GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Pseudomonas simiae WCS417

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate GFF4238 PS417_21710 acetylornithine aminotransferase

Query= curated2:Q5HJI8
         (394 letters)



>FitnessBrowser__WCS417:GFF4238
          Length = 406

 Score =  241 bits (616), Expect = 2e-68
 Identities = 138/385 (35%), Positives = 212/385 (55%), Gaps = 9/385 (2%)

Query: 15  NYAPLKLVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLSIISR 74
           NYAP   +  +G+G +VWD  G++ ID   G +V   GH HP +V A+TEQA KL  +S 
Sbjct: 20  NYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSN 79

Query: 75  VLYSDNLGKWEEKICHLAKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIAM 134
           V  ++   +   K+      ++V   NSG EA EAA K+AR+   +  G    + EIIA 
Sbjct: 80  VFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFG--SEKYEIIAA 137

Query: 135 NNNFHGRTLGSLSLSNHDAYKAGFHPLLQGTTTVDFGDIEQLTQAISPNTAAIILEPIQG 194
            N+FHGRTL ++++     Y  GF P + G T V + D++ L  A+S  T A++LEPIQG
Sbjct: 138 LNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKTCAVVLEPIQG 197

Query: 195 EGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFAMEWEQVVPDIYILGKAL 254
           EGGV      Y+Q  R LCD +  LL+ DE+Q G+GR+G  FA +   V PDI    K+L
Sbjct: 198 EGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAKSL 257

Query: 255 GGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAALDVLKDEQLVERSERLGS 314
           GGG +P++A+L    + + L  GTHG+T+GGNPLA A++ A +DV+   +++        
Sbjct: 258 GGG-FPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKHD 316

Query: 315 FLLKALLQL--KHPSIKEIRGRGLFIGIELNT----DAAPFVDQLIQRGILCKDTHRTII 368
                L Q+  ++    E+RG GL +G  L+      A    +   +  ++       ++
Sbjct: 317 LFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLMILQAGPDVV 376

Query: 369 RLSPPLVIDKEEIHQIVAAFQDVFK 393
           R +P LV++  +I + +  F+   K
Sbjct: 377 RFAPSLVVEDADIKEGLDRFERAVK 401


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: 392
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 394
Length of database: 406
Length adjustment: 31
Effective length of query: 363
Effective length of database: 375
Effective search space:   136125
Effective search space used:   136125
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