Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__ANA3:7025943 Length = 425 Score = 247 bits (631), Expect = 5e-70 Identities = 148/414 (35%), Positives = 213/414 (51%), Gaps = 19/414 (4%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P+ R E V+DV+G F DFA G+ V+N GH HP+V A+ Q E F+H Y Sbjct: 25 PVFTARAENATVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGY 84 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 E+ I + EKL +L PGD +K SG+EA E A+K+ + T R +AF +HGRT Sbjct: 85 ESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGVIAFTSGYHGRTM 144 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 A L+LT G V +P + G + D + + IE Sbjct: 145 AALALTGKVAPYSKGMGLMSANVFRAEFP------CALHGVSDDDAMAS-----IERIFK 193 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 P I AI EP+QGEGG+ F + L+ D GI+L DEVQ G GRTG F+ Sbjct: 194 NDAEPSNIAAIILEPVQGEGGFYAASPEFMQRLRALCDREGIMLIADEVQTGAGRTGTFF 253 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335 A+E GV D+ F K+I GG PL+G+ +A++ PG T+GGNP+A AA + V+ Sbjct: 254 AMEQMGVSADITTFAKSIAGGFPLSGITGKAEVMDAIGPGGLGGTYGGNPLACAAALAVL 313 Query: 336 EIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPEL 393 E+ +E LL +G+ + L + ++ I D RGLG A+E++ E + P+ Sbjct: 314 EVFEEEKLLERANAIGERIKSALNTMQVEHPQIADVRGLGAMIAIELM---EEGKPAPQY 370 Query: 394 RDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALKAALK 445 +I+ E+ RGL+LL CG N +R + PL V E++ + I + A LK Sbjct: 371 CAQILAEARNRGLILLSCGTYGNVLRILVPLTVPDEQLAAGLGILKSCFDAVLK 424 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: 452 Number of extensions: 23 Number of successful extensions: 5 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: 425 Length adjustment: 32 Effective length of query: 413 Effective length of database: 393 Effective search space: 162309 Effective search space used: 162309 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