GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Dyella japonica UNC79MFTsu3.2

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3950
          Length = 239

 Score =  141 bits (356), Expect = 1e-38
 Identities = 76/234 (32%), Positives = 133/234 (56%), Gaps = 2/234 (0%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           MLS + +   +   Q + D +  +++GE+V L+G NGAGK+T    + G  +A +G+I+ 
Sbjct: 1   MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELF 120
           +  ++ GLP     +  I  +P+   VF RLTV +N+       +    + +  ++  L 
Sbjct: 61  DKYDITGLPMHARAKLGIGYLPQEPSVFRRLTVADNIMAVLELRENLSAKQRAGELESLL 120

Query: 121 PRLKERY--EQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQ 178
             LK  +  +QR  ++SGGE++ + I RAL ++P+ +LLDEP  G+ PI + +I  I+  
Sbjct: 121 DELKIAHIADQRGISLSGGERRRVEIARALAAEPRYMLLDEPFAGVDPISVGEIQRIVRH 180

Query: 179 LRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232
           L+  G+ V + + N  + L + DRAY+L +G ++   T A +L + KVR+ YLG
Sbjct: 181 LKERGIGVLITDHNVRETLGICDRAYILNDGEVLSRGTPAHILADEKVREVYLG 234


Lambda     K      H
   0.318    0.136    0.374 

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: 144
Number of extensions: 7
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: 233
Length of database: 239
Length adjustment: 23
Effective length of query: 210
Effective length of database: 216
Effective search space:    45360
Effective search space used:    45360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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