I-TASSER results

Input Sequence in FASTA format

>protein (80 residues)
MSAVVVDAVEHLVRGIVDNPDDVRVDLITSRRGRTVEVHVHPDDLGKVIGRGGRTATALR
TLVAGIGGRGIRVDVVDTDQ

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MSAVVVDAVEHLVRGIVDNPDDVRVDLITSRRGRTVEVHVHPDDLGKVIGRGGRTATALRTLVAGIGGRGIRVDVVDTDQ
Prediction	CCCHHHHHHHHHHHHHCCCCCEEEEEEEHCCCEEEEEEEHCCCCCEEEHCCCCHHHHHHHHHHHHHHCCCCEEEEEHCCC
Conf.Score	98569999999999975896558999999599899999979766868976898589999999999965775799997699
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MSAVVVDAVEHLVRGIVDNPDDVRVDLITSRRGRTVEVHVHPDDLGKVIGRGGRTATALRTLVAGIGGRGIRVDVVDTDQ
Prediction	86731440032004310643650404346576223030303672203021474440400220041135471313023368
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHCCCCCEEEEEEEHCCCEEEEEEEHCCCCCEEEHCCCCHHHHHHHHHHHHHHCCCCEEEEEHCCC
MSAVVVDAVEHLVRGIVDNPDDVRVDLITSRRGRTVEVHVHPDDLGKVIGRGGRTATALRTLVAGIGGRGIRVDVVDTDQ

2cxcA2

0.23

0.20

0.88

1.57

MUSTER

-SSDLERIVKNLFPGV----KIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFG--VEKVVIR---

2cxcA2

0.20

0.17

0.88

2.18

dPPAS

-----SSDLERIVKNLFPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVEKVVIR-----

2cxcA2

0.22

0.19

0.85

1.84

wdPPAS

-SSDLERIVKNL------PGKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLF--GVEKVVIR---

2cxcA

0.21

0.19

0.88

1.10

wMUSTER

YSSDLERIVKNLF-----PGKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFG--VEKVVIR---

2cxcA2

0.22

0.19

0.84

1.45

wPPAS

-SSDLERIVKNL------PGKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFG---EKVVIR---

2cxcA2

0.22

0.19

0.86

4.16

dPPAS2

-SSDLERIVKNLF-----PGKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFG--VEKVVIR---

2cxcA2

0.22

0.19

0.85

1.60

PPAS

-SSDLERIVKNL------PGKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLF--GVEKVVIR---

2cxcA2

0.23

0.20

0.88

1.96

Env-PPAS

-SSDLERIVKNLFPGV----KIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLF--GVEKVVIR---

1l2fA4

0.24

0.20

0.84

1.16

MUSTER

-SD---DPKQLIANAL--APATVEVEILDKENK-AARVLVPPTQLSLAIGKGGQNARLAAKLTG------WKIDIKPINL

2pt7G1

0.14

0.95

1.23

dPPAS

KLHEIKQELKDLFSHLPYKINKVEVSLYEPG---VLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIHTYGYSIRLEIS-

(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 4 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=0.05

Estimated TM-score = 0.72±0.11

Estimated RMSD = 3.4±2.4Å

Download Model 2

C-score=-1.95

Download Model 3

C-score=-0.53

Download Model 4

C-score=-1.51

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	3ieuA	0.787	1.90	0.076	0.988
2	3ievA	0.760	1.97	0.114	0.988
3	1wf3A2	0.757	2.03	0.139	0.988
4	2zkqc1	0.755	1.71	0.123	0.912
5	2cxcA2	0.751	1.45	0.186	0.863
6	3kiqc	0.742	1.79	0.274	0.912
7	2aw7C	0.741	1.73	0.205	0.912
8	3bbnC	0.718	2.50	0.103	0.975
9	1l2fA4	0.694	2.02	0.179	0.838
10	2ywcA	0.690	2.26	0.108	0.925

(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	0.24	13	3ievA	NUC	Rep, Mult	14,20,31,45,46,47,49,50,51,52,53,54,55,56,57,60,61,64,70,72,74,75,76
2	0.06	3	4d2eC	78M	Rep, Mult	59,63
3	0.04	2	2j4w2	III	Rep, Mult	9,10,14,20,21,22,23,24,40,41
4	0.04	2	3vvkA	22B	Rep, Mult	9,13,16,56
5	0.02	1	3byr0	III	Rep, Mult	28,37,74,75,76
6	0.02	1	2axtl	UNK	Rep, Mult	63,66
7	0.02	1	4lq3A	20V	Rep, Mult	15,16,18,50,55
8	0.02	1	1iv2B	CDP	Rep, Mult	40,44,45,48,49,56,76,77,78,80
9	0.02	1	1nipA	MG	Rep, Mult	53,55
10	0.02	1	3i8gF	MG	Rep, Mult	51,52
11	0.02	1	3d5cC	MG	Rep, Mult	6,25,27

