GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Sporolactobacillus vineae SL153

Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate WP_010632451.1 RH97_RS11210 SDR family oxidoreductase

Query= curated2:P37079
         (267 letters)



>NCBI__GCF_000246965.1:WP_010632451.1
          Length = 246

 Score =  129 bits (323), Expect = 8e-35
 Identities = 92/267 (34%), Positives = 146/267 (54%), Gaps = 25/267 (9%)

Query: 1   MNTWLNLKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGD--RHHNGDNYHFWST 58
           MN ++N     +++TGG SGIGLA     +S+GA V ++D    +  RH + D Y     
Sbjct: 1   MNRFVNKS---VLITGGGSGIGLATAKLFISEGAAVSVLDYKVSEALRHLDCDTYQ---A 54

Query: 59  DISSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNI 118
           DI  A +V++ +  +I++  +ID LVN AG+            A   +  E A++++++ 
Sbjct: 55  DIRKADQVEEAVTKVIKKKKQIDILVNTAGIELV---------ASLEQTTEDAWDRVLDT 105

Query: 119 NQKGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKEL 178
           N KGVF +++AV    +K+  GVIVN +S+    GS   + Y A+KAA+ +FTRS + E+
Sbjct: 106 NLKGVFLVTRAVL-PFLKETHGVIVNTASQLAYVGSALFTAYTASKAAILNFTRSLAIEM 164

Query: 179 GKYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAIPIGRAGKLSEV 238
            K GIRV  V PG ++ T L   ++E      +  T++ L   +     PIGR GK  E+
Sbjct: 165 AKDGIRVNSVCPGAVD-TPLLNRQFENGKTGPQG-TIDDLIRMH-----PIGRLGKPEEI 217

Query: 239 ADFVCYLLSARASYITGVTTNIAGGKT 265
           A  + +L S  AS++TG    + GG T
Sbjct: 218 ARPILFLCSDDASFMTGSALVVDGGYT 244


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: 136
Number of extensions: 6
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: 267
Length of database: 246
Length adjustment: 24
Effective length of query: 243
Effective length of database: 222
Effective search space:    53946
Effective search space used:    53946
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 24 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