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
P51005 UniProt NPD GO	PAPO2_XENLA	Poly(A) polymerase alpha-B (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase)	0.77	+	nuc	0	Nucleus				484
Q9TXQ1 UniProt NPD GO	PME5_CAEEL	Poly(ADP-ribose) polymerase pme-5 (EC 2.4.2.30) (Poly ADP-ribose metabolism enzyme 5)	0.77	-	nuc	0	Nucleus (Probable)				2276
Q8CHP6 UniProt NPD GO	PHC3_MOUSE	Polyhomeotic-like protein 3	0.77	-	nuc	0	Nucleus (By similarity)				981
Q96L42 UniProt NPD GO	KCNH8_HUMAN	Potassium voltage-gated channel subfamily H member 8 (Voltage-gated potassium channel subunit Kv12.1 ...	0.77	-	nuc	6	Membrane; multi-pass membrane protein		608260		1107
Q9JKA8 UniProt NPD GO	HCN3_RAT	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3	0.77	-	end	1	Membrane; multi-pass membrane protein				780
Q9TV66 UniProt NPD GO	HCN4_RABIT	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 (Hyperpolarization-ac ...	0.77	-	nuc	5	Membrane; multi-pass membrane protein				1175
O94906 UniProt NPD GO	PRP6_HUMAN	Pre-mRNA-processing factor 6 homolog (U5 snRNP-associated 102 kDa protein) (U5-102 kDa protein)	0.77	-	nuc	0	Nucleus	nucleus [IDA] spliceosome complex [NAS]			941
Q5AP89 UniProt NPD GO	CWC21_CANAL	Pre-mRNA-splicing factor CWC21	0.77	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				162
Q04693 UniProt NPD GO	RSE1_YEAST	Pre-mRNA-splicing factor RSE1 (RNA splicing and ER to Golgi transport factor 1) (Spliceosome-associa ...	0.77	-	nuc	0	Nucleus (By similarity)	snRNP U2 [IDA]			1361
Q5B020 UniProt NPD GO	CWC15_EMENI	Pre-mRNA-splicing factor cwc15	0.77	+	nuc	0	Nucleus (Probable)				232
Q9P6R9 UniProt NPD GO	CWC22_SCHPO	Pre-mRNA-splicing factor cwc22 (Complexed with cdc5 protein 22) (Cell cycle control protein cwf22)	0.77	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				834
O59800 UniProt NPD GO	SLT11_SCHPO	Pre-mRNA-splicing factor slt11 (Complexed with cdc5 protein 5) (Cell cycle control protein cwf5)	0.77	+	nuc	0	Nucleus	spliceosome complex [IDA]			354
Q4WKN3 UniProt NPD GO	PAM17_ASPFU	Presequence translocated-associated motor subunit pam17, mitochondrial precursor	0.77	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				247
Q99PT0 UniProt NPD GO	DDX52_RAT	Probable ATP-dependent RNA helicase DDX52 (EC 3.6.1.-) (DEAD box protein 52) (ATP-dependent RNA heli ...	0.77	+	cyt	0	Nucleus; nucleolus (By similarity)				598
Q9NY93 UniProt NPD GO	DDX56_HUMAN	Probable ATP-dependent RNA helicase DDX56 (EC 3.6.1.-) (DEAD box protein 56) (ATP-dependent 61 kDa n ...	0.77	+	cyt	0	Nucleus; nucleolus	nucleolus [TAS]	608023		547
Q9ZSM8 UniProt NPD GO	EZA1_ARATH	Probable Polycomb group protein EZA1 (CURLY LEAF-like 1) (Protein SET DOMAIN GROUP 10)	0.77	-	nuc	0	Nucleus (Probable)				856
P36036 UniProt NPD GO	YKV4_YEAST	Probable RNA-binding protein YKL214C	0.77	-	nuc	0		nucleus [IDA]			203
Q9C557 UniProt NPD GO	WRK64_ARATH	Probable WRKY transcription factor 64 (WRKY DNA-binding protein 64)	0.77	-	nuc	0	Nucleus (Probable)				249
O74760 UniProt NPD GO	IF3A_SCHPO	Probable eukaryotic translation initiation factor 3 110 kDa subunit (eIF3 p110) (Translation initiat ...	0.77	-	nuc	0					932
Q33446 UniProt NPD GO	GATB_EMENI	Probable glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrial precursor (EC 6.3.5.-) (GLU-AD ...	0.77	-	mit	0	Mitochondrion (Probable)				581
Q9I8J6 UniProt NPD GO	EBP2_XENLA	Probable rRNA-processing protein EBP2 (Nucleolar protein p40-like protein)	0.77	-	nuc	0	Nucleus; nucleolus (By similarity)				312
Q8RXF1 UniProt NPD GO	SF3A1_ARATH	Probable splicing factor 3 subunit 1	0.77	-	nuc	0	Nucleus (By similarity)			1WE6	785
P38082 UniProt NPD GO	NRG2_YEAST	Probable transcriptional regulator NRG2	0.77	-	nuc	0	Nucleus (Potential)	nucleus [IC]			220
