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
P48415 UniProt NPD GO	SEC16_YEAST	Multidomain vesicle coat protein	0.98	-	nuc	0	Endoplasmic reticulum. On the endoplasmic reticulum and on vesicles which bud from it	COPII vesicle coat [IDA] endoplasmic reticulum membrane [IDA] extrinsic to membrane [TAS]			2195
P70475 UniProt NPD GO	MYT1L_RAT	Myelin transcription factor 1-like protein (MyT1L protein) (Neural zinc finger factor 1) (NZF-1)	0.98	-	nuc	0	Nucleus			1PXE	1187
P97500 UniProt NPD GO	MYT1L_MOUSE	Myelin transcription factor 1-like protein (MyT1L protein) (Postmitotic neural gene 1 protein) (Zinc ...	0.98	-	nuc	0	Nucleus (By similarity)				1187
Q8BRH4 UniProt NPD GO	MLL3_MOUSE	Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 ...	0.98	+	nuc	0	Nucleus (Probable)				4903
Q8NEZ4 UniProt NPD GO	MLL3_HUMAN	Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 ...	0.98	+	nuc	0	Nucleus (Probable)		606833		4911
Q6WCQ1 UniProt NPD GO	MRIP_HUMAN	Myosin phosphatase Rho-interacting protein (Rho-interacting protein 3) (M-RIP) (RIP3) (p116Rip)	0.98	+	nuc	0	Cytoplasm. Colocalizes with F-actin				1024
P97434 UniProt NPD GO	MRIP_MOUSE	Myosin phosphatase Rho-interacting protein (Rho-interacting protein 3) (p116Rip) (RIP3)	0.98	+	nuc	0	Cytoplasm. Colocalizes with F-actin				1024
Q9ERE6 UniProt NPD GO	MRIP_RAT	Myosin phosphatase Rho-interacting protein (Rho-interacting protein 3) (p116Rip) (RIP3)	0.98	+	nuc	0	Cytoplasm. Colocalizes with F-actin (By similarity)				1029
Q9JMH9 UniProt NPD GO	MY18A_MOUSE	Myosin-18A (Myosin XVIIIa) (Myosin containing PDZ domain) (Molecule associated with JAK3 N-terminus) ...	0.98	-	nuc	0	Isoform 1: Endoplasmic reticulum-Golgi intermediate compartment. Isoform 2: Cytoplasm. Isoform 2, wh ...	cytoskeleton [IDA]			2035
Q63358 UniProt NPD GO	MYO9B_RAT	Myosin-9B (Myosin IXb) (Unconventional myosin-9b)	0.98	-	nuc	0	Cytoplasm; cell cortex. Cytoplasm; perinuclear region (By similarity). In undifferentiated cells col ...				1980
Q8CIB9 UniProt NPD GO	ESCO2_MOUSE	N-acetyltransferase ESCO2 (EC 2.3.1.-) (Establishment of cohesion 1 homolog 2) (ECO1 homolog 2)	0.98	+	nuc	0	Nucleus (By similarity)				592
Q9VS50 UniProt NPD GO	ECO_DROME	N-acetyltransferase eco (EC 2.3.1.-) (Establishment of cohesion 1 homolog) (ECO1 homolog)	0.98	-	nuc	0	Nucleus (By similarity)	nuclear chromatin [ISS]			1052
P30415 UniProt NPD GO	NKTR_MOUSE	NK-tumor recognition protein (Natural-killer cells cyclophilin-related protein) (NK-TR protein)	0.98	+	nuc	0					1453
P32634 UniProt NPD GO	PMD1_YEAST	Negative regulator of sporulation PMD1	0.98	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1753
Q9R207 UniProt NPD GO	NBN_MOUSE	Nibrin (Nijmegen breakage syndrome protein 1 homolog) (Cell cycle regulatory protein p95)	0.98	-	nuc	0	Nucleus. Localizes to discrete nuclear foci after treatment with genotoxic agents (By similarity)	Mre11 complex [ISS] nuclear inclusion body [ISS] nucleus [IDA] replication fork [IDA]			751
Q95XZ5 UniProt NPD GO	NPBL_CAEEL	Nipped-B-like protein pqn-85 (Prion-like-(Q/n-rich)-domain-bearing protein 85) (SCC2 homolog)	0.98	+	nuc	0	Nucleus (By similarity)				2203
