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:Q30ZX9 (388 letters) >FitnessBrowser__Cola:Echvi_0124 Length = 386 Score = 293 bits (749), Expect = 7e-84 Identities = 151/381 (39%), Positives = 225/381 (59%), Gaps = 3/381 (0%) Query: 7 ADRLATLPPYLFAQIDKVKAEVAARGVDIISLGIGDPDMPTPDFVIEALKKAAEKPANHQ 66 A RLA + Y F++ + A + A G II++GIG PD+P V EAL ++ +P +H Sbjct: 5 AHRLANVKEYYFSKKLREVARLKAEGHPIINMGIGSPDLPPHPSVTEALNHSSAQPTSHG 64 Query: 67 YPSYTGMLAFRQEVANWYKRRYAVELDPKTEVLTLIGSKEGIAHFPTAFVNPGDLVLVCP 126 Y SY G+ A R+ +A++Y++ YAV L P E+L ++GSKE I H A++NPGD VL+ Sbjct: 65 YQSYQGIPALREAIASFYQKHYAVSLSPTDEILPMMGSKEAIMHISLAYLNPGDKVLIPN 124 Query: 127 PCYPVYAIASRFMGGVVQELPLLEENDFLPDLDAVDEATWEKARCIFVNYPNNPTAAMAP 186 P YP Y+ + +G L EEN +LPD+ ++E + +++NYP+ PT A A Sbjct: 125 PGYPTYSSVTELVGAKAVYYDLKEENQWLPDIGQLEELAQSGIKLMWINYPHMPTGANAS 184 Query: 187 RSFFEKLIGIARKHNVIVVHDAAYTEMYYNENNRPLSIMEIPGAMDVAIEFNSLSKPYNM 246 R E L+ A+KH +++V+D Y+ + P+SI+ I GA D+A+E NSLSK +NM Sbjct: 185 REALEALVTFAKKHQILLVNDNPYS---FILTQSPISILSIDGAKDIALELNSLSKTFNM 241 Query: 247 TGWRIAMAVGNASLVAGLGKVKENMDSGAFQAVQEAAIVALRDGDAFLAEIRDIYRKRRD 306 GWR+ M G AS + + KVK NMDSG F +QE AI AL + ++ IY KRR+ Sbjct: 242 PGWRVGMLCGQASYLQEVLKVKSNMDSGMFLGIQEGAIAALNLDQRWFDQMDAIYHKRRE 301 Query: 307 TVIAALNKIGITCRVPEASLYVWARVPEGYTSSDFVTRVLQETGVVMTPGNGFGAAGEGY 366 V ++G C A ++VWA++ T S V ++L E + +TPG+ FG+ G GY Sbjct: 302 AVWKLAERVGAICERNSAGMFVWAKLATQTTPSALVDKLLYENHIFITPGDIFGSNGHGY 361 Query: 367 FRISLTVNDERLEEAVSRIAS 387 R SL V + ++EA R+ S Sbjct: 362 IRFSLCVPENLIQEAFDRVNS 382 Lambda K H 0.320 0.136 0.403 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: 418 Number of extensions: 16 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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