I-TASSER results

I-TASSER results for job id Rv3040c

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

Input Sequence in FASTA format

>protein (288 residues)
MNSPREPLVPPPTPRPAATVMLVRDPDAGSASGLAVFLMRRHAAMDFAAGVMVFPGGGVD
DRDRDADLGRLGAWAGPPPQWWAQRFGIEPDLAEALVCAAARETFEESGVLFAGPVDQDH
SAPNSIVSDASVYGDARRALADRTLSFADFLQREKLVLRSDLLRPWANWVTPEAELTRRY
DTYFFVGALPEGQRADGENTESDRAGWVLPADAIADFAAGRNFLLPPTWTQLDSLAGHTV
ADVLAVERQIVPVQPQLARNGDNWEIEFFDSDRYNQARRSGGSTGWPL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MNSPREPLVPPPTPRPAATVMLVRDPDAGSASGLAVFLMRRHAAMDFAAGVMVFPGGGVDDRDRDADLGRLGAWAGPPPQWWAQRFGIEPDLAEALVCAAARETFEESGVLFAGPVDQDHSAPNSIVSDASVYGDARRALADRTLSFADFLQREKLVLRSDLLRPWANWVTPEAELTRRYDTYFFVGALPEGQRADGENTESDRAGWVLPADAIADFAAGRNFLLPPTWTQLDSLAGHTVADVLAVERQIVPVQPQLARNGDNWEIEFFDSDRYNQARRSGGSTGWPL
Prediction	CCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCEEEEEEEHCCCCCCCCCEEHCCCCCCCCCCCCCHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCEEHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCEEEEEHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHCCCCCCCEEEEHCCCEEEEEHCCCCCCCCCCCCCCCCCCCC
Conf.Score	998878999999887775999998689998889589999958877777996887898899776875676655556889899998869996777999999999999998957755789888887766677678999999999798559999999899679988665664348998898755568999986889866778885567787699999999998999878878999999995997999999778887555898669979999779877777777888888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MNSPREPLVPPPTPRPAATVMLVRDPDAGSASGLAVFLMRRHAAMDFAAGVMVFPGGGVDDRDRDADLGRLGAWAGPPPQWWAQRFGIEPDLAEALVCAAARETFEESGVLFAGPVDQDHSAPNSIVSDASVYGDARRALADRTLSFADFLQREKLVLRSDLLRPWANWVTPEAELTRRYDTYFFVGALPEGQRADGENTESDRAGWVLPADAIADFAAGRNFLLPPTWTQLDSLAGHTVADVLAVERQIVPVQPQLARNGDNWEIEFFDSDRYNQARRSGGSTGWPL
Prediction	855476464634402300000000235544451010000212651422341200100313463444613521424424253126426254620200000000101410210002346444344433234453145014303745330251046260203042022000001164524220101000010254351544531243234120430043046450200101220033007252142025527242020101447411100002252155446463454246
	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                 220                 240                 260                 280

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCEEEEEEEHCCCCCCCCCEEHCCCCCCCCCCCCCHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCEEHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCEEEEEHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHCCCCCCCEEEEHCCCEEEEEHCCCCCCCCCCCCCCCCCCCC
MNSPREPLVPPPTPRPAATVMLVRDPDAGSASGLAVFLMRRHAAMDFAAGVMVFPGGGVDDRDRDADLGRLGAWAGPPPQWWAQRFGIEPDLAEALVCAAARETFEESGVLFAGPVDQDHSAPNSIVSDASVYGDARRALADRTLSFADFLQREKLVLRSDLLRPWANWVTPEAELTRRYDTYFFVGALPEGQRADGENTESDRAGWVLPADAIADFAAGRNFLLPPTWTQLDSLAGHTVADVLAVERQIVPVQPQLARNGDNWEIEFFDSDRYNQARRSGGSTGWPL

