GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Marivita geojedonensis DPG-138

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_085634949.1 MGEO_RS01660 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ

Query= CharProtDB::CH_000559
         (406 letters)



>NCBI__GCF_002115805.1:WP_085634949.1
          Length = 409

 Score =  280 bits (715), Expect = 7e-80
 Identities = 173/408 (42%), Positives = 239/408 (58%), Gaps = 14/408 (3%)

Query: 5   LTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIA 64
           L  K   +LP I G+   TA AGVK  G TD+ L  +  GS V   FT +   +A V   
Sbjct: 10  LAPKNFPELPVIKGVRFATAAAGVKYSGRTDVMLAVLDPGSRVAGAFTKSATRSANVLDC 69

Query: 65  KSHL-FDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVIL 123
           +S +   +D   A+++N+GN+NA TG  G     A+CA  AR      N+V   STGVI 
Sbjct: 70  QSKIRLTDDRGAAIIVNSGNSNAFTGRAGDESVQAICAEVARVTDLPANRVFTSSTGVIG 129

Query: 124 EPLPADKIIAALPKM----QPAFWNEAARAIMTTDTVPKAASREGKV-GDQHTVRATGIA 178
           E LP D+I A + ++      A    AA+AIMTTDT PK ++    + G + T+   GIA
Sbjct: 130 ERLPHDRIAAKVEELYGNLDEAGLPNAAKAIMTTDTFPKGSTTSVDLPGGKVTI--AGIA 187

Query: 179 KGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIAT 238
           KGSGMI P+MATML +I TDAK++Q  LQ +  EI ++TFN+ITVD DTST+D+ ++ AT
Sbjct: 188 KGSGMIAPDMATMLVYIFTDAKIAQSDLQALVSEINEKTFNSITVDSDTSTSDTLLVAAT 247

Query: 239 GKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQ 298
           G +  S        +    ++ L  +  +LA  +VRDGEGATKF+ + V  A    +A+ 
Sbjct: 248 GASGVS-----VTAKDTAFRDGLHHVMQDLAHQVVRDGEGATKFLQITVTGALNDADAKT 302

Query: 299 AAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAAS 358
            A + A SPLVKTA    DPN G+ + AIG +  A  D D + +   D+ VA +G     
Sbjct: 303 HAMSIANSPLVKTAIAGEDPNWGRVVMAIGKSG-APADRDTLSISFGDVKVATNGWVDPD 361

Query: 359 YTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
           Y E QG A+M ++ I++ + L  G   ATV+TCDL+HGY+SINADYRS
Sbjct: 362 YREEQGAAIMKQENISMTVDLGMGSGEATVWTCDLTHGYISINADYRS 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: 385
Number of extensions: 21
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 Jul 26 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