I-TASSER results

I-TASSER results for job id Rv2288

[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)
MSRRRPLIEPATVQVLAIAFTDSFSVSLHWPQREQGCRTAILAPMRRWCDGDVDGRKLLP
PARRTGTQQRRIRPAAPRVYTTGDILRDRKGIAPWQEQREPGWAPFGWLHEPSGARCPKA
DGQSV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSRRRPLIEPATVQVLAIAFTDSFSVSLHWPQREQGCRTAILAPMRRWCDGDVDGRKLLPPARRTGTQQRRIRPAAPRVYTTGDILRDRKGIAPWQEQREPGWAPFGWLHEPSGARCPKADGQSV
Prediction	CCCCCCCCCCCEEEEEEEEEHCCEEEEEHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEHHHHHHHCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98666777764568888876565688987577555645667776577746899876568764544754433457898455434555555688876765788888766567898888888888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSRRRPLIEPATVQVLAIAFTDSFSVSLHWPQREQGCRTAILAPMRRWCDGDVDGRKLLPPARRTGTQQRRIRPAAPRVYTTGDILRDRKGIAPWQEQREPGWAPFGWLHEPSGARCPKADGQSV
Prediction	87554431442303010022244242324145466403310222044115352534422441554445544244324422332421454642441475564312221213446445145466677
	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

CCCCCCCCCCCEEEEEEEEEHCCEEEEEHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEHHHHHHHCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MSRRRPLIEPATVQVLAIAFTDSFSVSLHWPQREQGCRTAILAPMRRWCDGDVDGRKLLPPARRTGTQQRRIRPAAPRVYTTGDILRDRKGIAPWQEQREPGWAPFGWLHEPSGARCPKADGQSV

3chnS

0.17

0.96

0.79

MUSTER

ELVYEDLRGSVTFHCALGPEVANVAKFLCRQSSGENCD--VVVNTLGKRAPAFEGRILLNPQDKDGSFSVVITGLRKE---AGRYLCGAHSDGQLQEGSPIQAWQLFVNEESTIPRSPTVAGSSV

1wxaA

0.14

0.12

0.85

0.61

dPPAS

GSSGSS-GSGGTLRIYADSLKNIPYKTILLSTTDT-ADFAVAESLEKYGLEKENPKDMLPPHSDERGAKEIILDDDECPLQIFREWPSDKGILVFQLKRRPPSGPSSG-----------------

4kt0D

0.33

0.29

0.86

0.66

wdPPAS

LSGQPPLLSKANREKYAITWTSASEQVFEMPT---G--AAI---MN-------EGENLLYLARKLGTQLRKFKPKIQRVYPSGEVLHPADGVFP--EKVNEGREAQGTKTRRIGQNPPKFSGKAP

2l6nA

0.17

0.14

0.86

0.63

wMUSTER

MTPQSDTPKVTGLKLKR----KSRQLEISF---DNGQQFTLCELLRVYSEVHGHGNPVLVTHKKNVN--NAITPVG-KVFDDG-----DTGLYSWKVLYDLAWE--NYLAR-AKAREPLIDMAVK

4kt0D

0.37

0.30

0.79

0.53

wPPAS

LSGQPPLLSKANREKYAITWTSAFEM----PT---GA--AI---MN-------EGENLL--ARK-GTQLRKFKPKIQRVYPSGEVLHPADGVFP--EKVNEGREAQG--TKTRGQNPPKFSGKAP

2dnfA

0.29

0.22

0.75

0.61

dPPAS2

SSGRKPLQEPCTIFLIANG--DLINSRLLIPRKTLNQWDHVLQMVTEKIT--------LR----SG--------AVHRLYTLGKLVESGAGVAVGRDKFKK--LPYGELLFDSG----PSSG---

2l6nA

0.23

0.19

0.82

0.61

PPAS

MTPQSDTPKVTKLKQLEISFDNQFTLSCEL--RVY-SPSA-------EVHGH--GNPVLVTHKKNVN--NAITPVAVKVFDDG-----DTGLYSWKVLYDLAWE--NYLAR-AKAREPLIDMAVK

2l6nA

0.17

0.15

0.90

0.75

Env-PPAS

MTPQSDTPKVTGLKLKR----KSRQLEISFD---NGQQFTLCELLRVYSSAEVHGNPVLVTHKK-NVNINAITPVAVKVFDDG----HDTGLYSWKVLYDLAQVDL-WLRAAKASREPLIDMAVK

