I-TASSER results

I-TASSER results for job id Rv3421c

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

Input Sequence in FASTA format

>protein (211 residues)
MSRVQISTVLAIDTATPAVTAGIVRRHDLVVLGERVTVDARAHAERLTPNVLAALADAAL
TMADLDAVVVGCGPGPFTGLRAGMASAAAYGHALGIPVYGVCSLDAIGGQTIGDTLVVTD
ARRREVYWARYCDGIRTVGPAVNAAADVDPGPALAVAGAPEHAALFALPCVEPSRPSPAG
LVAAVNWADKPAPLVPLYLRRPDAKPLAVCT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSRVQISTVLAIDTATPAVTAGIVRRHDLVVLGERVTVDARAHAERLTPNVLAALADAALTMADLDAVVVGCGPGPFTGLRAGMASAAAYGHALGIPVYGVCSLDAIGGQTIGDTLVVTDARRREVYWARYCDGIRTVGPAVNAAADVDPGPALAVAGAPEHAALFALPCVEPSRPSPAGLVAAVNWADKPAPLVPLYLRRPDAKPLAVCT
Prediction	CCCCCCCEEEEEHCCCCCEEEEEEHCCCEEEEEEEEEHCCHHHHHHHHHHHHHHHHHHCCCHHHCCEEEEHCCCCCCHHHHHHHHHHHHHHHHHCCCEEHCCHHHHHHHHCCCCEEEEHCCCCCCEEEEEEHCCCCCCCHHHHCHHHCCCCCEEEHCCCHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHCCCCCCCCCCCCC
Conf.Score	9988764467765699746899998996999999998566589999999999999998999888888999779987589999999999999997998998585999987558887999758999679999866975445455456666788879985756667765776666667798999999888999655788655745576666689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSRVQISTVLAIDTATPAVTAGIVRRHDLVVLGERVTVDARAHAERLTPNVLAALADAALTMADLDAVVVGCGPGPFTGLRAGMASAAAYGHALGIPVYGVCSLDAIGGQTIGDTLVVTDARRREVYWARYCDGIRTVGPAVNAAADVDPGPALAVAGAPEHAALFALPCVEPSRPSPAGLVAAVNWADKPAPLVPLYLRRPDAKPLAVCT
Prediction	8653611200001001530000003455120102223424440033024003300651714262010000021112100100000000000313712011000010103413430000010334100000034444313421330450464210000214423621526414322220020022344644123033162345414332438
	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                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCEEEEEHCCCCCEEEEEEHCCCEEEEEEEEEHCCHHHHHHHHHHHHHHHHHHCCCHHHCCEEEEHCCCCCCHHHHHHHHHHHHHHHHHCCCEEHCCHHHHHHHHCCCCEEEEHCCCCCCEEEEEEHCCCCCCCHHHHCHHHCCCCCEEEHCCCHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHCCCCCCCCCCCCC
MSRVQISTVLAIDTATPAVTAGIVRRHDLVVLGERVTVDARAHAERLTPNVLAALADAALTMADLDAVVVGCGPGPFTGLRAGMASAAAYGHALGIPVYGVCSLDAIGGQTIGDTLVVTDARRREVYWARYCDGIRTVGPAVNAAADVDPGPALAVAGAPEHAALFALPCVEPSRPSPAGLVAAVNWADKPAPLVPLYLRRPDAKPLAVCT

5br9A

0.28

0.26

0.91

2.78

MUSTER

----HMSTLLALDTSTEACSVALLHEG---RALSHYEVIPRLHAQRLLPMVRDLLDEAGVALSAVDAIAFGRGPGAFTGVRIAIGVVQGLAFALQRPVLAVSDLAILAQRAAERVAAAIDARMDEVYWGCYQLQQGEMREAVLPPERVAADWFGAGTGWGYVERMPQRPVDASLLPHAEDLLSLAGEGVEAEQALPVYLR-----------

5br9A

0.28

0.26

0.91

4.12

dPPAS

----HMSTLLALDTSTEACSVALLHEG---RALSHYEVIPRLHAQRLLPMVRDLLDEAGVALSAVDAIAFGRGPGAFTGVRIAIGVVQGLAFALQRPVLAVSDLAILAQRAAERVAAAIDARMDEVYWGCYQLQQGEMSEAVLPPERVAADWFGAGTGWGYVERMPQRPVAASLLPHAEDLLSLAGEGVEAEQALPVYLR-----------

