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
P70697 UniProt NPD GO	DCUP_MOUSE	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD)	0.13	-	mit	0	Cytoplasm				367
P10746 UniProt NPD GO	HEM4_HUMAN	Uroporphyrinogen-III synthase (EC 4.2.1.75) (UROS) (Uroporphyrinogen-III cosynthetase) (Hydroxymethy ...	0.13	-	nuc	0			263700	1JR2	265
Q43432 UniProt NPD GO	VATB1_GOSHI	Vacuolar ATP synthase subunit B isoform 1 (EC 3.6.3.14) (V-ATPase B subunit 1) (Vacuolar proton pump ...	0.13	-	cyt	0					488
Q5R5V5 UniProt NPD GO	VATB2_PONPY	Vacuolar ATP synthase subunit B, brain isoform (EC 3.6.3.14) (V-ATPase B2 subunit) (Vacuolar proton ...	0.13	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Endomembrane (By similarity)				511
Q08743 UniProt NPD GO	YO292_YEAST	Vacuolar membrane protein YOR292C	0.13	-	nuc	5	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			309
O75436 UniProt NPD GO	VP26A_HUMAN	Vacuolar protein sorting 26A (Vesicle protein sorting 26A) (hVPS26)	0.13	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein	cytosol [IDA]	605506	2FAU	327
O22925 UniProt NPD GO	VSR2_ARATH	Vacuolar sorting receptor 2 precursor (AtVSR2) (Epidermal growth factor receptor-like protein 4) (At ...	0.13	-	end	2 *					625
P49042 UniProt NPD GO	VPE_RICCO	Vacuolar-processing enzyme precursor (EC 3.4.22.-) (VPE)	0.13	-	exc	1 *					497
Q8R164 UniProt NPD GO	BPHL_MOUSE	Valacyclovir hydrolase precursor (EC 3.1.-.-) (VACVase) (Biphenyl hydrolase-like protein)	0.13	-	mit	0	Cytoplasm (By similarity)	mitochondrion [IDA]			291
P20950 UniProt NPD GO	VSG2_TRYEQ	Variant surface glycoprotein 20 precursor (VSG-20)	0.13	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				457
Q6J936 UniProt NPD GO	TXVE_BOTER	Vascular endothelial growth factor toxin precursor (svVEGF)	0.13	-	end	1 *	Secreted protein				146
Q90X23 UniProt NPD GO	TXVE_BOTJA	Vascular endothelial growth factor toxin precursor (svVEGF)	0.13	-	end	1 *	Secreted protein				146
P14326 UniProt NPD GO	VSH5_DICDI	Vegetative-specific protein H5	0.13	-	nuc	0					316
P35776 UniProt NPD GO	VA2_SOLRI	Venom allergen 2 (Venom allergen II) (Allergen Sol r 2) (Sol r II)	0.13	-	nuc	0					119
P35785 UniProt NPD GO	VA5_VESPE	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Ves p 5) (Ves p V)	0.13	-	nuc	0	Secreted protein. Venom reservoirs				204
P00992 UniProt NPD GO	IVBI3_VIPAA	Venom basic protease inhibitor 3 (Venom chymotrypsin inhibitor)	0.13	-	nuc	0	Secreted protein				65
O94499 UniProt NPD GO	YBS9_SCHPO	Very hypothetical protein C18E5.09c in chromosome II	0.13	-	mit	0					128
Q9Y7S3 UniProt NPD GO	YQO4_SCHPO	Very hypothetical protein C569.04 in chromosome III	0.13	-	cyt	0					121
Q10263 UniProt NPD GO	YD2F_SCHPO	Very hypothetical protein C56F8.15 in chromosome I	0.13	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				176
P38317 UniProt NPD GO	YB69_YEAST	Very hypothetical protein YBR219C	0.13	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				127
P48818 UniProt NPD GO	ACADV_BOVIN	Very-long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.-) (VLCAD)	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane				655
O95183 UniProt NPD GO	VAMP5_HUMAN	Vesicle-associated membrane protein 5 (VAMP-5) (Myobrevin)	0.13	-	mit	1	Cell membrane; single-pass type IV membrane protein (Probable). Intracellular membrane; single-pass ...	plasma membrane [TAS]	607029		116
Q06432 UniProt NPD GO	CCG1_HUMAN	Voltage-dependent calcium channel gamma-1 subunit (Dihydropyridine-sensitive L-type, skeletal muscle ...	0.13	-	end	4 *	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	114209		222
Q8VHW4 UniProt NPD GO	CCG5_MOUSE	Voltage-dependent calcium channel gamma-5 subunit (Neuronal voltage-gated calcium channel gamma-5 su ...	0.13	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				275
