GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Erythrobacter gangjinensis K7-2

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_047005555.1 AAW01_RS01220 3-oxoacyl-[acyl-carrier-protein] reductase

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



>NCBI__GCF_001010925.1:WP_047005555.1
          Length = 254

 Score =  109 bits (273), Expect = 5e-29
 Identities = 79/263 (30%), Positives = 129/263 (49%), Gaps = 37/263 (14%)

Query: 14  VTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQS-------------SGNYNFWPTDI 60
           VTG + GIG +I   L  QGA + +   +G DK ++             +G++     ++
Sbjct: 11  VTGASGGIGSSIAYALAKQGARLALSGSNG-DKLRAFREQLIADCGSPEAGDHVEITCNL 69

Query: 61  SSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQ 120
           S  ++V + +   I   G +D LVNNAG+    L +          + +  +E+++ +N 
Sbjct: 70  SDTTQVEELIPAAIDTLGGLDILVNNAGITRDNLAM---------RMKDEEWEQVIQVNL 120

Query: 121 KGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGK 180
           + VF + +A AR M+K R G I+N++S  G  G+ GQ  Y A KA +   ++S ++EL  
Sbjct: 121 EAVFRLMRASARPMMKARFGRIINITSVVGTTGNPGQMNYCAAKAGVVGMSKSLAQELAA 180

Query: 181 HGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVAD 240
            GI V  VAPG +           EAL        +  ++      IP+GR G   ++  
Sbjct: 181 RGITVNCVAPGFIRSA------MTEAL--------DDKQKDAINGRIPMGRMGEGGDIGA 226

Query: 241 FVCYLLSERASYMTGVTTNIAGG 263
            V YL S+ ASY+TG T ++ GG
Sbjct: 227 AVAYLASKEASYVTGQTLHVNGG 249


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: 164
Number of extensions: 7
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: 254
Length adjustment: 24
Effective length of query: 243
Effective length of database: 230
Effective search space:    55890
Effective search space used:    55890
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.

Links

Downloads

Related tools

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