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
O14468 UniProt NPD GO	YO304_YEAST	Uncharacterized protein YOR304C-A	0.21	-	nuc	0	Cytoplasm. Bud. Bud neck	bud neck [IDA] cytoplasm [IDA]			76
Q3E806 UniProt NPD GO	YO316_YEAST	Uncharacterized protein YOR316C-A	0.21	-	mit	0					69
Q3E752 UniProt NPD GO	YP036_YEAST	Uncharacterized protein YPR036W-A	0.21	-	nuc	0					67
O13465 UniProt NPD GO	UREA_CRYNV	Urease (EC 3.5.1.5) (Urea amidohydrolase)	0.21	-	nuc	0					832
P16708 UniProt NPD GO	UFAP_PIG	Uteroferrin-associated protein precursor (UFAP)	0.21	-	mit	0	Secreted protein; extracellular space				417
Q5RCF0 UniProt NPD GO	LMA2L_PONPY	VIP36-like protein precursor (Lectin, mannose-binding 2-like) (LMAN2-like protein)	0.21	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				348
O82629 UniProt NPD GO	VATG2_ARATH	Vacuolar ATP synthase subunit G 2 (EC 3.6.3.14) (V-ATPase G subunit 2) (Vacuolar proton pump G subun ...	0.21	-	nuc	0					106
Q6NWF4 UniProt NPD GO	VPS25_BRARE	Vacuolar protein sorting protein 25	0.21	-	cyt	0	Cytoplasm (By similarity)				174
Q93050 UniProt NPD GO	VPP1_HUMAN	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1 (V-ATPase 116 kDa isoform a1) (Clat ...	0.21	-	end	7	Integral membrane protein. Coated vesicle		192130		837
Q9Z1G4 UniProt NPD GO	VPP1_MOUSE	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1 (V-ATPase 116 kDa isoform a1) (Clat ...	0.21	-	end	6	Integral membrane protein. Coated vesicle	cytoplasm [IDA] nucleus [ISS] transcription factor complex [ISS]			839
Q00788 UniProt NPD GO	V2R_RAT	Vasopressin V2 receptor (Renal-type arginine vasopressin receptor) (Antidiuretic hormone receptor) ( ...	0.21	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			371
P01184 UniProt NPD GO	NEU2_BALPH	Vasopressin-neurophysin 2 precursor [Contains: Arg-vasopressin; Neurophysin 2] (Fragment)	0.21	-	nuc	0	Secreted protein				107
P30431 UniProt NPD GO	DISJ_BOTJA	Venom metalloproteinase jararhagin precursor (EC 3.4.24.73) (HF2-proteinase) [Contains: Disintegrin ...	0.21	-	nuc	0				1C9G	571
Q9C110 UniProt NPD GO	YKIF_SCHPO	Very hypothetical protein C630.15 in chromosome I	0.21	-	mit	0					105
P53342 UniProt NPD GO	YG64_YEAST	Very hypothetical protein YGR293C	0.21	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				153
P47193 UniProt NPD GO	VAMP2_XENLA	Vesicle-associated membrane protein 2 (VAMP-2) (Synaptobrevin-2) (SYBII)	0.21	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...				113
Q15836 UniProt NPD GO	VAMP3_HUMAN	Vesicle-associated membrane protein 3 (VAMP-3) (Synaptobrevin-3) (Cellubrevin) (CEB)	0.21	-	nuc	1	Membrane; single-pass type IV membrane protein (Probable)	integral to membrane [TAS]	603657		99
Q16943 UniProt NPD GO	VP33_APLCA	Vesicle-associated membrane protein/synaptobrevin-binding protein (VAP-33)	0.21	-	cyt	1	Membrane; single-pass type IV membrane protein (Potential)				260
Q874L4 UniProt NPD GO	TPN1_SACPS	Vitamin B6 transporter TPN1 (Transport of pyridoxine protein 1)	0.21	-	end	10	Membrane; multi-pass membrane protein (Potential)				579
O35505 UniProt NPD GO	CAC1C_CAVPO	Voltage-dependent L-type calcium channel subunit alpha-1C (Voltage-gated calcium channel subunit alp ...	0.21	-	mit	1	Membrane; multi-pass membrane protein				169
Q9WUF1 UniProt NPD GO	VN1B2_MOUSE	Vomeronasal type-1 receptor B2 (Vomeronasal receptor VRi2)	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q9EQ47 UniProt NPD GO	VN1B4_MOUSE	Vomeronasal type-1 receptor B4 (Vomeronasal type-1 receptor A10) (Vomeronasal type-1 receptor B11)	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q9EQ46 UniProt NPD GO	VN1B7_MOUSE	Vomeronasal type-1 receptor B7 (Vomeronasal type-1 receptor A11)	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q5J3M9 UniProt NPD GO	VN1B9_RAT	Vomeronasal type-1 receptor B9 (Vomeronasal type-1 receptor B12) (Vomeronasal receptor 5) (Pheromone ...	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q96P53 UniProt NPD GO	WDFY2_HUMAN	WD repeat and FYVE domain-containing protein 2 (WD40- and FYVE domain-containing protein 2) (Zinc fi ...	0.21	-	cyt	0					400
