Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate AO353_03025 AO353_03025 acetylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03025 Length = 406 Score = 249 bits (635), Expect = 1e-70 Identities = 140/369 (37%), Positives = 210/369 (56%), Gaps = 24/369 (6%) Query: 11 VRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE 70 VRG G VWD+ GR +D GI VNVLGHAHP V ++ Q K+ +F ++ Sbjct: 29 VRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQANKLWHVSNVFTNEPALR 88 Query: 71 MLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR------LATGRSEIVAMTNAFHGRTLGS 124 + +L + V+ NSG EA EAA K AR + + EI+A N+FHGRTL + Sbjct: 89 LAHKLIDATFADRVFFCNSGAEANEAAFKLARRVAHDRFGSEKYEIIAALNSFHGRTLFT 148 Query: 125 LSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEF 184 ++ + KY +GFGP + G H+ FN+++A K AI+ +T AV+ EPIQGEGG++PAD + Sbjct: 149 VNVGGQSKYSDGFGPKITGITHVKFNDLDALKAAISDKTCAVVLEPIQGEGGVLPADLAY 208 Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLT 243 ++ R+L ALLI DEVQ+G+ R+G+ A +HYGV PDI+T K +G GFP++ LT Sbjct: 209 LQGARELCTQHNALLIFDEVQTGMGRSGELFAYQHYGVTPDILTSAKSLGGGFPIAAMLT 268 Query: 244 DLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVE--KAGEKFMEFSGERV--- 294 ++ + G HG+T+GGNPLAC + ++ ++ KA + E++ Sbjct: 269 TEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVVNTPEVLNGVKAKHDLFKTRLEQIGAK 328 Query: 295 ----VKTRGRGLMIGIVL----RRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDT 346 + RG GL++G VL + A + A + G+++ AG VIR P L++E Sbjct: 329 YGLFTQVRGLGLLLGCVLSEAWKGKAKDVFNAAEREGLMILQAGPDVIRFAPSLVVEDAD 388 Query: 347 LEEARKEIE 355 +EE + E Sbjct: 389 IEEGLERFE 397 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: 327 Number of extensions: 11 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: 406 Length adjustment: 30 Effective length of query: 332 Effective length of database: 376 Effective search space: 124832 Effective search space used: 124832 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