Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_093395028.1 BM091_RS08615 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_900114975.1:WP_093395028.1 Length = 385 Score = 219 bits (558), Expect = 1e-61 Identities = 130/376 (34%), Positives = 207/376 (55%), Gaps = 16/376 (4%) Query: 17 IRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAV-Q 75 + K L + D+I L IG+PDF TP +K A +A++ T YT + G ELR+A+ + Sbjct: 18 LEKAQELEKRGCDIIHLEIGEPDFDTPLPIKQAGIRALEAGETHYTHSLGIQELREAICR 77 Query: 76 LYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGA 135 Y + + D + +++IT+G S A A +L PGDE+I+ P YP Y G Sbjct: 78 NYEAEYGIYGLDPD-QVVITSGTSPAFLVALGAVLEPGDELIITNPCYPCYPNFARFLGI 136 Query: 136 KPVIVDT-TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRN 194 P V GF+ +++A+ P TK +++ P+NPTG L + LK +A L Sbjct: 137 IPKFVKVYEEEGFQYRIEDVKNAIGPRTKGILINSPANPTGHLLDADRLKGLAGL----G 192 Query: 195 VFVLSDEIYSELTYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHIL 254 +++ SDEIY L YD D+ V NG SK ++MTGWR+G++ PK + + Sbjct: 193 LWIFSDEIYHGLVYDGERAHSILEFTDKCFVFNGFSKKYAMTGWRLGYVIIPKPFKRTVQ 252 Query: 255 KVHQYNVSCASSISQKAALEAVTNGFDDALI-----MREQYKKRLDYVYDRLVSMGLDVV 309 + Q A++ SQ+AAL A+T DD ++ M ++Y +R ++ RL +G + Sbjct: 253 CMVQNFFISANAASQRAALVALT---DDRVVTETKKMVDEYDRRRKFMISRLKEIGFGID 309 Query: 310 -KPSGAFYIFPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTL 368 +P GAFY+F + KSFG S+ + LLE A V + PG F T GEGY+R S+A S++ + Sbjct: 310 HEPKGAFYVFANAKSFGSDSYRLAFELLEQAHVGVAPGIDFGTNGEGYLRFSYANSIEKI 369 Query: 369 REGLDRLELFVLKKRE 384 E L+R+ ++ ++++ Sbjct: 370 DEALNRIAQYLEQRKK 385 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: 18 Number of successful extensions: 5 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: 385 Length adjustment: 30 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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