GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Echinicola vietnamensis KMM 6221, DSM 17526

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__Cola:Echvi_2123
          Length = 318

 Score =  130 bits (327), Expect = 4e-35
 Identities = 79/246 (32%), Positives = 139/246 (56%), Gaps = 17/246 (6%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86
           AL+D SL + +G ++ ++GESG+GK++L R+I GL+  ++G V      I    +K+   
Sbjct: 19  ALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLGDQKILNPAQKLVPG 78

Query: 87  YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146
           Y  ++QLI Q+ Y   P N TVEE +  P+L ++K  + E    ++ LL L        F
Sbjct: 79  Y-DEIQLIHQE-YKLYP-NSTVEENIARPLLLYDKAYQKERTAEILELLSL------RAF 129

Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206
             K P QLSGGQ+Q+++I R+LS+ P +++ DEP + +DA  +  ++  L EI + L +T
Sbjct: 130 KDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKEIFDALEVT 189

Query: 207 MVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDL---IKLTP 263
           ++F+THD+  A     L      +++  G+++++ ++ E+ + P   Y   L   + L P
Sbjct: 190 VIFVTHDVDDA-----LLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFGYLNLIP 244

Query: 264 SIDNLY 269
             +  Y
Sbjct: 245 GAEEAY 250


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: 244
Number of extensions: 15
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: 318
Length adjustment: 28
Effective length of query: 296
Effective length of database: 290
Effective search space:    85840
Effective search space used:    85840
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: 48 (23.1 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