I-TASSER results

I-TASSER results for job id Rv0762c

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

Input Sequence in FASTA format

>protein (181 residues)
MAGYPRDELEDVVHRWLQANRTAERRGDWTLLADFYTDDATYGWNVGPNEDVMCVGIDEI
RDIALGQEMDGLQGWRYPYQRVVIDEKQGEVVGFWKQVATDANGAEQEVYGIGGSWFRYA
GGGKWNWQRDFFDFGHVSALYLELIKAGKLSPGMQKRIERAVSGNKVPGYYPLGKTPVPL
W

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MAGYPRDELEDVVHRWLQANRTAERRGDWTLLADFYTDDATYGWNVGPNEDVMCVGIDEIRDIALGQEMDGLQGWRYPYQRVVIDEKQGEVVGFWKQVATDANGAEQEVYGIGGSWFRYAGGGKWNWQRDFFDFGHVSALYLELIKAGKLSPGMQKRIERAVSGNKVPGYYPLGKTPVPLW
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCEEEEHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEEHCCCCEEEEEEHCCCCCCCCCEEEEHCCEEEEEEHCCCCCEEEHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Conf.Score	9999999999999999999999999889588887656874566557887655457799999988754457789975566789996899879999966656999985677565556999878986787634457789999999999989999999999998668888887656787898899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MAGYPRDELEDVVHRWLQANRTAERRGDWTLLADFYTDDATYGWNVGPNEDVMCVGIDEIRDIALGQEMDGLQGWRYPYQRVVIDEKQGEVVGFWKQVATDANGAEQEVYGIGGSWFRYAGGGKWNWQRDFFDFGHVSALYLELIKAGKLSPGMQKRIERAVSGNKVPGYYPLGKTPVPLW
Prediction	8661436204500540351045016544143005200430310231234352233126202611234405427414122322113374130002034206446344241431110103123633033132212133014004302744513750352046317565222224247352646
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCEEEEHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEEHCCCCEEEEEEHCCCCCCCCCEEEEHCCEEEEEEHCCCCCEEEHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
MAGYPRDELEDVVHRWLQANRTAERRGDWTLLADFYTDDATYGWNVGPNEDVMCVGIDEIRDIALGQEMDGLQGWRYPYQRVVIDEKQGEVVGFWKQVATDANGAEQEVYGIGGSWFRYAGGGKWNWQRDFFDFGHVSALYLELIKAGKLSPGMQKRIERAVSGNKVPGYYPLGKTPVPLW

5aifA

0.15

0.10

0.69

1.34

MUSTER

MT----------PIETVTAFIAHWNSGDMEAMYDLCAEDVVWHNIPMEP----IAGKPAMRAAVEGF-MANVSQCDWQVHAIAANGA--TVLTERTDGFTFTNGRRATIR--VMGTFECDAERRIIAWRDYFDMLEFQREFAG--------------------------------------

5aifA

0.15

0.10

0.69

1.71

dPPAS

----------MTPIETVTAFIAHWNSGDMEAMYDLCAEDVVWHNIPMEPI----AGKPAMRAAVEGF-MANVSQCDWQVHAIAANG--ATVLTERTDGFTFTNGRRATIR--VMGTFECDAERRIIAWRDYFDMLEFQREFAG--------------------------------------

5aifA

0.15

0.10

0.68

1.93

wdPPAS

MT--PIETVTAFIAHWNS---------DMEAMYDLCAEDVVWHNIPMEPI----AGKPAMRAAVEGF-MANVSQCDWQVHAIAANGA--TVLTERTDGFTFTNGRRATIR--VMGTFECDAERRIIAWRDYFDMLEFQREFAG--------------------------------------

5aifA

0.16

0.10

0.67

1.55

wMUSTER

------------PIETVTAFIAHWNSGDMEAMYDLCAEDVVWHNIPMEP----IAGKPAMRAAVEGF-MANVSQCDWQVHAIAANGA--TVLTERTDGFTFTNGRRATIR--VMGTFECDAERRIIAWRDYFDMLEFQREFA-----G---------------------------------

