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I-TASSER results for job id S775057

(Click on S775057_results.tar.bz2 to download the tarball file including all modeling results listed on this page. Click on Annotation of I-TASSER Output to read the instructions for how to interpret the results on this page. Model results are kept on the server for 60 days, there is no way to retrieve the modeling data older than 2 months)

Submitted Sequence in FASTA format

>protein
MDERHNSYKDMLLDVSLLIDKDDLQRMKFKCDQVIKKRQNEKITQPTELFTALEERGYLN
ETNVDFLKNLLRTCCGGKIDAIRALESYERVYIPGFVPTVQQAQAPHLGQANVQLGPGIP
QASGQQIVY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDERHNSYKDMLLDVSLLIDKDDLQRMKFKCDQVIKKRQNEKITQPTELFTALEERGYLNETNVDFLKNLLRTCCGGKIDAIRALESYERVYIPGFVPTVQQAQAPHLGQANVQLGPGIPQASGQQIVY
Prediction	CCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	984303599999999974599999999998254166777753398999999999849888743899999999981288999999999886127555898877788545887544598998875558889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDERHNSYKDMLLDVSLLIDKDDLQRMKFKCDQVIKKRQNEKITQPTELFTALEERGYLNETNVDFLKNLLRTCCGGKIDAIRALESYERVYIPGFVPTVQQAQAPHLGQANVQLGPGIPQASGQQIVY
Prediction	856462503400240176046720440120036304664255154034004303736404772141023004403541430053056144444754346665445444454445354731664665347
	Values range from 0 (buried residue) to 9 (highly exposed residue)

Predicted normalized B-factor

(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

(I-TASSER modeling starts from the structure templates identified by LOMETS from the PDB library. LOMETS is a meta-server threading approach containing multiple threading programs, where each threading program can generate tens of thousands of template alignments. I-TASSER only uses the templates of the highest significance in the threading alignments, the significance of which are measured by the Z-score, i.e. the difference between the raw and average scores in the unit of standard deviation. The templates in this section are the 10 best templates selected from the LOMETS threading programs. Usually, one template of the highest Z-score is selected from each threading program, where the threading programs are sorted by the average performance in the large-scale benchmark test experiments.)

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Z-score

Download
Align.

                  20                  40                  60                  80                 100                 120
                   |                   |                   |                   |                   |                   |         

Sec.Str
Seq

CCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MDERHNSYKDMLLDVSLLIDKDDLQRMKFKCDQVIKKRQNEKITQPTELFTALEERGYLNETNVDFLKNLLRTCCGGKIDAIRALESYERVYIPGFVPTVQQAQAPHLGQANVQLGPGIPQASGQQIVY

1n3kA

0.17

0.20

0.91

1.76

Download

-----AEYGTLLQDLTNNITLEDLEQLKSACKEDIPSEKSEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEIS--RRPDLLTMVVDYRTRVLKISEEDELDTKLTRIPSAKKYKDIIRQPSEEE----

7lvjA

0.28

0.26

0.71

1.64

Download

-----MDFSRNLYDIGEQLDSEDLASLKFLSLDYIPQRKQEPIKDALMLFQRLQEKRMLEESNLSFLKELLFRI--NRLDLLITYLNTRKEETPGRAQI------------------------------

2gf5A

0.23

0.17

0.71

2.90

Download

----SDPFLVLLHSVSSSLSSSELTELKYLCLGRVGKRKLERVQSGLDLFSMLLEQNDLEPGHTELLRELLASL--RRHDLLRRVDDFEAGAAAGAA--------------------------------

1n3k

0.19

0.20

0.91

2.10

Download

----MAEYGTLLQDLTNNITLEDLEQLKSACKEDIPSEKSEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEIS--RRPDLLTMVVDYRTRVLKISELDTKLTRIPSAKKYKDIIR----QPS-EEEII

1n3kA

0.19

0.20

0.95

1.92

Download

----MAEYGTLLQDLTNNITLEDLEQLKSACKEDIPSEKSEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEIS--RRPDLLTMVVDYRTRVLKISEEDELDTKLTR-IPSAKKYKDIIRQPSEEEIIK

1n3k

0.22

0.20

0.67

3.38

Download

-----AEYGTLLQDLTNNITLEDLEQLKSACKEDIPSEKSEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEIS--RRPDLLTMVVDYRTRVL------------------------------------

