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
P07269 UniProt NPD GO	PHO2_YEAST	Regulatory protein PHO2 (General regulatory factor 10)	0.92	+	nuc	0	Nucleus	nucleus [IDA]			559
P15593 UniProt NPD GO	RTP1_TRYBG	Retrotransposable element SLACS 45 kDa protein (ORF1)	0.92	-	nuc	0					404
P42331 UniProt NPD GO	RHG25_HUMAN	Rho-GTPase-activating protein 25	0.92	-	nuc	0				1V89	638
Q9UNA1 UniProt NPD GO	RHG26_HUMAN	Rho-GTPase-activating protein 26 (Oligophrenin-1-like protein) (GTPase regulator associated with foc ...	0.92	-	nuc	0			605370	1UGV	814
Q92974 UniProt NPD GO	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2 (GEF-H1 protein) (Proliferating cell nucleolar antigen ...	0.92	-	nuc	0	Cytoplasm. Colocalizes with microtubules through the C-terminal coiled-coil domain	microtubule [ISS]	607560		893
Q59VF9 UniProt NPD GO	RSA3_CANAL	Ribosome assembly protein 3	0.92	+	nuc	0	Nucleus; nucleolus (By similarity)				195
Q6BWS4 UniProt NPD GO	RSA3_DEBHA	Ribosome assembly protein 3	0.92	+	nuc	0	Nucleus; nucleolus (By similarity)				191
P32102 UniProt NPD GO	RLP7_KLULA	Ribosome biogenesis protein RLP7	0.92	+	nuc	0	Nucleus; nucleolus (By similarity)				318
Q8L4E7 UniProt NPD GO	BP73_ORYSA	SAP-like protein BP-73 (OsBP-73) (Riaa1)	0.92	-	nuc	0					375
Q9QX74 UniProt NPD GO	SHAN2_RAT	SH3 and multiple ankyrin repeat domains protein 2 (Shank2) (Proline-rich synapse-associated protein ...	0.92	+	nuc	0	Cytoplasm; postsynaptic density of neuronal cells. Colocalizes with cortactin in growth cones in dif ...	postsynaptic membrane [IDA]			1474
Q95216 UniProt NPD GO	SMRA3_RABIT	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3 (EC 3. ...	0.92	+	nuc	0	Nucleus (By similarity)				1005
Q6PCN7 UniProt NPD GO	SMRA3_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3 (EC 3. ...	0.92	+	nuc	0	Nucleus				1003
Q99JR8 UniProt NPD GO	SMRD2_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 (60 kD ...	0.92	+	nuc	0	Nucleus (By similarity)				456
Q4WNY4 UniProt NPD GO	SWC4_ASPFU	SWR1-complex protein 4	0.92	-	nuc	0	Nucleus (By similarity)				588
Q5B4T5 UniProt NPD GO	SWC4_EMENI	SWR1-complex protein 4	0.92	-	nuc	0	Nucleus (By similarity)				586
P54792 UniProt NPD GO	DVL1L_HUMAN	Segment polarity protein dishevelled homolog DVL-1-like (Dishevelled-1-like) (DSH homolog 1-like)	0.92	+	nuc	0	Cytoplasm (Potential)	cytoplasm [NAS]	601225		670
Q9EP97 UniProt NPD GO	SENP3_MOUSE	Sentrin-specific protease 3 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP3) (SUMO-1-specific pr ...	0.92	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			568
Q80UG5 UniProt NPD GO	SEPT9_MOUSE	Septin-9 (SL3-3 integration site 1 protein)	0.92	-	nuc	0	Cell membrane (By similarity)				583
P15619 UniProt NPD GO	SRYC_DROME	Serendipity locus protein H-1 (Protein wings-down) (Protein pourquoi-pas)	0.92	-	nuc	0	Nucleus	nucleus [IDA]			869
Q8QZV4 UniProt NPD GO	ST32C_MOUSE	Serine/threonine-protein kinase 32C (EC 2.7.11.1)	0.92	-	mit	0					488
Q6FL58 UniProt NPD GO	ATG1_CANGA	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.92	-	nuc	0	Cytoplasm (By similarity)				942
Q6C842 UniProt NPD GO	BUR1_YARLI	Serine/threonine-protein kinase BUR1 (EC 2.7.11.22) (EC 2.7.11.23)	0.92	-	nuc	0	Nucleus (By similarity)				706
Q08732 UniProt NPD GO	HRK1_YEAST	Serine/threonine-protein kinase HRK1 (EC 2.7.11.1) (Hygromycin resistance kinase 1)	0.92	+	nuc	0	Cytoplasm	cytoplasm [IDA]			759
Q9JKV2 UniProt NPD GO	ICK_MOUSE	Serine/threonine-protein kinase ICK (EC 2.7.11.22) (Intestinal cell kinase) (mICK) (MAK-related kina ...	0.92	-	nuc	0	Cytoplasm (By similarity)				629
P38990 UniProt NPD GO	PAK1_YEAST	Serine/threonine-protein kinase PAK1 (EC 2.7.11.1)	0.92	-	nuc	1		cytoplasm [IDA]			1142
Q75DK7 UniProt NPD GO	STE20_ASHGO	Serine/threonine-protein kinase STE20 (EC 2.7.11.1)	0.92	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				971
Q5KFE0 UniProt NPD GO	ATM_CRYNE	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.92	-	nuc	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2967
