GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Dino:3607384
          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:

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