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
Q5U1X0 UniProt NPD GO	TAF11_RAT	Transcription initiation factor TFIID subunit 11 (Transcription initiation factor TFIID 28 kDa subun ...	0.29	-	nuc	0	Nucleus (By similarity)				211
Q9Z142 UniProt NPD GO	TMM33_RAT	Transmembrane protein 33 (DB83 protein)	0.29	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				247
P19813 UniProt NPD GO	TREA_RABIT	Trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.29	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				578
P04803 UniProt NPD GO	SYWM_YEAST	Tryptophanyl-tRNA synthetase, mitochondrial (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.29	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			379
Q58A48 UniProt NPD GO	TSK_BRARE	Tsukushi precursor (Z-TSK) (Leucine-rich repeat-containing protein 54)	0.29	-	exc	0	Secreted protein (Potential)				347
P40633 UniProt NPD GO	TBG_COCHE	Tubulin gamma chain (Gamma tubulin) (Fragment)	0.29	-	nuc	0					265
Q8C5W3 UniProt NPD GO	TBCEL_MOUSE	Tubulin-specific chaperone cofactor E-like protein (Leucine-rich repeat-containing protein 35)	0.29	-	nuc	0					424
P48023 UniProt NPD GO	TNFL6_HUMAN	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.29	-	nuc	1	Cell membrane; single-pass type II membrane protein. Secreted protein. May be released into the extr ...	integral to plasma membrane [TAS]	134638	1BZI	281
Q9BDN1 UniProt NPD GO	TNFL6_CERTO	Tumor necrosis factor ligand superfamily member 6 (Fas antigen ligand) (Fas ligand) (CD178 antigen) ...	0.29	-	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				280
P32970 UniProt NPD GO	TNFL7_HUMAN	Tumor necrosis factor ligand superfamily member 7 (CD27 ligand) (CD27-L) (CD70 antigen)	0.29	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	602840		193
P51435 UniProt NPD GO	TNFA_CAVPO	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.29	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				234
Q96RJ3 UniProt NPD GO	TR13C_HUMAN	Tumor necrosis factor receptor superfamily member 13C (B cell-activating factor receptor) (BAFF rece ...	0.29	-	nuc	1	Membrane; single-pass type III membrane protein (Probable)		606269	1P0T	184
P47741 UniProt NPD GO	TNR4_MOUSE	Tumor necrosis factor receptor superfamily member 4 precursor (OX40L receptor) (OX40 antigen)	0.29	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			272
P27512 UniProt NPD GO	TNR5_MOUSE	Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antig ...	0.29	-	exc	1	Isoform I, isoform III, isoform IV, isoform V: Cell membrane; single-pass type I membrane protein. I ...	external side of plasma membrane [IDA]			289
O43399 UniProt NPD GO	TPD54_HUMAN	Tumor protein D54 (hD54) (Tumor protein D52-like 2)	0.29	-	nuc	0			603747		206
P32434 UniProt NPD GO	CWG2_SCHPO	Type-1 protein geranylgeranyltransferase subunit beta (EC 2.5.1.59) (Type I protein geranylgeranyltr ...	0.29	-	mit	0					355
Q08410 UniProt NPD GO	TYRO_COTJA	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase) (Fragment)	0.29	-	exc	0	Melanosome; melanosomal membrane; single-pass type I membrane protein				273
P13115 UniProt NPD GO	SRC1_XENLA	Tyrosine-protein kinase Src-1 (EC 2.7.10.2) (p60-Src-1)	0.29	-	nuc	0					531
Q7ZW33 UniProt NPD GO	UTP15_BRARE	U3 small nucleolar RNA-associated protein 15 homolog	0.29	-	cyt	0	Nucleus; nucleolus (By similarity)				517
Q5F3D7 UniProt NPD GO	UTP15_CHICK	U3 small nucleolar RNA-associated protein 15 homolog	0.29	-	cyt	0	Nucleus; nucleolus (By similarity)				520
Q8VHZ7 UniProt NPD GO	IMP4_MOUSE	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4)	0.29	-	mit	0	Nucleus; nucleolus (By similarity)				291
Q5PQR5 UniProt NPD GO	IMP4_RAT	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4)	0.29	-	mit	0	Nucleus; nucleolus (By similarity)				291
