I-TASSER results

I-TASSER results for job id Rv1205

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

Input Sequence in FASTA format

>protein (187 residues)
MSAKIDITGDWTVAVYCAASPTHAELLELAAEVGAAIAGRGWTLVWGGGHVSAMGAVASA
ARACGGWTVGVIPKMLVYRELADHDADELIVTDTMWERKQIMEDRSDAFIVLPGGVGTLD
ELFDAWTDGYLGTHDKPIVMVDPWGHFDGLRAWLNGLLDTGYVSPTAMERLVVVDNVKDA
LRACAPS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSAKIDITGDWTVAVYCAASPTHAELLELAAEVGAAIAGRGWTLVWGGGHVSAMGAVASAARACGGWTVGVIPKMLVYRELADHDADELIVTDTMWERKQIMEDRSDAFIVLPGGVGTLDELFDAWTDGYLGTHDKPIVMVDPWGHFDGLRAWLNGLLDTGYVSPTAMERLVVVDNVKDALRACAPS
Prediction	CCCCCCCCCCCEEEEHCCCCCCCCHHHHHHHHHHHHHHHHCCEEEHCCCCCCHHHHHHHHHHHHCCCEEEEHCCCCHHHHCCCCCCCEEEEHCCHHHHHHHHHHHCCEEEHCCCCCHHHHHHHHHHHHHHHCCCCCCEEEHCCCCHHHHHHHHHHHHHHHCCCCHHHCCEEEHCCCHHHHHHHHHHC
Conf.Score	9876677788779998778999989999999999999998998998899998799999999998996899976776677467899867999689899999999989989996998746999999999999888899899988997579999999999998999987754588869999999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSAKIDITGDWTVAVYCAASPTHAELLELAAEVGAAIAGRGWTLVWGGGHVSAMGAVASAARACGGWTVGVIPKMLVYRELADHDADELIVTDTMWERKQIMEDRSDAFIVLPGGVGTLDELFDAWTDGYLGTHDKPIVMVDPWGHFDGLRAWLNGLLDTGYVSPTAMERLVVVDNVKDALRACAPS
Prediction	7655364564230000000255445105102500420164401000001430002000400373613000011333254434253033224053344033200530200000113300230210021123244261000000252114201410430175321457224102106205301531378
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCEEEEHCCCCCCCCHHHHHHHHHHHHHHHHCCEEEHCCCCCCHHHHHHHHHHHHCCCEEEEHCCCCHHHHCCCCCCCEEEEHCCHHHHHHHHHHHCCEEEHCCCCCHHHHHHHHHHHHHHHCCCCCCEEEHCCCCHHHHHHHHHHHHHHHCCCCHHHCCEEEHCCCHHHHHHHHHHC
MSAKIDITGDWTVAVYCAASPTHAELLELAAEVGAAIAGRGWTLVWGGGHVSAMGAVASAARACGGWTVGVIPKMLVYRELADHDADELIVTDTMWERKQIMEDRSDAFIVLPGGVGTLDELFDAWTDGYLGTHDKPIVMVDPWGHFDGLRAWLNGLLDTGYVSPTAMERLVVVDNVKDALRACAPS

3sbxA

0.83

0.79

0.95

3.72

MUSTER

---------RWTVAVYCAAAPTHPELLELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAARAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDALQACAP-

3sbxA

0.83

0.79

0.95

5.28

dPPAS

---------RWTVAVYCAAAPTHPELLELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAARAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDALQACAP-

3sbxA

0.83

0.79

0.95

4.79

wdPPAS

---------RWTVAVYCAAAPTHPELLELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAARAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDALQACAP-

3sbxA

0.84

0.79

0.94

4.37

wMUSTER

----------WTVAVYCAAAPTHPELLELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAARAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDALQACAP-

3sbxA

0.83

0.79

0.95

4.93

wPPAS

---------RWTVAVYCAAAPTHPELLELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAARAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDALQACAP-

3sbxA

0.83

0.79

0.95

8.08

dPPAS2

---------RWTVAVYCAAAPTHPELLELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAARAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDALQACAP-

3sbxA

0.83

0.79

0.95

4.57

PPAS

---------RWTVAVYCAAAPTHPELLELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAARAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDALQACAP-

3sbxA

0.83

0.79

0.95

6.00

Env-PPAS

---------RWTVAVYCAAAPTHPELLELAGAVGAAIAARGWTLVWGGGHVSAMGAVSSAARAHGGWTVGVIPKMLVHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGYLGMHDKSIVVLDPWGHFDGLRAWLSELADTGYVSRTAMERLIVVDNLDDALQACAP-

