I-TASSER results

I-TASSER results for job id Rv2551c

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

Input Sequence in FASTA format

>protein (139 residues)
MLAAAVLAWMGVLCVCDVRQRRLPNWLTLPGAGVILLFAGLAGRGVPALAGAAALAGVYL
LVHLALPAAMGAGDVKLAIGLGGLTGCFGVEVWFLAALAAPLLTAVCGVMVTPWGVRTLP
HGPSMCVASLGAVGLALLG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLAAAVLAWMGVLCVCDVRQRRLPNWLTLPGAGVILLFAGLAGRGVPALAGAAALAGVYLLVHLALPAAMGAGDVKLAIGLGGLTGCFGVEVWFLAALAAPLLTAVCGVMVTPWGVRTLPHGPSMCVASLGAVGLALLG
Prediction	HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCC
Conf.Score	6779999999999998776554787578999999999997655588999999999999999999857888876699999999999999999999999999999999999999867999998779999999999999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLAAAVLAWMGVLCVCDVRQRRLPNWLTLPGAGVILLFAGLAGRGVPALAGAAALAGVYLLVHLALPAAMGAGDVKLAIGLGGLTGCFGVEVWFLAALAAPLLTAVCGVMVTPWGVRTLPHGPSMCVASLGAVGLALLG
Prediction	3201122230220000133233012311332233221210333433322212333333332231134411121113202321331233333323333332333133312112345744101010011123213332337
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCC
MLAAAVLAWMGVLCVCDVRQRRLPNWLTLPGAGVILLFAGLAGRGVPALAGAAALAGVYLLVHLALPAAMGAGDVKLAIGLGGLTGCFGVEVWFLAALAAPLLTAVCGVMVTPWGVRTLPHGPSMCVASLGAVGLALLG

4huqS

0.14

0.97

1.00

wMUSTER

TLSMVTMGVLMALQLVISRFSVGNNFIKV----FTFLIVALIAKWFGPWWGMLTAAVVDVIGTLMTGGPFFIGFTVSAVLGSLIYAVFLWWRVIGASVLIALLVNTLLNTLWVTIMYQTPFWSLLPVRALKELIVTPVQ

4o6mA2

0.14

0.95

1.23

wPPAS

IAREINRKVSLRISRLLADTSVTPNQITVFSFFLSLVGSALFLL-----YLTTLLAGVIIQLHSII--GCGYGDFIIVFSITYVLSASNPVYWIIGFLAAFASLMIAYTGDKFVARTYSPEIDFRLLIIFACSVVNLPS

4pgrA

0.12

0.11

0.86

1.19

dPPAS2

VFTLLIATVGLFIGQF------------VPVALMLPLSILEVAMIILAFWMKAVGYAFVYTFAFVS-------GITLFPIVSHYASIAGAYVVLEAFGSTFVIFAVLGTIGAKMKKDLSFLWSFLLVAVLALAVVGIFN

4huqS

0.14

0.98

1.16

PPAS

TLSMVTMGVLMALQLVISRFSVGNNFIKVSF---TFLIVALIAKWFGPWWGMLTAAVVDVIGTLMTGGPFFIGFTVSAVLGSLIYAVFLWWRVIGASVLIALLVNTLLNTLWVTIMYQTPFWSLLPVRALKELIVTPVQ

4o6mA2

0.14

0.95

0.98

wMUSTER

IAREINRKVSLRISRLLADTSVTPNQITVFSFFLSLVGSALFLL-----YLTTLLAGVIIQLHSII--GCGEGDFIIVFSITYVLSASNPVYWIIGFLAAFASLMIAYTGDKFVAGFAIPITDFRLLIIFACSVVNLPS

4hzuS

0.14

0.12

0.87

1.21

wPPAS

LKENTIAAVLIAMTVALSILVVIPTLCEVGIYTSAILY--------GRRMGLLVGGASGFLIDILT----GYPSLVIHGTQGLVVGWLLIRSMLLPLLVGSLVMVIGYCLATTL------FGFGNVVQVGFGAGVTLSI

4mndA2

0.12

0.10

0.81

1.14

dPPAS2

PLAGLLYQFSSILDGCDGEI-----RFVDFLFLAIIALLYPKTATVAMFAIFGSVMVSYTSEKYKAEFGESIRERIFLIMIFCLLSAISLQWIFWMFLFVAAISLTRVVVTLLAVLVS---------------------

