I-TASSER results

I-TASSER results for job id Rv2661c

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

Input Sequence in FASTA format

>protein (129 residues)
MRARSDAGGQSVKSRTSNRSRSSRRSRVRSSISALVDNPQARPRELPVLCGWPVVRVEPV
CEFVPEPVCGQAEVLGEPAAAHRVTSARRSPSTTVCSRSQKASAVVISSVSSVARVRRAS
VSSVDATTA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRARSDAGGQSVKSRTSNRSRSSRRSRVRSSISALVDNPQARPRELPVLCGWPVVRVEPVCEFVPEPVCGQAEVLGEPAAAHRVTSARRSPSTTVCSRSQKASAVVISSVSSVARVRRASVSSVDATTA
Prediction	CCCCCCCCCCEEHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEHCCCEEEEEEEHCCCCCCCCCCCEHCCCCCCCCCCCCCCCCCCCEEHCCCCCCCEEEEEEHHHHHHHHHCCCCCCCCCCC
Conf.Score	986446787544434455445677888998878875587777544555448857887444335899888864344886544444445668885454455677568876434445555434566665679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRARSDAGGQSVKSRTSNRSRSSRRSRVRSSISALVDNPQARPRELPVLCGWPVVRVEPVCEFVPEPVCGQAEVLGEPAAAHRVTSARRSPSTTVCSRSQKASAVVISSVSSVARVRRASVSSVDATTA
Prediction	754456444641454356454554454145304411644644345120104132230431052135411441522444333441353454443431444551312113314422414534255254458
	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

CCCCCCCCCCEEHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEHCCCEEEEEEEHCCCCCCCCCCCEHCCCCCCCCCCCCCCCCCCCEEHCCCCCCCEEEEEEHHHHHHHHHCCCCCCCCCCC
MRARSDAGGQSVKSRTSNRSRSSRRSRVRSSISALVDNPQARPRELPVLCGWPVVRVEPVCEFVPEPVCGQAEVLGEPAAAHRVTSARRSPSTTVCSRSQKASAVVISSVSSVARVRRASVSSVDATTA

4nx9A

0.09

1.00

0.69

MUSTER

VTAATASGTVDIAIDITGGSAVNGNETAEQAAAKIAAAVNDANVGIGAFTDGAQISYVSKASADGTTSAVSGVAITDTGSTGAGTAAGTTTFTEANDTVAKIDISTAKGAQSAVLVIDEAIKQIDAQRA

3r1fA

0.10

0.09

0.84

0.59

dPPAS

FDTVYPPGRGPHTSAEVIAALKAEGITSAPYLSQLRSGNRTNPSGA----------TAALANFIKAAYFTDDEYYEKLDKELQWLCTRDDGVRRIAQRAHGLPSAAQQKVLDRIDELR-----------

1wijA

0.30

0.20

0.68

0.57

wdPPAS

---------------SQFVLQDLQDATLGSLLSSLMDPPQRKPLEKGT---WPT---------------GNEE-LGLPKSQ---SPPYRKPH----KKMWKVGVLVINHMLPIAKIKRHSKCLQDKMTA

4w4iA

0.15

0.95

0.67

wMUSTER

IAETIGAGT-AITMPSDAAQRGAFVDRQRDELTRMLLSPQGVINPIKVVCF-P--DRWLDLRYVGPASADGACELLRGIVALRTGTGKKTGNGVVALRN--AQLVTFTAMDDPRALVPILGVGLAHRPP

2e1bA2

0.24

0.18

0.74

0.51

wPPAS

MRGNE--GEQLVGS-SVEKGRAENLNKYKEQIISLF-NKYVD-EGGEVIWWEGDRRYTQIRDFEVIP-CG-----G----TH-V---KD---I-----KE-IGHIKKLKRSSIGRKQR-----LEMWLE

2cp6A

0.32

0.29

0.91

0.65

dPPAS2

----GSSGSSGATPPISNLTKTASES-ISNLSEA--GSIKKGERELKVLVGGTVVRFLGETDFAKGEWCGKVTKIGFPSAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVA----SSVSSRPSRTG

2cp6A

0.31

0.29

0.95

0.71

PPAS

----GSSGSSGATPPISNLTKTASES-ISNLSEA--GSIKKGERELKVLVGGTVVRFLGETDFAKEPLCGKVTKIGFPSAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSSRPSRTGLLTETS

2e1bA2

0.22

0.17

0.77

0.70

Env-PPAS

MRLNEVLGEQLVGSGSVEKGRPENLNKYKEQIISLF-NKYVD-EGGEVIWWEGDRRYTQIRDFEVIP-CG-----G----TH-------------VKDIKEIGHIKKLKRSSIGRKQR-----LEMWLE

