I-TASSER results

I-TASSER results for job id Rv2991

[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)
MGTKQRADIVMSEAEIADFVNSSRTGTLATIGPDGQPHLTAMWYAVIDGEIWLETKAKSQ
KAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDE
CKPMVDQMMNKRVGVRIVARRTRSWDHRKLGLPHMSVGGSTAP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGTKQRADIVMSEAEIADFVNSSRTGTLATIGPDGQPHLTAMWYAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDECKPMVDQMMNKRVGVRIVARRTRSWDHRKLGLPHMSVGGSTAP
Prediction	CCCCHHHHCCCCHHHHHHHHHHCCEEEEEEHCCCCCEEEEEEEEEEHCCEEEEEHCCCCHHHHHHHHCCCEEEEEHCCCCCCCCEEEEEEEEEEEHCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCC
Conf.Score	9975566558999999999985988999998899977999999999899999997898889999998997899997799888757999999999968958999999999999878887665566776569889999998999986566667888778898999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGTKQRADIVMSEAEIADFVNSSRTGTLATIGPDGQPHLTAMWYAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDECKPMVDQMMNKRVGVRIVARRTRSWDHRKLGLPHMSVGGSTAP
Prediction	8655435634044720450055243021001256330100000102343200000155131141046332000000345534401102030303215466413400420044124634643442265336410001342430201112334335354654658
	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

CCCCHHHHCCCCHHHHHHHHHHCCEEEEEEHCCCCCEEEEEEEEEEHCCEEEEEHCCCCHHHHHHHHCCCEEEEEHCCCCCCCCEEEEEEEEEEEHCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCC
MGTKQRADIVMSEAEIADFVNSSRTGTLATIGPDGQPHLTAMWYAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDECKPMVDQMMNKRVGVRIVARRTRSWDHRKLGLPHMSVGGSTAP

1rfeA

0.90

0.84

0.93

3.45

MUSTER

---TKQRADIVSEAEIADFVNSSRTGTLATIGPDGQPHLTAW-YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDEKPVD-----NKRVGVRIVARRTRSWDHRKLGL-PHSVGGSTA-

1rfeA

0.90

0.84

0.94

6.49

dPPAS

---TKQRADIVSEAEIADFVNSSRTGTLATIGPDGQPHLTAW-YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDEKPVDQ----NKRVGVRIVARRTRSWDHRKLGL-PHSVGGSTA-

1rfeA

0.86

0.81

0.94

5.37

wdPPAS

---TKQRADIVSEAEIADFVNSSRTGTLATIGPDGQPHLTAWYAVIDG-EIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDEKPVDQ----NKRVGVRIVARRTRSWDHRKLGLP-HSVGGSTA-

1rfeA

0.90

0.84

0.93

4.13

wMUSTER

----KQRADIVSEAEIADFVNSSRTGTLATIGPDGQPHLTAW-YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDEKPVDQ----NKRVGVRIVARRTRSWDHRKLGL-PHSVGGSTA-

1rfeA

0.86

0.81

0.94

4.73

wPPAS

---TKQRADIVSEAEIADFVNSSRTGTLATIGPDGQPHLTAWYAVIDG-EIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDEKPVDQ----NKRVGVRIVARRTRSWDHRKLGLP-HSVGGSTA-

1rfeA

0.90

0.84

0.94

7.99

dPPAS2

---TKQRADIVSEAEIADFVNSSRTGTLATIGPDGQPHLTAW-YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDEKPVDQ----NKRVGVRIVARRTRSWDHRKLGL-PHSVGGSTA-

1rfeA

0.90

0.84

0.94

4.44

PPAS

---TKQRADIVSEAEIADFVNSSRTGTLATIGPDGQPHLTAW-YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDEKPVDQ----NKRVGVRIVARRTRSWDHRKLGL-PHSVGGSTA-

1rfeA

0.90

0.84

0.94

4.60

Env-PPAS

---TKQRADIVSEAEIADFVNSSRTGTLATIGPDGQPHLTAW-YAVIDGEIWLETKAKSQKAVNLRRDPRVSFLLEDGDTYDTLRGVSFEGVAEIVEEPEALHRVGVSVWERYTGPYTDEKPVDQ----NKRVGVRIVARRTRSWDHRKLGL-PHSVGGSTA-

1y30A

0.21

0.18

0.84

2.52

MUSTER

----------VFDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDKLLIQVSIAEPRAKTRNLRRDPRASILVDADDG---WSYAVAEGTAQLTPPAADTVEALIALYRNIAGEHSDWDDYRQAMVTDRRVLLTLPISHVYGLPPGMR-------------

1y30A

0.21

0.18

0.84

4.77

dPPAS

----------VFDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWS---YAVAEGTAQLTPPAADTVEALIALYRNIAGEHSDWDDYRQAMVTDRRVLLTLPISHVYGLPPGMR-------------

(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 4 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=1.35

