GapMind for catabolism of small carbon sources

 

Alignments for a candidate for snatA in Burkholderia phytofirmans PsJN

Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate BPHYT_RS17695 BPHYT_RS17695 membrane protein

Query= TCDB::Q8J305
         (216 letters)



>FitnessBrowser__BFirm:BPHYT_RS17695
          Length = 206

 Score =  141 bits (356), Expect = 8e-39
 Identities = 74/194 (38%), Positives = 122/194 (62%), Gaps = 4/194 (2%)

Query: 18  LFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKFFGSSTD 77
           L A+ NPVGA+P F+S+T + S  ERR      AISV   + +  LLGQ I  FFG S  
Sbjct: 10  LLALINPVGAIPFFMSLTANQSDVERRRTIRIAAISVFCVIAITTLLGQQIISFFGISVG 69

Query: 78  AFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPLAIPLISGPGA 137
           +  + GGI++  MA++ML+ ++ + + + EE  E  ++    + +A++PLAIPL++GPGA
Sbjct: 70  SLEVGGGIIMLLMAINMLNAQIGNSRSTPEERHEAEQK----DNIAVVPLAIPLLTGPGA 125

Query: 138 ITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGIKVMTRMMGLI 197
           I+T ++Y A S     R++++    ++    +F L  A  I   +GR GI + TR+MGL+
Sbjct: 126 ISTTIIYAAGSAHWYDRISLVAIGAVLAAICFFSLRLAEPIARWVGRTGINIGTRLMGLM 185

Query: 198 LTSMAVQMIINGIK 211
           L+++AV+ I++G+K
Sbjct: 186 LSALAVEFIVDGLK 199


Lambda     K      H
   0.327    0.141    0.396 

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: 110
Number of extensions: 5
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: 216
Length of database: 206
Length adjustment: 21
Effective length of query: 195
Effective length of database: 185
Effective search space:    36075
Effective search space used:    36075
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 (21.7 bits)
S2: 45 (21.9 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