GapMind for catabolism of small carbon sources

 

Aligments for a candidate for peb1B in Pseudomonas putida KT2440

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate PP_1070 PP_1070 glutamate / aspartate ABC transporter - permease subunit

Query= TCDB::A1VZQ3
         (250 letters)



>lcl|FitnessBrowser__Putida:PP_1070 PP_1070 glutamate / aspartate
           ABC transporter - permease subunit
          Length = 248

 Score =  120 bits (302), Expect = 2e-32
 Identities = 71/215 (33%), Positives = 121/215 (56%), Gaps = 13/215 (6%)

Query: 42  DAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIF 101
           D +I G  +T+ ++I A +IA + G++ GVM T   +++      YVELF+NVPL++Q+F
Sbjct: 23  DWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLF 82

Query: 102 FLFYALPVL---GIR------LDIFTIGVLGV----GAYHGAYVSEVVRSGILAVPRGQF 148
             ++ +P L   G++      L+  T  ++ V    G +  A V E VR+GI A+P+GQ 
Sbjct: 83  IWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQE 142

Query: 149 EASASQGFTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYA 208
            A+ + GF+  Q    +++PQ  RII+PP+T++ +N+ KN+SV  ++G  EL+      A
Sbjct: 143 AAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTA 202

Query: 209 ADYGNYAPAYIFAAVLYFIICYPLAYFAKAYENKL 243
               N   A+  A ++YF +   L    +  E K+
Sbjct: 203 EFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKV 237


Lambda     K      H
   0.328    0.143    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: 155
Number of extensions: 8
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: 250
Length of database: 248
Length adjustment: 24
Effective length of query: 226
Effective length of database: 224
Effective search space:    50624
Effective search space used:    50624
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: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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