I-TASSER results

I-TASSER results for job id Rv3337

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

Input Sequence in FASTA format

>protein (128 residues)
MPSPSTTGHHAACGTGGTGFSVGSMRSPIRVGSGEPVLLLHPFLMSQTVWEKVAQQLADT
GRFEVFAPTMAGHNGGPASGTRFCPRRCWPTTSNASSTNWAGKPAISSATRWAAGSRSNS
NDVAGHAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPSPSTTGHHAACGTGGTGFSVGSMRSPIRVGSGEPVLLLHPFLMSQTVWEKVAQQLADTGRFEVFAPTMAGHNGGPASGTRFCPRRCWPTTSNASSTNWAGKPAISSATRWAAGSRSNSNDVAGHAA
Prediction	CCCCCCCCCEEHCCCCCEEEEHCCEEEEEHCCCCCEEEEHCCCCCCHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCC
Conf.Score	99987666545556676578865467777648998599987998888999999999998798799997799989999999876545455545555566665544544444444444455554455579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPSPSTTGHHAACGTGGTGFSVGSMRSPIRVGSGEPVLLLHPFLMSQTVWEKVAQQLADTGRFEVFAPTMAGHNGGPASGTRFCPRRCWPTTSNASSTNWAGKPAISSATRWAAGSRSNSNDVAGHAA
Prediction	75435444342333443332423444231543624000000120123420450054027544030000002123444544332234321445443434413342314444443344444445245458
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCEEHCCCCCEEEEHCCEEEEEHCCCCCEEEEHCCCCCCHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCC
MPSPSTTGHHAACGTGGTGFSVGSMRSPIRVGSGEPVLLLHPFLMSQTVWEKVAQQLADTGRFEVFAPTMAGHNGGPASGTRFCPRRCWPTTSNASSTNWAGKPAISSATRWAAGSRSNSNDVAGHAA

3kdaA

0.18

0.17

0.93

1.98

MUSTER

FPVPN-GFESAYREVD------GVKLHYVKGGQGPLVMLVHGFGQTWYEWHQLMPELAK--RFTVIAPDLPGLGQSEPPKTGYSGEQVAVYLHKLARQFSPDRPDLVAHDIGIWNTYPMVVKNQADIA

4oseA1

0.11

0.95

2.14

dPPAS

MQINSIKIGPYINLLPLQYIP-QHKISYVEFGDKNIILCAHGLTRNAHDFDKIAKELCK--NYRIISINYPGRSDSENLKK---PYHYNYTTYIKDTLLFFKRLNIKNPIMGGIIGMVLASKYKNIFK

4oseA1

0.10

0.09

0.98

2.81

wdPPAS

MQINSIKIGPYIN-LLPLQYIPQHKISYVEFGDKNIILCAHGLTRNAHDFDKIAKELCK--NYRIISINYPGRSDSENLKKPYHYNYTTYIKDTLLFFKRLNIKNPILGTSMGGIIGMVLASKYKNKA

3kdaA

0.18

0.17

0.93

2.42

wMUSTER

FPVPN-GFESAYREVD------GVKLHYVKGGQGPLVMLVHGFGQTWYEWHQLMPELAK--RFTVIAPDLPGLGQSEPPKTGYSGEQVAVYLHKLARQFSPDRPDLVAHDIGIWNTYPMVVKNQADIA

4oseA1

0.11

0.10

0.91

2.83

wPPAS

MIGPYINLLP-------LQYIPQHKISYVEFGDKNIILCAHGLTRNAHDFDKIAKELCK--NYRIISINYPGRSDSENLKKPYHYNY---TTYIKDTLLFFKRLNIKNPIMGGIIGMVLASKYKNIFK

4q3lA1

0.10

0.08

0.77

3.38

dPPAS2

-----------------SIFTYEKDIYYEIDGNSDVIVILNGIMMSTKSWDAFVENFSK--NHVLLRYDMFDQGQSSKIEESYTQTIQVELLKNLLEHLYGASIALQFAAKYPTMIK-----------

4oseA1

0.11

0.95

2.69

PPAS

MQINSIKIGPYINLLPLQYIP-QHKISYVEFGDKNIILCAHGLTRNAHDFDKIAKELCK--NYRIISINYPGRSDSENLKK---PYHYNYTTYIKDTLLFFKRLNIKNPIMGGIIGMVLASKYKNIFK

4oseA1

0.11

0.95

2.84

Env-PPAS

MQINSIKIGPYINLLPLQYIP-QHKISYVEFGDKNIILCAHGLTRNAHDFDKIAKELCK--NYRIISINYPGRSDSENLKK---PYHYNYTTYIKDTLLFFKRLNIKNPIMGGIIGMVLASKYKNIFK

1zd4A

0.16

0.99

1.98

MUSTER

PAPLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAG-YRVLAMDMKGYGESSAPPEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVR

