Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= SwissProt::O50131 (454 letters) >MicrobesOnline__882:208056 Length = 542 Score = 192 bits (489), Expect = 2e-53 Identities = 146/439 (33%), Positives = 226/439 (51%), Gaps = 44/439 (10%) Query: 39 VIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPY 98 +I+ A+G + ID DGN LD S + G R+P + EAI++QLD V H+ Sbjct: 86 IIDAADGNHLIDTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQLDRVAHSTLLGLGGTP 145 Query: 99 QVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIA--------KWSTNRKMFIAFIGA 150 +ELA +L IAP + R VF S+SG+ A EAALKIA + R +AF A Sbjct: 146 SIELAARLTAIAPAGLTR-VFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAFSNA 204 Query: 151 FHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDY 210 +HG T G++SL + P + V P P+ YR P + P+ + Sbjct: 205 YHGDTIGSVSL-GGMSLFHGIYGPLLFDPVRAPAPHCYRCPADL----RPETCGMACLGE 259 Query: 211 IEEYLFEHYVPAEEVAGIFFEP-IQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMG 269 +E + H E+ + EP +QG G +V P+ + + L+ L D+HG+ ++ DEV +G Sbjct: 260 VERLMRHH---GHELCAVVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVAVG 316 Query: 270 MGRTGRMWAIEHFDIVPDIVTVAKALGGG-IPIGATIFRADLDFGVSG--------VHSN 320 G+TG M+A E +VPD++ +AK + GG +P+ AT+ + G G H + Sbjct: 317 FGKTGTMFACEQEGVVPDMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRTFFHGH 376 Query: 321 TFGGNTVAAAAALAVIEELQNGLIENAQKLEPLFRERLEEMK------EKYEIIGDVRGL 374 T+ GN +A AAALA ++ + E + LE L R R+E + +GD+R + Sbjct: 377 TYTGNALACAAALASLD-----VFEEERTLETL-RPRIERLATLLAPLNDLPHVGDIRRV 430 Query: 375 GLAWGVEFVKDRKTK-EYATKER--GEIVVEALKRGLALLGCGKSAIRLIPPLIISEEEA 431 G+ G+E V DR+T+ Y +ER + +EA +RG+ + G + L+PPL I+E E Sbjct: 431 GVMTGIELVADRETRTPYRPEERIGHRVTLEARRRGVIVRPLGDVMV-LMPPLSITETEL 489 Query: 432 KMGLDIFEEAIKVVSERHG 450 + + AI V+E HG Sbjct: 490 ETLVHTVRGAIIAVTE-HG 507 Lambda K H 0.319 0.139 0.410 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: 563 Number of extensions: 33 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: 454 Length of database: 542 Length adjustment: 34 Effective length of query: 420 Effective length of database: 508 Effective search space: 213360 Effective search space used: 213360 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 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