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 Pf6N2E2_5161 Valine--pyruvate aminotransferase (EC 2.6.1.66) ## AvtA
Query= SwissProt::E9L7A5 (479 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5161 Length = 390 Score = 190 bits (483), Expect = 6e-53 Identities = 129/397 (32%), Positives = 195/397 (49%), Gaps = 20/397 (5%) Query: 77 SPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHTRY 136 S R +++P +A+ +A L AG VI L GEPDF T PI++AG A+ G TRY Sbjct: 6 SARSRAIEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAEPIIQAGQAALAAGKTRY 65 Query: 137 TPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPY 196 T G ELR AI+ + G+ P +ILV+ G +++ A + PG L+ P Sbjct: 66 TAARGIPELREAIAGFYGQRYGVEIDPRRILVTPGGSGALLLASALLVDPGKHWLLADPG 125 Query: 197 WVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRK 256 + RL + ++P + L P L+ + S ++ SP+NPTG++ R Sbjct: 126 YPCNRHFLRLVEGAAQLVPVGPEVRYQLTPDLVNRHWDQDSVGALVASPANPTGTILTRD 185 Query: 257 LLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAMTG 316 L +++++ H LV+ DEIY + Y T AS+ + D +N FSK F MTG Sbjct: 186 ELAGLSKVIKGHNGHLVV-DEIYHGLTYG----TDAASVLEVDDDAFVLNSFSKYFGMTG 240 Query: 317 WRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRERR 376 WRLG++ P + K+ A S++Q AA+A A E+ F RR Sbjct: 241 WRLGWLVAPSAAVGELEKLAQNLYISAPSMAQYAALAC--FEPATIEIFEQRRAEFARRR 298 Query: 377 DYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQVAL 436 D+L+ + E+ EP GAFYL+ D+S++ G D F + C++ L+ VA Sbjct: 299 DFLLPALRELGFGIAVEPEGAFYLYADISAFGG---DAF-------AFCQHFLETEHVAF 348 Query: 437 VPGDAFGDDTC---IRISYAASLSTLQAAVERIKKAL 470 PG FG +R +Y SL L+ AV RI++ L Sbjct: 349 TPGLDFGRHQAGHHVRFAYTQSLPRLEEAVARIERGL 385 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: 420 Number of extensions: 17 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: 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 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