Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_011384093.1 AMB_RS08515 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000009985.1:WP_011384093.1 Length = 459 Score = 208 bits (530), Expect = 3e-58 Identities = 143/432 (33%), Positives = 228/432 (52%), Gaps = 29/432 (6%) Query: 33 PENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLT 92 PE P+VI RG+G+RVYD G + + +G+ ++G R+VEA +Q + Y L Sbjct: 29 PEVGPLVITRGQGVRVYDEAGRDYIEGLAGLWCTSLGWGEERLVEAAARQMRQLPFYHLF 88 Query: 93 DF-FYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY-----GT-GRKQFL 145 ++ + L +L+ +AP + KV SG+EAN+ A+KL+ Y GT +K+ + Sbjct: 89 SHKTHDVGVELCARLLAMAPVPMS-KVFLAGSGSEANDTAIKLIHYRANALGTPDKKKII 147 Query: 146 AFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTN 205 A A+HG T A SLT Q+ P +PGV P+ YR + DG E D + Sbjct: 148 AREKAYHGVTVATASLTGLVNNQRSFDLP-IPGVLRAACPHHYR--FAKDGESEED-FST 203 Query: 206 RVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEV 265 R+ +E + P + A F EP+ G GG +VPP G+F ++ D Y +LL DEV Sbjct: 204 RLAGELEAMILAE-GPDTVAAFFAEPVMGAGGVIVPPAGYFPKIQAVLDRYDVLLVVDEV 262 Query: 266 QMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRADI---TFDKPGR----- 316 G GRTGK + E FG+ PD++ K + G P++ ++ + ++ GR Sbjct: 263 ICGFGRTGKMFGTETFGIRPDMMTLAKGLSSGYAPISALMVNERVYGPVAEESGRIGVFG 322 Query: 317 HATTFGGNPVAIAAGIEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGL 374 H T+GG+PV+ A +E + I +++L V EVG L L + + ++G+ARG+GL Sbjct: 323 HGYTYGGHPVSAAVALETLNIYAERDILAQVAEVGPVLQDGLRALR-GHPLVGEARGVGL 381 Query: 375 AQAVEIVKSKETKEKYP---ELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDV 431 AVE+V K + +P + R+V ++ +G++L GD ++ F PPL+++K +I Sbjct: 382 IGAVELVADKANRAPFPPELAVGARVVAKAQAKGVILRAMGD-AVAFAPPLVISKADIAE 440 Query: 432 AMEIFEEALKAA 443 + F AL A Sbjct: 441 MLRRFGLALDEA 452 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: 567 Number of extensions: 35 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: 459 Length adjustment: 33 Effective length of query: 412 Effective length of database: 426 Effective search space: 175512 Effective search space used: 175512 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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