Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_012169089.1 AZC_RS02835 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000010525.1:WP_012169089.1 Length = 394 Score = 206 bits (523), Expect = 1e-57 Identities = 132/359 (36%), Positives = 183/359 (50%), Gaps = 6/359 (1%) Query: 29 AQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAVADWYARRFG 88 AQG D+I+LGIG PD TP+HI+EAA K LK H Y S G+ R AVA +RF Sbjct: 28 AQGRDIINLGIGQPDFRTPEHIVEAAVKALK-DGQHGYTPSVGIQPLREAVARDLHKRFD 86 Query: 89 VELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPVPLT 148 VE+DP V+ + G K + F +PG +L PDPG+P+Y G P PVP+ Sbjct: 87 VEVDPGL-VMIMPGGKVTMYAAILLFGEPGAEILYPDPGFPIYRSMIEYTGATPIPVPIR 145 Query: 149 AGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVDFAREYG-ILVCHDA 207 NGF A + +++ IN P NPTG V K ++V ++ + + D Sbjct: 146 EENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPKAEIDKLVKGLADHPHVALMSDE 205 Query: 208 AYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLKS 267 Y + FDG R + L R+ I + SKTY MTGWR G++ + + +L Sbjct: 206 IYDQFLFDGERHQTLLAYPEIRDRLILLNGWSKTYAMTGWRLGYSIWPQALYDKVRKLSV 265 Query: 268 NLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRLTRPRATFYI 326 N S V QYA IAAL GPQ+ V ++ + +RR LVV+ LN L G +P+ FY Sbjct: 266 NAWSCVNAATQYAGIAALEGPQEPVAAMLAEFDKRRRLVVEGLNALPGVTCAKPKGAFYA 325 Query: 327 WAPV--PAGHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERL 383 + V A + A +LE AGV G +G +GEGY R+S + A+ER+ Sbjct: 326 FPNVSRTGWTSAKALASALLEDAGVATIGGPDFGVHGEGYIRLSYANSAENIARALERM 384 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: 305 Number of extensions: 15 Number of successful extensions: 5 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 10 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