GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argJ in Dechlorosoma suillum PS

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate Dsui_0226 Dsui_0226 glutamate N-acetyltransferase/amino-acid acetyltransferase

Query= CharProtDB::CH_000559
         (406 letters)



>lcl|FitnessBrowser__PS:Dsui_0226 Dsui_0226 glutamate
           N-acetyltransferase/amino-acid acetyltransferase
          Length = 413

 Score =  425 bits (1093), Expect = e-123
 Identities = 230/415 (55%), Positives = 290/415 (69%), Gaps = 11/415 (2%)

Query: 1   MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60
           M VN      E L  + G+ L TA+AG++K    DLT+IA+  GSTV  VFT NRFCAAP
Sbjct: 1   MPVNYATPAPEALFPVAGVRLGTAEAGIRKANRRDLTVIALDPGSTVAGVFTQNRFCAAP 60

Query: 61  VHIAKSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGC-KPNQVMPFST 119
           V + + HL  E  +RALVINTG ANAGTG  G   A+  CA  A  +G  +  Q++PFST
Sbjct: 61  VQVCRKHLAGESEIRALVINTGIANAGTGETGLQAAMQTCATLAGLLGLDEDRQILPFST 120

Query: 120 GVILEPLPADKIIAALPK----MQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRAT 175
           GVILEPLP D++ A LP     ++   W+ AA  IMTTDTV KAASR+ ++G + +V  T
Sbjct: 121 GVILEPLPVDRLQAGLPAAIADLKADNWHAAAHGIMTTDTVAKAASRKVEIGGK-SVTIT 179

Query: 176 GIAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVI 235
           GI+KG+GMI PNMATMLGF+ATDA + Q +L+ + +E AD++FN ITVDGDTSTNDSF++
Sbjct: 180 GISKGAGMIKPNMATMLGFLATDAGIPQHLLEQVAKEAADQSFNCITVDGDTSTNDSFIV 239

Query: 236 IATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDE 295
           +ATG+ S   I + ADP +A LK  + ++++ELAQAIVRDGEGATKFITV VE  K  +E
Sbjct: 240 MATGQ-SGLRIKDGADPAWAPLKAAIVAVSIELAQAIVRDGEGATKFITVAVEGGKDLEE 298

Query: 296 ARQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYL----DDILVAE 351
            R+  YA   SPLVKTAFFASDPNLG+ LAAIGYA + DLD   + ++L    D +LVAE
Sbjct: 299 CRKVGYAIGHSPLVKTAFFASDPNLGRILAAIGYAGITDLDVGQIRVWLASGSDAVLVAE 358

Query: 352 HGGRAASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
            GGRAA+Y E  G  +M   EITVR+ L RG A   +Y+CD S+ YV INADYRS
Sbjct: 359 KGGRAAAYKEEDGSRIMKNAEITVRVDLARGTAQGCIYSCDFSYDYVKINADYRS 413


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: 440
Number of extensions: 15
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: 413
Length adjustment: 31
Effective length of query: 375
Effective length of database: 382
Effective search space:   143250
Effective search space used:   143250
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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