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
P58505 UniProt NPD GO	CU058_HUMAN	Protein C21orf58	0.63	-	nuc	0					239
Q5BMD4 UniProt NPD GO	DEPP_RAT	Protein DEPP	0.63	-	nuc	0					205
Q803T2 UniProt NPD GO	FA40A_BRARE	Protein FAM40A	0.63	-	end	0					813
Q8C079 UniProt NPD GO	FA40A_MOUSE	Protein FAM40A	0.63	-	end	0					837
Q8NCA5 UniProt NPD GO	FA98A_HUMAN	Protein FAM98A	0.63	+	nuc	0					519
Q80VD1 UniProt NPD GO	FA98B_MOUSE	Protein FAM98B	0.63	+	cyt	0					429
O81313 UniProt NPD GO	IND_ARATH	Protein INDEHISCENT	0.63	-	nuc	0	Nucleus (Probable)				169
Q14146 UniProt NPD GO	K0133_HUMAN	Protein KIAA0133	0.63	-	end	0	Membrane; multi-pass membrane protein (Potential)				1524
O15040 UniProt NPD GO	K0329_HUMAN	Protein KIAA0329/KIAA0297	0.63	+	nuc	0					1411
Q80V31 UniProt NPD GO	K0562_MOUSE	Protein KIAA0562	0.63	-	nuc	0					926
Q9H0B3 UniProt NPD GO	K1683_HUMAN	Protein KIAA1683	0.63	-	nuc	0					1180
Q14160 UniProt NPD GO	LAP4_HUMAN	Protein LAP4 (Protein scribble homolog) (hScrib)	0.63	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Localized to cell junctions		607733	1X5Q	1630
P27929 UniProt NPD GO	NAM9_YEAST	Protein NAM9, mitochondrial precursor	0.63	-	nuc	0	Mitochondrion (Probable)	mitochondrial small ribosomal subunit [IDA]			486
P33419 UniProt NPD GO	NIP29_YEAST	Protein NIP29	0.63	-	nuc	0		central plaque of spindle pole body [IDA]			253
Q6BKZ8 UniProt NPD GO	PBN1_DEBHA	Protein PBN1	0.63	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				450
O48559 UniProt NPD GO	UNI_PEA	Protein UNIFOLIATA	0.63	+	cyt	0	Nucleus (Probable)				395
P22745 UniProt NPD GO	BAM_DROME	Protein bag-of-marbles	0.63	-	nuc	0		cytoplasm [IDA] fusome [IDA] spectrosome [IDA]			442
Q25514 UniProt NPD GO	HUNB_MANSE	Protein hunchback (Fragment)	0.63	-	nuc	0	Nucleus (Probable)				327
Q9WVE8 UniProt NPD GO	PACN2_MOUSE	Protein kinase C and casein kinase substrate in neurons protein 2	0.63	-	nuc	0	Cytoplasmic vesicle (By similarity). Vesicle-like cytoplasmic distribution (By similarity)	cytoplasm [IDA] cytosol [IDA]			486
P48383 UniProt NPD GO	SAK1_SCHPO	Protein sak1	0.63	-	nuc	0	Nucleus (Probable)				766
P40482 UniProt NPD GO	SEC24_YEAST	Protein transport protein SEC24 (Abnormal nuclear morphology 1)	0.63	-	nuc	0	Cytoplasm	COPII vesicle coat [TAS]		1PD1	926
P09090 UniProt NPD GO	ZEN2_DROME	Protein zerknuellt 2 (ZEN-2)	0.63	+	nuc	0	Nucleus				252
Q96MG8 UniProt NPD GO	PCMD1_HUMAN	Protein-L-isoaspartate O-methyltransferase domain-containing protein 1	0.63	+	nuc	0	Cytoplasm (By similarity)				357
P16636 UniProt NPD GO	LYOX_RAT	Protein-lysine 6-oxidase precursor (EC 1.4.3.13) (Lysyl oxidase)	0.63	-	exc	0	Secreted protein; extracellular space				411
Q8HZP6 UniProt NPD GO	FOS_FELCA	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.63	+	nuc	0	Nucleus (By similarity)				381
P01100 UniProt NPD GO	FOS_HUMAN	Proto-oncogene protein c-fos (Cellular oncogene fos) (G0/G1 switch regulatory protein 7)	0.63	+	nuc	0	Nucleus	nucleus [TAS]	164810	1S9K	380
P22312 UniProt NPD GO	PU92_SCICO	Puff II/9-2 protein precursor	0.63	-	exc	0					286
Q6LFD5 UniProt NPD GO	RK18_PLAF7	Putative 50S ribosomal protein L18, apicoplast precursor	0.63	+	nuc	1 *	Plastid; apicoplast (Potential)				213
Q5ZI74 UniProt NPD GO	DHX30_CHICK	Putative ATP-dependent RNA helicase DHX30 (EC 3.6.1.-) (DEAH box protein 30)	0.63	-	end	0					1231
