Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_078716203.1 B5D49_RS03155 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900167125.1:WP_078716203.1 Length = 433 Score = 315 bits (807), Expect = 2e-90 Identities = 172/419 (41%), Positives = 248/419 (59%), Gaps = 12/419 (2%) Query: 31 QDPEN-LPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHY 89 Q P N LP + G + DV+G + DFA G+GV+N GH HP+VV A+++QAEKF H Sbjct: 17 QGPANMLPAFAAQARGATITDVEGREYIDFAGGIGVVNTGHCHPKVVRAVQEQAEKFLHT 76 Query: 90 SLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYH 149 YE + LAE+L LAPGD +K + NSGAEA E A+K+ +Y TGR +AF + Sbjct: 77 CFHVVMYEGYVELAERLNALAPGDFAKKSFFLNSGAEAVENAVKIARYETGRPAVIAFQN 136 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 FHGR+ +SLT+ + F P P V PY YR G+ D Sbjct: 137 GFHGRSLLTMSLTSKVKPYKYRFGPFAPEVYRAPYAYCYRCPLGL----THPACGAACAD 192 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 ++EE+ HV A+ EPIQGEGG+ PP +F L+ D+YGI L DEVQ G Sbjct: 193 YLEEFFVSHVAAERTAALVVEPIQGEGGFATPPPEYFPRLRSICDKYGIRLIVDEVQSGF 252 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKP--GRHATTFGGNPVA 327 GRTG +AIEH+GV PD+I K++ GG+PL+GV+ RA+I D P G T+GG+P A Sbjct: 253 GRTGTLFAIEHWGVAPDMITVAKSLAGGMPLSGVVGRAEI-MDAPHVGGLGGTYGGSPTA 311 Query: 328 IAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKE 385 AA + V++I+ E LL QE+G ++ K + F++++E++GD RGLG A+E+V+ ++ Sbjct: 312 CAAALAVLDILLEDGLLHRAQELGRHVRKVFDGFQQEFEIVGDVRGLGPMLALELVQDRQ 371 Query: 386 TKEKYPELRDRIVKESAKRGLVLLGCGD--NSIRFIPPLIVTKEEIDVAMEIFEEALKA 442 TK + +V +GL++L CG+ N IR + PL++T +E+D + I ++ L A Sbjct: 372 TKTPAADKAKALVAHCRAQGLIILACGNFGNVIRTLMPLVITDQELDRGLSILKDGLHA 430 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: 546 Number of extensions: 28 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: 433 Length adjustment: 32 Effective length of query: 413 Effective length of database: 401 Effective search space: 165613 Effective search space used: 165613 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