Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ga0059261_1558 Ga0059261_1558 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__Korea:Ga0059261_1558 Length = 389 Score = 152 bits (385), Expect = 1e-41 Identities = 110/372 (29%), Positives = 179/372 (48%), Gaps = 20/372 (5%) Query: 27 KAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIAKKFKRENN 86 +A+ I LG G PD + + +AA DA+ +Y P++G+P LR+AIA + R Sbjct: 23 RARAMGAINLGQGFPDGEGCVPVIRAAADALTTRSNQYPPMAGLPALRQAIATHYTRHQQ 82 Query: 87 LDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGTPVFVPTRQ 146 LD + + IV +G + + +F A + PGDEV++ P + +Y +V GG + + Sbjct: 83 LDLSPEEVIVTSGATEAIAASFTALIAPGDEVILIQPLYDAYLPLVQRAGGV-ARLARLE 141 Query: 147 ENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPHVWVLTDDM 206 +++L L+ A P+T+ V N+P NP+GA SH EL L ++ + + D++ Sbjct: 142 PGSWRLTPAALEAAAGPRTRLIVVNNPVNPAGAKLSHGELADLAAFCVERDLI-AICDEV 200 Query: 207 YEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHLIKAMDMIQG 266 +EH+ Y R P+ PG+ +RT+ + K +A+TGW++G+ L + Sbjct: 201 WEHVVYDSARH-IPLIAMPGMRDRTVKIGSAGKIFALTGWKVGWMCAAAPLAAVLARAHQ 259 Query: 267 QQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISCPTPEGAFYV 326 T A QWA E L +I + FQ RD + + L A + V Sbjct: 260 FLTFSTAPNLQWAVAEGLETQDAWIADSIVGFQRSRDRLAAGLTAA----------GYRV 309 Query: 327 YPSCAG--LIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAF----GLGPNFRISYAT 380 PS A L A SG + D F L+E GVA + SAF + R+ +A Sbjct: 310 LPSGATWFLSIDLAASGIALH-DAAFCDRLVEEIGVAAIPVSAFYAEAPVTHLARLCFAK 368 Query: 381 SEALLEEACRRI 392 ++A+L+ A R+ Sbjct: 369 ADAVLDTAIERM 380 Lambda K H 0.318 0.134 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: 363 Number of extensions: 18 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: 400 Length of database: 389 Length adjustment: 31 Effective length of query: 369 Effective length of database: 358 Effective search space: 132102 Effective search space used: 132102 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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