GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Pseudomonas fluorescens GW456-L13

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate PfGW456L13_4831 Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4831
         (340 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4831
           Glucosamine-6-phosphate deaminase [isomerizing],
           alternative (EC 3.5.99.6)
          Length = 340

 Score =  652 bits (1681), Expect = 0.0
 Identities = 340/340 (100%), Positives = 340/340 (100%)

Query: 1   LTSKMLEEALSSFEAVQAQLQQLDPQMIEIAGRLRRQPPQVAMTVARGSSDHAASYFAYL 60
           LTSKMLEEALSSFEAVQAQLQQLDPQMIEIAGRLRRQPPQVAMTVARGSSDHAASYFAYL
Sbjct: 1   LTSKMLEEALSSFEAVQAQLQQLDPQMIEIAGRLRRQPPQVAMTVARGSSDHAASYFAYL 60

Query: 61  TMQLLGIPVASLPMSVVTMQQAPLKVSGQVAFAFSQSGQSPDLVNSLRLLRKRGALSISL 120
           TMQLLGIPVASLPMSVVTMQQAPLKVSGQVAFAFSQSGQSPDLVNSLRLLRKRGALSISL
Sbjct: 61  TMQLLGIPVASLPMSVVTMQQAPLKVSGQVAFAFSQSGQSPDLVNSLRLLRKRGALSISL 120

Query: 121 VNAEDSPLEAACEFSLPLCAGTESSVAATKSFIATLSASARLIGHWKEDTELLDACRALP 180
           VNAEDSPLEAACEFSLPLCAGTESSVAATKSFIATLSASARLIGHWKEDTELLDACRALP
Sbjct: 121 VNAEDSPLEAACEFSLPLCAGTESSVAATKSFIATLSASARLIGHWKEDTELLDACRALP 180

Query: 181 EGLRDAAQQDWSQAIDALRDCQRLMVIGRGAGFAIAQEAALKFKETSAIQAEAFSSAEVR 240
           EGLRDAAQQDWSQAIDALRDCQRLMVIGRGAGFAIAQEAALKFKETSAIQAEAFSSAEVR
Sbjct: 181 EGLRDAAQQDWSQAIDALRDCQRLMVIGRGAGFAIAQEAALKFKETSAIQAEAFSSAEVR 240

Query: 241 HGPMALIGDNYPLLVFAPRGAEQAGLLSLAADMRQRGALVLLAAPDDVLERDLTLTRAEH 300
           HGPMALIGDNYPLLVFAPRGAEQAGLLSLAADMRQRGALVLLAAPDDVLERDLTLTRAEH
Sbjct: 241 HGPMALIGDNYPLLVFAPRGAEQAGLLSLAADMRQRGALVLLAAPDDVLERDLTLTRAEH 300

Query: 301 PALDPILAIQSFYVMAAGLAVARGMDPDQPRHLSKVTRTH 340
           PALDPILAIQSFYVMAAGLAVARGMDPDQPRHLSKVTRTH
Sbjct: 301 PALDPILAIQSFYVMAAGLAVARGMDPDQPRHLSKVTRTH 340


Lambda     K      H
   0.319    0.131    0.366 

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: 518
Number of extensions: 8
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: 340
Length of database: 340
Length adjustment: 28
Effective length of query: 312
Effective length of database: 312
Effective search space:    97344
Effective search space used:    97344
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 (21.8 bits)
S2: 49 (23.5 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, 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