I-TASSER results

I-TASSER results for job id Rv0970

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

Input Sequence in FASTA format

>protein (210 residues)
MIHDLMLRWVVTGLFVLTAAECGLAIIAKRRPWTLIVNHGLHFAMAVAMAVMAWPWGARV
PTTGPAVFFLLAAVWFGATAVVAVRGTATRGLYGYHGLMMLATAWMYAAMNPRLLPVRSC
TEYATEPDGSMPAMDMTAMNMPPNSGSPIWFSAVNWIGTVGFAVAAVFWACRFVMERRQE
ATQSRLPGSIGQAMMAAGMAMLFFAMLFPV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MIHDLMLRWVVTGLFVLTAAECGLAIIAKRRPWTLIVNHGLHFAMAVAMAVMAWPWGARVPTTGPAVFFLLAAVWFGATAVVAVRGTATRGLYGYHGLMMLATAWMYAAMNPRLLPVRSCTEYATEPDGSMPAMDMTAMNMPPNSGSPIWFSAVNWIGTVGFAVAAVFWACRFVMERRQEATQSRLPGSIGQAMMAAGMAMLFFAMLFPV
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	987589999999999999999999998468986435789999999999999985678889958999999999999999988645778766643578999999999999847788888888888888888888877777788888888866899999999999999999999999987578998766557899999999999999997569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MIHDLMLRWVVTGLFVLTAAECGLAIIAKRRPWTLIVNHGLHFAMAVAMAVMAWPWGARVPTTGPAVFFLLAAVWFGATAVVAVRGTATRGLYGYHGLMMLATAWMYAAMNPRLLPVRSCTEYATEPDGSMPAMDMTAMNMPPNSGSPIWFSAVNWIGTVGFAVAAVFWACRFVMERRQEATQSRLPGSIGQAMMAAGMAMLFFAMLFPV
Prediction	626332020000100011013001100146341322011001000030002001233251233211200332132100100233444433111011010021011000002332343444444444443423314234341434433331121021100101120002000111333445344443344001000032113013122244
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
MIHDLMLRWVVTGLFVLTAAECGLAIIAKRRPWTLIVNHGLHFAMAVAMAVMAWPWGARVPTTGPAVFFLLAAVWFGATAVVAVRGTATRGLYGYHGLMMLATAWMYAAMNPRLLPVRSCTEYATEPDGSMPAMDMTAMNMPPNSGSPIWFSAVNWIGTVGFAVAAVFWACRFVMERRQEATQSRLPGSIGQAMMAAGMAMLFFAMLFPV

4fbzA

0.14

0.11

0.81

1.03

wPPAS

MAAESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMYIITTFITTIAAAMYFAMATGFGVVVGDEALTIYWARYADWLFTTPLLL-AGANRN---TIATLIGLDVFMIGTGMIAAFAAT----------------------------------PGTRIAWWGISTGALLALLYVLVGTLSKDA--RGQSPEVASLFGRLRNLVIVLWLLYPV

4ke2A

0.13

0.12

0.92

1.24

dPPAS2

MNIDPAARAAAAAAASKAAVTAADAAAA------AATIAASAASVAAATAADD--------AAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKAL---ETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFA

4k5yA2

0.08

0.96

1.04

PPAS

--HYHVAAIINYLGHCISLVALLVAFVL-RSIRCLRNIIHANLIAAFILRNATWFVVQLLVTAAYNYFHVTNFFWMFGEGCYL------HTAIVLWDAYDRLRAWMFICIGWGVPFPIIVAWAIGKLYYDNEKCWAGKRPGVYTDYIYQGPMALVLLINFIFLFNIVRILMTKLRASTTSETIQARKAVKATLVLLPLLGITYMLAFVNE

4qi1A

0.13

0.11

0.86

1.03

wPPAS

VEGEGIWLALGTIGMLLGMLYFIADGLDVQDP--YVITILIPAIAAASYLSMFFGFGFTTPSQRDIGALVGIDAFMIVTGLVATLTKVVVARYAFWTISTISMVFLLYYLVAVFGEAVSDADEDTRS----------------------TFNALRNIILVTWAIYPVAWLVGT-----GLALTGLYGETLLFMVLDLVAKVGFGFILL-M