1n3kA

0.20

0.95

1.52

Download

----MAEYGTLLQDLTNNITLEDLEQLKSACKEDIPSEKSEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEIS--RRPDLLTMVVDYRTRVLKISEEDELDTKLTRIPSAK-KYKDIIRQPSEEEIIK

4zbwA

0.28

0.25

0.75

1.97

Download

------DFSRNLYDIGEQLDSEDLASLKFLSLDYIPQRKQEPIKDALMLFQRLQEKRMLEESNLSFLKELLFRIN--RLDLLITYLNTRKEEMERELQTPGRAQI------------------------

7lvjA

0.30

0.26

0.76

1.27

Download

MD-----FSRNLYDIGEQLDSEDLASLKFLSLDYIPQRKQEPIKDALMLFQRLQEKRMLEESNLSFLKELLFRI--NRLDLLITYLNTRKEEMERELQTPGRAQI------------------------

1n3kA

0.17

0.20

0.95

2.28

Download

----MAEYGTLLQDLTNNITLEDLEQLKSACKEDIPSEKSEEITTGSAWFSFLESHNKLDKDNLSYIEHIFEI--SRRPDLLTMVVDYRTRVEEDELDTKLTRIPSAKKYKDIIRQPSEEEIIKLAPPP

(a)	All the residues are colored in black; however, those residues in template which are identical to the residue in the query sequence are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade. (more about the colors used)
(b)	Rank of templates represents the top ten threading templates used by I-TASSER.
(c)	Ident1 is the percentage sequence identity of the templates in the threading aligned region with the query sequence.
(d)	Ident2 is the percentage sequence identity of the whole template chains with query sequence.
(e)	Cov represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein.
(f)	Norm. Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa.
(g)	Download Align. provides the 3D structure of the aligned regions of the threading templates.
(h)	The top 10 alignments reported above (in order of their ranking) are from the following threading programs:
	1: FFAS-3D 2: SPARKS-X 3: HHSEARCH2 4: HHSEARCH I 5: Neff-PPAS 6: HHSEARCH 7: pGenTHREADER 8: wdPPAS 9: PROSPECT2 10: SP3

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 a higher value signifies a model with a higher 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.)

(By right-click on the images, you can export image file or change the configurations, e.g. modifying the background color or stopping the spin of your models)

Download Model 1 C-score=-0.17 (Read more about C-score) Estimated TM-score = 0.69±0.12 Estimated RMSD = 4.8±3.1Å	Download Model 2 C-score = -3.86	Download Model 3 C-score = -4.00	Download Model 4 C-score = -4.24	Download Model 5 C-score = -3.82

Proteins structurally close to the target in the 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	Alignment
1	1n3kA	0.886	1.26	0.189	0.946	Download
2	2gf5A	0.628	3.24	0.180	0.853	Download
3	2bbzA	0.617	2.19	0.192	0.736	Download
4	6m6oA	0.614	2.23	0.149	0.729	Download
5	4zbwA	0.603	2.31	0.198	0.698	Download
6	4o7qA	0.587	2.01	0.133	0.698	Download
7	2do9A	0.571	2.66	0.120	0.744	Download
8	1a1wA	0.564	1.67	0.241	0.643	Download
9	2a5yB	0.560	3.17	0.075	0.744	Download
10	7pzcA	0.558	3.19	0.103	0.729	Download

(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 COFACTOR and COACH

(This section reports biological annotations of the target protein by COFACTOR and COACH based on the I-TASSER structure prediction. While COFACTOR deduces protein functions (ligand-binding sites, EC and GO) using structure comparison and protein-protein networks, COACH is a meta-server approach that combines multiple function annotation results (on ligand-binding sites) 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	0.07	3	4as2C	BTB	Rep, Mult	11,12,14,16,47,50,51
2	0.05	2	4z9vA	PEPTIDE	Rep, Mult	19,78,79,81,82,83,85
3	0.05	2	4s2mA	IOD	Rep, Mult	12,64,88
4	0.05	2	4m9zD	PEPTIDE	Rep, Mult	17,24,28
5	0.05	2	4fouB	CA	Rep, Mult	86,89

