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
O13684 UniProt NPD GO	PCS1_SCHPO	Chromosome segregation protein pcs1	0.28	-	nuc	0	Nucleus; nucleolus. During G2, nuclear; nucleolar. Centromere. Localizes to the centromeres througho ...				222
P07851 UniProt NPD GO	ICE1_ASCSU	Chymotrypsin/elastase isoinhibitor 1 (C/E-1 inhibitor) (AsC/E-1)	0.28	-	nuc	0	Secreted protein			1EAI	63
Q9LXS7 UniProt NPD GO	CISY1_ARATH	Citrate synthase 1, peroxisomal precursor (EC 2.3.3.1)	0.28	-	nuc	0	Peroxisome (Potential)				480
P21566 UniProt NPD GO	COF2_CHICK	Cofilin-2 (Cofilin, muscle isoform)	0.28	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)	nucleus [TAS]		1TVJ	166
Q7T312 UniProt NPD GO	CCD25_BRARE	Coiled-coil domain-containing protein 25	0.28	+	nuc	0					207
Q8R3Q6 UniProt NPD GO	CCD58_MOUSE	Coiled-coil domain-containing protein 58	0.28	-	nuc	0					144
P02460 UniProt NPD GO	CO2A1_CHICK	Collagen alpha-1(II) chain precursor (Fragment)	0.28	-	nuc	0					369
P32018 UniProt NPD GO	COEA1_CHICK	Collagen alpha-1(XIV) chain precursor (Undulin)	0.28	-	nuc	0	Secreted protein; extracellular space; extracellular matrix			1B9Q	1888
O93484 UniProt NPD GO	CO1A2_ONCMY	Collagen alpha-2(I) chain precursor	0.28	-	exc	0					1356
Q9BXJ3 UniProt NPD GO	C1QT4_HUMAN	Complement C1q tumor necrosis factor-related protein 4 precursor	0.28	-	mit	0	Secreted protein (Potential)				329
Q9WUW3 UniProt NPD GO	CFAI_RAT	Complement factor I precursor (EC 3.4.21.45) (C3B/C4B inactivator) [Contains: Complement factor I he ...	0.28	-	exc	0	Secreted protein; extracellular space				604
Q64735 UniProt NPD GO	CRRY_MOUSE	Complement regulatory protein Crry precursor (Protein p65)	0.28	-	nuc	1	Membrane; single-pass type I membrane protein			1NTL	483
Q80WM3 UniProt NPD GO	CPLX4_MOUSE	Complexin-4 (Complexin IV) (CPX IV)	0.28	-	nuc	0	Membrane; lipid-anchor. Enriched at the synaptic terminal	synapse [IDA]			160
Q5I4E6 UniProt NPD GO	CXX_CONTE	Conotoxin Gla-TxX precursor	0.28	-	exc	1 *	Secreted protein (By similarity)				82
Q6PN81 UniProt NPD GO	CX51_CONLE	Conotoxin Lp5.1 precursor	0.28	-	exc	0	Secreted protein (By similarity)				65
Q9UQ52 UniProt NPD GO	CNTN6_HUMAN	Contactin-6 precursor (Neural recognition molecule NB-3) (hNB-3)	0.28	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)		607220		1028
P35322 UniProt NPD GO	SPRR1_MACMU	Cornifin (Small proline-rich protein I) (SPR-I) (Small proline-rich squamous cell marker)	0.28	-	nuc	0	Cytoplasm				89
P35323 UniProt NPD GO	SPRR1_PIG	Cornifin (Small proline-rich protein I) (SPR-I) (Small proline-rich squamous cell marker) (SPRP)	0.28	-	nuc	0	Cytoplasm				97
P35321 UniProt NPD GO	SPR1A_HUMAN	Cornifin A (Small proline-rich protein IA) (SPR-IA) (SPRK) (19 kDa pancornulin)	0.28	-	nuc	0	Cytoplasm	cornified envelope [IDA]	182265		89
P22528 UniProt NPD GO	SPR1B_HUMAN	Cornifin B (Small proline-rich protein IB) (SPR-IB) (14.9 kDa pancornulin)	0.28	-	nuc	0	Cytoplasm	cornified envelope [IDA] cytoplasm [TAS]	182266		89
Q920J3 UniProt NPD GO	CORO6_RAT	Coronin-6	0.28	-	nuc	0					472
P20631 UniProt NPD GO	COL13_CAEEL	Cuticle collagen 13 precursor	0.28	-	nuc	1 *					316
Q03755 UniProt NPD GO	CUT1_CAEEL	Cuticlin-1 precursor	0.28	-	end	1	Secreted protein				424
P48127 UniProt NPD GO	RK19_CYAPA	Cyanelle 50S ribosomal protein L19	0.28	-	nuc	0	Plastid; cyanelle				131
P08463 UniProt NPD GO	CKS1_SCHPO	Cyclin-dependent kinases regulatory subunit (P13)	0.28	-	cyt	0				1SCE	112
Q9Z0H6 UniProt NPD GO	CST9_MOUSE	Cystatin-9 precursor (Testatin)	0.28	-	exc	0	Secreted protein (Potential)				137
Q96DT6 UniProt NPD GO	ATG4C_HUMAN	Cysteine protease ATG4C (EC 3.4.22.-) (Autophagy-related protein 4 homolog C) (Autophagin-3) (Autoph ...	0.28	-	cyt	0	Cytoplasm (Probable)	cytoplasm [ISS] cytosol [ISS] extracellular region [IDA] microtubule associated complex [ISS]			458