4k5yA2

0.08

0.96

1.21

dPPAS2

--HYHVAAIINYLGHCISLVALLVAFVLFRSIRCLRNIIHANLIAAFILRNATWFVVQLLVTAAYNYFHVTNFFWMFGEGCYLH------TAIVLWDAYDRLRAWMFICIGWGVPFPIIVAWAIGKLYYDNEKCWAGKRPGVYTDYIYQGPMALVLLINFIFLFNIVRILMTKLRASTTSETIQARKAVKATLVLLPLLGITYMLAFVNE

4ke2A

0.16

0.15

0.93

1.01

PPAS

MNIDPAARAAAAAAASKAAVTAADAAAA-----AATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAA-------SAAAAAVASAAKALETINVKAAYAAATANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP---

4hyjA

0.10

0.09

0.87

1.01

wPPAS

LLATQYMFWVGFVGMAAGTLYFLVERNSLAPEY-ATVAALVTFVAAIHYYFMKDAVGTSTPKLVIADVIMIVGGYIGESSINIA-GGFTQLGLWSYLIGCFAWIYIIYLLFTNVTKAAENKPAPIRD----------------------ALLKMRLFILIGWAIYPIGYAVTLFA----PGVEIQLVRELIYNFADLTNKVGFGLIAFFA

4w6vA2

0.11

0.96

1.16

dPPAS2

PINPVMIASLLVYVIAASVTLYFIYLFAFAKMSRKDRARLLVCFILLVSAAFFWVMGFEIPTVWFQSINALFIILLAPVFSWAPSSITK--FVIGILCAAAGFAVMMYAAQHVLSSGGAGVSTLGELCLSPIGLATMTLLAPDRMRG---QVMGLWFCASSLGNLAAGLIGGHVK---ADQLDMLPTLFARCSIALVICAAVLILLIVPI

3wt8A

0.15

0.12

0.80

1.00

wPPAS

FQTGTDAQWVVFAVMALAAIVFSIAVQFRPLPL-YYVNIAICTIAATAYYAMAVNGGDNKPADERQVIYARYIDWVFTTPLLL-TNMPAT---MIAWIMGADIAMIAFGIIGAFTVG-----------------------------------SYKWFYFVVGCIMLAVLAWGMINPIFKEE--LQKHKEYTGAYTTLLIYLIVLWVIYPI

4fbzA

0.11

0.10

0.88

1.10

dPPAS2

VGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMYIITTFITTIAAAMYFAMATGFGVTEANRNTIATLIGLDVFMIGTGMIAAFAATPGTRIAWWGISTGALLALLYVLVGTLSKDARGQSPEVA----------------------SLFGRLRNLVIVLWLLYPVVWILGTEGT---FGILPLYWETAAFMVLDLSAKVGFGVVLLRS

(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=-2.69

Estimated TM-score = 0.40±0.14

Estimated RMSD = 11.7±4.5Å

Download Model 2

C-score=-3.24

Download Model 3

C-score=-3.82

Download Model 4

C-score=-3.95

Download Model 5

C-score=-4.64

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	4fbzA	0.807	1.95	0.114	0.881
2	4qi1A	0.806	1.64	0.104	0.867
3	1uazA	0.804	1.69	0.077	0.867
4	1e0pA	0.801	1.73	0.082	0.867
5	4jr8A	0.799	1.75	0.132	0.867
6	4hyjA	0.797	1.78	0.092	0.876
7	3a7kA	0.796	1.66	0.083	0.857
8	2jafA	0.793	1.80	0.099	0.862
9	1h2sA	0.792	1.86	0.104	0.867
10	1xioA	0.791	1.96	0.099	0.867

(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	0.22	43	3a7kA	RET	Rep, Mult	61,76,80,96,99,100,103,162,165,166,169,196,200
2	0.09	12	1qhjA	PH1	Rep, Mult	14,21,157,194,197,198,201,202,205,209
3	0.03	5	1mgyA	BR	Rep, Mult	45,49,60,61,196,200
4	0.02	4	1p8hA	LI1	Rep, Mult	16,17,20,38,39,42,43,49
5	0.02	5	2i20A	LI1	Rep, Mult	111,152,155,156,159,160,163,167
6	0.01	2	3mbvA	BXC	Rep, Mult	20,23,35,38,39,42,49
7	0.01	3	1brrA	ARC	Rep, Mult	70,71,74,75,78,82
8	0.01	1	2i1xA	LI1	Rep, Mult	9,12,13,17,53
9	0.01	2	1brrA	ARC	Rep, Mult	149,150,153,157,202
10	0.01	3	1kmeA	SQU	Rep, Mult	40,43,44,47,51,60
11	0.01	2	1c8sA	LI1	Rep, Mult	96,100,103,104,166
12	0.01	2	2wscI	CLA	Rep, Mult	196,199,200
13	0.01	1	1jv6A	LI1	Rep, Mult	160,163,164,167,168
14	0.01	1	1c8sA	SQU	Rep, Mult	11,15,18,194,201
15	0.01	2	3am6A	CLR	Rep, Mult	17,18,21,22,205
16	0.01	1	1cwqA	TRD	Rep, Mult	13,42,43,49
17	0.01	2	1p8hA	LI1	Rep, Mult	111,156,159,160,163,164,167
18	0.00	1	1gzmB	C8E	Rep, Mult	10,190,191,194
19	0.00	1	3pdjB	3PJ	Rep, Mult	107,110
20	0.00	1	1jv6A	LI1	Rep, Mult	153,156,160,195,198

