NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P60024 UniProt NPD GO	UAP56_PANTR	Spliceosome RNA helicase BAT1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus (By similarity)				428
Q29024 UniProt NPD GO	UAP56_PIG	Spliceosome RNA helicase BAT1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus (By similarity)				428
Q5RE47 UniProt NPD GO	UAP56_PONPY	Spliceosome RNA helicase BAT1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus (By similarity)				428
Q13838 UniProt NPD GO	UAP56_HUMAN	Spliceosome RNA helicase BAT1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus	nucleus [TAS]	142560	1XTK	428
Q63413 UniProt NPD GO	UAP56_RAT	Spliceosome RNA helicase Bat1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus				428
Q9Z1N5 UniProt NPD GO	UAP56_MOUSE	Spliceosome RNA helicase Bat1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus (By similarity)				428
Q15427 UniProt NPD GO	SF3B4_HUMAN	Splicing factor 3B subunit 4 (Spliceosome-associated protein 49) (SAP 49) (SF3b50) (Pre-mRNA-splicin ...	0.19	-	nuc	0	Nucleus (By similarity)	spliceosome complex [IDA]	605593	1X5U	424
P42789 UniProt NPD GO	SDP_EIMBO	Sporozoite developmental protein (EC 3.4.99.-)	0.19	-	mit	0					596
P57675 UniProt NPD GO	STC2_CAVPO	Stanniocalcin-2 (STC-2) (Fragments)	0.19	-	nuc	0	Secreted protein (Potential)				197
Q7KV22 UniProt NPD GO	STEL8_DROME	Stellate protein CG33246	0.19	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			171
P55790 UniProt NPD GO	OMTA_ASPFL	Sterigmatocystin 8-O-methyltransferase precursor (EC 2.1.1.110)	0.19	-	cyt	0					418
P25628 UniProt NPD GO	ARE1_YEAST	Sterol O-acyltransferase 1 (EC 2.3.1.26) (Sterol-ester synthase 1)	0.19	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			610
P51070 UniProt NPD GO	THS2_VITVI	Stilbene synthase 2 (EC 2.3.1.95) (Resveratrol synthase 2) (Trihydroxystilbene synthase 2) (PSV21)	0.19	-	cyt	0	Cytoplasm				392
Q6Y4Q5 UniProt NPD GO	MMP3_CANFA	Stromelysin-1 precursor (EC 3.4.24.17) (Matrix metalloproteinase-3) (MMP-3)	0.19	-	exc	0					478
Q28397 UniProt NPD GO	MMP3_HORSE	Stromelysin-1 precursor (EC 3.4.24.17) (Matrix metalloproteinase-3) (MMP-3)	0.19	-	exc	0				1L9I	477
P03957 UniProt NPD GO	MMP3_RAT	Stromelysin-1 precursor (EC 3.4.24.17) (Matrix metalloproteinase-3) (MMP-3) (Transin-1) (SL-1) (PTR1 ...	0.19	-	exc	0					475
Q98982 UniProt NPD GO	NK1R_RANCA	Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykinin receptor 1)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				408
Q8L7R8 UniProt NPD GO	STP3_ARATH	Sugar transport protein 3 (Hexose transporter 3)	0.19	-	end	12 *	Membrane; multi-pass membrane protein				514
Q12650 UniProt NPD GO	MET3_PENCH	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase)	0.19	+	nuc	0				1M8P	572
Q62273 UniProt NPD GO	S26A2_MOUSE	Sulfate transporter (Diastrophic dysplasia protein homolog) (Solute carrier family 26 member 2) (ST- ...	0.19	+	end	9	Membrane; multi-pass membrane protein				739
Q15526 UniProt NPD GO	SURF1_HUMAN	Surfeit locus protein 1	0.19	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial electron transport chain [TAS]	256000		300
Q9R0M3 UniProt NPD GO	SRPX_MOUSE	Sushi-repeat-containing protein SRPX precursor (DRS protein)	0.19	-	exc	0					464
P26260 UniProt NPD GO	SDC1_RAT	Syndecan-1 precursor (SYND1)	0.19	-	end	1	Membrane; single-pass type I membrane protein	uropod [IMP]			313
Q764N2 UniProt NPD GO	CD3D_PIG	T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)	0.19	-	nuc	1	Membrane; single-pass type I membrane protein				171
O02757 UniProt NPD GO	CD28_FELCA	T-cell-specific surface glycoprotein CD28 precursor	0.19	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			221
Q3T084 UniProt NPD GO	TCPW_BOVIN	T-complex protein 1 subunit zeta-2 (TCP-1-zeta-2) (CCT-zeta-2)	0.19	-	nuc	0	Cytoplasm (By similarity)				530
