I-TASSER results

I-TASSER results for job id Rv3572

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

Input Sequence in FASTA format

>protein (176 residues)
MTRLIPGCTLVGLMLTLLPAPTSAAGSNTATTLFPVDEVTQLETHTFLDCHPNGSCDFVA
GANLRTPDGPTGFPPGLWARQTTEIRSTNRLAYLDAHATSQFERVMKAGGSDVITTVYFG
EGPPDKYQTTGVIDSTNWSTGQPMTDVNVIVCTHMQVVYPGVNLTSPSTCAQANFS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTRLIPGCTLVGLMLTLLPAPTSAAGSNTATTLFPVDEVTQLETHTFLDCHPNGSCDFVAGANLRTPDGPTGFPPGLWARQTTEIRSTNRLAYLDAHATSQFERVMKAGGSDVITTVYFGEGPPDKYQTTGVIDSTNWSTGQPMTDVNVIVCTHMQVVYPGVNLTSPSTCAQANFS
Prediction	CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEEHCCCCCEEEEEEEEHCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCEEEEEEHCCCCCCEEEEHCCCCCCHHHCCCCCCEEEEEEHCCCCCEEEEEHCEEEEEEHCCCCCCCCCCEEEEEEEEEEHCCEEHCCCCCCCCCCCC
Conf.Score	98644457899999997688876555567875676789976899999875689857888888864899987799987655667886488445465554788743434788858999997899965799975787665568998889978998678999687565786655445679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTRLIPGCTLVGLMLTLLPAPTSAAGSNTATTLFPVDEVTQLETHTFLDCHPNGSCDFVAGANLRTPDGPTGFPPGLWARQTTEIRSTNRLAYLDAHATSQFERVMKAGGSDVITTVYFGEGPPDKYQTTGVIDSTNWSTGQPMTDVNVIVCTHMQVVYPGVNLTSPSTCAQANFS
Prediction	64431432322101221133343434453432313165443131202130346340313121413447224212563134433413445331112032745244136534533010012252325414251434324144342446130000020203142241332631444628
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEEHCCCCCEEEEEEEEHCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCEEEEEEHCCCCCCEEEEHCCCCCCHHHCCCCCCEEEEEEHCCCCCEEEEEHCEEEEEEHCCCCCCCCCCEEEEEEEEEEHCCEEHCCCCCCCCCCCC
MTRLIPGCTLVGLMLTLLPAPTSAAGSNTATTLFPVDEVTQLETHTFLDCHPNGSCDFVAGANLRTPDGPTGFPPGLWARQTTEIRSTNRLAYLDAHATSQFERVMKAGGSDVITTVYFGEGPPDKYQTTGVIDSTNWSTGQPMTDVNVIVCTHMQVVYPGVNLTSPSTCAQANFS

4m00A

0.14

0.99

0.69

MUSTER

IDNQQSALTAKGYNYTSVDSSYASTYNDTNKTVKMTNAGQSVTYYFTDVKAPTVTVGNQTIEVGKTMNPIVLTTTD-NGTGTVTNTVTGLPSGLSYDATNSIIGTPTKIGQSTVTVVSTQANNKSTTTFTINVVDTTAPTVTPIGDQSSEVISPIKIATQDVTNTVTGLPSGLTFD

5aozA

0.12

0.10

0.78

0.75

dPPAS

--------------------PVANADVVFDFQNYTAKAGDEVTVDVLVD-SKNKPISADVKFKVDSPLTIEEIDKESLAFNTTVTNAILGANFKSLDDKGE-PLVPKDGAAVFTLYVNVPANTPDGTYYVGFNGKNEVHKSNDGSQFTVASKNGAITVGT----------------

4mboA2

0.21

0.16

0.79

0.60

wdPPAS

------------------NSPSTNVKTNVRSRIMKLDDERQTETYITQI-NPEGKEMYFASGNLYTIIGSDGSPVNLLNAEVKILKTNSKNL------TDSMDQNYDSPEFEDVTSQY--------YTNDGSKITIDWKTNSISSTTSYVVLVKI----SGVLYSTVSDINQTYGS

4mboA2

0.18

0.15

0.84

0.72

wMUSTER

----------------NSPSVTEHTNVKTRSRIMKLDDERQTETYITQINPEGKEMYFASGLNLYTIIGSDGSPVNLLNAEVKILKTNSKNL------TDSMDQNYDSPEFEDVTSQY-------SYTNDGSKITIDWKTNSISSTTSYVVLVKIGVLYSTVSDINQTYGSKYSYG

4mboA2

0.21

0.17

0.80

0.64

wPPAS

------------------NSPSTNVKTNVRSRIMKLDDERQTETYITQI-NPEGKEMYFASGNLYTIIGSDGSPVNLLNAEVKILKTNSKNL------TDSMDQNYDSPEFEDVTSQY-------SYTNDGSKITIDWKTNSISSTTSYVVLVKIQ---SGVLYSTVSDINQTYYS