5br9A

0.28

0.26

0.91

4.60

wdPPAS

----HMSTLLALDTSTEACSVALLHEG---RALSHYEVIPRLHAQRLLPMVRDLLDEAGVALSAVDAIAFGRGPGAFTGVRIAIGVVQGLAFALQRPVLAVSDLAILAQRAAERVAAAIDARMDEVYWGCYQLQQGEMREAVLPPERVAADWFGAGTGWGYVERMPQRPVAASLLPHAEDLLSLAGEGVEAEQALPVYLR-----------

5br9A

0.29

0.26

0.91

3.60

wMUSTER

M-----STLLALDTSTEACSVALLHEG---RALSHYEVIPRLHAQRLLPMVRDLLDEAGVALSAVDAIAFGRGPGAFTGVRIAIGVVQGLAFALQRPVLAVSDLAILAQRAAERVAAAIDARMDEVYWGCYQLQQGEMREAVLPPERVAADWFGAGTGWGYVERMPQRPVDASLLPHAEDLLSLAGEGVEAEQALPVYLR-----------

5br9A

0.28

0.26

0.91

4.79

wPPAS

----HMSTLLALDTSTEACSVALLHEG--RALSHYEVI-PRLHAQRLLPMVRDLLDEAGVALSAVDAIAFGRGPGAFTGVRIAIGVVQGLAFALQRPVLAVSDLAILAQRAAERVAAAIDARMDEVYWGCYQLQQGEMREAVLPPERVAADWFGAGTGWGYVERMPQRPVAASLLPHAEDLLSLAGEGVEAEQALPVYLR-----------

3r6mA

0.30

0.26

0.87

9.15

dPPAS2

------AKILAIDTATENCSVALLVNDQ---VISRSEVAPRDHTKKVLPMVDEVLKEAGLTLQDLDALAFGRGPGSFTGVRIGIGIAQGLAFGAELPMIGVSTLAAMAQASATDVAVAIDARMSEVYWARYSRQENGEARLAEEAQADSKTWTTAGTGWSAYQEELAGLPFEVLYPDSQDIVILAKNTVPVEE------------------

5br9A

0.28

0.26

0.91

3.94

PPAS

----HMSTLLALDTSTEACSVALLHEG---RALSHYEVIPRLHAQRLLPMVRDLLDEAGVALSAVDAIAFGRGPGAFTGVRIAIGVVQGLAFALQRPVLAVSDLAILAQRAAERVAAAIDARMDEVYWGCYQLQQGEMSEAVLPPERVAADWFGAGTGWGYVERMPQRPVAASLLPHAEDLLSLAGEGVEAEQALPVYLR-----------

5br9A

0.28

0.26

0.91

4.59

Env-PPAS

----HMSTLLALDTSTEACSVALLHEG---RALSHYEVIPRLHAQRLLPMVRDLLDEAGVALSAVDAIAFGRGPGAFTGVRIAIGVVQGLAFALQRPVLAVSDLAILAQRAAERVAAAIDARMDEVYWGCYQLQQGEMSEAVLPPERVAADWFGAGTGWGYVERMPQRPVAASLLPHAEDLLSLAGEGVEAEQALPVYLR-----------

1okjB

0.24

0.22

0.92

2.67

MUSTER

--KKAGLRILAIDTATEACSVALWNDG---TVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAATRVLAAIDARMGEVYWAEYQRDENGIWIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLEVLLPAAEDMLPIACKTVAVEHAEPVYL------------

3r6mA

0.30

0.26

0.87

4.11

dPPAS

------AKILAIDTATENCSVALLVNDQ---VISRSEVAPRDHTKKVLPMVDEVLKEAGLTLQDLDALAFGRGPGSFTGVRIGIGIAQGLAFGAELPMIGVSTLAAMAQASATDVAVAIDARMSEVYWARYSRQENGEARLAEEAQADSKTWTTAGTGWSAYQEELAGLPFEVLYPDSQDIVILAKNTVPVEE------------------