5aifA

0.16

0.11

0.67

1.81

wPPAS

MT--PIETVTAFIAHWNS---------DMEAMYDLCAEDVVWHNIPMEPI----AGKPAMRAAVEGF-MANVSQCDWQVHAIAANGA--TVLTERTDGFTFTNGRRATIR--VMGTFECDAERRIIAWRDYFDMLEFQREF------G---------------------------------

5aifA

0.15

0.10

0.69

3.59

dPPAS2

MT--PIETVTAFIAHWNSG--------DMEAMYDLCAEDVVWHNIPMEPI----AGKPAMRAAVEGF-MANVSQCDWQVHAIAANG--ATVLTERTDGFTFTNGRRATIR--VMGTFECDAERRIIAWRDYFDMLEFQREFAG--------------------------------------

5aifA

0.16

0.11

0.67

1.59

PPAS

MT--PIETVTAFIAHWNS---------DMEAMYDLCAEDVVWHNIPMEPI----AGKPAMRAAVEGF-MANVSQCDWQVHAIAANGA--TVLTERTDGFTFTNGRRATIR--VMGTFECDAERRIIAWRDYFDMLEFQREF------G---------------------------------

5aifA

0.15

0.10

0.69

1.91

Env-PPAS

MT--PIETVTAFIAHWNSG--------DMEAMYDLCAEDVVWHNIPMEP----IAGKPAMRAAVEGF-MANVSQCDWQVHAIAANGA--TVLTERTDGFTFTNGRRATIR--VMGTFECDAERRIIAWRDYFDMLEFQREFAG--------------------------------------

5cxoA

0.16

0.11

0.70

1.22

MUSTER

MQ--DEQKRKEIVAEYFRKVNE-----DVDAIVEMFTENATIEDPVGKD---VREGRAAQREYFNSNV-TAEVTIEPGHLSAGQDGKSVAVALAAEMNILDPNRTRVKIN--AVDVFTLTPEGKIDSMRVFWGMTDIGVW-----------------------------------------

3hx8A

0.17

0.12

0.69

1.59

dPPAS

-----GQSAKEAIEAANADFVKAYNSKDAAGVASKYDDAAAFP------PDARVDGRQNIQKLWQGA--DGISELKLTTLDVQESGDFAFESGSFSLKAPGKDSKLVDAAGKYVVVWRKGQDGGWKLYRDIWNSDPA--------------------------------------------

(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=-1.44

Estimated TM-score = 0.54±0.15

Estimated RMSD = 8.3±4.5Å

Download Model 2

C-score=-2.70

Download Model 3

C-score=-2.38

Download Model 4

C-score=-2.93

Download Model 5

C-score=-4.61

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	3rgaA	0.617	3.40	0.095	0.812
2	6stdA	0.608	3.27	0.075	0.801
3	2chcA	0.607	3.75	0.105	0.818
4	5aifA	0.605	1.90	0.146	0.680
5	4gb5A	0.602	2.42	0.092	0.718
6	3ef8A	0.597	2.78	0.112	0.729
7	3en1B	0.587	3.34	0.093	0.746
8	1wqlB	0.585	3.24	0.123	0.735
9	3gzxB	0.584	3.37	0.107	0.746
10	1nu3B	0.581	2.37	0.156	0.685

(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	0.35	31	3nhxA	ASD	Rep, Mult	16,44,63,67,96,100,109,115,128,130,132
2	0.10	9	5aigB	VPR	Rep, Mult	67,69,77,97,99,109,113,130,132,137,141
3	0.03	3	4xbyC	3ZS	Rep, Mult	20,42,64,74,128
4	0.01	1	3en8A	CA	Rep, Mult	38,39
5	0.01	1	1ohpB	ESR	Rep, Mult	97,101,109,132,137
6	0.01	1	3ov4A	EQU	Rep, Mult	16,20,44,74,98,100,109,132
7	0.01	1	3hx8A	IMD	Rep, Mult	10,13,77

