I-TASSER results

I-TASSER results for job id Rv3770c

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

Input Sequence in FASTA format

>protein (191 residues)
MLSGIQQNTLMDNDPLAHGYYVADLLVALAVVVLMLRARRTRPELARMLLLGTLIGLVWE
LPVFGLSAWTNTPIIEWATPLPLPTVVFLLAHSVWDGPLLTMGWLLARALTGEPAGALGL
TVQVLWGQLTALAVELSAILAGTWSYVDDLWFNPVMFWFRGHPVTAAMQLTWLLAPLCFA
ALVRRLALTAR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MLSGIQQNTLMDNDPLAHGYYVADLLVALAVVVLMLRARRTRPELARMLLLGTLIGLVWELPVFGLSAWTNTPIIEWATPLPLPTVVFLLAHSVWDGPLLTMGWLLARALTGEPAGALGLTVQVLWGQLTALAVELSAILAGTWSYVDDLWFNPVMFWFRGHPVTAAMQLTWLLAPLCFAALVRRLALTAR
Prediction	CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCEHCCCCCEEEHCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	98754445556778765457889999999999999877665589999999999999999754445444568865775688997467777765446764568999999987488887454577754555788999999888754444443345546788758754568899999999999999999998749
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MLSGIQQNTLMDNDPLAHGYYVADLLVALAVVVLMLRARRTRPELARMLLLGTLIGLVWELPVFGLSAWTNTPIIEWATPLPLPTVVFLLAHSVWDGPLLTMGWLLARALTGEPAGALGLTVQVLWGQLTALAVELSAILAGTWSYVDDLWFNPVMFWFRGHPVTAAMQLTWLLAPLCFAALVRRLALTAR
Prediction	73542454313554221301200100111000000020444344002001111111231312130032235331141134231200000002222422101101110311444322113010211233022112403111223132023222300010034231300130201001200000033122448
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCEHCCCCCEEEHCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MLSGIQQNTLMDNDPLAHGYYVADLLVALAVVVLMLRARRTRPELARMLLLGTLIGLVWELPVFGLSAWTNTPIIEWATPLPLPTVVFLLAHSVWDGPLLTMGWLLARALTGEPAGALGLTVQVLWGQLTALAVELSAILAGTWSYVDDLWFNPVMFWFRGHPVTAAMQLTWLLAPLCFAALVRRLALTAR

4or2A

0.20

0.19

0.96

0.67

MUSTER

QKYLIPVRYLEWSNIESIAFSCLGILVTLFVTLIFVLYRDTPVVKSRELCYIILAGIFLGYVCFTLIAKPTTTSCYLQR--LLVGLSSAMCYSA----LVTKTNRIARILARKPRF-MSAWAQVIASILISVQLTLVVTLIIMEPPMPILSYKEVYLICNTSNVVAPLGYNGLLIMSCTYYAFKTRNVPAN

4zowA2

0.14

0.12

0.82

0.58

dPPAS

QSPIIIITGE-QLSSYEYGLLQVPIFGALIAGNLLLARLTSRRTVRSLIIMGGWPIMIGLLVAAAATVIS--------SHAYLWMTAGLSIYAFGIGLANAGLVRLTLFASDMSKG----TVSAAMGMLQMLIFTVGIEISK---------------------HAWLNGGNGLFNLFNLVNGILWLSLMVI

4jq6A

0.18

0.15

0.85

0.62

wdPPAS

-------------DYVGISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLYMGVWIYAG-IDWLITVPLQIIEFYLIIAV----WKLLIASLVMLIGG--IGEAGLGDV--VVWWIVGMIAWLYIIYEIFLF---GWA-PIG-YA-GDGLEDALNIVYNLADLINKAAFGLAIWAAA

4jq6A

0.21

0.18

0.86

0.62

wMUSTER

---------------VGISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLYMGVWIETPTIDWLT--PLQIIEFYLIIAV---FWKLLIASLVMLIGG--IGEAGLGDVVVWWIVGMIAWLYIIYEIFLFNIV--GWA-PIG-YA-GDGLEDALNIVYNLADLINKAAFGLAIWAAA

4jq6A

0.19

0.16

0.83

0.55

wPPAS

-------------DYVGISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLYMGVWIETPTIDWLVPL-QIIEFYLIIAVFW---LIASLVMLIGGFIGEAGWIVG-MI-IIYEIFL---NTIKWIVTVGWAY-------PI--YA-GDGLEDALNIVYNLADLINKAAFGLAIWAAA

