GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cebG in Burkholderia phytofirmans PsJN

Align CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate BPHYT_RS17465 BPHYT_RS17465 glycerol-3-phosphate transporter membrane protein

Query= TCDB::Q9X9R5
         (276 letters)



>FitnessBrowser__BFirm:BPHYT_RS17465
          Length = 281

 Score =  139 bits (350), Expect = 7e-38
 Identities = 85/272 (31%), Positives = 137/272 (50%), Gaps = 16/272 (5%)

Query: 8   HAGPVTYVVLTVFALVSLAPLVWTAIAASRTNHRLAETPPPLWFGGNLFKNLEAAWEQ-- 65
           HA  +  VVL VF      P+     AA+ + H +   P  L    +L +N+   W Q  
Sbjct: 13  HAVLILGVVLVVF------PVYVAFCAATMSEHEVFSVPLSLVPSTHLLENIATVWSQGS 66

Query: 66  ----AGLGTAMLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQ 121
               A  G  + NS+++A  I++  +  S ++ +A    RF F  L   L   T+M+P +
Sbjct: 67  GNAAAPFGRMLFNSLVMALVISIGKIAVSMISAYAIVFFRFPFRNLAFWLIFITLMLPVE 126

Query: 122 LAVVPLYLWMSDLGWSNQLHTVILPSLVTAFGTFFMRQYLVQALPTELIEAARVDGASSL 181
           + + P    +S +  SN    + LP + +A  TF  RQ+ +  LP EL+EAAR+DGA ++
Sbjct: 127 VRIFPTVQVVSSMHLSNTYSGLTLPLIASATATFLFRQFFM-TLPDELMEAARIDGAGAM 185

Query: 182 RIVWHVVFPAARPAMAVLGLLTFVFAWNDFLWPIIALNQQNPT---VQVGPELARHRVLP 238
           R  W VV P ++  MA L ++TF++ WN +LWPI+  +QQ+ T   V +   +A      
Sbjct: 186 RFFWDVVLPLSKTNMAALFVITFIYGWNQYLWPILITSQQSLTTAVVGIKSMIASGDTAT 245

Query: 239 DQAVIMAGALLGTLPLLVAFLLFGKQIVGGIM 270
           +  ++M   LL  LP L   L   +  V G++
Sbjct: 246 EWHLVMTATLLAMLPPLAVVLTMQRWFVRGLV 277


Lambda     K      H
   0.327    0.140    0.434 

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: 241
Number of extensions: 16
Number of successful extensions: 2
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: 276
Length of database: 281
Length adjustment: 25
Effective length of query: 251
Effective length of database: 256
Effective search space:    64256
Effective search space used:    64256
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 (21.7 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