I-TASSER results

I-TASSER results for job id Rv1507c

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

Input Sequence in FASTA format

>protein (231 residues)
MKKVAIVQSNYIPWRGYFDLIAFVDEFIIYDDMQYTKRDWRNRNRIKTSQGLQWITVPVQ
VKGRFHQKIRETLIDGTDWAKAHWRALEFNYSAAAHFAEIADWLAPIYLEEQHTNLSLLN
RRLLNAICSYLGISTRLANSWDYELADGKTERLANLCQQAAATEYVSGPSARSYVDERVF
DELSIRVTWFDYDGYRDYKQLWGGFEPAVSILDLLFNVGAEAPDYLRYCRQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MKKVAIVQSNYIPWRGYFDLIAFVDEFIIYDDMQYTKRDWRNRNRIKTSQGLQWITVPVQVKGRFHQKIRETLIDGTDWAKAHWRALEFNYSAAAHFAEIADWLAPIYLEEQHTNLSLLNRRLLNAICSYLGISTRLANSWDYELADGKTERLANLCQQAAATEYVSGPSARSYVDERVFDELSIRVTWFDYDGYRDYKQLWGGFEPAVSILDLLFNVGAEAPDYLRYCRQ
Prediction	CCEEEEHCCCCCCCHHHHHHHHHCCEEEEEHCCCCCCCCCEEEEEHCCCCCEEEEEEEEHCCCCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHCCHHHHHHHCCCEEEHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHHCCC
Conf.Score	987999777778888999999989989999755666467554467658998589999976589888765689978958999999999999977997899999999999769988799999999999999989999689856556788765789999999788755578886554797888888995467657888765568899888854878876789799999998569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MKKVAIVQSNYIPWRGYFDLIAFVDEFIIYDDMQYTKRDWRNRNRIKTSQGLQWITVPVQVKGRFHQKIRETLIDGTDWAKAHWRALEFNYSAAAHFAEIADWLAPIYLEEQHTNLSLLNRRLLNAICSYLGISTRLANSWDYELADGKTERLANLCQQAAATEYVSGPSARSYVDERVFDELSIRVTWFDYDGYRDYKQLWGGFEPAVSILDLLFNVGAEAPDYLRYCRQ
Prediction	753100000200010000310240220000221414441121103133672330000003447646230322304566125301520450044032064025103500454625200300330041005207051513304404464654420240056242541142641451145740574615142162751340414545111200000000112540251045158
	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

CCEEEEHCCCCCCCHHHHHHHHHCCEEEEEHCCCCCCCCCEEEEEHCCCCCEEEEEEEEHCCCCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHCCHHHHHHHCCCEEEHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHHCCC
MKKVAIVQSNYIPWRGYFDLIAFVDEFIIYDDMQYTKRDWRNRNRIKTSQGLQWITVPVQVKGRFHQKIRETLIDGTDWAKAHWRALEFNYSAAAHFAEIADWLAPIYLEEQHTNLSLLNRRLLNAICSYLGISTRLANSWDYELADGKTERLANLCQQAAATEYVSGPSARSYVDERVFDELSIRVTWFDYDGYRDYKQLWGGFEPAVSILDLLFNVGAEAPDYLRYCRQ

1t1eA3

0.20

0.03

0.15

1.57

dPPAS2

--------------------------------------------------------------------------------------------------------------------------------------------------RQRGDELEAHVERQAAL----APHARVHLEREAFAASHG----------------------------------------------

3gbgA2

0.05

0.01

0.19

1.54

dPPAS2

------------------------------------------------------------------------------------------------------------------------------------------------DDLDAMEKISCLVKSDITRNWRWALRTNRMILKKELESRGVKF--------------------------------------------

3umgA

0.14

0.13

0.95

0.67

MUSTER

GRNVAVL--TVVDWTGIATAVADYLEVDAVAFADRWRARYQPSMDAILSGAREFVTLDILHRENLDFVLRESGIDPTNHDSGELDELARAWHVLTPWPDSVPGLTAIKAEYIIGPLSNGNTSLLLDMAKNAGIPWDVIIGSDINRKYKDPQAYLRTAQVLGLH-LAAA----HNGDLEAAHATGLATAFILRPVEHGPHQTDDLAPTG---WDISATDITDLAAQLRAGS-

2mr6A

0.06

0.03

0.55

0.84

dPPAS

-----------------------------------------------------------------MGVVILVLTGDERIAEELRKEVQKHDPNTKDKEKVKEEIEKARKQGRPIVVDDERAKDIAEYAQKEGLRVIVIIV---SQDEEALRKGYEDKKKKGYDVYTSRNEDEAKKKLKEALEKSGSLEHHHHHH-------------------------------------

