GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Sphingomonas koreensis DSMZ 15582

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Ga0059261_2293 Ga0059261_2293 cell division ATP-binding protein FtsE

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__Korea:Ga0059261_2293
          Length = 235

 Score = 87.4 bits (215), Expect = 3e-22
 Identities = 66/207 (31%), Positives = 106/207 (51%), Gaps = 7/207 (3%)

Query: 10  SVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEV 69
           +++  + VGL        L DVS +++ G    V G SGAGKT+L R++   Q+PT G V
Sbjct: 3   NIVQFENVGLRYGTGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRGIV 62

Query: 70  VYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRK 129
              G +     RK    +R+ + ++ QD +  LP     +   VA  LR   I + ++  
Sbjct: 63  RLFGEDAGALPRKRLPGFRRRIGVVFQD-FRLLPHLSAYDN--VALPLRVAGIPEADIEG 119

Query: 130 RLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLR 189
            +  ++  V L   +      P  LSGG++QR++IAR++   P I++ADEP   VD  + 
Sbjct: 120 PVREMIAWVGLKDRD---SAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMA 176

Query: 190 IGILNTLAEIKNRLNLTMVFITHDIPI 216
             +L+ L +  NRL  T+V  THD  +
Sbjct: 177 ERLLH-LFDSLNRLGTTVVVATHDFQL 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: 177
Number of extensions: 8
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: 235
Length adjustment: 25
Effective length of query: 299
Effective length of database: 210
Effective search space:    62790
Effective search space used:    62790
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 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