GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Burkholderia phytofirmans PsJN

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate BPHYT_RS12945 BPHYT_RS12945 glutamine synthetase

Query= reanno::BFirm:BPHYT_RS23160
         (444 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS12945 BPHYT_RS12945 glutamine
           synthetase
          Length = 471

 Score =  134 bits (337), Expect = 6e-36
 Identities = 134/465 (28%), Positives = 195/465 (41%), Gaps = 54/465 (11%)

Query: 3   DIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRS-----KFESGESMRLPQAVMIQTVTGD 57
           D+   +K   V  ++    D  G  +   +P S     KFESG +              D
Sbjct: 7   DVVQLVKDEDVKFVDFRFTDTRGKEQHVSVPVSAFDEDKFESGHAF-------------D 53

Query: 58  YPEDGTLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVH-FDGTPVAISPRRVLRR 116
                   G+   DM+ VPDA+T  + P+  + T  +  D V   DG      PR + +R
Sbjct: 54  GSSIAGWKGIEASDMLLVPDANTAFIDPFYEESTLVLTCDVVEPADGKGYERDPRSLAKR 113

Query: 117 VLELYKAKGWKPV--IAPELEFYLVDM---NKDP----------DLPLQPPI----GRTG 157
                K+ G        PE EF++ D    N D           + P         G TG
Sbjct: 114 AEAYLKSTGLGDTAFFGPEPEFFIFDSVQWNTDQSGCFIKIGSEEAPWSSAKEFEGGNTG 173

Query: 158 -RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEV-GAAQMEINFMHGDPLK 215
            RP T    + +  V+ F  +  ++    E   + V+   HEV G  Q EI       ++
Sbjct: 174 HRPGTKGGYFPVAPVDTFQDIRSEMCLLLEQIGIPVEVHHHEVAGQGQNEIGTKFSTLVQ 233

Query: 216 LADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGK 275
            AD +   K  +   A  +   ATFM KP+ G+ GS MH+HQS+  +  G NLF G    
Sbjct: 234 RADWLQQMKYIIHNVAHTYGKTATFMPKPVVGDNGSGMHVHQSIWKD--GANLFAGNGYA 291

Query: 276 PTSLFTS-YIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPH- 333
             S F   YI G+ K+  AL  I  P  NSY+RL     AP+ +A+   NR+   RIPH 
Sbjct: 292 GLSEFALFYIGGIIKHARALNAITNPSTNSYKRLVPHFEAPVKLAYSARNRSASIRIPHV 351

Query: 334 SGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQ------ 387
           S P  RRIE R P    NPYL  +A + AG  G+  K+   E    + Y+LP +      
Sbjct: 352 SNPKGRRIETRFPDPMANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYDLPPEEDAKIP 411

Query: 388 -LPRNLEEGLTLMGACEPI---AEVLGEKFVKAYLALKETEYEAF 428
            +   L++ L  + A         V  +  + AY+ LK  E + +
Sbjct: 412 TVCAGLDQALDALDADREFLTRGGVFTDSMLDAYIELKTGELQRY 456


Lambda     K      H
   0.321    0.138    0.418 

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: 529
Number of extensions: 32
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: 444
Length of database: 471
Length adjustment: 33
Effective length of query: 411
Effective length of database: 438
Effective search space:   180018
Effective search space used:   180018
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: 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 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