Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_013074657.1 BTUS_RS03025 aspartate aminotransferase family protein
Query= SwissProt::P38021 (401 letters) >NCBI__GCF_000092905.1:WP_013074657.1 Length = 466 Score = 247 bits (630), Expect = 6e-70 Identities = 156/405 (38%), Positives = 219/405 (54%), Gaps = 22/405 (5%) Query: 8 KEIIDQTSHYG-ANNYHPLPIVISEALG--AWVKDPEGNEYMDMLSAYSAVNQGHRHPKI 64 K++ D + G A YH + + E G + V D +G Y+D +S Y ++ GH + Sbjct: 8 KDLYDSYINPGLAKLYHLMGLSAGELRGEGSVVYDEDGKRYIDCVSGYGSLPFGHCPRPV 67 Query: 65 IQALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPM--NTGAEAVESAVKAARR 122 ++A++ Q D++ L+S+ G E A T ++ N+GAEAVE A+K AR Sbjct: 68 LEAVRRQMDRMALSSKVMPGRPAGELAEALAGWTPGDLQYSFFCNSGAEAVEGALKLAR- 126 Query: 123 WAYEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEAL 182 + +A G FHG+T A+S+S + Y+ F P+LPG+ L+P+GDVEAL Sbjct: 127 -------AVTGRPGFVAAEGGFHGKTFGALSVSGRQRYRAPFHPLLPGVTLVPFGDVEAL 179 Query: 183 RQAITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTF 242 ++A++ TAA + EPIQGE G+ P G+L A IC L I DE+QTG GRTG F Sbjct: 180 KRAVSQQTAAVILEPIQGEGGVHPAPRGYLTAAREICDRAGALLILDEVQTGFGRTGMPF 239 Query: 243 ACDWDGIVPDMYILGKALGGGVFPISCIAADREILGVF--NPGSHGSTFGGNPLACAVSI 300 A +G+VPD+ L KALGGGV PI C A E F +P H STFGGNPLA A + Sbjct: 240 AAQREGVVPDVMCLAKALGGGVMPIGCFIARPEAARAFWEDPLIHTSTFGGNPLAAAAGL 299 Query: 301 ASLEVLEDEKLADRSLELGEYFKSELESIDSPV---IKEVRGRGLFIGVELTEAARP--Y 355 A+L+ L+ E L + E G + K E E + I+EVRG GL +GVE + AR Sbjct: 300 ATLDWLQREDLPRAAAETGRWLKGEFEEMAKRYPGWIREVRGEGLLLGVEFVDEARGGLV 359 Query: 356 CERLKEEGLLCKETHD--TVIRFAPPLIISKEDLDWAIEKIKHVL 398 L E+G+L T + V+R P L I + L +E VL Sbjct: 360 MSGLVEKGVLTAFTLNEYRVVRVEPSLTIDRGLLIQVLEAWDAVL 404 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: 493 Number of extensions: 32 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: 466 Length adjustment: 32 Effective length of query: 369 Effective length of database: 434 Effective search space: 160146 Effective search space used: 160146 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: 51 (24.3 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