Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase
Query= curated2:Q89RB7 (404 letters) >NCBI__GCF_003173355.1:WP_109969613.1 Length = 384 Score = 244 bits (623), Expect = 3e-69 Identities = 140/370 (37%), Positives = 203/370 (54%), Gaps = 25/370 (6%) Query: 25 VVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAF---H 81 +++++G G V D DG +YLD ++ + S GHCHPK++ A+ EQA L S F H Sbjct: 23 IMITKGSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIHCSNLFYVPH 82 Query: 82 NDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADN 141 LA EI+ L G+ K NSGAEA+E A+K R + + E I C Sbjct: 83 QGALAKKLVEISGLPGNAKAFFSNSGAEAMEGALKLAR--------IRTGRKEFIACEGG 134 Query: 142 FHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAG 201 FHGRT+G + + P R F P P +P+GD AL+ AIT T A ++EPIQGE G Sbjct: 135 FHGRTMGSLACTHKPAIREPFMPLQPFTSFVPYGDVQALKGAITEETAAVILEPIQGEGG 194 Query: 202 VIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGG 261 VIIPP GY +VRE+C A V+L++DE+Q+G+GRTG A Q EGI D+ + KA+A G Sbjct: 195 VIIPPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFAFQEEGIHPDIITMAKAMASG 254 Query: 262 FYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLL 321 F P+ A+++ + +HGSTF G P+ACA A A++ V+ + ++ A +G R Sbjct: 255 F-PMGAIVAREGL--EFGKSEHGSTFAGGPIACAAALASIDVIGK--VLPEVAAKGERFR 309 Query: 322 EGLKDIRANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIAPPL 381 L + R +GLM+ + + ++ C G+L +R+ PPL Sbjct: 310 AALAHLNP------RVKGLMIGITIGDHCADVQKECAV---HGLLVNCAAHGNLRLVPPL 360 Query: 382 VITSDEVDWA 391 IT+ E+D A Sbjct: 361 TITNAEIDKA 370 Lambda K H 0.319 0.136 0.405 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: 454 Number of extensions: 19 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: 404 Length of database: 384 Length adjustment: 31 Effective length of query: 373 Effective length of database: 353 Effective search space: 131669 Effective search space used: 131669 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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