GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fcbT2 in Cupriavidus basilensis 4G11

Align FcbT2, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized)
to candidate RR42_RS24115 RR42_RS24115 C4-dicarboxylate ABC transporter permease

Query= TCDB::Q9RBR0
         (181 letters)



>FitnessBrowser__Cup4G11:RR42_RS24115
          Length = 172

 Score =  126 bits (317), Expect = 2e-34
 Identities = 69/168 (41%), Positives = 105/168 (62%), Gaps = 8/168 (4%)

Query: 20  RAEEILAAVACGLVLLMVLVICADVTLRATMRSGLT----SASAVAEYSLYAITFLAAPL 75
           R  + L  +AC L+L++V  I  DV LR  +  GL     +++ ++EY+LY  T LAAP 
Sbjct: 7   RLYDFLMVLACLLLLMIVGSITLDVLLRNLVIPGLPRGFPASNDISEYALYFCTLLAAPW 66

Query: 76  LLRKGQHIRVDLVLRAMPPRAAWLLEWAVDACGAAISGLFLTSSVHVLV--QSYSQSAMV 133
           LLR GQHIRVD+VLRA+P + AW  EW  D    A++G  + + + V++  +SY+  A+ 
Sbjct: 67  LLRAGQHIRVDIVLRAVPAKLAWACEWLSDV--IALTGCVVVAWMGVVMAFRSYASGAIQ 124

Query: 134 MREMMFPEWWLYIPMPISLALLTIEFLLRMRRLVQGERQMREEATSAA 181
           ++ ++ PEWW+  P+P++ ALL +EF  RM RL   +R  R +A S A
Sbjct: 125 IKSIVIPEWWVMAPLPVAFALLAVEFAFRMWRLAHSQRGPRSDAVSTA 172


Lambda     K      H
   0.327    0.134    0.405 

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: 109
Number of extensions: 6
Number of successful extensions: 1
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: 181
Length of database: 172
Length adjustment: 19
Effective length of query: 162
Effective length of database: 153
Effective search space:    24786
Effective search space used:    24786
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 44 (21.6 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