GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-small in Geotalea uraniireducens Rf4

Align Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8 (characterized)
to candidate WP_011937928.1 GURA_RS05055 molybdopterin cofactor-binding domain-containing protein

Query= SwissProt::Q4J6M5
         (163 letters)



>NCBI__GCF_000016745.1:WP_011937928.1
          Length = 931

 Score =  153 bits (387), Expect = 7e-42
 Identities = 82/156 (52%), Positives = 103/156 (66%), Gaps = 3/156 (1%)

Query: 10  VKVRVRVNGVWYEKYVSPRTLLVDFIRDELGLTGTKVGCDTTTCGACTVIMNGKSVKSCT 69
           +K  + VNG+     V    LL D +R +L LTGTKVGC T  CGAC VIM+GK V+SC 
Sbjct: 2   IKKVMVVNGIERTLIVDQEALLSDVLRKQLHLTGTKVGCGTGQCGACNVIMDGKLVRSCV 61

Query: 70  VLAAQADG-AEITTIEGLSSDSKLHPIQEAFKDNFALQCGFCTAGMIMQTYFFLKEHPNP 128
           V   + +  A+ITTIEG+ +   LHPIQ+AF  + ALQCGFCT G I+ T   L E+PNP
Sbjct: 62  VKMKKVENLAKITTIEGIGTPLNLHPIQKAFIFHGALQCGFCTPGFIVSTKALLDENPNP 121

Query: 129 TEEEVRDGI--HGNICRCTGYQNIVKAVLDASKRLR 162
           T E+VRD    + N CRCTGY  IV AV+DA+K +R
Sbjct: 122 TREDVRDWFQKYRNACRCTGYSMIVDAVMDAAKVMR 157


Lambda     K      H
   0.321    0.136    0.412 

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: 388
Number of extensions: 20
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: 163
Length of database: 931
Length adjustment: 30
Effective length of query: 133
Effective length of database: 901
Effective search space:   119833
Effective search space used:   119833
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 (21.9 bits)
S2: 50 (23.9 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