I-TASSER results

I-TASSER results for job id Rv0443

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

Input Sequence in FASTA format

>protein (171 residues)
MASTDAAAQELLRDAFTRLIEHVDELTDGLTDQLACYRPTPSANSIAWLLWHSARVQDIQ
VAHVAGVEEVWTRDGWVDRFGLDLPRHDTGYGHRPEDVAKVRAPADLLSGYYHAVHKLTL
EYIAGMTADELSRVVDTSWNPPVTVSARLVSIVDDCAQHLGQAAYLRGIAR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MASTDAAAQELLRDAFTRLIEHVDELTDGLTDQLACYRPTPSANSIAWLLWHSARVQDIQVAHVAGVEEVWTRDGWVDRFGLDLPRHDTGYGHRPEDVAKVRAPADLLSGYYHAVHKLTLEYIAGMTADELSRVVDTSWNPPVTVSARLVSIVDDCAQHLGQAAYLRGIAR
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHCCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	999887599999999999999999999799988998598998974889999999999999999869998555687788879999987788789988877753799999999999999999999979988886578899998654456889999999999999999997669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MASTDAAAQELLRDAFTRLIEHVDELTDGLTDQLACYRPTPSANSIAWLLWHSARVQDIQVAHVAGVEEVWTRDGWVDRFGLDLPRHDTGYGHRPEDVAKVRAPADLLSGYYHAVHKLTLEYIAGMTADELSRVVDTSWNPPVTVSARLVSIVDDCAQHLGQAAYLRGIAR
Prediction	666662412300330153036204511650447304422477232000011110223231114136454214475046217171466343332346204514342620340152025203510650457306532475251412201200000240031101002134238
	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

CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHCCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
MASTDAAAQELLRDAFTRLIEHVDELTDGLTDQLACYRPTPSANSIAWLLWHSARVQDIQVAHVAGVEEVWTRDGWVDRFGLDLPRHDTGYGHRPEDVAKVRAPADLLSGYYHAVHKLTLEYIAGMTADELSRVVDTSWNPPVTVSARLVSIVDDCAQHLGQAAYLRGIAR

3cexA

0.35

0.33

0.95

2.24

MUSTER

-----AKVTQLSSETLDRAHERFEETLAQ-TVAEANT-PAPLIKSVTWL-WHTARELDLQISALNHSDPLWLSQHWTEKFALDLPDETEDWHHTPEEAAKVVVEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDKNWTPPVT-RQVRLVSAIDDAVHSGQAVYTRRLVK

3cexA

0.33

0.32

0.95

3.67

dPPAS

-----AKVTQLSSETLDRAHERFEETLAQT--VAEANTPAPLIKSVTWL-WHTARELDLQISALNHSDPLWLSQHWTEKFALDLPDETEDWHHTPEEAAKVVVEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDKNWTPPVT-RQVRLVSAIDDAVHSGQAVYTRRLVI

3cexA

0.33

0.32

0.95

4.78

wdPPAS

-----AKVTQLSSETLDRAHERFEETLAQTVAEANT--PAPLIKSVTW-LWHTARELDLQISALNHSDPLWLSQHWTEKFALDLPDETEDWHHTPEEAAKVVVEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDKNWTPPVT-RQVRLVSAIDDAVHSGQAVYTRRLVI

3cexA

0.33

0.31

0.94

2.60

wMUSTER

------KVTQLSSETLDRAHERFEETLAQTVAEANT--PAPLIKSVTWL-WHTARELDLQISALNHSDPLWLSQHWTEKFALDLPDETEDWHHTPEEAAKVVVEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDKNWTPPVT-RQVRLVSAIDDAVHSGQAVYTRRLVK

3cexA

0.33

0.32

0.95

4.15

wPPAS

-----AKVTQLSSETLDRAHERFEETLAQTVAEANT--PAPLIKSVTW-LWHTARELDLQISALNHSDPLWLSQHWTEKFALDLPDETEDWHHTPEEAAKVVVEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDKNWTPPVT-RQVRLVSAIDDAVHSGQAVYTRRLVI

3cexA

0.35

0.33

0.95

11.01

dPPAS2

-----AKVTQLSSETLDRAHERFEETLAQ-TVAEANT-PAPLIKSVTWL-WHTARELDLQISALNHSDPLWLSQHWTEKFALDLPDETEDWHHTPEEAAKVVVEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDKNWTPPVT-RQVRLVSAIDDAVHSGQAVYTRRLVI

3cexA

0.34

0.32

0.95

3.26

PPAS

-----AKVTQLSSETLDRAHERFEETLAQT-VAEANT-PAPLIKSVTWL-WHTARELDLQISALNHSDPLWLSQHWTEKFALDLPDETEDWHHTPEEAAKVVVEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDKNWTPPVT-RQVRLVSAIDDAVHSGQAVYTRRLVI

