I-TASSER results

I-TASSER results for job id Rv2406c

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

Input Sequence in FASTA format

>protein (142 residues)
MRIADVLRNKGAAVVTINPDATVGELLAGLAEQNIGAMVVVGAEGVVGIVSERDVVRQLH
TYGASVLSRPVAKIMSTTVATCTKSDTVDKISVLMTENRVRHVPVLDGKKLIGIVSIGDV
VKSRMGELEAEQQQLQSYITQG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRIADVLRNKGAAVVTINPDATVGELLAGLAEQNIGAMVVVGAEGVVGIVSERDVVRQLHTYGASVLSRPVAKIMSTTVATCTKSDTVDKISVLMTENRVRHVPVLDGKKLIGIVSIGDVVKSRMGELEAEQQQLQSYITQG
Prediction	CCHHHHHHCCCCCEEEHCCCCCHHHHHHHHHHHCCCEEEEEHCCEEEEEEEHHHHHHHHHHHCCCCCCCCHHHHCCCCCEEHCCCCCHHHHHHHHHHHCCCEEEEEHCCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	8588987568998599789988999999999989988999879989999867899999999899966687578558997996899999999999999799778887799999998778999999999999999999999769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRIADVLRNKGAAVVTINPDATVGELLAGLAEQNIGAMVVVGAEGVVGIVSERDVVRQLHTYGASVLSRPVAKIMSTTVATCTKSDTVDKISVLMTENRVRHVPVLDGKKLIGIVSIGDVVKSRMGELEAEQQQLQSYITQG
Prediction	7404400455744111043732043005224746020000037740000002330022014544526724055152662230437230430041137450210011576400000122300431165364236304521678
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHCCCCCEEEHCCCCCHHHHHHHHHHHCCCEEEEEHCCEEEEEEEHHHHHHHHHHHCCCCCCCCHHHHCCCCCEEHCCCCCHHHHHHHHHHHCCCEEEEEHCCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCC
MRIADVLRNKGAAVVTINPDATVGELLAGLAEQNIGAMVVVGAEGVVGIVSERDVVRQLHTYGASVLSRPVAKIMSTTVATCTKSDTVDKISVLMTENRVRHVPVLDGKKLIGIVSIGDVVKSRMGELEAEQQQLQSYITQG

2rc3C

0.40

0.35

0.89

3.47

MUSTER

KTVKHLLQEKGHTVVAIGPDDSVFNAMQKMAADNIGALLVMKDEKLVGILTERDFSRKSYLLDKPVKDTQVKEIMTRQVAYVDLNNTNEDCMALITEMRVRHLPVLDDGKVIGLLSIGDLVKDAIS----------------

2rc3C

0.40

0.35

0.89

5.70

dPPAS

KTVKHLLQEKGHTVVAIGPDDSVFNAMQKMAADNIGALLVMKDEKLVGILTERDFSRKSYLLDKPVKDTQVKEIMTRQVAYVDLNNTNEDCMALITEMRVRHLPVLDDGKVIGLLSIGDLVKDAIS----------------

2rc3C

0.40

0.35

0.89

5.00

wdPPAS

KTVKHLLQEKGHTVVAIGPDDSVFNAMQKMAADNIGALLVMKDEKLVGILTERDFSRKSYLLDKPVKDTQVKEIMTRQVAYVDLNNTNEDCMALITEMRVRHLPVLDDGKVIGLLSIGDLVKDAIS----------------

2rc3C

0.40

0.35

0.89

3.80

wMUSTER

KTVKHLLQEKGHTVVAIGPDDSVFNAMQKMAADNIGALLVMKDEKLVGILTERDFSRKSYLLDKPVKDTQVKEIMTRQVAYVDLNNTNEDCMALITEMRVRHLPVLDDGKVIGLLSIGDLVKDAIS----------------

2rc3C

0.40

0.35

0.89

3.61

wPPAS

KTVKHLLQEKGHTVVAIGPDDSVFNAMQKMAADNIGALLVMKDEKLVGILTERDFSRKSYLLDKPVKDTQVKEIMTRQVAYVDLNNTNEDCMALITEMRVRHLPVLDDGKVIGLLSIGDLVKDAIS----------------

2rc3C

0.40

0.35

0.89

5.80

dPPAS2

KTVKHLLQEKGHTVVAIGPDDSVFNAMQKMAADNIGALLVMKDEKLVGILTERDFSRKSYLLDKPVKDTQVKEIMTRQVAYVDLNNTNEDCMALITEMRVRHLPVLDDGKVIGLLSIGDLVKDAIS----------------

