Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate Pf6N2E2_462 Aspartate aminotransferase (EC 2.6.1.1)
Query= curated2:B1I544 (392 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_462 Length = 394 Score = 169 bits (428), Expect = 1e-46 Identities = 112/361 (31%), Positives = 174/361 (48%), Gaps = 5/361 (1%) Query: 28 KAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAVADWYARRF 87 + QG+DV+ L +GDPD TP I++AA L+ H Y G+ R ++A + R Sbjct: 28 REQGMDVLLLSVGDPDFDTPRAIVDAAVGSLRAGETH-YSDIRGLHTLRTSIARRHRLRC 86 Query: 88 GVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPVPL 147 G + +VV L G++ + + C ++PGD V+V +P Y Y G PV + Sbjct: 87 GQPAGAE-QVVVLPGAQCAVYAVAQCLLNPGDEVIVAEPMYVTYEAVFGACGATVVPVAV 145 Query: 148 TAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVDFAREYGILVCHDA 207 NGF + A + R + M +N PNNP+GA + + E+ + + D Sbjct: 146 RPENGFRVEPADVARLVTPRTRAMLLNSPNNPSGASLPMPTWQALARLCIEHDLWLISDE 205 Query: 208 AYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLKS 267 YS++ +DG S + G E +S+SK++ MTGWR GW G + L L Sbjct: 206 VYSDLLYDG-EHISPASLPGMAERTATINSLSKSHAMTGWRIGWVIGPESLADHLANLSL 264 Query: 268 NLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRLTRPRATFYI 326 + G+ VQ AA AL V + + YR+RRDLV L+D G + RP ++ Sbjct: 265 CMLFGLPDFVQRAAQVALEQALPEVAQMHDEYRQRRDLVCAMLDDCPGLKPVRPDGGMFV 324 Query: 327 WAPV-PAGHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLRG 385 V G DA +FAE +L+ GV + G +G G+ R+ L + +L +A +R+ Sbjct: 325 MVDVRRTGLDAQAFAERLLDDYGVSVLAGEAFGPSAAGHIRLGLVVDQVKLADACQRITS 384 Query: 386 C 386 C Sbjct: 385 C 385 Lambda K H 0.321 0.139 0.430 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: 287 Number of extensions: 11 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: 392 Length of database: 394 Length adjustment: 31 Effective length of query: 361 Effective length of database: 363 Effective search space: 131043 Effective search space used: 131043 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 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