Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate RR42_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Cup4G11:RR42_RS26240 Length = 420 Score = 256 bits (654), Expect = 1e-72 Identities = 163/409 (39%), Positives = 235/409 (57%), Gaps = 24/409 (5%) Query: 41 ERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPYQV 100 ERAE DV+GN +DF++GI V+N G R+P++++A++ Q++ H A + Sbjct: 27 ERAENSELWDVEGNRYIDFAAGIAVLNTGHRHPRLVQAMQAQMERFTHTAYQIVPYASYI 86 Query: 101 ELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHGTMS 160 ELA+K+ APG +K +G EA E A+KIA+ +T R IAF G FHGRT M+ Sbjct: 87 ELAEKINARAPGAFAKKTAFFTTGAEAVENAIKIARAATGRPGVIAFSGGFHGRTMMGMA 146 Query: 161 LTASKPVQRSRMFPTMPG-VVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFEHY 219 LT K V F PG V H PYP +G+ G D IN + LF+ Sbjct: 147 LTG-KVVPYKVGFGPFPGDVFHAPYP------YGLHGVSVQDS-INAL-----HQLFKAD 193 Query: 220 VPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMWAI 279 V + VA I FEP+QGEGG+ V P F + L+ + D+HGILL+ DEVQ G GRTG+++A+ Sbjct: 194 VDPKRVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEVQTGFGRTGKLFAM 253 Query: 280 EHFDIVPDIVTVAKALGGGIPIGATIFRAD-LDFGVSGVHSNTFGGNTVAAAAALAVIEE 338 EH+D+ PD+ T+AK+L GG+P+ A RA+ +D G T+ GN +A A+ALAV++ Sbjct: 254 EHYDVTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGNPLAVASALAVLDV 313 Query: 339 LQN-GLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVK--DRKTKEYATKE 395 L++ LIE L +++L+ +K + IG+VRG+G VEF K R E+ Sbjct: 314 LESEKLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVEFRKADGRPDPEFTR-- 371 Query: 396 RGEIVVEALKRGLALLGCG--KSAIRLIPPLIISEEEAKMGLDIFEEAI 442 ++ AL+RGL LL CG + +R + PL I + GL I E A+ Sbjct: 372 --QVQDRALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGLGILEAAL 418 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: 520 Number of extensions: 31 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: 420 Length adjustment: 32 Effective length of query: 422 Effective length of database: 388 Effective search space: 163736 Effective search space used: 163736 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