I-TASSER results

I-TASSER results for job id Rv3222c

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

Input Sequence in FASTA format

>protein (183 residues)
MSSPVSSRRLANLVKESLQGSVLGGVVSDAVLPAVSDDVKPGAGEDAYRVPVVVAAGSGA
VVQVGGLEVGSAAVAGEVADTVAELFVCRPTEPDVGDFVGLAGGAGDAGQAGQQFGLGVG
VRGESFGARRRLALSTVGASGATAGLRKTHDGHHGCQARGALTQRRLYIGNPSEITDTRM
VHQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSSPVSSRRLANLVKESLQGSVLGGVVSDAVLPAVSDDVKPGAGEDAYRVPVVVAAGSGAVVQVGGLEVGSAAVAGEVADTVAELFVCRPTEPDVGDFVGLAGGAGDAGQAGQQFGLGVGVRGESFGARRRLALSTVGASGATAGLRKTHDGHHGCQARGALTQRRLYIGNPSEITDTRMVHQ
Prediction	CCCCCHHHHHHHHHHHHHCCCHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCEEEHCCCCCCCCHCCCCEHCCCEEEEEHCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Conf.Score	988765789999999875554434434454446777788888887655556899857885788767776543446644477578999858999878865454566654445555555555566666545544555457877555554445665445666667777776578765555434469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSSPVSSRRLANLVKESLQGSVLGGVVSDAVLPAVSDDVKPGAGEDAYRVPVVVAAGSGAVVQVGGLEVGSAAVAGEVADTVAELFVCRPTEPDVGDFVGLAGGAGDAGQAGQQFGLGVGVRGESFGARRRLALSTVGASGATAGLRKTHDGHHGCQARGALTQRRLYIGNPSEITDTRMVHQ
Prediction	864435543014113631433111212341113113661443445522403010114432304234353333323453254223010133344535404412343354343345334142244432334343204324354234324434544542534432444322344355145453348
	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                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHHCCCHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCEEEHCCCCCCCCHCCCCEHCCCEEEEEHCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
MSSPVSSRRLANLVKESLQGSVLGGVVSDAVLPAVSDDVKPGAGEDAYRVPVVVAAGSGAVVQVGGLEVGSAAVAGEVADTVAELFVCRPTEPDVGDFVGLAGGAGDAGQAGQQFGLGVGVRGESFGARRRLALSTVGASGATAGLRKTHDGHHGCQARGALTQRRLYIGNPSEITDTRMVHQ

2mu3A

0.16

0.97

0.59

MUSTER

ATGGASAGLISRVANALANTSTLRTVLRTGVSQQIASSVVQRAAQSTLGV--NLARFAVQAVSRLPAGSDTSAYAQAFS---SALFNAGVLNASIDTLGSRVLSALLNGVSSAAQGLGINVDSGSVQSDISSSSSFLSTSSSSASYSQASASSTGAGYTGPSGPSTGPSGYPGPLGGGAPFGQ

3la9A

0.18

0.16

0.89

0.54

dPPAS

SSITTNTTNLGNSTAAALGGGATYDPATGAISAPSYTTYN-ANGTTATNTSVGAAIDNINANGIKY-FHANSTDPDSVATGTNSVAIGPNAVANVDYSVAIGSGATTSAAVPVASAFGGFAGSAPIG-----VFS-VGAPGAERQITNVAAGRISAASTDAVNGSQLYATN------------

3grhA1

0.23

0.19

0.80

0.50

wdPPAS

ITLPAQ----PDFV--GPAGT--QGVIQAAVDAAIIKRVMPG-----YQGTVYVPAAPGGITLYGGEKPIDVKIGLSLDGGM--------SPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVLC----AVFWSQNNTLGDSVDAGNH---PA--AL---RT--GDQVQINNVNIL--

3grhA1

0.23

0.20

0.84

0.58

wMUSTER

NPSPITLPAQPDFV--GPAGT--QGVIQAAVDAAIIKRVMPG----EYQGTVYVPAAPGGITLYGGEKPIDVKIGLSLDGGM--------SPADWRHDVNPRGKYMPGKPAWYMYDSCQSKRSDSIGVLCSAVF-WSQNNGLTLGDSVDAGNH---PA--AL--R---DGDQVQINNVNIL--

3grhA1

0.23

0.17

0.77

0.57

wPPAS

ITLPAQ----PDFV--GPAGT--QGVIQAAV--AIIKRVMPG-----YQGTVYVPAAPGGITLYG---TG---------EKPIDVKIGLDGGMSPADWRHDVNPRGKYMPGKPAYDSCQSKRSDSIGVLC----AVFWSQNLTLGDSVDAGNH---PA--AL---RT--GDQVQINNVNIL--

