I-TASSER results

I-TASSER results for job id Rv3688c

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

Input Sequence in FASTA format

>protein (154 residues)
MAELKSQLRSDLTQAMKTQDKLRTATIRMLLAAIQTEEVSGKQARELSDDEVIKVLARES
RKRGEAAEIYTQNGRGELAATEHAEARIIDEYLPTPLTEGELADVADTAIAEVAEELGHR
PSMKQMGLVMKAATVIAAGKADGARLSAAVKERL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAELKSQLRSDLTQAMKTQDKLRTATIRMLLAAIQTEEVSGKQARELSDDEVIKVLARESRKRGEAAEIYTQNGRGELAATEHAEARIIDEYLPTPLTEGELADVADTAIAEVAEELGHRPSMKQMGLVMKAATVIAAGKADGARLSAAVKERL
Prediction	CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHC
Conf.Score	9889999999999999987589999999999999999987678889999999999999999999999999998999999999999999999878789999999999999999976547888888999999999887689889999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAELKSQLRSDLTQAMKTQDKLRTATIRMLLAAIQTEEVSGKQARELSDDEVIKVLARESRKRGEAAEIYTQNGRGELAATEHAEARIIDEYLPTPLTEGELADVADTAIAEVAEELGHRPSMKQMGLVMKAATVIAAGKADGARLSAAVKERL
Prediction	7551364046203501455354324003203330453535655766043630251045215514401530474626421550552051045112651556303500550055144545645445301400430265153422353025204748
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHC
MAELKSQLRSDLTQAMKTQDKLRTATIRMLLAAIQTEEVSGKQARELSDDEVIKVLARESRKRGEAAEIYTQNGRGELAATEHAEARIIDEYLPTPLTEGELADVADTAIAEVAEELGHRPSMKQMGLVMKAATVIAAGKADGARLSAAVKERL

1ng6A

0.33

0.31

0.95

2.95

MUSTER

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYLPEQLSEEELRTIVNETIAEVGA-----SSKADMGKVMGAIMPKVKGKADGSLINKLVSSQL

1ng6A

0.33

0.31

0.95

2.78

dPPAS

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYLPEQLSEEELRTIVNETIAEVGA-----SSKADMGKVMGAIMPKVKGKADGSLINKLVSSQL

1ng6A

0.33

0.31

0.95

3.98

wdPPAS

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYLPEQLSEEELRTIVNETIAEVGA-----SSKADMGKVMGAIMPKVKGKADGSLINKLVSSQL

1ng6A

0.33

0.31

0.95

3.23

wMUSTER

--SLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYLPEQLSEEELRTIVNETIAEVGA-----SSKADMGKVMGAIMPKVKGKADGSLINKLVSSQL

1ng6A

0.33

0.31

0.95

4.23

wPPAS

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYLPEQLSEEELRTIVNETIAEVGA-----SSKADMGKVMGAIMPKVKGKADGSLINKLVSSQL

1ng6A

0.33

0.31

0.95

6.40

dPPAS2

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYLPEQLSEEELRTIVNETIAEVGA-----SSKADMGKVMGAIMPKVKGKADGSLINKLVSSQL

1ng6A

0.33

0.31

0.95

3.43

PPAS

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYLPEQLSEEELRTIVNETIAEVGA-----SSKADMGKVMGAIMPKVKGKADGSLINKLVSSQL

1ng6A

0.33

0.31

0.95

6.36

Env-PPAS

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYLPEQLSEEELRTIVNETIAEVGA-----SSKADMGKVMGAIMPKVKGKADGSLINKLVSSQL

1ng6A1

0.29

0.17

0.59

1.78

MUSTER

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYL-------------------------------------------------------------

1ng6A1

0.29

0.17

0.59

1.78

dPPAS

-MSLLERLNQDMKLYMKNREKDKLTVVRMVKASLQNEAIKLK-KDSLTEDEELTVLSRELKQRKDSLQEFSNANRLDLVDKVQKELDILEVYL-------------------------------------------------------------