3quaA

0.73

0.70

0.96

3.69

MUSTER

--------RQWAVCVYCASGPTHPELLELAAEVGSSIAARGWTLVSGGGNVSAMGAVAQAARAKGGHTVGVIPKALVHRELADVDAAELIVTDTMRERKREMEHRSDAFIALPGGIGTLEEFFEAWTAGYLGMHDKPLILLDPFGHYDGLLTWLRGLVPTGYVSQRAMDSLVVVDNVEAALEACAPE

3quaA

0.73

0.70

0.96

5.22

dPPAS

--------RQWAVCVYCASGPTHPELLELAAEVGSSIAARGWTLVSGGGNVSAMGAVAQAARAKGGHTVGVIPKALVHRELADVDAAELIVTDTMRERKREMEHRSDAFIALPGGIGTLEEFFEAWTAGYLGMHDKPLILLDPFGHYDGLLTWLRGLVPTGYVSQRAMDSLVVVDNVEAALEACAPE

(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=1.00

Estimated TM-score = 0.85±0.08

Estimated RMSD = 3.2±2.3Å

Download Model 2

C-score=-0.36

Download Model 3

C-score=0.67

Download Model 4

C-score=-0.37

Download Model 5

C-score=-2.06

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	3quaA	0.927	0.95	0.726	0.957
2	3sbxA	0.927	0.76	0.831	0.947
3	5itsA	0.883	1.72	0.330	0.957
4	1wekA	0.877	1.92	0.247	0.973
5	5ajtA	0.868	1.75	0.307	0.947
6	3bq9A	0.846	2.14	0.167	0.963
7	2q4dA	0.832	1.99	0.280	0.914
8	2q4oA	0.823	1.68	0.314	0.888
9	3gh1A	0.821	2.38	0.182	0.941
10	1wehA	0.782	2.15	0.271	0.888

(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	0.97	16	3sbxF	AMP	Rep, Mult	17,18,19,54,76,80,95,98,99,115,116,117,118,120,121
2	0.05	1	3sbxE	AMP	Rep, Mult	124,127
3	0.05	1	3sbxD	AMP	Rep, Mult	127,131

