GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate H281DRAFT_01453 H281DRAFT_01453 carbohydrate ABC transporter membrane protein 1, CUT1 family

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



>FitnessBrowser__Burk376:H281DRAFT_01453
          Length = 319

 Score =  261 bits (667), Expect = 1e-74
 Identities = 119/275 (43%), Positives = 184/275 (66%)

Query: 23  LVLAPSMFIVLVGFYGYILWTFVLSFTNSTFLPTYKWAGLAQYARLFDNDRWWVASKNLA 82
           L L P +  V+  + G ++WT  +S +NS   P+  +AGL QY RLF+N RW ++ +N+ 
Sbjct: 38  LALLPMILTVVFAYLGTMVWTARVSLSNSRTFPSGDFAGLTQYVRLFNNARWLLSLQNIV 97

Query: 83  VFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLLNPGMGL 142
           ++G  FI   +VIG+ LAIF+DQ++  EG +RT++LYP A+S + TG  W+W+LNP +G 
Sbjct: 98  IYGACFIVACMVIGLLLAIFIDQRVVAEGALRTVFLYPYAMSFVATGLVWQWILNPELGA 157

Query: 143 DKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQSIVRAAQI 202
             +L   G+   R DW++D D  +Y +VIA VWQASG +MA+ LAGLRG+D  + +AA+I
Sbjct: 158 QAVLHKLGFVHARFDWIVDQDWAIYTIVIATVWQASGLVMALLLAGLRGIDDELWKAARI 217

Query: 203 DGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYS 262
           DG    R+Y S+V+P L P   +A ++L  + +K +D V AMT GGPG +S++PA F+  
Sbjct: 218 DGIPRWRVYASIVVPMLGPSISTAFVLLFVMVVKLYDAVVAMTQGGPGTASEVPAKFIMD 277

Query: 263 FTFSRGQMGMGSASAILMLGAILAIIVPYLYSELR 297
           + F R  +G+ SA++I++L  +LAI+ P+ Y+  R
Sbjct: 278 YLFGRANIGLASAASIVLLATVLAILTPFFYARSR 312


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: 331
Number of extensions: 15
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: 319
Length adjustment: 27
Effective length of query: 275
Effective length of database: 292
Effective search space:    80300
Effective search space used:    80300
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