GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Sphingobium czechense LL01

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_066599158.1 V473_RS00455 cell division ATP-binding protein FtsE

Query= TCDB::Q97VF4
         (324 letters)



>NCBI__GCF_001046645.1:WP_066599158.1
          Length = 236

 Score = 93.6 bits (231), Expect = 4e-24
 Identities = 66/207 (31%), Positives = 110/207 (53%), Gaps = 7/207 (3%)

Query: 10  SVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEV 69
           +++  + VGL        L DVS S+  G    + G SGAGKT+L +++   Q+P+ G +
Sbjct: 3   AIVQFENVGLRYGLDSETLSDVSFSLAGGGFYFLTGASGAGKTSLLKLLYLAQRPSRGVI 62

Query: 70  VYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRK 129
              G ++    RK    +R+ + ++ QD +  +P     + I +   LR   + + E+  
Sbjct: 63  RLFGEDVVTLPRKRLPGFRRRIGVVFQD-FRLVPHLSAYDNIALP--LRVSGMEEGEIDA 119

Query: 130 RLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLR 189
            ++ +L  V L    +     P  LSGG++QR++IAR++   P I+VADEP   VDA + 
Sbjct: 120 PVVEMLNWVGLGDRGQ---ARPATLSGGEQQRVAIARAVIGRPEILVADEPTGNVDADMA 176

Query: 190 IGILNTLAEIKNRLNLTMVFITHDIPI 216
             ++ TL E  NRL  T+V  THD+P+
Sbjct: 177 RRLM-TLFEALNRLGTTIVVATHDLPL 202


Lambda     K      H
   0.321    0.141    0.410 

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: 186
Number of extensions: 7
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: 324
Length of database: 236
Length adjustment: 25
Effective length of query: 299
Effective length of database: 211
Effective search space:    63089
Effective search space used:    63089
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 (21.8 bits)
S2: 47 (22.7 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