GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Sphingomonas koreensis DSMZ 15582

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate Ga0059261_1644 Ga0059261_1644 Predicted phosphosugar isomerases

Query= reanno::Korea:Ga0059261_1644
         (347 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1644 Ga0059261_1644 Predicted
           phosphosugar isomerases
          Length = 347

 Score =  663 bits (1710), Expect = 0.0
 Identities = 347/347 (100%), Positives = 347/347 (100%)

Query: 1   MVPNAAGASLGTLMEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAVVVTCARGSSD 60
           MVPNAAGASLGTLMEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAVVVTCARGSSD
Sbjct: 1   MVPNAAGASLGTLMEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAVVVTCARGSSD 60

Query: 61  HAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQR 120
           HAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQR
Sbjct: 61  HAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQR 120

Query: 121 KAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDEA 180
           KAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDEA
Sbjct: 121 KAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDEA 180

Query: 181 LETAVADLPAQLERAFALDWSAAVTALTGASGLFVLGRGYGYGIAQEAALKFKETCALHA 240
           LETAVADLPAQLERAFALDWSAAVTALTGASGLFVLGRGYGYGIAQEAALKFKETCALHA
Sbjct: 181 LETAVADLPAQLERAFALDWSAAVTALTGASGLFVLGRGYGYGIAQEAALKFKETCALHA 240

Query: 241 ESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLLADPAARQAG 300
           ESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLLADPAARQAG
Sbjct: 241 ESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLLADPAARQAG 300

Query: 301 LPAIAAHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNKVTETL 347
           LPAIAAHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNKVTETL
Sbjct: 301 LPAIAAHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNKVTETL 347


Lambda     K      H
   0.317    0.128    0.360 

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: 578
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: 347
Length of database: 347
Length adjustment: 29
Effective length of query: 318
Effective length of database: 318
Effective search space:   101124
Effective search space used:   101124
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: 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