GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pseudomonas putida KT2440

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_4864 PP_4864 High-affinity branched-chain amino acid transport ATP-binding protein BraF

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Putida:PP_4864
          Length = 291

 Score =  267 bits (682), Expect = 2e-76
 Identities = 137/293 (46%), Positives = 197/293 (67%), Gaps = 27/293 (9%)

Query: 9   MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68
           MSDD +L V++L M+FGG+ A++D S + +R  I ALIGPNGAGKTTVFNC+TGFYK + 
Sbjct: 1   MSDDIILSVDNLMMQFGGIKALSDVSLKVRRNQIFALIGPNGAGKTTVFNCLTGFYKASG 60

Query: 69  GMITFNQKSGKQYLLERL------PDF------------------RITKEARVARTFQNI 104
           G I  N +     +++ L       DF                   +   A +ARTFQNI
Sbjct: 61  GRIELNVRGSHTNVIQLLGERFQAADFVSPARFANRMYYKMFGGTHLVNRAGLARTFQNI 120

Query: 105 RLFSGLTVLENLLVAQHNKLMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDR 164
           RLF  ++V+ENLLVAQH   M  +   + G++    Y++  ++A++ A +WLE  DL+D 
Sbjct: 121 RLFKEMSVVENLLVAQH---MWVNRNLLAGVLNTKAYRKAESDALDHAFYWLEVVDLVDC 177

Query: 165 ADDPAGDLPYGAQRRLEIARAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTS 224
           A+  AG+L YG QRRLEIARAMCT P+++CLDEPAAGLNP+E+  L+ +++ +R E   +
Sbjct: 178 ANRLAGELSYGQQRRLEIARAMCTRPKIICLDEPAAGLNPQETEALSRMIRVLRDEHDIT 237

Query: 225 ILLIEHDMSVVMEISDHVVVLEYGQKISDGTPDHVKNDPRVIAAYLGVEDEEV 277
           ++LIEHDM +VM ISDH+VVL++G  I++G P  ++++P VIAAYLG ++EE+
Sbjct: 238 VVLIEHDMGMVMSISDHIVVLDHGNVIAEGAPQDIRHNPTVIAAYLGADEEEL 290


Lambda     K      H
   0.318    0.136    0.386 

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: 241
Number of extensions: 6
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: 292
Length of database: 291
Length adjustment: 26
Effective length of query: 266
Effective length of database: 265
Effective search space:    70490
Effective search space used:    70490
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: 48 (23.1 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