Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_035235405.1 Q366_RS00665 aspartate aminotransferase family protein
Query= SwissProt::P38021 (401 letters) >NCBI__GCF_000745975.1:WP_035235405.1 Length = 426 Score = 344 bits (882), Expect = 3e-99 Identities = 174/404 (43%), Positives = 258/404 (63%), Gaps = 15/404 (3%) Query: 10 IIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALK 69 I + +GA++Y+ + +V+ A G W+ D +GN+Y+D L+AYSA N GH HP I AL Sbjct: 21 IFNLEDKFGAHHYNRINLVVRGAKGCWLTDDKGNKYLDCLAAYSAANPGHHHPTITNALL 80 Query: 70 DQ--ADKITLTSRAFHNDQLGPFYEKTAKLTGK---------EMILPMNTGAEAVESAVK 118 + + ++ S D LG F + A + +L N G E+VE+A+K Sbjct: 81 NALTGNYASVISNVVFTDPLGIFLSECAAFAPQLAPGFGAHGNKVLAKNGGVESVETAIK 140 Query: 119 AARRWAYEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGD 178 A R + ++ KG+ D EII NFHGR++ VS SS ++Y+ GF P+ PG +P+GD Sbjct: 141 AMRYYGFKQKGIQDGNQEIIVFNNNFHGRSISVVSFSSSKKYREGFAPLTPGFVSVPFGD 200 Query: 179 VEALRQAITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRT 238 ++A+++A+TPNT L EP+QGE G+VIPP+GFL+ A+ E N+ + DEIQ G+GRT Sbjct: 201 LDAVKKAVTPNTCGILVEPLQGEGGMVIPPKGFLKGLRALADENNLFLVCDEIQVGMGRT 260 Query: 239 GKTFACDWDGIVPDMYILGKALGGGVFPISCIAADREILG-VFNPGSHGSTFGGNPLACA 297 GK F + +GIVPD ILGKAL GG+ P+S + I+ +F+ GS GSTFGG PLAC Sbjct: 261 GKRFCFEHEGIVPDGLILGKALSGGLVPLSVFMTNAGIMDMIFSKGSDGSTFGGYPLACV 320 Query: 298 VSIASLEVLEDEKLADRSLELGEYFKSELESID--SPVIKEVRGRGLFIGVELTEA-ARP 354 IA+L+V ++EKL ++S E G K +E I SP +KEVRG GLFIG+E+ +A A Sbjct: 321 AGIAALKVFQEEKLDEQSAEKGARLKKRIEDIGRRSPHVKEVRGLGLFIGIEVKDANAME 380 Query: 355 YCERLKEEGLLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398 +C +L +EGL+ ++H IR +PPL+I+ E++D+ +E+++ VL Sbjct: 381 FCRKLMKEGLIVNDSHGHTIRISPPLVINDEEMDFMVERLERVL 424 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: 477 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: 401 Length of database: 426 Length adjustment: 31 Effective length of query: 370 Effective length of database: 395 Effective search space: 146150 Effective search space used: 146150 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