Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_013419693.1 RVAN_RS10465 aspartate aminotransferase family protein
Query= curated2:C3P3K3 (396 letters) >NCBI__GCF_000166055.1:WP_013419693.1 Length = 453 Score = 195 bits (495), Expect = 3e-54 Identities = 142/408 (34%), Positives = 212/408 (51%), Gaps = 54/408 (13%) Query: 23 PIVISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRAFHSD 82 PI+ S+ EG + D EG Y+D LS V+ GH +++ A Q L++ AF + Sbjct: 34 PIIWSRGEGATLYDTEGRAYLDGLSGMWNVHLGHGRWELVEAASRQ-----LSTLAFATA 88 Query: 83 QLGPWYEKVAKLTNK---------EMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAE 133 G +E +L + E +G+EA +T+I+TAR W + + A + + Sbjct: 89 YAGATHEPAIRLAERLKKIAPAGIESFFFTTSGSEATDTSIRTAR-WFWRAQGKPA-KTK 146 Query: 134 IIVCEDNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPY-------GDLEA----LKAA 182 II E ++HG T+GA S + +E+ GFGP LPG + IP GD EA L+AA Sbjct: 147 IIAREWSYHGSTIGAASATGVDEFSEGFGPRLPGFLHIPSPYPYRFDGDGEAAADLLEAA 206 Query: 183 IT---PNT-AAFILEPIQGEAG-INIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGK 237 I P T AAFI EP+QG G + +PP G+ + E+C +VLF+ADE+ TG GRTGK Sbjct: 207 ILREGPETVAAFIAEPVQGGGGGVIVPPDGYFERIREICDSHDVLFIADEVITGFGRTGK 266 Query: 238 VFACDWDNVTPDMYILGKALGGGVFP---ISCAAANRDILGVFEPGS---HGSTFGGNPL 291 FA + + PD+ K + G P I +A +D+L E HG T +P+ Sbjct: 267 WFALEHWGIAPDIVQFAKGITSGYVPLGGIGISARIKDVLDGAESDRRWWHGFTASAHPV 326 Query: 292 ACAVSIAALEVLEEEKLTERSLQLGEKLVGQLKEI--DNPMITEVRGKGLFIGIELNEPA 349 ACAV++ L +++EE+L ER+ G L+G+L+E +P + EVRG GL G+EL Sbjct: 327 ACAVALETLRIIDEERLVERAAGQGGALLGRLREALGWHPHVGEVRGLGLLAGVELVADR 386 Query: 350 RPYCE-------------QLKAAGLLCKETHENVIRIAPPLVISEEDL 384 R +L A GL + ++ + +APPL ++ DL Sbjct: 387 RTRARFAPEFRIASKLRAELLARGLYTRIVNDTIC-LAPPLTTTDTDL 433 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: 437 Number of extensions: 24 Number of successful extensions: 7 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: 453 Length adjustment: 32 Effective length of query: 364 Effective length of database: 421 Effective search space: 153244 Effective search space used: 153244 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: 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