GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argJ in Azospirillum brasilense Sp245

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate AZOBR_RS02855 AZOBR_RS02855 N-acetylglutamate synthase

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__azobra:AZOBR_RS02855
          Length = 412

 Score =  294 bits (753), Expect = 3e-84
 Identities = 173/400 (43%), Positives = 232/400 (58%), Gaps = 9/400 (2%)

Query: 13  LPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDED 72
           LP + G+ + TA +G++  G  DL L  +  G+TV  V T +  C+APV   +  L    
Sbjct: 16  LPPVAGVRIATANSGIRYKGRDDLMLAVLDEGTTVAGVLTKSLTCSAPVIWCRDSL-PRG 74

Query: 73  GVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADKII 132
             RA+V+N GNANA TG  G     A   AAA+  GC  ++V   STGVI  PL AD I 
Sbjct: 75  SARAVVVNAGNANAFTGKAGDATVQATVEAAAKIAGCATDEVYVASTGVIGIPLAADAIA 134

Query: 133 AALPKMQPAFWNEAA------RAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHP 186
             LP M PA  +++A      RAIMTTDT  K ++R+  +G   TV  +G AKGSGMI P
Sbjct: 135 KVLPGMVPALKDDSAALEAGARAIMTTDTFAKGSTRQVAIGGT-TVTISGFAKGSGMIAP 193

Query: 187 NMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEI 246
           +MATMLGF+ TDA ++ P LQ M  E  + +FN ITVDGDTST+D+ ++ ATGK   + +
Sbjct: 194 DMATMLGFLFTDAAIAAPALQSMLSEFTERSFNAITVDGDTSTSDTLLLFATGKAGNAPV 253

Query: 247 DNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARS 306
            +   P  A  ++ L  + L+LA  IVRDGEGATKF+++ +  A+    A++ A   A S
Sbjct: 254 TDAQAPELAAFRKALEEVMLDLALQIVRDGEGATKFVSITLVGAENDVAAKRIALTVANS 313

Query: 307 PLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQA 366
           PLVKTA    D N G+ +AAIG A     D DL+++ +   L+   G     Y EA   A
Sbjct: 314 PLVKTALAGEDANWGRIVAAIGRAG-ERADRDLIKITIGGTLICAEGMEVPGYDEAPVAA 372

Query: 367 VMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
            M   EI V I L  G   + V+TCDL+HGY+ IN  YRS
Sbjct: 373 HMKGQEIDVHIDLGIGTGKSRVWTCDLTHGYIDINGSYRS 412


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: 388
Number of extensions: 19
Number of successful extensions: 5
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: 412
Length adjustment: 31
Effective length of query: 375
Effective length of database: 381
Effective search space:   142875
Effective search space used:   142875
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