GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Burkholderia phytofirmans PsJN

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate BPHYT_RS18670 BPHYT_RS18670 peptide ABC transporter ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__BFirm:BPHYT_RS18670
          Length = 339

 Score =  195 bits (495), Expect = 2e-54
 Identities = 107/313 (34%), Positives = 182/313 (58%), Gaps = 13/313 (4%)

Query: 16  KVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYN 75
           K G+F      AL  VS ++ +G  L V+GESG GK+TL R +  ++ P++G ++ DG +
Sbjct: 31  KRGMFASGTVKALNGVSFALERGKTLAVVGESGCGKSTLARQLTMIEAPSAGRLLIDGED 90

Query: 76  IWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLL 135
           +           R+ VQ++ Q+P+++L   KTVE+ L  P+    +++  E  +R+  ++
Sbjct: 91  VAGADHAKIAALRRRVQMVFQNPFASLNPRKTVEQTLGEPLAINTQLSATERAERIAQMM 150

Query: 136 ELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNT 195
             V L P  E   +YPH  SGGQ+QR++IAR++ ++P+I+VADEPV+ +D S++  ILN 
Sbjct: 151 RTVGLRP--EHAKRYPHMFSGGQRQRVAIARAMILDPQIVVADEPVSALDVSIQAQILNL 208

Query: 196 LAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYT 255
             +++ +   + VFI+H++ +     H+ D  + +VM+ G + E  D + I  +P HPYT
Sbjct: 209 FMDLQEQFKTSYVFISHNLSVVE---HIAD--DVMVMYFGGVAELGDKKRIFSNPRHPYT 263

Query: 256 NDLIKLTPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEPKLFKY-S 309
             L+  TPSI    + I +K+  E         GC +  RCP+ +D C++EEPKL +   
Sbjct: 264 RALMSATPSIFEADRTIKIKLQGEMPSPLNPPSGCTFHQRCPYVIDRCRSEEPKLREVDG 323

Query: 310 HEVACFLYGKVGE 322
            +V+C    +VG+
Sbjct: 324 RQVSCHRAEEVGD 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: 269
Number of extensions: 9
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: 339
Length adjustment: 28
Effective length of query: 296
Effective length of database: 311
Effective search space:    92056
Effective search space used:    92056
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.

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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