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
Q9NQ86 UniProt NPD GO	TRI36_HUMAN	Tripartite motif-containing protein 36 (Zinc-binding protein Rbcc728) (RING finger protein 98)	0.53	-	nuc	0	Cytoplasm (By similarity). Found in the acrosomal region of elongated spermatids and mature sperm (B ...		609317		728
Q9JLH8 UniProt NPD GO	TMOD4_MOUSE	Tropomodulin-4 (Skeletal muscle tropomodulin) (Sk-Tmod)	0.53	-	nuc	0					345
Q25145 UniProt NPD GO	TPM_HALRU	Tropomyosin	0.53	-	nuc	0					284
Q8T380 UniProt NPD GO	TPM_LEPSA	Tropomyosin	0.53	-	nuc	0					284
Q9U5M4 UniProt NPD GO	TPM2_PODCA	Tropomyosin 2	0.53	-	nuc	0					251
P17532 UniProt NPD GO	TPH1_MOUSE	Tryptophan 5-hydroxylase 1 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 1)	0.53	-	cyt	0					447
O75509 UniProt NPD GO	TNR21_HUMAN	Tumor necrosis factor receptor superfamily member 21 precursor (TNFR-related death receptor 6) (Deat ...	0.53	-	exc	1 *	Membrane; single-pass type I membrane protein (Probable)		605732		655
P17289 UniProt NPD GO	TY3H_BOVIN	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH)	0.53	-	nuc	0					490
Q91048 UniProt NPD GO	PTK7_CHICK	Tyrosine-protein kinase-like 7 precursor (Kinase-like protein)	0.53	+	end	1	Membrane; single-pass type I membrane protein				1051
P29350 UniProt NPD GO	PTN6_HUMAN	Tyrosine-protein phosphatase non-receptor type 6 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1C) (PT ...	0.53	-	mit	0	Cytoplasm	membrane [TAS]	176883	2B3O	595
Q03714 UniProt NPD GO	USA1_YEAST	U1 SNP1-associating protein 1	0.53	-	end	2	Membrane; multi-pass membrane protein (Potential)				838
Q00916 UniProt NPD GO	RU17_YEAST	U1 small nuclear ribonucleoprotein 70 kDa homolog	0.53	-	nuc	0		commitment complex [IPI] snRNP U1 [IDA]			300
Q921Y2 UniProt NPD GO	IMP3_MOUSE	U3 small nucleolar ribonucleoprotein protein IMP3 (U3 snoRNP protein IMP3)	0.53	-	cyt	0	Nucleus; nucleolus (By similarity)				184
O13835 UniProt NPD GO	IMP3_SCHPO	U3 small nucleolar ribonucleoprotein protein imp3 (U3 snoRNP protein imp3)	0.53	-	nuc	0	Nucleus; nucleolus (By similarity)				183
Q9NZ43 UniProt NPD GO	USE1_HUMAN	USE1-like protein (Hematopoietic stem/progenitor cells protein MDS032) (Putative MAPK-activating pro ...	0.53	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	endoplasmic reticulum [IDA]			259
Q9H347 UniProt NPD GO	UBQL3_HUMAN	Ubiquilin-3	0.53	-	nuc	0			605473	2DAH	655
Q06109 UniProt NPD GO	YP116_YEAST	Uncharacterized mitochondrial protein YPR116W	0.53	-	nuc	0	Mitochondrion	mitochondrion [IDA]			277
P23180 UniProt NPD GO	YHC1_YEAST	Uncharacterized oxidoreductase YHL021C (EC 1.14.11.-)	0.53	-	mit	0		mitochondrion [IDA]			465
P0C1G7 UniProt NPD GO	CJ026_RAT	Uncharacterized protein C10orf26 homolog	0.53	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				344
Q8NEA5 UniProt NPD GO	CS018_HUMAN	Uncharacterized protein C19orf18 precursor	0.53	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				215
Q8NC44 UniProt NPD GO	CB017_HUMAN	Uncharacterized protein C2orf17	0.53	-	end	1	Membrane; multi-pass membrane protein (Potential)				543
O16686 UniProt NPD GO	YK27_CAEEL	Uncharacterized protein K07E8.7	0.53	+	nuc	0					432
P38285 UniProt NPD GO	YB08_YEAST	Uncharacterized protein YBR158W	0.53	-	nuc	0		bud [IDA] cytoplasm [IDA] nucleus [IDA]			549
P38314 UniProt NPD GO	YB64_YEAST	Uncharacterized protein YBR214W	0.53	-	nuc	0		cytoplasm [IDA]			527
