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
Q27597 UniProt NPD GO	NCPR_DROME	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.34	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity). ...				679
Q9MZ37 UniProt NPD GO	NKG2D_PANTR	NKG2-D type II integral membrane protein (NKG2-D-activating NK receptor) (NK cell receptor D) (Kille ...	0.34	-	mit	1	Membrane; single-pass type II membrane protein				216
Q95MI1 UniProt NPD GO	NKG2F_PANTR	NKG2-F type II integral membrane protein (NKG2-F-activating NK receptor) (NK cell receptor F)	0.34	-	nuc	1	Membrane; single-pass type II membrane protein				158
Q9QZV9 UniProt NPD GO	NXT1_MOUSE	NTF2-related export protein 1	0.34	+	cyt	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm	nuclear pore [IDA]			140
Q920G2 UniProt NPD GO	NHRF2_RAT	Na(+)/H(+) exchange regulatory cofactor NHE-RF2 (NHERF-2) (Tyrosine kinase activator protein 1) (TKA ...	0.34	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein. Nucleus. Nuclear, in a punctate pattern				337
O46541 UniProt NPD GO	ANFB_SHEEP	Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic pepti ...	0.34	-	exc	0	Secreted protein				129
Q9HGY5 UniProt NPD GO	PHO85_CANAL	Negative regulator of the PHO system (EC 2.7.11.22) (Serine/threonine-protein kinase PHO85) (CaPHO85 ...	0.34	-	cyt	0					326
Q8C031 UniProt NPD GO	NGL1_MOUSE	Netrin-G1 ligand precursor (NGL-1) (Leucine-rich repeat-containing protein 4C)	0.34	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [ISS] membrane [ISS]			640
P70232 UniProt NPD GO	CHL1_MOUSE	Neural cell adhesion molecule L1-like protein precursor (Cell adhesion molecule with homology to L1C ...	0.34	-	exc	1	Membrane; single-pass type I membrane protein. Soluble forms produced by cleavage/shedding also exis ...	apical part of cell [IDA] dendrite [IDA]			1209
P20310 UniProt NPD GO	CADHN_XENLA	Neural-cadherin 1 precursor (N-cadherin 1)	0.34	-	end	1 *	Membrane; single-pass type I membrane protein				905
Q90275 UniProt NPD GO	CADH2_BRARE	Neural-cadherin precursor (N-cadherin) (Cadherin-2) (ZNCAD)	0.34	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	catenin complex [IDA] presynaptic membrane [IDA]			893
Q28146 UniProt NPD GO	NRX1A_BOVIN	Neurexin-1-alpha precursor (Neurexin I-alpha)	0.34	-	end	1	Membrane; single-pass type I membrane protein (Potential)			2H0B	1530
Q9CS84 UniProt NPD GO	NRX1A_MOUSE	Neurexin-1-alpha precursor (Neurexin I-alpha)	0.34	-	end	1	Membrane; single-pass type I membrane protein (Potential)	membrane fraction [TAS] presynaptic membrane [IDA]			1514
Q63372 UniProt NPD GO	NRX1A_RAT	Neurexin-1-alpha precursor (Neurexin I-alpha)	0.34	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1514
P39683 UniProt NPD GO	NPT1_YEAST	Nicotinate phosphoribosyltransferase (EC 2.4.2.11) (NAPRTase)	0.34	-	cyt	0	Cytoplasm. Nucleus	nucleus [IDA]		1VLP	429
Q5RK28 UniProt NPD GO	NMES1_RAT	Normal mucosa of esophagus-specific gene 1 protein	0.34	-	mit	1 *	Nucleus (By similarity)				83
Q944A9 UniProt NPD GO	NPS11_ARATH	Novel plant SNARE 11 (AtNPSN11)	0.34	-	nuc	1	Membrane; single-pass type IV membrane protein. Cell plate during cell division				265
O95760 UniProt NPD GO	NFHEV_HUMAN	Nuclear factor from high endothelial venules (NF-HEV)	0.34	-	nuc	0	Nucleus		608678		270
O17706 UniProt NPD GO	NH169_CAEEL	Nuclear hormone receptor family member nhr-169	0.34	-	nuc	0	Nucleus (Potential)				356
Q9NQ35 UniProt NPD GO	NRIP3_HUMAN	Nuclear receptor-interacting protein 3 (Sarcoma antigen NY-SAR-105)	0.34	-	nuc	0					241
Q84W66 UniProt NPD GO	NFYB6_ARATH	Nuclear transcription factor Y subunit B-6 (AtNF-YB-6) (Protein LEAFY COTYLEDON 1-LIKE)	0.34	-	nuc	0	Nucleus (Probable)				234
Q8BHY2 UniProt NPD GO	NOC4L_MOUSE	Nucleolar complex protein 4 homolog (NOC4 protein homolog) (NOC4-like protein) (Nucleolar complex-as ...	0.34	-	nuc	0	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Nucleus; nucleolus (By simil ...	small nucleolar ribonucleoprotein complex [ISS]			516
Q4R4J7 UniProt NPD GO	NUCL_MACFA	Nucleolin	0.34	+	nuc	0	Nucleus; nucleolus (By similarity)				710
