GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Escherichia coli BW25113

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 15367 b1247 oligopeptide transporter subunit (NCBI)

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__Keio:15367
          Length = 334

 Score =  185 bits (469), Expect = 2e-51
 Identities = 113/331 (34%), Positives = 184/331 (55%), Gaps = 32/331 (9%)

Query: 3   LMELKGVSVIFEDKVGLFKKRKFY-------ALKDVSLSMNQGDLLIVLGESGAGKTTLG 55
           L+E+  + V FE K G   K+ F+       A+  V+L + +G+ L V+GESG GK+T  
Sbjct: 11  LLEIADLKVHFEIKDG---KQWFWQPPKTLKAVDGVTLRLYEGETLGVVGESGCGKSTFA 67

Query: 56  RVIVGLQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAP 115
           R I+GL K T G V + G  +   K   ++  R D+Q+I QDP ++L    T+ EI+  P
Sbjct: 68  RAIIGLVKATDGHVAWLGKELLGMKPDEWRAVRSDIQMIFQDPLASLNPRMTIGEIIAEP 127

Query: 116 ILRWE-KINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRI 174
           +  +  K+++ E+R+R+  ++  V L P    + +YPH+ SGGQ QR+ IAR+L + P++
Sbjct: 128 LRTYHPKMSRQEVRERVKAMMLKVGLLP--NLINRYPHEFSGGQCQRIGIARALILEPKL 185

Query: 175 IVADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFA 234
           I+ DEPV+ +D S++  ++N L +++  + L+++FI HD+ + +   H+ D+   +VM+ 
Sbjct: 186 IICDEPVSALDVSIQAQVVNLLQQLQREMGLSLIFIAHDLAVVK---HISDR--VLVMYL 240

Query: 235 GRIVERADLEEILKDPLHPYTNDLIKLTP----------SIDNLYKEINVKINYERVEKG 284
           G  VE    +E+  +PLHPYT  L+   P          +I  L  E+   IN      G
Sbjct: 241 GHAVELGTYDEVYHNPLHPYTRALMSAVPIPDPDLEKNKTIQLLEGELPSPIN---PPSG 297

Query: 285 CPYRLRCPFAMDICKNEEPKL-FKYSHEVAC 314
           C +R RCP A   C    P L   + H V+C
Sbjct: 298 CVFRTRCPIAGPECAKTRPVLEGSFRHSVSC 328


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: 279
Number of extensions: 17
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: 334
Length adjustment: 28
Effective length of query: 296
Effective length of database: 306
Effective search space:    90576
Effective search space used:    90576
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