I-TASSER results

I-TASSER results for job id Rv3510c

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

Input Sequence in FASTA format

>protein (278 residues)
MTIDVWMQHPTQRFLHGDMFASLRRWTGGSIPETDIPIEATVSSMDAGGVTLGLLSAWRG
PNGQDLISNDAVAEWVRLYPNRFAGLAAVDLDRPMAAVRELRRRVGEGFVGLRVVPWLWG
APPTDRRYYPLFAECVQSAVPFCTQVGHTGPLRPSETGRPIPYIDQVALDFPELVIVCGH
VGYPWTEEMVAVARKHENVYIDTSAYTIKRLPGKLVRFMKTDTGQRKVLFGTNYPMIAHT
HALTGLDELGLSDEARRDFLHGNAVRVFKLDPRGKVQT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MTIDVWMQHPTQRFLHGDMFASLRRWTGGSIPETDIPIEATVSSMDAGGVTLGLLSAWRGPNGQDLISNDAVAEWVRLYPNRFAGLAAVDLDRPMAAVRELRRRVGEGFVGLRVVPWLWGAPPTDRRYYPLFAECVQSAVPFCTQVGHTGPLRPSETGRPIPYIDQVALDFPELVIVCGHVGYPWTEEMVAVARKHENVYIDTSAYTIKRLPGKLVRFMKTDTGQRKVLFGTNYPMIAHTHALTGLDELGLSDEARRDFLHGNAVRVFKLDPRGKVQT
Prediction	CEEEEHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCEEEEHCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEHCCCCCHHHHHHHHHHHHHHCCCEEEHCCCCCCCCCCCHHHHHHHHHHHHHCCCEEHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEHCCCCCHHHHHHHHHHCCCCEEEEHCCCCCCCCCHHHHHHHHHHCCCCCEEEHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	96899857888677557889888876488887778999999999999899899995799987654555999999999889978999857999879999999999998997999858888989998899999999999899699958999988887767778999999998999969998799865999999998599889985667888888999999999859775776578999998999999998799999999999799999989986566789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MTIDVWMQHPTQRFLHGDMFASLRRWTGGSIPETDIPIEATVSSMDAGGVTLGLLSAWRGPNGQDLISNDAVAEWVRLYPNRFAGLAAVDLDRPMAAVRELRRRVGEGFVGLRVVPWLWGAPPTDRRYYPLFAECVQSAVPFCTQVGHTGPLRPSETGRPIPYIDQVALDFPELVIVCGHVGYPWTEEMVAVARKHENVYIDTSAYTIKRLPGKLVRFMKTDTGQRKVLFGTNYPMIAHTHALTGLDELGLSDEARRDFLHGNAVRVFKLDPRGKVQT
Prediction	84733303021472044410430262242414644230430042037351120000013344220220032003005605714000000206315200400320173302000000222213011510230041036260000000000022222300200320130055126020000000101031002004625201000001025311430041006203553361000001131630041047170456114420241026244033535568
	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                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEEHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCEEEEHCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEHCCCCCHHHHHHHHHHHHHHCCCEEEHCCCCCCCCCCCHHHHHHHHHHHHHCCCEEHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEHCCCCCHHHHHHHHHHCCCCEEEEHCCCCCCCCCHHHHHHHHHHCCCCCEEEHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCC
MTIDVWMQHPTQRFLHGDMFASLRRWTGGSIPETDIPIEATVSSMDAGGVTLGLLSAWRGPNGQDLISNDAVAEWVRLYPNRFAGLAAVDLDRPMAAVRELRRRVGEGFVGLRVVPWLWGAPPTDRRYYPLFAECVQSAVPFCTQVGHTGPLRPSETGRPIPYIDQVALDFPELVIVCGHVGYPWTEEMVAVARKHENVYIDTSAYTIKRLPGKLVRFMKTDTGQRKVLFGTNYPMIAHTHALTGLDELGLSDEARRDFLHGNAVRVFKLDPRGKVQT

