I-TASSER results

I-TASSER results for job id Rv0801

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

Input Sequence in FASTA format

>protein (115 residues)
MALKVEMVTFDCSDPAKLAGWWAEQFDGTTRELLPGEFVVVARTDGPRLGFQKVPDPAPG
KNRVHLDFTTKDLDAEVLRLVAAGASEVGRHQVGESFRWVVLADPEGNAFCVAGQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MALKVEMVTFDCSDPAKLAGWWAEQFDGTTRELLPGEFVVVARTDGPRLGFQKVPDPAPGKNRVHLDFTTKDLDAEVLRLVAAGASEVGRHQVGESFRWVVLADPEGNAFCVAGQ
Prediction	CCEEEEEEEEHCCCHHHHHHHHHHHHCCCCCCCCCCCEEEEHCCCCEEEEEEHCCCCCCCCCEEEEEEHCCCHHHHHHHHHHHCCEEEEEHCCCCCCCEEEEHCCCCCEEEHCCC
Conf.Score	9858979998689999999999999799557889996899858997589999689999999858998767999999999999899576655579998689996899985665699
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MALKVEMVTFDCSDPAKLAGWWAEQFDGTTRELLPGEFVVVARTDGPRLGFQKVPDPAPGKNRVHLDFTTKDLDAEVLRLVAAGASEVGRHQVGESFRWVVLADPEGNAFCVAGQ
Prediction	7523133114533404421642152351424464442101133552120001314544434220000021652641153037132432444465752301000323513301358
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEEEEEHCCCHHHHHHHHHHHHCCCCCCCCCCCEEEEHCCCCEEEEEEHCCCCCCCCCEEEEEEHCCCHHHHHHHHHHHCCEEEEEHCCCCCCCEEEEHCCCCCEEEHCCC
MALKVEMVTFDCSDPAKLAGWWAEQFDGTTRELLPGEFVVVARTDGPRLGFQKVPDPAPGKNRVHLDFTTKDLDAEVLRLVAAGASEVGRHQVGESFRWVVLADPEGNAFCVAGQ

