I-TASSER results

I-TASSER results for job id Rv0326

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

Input Sequence in FASTA format

>protein (151 residues)
MVATDFSDVAVAQLRRSAQARGVSARVQPIVHDLRQPLPVKTGSIDGAFAHMALCMALST
SEIHAVVAEVGRVLRPGGKFIYTVRHTGDAHYGAGQAHGDDIFECAGFAVHFFRRELVAR
LATGWVLEEVHDFEEGELPRRLWRVTVTKPA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MVATDFSDVAVAQLRRSAQARGVSARVQPIVHDLRQPLPVKTGSIDGAFAHMALCMALSTSEIHAVVAEVGRVLRPGGKFIYTVRHTGDAHYGAGQAHGDDIFECAGFAVHFFRRELVARLATGWVLEEVHDFEEGELPRRLWRVTVTKPA
Prediction	CEEEHCCHHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCCCCCEEEEEEHHHHHHCCCHHHHHHHHHHHHHHCCCCCEEEEEHCCCCCCCCCCCEEHCCCEEEHCCEEEHCCCHHHHHHHHHCCCEEEEEEEHCCCCCCEEEEEEEEHCC
Conf.Score	8999699999999999999989988859998588778999988645776444677568977899999999998589959999987888765667766546758987888865899999999978867999875457777668999998689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MVATDFSDVAVAQLRRSAQARGVSARVQPIVHDLRQPLPVKTGSIDGAFAHMALCMALSTSEIHAVVAEVGRVLRPGGKFIYTVRHTGDAHYGAGQAHGDDIFECAGFAVHFFRRELVARLATGWVLEEVHDFEEGELPRRLWRVTVTKPA
Prediction	4000111450053036306754256403211110355131463101000011001112427404400420220023402000003134234134245235411433322220144610540076142440451663721330021314358
	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

CEEEHCCHHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCCCCCEEEEEEHHHHHHCCCHHHHHHHHHHHHHHCCCCCEEEEEHCCCCCCCCCCCEEHCCCEEEHCCEEEHCCCHHHHHHHHHCCCEEEEEEEHCCCCCCEEEEEEEEHCC
MVATDFSDVAVAQLRRSAQARGVSARVQPIVHDLRQPLPVKTGSIDGAFAHMALCMALSTSEIHAVVAEVGRVLRPGGKFIYTVRHTGDAHYGAGQAHGDDIFECAGFAVHFFRRELVARLATGWVLEEVHDFEEGELPRRLWRVTVTKPA

2p8jA

0.17

0.96

1.91

MUSTER

TYGIEISDLQLKKAENFSRENNF--KLNISKGD-IRKLPFKDESSFVYSYGTIFHR---KNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQEKVIHSYVSLEEADKYFKDKVLFKEDRVVELKIKQGYVDYIAEKFS

2p8jA

0.17

0.16

0.96

2.73

dPPAS

TYGIEISDLQLKKAENFSRENNF--KLNISKGDI-RKLPFKDESSFVYSYGTI---FHRKNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQEKVIHSYVSLEEADKYFKDKVLFKEDRVVERINDGLKIKQGYVDYI

2p8jA

0.17

0.96

2.49

wdPPAS

TYGIEISDLQLKKAENFSRENNF--KLNISKGDI-RKLPFKDESSFVYSYGTIFHR---KNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQEKVIHSYVSLEEADKYFKDKVLFKEDRVVELKIKQGYVDYIAEKFS

2p8jA

0.17

0.96

2.32

wMUSTER

TYGIEISDLQLKKAENFSRENNF--KLNISKGD-IRKLPFKDESSFVYSYGTIFHR---KNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQEKVIHSYVSLEEADKYFKDKVLFKEDRVVELKIKQGYVDYIAEKFS

2p8jA

0.17

0.95

2.57

wPPAS

TYGIEISDLQLKKAENFSRENNF--KLNISKGDI-RKLPFKDESSFVYSYGTIFHR---KNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQEKVIHSYVSLEEADKYFKDKVLFKEDRVVE-KIKQGYVDYIAEKKS

2p8jA

0.17

0.96

3.65

dPPAS2

TYGIEISDLQLKKAENFSRENNF--KLNISKGDI-RKLPFKDESSFVYSYGTIFHR---KNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQEKVIHSYVSLEEADKYFKDKVLFKEDRVVELKIKQGYVDYIAEKFS

2p8jA

0.17

0.96

2.39

PPAS

TYGIEISDLQLKKAENFSRENNF--KLNISKGDI-RKLPFKDESSFVYSYGTIFHR---KNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQEKVIHSYVSLEEADKYFKDKVLFKEDRVVELKIKQGYVDYIAEKFS

