Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4179 Length = 459 Score = 254 bits (648), Expect = 5e-72 Identities = 152/411 (36%), Positives = 219/411 (53%), Gaps = 18/411 (4%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 + I++ ++DV+G F DFA G+ V+N GH H V+ A+K Q + +TH YE Sbjct: 55 LFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQLDLYTHTCFQVVAYE 114 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQA 157 + + E+L LAPG +K + +GAEA E A+K+ + T R +AF +HGRT Sbjct: 115 PYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTKRPGVIAFTGGYHGRTNL 174 Query: 158 VLSLTASKWVQQDGFFPTMPGVT-HIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 L LT + GF P PG T H +PN + L +E Sbjct: 175 TLGLTGKVAPYKIGFGP-FPGETYHALFPNALHGV-----------SVEQALHSVELIFK 222 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 + P + A EP+QGEGG+ V P F LK AD YGILL DEVQ G GRTG ++ Sbjct: 223 NDIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTWF 282 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335 A E + V PDLI K++ GG PLAGV+ RAD+ PG T+ G+PVA AA + V+ Sbjct: 283 ASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAVI 342 Query: 336 EIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPEL 393 E ++LL Q++G L + L++ + IGD RGLG A+E+ ++ + L Sbjct: 343 EAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFENGDLSRPDAAL 402 Query: 394 RDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALKA 442 ++V E+A+RGL+LL CG N IR + PL + E + + I ++L+A Sbjct: 403 TKQVVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILADSLEA 453 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: 546 Number of extensions: 28 Number of successful extensions: 4 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