	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	1jswB	0.484	4.88	0.048	0.762	4.3.1.1	NA
2	0.060	3e04D	0.515	4.05	0.075	0.719	4.2.1.2	48
3	0.060	1y5nC	0.483	4.58	0.047	0.729	1.7.99.4	76
4	0.060	1f1oA	0.500	3.94	0.088	0.686	4.3.2.2	NA
5	0.060	1t3cA	0.411	5.37	0.066	0.681	3.4.24.69	NA
6	0.060	1occA	0.524	5.07	0.049	0.857	1.9.3.1	NA
7	0.060	3ig5A	0.489	5.70	0.068	0.848	6.3.2.2	NA
8	0.060	1i0aA	0.510	4.35	0.037	0.729	4.3.2.1	NA
9	0.060	1xmeA	0.561	4.74	0.078	0.852	1.9.3.1	NA
10	0.060	1k7wD	0.520	4.18	0.037	0.729	4.3.2.1	NA
11	0.060	1dofA	0.482	4.31	0.072	0.700	4.3.2.2	NA
12	0.060	2e9fB	0.513	4.32	0.037	0.724	4.3.2.1	NA
13	0.060	3iam4	0.469	5.17	0.060	0.729	1.6.99.5	NA
14	0.060	3gzhA	0.498	5.10	0.071	0.790	4.3.2.2	NA
15	0.060	1cc1L	0.495	5.06	0.031	0.767	1.12.99.6	NA
16	0.060	1qleA	0.486	4.98	0.069	0.781	1.9.3.1	NA
17	0.060	1vdkA	0.471	5.04	0.074	0.752	4.2.1.2	NA
18	0.060	2fenD	0.490	4.40	0.039	0.700	5.5.1.2	NA
19	0.060	1m56A	0.552	4.81	0.071	0.871	1.9.3.1	42

(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	0.41	0.789	2.06	0.08	0.87	1cwqA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
1	0.32	0.808	1.66	0.08	0.87	2z55A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
2	0.32	0.776	2.20	0.13	0.87	5awzA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
3	0.29	0.807	1.95	0.11	0.88	4fbzA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
4	0.28	0.801	1.70	0.13	0.87	4l35A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
5	0.28	0.795	1.68	0.08	0.86	3qbgA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
6	0.27	0.718	2.40	0.05	0.84	4yziA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220 GO:0046872
7	0.27	0.798	1.76	0.10	0.86	5ahzA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
8	0.26	0.806	1.64	0.10	0.87	4qi1A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
9	0.26	0.797	1.78	0.09	0.88	4hyjA	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
10	0.26	0.693	1.64	0.09	0.74	1c8sA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
11	0.25	0.782	2.10	0.09	0.89	5azdA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
12	0.25	0.775	2.09	0.12	0.86	3am6A	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
13	0.24	0.745	2.35	0.12	0.86	4klyB	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
14	0.23	0.781	2.42	0.05	0.89	4xtnA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
15	0.22	0.804	1.69	0.08	0.87	1uazA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
16	0.21	0.788	1.85	0.13	0.86	2ksyA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
17	0.21	0.698	2.58	0.04	0.84	4knfC	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
18	0.21	0.725	2.10	0.12	0.81	4jq6B	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220

Consensus prediction of GO terms

Molecular Function	GO:0005216	GO:0009881
GO-Score	0.86	0.71
Biological Processes	GO:0034220	GO:0015992	GO:0018298	GO:0007602
GO-Score	0.86	0.71	0.71	0.71
Cellular Component	GO:0016021	GO:0005886
GO-Score	0.86	0.71

(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.