Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_027720863.1 H589_RS0104130 aspartate aminotransferase family protein
Query= SwissProt::O50131 (454 letters) >NCBI__GCF_000425265.1:WP_027720863.1 Length = 444 Score = 215 bits (548), Expect = 2e-60 Identities = 145/418 (34%), Positives = 235/418 (56%), Gaps = 22/418 (5%) Query: 38 LVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNP 97 +++ EG+Y+ D G +DF S + +N+G +PKV +AIK Q+D + G + N Sbjct: 31 VLVTGCEGIYYWDETGKKYMDFGSQLVNLNIGHNHPKVQQAIKDQVDDICFI-GPQFANE 89 Query: 98 YQVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHG 157 + +LAKK++E+ P + K F + G +ANE A+K+A+ T + + ++HG T+G Sbjct: 90 TRGKLAKKIIELLPDNFG-KCFFTIGGADANENAIKMARAFTGKTKIFSRYRSYHGATYG 148 Query: 158 TMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFE 217 +SL+ +R + P +PGVV P YR P+G ++ PD + ++EE + Sbjct: 149 AISLSGDP--RRPPVEPGIPGVVRFFDPYCYRCPFG---HKYPDCKME-CATHLEEII-- 200 Query: 218 HYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMW 277 Y + A + E I G G VPP + ++L+++ D++ +LLI DEV G GRTG+M+ Sbjct: 201 GYENKDTCAAVLVESITGTNGVFVPPAGYMEKLREICDRNDMLLICDEVMTGFGRTGKMF 260 Query: 278 AIEHFDIVPDIVTVAKALGGG-IPIG-ATIFRADLDFGVSGV--HSNTFGGNTVAAAAAL 333 E+FDI PDI+T+AK + G +P+G A + + D+ S + T+ G+ V+ AAAL Sbjct: 261 GFENFDIKPDIITMAKGVNSGYVPLGVACVSQEIADWYESNMLWCGLTYSGHPVSCAAAL 320 Query: 334 AVIEEL-QNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVKDRKTKE-- 390 A IE + ++EN+ L + +E L MKEK+ IGDVR GL +E VKDR+T+E Sbjct: 321 ATIEAYEEEKIVENSAALGEVLKEELLAMKEKHPSIGDVRVKGLFACIETVKDRETREPL 380 Query: 391 ----YATKERGEIVVEALKRGLALLGCGKSAIRLIPPLIISEEEAKMGLDIFEEAIKV 444 A GE+ + + G+ + + I + PPL+I++EE GL EA+K+ Sbjct: 381 VPWNGAPGVMGEVAAKMKELGVTMF-VRWNFIFITPPLVITKEELLKGLSCISEALKI 437 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: 533 Number of extensions: 32 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: 454 Length of database: 444 Length adjustment: 33 Effective length of query: 421 Effective length of database: 411 Effective search space: 173031 Effective search space used: 173031 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 10 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