GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-alpha in Geotalea uraniireducens Rf4

Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate WP_011937928.1 GURA_RS05055 molybdopterin cofactor-binding domain-containing protein

Query= metacyc::MONOMER-20832
         (151 letters)



>NCBI__GCF_000016745.1:WP_011937928.1
          Length = 931

 Score = 96.7 bits (239), Expect = 9e-25
 Identities = 56/137 (40%), Positives = 75/137 (54%), Gaps = 4/137 (2%)

Query: 15  DADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTPVAGVVG-REITTIE 73
           D +  L  V+R  L LTGTK GCG  QCGAC+V++DG +VRSCV  +  V    +ITTIE
Sbjct: 18  DQEALLSDVLRKQLHLTGTKVGCGTGQCGACNVIMDGKLVRSCVVKMKKVENLAKITTIE 77

Query: 74  AIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKAQID---AAMINLC 130
            I T      +   ++ H   QCG+C  G +++  ALL   P P++  +        N C
Sbjct: 78  GIGTPLNLHPIQKAFIFHGALQCGFCTPGFIVSTKALLDENPNPTREDVRDWFQKYRNAC 137

Query: 131 RCGTYNAIHAAVDDLAK 147
           RC  Y+ I  AV D AK
Sbjct: 138 RCTGYSMIVDAVMDAAK 154


Lambda     K      H
   0.320    0.134    0.410 

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: 357
Number of extensions: 27
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: 151
Length of database: 931
Length adjustment: 29
Effective length of query: 122
Effective length of database: 902
Effective search space:   110044
Effective search space used:   110044
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 (21.8 bits)
S2: 49 (23.5 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