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
O03205 UniProt NPD GO	NU5M_CERSI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.18	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
P03921 UniProt NPD GO	NU5M_MOUSE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.18	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				607
Q36459 UniProt NPD GO	NU5M_ORNAN	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.18	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				604
O79678 UniProt NPD GO	NU5M_PELSU	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.18	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				605
Q95918 UniProt NPD GO	NU5M_POLOR	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.18	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				613
Q37622 UniProt NPD GO	NUGM_PROWI	NADH-ubiquinone oxidoreductase subunit 9 (EC 1.6.5.3) (EC 1.6.99.3)	0.18	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				192
Q02827 UniProt NPD GO	N4BM_BOVIN	NADH-ubiquinone oxidoreductase subunit B14.5b (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-B14.5b) (CI-B14. ...	0.18	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side				120
P16243 UniProt NPD GO	MAOC_MAIZE	NADP-dependent malic enzyme, chloroplast precursor (EC 1.1.1.40) (NADP-ME)	0.18	-	nuc	0	Plastid; chloroplast				636
Q9V4L4 UniProt NPD GO	KBRAS_DROME	NF-kappa-B inhibitor-interacting Ras-like protein (Kappa B-Ras) (KappaB-Ras)	0.18	-	cyt	0					201
Q5IFJ9 UniProt NPD GO	NTRK3_MACFA	NT-3 growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor type 3)	0.18	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)				825
Q5IS37 UniProt NPD GO	NTRK3_PANTR	NT-3 growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor type 3)	0.18	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)				825
Q16288 UniProt NPD GO	NTRK3_HUMAN	NT-3 growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor type 3) ( ...	0.18	-	nuc	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	191316	1WWC	839
P24786 UniProt NPD GO	NTRK3_PIG	NT-3 growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor type 3) ( ...	0.18	-	nuc	2 *	Membrane; single-pass type I membrane protein				825
O42701 UniProt NPD GO	NAH2_ZYGRO	Na(+)/H(+) antiporter 2	0.18	-	end	10 *	Membrane; multi-pass membrane protein				808
Q80WY3 UniProt NPD GO	NANO1_MOUSE	Nanos homolog 1	0.18	-	nuc	0	Cytoplasm; perinuclear region (By similarity)				267
P60321 UniProt NPD GO	NANO2_HUMAN	Nanos homolog 2	0.18	-	nuc	0			608228		138
Q09702 UniProt NPD GO	NRD1_SCHPO	Negative regulator of differentiation 1 (Multicopy suppressor of sporulation protein msa2)	0.18	+	mit	0		cytoplasm [IDA] nucleus [IDA]			529
Q9HB63 UniProt NPD GO	NET4_HUMAN	Netrin-4 precursor (Beta-netrin) (Hepar-derived netrin-like protein)	0.18	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component				628
Q9UMX5 UniProt NPD GO	NENF_HUMAN	Neudesin precursor (Neuron-derived neurotrophic factor) (Secreted protein of unknown function) (SPUF ...	0.18	-	exc	0	Secreted protein; extracellular space (By similarity)				172
Q9D0S4 UniProt NPD GO	NEUL2_MOUSE	Neuralized-like protein 2	0.18	-	cyt	0	Cytoplasm. In primary myoblasts, localized predominantly at the tips of differentiating myofibers				285
Q63373 UniProt NPD GO	NRX1B_RAT	Neurexin-1-beta precursor (Neurexin I-beta)	0.18	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)			1C4R	468
P30098 UniProt NPD GO	NK3R_CAVPO	Neuromedin K receptor (NKR) (Neurokinin B receptor) (NK-3 receptor) (NK-3R) (Tachykinin receptor 3)	0.18	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			440
