I-TASSER results

I-TASSER results for job id Rv3605c

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

Input Sequence in FASTA format

>protein (158 residues)
MGPTRKRDLTAAVVGAAAVGYLLVAVLYRWFPPITVWTGLSLLAVAVAEALWARYVRVKI
SDGEIGDGPGWLHPLVVARSLMVAKASAWVGALVTGWWIGVLAYFLPRRSWLRAAAEDTT
GTVVAAGSALALVVAALWLQHCCKSPQDPTEHADGAES

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGPTRKRDLTAAVVGAAAVGYLLVAVLYRWFPPITVWTGLSLLAVAVAEALWARYVRVKISDGEIGDGPGWLHPLVVARSLMVAKASAWVGALVTGWWIGVLAYFLPRRSWLRAAAEDTTGTVVAAGSALALVVAALWLQHCCKSPQDPTEHADGAES
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Conf.Score	98889999999999999999999999976799875789999999999999999999999975887778888889999999999999999999999999999999975678765545557899999999999999999999875699999999998889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGPTRKRDLTAAVVGAAAVGYLLVAVLYRWFPPITVWTGLSLLAVAVAEALWARYVRVKISDGEIGDGPGWLHPLVVARSLMVAKASAWVGALVTGWWIGVLAYFLPRRSWLRAAAEDTTGTVVAAGSALALVVAALWLQHCCKSPQDPTEHADGAES
Prediction	85514131010101321321222113344332333333333122203211320330132157565556454030120021002021002300231133202101101334424244431110000000122111000200210412576878776588
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
MGPTRKRDLTAAVVGAAAVGYLLVAVLYRWFPPITVWTGLSLLAVAVAEALWARYVRVKISDGEIGDGPGWLHPLVVARSLMVAKASAWVGALVTGWWIGVLAYFLPRRSWLRAAAEDTTGTVVAAGSALALVVAALWLQHCCKSPQDPTEHADGAES

2mgyA

0.12

0.11

0.98

1.07

wMUSTER

PESWPAVGLTLVPSLGGFMGAYFVRGEGLQKPSHPWTLAPIWGTLYSAMGYGSYIVWKELG-GFTEDAMVPLGLYTGQLALNWAWPPIFFGAMGWALADLLLVSGVATATTLAWHRVSPPAARLLYPYLAWLAFATVLNYYVWRDSGRRGGSRLAE--

4uc1A

0.10

0.09

0.92

1.16

wPPAS

MN-MDWALFLTFLAACGAPATTGALEWYDNLPWNPWVFPLAWTSLYFLMSLAAMRVAQ------LEGSGQALAFYAAQLAFNTLWTPVFFGMMATALAVVMVMWLFVAATMWAFFQLDTWAGVLFVPYLIWATATTGLNFEAMRLWNRPEAR------

4zowA2

0.11

0.08

0.77

1.17

dPPAS2

TSRRTVRSLIIMGGWPIMIGLLVAAAATVISSHAYLWMTAGLSIYAFGIGLANAGLVRLTLFASDMS---------------KGTVSAAMGMLQMLIFTVGIEISKH----AWLNGGNGLFNLFNLVNGILWLSLMVIFLK-----------------

2mgyA

0.10

0.97

1.10

PPAS

MPE-SWVPAVGLTLVPSLGGFMGAYFVRGSWHPPRWTLAPIWGTLYSAMGYGSYIVWKELG-GFTEDAMVPLGLYTGQLALNWAWPPIFFGAMGWALADLLLVSGVATATTLAWHRVSPPAARLLYPYLAWLAFATVLNYYVWRDSGRRGGSRLAE--

3j9tY

0.13

0.11

0.86

1.03

wMUSTER

I----CASAIIFTSLGAAYGTAKSGVGICATPDL-LFKNIVPVIMAGIIAIYGLVVSVLVCY-SLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFV-GMILILIFAEVLGLYGLIVALLLNSRAC---------------

5a43A

0.14

0.10

0.75

1.16

wPPAS

IK--SLFAVIIGGSVGCTLRWLLSTKFNSLFPNLPPGTLVVNLLAGLIIGTLAYFLRQ-----------PHLDPFWKL-------TTGLCGGL-FSTFSVEVFALLQA----GNYIWALTSVLVHVIGSLITALGFFIITILF---------------

5a43A

0.13

0.10

0.76

1.13

dPPAS2

IK--SLFAVIIGGSVGCTLRWLLSTKFNSLFPNLPPGTLVVNLLAGLIIGTLAYFLRQ-----------PHLDPFWKLITT------GLCGGLSFSTFSVEVFALLQAGNYIWALTSVLVHVIGSLITALGFFIITILF-------------------

4uc1A

0.10

0.09

0.91

1.03

PPAS

MNM-DWALFLTFLAACGAPATTGALLKPDENPP-RWVFPLAWTSLYFLMSLAAMRVAQ------LEGSGQALAFYAAQLAFNTLWTPVFFGMMATALAVVMVMWLFVAATMWAFFQLDTWAGVLFVPYLIWATATTGLNFEAMRLWNRPEAR------

