D-I-TASSER results for P09914

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

Summary of the Protein

Uniprot ID: P09914
Protein Name: Interferon-induced protein with tetratricopeptide repeats 1
Gene Name: IFIT1

Input Sequence in FASTA format

>P09914 (478 residues)
MSTNGDDHQVKDSLEQLRCHFTWELSIDDDEMPDLENRVLDQIEFLDTKYSVGIHNLLAY
VKHLKGQNEEALKSLKEAENLMQEEHDNQANVRSLVTWGNFAWMYYHMGRLAEAQTYLDK
VENICKKLSNPFRYRMECPEIDCEEGWALLKCGGKNYERAKACFEKVLEVDPENPESSAG
YAISAYRLDGFKLATKNHKPFSLLPLRQAVRLNPDNGYIKVLLALKLQDEGQEAEGEKYI
EEALANMSSQTYVFRYAAKFYRRKGSVDKALELLKKALQETPTSVLLHHQIGLCYKAQMI
QIKEATKGQPRGQNREKLDKMIRSAIFHFESAVEKKPTFEVAHLDLARMYIEAGNHRKAE
ENFQKLLCMKPVVEETMQDIHFHYGRFQEFQKKSDVNAIIHYLKAIKIEQASLTRDKSIN
SLKKLVLRKLRRKALDLESLSLLGFVYKLEGNMNEALEYYERALRLAADFENSVRQGP

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 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.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P09914-D1	1-67	67		MSTNGDDHQVKDSLEQLRCHFTWELSIDDDEMPDLENRVLDQIEFLDTKYSVGIHNLLAYVKHLKGQ
2	P09914-D2	68-155	88		NEEALKSLKEAENLMQEEHDNQANVRSLVTWGNFAWMYYHMGRLAEAQTYLDKVENICKKLSNPFRYRMECPEIDCEEGWALLKCGGK
3	P09914-D3	156-266	111		NYERAKACFEKVLEVDPENPESSAGYAISAYRLDGFKLATKNHKPFSLLPLRQAVRLNPDNGYIKVLLALKLQDEGQEAEGEKYIEEALANMSSQTYVFRYAAKFYRRKGS
4	P09914-D4	267-478	212		VDKALELLKKALQETPTSVLLHHQIGLCYKAQMIQIKEATKGQPRGQNREKLDKMIRSAIFHFESAVEKKPTFEVAHLDLARMYIEAGNHRKAEENFQKLLCMKPVVEETMQDIHFHYGRFQEFQKKSDVNAIIHYLKAIKIEQASLTRDKSINSLKKLVLRKLRRKALDLESLSLLGFVYKLEGNMNEALEYYERALRLAADFENSVRQGP

Top 1 final models from D-I-TASSER

SpinHigh qualityWhite background

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.88

(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

/jmol//j2s/core/package.js

-- required by ClazzNode ajax=false async=true

script 1 started

FileManager.getAtomSetCollectionFromFile(model1_3zgqA.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/P09914/model1_3zgqA.pdb.gz

/jmol//j2s/core/corezip.z.js

-- required by ClazzNode ajax=true async=false

The Resolver thinks Pdb

/jmol//j2s/core/corebio.z.js

-- required by ClazzNode ajax=true async=false

/jmol//j2s/J/render/MeshRenderer.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

/jmol//j2s/J/shape/Mesh.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

Time for openFile(model1_3zgqA.pdb.gz): 2572 ms

reading 11663 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

11663 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

JSmol exec jmolApplet2 start applet null

Jmol JavaScript applet jmolApplet2__3118787477867917__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet2__3118787477867917__)

vwrOptions:

{ "name":"jmolApplet2","applet":true,"documentBase":"https://zhanglab.comp.nus.edu.sg/HPmod/data/P09914/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet2__3118787477867917__","codePath":"https:/jmol//j2s/","display":"jmolApplet2_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3118787477867917","bgcolor":"#000000" }

setting document base to "https://zhanglab.comp.nus.edu.sg/HPmod/data/P09914/"

