GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Pseudomonas fluorescens FW300-N2E2

Align ATPase (characterized, see rationale)
to candidate Pf6N2E2_4455 Glutamate transport ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4455
          Length = 244

 Score =  246 bits (627), Expect = 4e-70
 Identities = 128/234 (54%), Positives = 168/234 (71%), Gaps = 1/234 (0%)

Query: 27  VEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL 86
           + K+YG+    L G+ L+V+ G+VV ++G SGSGKST LRTLN LES   G I ++G  L
Sbjct: 9   LHKYYGDH-HVLKGIDLSVEEGQVVAIIGRSGSGKSTLLRTLNGLESINDGVIEVDGEYL 67

Query: 87  SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVR 146
              R D+ ++RQ+VGMVFQQFNLFPHLTV +N+MLAP  V++ P A+A   ARQ+LERV 
Sbjct: 68  DAARADLRSLRQKVGMVFQQFNLFPHLTVGENVMLAPQVVQKVPKAKAAVLARQMLERVG 127

Query: 147 IAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLASE 206
           + E+ D +P +LSGGQQQRVAIARALAM P++LL DE TSALDPE+V EVL V+R LA E
Sbjct: 128 LGEKFDAFPDRLSGGQQQRVAIARALAMSPKVLLCDEITSALDPELVNEVLSVVRQLAKE 187

Query: 207 GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260
           GMT+++ THE+ FAREV D++V M  G++ E   P   F  PQ+     F+  +
Sbjct: 188 GMTLIMVTHEMRFAREVGDKLVFMHQGKVHEVGDPKVLFANPQTAELANFIGTV 241


Lambda     K      H
   0.321    0.134    0.387 

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: 185
Number of extensions: 4
Number of successful extensions: 1
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: 261
Length of database: 244
Length adjustment: 24
Effective length of query: 237
Effective length of database: 220
Effective search space:    52140
Effective search space used:    52140
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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