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_4610 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4610
          Length = 255

 Score =  198 bits (503), Expect = 1e-55
 Identities = 105/252 (41%), Positives = 161/252 (63%), Gaps = 3/252 (1%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           +L  + LS  FGGL AV+   + VKE  +  LIGPNGAGKTT+FN L+ F +P  G +L 
Sbjct: 5   ILKVENLSMRFGGLLAVNGVALSVKEKQVVALIGPNGAGKTTVFNCLTGFYKPSGGSILL 64

Query: 78  NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137
           +G++I  L  H+IAL+G VRTFQ  ++   +T +EN+L+A        FL  L      +
Sbjct: 65  DGEAIEGLPGHKIALKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFLSGLFKTPSFR 124

Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197
           K ER   + A   LE V L   A   AG L+ GQ++ LE+AR +M+ P++++LDEPAAG+
Sbjct: 125 KSEREAMDFAEFWLEKVNLKEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184

Query: 198 NPTLIGQICEHIVNWNRQ--GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQS 255
           NP     + + +++  R+   +T L+IEH+M ++M++  H+ V+ +G  LA+GTPEQI+ 
Sbjct: 185 NPKETEDL-KALISMLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLANGTPEQIRD 243

Query: 256 DPRVLEAYLGDS 267
           +P V++AYLG++
Sbjct: 244 NPEVIKAYLGEA 255


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: 180
Number of extensions: 10
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: 267
Length of database: 255
Length adjustment: 25
Effective length of query: 242
Effective length of database: 230
Effective search space:    55660
Effective search space used:    55660
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