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
Q90277 UniProt NPD GO	VSX1_CARAU	Visual system homeobox 1 (Transcription factor VSX1) (Homeobox protein VSX-1)	0.87	+	nuc	0	Nucleus (Probable)				341
O54898 UniProt NPD GO	CAC1G_RAT	Voltage-dependent T-type calcium channel subunit alpha-1G (Voltage-gated calcium channel subunit alp ...	0.87	+	end	17	Membrane; multi-pass membrane protein				2254
Q6X7K0 UniProt NPD GO	WOX1_ARATH	WUSCHEL-related homeobox 1 (PFS2-like protein)	0.87	-	nuc	0	Nucleus (By similarity)				350
Q8IX03 UniProt NPD GO	WWC1_HUMAN	WW domain-containing protein 1 (Kidney and brain protein) (KIBRA) (HBeAg-binding protein 3)	0.87	-	nuc	0	Cytoplasm				1113
P54350 UniProt NPD GO	WEE1_DROME	Wee1-like protein kinase (EC 2.7.10.2) (Dwee1)	0.87	-	nuc	0	Nucleus (By similarity)				609
Q92558 UniProt NPD GO	WASF1_HUMAN	Wiskott-Aldrich syndrome protein family member 1 (WASP-family protein member 1) (Protein WAVE-1) (Ve ...	0.87	+	nuc	0	Cytoplasm. Dot-like pattern in the cytoplasm. Concentrated in Rac-regulated membrane-ruffling areas	actin cytoskeleton [TAS]	605035		559
Q8SRY4 UniProt NPD GO	Z561_ENCCU	Zinc finger C2H2 protein ECU05_0610	0.87	-	nuc	0					281
Q8IWR0 UniProt NPD GO	Z3H7A_HUMAN	Zinc finger CCCH-type domain-containing protein 7A	0.87	-	nuc	0					971
Q6NZY4 UniProt NPD GO	ZCHC8_HUMAN	Zinc finger CCHC domain-containing protein 8	0.87	-	nuc	0					707
Q5R789 UniProt NPD GO	ZCHC8_PONPY	Zinc finger CCHC domain-containing protein 8	0.87	-	nuc	0					704
Q8NEG5 UniProt NPD GO	ZSWM2_HUMAN	Zinc finger SWIM domain-containing protein 2	0.87	-	nuc	0					633
P20662 UniProt NPD GO	ZFY2_MOUSE	Zinc finger Y-chromosomal protein 2	0.87	+	nuc	0	Nucleus				783
P24278 UniProt NPD GO	ZBT25_HUMAN	Zinc finger and BTB domain-containing protein 25 (Zinc finger protein 46) (Zinc finger protein KUP)	0.87	+	nuc	0	Nucleus		194541		433
Q8NBB4 UniProt NPD GO	ZSCA1_HUMAN	Zinc finger and SCAN domain-containing protein 1	0.87	-	nuc	0	Nucleus (Potential)				408
Q8C0Q2 UniProt NPD GO	ZHX3_MOUSE	Zinc finger and homeodomain protein 3 (Triple homeobox protein 1)	0.87	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			951
P52736 UniProt NPD GO	ZN133_HUMAN	Zinc finger protein 133	0.87	-	nuc	0	Nucleus (Potential)		604075		654
Q9ULJ3 UniProt NPD GO	ZN295_HUMAN	Zinc finger protein 295 (Zinc finger and BTB domain-containing protein 21)	0.87	+	nuc	0	Nucleus (Potential)			1WJP	1066
Q02975 UniProt NPD GO	TCF17_RAT	Zinc finger protein 354A (Transcription factor 17) (Renal transcription factor Kid-1) (Kidney, ische ...	0.87	-	nuc	0	Nucleus				576
O60765 UniProt NPD GO	TCF17_HUMAN	Zinc finger protein 354A (Transcription factor 17) (Zinc finger protein eZNF)	0.87	-	nuc	0	Nucleus (By similarity)		602444		605
Q8TF39 UniProt NPD GO	ZN483_HUMAN	Zinc finger protein 483	0.87	-	nuc	0	Nucleus (Probable)			2CTU	744
Q9I9K0 UniProt NPD GO	FOG1_XENLA	Zinc finger protein FOG (Friend of GATA) (xFOG) (Fragment)	0.87	-	nuc	0	Nucleus (By similarity)				1061
P56163 UniProt NPD GO	DPF1_RAT	Zinc-finger protein neuro-d4 (D4, zinc and double PHD fingers family 1)	0.87	+	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				397
Q99543 UniProt NPD GO	ZRF1_HUMAN	Zuotin-related factor 1 (M-phase phosphoprotein 11)	0.87	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	605502		568
