I-TASSER results

I-TASSER results for job id Rv1517

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

Input Sequence in FASTA format

>protein (254 residues)
MWTMVLLLGLGMAIDPARLGLAVVMLSRRRPMLNLFAFWVGGMVAGVGIALAVLVFMRDV
ALAAIQGVVSAANEFREAVGILAGGRLHIVIGVIMLLLAARMVARARAQVGVPVGPVGVA
DGGMSALALAQRPPGLVARLEVRTQQMLQGDVVWPAFVVGVASSAPPFESVVALTVIMAS
GAEIGTQLGAFVVFTLLVLAVIEIPLVAYLAIPQQTQQVMLRFQDWVRSNRRQISLTILI
GVGFLFLYQGVTSL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MWTMVLLLGLGMAIDPARLGLAVVMLSRRRPMLNLFAFWVGGMVAGVGIALAVLVFMRDVALAAIQGVVSAANEFREAVGILAGGRLHIVIGVIMLLLAARMVARARAQVGVPVGPVGVADGGMSALALAQRPPGLVARLEVRTQQMLQGDVVWPAFVVGVASSAPPFESVVALTVIMASGAEIGTQLGAFVVFTLLVLAVIEIPLVAYLAIPQQTQQVMLRFQDWVRSNRRQISLTILIGVGFLFLYQGVTSL
Prediction	CCHHHHHHHHHHHHCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	96569999999984766899889997698757899999999999999999999998644567764555445667777788765545678999999999999998565555667776666677777666677889866788999999875896477888888765898889999999998688667899999999999999999999999866688899999999999998756899999999999999856559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MWTMVLLLGLGMAIDPARLGLAVVMLSRRRPMLNLFAFWVGGMVAGVGIALAVLVFMRDVALAAIQGVVSAANEFREAVGILAGGRLHIVIGVIMLLLAARMVARARAQVGVPVGPVGVADGGMSALALAQRPPGLVARLEVRTQQMLQGDVVWPAFVVGVASSAPPFESVVALTVIMASGAEIGTQLGAFVVFTLLVLAVIEIPLVAYLAIPQQTQQVMLRFQDWVRSNRRQISLTILIGVGFLFLYQGVTSL
Prediction	52110132031103313200000000034411200001101122112132010000022133443433333344344344423233010000010021001101324454544444353444555244244654442440343034115540010000112022223320010001012343432220001321323133110110000001153033004302300443412000000112111101222355
	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                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCC
MWTMVLLLGLGMAIDPARLGLAVVMLSRRRPMLNLFAFWVGGMVAGVGIALAVLVFMRDVALAAIQGVVSAANEFREAVGILAGGRLHIVIGVIMLLLAARMVARARAQVGVPVGPVGVADGGMSALALAQRPPGLVARLEVRTQQMLQGDVVWPAFVVGVASSAPPFESVVALTVIMASGAEIGTQLGAFVVFTLLVLAVIEIPLVAYLAIPQQTQQVMLRFQDWVRSNRRQISLTILIGVGFLFLYQGVTSL

2n4xA

0.15

0.10

0.67

1.44

wPPAS

LM--AFALGILSVFSP------VLVV--PGRALDAFLIVAGLTISMLILGYTA---------------------------SLFFGFFRVVAMLFLLIFALILLS---------------------------ELDEKVSIFASRMTSGLSWKSFFFGMLLAFLWL-PILPFAGIAISQTLLSEN--------PLVMLSYGLGMAVTIAAVFKMGEK----------FVKANFRKVTGAIVLLYLAYFALTEVLLL

4bwzA2

0.15

0.12

0.78

1.30

dPPAS2

VGKEAFLVAVLGVALPFLGGYLYGLEI---GFETLPALFLGTALVSVGITARVLQELG-------------VLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVI--------AILGKVLGGFLGALTQGVRSALTVGCGMAPRGEVGLIVAALGLKAGA-VNEEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE--------------------------------

4bwzA2

0.14

0.11

0.78

1.24

PPAS

VGKEAFLVAVLGVALPFLGGYLYGLEIGFE--TLPALFLGTALVASVGITARVLQELGVLSRPYSRIILG-------------AAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVI--------AILGKVLGGFLGALTQGVRSALTVGCGMA-PRGEVGLIVAALGLKAGAVNEEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE--------------------------------

4bwzA2

0.13

0.10

0.76

1.16

wPPAS

VGKEAFLVAVLGVALPFLGGYLYGLE----GFETLPALFLGTALVATSVGITARVLQELGVLSRPYSRIILG-----------AAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGT------------AILGKVLGGFLGAL-TQGVRSALTVGCGMAPRGEVGLIVAALGLKAGA-VNEEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE--------------------------------

4ke2A

0.14

0.11

0.77

1.03

dPPAS2

-----------MNIDPAARAAAAAAA----SKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAA--ATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP-----------------------------------------