3cexA

0.34

0.32

0.95

5.60

Env-PPAS

-----AKVTQLSSETLDRAHERFEETLAQT-VAEANT-PAPLIKSVTWL-WHTARELDLQISALNHSDPLWLSQHWTEKFALDLPDETEDWHHTPEEAAKVVVEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDKNWTPPVT-RQVRLVSAIDDAVHSGQAVYTRRLVI

2ou6A

0.19

0.18

0.92

1.28

MUSTER

VQPDADPPHIGALVELTYARLTTLQAVEGLPEDQLWATAPGFANSIGTLLAHIAAVERVYHVLSFQGRDVTPEDDGAAYWGLTGKEGTAPARL---------PTLDELRAELADARAETLRVFAAKDDAWLAEPLGPGW----ANQHWAWFHVEDEVNHRGQLRLLRQVLA

2ou6A

0.20

0.18

0.92

1.71

dPPAS

DADPAFTPHIGALVELTYARLTTLQAVEGLPEDQLWATAPGFANSIGTLLAHIAAVERVYHVLSFQGRDVTPEDDGAAYWGLTGKEGTAPARL---------PTLDELRAELADARAETLRVFAAKDDAWLAEPLGPGW----ANQHWAWFHVEDEVNHRGQLRLLRQVLA

(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 4 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=1.17

Estimated TM-score = 0.87±0.07

Estimated RMSD = 2.8±2.0Å

Download Model 2

C-score=-1.72

Download Model 3

C-score=1.02

Download Model 4

C-score=-1.73

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	3cexA	0.918	0.95	0.340	0.947
2	2ou6A	0.698	3.01	0.179	0.848
3	4n6cA	0.694	3.16	0.094	0.860
4	5cogA	0.684	3.17	0.090	0.854
5	5civA	0.671	3.27	0.112	0.842
6	1rxqB	0.670	3.27	0.064	0.842
7	4x8bA	0.656	2.70	0.101	0.801
8	2qnlA	0.655	3.27	0.176	0.866
9	5cofA	0.638	3.08	0.112	0.807
10	2p1aB	0.632	3.00	0.081	0.766

(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	0.38	14	4x8bA	FE	Rep, Mult	52,156,159
2	0.05	2	3lu2B	ZN	Rep, Mult	52,58
3	0.03	1	1zyrN	STD	Rep, Mult	15,18,19,23
4	0.02	1	2qb0B	MN	Rep, Mult	69,92
5	0.02	1	4ea2A	MG	Rep, Mult	58,111
6	0.02	1	3t1gA	ZN	Rep, Mult	97,106
7	0.02	1	2p9i3	III	Rep, Mult	133,146,147,149,152,153,154,156
8	0.02	1	2b2rA	O	Rep, Mult	51,52

