GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Dinoroseobacter shibae DFL-12

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)

Query= curated2:C3P3K3
         (396 letters)



>FitnessBrowser__Dino:3607384
          Length = 393

 Score =  244 bits (624), Expect = 2e-69
 Identities = 130/378 (34%), Positives = 211/378 (55%), Gaps = 8/378 (2%)

Query: 19  YHPLPIVISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRA 78
           Y+  P+   K EG W+ + +G R++DL +  +    GH HP+++ AL DQA  +   S  
Sbjct: 9   YNRAPLSFVKGEGAWLIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQAQALWHVSNL 68

Query: 79  FHSDQLGPWYEKVAKLTNKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCE 138
           +         E +   T  + V   N+G E+ E A+K  R+  +D  + E  R EI+  E
Sbjct: 69  YQIPAQQKLAEMLVAETFADTVFFTNSGTESCELAVKMVRKHFHDAGQPE--RVEILTFE 126

Query: 139 DNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITPNTAAFILEPIQGE 198
            +FHGR+   ++ + +E+  +GFGP+LPG   +P+G+ EAL++A+   TAA ++EP+QGE
Sbjct: 127 GSFHGRSSAGIAAAGSEKMTKGFGPLLPGFRHLPFGNHEALQSAVNDRTAAIMVEPVQGE 186

Query: 199 AGINIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALG 258
            GI   P   LK   ++C +  +L + DE+Q G+GRTG++FA +W  V+PD+ ++ K +G
Sbjct: 187 GGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHEWAGVSPDIMMVAKGIG 246

Query: 259 GGVFPISCAAANRDILGVFEPGSHGSTFGGNPLACAVSIAALEVLEE----EKLTERSLQ 314
           GG FP+    A  D       G+HGST+GGNPL CAV  A LE +      E++  ++  
Sbjct: 247 GG-FPLGAVLATADAASGMTAGTHGSTYGGNPLGCAVGCAVLETVCADGFLEEVRRKAGL 305

Query: 315 LGEKLVGQLKEIDNPMITEVRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHENVIRIA 374
           + + L G + E    +  EVRG GL +G+    P     +    A +L     ENV+R+ 
Sbjct: 306 MRQALEGLVAEFPG-VFAEVRGAGLMLGLVCRAPNTDVVQAGYGAEVLVVPAAENVVRLL 364

Query: 375 PPLVISEEDLEWAFQKIK 392
           PPL I++ ++  A  +++
Sbjct: 365 PPLTITDAEIREALARLR 382


Lambda     K      H
   0.317    0.136    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: 411
Number of extensions: 21
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: 396
Length of database: 393
Length adjustment: 31
Effective length of query: 365
Effective length of database: 362
Effective search space:   132130
Effective search space used:   132130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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