I-TASSER results

I-TASSER results for job id Rv2732c

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

Input Sequence in FASTA format

>protein (204 residues)
MMSHEHDAGDLDALRAEIEAAERRVAREIEPGARALVVAILVFVLLGSFILPHTGSVRGW
DVLFSSHGAGRAAVALPSRVFAWLALVFGVGFSMLALLTRRWALAWVALAGSAMASGTGL
LAVWSRQTVAAGHPGPGIGLIVAWITAIVLTFHWAQVVWSRTIVQLAAEERRRRVVAQQQ
CKTLLDHVQTDSEAGTTPDRGTDR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MMSHEHDAGDLDALRAEIEAAERRVAREIEPGARALVVAILVFVLLGSFILPHTGSVRGWDVLFSSHGAGRAAVALPSRVFAWLALVFGVGFSMLALLTRRWALAWVALAGSAMASGTGLLAVWSRQTVAAGHPGPGIGLIVAWITAIVLTFHWAQVVWSRTIVQLAAEERRRRVVAQQQCKTLLDHVQTDSEAGTTPDRGTDR
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHCCEHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEHCCCCCCCCCHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Conf.Score	998888857999999999999999855444677556899999999999996656887757899757776544454547899999999999999999999999999999999999999999999985578889999865799999999999999999999869999999999999999999999999876567788888877899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MMSHEHDAGDLDALRAEIEAAERRVAREIEPGARALVVAILVFVLLGSFILPHTGSVRGWDVLFSSHGAGRAAVALPSRVFAWLALVFGVGFSMLALLTRRWALAWVALAGSAMASGTGLLAVWSRQTVAAGHPGPGIGLIVAWITAIVLTFHWAQVVWSRTIVQLAAEERRRRVVAQQQCKTLLDHVQTDSEAGTTPDRGTDR
Prediction	745558647415514530451145005414244322100102333331100021372401100021443443213213311132123212322230333332220120221123033322201001124447441000001113301210232103000332531342254136455554444335525555656642444568
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCHHHHHHHHHHHHHHHHHHHCCEHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEHCCCCCCCCCHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
MMSHEHDAGDLDALRAEIEAAERRVAREIEPGARALVVAILVFVLLGSFILPHTGSVRGWDVLFSSHGAGRAAVALPSRVFAWLALVFGVGFSMLALLTRRWALAWVALAGSAMASGTGLLAVWSRQTVAAGHPGPGIGLIVAWITAIVLTFHWAQVVWSRTIVQLAAEERRRRVVAQQQCKTLLDHVQTDSEAGTTPDRGTDR

5kk2E

0.14

0.10

0.72

0.97

wPPAS

----------------------RGVQMLL-----TVGAFAAFSLMTIAVGTDYRGEVSGWRTCCNFKDADYEAAVRASSIFPILSVILLFMGGLCIAASERHNIILSAGIFFVSAGLSNIIGIIVYISANAGYS--GWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARAT-----------------------------

4ke2A

0.16

0.14

0.87

1.10

dPPAS2

ASKAAVTAADAAAAAATIAASAASVA------AATAADDAAASIATINAASAAAKSIA-------AAAAMAAKDTAAAAASAAAAAVASAAKALEKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP-------------

4bwzA2

0.13

0.10

0.77

1.05

dPPAS2

VATSVGITARVLQELGVLSRPYSRII------LGAAVIDDVLGLIVLACVNGVAETGQ------ELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGMAPRGEVGLIVAALGLKAGAVNEEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE----------------------------------

5kk2E

0.10

0.07

0.73

1.01

dPPAS2

------------------RGVQMLLT--------TVGAFAAFSLMTIAVGTDYCCNFKGLCKQIDHEDADYEAAVRASSIFPILSVILLFMGGLCIAASERHNIILSAGIFFVSAGLSNIIGIIVYISANAGYS-YGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARAT-----------------------------

5cwoA

0.09

1.00

0.83

MUSTER

-PELEEWIRRAKEVAKEVEKVAQRAEEEGNPDLRDSAKELRRAVEEAIEEAKKQGNPELVEWVARAAKVAAEVIKVAEKEGNRDLFRAALELVRAVIEAIEEAVKQGNPELVEWVARAAKVAAEVIKVAIQAEKEGNRDLFRAALELVRAVIEAIEEAVKQGNPELVERVARLAKKAAELIKRAIRAEKEGNRDERREALERVR

4ke2A

0.14

0.96

0.78

dPPAS

--MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP------

5kk2E

0.12

0.08

0.72

0.87

wdPPAS

------------------RGVQMLLT--------TVGAFAAFSLMTIAVGTDYRGEVSGWRTCCNFKDADYERAVRASSIFPILSVILLFMGGLCIAASERHNIILSAGIFFVSAGLSNIIGIIVYISANAGYS--GWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARAT-----------------------------

