Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_026188837.1 RHE_RS30015 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B2A250 (386 letters) >NCBI__GCF_000092045.1:WP_026188837.1 Length = 405 Score = 337 bits (864), Expect = 4e-97 Identities = 164/385 (42%), Positives = 242/385 (62%), Gaps = 3/385 (0%) Query: 5 HRLNNLPPYLFADLDKMVQKEQAKGKEIIKLGIGDPGMKPPEGIIKAATQEMYKGENHGY 64 HR+ LPPY+F ++++ +A G +II LG+G+P + P+ I+ + + H Y Sbjct: 9 HRIQRLPPYVFEQVNRLKASARAGGADIIDLGMGNPDLPTPQSIVDKLCEVVQDPRTHRY 68 Query: 65 PAYDGIDKLKHAIKEYYQSRFGVELNPDREILTLIGSKEGIANISQAILNPGDINFIPDP 124 + GI L+ A YY RFGV+LNPD +++ +GSKEG AN++QAI PGD+ P+P Sbjct: 69 SSSKGIPGLRRAQAAYYARRFGVKLNPDTQVVATLGSKEGFANMAQAITAPGDVILCPNP 128 Query: 125 SYPVYKNGTILAGGTPHSMPLKQDNGFIPELESIPQSRLSKGKIVFMNYPNNPTSAVASK 184 +YP++ G ++AGG SM ++ D F P LE + + K + +NYP+NPT+ VA+ Sbjct: 129 TYPIHAFGFLMAGGVIRSMSVEPDESFFPPLERAVRHSIPKPLALILNYPSNPTALVATL 188 Query: 185 DFYSHAVKFCQKNKLLLCNDAAYSEIAFDDYQPQSLLSVPGAKEVAIEFNSLSKTFNMTG 244 DFY V F +K+ +++ +D AYSEI FD P S+L VPGA +V +EF S+SKTF+M G Sbjct: 189 DFYKDVVAFAKKHDIIVLSDLAYSEIYFDGAPPPSVLEVPGAMDVTVEFTSMSKTFSMPG 248 Query: 245 WRVGFVVGNEKAISALAKYKTNVDSGVFTPLQLAATHALENRHEYIPDILKAYKERRDLV 304 WR+GF VGNE+ I+AL + K+ +D G FTP+Q+AATHAL I ++ YK RRD++ Sbjct: 249 WRMGFAVGNERLIAALTRVKSYLDYGAFTPIQVAATHALNGDGSDIAEVRNVYKRRRDVM 308 Query: 305 IEFLEEAGFHVYHPKATFYVWAQVP---GNQDSFNFTKSLLTKTGVVVTPGIGFGKHGEG 361 +E +AGF V P AT + WA++P + S F+K L+ K V V PGIGFG+ G+ Sbjct: 309 VESFGKAGFDVPPPAATMFAWAKIPEKFRHLGSLEFSKLLVEKADVAVAPGIGFGEMGDD 368 Query: 362 YFRIALTVTKDRLKTAMEKICEYFS 386 Y R+AL + R++ A I + S Sbjct: 369 YVRLALVENEHRIRQAARNIKRWLS 393 Lambda K H 0.317 0.136 0.402 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: 482 Number of extensions: 18 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: 386 Length of database: 405 Length adjustment: 31 Effective length of query: 355 Effective length of database: 374 Effective search space: 132770 Effective search space used: 132770 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