Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_000566685.1:WP_025763135.1 Length = 384 Score = 188 bits (477), Expect = 3e-52 Identities = 115/374 (30%), Positives = 192/374 (51%), Gaps = 21/374 (5%) Query: 25 KGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRALYSDNLGKW 84 K +G+ +WD Y+D G +V++ GHCHP + L EQ +I+ S ++ + Sbjct: 17 KAQGSYLWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISFYSNSVQIPQQEEL 76 Query: 85 EEKICKLANKEN--VLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMNGNFHGRT 142 K+ L+ + + N+G EA E A+K+A + +++A FHGRT Sbjct: 77 ATKLGTLSGYPDYKLFLCNSGAEANENALKLA--------SFHTGRKKVVAFTKAFHGRT 128 Query: 143 LGSLSLSSQDSYKKGFGPLLNNIH--YADFGDIEQLKKLINNQTTAIILEPIQGEGGVNI 200 G+++ + S P+ N H + F DIE L+ I + A+I+E IQG GG+ + Sbjct: 129 AGAVAATDNPSI---VAPVNYNEHVSFLPFNDIEALQAGITEEVAAVIVEGIQGVGGIQV 185 Query: 201 PPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGGGLYP 260 F+Q +R+ C+E LI D +Q G GRTGK F+ ++ PD+ + K +G G +P Sbjct: 186 CSDEFLQALRKRCDETGAALILDSVQCGYGRTGKFFSHQFSGIHPDMMTMAKGMGNG-FP 244 Query: 261 ISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRLLKHL 320 I+ VL + G G+TFGGN LACA +A LD++ +E L+ NA +G L + Sbjct: 245 IAGVLIAPQFKASF--GLLGTTFGGNHLACAAGIAVLDIMKDEQLLDNATKIGAYLFHEI 302 Query: 321 QQIESELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQG-NIIRIAPPLVIDKD 379 +++ ++RGRGL IGIE + ++ +++ + + G +R+ P L I + Sbjct: 303 EELGG--YKDLRGRGLMIGIEFDFPVKELRNKLLFEHHIFTGVAGAYTLRLLPSLAISQK 360 Query: 380 EIDEVIRVITEVLE 393 E D+ + L+ Sbjct: 361 EADQFLEAYRSCLK 374 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: 353 Number of extensions: 20 Number of successful extensions: 6 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: 394 Length of database: 384 Length adjustment: 30 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 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: 50 (23.9 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