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
Q9UP52 UniProt NPD GO	TFR2_HUMAN	Transferrin receptor protein 2 (TfR2)	0.22	-	mit	1	Cell membrane; single-pass type II membrane protein. Isoform Beta: Cytoplasm (Probable). The beta is ...	integral to plasma membrane [NAS]	604720		801
Q9EPK8 UniProt NPD GO	TRPV4_MOUSE	Transient receptor potential cation channel subfamily V member 4 (TrpV4) (osm-9-like TRP channel 4) ...	0.22	+	end	6	Membrane; multi-pass membrane protein (Probable)	plasma membrane [ISS]			871
Q60HC7 UniProt NPD GO	TKT_MACFA	Transketolase (EC 2.2.1.1) (TK)	0.22	-	cyt	0					623
Q7YJU4 UniProt NPD GO	IF1C_CALFE	Translation initiation factor IF-1, chloroplast	0.22	-	nuc	0	Plastid; chloroplast				77
P79769 UniProt NPD GO	TSN_CHICK	Translin	0.22	-	end	0	Nucleus				229
Q5XI41 UniProt NPD GO	TRAM1_RAT	Translocation-associated membrane protein 1	0.22	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				373
Q9BZW4 UniProt NPD GO	TM6S2_HUMAN	Transmembrane 6 superfamily member 2 (Fragment)	0.22	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	membrane [NAS]	606563		350
Q9JIQ8 UniProt NPD GO	TMPS2_MOUSE	Transmembrane protease, serine 2 (EC 3.4.21.-) (Epitheliasin) (Plasmic transmembrane protein X) [Con ...	0.22	-	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				490
Q3ZC25 UniProt NPD GO	T106B_BOVIN	Transmembrane protein 106B	0.22	-	mit	1	Membrane; single-pass membrane protein (Potential)				275
Q5RJK0 UniProt NPD GO	T106C_RAT	Transmembrane protein 106C	0.22	-	mit	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				260
Q6DIE4 UniProt NPD GO	TM55A_XENTR	Transmembrane protein 55A (EC 3.1.3.-) (Type II phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.22	-	mit	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				276
Q3TWL2 UniProt NPD GO	TM55B_MOUSE	Transmembrane protein 55B (EC 3.1.3.-) (Type I phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.22	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				284
Q5PPM8 UniProt NPD GO	TM55B_RAT	Transmembrane protein 55B (EC 3.1.3.-) (Type I phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.22	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				284
Q9NQ34 UniProt NPD GO	TMM9B_HUMAN	Transmembrane protein 9B precursor	0.22	-	end	2 *	Membrane; single-pass membrane protein (Potential)				198
Q6TYI6 UniProt NPD GO	TREM1_PIG	Triggering receptor expressed on myeloid cells 1 precursor (TREM-1)	0.22	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				238
Q91ZE0 UniProt NPD GO	TMLH_MOUSE	Trimethyllysine dioxygenase, mitochondrial precursor (EC 1.14.11.8) (Epsilon-trimethyllysine 2-oxogl ...	0.22	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			421
Q810I2 UniProt NPD GO	TRI50_MOUSE	Tripartite motif-containing protein 50	0.22	-	cyt	0					483
P84451 UniProt NPD GO	ITR2_SECED	Trypsin inhibitor 2b (Trypsin inhibitor IIb) (SETI-IIb) [Contains: Trypsin inhibitor 2a (Trypsin inh ...	0.22	-	nuc	0	Secreted protein				32
O96771 UniProt NPD GO	SYW_ENCCU	Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.22	-	cyt	0					385
Q17299 UniProt NPD GO	TBB1_CAEBR	Tubulin beta-1 chain (Beta-1 tubulin)	0.22	-	cyt	0					441
P13602 UniProt NPD GO	TBB2_XENLA	Tubulin beta-2 chain (Beta-2 tubulin)	0.22	-	cyt	0					443
P45960 UniProt NPD GO	TBB4_ORYSA	Tubulin beta-4 chain (Beta-4 tubulin)	0.22	-	cyt	0					447
Q99867 UniProt NPD GO	TBB4Q_HUMAN	Tubulin beta-4q chain	0.22	-	cyt	0		cytoskeleton [TAS]			434
Q8WP14 UniProt NPD GO	TBB4Q_PANTR	Tubulin beta-4q chain	0.22	-	cyt	0					444
P29513 UniProt NPD GO	TBB5_ARATH	Tubulin beta-5 chain (Beta-5 tubulin)	0.22	-	cyt	0					449
P90548 UniProt NPD GO	TBG2_EUPOC	Tubulin gamma-2 chain (Gamma-2 tubulin)	0.22	-	cyt	0					461
Q15813 UniProt NPD GO	TBCE_HUMAN	Tubulin-specific chaperone E (Tubulin-folding cofactor E)	0.22	-	cyt	0		microtubule [TAS]	604934		527
Q5RBD9 UniProt NPD GO	TBCE_PONPY	Tubulin-specific chaperone E (Tubulin-folding cofactor E)	0.22	-	cyt	0					527
