GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Dechloromonas agitata is5

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_027457665.1 K420_RS0108410 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ

Query= CharProtDB::CH_000559
         (406 letters)



>NCBI__GCF_000519045.1:WP_027457665.1
          Length = 408

 Score =  444 bits (1142), Expect = e-129
 Identities = 236/410 (57%), Positives = 298/410 (72%), Gaps = 6/410 (1%)

Query: 1   MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60
           M VN     A+QL  + G+ L  A+A ++K    DLTL+A+  G TV  VFT NRFCAAP
Sbjct: 1   MPVNYATPAADQLLPVAGVRLGVAEAEIRKKNRRDLTLVALDGGCTVAGVFTQNRFCAAP 60

Query: 61  VHIAKSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTG 120
           V + ++HL     +RALVINTG ANAGTG  GR  A A C A A  +G   +QV+PFSTG
Sbjct: 61  VQLCRNHLATGKEIRALVINTGIANAGTGEPGRQTAQASCEAVAALLGIAADQVLPFSTG 120

Query: 121 VILEPLPADKIIAALPKMQPAF----WNEAARAIMTTDTVPKAASREGKVGDQHTVRATG 176
           VILEPLP D++ A LP  +       W+ AA AIMTTDTV KAASR   VG + T+  +G
Sbjct: 121 VILEPLPVDRLKAGLPAAKADLKADNWHAAAHAIMTTDTVAKAASRRITVGGK-TITVSG 179

Query: 177 IAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVII 236
           I+KG+GMI PNMATMLGF+ATDA ++Q +L  + +E AD +FN ITVDGDTSTNDSFV+I
Sbjct: 180 ISKGAGMIKPNMATMLGFVATDAGIAQSLLDKLVKEAADASFNCITVDGDTSTNDSFVMI 239

Query: 237 ATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEA 296
           ATG+ S +   + AD  + +++  + ++A+ELAQAIVRDGEGATKFIT+ V+  KT +E 
Sbjct: 240 ATGQ-SGAAFASEADAGWDEVRAAIVAVAVELAQAIVRDGEGATKFITIAVQGGKTVEEC 298

Query: 297 RQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRA 356
           RQ  YA   SPLVKTAFFASDPNLG+ LAA+GYA +ADLD D V+++LDD+LVAE+GGRA
Sbjct: 299 RQVGYAIGHSPLVKTAFFASDPNLGRILAAVGYAGIADLDVDGVKVWLDDVLVAENGGRA 358

Query: 357 ASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
           A+Y EA+G  VM++ EITVR+ L RG A A+V+TCD S+ YV INADYRS
Sbjct: 359 AAYQEAEGARVMAQAEITVRVDLGRGNAQASVFTCDFSYDYVKINADYRS 408


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: 444
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: 406
Length of database: 408
Length adjustment: 31
Effective length of query: 375
Effective length of database: 377
Effective search space:   141375
Effective search space used:   141375
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 Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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