GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Pseudomonas stutzeri RCH2

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate GFF305 Psest_0306 adenosylmethionine-8-amino-7-oxononanoate transaminase

Query= BRENDA::P31893
         (426 letters)



>FitnessBrowser__psRCH2:GFF305
          Length = 467

 Score = 98.6 bits (244), Expect = 4e-25
 Identities = 81/270 (30%), Positives = 123/270 (45%), Gaps = 26/270 (9%)

Query: 64  RAKGVSL-DMEGKRYFDFLSAYSAVNQGHCHPKIVNTMVEQAQRLTLTSRA-FYTDVLGE 121
           R  GV L D +GKRY D +S++     GH +P+I   + +Q  +L     A F    + E
Sbjct: 35  RGDGVWLEDFDGKRYLDAVSSWWVNVFGHANPRINQRIKDQVDQLEHVMLAGFSHQPVVE 94

Query: 122 YEEFLTKLF--NYDKVLPMNTGVEGGETACKIARCWAYMKKKVPENQAKIIFAENNFWGR 179
             E L  L     D+V   + G  G E A K++  + Y +      + + +   N++ G 
Sbjct: 95  LSERLVALTPAGLDRVFYTDNGSTGIEVALKMS--FHYWRNSGRGQKQRFVTLTNSYHGE 152

Query: 180 TLSAISASTDPMSYDELRPYM------PGFEIVKYNDTAALEK-------------AFQD 220
           T++A+S     +  D  +P +      P  +     D  + E+             A   
Sbjct: 153 TVAAMSVGDVALFTDTYKPLLLDTFKVPSPDCYLRPDGVSWEEHSRQMFAHMEQTLAEHH 212

Query: 221 PNVCAYMVEP-IQGEAGVVALDAGYLTEVRELCTKYNVLFIADEVQTGLARTGRMLAVDH 279
            ++ A +VEP IQG  G+      YL  +RE C +Y V  I DE+  G  RTG M A + 
Sbjct: 213 QDIAAVIVEPLIQGAGGMRMYHPVYLKLLREACDRYEVHLIHDEIAVGFGRTGTMFACEQ 272

Query: 280 EDVKPDLLILGKALSGGLYPVSAVLRDDHI 309
             + PD L L KAL+GG  P++AVL  D I
Sbjct: 273 AGITPDFLCLSKALTGGYLPMAAVLTTDRI 302


Lambda     K      H
   0.322    0.137    0.424 

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: 398
Number of extensions: 18
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: 426
Length of database: 467
Length adjustment: 32
Effective length of query: 394
Effective length of database: 435
Effective search space:   171390
Effective search space used:   171390
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 (21.9 bits)
S2: 51 (24.3 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