GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Pseudomonas fluorescens GW456-L13

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_84
          Length = 290

 Score =  134 bits (337), Expect = 2e-36
 Identities = 84/261 (32%), Positives = 146/261 (55%), Gaps = 15/261 (5%)

Query: 9   ENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFI 68
           + L +   ++L  + +S SF G RA+++ ++ +  G +  +IGPNGAGKTTL ++++   
Sbjct: 40  KGLNTRHGTILTLEDISVSFDGFRALNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKT 99

Query: 69  RPDQGEVLFNGD-SIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFL 127
           RP  G+  F     + Q++  QIA  G  R FQ   V   L+V EN+ LA   Q  +K +
Sbjct: 100 RPSHGKAWFGETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA---QKTDKSV 156

Query: 128 PRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKL 187
              +  R   ++    +++   +L+++ L +     AG LS GQ++ LE+   LM +P+L
Sbjct: 157 WASLRARLSGEQ----KDRIAQVLDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQL 212

Query: 188 ILLDEPAAGVNPT---LIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRN 244
           +LLDEP AG+         ++ + +   +    + +V+EH+M  + ++  HV VL +G  
Sbjct: 213 LLLDEPVAGMTDAETEFTAELFKSLAGKH----SLMVVEHDMGFVGSIADHVTVLHQGSV 268

Query: 245 LADGTPEQIQSDPRVLEAYLG 265
           LA+G+ EQ+Q + RV+E YLG
Sbjct: 269 LAEGSLEQVQDNERVIEVYLG 289


Lambda     K      H
   0.319    0.136    0.389 

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: 195
Number of extensions: 9
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: 267
Length of database: 290
Length adjustment: 25
Effective length of query: 242
Effective length of database: 265
Effective search space:    64130
Effective search space used:    64130
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 (21.7 bits)
S2: 47 (22.7 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