Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Pf6N2E2_5326 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= curated2:Q5HJI8 (394 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5326 Length = 396 Score = 276 bits (706), Expect = 7e-79 Identities = 154/376 (40%), Positives = 225/376 (59%), Gaps = 10/376 (2%) Query: 16 YAPLKLVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLSIISRV 75 Y PL L + G G ++WD DG++Y+D ++G +V N GH HP +V A++EQA L S + Sbjct: 15 YQPLALSFTHGLGTRLWDQDGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTSNL 74 Query: 76 LYSDNLGKWEEKICHLAKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIAMN 135 D + +K+ L+ ++ NSG EA E A+K+AR +G KGI Q ++ M+ Sbjct: 75 YSIDWQQRLAQKLTQLSGLERAFFNNSGAEANETALKLARLYGWH-KGIE--QPLVVVMD 131 Query: 136 NNFHGRTLGSLSLSNHDAYKAGFHPLLQGTTTVDFGDI---EQLTQAISPNTAAIILEPI 192 N FHGRTLG++ S+ + + GF+ L V FGD+ E + QA + A+++EPI Sbjct: 132 NAFHGRTLGTMCASDGPSVRLGFNRLPGDFIKVPFGDLAALEAIQQAHAERIVAVLVEPI 191 Query: 193 QGEGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFAMEWEQVVPDIYILGK 252 QGE GV + P GY++A+R+LC + LL+ DEIQ G+GRTG+WFA + E +VPD+ L K Sbjct: 192 QGESGVQLAPPGYLKALRELCSRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAK 251 Query: 253 ALGGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAALDVLKDEQLVERSERL 312 LG G+ P+ A LA + TPG+HGSTFGGNPLA + L++++ + LV+ + Sbjct: 252 GLGNGV-PIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLEIIEQQALVDNARHQ 310 Query: 313 GSFLLKAL-LQL-KHPSIKEIRGRGLFIGIELNTDAAPFVDQLIQ-RGILCKDTHRTIIR 369 G LL L ++L +P++ IRG+GL IGIEL + + G+L T IR Sbjct: 311 GDQLLGRLRIELADNPNVLAIRGQGLMIGIELKQPVRDLALRAARDHGLLINITRGQTIR 370 Query: 370 LSPPLVIDKEEIHQIV 385 L PPL ID E+ IV Sbjct: 371 LLPPLTIDGREVEMIV 386 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: 368 Number of extensions: 15 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: 396 Length adjustment: 31 Effective length of query: 363 Effective length of database: 365 Effective search space: 132495 Effective search space used: 132495 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: 50 (23.9 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