I-TASSER results

I-TASSER results for job id Rv1506c

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

Input Sequence in FASTA format

>protein (166 residues)
MRIVNAADPFSINDLGCGYGALLDYLDARGFKTDYTGIDVSPEMVRAAALRFEGRANADF
ICAARIDREADYSVASGIFNVRLKSLDTEWCAHIEATLDMLNAASRRGFSFNCLTSYSDA
SKMRDDLYYADPCALFDLCKRRYSKSVALLHDYGLYEFTILVRKAS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRIVNAADPFSINDLGCGYGALLDYLDARGFKTDYTGIDVSPEMVRAAALRFEGRANADFICAARIDREADYSVASGIFNVRLKSLDTEWCAHIEATLDMLNAASRRGFSFNCLTSYSDASKMRDDLYYADPCALFDLCKRRYSKSVALLHDYGLYEFTILVRKAS
Prediction	CCCCCCCCCCEEEEHCCCCCHHHHHHHHHCCCCEEEEEHCCHHHHHHHHHHCCCCCCEEEEHCCCCCCCCCEEEHCCHCCEHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEHCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCEEEEHCCCCCCEEEEEEHCC
Conf.Score	9767999998589977996599999999899868999979999999999988999875899778999998789984534644586578899999999999999859959998578888756645676448999999999997699689985888886799999689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRIVNAADPFSINDLGCGYGALLDYLDARGFKTDYTGIDVSPEMVRAAALRFEGRANADFICAARIDREADYSVASGIFNVRLKSLDTEWCAHIEATLDMLNAASRRGFSFNCLTSYSDASKMRDDLYYADPCALFDLCKRRYSKSVALLHDYGLYEFTILVRKAS
Prediction	4641647644442631300130031027442504000221055006303751673440412216136540000000000010234424401630350053026204300000002534446434531122314300410374114402022413430000002358
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCEEEEHCCCCCHHHHHHHHHCCCCEEEEEHCCHHHHHHHHHHCCCCCCEEEEHCCCCCCCCCEEEHCCHCCEHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEHCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHCCCCEEEEHCCCCCCEEEEEEHCC
MRIVNAADPFSINDLGCGYGALLDYLDARGFKTDYTGIDVSPEMVRAAALRFEGRANADFICAARIDREADYSVASGIFNVRLKSLDTEWCAHIEATLDMLNAASRRGFSFNCLTSYSDASKMRDDLYYADPCALFDLCKRRYSKSVALLHDYGLYEFTILVRKAS

3g5lA

0.19

0.18

0.96

1.60

MUSTER

KKMLPDFNQKTVLDLGCGFGWHCIYAAEHGAK-KVLGIDLSERMLTEAKRKT-TSPVVCYEQKAIED----IAIEPDAYNVVLSSLALHYIASFDDICKKVYINLKSSGSFIFSVEHPVFTADGRQDWYTDTGNKLHWPVDRYFNESMRTSHFLGEDVQKYHRTVT

3ofjA

0.12

0.11

0.94

2.10

dPPAS

RLSLSSGAVSNGLEIGCAAGAFTEKLAPHC--KRLTVIDVMPRAIGRACQRTKRWSHISWAATDSTAELFDLIVVAEVLYYLED------MTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHV--AGAETVITILTEALTERVQCQGQSADEDCLLARFRNP

4iscA

0.19

0.16

0.86

2.30

wdPPAS

LAALPRERYRAIFEPGCANGELSADLAER---CDLVCCDTSTQAVELARQRLADVPHARVVQARLP-HQW----PAGQFDLIVFSELYLDAADLHRLIDCALAALSPDGQLLACHWRP-----------LNAQAVHAILAERLSHRLFSHHE---QDFLLDLWSR-

4iscA

0.19

0.16

0.86

2.28

wMUSTER

LAALPRERYRAIFEPGCANGELSADLAER---CDLVCCDTSTQAVELARQRLADVPHARVVQARLPHQ-----WPAGQFDLIVFSELYLDAADLHRLIDCALAALSPDGQLLACHWRPL-----------NAQAVHAILAERLSHRLFSHHE---QDFLLDLWSR-

