GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lhgD in Pseudomonas putida KT2440

Align (S)-2-hydroxyglutarate oxidase (characterized)
to candidate PP_2910 PP_2910 L-2-hydroxyglutarate oxidase

Query= metacyc::G1G01-3089-MONOMER
         (416 letters)



>lcl|FitnessBrowser__Putida:PP_2910 PP_2910 L-2-hydroxyglutarate
           oxidase
          Length = 416

 Score =  835 bits (2158), Expect = 0.0
 Identities = 416/416 (100%), Positives = 416/416 (100%)

Query: 1   MYDFIIIGGGIVGMSTAMHLIKVYPDAKMLLLEKESGPARHQTGHNSGVIHAGVYYTPGS 60
           MYDFIIIGGGIVGMSTAMHLIKVYPDAKMLLLEKESGPARHQTGHNSGVIHAGVYYTPGS
Sbjct: 1   MYDFIIIGGGIVGMSTAMHLIKVYPDAKMLLLEKESGPARHQTGHNSGVIHAGVYYTPGS 60

Query: 61  LKARFCLEGNKATKAFCTQHGIRFDECGKLLVATNDLEMQRMKALWERTAANGLERYWLS 120
           LKARFCLEGNKATKAFCTQHGIRFDECGKLLVATNDLEMQRMKALWERTAANGLERYWLS
Sbjct: 61  LKARFCLEGNKATKAFCTQHGIRFDECGKLLVATNDLEMQRMKALWERTAANGLERYWLS 120

Query: 121 ADELREREPNIVGMGGIFVPSSGIVNYAQVTAAMAAEFQRAGGEIRYGAEVVGLQEQANE 180
           ADELREREPNIVGMGGIFVPSSGIVNYAQVTAAMAAEFQRAGGEIRYGAEVVGLQEQANE
Sbjct: 121 ADELREREPNIVGMGGIFVPSSGIVNYAQVTAAMAAEFQRAGGEIRYGAEVVGLQEQANE 180

Query: 181 VIVRTQRDELHSRFLVTCSGLMADRVVGMLGLRTEFVICPFRGEYYLLPKQHNQIVNHLI 240
           VIVRTQRDELHSRFLVTCSGLMADRVVGMLGLRTEFVICPFRGEYYLLPKQHNQIVNHLI
Sbjct: 181 VIVRTQRDELHSRFLVTCSGLMADRVVGMLGLRTEFVICPFRGEYYLLPKQHNQIVNHLI 240

Query: 241 YPIPDPSMPFLGVHLTRMIDGTVTVGPNAVLAMKREGYRKTDVSPSDLFQTLTTPGILKV 300
           YPIPDPSMPFLGVHLTRMIDGTVTVGPNAVLAMKREGYRKTDVSPSDLFQTLTTPGILKV
Sbjct: 241 YPIPDPSMPFLGVHLTRMIDGTVTVGPNAVLAMKREGYRKTDVSPSDLFQTLTTPGILKV 300

Query: 301 LAKNFRPGLIEMKNSLFKGGYLKQVQKYCPSIIKADLTPYPAGVRAQAVSRDGKLIDDFL 360
           LAKNFRPGLIEMKNSLFKGGYLKQVQKYCPSIIKADLTPYPAGVRAQAVSRDGKLIDDFL
Sbjct: 301 LAKNFRPGLIEMKNSLFKGGYLKQVQKYCPSIIKADLTPYPAGVRAQAVSRDGKLIDDFL 360

Query: 361 FVNTARSVNVCNAPSPAATSAIPIGAYIVEKVCEQVGLQGGSFPKADLSANQRAAS 416
           FVNTARSVNVCNAPSPAATSAIPIGAYIVEKVCEQVGLQGGSFPKADLSANQRAAS
Sbjct: 361 FVNTARSVNVCNAPSPAATSAIPIGAYIVEKVCEQVGLQGGSFPKADLSANQRAAS 416


Lambda     K      H
   0.321    0.137    0.409 

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: 807
Number of extensions: 17
Number of successful extensions: 1
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: 416
Length of database: 416
Length adjustment: 31
Effective length of query: 385
Effective length of database: 385
Effective search space:   148225
Effective search space used:   148225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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 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