GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Pseudomonas fluorescens FW300-N2E2

Align D-lactate transporter, ATP-binding component (characterized)
to candidate Pf6N2E2_2925 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= reanno::Phaeo:GFF1248
         (251 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2925
          Length = 255

 Score =  196 bits (499), Expect = 3e-55
 Identities = 99/253 (39%), Positives = 162/253 (64%), Gaps = 7/253 (2%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           IL+V+N+  RFGGL A++ V L+V+E  V A+IGPNGAGK+T+ NCL G   P  G+++ 
Sbjct: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64

Query: 63  DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRD-----GAFEMNAIS 117
           DG+ + G   + I + G+ R FQ   +F D++ +EN++I      +     G F+  A  
Sbjct: 65  DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124

Query: 118 AVSGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTA 177
               +R+ +E AE+ L+++N+ +  +  A +++ G +RRLEI  C+   PR+L+LDEP A
Sbjct: 125 --KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182

Query: 178 GMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIK 237
           G+   +T +   L+  ++ E ++T+ +IEHDM +V S++D I V+ QGTPL +  P+ I+
Sbjct: 183 GLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIR 242

Query: 238 GNPKVREAYLGES 250
            NP+V +AYLGE+
Sbjct: 243 DNPEVIKAYLGEA 255


Lambda     K      H
   0.318    0.135    0.379 

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: 182
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: 251
Length of database: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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