3wadA1

0.12

0.09

0.79

0.74

wdPPAS

MRVLMTVFANLYNMVPLAWALTTA-EVHIASHPDNVQ-------AISDSG-----AVPVGNDLNIMAALTLNE-LTWQYIHDVFAQYSQIYEYM---STMTADLVAHARQWQPD-IWDALTYAGPIAAEAVGA-PHVRMLFGLDQWGRMRDHFNRLTGERAADDRHDPL--ADWL-ATKGEPHGVAFTTLAVAP-----SFPSE-QPALS---------------------

2iyfB1

0.13

0.12

0.88

0.70

wMUSTER

PAHIAMFSIHVNPSLEVIRELVA-HRVTYAIPPVFADK-------VAAT-GPRPVLY--------HSTLPGPDADPEAWGSTLLDNVEPFLND---AIQALPQLADAYADDIPDLVHDITSYPARVLARRWGVPA-VSLSPNLVAWKG---YEEEVAEPM-WREPRQTERGRAYYAEAWLKENGITETFASHPPRSLVLIPK-ALQPHADRVDYTF-VGRRAADLIEAELP

3h05B

0.15

0.09

0.62

0.64

wPPAS

MKKIAIFGSAFNP-LGHKSVIESLDLVLLEPSINMLD---PIR--------CKLVDAFIKDMGLSN--VQRSDLEQ-ALYVTTYALLEKIQEIYPTADITPDNFFKFAKFYKAEEITECPEKVSTDIRNALIEGKDI---STY-------PTVSELLLNEG---YRETLSGK-----------------------------------------------------------

4xkhE

0.12

0.02

0.19

1.51

dPPAS2

---------------------------------------------------------------------------------------------------------------------------------------------NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSASE-----------------------------------------------

5bvrA

0.11

0.09

0.86

0.69

PPAS

LPSVFDLRKDLSDGILLIQLLEI----IGDENLGRYNRNPRMRVH------------RLENVNKALEYIKSKGMPLTNIGPADIVDGN----LKLILGLIWTLILRFTIADINEEGLTAKEGLLLWCQRKTANYHPEVDVQDFTRSWTNGLAFCALIHQHRPDDKKNHRANMQLAFDIAQKSIGI-------PRLIEVEDVCDVDRPDRSIMTYVAE--FHAFSTLDK---

4cl2A

0.15

0.14

0.92

0.76

Env-PPAS

VTVTTLVEASYQVTSADAIKIQNAD-LILCNGLHL--EETYMKYFTNLKKGTKIITV---TDGINPIGVSESEPNSLTNAMIYIENIRKALTALPYAREYSEKIRNSILPLK-TRIEKVDPEKLVYLAEDFGFK-SLYLWPINSRSPSMMRHAINQMRSHKIKFFSESTNSDQPA-KQVAYETNASYGGVLY-----VDSLSKPDGPAPTYLDLLRFSLTKIVDTLF----

(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=-2.15

Estimated TM-score = 0.46±0.15

Estimated RMSD = 10.5±4.6Å

Download Model 2

C-score=-3.74

Download Model 3

C-score=-4.87

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	2iyfB	0.690	3.54	0.088	0.883
2	2iyaA	0.676	3.46	0.099	0.853
3	3iaaA	0.654	3.98	0.080	0.866
4	3ia7A	0.642	3.80	0.083	0.844
5	2yjnA	0.635	4.32	0.058	0.879
6	5du2A1	0.631	3.80	0.095	0.831
7	3wadA	0.629	3.95	0.095	0.836
8	2p6pA	0.627	3.55	0.053	0.792
9	4rieA	0.627	3.40	0.111	0.788
10	2vg8A	0.620	4.13	0.086	0.836

(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	0.05	3	2acvB	UDP	Rep, Mult	6,8,118,121,123,124,127
2	0.05	3	4xk8a	CLA	Rep, Mult	83,84,87
3	0.03	2	3s29B	UDP	Rep, Mult	7,8,29,57,58,104,124,127
4	0.02	1	1k77A	MG	Rep, Mult	175,176
5	0.02	1	4il6R	HEM	Rep, Mult	93,100
6	0.02	1	5esrA	MG	Rep, Mult	24,224
7	0.02	1	1cqpB	803	Rep, Mult	5,137,218,222
8	0.02	1	3scxA	CA	Rep, Mult	43,47
9	0.02	1	2wpnA	SBY	Rep, Mult	3,5,116,118,222,226
10	0.02	1	3hosA	MG	Rep, Mult	31,142
11	0.02	1	1ahpA	PLP	Rep, Mult	7,57,105,126,127,130
12	0.02	1	3dylB	MG	Rep, Mult	25,83
13	0.02	1	1pn3B	III	Rep, Mult	9,10,120,121,122,175,176,190
14	0.02	1	3udtB	MG	Rep, Mult	184,213
15	0.02	1	2zhcA	MG	Rep, Mult	213,219
16	0.02	1	2z3hB	BLO	Rep, Mult	35,40
17	0.02	1	4l73A	CA	Rep, Mult	11,119,140,142
18	0.02	1	2wscJ	CLA	Rep, Mult	207,210
19	0.02	1	3leeD	MG	Rep, Mult	25,31
20	0.02	1	2acv0	III	Rep, Mult	13,16,17,20,24,49,219