4iscA

0.19

0.16

0.84

2.37

wPPAS

LAALPRERYRAIFEPGCANGELSADLAER---CDLVCCDTSTQAVELARQRLADVPHARVVQARLPAGQFDLIVFSELY---------LDAADLHRLIDCALAALSPDGQLLACHWRPL-----------NAQAVHAILAERLSHRLFSHHE---QDFLLDLWSR-

4iscA

0.19

0.16

0.84

2.76

dPPAS2

LAALPRERYRAIFEPGCANGELSADLAER---CDLVCCDTSTQAVELARQRLADVPHARVVQARWPAGQFDLIVFSELYL---------DAADLHRLIDCALAALSPDGQLLACHWRP-----------LNAQAVHAILAERLSHRLFSHHE---QDFLLDLWSR-

4iscA

0.19

0.16

0.84

2.14

PPAS

LAALPRERYRAIFEPGCANGELSADLAER---CDLVCCDTSTQAVELARQRLADVPHARVVQARWPAGQFDLIVFSELYL---------DAADLHRLIDCALAALSPDGQLLACHWRPL-----------NAQAVHAILAERLSHRLFSHHE---QDFLLDLWSR-

3i9fB

0.12

0.11

0.90

2.15

Env-PPAS

LPNIFEGKKGVIVDYGCGNGFYCKYLLEFAT--KLYCIDINVIALKEVKEKFD---SVITLSDPIPDNSVDFILFANSFH---------DMDDKQHVISEVKRILKDDGRVIIIDRKENTGIGPPLSIRMDEKDYMGWFSNFV---VEKRFNPTPYHFGLVLKRKT

4kwcA

0.19

0.18

0.96

1.53

MUSTER

YQLTFKKTPVSILDIGCGQGQMLEYISKQLPLADLTGIDSSEEAIHCANKL---NIKANFICTDIKNFSSH----AKIYDVILIHLCFGLFENPIELLEQLLPYLSNESMIYIVDNRDSIESGLSSVQSKEEELYIYDQYHASLTLEQLLTYITKPREDMMYKIGT

4iscA

0.19

0.16

0.84

2.09

dPPAS

LAALPRERYRAIFEPGCANGELSADLAER---CDLVCCDTSTQAVELARQRLADVPHARVVQARWPAGQFDLIVFSELYL---------DAADLHRLIDCALAALSPDGQLLACHWRP-----------LNAQAVHAILAERLSHRLFSHHE---QDFLLDLWSR-

(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=-0.57

Estimated TM-score = 0.64±0.13

Estimated RMSD = 6.1±3.8Å

Download Model 2

C-score=-0.59

Download Model 3

C-score=-2.46

Download Model 4

C-score=-3.09

Download Model 5

C-score=-4.65

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	3ofjA	0.800	2.44	0.141	0.940
2	3dh0B	0.780	2.79	0.133	0.952
3	4iscA	0.777	1.84	0.175	0.861
4	5egpA	0.765	3.02	0.138	0.958
5	4krgA	0.762	2.74	0.103	0.934
6	2iipA	0.762	2.83	0.108	0.952
7	5thyA	0.759	3.28	0.136	0.976
8	3sm3A	0.759	3.12	0.144	0.958
9	3dp7A	0.758	2.83	0.115	0.946
10	2a14A	0.757	2.97	0.119	0.958

(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	0.22	12	4er6A	AW2	Rep, Mult	3,14,16,17,18,22,39,40,41,63,83,85,112,113,160
2	0.21	12	2zbqA	SAH	Rep, Mult	16,17,18,22,39,40,41,63,66,85,86,93
3	0.04	2	3bgdB	PM6	Rep, Mult	2,5,110,112,149,162
4	0.02	1	2o06A	MG	Rep, Mult	5,80,108,109
5	0.02	1	1xcbA	NAD	Rep, Mult	21,22,25,153