5edlA

0.16

0.14

0.88

0.83

wMUSTER

IMS----SIVFAVVYLLFTHFGNVLAGMFGPIAYEPIYGIWFIVSVIAAYMIRKPGA----ALVSEIIAALVECLLGNPMVIVIGIVQGLGAEAVFLATKAYSLPVLMLAGMGSSVASFIYDLFVSGYAAYSPGYLLIMLVIRLISGALLAGLLGKAVSD--SLAYT----NGMALGKELKKKRKRASEHASL-----------

5edlA

0.19

0.15

0.76

wPPAS

V------YLLFTHFGNVLAGMFGPIAYEPIYG--VSVIAAYMIAALVSEIIAALV-----ECLLGNPSG---------PMVIVIGIVQGLGAEAVFLATKALPVLMLAGMGSSVASFIYDLFVSGYAAYSPG-----IMLVIRLISGALLAGLLGKAVSDST--GMALGKELKKKRKRASEHASL-------------------

5cwnA

0.13

0.12

0.92

0.95

dPPAS2

ASERGDEEEFRKAAEKALELAKRLVEQAKKEGDPELVLEAAKVALRVAELAAKNGDKE------VFKKAAESALEVAKRLVEVASKEGDPELVLEAAKVALRVAELAAKNGKEVFKKAAESALEVAKRLVEVASKEGDPELVEEAAKVAEEVRKLAKKQGDEEVYEKARETAREVKEELKRVREEKGGWLEHH-----------

(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=-3.69

Estimated TM-score = 0.31±0.10

Estimated RMSD = 14.2±3.8Å

Download Model 2

C-score=-4.31

Download Model 3

C-score=-4.34

Download Model 4

C-score=-3.18

Download Model 5

C-score=-4.32

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	4xydA	0.601	4.51	0.068	0.868
2	4he8M	0.601	3.98	0.061	0.804
3	4he8L	0.601	4.18	0.081	0.819
4	3o0rB	0.600	4.49	0.079	0.853
5	3rkoM	0.599	4.03	0.061	0.814
6	3rkoN	0.591	3.96	0.061	0.804
7	3ayfA2	0.591	4.73	0.068	0.892
8	1xmeA	0.587	4.34	0.089	0.853
9	2jswA	0.586	3.65	0.074	0.774
10	1tt9A	0.586	4.05	0.112	0.799

(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	0.07	4	4bmoA	FE2	Rep, Mult	44,115,147,150
2	0.05	3	2y00B	Y01	Rep, Mult	34,35,38,39,42
3	0.04	2	3fyeA	DMU	Rep, Mult	80,82,113,114,117,118,121
4	0.04	2	2jstB	HLT	Rep, Mult	83,86,113
5	0.04	2	5ajfA	CU1	Rep, Mult	37,87,91,111,154
6	0.04	2	3rkoN	LFA	Rep, Mult	42,43,46,87,88,91
7	0.04	2	1c6fA	AR	Rep, Mult	120,123,147
8	0.02	1	2q8hA	TF4	Rep, Mult	44,80,114,144,147
9	0.02	1	3rkoC	LFA	Rep, Mult	109,112,116,120
10	0.02	1	2q67A	CA	Rep, Mult	128,129
11	0.02	1	3ap1B	III	Rep, Mult	23,24,27
12	0.02	1	3ap2B	PO4	Rep, Mult	126,204
13	0.02	1	4zzbC	XE	Rep, Mult	45,81,84
14	0.02	1	3dtuC	DXC	Rep, Mult	122,125,126,129,136,140
15	0.02	1	2wse1	CLA	Rep, Mult	108,111
16	0.02	1	3rkoN	LFA	Rep, Mult	111,114,115,119,150,151
17	0.02	1	2jk8B	CL	Rep, Mult	137,139,140
18	0.02	1	3dtuC	TRD	Rep, Mult	47,119,122,123,126

	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	1fftA	0.563	4.67	0.074	0.843	1.10.3.-	NA
2	0.060	2wpnB	0.559	3.89	0.040	0.760	1.12.7.2	31
3	0.060	1y2mB	0.523	5.17	0.082	0.809	4.3.1.24	NA
4	0.060	1occA	0.554	4.78	0.052	0.868	1.9.3.1	NA
5	0.060	1xmeA	0.587	4.34	0.089	0.853	1.9.3.1	NA
6	0.060	1qd1B	0.376	4.79	0.090	0.588	2.1.2.5,4.3.1.4	4
7	0.060	1qleA	0.578	4.93	0.060	0.892	1.9.3.1	173,174
8	0.060	1w27A	0.515	4.67	0.022	0.760	4.3.1.24	NA
9	0.060	2pnrB	0.557	4.88	0.042	0.853	2.7.11.2	NA
10	0.060	2occN	0.553	4.81	0.058	0.873	1.9.3.1	76,81,84
11	0.060	2pfdB	0.587	4.17	0.130	0.799	2.1.2.5,4.3.1.4	NA
12	0.060	3djlA	0.520	4.49	0.050	0.770	1.3.99.-	NA
13	0.060	2ix6A	0.541	3.75	0.066	0.730	1.3.3.6	NA
14	0.060	1yrqI	0.541	3.95	0.020	0.750	1.12.2.1	52,86
15	0.060	1frvB	0.559	4.05	0.049	0.784	1.12.2.1	NA
16	0.060	1h2rL	0.565	3.93	0.059	0.779	1.12.2.1	43,84,140
17	0.060	1gkzA	0.541	4.61	0.046	0.799	2.7.11.4,2.7.1.115	NA
18	0.060	2r0nA	0.513	4.34	0.060	0.745	1.3.99.7	49,140
19	0.060	3no9A	0.512	4.68	0.035	0.765	4.2.1.2	47

