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
P31335 UniProt NPD GO	PUR9_CHICK	Bifunctional purine biosynthesis protein PURH [Includes: Phosphoribosylaminoimidazolecarboxamide for ...	0.14	-	cyt	0				1THZ	593
O46403 UniProt NPD GO	PGS1_HORSE	Biglycan precursor (Bone/cartilage proteoglycan I) (PG-S1)	0.14	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				372
Q02247 UniProt NPD GO	BCP4_RABIT	Blastocyst protein 4 precursor	0.14	-	nuc	0					95
P81705 UniProt NPD GO	IBB_ERYVA	Bowman-Birk type proteinase inhibitor (EBI)	0.14	-	nuc	0					61
P07679 UniProt NPD GO	IBB1_COILA	Bowman-Birk type trypsin inhibitor TI1	0.14	-	nuc	0					64
P30423 UniProt NPD GO	BPP3_BOTIN	Bradykinin-potentiating peptide S4,3,2 (10C) (Angiotensin-converting enzyme inhibitor)	0.14	-		0					11
P40842 UniProt NPD GO	BR2EF_RANES	Brevinin-2Ef precursor	0.14	-	exc	0	Secreted protein				74
Q62556 UniProt NPD GO	BT1A1_MOUSE	Butyrophilin subfamily 1 member A1 precursor (BT)	0.14	-	end	1	Membrane; single-pass type I membrane protein				524
Q6MG97 UniProt NPD GO	BTNL2_RAT	Butyrophilin-like protein 2 precursor	0.14	-	cyt	0	Secreted protein; extracellular space (Potential)				454
Q05611 UniProt NPD GO	BSC2_YEAST	Bypass of stop codon protein 2	0.14	-	cyt	1	Membrane-bound. Punctate lipid particles	lipid particle [IDA]			235
Q95ND1 UniProt NPD GO	CCR5_MANSP	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.14	-	end	6 *	Membrane; multi-pass membrane protein				352
Q99417 UniProt NPD GO	MYCBP_HUMAN	C-Myc-binding protein (Associate of Myc 1) (AMY-1)	0.14	-	nuc	0	Cytoplasm. Nucleus. Translocates into the nucleus in the S phase of the cell cycle upon an increase ...	cytoplasm [IDA] nucleus [TAS]	606535		102
Q5KSK8 UniProt NPD GO	CXCR3_CANFA	C-X-C chemokine receptor type 3 (CXC-R3) (CXCR-3) (Interferon-inducible protein 10 receptor) (IP-10 ...	0.14	+	end	7	Membrane; multi-pass membrane protein (By similarity)				365
Q07203 UniProt NPD GO	CRP_XENLA	C-reactive protein precursor (CRP)	0.14	-	end	0	Secreted protein				238
Q8WXI8 UniProt NPD GO	CLC4D_HUMAN	C-type lectin domain family 4 member D (C-type lectin superfamily member 8) (C-type lectin-like rece ...	0.14	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)		609964		215
P40756 UniProt NPD GO	ANFD_RANCA	C-type natriuretic peptide 2 precursor (CNP II)	0.14	-	mit	0	Secreted protein				118
Q16581 UniProt NPD GO	C3AR_HUMAN	C3a anaphylatoxin chemotactic receptor (C3a-R) (C3AR)	0.14	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	605246		482
O55197 UniProt NPD GO	C3AR_RAT	C3a anaphylatoxin chemotactic receptor (C3a-R) (C3AR)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				473
P79175 UniProt NPD GO	C5AR_GORGO	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen) (Fragment)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				340
P79188 UniProt NPD GO	C5AR_MACMU	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen) (Fragment)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				340
P79240 UniProt NPD GO	C5AR_PANTR	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen) (Fragment)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				340
P47154 UniProt NPD GO	STE24_YEAST	CAAX prenyl protease 1 (EC 3.4.24.84) (Prenyl protein-specific endoprotease 1) (PPSEP 1) (A-factor-c ...	0.14	-	mit	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA] mitochondrial outer membrane [IDA]			453
O75844 UniProt NPD GO	FACE1_HUMAN	CAAX prenyl protease 1 homolog (EC 3.4.24.84) (Prenyl protein-specific endoprotease 1) (Farnesylated ...	0.14	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...		608612		475
P27548 UniProt NPD GO	CD40L_MOUSE	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) (TNF-relate ...	0.14	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists a ...	integral to membrane [ISS] soluble fraction [ISS]		1CDA	260
