Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate AZOBR_RS07830 AZOBR_RS07830 aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__azobra:AZOBR_RS07830 Length = 424 Score = 350 bits (897), Expect = e-101 Identities = 165/390 (42%), Positives = 248/390 (63%), Gaps = 10/390 (2%) Query: 3 EARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENH 62 E RI+ LPPY+FA + A AR G DII LG+G+PD PTP H++DKL+ +P+ H Sbjct: 5 EFHRIKRLPPYVFAEVNAMKARARAAGEDIIDLGMGNPDQPTPQHIVDKLIEAVRDPKTH 64 Query: 63 RYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVP 122 RY S G+ R+A A +Y+R + VD+DP E + IGSKEG+A+++ PGDI LVP Sbjct: 65 RYSNSRGIPGLRKAHAAYYKRRFNVDVDPESECIVTIGSKEGLANLAQAITSPGDIILVP 124 Query: 123 DPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAK-------LMFINYPN 175 +P YP++ G +LAG +P+ ANG D+ + + R + + +NYP+ Sbjct: 125 NPSYPIHPFGFILAGASVRHLPVGQANGTSTDIDSFMIMLERAVRHSVPKPLALVLNYPS 184 Query: 176 NPTGAVADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNS 235 NPT V L F++ +VEF R + + + D AY+E+ +DG PS L+ P A+EV +EF S Sbjct: 185 NPTAEVVGLDFYRPIVEFCRKHGIYILSDLAYAEVFFDGEPPPSILEIPEAREVAVEFTS 244 Query: 236 VSKPYNMTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRR 295 +SK Y+M GWR+G+A G +I ALARIKS +D GAF +Q A AAL GPQE + +VR Sbjct: 245 MSKTYSMAGWRIGFATGNKKLITALARIKSYLDYGAFTPIQVAATAALNGPQECVEQVRT 304 Query: 296 VYQERRDIIVEGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPG 352 +Y++RRD+++EG S GW + P A+ + WAP+P + S F++++L++A V + PG Sbjct: 305 MYRQRRDVMIEGLASAGWTVPSPSASMFAWAPIPEPFAHLGSLEFSKLLLQEAKVAVAPG 364 Query: 353 NGYGNYGEGYFRIALTISKERMQEAIERLR 382 G+G YG+G+ R+AL + R+++A ++ Sbjct: 365 IGFGEYGDGHVRLALVENVHRIRQATRNIK 394 Lambda K H 0.320 0.139 0.421 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: 469 Number of extensions: 18 Number of successful extensions: 2 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: 390 Length of database: 424 Length adjustment: 31 Effective length of query: 359 Effective length of database: 393 Effective search space: 141087 Effective search space used: 141087 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