GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Shewanella oneidensis MR-1

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)

Query= curated2:Q5HJI8
         (394 letters)



>FitnessBrowser__MR1:199805
          Length = 405

 Score =  261 bits (667), Expect = 3e-74
 Identities = 144/381 (37%), Positives = 221/381 (58%), Gaps = 9/381 (2%)

Query: 15  NYAPLKLVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLSIISR 74
           NYAP  ++  +G+G +VWD +G ++ID   G +V   GHCHP +V A+  Q  KL  +S 
Sbjct: 19  NYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSN 78

Query: 75  VLYSDNLGKWEEKICHLAKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIAM 134
           V+ ++   +   K+ +    ++V   NSG EA EAA+K+AR++  E  G+     EIIA 
Sbjct: 79  VMTNEPALELATKLVNSTFAERVYFANSGAEANEAALKLARRYALEKHGVEKD--EIIAF 136

Query: 135 NNNFHGRTLGSLSLSNHDAYKAGFHPLLQGTTTVDFGDIEQLTQAISPNTAAIILEPIQG 194
           +  FHGRT  ++S+    AY  GF P  Q  T + F D+  L  A+S  T AI+LEP+QG
Sbjct: 137 DKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDVAALEAAVSDKTCAIMLEPLQG 196

Query: 195 EGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFAMEWEQVVPDIYILGKAL 254
           EGG+      +++AVR+L +KH  L+I DE+Q G+GRTG+ +A     +VPDI    KAL
Sbjct: 197 EGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDIVPDILTTAKAL 256

Query: 255 GGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAALDVLKDEQLVERSERLGS 314
           GGG +P++A+L   ++   L  GTHGST+GGNPLA AI  A LDV+   +++   +    
Sbjct: 257 GGG-FPIAAMLTTTEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHREQ 315

Query: 315 FLLKALLQL--KHPSIKEIRGRGLFIGIELNTD----AAPFVDQLIQRGILCKDTHRTII 368
            L   L ++  K+    E+RG+GL +G  LN      +  F+   +  G++       ++
Sbjct: 316 LLRDGLNKINEKYHVFSEVRGKGLLLGAVLNEQYQGRSRDFLVASVAEGLMSLMAGANVV 375

Query: 369 RLSPPLVIDKEEIHQIVAAFQ 389
           R +P LVI + +I + +A F+
Sbjct: 376 RFAPSLVIPEADIAEGLARFE 396


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: 369
Number of extensions: 14
Number of successful extensions: 6
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: 405
Length adjustment: 31
Effective length of query: 363
Effective length of database: 374
Effective search space:   135762
Effective search space used:   135762
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