(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=1.12

Estimated TM-score = 0.87±0.07

Estimated RMSD = 2.7±2.0Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.64

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	1ng6A	0.939	0.76	0.327	0.955
2	4w8yA	0.547	4.44	0.107	0.851
3	5doqA	0.524	4.24	0.027	0.818
4	2z1qB	0.510	4.69	0.093	0.799
5	3owaA	0.509	4.78	0.078	0.805
6	4j5tA	0.509	4.59	0.043	0.786
7	2eabA	0.507	4.73	0.092	0.812
8	4j7cI	0.507	4.30	0.055	0.812
9	2uxwA	0.500	4.82	0.086	0.799
10	4av3A	0.496	4.50	0.042	0.747

(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	3erzD	HG	Rep, Mult	71,75,79
2	0.07	4	2p06A	MG	Rep, Mult	63,66,82,85
3	0.05	3	3iouB	ZN	Rep, Mult	65,68,82
4	0.03	2	1xmeC	HAS	Rep, Mult	52,56
5	0.03	2	3iqvA	FSC	Rep, Mult	61,64,65,96
6	0.03	2	3p1nA	III	Rep, Mult	30,81,84,85,88,91
7	0.03	2	1is2A	FAD	Rep, Mult	14,26,27,30
8	0.03	2	1is2B	FAD	Rep, Mult	7,14,22,89,91,92
9	0.02	1	3p1qA	FSC	Rep, Mult	7,27,30,31,89,95
10	0.02	1	5da5A	CA	Rep, Mult	62,65
11	0.02	1	3owaA	FAD	Rep, Mult	31,34,54
12	0.02	1	1jm0B	MN	Rep, Mult	35,38
13	0.02	1	4ryqA	MPG	Rep, Mult	63,70,77,78,82,85
14	0.02	1	2w6dA	CPL	Rep, Mult	85,86,108,109,111,112
15	0.02	1	2w6dB	CPL	Rep, Mult	84,85,86,87,88,108,109,111
16	0.02	1	1r8eA	IMD	Rep, Mult	42,46
17	0.02	1	3touA	GSH	Rep, Mult	58,62

	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	1is2A	0.484	4.81	0.032	0.786	1.3.3.6	100,105
2	0.060	3b98A	0.456	5.23	0.041	0.799	5.3.99.4	NA
3	0.060	1r76A	0.468	4.68	0.152	0.779	4.2.2.2	87
4	0.060	2vn0A	0.462	5.03	0.053	0.779	1.14.14.1	99
5	0.060	2z1qB	0.510	4.69	0.093	0.799	1.3.99.3	NA
6	0.060	2ewbA	0.464	5.05	0.077	0.786	3.4.11.1,3.4.11.5	62
7	0.060	2vn7A	0.467	4.30	0.091	0.708	3.2.1.3	11,84,87
8	0.060	2gtqA	0.460	5.14	0.061	0.812	3.4.11.2	NA
9	0.060	2jg0A	0.496	4.23	0.069	0.701	3.2.1.28	NA
10	0.060	1qmgA	0.468	5.14	0.035	0.812	1.1.1.86	152
11	0.060	2sqcA	0.464	5.42	0.049	0.877	5.4.99.17	NA
12	0.060	1og5B	0.450	4.79	0.033	0.753	1.14.13.48,1.14.13.49,1.14.13.80	88
13	0.060	1gaiA	0.464	4.51	0.090	0.701	3.2.1.3	51
14	0.060	1ue8A	0.329	5.63	0.033	0.643	1.14.-.-	59
15	0.060	3b4xA	0.470	5.05	0.067	0.812	1.14.14.1	93
16	0.060	1h12A	0.469	4.41	0.078	0.721	3.2.1.8	71,75
17	0.060	1og2A	0.451	4.88	0.033	0.753	1.14.14.1	152
18	0.060	2yr4A	0.459	4.81	0.040	0.773	1.13.12.9	NA
19	0.060	2pffB	0.462	4.77	0.065	0.786	2.3.1.86	64

