D-I-TASSER results for P05067-D3

Input Sequence in FASTA format

>P05067 (398 residues)
DAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVI
QHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFN
MLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVP
AVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGE
FSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMD
AEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIH
HGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN

Predicted Secondary Structure

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Sequence
DAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN
Prediction
CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCSSSSCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHCC
Confidence
98765526899714899999999999999999999999999999999987557618999999999999999999999999999999999999999999999999999971488879999999999999999999999999999952988999999999999999999999999999972899999999999999998533036666556532101122112345444533311133222234334565653223455555544566320234443344445433333211013566522332224677764201122344556642128999999999999999999999851468987650575035688168999999861788861145565259

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360                 380
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Sequence
DAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN
Prediction
87424106264574135404503540454145414532551550453155145534640254035204403542553454035203420342146423521540351055545526401510430251244324230510430473555425533540253044125314501520442440164036304500561454445434533544544465545345444464426434565555466554445464554555565535544544456763454555534544455254452625444355152345634434653423300100011121111000000000002153432320103244423465520450353113200131156358

Values range from 0 (buried residue) to 8 (highly exposed residue)

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

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                 220                 240                 260                 280                 300                 320                 340                 360                 380                    |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |
							SS	CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCSSSSCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHCC
							Seq	DAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN
1	5tptA	0.68	0.33	9.52	2.39	FFAS-3D		-DVDVYFETSADDNEHARFQKAKEQLEIRHRNRMDRVKKEWEEAELQAKNLPKAERQTLIQHFQAMVKALEKEAASEKQQLVETHLARVEAMLNDRRRMALENYLAALQSDPPRPHRILQALRRYVRAENKDRLHTIRHYQHVLAVDPEKAAQMKSQVMTHLHVIEERRNQSLSLLYKVPYVAQEIQEEIDELLQEQR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
2	5tptA	0.68	0.33	9.52	1.99	SPARKS-K		-DVDVYFETSADDNEHARFQKAKEQLEIRHRNRMDRVKKEWEEAELQAKNLPKAERQTLIQHFQAMVKALEKEAASEKQQLVETHLARVEAMLNDRRRMALENYLAALQSDPPRPHRILQALRRYVRAENKDRLHTIRHYQHVLAVDPEKAAQMKSQVMTHLHVIEERRNQSLSLLYKVPYVAQEIQEEIDELLQEQR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
3	6tedQ	0.07	0.06	2.57	0.78	EigenThreader		VRLGMGHCFVKLNKLEKARLAFSRALELNALHAAMQAESCYQLARSFHVQEDYDQAFQYYYQATQFAFEKVLKAYEKRDIAKGHLKKVTEQWIELAQQGALSAYGTATRILQVPPEILNNVGALHFRL-------------------------------------GGEAKKYFLASLDRAKAAISVTTSYNLARLYEAMCEFHEAEKLYKNILREHPNYVDCYLRLGAMARDKGNFYEASDWFKEALQINQDHPDAWSLIGNLHLAKQEWGPGQKKFERILKQPSTQSDTYSMLALGNVWLQTLHQPT-------------RDREKEKRHQDRALAIYKQVLRNGIGAVLAHKGYFREFAQVREATADISDVWLNLAHIYVEQKQYISAVQMYENCLR
4	4yn0B	1.00	0.51	14.14	1.54	CNFpred		--------TPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPHHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMIS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
5	6uebA	0.08	0.05	2.12	0.67	DEthreader		CITLAH--SPPEGVL-CL---TY--YLFFHVITLYMNALDWDEEK----------DIGKDLVIVTKDFVDRYTLMLKDLFLSRFNSLMVLLSP-PRYSD-----------------------------------------------GNSGYEVIKILEPYVVNSLVQRAEKFRPL--------GLLDYSRVT--Y--AF--HL--DY-EKWNNH-YTCGLEGLRQKWSLSLLAQVLCPTYNAIYAVEEGASGLIIK---------------SNDQINTGLIWEKVTNVHVVKRALSLKESINWITRVFKRTDFESLSGRESSPRDYLRGAIYLQHVLRYNPYNEMIILVMIMIVFSNVCM--IYLSWSWSND--TS-VFK------------------
6	5tptA	0.68	0.33	9.52	1.33	MUSTER		-DVDVYFETSADDNEHARFQKAKEQLEIRHRNRMDRVKKEWEEAELQAKNLPKAERQTLIQHFQAMVKALEKEAASEKQQLVETHLARVEAMLNDRRRMALENYLAALQSDPPRPHRILQALRRYVRAENKDRLHTIRHYQHVLAVDPEKAAQMKSQVMTHLHVIEERRNQSLSLLYKVPYVAQEIQEEIDELLQEQR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
7	6af0A	0.07	0.07	2.96	0.84	MapAlign		YWMTVALAYAKQNKIDFAIEMLLRGALGIITCICWLYLWKSREAPRVAPDGVPASEAKTKEYYLQLATQSLNDASRILFLARGVLILLKANKAEQLRNALKSFEEAIRVSQGRNMLAVMGKARALFSLNILLGLYYLDASGHVP-TNSPEFIRLYKKAMTYTQKSFKLCATFAGYFLKQFGNVDALAHKALARKEHYDGNLERASDYYRRADDARGGAERGYAKFGAAQLSVLKNDLGEAKLRLEKMIQHSKNYEAMILLGTLYAEEVFANQSAAVKEDKSAEAKKAISLLEGVRSAWKDPKRNLSPDAAVLLNLARLYESESPDKALQCLQQVEQLEIDLATEFFQAALDSCARISQTENDLDIDALLTTIPFNLGRSYEYEGDIDKAIETYEQLLS
8	5tptA	0.68	0.33	9.52	4.79	HHsearch		-DVDVYFETSADDNEHARFQKAKEQLEIRHRNRMDRVKKEWEEAELQAKNLPKAERQTLIQHFQAMVKALEKEAASEKQQLVETHLARVEAMLNDRRRMALENYLAALQSDPPRPHRILQALRRYVRAENKDRLHTIRHYQHVLAVDPEKAAQMKSQVMTHLHVIEERRNQSLSLLYKVPYVAQEIQEEIDELLQEQR--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
9	3pmrA	0.51	0.25	7.21	2.37	FFAS-3D		DGVDIYFGMPGEISEHEGFLRAKMDLEERRMRQINEVMREWAMADNQSKNLPKADRQALNEHFQSILQTLEEQVSGERQRLVETHATRVIALINDQRRAALEGFLAALQADPPQAERVLLALRRYLRAEQKEQRHTLRHYQHVAAVDPEKAQQMRFQVHTHLQVIEERVNQSLGLLDQNPHLAQELRPQIQELLH-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
10	3pmrA	0.51	0.25	7.21	1.79	SPARKS-K		DGVDIYFGMPGEISEHEGFLRAKMDLEERRMRQINEVMREWAMADNQSKNLPKADRQALNEHFQSILQTLEEQVSGERQRLVETHATRVIALINDQRRAALEGFLAALQADPPQAERVLLALRRYLRAEQKEQRHTLRHYQHVAAVDPEKAQQMRFQVHTHLQVIEERVNQSLGLLDQNPHLAQELRPQIQELLH-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