(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	0.10	0.600	4.49	0.08	0.85	3o0rB	GO:0004129 GO:0005506 GO:0005886 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0019333 GO:0020037 GO:0046872 GO:0055114 GO:0070469 GO:1902600
1	0.07	0.601	4.51	0.07	0.87	4xydA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0016491 GO:0016966 GO:0020037 GO:0055114 GO:0070469 GO:1902600
2	0.07	0.574	3.76	0.08	0.76	4he8I	GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
3	0.07	0.572	4.59	0.06	0.84	5djqA	GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0005887 GO:0006119 GO:0009055 GO:0009060 GO:0015078 GO:0015990 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0016705 GO:0019411 GO:0019646 GO:0019825 GO:0020037 GO:0045154 GO:0045278 GO:0046872 GO:0055114 GO:0070069 GO:0070469 GO:0070470 GO:1902600
4	0.07	0.601	4.18	0.08	0.82	4he8F	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
5	0.07	0.591	4.71	0.06	0.89	3ayfA	GO:0004129 GO:0005506 GO:0009055 GO:0009060 GO:0016020 GO:0016021 GO:0020037 GO:0046872 GO:0055114 GO:1902600
6	0.07	0.473	2.50	0.05	0.56	2rldC	GO:0046872
7	0.07	0.601	3.90	0.06	0.80	4he8G	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
8	0.06	0.576	4.83	0.10	0.86	2yevA	GO:0004129 GO:0005506 GO:0005507 GO:0005886 GO:0006119 GO:0006810 GO:0006811 GO:0009055 GO:0009060 GO:0015002 GO:0015992 GO:0016020 GO:0016021 GO:0016491 GO:0020037 GO:0022900 GO:0022904 GO:0046872 GO:0055114 GO:0070469 GO:1902600
9	0.06	0.374	4.90	0.04	0.54	4fluA	GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0006260 GO:0008408 GO:0016740 GO:0016779 GO:0071897 GO:0090305
10	0.06	0.491	4.99	0.03	0.76	1tj7A	GO:0003824 GO:0004056 GO:0005737 GO:0005829 GO:0006526 GO:0008652 GO:0016829 GO:0042450 GO:0051262
11	0.06	0.354	5.13	0.05	0.56	4aq4A	GO:0001407 GO:0005215 GO:0006810 GO:0015794 GO:0030288 GO:0042597
12	0.06	0.271	5.38	0.02	0.45	2af3C	GO:0005886 GO:0006085 GO:0008152 GO:0008959 GO:0016020 GO:0016407 GO:0016740 GO:0016746
13	0.06	0.322	6.00	0.10	0.57	3swxB	GO:0003824 GO:0008152 GO:0016853
14	0.06	0.338	5.39	0.03	0.56	2uxyA	GO:0004040 GO:0006807 GO:0015976 GO:0016787 GO:0016810 GO:0043605
15	0.06	0.328	5.83	0.04	0.59	2ohfA	GO:0000166 GO:0005524 GO:0005525 GO:0005634 GO:0005730 GO:0005737 GO:0005813 GO:0005913 GO:0016020 GO:0016787 GO:0016887 GO:0043022 GO:0043023 GO:0046034 GO:0046872 GO:0070062 GO:0098609 GO:0098641
16	0.06	0.289	4.73	0.10	0.44	2isjA	GO:0000166 GO:0009236 GO:0016491 GO:0016705 GO:0055114
17	0.06	0.287	4.87	0.08	0.43	3dbaA	GO:0000166 GO:0004114 GO:0005886 GO:0007165 GO:0007601 GO:0008081 GO:0016020 GO:0016787 GO:0030553 GO:0046872 GO:0047555 GO:0050896
18	0.06	0.303	4.95	0.07	0.48	3fkkA	GO:0003824 GO:0005975 GO:0008152 GO:0016829 GO:0019568 GO:0019570 GO:0042803 GO:0047449
19	0.06	0.240	5.75	0.06	0.43	3ktyB	GO:0001510 GO:0003723 GO:0006396 GO:0008168 GO:0008173 GO:0016740 GO:0032259

Consensus prediction of GO terms

Molecular Function	GO:0009055	GO:0015002	GO:0046906	GO:0046914	GO:0016676	GO:0015078	GO:0016662
GO-Score	0.45	0.45	0.45	0.45	0.45	0.45	0.34
Biological Processes	GO:0098662	GO:0045333	GO:0015992
GO-Score	0.45	0.45	0.45
Cellular Component	GO:0071944	GO:0016021
GO-Score	0.54	0.32

(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.