I-TASSER results

I-TASSER results for job id Rv0123

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

Input Sequence in FASTA format

>protein (122 residues)
MTKKPRNPADYVIGDDVEVSDVDLKQEEVYVDGERLTDERVEQMASESLRLAREREANLI
PGGKSLSGGSAHSPAVQVVVSKATHAKLKELARSRKMSVSKLLRPVLDEFVQRETGRILP
RR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTKKPRNPADYVIGDDVEVSDVDLKQEEVYVDGERLTDERVEQMASESLRLAREREANLIPGGKSLSGGSAHSPAVQVVVSKATHAKLKELARSRKMSVSKLLRPVLDEFVQRETGRILPRR
Prediction	CCCCCCCCCCCCCCCCEEEEEHCCCCCEEEEEEEEHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEHCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCC
Conf.Score	99889986555456765776555786479996587454558999999999999999876788755688987776689998688899999999997786889999999999998757788899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTKKPRNPADYVIGDDVEVSDVDLKQEEVYVDGERLTDERVEQMASESLRLAREREANLIPGGKSLSGGSAHSPAVQVVVSKATHAKLKELARSRKMSVSKLLRPVLDEFVQRETGRILPRR
Prediction	85654653242112451415525155640413154135643563446414233443541343255146645433303121355346404520554724145113520551154534433478
	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

CCCCCCCCCCCCCCCCEEEEEHCCCCCEEEEEEEEHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEHCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCC
MTKKPRNPADYVIGDDVEVSDVDLKQEEVYVDGERLTDERVEQMASESLRLAREREANLIPGGKSLSGGSAHSPAVQVVVSKATHAKLKELARSRKMSVSKLLRPVLDEFVQRETGRILPRR

5cwpA1

0.22

0.20

0.89

0.72

MUSTER

MSEEARELIE-------RAKEA---AERAQEAAERTGDPRVRELARELKRLAQEAAEEVK--RDPSSSDVNEALKLIVEAIEAAVRALEAAERTGDPEVRELARELVRLAVEAAEE--VQRN

2k9iA

0.15

0.07

0.45

0.57

dPPAS

----------------------------------------------------------------GRPYKLLNGIKLGVYIPQEWHDRLMEIAKEKNLTLSDVCRLAIKEYLDNHDKQKK---

1na6B3

0.18

0.16

0.86

0.54

wdPPAS

ITEGNKKP-DFLFPSAGAYHDTEFPVENLRMLAVKTTKDRWRQILNE---ADKIHQVHLFTLQEGVSLA-ESG--VRLVVPSSLHKKYPEAVRAELMTLGAFIAELTGLYAD----------

1ygmA

0.22

0.18

0.83

0.70

wMUSTER

FEKHHRK--------DILLEKSTGVMEAM-----KVTSEEKEQLSTAIDRMNEGLDAFIQLYNESE----IDEPLIQL---DDDTAELMKQARDMQEKLNEKLNTIIKQILSIEEGELVPR-

3gniA1

0.26

0.19

0.74

0.55

wPPAS

FGKSHKSPADIVLKESMAV----LEKQD--------ISDKKAEKATEEVSKNLVAMKEI------LYGTNEKEP-----QTEAVAQLAQELYNS--TLVADLQL----DFEGKKD--IL-RR

2k9iA

0.21

0.09

0.43

0.63

dPPAS2

--------------------------------------------------------------GRKLLNGIKLG----VYIPQEWHDRLMEIAKEKNLTLSDVCRLAIKEYLDNHDKQKK---

1jokA

0.12

0.11

0.99

0.60

PPAS

TKKLHKEPAIKAIGDTVKLMYKG-QPMTFRLLLVDTPETKHPKKGVEKYGEASAFTKKMVENAKGQRTDKYGRGLAYIYADALVRQGLAKVAYVYKPNNTHEQLLRKSEAQAKKEKLNIADS

