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
Q9LRR4 UniProt NPD GO	R13L1_ARATH	Putative disease resistance RPP13-like protein 1	0.75	-	nuc	0					1054
Q10105 UniProt NPD GO	YAQ5_SCHPO	Putative translational activator C18G6.05c (GCN1 homolog)	0.75	-	nuc	0					2670
P34225 UniProt NPD GO	YBG0_YEAST	Putative uncharacterized protein YBL060W	0.75	-	nuc	0		bud neck [IDA] cytoplasm [IDA]			687
O23379 UniProt NPD GO	COL11_ARATH	Putative zinc finger protein CONSTANS-LIKE 11	0.75	-	nuc	0	Nucleus (Potential)				330
Q90WN5 UniProt NPD GO	RCOR1_XENLA	REST corepressor 1 (Protein CoREST) (xCoREST)	0.75	+	nuc	0	Nucleus (By similarity)				431
Q5E9N3 UniProt NPD GO	RNF25_BOVIN	RING finger protein 25 (EC 6.3.2.-)	0.75	-	nuc	0					458
Q96BH1 UniProt NPD GO	RNF25_HUMAN	RING finger protein 25 (EC 6.3.2.-)	0.75	-	nuc	0				2DAY	459
Q12161 UniProt NPD GO	PSH1_YEAST	RING finger protein PSH1 (POB3/SPT16 histone-associated protein 1)	0.75	-	nuc	0	Nucleus	nucleus [IDA]			406
Q9P7Y4 UniProt NPD GO	MED14_SCHPO	RNA polymerase II mediator complex subunit 14 (RNA polymerase II mediator complex protein pmc1)	0.75	-	cyt	0	Nucleus (Probable)				879
O94763 UniProt NPD GO	RMP_HUMAN	RNA polymerase II subunit 5-mediating protein (RPB5-mediating protein)	0.75	-	nuc	0	Nucleus	cytoplasm [TAS] DNA-directed RNA polymerase II, core complex [TAS] nucleus [TAS]	603494		508
P21328 UniProt NPD GO	RTJK_DROME	RNA-directed DNA polymerase from mobile element jockey (EC 2.7.7.49) (Reverse transcriptase)	0.75	+	cyt	0					916
Q8N2Y8 UniProt NPD GO	RUSC2_HUMAN	RUN and SH3 domain-containing protein 2	0.75	-	nuc	0					1516
O54828 UniProt NPD GO	RGS9_MOUSE	Regulator of G-protein signaling 9 (RGS9)	0.75	-	nuc	0					675
P49805 UniProt NPD GO	RGS9_RAT	Regulator of G-protein signaling 9 (RGS9)	0.75	-	nuc	0					677
O42567 UniProt NPD GO	RXB_XENLA	Retinal homeobox protein Rx-B (Rx2A)	0.75	+	nuc	0	Nucleus (By similarity)				325
Q8K0Q5 UniProt NPD GO	RHG18_MOUSE	Rho-GTPase-activating protein 18	0.75	+	nuc	0					663
P51211 UniProt NPD GO	RNE_PORPU	Ribonuclease E homolog (EC 3.1.4.-) (RNase E)	0.75	-	cyt	0	Plastid; chloroplast				511
Q13309 UniProt NPD GO	SKP2_HUMAN	S-phase kinase-associated protein 2 (F-box protein Skp2) (Cyclin A/CDK2-associated protein p45) (p45 ...	0.75	+	nuc	0			601436	2AST	424
Q5H9R7 UniProt NPD GO	SAPS3_HUMAN	SAPS domain family member 3 (Sporulation-induced transcript 4-associated protein SAPL) (Protein phos ...	0.75	-	nuc	0					873
Q8K352 UniProt NPD GO	SLY_MOUSE	SH3 protein expressed in lymphocytes	0.75	-	nuc	0					380
Q9CZV5 UniProt NPD GO	ST65G_MOUSE	STAGA complex 65 subunit gamma (STAF65gamma) (SPTF-associated factor 65 gamma) (Suppressor of Ty 7-l ...	0.75	-	nuc	0	Nucleus (By similarity)				412
Q5BIN2 UniProt NPD GO	SNF5_BOVIN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	0.75	-	nuc	0	Nucleus (By similarity)				385
Q9NSC2 UniProt NPD GO	SALL1_HUMAN	Sal-like protein 1 (Zinc finger protein SALL1) (Spalt-like transcription factor 1) (HSal1)	0.75	-	nuc	0	Nucleus (By similarity)		602218		1324
Q00725 UniProt NPD GO	SGS4_DROME	Salivary glue protein Sgs-4 precursor	0.75	-	nuc	0	Secreted protein (Potential)				297
Q60838 UniProt NPD GO	DVL2_MOUSE	Segment polarity protein dishevelled homolog DVL-2 (Dishevelled-2) (DSH homolog 2)	0.75	+	nuc	0	Cytoplasm (By similarity)				736
P48010 UniProt NPD GO	SPN5_SCHPO	Septin homolog spn5 (Mei4-dependent protein 9) (Meiotic expression up-regulated protein 28)	0.75	-	nuc	0					464
P54359 UniProt NPD GO	SEPT2_DROME	Septin-2	0.75	-	mit	0		ring canal (sensu Insecta) [NAS]			419
Q5ZJK4 UniProt NPD GO	STK4_CHICK	Serine/threonine-protein kinase 4 (EC 2.7.11.1)	0.75	-	nuc	0	Cytoplasm. The caspase-cleaved form cycles between the nucleus and cytoplasm (By similarity)				486
O14965 UniProt NPD GO	STK6_HUMAN	Serine/threonine-protein kinase 6 (EC 2.7.11.1) (Serine/threonine kinase 15) (Aurora/IPL1-related ki ...	0.75	-	nuc	0	Centrosome. Spindle. Localizes on centrosomes in interphase cells and at each spindle pole in mitosi ...	nucleus [TAS] spindle [TAS]	602687	2C6E	403
