I-TASSER results

I-TASSER results for job id Rv3354

[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)
MNLRRHQTLTLRLLAASAGILSAAAFAAPAQANPVDDAFIAALNNAGVNYGDPVDAKALG
QSVCPILAEPGGSFNTAVASVVARAQGMSQDMAQTFTSIAISMYCPSVMADVASGNLPAL
PDMPGLPGS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MNLRRHQTLTLRLLAASAGILSAAAFAAPAQANPVDDAFIAALNNAGVNYGDPVDAKALGQSVCPILAEPGGSFNTAVASVVARAQGMSQDMAQTFTSIAISMYCPSVMADVASGNLPALPDMPGLPGS
Prediction	CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHHHHCCCCCCCCCCCCCCCCC
Conf.Score	988665467899999999999999857888889875999999998599999999999999999999986799879999999987899999999999999999959788876578888888888999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MNLRRHQTLTLRLLAASAGILSAAAFAAPAQANPVDDAFIAALNNAGVNYGDPVDAKALGQSVCPILAEPGGSFNTAVASVVARAQGMSQDMAQTFTSIAISMYCPSVMADVASGNLPALPDMPGLPGS
Prediction	653444332313200130133122323332324443440142047450426336201420330043036544434421341356347144730130002004311241236247543444253654458
	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

CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHHHHCCCCCCCCCCCCCCCCC
MNLRRHQTLTLRLLAASAGILSAAAFAAPAQANPVDDAFIAALNNAGVNYGDPVDAKALGQSVCPILAEPGGSFNTAVASVVARAQGMSQDMAQTFTSIAISMYCPSVMADVASGNLPALPDMPGLPGS

4jkzA2

0.18

0.14

0.76

1.17

dPPAS2

-RMPKTDDVTADLASWAGTLAAALT-------TRRGHAMLKTLMAASLEHEDEGFSRPLIESVRDRLRDEDIDLGAVVNAVLSEGRSYSRQRAETSARIIVAGLRP-----------------------

5cwdA

0.16

0.98

1.11

dPPAS2

AKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGM--PTKEAARSFCEAAARAAAESNDEIAAKACLEVAKQAGMPTKEAARSFCEAAKRAADEEVEKIAKKACKEVAKQAGMPWL

2n3eA

0.18

0.17

0.92

0.79

MUSTER

MGQANTPWSSKANADAFINSFISAASNTGSFSSLIGNTLMAAMDNMGGRITPQALDMAFASSVAQIAASQGGDIADALTSAFYQTTGVVNSRFISEIRSLIGMFAQASANDVYASAGSG----------

2n3eA

0.18

0.17

0.92

0.70

dPPAS

MGQANTPWSSKANADAFINSFISAASNTGSFSSLIGNTLMAAMDNMGGRITPQALDMAFASSVAQIAASQGGDIADALTSAFYQTTGVVNSRFISEIRSLIGMFAQASANDVYASAGSG----------

4k82A2

0.17

0.13

0.80

0.66

wdPPAS

---------DETVFNAVCDVTKKMLDNKPKILQGDLVKFLKDLKYK-IEGGDPELIIKDLKIILERLPC-GVGLDDLFKNIFVKDGILSEGIAKPLGDLLILVLCPNVKNNVSS---------------

2n3eA

0.19

0.17

0.91

0.78

wMUSTER

MGQANSSKANADAFINSFISAASNTGSFSQD-SLIGNTLMAAMDNMGGRITPQALDMAFASSVAQIAASQGGDIADALTSAFYQTTGVVNSRFISEIRSLIGMFAQASANDVYASA-----------GS

4k82A2

0.17

0.13

0.78

0.71

wPPAS

---------DETVFNAVCDVTKKMLDNKPKILQGDLVKFLKDLKYK-IEGGDPELIIKDLKIILERL---GVGLDDLFKNIFVKDGILSEGIAKPLGDLLILVLCPNVKNNVSS---------------

