GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Burkholderia phytofirmans PsJN

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate BPHYT_RS27000 BPHYT_RS27000 aspartate aminotransferase

Query= BRENDA::A0LEA5
         (388 letters)



>FitnessBrowser__BFirm:BPHYT_RS27000
          Length = 392

 Score =  186 bits (472), Expect = 1e-51
 Identities = 117/367 (31%), Positives = 181/367 (49%), Gaps = 5/367 (1%)

Query: 19  EIDRLKAELTAKGVDVINLGVGDPDLPTPDHIIARLKTAAEDPSTHQYPSYSGMNDFKVS 78
           EI R+  +  A+G DVI L VGDPD  TP  I+ R   A     TH Y + SG    + +
Sbjct: 19  EIHRVAQQAEARGEDVIVLSVGDPDFATPAPIVERAIEALRGGDTH-YSAVSGREPVRAA 77

Query: 79  VAGWYKRRFGVELDPLSEVLTLIGSKEGLAHFPLAVINPGDLALVPTPAYPVYHVATMFA 138
           +A  + R  G      + +LT  G++ G+    L ++  GD  +VP P Y  Y      A
Sbjct: 78  IAAEHTRMTGCAASAANVILTA-GAQNGVFAASLCLLEAGDEVIVPEPMYLTYEACVRAA 136

Query: 139 GGESYFMPLVRENGFLPDLDSIPADVARRAKVMFINYPNNPTGATAERDFFEKVIAFARE 198
           G     +P+     F  D D++ A V  R K +F   P NPTG   +R   E++   A  
Sbjct: 137 GATLVTVPVDAARAFHVDCDALEAAVTSRTKAIFFATPCNPTGVVMQRADLERIARLACR 196

Query: 199 YDVIVCHDAAYTEMAFGGYRPLSFLELPGAGEVGVEFHSLSKTYNMTGWRLGFAVGNADI 258
           +D+ V  D  Y E+ F     +S   LPG  E  V   SLSK++ M GWR+G+A+G  ++
Sbjct: 197 HDLWVLSDEVYAELTF-EREHVSIAALPGMAERTVTLGSLSKSHAMAGWRVGWAIGPTEL 255

Query: 259 LAGLGQVKSNIDSGAFNAVQWAGITALEGDQGCVVEMQRIYKERLDILIEGLKRI-GLHP 317
           +  +G++   +  G    +Q A +TA++       EM+ IY+ R D++ E L R+ GL  
Sbjct: 256 IEHMGRLALAMLYGLPGFIQQAALTAVQHKARIAAEMREIYRRRRDVVFERLHRVPGLRC 315

Query: 318 EVPRATFYVWCP-TPPGYSSKDFSSLLLREAGIVATPGSGFGAPGEGYIRMALTVDKERV 376
            +P A  ++    +  G  + DF+  L R  G+     S FG    G++R+   VD+ R+
Sbjct: 316 LLPEAGMFMMVDVSGTGLDTVDFTWQLFRARGVSLLDASAFGETANGFVRLGFVVDEARL 375

Query: 377 REAVERM 383
            +A ER+
Sbjct: 376 IDACERI 382


Lambda     K      H
   0.321    0.140    0.423 

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: 343
Number of extensions: 16
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: 388
Length of database: 392
Length adjustment: 31
Effective length of query: 357
Effective length of database: 361
Effective search space:   128877
Effective search space used:   128877
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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