Q8TAZ6 UniProt NPD GO	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain-containing protein 2 (Chemokine-like factor superfamily member ...	0.14	-	end	3	Membrane; multi-pass membrane protein		607885		248
Q9SRT7 UniProt NPD GO	COBL1_ARATH	COBRA-like protein 1 precursor	0.14	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	anchored to membrane [TAS]			452
Q9CZG3 UniProt NPD GO	COMD8_MOUSE	COMM domain-containing protein 8	0.14	-	cyt	0					183
Q75CD6 UniProt NPD GO	CSN11_ASHGO	COP9 signalosome complex subunit 11	0.14	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)				420
Q8W1P0 UniProt NPD GO	CSN6B_ARATH	COP9 signalosome complex subunit 6b (Signalosome subunit 6b) (AtCSN6b)	0.14	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)				317
Q09722 UniProt NPD GO	CSN7B_SCHPO	COP9 signalosome complex subunit 7B	0.14	-	nuc	0		cytoplasm [IDA] eukaryotic translation initiation factor 3 ... [IDA]			402
Q6P3W2 UniProt NPD GO	ZCSL3_HUMAN	CSL-type zinc finger-containing protein 3	0.14	-	cyt	0					148
Q8SQI7 UniProt NPD GO	PYRG_ENCCU	CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) (CTP synthetase)	0.14	-	cyt	0					535
P49594 UniProt NPD GO	FEM2_CAEEL	Ca(2+)/calmodulin-dependent protein kinase phosphatase (EC 3.1.3.16) (CaM-kinase phosphatase) (CaMKP ...	0.14	-	cyt	0					449
Q9HDE1 UniProt NPD GO	CANB_CRYNE	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.14	-	cyt	0					175
Q14206 UniProt NPD GO	CCP2_HUMAN	Calcipressin-2 (Thyroid hormone-responsive protein ZAKI-4) (Down syndrome candidate region 1-like 1) ...	0.14	-	nuc	0			604876		197
O46372 UniProt NPD GO	KCMB1_RABIT	Calcium-activated potassium channel subunit beta 1 (Calcium-activated potassium channel, subfamily M ...	0.14	-	mit	2 *	Membrane; multi-pass membrane protein				190
O75746 UniProt NPD GO	CMC1_HUMAN	Calcium-binding mitochondrial carrier protein Aralar1 (Mitochondrial aspartate glutamate carrier 1) ...	0.14	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to plasma membrane [TAS] mitochondrion [TAS]	603667		678
Q8BH59 UniProt NPD GO	CMC1_MOUSE	Calcium-binding mitochondrial carrier protein Aralar1 (Mitochondrial aspartate glutamate carrier 1) ...	0.14	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			677
Q9JLK3 UniProt NPD GO	CABP5_MOUSE	Calcium-binding protein 5 (CaBP5)	0.14	-	cyt	0					173
Q9XES1 UniProt NPD GO	ECA4_ARATH	Calcium-transporting ATPase 4, endoplasmic reticulum-type (EC 3.6.3.8)	0.14	-	end	8	Membrane; multi-pass membrane protein				1061
Q14012 UniProt NPD GO	KCC1A_HUMAN	Calcium/calmodulin-dependent protein kinase type 1 (EC 2.7.11.17) (CaM kinase I) (CaM-KI) (CaM kinas ...	0.14	-	cyt	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity)		604998		370
O42844 UniProt NPD GO	KCC2_SCHPO	Calcium/calmodulin-dependent protein kinase type II (EC 2.7.11.17) (CAM kinase II)	0.14	-	cyt	0	Cytoplasm	cytoplasm [IDA]			504
P61861 UniProt NPD GO	CALM_COLGL	Calmodulin (CaM)	0.14	-	cyt	0					148
P61860 UniProt NPD GO	CALM_COLTR	Calmodulin (CaM)	0.14	-	cyt	0					148
Q9UWF0 UniProt NPD GO	CALM_MAGGR	Calmodulin (CaM)	0.14	-	cyt	0					148
P61859 UniProt NPD GO	CALM_NEUCR	Calmodulin (CaM)	0.14	-	cyt	0					148
Q61KR9 UniProt NPD GO	CALR_CAEBR	Calreticulin precursor	0.14	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				396
P05434 UniProt NPD GO	CATR_CHLRE	Caltractin (Centrin) (20 kDa calcium-binding protein)	0.14	-	cyt	0				2AMI	169
P06833 UniProt NPD GO	CALT_BOVIN	Caltrin precursor (Calcium transport inhibitor) (Seminalplasmin) (SPLN)	0.14	-	exc	1 *					80
P07756 UniProt NPD GO	CPSM_RAT	Carbamoyl-phosphate synthase [ammonia], mitochondrial precursor (EC 6.3.4.16) (Carbamoyl-phosphate s ...	0.14	-	mit	0	Mitochondrion				1500

You are viewing entries 58051 to 58100 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.