Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_010531968.1 ON01_RS15370 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000224785.1:WP_010531968.1 Length = 395 Score = 357 bits (917), Expect = e-103 Identities = 166/387 (42%), Positives = 243/387 (62%), Gaps = 1/387 (0%) Query: 2 SFVEAKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIP 61 +F ++ ++ LP FA++ + K QG DVI+LG G+PD+PTPDHII+ ++ K P Sbjct: 4 NFEQSDMLKRLPEQFFAKLVGRTQEFKQQGHDVINLGQGNPDLPTPDHIIQEVQEAAKNP 63 Query: 62 ANHQYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVV 121 ANH+Y G ++ A A++Y R +GV LDP+ E+ L G K G+ + C ++P D Sbjct: 64 ANHKYAPFRGFHYFKEAAANYYKREYGVSLDPETEIAVLFGGKAGLVEISQCLLNPNDTA 123 Query: 122 LVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTG 181 L+PDPGYP Y G +A P+ +PL N FLPD + IP ET +AK+MF+NYPNNPT Sbjct: 124 LLPDPGYPDYMSGIAMADADPYFMPLQKDNHFLPDYSTIPGETLNQAKLMFLNYPNNPTA 183 Query: 182 AVASKEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKT 241 A+K+F+ V A+++ I V D AY + FDG +P SFL+ GA+++GIE +++SKT Sbjct: 184 VTANKDFYDETVKLAKDHHICVVQDFAYGALGFDGQKPQSFLQSEGAKDIGIEIYTLSKT 243 Query: 242 YNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRE 301 YNM GWR +AAGN +EAL +++ ++ +F +Q AA ALN Q VQ L + Y E Sbjct: 244 YNMAGWRVAFAAGNPSVIEALNKIQDHMYVSLFGAIQSAAAKALNSDQSAVQRLIDTYTE 303 Query: 302 RRDLVVDTLNDLGWRLTRPRATFYIWAPVPAGHDASSFAEMVLEKAGVVITPGTGYGTYG 361 RRD + + ++GW + P +F+ W PVP+ + + F+ ++LE A VV+ PG G+G YG Sbjct: 304 RRDRFIRAIREIGWDVDTPEGSFFAWLPVPSNYTSEEFSNLLLENAHVVVAPGRGFGKYG 363 Query: 362 EGYFRISLTLPTPRLVEAMERLRGCLG 388 +GY R+ L RL EA R+ G LG Sbjct: 364 DGYVRVGLLESAERLEEAAARI-GRLG 389 Lambda K H 0.321 0.139 0.430 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: 360 Number of extensions: 12 Number of successful extensions: 1 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: 392 Length of database: 395 Length adjustment: 31 Effective length of query: 361 Effective length of database: 364 Effective search space: 131404 Effective search space used: 131404 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 Jul 26 2024. The underlying query database was built on Jul 25 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