I-TASSER results

I-TASSER results for job id Rv2799

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

Input Sequence in FASTA format

>protein (209 residues)
MYTPGKGPPRAGGVVFTRVRLIGGLGALTAAVVVVGTVGWQGIPPAPTGGDAVQLRSTAA
PMSTTMKSPIVATTDPSPFDPCRDIPFDVIQRLGLAYTPPEAEEGLRCHFDAGNYQMAVE
PIIWRTYAQTLPPDAIETTIAGHRAAQYWVRKPTYHNSFWYSSCMVTFKTSYGVIQQSLF
YSTVYSEPDVDCPSTNLQRANDLVPYYRF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MYTPGKGPPRAGGVVFTRVRLIGGLGALTAAVVVVGTVGWQGIPPAPTGGDAVQLRSTAAPMSTTMKSPIVATTDPSPFDPCRDIPFDVIQRLGLAYTPPEAEEGLRCHFDAGNYQMAVEPIIWRTYAQTLPPDAIETTIAGHRAAQYWVRKPTYHNSFWYSSCMVTFKTSYGVIQQSLFYSTVYSEPDVDCPSTNLQRANDLVPYYRF
Prediction	CCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCEEEEEHCCCEEEEEEEEEEHHHHHHCCCCCEHCCCCHHHHHHHEEHCCCCCCCCEEEEEEEEEHCCCCEEEEEEEEHCCCCCCCCCCHHHHHHHHHHHCCCCCC
Conf.Score	99998898887756776654788999999999998534566788888888876556677887777778765578999898877898899999878789999777756888578768988876543467768987444444455554444446766676557899999865644455444444566899988656788988775554469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MYTPGKGPPRAGGVVFTRVRLIGGLGALTAAVVVVGTVGWQGIPPAPTGGDAVQLRSTAAPMSTTMKSPIVATTDPSPFDPCRDIPFDVIQRLGLAYTPPEAEEGLRCHFDAGNYQMAVEPIIWRTYAQTLPPDAIETTIAGHRAAQYWVRKPTYHNSFWYSSCMVTFKTSYGVIQQSLFYSTVYSEPDVDCPSTNLQRANDLVPYYRF
Prediction	74457644342110010303211111220010111023314433444444541504345341433143331524546315204512240034122423345356424041434413100310113214641446315241433400321113034244300000001243432203311221313364527134541540441243257
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCEEEEEHCCCEEEEEEEEEEHHHHHHCCCCCEHCCCCHHHHHHHEEHCCCCCCCCEEEEEEEEEHCCCCEEEEEEEEHCCCCCCCCCCHHHHHHHHHHHCCCCCC
MYTPGKGPPRAGGVVFTRVRLIGGLGALTAAVVVVGTVGWQGIPPAPTGGDAVQLRSTAAPMSTTMKSPIVATTDPSPFDPCRDIPFDVIQRLGLAYTPPEAEEGLRCHFDAGNYQMAVEPIIWRTYAQTLPPDAIETTIAGHRAAQYWVRKPTYHNSFWYSSCMVTFKTSYGVIQQSLFYSTVYSEPDVDCPSTNLQRANDLVPYYRF

5bmqA

0.13

0.11

0.87

0.57

MUSTER

TPTTDHDCGKAGE----------YQKDLETTLASLADYGTIFADGKQSKEDCAAIKK----FQKRGIQPAEGYAGKLTLDV-----AQRIAKSSFDKCQE-AKKGKTVCVDTHQTLWVVEKRIFEPTVVRTGAGY--ATQPGAWKIFVKEGTHWSKKYKVWLPYWQNFNNGEGLHTTTTYIHEPWIGSH--CVNLLPSDSKKL---YDF

5fhhA2

0.08

0.92

0.67

dPPAS

TASHKVGRDGIVATRLCTHQDDVALTNERRLQELPGKVHRFEAMDSNPELASTLDAQCPVSQLLQLKLGVKNLSVSRGLVNGARGVVLPQVRFLCGVTEVIHADRWTVQATGGQLLSRQQLPLQLAWAMSIHKSQGMTLDC------VEISLGRVFASGQAYVALSRARSLQGLRVLDFDPMAVRCDPRVLHFYATLR-----------

4c0dB

0.17

0.13

0.75

0.58

wdPPAS

--------------MVT------GMIGLLTFIRAAET-----DPGMVHLALGSDLTTLGLNLNSKFASP-WASSPCRPQDIDFHVPSEYLTNIHIRDKLAAGEDLL---Y----YMNG------GDVLQLL---AVELFNRDHKEERVWITRPTMKTNTYERGTYYFFDLNWRKVAKEFHLE--YDK---------LEERPHLPSTFNY

4fweA

0.15

0.14

0.94

0.58

wMUSTER

KESGIQFSELEGQVLFHLSNLEYACGSNLHQVSARSWDHFAQFAGDLTPGYSVIIEKLAEGLDIQLKSPVVTTTDGTGYSA--QVPLALLQKGAIQFNPPLSEK-KMKAINSLGAGIIEKIALQ------FPYRFWDSKVQG---ADFFGHVPPSASKRGLFAVFYDMDPQKKSVLMSVIAGEVRTLDDKQVLQQCMATLRELFKEQEV

