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
Q4ICM0 UniProt NPD GO	NUDF_GIBZE	Nuclear distribution protein PAC1 (nudF homolog)	0.09	-	mit	0	Cytoplasm. Localizes to the plus ends of microtubules and the mitotic spindle poles (By similarity)				464
Q00664 UniProt NPD GO	NUDF_EMENI	Nuclear distribution protein nudF	0.09	-	cyt	0	Cytoplasm. Localizes to the plus ends of microtubules, and this requires clipA and nudE. Localizes t ...				444
O75002 UniProt NPD GO	MOG1_SCHPO	Nuclear import protein mog1	0.09	-	cyt	0	Nucleus	nucleus [IDA]			190
Q62792 UniProt NPD GO	NRF1_RAT	Nuclear respiratory factor 1 (NRF-1) (Alpha palindromic-binding protein) (Alpha-pal) (Fragment)	0.09	-	cyt	0	Nucleus				52
Q9FGP7 UniProt NPD GO	NFYC6_ARATH	Nuclear transcription factor Y subunit C-6 (AtNF-YC-6)	0.09	-	nuc	0	Nucleus (By similarity)				202
Q9FGP8 UniProt NPD GO	NFYC7_ARATH	Nuclear transcription factor Y subunit C-7 (AtNF-YC-7)	0.09	-	nuc	0	Nucleus (By similarity)				212
P87355 UniProt NPD GO	NDKM_COLLI	Nucleoside diphosphate kinase, mitochondrial precursor (EC 2.7.4.6) (NDP kinase, mitochondrial) (NDK ...	0.09	-	mit	0	Mitochondrion; mitochondrial intermembrane space				181
P31381 UniProt NPD GO	FUN26_YEAST	Nucleoside transporter FUN26	0.09	-	end	11	Membrane; multi-pass membrane protein (Potential)	intracellular [IDA] membrane [IDA]			517
Q687E1 UniProt NPD GO	NPP_HORVU	Nucleotide pyrophosphatase/phosphodiesterase (EC 3.-.-.-) (Fragments)	0.09	-	cyt	0	Plastid; chloroplast				368
Q52K88 UniProt NPD GO	NUD13_ARATH	Nudix hydrolase 13, mitochondrial precursor (EC 3.6.1.-) (AtNUDT13)	0.09	-	nuc	0	Mitochondrion (Potential)				202
Q9SJC6 UniProt NPD GO	NUDT5_ARATH	Nudix hydrolase 5 (EC 3.6.1.-) (AtNUDT5)	0.09	-	cyt	0					327
Q8T6Z0 UniProt NPD GO	OBL_OBEGE	Obelin precursor (OBL)	0.09	-	cyt	0					195
Q4LBB6 UniProt NPD GO	OCTB3_DROME	Octopamine receptor beta-3R (DmOct-beta-3R)	0.09	-	vac	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			440
P81912 UniProt NPD GO	OR23A_DROME	Odorant receptor 23a	0.09	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			379
P81915 UniProt NPD GO	OR33B_DROME	Odorant receptor 33b	0.09	-	nuc	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			379
Q9NY56 UniProt NPD GO	OBP2A_HUMAN	Odorant-binding protein 2a precursor (OBPIIa)	0.09	-	cyt	0	Secreted protein (Probable)		164320		170
Q42431 UniProt NPD GO	OLEO4_ARATH	Oleosin 20.3 kDa (Oleosin type 4)	0.09	-	end	2	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface (By similarity)				191
Q8VFL5 UniProt NPD GO	O1030_MOUSE	Olfactory receptor 1030 (Olfactory receptor 196-2)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				318
Q8NHC4 UniProt NPD GO	O10J5_HUMAN	Olfactory receptor 10J5	0.09	-	end	7 *	Membrane; multi-pass membrane protein				309
Q8NGQ4 UniProt NPD GO	O10Q1_HUMAN	Olfactory receptor 10Q1	0.09	-	end	7 *	Membrane; multi-pass membrane protein				319
Q8NGZ3 UniProt NPD GO	O13G1_HUMAN	Olfactory receptor 13G1	0.09	-	end	7 *	Membrane; multi-pass membrane protein				307
Q9QY00 UniProt NPD GO	OL154_MOUSE	Olfactory receptor 154 (Olfactory receptor 175-1)	0.09	-	end	6 *	Membrane; multi-pass membrane protein				318
Q9JHB2 UniProt NPD GO	OLF19_MOUSE	Olfactory receptor 19 (Olfactory receptor 140-1) (Odorant receptor M12)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				309
Q8NG77 UniProt NPD GO	O2T12_HUMAN	Olfactory receptor 2T12 (Olfactory receptor OR1-57)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				320
