GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Pedobacter sp. GW460-11-11-14-LB5

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate CA265_RS08355 CA265_RS08355 short-chain dehydrogenase

Query= BRENDA::Q4J9F2
         (255 letters)



>FitnessBrowser__Pedo557:CA265_RS08355
          Length = 254

 Score =  118 bits (295), Expect = 1e-31
 Identities = 87/257 (33%), Positives = 128/257 (49%), Gaps = 13/257 (5%)

Query: 5   SLKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEVLGVKA 64
           SLKNK  +VTG GSGIG+AIA   A   + V  +EL  +     + E++  G        
Sbjct: 3   SLKNKKAVVTGGGSGIGKAIATILAKQGAEVHIIELGTEHAQDTLDEIKTNGGVAFSYGC 62

Query: 65  DVSKKKDVEEFVRRTFETYSRIDVLCNNAGIMDGVTPVAEVSDEL-WERVLAVNLYSAFY 123
           DVS      + V   F     I++L NNAGI       A+ +DE  ++RV+ VN+   + 
Sbjct: 63  DVSD----HQAVAAVFNEIGNINILINNAGIAH--IGKADTTDEADFDRVMRVNVKGVYN 116

Query: 124 SSRAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRA 183
              A IP +   G GVI+N ASIA + G      Y+ AK  +  +T S+A  Y  + IR 
Sbjct: 117 CLHAAIPQIRLSGGGVIINMASIAALIGLPDRFVYSAAKGAVKAITMSVAKDYIGENIRC 176

Query: 184 VAVLPGTVKTNI---GLGSSKPSELG--MRTLTKLMSLSSRLAEPEDIANVIVFLASDEA 238
            ++ P  V T      L  + P  +      L+K   +  R+A+PE++  + ++L SDEA
Sbjct: 177 NSISPARVHTPFVDGFLQKNYPDNIPEMFEKLSKTQPI-GRMAKPEEVGALALYLCSDEA 235

Query: 239 SFVNGDAVVVDGGLTVL 255
           SF+ G    +DGG T L
Sbjct: 236 SFITGCDYPIDGGFTTL 252


Lambda     K      H
   0.318    0.135    0.369 

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: 170
Number of extensions: 12
Number of successful extensions: 4
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: 254
Length adjustment: 24
Effective length of query: 231
Effective length of database: 230
Effective search space:    53130
Effective search space used:    53130
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