4c0dB

0.16

0.12

0.76

0.52

wPPAS

MVT---DQ---G------------MIGLLTFIRAAET-----DPGMVHLALGSDLTTSPENLYPKFASP-WASSPCRPQDIDFHVP---------EYLTHIRDKLAAIKLG----RYGEDLYLYGDVLQLL--AAVELFNRDHKEERVWITRPTMKTNTYERGTYYFFDCNWRKVAKEFHLE--YDK---------LEERPHLPSTFNY

2v5dA1

0.24

0.14

0.57

0.62

dPPAS2

NPTPENLEVVGDGFKITSINLVGEEEADENAVNALREF---------LTANNIEINSENDPNSTTL---IIGEVD--------DDIPELDEALNGTTAENLKEEGYALVSNDG--KIAIEGTFYQTFKQLVKESNIEVNITD-------------------------------------------------------------------

5bmqA

0.12

0.11

0.87

0.66

PPAS

TPTTDHDCGKAGE----------YQKDLETTLASLADYGTIFADGKQSKEDCAAIKK----FQKRGIQPAEGYAGKLTLD------VAQRIAKSSFDKCQEAKKGKTVCVDTHQTLWVVEKRIFEPTVVRTGAGY--ATQPGAWKIFVKEGTHWSKKYKVWLPYWQNFNNGEGLHTTTTYIHEPWSH----C-PSDSKKLYELDFFGNR

4c0dB

0.18

0.14

0.81

0.71

Env-PPAS

--------------MVTQFGMIGLLTFIRAAETDPGMVHLALGSDLTTLGLNL---NSPENLYPKFASPWASSP-CRPQDIDFHVP--------SEYLTNIHIRDKLAAIKLGRYGEDLLFYLYGDVLQLL--AAVELFNRDHKEERVWITRPTMKTNTYERGTYYFFDCNWRKVAKEFHLE--YDK---------LEERPHLPSTFNY

5fhhA2

0.09

0.08

0.90

0.57

MUSTER

TASHKVGRDGIVATRLCTHQDDVALTNERRLQELPGKVHRFEAMDSNPELASTLDAQCPVSQLLQLKLGLVKNLSVSRGLVNGVVLPQVRFLCGVTEVIHADR--WTVQATGGQLLSRQQLPLQLAW-------AMSIHKSQGMTLDCVEISLGRVFASGQAYVALSRARSLGLRVLDFDPMAVRCDPR------VLHFYATLR-----

4m6tA

0.11

0.09

0.81

0.61

dPPAS

-----------------KDRDSQITAIEKTFEDAQKSISQHYSKPRVTPVEVMPVFPDFNPCAQVIFDSDPAPKDTSGAAALEMMSQAMIRGMMSGENLYFQSGNDLYFVKLPNFSVEPRPFDPQYYEDEFEEEGRTRLKLKVENTIRWRIRRDEEGNEIKESNARIVKWSDGSMSLHLEVFDVYKA----------------------

(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=-3.82

Estimated TM-score = 0.30±0.10

Estimated RMSD = 14.6±3.7Å

Download Model 2

C-score=-4.49

Download Model 3

C-score=-4.29

Download Model 4

C-score=-4.86

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	5bmqA	0.670	3.50	0.093	0.847
2	4lpqA	0.466	4.94	0.075	0.713
3	1lmlA	0.441	5.71	0.025	0.780
4	4lzhA	0.439	4.63	0.080	0.632
5	3lwtX	0.438	5.78	0.055	0.751
6	3hc1A	0.436	4.77	0.060	0.675
7	3eh1A	0.427	5.57	0.030	0.718
8	3cskA	0.426	5.56	0.051	0.732
9	3memA	0.426	5.02	0.039	0.694
10	4icqA	0.425	5.59	0.065	0.732

(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	0.20	9	1cnzA	MN	Rep, Mult	84,88
2	0.07	3	4dcaA	MG	Rep, Mult	114,134
3	0.05	2	2xybA	ZN	Rep, Mult	143,157
4	0.05	2	2ek8A	ZN	Rep, Mult	80,84
5	0.02	1	3fw6A	ZN	Rep, Mult	134,156
6	0.02	1	2y2gA	NA	Rep, Mult	163,193,194
7	0.02	1	1c8nA	CA	Rep, Mult	139,196
8	0.02	1	3rr5A	MG	Rep, Mult	79,137
9	0.02	1	2y6pC	MG	Rep, Mult	84,191
10	0.02	1	3lw52	CLA	Rep, Mult	168,170

