GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Kocuria flava HO-9041

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_058858690.1 AS188_RS09780 beta-ketoacyl-ACP reductase

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



>NCBI__GCF_001482365.1:WP_058858690.1
          Length = 242

 Score =  117 bits (292), Expect = 3e-31
 Identities = 76/245 (31%), Positives = 121/245 (49%), Gaps = 19/245 (7%)

Query: 15  VLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDAAQIEA 74
           VL++GG  GIG  +A A+ +AG  V V   S  A         G +A +ADV+DAA I+A
Sbjct: 13  VLVTGGNRGIGRAIAQAFKDAGDNVAVTHRSGEAPE-------GFLAVQADVTDAASIDA 65

Query: 75  VFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPMLKE 134
            FK      G ++V+V NAGI   T  +  + + ++Q  ++ NLT  +R    A      
Sbjct: 66  AFKAVEAEFGPVEVVVANAGITRDTLLL-RMKEQDFQDVVDTNLTGAFRVVQRAAKGFMR 124

Query: 135 SSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIVEGP 194
              G ++ I+SV G  G   +  YAA+K  +VG+ +S+  ELG  ++  N + PG +   
Sbjct: 125 LKRGRVVLISSVVGLYGSPGQVNYAASKAGLVGMARSITRELGGRNVTANVVAPGFI--- 181

Query: 195 RMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQAIS 254
                     E       + +++YL  I   R    E+VAA+  ++ S  A+ ++G  I 
Sbjct: 182 --------NTEMTAALPEDTQRDYLASIPAGRFAEPEEVAAVVRWIASDEAKYISGAVIP 233

Query: 255 VDGNV 259
           VDG +
Sbjct: 234 VDGGL 238


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: 161
Number of extensions: 10
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: 262
Length of database: 242
Length adjustment: 24
Effective length of query: 238
Effective length of database: 218
Effective search space:    51884
Effective search space used:    51884
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: 46 (22.3 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