Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_011033352.1 MM_RS07280 aspartate aminotransferase family protein
Query= SwissProt::P38021 (401 letters) >NCBI__GCF_000007065.1:WP_011033352.1 Length = 395 Score = 292 bits (747), Expect = 1e-83 Identities = 155/387 (40%), Positives = 236/387 (60%), Gaps = 12/387 (3%) Query: 10 IIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALK 69 +ID+ S Y Y P+V+S+ GA V+D G EY+D ++ + N GH HP +++A++ Sbjct: 18 VIDKDSKYVMQTYGRQPLVLSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQ 77 Query: 70 DQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKG 129 QA+K+ S ++ + F E A +TG E + N+GAEAVE+A+K AR Sbjct: 78 AQAEKLIHVSNLYYTEIQAEFAETLASITGMECVFFCNSGAEAVEAAMKLAR-------- 129 Query: 130 VADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPG-IKLIPYGDVEALRQAITP 188 VA ++ +A +FHGRT+ A+S++ + Y+ F P + +PY D +A+R+AI+ Sbjct: 130 VATGKSAFVAAEHSFHGRTIGALSVTHKSMYRDPFMPPVSSKTSFVPYSDADAIRKAISE 189 Query: 189 NTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDG 248 +TAA + EPIQGE G+ +P G+L+E IC E L I DE+QTG GRTG F + G Sbjct: 190 DTAAVVLEPIQGEGGVNVPDPGYLKEVREICDETGTLLIFDEVQTGFGRTGTWFCKEQFG 249 Query: 249 IVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLED 308 + PD+ + KA+GGG FP+ IAA + F G H STFGG PLACA ++AS++ +++ Sbjct: 250 VEPDIMSMAKAIGGG-FPMGAIAARSGLS--FGRGQHASTFGGGPLACAAALASIQAIKE 306 Query: 309 EKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTEAARPYCERLKEEGLLCKE 368 EKL +RS E+G YF +L + I EVRG+GL IGVE+ + + +E G+L Sbjct: 307 EKLLERSKEMGAYFTKKLSGMARDDIVEVRGKGLMIGVEIKYPCGKFVDFAREHGVLVNC 366 Query: 369 THDTVIRFAPPLIISKEDLDWAIEKIK 395 T D+V+R PPL+I+KE +D ++ ++ Sbjct: 367 TSDSVLRLVPPLVITKEQIDSVVDVLE 393 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: 409 Number of extensions: 17 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: 401 Length of database: 395 Length adjustment: 31 Effective length of query: 370 Effective length of database: 364 Effective search space: 134680 Effective search space used: 134680 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 10 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