2n4xA

0.13

0.09

0.70

1.10

PPAS

LM--AFALGILSVFSP------VLVVGSRGRALDAFLIVAGLTISMLILGYTA---------------------------SLFFGFFRVVAMLFLLIFALILLSDELDE--------------------------KVSIFASRMTSGLSWKSFFFGMLLAFLWLPAILPFAGIAISQTLLSEN--------PLVMLSYGLGMAVTIAAVFKMGEK------FVKANFQLIR-KVTGAIVLLYLAYFALTEVLLL

4czbA2

0.09

0.07

0.75

1.15

wPPAS

VIKTVVRLDITFLITLLISGFIFNMV--NLPYTSPVGYLFGAITA-----ATLIPVFSRVRTNP----------------AITLEAESIFNDPLGIVSTSVILGLFGLFSLS-----------------------------MLENYFI----PGLLVALGSIFL---ARPLGVFLGLIGSKHSFKEKLYFALE--VVPAALAVTVGIEILKNADKIPASITKYITPTDIAG-TIIIGTFMTILLSVILEASW-L

4czbA2

0.09

0.07

0.76

1.07

PPAS

VIKTVVRLDITFLITLLISGFIFNMVL-NLPYTSPVGYLFGAITA-----ATLIPVFSRVRTNP----------------AITLEAESIFNDPLGIVSTSVILGLFGLFSLS-----------------------------MLENYFI----PGLLVALGSIFL---ARPLGVFLGLIGSKHSFKEKLYFALE--VVPAALAVTVGIEILKNADKIPASITKYITPTDIAGTIIIGTFMTILLSVILEASWAGM

4cadC

0.08

0.07

0.86

1.01

PPAS

--NPKLYFLSTFVVTILWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIISTILIAKK-------------KDFINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIP--------------FGGSISQFQFSGGDFVPVLFLLLLAAT--SLFKASILFGIFW----SLWHFPLIFVNNSYQYEIFNQSIWYGLNFFLSILPMGIIITWMCLAIIFHFLINLNQELITQDTKIIETGVLFLVAAAIILYDKKMF

4ikvA2

0.09

0.08

0.92

1.00

PPAS

ETFISLVGILGIII--PIIYFVVMYRSPKTTAEERSRVIAYIPLFVASAMFWAIQEQGSTILANYADKRTQLDVAGIHLSPAWFQSLNPLFIIILAPVFAWMWVKLGKRQPTIPQKFALGLLFAGL--------SFIVILVPGHLSGGGLVHPIWLVLSYFIVVLGELCLSPVGLSATTKLAPAAFSQTMSLWFLSNAAAQAINAQLVRFYTPE--------NETAYFGT--IGGAALVLGLILLAIAPRIGRL

(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=-3.22

Estimated TM-score = 0.35±0.12

Estimated RMSD = 13.5±4.0Å

Download Model 2

C-score=-3.61

Download Model 3

C-score=-4.40

Download Model 4

C-score=-4.72

Download Model 5

C-score=-4.44

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	4bwzA	0.642	2.68	0.111	0.752
2	4czbA2	0.604	3.28	0.078	0.744
3	4cz8A2	0.584	3.26	0.117	0.721
4	4n7wA	0.569	3.86	0.100	0.740
5	3zuxA	0.567	3.70	0.070	0.721
6	1zcdA	0.553	3.66	0.123	0.697
7	2j2fA	0.450	5.57	0.081	0.728
8	3dhiA	0.441	5.43	0.069	0.717
9	1mhzD	0.439	5.57	0.055	0.724
10	5aezA	0.431	5.65	0.068	0.709

(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	0.06	3	3bvdA	XE	Rep, Mult	158,161,206,207
2	0.06	3	1brrC	ARC	Rep, Mult	170,192,196
3	0.06	3	1xvgA	BRJ	Rep, Mult	12,13,16,88,91,92
4	0.04	2	3cz3A	NUC	Rep, Mult	203,205,206
5	0.02	1	1vf5S	III	Rep, Mult	25,26
6	0.02	1	1ocoB	HEA	Rep, Mult	198,199
7	0.02	1	3zuyA	PTY	Rep, Mult	13,17,20,41,95,98,99,102
8	0.02	1	4bo3B	U98	Rep, Mult	10,83,90,91
9	0.02	1	1mhy1	III	Rep, Mult	6,7,10,11,13,14,15,18,19,140,144
10	0.02	1	3zvwC	MG	Rep, Mult	113,114
11	0.02	1	1vltA	ASP	Rep, Mult	101,105
12	0.02	1	3ri5B	UND	Rep, Mult	28,31
13	0.02	1	3d9sB	PS6	Rep, Mult	6,181
14	0.02	1	4ub8h	CLA	Rep, Mult	89,92
15	0.02	1	2bhwA	CLA	Rep, Mult	17,19
16	0.02	1	2wyiA	PG0	Rep, Mult	143,209
17	0.02	1	3k7tA	GP7	Rep, Mult	134,135
18	0.02	1	3asoA	DMU	Rep, Mult	194,197
19	0.02	1	3zuxA	TCH	Rep, Mult	4,8,148,149,150