Q8TE23 UniProt NPD GO	TS1R2_HUMAN	Taste receptor type 1 member 2 precursor (G-protein coupled receptor 71) (Sweet taste receptor T1R2) ...	0.19	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IC]	606226		839
Q645T2 UniProt NPD GO	T2R14_MACMU	Taste receptor type 2 member 14 (T2R14)	0.19	-	end	6 *	Membrane; multi-pass membrane protein				319
Q9NYV8 UniProt NPD GO	T2R14_HUMAN	Taste receptor type 2 member 14 (T2R14) (Taste receptor family B member 1) (TRB1)	0.19	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604790		317
Q645U5 UniProt NPD GO	T2R40_PONPY	Taste receptor type 2 member 40 (T2R40)	0.19	-	end	6 *	Membrane; multi-pass membrane protein				323
Q645V9 UniProt NPD GO	TA2R9_PONPY	Taste receptor type 2 member 9 (T2R9)	0.19	-	end	8 *	Membrane; multi-pass membrane protein				312
Q71U07 UniProt NPD GO	TRBM_SAISC	Thrombomodulin precursor (TM) (CD141 antigen)	0.19	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				575
P07204 UniProt NPD GO	TRBM_HUMAN	Thrombomodulin precursor (TM) (Fetomodulin) (CD141 antigen)	0.19	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	188040	2ADX	575
Q07212 UniProt NPD GO	THY1_CHICK	Thy-1 membrane glycoprotein precursor (Thy-1 antigen)	0.19	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	cytosol [ISS] external side of plasma membrane [ISS] growth cone [ISS] lipid raft [ISS] plasma membrane [ISS]			160
Q43054 UniProt NPD GO	TCMO_POPKI	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.19	-	end	0					505
O24312 UniProt NPD GO	TCMO_POPTM	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.19	-	end	0					505
Q9H4W6 UniProt NPD GO	COE3_HUMAN	Transcription factor COE3 (Early B-cell factor 3) (EBF-3) (Olf-1/EBF-like 2) (OE-2) (O/E-2)	0.19	-	nuc	0	Nucleus (Potential)		607407		596
O08791 UniProt NPD GO	COE3_MOUSE	Transcription factor COE3 (Early B-cell factor 3) (EBF-3) (Olf-1/EBF-like 2) (OE-2) (O/E-2)	0.19	-	nuc	0	Nucleus (Potential)				596
P32773 UniProt NPD GO	TOA1_YEAST	Transcription initiation factor IIA large subunit (TFIIA 32 kDa subunit)	0.19	-	nuc	0	Nucleus	transcription factor TFIIA complex [IDA]		1YTF	286
P69041 UniProt NPD GO	IF1C_ANTMA	Translation initiation factor IF-1, chloroplast	0.19	-	nuc	0	Plastid; chloroplast				77
P69042 UniProt NPD GO	IF1C_LAMPU	Translation initiation factor IF-1, chloroplast	0.19	-	nuc	0	Plastid; chloroplast				77
Q8VHJ4 UniProt NPD GO	TM11D_RAT	Transmembrane protease, serine 11D precursor (EC 3.4.21.-) (Airway trypsin-like protease) (AT) (Adre ...	0.19	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	cell surface [IDA]			417
P69525 UniProt NPD GO	TMPS9_MOUSE	Transmembrane protease, serine 9 (EC 3.4.21.-) (Polyserase-1) (Polyserine protease 1) (Polyserase-I) ...	0.19	-	mit	0	Cell membrane; single-pass type II membrane protein (By similarity)				1065
Q86YD3 UniProt NPD GO	TMM25_HUMAN	Transmembrane protein 25 precursor	0.19	-	end	1	Isoform 1, isoform 4: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2, iso ...				366
Q8R3Q0 UniProt NPD GO	TMM66_MOUSE	Transmembrane protein 66 precursor	0.19	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				334
P38778 UniProt NPD GO	SMF2_YEAST	Transporter protein SMF2	0.19	-	end	11	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)	cytoplasmic membrane-bound vesicle [IDA] mitochondrion [IDA]			549
Q8NJA1 UniProt NPD GO	TRI5_FUSMI	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.19	-	cyt	0					375
Q00909 UniProt NPD GO	TRI5_GIBZE	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.19	-	cyt	0					375
Q99JY0 UniProt NPD GO	ECHB_MOUSE	Trifunctional enzyme subunit beta, mitochondrial precursor (TP-beta) [Includes: 3-ketoacyl-CoA thiol ...	0.19	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			475
P01086 UniProt NPD GO	IAAE_HORVU	Trypsin inhibitor CMe precursor (Chloroform/methanol-soluble protein CMe) (Alpha-amylase/trypsin inh ...	0.19	-	exc	1 *	Secreted protein	intracellular [IDA]			148

You are viewing entries 52501 to 52550 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.