3d5nA

0.10

0.08

0.81

0.52

dPPAS2

FGGDIDNTPIIRTIRIYGDLEK---II---IVGKYVNEL-PLLD-----QIVIYNPFWNE-----GIS-TSLKLGLRFFKDYDAVLVA-LGDPTKEDVNKIINTFKPNCKAVIPTHKGERGNPVLISKSLFNEIEKLGDVGARVILNKIK-----------IEELCFIECSEGVLIDKK----

3grhA1

0.21

0.17

0.83

0.67

PPAS

NPSPITLPAQPDFV--GPAGT--QGVIQAAVDAAIIKRVMPG-----YQGTVYVPAAPGGITLYG---TGEKP-------IDVKIGLSLDGGMSPADWRHDVNPRGKY-MPGKPAWYMYDSCQSKRSDSIGVLCSVFWSQNNTLGDSVDAGNH---PA--AL---RT--GDQVQINNVNIL--

2vbgA1

0.21

0.18

0.85

0.64

Env-PPAS

HSSGL-MYTVGDYLLDRLHGEEIFGVPGDYNLQQIREDMKLNASADGYKAAAFLTT-FG----VGEL---SAGLAGSYAENLPVVEIVGPT-------SKVQN--DGKFVHHT-LADGD------F---KHFMKMHEPVTAARTLLTAENATYEIDRVLSQLLKERVYINLPVDVAAAKAEKP

2jl1A2

0.16

0.14

0.91

0.55

MUSTER

EESIIPLAHVHLATEYAIRTT---NIPYTFLRNALYTDFFVNEGLRAST-AIVTNAGSGIVNSVTRNELALAAATVLTEEGHKTYNLVSNQPWTFDELAQILSEV---------SGKKVVHQPVSFEEEKNFLVNA-GVPEPFTITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETKM---

3fg2P1

0.12

0.11

0.93

0.54

dPPAS

GAGHAGFQVAVSLRQAKYPGRIARPPLSKAYLKSGGDPNSLMFRPEKFFQDQAIELISDRMVSIDREGRKLLLASGTAIEYGHLVLATGARVIPNVEIAAAAGLPTAAGIIVDQQLLTSDPHISAIG-------DCALFESVRFGETMRVESVQNATDQARCVAARLT-GDAKPYDGYP----

(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=-3.97

Estimated TM-score = 0.29±0.09

Estimated RMSD = 14.7±3.6Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-4.79

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	3grhA	0.512	5.03	0.117	0.869
2	4pmhA	0.512	4.84	0.108	0.847
3	4qjyA	0.480	5.49	0.048	0.831
4	3wkwA	0.479	5.61	0.053	0.853
5	3qpfA	0.462	4.86	0.043	0.770
6	4n5cA	0.458	4.98	0.049	0.738
7	2iwhB	0.455	4.98	0.068	0.743
8	4fwiB	0.453	4.52	0.070	0.689
9	2p0vA	0.452	5.13	0.036	0.765
10	2pclA	0.451	4.58	0.063	0.689

(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	0.06	3	3du7B	HOS	Rep, Mult	27,28,73,74
2	0.06	3	3b8iB	MG	Rep, Mult	97,107
3	0.04	2	3cknA	MN	Rep, Mult	80,150
4	0.04	2	2a68F	MG	Rep, Mult	10,11,67
5	0.04	2	3hkeB	T13	Rep, Mult	66,77,79,81,181
6	0.04	2	3hkeB	T13	Rep, Mult	9,10,12,13,40
7	0.04	2	7insB	UNK	Rep, Mult	166,167,170
8	0.02	1	3wmn2	BCL	Rep, Mult	14,18
9	0.02	1	3t9wA	CU	Rep, Mult	153,154
10	0.02	1	4imaD	ADN	Rep, Mult	131,157,161
11	0.02	1	2wse4	CLA	Rep, Mult	5,9
12	0.02	1	3du7D	HOS	Rep, Mult	92,94,95
13	0.02	1	4fc5A	ZN	Rep, Mult	77,107,114
14	0.02	1	4h6fE	NUC	Rep, Mult	7,176
15	0.02	1	4as2B	BTB	Rep, Mult	132,164
16	0.02	1	1aeiC	CA	Rep, Mult	2,171
17	0.02	1	3auyA	ADP	Rep, Mult	2,3,4,5,6,35,171

