D-I-TASSER P05305-D1

D-I-TASSER results for P05305-D1

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>P05305 (212 residues)
MDYLLMIFSLLFVACQGAPETAVLGAELSAVGENGGEKPTPSPPWRLRRSKRCSCSSLMD
KECVYFCHLDIIWVNTPEHVVPYGLGSPRSKRALENLLPTKATDRENRCQCASQKDKKCW
NFCQAGKELRAEDIMEKDWNNHKKGKDCSKLGKKCIYQQLVRGRKIRRSSEEHLRQTRSE
TMRNSVKSSFHDPKLKGKPSRERYVTHNRAHW

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MDYLLMIFSLLFVACQGAPETAVLGAELSAVGENGGEKPTPSPPWRLRRSKRCSCSSLMDKECVYFCHLDIIWVNTPEHVVPYGLGSPRSKRALENLLPTKATDRENRCQCASQKDKKCWNFCQAGKELRAEDIMEKDWNNHKKGKDCSKLGKKCIYQQLVRGRKIRRSSEEHLRQTRSETMRNSVKSSFHDPKLKGKPSRERYVTHNRAHW
Prediction	CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCSSSSCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCHHHCCCHHHHCHHHHHHHHHHHCCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Confidence	94588999999998358730110345556644445678999998654445655444445531035542115885389852334589976566667788754678988731479999178887467875433554444543212057735533355468887412101122443223441889999987535677641321135567776779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MDYLLMIFSLLFVACQGAPETAVLGAELSAVGENGGEKPTPSPPWRLRRSKRCSCSSLMDKECVYFCHLDIIWVNTPEHVVPYGLGSPRSKRALENLLPTKATDRENRCQCASQKDKKCWNFCQAGKELRAEDIMEKDWNNHKKGKDCSKLGKKCIYQQLVRGRKIRRSSEEHLRQTRSETMRNSVKSSFHDPKLKGKPSRERYVTHNRAHW
Prediction	44103012000101031225442435635343454456457645455445431414524444012103221022437431000011344444536545556455454204034571540240044355254464456447556545514513550244422545413544554355341541353145414145246524565435254547
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCSSSSCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCHHHCCCHHHHCHHHHHHHHHHHCCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
MDYLLMIFSLLFVACQGAPETAVLGAELSAVGENGGEKPTPSPPWRLRRSKRCSCSSLMDKECVYFCHLDIIWVNTPEHVVPYGLGSPRSKRALENLLPTKATDRENRCQCASQKDKKCWNFCQAGKELRAEDIMEKDWNNHKKGKDCSKLGKKCIYQQLVRGRKIRRSSEEHLRQTRSETMRNSVKSSFHDPKLKGKPSRERYVTHNRAHW

1vt4I3

0.06

2.53

0.59

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

6y5rA1

0.07

2.71

0.50

EigenThreader

SIPIGTILAILTTSFVYLSNVVLFGACIEGVVLRDKFGDAVKGNLVVGTLSWPSPWVIVIGSFF-----------STCGAGLQSLTGAPRLLQAIAKDNIIPFLRVFGHSKANGEPTWALLLTAAIAELGILSMFFLMCYLFVNLACALQTLLLSFMGMSICLALMFISSWYYAIVAMVIAGMIYKYIEYQGAEKEWGDGGPPHTKN-----

6xkwo

0.09

0.08

2.92

0.40

FFAS-3D

LEKNATLLLIFAFLVVTIGGIVEIAPLFYLENTIEKVEGMRPYTPLELTGRDI----YIREGCY-VCHSQ-MIRPMRDEVERYGHYSLAAESMYDHPFQWGSKRTGPDLARGRYSDAWHVEHLSNPQSVVPESVMPSYSYLANVPLDSTWIEDRVSTDALVGVPY---SAEMIAAATEMDALVAYLQVLGTMVDFS----------------

3j3iA

0.10

0.09

3.51

0.87

SPARKS-K

RRVSEVPLAHVSPRWLTREGPQLTRRVPIIDEPPAYESGRSSSPVTSSTSQHEEEMGLFDAEEL----PMQQTVIATEARRRLGRGTLERIQEAAEGQVAQGEVTAEK---NRRIELSARDPQFTGREQITKMLSDGGLELVDKTVGVKGLKEVRSIDGIRRHLGFAVVRTLLSGNSKHVRRINQLIRESNPSAFETEASRMRRLRADWDGD

