D-I-TASSER results for P24387-D1

Input Sequence in FASTA format

>P24387 (182 residues)
MSPNFKLQCHFILIFLTALRGESRYLELREAADYDPFLLFSANLKRELAGEQPYRRALRC
LDMLSLQGQFTFTADRPQLHCAAFFISEPEEFITIHYDQVSIDCQGGDFLKVFDGWILKG
EKFPSSQDHPLPSAERYIDFCESGLSRRSIRSSQNVAMIFFRVHEPGNGFTLTIKTDPNL
FP

Predicted Secondary Structure

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Sequence
MSPNFKLQCHFILIFLTALRGESRYLELREAADYDPFLLFSANLKRELAGEQPYRRALRCLDMLSLQGQFTFTADRPQLHCAAFFISEPEEFITIHYDQVSIDCQGGDFLKVFDGWILKGEKFPSSQDHPLPSAERYIDFCESGLSRRSIRSSQNVAMIFFRVHEPGNGFTLTIKTDPNLFP
Prediction
CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCSSSCCCCCCCCCCCCCCCCCHHHHSSSSSCCCSSSSSCCCCCCSSSSSSSSCCCSSSSSSSSSSSCCCCCCCSSSSSSSSSSCCCSCCCCCCCCCCHHHHHHHHCCCCCCCCSSSSCCCSSSSSSSSCCCCCCSSSSSSSCCCCCC
Confidence
99313457889999998751842467776404688523246101346786433232010023563484489972899956999997088818999998874158999779998601875625778456888546667875079999850551132589998705899827999994589999

H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

                  20                  40                  60                  80                 100                 120                 140                 160                 180
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Sequence
MSPNFKLQCHFILIFLTALRGESRYLELREAADYDPFLLFSANLKRELAGEQPYRRALRCLDMLSLQGQFTFTADRPQLHCAAFFISEPEEFITIHYDQVSIDCQGGDFLKVFDGWILKGEKFPSSQDHPLPSAERYIDFCESGLSRRSIRSSQNVAMIFFRVHEPGNGFTLTIKTDPNLFP
Prediction
85451333000000001014453433424632753212023462456347643143023002011452403131754622000000142643040305314040643210101212313354123664253325620331057644443131222000010203444420102043364468

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 AttentionPotential. 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                    |                   |                   |                   |                   |                   |                   |                   |                   |
							SS	CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCSSSCCCCCCCCCCCCCCCCCHHHHSSSSSCCCSSSSSCCCCCCSSSSSSSSCCCSSSSSSSSSSSCCCCCCCSSSSSSSSSSCCCSCCCCCCCCCCHHHHHHHHCCCCCCCCSSSSCCCSSSSSSSSCCCCCCSSSSSSSCCCCCC
							Seq	MSPNFKLQCHFILIFLTALRGESRYLELREAADYDPFLLFSANLKRELAGEQPYRRALRCLDMLSLQGQFTFTADRPQLHCAAFFISEPEEFITIHYDQVSIDCQGGDFLKVFDGWILKGEKFPSSQDHPLPSAERYIDFCESGLSRRSIRSSQNVAMIFFRVHEPGNGFTLTIKTDPNLFP
1	1sfpA	0.21	0.13	4.01	1.21	SPARKS-K		-----------------------------------------------------LPRNTNCGGILKEESGVIATYYGPKTNCVWTIQMPPEYHVRVSIQYLQLNCNK-ESLEIIDG---------------LPGSPVLGKICE--GSLMDYRSSGSIMTVKYIREPPASFYEVLYFQDPQA--
2	2qqmA	0.17	0.10	3.26	2.30	HHsearch		---------------------------------------------------------PECSQNYTTPGV--IKSPGNSLECTYIVFAPKMSEIILEFESFDLECR-YDRLEIWDGFPDV--------------GPHIGRYCGQK-TPGRIRSSSGILSMVFYTDIAKEGFSANYSVLQSSVS
3	1sppB	0.13	0.08	2.66	1.55	CNFpred		-----------------------------------------------------INGPDECGRVIK-DTSGSISNTDQKNLCTWTILMKPDQKVRMAIPYLNLACG-KEYVEVFDGLLS---------------GPSYGKLCAGA--AIVFLSTANTMTIKYNRISGSSPFLIYFYGSS----
4	5mqrA	0.07	0.05	2.32	1.00	DEthreader		-KEG-LSPVV-GVHNIQL-KDGY-WATVYNPSWPLVHPQVSYSVKEDWI-------IYSPAPVSL--EWLKLQDKDPFDYAKVERKIPASELKVSFDLSAGQNDK--GILQIDFLDEN---SIA------C----SRLELTPGNYTYVEAVLSIERIVFRTGEQEPLAEYRIAVKTS-STDK
5	5fwsA2	0.14	0.08	2.64	1.14	SPARKS-K		---------------------------------------------------------GACGGNYSAM-SSVVYSPDTGRVCYWTIRVPGASHIHFSFPLFDIRDSA-DMVELLDG----------------YTHRVLARFHGRSRPPLSFNVSLDFVILYFFSDNQAQGFAVLYQAVK----
6	2qqmA1	0.15	0.09	2.97	0.82	MapAlign		--------------------------------------------------------PECSQNYTTPSGVIKSPKYPNSLECTYIVFAPKMSEIILEFESFDLEPDRYDRLEIWDGFP-----------DVG---PHIGRYCGQKTP-GRIRSSSGILSMVFYTDIAKEGFSANYSVLQS---
7	2qqmA1	0.16	0.10	3.27	0.75	CEthreader		---------------------------------------------------------PECSQNYTTSGVIKSPKYPNSLECTYIVFAPKMSEIILEFESFDLEPDRYDRLEIWDGFPDVG--------------PHIGRYCGQKTP-GRIRSSSGILSMVFYTDIAKEGFSANYSVLQSSVS
8	6fzvD	0.22	0.20	6.24	0.80	MUSTER		LELHPACRYDALEVFLGRFCGTFRPAPLV-APGNQVTLRMTTDEGTGGRGLLWYSGRAFCGGRLKAQGTLTWPESDPGISCSWHIIAPPDQVIALTFEKFDLECR-YDSVSVFNGAVSDDSR-------------RLGKFCGDAVPGS-ISSEGNELLVQFVSSVTADGFSASYKTLPR---
9	2qqoA	0.18	0.10	3.41	2.11	HHsearch		----------------------------------------------------------DCSKNFTSPN-GTIESPGHNLDCTFTILAKPKMEIILQFLIFDLECK-YDWLDIWDGIPHV--------------GPLIGKYCGTK-TPSELRSSTGILSLTFHTDVAKDGFSARYYLVHCNVP
10	1sppB	0.18	0.10	3.38	0.70	FFAS-3D		----------------------------------------------------------ECGRVIKDTSGSISNTDRQKNLCTWTILMKPDQKVRMAIPYLNLACGK-EYVEVFDG---------------LLSGPSYGKLCAGA--AIVFLSTANTMTIKYNRISSSSPFLIYFYGSS---P