	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	2azdB	0.495	4.96	0.025	0.753	2.4.1.1	NA
2	0.060	2jg1A	0.524	4.36	0.053	0.740	2.7.1.144	NA
3	0.060	1o6cA	0.522	4.52	0.060	0.727	5.1.3.14	45
4	0.060	1wyeA	0.511	4.66	0.067	0.749	2.7.1.45	NA
5	0.060	2fv7A	0.530	4.14	0.082	0.736	2.7.1.15	NA
6	0.060	2c1zA	0.588	4.38	0.055	0.831	2.4.1.115	110
7	0.060	1v4vA	0.521	4.29	0.073	0.714	5.1.3.14	45
8	0.060	1ahpA	0.505	4.99	0.030	0.775	2.4.1.1	NA
9	0.060	3ewmA	0.539	4.51	0.067	0.771	2.7.1.-	NA
10	0.060	3k9eB	0.519	4.25	0.092	0.740	2.7.1.-	101,103
11	0.060	1f6dA	0.524	4.02	0.093	0.697	5.1.3.14	NA
12	0.060	2i6aA	0.551	4.12	0.045	0.762	2.7.1.20	213
13	0.060	1fa9A	0.568	4.88	0.064	0.866	2.4.1.1	NA
14	0.060	1gz5A	0.526	5.25	0.058	0.823	2.4.1.15	NA
15	0.060	3c4qA	0.549	3.93	0.058	0.723	2.4.1.14	34,90
16	0.060	2r4uA	0.572	4.35	0.078	0.788	2.4.1.21	NA
17	0.060	1gqtB	0.527	4.05	0.118	0.719	2.7.1.15	NA
18	0.060	1ua4A	0.516	4.20	0.086	0.727	2.7.1.147	NA
19	0.060	2qvbB	0.510	4.49	0.094	0.723	3.8.1.5	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	0.10	0.689	3.51	0.09	0.88	4m7pA	GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0016999 GO:0046677
1	0.09	0.676	3.46	0.10	0.85	2iyaA	GO:0000166 GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0016999
2	0.09	0.642	3.80	0.08	0.84	3ia7A	GO:0008152 GO:0016758 GO:0016999 GO:0046872
3	0.09	0.657	3.96	0.09	0.87	3rscA	GO:0008152 GO:0016758 GO:0016999
4	0.08	0.625	3.99	0.10	0.84	3wadB	GO:0008152 GO:0016740 GO:0016757 GO:0016758
5	0.08	0.617	3.46	0.07	0.78	3uykA	GO:0016740
6	0.07	0.635	4.32	0.06	0.88	2yjnA	GO:0008152 GO:0016740 GO:0016757 GO:0016758 GO:0017000
7	0.07	0.627	3.55	0.05	0.79	2p6pA	GO:0016740
8	0.07	0.627	3.65	0.08	0.79	3othA	GO:0005975 GO:0008152 GO:0016758 GO:0030259
9	0.07	0.620	4.13	0.09	0.84	2vg8A	GO:0006805 GO:0008152 GO:0008194 GO:0009636 GO:0009651 GO:0009813 GO:0016740 GO:0016757 GO:0016758 GO:0035251 GO:0042178 GO:0043231 GO:0050505 GO:0052696 GO:0080043 GO:0080044
10	0.07	0.610	4.52	0.07	0.86	4relA	GO:0000166 GO:0008152 GO:0016740 GO:0016757 GO:0016758
11	0.07	0.619	3.69	0.10	0.80	4rifB	GO:0016740
12	0.07	0.601	3.81	0.10	0.78	4ambB	GO:0008152 GO:0016740 GO:0016758 GO:0042802
13	0.07	0.588	4.38	0.06	0.83	2c1zA	GO:0008152 GO:0009718 GO:0016740 GO:0016757 GO:0016758 GO:0033303 GO:0033330 GO:0033485 GO:0047213
14	0.07	0.609	3.83	0.07	0.80	4leiA	GO:0016740 GO:0016757
15	0.07	0.576	3.80	0.08	0.75	4an4D	GO:0008152 GO:0016740 GO:0016758 GO:0042802
16	0.07	0.596	3.77	0.06	0.77	4g2tA	GO:0008152 GO:0016758
17	0.07	0.580	4.74	0.09	0.86	3hbjA	GO:0008152 GO:0009698 GO:0009813 GO:0016740 GO:0016757 GO:0016758
18	0.07	0.586	4.00	0.08	0.78	3d0rB	GO:0046527

Consensus prediction of GO terms

Molecular Function	GO:0016758
GO-Score	0.38
Biological Processes	GO:0016999
GO-Score	0.33
Cellular Component
GO-Score

(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.