GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Pseudomonas stutzeri RCH2

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC

Query= uniprot:B2TBJ8
         (250 letters)



>FitnessBrowser__psRCH2:GFF18
          Length = 219

 Score = 95.5 bits (236), Expect = 8e-25
 Identities = 70/220 (31%), Positives = 112/220 (50%), Gaps = 11/220 (5%)

Query: 8   LFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPL 67
           + + +  LL     T+ + F   +L    +L+    R+SP       A  YI VFRGS L
Sbjct: 1   MIELLPLLLQGAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSL 60

Query: 68  LIQMFLVYY--GMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAVPV 125
           L+Q+F +Y+   M  F +   +F           AV+ L L    Y AE++RG + +V  
Sbjct: 61  LVQLFWLYFVLPMPPFNIEMSAFA---------VAVVGLGLNIGAYGAEVLRGAIRSVHR 111

Query: 126 GQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQ 185
           GQ EA  ++ ++    +RR+I P AL   +P  +   + L+K+T+L SL+T+ ++   A+
Sbjct: 112 GQHEACQALNMTPLTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRAR 171

Query: 186 QIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSR 225
           Q+ Q T  T E+F  A +IY  L   I   +  LE RL+R
Sbjct: 172 QLDQATLMTMEIFGLALVIYFVLAQTINFGMRQLERRLAR 211


Lambda     K      H
   0.331    0.143    0.431 

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: 115
Number of extensions: 8
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: 250
Length of database: 219
Length adjustment: 23
Effective length of query: 227
Effective length of database: 196
Effective search space:    44492
Effective search space used:    44492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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