4ut1A2

0.21

0.13

0.64

0.94

dPPAS2

--------------------LAAGVATNSGTGVIS---QGSVSAGYQL---PSGTTTLAYNA---ASKTLSGFPVG----TTVTIAGTPPTSINITSATTP---VPYDPSKGASMTISSTTQPA----PSGVMNGVSVSSGTPADGDQFTIG------------------------

4mboA2

0.18

0.15

0.84

0.76

PPAS

----------------NSPSVTEHTNVKTNSRIMKLDDERQTETYITQINPEGKEMYFASGGNLYTIIGSDGSPVNLLNAEVKILKTNSKNL------TDSMDQNYDSPEFEDVTSQY-------SYTNDGSKITIDWKTNSISSTTSYVVLVKIGVLYSTVSDINQTYGSKYSYG

1m5hA1

0.13

0.10

0.79

0.69

Env-PPAS

IKRVL--ITGYDYYWAWV---AANEATGFGTSVIMCPAEAGIEIKAKPSETPDGRP--GYYIQICHMSK-KGLEEQLLARQCV-LTAPTTAVFNGLPDAEEKDDTGFKLK-------FFADGYQKEVEVGG---RKCWAV--PMMEGDFIIENDIGYTNG----------------

4lgnA

0.14

0.96

0.69

MUSTER

TWSQMTNFPDVGTYIANPTDTTGYQSDIQGVVWVAFDKSSQASKTIFVGVADPNNPVFWSRDGGATWQAVPGAPTG-FIPHKGVFDPVNHVLYIATSNTGGPY----DGSSGDVWKFSVTSGTWTRISPVPSTDTANDYFGDRQHPNTIMVATQISWWPDTIIFRSTDGGA--TWT

4c2lA1

0.14

0.12

0.91

0.70

dPPAS

AGGDSSTDDVPAITEAL------SSCGNGGTIVFP--EGSTYYLNSVLDLGSCSDCDIQVEGLLKFASDTDYWSGRTANVDGLKLRSLTGSGVIDGNGQDAWDLFASDSSYSRPTLLYITG--GSNLEISGLRQKN------PPNVFNSVKGGATNVVFSNLKMDANSKSDNPPKN

(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=-3.39

Estimated TM-score = 0.34±0.11

Estimated RMSD = 13.0±4.2Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-3.93

Download Model 4

C-score=-5.00

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	4mboA	0.652	3.32	0.107	0.835
2	4mbrA	0.611	3.60	0.075	0.818
3	3aswA	0.594	4.05	0.047	0.841
4	5cf3A	0.586	4.05	0.096	0.830
5	1n67A	0.584	4.17	0.095	0.824
6	4b5zA	0.582	4.07	0.048	0.835
7	1r17A	0.580	4.05	0.075	0.835
8	4jdzB	0.572	4.13	0.068	0.824
9	3irpX	0.553	3.87	0.072	0.773
10	3txaA2	0.552	3.61	0.075	0.744

(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	0.10	5	2y58A	V38	Rep, Mult	37,44,85,150,152
2	0.08	4	2a7aA	CA	Rep, Mult	116,118,125
3	0.04	2	1gqgA	UUU	Rep, Mult	162,163
4	0.04	2	3q2wA	MAN	Rep, Mult	33,43
5	0.04	2	2fynC	SMA	Rep, Mult	152,154
6	0.04	2	3d48R	CO3	Rep, Mult	83,84,85,150,152
7	0.02	1	3oqqA	CA	Rep, Mult	84,112,115
8	0.02	1	1agmA	MAN	Rep, Mult	166,167
9	0.02	1	1aczA	GLC	Rep, Mult	78,138
10	0.02	1	5fy1A	0R0	Rep, Mult	42,154
11	0.02	1	1j2qH	CIB	Rep, Mult	49,151
12	0.02	1	4f24A	MG	Rep, Mult	37,38,40,41,157
13	0.02	1	1ohtA	ZN	Rep, Mult	45,154,170
14	0.02	1	3mflB	DHY	Rep, Mult	74,93
15	0.02	1	1vtzi	CA	Rep, Mult	140,141

