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
Q75BD5 UniProt NPD GO	MRL1_ASHGO	Mannose 6-phosphate receptor-like protein 1 precursor	0.33	-	end	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...				273
P33300 UniProt NPD GO	SUR1_YEAST	Mannosyl phosphorylinositol ceramide synthase SUR1 (EC 2.-.-.-)	0.33	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)	intracellular [IC]			382
P43481 UniProt NPD GO	KIT_BOVIN	Mast/stem cell growth factor receptor precursor (EC 2.7.10.1) (SCFR) (Proto-oncogene tyrosine-protei ...	0.33	-	end	2	Membrane; single-pass type I membrane protein				977
O97799 UniProt NPD GO	KIT_CANFA	Mast/stem cell growth factor receptor precursor (EC 2.7.10.1) (SCFR) (Proto-oncogene tyrosine-protei ...	0.33	-	end	2	Membrane; single-pass type I membrane protein				975
Q28317 UniProt NPD GO	KIT_CAPHI	Mast/stem cell growth factor receptor precursor (EC 2.7.10.1) (SCFR) (Proto-oncogene tyrosine-protei ...	0.33	-	end	2	Membrane; single-pass type I membrane protein				978
O59851 UniProt NPD GO	MAT1_FUSOX	Mating-type protein MAT-1	0.33	-	cyt	0	Nucleus (Potential)				357
O42413 UniProt NPD GO	MGP_CHICK	Matrix Gla-protein precursor (MGP)	0.33	-	exc	0	Secreted protein				103
Q58T70 UniProt NPD GO	M3H32_BOMMX	Maximins 3/H3 type 2 precursor [Contains: Maximin-3; Maximin-H3]	0.33	-	end	0	Secreted protein				145
Q8HYX8 UniProt NPD GO	MCP_CALJA	Membrane cofactor protein precursor (CD46 antigen)	0.33	-	nuc	1	Acrosome; acrosomal inner membrane; single-pass type I membrane protein. Inner acrosomal membrane of ...				392
O62837 UniProt NPD GO	MCP_SAGOE	Membrane cofactor protein precursor (CD46 antigen)	0.33	-	nuc	1	Acrosome; acrosomal inner membrane; single-pass type I membrane protein (By similarity). Inner acros ...				370
P19260 UniProt NPD GO	MSA2_PLAFG	Merozoite surface antigen 2 precursor (MSA-2) (Allelic form 2) (Membrane protein PF7)	0.33	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				287
Q09165 UniProt NPD GO	DIG1_CAEEL	Mesocentin precursor	0.33	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				13100
O97563 UniProt NPD GO	TIMP4_BOVIN	Metalloproteinase inhibitor 4 precursor (TIMP-4) (Tissue inhibitor of metalloproteinases 4)	0.33	-	nuc	0	Secreted protein				224
Q6Y4S4 UniProt NPD GO	KISS1_MOUSE	Metastasis-suppressor KiSS-1 precursor (Kisspeptin-1) [Contains: Metastin (Kisspeptin-52); Kisspepti ...	0.33	-	exc	0	Secreted protein				130
Q9MBC2 UniProt NPD GO	MMT1_HORVU	Methionine S-methyltransferase (EC 2.1.1.12) (AdoMet:Met S-methyltransferase) (Hv-MMT1)	0.33	-	cyt	0	Cytoplasm (By similarity)				1088
P56192 UniProt NPD GO	SYM_HUMAN	Methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.33	-	nuc	0	Cytoplasm (Probable)		156560		900
P19879 UniProt NPD GO	MIME_BOVIN	Mimecan precursor (Osteoglycin) [Contains: Corneal keratan sulfate proteoglycan 25 core protein (KSP ...	0.33	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				299
P48955 UniProt NPD GO	RM16_CHOCR	Mitochondrial 60S ribosomal protein L16	0.33	-	mit	0	Mitochondrion				138
Q66HG9 UniProt NPD GO	MAVS_RAT	Mitochondrial antiviral signaling protein (Interferon-beta promoter stimulator protein 1) (IPS-1) (V ...	0.33	-	nuc	0	Mitochondrion; mitochondrial outer membrane (By similarity)				507
Q9R1B1 UniProt NPD GO	TIM9B_RAT	Mitochondrial import inner membrane translocase subunit Tim9 B (TIMM10B) (Tim10b) (Fracture callus p ...	0.33	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				100
Q9Y8A7 UniProt NPD GO	TIM9_EMENI	Mitochondrial import inner membrane translocase subunit tim9	0.33	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
P46742 UniProt NPD GO	RT10_PROWI	Mitochondrial ribosomal protein S10	0.33	-	cyt	0	Mitochondrion				107
Q9NYZ2 UniProt NPD GO	MFRN1_HUMAN	Mitoferrin-1 (Mitochondrial iron transporter 1) (Solute carrier family 25 member 37) (Mitochondrial ...	0.33	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				347
Q40353 UniProt NPD GO	MMK2_MEDSA	Mitogen-activated protein kinase homolog MMK2 (EC 2.7.11.24)	0.33	-	cyt	0					371
