GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PGA1_c12640 in Dechlorosoma suillum PS

Align D-lactate transporter, ATP-binding component (characterized)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component

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



>lcl|FitnessBrowser__PS:Dsui_0627 Dsui_0627 ABC-type branched-chain
           amino acid transport systems, ATPase component
          Length = 267

 Score =  186 bits (473), Expect = 3e-52
 Identities = 103/254 (40%), Positives = 154/254 (60%), Gaps = 8/254 (3%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           +LE  +V K FGG++AL  V+L++RE  ++ +IGPNGAGK+T  NCL G  +P+ G ++F
Sbjct: 7   LLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGGRIVF 66

Query: 63  DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAK-RDGAFEMNAISAVSG 121
            G  +   AP+++   GI+R FQ   +F  ++ LEN+M+    + R G F   AI    G
Sbjct: 67  AGAELDTSAPHKVAARGIARTFQNIRLFAHMTALENVMVGRHQRTRAGVF--GAIFRTPG 124

Query: 122 QR----DILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTA 177
            R     I  +AE +L  + +AD+ H  A  +S GD+RRLEI   L+ EP+LL LDEP A
Sbjct: 125 TRAEEAAIQRRAEELLHYVGIADRAHDLAKHLSYGDQRRLEIARALATEPKLLALDEPAA 184

Query: 178 GMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIK 237
           GM  ++T     L++ I+ +  IT+ +IEHD+ +V  L DR+ VL  G  + ED P  ++
Sbjct: 185 GMNASETGELRTLIEGIRKD-GITVLLIEHDVKLVMGLCDRVAVLDYGEKICEDVPAVVQ 243

Query: 238 GNPKVREAYLGESA 251
            +P+V  AYLG  A
Sbjct: 244 KDPRVITAYLGAEA 257


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: 179
Number of extensions: 10
Number of successful extensions: 3
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: 267
Length adjustment: 24
Effective length of query: 227
Effective length of database: 243
Effective search space:    55161
Effective search space used:    55161
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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