Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate AO353_28150 AO353_28150 arginine aminotransferase
Query= curated2:B1I544 (392 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28150 Length = 667 Score = 179 bits (454), Expect = 2e-49 Identities = 119/361 (32%), Positives = 178/361 (49%), Gaps = 5/361 (1%) Query: 26 DKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAVADWYAR 85 D + +G DVI L +GDPD PTPD I +AA L+ H Y AG A R A+A Y++ Sbjct: 26 DAQRRGEDVIILSVGDPDFPTPDFITDAAVDALREGDTH-YTEIAGRLALREAIAARYSQ 84 Query: 86 RFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPV 145 FG EL V+++ G++ + C + GD VL DP Y Y +G V Sbjct: 85 LFGRELQASN-VINVAGAQNALFITSLCLLTAGDEVLALDPMYVTYEATLKASGATLVRV 143 Query: 146 PLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVDFAREYGILVCH 205 P A +GF D A + R + +F++ PNNPTG V ++E + D A + + V Sbjct: 144 PCAADSGFRLDAAVLAKAITPRTRAIFLSNPNNPTGVVLNREELQAIADLAITHDLWVVV 203 Query: 206 DAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRL 265 D Y +AF+ S + G E + S+SK++ MTGWR GW + V L Sbjct: 204 DEVYESLAFE-REHLSLAALPGMAERCVVIGSLSKSHAMTGWRIGWIVADETLVAHAETL 262 Query: 266 KSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRLTRPRATF 324 ++ G+ V AA+ A+ ++ + E+YR RRDLVV L+D G + P A Sbjct: 263 MLSMLYGLPGFVMEAALKAVQAHEEVTHGMREIYRRRRDLVVKGLSDCPGISVLTPDAGM 322 Query: 325 YIWAPV-PAGHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERL 383 ++ V G + FA +L +A V + +G +G+ R+S TL RL +A +R+ Sbjct: 323 FVLVDVRGTGLSSLEFAWRLLREARVSVLDAAAFGEPAQGFVRLSFTLGEERLAQACQRI 382 Query: 384 R 384 R Sbjct: 383 R 383 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: 472 Number of extensions: 14 Number of successful extensions: 4 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: 667 Length adjustment: 34 Effective length of query: 358 Effective length of database: 633 Effective search space: 226614 Effective search space used: 226614 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: 52 (24.6 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