3irsA

0.25

0.24

0.97

2.67

MUSTER

LIIDFRLRPPARIYTRPDIRNRFTRQLGFEPAPEEKSLELMFEEMAAAGIEQGVCVGRNSSV-LGSVSNADVAAVAKAYPDKFHPVGSIEAATRKEAMAQMQEILDLGIRIVNLEPGVWPMHVDDRRLYPLYAFCEDNGIPVIMMTGGNA--GPDITYTNPEHIDRVLGDFPDLTVVSSHGNWPWVQEIIHVAFRRPNLYLSPDMYLYNLPGHADFIQAANSFLADRMLFGTAYPMCPLKEYTEWFLTLPIKPDAMEKILHGNAERLLAQAGR-----

3irsA

0.25

0.24

0.97

4.41

dPPAS

KIIDFRLRPPARIYTRPDIRNRFTRQLGFEPAAEEKSLELMFEEMAAAGIEQGVCVGRNS-SVLGSVSNADVAAVAKAYPDKFHPVGSIEAATRKEAMAQMQEILDLGIRIVNLEPWATPMHVDDRRLYPLYAFCEDNGIPVIMMTGGN--AGPDITYTNPEHIDRVLGDFPDLTVVSSHGNWPWVQEIIHVAFRRPNLYLSPDMYLYNLPGHADFIQAANSFLADRMLFGTAYPMCPLKEYTEWFLTLPIKPDAMEKILHGNAERLLAQAGR-----

3irsA

0.24

0.97

4.38

wdPPAS

LIIDFRLRPPAMGFLNARIYTRPDIRNEPAPSAEEKSLELMFEEMAAAGIEQGVCVGRNS-SVLGSVSNADVAAVAKAYPDKFHPVGSIEAATRKEAMAQMQEILDLGIRIVNLEPWATPMHVDDRRLYPLYAFCEDNGIPVIMMTGGN--AGPDITYTNPEHIDRVLGDFPDLTVVSSHGNWPWVQEIIHVAFRRPNLYLSPDMYLYNLPGHADFIQAANSFLADRMLFGTAYPMCPLKEYTEWFLTLPIKPDAMEKILHGNAERLLAQAGR-----

3irsA

0.25

0.24

0.97

3.37

wMUSTER

KIIDFRLRPPARIYTRPDIRNRFTRQLGFEPAPEEKSLELMFEEMAAAGIEQGVCVGRNS-SVLGSVSNADVAAVAKAYPDKFHPVGSIEAATRKEAMAQMQEILDLGIRIVNLEPGVWPMHVDDRRLYPLYAFCEDNGIPVIMMTGGNA--GPDITYTNPEHIDRVLGDFPDLTVVSSHGNWPWVQEIIHVAFRRPNLYLSPDMYLYNLPGHADFIQAANSFLADRMLFGTAYPMCPLKEYTEWFLTLPIKPDAMEKILHGNAERLLAQAGR-----

3irsA

0.25

0.24

0.97

4.12

wPPAS

LIIDFRLRPPAMGFLNARIYTRPDIR-EPAPSAEEKSLELMFEEMAAAGIEQGVCVGRN-SSVLGSVSNADVAAVAKAYPDKFHPVGSIEAATRKEAMAQMQEILDLGIRIVNLEPGVWPMHVDDRRLYPLYAFCEDNGIPVIMMTGGNA--GPDITYTNPEHIDRVLGDFPDLTVVSSHGNWPWVQEIIHVAFRRPNLYLSPDMYLYNLPGHADFIQAANSFLADRMLFGTAYPMCPLKEYTEWFLTLPIKPDAMEKILHGNAERLLAQAGR-----

3irsA

0.25

0.24

0.97

8.38

dPPAS2

LIIDFRLRPPARIYTRPDIRNRFTRQLGFEPAAEEKSLELMFEEMAAAGIEQGVCVGRNS-SVLGSVSNADVAAVAKAYPDKFHPVGSIEAATRKEAMAQMQEILDLGIRIVNLEPWATPMHVDDRRLYPLYAFCEDNGIPVIMMTGGN--AGPDITYTNPEHIDRVLGDFPDLTVVSSHGNWPWVQEIIHVAFRRPNLYLSPDMYLYNLPGHADFIQAANSFLADRMLFGTAYPMCPLKEYTEWFLTLPIKPDAMEKILHGNAERLLAQAGR-----

