D-I-TASSER Q5HYA8

D-I-TASSER results for Q5HYA8

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

Summary of the Protein

Uniprot ID: Q5HYA8
Protein Name: Meckelin
Gene Name: TMEM67

Input Sequence in FASTA format

>Q5HYA8 (995 residues)
MATRGGAGVAMAVWSLLSARAVTAFLLLFLPRFLQAQTFSFPFQQPEKCDNNQYFDISAL
SCVPCGANQRQDARGTSCVCLPGFQMISNNGGPAIICKKCPENMKGVTEDGWNCISCPSD
LTAEGKCHCPIGHILVERDINGTLLSQATCELCDGNENSFMVVNALGDRCVRCEPTFVNT
SRSCACSEPNILTGGLCFSSTGNFPLRRISAARYGEVGMSLTSEWFAKYLQSSAAACWVY
ANLTSCQALGNMCVMNMNSYDFATFDACGLFQFIFENTAGLSTVHSISFWRQNLPWLFYG
DQLGLAPQVLSSTSLPTNFSFKGENQNTKLKFVAASYDIRGNFLKWQTLEGGVLQLCPDT
ETRLNAAYSFGTTYQQNCEIPISKILIDFPTPIFYDVYLEYTDENQHQYILAVPVLNLNL
QHNKIFVNQDSNSGKWLLTRRIFLVDAVSGRENDLGTQPRVIRVATQISLSVHLVPNTIN
GNIYPPLITIAYSDIDIKDANSQSVKVSFSVTYEMDHGEAHVQTDIALGVLGGLAVLASL
LKTAGWKRRIGSPMIDLQTVVKFLVYYAGDLANVFFIITVGTGLYWLIFFKAQKSVSVLL
PMPIQEERFVTYVGCAFALKALQFLHKLISQITIDVFFIDWERPKGKVLKAVEGEGGVRS
ATVPVSIWRTYFVANEWNEIQTVRKINSLFQVLTVLFFLEVVGFKNLALMDSSSSLSRNP
PSYIAPYSCILRYAVSAALWLAIGIIQVVFFAVFYERFIEDKIRQFVDLCSMSNISVFLL
SHKCFGYYIHGRSVHGHADTNMEEMNMNLKREAENLCSQRGLVPNTDGQTFEIAISNQMR
QHYDRIHETLIRKNGPARLLSSSASTFEQSIKAYHMMNKFLGSFIDHVHKEMDYFIKDKL
LLERILGMEFMEPMEKSIFYNDEGYSFSSVLYYGNEATLLIFDLLFFCVVDLACQNFILA
SFLTYLQQEIFRYIRNTVGQKNLASKTLVDQRFLI

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	Q5HYA8-D1	1-99,204-517	413		MATRGGAGVAMAVWSLLSARAVTAFLLLFLPRFLQAQTFSFPFQQPEKCDNNQYFDISALSCVPCGANQRQDARGTSCVCLPGFQMISNNGGPAIICKKFPLRRISAARYGEVGMSLTSEWFAKYLQSSAAACWVYANLTSCQALGNMCVMNMNSYDFATFDACGLFQFIFENTAGLSTVHSISFWRQNLPWLFYGDQLGLAPQVLSSTSLPTNFSFKGENQNTKLKFVAASYDIRGNFLKWQTLEGGVLQLCPDTETRLNAAYSFGTTYQQNCEIPISKILIDFPTPIFYDVYLEYTDENQHQYILAVPVLNLNLQHNKIFVNQDSNSGKWLLTRRIFLVDAVSGRENDLGTQPRVIRVATQISLSVHLVPNTINGNIYPPLITIAYSDIDIKDANSQSVKVSFSVTYEMDH
2	Q5HYA8-D2	100-203	104		CPENMKGVTEDGWNCISCPSDLTAEGKCHCPIGHILVERDINGTLLSQATCELCDGNENSFMVVNALGDRCVRCEPTFVNTSRSCACSEPNILTGGLCFSSTGN
3	Q5HYA8-D3	518-995	478		GEAHVQTDIALGVLGGLAVLASLLKTAGWKRRIGSPMIDLQTVVKFLVYYAGDLANVFFIITVGTGLYWLIFFKAQKSVSVLLPMPIQEERFVTYVGCAFALKALQFLHKLISQITIDVFFIDWERPKGKVLKAVEGEGGVRSATVPVSIWRTYFVANEWNEIQTVRKINSLFQVLTVLFFLEVVGFKNLALMDSSSSLSRNPPSYIAPYSCILRYAVSAALWLAIGIIQVVFFAVFYERFIEDKIRQFVDLCSMSNISVFLLSHKCFGYYIHGRSVHGHADTNMEEMNMNLKREAENLCSQRGLVPNTDGQTFEIAISNQMRQHYDRIHETLIRKNGPARLLSSSASTFEQSIKAYHMMNKFLGSFIDHVHKEMDYFIKDKLLLERILGMEFMEPMEKSIFYNDEGYSFSSVLYYGNEATLLIFDLLFFCVVDLACQNFILASFLTYLQQEIFRYIRNTVGQKNLASKTLVDQRFLI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.747

