D-I-TASSER Q9H694

D-I-TASSER results for Q9H694

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

Summary of the Protein

Uniprot ID: Q9H694
Protein Name: Protein bicaudal C homolog 1
Gene Name: BICC1

Input Sequence in FASTA format

>Q9H694 (974 residues)
MAAQGEPGYLAAQSDPGSNSERSTDSPVPGSEDDLVAGATLHSPEWSEERFRVDRKKLEA
MLQAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKE
MIMSVLDTKSNRVTLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKS
NQVSIAGQPAGVESARVRIRELLPLVLMFELPIAGILQPVPDPNSPSIQHISQTYNISVS
FKQRSRMYGATVIVRGSQNNTSAVKEGTAMLLEHLAGSLASAIPVSTQLDIAAQHHLFMM
GRNGSNIKHIMQRTGAQIHFPDPSNPQKKSTVYLQGTIESVCLARQYLMGCLPLVLMFDM
KEEIEVDPQFIAQLMEQLDVFISIKPKPKQPSKSVIVKSVERNALNMYEARKCLLGLESS
GVTIATSPSPASCPAGLACPSLDILASAGLGLTGLGLLGPTTLSLNTSTTPNSLLNALNS
SVSPLQSPSSGTPSPTLWAPPLANTSSATGFSAIPHLMIPSTAQATLTNILLSGVPTYGH
TAPSPPPGLTPVDVHINSMQTEGKKISAALNGHAQSPDIKYGAISTSSLGEKVLSANHGD
PSIQTSGSEQTSPKSSPTEGCNDAFVEVGMPRSPSHSGNAGDLKQMMCPSKVSCAKRQTV
ELLQGTKNSHLHSTDRLLSDPELSATESPLADKKAPGSERAAERAAAAQQNSERAHLAPR
SSYVNMQAFDYEQKKLLATKAMLKKPVVTEVRTPTNTWSGLGFSKSMPAETIKELRRANH
VSYKPTMTTTYEGSSMSLSRSNSREHLGGGSESDNWRDRNGIGPGSHSEFAASIGSPKRK
QNKSTEHYLSSSNYMDCISSLTGSNGCNLNSSFKGSDLPELFSKLGLGKYTDVFQQQEID
LQTFLTLTDQDLKELGITTFGARRKMLLAISELNKNRRKLFESPNARTSFLEGGASGRLP
RQYHSDIASVSGRW

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

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q9H694-D1	1-39,723-847	164		MAAQGEPGYLAAQSDPGSNSERSTDSPVPGSEDDLVAGAYVNMQAFDYEQKKLLATKAMLKKPVVTEVRTPTNTWSGLGFSKSMPAETIKELRRANHVSYKPTMTTTYEGSSMSLSRSNSREHLGGGSESDNWRDRNGIGPGSHSEFAASIGSPKRKQNKSTEH
2	Q9H694-D2	40-133	94		TLHSPEWSEERFRVDRKKLEAMLQAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSVLDTKSNRV
3	Q9H694-D3	134-202	69		TLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVESARVRIREL
4	Q9H694-D4	203-284	82		LPLVLMFELPIAGILQPVPDPNSPSIQHISQTYNISVSFKQRSRMYGATVIVRGSQNNTSAVKEGTAMLLEHLAGSLASAIP
5	Q9H694-D5	285-423	139		VSTQLDIAAQHHLFMMGRNGSNIKHIMQRTGAQIHFPDPSNPQKKSTVYLQGTIESVCLARQYLMGCLPLVLMFDMKEEIEVDPQFIAQLMEQLDVFISIKPKPKQPSKSVIVKSVERNALNMYEARKCLLGLESSGVT
6	Q9H694-D6	424-534	111		IATSPSPASCPAGLACPSLDILASAGLGLTGLGLLGPTTLSLNTSTTPNSLLNALNSSVSPLQSPSSGTPSPTLWAPPLANTSSATGFSAIPHLMIPSTAQATLTNILLSG
7	Q9H694-D7	535-652	118		VPTYGHTAPSPPPGLTPVDVHINSMQTEGKKISAALNGHAQSPDIKYGAISTSSLGEKVLSANHGDPSIQTSGSEQTSPKSSPTEGCNDAFVEVGMPRSPSHSGNAGDLKQMMCPSKV
8	Q9H694-D8	653-722	70		SCAKRQTVELLQGTKNSHLHSTDRLLSDPELSATESPLADKKAPGSERAAERAAAAQQNSERAHLAPRSS
9	Q9H694-D9	848-875,925-974	78		YLSSSNYMDCISSLTGSNGCNLNSSFKGKMLLAISELNKNRRKLFESPNARTSFLEGGASGRLPRQYHSDIASVSGRW
10	Q9H694-D10	876-924	49		SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.44