2p8jA

0.17

0.96

2.40

Env-PPAS

TYGIEISDLQLKKAENFSRENNF--KLNISKGDI-RKLPFKDESSFVYSYGTIFHR---KNDVKEAIDEIKRVLKPGGLACINFLTTKDERYNKGEKIGEGEFLQEKVIHSYVSLEEADKYFKDKVLFKEDRVVELKIKQGYVDYIAEKFS

5cm2Z

0.16

0.15

0.93

1.72

MUSTER

IVGSDRSDELVKLAHDMD------PSREVVVCD-AIDNAHPEGRFDFAISIAVIHHFSTPERRREAVRAILNTLRPDGRALIYVWALEQDVMVPWVKKVDGVEEVRYRYYHLYREGEITSDVEASGGKVLETGYEKD----NWWVVAKRGD

5cm2Z

0.16

0.15

0.93

2.48

dPPAS

IVGSDRSDELVKLAHDMD------PSREVVVCDA-IDNAHPEGRFDFAISIAVIHHFSTPERRREAVRAILNTLRPDGRALIYVWALEQDQMVPWVKKVDGVEEVRYRYYHLYREGEITSDVEASGGKVLETGYEKD----NWWVVAKRGD

(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=0.71

Estimated TM-score = 0.81±0.09

Estimated RMSD = 3.4±2.3Å

Download Model 2

C-score=-1.45

Download Model 3

C-score=-2.32

Download Model 4

C-score=-4.02

Download Model 5

C-score=-4.59

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	2p8jA	0.915	1.13	0.172	0.960
2	3sm3A	0.846	2.31	0.154	0.974
3	1d2gA	0.782	2.70	0.115	0.947
4	3d2lC	0.779	2.38	0.127	0.914
5	3g5lA	0.778	2.40	0.128	0.927
6	4iv0A	0.777	2.27	0.094	0.901
7	1y8cA	0.776	2.41	0.119	0.914
8	4ineA2	0.775	2.36	0.167	0.907
9	5jdyA	0.774	2.70	0.160	0.954
10	5gm1A	0.773	2.56	0.199	0.927

(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	0.37	18	3lhdD	SAH	Rep, Mult	5,6,7,10,33,35,36,50,52,53,85,113
2	0.04	2	3zkrG	B4M	Rep, Mult	80,81,82,147
3	0.02	1	3wmnA	MQ8	Rep, Mult	70,74
4	0.02	1	1d2hC	SAH	Rep, Mult	5,6,7,10,32,33
5	0.02	1	4qjsU	MG	Rep, Mult	68,72
6	0.02	1	1yz30	III	Rep, Mult	86,115,116,119,130,131

	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	0.067	1wznA	0.757	2.44	0.116	0.887	2.1.1.-	NA
2	0.067	3eppB	0.765	3.10	0.173	0.993	2.1.1.56	30
3	0.067	3bgdA	0.710	2.68	0.083	0.881	2.1.1.67	57
4	0.066	2fcaA	0.640	2.85	0.113	0.821	2.1.1.33	NA
5	0.066	2iftA	0.616	2.36	0.107	0.742	2.1.1.52	69,75
6	0.066	3e05D	0.615	2.75	0.111	0.775	2.1.1.132	27
7	0.066	1pjzA	0.607	3.31	0.102	0.828	2.1.1.67	2,10
8	0.066	3ckkA	0.598	2.99	0.095	0.755	2.1.1.33	NA
9	0.066	1yzhB	0.619	3.03	0.124	0.788	2.1.1.33	NA
10	0.060	1ri5A	0.751	3.14	0.161	0.980	2.1.1.56	33
11	0.060	1xxlA	0.782	2.46	0.151	0.920	2.1.1.-	NA
12	0.060	1sqfA	0.664	2.78	0.098	0.815	2.1.1.-	31
13	0.060	2ex4A	0.725	2.40	0.128	0.881	2.1.1.-	NA
14	0.060	1l1eA	0.740	2.67	0.094	0.907	2.1.1.79	NA
15	0.060	3i58A	0.674	3.05	0.157	0.887	2.1.1.-	NA
16	0.060	1nt2A	0.645	2.81	0.082	0.781	2.1.1.-	NA
17	0.060	2h11B	0.713	2.59	0.083	0.874	2.1.1.67	NA
18	0.060	3dxxA	0.646	2.99	0.129	0.815	2.1.1.33	63
19	0.060	3g07A	0.649	2.93	0.140	0.815	2.1.1.-	NA
20	0.060	3ccfB	0.732	2.16	0.146	0.861	2.1.1.144	5,50
21	0.060	3hnrA	0.691	3.03	0.118	0.861	2.1.1.-	NA
22	0.060	1tw2B	0.691	3.18	0.186	0.927	2.1.1.-	54
23	0.060	2ip2A	0.657	2.89	0.138	0.861	2.1.1.-	NA
24	0.060	2opbB	0.747	2.72	0.152	0.914	2.1.1.28	5,38,50
25	0.060	2frxA	0.671	2.83	0.153	0.815	2.1.1.-	NA
26	0.060	1tpyA	0.746	2.46	0.108	0.901	2.1.1.79	NA
27	0.060	3lccA	0.700	2.60	0.128	0.881	2.1.1.-	NA
28	0.060	1ri1A	0.753	3.22	0.161	0.987	2.1.1.56	5

