Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate Ga0059261_1558 Ga0059261_1558 Aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Korea:Ga0059261_1558 Length = 389 Score = 160 bits (404), Expect = 8e-44 Identities = 121/392 (30%), Positives = 193/392 (49%), Gaps = 23/392 (5%) Query: 19 SSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALD 78 S++G + + +RA AM I LG G PD + V +AA+DA+ +Y + Sbjct: 10 SALGTTIFETMSSRARAMG-----AINLGQGFPDGEGCVPVIRAAADALTTRSNQYPPMA 64 Query: 79 GTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSY 138 G P L++AI + R L +E+ V +GA + + + A + PGDEVI+ P + +Y Sbjct: 65 GLPALRQAIATHYTRHQQLDLSPEEVIVTSGATEAIAASFTALIAPGDEVILIQPLYDAY 124 Query: 139 SDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRP 198 +V G L + S +RLT LEAA PRTR +++N+P NP+GA S + Sbjct: 125 LPLVQRAGGVARLARLEPGS-WRLTPAALEAAAGPRTRLIVVNNPVNPAGAKLSHGELAD 183 Query: 199 LLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRI 258 L + + + D+++EH+VYD R + P PG+++RT+ + K +A+TGW++ Sbjct: 184 LAAFCVERDLI-AICDEVWEHVVYDSARHI-PLIAMPGMRDRTVKIGSAGKIFALTGWKV 241 Query: 259 GYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNG 318 G+ L +A T + Q A L ++ + FQR RD + G Sbjct: 242 GWMCAAAPLAAVLARAHQFLTFSTAPNLQWAVAEGLETQDAWIADSIVGFQRSRDRLAAG 301 Query: 319 LNAIDGLDCRV-PEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSA 377 L A RV P GA + S + SG + D FC L+E+ VA +P SA Sbjct: 302 LTA---AGYRVLPSGATWFLS------IDLAASGIALH-DAAFCDRLVEEIGVAAIPVSA 351 Query: 378 F----GLSPFFRISYATSEAELKEALERIAAA 405 F ++ R+ +A ++A L A+ER++AA Sbjct: 352 FYAEAPVTHLARLCFAKADAVLDTAIERMSAA 383 Lambda K H 0.318 0.134 0.393 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: 374 Number of extensions: 22 Number of successful extensions: 5 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: 410 Length of database: 389 Length adjustment: 31 Effective length of query: 379 Effective length of database: 358 Effective search space: 135682 Effective search space used: 135682 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 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