(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	0.57	0.939	0.76	0.33	0.95	1ng6A	GO:0016884
1	0.06	0.386	5.40	0.05	0.71	3ju8A	GO:0004029 GO:0006525 GO:0006527 GO:0008152 GO:0016491 GO:0016620 GO:0019544 GO:0019545 GO:0043824 GO:0055114
2	0.06	0.344	5.55	0.09	0.67	4jo0A	GO:0046872
3	0.06	0.357	5.06	0.02	0.62	2ol2A	GO:0001972 GO:0002020 GO:0002080 GO:0004867 GO:0005539 GO:0005576 GO:0005615 GO:0006810 GO:0006869 GO:0007283 GO:0007338 GO:0007342 GO:0007596 GO:0008201 GO:0009897 GO:0010466 GO:0010951 GO:0016020 GO:0030414 GO:0031091 GO:0031094 GO:0031210 GO:0032190 GO:0036024 GO:0036025 GO:0036026 GO:0036027 GO:0036028 GO:0036029 GO:0036030 GO:0043234 GO:0045861 GO:0051346 GO:0070062 GO:0097181 GO:0097182 GO:0097183
4	0.06	0.358	4.98	0.05	0.62	3x1lA	GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
5	0.06	0.365	5.16	0.07	0.62	4dozA	GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
6	0.06	0.322	5.37	0.06	0.58	3bw8A	GO:0005576 GO:0006471 GO:0009405 GO:0016740 GO:0016757 GO:0016763
7	0.06	0.335	5.62	0.04	0.60	3w2wA	GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
8	0.06	0.547	4.44	0.11	0.85	4w8yA	GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
9	0.06	0.341	5.24	0.05	0.61	1jilA	GO:0000166 GO:0003723 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874
10	0.06	0.342	5.17	0.04	0.60	2ts1A	GO:0000166 GO:0003723 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874
11	0.06	0.373	4.03	0.02	0.52	4xeaA	GO:0003824 GO:0046872
12	0.06	0.280	5.55	0.05	0.53	2q3sA	GO:0003676 GO:0005634 GO:0005737 GO:0005773 GO:0005774 GO:0006139 GO:0008408 GO:0090305
13	0.06	0.306	5.11	0.07	0.52	1yyaA	GO:0003824 GO:0004807 GO:0005737 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853
14	0.06	0.360	5.17	0.02	0.64	3kowB	GO:0003824 GO:0008152 GO:0016853 GO:0031419 GO:0046872 GO:0046983 GO:0047831
15	0.06	0.298	5.37	0.04	0.55	1uj3B
16	0.06	0.275	5.17	0.04	0.48	3eu7A	GO:0000724 GO:0000731 GO:0000732 GO:0001701 GO:0001756 GO:0001833 GO:0003677 GO:0005634 GO:0005654 GO:0006281 GO:0006310 GO:0006974 GO:0007498 GO:0009887 GO:0031052 GO:0035264 GO:0036342 GO:0043066 GO:0048568
17	0.06	0.261	4.16	0.07	0.39	1ob8B	GO:0003676 GO:0003677 GO:0004518 GO:0004519 GO:0006281 GO:0006310 GO:0006974 GO:0008821 GO:0016787 GO:0046872 GO:0090305
18	0.06	0.289	5.50	0.04	0.55	2ojzH

Consensus prediction of GO terms

Molecular Function	GO:0016884
GO-Score	0.57
Biological Processes	GO:0019545	GO:0019544	GO:0055114	GO:0007596	GO:0007342	GO:0006869	GO:0010951	GO:0007283	GO:0051607
GO-Score	0.07	0.07	0.07	0.06	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0097182	GO:0031091	GO:0036027	GO:0036028	GO:0005615	GO:0070062	GO:0097183	GO:0036030	GO:0036025	GO:0031094	GO:0097181	GO:0036024	GO:0036026	GO:0036029	GO:0002080	GO:0009897
GO-Score	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	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.