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
Q5R911 UniProt NPD GO	NUAM_PONPY	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.16	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				727
Q96126 UniProt NPD GO	NU1M_HYLLA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.16	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q534E0 UniProt NPD GO	NU2M_AILFU	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q9ZZ65 UniProt NPD GO	NU2M_CANFA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	10 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
O21326 UniProt NPD GO	NU2M_DASNO	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P55780 UniProt NPD GO	NU2M_GADMO	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				348
Q9T9Y9 UniProt NPD GO	NU2M_GORGO	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
P48653 UniProt NPD GO	NU2M_HORSE	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				346
Q36426 UniProt NPD GO	NU2M_LOCMI	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				342
Q9T9X1 UniProt NPD GO	NU2M_PANPA	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	9 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q2TQ18 UniProt NPD GO	NU2M_SYLME	NADH-ubiquinone oxidoreductase chain 2 (EC 1.6.5.3) (NADH dehydrogenase subunit 2)	0.16	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				347
Q35542 UniProt NPD GO	NU4M_PETMA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.16	-	end	13 *					458
P92613 UniProt NPD GO	NU4M_AGKRH	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.16	-	exc	6 *					231
P11993 UniProt NPD GO	NU5M_ASTPE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.16	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				643
P41299 UniProt NPD GO	NU5M_BALMU	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.16	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
Q9ZZ57 UniProt NPD GO	NU5M_CANFA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.16	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
Q76LN2 UniProt NPD GO	NU5M_ROUAM	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.16	-	end	14 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				605
O78756 UniProt NPD GO	NU5M_SHEEP	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.16	-	end	16 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				606
Q36284 UniProt NPD GO	NU5M_MAIZE	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5) (Fragment)	0.16	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				180
Q34050 UniProt NPD GO	NU6M_CERCA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.16	-	end	4 *					174
P37201 UniProt NPD GO	NCPR_CANTR	NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R)	0.16	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				680
P48360 UniProt NPD GO	ADRO_YEAST	NADPH:adrenodoxin oxidoreductase homolog, mitochondrial precursor (Adrenodoxin reductase homolog)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA]			493
Q12059 UniProt NPD GO	ULA1_YEAST	NEDD8-activating enzyme E1 regulatory subunit (Ubiquitin-like activation protein 1) (Ubiquitin-activ ...	0.16	-	cyt	0					462
Q9LYC2 UniProt NPD GO	NPL41_ARATH	NPL4-like protein 1	0.16	-	cyt	0				1WF9	413
Q05964 UniProt NPD GO	FL3H_DIACA	Naringenin,2-oxoglutarate 3-dioxygenase (EC 1.14.11.9) (Flavonone-3-hydroxylase) (F3H) (FHT)	0.16	-	cyt	0					365
Q45FF9 UniProt NPD GO	NACA_BABDI	Nascent polypeptide-associated complex subunit alpha (NAC-alpha) (Alpha-NAC)	0.16	-	nuc	0					197
