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
Q9PTJ6 UniProt NPD GO	CTDSL_CHICK	CTD small phosphatase-like protein (CTDSP-like) (Small C-terminal domain phosphatase 3) (Nuclear LIM ...	0.22	-	cyt	0	Nucleus (Potential)				275
Q5F3Z1 UniProt NPD GO	PYRG2_CHICK	CTP synthase 2 (EC 6.3.4.2) (UTP--ammonia ligase 2) (CTP synthetase 2)	0.22	-	cyt	0					586
P70408 UniProt NPD GO	CAD10_MOUSE	Cadherin-10 (T2-cadherin) (Fragment)	0.22	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				265
P81658 UniProt NPD GO	TXCA_DENAN	Calcicludin (Calcicludine) (CAC) (L-type calcium channel blocker)	0.22	-	nuc	0	Secreted protein			1BF0	60
O81223 UniProt NPD GO	CNBL4_ARATH	Calcineurin B-like protein 4 (Protein SALT OVERLY SENSITIVE 3)	0.22	-	cyt	0	Cell membrane; lipid-anchor			1V1G	221
P87072 UniProt NPD GO	CANB_NEUCR	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.22	+	cyt	0					174
P22947 UniProt NPD GO	TXCAS_DENPO	Calciseptin (Calciseptine) (CaS) (L-type calcium channel blocker)	0.22	-	mit	0	Secreted protein				60
Q9NZU7 UniProt NPD GO	CABP1_HUMAN	Calcium-binding protein 1 (CaBP1) (Calbrain)	0.22	-	cyt	0	Cytoplasm. Cytoskeleton. Cell membrane; lipid-anchor; cytoplasmic side. L-CaBP1 is associated most l ...		605563		226
P53684 UniProt NPD GO	CDPK3_ORYSA	Calcium-dependent protein kinase, isoform 11 (EC 2.7.11.1) (CDPK 11)	0.22	-	mit	0					542
O81108 UniProt NPD GO	ACA2_ARATH	Calcium-transporting ATPase 2, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 2)	0.22	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				1014
P22189 UniProt NPD GO	ATC3_SCHPO	Calcium-transporting ATPase 3 (EC 3.6.3.8)	0.22	-	end	9	Membrane; multi-pass membrane protein				1037
Q6P2M8 UniProt NPD GO	KCC1B_HUMAN	Calcium/calmodulin-dependent protein kinase type 1B (EC 2.7.11.17) (CaM kinase IB) (CaM kinase I bet ...	0.22	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				343
Q5RCC4 UniProt NPD GO	KCC2A_PONPY	Calcium/calmodulin-dependent protein kinase type II alpha chain (EC 2.7.11.17) (CaM-kinase II alpha ...	0.22	-	mit	0					478
P25071 UniProt NPD GO	TCH3_ARATH	Calmodulin-related protein 3, touch-induced	0.22	-	cyt	0					324
Q27970 UniProt NPD GO	CAN1_BOVIN	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.22	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				716
P35750 UniProt NPD GO	CAN1_PIG	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.22	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				714
Q2HJ38 UniProt NPD GO	CNN1_BOVIN	Calponin-1 (Calponin H1, smooth muscle) (Basic calponin)	0.22	-	nuc	0					297
O81919 UniProt NPD GO	CALR_BETVU	Calreticulin precursor	0.22	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				416
P23589 UniProt NPD GO	CAH5A_MOUSE	Carbonic anhydrase 5A, mitochondrial precursor (EC 4.2.1.1) (Carbonic anhydrase VA) (Carbonate dehyd ...	0.22	-	mit	0	Mitochondrion	mitochondrion [IDA]		1URT	299
P38930 UniProt NPD GO	CSK2C_YEAST	Casein kinase II subunit beta' (CK II beta')	0.22	-	cyt	0		protein kinase CK2 complex [IDA]			258
P81138 UniProt NPD GO	CAT1_PENJA	Catalase (EC 1.11.1.6)	0.22	-	mit	0					696
P24270 UniProt NPD GO	CATA_MOUSE	Catalase (EC 1.11.1.6)	0.22	-	cyt	0	Peroxisome	mitochondrion [IDA] peroxisomal membrane [IDA]			526
P49315 UniProt NPD GO	CATA1_NICPL	Catalase isozyme 1 (EC 1.11.1.6) (Fragment)	0.22	-	cyt	0	Peroxisome (Potential)				485
P29756 UniProt NPD GO	CATA1_SOYBN	Catalase-1/2 (EC 1.11.1.6)	0.22	-	nuc	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
P25819 UniProt NPD GO	CATA2_ARATH	Catalase-2 (EC 1.11.1.6)	0.22	-	cyt	0	Peroxisome. Glyoxysome				492
O14072 UniProt NPD GO	ATC4_SCHPO	Cation-transporting ATPase 4 (EC 3.6.3.-)	0.22	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			1211
Q06689 UniProt NPD GO	YL413_YEAST	Cell membrane protein YLR413W precursor	0.22	-	end	4 *	Cell membrane; multi-pass membrane protein (Potential)				675
