Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate CCNA_02326 CCNA_02326 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Caulo:CCNA_02326 Length = 405 Score = 188 bits (477), Expect = 3e-52 Identities = 136/418 (32%), Positives = 206/418 (49%), Gaps = 51/418 (12%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+ ERG G R+ +G + D +G+ +GH+HP +VE +K QAEK H S Sbjct: 22 PLAFERGRGARLISTEGEEYLDCVAGIATNGLGHAHPALVEVLKAQAEKLWHVSNIYRIP 81 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV-KYGTGRKQ-----FLAFYHA 150 E LA+ L + D+ V + NSG EA E A+K KY + Q F + Sbjct: 82 EQEE-LADALCANSFADV---VFFTNSGTEAVECALKTARKYHSANGQPERIDIYGFDGS 137 Query: 151 FHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDF 210 FHGRT A ++ + + DGF P +PG + + + + Sbjct: 138 FHGRTYAAVNASGNP-SYVDGFGPRLPGYSQLTFGD------------------------ 172 Query: 211 IEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIG 270 + + + AI EP+QGEGG P L++ DE+G+LL DEVQ G+G Sbjct: 173 -HDAIKAAIASPTTAAIIVEPVQGEGGARSIPTQCLVGLRQLCDEHGVLLIYDEVQCGMG 231 Query: 271 RTGKFWAIEHF-GVEPDLIQFGKAIGGGLPLAGVIHRADITFDKP-GRHATTFGGNPVAI 328 RTGK +A E G EP ++ KA+GGG P+ + + H +TFGGNP+A+ Sbjct: 232 RTGKLFAYEWAEGGEPHIMAVAKALGGGFPIGACLATTEAAKGMTVAAHGSTFGGNPLAM 291 Query: 329 AAGIEVVEIVK--ELLPHVQEVGDYLHKYLEEFKEKY-EVIGDARGLGLAQAVEIVKSKE 385 A G +EI+K E L +V+ V + + L K+++ +VI D RG G+ V+++ Sbjct: 292 AVGKAALEIIKSPETLDNVKTVSGFFTQQLNGLKDRFPDVIVDVRGKGMLIGVKLI---- 347 Query: 386 TKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALKAA 443 P RD +V ++ L++ G GDN +R +PPL +T EE A+ E+A +AA Sbjct: 348 -----PNNRDFMVLARDEK-LLIAGGGDNCVRLLPPLNLTIEEASEAIAKLEKACEAA 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: 432 Number of extensions: 29 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: 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