GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Phaeobacter inhibens BS107

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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