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
Q6FML5 UniProt NPD GO	PRP5_CANGA	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.98	+	nuc	0	Nucleus (By similarity)				816
Q5APG6 UniProt NPD GO	CEF1_CANAL	Pre-mRNA-splicing factor CEF1	0.98	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				610
Q6BLT3 UniProt NPD GO	CEF1_DEBHA	Pre-mRNA-splicing factor CEF1	0.98	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				668
Q4P652 UniProt NPD GO	CEF1_USTMA	Pre-mRNA-splicing factor CEF1	0.98	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				820
Q4IRI9 UniProt NPD GO	CWC25_GIBZE	Pre-mRNA-splicing factor CWC25	0.98	+	nuc	0	Nucleus (By similarity)				393
Q6C1V6 UniProt NPD GO	CWC25_YARLI	Pre-mRNA-splicing factor CWC25	0.98	+	nuc	0	Nucleus (By similarity)				561
P19736 UniProt NPD GO	PRP9_YEAST	Pre-mRNA-splicing factor PRP9	0.98	-	nuc	0	Nucleus	snRNP U2 [IDA]			530
O93383 UniProt NPD GO	NRG1_XENLA	Pro-neuregulin-1, membrane-bound isoform precursor (Pro-NRG1) [Contains: Neuregulin-1]	0.98	+	nuc	0	Pro-neuregulin-1, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...				677
Q9H8H2 UniProt NPD GO	DDX31_HUMAN	Probable ATP-dependent RNA helicase DDX31 (EC 3.6.1.-) (DEAD box protein 31) (Helicain)	0.98	-	nuc	0	Nucleus; nucleolus				851
P49756 UniProt NPD GO	RBM25_HUMAN	Probable RNA-binding protein 25 (RNA-binding motif protein 25) (RNA-binding region-containing protei ...	0.98	+	nuc	0					784
Q8MT36 UniProt NPD GO	MES4_DROME	Probable histone methyltransferase Mes-4 (Maternal-effect sterile 4)	0.98	+	nuc	0	Nucleus (Probable)	nuclear chromosome [ISS]			1427
Q6BW57 UniProt NPD GO	NOP14_DEBHA	Probable nucleolar complex protein 14	0.98	+	nuc	0	Nucleus; nucleolus (By similarity)				795
P38114 UniProt NPD GO	YB00_YEAST	Probable transcriptional regulatory protein YBR150C	0.98	+	nuc	0	Nucleus (Probable)	cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			1094
Q8BHE0 UniProt NPD GO	PRR11_MOUSE	Proline-rich protein 11	0.98	+	nuc	0					368
P39969 UniProt NPD GO	BOI2_YEAST	Protein BOI2 (Protein BEB1)	0.98	-	nuc	0		bud neck [IDA]			1040
Q7Z3E2 UniProt NPD GO	CJ118_HUMAN	Protein C10orf118 (CTCL tumor antigen HD-CL-01/L14-2)	0.98	-	nuc	0					898
Q6P9P0 UniProt NPD GO	CJ006_MOUSE	Protein C10orf6 homolog	0.98	-	nuc	0					1278
Q9P7M1 UniProt NPD GO	YOS2_SCHPO	Protein C21C3.02c in chromosome II	0.98	-	nuc	0	Nucleus				491
Q66JQ7 UniProt NPD GO	CASC5_MOUSE	Protein CASC5 (Cancer susceptibility candidate gene 5 protein homolog)	0.98	-	nuc	0	Nucleus (By similarity)				1612
Q00816 UniProt NPD GO	HEX2_YEAST	Protein HEX2 (Protein SRN1) (Protein REG1)	0.98	-	nuc	0	Nucleus	cytoplasm [IDA] protein phosphatase type 1 complex [TAS]			1014
Q6ZQK0 UniProt NPD GO	K0056_MOUSE	Protein KIAA0056	0.98	+	nuc	0					1506
P59281 UniProt NPD GO	K1688_MOUSE	Protein KIAA1688	0.98	-	nuc	0	Nucleus (Potential)				1107
P36044 UniProt NPD GO	MNN4_YEAST	Protein MNN4	0.98	+	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)				1178
P32380 UniProt NPD GO	NUF1_YEAST	Protein NUF1 (Spindle poly body spacer protein SPC110)	0.98	+	nuc	0	Nucleus. Tightly associated with the nucleus. It is present in a granular pattern that excludes the ...	central plaque of spindle pole body [IDA] inner plaque of spindle pole body [IDA]			944
