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 Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::E9L7A5 (479 letters) >FitnessBrowser__PS:Dsui_0132 Length = 385 Score = 184 bits (466), Expect = 6e-51 Identities = 126/400 (31%), Positives = 197/400 (49%), Gaps = 26/400 (6%) Query: 77 SPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHTRY 136 +PR+ + P + + +A L G +I + GEPDF TP PI+ A +++G Y Sbjct: 5 APRLADIAPFHVMELLGRARELEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGRVFY 64 Query: 137 TPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPY 196 TP G ELR AIS ++ G++ +I ++ GA ++ A+ + +PG E L+ P Sbjct: 65 TPALGLPELREAISGFYRQRYGIAVPASRIAITAGASGALTLALACLAAPGSEWLLTDPG 124 Query: 197 WVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRK 256 + R + PV +P + +F LE E++ + SP+NPTG++ Sbjct: 125 YPCNRHFVRAFEGVPVSIPVGAASNFQPTRLDLEQHWNERTAGALFASPANPTGTMLDAA 184 Query: 257 LLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAMTG 316 L IA+ V + L+I DEIY + Y T+ A+ D V FSK F MTG Sbjct: 185 ELADIADFVRQRQGQLII-DEIYHGLTYNGDAPTALAA----GDNIFVVQSFSKYFQMTG 239 Query: 317 WRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVK---SFR 373 WRLG++ P+ F+ K+ AS+ +Q AA+AA E +A + + F+ Sbjct: 240 WRLGWLVIPEPFVRDVEKLAQNLFISASTPAQHAALAAF-----QPETIALLEQRRAEFK 294 Query: 374 ERRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQ 433 RRDYL + I ++P GAFYL+ D S+ + D FG R LL++A Sbjct: 295 ARRDYLAPALEAIGFRITAQPEGAFYLYADCST---LTDDSFG-------FARRLLEEAG 344 Query: 434 VALVPGDAFGD---DTCIRISYAASLSTLQAAVERIKKAL 470 VA+ PG FG+ + +R +Y + + L VERI++ L Sbjct: 345 VAITPGIDFGNHGASSHVRFAYTNAQARLAEGVERIRQLL 384 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: 402 Number of extensions: 22 Number of successful extensions: 4 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: 385 Length adjustment: 32 Effective length of query: 447 Effective length of database: 353 Effective search space: 157791 Effective search space used: 157791 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