Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_005458846.1 SACCYDRAFT_RS19655 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000244975.1:WP_005458846.1 Length = 418 Score = 268 bits (685), Expect = 2e-76 Identities = 159/411 (38%), Positives = 222/411 (54%), Gaps = 18/411 (4%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+V++ GEG +YD G DF +G+GV + GH HPRVV A ++Q K H T + Sbjct: 13 PVVVDHGEGAYLYDTSGRRHLDFTAGIGVTSTGHCHPRVVAAAQEQVGKLIHGQYTTVMH 72 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 + L+E+L E+ P ++ + + NSG+EA EAA++L + TGR + F FHGRT Sbjct: 73 RPLLELSERLGEVLPKGLD-SLFFANSGSEAVEAALRLTRQATGRPNVVVFQGGFHGRTV 131 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 A S+T S GF P M GV P+P Y W E R LD++ Sbjct: 132 AAASMTTSGTRFSAGFSPLMGGVHVAPFPYAYHYGWD---ERTATEFALRELDYL---FA 185 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 P E A F EP+ GEGGYV F L++ ADE+GILL DE+Q G GRTG+FW Sbjct: 186 TQTSPQETAAFFVEPMLGEGGYVPANTEFMAGLRRRADEHGILLVVDEIQTGFGRTGRFW 245 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDK-PGRHATTFGGNPVAIAAGIEVV 335 EHF V PD++ K + G PL+G+ D+ PG T+GGN V+ AA I + Sbjct: 246 GHEHFDVRPDVVLIAKGLASGFPLSGIAASKDLMGKAWPGSQGGTYGGNAVSCAAAIATL 305 Query: 336 EIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPE- 392 ++++E L+ + G L + EK IGD RGLGL E V T + P+ Sbjct: 306 DVIREENLVENAAARGRQLLDGAKAVGEKTPGIGDVRGLGLLVGSEFV----TADGKPDG 361 Query: 393 -LRDRIVKESAKRGLVLLGCGD--NSIRFIPPLIVTKEEIDVAMEIFEEAL 440 + K +A++GL+LL CG N +R IPPL+VT E+ID A+EI+ + + Sbjct: 362 ATAQAVQKAAAEKGLLLLTCGAFMNVVRMIPPLVVTAEQIDEALEIWADVV 412 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: 478 Number of extensions: 17 Number of successful extensions: 7 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: 418 Length adjustment: 32 Effective length of query: 413 Effective length of database: 386 Effective search space: 159418 Effective search space used: 159418 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