(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=0.85

Estimated TM-score = 0.83±0.08

Estimated RMSD = 3.7±2.6Å

Download Model 2

C-score=-0.77

Download Model 3

C-score=0.88

Download Model 4

C-score=-3.32

Download Model 5

C-score=-1.47

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	5br9A	0.865	1.51	0.275	0.915
2	1okjB	0.839	1.98	0.226	0.924
3	3r6mA	0.812	1.69	0.303	0.877
4	2a6aA	0.702	2.61	0.276	0.825
5	3zetB	0.681	3.45	0.188	0.863
6	3enoA	0.678	3.56	0.146	0.863
7	3en9A	0.674	3.67	0.157	0.872
8	2ivoA	0.674	3.35	0.191	0.839
9	4k25A	0.660	3.64	0.167	0.848
10	5e84A	0.641	4.09	0.110	0.881

(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	0.07	2	4yduD	ADP	Rep, Mult	41,42,43,44,76,78,82,122
2	0.06	2	2vypA	RH9	Rep, Mult	99,109,110,111,112,113,139,140,183,184
3	0.06	2	1yt3A	ZN	Rep, Mult	13,64
4	0.06	2	2ivoA	WO4	Rep, Mult	77,78,81
5	0.06	2	3eksA	CY9	Rep, Mult	99,101,102,105,109,139,140,184
6	0.03	1	3mr2A	MG	Rep, Mult	13,120,125
7	0.03	1	2iocB	MN	Rep, Mult	13,120
8	0.03	1	3i9dL	MG	Rep, Mult	120,122
9	0.03	1	3m6gA	LO3	Rep, Mult	13,14,80,83,84,87,88
10	0.03	1	3gocA	MG	Rep, Mult	13,203
11	0.03	1	1m1bA	MG	Rep, Mult	120,200

	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	0.066	2ivpA	0.669	3.50	0.181	0.844	3.4.24.57	15,74
2	0.066	3enoA	0.678	3.56	0.146	0.863	3.4.24.57	74
3	0.060	1hkgA	0.554	4.90	0.107	0.848	2.7.1.1	NA
4	0.060	3jvpD	0.543	4.64	0.082	0.787	2.7.1.16	89
5	0.060	3b8aX	0.561	4.86	0.106	0.858	2.7.1.1	NA
6	0.060	2hoeA	0.568	4.66	0.108	0.844	2.7.1.59	NA
7	0.060	3flcX	0.574	4.38	0.092	0.796	2.7.1.30	54
8	0.060	2w41B	0.541	4.30	0.072	0.763	2.7.1.30	NA
9	0.060	2uytA	0.539	4.73	0.065	0.820	2.7.1.5	110
10	0.060	2q2rA	0.539	5.09	0.116	0.844	2.7.1.2	NA
11	0.060	3f9mA	0.550	4.63	0.081	0.825	2.7.1.2	NA
12	0.060	1qhaA	0.562	4.70	0.063	0.834	2.7.1.1	NA
13	0.060	3hz6A	0.548	4.39	0.103	0.791	2.7.1.17	79,82
14	0.060	1woqA	0.554	4.68	0.188	0.825	2.7.1.63	NA
15	0.060	1zc6B	0.563	4.58	0.079	0.834	2.7.1.59	13
16	0.060	1q18A	0.545	4.56	0.095	0.820	2.7.1.2	NA
17	0.060	3mdqA	0.549	4.48	0.094	0.806	3.6.1.11	NA
18	0.060	3htvA	0.564	4.33	0.104	0.810	2.7.1.55	NA
19	0.060	2d4wA	0.554	4.26	0.128	0.772	2.7.1.30	16,174
20	0.060	3gbtA	0.535	4.26	0.037	0.754	2.7.1.12	71
21	0.060	2i7pB	0.536	4.31	0.096	0.782	2.7.1.33	78

