spacer

Tempura webservice results format

The table below shows examples of the various line types output from the Tempura webservice. The output is designed to be parsable and the notation involving numbers in square brackets refers to three levels of organisation:
  • First layer = certainty class*
  • Second layer = rank within certainty class
  • Third layer = rank within second layer
* Certainty classes are defined as:
[1] = "certain"
[2] = "probable"
[3] = "possible"
[4] = "long shot"

As an example, SITE_RESIDUE_NAME[1][2][3] = the residue name for the third residue[3] of the second match [2] within the "certain" hits[1].

Table of results from the Tempura webservice

Line from results:   Explanation:   In this example:  
     
SITE_NTEMPLATES 75 = Total number of templates75
SITE_NSIGNIF_HITS 489 = Number of hits489
SITE_NSHOWN 13 = Number of top hits shown13
SITE_NHITS[1] 1 = Number of "certain" matches [1]1
SITE_NHITS[2] 2 = Number of "probable" matches [2]2
SITE_NHITS[3] 0 = Number of "possible" matches [3]0
SITE_NHITS[4] 10 = Number of "long shot" matches [4]10
SITE_TEMPLATE_REF[1][1] TMP00290= NOT RELEVANT
SITE_HIT_NUMBER[1][1] 1 = 1st hit of certain matches [1][1]1
SITE_HIT_REF[1][1] 10_1090 = NOT RELEVANT
SITE_QUERY_SEQLEN[1][1] 294 = Query sequence length294
SITE_TARGET_SEQLEN[1][1] 294 = Target/Hit sequence length294
SITE_NIDENTICAL[1][1] 294 = Number of identical residues294
SITE_PERCENT_ID[1][1] 100.00 = % sequence identity100.00
SITE_NOVERLAP[1][1] 294 = Number residues overlapping294
SITE_STRUCT_SIMILARITY[1][1] 99.7 = % structural similarity99.7
SITE_LONGEST_FIT[1][1] 293 = Longest fit-able region293
SITE_NFIT_RES[1][1] 293 = Number of fit-able residues293
SITE_FIT_RMSD[1][1] 0.00 = R.m.s.d. of superposition0.00
SITE_PDB_CODE[1][1] 3b2m = PDB code of hit3b2m
SITE_CHAIN[1][1] A = Hit chain identifierA
SITE_QUERY_CHAIN[1][1] A = Query chain identifierA
SITE_NMATCHES[1][1] 43 = Number of matches to hit PDB code43
SITE_PROTEIN_NAME[1][1] Major pilin = Hit Protein NameMajor pilin
SITE_HIT_RMSD[1][1] 0.00 = Hit template match r.m.s.d.0.00
SITE_NRMSD_ATOMS[1][1] 19 = Number of atoms used in r.m.s.d.19
SITE_SCORE[1][1] 840.00 = ProFunc score for template match840.00
SITE_EVALUE[1][1] 0.00E+00 = E-value for template match0.00E+00
SITE_NIDENT[1][1] 43 = No of identical residues43
SITE_NSIMIL[1][1] 0 = No of similar residues0
SITE_PATH_LEN[1][1] 43 = NOT RELEVANT
SITE_ZONE_PERCENT[1][1] 100.00 = Local % sequence identity100.00
SITE_NALIGN_GIFS[1][1] 1 = NOT RELEVANT
SITE_RESIDUE_NAME[1][1][1] Lys36(A) = Hit residue 1 [1][1][1]Lys36(A)
SITE_RES_NAME[1][1][1] LYS = Hit residue 1 - nameLYS
SITE_RES_NUM[1][1][1] 36 = Hit residue 1 - number36
SITE_RES_CHAIN[1][1][1] A = Hit residue 1 - chainA
SITE_RES_CONSERV[1][1][1] 1.000 = Hit residue 1 - conservation score1.000
SITE_RESIDUE_NAME[1][1][2] Phe52(A) = Hit residue 2 [1][1][2]Phe52(A)
SITE_RES_NAME[1][1][2] PHE = Hit residue 2 - namePHE
SITE_RES_NUM[1][1][2] 52 = Hit residue 2 - number52
SITE_RES_CHAIN[1][1][2] A = Hit residue 2 - chainA
SITE_RES_CONSERV[1][1][2] 1.000 = Hit residue 2 - conservation score1.000
SITE_RESIDUE_NAME[1][1][3] Thr53(A) = Hit residue 3 [1][1][3]Thr53(A)
SITE_RES_NAME[1][1][3] THR = Hit residue 3 - nameTHR
SITE_RES_NUM[1][1][3] 53 = Hit residue 3 - number53
SITE_RES_CHAIN[1][1][3] A = Hit residue 3 - chainA
SITE_RES_CONSERV[1][1][3] 1.000 = Hit residue 3 - conservation score1.000
SITE_NRESID[1][1] 3 = Number of hit residues3
SITE_TEMP_RESIDUE_NAME[1][1][1] Lys36(A) = Template residue 1 [1][1][1]Lys36(A)
SITE_TEMP_RESIDUE_NAME[1][1][2] Phe52(A) = Template residue 2 [1][1][2]Phe52(A)
SITE_TEMP_RESIDUE_NAME[1][1][3] Thr53(A) = Template residue 3 [1][1][3]Thr53(A)
SITE_NTEMP_RESID[1][1] 3 = Number of template residues3
spacer
spacer