(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	0.7182


(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 AttentionPotential, 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	3kq4B	0.58	3.40	0.126	0.725
2	4es8A	0.55	4.63	0.086	0.813
3	5mqrA	0.54	4.74	0.061	0.830
4	3hbzA	0.54	4.56	0.085	0.824
5	2wnoA	0.52	2.24	0.128	0.599
6	1sppB	0.52	2.35	0.156	0.599
7	2qqmA1	0.51	2.30	0.155	0.593
8	3s30A	0.51	4.68	0.083	0.775
9	4gzaH	0.51	2.15	0.200	0.577
10	2qqoA1	0.50	2.16	0.171	0.577



(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:0042562	1.00	hormone binding
GO:0051424	0.96	corticotropin-releasing hormone 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:0010817	1.00	regulation of hormone levels
GO:0050794	0.97	regulation of cellular process
GO:0044699	0.97	single-organism process
GO:0009987	0.97	cellular process
GO:2000310	0.96	regulation of N-methyl-D-aspartate selective glutamate receptor activity
GO:1900011	0.96	negative regulation of corticotropin-releasing hormone receptor activity
GO:0097211	0.96	cellular response to gonadotropin-releasing hormone
GO:0071392	0.96	cellular response to estradiol stimulus
GO:0071391	0.96	cellular response to estrogen stimulus
GO:0071356	0.96	cellular response to tumor necrosis factor
GO:0071320	0.96	cellular response to cAMP
GO:0071314	0.96	cellular response to cocaine
GO:0071277	0.96	cellular response to calcium ion
GO:0051460	0.96	negative regulation of corticotropin secretion
GO:0048149	0.96	behavioral response to ethanol
GO:0045055	0.96	regulated exocytosis
GO:0035865	0.96	cellular response to potassium ion
GO:0035690	0.96	cellular response to drug
GO:0033554	0.96	cellular response to stress
GO:0009755	0.96	hormone-mediated signaling pathway
GO:0007565	0.96	female pregnancy
GO:0006954	0.96	inflammatory response
GO:0001963	0.96	synaptic transmission, dopaminergic
GO:0051705	0.70	multi-organism behavior
GO:0002125	0.69	maternal aggressive behavior
GO:0008152	0.60	metabolic process
GO:0042445	0.52	hormone 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:0005615	1.00	extracellular space
GO:0044464	0.98	cell part
GO:0044444	0.97	cytoplasmic part
GO:0043679	0.96	axon terminus
GO:0043204	0.96	perikaryon
GO:0043196	0.96	varicosity
GO:0031045	0.96	dense core granule
GO:0030425	0.96	dendrite
GO:0005874	0.96	microtubule
GO:0005794	0.96	Golgi apparatus
GO:0005783	0.96	endoplasmic reticulum
GO:0005771	0.96	multivesicular body
GO:0005767	0.96	secondary lysosome
GO:0005634	0.96	nucleus
GO:0005622	0.96	intracellular






(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	2hykA	0.464	4.21	0.067	0.681	3.2.1.39	NA
2	0.060	3gtnA	0.478	4.12	0.037	0.703	3.2.1.136	NA
3	0.060	1olrA	0.474	4.30	0.073	0.709	3.2.1.4	NA
4	0.060	1nt0A	0.471	2.59	0.119	0.555	3.4.21.104	79,83,108,111,141,165
5	0.060	2wgqB	0.484	5.29	0.043	0.819	1.4.3.21	120



(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	Predicted binding site residues
1	0.02	1spp0	0.499	2.37	0.142	0.577	0.47	III	67,69,94,173,175,176,178



(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.

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.