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
Q3E827 UniProt NPD GO	YJ005_YEAST	Uncharacterized protein YJR005C-A	0.73	-	nuc	0					93
Q61069 UniProt NPD GO	USF1_MOUSE	Upstream stimulatory factor 1 (Major late transcription factor 1)	0.73	+	nuc	0	Nucleus	transcription factor complex [IC]			310
O75445 UniProt NPD GO	USH2A_HUMAN	Usherin precursor (Usher syndrome type-2A protein) (Usher syndrome type IIa protein)	0.73	-	nuc	2 *	Membrane; single-pass type I membrane protein. Probable component of the interstereocilia ankle link ...	basal lamina [TAS]	608400		5202
Q7SAN9 UniProt NPD GO	BRO1_NEUCR	Vacuolar protein-sorting protein bro-1 (BRO domain-containing protein 1)	0.73	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				1012
Q6QD59 UniProt NPD GO	SEC20_MOUSE	Vesicle transport protein SEC20	0.73	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...	endoplasmic reticulum [ISS] integral to endoplasmic reticulum membrane [ISS] SNARE complex [ISS]			228
Q8VHI8 UniProt NPD GO	SEC20_RAT	Vesicle transport protein SEC20	0.73	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...	endoplasmic reticulum [ISS] integral to endoplasmic reticulum membrane [ISS] nuclear envelope [ISS] SNARE complex [ISS]			228
Q07175 UniProt NPD GO	VKGC_BOVIN	Vitamin K-dependent gamma-carboxylase (EC 6.4.-.-) (Gamma-glutamyl carboxylase) (Vitamin K gamma glu ...	0.73	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				758
P55155 UniProt NPD GO	VIT1_CAEEL	Vitellogenin-1 precursor	0.73	-	mit	0	Secreted protein				1616
Q6ZQL4 UniProt NPD GO	WDR43_MOUSE	WD repeat protein 43 (Fragment)	0.73	-	nuc	0	Nucleus; nucleolus (By similarity)				665
P45441 UniProt NPD GO	YBX2B_XENLA	Y-box-binding protein 2-B (Cytoplasmic RNA-binding protein p54) (mRNP3)	0.73	-	nuc	0	Cytoplasm. Either free or associated with ribonucleoprotein particles				324
O35986 UniProt NPD GO	ZRAB2_RAT	Zinc finger Ran-binding domain-containing protein 2 (Zinc finger protein 265) (Zinc finger, splicing ...	0.73	+	nuc	0	Nucleus (Potential)				332
Q8K3J5 UniProt NPD GO	ZN131_MOUSE	Zinc finger protein 131	0.73	-	cyt	0	Nucleus (By similarity)				619
P10077 UniProt NPD GO	ZFP27_MOUSE	Zinc finger protein 27 (Zfp-27) (Protein mKR4)	0.73	-	nuc	0	Nucleus (Potential)				819
Q9NRM2 UniProt NPD GO	ZN277_HUMAN	Zinc finger protein 277	0.73	-	cyt	0	Nucleus (Potential)	nucleus [NAS]	605465		438
Q8NHY6 UniProt NPD GO	ZFP28_HUMAN	Zinc finger protein 28 homolog (Zfp-28) (Krueppel-like zinc finger factor X6)	0.73	-	nuc	0	Nucleus (Potential)				868
Q5RJR4 UniProt NPD GO	ZN467_RAT	Zinc finger protein 467	0.73	-	nuc	0	Nucleus (By similarity)				594
Q8N8L2 UniProt NPD GO	ZN491_HUMAN	Zinc finger protein 491	0.73	-	nuc	0	Nucleus (Potential)				437
Q95K49 UniProt NPD GO	ZN614_MACFA	Zinc finger protein 614	0.73	-	nuc	0	Nucleus (Probable)				582
Q96502 UniProt NPD GO	COL2_ARATH	Zinc finger protein CONSTANS-LIKE 2	0.73	-	nuc	0	Nucleus (Probable)				347
P24349 UniProt NPD GO	SDC1_CAEEL	Zinc finger protein sdc-1 (Egg-laying defective protein 16)	0.73	-	nuc	0	Nucleus	nuclear chromosome [IDA]			1203
P10734 UniProt NPD GO	KNIR_DROME	Zygotic gap protein knirps	0.73	-	nuc	0	Nucleus				429
Q03043 UniProt NPD GO	KGP24_DROME	cGMP-dependent protein kinase, isozyme 2 forms cD4/T1/T3A/T3B (EC 2.7.11.12) (CGK) (Foraging protein ...	0.73	-	mit	0					1088
P32783 UniProt NPD GO	ABD1_YEAST	mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56)	0.73	-	nuc	0		DNA-directed RNA polymerase II, holoenzyme [IPI] nucleus [IPI]		1IC3	436
