I-TASSER results

I-TASSER results for job id Rv1056

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

Input Sequence in FASTA format

>protein (254 residues)
MSVDYPQMAATRGRIEPAPRRVRGYLGHVLVFDTSAARYVWEVPYYPQYYIPLADVRMEF
LRDENHPQRVQLGPSRLHSLVSAGQTHRSAARVFDVDGDSPVAGTVRFNWDPLRWFEEDE
PIYGHPRNPYQRADALRSHRHVRVELDGIVLADTRSPVLLFETGIPTRYYIDPADIAFEH
LEPTSTQTLCPYKGTTSGYWSVRVGDAVHRDLAWTYHYPLPAVAPIAGLVAFYNEKVDLT
VDGVALPRPHTQFS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MSVDYPQMAATRGRIEPAPRRVRGYLGHVLVFDTSAARYVWEVPYYPQYYIPLADVRMEFLRDENHPQRVQLGPSRLHSLVSAGQTHRSAARVFDVDGDSPVAGTVRFNWDPLRWFEEDEPIYGHPRNPYQRADALRSHRHVRVELDGIVLADTRSPVLLFETGIPTRYYIDPADIAFEHLEPTSTQTLCPYKGTTSGYWSVRVGDAVHRDLAWTYHYPLPAVAPIAGLVAFYNEKVDLTVDGVALPRPHTQFS
Prediction	CCCCCCCCCCCCCEEHCCCCEEEEEHCCEEEEEHCCCEEEHCCCCCCEEHCCHHHHHHHHCCCCCCCCCCCCCCCEEEEEEHCCEEHCCEEEHCCCCCCHHHCCCEEHCCCCCCCEHCCCCCCCCCCCCCCCEEEEHCCCEEEEEHCCEEEEEHCCCEEEEHCCCCCCEHCCHHHCCHHHCHCCCCCEHCCCCCEEEEEEEEEHCCEEHCCEEEHCCCCCHHHHHHCCCEEHCCCCEEEEEHCEHCCCCCCCCC
Conf.Score	99899998888865665798699999999999959958998589998588699886677656789986666787579999989888655577679999877778588656677655556666568999887668986699699999999999859968999679998577798885667644469856588775677789998598787558997799998899876958875886899995677689999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MSVDYPQMAATRGRIEPAPRRVRGYLGHVLVFDTSAARYVWEVPYYPQYYIPLADVRMEFLRDENHPQRVQLGPSRLHSLVSAGQTHRSAARVFDVDGDSPVAGTVRFNWDPLRWFEEDEPIYGHPRNPYQRADALRSHRHVRVELDGIVLADTRSPVLLFETGIPTRYYIDPADIAFEHLEPTSTQTLCPYKGTTSGYWSVRVGDAVHRDLAWTYHYPLPAVAPIAGLVAFYNEKVDLTVDGVALPRPHTQFS
Prediction	67252153345413114143201020442000005300201036210000013610444214467344324434012020304554263001303436254033101132551413637240241244431403034164202020442000106400201005242120003400435204627441302131403200203275630420022044136204503300001643010103545255376558
	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

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

Sec.Str
Seq

CCCCCCCCCCCCCEEHCCCCEEEEEHCCEEEEEHCCCEEEHCCCCCCEEHCCHHHHHHHHCCCCCCCCCCCCCCCEEEEEEHCCEEHCCEEEHCCCCCCHHHCCCEEHCCCCCCCEHCCCCCCCCCCCCCCCEEEEHCCCEEEEEHCCEEEEEHCCCEEEEHCCCCCCEHCCHHHCCHHHCHCCCCCEHCCCCCEEEEEEEEEHCCEEHCCEEEHCCCCCHHHHHHCCCEEHCCCCEEEEEHCEHCCCCCCCCC
MSVDYPQMAATRGRIEPAPRRVRGYLGHVLVFDTSAARYVWEVPYYPQYYIPLADVRMEFLRDENHPQRVQLGPSRLHSLVSAGQTHRSAARVFDVDGDSPVAGTVRFNWDPLRWFEEDEPIYGHPRNPYQRADALRSHRHVRVELDGIVLADTRSPVLLFETGIPTRYYIDPADIAFEHLEPTSTQTLCPYKGTTSGYWSVRVGDAVHRDLAWTYHYPLPAVAPIAGLVAFYNEKVDLTVDGVALPRPHTQFS

3djmB

0.25

0.11

0.43

1.47

MUSTER

--------------------------------------------------------------------------------------------------------------------------------QNNHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVA--VFDKSEKVTACPLKGEASYYSIVG--SGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY------------

3hxjA1

0.08

0.06

0.72

1.17

dPPAS

WEFLIGNSIDSSPILAKNGTIYLGSSNKNLYAINTDGSVKWFFKSGEIIE---------CRPSIGKDGTIYFGSDKVYAINPDGTEK----WRFDTVTRPAISGTIYVTSLDGHLYAINPDRFKTGKRIESSPVIGNTDTIYFGSYDGHLYAINPDGTEKWNFETGSWII------ATPVIDENGTIYFGTRNGKFYALFN-----------------------------------------------------