O43684 UniProt NPD GO	BUB3_HUMAN	Mitotic checkpoint protein BUB3	0.33	-	nuc	0	Nucleus	kinetochore [TAS]	603719		328
Q5RB58 UniProt NPD GO	BUB3_PONPY	Mitotic checkpoint protein BUB3	0.33	-	nuc	0	Nucleus (By similarity)				328
O70451 UniProt NPD GO	MOT2_MOUSE	Monocarboxylate transporter 2 (MCT 2)	0.33	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)				484
Q8VHF2 UniProt NPD GO	MUCDL_MOUSE	Mucin and cadherin-like protein precursor (Mu-protocadherin)	0.33	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [ISS]			831
Q9JIK1 UniProt NPD GO	MUCDL_RAT	Mucin and cadherin-like protein precursor (Mu-protocadherin) (GP100)	0.33	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	coated pit [IDA] integral to membrane [NAS]			862
Q8R4F0 UniProt NPD GO	MCLN3_MOUSE	Mucolipin-3	0.33	-	end	5	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] plasma membrane [IDA]			553
Q8BH27 UniProt NPD GO	MEGF9_MOUSE	Multiple epidermal growth factor-like domains 9 precursor (EGF-like domain-containing protein 5) (Mu ...	0.33	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				600
Q4WX89 UniProt NPD GO	MBF1_ASPFU	Multiprotein-bridging factor 1	0.33	-	nuc	0					154
P54296 UniProt NPD GO	MYOM2_HUMAN	Myomesin-2 (M-protein) (165 kDa titin-associated protein) (165 kDa connectin-associated protein)	0.33	-	nuc	0			603509		1465
O88599 UniProt NPD GO	MYBPH_RAT	Myosin-binding protein H (MyBP-H) (H-protein)	0.33	-	nuc	0					484
Q8BJ48 UniProt NPD GO	NAGPA_MOUSE	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase precursor (EC 3.1.4.45) (Phosphod ...	0.33	-	end	2 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type I membrane protein. Cis/medial ...				517
Q9UJJ9 UniProt NPD GO	GNPTG_HUMAN	N-acetylglucosamine-1-phosphotransferase subunit gamma precursor (GlcNAc-1-phosphotransferase subuni ...	0.33	-	exc	0	Secreted protein (By similarity). Golgi apparatus (By similarity)		607838		305
Q85A84 UniProt NPD GO	NUIC_ANTFO	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.33	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				183
Q29259 UniProt NPD GO	NDUB6_PIG	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.33	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				127
Q06892 UniProt NPD GO	POS5_YEAST	NADH kinase POS5, mitochondrial precursor (EC 2.7.1.86)	0.33	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			414
O00217 UniProt NPD GO	NUIM_HUMAN	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.33	-	mit	0			602141		210
Q8K3J1 UniProt NPD GO	NUIM_MOUSE	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.33	-	mit	0					212
P25284 UniProt NPD GO	NDUA9_NEUCR	NADH-ubiquinone oxidoreductase 40 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.33	-	mit	0	Mitochondrion; mitochondrial matrix				375
O21406 UniProt NPD GO	NU4M_STRCA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.33	-	end	12 *					458
Q5R5C5 UniProt NPD GO	NOX4_PONPY	NADPH oxidase 4 (EC 1.6.3.-)	0.33	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				578
P08165 UniProt NPD GO	ADRO_BOVIN	NADPH:adrenodoxin oxidoreductase, mitochondrial precursor (EC 1.18.1.2) (Adrenodoxin reductase) (AR) ...	0.33	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]		1E6E	492
Q9V3H8 UniProt NPD GO	NXT1_DROME	NTF2-related export protein (p15)	0.33	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nuclear envelope [IDA] nucleoplasm [IDA]			133
Q2KIW0 UniProt NPD GO	NXT1_BOVIN	NTF2-related export protein 1	0.33	+	cyt	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm (By similarity)				140
Q9ULB1 UniProt NPD GO	NRX1A_HUMAN	Neurexin-1-alpha precursor (Neurexin I-alpha)	0.33	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	600565		1477
P12037 UniProt NPD GO	NFH_PIG	Neurofilament triplet H protein (200 kDa neurofilament protein) (Neurofilament heavy polypeptide) (N ...	0.33	-	nuc	0					142
Q8R493 UniProt NPD GO	ACHB4_MOUSE	Neuronal acetylcholine receptor protein subunit beta-4 precursor	0.33	-	end	4	Membrane; multi-pass membrane protein (By similarity)				495

You are viewing entries 37751 to 37800 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.