I-TASSER results

I-TASSER results for job id Rv2774c

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

Input Sequence in FASTA format

>protein (134 residues)
MGTAVEVGWRDPCGLAVGELRCAPAVSDQPVVGCAGCPLVDMVDFAPVTGCVAVGSTMGA
VPALLRVRFPWPPFEPDVRLSPYLALHGICRWGGSDSCDRTTVQVFHLHSINKRLTAHAG
FGAAAVVGLEDGPV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGTAVEVGWRDPCGLAVGELRCAPAVSDQPVVGCAGCPLVDMVDFAPVTGCVAVGSTMGAVPALLRVRFPWPPFEPDVRLSPYLALHGICRWGGSDSCDRTTVQVFHLHSINKRLTAHAGFGAAAVVGLEDGPV
Prediction	CCCEEEEHCCCCCCCEEEEEEHCCCCCCCCCEHCCCCCCCCCCCCCCCCCEEEHCCCCCCCCEEEEEHCCCCCCCCCCCCCHHHHHHHCHHCCCCCCCCCCEEEEEEEEHHHHHHHHHCCCCCEEEEHCCCCCC
Conf.Score	98568876568865455556546777889865556888654445565555466545555544467765799999988655544455433335898888764788887643455666545776456775677899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGTAVEVGWRDPCGLAVGELRCAPAVSDQPVVGCAGCPLVDMVDFAPVTGCVAVGSTMGAVPALLRVRFPWPPFEPDVRLSPYLALHGICRWGGSDSCDRTTVQVFHLHSINKRLTAHAGFGAAAVVGLEDGPV
Prediction	74342533143312212341412422574311102413223224234131022234334213011314142442436241332120201042235641442203113134145413331322111112156458
	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

CCCEEEEHCCCCCCCEEEEEEHCCCCCCCCCEHCCCCCCCCCCCCCCCCCEEEHCCCCCCCCEEEEEHCCCCCCCCCCCCCHHHHHHHCHHCCCCCCCCCCEEEEEEEEHHHHHHHHHCCCCCEEEEHCCCCCC
MGTAVEVGWRDPCGLAVGELRCAPAVSDQPVVGCAGCPLVDMVDFAPVTGCVAVGSTMGAVPALLRVRFPWPPFEPDVRLSPYLALHGICRWGGSDSCDRTTVQVFHLHSINKRLTAHAGFGAAAVVGLEDGPV

3u0oA1

0.22

0.19

0.87

0.59

MUSTER

LHSEQA-KFVDP-GNETRD--AADLGNGTSVISTTDFPIVNPFDFGRIAATNAISFAMGGKPAIAILGWP-----IN-KL-SPEIAREVTE-GGRYACRQAGIALAGGHSIAPEPIF-----GLAVTGIPTERV

4cp6A4

0.12

0.10

0.80

0.60

dPPAS

----------FYGNLELKELILPDNVKNFGKHVMNGLPKLKSLTIGNNINSLPSFFLSGVLDSLKEIHIKNKSTEFSVKKDTF------------AIPETVKFYVTSEHIKDVLKSNLSTSNDIIVEKV-----

4q0cA3

0.23

0.15

0.66

0.56

wdPPAS

---------------------------DHPVVMPIGARHVPASNLAGQRLAVDINYLP---KETLARAY------PQATLSSEQALAAVAY-GQAD------VFIGDALTTSHLVSQS-YFNDVRVVA--PAHI

3u0oA1

0.24

0.21

0.86

0.60

wMUSTER

LHSEQA-KFVDP-GNETRD--AADLGNGTSVISTTDF-FMPIVD-NPFDGAATNASAMGGKPAIAILGWP-----IN-KL-SPEIAREVTE-GGRYACRQAGIALAGGHSIAPEPI----FG-LAVTGIPTERV

2ysmA

0.20

0.13

0.63

0.52

wPPAS

-GSS---GSSANCAV------CD---PGDLQFFCTTC---GQ--YHGM--CL--DIAVTPLK-----RAGW--QCPECKV--------NCKQSGEDTCDK----GYHTFCLQPVMKSTNGWPSSG---------

4q0cA3

0.23

0.15

0.66

0.68

dPPAS2

---------------------------DHPVVMPIGARHVPASNLAGQRLAVDINYLP---KETLARAY------PQATLSSEQALAAVAY-GQAD------VFIGDALTTSHLVSQS-YFNDVRVVA--PAHI

