GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Azospirillum brasilense Sp245

Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate AZOBR_RS03285 AZOBR_RS03285 acetylglutamate kinase

Query= BRENDA::Q0ASS9
         (441 letters)



>FitnessBrowser__azobra:AZOBR_RS03285
          Length = 299

 Score =  117 bits (293), Expect = 5e-31
 Identities = 95/297 (31%), Positives = 143/297 (48%), Gaps = 30/297 (10%)

Query: 16  LSHMRDGKEIREYLHRFSGIDQERFAVIKVGGAVIQDD--LPGLASALAFLQTVGLTPVV 73
           L+  R   E   Y+ R++G    R  VIK GG  + DD      A  +  L+ VG+ PVV
Sbjct: 10  LAKARTLSEALPYMRRYAG----RTFVIKYGGHAMGDDSLAEKFARDIVLLKQVGINPVV 65

Query: 74  VHGGGPQLDAALEAADIPTERVDGLRVTRDEAIPIIRDTLT-QANLALVDAIRDAGGRAA 132
           VHGGGPQ+   L+   I +  +DGLRVT  E + ++   L    N  +V AI +AGGRA 
Sbjct: 66  VHGGGPQIGQMLQRLAIKSSFIDGLRVTDKETVEVVEMVLAGSINKQIVAAINNAGGRAV 125

Query: 133 AVPRGVFEADIVDADK-----------------LGRVGEPRHIHLDLVGSAARAGQAAIL 175
            +     +  ++ A K                 LG VGEP  ++  ++ S A++    ++
Sbjct: 126 GLSGK--DGSLITARKLRRTQRDPDSNIEKVLDLGFVGEPYQVNPQIITSLAQSDIIPVI 183

Query: 176 ACLGETPDGTLVNINADVAVRALVHALQPYKVVFLTGTGGLLDEDGDILSSINLATDFGD 235
           A +G   +G   NINAD A  A+  AL   +   LT   G+LD++ +++  ++L  D   
Sbjct: 184 APIGFDRNGDTYNINADTAAGAVASALGATRFFLLTDVAGVLDKNKELVPRMSL--DQAR 241

Query: 236 LMQAD-WVNGGMRLKLEE-IKRLLDDLPLSSSVSITRPSELARELFTHAGSGTLIRR 290
              AD    GGM  K+E  I  +   +  +  +    P  L  E+FT  G+GTLI R
Sbjct: 242 AAIADGTATGGMIPKIETCIDAVEQGVDAAVILDGRVPHALLLEIFTEGGAGTLIGR 298


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: 294
Number of extensions: 16
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: 299
Length adjustment: 29
Effective length of query: 412
Effective length of database: 270
Effective search space:   111240
Effective search space used:   111240
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.

Links

Downloads

Related tools

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