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
P08081 UniProt NPD GO	CLCA_RAT	Clathrin light chain A (Lca)	0.14	-	cyt	0	Cytoplasmic face of coated pits and vesicles	clathrin coat of coated pit [NAS] clathrin vesicle coat [NAS]			248
Q11085 UniProt NPD GO	CLC2_CAEEL	Clc-like protein 2	0.14	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	membrane [NAS]			252
Q7T3C6 UniProt NPD GO	CPSF5_BRARE	Cleavage and polyadenylation specificity factor 5	0.14	-	mit	0	Nucleus (By similarity)	paraspeckles [ISS]			228
P79101 UniProt NPD GO	CPSF3_BOVIN	Cleavage and polyadenylation specificity factor 73 kDa subunit (CPSF 73 kDa subunit)	0.14	-	cyt	0	Nucleus				684
P22457 UniProt NPD GO	FA7_BOVIN	Coagulation factor VII precursor (EC 3.4.21.21) (Serum prothrombin conversion accelerator) [Contains ...	0.14	-	exc	1 *					447
Q8K3U6 UniProt NPD GO	FA7_RAT	Coagulation factor VII precursor (EC 3.4.21.21) (Serum prothrombin conversion accelerator) [Contains ...	0.14	-	exc	0					446
Q08058 UniProt NPD GO	COQ10_YEAST	Coenzyme Q-binding protein COQ10, mitochondrial precursor	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	mitochondrial inner membrane [IDA]			207
P08125 UniProt NPD GO	COAA1_CHICK	Collagen alpha-1(X) chain precursor	0.14	-	exc	0					674
Q05306 UniProt NPD GO	COAA1_MOUSE	Collagen alpha-1(X) chain precursor	0.14	-	exc	0					680
P12108 UniProt NPD GO	CO9A2_CHICK	Collagen alpha-2(IX) chain precursor	0.14	-	exc	0					677
Q8CG08 UniProt NPD GO	CTHR1_RAT	Collagen triple helix repeat-containing protein 1 precursor	0.14	-	exc	1 *	Secreted protein; extracellular space				245
P02745 UniProt NPD GO	C1QA_HUMAN	Complement C1q subcomponent subunit A precursor	0.14	-	exc	0	Secreted protein	complement component C1q complex [TAS]	120550	1PK6	245
Q9BXI9 UniProt NPD GO	C1QT6_HUMAN	Complement C1q tumor necrosis factor-related protein 6 precursor	0.14	-	mit	1 *	Secreted protein (Probable)				259
P12082 UniProt NPD GO	CO5_BOVIN	Complement C5a anaphylatoxin	0.14	-	nuc	0					74
P07360 UniProt NPD GO	CO8G_HUMAN	Complement component C8 gamma chain precursor	0.14	-	vac	0	Secreted protein		120930	1LF7	202
P48740 UniProt NPD GO	MASP1_HUMAN	Complement-activating component of Ra-reactive factor precursor (EC 3.4.21.-) (Ra-reactive factor se ...	0.14	-	mit	0			600521		699
Q5K0D1 UniProt NPD GO	CXO1_CONVX	Conotoxin-1 precursor	0.14	-	exc	0	Secreted protein (By similarity)				79
P14781 UniProt NPD GO	CNTN1_CHICK	Contactin-1 precursor (Neural cell recognition molecule F11)	0.14	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				1010
Q12860 UniProt NPD GO	CNTN1_HUMAN	Contactin-1 precursor (Neural cell surface protein F3) (Glycoprotein gp135)	0.14	-	end	0	Isoform 1, isoform 2: Cell membrane; lipid-anchor; GPI-anchor; extracellular side	membrane fraction [TAS]	600016		1018
P28685 UniProt NPD GO	CNTN2_CHICK	Contactin-2 precursor (Axonin-1)	0.14	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Attached to the neuronal membrane by a GPI-anchor			1CS6	1036
P55947 UniProt NPD GO	MTCU_HELPO	Copper-metallothionein (Cu-MT)	0.14	-	nuc	0					64
P35670 UniProt NPD GO	ATP7B_HUMAN	Copper-transporting ATPase 2 (EC 3.6.3.4) (Copper pump 2) (Wilson disease-associated protein)	0.14	-	end	7	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein (By ...	extracellular region [ISS] extracellular space [ISS] integral to plasma membrane [TAS] late endosome [IDA]	277900	2EW9	1465
P16232 UniProt NPD GO	DHI1_RAT	Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) (11-DH) (11-beta-hydroxysteroid dehydr ...	0.14	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				288
P31225 UniProt NPD GO	CBP1_CANAL	Corticosteroid-binding protein	0.14	-	cyt	0					489
Q76LL8 UniProt NPD GO	CRFR1_MACMU	Corticotropin-releasing factor receptor 1 precursor	0.14	-	end	7	Membrane; multi-pass membrane protein				415
