GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Collimonas arenae Ter10

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_061532684.1 CAter10_RS05885 SDR family oxidoreductase

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



>NCBI__GCF_001584165.1:WP_061532684.1
          Length = 254

 Score =  120 bits (300), Expect = 4e-32
 Identities = 80/251 (31%), Positives = 131/251 (52%), Gaps = 10/251 (3%)

Query: 12  GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESAL----AVFRDKYPGTVATRADVS 67
           G R+L++    GIG   A A+   GAQV   D++++AL    A  RD          DV+
Sbjct: 5   GKRILVTAAGQGIGRASALAFAREGAQVLATDINQAALDETAAAARDGGHPITTRLLDVT 64

Query: 68  DAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHH 127
           D   + A+     +   G DVL N AG     G I   S+ +W+ + +IN+++ YR    
Sbjct: 65  DDRAVAAL----AQSGSGFDVLFNCAGYVHH-GSILDCSEEDWRFSWDINVSSMYRLIRA 119

Query: 128 AVPMLKESSHGHLLHIASVAGRL-GYAWRTPYAATKWAIVGLMKSLASELGESDIRVNAL 186
            +P +     G +++++S A  + G   R  Y  TK A++GL K++A++     IR NA+
Sbjct: 120 LLPGMVAQGGGSIINMSSAASSVKGVPNRFVYGTTKAAVIGLTKAVAADFVAKGIRCNAI 179

Query: 187 LPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAAR 246
            PG VE P ++  IR +A Q GV  AE++  ++ +  + R+   E++AA+AL+L S  + 
Sbjct: 180 CPGTVESPSLEVRIREQARQQGVDIAEVQAAFVARQPMGRIGKTEEIAALALYLASDESS 239

Query: 247 NVTGQAISVDG 257
             TG    +DG
Sbjct: 240 FTTGAIHLIDG 250


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: 139
Number of extensions: 5
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: 254
Length adjustment: 24
Effective length of query: 238
Effective length of database: 230
Effective search space:    54740
Effective search space used:    54740
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 24 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