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I-TASSER-MTD Results for job ITM118

[Click on ITM118_results.tar.bz2 to download the tarball file including all results listed on this page]



Query Sequence and Predicted Domain Definition

>example (230 residues)
MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV
  • domain 1: 1-66
  • domain 2: 67-141
  • domain 3: 142-230
  • 3 domains in total. Different colors represent different domains. The domain definition is used for the domain structure modeling, see the domain boundary prediction part for details.

    Final Full-length Models Predicted by I-TASSER-MTD

    Top 5 models constructed by I-TASSER-MTD

    Click
    to view
    eTM-score eRMSD(Å) P-score PDB file
    Model 1 0.92+-0.08 2.8+-0.7 0.25 Download model
    Model 2 0.78+-0.11 4.2+-1.2 0.24 Download model
    Model 3 0.74+-0.15 4.8+-1.1 0.20 Download model
    Model 4 0.72+-0.14 5.0+-1.4 0.19 Download model
    Model 5 0.70+-0.16 5.3+-1.6 0.12 Download model

    Probabilties of inter-domain interactions
        domain1-domain2: 1.00; domain1-domain3: 0.17; domain2-domain3: 0.85;


    (a)Colored by domain: domain 1 in red; domain 2 in blue; domain 3 in green.
    (b)For each target, I-TASSER-MTD generates an ensemble of structural conformations by starting from a set of initial models generated by different templates. The server reports up to five final models sorted by the energy. The accuracy of each model is quantitatively evaluated by estimated TM-score (eTM-score) and estimated RMSD (eRMSD) that are calculated based on the significance of the structural analogous templates for domain models assembly, convergence parameters of the domain assembly simulations, satisfaction degrees of the inter-domain distances/interfaces, and the estimated accuracy of the individual domain model. eTM-score is typically in the range of [0,1], where an eTM-score of higher value signifies a model with a high confidence and vice-versa.
    (d)Since the top 5 models are ranked by the energy or cluster size, it is possible that the lower-rank models have a higher eTM-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests.
    More about eTM-score
    (e)P-score is used to estimate the population formed in the modeling simulations based on the structural similarity or SPICKER clustering. P-score ranges from 0 to 1, and a higher value means the structure occurs more often in the simulation trajectory.
    (f)The inter-domain interaction is defined as ≥1 residue pairs with distance <8Å apart from the linker region. The probability ranges from 0 to 1, and a large value indicates the two domains have a large probability of interaction.

    Predicted Individual Domain Structures

    Structure of domain 1
    Download dom1.pdb
    eTM-score=0.76

    Estimated distance error of domain 1 Download distance error of domain 1

    Click to view the predicted function

    Structure of domain 2
    Download dom2.pdb
    eTM-score=0.77

    Estimated distance error of domain 2 Download distance error of domain 2

    Click to view the predicted function

    Structure of domain 3
    Download dom3.pdb
    eTM-score=0.7

    Estimated distance error of domain 3 Download distance error of domain 3

    Click to view the predicted function

     

    Predicted Secondary Structure

    1                 20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 
    |                  |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   
    Sequence MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV
     
    Prediction CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCSSSCCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCSSSSSSSSSCCCCCCCHHHHHHHHHHCCCCCCSSSSSSSCCCCSSSSSSCCSSSSCCHHHHCCCSSSSC
     
    Conf.Score 97567689999999999996189866999999979993799999999999197898179726458889999999999999779999998499989999999998636989999999998379887999997897333666676543221211044348994289999994112357999999999909999829999995699749999699389848888412047759
     
    H: Helix; S: Strand; C: Coil

    Predicted Solvent Accessibility

    1                 20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 
    |                  |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   
    Sequence MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV
     
    Conf.Score 87524643130020003026675413143006317144210140043036431022254330202640351044004202002410341060436302620240111326500510261173054044342025364324245443334222303404644402000210253265244004203726031424030343574311021466541502460054020558
     
    Values range from 0 (buried residue) to 8 (highly exposed residue)

    Information for Domain Boundary Detection

    Predicted domain boundary on contact map FU-score curve of continuous domain FU-score heatmap of discontinuous domain    Predicted domain(s)   
    Contact map
    Download contact map
    Contact map
    Download the FU-score (continuous)
    Contact map
    Download the FU-score (discontinuous)

    Modelinga
    Domain 1(D1): 1-66
    Domain 2(D2): 67-141
    Domain 3(D3): 142-230
    Without linkerb
    Domain 1(D1): 1-64
    Domain 2(D2): 73-141
    Domain 3(D3): 151-230

    (a) Domain definition for the domain structure modeling. (b) Domain definition without including the linker.

