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
Q9H5J0 UniProt NPD GO	ZBTB3_HUMAN	Zinc finger and BTB domain-containing protein 3	0.72	-	nuc	0	Nucleus (Potential)				574
O43670 UniProt NPD GO	ZN207_HUMAN	Zinc finger protein 207	0.72	+	nuc	0	Nucleus (Probable)	nucleus [NAS]	603428		478
Q5RCA4 UniProt NPD GO	ZN326_PONPY	Zinc finger protein 326	0.72	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)				579
Q8BXJ8 UniProt NPD GO	ZN533_MOUSE	Zinc finger protein 533	0.72	-	nuc	0	Nucleus (Potential)				482
Q96ND8 UniProt NPD GO	ZN583_HUMAN	Zinc finger protein 583 (Zinc finger protein L3-5)	0.72	-	nuc	0	Nucleus (Potential)				569
Q8N883 UniProt NPD GO	ZN614_HUMAN	Zinc finger protein 614	0.72	-	nuc	0	Nucleus (Probable)				585
Q5RCJ2 UniProt NPD GO	ZN614_PONPY	Zinc finger protein 614	0.72	-	nuc	0	Nucleus (Probable)				585
Q99KE8 UniProt NPD GO	ZFP64_MOUSE	Zinc finger protein 64 (Zfp-64)	0.72	-	nuc	0	Nucleus (Probable)				643
Q02085 UniProt NPD GO	SNAI_MOUSE	Zinc finger protein SNAI1 (Protein snail homolog) (Protein sna)	0.72	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			264
Q42430 UniProt NPD GO	ZFP1_WHEAT	Zinc-finger protein 1 (WZF1)	0.72	-	nuc	0	Nucleus (Probable)				261
Q8IRU4 UniProt NPD GO	PDE4E_DROME	cAMP-specific 3',5'-cyclic phosphodiesterase, isoform F (EC 3.1.4.17) (Learning/memory process prote ...	0.72	-	nuc	0					662
Q91YD3 UniProt NPD GO	DCP1A_MOUSE	mRNA decapping enzyme 1A (EC 3.-.-.-) (Transcription factor SMIF) (MAD homolog 4-interacting transcr ...	0.72	-	nuc	0	Cytoplasm (By similarity). Predominantly cytoplasmic, in processing bodies (PB). Nucleus (By similar ...				602
Q06053 UniProt NPD GO	DUS3_YEAST	tRNA-dihydrouridine synthase 3 (EC 1.-.-.-)	0.72	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			609
Q62935 UniProt NPD GO	VWF_RAT	von Willebrand factor (Fragment)	0.72	-	cyt	0	Secreted protein (By similarity). Localized to storage granules (By similarity)				430
Q9DC71 UniProt NPD GO	RT15_MOUSE	28S ribosomal protein S15, mitochondrial precursor (S15mt) (MRP-S15)	0.71	+	mit	0	Mitochondrion (By similarity)				258
Q9ZST1 UniProt NPD GO	RR17_ORYSA	30S ribosomal protein S17, chloroplast precursor (CS17)	0.71	-	nuc	0	Plastid; chloroplast (Probable)				145
Q09757 UniProt NPD GO	RS9A_SCHPO	40S ribosomal protein S9-A	0.71	-	mit	0					190
Q56JZ1 UniProt NPD GO	RL13_BOVIN	60S ribosomal protein L13	0.71	-	nuc	0					210
Q6FS31 UniProt NPD GO	RM02_CANGA	60S ribosomal protein L2, mitochondrial precursor	0.71	-	nuc	0	Mitochondrion (By similarity)				368
Q752U6 UniProt NPD GO	RL24_ASHGO	60S ribosomal protein L24	0.71	-	nuc	0					155
Q9VJY6 UniProt NPD GO	RL24_DROME	60S ribosomal protein L24	0.71	-	nuc	0					155
P04359 UniProt NPD GO	RL32_DROME	60S ribosomal protein L32 (Ribosomal protein 49)	0.71	-	nuc	0					134
P61128 UniProt NPD GO	RL32_DROSI	60S ribosomal protein L32 (Ribosomal protein 49)	0.71	-	nuc	0					134
P61127 UniProt NPD GO	RL32_DROYA	60S ribosomal protein L32 (Ribosomal protein 49)	0.71	-	nuc	0					134
P47964 UniProt NPD GO	RL36_MOUSE	60S ribosomal protein L36	0.71	-	nuc	0					104
Q9M352 UniProt NPD GO	RL362_ARATH	60S ribosomal protein L36-2	0.71	-	nuc	0					112
Q9P0M2 UniProt NPD GO	AKA7G_HUMAN	A-kinase anchor protein 7 isoform gamma (Protein kinase A-anchoring protein 7 isoform gamma) (A-kina ...	0.71	+	nuc	0	Cytoplasm	cytosol [IDA]	604693		326
Q8R5G2 UniProt NPD GO	MUTYH_RAT	A/G-specific adenine DNA glycosylase (EC 3.2.2.-) (MutY homolog) (rMYH)	0.71	-	nuc	0	Nucleus (By similarity)				516
