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I-TASSER results for job id Rv3367

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

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 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 higher value signifies a model with a high 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.)
 Proteins structureally close to the target in 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.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.09 5 3smrB NP7 Rep, Mult 142,143,184,185,186,201,227,259,261,277,391,407
20.06 3 1af0A CA Rep, Mult 454,455,456,458,465,466,467,470
30.04 2 3sbpA CUK Rep, Mult 144,145,262,305,344,345,365,393
40.04 2 2z2pA III Rep, Mult 142,158,185,227,259,261,303,318,342,344,365,407
50.02 1 1g9kA CA Rep, Mult 321,322,323,325,335,356,357,360
60.02 1 3iurA III Rep, Mult 178,184,200,209,210
70.02 1 3odtA CA Rep, Mult 140,407,413
80.02 1 3ucpA MG Rep, Mult 398,401,404
90.02 1 1yo8A UUU Rep, Mult 247,264,268
100.02 1 3sbpA CUA Rep, Mult 438,440,444
110.02 1 1fwxA CUA Rep, Mult 342,364,366,372,375
120.02 1 4v0oF PB Rep, Mult 145,187,188,394
130.02 1 1om7A CA Rep, Mult 335,337,339,352,354,357
140.02 1 1o0tA CA Rep, Mult 353,354,355,357,371,373,376
150.02 1 3sfzA GBL Rep, Mult 96,111,114
160.02 1 1sqj0 III Rep, Mult 150,163,176,212
170.02 1 1jiwP CA Rep, Mult 459,460,461,462,464,479,486
180.02 1 3fvzA CA Rep, Mult 144,186,392
190.02 1 2qubE CA Rep, Mult 466,468,470,481,482,483,486

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

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0601yr2A0.4406.610.0610.6333.4.21.26NA
20.0602aeyA0.3656.340.0480.5073.2.1.80NA
30.0602h47H0.3984.280.0650.4741.4.99.4NA
40.0601e5tA0.4195.350.0260.5463.4.21.26NA
50.0603c75J0.3214.430.0540.3911.4.99.3269
60.0602qr5A0.4125.330.0880.5313.4.19.1NA
70.0603elqB0.3825.830.0510.5122.8.2.22NA
80.0601yrzA0.3766.510.0600.5413.2.1.37NA
90.0601fwxA0.4435.380.0400.5591.7.99.6425
100.0601orvA0.3926.310.0480.5463.4.14.5312
110.0602bklB0.4095.980.0580.5463.4.21.26NA
120.0601simA0.3724.560.0500.4583.2.1.18NA
130.0602ac1A0.3686.440.0540.5153.2.1.26NA
140.0601yifA0.3746.530.0510.5413.2.1.37NA
150.0601y9mA0.3736.230.0820.5173.2.1.80NA
160.0601w6sC0.3975.080.0540.5051.1.99.8NA
170.0601r9mB0.3916.230.0500.5413.4.14.5NA
180.0601qksB0.4085.170.0330.5271.7.2.1436,486,530
190.0602gc7A0.3924.310.0710.4711.4.99.3150,193