P43681 UniProt NPD GO	ACHA4_HUMAN	Neuronal acetylcholine receptor protein subunit alpha-4 precursor	0.18	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [TAS]	600513		627
P68007 UniProt NPD GO	NEUY_ALLMI	Neuropeptide Y (NPY)	0.18	-	nuc	0	Secreted protein				36
P68008 UniProt NPD GO	NEUY_CAVPO	Neuropeptide Y (NPY)	0.18	-	nuc	0	Secreted protein				36
P68006 UniProt NPD GO	NEUY_RABIT	Neuropeptide Y (NPY)	0.18	-	nuc	0	Secreted protein				36
P19630 UniProt NPD GO	NEU2_ANSAN	Neurophysin 2 (MSEL-neurophysin)	0.18	-	nuc	0	Secreted protein				131
P56743 UniProt NPD GO	SCX6_ANDAU	Neurotoxin 6 (Neurotoxin VI) (AaH VI) (AaHVI) (AaH6)	0.18	-	nuc	0	Secreted protein				66
P01526 UniProt NPD GO	NXB2_CERLA	Neurotoxin B-II	0.18	-	nuc	0	Secreted protein				55
P57716 UniProt NPD GO	NICA_MOUSE	Nicastrin precursor	0.18	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to plasma membrane [ISS] membrane fraction [IDA]			708
Q9UHC9 UniProt NPD GO	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 precursor	0.18	-	end	12	Cell membrane; apical cell membrane; multi-pass membrane protein. Cell membrane; multi-pass membrane ...		608010		1359
P39865 UniProt NPD GO	NIA1_PHAVU	Nitrate reductase [NADH] 1 (EC 1.7.1.1) (NR-1)	0.18	-	cyt	0					881
P08509 UniProt NPD GO	NIA2_TOBAC	Nitrate reductase [NADH] 2 (EC 1.7.1.1) (NR2)	0.18	-	nuc	0					904
P43100 UniProt NPD GO	NIA_BEABA	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.18	-	nuc	0					894
Q28314 UniProt NPD GO	NOS2_CAPHI	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.18	-	cyt	0					110
Q5JPE7 UniProt NPD GO	NOMO2_HUMAN	Nodal modulator 2 precursor (pM5 protein 2)	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein		609158		1267
Q53EK2 UniProt NPD GO	NSE1_SCHPO	Non-structural maintenance of chromosome element 1 (Non-SMC element 1)	0.18	-	cyt	0	Nucleus	Smc5-Smc6 complex [IDA]			232
P84000 UniProt NPD GO	TXC5_PHORI	Non-toxic venom protein PRTx22C5 (Fragment)	0.18	-	nuc	0	Secreted protein				34
Q5ZL79 UniProt NPD GO	NOL11_CHICK	Nucleolar protein 11	0.18	-	cyt	0	Nucleus; nucleolus (By similarity)				723
P81918 UniProt NPD GO	OR43B_DROME	Odorant receptor 43b	0.18	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			403
Q9TU99 UniProt NPD GO	OR1G1_PANTR	Olfactory receptor 1G1	0.18	-	end	7 *	Membrane; multi-pass membrane protein				313
Q8NH94 UniProt NPD GO	OR1L1_HUMAN	Olfactory receptor 1L1 (Olfactory receptor 9-C) (OR9-C)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				310
Q6IEY1 UniProt NPD GO	O4F29_HUMAN	Olfactory receptor 4F29 (Olfactory receptor OR1-1)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				312
Q17758 UniProt NPD GO	OPT1_CAEEL	Oligopeptide transporter 1 (Di-/tri-peptide transporter CPTA)	0.18	-	end	10	Membrane; multi-pass membrane protein (Potential)				785
P81597 UniProt NPD GO	TOT1D_HADVE	Omega-atracotoxin-Hv1d (Omega-AcTx-Hv1d)	0.18	-	nuc	0	Secreted protein				37
P02631 UniProt NPD GO	ONCO_RAT	Oncomodulin (OM) (Parvalbumin beta)	0.18	-	nuc	0				1RRO	108
Q94741 UniProt NPD GO	OPS1_SCHGR	Opsin-1	0.18	-	end	7	Membrane; multi-pass membrane protein				381
Q9P8X9 UniProt NPD GO	PYRF_AURPU	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.18	-	mit	0					270
Q41806 UniProt NPD GO	PSBQ2_MAIZE	Oxygen-evolving enhancer protein 3-2, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolvin ...	0.18	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				213
P47900 UniProt NPD GO	P2RY1_HUMAN	P2Y purinoceptor 1 (ATP receptor) (P2Y1) (Purinergic receptor)	0.18	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601167		373

You are viewing entries 53351 to 53400 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.