Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__azobra:AZOBR_RS19630 Length = 428 Score = 286 bits (732), Expect = 9e-82 Identities = 160/413 (38%), Positives = 236/413 (57%), Gaps = 18/413 (4%) Query: 36 LPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF 95 +P+ ++R E ++DV+GN F DFA G+ V+N GH HP+++EA+K Q ++FTH Sbjct: 22 MPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHTCAMVTP 81 Query: 96 YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRT 155 YE+ + LAE+L L PG +K + +GAEA E A+K+ + TGR +AF AFHGRT Sbjct: 82 YESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGAFHGRT 141 Query: 156 QAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYV 215 ++LT + GF P V H P+PN YR D L +E+ Sbjct: 142 LLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDS-----------LKALEQLF 190 Query: 216 FRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKF 275 V + AI EP+QGEGG+ + P F +AL+K DE GILL DE+Q G RTGK Sbjct: 191 KSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGKM 250 Query: 276 WAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEV 334 +AIEH GVEPDL+ K++ GG PL+ V +A+I PG T+ G+P+A A + V Sbjct: 251 FAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGSPLATTAALAV 310 Query: 335 VEIVKE--LLPHVQEVGDYLHKYLEEFKEK--YEVIGDARGLGLAQAVEIVKSKETKEKY 390 +++++E L+ ++G+ + ++ VIGD R LG A+E+VK + TKE Sbjct: 311 LDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTKEPA 370 Query: 391 PELRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441 EL +V ++A++GLVLL CG N IR + PL + +D ++I E +L+ Sbjct: 371 AELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERSLE 423 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: 477 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: 428 Length adjustment: 32 Effective length of query: 413 Effective length of database: 396 Effective search space: 163548 Effective search space used: 163548 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 09 2024. 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