Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_012383166.1 BIND_RS00765 acetylornithine transaminase
Query= curated2:C3P3K3 (396 letters) >NCBI__GCF_000019845.1:WP_012383166.1 Length = 405 Score = 263 bits (672), Expect = 7e-75 Identities = 141/379 (37%), Positives = 220/379 (58%), Gaps = 8/379 (2%) Query: 19 YHPLPIVISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRA 78 Y PI + EG W+ G R++D + + G+ HP +I AL +Q +++ TS Sbjct: 9 YARAPIAFERGEGAWLTSTTGERFLDFGGGIAVASLGYSHPHLIKALHEQGDKLWHTSNL 68 Query: 79 FHSDQLGPWYEKVAKLTNKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCE 138 F Q E++ ++ + V N+GAEA+E IKTAR++ E NR II + Sbjct: 69 FQIPQAERLAERLTAVSFADFVFFTNSGAEAMEGVIKTARKYHAACGHPEKNR--IITFQ 126 Query: 139 DNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITPNTAAFILEPIQGE 198 FHGRT+ ++ + NE+Y GF P LPG +P+GDLEA+KAAI P T A ++EPIQGE Sbjct: 127 GAFHGRTLATIAAAGNEKYLDGFEPRLPGFDNVPFGDLEAVKAAIKPETGAILIEPIQGE 186 Query: 199 AGINIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALG 258 GI + FL+ ++C ++ +L + DE+Q+G+GR+GK+FA +W V PD+ + K +G Sbjct: 187 GGIRVVSPDFLQALRKLCDEQGLLLLLDEVQSGVGRSGKLFAYEWAGVEPDVMAIAKGIG 246 Query: 259 GGVFPISCAAANRDILGVFEPGSHGSTFGGNPLACAVSIAALEVLEEEK----LTERSLQ 314 GG FP+ A R+ G+HGST+GGNPLA ++ A L+++ E + + Sbjct: 247 GG-FPLGAFMATREAAKGMVVGTHGSTYGGNPLATSIGNAVLDIVLEPSFLAHVEATGVL 305 Query: 315 LGEKLVGQLKEIDNPMITEVRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHENVIRIA 374 L ++LV L+E +I E+RG GL GI++ P + +A LL +NV+R+ Sbjct: 306 LQQRLVA-LRERHPEVIAELRGAGLMRGIKVTLPVADFAAAARAEKLLVIPAGDNVVRLL 364 Query: 375 PPLVISEEDLEWAFQKIKA 393 PPL+I EE+++ A +++ A Sbjct: 365 PPLIIGEEEVDGAIERLDA 383 Lambda K H 0.317 0.136 0.402 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: 436 Number of extensions: 23 Number of successful extensions: 4 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: 396 Length of database: 405 Length adjustment: 31 Effective length of query: 365 Effective length of database: 374 Effective search space: 136510 Effective search space used: 136510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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