I-TASSER results

I-TASSER results for job id Rv0310c

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

Input Sequence in FASTA format

>protein (163 residues)
MCCNGVVTPGDPADIAAIKQLKYRYLRALDTKHWDDFTDTLAEDVTGDYGSSVGTELHFT
NRADLVDYLRQALGPGVITEHRVTHPEITVTGDTATGIWYLQDRVIVAEFNFMLIGAAFY
HDQYRRTTDGWRISATGYDRTYEATMSLAGLNFNIRPGRALAD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MCCNGVVTPGDPADIAAIKQLKYRYLRALDTKHWDDFTDTLAEDVTGDYGSSVGTELHFTNRADLVDYLRQALGPGVITEHRVTHPEITVTGDTATGIWYLQDRVIVAEFNFMLIGAAFYHDQYRRTTDGWRISATGYDRTYEATMSLAGLNFNIRPGRALAD
Prediction	CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCEEEEHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEHCCEEEEEHCCEEEEEEEEEEEEEHCCCCEEEEEEEEEEEEEEEHCCEEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCC
Conf.Score	9875678989999999999999999999867999999885569789997888888766689999999999985878755887565699997998999999999999689985899999999999997998999999999999866788888888888777789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MCCNGVVTPGDPADIAAIKQLKYRYLRALDTKHWDDFTDTLAEDVTGDYGSSVGTELHFTNRADLVDYLRQALGPGVITEHRVTHPEITVTGDTATGIWYLQDRVIVAEFNFMLIGAAFYHDQYRRTTDGWRISATGYDRTYEATMSLAGLNFNIRPGRALAD
Prediction	6456433426304024204500320031034431530240103302011333434434142142024103521552331212113330304363030101231212336443201010102132223775234341423322344331662516243243368
	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

CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCEEEEHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEHCCEEEEEHCCEEEEEEEEEEEEEHCCCCEEEEEEEEEEEEEEEHCCEEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCC
MCCNGVVTPGDPADIAAIKQLKYRYLRALDTKHWDDFTDTLAEDVTGDYGSSVGTELHFTNRADLVDYLRQALGPGVITEHRVTHPEITVTGDTATGIWYLQDRVIVAEFNFMLIGAAFYHDQYRRTTDGWRISATGYDRTYEATMSLAGLNFNIRPGRALAD

2chcA

0.20

0.18

0.91

2.19

MUSTER

--GAMGPVDEQWIEILRIQALCARYCLTINTQDGEGWAGCFTEDGAFEFDG-----WVIRGRPALREYADAHA-RVVRGRHLTTDLLYEVDGDVATGRSASVVTLATAAG-YKILGSGEYQDRLIKQDGQWRIAYRRLRNDRLVSDP------SVAVNVADAD

4l8oA

0.33

0.31

0.94

5.12

dPPAS

RLEALEKEIQKMKDIEEIKKLKGQYFRCLDGKFWDELETTLSPNIVT-------SYLVFHGPKEVTDYFKKAMPREEISMHMGHTPEITIDSETATGRWYLEDKLIFTEESSGVNGGAFYTDKYEKVDGKWYILETGYLRVYEEHFMRDP-KIKITMNMHKT-

4l8oA

0.34

0.33

0.94

5.28

wdPPAS

MSEALEKEIQKMKDIEEIKKLKGQYFRCLDGKFWDELETTLSPNIVTSY-------LVFHGPKEVTDYFKKAMPREEISMHMGHTPEITIDSETATGRWYLEDKLIFTEESSGVNGGAFYTDKYEKVDGKWYILETGYLRVYEEHFMRDP-KIKITMNMHKT-

4l8oA

0.33

0.31

0.94

4.07

wMUSTER

ILEALEKEIQKMKDIEEIKKLKGQYFRCLDGKFWDELETTLSPNIVTSYLV-------FHGPKEVTDYFKKAMPREEISMHMGHTPEITIDSETATGRWYLEDKLIFTEEGSGVNGGAFYTDKYEKVDGKWYILETGYLRVYEEHFMR-DPKIKITMNMHKT-

4l8oA

0.34

0.33

0.94

5.11

wPPAS

MSEALEKEIQKMKDIEEIKKLKGQYFRCLDGKFWDELETTLSPNIVTSY-------LVFHGPKEVTDYFKKAMPREEISMHMGHTPEITIDSETATGRWYLEDKLIFTEEGSGVNGGAFYTDKYEKVDGKWYILETGYLRVYEEHFM-RDPKIKITMNMHKT-

4l8oA

0.34

0.32

0.94

8.11

dPPAS2

MSEALEKEIQKMKDIEEIKKLKGQYFRCLDGKFWDELETTLSPNIVTSYLV-------FHGPKEVTDYFKKAMPREEISMHMGHTPEITIDSETATGRWYLEDKLIFTEESSGVNGGAFYTDKYEKVDGKWYILETGYLRVYEEHFMRDP-KIKITMNMHKT-

