I-TASSER results

I-TASSER results for job id Rv1974

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

Input Sequence in FASTA format

>protein (125 residues)
MQRQSLMPQQTLAAGVFVGALLCGVVTAAVPPHARADVVAYLVNVTVRPGYNFANADAAL
SYGHGLCEKVSRGRPYAQIIADVKADFDTRDQYQASYLLSQAVNELCPALIWQLRNSAVD
NRRSG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MQRQSLMPQQTLAAGVFVGALLCGVVTAAVPPHARADVVAYLVNVTVRPGYNFANADAALSYGHGLCEKVSRGRPYAQIIADVKADFDTRDQYQASYLLSQAVNELCPALIWQLRNSAVDNRRSG
Prediction	CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCC
Conf.Score	99888864677899999999999887646888888876899999987469998998999999899999998699999999999986899864567899999999979999999987567888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MQRQSLMPQQTLAAGVFVGALLCGVVTAAVPPHARADVVAYLVNVTVRPGYNFANADAALSYGHGLCEKVSRGRPYAQIIADVKADFDTRDQYQASYLLSQAVNELCPALIWQLRNSAVDNRRSG
Prediction	86466444432222221332232112323443525263022002023444251643620132034004315664534401430365254454230121123004421352024035445644468
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCC
MQRQSLMPQQTLAAGVFVGALLCGVVTAAVPPHARADVVAYLVNVTVRPGYNFANADAALSYGHGLCEKVSRGRPYAQIIADVKADFDTRDQYQASYLLSQAVNELCPALIWQLRNSAVDNRRSG

4ci6B

0.10

1.00

0.66

MUSTER

TDVRRITPYYLRELSDLLRTHLSSAATKQLDMGVVDTMLVALDKAEREGGVDKDQLKSFNSLILKTYSVIGAYIIVEPSLQRIQKHLDQTHSFSDIGSLMRAHKHLETLLEVLVTLSQQGQPVSS

5appA

0.07

0.97

0.60

dPPAS

IEEILSKIYHIENEIARIKKLIQNVDVRSTENAARSRANEQKIAENKKAIENKADKADVEKNRADIAANSRAIATFRSSSQNIAALTTKMKQIEDKIEEILSKIYHIENEIARIKKLIKLH----

4k82A2

0.10

0.09

0.84

0.57

wdPPAS

---------DETVFNAVCDVTKKMLDNKCLPKILQGDLVKFLKDLKYKVCIEGGDPELIIKDLKIILERLPC-VGLDDLFKNIFVKDGIL-EGIAKPLGDLLILVLCPNVKN---NVSS------

1ztdA

0.12

0.11

0.92

0.75

wMUSTER

ID----KGLAKFGDSLINFLYSLALTEFLGKPTGDRVPNASLAIALELTGLNLRRVDKGDYAEALIAKAWLMGLSEREAVEIIKKNLYPLDFSKKKEAIGRALAPLLVIISERLYSSQV------

4x82B2

0.22

0.12

0.55

0.75

wPPAS

--------------------------------NTPNISVAELAALMQRLGVGGVNSSSDT---DTVC-------SARDVMAVYLSEQTGVT--------PEAWAQLSPALLQQQLSGAC------

2mqaA

0.13

0.11

0.87

0.83

dPPAS2

----GNAFAQSLSSNLLSSGDFVQMISSTTSTQAVSVATSVAQNVGNQLGLDANAMNSLLGAVSGYVSTLGNAISISSAIGNVLANSGSISESSAASSVTTTLTSYGPAVFYA------------

2mqaA

0.13

0.11

0.87

0.83

PPAS

----GNAFAQSLSSNLLSSGDFVQMISSTSTDQAVSVATSVAQNVGNQLGLDANAMNSLLGAVSGYVSTLGNAISISSAIGNVLANSGSISESSAASSVTTTLTSYGPAVFYA------------

4qiwF

0.08

0.98

0.81

Env-PPAS

MIGRKKLEEHYITIAEAKELLERRHAEGLAENPEEPMFYEARVSLEHAERFAKLKPEQARELKEKLMGLFDWIN--ERIAAKLVDILP-EDYLDIRVIFAKEEYMPTPEEAEEIIKVIDEYRPLE

1u6gC

0.13

1.00

0.64

MUSTER

DELPPLISESDMHVSQMAISFLTTLAKVYPSSKISGSILNELIGLVRSPLLQGGALSAMLDFFQALVVTGTNNLGYMDLLRMLTGPVYSQTHKQSYYSIAKCVAALTPAVVGQFIQDVKNSRSTD

5cwmA1

0.04

0.91

0.60

dPPAS

----DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTAEEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGSEEALERALRVAEEAARLAKRVLELAEKQG-------

(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=-3.08

Estimated TM-score = 0.37±0.12

Estimated RMSD = 11.3±4.5Å

Download Model 2

C-score=-3.22

Download Model 3

C-score=-4.69

Download Model 4

C-score=-4.28

Download Model 5

C-score=-4.65

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	1ztdA	0.673	2.79	0.078	0.904
2	3vvnA	0.573	4.41	0.024	0.912
3	3ixzA4	0.565	3.81	0.061	0.864
4	3kdpA4	0.558	3.93	0.053	0.864
5	2xzmG	0.547	3.66	0.061	0.824
6	3b9zA	0.544	4.02	0.090	0.880
7	4x9eA	0.543	4.16	0.042	0.872
8	3qnqA	0.539	4.33	0.052	0.920
9	4z3nA	0.531	4.77	0.064	0.920
10	3b8cA2	0.530	4.11	0.027	0.824