Q7ZXZ0 UniProt NPD GO	MCM3Z_XENLA	Zygotic DNA replication licensing factor mcm3 (Zygotic minichromosome maintenance protein 3) (zMCM3) ...	0.87	+	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	MCM complex [IDA]			806
P51985 UniProt NPD GO	CREB_HYDAT	cAMP response element-binding protein	0.87	+	nuc	0	Nucleus				217
P27699 UniProt NPD GO	CREM_MOUSE	cAMP-responsive element modulator	0.87	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			341
Q07343 UniProt NPD GO	PDE4B_HUMAN	cAMP-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) (DPDE4) (PDE32)	0.87	+	nuc	0		insoluble fraction [TAS] soluble fraction [TAS]	600127	2CHM	736
Q9W4T4 UniProt NPD GO	PDE4A_DROME	cAMP-specific 3',5'-cyclic phosphodiesterase, isoform I (EC 3.1.4.17) (Learning/memory process prote ...	0.87	-	nuc	0					1209
Q9Z0X4 UniProt NPD GO	PDE3A_MOUSE	cGMP-inhibited 3',5'-cyclic phosphodiesterase A (EC 3.1.4.17) (Cyclic GMP-inhibited phosphodiesteras ...	0.87	+	end	5	Membrane; peripheral membrane protein (Potential)				1141
Q6BJD8 UniProt NPD GO	RNA14_DEBHA	mRNA 3'-end processing protein RNA14	0.87	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				742
Q9QWI6 UniProt NPD GO	SNIP_MOUSE	p130Cas-associated protein (p140Cap) (SNAP-25-interacting protein) (SNIP)	0.87	-	nuc	0					1250
Q9QXY2 UniProt NPD GO	SNIP_RAT	p130Cas-associated protein (p140Cap) (SNAP-25-interacting protein) (SNIP)	0.87	-	nuc	0	Localized to the perinuclear region, lamellopodia, cortical actin and actin stress fibers but not to ...				1197
Q6BWG3 UniProt NPD GO	TRM10_DEBHA	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.87	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				360
O75038 UniProt NPD GO	PLCL4_HUMAN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase-like 4 (EC 3.1.4.11) (Phosphoinositide pho ...	0.86	+	nuc	0					1182
Q12368 UniProt NPD GO	SNU23_YEAST	23 kDa U4/U6.U5 small nuclear ribonucleoprotein component	0.86	-	nuc	0	Nucleus	U4/U6 x U5 tri-snRNP complex [IDA]			194
Q9M3V8 UniProt NPD GO	RS6_ASPOF	40S ribosomal protein S6	0.86	-	nuc	0					251
P29327 UniProt NPD GO	RS6_DROME	40S ribosomal protein S6	0.86	+	nuc	0					248
Q9YGF2 UniProt NPD GO	RS6_ONCMY	40S ribosomal protein S6	0.86	+	nuc	0					249
Q95V32 UniProt NPD GO	RS6_SPOFR	40S ribosomal protein S6	0.86	+	nuc	0					253
P29345 UniProt NPD GO	RS6_TOBAC	40S ribosomal protein S6 (Fragment)	0.86	-	nuc	0					199
Q3T0W9 UniProt NPD GO	RL19_BOVIN	60S ribosomal protein L19	0.86	+	nuc	0					196
P84098 UniProt NPD GO	RL19_HUMAN	60S ribosomal protein L19	0.86	+	nuc	0			180466		196
Q90YU8 UniProt NPD GO	RL19_ICTPU	60S ribosomal protein L19	0.86	+	nuc	0					196
Q8HXN9 UniProt NPD GO	RL19_MACFA	60S ribosomal protein L19	0.86	+	nuc	0					196
P84099 UniProt NPD GO	RL19_MOUSE	60S ribosomal protein L19	0.86	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [IDA]			196
Q5RB99 UniProt NPD GO	RL19_PONPY	60S ribosomal protein L19	0.86	+	nuc	0					196
P84100 UniProt NPD GO	RL19_RAT	60S ribosomal protein L19	0.86	+	nuc	0					196
P22354 UniProt NPD GO	RM20_YEAST	60S ribosomal protein L20, mitochondrial precursor (YmL20)	0.86	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			195
Q6YLX4 UniProt NPD GO	RL41_CYPCA	60S ribosomal protein L41	0.86	+	nuc	0					25
Q71H53 UniProt NPD GO	RL41_EPICO	60S ribosomal protein L41	0.86	+	nuc	0					25

You are viewing entries 5901 to 5950 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.