4l8oA

0.34

0.32

0.94

4.60

PPAS

MSEALEKEIQKMKDIEEIKKLKGQYFRCLDGKFWDELETTLSPNIVTSYL-------VFHGPKEVTDYFKKAMPREEISMHMGHTPEITIDSETATGRWYLEDKLIFTEEGSGVNGGAFYTDKYEKVDGKWYILETGYLRVYEEHFM-RDPKIKITMNMHKT-

4l8oA

0.34

0.32

0.94

3.74

Env-PPAS

MSEALEKEIQKMKDIEEIKKLKGQYFRCLDGKFWDELETTLSPNIVTSYL-------VFHGPKEVTDYFKKAMPREEISMHMGHTPEITIDSETATGRWYLEDKLIFTEESSGVNGGAFYTDKYEKVDGKWYILETGYLRVYEEHFMR-DPKIKITMNMHKT-

3a76A

0.20

0.18

0.89

2.17

MUSTER

-----MSDLDRLASRAAIQDLYSDKLIAVDKRQEGRLASIWWDDAEWTIEGI----GTYKGPEGALDLANNVWPMFHECIHYGTNLRLEFSADKVNGIGDVLLLGNLVEGNQSILIAAVFTDEYERRDGVWKFSKRNACTNYFT--PLAGIHFAPP-------

3a76A

0.17

0.15

0.89

4.97

dPPAS

-----MSDLDRLASRAAIQDLYSDKLIAVDKRQEGRLASIWWDDAEWTIEGI----GTYKGPEGALDLANNVWPMFHECIHYGTNLRLEFSADKVNGIGDVLLLGNLVEGNQSILIAAVFTDEYERRDGVWKFSKRNACTNYFTPLAGIHFAPP---------

(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=1.13

Estimated TM-score = 0.87±0.07

Estimated RMSD = 2.7±2.0Å

Download Model 2

C-score=-2.28

Download Model 3

C-score=-4.67

Download Model 4

C-score=-2.15

Download Model 5

C-score=-1.60

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	4l8oA	0.879	1.45	0.331	0.945
2	3a76A	0.791	2.01	0.200	0.890
3	6stdA	0.755	2.38	0.144	0.853
4	4gb5A	0.754	2.07	0.257	0.841
5	2rfrA	0.728	2.41	0.189	0.841
6	2chcA	0.727	2.78	0.175	0.859
7	3ef8A	0.714	1.77	0.163	0.791
8	3robA	0.711	1.63	0.220	0.779
9	3soyA	0.709	1.81	0.118	0.785
10	3b8lA	0.706	2.16	0.210	0.797

(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	0.45	108	4stdA	BFS	Rep, Mult	29,49,72,73,101,103,105,116,118,120,136,138,140
2	0.02	4	2a15A	NCA	Rep, Mult	25,37,49,79,103,120,122,136
3	0.01	3	4j8tA	DOG	Rep, Mult	26,29,37,49,53,68,69,73,118,136,138,140
4	0.01	3	2z77C	HE7	Rep, Mult	25,26,29,49,53,68,72,73,77,79,81,103,107,122,136,140,143
5	0.01	2	3cnxB	MG	Rep, Mult	30,81
6	0.01	4	3hx8D	IMD	Rep, Mult	22,25,83,97,120,122,133
7	0.01	3	3junB	AJD	Rep, Mult	33,37,65,68,69,72,79,81,137
8	0.01	2	3vgnA	FNN	Rep, Mult	25,49,101,120,136,138
9	0.00	1	2z77C	HE7	Rep, Mult	73,107,108,112
10	0.00	1	4fcmB	III	Rep, Mult	17,20,21,24,39,40,41,127,130,131,132
11	0.00	1	2z77B	HE7	Rep, Mult	53,72,77,79,103,105,107,114,146
12	0.00	1	3hx8A	IMD	Rep, Mult	19,22,83
13	0.00	1	2bngB	CA	Rep, Mult	14,126

	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	0.303	8choA	0.663	2.00	0.107	0.749	5.3.3.1	24,28,42,46
2	0.279	1e3vB	0.661	2.37	0.127	0.767	5.3.3.1	25,48
3	0.184	2ux0A	0.654	2.94	0.112	0.822	2.7.11.17	38,46
4	0.134	1o7hB	0.663	2.86	0.114	0.816	1.14.12.12	79
5	0.126	4stdA	0.761	2.31	0.144	0.853	4.2.1.94	23
6	0.060	3e99A	0.635	3.08	0.146	0.797	1.14.12.10	23,27
7	0.060	1cdgA	0.420	4.59	0.034	0.669	2.4.1.19	103
8	0.060	1buqA	0.626	2.47	0.106	0.755	5.3.3.1	25,122
9	0.060	3kvnX	0.437	4.67	0.053	0.687	3.1.1.1	69
10	0.060	1yiqA	0.488	4.56	0.045	0.773	1.1.99.-	NA
11	0.060	1qgxA	0.454	4.78	0.053	0.749	3.1.3.7	19,83
12	0.060	1cgtA	0.418	4.55	0.041	0.669	2.4.1.19	30,79,121,122
13	0.060	2e1qA	0.436	5.28	0.051	0.761	1.17.3.2,1.17.1.4	NA
14	0.060	2x4mA	0.455	4.61	0.038	0.724	3.4.23.48	86,96
15	0.060	1hkxA	0.651	3.15	0.110	0.828	2.7.11.17	28,88
16	0.060	3gzxB	0.655	3.04	0.140	0.816	1.14.12.18	23,30
17	0.060	2d0vA	0.532	4.42	0.065	0.804	1.1.99.8	NA
18	0.060	9cgtA	0.409	4.75	0.041	0.681	2.4.1.19	13
19	0.060	2v7oA	0.331	5.53	0.047	0.607	2.7.11.17	39,61
20	0.060	3b9jC	0.350	5.56	0.042	0.675	1.17.3.2,1.17.1.4	NA
21	0.060	3elqB	0.441	4.51	0.051	0.663	2.8.2.22	NA
22	0.060	2bngC	0.680	2.22	0.121	0.785	3.3.2.8	138
23	0.060	3en1B	0.654	3.31	0.146	0.828	1.14.12.3,1.14.12.11	20,23,41
24	0.060	1d7fA	0.419	4.53	0.034	0.663	2.4.1.19	24,121,122

