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
Q28265 UniProt NPD GO	KCMA1_CANFA	Calcium-activated potassium channel subunit alpha 1 (Calcium-activated potassium channel, subfamily ...	0.56	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				1159
P11730 UniProt NPD GO	KCC2G_RAT	Calcium/calmodulin-dependent protein kinase type II gamma chain (EC 2.7.11.17) (CaM-kinase II gamma ...	0.56	-	mit	0		calcium- and calmodulin-dependent protein k... [TAS]			527
P16259 UniProt NPD GO	CAN3_RAT	Calpain-3 (EC 3.4.22.-) (Calpain L3) (Calpain p94) (Calcium-activated neutral proteinase 3) (CANP 3) ...	0.56	-	cyt	0	Cytoplasm				821
Q92887 UniProt NPD GO	MRP2_HUMAN	Canalicular multispecific organic anion transporter 1 (ATP-binding cassette sub-family C member 2) ( ...	0.56	+	end	14 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601107		1545
O88199 UniProt NPD GO	CHST3_MOUSE	Carbohydrate sulfotransferase 3 (EC 2.8.2.17) (Chondroitin 6-O-sulfotransferase 1) (C6ST-1) (Galacto ...	0.56	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				472
Q00372 UniProt NPD GO	SNF1_CANGA	Carbon catabolite derepressing protein kinase (EC 2.7.11.1)	0.56	-	nuc	0	Nucleus; nuclear membrane; peripheral membrane protein (By similarity)				612
P18915 UniProt NPD GO	CAH6_BOVIN	Carbonic anhydrase 6 precursor (EC 4.2.1.1) (Carbonic anhydrase VI) (Carbonate dehydratase VI) (CA-V ...	0.56	-	exc	0	Secreted protein				319
P48730 UniProt NPD GO	KC1D_HUMAN	Casein kinase I isoform delta (EC 2.7.11.1) (CKI-delta) (CKId)	0.56	-	nuc	0	Cytoplasm		600864		415
Q499V3 UniProt NPD GO	RAD9B_RAT	Cell cycle checkpoint control protein RAD9B homolog (RAD9 homolog B)	0.56	-	nuc	0					398
P39827 UniProt NPD GO	CDC10_CANAL	Cell division control protein 10	0.56	-	nuc	0	Bud neck. Present at the bud neck during cell division (By similarity)				357
Q9USK8 UniProt NPD GO	MOK1_SCHPO	Cell wall alpha-1,3-glucan synthase mok1 (EC 2.4.1.183)	0.56	-	end	11 *					2410
P10360 UniProt NPD GO	P53_CHICK	Cellular tumor antigen p53 (Tumor suppressor p53)	0.56	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				367
Q12493 UniProt NPD GO	NKP1_YEAST	Central kinetochore subunit NKP1 (Non-essential kinetochore protein 1)	0.56	-	nuc	0	Nucleus. Associated with kinetochores	kinetochore [IDA]			238
O13356 UniProt NPD GO	CHS1_CRYNV	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-IV chitin synt ...	0.56	-	end	6	Cell membrane; multi-pass membrane protein				1041
P51289 UniProt NPD GO	RR12_PORPU	Chloroplast 30S ribosomal protein S12	0.56	-	nuc	0	Plastid; chloroplast				124
P56353 UniProt NPD GO	RR18_CHLVU	Chloroplast 30S ribosomal protein S18	0.56	-	nuc	0	Plastid; chloroplast				103
P36454 UniProt NPD GO	RR4_DENGI	Chloroplast 30S ribosomal protein S4 (Fragment)	0.56	-	mit	0	Plastid; chloroplast				196
O20231 UniProt NPD GO	RR4_HEAMA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.56	-	nuc	0	Plastid; chloroplast				182
P62729 UniProt NPD GO	RR7_ATRBE	Chloroplast 30S ribosomal protein S7	0.56	-	nuc	0	Plastid; chloroplast				155
