GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudomonas putida KT2440

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_1139 PP_1139 branched chain amino acid transporter - permease subunit

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__Putida:PP_1139
          Length = 418

 Score =  356 bits (914), Expect = e-103
 Identities = 218/446 (48%), Positives = 279/446 (62%), Gaps = 42/446 (9%)

Query: 16  VRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAI-FVAVAAIGRFAMV 74
           + + L +A F+A+L + +    +GLK   +I    ++V   G   I  +AV ++  F  V
Sbjct: 1   MNRNLKQAFFSALLVWAVAFPVLGLKL--SIDGISLVVHSQGSFTISIIAVCSVLMFLRV 58

Query: 75  VFIRP-------NIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIKG 127
           +F +          DR+ +  A    L +   + +             ++  ++VVA+  
Sbjct: 59  LFDKQWSSVMGRRSDRKLIPPAVSNYLTLPKTQRY-------------VIIGLIVVALVW 105

Query: 128 PQ-GSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGL 186
           P  GS   VD     ILIYV+L  GLNIVVGLAGLLDLGYV FYAVGAYSYA+LS Y G 
Sbjct: 106 PFFGSRGAVD-IATLILIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYAMLSHYLGW 164

Query: 187 SFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGI 246
           SFWV LP++G+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD T G  GI
Sbjct: 165 SFWVCLPIAGLMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDWTGGPNGI 224

Query: 247 SSIPKATLFGIPFDATAGGFAKLFH----LPISSAYYKIFLFYLILALCMLTAYVTIRLR 302
           S+IPK   FG+ F+  A    + FH    L  +S    IFL+ + L L +L  +V  RL 
Sbjct: 225 SNIPKPEFFGLTFERRAAEGMQTFHEFFGLQYNSINKVIFLYLVALLLALLALFVINRLL 284

Query: 303 RMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFV 362
           RMPIGRAWEALREDEIACR+LG+N    KL+AF  GA FAGFAGSFFAARQG V+PESF 
Sbjct: 285 RMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGACFAGFAGSFFAARQGLVTPESFT 344

Query: 363 FLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIF 422
           F+ESA+ILAIVVLGGMGS  G+ +AAIVM+   EL+RE S              YRML+F
Sbjct: 345 FIESAIILAIVVLGGMGSQLGVILAAIVMILLPELMREFS-------------EYRMLMF 391

Query: 423 GLAMVVVMLFKPRGFVGSREPTAFLR 448
           G  MV++M+++P+G +  + P   LR
Sbjct: 392 GALMVLMMIWRPQGLLPMQRPHMELR 417


Lambda     K      H
   0.330    0.145    0.432 

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: 630
Number of extensions: 46
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: 463
Length of database: 418
Length adjustment: 32
Effective length of query: 431
Effective length of database: 386
Effective search space:   166366
Effective search space used:   166366
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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