GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Thiohalomonas denitrificans HLD2

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_092992063.1 BLP65_RS02000 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ

Query= CharProtDB::CH_000559
         (406 letters)



>NCBI__GCF_900102855.1:WP_092992063.1
          Length = 404

 Score =  370 bits (951), Expect = e-107
 Identities = 202/399 (50%), Positives = 263/399 (65%), Gaps = 8/399 (2%)

Query: 12  QLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDE 71
           +L  + G+ L T  AG+KKPG  DL LI +A G+T  AVFT N FCAAPV +A+ HL   
Sbjct: 10  KLHPVGGVRLGTTAAGIKKPGRPDLVLIELARGATASAVFTRNAFCAAPVILAREHLSAR 69

Query: 72  DGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADKI 131
           +    L++NTGNANAGTG QG +DA   C A A + GC+   V+PFSTGVI EPLP   +
Sbjct: 70  EP-SYLLVNTGNANAGTGRQGLVDAQTCCEAVASRGGCEAADVLPFSTGVIGEPLPVATL 128

Query: 132 IAALPKMQPAF----WNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHPN 187
              +P    A     W  AA  I+TTDTVPK +SR+ ++G +  V  TGI+KG+GMI P+
Sbjct: 129 TQGIPAAFSALVAEGWANAADGILTTDTVPKGSSRQVEIGGR-PVTITGISKGAGMIRPD 187

Query: 188 MATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEID 247
           MATML FIATDA V + VL  + +  A  +FN I+VDGDTSTND+ V++ATG +      
Sbjct: 188 MATMLAFIATDAVVERDVLDGLLKRAAGLSFNRISVDGDTSTNDACVLMATGASGVKPEP 247

Query: 248 NIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARSP 307
              D  +  L+  + ++  ELAQ IVRDGEGATKFI ++V   +   E    AY  A SP
Sbjct: 248 GSDD--FETLETAVTAVCRELAQLIVRDGEGATKFIAIKVVKGRDQKECTDVAYTIAHSP 305

Query: 308 LVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQAV 367
           LVKTAFFASDPN G+ LAA+G A V DL+   V ++L+++ +   GGRAA Y EA+GQ V
Sbjct: 306 LVKTAFFASDPNWGRILAAVGRAGVPDLNLQAVTIHLNEVCIVSDGGRAADYEEARGQLV 365

Query: 368 MSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
           M ++EIT+R+ L RG A ATV+TCD S+ YV INA+YR+
Sbjct: 366 MDQEEITIRVDLSRGSAEATVWTCDFSYDYVRINAEYRT 404


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: 402
Number of extensions: 17
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: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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 Jul 25 2024. The underlying query database was built on Jul 25 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