I-TASSER results

I-TASSER results for job id Rv0883c

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

Input Sequence in FASTA format

>protein (253 residues)
MRELKVVGLDADGKNIICQGAIPSEQFKLPVDDRLRAALRDDSVQPEQAQLDIEVTNVLS
PKEIQARIRAGASVEQVAAASGSDIARIRRFAHPVLLERSRAAELATAAHPVLADGPAVL
TMQETVAAALVARGLNPDSLTWDAWRNEDSRWTVQLAWKAGRSDNLAHFRFTPGAHGGTA
TAIDDTAHELINPTFNRPLRPLAPVAHLDFDEPEPAQPTLTVPSAQPVSNRRGKPAIPAW
EDVLLGVRSGGRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MRELKVVGLDADGKNIICQGAIPSEQFKLPVDDRLRAALRDDSVQPEQAQLDIEVTNVLSPKEIQARIRAGASVEQVAAASGSDIARIRRFAHPVLLERSRAAELATAAHPVLADGPAVLTMQETVAAALVARGLNPDSLTWDAWRNEDSRWTVQLAWKAGRSDNLAHFRFTPGAHGGTATAIDDTAHELINPTFNRPLRPLAPVAHLDFDEPEPAQPTLTVPSAQPVSNRRGKPAIPAWEDVLLGVRSGGRR
Prediction	CCEEEEEEHCCCCCEEEEEHCCCCEEEEEHCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHCCEEEEHCCCCCEEEEEEEHCCCCCCEEEEEEHCCCCCCEEEHCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHEEEHCCCCCCC
Conf.Score	9758999867999889998589985999967889999998676666777766677889998999999986999999999989998897656678999999999999878888899988879999999999998999877755567769986899999985887555899995788898566577899998698888888777777888888888778888888877654568889998455455545789999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MRELKVVGLDADGKNIICQGAIPSEQFKLPVDDRLRAALRDDSVQPEQAQLDIEVTNVLSPKEIQARIRAGASVEQVAAASGSDIARIRRFAHPVLLERSRAAELATAAHPVLADGPAVLTMQETVAAALVARGLNPDSLTWDAWRNEDSRWTVQLAWKAGRSDNLAHFRFTPGAHGGTATAIDDTAHELINPTFNRPLRPLAPVAHLDFDEPEPAQPTLTVPSAQPVSNRRGKPAIPAWEDVLLGVRSGGRR
Prediction	5550411302640420003137523302030044023114455445645536364745030430032234433043007427143630441120031014201520471424367454322013003410453625375140402247743030202043645524020303263453204021620440355645434442442464437546466454754566446745643312113100001155588
	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                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEEEHCCCCCEEEEEHCCCCEEEEEHCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHCCEEEEHCCCCCEEEEEEEHCCCCCCEEEEEEHCCCCCCEEEHCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHEEEHCCCCCCC
MRELKVVGLDADGKNIICQGAIPSEQFKLPVDDRLRAALRDDSVQPEQAQLDIEVTNVLSPKEIQARIRAGASVEQVAAASGSDIARIRRFAHPVLLERSRAAELATAAHPVLADGPAVLTMQETVAAALVARGLNPDSLTWDAWRNEDSRWTVQLAWKAGRSDNLAHFRFTPGAHGGTATAIDDTAHELINPTFNRPLRPLAPVAHLDFDEPEPAQPTLTVPSAQPVSNRRGKPAIPAWEDVLLGVRSGGRR

2mxxA

0.09

0.06

0.68

1.01

dPPAS

---------------------------------------MADEATDAARNNDGAYYLQTQ----------FTNADKVNEYL---AQHDGEIRAEAAADPAVVAAKAALDAVEGGSHNYGEVKAAYEAAFNNAFNAVRNKY-------------VQRFQATYNNATE------QEGKTYIQGETPEQANARYLKRVGAANNQNPAAEDKGATTPASKEEAKKSEAAAKNAGKAAGKALP---------KTSAVK

5af3A2

0.20

0.04

0.22

1.68

dPPAS2

--------------------------------------IRLPQYGDANVVLDPRDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---------------------------------------------------------------------------------------------------------------------------------------------------------------

2kb4A

0.14

0.03

0.23

1.45

dPPAS2

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MSDNNGTPEPQVETTSVFRADLLKEMESSTGTAPASTGAENLPAGSA---LLVVKRGPNAG

4cwuT

0.15

0.04

0.23

1.27

dPPAS2

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------APGLGVQTVD------VQETQTSPVASAVADAAVQAVAAAASKTSTEMFRVSAPRRPRGSALLPE--------------

2kfuA

0.13

0.03

0.24

1.24

dPPAS2

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------VTDMNPDIEKDQTSDEVTVEADFLSELDAPAQAGTESAVSGVEGLPPGSA---LLVVKRGPNAG

5af3A

0.14

0.04

0.32

1.20

dPPAS2

EHYLQQISFADDNLASMIRLPQYGDA-NVVLD------------PRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---------------------------------------------------------------------------------------------------------------------------------------------------------------

