Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate 8500663 DvMF_1411 aminotransferase class I and II (RefSeq)
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Miya:8500663 Length = 394 Score = 167 bits (424), Expect = 4e-46 Identities = 123/396 (31%), Positives = 189/396 (47%), Gaps = 26/396 (6%) Query: 7 RVQAMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKT-KYA 65 R+ + P VN ++LRRQ VD+V L G PD TP+H+ + A +G +Y+ Sbjct: 6 RMHRLPPYVFATVNELKMQLRRQNVDIVDLGMGNPDIPTPQHIVDKLVEASGKGVNHRYS 65 Query: 66 PPAGIPELREALAEKFRRENGLSVTPE-ETIVTVGGKQALFNLFQAILDPGDEVIVLSPY 124 GIP LR+A+ + + R G+ + P+ E + T+G K+ L +L A+L PGD V P Sbjct: 66 VSRGIPNLRKAICDWYMRRFGVYLDPDTEAVATMGAKEGLSHLSLAMLSPGDVVFAPDPT 125 Query: 125 WVSYPEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKE 184 + + AG V + F D R P+ K L ++ P+NPT + E Sbjct: 126 YPIHTYAPIIAGADVRRIPIGRGRDFFEDLLVATRQTWPQPKLLFISYPHNPTCEIAAPE 185 Query: 185 VLEALARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRVAPEHTLTVN----GAAKAFAMTG 240 + + A EH Y++ D Y L ++G H P + E V +K+++M G Sbjct: 186 FFQKVVDFAKEHKIYVIHDFAYADLAFDG-HMPPSFMQAEGAKDVGVEFFSMSKSYSMAG 244 Query: 241 WRIGYACGPKEVIKAMASVSSQSTTSPDTIAQWATLEALTN-QEASRAFVEMAREAYRRR 299 WR+G+ G ++++ A+ + S Q A AL QE V + YR+R Sbjct: 245 WRVGFCVGNRDLVYALTRIKSYLDYGHFQPIQIAATVALNGPQECVTEIV----DTYRKR 300 Query: 300 RDLLLEGLTALGLKAVRPSGAFYVLMDTSPIAPDEVRA------AERLLEAG-VAVVPGT 352 RD+L+EGL G P G +V P+E RA ++ LL+ G VAV PG Sbjct: 301 RDVLIEGLGRAGWVVPPPKGTMFVWAQ----IPEEFRAMGSVEFSKLLLKEGHVAVSPGL 356 Query: 353 DFAAFG--HVRLSYATSEENLRKALERFARVL-GRA 385 F A G HVR + +E ++A++ +VL GRA Sbjct: 357 GFGAHGDDHVRFALIENEHRTKQAMKGIKKVLSGRA 392 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: 394 Number of extensions: 23 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: 385 Length of database: 394 Length adjustment: 30 Effective length of query: 355 Effective length of database: 364 Effective search space: 129220 Effective search space used: 129220 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