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
P61845 UniProt NPD GO	RK23_ARATH	Chloroplast 50S ribosomal protein L23	0.19	-	cyt	0	Plastid; chloroplast				93
Q9TLT4 UniProt NPD GO	RK23_CYACA	Chloroplast 50S ribosomal protein L23	0.19	+	nuc	0	Plastid; chloroplast				101
P61846 UniProt NPD GO	RK23_SINAL	Chloroplast 50S ribosomal protein L23	0.19	-	cyt	0	Plastid; chloroplast				93
Q9BBR2 UniProt NPD GO	RK33_LOTJA	Chloroplast 50S ribosomal protein L33	0.19	-	nuc	0	Plastid; chloroplast				66
P52764 UniProt NPD GO	CEMA_PINTH	Chloroplast envelope membrane protein	0.19	-	end	3	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				261
P45639 UniProt NPD GO	SCXL_LEIQU	Chlorotoxin (CTX)	0.19	-	nuc	0	Secreted protein			1CHL	36
P47896 UniProt NPD GO	CETP_MACFA	Cholesteryl ester transfer protein precursor (Lipid transfer protein I)	0.19	-	exc	0	Secreted protein				493
Q8BJ64 UniProt NPD GO	CHDH_MOUSE	Choline dehydrogenase, mitochondrial precursor (EC 1.1.99.1) (CHD) (CDH)	0.19	-	mit	0	Mitochondrion (Potential)	mitochondrial inner membrane [IDA]			596
P32178 UniProt NPD GO	CHMU_YEAST	Chorismate mutase (EC 5.4.99.5) (CM)	0.19	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		5CSM	256
Q75BT5 UniProt NPD GO	EAF6_ASHGO	Chromatin modification-related protein EAF6	0.19	-	nuc	0	Nucleus (By similarity)				98
P08673 UniProt NPD GO	CSP_PLACC	Circumsporozoite protein precursor (CS)	0.19	-	nuc	1					398
P15979 UniProt NPD GO	HA1F_CHICK	Class I histocompatibility antigen, F10 alpha chain precursor (B-F histocompatibility F10 antigen) ( ...	0.19	-	end	1	Membrane; single-pass type I membrane protein				345
P56750 UniProt NPD GO	CLD17_HUMAN	Claudin-17	0.19	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [ISS] tight junction [ISS]			224
P48444 UniProt NPD GO	COPD_HUMAN	Coatomer subunit delta (Delta-coat protein) (Delta-COP) (Archain)	0.19	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [ISS]	600820		511
Q5RA77 UniProt NPD GO	COPD_PONPY	Coatomer subunit delta (Delta-coat protein) (Delta-COP) (Archain)	0.19	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				511
P18395 UniProt NPD GO	CSDE1_RAT	Cold shock domain-containing protein E1 (UNR protein)	0.19	-	cyt	0	Cytoplasm				798
Q04857 UniProt NPD GO	CO6A1_MOUSE	Collagen alpha-1(VI) chain precursor	0.19	-	mit	0					1025
Q86Y22 UniProt NPD GO	CONA1_HUMAN	Collagen alpha-1(XXIII) chain	0.19	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)		610043		540
P27393 UniProt NPD GO	CO4A2_ASCSU	Collagen alpha-2(IV) chain precursor	0.19	-	nuc	1 *					1763
Q96CG8 UniProt NPD GO	CTHR1_HUMAN	Collagen triple helix repeat-containing protein 1 precursor (NMTC1 protein)	0.19	-	nuc	0	Secreted protein; extracellular space (By similarity)				243
Q9ESG3 UniProt NPD GO	TMM27_RAT	Collectrin precursor (Transmembrane protein 27)	0.19	-	end	1	Membrane; single-pass type I membrane protein (Potential)	cytoplasm [TAS] membrane [TAS]			222
Q8VCG4 UniProt NPD GO	CO8G_MOUSE	Complement component C8 gamma chain precursor	0.19	-	exc	0	Secreted protein				202
P36980 UniProt NPD GO	FHR2_HUMAN	Complement factor H-related protein 2 precursor (FHR-2) (H factor-like protein 2) (H factor-like 3) ...	0.19	-	nuc	0	Secreted protein		600889		270
P36551 UniProt NPD GO	HEM6_HUMAN	Coproporphyrinogen III oxidase, mitochondrial precursor (EC 1.3.3.3) (Coproporphyrinogenase) (Coprog ...	0.19	-	nuc	0	Mitochondrion; mitochondrial intermembrane space	mitochondrion [TAS]	121300	2AEX	454
O35828 UniProt NPD GO	CORO7_RAT	Coronin-7 (70 kDa WD repeat tumor rejection antigen) (Fragment)	0.19	-	mit	0	Cytoplasm; cytosol (By similarity). Predominantly. Membrane (By similarity). Also found in membrane ...	Golgi apparatus [ISS] integral to membrane of membrane fraction [ISS] soluble fraction [ISS]			443
P68000 UniProt NPD GO	COLI_BALBO	Corticotropin-lipotropin (Pro-opiomelanocortin) (POMC) [Contains: Corticotropin (Adrenocorticotropic ...	0.19	-	nuc	0					39
