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
Q6KGX9 UniProt NPD GO	RR7_LILSU	Chloroplast 30S ribosomal protein S7	0.50	-	nuc	0	Plastid; chloroplast				155
Q68RU7 UniProt NPD GO	RR7_PANGI	Chloroplast 30S ribosomal protein S7	0.50	-	nuc	0	Plastid; chloroplast				155
Q4VZN1 UniProt NPD GO	RK16_CUCSA	Chloroplast 50S ribosomal protein L16	0.50	-	nuc	0	Plastid; chloroplast				135
Q2L944 UniProt NPD GO	RK2_GOSHI	Chloroplast 50S ribosomal protein L2	0.50	+	nuc	0	Plastid; chloroplast				274
Q5SD13 UniProt NPD GO	RK2_HUPLU	Chloroplast 50S ribosomal protein L2	0.50	-	nuc	0	Plastid; chloroplast				278
Q589A7 UniProt NPD GO	RK2_SILLA	Chloroplast 50S ribosomal protein L2	0.50	-	nuc	0	Plastid; chloroplast				274
Q3C1L5 UniProt NPD GO	RK22_NICSY	Chloroplast 50S ribosomal protein L22	0.50	-	nuc	0	Plastid; chloroplast				155
Q2VEE1 UniProt NPD GO	RK22_SOLTU	Chloroplast 50S ribosomal protein L22	0.50	-	nuc	0	Plastid; chloroplast				155
P06389 UniProt NPD GO	RK22_TOBAC	Chloroplast 50S ribosomal protein L22	0.50	-	nuc	0	Plastid; chloroplast				155
P51312 UniProt NPD GO	RK23_PORPU	Chloroplast 50S ribosomal protein L23	0.50	-	nuc	0	Plastid; chloroplast				110
P12196 UniProt NPD GO	RK32_MARPO	Chloroplast 50S ribosomal protein L32	0.50	-	mit	0	Plastid; chloroplast				68
P06392 UniProt NPD GO	RK33_MARPO	Chloroplast 50S ribosomal protein L33	0.50	-	nuc	0	Plastid; chloroplast				64
Q85FW2 UniProt NPD GO	RK4_CYAME	Chloroplast 50S ribosomal protein L4	0.50	-	nuc	0	Plastid; chloroplast				200
P20485 UniProt NPD GO	KICH_YEAST	Choline kinase (EC 2.7.1.32)	0.50	-	mit	0	Cytoplasm				582
P34618 UniProt NPD GO	CEC1_CAEEL	Chromo domain protein cec-1	0.50	-	nuc	0	Nucleus. During mitosis it seems to dissociate from the condensing chromosomes				304
P05059 UniProt NPD GO	CMGA_BOVIN	Chromogranin A precursor (CgA) (Pituitary secretory protein I) (SP-I) [Contains: Vasostatin-1; Chrom ...	0.50	-	exc	0	Neuroendocrine and endocrine secretory granules	extracellular region [IDA] secretory granule [IDA]		1N2Y	449
O45952 UniProt NPD GO	CSC1_CAEEL	Chromosome segregation and cytokinesis defective protein 1	0.50	-	nuc	0	Localizes on chromosome arms and inner centromeres from prophase through metaphase and then transfer ...				249
Q6IRU5 UniProt NPD GO	CLCB_MOUSE	Clathrin light chain B (Lcb)	0.50	-	nuc	0	Cytoplasmic face of coated pits and vesicles				229
P53618 UniProt NPD GO	COPB_HUMAN	Coatomer subunit beta (Beta-coat protein) (Beta-COP)	0.50	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [ISS] cytosol [TAS] Golgi membrane [TAS] Golgi-associated vesicle [TAS]	600959		953
Q96CS2 UniProt NPD GO	CCDC5_HUMAN	Coiled-coil domain-containing protein 5 (Enhancer of invasion-cluster) (HEI-C)	0.50	-	nuc	0	Cytoplasm. Localizes with the spindle poles in mitotic cells. In metaphase it localizes to the mitot ...		608775		278
P12107 UniProt NPD GO	COBA1_HUMAN	Collagen alpha-1(XI) chain precursor	0.50	-	nuc	0		collagen type XI [TAS] extracellular matrix (sensu Metazoa) [NAS]	604841		1806
P04186 UniProt NPD GO	CFAB_MOUSE	Complement factor B precursor (EC 3.4.21.47) (C3/C5 convertase) [Contains: Complement factor B Ba fr ...	0.50	-	cyt	0	Secreted protein				761
Q6ZQ73 UniProt NPD GO	CAND2_MOUSE	Cullin-associated NEDD8-dissociated protein 2 (Cullin-associated and neddylation-dissociated protein ...	0.50	-	cyt	0	Nucleus (By similarity)	nucleus [IDA]			1235
P15764 UniProt NPD GO	RK2_CYAPA	Cyanelle 50S ribosomal protein L2	0.50	-	nuc	0	Plastid; cyanelle				275
P42752 UniProt NPD GO	CCND2_ARATH	Cyclin delta-2	0.50	-	nuc	0					361
P43449 UniProt NPD GO	CCNA2_CHICK	Cyclin-A2 (Cyclin-A)	0.50	-	nuc	0					395
