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
Q9JL89 UniProt NPD GO	NINJ2_MOUSE	Ninjurin-2 (Nerve injury-induced protein 2)	0.06	-	end	2	Membrane; multi-pass membrane protein				143
P17571 UniProt NPD GO	NIA1_MAIZE	Nitrate reductase [NADH] (EC 1.7.1.1) (NR) (Fragment)	0.06	-	mit	0				2CND	621
P80255 UniProt NPD GO	MP2_NERDI	Non-metallothionein cadmium-binding protein (CD-BP) (MP II)	0.06	-	cyt	0					119
Q07913 UniProt NPD GO	NSE1_YEAST	Non-structural maintenance of chromosome element 1 (Non-SMC element 1)	0.06	-	cyt	0	Nucleus	nucleus [IDA] Smc5-Smc6 complex [IPI]			336
P16270 UniProt NPD GO	LECN_PEA	Nonseed lectin precursor	0.06	-	end	1 *					265
P81651 UniProt NPD GO	NLTP1_PRUAR	Nonspecific lipid-transfer protein 1 (LTP 1) (Major allergen Pru ar 3)	0.06	-	nuc	0					91
Q8VEJ4 UniProt NPD GO	NLE1_MOUSE	Notchless homolog 1	0.06	-	cyt	0	Nucleus; nucleolus (By similarity)				484
Q7RY30 UniProt NPD GO	NUDFA_NEUCR	Nuclear distribution protein pac-1a (nudF homolog A)	0.06	-	mit	0	Cytoplasm. Localizes to the plus ends of microtubules and the mitotic spindle poles (By similarity)				441
O75607 UniProt NPD GO	NPM3_HUMAN	Nucleoplasmin-3	0.06	-	cyt	0	Nucleus		606456		177
Q9CPP0 UniProt NPD GO	NPM3_MOUSE	Nucleoplasmin-3	0.06	-	cyt	0	Nucleus (By similarity)	nucleolus [IDA]			174
Q5RC37 UniProt NPD GO	NPM3_PONPY	Nucleoplasmin-3	0.06	-	cyt	0	Nucleus (By similarity)				179
Q93454 UniProt NPD GO	NPP17_CAEEL	Nucleoporin-17 (Nuclear pore complex protein 17) (CeRAE1)	0.06	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex				373
P81648 UniProt NPD GO	OBP2_HYSCR	Odorant-binding protein 2 (Odorant-binding protein II) (OBP II) (Olfactory mucosa pyrazine-binding p ...	0.06	-	nuc	0	Secreted protein; extracellular space				38
Q07081 UniProt NPD GO	OLFM_RANCA	Olfactomedin precursor (Olfactory mucus protein)	0.06	-	mit	0	Secreted protein; extracellular space				464
P23265 UniProt NPD GO	O1078_RAT	Olfactory receptor 1078 (Olfactory receptor-like protein F3)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				333
Q8NGN3 UniProt NPD GO	O10G4_HUMAN	Olfactory receptor 10G4 (Olfactory receptor OR11-278)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				311
Q8NGX6 UniProt NPD GO	O10R2_HUMAN	Olfactory receptor 10R2	0.06	-	end	7 *	Membrane; multi-pass membrane protein				324
Q8NGC9 UniProt NPD GO	O11H4_HUMAN	Olfactory receptor 11H4 (Olfactory receptor OR14-36)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				324
P23266 UniProt NPD GO	O1361_RAT	Olfactory receptor 1361 (Olfactory receptor-like protein F5)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				313
Q8NGS5 UniProt NPD GO	O13C4_HUMAN	Olfactory receptor 13C4	0.06	-	end	7 *	Membrane; multi-pass membrane protein				318
Q8NGS8 UniProt NPD GO	O13C5_HUMAN	Olfactory receptor 13C5	0.06	-	end	7 *	Membrane; multi-pass membrane protein				318
Q8NGT2 UniProt NPD GO	O13J1_HUMAN	Olfactory receptor 13J1	0.06	-	end	7 *	Membrane; multi-pass membrane protein				312
Q60878 UniProt NPD GO	OL140_MOUSE	Olfactory receptor 140 (Olfactory receptor 4A) (Olfactory receptor 235-1) (Odorant receptor A16)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				302
P23269 UniProt NPD GO	O1496_RAT	Olfactory receptor 1496 (Olfactory receptor-like protein I3)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				310
P30953 UniProt NPD GO	OR1E1_HUMAN	Olfactory receptor 1E1 (Olfactory receptor-like protein HGMP07I) (Olfactory receptor 17-2/17-32) (OR ...	0.06	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			314
Q8NHA8 UniProt NPD GO	OR1FC_HUMAN	Olfactory receptor 1F12 (Hs6M1-35P)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				337
