Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_013461156.1 SULKU_RS11575 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::O66630 (387 letters) >NCBI__GCF_000183725.1:WP_013461156.1 Length = 408 Score = 309 bits (792), Expect = 8e-89 Identities = 162/388 (41%), Positives = 233/388 (60%), Gaps = 10/388 (2%) Query: 6 DRLKVLPPYLFAELDRKKQEKIEQGVDVIDLGVGDPDMPTPKPIVEAAKKALENPENHKY 65 DR+K LP Y+FAE++ K + G DVID +G+PD TP+ I + ++ E + H Y Sbjct: 8 DRIKRLPKYVFAEVNELKMARRRAGADVIDFSMGNPDGDTPEHIRKKLVESAEKTKTHGY 67 Query: 66 PSYVGKYEFRKAVADWYKRRFDVDLDPNTEVITLIGSKEGIAHFPLAFVNPGDIVLCPDP 125 G + R+A+ DWYKRR+DVDLDP+TE + +GSKEG AH A NPGD+V+ PDP Sbjct: 68 SVSKGIPKLRQAICDWYKRRYDVDLDPDTEAVATMGSKEGYAHLAYAITNPGDVVVVPDP 127 Query: 126 AYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAK-------KAKIIWINYPNNP 178 YP++ G I AGG + L + ++ D D E + K K + +N+P+NP Sbjct: 128 TYPIHSYGFILAGGNVQKMELPFDEDYKVDEDLFFERLEHAFHVSFPKPKYLVVNFPHNP 187 Query: 179 TSAPPTLEFYKKLVDWAKEYNVIIASDNAYSEIYTGQEKPPSILQVPGAKDVAIEFHSLS 238 T+A T EFY ++V+ AK + SD AY ++ K PSIL VPGAKDVA+E +LS Sbjct: 188 TTATVTPEFYVRVVEMAKRERFYVISDIAYGDLTFDGYKTPSILSVPGAKDVAVEAFTLS 247 Query: 239 KTYNMTGWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVY 298 K+YNM GWR+G VGN +L+ L K+K+ +D G F +Q A VAL + V++I D Y Sbjct: 248 KSYNMAGWRVGFFVGNAKLIGALQKIKSWLDYGMFTPIQVAATVALTGDQTCVQEITDKY 307 Query: 299 RERKKIMTEALEKIGLEIYRSDYTFYLWIKVPE---GYTSAEFVGRLIDEAGIVCTPGNG 355 R+ ++ +A + G I R+ + ++W K+PE S EF RL+ EA + PG G Sbjct: 308 DHRQNVLLDAFNRAGWPIRRNQASMFVWAKIPECAIHMGSLEFSKRLLVEANVAVAPGIG 367 Query: 356 FGEYGEGYFRISLTVPTERLLEAAERIK 383 FG+YG+ Y RI+L +R+ +AA+ IK Sbjct: 368 FGDYGDEYVRIALIENDQRIRQAAKNIK 395 Lambda K H 0.317 0.139 0.413 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: 458 Number of extensions: 22 Number of successful extensions: 3 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: 387 Length of database: 408 Length adjustment: 31 Effective length of query: 356 Effective length of database: 377 Effective search space: 134212 Effective search space used: 134212 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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