GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Pseudomonas putida KT2440

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate PP_3970 PP_3970 putative oxidoreductase, Zn-dependent and NAD(P)-binding

Query= BRENDA::Q86ZV0
         (358 letters)



>FitnessBrowser__Putida:PP_3970
          Length = 400

 Score =  107 bits (268), Expect = 4e-28
 Identities = 87/268 (32%), Positives = 124/268 (46%), Gaps = 33/268 (12%)

Query: 17  GIHKVKFEDRPIPQLRDAHDVLVDVRFTGICGSDVHYWEHGSIGQFVVKDPMVLGHESSG 76
           G + V+ +  P P L+DA D+++ V  T ICGSD+H +  G I +    D  + GHE  G
Sbjct: 8   GANDVRVDSVPDPILQDADDIILRVTATAICGSDLHLYR-GKIPETEQGD--IFGHEFMG 64

Query: 77  VISKVGSAVTTLKVGDHVAMEPGIPCRRCEPCKEGKYNLCEKMAFA--------ATPP-- 126
           ++ +VG  VTTL+VGD V +   I C  C  C++  +  CE               PP  
Sbjct: 65  IVEEVGRDVTTLQVGDRVVIPFVIACGSCFFCQQDLFAACETTNTGRGSIINKKGIPPGA 124

Query: 127 -----------YDGTLAKYYVLPEDFC--YKLPENINLQEAAVMEP-LSVAVHIVKQANV 172
                        G  A Y  +P+     +K+P  +   +   +   L  A   V  A +
Sbjct: 125 ALFGYSHLYGGIPGGQADYVRVPKGNVGPFKVPTTLADDKVLFLSDILPTAWQAVINAEI 184

Query: 173 APGQSVVVFGAGPVGLLCCAVARAFGSPKVIAVDIQKGRLEFAKK-YAATAI-FEPSKVS 230
             G SV ++GAGPVGLL  A AR  G+  V  VD    RL +A++ Y    I FE     
Sbjct: 185 GEGSSVAIYGAGPVGLLSAACARMLGAHTVFMVDDNDYRLAYAQEAYGVIPINFEKDD-- 242

Query: 231 ALENAERIVNENDLGRGADIVIDASGAE 258
             + A+ I+ +    RG D VIDA G E
Sbjct: 243 --DPADSIIRQTPGMRGVDAVIDAVGFE 268


Lambda     K      H
   0.319    0.137    0.406 

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: 398
Number of extensions: 20
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 400
Length adjustment: 30
Effective length of query: 328
Effective length of database: 370
Effective search space:   121360
Effective search space used:   121360
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 (21.7 bits)
S2: 50 (23.9 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