Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__Korea:Ga0059261_4131 Length = 398 Score = 198 bits (504), Expect = 2e-55 Identities = 135/355 (38%), Positives = 189/355 (53%), Gaps = 24/355 (6%) Query: 12 RGEGVYVWD-EKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE 70 RGEG +++ + G YLD +AG+ N LGH HP V + Q K+ MFE + Sbjct: 18 RGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISNMFEMPGQNA 77 Query: 71 MLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR---LATG---RSEIVAMTNAFHGRTLGS 124 + E L+ + V+ NSGTEAVE AIK AR A G R ++ + AFHGRT G+ Sbjct: 78 LAERLTTASFADTVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVIGFSGAFHGRTYGA 137 Query: 125 LSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAIT-KETAAVIFEPIQGEGGIVPADEE 183 ++A + +GFG +PGF H +N A AI TAAV+ EP+QGEGG E Sbjct: 138 MNAAGNPAHLDGFGDRLPGFVHFAVDNWPALALAIADSATAAVVVEPVQGEGGARAMTEP 197 Query: 184 FVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHY-GVRPDIVTMGKGIGNGFPVSLT 241 F+ LR G LLI DEVQ+G+ RTGK A + Y PDI+ + K +G+GFPV Sbjct: 198 FLDKLRAACTAHGVLLIYDEVQTGMGRTGKLFAHQWYPDATPDIMALAKALGSGFPVGAC 257 Query: 242 LTDLEIPRGK----HGSTFGGNPLACR-AVATTLRILRRDRLVE--------KAGEKFME 288 L E G HG+T GGNPLA A+A I + + L +AG + Sbjct: 258 LATAEAASGMVPGVHGTTAGGNPLAMAVAIAAFDEIAKPETLTHAREVAQHLRAGLDRLA 317 Query: 289 FSGERVV-KTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLII 342 + V+ + RG+GL++G+ L ++ A +E+ +LV G+ +RLLPPL + Sbjct: 318 ATHPGVISEIRGKGLLVGVRLVPNNRAFMAAAREQRLLVAGGGDNCVRLLPPLTL 372 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: 355 Number of extensions: 18 Number of successful extensions: 6 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: 398 Length adjustment: 30 Effective length of query: 332 Effective length of database: 368 Effective search space: 122176 Effective search space used: 122176 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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