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
Q9P0G3 UniProt NPD GO	KLK14_HUMAN	Kallikrein-14 precursor (EC 3.4.21.-) (Kallikrein-like protein 6) (KLK-L6)	0.37	-	nuc	0	Secreted protein (Probable)	extracellular region [NAS]	606135		251
Q8BNW9 UniProt NPD GO	KBTBB_MOUSE	Kelch repeat and BTB domain-containing protein 11	0.37	-	mit	0					633
Q5RGB8 UniProt NPD GO	KLH26_BRARE	Kelch-like protein 26	0.37	-	nuc	0					605
Q96PQ7 UniProt NPD GO	KLHL5_HUMAN	Kelch-like protein 5	0.37	-	mit	1 *		cytoplasm [ISS]	608064		755
P02438 UniProt NPD GO	KRB2A_SHEEP	Keratin, high-sulfur matrix protein, B2A	0.37	-	mit	0					171
O76014 UniProt NPD GO	K1H7_HUMAN	Keratin, type I cuticular Ha7 (Hair keratin, type I Ha7)	0.37	-	exc	0			604541		449
P08727 UniProt NPD GO	K1C19_HUMAN	Keratin, type I cytoskeletal 19 (Cytokeratin-19) (CK-19) (Keratin-19) (K19)	0.37	-	nuc	0		costamere [IDA] intermediate filament [TAS]	148020		400
Q5R8S9 UniProt NPD GO	K1C19_PONPY	Keratin, type I cytoskeletal 19 (Cytokeratin-19) (CK-19) (Keratin-19) (K19)	0.37	-	nuc	0					400
P02538 UniProt NPD GO	K2C6A_HUMAN	Keratin, type II cytoskeletal 6A (Cytokeratin-6A) (CK 6A) (K6a keratin)	0.37	-	cyt	0		intermediate filament [TAS]	167200		563
P60412 UniProt NPD GO	KR10B_HUMAN	Keratin-associated protein 10-11 (Keratin-associated protein 10.11) (High sulfur keratin-associated ...	0.37	-	exc	0					298
P60368 UniProt NPD GO	KR102_HUMAN	Keratin-associated protein 10-2 (Keratin-associated protein 10.2) (High sulfur keratin-associated pr ...	0.37	-	nuc	0					255
P60370 UniProt NPD GO	KR105_HUMAN	Keratin-associated protein 10-5 (Keratin-associated protein 10.5) (High sulfur keratin-associated pr ...	0.37	-	exc	0					271
Q3LI77 UniProt NPD GO	KR134_HUMAN	Keratin-associated protein 13-4	0.37	-	mit	0					160
Q8K201 UniProt NPD GO	KCT2_MOUSE	Keratinocytes-associated transmembrane protein 2 precursor	0.37	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				259
P43629 UniProt NPD GO	KI3L1_HUMAN	Killer cell immunoglobulin-like receptor 3DL1 precursor (MHC class I NK cell receptor) (Natural kill ...	0.37	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	604946		444
Q95237 UniProt NPD GO	LYAM1_PANTR	L-selectin precursor (Lymph node homing receptor) (Leukocyte adhesion molecule 1) (LAM-1) (Leukocyte ...	0.37	-	nuc	1	Membrane; single-pass type I membrane protein				372
Q9JI93 UniProt NPD GO	A4GAT_RAT	Lactosylceramide 4-alpha-galactosyltransferase (EC 2.4.1.228) (Alpha-1,4-galactosyltransferase) (UDP ...	0.37	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to Golgi membrane [ISS]			360
Q9MYL0 UniProt NPD GO	LEPR_MACMU	Leptin receptor precursor (LEP-R) (OB receptor) (OB-R) (CD295 antigen)	0.37	-	end	3 *	Membrane; single-pass type I membrane protein				1163
Q27333 UniProt NPD GO	NT56_DROME	Lethal(2)neighbour of tid protein (NOT56) (NOT45)	0.37	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				510
Q8BYR1 UniProt NPD GO	LCMT2_MOUSE	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-) (p21WAF1/CIP1 promoter-interacting protein)	0.37	-	mit	0					686
Q80WG5 UniProt NPD GO	LRC8A_MOUSE	Leucine-rich repeat-containing protein 8A	0.37	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				810
Q5U308 UniProt NPD GO	LRC8D_RAT	Leucine-rich repeat-containing protein 8D	0.37	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				858
P97629 UniProt NPD GO	LCAP_RAT	Leucyl-cystinyl aminopeptidase (EC 3.4.11.3) (Cystinyl aminopeptidase) (Oxytocinase) (OTase) (Insuli ...	0.37	-	nuc	1	Cell membrane; single-pass type II membrane protein. Intracellular membrane; single-pass type II mem ...				1025
P08923 UniProt NPD GO	LTK_MOUSE	Leukocyte tyrosine kinase receptor precursor (EC 2.7.10.1)	0.37	-	end	1	Cell membrane; single-pass type I membrane protein. Isoform A, isoform B: Endoplasmic reticulum. Iso ...				888
O13476 UniProt NPD GO	LIPB_KLULA	Lipoate-protein ligase, mitochondrial precursor (EC 6.-.-.-) (Lipoate biosynthesis protein) (Lipoyl ...	0.37	-	mit	0	Mitochondrion (Probable)				332
P14612 UniProt NPD GO	NXLH_PSEAU	Long neurotoxin homolog Pa ID	0.37	-	nuc	0	Secreted protein				68
P39518 UniProt NPD GO	LCF2_YEAST	Long-chain-fatty-acid--CoA ligase 2 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 2) (Fatty acid acti ...	0.37	-	cyt	0	Cytoplasm. The FAM1-1 mutant is imported in the mitochondria	mitochondrion [IDA] peroxisome [IDA]			744
