GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Nocardiopsis gilva YIM 90087

Align glyoxylate reductase (EC 1.1.1.26); glycerate dehydrogenase (EC 1.1.1.29); hydroxypyruvate reductase (EC 1.1.1.81) (characterized)
to candidate WP_017618255.1 CDO52_RS17960 2-hydroxyacid dehydrogenase

Query= BRENDA::Q9C9W5
         (386 letters)



>NCBI__GCF_002263495.1:WP_017618255.1
          Length = 352

 Score =  107 bits (267), Expect = 5e-28
 Identities = 78/258 (30%), Positives = 123/258 (47%), Gaps = 20/258 (7%)

Query: 99  NVDVEAANKYGIAVGNTPGVLTETTAELAASLSLAAARRIVEADEFMRGGLYEG-WLPHL 157
           NV+VEAA ++G+AV   PG     TAE    L L+AARRI +    +R G + G +  + 
Sbjct: 100 NVNVEAATRHGVAVCYAPGRNAAATAEHTLGLILSAARRIPDLHADLRHGRWRGDFYDYD 159

Query: 158 FVGNLLKGQTVGVIGAGRIGSAYARMMVEGFKMNLIYFDLYQSTRLEKFVTAYGQFLKAN 217
             G  ++G TVG++G G IG   A  +       L++         + +VT         
Sbjct: 160 NCGVEIEGATVGLVGYGAIGRRVAAALAALGARVLVH---------DPYVT--------- 201

Query: 218 GEQPVTWKRASSMEEVLREADLISLHPVLDKTTYHLVNKERLAMMKKEAILVNCSRGPVI 277
           G+         +++ +L EA ++SLH  L   T  L+    +A M+  A+LVNC+RG ++
Sbjct: 202 GDALAGTATKVALDHLLAEAHIVSLHARLTPETTGLLGPSEIAAMRPGAVLVNCARGGLV 261

Query: 278 DEAALVEHLKENPMFRVGLDVFEEEPFMKPG-LADTKNAIVVPHIASASKWTREGMATLA 336
           D  A+ + L+   +     DV+ EEP      L    N ++ PH+A AS+      A + 
Sbjct: 262 DYDAVCDALERGHLHAAAFDVYAEEPVPADSRLLSAPNVVLTPHVAGASRQVAHKAADIV 321

Query: 337 ALNVLGRVKGYPIWHDPN 354
           A  V   + G P+ H  N
Sbjct: 322 AAEVGRFLTGRPLAHCAN 339


Lambda     K      H
   0.318    0.135    0.399 

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: 282
Number of extensions: 10
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: 386
Length of database: 352
Length adjustment: 30
Effective length of query: 356
Effective length of database: 322
Effective search space:   114632
Effective search space used:   114632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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