I-TASSER results

I-TASSER results for job id Rv2557

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

Input Sequence in FASTA format

>protein (224 residues)
MTGGATGALPRTMKEGWIVYARSTTIQAQSECIDTGIAHVRDVVMPALQGMDGCIGVSLL
VDRQSGRCIATSAWETAEAMHASREQVTPIRDRCAEMFGGTPAVEEWEIAAMHRDHRSAE
GACVRATWVKVPADQVDQGIEYYKSSVLPQIEGLDGFCSASLLVDRTSGRAVSSATFDSF
DAMERNRDQSNALKATSLREAGGEELDECEFELALAHLRVPELV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTGGATGALPRTMKEGWIVYARSTTIQAQSECIDTGIAHVRDVVMPALQGMDGCIGVSLLVDRQSGRCIATSAWETAEAMHASREQVTPIRDRCAEMFGGTPAVEEWEIAAMHRDHRSAEGACVRATWVKVPADQVDQGIEYYKSSVLPQIEGLDGFCSASLLVDRTSGRAVSSATFDSFDAMERNRDQSNALKATSLREAGGEELDECEFELALAHLRVPELV
Prediction	CCCCCCCCCCCCCCCCCCEEEEEEEEEHCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEHCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEHCCCCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEHCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEHCCCCCCCC
Conf.Score	99876544567778888768999999976555689999999888888875899657999996899959999864898999988999999999999998998544335677776478888986699999985765667789999888757888779855788987577787678876489999999999999999999999888344344445554346787789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTGGATGALPRTMKEGWIVYARSTTIQAQSECIDTGIAHVRDVVMPALQGMDGCIGVSLLVDRQSGRCIATSAWETAEAMHASREQVTPIRDRCAEMFGGTPAVEEWEIAAMHRDHRSAEGACVRATWVKVPADQVDQGIEYYKSSVLPQIEGLDGFCSASLLVDRTSGRAVSSATFDSFDAMERNRDQSNALKATSLREAGGEELDECEFELALAHLRVPELV
Prediction	86443413033526344201010021404253144004213530141057253120000001364120000011434532543464045115402631614241450200001442545621101011141435416300411344104305714010100000136433000001143362155346414503552156242421423513101241423647
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCEEEEEEEEEHCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEHCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEHCCCCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEHCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEHCCCCCCCC
MTGGATGALPRTMKEGWIVYARSTTIQAQSECIDTGIAHVRDVVMPALQGMDGCIGVSLLVDRQSGRCIATSAWETAEAMHASREQVTPIRDRCAEMFGGTPAVEEWEIAAMHRDHRSAEGACVRATWVKVPADQVDQGIEYYKSSVLPQIEGLDGFCSASLLVDRTSGRAVSSATFDSFDAMERNRDQSNALKATSLREAGGEELDECEFELALAHLRVPELV

3mcsA

0.11

0.10

0.91

1.05

MUSTER

---------------YAVPILNVYDFEVKKDK-ETSYKSATEDYVNKTGVEQGVLGLFAATDERKTTSYIVEIYNDAFSNHTKNQASKDFKAVIPQIAEGNLNSAEIDVQIAKDKKEQNDNTFAVYTVIDVKPENDKEFAEIIKNIVETTFNE-EGTLLVYLGTDRRNNKWCLFEVYKDIDSYLNHRSA-KYFKDYITQTKDIAGKKRAELQVLKI-LDYKKL-

3mcsA

0.11

0.10

0.92

1.17

dPPAS

---------------YAVPILNVYDFEVKKDK-ETSYKSATEDYVNKTGVEQGVLGLFAATDERDKTSYIVEIYNDAFSNHTKNQASKDFKAVIPQIAEGNLNSAEIDVQIAKDKKEQNDNTFAVYTVIDVKPENDKEFAEIIKNIVETTFNE-EGTLLVYLGTDRRNNKWCLFEVYKDIDSYLNHRSAKYFKDYITQTKDIAGKKRAELQVLKIENLDYKKL-

3mcsA

0.11

0.10

0.89

1.21

wdPPAS

---------------YAVPILNVYDFEVKKDKETSYKSATEDYVNKTGVE-QGVLGLFAATDERDKTSYIVEIYNDAFSNHTKNQASKDFKAVIPQIAEGNLNSAEIDVQIAKDKKEQNDNTFAVYTVIDVKPENDKEFAEIIKNIVETTFNE-EGTLLVYLGTDRRNNKWCLFEVYKDIDSYLNHRSA--KYFKDYITQT-KDIAGKKRAELQVLKIKL----

3mcsA

0.12

0.11

0.91

1.17

wMUSTER

----------------AVPILNVYDFEVKKDKETSYKSATEDYVNKTGVE-QGVLGLFAATDERDTTSYIVEIYNDAFSNHTKNQASKDFKAVIPQIAEGNLNSAEIDVQIAKDKKEQNDNTFAVYTVIDVKPENDKEFAEIIKNIVETTFNE-EGTLLVYLGTDRRNNKWCLFEVYKDIDSYLNHRSA-KYFKDYITQTKDIAGKKRAELQVLKI-LDYKKL-

