GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysJ in Dinoroseobacter shibae DFL-12

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.-; EC 2.6.1.118 (characterized, see rationale)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)

Query= uniprot:Q5JFW3
         (362 letters)



>lcl|FitnessBrowser__Dino:3607384 Dshi_0798 acetylornithine and
           succinylornithine aminotransferase (RefSeq)
          Length = 393

 Score =  246 bits (629), Expect = 6e-70
 Identities = 147/373 (39%), Positives = 206/373 (55%), Gaps = 24/373 (6%)

Query: 1   MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59
           +P Y R  L  V+GEG ++ +  GRR+LDL AGI VN LGHAHP  V  ++ Q + +   
Sbjct: 6   LPTYNRAPLSFVKGEGAWLIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQAQALWHV 65

Query: 60  GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL------ATGRSEIVAM 113
             +++   ++++ E L      + V+  NSGTE+ E A+K  R          R EI+  
Sbjct: 66  SNLYQIPAQQKLAEMLVAETFADTVFFTNSGTESCELAVKMVRKHFHDAGQPERVEILTF 125

Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173
             +FHGR+   ++A   +K  +GFGPL+PGF+H+PF N EA + A+   TAA++ EP+QG
Sbjct: 126 EGSFHGRSSAGIAAAGSEKMTKGFGPLLPGFRHLPFGNHEALQSAVNDRTAAIMVEPVQG 185

Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGI 232
           EGGI    +  +K LRDL +  G L+I DEVQ G+ RTG+  A E  GV PDI+ + KGI
Sbjct: 186 EGGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHEWAGVSPDIMMVAKGI 245

Query: 233 GNGFPVSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEK--- 285
           G GFP+   L   +    +  G HGST+GGNPL C      L  +  D  +E+   K   
Sbjct: 246 GGGFPLGAVLATADAASGMTAGTHGSTYGGNPLGCAVGCAVLETVCADGFLEEVRRKAGL 305

Query: 286 --------FMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLL 337
                     EF G    + RG GLM+G+V R P  + V+A     +LV  A   V+RLL
Sbjct: 306 MRQALEGLVAEFPGV-FAEVRGAGLMLGLVCRAPNTDVVQAGYGAEVLVVPAAENVVRLL 364

Query: 338 PPLIIEGDTLEEA 350
           PPL I    + EA
Sbjct: 365 PPLTITDAEIREA 377


Lambda     K      H
   0.320    0.140    0.410 

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: 372
Number of extensions: 21
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: 362
Length of database: 393
Length adjustment: 30
Effective length of query: 332
Effective length of database: 363
Effective search space:   120516
Effective search space used:   120516
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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