O42602 UniProt NPD GO	CRFR1_XENLA	Corticotropin-releasing factor receptor 1 precursor (CRF-R) (CRF1) (Corticotropin-releasing hormone ...	0.14	-	end	8 *	Membrane; multi-pass membrane protein				415
P18294 UniProt NPD GO	KCRF_STRPU	Creatine kinase, flagellar (EC 2.7.3.2)	0.14	-	nuc	0	Axoneme. Associates specifically with the axoneme and may bind directly to polymerized microtubules				1174
P47941 UniProt NPD GO	CRKL_MOUSE	Crk-like protein	0.14	-	nuc	0					303
Q25589 UniProt NPD GO	CHH1_ORCLI	Crustacean hyperglycemic hormones A precursor (CHH A) [Contains: CHH precursor-related peptide A (CP ...	0.14	-	exc	1 *	Secreted protein				135
P34687 UniProt NPD GO	COL34_CAEEL	Cuticle collagen 34 (Abnormal ray morphology protein 4)	0.14	-	nuc	1 *		extracellular region [NAS]			299
P15768 UniProt NPD GO	RK22_CYAPA	Cyanelle 50S ribosomal protein L22	0.14	-	nuc	0	Plastid; cyanelle				114
P51480 UniProt NPD GO	CD2A1_MOUSE	Cyclin-dependent kinase inhibitor 2A, isoforms 1/2 (Cyclin-dependent kinase 4 inhibitor A) (CDK4I) ( ...	0.14	-	cyt	0		cytoplasm [IDA] nucleolus [IDA] nucleoplasm [IDA]		1LNN	168
Q640G7 UniProt NPD GO	ATG4B_XENLA	Cysteine protease ATG4B (EC 3.4.22.-) (Autophagy-related protein 4 homolog B)	0.14	-	cyt	0	Cytoplasm (Probable)				384
P43296 UniProt NPD GO	RD19A_ARATH	Cysteine proteinase RD19a precursor (EC 3.4.22.-) (RD19)	0.14	-	exc	0					368
P56101 UniProt NPD GO	CSP_TORCA	Cysteine string protein (CCCS1)	0.14	-	nuc	0	Membrane; lipid-anchor (By similarity)				195
Q9DBE0 UniProt NPD GO	CSAD_MOUSE	Cysteine sulfinic acid decarboxylase (EC 4.1.1.29) (Sulfinoalanine decarboxylase) (Cysteine-sulfinat ...	0.14	-	mit	0					493
Q7ZZN9 UniProt NPD GO	CRVP_TRIJE	Cysteine-rich venom protein precursor (TJ-CRVP)	0.14	-	exc	0	Secreted protein				240
O60931 UniProt NPD GO	CTNS_HUMAN	Cystinosin	0.14	-	end	7	Lysosome; lysosomal membrane; multi-pass membrane protein	lysosomal membrane [TAS]	606272		367
Q9VCR7 UniProt NPD GO	CTNS_DROME	Cystinosin homolog	0.14	-	end	7 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				397
P27786 UniProt NPD GO	CP17A_MOUSE	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.14	-	end	0		mitochondrion [IDA]			507
Q91Z85 UniProt NPD GO	CP17A_PERLE	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.14	-	nuc	0					509
Q92112 UniProt NPD GO	CP19A_POEGU	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.14	-	end	2 *	Membrane; peripheral membrane protein				509
P24460 UniProt NPD GO	CP2BB_CANFA	Cytochrome P450 2B11 (EC 1.14.14.1) (CYPIIB11) (P450 PBD-2)	0.14	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				494
P33260 UniProt NPD GO	CP2CI_HUMAN	Cytochrome P450 2C18 (EC 1.14.14.1) (CYPIIC18) (P450-6B/29C)	0.14	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		601131		490
P33265 UniProt NPD GO	CP2CS_MESAU	Cytochrome P450 2C28 (EC 1.14.14.1) (CYPIIC28) (P450 HSM4)	0.14	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P00182 UniProt NPD GO	CP2C3_RABIT	Cytochrome P450 2C3 (EC 1.14.14.1) (CYPIIC3) (P450 PBC3) (P450 form 3B)	0.14	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				489
Q27712 UniProt NPD GO	CP2L1_PANAR	Cytochrome P450 2L1 (EC 1.14.14.1) (CYPIIL1)	0.14	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				492
Q8TAV3 UniProt NPD GO	CP2W1_HUMAN	Cytochrome P450 2W1 (EC 1.14.14.-) (CYPIIW1)	0.14	-	cyt	0	Membrane; peripheral membrane protein (Potential)				434
O42563 UniProt NPD GO	CP3AR_ONCMY	Cytochrome P450 3A27 (EC 1.14.14.1) (CYPIIIA27)	0.14	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				518
P49602 UniProt NPD GO	CP51_USTMA	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Lanosterol 14- ...	0.14	-	end	2 *					561

You are viewing entries 58151 to 58200 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.