Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family
Query= SwissProt::P38021 (401 letters) >FitnessBrowser__psRCH2:GFF2666 Length = 406 Score = 256 bits (653), Expect = 1e-72 Identities = 144/383 (37%), Positives = 218/383 (56%), Gaps = 9/383 (2%) Query: 22 YHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADKITLTSRA 81 + P V LG+ V D G E +D + GH HP ++ AL +QA K+ S Sbjct: 21 FAPAAFVPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHISNI 80 Query: 82 FHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAEIIACV 141 + N+ +K T + N+GAEA E+A K ARR+A++V G + EII+ + Sbjct: 81 YTNEPALRLAKKLVAATFADRAFFCNSGAEANEAAFKLARRYAHDVYG--PQKFEIISAL 138 Query: 142 GNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAFLFEPIQGE 201 +FHGRT+ V++ + +Y GFGP + GI +PY D+EAL+ AI+ T A + EPIQGE Sbjct: 139 NSFHGRTLFTVTVGGQSKYSDGFGPKIEGITHVPYNDLEALKAAISDKTCAVVLEPIQGE 198 Query: 202 AGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYILGKALG 261 +GI+ + +L+ A +C E N L I DE+QTG+GRTG+ FA GI PD+ K+LG Sbjct: 199 SGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELFAYMHYGITPDILTNAKSLG 258 Query: 262 GGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLADRSLELGEY 321 GG FPI + EI + G+HG+T+GGNPLACAV+ A ++++ ++ + E Sbjct: 259 GG-FPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAEAVVDIVNTPEVLEGVKAKHER 317 Query: 322 FKSELESIDS--PVIKEVRGRGLFIGVELTEA----ARPYCERLKEEGLLCKETHDTVIR 375 FK+ L I V VRGRGL IG L++A A +C ++E L+ + V+R Sbjct: 318 FKARLTQIGERYGVFSLVRGRGLLIGCVLSDAWKGKAGAFCAAAEKEALMVLQAGPDVVR 377 Query: 376 FAPPLIISKEDLDWAIEKIKHVL 398 AP L+I + D+D +++++ + Sbjct: 378 LAPSLVIDQADIDEGLDRLERAV 400 Lambda K H 0.318 0.136 0.401 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: 405 Number of extensions: 19 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: 401 Length of database: 406 Length adjustment: 31 Effective length of query: 370 Effective length of database: 375 Effective search space: 138750 Effective search space used: 138750 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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