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
P17680 UniProt NPD GO	ITR1_MOMRE	Trypsin inhibitor 1 (Trypsin inhibitor I) (MRTI-I)	0.14	-	nuc	0	Secreted protein				29
O93267 UniProt NPD GO	TRP3_PSEAM	Trypsinogen-like protein 3 precursor	0.14	-	exc	0					256
Q9XSM2 UniProt NPD GO	TRYT_SHEEP	Tryptase-2 precursor (EC 3.4.21.59)	0.14	-	exc	0	Released from the secretory granules upon mast cell activation				273
Q8SRI6 UniProt NPD GO	TBA_ENCCU	Tubulin alpha chain	0.14	-	cyt	0					441
Q9ZRB7 UniProt NPD GO	TBA_WHEAT	Tubulin alpha chain	0.14	-	cyt	0					451
Q9SCC8 UniProt NPD GO	TBAN_GUITH	Tubulin alpha chain, nucleomorph (Nucleomorph alpha tubulin)	0.14	-	cyt	0					448
Q6VAG1 UniProt NPD GO	TBA1_GOSHI	Tubulin alpha-1 chain (Alpha-1 tubulin)	0.14	-	cyt	0					451
Q96460 UniProt NPD GO	TBA2_HORVU	Tubulin alpha-2 chain	0.14	-	cyt	0					451
P29510 UniProt NPD GO	TBA2_ARATH	Tubulin alpha-2/alpha-4 chain	0.14	-	cyt	0					450
P22275 UniProt NPD GO	TBA3_MAIZE	Tubulin alpha-3 chain (Alpha-3 tubulin)	0.14	-	cyt	0					450
P20363 UniProt NPD GO	TBA3_ARATH	Tubulin alpha-3/alpha-5 chain	0.14	-	cyt	0					450
P09644 UniProt NPD GO	TBA5_CHICK	Tubulin alpha-5 chain	0.14	-	cyt	0					448
Q02245 UniProt NPD GO	TBA5_MAIZE	Tubulin alpha-5 chain (Alpha-5 tubulin)	0.14	-	cyt	0					450
P29511 UniProt NPD GO	TBA6_ARATH	Tubulin alpha-6 chain	0.14	-	cyt	0					450
Q4HZS8 UniProt NPD GO	TBB_GIBZE	Tubulin beta chain (Beta tubulin)	0.14	-	cyt	0					446
P41386 UniProt NPD GO	TBB_HALDI	Tubulin beta chain (Beta tubulin) (Fragment)	0.14	-	cyt	0					341
Q42480 UniProt NPD GO	TBB1_CHOCR	Tubulin beta-1 chain (Beta-1 tubulin)	0.14	-	cyt	0					453
Q43695 UniProt NPD GO	TBB3_MAIZE	Tubulin beta-3 chain (Beta-3 tubulin)	0.14	-	cyt	0					445
Q40665 UniProt NPD GO	TBB3_ORYSA	Tubulin beta-3 chain (Beta-3 tubulin)	0.14	-	cyt	0					446
Q41785 UniProt NPD GO	TBB8_MAIZE	Tubulin beta-8 chain (Beta-8 tubulin)	0.14	-	cyt	0					445
Q02223 UniProt NPD GO	TNR17_HUMAN	Tumor necrosis factor receptor superfamily member 17 (B-cell maturation protein) (CD269 antigen)	0.14	-	nuc	1	Cell membrane; single-pass type III membrane protein. Intracellular membrane; single-pass type III m ...	integral to membrane [TAS] plasma membrane [TAS]	109545	1XU2	184
O35714 UniProt NPD GO	TNR18_MOUSE	Tumor necrosis factor receptor superfamily member 18 precursor (Glucocorticoid-induced TNFR-related ...	0.14	-	nuc	1	Isoform A, isoform B, isoform C: Cell membrane; single-pass type I membrane protein. Isoform D: Secr ...				228
Q9Y5U5 UniProt NPD GO	TNR18_HUMAN	Tumor necrosis factor receptor superfamily member 18 precursor (Glucocorticoid-induced TNFR-related ...	0.14	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein		603905		241
P19473 UniProt NPD GO	TUR8_MOUSE	Tumor rejection antigen P815A	0.14	-	cyt	1 *					224
O17185 UniProt NPD GO	SUP9_CAEEL	Two pore potassium channel protein sup-9 (Suppressor of unc-93 protein 9) (n2P38)	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential). Associated with dense bodies	integral to plasma membrane [NAS]			329
Q61153 UniProt NPD GO	IOD1_MOUSE	Type I iodothyronine deiodinase (EC 1.97.1.10) (Type-I 5'deiodinase) (DIOI) (Type 1 DI) (5DI)	0.14	-	mit	1 *					257
P10936 UniProt NPD GO	YES_XENLA	Tyrosine-protein kinase Yes (EC 2.7.10.2) (p61-Yes)	0.14	-	cyt	0					536
P42690 UniProt NPD GO	SRK4_SPOLA	Tyrosine-protein kinase isoform SRK4 (EC 2.7.10.2)	0.14	-	cyt	0	Cytoplasm (Probable)				506