	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	0.245	8choA	0.561	2.64	0.240	0.685	5.3.3.1	15,19,41,61,124
2	0.129	1hkxA	0.504	3.42	0.088	0.685	2.7.11.17	8,19,124
3	0.117	2ux0A	0.505	3.37	0.073	0.674	2.7.11.17	19,41
4	0.077	1e3vB	0.561	2.80	0.119	0.691	5.3.3.1	36
5	0.067	3gzxB	0.584	3.37	0.107	0.746	1.14.12.18	18,33,76
6	0.060	2p0mB	0.429	5.01	0.070	0.685	1.13.11.33	8
7	0.060	1buqA	0.534	2.95	0.232	0.674	5.3.3.1	35
8	0.060	2qnoA	0.445	5.64	0.029	0.790	3.2.1.4	75
9	0.060	3bfjA	0.429	5.19	0.085	0.735	1.1.1.202	NA
10	0.060	1l2aE	0.404	5.49	0.046	0.718	3.2.1.4	NA
11	0.060	2p0mA	0.432	5.03	0.070	0.696	1.13.11.33	NA
12	0.060	2welA	0.281	5.75	0.040	0.525	2.7.11.17	41
13	0.060	3en1B	0.587	3.34	0.093	0.746	1.14.12.3,1.14.12.11	26,76
14	0.060	1z45A	0.431	5.30	0.049	0.740	5.1.3.2,5.1.3.3	NA
15	0.060	1sa3A	0.422	4.62	0.060	0.635	3.1.21.4	68,93,100
16	0.060	1f1sA	0.451	5.45	0.071	0.784	4.2.2.1	NA
17	0.060	1rw9A	0.440	5.65	0.065	0.790	4.2.2.5	NA
18	0.060	1o7hB	0.581	3.27	0.066	0.729	1.14.12.12	NA
19	0.060	2bngC	0.538	3.05	0.123	0.680	3.3.2.8	45
20	0.060	3lrkA	0.449	5.34	0.062	0.784	3.2.1.22	165
21	0.060	3e99A	0.539	3.36	0.082	0.713	1.14.12.10	95
22	0.060	2v7oA	0.288	6.36	0.044	0.591	2.7.11.17	34
23	0.060	4stdA	0.614	3.28	0.068	0.801	4.2.1.94	NA
24	0.060	1nu3B	0.581	2.37	0.156	0.685	3.3.2.8	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	0.31	0.534	2.95	0.23	0.67	1buqA	GO:0004769 GO:0005622 GO:0006629 GO:0006810 GO:0008202 GO:0016853
1	0.25	0.593	2.54	0.17	0.71	4xbxC	GO:0016787 GO:0018744
2	0.23	0.602	2.83	0.13	0.73	4r9kC	GO:0016787 GO:0018744
3	0.21	0.541	2.47	0.09	0.64	1qmaA	GO:0000060 GO:0005622 GO:0005640 GO:0005737 GO:0006611 GO:0006810 GO:0008536 GO:0015031 GO:0042307 GO:0044613 GO:0070062 GO:1904046
4	0.16	0.620	3.45	0.08	0.81	4rzmB	GO:0016853 GO:0017000
5	0.16	0.526	2.14	0.13	0.61	3ujmA	GO:0000166 GO:0000398 GO:0001752 GO:0003676 GO:0003729 GO:0005622 GO:0005737 GO:0005811 GO:0005829 GO:0006810 GO:0007265 GO:0008069 GO:0010628 GO:0016318 GO:0030529 GO:0045571 GO:0071011 GO:0071013
6	0.15	0.544	2.48	0.14	0.65	2qiyA	GO:0000932 GO:0003676 GO:0003723 GO:0005622 GO:0006810 GO:0016579 GO:0034517 GO:0042802 GO:0060628 GO:1990861 GO:2000156
7	0.15	0.564	2.30	0.12	0.66	4fcmB	GO:0000166 GO:0003676 GO:0003677 GO:0003723 GO:0003729 GO:0004003 GO:0004004 GO:0004386 GO:0004518 GO:0004519 GO:0005524 GO:0005622 GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0005925 GO:0006810 GO:0007265 GO:0010494 GO:0016020 GO:0016787 GO:0032508 GO:0044822 GO:0090090 GO:0090305
8	0.14	0.561	3.24	0.09	0.72	4l8pA	GO:0016829 GO:0033988