Jmol Version: 14.2.13_2015.03.07 2015-03-07 10:45

java.vendor: Java2Script (HTML5)

java.version: 2015-03-01 07:13:29 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet2 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #000000

backgroundColor = "#000000"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet2__3118787477867917__ ready

SpinHigh qualityWhite background

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3zgqA	0.72	4.08	0.384	0.829	model1_3zgqA.pdb.gz
2	6swy5	0.63	5.91	0.063	0.912	model1_6swy5.pdb.gz
3	4n5cA	0.63	5.01	0.058	0.818	model1_4n5cA.pdb.gz
4	6gmhQ	0.63	4.81	0.113	0.810	model1_6gmhQ.pdb.gz
5	5udiA	0.62	4.99	0.637	0.803	model1_5udiA.pdb.gz
6	5c6gA	0.62	5.06	0.062	0.816	model1_5c6gA.pdb.gz
7	5u1sA	0.62	4.96	0.074	0.805	model1_5u1sA.pdb.gz
8	6tedQ	0.61	4.84	0.114	0.799	model1_6tedQ.pdb.gz
9	4xdnA	0.61	5.16	0.067	0.814	model1_4xdnA.pdb.gz
10	5dseA	0.61	4.14	0.109	0.736	model1_5dseA.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	0.93	heterocyclic compound binding
GO:0097159	0.93	organic cyclic compound binding
GO:0003676	0.91	nucleic acid binding
GO:0003723	0.88	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:0009987	0.99	cellular process
GO:0050896	0.92	response to stimulus
GO:0043207	0.91	response to external biotic stimulus
GO:0009615	0.90	response to virus
GO:0006950	0.85	response to stress
GO:0002376	0.85	immune system process
GO:0051607	0.84	defense response to virus

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:0005737	0.78	cytoplasm
GO:0043226	0.75	organelle
GO:0043229	0.74	intracellular organelle
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0044444	0.68	cytoplasmic part

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

SpinHigh qualityWhite background

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	0.086	1w3bA	0.582	3.74	0.120	0.686	2.4.1.-	NA
2	0.067	1w3bB	0.548	3.65	0.130	0.644	2.4.1.-	71
3	0.060	1hxgA	0.381	6.59	0.046	0.571	4.2.3.9 4.1.99.7	NA
4	0.060	1ofdA	0.360	7.25	0.032	0.588	1.4.7.1	60
5	0.060	1lf6A	0.371	6.33	0.065	0.548	3.2.1.3	144

	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

/jmol//j2s/core/core.z.js

-- required by ClazzNode ajax=false async=true

JSmol exec jmolApplet0 start applet null

/jmol//j2s/java/util/Hashtable.js

-- required by ClazzNode ajax=true async=false

/jmol//j2s/java/util/NoSuchElementException.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/lang/RuntimeException.js

-- required by java.util.NoSuchElementException ajax=true async=false

/jmol//j2s/java/lang/Exception.js

-- required by java.lang.RuntimeException ajax=true async=false

/jmol//j2s/java/lang/Throwable.js

-- required by java.lang.Exception ajax=true async=false

/jmol//j2s/java/util/MapEntry.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/util/Map.js

-- required by java.util.MapEntry ajax=true async=false

/jmol//j2s/java/util/Iterator.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/util/Enumeration.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/util/Dictionary.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/lang/IllegalArgumentException.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/lang/IllegalStateException.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/lang/NullPointerException.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/lang/StringBuilder.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/lang/AbstractStringBuilder.js

