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
P97802 UniProt NPD GO	ANG3_MOUSE	Angiogenin-3 precursor (EC 3.1.27.-) (Angiogenin-related protein 2) (EF-5)	0.40	-	exc	0					145
Q9GLN6 UniProt NPD GO	ACET_PANTR	Angiotensin-converting enzyme, testis-specific isoform precursor (EC 3.4.15.1) (EC 3.2.1.-) (ACE-T) ...	0.40	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				732
Q8K0L0 UniProt NPD GO	ASB2_MOUSE	Ankyrin repeat and SOCS box protein 2 (ASB-2)	0.40	-	nuc	0					634
P15714 UniProt NPD GO	LP61_EIMTE	Antigen LPMC-61 (Fragment)	0.40	-	exc	0					255
Q9Z0F3 UniProt NPD GO	B2L10_MOUSE	Apoptosis regulator Bcl-B (Bcl-2-like 10 protein) (Bcl2-L-10) (Anti-apoptotic protein Boo) (Bcl-2 ho ...	0.40	-	cyt	1	Mitochondrion (By similarity). Nuclear membrane (By similarity)				191
Q400C9 UniProt NPD GO	AMZ1_RAT	Archaemetzincin-1 (EC 3.-.-.-) (Archeobacterial metalloproteinase-like protein 1)	0.40	-	cyt	0					501
Q766C2 UniProt NPD GO	NEP2_NEPGR	Aspartic proteinase nepenthesin-2 precursor (EC 3.4.23.-) (Nepenthesin-II)	0.40	-	nuc	0	Secreted protein (By similarity)				438
Q6FXR8 UniProt NPD GO	ATG8_CANGA	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.40	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				118
Q6ZL57 UniProt NPD GO	IAA24_ORYSA	Auxin-responsive protein IAA24 (Indoleacetic acid-induced protein 24)	0.40	-	exc	0	Nucleus (By similarity)				219
P0C128 UniProt NPD GO	IAA25_ORYSA	Auxin-responsive protein IAA25 (Indoleacetic acid-induced protein 25)	0.40	-	nuc	0	Nucleus (By similarity)				246
Q6Z5M0 UniProt NPD GO	IAA8_ORYSA	Auxin-responsive protein IAA8 (Indoleacetic acid-induced protein 8)	0.40	-	nuc	0	Nucleus (By similarity)				205
Q8HZP2 UniProt NPD GO	BKRB1_MACMU	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.40	+	end	7 *	Membrane; multi-pass membrane protein				352
Q8CI61 UniProt NPD GO	BAG4_MOUSE	BAG family molecular chaperone regulator 4 (BCL2-associated athanogene 4) (BAG-4) (Silencer of death ...	0.40	-	nuc	0	Cytoplasm				457
Q5RKQ0 UniProt NPD GO	BCAS2_BRARE	BCAS2 protein homolog	0.40	-	nuc	0	Nucleus (By similarity)				225
Q9D0L6 UniProt NPD GO	BAMBI_MOUSE	BMP and activin membrane-bound inhibitor homolog precursor (Putative transmembrane protein NMA)	0.40	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				260
Q5XKL5 UniProt NPD GO	BTBD8_HUMAN	BTB/POZ domain-containing protein 8	0.40	-	mit	0					378
Q96Q07 UniProt NPD GO	BTBD9_HUMAN	BTB/POZ domain-containing protein 9	0.40	-	cyt	0					612
P04280 UniProt NPD GO	PRP1_HUMAN	Basic salivary proline-rich protein 1 precursor (Salivary proline-rich protein) [Contains: Basic pep ...	0.40	-	exc	0		extracellular region [NAS]	180989		392
Q99JU7 UniProt NPD GO	BNIPL_MOUSE	Bcl-2/adenovirus E1B 19 kDa-interacting protein 2-like protein	0.40	-	cyt	0					328
Q9M367 UniProt NPD GO	BCN1_ARATH	Beclin-1-like protein	0.40	-	nuc	0					443
P17549 UniProt NPD GO	CP53_ASPNG	Benzoate 4-monooxygenase (EC 1.14.13.12) (Benzoate-para-hydroxylase) (Cytochrome P450 53) (BpH)	0.40	+	nuc	1 *		microsome [IDA]			517
Q9USX0 UniProt NPD GO	PVG3_SCHPO	Beta-1,3-galactosyltransferase pvg3 (EC 2.4.1.134) (Pyruvylated Gal-beta-1,3-epitope synthesis prote ...	0.40	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				378
P35224 UniProt NPD GO	CTNB_URECA	Beta-catenin	0.40	-	nuc	0					818
P87023 UniProt NPD GO	KRE6_CANAL	Beta-glucan synthesis-associated protein KRE6	0.40	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				740
O02604 UniProt NPD GO	DRTS_PLAVI	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.40	-	cyt	0				2BLC	623
O59778 UniProt NPD GO	BIOB_SCHPO	Biotin synthase (EC 2.8.1.6) (Biotin synthetase)	0.40	-	mit	0					363
Q9R229 UniProt NPD GO	BMP10_MOUSE	Bone morphogenetic protein 10 precursor (BMP-10)	0.40	-	mit	0	Secreted protein (By similarity)	extracellular region [IC]			420
