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
Q8CBR6 UniProt NPD GO	TSK_MOUSE	Tsukushi precursor (Leucine-rich repeat-containing protein 54)	0.28	-	nuc	0	Secreted protein (Potential)				354
Q6QMY6 UniProt NPD GO	TSK_RAT	Tsukushi precursor (Leucine-rich repeat-containing protein 54) (Early insulin-induced hepatic gene p ...	0.28	-	exc	0	Secreted protein (Potential)				353
P12460 UniProt NPD GO	TBB2_SOYBN	Tubulin beta-2 chain (Beta-2 tubulin)	0.28	-	cyt	0					449
P38584 UniProt NPD GO	TTL_BOVIN	Tubulin--tyrosine ligase (EC 6.3.2.25) (TTL)	0.28	-	cyt	0					377
P48427 UniProt NPD GO	TBCA_BOVIN	Tubulin-specific chaperone A (Tubulin-folding cofactor A) (CFA) (TCP1-chaperonin cofactor A)	0.28	-	nuc	0					107
O35235 UniProt NPD GO	TNF11_MOUSE	Tumor necrosis factor ligand superfamily member 11 (Receptor activator of nuclear factor kappa B lig ...	0.28	-	mit	1 *	Isoform 1, isoform 2: Cell membrane; single-pass type II membrane protein. Processed isoform 1, proc ...			1S55	316
Q9I8F4 UniProt NPD GO	TPD53_CHICK	Tumor protein D53 homolog (Tumor protein D52-like 1)	0.28	-	nuc	0		cytoplasm [ISS] early endosome [IDA] perinuclear region [ISS]			210
Q7ZXP0 UniProt NPD GO	TWF2A_XENLA	Twinfilin-2-A	0.28	-	cyt	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Perinuclear and G-actin-ri ...				349
P78324 UniProt NPD GO	SHPS1_HUMAN	Tyrosine-protein phosphatase non-receptor type substrate 1 precursor (SHP substrate 1) (SHPS-1) (Inh ...	0.28	-	exc	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	602461		503
P57784 UniProt NPD GO	RU2A_MOUSE	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.28	-	nuc	0	Nucleus (By similarity)				255
Q9CQI7 UniProt NPD GO	RU2B_MOUSE	U2 small nuclear ribonucleoprotein B''	0.28	-	nuc	0	Nucleus (By similarity)				225
Q06406 UniProt NPD GO	LSM6_YEAST	U6 snRNA-associated Sm-like protein LSm6	0.28	-	nuc	0	Nucleus	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI] snRNP U6 [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			123
Q9V968 UniProt NPD GO	U195B_DROME	UPF0195 protein CG30152	0.28	-	nuc	0					218
Q9GP40 UniProt NPD GO	UCR6_ECHMU	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2)	0.28	-	cyt	0	Mitochondrion; mitochondrial inner membrane				130
P43264 UniProt NPD GO	UQCR1_EUGGR	Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor (EC 1.10.2.2)	0.28	-	cyt	0	Mitochondrion; mitochondrial inner membrane				494
Q920M9 UniProt NPD GO	SIAH1_RAT	Ubiquitin ligase SIAH1 (EC 6.3.2.-) (Seven in absentia homolog 1) (Siah-1) (Siah-1a)	0.28	-	mit	0	Cytoplasm. Predominantly. Nucleus. Partially				282
P61092 UniProt NPD GO	SIA1A_MOUSE	Ubiquitin ligase SIAH1A (EC 6.3.2.-) (Seven in absentia homolog 1a) (Siah1a) (Siah-1a) (mSiah-1a)	0.28	-	mit	0	Cytoplasm. Predominantly. Nucleus. Partially			1K2F	282
P29304 UniProt NPD GO	SINA_DROVI	Ubiquitin ligase sina (EC 6.3.2.-) (Seven in absentia protein)	0.28	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [ISS]			314
Q8I147 UniProt NPD GO	SINA_DROWI	Ubiquitin ligase sina (EC 6.3.2.-) (Seven in absentia protein)	0.28	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [ISS]			331
P43102 UniProt NPD GO	UBC4_CANAL	Ubiquitin-conjugating enzyme E2 4 (EC 6.3.2.19) (Ubiquitin-protein ligase 4) (Ubiquitin carrier prot ...	0.28	-	nuc	0					147
Q13432 UniProt NPD GO	UN119_HUMAN	Unc-119 protein homolog (Retinal protein 4) (HRG4)	0.28	-	nuc	0		cytosol [TAS] soluble fraction [TAS]	604011		240
Q9NUR3 UniProt NPD GO	CT046_HUMAN	Uncharacterized protein C20orf46	0.28	-	end	2	Membrane; multi-pass membrane protein (Potential)				256
P39996 UniProt NPD GO	YEB7_YEAST	Uncharacterized protein YEL017W	0.28	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				337
Q3E838 UniProt NPD GO	YF012_YEAST	Uncharacterized protein YFR012W-A	0.28	-	nuc	0					28
P53136 UniProt NPD GO	YGL1_YEAST	Uncharacterized protein YGL111W	0.28	-	mit	0		nucleolus [IDA] nucleus [IDA]			463
