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
P21591 UniProt NPD GO	BOMB_BOMOR	Bombesin precursor	0.31	-	exc	0	Secreted protein				119
P19860 UniProt NPD GO	IBB2_SETIT	Bowman-Birk type major trypsin inhibitor (FMTI-II)	0.31	-	nuc	0					67
P81713 UniProt NPD GO	IBB3_WHEAT	Bowman-Birk type trypsin inhibitor (WTI)	0.31	-	nuc	0					71
P25429 UniProt NPD GO	BDNF_CHICK	Brain-derived neurotrophic factor precursor (BDNF)	0.31	-	nuc	0	Secreted protein				246
P55068 UniProt NPD GO	PGCB_RAT	Brevican core protein precursor (Brain-enriched hyaluronan-binding protein) (Protein BEHAB) [Contain ...	0.31	-	exc	0	Isoform 1: Secreted protein; extracellular space; extracellular matrix. Isoform 2: Membrane; lipid-a ...	synapse [IPI] synaptic vesicle membrane [IPI]			883
O88201 UniProt NPD GO	CLC11_RAT	C-type lectin domain family 11 member A precursor (Stem cell growth factor) (Lymphocyte secreted C-t ...	0.31	-	vac	0	Cytoplasm (By similarity). Secreted protein (By similarity)	extracellular region [ISS]			328
Q805D3 UniProt NPD GO	ANFC4_FUGRU	C-type natriuretic peptide 4 precursor	0.31	-	nuc	0	Secreted protein				120
P41319 UniProt NPD GO	ANFC_SQUAC	C-type natriuretic peptide precursor	0.31	-	exc	0	Secreted protein				135
Q91ZW9 UniProt NPD GO	C209C_MOUSE	CD209 antigen-like protein C (DC-SIGN-related protein 2) (DC-SIGNR2)	0.31	-	mit	0					178
Q9BDM3 UniProt NPD GO	CD40L_AOTTR	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.31	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			261
Q9DAC0 UniProt NPD GO	CLF2B_MOUSE	CKLF-like MARVEL transmembrane domain-containing protein 2B (Chemokine-like factor superfamily membe ...	0.31	-	end	4 *	Membrane; multi-pass membrane protein				210
Q64690 UniProt NPD GO	SIA8D_CRIGR	CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase (EC 2.4.99.-) (Alpha-2,8-sialyltransferase ...	0.31	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				359
Q8N668 UniProt NPD GO	COMD1_HUMAN	COMM domain-containing protein 1 (Protein Murr1)	0.31	-	nuc	0			607238		190
Q9GZQ3 UniProt NPD GO	COMD5_HUMAN	COMM domain-containing protein 5 (Hypertension-related calcium-regulated gene protein) (HCaRG)	0.31	-	cyt	0	Nucleus (By similarity)		608216		224
Q9ERR2 UniProt NPD GO	COMD5_RAT	COMM domain-containing protein 5 (Hypertension-related calcium-regulated gene protein) (HCaRG)	0.31	-	nuc	0	Nucleus				224
Q8K2Q0 UniProt NPD GO	COMD9_MOUSE	COMM domain-containing protein 9	0.31	-	nuc	0					198
Q4P8T5 UniProt NPD GO	CSN12_USTMA	COP9 signalosome complex subunit 12	0.31	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				454
Q7ZTN8 UniProt NPD GO	CSN3_XENLA	COP9 signalosome complex subunit 3 (Signalosome subunit 3)	0.31	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				423
Q2M197 UniProt NPD GO	PYRG_DROPS	CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) (CTP synthetase)	0.31	-	cyt	0					637
P79883 UniProt NPD GO	CADH4_XENLA	Cadherin-4 precursor (Maternally expressed neural cadherin) (XmN-cadherin)	0.31	-	end	1	Membrane; single-pass type I membrane protein				922
O02840 UniProt NPD GO	CADH5_PIG	Cadherin-5 precursor (Vascular endothelial-cadherin) (VE-cadherin) (CD144 antigen)	0.31	+	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein (By similarity). Cell membran ...				782
Q9JHG6 UniProt NPD GO	CCP1_MOUSE	Calcipressin-1 (Down syndrome critical region protein 1 homolog) (Myocyte-enriched calcineurin-inter ...	0.31	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1WEY	198
O35847 UniProt NPD GO	CCP1_CRIGR	Calcipressin-1 (Down syndrome critical region protein 1 homolog) (Oxidative-induced protein Adapt78) ...	0.31	-	nuc	0					197
Q60482 UniProt NPD GO	CRCP_CAVPO	Calcitonin gene-related peptide-receptor component protein (CGRP-receptor component protein) (CGRP-R ...	0.31	-	nuc	0					146
P70160 UniProt NPD GO	CALC_MOUSE	Calcitonin precursor	0.31	-	exc	0	Secreted protein	extracellular region [IDA] intracellular [IDA]			136
P32214 UniProt NPD GO	CALCR_RAT	Calcitonin receptor precursor (CT-R) (C1A/C1B)	0.31	-	end	7	Membrane; multi-pass membrane protein				516
