Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_084199387.1 C0029_RS09770 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_002869505.1:WP_084199387.1 Length = 467 Score = 153 bits (386), Expect = 1e-41 Identities = 116/436 (26%), Positives = 206/436 (47%), Gaps = 72/436 (16%) Query: 8 TDKYSSKNY-SPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQS 66 + K +SK Y P + + + G VWD++ N YID +G++ G+CHP+I++A+ E Sbjct: 31 SQKSASKGYVPPAQFIVGRAEGDYVWDLDGNQYIDFQNGWATNPLGNCHPEILEAVHEAQ 90 Query: 67 QRITMVSRALYSDNLGKWEEKI-CKLANK-ENVLPMN---------TGTEAVETAIKMAR 115 ++ +WE + LA + +++P +GTEA E+AI +A Sbjct: 91 RQYGF-----------QWEHPLRIPLAERLASIMPSGSLPRFSFEVSGTEAAESAIHLAL 139 Query: 116 KWGADIKNIDESSSEIIAMNGNFHGRTLGSLSLSSQDS----YKKGFGPLLNNIHYADFG 171 I++ FHG LG+ +S+ +S Y +G+ + A F Sbjct: 140 --------CHTQRRYIVSFTSCFHGEGLGTKMVSAYNSDNNLYMEGWA---GGVLKAPFP 188 Query: 172 DIEQLKKLIN-----------------------NQTTAIILEPIQGEGGVNIPPTHFIQE 208 E++ ++ AI++EP EGG IP F+Q Sbjct: 189 YSEEIPAGMDQAQYTEYCLWYIETHLTEYVVPAENIAAILVEPGLAEGGNWIPSKAFMQG 248 Query: 209 VRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGGGLYPISAVLANQ 268 +R++C++++ LLIADE+ GLGRTG M+A+E + PDI + GK+L GG+ P + V A Sbjct: 249 LRRICDKFDWLLIADEVLTGLGRTGTMWAVEHFDVVPDILVAGKNLSGGIEPCAGVAARD 308 Query: 269 DVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRLLKHLQQIES--E 326 +++ T GSTF G P CA ++ L++ + ++ + L ++ + ES E Sbjct: 309 EILGDNPRATAGSTFAGTPGGCAAALKTLEIYERDAVLTHTQHLAGVAMQRMSDWESRYE 368 Query: 327 LIVEVRGRGLFIGIELNVAAQD---------YCEQMINKGVLCKETQGNIIRIAPPLVID 377 ++ +VRG GL +G+ +D ++M+ +G+ +R+ P L + Sbjct: 369 IVSQVRGLGLLLGVSFRAGREDIEDFHIARSVRDEMLKRGLWAICDNEPQVRMYPALNMA 428 Query: 378 KDEIDEVIRVITEVLE 393 +D + E + + E +E Sbjct: 429 EDVLLEGLSRMEEAIE 444 Lambda K H 0.317 0.136 0.396 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: 408 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 394 Length of database: 467 Length adjustment: 32 Effective length of query: 362 Effective length of database: 435 Effective search space: 157470 Effective search space used: 157470 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 Sep 24 2021. 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