GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0029 in Pedobacter sp. GW460-11-11-14-LB5

Align TM0029, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate CA265_RS18010 CA265_RS18010 peptide transporter

Query= TCDB::Q9WXN6
         (280 letters)



>FitnessBrowser__Pedo557:CA265_RS18010
          Length = 380

 Score =  105 bits (262), Expect = 2e-27
 Identities = 71/222 (31%), Positives = 119/222 (53%), Gaps = 10/222 (4%)

Query: 57  LGTDTYGRDVLAQLLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNI 116
           LGTD YGRD+L++L+ GIR SL +G +A +ISL IG  +G+ +    G VD  +    N+
Sbjct: 157 LGTDIYGRDLLSRLILGIRVSLSVGLMAVLISLFIGVSLGAIAGYFGGRVDAAISWFMNV 216

Query: 117 VLTTPSILIAILIASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMA 176
           V + PS+L+ I I S+   +    + + +GL  W   AR +R Q+M++   E+V  +   
Sbjct: 217 VWSLPSLLLVIAI-SFALGKGFWQIFIAVGLSTWVDVARLVRGQVMALKEVEFVEAARAL 275

Query: 177 GYSDLRLVIEDLIPTIATYAFMSFVLFINGGIMGEAGLSLIGLGPTQGI-SLGIMLQ--- 232
           G+S  R +I+ ++P IA    +         I+ E GLS +G G    + S G M++   
Sbjct: 276 GFSTSRTIIKHILPNIAGPILVVASSNFASAILLETGLSFLGFGAQPPMPSWGSMIKEHY 335

Query: 233 WAVLMEAVRRGLWWWFVPPGLAIVAVTASLLVISTAMDEVFN 274
             ++M+A      +  V PGLAI+    +  V++  + + F+
Sbjct: 336 GYIIMDAA-----YLAVLPGLAIMFTVYAFNVLAIGLRDAFD 372


Lambda     K      H
   0.330    0.144    0.441 

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: 231
Number of extensions: 14
Number of successful extensions: 2
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: 280
Length of database: 380
Length adjustment: 28
Effective length of query: 252
Effective length of database: 352
Effective search space:    88704
Effective search space used:    88704
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: 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