I-TASSER results

I-TASSER results for job id Rv2879c

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

Input Sequence in FASTA format

>protein (189 residues)
WGEPLANYARVLAAVQRITARPPSGFGISARAVTVSTVGLAPAIRNLADARLGVTLALSL
HAPDDGLRDTLVPVNNRWRISEALDAARYYANVTGRRVSIEYALIRDVNDQPWRADLLGK
RLHRVLGPLAHVNLIPLNPTPGSDWDASPKPVEREFVKRVRAKGVSCTVRDTRGREISAA
CGQLAAVGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| WGEPLANYARVLAAVQRITARPPSGFGISARAVTVSTVGLAPAIRNLADARLGVTLALSLHAPDDGLRDTLVPVNNRWRISEALDAARYYANVTGRRVSIEYALIRDVNDQPWRADLLGKRLHRVLGPLAHVNLIPLNPTPGSDWDASPKPVEREFVKRVRAKGVSCTVRDTRGREISAACGQLAAVGG
Prediction	CCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEHCCHHHHHHHHHHHCCCEEEEEEHCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCEEEEHHHHHHHHCCCHHHHHHHHHHHHHHCCCCEEEEHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEHCCCCHHHHHHHHHHHHHCC
Conf.Score	998757999999999998589999986555565776544688999998759977899985799856557555687667799999999999998899566545676654676799999999999985996688756899999998788996899999999999899866766997678899988877569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| WGEPLANYARVLAAVQRITARPPSGFGISARAVTVSTVGLAPAIRNLADARLGVTLALSLHAPDDGLRDTLVPVNNRWRISEALDAARYYANVTGRRVSIEYALIRDVNDQPWRADLLGKRLHRVLGPLAHVNLIPLNPTPGSDWDASPKPVEREFVKRVRAKGVSCTVRDTRGREISAACGQLAAVGG
Prediction	864244214301400341253436122223440202001012103403757130200000102456135421323441404300400340064343301021010322353512042005203744442010000103133445143445733540052057441302031144551331023123788
	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

CCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEHCCHHHHHHHHHHHCCCEEEEEEHCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCEEEEHHHHHHHHCCCHHHHHHHHHHHHHHCCCCEEEEHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEHCCCCHHHHHHHHHHHHHCC
WGEPLANYARVLAAVQRITARPPSGFGISARAVTVSTVGLAPAIRNLADARLGVTLALSLHAPDDGLRDTLVPVNNRWRISEALDAARYYANVTGRRVSIEYALIRDVNDQPWRADLLGKRLHRVLGPLAHVNLIPLNPTPGSDWDASPKPVEREFVKRVRAKGVSCTVRDTRGREISAACGQLAAVGG

3rf9A

0.38

0.37

0.96

2.50

MUSTER

MGEPLLNLNNVVPAMEIMLD--DFGFGLSKRRVTLSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A2

0.37

0.30

0.79

4.39

dPPAS

----------------------------------LSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A2

0.37

0.30

0.79

4.08

wdPPAS

----------------------------------LSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A

0.38

0.37

0.96

2.85

wMUSTER

MGEPLLNLNNVVPAMEIMLD--DFGFGLSKRRVTLSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A2

0.37

0.30

0.79

3.27

wPPAS

----------------------------------LSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A2

0.37

0.30

0.79

8.71

dPPAS2

----------------------------------LSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A2

0.37

0.30

0.79

3.11

PPAS

----------------------------------LSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A2

0.37

0.30

0.79

4.56

Env-PPAS

----------------------------------LSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A2

0.37

0.30

0.79

2.03

MUSTER

----------------------------------LSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNGRVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

3rf9A

0.38

0.37

0.96

2.70

dPPAS

MGEPLLNLNNVVPAMEIMLD--DFGFGLSKRRVTLSTSGVVPALDKLGDM-IDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNARVTIEYVMLDHVNDGTEHAHQLAELLK---DTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDRTKRTLRKRM-

