Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate PP_4481 PP_4481 Succinylornithine transaminase/acetylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__Putida:PP_4481 Length = 406 Score = 248 bits (633), Expect = 2e-70 Identities = 140/374 (37%), Positives = 207/374 (55%), Gaps = 34/374 (9%) Query: 11 VRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE 70 VRGEG VWD+ GR +D GI VN LGH HP V ++ Q + +F ++ Sbjct: 29 VRGEGSRVWDQSGRELIDFAGGIAVNALGHCHPALVKALTEQANTLWHVSNVFTNEPALR 88 Query: 71 MLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR------LATGRSEIVAMTNAFHGRTLGS 124 + +L + + NSG E+ EAA K AR + EI+A N+FHGRTL + Sbjct: 89 LAHKLVDATFADRAFFCNSGAESNEAAFKLARRVAHDRFGPQKHEIIATVNSFHGRTLFT 148 Query: 125 LSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEF 184 +S + KY +GFGP + G H+P+N++EA K I+ +T AV+ EPIQGE G+VPAD+ + Sbjct: 149 VSVGGQPKYSDGFGPKITGISHVPYNDLEALKAQISDKTCAVVIEPIQGESGVVPADKAY 208 Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLT 243 ++ R L ++ ALLI DEVQ+G+ RTG A +HYGV PDI+T K +G GFP+ LT Sbjct: 209 LEGARKLCDEHNALLIFDEVQTGVGRTGSLYAYQHYGVIPDILTSAKSLGGGFPIGAMLT 268 Query: 244 DLEIPR----GKHGSTFGGNPLACRAVATTLRIL--------------RRDRLVEKAGEK 285 E+ + G HG+T+GGNPL C L ++ R +E+ G++ Sbjct: 269 TTELAKHLAVGTHGTTYGGNPLGCAVACAVLDVVNTPETLAGIKAKHERFKTRLEQIGQQ 328 Query: 286 FMEFSGERVVKTRGRGLMIGIVL----RRPAGNYVKALQERGILVNTAGNRVIRLLPPLI 341 + FS + RG GL++G VL + A + + A ++ G++V AG V+R P L+ Sbjct: 329 YNLFS-----QVRGVGLLLGCVLTEAWKGKAKDVLNAAEKEGVMVLQAGPDVVRFAPSLV 383 Query: 342 IEGDTLEEARKEIE 355 +E ++E E Sbjct: 384 VEDADIDEGLDRFE 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: 339 Number of extensions: 12 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