GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pantoea rwandensis LMG 26275

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_084936983.1 HA51_RS22390 SDR family oxidoreductase

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>NCBI__GCF_002095475.1:WP_084936983.1
          Length = 246

 Score =  113 bits (282), Expect = 4e-30
 Identities = 77/249 (30%), Positives = 138/249 (55%), Gaps = 13/249 (5%)

Query: 12  GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGVADVSDCAQ 71
           G RVLI+ A  GIG A A+ F + GANV   D++  A+   +   P       DV+D A 
Sbjct: 5   GKRVLITAAGQGIGLASARYFAEQGANVVGSDINITALQDLQNVTPYR----LDVTDRAA 60

Query: 72  VDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAVP- 130
           +   +++    LG +D+L N AG+   +G +      EW+  +  N+++ F+ ++  +P 
Sbjct: 61  IRAAVEE----LGPVDVLFNCAGVVH-SGNLLACTEQEWQFALDLNVSAMFHMIQAFLPG 115

Query: 131 LLKETSANPGIIAMASVAGRL-GYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAILP 189
           +L +   +  II M+SVA  + G A R  Y+A+K A++G+ +S+A +   + +R NAI P
Sbjct: 116 MLAQKKGS--IINMSSVASSVKGVANRFAYSATKAAVIGLTRSVAADFIADGIRCNAICP 173

Query: 190 GVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQNI 249
           G V+   + + I+ +A++ G   D++   ++ +  + R+ TV ++A +A +LAS A    
Sbjct: 174 GTVDSPSLRQRIATQAQAEGKSEDEVYAAFVARQPIGRIGTVEEIAYLAAYLASDASNYT 233

Query: 250 SGQAISVDG 258
           +G A  +DG
Sbjct: 234 TGTAQVIDG 242


Lambda     K      H
   0.320    0.136    0.391 

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: 140
Number of extensions: 6
Number of successful extensions: 2
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: 263
Length of database: 246
Length adjustment: 24
Effective length of query: 239
Effective length of database: 222
Effective search space:    53058
Effective search space used:    53058
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 (21.8 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