Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 5208501 Shew_1012 glutamate-1-semialdehyde-2,1-aminomutase (RefSeq)
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__PV4:5208501 Length = 428 Score = 136 bits (343), Expect = 1e-36 Identities = 94/304 (30%), Positives = 143/304 (47%), Gaps = 27/304 (8%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P IE+ +G +YD DG + D+ G + +GH+HP++ +A+ E + Sbjct: 33 PRFIEKADGAYIYDADGKAYIDYVGSWGPMILGHNHPKIRQAVLDAVENGLSFGAPT--- 89 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 E + +AEK+IE+ P + ++V +SG EA +A++L + T R + L F +HG Sbjct: 90 ELEVRMAEKVIEMVPSMEQVRMV--SSGTEATMSAIRLARGFTNRDKILKFEGCYHGHAD 147 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 +L S + P+ PG+ P + Y E + V E+Y Sbjct: 148 CLLVKAGSGALTLGQ--PSSPGI-----PEDFAKHTLTAVYNELES----VKTLFEQY-- 194 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 P EI I EP+ G + P GF + L+ D+YG LL DEV G R K Sbjct: 195 ----PEEIACIILEPVAGNMNCIPPIPGFLEGLRALCDQYGALLIIDEVMTGF-RVSKSG 249 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRAD----ITFDKPGRHATTFGGNPVAIAAGI 332 A H+G+ PDL GK IGGG+P+ R + I P A T GNP+A++AG+ Sbjct: 250 AQGHYGITPDLTTLGKVIGGGMPVGAFGGRKEVMQFIAPTGPVYQAGTLSGNPIAMSAGL 309 Query: 333 EVVE 336 +E Sbjct: 310 AQME 313 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: 449 Number of extensions: 23 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: 428 Length adjustment: 32 Effective length of query: 413 Effective length of database: 396 Effective search space: 163548 Effective search space used: 163548 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