Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate Ga0059261_1558 Ga0059261_1558 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Korea:Ga0059261_1558 Length = 389 Score = 186 bits (472), Expect = 1e-51 Identities = 126/369 (34%), Positives = 189/369 (51%), Gaps = 16/369 (4%) Query: 22 KALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKF 81 + + R + + + L G PD + V AA AL +Y P AG+P LR+A+A + Sbjct: 18 ETMSSRARAMGAINLGQGFPDGEGCVPVIRAAADALTTRSNQYPPMAGLPALRQAIATHY 77 Query: 82 RRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVE 141 R L ++PEE IVT G +A+ F A++ PGDEVI++ P + +Y +V+ AGG V Sbjct: 78 TRHQQLDLSPEEVIVTSGATEAIAASFTALIAPGDEVILIQPLYDAYLPLVQRAGG-VAR 136 Query: 142 VETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLV 201 + L + P + A PRT+ +VVN+P NP GA L LA VE D + Sbjct: 137 LARLEPGSWRLTPAALEAAAGPRTRLIVVNNPVNPAGAKLSHGELADLAAFCVERDLIAI 196 Query: 202 SDEIYEHLLYEGEHFSPGRVAP---EHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMAS 258 DE++EH++Y+ P P + T+ + A K FA+TGW++G+ C + +A Sbjct: 197 CDEVWEHVVYDSARHIPLIAMPGMRDRTVKIGSAGKIFALTGWKVGWMCAAAPLAAVLAR 256 Query: 259 VSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPS 318 T S QWA E L Q+ A++ + ++R RD L GLTA G + V PS Sbjct: 257 AHQFLTFSTAPNLQWAVAEGLETQD---AWIADSIVGFQRSRDRLAAGLTAAGYR-VLPS 312 Query: 319 GAFYVL---MDTSPIAPDEVRAAERLL-EAGVAVVPGTDFAAFGHV----RLSYATSEEN 370 GA + L + S IA + +RL+ E GVA +P + F A V RL +A ++ Sbjct: 313 GATWFLSIDLAASGIALHDAAFCDRLVEEIGVAAIPVSAFYAEAPVTHLARLCFAKADAV 372 Query: 371 LRKALERFA 379 L A+ER + Sbjct: 373 LDTAIERMS 381 Lambda K H 0.317 0.133 0.379 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: 318 Number of extensions: 16 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: 385 Length of database: 389 Length adjustment: 30 Effective length of query: 355 Effective length of database: 359 Effective search space: 127445 Effective search space used: 127445 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 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