Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__MR1:199805 Length = 405 Score = 217 bits (552), Expect = 6e-61 Identities = 143/412 (34%), Positives = 209/412 (50%), Gaps = 46/412 (11%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 ++ RGEG RV+D +GN F DFA G+ V +GH HP +V A+K Q EK H S E Sbjct: 25 VIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSNV-MTNE 83 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV------KYGTGRKQFLAFYHAF 151 A+ LA KL+ +V + NSGAEANEAA+KL K+G + + +AF AF Sbjct: 84 PALELATKLVN---STFAERVYFANSGAEANEAALKLARRYALEKHGVEKDEIIAFDKAF 140 Query: 152 HGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFI 211 HGRT +S+ + DGF P +TH+P+ + L V D Sbjct: 141 HGRTFFTVSV-GGQAAYSDGFGPKPQSITHLPF-------------NDVAALEAAVSD-- 184 Query: 212 EEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGR 271 + AI EP+QGEGG + F KA+++ A+++ L+ DEVQ G+GR Sbjct: 185 -----------KTCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGR 233 Query: 272 TGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIAA 330 TG+ +A + PD++ KA+GGG P+A ++ +I K G H +T+GGNP+A A Sbjct: 234 TGELYAYMGTDIVPDILTTAKALGGGFPIAAMLTTTEIAEHLKVGTHGSTYGGNPLACAI 293 Query: 331 GIEVVEIVK--ELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKE 388 G V+++V E+L V+ L L + EKY V + RG GL + E Sbjct: 294 GNAVLDVVNTPEVLNGVKHREQLLRDGLNKINEKYHVFSEVRGKGLLLGAVL------NE 347 Query: 389 KYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEAL 440 +Y + S GL+ L G N +RF P L++ + +I + FE A+ Sbjct: 348 QYQGRSRDFLVASVAEGLMSLMAGANVVRFAPSLVIPEADIAEGLARFERAV 399 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: 419 Number of extensions: 27 Number of successful extensions: 8 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: 405 Length adjustment: 32 Effective length of query: 413 Effective length of database: 373 Effective search space: 154049 Effective search space used: 154049 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: 51 (24.3 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