GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA 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)



>FitnessBrowser__PS:Dsui_0226
          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:

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