GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-alpha in Photobacterium gaetbulicola Gung47

Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate WP_044623709.1 H744_RS21450 (2Fe-2S)-binding protein

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



>NCBI__GCF_000940995.1:WP_044623709.1
          Length = 162

 Score =  114 bits (285), Expect = 7e-31
 Identities = 58/150 (38%), Positives = 93/150 (62%), Gaps = 5/150 (3%)

Query: 1   MELRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTP 60
           + L +N + YQ+    +T LL ++R DLGLTGTK GC + +CGAC+V+++   V SC+  
Sbjct: 11  LSLSVNGRPYQLSVTGNTRLLDLLRQDLGLTGTKEGCAVGECGACTVVMNSEAVCSCMIL 70

Query: 61  VAGVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKA 120
            A     +I TIE ++ D + +++  ++++    QCG+C  G +M++ ALLK    PS+ 
Sbjct: 71  AAQCQESQIVTIEGLKDDPLAQQLQQSFIKRGGVQCGFCTPGVLMSSWALLKKYQRPSQQ 130

Query: 121 QI-DAAMINLCRCGTY----NAIHAAVDDL 145
           Q+ DA   NLCRC  Y    NAI+A ++D+
Sbjct: 131 QVLDALEGNLCRCTGYQPILNAINAVIEDI 160


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: 98
Number of extensions: 7
Number of successful extensions: 2
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: 162
Length adjustment: 17
Effective length of query: 134
Effective length of database: 145
Effective search space:    19430
Effective search space used:    19430
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: 43 (21.2 bits)

This GapMind analysis is from Sep 24 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