Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate PP_1588 PP_1588 N-succinyl-L,L-diaminopimelate aminotransferase alternative
Query= curated2:B1I544 (392 letters) >FitnessBrowser__Putida:PP_1588 Length = 398 Score = 192 bits (489), Expect = 1e-53 Identities = 128/398 (32%), Positives = 200/398 (50%), Gaps = 26/398 (6%) Query: 9 IRNLPPYLFARIEQLIAD-KKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYP 67 + L PY F ++ L+ K A I+L IG+P +P + +A L A YP Sbjct: 5 LTQLQPYPFEKLRALLGSVKPAADKRAIALSIGEPKHESPAFVAQAMADNLDKLA--VYP 62 Query: 68 SSAGMPAYRRAVADWYARRFGVE---LDPQREVVSLIGSKEGIAHLPWCFVDPGD--VVL 122 S+ G+PA R+A+ W RRFGV LD R ++ + G++E + V+ D +V+ Sbjct: 63 STLGLPALRQAIGQWCERRFGVPAGWLDADRHILPVNGTREALFAFTQAVVNRADDGLVI 122 Query: 123 VPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGA 182 P+P Y +Y G +LAG PH +P NGF PD A+PAE +R +++F+ P NPTGA Sbjct: 123 SPNPFYQIYEGAALLAGATPHYLPCLENNGFNPDFDAVPAEVWKRCQILFLCSPGNPTGA 182 Query: 183 VASKEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVG-------IEF 235 + +++ A E+ ++ D YSE+ FD PP L ++ E+G + F Sbjct: 183 LVPMNTLKKLIALADEHDFVIAADECYSELYFDEDAPPPGL-LSACAELGRSDFARCVVF 241 Query: 236 HSVSKTYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSL 295 HS+SK N+ G R+G+ AG+A ++ ++ + Q A+IAA + V+ Sbjct: 242 HSLSKRSNLPGLRSGFVAGDAQIIKPFLLYRTYHGCAMPVQTQLASIAAWQ-DEAHVREN 300 Query: 296 CEMYRERRDLVVDTLNDLGWRLTRPRATFYIWAPVPAGHDASSFAEMVLEKAGVVITPGT 355 + YR + D V+D L + + RP +FY+WA VP D + F + E V + PG+ Sbjct: 301 RDQYRAKYDAVLDILQPV-LDVQRPDGSFYLWAKVPG--DDAEFTRDLFEAQHVTVVPGS 357 Query: 356 GYG------TYGEGYFRISLTLPTPRLVEAMERLRGCL 387 G G R++L P +EA ER+R L Sbjct: 358 YLSREVDGVNPGAGRVRMALVAPLAECIEAAERIRAFL 395 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: 349 Number of extensions: 18 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: 398 Length adjustment: 31 Effective length of query: 361 Effective length of database: 367 Effective search space: 132487 Effective search space used: 132487 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