTP---LTEPTAAHVKD 298 G YA+SL+ G +VR P L++ T +KD Sbjct: 247 GLVGAKYALSLL-------GKCSEDVRLPLLGLSDGTKVLIKD 282 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: 202 Number of extensions: 15 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: 291 Length adjustment: 27 Effective length of query: 293 Effective length of database: 264 Effective search space: 77352 Effective search space used: 77352 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