4q3lA1

0.09

0.07

0.77

2.04

dPPAS

----------------SIFTYQEKDIYYEIDGNSDVIVILNGIMMSTKSWDAFVENFSK--NHVLLRYDMFDQGQSSKIEESYTQTIQVELLKNLLEHLYGASIALQFAAKYPTMIK-----------

(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=0.46

Estimated TM-score = 0.77±0.10

Estimated RMSD = 3.5±2.4Å

Download Model 2

C-score=-3.12

Download Model 3

C-score=-4.17

Download Model 4

C-score=-3.93

Download Model 5

C-score=-4.20

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	2cjpA	0.763	1.84	0.133	0.883
2	1k8qA	0.756	2.07	0.147	0.906
3	3wzlA	0.751	2.05	0.114	0.891
4	2xt0A	0.748	2.32	0.103	0.914
5	3qitA	0.747	2.03	0.167	0.891
6	4oseA1	0.745	2.32	0.096	0.914
7	1cijA	0.742	2.36	0.103	0.914
8	4i3fA	0.741	2.02	0.142	0.883
9	5a62A	0.740	2.07	0.195	0.883
10	5cw2C	0.740	2.16	0.175	0.891

(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	14	1ek1A	CIU	Rep, Mult	43,99,100,103,127
2	0.10	10	1be0A	ACY	Rep, Mult	43,99,100
3	0.08	8	1bezA	ACY	Rep, Mult	99,100,103
4	0.04	4	2wm2A	CL	Rep, Mult	42,43,110,111
5	0.02	2	3g0bC	NAG	Rep, Mult	8,9,26,71,92,95
6	0.02	2	5curA	CL	Rep, Mult	41,42,45,49,109
7	0.02	2	1b6gA	GOL	Rep, Mult	23,77
8	0.02	2	3hssA	NA	Rep, Mult	54,55,57,58,64
9	0.02	2	4c01C	QY9	Rep, Mult	3,27,46,50,69
10	0.01	1	1b6gA	GOL	Rep, Mult	52
11	0.01	1	1j1i0	III	Rep, Mult	51,54,59,64,65,66,67,68,69,70,72,73,92,95,99
12	0.01	1	1g5fA	DCE	Rep, Mult	99
13	0.01	1	1g42A	CP2	Rep, Mult	34,35
14	0.01	1	3a2mA	SUC	Rep, Mult	51,54,65,66,67

