GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Acidovorax sp. GW101-3H11

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate Ac3H11_4758 Glutamate N-acetyltransferase (EC 2.3.1.35) / N-acetylglutamate synthase (EC 2.3.1.1)

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4758
          Length = 412

 Score =  443 bits (1139), Expect = e-129
 Identities = 233/413 (56%), Positives = 291/413 (70%), Gaps = 8/413 (1%)

Query: 1   MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60
           M VNL    A  L  I G+ +  A+AGV+K    DLT+  +  G++V  VFT NRFCAAP
Sbjct: 1   MPVNLVAPVAADLYPIAGVRIGVAEAGVRKANRKDLTVFLLDEGASVAGVFTQNRFCAAP 60

Query: 61  VHIAKSHLFDEDG---VRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPF 117
           V I++ HL  +     +RA+VINTGNANAGTGA G   A + C A ARQ+   P Q++PF
Sbjct: 61  VQISREHLSQQQAGQPIRAMVINTGNANAGTGADGLARARSTCVALARQLSVAPEQILPF 120

Query: 118 STGVILEPLPADKIIAALPKM----QPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVR 173
           STGVI+EPLP D+I A LP      QP  W  AA  IMTTDT+PKA S + ++G   TV 
Sbjct: 121 STGVIMEPLPNDRIEAGLPAAIADAQPGHWARAAEGIMTTDTLPKAFSAQAQIGGA-TVS 179

Query: 174 ATGIAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSF 233
            TGI+KG+GMI PNMATMLGF+ATDA V+  V+Q + +E+AD +FN +T+DGDTSTNDSF
Sbjct: 180 ITGISKGAGMIRPNMATMLGFLATDACVAPAVMQQLARELADGSFNRVTIDGDTSTNDSF 239

Query: 234 VIIATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTC 293
           V++AT K + + I ++       LK  + +++ +LAQAIVRDGEGATKFITVRVE  KT 
Sbjct: 240 VVVATNKAAHAPITSLDSAEGQALKAAMLAVSQKLAQAIVRDGEGATKFITVRVEGGKTG 299

Query: 294 DEARQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHG 353
           DE R+ AYA A SPLVKTAFFASDPNLG+ LAA+GYA + DLD   +++YLDD+ VA  G
Sbjct: 300 DECRKVAYAIAHSPLVKTAFFASDPNLGRILAAVGYAGIDDLDQTGIDLYLDDVHVAVQG 359

Query: 354 GRAASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
           GR  +Y E  GQ VM + EITVR+ L RG AA TV+TCD SH YV+INADYRS
Sbjct: 360 GRNPAYREEDGQRVMKQAEITVRVLLGRGNAADTVWTCDFSHEYVTINADYRS 412


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: 453
Number of extensions: 14
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: 412
Length adjustment: 31
Effective length of query: 375
Effective length of database: 381
Effective search space:   142875
Effective search space used:   142875
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.

Links

Downloads

Related tools

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