I-TASSER results

I-TASSER results for job id Rv0461

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

Input Sequence in FASTA format

>protein (174 residues)
MPDFDTGAHSQRFLSLAGQQDRAGKSWPGSTPKPQEDPVGVAPSASVEVLGSEPAATLAH
SVTVPGRYTYLKWWKFVLVVLGVWIGAGEVGLSLFYWWYHTLDKTAAVFVVLVYVVACTV
GGLILALVPGRPLITALSLGVMSGPFASVAAAAPLYGYYYCERMSHCLVGVIPY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPDFDTGAHSQRFLSLAGQQDRAGKSWPGSTPKPQEDPVGVAPSASVEVLGSEPAATLAHSVTVPGRYTYLKWWKFVLVVLGVWIGAGEVGLSLFYWWYHTLDKTAAVFVVLVYVVACTVGGLILALVPGRPLITALSLGVMSGPFASVAAAAPLYGYYYCERMSHCLVGVIPY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEHCCC
Conf.Score	998889999998889999887788999899999999999888899899999999999998888887589986457899999999988888888888887655554679999999999999999999858986567888998876789998888778888777446656765689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPDFDTGAHSQRFLSLAGQQDRAGKSWPGSTPKPQEDPVGVAPSASVEVLGSEPAATLAHSVTVPGRYTYLKWWKFVLVVLGVWIGAGEVGLSLFYWWYHTLDKTAAVFVVLVYVVACTVGGLILALVPGRPLITALSLGVMSGPFASVAAAAPLYGYYYCERMSHCLVGVIPY
Prediction	634244463664344344445566554554545366553455545447445653454446333243434204302000001122322232020022213331442120000013133133111011104733211010212232333222232312021003224311003246
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEHCCC
MPDFDTGAHSQRFLSLAGQQDRAGKSWPGSTPKPQEDPVGVAPSASVEVLGSEPAATLAHSVTVPGRYTYLKWWKFVLVVLGVWIGAGEVGLSLFYWWYHTLDKTAAVFVVLVYVVACTVGGLILALVPGRPLITALSLGVMSGPFASVAAAAPLYGYYYCERMSHCLVGVIPY

4mfjA1

0.17

0.96

0.95

MUSTER

MMDPETGLEERTAAWLTELDELGPPAEPVRLPRGEEARDLLRRLEVPELDAEEIVAAAPDPDRDPAL-----WWLLERTHHAIVRHMGDHRAKPRGGPPLPYEGGAAARYFHVYVFLATVPAVRRFHAEGIPEVGWETLTQLGELVAIHRRKYGQGGMNMQWWTTYHLRGIL--

4ozvA1

0.07

0.95

0.69

dPPAS

------ADLVPPPGYYAAVGERKAGSCPAVPPPYTGSLVFTSKYEGSDSARATLNVKAEKTFRSQIKERGATKLVTQYMRSGRDGDLACALNWMSAWARADDFNHTGKSMRKWALGSLSGAYMRLKFSSSRPLAAHAEQSREIEDWFARLGTQVVRDWSSFRLGGEVTRVFS--

4ryiA

0.20

0.11

0.57

0.71

wdPPAS

----------------------------------------------------------------------MK--KSSIIVFFLTYGLFYVSSVLFRTWYDALEKTIGMIWAVLFGLIALSVAIIYNNYGFKYFQFSLFLATVDCLLVAITTLLLIMFSSNLSKVSAWL--LIPY

5an8A

0.09

1.00

0.80

wMUSTER

ILQREFSAPCQSLSRKFTEWCYGPVRVSLYDLASVDSWEENSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLCFLAIELLVSSLVL

4ryiA

0.19

0.11

0.56

0.87

wPPAS

----------------------------------------------------------------------MK--KSSIIVFFLTYGLFYVSSVLFRTWYDALEKTIGMIWAVLFGLIALSVAIIYNNYGFKYFQFSLFLATVDCLLVAITTLLLIMFSSNLSKVS----ALIPY

4ryiA

0.13

0.08

0.60

0.83

dPPAS2

---------------------------------------------------------------------MKKSSIIVFFLTYGLFYVSSVLFPIDRTWYDALEKTIGMIWAVLFGLIALSVAIIYNNYGFKPAFSYFQFSLFLATVDCLLVAITTLLLIMFSSNLSKVSALIPY

4mfjA1

0.17

0.95

0.93

PPAS

MMDPETGLEERTAAWLTELDELGPPAEPVRLPRGEEARDLLRRLEVPELDAEEIVAAAPDPDRDPA-----LWWLLERTHHAIVRHMGDHRAKPRGGPPLPYEGGAAARYFHVYVFLATVPAVRRFH-AERGIPDEVGWETLTQLGELVAIHRRKYGQGMQWWTTYHLRGIL--