Q3T0Q6 UniProt NPD GO	CNBP_BOVIN	Cellular nucleic acid-binding protein (CNBP) (Zinc finger protein 9)	0.22	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity)				170
O42395 UniProt NPD GO	CNBP_CHICK	Cellular nucleic acid-binding protein (CNBP) (Zinc finger protein 9)	0.22	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity)				172
P62633 UniProt NPD GO	CNBP_HUMAN	Cellular nucleic acid-binding protein (CNBP) (Zinc finger protein 9)	0.22	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity)		602668		177
Q5R5R5 UniProt NPD GO	CNBP_PONPY	Cellular nucleic acid-binding protein (CNBP) (Zinc finger protein 9)	0.22	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity)				177
P62634 UniProt NPD GO	CNBP_RAT	Cellular nucleic acid-binding protein (CNBP) (Zinc finger protein 9)	0.22	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity)				177
P12271 UniProt NPD GO	CRAL_HUMAN	Cellular retinaldehyde-binding protein (CRALBP)	0.22	-	nuc	0	Cytoplasm	soluble fraction [TAS]	607476		316
P38696 UniProt NPD GO	ARP1_YEAST	Centractin (Actin-like protein)	0.22	-	cyt	0		dynactin complex [IDA]			384
Q9SEP4 UniProt NPD GO	CHSY_ARAAL	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.22	-	cyt	0					391
P48385 UniProt NPD GO	CHSY_CALCH	Chalcone synthase (EC 2.3.1.74) (Naringenin-chalcone synthase)	0.22	-	nuc	0					398
P53414 UniProt NPD GO	CHS1_SECCE	Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1)	0.22	-	cyt	0					392
P51081 UniProt NPD GO	CHSA_PEA	Chalcone synthase 1A (EC 2.3.1.74) (Naringenin-chalcone synthase 1A)	0.22	-	nuc	0					389
P51082 UniProt NPD GO	CHSB_PEA	Chalcone synthase 1B (EC 2.3.1.74) (Naringenin-chalcone synthase 1B)	0.22	-	cyt	0					389
P13417 UniProt NPD GO	CHS3_SINAL	Chalcone synthase 3 (EC 2.3.1.74) (Naringenin-chalcone synthase 3)	0.22	-	cyt	0					395
Q5E994 UniProt NPD GO	CHM1B_BOVIN	Charged multivesicular body protein 1b (Chromatin-modifying protein 1b) (CHMP1b)	0.22	-	nuc	0	Cytoplasm; cytosol (By similarity). Endosome (By similarity)				199
P46094 UniProt NPD GO	XCR1_HUMAN	Chemokine XC receptor 1 (XC chemokine receptor 1) (Lymphotactin receptor) (G-protein coupled recepto ...	0.22	+	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600552		333
P30595 UniProt NPD GO	CHS2_RHIOL	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2)	0.22	-	end	7	Cell membrane; multi-pass membrane protein				858
Q8MM24 UniProt NPD GO	IDGF1_DROME	Chitinase-like protein Idgf1 precursor (Imaginal disk growth factor protein 1)	0.22	-	exc	0	Secreted protein. Secreted in hemolymph. It is probably transported to target tissues via hemolymph	extracellular region [NAS]			439
P16661 UniProt NPD GO	ALG1_YEAST	Chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) (GDP-mannose-dolichol diphospho ...	0.22	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (Potenti ...	endoplasmic reticulum [IPI]			449
Q5E9B7 UniProt NPD GO	CLIC1_BOVIN	Chloride intracellular channel protein 1	0.22	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	brush border [ISS] cytoplasm [ISS] membrane fraction [ISS] soluble fraction [ISS]			240
Q5R957 UniProt NPD GO	CLIC4_PONPY	Chloride intracellular channel protein 4	0.22	-	nuc	0					252
Q9Y696 UniProt NPD GO	CLIC4_HUMAN	Chloride intracellular channel protein 4 (Intracellular chloride ion channel protein p64H1)	0.22	-	nuc	0	Cytoplasmic vesicle. Present in an intracellular vesicular compartment that likely represent trans-G ...	actin cytoskeleton [TAS] cytoplasm [IDA] microvillus [IDA] soluble fraction [IDA]	606536	2D2Z	252
Q9EPT8 UniProt NPD GO	CLIC5_RAT	Chloride intracellular channel protein 5	0.22	-	cyt	0		actin cytoskeleton [ISS] insoluble fraction [ISS] microvillus [ISS]			251
P49499 UniProt NPD GO	RR11_ODOSI	Chloroplast 30S ribosomal protein S11	0.22	+	nuc	0	Plastid; chloroplast				130

You are viewing entries 48201 to 48250 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.