4o6mA2

0.14

0.97

1.16

PPAS

IAREINRKVSLRISRLLADTSVTPNQITVFSFFLSLVGSALFLLNS---YLTTLLAGVIIQLHSII-KFMEYGDFIIVFSITYVLSASNPVYWIIGFLAAFASLMIAYTGDKFVAGFAIPITDFRLLIIFACSVVNLPS

4mndA2

0.13

0.12

0.88

1.12

wPPAS

KINRKISTRISAAI-----NKVNPNQMTLISFLVGAFSALASFF-------SIPLAGLLYQFSSIL--GCGKGDFLFLAIIALL---PKTATVAMFAIFGSVMVSYTSEKYKAEFGESIRYIDERIFLIMIFCLLSAIS

4huqS

0.13

0.12

0.92

1.13

dPPAS2

VTMGVLMALQLVISRF-----------SVGNNFITFLIVALIAKWFGPWWGMLTAAVVDVIGTLMTGGPFFIGFTVSAVLGSLIYAVFLWWRVIGASVLIALLVNTLLNTLWVTIMYQTPFWSLLPVRALKELIVTPVQ

(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=-1.22

Estimated TM-score = 0.56±0.15

Estimated RMSD = 7.2±4.2Å

Download Model 2

C-score=-2.65

Download Model 3

C-score=-4.83

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	4huqS	0.828	2.23	0.133	0.971
2	4z7fA	0.780	2.63	0.141	0.964
3	4hzuS	0.774	2.81	0.102	0.986
4	3rlbA	0.766	2.58	0.135	0.957
5	4tkrA	0.752	2.73	0.097	0.964
6	5d0yA	0.748	2.58	0.090	0.942
7	4rfsS	0.745	2.97	0.140	0.971
8	4m58A	0.723	2.84	0.068	0.942
9	5kbwA	0.709	2.96	0.096	0.964
10	3p5nA	0.702	3.11	0.068	0.957

(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	2	3lsjA	COA	Rep, Mult	35,78,79,82
2	0.06	2	3rumA	UUU	Rep, Mult	71,76
3	0.03	1	3aqtA	RCO	Rep, Mult	14,32,35,36,39,61,62
4	0.03	1	2h2pB	SEK	Rep, Mult	66,68,92,95
5	0.03	1	2q69A	CA	Rep, Mult	69,70,71
6	0.03	1	2h2pA	SEK	Rep, Mult	66,68
7	0.03	1	2h2sB	SEK	Rep, Mult	66,67,68,89
8	0.03	1	1bjyB	CTC	Rep, Mult	77,81,84
9	0.03	1	3dl9B	BCD	Rep, Mult	119,120,122
10	0.03	1	3angD	DCC	Rep, Mult	9,13,17,18,31,34
11	0.03	1	2yqcA	MG	Rep, Mult	25,28
12	0.03	1	4z7fC	FOL	Rep, Mult	28,59,68,69,70,71,74,75,104,108,112,128,131
13	0.03	1	3rlbB	VIB	Rep, Mult	74,75,108,112,123,127,128
14	0.03	1	1yklG	DHB	Rep, Mult	122,123