Q8TGK1 UniProt NPD GO	YH21B_YEAST	Uncharacterized protein YHR213W-B	0.28	-	nuc	0					99
P25040 UniProt NPD GO	YO022_YEAST	Uncharacterized protein YOL022C	0.28	-	nuc	0		cytoplasm [IDA]			408
Q08219 UniProt NPD GO	YO048_YEAST	Uncharacterized protein YOL048C	0.28	-	end	5	Membrane; multi-pass membrane protein (Potential). Lipid particle	lipid particle [IDA]			342
Q12239 UniProt NPD GO	YO107_YEAST	Uncharacterized protein YOL107W	0.28	-	end	2 *	Golgi apparatus; Golgi apparatus membrane; multi-pass membrane protein (Potential)	Golgi apparatus [IDA]			342
Q3E804 UniProt NPD GO	YO381_YEAST	Uncharacterized protein YOR381W-A	0.28	-	nuc	0					55
P38125 UniProt NPD GO	YB30_YEAST	Uncharacterized transporter YBR180W	0.28	-	end	12	Membrane; multi-pass membrane protein (Probable)	prospore membrane [IDA]			572
Q9GK79 UniProt NPD GO	UPAR_CERAE	Urokinase plasminogen activator surface receptor precursor (uPAR) (U-PAR)	0.28	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				335
Q91X17 UniProt NPD GO	UROM_MOUSE	Uromodulin precursor (Tamm-Horsfall urinary glycoprotein) (THP)	0.28	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Secreted protein (By similarity). Secreted ...				642
P87214 UniProt NPD GO	HEM4_SCHPO	Uroporphyrinogen-III synthase (EC 4.2.1.75) (UROS) (Uroporphyrinogen-III cosynthetase) (Hydroxymethy ...	0.28	-	cyt	0					251
P47082 UniProt NPD GO	AVT1_YEAST	Vacuolar amino acid transporter 1	0.28	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuole [IMP]			602
Q5R436 UniProt NPD GO	VP26B_PONPY	Vacuolar protein sorting 26B (Vesicle protein sorting 26B)	0.28	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Does not localize to endosomes (By similarity)				336
Q7ZVK4 UniProt NPD GO	VPS36_BRARE	Vacuolar protein sorting protein 36	0.28	-	cyt	0	Cytoplasm (By similarity)				382
P83548 UniProt NPD GO	VNNL3_DROME	Vanin-like protein 3 precursor	0.28	-	mit	1		extrinsic to membrane [ISS]			523
P20948 UniProt NPD GO	VSY1_TRYCO	Variant surface glycoprotein YnAT 1.1 precursor (VSG)	0.28	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				419
P38268 UniProt NPD GO	YBW6_YEAST	Very hypothetical protein YBR116C	0.28	-	mit	1					175
P53967 UniProt NPD GO	YNC8_YEAST	Very hypothetical protein YNL028W	0.28	-	mit	1 *					105
Q9N0Y0 UniProt NPD GO	VAMP2_MACMU	Vesicle-associated membrane protein 2 (VAMP-2) (Synaptobrevin-2)	0.28	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein (By similarity). N ...				115
O70480 UniProt NPD GO	VAMP4_MOUSE	Vesicle-associated membrane protein 4 (VAMP-4)	0.28	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				141
P27587 UniProt NPD GO	VIT2_CERCA	Vitellogenin-2 precursor (Vitellogenin II) (Yolk protein 2)	0.28	-	nuc	0	Secreted protein				422
P06607 UniProt NPD GO	VIT3_DROME	Vitellogenin-3 precursor (Vitellogenin III) (Yolk protein 3)	0.28	-	mit	0	Secreted protein	extracellular region [IMP]			420
P62483 UniProt NPD GO	KCAB2_RAT	Voltage-gated potassium channel subunit beta-2 (K(+) channel subunit beta-2) (Kv-beta-2)	0.28	-	nuc	0	Cytoplasm (Potential)			2A79	367
P62482 UniProt NPD GO	KCAB2_MOUSE	Voltage-gated potassium channel subunit beta-2 (K(+) channel subunit beta-2) (Kv-beta-2) (Neuroimmun ...	0.28	-	nuc	0	Cytoplasm (Potential)				367
Q9DB94 UniProt NPD GO	WDR53_MOUSE	WD repeat protein 53	0.28	-	nuc	0					358
Q94130 UniProt NPD GO	WRT8_CAEEL	Warthog protein 8 precursor (M89 protein) [Contains: Warthog protein 8 N-product; Warthog protein 8 ...	0.28	-	mit	0	Warthog protein 8: Secreted protein (By similarity). Cell surface (By similarity). Warthog protein 8 ...	extracellular region [NAS] plasma membrane [NAS]			550
Q9VFX1 UniProt NPD GO	WNT8_DROME	Wnt inhibitor of Dorsal protein precursor (Protein Wnt-8) (dWnt-8)	0.28	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [NAS]			309

You are viewing entries 42801 to 42850 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.