    Top 10 Full-length Templates for Domain Assembly

     Rank  Template  SeqId  TplScore  1                 20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 
    |                  |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   
    QueryMNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV 
    14o6jA0.290.76-----VTEEDYLKIIQELVLYKGYATLADISRSLNVKRQSVRDEINHLISLSMAEK----------SGDREANRFLRKHRTAEILLSRCIGIPWERVDEEAMGIE-HGM--T-EEIIQRTEGVDRCPHGNP--------------PV--ADVRITSL-L-PDSTARISRIVYE-T--DDILHFLALNGLIPGKDIKIESVK-DTVRVLV-DGRSIEIPTD----------
    26o5cA0.270.76----TPNKEDYLKCIYEIGEQEPKITNKMVAEKMHVSAPAVSEMIKKMISQGWIVK----------KGYALVANLYRKHRLIEVFLIHQLGYNTQEVHQEAEVLEHTVSDTFIDRLDKILDFPDFCPHGGT--------------EM--NTTTLNTITE-L-GRFRLSRIHD--H-FD-LIQYLETHHLNINTELTLTIDTFKTYTICY-GDKELVIPEN----------
    35cviB0.270.72-----PNKEDYLKIIYELSERDEKISNKQIAEK-SVSAPAVSE-VKKLLLEDLVLK----------KKQILASSLYRKHRLIEVFL-NHLNYTADEIHEEAEVLEHTVSDVFVERLDKFLNYPKVCPHGGT--------------ER--YRTTLKGVTE---GVYLLKRVQDN-F--Q-LLKY-EQHHLKIGDELRLLYDAFGAYTIEK-DGEQLQVTSA----------
    46ndlA0.190.54----SKYSQDVLQLLYKNK--PNYISGQSIAESLNISRTAVKKVIDQLKLEGCKID-----------AFSMISKFNLFIALGIRDAIQ-HFSQFLERLLQEIEKRYNQLFSEIREEYIAASNI------------------GRF-RH-----KWPND---WNRTLLFTEN-------------------DKQFKGQAIDLDYGYLIVRDEAGESHRL-I-----------
    53rirA0.190.53----SKYSQDVLQLLYKNK--PNYISGQSIAESLNISRTAVKKVIDQLKLEGCKID-----------AFSMISKFNLFIALGIRDAIQ-HFSQFLERLLQEIEKRYNQLFSEIREEYNAASNI------------------GRF-RH-----KWPND---WNRTLLFTEN-------------------DKQFKGQAIDLDYDYLIVRDEAGESHRL-I-----------
    62ewnA0.210.51---DNTVPLKLIALLANGE----FHSGEQLGETLGMSRAAINKHIQTLRDWGVDVF----------QGPAAAIGLSLVIGIVMAEVLRKLGILLAAMLIRELRAALELELAPYLSRWEKL-DNF-----------------NDLY-LQDRK-----------INRPV-KL-I--I-GD--KE-I----F---G-ISRGIDKQGALLLEQ-DGIIKPWM-G----------
    73qphA0.240.50KEILTYWTLLVYGPSTAKE-----IST-KSGIPY-NR--VY-DTISSLKLRGFVTE--------------------------EVIGMTVVKSIIFSQYSLIIEIFKESTLEK-EI-IG--DIRFFA---MF----------NTVNF-NPK--HAVDFVKNLKRNIYAE-I-T----GKNLGRLET---LT--G-RVVGYTLSVNNIHLETENGVVKVGGM----------
    84gygA0.260.48TMRLTAEDWRVLTAVEMGSKNHEIVPTPLIEKI------GVHKSIATLAKAGLIAR----------WMYLSRLAAIKEFAFMKALYEEGF---------EPAVMS---FNIDFPQ-MV-SMLDAAL--ASG---------------------KL------------DRAH-LTGGLDLALHTH-ADVYS---VGSRIGV-GKESDIMIVAKQKVLKIHRL----------
    96k8nA0.290.48VSSAGRVQSPTLVQVVNSEIERSRYTKVSLLKWMSNTEATRGRIIEILVKRKYLTN----------ELCKYHYEAKVRLLDAVEIWKERTKYDHKKILKRISSSTGK--------------------M-------------TKSDILS----GLISFPTNSQKIPSIYNKGEN-SSYRKLVDLVRKITGG-KYVVKQAI--KILIRFSVSADNWIYH-------------
    104xgcC0.290.47HTALPPDLSVVYKLHLECGR---MINLFDWLQAFRVIQARFTRAVAELQFLGYIKM----------RDLLHFLLFRCSLEFLTELVGDLPRC--GKLRRELYVNCLAII---------KVNALERT---QF----------FHFFGG--NAFAL-CTDYSKLGKLTMETRLP--SFRP-YVEI-CRIAVLTDD----------------DYLKKKQLLCP----------
    (a)All the residues are colored in black; however, those residues in template which are identical to the residue in the query sequence are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade. (more about the colors used) 
    (b)Rank of templates represents the top five structural aligenment templates identified by using TM-align.
    (c)SeqId is the ratio between the number of identical residues and query length.
    (d)TplScore is the score of the template calculated based on harmonic mean of TM-scores between all domain models and the template.

    Predicted Distance/Interface Map for Domain Assembly

    CA distance map with distance < 20Å CB distance map with distance < 20Å CA interface map with distance < 18Å CB interface map with distance < 18Å
    CA20
    Download CA distance map
    CB20
    Download CB distance map
    cnt_CA
    Download CA interface map
    cnt_CB
    Download CB interface map

    Proteins Structurally Close to the Query Protein

    Top 10 structural analogs in PDB (as identified by TM-align)

    Click
    to view
    RankPDB
    Hit
    TM-scoreRMSDaIDENaCov.Download
    Alignment
    11c0wB0.891.590.5890.952model1_1c0wB.pdb.gz
    23hrsA0.772.860.2410.922model1_3hrsA.pdb.gz
    37b1vA0.773.100.6190.926model1_7b1vA.pdb.gz
    41fx7A0.763.210.7780.930model1_1fx7A.pdb.gz
    56o5cA0.723.300.2440.887model1_6o5cA.pdb.gz
    65zr4A0.721.960.2910.791model1_5zr4A.pdb.gz
    74o6jA0.723.310.2710.909model1_4o6jA.pdb.gz
    85cviA0.703.320.2380.878model1_5cviA.pdb.gz
    92f5cA0.481.930.2210.517model1_2f5cA.pdb.gz
    102x4hA0.482.390.2520.552model1_2x4hA.pdb.gz

    (a)Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
    (b)Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
    (c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
    (d)IDENa is the percentage sequence identity in the structurally aligned region.
    (e)Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

    Predicted Gene Ontology (GO) Terms


    GOsearchresult_final_MF.svg
    Molecular Function (MF)
    GO termCscoreGOName
    GO:19013630.89heterocyclic compound binding
    GO:00971590.89organic cyclic compound binding
    GO:00037000.86transcription factor activity, sequence-specific DNA binding
    GO:00036770.86DNA binding
    GO:00469830.84protein dimerization activity

    Download full result of the above consensus prediction.

    Click the graph to show a high resolution version.
    (a)CscoreGO is the confidence score of predicted GO terms. CscoreGO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.
    (b)The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by CscoreGO:
    [0.4,0.5)[0.5,0.6)[0.6,0.7)[0.7,0.8)[0.8,0.9)[0.9,1.0]

    GOsearchresult_final_BP.svg
    Biological Process (BP)
    GO termCscoreGOName
    GO:00081520.83metabolic process
    GO:00508960.81response to stimulus
    GO:00099870.81cellular process
    GO:00442370.80cellular metabolic process
    GO:00717040.77organic substance metabolic process
    GO:00090580.73biosynthetic process
    GO:00442490.72cellular biosynthetic process
    GO:00068070.72nitrogen compound metabolic process
    GO:00100430.70response to zinc ion
    GO:19015760.69organic substance biosynthetic process
    GO:00346410.64cellular nitrogen compound metabolic process
    GO:19013600.63organic cyclic compound metabolic process
    GO:00067250.63cellular aromatic compound metabolic process
    GO:00442710.60cellular nitrogen compound biosynthetic process
    GO:00446990.55single-organism process
    GO:00442380.55primary metabolic process

    Download full result of the above consensus prediction.

    Click the graph to show a high resolution version.
    (a)CscoreGO is the confidence score of predicted GO terms. CscoreGO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.
    (b)The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by CscoreGO:
    [0.4,0.5)[0.5,0.6)[0.6,0.7)[0.7,0.8)[0.8,0.9)[0.9,1.0]

    GOsearchresult_final_CC.svg
    Cellular Component (CC)
    GO termCscoreGOName
    GO:00444241.00intracellular part
    GO:00058860.93plasma membrane
    GO:00057370.87cytoplasm

    Download full result of the above consensus prediction.

    Click the graph to show a high resolution version.
    (a)CscoreGO is the confidence score of predicted GO terms. CscoreGO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.
    (b)The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by CscoreGO:
    [0.4,0.5)[0.5,0.6)[0.6,0.7)[0.7,0.8)[0.8,0.9)[0.9,1.0]


    Predicted Enzyme Commission (EC) Numbers

    Top 5 enzyme homologs in PDB

    Click
    to view
    RankCscoreECPDB
    Hit
    TM-scoreRMSDaIDENaCov.EC NumberPredicted Active Site Residues
    10.0601fxxA0.4115.680.1000.6743.1.11.1 9,79
    20.0602a1sC0.2756.520.0290.5303.1.13.4 NA
    30.0601mdwA0.3166.260.0430.5743.4.22.53 NA
    40.0602qxfA0.4145.680.0170.7133.1.11.1 NA
    50.0601mioD0.4096.110.0550.7261.18.6.1 NA

     Click on the radio buttons to visualize predicted active site residues.
    (a)CscoreEC is the confidence score for the Enzyme Commission (EC) number prediction. CscoreEC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
    (b)TM-score is a measure of global structural similarity between query and template protein.
    (c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
    (d)IDENa is the percentage sequence identity in the structurally aligned region.
    (e)Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

    Predicted Ligand Binding Sites

    Template proteins with similar binding site

    Click
    to view
    RankCscoreLBPDB
    Hit
    TM-scoreRMSDaIDENaCov.BS-scoreLig. NameDownload
    Complex
    Predicted binding site residues
    10.371c0wD0.7411.030.6970.7611.91QNAcomplex1.pdb.gz7,36,37,39,40,43,47,50
    20.101c0wA0.7340.970.7050.7520.80COcomplex2.pdb.gz79,98,172,175
    30.042h0900.4622.360.2580.5170.94IIIcomplex3.pdb.gz32,34,85,90,92,93,96,100,103,104,107,108,109
    40.033jsoB0.2973.250.1190.3481.23QNAcomplex4.pdb.gz5,7,36,37,39,40,43,44,50,59
    50.012ff4B0.4145.270.0690.6480.66IIIcomplex5.pdb.gz51,52,53,54,55,66,67

      Click on the radio buttons to visualize predicted binding site and residues.
    (a)CscoreLB is the confidence score of predicted binding site. CscoreLB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
    (b)BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
    (c)TM-score is a measure of global structural similarity between query and template protein.
    (d)RMSDa the RMSD between residues that are structurally aligned by TM-align.
    (e)IDENa is the percentage sequence identity in the structurally aligned region.
    (f)Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

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    Reference:
  • Xiaogen Zhou, Wei Zheng, Yang Li, Robin Pearce, Chengxin Zhang, Eric W. Bell, Guijun Zhang, and Yang Zhang. I-TASSER-MTD: A deep-learning based platform for multi-domain protein structure and function prediction, to be submitted.
  • yangzhanglabumich.edu | (734) 647-1549 | 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218