GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Dinoroseobacter shibae DFL-12

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate 3607850 Dshi_1258 short-chain dehydrogenase/reductase SDR (RefSeq)

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



>FitnessBrowser__Dino:3607850
          Length = 247

 Score =  109 bits (273), Expect = 5e-29
 Identities = 83/254 (32%), Positives = 125/254 (49%), Gaps = 25/254 (9%)

Query: 14  VTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSS--GNYNFWPTDISSASEVHKTVD 71
           +TGGA GIG A  + L A+GA + + DI    +  ++  G   +   D+  A+ V    D
Sbjct: 9   ITGGAQGIGYACAEALAAEGARIILADIQDSVQEAAARLGGAGYL-CDMGDAAAVGALFD 67

Query: 72  HIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKGVFLMSQAVA 131
            I    G +  LVNNAG+  P   +D       Y+L  A F+++++IN +GVF+ +Q   
Sbjct: 68  RIEAEHGAVTYLVNNAGIAAPGDFLD-------YDL--ATFDRVLDINLRGVFVATQRAG 118

Query: 132 RQMVKQR-SGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHGIRVVGVAP 190
           R MV     G +VN+SS +          Y A+K  L   T+  +  L  HGIRV  V P
Sbjct: 119 RSMVAHGIKGAVVNMSSINAQVAIPSIPAYCASKGGLMQLTKVAALALAPHGIRVNAVGP 178

Query: 191 GILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFVCYLLSERA 250
           G ++          E +A   N   E +    S+   PL R G   E+A+ V +L S++A
Sbjct: 179 GSIDT---------EMMAGV-NANPEAMNMVLSRT--PLKRVGTAQEIANVVAFLCSDKA 226

Query: 251 SYMTGVTTNIAGGK 264
           SY+TG T  + GG+
Sbjct: 227 SYVTGETIYVDGGR 240


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: 153
Number of extensions: 11
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: 247
Length adjustment: 24
Effective length of query: 243
Effective length of database: 223
Effective search space:    54189
Effective search space used:    54189
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 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