Q8NGL6 UniProt NPD GO	O4A15_HUMAN	Olfactory receptor 4A15 (Olfactory receptor OR11-118)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NGJ1 UniProt NPD GO	OR4D6_HUMAN	Olfactory receptor 4D6 (Olfactory receptor OR11-250)	0.09	-	end	6 *	Membrane; multi-pass membrane protein				314
Q8NGB9 UniProt NPD GO	OR4F6_HUMAN	Olfactory receptor 4F6	0.09	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8TCB6 UniProt NPD GO	O51E1_HUMAN	Olfactory receptor 51E1	0.09	-	end	7 *	Membrane; multi-pass membrane protein				317
Q8NGK2 UniProt NPD GO	O52B4_HUMAN	Olfactory receptor 52B4 (Olfactory receptor OR11-3)	0.09	-	end	5 *	Membrane; multi-pass membrane protein				314
Q8N127 UniProt NPD GO	O5AS1_HUMAN	Olfactory receptor 5AS1	0.09	-	end	7 *	Membrane; multi-pass membrane protein				324
Q8NGC5 UniProt NPD GO	OR6J1_HUMAN	Olfactory receptor 6J1	0.09	-	end	7 *	Membrane; multi-pass membrane protein				347
Q8NGU2 UniProt NPD GO	OR9A4_HUMAN	Olfactory receptor 9A4	0.09	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NGE7 UniProt NPD GO	OR9K2_HUMAN	Olfactory receptor 9K2	0.09	-	end	5 *	Membrane; multi-pass membrane protein				313
P30955 UniProt NPD GO	OLFD_CANFA	Olfactory receptor-like protein DTMT	0.09	-	end	6 *	Membrane; multi-pass membrane protein				313
Q9T095 UniProt NPD GO	OPT6_ARATH	Oligopeptide transporter 6 (AtOPT6)	0.09	-	end	14 *	Membrane; multi-pass membrane protein (Probable)				736
Q9ZVE0 UniProt NPD GO	ORN_ARATH	Oligoribonuclease (EC 3.1.-.-)	0.09	-	cyt	0					222
P46313 UniProt NPD GO	FAD6E_ARATH	Omega-6 fatty acid desaturase, endoplasmic reticulum (EC 1.14.19.-) (Delta-12 desaturase)	0.09	-	mit	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				383
P83580 UniProt NPD GO	TOT1A_ATRRO	Omega-atracotoxin-Ar1a (Omega-AcTx-Ar1a)	0.09	-	nuc	0	Secreted protein	extracellular region [NAS]			37
P17772 UniProt NPD GO	OSS2_PEA	Organ-specific protein S2	0.09	-	exc	0					181
Q9Y226 UniProt NPD GO	ORCT3_HUMAN	Organic-cation transporter-like 3 (Solute carrier family 22 member 13)	0.09	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS] membrane fraction [TAS]	604047		551
P25512 UniProt NPD GO	ORNC_PLAOR	Ornatin-C	0.09	-	nuc	0	Secreted protein				52
P14170 UniProt NPD GO	OSMO_TOBAC	Osmotin precursor	0.09	-	exc	1 *	Vacuolar inclusion bodies			1PCV	246
P50702 UniProt NPD GO	OS81_SOLCO	Osmotin-like protein OSML81 precursor (PA81)	0.09	-	exc	0					247
Q5ZJJ9 UniProt NPD GO	OSTF1_CHICK	Osteoclast-stimulating factor 1	0.09	-	cyt	0	Cytoplasm (By similarity)				202
P32306 UniProt NPD GO	OXYR_PIG	Oxytocin receptor (OT-R)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				386
Q9VTL1 UniProt NPD GO	PCID_DROME	PCI domain-containing protein (CSN12-like protein)	0.09	-	nuc	0					395
Q5E9E1 UniProt NPD GO	PDLI1_BOVIN	PDZ and LIM domain protein 1 (Elfin)	0.09	-	nuc	0	Cytoplasm (By similarity). Associates with the actin stress fibers (By similarity)				327
Q86UT5 UniProt NPD GO	PDZD3_HUMAN	PDZ domain-containing protein 3 (PDZ domain-containing protein 2) (Intestinal and kidney-enriched PD ...	0.09	-	cyt	0	Cell membrane; peripheral membrane protein. Cytoplasm. Preferentially accumulates at the apical surf ...	apical part of cell [IDA]	607146		571
Q8TF65 UniProt NPD GO	GIPC2_HUMAN	PDZ domain-containing protein GIPC2	0.09	-	cyt	0	Cytoplasm (Probable)				315
Q8R5M0 UniProt NPD GO	GIPC3_MOUSE	PDZ domain-containing protein GIPC3 (Regulator of G-protein signaling 19-interacting protein 3)	0.09	-	cyt	0					297

You are viewing entries 66651 to 66700 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.