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
Q00204 UniProt NPD GO	PALB_EMENI	Calpain-like protease palB (EC 3.4.22.-) (Cysteine protease palB)	0.32	-	mit	0					847
Q4VIT5 UniProt NPD GO	CALR_CERAE	Calreticulin precursor	0.32	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				417
Q4R6K8 UniProt NPD GO	CALR_MACFA	Calreticulin precursor	0.32	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				417
Q2HWU3 UniProt NPD GO	CALR_MACFU	Calreticulin precursor	0.32	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				417
P27797 UniProt NPD GO	CALR_HUMAN	Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (grp60)	0.32	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Cytoplasm; cytosol. Secreted protein; extracellu ...	cytosol [IDA] endoplasmic reticulum [TAS] endoplasmic reticulum lumen [IDA]	109091	2CLR	417
P07090 UniProt NPD GO	CALB2_CHICK	Calretinin (CR)	0.32	-	cyt	0					269
O42778 UniProt NPD GO	CARP8_CANAL	Candidapepsin-8 precursor (EC 3.4.23.24) (Aspartate protease 8) (ACP 8) (Secreted aspartic protease ...	0.32	-	exc	0	Secreted protein				405
Q76EC5 UniProt NPD GO	CHST9_MOUSE	Carbohydrate sulfotransferase 9 (EC 2.8.2.-) (N-acetylgalactosamine-4-O-sulfotransferase 2) (GalNAc- ...	0.32	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				413
Q704S8 UniProt NPD GO	CACP_RAT	Carnitine O-acetyltransferase (EC 2.3.1.7) (Carnitine acetylase) (CAT) (Carnitine acetyltransferase) ...	0.32	-	pox	0	Endoplasmic reticulum (Potential). Peroxisome (Potential). Mitochondrion; mitochondrial inner membra ...				626
O59906 UniProt NPD GO	CSK2B_CANAL	Casein kinase II subunit beta (CK II beta)	0.32	-	cyt	0					294
P42575 UniProt NPD GO	CASP2_HUMAN	Caspase-2 precursor (EC 3.4.22.-) (CASP-2) (ICH-1 protease) (ICH-1L/1S) [Contains: Caspase-2 subunit ...	0.32	-	cyt	0			600639	1PYO	452
Q8MJU1 UniProt NPD GO	CASP3_FELCA	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) [Contains: Caspase-3 p17 subunit; Caspase-3 p12 subunit]	0.32	-	nuc	0	Cytoplasm				277
Q2YDG3 UniProt NPD GO	CD123_BOVIN	Cell division cycle protein 123 homolog	0.32	-	cyt	0	Cytoplasm (By similarity)				335
Q2PG37 UniProt NPD GO	CD123_MACFA	Cell division cycle protein 123 homolog	0.32	-	cyt	0	Cytoplasm (By similarity)				336
Q9CWM2 UniProt NPD GO	CDCA4_MOUSE	Cell division cycle-associated protein 4 (Hematopoietic progenitor protein)	0.32	-	nuc	0					237
Q9JKA5 UniProt NPD GO	GPA33_MOUSE	Cell surface A33 antigen precursor (Glycoprotein A33) (mA33)	0.32	-	mit	1	Membrane; single-pass type I membrane protein (By similarity)	plasma membrane [IDA]			319
P50112 UniProt NPD GO	KNH1_YEAST	Cell wall synthesis protein KNH1 precursor	0.32	-	cyt	0	Cell surface. Secreted, probably found at cell surface	cell wall (sensu Fungi) [NAS] extracellular region [IDA]			268
O44219 UniProt NPD GO	ZW10_DROGR	Centromere/kinetochore protein zw10 (Mitotic 15 protein)	0.32	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Excluded from the nucleus during interphase but ...				714
Q5ZKX1 UniProt NPD GO	CHM1B_CHICK	Charged multivesicular body protein 1b (Chromatin-modifying protein 1b) (CHMP1b)	0.32	-	nuc	0	Cytoplasm (By similarity)				199
Q12114 UniProt NPD GO	CHS5_YEAST	Chitin biosynthesis protein CHS5 (Protein CAL3)	0.32	+	nuc	0	Golgi apparatus	cytoplasm [IDA]			671
Q00757 UniProt NPD GO	CHSB_EMENI	Chitin synthase B (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase B) (Class-III chitin syn ...	0.32	-	end	7	Cell membrane; multi-pass membrane protein				916
Q8T0R7 UniProt NPD GO	IDGF5_DROME	Chitinase-like protein Idgf5 precursor (Imaginal disk growth factor protein 5)	0.32	-	end	0	Secreted protein (By similarity). Secreted in hemolymph (By similarity). It is probably transported ...	extracellular region [NAS]			444