Q9TUJ2 UniProt NPD GO	CMAH_MACMU	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.28	-	cyt	0	Cytoplasm (By similarity)				590
P14137 UniProt NPD GO	CP11A_RAT	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.28	-	cyt	0	Mitochondrion				526
O73853 UniProt NPD GO	CP17A_ICTPU	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.28	-	nuc	1 *					514
P04798 UniProt NPD GO	CP1A1_HUMAN	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1) (P450-P1) (P450 form 6) (P450-C)	0.28	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		108330		512
Q5RBQ1 UniProt NPD GO	CP1A2_PONPY	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2)	0.28	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				515
P11711 UniProt NPD GO	CP2A1_RAT	Cytochrome P450 2A1 (EC 1.14.14.1) (CYPIIA1) (Steroid hormones 7-alpha-hydroxylase) (Testosterone 7- ...	0.28	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			492
Q05556 UniProt NPD GO	CP2AB_RABIT	Cytochrome P450 2A11 (EC 1.14.14.1) (CYPIIA11) (P450-IIA11)	0.28	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				494
P15149 UniProt NPD GO	CP2A2_RAT	Cytochrome P450 2A2 (EC 1.14.14.1) (CYPIIA2) (Testosterone 15-alpha-hydroxylase) (P450-UT-4)	0.28	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				492
P20852 UniProt NPD GO	CP2A5_MOUSE	Cytochrome P450 2A5 (EC 1.14.14.1) (CYPIIA5) (Coumarin 7-hydroxylase) (P450-15-COH) (P450-IIA3.2)	0.28	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				494
Q91W64 UniProt NPD GO	CP270_MOUSE	Cytochrome P450 2C70 (EC 1.14.14.1) (CYPIIC70)	0.28	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [ISS]			489
P13584 UniProt NPD GO	CP4B1_HUMAN	Cytochrome P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-HP)	0.28	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		124075		511
Q12664 UniProt NPD GO	CP51_PENIT	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Eburicol 14-al ...	0.28	+	nuc	2 *	Microsome (Potential)				515
P58047 UniProt NPD GO	C71AS_ARATH	Cytochrome P450 71A28 (EC 1.14.-.-)	0.28	-	nuc	0					488
P37117 UniProt NPD GO	C71A4_SOLME	Cytochrome P450 71A4 (EC 1.14.-.-) (CYPLXXIA4) (P-450EG2)	0.28	-	nuc	1 *					507
Q5R7U6 UniProt NPD GO	COX11_PONPY	Cytochrome c oxidase assembly protein COX11, mitochondrial precursor	0.28	-	mit	1	Mitochondrion (By similarity)				277
Q75AF9 UniProt NPD GO	COX19_ASHGO	Cytochrome c oxidase assembly protein COX19	0.28	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial intermembrane space (By similarity)				99
P29872 UniProt NPD GO	COX2_CTEFE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.28	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q6YFQ1 UniProt NPD GO	CX6B2_RAT	Cytochrome c oxidase subunit VIb isoform 2 (EC 1.9.3.1) (COX VIb-2) (Cytochrome c oxidase subunit VI ...	0.28	-	nuc	0					88
Q9BXI3 UniProt NPD GO	5NT1A_HUMAN	Cytosolic 5'-nucleotidase 1A (EC 3.1.3.5) (Cytosolic 5'-nucleotidase IA) (cN1A) (cN-IA) (cN-I)	0.28	+	cyt	0	Cytoplasm	cytosol [NAS]			368
Q64559 UniProt NPD GO	BACH_RAT	Cytosolic acyl coenzyme A thioester hydrolase (EC 3.1.2.2) (Long chain acyl-CoA thioester hydrolase) ...	0.28	-	cyt	0	Cytoplasm	cytosol [IDA]			381
O00154 UniProt NPD GO	BACH_HUMAN	Cytosolic acyl coenzyme A thioester hydrolase (EC 3.1.2.2) (Long chain acyl-CoA thioester hydrolase) ...	0.28	-	mit	0	Isoform 4, isoform 6: Cytoplasm. Isoform 1, isoform 5: Mitochondrion	cytoplasm [TAS]			380
Q9UP65 UniProt NPD GO	PA24C_HUMAN	Cytosolic phospholipase A2 gamma precursor (EC 3.1.1.4) (cPLA2-gamma) (Phospholipase A2 group IVC)	0.28	-	cyt	0	Membrane; lipid-anchor	cytosol [TAS] membrane [TAS]	603602		541
P46555 UniProt NPD GO	GLCE_CAEEL	D-glucuronyl C5 epimerase (EC 5.1.3.-) (Heparin/heparan sulfate:glucuronic acid C5 epimerase)	0.28	-	mit	1 *	Cell membrane; single-pass type II membrane protein (Potential). Secreted protein; extracellular spa ...				616

You are viewing entries 42151 to 42200 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.