	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	0.165	2iftA	0.666	2.95	0.094	0.837	2.1.1.52	29
2	0.101	3hnrA	0.723	2.95	0.112	0.916	2.1.1.-	NA
3	0.095	3e05B	0.731	2.43	0.075	0.879	2.1.1.132	NA
4	0.093	1f38A	0.705	2.55	0.112	0.861	2.1.1.-	NA
5	0.081	3grzB	0.697	2.71	0.113	0.855	2.1.1.-	NA
6	0.080	2ex4A	0.745	3.04	0.096	0.940	2.1.1.-	NA
7	0.079	3dxxA	0.687	3.01	0.132	0.861	2.1.1.33	21,40
8	0.076	2pxxA	0.716	2.80	0.171	0.879	3.4.24.71	NA
9	0.069	2fcaA	0.712	2.65	0.092	0.855	2.1.1.33	NA
10	0.067	1pjzA	0.662	3.69	0.082	0.934	2.1.1.67	NA
11	0.067	1yzhB	0.703	2.56	0.121	0.837	2.1.1.33	21
12	0.067	3ckkA	0.668	2.93	0.150	0.819	2.1.1.33	17,19,83
13	0.060	2b3tA	0.717	2.67	0.143	0.885	2.1.1.-	67
14	0.060	3bwmA	0.718	2.79	0.087	0.885	2.1.1.6	NA
15	0.060	3e05D	0.735	2.37	0.068	0.879	2.1.1.132	NA
16	0.060	1o54A	0.719	2.65	0.103	0.874	2.1.1.-	NA
17	0.060	2fk8A	0.737	3.01	0.089	0.952	2.1.1.-	95
18	0.060	2frxA	0.733	2.98	0.166	0.910	2.1.1.-	NA
19	0.060	3bgdA	0.720	3.08	0.102	0.940	2.1.1.67	67
20	0.060	2iipA	0.762	2.83	0.108	0.952	2.1.1.1	16,18,39,67
21	0.060	1nt2A	0.716	3.04	0.078	0.916	2.1.1.-	NA
22	0.060	2a14A	0.757	2.97	0.119	0.958	2.1.1.49	16,18,46,83
23	0.060	1jq3A	0.725	3.26	0.110	0.928	2.5.1.16	NA
24	0.060	2cl5A	0.721	2.77	0.100	0.885	2.1.1.6	NA
25	0.060	3g5tA	0.727	3.51	0.119	0.946	2.1.1.145	17,26
26	0.060	3ccfB	0.714	2.89	0.173	0.898	2.1.1.144	16,39
27	0.060	3i58A	0.718	3.21	0.173	0.940	2.1.1.-	NA
28	0.060	2ip2A	0.754	2.88	0.115	0.940	2.1.1.-	NA
29	0.060	1wznA	0.720	3.17	0.158	0.922	2.1.1.-	NA
30	0.060	1xxlA	0.746	3.08	0.121	0.946	2.1.1.-	NA
31	0.060	1bhjA	0.736	3.24	0.155	0.964	2.1.1.20	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	0.784	1.83	0.17	0.87	4iscA	GO:0008168 GO:0008757 GO:0009312 GO:0009877 GO:0016740 GO:0032259
1	0.25	0.721	2.99	0.17	0.92	3ccfB	GO:0008152 GO:0008168 GO:0016740 GO:0030798 GO:0032259
2	0.22	0.701	3.24	0.18	0.92	2p35A	GO:0005737 GO:0008168 GO:0016740 GO:0030798 GO:0032259
3	0.22	0.759	3.12	0.14	0.96	3sm3A	GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872
4	0.20	0.758	2.78	0.17	0.93	3l8dA	GO:0008152 GO:0008168 GO:0016740 GO:0032259
5	0.19	0.705	2.55	0.11	0.86	1f38A	GO:0006479 GO:0008168 GO:0008276 GO:0009236 GO:0016740 GO:0032259 GO:0046140
6	0.18	0.738	3.11	0.10	0.95	4krhA	GO:0008152 GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
7	0.16	0.780	2.79	0.13	0.95	3dh0B	GO:0005737 GO:0008757 GO:0032259 GO:0046872 GO:0051536 GO:0051539
