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
Q16384 UniProt NPD GO	SSX1_HUMAN	Protein SSX1 (Synovial sarcoma, X breakpoint 1)	0.61	-	nuc	0		nucleus [TAS]	312820		188
Q24174 UniProt NPD GO	ABRU_DROME	Protein abrupt (Protein clueless)	0.61	-	nuc	0	Nucleus	nucleus [NAS]			904
Q9Y6X2 UniProt NPD GO	PIAS3_HUMAN	Protein inhibitor of activated STAT protein 3	0.61	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Mostly (By similarity)		605987		628
P16911 UniProt NPD GO	KDC1_DROME	Protein kinase DC1 (EC 2.7.11.1)	0.61	-	cyt	0					376
Q91VC7 UniProt NPD GO	PP14A_MOUSE	Protein phosphatase 1 regulatory subunit 14A (17 kDa PKC-potentiated inhibitory protein of PP1) (CPI ...	0.61	-	mit	0	Cytoplasm (By similarity)				147
Q9SZ77 UniProt NPD GO	SEC1B_ARATH	Protein transport Sec1b (AtSec1b)	0.61	-	cyt	0					662
P20153 UniProt NPD GO	USP_DROME	Protein ultraspiracle (XR2C) (Chorion factor 1)	0.61	+	nuc	0	Nucleus	ecdysone receptor holocomplex [TAS] nucleus [IDA]		1R0O	508
Q9NHV9 UniProt NPD GO	VAV_DROME	Protein vav (DroVav)	0.61	-	nuc	0					793
Q9SA27 UniProt NPD GO	RH36_ARATH	Putative DEAD-box ATP-dependent RNA helicase 36 (EC 3.6.1.-)	0.61	+	cyt	0					491
Q9VUV9 UniProt NPD GO	U520_DROME	Putative U5 small nuclear ribonucleoprotein 200 kDa helicase (EC 3.6.1.-)	0.61	-	nuc	0	Nucleus (Potential)	nucleus [IC] spliceosome complex [ISS]			2142
P34815 UniProt NPD GO	UNC18_CAEEL	Putative acetylcholine regulator unc-18 (Uncoordinated protein 18)	0.61	-	cyt	0					591
Q8VYT2 UniProt NPD GO	CAP6_ARATH	Putative clathrin assembly protein At4g25940	0.61	-	nuc	0					601
Q9SIZ0 UniProt NPD GO	DRE2H_ARATH	Putative dehydration-responsive element-binding protein 2H (DREB2H protein)	0.61	-	nuc	0	Nucleus (Probable)				164
Q8W3K3 UniProt NPD GO	DRL8_ARATH	Putative disease resistance protein At1g58400	0.61	-	cyt	0					910
Q9HCE1 UniProt NPD GO	MOV10_HUMAN	Putative helicase MOV-10 (EC 3.6.1.-) (Moloney leukemia virus 10 protein)	0.61	-	cyt	0					1003
Q9M081 UniProt NPD GO	SC24B_ARATH	Putative protein transport protein Sec24-like At4g32640	0.61	-	nuc	0					1069
P39728 UniProt NPD GO	YAD7_YEAST	Putative uncharacterized protein YAL037W	0.61	-	nuc	0					267
Q9C9A9 UniProt NPD GO	COL7_ARATH	Putative zinc finger protein CONSTANS-LIKE 7	0.61	+	nuc	0	Nucleus (Potential)				392
Q99N57 UniProt NPD GO	RAF1_MOUSE	RAF proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (Raf-1) (C-RAF) (cRaf)	0.61	-	nuc	0		cytosol [TAS] plasma membrane [TAS]			648
Q9R1W3 UniProt NPD GO	RN103_MOUSE	RING finger protein 103 (Zinc finger protein 103) (Zfp-103) (KF-1) (mKF-1)	0.61	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				683
Q5REL3 UniProt NPD GO	RN146_PONPY	RING finger protein 146	0.61	+	nuc	0					358
Q8VC70 UniProt NPD GO	RBMS2_MOUSE	RNA-binding motif, single-stranded-interacting protein 2	0.61	-	nuc	0	Nucleus (Potential)				383
Q4R537 UniProt NPD GO	NOB1_MACFA	RNA-binding protein NOB1	0.61	-	nuc	0	Nucleus (By similarity)				412
Q9ULX3 UniProt NPD GO	NOB1_HUMAN	RNA-binding protein NOB1 (Protein ART-4) (Phosphorylation regulatory protein HP-10)	0.61	-	nuc	0	Nucleus				412
Q6NXK5 UniProt NPD GO	DUS11_MOUSE	RNA/RNP complex-1-interacting phosphatase (EC 3.1.3.-) (Phosphatase that interacts with RNA/RNP comp ...	0.61	-	nuc	0	Nucleus (By similarity)				321
Q6NW29 UniProt NPD GO	RWDD4_HUMAN	RWD domain-containing protein 4A (Protein FAM28A)	0.61	+	nuc	0					188
Q91WG2 UniProt NPD GO	RABE2_MOUSE	Rab GTPase-binding effector protein 2 (Rabaptin-5beta)	0.61	-	nuc	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity)				511
Q8R361 UniProt NPD GO	RFIP5_MOUSE	Rab11 family-interacting protein 5 (Rab11-FIP5) (Rab11-interacting protein Rip11)	0.61	-	nuc	0	Cytoplasm (By similarity). Endosome; recycling endosome; recycling endosomal membrane; peripheral me ...	mitochondrial outer membrane [ISS]			645