P43124 UniProt NPD GO	NSE4_YEAST	Non-structural maintenance of chromosome element 4 (Non-SMC element 4) (Protein QRI2)	0.98	-	nuc	0	Nucleus	nucleus [IDA] Smc5-Smc6 complex [IPI]			402
Q13342 UniProt NPD GO	LY10_HUMAN	Nuclear body protein SP140 (Nuclear autoantigen Sp-140) (Speckled 140 kDa) (LYSp100 protein) (Lympho ...	0.98	+	nuc	0	Nucleus. Cytoplasm. Localized to nuclear structures termed LANDS, for LYSp100-associated nuclear dom ...	nuclear envelope [TAS] nucleoplasm [TAS] nucleus [TAS]	608602		882
Q9UHK0 UniProt NPD GO	NUFP1_HUMAN	Nuclear fragile X mental retardation-interacting protein 1 (Nuclear FMRP-interacting protein 1)	0.98	+	nuc	0	Nucleus. Distributed in the nucleus in a dot-like pattern	nucleus [TAS]	604354		495
Q9QXX8 UniProt NPD GO	NUFP1_MOUSE	Nuclear fragile X mental retardation-interacting protein 1 (Nuclear FMRP-interacting protein 1)	0.98	+	nuc	0	Nucleus. Distributed in the nucleus in a dot-like pattern	nucleus [IDA]			484
P29258 UniProt NPD GO	STP2_PIG	Nuclear transition protein 2 (TP-2) (TP2)	0.98	-	nuc	0	Nucleus				137
Q9BSC4 UniProt NPD GO	NOL10_HUMAN	Nucleolar protein 10	0.98	-	nuc	0	Nucleus; nucleolus				688
Q5RJG1 UniProt NPD GO	NOL10_MOUSE	Nucleolar protein 10	0.98	-	nuc	0	Nucleus; nucleolus (By similarity)				687
Q9D7Z3 UniProt NPD GO	NOL7_MOUSE	Nucleolar protein 7	0.98	+	nuc	0	Nucleus; nucleolus (By similarity)				254
P25976 UniProt NPD GO	UBF1_MOUSE	Nucleolar transcription factor 1 (Upstream-binding factor 1) (UBF-1)	0.98	-	nuc	0	Nucleus	nucleolus [IDA]		1WGF	765
P25977 UniProt NPD GO	UBF1_RAT	Nucleolar transcription factor 1 (Upstream-binding factor 1) (UBF-1)	0.98	-	nuc	0	Nucleus				764
P17480 UniProt NPD GO	UBF1_HUMAN	Nucleolar transcription factor 1 (Upstream-binding factor 1) (UBF-1) (Autoantigen NOR-90)	0.98	-	nuc	0	Nucleus	nucleolus [TAS]	600673	1L8Z	764
P25979 UniProt NPD GO	UBF1A_XENLA	Nucleolar transcription factor 1-A (Upstream-binding factor 1-A) (UBF-1-A) (xUBF-1)	0.98	-	nuc	0	Nucleus				677
Q32PJ3 UniProt NPD GO	ORC3_BOVIN	Origin recognition complex subunit 3	0.98	-	nuc	0	Nucleus (By similarity)				712
Q8MJ05 UniProt NPD GO	RP1_BOVIN	Oxygen-regulated protein 1 (Retinitis pigmentosa RP1 protein homolog)	0.98	-	nuc	0					2105
P56716 UniProt NPD GO	RP1_MOUSE	Oxygen-regulated protein 1 (Retinitis pigmentosa RP1 protein homolog)	0.98	+	nuc	0		cilium [IDA] soluble fraction [IDA]			2095
Q8MJ06 UniProt NPD GO	RP1_PAPHA	Oxygen-regulated protein 1 (Retinitis pigmentosa RP1 protein homolog)	0.98	-	nuc	0					2152
O14340 UniProt NPD GO	YB35_SCHPO	Oxysterol-binding protein homolog C2F12.05c	0.98	+	nuc	0					1310
Q9QY39 UniProt NPD GO	PDZK4_MOUSE	PDZ domain-containing protein 4 (PDZ domain-containing RING finger protein 4-like protein)	0.98	+	nuc	0	Cytoplasm; cell cortex (By similarity). Mainly localized under the plasma membrane (By similarity)				772
Q9BVI0 UniProt NPD GO	PHF20_HUMAN	PHD finger protein 20 (Hepatocellular carcinoma-associated antigen 58) (Glioma-expressed antigen 2) ...	0.98	+	nuc	0	Nucleus (Probable)				1012
Q4P7H2 UniProt NPD GO	CWC27_USTMA	Peptidyl-prolyl isomerase CWC27 (EC 5.2.1.8)	0.98	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				485
