GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Pseudomonas putida KT2440

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate PP_2021 PP_2021 L-alpha-hydroxyglutaric acid gamma-lactonase

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__Putida:PP_2021
          Length = 376

 Score =  334 bits (857), Expect = 2e-96
 Identities = 188/380 (49%), Positives = 249/380 (65%), Gaps = 16/380 (4%)

Query: 10  LALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSV-KGPLRVAHTSNPS 68
           L  A L  +   A AA+L   LVG+YT+G+S+GI  Y FD   G +   PL+V  + +PS
Sbjct: 8   LLTASLMSLTISAHAATL---LVGSYTDGASQGIYRYHFDDKAGQIGPTPLQVVKSVSPS 64

Query: 69  YLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLS 128
           +L  + DQR LF VNE  +G        A+S+      G ++ ++QV T  D PT++SLS
Sbjct: 65  WLVLSADQRQLFAVNETPQG-------HASSFSISS-KGEIKPLNQVVTQGDEPTHASLS 116

Query: 129 HDGRYLFVANYSVQPE--GSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSVV 185
            D RYLFVANY+V P+  GS+ V+PV  DG+L PVVQ   H+AS V+P RQ   HVHS+V
Sbjct: 117 RDQRYLFVANYAVNPDPGGSLVVIPVAKDGTLKPVVQQARHKASGVNPERQAGAHVHSLV 176

Query: 186 SSPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFA 245
            SPDGQ+L+A DLGADKVF+YRY    A+ PL AA PA V  PPGSGPRHL+F A GR A
Sbjct: 177 LSPDGQHLYASDLGADKVFIYRYDGASADHPLTAAIPASVALPPGSGPRHLLFDAKGRHA 236

Query: 246 YLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDD 305
           YLTLE++ +V++F  + +G L + Q   L          AG LHLSADGRFL V NRG  
Sbjct: 237 YLTLEMNAEVVMFDVQ-DGNLVERQRLPLTERQEAAAKAAGGLHLSADGRFLYVSNRGTA 295

Query: 306 NQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSG 365
           N++V F+V    GQL F++RR  EG  PREFA  P   F+LVANQ S+Q+ V  RDP+SG
Sbjct: 296 NEIVAFSVGKQDGQLTFLQRRPAEGDHPREFALDPSDNFLLVANQKSNQIVVIRRDPRSG 355

Query: 366 QVGKTLQSVEVGSPSDLRFV 385
           ++ +T+Q+++  +PSDL+F+
Sbjct: 356 KLLETVQTLKQDAPSDLKFI 375


Lambda     K      H
   0.318    0.135    0.395 

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: 557
Number of extensions: 32
Number of successful extensions: 10
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: 388
Length of database: 376
Length adjustment: 30
Effective length of query: 358
Effective length of database: 346
Effective search space:   123868
Effective search space used:   123868
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: 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