2rc3C

0.40

0.35

0.89

3.63

PPAS

KTVKHLLQEKGHTVVAIGPDDSVFNAMQKMAADNIGALLVMKDEKLVGILTERDFSRKSYLLDKPVKDTQVKEIMTRQVAYVDLNNTNEDCMALITEMRVRHLPVLDDGKVIGLLSIGDLVKDAIS----------------

2rc3C

0.40

0.35

0.89

4.15

Env-PPAS

KTVKHLLQEKGHTVVAIGPDDSVFNAMQKMAADNIGALLVMKDEKLVGILTERDFSRKSYLLDKPVKDTQVKEIMTRQVAYVDLNNTNEDCMALITEMRVRHLPVLDDGKVIGLLSIGDLVKDAIS----------------

4fryA

0.37

0.35

0.94

3.34

MUSTER

TTVAQILKAKPRTIYTVTKNDFVYDAIKLMAEKGIGALLVVDGDDIAGIVTERDYARKVVLQERSSKATRVEEIMTAKVRYVEPSQSTDECMALMTEHRMRHLPVLDGGKLIGLISIGDLVKSVIADQQFTIS---------

4fryA

0.38

0.35

0.94

5.41

dPPAS

TTVAQILKAKGRTIYTVTKNDFVYDAIKLMAEKGIGALLVVDGDDIAGIVTERDYARKVVLQERSSKATRVEEIMTAKVRYVEPSQSTDECMALMTEHRMRHLPVLDGGKLIGLISIGDLVKSVIADQQFTIS---------

(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=0.71

Estimated TM-score = 0.81±0.09

Estimated RMSD = 3.3±2.3Å

Download Model 2

C-score=-0.92

Download Model 3

C-score=0.98

Download Model 4

C-score=-3.57

Download Model 5

C-score=-3.42

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	2rc3C	0.881	0.38	0.397	0.887
2	4fryA	0.869	1.44	0.376	0.922
3	3fhmA	0.836	1.24	0.421	0.887
4	3fwrB	0.798	1.57	0.232	0.880
5	3ddjA2	0.797	1.88	0.172	0.901
6	3kh5A	0.787	1.87	0.203	0.901
7	3kpcA	0.786	1.36	0.242	0.845
8	2qh1B	0.781	1.63	0.180	0.859
9	5aweA	0.779	2.30	0.217	0.908
10	3pc2A2	0.776	1.68	0.228	0.866

(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	0.74	94	3fhmA	NAI	Rep, Mult	10,13,14,15,35,36,37,102,114,116,118,119,122
2	0.38	54	2yzqA	SAM	Rep, Mult	36,49,51,53,54,58,76,78,79,80,98,99,100,101,102,104
3	0.14	16	2rc3A	NAD	Rep, Mult	53,95,96,99,100,101,117
4	0.07	11	3k2vA	CMK	Rep, Mult	34,35,36,52,116,118
5	0.03	7	3fwsA	MG	Rep, Mult	36,37,51,101
6	0.03	7	3fwsB	PO4	Rep, Mult	36,114,116,118
7	0.01	2	3kh5A	ADP	Rep, Mult	51,53,54,101
8	0.00	1	3fwsA	ANP	Rep, Mult	34,52
9	0.00	1	2nyc0	III	Rep, Mult	24,28,31,34,36,51,52,53,56,58,60,61,92,93,95,96,98,99,100,101,117,121,122,124,125
10	0.00	1	1xkf0	III	Rep, Mult	5,12,13,14,15,32,33,43,44,110,123
11	0.00	1	2zy9A	MG	Rep, Mult	96,97,99
12	0.00	1	3kh5A	AMP	Rep, Mult	5

