Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= curated2:Q5HJI8 (394 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4179 Length = 459 Score = 198 bits (503), Expect = 3e-55 Identities = 137/407 (33%), Positives = 206/407 (50%), Gaps = 49/407 (12%) Query: 21 LVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLSIISRVLYSDN 80 L I K + ++WD +G+++ID G +V N GH H ++ A+ Q L + + + Sbjct: 55 LFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQ---LDLYTHTCFQVV 111 Query: 81 LGKWEEKICHL-------AKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIA 133 + ++C A K L L +G EAVE AIKIAR + + +IA Sbjct: 112 AYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTK--------RPGVIA 163 Query: 134 MNNNFHGRTLGSLSLSNHDA-YKAGFHPLLQGTTTVDFGD------IEQLTQAIS----- 181 +HGRT +L L+ A YK GF P T F + +EQ ++ Sbjct: 164 FTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQALHSVELIFKN 223 Query: 182 ----PNTAAIILEPIQGEGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFA 237 AA I+EP+QGEGG + P +I ++ L D++ ILLIADE+Q G GRTG WFA Sbjct: 224 DIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTWFA 283 Query: 238 MEWEQVVPDIYILGKALGGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAAL 297 E V PD+ K+L GG +P++ V+ DVM PG G T+ G+P+A A S A + Sbjct: 284 SEQWPVAPDLITTAKSLAGG-FPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAVI 342 Query: 298 DVLKDEQLVERSERLGSFLLKAL--LQLKHPSIKEIRGRGLFIGIEL-------NTDAA- 347 + E+L+ RS+ +G+ L+++L L + P+I ++RG G + IEL DAA Sbjct: 343 EAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFENGDLSRPDAAL 402 Query: 348 --PFVDQLIQRG--ILCKDTHRTIIRLSPPLVIDKEEIHQIVAAFQD 390 V + +RG +L TH +IR+ PL E +H+ +A D Sbjct: 403 TKQVVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILAD 449 Lambda K H 0.319 0.137 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: 420 Number of extensions: 20 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: 394 Length of database: 459 Length adjustment: 32 Effective length of query: 362 Effective length of database: 427 Effective search space: 154574 Effective search space used: 154574 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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