5uanB

0.08

0.05

2.06

0.59

CNFpred

LKAACLDILILRICTRYTPE----------------------------------------QDTMTFSDGLTLNRTQ-----MHNAGFGPLTDLVFTFANQLLPLEMDDTETG---LLSAICLICGD---------RQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKHMFPKILMITDLRSISAKGAERVITLKME----------------

3ripA

0.05

0.04

1.73

0.83

DEthreader

--C---PSYIPRVAEKILFVGE-S-VQMFEN----------LWMSLQLIIDFY-LGR-------GELFQAF-------------ID-TAQHMLTPTAV-T-H--DVNVAFQ--LPLLHLT-WLGLEKYNVVFL--EQFSQLLHQINS-----TRD-FESIRLAHDHFLSNLLAQSFILLKPVFHCLNEILDLCHSFSLVSQNLLD-------

2pffB

0.06

2.66

0.74

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVILSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM

1kanA

0.07

2.74

0.48

MUSTER

MKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSTEEAEFSHEWTTGEW-----KVE---VNFYSEEILYASQVESDWPLTHGQFFSILKVYQTAKSVEAQKFHDA-ICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVMAGAMLTSASVLTEAVKQSDLPSGYDHLCQFGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKR

2pffB

0.14

0.12

4.17

0.94

HHsearch

DSWESFFVSVRKAITVLFFIG-VRCYPNTSLPPSNEGVPSPLSISNLTQEQVQKTNSHLPAGKQV----EISLVNGAKNLVVYGLNLTLRKAK----APSGLD--QSRIPFSERK----LKFS--NRFLPVASPFHSH--LLVPA-------SDLINKDLVKNNDIQIPVYDTFDGSDLRVLSGSISERIVDCIIR---LPVKWEQFKATHI

5wlcLJ

0.08

3.29

0.59

CEthreader

ELTGATDYVRTLSFIPAAPHLVATGSYDGLIRLYDTRSSGSTPIYSLNHDQPVENVIAVSPTQIVSCGGNNFKVWDLTSNKKLYERGNFNKAVTCLDYVENFDSPMQSALIASSLDGHVKVFDPLDNFQVKFGWKFSGPVLSCAVSPSTAQGNRHLVAGLSSGLLAIRTKKKKSNNFQRMMRGSEYQGDQEHIIHNDKVRSQRRMRAFERNI

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 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 and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3884

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5wlcLO	0.45	5.70	0.057	0.764	model1_5wlcLO.pdb.gz
2	3rkoL	0.44	5.84	0.032	0.764	model1_3rkoL.pdb.gz
3	1gjwA	0.44	5.57	0.078	0.736	model1_1gjwA.pdb.gz
4	1e1cA1	0.44	5.24	0.035	0.717	model1_1e1cA1.pdb.gz
5	7a23a	0.44	5.75	0.032	0.755	model1_7a23a.pdb.gz
6	4r3uA	0.44	5.54	0.024	0.736	model1_4r3uA.pdb.gz
7	7reqB1	0.41	5.42	0.043	0.708	model1_7reqB1.pdb.gz
8	3bicA1	0.35	5.75	0.081	0.627	model1_3bicA1.pdb.gz
9	4xc6A2	0.35	6.31	0.047	0.651	model1_4xc6A2.pdb.gz
10	1ea9C2	0.33	6.21	0.040	0.590	model1_1ea9C2.pdb.gz