(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

Rank^a	Estimated TM-score^b
1	0.6171


(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.
1	6uebA	0.46	6.43	0.039	0.719
2	3k66A	0.45	3.40	0.293	0.523
3	3pmrA	0.42	3.22	0.503	0.487
4	5tptA	0.42	3.11	0.634	0.487
5	5yfpE	0.41	5.65	0.046	0.588
6	6wjvA	0.40	6.59	0.035	0.648
7	1rw6A	0.40	3.60	0.721	0.477
8	5yfpC	0.40	5.72	0.067	0.573
9	5ganA	0.40	6.34	0.049	0.616
10	3g61A	0.40	5.69	0.020	0.573



(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	0.77	heterocyclic compound binding
GO:0097159	0.77	organic cyclic compound binding
GO:0003677	0.75	DNA binding






(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:

Biological Process (BP)


GO term	Cscore^GO	Name
GO:0044699	1.00	single-organism process
GO:0048856	0.97	anatomical structure development
GO:0044767	0.97	single-organism developmental process
GO:0009653	0.94	anatomical structure morphogenesis
GO:0009987	0.78	cellular process
GO:0044763	0.73	single-organism cellular process
GO:0065007	0.72	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0016043	0.67	cellular component organization
GO:0050794	0.66	regulation of cellular process
GO:0048869	0.62	cellular developmental process
GO:0060560	0.61	developmental growth involved in morphogenesis
GO:0048588	0.61	developmental cell growth
GO:0031175	0.61	neuron projection development
GO:0007409	0.61	axonogenesis
GO:0048731	0.55	system development
GO:0007417	0.53	central nervous system development
GO:0060026	0.52	convergent extension
GO:0001944	0.52	vasculature development
GO:0008152	0.51	metabolic process
GO:0007165	0.51	signal transduction
GO:0080090	0.50	regulation of primary metabolic process
GO:0031323	0.50	regulation of cellular metabolic process






(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:

Cellular Component (CC)


GO term	Cscore^GO	Name
GO:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043227	0.97	membrane-bounded organelle
GO:0044444	0.96	cytoplasmic part
GO:0043229	0.96	intracellular organelle
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0005794	0.80	Golgi apparatus
GO:0044425	0.79	membrane part
GO:0016021	0.78	integral component of membrane
GO:0097458	0.73	neuron part
GO:0043005	0.72	neuron projection
GO:0030424	0.71	axon
GO:0005737	0.71	cytoplasm
GO:0016020	0.54	membrane






(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:

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	3btaA	0.358	6.49	0.033	0.545	3.4.24.69	NA
2	0.060	1mhyD	0.341	5.94	0.076	0.502	1.14.13.25	NA
3	0.060	1fziA	0.338	5.74	0.044	0.492	1.14.13.25	NA
4	0.060	1tiwA	0.270	5.55	0.063	0.384	1.5.1.12 1.5.99.8	NA
5	0.060	1f1sA	0.348	7.02	0.038	0.578	4.2.2.1	NA



(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:

No Binding sites was predicted

References:
1. Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.