3mcsA

0.11

0.10

0.91

1.04

wPPAS

-----YAV-----------ILNVYDFEVKKDKETSYKSATEDYVNKTGVE-QGVLGLFAATDERDKTSYIVEIYNDFSNHTKN-QASKDFKAVIPQIAEGNLNSAEIDVQIAKDKKEQNDNTFAVYTVIDVKPENDKEFAEIIKNIVETTFNE-EGTLLVYLGTDRRNNKWCLFEVYKDIDSYLNHRSA-KYFKDYITQTKDAGKKRAELQVLKIENLDYKKL-

3mcsA

0.10

0.09

0.89

1.84

dPPAS2

---------------YAVPILNVYDFEVKKDKETSYKSATEDYVNKTGVE-QGVLGLFAATDERDKTSYIVEIYNDFSNHTKN-QASKDFKAVIPQIAEGNLNSAEIDVQIAKDKKEQNDNTFAVYTVIDVKPENDKEFAEIIKNIVETTFNE-EGTLLVYLGTDRRNNKWCLFEVYKDIDSYLNHRSAKYFKDYITQTKDIAGKKRAELQVLKIENL------

3mcsA

0.10

0.09

0.91

1.03

PPAS

-----YAV-----------ILNVYDFEVKKDKETSYKSATEDYVNKTGVE-QGVLGLFAATDERDKTSYIVEIYNDFSNHTKN-QASKDFKAVIPQIAEGNLNSAEIDVQIAKDKKEQNDNTFAVYTVIDVKPENDKEFAEIIKNIVETTFNE-EGTLLVYLGTDRRNNKWCLFEVYKDIDSYLNHRSAKYFKDYITQTKDIAGKKRAELQVLKIENLDYKKL-

3f44A

0.10

0.08

0.88

1.15

Env-PPAS

----------------ETPIFKIKKLTIAENDRSEYIRYAEKNHDS-IPAEEGTLLIGSGHDDAHGDNYEIEVFRNKGAEDLHIASHADDFVETVNKIATKQKVIDLHPEVIT---TKAQDNFVRLIKVEVKDADAEKFSHAVKKETTSASE--PG---EISGTNIDNNEWYFIEVYANDEAYDIHVK-TPHYKEYIEETDGVKSRDVKTLVRDTLATQ-GAIV

3f44A

0.09

0.08

0.88

0.97

MUSTER

----------------ETPIFKIKKLTIAENDRSEYIRYAEKNHDS-IPAEEGTLLIGSGHDDAHGDNYEIEVFRNKGAEDLHIASHADDFVETVNKIATKQKVIDLHPEVITTKAQDNF---VRLIKVEVKDADAEKFSHAVKKETTSASE--PG---EISGTNIDNNEWYFIEVYANDEAYDIHVK-TPHYKEYIEETDGVKSRDVKTLVRDTLATQ-GAIV

3f44A

0.10

0.09

0.88

1.11

dPPAS

----------------ETPIFKIKKLTIAENDRSEYIRYAEKNHDS-IPAEEGTLLIGSGHDDAHGDNYEIEVFRNKGAEDLHIASHADDFVETVNKIATKQKVIDLHPEVIT---TKAQDNFVRLIKVEVKDADAEKFSHAVKKETTSASE--PG--EISGTNIDNPNEWYFIEVYANDEAYDIHVK-TPHYKEYIEETDGVKSRDVKTLVRDTLATQ-GAIV

(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=-1.23

Estimated TM-score = 0.56±0.15

Estimated RMSD = 8.3±4.5Å

Download Model 2

C-score=-1.51

Download Model 3

C-score=-1.22

Download Model 4

C-score=-2.53

Download Model 5

C-score=-1.80

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	3mcsA	0.883	1.28	0.101	0.924
2	3f44A	0.802	1.81	0.076	0.879
3	3gn6C	0.734	3.04	0.098	0.906
4	2cb2A	0.728	3.14	0.122	0.911
5	2pgcA	0.694	2.94	0.106	0.839
6	2hagA	0.635	4.13	0.062	0.862
7	4gu7A	0.631	4.17	0.093	0.871
8	4gs1A	0.629	4.29	0.062	0.888
9	4g2cA	0.628	4.10	0.037	0.875
10	2gvkA	0.626	4.21	0.052	0.866

