GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cebG in Dinoroseobacter shibae DFL-12

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 3607838 Dshi_1246 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::Q9X9R5
         (276 letters)



>FitnessBrowser__Dino:3607838
          Length = 282

 Score =  123 bits (309), Expect = 4e-33
 Identities = 88/276 (31%), Positives = 138/276 (50%), Gaps = 14/276 (5%)

Query: 9   AGPVTYVVLTVFALVS-LAPLVWTAIAASRTNHRLAETPPPLW---FGGNLFKNLEAAWE 64
           A  +TY  +   AL+  L PL+  AI + +     A      W   F G  F+N    + 
Sbjct: 12  AAQLTYQGMIPLALILWLLPLIAVAIFSVKPAGDFAAGNYWGWPAEFAG--FENYARVFT 69

Query: 65  QAGLGTAMLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAV 124
            + +   +LNS ++     +  V  S + GFA    RFR + L+  + I    +P Q+ +
Sbjct: 70  DSEMPRYILNSFMITIPTVIGAVALSCMTGFALGIYRFRGNLLIFFMFIAGNFVPFQILM 129

Query: 125 VPLYLWMSDLGWSNQLHTVILPSLV--TAFGTFFMRQYLVQALPTELIEAARVDGASSLR 182
           VP+     D+G  N    ++L  +   T F T FMR + ++ALP ELIEAARV+G +  R
Sbjct: 130 VPVRDLTVDMGLYNTKTGLVLFHIAFQTGFCTLFMRNF-IRALPYELIEAARVEGVAEWR 188

Query: 183 IVWHVVFPAARPAMAVLGLLTFVFAWNDFLWPIIAL---NQQNPTVQVGPELARHRVLPD 239
           I W VV P  +PA+A L +L F F WND+ W ++     N Q  T  +    A+  +  +
Sbjct: 189 IFWFVVLPLMKPAIAALSVLIFTFIWNDYFWAVVLTQGPNAQPVTAGITSFNAQFGIAYN 248

Query: 240 QAVIMAGALLGTLPLLVAFLLFGKQIVGGIMQGAIK 275
             ++ AG+L+  LP ++ F L  K  + G+  GA+K
Sbjct: 249 --MLSAGSLIAALPPVMMFFLMQKHFIAGLTLGAVK 282


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: 239
Number of extensions: 12
Number of successful extensions: 3
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: 282
Length adjustment: 26
Effective length of query: 250
Effective length of database: 256
Effective search space:    64000
Effective search space used:    64000
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