Q86TL0 UniProt NPD GO	ATG4D_HUMAN	Cysteine protease ATG4D (EC 3.4.22.-) (Autophagy-related protein 4 homolog D) (Autophagin-4) (Autoph ...	0.50	-	mit	0	Cytoplasm (Probable)	cytoplasm [ISS] cytosol [ISS] microtubule associated complex [ISS]			474
Q4H4C3 UniProt NPD GO	CP1A2_MACFU	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2)	0.50	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				515
P20816 UniProt NPD GO	CP4A2_RAT	Cytochrome P450 4A2 precursor (EC 1.14.15.3) (CYPIVA2) (Lauric acid omega-hydroxylase) (P450-LA-omeg ...	0.50	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				504
Q99N16 UniProt NPD GO	CP4F3_MOUSE	Cytochrome P450 4F3 (EC 1.14.13.30) (CYPIVF3) (Leukotriene-B(4) omega-hydroxylase) (Leukotriene-B(4) ...	0.50	-	vac	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				524
P98187 UniProt NPD GO	CP4F8_HUMAN	Cytochrome P450 4F8 (EC 1.14.14.1) (CYPIVF8)	0.50	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				520
O64638 UniProt NPD GO	C76C3_ARATH	Cytochrome P450 76C3 (EC 1.14.-.-)	0.50	-	nuc	1 *					515
O46491 UniProt NPD GO	CP7A1_PIG	Cytochrome P450 7A1 (EC 1.14.13.17) (Cholesterol 7-alpha-monooxygenase) (CYPVII) (Cholesterol 7-alph ...	0.50	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				501
Q42602 UniProt NPD GO	C89A2_ARATH	Cytochrome P450 89A2 (EC 1.14.-.-) (CYPLXXXIX) (ATH 6-1)	0.50	-	end	0					506
P50392 UniProt NPD GO	PA24A_BRARE	Cytosolic phospholipase A2 (cPLA2) (Phospholipase A2 group IVA) [Includes: Phospholipase A2 (EC 3.1. ...	0.50	-	cyt	0	Cytoplasm (By similarity). Cytoplasmic vesicle (By similarity). Translocates to membrane vesicles in ...				741
Q94F88 UniProt NPD GO	CMT3_ARATH	DNA (cytosine-5)-methyltransferase CMT3 (EC 2.1.1.37) (Chromomethylase 3) (Protein CHROMOMETHYLASE3) ...	0.50	+	cyt	0	Nucleus (By similarity)				839
P07903 UniProt NPD GO	ERCC1_MOUSE	DNA excision repair protein ERCC-1	0.50	-	nuc	0	Nucleus	nucleotide-excision repair complex [ISS]			298
Q6C6M5 UniProt NPD GO	DPB3_YARLI	DNA polymerase epsilon subunit C (EC 2.7.7.7) (DNA polymerase II subunit C)	0.50	-	nuc	0	Nucleus (By similarity)				114
Q9HCU8 UniProt NPD GO	DPOD4_HUMAN	DNA polymerase subunit delta 4 (DNA polymerase subunit delta p12)	0.50	-	mit	0	Nucleus	nucleus [TAS]			107
Q96UP6 UniProt NPD GO	RAD52_EMENI	DNA repair and recombination protein radC (RAD52 homolog)	0.50	-	nuc	0	Nucleus (By similarity)				582
P48379 UniProt NPD GO	RFX2_MOUSE	DNA-binding protein RFX2	0.50	+	nuc	0	Nucleus (Probable)				692
P13911 UniProt NPD GO	RPOA_PEA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.50	-	cyt	0	Plastid; chloroplast				334
Q8MC99 UniProt NPD GO	RPOA_PHAAN	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.50	-	cyt	0	Plastid; chloroplast				333
Q7YJX9 UniProt NPD GO	RPOC1_CALFE	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.50	-	mit	0	Plastid; chloroplast				678
Q2VEI5 UniProt NPD GO	RPOC1_SOLTU	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.50	-	cyt	0	Plastid; chloroplast				687
Q9MUS7 UniProt NPD GO	RPOC2_MESVI	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.50	-	cyt	0	Plastid; chloroplast				1223
O93227 UniProt NPD GO	DEM_AGAAN	Dermorphin precursor [Contains: Dermorphin] (Fragment)	0.50	-	nuc	0	Secreted protein	extracellular region [ISS]			86
Q14574 UniProt NPD GO	DSC3_HUMAN	Desmocollin-3 precursor (Desmocollin-4) (HT-CP)	0.50	-	end	1	Membrane; single-pass type I membrane protein	intercellular junction [TAS] membrane fraction [TAS] plasma membrane [TAS]	600271		896
P29382 UniProt NPD GO	SEP1_ARATH	Developmental protein SEPALLATA1 (Agamous-like MADS-box protein AGL2)	0.50	-	nuc	0	Nucleus				251
P29384 UniProt NPD GO	SEP2_ARATH	Developmental protein SEPALLATA2 (Agamous-like MADS-box protein AGL4)	0.50	-	nuc	0	Nucleus				250

You are viewing entries 24901 to 24950 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.