(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

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.120.5255.240.090.662ymuA GO:0016020 GO:0016021
10.070.5765.720.040.773j2tA GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007399 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043065 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0072432 GO:0097190 GO:0097193 GO:1902510 GO:2001235
20.070.5475.470.060.704nsxA GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0030529 GO:0031167 GO:0032040 GO:0034388 GO:0042254 GO:0042274
30.070.5386.140.040.743sfzA GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0097190 GO:1902510 GO:2001235
40.070.5095.340.050.654xfvA GO:0002098 GO:0005634 GO:0005654 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006810 GO:0008017 GO:0015031 GO:0032447 GO:0033588
50.070.5015.050.060.631nr0A GO:0003779 GO:0005737 GO:0005856 GO:0016528 GO:0030016 GO:0030240 GO:0030836 GO:0030837 GO:0040011 GO:0040012 GO:0042643 GO:0051015 GO:0071689
60.070.5056.100.080.694ci8A GO:0000226 GO:0002244 GO:0005509 GO:0005737 GO:0005829 GO:0005856 GO:0005874 GO:0005875 GO:0007052 GO:0007405 GO:0007420 GO:0008017 GO:0015631 GO:0048471 GO:0097431 GO:1990023
70.070.4994.970.080.621pguB GO:0003779 GO:0005737 GO:0005856 GO:0005884 GO:0006970 GO:0030042 GO:0030479 GO:0032466 GO:0051016
80.060.4514.710.060.555cvlA GO:0000724 GO:0005634 GO:0005737 GO:0005764 GO:0005768 GO:0005770 GO:0006974 GO:0007283 GO:0007338 GO:0008584 GO:0016032 GO:0016579 GO:0035264 GO:0043588 GO:0048568 GO:0048705 GO:0048872 GO:0050679 GO:0072520 GO:1902525
90.060.4042.890.060.441vyhC GO:0000132 GO:0000226 GO:0000235 GO:0000776 GO:0001667 GO:0001675 GO:0001764 GO:0001961 GO:0005634 GO:0005635 GO:0005737 GO:0005813 GO:0005815 GO:0005819 GO:0005829 GO:0005856 GO:0005871 GO:0005874 GO:0005875 GO:0005938 GO:0006629 GO:0006810 GO:0007017 GO:0007049 GO:0007067 GO:0007097 GO:0007268 GO:0007275 GO:0007399 GO:0007405 GO:0007420 GO:0007611 GO:0008017 GO:0008090 GO:0008344 GO:0009306 GO:0010977 GO:0015630 GO:0016020 GO:0016042 GO:0016477 GO:0017145 GO:0019226 GO:0021540 GO:0021766 GO:0021819 GO:0021895 GO:0021987 GO:0030036 GO:0030154 GO:0030424 GO:0030426 GO:0031023 GO:0031252 GO:0031512 GO:0031965 GO:0031982 GO:0032403 GO:0032420 GO:0036035 GO:0040019 GO:0042249 GO:0042803 GO:0043005 GO:0043025 GO:0043087 GO:0043622 GO:0045502 GO:0045505 GO:0045773 GO:0045931 GO:0046329 GO:0047496 GO:0048471 GO:0048854 GO:0050885 GO:0051081 GO:0051130 GO:0051219 GO:0051301 GO:0051660 GO:0051661 GO:0060117 GO:0061003 GO:0070062 GO:0070507 GO:0090102 GO:0090176 GO:1904115 GO:2000574
100.060.3493.190.040.393w15A GO:0005053 GO:0005737 GO:0005777 GO:0005829 GO:0006810 GO:0015031 GO:0016560
110.060.3753.390.060.425a2qg GO:0001649 GO:0001891 GO:0001934 GO:0005080 GO:0005102 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0005913 GO:0006417 GO:0006915 GO:0006919 GO:0007049 GO:0007275 GO:0007369 GO:0008200 GO:0008656 GO:0010629 GO:0010803 GO:0015935 GO:0016020 GO:0016032 GO:0017148 GO:0019899 GO:0019903 GO:0030178 GO:0030292 GO:0030308 GO:0030335 GO:0030425 GO:0030496 GO:0030822 GO:0030971 GO:0032436 GO:0032464 GO:0032880 GO:0032947 GO:0033137 GO:0035591 GO:0040008 GO:0042169 GO:0042803 GO:0042995 GO:0042998 GO:0043005 GO:0043025 GO:0043065 GO:0043204 GO:0043547 GO:0044297 GO:0044822 GO:0048471 GO:0048511 GO:0050765 GO:0051302 GO:0051343 GO:0051726 GO:0051898 GO:0051901 GO:0061099 GO:0070062 GO:0071333 GO:0071363 GO:0090003 GO:0098609 GO:0098641 GO:1900102 GO:1903208 GO:1990630 GO:2000114 GO:2000304 GO:2000543 GO:2001244