(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	0.41	0.929	0.97	0.16	0.97	2p8jB	GO:0008152 GO:0008168 GO:0016740 GO:0032259
1	0.25	0.787	2.32	0.11	0.92	1y8cA	GO:0008168 GO:0016740 GO:0032259
2	0.23	0.781	2.54	0.12	0.94	1bhjA	GO:0001887 GO:0005542 GO:0005634 GO:0005737 GO:0005829 GO:0006544 GO:0008168 GO:0008757 GO:0016594 GO:0016740 GO:0017174 GO:0032259 GO:0046498 GO:0046500 GO:0046655 GO:0051262 GO:0051289 GO:0098603 GO:1901052
3	0.23	0.742	1.75	0.17	0.83	5cm2Z	GO:0000049 GO:0002098 GO:0005634 GO:0005737 GO:0005829 GO:0008152 GO:0008168 GO:0008198 GO:0016300 GO:0016706 GO:0030488 GO:0032259 GO:0055114
4	0.22	0.785	2.43	0.17	0.92	1vl5A	GO:0008152 GO:0008168 GO:0016740 GO:0032259
5	0.17	0.846	2.31	0.15	0.97	3sm3A	GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872
6	0.17	0.783	2.32	0.15	0.91	2gluA	GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259
7	0.17	0.781	2.44	0.19	0.91	3busA	GO:0008152 GO:0008168 GO:0016740 GO:0032259
8	0.16	0.798	2.36	0.12	0.93	3d2lC	GO:0008168 GO:0016740 GO:0032259
9	0.16	0.771	2.34	0.20	0.90	4pneB	GO:0008152 GO:0008168 GO:0016740 GO:0032259
10	0.15	0.776	2.49	0.09	0.91	4iv8A	GO:0000234 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
11	0.15	0.769	2.39	0.20	0.91	1ve3B	GO:0046872 GO:0051536 GO:0051539
12	0.15	0.757	2.29	0.21	0.89	4htfB	GO:0008033 GO:0008168 GO:0016740 GO:0032259
13	0.15	0.775	2.36	0.17	0.91	4ineA	GO:0000773 GO:0005737 GO:0006656 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0080101
14	0.15	0.771	2.72	0.16	0.95	5je1A	GO:0008168 GO:0016740 GO:0032259
15	0.14	0.745	2.15	0.15	0.87	3ccfB	GO:0008152 GO:0008168 GO:0016740 GO:0030798 GO:0032259
16	0.14	0.774	2.39	0.11	0.90	3uj7A	GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
17	0.14	0.757	2.44	0.12	0.89	1wznA
18	0.14	0.727	2.27	0.08	0.85	4qdkA	GO:0005737 GO:0008168 GO:0008757 GO:0015979 GO:0015995 GO:0016740 GO:0032259 GO:0036068 GO:0046406
19	0.14	0.734	2.99	0.13	0.91	3kkzA	GO:0046872 GO:0051536 GO:0051539
20	0.08	0.704	2.52	0.19	0.85	2i6gB	GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046690
21	0.07	0.725	2.47	0.17	0.87	2xvaA	GO:0005737 GO:0005829 GO:0008168 GO:0008757 GO:0009636 GO:0016740 GO:0032259 GO:0046677 GO:0046690
22	0.07	0.736	2.78	0.12	0.90	3e7pA	GO:0046872 GO:0051536 GO:0051539
23	0.07	0.730	2.44	0.09	0.87	3m70A	GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046690

Consensus prediction of GO terms

Molecular Function	GO:0003723	GO:0008170	GO:0016597	GO:0051213	GO:0019842	GO:0008175	GO:0043177	GO:0005506	GO:0016705	GO:0072341	GO:0033218
GO-Score	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45
Biological Processes	GO:0051260	GO:0051262	GO:0043603	GO:0006760	GO:0001510	GO:0009069	GO:0002097	GO:0006767	GO:0006520	GO:0006790	GO:0046128
GO-Score	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45	0.45
Cellular Component	GO:0005829	GO:0005634
GO-Score	0.40	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.