Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein
Query= SwissProt::Q5JEW1 (445 letters) >NCBI__GCF_000182725.1:WP_008507916.1 Length = 403 Score = 202 bits (515), Expect = 1e-56 Identities = 142/413 (34%), Positives = 208/413 (50%), Gaps = 55/413 (13%) Query: 41 ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100 ERGEGI + DG + DFA+G+ V ++GHSHP +VE +K QAEK H S YE I Sbjct: 22 ERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEKLWHLSN---IYE--I 76 Query: 101 ILAEKL-IELAPGDIERKVVYGNSGAEANEAAMKLVK---YGTG---RKQFLAFYHAFHG 153 EKL L KV + NSGAEA E A+K + Y +G R + + F AFHG Sbjct: 77 PAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQYVSGHPERFRIITFEGAFHG 136 Query: 154 RTQAVLSLTA-SKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIE 212 RT A ++ +K+++ GF P + G +P F + Sbjct: 137 RTLATIAAGGQAKYLE--GFGPKVEGFDQVP--------------------------FGD 168 Query: 213 EYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRT 272 E R E I EPIQGEGG P+ F + +++ DE G+LL DEVQ G+GRT Sbjct: 169 EAALRAAITPETAGILLEPIQGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGVGRT 228 Query: 273 GKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIAAG 331 GKF+A E G+ PD++ K IGGG P+ + A+ G H TT+GGNP+ +A G Sbjct: 229 GKFFAHEWAGIRPDIMAIAKGIGGGFPIGACLATAEAAKGMTAGMHGTTYGGNPLGMAVG 288 Query: 332 IEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKY-EVIGDARGLGLAQAVEIVKSKETKE 388 V+++V + +VQ + + L ++Y V+ + RG GL ++ V + Sbjct: 289 NAVLDVVLADGFMENVQATALVMKQGLASLVDRYPNVVSEIRGRGLLMGLKCVVPNTS-- 346 Query: 389 KYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALK 441 +++ ++ +G GDN +R +PPLI T EE A++ E A++ Sbjct: 347 --------LIQALRDEHVLSVGAGDNVVRLLPPLITTPEEAREALKHIETAVE 391 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: 497 Number of extensions: 22 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: 403 Length adjustment: 32 Effective length of query: 413 Effective length of database: 371 Effective search space: 153223 Effective search space used: 153223 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 24 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