	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	2fp0B	0.380	6.06	0.058	0.738	3.2.1.143	NA
2	0.060	1w6sC	0.418	6.07	0.048	0.792	1.1.99.8	NA
3	0.060	2o1sA	0.432	5.33	0.052	0.765	2.2.1.7	43
4	0.060	1b90A	0.430	5.51	0.046	0.754	3.2.1.2	NA
5	0.060	1hcuB	0.449	5.23	0.075	0.765	3.2.1.113	NA
6	0.060	2d0vA	0.425	5.86	0.065	0.787	1.1.99.8	NA
7	0.060	3lmdA	0.423	5.52	0.064	0.732	2.5.1.30	NA
8	0.060	2x1cA	0.426	5.54	0.078	0.765	2.3.1.164	7,19
9	0.060	2o1xC	0.408	5.51	0.038	0.716	2.2.1.7	NA
10	0.060	1kktA	0.400	5.81	0.052	0.732	3.2.1.113	NA
11	0.060	1cb7B	0.434	5.13	0.048	0.727	5.4.99.1	NA
12	0.060	3ctzA	0.422	5.96	0.057	0.776	3.4.11.9	68
13	0.060	2uveA	0.374	5.76	0.085	0.705	3.2.1.82	NA
14	0.060	1veoA	0.403	5.00	0.025	0.678	3.2.1.2	NA
15	0.060	1fp3A	0.423	5.22	0.074	0.721	5.1.3.8	NA
16	0.060	2o1xB	0.425	5.54	0.038	0.770	2.2.1.7	NA
17	0.060	2pbgA	0.422	5.63	0.017	0.792	3.2.1.85	NA
18	0.060	2gruA	0.427	4.94	0.076	0.694	4.2.3.-	NA
19	0.060	1p8jA	0.434	5.16	0.043	0.716	3.4.21.75	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	0.07	0.512	5.03	0.12	0.87	3grhA	GO:0005618 GO:0009279 GO:0016020 GO:0016787 GO:0030599 GO:0042545 GO:0045330
1	0.07	0.457	5.78	0.06	0.85	3wrgA	GO:0000272 GO:0003824 GO:0005975 GO:0008152 GO:0016787 GO:0016798
2	0.07	0.512	4.84	0.11	0.85	4pmhA	GO:0005618 GO:0016787 GO:0030599 GO:0042545 GO:0045330 GO:0045490
3	0.07	0.480	5.49	0.05	0.83	4qjyA	GO:0003824
4	0.06	0.417	4.93	0.02	0.68	1xg2A	GO:0004857 GO:0005576 GO:0005618 GO:0009835 GO:0016787 GO:0030599 GO:0042545 GO:0043086 GO:0045330 GO:0045490 GO:0046910 GO:0071555 GO:0071944
5	0.06	0.381	5.28	0.05	0.66	3uw0A	GO:0005618 GO:0016787 GO:0030599 GO:0042545 GO:0045330 GO:0045490
6	0.06	0.403	4.69	0.10	0.65	2nspA	GO:0005576 GO:0005618 GO:0016787 GO:0030599 GO:0042545 GO:0045330 GO:0045490 GO:0071555
7	0.06	0.382	5.33	0.01	0.63	2d8lA	GO:0003824 GO:0005737 GO:0008152 GO:0016787 GO:0016798 GO:0102211
8	0.06	0.396	5.66	0.07	0.70	1gq8A	GO:0005576 GO:0005618 GO:0016787 GO:0030599 GO:0042545 GO:0045330 GO:0045490 GO:0071555
9	0.06	0.404	5.47	0.06	0.72	5c1cA	GO:0005576 GO:0005618 GO:0016787 GO:0030599 GO:0042545 GO:0045330 GO:0045490 GO:0071555
10	0.06	0.329	5.84	0.09	0.62	1v1mA	GO:0003826 GO:0003863 GO:0005739 GO:0005759 GO:0005947 GO:0008152 GO:0009083 GO:0016491 GO:0016624 GO:0016831 GO:0046487 GO:0046872 GO:0055114
11	0.06	0.306	5.98	0.07	0.56	2c2nA	GO:0003824 GO:0004314 GO:0005739 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0044822
12	0.06	0.370	5.57	0.06	0.67	3wogB	GO:0005537 GO:0006952 GO:0030246
13	0.06	0.354	5.65	0.05	0.66	2as0A	GO:0003723 GO:0008168 GO:0032259
14	0.06	0.347	5.72	0.03	0.63	3wi9A	GO:0005507 GO:0006807 GO:0016491 GO:0046872 GO:0050421 GO:0055114
15	0.06	0.314	5.94	0.05	0.60	2bffA	GO:0003826 GO:0003863 GO:0005739 GO:0005759 GO:0005947 GO:0008152 GO:0009083 GO:0016491 GO:0016624 GO:0016831 GO:0046487 GO:0046872 GO:0055114
16	0.06	0.339	4.92	0.08	0.55	2xhkB	GO:0003677 GO:0003700 GO:0005622 GO:0006351 GO:0006355
17	0.06	0.322	6.22	0.05	0.65	3fpkA	GO:0000166 GO:0004324 GO:0005829 GO:0016491 GO:0055114 GO:0071949
18	0.06	0.312	5.93	0.04	0.58	3kbrA	GO:0003824 GO:0004664 GO:0005215 GO:0006810 GO:0008152 GO:0008652 GO:0009073 GO:0009094 GO:0016829 GO:0042597 GO:0047769

Consensus prediction of GO terms

Molecular Function	GO:0052689
GO-Score	0.37
Biological Processes	GO:0071555
GO-Score	0.37
Cellular Component	GO:0030312
GO-Score	0.37

(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.