	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	2vf2A	0.732	2.22	0.139	0.898	3.7.1.8	NA
2	0.060	3g0iA	0.707	2.38	0.140	0.891	3.3.2.3	40
3	0.060	2pu5A	0.734	2.51	0.102	0.914	3.7.1.8	NA
4	0.060	1u2eA	0.731	2.25	0.113	0.898	3.7.1.-	NA
5	0.060	1b6gA	0.742	2.35	0.111	0.914	3.8.1.5	NA
6	0.060	1k8qA	0.756	2.07	0.147	0.906	3.1.1.3	NA
7	0.060	1vj5A	0.732	2.30	0.165	0.898	3.3.2.10,3.3.2.3	NA
8	0.060	1iunB	0.724	2.36	0.168	0.883	3.7.1.9	NA
9	0.060	1l7aA	0.719	2.71	0.072	0.914	3.1.1.72,3.1.1.41	NA
10	0.060	1mt3A	0.730	2.12	0.088	0.883	3.4.11.5	NA
11	0.060	1j1iA	0.734	2.00	0.188	0.875	3.7.1.8	5
12	0.060	1a88B	0.722	2.06	0.144	0.867	1.11.1.10	47
13	0.060	3c5vA	0.734	2.67	0.092	0.930	3.1.1.-	NA
14	0.060	2pl5A	0.700	2.66	0.056	0.914	2.3.1.31	NA
15	0.060	1cqzB	0.728	2.34	0.157	0.898	3.3.2.10,3.3.2.3	NA
16	0.060	3fcyA	0.702	2.80	0.072	0.906	3.1.1.41	NA
17	0.060	3a2lA	0.737	2.00	0.125	0.875	3.8.1.5	NA
18	0.060	2og1A	0.733	2.53	0.102	0.914	3.7.1.8	NA
19	0.060	2zjfA	0.726	2.21	0.133	0.883	3.3.2.3	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	0.21	0.732	2.15	0.09	0.88	3e3aB	GO:0003824 GO:0004601 GO:0009062 GO:0016298 GO:0016491 GO:0055114 GO:0098869
1	0.21	0.707	2.42	0.17	0.88	4rncA	GO:0016787 GO:0052689
2	0.17	0.717	2.29	0.17	0.88	3b12A	GO:0003824 GO:0016787 GO:0018785
3	0.16	0.748	2.32	0.10	0.91	2xt0A	GO:0003824
4	0.14	0.741	2.36	0.11	0.91	1be0A	GO:0003824 GO:0009636 GO:0016787 GO:0018786 GO:0019260
5	0.14	0.738	2.03	0.16	0.88	3kxpA	GO:0016787 GO:0042803 GO:0042820 GO:0047411
6	0.14	0.731	2.25	0.11	0.90	1u2eA	GO:0003824 GO:0005737 GO:0016787 GO:0018771 GO:0019380 GO:0019439 GO:0019622 GO:0042803 GO:0052823
7	0.14	0.764	1.83	0.13	0.88	4ufoA	GO:0003824 GO:0016787
8	0.14	0.724	2.36	0.17	0.88	1iunB	GO:0003824 GO:0016787
9	0.14	0.733	2.00	0.14	0.87	1a8qA	GO:0003824 GO:0004601 GO:0016491 GO:0017000 GO:0055114 GO:0098869
10	0.14	0.735	2.18	0.10	0.89	4mj3B	GO:0003824 GO:0016787 GO:0018786
11	0.14	0.736	2.07	0.12	0.88	4lxhA	GO:0016787
12	0.14	0.741	2.02	0.14	0.88	4i3fA	GO:0016787
13	0.14	0.719	2.52	0.12	0.91	4f0jA	GO:0003824 GO:0016787
14	0.14	0.734	2.67	0.09	0.93	3c5vA	GO:0004864 GO:0005913 GO:0006482 GO:0008601 GO:0016787 GO:0019901 GO:0019903 GO:0034047 GO:0043086 GO:0051721 GO:0051722 GO:0052689 GO:0098609 GO:0098641
15	0.13	0.728	2.34	0.16	0.90	1cqzB	GO:0000287 GO:0003824 GO:0004301 GO:0005102 GO:0005737 GO:0005777 GO:0005829 GO:0006629 GO:0008152 GO:0009636 GO:0010628 GO:0015643 GO:0016311 GO:0016787 GO:0016791 GO:0019439 GO:0033885 GO:0042577 GO:0042632 GO:0042803 GO:0046272 GO:0046839 GO:0046872 GO:0070062 GO:0090181
16	0.13	0.722	2.39	0.17	0.90	4x00A	GO:0016787
17	0.13	0.735	2.01	0.11	0.87	3fobA	GO:0003824 GO:0004601 GO:0009636 GO:0016491 GO:0016691 GO:0016787 GO:0019806 GO:0055114 GO:0098869
18	0.13	0.732	2.29	0.17	0.90	4haiA	GO:0000287 GO:0003824 GO:0004301 GO:0005102 GO:0005737 GO:0005777 GO:0005829 GO:0006629 GO:0006805 GO:0006874 GO:0006954 GO:0008152 GO:0008217 GO:0009636 GO:0010628 GO:0015643 GO:0016311 GO:0016787 GO:0016791 GO:0017144 GO:0019373 GO:0019439 GO:0033885 GO:0042577 GO:0042632 GO:0042803 GO:0045909 GO:0046272 GO:0046839 GO:0046872 GO:0070062 GO:0072593 GO:0090181
19	0.13	0.733	2.53	0.10	0.91	2og1A	GO:0003824 GO:0016787 GO:0016823 GO:0018771 GO:0018774 GO:0019439
20	0.13	0.731	2.05	0.12	0.87	1hkhA	GO:0003824 GO:0004601 GO:0098869
21	0.07	0.751	2.05	0.11	0.89	3wzlA	GO:0016787
22	0.07	0.718	2.24	0.18	0.88	4ns4A	GO:0016787 GO:0016788
23	0.07	0.734	2.00	0.19	0.88	1j1iA	GO:0016787
24	0.07	0.722	2.39	0.14	0.89	3wmrA	GO:0006508 GO:0008233 GO:0016787
25	0.07	0.732	2.22	0.14	0.90	2vf2A	GO:0005618 GO:0005886 GO:0006629 GO:0006694 GO:0016042 GO:0016787 GO:0018774 GO:0019439 GO:0034820 GO:0044117 GO:0102296
26	0.07	0.733	2.04	0.14	0.87	1a8sA	GO:0003824 GO:0004601 GO:0016491 GO:0016691 GO:0055114 GO:0098869
27	0.07	0.707	2.17	0.08	0.86	2xuaH	GO:0016787 GO:0042952 GO:0047570
28	0.07	0.718	2.25	0.11	0.88	4g8bA	GO:0003824 GO:0016787 GO:0016788

Consensus prediction of GO terms

Molecular Function	GO:0016788	GO:0016209	GO:0016684	GO:0019120
GO-Score	0.42	0.42	0.42	0.35
Biological Processes	GO:1990748	GO:0006631	GO:0044242	GO:0072329
GO-Score	0.42	0.42	0.42	0.42
Cellular Component
GO-Score

(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.