5tj5D

0.10

0.09

0.87

1.03

wMUSTER

A----CAAAMVLSCLGAAIGTAKSGIGIAGIPEL-IMKSLIPVVMSGILAIYGLVVAVLIAGNSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRKYMHQPRL-FVGIVLILIFSEVLGLYGMIVALILNTRG-S--------------

2mgyA

0.11

0.09

0.84

1.15

wPPAS

MPE-SWVPAVGLTLVPSLGGFMGAYFVRGEGPSHPWTLAPIWGTLYSAMGYGSYIVWKELGGFT--------------EDAMVPLGLYTGQLALNWAW--PPIFFGARQMGW------ALADLLLVSGVATATTLAWHVSPPA-YPSGRRGGSRLAE-

(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=-1.63

Estimated TM-score = 0.52±0.15

Estimated RMSD = 8.4±4.5Å

Download Model 2

C-score=-3.28

Download Model 3

C-score=-4.81

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.71

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	4ryiA	0.741	2.65	0.070	0.899
2	4uc1A	0.740	2.43	0.103	0.880
3	2jswA	0.680	3.49	0.100	0.949
4	2mgyA	0.662	3.69	0.098	0.968
5	1r0dA	0.642	3.99	0.045	0.937
6	3ay5A	0.639	3.79	0.096	0.918
7	2zw3A	0.613	3.27	0.091	0.835
8	4hr0A	0.603	3.82	0.045	0.848
9	3myrB	0.599	4.03	0.052	0.873
10	3ee4A	0.598	3.70	0.038	0.829

(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	3	4ryrA	MPG	Rep, Mult	41,44,45,130,131,134,137
2	0.07	3	1biqB	UUU	Rep, Mult	45,49,52,107,125,128
3	0.05	2	4ryqA	MPG	Rep, Mult	130,131,134,137
4	0.05	2	3locA	URA	Rep, Mult	137,140
5	0.03	1	4ryrA	DMS	Rep, Mult	38,42,85,131,135
6	0.02	1	4amjB	2CV	Rep, Mult	1,5
7	0.02	1	1ijdD	BCL	Rep, Mult	96,99
8	0.02	1	1xmeC	HAS	Rep, Mult	77,81
9	0.02	1	2wse1	CLA	Rep, Mult	84,91
10	0.02	1	1g42A	CA	Rep, Mult	74,77
11	0.02	1	2y00A	2CV	Rep, Mult	53,56,75,82
12	0.02	1	4rynA	MPG	Rep, Mult	44,51,55,59,118
13	0.02	1	1kf6O	CE1	Rep, Mult	42,43,46
14	0.02	1	1rsrB	UUU	Rep, Mult	42,100,103,132,135

	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	2htnG	0.560	3.88	0.072	0.772	1.16.3.1	NA
2	0.060	1h2aL	0.584	4.19	0.090	0.873	1.12.2.1	NA
3	0.060	2ix6A	0.554	4.87	0.073	0.892	1.3.3.6	NA
4	0.060	1rsrB	0.578	3.97	0.058	0.829	1.17.4.1	130,136
5	0.060	2wpnB	0.575	4.03	0.059	0.835	1.12.7.2	40
6	0.060	1cc1L	0.564	4.33	0.063	0.867	1.12.99.6	NA
7	0.060	1ivhA	0.547	4.76	0.049	0.867	1.3.99.10	129
8	0.060	1o9iA	0.580	4.23	0.071	0.854	1.11.1.6	40,43
9	0.060	2j2fA	0.561	3.87	0.047	0.772	1.14.19.2,1.14.99.6	NA
10	0.060	2rccA	0.541	4.35	0.026	0.797	1.17.4.1	NA
11	0.060	1smsA	0.581	3.78	0.059	0.791	1.17.4.1	NA
12	0.060	1uzrB	0.573	3.97	0.071	0.829	1.17.4.1	NA
13	0.060	2pfdB	0.535	4.30	0.059	0.804	2.1.2.5,4.3.1.4	132
14	0.060	1h2rL	0.586	4.16	0.090	0.873	1.12.2.1	46,51
15	0.060	2frvD	0.567	4.14	0.092	0.861	1.12.2.1	NA
16	0.060	1jkuA	0.578	4.33	0.065	0.861	1.11.1.6	NA
17	0.060	1u8vA	0.555	4.35	0.070	0.817	5.3.3.3	NA
18	0.060	2pnrB	0.527	4.25	0.046	0.778	2.7.11.2	NA
19	0.060	1fziA	0.582	4.00	0.076	0.829	1.14.13.25	NA
20	0.060	1xvgC	0.570	4.35	0.120	0.848	1.14.13.25	46,51

