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
Q64707 UniProt NPD GO	U2AFL_MOUSE	U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2(RNU2) small ...	1.00	+	nuc	0	Nucleus				428
P34537 UniProt NPD GO	BRE1_CAEEL	Ubiquitin-protein ligase bre-1 (EC 6.3.2.-) (RING finger protein rfp-1) (Bt toxin-resistant protein ...	1.00	+	nuc	0	Nucleus				837
P15919 UniProt NPD GO	RAG1_MOUSE	V(D)J recombination-activating protein 1 (RAG-1)	1.00	+	nuc	0	Nucleus			1RMD	1040
Q03388 UniProt NPD GO	VPS72_YEAST	Vacuolar protein sorting protein 72 (SWR complex protein 2)	1.00	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA] SWR1 complex [IPI]			795
Q5VUA4 UniProt NPD GO	ZN318_HUMAN	Zinc finger protein 318 (Endocrine regulatory protein)	1.00	+	nuc	0	Nucleus				2099
P15822 UniProt NPD GO	ZEP1_HUMAN	Zinc finger protein 40 (Human immunodeficiency virus type I enhancer-binding protein 1) (HIV-EP1) (M ...	1.00	+	nuc	0	Nucleus	nucleus [TAS]	194540	4ZNF	2717
P51432 UniProt NPD GO	PLCB3_MOUSE	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 3 (EC 3.1.4.11) (Phosphoinositide pho ...	0.99	+	nuc	0	Nucleus				1234
P36495 UniProt NPD GO	YCX7_CHLRE	232.2 kDa protein (ORF1995) (ORF-S) (ORFA)	0.99	+	end	8 *	Membrane; multi-pass membrane protein (Potential)				1995
Q9Y2D5 UniProt NPD GO	AKAP2_HUMAN	A-kinase anchor protein 2 (Protein kinase A-anchoring protein 2) (PRKA2) (AKAP-2)	0.99	+	nuc	0			604582		1103
P24275 UniProt NPD GO	AKAP5_BOVIN	A-kinase anchor protein 5 (A-kinase anchor protein 75 kDa) (AKAP 75) (cAMP-dependent protein kinase ...	0.99	+	nuc	0	Membrane. Associated with particulate fractions				428
Q99996 UniProt NPD GO	AKAP9_HUMAN	A-kinase anchor protein 9 (Protein kinase A-anchoring protein 9) (PRKA9) (A-kinase anchor protein 45 ...	0.99	-	nuc	0	Centrosome. In parietal cells: Cytoplasm	centrosome [TAS] cytoskeleton [TAS]	604001		3911
P29374 UniProt NPD GO	ARI4A_HUMAN	AT-rich interactive domain-containing protein 4A (ARID domain-containing protein 4A) (Retinoblastoma ...	0.99	+	nuc	0	Nucleus	nucleus [TAS] transcriptional repressor complex [IDA]	180201		1257
Q5RDX4 UniProt NPD GO	ATAD2_PONPY	ATPase family AAA domain-containing protein 2	0.99	+	nuc	0					1091
P70039 UniProt NPD GO	APC_XENLA	Adenomatous polyposis coli homolog (Protein APC)	0.99	-	nuc	0					2829
P25054 UniProt NPD GO	APC_HUMAN	Adenomatous polyposis coli protein (Protein APC)	0.99	-	nuc	0		lateral plasma membrane [IDA] nucleus [IDA]	135290	1V18	2843
P70478 UniProt NPD GO	APC_RAT	Adenomatous polyposis coli protein (Protein APC)	0.99	-	nuc	0					2842
Q6UB99 UniProt NPD GO	ANR11_HUMAN	Ankyrin repeat domain-containing protein 11 (Ankyrin repeat-containing cofactor 1)	0.99	+	nuc	0	Nucleus				2664
Q6UB98 UniProt NPD GO	ANR12_HUMAN	Ankyrin repeat domain-containing protein 12 (Ankyrin repeat-containing cofactor 2) (GAC-1 protein)	0.99	-	nuc	0	Nucleus				2062