Q6ICZ8 UniProt NPD GO	NACA3_ARATH	Nascent polypeptide-associated complex subunit alpha-like protein 3 (NAC-alpha-like protein 3) (Alph ...	0.16	-	nuc	0					204
P82972 UniProt NPD GO	NFNP_PSEPC	Natriuretic peptide PNP	0.16	-	nuc	0	Secreted protein	extracellular region [IDA]			37
Q6WZ20 UniProt NPD GO	NGB_MACMU	Neuroglobin	0.16	-	cyt	0					151
P55099 UniProt NPD GO	TKNK_MOUSE	Neurokinin-B precursor (NKB) (Neuromedin-K) (Preprotachykinin B) (PPT-B) (Neurokinin B-like protein ...	0.16	-	exc	0	Secreted protein				116
P24053 UniProt NPD GO	NMBR_RAT	Neuromedin-B receptor (NMB-R) (Neuromedin-B-preferring bombesin receptor)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				390
Q9UGM1 UniProt NPD GO	ACHA9_HUMAN	Neuronal acetylcholine receptor protein subunit alpha-9 precursor (Nicotinic acetylcholine receptor ...	0.16	-	end	4	Membrane; multi-pass membrane protein (Probable)		605116		479
P01182 UniProt NPD GO	NEU2_HORSE	Neurophysin 2 (Fragment)	0.16	-	nuc	0	Secreted protein				92
P41536 UniProt NPD GO	NEUT_RANTE	Neurotensin (NT)	0.16	-		0	Secreted protein				13
P84473 UniProt NPD GO	TX12B_BUNCA	Neurotoxin T1-2 B chain (Fragment)	0.16	-		0	Secreted protein				15
P11478 UniProt NPD GO	DEF1A_CAVPO	Neutrophil cationic peptide 1 type A precursor (GNCP-1A) [Contains: Neutrophil cationic peptide 1 (N ...	0.16	-	exc	0	Secreted protein				93
P19878 UniProt NPD GO	NCF2_HUMAN	Neutrophil cytosol factor 2 (NCF-2) (Neutrophil NADPH oxidase factor 2) (67 kDa neutrophil oxidase f ...	0.16	-	cyt	0	Cytoplasm		233710	2DMO	526
P33183 UniProt NPD GO	NIGB_SAMNI	Nigrin b precursor (Agglutinin V) (SNAV) [Contains: Nigrin b A chain (EC 3.2.2.22) (rRNA N-glycosida ...	0.16	-	mit	1 *					563
P49050 UniProt NPD GO	NIA_PICAN	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.16	-	cyt	0				2BII	859
P46010 UniProt NPD GO	NRL3_ARATH	Nitrilase 3 (EC 3.5.5.1)	0.16	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Tightly associated with the plasma mem ...				346
P43504 UniProt NPD GO	NIR_LEPMC	Nitrite reductase [NAD(P)H] (EC 1.7.1.4) (Fragment)	0.16	-	cyt	0					185
Q43460 UniProt NPD GO	NO20A_SOYBN	Nodulin 20a precursor (N-20A) (Nod-20A)	0.16	-	exc	0	Peribacteroid membrane or peribacteroid space (Potential)				195
Q9QY81 UniProt NPD GO	PO210_MOUSE	Nuclear pore membrane glycoprotein 210 precursor (POM210) (Nuclear pore protein gp210)	0.16	-	end	1	Nucleus; nuclear envelope; nuclear pore complex; single-pass type I membrane protein (By similarity) ...	nuclear envelope [IDA]			1886
Q65XK1 UniProt NPD GO	NFYB4_ORYSA	Nuclear transcription factor Y subunit B-4 (OsNF-YB-4) (Transcriptional activator HAP3C)	0.16	-	cyt	0	Nucleus (Probable)				143
Q6BWC0 UniProt NPD GO	NTF2_DEBHA	Nuclear transport factor 2 (NTF-2)	0.16	-	cyt	0	Cytoplasm (By similarity)				124
Q27415 UniProt NPD GO	NLP_DROME	Nucleoplasmin-like protein (dNLP) (Chromatin decondensation protein 1)	0.16	-	cyt	0	Nucleus			1NLQ	152
Q5E9Y9 UniProt NPD GO	NDK7_BOVIN	Nucleoside diphosphate kinase 7 (EC 2.7.4.6) (NDK 7) (NDP kinase 7)	0.16	-	cyt	0					377
Q8WVJ2 UniProt NPD GO	NUDC2_HUMAN	NudC domain-containing protein 2	0.16	-	cyt	0					157
Q9V6H2 UniProt NPD GO	OR49B_DROME	Odorant receptor 49b	0.16	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			375
Q8VGI1 UniProt NPD GO	OLF1_MOUSE	Olfactory receptor 1 (Olfactory receptor 135-13) (Odorant receptor I54)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				314

You are viewing entries 55951 to 56000 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.