GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Burkholderia phytofirmans PsJN

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate BPHYT_RS15580 BPHYT_RS15580 acetylornithine aminotransferase

Query= curated2:Q5HJI8
         (394 letters)



>FitnessBrowser__BFirm:BPHYT_RS15580
          Length = 394

 Score =  224 bits (571), Expect = 3e-63
 Identities = 132/380 (34%), Positives = 208/380 (54%), Gaps = 16/380 (4%)

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

Query: 80  NLGKWEEKICHLAKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIAMNNNFH 139
            + +    +   +  DKV   NSG EA E AIK+ARKWG + K   DG  EII  +++FH
Sbjct: 79  PMAQLAGLLTQHSCFDKVFFANSGAEANEGAIKLARKWGKKFK---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   + PDI  LGK +GGG+ 
Sbjct: 196 PATREFMQQLRELTKKHNLLLIVDEVQSGCGRAGTLFAYELSDIEPDIMTLGKGIGGGV- 254

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

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

Query: 372 PPLVIDKEEIHQIVAAFQDV 391
           P L +  EEI Q++   + +
Sbjct: 371 PALNVTNEEIDQMMTMLRSI 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: 337
Number of extensions: 13
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:

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