Q80TT8 UniProt NPD GO	PARC_MOUSE	p53-associated parkin-like cytoplasmic protein	0.73	-	nuc	0	Cytoplasm				1865
Q8WZL4 UniProt NPD GO	PALA_YARLI	pH-response regulator protein RIM20	0.73	-	nuc	0					773
Q05022 UniProt NPD GO	RRP5_YEAST	rRNA biogenesis protein RRP5	0.73	-	nuc	0	Nucleus; nucleolus	nucleolus [TAS] small nucleolar ribonucleoprotein complex [IPI]			1729
Q9H3H1 UniProt NPD GO	MOD5_HUMAN	tRNA isopentenyltransferase, mitochondrial precursor (EC 2.5.1.8) (Isopentenyl-diphosphate:tRNA isop ...	0.73	+	mit	0	Isoform 1, isoform 4: Mitochondrion (Potential). Isoform 2, isoform 3, isoform 5: Cytoplasm (Potenti ...				467
Q5ZIN2 UniProt NPD GO	SEN2_CHICK	tRNA-splicing endonuclease subunit Sen2 (EC 3.1.27.9) (tRNA-intron endonuclease Sen2)	0.73	-	nuc	0	Nucleus (By similarity)				461
P40327 UniProt NPD GO	PRS4_YEAST	26S protease regulatory subunit 4 homolog (TAT-binding homolog 5)	0.72	+	nuc	0	Cytoplasm (Potential). Nucleus (Potential)	nucleus [IDA] proteasome regulatory particle, base subcom... [IPI]			436
Q9TJN6 UniProt NPD GO	RR17_MAIZE	30S ribosomal protein S17, chloroplast precursor	0.72	-	nuc	0	Plastid; chloroplast (Probable)				132
Q9VHN6 UniProt NPD GO	RM19_DROME	39S ribosomal protein L19, mitochondrial precursor (L19mt)	0.72	-	mit	0	Mitochondrion				306
Q9C0Z7 UniProt NPD GO	RS6B_SCHPO	40S ribosomal protein S6-B	0.72	-	nuc	0					239
P25204 UniProt NPD GO	RS8_LEIMA	40S ribosomal protein S8	0.72	+	nuc	0					220
Q08069 UniProt NPD GO	RS8_MAIZE	40S ribosomal protein S8	0.72	+	nuc	0					221
O59675 UniProt NPD GO	RS9B_SCHPO	40S ribosomal protein S9-B	0.72	-	mit	0					191
Q95ZQ4 UniProt NPD GO	AAPK2_CAEEL	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1) (AMP-activated kinase 2)	0.72	-	nuc	0					626
P82244 UniProt NPD GO	RK34_SPIOL	50S ribosomal protein L34, chloroplast precursor	0.72	+	mit	0	Plastid; chloroplast				152
P05748 UniProt NPD GO	RL15A_YEAST	60S ribosomal protein L15-A (YL10) (L13) (RP15R) (YP18)	0.72	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	203
Q8SSF6 UniProt NPD GO	RL24_ENCCU	60S ribosomal protein L24	0.72	-	nuc	0					155
Q90YU3 UniProt NPD GO	RL24_ICTPU	60S ribosomal protein L24	0.72	-	nuc	0					157
Q9FHG2 UniProt NPD GO	RL322_ARATH	60S ribosomal protein L32-2	0.72	-	nuc	0					133
P40590 UniProt NPD GO	RL34_PEA	60S ribosomal protein L34	0.72	-	mit	0					120
Q3SZ59 UniProt NPD GO	RL36A_BOVIN	60S ribosomal protein L36a	0.72	-	nuc	0	Cytoplasm (By similarity)				105
P83882 UniProt NPD GO	RL36A_MOUSE	60S ribosomal protein L36a (60S ribosomal protein L44)	0.72	-	nuc	0	Cytoplasm	ribosome [ISS]			105
P83884 UniProt NPD GO	RL36A_PIG	60S ribosomal protein L36a (60S ribosomal protein L44)	0.72	-	nuc	0	Cytoplasm	ribosome [ISS]			105
P83883 UniProt NPD GO	RL36A_RAT	60S ribosomal protein L36a (60S ribosomal protein L44)	0.72	-	nuc	0	Cytoplasm				105
P83881 UniProt NPD GO	RL36A_HUMAN	60S ribosomal protein L36a (60S ribosomal protein L44) (Migration-inducing gene 6 protein)	0.72	-	nuc	0	Cytoplasm	cytoplasm [NAS] ribosome [NAS]			105
Q969Q0 UniProt NPD GO	RL36L_HUMAN	60S ribosomal protein L36a-like	0.72	-	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS] ribosome [ISS]	180469		105
Q43292 UniProt NPD GO	RL372_ARATH	60S ribosomal protein L37-2	0.72	-	mit	0					95
P08429 UniProt NPD GO	RL4A_XENLA	60S ribosomal protein L4-A (L1A)	0.72	+	nuc	0					396

You are viewing entries 12601 to 12650 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.