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
Q6L369 UniProt NPD GO	RR11_SACHY	Chloroplast 30S ribosomal protein S11	0.42	-	nuc	0	Plastid; chloroplast				143
Q6ENT1 UniProt NPD GO	RR11_SACOF	Chloroplast 30S ribosomal protein S11	0.42	-	nuc	0	Plastid; chloroplast				143
P42344 UniProt NPD GO	RR12_SPIMX	Chloroplast 30S ribosomal protein S12	0.42	-	nuc	0	Plastid; chloroplast				123
Q4G349 UniProt NPD GO	RR13_EMIHU	Chloroplast 30S ribosomal protein S13	0.42	-	nuc	0	Plastid; chloroplast				124
Q68RU9 UniProt NPD GO	RR15_PANGI	Chloroplast 30S ribosomal protein S15	0.42	-	nuc	0	Plastid; chloroplast				90
Q5D704 UniProt NPD GO	RR16_PHATR	Chloroplast 30S ribosomal protein S16	0.42	-	nuc	0	Plastid; chloroplast				78
P51352 UniProt NPD GO	RR16_PORPU	Chloroplast 30S ribosomal protein S16	0.42	-	mit	0	Plastid; chloroplast				82
P49504 UniProt NPD GO	RR17_ODOSI	Chloroplast 30S ribosomal protein S17	0.42	-	nuc	0	Plastid; chloroplast				84
O22029 UniProt NPD GO	RR4B_CYACA	Chloroplast 30S ribosomal protein S4	0.42	-	mit	0	Plastid; chloroplast				192
Q9FT08 UniProt NPD GO	RR4_BUCRO	Chloroplast 30S ribosomal protein S4	0.42	-	mit	0	Plastid; chloroplast				202
Q5SD08 UniProt NPD GO	RR4_HUPLU	Chloroplast 30S ribosomal protein S4	0.42	-	nuc	0	Plastid; chloroplast				202
P59140 UniProt NPD GO	RR4_HYLSP	Chloroplast 30S ribosomal protein S4	0.42	-	mit	0	Plastid; chloroplast				202
Q332X6 UniProt NPD GO	RR4_LACSA	Chloroplast 30S ribosomal protein S4	0.42	-	mit	0	Plastid; chloroplast				201
Q9FSD9 UniProt NPD GO	RR4_PELNE	Chloroplast 30S ribosomal protein S4	0.42	-	mit	0	Plastid; chloroplast				200
O19986 UniProt NPD GO	RR4_ALOVE	Chloroplast 30S ribosomal protein S4 (Fragment)	0.42	-	nuc	0	Plastid; chloroplast				182
O36057 UniProt NPD GO	RR4_TIGSP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.42	-	nuc	0	Plastid; chloroplast				182
Q8WHY7 UniProt NPD GO	RR8_PSINU	Chloroplast 30S ribosomal protein S8	0.42	-	cyt	0	Plastid; chloroplast				132
Q6YXK9 UniProt NPD GO	RK16_PHYPA	Chloroplast 50S ribosomal protein L16	0.42	-	mit	0	Plastid; chloroplast				138
Q32RV3 UniProt NPD GO	RK16_STAPU	Chloroplast 50S ribosomal protein L16	0.42	-	mit	0	Plastid; chloroplast				141
Q32RN5 UniProt NPD GO	RK16_ZYGCR	Chloroplast 50S ribosomal protein L16	0.42	-	mit	0	Plastid; chloroplast				141
Q9MUT9 UniProt NPD GO	RK2_MESVI	Chloroplast 50S ribosomal protein L2	0.42	+	nuc	0	Plastid; chloroplast				276
Q1KXR9 UniProt NPD GO	RK22_HELAN	Chloroplast 50S ribosomal protein L22	0.42	-	mit	0	Plastid; chloroplast				154
P51306 UniProt NPD GO	RK29_PORPU	Chloroplast 50S ribosomal protein L29	0.42	-	nuc	0	Plastid; chloroplast				67
Q6EW02 UniProt NPD GO	RK32_NYMAL	Chloroplast 50S ribosomal protein L32	0.42	-	mit	0	Plastid; chloroplast				52
Q811Q9 UniProt NPD GO	PCY1B_MOUSE	Choline-phosphate cytidylyltransferase B (EC 2.7.7.15) (Phosphorylcholine transferase B) (CTP:phosph ...	0.42	-	nuc	0	Endoplasmic reticulum (By similarity)				369
Q9QZC4 UniProt NPD GO	PCY1B_RAT	Choline-phosphate cytidylyltransferase B (EC 2.7.7.15) (Phosphorylcholine transferase B) (CTP:phosph ...	0.42	-	nuc	0	Endoplasmic reticulum (By similarity)				369
O55226 UniProt NPD GO	CHAD_MOUSE	Chondroadherin precursor (Cartilage leucine-rich protein)	0.42	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				358
Q00657 UniProt NPD GO	CSPG4_RAT	Chondroitin sulfate proteoglycan 4 precursor (Chondroitin sulfate proteoglycan NG2) (HSN tumor-speci ...	0.42	-	end	1	Cell membrane; single-pass type I membrane protein. Localizes to the plasma membrane of oligodendroc ...	extracellular matrix [TAS] integral to plasma membrane [TAS]			2326
P83917 UniProt NPD GO	CBX1_MOUSE	Chromobox protein homolog 1 (Heterochromatin protein 1 homolog beta) (HP1 beta) (Modifier 1 protein) ...	0.42	+	nuc	0	Nucleus (By similarity). Unassociated with chromosomes during mitosis (By similarity)	centric heterochromatin [IDA] female pronucleus [IDA] male pronucleus [IDA] nuclear heterochromatin [ISS] nucleoplasm [ISS] polytene chromosome chromocenter [IDA]		1GUW	185
