Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 207835 DVU2347 acetylornithine aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >MicrobesOnline__882:207835 Length = 399 Score = 168 bits (426), Expect = 2e-46 Identities = 127/415 (30%), Positives = 190/415 (45%), Gaps = 53/415 (12%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 PI ++R EG R++D +G + D SG+ V ++GH HP + E + +QA K H S F+ Sbjct: 24 PISVQRAEGSRMWDHEGREYIDLLSGIAVTSLGHCHPELAEVMARQARKLVHVSNL-FYQ 82 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY------GTGRKQFLAFYHA 150 E + LAEKL+ K + NSGAEANEAA+KL + G + + A Sbjct: 83 EEQLDLAEKLLSTLHCT---KAFFCNSGAEANEAAIKLARRYMQRVRGVDAHEVVTLTGA 139 Query: 151 FHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWG-IDGYEEPDELTNRVLD 209 FHGRT A ++ T + Q DGF P G WG ID Sbjct: 140 FHGRTLATVAATGQERFQ-DGFAPMPAGFRQAE--------WGDIDALRAA--------- 181 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 + P G + E +QGEGG + + +A+ E G+LL DE+Q G+ Sbjct: 182 ---------ITPATAG-VLVEMVQGEGGVRPMTQDYARAVADLCREKGVLLMVDEIQTGL 231 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAI 328 RTG+FWA +H+GVEPD++ KA+ GLP+ ++ ++ G HATTFG + Sbjct: 232 CRTGRFWAHQHYGVEPDIVTSAKALANGLPMGAMMTTDEVAQGFVAGSHATTFGAGALVS 291 Query: 329 AAGIEVVEIVK--ELLPHVQEVGDYLHKYLEEFKEKYE-VIGDARGLGLAQAVEIVKSKE 385 + ++I+K L VG + K I + RG GL + IV + Sbjct: 292 SVAAATLDIMKRDRLDERATAVGGRAMERFRAIGAKLPGTIEEVRGYGL--MIGIVLTFS 349 Query: 386 TKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEAL 440 KE + KE RG V + +R +P L + + ++ + E+ L Sbjct: 350 GKE--------VWKELVARGFVCNNTQEKVLRLVPALTIDEADLTAFADTLEDIL 396 Lambda K H 0.320 0.141 0.418 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: 416 Number of extensions: 27 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: 445 Length of database: 399 Length adjustment: 32 Effective length of query: 413 Effective length of database: 367 Effective search space: 151571 Effective search space used: 151571 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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