GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Herbaspirillum autotrophicum IAM 14942

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_050463092.1 AKL27_RS12160 acetylornithine transaminase

Query= BRENDA::A0A3B6MXE9
         (473 letters)



>NCBI__GCF_001189915.1:WP_050463092.1
          Length = 400

 Score =  216 bits (549), Expect = 1e-60
 Identities = 138/389 (35%), Positives = 210/389 (53%), Gaps = 16/389 (4%)

Query: 60  MVFSKGEGSHILDPEGNKYIDFLSAYSAVNQGHCHPKVLRALIEQAERLTLSSRAFYNDK 119
           ++F++G G  + D  G +Y+D+L  ++    GH    ++ AL  QA++L   S AFYN  
Sbjct: 20  LIFTEGSGMWMTDHTGKRYLDYLQGWAVNALGHSPQCMVDALTAQAKKLINPSPAFYNAP 79

Query: 120 FPVFAEYLTSMFGYDMMLPMNTGAEGVETAIKLARKWGYEKKNIPKNEAL----IVSCCG 175
               A+ LT    +D +   N+GAE  E AIKLARKWG  KKN P +E      I++   
Sbjct: 80  SIELADLLTENSVFDRVFFANSGAEANEGAIKLARKWG--KKN-PDSEGQDRFEIITFDH 136

Query: 176 CFHGRTLGVISMSCDNDATRGFGPLVPGHLKVDFGDIDGLEKIFKEHGDRICGFLFEPIQ 235
            FHGRT+  +S S        F P VPG  K +  D+  +E++  +   +    + EP+Q
Sbjct: 137 SFHGRTIATMSASGKPGWDTMFAPQVPGFKKAELNDLTSVERLITK---KTVAVMLEPVQ 193

Query: 236 GEAGVIIPPDGYLKAVRDLCSRHNILMIDDEIQTGIARTGKMLACDWEDVRPDMVILGKA 295
           GE GVI     +++ +R L  + N+L+I DE+QTG  RTG++ A    D+ PD++ LGK 
Sbjct: 194 GEGGVIPATREFMQGLRRLTKQANLLLIVDEVQTGFGRTGELFAYQLSDIEPDIMTLGKG 253

Query: 296 LGAGVVPVSAVLADKDIMLCIKPGEHGSTFGGNPLASAVAVASLKVVKDEGLVERAAELG 355
           +G G VP++A+LA ++I  C + GE G T+ GNPL +AV  A LK +   G ++   + G
Sbjct: 254 IGGG-VPLAALLAREEI-ACFEAGEQGGTYNGNPLMTAVGAAVLKELLKPGFLQSVKDQG 311

Query: 356 QEFRDQLQKVQQKFPHIIREIRGRGLLNAVDLCSKALYPASAYDICIKLKERGILAKPTH 415
           Q    +L K+  K  H     RG GLL A+ L  K + P    +    L   G+L     
Sbjct: 312 QYLSSELIKLSDK--HGFEGERGEGLLRALKL-GKDIGP-QIVEAARDLNPIGLLINSPR 367

Query: 416 DTIIRLAPPLSISSEELAEASKALSDVLE 444
             ++R  P L++S +E+ +    LSDVL+
Sbjct: 368 PNLLRFMPSLNVSKDEIDQMLSMLSDVLK 396


Lambda     K      H
   0.321    0.137    0.409 

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: 381
Number of extensions: 25
Number of successful extensions: 5
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: 473
Length of database: 400
Length adjustment: 32
Effective length of query: 441
Effective length of database: 368
Effective search space:   162288
Effective search space used:   162288
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: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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