Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_012283431.1 HM1_RS10910 LL-diaminopimelate aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_000019165.1:WP_012283431.1 Length = 393 Score = 426 bits (1094), Expect = e-124 Identities = 201/381 (52%), Positives = 272/381 (71%), Gaps = 1/381 (0%) Query: 4 ARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHR 63 ARR+ L +F+R++ E GVD+I+LGIG PD P HV L+ + + Sbjct: 7 ARRMASLSSAMFSRMDALRQEVEASGVDVINLGIGSPDRPPAPHVRQTLMDALVRDDAYG 66 Query: 64 YPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPD 123 Y ++GL+ F+ AVADWYQ +GV LDP+ EV++L+GS++G+ H+ L +DPGD+ L+PD Sbjct: 67 YALTDGLIEFKSAVADWYQERFGVALDPKTEVLSLMGSQDGLGHLGLALLDPGDVALIPD 126 Query: 124 PGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVAD 183 PGYP+Y G LLA G Y +PL +LPDL A+P D+ RRAKLM +NYP+NP A A+ Sbjct: 127 PGYPIYRAGVLLAEGFPYPLPLERERDYLPDLDAVPEDILRRAKLMILNYPSNPVAATAE 186 Query: 184 LKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMT 243 L FF VV+FAR ++IV HD AYSE+ YDGYR SFLQAPGAKEVGIEF+S+SK YN+ Sbjct: 187 LNFFTGVVDFARRNNIIVLHDIAYSELAYDGYRPVSFLQAPGAKEVGIEFHSLSKSYNLA 246 Query: 244 GWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDI 303 G RLG A G +V+ LA +KSNID G F+AVQ+A +AAL GPQ + E R YQ RRD+ Sbjct: 247 GCRLGMAVGNREVLALLANLKSNIDYGVFKAVQWAAVAALRGPQAIVEENARAYQRRRDV 306 Query: 304 IVEGFNSLGWHLEKPKATFYVWAPVPRGYTSA-SFAEMVLEKAGVIITPGNGYGNYGEGY 362 +V+G N +GW ++KPKA+ +VWAPVP+G+TS+ +FAE +L + GV++ PGN +G GEGY Sbjct: 307 LVDGLNRIGWQMDKPKASMFVWAPVPKGFTSSFAFAEELLRETGVLVVPGNAFGERGEGY 366 Query: 363 FRIALTISKERMQEAIERLRR 383 RIAL + + R++EA+ER+ R Sbjct: 367 VRIALVVPEGRLEEAVERIAR 387 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: 509 Number of extensions: 29 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: 393 Length adjustment: 31 Effective length of query: 359 Effective length of database: 362 Effective search space: 129958 Effective search space used: 129958 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