Q9EQT5 UniProt NPD GO	TINAL_RAT	Tubulointerstitial nephritis antigen-like precursor (Glucocorticoid-inducible protein 5)	0.22	+	vac	0	Secreted protein (By similarity)				467
P36940 UniProt NPD GO	TNFL6_RAT	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.22	-	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				278
Q861W5 UniProt NPD GO	TNFL6_FELCA	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.22	-	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				280
O55237 UniProt NPD GO	TNFL7_MOUSE	Tumor necrosis factor ligand superfamily member 7 (CD27 ligand) (CD27-L) (CD70 antigen)	0.22	-	mit	1 *	Membrane; single-pass type II membrane protein				195
P59695 UniProt NPD GO	TNFA_PAPAN	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.22	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P18519 UniProt NPD GO	TNR16_CHICK	Tumor necrosis factor receptor superfamily member 16 precursor (Low-affinity nerve growth factor rec ...	0.22	-	exc	1	Membrane; single-pass type I membrane protein				416
Q93038 UniProt NPD GO	TNR25_HUMAN	Tumor necrosis factor receptor superfamily member 25 precursor (WSL-1 protein) (Apoptosis-mediating ...	0.22	-	exc	1	Isoform 1, isoform 2, isoform 9, isoform 11: Cell membrane; single-pass type I membrane protein. Iso ...	cytosol [NAS] integral to plasma membrane [TAS] plasma membrane [IDA]	603366		417
P09758 UniProt NPD GO	TACD2_HUMAN	Tumor-associated calcium signal transducer 2 precursor (Pancreatic carcinoma marker protein GA733-1) ...	0.22	-	end	1	Membrane; single-pass type I membrane protein	cytosol [TAS] integral to plasma membrane [TAS] membrane [TAS]	204870		323
P70551 UniProt NPD GO	IOD2_RAT	Type II iodothyronine deiodinase (EC 1.97.1.10) (Type-II 5'deiodinase) (DIOII) (Type 2 DI) (5DII)	0.22	-	nuc	0					262
P49898 UniProt NPD GO	IOD3_RANCA	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.22	-	exc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Endosome; endosomal membrane; s ...				269
P80961 UniProt NPD GO	AFP4_MYOOC	Type-4 ice-structuring protein LS-12 precursor (ISP LS-12) (Antifreeze protein LS-12)	0.22	-	exc	0	Secreted protein				128
Q8J130 UniProt NPD GO	TYRO_ASPFU	Tyrosinase (EC 1.14.18.1) (Monophenol monooxygenase)	0.22	-	mit	0					630
P55026 UniProt NPD GO	TYRO_TRISI	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase) (Fragment)	0.22	-	exc	0	Melanosome; melanosomal membrane; single-pass type I membrane protein				273
Q9Z222 UniProt NPD GO	B3GN1_MOUSE	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1 (EC 2.4.1.-) (Beta3Gn-T1) (BGnT-1) (Be ...	0.22	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				397
P08430 UniProt NPD GO	UD16_RAT	UDP-glucuronosyltransferase 1-6 precursor (EC 2.4.1.17) (UDPGT) (UGT1*6) (UGT1-06) (UGT1.6) (UGT1A6) ...	0.22	-	end	1	Microsome				529
Q9HD40 UniProt NPD GO	UGTAP_HUMAN	UGA suppressor tRNA-associated protein (tRNA(Ser/Sec)-associated antigenic protein) (SLA/LP autoanti ...	0.22	-	nuc	0	Cytoplasm	cytoplasm [ISS] nucleus [ISS]			501
P06580 UniProt NPD GO	UTS2G_CYPCA	UII gamma precursor [Contains: Urophysin gamma; Urotensin II-gamma (UII-gamma) (U-II-gamma)]	0.22	-	exc	0	Secreted protein				125
Q8CAV0 UniProt NPD GO	CU057_MOUSE	UPF0054 protein C21orf57 homolog	0.22	-	mit	0					164
O01369 UniProt NPD GO	UCR6_FASHE	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2)	0.22	-	mit	0	Mitochondrion; mitochondrial inner membrane				130
P14927 UniProt NPD GO	UCR6_HUMAN	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VI) (QP-C ...	0.22	-	cyt	0	Mitochondrion; mitochondrial inner membrane	mitochondrial electron transport chain [TAS]	191330		110
P51132 UniProt NPD GO	UCRI2_TOBAC	Ubiquinol-cytochrome c reductase iron-sulfur subunit 2, mitochondrial precursor (EC 1.10.2.2) (Riesk ...	0.22	-	mit	1	Mitochondrion; mitochondrial inner membrane				272
P91428 UniProt NPD GO	COQ4_CAEEL	Ubiquinone biosynthesis protein coq-4	0.22	-	mit	0					263

You are viewing entries 49001 to 49050 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.