2fflA3

0.13

0.12

0.90

0.54

Env-PPAS

-----TGPVASKVLALYEKYESSGGSKHIAAQTVSRSLAVPIPSGTIPFL----IRLLQIALTPHVKLELLGDAFLKCSLALHLHALPTLTEGALTRMRQSANSVLGRLTKRFPSVVSEVIIESHPKIQPDS-------KVYGDTFEAILAAILLACEEAAGAFVREH--VLPQ

4ozvA1

0.09

0.08

0.93

0.88

MUSTER

VPPPG------YYAAVGERKAGSCPAVPPPYTGSLVFTSKYEGSDSARATLNVKAEKTFRSQIKDITERGATKLVTQYMRSGRDGDLACALNWMSAWARASDDFNHTGKSMRKWALGSLSGAYMRLKFSSRPLAAHAEQSREIEDWFARLGTQVVRDWS--FRLGGEV-----F

2mfzA

0.07

0.05

0.72

0.65

dPPAS

---------------------------GSGNSVTSGGYGYGTSAAAGAGVAAGSYAGAVNRLSSAEAASRVSSNIAAIASGGASALPSVISNIYSGVVASGVSSNEALIQALLELLSALVHVLSSASIGNVSSVGVDSTLNVVQDSVGQYVG----------------------

(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=-3.01

Estimated TM-score = 0.37±0.13

Estimated RMSD = 12.0±4.4Å

Download Model 2

C-score=-4.73

Download Model 3

C-score=-3.72

Download Model 4

C-score=-5.00

Download Model 5

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	4mfjA	0.854	2.01	0.161	0.966
2	2pulA	0.514	4.68	0.031	0.828
3	2pywA	0.509	4.74	0.049	0.839
4	4av3A	0.492	4.99	0.048	0.782
5	4aeeA	0.486	5.66	0.061	0.897
6	3k92A	0.484	5.00	0.061	0.776
7	2dqbE	0.482	4.34	0.095	0.701
8	3m1cA	0.482	4.87	0.078	0.776
9	5f7sA	0.481	5.01	0.055	0.828
10	3aoeE	0.481	5.04	0.067	0.782

(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	4	3ehbB	HEA	Rep, Mult	113,149
2	0.08	4	2e76A	CLA	Rep, Mult	149,156
3	0.06	3	3glnA	XE	Rep, Mult	78,79,95
4	0.04	2	3hb3A	CA	Rep, Mult	83,86,88,90,92
5	0.04	2	3zvmA	MG	Rep, Mult	93,103
6	0.02	1	1xmeC	HAS	Rep, Mult	108,112
7	0.02	1	4zbiB	4M6	Rep, Mult	76,79,83,96,98,99,108,112,115,116,142
8	0.02	1	2h8pC	GOA	Rep, Mult	157,158
9	0.02	1	3aoeD	LEU	Rep, Mult	78,81,82,83,86
10	0.02	1	3klzB	FMT	Rep, Mult	135,137
11	0.02	1	2q69A	CA	Rep, Mult	119,120,121
12	0.02	1	3k7tA	GP7	Rep, Mult	28,29
13	0.02	1	2xtvA	MC3	Rep, Mult	74,78
14	0.02	1	4ub8h	CLA	Rep, Mult	141,144
15	0.02	1	2o012	CLA	Rep, Mult	91,92
16	0.02	1	1ucgA	MN	Rep, Mult	100,104