5cwpA

0.12

0.11

0.87

0.67

MUSTER

EEEARIERAKEAAERAQEAAERTGDPRVRELARELKRLAQEAAEEVKRDPSSSDVNE--ALKLIVEAIEAAVRALEAAERTGD--PEVRELARELVRLAVEAAEEVQRN-------PSSSDVNEALKLIVEAIEAAVRALE--------------AAERTGDPEVR-------ELARELVRLAVEAAEEVQRNPSSEEVNEALKKIVKAIQEAVESLREAEESGDPEKREKARERVREAVERAVQRDPSGWLE

1ub1A

0.10

0.05

0.48

0.77

dPPAS

-------------------------------------------------------------------------------------------------------------APAVPEASASPKQ---------RRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTGSPSRREQRPPKKAKSPKSPGSGRGRGRPKGSG--------------

1hdoA

0.12

0.08

0.71

0.68

wdPPAS

VKKIAIFGAT--GLTTLAQAVQAG---------EVTVLVRDSSRLPSEGPRPAHVGDVLQAADVDKTVA-GQDA--VIVLLGTRNDL----TTVMSEGARNIVAAMKAHGVDK--LWDPTKVPPRLQAVTDDHIRMHKVL-----RESGLKYVAV-HIGDQPLTGAYTVTLDGRGPSRVIS--HDLGHFMLR-TTDEYDGHSTYPSHQY--------------------------------------------

3c1aA

0.19

0.18

0.95

0.70

wMUSTER

V-RLALIGAGRWGKNYIIAGLPGAALVRLA-SDNLALVPPGCVIESDWRSVEVETPPATHAEITLAAIASGLDVAAAAKATGV-VEHTQLFNPAWEALKADLTSIGPEAGNHGPYRPGGVPLWDWGAHDVSVLGRDPDSASWAARGEKDGGGDVTLTLAFST--VEAHIRLCNTDKCRRLAVFGEAG--LVDDRATDKLTLHPPQPDGNWPVGQGHALTVTDEPLTRA--RQPEPGPSPLELGLRVVRS----

(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 = 14.0±3.9Å

Download Model 2

C-score=-4.33

Download Model 3

C-score=-4.70

Download Model 4

C-score=-3.57

Download Model 5

C-score=-4.02

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	3c1aA	0.628	4.83	0.136	0.921
2	3evnA	0.619	4.82	0.078	0.893
3	2poqX	0.619	4.68	0.115	0.893
4	3uuwA	0.613	4.64	0.071	0.877
5	1zh8A	0.610	4.64	0.063	0.877
6	3e9mA	0.610	4.81	0.066	0.885
7	3rbvA	0.609	4.99	0.078	0.901
8	1tltB	0.609	4.61	0.111	0.874
9	3moiA	0.606	5.04	0.065	0.901
10	4h3vA	0.606	4.64	0.112	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	0.08	4	2nr9A	PA6	Rep, Mult	126,130
2	0.04	2	2wtgA	OXY	Rep, Mult	91,243
3	0.04	2	4r6cA	6BP	Rep, Mult	124,127,128
4	0.04	2	2wpnB	UUU	Rep, Mult	40,110
5	0.04	2	2ek8A	ZN	Rep, Mult	168,184,211
6	0.02	1	1lc3A	PO4	Rep, Mult	92,93,97,98,99
7	0.02	1	2wssX	III	Rep, Mult	122,126
8	0.02	1	1h6dA	NDP	Rep, Mult	130,136,137,139,140,141
9	0.02	1	3kd3A	MG	Rep, Mult	10,12,185
10	0.02	1	1v51A	ZN	Rep, Mult	185,189
11	0.02	1	3rbvA	NA	Rep, Mult	106,107,108,109,111
12	0.02	1	4ep7B	MG	Rep, Mult	130,133
13	0.02	1	1shkA	MG	Rep, Mult	69,70,71
14	0.02	1	4dcaA	MG	Rep, Mult	165,184
15	0.02	1	2pnqA	MG	Rep, Mult	115,116
16	0.02	1	1c66A	AR	Rep, Mult	129,171
17	0.02	1	3oceC	CO	Rep, Mult	121,124
18	0.02	1	1h74B	MG	Rep, Mult	73,104

