Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate H281DRAFT_06342 H281DRAFT_06342 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Burk376:H281DRAFT_06342 Length = 473 Score = 164 bits (415), Expect = 6e-45 Identities = 125/423 (29%), Positives = 206/423 (48%), Gaps = 29/423 (6%) Query: 39 VIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPY 98 V+E A G + D GN LLD SG+ +NVG ++EA Q+ + +A ++ Sbjct: 31 VLESASGAFLRDAAGNELLDAFSGLWCVNVGYGQQSIVEAATAQMKKLPYATSYFHFGSE 90 Query: 99 Q-VELAKKLVEIAPGDIERKVFLSNSGTEANEAALKI------AKWSTNRKMFIAFIGAF 151 +ELA+KL +AP ++ V+ + G++A ++A++ A ++K IA + Sbjct: 91 PAIELAQKLASVAPASLQH-VYFTLGGSDAVDSAIRFITHYFNATGRPSKKHIIALQRGY 149 Query: 152 HGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYI 211 HG + LTA R+ P +P H+P P YR+ + D LI + + Sbjct: 150 HGSSSMGAGLTALPAFHRNFDLP-LPNQHHLPSPYAYRSNFADDA-----ALIAASVAAL 203 Query: 212 EEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMG 271 E + E + A+ VA F EPIQG GG +VPP + K +++ K GIL + DEV G G Sbjct: 204 EAKVAE--LGADNVAAFFCEPIQGSGGVIVPPFGWLKAMRESCRKLGILFLADEVITGFG 261 Query: 272 RTGRMWAIEHFDIVPDIVTVAKALGGG-IPIGATIFRADLDFGVSG-------VHSNTFG 323 RTG ++A + + PD++TVAK L G P+GA + ++ G++ H +T+ Sbjct: 262 RTGPLFACQGESVEPDLMTVAKGLTAGYAPMGAVLMSDEIYQGIADGDAEAIVGHGHTYS 321 Query: 324 GNTVAAAAALAVIEEL-QNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEF 382 + V+AA L V+ + GL+ N P F L+ + E + ++GD R GL +E Sbjct: 322 AHPVSAAIGLEVLRLYHEGGLLANGAARAPRFARGLDALLE-HPLVGDSRHRGLLGALEL 380 Query: 383 VKDRKTK---EYATKERGEIVVEALKRGLALLGCGKSAIRLIPPLIISEEEAKMGLDIFE 439 V ++ +K + A K I A + L G + + P L +E + M + E Sbjct: 381 VSNKDSKAQFDPALKLSERIAAAAYENRLIFRAFGDNILGFAPALSYTESDFDMMFERLE 440 Query: 440 EAI 442 + + Sbjct: 441 KTL 443 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: 472 Number of extensions: 21 Number of successful extensions: 3 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: 473 Length adjustment: 33 Effective length of query: 421 Effective length of database: 440 Effective search space: 185240 Effective search space used: 185240 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