(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	0.50	0.837	2.02	0.23	0.91	3zeuA	GO:0002949
1	0.47	0.860	1.87	0.27	0.92	5br9C	GO:0000408 GO:0002949
2	0.47	0.812	1.69	0.30	0.88	3r6mA	GO:0002949 GO:0005737 GO:0008033
3	0.46	0.843	2.01	0.22	0.92	4yduC	GO:0000408 GO:0002949 GO:0005737 GO:0005829 GO:0006508 GO:0008033 GO:0008237 GO:0042802
4	0.32	0.710	2.60	0.27	0.83	2a6aA	GO:0000408 GO:0002949 GO:0005737 GO:0008033
5	0.13	0.678	3.56	0.15	0.86	3enoA	GO:0000166 GO:0002949 GO:0003824 GO:0004222 GO:0004674 GO:0004712 GO:0005506 GO:0005524 GO:0005737 GO:0006468 GO:0006508 GO:0008033 GO:0008152 GO:0008270 GO:0016301 GO:0016310 GO:0016740 GO:0016746 GO:0016747 GO:0046872 GO:0061711
6	0.11	0.682	3.35	0.18	0.86	4yduB	GO:0000287 GO:0000408 GO:0001948 GO:0002949 GO:0004222 GO:0005506 GO:0005737 GO:0005829 GO:0006508 GO:0008033 GO:0016740 GO:0016746 GO:0016747 GO:0042802 GO:0046872 GO:0061711
7	0.10	0.671	3.43	0.18	0.84	2ivnA	GO:0000049 GO:0000408 GO:0002949 GO:0003727 GO:0005737 GO:0008033 GO:0016740 GO:0016746 GO:0046872 GO:0061711
8	0.10	0.674	3.67	0.16	0.87	3en9A	GO:0000166 GO:0000408 GO:0002949 GO:0003824 GO:0004222 GO:0004672 GO:0004674 GO:0004712 GO:0005506 GO:0005524 GO:0005737 GO:0006468 GO:0006508 GO:0008033 GO:0008152 GO:0008270 GO:0016301 GO:0016310 GO:0016740 GO:0016746 GO:0016747 GO:0046872 GO:0061711
9	0.07	0.592	4.05	0.15	0.78	3venA	GO:0000166 GO:0003824 GO:0005506 GO:0005524 GO:0009058 GO:0016743 GO:0016787 GO:0016874 GO:0017000 GO:0046872 GO:1901121 GO:1901133
10	0.07	0.673	3.63	0.16	0.86	4k25A	GO:0002949 GO:0004222 GO:0005739 GO:0006508 GO:0008033 GO:0016740 GO:0016746 GO:0016747 GO:0046872 GO:0061711 GO:0072670
11	0.06	0.397	5.23	0.10	0.61	5dwzE	GO:0003824 GO:0008152 GO:0044550
12	0.06	0.376	5.22	0.07	0.62	1f05A	GO:0003824 GO:0004801 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0005999 GO:0006002 GO:0006098 GO:0009052 GO:0016740 GO:0019682 GO:0030246 GO:0043231 GO:0048029 GO:0070062
13	0.06	0.358	5.54	0.05	0.60	4e21B	GO:0004616 GO:0006098 GO:0016491 GO:0055114
14	0.06	0.284	5.47	0.05	0.49	5abbA	GO:0005622 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
15	0.06	0.306	5.52	0.04	0.53	4clqA	GO:0000447 GO:0000472 GO:0000480 GO:0003723 GO:0003824 GO:0003963 GO:0004521 GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0006396 GO:0008047 GO:0030686 GO:0031167 GO:0042254 GO:0043085
16	0.06	0.326	4.05	0.03	0.44	2du2A	GO:0000166 GO:0003824 GO:0010181 GO:0016491 GO:0046872 GO:0055114
17	0.06	0.286	6.39	0.05	0.55	2yvkA	GO:0005737 GO:0008652 GO:0009086 GO:0016853 GO:0019284 GO:0019509 GO:0044237 GO:0044249 GO:0046523
18	0.06	0.251	5.75	0.06	0.45	4qi1A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
19	0.06	0.301	4.83	0.10	0.47	3umbA	GO:0008152 GO:0016787 GO:0019120

Consensus prediction of GO terms

Molecular Function	GO:0042802	GO:0008237
GO-Score	0.46	0.46
Biological Processes	GO:0002949	GO:0006508
GO-Score	0.95	0.46
Cellular Component	GO:0000408	GO:0005829
GO-Score	0.81	0.46

(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.