3tjqA

0.28

0.20

0.72

0.57

PPAS

-------GCPDRCEPA----RCPPQ----P----EHCEGGRARD---ACGCCEV----GAPEAACGLQEG-EGLQCVVPFAGL----CVCASSGSD--ANTYANLCQLRAASRRSERL---HRPPVIVLQRGA-

3ontA

0.34

0.22

0.66

0.68

Env-PPAS

----------------------------YP----KNC-LLTVDRYSAVVRNEQV---V--IPSLLRV--QLPSVQDGAPLYTYFTLKSIVDHGISEELD--LEAQFHLHHILTHLTRK----AQEVTRQETGQV

3cbnA

0.25

0.21

0.85

0.57

MUSTER

LGVLRYTLRRHPNVTATFEVTVDPEIGD--IIGV--SSSDSISTLPDEKRAIARESL---VRVILRTENGY--DEPELTLD-----HPVCR--KSDICSRTLIRA----DLDENLVRDLRKGRELKVEIEYEGH

4q0cA3

0.23

0.15

0.66

0.60

dPPAS

---------------------------DHPVVMPIGARHVPASNLAGQRLAVDINYLP---KETLARAY------PQATLSSEQALAAVAY-GQAD------VFIGDALTTSHLVSQS-YFNDVRVVA--PAHI

(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=-4.36

Estimated TM-score = 0.26±0.08

Estimated RMSD = 14.9±3.6Å

Download Model 2

C-score=-4.48

Download Model 3

C-score=-4.46

Download Model 4

C-score=-4.87

Download Model 5

C-score=-4.91

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	1sbpA	0.504	3.93	0.074	0.784
2	3ix1A	0.502	4.05	0.109	0.784
3	1pc3A	0.501	4.40	0.120	0.806
4	2q89A	0.496	4.33	0.099	0.813
5	4x6gA	0.493	4.26	0.074	0.791
6	2q2aA	0.493	3.78	0.068	0.754
7	5dtbA	0.493	4.44	0.066	0.784
8	3tmgA	0.492	4.41	0.025	0.798
9	4io2A	0.491	4.25	0.059	0.784
10	4q0cA	0.487	3.71	0.085	0.702

(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	0.09	5	3pm6B	IOD	Rep, Mult	110,111,114
2	0.04	2	2a69P	MG	Rep, Mult	114,118
3	0.04	2	3fxuA	TSU	Rep, Mult	27,28,133
4	0.04	2	3fxuB	TSU	Rep, Mult	51,88,89
5	0.04	2	4dwzE	ZN	Rep, Mult	109,113
6	0.04	2	3fxrA	SO4	Rep, Mult	45,50,51,105
7	0.02	1	3fxuA	TSU	Rep, Mult	20,21,55,58,59,63
8	0.02	1	1a0fA	GTS	Rep, Mult	112,116,117
9	0.02	1	4plrA	CA	Rep, Mult	119,120
10	0.02	1	3fxuA	TSU	Rep, Mult	29,30,106,108
11	0.02	1	3n6uA	TSU	Rep, Mult	20,51,52,53,62,63
12	0.02	1	2f7aB	CCU	Rep, Mult	52,56,86
13	0.02	1	1xnyA	BTN	Rep, Mult	36,48,49
14	0.02	1	1pegB	ZN	Rep, Mult	90,98
15	0.02	1	4sbvA	CA	Rep, Mult	41,44
16	0.02	1	3gdcA	CU	Rep, Mult	87,107
17	0.02	1	3kjhA	ZN	Rep, Mult	34,37
18	0.02	1	2xvjC	IND	Rep, Mult	9,110
19	0.02	1	2wse1	CLA	Rep, Mult	25,33