(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 Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0031705	1.00	bombesin receptor binding
GO:0031708	0.95	endothelin B receptor binding
GO:0005179	0.75	hormone activity
GO:0031707	0.70	endothelin A receptor binding
GO:0005125	0.51	cytokine activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0032501	0.95	multicellular organismal process
GO:0065007	0.94	biological regulation
GO:0050789	0.94	regulation of biological process
GO:0044699	0.88	single-organism process
GO:0009987	0.85	cellular process
GO:0065008	0.84	regulation of biological quality
GO:0051239	0.84	regulation of multicellular organismal process
GO:0050794	0.84	regulation of cellular process
GO:0003008	0.84	system process
GO:0050880	0.83	regulation of blood vessel size
GO:0044057	0.83	regulation of system process
GO:0044763	0.82	single-organism cellular process
GO:0048518	0.76	positive regulation of biological process
GO:0032879	0.76	regulation of localization
GO:0008217	0.76	regulation of blood pressure
GO:0048522	0.75	positive regulation of cellular process
GO:0019222	0.72	regulation of metabolic process
GO:0007165	0.71	signal transduction
GO:0051049	0.69	regulation of transport
GO:1903530	0.68	regulation of secretion by cell
GO:0051240	0.67	positive regulation of multicellular organismal process
GO:1903522	0.66	regulation of blood circulation
GO:0042310	0.66	vasoconstriction
GO:0031323	0.66	regulation of cellular metabolic process
GO:0080090	0.65	regulation of primary metabolic process
GO:0060255	0.65	regulation of macromolecule metabolic process
GO:0051047	0.65	positive regulation of secretion
GO:0048583	0.65	regulation of response to stimulus
GO:0009893	0.65	positive regulation of metabolic process
GO:0048584	0.64	positive regulation of response to stimulus
GO:0023051	0.64	regulation of signaling
GO:0010646	0.64	regulation of cell communication
GO:0048519	0.63	negative regulation of biological process
GO:0042127	0.63	regulation of cell proliferation
GO:0040012	0.63	regulation of locomotion
GO:0035556	0.63	intracellular signal transduction
GO:0048523	0.62	negative regulation of cellular process
GO:0046883	0.62	regulation of hormone secretion
GO:0030335	0.62	positive regulation of cell migration
GO:0014829	0.62	vascular smooth muscle contraction
GO:0008284	0.62	positive regulation of cell proliferation
GO:0008152	0.61	metabolic process
GO:0014824	0.59	artery smooth muscle contraction
GO:0044237	0.58	cellular metabolic process
GO:0031325	0.58	positive regulation of cellular metabolic process
GO:0010604	0.58	positive regulation of macromolecule metabolic process
GO:0006874	0.58	cellular calcium ion homeostasis
GO:0010468	0.57	regulation of gene expression
GO:0006810	0.57	transport
GO:0044765	0.56	single-organism transport
GO:0032502	0.56	developmental process
GO:0071705	0.55	nitrogen compound transport
GO:0071702	0.55	organic substance transport
GO:0048856	0.55	anatomical structure development
GO:0046903	0.55	secretion
GO:0044767	0.55	single-organism developmental process
GO:0090257	0.54	regulation of muscle system process
GO:0007204	0.54	positive regulation of cytosolic calcium ion concentration
GO:1903532	0.51	positive regulation of secretion by cell
GO:0065009	0.51	regulation of molecular function
GO:0032268	0.51	regulation of cellular protein metabolic process
GO:0051171	0.50	regulation of nitrogen compound metabolic process
GO:0043085	0.50	positive regulation of catalytic activity
GO:0031326	0.50	regulation of cellular biosynthetic process
GO:0007166	0.50	cell surface receptor signaling pathway

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0005615	1.00	extracellular space
GO:0044464	0.91	cell part
GO:0044424	0.83	intracellular part
GO:0005576	0.52	extracellular region
GO:0005737	0.51	cytoplasm

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2v7oA	0.356	5.96	0.037	0.618	2.7.11.17	70
2	0.060	2ow6A	0.399	6.25	0.043	0.745	3.2.1.114	60
3	0.060	1fo4A	0.336	5.15	0.005	0.528	1.17.1.4	NA
4	0.060	2b3xA	0.426	5.38	0.049	0.722	4.2.1.3	NA
5	0.060	1gq2A	0.331	5.85	0.031	0.580	1.1.1.40	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (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.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	1pk0B	0.300	6.06	0.018	0.552	0.10	EMA	complex1.pdb.gz	73,81,84
2	0.01	1b0pA	0.346	5.45	0.025	0.585	0.21	SF4	complex2.pdb.gz	67,69,89
3	0.01	1b0pA	0.346	5.45	0.025	0.585	0.34	SF4	complex3.pdb.gz	70,83,84,86
4	0.01	2c3uA	0.364	6.10	0.024	0.660	0.36	SF4	complex4.pdb.gz	58,63,65,84
5	0.01	2c3oB	0.366	6.09	0.029	0.665	0.23	SF4	complex5.pdb.gz	67,68,82,83
6	0.01	1tuuB	0.345	5.61	0.041	0.585	0.31	AMP	complex6.pdb.gz	56,57,71,86,87
7	0.01	2c3oB	0.366	6.09	0.029	0.665	0.26	SF4	complex7.pdb.gz	59,73,74

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	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.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.