I-TASSER results

I-TASSER results for job id Rv1508A

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

Input Sequence in FASTA format

>protein (120 residues)
MKRALITGITGPDGSYLAKLPLKGYVAAGSPAEVYFCWATRNYRELYGLLAVNSIWFNHE
SPRHGETFMTRNPAPYRGRQRGADRCADADAPAHPDRYQYWGVPASVRGVIDRAMGVCVE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MKRALITGITGPDGSYLAKLPLKGYVAAGSPAEVYFCWATRNYRELYGLLAVNSIWFNHESPRHGETFMTRNPAPYRGRQRGADRCADADAPAHPDRYQYWGVPASVRGVIDRAMGVCVE
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEHCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Conf.Score	997555588899998899999999887568999999999999999989867875546899999998743368999999999996999958868986555678489999999999987579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MKRALITGITGPDGSYLAKLPLKGYVAAGSPAEVYFCWATRNYRELYGLLAVNSIWFNHESPRHGETFMTRNPAPYRGRQRGADRCADADAPAHPDRYQYWGVPASVRGVIDRAMGVCVE
Prediction	754133224454476463533342433330002110220032034224110010221326044366410133014110313245635530402314143312143104000430263038
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEHCCCCCCCCCCHHHHHHHHHHHHHHHHCC
MKRALITGITGPDGSYLAKLPLKGYVAAGSPAEVYFCWATRNYRELYGLLAVNSIWFNHESPRHGETFMTRNPAPYRGRQRGADRCADADAPAHPDRYQYWGVPASVRGVIDRAMGVCVE

1t2aA

0.26

0.25

0.95

2.09

MUSTER

ASTSELYGVQEIPQKETTPFPRSP----YGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLG--QLECFSLGNLDAKRDWGAKDYVEAMWLMLQNDEPE

1rpnC

0.26

0.25

0.95

1.88

dPPAS

ASTSEMFGIQAERQDENTPFPRSP----YGVAKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARIKLG--KQQELRLGNVDAKRDWGAGDYVEAMWLMLQQDKAD

1rpnC

0.26

0.25

0.95

2.36

wdPPAS

ASTSEMFGIQAERQDENTPFPRSP----YGVAKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARIKLG--KQQELRLGNVDAKRDWGAGDYVEAMWLMLQQDKAD

1rpnC

0.26

0.25

0.95

1.48

wMUSTER

PETSEMFGIQAERQDENTPFPRSP----YGVAKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARIKLG--KQQELRLGNVDAKRDWGAGDYVEAMWLMLQQDKAD

1rpnC

0.26

0.25

0.95

1.87

wPPAS

ASTSEMFGIQAERQDENTPFPRSP----YGVAKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARIKLG--KQQELRLGNVDAKRDWGAGDYVEAMWLMLQQDKAD

1rpnC

0.26

0.25

0.95

4.64

dPPAS2

ASTSEMFGIQAERQDENTPFPRSP----YGVAKLYGHWITVNYRESFGLHASSGILFNHESPLRGIEFVTRKVTDAVARIKLG--KQQELRLGNVDAKRDWGAGDYVEAMWLMLQQDKAD

2pk3A

0.15

0.14

0.96

1.57

PPAS

LDCSEEYGMIESPVSEENQLPMSP----YGVSKASVGMLARQYVKAYGMDIIHTRTFNHIGPGQSLGFVTQDFAKQIVDIEMEKQ-EPIIKVGNLEAVRDFTVRDIVQAYWLLSQYGKTG

2pk3A

0.15

0.14

0.96

1.73

Env-PPAS

LDCSEEYGMILSPVSEENQLPMSP----YGVSKASVGMLARQYVKAYGMDIIHTRTFNHIGPGQSLGFVTQDFAKQIVDIEMEKQ-EPIIKVGNLEAVRDFTVRDIVQAYWLLSQYGKTD

1n7gB

0.30

0.28

0.95

1.95

MUSTER

GRTSEMFGSTPPPQSETTPFPRSP----YAASKCAAHWYTVNYREAYGLFACNGILFNHESPRRGENFVTRKITRALGRIKVG--LQTKLFLGNLQASRDWGAGDYVEAMWLMLQQEKPD

2pk3A

0.15

0.14

0.96

1.85

dPPAS

IGSSEEYGMILSPVSEENQLPMSP----YGVSKASVGMLARQYVKAYGMDIIHTRTFNHIGPGQSLGFVTQDFAKQIVDIEMEK-QEPIIKVGNLEAVRDFTVRDIVQAYWLLSQYGKTG

(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 1 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=0.51

Estimated TM-score = 0.78±0.10

Estimated RMSD = 3.3±2.3Å

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	1rpnC	0.889	1.18	0.226	0.958
2	1n7gB	0.882	1.16	0.298	0.950
3	1t2aA	0.877	1.29	0.252	0.958
4	2pk3A	0.866	1.42	0.148	0.958
5	2z95C	0.851	1.52	0.217	0.958
6	1db3A	0.842	1.62	0.278	0.958
7	1orrA	0.810	1.94	0.052	0.958
8	4b8wA	0.809	2.01	0.113	0.958
9	1sb8A	0.805	1.62	0.082	0.917
10	1kerB	0.802	1.67	0.109	0.917

(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	0.42	25	1a9yA	UPG	Rep, Mult	3,4,5,28,57,58,67,68,69,91,92,93,97,99,101
2	0.05	2	2z1mA	NDP	Rep, Mult	1,2,3,29,33,56,58,59,64
3	0.02	1	1kepA	TDX	Rep, Mult	3,5,58,68,99
4	0.02	1	1rkxA	NAD	Rep, Mult	29,33,59,60,61,62