P38276 UniProt NPD GO	YBY7_YEAST	UPF0303 protein YBR137W	0.29	-	cyt	0	Cytoplasm	cytoplasm [IDA]			179
Q8J0M4 UniProt NPD GO	YCB2_YEAST	UPF0357 protein YCL012C precursor	0.29	-	mit	1 *					134
P54728 UniProt NPD GO	RD23B_MOUSE	UV excision repair protein RAD23 homolog B (mHR23B) (XP-C repair-complementing complex 58 kDa protei ...	0.29	-	nuc	0	Nucleus (Probable)			2F4O	416
Q84JL3 UniProt NPD GO	SINA3_ARATH	Ubiquitin ligase SINAT3 (EC 6.3.2.-) (Seven in absentia homolog 3)	0.29	-	nuc	0					326
Q7ZVG6 UniProt NPD GO	SIAH1_BRARE	Ubiquitin ligase Siah1 (EC 6.3.2.-) (Seven in absentia homolog 1) (Siah-1)	0.29	-	mit	0					282
Q5M7A4 UniProt NPD GO	UE1D1_RAT	Ubiquitin-activating enzyme E1 domain-containing protein 1 (UFM1-activating enzyme)	0.29	-	nuc	0					403
Q75EB8 UniProt NPD GO	UBC2_ASHGO	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.29	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				170
P25868 UniProt NPD GO	UBC7_WHEAT	Ubiquitin-conjugating enzyme E2 7 (EC 6.3.2.19) (Ubiquitin-protein ligase 7) (Ubiquitin carrier prot ...	0.29	-	mit	0					168
O00103 UniProt NPD GO	UBC11_SCHPO	Ubiquitin-conjugating enzyme E2-20 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.29	-	nuc	0					176
Q9JJR6 UniProt NPD GO	CK016_MOUSE	Uncharacterized protein C11orf16 homolog	0.29	-	nuc	0					402
Q5XIL6 UniProt NPD GO	CT135_RAT	Uncharacterized protein C20orf135 homolog	0.29	-	mit	0					474
Q8R100 UniProt NPD GO	CF188_MOUSE	Uncharacterized protein C6orf188 homolog	0.29	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				309
P40084 UniProt NPD GO	YEW9_YEAST	Uncharacterized protein YER139C	0.29	-	nuc	0		cytoplasm [IDA]			226
P38878 UniProt NPD GO	YHZ2_YEAST	Uncharacterized protein YHR192W	0.29	-	nuc	2	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			278
P40481 UniProt NPD GO	YIL0_YEAST	Uncharacterized protein YIL110W	0.29	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			377
Q3E7A3 UniProt NPD GO	YJ133_YEAST	Uncharacterized protein YJL133C-A	0.29	-	mit	0	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein (Potential)				74
Q3E7A0 UniProt NPD GO	YK106_YEAST	Uncharacterized protein YKL106C-A	0.29	-	nuc	0					39
Q3E7Z0 UniProt NPD GO	YN227_YEAST	Uncharacterized protein YNL277W-A	0.29	-	mit	0					62
Q3E7B3 UniProt NPD GO	YPR08_YEAST	Uncharacterized protein YPR108W-A	0.29	-	nuc	0					70
P53932 UniProt NPD GO	YNJ5_YEAST	Uncharacterized transporter YNL095C	0.29	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				642
Q9V359 UniProt NPD GO	VPS28_DROME	VPS28 protein homolog	0.29	-	cyt	0					210
O00780 UniProt NPD GO	VATE_DICDI	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit)	0.29	-	nuc	0					233
P39968 UniProt NPD GO	VAC8_YEAST	Vacuolar protein 8	0.29	-	nuc	0	Vacuole; vacuolar membrane; lipid-anchor	vacuole (sensu Fungi) [IDA]			577
Q9BGZ0 UniProt NPD GO	VP13A_MACFA	Vacuolar protein sorting 13A (Chorein) (Chorea-acanthocytosis protein homolog) (Fragment)	0.29	-	cyt	0					619
P0C0A2 UniProt NPD GO	VPS36_RAT	Vacuolar protein sorting protein 36 (ELL-associated protein of 45 kDa)	0.29	-	cyt	0	Cytoplasm. Endosome; late endosome (By similarity). Colocalizes with ubiquitinated proteins on late ...				386
P26329 UniProt NPD GO	VSI4_TRYBB	Variant surface glycoprotein ILTAT 1.24 precursor (VSG)	0.29	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...			2VSG	514
P06014 UniProt NPD GO	VSI6_TRYBB	Variant surface glycoprotein ILTAT 1.3 precursor (VSG)	0.29	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				503
Q9WU02 UniProt NPD GO	V1BR_MOUSE	Vasopressin V1b receptor (V1bR) (AVPR V1b) (Vasopressin V3 receptor) (AVPR V3) (Antidiuretic hormone ...	0.29	-	end	7 *	Membrane; multi-pass membrane protein				421

You are viewing entries 41851 to 41900 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.