Q92325 UniProt NPD GO	LAG2_YEAST	Longevity-assurance protein 2	0.37	-	mit	1 *		mitochondrion [IDA]			680
Q9TTB4 UniProt NPD GO	LUM_PIG	Lumican (Keratan sulfate proteoglycan lumican) (KSPG lumican) (Fragment)	0.37	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				147
P83673 UniProt NPD GO	LYC_CRAVI	Lysozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase) (Fragments)	0.37	-	nuc	0	Secreted protein	extracellular region [IDA]			119
O22815 UniProt NPD GO	MLO5_ARATH	MLO-like protein 5 (AtMlo5)	0.37	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				501
Q9LD46 UniProt NPD GO	CRD1_CHLRE	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase 1, chloroplast precursor (EC 1.14.1 ...	0.37	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				407
P05532 UniProt NPD GO	KIT_MOUSE	Mast/stem cell growth factor receptor precursor (EC 2.7.10.1) (SCFR) (Proto-oncogene tyrosine-protei ...	0.37	-	end	2	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			975
Q9H204 UniProt NPD GO	MED28_HUMAN	Mediator of RNA polymerase II transcription subunit 28 (Mediator complex subunit 28) (Tumor angiogen ...	0.37	-	nuc	0	Nucleus. Cytoplasm. Membrane; peripheral membrane protein. According to Ref.6, it is cytoplasmic and ...				178
Q8TCY5 UniProt NPD GO	MRAP_HUMAN	Melanocortin 2 receptor accessory protein (Fat cell-specific low molecular weight protein) (Fat tiss ...	0.37	-	nuc	1 *	Cytoplasm; perinuclear region. Concentrated at the perinuclear membrane region. Cytoplasm (By simila ...		609196		173
Q96MG7 UniProt NPD GO	MAGG1_HUMAN	Melanoma-associated antigen G1 (MAGE-G1 antigen) (Necdin-like protein 2) (Hepatocellular carcinoma-a ...	0.37	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		608243		304
Q5XIE5 UniProt NPD GO	MARH3_RAT	Membrane-associated RING finger protein 3 (Membrane-associated RING-CH protein III) (MARCH-III)	0.37	-	end	2	Membrane; multi-pass membrane protein (Potential)				253
P50498 UniProt NPD GO	MSA2_PLAF7	Merozoite surface antigen 2 precursor (MSA-2) (45 kDa merozoite surface antigen)	0.37	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				272
P19599 UniProt NPD GO	MSA2_PLAFF	Merozoite surface antigen 2 precursor (MSA-2) (Merozoite 45 kDa surface antigen) (AG513)	0.37	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				264
Q863I4 UniProt NPD GO	MGR6_RABIT	Metabotropic glutamate receptor 6 precursor (mGluR6)	0.37	-	end	6	Membrane; multi-pass membrane protein				868
O08663 UniProt NPD GO	AMPM2_MOUSE	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (Peptidase M 2) (Initiation factor 2-associated ...	0.37	+	nuc	0		cytoplasm [ISS]			478
Q924T2 UniProt NPD GO	RT02_MOUSE	Mitochondrial 28S ribosomal protein S2 (S2mt) (MRP-S2)	0.37	-	mit	0	Mitochondrion	mitochondrion [IDA]			291
P82931 UniProt NPD GO	RT06_BOVIN	Mitochondrial 28S ribosomal protein S6 (S6mt) (MRP-S6)	0.37	-	mit	0	Mitochondrion				123
P15765 UniProt NPD GO	RM02_PARTE	Mitochondrial 60S ribosomal protein L2	0.37	-	mit	0	Mitochondrion				259
Q8BG51 UniProt NPD GO	MIRO1_MOUSE	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (MIRO-1) (Ras homolog gene family member T1)	0.37	-	mit	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)	mitochondrion [IDA]			631
Q7Z434 UniProt NPD GO	MAVS_HUMAN	Mitochondrial antiviral signaling protein (Interferon-beta promoter stimulator protein 1) (IPS-1) (V ...	0.37	-	nuc	1	Mitochondrion; mitochondrial outer membrane		609676		540
P38228 UniProt NPD GO	TCM62_YEAST	Mitochondrial chaperone TCM62	0.37	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA]			572
Q758C9 UniProt NPD GO	TIM54_ASHGO	Mitochondrial import inner membrane translocase subunit TIM54	0.37	-	nuc	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				472
Q9XGX7 UniProt NPD GO	TIM9_ORYSA	Mitochondrial import inner membrane translocase subunit Tim9	0.37	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				93
Q9WV96 UniProt NPD GO	TIM9B_MOUSE	Mitochondrial import inner membrane translocase subunit Tim9 B (TIMM10B) (Tim10b)	0.37	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)	mitochondrion [IDA]			100

You are viewing entries 34301 to 34350 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.