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
Q28902 UniProt NPD GO	COCA1_RABIT	Collagen alpha-1(XII) chain (Fragment)	0.23	-	mit	0					639
P39060 UniProt NPD GO	COIA1_HUMAN	Collagen alpha-1(XVIII) chain precursor [Contains: Endostatin]	0.23	-	exc	0		collagen [TAS]	120328	1BNL	1516
O46392 UniProt NPD GO	CO1A2_CANFA	Collagen alpha-2(I) chain precursor	0.23	-	exc	0					1366
P17140 UniProt NPD GO	CO4A2_CAEEL	Collagen alpha-2(IV) chain precursor (Lethal protein 2)	0.23	-	mit	0		collagen type IV [IMP]			1758
P32017 UniProt NPD GO	CO9A3_CHICK	Collagen alpha-3(IX) chain precursor	0.23	-	exc	0					675
Q8CG16 UniProt NPD GO	C1RA_MOUSE	Complement C1r-A subcomponent precursor (EC 3.4.21.41) (Complement component 1, r-A subcomponent) [C ...	0.23	-	cyt	0					707
Q91ZQ1 UniProt NPD GO	PDE6C_MOUSE	Cone cGMP-specific 3',5'-cyclic phosphodiesterase alpha'-subunit (EC 3.1.4.35) (cGMP phosphodiestera ...	0.23	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				861
P69765 UniProt NPD GO	CX5A_CONVC	Conotoxin Vc5a precursor (Conotoxin Vc5.1) (Fragment)	0.23	-	exc	0	Secreted protein				54
Q69Z26 UniProt NPD GO	CNTN4_MOUSE	Contactin-4 precursor (Brain-derived immunoglobulin superfamily protein 2) (BIG-2)	0.23	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	axon [ISS] plasma membrane [ISS]			1026
Q9UBL6 UniProt NPD GO	CPNE7_HUMAN	Copine-7 (Copine VII)	0.23	-	cyt	0			605689		633
P49015 UniProt NPD GO	ATP7A_CRIGR	Copper-transporting ATPase 1 (EC 3.6.3.4) (Copper pump 1) (Fragment)	0.23	-	end	7	Membrane; multi-pass membrane protein				1476
Q92176 UniProt NPD GO	COR1A_BOVIN	Coronin-1A (Coronin-like protein p57) (Coronin-like protein A) (CLIPINA) (Tryptophan aspartate-conta ...	0.23	-	end	0	In non-infected macrophages, associated with the cortical microtubule network; in mycobacteria-infec ...				460
P21252 UniProt NPD GO	COLI_LOXAF	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: Corticotropin (Adrenocor ...	0.23	-	nuc	0					134
Q90812 UniProt NPD GO	CRFR1_CHICK	Corticotropin-releasing factor receptor 1 precursor (CRF-R) (CRF1) (Corticotropin-releasing hormone ...	0.23	-	end	7 *	Membrane; multi-pass membrane protein				420
P30275 UniProt NPD GO	KCRU_MOUSE	Creatine kinase, ubiquitous mitochondrial precursor (EC 2.7.3.2) (U-MtCK) (Mia-CK) (Acidic-type mito ...	0.23	-	mit	0	Mitochondrion; mitochondrial inner membrane; intermembrane side	mitochondrion [IDA]			418
P25809 UniProt NPD GO	KCRU_RAT	Creatine kinase, ubiquitous mitochondrial precursor (EC 2.7.3.2) (U-MtCK) (Mia-CK) (Acidic-type mito ...	0.23	-	mit	0	Mitochondrion; mitochondrial inner membrane; intermembrane side	mitochondrion [TAS]			418
P40821 UniProt NPD GO	CRJ1C_TRICY	Crystallin J1C	0.23	-	nuc	0					322
Q39547 UniProt NPD GO	CUCM1_CUCME	Cucumisin precursor (EC 3.4.21.25) (Allergen Cuc m 1)	0.23	-	mit	0	Secreted protein				731
Q03041 UniProt NPD GO	CNGA2_BOVIN	Cyclic nucleotide-gated olfactory channel (Cyclic nucleotide-gated cation channel 2) (CNG channel 2) ...	0.23	-	end	4	Membrane; multi-pass membrane protein			1SY9	663
P41384 UniProt NPD GO	CKS1_PATVU	Cyclin-dependent kinases regulatory subunit (SUC1 homolog)	0.23	-	cyt	0					76
O19093 UniProt NPD GO	CYTC_SAISC	Cystatin C precursor	0.23	-	exc	1 *					146
Q8K5A3 UniProt NPD GO	CST11_RAT	Cystatin-11 precursor	0.23	-	vac	1 *	Secreted protein (Potential)				139
Q03751 UniProt NPD GO	CSP_DROME	Cysteine string protein	0.23	-	nuc	0	Membrane; lipid-anchor	synaptic vesicle [TAS]			249
P60623 UniProt NPD GO	CRVP_TRIST	Cysteine-rich secretory protein precursor (Stecrisp) (Fragment)	0.23	-	nuc	0	Secreted protein			1RC9	233
P07253 UniProt NPD GO	CBP6_YEAST	Cytochrome B pre-mRNA-processing protein 6	0.23	-	nuc	0	Mitochondrion	mitochondrion [IDA]			162
Q29552 UniProt NPD GO	C11B1_PIG	Cytochrome P450 11B1, mitochondrial precursor (EC 1.14.15.4) (CYPXIB1) (P450C11) (Steroid 11-beta-hy ...	0.23	-	cyt	0	Mitochondrion				503