4zowA2

0.13

0.10

0.78

0.64

dPPAS2

GE-QL--------SSYEYGLLQVPIFGALIAGNLLLARLTSRRTVRSLIIMGGWPIMIGLLVAAAATVISSHAYL-WMT---AGLSIYAFGIGL----ANAGLVRLTLFASDMSKG----TVSAAMGMLQMLIFTVGIEISK---------------------HAWLNGGNGLFNLFNLVNGILWLSLMVI

4jq6A

0.21

0.18

0.87

0.63

PPAS

-------------DYVGISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLYMGVWIETPTIDWLT--PLQIIEFYLIIAV---FWKLLIASLVMLIGG--IGEAGLGDVVVWWIVGMIAWLYIIYEIFLFNIV--GWA-PI-GYA-GDGLEDALNIVYNLADLINKAAFGLAIWAAA

3j3vO

0.29

0.17

0.59

Env-PPAS

MITKTSKNAA-----------------------RLKRHARVR-----AKLSGT--AERPRLNVF----RSNKHI--YAQ--------------IIDD---VNGVTLASASTLDKDLNVESTGDTSAATKVGELVAKRAAEKG----ISDVVFD------RGYL---------------YHGRVKALADAAR

4xydA

0.17

0.16

0.91

0.66

MUSTER

LLLGWIPNFLSEILPLIVWLLLGFMGAAYFVIPEESEREIHSPLLAYLQLAIMVLGTLGVVVTYNLFELLGKEGREF---LEQPVWVKMGIVVA----ALIFMYNISMTV---QGRKTAITNVLLLGLWGLTLLFLFAFYNPSNLALDKMYW----WYV----VHLWVEGTWELVMASVLAFLMLKLTGVD

4o6yA

0.15

0.14

0.95

0.57

dPPAS

YRGGL---ALSSDNKDVHPVMMVIGLILFNGEAMLAYKSVQGTKNLKKLVHLTLQLTAFILSLIGVWAALKFHIDKGIENFYSLHSWLGLACLF----LFAFQWAAGFVTYWYPGGSRNSRASLMWHVFLGISIYALALVTATTGILEKVTFLQVNQVITRYSTEAMLVNTMGVLILILGGFVILGVVT--

(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=-2.30

Estimated TM-score = 0.44±0.14

Estimated RMSD = 10.4±4.6Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-4.92

Download Model 4

C-score=-4.16

Download Model 5

C-score=-4.72

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	5b2nA	0.831	2.40	0.084	0.953
2	4hyjA	0.828	2.43	0.147	0.953
3	4jq6A	0.824	1.83	0.179	0.906
4	4xtlA	0.822	2.53	0.100	0.948
5	3ddlA	0.821	2.34	0.128	0.948
6	5azdA	0.818	2.31	0.151	0.942
7	1xioA	0.807	2.49	0.146	0.932
8	1uazA	0.800	2.59	0.137	0.942
9	2jafA	0.798	2.53	0.154	0.937
10	3a7kA	0.795	2.56	0.137	0.937

(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	12	3iseR	HEM	Rep, Mult	31,35,50,54,57
2	0.08	13	1brxA	RET	Rep, Mult	77,81,84,108,112,127,130,131,134,151,158,176,180
3	0.06	8	3qbkA	BR	Rep, Mult	58,62,76,77,80,180
4	0.05	7	2at9A	2DP	Rep, Mult	27,28,31,49,52,53,56,57,60,64
5	0.05	6	1qhjA	PH1	Rep, Mult	26,33,146,174,177,178,181,182,185,189
6	0.04	6	1brrC	ARC	Rep, Mult	35,38,49,50,53,54
7	0.02	3	2i1xA	SQU	Rep, Mult	22,29,173,174,177,178,182,186
8	0.02	4	1p8hA	LI1	Rep, Mult	20,24,25,27,28,60,64
9	0.02	4	3e1nE	UNK	Rep, Mult	30,56
10	0.02	3	1kmeA	SQU	Rep, Mult	47,50,51,54,58,83
11	0.01	2	3am6A	CLR	Rep, Mult	29,30,33,34,185,191
12	0.01	1	2r9rB	PGW	Rep, Mult	32,36
13	0.01	1	2i20A	LI1	Rep, Mult	53,57,58,62
14	0.01	1	1rkvB	MG	Rep, Mult	148,162
15	0.01	1	2i1xA	LI1	Rep, Mult	50,54,55,57,58
16	0.01	1	2hawA	MG	Rep, Mult	14,76,92,148
17	0.01	1	2zzlA	SOG	Rep, Mult	140,141,142,143,146
18	0.01	2	3oaxB	4E6	Rep, Mult	18,22,25,29,182
19	0.01	1	2hawA	F	Rep, Mult	12,14,76,148
20	0.01	1	2i1xA	LI1	Rep, Mult	28,31,32,36,60

