GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Magnetospirillum magneticum AMB-1

Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_011386705.1 AMB_RS22045 acetylglutamate kinase

Query= BRENDA::Q0ASS9
         (441 letters)



>NCBI__GCF_000009985.1:WP_011386705.1
          Length = 300

 Score =  107 bits (267), Expect = 5e-28
 Identities = 78/223 (34%), Positives = 114/223 (51%), Gaps = 19/223 (8%)

Query: 42  VIKVGG-AVIQDDLPGL-ASALAFLQTVGLTPVVVHGGGPQLDAALEAADIPTERVDGLR 99
           VIK GG A+  DDL  L A  +  L+ VG+ PVVVHGGGPQ+DA L+  DI T RVDGLR
Sbjct: 39  VIKFGGHAMESDDLARLFARDVVLLKQVGINPVVVHGGGPQIDAMLKRLDIQTPRVDGLR 98

Query: 100 VTRDEAIPIIRDTLT-QANLALVDAIRDAGG-------------RAAAVPRGVFEAD--I 143
            T +  + ++   L  + N  +V AI +AGG             RA  + R   + D  I
Sbjct: 99  FTDEATVEVVEMILAGKINKQIVSAINEAGGFAVGLSGKDGHLIRARKLRRTKKDPDSNI 158

Query: 144 VDADKLGRVGEPRHIHLDLVGSAARAGQAAILACLGETPDGTLVNINADVAVRALVHALQ 203
                LG VGEP  I+  ++    ++    ++A +G    G   NINAD A  A+  A  
Sbjct: 159 EKVLDLGFVGEPAEINPHILDQFKKSDTIPVIAPVGMGGAGETYNINADTAAGAIAGATN 218

Query: 204 PYKVVFLTGTGGLLDEDGDILSSINLATDFGDLMQADWVNGGM 246
             +++ LT   G+LD+ G+++  +  A     +     ++GGM
Sbjct: 219 AKRLLMLTDVAGVLDKSGNLIPEMTAAQVHAYIADGT-ISGGM 260


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: 280
Number of extensions: 11
Number of successful extensions: 2
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: 300
Length adjustment: 29
Effective length of query: 412
Effective length of database: 271
Effective search space:   111652
Effective search space used:   111652
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