Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_092053439.1 BQ4888_RS01605 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_900111775.1:WP_092053439.1 Length = 449 Score = 185 bits (469), Expect = 3e-51 Identities = 138/429 (32%), Positives = 221/429 (51%), Gaps = 39/429 (9%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 PI I RG+G +YD DG + D S V GH+HPR+ A+ KQA K H+ F + Sbjct: 29 PIPIARGDGAYLYDFDGKGYIDGVSSWWVNLFGHNHPRLNRALSKQAGKVAHHIFAGFTH 88 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV-----KYGTGRK-QFLAFYHA 150 E A LA +L ELAP +E KV + ++G+ A EAA+K+ + G G K +F++ A Sbjct: 89 EPAATLAARLCELAPPGLE-KVFFTDNGSAAVEAALKMSFQYWRQTGQGEKTRFVSITEA 147 Query: 151 FHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDF 210 +HG T LS+ + +D + P + + P+ +R +G E + Sbjct: 148 YHGETLGALSV-GGCGLYKDIYQPLLLDGFQVQGPDCFRCPYGC----ERESCNAECFAA 202 Query: 211 IEEYVFRHVPPHEIGAIFFEP-IQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 +EE V H +I A+ EP IQ G + P + K L++ D + I DE+ +G Sbjct: 203 MEEVVAEH--HRQIAAVIIEPLIQCAAGMRIYPPIYLKKLRELCDRWRIHYIADEIAVGF 260 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRA---DITFD-----KPGRHATT 320 GRTG+ +A EH GV PDL+ K I GG +PL+ V+ R D +D K H+ + Sbjct: 261 GRTGRLFANEHAGVSPDLLCLSKGITGGYMPLSVVLTRQEMYDAFYDDYATLKAFLHSHS 320 Query: 321 FGGNPVAIAAGIEVV------EIVKELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGL 374 + GNP+A A EV+ +I+++++P + + H++ E +G+ R LGL Sbjct: 321 YSGNPLACALACEVLNIFTEEKILEKMVPKMAILASQKHRF-----EALPQVGEFRQLGL 375 Query: 375 AQAVEIVKSKETKEKYPELRDR---IVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDV 431 A+E+V+ K K YP R + +++ ++G +L G N + F+PPL + K ++ Sbjct: 376 VGAIELVRDKVGKTPYPWQERRGYAVYRKALEKGALLRPLG-NVVYFMPPLTIEKADLSR 434 Query: 432 AMEIFEEAL 440 ++I EA+ Sbjct: 435 LVDIAYEAI 443 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: 528 Number of extensions: 30 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: 449 Length adjustment: 33 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 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