	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	2fonB	0.391	5.61	0.045	0.614	1.3.3.6	141
2	0.060	1mhyB	0.388	5.27	0.061	0.618	1.14.13.25	35,99
3	0.060	2vycA	0.382	5.30	0.045	0.583	4.1.1.19	NA
4	0.060	1hm7B	0.405	5.07	0.056	0.602	4.2.3.7,4.6.1.5	NA
5	0.060	1hm7A	0.377	5.65	0.056	0.598	4.2.3.7,4.6.1.5	NA
6	0.060	1fziA	0.434	5.48	0.063	0.713	1.14.13.25	NA
7	0.060	2yyjA	0.390	5.87	0.052	0.642	1.14.13.3	NA
8	0.060	2vuaA	0.307	6.01	0.051	0.524	3.4.24.69	188
9	0.060	1js4A	0.387	5.56	0.079	0.598	3.2.1.4	NA
10	0.060	2bq1I	0.384	5.26	0.108	0.610	1.17.4.1	NA
11	0.060	3dy5A	0.385	6.06	0.023	0.665	1.13.11.40,4.2.1.92	NA
12	0.060	1q5nA	0.393	5.79	0.025	0.646	5.5.1.2	NA
13	0.060	1w07B	0.397	5.73	0.045	0.630	1.3.3.6	NA
14	0.060	1h19A	0.385	5.82	0.044	0.653	3.3.2.6	171
15	0.060	1g87B	0.384	5.91	0.056	0.630	3.2.1.4	NA
16	0.060	2z1qB	0.383	5.56	0.052	0.598	1.3.99.3	141
17	0.060	2p0mB	0.390	5.77	0.043	0.642	1.13.11.33	NA
18	0.060	1ks8A	0.400	5.71	0.033	0.650	3.2.1.4	NA
19	0.060	1ksdA	0.401	5.70	0.055	0.646	3.2.1.4	211

(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	0.09	0.642	2.68	0.11	0.75	4bwzA	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
1	0.07	0.567	3.70	0.07	0.72	3zuxA	GO:0016020 GO:0016021
2	0.07	0.434	5.68	0.09	0.72	2uw1B
3	0.06	0.439	5.54	0.08	0.73	2xz1A	GO:0006629 GO:0006631 GO:0006633 GO:0009507 GO:0009536 GO:0016491 GO:0045300 GO:0046872 GO:0055114
4	0.06	0.583	3.84	0.10	0.76	4cz8A	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
5	0.06	0.610	3.57	0.10	0.78	4czbB	GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600
6	0.06	0.312	5.68	0.05	0.51	4rpfA	GO:0000166 GO:0004413 GO:0005524 GO:0005737 GO:0006566 GO:0008652 GO:0009088 GO:0016301 GO:0016310 GO:0016740
7	0.06	0.571	3.53	0.11	0.71	4atvA	GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0006885 GO:0015081 GO:0015297 GO:0015491 GO:0015992 GO:0016020 GO:0016021 GO:0035725 GO:0055085 GO:0098655
8	0.06	0.262	5.80	0.05	0.43	3i48A	GO:0005576 GO:0008081 GO:0046872
9	0.06	0.277	5.17	0.05	0.41	1za0A	GO:0005618 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0040007 GO:0045300 GO:0046872 GO:0055114
10	0.06	0.569	3.86	0.10	0.74	4n7wA	GO:0016020 GO:0016021
11	0.06	0.276	5.47	0.06	0.44	1u0uA	GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
12	0.06	0.230	6.04	0.03	0.39	2w2hA	GO:0000307 GO:0003677 GO:0003682 GO:0005634 GO:0005654 GO:0006351 GO:0006355 GO:0006468 GO:0007049 GO:0008024 GO:0016032 GO:0016538 GO:0017069 GO:0044212 GO:0045737 GO:0045944 GO:0051301 GO:0097322 GO:1900364 GO:1901409
13	0.06	0.243	5.91	0.05	0.41	1pv9B	GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
14	0.06	0.300	6.25	0.04	0.52	3ug4C	GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046373 GO:0046556
15	0.06	0.243	6.20	0.04	0.42	1t6lA	GO:0003677 GO:0006260 GO:0019012 GO:0019079 GO:0030337 GO:0039686 GO:0042025
16	0.06	0.214	6.08	0.07	0.37	2fckA	GO:0008080 GO:0016740 GO:0016746
17	0.06	0.250	5.60	0.04	0.40	3lb9A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176 GO:0045493
18	0.06	0.233	4.46	0.06	0.33	2m89A	GO:0006950

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0015298	GO:0015078
GO-Score	0.30	0.30	0.30
Biological Processes	GO:0015992	GO:0098662
GO-Score	0.30	0.30
Cellular Component	GO:0031224
GO-Score	0.33

(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.