GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0027 in Chryseobacterium viscerum 687B-08

Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate WP_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= TCDB::Q9WXN4
         (268 letters)



>NCBI__GCF_002899945.2:WP_103234822.1
          Length = 416

 Score =  110 bits (276), Expect = 4e-29
 Identities = 83/275 (30%), Positives = 134/275 (48%), Gaps = 25/275 (9%)

Query: 3   RLVVKNLTKIFSL-----------GFFSKRRIE------AVKNVSFEVKEKEIVSLVGES 45
           +L V++LT IF             GF  K  +E       +   SFE+ E E   ++G S
Sbjct: 11  KLKVEDLTIIFGKNKEKAQELLDKGFSKKEILEKTGCTIGINKASFEIYEGEFFVIMGLS 70

Query: 46  GSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPF 105
           GSGK+T  + + RL  PTSG++Y    DI    K+ + L+E RR   ++    F      
Sbjct: 71  GSGKSTLLRCLNRLNEPTSGKVYINDDDITS--KNNKELLEVRRTEMSMVFQKFG----L 124

Query: 106 YPVERTLWQAISLLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMI 165
            P    L  A   LE +  +K    E  +++L  VG++  +   +YP Q+SGG +QR+ +
Sbjct: 125 LPHHTILDNAGFGLEIRGEDKASRNEKAQKALDIVGLNGFE--NQYPSQLSGGMQQRVGL 182

Query: 166 ARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNI 225
           AR     P +++ DE  S +D   +  +   + EL+     +I+FITHDL  A  + D I
Sbjct: 183 ARALANDPEVLLMDEAFSALDPLIKSEMQDQMLELQNTLQKTIVFITHDLDEAIKIGDRI 242

Query: 226 FVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIPK 260
            +MK+G I + G  + ++  P  +Y K  V  + +
Sbjct: 243 VIMKDGVIEQIGTAEDILTNPASDYVKAFVEKVDR 277


Lambda     K      H
   0.319    0.139    0.397 

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: 279
Number of extensions: 19
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: 268
Length of database: 416
Length adjustment: 28
Effective length of query: 240
Effective length of database: 388
Effective search space:    93120
Effective search space used:    93120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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