Q9VAD6 UniProt NPD GO	COG7_DROME	Putative conserved oligomeric Golgi complex component 7	0.63	-	nuc	0	Golgi apparatus (By similarity)				742
Q7XA42 UniProt NPD GO	RGA1_SOLBU	Putative disease resistance protein RGA1 (RGA3-blb)	0.63	-	cyt	0					1025
Q17574 UniProt NPD GO	MTRR_CAEEL	Putative methionine synthase reductase (EC 1.16.1.8) (MSR)	0.63	-	cyt	0					682
Q09452 UniProt NPD GO	YQ23_CAEEL	Putative zinc finger protein C09F5.3	0.63	-	nuc	0	Nucleus (Potential)				359
Q5RBB3 UniProt NPD GO	NOB1_PONPY	RNA-binding protein NOB1	0.63	-	nuc	0	Nucleus (By similarity)				411
O35141 UniProt NPD GO	RASF5_RAT	Ras association domain-containing family protein 5 (New ras effector 1) (Maxp1)	0.63	-	nuc	0	Cytoplasm. Mainly located in the perinuclear region of unstimulated primary T cells; upon stimulatio ...				413
P24348 UniProt NPD GO	LET23_CAEEL	Receptor tyrosine-protein kinase let-23 precursor (EC 2.7.10.1) (Lethal protein 23)	0.63	-	end	2 *	Cell membrane; apical cell membrane; single-pass type I membrane protein. Cell membrane; basolateral ...	basolateral plasma membrane [IDA]			1323
Q9UBG7 UniProt NPD GO	RBPSL_HUMAN	Recombining binding protein suppressor of hairless-like protein (Transcription factor RBP-L)	0.63	-	cyt	0	Nucleus (Probable)				516
Q9Z2H1 UniProt NPD GO	RGS11_MOUSE	Regulator of G-protein signaling 11 (RGS11) (Fragment)	0.63	-	cyt	0					438
Q24762 UniProt NPD GO	ZEST_DROVI	Regulatory protein zeste	0.63	-	nuc	0	Nucleus (By similarity)				618
P51456 UniProt NPD GO	RELH_RABIT	Relaxin-like protein SQ10 precursor [Contains: Relaxin-like protein SQ10 B chain; Relaxin-like prote ...	0.63	-	exc	0	Secreted protein (By similarity)				178
Q9NQC3 UniProt NPD GO	RTN4_HUMAN	Reticulon-4 (Neurite outgrowth inhibitor) (Nogo protein) (Foocen) (Neuroendocrine-specific protein) ...	0.63	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Anchored to the ...	endoplasmic reticulum [NAS] integral to endoplasmic reticulum membrane [IEP] nuclear envelope [IDA]	604475		1192
Q7SYN5 UniProt NPD GO	RXRB_BRARE	Retinoic acid receptor RXR-beta (Retinoid X receptor beta)	0.63	+	nuc	0	Nucleus	nucleus [NAS]			471
P18515 UniProt NPD GO	RARB_NOTVI	Retinoic acid receptor beta (RAR-beta) (Fragment)	0.63	+	nuc	0	Nucleus				158
P10401 UniProt NPD GO	POLY_DROME	Retrovirus-related Pol polyprotein from transposon gypsy [Includes: Reverse transcriptase (EC 2.7.7. ...	0.63	-	cyt	0					1035
Q8IUC4 UniProt NPD GO	RHPN2_HUMAN	Rhophilin-2 (GTP-Rho-binding protein 2) (76 kDa RhoB effector protein) (p76RBE)	0.63	-	cyt	0	Cytoplasm; perinuclear region				686
Q3ZE13 UniProt NPD GO	RPP30_DICDI	Ribonuclease P protein subunit drpp30 (EC 3.1.26.5) (RNaseP protein 1)	0.63	-	nuc	0	Nucleus (Potential)				366
Q6CNW3 UniProt NPD GO	RLP24_KLULA	Ribosome biogenesis protein RLP24	0.63	+	nuc	0	Nucleus; nucleolus (By similarity)				198
P50243 UniProt NPD GO	DCAM_BOVIN	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.63	-	cyt	0					334
P17707 UniProt NPD GO	DCAM_HUMAN	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.63	-	cyt	0			180980	1MSV	334
P28918 UniProt NPD GO	DCAM_MESAU	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.63	-	cyt	0					334

You are viewing entries 17601 to 17650 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.