5fmwA

0.15

0.14

0.98

0.78

MUSTER

MFRSRSIEVFGQFNGKRCAVGDRRQCVPTEPCECGNCSTGRCIKMRLRCNGDNDCGDFSDEDDCESEPRPPCRDRVVEESELARTA--GYGINILG-MDPLSTPFDNEFYNGLCNRDRDGNTLTY

1ss6A

0.20

0.16

0.79

0.61

dPPAS

GSEKRQ-HSSQDVHVVLKLWKSGFSLELRSYQDPS--NAQFLESIRRG---------------EVPAELRRLAH-GGQVNLDMEDHRDEDFVKP-----KGAFKAFTGEGQKLGSTAPQVLST--

(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=-3.85

Estimated TM-score = 0.30±0.10

Estimated RMSD = 13.3±4.1Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-4.80

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	2l6nA	0.507	4.20	0.090	0.864
2	2l6pA	0.456	4.15	0.146	0.760
3	5a22A	0.452	5.13	0.035	0.848
4	3nepX	0.448	4.31	0.098	0.768
5	1uxiA	0.444	4.72	0.067	0.808
6	4bgvA	0.444	4.39	0.056	0.768
7	1sevA	0.443	4.30	0.104	0.752
8	2dfdA	0.442	4.69	0.073	0.800
9	4plcA	0.442	4.26	0.028	0.760
10	2v7pA	0.440	4.24	0.101	0.752

(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	0.09	4	1lziA	MN	Rep, Mult	52,54
2	0.05	2	1fk0A	DKA	Rep, Mult	45,48,79,85,92
3	0.05	2	4qvpK	MG	Rep, Mult	41,45
4	0.05	2	1k61C	NUC	Rep, Mult	43,47
5	0.05	2	2npiA	MG	Rep, Mult	39,123
6	0.02	1	3e27A	MG	Rep, Mult	84,99
7	0.02	1	2dfdB	HIS	Rep, Mult	46,61,62
8	0.02	1	3tvwB	07H	Rep, Mult	11,14,15
9	0.02	1	4h7oA	ARG	Rep, Mult	24,46
10	0.02	1	1j3gA	ZN	Rep, Mult	29,110,121
11	0.02	1	2bkmA	OXY	Rep, Mult	52,103
12	0.02	1	2wse4	CLA	Rep, Mult	92,96
13	0.02	1	4zk0A	ZN	Rep, Mult	14,74
14	0.02	1	1gwvA	MN	Rep, Mult	52,54,119

