Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_084056111.1 B9A12_RS02895 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_900176285.1:WP_084056111.1 Length = 398 Score = 246 bits (629), Expect = 6e-70 Identities = 140/374 (37%), Positives = 221/374 (59%), Gaps = 19/374 (5%) Query: 19 KFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYM 78 K L AQ + VIS +G+PDF TPHH+ AA +A+ T YT G EL++A+ + Sbjct: 21 KAKALRAQGKKVISFGVGEPDFDTPHHIGQAAIQAVQRGQTRYTAVQGIPELKEAIIDVV 80 Query: 79 KKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPV 138 + +Y E E++++ G ++ F+ +L PGD+VI+P P + Y ++ L GA+PV Sbjct: 81 RADYGLDYSPE-EVLVSCGGKHSLYNLFQAVLDPGDQVIIPAPYWVSYPDMVRLAGAEPV 139 Query: 139 IVDTT-SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNVF 196 IVD S FKL + + +A+T T+ ++L PSNPTGV + EEL+ +A LL V Sbjct: 140 IVDCPMSTSFKLEPQALREAITERTRMLILNSPSNPTGVHYTPEELRGLAQVLLDHEQVV 199 Query: 197 VLSDEIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKH 252 ++SD+IY L Y ++ + L+D+T ++NG+SK+++MTGWRIG+L D+ K Sbjct: 200 IVSDDIYYRLLYKGAQWANMAMVEPRLKDRTFIVNGVSKTYAMTGWRIGYLLGDADVIKA 259 Query: 253 ILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKP 311 K+ + S S++Q AA+ A+ +D MR+ + +R +YV +RL + G+ P Sbjct: 260 AGKIQSQSTSNPCSVAQWAAVAALRGSQEDVQTMRQAFARRREYVMERLGRLPGVTCPDP 319 Query: 312 SGAFYIFPSIKSFG---------MTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFA 362 +GAFY+FP++ ++ S D S L+E+A +A+VPG++F + +RLSFA Sbjct: 320 NGAFYVFPNVSAYYGKKAGERSIQGSLDLSDYLMEEAHLAVVPGAAFGE--DRCIRLSFA 377 Query: 363 CSMDTLREGLDRLE 376 SM+ L EG DRLE Sbjct: 378 LSMEELEEGFDRLE 391 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: 358 Number of extensions: 25 Number of successful extensions: 8 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: 398 Length adjustment: 31 Effective length of query: 362 Effective length of database: 367 Effective search space: 132854 Effective search space used: 132854 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