GapMind for Amino acid biosynthesis

 

Aligments for a candidate for OAT in Paraburkholderia bryophila 376MFSha3.1

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme

Query= curated2:Q5HJI8
         (394 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04057 H281DRAFT_04057
           acetylornithine aminotransferase apoenzyme
          Length = 394

 Score =  229 bits (584), Expect = 1e-64
 Identities = 138/380 (36%), Positives = 208/380 (54%), Gaps = 16/380 (4%)

Query: 20  KLVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLSIISRVLYSD 79
           ++V + GKG  ++D +GK+Y+D I G++V   GHC   +++A+ +QA  L   S   Y++
Sbjct: 19  EIVFTHGKGSWLYDNNGKRYLDFIQGWAVNCLGHCDEGMIEALNQQAKLLFNPSPAFYNE 78

Query: 80  NLGKWEEKICHLAKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIAMNNNFH 139
            + K    +   +  DKV   NSG EA E AIK+ARKWG + K   DG  EII  +++FH
Sbjct: 79  PMAKLAALLTQHSCFDKVFFANSGAEANEGAIKLARKWGKKFK---DGAFEIITFDHSFH 135

Query: 140 GRTLGSLSLSNHDAYKAGFHPLLQGTTTVDFGDIEQLTQAISPNTAAIILEPIQGEGGVN 199
           GRTL ++S S    +   + P + G    D  DI  + + I+  T A++LEPIQGEGGV 
Sbjct: 136 GRTLATMSASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKTVAVMLEPIQGEGGVI 195

Query: 200 IPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFAMEWEQVVPDIYILGKALGGGLY 259
              + ++Q +R+L  KH +LLI DE+Q G GR G  FA E   V PDI  LGK +GGG+ 
Sbjct: 196 PATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGTLFAYELSGVEPDIMTLGKGIGGGV- 254

Query: 260 PVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAALDVLKDEQLVERSERLGSFLLKA 319
           P++A+LA  +V  V   G  G T+ GNPL  A+  + +  L     +E     G +L   
Sbjct: 255 PLAALLAKAEV-AVFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGVRARGEYLRAK 313

Query: 320 LLQL-KHPSIKEIRGRGLFIGIELNTDAAPFVDQLIQR-------GILCKDTHRTIIRLS 371
           LL+L +    K  RG GL   + L  D     +Q++++       G+L       ++R  
Sbjct: 314 LLELSEERGFKGERGEGLLRALLLGKDIG---NQIVEKARDMQPDGLLLNAARPNLLRFM 370

Query: 372 PPLVIDKEEIHQIVAAFQDV 391
           P L +  EEI Q++A  + +
Sbjct: 371 PALNVTNEEIDQMMAMLRSI 390


Lambda     K      H
   0.319    0.137    0.402 

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: 338
Number of extensions: 12
Number of successful extensions: 4
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 (21.7 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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