1na6B3

0.19

0.16

0.87

0.71

Env-PPAS

ITEGNKKP-DFLFPSAGAYHDTEFPVENLRMLAVKTTKDRWRQILNEADKIHQVHLFTLQEG---VSLARESG--VRLVVPSSLHKKYPEAVRAELMTLGAFIAELTGLYAD----------

4tkoB3

0.14

0.12

0.87

0.71

MUSTER

--------------LHISLSAKKLKVESLKKKREALRKLLQVEEKIKLVKLDWERYKSLFQKG-LIPRRKFEEVDTNLKVLLHEREYLEKSIQEINTEIKRAKKGIENARNEFKTIEELKK-

4ix7A

0.12

0.10

0.84

0.56

dPPAS

------------------DNVVSIGPNNTCVPASVFSVCSLATRKLLVTIFDRETLATHSVTGKPSPAFKDQDKPLKRLDPGKIQDIIFAVTHKCNAS-EKEVRNAITTKCADENKKIQNVK

(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=-4.03

Estimated TM-score = 0.28±0.09

Estimated RMSD = 13.7±4.0Å

Download Model 2

C-score=-4.22

Download Model 3

C-score=-4.50

Download Model 4

C-score=-4.70

Download Model 5

C-score=-4.98

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	4r1iA	0.541	4.18	0.087	0.869
2	4r0cA	0.534	4.40	0.033	0.893
3	1n63B	0.521	4.24	0.018	0.885
4	1ffvB3	0.520	4.31	0.064	0.877
5	1sb3D	0.518	4.30	0.045	0.885
6	5g5gC2	0.517	4.25	0.018	0.877
7	3cmmC	0.516	3.97	0.087	0.795
8	4p1tA	0.512	4.11	0.028	0.836
9	3bqkA	0.511	4.09	0.037	0.820
10	3g3nA	0.510	4.53	0.017	0.853

(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	0.12	6	2bsqH	NUC	Rep, Mult	89,93,98,99,100,104
2	0.04	2	3bdcA	CA	Rep, Mult	15,35,37,39
3	0.04	2	1rm6A	NA	Rep, Mult	56,57,59
4	0.04	2	4rkuL	CLA	Rep, Mult	103,107
5	0.04	2	3cknA	MN	Rep, Mult	23,85
6	0.02	1	1revA	MG	Rep, Mult	12,15
7	0.02	1	1tkoB	FE	Rep, Mult	109,112
8	0.02	1	1t9rA	PO4	Rep, Mult	15,49,113
9	0.02	1	3jwqA	VIA	Rep, Mult	11,49,53,56
10	0.02	1	4h6pC	FMN	Rep, Mult	30,67
11	0.02	1	2hzaA	3CM	Rep, Mult	91,92,95,97,106
12	0.02	1	2ch1A	LLP	Rep, Mult	30,37
13	0.02	1	3zjoB	AZI	Rep, Mult	78,106,110
14	0.02	1	3zq4D	CA	Rep, Mult	54,117
15	0.02	1	3jwqB	MG	Rep, Mult	16,32,48
16	0.02	1	3e25A	MG	Rep, Mult	21,23