	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	2fiqC	0.442	5.46	0.083	0.789	2.7.1.144	76,125
2	0.060	1jtnA	0.323	5.57	0.060	0.550	3.2.1.17	130,136
3	0.060	2rgzB	0.451	4.96	0.099	0.766	1.14.99.3	112,150
4	0.060	2rd3D	0.464	4.90	0.068	0.778	3.5.99.2	47,53,111
5	0.060	1otwA	0.471	4.74	0.095	0.784	1.3.3.11	9,12,14,21,118
6	0.060	2z8yD	0.456	3.82	0.094	0.643	1.2.7.4,1.2.99.2	109
7	0.060	2pmzQ	0.481	4.81	0.031	0.760	2.7.7.6	150
8	0.060	2uuvD	0.427	5.35	0.019	0.754	2.5.1.26	NA
9	0.060	3i39X	0.456	3.80	0.040	0.626	1.2.99.2	116
10	0.060	1kraC	0.447	5.22	0.031	0.795	3.5.1.5	150
11	0.060	2qppB	0.456	5.00	0.087	0.778	1.14.99.3	125
12	0.060	1ynnJ	0.272	5.30	0.045	0.468	2.7.7.6	57,115,117
13	0.060	1a5lC	0.435	5.24	0.070	0.743	3.5.1.5	NA
14	0.060	3iam4	0.480	4.56	0.048	0.743	1.6.99.5	NA
15	0.060	1ynnD	0.442	5.36	0.061	0.795	2.7.7.6	NA
16	0.060	1ix3A	0.445	4.93	0.088	0.760	1.14.99.3	NA
17	0.060	3la4A	0.443	5.31	0.019	0.789	3.5.1.5	33
18	0.060	1tlbA	0.447	5.25	0.046	0.778	1.3.3.3	148,160
19	0.060	1frvB	0.474	4.18	0.084	0.690	1.12.2.1	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	0.45	0.711	3.15	0.19	0.87	2ou6A
1	0.32	0.682	3.07	0.07	0.85	1rxqB	GO:0005737 GO:0008270 GO:0016787 GO:0046872
2	0.16	0.683	3.17	0.09	0.85	5cogB	GO:0005634 GO:0005737 GO:0006312
3	0.07	0.476	4.51	0.06	0.76	1rcwB	GO:0005576 GO:0046872
4	0.06	0.373	5.78	0.06	0.71	5ee0A	GO:0000166 GO:0003924 GO:0005524 GO:0005525 GO:0005737 GO:0005829 GO:0005886 GO:0009651 GO:0016020 GO:0016787 GO:0016887 GO:0043022 GO:0043023 GO:0046872 GO:1901001
5	0.06	0.344	5.83	0.06	0.65	1z6tB	GO:0000166 GO:0001666 GO:0001843 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0006919 GO:0007275 GO:0007399 GO:0007420 GO:0007568 GO:0007584 GO:0008635 GO:0008656 GO:0010659 GO:0030154 GO:0030900 GO:0031072 GO:0034349 GO:0042802 GO:0042981 GO:0043065 GO:0043293 GO:0043531 GO:0051260 GO:0051402 GO:0070059 GO:0070062 GO:0071560 GO:0072432 GO:0097190 GO:0097193 GO:1902510 GO:2001235
6	0.06	0.345	4.94	0.04	0.56	3lomA	GO:0004311 GO:0004337 GO:0008299 GO:0016740 GO:0033386
7	0.06	0.324	5.50	0.04	0.55	4hkaA	GO:0004833 GO:0006569 GO:0006727 GO:0016491 GO:0019441 GO:0019442 GO:0020037 GO:0046872 GO:0048072 GO:0051213 GO:0055114 GO:0070189 GO:1901216
8	0.06	0.321	5.41	0.07	0.54	3npiA	GO:0003677 GO:0006351 GO:0006355
9	0.06	0.337	4.77	0.06	0.56	4a82A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042626 GO:0055085
10	0.06	0.336	5.38	0.05	0.59	2akzA	GO:0000015 GO:0000287 GO:0001917 GO:0004634 GO:0005615 GO:0005622 GO:0005737 GO:0005829 GO:0005886 GO:0006094 GO:0006096 GO:0016020 GO:0016829 GO:0043025 GO:0043204 GO:0043209 GO:0046872 GO:0061621 GO:0070062
11	0.06	0.373	5.32	0.07	0.64	1w36B	GO:0000166 GO:0000287 GO:0000724 GO:0003677 GO:0004003 GO:0004386 GO:0004518 GO:0004519 GO:0004527 GO:0005524 GO:0006281 GO:0006302 GO:0006310 GO:0006974 GO:0008854 GO:0009338 GO:0016787 GO:0032508 GO:0044355 GO:0046872 GO:0090305
12	0.06	0.309	5.74	0.06	0.58	3h70A	GO:0000287 GO:0003824 GO:0008152 GO:0009234 GO:0016829 GO:0016836 GO:0046872
13	0.06	0.331	5.63	0.05	0.59	2pqiB	GO:0006952 GO:0016787 GO:0017148 GO:0030598
14	0.06	0.302	4.92	0.04	0.49	5a9zAI	GO:0003723 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529 GO:0042254 GO:0070180
15	0.06	0.277	5.09	0.02	0.47	2qc1B	GO:0003009 GO:0004889 GO:0005216 GO:0005230 GO:0005886 GO:0005892 GO:0006810 GO:0006811 GO:0006812 GO:0007165 GO:0007271 GO:0007274 GO:0007528 GO:0009986 GO:0015464 GO:0016020 GO:0016021 GO:0019228 GO:0030054 GO:0031594 GO:0035094 GO:0042166 GO:0042391 GO:0045202 GO:0045211 GO:0046716 GO:0048630 GO:0050881 GO:0050905 GO:0070050 GO:0098655 GO:0099565
16	0.06	0.273	5.64	0.03	0.49	2xhfA	GO:0016491 GO:0051920 GO:0055114 GO:0098869
17	0.06	0.283	5.06	0.04	0.48	2pqgA	GO:0005737 GO:0006952 GO:0016787 GO:0017148 GO:0030598
18	0.06	0.321	5.07	0.07	0.53	2gviA	GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0016787	GO:0008270
GO-Score	0.36	0.32
Biological Processes	GO:0006310
GO-Score	0.31
Cellular Component	GO:0005737	GO:0043231
GO-Score	0.46	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.