GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cebG in Rhodobacter viridis JA737

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 WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease

Query= TCDB::Q9X9R5
         (276 letters)



>NCBI__GCF_003217355.1:WP_110804034.1
          Length = 382

 Score =  105 bits (263), Expect = 1e-27
 Identities = 74/239 (30%), Positives = 118/239 (49%), Gaps = 19/239 (7%)

Query: 47  PPLWFGGNLFKNLEAAWEQAGLGTAMLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSG 106
           PP    GN  + + A     G+G A LN++ V    TV  +L +  A +A A +RF    
Sbjct: 153 PPRLTTGNYARVITAE----GIGRAFLNTMTVTIPATVIPILIAAFAAYALAWMRFPGRA 208

Query: 107 LLLLLTIGTMMIPPQLAVVPLYLWMSDLGWSNQLHTVILPSLVTAFGT----FFMRQYLV 162
           LL+   +G +++P QLA++PL    + +G +     + L    T FG     + +R Y+V
Sbjct: 209 LLVATIVGLLVVPLQLALIPLLKLHNQIGLNQSYLGIWLAH--TGFGLPLAIYLLRNYMV 266

Query: 163 QALPTELIEAARVDGASSLRIVWHVVFPAARPAMAVLGLLTFVFAWNDFLWPIIALNQQN 222
             LP E+IE+ARVDGA+  +I   +V P + PA+A   +  F++ WND L   + L    
Sbjct: 267 -GLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFLGNAT 325

Query: 223 PTVQVGPELARHRVL-----PDQAVIMAGALLGTLPLLVAFLLFGKQIVGGIMQGAIKG 276
            T  +   L   R L      D  ++ A A +     L+ F    K +V G++ G++KG
Sbjct: 326 DTQVMTGAL---RALLGSRGGDWEILAASAFVSIAVPLIVFFALQKYLVRGLLAGSVKG 381


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: 313
Number of extensions: 15
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: 382
Length adjustment: 28
Effective length of query: 248
Effective length of database: 354
Effective search space:    87792
Effective search space used:    87792
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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