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
P81272 UniProt NPD GO	NOS2B_HUMAN	Nitric-oxide synthase IIB (EC 1.14.13.39) (NOS type II B) (NOSIIb) (Fragments)	0.01	-	mit	1 *			600719		79
Q26239 UniProt NPD GO	NP1_RHOPR	Nitrophorin-1 precursor (NP1)	0.01	-	mit	1 *	Secreted protein			4NP1	207
P26415 UniProt NPD GO	NO14_PEA	Nodulin 14 precursor (N-14) (Fragment)	0.01	-	exc	1 *					61
P82598 UniProt NPD GO	NGIF_RAT	Non-arginase growth inhibitory factor (NAGIF) (Fragment)	0.01	-		0					8
Q42831 UniProt NPD GO	HBL_HORVU	Non-symbiotic hemoglobin (HORvu GLB1) (Nonlegume hemoglobin)	0.01	-	cyt	0					162
Q9FVL0 UniProt NPD GO	HBL1_MEDSA	Non-symbiotic hemoglobin 1 (MEDsa GLB1)	0.01	-	cyt	0	Nucleus; nucleoplasm; nuclear matrix. Cytoplasm. But not in the nucleolus, and to a lower extent, cy ...				160
Q941Q2 UniProt NPD GO	HBL2_BRANA	Non-symbiotic hemoglobin 2 (Hb2) (BRAna GLB2)	0.01	-	cyt	0					161
Q43766 UniProt NPD GO	NLTP3_HORVU	Nonspecific lipid-transfer protein 3 precursor (LTP 3) (CW20) (CW-20) (CW-19)	0.01	-	exc	1 *					118
P82007 UniProt NPD GO	NLTP1_HELAN	Nonspecific lipid-transfer protein AP10 (LTP) (NsLTP) (HA-AP10) (Fragment)	0.01	-		0	Secreted protein; extracellular space				20
P80275 UniProt NPD GO	NLTP1_VITSX	Nonspecific lipid-transfer protein P1 (LTP P1) (Fragment)	0.01	-	nuc	0					38
P33556 UniProt NPD GO	NLTP2_VITSX	Nonspecific lipid-transfer protein P2 (LTP P2) (Fragment)	0.01	-	nuc	0					38
Q9M5X6 UniProt NPD GO	NLTP_PYRCO	Nonspecific lipid-transfer protein precursor (LTP) (Allergen Pyr c 3)	0.01	-	exc	1 *					115
P10976 UniProt NPD GO	NLTP_SPIOL	Nonspecific lipid-transfer protein precursor (LTP) (Phospholipid transfer protein) (PLTP)	0.01	-	exc	1 *					117
P81203 UniProt NPD GO	NUC1_CUNEE	Nuclease C1 (EC 3.1.30.-)	0.01	-	nuc	0	Secreted protein				252
Q96559 UniProt NPD GO	NDK_HELAN	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.01	-	cyt	0					148
P49740 UniProt NPD GO	NDK_SCHPO	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.01	-	cyt	0		cytosol [IDA] mitochondrial intermembrane space [IDA]			151
Q6XI71 UniProt NPD GO	NDKA_DROYA	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase) (Abnormal wing disks protein) (Fragmen ...	0.01	-	cyt	0		nuclear microtubule [ISS]			150
P08879 UniProt NPD GO	NDKA_DROME	Nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase) (Abnormal wing disks protein) (Killer ...	0.01	-	cyt	0	Cytoplasm. Microtubule-associated	nuclear microtubule [IMP]		1NSQ	152
Q07661 UniProt NPD GO	NDK1_ORYSA	Nucleoside diphosphate kinase 1 (EC 2.7.4.6) (Nucleoside diphosphate kinase I) (NDK I) (NDP kinase I ...	0.01	-	cyt	0				1PKU	149
Q02254 UniProt NPD GO	NDK1_SPIOL	Nucleoside diphosphate kinase 1 (EC 2.7.4.6) (Nucleoside diphosphate kinase I) (NDK I) (NDP kinase I ...	0.01	-	cyt	0					148
P93554 UniProt NPD GO	NDK1_SACOF	Nucleoside diphosphate kinase 1 (EC 2.7.4.6) (Nucleoside diphosphate kinase I) (NDK I) (NDP kinase I ...	0.01	-	cyt	0					149
P13420 UniProt NPD GO	NUDT6_XENLA	Nucleoside diphosphate-linked moiety X motif 6 (Nudix motif 6) (Protein GFG)	0.01	-	cyt	0					217
Q9Y5Y2 UniProt NPD GO	NUBP2_HUMAN	Nucleotide-binding protein 2 (NBP 2)	0.01	-	cyt	0					271
Q9VP04 UniProt NPD GO	ORMDL_DROME	ORM1-like protein (dORMDL)	0.01	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]			154