120.060.3964.110.060.474lg9A GO:0000118 GO:0000122 GO:0002021 GO:0003677 GO:0003714 GO:0005634 GO:0005654 GO:0005876 GO:0006351 GO:0006355 GO:0008013 GO:0010468 GO:0016042 GO:0016568 GO:0016575 GO:0017053 GO:0030814 GO:0035264 GO:0042393 GO:0043161 GO:0044212 GO:0044255 GO:0045892 GO:0045893 GO:0045944 GO:0047485 GO:0050872 GO:0060070 GO:0060612 GO:0060613 GO:0090207
130.060.3753.480.070.424v6wAg GO:0000398 GO:0005080 GO:0005737 GO:0005776 GO:0005829 GO:0005875 GO:0007626 GO:0009267 GO:0016243 GO:0018991 GO:0035220 GO:0042335 GO:0044829 GO:0045725 GO:0046716 GO:0048477 GO:0071011 GO:0071013 GO:0075522
140.060.4053.250.060.452h9lA GO:0000123 GO:0001501 GO:0005622 GO:0005634 GO:0005654 GO:0005671 GO:0006351 GO:0006355 GO:0016568 GO:0018024 GO:0031175 GO:0035064 GO:0035097 GO:0035948 GO:0042800 GO:0043966 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0044666 GO:0046972 GO:0048188 GO:0051568 GO:0071339
150.060.3724.040.040.442ybaB GO:0000122 GO:0000281 GO:0003682 GO:0005634 GO:0005667 GO:0005700 GO:0006281 GO:0006334 GO:0006335 GO:0006342 GO:0006351 GO:0006355 GO:0007307 GO:0007346 GO:0007379 GO:0007517 GO:0008284 GO:0016568 GO:0016571 GO:0016573 GO:0016581 GO:0016584 GO:0016589 GO:0016590 GO:0031491 GO:0031497 GO:0031523 GO:0033186 GO:0035035 GO:0035097 GO:0035098 GO:0042054 GO:0042393 GO:0042766 GO:0042803 GO:0042826 GO:0046974 GO:0046976 GO:0048666 GO:0048812 GO:0048813 GO:0051567 GO:0061085 GO:0070615 GO:0070734 GO:0070822
160.060.3993.240.070.453i2nA GO:0006915 GO:0043130
170.060.4013.150.070.453jcrD GO:0000375 GO:0000398 GO:0005634 GO:0005654 GO:0005681 GO:0005682 GO:0005732 GO:0005737 GO:0006396 GO:0006397 GO:0008380 GO:0044822 GO:0071011 GO:0071013
180.060.3963.140.070.444lg8A GO:0000209 GO:0000244 GO:0000245 GO:0000398 GO:0000974 GO:0001833 GO:0004842 GO:0005634 GO:0005654 GO:0005662 GO:0005681 GO:0005737 GO:0005811 GO:0005819 GO:0005856 GO:0006281 GO:0006283 GO:0006303 GO:0006397 GO:0006974 GO:0008380 GO:0008610 GO:0010498 GO:0016020 GO:0016567 GO:0016607 GO:0016874 GO:0034450 GO:0034613 GO:0035861 GO:0042802 GO:0045665 GO:0048026 GO:0048711 GO:0061630 GO:0070534 GO:0071013 GO:0072422


Consensus prediction of GO terms
 
Molecular Function GO:0008656 GO:0005524 GO:0031072 GO:0042802 GO:0043531 GO:0008017
GO-Score 0.13 0.13 0.13 0.13 0.13 0.07
Biological Processes GO:0071560 GO:0008635 GO:0007568 GO:0051260 GO:0030154 GO:0051402 GO:2001235 GO:0034349 GO:1902510 GO:0010659 GO:0030900 GO:0001666 GO:0007584 GO:0070059 GO:0001843 GO:0015031 GO:0042274 GO:0072432 GO:0032447 GO:0002098 GO:0006357 GO:0031167
GO-Score 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0043231
GO-Score 0.48

(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 result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.