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
P15684 UniProt NPD GO	AMPN_RAT	Aminopeptidase N (EC 3.4.11.2) (rAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (Aminopept ...	0.31	-	exc	1 *	Membrane; single-pass type II membrane protein				964
Q86SJ2 UniProt NPD GO	AMGO2_HUMAN	Amphoterin-induced protein 2 precursor (AMIGO-2) (Alivin-1) (Differentially expressed in gastric ade ...	0.31	-	nuc	1	Cell membrane; single-pass type I membrane protein (By similarity). Nucleus (By similarity). Associa ...	integral to plasma membrane [ISS]			522
P12023 UniProt NPD GO	A4_MOUSE	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid protein homolog) (Amyloido ...	0.31	-	end	1	Membrane; single-pass type I membrane protein. Cell surface protein that rapidly becomes internalize ...	apical part of cell [IDA] axon [IDA] ciliary rootlet [IDA] cytoplasm [IDA] cytoplasmic vesicle [IDA] Golgi apparatus [IDA] integral to membrane [IDA] membrane [IDA] membrane fraction [IDA] neuromuscular junction [IDA] perinuclear region [IDA] spindle midzone [IDA]			770
P08592 UniProt NPD GO	A4_RAT	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid protein homolog) (Amyloido ...	0.31	-	end	1	Membrane; single-pass type I membrane protein. Cell surface protein that rapidly becomes internalize ...			1OQN	770
O42659 UniProt NPD GO	APC14_SCHPO	Anaphase-promoting complex subunit 14 (20S cyclosome/APC complex protein apc14) (Overlapping meiotic ...	0.31	-	nuc	0	Outer spore wall	anaphase-promoting complex [IDA]			107
Q8WN63 UniProt NPD GO	ANGI_MACMU	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.31	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q8WN62 UniProt NPD GO	ANGI_SAGOE	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.31	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q6UX02 UniProt NPD GO	AN36A_HUMAN	Ankyrin repeat domain-containing protein 36A	0.31	-	nuc	0					151
Q8N2N9 UniProt NPD GO	AN36B_HUMAN	Ankyrin repeat domain-containing protein 36B	0.31	-	mit	0					239
Q5TZF3 UniProt NPD GO	ANR45_HUMAN	Ankyrin repeat domain-containing protein 45	0.31	-	cyt	0					282
P14087 UniProt NPD GO	ANXA1_CAVCU	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin-9) (p35) (Phospholipase A2 inhibi ...	0.31	-	cyt	0					346
Q9UJ72 UniProt NPD GO	ANX10_HUMAN	Annexin A10 (Annexin-14)	0.31	-	cyt	0			608008		324
P14669 UniProt NPD GO	ANXA3_RAT	Annexin A3 (Annexin III) (Lipocortin III) (Placental anticoagulant protein III) (PAP-III) (35-alpha ...	0.31	-	cyt	0					323
Q8TD06 UniProt NPD GO	AGR3_HUMAN	Anterior gradient protein 3 homolog precursor (AG-3 protein) (hAG-3) (AG3) (Breast cancer membrane p ...	0.31	-	vac	0	Secreted protein (Probable)		609482		166
Q07840 UniProt NPD GO	EM13_ECHMU	Antigen EM13	0.31	-	nuc	0					426
O97666 UniProt NPD GO	APJ_MACMU	Apelin receptor (G-protein coupled receptor APJ) (Angiotensin receptor-like 1)	0.31	+	end	7 *	Membrane; multi-pass membrane protein				380
Q9JHG3 UniProt NPD GO	APJ_RAT	Apelin receptor (G-protein coupled receptor APJ) (Angiotensin receptor-like 1) (B78) (GPCR34)	0.31	+	end	7 *	Membrane; multi-pass membrane protein	cytoplasmic vesicle [IMP] nucleus [IMP] plasma membrane [IMP]			377
P35414 UniProt NPD GO	APJ_HUMAN	Apelin receptor (G-protein coupled receptor APJ) (Angiotensin receptor-like 1) (HG11)	0.31	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600052		380
O42296 UniProt NPD GO	APOA1_ANAPL	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.31	-	exc	0	Secreted protein				264
P08250 UniProt NPD GO	APOA1_CHICK	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.31	-	exc	0	Secreted protein				264
Q9Z2L4 UniProt NPD GO	APOA1_MESAU	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.31	-	cyt	0	Secreted protein				264
Q00623 UniProt NPD GO	APOA1_MOUSE	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.31	-	exc	0	Secreted protein	extracellular space [IDA]			264
P18648 UniProt NPD GO	APOA1_PIG	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.31	-	exc	0	Secreted protein				265
P41958 UniProt NPD GO	CED9_CAEEL	Apoptosis regulator ced-9 (Cell death protein 9)	0.31	-	nuc	1	Intracytoplasmic membrane; peripheral membrane protein. Mitochondrion; mitochondrial membrane; perip ...	membrane fraction [IDA] organelle membrane [IDA] perinuclear region [IDA]		2A5Y	280
P61799 UniProt NPD GO	APTX_BRARE	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.31	-	nuc	0	Nucleus (Probable)				324