8	0.15	0.801	2.37	0.15	0.93	3ofkA	GO:0008168 GO:0008757 GO:0009312 GO:0009877 GO:0016740 GO:0032259
9	0.15	0.777	2.76	0.11	0.95	4krgA	GO:0008152 GO:0008168 GO:0032259
10	0.15	0.744	3.15	0.12	0.95	3bkxA	GO:0008168 GO:0016740 GO:0032259
11	0.15	0.734	3.08	0.11	0.93	3duwA	GO:0008168 GO:0008171 GO:0016740 GO:0032259
12	0.15	0.662	3.03	0.11	0.84	3fycA	GO:0000154 GO:0000179 GO:0003723 GO:0005737 GO:0006364 GO:0008168 GO:0008649 GO:0016433 GO:0016740 GO:0031167 GO:0032259
13	0.14	0.769	2.83	0.09	0.95	1vl5A	GO:0008152 GO:0008168 GO:0016740 GO:0032259
14	0.14	0.745	3.20	0.12	0.96	3uj7A	GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
15	0.14	0.731	2.91	0.10	0.92	3dliA
16	0.14	0.739	3.15	0.12	0.94	3lccA	GO:0005886 GO:0006952 GO:0008168 GO:0008757 GO:0016740 GO:0018708 GO:0019762 GO:0032259
17	0.14	0.739	3.17	0.16	0.96	1y8cA	GO:0008168 GO:0016740 GO:0032259
18	0.14	0.765	3.02	0.14	0.96	5egpA	GO:0008168 GO:0016740 GO:0032259
19	0.14	0.754	3.02	0.18	0.95	3d2lC	GO:0008168 GO:0016740 GO:0032259
20	0.14	0.751	3.01	0.11	0.95	2gluA	GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259
21	0.14	0.725	3.02	0.14	0.93	3bkwA	GO:0008152 GO:0008168 GO:0032259
22	0.14	0.749	3.15	0.15	0.95	4pneB	GO:0008152 GO:0008168 GO:0016740 GO:0032259
23	0.14	0.723	2.53	0.12	0.88	3tmaA	GO:0003723 GO:0008168 GO:0016740 GO:0032259
24	0.14	0.740	3.26	0.16	0.96	4mwzB	GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
25	0.13	0.724	2.78	0.14	0.89	3i9fB	GO:0008152 GO:0008168 GO:0032259 GO:0046872
26	0.10	0.694	2.75	0.13	0.86	2pjdA	GO:0003676 GO:0005737 GO:0005829 GO:0006364 GO:0008168 GO:0008649 GO:0008990 GO:0016740 GO:0031167 GO:0032259 GO:0052914 GO:0070475
27	0.08	0.750	2.87	0.16	0.95	3dtnA	GO:0046872
28	0.08	0.693	3.28	0.13	0.90	3cc8A
29	0.07	0.738	3.02	0.17	0.95	5je1A	GO:0008168 GO:0016740 GO:0032259
30	0.07	0.749	2.99	0.11	0.96	2an3B	GO:0004603 GO:0005829 GO:0008168 GO:0016740 GO:0032259 GO:0042418 GO:0042423
31	0.07	0.720	3.17	0.16	0.92	1wznA
32	0.07	0.761	2.79	0.11	0.95	2i62B	GO:0005737 GO:0005829 GO:0008112 GO:0008168 GO:0010243 GO:0016740 GO:0031100 GO:0032259 GO:0042493

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0030798
GO-Score	0.44	0.42
Biological Processes	GO:0032259	GO:0009312	GO:0009877
GO-Score	0.75	0.31	0.31
Cellular Component	GO:0044424
GO-Score	0.44

(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.