	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	1gpmA	0.633	2.69	0.079	0.950	6.3.5.2	NA
2	0.060	3imlD	0.550	3.01	0.059	0.838	2.5.1.6	NA
3	0.060	3gtdA	0.569	3.36	0.026	0.950	4.2.1.2	NA
4	0.060	2ayaA	0.622	2.97	0.114	0.863	2.7.7.7	12,39
5	0.060	3d0oB	0.559	2.80	0.026	0.812	1.1.1.27	NA
6	0.060	3cmqA	0.570	2.81	0.138	0.812	6.1.1.20	14
7	0.060	2dplA	0.678	2.27	0.147	0.938	6.3.5.2	NA
8	0.060	1u6zB	0.574	3.07	0.056	0.875	3.6.1.11	11
9	0.060	1nyeD	0.627	3.12	0.039	0.950	1.11.1.15	26,56,63
10	0.060	1bibA	0.570	2.78	0.078	0.825	6.3.4.15	34
11	0.060	3bt7A	0.619	2.95	0.135	0.925	2.1.1.35	NA
12	0.060	1fimA	0.575	3.31	0.038	0.963	5.3.2.1	62
13	0.060	1fugA	0.552	2.95	0.074	0.850	2.5.1.6	NA
14	0.060	3d4pB	0.560	2.81	0.026	0.812	1.1.1.27	49
15	0.060	3hx0A	0.570	3.16	0.093	0.912	2.7.7.7,	74
16	0.060	2zzgA	0.559	2.78	0.087	0.863	6.1.1.7	NA
17	0.060	1w27A	0.580	2.85	0.117	0.825	4.3.1.24	NA
18	0.060	3djiF	0.560	3.32	0.078	0.963	5.3.2.1	23,25,41,59,73
19	0.060	1bpxA	0.573	3.02	0.129	0.875	2.7.7.7	74

