Align Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase; PhPPA-AT; EC 2.6.1.1; EC 2.6.1.78; EC 2.6.1.79 (characterized)
to candidate 352902 BT3375 aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::E9L7A5 (479 letters) >FitnessBrowser__Btheta:352902 Length = 386 Score = 232 bits (591), Expect = 2e-65 Identities = 138/398 (34%), Positives = 219/398 (55%), Gaps = 21/398 (5%) Query: 74 ISLSPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGH 133 I LS NS+ PS +T + L Q VI G+PD I EAG AI EG Sbjct: 2 IQLSEITNSISPS----LTRRLFNLAQKYDNVIDFTLGDPDIHPHDKIKEAGCKAILEGR 57 Query: 134 TRYTPNAGTMELRSAISHKLKEENGLSYTP-DQILVSNGAKQSIIQAVLAVCSPGDEVLI 192 TRY+PNAG +ELR IS + K + + Y P ++I+V+ G + + +LA+ + GDEV+I Sbjct: 58 TRYSPNAGLLELREIISSRYKLQYNIEYNPTNEIMVTVGGMEGLYLTLLAILNRGDEVII 117 Query: 193 PAPYWVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSV 252 PAPYW++Y +M + P+I + D + + + +T K++ +IL +PSNP+G + Sbjct: 118 PAPYWINYVQMVCMCSGEPIITAPVSTNDLSISIENIRKAITPKTKAIILNTPSNPSGRI 177 Query: 253 YPRKLLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAF 312 ++QIA+I + L+VI+DE+Y+ ++Y A S + M +RT+ +N SK F Sbjct: 178 ISDDSIQQIAQIAIEND-LIVITDEVYKTLLYDNAHFKSIVTCDKMKERTVVINSLSKEF 236 Query: 313 AMTGWRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSF 372 MTGWRLGYIA P I+ Q + A SQ AA+ AL + A M++ F Sbjct: 237 CMTGWRLGYIAAPSELISVMTMFQENIAACAPLPSQYAAIEAL---RNSEKYSAGMIEEF 293 Query: 373 RERRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKA 432 RR+ L++ +I+ + + P+G FY +++ S G++ SE LL+K Sbjct: 294 TLRRNVLLEEVAKIKTITVDAPQGTFYAMLNIKS-TGLK---------SEEFAYALLEKE 343 Query: 433 QVALVPGDAFGD--DTCIRISYAASLSTLQAAVERIKK 468 QVA+VPG +GD + IRI++ + ++ ++R+K+ Sbjct: 344 QVAVVPGITYGDCCEDFIRIAFTLDIYKIKEGIQRLKR 381 Lambda K H 0.317 0.132 0.375 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: 399 Number of extensions: 21 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: 479 Length of database: 386 Length adjustment: 32 Effective length of query: 447 Effective length of database: 354 Effective search space: 158238 Effective search space used: 158238 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: 51 (24.3 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