Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_012169089.1 AZC_RS02835 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000010525.1:WP_012169089.1 Length = 394 Score = 220 bits (560), Expect = 6e-62 Identities = 132/376 (35%), Positives = 208/376 (55%), Gaps = 8/376 (2%) Query: 17 IRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQL 76 + + + L AQ D+I+L IGQPDF TP H+ AA KA+ + YTP+ G LR+AV Sbjct: 20 LARATTLAAQGRDIINLGIGQPDFRTPEHIVEAAVKALKDGQHGYTPSVGIQPLREAVAR 79 Query: 77 YMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAK 136 + K+ D D ++I G + AA PG E++ P P +P Y +I GA Sbjct: 80 DLHKRFDVEVD-PGLVMIMPGGKVTMYAAILLFGEPGAEILYPDPGFPIYRSMIEYTGAT 138 Query: 137 PVIVD-TTSHGFKLTARLIEDALTPNTKCVVLPYPSNPT-GVTLSEEELKSIAALLKGRN 194 P+ V +GF +A +TP T+ +++ P+NPT GVT E K + L + Sbjct: 139 PIPVPIREENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPKAEIDKLVKGLADHPH 198 Query: 195 VFVLSDEIYSELTYD-RPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAK 251 V ++SDEIY + +D H ++ Y +RD+ I++NG SK+++MTGWR+G+ P+ + Sbjct: 199 VALMSDEIYDQFLFDGERHQTLLAYPEIRDRLILLNGWSKTYAMTGWRLGYSIWPQALYD 258 Query: 252 HILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVK 310 + K+ SC ++ +Q A + A+ + M ++ KR V + L ++ G+ K Sbjct: 259 KVRKLSVNAWSCVNAATQYAGIAALEGPQEPVAAMLAEFDKRRRLVVEGLNALPGVTCAK 318 Query: 311 PSGAFYIFPSIKSFGMTSFD-FSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLR 369 P GAFY FP++ G TS + ALLEDAGVA + G F +GEGY+RLS+A S + + Sbjct: 319 PKGAFYAFPNVSRTGWTSAKALASALLEDAGVATIGGPDFGVHGEGYIRLSYANSAENIA 378 Query: 370 EGLDRLELFVLKKREA 385 L+R+ F+ +++ A Sbjct: 379 RALERMGAFLSERKVA 394 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: 392 Number of extensions: 16 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: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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