GapMind for catabolism of small carbon sources

 

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

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate CA265_RS04175 CA265_RS04175 phosphonate ABC transporter ATP-binding protein

Query= TCDB::G3LHY8
         (358 letters)



>FitnessBrowser__Pedo557:CA265_RS04175
          Length = 232

 Score = 89.7 bits (221), Expect = 7e-23
 Identities = 61/181 (33%), Positives = 91/181 (50%), Gaps = 7/181 (3%)

Query: 21  DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMP------VQKRN 74
           +L +  G    ++GP+  GK++L+ +M  LD+P  GS  F  T++  +        +KRN
Sbjct: 25  NLHVAAGEFVSIMGPSGCGKSTLLNVMGLLDKPENGSYKFIDTELLTLNDRERSNFRKRN 84

Query: 75  VAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSG 134
           +  V+Q F     LTV+ NI  P+  +   A    + V +  E + +       P  LSG
Sbjct: 85  MGFVFQNFNLIDELTVFENIELPLIYNKIPAGERKKLVNEIIERMNIVNRSGHFPQQLSG 144

Query: 135 GQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSE 194
           GQQQR A+ARALV    LVL DEP  NLD     E+ E L ++  ++G   V  T    +
Sbjct: 145 GQQQRVAVARALVTKPKLVLADEPTGNLDSSHGNEVMELLCEL-NETGTTIVMVTHSSHD 203

Query: 195 A 195
           A
Sbjct: 204 A 204


Lambda     K      H
   0.319    0.136    0.392 

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: 175
Number of extensions: 9
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: 358
Length of database: 232
Length adjustment: 26
Effective length of query: 332
Effective length of database: 206
Effective search space:    68392
Effective search space used:    68392
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 (21.7 bits)
S2: 47 (22.7 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