Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_035242472.1 Q366_RS19250 aspartate aminotransferase family protein
Query= curated2:Q4A0N2 (394 letters) >NCBI__GCF_000745975.1:WP_035242472.1 Length = 398 Score = 255 bits (652), Expect = 1e-72 Identities = 141/391 (36%), Positives = 224/391 (57%), Gaps = 9/391 (2%) Query: 8 TDKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQ 67 T + K Y+ KGRG +++D + N Y D ++G +V N GHCHP I A+ Q+ Sbjct: 6 TQDHVFKTYARQGRPFVKGRGTQLYDDQGNVYTDFLAGIAVCNLGHCHPDITAAISAQAG 65 Query: 68 RITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDES 127 + VS Y+ + + + + + + V N+G EA E AIK+AR++ + Sbjct: 66 TLVHVSNLFYTRPQAELAKVLTEKSFADRVFFANSGAEANEAAIKLARRFFQ--AKGEAG 123 Query: 128 SSEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAI 187 +I+ M +FHGRT+ +LS + QD KKGF PLL+ + F DIE LK +++ A+ Sbjct: 124 RFKIVTMQQSFHGRTMATLSATGQDKIKKGFFPLLDGFIHVPFNDIEALKAVMDGTVCAV 183 Query: 188 ILEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDI 247 ++EP+QGEGGV +I+ VRQLC + LLI DEIQ G+GR G +FA E + PDI Sbjct: 184 MMEPVQGEGGVIPADPEYIKAVRQLCTDTGTLLIFDEIQTGMGRCGTLFAHESYDVVPDI 243 Query: 248 YLLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQ 307 L K+L G+ PI A+LA+++ G+HGSTFGG PLA A ++ + +++E+ + Sbjct: 244 MTLAKALANGV-PIGAMLASEEAALGFEVGSHGSTFGGTPLATAAALEVVRLISEQGFLA 302 Query: 308 NALDLGDRLLKHLQQIES--ELIVEVRGRGLFIGIELNVA----AQDYCEQMINKGVLCK 361 + + L L ++ + +V+VRG+GL IG+EL+++ A DY + KG + Sbjct: 303 SVREKSAYFLAQLNGLKEKHKKVVDVRGKGLLIGMELDISKGKTATDYVSECFKKGFIIN 362 Query: 362 ETQGNIIRIAPPLVIDKDEIDEVIRVITEVL 392 Q ++R APPL+I EI++++ + +L Sbjct: 363 AIQDKVLRFAPPLIIGTVEINQLVAELDSLL 393 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: 342 Number of extensions: 13 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: 394 Length of database: 398 Length adjustment: 31 Effective length of query: 363 Effective length of database: 367 Effective search space: 133221 Effective search space used: 133221 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 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