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 WP_013843674.1 DESRU_RS18780 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::E9L7A5 (479 letters) >NCBI__GCF_000215085.1:WP_013843674.1 Length = 390 Score = 263 bits (671), Expect = 1e-74 Identities = 169/369 (45%), Positives = 223/369 (60%), Gaps = 20/369 (5%) Query: 105 VIRLAAGEPDFDTPAPIVEAGINAIREGHTRYTPNAGTMELRSAISHKLKEENGLSYTP- 163 VI L GEPDF TP I EA I ++ +G T YT N G +ELR +IS L + G+ Y P Sbjct: 35 VISLGVGEPDFVTPWHIREACIYSLHKGSTTYTSNHGLLELRESISQYLGNQ-GVRYNPQ 93 Query: 164 DQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPYWVSYPEMARLADATPVILPTSISEDFL 223 D+ILV+ G +++ A+ V SPGDEVLIP P +VSY LA PV + T + + F Sbjct: 94 DEILVTVGVSEALDLALRTVISPGDEVLIPTPCYVSYIPCTTLAGGVPVTVATHMEDHFK 153 Query: 224 LDPKLLESKLTEKSRLLILCSPSNPTGSVYPRKLLEQIAEIVARHPRLLVISDEIYEHII 283 L LE+ +T KS++L+LC P+NPTG+V R+ L QIAE+V R+ LLVISDEIY+ + Sbjct: 154 LTAGKLEAAITPKSKVLLLCFPNNPTGAVMSREELLQIAEVVRRYD-LLVISDEIYDRLT 212 Query: 284 YAPATHTSFASLPGMWDRTLTVNGFSKAFAMTGWRLGYIAGPKHFIAACNKIQSQFTSGA 343 Y HT FASLPGM DRT+T+NGFSKA+AMTGWRLGY A FIAA KI A Sbjct: 213 YT-GEHTCFASLPGMRDRTITLNGFSKAYAMTGWRLGYAAANAEFIAAMTKIHQYTMLCA 271 Query: 344 SSISQKAAVAALGLGYAGGELVATMVKSFRERRDYLVKSFGEIEGVKISEPRGAFYLFID 403 +Q +A+ AL G + E MV + RR +++ F EI G+ EP GAFY F Sbjct: 272 PITAQISAMEALRNGKSAME---GMVAHYNRRRRLILQGFKEI-GLPCFEPGGAFYAF-- 325 Query: 404 LSSYYGVEVDGFGSINNSESLCRYLLDKAQVALVPGDAF--GDDTCIRISYAASLSTLQA 461 Y G G + +E LL + +VA++PGD F G + C+R SYA+S+ L Sbjct: 326 --PYIG--ETGLTAAEFAEE----LLVEEKVAVIPGDVFGPGGENCVRCSYASSVEDLTE 377 Query: 462 AVERIKKAL 470 A+ER+ + L Sbjct: 378 ALERMGRFL 386 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: 422 Number of extensions: 27 Number of successful extensions: 6 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: 390 Length adjustment: 32 Effective length of query: 447 Effective length of database: 358 Effective search space: 160026 Effective search space used: 160026 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 Apr 10 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