Estimated TM-score = 0.90±0.06

Estimated RMSD = 2.3±1.8Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

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	1rfeA	0.904	1.04	0.902	0.939
2	4ybnA	0.774	2.60	0.114	0.932
3	2furA	0.738	2.42	0.131	0.859
4	1w3oA	0.728	2.98	0.140	0.890
5	2ol5B	0.721	2.74	0.103	0.865
6	2fg9A	0.697	2.65	0.112	0.828
7	2arzA	0.695	2.67	0.129	0.822
8	1y30A	0.692	2.59	0.213	0.834
9	5bncA	0.684	3.11	0.174	0.834
10	3dnhA	0.683	2.91	0.187	0.816

(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	0.53	26	1wv4A	FMN	Rep, Mult	40,41,42,43,45,54,55,59,60,61,132
2	0.09	6	4ybnB	FAD	Rep, Mult	76,84,86,87,88,90,143,145
3	0.04	3	1ty9A	FMN	Rep, Mult	29,72,90,141
4	0.03	2	3gasA	UUU	Rep, Mult	55,56,58,59,61,129,132
5	0.02	2	2iab0	III	Rep, Mult	25,27,29,30,31,32,33,35,36,37,38,39,41,68,70,72,73,74,86,88,145
6	0.01	1	1w3rA	2MN	Rep, Mult	40,41
7	0.01	1	2i02A	FMN	Rep, Mult	25,40,41,42,43,54,55,59,60,61,113,114
8	0.01	1	1vl70	III	Rep, Mult	23,24,25,27,29,31,35,36,37,38,39,41,43,56,70,72,74,86,113