(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	0.55	0.906	1.30	0.34	0.96	4lehA	GO:0016829 GO:0033988
1	0.44	0.880	1.62	0.34	0.96	4l8pA	GO:0016829 GO:0033988
2	0.39	0.879	1.45	0.33	0.94	4l8oA	GO:0016829 GO:0033988
3	0.31	0.794	2.08	0.20	0.90	3a76B	GO:0009636 GO:0016829 GO:0042597
4	0.25	0.633	3.04	0.10	0.79	1z1sA	GO:0017000
5	0.22	0.761	2.31	0.14	0.85	4stdA	GO:0006582 GO:0016829 GO:0030411 GO:0042438 GO:0043581
6	0.19	0.672	2.30	0.13	0.78	3t8nB	GO:0004769 GO:0006629 GO:0008202 GO:0016853
7	0.18	0.630	2.62	0.12	0.76	4cdlA	GO:0004769 GO:0006629 GO:0008202 GO:0016853
8	0.16	0.660	2.67	0.12	0.80	5cxoB	GO:0016787
9	0.06	0.337	5.12	0.04	0.58	3alnA	GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004702 GO:0004713 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006468 GO:0006915 GO:0007165 GO:0007254 GO:0009611 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0035897 GO:0038095 GO:0071260 GO:2000672
10	0.06	0.302	5.27	0.02	0.54	2refA	GO:0003824 GO:0008080 GO:0008152 GO:0016740 GO:0031177
11	0.06	0.310	5.56	0.03	0.56	5d80B	GO:0000166 GO:0000221 GO:0000329 GO:0003677 GO:0004518 GO:0004519 GO:0005524 GO:0005773 GO:0005774 GO:0006314 GO:0006810 GO:0006811 GO:0007035 GO:0012505 GO:0015991 GO:0015992 GO:0016020 GO:0016539 GO:0016787 GO:0016820 GO:0030908 GO:0033178 GO:0044267 GO:0046034 GO:0046961 GO:0090305
12	0.06	0.271	5.36	0.06	0.48	3n2nA	GO:0004872 GO:0004888 GO:0005518 GO:0005886 GO:0007165 GO:0009986 GO:0010008 GO:0016020 GO:0016021 GO:0022414 GO:0031258 GO:0031527 GO:0031532 GO:0034446 GO:0042995 GO:0046872 GO:0051015 GO:0070062
13	0.06	0.285	5.14	0.01	0.50	2r2iA	GO:0001750 GO:0005509 GO:0005886 GO:0007601 GO:0007602 GO:0008048 GO:0030249 GO:0031282 GO:0031284 GO:0046872 GO:0050896 GO:0071277
14	0.06	0.297	5.72	0.03	0.53	3f0hA
15	0.06	0.276	5.28	0.04	0.48	1bs4A	GO:0005506 GO:0005829 GO:0006412 GO:0008198 GO:0008270 GO:0016787 GO:0031365 GO:0042586 GO:0043022 GO:0043686 GO:0046872
16	0.06	0.288	5.59	0.02	0.53	1xx6A	GO:0000166 GO:0004797 GO:0005524 GO:0005737 GO:0006259 GO:0008270 GO:0009157 GO:0016301 GO:0016310 GO:0016740 GO:0046872 GO:0071897
17	0.06	0.263	5.96	0.06	0.52	2gieA	GO:0003677 GO:0004518 GO:0004519 GO:0009036 GO:0009307 GO:0016787 GO:0090305
18	0.06	0.291	4.18	0.01	0.45	1nh2D	GO:0001129 GO:0001132 GO:0003713 GO:0005634 GO:0005672 GO:0005737 GO:0006351 GO:0006355 GO:0006367 GO:0017025 GO:0045944 GO:0051091 GO:0051123

Consensus prediction of GO terms

Molecular Function	GO:0033988
GO-Score	0.85
Biological Processes	GO:0044249	GO:0016999	GO:0009636
GO-Score	0.50	0.50	0.31
Cellular Component	GO:0042597
GO-Score	0.31

(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.