P83916 UniProt NPD GO	CBX1_HUMAN	Chromobox protein homolog 1 (Heterochromatin protein 1 homolog beta) (HP1 beta) (Modifier 1 protein) ...	0.42	+	nuc	0	Nucleus. Unassociated with chromosomes during mitosis	nuclear heterochromatin [TAS] nucleoplasm [TAS]	604511	2FMM	185
Q24764 UniProt NPD GO	CCCP_DROYA	Circadian clock-controlled protein precursor	0.42	-	mit	0					260
P43635 UniProt NPD GO	CISY3_YEAST	Citrate synthase 3 (EC 2.3.3.1)	0.42	-	mit	0		mitochondrial matrix [NAS]			486
Q10569 UniProt NPD GO	CPSF1_BOVIN	Cleavage and polyadenylation specificity factor 160 kDa subunit (CPSF 160 kDa subunit)	0.42	-	nuc	0	Nucleus; nucleoplasm				1444
Q99LI7 UniProt NPD GO	CSTF3_MOUSE	Cleavage stimulation factor 77 kDa subunit (CSTF 77 kDa subunit) (CF-1 77 kDa subunit) (CstF-77)	0.42	+	cyt	0	Nucleus (By similarity)				717
Q91132 UniProt NPD GO	CO3_NAJKA	Cobra venom factor precursor (CVF) (Complement C3 homolog) [Contains: Cobra venom factor alpha chain ...	0.42	-	mit	1 *	Secreted protein				1642
P56388 UniProt NPD GO	CART_MOUSE	Cocaine- and amphetamine-regulated transcript protein precursor [Contains: CART(1-52); CART(55-102); ...	0.42	-	exc	0	Secreted protein (Potential)				129
P12111 UniProt NPD GO	CO6A3_HUMAN	Collagen alpha-3(VI) chain precursor	0.42	-	cyt	0		collagen type VI [TAS]	120250	2KNT	3176
P01031 UniProt NPD GO	CO5_HUMAN	Complement C5 precursor [Contains: Complement C5 beta chain; Complement C5 alpha chain; C5a anaphyla ...	0.42	+	end	0		extracellular space [TAS]	120900	1XWE	1676
Q96MW5 UniProt NPD GO	COG8_HUMAN	Conserved oligomeric Golgi complex component 8	0.42	-	nuc	0	Golgi apparatus	Golgi transport complex [NAS]	606979		612
Q8AXZ4 UniProt NPD GO	CNT1A_BRARE	Contactin-1a precursor (Neural cell recognition molecule F11) (F3/F11/contactin)	0.42	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				1032
P49188 UniProt NPD GO	CRF_XENLA	Corticoliberin precursor (Corticotropin-releasing factor) (CRF) (Corticotropin-releasing hormone)	0.42	-	exc	0	Secreted protein				162
Q04618 UniProt NPD GO	COLI2_ONCMY	Corticotropin-lipotropin B precursor (Pro-opiomelanocortin B) (POMC B) [Contains: NPP 2; Corticotrop ...	0.42	-	nuc	0					240
P10000 UniProt NPD GO	COLI_ONCKE	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: Corticotropin (Adrenocor ...	0.42	-	exc	0					226
O70244 UniProt NPD GO	CUBN_RAT	Cubilin precursor (Intrinsic factor-cobalamin receptor) (Intrinsic factor-vitamin B12 receptor) (Gly ...	0.42	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein. Lysosome; lysosomal membrane; peripheral ...	membrane fraction [IDA]			3623
P15760 UniProt NPD GO	RR18_CYAPA	Cyanelle 30S ribosomal protein S18	0.42	-	mit	0	Plastid; cyanelle				71
Q14028 UniProt NPD GO	CNGB1_HUMAN	Cyclic nucleotide-gated cation channel 4 (CNG channel 4) (CNG-4) (CNG4) (Cyclic nucleotide-gated cat ...	0.42	-	mit	0	Membrane; multi-pass membrane protein	intracellular cyclic nucleotide activated c... [NAS]	600724		909
Q29441 UniProt NPD GO	CNGA3_BOVIN	Cyclic nucleotide-gated cation channel alpha 3 (CNG channel alpha 3) (CNG-3) (CNG3) (Cyclic nucleoti ...	0.42	-	end	3	Membrane; multi-pass membrane protein				706
Q9D9G3 UniProt NPD GO	CHIC2_MOUSE	Cysteine-rich hydrophobic domain 2 protein	0.42	-	cyt	1	Membrane; peripheral membrane protein (By similarity). Golgi apparatus (By similarity). Associated a ...	Golgi apparatus [IDA] Golgi-associated vesicle [IDA] plasma membrane [IDA]			165
Q9JLL0 UniProt NPD GO	CRIM1_MOUSE	Cysteine-rich motor neuron 1 protein precursor (CRIM-1) (Fragment)	0.42	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				1028
Q9XSD3 UniProt NPD GO	CRIS1_MACMU	Cysteine-rich secretory protein 1 precursor (CRISP-1) (Androgen-dependent acidic epididymal glycopro ...	0.42	-	nuc	0	Located in the lumen and epithelium of distal ductus efferentes and epididymal ducts, and on the pos ...				249

You are viewing entries 30251 to 30300 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.