GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate BPHYT_RS29185 BPHYT_RS29185 sugar ABC transporter permease

Query= reanno::WCS417:GFF4323
         (302 letters)



>FitnessBrowser__BFirm:BPHYT_RS29185
          Length = 314

 Score =  266 bits (680), Expect = 5e-76
 Identities = 121/275 (44%), Positives = 186/275 (67%)

Query: 23  LVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKWAGLAQYARLFDNDRWWVASKNLA 82
           L L P +  V+  + G ++WT  +S +NS   P+  +AG  QYARLF+NDRW ++ +N+ 
Sbjct: 33  LALLPMVMTVVFAYLGTMVWTARVSLSNSRTFPSGDFAGFTQYARLFNNDRWLLSLQNIV 92

Query: 83  VFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGL 142
           ++G  FI   +VIG+ LAIF+DQ++  EG +RT++LYP A+S + TG  W+W+LNP +G 
Sbjct: 93  IYGACFIVACMVIGLLLAIFIDQRVVAEGALRTVFLYPYAMSFVATGLVWQWILNPELGA 152

Query: 143 DKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQI 202
             +L   G+   R DW++D D V+Y +VIA VWQASG +MA+ LAGLRG+D  + +AA+I
Sbjct: 153 QAVLHKLGFAHARFDWIVDQDWVIYTIVIATVWQASGLVMALLLAGLRGIDDELWKAARI 212

Query: 203 DGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYS 262
           DG    R+Y S+V+P L P   +A ++L  + +K +D V AMT GGPG +S++PA F+  
Sbjct: 213 DGIPRWRVYVSIVVPMLGPSISTAFVLLFVMVVKLYDAVVAMTQGGPGTASEVPAKFIMD 272

Query: 263 FTFSRGQMGMGSASAILMLGAILAIIVPYLYSELR 297
           + F R  +G+ SA++I++L  +LAI+ P+ Y+  R
Sbjct: 273 YLFGRANIGLASAASIVLLATVLAILAPFFYARSR 307


Lambda     K      H
   0.330    0.141    0.455 

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: 335
Number of extensions: 16
Number of successful extensions: 1
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: 302
Length of database: 314
Length adjustment: 27
Effective length of query: 275
Effective length of database: 287
Effective search space:    78925
Effective search space used:    78925
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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