Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_086510442.1 BZY95_RS13490 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_002151265.1:WP_086510442.1 Length = 386 Score = 169 bits (427), Expect = 2e-46 Identities = 130/372 (34%), Positives = 179/372 (48%), Gaps = 15/372 (4%) Query: 23 AEARER-GVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYPTSEGLLAFRQAVADWY 81 A+ARE G D+I L +G+PD TP V+ A A RY + GL A R+A+A Y Sbjct: 22 AQAREAAGHDVIHLEVGEPDFATPEPVVAAGQA-ALAAGLTRYSPAAGLPALREAIAGHY 80 Query: 82 QRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPGYPVYNIGTLLAGGESY 141 +G D+DPRR +VT G+ + S V PGD L+ DP YP LAG E Sbjct: 81 GEHFGADVDPRRVLVTP-GASGALLLASQLLVGPGDRVLMADPNYPCNRHFMALAGAEVD 139 Query: 142 FMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLKFFQEVVEF--ARSYDL 199 +P+ +G+ D + +L + P+NPTG + D + V + AR L Sbjct: 140 TVPIGPQSGWQLDANLVARHWQDATRLAMLATPSNPTGHMLDAAQLKAVADTVAARGGHL 199 Query: 200 IVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGWRLGWACGRADVIEA 259 +V D Y ++YD AP L NS SK + MTGWRLGW +E Sbjct: 200 LV--DEIYQGLSYD--IAP--LSVASLTADAFVVNSFSKYFGMTGWRLGWLLAPQAAVEP 253 Query: 260 LARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRR-VYQERRDIIVEGFNSLGWHLE-K 317 L R+ N+ A Q+A +AA T L E RR RRD ++ G LG Sbjct: 254 LTRLAQNVFLAAPTPAQHAALAAFTPECRALLEARRSELGRRRDALLAGLARLGLAPSLP 313 Query: 318 PKATFYVWAPVPR-GYTSASFAEMVLEKAGVIITPGNGYG-NYGEGYFRIALTISKERMQ 375 P+ FY+W + R S +F + +LE+ V ITPG + GE + RIA T ER++ Sbjct: 314 PQGAFYLWLDISRYSRDSQAFCQRLLEEENVAITPGIDFAVTGGEYHVRIAFTTGIERLE 373 Query: 376 EAIERLRRVLGK 387 EA+ RL R L + Sbjct: 374 EAVSRLERFLAR 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: 358 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 390 Length of database: 386 Length adjustment: 30 Effective length of query: 360 Effective length of database: 356 Effective search space: 128160 Effective search space used: 128160 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