Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_012853702.1 TCUR_RS16645 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000024385.1:WP_012853702.1 Length = 431 Score = 210 bits (535), Expect = 6e-59 Identities = 146/421 (34%), Positives = 221/421 (52%), Gaps = 33/421 (7%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 PI I G+G+RV D +GN + DF +G+ +G+ V +A+++Q ++ T + Sbjct: 23 PIEIVSGKGVRVTDAEGNTYLDFFAGIITNILGYDVEEVRQAVERQLATGVVHTSTAYLL 82 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 + LAEK++ L+ G + KV + NSG EANE A+ L Y Q LA ++HGR+ Sbjct: 83 RGQVELAEKIVALS-GIKDAKVFFVNSGTEANETALLLATYARKSNQVLAMRQSYHGRSF 141 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIE---- 212 + +TA++ + + + P H G D + P DFI+ Sbjct: 142 GAIGVTANRSWKNNAYTPLTVHFLH-----------GGDRHL-PQFAHLSDADFIKVCTE 189 Query: 213 --EYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIG 270 +V ++ A+ EPIQG GG+ +PP G + A K+ DEYG L DEVQ G G Sbjct: 190 DLRHVLATATGGDVAALIAEPIQGVGGFTMPPDGLYAAYKEVLDEYGALFISDEVQTGWG 249 Query: 271 RTGK-FWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHAT---TFGGNPV 326 RTG+ F+ I + GV PD++ F K +G G + GV+ R D+ D P HAT TFGGNP+ Sbjct: 250 RTGQSFFGIHNHGVTPDIMTFAKGLGNGFAVGGVVARGDL-MDAP--HATGLSTFGGNPI 306 Query: 327 AIAAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSK 384 A+AA ++ + +L + G L L+E + V+G RG GL AVE+V+ Sbjct: 307 AMAAANATLDYILDHDLQSNAARQGALLLDGLKEAAPRLPVVGAVRGKGLMFAVELVE-P 365 Query: 385 ETKEKYPELRDRIVKESAKRGLVLLGCG---DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441 T E P L +++E+ KRGL L+G G N IR PPL +T+E+ + I ++L+ Sbjct: 366 GTGEPSPPLAAAVMEETRKRGL-LVGKGGLYGNVIRMAPPLTITEEDAREGLGILIDSLE 424 Query: 442 A 442 A Sbjct: 425 A 425 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: 521 Number of extensions: 28 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: 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 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