(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	0.28	0.741	2.72	0.07	0.90	4rymA	GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0033013 GO:0046906
1	0.26	0.738	2.44	0.10	0.88	5duoA	GO:0005886 GO:0006810 GO:0008289 GO:0016020 GO:0016021 GO:0033013 GO:0046906
2	0.22	0.680	3.49	0.10	0.95	2jswA	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
3	0.18	0.653	3.65	0.10	0.93	1r0dA	GO:0003779 GO:0005543 GO:0005737 GO:0005856 GO:0005905 GO:0006897 GO:0006898 GO:0006915 GO:0012505 GO:0016020 GO:0030136 GO:0030276 GO:0030665 GO:0031410 GO:0035091 GO:0043231 GO:0048471 GO:0072583
4	0.16	0.639	3.79	0.10	0.92	3ay5A	GO:0005634 GO:0005654 GO:0005737 GO:0007049 GO:0051726
5	0.15	0.613	3.27	0.09	0.84	2zw3A	GO:0005243 GO:0005737 GO:0005793 GO:0005886 GO:0005921 GO:0005922 GO:0006810 GO:0007154 GO:0007267 GO:0007565 GO:0007605 GO:0016020 GO:0016021 GO:0016264 GO:0016328 GO:0030054 GO:0030539 GO:0032355 GO:0032570 GO:0034599 GO:0044752 GO:0046697 GO:0055085
6	0.15	0.662	3.69	0.10	0.97	2mgyA	GO:0005497 GO:0005737 GO:0005739 GO:0005741 GO:0006694 GO:0006810 GO:0006811 GO:0006821 GO:0006869 GO:0007268 GO:0007568 GO:0008347 GO:0008503 GO:0010042 GO:0010266 GO:0010823 GO:0010940 GO:0014012 GO:0016020 GO:0016021 GO:0030325 GO:0031397 GO:0031965 GO:0031966 GO:0032570 GO:0032720 GO:0033574 GO:0042493 GO:0043065 GO:0043231 GO:0044325 GO:0045019 GO:0048265 GO:0048266 GO:0048678 GO:0050810 GO:0051901 GO:0051928 GO:0060242 GO:0060252 GO:0060253 GO:0070062 GO:0071222 GO:0071294 GO:0071476 GO:0072655 GO:0072656 GO:0098794 GO:0099565 GO:1903147 GO:1903579 GO:2000379
7	0.08	0.590	3.59	0.04	0.79	1h0nA	GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009262 GO:0009263 GO:0016491 GO:0046872 GO:0051259 GO:0051290 GO:0055114
8	0.07	0.593	3.74	0.03	0.81	4c3oA	GO:0008901 GO:0016151 GO:0016491 GO:0046872 GO:0055114
9	0.07	0.550	4.12	0.05	0.82	1e3dB	GO:0008901 GO:0016151 GO:0016491 GO:0046872 GO:0055114
10	0.07	0.534	3.93	0.04	0.78	4iubL	GO:0005886 GO:0008901 GO:0016020 GO:0016151 GO:0016491 GO:0033748 GO:0046872 GO:0055114
11	0.07	0.604	3.93	0.04	0.84	4ac8A	GO:0004748 GO:0005506 GO:0005829 GO:0005971 GO:0009186 GO:0009263 GO:0016491 GO:0030145 GO:0046872 GO:0055114
12	0.07	0.602	4.04	0.05	0.87	3myrD	GO:0008901 GO:0016151 GO:0016491 GO:0046872 GO:0055114
13	0.07	0.575	3.72	0.07	0.80	4ci0A	GO:0008901 GO:0016151 GO:0016491 GO:0046872 GO:0050454 GO:0050660 GO:0051536 GO:0055114
14	0.07	0.593	3.72	0.07	0.81	5a4mL	GO:0005886 GO:0006113 GO:0008901 GO:0009055 GO:0009061 GO:0016020 GO:0016151 GO:0016491 GO:0030288 GO:0033748 GO:0044569 GO:0046872 GO:0055114
15	0.07	0.592	3.69	0.03	0.80	3ayxA	GO:0008901 GO:0016151 GO:0016491 GO:0046872 GO:0055114
16	0.07	0.603	3.83	0.04	0.85	5dcsA	GO:0004748 GO:0009186 GO:0016491 GO:0046872 GO:0055114
17	0.07	0.574	4.41	0.05	0.86	2wpnB	GO:0008901 GO:0016151 GO:0016491 GO:0046872 GO:0051536 GO:0051539 GO:0055114
18	0.07	0.591	4.25	0.08	0.88	5aa5C	GO:0016151

Consensus prediction of GO terms

Molecular Function	GO:0046906	GO:0050839	GO:0005198	GO:0005102	GO:0032403	GO:0019904	GO:0003779
GO-Score	0.46	0.45	0.45	0.45	0.45	0.45	0.36
Biological Processes	GO:0033013	GO:0032507	GO:0030168	GO:0034329	GO:0030036	GO:0030865	GO:0034109	GO:0006897	GO:0012501	GO:0050794	GO:0007049
GO-Score	0.46	0.45	0.45	0.45	0.45	0.45	0.45	0.36	0.36	0.31	0.31
Cellular Component	GO:0016021	GO:0031256	GO:0005924	GO:0015630	GO:0031253	GO:1903561	GO:0044430	GO:0030662	GO:0098589	GO:0031981
GO-Score	0.46	0.45	0.45	0.45	0.45	0.45	0.45	0.36	0.36	0.31

(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.