Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__HerbieS:HSERO_RS19685 Length = 456 Score = 264 bits (675), Expect = 4e-75 Identities = 158/437 (36%), Positives = 248/437 (56%), Gaps = 19/437 (4%) Query: 11 PGPKARKVIEEHHKYMATTTNDPNEYFLVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGL 70 PGPK +E + + + +++A GV + D DGN +D S+G+GV +VG Sbjct: 23 PGPKTAAALELSAR-TESMARGGGRMPIAMDQAFGVTFKDPDGNTFIDLSAGVGVSSVGR 81 Query: 71 RNPKVIEAIKKQLDLVLHAAGTDYYNPYQVELAKKLVEIAPGDIERK--VFLSNSGTEAN 128 NP+V+EAI+KQ + ++H+ + + + ELA K+ EI P + F + G++A Sbjct: 82 CNPRVVEAIRKQSESLMHSMEVN--SSKRTELAAKISEIMPDGLRGDCITFFTQGGSDAL 139 Query: 129 EAALKIAKWSTNRKMFIAFIGAFHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPY 188 EAA+K AK T R IAF G +HG + + +LT R P M GV+H PYP Y Sbjct: 140 EAAVKFAKRVTGRHQIIAFHGGYHGIWNASNALTTGT-AYRKGFGPFMGGVIHAPYPYAY 198 Query: 189 RNPWGIDGYENPDELINRVIDYIEEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFK 248 R P+ +++ +++ +DY+ L Y A++VA + EP+QGEGGYV P F + Sbjct: 199 RFPFDTS-HKSAEQIAGEYVDYL---LNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFLQ 254 Query: 249 ELKKLADKHGILLIDDEVQMGMGRTGRMWAIEHFDIVPDIVTVAKALGGGIPIGATIFRA 308 L+K D+ G LLI DEVQ G GRTG+MWA+EH + PD++T K +GG +P+ + R+ Sbjct: 255 ILRKACDRSGALLIVDEVQAGAGRTGKMWAVEHSGVKPDMLTFGKGIGGDMPMAGLVMRS 314 Query: 309 DLDFGV-SGVHSNTFGGNTVAAAAALAVIEELQN---GLIENAQKLEPLFRERLEEMKEK 364 DL + G NTF N+++AA AL I LQ+ L+ A L +ER+ Sbjct: 315 DLAAKIPDGSQPNTFAANSISAAVALTNISILQDPRLDLVNRAHTLGLEAQERIRSFNSP 374 Query: 365 YEIIGDVRGLGLAWGVEFVKDRKTKEYATKER-GEIVVEALKRGLALLGCGK--SAIRLI 421 + +G+VRG GL G+E V++R+T+E ++E+ G+++ + G+ ++ CG+ + +R++ Sbjct: 375 W--VGEVRGRGLMIGIELVENRETREPLSREKLGKLMDYVVGHGVLMIPCGRYTNVMRVM 432 Query: 422 PPLIISEEEAKMGLDIF 438 P L I GLDIF Sbjct: 433 PSLTIPRSLMFKGLDIF 449 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: 528 Number of extensions: 25 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: 456 Length adjustment: 33 Effective length of query: 421 Effective length of database: 423 Effective search space: 178083 Effective search space used: 178083 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