(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	6vr4A	0.33	9.19	0.031	0.533	model1_6vr4A.pdb.gz
2	5w1hA	0.31	9.11	0.033	0.499	model1_5w1hA.pdb.gz
3	6kldA	0.31	9.16	0.032	0.497	model1_6kldA.pdb.gz
4	6r9tA	0.30	9.26	0.056	0.489	model1_6r9tA.pdb.gz
5	4f91B	0.30	9.04	0.042	0.477	model1_4f91B.pdb.gz
6	6um1A	0.30	9.48	0.043	0.494	model1_6um1A.pdb.gz
7	6w2jA	0.29	8.68	0.032	0.456	model1_6w2jA.pdb.gz
8	5amqA	0.28	8.88	0.025	0.448	model1_5amqA.pdb.gz
9	7cpxA	0.28	9.19	0.028	0.457	model1_7cpxA.pdb.gz
10	3qmzA	0.28	9.28	0.030	0.455	model1_3qmzA.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:1901363	0.90	heterocyclic compound binding
GO:0097159	0.90	organic cyclic compound binding
GO:0003676	0.84	nucleic acid binding
GO:0003723	0.79	RNA binding
GO:0044822	0.75	poly(A) RNA binding

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:0065007	0.86	biological regulation
GO:0050794	0.81	regulation of cellular process
GO:0009987	0.69	cellular process
GO:0048523	0.67	negative regulation of cellular process
GO:0044699	0.59	single-organism process
GO:0048583	0.56	regulation of response to stimulus
GO:0009966	0.55	regulation of signal transduction
GO:0048585	0.53	negative regulation of response to stimulus
GO:0009968	0.52	negative regulation of signal transduction
GO:0060828	0.51	regulation of canonical Wnt signaling pathway
GO:0090090	0.50	negative regulation of canonical Wnt 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:0044424	1.00	intracellular part
GO:0043226	0.87	organelle
GO:0043229	0.86	intracellular organelle
GO:0005737	0.85	cytoplasm
GO:0044444	0.75	cytoplasmic part
GO:0043232	0.67	intracellular non-membrane-bounded organelle
GO:0043227	0.65	membrane-bounded organelle
GO:0043231	0.63	intracellular membrane-bounded organelle
GO:0044422	0.62	organelle part
GO:0032991	0.62	macromolecular complex
GO:0044446	0.61	intracellular organelle part
GO:0005634	0.52	nucleus

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	2fgeA	0.260	9.10	0.038	0.413	3.4.24.-	NA
2	0.060	1ofdA	0.259	8.93	0.026	0.406	1.4.7.1	NA
3	0.060	2e1qA	0.257	9.55	0.039	0.427	1.17.3.2 1.17.1.4	NA
4	0.060	1ob2A	0.152	6.87	0.012	0.205	3.6.1.48	NA
5	0.060	3b9jC	0.182	8.75	0.022	0.280	1.17.3.2 1.17.1.4	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	1rkcA	0.109	6.44	0.085	0.143	0.15	III	complex1.pdb.gz	72,76,77,81
2	0.01	1u6hA	0.114	6.03	0.040	0.146	0.17	III	complex2.pdb.gz	52,53,58,61,62,65,68,69
3	0.01	1t01A	0.115	5.94	0.034	0.146	0.17	III	complex3.pdb.gz	68,69,73,118,119,122,125,127,128
4	0.01	1syqA	0.117	5.50	0.065	0.144	0.17	III	complex4.pdb.gz	69,73,115,118,119,122,125,126,127
5	0.01	1xmsA	0.112	6.33	0.048	0.146	0.19	ANP	complex5.pdb.gz	72,76,77,78
6	0.01	3s90A	0.113	5.60	0.076	0.141	0.18	III	complex6.pdb.gz	69,76,118
7	0.01	3cmvG	0.213	8.37	0.028	0.318	0.18	ANP	complex7.pdb.gz	71,73,74,75,76,77
8	0.01	3cmvB	0.216	8.81	0.046	0.338	0.16	ANP	complex8.pdb.gz	74,75,76,77
9	0.01	3cmvG	0.213	8.37	0.028	0.318	0.34	ANP	complex9.pdb.gz	71,72,73,74,75,76,77
10	0.01	1rke0	0.117	6.09	0.027	0.151	0.13	III	complex10.pdb.gz	72,75,76,79,80,83,84

	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.