Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase
Query= curated2:C3P3K3 (396 letters) >FitnessBrowser__azobra:AZOBR_RS19025 Length = 389 Score = 243 bits (619), Expect = 9e-69 Identities = 139/372 (37%), Positives = 206/372 (55%), Gaps = 6/372 (1%) Query: 19 YHPLPIVISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRA 78 Y IV + EG ++ +G R++D + + GH +P ++ AL QA+++ TS Sbjct: 9 YARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNL 68 Query: 79 FHSDQLGPWYEKVAKLTNKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIVCE 138 F +++ + T + V N+GAEA E K R++ Y+ K + R II E Sbjct: 69 FRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYE--KGDKARTRIITFE 126 Query: 139 DNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAAITPNTAAFILEPIQGE 198 FHGRT+ AVS + E+ +GFGP+L G ++P+GDLEA++ A+T TA LEPIQGE Sbjct: 127 QAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGE 186 Query: 199 AGINIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILGKALG 258 GI FL+ E+C + +L DEIQ G+GRTGK+FA +W +TPD+ + K +G Sbjct: 187 GGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIG 246 Query: 259 GGVFPISCAAANRDILGVFEPGSHGSTFGGNPLACAVSIAALEVLEEEKLTERSLQLGEK 318 GG FP+ A G+HGST+GGNPLA AV A L+ + E + ++G Sbjct: 247 GG-FPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGL 305 Query: 319 LVGQLKEI--DNPMITE-VRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHENVIRIAP 375 L +L + +NP + + VRGKGL +G+ L+A GLL +NV+R+ P Sbjct: 306 LQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLLP 365 Query: 376 PLVISEEDLEWA 387 PL I E ++E A Sbjct: 366 PLNIGEAEVEEA 377 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: 393 Number of extensions: 19 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: 389 Length adjustment: 31 Effective length of query: 365 Effective length of database: 358 Effective search space: 130670 Effective search space used: 130670 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 17 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