GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Pseudomonas simiae WCS417

Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate GFF1410 PS417_07165 dihydrodipicolinate synthase

Query= curated2:B9KW45
         (301 letters)



>FitnessBrowser__WCS417:GFF1410
          Length = 292

 Score = 88.2 bits (217), Expect = 2e-22
 Identities = 76/229 (33%), Positives = 107/229 (46%), Gaps = 13/229 (5%)

Query: 19  VTPFDAENRFAAAPYQKHVEWLSGFDAPVLFAAGGTGEFFSLTPDE-IPAIVRAAKESAG 77
           VTP DA+         K V++        + A G TGE  +L  +E I  I    K  AG
Sbjct: 10  VTPMDAQGHLDWDSLGKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIEFVVKRVAG 69

Query: 78  KTAIVSGCGYG-TEIARGIARSVEAAGGDGILLLPHYLIDAPQEGLYAHVRAVCQATGMG 136
           + A+++G G   T  A  + ++ + AG D  LL+  Y     QEGLY H RA+ +A  + 
Sbjct: 70  RIAVIAGTGANSTREAIELTKNAKKAGADACLLVTPYYNKPTQEGLYQHFRAIAEAVDIP 129

Query: 137 VMVYN---RDNAVLQADTLARLCDDCPNLVGFKDGTGDIGLVRQITAKM-GDRLTYLGGM 192
            ++YN   R    +QA T+ RL    PN++G K+ TGD+   + I A +  D L Y G  
Sbjct: 130 QILYNVPGRTACDMQAATVIRL-STVPNIIGIKEATGDLQRAKDILAGVSSDFLVYSGDD 188

Query: 193 PTA-ELFAEAYLGASFTTYSSAVFNFVPALANKFYAALRAGDRATCESI 240
            TA EL     LG       S   N  P   ++  AA  AGD  T  +I
Sbjct: 189 ATAVELI---LLGGKGNI--SVTANVAPRAMSEMCAAAIAGDAVTARAI 232


Lambda     K      H
   0.321    0.138    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: 195
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: 301
Length of database: 292
Length adjustment: 26
Effective length of query: 275
Effective length of database: 266
Effective search space:    73150
Effective search space used:    73150
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