Q9TT16 UniProt NPD GO	CLCN6_RABIT	Chloride channel protein 6 (ClC-6)	0.32	-	end	9	Membrane; multi-pass membrane protein (Potential)				869
P35524 UniProt NPD GO	CLCN1_RAT	Chloride channel protein, skeletal muscle (Chloride channel protein 1) (ClC-1)	0.32	-	end	11	Membrane; multi-pass membrane protein				994
Q70XX6 UniProt NPD GO	RR11_AMBTC	Chloroplast 30S ribosomal protein S11	0.32	-	nuc	0	Plastid; chloroplast				138
Q6YXJ8 UniProt NPD GO	RR11_PHYPA	Chloroplast 30S ribosomal protein S11	0.32	-	mit	0	Plastid; chloroplast				130
P41630 UniProt NPD GO	RR11_PINTH	Chloroplast 30S ribosomal protein S11	0.32	-	nuc	0	Plastid; chloroplast				130
Q2PMQ2 UniProt NPD GO	RR11_SOYBN	Chloroplast 30S ribosomal protein S11	0.32	-	nuc	0	Plastid; chloroplast				138
P06506 UniProt NPD GO	RR11_SPIOL	Chloroplast 30S ribosomal protein S11	0.32	-	mit	0	Plastid; chloroplast				137
Q8W8R9 UniProt NPD GO	RR12_PSINU	Chloroplast 30S ribosomal protein S12	0.32	-	mit	0	Plastid; chloroplast				123
Q70XV7 UniProt NPD GO	RR15_AMBTC	Chloroplast 30S ribosomal protein S15	0.32	-	nuc	0	Plastid; chloroplast				87
Q3V4Z8 UniProt NPD GO	RR8_ACOCL	Chloroplast 30S ribosomal protein S8	0.32	-	nuc	0	Plastid; chloroplast				132
Q4VZK0 UniProt NPD GO	RR8_CUCSA	Chloroplast 30S ribosomal protein S8	0.32	-	nuc	0	Plastid; chloroplast				134
P49554 UniProt NPD GO	RK18_ODOSI	Chloroplast 50S ribosomal protein L18	0.32	-	nuc	0	Plastid; chloroplast				135
Q85FH8 UniProt NPD GO	RK21_ADICA	Chloroplast 50S ribosomal protein L21	0.32	-	cyt	0	Plastid; chloroplast				127
O46896 UniProt NPD GO	RK23_GUITH	Chloroplast 50S ribosomal protein L23	0.32	-	cyt	0	Plastid; chloroplast				95
P49564 UniProt NPD GO	RK32_ODOSI	Chloroplast 50S ribosomal protein L32	0.32	-	nuc	0	Plastid; chloroplast				57
Q9BBQ2 UniProt NPD GO	RK36_LOTJA	Chloroplast 50S ribosomal protein L36	0.32	-	mit	0	Plastid; chloroplast				37
Q9TLU4 UniProt NPD GO	RK5_CYACA	Chloroplast 50S ribosomal protein L5	0.32	-	cyt	0	Plastid; chloroplast				182
P80344 UniProt NPD GO	CCKN_RANCA	Cholecystokinins precursor (CCK) [Contains: Cholecystokinin 58 (CCK58); Cholecystokinin 33 (CCK33); ...	0.32	-	exc	0					130
Q9H2X0 UniProt NPD GO	CHRD_HUMAN	Chordin precursor	0.32	-	exc	0	Secreted protein (By similarity)		603475		955
Q757R4 UniProt NPD GO	EAF5_ASHGO	Chromatin modification-related protein EAF5	0.32	-	cyt	0	Nucleus (By similarity)				221
P02894 UniProt NPD GO	CSP_PLAKH	Circumsporozoite protein precursor (CS)	0.32	-	mit	1					363
O95639 UniProt NPD GO	CPSF4_HUMAN	Cleavage and polyadenylation specificity factor 30 kDa subunit (CPSF 30 kDa subunit) (NS1 effector d ...	0.32	-	nuc	0	Nucleus		603052		269
P33240 UniProt NPD GO	CSTF2_HUMAN	Cleavage stimulation factor 64 kDa subunit (CSTF 64 kDa subunit) (CF-1 64 kDa subunit) (CstF-64)	0.32	-	nuc	0	Nucleus	nucleus [TAS]	600368	1P1T	577
Q5RDA3 UniProt NPD GO	CSTF2_PONPY	Cleavage stimulation factor 64 kDa subunit (CSTF 64 kDa subunit) (CF-1 64 kDa subunit) (CstF-64)	0.32	-	nuc	0	Nucleus (By similarity)				577
Q3T0E3 UniProt NPD GO	CCD56_BOVIN	Coiled-coil domain-containing protein 56	0.32	-	nuc	1	Membrane; single-pass membrane protein (Potential)				106
Q9BSY4 UniProt NPD GO	CHCH5_HUMAN	Coiled-coil-helix-coiled-coil-helix domain-containing protein 5	0.32	-	nuc	0					110
P02453 UniProt NPD GO	CO1A1_BOVIN	Collagen alpha-1(I) chain precursor	0.32	-	exc	0					1463
P02454 UniProt NPD GO	CO1A1_RAT	Collagen alpha-1(I) chain precursor	0.32	-	exc	0				1YGV	1453

You are viewing entries 38351 to 38400 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.