GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Phyllobacterium brassicacearum STM 196

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_106711239.1 CU102_RS11545 2-hydroxy-3-oxopropionate reductase

Query= BRENDA::Q9LSV0
         (289 letters)



>NCBI__GCF_003010955.1:WP_106711239.1
          Length = 294

 Score =  148 bits (374), Expect = 1e-40
 Identities = 86/284 (30%), Positives = 148/284 (52%)

Query: 2   EVGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTI 61
           ++GF+GLGIMG  M+ +L   G  V+     ++   EL+++G  + ESP  + +K    I
Sbjct: 3   DIGFIGLGIMGTPMARHLQDAGHDVSTSKFFIAPKQELIDNGLKIVESPKALAEKTDIII 62

Query: 62  AMLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVS 121
            ML D      V+F + GV+  +  GK  IDMS++    + +    +   G  +++ PVS
Sbjct: 63  LMLPDTPEVKDVLFGENGVVFGLKPGKLVIDMSSISPIDTKEFARKVRETGSEYIDAPVS 122

Query: 122 GSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMM 181
           G +  A++  L I+A G ++ F+ ++P F ++GK    +G  G+G   K+   +I+   +
Sbjct: 123 GGEVGAKNASLSIMAGGTQSAFDRALPLFKLMGKNITLVGDCGDGQVTKVANQIIVALTI 182

Query: 182 NAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMR 241
            A SE LVLA K+G +   + + L  G  ++ + +  G  M K ++ P F +   QKD+ 
Sbjct: 183 EAISEALVLASKAGANPARVREALMGGFASSRILELHGDRMIKRTFEPGFRISLHQKDLN 242

Query: 242 LALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVK 285
           LAL       VS+P  A+  E F    + G   LD S ++ A++
Sbjct: 243 LALQSAKTLGVSLPNTASTQELFNSCAANGESGLDHSGLVRALE 286


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: 195
Number of extensions: 6
Number of successful extensions: 1
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: 294
Length adjustment: 26
Effective length of query: 263
Effective length of database: 268
Effective search space:    70484
Effective search space used:    70484
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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