(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	7fh1A	0.74	2.20	0.853	0.769	model1_7fh1A.pdb.gz
2	5nrlA	0.35	9.01	0.043	0.548	model1_5nrlA.pdb.gz
3	6lk8A	0.33	8.64	0.033	0.505	model1_6lk8A.pdb.gz
4	7wb4A	0.33	9.23	0.035	0.520	model1_7wb4A.pdb.gz
5	8d4xA	0.32	9.54	0.049	0.524	model1_8d4xA.pdb.gz
6	7abiA	0.32	8.95	0.035	0.490	model1_7abiA.pdb.gz
7	8bbgD	0.31	9.10	0.036	0.493	model1_8bbgD.pdb.gz
8	6um1A	0.31	8.93	0.038	0.488	model1_6um1A.pdb.gz
9	7n84X	0.31	8.79	0.049	0.479	model1_7n84X.pdb.gz
10	6r9tA	0.31	8.46	0.038	0.461	model1_6r9tA.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:0051082	0.95	unfolded protein binding
GO:0031005	0.95	filamin 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:0044699	0.92	single-organism process
GO:0009987	0.92	cellular process
GO:0032502	0.91	developmental process
GO:0044763	0.90	single-organism cellular process
GO:0044767	0.89	single-organism developmental process
GO:0016043	0.89	cellular component organization
GO:0042384	0.88	cilium assembly
GO:0009653	0.84	anatomical structure morphogenesis
GO:0065007	0.67	biological regulation
GO:0050789	0.65	regulation of biological process
GO:0050794	0.63	regulation of cellular process
GO:0048869	0.60	cellular developmental process
GO:0048858	0.58	cell projection morphogenesis
GO:0060271	0.57	cilium morphogenesis
GO:0051726	0.50	regulation of cell cycle

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:0044464	0.99	cell part
GO:0044422	0.98	organelle part
GO:0044441	0.97	ciliary part
GO:0044424	0.93	intracellular part
GO:0044444	0.90	cytoplasmic part
GO:0044446	0.89	intracellular organelle part
GO:0032991	0.89	macromolecular complex
GO:0016020	0.89	membrane
GO:0044425	0.88	membrane part
GO:0043234	0.88	protein complex
GO:0036038	0.87	MKS complex
GO:0030659	0.87	cytoplasmic vesicle membrane
GO:0005789	0.87	endoplasmic reticulum membrane
GO:0043226	0.73	organelle
GO:0035869	0.70	ciliary transition zone
GO:0043229	0.67	intracellular organelle
GO:0044430	0.65	cytoskeletal part
GO:0043232	0.62	intracellular non-membrane-bounded organelle
GO:0098588	0.61	bounding membrane of organelle
GO:0005815	0.61	microtubule organizing center
GO:0060170	0.60	ciliary membrane
GO:0005813	0.60	centrosome

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	3dnyT	0.159	8.55	0.029	0.243	3.6.5.3	NA
2	0.060	1ea0A	0.214	9.36	0.040	0.346	1.4.1.13	978
3	0.060	2vz9B	0.271	9.41	0.035	0.438	2.3.1.85	NA
4	0.060	1ileA	0.245	8.52	0.036	0.372	6.1.1.5	NA
5	0.060	1l5jA	0.229	8.72	0.053	0.354	4.2.1.3	58

	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	1xmvA	0.094	6.83	0.036	0.127	0.17	ADP	complex1.pdb.gz	67,70,90
2	0.01	1xmsA	0.127	6.68	0.040	0.169	0.16	ANP	complex2.pdb.gz	71,72,80,81,124,125
3	0.01	3cmvC	0.230	9.23	0.030	0.369	0.13	ANP	complex3.pdb.gz	66,88,91
4	0.01	3cmvF	0.237	9.38	0.029	0.386	0.19	ANP	complex4.pdb.gz	66,67,68,69
5	0.01	3ho8C	0.296	9.10	0.043	0.470	0.18	COA	complex5.pdb.gz	88,89,91,92,293
6	0.01	3bg5B	0.301	8.98	0.041	0.474	0.12	BTI	complex6.pdb.gz	91,92,93
7	0.01	3ho8C	0.296	9.10	0.043	0.470	0.18	BTI	complex7.pdb.gz	67,70,83,84

	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.