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
Q8N488 UniProt NPD GO	RYBP_HUMAN	RING1 and YY1-binding protein (Death effector domain-associated factor) (DED-associated factor) (YY1 ...	0.73	+	nuc	0	Nucleus. Cytoplasm. Primarily found in the nucleus		607535		228
P40561 UniProt NPD GO	SGN1_YEAST	RNA-binding protein SGN1	0.73	-	nuc	0	Cytoplasm	cytoplasm [IDA]			250
O75154 UniProt NPD GO	RFIP3_HUMAN	Rab11 family-interacting protein 3 (Rab11-FIP3) (EF hands-containing Rab-interacting protein) (Eferi ...	0.73	-	nuc	0	Endosome; recycling endosome. Colocalizes with RAB11A at recycling endosomes		608738		756
Q9Y2J0 UniProt NPD GO	RP3A_HUMAN	Rabphilin-3A (Exophilin-1)	0.73	-	nuc	0					694
Q8NHQ8 UniProt NPD GO	RASF8_HUMAN	Ras association domain-containing protein 8 (Carcinoma-associated protein HOJ-1)	0.73	+	nuc	0			608180	2CS4	419
Q8K072 UniProt NPD GO	REEP4_MOUSE	Receptor expression-enhancing protein 4	0.73	-	end	2 *	Membrane; multi-pass membrane protein (By similarity)				257
Q60855 UniProt NPD GO	RIPK1_MOUSE	Receptor-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (Serine/threonine-protein kinas ...	0.73	-	nuc	0	Cytoplasm				656
Q4VSN4 UniProt NPD GO	RIPK5_CANFA	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.73	-	cyt	0	Cytoplasm (Probable)				931
P34891 UniProt NPD GO	KIN15_CAEEL	Receptor-like tyrosine-protein kinase kin-15 precursor (EC 2.7.10.1)	0.73	-	exc	2 *					488
P09956 UniProt NPD GO	ZEST_DROME	Regulatory protein zeste	0.73	-	nuc	0	Nucleus				574
O42201 UniProt NPD GO	RXA_XENLA	Retinal homeobox protein Rx-A (xRx1)	0.73	+	nuc	0	Nucleus (By similarity)				322
P28702 UniProt NPD GO	RXRB_HUMAN	Retinoic acid receptor RXR-beta (Retinoid X receptor beta)	0.73	+	nuc	0	Nucleus		180246	1UHL	533
P28704 UniProt NPD GO	RXRB_MOUSE	Retinoic acid receptor RXR-beta (Retinoid X receptor beta) (MHC class I regulatory element-binding p ...	0.73	+	nuc	0	Nucleus				520
P28699 UniProt NPD GO	RARG_XENLA	Retinoic acid receptor gamma (RAR-gamma)	0.73	+	nuc	0	Nucleus				476
P22932 UniProt NPD GO	RARG2_HUMAN	Retinoic acid receptor gamma-2 (RAR-gamma-2)	0.73	+	nuc	0	Nucleus		180190	4LBD	443
Q2PP52 UniProt NPD GO	RHBL6_TOXGO	Rhomboid-like protease 6 (EC 3.4.21.105)	0.73	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				531
Q6V7V2 UniProt NPD GO	RTKN_RAT	Rhotekin	0.73	-	nuc	0					548
Q8C050 UniProt NPD GO	KS6A5_MOUSE	Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1) (Nuclear mitogen-and stress-activated protein kina ...	0.73	-	nuc	0	Nucleus (By similarity)	nucleus [IEP]			863
O75582 UniProt NPD GO	KS6A5_HUMAN	Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1) (Nuclear mitogen-and stress-activated protein kina ...	0.73	+	cyt	0	Nucleus. Predominantly. Cytoplasm. Partially	nucleus [IEP]	603607	1VZO	802
Q24498 UniProt NPD GO	RY44_DROME	Ryanodine receptor 44F	0.73	+	end	6	Membrane; multi-pass membrane protein (Probable)	integral to membrane [NAS]			5127
Q9Z0Z3 UniProt NPD GO	SKP2_MOUSE	S-phase kinase-associated protein 2 (F-box protein Skp2) (Cyclin A/CDK2-associated protein p45) (F-b ...	0.73	-	nuc	0		ubiquitin ligase complex [TAS]			424
Q6NRF1 UniProt NPD GO	SAP3B_XENLA	SAPS domain family member 3-B	0.73	-	nuc	0					850
Q9V785 UniProt NPD GO	3BP5_DROME	SH3 domain-binding protein 5-like (Protein parcase)	0.73	-	nuc	0	Cytoplasm (By similarity)				476
O94933 UniProt NPD GO	SLIK3_HUMAN	SLIT and NTRK-like protein 3 precursor	0.73	+	nuc	2 *	Membrane; single-pass membrane protein (Potential)		609679		977
Q9H5Y7 UniProt NPD GO	SLIK6_HUMAN	SLIT and NTRK-like protein 6 precursor	0.73	+	nuc	1	Membrane; single-pass membrane protein (Potential)		609681		841
