Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF4212 Psest_4285 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__psRCH2:GFF4212 Length = 452 Score = 198 bits (503), Expect = 3e-55 Identities = 126/411 (30%), Positives = 230/411 (55%), Gaps = 30/411 (7%) Query: 39 VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF--- 95 +I + G+ ++D +G+ D +G+ +N+G+ +VEA +Q + +Y+L FF Sbjct: 34 IITKASGVYLWDSEGHKILDAMAGLWCVNLGYGREELVEAATRQMRELPYYNL--FFQTA 91 Query: 96 YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY------GTGRKQFLAFYH 149 + A+ LA+ + ++AP + V + SG+EAN+ +++V++ +K + ++ Sbjct: 92 HPPAVALAKAIADIAPAGMNH-VFFTGSGSEANDTVLRMVRHYWAIKGQPAKKVVIGRWN 150 Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209 +HG T A SL K + + P +PG+ HI P + G G P+E R+ D Sbjct: 151 GYHGSTIAGASLGGMKAMHEQSDGP-IPGIEHIDQPYWF----GEGGDMSPEEFGVRIAD 205 Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269 +E+ + V ++ A EPIQG GG ++PP+ ++ +K+ Y IL DEV G Sbjct: 206 QLEQKILE-VGEDKVAAFIAEPIQGAGGVIIPPETYWPRIKEILARYDILFIADEVICGF 264 Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRADI--TFDKPGR--HATTFGGN 324 GRTG+++ +++G+EPDL+ K + G +P+ GVI R ++ T ++ G H T+ G+ Sbjct: 265 GRTGEWFGSDYYGLEPDLMPIAKGLTSGYIPMGGVIVRDEVVQTLNEGGEFYHGFTYSGH 324 Query: 325 PVAIAAGIEVVEIVKE--LLPHVQ-EVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIV 381 PVA A +E + I++E ++ V+ + YL +E + + ++G+ARG+GL A+E+V Sbjct: 325 PVAAAVALENIRILREEKIVERVKTKTAPYLQSRWQELLD-HPLVGEARGVGLLGALELV 383 Query: 382 KSKETKEKY--PELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEID 430 K+K+T+E++ P + + + GLV+ GD I PPL++++E+ID Sbjct: 384 KNKKTRERFADPGVGMLCREHCFRNGLVMRAVGDTMI-ISPPLVISEEQID 433 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: 562 Number of extensions: 40 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: 452 Length adjustment: 33 Effective length of query: 412 Effective length of database: 419 Effective search space: 172628 Effective search space used: 172628 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