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
P41387 UniProt NPD GO	TBB_ONCGI	Tubulin beta chain (Beta tubulin)	0.33	-	cyt	0					444
P54403 UniProt NPD GO	TBG1_EUPCR	Tubulin gamma-1 chain (Gamma-1 tubulin)	0.33	-	cyt	0					462
Q41808 UniProt NPD GO	TBG2_MAIZE	Tubulin gamma-2 chain (Gamma-2 tubulin)	0.33	-	cyt	0					469
O75347 UniProt NPD GO	TBCA_HUMAN	Tubulin-specific chaperone A (Tubulin-folding cofactor A) (CFA) (TCP1-chaperonin cofactor A)	0.33	-	nuc	0		cytoplasm [TAS]		1H7C	107
O14788 UniProt NPD GO	TNF11_HUMAN	Tumor necrosis factor ligand superfamily member 11 (Receptor activator of nuclear factor kappa B lig ...	0.33	-	mit	1 *	Isoform 1, isoform 3: Cell membrane; single-pass type II membrane protein. Isoform 2, processed isof ...	extracellular region [NAS] integral to plasma membrane [NAS]	602642		317
Q28203 UniProt NPD GO	TNR5_BOVIN	Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antig ...	0.33	-	end	1	Membrane; single-pass type I membrane protein				269
Q9TSN4 UniProt NPD GO	TNR6_MACFA	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.33	-	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				331
O54818 UniProt NPD GO	TPD53_MOUSE	Tumor protein D53 (mD53) (Tumor protein D52-like 1)	0.33	-	nuc	0		cytoplasm [ISS] perinuclear region [ISS]			204
Q9WUE4 UniProt NPD GO	TUSC4_MOUSE	Tumor suppressor candidate 4 (NPR2-like) (Gene 21 protein) (G21 protein)	0.33	-	cyt	0					380
Q6GMH3 UniProt NPD GO	TWF2_BRARE	Twinfilin-2	0.33	-	cyt	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Perinuclear and G-actin-ri ...				347
Q5RFH1 UniProt NPD GO	TWF2_PONPY	Twinfilin-2 (Fragment)	0.33	-	cyt	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Perinuclear and G-actin-ri ...				341
Q9Z0P5 UniProt NPD GO	TWF2_MOUSE	Twinfilin-2 (Twinfilin-1-like protein) (A6-related protein) (mA6RP)	0.33	-	cyt	0	Cytoplasm. Cytoplasm; perinuclear region. Perinuclear and G-actin-rich cortical actin structures sub ...				349
Q7G8V2 UniProt NPD GO	ARR15_ARATH	Two-component response regulator ARR15	0.33	+	nuc	0	Nucleus				206
P13116 UniProt NPD GO	SRC2_XENLA	Tyrosine-protein kinase Src-2 (EC 2.7.10.2) (p60-Src-2)	0.33	-	nuc	0					531
Q62270 UniProt NPD GO	SRMS_MOUSE	Tyrosine-protein kinase Srms (EC 2.7.10.2) (PTK70)	0.33	-	exc	0					496
P48527 UniProt NPD GO	SYYM_YEAST	Tyrosyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrRS)	0.33	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			492
P09234 UniProt NPD GO	RU1C_HUMAN	U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C)	0.33	-	nuc	0	Nucleus	snRNP U1 [TAS]	603522	1UW2	159
Q62241 UniProt NPD GO	RU1C_MOUSE	U1 small nuclear ribonucleoprotein C (U1 snRNP protein C) (U1C protein) (U1-C)	0.33	-	nuc	0	Nucleus				159
Q755D2 UniProt NPD GO	RU2A_ASHGO	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A')	0.33	-	nuc	0	Nucleus (By similarity)				237
Q9CQQ8 UniProt NPD GO	LSM7_MOUSE	U6 snRNA-associated Sm-like protein LSm7	0.33	-	nuc	0	Nucleus (Potential)				103
Q5R885 UniProt NPD GO	UXS1_PONPY	UDP-glucuronic acid decarboxylase 1 (EC 4.1.1.35) (UDP-glucuronate decarboxylase 1) (UGD) (UXS-1)	0.33	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				420
Q9M2D2 UniProt NPD GO	YU88_ARATH	UPF0187 protein At3g61320, chloroplast precursor	0.33	-	end	1	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				410
P00129 UniProt NPD GO	UCR6_BOVIN	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VI)	0.33	-	nuc	0	Mitochondrion; mitochondrial inner membrane			3BCC	110
P48510 UniProt NPD GO	DSK2_YEAST	Ubiquitin domain-containing protein DSK2	0.33	-	nuc	0	Nucleus (Probable)	nucleus [TAS]		2BWF	373
Q8S3N1 UniProt NPD GO	SINA5_ARATH	Ubiquitin ligase SINAT5 (EC 6.3.2.-) (Seven in absentia homolog 5)	0.33	-	nuc	0	Nucleus. Predominantly. Cytoplasm. Partially				309
