GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized)
to candidate WP_279338484.1 HTA01S_RS01495 NAD(P)-dependent oxidoreductase

Query= BRENDA::Q9LSV0
         (289 letters)



>NCBI__GCF_001592305.1:WP_279338484.1
          Length = 301

 Score =  132 bits (333), Expect = 7e-36
 Identities = 85/278 (30%), Positives = 135/278 (48%), Gaps = 2/278 (0%)

Query: 3   VGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIA 62
           +  LG+G+MG  ++  L   G++V+ WNR+  K + L   GA VC++PA+ + +    I 
Sbjct: 15  IAVLGIGMMGWPIARRLCVAGYQVSAWNRSPDKAERLRPFGAQVCDTPAQAVAQADLVIT 74

Query: 63  MLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSG 122
           +L D      V+F + G  E +  G   +DMS++    +      +   G   ++ PVSG
Sbjct: 75  LLEDGKVVEDVLF-RQGTTEGLRPGALVVDMSSIQPRQARDHAARLAAIGVHHLDAPVSG 133

Query: 123 SKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMN 182
               AE   L I+A G  A FE + P F+ LG R  ++G  G+G   KL   MI+G  + 
Sbjct: 134 GTVGAEQATLAIMAGGKPADFERARPVFEHLG-RPTHVGPHGSGQLAKLANQMIVGITIG 192

Query: 183 AFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMRL 242
           A +E L+L +K G     +   +  G   + + +  G  M +  +     +  Q KDMR 
Sbjct: 193 AVAEALLLCEKGGADMAKVRQAITGGFADSRILQVHGQRMVERDFAKRGAISVQLKDMRN 252

Query: 243 ALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAV 280
           A+A   E     P+ A   + F +A   GL DLD SA+
Sbjct: 253 AMATAREIGFEAPITALFEQLFAQAADHGLADLDHSAL 290


Lambda     K      H
   0.317    0.134    0.379 

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: 176
Number of extensions: 7
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: 289
Length of database: 301
Length adjustment: 26
Effective length of query: 263
Effective length of database: 275
Effective search space:    72325
Effective search space used:    72325
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 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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