Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate YP_427128.1 Rru_A2041 aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000013085.1:YP_427128.1 Length = 455 Score = 208 bits (529), Expect = 3e-58 Identities = 138/427 (32%), Positives = 229/427 (53%), Gaps = 28/427 (6%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDF-F 95 P++ RGEG+RV+D G + + +G+ ++G S PR+ A +Q + + + Sbjct: 29 PLIAVRGEGVRVFDDKGKDYIEGMAGLWCASLGFSEPRLAAAAARQMAELPFFHMFSHKS 88 Query: 96 YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY---GTGR---KQFLAFYH 149 +E I L+E+L++ AP + R + NSG+EAN+ A+K++ Y GR K+ +A Sbjct: 89 HEPGIRLSEELVKRAPVPMAR-AFFCNSGSEANDTAIKMIWYINNALGRPQKKKIIARKR 147 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 A+HG T A SLT +D P + + H P+ YR G G E + R D Sbjct: 148 AYHGVTVASASLTGLPANHRDFDLP-IANILHTSSPDYYRE--GKPG-ESEEAFAKRCAD 203 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 +E + P+ + A F EPI G GG V+PPKG+F+ ++ +Y ILL DEV G Sbjct: 204 ELEAMILAE-DPNTVAAFFAEPIMGAGGVVLPPKGYFEHIQAVLKKYDILLVADEVICGF 262 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRADI---TFDKPGR-----HATT 320 GRTG++W + FG++PD++ KA+ +P++ V+ ++ D G+ H T Sbjct: 263 GRTGQYWGSQTFGLKPDILTCAKALSSAYMPISAVLVTEEVYKPLRDNSGKIGTFGHGYT 322 Query: 321 FGGNPVAIAAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAV 378 + +PVA A +E + I +++L +V G L + L F + + ++G+ RG+GL A+ Sbjct: 323 YSAHPVAAAVALETLAIYDERDILGNVAVSGARLQERLRSFAD-HPLVGNVRGIGLIGAI 381 Query: 379 EIVKSKETKEKYP---ELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEI 435 E+V K T +P + R+V ++ + G++L + + F PPLI+T EE+D M+ Sbjct: 382 ELVADKATHGAFPASDAVGPRVVTKAEEAGVILRAMAGDVVAFSPPLIITPEEVDQMMDR 441 Query: 436 FEEALKA 442 F AL+A Sbjct: 442 FTVALEA 448 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: 519 Number of extensions: 28 Number of successful extensions: 6 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: 455 Length adjustment: 33 Effective length of query: 412 Effective length of database: 422 Effective search space: 173864 Effective search space used: 173864 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 Apr 10 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