	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	4mdhA	0.429	4.36	0.019	0.728	1.1.1.37	NA
2	0.060	2v65A	0.430	4.82	0.024	0.800	1.1.1.27	NA
3	0.060	1a59A	0.427	4.51	0.036	0.736	2.3.3.1	NA
4	0.060	3msuA	0.427	4.45	0.063	0.744	2.3.3.1	NA
5	0.060	1iz9A	0.430	4.24	0.056	0.728	1.1.1.37	11,85,93
6	0.060	1guzA	0.431	4.43	0.050	0.768	1.1.1.37	NA
7	0.060	1uxgA	0.421	4.88	0.045	0.760	1.1.1.37	NA
8	0.060	1ldxA	0.416	4.33	0.046	0.720	1.1.1.27	27,38
9	0.060	5ldhA	0.416	4.94	0.045	0.760	1.1.1.27	NA
10	0.060	1y6jA	0.436	4.54	0.071	0.768	1.1.1.37	NA
11	0.060	1b8pA	0.376	5.11	0.087	0.744	1.1.1.37	NA
12	0.060	1a39A	0.434	5.15	0.041	0.864	3.2.1.4	19
13	0.060	3gvhA	0.431	4.66	0.037	0.776	1.1.1.37	47
14	0.060	3ovwA	0.435	5.24	0.042	0.864	3.2.1.4	NA
15	0.060	1sowB	0.436	4.37	0.056	0.768	1.1.1.27	NA
16	0.060	1bdmB	0.387	5.04	0.054	0.744	1.1.1.37	NA
17	0.060	1smkA	0.443	4.47	0.061	0.760	1.1.1.37	NA
18	0.060	2e37C	0.357	5.47	0.025	0.728	1.1.1.27	NA
19	0.060	1ldnA	0.432	4.54	0.056	0.768	1.1.1.27	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	0.07	0.507	4.20	0.09	0.86	2l6nA
1	0.07	0.456	4.15	0.15	0.76	2l6pA	GO:0016853
2	0.06	0.384	4.24	0.06	0.65	3luuA	GO:0046872
3	0.06	0.347	4.79	0.04	0.61	1xi6A	GO:0046854
4	0.06	0.251	5.37	0.10	0.51	4ubqA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0046677 GO:0046872
5	0.06	0.333	4.92	0.01	0.64	1qftA	GO:0005576 GO:0030682 GO:0043176
6	0.06	0.276	5.09	0.03	0.51	1tuzA	GO:0000166 GO:0004143 GO:0005509 GO:0005524 GO:0005543 GO:0005829 GO:0005886 GO:0007205 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0030168 GO:0035556 GO:0046872
7	0.06	0.318	5.51	0.04	0.67	1c9wA	GO:0004032 GO:0005737 GO:0016491 GO:0055114
8	0.06	0.317	5.78	0.04	0.70	2cb1A	GO:0003824 GO:0016829 GO:0030170
9	0.06	0.281	5.13	0.04	0.53	2q0aA	GO:0000166 GO:0005216 GO:0005222 GO:0005244 GO:0005248 GO:0005249 GO:0005267 GO:0005272 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0016020 GO:0016021 GO:0030552 GO:0034765 GO:0035725 GO:0042391 GO:0042802 GO:0055085 GO:0060078 GO:0071320 GO:0071321 GO:0071805
10	0.06	0.342	5.19	0.04	0.65	5chsB	GO:0000166 GO:0001172 GO:0003824 GO:0003968 GO:0004482 GO:0005524 GO:0006139 GO:0006370 GO:0006397 GO:0008152 GO:0008168 GO:0016740 GO:0016779 GO:0019012 GO:0030430 GO:0032259 GO:0036265 GO:0039689
11	0.06	0.323	5.22	0.03	0.65	4cnjA	GO:0000166 GO:0016491 GO:0055114
12	0.06	0.320	5.14	0.10	0.62	3bo5A	GO:0000014 GO:0000729 GO:0000737 GO:0000793 GO:0003677 GO:0003690 GO:0003697 GO:0003824 GO:0004518 GO:0004519 GO:0005634 GO:0005694 GO:0006281 GO:0006303 GO:0006974 GO:0008152 GO:0008168 GO:0008270 GO:0008283 GO:0010452 GO:0015074 GO:0016568 GO:0016740 GO:0016787 GO:0018024 GO:0031297 GO:0032259 GO:0034968 GO:0035861 GO:0042800 GO:0042803 GO:0043566 GO:0044547 GO:0044774 GO:0046872 GO:0046975 GO:0051568 GO:0071157 GO:0090305 GO:0097676 GO:2000373 GO:2001034 GO:2001251
13	0.06	0.272	4.28	0.03	0.45	2ip2A	GO:0008168 GO:0008171 GO:0008757 GO:0016740 GO:0019438 GO:0032259
14	0.06	0.289	5.05	0.06	0.52	1b4wA	GO:0004623 GO:0005509 GO:0005576 GO:0006629 GO:0016042 GO:0016787 GO:0046872
15	0.06	0.304	5.34	0.03	0.58	1qzzA	GO:0008168 GO:0008171 GO:0016829 GO:0016831 GO:0017000 GO:0032259
16	0.06	0.353	4.28	0.05	0.60	3ictA	GO:0000166 GO:0003756 GO:0005623 GO:0016491 GO:0045454 GO:0050451 GO:0050660 GO:0050661 GO:0055114
17	0.06	0.291	4.99	0.03	0.54	1a0iA	GO:0000166 GO:0003677 GO:0003909 GO:0003910 GO:0005524 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0016874 GO:0046872 GO:0051103
18	0.06	0.288	5.41	0.03	0.56	1sezA	GO:0004729 GO:0005739 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016853	GO:0008800	GO:0008270
GO-Score	0.07	0.06	0.06
Biological Processes	GO:0046854	GO:0046677	GO:0017001
GO-Score	0.06	0.06	0.06
Cellular Component
GO-Score

(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.