GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaF in Cupriavidus basilensis 4G11

Align 2-aminomuconate deaminase (EC 3.5.99.5) (characterized)
to candidate RR42_RS05085 RR42_RS05085 2-aminomuconate deaminase

Query= metacyc::MONOMER-13362
         (143 letters)



>FitnessBrowser__Cup4G11:RR42_RS05085
          Length = 140

 Score =  213 bits (543), Expect = 7e-61
 Identities = 104/138 (75%), Positives = 116/138 (84%)

Query: 1   MSTEAKLVEGKALPRGKFPHIKRAGDFLFVSGTSSRRPDNTLVGVEVDAMGTTRLDIVAQ 60
           M+T +K++ GKA PRG+FPH+KRAGDFLFVSGTSSRR DN+  G   DAMG T LDI  Q
Sbjct: 1   MTTLSKVLTGKATPRGRFPHVKRAGDFLFVSGTSSRRADNSFAGASADAMGVTALDIHEQ 60

Query: 61  TTAVIENIRDILGSVGATLDDVVEISTFLVNMNDFAGYNEVYGTYFGYEGPTRTTVAVHQ 120
           T AVI NIR+IL SVG  L D+VEI+TFLVNMNDF GYNEVYG YF Y+GPTRTTVAVHQ
Sbjct: 61  TRAVIGNIREILQSVGCDLSDLVEITTFLVNMNDFGGYNEVYGEYFDYDGPTRTTVAVHQ 120

Query: 121 LPHPHLLIEIKAVAYKPL 138
           LPHPHLLIEIKAVAY+PL
Sbjct: 121 LPHPHLLIEIKAVAYQPL 138


Lambda     K      H
   0.318    0.136    0.388 

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: 132
Number of extensions: 2
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: 143
Length of database: 140
Length adjustment: 16
Effective length of query: 127
Effective length of database: 124
Effective search space:    15748
Effective search space used:    15748
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: 42 (20.8 bits)

This GapMind analysis is from Sep 17 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