Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__Caulo:CCNA_00620 Length = 392 Score = 264 bits (674), Expect = 3e-75 Identities = 155/371 (41%), Positives = 213/371 (57%), Gaps = 21/371 (5%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R + +VRGEG +++D+ GR YLDL AG+ VN LGH P V + Q + + A ++ Sbjct: 10 RANIDIVRGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWHASNLYR 69 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL---ATGRSE---IVAMTNAFH 118 +E + +L+ + V+ NSG EAVEAAIK AR A GR E ++ NAFH Sbjct: 70 LPAQEALATKLTDATFADRVFFANSGAEAVEAAIKTARRWQGAKGRPERYRVLTFGNAFH 129 Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIV 178 GRTL ++SAT + K REGF PL F PFN++E A AIT +TAA++ EPIQGEGG+ Sbjct: 130 GRTLATISATDQMKVREGFTPLYDAFDTTPFNDIEGAARAITPQTAAILVEPIQGEGGLT 189 Query: 179 PADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFP 237 PA F+ LR L + LLI DEVQ+G+ RTG A E YGVRPDI+ + KG+G GFP Sbjct: 190 PATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHELYGVRPDIIAVAKGLGGGFP 249 Query: 238 VSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTL----------RILRRDRLVEKAG 283 + L + + G HGST+GGNPLAC + L + R LV+ Sbjct: 250 IGACLATEDAASGMTPGSHGSTYGGNPLACAVASAVLDAVLAPGFLETVRERAALVDALL 309 Query: 284 EKFMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIE 343 E+ + + V+ +G GLM G+ +R A + V L++ G++ AG V+RLLPPL I Sbjct: 310 ERLLRRHSDLFVRAQGHGLMRGLQVRASARDVVAHLRDFGVMTVAAGADVVRLLPPLTIS 369 Query: 344 GDTLEEARKEI 354 + EA + Sbjct: 370 ELEIAEAEARL 380 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: 349 Number of extensions: 20 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: 392 Length adjustment: 30 Effective length of query: 332 Effective length of database: 362 Effective search space: 120184 Effective search space used: 120184 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