GapMind for catabolism of small carbon sources

 

Alignments for a candidate for udh in Echinicola vietnamensis KMM 6221, DSM 17526

Align uronate dehydrogenase (EC 1.1.1.203) (characterized)
to candidate Echvi_3804 Echvi_3804 Nucleoside-diphosphate-sugar epimerases

Query= BRENDA::Q888H1
         (275 letters)



>FitnessBrowser__Cola:Echvi_3804
          Length = 357

 Score = 60.1 bits (144), Expect = 7e-14
 Identities = 45/144 (31%), Positives = 71/144 (49%), Gaps = 9/144 (6%)

Query: 60  DLADKDAVHRLVEG--VDAILHFGG-----VSVERPFEEILGANICGVFHIYEAARRHGV 112
           DLADK  +  L+    VD ++H         S+E P +  + ANI G  ++ EA R++ V
Sbjct: 76  DLADKALLFELMAANKVDVVIHLAAQAGVRYSLEHP-DAYVQANIQGFLNVLEACRQYPV 134

Query: 113 KRVIFASSNHVIGFYKQNETIDAHSPRRPDSYYGLSKSYGEDMASFYFDRYGIETVSIRI 172
           K++++ASS+ V G  K       H+   P S Y  +K   E MA  Y   +GI T  +R 
Sbjct: 135 KQLVYASSSSVYGANKAMPFSTEHAVDHPVSLYAATKKSNELMAHTYSHLFGIPTTGLRF 194

Query: 173 GSSFPEPQNRRMMSTWLSFDDLTR 196
            + +  P  R  M+ +L  D + +
Sbjct: 195 FTVY-GPWGRPDMAMFLFADAIRK 217


Lambda     K      H
   0.320    0.137    0.413 

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: 234
Number of extensions: 14
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: 275
Length of database: 357
Length adjustment: 27
Effective length of query: 248
Effective length of database: 330
Effective search space:    81840
Effective search space used:    81840
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: 48 (23.1 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