GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Desulfovibrio vulgaris Hildenborough

Align BadH (characterized)
to candidate 208656 DVU3137 oxidoreductase, short chain dehydrogenase/reductase family

Query= metacyc::MONOMER-893
         (255 letters)



>MicrobesOnline__882:208656
          Length = 258

 Score =  134 bits (338), Expect = 1e-36
 Identities = 85/248 (34%), Positives = 120/248 (48%), Gaps = 7/248 (2%)

Query: 4   LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63
           +Q++  ++TG   GIG      FA  GA++ + DL+ +  E    A R  G        D
Sbjct: 5   MQDRRVMVTGSAKGIGKGIAEAFASRGARVFLADLSAEHVEATGNAFRAKGYNVAWGVAD 64

Query: 64  IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123
           + D+ SV+   +     LG +D+L  NAG     P       +W+ ++ +NL G      
Sbjct: 65  VKDKASVEQVASKAVEQLGGLDVLCANAGIFPAAPLETMTEEQWDTVLDVNLKGMFLTVQ 124

Query: 124 AVLPGMVERRHGRIVNIASDAARV-GSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182
           A +P + E   GRIV  +S    V G  G   Y A K G + F +T A E AR+GIT+N 
Sbjct: 125 ACIPALKESTSGRIVVTSSITGPVTGYPGWCHYGASKAGQMGFIRTAAIELARYGITINA 184

Query: 183 VCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITG 242
           V PG   T  L +        E  + +   +IPL RLG P D+A A  F  S DAG+ITG
Sbjct: 185 VQPGNIATEGLQE------QGEAYMASMASSIPLRRLGLPADIAAAAVFLASPDAGYITG 238

Query: 243 QVLSVSGG 250
           Q + V GG
Sbjct: 239 QGIIVDGG 246


Lambda     K      H
   0.318    0.135    0.398 

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: 161
Number of extensions: 5
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: 255
Length of database: 258
Length adjustment: 24
Effective length of query: 231
Effective length of database: 234
Effective search space:    54054
Effective search space used:    54054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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