	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	1sqfA	0.429	4.98	0.056	0.753	2.1.1.-	NA
2	0.060	2z8kC	0.335	5.48	0.049	0.627	2.3.2.2	21,24,38
3	0.060	1ybqA	0.427	4.79	0.070	0.704	3.4.19.1	86
4	0.060	3e4qB	0.447	4.56	0.060	0.753	2.7.13.3	NA
5	0.060	1ra0A	0.417	4.69	0.053	0.697	3.5.4.1	34
6	0.060	3cf4A	0.428	5.24	0.022	0.803	1.2.99.2	NA
7	0.060	3l4uA	0.423	5.32	0.043	0.796	3.2.1.20,3.2.1.3	NA
8	0.060	1od2A	0.366	4.74	0.076	0.641	6.3.4.14,6.4.1.2	118
9	0.060	1gytA	0.442	5.01	0.063	0.810	3.4.11.1	NA
10	0.060	1jcnB	0.438	3.08	0.052	0.563	1.1.1.205	48
11	0.060	2z8kD	0.301	5.08	0.057	0.542	2.3.2.2	NA
12	0.060	1wkyA	0.424	4.90	0.094	0.753	3.2.1.78	NA
13	0.060	1qi9B	0.382	5.64	0.038	0.753	1.11.1.10	NA
14	0.060	1uyvA	0.393	4.97	0.056	0.697	6.3.4.14,6.4.1.2	24
15	0.060	1n63B	0.423	5.04	0.033	0.747	1.2.99.2	NA
16	0.060	3ij3A	0.425	4.95	0.061	0.753	3.4.11.1	NA
17	0.060	3ma8A	0.426	4.99	0.048	0.747	2.7.1.40	98
18	0.060	3pvaA	0.442	5.10	0.047	0.775	3.5.1.11	NA
19	0.060	1j33A	0.430	5.11	0.055	0.782	2.4.2.21	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	0.58	0.836	1.24	0.42	0.89	3fhmA	GO:0000166
1	0.56	0.881	0.38	0.40	0.89	2rc3C	GO:0000166
2	0.51	0.870	1.41	0.37	0.92	4fryB	GO:0000166
3	0.44	0.767	1.84	0.24	0.87	4gqyA	GO:0009507 GO:0009536 GO:0009570 GO:0045454
4	0.43	0.797	1.60	0.22	0.88	3fv6B	GO:0003677 GO:0006351 GO:0006355 GO:0045013
5	0.42	0.824	2.25	0.23	0.96	5aweA	GO:0003824
6	0.41	0.730	1.79	0.24	0.82	2p9mB
7	0.40	0.760	1.85	0.20	0.86	4o9kA	GO:0005975 GO:0016853 GO:0019146 GO:0030246
8	0.39	0.731	1.93	0.20	0.83	2yziB
9	0.37	0.694	2.10	0.25	0.82	1pbjA
10	0.37	0.759	2.26	0.20	0.91	2o16B
11	0.37	0.718	1.80	0.19	0.81	3fnaB
12	0.36	0.694	2.53	0.26	0.85	4esyA	GO:0006950
13	0.36	0.789	1.87	0.20	0.90	3lfzA
14	0.36	0.786	1.36	0.24	0.85	3kpcA	GO:0003824
15	0.35	0.616	3.13	0.15	0.84	2ef7A
16	0.34	0.749	2.46	0.13	0.91	4qfsC	GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
17	0.34	0.733	2.64	0.23	0.89	2ooxE	GO:0000166 GO:0003824 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0006351 GO:0006355 GO:0006357 GO:0007165 GO:0016208 GO:0030295 GO:0031588 GO:0032147
18	0.32	0.764	2.17	0.23	0.89	2v8qE	GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
19	0.31	0.737	1.82	0.20	0.84	3k2vA	GO:0005975 GO:0016853 GO:0019146 GO:0030246 GO:0046872
20	0.31	0.700	2.26	0.21	0.85	1xkfB	GO:0001666 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0046872 GO:0052553 GO:0052572
21	0.31	0.699	2.56	0.24	0.86	4gqwA	GO:0009507 GO:0009536 GO:0045454
22	0.29	0.828	1.88	0.18	0.94	3ddjA	GO:0000166 GO:0003824
23	0.28	0.716	2.54	0.18	0.89	2emqA
24	0.27	0.677	2.35	0.20	0.83	1vr9A	GO:0008152 GO:0016597
25	0.23	0.781	1.63	0.18	0.86	2qh1B	GO:0046872
26	0.22	0.734	1.77	0.26	0.82	2yzqA	GO:0003824 GO:0046872 GO:0051536 GO:0051539
27	0.19	0.704	2.05	0.19	0.82	3l31A	GO:0000166 GO:0004427 GO:0005737 GO:0006796 GO:0016208 GO:0016462 GO:0016787 GO:0030145 GO:0046872 GO:0050897

Consensus prediction of GO terms

Molecular Function	GO:0000166	GO:0003677
GO-Score	0.91	0.43
Biological Processes	GO:0045454	GO:0045013
GO-Score	0.44	0.43
Cellular Component	GO:0009570
GO-Score	0.44

(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.