Q00083 UniProt NPD GO	APSA_EMENI	Anucleate primary sterigmata protein A	0.99	-	nuc	0	Membrane; peripheral membrane protein				1676
Q96IZ7 UniProt NPD GO	RSRC1_HUMAN	Arginine/serine-rich coiled coil protein 1	0.99	+	nuc	0					334
O15265 UniProt NPD GO	ATX7_HUMAN	Ataxin-7 (Spinocerebellar ataxia type 7 protein)	0.99	-	nuc	0	Nucleus. Nucleus; nucleolus. Nucleus; nuclear matrix. In addition to a diffuse distribution througho ...	nucleus [TAS]	607640		892
Q9V407 UniProt NPD GO	AXN_DROME	Axin (Axis inhibition protein) (dAxin) (d-Axin)	0.99	-	nuc	0	Cytoplasm (By similarity)				745
P40450 UniProt NPD GO	BNR1_YEAST	BNI1-related protein 1	0.99	-	nuc	0		contractile ring (sensu Saccharomyces) [IDA]			1375
P54132 UniProt NPD GO	BLM_HUMAN	Bloom syndrome protein (EC 3.6.1.-) (RecQ protein-like 3) (DNA helicase, RecQ-like type 2)	0.99	+	nuc	0	Nucleus		604610		1417
O88700 UniProt NPD GO	BLM_MOUSE	Bloom syndrome protein homolog (EC 3.6.1.-) (mBLM)	0.99	+	nuc	0	Nucleus (By similarity)	replication fork [IDA]			1416
P48754 UniProt NPD GO	BRCA1_MOUSE	Breast cancer type 1 susceptibility protein homolog	0.99	-	nuc	0	Nucleus (Potential)	centrosome [TAS] condensed chromosome [IDA] cytoplasm [IDA] gamma-tubulin ring complex [ISS] nucleus [ISS]			1812
Q864S8 UniProt NPD GO	BRCA2_FELCA	Breast cancer type 2 susceptibility protein homolog (Fanconi anemia group D1 protein homolog)	0.99	-	nuc	0					3372
O35923 UniProt NPD GO	BRCA2_RAT	Breast cancer type 2 susceptibility protein homolog (Fanconi anemia group D1 protein homolog)	0.99	-	nuc	0				1IYJ	3343
Q9UIF8 UniProt NPD GO	BAZ2B_HUMAN	Bromodomain adjacent to zinc finger domain 2B (hWALp4)	0.99	+	nuc	0			605683		1972
Q9Z277 UniProt NPD GO	BAZ1B_MOUSE	Bromodomain adjacent to zinc finger domain protein 1B (Williams-Beuren syndrome chromosome region 9 ...	0.99	+	nuc	0	Nucleus (Potential). Accumulates in pericentromeric heterochromatin during replication (By similarit ...	centric heterochromatin [IDA] condensed chromosome [IDA] nucleus [IDA]			1479
Q9UIG0 UniProt NPD GO	BAZ1B_HUMAN	Bromodomain adjacent to zinc finger domain protein 1B (Williams-Beuren syndrome chromosome region 9 ...	0.99	+	nuc	0	Nucleus (Potential). Accumulates in pericentromeric heterochromatin during replication	nucleus [NAS]	194050	1F62	1483
Q9NSI6 UniProt NPD GO	BRWD1_HUMAN	Bromodomain and WD repeat domain-containing protein 1 (WD repeat protein 9)	0.99	+	nuc	0	Cytoplasm. Nucleus (By similarity)				2320
Q5R8B0 UniProt NPD GO	BRD7_PONPY	Bromodomain-containing protein 7	0.99	+	nuc	0	Nucleus (By similarity)				651
O88665 UniProt NPD GO	BRD7_MOUSE	Bromodomain-containing protein 7 (75 kDa bromodomain protein)	0.99	+	nuc	0	Nucleus	nucleus [IDA]			651
Q6GLP7 UniProt NPD GO	BRD9_XENLA	Bromodomain-containing protein 9	0.99	+	nuc	0					527
Q04347 UniProt NPD GO	BUD22_YEAST	Bud site selection protein 22	0.99	+	nuc	0	Nucleus	nucleus [IDA]			519
