GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Acidovorax sp. GW101-3H11

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= curated2:Q5HJI8
         (394 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1332
          Length = 398

 Score =  280 bits (717), Expect = 4e-80
 Identities = 154/397 (38%), Positives = 229/397 (57%), Gaps = 8/397 (2%)

Query: 1   MNSIIELTDYYSSNNYAPLKLVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVK 60
           M + IE    +  N Y  + + + +G+G +VWD +GK+YID + G +V   GH H  +V 
Sbjct: 1   MTAFIEAASPHVMNTYGRVPIALERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVP 60

Query: 61  AMTEQASKLSIISRVLYSDNLGKWEEKICHLAKKDKVLPLNSGTEAVEAAIKIARKWGSE 120
           A+ +Q +KL   S   +     K   K+  L+    V   NSG EA EAA+KIARK+G +
Sbjct: 61  ALQDQIAKLIHTSNYYHVPLQEKLATKLVELSGMQNVFFCNSGLEANEAALKIARKFGVD 120

Query: 121 VKGITDGQVEIIAMNNNFHGRTLGSLSLSNHDAYKAGFHPLLQGTTTVDFGDIEQLTQAI 180
            KGI   + EI+     FHGR++ ++S + +     GF PL++G   V   DIE + QA 
Sbjct: 121 -KGIA--KPEIVVYEKAFHGRSIATMSATGNPKIHNGFGPLVEGFVRVPMNDIEAIKQAT 177

Query: 181 --SPNTAAIILEPIQGEGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFAM 238
             +PN  A+  E IQGEGG+N     Y+Q +R+LCD+   L++ DE+Q G+GRTGKWFA 
Sbjct: 178 EGNPNVVAVFFETIQGEGGINGMRIEYLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAH 237

Query: 239 EWEQVVPDIYILGKALGGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAALD 298
           +W  +VPD+  L K LG G+ P+ AV+A      VL PG HG+TFGGNPLA+      + 
Sbjct: 238 QWAGIVPDVMPLAKGLGSGV-PIGAVVAGPKAANVLQPGNHGTTFGGNPLAMRAGVETIR 296

Query: 299 VLKDEQLVERSERLGSFLLKALLQL--KHPSIKEIRGRGLFIGIELNTDAAPFVDQLIQR 356
           +++++ L+  + ++G  L  AL +     P +KEIRG+GL +GIELN      + +  + 
Sbjct: 297 IMEEDGLLHNAAQVGDHLRAALQRELGSLPGVKEIRGQGLMLGIELNKPCGALIGRAAEA 356

Query: 357 GILCKDTHRTIIRLSPPLVIDKEEIHQIVAAFQDVFK 393
           G+L   T  ++IRL PPL++   E   IVA    + K
Sbjct: 357 GLLLSVTADSVIRLVPPLILTTAEADAIVAILTPLVK 393


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: 401
Number of extensions: 18
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: 394
Length of database: 398
Length adjustment: 31
Effective length of query: 363
Effective length of database: 367
Effective search space:   133221
Effective search space used:   133221
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