Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate Echvi_0124 Echvi_0124 Aspartate/tyrosine/aromatic aminotransferase
Query= curated2:C6BUK3 (388 letters) >FitnessBrowser__Cola:Echvi_0124 Length = 386 Score = 293 bits (749), Expect = 7e-84 Identities = 151/380 (39%), Positives = 225/380 (59%), Gaps = 3/380 (0%) Query: 7 ADRLATLPPYLFAEIDRLKAEVAAQGVDIISLGIGDPDLPTPDFIIEALHKAAKNPVNHQ 66 A RLA + Y F++ R A + A+G II++GIG PDLP + EAL+ ++ P +H Sbjct: 5 AHRLANVKEYYFSKKLREVARLKAEGHPIINMGIGSPDLPPHPSVTEALNHSSAQPTSHG 64 Query: 67 YPSYVGLLTFRQAVADWYKERFDVELDATKEVVSLIGSKEGIAHFPLAFVNPGDLVLVAS 126 Y SY G+ R+A+A +Y++ + V L T E++ ++GSKE I H LA++NPGD VL+ + Sbjct: 65 YQSYQGIPALREAIASFYQKHYAVSLSPTDEILPMMGSKEAIMHISLAYLNPGDKVLIPN 124 Query: 127 PNYPVYPVASGFAGGEVEIVPLLEENDFLPNLDAISDEKWDKCKIFFVNYPNNPTSATAT 186 P YP Y + G + L EEN +LP++ + + K+ ++NYP+ PT A A+ Sbjct: 125 PGYPTYSSVTELVGAKAVYYDLKEENQWLPDIGQLEELAQSGIKLMWINYPHMPTGANAS 184 Query: 187 PEFYAELVAKAKKHNVIIAADAAYTEVYYDEDKKPISILETPGAKDVAIEFHSLSKTYNM 246 E LV AKKH +++ D Y+ + + PISIL GAKD+A+E +SLSKT+NM Sbjct: 185 REALEALVTFAKKHQILLVNDNPYSFIL---TQSPISILSIDGAKDIALELNSLSKTFNM 241 Query: 247 TGWRCGMAVGNASLVAGLGKIKENVDSGIFQAVQEAGIVALKEGEPYVKEFRKIYKERRD 306 GWR GM G AS + + K+K N+DSG+F +QE I AL + + + IY +RR+ Sbjct: 242 PGWRVGMLCGQASYLQEVLKVKSNMDSGMFLGIQEGAIAALNLDQRWFDQMDAIYHKRRE 301 Query: 307 CVIEALEKINISCKVPDASIFVWAKTPEGYTSSEFVSKLLKETGVVVTPGNGFGESGEGY 366 V + E++ C+ A +FVWAK T S V KLL E + +TPG+ FG +G GY Sbjct: 302 AVWKLAERVGAICERNSAGMFVWAKLATQTTPSALVDKLLYENHIFITPGDIFGSNGHGY 361 Query: 367 FRISLTVDTDRLKEAVSRIS 386 R SL V + ++EA R++ Sbjct: 362 IRFSLCVPENLIQEAFDRVN 381 Lambda K H 0.317 0.136 0.398 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: 425 Number of extensions: 17 Number of successful extensions: 2 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: 388 Length of database: 386 Length adjustment: 30 Effective length of query: 358 Effective length of database: 356 Effective search space: 127448 Effective search space used: 127448 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