Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Ga0059261_1288 Ga0059261_1288 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__Korea:Ga0059261_1288 Length = 401 Score = 332 bits (852), Expect = 9e-96 Identities = 163/381 (42%), Positives = 235/381 (61%), Gaps = 3/381 (0%) Query: 11 RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70 RI++LPPYV A ++ ++A AR G D+IDLGMGNPD PQ V+D + Q P HGY Sbjct: 7 RIKRLPPYVIAEVNGMRAAARAAGEDIIDLGMGNPDLPPPQHVIDKLCEVAQKPSAHGYS 66 Query: 71 PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130 +G RRA N+Y RR+GV +DP+SE + +GSKEGL+ LA A PGDV+L P+P+ Sbjct: 67 QSKGIPGLRRAQANYYGRRFGVDVDPESEVVVTMGSKEGLASLATAITAPGDVILAPNPS 126 Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190 YP H G +IAG T+ ++ P+ + L + IL NYPSNPT T Sbjct: 127 YPIHTFGFIIAGATIRAVPTTPDEHYFESLERAMNFTVPRPSILVVNYPSNPTAETVDLA 186 Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250 F+E +VA+A++ ++ ++ DL Y+EL +DG S+L++ GAKD+ +EF +LSKTY+MAGW Sbjct: 187 FYERLVAWAKENKVWIISDLAYSELYYDGKPTVSILQVKGAKDVAIEFTSLSKTYSMAGW 246 Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310 R+GF VGN+ +I + +K+ LDYG F +Q AA AL P + +Q Y RRD L+ Sbjct: 247 RIGFAVGNKQLIAAMTRVKSYLDYGAFTPVQAAACAALNGPQDIVEANRQLYHKRRDVLV 306 Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367 + G GWD+P A+M+ W P +GS +F+ LL V V PG +G GEG+ Sbjct: 307 ESFGRAGWDIPAPPASMFAWAPLPPALAHLGSLEFSKQLLSHAKVAVAPGVGYGENGEGF 366 Query: 368 VRISLIADCDRLGEALDRIKQ 388 VRI+++ + RL +A +++ Sbjct: 367 VRIAMVENEQRLRQAARNVRK 387 Lambda K H 0.321 0.140 0.427 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: 457 Number of extensions: 24 Number of successful extensions: 2 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: 403 Length of database: 401 Length adjustment: 31 Effective length of query: 372 Effective length of database: 370 Effective search space: 137640 Effective search space used: 137640 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 (21.8 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