3irsA

0.25

0.24

0.97

3.61

PPAS

LIIDFRLRPPARIYTRPDIRNRFTRQLGFEPAPEEKSLELMFEEMAAAGIEQGVCVGRNS-SVLGSVSNADVAAVAKAYPDKFHPVGSIEAATRKEAMAQMQEILDLGIRIVNLEPWATPMHVDDRRLYPLYAFCEDNGIPVIMMTGGNA--GPDITYTNPEHIDRVLGDFPDLTVVSSHGNWPWVQEIIHVAFRRPNLYLSPDMYLYNLPGHADFIQAANSFLADRMLFGTAYPMCPLKEYTEWFLTLPIKPDAMEKILHGNAERLLAQAGR-----

3irsA

0.25

0.24

0.97

4.71

Env-PPAS

LIIDFRLRPPARIYTRPDIRNRFTRQLGFEPAPEEKSLELMFEEMAAAGIEQGVCVGRNSSV-LGSVSNADVAAVAKAYPDKFHPVGSIEAATRKEAMAQMQEILDLGIRIVNLEPGVWAMHVDDRRLYPLYAFCEDNGIPVIMMTGGN--AGPDITYTNPEHIDRVLGDFPDLTVVSSHGNWPWVQEIIHVAFRRPNLYLSPDMYLYNLPGHADFIQAANSFLADRMLFGTAYPMCPLKEYTEWFLTLPIKPDAMEKILHGNAERLLAQAGR-----

3cjpA

0.18

0.16

0.91

2.17

MUSTER

LIIDGHTHVILPVEKHIKIMDEAG-FSTSIHPETAVNLRDVKKEMKKLND---VVNGKTNSMIVRRNSIKELTNVIQAYPSRYVGFGNVPVGSENDTNSYIEENIVNNLVGIGELTPASG---QIKSLKPIFKYSMDSGLPIWIHAFNPLVL------QDIKEIAELCKAFPKVPVILGHMGGSNWMTAVELAKEIQNLYLDTSAY----FSTFVLKIVINE-LPLKCIFGTDMPFGDLQLSIEAIKKMSNDSYVANAVLGDNISRLLNI--------

3cjpA

0.18

0.17

0.91

3.40

dPPAS

LIIDGHTHVILPVEKHIKIMDEAGLFSTSIHPETAVNLRDVKKEMKKL---NDVVNGKTNSMDVRRNSIKELTNVIQAYPSRYVGFGNVPVGLNDTNSYIEENIVNNKLVGIGELTPASG---QIKSLKPIFKYSMDSGLPIWIHAFNPL------VLQDIKEIAELCKAFPKVPVILGHMGGSNWMTAVELAKEIQNLYLDTSAYFS-----TFVLKIVINELPLKCIFGTDMPFGDLQLSIEAIKKMSNDSYVANAVLGDNISRLLNI--------

(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 1 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=1.44

Estimated TM-score = 0.91±0.06

Estimated RMSD = 3.1±2.2Å

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	3irsA	0.928	1.31	0.238	0.968
2	2dvtA	0.766	3.46	0.238	0.928
3	2f6kA	0.751	3.54	0.142	0.906
4	2qpxA	0.750	3.58	0.103	0.921
5	4l5pA	0.749	3.59	0.207	0.914
6	4b90A	0.749	3.39	0.098	0.906
7	2vr2A	0.747	3.43	0.125	0.906
8	4infA	0.747	3.76	0.204	0.932
9	2ftwA	0.745	3.45	0.129	0.906
10	1kcxA	0.743	3.47	0.125	0.906

(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	0.45	43	1k6wA	FE	Rep, Mult	6,8,145,180,233
2	0.06	6	2dvuA	GRE	Rep, Mult	8,21,145,233,236
3	0.05	5	4kirB	MN	Rep, Mult	6,113,115,145,180,233
4	0.03	3	2vc5B	CO	Rep, Mult	6,113,145,180,205,233
5	0.01	1	1gkp0	III	Rep, Mult	125,126,133,163,166,167,170