(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	0.20	16	3e8oB	UNL	Rep, Mult	146,160,175,186,207
2	0.04	3	3twaA	MG	Rep, Mult	165,212,222
3	0.03	2	2xctS	CPF	Rep, Mult	63,66
4	0.03	2	1n5vA	NOM	Rep, Mult	125,127,160,173,175,177,183,186,195,196,205,207
5	0.03	2	3fgvB	UNL	Rep, Mult	24,70,102
6	0.03	2	3bguA	NBZ	Rep, Mult	125,127,129,143,173,186,192,196,199,205
7	0.01	1	1x8gA	ZN	Rep, Mult	52,158,217
8	0.01	1	1zqqA	NUC	Rep, Mult	53,55,56,58,59
9	0.01	1	3l76B	THR	Rep, Mult	28,33,36,37,60,69
10	0.01	1	3l76A	THR	Rep, Mult	37,38,39,40,41,58
11	0.01	1	1s2vB	MG	Rep, Mult	34,62
12	0.01	1	5b09A	4MX	Rep, Mult	22,39,43,81,82,87,90,98,102
13	0.01	1	3a16B	PXO	Rep, Mult	127,206,207
14	0.01	1	3rj8A	ZN	Rep, Mult	115,116
15	0.01	1	1n5sB	ADL	Rep, Mult	24,26,57,59,70,72,74,78,81,90,91,94
16	0.01	1	1s2vC	MG	Rep, Mult	3,34,62
17	0.01	1	3jcmM	NUC	Rep, Mult	42,88
18	0.01	1	3l76A	THR	Rep, Mult	131,136,138,139,140,165

	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	2v5aB	0.430	5.64	0.056	0.723	6.3.4.14	163
2	0.060	2vqdA	0.433	5.86	0.056	0.746	6.3.4.14,6.4.1.2	NA
3	0.060	3bxvA	0.732	3.20	0.131	0.920	1.13.11.55	20,78,81
4	0.060	2jb2A	0.420	5.31	0.046	0.665	1.4.3.2	NA
5	0.060	1gsoA	0.438	5.65	0.048	0.728	6.3.4.13	NA
6	0.060	1k2yX	0.455	4.77	0.067	0.679	5.4.2.2,5.4.2.8	NA
7	0.060	2qf7B	0.360	5.61	0.053	0.598	6.4.1.1	NA
8	0.060	1hbmA	0.437	5.15	0.046	0.679	2.8.4.1	NA
9	0.060	3lp8A	0.441	5.64	0.053	0.741	6.3.4.13	24
10	0.060	1t3tA	0.419	5.86	0.052	0.705	6.3.5.3	NA
11	0.060	3eoqB	0.426	5.27	0.034	0.670	3.4.24.56	NA
12	0.060	1f1hA	0.424	5.22	0.047	0.683	6.3.1.2	NA
13	0.060	1oj9A	0.424	5.38	0.045	0.683	1.4.3.4	NA
14	0.060	1f1hL	0.424	5.22	0.047	0.683	6.3.1.2	45,51,56
15	0.060	1msvB	0.419	5.25	0.050	0.652	4.1.1.50	NA
16	0.060	1htoA	0.428	5.11	0.057	0.670	6.3.1.2	NA
17	0.060	2g49A	0.409	4.95	0.015	0.612	3.4.24.56	NA
18	0.060	1lgrA	0.413	5.25	0.035	0.661	6.3.1.2	NA
19	0.060	2z5xA	0.427	5.21	0.067	0.674	1.4.3.4	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	0.26	0.885	1.33	0.10	0.93	3mcsB
1	0.25	0.802	1.81	0.08	0.88	3f44A
2	0.13	0.747	2.99	0.09	0.92	3gn6C	GO:0046872
3	0.12	0.732	3.20	0.13	0.92	3bxvA	GO:0046872
4	0.11	0.731	3.15	0.12	0.92	2cb2A	GO:0005737 GO:0016491 GO:0033755 GO:0046872 GO:0055114
5	0.09	0.635	4.27	0.05	0.89	5fw4A	GO:0004096 GO:0004601 GO:0005576 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
6	0.08	0.628	4.17	0.06	0.87	3qnsA	GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
7	0.08	0.631	4.17	0.09	0.87	4gu7A	GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
8	0.08	0.654	3.97	0.07	0.88	2hagA	GO:0004601 GO:0006582 GO:0020037 GO:0046872 GO:0055114 GO:0098869
9	0.08	0.623	4.49	0.06	0.89	4gt2A	GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
10	0.08	0.646	3.94	0.05	0.87	2gvkA	GO:0004601 GO:0020037 GO:0055114 GO:0098869
11	0.08	0.626	4.42	0.07	0.88	2y4eA	GO:0004601 GO:0006974 GO:0015684 GO:0016491 GO:0016675 GO:0020037 GO:0033212 GO:0042597 GO:0046872 GO:0055114 GO:0098869
12	0.07	0.628	4.32	0.05	0.88	4gs1B	GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
13	0.07	0.401	1.73	0.17	0.43	3qmqC
14	0.07	0.614	4.28	0.05	0.85	4grcA	GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
15	0.07	0.619	4.26	0.07	0.86	5de0B	GO:0004601 GO:0006582 GO:0020037 GO:0055114 GO:0098869
16	0.06	0.425	1.63	0.10	0.46	3kkfA	GO:0046872
17	0.06	0.381	2.21	0.14	0.43	1iujB
18	0.06	0.397	1.90	0.15	0.43	2gffB	GO:0005737 GO:0016853

Consensus prediction of GO terms

Molecular Function	GO:0046872
GO-Score	0.32
Biological Processes	GO:0055114
GO-Score	0.11
Cellular Component	GO:0005737
GO-Score	0.11

(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.