Q8VHW8 UniProt NPD GO	CCG5_RAT	Voltage-dependent calcium channel gamma-5 subunit (Neuronal voltage-gated calcium channel gamma-5 su ...	0.13	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				275
Q9BXT2 UniProt NPD GO	CCG6_HUMAN	Voltage-dependent calcium channel gamma-6 subunit (Neuronal voltage-gated calcium channel gamma-6 su ...	0.13	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)	voltage-gated calcium channel complex [NAS]	606898		260
Q8VHW3 UniProt NPD GO	CCG6_MOUSE	Voltage-dependent calcium channel gamma-6 subunit (Neuronal voltage-gated calcium channel gamma-6 su ...	0.13	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				260
O43448 UniProt NPD GO	KCAB3_HUMAN	Voltage-gated potassium channel subunit beta-3 (K(+) channel subunit beta-3) (Kv-beta-3)	0.13	-	cyt	0	Cytoplasm (Potential)		604111		404
Q63494 UniProt NPD GO	KCAB3_RAT	Voltage-gated potassium channel subunit beta-3 (K(+) channel subunit beta-3) (Kv-beta-3) (RCK beta3) ...	0.13	-	cyt	0	Cytoplasm (Potential)				404
Q63751 UniProt NPD GO	VOME_RAT	Vomeromodulin (Fragment)	0.13	-	nuc	0					98
Q8WN92 UniProt NPD GO	VN1R1_GORGO	Vomeronasal type-1 receptor 1 (V1r-like receptor 1)	0.13	-	nuc	6	Membrane; multi-pass membrane protein				353
Q7YRP3 UniProt NPD GO	VN1R3_PANTR	Vomeronasal type-1 receptor 3 (V1r-like receptor 3)	0.13	-	end	3 *	Membrane; multi-pass membrane protein				310
Q7Z5H4 UniProt NPD GO	VN1R5_HUMAN	Vomeronasal type-1 receptor 5 (V1r-like receptor 5) (hGPCR26)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				357
Q9EQ45 UniProt NPD GO	VN1B8_MOUSE	Vomeronasal type-1 receptor B8 (Vomeronasal type-1 receptor A13)	0.13	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				309
Q6DCV0 UniProt NPD GO	WIPI4_XENLA	WD repeat domain phosphoinositide-interacting protein 4 (WIPI-4) (WD repeat protein 45)	0.13	-	cyt	0					355
Q9P2L0 UniProt NPD GO	WDR35_HUMAN	WD repeat protein 35	0.13	-	nuc	0					1181
O76071 UniProt NPD GO	WDR39_HUMAN	WD repeat protein 39 (Ciao 1 protein)	0.13	-	cyt	0	Nucleus		604333		339
Q5BK30 UniProt NPD GO	WDR69_RAT	WD repeat protein 69	0.13	-	cyt	0					415
Q26544 UniProt NPD GO	WS17_SCHMA	WD repeat protein SL1-17	0.13	-	cyt	0					301
Q9CYF5 UniProt NPD GO	WBS16_MOUSE	Williams-Beuren syndrome chromosome region 16 protein homolog	0.13	-	mit	0					461
Q9H6D5 UniProt NPD GO	WBS23_HUMAN	Williams-Beuren syndrome chromosome region 23 protein	0.13	-	cyt	0	Membrane; single-pass membrane protein (Potential)		194050		173
Q9P8K9 UniProt NPD GO	HEX1_EMENI	Woronin body major protein	0.13	-	cyt	0	Peroxisome. Woronin bodies				221
P47165 UniProt NPD GO	XPT1_YEAST	Xanthine phosphoribosyltransferase 1 (EC 2.4.2.-) (XPRT)	0.13	-	cyt	0	Cytoplasm	cytoplasm [IDA]			209
O88939 UniProt NPD GO	ZBT7A_MOUSE	Zinc finger and BTB domain-containing protein 7A (Leukemia/lymphoma-related factor)	0.13	-	cyt	0	Nucleus	nucleus [NAS]			565
P53786 UniProt NPD GO	ZP3_CALSQ	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Zona pellucida p ...	0.13	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				424
P18142 UniProt NPD GO	D2_DICDI	cAMP-regulated D2 protein precursor	0.13	-	end	0	Membrane. Membrane-enclosed crystals (esterosome)				535
Q759Y2 UniProt NPD GO	PALI_ASHGO	pH-response regulator protein palI/RIM9	0.13	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				266
Q32M08 UniProt NPD GO	DUS4L_MOUSE	tRNA-dihydrouridine synthase 4-like (EC 1.-.-.-)	0.13	-	cyt	0					324
Q39522 UniProt NPD GO	SMT_COPJA	(S)-scoulerine 9-O-methyltransferase (EC 2.1.1.117)	0.12	-	cyt	0					381
Q6PBX5 UniProt NPD GO	MTND_BRARE	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.12	-	cyt	0		cytoplasm [ISS] nucleus [ISS] plasma membrane [ISS]			181

You are viewing entries 60651 to 60700 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.