Q9JIR0 UniProt NPD GO	RIMB1_RAT	Peripheral-type benzodiazepine receptor-associated protein 1 (PRAX-1) (RIM-binding protein 1) (RIM-B ...	0.98	+	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA] mitochondrion [IDA]			1847
Q6RFY2 UniProt NPD GO	PHAR3_RAT	Phosphatase and actin regulator 3 (Scapinin) (Scaffold-associated PP1-inhibiting protein)	0.98	-	nuc	0	Nucleus; nuclear matrix (By similarity). Localized to the nuclear matrix-intermediate filament scaff ...				517
O02810 UniProt NPD GO	PI4KB_BOVIN	Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) (PtdIns 4-kinase beta) (PI4Kbeta) (PI4K-beta)	0.98	-	nuc	0	Intracytoplasmic membrane (By similarity). Mitochondrion; mitochondrial outer membrane; peripheral m ...				816
O08561 UniProt NPD GO	PI4KB_RAT	Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) (PtdIns 4-kinase beta) (PI4Kbeta) (PI4K-beta)	0.98	-	nuc	0	Intracytoplasmic membrane (By similarity). Mitochondrion; mitochondrial outer membrane; peripheral m ...	cytoplasm [IDA]			816
Q9UBF8 UniProt NPD GO	PI4KB_HUMAN	Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) (PtdIns 4-kinase beta) (PI4Kbeta) (PI4K-beta) (NPIK ...	0.98	-	nuc	0	Intracytoplasmic membrane. Mitochondrion; mitochondrial outer membrane; peripheral membrane protein. ...	cytoplasm [TAS] endosome [TAS]	602758		816
O59722 UniProt NPD GO	FAB1_SCHPO	Phosphatidylinositol-4-phosphate 5-kinase fab1 (EC 2.7.1.68) (1-phosphatidylinositol-4-phosphate kin ...	0.98	-	nuc	0	Cytoplasm. During cell fusion of opposite mating types, migrates to the isthmus				1932
P20824 UniProt NPD GO	NUC1_NEUCR	Phosphorus acquisition-controlling protein	0.98	-	nuc	0					823
Q8W2F3 UniProt NPD GO	PIF4_ARATH	Phytochrome-interacting factor 4 (Basic helix-loop-helix protein 9) (bHLH9) (AtbHLH009) (Short under ...	0.98	+	nuc	0	Nucleus				430
Q9H307 UniProt NPD GO	PININ_HUMAN	Pinin (140 kDa nuclear and cell adhesion-related phosphoprotein) (Domain-rich serine protein) (DRS-p ...	0.98	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Cell membrane; cell-cell junction. Cell-cell contact area, pr ...		603154		716
Q9ULL1 UniProt NPD GO	PKHG1_HUMAN	Pleckstrin homology domain-containing family G member 1	0.98	-	nuc	0					1385
Q86SQ0 UniProt NPD GO	PHLB2_HUMAN	Pleckstrin homology-like domain family B member 2 (Protein LL5-beta)	0.98	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Translocates to the plasma membrane at high levels ...				1253
Q9NJG9 UniProt NPD GO	SUZ12_DROME	Polycomb protein Su(z)12 (Suppressor 12 of zeste protein)	0.98	-	nuc	0	Nucleus	ESC/E(Z) complex [IDA] nuclear chromatin [NAS]			900
O74747 UniProt NPD GO	RAD18_SCHPO	Postreplication repair ubiquitin-protein ligase E3 rad18 (EC 6.-.-.-) (RAD18 homolog)	0.98	-	nuc	0	Nucleus (By similarity)				387
O94913 UniProt NPD GO	PCF11_HUMAN	Pre-mRNA cleavage complex 2 protein Pcf11 (Pre-mRNA cleavage complex II protein Pcf11) (Fragment)	0.98	+	nuc	0	Nucleus	mRNA cleavage factor complex [NAS]	608876		1654

You are viewing entries 701 to 750 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.