Q03001 UniProt NPD GO	BPA1_HUMAN	Bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kDa bullous pemphigoid antigen) (BPA) (Hemide ...	0.99	-	nuc	0	Cytoplasm	basement membrane [TAS] cytoplasm [IEP] cytoplasmic membrane-bound vesicle [IDA] hemidesmosome [TAS]	600088		3214
Q91ZU8 UniProt NPD GO	BPAEA_MOUSE	Bullous pemphigoid antigen 1, isoform 5 (BPA) (Hemidesmosomal plaque protein) (Dystonia musculorum p ...	0.99	+	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] hemidesmosome [IDA]			2611
Q9UKL3 UniProt NPD GO	C8AP2_HUMAN	CASP8-associated protein 2 (FLICE-associated huge protein)	0.99	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]	606880		1982
Q92793 UniProt NPD GO	CBP_HUMAN	CREB-binding protein (EC 2.3.1.48)	0.99	+	nuc	0	Nucleus	cytoplasm [TAS] nucleus [TAS]	180849	2D82	2442
P45481 UniProt NPD GO	CBP_MOUSE	CREB-binding protein (EC 2.3.1.48)	0.99	+	nuc	0	Nucleus	histone acetyltransferase complex [IDA] nucleus [IDA] outer kinetochore of condensed chromosome [IDA]		2C52	2441
Q9Y6J0 UniProt NPD GO	CABIN_HUMAN	Calcineurin-binding protein Cabin 1 (Calcineurin inhibitor) (CAIN)	0.99	-	nuc	0	Nucleus	nucleus [NAS]	604251	1N6J	2220
Q9EPY0 UniProt NPD GO	CARD9_RAT	Caspase recruitment domain-containing protein 9 (rCARD9)	0.99	+	nuc	0	Cytoplasm (By similarity)				536
Q2KJC1 UniProt NPD GO	CDC5L_BOVIN	Cell division cycle 5-like protein (Cdc5-like protein)	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. May shuttle between cytoplasm and nucleus (By similarity)				802
Q99459 UniProt NPD GO	CDC5L_HUMAN	Cell division cycle 5-like protein (Cdc5-like protein) (Pombe cdc5-related protein)	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. May shuttle between cytoplasm and nucleus	nucleus [NAS]	602868		802
Q6A068 UniProt NPD GO	CDC5L_MOUSE	Cell division cycle 5-related protein (Cdc5-like protein)	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. May shuttle between cytoplasm and nucleus				802
O08837 UniProt NPD GO	CDC5L_RAT	Cell division cycle 5-related protein (Cdc5-like protein) (Pombe Cdc5-related protein)	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. May shuttle between cytoplasm and nucleus	nuclear speck [IDA] nucleus [IDA]			802
Q641G3 UniProt NPD GO	CCAR1_XENLA	Cell division cycle and apoptosis regulator protein 1	0.99	+	nuc	0	Cytoplasm; perinuclear region (By similarity)				1157
Q9QWF0 UniProt NPD GO	CAF1A_MOUSE	Chromatin assembly factor 1 subunit A (CAF-1 subunit A) (Chromatin assembly factor I p150 subunit) ( ...	0.99	+	nuc	0	Nucleus. DNA replication foci			1S4Z	911
Q12495 UniProt NPD GO	CAC1_YEAST	Chromatin assembly factor 1 subunit p90 (CAF-1 90 kDa subunit) (RAP1 localization factor 2)	0.99	+	nuc	0	Nucleus	chromatin assembly complex [IDA] chromosome, pericentric region [IDA] nucleus [IDA]			606

You are viewing entries 201 to 250 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.