	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	1nrgA	0.629	3.33	0.146	0.791	1.4.3.5	136
2	0.060	1kigH	0.440	4.27	0.066	0.632	3.4.21.6	89
3	0.060	1bruP	0.425	4.10	0.044	0.607	3.4.21.71	NA
4	0.060	2qy0C	0.249	4.45	0.047	0.393	3.4.21.41,3.4.21.42	56,60
5	0.060	1rtkA	0.426	4.04	0.041	0.626	3.4.21.47	93
6	0.060	2a2jA	0.647	2.96	0.146	0.785	1.4.3.5	NA
7	0.060	1c5mD	0.440	4.13	0.074	0.626	3.4.21.6	NA
8	0.060	1gpzA	0.413	4.18	0.117	0.607	3.4.21.41	88
9	0.060	2iphA	0.414	3.75	0.048	0.577	3.4.22.66	93
10	0.060	1pfxC	0.439	4.18	0.045	0.626	3.4.21.22	38
11	0.060	1wv4A	0.621	2.60	0.174	0.718	1.4.3.5	NA
12	0.060	2ok5A	0.427	4.08	0.040	0.626	3.4.21.47	88
13	0.060	1dlmB	0.439	4.57	0.040	0.681	1.13.11.1	NA
14	0.060	1autC	0.435	4.19	0.043	0.626	3.4.21.69	64
15	0.060	1ci0A	0.625	3.35	0.145	0.791	1.4.3.5	136
16	0.060	1yc0A	0.414	4.09	0.028	0.601	3.4.21.-	86
17	0.060	1ym0A	0.413	4.13	0.080	0.601	3.4.21.-	NA
18	0.060	1ty9B	0.644	3.05	0.130	0.791	1.4.-.-	29,37,72,145
19	0.060	1eltA	0.419	4.14	0.037	0.595	3.4.21.36	NA
20	0.060	1dlmA	0.435	4.58	0.048	0.681	1.13.11.1	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	0.69	0.928	1.00	0.90	0.96	1rfeA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
1	0.39	0.698	2.57	0.22	0.84	4qvbB	GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
2	0.36	0.668	2.56	0.16	0.75	2fhqA	GO:0010181 GO:0016491 GO:0055114
3	0.35	0.675	2.07	0.17	0.76	3db0B	GO:0010181 GO:0016491 GO:0055114
4	0.30	0.671	2.94	0.18	0.83	3tgvA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
5	0.28	0.638	2.64	0.24	0.76	3f7eA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
6	0.26	0.658	2.42	0.14	0.76	2i02A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
7	0.26	0.668	2.53	0.17	0.77	2re7A	GO:0010181 GO:0016491 GO:0055114
8	0.25	0.640	3.26	0.16	0.81	3dmbA	GO:0010181 GO:0016491 GO:0055114
9	0.25	0.652	2.65	0.15	0.77	3fkhD	GO:0010181 GO:0016491 GO:0055114
10	0.25	0.689	2.90	0.18	0.82	3dnhA	GO:0010181 GO:0016491 GO:0055114
11	0.25	0.765	2.40	0.13	0.89	2furA	GO:0010181 GO:0016491 GO:0055114
12	0.25	0.656	2.23	0.18	0.75	3u5wA	GO:0010181 GO:0016491 GO:0055114
13	0.24	0.774	2.60	0.11	0.93	4ybnA	GO:0010181 GO:0016491 GO:0055114
14	0.24	0.729	2.97	0.14	0.89	2x1kA	GO:0010181 GO:0016491 GO:0055114
15	0.23	0.684	3.11	0.17	0.83	5bncA	GO:0010181 GO:0016491 GO:0055114
16	0.23	0.695	2.67	0.13	0.82	2arzA	GO:0010181 GO:0016491 GO:0055114
17	0.23	0.633	3.04	0.17	0.77	2ou5A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
18	0.22	0.668	2.46	0.18	0.77	2htiA	GO:0000166 GO:0010181 GO:0016491 GO:0055114
19	0.20	0.655	2.63	0.18	0.77	2hq9B	GO:0000166 GO:0010181 GO:0016491 GO:0055114
20	0.19	0.730	2.62	0.11	0.86	2fg9A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
21	0.18	0.664	2.40	0.17	0.77	1vl7A	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
22	0.18	0.742	2.95	0.09	0.90	2ol5B	GO:0010181 GO:0016491 GO:0055114
23	0.17	0.647	2.37	0.19	0.73	3ec6A	GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
24	0.07	0.618	3.51	0.14	0.79	2qeaA	GO:0010181 GO:0016491 GO:0046872 GO:0055114
25	0.06	0.326	5.63	0.03	0.62	1gviA	GO:0003824 GO:0004553 GO:0005975
26	0.06	0.413	4.18	0.12	0.61	1gpzA	GO:0002376 GO:0004252 GO:0005509 GO:0005576 GO:0006508 GO:0006955 GO:0006956 GO:0006958 GO:0008233 GO:0008236 GO:0016787 GO:0045087 GO:0070062 GO:0072562
27	0.06	0.330	4.90	0.03	0.56	2p52A	GO:0000060 GO:0000122 GO:0000733 GO:0000785 GO:0000790 GO:0000977 GO:0000979 GO:0000981 GO:0001046 GO:0001077 GO:0001085 GO:0001228 GO:0001701 GO:0001756 GO:0001836 GO:0002020 GO:0002039 GO:0002309 GO:0002326 GO:0002360 GO:0002931 GO:0003677 GO:0003682 GO:0003684 GO:0003700 GO:0005507 GO:0005524 GO:0005634 GO:0005654 GO:0005657 GO:0005667 GO:0005669 GO:0005730 GO:0005737 GO:0005739 GO:0005759 GO:0005783 GO:0005829 GO:0006289 GO:0006302 GO:0006351 GO:0006355 GO:0006357 GO:0006366 GO:0006461 GO:0006915 GO:0006974 GO:0006977 GO:0006978 GO:0006979 GO:0006983 GO:0007049 GO:0007050 GO:0007179 GO:0007275 GO:0007369 GO:0007406 GO:0007417 GO:0007507 GO:0007569 GO:0007623 GO:0008104 GO:0008134 GO:0008156 GO:0008285 GO:0008340 GO:0009303 GO:0009411 GO:0009651 GO:0009792 GO:0010165 GO:0010332 GO:0010628 GO:0010629 GO:0010666 GO:0012501 GO:0016032 GO:0016363 GO:0016604 GO:0016605 GO:0019899 GO:0019901 GO:0019903 GO:0021549 GO:0030308 GO:0030330 GO:0030512 GO:0030971 GO:0031052 GO:0031065 GO:0031497 GO:0031571 GO:0031625 GO:0032461 GO:0033077 GO:0034103 GO:0034613 GO:0034644 GO:0035033 GO:0035035 GO:0035264 GO:0035794 GO:0035861 GO:0042127 GO:0042149 GO:0042493 GO:0042771 GO:0042802 GO:0042981 GO:0043065 GO:0043066 GO:0043153 GO:0043234 GO:0043504 GO:0043523 GO:0043525 GO:0043621 GO:0044212 GO:0045861 GO:0045892 GO:0045893 GO:0045930 GO:0045944 GO:0046872 GO:0046982 GO:0047485 GO:0048147 GO:0048511 GO:0048512 GO:0048568 GO:0050731 GO:0050821 GO:0051087 GO:0051262 GO:0051276 GO:0051402 GO:0051721 GO:0051726 GO:0051974 GO:0060411 GO:0061419 GO:0070059 GO:0070243 GO:0070245 GO:0070266 GO:0071158 GO:0071479 GO:0071480 GO:0071494 GO:0071850 GO:0072332 GO:0072363 GO:0090200 GO:0090343 GO:0090399 GO:0090403 GO:0097252 GO:0097371 GO:1900119 GO:1901525 GO:1902108 GO:1902253 GO:1904024 GO:1990144 GO:1990440 GO:2000269 GO:2000378 GO:2000379 GO:2000772 GO:2001244

Consensus prediction of GO terms

Molecular Function	GO:0010181	GO:0004733	GO:0030170	GO:0042803
GO-Score	0.94	0.87	0.39	0.39
Biological Processes	GO:0055114	GO:0042823	GO:0042816
GO-Score	0.94	0.87	0.39
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.