GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Paraburkholderia bryophila 376MFSha3.1

Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate H281DRAFT_00444 H281DRAFT_00444 N-acetylglutamate synthase

Query= curated2:A4J169
         (287 letters)



>FitnessBrowser__Burk376:H281DRAFT_00444
          Length = 462

 Score =  144 bits (364), Expect = 3e-39
 Identities = 86/273 (31%), Positives = 151/273 (55%), Gaps = 5/273 (1%)

Query: 16  PYIKKFSGKTIVIKYGGHAMLNADLKKAVMTDLVLMKFVGINPVVVHGGGPEITGMLHRL 75
           PYI  F  KT V+ +GG  +++  L  A+++D+ L++ +GI  V+VHG  P++   +   
Sbjct: 39  PYIHAFRNKTFVVGFGGE-VVHQGLLNALVSDIALLQAMGIQIVLVHGSRPQVEEQMSLH 97

Query: 76  GIESQFVSGLRVTDAPTMEVVEMVLGKLNKEIVALIN-GLGGRSVG---LSGKDANLIMA 131
           G+ES+F  G+R+TDA  +E  +   G++  +I A I+ GL    +    +S    N + A
Sbjct: 98  GVESEFSHGMRITDARALESAKEAAGEVRLDIEAAISQGLPNTPMAHAHISVVSGNFVTA 157

Query: 132 NKKYSNDCQDIGFVGEVTGVNPQLLQTVIQEGYIPVVSPVGISTEGETYNINADTVASAI 191
                 D  D    G V  ++   ++  +    + ++SP+G S  GE +N+  + VASA 
Sbjct: 158 RPVGILDGVDFAHTGVVRKIDADSIRHSLASRKLVLLSPLGFSPTGEAFNLAMEDVASAA 217

Query: 192 ATALKADKLIILTDVEGILEDRQDKGTLISTVKMEDIPRLIERGVIQGGMIPKVECCMQA 251
           A AL+ADK++ LT+  G+++  +D   LI  + ++D  +L E G + G     ++  ++A
Sbjct: 218 AIALRADKIVFLTETPGLMQAGEDGTELIRELSLDDAYKLHESGEVTGDAGFYLKHSIRA 277

Query: 252 IQTGVATTHILDGRVPHSILLEVFTDKGIGTMV 284
            + GVA  HI+   +  S+LLE+F   G+GTM+
Sbjct: 278 CRGGVARAHIIPYALDGSLLLELFLHDGVGTMI 310


Lambda     K      H
   0.318    0.138    0.387 

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: 304
Number of extensions: 14
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: 287
Length of database: 462
Length adjustment: 29
Effective length of query: 258
Effective length of database: 433
Effective search space:   111714
Effective search space used:   111714
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: 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