GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Caulobacter crescentus NA1000

Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate CCNA_00285 CCNA_00285 acetylglutamate kinase

Query= BRENDA::Q0ASS9
         (441 letters)



>FitnessBrowser__Caulo:CCNA_00285
          Length = 304

 Score =  106 bits (264), Expect = 1e-27
 Identities = 96/295 (32%), Positives = 147/295 (49%), Gaps = 31/295 (10%)

Query: 23  KEIREYLHRFSGIDQERFAVIKVGG-AVIQDDLPGLASALA-FLQTVGLTPVVVHGGGPQ 80
           K + E L      D+E   VIK GG A+ Q+D+  + +A A  L+ +G+ PVVVHGGGPQ
Sbjct: 14  KTLAEALPYIQIYDRET-VVIKYGGHAMGQEDVAKVFAADAVLLKLLGVHPVVVHGGGPQ 72

Query: 81  LDAALEAADIPTERVDGLRVTRDEAIPIIRDTLTQA-NLALVDAIRDAGGRAAAVPRGV- 138
           +   L+ A + +  VDGLRVT +  + +    L+ A N  + + I  AG  A A  RGV 
Sbjct: 73  ISRMLDKAGVKSTFVDGLRVTDEATMEVAEMVLSGAINKEIANWITLAG--AEADVRGVG 130

Query: 139 ---FEADIVDADK-----------------LGRVGEPRHIHLDLVGS--AARAGQAAILA 176
               +A ++ A+K                 LG VGEP  +   L+ +   +      ++A
Sbjct: 131 LSGKDARLITAEKVTRTKKDPDSNIEQAVDLGFVGEPTKVDPQLIEALLTSEHDYIPVVA 190

Query: 177 CLGETPDGTLVNINADVAVRALVHALQPYKVVFLTGTGGLLDEDGDILSSINLATDFGDL 236
            +G +PDG   NINAD    AL  AL+  +++ LT   G+LD +G+++  + +      L
Sbjct: 191 PIGVSPDGDTFNINADTVAGALAGALKAKRMLMLTDIKGVLDGNGELIREMTI-EQARAL 249

Query: 237 MQADWVNGGMRLKLEE-IKRLLDDLPLSSSVSITRPSELARELFTHAGSGTLIRR 290
           +      GGM  KLE  I  +   +     +   RP  +  ELF+  G+GTLI+R
Sbjct: 250 IDTGVATGGMIPKLENAIHAIESGVEAVVILDGRRPHAMLVELFSEYGAGTLIKR 304


Lambda     K      H
   0.320    0.139    0.411 

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: 275
Number of extensions: 13
Number of successful extensions: 3
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: 441
Length of database: 304
Length adjustment: 30
Effective length of query: 411
Effective length of database: 274
Effective search space:   112614
Effective search space used:   112614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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