3qsjA

0.29

0.22

0.75

2.26

MUSTER

----------ATDIRKAATLVVIRDGANK---DIEVLVVRRAK-TRFLPGFVAFPGGAADPSDAEAKR----AFGRP--------VCAEDDDDPALAVTALRETAEEIGWLLAVRDGEGTKDTPLA-------PDEQADLCKGGDALSAWLSARGLAFDLGLLRRIGRFVTPPTQ-PVRFDTRFFLCVGQHLGEPRLHGAELDAALWT-PARDLTRIQSGELPAVRPTIAVLKALVACPNAEI-ASTLSIGP------------------------------------

3qsjA

0.27

0.20

0.75

3.13

dPPAS

----------ATDIRKAATLVVIRDG----ANKDIEVLVVRRAKTRFLPGFVAFPGGAADPSDAEAKRAFGRP------------VCAEDDDDPALAVTALRETAEEIGWLLAVRDGEGTKDTPLA-------PDEQADLCKGGDALSAWLSARGLAFDLGLLRRIGRFVTPPTQ-PVRFDTRFFLCVGQHLGEPRLHGAELDAALWT-PARDLTRIQSGELPAVRPTIAVLKALVACPNAEIASTLSIGP-------------------------------------

3qsjA

0.28

0.21

0.75

4.74

wdPPAS

----------ATDIRKAATLVVIRDG----ANKDIEVLVVRRAKTRFLPGFVAFPGGAADPSDAEAKRAFGRP------------VCAEDDDDPALAVTALRETAEEIGWLLAVRDGEGTKDTPLA-------PDEQADLCKGGDALSAWLSARGLAFDLGLLRRIGRFVTPPTQ-PVRFDTRFFLCVGQHLGEPRLHGAELDAALWT-PARDLTRIQSGELPAVRPTIAVLKALVACPNAEIASTLS----IGP---------------------------------

3qsjA

0.29

0.22

0.75

2.78

wMUSTER

-----------TDIRKAATLVVIRDG----ANKDIEVLVVRRAKTRFLPGFVAFPGGAADPSDAEAKRAFGRP------------VCAEDDDDPALAVTALRETAEEIGWLLAVRDGEGTKDTPLA-------PDEQADLCKGGDALSAWLSARGLAFDLGLLRRIGRFVTPPTQ-PVRFDTRFFLCVGQHLGEPRLHGAELDAALWT-PARDLTRIQSGELPAVRPTIAVLKALVACPNAEI-ASTLSIGP------------------------------------

3qsjA

0.28

0.21

0.75

4.79

wPPAS

----------ATDIRKAATLVVIRDG----ANKDIEVLVVRRAKTRFLPGFVAFPGGAADPSDAEAKRAFGRP------------VCAEDDDDPALAVTALRETAEEIGWLLAVRDGEGTKDT-------PLAPDEQADLCKGGDALSAWLSARGLAFDLGLLRRIGRFVTPPTQ-PVRFDTRFFLCVGQHLGEPRLHGAELDAALWT-PARDLTRIQSGELPAVRPTIAVLKALVACPNAEIASTLS----IGP---------------------------------

3qsjA

0.27

0.20

0.75

9.29

dPPAS2

----------ATDIRKAATLVVIRDG----ANKDIEVLVVRRAKTRFLPGFVAFPGGAADPSDAEAKRAFGRP------------VCAEDDDDPALAVTALRETAEEIGWLLAVRDGEGTKDTPLA-------PDEQADLCKGGDALSAWLSARGLAFDLGLLRRIGRFVTPPTQ-PVRFDTRFFLCVGQHLGEPRLHGAELDAALWT-PARDLTRIQSGELPAVRPTIAVLKALVACPNAEIASTLSIGP-------------------------------------

3qsjA

0.27

0.20

0.75

3.80

PPAS

----------ATDIRKAATLVVIRDG----ANKDIEVLVVRRAKTRFLPGFVAFPGGAADPSDAEAKRAFGRP------------VCAEDDDDPALAVTALRETAEEIGWLLAVRDGEGTKDTPLA-------PDEQADLCKGGDALSAWLSARGLAFDLGLLRRIGRFVTPPTQ-PVRFDTRFFLCVGQHLGEPRLHGAELDAALWT-PARDLTRIQSGELPAVRPTIAVLKALVACPNAEIASTLSIGP-------------------------------------