	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	0.451	2q4dA	0.832	1.99	0.280	0.914	3.2.2.-	17,45,47,49,99,110,115,117,122
2	0.431	2q4oA	0.823	1.68	0.314	0.888	3.2.2.-	17,48,55,99,114,119,121
3	0.132	1qzuC	0.529	4.21	0.076	0.759	4.1.1.36	30
4	0.132	1f8xA	0.518	3.71	0.072	0.695	2.4.2.6	121
5	0.066	1wo8A	0.469	3.28	0.086	0.615	4.2.3.3	NA
6	0.066	2a0kA	0.518	3.77	0.079	0.701	2.4.2.6	121
7	0.066	1h0rA	0.452	4.03	0.164	0.642	4.2.1.10	NA
8	0.066	1e20A	0.552	4.00	0.063	0.765	4.1.1.36	NA
9	0.066	1g63B	0.529	4.11	0.064	0.754	4.1.1.-	NA
10	0.060	1i3kA	0.568	4.00	0.107	0.797	5.1.3.2	NA
11	0.060	2rh4B	0.571	4.22	0.105	0.818	1.3.1.-	NA
12	0.060	1g6kA	0.572	4.03	0.101	0.802	1.1.1.47	NA
13	0.060	1iy8A	0.572	3.76	0.122	0.786	1.1.1.-	NA
14	0.060	1z45A	0.570	3.86	0.100	0.791	5.1.3.2,5.1.3.3	NA
15	0.060	3i39X	0.584	4.17	0.069	0.840	1.2.99.2	17,173
16	0.060	3gr6D	0.566	4.25	0.098	0.807	1.3.1.9	54
17	0.060	1rzuB	0.567	3.72	0.190	0.765	2.4.1.21	110,117
18	0.060	1fduC	0.569	3.91	0.144	0.797	1.1.1.62	122
19	0.060	1jqkF	0.588	4.14	0.124	0.840	1.2.99.2	22,119
20	0.060	2z8yD	0.596	3.88	0.065	0.818	1.2.7.4,1.2.99.2	NA
21	0.060	1q0lA	0.569	4.09	0.099	0.813	1.1.1.267	20,34,46,59,111,121
22	0.060	3cf4A	0.569	3.65	0.086	0.770	1.2.99.2	NA
23	0.060	1gz5A	0.579	3.59	0.110	0.775	2.4.1.15	NA
24	0.060	1sb8A	0.569	3.93	0.057	0.791	5.1.3.7	NA
25	0.060	3enkA	0.574	3.87	0.145	0.802	5.1.3.2	NA
26	0.060	1xhlA	0.567	3.96	0.097	0.797	1.1.1.236	NA
27	0.060	3dzcB	0.587	3.15	0.086	0.749	5.1.3.14	114
28	0.060	1enpA	0.567	4.45	0.073	0.834	1.3.1.9	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	0.65	0.846	1.62	0.33	0.91	2a33A	GO:0005634 GO:0005737 GO:0009691 GO:0016787 GO:0016799
1	0.60	0.927	0.95	0.73	0.96	3quaA	GO:0009691 GO:0016787 GO:0016799
2	0.48	0.882	1.97	0.26	0.98	1wekA	GO:0009691 GO:0016787 GO:0016799
3	0.47	0.791	2.15	0.27	0.90	1wehA	GO:0016020 GO:0016021
4	0.44	0.818	2.23	0.28	0.94	1t35E	GO:0005829 GO:0009691 GO:0016799
5	0.44	0.871	1.82	0.29	0.95	2q4dA	GO:0005634 GO:0005737 GO:0005829 GO:0009691 GO:0016787 GO:0016799 GO:0042803
6	0.30	0.733	2.28	0.24	0.83	2iz7A	GO:0005829 GO:0009691 GO:0016799
7	0.28	0.855	2.08	0.18	0.96	3gh1A	GO:0005829 GO:0009691 GO:0016799
8	0.27	0.749	2.47	0.21	0.87	1rcuA	GO:0005829 GO:0009691 GO:0016799
9	0.07	0.469	4.35	0.06	0.69	3gk0A	GO:0003824 GO:0005737 GO:0008615 GO:0016740 GO:0016769 GO:0033856
10	0.07	0.430	4.76	0.05	0.68	2z0mA	GO:0000166 GO:0003676 GO:0004386 GO:0005524 GO:0016787
11	0.07	0.452	5.11	0.05	0.74	2xtzC	GO:0000166 GO:0001789 GO:0003924 GO:0004871 GO:0005095 GO:0005525 GO:0005789 GO:0005834 GO:0005886 GO:0006571 GO:0007165 GO:0007186 GO:0008219 GO:0009094 GO:0009506 GO:0009738 GO:0009740 GO:0009749 GO:0009785 GO:0009788 GO:0009789 GO:0009845 GO:0010027 GO:0010119 GO:0010244 GO:0016020 GO:0016247 GO:0019001 GO:0031683 GO:0034260 GO:0042127 GO:0046872 GO:0071215 GO:0072593
12	0.06	0.379	5.76	0.05	0.70	1acoA	GO:0003994 GO:0005506 GO:0005634 GO:0005739 GO:0006099 GO:0006101 GO:0008152 GO:0016829 GO:0043209 GO:0046872 GO:0051536 GO:0051539
13	0.06	0.359	5.60	0.07	0.63	2b3tB	GO:0003747 GO:0005737 GO:0005829 GO:0006412 GO:0006415 GO:0016149 GO:0043022
14	0.06	0.362	5.19	0.05	0.60	3icqT	GO:0000049 GO:0003723 GO:0005525 GO:0005634 GO:0005635 GO:0005643 GO:0005737 GO:0005829 GO:0006409 GO:0006605 GO:0006810 GO:0008033 GO:0008536 GO:0015932 GO:0016363 GO:0071528
15	0.06	0.260	6.01	0.06	0.50	3pu2B	GO:0006950
16	0.06	0.181	4.89	0.05	0.29	2cs4A	GO:0007165
17	0.06	0.178	4.70	0.08	0.29	2gagD	GO:0008115 GO:0046653 GO:0046872 GO:0055114
18	0.06	0.174	4.10	0.06	0.25	1x4pA	GO:0003676 GO:0003723 GO:0005634 GO:0005654 GO:0006396 GO:0006397 GO:0008380 GO:0044822

Consensus prediction of GO terms

Molecular Function	GO:0016799
GO-Score	0.96
Biological Processes	GO:0009691
GO-Score	0.96
Cellular Component	GO:0005634	GO:0016021	GO:0005829
GO-Score	0.65	0.47	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.