Q6BV76 UniProt NPD GO	ATM_DEBHA	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.92	-	end	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2948
Q4IB89 UniProt NPD GO	ATM_GIBZE	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.92	+	nuc	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2813
Q7RX99 UniProt NPD GO	ATG1_NEUCR	Serine/threonine-protein kinase atg-1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.92	-	nuc	0	Cytoplasm (By similarity)				932
Q09898 UniProt NPD GO	SID2_SCHPO	Serine/threonine-protein kinase sid2 (EC 2.7.11.1)	0.92	-	nuc	0	Spindle pole body	medial ring [IDA]			607
P26570 UniProt NPD GO	PPZ1_YEAST	Serine/threonine-protein phosphatase PP-Z1 (EC 3.1.3.16)	0.92	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			691
P38688 UniProt NPD GO	SRP72_YEAST	Signal recognition particle subunit SRP72 (Signal recognition particle 72 kDa protein homolog)	0.92	+	nuc	0	Cytoplasm (By similarity). Nucleus	signal recognition particle (sensu Eukaryota) [IDA]			640
P52630 UniProt NPD GO	STAT2_HUMAN	Signal transducer and activator of transcription 2 (p113)	0.92	-	nuc	0	Cytoplasm. Translocated into the nucleus upon activation by IFN-alpha/beta		600556		851
Q750S2 UniProt NPD GO	SCC2_ASHGO	Sister chromatid cohesion protein 2	0.92	-	nuc	0	Nucleus (By similarity)				1479
Q04264 UniProt NPD GO	PDS5_YEAST	Sister chromatid cohesion protein PDS5 (Precocious dissociation of sisters protein 5)	0.92	-	nuc	0		condensed nuclear chromosome [IDA]			1277
Q4R503 UniProt NPD GO	SNX1_MACFA	Sorting nexin-1	0.92	-	nuc	0					522
P83266 UniProt NPD GO	PRT31_HYDCO	Sperm protamine R3 isoform 1	0.92	+	nuc	0	Nucleus	nucleosome [TAS] nucleus [TAS]			48
P83267 UniProt NPD GO	PRT32_HYDCO	Sperm protamine R3 isoform 2	0.92	+	nuc	0	Nucleus	nucleosome [TAS] nucleus [TAS]			48
Q7M2P1 UniProt NPD GO	STP3_PIG	Spermatid nuclear transition protein 3 (STP-3) (TP-3) (TP3)	0.92	+	mit	0	Nucleus				76
Q6CMM2 UniProt NPD GO	MAD1_KLULA	Spindle assembly checkpoint component MAD1 (Mitotic arrest deficient protein 1)	0.92	+	nuc	0	Nucleus (By similarity)				648
O59755 UniProt NPD GO	CUT12_SCHPO	Spindle pole body-associated protein cut12 (Cell untimely torn protein 12)	0.92	+	nuc	0	Spindle pole body	spindle pole body [IDA]			548
Q8CH02 UniProt NPD GO	SF04_MOUSE	Splicing factor 4	0.92	-	nuc	0	Nucleus (Probable)			1X4O	643
Q8IWZ8 UniProt NPD GO	SF04_HUMAN	Splicing factor 4 (RNA-binding protein RBP)	0.92	-	nuc	0	Nucleus (Probable)		607992		645
P90727 UniProt NPD GO	U2AF2_CAEBR	Splicing factor U2AF 65 kDa subunit (U2 auxiliary factor 65 kDa subunit) (U2 snRNP auxiliary factor ...	0.92	+	nuc	0	Nucleus				488
Q9US08 UniProt NPD GO	SPO3_SCHPO	Sporulation-specific protein 3	0.92	-	nuc	0	Associated with the plasma and forespore membranes	prospore membrane [IDA]			1028
Q12151 UniProt NPD GO	UPC2_YEAST	Sterol uptake control protein 2 (Mannoprotein regulation by oxygen protein 4)	0.92	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IPI]			913
Q6ZVD7 UniProt NPD GO	STOX1_HUMAN	Storkhead-box protein 1 (Winged helix domain-containing protein)	0.92	-	exc	0	Isoform A: Cytoplasm. Isoform A, isoform B: Nucleus. Isoform A is either found in the cytoplasm or i ...		609404		989
O97593 UniProt NPD GO	SMC1A_BOVIN	Structural maintenance of chromosome 1-like 1 protein (SMC-protein)	0.92	+	nuc	0	Nucleus. Associates with chromatin. The phosphorylated form on Ser-957 and Ser-966 associates with c ...	cohesin core heterodimer [ISS] kinetochore [ISS] nucleus [ISS]			1233
Q9Z1M9 UniProt NPD GO	SMC1A_RAT	Structural maintenance of chromosome 1-like 1 protein (SMC-protein)	0.92	+	nuc	0	Nucleus (By similarity). Associates with chromatin. Before prophase it is scattered along chromosome ...	cohesin core heterodimer [ISS] kinetochore [ISS] nucleus [ISS]			1233

You are viewing entries 3451 to 3500 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.