GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deh in Williamsia sterculiae CPCC 203464

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate WP_076482685.1 BW971_RS19165 MHS family MFS transporter

Query= TCDB::F8SVK1
         (552 letters)



>NCBI__GCF_900156495.1:WP_076482685.1
          Length = 446

 Score =  197 bits (500), Expect = 9e-55
 Identities = 106/315 (33%), Positives = 177/315 (56%), Gaps = 3/315 (0%)

Query: 18  KRVIFASSLGTVFEWYDFYLAGSLAAFI-SKSFFSGVNPTAAFIFTLLGFAAGFAVRPFG 76
           + V  AS LGT  EWYDF+L  + A+ + +K FF   +     + +   FA GF +RP G
Sbjct: 28  RTVTAASLLGTTVEWYDFFLYATAASLVFNKLFFPDQSSLVGTLLSFATFAVGFVMRPIG 87

Query: 77  ALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLALG 136
            LVFG +GD +GRK T  +T+V+MGL+T ++G LP  AA+G+A+P++ + +R++QG ALG
Sbjct: 88  GLVFGHIGDRIGRKRTLALTMVLMGLATTLMGVLPTAAAVGVAAPILLLVLRMIQGFALG 147

Query: 137 GEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWGWRI 196
           GE+ GA     EH+PA +RG + +  Q    LGL L   V   ++  + + AF  +GWRI
Sbjct: 148 GEWAGAVLLAVEHSPARKRGLFGSIPQVGLALGLALGTAVFALLQVVLDDKAFLDYGWRI 207

Query: 197 PFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALIGVT 256
            F  SL+L+ + + +R+++ E+PAF  +    + + AP+ +      N +  +L L+   
Sbjct: 208 AFGISLILVVVGLVVRLKVDETPAFRELDRLSRKASAPIKDVVIP-PNTRNTVLGLLS-R 265

Query: 257 AGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRKPII 316
            G+   + T   +A+ + T +L +      + ++IA ++        G L+DR+G + I 
Sbjct: 266 WGEGAAFNTWGVFAISYATGSLGLHRVPVLVGVSIAAVVMALLLPVSGILTDRLGARRIY 325

Query: 317 LAGCLIAALTYFPLF 331
             G     +  FP+F
Sbjct: 326 TIGIAAYGVLVFPVF 340



 Score = 42.0 bits (97), Expect = 5e-08
 Identities = 21/96 (21%), Positives = 44/96 (45%), Gaps = 3/96 (3%)

Query: 454 TVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVA 513
           T+ ++ +  +   + YG    +   ++PT IRYT +S+ Y +   +  G  P    +++A
Sbjct: 352 TIAMVAVFGVVHALFYGAQGTLYASLYPTEIRYTGLSVVYQMSGIYASGLTPLILTSLIA 411

Query: 514 AKGNIYSGLWYPIIIALATFVIGLLFVRETKDSNIY 549
           A G      W      + T VI ++     + S+++
Sbjct: 412 AGGGT---PWIACAYLVGTAVISVIATSLIRRSDVH 444


Lambda     K      H
   0.325    0.139    0.422 

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: 625
Number of extensions: 46
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 552
Length of database: 446
Length adjustment: 34
Effective length of query: 518
Effective length of database: 412
Effective search space:   213416
Effective search space used:   213416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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