Q99733 UniProt NPD GO	NP1L4_HUMAN	Nucleosome assembly protein 1-like 4 (Nucleosome assembly protein 2) (NAP2)	0.34	+	cyt	0	Nucleus	chromatin assembly complex [TAS] cytoplasm [TAS]	601651		375
Q9NRN5 UniProt NPD GO	OLFL3_HUMAN	Olfactomedin-like protein 3 precursor (HNOEL-iso) (hOLF44)	0.34	-	end	0	Secreted protein				406
P51839 UniProt NPD GO	GUC2D_RAT	Olfactory guanylyl cyclase GC-D precursor (EC 4.6.1.2) (Guanylate cyclase, olfactory)	0.34	-	end	2 *	Membrane; single-pass type I membrane protein	integral to membrane [IDA]			1110
Q8NGI4 UniProt NPD GO	OR4DB_HUMAN	Olfactory receptor 4D11	0.34	-	end	7 *	Membrane; multi-pass membrane protein				311
P23515 UniProt NPD GO	OMGP_HUMAN	Oligodendrocyte-myelin glycoprotein precursor	0.34	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor		164345		440
Q9XZL5 UniProt NPD GO	CXS62_CONST	Omega-conotoxin SVIA mutant 2 precursor	0.34	-	exc	0	Secreted protein				72
P54361 UniProt NPD GO	OAZ_DROME	Ornithine decarboxylase antizyme (ODC-Az) (Protein gutfeeling)	0.34	-	nuc	0					254
P62044 UniProt NPD GO	NR1I3_CALUR	Orphan nuclear receptor NR1I3 (Constitutive androstane receptor) (CAR)	0.34	-	cyt	0	Nucleus (By similarity)				348
P02822 UniProt NPD GO	OSTC_CHICK	Osteocalcin precursor (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.34	-	exc	0	Secreted protein				97
Q01456 UniProt NPD GO	OAM_ASCSU	Ovarian abundant message protein (Protein OAM)	0.34	-	vac	5					590
Q86VZ1 UniProt NPD GO	P2RY8_HUMAN	P2Y purinoceptor 8 (P2Y8)	0.34	-	end	6 *	Membrane; multi-pass membrane protein		300525		359
Q6P8I4 UniProt NPD GO	PCNP_MOUSE	PEST proteolytic signal-containing nuclear protein (PEST-containing nuclear protein) (PCNP)	0.34	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			178
Q9UKN5 UniProt NPD GO	PRDM4_HUMAN	PR domain zinc finger protein 4 (PR domain-containing protein 4)	0.34	-	nuc	0	Nucleus (Potential)		605780		801
P83984 UniProt NPD GO	IGWP_GINCI	Pancreatic IgW, short secretory form (Fragment)	0.34	-	nuc	0	Secreted protein				190
Q9GK30 UniProt NPD GO	PTHR_SHEEP	Parathyroid hormone-related protein precursor (PTH-rP) (PTHrP) (Fragment)	0.34	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Secreted protein (By similarity)				121
Q9BYG5 UniProt NPD GO	PAR6B_HUMAN	Partitioning defective 6 homolog beta (PAR-6 beta) (PAR-6B)	0.34	-	nuc	0	Cytoplasm (Probable)	plasma membrane [IDA] tight junction [IDA]	608975		372
Q56ZI2 UniProt NPD GO	PATL2_ARATH	Patellin-2	0.34	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Mainly membrane-associated. Cytoplasm (By sim ...				683
P47189 UniProt NPD GO	PLNC_PENCI	Penicillolysin precursor (EC 3.4.24.39) (Deuterolysin)	0.34	-	exc	0					351
Q70PY2 UniProt NPD GO	PGSB1_DROME	Peptidoglycan-recognition protein-SB1 precursor (EC 3.5.1.28)	0.34	-	exc	1 *	Secreted protein (Potential)	extracellular region [IDA]			190
Q4P0V4 UniProt NPD GO	PPID_USTMA	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.34	-	nuc	0	Cytoplasm (By similarity)				398
P19135 UniProt NPD GO	PER2_CUCSA	Peroxidase 2 (EC 1.11.1.7) (CUP2) (Fragment)	0.34	-	nuc	0					292
Q01548 UniProt NPD GO	PER2_HORVU	Peroxidase 2 (EC 1.11.1.7) (Fragment)	0.34	-	nuc	0					170
Q9NR77 UniProt NPD GO	PXMP2_HUMAN	Peroxisomal membrane protein 2 (22 kDa peroxisomal membrane protein)	0.34	+	mit	4 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein				194
Q9D0K1 UniProt NPD GO	PEX13_MOUSE	Peroxisomal membrane protein PEX13 (Peroxin-13)	0.34	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)	peroxisome [IDA]		1WXU	405
Q9CA86 UniProt NPD GO	PEX2_ARATH	Peroxisome assembly protein 2 (Peroxin-2) (AthPEX2) (Pex2p)	0.34	-	cyt	0	Peroxisome; peroxisomal membrane; peripheral membrane protein (Potential)				333
O42849 UniProt NPD GO	SYFB_SCHPO	Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chain) (PheRS ...	0.34	-	cyt	0	Cytoplasm (By similarity)				589
Q9FYC2 UniProt NPD GO	PAO_ARATH	Pheophorbide a oxygenase, chloroplast precursor (EC 1.-.-.-) (Pheide a oxygenase) (AtPaO) (Accelerat ...	0.34	-	cyt	0	Plastid; chloroplast; chloroplast inner membrane (By similarity)				537

You are viewing entries 36901 to 36950 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.