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.
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:
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