GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas stutzeri RCH2

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate GFF1097 Psest_1130 glutamate N-acetyltransferase/amino-acid acetyltransferase

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__psRCH2:GFF1097
          Length = 405

 Score =  395 bits (1016), Expect = e-115
 Identities = 211/398 (53%), Positives = 274/398 (68%), Gaps = 7/398 (1%)

Query: 13  LPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDED 72
           L  + G  L  A AG+K+PG  D+ ++  A GS V  V TTN FCAAPV + +  +    
Sbjct: 11  LHPVPGFELGIASAGIKRPGRKDVVIMRCAEGSRVAGVTTTNAFCAAPVIVTRERMHGP- 69

Query: 73  GVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADKII 132
            VR L+ NTGNANAGTG QG  DA   CAA A   G     V+PFSTGVI EPLP  KI 
Sbjct: 70  -VRYLLTNTGNANAGTGPQGLADARHTCAALAAITGVDETAVLPFSTGVIGEPLPVQKIE 128

Query: 133 AALPK----MQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHPNM 188
           AAL      + P  W EAA  IMTTDT+PK ASR+ +  D  TV  TGI+KG+GMI PNM
Sbjct: 129 AALQAALDDLSPDHWAEAATGIMTTDTLPKGASRQFQ-HDGVTVTVTGISKGAGMIRPNM 187

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

Query: 249 IADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARSPL 308
                +A+LK+ +  + +E+AQAIVRDGEGATKF+TV+V    T  E    AYA A SPL
Sbjct: 248 ATGELFAKLKQAVLEVFMEVAQAIVRDGEGATKFVTVQVNGGGTHQECLDVAYAVAHSPL 307

Query: 309 VKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQAVM 368
           +KTA FASDPN G+ LAA+GYA V++LD   ++++L ++ +A  GGR++SYTE QG AVM
Sbjct: 308 IKTALFASDPNWGRILAAVGYAGVSNLDVSKIDVFLGEVCIASQGGRSSSYTEEQGAAVM 367

Query: 369 SKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
           +++EIT+RI+L RG  + T++T DLSH YV INA+YR+
Sbjct: 368 AREEITIRIELGRGDCSETIWTTDLSHEYVKINAEYRT 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: 426
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: 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