(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=0.42

Estimated TM-score = 0.77±0.10

Estimated RMSD = 4.4±2.9Å

Download Model 2

C-score=-1.33

Download Model 3

C-score=-1.88

Download Model 4

C-score=-2.04

Download Model 5

C-score=-0.72

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	3rf9A	0.877	0.91	0.372	0.899
2	3c8fA	0.707	2.34	0.174	0.820
3	2a5hB	0.696	2.91	0.151	0.852
4	1tv8A	0.690	3.21	0.145	0.868
5	4wcxA	0.689	3.22	0.095	0.878
6	4rtbA	0.688	3.13	0.113	0.878
7	3canA	0.688	2.28	0.212	0.799
8	1r30B	0.687	2.98	0.092	0.857
9	4k36A	0.685	3.53	0.103	0.899
10	3t7vA	0.680	3.06	0.129	0.862

(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	0.41	8	3rfaA	SAM	Rep, Mult	2,3,4,36,37,59,61,103,135,137,138
2	0.09	2	3rf9B	SF4	Rep, Mult	2,38
3	0.09	3	3figA	LEU	Rep, Mult	64,65,66,68,73,74,75
4	0.06	2	3deqA	MG	Rep, Mult	57,101,133,170
5	0.03	1	3hpsA	LEU	Rep, Mult	63,64,65,83,84
6	0.03	1	3can0	III	Rep, Mult	14,17,18,28,138,150,168,169

	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	0.070	3cb8A	0.708	2.32	0.181	0.820	1.97.1.4	2
2	0.060	1uhvB	0.627	4.33	0.068	0.910	3.2.1.37	3,41
3	0.060	3i68A	0.637	4.03	0.067	0.878	1.3.5.2	NA
4	0.060	1w3hA	0.634	3.88	0.085	0.894	3.2.1.8	NA
5	0.060	2cw6E	0.654	3.58	0.104	0.868	4.1.3.4	60
6	0.060	1q45B	0.618	3.90	0.086	0.841	1.3.1.42	NA
7	0.060	1px8A	0.623	4.17	0.057	0.905	3.2.1.37	NA
8	0.060	1twiB	0.623	4.15	0.074	0.899	4.1.1.20	12,36,58
9	0.060	2a5hD	0.696	3.05	0.151	0.857	5.4.3.2	106,109,155
10	0.060	1rh9A	0.633	3.71	0.017	0.847	3.2.1.78	102
11	0.060	1de5A	0.624	3.75	0.064	0.852	5.3.1.14	NA
12	0.060	1knwA	0.639	3.81	0.095	0.873	4.1.1.20	NA
13	0.060	3cbhA	0.636	4.19	0.094	0.905	3.2.1.91	68,69
14	0.060	2bs9E	0.625	4.09	0.063	0.899	3.2.1.37	102
15	0.060	2eqdA	0.632	4.31	0.049	0.926	3.2.1.151	NA
16	0.060	3n2oA	0.641	4.03	0.073	0.926	4.1.1.19	133
17	0.060	1isvA	0.629	4.23	0.091	0.910	3.2.1.8	NA
18	0.060	1r30B	0.687	2.98	0.092	0.857	2.8.1.6	NA
19	0.060	2dgaA	0.636	4.00	0.071	0.884	3.2.1.21	NA
20	0.060	3aboA	0.648	3.56	0.103	0.852	4.3.1.7	36,82,147