(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	0.31	0.717	2.12	0.12	0.93	1wh9A	GO:0000184 GO:0003677 GO:0003684 GO:0003723 GO:0003729 GO:0003735 GO:0003906 GO:0004520 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005739 GO:0005743 GO:0005759 GO:0005819 GO:0005829 GO:0005840 GO:0005844 GO:0005856 GO:0005886 GO:0005925 GO:0006281 GO:0006351 GO:0006355 GO:0006364 GO:0006412 GO:0006413 GO:0006417 GO:0006614 GO:0006915 GO:0006974 GO:0006979 GO:0007049 GO:0007059 GO:0007067 GO:0008017 GO:0008134 GO:0010628 GO:0015631 GO:0015935 GO:0016020 GO:0016829 GO:0017148 GO:0019083 GO:0019104 GO:0019899 GO:0019900 GO:0019901 GO:0022627 GO:0030529 GO:0030544 GO:0031012 GO:0031116 GO:0031397 GO:0032079 GO:0032183 GO:0032357 GO:0032358 GO:0032587 GO:0042769 GO:0042981 GO:0043507 GO:0044390 GO:0044822 GO:0045738 GO:0045739 GO:0051018 GO:0051225 GO:0051301 GO:0051536 GO:0051879 GO:0061481 GO:0070062 GO:0070181 GO:0070301 GO:0072686 GO:0097100 GO:1901224 GO:1902231 GO:1902546 GO:1905053 GO:2001235 GO:2001272
1	0.16	0.699	2.53	0.14	0.96	4kzxD	GO:0003723 GO:0003735 GO:0003906 GO:0005737 GO:0005840 GO:0006259 GO:0006412 GO:0015935 GO:0030529
2	0.15	0.751	1.45	0.18	0.86	2cxcA	GO:0003676 GO:0003723 GO:0005737 GO:0006351 GO:0006353 GO:0006355
3	0.14	0.791	1.83	0.09	0.99	1egaB	GO:0000028 GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0006468 GO:0016020 GO:0019843 GO:0042254 GO:0042274 GO:0043024 GO:0070181
4	0.10	0.429	3.89	0.07	0.74	1lnzA	GO:0000166 GO:0000287 GO:0003924 GO:0005525 GO:0005737 GO:0016787 GO:0030435 GO:0042254 GO:0046872
5	0.09	0.621	2.83	0.08	0.91	3j8gX	GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005829 GO:0032794 GO:0042254 GO:0043022
6	0.09	0.638	2.73	0.10	0.91	4dcsA	GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0042254 GO:0043022
7	0.08	0.760	1.97	0.11	0.99	3ievA	GO:0000028 GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0016020 GO:0019843 GO:0042254 GO:0042274 GO:0043024 GO:0070181
8	0.07	0.633	2.81	0.14	0.93	5dn8A	GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0042254 GO:0043022
9	0.07	0.595	3.16	0.13	0.95	5dcxA	GO:0000166 GO:0005524 GO:0006260 GO:0016032 GO:0016787 GO:0019079 GO:0039592 GO:0039645 GO:0039665 GO:0039693 GO:0046718 GO:0060153
10	0.07	0.530	3.47	0.07	0.94	4ttbA	GO:0004447 GO:0005886 GO:0006590 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
11	0.07	0.757	2.03	0.14	0.99	1wf3A	GO:0000028 GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0005886 GO:0016020 GO:0019843 GO:0042254 GO:0042274 GO:0043024 GO:0070181
12	0.07	0.578	3.23	0.11	0.93	1mkyA	GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0042254 GO:0043022
13	0.07	0.531	3.36	0.07	0.93	4ttcA	GO:0004447 GO:0005886 GO:0006590 GO:0016020 GO:0016021 GO:0016491 GO:0055114 GO:0098869
14	0.07	0.427	3.89	0.09	0.72	3ec1A	GO:0005525
15	0.07	0.455	3.10	0.15	0.72	3vr1A	GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0006412 GO:0006415 GO:0006449 GO:0016149
16	0.07	0.373	3.88	0.07	0.68	3gehA	GO:0000166 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006400 GO:0008033 GO:0016787 GO:0046872
17	0.07	0.415	3.50	0.04	0.62	3w5iB	GO:0005525 GO:0005886 GO:0006810 GO:0015093 GO:0015684 GO:0016020 GO:0016021 GO:0055072 GO:1903874
18	0.07	0.377	3.94	0.03	0.69	2lkcA	GO:0000166 GO:0003743 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006412 GO:0006413
19	0.06	0.389	4.36	0.09	0.76	2e87A	GO:0005525
20	0.06	0.374	4.28	0.01	0.70	3rwmB	GO:0000139 GO:0000166 GO:0003924 GO:0005525 GO:0005768 GO:0005794 GO:0005829 GO:0006810 GO:0006887 GO:0006914 GO:0007264 GO:0015031 GO:0016020 GO:0016192 GO:0034498 GO:0055037
21	0.06	0.387	3.75	0.10	0.69	1sulB	GO:0000166 GO:0000287 GO:0003924 GO:0005525 GO:0005829 GO:0007049 GO:0046872 GO:0051301

Consensus prediction of GO terms

Molecular Function	GO:0017111	GO:0035639	GO:0032561	GO:0032550	GO:0003735	GO:0003906	GO:0070181	GO:0051879	GO:0097100	GO:0008017	GO:0019901	GO:0032183	GO:0032357	GO:0051536	GO:0044390	GO:0019104	GO:0051018	GO:0032358	GO:0008134	GO:0030544	GO:0003729
GO-Score	0.45	0.45	0.45	0.45	0.41	0.41	0.41	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31
Biological Processes	GO:0006355	GO:1902546	GO:2001272	GO:0007067	GO:0031116	GO:0017148	GO:0051301	GO:0019083	GO:1902231	GO:0010628	GO:0000184	GO:1901224	GO:0043507	GO:0032079	GO:0006614	GO:0045738	GO:0031397	GO:0070301	GO:0006364	GO:0042769	GO:0051225	GO:1905053	GO:0006413	GO:0007059	GO:0061481
GO-Score	0.41	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31
Cellular Component	GO:0022627	GO:0070062	GO:0005925	GO:0005759	GO:0031012	GO:0072686	GO:0005730	GO:0005743	GO:0032587	GO:0005654	GO:0005844
GO-Score	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31	0.31

(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.

I-TASSER results for job id Rv2908c

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

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