GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Burkholderia phytofirmans PsJN

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate BPHYT_RS35660 BPHYT_RS35660 membrane protein

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__BFirm:BPHYT_RS35660
          Length = 283

 Score =  134 bits (338), Expect = 2e-36
 Identities = 84/259 (32%), Positives = 133/259 (51%), Gaps = 9/259 (3%)

Query: 18  LLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEA--FRPKFQNSVVLAVSATL 75
           L P  +++ TALK  + I +      P    W +F   W A  F    +NS V+++ +T 
Sbjct: 25  LFPFAVMLFTALKPASEIFVYPARWLPVHWQWSNFSDMWVAANFGVALRNSTVISLLSTA 84

Query: 76  LSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSI-----GLYGS 130
           L+  V     Y LA++PFRG GL    +L    +    +++ LF+    I      L  S
Sbjct: 85  LALAVSLPAAYALARFPFRGRGLYRQFLLVTQMLSPILLVVGLFRLAAMIPYGDGNLVDS 144

Query: 131 LFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPAFVV 190
             G+++ +  + I     +  +Y+  +P +L E+A ++G G       V LPL+VPA VV
Sbjct: 145 KIGVIVSYAAFNIAFAVWMLSSYFQTVPRDLEESAWLEGCGRTKAVFKVFLPLAVPAIVV 204

Query: 191 VAIWQFTQIWNEFLFAVTLTR-PESQPITVALAQLAGGE-AVKWNLPMAGAILAALPTLL 248
            AI+ F   WNEF    TL R PE++ +TV +  +  G+  V+W+L MA  + A LP  +
Sbjct: 205 TAIFTFINAWNEFAVVYTLIRSPENKTLTVQVTDMVAGKYVVQWHLVMAATLCATLPVSV 264

Query: 249 VYILLGRYFLRGLLAGSVK 267
           V+  L RY ++GL  G+VK
Sbjct: 265 VFAWLQRYLVKGLALGAVK 283


Lambda     K      H
   0.330    0.146    0.461 

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: 225
Number of extensions: 17
Number of successful extensions: 4
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: 268
Length of database: 283
Length adjustment: 25
Effective length of query: 243
Effective length of database: 258
Effective search space:    62694
Effective search space used:    62694
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: 47 (22.7 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