3lr0A1

0.23

0.07

0.31

0.97

dPPAS2

-----AQRVALQLVAIVKLTRTALLYSDP---DLRRALLQDLESNEGV---------------------------------------------------------------------------------

2mqaA

0.15

0.13

0.85

0.87

PPAS

-GNAFAQSLSSNLLSSGDFVQMISSTTSTDQASVATSVAQNVGNQLGLDANAMNSLLGAVSGYVSTLGNAISDISSAIGNVLANSGSISASSAASSVTTTLTSYGPAVFYA------------------

1ta9B2

0.12

0.11

0.91

0.75

Env-PPAS

AIHGPVHRLMHGEKVAYGTLVQVVLEDWPLEDFNNLASFMAKCEELGIPNVTDEELLMVGRATLR----PDE-------SIHNMSKKFN-PSQIADAIKAVDSYSQKWQEQTGWTERFRLPPSRHSPHL

(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=-2.10

Estimated TM-score = 0.47±0.15

Estimated RMSD = 9.0±4.6Å

Download Model 2

C-score=-2.74

Download Model 3

C-score=-4.37

Download Model 4

C-score=-4.78

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	2j8sA3	0.601	3.57	0.081	0.853
2	1cqxA1	0.540	4.18	0.044	0.798
3	1gvhA	0.533	3.97	0.043	0.767
4	2cse1	0.533	4.35	0.071	0.891
5	1mhsA	0.532	3.94	0.065	0.822
6	2ig3A	0.530	4.07	0.057	0.767
7	2wy4A	0.529	3.70	0.038	0.744
8	1rsrB	0.521	4.46	0.048	0.837
9	4vhbA	0.518	3.98	0.048	0.744
10	3hi0A	0.516	4.41	0.041	0.845

(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	3kziT	CLA	Rep, Mult	96,100
2	0.08	4	1vhbA	HEM	Rep, Mult	39,67,74,75,78,96,100
3	0.06	3	3qb5K	MN	Rep, Mult	61,104
4	0.06	3	1pssL	BCL	Rep, Mult	89,92,93,96,97
5	0.06	3	1n38A	CH1	Rep, Mult	35,36,61,65,66,67
6	0.02	1	3leeE	MG	Rep, Mult	25,104,108
7	0.02	1	2o01G	CLA	Rep, Mult	106,107
8	0.02	1	2h2pA	SEK	Rep, Mult	28,30
9	0.02	1	1cb2A	MAN	Rep, Mult	72,76
10	0.02	1	3go9A	ZN	Rep, Mult	36,49
11	0.02	1	3ozvB	ECN	Rep, Mult	17,18,21,39,78,81
12	0.02	1	1lghA	BCL	Rep, Mult	33,34,37
13	0.02	1	3eerA	ZN	Rep, Mult	64,105,106
14	0.02	1	3ze3B	78N	Rep, Mult	23,32

	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	3f93A	0.498	4.55	0.059	0.853	3.2.1.-	NA
2	0.060	1mhsA	0.532	3.94	0.065	0.822	3.6.3.6	NA
3	0.060	2uu7A	0.498	4.06	0.049	0.767	6.3.1.2	NA
4	0.060	1hbmA	0.487	4.01	0.058	0.736	2.8.4.1	NA
5	0.060	2debA	0.498	4.34	0.082	0.814	2.3.1.21	NA
6	0.060	1f1hL	0.506	4.18	0.073	0.783	6.3.1.2	67,70
7	0.060	3fkyC	0.507	4.09	0.076	0.783	6.3.1.2	NA
8	0.060	2fknB	0.495	3.90	0.088	0.775	4.2.1.49	37
9	0.060	3g4dA	0.515	4.51	0.081	0.845	4.2.3.13	NA
10	0.060	1cqxB	0.537	3.95	0.040	0.798	1.14.12.17	NA
11	0.060	1eulA	0.464	4.32	0.076	0.767	3.6.3.8	NA
12	0.060	2r7oA	0.496	4.68	0.073	0.868	2.7.7.48	NA
13	0.060	1e6yA	0.498	4.75	0.089	0.853	2.8.4.1	NA
14	0.060	1n1hA	0.531	4.22	0.065	0.884	2.7.7.48	NA
15	0.060	1u6zB	0.505	3.94	0.073	0.791	3.6.1.11	NA
16	0.060	1dgjA	0.498	4.38	0.100	0.806	1.2.-.-	12
17	0.060	2df4A	0.484	4.25	0.073	0.798	6.3.5.-	102
18	0.060	1wchA	0.498	3.78	0.061	0.760	3.1.3.48	NA
19	0.060	1uwkA	0.497	3.90	0.088	0.775	4.2.1.49	91

