GapMind for catabolism of small carbon sources

 

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

Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate Echvi_2940 Echvi_2940 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= curated2:P37079
         (267 letters)



>FitnessBrowser__Cola:Echvi_2940
          Length = 251

 Score =  113 bits (282), Expect = 5e-30
 Identities = 88/266 (33%), Positives = 134/266 (50%), Gaps = 30/266 (11%)

Query: 7   LKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIH-------GGDRHHNGDNYHFWSTD 59
           +K+  I++TGGASGIGLA+      +G +V  ID           +    G    F   D
Sbjct: 1   MKNKTILITGGASGIGLAMTKRFAEEGGNVYFIDYDQKTGEKVAEELTSKGHRVTFLQGD 60

Query: 60  ISSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNIN 119
           +S   E++QTI +I      ID LVNNAG++    L +           E  F+++  +N
Sbjct: 61  VSQTEEMKQTISSIS---GSIDVLVNNAGISHVGNLENTA---------EEDFDRLYQVN 108

Query: 120 QKGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELG 179
            KG++  S A   +M K++ G I+N++S +   G   +  Y+ TK A+ S T S +++  
Sbjct: 109 VKGIYNCSLASLPKM-KEKGGSIINMASVASTMGLPDRFAYSMTKGAVFSMTLSMARDYV 167

Query: 180 KYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAI--PIGRAGKLSE 237
           +Y IRV  +APG      + TP  +  LA  +N   ++ +E + K A   PIGR GK  E
Sbjct: 168 EYNIRVNSIAPG-----RVHTPFVDGFLA--KNYPGKE-KEMFDKLAATQPIGRMGKPEE 219

Query: 238 VADFVCYLLSARASYITGVTTNIAGG 263
           +A    YL S  AS++TG    I GG
Sbjct: 220 IAAMAVYLSSDEASFLTGGNYPIDGG 245


Lambda     K      H
   0.316    0.133    0.386 

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: 134
Number of extensions: 8
Number of successful extensions: 5
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: 267
Length of database: 251
Length adjustment: 24
Effective length of query: 243
Effective length of database: 227
Effective search space:    55161
Effective search space used:    55161
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 (21.6 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