GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Collimonas arenae Ter10

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_061534238.1 CAter10_RS16300 3-oxoacyl-ACP reductase FabG

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_001584165.1:WP_061534238.1
          Length = 252

 Score =  116 bits (290), Expect = 5e-31
 Identities = 81/250 (32%), Positives = 131/250 (52%), Gaps = 16/250 (6%)

Query: 11  LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAA-ESSLALCEKVAAQTGQAPHFIQ 69
           L  +   + GG  GIGAA+ +  AR GA VA   I++ E +L + + + A  G+A   I+
Sbjct: 10  LAGKVAFIQGGSRGIGAAVAKRLARDGAAVALTYISSGERALQMVKDIEAAGGRA-LAIK 68

Query: 70  ADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFM 129
           AD  + EA++AA  + + K G + +LVNNA       L   + E +D +L++N+R +F  
Sbjct: 69  ADSADAEAIKAAIGQTMTKFGRLDILVNNAGVLAIAPLADFSLEDFDRTLAINVRSVFIA 128

Query: 130 CQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIP-----AYSTAKAGIIGLTKSLAGKLGPD 184
            Q  A HM   GGG I+N  S     N   +P      Y+ +K+ ++GLT+ LA  LGP 
Sbjct: 129 SQEAARHM--GGGGRIINIGS----TNADRMPFAGGGPYAMSKSALVGLTRGLARDLGPR 182

Query: 185 NIRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAM 244
            I +N + PG + T+         +  A ++    + R   A+++ G   +LAS  +A +
Sbjct: 183 GITINNVQPGPVDTDMNP---AGSDFAASLKAMMPVGRYGTAEEVAGFVAYLASPEAAYI 239

Query: 245 TAQAMIIDGG 254
           T  ++ IDGG
Sbjct: 240 TGASLSIDGG 249


Lambda     K      H
   0.321    0.133    0.377 

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: 122
Number of extensions: 9
Number of successful extensions: 4
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: 256
Length of database: 252
Length adjustment: 24
Effective length of query: 232
Effective length of database: 228
Effective search space:    52896
Effective search space used:    52896
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: 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