GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Paraburkholderia bryophila 376MFSha3.1

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate H281DRAFT_06249 H281DRAFT_06249 glutamate N-acetyltransferase

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__Burk376:H281DRAFT_06249
          Length = 413

 Score =  441 bits (1134), Expect = e-128
 Identities = 233/414 (56%), Positives = 288/414 (69%), Gaps = 9/414 (2%)

Query: 1   MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60
           MAVN       QL  + G+ L  A+A ++KP   D+ +I+V  G+TVG VFT NRFCAAP
Sbjct: 1   MAVNFPSIDPAQLHPVAGVTLGWAEANIRKPNRKDVLVISVDEGATVGGVFTQNRFCAAP 60

Query: 61  VHIAKSHL----FDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMP 116
           V + + +L         +RALVINTGNANAGTG  G + A   C   AR     P QV+P
Sbjct: 61  VTVCRENLERVRAGGKPIRALVINTGNANAGTGEPGLVAARETCVELARLADIAPEQVLP 120

Query: 117 FSTGVILEPLPADKIIAALP----KMQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTV 172
           FSTGVILEPLP D++ A LP      + A W +AA+AIMTTDT+PKA SR+  + D HTV
Sbjct: 121 FSTGVILEPLPVDRLKAGLPAALANRKEANWYDAAQAIMTTDTLPKATSRQVTI-DGHTV 179

Query: 173 RATGIAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDS 232
             TGI+KG+GMI PNMATMLGF+A DA V+QPVL  + + +AD +FN IT+DGDTSTNDS
Sbjct: 180 TLTGISKGAGMIKPNMATMLGFLAFDAAVAQPVLDALVKHVADRSFNCITIDGDTSTNDS 239

Query: 233 FVIIATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKT 292
           F++IA+GK+S   I +   P YA L++ +  +A  LAQ IVRDGEGATKF+TV VE   +
Sbjct: 240 FILIASGKSSLPAITSTDSPAYAALRDAVTEVAQTLAQLIVRDGEGATKFMTVHVEGGSS 299

Query: 293 CDEARQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEH 352
             E RQ AYA   SPLVKTAF+ASDPNLG+ LAAIGYA + DLD   +++YLDD+LVA  
Sbjct: 300 VGECRQIAYAIGHSPLVKTAFYASDPNLGRILAAIGYAGIDDLDVGKIDLYLDDVLVATA 359

Query: 353 GGRAASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
           GGR  +Y E  GQ VM K EI +R+ L RG A AT++TCDLSH YVSINADYRS
Sbjct: 360 GGRNPAYREEDGQRVMKKSEIGIRVVLGRGNAQATIWTCDLSHDYVSINADYRS 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: 443
Number of extensions: 13
Number of successful extensions: 4
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