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
Q76FK4 UniProt NPD GO	NOL8_HUMAN	Nucleolar protein 8 (Nucleolar protein Nop132)	1.00	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			1167
Q9XTY6 UniProt NPD GO	NUMB1_CAEEL	Numb-related protein 1 (Protein kinase C adapter 1) (CKA1)	1.00	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Expressed at the inner surface of the plasma membr ...	cytoplasm [IDA] integral to plasma membrane [IDA]			593
Q99MR1 UniProt NPD GO	PERQ1_MOUSE	PERQ amino acid rich with GYF domain protein 1	1.00	+	nuc	0					1011
Q92576 UniProt NPD GO	PHF3_HUMAN	PHD finger protein 3	1.00	-	nuc	0			607789		2039
P24788 UniProt NPD GO	CD2L1_MOUSE	PITSLRE serine/threonine-protein kinase CDC2L1 (EC 2.7.11.22) (Galactosyltransferase-associated prot ...	1.00	+	nuc	0		nucleus [IDA]			784
Q9UQ88 UniProt NPD GO	CD2L2_HUMAN	PITSLRE serine/threonine-protein kinase CDC2L2 (EC 2.7.11.22) (Galactosyltransferase-associated prot ...	1.00	+	nuc	0	Cytoplasm. Nucleus	nucleus [IEP]	116951		780
P31369 UniProt NPD GO	PDM2_DROME	POU domain protein 2 (didymous protein) (Pdm-2) (dPOU-28) (dOct2) (miti-mere)	1.00	+	nuc	0	Nucleus				498
P27715 UniProt NPD GO	UNC13_CAEEL	Phorbol ester/diacylglycerol-binding protein unc-13 (Uncoordinated protein 13)	1.00	+	nuc	0					2155
Q96KR7 UniProt NPD GO	PHAR3_HUMAN	Phosphatase and actin regulator 3 (Scapinin) (Scaffold-associated PP1-inhibiting protein)	1.00	-	nuc	0	Nucleus; nuclear matrix. Localized to the nuclear matrix-intermediate filament scaffold. Isoform 2 i ...		608725		559
Q24459 UniProt NPD GO	PCL_DROME	Polycomb protein Pcl (Polycomblike protein)	1.00	+	nuc	0	Nucleus. Associated with chromatin. Colocalizes with many PcG sites on polytene chromosomes. It also ...	nucleus [IDA]			1043
O75400 UniProt NPD GO	PRP40_HUMAN	Pre-mRNA-processing factor 40 homolog A (Formin-binding protein 3) (Huntingtin yeast partner A) (Hun ...	1.00	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)			2CQN	957
O94406 UniProt NPD GO	PRP18_SCHPO	Pre-mRNA-splicing factor 18	1.00	+	nuc	0	Nucleus (By similarity)				343
P25357 UniProt NPD GO	SNT1_YEAST	Probable DNA-binding protein SNT1	1.00	+	nuc	0	Nucleus (Probable)	histone deacetylase complex [IDA]			1226
P32862 UniProt NPD GO	YKD8_YEAST	Probable transcriptional regulatory protein YKL038W	1.00	+	mit	0	Nucleus (Probable)	nucleus [IC]			1170
Q8N655 UniProt NPD GO	CJ012_HUMAN	Protein C10orf12	1.00	+	nuc	0					1247
Q14684 UniProt NPD GO	K0179_HUMAN	Protein KIAA0179	1.00	+	nuc	0	Nucleus; nucleolus				758
Q14687 UniProt NPD GO	K0182_HUMAN	Protein KIAA0182 (Fragment)	1.00	+	nuc	0					1157
Q9UKJ3 UniProt NPD GO	K0553_HUMAN	Protein KIAA0553	1.00	+	nuc	0					1089
Q80TG1 UniProt NPD GO	K1267_MOUSE	Protein KIAA1267	1.00	-	nuc	0					1036
Q80VC9 UniProt NPD GO	K1543_MOUSE	Protein KIAA1543	1.00	-	mit	0				1UGJ	1252
P38904 UniProt NPD GO	SPP41_YEAST	Protein SPP41	1.00	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			1435
P24276 UniProt NPD GO	SSD1_YEAST	Protein SSD1 (Protein SRK1)	1.00	+	nuc	0		cytoplasm [IDA]			1250
P28466 UniProt NPD GO	WNT5_DROME	Protein Wnt-5 precursor (dWnt-5) (dWnt-3)	1.00	+	nuc	0	Secreted protein; extracellular space; extracellular matrix				1004
Q9NK54 UniProt NPD GO	CHIF_DROME	Protein chiffon	1.00	-	nuc	0					1711
Q9NSV4 UniProt NPD GO	DIAP3_HUMAN	Protein diaphanous homolog 3 (Diaphanous-related formin-3) (DRF3)	1.00	-	nuc	0					1110
P34427 UniProt NPD GO	LIN36_CAEEL	Protein lin-36 (Abnormal cell lineage protein 36)	1.00	+	nuc	0	Nucleus				962