P30886 UniProt NPD GO	BMP7_XENLA	Bone morphogenetic protein 7 precursor (BMP-7) (Osteogenic protein 1) (OP-1) (xBMP7)	0.40	-	exc	0	Secreted protein (By similarity)				426
O00238 UniProt NPD GO	BMR1B_HUMAN	Bone morphogenetic protein receptor type IB precursor (EC 2.7.11.30) (CDw293 antigen)	0.40	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [IC] receptor complex [TAS]	609441		502
P81993 UniProt NPD GO	CRVP_BUNCA	Bucarin (Fragment)	0.40	-	nuc	0	Secreted protein				67
Q8BWY2 UniProt NPD GO	CLC1A_MOUSE	C-type lectin domain family 1 member A	0.40	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)				269
P10716 UniProt NPD GO	CLC4F_RAT	C-type lectin domain family 4 member F (C-type lectin superfamily member 13) (C-type lectin 13) (Kup ...	0.40	-	nuc	1 *	Membrane; single-pass type II membrane protein				550
P42292 UniProt NPD GO	CD166_CHICK	CD166 antigen precursor (Activated leukocyte-cell adhesion molecule) (SC1 glycoprotein) (BEN glycopr ...	0.40	-	mit	2 *	Membrane; single-pass type I membrane protein				588
Q9LFW3 UniProt NPD GO	COBL4_ARATH	COBRA-like protein 4 precursor	0.40	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				431
Q75AS3 UniProt NPD GO	CSN10_ASHGO	COP9 signalosome complex subunit 10	0.40	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				553
Q6CRJ8 UniProt NPD GO	CSN5_KLULA	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.40	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				373
Q9V4S8 UniProt NPD GO	CSN7_DROME	COP9 signalosome complex subunit 7 (Signalosome subunit 7) (Dch7)	0.40	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IMP]			278
Q5R9X1 UniProt NPD GO	CADH2_PONPY	Cadherin-2 precursor (Neural-cadherin) (N-cadherin) (CDw325 antigen)	0.40	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				906
Q5RES7 UniProt NPD GO	CCP1_PONPY	Calcipressin-1 (Down syndrome critical region protein 1 homolog)	0.40	-	exc	0					197
Q99JA0 UniProt NPD GO	CALCA_MOUSE	Calcitonin gene-related peptide 1 precursor (Calcitonin gene-related peptide I) (CGRP-I) (Alpha-type ...	0.40	-	exc	0	Secreted protein	extracellular region [IDA] intracellular [IDA]			128
Q811Q0 UniProt NPD GO	KCMB2_RAT	Calcium-activated potassium channel subunit beta 2 (Calcium-activated potassium channel, subfamily M ...	0.40	-	mit	2 *	Membrane; multi-pass membrane protein (By similarity)				235
Q8VBY2 UniProt NPD GO	KKCC1_MOUSE	Calcium/calmodulin-dependent protein kinase kinase 1 (EC 2.7.11.17) (Calcium/calmodulin-dependent pr ...	0.40	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				505
P11925 UniProt NPD GO	ELHC_APLCA	Califin-C [Contains: Califin-C large subunit; Califin-C small subunit]	0.40	-	nuc	0	Secreted protein				54
Q39994 UniProt NPD GO	CALX_HELTU	Calnexin homolog precursor	0.40	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				540
P27730 UniProt NPD GO	CAN_SCHMA	Calpain (EC 3.4.22.-) (Calcium-activated neutral proteinase) (CANP)	0.40	-	cyt	0					758
Q27971 UniProt NPD GO	CAN2_BOVIN	Calpain-2 catalytic subunit (EC 3.4.22.53) (Calpain-2 large subunit) (Calcium-activated neutral prot ...	0.40	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				207
P06814 UniProt NPD GO	CAN2_RABIT	Calpain-2 catalytic subunit (EC 3.4.22.53) (Calpain-2 large subunit) (Calcium-activated neutral prot ...	0.40	-	cyt	0	Cytoplasm. Cell membrane. Translocates to the plasma membrane upon Ca(2+) binding				422
O08529 UniProt NPD GO	CAN2_MOUSE	Calpain-2 catalytic subunit precursor (EC 3.4.22.53) (Calpain-2 large subunit) (Calcium-activated ne ...	0.40	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				699
O08688 UniProt NPD GO	CAN5_MOUSE	Calpain-5 (EC 3.4.22.-) (nCL-3)	0.40	-	cyt	0					640
Q9HFC8 UniProt NPD GO	PALB_YARLI	Calpain-like protease palB/RIM13 (EC 3.4.22.-) (Cysteine protease RIM13)	0.40	-	cyt	0					795

You are viewing entries 31651 to 31700 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.