Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_067072365.1 MCUHO_RS00805 aspartate aminotransferase family protein
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_001602375.1:WP_067072365.1 Length = 374 Score = 236 bits (602), Expect = 8e-67 Identities = 136/364 (37%), Positives = 195/364 (53%), Gaps = 22/364 (6%) Query: 29 RGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQLAPF 88 RG G VWD G +YLDC++ + S GHCHP ++ A+ QA L S ++ A Sbjct: 25 RGAGSRVWDDRGRQYLDCVAGIAVCSTGHCHPLVVEALCNQAKELIHCSNLYYIPNQAEL 84 Query: 89 YEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFHGRTLG 148 E++ +TG K NSGAEA + AIK R V + + FHGRT G Sbjct: 85 AEKLVGITGLSKAFFSNSGAEANDGAIKLAR--------VRTGRKNFVAFTHGFHGRTCG 136 Query: 149 IVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVIIPPAG 208 + + P R F P + + +GD AL +A+ +T VEPIQGEAGV+IPP Sbjct: 137 SLAVTHKPAIREPFEPLSTPCTFVDYGDLDALAKAVNKDTAGVFVEPIQGEAGVLIPPDE 196 Query: 209 YFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGGFYPVSAV 268 + VR++C ++++DE+QTG+GRTGK A QH GI D+ K LA GF P+ A+ Sbjct: 197 FLRGVRDICDDTGALMIVDEVQTGMGRTGKWFAFQHAGILPDIVTTAKGLASGF-PIGAL 255 Query: 269 LSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGLKDIR 328 ++ + + G+HGSTF G PLACA A A + V+ E ++ + R+G R +GL R Sbjct: 256 VAREGL--EFKKGEHGSTFAGGPLACATALATIGVI--EEILPDVTRKGERFKKGL--AR 309 Query: 329 ANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIAPPLVITSDEV 388 N RGRGL++ + + ++ C A G+L +R+ PPLVIT +E+ Sbjct: 310 HNP----RGRGLIIGMSIGDRCAEVQQTCAA---NGVLVNCAADGNLRLIPPLVITDNEI 362 Query: 389 DWAL 392 D AL Sbjct: 363 DCAL 366 Lambda K H 0.319 0.136 0.405 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: 435 Number of extensions: 23 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: 404 Length of database: 374 Length adjustment: 30 Effective length of query: 374 Effective length of database: 344 Effective search space: 128656 Effective search space used: 128656 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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