Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >MicrobesOnline__882:208056 Length = 542 Score = 166 bits (419), Expect = 2e-45 Identities = 128/434 (29%), Positives = 210/434 (48%), Gaps = 43/434 (9%) Query: 37 PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96 P +I+ +G + D DGN + D S + GH HP + EAI++Q ++ H +L Sbjct: 84 PCIIDAADGNHLIDTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQLDRVAHSTLLGLGG 143 Query: 97 ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV--------KYGTGRKQFLAFY 148 +I LA +L +AP + R V Y +SG+ A EAA+K+ + R + +AF Sbjct: 144 TPSIELAARLTAIAPAGLTR-VFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAFS 202 Query: 149 HAFHGRTQAVLSLTASKWVQQDGFF-PTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRV 207 +A+HG T +SL G + P + P P+ YR + P+ Sbjct: 203 NAYHGDTIGSVSLGGMSLFH--GIYGPLLFDPVRAPAPHCYRCPADL----RPETCGMAC 256 Query: 208 LDFIEEYVFRHVPPHEIGAIFFEP-IQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQ 266 L +E + H HE+ A+ EP +QG G +V P+G+ + L+ D +G+ + DEV Sbjct: 257 LGEVERLMRHH--GHELCAVVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVA 314 Query: 267 MGIGRTGKFWAIEHFGVEPDLIQFGKAIGGG-LPLAGVIHRADITFDKPGR--------H 317 +G G+TG +A E GV PD++ K I GG LPLA + I G H Sbjct: 315 VGFGKTGTMFACEQEGVVPDMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRTFFH 374 Query: 318 ATTFGGNPVAIAAGIEVVEIVKE------LLPHVQEVGDYLHKYLEEFKEKYEVIGDARG 371 T+ GN +A AA + +++ +E L P ++ + L L + +GD R Sbjct: 375 GHTYTGNALACAAALASLDVFEEERTLETLRPRIERLATLLAP-LNDLPH----VGDIRR 429 Query: 372 LGLAQAVEIVKSKETKEKY-PELR--DRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEE 428 +G+ +E+V +ET+ Y PE R R+ E+ +RG+++ GD + +PPL +T+ E Sbjct: 430 VGVMTGIELVADRETRTPYRPEERIGHRVTLEARRRGVIVRPLGDVMV-LMPPLSITETE 488 Query: 429 IDVAMEIFEEALKA 442 ++ + A+ A Sbjct: 489 LETLVHTVRGAIIA 502 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: 558 Number of extensions: 32 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: 542 Length adjustment: 34 Effective length of query: 411 Effective length of database: 508 Effective search space: 208788 Effective search space used: 208788 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: 52 (24.6 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