GapMind for catabolism of small carbon sources

 

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

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate Echvi_3928 Echvi_3928 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= SwissProt::Q92RN6
         (256 letters)



>FitnessBrowser__Cola:Echvi_3928
          Length = 252

 Score =  111 bits (278), Expect = 1e-29
 Identities = 80/248 (32%), Positives = 122/248 (49%), Gaps = 12/248 (4%)

Query: 11  LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70
           L  +  +VTGG SGIG +  +    +GA+V     +AE         AA+ G     I A
Sbjct: 4   LNGKVAVVTGGNSGIGYSTAKKLKEEGAQVIITGRSAEK----VNVAAAELGVTG--ITA 57

Query: 71  DLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMC 130
           D+  + A+ AA ++  A  G V +L  NA       +   TE+ +D+ + +NL+   F  
Sbjct: 58  DVLELAAIDAAVNQVKADFGHVDILFVNAGIFLPAPIGQTTEDLFDQQMDINLKGAVFTI 117

Query: 131 QAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVNA 190
           +   P ++   GGSI+N SSI     MP    Y  +KA +   T++ A +L P  IRVNA
Sbjct: 118 EKFLPILK--DGGSIINLSSINAYTGMPNTSIYGASKAALNSYTRTAATELAPRKIRVNA 175

Query: 191 ILPGMIVTERQRRLWLTEESI----ARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTA 246
           + PG + T    +  ++E+ +    A MQ R  LKR    +D+     FLASD ++ +T 
Sbjct: 176 VNPGPVYTPIFSKTGMSEDQLNGMAAAMQNRIPLKRYGKPEDIAELVAFLASDRASFITG 235

Query: 247 QAMIIDGG 254
               IDGG
Sbjct: 236 AEYNIDGG 243


Lambda     K      H
   0.321    0.133    0.377 

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: 111
Number of extensions: 6
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: 256
Length of database: 252
Length adjustment: 24
Effective length of query: 232
Effective length of database: 228
Effective search space:    52896
Effective search space used:    52896
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 (21.9 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