	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	2glxE	0.599	4.82	0.085	0.877	1.1.1.263	157
2	0.060	2ph5A	0.466	5.78	0.087	0.767	2.5.1.44	8,55
3	0.060	1ml4A	0.459	5.10	0.044	0.696	2.1.3.2	NA
4	0.060	3euwD	0.565	5.14	0.094	0.874	1.1.1.18	11,60
5	0.060	2o48X	0.619	4.67	0.115	0.893	1.1.1.179,1.3.1.20	NA
6	0.060	1dpgA	0.555	5.50	0.068	0.893	1.1.1.49	NA
7	0.060	1gcuA	0.592	4.73	0.059	0.870	1.3.1.24	NA
8	0.060	1ydwB	0.596	5.29	0.096	0.909	1.-.-.-	128
9	0.060	2ixaA	0.597	5.08	0.054	0.909	3.2.1.49	128
10	0.060	2o4uX	0.619	4.66	0.115	0.893	1.3.1.20	91
11	0.060	1e5qA	0.474	5.78	0.043	0.775	1.5.1.10	101,105
12	0.060	1e5lA	0.462	5.57	0.034	0.739	1.5.1.10	NA
13	0.060	1p1jA	0.489	4.91	0.070	0.739	5.5.1.4	96,100,222
14	0.060	2ejwA	0.489	5.34	0.085	0.767	1.1.1.3	NA
15	0.060	1o0sA	0.475	5.43	0.055	0.751	1.1.1.38	NA
16	0.060	1ebfA	0.483	5.37	0.053	0.767	1.1.1.3	NA
17	0.060	3mtjA	0.496	5.72	0.090	0.806	1.1.1.3	96,98,127
18	0.060	1dxhA	0.464	5.45	0.033	0.727	2.1.3.3	69
19	0.060	2h63D	0.585	4.71	0.051	0.858	1.3.1.24	NA
20	0.060	2glxA	0.598	4.80	0.077	0.874	1.1.1.292	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	0.25	0.606	4.73	0.06	0.89	3q2kC	GO:0000166 GO:0008152 GO:0016491 GO:0055114
1	0.08	0.639	4.75	0.14	0.93	3c1aA	GO:0016491 GO:0055114
2	0.08	0.609	4.70	0.09	0.88	4nheB	GO:0016491 GO:0055114
3	0.08	0.604	4.97	0.07	0.90	5a03C	GO:0008152 GO:0016491 GO:0055114
4	0.07	0.615	4.89	0.09	0.90	3rc1A	GO:0000166 GO:0016491 GO:0055114
5	0.07	0.619	4.67	0.12	0.89	2o48X	GO:0016491 GO:0047115 GO:0047837 GO:0055114
6	0.07	0.619	4.82	0.08	0.89	3evnA	GO:0016491 GO:0055114
7	0.07	0.600	4.71	0.09	0.87	1xeaA	GO:0016491 GO:0055114
8	0.07	0.593	4.93	0.08	0.88	3kuxA	GO:0008152 GO:0016491 GO:0055114
9	0.07	0.612	4.61	0.12	0.89	4h3vA	GO:0008152 GO:0016491 GO:0055114
10	0.07	0.596	4.88	0.11	0.89	3u3xA	GO:0008152 GO:0016491 GO:0055114
11	0.07	0.611	4.78	0.04	0.90	3dtyA	GO:0008152 GO:0016491 GO:0055114
12	0.07	0.613	4.83	0.07	0.89	3e9mA	GO:0016491 GO:0055114
13	0.07	0.602	4.73	0.09	0.88	4fb5A	GO:0008152 GO:0016491 GO:0055114
14	0.07	0.599	5.01	0.08	0.89	3db2A	GO:0008152 GO:0016491 GO:0055114
15	0.07	0.608	4.47	0.12	0.87	4gqaC	GO:0008152 GO:0016491 GO:0055114
16	0.07	0.606	5.04	0.07	0.90	3moiA	GO:0008152 GO:0016491 GO:0055114
17	0.07	0.596	4.84	0.10	0.88	2p2sA	GO:0008152 GO:0016491 GO:0055114
18	0.07	0.598	4.82	0.10	0.88	4koaA	GO:0008152 GO:0016491 GO:0033712 GO:0055114
19	0.07	0.597	5.04	0.09	0.89	3gfgB	GO:0008152 GO:0016491 GO:0055114
20	0.07	0.585	4.71	0.05	0.86	2h63D	GO:0004074 GO:0005737 GO:0005829 GO:0008270 GO:0016491 GO:0042167 GO:0046872 GO:0055114 GO:0070062
21	0.07	0.592	4.73	0.06	0.87	1gcuA	GO:0004074 GO:0005737 GO:0008270 GO:0016491 GO:0042167 GO:0046872 GO:0055114
22	0.07	0.585	4.96	0.05	0.87	4ew6A	GO:0016491 GO:0019151 GO:0055114
23	0.07	0.606	4.96	0.07	0.90	4hadA	GO:0016491 GO:0055114
24	0.07	0.600	4.80	0.10	0.88	3m2tA	GO:0000166 GO:0016491 GO:0055114
25	0.07	0.591	4.68	0.08	0.86	3ezyA	GO:0008152 GO:0016491 GO:0050112 GO:0055114
26	0.07	0.598	4.80	0.08	0.87	2glxA	GO:0008152 GO:0016491 GO:0033712 GO:0055114
27	0.07	0.595	4.90	0.09	0.89	3q2iA	GO:0000166 GO:0008152 GO:0016491 GO:0055114
28	0.07	0.583	5.09	0.05	0.88	3fhlC	GO:0008152 GO:0016491 GO:0055114
29	0.07	0.595	4.82	0.09	0.88	3f4lA	GO:0005829 GO:0008152 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016491	GO:0000166
GO-Score	0.46	0.31
Biological Processes	GO:0055114
GO-Score	0.46
Cellular Component
GO-Score

(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.