4lqbA

0.30

0.28

0.93

2.79

MUSTER

HRSRVSTVLIDVPQASRSAQFWAGALGVRADSPPEPQYVTLHALPGLVTAVQALEE---GEARYHLDIETDDVDAEVERLVGLGAVEESSWQ-----GCRTLRVPGGQLVCVIPL

4lqbA

0.29

0.27

0.93

3.81

dPPAS

HRSRVSTVLIDVEQASRSAQFWAGALGVRADSPPGEPVTLHGALPGLVTAVQALEE---GEARYHLDIETDDVDAEVERLVGLGAVEESSWQ-----GCRTLRVPGGQLVCVIPL

4lqbA

0.29

0.28

0.95

3.47

wdPPAS

HRSRVSTVLIDVEQASRSAQFWAGALGVRADSPPGEPQYVTLHGALPGL-VTAVQALEEGEARYHLDIETDDVDAEVERLVGLGAVEESSW-----QGCRTLRVPGGQLVCVIPL

4lqbA

0.30

0.28

0.93

3.20

wMUSTER

HRSRVSTVLIDVPQASRSAQFWAGALGVRADSPPGEQYVTLHALPGLVTAVQALEE---GEARYHLDIETDDVDAEVERLVGLGAVEESSWQ-----GCRTLRVPGGQLVCVIPL

4lqbA

0.30

0.29

0.95

3.68

wPPAS

HRSRVSTVLIDVEQASRSAQFWAGALGVRADSPPGEPQYVTLHGALPGL-VTAVQALEEGEARYHLDIETDDVDAEVERLVGLGAVEESSWQ-----GCRTLRVPGGQLVCVIPL

4lqbA

0.29

0.27

0.93

6.85

dPPAS2

HRSRVSTVLIDVEQASRSAQFWAGALGVRADSPPGEPVTLHGALPGLVTAVQALEE---GEARYHLDIETDDVDAEVERLVGLGAVEESSWQ-----GCRTLRVPGGQLVCVIPL

4lqbA

0.29

0.27

0.93

3.63

PPAS

HRSRVSTVLIDVEQASRSAQFWAGALGVRADSPPGEPVTLHGALPGLVTAVQALEE---GEARYHLDIETDDVDAEVERLVGLGAVEESSWQ-----GCRTLRVPGGQLVCVIPL

4lqbA

0.29

0.27

0.93

3.65

Env-PPAS

HRSRVSTVLIDVEQASRSAQFWAGALGVRADSPPGEPVTLHGALPGLVTAVQALEE---GEARYHLDIETDDVDAEVERLVGLGAVEESSWQ-----GCRTLRVPGGQLVCVIPL

4hc5A

0.19

0.99

2.24

MUSTER

LIAYVHSATIIVSDQEKALDFYVNTLGFEKVQLDPNRFVTVVPPGATQVALGLYEDGRKPGGYTGISLITRDIDEAYKTLTERGVTFTKP-PEPWGQRATWFSDPDGNQFFLVEE

4n04A

0.16

0.15

0.95

2.69

dPPAS

--SLNLFAGVAVGDFGAALAWYRSLLGAEPTFYPHETEAVWQLEEGRLLYIVERPEHAGH----AQTLIVEDLDAVLSGASERGVEAAKQETYANGVRKVTYLDPDGSEIAFGEV

(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=0.41

Estimated TM-score = 0.77±0.10

Estimated RMSD = 3.4±2.4Å

Download Model 2

C-score=-0.29

Download Model 3

C-score=-2.43

Download Model 4

C-score=-2.80

Download Model 5

C-score=-0.21

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	4hc5A	0.727	2.64	0.149	0.939
2	4huzA	0.726	2.70	0.114	0.991
3	3ghjA	0.723	2.60	0.144	0.939
4	1zswA	0.720	3.13	0.168	0.983
5	2zw6A	0.719	3.19	0.211	0.974
6	2kjzA	0.719	2.68	0.134	0.930
7	1bylA	0.718	2.83	0.144	0.930
8	1mh6A	0.715	2.65	0.148	0.922
9	4ro6A	0.714	3.17	0.104	1.000
10	1jifA	0.712	2.90	0.144	0.930

(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	0.36	23	1lqpA	FCN	Rep, Mult	65,67,109,111
2	0.05	4	2zhpB	BY6	Rep, Mult	38,50,52,53,54
3	0.05	4	2zhpB	BY6	Rep, Mult	61,62,63,64,66,88,101,103,107,109,111
4	0.04	3	1lqpA	FCN	Rep, Mult	65,89,93,101,111
5	0.04	3	2p7qD	GG6	Rep, Mult	7,9,49,51
6	0.02	2	1byl0	III	Rep, Mult	8,9,28,37,43,44,45,46,50,52,62,64,66,67,69,70,71,72,75,76,115
7	0.01	1	1ecs0	III	Rep, Mult	9,37,40,45,49,50,52,54,63,64,65,66,67,68,69,70,71,111,115

	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	0.179	1lqoB	0.670	2.99	0.136	0.913	2.5.1.18	68,105,107
2	0.100	1fa7B	0.656	3.16	0.071	0.930	4.4.1.5	105,107
3	0.086	1lqkA	0.673	2.95	0.136	0.913	2.5.1.18	NA
4	0.060	1f9zA	0.642	3.28	0.071	0.948	4.4.1.5	NA
5	0.060	1kmyA	0.636	3.30	0.080	0.939	1.13.11.39	NA
6	0.060	1q78A	0.458	4.11	0.045	0.748	2.7.7.19	22
7	0.060	1ydwB	0.459	4.25	0.066	0.783	1.-.-.-	82
8	0.060	1ei5A	0.456	4.70	0.039	0.800	3.4.11.19	NA
9	0.060	2jkbA	0.463	4.22	0.088	0.713	3.2.1.18,4.2.2.15	NA
10	0.060	3fkyC	0.457	4.68	0.067	0.809	6.3.1.2	63
11	0.060	2p25A	0.673	2.97	0.107	0.930	4.4.1.5	NA
12	0.060	1npbA	0.662	2.98	0.164	0.904	2.5.1.18	9,29,68,105
13	0.060	1fx2A	0.470	3.88	0.065	0.739	4.6.1.1	NA
14	0.060	1qipB	0.658	3.08	0.117	0.904	4.4.1.5	NA
15	0.060	1f1uA	0.665	3.16	0.115	0.922	1.13.11.15	NA
16	0.060	2c21A	0.649	3.43	0.099	0.930	4.1.1.-	NA
17	0.060	2cjbB	0.465	4.25	0.067	0.765	6.1.1.11	NA
18	0.060	2uu7A	0.461	4.74	0.086	0.826	6.3.1.2	NA
19	0.060	1jmsA	0.474	4.06	0.020	0.765	2.7.7.31	NA
20	0.060	1eilA	0.641	3.11	0.062	0.930	1.13.11.39	NA
21	0.060	2glxE	0.471	4.30	0.037	0.783	1.1.1.263	NA
22	0.060	1sqiA	0.655	3.31	0.114	0.957	1.13.11.27	84

