GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Sphingomonas koreensis DSMZ 15582

Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Ga0059261_2530 Ga0059261_2530 N-acetylglutamate kinase (EC 2.7.2.8)

Query= BRENDA::Q0ASS9
         (441 letters)



>FitnessBrowser__Korea:Ga0059261_2530
          Length = 299

 Score =  100 bits (248), Expect = 8e-26
 Identities = 90/284 (31%), Positives = 133/284 (46%), Gaps = 28/284 (9%)

Query: 28  YLHRFSGIDQERFAVIKVGGAVIQDDLPGLASALA----FLQTVGLTPVVVHGGGPQLDA 83
           Y+ R++G    +  V+K GG  + D  P LA   A     L+ VG+ PVVVHGGGPQ+  
Sbjct: 23  YMQRYAG----KTFVVKYGGHAMGD--PELARDFAEDVVLLKAVGINPVVVHGGGPQIGQ 76

Query: 84  ALEAADIPTERVDGLRVTRDEAIPIIRDTLT-QANLALVDAIRDAGGRAAAV---PRGVF 139
            L+   + +E V GLRVT  E   I    L    N  +V  I  AGG+A  +     G+ 
Sbjct: 77  MLKRLGVESEFVGGLRVTDAETARIAEMVLAGSINKEIVSWISAAGGKAIGISGKDSGLV 136

Query: 140 EADIV---DAD---------KLGRVGEPRHIHLDLVGSAARAGQAAILACLGETPDGTLV 187
            A  V   +AD          LG VGEP  +   ++ + +  G   ++A +    DG   
Sbjct: 137 TARKVTRSEADPLQGIERHVDLGFVGEPVAVDASVLTTLSAQGFIPVIAPIALGADGHTY 196

Query: 188 NINADVAVRALVHALQPYKVVFLTGTGGLLDEDGDILSSINLATDFGDLMQADWVNGGMR 247
           NINAD    A+  AL   +   LT   G+L +D  +LS ++       L     ++GGM 
Sbjct: 197 NINADTMAGAIAGALGASRFFLLTDVPGVLSKDKQLLSDLDPGR-IAALKADGTISGGMI 255

Query: 248 LKLEEIKRLLDDLPLSSSVSITR-PSELARELFTHAGSGTLIRR 290
            K+E     +D    ++ +   R P  +  E+FT  G+GTL+ R
Sbjct: 256 PKVETCVAAVDAGVDAAVILDGRVPHSMLLEIFTPQGAGTLVHR 299


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: 262
Number of extensions: 10
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.

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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