(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	0.27	0.707	2.34	0.17	0.82	3c8fA	GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006974 GO:0016491 GO:0018307 GO:0043365 GO:0046872 GO:0051536 GO:0051539 GO:0055114
1	0.22	0.696	2.31	0.21	0.81	3canA	GO:0003824 GO:0016491 GO:0016829 GO:0051536 GO:0051539 GO:0055114
2	0.18	0.863	1.48	0.38	0.91	5hr7A	GO:0000049 GO:0002935 GO:0003824 GO:0005737 GO:0005829 GO:0006364 GO:0008033 GO:0008168 GO:0008173 GO:0016740 GO:0019843 GO:0030488 GO:0032259 GO:0046677 GO:0046872 GO:0051536 GO:0051539 GO:0070040 GO:0070475
3	0.15	0.680	3.06	0.13	0.86	3t7vA	GO:0003824 GO:0008652 GO:0016765 GO:0016853 GO:0016866 GO:0046872 GO:0051188 GO:0051536 GO:0051539 GO:0071524
4	0.11	0.690	3.17	0.15	0.86	2fb2A	GO:0000166 GO:0003824 GO:0005525 GO:0006777 GO:0016829 GO:0019008 GO:0032324 GO:0046872 GO:0051536 GO:0051539 GO:0061597
5	0.11	0.703	2.89	0.15	0.86	2a5hB	GO:0003824 GO:0016853 GO:0019475 GO:0046872 GO:0050066 GO:0051536 GO:0051539
6	0.10	0.688	3.13	0.11	0.88	4rtbA	GO:0003824 GO:0009228 GO:0046872 GO:0051536 GO:0051539
7	0.10	0.685	3.53	0.10	0.90	4k36A	GO:0003824 GO:0016491 GO:0046872 GO:0051536 GO:0051539 GO:0055114
8	0.10	0.673	3.46	0.09	0.89	4r33A	GO:0003824 GO:0046872 GO:0051536 GO:0051539
9	0.10	0.689	3.22	0.10	0.88	4wcxA	GO:0003824 GO:0046872 GO:0051536 GO:0051539
10	0.09	0.667	3.27	0.10	0.87	5ff2A	GO:0003824 GO:0016491 GO:0016765 GO:0046872 GO:0051188 GO:0051536 GO:0051537 GO:0051539 GO:0055114
11	0.07	0.589	3.91	0.04	0.83	4aibA	GO:0003824 GO:0004586 GO:0005737 GO:0006596 GO:0016829 GO:0033387
12	0.07	0.525	4.08	0.05	0.76	4q3mA	GO:0016491 GO:0055114
13	0.07	0.553	3.61	0.07	0.76	3lu2A	GO:0006508 GO:0016805
14	0.07	0.501	4.00	0.07	0.70	2h6rB	GO:0003824 GO:0004807 GO:0005737 GO:0005829 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853 GO:0019563 GO:0046166
15	0.07	0.460	4.79	0.08	0.72	1dj3A	GO:0000166 GO:0004019 GO:0005525 GO:0006164 GO:0009507 GO:0009536 GO:0016874 GO:0044208 GO:0046872
16	0.07	0.461	4.13	0.11	0.65	3tznB	GO:0004156 GO:0009396 GO:0016740 GO:0042558 GO:0044237 GO:0046654 GO:0046656 GO:0046872
17	0.07	0.457	4.93	0.05	0.73	2v40A	GO:0000166 GO:0000287 GO:0002376 GO:0004019 GO:0005525 GO:0005737 GO:0005829 GO:0005886 GO:0006164 GO:0006167 GO:0006531 GO:0009168 GO:0014074 GO:0016874 GO:0042301 GO:0044208 GO:0046040 GO:0046872 GO:0060359 GO:0070062 GO:0071257
18	0.06	0.408	4.59	0.05	0.60	4q1hA	GO:0003824 GO:0005737 GO:0005829 GO:0008152 GO:0008935 GO:0016829 GO:0017000 GO:0042181

Consensus prediction of GO terms

Molecular Function	GO:0051539	GO:0046872	GO:0043364	GO:0070283	GO:0016491	GO:0008169	GO:0003723	GO:0016426	GO:0016433
GO-Score	0.64	0.54	0.54	0.54	0.43	0.36	0.36	0.36	0.36
Biological Processes	GO:0006464	GO:0019318	GO:0033554	GO:0055114	GO:0031167	GO:0042221	GO:0006400
GO-Score	0.54	0.54	0.54	0.43	0.36	0.36	0.36
Cellular Component	GO:0005829
GO-Score	0.40

(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.