5dfzB

0.09

1.00

0.66

MUSTER

VMAANPNLKNVFVQLEPTSYHMHSPNHGLKDNANVKPERKVVVSNEKFLSTFKILPLRDYKEFGPIQEIVRSPNMGNLRGATLMENEPNSITSSAVSPGETPGVIKIWNLKEIIVEVYSSSLTYDCSST

2cp6A

0.29

0.27

0.95

0.57

dPPAS

----GSSGSSGATPPISNLTKTASES---ISNLSEAGSIKKGERELKVLVGGTVVRFLGETDFAKGEWCGKVTKIGFPSAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTE

(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=-4.40

Estimated TM-score = 0.25±0.08

Estimated RMSD = 14.9±3.6Å

Download Model 2

C-score=-4.50

Download Model 3

C-score=-4.92

Download Model 4

C-score=-4.42

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	2ihvA	0.466	4.55	0.046	0.806
2	2wmfA	0.460	4.69	0.053	0.822
3	3s3uA	0.449	4.95	0.052	0.845
4	1ry2A1	0.446	4.80	0.098	0.783
5	3ahcA2	0.444	5.10	0.050	0.806
6	3tsyA	0.443	4.51	0.071	0.729
7	2hctA	0.443	4.66	0.050	0.767
8	2ccdA1	0.442	4.78	0.059	0.791
9	3a9uA1	0.442	4.63	0.061	0.744
10	3nl2A	0.441	5.31	0.056	0.868

(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	0.08	4	1upaA	TPP	Rep, Mult	59,62,112,113,116
2	0.08	4	4il6H	CLA	Rep, Mult	28,32,35
3	0.06	3	2xquA	CVM	Rep, Mult	24,28
4	0.04	2	1ci7A	UMP	Rep, Mult	42,44
5	0.04	2	3uilB	DAO	Rep, Mult	34,35
6	0.02	1	1i6qA	CO3	Rep, Mult	15,16
7	0.02	1	3hl2A	TS6	Rep, Mult	98,99,100
8	0.02	1	4llhA	CM5	Rep, Mult	21,25
9	0.02	1	1lbgD	NUC	Rep, Mult	38,41
10	0.02	1	1qbhA	ZN	Rep, Mult	61,69,82,96
11	0.02	1	3dzfA	RF5	Rep, Mult	111,112,113,117
12	0.02	1	4adsA	PO4	Rep, Mult	82,88,89
13	0.02	1	5awvC	3FG	Rep, Mult	23,24,27
14	0.02	1	3pyoE	MG	Rep, Mult	15,32
15	0.02	1	1dd1B	SO4	Rep, Mult	17,18,21
16	0.02	1	1s2vB	MG	Rep, Mult	6,37

