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
P08251 UniProt NPD GO	AT1B1_CHICK	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.08	-	mit	1 *	Membrane; single-pass type II membrane protein				305
P33879 UniProt NPD GO	AT1B3_CHICK	Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent ATPase beta-3 subuni ...	0.08	-	mit	1 *	Membrane; single-pass type II membrane protein				280
O02298 UniProt NPD GO	GCY35_CAEEL	Soluble guanylate cyclase gcy-35 (EC 4.6.1.2)	0.08	-	nuc	0	Cytoplasm (By similarity)				688
Q63632 UniProt NPD GO	S12A4_RAT	Solute carrier family 12 member 4 (Electroneutral potassium-chloride cotransporter 1) (Erythroid K-C ...	0.08	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [ISS]			1085
Q28615 UniProt NPD GO	S13A2_RABIT	Solute carrier family 13 member 2 (Renal sodium/dicarboxylate cotransporter) (Na(+)/dicarboxylate co ...	0.08	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				593
Q9Z0Z5 UniProt NPD GO	S13A3_RAT	Solute carrier family 13 member 3 (Sodium-dependent high-affinity dicarboxylate transporter 2) (Na(+ ...	0.08	-	end	11 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			600
Q9BYW1 UniProt NPD GO	GTR11_HUMAN	Solute carrier family 2, facilitated glucose transporter member 11 (Glucose transporter type 11) (Gl ...	0.08	-	end	10 *	Membrane; multi-pass membrane protein				496
Q9WTW8 UniProt NPD GO	S23A2_RAT	Solute carrier family 23 member 2 (Sodium-dependent vitamin C transporter 2) (Na(+)/L-ascorbic acid ...	0.08	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			592
Q91YY5 UniProt NPD GO	SO1A5_MOUSE	Solute carrier organic anion transporter family member 1A5 (Solute carrier family 21 member 7) (Sodi ...	0.08	-	end	9 *	Membrane; multi-pass membrane protein				670
P81029 UniProt NPD GO	SMS2_ORENI	Somatostatin-2 precursor (Somatostatin II) [Contains: [Tyr21,Gly24]-somatostatin-28; [Tyr7,Gly10]-so ...	0.08	-	nuc	0	Secreted protein				28
P16065 UniProt NPD GO	GCY_STRPU	Speract receptor precursor (Guanylate cyclase) (EC 4.6.1.2)	0.08	-	end	2 *	Membrane; single-pass type I membrane protein				1125
Q8VBV2 UniProt NPD GO	SPG11_RAT	Sperm-associated antigen 11 precursor (Antimicrobial-like protein Bin-1b)	0.08	-	exc	0	Secreted protein (By similarity)				68
Q9ZTR1 UniProt NPD GO	SPD1_PEA	Spermidine synthase 1 (EC 2.5.1.16) (Putrescine aminopropyltransferase 1) (SPDSY 1)	0.08	-	cyt	0					334
P97355 UniProt NPD GO	SPSY_MOUSE	Spermine synthase (EC 2.5.1.22) (Spermidine aminopropyltransferase) (SPMSY)	0.08	-	mit	0					366
Q9DA37 UniProt NPD GO	SAMD8_MOUSE	Sphingomyelin synthase-related 1 (Sterile alpha motif domain-containing 8)	0.08	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			478
O65404 UniProt NPD GO	ERG11_ARATH	Squalene monooxygenase 1,1 (EC 1.14.99.7) (Squalene epoxidase 1,1) (SE 1,1)	0.08	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				516
Q96DR4 UniProt NPD GO	STAR4_HUMAN	StAR-related lipid transfer protein 4 (StARD4) (START domain-containing protein 4)	0.08	-	cyt	0			607049		205
Q875K1 UniProt NPD GO	ERG6_CLALS	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.08	-	nuc	0					375
O77759 UniProt NPD GO	SOAT2_CERAE	Sterol O-acyltransferase 2 (EC 2.3.1.26) (Cholesterol acyltransferase 2) (Acyl coenzyme A:cholestero ...	0.08	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				526
Q9U6D2 UniProt NPD GO	JNK1_ANCCA	Stress-activated protein kinase JNK-1 (EC 2.7.11.24)	0.08	-	cyt	0					376
Q9SW70 UniProt NPD GO	SRP_VITRI	Stress-related protein	0.08	-	nuc	0					248
P92976 UniProt NPD GO	STS3_ARATH	Strictosidine synthase 3 precursor (EC 4.3.3.2) (SS-3)	0.08	-	mit	0	Vacuole (By similarity)				329
P83514 UniProt NPD GO	SCAL1_STRCA	Struthiocalcin-1 (SCA-1)	0.08	-	cyt	0	Eggshell matrix				132
P05363 UniProt NPD GO	NK2R_BOVIN	Substance-K receptor (SKR) (Neurokinin A receptor) (NK-2 receptor) (NK-2R) (Tachykinin receptor 2)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				384
Q5DUB2 UniProt NPD GO	NK2R_CANFA	Substance-K receptor (SKR) (Neurokinin A receptor) (NK-2 receptor) (NK-2R) (Tachykinin receptor 2)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				384
