Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate CCNA_03233 CCNA_03233 Acetyl ornithine aminotransferase
Query= reanno::pseudo5_N2C3_1:AO356_13150 (454 letters) >FitnessBrowser__Caulo:CCNA_03233 Length = 467 Score = 519 bits (1337), Expect = e-152 Identities = 252/438 (57%), Positives = 314/438 (71%), Gaps = 4/438 (0%) Query: 5 NPQTREWQALSNDHHLAPFSDFKQLKEKG-PRIITHAKGVYLWDSEGNKILDGMAGLWCV 63 N E + L HHL +D K + E G RI+T A G Y+ D +G++ILDGMAGLWCV Sbjct: 7 NHDVAELKRLDLAHHLPAQADHKVIAELGGSRIVTRADGCYITDGDGHRILDGMAGLWCV 66 Query: 64 AVGYGREELADAASQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGSGSE 123 VGYGR+ELADAA +QM ELPYYN FF+TA PP ++L+ IA+ + HVFF SGSE Sbjct: 67 NVGYGRKELADAAYEQMLELPYYNTFFKTATPPTVKLAAKIAEKMGGHLTHVFFNSSGSE 126 Query: 124 GNDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVH 183 NDT+ R+VRHYW +KGQPN+ V ISR N YHGSTVAG SLGGM +MH QGDLPIPG+ H Sbjct: 127 ANDTVFRLVRHYWKLKGQPNRTVFISRWNAYHGSTVAGVSLGGMKHMHVQGDLPIPGVEH 186 Query: 184 IAQPYWFGEGGDMSPEEFGVWAANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPDSYW 243 + QPY FGEG P F A ++E+KILE+G +NV AFI EP+QGAGGVI+PPD YW Sbjct: 187 VMQPYPFGEGFGEDPAAFRDRAVKEIEDKILEVGPENVAAFIGEPVQGAGGVIIPPDGYW 246 Query: 244 PRMKEILAKYDILFVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGGLIV 303 P ++ + KY IL V DEVICGFGR G+WFG HYG+KP ++ +AKGL+SGY+P+ + V Sbjct: 247 PAVEAVCRKYGILLVCDEVICGFGRLGQWFGHQHYGIKPDLIAMAKGLSSGYLPISAVGV 306 Query: 304 RDDVVAVLNE-GGDFNHGFTYSGHPVAAAVALENIRILRDEKIIERVHSETAPYLQKRLR 362 D +VA L E GGDF HGFTYSGHP AAVAL+NI I+ E +I R +T PYL K L Sbjct: 307 ADHIVAELREKGGDFIHGFTYSGHPTCAAVALKNIEIIEREDLITRTREDTGPYLAKALA 366 Query: 363 ELNDHPLVGEVRGVGLLGAIELVQDKATRKRYEGK--GVGMICRQFCFDNGLIMRAVGDT 420 LNDHPLVGE R +GL+GA+E+V++K T R+ K G I R C NGL++RA+ D+ Sbjct: 367 RLNDHPLVGETRSLGLIGAVEIVREKGTNHRFLDKEGEAGPIVRDICIRNGLMVRAIRDS 426 Query: 421 MIIAPPLVISKAEIDELV 438 ++ PPL++S AEIDELV Sbjct: 427 IVCCPPLIVSHAEIDELV 444 Lambda K H 0.320 0.139 0.431 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: 719 Number of extensions: 41 Number of successful extensions: 3 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: 454 Length of database: 467 Length adjustment: 33 Effective length of query: 421 Effective length of database: 434 Effective search space: 182714 Effective search space used: 182714 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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