	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	1hxgA	0.486	5.01	0.034	0.780	4.2.3.9,4.1.99.7	NA
2	0.060	1n1zA	0.481	5.31	0.060	0.822	5.5.1.8	NA
3	0.060	1jswB	0.485	4.86	0.064	0.775	4.3.1.1	NA
4	0.060	1vdkA	0.536	4.09	0.094	0.754	4.2.1.2	NA
5	0.060	1f1oA	0.552	3.94	0.058	0.764	4.3.2.2	NA
6	0.060	2pfmA	0.545	3.72	0.053	0.749	4.3.2.2	NA
7	0.060	1k7wD	0.503	4.31	0.030	0.754	4.3.2.1	NA
8	0.060	1q5nA	0.521	4.11	0.044	0.738	5.5.1.2	NA
9	0.060	3bhgA	0.508	3.98	0.056	0.733	4.3.2.2	NA
10	0.060	2o6yA	0.514	4.36	0.054	0.749	4.3.1.-	NA
11	0.060	2qb0B	0.359	5.79	0.064	0.639	3.2.1.17	NA
12	0.060	1k62B	0.539	4.04	0.069	0.728	4.3.2.1	NA
13	0.060	2ewgA	0.481	5.10	0.127	0.785	2.5.1.10	NA
14	0.060	1qleA	0.513	4.71	0.053	0.775	1.9.3.1	NA
15	0.060	3npkA	0.499	4.29	0.060	0.744	2.5.1.10	NA
16	0.060	1tj7A	0.533	3.99	0.063	0.723	4.3.2.1	NA
17	0.060	1dcnB	0.532	4.10	0.057	0.728	4.3.2.1	NA
18	0.060	1m56A	0.509	4.89	0.058	0.791	1.9.3.1	NA
19	0.060	3gzhA	0.480	4.89	0.024	0.764	4.3.2.2	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	0.39	0.788	2.55	0.13	0.93	1cwqA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
1	0.33	0.797	2.57	0.13	0.94	3qbgA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
2	0.32	0.835	2.14	0.12	0.93	4klyB	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
3	0.30	0.729	2.79	0.09	0.88	4yziA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220 GO:0046872
4	0.30	0.797	2.68	0.16	0.95	2z55A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
5	0.30	0.828	2.43	0.15	0.95	4hyjA	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
6	0.28	0.835	2.21	0.15	0.94	4knfC	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
7	0.28	0.818	2.31	0.15	0.94	5azdA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
8	0.27	0.817	2.52	0.10	0.95	4xtnA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
9	0.25	0.761	2.74	0.12	0.90	1c8sA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
10	0.18	0.832	1.93	0.18	0.92	4jq6B	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
11	0.17	0.790	2.51	0.12	0.92	2ksyA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
12	0.17	0.800	2.59	0.14	0.94	1uazA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
13	0.17	0.821	2.34	0.13	0.95	3ddlA	GO:0005216 GO:0006811 GO:0007602 GO:0010461 GO:0016020 GO:0016021 GO:0018298 GO:0034220
14	0.16	0.793	2.49	0.10	0.93	4qi1A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
15	0.16	0.789	2.55	0.11	0.93	4l35A	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
16	0.13	0.704	3.40	0.14	0.92	2m3gA	GO:0005216 GO:0006811 GO:0016020 GO:0016021 GO:0034220
17	0.13	0.707	3.55	0.12	0.96	2l6xA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0010461 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
18	0.12	0.690	2.62	0.08	0.83	1brdA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0015992 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896

Consensus prediction of GO terms

Molecular Function	GO:0009881	GO:0043169	GO:0010461
GO-Score	0.81	0.60	0.32
Biological Processes	GO:0034220	GO:0018298	GO:0007602	GO:0015992
GO-Score	0.86	0.81	0.81	0.71
Cellular Component	GO:0016021	GO:0005886
GO-Score	0.86	0.81

(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.