Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_012283547.1 HM1_RS11430 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000019165.1:WP_012283547.1 Length = 395 Score = 195 bits (495), Expect = 2e-54 Identities = 118/382 (30%), Positives = 189/382 (49%), Gaps = 7/382 (1%) Query: 9 IRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPS 68 I NLPP R L+A+ K VISLG+G+PD TP H+ E+ L+ Y S Sbjct: 13 ILNLPPSGIRRFFDLVANTKG----VISLGVGEPDFVTPWHVRESCFYALE-RGYTMYTS 67 Query: 69 SAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGY 128 + G P R+ + + R +GV+ DP EV+ +G+ E + + PGD VLVP+P Y Sbjct: 68 NFGTPELRKEITRFIQRSYGVDYDPLSEVLVTVGASEAVDLAMRMLLCPGDEVLVPEPSY 127 Query: 129 PVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEF 188 Y+ +AGG+ VP + F + A+ + + R K++ + YPNNPTGA+ ++ Sbjct: 128 VSYSPTVTMAGGVAVAVPTYVKDDFQLTVEALEKKVSPRTKMLVLCYPNNPTGAIMTRPE 187 Query: 189 FARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWR 248 + FA E ++V D Y+E+ ++ + F + G R+ + + +SK++ MTGWR Sbjct: 188 LEAIARFAEERDLIVLADEIYAELTYE-EQHVCFAGLPGMRDRTVLINGLSKSHAMTGWR 246 Query: 249 AGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVD 308 G+ GN + + ++ + Q AA+ AL + Y +RR VV Sbjct: 247 IGYVCGNKDFIAQMTKIHQYTILCAPIMGQMAALEALRNGDLEKSRMVNQYDQRRRFVVA 306 Query: 309 TLNDLGWRLTRPRATFYIWAPVPA-GHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRI 367 N +G PR FY + + A G + F E +L + V + PGT +G GEG+ R+ Sbjct: 307 RFNQMGLTCFNPRGAFYAFPSITATGLSSDDFCEQLLAEEKVAVVPGTAFGASGEGFIRV 366 Query: 368 SLTLPTPRLVEAMERLRGCLGR 389 S L A++R+ + R Sbjct: 367 SYASSMANLTTALDRIEAFVQR 388 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: 297 Number of extensions: 15 Number of successful extensions: 4 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 Apr 09 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