GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Paraburkholderia bryophila 376MFSha3.1

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate H281DRAFT_00452 H281DRAFT_00452 L-glutamine synthetase

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



>FitnessBrowser__Burk376:H281DRAFT_00452
          Length = 471

 Score =  135 bits (340), Expect = 3e-36
 Identities = 136/465 (29%), Positives = 198/465 (42%), 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 AEAYLKSSGLGDTAFFGPEPEFFIFDSVQWNTDQSGCFVKIGSEEAPWSSSKEFEGGNTG 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 RADWLQQMKYIIQNVAHTYGKTATFMPKPIVGDNGSGMHVHQSIWKD--GQNLFAGNGYA 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 -LPRNLEEGL-TLMGACEPIAE--VLGEKFVKAYLALKETEYEAF 428
            +   L++ L  L G  E +    V  +  + AY+ LK  E + +
Sbjct: 412 TVCAGLDQALDALDGDREFLTRGGVFTDSMLDAYIELKTNELQRY 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: 519
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.

Links

Downloads

Related tools

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