Q7YU81 UniProt NPD GO	CHN_DROME	Protein charlatan	0.98	+	nuc	0	Nucleus (Probable)	nucleus [IC]			1108
O70566 UniProt NPD GO	DIAP2_MOUSE	Protein diaphanous homolog 2 (Diaphanous-related formin-2) (DRF2) (mDia3)	0.98	+	nuc	0					1098
Q9Z207 UniProt NPD GO	DIAP3_MOUSE	Protein diaphanous homolog 3 (Diaphanous-related formin-3) (DRF3) (mDIA2) (p134mDIA2)	0.98	-	nuc	0					1171
O44757 UniProt NPD GO	LIN59_CAEEL	Protein lin-59 (Abnormal cell lineage protein 59)	0.98	+	nuc	0	Nucleus (Probable)				1312
Q9JKS6 UniProt NPD GO	PCLO_RAT	Protein piccolo (Aczonin) (Multidomain presynaptic cytomatrix protein)	0.98	-	nuc	0	Concentrated at presynaptic side of synaptic junctions	synapse [IDA]		1RH8	5085
Q90941 UniProt NPD GO	PB1_CHICK	Protein polybromo-1	0.98	+	nuc	0	Nucleus			1W4S	1633
Q00333 UniProt NPD GO	NPBL_COPCI	Protein rad9 (SCC2 homolog)	0.98	-	nuc	0	Nucleus (Probable)				2157
P40798 UniProt NPD GO	STC_DROME	Protein shuttle craft	0.98	+	nuc	0	Nucleus				1106
P26675 UniProt NPD GO	SOS_DROME	Protein son of sevenless	0.98	-	nuc	0				1AZE	1596
Q8SX83 UniProt NPD GO	SPEN_DROME	Protein split ends	0.98	+	nuc	0	Nucleus	nucleus [IDA]			5560
O17482 UniProt NPD GO	TIM_DROVI	Protein timeless	0.98	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				1343
O13817 UniProt NPD GO	SEC73_SCHPO	Protein transport protein sec73	0.98	-	nuc	0					1082
P20659 UniProt NPD GO	TRX_DROME	Protein trithorax	0.98	+	nuc	0	Nucleus. Binds to 16 discrete sites on larval salivary gland polytene chromosomes	histone methyltransferase complex [IDA]			3726
Q24742 UniProt NPD GO	TRX_DROVI	Protein trithorax	0.98	+	nuc	0	Nucleus				3828
P61241 UniProt NPD GO	YCF2_AMBTC	Protein ycf2	0.98	-	nuc	0	Plastid; chloroplast; chloroplast stroma (By similarity)				2304
Q1KXP6 UniProt NPD GO	YCF2_HELAN	Protein ycf2	0.98	+	end	2	Plastid; chloroplast; chloroplast stroma (By similarity)				2131
Q9B1K6 UniProt NPD GO	YCF2_LOTJA	Protein ycf2	0.98	-	end	0	Plastid; chloroplast; chloroplast stroma (By similarity)				2298
P09975 UniProt NPD GO	YCF2_MARPO	Protein ycf2	0.98	+	mit	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2136
Q8WHW9 UniProt NPD GO	YCF2_PSINU	Protein ycf2	0.98	-	nuc	0	Plastid; chloroplast; chloroplast stroma (By similarity)				2313
Q2PMM5 UniProt NPD GO	YCF2_SOYBN	Protein ycf2	0.98	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2287
P08973 UniProt NPD GO	YCF2_SPIOL	Protein ycf2	0.98	-	end	1	Plastid; chloroplast; chloroplast stroma				2131
Q9HDY4 UniProt NPD GO	YK16_SCHPO	Putative ATP-dependent RNA helicase PB1A10.06c (EC 3.6.1.-)	0.98	-	nuc	0	Nucleus; nucleolus				1183
Q10752 UniProt NPD GO	CDC28_SCHPO	Putative ATP-dependent RNA helicase cdc28 (EC 3.6.1.-)	0.98	+	nuc	0	Nucleus (Probable)				1055
Q872I5 UniProt NPD GO	INO80_NEUCR	Putative DNA helicase ino-80 (EC 3.6.1.-)	0.98	+	nuc	0	Nucleus (By similarity)				2001
Q4WTV7 UniProt NPD GO	INO80_ASPFU	Putative DNA helicase ino80 (EC 3.6.1.-)	0.98	+	nuc	0	Nucleus (By similarity)				1708
Q10124 UniProt NPD GO	PQE1_CAEEL	Putative RNA exonuclease pqe-1 (PolyQ enhancer protein 1)	0.98	+	nuc	0	Nucleus				1647

You are viewing entries 751 to 800 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.