Q9V6K3 UniProt NPD GO	ROR2_DROME	Tyrosine-protein kinase transmembrane receptor Ror2 precursor (EC 2.7.10.1) (Neurospecific receptor ...	0.14	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				724
P28207 UniProt NPD GO	PTP15_STYPL	Tyrosine-protein phosphatase 15 (EC 3.1.3.48) (Fragment)	0.14	-	cyt	0					113
P28210 UniProt NPD GO	PTP18_STYPL	Tyrosine-protein phosphatase 18 (EC 3.1.3.48) (Fragment)	0.14	-	cyt	0					115
P28211 UniProt NPD GO	PTP19_STYPL	Tyrosine-protein phosphatase 19 (EC 3.1.3.48) (Fragment)	0.14	-	cyt	0					115
Q91YN5 UniProt NPD GO	UAP1_MOUSE	UDP-N-acetylhexosamine pyrophosphorylase [Includes: UDP-N-acetylgalactosamine pyrophosphorylase (EC ...	0.14	-	cyt	0	Cytoplasm (By similarity)			1VM8	522
O77649 UniProt NPD GO	UDB20_MACFA	UDP-glucuronosyltransferase 2B20 precursor (EC 2.4.1.17) (UDPGT)	0.14	-	end	1	Microsome				530
Q9Y115 UniProt NPD GO	UN93L_DROME	UNC93-like protein	0.14	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS] plasma membrane [ISS]			538
Q09906 UniProt NPD GO	YAJ6_SCHPO	UPF0206 protein C30D11.06c	0.14	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				426
Q8AV19 UniProt NPD GO	CI021_FUGRU	UPF0308 protein C9orf21 homolog (fmHP)	0.14	-	nuc	0					226
Q8WWR9 UniProt NPD GO	CH022_HUMAN	UPF0362 protein C8orf22	0.14	-	nuc	0					84
Q9D1H7 UniProt NPD GO	CG020_MOUSE	UPF0363 protein C7orf20 homolog	0.14	-	nuc	0					327
P08800 UniProt NPD GO	UGPA_DICDI	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) (UDPGP) (U ...	0.14	-	nuc	0					511
O15205 UniProt NPD GO	UBD_HUMAN	Ubiquitin D (Ubiquitin-like protein FAT10) (Diubiquitin)	0.14	-	nuc	0			606050		165
P23356 UniProt NPD GO	UCHL1_BOVIN	Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (EC 6.-.-.-) (UCH-L1) (Ubiquitin thi ...	0.14	-	nuc	0	Cytoplasm				252
Q64339 UniProt NPD GO	UCRP_MOUSE	Ubiquitin cross-reactive protein precursor (Interferon-stimulated protein 15) (IP17)	0.14	-	cyt	0	Cytoplasm. UCRP conjugates seem to be noncovalently associated with the intermediate filaments and d ...				160
O94289 UniProt NPD GO	LUB1_SCHPO	Ubiquitin homeostasis protein lub1	0.14	-	nuc	0	Nucleus. Cytoplasm				713
Q8R516 UniProt NPD GO	MIB2_MOUSE	Ubiquitin ligase protein MIB2 (EC 6.3.2.-) (Mind bomb homolog 2) (Mind bomb-2) (Skeletrophin) (Dystr ...	0.14	-	nuc	0	Cytoplasm. Endosome. Colocalizes with endosomal compartments	early endosome [IDA] ubiquitin ligase complex [IDA]			973
O00762 UniProt NPD GO	UBE2C_HUMAN	Ubiquitin-conjugating enzyme E2 C (EC 6.3.2.19) (Ubiquitin-protein ligase C) (Ubiquitin carrier prot ...	0.14	-	nuc	0			605574	1I7K	179
Q4R4I1 UniProt NPD GO	UBE2N_MACFA	Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) (Ubiquitin-protein ligase N) (Ubiquitin carrier prot ...	0.14	-	mit	0					152
Q9EQX9 UniProt NPD GO	UBE2N_RAT	Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) (Ubiquitin-protein ligase N) (Ubiquitin carrier prot ...	0.14	-	mit	0					152
Q13404 UniProt NPD GO	UB2V1_HUMAN	Ubiquitin-conjugating enzyme E2 variant 1 (UEV-1) (CROC-1) (Ubiquitin-conjugating enzyme variant Kua ...	0.14	-	mit	0	Nucleus. Isoform 3, isoform 5: Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] nucleus [TAS] ubiquitin conjugating enzyme complex [IDA]	602995	2C2V	221
P29340 UniProt NPD GO	UBCX_YEAST	Ubiquitin-conjugating enzyme E2-21 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.14	-	nuc	0	Peroxisome	peroxisome [IDA]			183

You are viewing entries 59151 to 59200 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.