	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	1trkA	0.437	5.05	0.045	0.822	2.2.1.1	51
2	0.060	1r9jB	0.429	5.05	0.045	0.814	2.2.1.1	17
3	0.060	2e6kA	0.437	5.03	0.087	0.822	2.2.1.1	NA
4	0.060	3e7wA	0.440	4.45	0.049	0.744	6.1.1.13	NA
5	0.060	1iq8A	0.443	5.05	0.070	0.822	2.4.2.29	NA
6	0.060	2yvkD	0.429	4.87	0.029	0.760	5.3.1.23	15,20,34,46
7	0.060	2o1sB	0.418	5.36	0.009	0.845	2.2.1.7	NA
8	0.060	2ps1B	0.434	4.40	0.037	0.721	2.4.2.10	32,38,48
9	0.060	1ultA	0.433	4.46	0.075	0.760	6.2.1.3	NA
10	0.060	1ry2A	0.446	4.80	0.098	0.783	6.2.1.1	NA
11	0.060	1qs1A	0.432	4.93	0.048	0.798	2.4.2.30	73
12	0.060	1v5eA	0.430	5.11	0.018	0.822	1.2.3.3	NA
13	0.060	2o1sA	0.436	5.02	0.057	0.806	2.2.1.7	NA
14	0.060	2fxhA	0.438	4.61	0.042	0.775	1.11.1.7,1.11.1.6	NA
15	0.060	1kwgA	0.435	4.98	0.036	0.806	3.2.1.23	NA
16	0.060	3fccA	0.431	4.60	0.039	0.752	6.1.1.13	NA
17	0.060	1y9dD	0.432	4.96	0.056	0.806	1.2.3.3	NA
18	0.060	1zvmC	0.437	4.81	0.050	0.775	3.2.2.5	NA
19	0.060	3ivrA	0.432	4.62	0.133	0.744	6.2.1.3	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	0.06	0.411	4.97	0.06	0.75	3e9yA	GO:0000287 GO:0003824 GO:0003984 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0009507 GO:0009536 GO:0009570 GO:0009635 GO:0016740 GO:0030976 GO:0046872 GO:0050660
1	0.06	0.437	5.01	0.05	0.81	3ey9A	GO:0000287 GO:0003824 GO:0005829 GO:0005886 GO:0006090 GO:0008289 GO:0016020 GO:0016491 GO:0030976 GO:0042802 GO:0042867 GO:0050660 GO:0051289 GO:0052737 GO:0055114
2	0.06	0.433	5.09	0.06	0.81	4feeA	GO:0000287 GO:0003824 GO:0030976 GO:0047112 GO:0055114
3	0.06	0.388	5.10	0.07	0.74	4q9dB	GO:0000287 GO:0003824 GO:0016829 GO:0030976 GO:0046872 GO:0050695
4	0.06	0.410	4.95	0.06	0.75	5ahkA	GO:0000287 GO:0003824 GO:0030976
5	0.06	0.357	5.14	0.02	0.70	2q5lA	GO:0000287 GO:0003824 GO:0009851 GO:0016829 GO:0016831 GO:0030976 GO:0046872 GO:0047434
6	0.06	0.412	5.14	0.10	0.79	2vjyA	GO:0000287 GO:0003824 GO:0004737 GO:0016829 GO:0016831 GO:0030976 GO:0046872
7	0.06	0.392	5.22	0.10	0.78	4qq8C	GO:0000287 GO:0003824 GO:0016829 GO:0030976 GO:0046872
8	0.06	0.413	5.19	0.07	0.78	2vk1A	GO:0000287 GO:0000949 GO:0000955 GO:0003824 GO:0004737 GO:0005634 GO:0005737 GO:0005829 GO:0006090 GO:0006559 GO:0006569 GO:0008152 GO:0009083 GO:0016829 GO:0016831 GO:0019655 GO:0030976 GO:0046872 GO:0047433 GO:0047434 GO:0050177
9	0.06	0.433	4.76	0.05	0.78	4d5eB	GO:0000287 GO:0003824 GO:0016787 GO:0030976 GO:0046872
10	0.06	0.432	4.96	0.06	0.81	1y9dD	GO:0000287 GO:0003824 GO:0016491 GO:0030976 GO:0046872 GO:0047112 GO:0055114
11	0.06	0.337	4.99	0.07	0.64	1ovmA	GO:0000287 GO:0003824 GO:0009851 GO:0016829 GO:0016831 GO:0030976 GO:0046872 GO:0047434
12	0.06	0.375	5.62	0.03	0.78	5femA	GO:0000287 GO:0003824 GO:0003984 GO:0005739 GO:0005948 GO:0008652 GO:0009082 GO:0009097 GO:0009099 GO:0016740 GO:0030976 GO:0046872 GO:0050660
13	0.06	0.420	5.10	0.03	0.78	2vbiA	GO:0000287 GO:0003824 GO:0004737 GO:0016829 GO:0016831 GO:0030976 GO:0046872
14	0.06	0.431	4.79	0.06	0.77	4rjiC	GO:0000287 GO:0003824 GO:0003984 GO:0016740 GO:0030976 GO:0034077
15	0.06	0.318	5.22	0.06	0.62	1x94A	GO:0005737 GO:0005975 GO:0008270 GO:0008968 GO:0009103 GO:0009244 GO:0016853 GO:0030246 GO:0046872 GO:2001061
16	0.06	0.337	4.99	0.05	0.61	4mx6A	GO:0006810 GO:0030288
17	0.06	0.380	5.02	0.07	0.73	2q28A	GO:0000166 GO:0000287 GO:0003824 GO:0008949 GO:0016829 GO:0016831 GO:0030976 GO:0033611 GO:0042802 GO:0043531 GO:0046872 GO:0071468
18	0.06	0.340	5.68	0.05	0.71	2panA	GO:0000287 GO:0003824 GO:0009028 GO:0009436 GO:0016829 GO:0030976 GO:0042802 GO:0046296 GO:0071949

Consensus prediction of GO terms

Molecular Function	GO:0050662	GO:0019842	GO:0046872	GO:0097159	GO:1901363
GO-Score	0.56	0.56	0.56	0.54	0.54
Biological Processes	GO:0055114	GO:0042867	GO:0009097	GO:0009099	GO:0051289	GO:0009635
GO-Score	0.12	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0005829	GO:0009570	GO:0005886
GO-Score	0.06	0.06	0.06

(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.