	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	2z00A	0.695	3.39	0.115	0.845	3.5.2.3	NA
2	0.060	1xrtA	0.687	3.15	0.130	0.827	3.5.2.3	232
3	0.060	3griB	0.682	3.38	0.138	0.831	3.5.2.3	NA
4	0.060	1k1dA	0.725	3.59	0.118	0.896	3.5.2.-	NA
5	0.060	3giqA	0.696	3.35	0.131	0.853	3.5.1.82	97,105,108,114
6	0.060	1m7jA	0.684	3.57	0.117	0.856	3.5.1.81	NA
7	0.060	2ftyA	0.716	3.69	0.123	0.896	3.5.2.2	NA
8	0.060	1gkpA	0.738	3.55	0.125	0.906	3.5.2.2	232
9	0.060	3iarA	0.680	4.07	0.104	0.881	3.5.4.4	180
10	0.060	3ihnA	0.690	3.35	0.112	0.842	3.5.2.3	NA
11	0.060	1j5sA	0.709	4.09	0.100	0.928	5.3.1.12	184
12	0.060	2vr2A	0.747	3.43	0.125	0.906	3.5.2.2	232
13	0.060	3iacA	0.694	4.36	0.085	0.928	5.3.1.12	NA
14	0.060	1zzmA	0.678	3.21	0.102	0.809	3.1.21.-	232
15	0.060	1ie7C	0.667	3.54	0.108	0.831	3.5.1.5	119
16	0.060	3hm7B	0.697	3.62	0.094	0.856	3.5.2.5	202
17	0.060	2vunD	0.702	3.26	0.122	0.853	3.5.2.18	NA
18	0.060	2q01C	0.704	4.28	0.071	0.942	5.3.1.12	230
19	0.060	1a4lA	0.677	4.11	0.100	0.885	3.5.4.4	180,183

(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	0.53	0.928	1.31	0.24	0.97	3irsA	GO:0016787
1	0.35	0.722	3.77	0.17	0.91	3ij6A	GO:0016787 GO:0046872
2	0.34	0.770	3.66	0.24	0.94	4qroA	GO:0016787 GO:0046872
3	0.31	0.741	3.66	0.17	0.91	4eraA	GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
4	0.29	0.746	3.92	0.13	0.93	4hjwC	GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
5	0.28	0.746	3.88	0.14	0.93	4hk5D	GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
6	0.28	0.741	3.65	0.21	0.91	4ofcA	GO:0001760 GO:0005829 GO:0006568 GO:0006569 GO:0008270 GO:0016787 GO:0016829 GO:0016831 GO:0046872 GO:0046874 GO:0051259 GO:0070062 GO:1904984 GO:1905004 GO:1905012
7	0.25	0.736	3.96	0.18	0.95	4dziC	GO:0016787
8	0.24	0.747	3.71	0.20	0.93	4qrnA	GO:0016787 GO:0046872
9	0.23	0.747	3.62	0.20	0.91	4icmA	GO:0016787 GO:0046872
10	0.19	0.759	3.44	0.14	0.91	2f6kA	GO:0016787 GO:0046872
11	0.15	0.766	3.46	0.24	0.93	2dvtA	GO:0016787 GO:0046872
12	0.14	0.709	3.80	0.22	0.88	2gwgA	GO:0016787 GO:0046872
13	0.13	0.729	3.52	0.23	0.89	3nurA	GO:0016787
14	0.07	0.574	4.71	0.07	0.81	1bgaA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
15	0.07	0.541	3.78	0.10	0.70	3ve7A	GO:0003824 GO:0004590 GO:0006207 GO:0008152 GO:0016829
16	0.06	0.414	5.88	0.06	0.68	2d5lA	GO:0004177 GO:0006508 GO:0008233 GO:0008236 GO:0016787
17	0.06	0.399	6.26	0.05	0.67	2vn4A
18	0.06	0.366	6.59	0.03	0.67	2c2xA	GO:0000105 GO:0003824 GO:0004477 GO:0004488 GO:0005576 GO:0005829 GO:0005886 GO:0006164 GO:0006730 GO:0008152 GO:0008652 GO:0009086 GO:0009396 GO:0016491 GO:0016787 GO:0035999 GO:0040007 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016787	GO:0046872	GO:0001760
GO-Score	0.90	0.79	0.51
Biological Processes	GO:1904984	GO:0006568
GO-Score	0.51	0.51
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.