Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_018126051.1 B149_RS0115315 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000375485.1:WP_018126051.1 Length = 390 Score = 219 bits (558), Expect = 1e-61 Identities = 137/368 (37%), Positives = 199/368 (54%), Gaps = 16/368 (4%) Query: 19 KFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYM 78 K L AQ +++SL +GQPDF TP HV AAK A+DE T YTP G ELR+AV Y Sbjct: 21 KAQELRAQGREIVSLAVGQPDFGTPAHVVEAAKAALDEGFTRYTPVPGIPELREAVADYY 80 Query: 79 KKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPV 138 + E+ II + G Q + +++PGDEV++P P + Y +I L + V Sbjct: 81 GRFYGITAVQENAII-SNGGKQVLYNLLMALVNPGDEVLVPAPYWVSYPAMIELAEGRCV 139 Query: 139 IVDTTSHG-FKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFV 197 V T + F ++ +E A T T+ +VL PSNPTG ++++L IA VF+ Sbjct: 140 TVPTEAENDFLVSVEGLEAARTERTRVLVLNSPSNPTGCCYTQDQLDGIAQWALDNGVFI 199 Query: 198 LSDEIYSELTYDRPHYSIATYLR------DQTIVINGLSKSHSMTGWRIGFLFAPKDIAK 251 +SDE+Y L Y AT R + ++ LSKS MTGWR+G+ A +++ K Sbjct: 200 ISDEVYDRLVY--APVEPATLARFWQKHPESCALVGALSKSFCMTGWRLGWALAAEELVK 257 Query: 252 HILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKP 311 + K+ + S SS SQKA + A+ +D M+E + +R D ++ + S G KP Sbjct: 258 AMSKIQGQSTSNVSSFSQKAGVVALAGEWDIVEQMKEAFVRRRDIAHEIITSWGAPCPKP 317 Query: 312 SGAFYIFPSIKSFGMTSFDFSMA----LLEDAGVALVPGSSFSTYGEGYVRLSFACSMDT 367 GAFY+FP + +F S A +LE+AGVALVPGS+F + +R S+A DT Sbjct: 318 DGAFYLFPVLDAFYTEDAPDSAAMCNKILEEAGVALVPGSAFG--DDRCIRFSYAVDDDT 375 Query: 368 LREGLDRL 375 LR+ L R+ Sbjct: 376 LRDALTRV 383 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: 338 Number of extensions: 20 Number of successful extensions: 6 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: 390 Length adjustment: 31 Effective length of query: 362 Effective length of database: 359 Effective search space: 129958 Effective search space used: 129958 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