GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argJ in Phaeobacter inhibens BS107

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate GFF3407 PGA1_c34600 arginine biosynthesis bifunctional protein ArgJ

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__Phaeo:GFF3407
          Length = 409

 Score =  274 bits (701), Expect = 3e-78
 Identities = 168/403 (41%), Positives = 235/403 (58%), Gaps = 16/403 (3%)

Query: 12  QLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDE 71
           +LP I G+   +A AGVK    TD+ L  +  GS V  VFT +   +APV   ++ L   
Sbjct: 15  KLPQIAGVRFASAAAGVKYKNRTDVMLAVMDPGSAVAGVFTRSATRSAPVLDCQAKLASN 74

Query: 72  DGVRA----LVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLP 127
           D   A    +++N+GN+NA TG  G+     +    A   G    +V   STGVI EPLP
Sbjct: 75  DNHTAHGAAILVNSGNSNAFTGHYGQTSVAEITRTVADITGIPAARVFTASTGVIGEPLP 134

Query: 128 ADKIIAALPKMQPAFW----NEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGM 183
            D+I++ +  +          +AA AIMTTDT  K A    +VG + TV   GIAKGSGM
Sbjct: 135 HDRIVSQIATLNDGLVATAIEDAAEAIMTTDTFAKGAGATIEVGGK-TVSIAGIAKGSGM 193

Query: 184 IHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQ 243
           I P+MATML +I TDA+++Q  LQ++  +I D TFN ITVD DTST+DS ++ A+G    
Sbjct: 194 IAPDMATMLVYIFTDAQIAQNDLQVLLSQICDRTFNCITVDSDTSTSDSLMLCASG---A 250

Query: 244 SEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAA 303
           S ID   +  +A   E   ++ L+L+  +VRDGEGATKF+ ++V  A    +A+    + 
Sbjct: 251 SGIDVTGNTDFALALE---NVMLDLSHQVVRDGEGATKFVEIQVTGAMNDHDAKVHGLSI 307

Query: 304 ARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQ 363
           A SPLVKTA    DPN G+ + AIG +  A  D D + +   ++LVAE G  +  Y E  
Sbjct: 308 ANSPLVKTAIAGEDPNWGRVVMAIGKSGAA-ADRDKLSISFGEVLVAEKGWVSPDYKETD 366

Query: 364 GQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
           G A M+K EI +++ L   +  +TV+TCDL+H Y+SINADYRS
Sbjct: 367 GAAEMAKPEIVIKVDLGLAEGKSTVWTCDLTHQYISINADYRS 409


Lambda     K      H
   0.317    0.130    0.367 

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: 379
Number of extensions: 18
Number of successful extensions: 6
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: 406
Length of database: 409
Length adjustment: 31
Effective length of query: 375
Effective length of database: 378
Effective search space:   141750
Effective search space used:   141750
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: 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