I-TASSER results

I-TASSER results for job id Rv1961

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

Input Sequence in FASTA format

>protein (164 residues)
MFLPTNAQYQLLVVGVSPWDTPSPSGRISWGSAWPHQARRAQTCQRVRRHWMIDTTEAAY
RLTYQPDGTSITVRENLVDILARELLGPIRGPQEVLPFSPRSQYLVGHLAPVKLTGAALI
DDNAVQARANAEALAEGGGVPAYAADETTPTPTTTPKTAHPSRA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MFLPTNAQYQLLVVGVSPWDTPSPSGRISWGSAWPHQARRAQTCQRVRRHWMIDTTEAAYRLTYQPDGTSITVRENLVDILARELLGPIRGPQEVLPFSPRSQYLVGHLAPVKLTGAALIDDNAVQARANAEALAEGGGVPAYAADETTPTPTTTPKTAHPSRA
Prediction	CCCCCCCCEEEEEEHCCCCCCCCCCCCEHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHCCCCCCCEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98888865689998678888899887655567787689999999999888877655665444578898857999999999999846899998655579965335666775676676556777655677666667767888888888889988888777787779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MFLPTNAQYQLLVVGVSPWDTPSPSGRISWGSAWPHQARRAQTCQRVRRHWMIDTTEAAYRLTYQPDGTSITVRENLVDILARELLGPIRGPQEVLPFSPRSQYLVGHLAPVKLTGAALIDDNAVQARANAEALAEGGGVPAYAADETTPTPTTTPKTAHPSRA
Prediction	74234634130000102324344362414234323453534523641443410541544240444376432512540251045300213715644274524420000101134244544455445535656463564452525445665445564656642578
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(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

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCEEEEEEHCCCCCCCCCCCCEHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHCCCCCCCEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MFLPTNAQYQLLVVGVSPWDTPSPSGRISWGSAWPHQARRAQTCQRVRRHWMIDTTEAAYRLTYQPDGTSITVRENLVDILARELLGPIRGPQEVLPFSPRSQYLVGHLAPVKLTGAALIDDNAVQARANAEALAEGGGVPAYAADETTPTPTTTPKTAHPSRA

1vddA

0.20

0.18

0.91

1.14

MUSTER

MKYPPSLVSLIRELSRLPGIGPKSAQRLRLASALLEAKRDLHVCPICFNITDAEKCDVCA--DPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLH---------GVLSPMNGVGPDKLHIKPLLPRV--GQGMEVILATGTTVE-GDATALYLQRLLEPLGA

4cwuU

0.14

0.12

0.82

1.02

dPPAS2

SLAPRHGSRPF----MGNWQDTSNMSAFSWGSLWSFGSTVKNYGSKAWNSSTGQMLDKLKEQNFQQKGIS-----GVVDLANQAV-------QNKINSK---------LDPRPPVEEPPPAVETVSPEGRGEKRPRPDREETLVTQIDEPPSYEEALKQ-----

3vdpA

0.17

0.16

0.92

1.12

MUSTER

-YYSTSVAKLIEELSKLPGIGPKTAQRLSLSQAIIEAKEKLRYCKICFNITDKEVCDICS--DENRDHSTICVVSHPMDVVAMEKVKEYKGVYHVLH---------GVISPIEGVGPEDIRIKELLERVRDGSVKEVILATNPDIE-GEATAMYIAKLLKPFGA

2mxxA

0.12

0.11

0.90

1.00

dPPAS2

ADEATDAA------RNNDGAYYLQTQFTN--------ADKVNEYLAQHDGEIRAEAAAKAALDAVEGGSHNAVRNKYVQRFQATYNNATEGKTYIQGETPEQA---NARYLKRVGAANNQNPAAEDKGATTPASKEEAKKSEAAAKNAGKAAGKALPKTSAVKH

5an9D

0.10

0.94

0.76

MUSTER

MVDPSEK--VEVFLRVCGGEAGAMST---LAPKLPLGVSPKKVGDDIAKATQPWKGMKVSKLTIQNRIAVPEVLPSASALVIKA-LKEPPRDRKKEKNIKH----NGNIPLEEICKIAKTMRFKSLAVDFKGSVLEILGTAHSKVNGKSPRDIQAGEIEVVEPK

2mxxA

0.08

0.95

0.88

dPPAS

ADEATDAA------RNNDGAYYLQTQFTNADKVNEYLAQHDGEIRAEAAADPAVVAAKAALDAVEGGSHNYGEVKAAYEAAFNNAATEQEGKTYIQGETPEQA---NARYLKRVGAANNQNPAAEDKGATTPASKEEAKKSEAAAKNAGKAAGKALPKTSAVKH

2mxxA

0.15

0.13

0.87

0.80

wdPPAS

MADATDAA------RNNDGAYYLQTQFIR--AADPAVVAAKAALDAVNYGEVKAAYEAAF------NNAFNAVRNKYVQRFQATYATEQEGKTYIQGETPEQA--------ARYLKRVGAANNQNPAAEDKGATTPASKEEAKKSEAAAKNAGKAAGKALPTSA