Q9Y6V0 UniProt NPD GO	PCLO_HUMAN	Protein piccolo (Aczonin)	1.00	+	nuc	0	Concentrated at the presynaptic side of synaptic junctions (By similarity)	cytoskeleton [NAS] synapse [ISS]	604918	1UJD	5183
Q18221 UniProt NPD GO	SET2_CAEEL	Protein set-2	1.00	+	nuc	0	Nucleus. Localized in mitotic and mid-late-stage meiotic nuclei but is undetectable in early pachyte ...				1507
Q9VTE2 UniProt NPD GO	SUUR_DROME	Protein suppressor of underreplication	1.00	+	nuc	0	Nucleus. Binds to polytene chromosomes from salivary glands; localized at late-replicating intercala ...	centric heterochromatin [IDA] intercalary heterochromatin [IDA] nuclear telomeric heterochromatin [IDA] polytene chromosome [IDA]			962
P12297 UniProt NPD GO	SUWA_DROME	Protein suppressor of white apricot	1.00	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Speckled subnuclear compartment				963
P42282 UniProt NPD GO	TTKA_DROME	Protein tramtrack, alpha isoform (Tramtrack p88) (Repressor protein fushi tarazu)	1.00	+	nuc	0		polytene chromosome [IDA]			813
Q8S8V2 UniProt NPD GO	YCF2A_ATRBE	Protein ycf2	1.00	-	nuc	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2291
Q8S8U1 UniProt NPD GO	YCF2B_ATRBE	Protein ycf2	1.00	-	nuc	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2291
P56786 UniProt NPD GO	YCF2_ARATH	Protein ycf2	1.00	-	end	0	Plastid; chloroplast; chloroplast stroma (By similarity)				2294
Q49KT6 UniProt NPD GO	YCF2_EUCGG	Protein ycf2	1.00	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2280
Q332R7 UniProt NPD GO	YCF2_LACSA	Protein ycf2	1.00	+	end	2	Plastid; chloroplast; chloroplast stroma (By similarity)				2264
Q3C1N4 UniProt NPD GO	YCF2_NICSY	Protein ycf2	1.00	-	nuc	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2280
Q33BV3 UniProt NPD GO	YCF2_NICTO	Protein ycf2	1.00	-	nuc	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2280
Q68RU4 UniProt NPD GO	YCF2_PANGI	Protein ycf2	1.00	+	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2110
Q3BAH3 UniProt NPD GO	YCF2_PHAAO	Protein ycf2	1.00	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2290
P09976 UniProt NPD GO	YCF2_TOBAC	Protein ycf2	1.00	-	nuc	1	Plastid; chloroplast; chloroplast stroma				2280
P31380 UniProt NPD GO	YAB9_YEAST	Putative ATP-dependent helicase YAL019W (EC 3.6.1.-)	1.00	-	nuc	0	Nucleus (Potential)	mitochondrion [IDA] nucleus [IDA]			1131
Q6FV37 UniProt NPD GO	INO80_CANGA	Putative DNA helicase INO80 (EC 3.6.1.-)	1.00	+	nuc	0	Nucleus (By similarity)				1484
Q6CNY4 UniProt NPD GO	INO80_KLULA	Putative DNA helicase INO80 (EC 3.6.1.-)	1.00	+	nuc	0	Nucleus (By similarity)				1489
P53115 UniProt NPD GO	INO80_YEAST	Putative DNA helicase INO80 (EC 3.6.1.-) (Inositol-requiring protein 80)	1.00	-	nuc	0	Nucleus	INO80 complex [IDA]			1489
Q9VGW1 UniProt NPD GO	YCDA_DROME	Putative cadherin CG4509 precursor	1.00	+	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			1483
Q9FLH0 UniProt NPD GO	NMCP_ARATH	Putative nuclear matrix constituent protein 1-like protein (NMCP1-like)	1.00	+	nuc	0	Nucleus (Potential)				1042
Q03002 UniProt NPD GO	YP141_YEAST	Putative serine/threonine-protein kinase YPL141C (EC 2.7.11.1)	1.00	+	nuc	0	Cytoplasm	cytoplasm [IDA]			865
P34437 UniProt NPD GO	YL57_CAEEL	Putative zinc finger protein F44E2.7	1.00	+	nuc	0	Nucleus (Potential)				471
Q9UQ26 UniProt NPD GO	RIMS2_HUMAN	Regulating synaptic membrane exocytosis protein 2 (Rab3-interacting molecule 2) (RIM 2)	1.00	+	nuc	0			606630	1WFG	1411

You are viewing entries 101 to 150 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.