Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate PfGW456L13_4713 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)
Query= curated2:B1I544 (392 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713 Length = 399 Score = 184 bits (468), Expect = 3e-51 Identities = 131/405 (32%), Positives = 206/405 (50%), Gaps = 36/405 (8%) Query: 9 IRNLPPYLFARIEQLIA------DKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPA 62 + L PY F ++ L+ DK+ I+L IG+P +P + EA L+ A Sbjct: 5 LSQLQPYPFEKLRALLGSVTPNPDKRP-----IALSIGEPKHRSPSFVAEALAGNLEKMA 59 Query: 63 NHQYPSSAGMPAYRRAVADWYARRFGVE---LDPQREVVSLIGSKEGIAHLPWCFVDPGD 119 YP++ G+P R A+A W RRF V +DP R V+ + G++E + V+ GD Sbjct: 60 --VYPTTLGIPELREAIAAWCERRFDVPKGWIDPARNVLPVNGTREALFAFTQTVVNRGD 117 Query: 120 VVLV--PDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPN 177 LV P+P Y +Y G LAG PH +P NGF PD A+ + +R +++F+ P Sbjct: 118 DALVVSPNPFYQIYEGAAFLAGAKPHYLPCLDENGFNPDFDAVSPDIWKRCQILFLCSPG 177 Query: 178 NPTGAVASKEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVG----- 232 NPTGA+ E +++ A EY ++ D YSE+ FD PP L ++ E+G Sbjct: 178 NPTGALIPVETLKKLIALADEYDFVIAADECYSELYFDEQTPPPGL-LSACAELGRKDFK 236 Query: 233 --IEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQD 290 + FHS+SK N+ G R+G+ AG+A ++ ++ + Q A++AA N + Sbjct: 237 RCVVFHSLSKRSNLPGLRSGFVAGDADVLKGFLLYRTYHGCAMPVQTQLASVAAWN-DEV 295 Query: 291 GVQSLCEMYRERRDLVVDTLNDLGWRLTRPRATFYIWAPVPAGHDASSFAEMVLEKAGVV 350 V++ +YRE+ D V++ L+ + + RP +FY+W P AG DA +F + E+ V Sbjct: 296 HVRANRALYREKFDAVLEILSPV-LDVQRPDGSFYLW-PNVAGDDA-AFCRDLFEQEHVT 352 Query: 351 ITPGTGYG------TYGEGYFRISLTLPTPRLVEAMERLRGCLGR 389 + PG+ G G R++L P VEA ER+R + R Sbjct: 353 VVPGSYLSRDVDGVNPGAGRVRMALVAPLAECVEAAERIRDFIQR 397 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: 349 Number of extensions: 16 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: 399 Length adjustment: 31 Effective length of query: 361 Effective length of database: 368 Effective search space: 132848 Effective search space used: 132848 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