1vddA

0.20

0.18

0.90

0.93

wMUSTER

KY-PPSLVSLIRELSRLPGIGPKSAQRLRLASALLEAKRDLHVCPICFNITDAEKCDVCA--DPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLH---------GVLSPMNGVGPDKLHIKPLLPRV--GQGMEVILATGTTVE--DATALYLQRLLEPLGA

4cwuU

0.22

0.16

0.76

0.87

wPPAS

-FLPRHGSRPF----MGNWQDTSNMSAFSWGSLWSFGSTVKNYGSKAWNS------------------TGQMLRDKLKE---QNFQQ--KGISGVVD--------LANQAVQNKINSKLDPEEPPPAVETVSPEGRGEKRPRPDREETLVTQIDEP----PSEA

4cwuT

0.20

0.07

0.34

0.93

dPPAS2

-------------------------------------------------------------------------------------------------------------APGLQTVDVQETQTSPVASAVADAAVQAVAAAASKTSTEVQTDPWMFRVSAPRRP

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

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.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-2.07

Estimated TM-score = 0.47±0.15

Estimated RMSD = 9.5±4.6Å

Download Model 2

C-score=-4.65

Download Model 3

C-score=-4.60

Download Model 4

C-score=-3.99

Download Model 5

C-score=-3.94

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.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	1vddA	0.783	2.16	0.168	0.896
2	3vdpA	0.776	2.28	0.133	0.908
3	1k30A	0.519	5.31	0.037	0.908
4	2xt6A	0.519	3.87	0.065	0.750
5	3mveA	0.517	4.54	0.043	0.805
6	2bklB	0.509	4.87	0.056	0.829
7	2xe4A	0.507	4.88	0.039	0.848
8	4hvtA	0.504	4.83	0.020	0.823
9	3iujA	0.502	5.20	0.053	0.848
10	1yr2A	0.501	4.76	0.050	0.823

(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)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a 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 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
1	0.15	9	5cdoS	NUC	Rep, Mult	75,77,107,108,146
2	0.07	4	2bgrB	UUU	Rep, Mult	97,104,105,106,107
3	0.05	3	2xt6A	CA	Rep, Mult	84,87,89
4	0.03	2	2v1c0	III	Rep, Mult	6,18,26,31,34,35,38,39,41,42,43,49,50,57,58,77,78,80,81
5	0.03	2	1c9uA	CA	Rep, Mult	74,87,88
6	0.03	2	2dkiA	XE	Rep, Mult	62,81,88,89,104
7	0.03	2	1c9uB	CA	Rep, Mult	94,104
8	0.02	1	3e3gB	SO4	Rep, Mult	49,74
9	0.02	1	1c8fA	CA	Rep, Mult	90,94
10	0.02	1	1tk3B	NDG	Rep, Mult	95,97,106,107,108
11	0.02	1	1nuiA	MG	Rep, Mult	75,142
12	0.02	1	2yclA	SF4	Rep, Mult	73,75,76,80,83

	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

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	3d66A	0.477	4.94	0.043	0.780	3.4.17.20	NA
2	0.060	1gz7A	0.424	5.17	0.034	0.713	3.1.1.3	NA
3	0.060	1orvA	0.498	5.23	0.040	0.860	3.4.14.5	NA
4	0.060	3fegA	0.481	5.36	0.055	0.817	2.7.1.82	107,109
5	0.060	1peuA	0.465	4.77	0.032	0.780	1.17.4.1	NA
6	0.060	2vdcA	0.466	4.87	0.043	0.738	1.4.1.13	NA
7	0.060	1ayeA	0.484	5.12	0.045	0.817	3.4.17.15	NA
8	0.060	1pcaA	0.480	5.06	0.045	0.817	3.4.17.1	NA
9	0.060	3g0bB	0.498	5.16	0.027	0.848	3.4.14.5	NA
10	0.060	3mwdA	0.465	4.50	0.037	0.768	2.3.3.8	156
11	0.060	3dgvA	0.344	5.61	0.027	0.628	3.4.17.20	NA
12	0.060	3g0iA	0.467	4.60	0.049	0.750	3.3.2.3	NA
13	0.060	1ea0A	0.445	5.07	0.029	0.750	1.4.1.13	NA
14	0.060	1pytA	0.226	4.17	0.034	0.335	3.4.17.1	98
15	0.060	2bklB	0.509	4.87	0.056	0.829	3.4.21.26	NA
16	0.060	1cleA	0.466	4.93	0.027	0.774	3.1.1.3	NA
17	0.060	2boaA	0.486	5.16	0.045	0.829	3.4.17.-	NA
18	0.060	2d5lA	0.496	5.14	0.052	0.848	3.4.14.-	NA
19	0.060	2gbcA	0.500	5.29	0.047	0.866	3.4.14.5,3.4.15.5	NA

