Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_035238275.1 Q366_RS09090 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_000745975.1:WP_035238275.1 Length = 385 Score = 179 bits (454), Expect = 1e-49 Identities = 119/387 (30%), Positives = 191/387 (49%), Gaps = 8/387 (2%) Query: 1 MQEARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPE 60 M A+R ++ P++ + +KI RGVD+I + IG+PD P ++++ EA Sbjct: 1 MSVAKRCEQMKPFIAMDVMEKIHNMEARGVDVIHMEIGEPDFNVPE-CVNRVCGEALAQN 59 Query: 61 NHRYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINL 120 Y S G L RQA++D+++R+YG +DP + +VT G+ + + +DPGD + Sbjct: 60 ETCYTHSLGDLRLRQAISDYHKRIYGTTVDPGQILVTS-GTSPAMLLVFSALIDPGDEVI 118 Query: 121 VPDPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGA 180 V DP Y Y GE F+ + +GF+ AI + + K +F+N P+NPTG+ Sbjct: 119 VSDPHYACYANFIRYVQGEPVFVKVYEKDGFVYTPQAILEKITPKTKAIFVNSPSNPTGS 178 Query: 181 VADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPY 240 V +++V+ AR + L + D Y +TY+G + S ++ + N SK + Sbjct: 179 VIPEARMRQIVDLAREHGLYIVSDEIYHGLTYEG-KDHSIME---FTDQAFVLNGFSKLF 234 Query: 241 NMTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQER 300 MTG RLG+ I AL ++ N A Q AG ALT +R Y ER Sbjct: 235 AMTGLRLGYLIAPPKFIRALQVLQQNFFICANSITQLAGAVALTDAGRETQAMRDTYNER 294 Query: 301 RDIIVEGFNSLGWH-LEKPKATFYVWAPVPRGYT-SASFAEMVLEKAGVIITPGNGYGNY 358 R ++ +G + +P FYV+ T S + A +LEKA + +TPG +G Sbjct: 295 RIFMIRRLKEMGLSMMVEPTGAFYVFVNFKHISTDSYALAFDILEKAHIGVTPGIDFGAN 354 Query: 359 GEGYFRIALTISKERMQEAIERLRRVL 385 GEGY R + S + ++ ++RL L Sbjct: 355 GEGYLRFSYANSLDNLKIGMDRLENYL 381 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: 364 Number of extensions: 25 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: 390 Length of database: 385 Length adjustment: 30 Effective length of query: 360 Effective length of database: 355 Effective search space: 127800 Effective search space used: 127800 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