Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate PP_4692 PP_4692 putative aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__Putida:PP_4692 Length = 390 Score = 144 bits (364), Expect = 3e-39 Identities = 117/391 (29%), Positives = 182/391 (46%), Gaps = 24/391 (6%) Query: 6 RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENH-RY 64 R R + P+ + + E + G D+I L IG+PD T + ++ +A H RY Sbjct: 8 RSRAIEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAAPIV--AAGQAALAAGHTRY 65 Query: 65 PTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDP 124 + GL A R+A+A +Y + YG+++DP R ++T GS + SL VDPG L+ DP Sbjct: 66 TAARGLPALREAIAGFYGQRYGLNIDPERILITPGGSGALLLASSLL-VDPGKHWLLADP 124 Query: 125 GYPVYNIGTLLAGGESYFMPLTAANGFLPDLG-AIPSDVARR-----AKLMFINYPNNPT 178 GYP L G + +P+ PD+ + +D+ R + P NPT Sbjct: 125 GYPCNRHFLRLVEGGAQLVPVG------PDVNYQLTADLVERYWDKDTVGALVASPANPT 178 Query: 179 GAVADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSK 238 G V + + + D Y +TY G APS L+ + V NS SK Sbjct: 179 GTVLGREALACLARTTHERHGHLVVDEIYHGLTY-GMDAPSVLEVDDSAFV---LNSFSK 234 Query: 239 PYNMTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRV-Y 297 + MTGWRLGW + L ++ N+ A Q+A +A + E RR + Sbjct: 235 YFGMTGWRLGWLVAPPGAVADLEKLAQNLYISAPSMAQHAALACFQPEALAIFEERRAEF 294 Query: 298 QERRDIIVEGFNSLGWHLE-KPKATFYVWAPVPR-GYTSASFAEMVLEKAGVIITPGNGY 355 RRD ++ LG+ + +P+ FY++A + G + +F LE V TPG + Sbjct: 295 ARRRDYLLPALRELGFRIAVEPQGAFYLYADISAFGGDAFAFCRHFLETQHVAFTPGLDF 354 Query: 356 GNYGEG-YFRIALTISKERMQEAIERLRRVL 385 G + G + R A T S R++EA++R+ R L Sbjct: 355 GRHLAGHHVRFAYTQSLPRLEEAVQRIARGL 385 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: 384 Number of extensions: 23 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: 390 Length of database: 390 Length adjustment: 31 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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