Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_011317102.1 AVA_RS01075 acetyl ornithine aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000204075.1:WP_011317102.1 Length = 431 Score = 360 bits (923), Expect = e-104 Identities = 193/437 (44%), Positives = 271/437 (62%), Gaps = 24/437 (5%) Query: 7 VKELPGPKAKEVIERNFKYLAMTTQD-PENLPIVIERGEGIRVYDVDGNVFYDFASGVGV 65 V LPGP+AK ++ER+ A+T+ + P+V+ RGEG V DVDGNVF D +G+ V Sbjct: 17 VTSLPGPRAKAIVERD---RAVTSPSYTRDYPLVVNRGEGCMVEDVDGNVFLDMTAGIAV 73 Query: 66 INVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGA 125 GH+HP VV AI++Q+ + H S TDF+YE + LAE L AP + KV + NSGA Sbjct: 74 TATGHAHPEVVRAIQEQSARLIHMSGTDFYYEPMVELAENLASQAPFVHDTKVFFTNSGA 133 Query: 126 EANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYP 185 E+NE A+KL +Y T R +AF AFHGRT +SLT SK VQ+ F P +PGVTHIPY Sbjct: 134 ESNEGAIKLARYYTKRSLIIAFLGAFHGRTYGAMSLTGSKTVQRANFGPLVPGVTHIPYG 193 Query: 186 NPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGF 245 + D L N +L I +P HE+ AI EPIQGEGGY+VP GF Sbjct: 194 T----------HASLDYLENNLLTTI-------IPAHEVAAIVVEPIQGEGGYIVPEDGF 236 Query: 246 FKALKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIH 305 + ++ D YGIL+ DEVQ G+GRTG+ +AIEH+ V PD+I K I G+PL ++ Sbjct: 237 LQRIRNICDRYGILMVVDEVQSGMGRTGRLFAIEHWNVTPDIITTAKGIASGMPLGAILA 296 Query: 306 RADITFDKPGRHATTFGGNPVAIAAGIEVVEIVKE-LLPHVQEVGDYLHKYLEEFKEKYE 364 RA++ PG HATTFGGNPVA AAGI +++++ L+ + ++G+ L L + +++ Sbjct: 297 RAELMTWPPGSHATTFGGNPVACAAGIVTLKLLESGLMDNATQMGELLQTGLTQLHQQFP 356 Query: 365 VIGDARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIV 424 + RG GL AV+++ + +LRDRI++E+ GL+LLGCG +IRF PPL++ Sbjct: 357 RMSLPRGKGLMVAVDLLDEDGNFDS--KLRDRIIQEAFYHGLLLLGCGKAAIRFCPPLVI 414 Query: 425 TKEEIDVAMEIFEEALK 441 +E+I ++I E L+ Sbjct: 415 NREQIQTTLDILAEILR 431 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: 516 Number of extensions: 20 Number of successful extensions: 4 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: 431 Length adjustment: 32 Effective length of query: 413 Effective length of database: 399 Effective search space: 164787 Effective search space used: 164787 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 09 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