P04808 UniProt NPD GO	REL1_HUMAN	Prorelaxin H1 precursor [Contains: Relaxin B chain; Relaxin A chain]	0.77	-	nuc	0	Secreted protein		179730		185
P12818 UniProt NPD GO	PRT3A_ONCMY	Protamine 3A	0.77	+	nuc	0	Nucleus				32
P02326 UniProt NPD GO	PRTIB_ONCMY	Protamine IB (Iridine IB)	0.77	+	nuc	0	Nucleus				33
Q5KBS9 UniProt NPD GO	BFR2_CRYNE	Protein BFR2	0.77	+	nuc	0	Nucleus; nucleolus (By similarity)				463
Q9NVM9 UniProt NPD GO	CL011_HUMAN	Protein C12orf11 (Sarcoma antigen NY-SAR-95)	0.77	+	nuc	0					706
Q8QZV7 UniProt NPD GO	CL011_MOUSE	Protein C12orf11 homolog	0.77	+	nuc	0					732
Q6NW34 UniProt NPD GO	CC017_HUMAN	Protein C3orf17	0.77	+	end	0	Membrane; single-pass membrane protein (Potential)				567
Q5VZ89 UniProt NPD GO	CI055_HUMAN	Protein C9orf55	0.77	-	end	0	Membrane; multi-pass membrane protein (Potential)				1620
Q9NZ63 UniProt NPD GO	CI078_HUMAN	Protein C9orf78 (Hepatocellular carcinoma-associated antigen 59)	0.77	-	nuc	0					289
P34237 UniProt NPD GO	CASP_YEAST	Protein CASP	0.77	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein	Golgi membrane [IGI]			679
Q9Y3C1 UniProt NPD GO	CG117_HUMAN	Protein CGI-117	0.77	-	mit	0	Nucleus; nucleolus				178
Q9Y3M2 UniProt NPD GO	PGEA1_HUMAN	Protein Chibby (PKD2 interactor, Golgi and endoplasmic reticulum associated 1) (PIGEA-14) (Cytosolic ...	0.77	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear, in a punctate manner. Golgi apparatus; trans-Golgi n ...	Golgi trans face [IDA] nucleus [IDA]	607757		126
Q9D1C2 UniProt NPD GO	PGEA1_MOUSE	Protein Chibby (PKD2 interactor, Golgi and endoplasmic reticulum associated 1) (PIGEA-14) (Cytosolic ...	0.77	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nuclear, in a punctate manner. Golgi apparatu ...				127
Q9Y247 UniProt NPD GO	FA50B_HUMAN	Protein FAM50B (XAP-5-like protein)	0.77	+	nuc	0					325
O35242 UniProt NPD GO	FAN_MOUSE	Protein FAN (Factor associated with N-SMase activation) (Factor associated with neutral sphingomyeli ...	0.77	-	cyt	0					920
Q04429 UniProt NPD GO	HLR1_YEAST	Protein HLR1 (LRE1 homolog)	0.77	-	nuc	0	Cytoplasm	cytoplasm [IDA]			423
Q9BVV6 UniProt NPD GO	K0586_HUMAN	Protein KIAA0586	0.77	-	nuc	0					1533
Q96JH8 UniProt NPD GO	K1849_HUMAN	Protein KIAA1849	0.77	-	nuc	0				1UM1	1073
Q946J8 UniProt NPD GO	LHP1_ARATH	Protein LIKE HETEROCHROMATIN PROTEIN1 (LHP1) (Protein TERMINAL FLOWER 2)	0.77	+	nuc	0	Nucleus; punctuated distribution and in heterochromatic chromocenters				445
Q9UU83 UniProt NPD GO	YQM4_SCHPO	Protein P1E11.04c in chromosome III	0.77	-	nuc	0	Nucleus	cell tip [IDA] medial ring [IDA]			425
Q5RJH6 UniProt NPD GO	SMG7_MOUSE	Protein SMG7 (SMG-7 homolog) (EST1-like protein C)	0.77	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Predominantly cytoplasmic, and nuclear. Shuttles ...	cytoplasm [ISS] nucleus [ISS]			1138
Q758Y4 UniProt NPD GO	VTS1_ASHGO	Protein VTS1	0.77	-	nuc	0	Cytoplasm (By similarity)				490
Q7RZQ3 UniProt NPD GO	VTS1_NEUCR	Protein VTS1	0.77	-	mit	0	Cytoplasm (By similarity)				610
P40794 UniProt NPD GO	BNK_DROME	Protein bottleneck	0.77	-	nuc	0	Colocalizes with the structural transitions in the microfilament network during cellularization. Ass ...	actin filament [IDA]			303
P07713 UniProt NPD GO	DECA_DROME	Protein decapentaplegic precursor (Protein DPP-C)	0.77	-	nuc	0	Secreted protein. Is internalized by receptor-mediated endocytosis	extracellular space [IDA] intracellular [IDA]			588
P91706 UniProt NPD GO	DECA_DROSI	Protein decapentaplegic precursor (Protein DPP-C)	0.77	-	nuc	0	Secreted protein. Is internalized by receptor-mediated endocytosis (By similarity)				593
Q9VNA8 UniProt NPD GO	DONS_DROME	Protein downstream neighbor of son homolog (Protein humpty dumpty)	0.77	-	nuc	0	Nucleus				568

You are viewing entries 10501 to 10550 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.