GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Pseudomonas putida KT2440

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate PP_1070 PP_1070 glutamate / aspartate ABC transporter - permease subunit

Query= TCDB::Q8YPM8
         (308 letters)



>FitnessBrowser__Putida:PP_1070
          Length = 248

 Score =  127 bits (320), Expect = 2e-34
 Identities = 86/239 (35%), Positives = 124/239 (51%), Gaps = 22/239 (9%)

Query: 72  TDTYSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPL 131
           ++TY      GL  ++ IA    I+  ++G L G+ R   N LV  I+  YVE+FRN PL
Sbjct: 18  SETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPL 77

Query: 132 LLQLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFT--FSPEFSALLLGLI---F 186
           L+QL  WYF V   LP            GL +      WF    +P  SAL+  +I    
Sbjct: 78  LVQLFIWYFLVPDLLPE-----------GLQE------WFKQDLNPTTSALISVVICLGL 120

Query: 187 YTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLT 246
           +T A + E VR GIQ++ KGQ  A R++G +   I   V+ PQA R+IIPPLTS++LN+ 
Sbjct: 121 FTAARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVF 180

Query: 247 KNSSLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTVQI 305
           KNSS+A  IG  ++      T   +    E   L  L Y +L++ + L+M    + V +
Sbjct: 181 KNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAV 239


Lambda     K      H
   0.328    0.143    0.430 

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: 200
Number of extensions: 9
Number of successful extensions: 2
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: 308
Length of database: 248
Length adjustment: 25
Effective length of query: 283
Effective length of database: 223
Effective search space:    63109
Effective search space used:    63109
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: 47 (22.7 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