Q9NRM7 UniProt NPD GO	LATS2_HUMAN	Serine/threonine-protein kinase LATS2 (EC 2.7.11.1) (Large tumor suppressor homolog 2) (Serine/threo ...	0.75	-	nuc	0	Centrosome. Cytoplasm. Co-localizes with STK6 at the centrosomes during interphase, early prophase a ...	nucleus [NAS] spindle pole [IDA]	604861		1088
O35942 UniProt NPD GO	NEK2_MOUSE	Serine/threonine-protein kinase Nek2 (EC 2.7.11.1) (NimA-related protein kinase 2)	0.75	-	nuc	0	Nucleus. Localizes at the centromere	condensed nuclear chromosome [IDA] midbody [IDA] spindle pole [IDA]			443
O00444 UniProt NPD GO	PLK4_HUMAN	Serine/threonine-protein kinase PLK4 (EC 2.7.11.21) (Polo-like kinase 4) (PLK-4) (Serine/threonine-p ...	0.75	-	nuc	0			605031		970
Q6CP76 UniProt NPD GO	ATM_KLULA	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.75	-	end	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2761
O75011 UniProt NPD GO	NAK1_SCHPO	Serine/threonine-protein kinase nak1 (EC 2.7.11.1) (N-rich kinase 1)	0.75	-	nuc	0	Cytoplasm	cytoplasm [IDA] spindle pole body [IDA]			652
Q17850 UniProt NPD GO	PAK1_CAEEL	Serine/threonine-protein kinase pak-1 (EC 2.7.11.1) (p21-activated kinase 1) (PAK1) (CePAK)	0.75	-	nuc	0	Cell surface. Preferentially localized at the cell surface and especially condensed at cell boundari ...	integral to membrane [IDA]			572
P50528 UniProt NPD GO	PLO1_SCHPO	Serine/threonine-protein kinase plo1 (EC 2.7.11.21)	0.75	-	nuc	0		spindle pole body [IDA]			683
Q2ULU3 UniProt NPD GO	STE20_ASPOR	Serine/threonine-protein kinase ste20 (EC 2.7.11.1)	0.75	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				848
Q5BHE2 UniProt NPD GO	ATM_EMENI	Serine/threonine-protein kinase tel1 (EC 2.7.11.1) (DNA-damage checkpoint kinase tel1) (Telomere len ...	0.75	-	nuc	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2793
Q29090 UniProt NPD GO	2ABA_PIG	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A, subunit B, ...	0.75	-	nuc	0					426
Q16537 UniProt NPD GO	2A5E_HUMAN	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform (PP2A, B subunit, ...	0.75	-	cyt	0	Cytoplasm	cytoplasm [TAS]	601647		467
Q06190 UniProt NPD GO	2ACA_HUMAN	Serine/threonine-protein phosphatase 2A 72/130 kDa regulatory subunit B (PP2A, subunit B, B''-PR72/P ...	0.75	-	nuc	0		protein phosphatase type 2A complex [ISS]	604944		1150
P32945 UniProt NPD GO	PPQ1_YEAST	Serine/threonine-protein phosphatase PPQ (EC 3.1.3.16)	0.75	-	mit	0		cytoplasm [IDA]			549
P48595 UniProt NPD GO	SPB10_HUMAN	Serpin B10 (Bomapin) (Protease inhibitor 10)	0.75	-	nuc	0	Cytoplasm (By similarity)		602058		397
Q6TC39 UniProt NPD GO	SRY_MIRAN	Sex-determining region Y protein (Testis-determining factor)	0.75	+	nuc	0	Nucleus				218
Q6TC38 UniProt NPD GO	SRY_MIRLE	Sex-determining region Y protein (Testis-determining factor)	0.75	+	nuc	0	Nucleus				218
P36393 UniProt NPD GO	SRY_PIG	Sex-determining region Y protein (Testis-determining factor)	0.75	+	nuc	0	Nucleus				208
P42900 UniProt NPD GO	SLS1_YEAST	Sigma-like sequence protein 1, mitochondrial precursor (Protein SLS1)	0.75	+	nuc	0	Mitochondrion; mitochondrial inner membrane	integral to membrane [IDA] mitochondrial inner membrane [IDA] mitochondrial nucleoid [IDA]			643
Q9WVC1 UniProt NPD GO	SLIT2_RAT	Slit homolog 2 protein precursor (Slit-2) (Fragment)	0.75	-	nuc	0	Secreted protein (By similarity)				766
P02318 UniProt NPD GO	HSP1_BOVIN	Sperm protamine P1 (Cysteine-rich protamine)	0.75	+	mit	0	Nucleus				50
P87244 UniProt NPD GO	ALP16_SCHPO	Spindle pole body component alp16 (Altered polarity protein 16)	0.75	-	nuc	0	Spindle pole body. And the microtubule organizing center (MTOC)	equatorial microtubule organizing center [IDA] gamma-tubulin complex [IDA] spindle pole body [IC]			759

You are viewing entries 11551 to 11600 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.