GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pseudomonas putida KT2440

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate PP_1946 PP_1946 Oxidoreductase, short chain dehydrogenase/reductase family

Query= metacyc::MONOMER-20835
         (262 letters)



>FitnessBrowser__Putida:PP_1946
          Length = 262

 Score =  125 bits (313), Expect = 1e-33
 Identities = 80/254 (31%), Positives = 129/254 (50%), Gaps = 15/254 (5%)

Query: 10  YPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVS--ESALAVFRDKYPGTVAT--RAD 65
           + G  VL++G  +GIG   A A+ ++GA V V D+S       V   K  G  AT    D
Sbjct: 7   FSGKVVLVTGAGSGIGRATALAFAQSGASVAVADISTDHGLKTVELVKAEGGEATFFHVD 66

Query: 66  VSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFA 125
           V     ++++      H GGLD+  NNAGI      +  +    W+  I++NL++ +   
Sbjct: 67  VGSEPSVQSMLAGVVAHYGGLDIAHNNAGIEANIVPLAELDSDNWRRVIDVNLSSVFYCL 126

Query: 126 HHAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185
              +P++ +   G +++ AS +G +G    + Y ATK  +VGL K+ A +    +IR+NA
Sbjct: 127 KGEIPLMLKRGGGAIVNTASASGLIGGYRLSGYTATKHGVVGLTKAAAIDYANQNIRINA 186

Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAA 245
           + PG V+ P +            +P+  MR   L    + R+ TAE++A   L+LCS  A
Sbjct: 187 VCPGPVDSPFL----------ADMPQ-PMRDRLLFGTPIGRLATAEEIARSVLWLCSDDA 235

Query: 246 RNVTGQAISVDGNV 259
           + V G ++SVDG V
Sbjct: 236 KYVVGHSMSVDGGV 249


Lambda     K      H
   0.318    0.133    0.383 

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: 184
Number of extensions: 14
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: 262
Length of database: 262
Length adjustment: 25
Effective length of query: 237
Effective length of database: 237
Effective search space:    56169
Effective search space used:    56169
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: 47 (22.7 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