GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Burkholderia phytofirmans PsJN

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate BPHYT_RS23405 BPHYT_RS23405 glucosamine--fructose-6-phosphate aminotransferase

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



>FitnessBrowser__BFirm:BPHYT_RS23405
          Length = 605

 Score =  117 bits (292), Expect = 1e-30
 Identities = 110/361 (30%), Positives = 163/361 (45%), Gaps = 43/361 (11%)

Query: 14  MEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAVVVTCAR------GSSDHAATYAK 67
           M++E  E   AVS+    N  A +  A+   A+ P       R      G+S ++A  AK
Sbjct: 251 MQKEIFEQPLAVSKTFPRN-SAFD--ASLFGATDPQAFAQIDRILLLGCGTSHYSALTAK 307

Query: 68  YLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGA-FV 126
              E++  +PT    +S    Y   +   N L + ISQSG++ D L  + H +  G    
Sbjct: 308 AWFESIAKIPT-QVEISSEYRYRETIPGKNTLVVPISQSGETADTLGALMHAQSLGQDHT 366

Query: 127 VAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDEALETAVA 186
           +A+ N   S +   +      +AGPE  VA+TK++   L A+  L         L  A  
Sbjct: 367 LAICNVATSAIVRQSRWSFITQAGPEIGVASTKAFTTQLVALFVLAVT------LGRARG 420

Query: 187 DLPAQLERAFALDWSAAVTALTGA------------------SGLFVLGRGYGYGIAQEA 228
            + AQ E ++    S   TAL G                   S +F LGRG  + IA E 
Sbjct: 421 YVDAQQEASYRSQLSGLSTALQGVLAREPQIIAWAHEIARTDSAIF-LGRGSHFPIALEG 479

Query: 229 ALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAE 288
           ALK KE   +HAE + A E++HGP+A+V +A  V+  A +D   E ++  + E R+R  +
Sbjct: 480 ALKLKEISYIHAEGYPAGELKHGPLALVTDAMPVVVTAPNDGLLEKLKSNIQEVRARRGQ 539

Query: 289 V-LLADPAA---RQAGLPAIAA---HPAIEPILIVQSFYKMANALALARGCDPDSPPHLN 341
           V + AD  A    + GL  I     + A+ PIL V     +A   A  RG D D P +L 
Sbjct: 540 VYVFADADANLSNEEGLRVIQMPEYYGALSPILHVLPLQLLAYHTACTRGTDVDKPRNLA 599

Query: 342 K 342
           K
Sbjct: 600 K 600


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: 398
Number of extensions: 17
Number of successful extensions: 4
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: 605
Length adjustment: 33
Effective length of query: 314
Effective length of database: 572
Effective search space:   179608
Effective search space used:   179608
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: 51 (24.3 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