GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Pseudomonas putida KT2440

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate PP_1298 PP_1298 putative amino acid ABC transporter - permease subunit

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__Putida:PP_1298
          Length = 392

 Score =  300 bits (768), Expect = 5e-86
 Identities = 184/410 (44%), Positives = 245/410 (59%), Gaps = 35/410 (8%)

Query: 20  DTRFRSITIQIVVLLLFLAGLVW-LLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPY 78
           D R R+   QI+ ++ F+ GL W L +N   NL+ +G    F FL   AG+ +AQ LIPY
Sbjct: 15  DPRVRAWLFQILTIV-FVVGLGWYLFHNTQTNLQHRGITSGFDFLDRSAGFGIAQHLIPY 73

Query: 79  SNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNI 138
              D++ R  + GLLNTLLV+ +G ILATILG IIGV RLS NW++ ++ TVYVETFRNI
Sbjct: 74  VESDSYARVFVIGLLNTLLVTFIGVILATILGFIIGVARLSPNWMINKLATVYVETFRNI 133

Query: 139 PLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAF 198
           P LL IL     +  T P                 P+ S+   D   ++NRG N+P  + 
Sbjct: 134 PPLLQILFWYFAVFLTLP----------------GPRGSINIEDMFFISNRGLNMPGAS- 176

Query: 199 DHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLI 258
                + D  W   V+L ALAI A+     +  +RF          TG     +W  LL+
Sbjct: 177 -----IADGFWPFVVAL-ALAIAAIALMVRYANKRF--------NETGVPFHKFWAGLLL 222

Query: 259 LFA--PISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAG 316
             A   +S LL+G     D PQ+  F+F GG+ ++    AL +ALT+YTAAFIAEIVR+G
Sbjct: 223 FIAIPSLSVLLFGSPVTWDMPQLKGFNFVGGWVLIPELLALTLALTIYTAAFIAEIVRSG 282

Query: 317 IQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMD 376
           I+++S GQTEAA +LGLR G T+  VI+PQALRVI+PPL SQ+LNL KNSSLA  + Y +
Sbjct: 283 IRSVSHGQTEAARSLGLREGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPE 342

Query: 377 LRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426
           +     G  LNQTG+ +E + + M +YL IS++IS LMN YNK I L ER
Sbjct: 343 MVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIER 392


Lambda     K      H
   0.326    0.139    0.419 

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: 408
Number of extensions: 21
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: 426
Length of database: 392
Length adjustment: 31
Effective length of query: 395
Effective length of database: 361
Effective search space:   142595
Effective search space used:   142595
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 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