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

GapMind for Amino acid biosynthesis

Aligments 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.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis