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I-TASSER results for job id S778584

(Click on S778584_results.tar.bz2 to download the tarball file including all modeling results listed on this page. Click on Annotation of I-TASSER Output to read the instructions for how to interpret the results on this page. Model results are kept on the server for 60 days, there is no way to retrieve the modeling data older than 2 months)

  Submitted Sequence in FASTA format

>protein
MMKPFARVAGIEVPSDPLPNSASVEQIQNKMQELNDILDDLRDSFEGCVGGNAFAYQIQL
NFRIPQAQQQGQGQQQQQAQATVQEAAAAAAVRVLNNNDQIIQLYKDLVKLKRHAGIKKA
MEKLADQDGGGDGGGNNKKRGASEDYDAGASKGGKGKETEFDLSMIVGQVKLYADLITTE
SFSIYAGLGAGLAYTYGKIDNKDINRAYRHGCIRSTWCSTLHAAVGVCLW

  Predicted Secondary Structure

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |          
MMKPFARVAGIEVPSDPLPNSASVEQIQNKMQELNDILDDLRDSFEGCVGGNAFAYQIQLNFRIPQAQQQGQGQQQQQAQATVQEAAAAAAVRVLNNNDQIIQLYKDLVKLKRHAGIKKAMEKLADQDGGGDGGGNNKKRGASEDYDAGASKGGKGKETEFDLSMIVGQVKLYADLITTESFSIYAGLGAGLAYTYGKIDNKDINRAYRHGCIRSTWCSTLHAAVGVCLW
PredictionCCCCHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHSSSSCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHCCSSSSSSCCCCCCSSSCCCCCCCCCCCCCCCCSSSCHHHHHHHHCCCSSSC
Conf.Score97504344076589998998311999999999999999999987314033214455551201257899864000116899999999999999986584789999999999998775999999998754667677505422665433112232467753121366743456555546301214555224632102226556632244666646510134200030225509
H:Helix; S:Strand; C:Coil

  Predicted Solvent Accessibility

Sequence                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |          
MMKPFARVAGIEVPSDPLPNSASVEQIQNKMQELNDILDDLRDSFEGCVGGNAFAYQIQLNFRIPQAQQQGQGQQQQQAQATVQEAAAAAAVRVLNNNDQIIQLYKDLVKLKRHAGIKKAMEKLADQDGGGDGGGNNKKRGASEDYDAGASKGGKGKETEFDLSMIVGQVKLYADLITTESFSIYAGLGAGLAYTYGKIDNKDINRAYRHGCIRSTWCSTLHAAVGVCLW
Prediction73331161261413744135433164035314413510540362041102341103303031313444456644645444434454323210301244630140033013034332134105402765456645454555434564654456645444241302101230312020232431202112111112132404443144333111021011101311411133
Values range from 0 (buried residue) to 9 (highly exposed residue)

   Predicted normalized B-factor

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. Click here to read more about predicted normalized B-factor)


  Top 10 threading templates used by I-TASSER

(I-TASSER modeling starts from the structure templates identified by LOMETS from the PDB library. LOMETS is a meta-server threading approach containing multiple threading programs, where each threading program can generate tens of thousands of template alignments. I-TASSER only uses the templates of the highest significance in the threading alignments, the significance of which are measured by the Z-score, i.e. the difference between the raw and average scores in the unit of standard deviation. The templates in this section are the 10 best templates selected from the LOMETS threading programs. Usually, one template of the highest Z-score is selected from each threading program, where the threading programs are sorted by the average performance in the large-scale benchmark test experiments.)

Rank PDB
Hit		Iden1Iden2CovNorm.
Z-score		Download
Align.		                   20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220
                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |          
Sec.Str
Seq		CCCCHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHSSSSCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHCCSSSSSSCCCCCCSSSCCCCCCCCCCCCCCCCSSSCHHHHHHHHCCCSSSC
MMKPFARVAGIEVPSDPLPNSASVEQIQNKMQELNDILDDLRDSFEGCVGGNAFAYQIQLNFRIPQAQQQGQGQQQQQAQATVQEAAAAAAVRVLNNNDQIIQLYKDLVKLKRHAGIKKAMEKLADQDGGGDGGGNNKKRGASEDYDAGASKGGKGKETEFDLSMIVGQVKLYADLITTESFSIYAGLGAGLAYTYGKIDNKDINRAYRHGCIRSTWCSTLHAAVGVCLW
14wheA 0.23 0.15 0.52 0.94Download IFSRFADIVNANI-NALLED--PQKLVRLMIQEMEDTLVEVRSTS-----ARALAEKKQLTRRIEQASAREVEWQEKAELALLEDLARAALIEKQKLTDLIKSLEHEVTLVDDTLAMKKEIGELENK-------------------------------------------------------------------------------------------------------
28ugcA 0.13 0.19 0.78 0.65Download AFEAFAAIAAAEAFSDS-TGETVAEAVAKALKAAMEAFAEIAKAVAQAAKQGASEAAFEAFAAIAAAAAEAAAAAFEAFSDSTGETVAEAVAKALKAAEAFAEIAKAVAQAAKQGASEEAFEKFAAIAAEAAEAAAAAFERFSDSTG------------ETEAEKVAKELKQLMEEFAERAKSVAEQAKNGAS-------------------------------------
34tqlA 0.12 0.20 0.92 0.64Download MVQELEKARD-RMEKLY---KEMVELIQKAIELMRKIFQEVKQEVEKAIEEKKLYDEAKKKIEMIQQIKQGGDKQKMEELLKRAKEEMKKVKDKMEKLLEKLKQIMQEAKQKMEKLLKQLKEEMKKMKEKKQRMEEVKKKMDDELLEKIKKNIDDLKKIAEDAEENIKEAKKIAEQLVKRAKQLIEKAKQVAEELIKKILQL----------IEKAKEIAEKVLKG----
46vrb 0.38 0.17 0.13 0.83Download --------------------SQKYNQIQGKIQEINKEIATLYESSEDYI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
56v1vA 0.23 0.20 0.85 0.41Download LPKITSMLNEVMKQNHVL--SLQIEFLSKQLQEISDKLDN--------VLINSTLTEI-----TP-AYQRIKYVNEKFDELTS---TVEKNPKSYQDNKEVIENLNELTELAKSVSFEFYLQTFHDVMTGNNLFGRSALKTASETKENVTTRGSEGKVYNFLIVLTSLQAKAFLTLTACRKL---LGL-TDIDYT--QIMNHHIDGQKREF--RINILPTLS--------
65cwqA 0.11 0.16 0.91 0.80Download --------------------ERESEEAERRLQEARKRSEEARERGDLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARKVSEEDDEVLALALIAIALAVLALAEVACCRGNSEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVACCRGNKEEAERAYEDARRVEEEARKVKESAEEEEAEQLAREARRHVQECRGGW
76r5k 0.21 0.23 0.82 0.73Download IFSPIGSVSSIRVCIKNLHPDIDN--------------KALYDTFSVFGD--I------LSSKIATDEN---G--KSKGFGHEEEGAAKEAIDALNGMLQEIYLYEQFQELFKHEDAVKAVEALNDSEL---NGEKLYVGRA----------QK-KNERMHVLKKQYEAYRL-EKMAKYQGVNLFVKLDDSEFAPYGTITSAKVMRTKGFGFVCFSTTKAITEKNQQIVA
84wheA 0.19 0.15 0.52 0.63Download IFSRFADIVNANI-NALLED--PQKLVRLMIQEMEDTLVEVRSTS-----ARALAEKKQLTRRIEQASAREVEWQEKAELALLKDLIKSLEHEVTLVDDTLARMKKEIGELENKLSETRARQQALMLR------------------------------------------------------------------------------------------------------
96r5k 0.19 0.23 0.83 0.65Download IFSPIGSVSSIRVCIKNLHPDIDN--------------KALYDTFSVFGD--I------LSSKIATDE--NGKS-KGFGFVFEEEGAAKEAIDALNGMLQEIYVYEQFQELFAHEDAVKAVEALNDS---ELNGEKLYVGRA---------QKKNERMH--VLKKQYEAYRL-EKMAKYQGVNLFVKLDDSEFAPYGTITSAKVMRTENGFVCFSTATKAITEKNQQIVA
108g9jA 0.12 0.17 0.79 0.89Download SEEIVEEAEALKALLEEAEKGGKEDALEIAEKLAELAKEALEVLLEAGASPELIVRLAETALKALLAIAELGGEELALEIARILAELAEVALEVLASPELIVRLAETALEALLAILAELAEVALEVLLELGASPELIKKLAETAEEALEAIAKLGGEELAEEIAKILAELAEVAKEVQKE-------------------------------------------------L
(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 ten threading templates used by I-TASSER.
(c)Ident1 is the percentage sequence identity of the templates in the threading aligned region with the query sequence.
(d)Ident2 is the percentage sequence identity of the whole template chains with query sequence.
(e)Cov represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein.
(f)Norm. Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa.
(g)Download Align. provides the 3D structure of the aligned regions of the threading templates.
(h)The top 10 alignments reported above (in order of their ranking) are from the following threading programs:
       1: FFAS-3D   2: SPARKS-X   3: SP3   4: HHSEARCH   5: wdPPAS   6: Neff-PPAS   7: HHSEARCH2   8: pGenTHREADER   9: HHSEARCH I   10: PROSPECT2   

   Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of a higher value signifies a model with a higher confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-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. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated; this is usually an indication that the models have a good quality because of the converged simulations.)
    (By right-click on the images, you can export image file or change the configurations, e.g. modifying the background color or stopping the spin of your models)
  • Download Model 1
  • C-score=-3.42 (Read more about C-score)
  • Estimated TM-score = 0.34±0.11
  • Estimated RMSD = 13.8±3.9Å

  • Download Model 2
  • C-score = -4.38

  • Download Model 3
  • C-score = -4.18

  • Download Model 4
  • C-score = -4.70

  • Download Model 5
  • C-score = -3.91


  Proteins structurally close to the target in the PDB (as identified by TM-align)

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


Top 10 Identified stuctural analogs in PDB

Click
to view		RankPDB HitTM-scoreRMSDaIDENaCovAlignment
15cwqA0.887 1.350.1130.926Download
26xr1A0.747 3.610.0960.961Download
33m71A0.735 3.770.0580.978Download
47en0A0.686 3.960.0680.930Download
58qt5A0.675 3.090.0630.830Download
67wnqA0.675 4.350.0620.961Download
78fitA0.669 3.760.0860.891Download
82o98B0.665 2.900.0490.809Download
98qtcA0.664 3.250.0540.826Download
106a5qB0.662 3.060.0540.813Download

(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 function using COFACTOR and COACH

(This section reports biological annotations of the target protein by COFACTOR and COACH based on the I-TASSER structure prediction. While COFACTOR deduces protein functions (ligand-binding sites, EC and GO) using structure comparison and protein-protein networks, COACH is a meta-server approach that combines multiple function annotation results (on ligand-binding sites) from the COFACTOR, TM-SITE and S-SITE programs.)

  Ligand binding sites


Click
to view		RankC-scoreCluster
size		 PDB
Hit		 Lig
Name		 Download
Complex		 Ligand Binding Site Residues
10.14 18 3p1qA FSC Rep, Mult 52,56,104,107,108,160,161,212,213
20.13 18 4ieaA PEPTIDE Rep, Mult 58,59,65,69,107,114,115,164,167,168,171,175,212,215,219,224
30.09 14 4dauA PEPTIDE Rep, Mult 58,62,69,110,117,118,168,171,172,175,179,215,222,225
40.04 6 4n7yB PEPTIDE Rep, Mult 52,55,56,58,104,107,114,115,160,164,167,168,171,213,215,219
50.03 5 5d2dB PEPTIDE Rep, Mult 52,55,58,65,104,107,114,115,161,164,167,168


Download the residue-specific ligand binding probability, which is estimated by SVM.
Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites


Click
to view		RankCscoreECPDB
Hit		TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.1021fp3A0.628 4.500.0450.913 5.1.3.8  NA
20.0931rw9A0.621 4.330.0680.874 4.2.2.5  196
30.0932f6dA0.602 5.010.0410.935 3.2.1.3  NA
40.0932qnoA0.606 4.770.0640.891 3.2.1.4  100
50.0931l2aE0.614 4.790.0450.917 3.2.1.4  107

 Click on the radio buttons to visualize predicted active site residues.
(a)CscoreEC is the confidence score for the 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.

  Gene Ontology (GO) terms
Top 10 homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
1 0.130.6573 3.09 0.07 0.811qjbB GO:0005739 GO:0005634 GO:0006605 GO:0042470 GO:0005737 GO:0008134 GO:0019904 GO:0006916 GO:0002553 GO:0043234 GO:0005515 GO:0005829 GO:0005625 GO:0006626 GO:0042493 GO:0007165 GO:0030168 GO:0016071 GO:0014069 GO:0016070 GO:0032403 GO:0007596
2 0.120.6559 2.95 0.07 0.803iqjA GO:0043154 GO:0005737 GO:0008426 GO:0008630 GO:0043616 GO:0008285 GO:0008283 GO:0005615 GO:0007165 GO:0005576 GO:0000079 GO:0006469 GO:0030307 GO:0005515 GO:0001836 GO:0006915 GO:0043588 GO:0030216 GO:0005634 GO:0019904 GO:0051726
3 0.100.6576 2.95 0.07 0.802btpA GO:0006605 GO:0005730 GO:0019904 GO:0005737 GO:0005625 GO:0005813 GO:0005634 GO:0047485 GO:0045892 GO:0043234 GO:0005515 GO:0007264
4 0.100.6278 4.50 0.04 0.911fp3A GO:0050121 GO:0006013 GO:0006044 GO:0016853 GO:0004476 GO:0003824
5 0.100.6450 4.30 0.09 0.913gt5A GO:0003824 GO:0004476 GO:0006013
6 0.100.7332 3.79 0.06 0.983m73A GO:0006810 GO:0016021 GO:0046690 GO:0046677 GO:0005886 GO:0016020 GO:0006811 GO:0005216 GO:0055085
7 0.100.6650 2.90 0.05 0.812o98B GO:0019904
8 0.100.6371 4.18 0.07 0.892zzrA GO:0008152 GO:0016787 GO:0003824
9 0.100.6471 4.46 0.09 0.913aflA GO:0016829
10 0.100.6534 3.17 0.07 0.802br9A GO:0005737 GO:0006605 GO:0005622 GO:0005739 GO:0000278 GO:0048011 GO:0032403 GO:0019904 GO:0001764 GO:0021987 GO:0033267 GO:0035308 GO:0050815 GO:0006915 GO:0008624 GO:0042470 GO:0051219 GO:0044419 GO:0000086 GO:0042826 GO:0005871 GO:0005515 GO:0035556 GO:0019899 GO:0005829 GO:0021766


Consensus prediction of GO terms		 
Molecular Function GO:0016861 GO:0019904
GO-Score 0.38 0.31
Biological Process GO:0023052 GO:0050794 GO:0051716 GO:0007154 GO:0046907 GO:0045184 GO:0034613 GO:0019318
GO-Score 0.47 0.47 0.47 0.47 0.43 0.43 0.43 0.38
Cellular Component GO:0000267 GO:0032991 GO:0005737 GO:0005634
GO-Score 0.43 0.43 0.31 0.31

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.


[Click on S778584_results.tar.bz2 to download the tarball file including all modeling results listed on this page]


Please cite the following articles when you use the I-TASSER server:
  • Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1: 100014 (2021).
  • Chengxin Zhang, Peter L. Freddolino, and Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017).
  • Jianyi Yang, Yang Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.