GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcE in Desulfovibrio vulgaris Miyazaki F

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate 8500826 DvMF_1567 D-lactate dehydrogenase (cytochrome) (RefSeq)

Query= reanno::Cup4G11:RR42_RS17310
         (374 letters)



>FitnessBrowser__Miya:8500826
          Length = 474

 Score = 79.3 bits (194), Expect = 2e-19
 Identities = 60/194 (30%), Positives = 90/194 (46%), Gaps = 9/194 (4%)

Query: 11  TLTAFRDAIRHATGTRTPLRLRGGGSKDFYG--QHPQGTLLDTRAYSGIVDYDPPELVIT 68
           T+   +  +R A+    P+  RGGG+    G      G +L     + I   D   LV  
Sbjct: 65  TVEQVQALLRCASAHAIPVIPRGGGTGLAGGCLAVRGGVVLSLERMNRIRAIDTRNLVAE 124

Query: 69  ARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALR 128
              G    ++  A AE+      +P        G D +TIGG VA    GP     G  R
Sbjct: 125 VEAGVISQRVRDAAAEQGLYYPPDPA-------GMDRSTIGGNVATNAGGPACVKYGVTR 177

Query: 129 DFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDA 188
           D+VLG   +   G++L  G +  K V GYD++ L+ GS GTLG+I  ++LK++P+P    
Sbjct: 178 DYVLGVEAVLPDGELLRAGVRTRKGVVGYDMAHLLCGSEGTLGVITALTLKLVPLPPATV 237

Query: 189 TLRFALDEAAALDR 202
           ++  A  + AA  R
Sbjct: 238 SMAVAFPDMAAAMR 251


Lambda     K      H
   0.321    0.136    0.414 

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: 401
Number of extensions: 26
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 374
Length of database: 474
Length adjustment: 32
Effective length of query: 342
Effective length of database: 442
Effective search space:   151164
Effective search space used:   151164
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: 50 (23.9 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