Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_044136428.1 TERY_RS04760 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B8CX89 (389 letters) >NCBI__GCF_000014265.1:WP_044136428.1 Length = 394 Score = 398 bits (1022), Expect = e-115 Identities = 176/386 (45%), Positives = 262/386 (67%) Query: 4 ADRIKNLPPYLFAEIDKMIARAKKEGVDVISFGIGDPDQPTPDNIINKMIEAVKDPSTHS 63 A R++ LPPY+FA +D++ ARA+++G+D+I G+G+PD TP ++ I A++D + H Sbjct: 9 AKRVQALPPYVFARLDELKARAREQGLDLIDLGMGNPDGATPKPVVEAAIAALQDSTNHG 68 Query: 64 YPSYEGMYEYRKTVADWYKNNYGRELDPDKEVVSLIGSKEGIAHLPFCYINPGDIALVPD 123 YP +EG +RK + DWY Y +LDPD E + L+GSKEG+ HL YINPG++ L P+ Sbjct: 69 YPPFEGTASFRKAITDWYFRRYSVKLDPDGEALPLLGSKEGLTHLALAYINPGNLVLAPN 128 Query: 124 PGYPVYKTSVLLAGGKPVQVPLVEENNFLPDLKAIDEDIARKAKLFFINYPNNPTGAIAP 183 P YP + L+AGGK + L EN+++ DL I + +A +AK+F+ NYP+NPTGA AP Sbjct: 129 PAYPAHFRGPLIAGGKVHSILLKPENDWIIDLADIPDSVAEQAKVFYFNYPSNPTGATAP 188 Query: 184 EEFYEELIDFADKYDIIIAHDAAYSEIGLDGYNPPSFMQFEGAKKVGIEFNSLSKPFNMT 243 EF+++++ FA KY+I++ HD Y+E+ DGY P S +Q G K +G+EF+++SK +NM Sbjct: 189 REFFQDIVTFAKKYEILLVHDLCYAELAFDGYQPTSLLQIPGGKDIGVEFHTMSKTYNMA 248 Query: 244 GWRVGWAVGRSDVIESLGRIKTNIDSGIFEAIQYAGIEALTGPEDNIEKMTELYSKRRDL 303 GWR+G+ VG S+VI+ L +KTN+D G+F A+Q A AL P++ + ++ E Y +RRD Sbjct: 249 GWRIGFVVGNSNVIQGLRTLKTNMDYGVFSALQLAAKTALQLPDEYLSQVQERYRQRRDF 308 Query: 304 LVEGLRELGWEVPVNKATFYIWAKVPEGYNSTEFSTHVFEKTGIFFTPGNGYGEFGEGYV 363 L++GL +LGW V AT Y+W P G ST+F+ V +KTG+ TPGN +G GEGYV Sbjct: 309 LIQGLGKLGWNVQKTMATMYLWVPCPPGIGSTDFALSVLQKTGVVVTPGNAFGSGGEGYV 368 Query: 364 RIALTVTEERIKEALERLKNSDIKFK 389 RI+L +R+ EAL R K + I ++ Sbjct: 369 RISLIAECKRLDEALNRFKKAGIYYQ 394 Lambda K H 0.316 0.139 0.414 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: 524 Number of extensions: 21 Number of successful extensions: 1 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: 389 Length of database: 394 Length adjustment: 31 Effective length of query: 358 Effective length of database: 363 Effective search space: 129954 Effective search space used: 129954 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