Q92110 UniProt NPD GO	CP1A1_ONCMY	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1) (CYP1A2)	0.23	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				522
P11372 UniProt NPD GO	CP2CF_RABIT	Cytochrome P450 2C15 (EC 1.14.14.1) (CYPIIC15) (B32-3) (Fragment)	0.23	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				378
P56656 UniProt NPD GO	CP239_MOUSE	Cytochrome P450 2C39 (EC 1.14.14.1) (CYPIIC39)	0.23	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
Q64680 UniProt NPD GO	CP2DI_RAT	Cytochrome P450 2D18 (EC 1.14.14.1) (CYPIID18) (P450 2D-29/2D-35)	0.23	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
O46658 UniProt NPD GO	CP2DP_PIG	Cytochrome P450 2D25 (EC 1.14.14.-) (CYPIID25) (Vitamin D(3) 25-hydroxylase)	0.23	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				499
O22307 UniProt NPD GO	C71DB_LOTJA	Cytochrome P450 71D11 (EC 1.14.-.-) (Fragment)	0.23	-	nuc	0					490
O23365 UniProt NPD GO	C97B3_ARATH	Cytochrome P450 97B3 (EC 1.14.-.-)	0.23	-	cyt	0					580
Q9W130 UniProt NPD GO	CP9C1_DROME	Cytochrome P450 9c1 (EC 1.14.-.-) (CYPIXC1)	0.23	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				522
P00175 UniProt NPD GO	CYB2_YEAST	Cytochrome b2, mitochondrial precursor (EC 1.1.2.3) (L-lactate dehydrogenase [Cytochrome]) (L-lactat ...	0.23	-	nuc	0	Mitochondrion; mitochondrial intermembrane space	mitochondrial intermembrane space [IDA]		1SZG	591
P31172 UniProt NPD GO	CCSA_PEA	Cytochrome c biogenesis protein ccsA (Fragment)	0.23	-	mit	2 *	Plastid; chloroplast				65
P53700 UniProt NPD GO	CCHL_CANAL	Cytochrome c heme lyase (EC 4.4.1.17) (CCHL) (Holocytochrome-c synthase)	0.23	-	nuc	0	Mitochondrion; mitochondrial inner membrane				264
Q7YRF4 UniProt NPD GO	COX83_EULFU	Cytochrome c oxidase polypeptide 8 isoform 3, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxi ...	0.23	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				71
P13184 UniProt NPD GO	CX7A2_BOVIN	Cytochrome c oxidase polypeptide VIIa-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.23	-	mit	1	Mitochondrion; mitochondrial inner membrane				83
P05489 UniProt NPD GO	COX1_PARTE	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.23	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				645
O99819 UniProt NPD GO	COX2_RHISA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.23	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				225
P14854 UniProt NPD GO	CX6B1_HUMAN	Cytochrome c oxidase subunit VIb isoform 1 (EC 1.9.3.1) (COX VIb-1)	0.23	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)		124089		85
Q5RCT0 UniProt NPD GO	CX6B1_PONPY	Cytochrome c oxidase subunit VIb isoform 1 (EC 1.9.3.1) (COX VIb-1)	0.23	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				85
P07142 UniProt NPD GO	CY1_NEUCR	Cytochrome c1, heme protein, mitochondrial precursor	0.23	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein; intermembrane side				332
Q9H227 UniProt NPD GO	GBA3_HUMAN	Cytosolic beta-glucosidase (EC 3.2.1.21) (Cytosolic beta-glucosidase-like protein 1)	0.23	-	cyt	0	Cytoplasm; cytosol		606619		469
Q5BN22 UniProt NPD GO	RGA2_BRACM	DELLA protein RGA2 (RGA-like protein 2) (BrRGA2)	0.23	-	cyt	0	Nucleus (By similarity)				579
P28352 UniProt NPD GO	APEX1_MOUSE	DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP endonuclease 1) (APEX nuclease) (APEN)	0.23	-	nuc	0	Nucleus	cytoplasm [IDA] endoplasmic reticulum [ISS] nucleus [ISS] perinuclear region [ISS] ribosome [ISS]			316
P47928 UniProt NPD GO	ID4_HUMAN	DNA-binding protein inhibitor ID-4 (Inhibitor of DNA binding 4)	0.23	-	nuc	0	Nucleus	nucleus [IC]	600581		161
Q8WHZ1 UniProt NPD GO	RPOA_PSINU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.23	-	cyt	0	Plastid; chloroplast				340
Q9FHD5 UniProt NPD GO	UDU1_ARATH	DUF26 domain-containing protein 1 precursor	0.23	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			286

You are viewing entries 47251 to 47300 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.