Q8NGS2 UniProt NPD GO	OR1J2_HUMAN	Olfactory receptor 1J2 (OST044) (HSA5) (HTPCRX15) (Olfactory receptor OR9-19)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				313
Q8NHA4 UniProt NPD GO	O2AE1_HUMAN	Olfactory receptor 2AE1	0.06	-	end	7 *	Membrane; multi-pass membrane protein				323
Q9H205 UniProt NPD GO	O2AG1_HUMAN	Olfactory receptor 2AG1 (HT3)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				316
Q8NG84 UniProt NPD GO	O2AK2_HUMAN	Olfactory receptor 2AK2 (Olfactory receptor OR1-47)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				320
Q9H210 UniProt NPD GO	OR2D2_HUMAN	Olfactory receptor 2D2 (Olfactory receptor 11-610) (OR11-610) (HB2) (Olfactory receptor OR11-88)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	608494		308
Q8NHC8 UniProt NPD GO	OR2T6_HUMAN	Olfactory receptor 2T6 (OST703)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				309
Q8NGV0 UniProt NPD GO	OR2Y1_HUMAN	Olfactory receptor 2Y1 (Olfactory receptor OR5-2)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				311
Q8VF66 UniProt NPD GO	OL469_MOUSE	Olfactory receptor 469 (Olfactory receptor 204-21)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8VF65 UniProt NPD GO	OL470_MOUSE	Olfactory receptor 470 (Olfactory receptor 204-22)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NH70 UniProt NPD GO	O4A16_HUMAN	Olfactory receptor 4A16 (Olfactory receptor OR11-117)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				328
Q8NH41 UniProt NPD GO	OR4KF_HUMAN	Olfactory receptor 4K15	0.06	-	end	7 *	Membrane; multi-pass membrane protein				324
Q8NH73 UniProt NPD GO	OR4S2_HUMAN	Olfactory receptor 4S2	0.06	-	end	7 *	Membrane; multi-pass membrane protein				311
Q8NGL1 UniProt NPD GO	OR5DI_HUMAN	Olfactory receptor 5D18	0.06	-	end	7 *	Membrane; multi-pass membrane protein				313
Q8NGA2 UniProt NPD GO	OR7A2_HUMAN	Olfactory receptor 7A2	0.06	-	end	7 *	Membrane; multi-pass membrane protein				310
Q8NH50 UniProt NPD GO	OR8K5_HUMAN	Olfactory receptor 8K5	0.06	-	end	6 *	Membrane; multi-pass membrane protein				307
Q8NGT5 UniProt NPD GO	OR9A2_HUMAN	Olfactory receptor 9A2	0.06	-	end	7 *	Membrane; multi-pass membrane protein				310
Q95156 UniProt NPD GO	OLF3_CANFA	Olfactory receptor-like protein OLF3	0.06	-	end	7 *	Membrane; multi-pass membrane protein				317
P15971 UniProt NPD GO	TOG2A_AGEAP	Omega-agatoxin-2A (Omega-agatoxin IIA) (Omega-Aga-IIA) (Fragment)	0.06	-	nuc	0	Secreted protein				28
Q9H1Y3 UniProt NPD GO	OPN3_HUMAN	Opsin-3 (Encephalopsin) (Panopsin)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606695		402
P83683 UniProt NPD GO	OX26_RANES	Orexigenic neuropeptide 26RFa	0.06	-	cyt	0	Secreted protein				26
Q9Z306 UniProt NPD GO	S22A4_MOUSE	Organic cation/carnitine transporter 1 (Solute carrier family 22 member 4)	0.06	-	end	11 *	Membrane; multi-pass membrane protein	mitochondrion [IDA]			553
Q9R141 UniProt NPD GO	S22A4_RAT	Organic cation/carnitine transporter 1 (Solute carrier family 22 member 4)	0.06	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				553
Q9Z0E8 UniProt NPD GO	S22A5_MOUSE	Organic cation/carnitine transporter 2 (Solute carrier family 22 member 5) (High-affinity sodium-dep ...	0.06	-	end	11 *	Cell membrane; apical cell membrane; multi-pass membrane protein. Colocalizes with PDZK1 on apical m ...				557
Q7RT90 UniProt NPD GO	OAT_PLAYO	Ornithine aminotransferase (EC 2.6.1.13) (Ornithine--oxo-acid aminotransferase)	0.06	-	cyt	0	Cytoplasm (Probable)			1Z7D	414

You are viewing entries 72651 to 72700 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.