P39655 UniProt NPD GO	LOX12_MOUSE	Arachidonate 12-lipoxygenase, 12S-type (EC 1.13.11.31) (12-LOX) (Platelet-type lipoxygenase 12)	0.31	-	mit	1 *	Cytoplasm	cytosol [ISS]			662
Q9NZN9 UniProt NPD GO	AIPL1_HUMAN	Aryl-hydrocarbon-interacting protein-like 1	0.31	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]	604393		384
P28658 UniProt NPD GO	ATX10_MOUSE	Ataxin-10 (Spinocerebellar ataxia type 10 protein homolog) (Brain protein E46)	0.31	-	cyt	0					475
P01361 UniProt NPD GO	ELHL_APLCA	Atrial gland peptide B precursor (ELH-1L)	0.31	-	exc	1 *	Secreted protein				122
P18909 UniProt NPD GO	ANF_RANCA	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP)	0.31	-	exc	0	Secreted protein				145
Q6CPX2 UniProt NPD GO	ATG16_KLULA	Autophagy protein 16	0.31	-	nuc	0	Vacuole (By similarity). Cytoplasmic vesicle (By similarity). Vesicular and vacuolar. Found in punct ...				126
Q51Y68 UniProt NPD GO	ATG17_MAGGR	Autophagy-related protein 17	0.31	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				504
Q8J282 UniProt NPD GO	ATG8_PODAN	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8) (Induced duri ...	0.31	-	cyt	0	Cytoplasm (By similarity). Membrane; lipid-anchor (By similarity). Punctate structures under nutrien ...				121
Q5VRD1 UniProt NPD GO	IAA1_ORYSA	Auxin-responsive protein IAA1 (Indoleacetic acid-induced protein 1)	0.31	-	nuc	0	Nucleus (By similarity)				199
Q75GK1 UniProt NPD GO	IAA12_ORYSA	Auxin-responsive protein IAA12 (Indoleacetic acid-induced protein 12)	0.31	-	nuc	0	Nucleus (By similarity)				226
Q7Z6A9 UniProt NPD GO	BTLA_HUMAN	B- and T-lymphocyte attenuator precursor (B- and T-lymphocyte-associated protein) (CD272 antigen)	0.31	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)		607925	2AW2	289
Q9Z2F7 UniProt NPD GO	BNI3L_MOUSE	BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like (NIP3L) (NIP3-like protein X)	0.31	-	nuc	1	Mitochondrion	mitochondrion [ISS]			218
Q9NYM9 UniProt NPD GO	BET1L_HUMAN	BET1-like protein (Vesicle transport protein GOS15) (Golgi SNARE with a size of 15 kDa) (GS15) (GOS- ...	0.31	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				111
Q28739 UniProt NPD GO	BPI_RABIT	Bactericidal permeability-increasing protein (BPI) (Fragment)	0.31	-	nuc	0	Membrane-associated in polymorphonuclear Leukocytes (PMN) granules (By similarity)				445
Q8C1Z7 UniProt NPD GO	BBS4_MOUSE	Bardet-Biedl syndrome 4 protein homolog	0.31	-	cyt	0		centrosome [IDA]			520
O09009 UniProt NPD GO	RFNG_MOUSE	Beta-1,3-N-acetylglucosaminyltransferase radical fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.31	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				332
Q9Y5Z6 UniProt NPD GO	B3GT1_HUMAN	Beta-1,3-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,3-GalTase 1) (Beta3GalT1) (UDP-galactose:beta- ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to membrane [NAS]	603093		326
O54904 UniProt NPD GO	B3GT1_MOUSE	Beta-1,3-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,3-GalTase 1) (Beta3GalT1) (UDP-galactose:beta- ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	Golgi membrane [IDA]			326
Q7JK24 UniProt NPD GO	B3GT1_GORGO	Beta-1,3-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,3-GalTase 1) (UDP-galactose:beta-N-acetyl-gluc ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				326
Q7JK25 UniProt NPD GO	B3GT1_PANPA	Beta-1,3-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,3-GalTase 1) (UDP-galactose:beta-N-acetyl-gluc ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				326
Q7JK26 UniProt NPD GO	B3GT1_PANTR	Beta-1,3-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,3-GalTase 1) (UDP-galactose:beta-N-acetyl-gluc ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				326
Q9MYM7 UniProt NPD GO	B3GT1_PONPY	Beta-1,3-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,3-GalTase 1) (UDP-galactose:beta-N-acetyl-gluc ...	0.31	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				326
Q80XD1 UniProt NPD GO	CHIO_MOUSE	Beta-chimaerin (Beta-chimerin) (Rho-GTPase-activating protein 3)	0.31	+	cyt	0	Membrane; peripheral membrane protein (Potential)				332
Q5J601 UniProt NPD GO	DB120_MACMU	Beta-defensin 120 precursor (Defensin, beta 120)	0.31	-	cyt	0	Secreted protein (Potential)				88
P49776 UniProt NPD GO	APH1_SCHPO	Bis(5'-nucleosyl)-tetraphosphatase [Asymmetrical] (EC 3.6.1.17) (Diadenosine 5',5'''-P1,P4-tetraphos ...	0.31	-	mit	0					181

You are viewing entries 39201 to 39250 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.