Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_020174095.1 A3OQ_RS0104145 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000385335.1:WP_020174095.1 Length = 400 Score = 216 bits (549), Expect = 1e-60 Identities = 140/378 (37%), Positives = 214/378 (56%), Gaps = 20/378 (5%) Query: 18 RKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLY 77 +K +L A D+ISL++G+PDF TP ++K AA AI+ T YTP AG LR+A+ Sbjct: 21 QKARDLRAAGRDIISLSVGEPDFDTPDNIKKAAIAAIERGDTKYTPVAGIQPLREAIAQK 80 Query: 78 MKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKP 137 K++ +Y S+ I+ TG + AF ++PGDEVI+P P + Y ++ + G P Sbjct: 81 FKRENGLDY-KPSQTIVGTGGKHILFNAFLATVNPGDEVIIPAPYWVSYPDMVAIAGGVP 139 Query: 138 VIVDT-TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNV 195 VIV T H FKL A ++ A+TP TK ++L PSNP+G + +LK++ LL+ +V Sbjct: 140 VIVPTKMEHEFKLQAEDLDRAITPKTKWLLLNSPSNPSGAAYTRAQLKALTDVLLRHPHV 199 Query: 196 FVLSDEIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAK 251 +VL+D+IY LTY ++ + L D+T+ +NG+SKS++MTGWRIG+ P + K Sbjct: 200 WVLTDDIYEHLTYGDFTFTTPAQVEPALIDRTLTMNGVSKSYAMTGWRIGYAAGPDVLIK 259 Query: 252 HILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVK 310 + + S A SI+Q A++EA+T D R+ ++ R D V L + L Sbjct: 260 AMDMLQGQQTSGACSIAQWASVEALTGPQDFIAERRKIFESRRDLVVSMLNQAKYLKCPS 319 Query: 311 PSGAFYIFPS-IKSFG---------MTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLS 360 P GAFY++PS ++ G + DF ALLE GVA+V GS+F G + R+S Sbjct: 320 PEGAFYVYPSCAEAIGKKTPDGKVIASDEDFVSALLEMEGVAVVQGSAFG-LGPNF-RIS 377 Query: 361 FACSMDTLREGLDRLELF 378 +A S L + +++ F Sbjct: 378 YATSTSVLEDACTKIQRF 395 Lambda K H 0.319 0.135 0.388 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: 21 Number of successful extensions: 7 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: 393 Length of database: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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