GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas fluorescens FW300-N1B4

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate Pf1N1B4_656 Glutamate N-acetyltransferase (EC 2.3.1.35) / N-acetylglutamate synthase (EC 2.3.1.1)

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_656
          Length = 405

 Score =  380 bits (977), Expect = e-110
 Identities = 205/398 (51%), Positives = 269/398 (67%), Gaps = 7/398 (1%)

Query: 13  LPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDED 72
           L  + G  L  A AG+K+PG  D+ ++  A GSTV  VFT N FCAAPV +AK  +  + 
Sbjct: 11  LHPVAGFELGIASAGIKRPGRKDVVVMRCAEGSTVAGVFTLNAFCAAPVILAKQRV--QG 68

Query: 73  GVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADKII 132
            VR L+ NTGNANAGTG  G   A   CA  A   G   + V+P+STGVI EPLP +KI 
Sbjct: 69  PVRYLLTNTGNANAGTGEPGLAAAERTCAKLAELTGVDASLVLPYSTGVIGEPLPVEKIE 128

Query: 133 ----AALPKMQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHPNM 188
               AAL  +    W  AA  IMTTDT+PK ASR+ +  D  T+  TGI+KG+GMI PNM
Sbjct: 129 GALQAALDDLSVDNWEAAATGIMTTDTLPKGASRQFQ-HDGVTITVTGISKGAGMIRPNM 187

Query: 189 ATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEIDN 248
           ATMLG+IATDAKVS+ VLQ +  + A+++FN IT+DGDTSTND  ++IATG+ +  EI  
Sbjct: 188 ATMLGYIATDAKVSREVLQNLLLDGANKSFNRITIDGDTSTNDCCMLIATGQAALPEITE 247

Query: 249 IADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARSPL 308
            + P +A LK+ +  + +++AQAIVRDGEGATKF+TV V       E     Y  A SPL
Sbjct: 248 ASGPLFALLKQAVFEVCMDVAQAIVRDGEGATKFVTVEVNGGGNHQECLDVGYTVAHSPL 307

Query: 309 VKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQAVM 368
           +KTA FASDPN G+ LAA+G A V +LD   ++++L D+ +A  G R+A+YTEAQG AVM
Sbjct: 308 IKTALFASDPNWGRILAAVGRAGVPNLDVSKIDVFLGDVCIASRGARSATYTEAQGAAVM 367

Query: 369 SKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
            ++EIT+RI+L RG+ + T++T DLSH YV INA+YR+
Sbjct: 368 QQEEITIRIELGRGECSETIWTTDLSHEYVKINAEYRT 405


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: 434
Number of extensions: 16
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: 405
Length adjustment: 31
Effective length of query: 375
Effective length of database: 374
Effective search space:   140250
Effective search space used:   140250
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