Q8JFB7 UniProt NPD GO	ORML1_BRARE	ORM1-like protein 1	0.01	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q5ZIU0 UniProt NPD GO	ORML2_CHICK	ORM1-like protein 2	0.01	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q5XJR6 UniProt NPD GO	ORML3_BRARE	ORM1-like protein 3	0.01	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
Q9CPZ6 UniProt NPD GO	ORML3_MOUSE	ORM1-like protein 3	0.01	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				153
P35361 UniProt NPD GO	OPSO_LIMPO	Ocellar opsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				376
P14803 UniProt NPD GO	OAR_PHOPY	Octopamine receptor (Octopamine-binding protein) (Fragment)	0.01	-		0	Membrane; multi-pass membrane protein				20
P81916 UniProt NPD GO	OR33C_DROME	Odorant receptor 33c	0.01	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			384
P81245 UniProt NPD GO	OBP_PIG	Odorant-binding protein (OBP)	0.01	-	cyt	0	Secreted protein			1HQP	157
P07435 UniProt NPD GO	OBP_BOVIN	Odorant-binding protein (OBP) (Olfactory mucosa pyrazine-binding protein)	0.01	-	cyt	0	Secreted protein			1PBO	159
P20005 UniProt NPD GO	VSP1_TRIOK	Okinaxobin-1 (EC 3.4.21.-) (Okinaxobin I) (Fragment)	0.01	-		0	Secreted protein				20
O95223 UniProt NPD GO	O10A1_HUMAN	Olfactory receptor 10A1 (Olfactory receptor 11-403) (OR11-403) (Fragment)	0.01	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	608493		227
Q8NGE0 UniProt NPD GO	O10AD_HUMAN	Olfactory receptor 10AD1	0.01	-	end	7 *	Membrane; multi-pass membrane protein				317
Q8NH81 UniProt NPD GO	O10G6_HUMAN	Olfactory receptor 10G6 (Olfactory receptor OR11-280)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				332
Q8NGN4 UniProt NPD GO	O10G9_HUMAN	Olfactory receptor 10G9	0.01	-	end	7 *	Membrane; multi-pass membrane protein				311
Q9Y4A9 UniProt NPD GO	O10H1_HUMAN	Olfactory receptor 10H1	0.01	-	end	7 *	Membrane; multi-pass membrane protein				318
Q8NGA5 UniProt NPD GO	O10H4_HUMAN	Olfactory receptor 10H4	0.01	-	end	7 *	Membrane; multi-pass membrane protein				316
Q8NGX3 UniProt NPD GO	O10T2_HUMAN	Olfactory receptor 10T2 (Olfactory receptor OR1-3)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NGF6 UniProt NPD GO	O10W1_HUMAN	Olfactory receptor 10W1 (Olfactory receptor OR11-236)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				305
Q8NG94 UniProt NPD GO	O11H1_HUMAN	Olfactory receptor 11H1 (Olfactory receptor 22-1) (OR22-1)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				315
Q8NGC7 UniProt NPD GO	O11H6_HUMAN	Olfactory receptor 11H6 (Olfactory receptor OR14-35)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				330
P58182 UniProt NPD GO	O12D2_HUMAN	Olfactory receptor 12D2 (Hs6M1-20)	0.01	-	vac	7 *	Membrane; multi-pass membrane protein				307
Q9UGF7 UniProt NPD GO	O12D3_HUMAN	Olfactory receptor 12D3 (Hs6M1-27)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				316
Q60882 UniProt NPD GO	OL145_MOUSE	Olfactory receptor 145 (Olfactory receptor 7C) (Olfactory receptor 161-6) (Odorant receptor K21)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				310
Q60888 UniProt NPD GO	OL149_MOUSE	Olfactory receptor 149 (Olfactory receptor 7G) (Olfactory receptor 224-8) (Odorant receptor M31)	0.01	-	end	6 *	Membrane; multi-pass membrane protein				311
Q9TUA7 UniProt NPD GO	OR1A1_PANTR	Olfactory receptor 1A1	0.01	-	end	7 *	Membrane; multi-pass membrane protein				309
Q9P1Q5 UniProt NPD GO	OR1A1_HUMAN	Olfactory receptor 1A1 (Olfactory receptor 17-7) (OR17-7) (Olfactory receptor OR17-11)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			309

You are viewing entries 89951 to 90000 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.