Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate AO356_27515 AO356_27515 4-aminobutyrate aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27515 Length = 457 Score = 255 bits (651), Expect = 2e-72 Identities = 157/440 (35%), Positives = 245/440 (55%), Gaps = 15/440 (3%) Query: 10 IPGPKARKVIEEHHKYMATTTNDPNEYFLVIERAEGVYWIDVDGNVLLDFSSGIGVMNVG 69 IPGP+ + + + + + ++RA G + D D N +D S+G+GV +VG Sbjct: 21 IPGPRTTEALALSAR-TESMARGGGRMPVAMDRAFGATFKDADDNTYIDLSAGVGVSSVG 79 Query: 70 LRNPKVIEAIKKQLDLVLHAAGTDYYNPYQVELAKKLVEIAPGDIERK--VFLSNSGTEA 127 +PKV++AI++Q ++++HA + + + ELA KL EIAP + F + SG++A Sbjct: 80 RCHPKVVQAIREQSEVLMHALEVN--STRRTELAAKLSEIAPDGLRGDCITFFTQSGSDA 137 Query: 128 NEAALKIAKWSTNRKMFIAFIGAFHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNP 187 EAA+K AK T R IAF G +HG + + +LT R M GV+H PYP Sbjct: 138 LEAAIKFAKRVTGRHQIIAFHGGYHGVWNASGALTTGT-AYRKGYGAQMGGVIHAPYPYA 196 Query: 188 YRNPWGIDGYENPDELINRVIDYIEEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFF 247 YR P+ +++ +++ +DY+ L Y A++VA + EP+QGEGGYV P F Sbjct: 197 YRFPFDTT-HKSAEQIAGEYVDYL---LNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFL 252 Query: 248 KELKKLADKHGILLIDDEVQMGMGRTGRMWAIEHFDIVPDIVTVAKALGGGIPIGATIFR 307 + L+K D+ G LLI DEVQ G GRTG+MWA+EH + PD++T K +G +P+ I R Sbjct: 253 QLLRKACDRSGTLLIVDEVQSGAGRTGKMWAVEHSGVKPDMLTFGKGIGSDLPMAGLIMR 312 Query: 308 ADLDFGV-SGVHSNTFGGNTVAAAAALAVIEELQNGLIENAQKLEPLFRERLEEMKE-KY 365 +DL + G NTF N+++AA AL I LQ+ ++ + L E E ++ Sbjct: 313 SDLAAAIPDGSMPNTFAANSLSAAVALTNISILQDPELDLLNRAHTLGLEAQERIRGFGS 372 Query: 366 EIIGDVRGLGLAWGVEFVKDRKTKEYATKER-GEIVVEALKRGLALLGCGK--SAIRLIP 422 ++G+VRG GL G+E V D TK E+ G+++ L G+ ++ CG+ + +R++P Sbjct: 373 PLVGEVRGRGLMIGIELVSDPTTKAPLAPEKIGQLMGYLLSHGVLMIPCGRYSNVMRVMP 432 Query: 423 PLIISEEEAKMGLDIFEEAI 442 L IS LDIF +A+ Sbjct: 433 SLTISRALFFKALDIFGDAL 452 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: 500 Number of extensions: 18 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: 457 Length adjustment: 33 Effective length of query: 421 Effective length of database: 424 Effective search space: 178504 Effective search space used: 178504 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