Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF3809 PS417_19505 2,4-diaminobutyrate 4-aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__WCS417:GFF3809 Length = 464 Score = 229 bits (585), Expect = 1e-64 Identities = 146/425 (34%), Positives = 226/425 (53%), Gaps = 16/425 (3%) Query: 33 PENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLT 92 P +P+ ++R +G+ V DV+G F D +G G + +GH+HP V+EAI++ Sbjct: 40 PRRIPLALKRAKGLYVEDVEGRRFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTL 99 Query: 93 DFFYENAIILAEKLIELAPGDIERKVVY---GNSGAEANEAAMKLVKYGTGRKQFLAFYH 149 D + L L P + R+ G +G +A EAA+KLV+ TGR L+F Sbjct: 100 DLTTPVKDQFVQDLFGLLPPALAREAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQG 159 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 +HG +Q LSL S ++ GV +PYP YR +G+ G E + + + Sbjct: 160 GYHGMSQGALSLMGSLGPKKPLGALLGNGVQFLPYPYDYRCPFGLGGAEGVRVNLHYLDN 219 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 + + + P A+ E +QGEGG + + + L++ ++ G+ L DE+Q G Sbjct: 220 LLNDPEAGVLLP---AAVIVEVVQGEGGVIPADLDWLRGLRRITEQAGVALIVDEIQSGF 276 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAIA 329 GRTGK +A EH G+ PD++ KAIGG LPLA V++R + PG HA TF GN +A+A Sbjct: 277 GRTGKLFAFEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWLPGAHAGTFRGNQMAMA 336 Query: 330 AGIEVVEIVK--ELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETK 387 AG V+ +K +L H +G+ L ++L + + +GD RG GL VE+V T Sbjct: 337 AGSAVMRYLKDHDLAGHAAAMGERLGEHLRILQRDFPHLGDIRGRGLMLGVELVDPNGTL 396 Query: 388 E------KYPELRDRIVKESAKRGLVL-LGCGDNS-IRFIPPLIVTKEEIDVAMEIFEEA 439 + + +L + +E KRGL+L LG S +RF+PPL++T E+D+ +IF A Sbjct: 397 DVQGHPPVHRQLAPLVQRECLKRGLILELGGRHGSVVRFLPPLVITAVEVDLVADIFGRA 456 Query: 440 LKAAL 444 L AA+ Sbjct: 457 LAAAV 461 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: 543 Number of extensions: 37 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: 464 Length adjustment: 33 Effective length of query: 412 Effective length of database: 431 Effective search space: 177572 Effective search space used: 177572 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 Apr 09 2024.
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