	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	2g8eA	0.350	5.52	0.025	0.603	3.4.22.52	NA
2	0.060	3lmdA	0.404	5.15	0.024	0.646	2.5.1.30	138
3	0.060	2vdcF	0.407	5.81	0.036	0.737	1.4.1.13	132
4	0.060	3fsnB	0.406	5.89	0.034	0.727	5.2.1.7	NA
5	0.060	3ij3A	0.409	5.12	0.047	0.651	3.4.11.1	111
6	0.060	3fwmA	0.422	6.10	0.041	0.780	2.4.1.129,	NA
7	0.060	1e6yA	0.404	5.32	0.022	0.670	2.8.4.1	NA
8	0.060	2jgdA	0.408	5.81	0.039	0.713	1.2.4.2	NA
9	0.060	3ipiA	0.399	5.34	0.063	0.655	2.5.1.-	84
10	0.060	1qxpB	0.402	6.09	0.048	0.761	3.4.22.53,3.4.22.52	201
11	0.060	3f2bA	0.405	5.73	0.039	0.694	2.7.7.7	200
12	0.060	2fahA	0.404	5.67	0.056	0.703	4.1.1.32	NA
13	0.060	2zufA	0.405	6.09	0.052	0.737	6.1.1.19	90
14	0.060	3cskA	0.426	5.56	0.051	0.732	3.4.14.4	193
15	0.060	1xc6A	0.391	6.48	0.059	0.761	3.2.1.23	110
16	0.060	2ebsB	0.405	5.90	0.055	0.732	3.2.1.150	131
17	0.060	2p4eA	0.414	6.02	0.076	0.775	3.4.21.-	NA
18	0.060	1vncA	0.396	5.32	0.080	0.665	1.11.1.10	NA
19	0.060	1htoA	0.402	5.60	0.044	0.694	6.3.1.2	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	0.10	0.674	3.68	0.09	0.86	5bmqA	GO:0016020 GO:0016021 GO:0016740
1	0.07	0.480	4.81	0.08	0.72	4lpqA	GO:0016740
2	0.07	0.440	4.77	0.04	0.69	3memA	GO:0002161 GO:0006450
3	0.07	0.441	5.71	0.03	0.78	1lmlA	GO:0004222 GO:0005886 GO:0006508 GO:0007155 GO:0008233 GO:0008237 GO:0016020 GO:0016787 GO:0031225 GO:0046872 GO:0052014 GO:0052032
4	0.07	0.438	5.78	0.06	0.75	3lwtX	GO:0004438 GO:0005783 GO:0005789 GO:0005797 GO:0016020 GO:0016021 GO:0016787 GO:0016791 GO:0030173 GO:0030176 GO:0035339 GO:0036092 GO:0042578 GO:0043812 GO:0043813 GO:0046856
5	0.06	0.435	4.65	0.06	0.67	3hc1A	GO:0005730 GO:0016787 GO:0046872
6	0.06	0.441	4.66	0.07	0.63	4lzhA	GO:0016740
7	0.06	0.388	4.40	0.07	0.54	4xxtA	GO:0004180 GO:0006508 GO:0016740 GO:0016787
8	0.06	0.398	3.93	0.06	0.53	2hklA	GO:0016020 GO:0016021 GO:0016740
9	0.06	0.383	5.12	0.09	0.63	3p3qB	GO:0000160 GO:0005622
10	0.06	0.361	4.24	0.06	0.51	4jmnA	GO:0005576 GO:0006508 GO:0008360 GO:0009252 GO:0016740 GO:0016746 GO:0018104 GO:0042597 GO:0071555 GO:0071972
11	0.06	0.360	4.13	0.05	0.50	4xvoA	GO:0016740
12	0.06	0.316	6.22	0.05	0.60	4a2mB	GO:0000155 GO:0000160 GO:0003677 GO:0003700 GO:0005622 GO:0006351 GO:0006355 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016772 GO:0023014 GO:0043565
13	0.06	0.374	5.39	0.06	0.62	4hzdA	GO:0005737 GO:0006535 GO:0009001 GO:0016740
14	0.06	0.365	3.95	0.02	0.48	4qr7A	GO:0005886 GO:0008360 GO:0009252 GO:0016020 GO:0016740 GO:0016746 GO:0046872 GO:0071555
15	0.06	0.382	3.72	0.04	0.49	4k73A	GO:0008360 GO:0009252 GO:0016740 GO:0016746 GO:0071555
16	0.06	0.345	5.51	0.06	0.58	2hekA	GO:0006203 GO:0008832 GO:0046872
17	0.06	0.338	5.95	0.03	0.61	1lbuA	GO:0004180 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009046 GO:0016787 GO:0046872 GO:0071555
18	0.06	0.386	5.36	0.05	0.63	2ongA	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0016740	GO:0004222	GO:0043813	GO:0043812	GO:0046872	GO:0004438	GO:0002161
GO-Score	0.16	0.07	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0006450	GO:0007155	GO:0006508	GO:0036092	GO:0052032	GO:0052014	GO:0046856
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0030173	GO:0005886	GO:0030176	GO:0035339	GO:0031225	GO:0005797
GO-Score	0.07	0.07	0.07	0.07	0.07	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.