Q8WWW0 UniProt NPD GO	RASF5_HUMAN	Ras association domain-containing family protein 5 (New ras effector 1) (Regulator for cell adhesion ...	0.61	-	nuc	0	Cytoplasm. Isoform 2 is mainly located in the perinuclear region of unstimulated primary T cells; up ...		607020		418
Q5U651 UniProt NPD GO	RAIN_HUMAN	Ras-interacting protein 1 (Rain)	0.61	-	nuc	0	Cytoplasm; perinuclear region. Associated with perinuclear vesicles. Golgi apparatus; Golgi stack. I ...		609623		963
P48555 UniProt NPD GO	RALA_DROME	Ras-related protein Ral-a	0.61	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q3ZCI8 UniProt NPD GO	REEP4_BOVIN	Receptor expression-enhancing protein 4	0.61	-	end	2 *	Membrane; multi-pass membrane protein (By similarity)				257
Q13546 UniProt NPD GO	RIPK1_HUMAN	Receptor-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (Serine/threonine-protein kinas ...	0.61	-	nuc	0	Cytoplasm		603453		671
P58801 UniProt NPD GO	RIPK2_MOUSE	Receptor-interacting serine/threonine-protein kinase 2 (EC 2.7.11.1)	0.61	-	nuc	0	Cytoplasm (Probable)				539
O02695 UniProt NPD GO	PTPR2_MACNE	Receptor-type tyrosine-protein phosphatase N2 precursor (EC 3.1.3.48) (R-PTP-N2) (M1851)	0.61	-	end	0	Membrane; single-pass type I membrane protein (Probable)				1013
P80560 UniProt NPD GO	PTPR2_MOUSE	Receptor-type tyrosine-protein phosphatase N2 precursor (EC 3.1.3.48) (R-PTP-N2) (PTP IA-2beta) (Pro ...	0.61	-	end	0	Membrane; single-pass type I membrane protein (Probable)				1001
P23471 UniProt NPD GO	PTPRZ_HUMAN	Receptor-type tyrosine-protein phosphatase zeta precursor (EC 3.1.3.48) (R-PTP-zeta)	0.61	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	176891		2314
Q62656 UniProt NPD GO	PTPRZ_RAT	Receptor-type tyrosine-protein phosphatase zeta precursor (EC 3.1.3.48) (R-PTP-zeta) (Phosphacan) (3 ...	0.61	-	exc	1	Membrane; single-pass type I membrane protein				2316
O93574 UniProt NPD GO	RELN_CHICK	Reelin (EC 3.4.21.-) (Fragment)	0.61	-	nuc	0	Secreted protein (By similarity)				3209
P78509 UniProt NPD GO	RELN_HUMAN	Reelin precursor (EC 3.4.21.-)	0.61	-	nuc	0	Secreted protein (By similarity)		600514		3460
Q99PG4 UniProt NPD GO	RGS18_MOUSE	Regulator of G-protein signaling 18 (RGS18)	0.61	-	nuc	0	Cytoplasm	cytoplasm [IDA]			235
P41220 UniProt NPD GO	RGS2_HUMAN	Regulator of G-protein signaling 2 (RGS2) (G0/G1 switch regulatory protein 8)	0.61	-	nuc	0			600861	2AF0	211
P40418 UniProt NPD GO	SWI6_KLULA	Regulatory protein SWI6 (Cell-cycle box factor, chain SWI6) (Trans-acting activator of HO endonuclea ...	0.61	-	nuc	0					769
P22336 UniProt NPD GO	RFA1_YEAST	Replication factor-A protein 1 (RF-A) (Single-stranded DNA-binding protein) (DNA-binding protein BUF ...	0.61	-	nuc	0	Nucleus	chromosome, telomeric region [IMP] cytoplasm [IDA] DNA replication factor A complex [TAS] nucleus [IDA]		1YNX	621
Q6P1E1 UniProt NPD GO	ZIM10_MOUSE	Retinoic acid-induced protein 17 (PIAS-like protein Zimp10)	0.61	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cytoplasm (By similarity)				1072
Q9Z0J1 UniProt NPD GO	RECK_MOUSE	Reversion-inducing cysteine-rich protein with Kazal motifs precursor (mRECK)	0.61	+	exc	0	Cell membrane; lipid-anchor; GPI-anchor				971
Q9NSG0 UniProt NPD GO	RHG08_HUMAN	Rho-GTPase-activating protein 8	0.61	-	mit	0					718
Q6GV23 UniProt NPD GO	RHBL5_TOXGO	Rhomboid-like protease 5 (EC 3.4.21.105) (Microneme protein protease 1) (MPP-1)	0.61	-	nuc	6	Membrane; multi-pass membrane protein. Detected primarily at the posterior surface of intracellular ...				841
Q07762 UniProt NPD GO	RNH1_CRIFA	Ribonuclease H (EC 3.1.26.4) (RNase H)	0.61	-	mit	0					494
Q8IY67 UniProt NPD GO	RAVR1_HUMAN	Ribonucleoprotein PTB-binding 1 (Protein raver-1)	0.61	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear, in perinucleolar structures. Shuttles b ...		609950		606

You are viewing entries 18701 to 18750 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.