(a)	Cscore^EC is the confidence score for the EC number prediction. Cscore^EC 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)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a 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

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.20	0.666	3.64	0.10	0.90	4o6oD	GO:0003677 GO:0006281 GO:0006310 GO:0006974 GO:0046872
1	0.18	0.783	2.16	0.17	0.90	1vddA	GO:0003677 GO:0006281 GO:0006302 GO:0006310 GO:0006974 GO:0046872
2	0.08	0.490	4.54	0.10	0.76	2y0pC	GO:0003824 GO:0004149 GO:0004591 GO:0006099 GO:0008152 GO:0008683 GO:0016491 GO:0016624 GO:0016740 GO:0016746 GO:0016829 GO:0016831 GO:0030976 GO:0046872 GO:0050439 GO:0055114
3	0.07	0.519	5.31	0.04	0.91	1k30A	GO:0004366 GO:0006629 GO:0006650 GO:0008152 GO:0008654 GO:0009507 GO:0009536 GO:0009570 GO:0016024 GO:0016740 GO:0016746
4	0.06	0.443	4.49	0.03	0.66	4ddtA	GO:0000166 GO:0000287 GO:0003676 GO:0003677 GO:0003916 GO:0003917 GO:0003918 GO:0004386 GO:0005524 GO:0006265 GO:0006268 GO:0008270 GO:0016787 GO:0016853 GO:0046872
5	0.06	0.410	4.55	0.04	0.66	2jgdA	GO:0000287 GO:0004591 GO:0005829 GO:0006096 GO:0006099 GO:0008152 GO:0016491 GO:0016624 GO:0030976 GO:0042802 GO:0045252 GO:0055114
6	0.06	0.368	4.38	0.02	0.58	5a2aA	GO:0003824 GO:0004556 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798
7	0.06	0.316	4.61	0.02	0.51	4uw0A	GO:0004672 GO:0005524 GO:0006468
8	0.06	0.325	5.54	0.07	0.60	3exeA	GO:0004738 GO:0004739 GO:0005634 GO:0005739 GO:0005759 GO:0005975 GO:0006006 GO:0006086 GO:0006090 GO:0006099 GO:0008152 GO:0010510 GO:0016491 GO:0016624 GO:0034604 GO:0043209 GO:0043231 GO:0045254 GO:0046487 GO:0055114 GO:0061732
9	0.06	0.364	5.45	0.04	0.68	4ax8A	GO:0000166 GO:0004672 GO:0005524 GO:0005886 GO:0006468 GO:0008168 GO:0009103 GO:0009243 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0032259
10	0.06	0.311	5.81	0.08	0.62	3b8kA	GO:0004742 GO:0005739 GO:0005759 GO:0005967 GO:0005975 GO:0006006 GO:0006086 GO:0006090 GO:0006099 GO:0008152 GO:0010510 GO:0016740 GO:0016746 GO:0030431 GO:0034604 GO:0043209 GO:0045254 GO:0046487
11	0.06	0.319	5.43	0.04	0.60	4p8mB	GO:0003824 GO:0003885 GO:0016020 GO:0016491 GO:0016614 GO:0045227 GO:0050660 GO:0055114 GO:0071555
12	0.06	0.329	5.22	0.09	0.60	4b7cK	GO:0000166 GO:0008270 GO:0016491 GO:0055114
13	0.06	0.335	4.73	0.09	0.53	1a82A	GO:0000166 GO:0000287 GO:0004141 GO:0005524 GO:0005737 GO:0005829 GO:0009102 GO:0016874 GO:0046872
14	0.06	0.334	5.52	0.06	0.64	1sczA	GO:0004149 GO:0005829 GO:0006099 GO:0008152 GO:0016740 GO:0016746 GO:0031405 GO:0033512 GO:0045252
15	0.06	0.292	5.16	0.06	0.49	4memB	GO:0004197 GO:0004843 GO:0005634 GO:0005737 GO:0006508 GO:0006511 GO:0008233 GO:0008234 GO:0016579 GO:0016787 GO:0036459
16	0.06	0.346	5.08	0.01	0.59	1umbA	GO:0003863 GO:0008152 GO:0016491 GO:0016624 GO:0046872 GO:0055114
17	0.06	0.312	5.49	0.06	0.57	3dufA	GO:0004739 GO:0006096 GO:0008152 GO:0016491 GO:0016624 GO:0055114
18	0.06	0.326	4.20	0.08	0.49	1djlA	GO:0003957 GO:0005739 GO:0005743 GO:0005746 GO:0006099 GO:0006740 GO:0008746 GO:0008750 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0045454 GO:0050661 GO:0051287 GO:0055114 GO:0072593 GO:1902600

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0003677
GO-Score	0.44	0.39
Biological Processes	GO:0006310	GO:0006281
GO-Score	0.34	0.34
Cellular Component	GO:0009570
GO-Score	0.07

(a)	Cscore^GO 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)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a 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 Cscore^GO 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.