P21452 UniProt NPD GO	NK2R_HUMAN	Substance-K receptor (SKR) (Neurokinin A receptor) (NK-2 receptor) (NK-2R) (Tachykinin receptor 2)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	162321		398
P58371 UniProt NPD GO	SPM1_MAGGR	Subtilisin-like proteinase Spm1 precursor (EC 3.4.21.-) (Serine protease of Magnaporthe 1)	0.08	-	end	0	Vacuole (Potential)				536
Q9P2R7 UniProt NPD GO	SUCB1_HUMAN	Succinyl-CoA ligase [ADP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.5) (Succinyl-CoA syn ...	0.08	-	cyt	0	Mitochondrion	mitochondrion [TAS]	603921		463
Q00917 UniProt NPD GO	SUS2_ARATH	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase)	0.08	-	cyt	1 *					805
P31923 UniProt NPD GO	SUS2_HORVU	Sucrose synthase 2 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 2)	0.08	-	cyt	0					816
P50227 UniProt NPD GO	ST1A1_BOVIN	Sulfotransferase 1A1 (EC 2.8.2.1) (Aryl sulfotransferase) (Phenol sulfotransferase) (Phenol-sulfatin ...	0.08	-	cyt	0	Cytoplasm				294
P19333 UniProt NPD GO	VAT1_TORCA	Synaptic vesicle membrane protein VAT-1 (EC 1.-.-.-)	0.08	-	cyt	0	Membrane				379
Q99KW9 UniProt NPD GO	TIP_MOUSE	T-cell immunomodulatory protein precursor (Protein TIP) (Integrin alpha FG-GAP repeat-containing pro ...	0.08	-	end	1 *	Secreted protein (Potential). Membrane; single-pass type I membrane protein (Potential)				610
Q8R4E1 UniProt NPD GO	TIP_RAT	T-cell immunomodulatory protein precursor (Protein TIP) (Integrin alpha FG-GAP repeat-containing pro ...	0.08	-	end	2 *	Secreted protein (By similarity). Cell membrane; single-pass type I membrane protein (Potential)				610
P01850 UniProt NPD GO	TCB_HUMAN	T-cell receptor beta chain C region	0.08	-	cyt	1		membrane [NAS]		2BNU	177
P03986 UniProt NPD GO	TCC_HUMAN	T-cell receptor gamma chain C region PT-gamma-1/2	0.08	-	nuc	1		integral to plasma membrane [NAS]		1HXM	189
P03979 UniProt NPD GO	TVC_HUMAN	T-cell receptor gamma chain V region PT-gamma-1/2 precursor	0.08	-	exc	0		plasma membrane [NAS]			136
P06126 UniProt NPD GO	CD1A_HUMAN	T-cell surface glycoprotein CD1a precursor (CD1a antigen) (T-cell surface antigen T6/Leu-6) (hTa1 th ...	0.08	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	188370	1XZ0	327
P53451 UniProt NPD GO	TCPD_FUGRU	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.08	-	cyt	0	Cytoplasm				536
Q2NKZ1 UniProt NPD GO	TCPH_BOVIN	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta)	0.08	-	cyt	0	Cytoplasm (By similarity)				543
Q5R5C8 UniProt NPD GO	TCPH_PONPY	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta)	0.08	-	cyt	0	Cytoplasm (By similarity)				543
Q99832 UniProt NPD GO	TCPH_HUMAN	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta) (HIV-1 Nef-interacting protein)	0.08	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]	605140		543
O00782 UniProt NPD GO	TCPG_OXYGR	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma) (Chaperonin subunit CCTV gamma)	0.08	-	cyt	0	Cytoplasm				559
P47079 UniProt NPD GO	TCPQ_YEAST	T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta)	0.08	-	cyt	0	Cytoplasm (By similarity)	chaperonin-containing T-complex [IPI] cytoplasm [IDA] cytoskeleton [TAS]			568
P39079 UniProt NPD GO	TCPZ_YEAST	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta)	0.08	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IPI] cytoplasm [TAS] cytoskeleton [TAS]			546
Q6DHU8 UniProt NPD GO	TOPK_BRARE	T-lymphokine-activated killer cell-originated protein kinase homolog (EC 2.7.12.2) (PDZ-binding kina ...	0.08	-	cyt	0					339
P62340 UniProt NPD GO	TBPL1_MOUSE	TATA box-binding protein-like protein 1 (TBP-like protein 1) (TATA box-binding protein-related facto ...	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			186
P62380 UniProt NPD GO	TBPL1_HUMAN	TATA box-binding protein-like protein 1 (TBP-like protein 1) (TATA box-binding protein-related facto ...	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)		605521		186
Q9YGV8 UniProt NPD GO	TBPL1_CHICK	TATA box-binding protein-like protein 1 (TBP-like protein 1) (TBP-like factor)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				183
P48511 UniProt NPD GO	TBP_MESCR	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.08	-	mit	0	Nucleus				200

You are viewing entries 69051 to 69100 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.