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) (characterized)
to candidate WP_010631563.1 RH97_RS06600 SDR family oxidoreductase

Query= reanno::Koxy:BWI76_RS01745
         (267 letters)



>NCBI__GCF_000246965.1:WP_010631563.1
          Length = 267

 Score =  299 bits (765), Expect = 5e-86
 Identities = 154/265 (58%), Positives = 191/265 (72%), Gaps = 1/265 (0%)

Query: 3   TWLNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYNFWPTDISS 62
           +WL L++K+I VTGGASGIG  IV  L A GA V + DIH     QS     +   D++S
Sbjct: 4   SWLGLEKKVIVVTGGASGIGKHIVATLAAAGAQVVVCDIHVKTGDQSENGVYYVQMDVTS 63

Query: 63  ASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKG 122
              V   V H+  +FG IDGLVN+AG+N PRLLVD +    +YEL+E  F  M+ +N KG
Sbjct: 64  KESVENMVSHVAAKFGGIDGLVNDAGINLPRLLVDFRGEKPQYELSEKDFNLMIGVNVKG 123

Query: 123 VFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHG 182
           VFL SQAV RQ +K+ SGVIVN+SSE+G+EGS GQS Y+ATK A+N FTRSW+KELG H 
Sbjct: 124 VFLTSQAVVRQFLKKGSGVIVNISSEAGMEGSNGQSVYSATKGAVNGFTRSWAKELGSHH 183

Query: 183 IRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFV 242
           IRVVGVAPGI EKTGL T  Y EALA+TRNI+V +L   YSK +IPLGR G+L ++ + V
Sbjct: 184 IRVVGVAPGINEKTGLTTDTYNEALAYTRNISVSELGTDYSK-AIPLGRPGKLDDIGNLV 242

Query: 243 CYLLSERASYMTGVTTNIAGGKTRG 267
            YLLS+RA+Y+TG T NI GGK+RG
Sbjct: 243 TYLLSDRAAYITGTTVNITGGKSRG 267


Lambda     K      H
   0.315    0.132    0.378 

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: 220
Number of extensions: 10
Number of successful extensions: 2
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: 267
Length adjustment: 25
Effective length of query: 242
Effective length of database: 242
Effective search space:    58564
Effective search space used:    58564
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: 42 (22.0 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