Q13239 UniProt NPD GO	SLAP1_HUMAN	SRC-like-adapter (Src-like-adapter protein 1) (hSLAP)	0.73	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity). Colocalizes with endosomes (By similarity)		601099	2CUD	275
Q9UJQ4 UniProt NPD GO	SALL4_HUMAN	Sal-like protein 4 (Zinc finger protein SALL4)	0.73	-	nuc	0	Nucleus (Probable)		607343		1053
P49907 UniProt NPD GO	SEPP1_BOVIN	Selenoprotein P-like protein precursor	0.73	-	end	0	Secreted protein (By similarity)				402
Q13591 UniProt NPD GO	SEM5A_HUMAN	Semaphorin-5A precursor (Semaphorin F) (Sema F)	0.73	-	exc	1	Membrane; single-pass type I membrane protein				1074
Q6CFS5 UniProt NPD GO	CBK1_YARLI	Serine/threonine-protein kinase CBK1 (EC 2.7.11.1)	0.73	-	nuc	0					588
P06784 UniProt NPD GO	STE7_YEAST	Serine/threonine-protein kinase STE7 (EC 2.7.12.2)	0.73	-	nuc	0		cytoplasm [IDA] mating projection tip [IDA]			515
Q00005 UniProt NPD GO	2ABB_HUMAN	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, B ...	0.73	-	nuc	0			604326		443
Q4R8L3 UniProt NPD GO	2ABB_MACFA	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, B ...	0.73	-	nuc	0					443
Q6ZWR4 UniProt NPD GO	2ABB_MOUSE	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, B ...	0.73	-	nuc	0					443
Q5R4A2 UniProt NPD GO	2ABB_PONPY	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, B ...	0.73	-	nuc	0					443
Q15172 UniProt NPD GO	2A5A_HUMAN	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform (PP2A, B subunit, B' ...	0.73	-	cyt	0	Cytoplasm	cytoplasm [TAS]	601643		486
Q14738 UniProt NPD GO	2A5D_HUMAN	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PP2A, B subunit, B' ...	0.73	-	nuc	0	Cytoplasm. Nucleus. Nuclear in interphase, nuclear during mitosis	nucleus [TAS]	601646		602
O76094 UniProt NPD GO	SRP72_HUMAN	Signal recognition particle 72 kDa protein (SRP72)	0.73	+	nuc	0	Cytoplasm		602122		670
Q20977 UniProt NPD GO	STATB_CAEEL	Signal transducer and activator of transcription b (Zinc finger protein STAT-B)	0.73	-	end	3	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation (By similarity)				966
Q8IPH9 UniProt NPD GO	SLOB_DROME	Slowpoke-binding protein	0.73	-	nuc	0	Cytoplasm (Probable). Enriched in synaptic boutons	cytoplasm [NAS]			515
Q9H2A7 UniProt NPD GO	SCYBG_HUMAN	Small inducible cytokine B16 precursor (Transmembrane chemokine CXCL16) (SR-PSOX) (Scavenger recepto ...	0.73	-	exc	1 *	Cell membrane; single-pass type I membrane protein (Potential). Secreted protein. Also exists as a s ...	extracellular region [NAS] integral to membrane [NAS] membrane [TAS]	605398		254
Q6CHY6 UniProt NPD GO	MVP1_YARLI	Sorting nexin MVP1	0.73	-	nuc	0	Cytoplasm (By similarity)				605
Q91WL6 UniProt NPD GO	SNX11_MOUSE	Sorting nexin-11	0.73	-	nuc	0					271
Q9D8U8 UniProt NPD GO	SNX5_MOUSE	Sorting nexin-5	0.73	-	cyt	0					404
P56225 UniProt NPD GO	SPRM1_RAT	Sperm 1 POU-domain transcription factor (SPRM-1)	0.73	+	nuc	0	Nucleus				335
Q8WMC7 UniProt NPD GO	HSP1_EPTBR	Sperm protamine P1	0.73	+	nuc	0	Nucleus (By similarity)				47
Q7JH05 UniProt NPD GO	HSP1_EPTFU	Sperm protamine P1	0.73	+	nuc	0	Nucleus (By similarity)				47
Q95ZG4 UniProt NPD GO	SPC98_DICDI	Spindle pole body component 98 (Spc98) (DdSpc98) (Fragment)	0.73	-	nuc	0	Centrosome. Cytoplasm				812
Q9Y7J1 UniProt NPD GO	SPO6_SCHPO	Sporulation-specific protein 6	0.73	-	nuc	0	Nucleus				474
Q923Q2 UniProt NPD GO	STA13_MOUSE	StAR-related lipid transfer protein 13 (StARD13) (START domain-containing protein 13)	0.73	-	nuc	0					1113

You are viewing entries 12501 to 12550 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.