GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deh in Pseudomonas stutzeri RCH2

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate GFF1547 Psest_1584 Arabinose efflux permease

Query= TCDB::F8SVK1
         (552 letters)



>FitnessBrowser__psRCH2:GFF1547
          Length = 452

 Score =  183 bits (465), Expect = 1e-50
 Identities = 103/314 (32%), Positives = 160/314 (50%), Gaps = 4/314 (1%)

Query: 18  KRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVRPFGA 77
           K  + A+ +G   EWYDF + G LA  IS+ FF   +  +A +     F  GF +RP G 
Sbjct: 10  KNQVLAAVIGNALEWYDFIVFGFLAVVISRLFFPAESEYSALLMATATFGVGFFMRPIGG 69

Query: 78  LVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLALGG 137
           ++ G   D  GRK    + I +M LS  ++ F P +AAIG+A+P++ +  RL+QG A GG
Sbjct: 70  VLLGIYADRKGRKAALQLIISLMTLSIAMIAFAPPFAAIGIAAPLLIVLARLMQGFATGG 129

Query: 138 EYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWGWRIP 197
           E+  A +++ E APANRRG Y +W      L +F    V   V + +  +   +WGWRIP
Sbjct: 130 EFASATSFLIESAPANRRGLYGSWQMFGQGLAVFCGAGVTALVTSNLSPEDLDSWGWRIP 189

Query: 198 FVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALIGVTA 257
           F+  L++  + +W+R  L E+ AF   +   K  K  L+          + ++AL   T 
Sbjct: 190 FIIGLIIGPVGLWMRRNLSETEAFLEARQAPK-EKQSLARMLRSHLRQVVTVMAL---TV 245

Query: 258 GQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRKPIIL 317
              V +Y    Y   F  + L +    A     +A+ + T     FG+LSDR+GRK +++
Sbjct: 246 CGTVAFYVILVYMPTFANRQLGMQLKDAFTAQVVAVAVLTLLMPVFGALSDRVGRKLLMI 305

Query: 318 AGCLIAALTYFPLF 331
              L   +  +PLF
Sbjct: 306 VATLGLLVALYPLF 319



 Score = 42.0 bits (97), Expect = 5e-08
 Identities = 22/88 (25%), Positives = 47/88 (53%), Gaps = 5/88 (5%)

Query: 453 MTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIV 512
           M +++ ++L ++    +GP +A + E FP  +R T ++L Y++    FGGF       ++
Sbjct: 334 MQLILCSLLAVF----FGPFSAAVAEQFPAGVRSTGLALAYNLAVMIFGGFAQFIVTWLI 389

Query: 513 AAKGNIYSGLWYPIIIALATFVIGLLFV 540
              G   + ++Y ++ A+   +IG  F+
Sbjct: 390 QNTGMAIAPVFY-VLFAVTLGLIGSFFL 416


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: 590
Number of extensions: 42
Number of successful extensions: 4
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: 452
Length adjustment: 34
Effective length of query: 518
Effective length of database: 418
Effective search space:   216524
Effective search space used:   216524
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 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