(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	0.31	0.687	2.94	0.16	0.94	3l7tA	GO:0004462 GO:0046872
1	0.31	0.737	2.44	0.17	0.94	4hc5D	GO:0051213 GO:0055114
2	0.27	0.673	2.95	0.14	0.91	1lqkA	GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
3	0.27	0.682	3.14	0.13	0.96	2rk0A	GO:0051213 GO:0055114
4	0.26	0.722	2.79	0.17	0.95	4g6xA	GO:0051213 GO:0055114
5	0.24	0.691	2.77	0.16	0.91	4n04A	GO:0051213 GO:0055114
6	0.24	0.677	3.01	0.13	0.93	3hnqA	GO:0009405
7	0.23	0.716	2.82	0.18	0.93	5cj3A	GO:0008144 GO:0046677
8	0.22	0.662	2.98	0.16	0.90	1npbA	GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
9	0.21	0.675	3.06	0.13	0.93	4mymA	GO:0051213 GO:0055114
10	0.20	0.661	3.33	0.15	0.95	3kolA	GO:0004462 GO:0046872 GO:0051213 GO:0055114
11	0.20	0.712	2.87	0.14	0.93	1jieA	GO:0008144 GO:0046677
12	0.19	0.648	3.24	0.12	0.93	4jh1A	GO:0000287 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
13	0.18	0.677	3.20	0.13	0.96	2r5vA	GO:0003868 GO:0005506 GO:0009072 GO:0016491 GO:0016701 GO:0017000 GO:0033072 GO:0046872 GO:0050585 GO:0055114
14	0.18	0.673	2.97	0.11	0.93	2p25A
15	0.17	0.622	3.00	0.12	0.86	4nazA	GO:0000287 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
16	0.17	0.680	2.85	0.11	0.92	3ey7A	GO:0003824 GO:0051213 GO:0055114
17	0.16	0.718	2.83	0.14	0.93	1bylA	GO:0008144 GO:0046677
18	0.16	0.644	3.29	0.14	0.93	4jd1B	GO:0000287 GO:0004364 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
19	0.14	0.657	3.24	0.15	0.92	4kykA	GO:0004462 GO:0005975 GO:0006357 GO:0006749 GO:0008270 GO:0009438 GO:0016829 GO:0019243 GO:0030316 GO:0043066 GO:0046872 GO:0070062
20	0.12	0.657	3.29	0.11	0.96	1sqiB	GO:0000139 GO:0003868 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0006559 GO:0006572 GO:0009072 GO:0016020 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
21	0.10	0.720	3.13	0.17	0.98	1zswA	GO:0046872
22	0.10	0.636	3.30	0.08	0.94	1kmyA	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
23	0.10	0.726	2.70	0.11	0.99	4huzA	GO:0016491 GO:0046872 GO:0051213 GO:0055114
24	0.09	0.709	3.01	0.10	0.98	3oajA	GO:0005737 GO:0009636 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0051213	GO:0016765	GO:0046872	GO:0004462
GO-Score	0.62	0.54	0.50	0.31
Biological Processes	GO:0055114	GO:0042221
GO-Score	0.62	0.54
Cellular Component	GO:0044424
GO-Score	0.54

(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.