Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Ga0059261_2226 Ga0059261_2226 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Korea:Ga0059261_2226 Length = 399 Score = 183 bits (465), Expect = 7e-51 Identities = 121/372 (32%), Positives = 194/372 (52%), Gaps = 16/372 (4%) Query: 30 QGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQA 89 QG +++ L G+PDFDTP + +AAI+++ G T Y +V G L+ I + R +G Sbjct: 28 QGIDVIGLGAGEPDFDTPDFVKEAAIEAIRKGITKYTNVDGTPELKAAIVGKFARDNGLT 87 Query: 90 VDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSEN 149 Q+ V +G + L+ ++ GDEV++ P +V+Y V G + V + +E Sbjct: 88 YAENQISVNSGGKHTLFNAFCATIDAGDEVVIPAPYWVSYPDVVEFAGGKPVFIAAGAEA 147 Query: 150 GFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYS 208 ++++ E++ A IT RT+ + LNSP NP+GA+ A +AL E+ H ++ + +D++Y Sbjct: 148 NYKIKPEQLEAAITARTKWVVLNSPSNPTGAAYSAAELKALGEVLERHPNVLIYADDMYE 207 Query: 209 ELLFDG-EHVSPASL-PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCM 266 +L+DG E + A + P + +RT T N +SK++AMTGWR+G+ GP L + L Sbjct: 208 HILYDGFEFATIAQVCPSLYERTLTANGVSKAYAMTGWRIGYAGGPQWLIKAMGKLQSQS 267 Query: 267 LYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMV 326 Q A+ AL L+ A+++RRDLV+ L G+ RP+G +V Sbjct: 268 TSNPCSVSQAASVAALNGDQSFLKDRAAAFQKRRDLVVSMLGQINGMNCPRPEGAFYVYP 327 Query: 327 DI-------RPTGL---SAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLR 376 + P GL + + LLD V+ + G AFG S A +R+ + L Sbjct: 328 EFSQLIGKTTPKGLVIDTDETMVGYLLDDAKVAAVHGGAFGFSPA--LRISYATSEDVLA 385 Query: 377 EACRRI-ALCAA 387 EAC RI CAA Sbjct: 386 EACGRIQEACAA 397 Lambda K H 0.322 0.136 0.411 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: 392 Number of extensions: 22 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: 393 Length of database: 399 Length adjustment: 31 Effective length of query: 362 Effective length of database: 368 Effective search space: 133216 Effective search space used: 133216 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 (21.9 bits) S2: 50 (23.9 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