P68001 UniProt NPD GO	COLI_BALPH	Corticotropin-lipotropin (Pro-opiomelanocortin) (POMC) [Contains: Corticotropin (Adrenocorticotropic ...	0.19	-	nuc	0					39
P35353 UniProt NPD GO	CRFR1_RAT	Corticotropin-releasing factor receptor 1 precursor (CRF-R) (CRF1) (Corticotropin-releasing hormone ...	0.19	-	end	7	Membrane; multi-pass membrane protein				415
P83399 UniProt NPD GO	THGC_VIGUN	Cp-thionin	0.19	-	nuc	0					47
P11009 UniProt NPD GO	KCRS_CHICK	Creatine kinase, sarcomeric mitochondrial precursor (EC 2.7.3.2) (S-MtCK) (Mib-CK) (Basic-type mitoc ...	0.19	-	cyt	0	Mitochondrion; mitochondrial inner membrane; intermembrane side			1CRK	419
P81206 UniProt NPD GO	CHH1_MACRS	Crustacean hyperglycemic hormone isoform 1 (Crustacean hyperglycemic hormone isoform I) (CHH I) (MAR ...	0.19	-	cyt	0	Secreted protein				71
Q09184 UniProt NPD GO	CDB4_SCHPO	Curved DNA-binding protein (42 kDa protein)	0.19	-	nuc	0	Nucleus				381
Q8IX95 UniProt NPD GO	CTGE3_HUMAN	Cutaneous T-cell lymphoma-associated antigen 3 (cTAGE-3 protein)	0.19	-	nuc	0			608857		158
P14826 UniProt NPD GO	RR8_CYAPA	Cyanelle 30S ribosomal protein S8	0.19	-	cyt	0	Plastid; cyanelle				132
P25374 UniProt NPD GO	NFS1_YEAST	Cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7) (tRNA-splicing protein SPL1)	0.19	+	mit	0	Mitochondrion	mitochondrion [IDA] nucleus [IMP]			497
Q8C9S8 UniProt NPD GO	ATG4A_MOUSE	Cysteine protease ATG4A (EC 3.4.22.-) (Autophagy-related protein 4 homolog A) (Autophagin-2) (Autoph ...	0.19	-	cyt	0	Cytoplasm (Probable)	cytoplasm [ISS] cytosol [ISS] microtubule associated complex [ISS]			396
P04989 UniProt NPD GO	CYSP2_DICDI	Cysteine proteinase 2 precursor (EC 3.4.22.-) (Prestalk cathepsin)	0.19	-	mit	0	Lysosome				376
Q95N02 UniProt NPD GO	CLTR1_PIG	Cysteinyl leukotriene receptor 1 (CysLTR1)	0.19	-	end	6 *	Membrane; multi-pass membrane protein				340
P00189 UniProt NPD GO	CP11A_BOVIN	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.19	-	cyt	0	Mitochondrion			1SCC	520
P30437 UniProt NPD GO	CP17A_ONCMY	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.19	-	mit	1 *					514
O42231 UniProt NPD GO	CP1A1_LIZAU	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.19	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
P33264 UniProt NPD GO	CP2CR_MESAU	Cytochrome P450 2C27 (EC 1.14.14.1) (CYPIIC27) (P450 HSM3)	0.19	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
Q01361 UniProt NPD GO	CP2DE_BOVIN	Cytochrome P450 2D14 (EC 1.14.14.1) (CYPIID14) (Fragment)	0.19	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				487
Q2XNC9 UniProt NPD GO	CP2D6_PANPA	Cytochrome P450 2D6 (EC 1.14.14.1) (CYPIID6)	0.19	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				497
Q2XNC8 UniProt NPD GO	CP2D6_PANTR	Cytochrome P450 2D6 (EC 1.14.14.1) (CYPIID6)	0.19	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				497
P11714 UniProt NPD GO	CP2D9_MOUSE	Cytochrome P450 2D9 (EC 1.14.14.1) (CYPIID9) (P450-16-alpha) (CA) (Testosterone 16-alpha hydroxylase ...	0.19	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			504
P24463 UniProt NPD GO	CP3AC_CANFA	Cytochrome P450 3A12 (EC 1.14.14.1) (CYPIIIA12) (P450-PBD-1)	0.19	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]			503
Q64581 UniProt NPD GO	CP3AI_RAT	Cytochrome P450 3A18 (EC 1.14.14.1) (CYPIIIA18) (P450(6)beta-2)	0.19	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				497
P50859 UniProt NPD GO	CP51_CANGA	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha-demethylase) (Lanosterol 14- ...	0.19	-	cyt	0					533
Q04552 UniProt NPD GO	CP6B1_PAPPO	Cytochrome P450 6B1 (EC 1.14.14.1) (CYPVIB1) (CYP6B1V1/CYP6B1V2/ CYP6B1V3)	0.19	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				498

You are viewing entries 51701 to 51750 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.