Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 353461 BT3935 aminotransferase (NCBI ptt file)
Query= BRENDA::O66630 (387 letters) >FitnessBrowser__Btheta:353461 Length = 393 Score = 297 bits (761), Expect = 3e-85 Identities = 160/382 (41%), Positives = 223/382 (58%), Gaps = 3/382 (0%) Query: 5 SDRLKVLPPYLFAELDRKKQEKIEQGVDVIDLGVGDPDMPTPKPIVEAAKKALENPENHK 64 ++RL + Y F++ ++ + +G DVI LG+G PDMP K +E +P H Sbjct: 13 AERLASVSEYYFSKKLKEVAQMNAEGKDVISLGIGSPDMPPSKVTIETLCNNAHDPNGHG 72 Query: 65 YPSYVGKYEFRKAVADWYKRRFDVDLDPNTEVITLIGSKEGIAHFPLAFVNPGDIVLCPD 124 Y YVG E RK A WY+R + V+L+PNTE+ LIGSKEGI H LAFVNPG+ VL P+ Sbjct: 73 YQPYVGIPELRKGFAAWYQRWYGVELNPNTEIQPLIGSKEGILHVTLAFVNPGEQVLVPN 132 Query: 125 PAYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAKKAKIIWINYPNNPTSAPPT 184 P YP Y + G + LKEE+ ++PD +++ + + K++W NYPN PT A T Sbjct: 133 PGYPTYTSLSKILGAEVISYDLKEEDGWMPDFEALEKMDLNRVKLMWTNYPNMPTGANAT 192 Query: 185 LEFYKKLVDWAKEYNVIIASDNAYSEIYTGQEKPPSILQVPGAKDVAIEFHSLSKTYNMT 244 E Y++LVD+A+ N++I +DN YS I EKP SIL VPGAK+ IEF+S+SK++NM Sbjct: 193 PELYERLVDFARRKNIVIVNDNPYSFIL--NEKPISILSVPGAKECCIEFNSMSKSHNMP 250 Query: 245 GWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYRERKKI 304 GWRIGM N E V + KVK+N+DSG F A+Q A AL + E YR R+ + Sbjct: 251 GWRIGMLASNAEFVQWILKVKSNIDSGMFRAMQLAAATALEAEADWYEGNNHNYRGRRHL 310 Query: 305 MTEALEKIGLEIYRSDYTFYLWIKVPEGYTSA-EFVGRLIDEAGIVCTPGNGFGEYGEGY 363 E ++ +G + +LW K+P E +++ +A + TPG FG G + Sbjct: 311 AGEIMKTLGCTYDENQVGMFLWGKIPASCKDVEELTEKVLHQARVFITPGFIFGSNGARF 370 Query: 364 FRISLTVPTERLLEAAERIKNL 385 RISL +L EA ERIK L Sbjct: 371 IRISLCCKDAKLAEALERIKKL 392 Lambda K H 0.317 0.139 0.413 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: 462 Number of extensions: 17 Number of successful extensions: 3 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: 387 Length of database: 393 Length adjustment: 31 Effective length of query: 356 Effective length of database: 362 Effective search space: 128872 Effective search space used: 128872 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 (21.6 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