Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_011020683.1 MA_RS03340 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000007345.1:WP_011020683.1 Length = 394 Score = 185 bits (470), Expect = 2e-51 Identities = 121/384 (31%), Positives = 186/384 (48%), Gaps = 8/384 (2%) Query: 6 AKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQ 65 +K+ ++PP+ + + + +AQG +I L +G+PD PT HI EAA + + Sbjct: 11 SKQSEDIPPFYVMEVLESAKELEAQGRHIIHLEVGEPDFPTAPHICEAACAAIGKGLT-K 69 Query: 66 YPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPD 125 Y S G+PA R A+A+ Y R+FGV+LDP + +V+ G+ G+ + ++ D V++ + Sbjct: 70 YTHSQGLPALREAIAESYYRKFGVDLDPNQVIVTS-GTSPGLLMVFMALLEKRDEVIMSN 128 Query: 126 PGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVAS 185 P Y Y GG P V + NGF + + + K + IN P+NP G V S Sbjct: 129 PHYACYPNFVKYLGGTPVFVYTSEANGFALEPETVRQCLSPNTKAILINSPSNPGGHVMS 188 Query: 186 KEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMT 245 + + A E GI V D Y + + G S LE + + SK Y MT Sbjct: 189 PDTLQGLAAIADEKGIPVVSDEIYQGLIYSG-EEHSILEYT---KNAFVLNGFSKLYAMT 244 Query: 246 GWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDL 305 GWR G+ G V A+ ++ N VQ A IAAL G Q+ V + ++Y RR Sbjct: 245 GWRLGYIICPPGCVRAIQKIHQNFFICANSFVQEAGIAALKGSQEHVVEMVQIYNMRRQY 304 Query: 306 VVDTLNDLGWRLTR-PRATFYIWAPV-PAGHDASSFAEMVLEKAGVVITPGTGYGTYGEG 363 ++ L +G + + P FY+ A G+D+ + +L +AGV +TPG +G EG Sbjct: 305 MLKRLLGMGLEVRKEPMGAFYVLADARKFGNDSLELSRSILNEAGVAVTPGVDFGNGAEG 364 Query: 364 YFRISLTLPTPRLVEAMERLRGCL 387 Y R S + E M+RL L Sbjct: 365 YLRFSYANSLENIAEGMDRLEAFL 388 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: 317 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: 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