GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Desulfovibrio vulgaris Hildenborough

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 207249 DVU1784 oxidoreductase, short-chain dehydrogenase/reductase family

Query= BRENDA::B8H1Z0
         (248 letters)



>MicrobesOnline__882:207249
          Length = 253

 Score = 84.3 bits (207), Expect = 2e-21
 Identities = 60/184 (32%), Positives = 89/184 (48%), Gaps = 17/184 (9%)

Query: 14  VVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKRCDLMNLE 73
           + ITG  +G G      FA +G  +I      E    L AEL      P+    D+ + +
Sbjct: 5   ICITGATAGFGEACARRFAAEGCRLIITGRRKERLEKLAAELGEDRCLPLV--FDVRDRK 62

Query: 74  AIKAVFAEI----GDVDVLVNNAG------NDDRHKLADVTGAYWDERINVNLRHMLFCT 123
           A++A FA +     +VDVL+NNAG         R  L D     W+  I+ NL+ +++CT
Sbjct: 63  AVEAAFAALPEAFANVDVLINNAGLALGLEPAHRASLED-----WETMIDTNLKGLMYCT 117

Query: 124 QAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTC 183
           +A+ PGM +RG G V+N GSI+          Y   KA +   +R L  +L    +RVT 
Sbjct: 118 RALLPGMVERGKGHVVNLGSIAGSYPYPGGNTYGATKAFVMQFSRNLRADLHGTGVRVTN 177

Query: 184 VVPG 187
           + PG
Sbjct: 178 IEPG 181


Lambda     K      H
   0.319    0.137    0.416 

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: 156
Number of extensions: 8
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: 248
Length of database: 253
Length adjustment: 24
Effective length of query: 224
Effective length of database: 229
Effective search space:    51296
Effective search space used:    51296
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 (21.7 bits)
S2: 46 (22.3 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