	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	3hf1B	0.469	4.95	0.061	0.776	1.17.4.1	NA
2	0.060	1j0hA	0.464	5.52	0.042	0.822	3.2.1.135	98
3	0.060	1z45A	0.460	5.32	0.066	0.810	5.1.3.2,5.1.3.3	101
4	0.060	3etdA	0.470	5.21	0.087	0.822	1.4.1.3	143
5	0.060	2z8yP	0.470	4.66	0.036	0.747	2.3.1.169	31,58,118
6	0.060	1j0kA	0.465	5.67	0.054	0.839	3.2.1.135	147
7	0.060	2nvrA	0.466	5.30	0.082	0.782	3.5.1.98	103,105
8	0.060	2occN	0.474	4.89	0.088	0.759	1.9.3.1	146,155,165
9	0.060	1euzF	0.467	5.07	0.048	0.764	1.4.1.3	NA
10	0.060	2pulA	0.514	4.68	0.031	0.828	2.7.1.100	NA
11	0.060	1bvzA	0.455	5.64	0.071	0.816	3.2.1.135	92
12	0.060	1ah7A	0.476	4.03	0.058	0.684	3.1.4.3	NA
13	0.060	3fvyA	0.471	5.44	0.070	0.851	3.4.14.4	NA
14	0.060	3k92A	0.484	5.00	0.061	0.776	1.4.1.2	51,111
15	0.060	1jk0A	0.467	5.14	0.068	0.810	1.17.4.1	NA
16	0.060	2dqbA	0.448	4.23	0.055	0.695	3.1.5.1	119,139
17	0.060	3l4uA	0.461	5.40	0.061	0.828	3.2.1.20,3.2.1.3	NA
18	0.060	1ea9C	0.463	5.44	0.067	0.810	3.2.1.54	NA
19	0.060	1gaxA	0.468	4.66	0.040	0.724	6.1.1.9	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	0.19	0.854	2.01	0.16	0.97	4mfjA	GO:0016757
1	0.07	0.514	4.68	0.03	0.83	2pulA	GO:0000166 GO:0005524 GO:0008652 GO:0009086 GO:0016301 GO:0016310 GO:0016740 GO:0019284 GO:0019509 GO:0046522
2	0.07	0.509	4.74	0.05	0.84	2pywA	GO:0000166 GO:0005524 GO:0005829 GO:0008652 GO:0009086 GO:0016301 GO:0016310 GO:0016740 GO:0019509 GO:0042802 GO:0046522 GO:0071281 GO:0071369 GO:0071732
3	0.07	0.498	4.78	0.04	0.77	4av3B	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
4	0.07	0.497	4.90	0.07	0.80	4av6A	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
5	0.07	0.438	5.12	0.07	0.71	4a01A	GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
6	0.06	0.431	5.13	0.06	0.76	2ig7B	GO:0000166 GO:0004103 GO:0004305 GO:0005524 GO:0005829 GO:0006629 GO:0006646 GO:0006656 GO:0006657 GO:0008654 GO:0016301 GO:0016310 GO:0016740 GO:0046474
7	0.06	0.378	5.24	0.08	0.65	3f7wA
8	0.06	0.380	4.39	0.06	0.57	3l0iC	GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
9	0.06	0.355	5.52	0.05	0.62	2ckpB	GO:0000166 GO:0004103 GO:0004104 GO:0004305 GO:0004871 GO:0005524 GO:0005737 GO:0005829 GO:0006580 GO:0006629 GO:0006646 GO:0006656 GO:0006657 GO:0006869 GO:0007165 GO:0008144 GO:0008654 GO:0009636 GO:0016301 GO:0016310 GO:0016740 GO:0019695 GO:0033265 GO:0042803 GO:1904681
10	0.06	0.434	5.28	0.06	0.75	3i0oA	GO:0000166 GO:0016740
11	0.06	0.377	4.39	0.05	0.57	4v7oA5	GO:0000502 GO:0005634 GO:0005737 GO:0005839 GO:0006281 GO:0006974 GO:0010499 GO:0010952 GO:0016504 GO:0034515 GO:0043248 GO:0043486 GO:0061136 GO:0070577 GO:0070628 GO:1990236 GO:1990237
12	0.06	0.312	6.17	0.01	0.60	5bv7A	GO:0004607 GO:0004623 GO:0005576 GO:0005615 GO:0006629 GO:0006644 GO:0006656 GO:0008202 GO:0008203 GO:0008374 GO:0016740 GO:0016746 GO:0030301 GO:0034186 GO:0034364 GO:0034372 GO:0034375 GO:0034435 GO:0042157 GO:0042158 GO:0042632 GO:0043691 GO:0046470 GO:0046688 GO:0051384 GO:0070062 GO:0090107
13	0.06	0.341	4.77	0.06	0.53	3hr8A	GO:0000150 GO:0000166 GO:0000400 GO:0000730 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0004520 GO:0005524 GO:0005737 GO:0005829 GO:0006259 GO:0006281 GO:0006310 GO:0006312 GO:0006974 GO:0008094 GO:0009432 GO:0010212 GO:0042148
14	0.06	0.379	4.66	0.06	0.59	3l0mA	GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
15	0.06	0.254	5.72	0.05	0.47	1sskA	GO:0003723 GO:0019012 GO:0019013 GO:0030430 GO:0044172 GO:0044177 GO:0044220
16	0.06	0.330	4.81	0.06	0.53	3s6fA	GO:0008080
17	0.06	0.201	3.82	0.05	0.29	1aoyA	GO:0003677 GO:0003700 GO:0005737 GO:0006310 GO:0006351 GO:0006355 GO:0006525 GO:0006526 GO:0008652 GO:0034618 GO:0042150 GO:0044212 GO:0051259 GO:2000143
18	0.06	0.236	3.93	0.08	0.34	1y9oA	GO:0003998 GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0016740
GO-Score	0.38
Biological Processes	GO:0019509	GO:0016310	GO:0015992	GO:0035725	GO:0071369	GO:0019284	GO:0071732	GO:0071281
GO-Score	0.13	0.13	0.13	0.13	0.07	0.07	0.07	0.07
Cellular Component	GO:0005887	GO:0005829
GO-Score	0.13	0.07

(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.