GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Azospirillum brasilense Sp245

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate AZOBR_RS29790 AZOBR_RS29790 3-ketoacyl-ACP reductase

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



>FitnessBrowser__azobra:AZOBR_RS29790
          Length = 250

 Score =  125 bits (313), Expect = 1e-33
 Identities = 85/263 (32%), Positives = 136/263 (51%), Gaps = 24/263 (9%)

Query: 7   LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYNFWPTDISS---- 62
           L  K+  +TG A G+GLA+ +  + +G  V ++DI+G      +         I++    
Sbjct: 5   LDGKVALITGAAQGLGLAMAETFVREGGRVAVVDINGDAAKAVAERLGESAIGIAANVTR 64

Query: 63  ASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYE-LNEAAFEKMVNINQK 121
            ++V  T+   +++FGR+D LVNNAG             +G +E + E  F+++  +N K
Sbjct: 65  MADVEMTIAATVEKFGRLDILVNNAGSTHA---------NGPFENVTEEEFDRVFALNVK 115

Query: 122 GVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKH 181
            ++L S+AV   M  Q+SGVI+N+ S +GL    G   Y ATK A+++ T+S + EL   
Sbjct: 116 SIYLYSKAVVATMRAQKSGVILNLGSTAGLRPRPGLVWYNATKGAVHNITKSLALELAPD 175

Query: 182 GIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADF 241
            IRV  +AP   E   L T        +    T E  +       +PLGR G+ T+VA+ 
Sbjct: 176 NIRVCALAPVATETPLLAT--------FMGGDTPE--KRARMMGIVPLGRLGQPTDVANA 225

Query: 242 VCYLLSERASYMTGVTTNIAGGK 264
             YL S+ A+++TGV   I GG+
Sbjct: 226 ALYLASDEAAFLTGVVLEIDGGR 248


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: 170
Number of extensions: 9
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: 250
Length adjustment: 24
Effective length of query: 243
Effective length of database: 226
Effective search space:    54918
Effective search space used:    54918
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.

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