Align acetylornithine aminotransferase (EC 2.6.1.11); succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 Length = 430 Score = 225 bits (574), Expect = 2e-63 Identities = 128/402 (31%), Positives = 224/402 (55%), Gaps = 33/402 (8%) Query: 28 RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NVMTNEPALR 86 R +GS +WD +G+ ++D GGI V +GH+HP +V A+ Q +KI H V+ +P L Sbjct: 33 RAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKISHACFQVVAYKPYLD 92 Query: 87 LAKTLCDLTFAERVF---FANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRT 143 LA+ LC++ + + F SGAEA E A K+AR + ++ +I+F+ FHGRT Sbjct: 93 LAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHT------NRSAVIAFRGGFHGRT 146 Query: 144 LFTVSVGGQPK-YLEGFEPAPGGIHHAEFND----------LESVKKL----ISKEKTCA 188 L ++ G + Y + F P + H + + L+++ +L ++ E+ A Sbjct: 147 LLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSAMALQALDELLATQVAPERVAA 206 Query: 189 IVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPD 248 I++EP+QG+GG + FLQGLR L ++ +L+ DE+Q+G GR+G ++ +Q G+ PD Sbjct: 207 IIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFGRTGKWFGFQHAGIQPD 266 Query: 249 ILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILK 308 +++ AK L GG P++ ++ A++ + G G TYGGNAL+CA A V++ Q ++L Sbjct: 267 LVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEAYEQEQLLA 326 Query: 309 GVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKD------FLNAGLE 362 + ++LR+G++ + RY +VRG+G +L L + + + D ++ Sbjct: 327 RGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLAIELIKHDEARTPDADLNQRLIDEARA 386 Query: 363 EGVMVLVAGA--NVIRLAPSLIIPEPDIELALERFEAAVKKL 402 G++V+ G NV+R L+ E I+ AL+ + A+ ++ Sbjct: 387 GGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQILDGALARV 428 Lambda K H 0.318 0.137 0.406 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: 484 Number of extensions: 20 Number of successful extensions: 4 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: 430 Length adjustment: 31 Effective length of query: 373 Effective length of database: 399 Effective search space: 148827 Effective search space used: 148827 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 Apr 09 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