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
Q8VHC5 UniProt NPD GO	CABP4_MOUSE	Calcium-binding protein 4 (CaBP4)	0.54	-	nuc	0	Presynapses from both types of photoreceptors: rod spherules and cone pedicles				271
Q8ICR0 UniProt NPD GO	CDPK2_PLAF7	Calcium-dependent protein kinase 2 (EC 2.7.11.1) (PfCDPK2)	0.54	+	nuc	0					508
Q9NJU9 UniProt NPD GO	CDPK3_PLAF7	Calcium-dependent protein kinase 3 (EC 2.7.11.1) (PfCDPK3)	0.54	+	cyt	0					562
Q8IBS5 UniProt NPD GO	CDPK4_PLAF7	Calcium-dependent protein kinase 4 (EC 2.7.11.1)	0.54	-	nuc	0					527
P13586 UniProt NPD GO	ATC1_YEAST	Calcium-transporting ATPase 1 (EC 3.6.3.8) (Golgi Ca(2+)-ATPase)	0.54	-	end	7	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [TAS]			950
Q13554 UniProt NPD GO	KCC2B_HUMAN	Calcium/calmodulin-dependent protein kinase type II beta chain (EC 2.7.11.17) (CaM-kinase II beta ch ...	0.54	-	nuc	0			607707		664
Q9ES66 UniProt NPD GO	CAN10_RAT	Calpain-10 (EC 3.4.22.-) (Calcium-activated neutral proteinase 10) (CANP 10)	0.54	-	mit	0	Cytoplasm. Nucleus				666
P51186 UniProt NPD GO	CAN3_BOVIN	Calpain-3 (EC 3.4.22.-) (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) ...	0.54	-	cyt	0	Cytoplasm				822
O14815 UniProt NPD GO	CAN9_HUMAN	Calpain-9 (EC 3.4.22.-) (Digestive tract-specific calpain) (nCL-4) (CG36 protein)	0.54	-	cyt	0			606401	1ZIV	690
P08060 UniProt NPD GO	CAH6_SHEEP	Carbonic anhydrase 6 (EC 4.2.1.1) (Carbonic anhydrase VI) (Carbonate dehydratase VI) (CA-VI) (Secret ...	0.54	-	cyt	0	Secreted protein				307
Q5U901 UniProt NPD GO	CBPA6_MOUSE	Carboxypeptidase A6 precursor (EC 3.4.17.1)	0.54	-	cyt	0	Secreted protein (By similarity)				438
P18886 UniProt NPD GO	CPT2_RAT	Carnitine O-palmitoyltransferase 2, mitochondrial precursor (EC 2.3.1.21) (Carnitine palmitoyltransf ...	0.54	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			658
Q9JMK2 UniProt NPD GO	KC1E_MOUSE	Casein kinase I isoform epsilon (EC 2.7.11.1) (CKI-epsilon) (CKIe)	0.54	-	nuc	0	Cytoplasm (By similarity)				416
O76484 UniProt NPD GO	CSK2A_SPOFR	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II subunit alpha)	0.54	-	mit	0					353
P31944 UniProt NPD GO	CASPE_HUMAN	Caspase-14 precursor (EC 3.4.22.-) (CASP-14) [Contains: Caspase-14 subunit 1; Caspase-14 subunit 2]	0.54	-	cyt	0	Cytoplasm (By similarity)		605848		242
P08169 UniProt NPD GO	MPRI_BOVIN	Cation-independent mannose-6-phosphate receptor precursor (CI Man-6-P receptor) (CI-MPR) (M6PR) (Ins ...	0.54	-	nuc	1	Lysosome; lysosomal membrane; single-pass type I membrane protein			1SZ0	2499
Q96372 UniProt NPD GO	CDC48_CAPAN	Cell division cycle protein 48 homolog	0.54	-	cyt	0					805
P54774 UniProt NPD GO	CDC48_SOYBN	Cell division cycle protein 48 homolog (Valosin-containing protein homolog) (VCP)	0.54	-	nuc	0	Cell membrane; peripheral membrane protein				807
Q38813 UniProt NPD GO	DNAJ1_ARATH	Chaperone protein dnaJ 1, mitochondrial precursor (AtJ1) (AtDjB1)	0.54	-	nuc	0	Mitochondrion				408
Q7ZW25 UniProt NPD GO	CHM2A_BRARE	Charged multivesicular body protein 2a (Chromatin-modifying protein 2a) (CHMP2a)	0.54	-	nuc	0	Cytoplasm; cytosol (By similarity)				220
P29465 UniProt NPD GO	CHS3_YEAST	Chitin synthase 3 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 3) (Class-IV chitin synt ...	0.54	-	end	6	Membrane; multi-pass membrane protein	bud neck [IDA] chitosome [IDA] cytoplasm [IDA] incipient bud site [IDA] prospore membrane [IDA]			1165
P49507 UniProt NPD GO	RR20_ODOSI	Chloroplast 30S ribosomal protein S20	0.54	-	nuc	0	Plastid; chloroplast				93
P49492 UniProt NPD GO	RR4_ODOSI	Chloroplast 30S ribosomal protein S4	0.54	-	mit	0	Plastid; chloroplast				206