	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	3it3A	0.444	4.72	0.047	0.754	3.1.3.2	125
2	0.060	1qwoA	0.436	4.77	0.047	0.761	3.1.3.8	NA
3	0.060	2hhjA	0.436	4.88	0.103	0.769	3.1.3.13,5.4.2.1,5.4.2.4	NA
4	0.060	3i39X	0.429	5.18	0.066	0.821	1.2.99.2	51,89,111,126
5	0.060	2gfiA	0.436	4.78	0.031	0.761	3.1.3.8	NA
6	0.060	2de3B	0.436	4.74	0.056	0.754	3.13.1.3	88
7	0.060	3e9cA	0.432	4.84	0.063	0.746	3.1.3.46	107
8	0.060	3e9dA	0.441	4.88	0.060	0.761	3.1.3.46	107
9	0.060	1nd6B	0.443	4.75	0.039	0.761	3.1.3.2	NA
10	0.060	3gp5A	0.437	4.94	0.068	0.769	5.4.2.1	66
11	0.060	1h3dA	0.430	4.64	0.056	0.694	2.4.2.17	110,115
12	0.060	2be7A	0.437	4.82	0.041	0.754	2.1.3.2	NA
13	0.060	1ultA	0.433	4.72	0.080	0.746	6.2.1.3	NA
14	0.060	1qfxB	0.435	4.73	0.054	0.754	3.1.3.8	10
15	0.060	1u7nA	0.430	4.36	0.093	0.672	2.3.1.-	112
16	0.060	1ihpA	0.437	4.82	0.047	0.761	3.1.3.8	10
17	0.060	2jc9A	0.435	5.11	0.074	0.813	3.1.3.5	33
18	0.060	3kbrA	0.454	4.16	0.079	0.709	4.2.1.91,4.2.1.51	NA
19	0.060	1gq2A	0.382	4.88	0.056	0.687	1.1.1.40	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	0.07	0.502	4.05	0.11	0.78	3ix1A	GO:0005886 GO:0006810 GO:0009228 GO:0009229 GO:0016020
1	0.07	0.504	3.93	0.07	0.78	1sbpA	GO:0006810 GO:0008271 GO:0008272 GO:0015419 GO:0030288 GO:0042597 GO:1902358
2	0.07	0.474	4.68	0.07	0.80	4h67C	GO:0009228 GO:0009229
3	0.07	0.494	4.15	0.12	0.80	2q88A	GO:0005886 GO:0033294 GO:0051470 GO:0051471
4	0.07	0.494	4.44	0.04	0.79	3fasA	GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007268 GO:0008328 GO:0014069 GO:0016020 GO:0016021 GO:0030054 GO:0030425 GO:0032281 GO:0032983 GO:0034220 GO:0035235 GO:0042995 GO:0043025 GO:0043195 GO:0045202 GO:0045211 GO:0050803 GO:0050804 GO:0051968 GO:0060992
5	0.07	0.457	4.31	0.07	0.75	4h6dE	GO:0009228 GO:0009229
6	0.07	0.493	3.78	0.07	0.75	2q2aA	GO:0004970 GO:0016020 GO:0035235
7	0.07	0.476	4.41	0.04	0.75	4f1yA	GO:0001919 GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0008328 GO:0010226 GO:0014069 GO:0016020 GO:0016021 GO:0030054 GO:0030165 GO:0030425 GO:0032279 GO:0032281 GO:0034220 GO:0035235 GO:0043025 GO:0043083 GO:0043195 GO:0043197 GO:0043198 GO:0043204 GO:0043234 GO:0045202 GO:0045211 GO:0060992
8	0.07	0.478	4.53	0.07	0.78	1a40A	GO:0005886 GO:0006810 GO:0006817 GO:0006974 GO:0015415 GO:0016036 GO:0035435 GO:0042301 GO:0042597 GO:0043190
9	0.07	0.470	4.15	0.05	0.74	4f3pA	GO:0004970 GO:0016020 GO:0035235
10	0.07	0.486	4.07	0.06	0.78	4io7B	GO:0004930 GO:0004970 GO:0006810 GO:0006811 GO:0007186 GO:0016020 GO:0016021 GO:0035235
11	0.07	0.485	3.73	0.09	0.73	4ymxA	GO:0004970 GO:0005215 GO:0006810 GO:0016020 GO:0035235
12	0.07	0.468	4.10	0.06	0.75	1wdnA	GO:0004970 GO:0005215 GO:0006810 GO:0006865 GO:0016020 GO:0030288 GO:0035235 GO:0042597
13	0.07	0.461	3.78	0.07	0.69	3tqlA	GO:0003333 GO:0004970 GO:0006865 GO:0015424 GO:0016020 GO:0035235 GO:0042626 GO:0055085
14	0.07	0.466	4.06	0.09	0.75	4jb7A	GO:0008272 GO:0009405 GO:0015419 GO:1902358
15	0.07	0.468	4.45	0.05	0.78	2ylnA	GO:0005215 GO:0006810
16	0.07	0.450	4.43	0.09	0.75	3firA	GO:0008272 GO:0015419 GO:1902358
17	0.07	0.474	4.17	0.08	0.77	1hpbP	GO:0005215 GO:0006810 GO:0006865 GO:0030288 GO:0042597
18	0.07	0.456	4.26	0.07	0.70	4la9A	GO:0004970 GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0035235

Consensus prediction of GO terms

Molecular Function	GO:0015419	GO:0051471	GO:0008271	GO:0033294	GO:0004971	GO:0005234
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0051234
GO-Score	0.37
Cellular Component	GO:0071944
GO-Score	0.37

(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.