	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	1fo4A	0.506	3.93	0.056	0.811	1.17.1.4	NA
2	0.060	2ouyA	0.499	4.36	0.049	0.836	3.1.4.17	52,57,104
3	0.060	1rm6A	0.523	4.23	0.055	0.885	1.3.99.20	NA
4	0.060	3dysB	0.497	4.53	0.026	0.828	3.1.4.35	109
5	0.060	3djlA	0.479	4.66	0.033	0.803	1.3.99.-	NA
6	0.060	1fa9A	0.487	4.11	0.078	0.770	2.4.1.1	35
7	0.060	2pywA	0.481	4.15	0.114	0.787	2.7.1.100	NA
8	0.060	1tazA	0.502	4.65	0.065	0.861	3.1.4.17	54
9	0.060	2o2dB	0.485	4.11	0.069	0.770	5.3.1.9	85
10	0.060	2e1qA	0.504	4.44	0.055	0.869	1.17.3.2,1.17.1.4	NA
11	0.060	1t3qB	0.502	4.31	0.046	0.877	1.3.99.17	NA
12	0.060	3b8cA	0.487	4.75	0.043	0.844	3.6.3.6	NA
13	0.060	2pulA	0.476	4.38	0.111	0.811	2.7.1.100	NA
14	0.060	1jroB	0.500	4.04	0.065	0.828	1.1.1.204	NA
15	0.060	1z1wA	0.479	4.44	0.055	0.811	3.4.11.-	18
16	0.060	3b9jJ	0.416	4.95	0.081	0.746	1.17.1.4,1.17.3.2	57
17	0.060	1zklA	0.509	4.58	0.017	0.853	3.1.4.17	106,110
18	0.060	2qykB	0.500	4.71	0.063	0.869	3.1.4.17	21
19	0.060	3hfwA	0.485	4.60	0.065	0.844	3.2.2.19	14

(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	0.24	0.523	4.23	0.06	0.89	1rm6A	GO:0016491 GO:0018525 GO:0055114
1	0.07	0.500	4.04	0.07	0.83	1jroB	GO:0016491 GO:0030151 GO:0046872 GO:0055114
2	0.07	0.521	4.24	0.02	0.89	1n63B	GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
3	0.07	0.510	4.10	0.06	0.86	1ffuB	GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
4	0.07	0.502	4.31	0.05	0.88	1t3qB	GO:0016491 GO:0055114
5	0.07	0.480	4.36	0.05	0.84	3zyvB	GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0030151 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114
6	0.07	0.504	4.44	0.06	0.87	2e1qA	GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
7	0.07	0.495	4.12	0.03	0.84	1dgjA	GO:0009055 GO:0016491 GO:0046872 GO:0051536 GO:0051537 GO:0055114
8	0.07	0.506	3.93	0.06	0.81	1fo4A	GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
9	0.06	0.493	4.13	0.08	0.82	2ckjA	GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
10	0.06	0.415	4.77	0.07	0.71	3hrdA	GO:0016491 GO:0046872 GO:0050138 GO:0051187 GO:0055114
11	0.06	0.499	4.13	0.04	0.82	4uhxA	GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0006954 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0042816 GO:0043546 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114 GO:0070062 GO:0072593
12	0.06	0.497	4.11	0.06	0.81	4zohA	GO:0016491 GO:0055114
13	0.06	0.407	4.87	0.09	0.72	3fahA	GO:0009055 GO:0016491 GO:0033727 GO:0046872 GO:0051536 GO:0051537 GO:0055114
14	0.06	0.408	4.76	0.06	0.77	3gp5A	GO:0003824 GO:0004619 GO:0006094 GO:0006096 GO:0008152 GO:0016853 GO:0016868 GO:0046538
15	0.06	0.382	5.04	0.04	0.69	5a5bW	GO:0000502 GO:0005198 GO:0005634 GO:0005829 GO:0006511 GO:0008540 GO:0031593 GO:0043161 GO:0043248
16	0.06	0.395	5.35	0.03	0.73	4r0cD	GO:0015558 GO:0016020 GO:0016021 GO:1902604
17	0.06	0.321	4.85	0.10	0.60	1xhnA	GO:0003714 GO:0005576 GO:0005615 GO:0005667 GO:0006355 GO:0006357 GO:0007275 GO:0008134 GO:0008283 GO:0010181 GO:0016491 GO:0040008 GO:0055114 GO:0070062 GO:1903507
18	0.06	0.407	4.77	0.03	0.67	3hrdB	GO:0016491 GO:0046872 GO:0050138 GO:0051187 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016636	GO:0046914
GO-Score	0.47	0.37
Biological Processes	GO:0055114
GO-Score	0.42
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.