9	0.14	0.548	2.22	0.13	0.64	5drvA	GO:0000166 GO:0003676 GO:0003723 GO:0005622 GO:0005737 GO:0006810 GO:0007253 GO:0007265 GO:0030159 GO:0044822 GO:0051028
10	0.13	0.512	2.97	0.07	0.65	1gy7B	GO:0005622 GO:0005635 GO:0005737 GO:0006606 GO:0006810 GO:0006913 GO:0008536 GO:0015031
11	0.13	0.556	3.11	0.13	0.70	1z1sA	GO:0017000
12	0.13	0.561	2.56	0.14	0.69	5cxoB	GO:0016787
13	0.12	0.544	2.99	0.12	0.69	2bngC	GO:0004301 GO:0005886 GO:0016787 GO:0033963 GO:0097176
14	0.11	0.556	2.98	0.08	0.70	4l8oA	GO:0016829 GO:0033988
15	0.11	0.565	2.76	0.13	0.69	3t8nB	GO:0004769 GO:0006629 GO:0008202 GO:0016853
16	0.11	0.565	2.82	0.13	0.70	3wmdB	GO:0016853
17	0.11	0.354	5.37	0.10	0.62	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
18	0.07	0.614	3.28	0.07	0.80	4stdA	GO:0006582 GO:0016829 GO:0030411 GO:0042438 GO:0043581
19	0.07	0.522	2.83	0.13	0.65	1zo2A	GO:0005622 GO:0006810
20	0.07	0.506	2.98	0.09	0.64	3nv0B	GO:0005622 GO:0005634 GO:0006810 GO:0015031 GO:0051028
21	0.07	0.520	3.14	0.09	0.67	1jkgA	GO:0005622 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006405 GO:0006406 GO:0006611 GO:0006810 GO:0008536 GO:0015031 GO:0016607
22	0.07	0.522	3.20	0.11	0.66	4xb5A	GO:0005622 GO:0006810 GO:0007165 GO:0009579 GO:0009881 GO:0016020 GO:0016037 GO:0018298 GO:0030089 GO:0031404 GO:0042651 GO:0050896
23	0.06	0.347	5.07	0.02	0.58	4i5jA	GO:0000159 GO:0001754 GO:0005509 GO:0006470 GO:0007525 GO:0008601 GO:0030674 GO:0034047 GO:0045732 GO:0046872 GO:0061053 GO:0090090 GO:0090244 GO:0090249 GO:0090263
24	0.06	0.332	6.17	0.05	0.66	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
25	0.06	0.519	3.23	0.09	0.66	1m98A	GO:0005622 GO:0006810 GO:0007165 GO:0009579 GO:0009881 GO:0016020 GO:0016037 GO:0018298 GO:0030089 GO:0031404 GO:0042651 GO:0050896
26	0.06	0.302	5.99	0.09	0.56	1bs4A	GO:0005506 GO:0005829 GO:0006412 GO:0008198 GO:0008270 GO:0016787 GO:0031365 GO:0042586 GO:0043022 GO:0043686 GO:0046872
27	0.06	0.311	5.50	0.07	0.52	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

Consensus prediction of GO terms

Molecular Function	GO:0017016	GO:0018744	GO:0004769
GO-Score	0.43	0.42	0.31
Biological Processes	GO:0010574	GO:0090316	GO:1904591	GO:1900182	GO:0042306	GO:0001818	GO:0046824	GO:0051168	GO:0044249	GO:0016999	GO:0008202
GO-Score	0.43	0.43	0.43	0.43	0.43	0.43	0.43	0.43	0.32	0.32	0.31
Cellular Component	GO:0031965	GO:0031988	GO:1903561	GO:0043234	GO:0031968	GO:0042175	GO:0005643	GO:0044425
GO-Score	0.43	0.43	0.43	0.43	0.43	0.43	0.43	0.33

(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.