Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate 207835 DVU2347 acetylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >MicrobesOnline__882:207835 Length = 399 Score = 256 bits (655), Expect = 6e-73 Identities = 145/375 (38%), Positives = 214/375 (57%), Gaps = 21/375 (5%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R + + R EG +WD +GR Y+DL++GI V LGH HPE M+RQ K+V +F Sbjct: 22 RYPISVQRAEGSRMWDHEGREYIDLLSGIAVTSLGHCHPELAEVMARQARKLVHVSNLFY 81 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGR------SEIVAMTNAFH 118 +E+ ++ E+L + + NSG EA EAAIK AR R E+V +T AFH Sbjct: 82 QEEQLDLAEKLLSTLHCTKAFFCNSGAEANEAAIKLARRYMQRVRGVDAHEVVTLTGAFH 141 Query: 119 GRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIV 178 GRTL +++AT ++++++GF P+ GF+ + +++A + AIT TA V+ E +QGEGG+ Sbjct: 142 GRTLATVAATGQERFQDGFAPMPAGFRQAEWGDIDALRAAITPATAGVLVEMVQGEGGVR 201 Query: 179 PADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFP 237 P +++ + + DL + G LL+ DE+Q+GL RTG+F A +HYGV PDIVT K + NG P Sbjct: 202 PMTQDYARAVADLCREKGVLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKALANGLP 261 Query: 238 VSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVEKAG-------EKF 286 + +T E+ + G H +TFG L A TL I++RDRL E+A E+F Sbjct: 262 MGAMMTTDEVAQGFVAGSHATTFGAGALVSSVAAATLDIMKRDRLDERATAVGGRAMERF 321 Query: 287 MEFSGE---RVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIE 343 + + + RG GLMIGIVL K L RG + N +V+RL+P L I+ Sbjct: 322 RAIGAKLPGTIEEVRGYGLMIGIVLTFSGKEVWKELVARGFVCNNTQEKVLRLVPALTID 381 Query: 344 GDTLEEARKEIEGVL 358 L +E +L Sbjct: 382 EADLTAFADTLEDIL 396 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: 341 Number of extensions: 10 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: 399 Length adjustment: 30 Effective length of query: 332 Effective length of database: 369 Effective search space: 122508 Effective search space used: 122508 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