GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-small in Dethiosulfovibrio salsuginis USBA 82

Align Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8 (characterized)
to candidate WP_085544052.1 B9Y55_RS03880 (2Fe-2S)-binding protein

Query= SwissProt::Q4J6M5
         (163 letters)



>NCBI__GCF_900177735.1:WP_085544052.1
          Length = 157

 Score =  169 bits (429), Expect = 2e-47
 Identities = 84/153 (54%), Positives = 106/153 (69%)

Query: 10  VKVRVRVNGVWYEKYVSPRTLLVDFIRDELGLTGTKVGCDTTTCGACTVIMNGKSVKSCT 69
           + +++ VNG      +S    L+D +RD LGLT  K GC    CGACTV+M+GK+V SCT
Sbjct: 1   MNIQLTVNGQGRTVEISSEMRLLDLLRDVLGLTSVKEGCSEGECGACTVVMDGKAVTSCT 60

Query: 70  VLAAQADGAEITTIEGLSSDSKLHPIQEAFKDNFALQCGFCTAGMIMQTYFFLKEHPNPT 129
           V+A QA+G++I T EGL+   +L  IQ+AF DN A+QCGFCT GMIM T   L    NPT
Sbjct: 61  VMAFQAEGSDILTTEGLARMGELDRIQQAFIDNDAVQCGFCTPGMIMSTKALLMHKENPT 120

Query: 130 EEEVRDGIHGNICRCTGYQNIVKAVLDASKRLR 162
           EEE R  + GNICRCTGY  IVKAV+DA++RLR
Sbjct: 121 EEEARRALEGNICRCTGYIPIVKAVMDAARRLR 153


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: 118
Number of extensions: 3
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: 163
Length of database: 157
Length adjustment: 17
Effective length of query: 146
Effective length of database: 140
Effective search space:    20440
Effective search space used:    20440
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: 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