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I-TASSER results for job id S777124

(Click on S777124_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

>seq
MHCVANESHWARIVISWANATHANANANTHASCMRAMANIAN

Predicted Secondary Structure

Sequence	20 40 \| \| MHCVANESHWARIVISWANATHANANANTHASCMRAMANIAN
Prediction	CCCCCCCCHHHHHHSSSCCCCCCCCCCCCHHHHHHHHHHHCC
Conf.Score	953224010453001303324245675415999999874339
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MHCVANESHWARIVISWANATHANANANTHASCMRAMANIAN
Prediction	741335463113010312434444343633340243235348
	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
                   |                   |  

Sec.Str
Seq

CCCCCCCCHHHHHHSSSCCCCCCCCCCCCHHHHHHHHHHHCC
MHCVANESHWARIVISWANATHANANANTHASCMRAMANIAN

2xphA

0.11

0.17

0.86

0.28

Download

---IHLGVHWCLAVVDFRKKNYYDSMGGINNEACRILLQ---

7u65G

0.07

0.14

1.00

0.86

Download

DDWYDAYTRKDCIRLRIEDRSGNLIDTSTFNMCTDWLNHMYD

4xkhE

0.17

0.14

1.00

0.93

Download

NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSAS

7wjiA

0.21

0.41

0.81

0.80

Download

------NMSWLHVMILLCNQQSFICTHVHSRSCARLVRAI--

6gtrC

0.22

0.17

0.88

0.85

Download

QHVILNEESWTRVMDALSNPPSPGEKLKRAAKRLQGM-----

3gv2A

0.12

0.17

0.98

0.92

Download

QGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGA-

7wji

0.17

0.41

1.00

0.72

Download

TNNYHRNMSWLHVMILLCNQQSFICTHVHSRSCARLVRAIKL

2pz0A

0.39

0.19

0.55

0.25

Download

-------------------KTSKNVPENTIAAFKRAMELGAD

7wji

0.17

0.41

1.00

0.52

Download

TNNYHRNMSWLHVMILLCNQQSFICTHVHSRSCARLVRAIKL

7r6qV

0.10

1.00

0.40

Download

RSQSEREEEWEKLYKKHGDDYKKNIYQQSEGDLKRRLLRWKG

(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: SP3 4: HHSEARCH 5: wdPPAS 6: Neff-PPAS 7: HHSEARCH2 8: pGenTHREADER 9: HHSEARCH I 10: PROSPECT2

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=-1.93 (Read more about C-score) Estimated TM-score = 0.48±0.15 Estimated RMSD = 6.1±3.8Å	Download Model 2 C-score = -3.46	Download Model 3 C-score = -2.23	Download Model 4 C-score = -3.89	Download Model 5 C-score = -4.54

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	6wbrA	0.653	1.79	0.025	0.905	Download
2	8d2kA	0.639	1.80	0.025	0.905	Download
3	6jooA1	0.631	1.95	0.077	0.929	Download
4	4djaA2	0.624	1.95	0.100	0.929	Download
5	3qxyA	0.620	2.08	0.025	0.929	Download
6	6jsjA	0.617	2.40	0.050	0.952	Download
7	4b46A	0.617	2.33	0.024	0.929	Download
8	3jcrV	0.616	2.16	0.000	0.929	Download
9	1mqwA	0.610	2.54	0.098	0.976	Download
10	6k6lA	0.610	2.30	0.053	0.905	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	0.13	134	4c9iF	KXN	Rep, Mult	31,34,35,38,39,42
2	0.12	132	5f9fA	BU3	Rep, Mult	27,28,29,30
3	0.10	110	2q7mA	2CS	Rep, Mult	35,37,38,39,41,42
4	0.09	96	4hytG	17F	Rep, Mult	31,32,35,36,39
5	0.07	79	1pcrM	BCL	Rep, Mult	27,30,31,33,34

	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	0.177	1x0xA	0.600	2.35	0.075	0.857	1.1.1.8	NA
2	0.166	1mqwA	0.610	2.54	0.098	0.976	3.6.1.13	NA
3	0.163	1ia7A	0.599	2.42	0.024	1.000	3.2.1.4	NA
4	0.161	1wchA	0.587	2.34	0.103	0.929	3.1.3.48	NA
5	0.157	1ut9A	0.581	2.53	0.071	1.000	3.2.1.4	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	0.18	0.5996	2.35	0.07	0.86	1x0xA	GO:0006734 GO:0051287 GO:0005975 GO:0006094 GO:0005739 GO:0004368 GO:0046486 GO:0006116 GO:0044255 GO:0005829 GO:0055114 GO:0004367 GO:0005737 GO:0006072 GO:0016491 GO:0005625 GO:0019432 GO:0005488 GO:0009331 GO:0016614 GO:0016616 GO:0042803 GO:0046168 GO:0050662
2	0.17	0.5961	2.32	0.03	0.93	1ni7A	GO:0005515
3	0.17	0.4114	2.83	0.03	0.67	1mskA	GO:0005622 GO:0008270 GO:0008705 GO:0009086 GO:0031419
4	0.17	0.5876	2.32	0.07	0.93	1v74B	GO:0030153 GO:0005515
5	0.17	0.5907	2.98	0.05	0.90	3lpzA	GO:0005488
6	0.17	0.6101	2.54	0.10	0.98	1mqwA	GO:0030145 GO:0016787
7	0.16	0.5988	2.42	0.02	1.00	1ia7A	GO:0003824 GO:0004553 GO:0005975
8	0.16	0.5902	2.62	0.08	0.88	3h95A	GO:0016787
9	0.16	0.5866	2.76	0.05	0.88	3lkuE	GO:0016192 GO:0005515 GO:0045048 GO:0003674 GO:0005737 GO:0072380 GO:0006810 GO:0006620
10	0.15	0.5958	2.96	0.05	0.95	2jkrA	GO:0005488 GO:0006886 GO:0016192 GO:0030117

Consensus prediction of GO terms

Molecular Function GO:0042802 GO:0016901 GO:0046906 GO:0008172 GO:0043167 GO:0042084 GO:0019842

GO-Score 0.36 0.36 0.34 0.34 0.34 0.34 0.34

Biological Process GO:0019563 GO:0006641 GO:0019319 GO:0019637 GO:0019674 GO:0006796 GO:0046463 GO:0009067 GO:0006555 GO:0009404

GO-Score 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.34 0.34 0.34

Cellular Component GO:0043231 GO:0044444 GO:0032991 GO:0000267

GO-Score 0.36 0.36 0.36 0.36

(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 S777124_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.