Q80W47 UniProt NPD GO	WIPI2_MOUSE	WD repeat domain phosphoinositide-interacting protein 2 (WIPI-2)	0.21	-	nuc	0					445
Q5U4F6 UniProt NPD GO	WDR34_MOUSE	WD repeat protein 34	0.21	+	mit	0					535
O42255 UniProt NPD GO	TXW5_NAJSP	Weak neurotoxin 5 precursor (Wntx-5)	0.21	-	nuc	1 *	Secreted protein				86
P29180 UniProt NPD GO	TXW6_NAJNA	Weak neurotoxin 6	0.21	-	nuc	0	Secreted protein			1LN9	65
O42256 UniProt NPD GO	TXW6_NAJSP	Weak neurotoxin 6 precursor (Wntx-6)	0.21	-	nuc	1 *	Secreted protein				86
Q802B3 UniProt NPD GO	TXW8_NAJSP	Weak neurotoxin 8 precursor (Wntx-8)	0.21	-	nuc	1 *	Secreted protein				86
Q9W7I3 UniProt NPD GO	TXW9_NAJSP	Weak neurotoxin 9 precursor (Wntx-9)	0.21	-	nuc	1 *	Secreted protein				86
O76024 UniProt NPD GO	WFS1_HUMAN	Wolframin	0.21	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to membrane [TAS] membrane fraction [TAS]	606201		890
Q49LS8 UniProt NPD GO	XKR6_TETNG	XK-related protein 6	0.21	-	end	6	Membrane; multi-pass membrane protein (Potential)				578
Q03938 UniProt NPD GO	ZNF90_HUMAN	Zinc finger protein 90 (Zinc finger protein HTF9) (Fragment)	0.21	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	603973		195
P34482 UniProt NPD GO	ZIF1_CAEEL	Zinc finger-interacting factor 1 (Protein zif-1)	0.21	-	cyt	0					489
Q80VX4 UniProt NPD GO	ZHX2_RAT	Zinc fingers and homeoboxes protein 2 (Zinc finger and homeodomain protein 2) (Alpha-fetoprotein reg ...	0.21	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			164
Q21181 UniProt NPD GO	NAS19_CAEEL	Zinc metalloproteinase nas-19 precursor (EC 3.4.24.21) (Nematode astacin 19)	0.21	-	mit	1 *	Secreted protein (Potential)				479
Q9U3S9 UniProt NPD GO	NAS6_CAEEL	Zinc metalloproteinase nas-6 precursor (EC 3.4.24.21) (Nematode astacin 6)	0.21	-	mit	0	Secreted protein (Potential)				344
P47984 UniProt NPD GO	ZP2_FELCA	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.21	-	end	2 *	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				716
Q6AWN0 UniProt NPD GO	MTND_DROME	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.20	-	cyt	0		cytoplasm [ISS] nucleus [ISS] plasma membrane [ISS]			186
Q99JT9 UniProt NPD GO	MTND_MOUSE	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.20	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Nucleus (By similarity ...	cytoplasm [ISS] nucleus [ISS] plasma membrane [ISS]		1VR3	179
Q6DIY2 UniProt NPD GO	MTND_XENTR	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.20	-	cyt	0		cytoplasm [ISS] nucleus [ISS] plasma membrane [ISS]			179
Q9SAR0 UniProt NPD GO	1A16_ARATH	1-aminocyclopropane-1-carboxylate synthase 6 (EC 4.4.1.14) (ACC synthase 6) (S-adenosyl-L-methionine ...	0.20	-	cyt	0					495
Q91896 UniProt NPD GO	1433Z_XENLA	14-3-3 protein zeta	0.20	-	nuc	0	Cytoplasm				245
Q9SP07 UniProt NPD GO	1433_LILLO	14-3-3-like protein	0.20	-	cyt	0					259
P54190 UniProt NPD GO	TES26_TOXCA	26 kDa secreted antigen precursor (Toxocara excretory-secretory antigen 26) (TES-26)	0.20	-	exc	0	Secreted protein				262
Q16401 UniProt NPD GO	PSD5_HUMAN	26S proteasome non-ATPase regulatory subunit 5 (26S proteasome subunit S5B) (26S protease subunit S5 ...	0.20	-	cyt	0		proteasome complex (sensu Eukaryota) [TAS]	604452		503
Q5IFJ8 UniProt NPD GO	PSD5_MACFA	26S proteasome non-ATPase regulatory subunit 5 (26S proteasome subunit S5B) (26S protease subunit S5 ...	0.20	-	cyt	0					503
P36599 UniProt NPD GO	PDE1_SCHPO	3',5'-cyclic-nucleotide phosphodiesterase (EC 3.1.4.17) (PDEase)	0.20	-	cyt	0					346

You are viewing entries 50201 to 50250 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.