3qsjA

0.28

0.21

0.75

5.12

Env-PPAS

----------ATDIRKAATLVVIRDG----ANKDIEVLVVRRAKTRFLPGFVAFPGGAADPSDAEAKR------------AFGRPVCAEDDDDPALAVTALRETAEEIGWLLAVRDGEGTKDT-------PLAPDEQADLCKGGDALSAWLSARGLAFDLGLLRRIGRFVTPPTQ-PVRFDTRFFLCVGQHLGEPRLHGAELDAALWT-PARDLTRIQSGELPAVRPTIAVLKALVACPNAEIASTLS----IGP---------------------------------

4zb3A2

0.16

0.09

0.59

0.78

MUSTER

----------NASHVVGAGALVINKNTK------EVLVVQERSGFFKDKNVWKLPTGVINEGED-------------------------------IWTGVAREVEEETGI------------------------------------------------IADFVEVLAFRQSHKAILKKKTDMFFLCVLSPRSYDITEQKSEILQAKWMPIQEYVDQPWNKKN-------EMFKFMAN---ICQKKCEEEYLGFAIVPTTTSSGKESFI-----YCNADHA--------

4zb3A2

0.15

0.09

0.59

0.78

dPPAS

----------NASHVVGAGALVINKNTK------EVLVVQERSGFFKDKNVWKLPTGVINEGED-------------------------------IWTGVAREVEEETGI------------------------------------------------IADFVEVLAFRQSHKAILKKKTDMFFLCVLSPRSYDITEQKSEILQAKWMPIQEYVDQPWNKKN----------EMFKFMANICQKKCEEEYLGFAIVPTTTSSGKESFI-----YCNADHA--------

(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=-0.58

Estimated TM-score = 0.64±0.13

Estimated RMSD = 7.4±4.2Å

Download Model 2

C-score=-1.51

Download Model 3

C-score=-2.37

Download Model 4

C-score=-2.76

Download Model 5

C-score=-3.69

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	3qsjA	0.705	1.65	0.264	0.750
2	2pnyA	0.490	4.02	0.096	0.628
3	2i6kA	0.485	4.03	0.108	0.625
4	1viqA	0.460	3.00	0.122	0.542
5	3dupA	0.455	3.84	0.141	0.576
6	1qvjA	0.451	4.12	0.135	0.573
7	2qkmB	0.447	4.31	0.138	0.583
8	1mqwA	0.444	3.86	0.116	0.552
9	2fmlA	0.444	3.72	0.105	0.545
10	5bonA	0.443	2.85	0.133	0.514

(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	0.52	16	2r5wB	MG	Rep, Mult	56,57,103,107
2	0.12	6	2a8sA	GTP	Rep, Mult	19,41,54,56,57,58,103,106,107,182,201,225,227,228,231
3	0.06	3	1g9qB	APR	Rep, Mult	14,17,43,56,57,58,103
4	0.02	1	2qjtB	MN	Rep, Mult	58,60,102,103
5	0.02	1	3i9x0	III	Rep, Mult	15,16,59,61,96,168,170,172,179,181,183

