Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__psRCH2:GFF3586 Length = 426 Score = 252 bits (644), Expect = 1e-71 Identities = 150/407 (36%), Positives = 213/407 (52%), Gaps = 16/407 (3%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 PI + + V DV+G F DFA G+ V+N GH HP++++A++ Q K TH Y Sbjct: 25 PIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKLTHTCFQVLAY 84 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156 E + L EK+ PGD +K + +G+EA E A+K+ + TGR +AF A+HGRT Sbjct: 85 EPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTM 144 Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216 L LT G G+ YP I G D + + IE Sbjct: 145 MTLGLTGKVAPYSAGMGLMPGGIFRALYP------CAIYGVSVDDSIAS-----IERIFK 193 Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276 P +I AI EP+QGEGG+ V PK F L+ DE+GILL DEVQ G GRTG F+ Sbjct: 194 NDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIADEVQTGAGRTGTFF 253 Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335 A+E GV DL F K++GGG P+AGV +A+I PG T+ GNP++ AA + V+ Sbjct: 254 AMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYAGNPLSCAAALAVL 313 Query: 336 EIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPEL 393 E+ +E LL + V + L L+ + K++ IG+ RGLG A+E+ + + L Sbjct: 314 EVFEEEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIELFEDGDHARPAAAL 373 Query: 394 RDRIVKESAKRGLVLLGCGD--NSIRFIPPLIVTKEEIDVAMEIFEE 438 +IV + +GL+LL CG N +R + PL E +D + I E Sbjct: 374 TSQIVARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGLAIIGE 420 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: 23 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: 426 Length adjustment: 32 Effective length of query: 413 Effective length of database: 394 Effective search space: 162722 Effective search space used: 162722 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