	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	2agsA	0.426	5.02	0.046	0.722	3.2.1.18	NA
2	0.060	3ovwA	0.441	5.18	0.052	0.784	3.2.1.4	NA
3	0.060	1lfwA	0.414	5.70	0.044	0.773	3.4.13.3	NA
4	0.060	2frvD	0.447	5.09	0.052	0.767	1.12.2.1	NA
5	0.060	1g87B	0.442	3.65	0.023	0.614	3.2.1.4	NA
6	0.060	1ui7A	0.414	4.72	0.087	0.665	1.4.3.21	136
7	0.060	1a39A	0.438	5.42	0.056	0.818	3.2.1.4	NA
8	0.060	1pz2A	0.421	4.28	0.083	0.636	3.2.1.55	NA
9	0.060	1av4A	0.416	4.82	0.062	0.682	1.4.3.21,1.4.3.6	NA
10	0.060	2a1xA	0.418	4.47	0.090	0.653	1.14.11.18	NA
11	0.060	1mdwA	0.265	5.97	0.054	0.494	3.4.22.53	NA
12	0.060	1nlrA	0.451	4.90	0.059	0.750	3.2.1.4	43
13	0.060	1sdwA	0.461	4.51	0.029	0.733	4.3.2.5,1.14.17.3	NA
14	0.060	1olrA	0.424	4.96	0.037	0.722	3.2.1.4	43
15	0.060	2zxqA	0.419	4.82	0.046	0.705	3.2.1.97	33,112
16	0.060	1s0kA	0.420	5.04	0.062	0.710	3.2.1.18	NA
17	0.060	2nqaB	0.269	5.26	0.054	0.472	3.4.22.53,3.4.22.52	138
18	0.060	1ddtA	0.461	4.24	0.046	0.688	2.4.2.36	NA
19	0.060	1sg3A	0.431	4.52	0.070	0.693	3.5.3.4	NA

(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	0.09	0.652	3.32	0.11	0.84	4mboA	GO:0005576 GO:0005618 GO:0007155 GO:0009986 GO:0030260 GO:1990254
1	0.08	0.536	3.11	0.10	0.67	4rmbB	GO:0005576 GO:0005618 GO:0007155 GO:0009986 GO:0030260 GO:1990254
2	0.07	0.611	3.60	0.07	0.82	4mbrA	GO:0005576 GO:0005618 GO:0007155
3	0.07	0.584	4.17	0.10	0.82	1n67A	GO:0005576 GO:0005618 GO:0007155 GO:0009405 GO:0016020
4	0.07	0.581	4.05	0.08	0.84	2ralA	GO:0005576 GO:0005618 GO:0007155 GO:0009405 GO:0016020 GO:0046872
5	0.07	0.580	4.05	0.07	0.84	1r17A	GO:0005576 GO:0005618 GO:0007155 GO:0009405 GO:0016020 GO:0046872
6	0.07	0.598	3.88	0.05	0.84	3au0A	GO:0005576 GO:0005618 GO:0007155 GO:0009405 GO:0016020
7	0.07	0.582	4.07	0.05	0.84	4b5zA	GO:0005576 GO:0005618 GO:0007155 GO:0009405 GO:0016020
8	0.07	0.572	4.13	0.07	0.82	4jdzB	GO:0005576 GO:0005618 GO:0007155 GO:0016020 GO:0016021
9	0.06	0.553	3.87	0.07	0.77	3irpX	GO:0005576 GO:0005618 GO:0007155 GO:0009405 GO:0016020
10	0.06	0.308	5.84	0.05	0.59	3c0kA	GO:0003723 GO:0005737 GO:0005829 GO:0006364 GO:0008168 GO:0008649 GO:0009383 GO:0016434 GO:0016740 GO:0031167 GO:0032259 GO:0044010 GO:0070475
11	0.06	0.441	3.76	0.06	0.62	2xbtA	GO:0000272 GO:0005975 GO:0030246 GO:0030248
12	0.06	0.329	5.94	0.07	0.64	4ljyA	GO:0000166 GO:0000348 GO:0003676 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0006397 GO:0008186 GO:0008380 GO:0010468 GO:0010501 GO:0016787
13	0.06	0.582	4.10	0.10	0.83	5cfaB	GO:0005576 GO:0005618 GO:0007155 GO:0009405 GO:0016020
14	0.06	0.309	4.08	0.04	0.44	2fqpC	GO:0046872
15	0.06	0.304	5.54	0.03	0.56	3hyiA	GO:0003677 GO:0004519 GO:0006351 GO:0006355 GO:0043937 GO:0090305
16	0.06	0.286	5.83	0.05	0.53	4o0lA	GO:0000166 GO:0016491 GO:0055114
17	0.06	0.300	6.02	0.06	0.56	3s6tA	GO:0004553 GO:0004563 GO:0005975 GO:0008152 GO:0016787 GO:0016798
18	0.06	0.282	5.62	0.04	0.52	4chcA	GO:0001172 GO:0003723 GO:0003968 GO:0006351

Consensus prediction of GO terms

Molecular Function	GO:0019215
GO-Score	0.33
Biological Processes	GO:0051806	GO:0044409	GO:0007155
GO-Score	0.33	0.33	0.32
Cellular Component	GO:0005618	GO:0005576
GO-Score	0.32	0.32

(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.