	Download the residue-specific ligand binding probability, which is estimated by SVM.
	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	0.220	2hoqA	0.519	4.36	0.045	0.837	3.-.-.-	NA
2	0.200	2w4mA	0.497	4.42	0.055	0.830	3.1.3.29	NA
3	0.200	1ci8A	0.490	4.64	0.056	0.845	3.1.1.1	NA
4	0.199	1s9rA	0.491	4.39	0.049	0.806	3.5.3.6	NA
5	0.178	3c46B	0.524	4.43	0.048	0.868	2.7.7.6	NA

	Click on the radio buttons to visualize predicted active site residues.
(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
Top 10 homologous GO templates in PDB
1	0.35	0.8858	1.26	0.19	0.95	1n3kA	GO:0042981 GO:0006810 GO:0006915 GO:0005515 GO:0005737 GO:0008643
2	0.26	0.6284	3.24	0.18	0.85	2gf5A	GO:0043005 GO:0043234 GO:0005123 GO:0071260 GO:0051607 GO:0006919 GO:0070265 GO:0005515 GO:0043123 GO:0005829 GO:0045087 GO:0042981 GO:0031264 GO:0006915 GO:0060340 GO:0008625 GO:0042802 GO:0008624 GO:0031265 GO:0045121 GO:0005737 GO:0032757 GO:0051291 GO:0044297 GO:0044419 GO:0045944 GO:0032813 GO:0032760 GO:0008633 GO:0007165
3	0.25	0.6169	2.19	0.19	0.74	2bbzA	GO:0044419 GO:0006915 GO:0004197 GO:0005515 GO:0006508 GO:0042981
4	0.24	0.5639	1.67	0.24	0.64	1a1wA	GO:0044419 GO:0044297 GO:0032813 GO:0032760 GO:0043234 GO:0043005 GO:0008633 GO:0005123 GO:0071260 GO:0051607 GO:0006919 GO:0070265 GO:0005515 GO:0043123 GO:0005829 GO:0045087 GO:0042981 GO:0031264 GO:0006915 GO:0060340 GO:0008625 GO:0042802 GO:0008624 GO:0031265 GO:0045121 GO:0005737 GO:0032757 GO:0051291 GO:0045944
5	0.23	0.5393	3.27	0.09	0.73	1vt4I	GO:0005524 GO:0006915
6	0.22	0.5528	3.11	0.07	0.74	3lqqA	GO:0051432 GO:0006915 GO:0005829 GO:0005624 GO:0005524 GO:0005634 GO:0043281 GO:0048598 GO:0048471 GO:0005625 GO:0000166 GO:0005739 GO:0043065 GO:0008219 GO:0008361 GO:0005515 GO:0051434 GO:0005622 GO:0042981
7	0.22	0.5191	4.36	0.04	0.84	2hoqA	GO:0008152 GO:0003824 GO:0008967 GO:0016787
8	0.22	0.5196	3.07	0.13	0.71	3mopA	GO:0005515 GO:0007165
9	0.22	0.5230	2.82	0.19	0.67	3cl3A	GO:0004197 GO:0005515 GO:0006508 GO:0042981
10	0.22	0.5219	3.27	0.11	0.73	1e3yA	GO:0045087 GO:0005829 GO:0031264 GO:0006915 GO:0060340 GO:0008625 GO:0042802 GO:0008624 GO:0031265 GO:0045121 GO:0005737 GO:0032757 GO:0051291 GO:0044297 GO:0044419 GO:0045944 GO:0032813 GO:0032760 GO:0043234 GO:0043005 GO:0008633 GO:0005123 GO:0071260 GO:0051607 GO:0006919 GO:0070265 GO:0005515 GO:0043123 GO:0042981 GO:0007165

Consensus prediction of GO terms

Molecular Function GO:0004175 GO:0032559 GO:0035639 GO:0042802 GO:0005123 GO:0008234

GO-Score 0.51 0.46 0.46 0.44 0.44 0.31

Biological Process GO:0044419 GO:0019538 GO:0051607 GO:0045944 GO:0032757 GO:0043123 GO:0008633 GO:0051291 GO:0032760 GO:0008625

GO-Score 0.58 0.45 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44

Cellular Component GO:0005829 GO:0044297 GO:0043005 GO:0031265 GO:0045121

GO-Score 0.44 0.44 0.44 0.44 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 S775057_results.tar.bz2 to download the tarball file including all modeling results listed on this page]

Please cite the following articles when you use the I-TASSER server:

Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1: 100014 (2021).
Chengxin Zhang, Peter L. Freddolino, and Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017).
Jianyi Yang, Yang Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.