Q12515 UniProt NPD GO	YD173_YEAST	Uncharacterized protein YDL173W	0.53	+	nuc	0	Cytoplasm	cytoplasm [IDA]			295
P48235 UniProt NPD GO	YG3K_YEAST	Uncharacterized protein YGR146C	0.53	-	nuc	0					211
P47158 UniProt NPD GO	YJ92_YEAST	Uncharacterized protein YJR122W	0.53	+	mit	0		mitochondrion [IDA]			497
P53754 UniProt NPD GO	YN97_YEAST	Uncharacterized protein YNR068C	0.53	-	nuc	0					272
Q03080 UniProt NPD GO	YP039_YEAST	Uncharacterized protein YPL039W	0.53	-	nuc	0					316
Q9LKA5 UniProt NPD GO	UMP1_ARATH	Unknown mitochondrial protein At3g15000	0.53	+	mit	0	Mitochondrion				395
Q08747 UniProt NPD GO	UAF30_YEAST	Upstream activation factor subunit UAF30 (Upstream activation factor 30 KDa subunit) (p30)	0.53	-	nuc	0	Nucleus; nucleolus	RNA polymerase I upstream activating factor... [IMP]			228
Q9EQH3 UniProt NPD GO	VPS35_MOUSE	Vacuolar protein sorting 35 (Vesicle protein sorting 35) (Maternal-embryonic 3)	0.53	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				796
Q06385 UniProt NPD GO	VPS74_YEAST	Vacuolar protein sorting-associated protein 74	0.53	-	mit	0		cytoplasm [IDA] nucleus [IDA]			345
P67863 UniProt NPD GO	TXVE_VIPAA	Vascular endothelial growth factor toxin (svVEGF) (Vammin)	0.53	+	nuc	0	Secreted protein				110
Q3HXZ0 UniProt NPD GO	NGFV2_OXYMI	Venom nerve growth factor 2 precursor (vNGF-2)	0.53	-	exc	0	Secreted protein				243
Q9PVN2 UniProt NPD GO	VAX1_CHICK	Ventral anterior homeobox 1	0.53	+	nuc	0	Nucleus (By similarity)				327
Q9SEL6 UniProt NPD GO	VTI11_ARATH	Vesicle transport v-SNARE 11 (AtVTI11) (Vesicle transport v-SNARE protein VTI1a) (Vesicle soluble NS ...	0.53	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				221
O15195 UniProt NPD GO	VILL_HUMAN	Villin-like protein	0.53	-	cyt	0		actin cytoskeleton [TAS]			856
P09654 UniProt NPD GO	VIME_CHICK	Vimentin	0.53	-	mit	0					459
P02543 UniProt NPD GO	VIME_PIG	Vimentin (Fragments)	0.53	-	mit	0					275
P00745 UniProt NPD GO	PROC_BOVIN	Vitamin K-dependent protein C precursor (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein ...	0.53	+	end	0		extracellular region [ISS]			456
Q12523 UniProt NPD GO	YP247_YEAST	WD repeat protein YPL247C	0.53	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			523
Q80VW5 UniProt NPD GO	WHRN_MOUSE	Whirlin	0.53	-	nuc	0	Cytoplasm. Detected at the level of stereocilia in inner hair cells and in outer hair cells in the c ...	actin filament [IDA] cilium [IDA]			906
Q93YS4 UniProt NPD GO	WBC23_ARATH	White-brown complex homolog protein 23	0.53	-	end	5	Membrane; multi-pass membrane protein (By similarity)				751
P59041 UniProt NPD GO	WBS18_MOUSE	Williams-Beuren syndrome chromosome region 18 protein homolog	0.53	+	nuc	0					219
Q9ERS6 UniProt NPD GO	IRPL2_MOUSE	X-linked interleukin-1 receptor accessory protein-like 2 precursor (IL1RAPL-2-related protein) (TIGI ...	0.53	-	end	1	Membrane; single-pass type I membrane protein				686
P17010 UniProt NPD GO	ZFX_HUMAN	Zinc finger X-chromosomal protein	0.53	+	nuc	0	Nucleus		314980		805
P52740 UniProt NPD GO	ZN132_HUMAN	Zinc finger protein 132	0.53	-	nuc	0	Nucleus (Potential)		604074		589
P10755 UniProt NPD GO	ZFP14_MOUSE	Zinc finger protein 14 (Zfp-14) (Krox-9 protein)	0.53	-	nuc	0	Nucleus (Potential)				501
P17020 UniProt NPD GO	ZNF16_HUMAN	Zinc finger protein 16 (Zinc finger protein KOX9)	0.53	-	nuc	0	Nucleus (Potential)		601262		682

You are viewing entries 23451 to 23500 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.