Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_012281785.1 HM1_RS02935 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000019165.1:WP_012281785.1 Length = 397 Score = 182 bits (463), Expect = 1e-50 Identities = 117/376 (31%), Positives = 189/376 (50%), Gaps = 16/376 (4%) Query: 28 KAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAVADWYARRF 87 +++GVDVI G G+PD TPDH+ +AA ++ P+S G ++A+ D Sbjct: 26 RSEGVDVIGFGAGEPDFDTPDHVKQAAIAAIEAGFTKYTPAS-GTLELKQAICDKLKAEN 84 Query: 88 GVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPVPL 147 GV+ P +VS G+K + + +PGD V++P P + Y L +P V Sbjct: 85 GVDYAPANIIVSN-GAKHSLVNAFEAICNPGDEVIIPAPYWVSYPEMVKLVDAVPVFVYT 143 Query: 148 TAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVDFAREYGILVCHDA 207 T + F + I + K + +N P+NPTG V SKE A + D A EYGI V D Sbjct: 144 TEESRFKFTVEQIKQALTSKTKALVLNSPSNPTGMVYSKEELAEIADLAVEYGIFVISDE 203 Query: 208 AYSEIAFDGYRPPSFLEVAG-AREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLK 266 Y ++ +D + S + +E I + VSK Y+MTGWR G+ A NA + + ++ Sbjct: 204 IYEKLIYDDFEHVSIASINDKIKEQTIIVNGVSKAYSMTGWRIGYTASNAPIAKIMANIQ 263 Query: 267 SNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRLTRPRATFY 325 S+ S + Q AA+AA+ GPQD V ++ + RRD +V+ +N + G +P FY Sbjct: 264 SHATSNPNSIAQKAALAAITGPQDIVGTMVGEFVRRRDYMVERINAIPGLSCLKPNGAFY 323 Query: 326 IWAPVP-------AG---HDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPR 375 + + AG + + FA+++LE+A V + PG+G+G + + R+S Sbjct: 324 VMMNISKIIGSTFAGRRINGSDDFADLLLEQAQVALVPGSGFGI--DTHVRLSYATSMEN 381 Query: 376 LVEAMERLRGCLGRVT 391 + E + R+ L +T Sbjct: 382 ITEGLNRIENFLLSLT 397 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: 289 Number of extensions: 14 Number of successful extensions: 3 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: 397 Length adjustment: 31 Effective length of query: 361 Effective length of database: 366 Effective search space: 132126 Effective search space used: 132126 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