P48233 UniProt NPD GO	CMC1_YEAST	Calcium-binding mitochondrial carrier SAL1 (Suppressor of AAC2 lethality)	0.31	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				545
P28583 UniProt NPD GO	CDPK_SOYBN	Calcium-dependent protein kinase SK5 (EC 2.7.11.1) (CDPK)	0.31	-	mit	0				1S6J	508
Q42883 UniProt NPD GO	ECAP_LYCES	Calcium-transporting ATPase, endoplasmic reticulum-type (EC 3.6.3.8)	0.31	+	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			1048
P97756 UniProt NPD GO	KKCC1_RAT	Calcium/calmodulin-dependent protein kinase kinase 1 (EC 2.7.11.17) (Calcium/calmodulin-dependent pr ...	0.31	-	nuc	0	Cytoplasm. Nucleus			1CKK	505
O88501 UniProt NPD GO	CAN6_RAT	Calpain-6	0.31	-	nuc	0					641
Q27178 UniProt NPD GO	CATR3_PARTE	Caltractin ICL1C (Centrin)	0.31	-	mit	0	ICL, innermost fibrous network of the cortical cytoskeleton				183
P32198 UniProt NPD GO	CPT1A_RAT	Carnitine O-palmitoyltransferase I, liver isoform (EC 2.3.1.21) (CPT I) (CPTI-L) (Carnitine palmitoy ...	0.31	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial outer membrane [IDA]			773
O75718 UniProt NPD GO	CRTAP_HUMAN	Cartilage-associated protein precursor	0.31	-	end	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)		605497		401
P67827 UniProt NPD GO	KC1A_BOVIN	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1)	0.31	-	nuc	0	Cytoplasm				325
P67828 UniProt NPD GO	KC1A_RABIT	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1)	0.31	-	nuc	0	Cytoplasm				325
P67829 UniProt NPD GO	KC1A_SHEEP	Casein kinase I isoform alpha (EC 2.7.11.1) (CKI-alpha) (CK1)	0.31	-	nuc	0	Cytoplasm				325
Q8JZX9 UniProt NPD GO	BORG1_MOUSE	Cdc42 effector protein 2 (Binder of Rho GTPases 1)	0.31	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)				214
P26449 UniProt NPD GO	BUB3_YEAST	Cell cycle arrest protein BUB3	0.31	-	mit	0	Nucleus (Probable)	condensed nuclear chromosome kinetochore [IPI]		1YFQ	341
Q8CII2 UniProt NPD GO	CD123_MOUSE	Cell division cycle protein 123 homolog	0.31	-	cyt	0	Cytoplasm (By similarity)				336
Q5BKN5 UniProt NPD GO	CD123_XENTR	Cell division cycle protein 123 homolog	0.31	-	cyt	0	Cytoplasm (By similarity)				335
Q8R349 UniProt NPD GO	CDC16_MOUSE	Cell division cycle protein 16 homolog (Anaphase-promoting complex subunit 6) (APC6) (Cyclosome subu ...	0.31	-	cyt	0		nucleus [IDA]			620
O74226 UniProt NPD GO	KRE9_CANAL	Cell wall synthesis protein KRE9 precursor	0.31	-	exc	0	Cell surface (By similarity). Secreted, probably found at cell surface (By similarity)				271
P39005 UniProt NPD GO	KRE9_YEAST	Cell wall synthesis protein KRE9 precursor	0.31	-	exc	1 *	Cell surface. Secreted, probably found at cell surface	extracellular region [IDA]			276
Q32LE3 UniProt NPD GO	CETN1_BOVIN	Centrin-1	0.31	-	mit	0	Centrosome. Centrosome of interphase and mitotic cells (By similarity)				172
Q6NUD8 UniProt NPD GO	CHM1A_XENLA	Charged multivesicular body protein 1a (Chromatin-modifying protein 1a) (CHMP1a)	0.31	-	nuc	0	Cytoplasm (By similarity)				196
O59732 UniProt NPD GO	CHR1_SCHPO	Chitin synthase regulatory factor 1 (Chs four homolog 4)	0.31	-	nuc	0					456
Q6C3K2 UniProt NPD GO	ALG1_YARLI	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.31	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				463
P51791 UniProt NPD GO	CLCN3_MOUSE	Chloride channel protein 3 (ClC-3)	0.31	-	end	11	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein (By similarity). End ...	cell surface [ISS] early endosome [ISS] Golgi apparatus [ISS] integral to membrane [ISS] late endosome [ISS] vesicle membrane [ISS]			760
P51792 UniProt NPD GO	CLCN3_RAT	Chloride channel protein 3 (ClC-3)	0.31	-	end	11	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein (By similarity). End ...	apical plasma membrane [IDA] cell surface [ISS] early endosome [ISS] Golgi apparatus [ISS] integral to membrane [ISS] late endosome [ISS] membrane [IDA] vesicle membrane [ISS]			760

You are viewing entries 39251 to 39300 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.