	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	2yy7A	0.754	2.18	0.072	0.925	1.1.1.103	NA
2	0.060	2c29F	0.672	2.97	0.113	0.883	1.1.1.219	23,35
3	0.060	1ujmA	0.645	2.99	0.057	0.883	1.1.1.2	NA
4	0.060	2gn4A	0.675	1.85	0.074	0.792	4.2.1.-	NA
5	0.060	1bsvA	0.784	2.48	0.095	0.958	1.1.1.271	NA
6	0.060	1kerB	0.802	1.67	0.109	0.917	4.2.1.46	25
7	0.060	1n7gB	0.882	1.16	0.298	0.950	4.2.1.47	25
8	0.060	2ggsA	0.675	2.05	0.031	0.817	1.1.1.133	NA
9	0.060	1keuA	0.787	1.84	0.145	0.917	4.2.1.46	NA
10	0.060	3m2pA	0.715	2.39	0.065	0.892	5.1.3.7	21,100
11	0.060	1eq2D	0.718	2.48	0.099	0.925	5.1.3.20	25
12	0.060	1t2aA	0.877	1.29	0.252	0.958	4.2.1.47	NA
13	0.060	1z7eD	0.775	2.24	0.106	0.942	2.1.2.-,1.1.1.-	NA
14	0.060	1wvgA	0.785	1.85	0.082	0.917	4.2.1.45	30
15	0.060	2c59A	0.771	2.04	0.099	0.925	5.1.3.18	NA
16	0.060	1udpB	0.764	2.12	0.081	0.925	5.1.3.2	NA
17	0.060	1z45A	0.770	2.08	0.090	0.917	5.1.3.2,5.1.3.3	25
18	0.060	1db3A	0.842	1.62	0.278	0.958	4.2.1.47	NA
19	0.060	1eq2A	0.648	2.60	0.108	0.850	5.1.3.20	25

(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	0.26	0.880	1.26	0.22	0.96	2z1mA	GO:0000166 GO:0008446 GO:0016829 GO:0019673 GO:0070401
1	0.26	0.882	1.16	0.30	0.95	1n7gB	GO:0000166 GO:0005525 GO:0005829 GO:0008446 GO:0009826 GO:0016829 GO:0019673 GO:0042351
2	0.25	0.877	1.29	0.25	0.96	1t2aA	GO:0005737 GO:0005829 GO:0007219 GO:0008446 GO:0016829 GO:0019673 GO:0042351 GO:0070062 GO:0070401
3	0.25	0.889	1.18	0.23	0.96	1rpnC	GO:0008446 GO:0009103 GO:0016829 GO:0019673 GO:0070401
4	0.23	0.842	1.62	0.28	0.96	1db3A	GO:0008446 GO:0009242 GO:0016829 GO:0019673 GO:0042351 GO:0070401
5	0.18	0.866	1.42	0.15	0.96	2pk3A	GO:0016491 GO:0033705 GO:0055114
6	0.18	0.802	1.66	0.11	0.92	2b69A	GO:0005739 GO:0005794 GO:0016020 GO:0016021 GO:0016829 GO:0016831 GO:0032580 GO:0033320 GO:0042803 GO:0048040 GO:0051262 GO:0070062 GO:0070403
7	0.18	0.774	1.94	0.14	0.92	1bxkB	GO:0008460 GO:0009103 GO:0009225 GO:0009246 GO:0016829 GO:0045226
8	0.17	0.794	1.77	0.12	0.92	4egbA	GO:0000166 GO:0008460 GO:0009225 GO:0016829
9	0.17	0.776	2.04	0.13	0.93	4twrA	GO:0000166 GO:0003824 GO:0003978 GO:0006012 GO:0016853 GO:0046872 GO:0050662
10	0.17	0.777	1.88	0.07	0.92	3vpsA	GO:0000166 GO:0003824 GO:0050662
11	0.17	0.810	1.94	0.05	0.96	1orrA	GO:0009103 GO:0016853 GO:0047732
12	0.17	0.805	1.62	0.08	0.92	1sb8A	GO:0000166 GO:0003824 GO:0005975 GO:0016857 GO:0050662
13	0.16	0.799	1.68	0.08	0.92	3lu1A	GO:0000166 GO:0003824 GO:0003974 GO:0005975 GO:0009243 GO:0016853 GO:0016857 GO:0050662
14	0.16	0.770	2.08	0.09	0.92	1z45A	GO:0003824 GO:0003978 GO:0004034 GO:0005829 GO:0005975 GO:0006012 GO:0008152 GO:0016853 GO:0019318 GO:0030246 GO:0033499
15	0.16	0.799	2.35	0.15	0.97	1gy8C	GO:0000166 GO:0003824 GO:0003978 GO:0006012 GO:0016853 GO:0050662
16	0.16	0.781	1.85	0.13	0.92	4zrnA	GO:0003824 GO:0003978 GO:0005975 GO:0016853 GO:0016857 GO:0050662
17	0.16	0.779	1.75	0.12	0.91	4lw8A	GO:0003824 GO:0050662
18	0.16	0.779	1.82	0.12	0.91	3aw9A	GO:0000166 GO:0003824 GO:0016491 GO:0050662 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0008446	GO:0070401	GO:0032561	GO:0032550	GO:0035639
GO-Score	0.76	0.68	0.51	0.51	0.51
Biological Processes	GO:0019673	GO:0042351	GO:0000902	GO:0016049	GO:0060560	GO:0007166	GO:0008653	GO:0008610	GO:0033692	GO:0046377
GO-Score	0.76	0.57	0.51	0.51	0.51	0.50	0.50	0.50	0.50	0.46
Cellular Component	GO:1903561	GO:0031988	GO:0005829
GO-Score	0.50	0.50	0.44

(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.