	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	1ry2A	0.368	6.79	0.038	0.674	6.2.1.1	NA
2	0.060	2g3fA	0.373	6.02	0.057	0.611	3.5.2.7	NA
3	0.060	2a6tA	0.412	3.79	0.138	0.514	3.6.1.30	16,60,97,103,106
4	0.060	2pnyA	0.490	4.02	0.096	0.628	5.3.3.2	109
5	0.060	1f3yA	0.383	3.51	0.177	0.472	3.6.1.17	15,58,103,107,185,201
6	0.060	1yq2A	0.382	6.13	0.066	0.625	3.2.1.23	103
7	0.060	1qlaD	0.377	6.57	0.013	0.653	1.3.99.1	167,182
8	0.060	3kvnX	0.396	6.20	0.069	0.674	3.1.1.1	162
9	0.060	1hx3B	0.420	3.43	0.122	0.510	5.3.3.2	NA
10	0.060	1yq3A	0.373	5.90	0.058	0.611	1.3.5.1	240
11	0.060	2yvmA	0.418	3.43	0.187	0.517	3.6.1.-	41,201
12	0.060	3ezwG	0.371	5.99	0.058	0.608	2.7.1.30	229
13	0.060	1q33A	0.452	3.95	0.124	0.569	3.6.1.13	56,60,103,106
14	0.060	1xsbA	0.417	3.62	0.118	0.517	3.6.1.17	96,107
15	0.060	2q9pA	0.366	3.03	0.233	0.431	3.6.1.52	58,103,107
16	0.060	1thgA	0.380	6.30	0.073	0.656	3.1.1.3	NA
17	0.060	2dsbA	0.426	3.66	0.123	0.531	3.6.1.13	NA
18	0.060	1viqA	0.460	3.00	0.122	0.542	3.6.1.13	17,103,106,109,204
19	0.060	1jnrA	0.366	6.03	0.061	0.611	1.8.99.2	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	0.52	0.717	1.76	0.26	0.77	3qsjA	GO:0016787 GO:0046872
1	0.23	0.396	3.23	0.18	0.48	3sonA	GO:0016787
2	0.16	0.436	3.32	0.15	0.52	3o61D	GO:0000287 GO:0016787 GO:0016818 GO:0046872 GO:0052751
3	0.12	0.428	3.23	0.18	0.51	5hzxA	GO:0006281 GO:0008413 GO:0016787
4	0.10	0.443	2.85	0.13	0.51	5bonA	GO:0005829 GO:0006203 GO:0008413 GO:0016787 GO:0017110 GO:0034656 GO:0035539 GO:0046872
5	0.09	0.407	3.49	0.12	0.50	3fk9A	GO:0016787
6	0.08	0.395	3.05	0.12	0.47	4kyxA	GO:0016787
7	0.08	0.403	3.01	0.16	0.47	2b0vA	GO:0016787
8	0.07	0.421	3.37	0.19	0.51	1su2A	GO:0000166 GO:0005524 GO:0016787
9	0.07	0.408	2.93	0.17	0.48	3q91D	GO:0005737 GO:0005829 GO:0008768 GO:0016787 GO:0016818 GO:0018279 GO:0046872 GO:0047631 GO:0070062
10	0.07	0.488	4.04	0.11	0.63	2i6kA	GO:0000287 GO:0004452 GO:0005777 GO:0005829 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008299 GO:0016126 GO:0016787 GO:0016853 GO:0030145 GO:0046872 GO:0050992
11	0.07	0.490	4.02	0.10	0.63	2pnyA	GO:0004452 GO:0005777 GO:0005829 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008299 GO:0016126 GO:0016787 GO:0016853 GO:0046490 GO:0046872 GO:0050992
12	0.07	0.458	3.02	0.13	0.54	1g9qA	GO:0000287 GO:0005829 GO:0009408 GO:0016787 GO:0016818 GO:0019144 GO:0046872 GO:0047631
13	0.07	0.444	3.86	0.12	0.55	1mqwA	GO:0016787 GO:0030145 GO:0046872
14	0.06	0.438	3.26	0.14	0.53	5c7qA	GO:0016787 GO:0047631
15	0.06	0.419	3.38	0.12	0.51	2b2kB	GO:0004452 GO:0005737 GO:0006974 GO:0008299 GO:0016787 GO:0016853 GO:0046872 GO:0050992
16	0.06	0.399	3.42	0.15	0.49	2fkbC	GO:0005829 GO:0016787 GO:0016817 GO:0046872
17	0.06	0.410	2.97	0.14	0.49	3hyqA	GO:0004452 GO:0005737 GO:0008299 GO:0016787 GO:0016853 GO:0046872 GO:0050992
18	0.06	0.405	3.94	0.14	0.52	1vhzA	GO:0000287 GO:0005829 GO:0016787 GO:0019144 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0047429
GO-Score	0.64	0.41
Biological Processes	GO:0006281	GO:0034656	GO:0006203
GO-Score	0.12	0.10	0.10
Cellular Component	GO:0005829
GO-Score	0.10

(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.