(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	0.536	4.20	0.05	0.81	1cqxA	GO:0005344 GO:0005737 GO:0006810 GO:0008941 GO:0009636 GO:0015671 GO:0016491 GO:0019825 GO:0020037 GO:0046872 GO:0051409 GO:0055114 GO:0071949
1	0.07	0.537	4.05	0.05	0.76	3tm9A	GO:0005344 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
2	0.07	0.533	3.97	0.04	0.77	1gvhA	GO:0005344 GO:0005504 GO:0005737 GO:0006810 GO:0008941 GO:0009636 GO:0015671 GO:0016491 GO:0019825 GO:0020037 GO:0032843 GO:0046872 GO:0051409 GO:0055114 GO:0071949
3	0.07	0.520	4.22	0.06	0.81	4g1bA	GO:0000166 GO:0016491 GO:0019825 GO:0020037 GO:0046872 GO:0055114
4	0.07	0.594	3.75	0.08	0.86	3d9bA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
5	0.07	0.508	4.56	0.08	0.89	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
6	0.07	0.472	4.35	0.10	0.79	2dc3A	GO:0001666 GO:0004096 GO:0004601 GO:0005344 GO:0005506 GO:0005737 GO:0005829 GO:0006810 GO:0006979 GO:0008941 GO:0010764 GO:0015671 GO:0019395 GO:0019825 GO:0020037 GO:0032966 GO:0043005 GO:0043025 GO:0046872 GO:0047888 GO:0050999 GO:0098869 GO:2000490
7	0.07	0.410	4.82	0.07	0.72	3bcqA	GO:0005344 GO:0005506 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
8	0.07	0.416	4.72	0.05	0.71	1binA	GO:0005344 GO:0006810 GO:0009399 GO:0009877 GO:0015671 GO:0019825 GO:0020037 GO:0046872
9	0.07	0.460	4.94	0.06	0.84	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
10	0.07	0.473	4.35	0.08	0.78	2olpA	GO:0005344 GO:0005737 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
11	0.07	0.456	4.31	0.06	0.71	3qqqA	GO:0019825 GO:0020037 GO:0046872
12	0.07	0.491	4.05	0.05	0.74	1oj6B	GO:0005344 GO:0005737 GO:0005739 GO:0006810 GO:0006915 GO:0015671 GO:0019825 GO:0020037 GO:0043204 GO:0046872
13	0.07	0.418	4.40	0.02	0.69	1cg5B	GO:0005344 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
14	0.07	0.447	4.72	0.10	0.76	1hlmA	GO:0005344 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
15	0.07	0.482	4.37	0.03	0.74	3vreA	GO:0005344 GO:0005506 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
16	0.07	0.470	4.10	0.04	0.73	3zhwA	GO:0001666 GO:0005344 GO:0005618 GO:0005829 GO:0005886 GO:0009506 GO:0019825 GO:0020037 GO:0046872
17	0.07	0.529	3.70	0.04	0.74	2wy4A	GO:0005344 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
18	0.07	0.430	4.52	0.08	0.74	1hlbA	GO:0005344 GO:0005506 GO:0005576 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0046906	GO:0043169	GO:0022892
GO-Score	0.48	0.48	0.37
Biological Processes	GO:0015669	GO:0044710
GO-Score	0.37	0.37
Cellular Component	GO:0005737	GO:0005887
GO-Score	0.13	0.07

(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.