P36447 UniProt NPD GO	RR4_ANTOD	Chloroplast 30S ribosomal protein S4 (Fragment)	0.54	-	mit	0	Plastid; chloroplast				196
O20213 UniProt NPD GO	RR4_FURGI	Chloroplast 30S ribosomal protein S4 (Fragment)	0.54	-	mit	0	Plastid; chloroplast				194
P36464 UniProt NPD GO	RR4_LYGSP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.54	-	mit	0	Plastid; chloroplast				196
O20399 UniProt NPD GO	RR4_WATAN	Chloroplast 30S ribosomal protein S4 (Fragment)	0.54	-	mit	0	Plastid; chloroplast				195
Q9GFN5 UniProt NPD GO	RR7_ACOCL	Chloroplast 30S ribosomal protein S7	0.54	-	nuc	0	Plastid; chloroplast				155
P06360 UniProt NPD GO	RR7_MARPO	Chloroplast 30S ribosomal protein S7	0.54	-	nuc	0	Plastid; chloroplast				155
Q6ENC1 UniProt NPD GO	RR7_ORYNI	Chloroplast 30S ribosomal protein S7	0.54	-	nuc	0	Plastid; chloroplast				156
P62730 UniProt NPD GO	RR7_ORYSA	Chloroplast 30S ribosomal protein S7	0.54	-	nuc	0	Plastid; chloroplast				156
P62733 UniProt NPD GO	RR7_WHEAT	Chloroplast 30S ribosomal protein S7	0.54	-	nuc	0	Plastid; chloroplast				156
Q6EW16 UniProt NPD GO	RR8_NYMAL	Chloroplast 30S ribosomal protein S8	0.54	-	nuc	0	Plastid; chloroplast				132
P18663 UniProt NPD GO	RK2A_SOYBN	Chloroplast 50S ribosomal protein L2-1	0.54	+	nuc	0	Plastid; chloroplast				274
P06387 UniProt NPD GO	RK21_MARPO	Chloroplast 50S ribosomal protein L21	0.54	-	nuc	0	Plastid; chloroplast				116
Q7YJT5 UniProt NPD GO	RK32_CALFE	Chloroplast 50S ribosomal protein L32	0.54	-	mit	0	Plastid; chloroplast				57
Q6B934 UniProt NPD GO	RK32_GRATL	Chloroplast 50S ribosomal protein L32	0.54	-	nuc	0	Plastid; chloroplast				57
P12198 UniProt NPD GO	RK32_TOBAC	Chloroplast 50S ribosomal protein L32	0.54	-	nuc	0	Plastid; chloroplast				54
O19912 UniProt NPD GO	RK34_CYACA	Chloroplast 50S ribosomal protein L34	0.54	-	nuc	0	Plastid; chloroplast				45
Q63931 UniProt NPD GO	CCKAR_CAVPO	Cholecystokinin type A receptor (CCK-A receptor) (CCK-AR) (Cholecystokinin-1 receptor) (CCK1-R)	0.54	-	end	7 *	Membrane; multi-pass membrane protein				430
Q6C9M9 UniProt NPD GO	EAF3_YARLI	Chromatin modification-related protein EAF3	0.54	+	cyt	0	Nucleus (By similarity)				387
P06914 UniProt NPD GO	CSP_PLAYO	Circumsporozoite protein precursor (CS)	0.54	-	exc	1					367
Q9JIG7 UniProt NPD GO	CCD22_MOUSE	Coiled-coil domain-containing protein 22	0.54	-	nuc	0					627
Q6AY97 UniProt NPD GO	CCD91_RAT	Coiled-coil domain-containing protein 91 (GGA-binding partner)	0.54	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Golgi apparatus; trans-Golgi network; trans-G ...				442
Q9JMH4 UniProt NPD GO	COHA1_MESAU	Collagen alpha-1(XVII) chain (Bullous pemphigoid antigen 2) (180 kDa bullous pemphigoid antigen 2)	0.54	-	nuc	1	Membrane; single-pass type II membrane protein (By similarity)				1431
P01024 UniProt NPD GO	CO3_HUMAN	Complement C3 precursor [Contains: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphyla ...	0.54	-	end	0			120700	2A74	1663
Q864W1 UniProt NPD GO	CFAB_PONPY	Complement factor B precursor (EC 3.4.21.47) (C3/C5 convertase) [Contains: Complement factor B Ba fr ...	0.54	-	mit	0	Secreted protein				764
Q21346 UniProt NPD GO	CUL6_CAEEL	Cullin-6	0.54	-	cyt	0					729
Q13319 UniProt NPD GO	CD5R2_HUMAN	Cyclin-dependent kinase 5 activator 2 precursor (CDK5 activator 2) (Cyclin-dependent kinase 5 regula ...	0.54	-	nuc	0			603764		367
Q92045 UniProt NPD GO	CP11A_DASAM	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(SCC)) (Cholesterol side ...	0.54	-	mit	0	Mitochondrion				514

You are viewing entries 22401 to 22450 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.