GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Caulobacter crescentus NA1000

Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate CCNA_03162 CCNA_03162 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase

Query= CharProtDB::CH_000559
         (406 letters)



>FitnessBrowser__Caulo:CCNA_03162
          Length = 481

 Score =  278 bits (711), Expect = 2e-79
 Identities = 167/400 (41%), Positives = 226/400 (56%), Gaps = 8/400 (2%)

Query: 13  LPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDED 72
           +P I G+ + T +AG  K    DL L+  A G++   VFT +   +APV   K  L    
Sbjct: 84  IPPIAGVEIATGRAGFYKHEREDLLLMRFAEGTSAAGVFTRHGVGSAPVDWCKRQLAATG 143

Query: 73  G--VRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADK 130
           G  VRALV+N G AN+ TG  G      V  A  ++  C+   VM  STGVI   L   K
Sbjct: 144 GADVRALVVNAGCANSFTGKPGADAVRRVATAVGKRFDCRQRDVMMASTGVIGVILDDSK 203

Query: 131 IIAALPKMQPAF----WNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHP 186
           I A LP+++       W EA RAIMTTDT PK A     + D H V+  GIAKGSGMI P
Sbjct: 204 ITARLPEVESRLKADAWAEAGRAIMTTDTFPKGAYATAVI-DGHEVKIAGIAKGSGMIAP 262

Query: 187 NMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEI 246
           +MATML F+ATDA ++   LQ +       TFN +TVDGD STND+ ++ ATG++   +I
Sbjct: 263 DMATMLAFVATDAAIAPAALQTLVSLYTRTTFNCVTVDGDRSTNDTLLLFATGQSGAPKI 322

Query: 247 DNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARS 306
               D R A  +E L  + L+LA  +V+DGEGATKF+ + V  A++   AR+ A   A S
Sbjct: 323 HRAGDKRLADFREKLEGVLLDLALQLVKDGEGATKFVKITVNGAESPASARKIARTIAES 382

Query: 307 PLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQA 366
           PLVKTAF   D N G+ + A+G AD   +  + + +   D+  A  G  +A Y EA+  A
Sbjct: 383 PLVKTAFAGEDANWGRIVMAVGRAD-EPVAREKISVKFGDLYAARDGLISAEYDEAKMSA 441

Query: 367 VMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406
            +      V + +  G+ +ATV+TCDL+  YV+IN DYRS
Sbjct: 442 YVKNQAFEVSVDVGVGRGSATVWTCDLTKQYVAINGDYRS 481


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: 412
Number of extensions: 18
Number of successful extensions: 5
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: 481
Length adjustment: 32
Effective length of query: 374
Effective length of database: 449
Effective search space:   167926
Effective search space used:   167926
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: 51 (24.3 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