	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	3bkkA	0.522	4.15	0.050	0.835	3.4.15.1	121
2	0.060	1jroB	0.530	4.53	0.106	0.871	1.1.1.204	NA
3	0.060	1yewB	0.565	3.77	0.082	0.863	1.14.13.25	80
4	0.060	2j5cB	0.536	4.99	0.036	0.928	4.2.3.-	NA
5	0.060	1pgjA	0.507	3.40	0.060	0.719	1.1.1.44	76
6	0.060	2c6fA	0.524	3.89	0.089	0.763	3.4.15.1	NA
7	0.060	1hxgA	0.533	4.88	0.104	0.899	4.2.3.9,4.1.99.7	NA
8	0.060	3fwnA	0.519	4.06	0.065	0.777	1.1.1.44	NA
9	0.060	1n63B	0.544	4.68	0.053	0.914	1.2.99.2	NA
10	0.060	2i2xA	0.550	4.61	0.105	0.935	2.1.1.90	106
11	0.060	1n1zA	0.551	4.40	0.072	0.885	5.5.1.8	NA
12	0.060	3b9jC	0.520	4.66	0.085	0.921	1.17.3.2,1.17.1.4	NA
13	0.060	1vlbA	0.535	4.56	0.046	0.878	1.2.99.7	NA
14	0.060	1ivhA	0.511	3.88	0.117	0.748	1.3.99.10	132
15	0.060	3hfwA	0.532	4.29	0.063	0.849	3.2.2.19	18,33
16	0.060	1ezfB	0.549	4.35	0.078	0.878	2.5.1.21	58,81
17	0.060	1dgjA	0.526	4.62	0.094	0.906	1.2.-.-	NA
18	0.060	1y791	0.508	4.63	0.076	0.813	3.4.15.5	59
19	0.060	1ffuB	0.550	3.98	0.081	0.863	1.2.99.2	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	0.31	0.772	2.56	0.13	0.96	4z7fB	GO:0005215 GO:0006810 GO:0016020 GO:0016021
1	0.30	0.774	2.81	0.10	0.99	4hzuS	GO:0016020 GO:0016021
2	0.30	0.828	2.23	0.13	0.97	4huqS	GO:0005215 GO:0006810 GO:0016020 GO:0016021
3	0.29	0.766	2.57	0.14	0.96	4muuA	GO:0005886 GO:0015234 GO:0015888 GO:0016020 GO:0016021 GO:0071934
4	0.28	0.748	2.75	0.10	0.96	4tkrB	GO:0005886 GO:0015234 GO:0015888 GO:0016020 GO:0016021 GO:0071934
5	0.26	0.735	2.87	0.10	0.93	5d3mC	GO:0005215 GO:0006810 GO:0016020 GO:0016021
6	0.22	0.745	2.97	0.14	0.97	4rfsS	GO:0005215 GO:0006810 GO:0016020 GO:0016021
7	0.14	0.712	2.96	0.12	0.96	4dveA	GO:0005886 GO:0006810 GO:0015225 GO:0015878 GO:0016020 GO:0016021
8	0.14	0.702	3.11	0.07	0.96	3p5nA	GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0032217 GO:0032218
9	0.12	0.723	2.84	0.07	0.94	4m58A	GO:0000041 GO:0016020 GO:0016021
10	0.07	0.633	3.58	0.06	0.91	5do7D	GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010949 GO:0015248 GO:0015914 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045796 GO:0046982 GO:0055085 GO:0055092
11	0.07	0.413	5.02	0.06	0.73	3na8A	GO:0003824 GO:0008152 GO:0016829 GO:0046872
12	0.07	0.461	5.01	0.03	0.78	4m1mA	GO:0000086 GO:0000166 GO:0002481 GO:0002485 GO:0002489 GO:0002591 GO:0005524 GO:0005886 GO:0006810 GO:0006855 GO:0008559 GO:0009986 GO:0015893 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042623 GO:0042626 GO:0042908 GO:0046581 GO:0055085 GO:0070062 GO:0072089
13	0.06	0.449	4.66	0.06	0.76	2iw3B	GO:0000166 GO:0001933 GO:0003723 GO:0003746 GO:0005524 GO:0005737 GO:0005840 GO:0006412 GO:0006414 GO:0006415 GO:0006469 GO:0010494 GO:0016887 GO:0019843 GO:0022626 GO:0042788
14	0.06	0.371	4.49	0.09	0.63	2yz2A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016787 GO:0016887 GO:0032217 GO:0032218
15	0.06	0.435	4.22	0.09	0.70	3rdpB	GO:0000166 GO:0004797 GO:0005524 GO:0006230 GO:0016301 GO:0016310 GO:0016740 GO:0071897
16	0.06	0.376	6.14	0.04	0.83	2vbfA	GO:0000287 GO:0003824 GO:0009082 GO:0016831 GO:0030976 GO:0046872 GO:0047433
17	0.06	0.315	4.03	0.07	0.47	3b5wA	GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0008144 GO:0008289 GO:0015437 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085 GO:1901264
18	0.06	0.407	4.87	0.04	0.67	5c73A	GO:0000166 GO:0005524 GO:0006810 GO:0016021 GO:0016887 GO:0042626 GO:0055085

Consensus prediction of GO terms

Molecular Function	GO:0015234
GO-Score	0.49
Biological Processes	GO:0071934
GO-Score	0.49
Cellular Component	GO:0016021	GO:0005886
GO-Score	0.83	0.49

(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.