Q9Z0F8 UniProt NPD GO	ADA17_MOUSE	ADAM 17 precursor (EC 3.4.24.86) (A disintegrin and metalloproteinase domain 17) (TNF-alpha-converti ...	0.71	-	end	1	Isoform Long: Cell membrane; single-pass type I membrane protein. Isoform Short: Secreted protein	cytoplasm [IDA]			827
Q9Z1K9 UniProt NPD GO	ADA17_RAT	ADAM 17 precursor (EC 3.4.24.86) (A disintegrin and metalloproteinase domain 17) (TNF-alpha-converti ...	0.71	-	end	1	Membrane; single-pass type I membrane protein				827
O62827 UniProt NPD GO	ADML_BOVIN	ADM precursor [Contains: Adrenomedullin (AM); Adrenomedullin 11-26 (AM 11-26); Proadrenomedullin N-2 ...	0.71	-	exc	0	Secreted protein				188
Q06336 UniProt NPD GO	GGA1_YEAST	ADP-ribosylation factor-binding protein GGA1 (Golgi-localized, gamma ear-containing, ARF-binding pro ...	0.71	-	nuc	0		Golgi trans face [IDA]			557
P42736 UniProt NPD GO	AP23_ARATH	AP2 domain transcription factor RAP2.3 (Related to AP2 protein 3) (Cadmium-induced protein AS30)	0.71	+	nuc	0	Nucleus (Probable)				248
P53731 UniProt NPD GO	ARPC2_YEAST	ARP2/3 complex 34 kDa subunit (p34-ARC)	0.71	-	cyt	0		Arp2/3 protein complex [IDA] cytosol [IPI]			342
Q6CDN5 UniProt NPD GO	DBP6_YARLI	ATP-dependent RNA helicase DBP6 (EC 3.6.1.-)	0.71	+	cyt	0	Nucleus; nucleolus (By similarity)				607
Q75F95 UniProt NPD GO	DRS1_ASHGO	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.71	+	cyt	0	Nucleus; nucleolus (By similarity)				734
Q750Q4 UniProt NPD GO	MS116_ASHGO	ATP-dependent RNA helicase MSS116, mitochondrial precursor (EC 3.6.1.-)	0.71	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				658
Q2UMY7 UniProt NPD GO	MAK5_ASPOR	ATP-dependent RNA helicase mak5 (EC 3.6.1.-)	0.71	+	nuc	0	Nucleus; nucleolus (By similarity)				757
O74393 UniProt NPD GO	MAK5_SCHPO	ATP-dependent RNA helicase mak5 (EC 3.6.1.-)	0.71	+	nuc	0	Nucleus; nucleolus (By similarity)				648
Q5KBE2 UniProt NPD GO	RRP3_CRYNE	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.71	-	nuc	0	Nucleus (Probable)				484
Q6CT85 UniProt NPD GO	RRP3_KLULA	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.71	-	nuc	0	Nucleus (Probable)				487
Q6BSM3 UniProt NPD GO	SPB4_DEBHA	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-)	0.71	+	nuc	0	Nucleus; nucleolus (By similarity)				614
Q5B8F4 UniProt NPD GO	SPB4_EMENI	ATP-dependent rRNA helicase spb4 (EC 3.6.1.-)	0.71	-	nuc	0	Nucleus; nucleolus (By similarity)				638
Q925I1 UniProt NPD GO	ATAD3_MOUSE	ATPase family AAA domain-containing protein 3 (AAA-ATPase TOB3)	0.71	-	nuc	0		mitochondrial inner membrane [IDA] mitochondrion [IDA]			591
Q9NDG8 UniProt NPD GO	ACE4_CAEBR	Acetylcholinesterase 4 precursor (EC 3.1.1.7) (AChE 4)	0.71	+	end	0	Secreted protein (Potential)				604
P29385 UniProt NPD GO	AGL5_ARATH	Agamous-like MADS-box protein AGL5	0.71	-	nuc	0	Nucleus				246
Q99JA2 UniProt NPD GO	ASIP_RAT	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.71	-	nuc	1 *	Secreted protein (By similarity)				131
Q91081 UniProt NPD GO	ADRA2_LABOS	Alpha-2 adrenergic receptor (Alpha-2 adrenoceptor) (Alpha-2 adrenoreceptor)	0.71	+	end	7 *	Membrane; multi-pass membrane protein				432
Q92075 UniProt NPD GO	SCNNA_CHICK	Amiloride-sensitive sodium channel subunit alpha (Epithelial Na+ channel subunit alpha) (Alpha ENaC) ...	0.71	-	end	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				637
P51169 UniProt NPD GO	SCNNB_XENLA	Amiloride-sensitive sodium channel subunit beta (Epithelial Na+ channel subunit beta) (Beta ENaC) (N ...	0.71	-	mit	2	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				647

You are viewing entries 13101 to 13150 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.