GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Dechlorosoma suillum PS

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Dsui_0414 Dsui_0414 oligopeptide/dipeptide ABC transporter, ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__PS:Dsui_0414
          Length = 352

 Score =  171 bits (434), Expect = 2e-47
 Identities = 104/308 (33%), Positives = 174/308 (56%), Gaps = 19/308 (6%)

Query: 19  LFKKRKF-YALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIW 77
           L ++RKF +A+  V+ S+ +G  L ++GESG GK+T  R++  L    +GE+++DG  + 
Sbjct: 38  LDRERKFVHAVDGVNFSVPKGKTLGIVGESGCGKSTTARLVARLMPADAGELIFDGEGVE 97

Query: 78  KNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLEL 137
           + +    K++R+++Q++ QD +++L    T+ E  +A   R   I + + + R   LL+ 
Sbjct: 98  EFRGLRLKEFRRNLQMVFQDSFASLNPRLTIAET-IAYGPRVHGIARADHQAR--ELLDR 154

Query: 138 VKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLA 197
           V L P+  F G+YPH+LSGGQ+QR++IAR+L+ +PR+++ DE V  +D S++  +LN L 
Sbjct: 155 VGLDPSH-FAGRYPHELSGGQRQRVNIARALAFDPRLVILDEAVAALDKSVQAQVLNLLQ 213

Query: 198 EIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTND 257
           E+K    LT +FI+HD+ +  Y          +VM+ G+++E   +E I   P HPYT  
Sbjct: 214 ELKAERQLTYLFISHDLHVVHYL-----SDYVMVMYLGQVIESGPVERIYGQPAHPYTRA 268

Query: 258 LIKLTPSIDNLYKEINVKI-----NYERVEKGCPYRLRCPFAMDICKNEEPKLFKY---- 308
           L+   PS+D  ++     +     N      GC +R RCP A  +C +  P L       
Sbjct: 269 LLSAVPSMDPEHRTQASPLAGDPPNPINPPSGCRFRDRCPHAHAVCASATPALRDMGRHS 328

Query: 309 SHEVACFL 316
            H  AC L
Sbjct: 329 EHLAACHL 336


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: 300
Number of extensions: 11
Number of successful extensions: 4
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: 352
Length adjustment: 28
Effective length of query: 296
Effective length of database: 324
Effective search space:    95904
Effective search space used:    95904
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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