GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Cupriavidus basilensis 4G11

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate RR42_RS18020 RR42_RS18020 ornithine acetyltransferase

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__Cup4G11:RR42_RS18020
          Length = 409

 Score =  455 bits (1171), Expect = e-132
 Identities = 243/410 (59%), Positives = 290/410 (70%), Gaps = 5/410 (1%)

Query: 1   MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60
           MAVNL    AE L  + G+ L  A+AGV+K    D+ ++ VA GSTV  VFT NRFCAAP
Sbjct: 1   MAVNLPLPLAENLKPVAGVELGWAEAGVRKANRKDVLVVRVAQGSTVAGVFTRNRFCAAP 60

Query: 61  VHIAKSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTG 120
           V + + HL    G+RA+V+NTGNANAGTG  G  +A A C A A Q+G  P QV+PFSTG
Sbjct: 61  VQVCREHLAAGKGIRAIVVNTGNANAGTGEPGLANARATCDALAAQLGIAPEQVLPFSTG 120

Query: 121 VILEPLPADKIIAALP----KMQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATG 176
           VILEPLP D+I AALP      +P  W  AA +IMTTDT PKAASR  ++G + TV  +G
Sbjct: 121 VILEPLPVDRITAALPAAIANAKPDNWLAAAESIMTTDTQPKAASRTVQIGGK-TVTLSG 179

Query: 177 IAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVII 236
           I+KG+GMI PNMATMLGF+ATDA VSQ VLQ +    AD +FN+IT+DGDTSTNDSFV+I
Sbjct: 180 ISKGAGMIRPNMATMLGFVATDATVSQDVLQALVSYAADHSFNSITIDGDTSTNDSFVLI 239

Query: 237 ATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEA 296
           A+GK     I+      +  L+  L  L+ ELAQ IVRDGEGATK +T++VE  K   E 
Sbjct: 240 ASGKAGAPAIERAEGADFEALRAALTDLSQELAQMIVRDGEGATKLMTIQVEGGKDVAEC 299

Query: 297 RQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRA 356
           R  AYA A SPLVKTAF+ASDPNLG+ LAA+GYA V DLD + V ++LDD+LVA  GGR 
Sbjct: 300 RLIAYAVAHSPLVKTAFYASDPNLGRILAAVGYAGVDDLDVERVNLWLDDVLVARDGGRN 359

Query: 357 ASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
             Y E  GQ VM + EITVRI L RG AAATV+TCDLSH YVSINADYRS
Sbjct: 360 PEYREEDGQRVMKQAEITVRIALGRGDAAATVWTCDLSHDYVSINADYRS 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: 433
Number of extensions: 8
Number of successful extensions: 3
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