3djmB

0.23

0.10

0.44

5.52

dPPAS

--------------------------------------------------------------------------------------------------------------------------------QNNHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVA--VFDKSEKVTACPLK-GEASYYSIVGASGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY------------

3djmB

0.25

0.11

0.43

4.27

wdPPAS

--------------------------------------------------------------------------------------------------------------------------------QNNHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVA--VFDKSEKVTACPLKGEASYYSIVG--SGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY------------

3djmB

0.25

0.11

0.43

1.77

wMUSTER

----------------------------------------------------------------------------------------------------------------------------------NHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVA--VFDKSEKVTACPLKGEASYYSIVG--SGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY------------

3djmB

0.25

0.11

0.43

2.77

wPPAS

--------------------------------------------------------------------------------------------------------------------------------QNNHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVA--VFDKSEKVTACPLKGEASYYSIVG--SGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY------------

3djmB

0.23

0.10

0.44

15.17

dPPAS2

--------------------------------------------------------------------------------------------------------------------------------QNNHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVA--VFDKSEKVTACPLK-GEASYYSIVGASGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY------------

3djmB

0.23

0.10

0.44

2.37

PPAS

--------------------------------------------------------------------------------------------------------------------------------QNNHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVA--VFDKSEKVTACPLK-GEASYYSIVGASGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY------------

3djmB

0.23

0.10

0.44

4.30

Env-PPAS

--------------------------------------------------------------------------------------------------------------------------------QNNHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVA--VFDKSEKVTACPLK-GEASYYSIVGASGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY------------

4le7A

0.10

0.09

0.91

0.69

MUSTER

ASS-APRQVRDGQFITSPNGKYKLVMDGNLVLYEDGTKPIWNTTPVGNLYNKAG--QVAWSSNVYTAYLFEEFKDEAYLNLQDD---GDFGIFSDEAK-------WGSIVLSRPEVGVKNKIIPTGTVMVPGTEYINGNYRLAFQGDGLVIYQINPQVVIWATYMGADRAVVQEDGNFVIYKGTTALWHTHTATGMPAYLKFTNTGKLF-TLLWTLK--RGSLSKPPKVIPGQHGP----LDTTPISWPHDY--

(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=-3.48

Estimated TM-score = 0.33±0.11

Estimated RMSD = 14.2±3.8Å

Download Model 2

C-score=-3.82

Download Model 3

C-score=-3.96

Download Model 4

C-score=-4.12

Download Model 5

C-score=-4.06

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	3djmB	0.419	1.31	0.243	0.437
2	5annA	0.407	6.16	0.069	0.701
3	4a01A	0.401	6.44	0.050	0.728
4	3ldkA	0.401	6.00	0.078	0.693
5	3ikmD1	0.400	6.07	0.050	0.669
6	3pigA	0.400	5.93	0.051	0.685
7	2eceA	0.393	6.34	0.061	0.697
8	4yixA	0.390	6.27	0.088	0.685
9	3ugfA	0.390	5.94	0.034	0.669
10	4ci1B	0.389	5.63	0.041	0.626

(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	0.05	3	2pq3A	ZN	Rep, Mult	172,175
2	0.03	2	3o5uB	FE	Rep, Mult	49,139,141
3	0.03	2	3sy9C	C8E	Rep, Mult	199,213
4	0.03	2	3hncA	TTP	Rep, Mult	169,190,191,192,197
5	0.03	2	1yd4A	MN	Rep, Mult	145,238,240
6	0.02	1	1y9mA	UUU	Rep, Mult	194,196,227,228
7	0.02	1	2wghA	DTP	Rep, Mult	50,55,56
8	0.02	1	2wghB	DTP	Rep, Mult	135,226,230,231,232
9	0.02	1	2ovzA	CA	Rep, Mult	185,188,191
10	0.02	1	4iikA	MG	Rep, Mult	33,238
11	0.02	1	2g8sA	CA	Rep, Mult	162,170
12	0.02	1	3o32B	FE	Rep, Mult	139,141
13	0.02	1	2wn9A	ZY5	Rep, Mult	123,214
14	0.02	1	1pm1X	IMD	Rep, Mult	142,144,152,154
15	0.02	1	3rbhD	C8E	Rep, Mult	197,229
16	0.02	1	3ugfB	UUU	Rep, Mult	153,155,156,158,171,173
17	0.02	1	3hncB	TTP	Rep, Mult	169,170,171,172
18	0.02	1	2cvtA	ANP	Rep, Mult	144,151,171,172,232
19	0.02	1	2y68A	AZI	Rep, Mult	146,236,237
20	0.02	1	3dgdA	ZN	Rep, Mult	143,242

