Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate H281DRAFT_02621 H281DRAFT_02621 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Burk376:H281DRAFT_02621 Length = 447 Score = 194 bits (494), Expect = 4e-54 Identities = 137/435 (31%), Positives = 219/435 (50%), Gaps = 32/435 (7%) Query: 35 NLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDF 94 +LPI + RG+GI + D G + D G V +GHSHPRV+EAI++Q ++ + + F Sbjct: 12 SLPIAV-RGDGIEIVDSTGTRYIDACGGAAVSCLGHSHPRVIEAIQRQVQQLPYAHTSFF 70 Query: 95 FYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV------KYGTGRKQFLAFY 148 E A LA+ LIE AP ++ V + + G+EA EAA+KL K R+ F+A Sbjct: 71 TTEPAEALADLLIEAAPRNLGH-VYFVSGGSEAMEAALKLARQYFVEKGQPERRHFIARR 129 Query: 149 HAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVL 208 ++HG T L++ + W +++ F P + H+ YR E + R+ Sbjct: 130 QSYHGNTLGALAIGGNAW-RREPFLPILIEAHHVTPCFAYREQ---QAGETDEAFAQRLA 185 Query: 209 DFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPP-KGFFKALKKFADEYGILLADDEVQM 267 D +E + + + A E + G VPP + +F+ ++ D+YG+LL DEV Sbjct: 186 DELEAKIL-ELGAQSVAAFVAETVVGATAGAVPPVREYFRKIRAVCDKYGVLLILDEVMS 244 Query: 268 GIGRTGKFWAIEHFGVEPDLIQFGKAIGGGL-PLAGVIHRADITFDKPG-----RHATTF 321 G+GRTG +A E GV PD++ K +G G P+ + +I G +H T+ Sbjct: 245 GMGRTGHLFACEEDGVSPDILAIAKGLGAGYQPIGATLVSNEIFNTIVGGSGFFQHGHTY 304 Query: 322 GGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVE 379 G+ A AA +EV +++ E LL +V+ G+ L L E++ + IGD RG GL VE Sbjct: 305 IGHATACAAALEVQKVIAEEQLLDNVKARGEQLRARLREWQANHPFIGDVRGRGLFTGVE 364 Query: 380 IVKSKETKEKYP---ELRDRIVKESAKRGLVLLGCG-------DNSIRFIPPLIVTKEEI 429 +V+ + +K + +L I E+ KRGL++ G + + PP I T +I Sbjct: 365 LVQDRASKTAFDPKHKLHAIIKSEAMKRGLMVYPMGGTVDGRIGDHVLIAPPFITTSAQI 424 Query: 430 DVAMEIFEEALKAAL 444 D +E +A+ AL Sbjct: 425 DTIVERLADAIDGAL 439 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: 503 Number of extensions: 30 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: 447 Length adjustment: 32 Effective length of query: 413 Effective length of database: 415 Effective search space: 171395 Effective search space used: 171395 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