P61093 UniProt NPD GO	SINA_DROER	Ubiquitin ligase sina (EC 6.3.2.-) (Seven in absentia protein)	0.33	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [ISS]			314
P21461 UniProt NPD GO	SINA_DROME	Ubiquitin ligase sina (EC 6.3.2.-) (Seven in absentia protein)	0.33	-	mit	0	Cytoplasm. Nucleus	nucleus [IDA]			314
P11441 UniProt NPD GO	UBL4A_HUMAN	Ubiquitin-like protein 4A (Ubiquitin-like protein GDX)	0.33	-	nuc	0			312070		157
Q9H2U6 UniProt NPD GO	CO005_HUMAN	Uncharacterized protein C15orf5	0.33	-	nuc	0					94
P25625 UniProt NPD GO	YCT4_YEAST	Uncharacterized protein YCR044C	0.33	-	end	6		vacuolar membrane (sensu Fungi) [IDA]			357
P25651 UniProt NPD GO	YCX6_YEAST	Uncharacterized protein YCR086W	0.33	-	nuc	0		condensed nuclear chromosome kinetochore [IDA] nuclear envelope [IDA] nucleolus [IDA]			190
Q3E7Y6 UniProt NPD GO	YH199_YEAST	Uncharacterized protein YHR199C-A	0.33	-	nuc	0					73
P40186 UniProt NPD GO	YIF0_YEAST	Uncharacterized protein YIL050W	0.33	-	nuc	0		cyclin-dependent protein kinase holoenzyme ... [TAS]			285
P34234 UniProt NPD GO	YKS3_YEAST	Uncharacterized protein YKL183W	0.33	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			306
Q06071 UniProt NPD GO	YL408_YEAST	Uncharacterized protein YLR408C	0.33	-	nuc	0	Endosome	endosome [IDA]			122
Q96RP3 UniProt NPD GO	UCN2_HUMAN	Urocortin-2 precursor (Urocortin II) (Ucn II) (Stresscopin-related peptide) (Urocortin-related pepti ...	0.33	-	mit	1 *	Secreted protein	extracellular region [NAS]	605902		112
Q9QZQ4 UniProt NPD GO	UTS2_RAT	Urotensin-2 precursor (Urotensin-II) (U-II) (UII)	0.33	-	exc	0	Secreted protein				123
Q9HDW6 UniProt NPD GO	VATC_SCHPO	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.33	-	nuc	0					394
P57746 UniProt NPD GO	VATD_MOUSE	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit) ...	0.33	-	cyt	0					247
Q12042 UniProt NPD GO	YP162_YEAST	Vacuolar membrane protein YPL162C	0.33	-	end	5 *	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential)	vacuolar membrane (sensu Fungi) [IDA]			273
Q9P253 UniProt NPD GO	VPS18_HUMAN	Vacuolar protein sorting 18 (hVPS18)	0.33	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein. Lysosome; lysosomal membrane; p ...		608551		973
Q8C754 UniProt NPD GO	VPS52_MOUSE	Vacuolar protein sorting protein 52	0.33	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				723
O55166 UniProt NPD GO	VPS52_RAT	Vacuolar protein sorting protein 52 (SAC2 suppressor of actin mutations 2-like protein)	0.33	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				723
P62583 UniProt NPD GO	VPS74_ASHGO	Vacuolar protein sorting-associated protein 74	0.33	-	cyt	0					331
Q9Z1Q9 UniProt NPD GO	SYV_MOUSE	Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS) (Protein G7a)	0.33	-	cyt	0		mitochondrion [IDA]			1263
P06016 UniProt NPD GO	VSAC_TRYBB	Variant surface glycoprotein ANTAT 1.1C precursor (VSG) (Fragment)	0.33	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				482
P49766 UniProt NPD GO	VEGFB_MOUSE	Vascular endothelial growth factor B precursor (VEGF-B) (VEGF-related factor) (VRF)	0.33	-	exc	0	Secreted protein. Secreted but remains associated to cells or to the extracellular matrix unless rel ...				207
Q9WTV9 UniProt NPD GO	V1AR_MICOH	Vasopressin V1a receptor (V1aR) (Vascular/hepatic-type arginine vasopressin receptor) (Antidiuretic ...	0.33	-	end	7	Membrane; multi-pass membrane protein				420
Q5YF89 UniProt NPD GO	NGFV2_NAJSP	Venom nerve growth factor 2 precursor (vNGF-2) (Nerve growth factor II)	0.33	-	exc	0	Secreted protein				241
Q9C120 UniProt NPD GO	YIZL_SCHPO	Very hypothetical protein C1002.21 in chromosome I	0.33	-	mit	0					148

You are viewing entries 38101 to 38150 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.