(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	0.10	5	3edvB	MG	Rep, Mult	104,108
2	0.09	5	1mz9B	VDY	Rep, Mult	103,106,110
3	0.05	3	1vdfB	CL	Rep, Mult	110,113
4	0.03	2	4rgsA	V55	Rep, Mult	96,97
5	0.03	2	1pprM	PID	Rep, Mult	98,102
6	0.03	2	3fgoA	CZA	Rep, Mult	69,76,78,79,82,106,109,110
7	0.03	2	1wpgA	NA	Rep, Mult	82,83,84,85,86
8	0.02	1	2h8pC	GOA	Rep, Mult	50,51
9	0.02	1	3nyhA	IOD	Rep, Mult	12,29,74
10	0.02	1	3fgoB	CZA	Rep, Mult	82,83,85,86,89,98,101,102
11	0.02	1	1uf3A	CA	Rep, Mult	50,57
12	0.02	1	2agvA	BHQ	Rep, Mult	17,21,79,103,108
13	0.02	1	3gxqA	NUC	Rep, Mult	61,64,66
14	0.02	1	3a95A	RH3	Rep, Mult	84,91
15	0.02	1	2eulA	ZN	Rep, Mult	101,105

	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	2nsmA	0.492	4.26	0.035	0.824	3.4.17.3	78
2	0.060	3ig5A	0.495	4.77	0.068	0.864	6.3.2.2	NA
3	0.060	3dslA	0.496	4.46	0.087	0.776	3.4.24.49	NA
4	0.060	1zxvA	0.517	3.56	0.052	0.768	3.4.24.83	NA
5	0.060	2qykB	0.468	4.79	0.049	0.872	3.1.4.17	NA
6	0.060	3n2zB	0.497	4.42	0.052	0.776	3.4.16.2	100
7	0.060	3ixzA	0.526	4.24	0.050	0.888	3.6.3.10	NA
8	0.060	3hkzJ	0.484	4.55	0.062	0.840	2.7.7.6	20,106
9	0.060	1r3nA	0.356	5.02	0.022	0.664	3.5.1.6	NA
10	0.060	1ca1A	0.498	4.04	0.049	0.776	3.1.4.3	NA
11	0.060	2dqbA	0.390	5.16	0.042	0.744	3.1.5.1	106
12	0.060	1iduA	0.492	4.08	0.036	0.752	1.11.1.10	NA
13	0.060	3b8eA	0.562	3.85	0.043	0.864	3.6.3.9	NA
14	0.060	3b8cB	0.531	4.18	0.027	0.832	3.6.3.6	45,80
15	0.060	1olpA	0.500	3.92	0.056	0.784	3.1.4.3	NA
16	0.060	1o0wB	0.510	3.56	0.058	0.760	3.1.26.3	12,16
17	0.060	1khoA	0.503	4.18	0.058	0.768	3.1.4.3	NA
18	0.060	3b8eC	0.560	3.99	0.052	0.880	3.6.3.9	26,34
19	0.060	3gtgB	0.486	4.53	0.063	0.840	2.7.7.6	100

(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	0.16	0.673	2.79	0.08	0.90	1ztdA	GO:0003723 GO:0004525 GO:0006396 GO:0090501 GO:0090502
1	0.07	0.568	4.33	0.05	0.90	4mlbB	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
2	0.07	0.523	4.16	0.05	0.80	5c6nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
3	0.07	0.559	3.97	0.04	0.87	3a3yA	GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
4	0.07	0.497	4.38	0.05	0.78	3vvpA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
5	0.07	0.472	4.78	0.04	0.82	3mktA
6	0.07	0.531	4.77	0.06	0.92	4z3nA	GO:0006855 GO:0015238 GO:0015297 GO:0016020 GO:0016021 GO:0055085
7	0.07	0.526	4.24	0.05	0.89	3ixzA	GO:0000166 GO:0000287 GO:0005391 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0008900 GO:0010107 GO:0010248 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0036376 GO:0043231 GO:0046872
8	0.07	0.562	3.85	0.04	0.86	3b8eA	GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
9	0.07	0.448	4.41	0.04	0.76	4bbjA	GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
10	0.06	0.511	4.03	0.07	0.79	1mhsA	GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
11	0.06	0.377	4.48	0.05	0.62	2ayxA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0005887 GO:0006355 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0044010 GO:0046777 GO:0071470
12	0.06	0.383	5.08	0.06	0.73	3j09A	GO:0000166 GO:0005507 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
13	0.06	0.413	4.59	0.09	0.70	5it9C	GO:0003723 GO:0003735 GO:0005840 GO:0006407 GO:0006412 GO:0015935 GO:0022627 GO:0030529 GO:0032040 GO:0045903 GO:0070181
14	0.06	0.402	4.52	0.03	0.66	4qx6D	GO:0000166 GO:0006006 GO:0016491 GO:0016620 GO:0050661 GO:0051287 GO:0055114
15	0.06	0.319	5.40	0.05	0.62	4ffcA	GO:0003824 GO:0003867 GO:0008483 GO:0009448 GO:0016740 GO:0030170
16	0.06	0.530	4.11	0.03	0.82	3b8cA	GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0046872 GO:0051453
17	0.06	0.320	4.38	0.08	0.54	4ruwA	GO:0004519 GO:0004527 GO:0046872 GO:0090305
18	0.06	0.433	4.96	0.07	0.81	4umvA	GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655

Consensus prediction of GO terms

Molecular Function	GO:0015291	GO:0090484	GO:0016891	GO:0003676	GO:0032296
GO-Score	0.37	0.37	0.33	0.33	0.33
Biological Processes	GO:0055085	GO:0015893	GO:0016070	GO:0090305	GO:0010467
GO-Score	0.37	0.37	0.33	0.33	0.33
Cellular Component	GO:0031224
GO-Score	0.38

(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.