-- required by java.lang.StringBuilder ajax=true async=false

/jmol//j2s/java/io/InvalidObjectException.js

-- required by java.lang.AbstractStringBuilder ajax=true async=false

/jmol//j2s/java/io/ObjectStreamException.js

-- required by java.io.InvalidObjectException ajax=true async=false

/jmol//j2s/java/io/IOException.js

-- required by java.io.ObjectStreamException ajax=true async=false

/jmol//j2s/java/lang/ArrayIndexOutOfBoundsException.js

-- required by java.lang.AbstractStringBuilder ajax=true async=false

/jmol//j2s/java/lang/IndexOutOfBoundsException.js

-- required by java.lang.ArrayIndexOutOfBoundsException ajax=true async=false

/jmol//j2s/java/lang/NegativeArraySizeException.js

-- required by java.lang.AbstractStringBuilder ajax=true async=false

/jmol//j2s/java/lang/StringIndexOutOfBoundsException.js

-- required by java.lang.AbstractStringBuilder ajax=true async=false

/jmol//j2s/java/lang/Double.js

-- required by java.lang.StringBuilder ajax=true async=false

/jmol//j2s/java/lang/Number.js

-- required by java.lang.Double ajax=true async=false

/jmol//j2s/java/lang/Float.js

-- required by java.lang.StringBuilder ajax=true async=false

/jmol//j2s/java/lang/Long.js

-- required by java.lang.StringBuilder ajax=true async=false

/jmol//j2s/java/util/AbstractCollection.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/util/Collection.js

-- required by java.util.AbstractCollection ajax=true async=false

/jmol//j2s/java/lang/UnsupportedOperationException.js

-- required by java.util.AbstractCollection ajax=true async=false

/jmol//j2s/java/lang/reflect/Array.js

-- required by java.util.AbstractCollection ajax=true async=false

/jmol//j2s/java/util/AbstractSet.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/util/Set.js

-- required by java.util.AbstractSet ajax=true async=false

/jmol//j2s/java/util/Arrays.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/util/AbstractList.js

-- required by java.util.Arrays ajax=true async=false

/jmol//j2s/java/util/List.js

-- required by java.util.AbstractList ajax=true async=false

/jmol//j2s/java/util/ListIterator.js

-- required by java.util.AbstractList ajax=true async=false

/jmol//j2s/java/util/RandomAccess.js

-- required by java.util.AbstractList ajax=true async=false

/jmol//j2s/java/util/ConcurrentModificationException.js

-- required by java.util.AbstractList ajax=true async=false

/jmol//j2s/java/util/Collections.js

-- required by java.util.Hashtable ajax=true async=false

/jmol//j2s/java/util/AbstractMap.js

-- required by java.util.Collections ajax=true async=false

/jmol//j2s/java/util/SortedMap.js

-- required by java.util.Collections ajax=true async=false

/jmol//j2s/java/util/SortedSet.js

-- required by java.util.Collections ajax=true async=false

/jmol//j2s/java/lang/ClassCastException.js

-- required by java.util.Collections ajax=true async=false

/jmol//j2s/java/util/ArrayList.js

-- required by java.util.Collections ajax=true async=false

/jmol//j2s/java/util/Random.js

-- required by java.util.Collections ajax=true async=false

JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__3118787477867917__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__3118787477867917__)

vwrOptions:

{ "name":"jmolApplet1","applet":true,"documentBase":"https://zhanglab.comp.nus.edu.sg/HPmod/data/P09914/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__3118787477867917__","codePath":"https:/jmol//j2s/","display":"jmolApplet1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3118787477867917","bgcolor":"#000000" }

setting document base to "https://zhanglab.comp.nus.edu.sg/HPmod/data/P09914/"

Jmol Version: 14.2.13_2015.03.07 2015-03-07 10:45

java.vendor: Java2Script (HTML5)

java.version: 2015-03-01 07:13:29 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet1 (signed)

/jmol//j2s/core/corescript.z.js

-- required by ClazzNode ajax=true async=false

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #000000

backgroundColor = "#000000"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet1__3118787477867917__ ready

SpinHigh qualityWhite background

Template proteins with similar binding site:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.04	3hymD	0.465	3.40	0.135	0.529	0.58	III	complex1.pdb.gz	59,100,106,125,140,144,150,174,176,179,180,183,186,218,221,222,225,228,229,233,254,260,263,264,300
	2	0.02	3hymH	0.479	4.42	0.117	0.594	0.56	III	complex2.pdb.gz	60,63,82,96,100,103,138,140,143,144,147,150,176,179,180,183,225,228,229,233,254,258,259

	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, 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.