GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Leeuwenhoekiella blandensis MED217

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_040533847.1 MED217_RS18300 ABC transporter ATP-binding protein

Query= TCDB::G3LHY9
         (356 letters)



>NCBI__GCF_000152985.1:WP_040533847.1
          Length = 308

 Score =  116 bits (291), Expect = 7e-31
 Identities = 70/222 (31%), Positives = 120/222 (54%), Gaps = 7/222 (3%)

Query: 25  LKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVT----NLSTQS 80
           LK +D     G   ++LG SGCGK+TLL II GLL   +G + ++  ++     NL    
Sbjct: 17  LKNLDFTVEKGKHISILGESGCGKSTLLKIIYGLLHVENGTVFWNDNELLGPNFNLVPGE 76

Query: 81  RNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGL 140
             I  + Q   +   ++V DN+   L  R + + +   R+ ++LE++D+ ++A    + L
Sbjct: 77  PFIKYLAQDFDLMPYISVADNIGKHLSRRFMQQRE--ERINELLEVVDMTAFADVHVKLL 134

Query: 141 TADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHD 200
           +  QKQ+++L R + + +   +L DEP + ID   +  LR  L    K+   T +  THD
Sbjct: 135 SGGQKQRVALARAIAK-EPELLLLDEPFSHIDNFRRNALRRNLYAYLKKENITCITATHD 193

Query: 201 QTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIG 242
             EAL+F++++ +M +GQ +Q  TP  LF+ P + +V  F G
Sbjct: 194 SEEALSFSDEIKMMREGQFIQTATPEALFKNPKNAYVASFFG 235


Lambda     K      H
   0.321    0.137    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: 192
Number of extensions: 14
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: 356
Length of database: 308
Length adjustment: 28
Effective length of query: 328
Effective length of database: 280
Effective search space:    91840
Effective search space used:    91840
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 24 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