Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_230973858.1 G579_RS0114350 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000423825.1:WP_230973858.1 Length = 473 Score = 170 bits (430), Expect = 1e-46 Identities = 141/432 (32%), Positives = 206/432 (47%), Gaps = 39/432 (9%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 ++ RG G +YD+DG + D S + GH HPR+ A++ Q + H + Sbjct: 47 VIFARGAGNYLYDLDGKAYLDAISSLWCNVHGHRHPRLDAALQAQMGRVAHSTTLGASNP 106 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY---GTGR---KQFLAFYHAF 151 AI+LA++L ELAP +ER V Y GAEA E A+K+ + +GR ++FL +A+ Sbjct: 107 PAILLAKRLAELAPAGLER-VFYSEDGAEAVEIAVKMAFHFWRNSGRPEKRRFLTLDNAY 165 Query: 152 HGRTQAVLSLTASKW---VQQDGFFPTMPGVTHIPYPNPY---RNTWGIDGYEEPDELTN 205 HG T +S+ V QD F P+PY R +G +++P T Sbjct: 166 HGDTVGAVSVGGMDLFHNVYQDLLFHADR------LPSPYGLARALFGARDWDQP-AATA 218 Query: 206 RVLDFIEEYVFRHVPPHEIGAIFFEP-IQGEGGYVVPPKGFFKALKKFADEYGILLADDE 264 L +EE + EI A+ E IQG G + PKG + D + +LL DE Sbjct: 219 AWLQRLEEMLRER--GGEIAALVMESGIQGAAGLLPFPKGILAGARALCDRHDVLLILDE 276 Query: 265 VQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRADITFDKPGR------- 316 V G GRTG+ +A EH V PDL+ GK + GG LPLA + I G Sbjct: 277 VATGFGRTGRLFACEHEAVRPDLMALGKGLSGGYLPLAATLTTQRIYDAFLGEFGETRQF 336 Query: 317 -HATTFGGNPVAIAAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLG 373 H TF GNP+A A +E ++I +++L + +LH L F + + +G R G Sbjct: 337 YHGHTFTGNPLACAVALENLQIFEDEQILERLAGRIRHLHDGLAAFWQ-HPHVGAVRQFG 395 Query: 374 LAQAVEIVKSKETKEKYP---ELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEID 430 L +E+V K T YP + I + + +RG+ GD + +PPL +T EEID Sbjct: 396 LMVGIEVVADKSTGSAYPYGERVEYAISRAAIERGVYTRPLGDTLV-LMPPLSITAEEID 454 Query: 431 VAMEIFEEALKA 442 + EAL A Sbjct: 455 RILATLAEALDA 466 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: 532 Number of extensions: 31 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: 473 Length adjustment: 33 Effective length of query: 412 Effective length of database: 440 Effective search space: 181280 Effective search space used: 181280 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 Jul 25 2024. The underlying query database was built on Jul 25 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