	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	2h12B	0.382	6.25	0.070	0.673	2.3.3.1	NA
2	0.060	1mc1B	0.379	6.08	0.050	0.646	6.3.3.4	217
3	0.060	3hwkE	0.370	6.35	0.073	0.657	2.3.3.1	NA
4	0.060	1qdbA	0.376	5.76	0.045	0.618	1.7.2.2	98,102
5	0.060	2wghB	0.381	6.06	0.052	0.646	1.17.4.1	NA
6	0.060	2b3xA	0.380	6.21	0.061	0.673	4.2.1.3	NA
7	0.060	3hztA	0.291	6.42	0.069	0.520	2.7.11.17	NA
8	0.060	2cvtA	0.381	6.13	0.042	0.650	1.17.4.1	NA
9	0.060	1pg3B	0.373	6.00	0.040	0.630	6.2.1.1	34,160,164
10	0.060	1i19A	0.374	6.01	0.024	0.618	1.1.3.6	162
11	0.060	3bnjA	0.380	5.93	0.045	0.642	1.7.2.2	NA
12	0.060	1y9mA	0.374	6.09	0.059	0.665	3.2.1.80	162
13	0.060	3fsnB	0.371	6.14	0.034	0.646	5.2.1.7	25
14	0.060	2hb6A	0.371	6.79	0.068	0.697	3.4.11.1	153
15	0.060	2q5lA	0.373	6.59	0.030	0.689	4.1.1.74,4.1.1.43	NA
16	0.060	1vlbA	0.370	6.72	0.033	0.681	1.2.99.7	NA
17	0.060	1g72A	0.370	5.79	0.066	0.626	1.1.99.8	NA
18	0.060	2ipyA	0.284	6.78	0.030	0.539	4.2.1.3	78
19	0.060	1z45A	0.374	6.12	0.069	0.646	5.1.3.2,5.1.3.3	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	0.06	0.400	6.47	0.04	0.71	4av3B	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
1	0.06	0.389	6.17	0.05	0.69	3ugfB	GO:0004553 GO:0004564 GO:0004575 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016740 GO:0016787 GO:0016798
2	0.06	0.406	6.05	0.07	0.69	3pigB	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
3	0.06	0.366	6.14	0.02	0.65	3rwkX	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051670
4	0.06	0.401	6.44	0.05	0.73	4a01A	GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
5	0.06	0.399	6.53	0.05	0.72	4av6A	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
6	0.06	0.306	6.54	0.04	0.56	2berA	GO:0004308 GO:0005576 GO:0008152 GO:0016787 GO:0016798 GO:0052794 GO:0052795 GO:0052796
7	0.06	0.407	6.16	0.07	0.70	5annA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
8	0.06	0.381	6.15	0.04	0.66	1y4wA	GO:0000272 GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051669
9	0.06	0.333	6.46	0.06	0.60	2ac1A	GO:0004553 GO:0004564 GO:0004575 GO:0005576 GO:0005618 GO:0005886 GO:0005975 GO:0008152 GO:0009611 GO:0016787 GO:0016798 GO:0048046 GO:0080167
10	0.06	0.314	6.07	0.05	0.55	1yxoA	GO:0000287 GO:0005737 GO:0008270 GO:0008615 GO:0016491 GO:0016616 GO:0042823 GO:0046872 GO:0050570 GO:0050897 GO:0051287 GO:0055114
11	0.06	0.401	6.00	0.08	0.69	3ldkA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
12	0.06	0.332	6.46	0.06	0.60	4eqvA	GO:0004553 GO:0004564 GO:0004575 GO:0005576 GO:0005737 GO:0005975 GO:0005987 GO:0008152 GO:0010147 GO:0016787 GO:0016798 GO:0034484 GO:0051670 GO:1902927
13	0.06	0.326	6.55	0.05	0.60	2addA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051669
14	0.06	0.284	6.72	0.05	0.54	1ksiA	GO:0005507 GO:0008131 GO:0009308 GO:0016491 GO:0046872 GO:0048038 GO:0052593 GO:0052594 GO:0052595 GO:0052596 GO:0052597 GO:0055114 GO:0097185
15	0.06	0.365	6.08	0.03	0.64	3kf5A	GO:0004553 GO:0004564 GO:0004575 GO:0005975 GO:0008152 GO:0016787 GO:0016798
16	0.06	0.271	6.64	0.04	0.50	2vf7B	GO:0000166 GO:0003677 GO:0004518 GO:0005524 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0009380 GO:0009381 GO:0016887 GO:0046872 GO:0090305
17	0.06	0.282	5.84	0.02	0.48	3t66A	GO:0043190 GO:0055085
18	0.06	0.376	6.17	0.06	0.64	1uypA	GO:0004553 GO:0004564 GO:0004575 GO:0005975 GO:0005987 GO:0008152 GO:0016787 GO:0016798

Consensus prediction of GO terms

Molecular Function	GO:0003824
GO-Score	0.40
Biological Processes	GO:0044238
GO-Score	0.31
Cellular Component	GO:0005887	GO:0005576	GO:0005774
GO-Score	0.07	0.06	0.06

(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.