P12339 UniProt NPD GO	RR7_MAIZE	Chloroplast 30S ribosomal protein S7	0.56	-	nuc	0	Plastid; chloroplast				156
Q6L3C6 UniProt NPD GO	RR7_SACHY	Chloroplast 30S ribosomal protein S7	0.56	-	nuc	0	Plastid; chloroplast				156
Q6ENQ9 UniProt NPD GO	RR7_SACOF	Chloroplast 30S ribosomal protein S7	0.56	-	nuc	0	Plastid; chloroplast				156
P62731 UniProt NPD GO	RR7_SOLNI	Chloroplast 30S ribosomal protein S7	0.56	-	nuc	0	Plastid; chloroplast				155
P62732 UniProt NPD GO	RR7_TOBAC	Chloroplast 30S ribosomal protein S7	0.56	-	nuc	0	Plastid; chloroplast				155
Q9TLV4 UniProt NPD GO	RR9_CYACA	Chloroplast 30S ribosomal protein S9	0.56	-	nuc	0	Plastid; chloroplast				128
Q8LVH2 UniProt NPD GO	RK2_PHAAN	Chloroplast 50S ribosomal protein L2	0.56	+	nuc	0	Plastid; chloroplast				275
Q8S8U0 UniProt NPD GO	RK2B_ATRBE	Chloroplast 50S ribosomal protein L2-2	0.56	+	nuc	0	Plastid; chloroplast				274
Q2PMM3 UniProt NPD GO	RK2B_SOYBN	Chloroplast 50S ribosomal protein L2-2	0.56	+	nuc	0	Plastid; chloroplast				274
P61847 UniProt NPD GO	RK32_ARATH	Chloroplast 50S ribosomal protein L32	0.56	-	nuc	0	Plastid; chloroplast				51
P61848 UniProt NPD GO	RK32_BRARA	Chloroplast 50S ribosomal protein L32	0.56	-	nuc	0	Plastid; chloroplast				51
Q85AL7 UniProt NPD GO	RK36_ANTFO	Chloroplast 50S ribosomal protein L36	0.56	-	nuc	0	Plastid; chloroplast				37
Q8M9V5 UniProt NPD GO	RK36_CHAGL	Chloroplast 50S ribosomal protein L36	0.56	-	mit	0	Plastid; chloroplast				37
Q5SD21 UniProt NPD GO	RK36_HUPLU	Chloroplast 50S ribosomal protein L36 (Fragment)	0.56	-	mit	0	Plastid; chloroplast				37
P20385 UniProt NPD GO	CF2_DROME	Chorion transcription factor Cf2, isoforms I/II	0.56	-	nuc	0	Nucleus	nucleus [IDA]			510
Q03124 UniProt NPD GO	RSC9_YEAST	Chromatin structure remodeling complex protein RSC9 (Remodel the structure of chromatin complex subu ...	0.56	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	RSC complex [IDA]			581
O35218 UniProt NPD GO	CPSF2_MOUSE	Cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF 100 kDa subunit)	0.56	-	cyt	0	Nucleus (Potential)				782
Q6NVF9 UniProt NPD GO	CPSF6_MOUSE	Cleavage and polyadenylation specificity factor 6	0.56	+	nuc	0	Nucleus (By similarity). In punctate subnuclear structures localized adjacent to nuclear speckles, c ...				551
Q9D024 UniProt NPD GO	CC47_MOUSE	Coiled-coil domain-containing protein 47 precursor (Adipocyte-specific protein 4)	0.56	-	end	0	Membrane; single-pass membrane protein (Potential)				483
Q8K182 UniProt NPD GO	CO8A_MOUSE	Complement component C8 alpha chain precursor (Complement component 8 subunit alpha)	0.56	-	nuc	0	Secreted protein				587
Q17390 UniProt NPD GO	CUL2_CAEEL	Cullin-2	0.56	-	nuc	0	Cytoplasm. Nucleus. Nuclear in oocytes				776
Q9NPC3 UniProt NPD GO	CIP1_HUMAN	Cyclin-B1-interacting protein 1 (EC 6.3.2.-) (Human enhancer of invasion 10) (E3 ubiquitin-protein l ...	0.56	-	nuc	0	Nucleus. May associate with segregating chromosomes during metaphase and anaphase		608249		277
P30099 UniProt NPD GO	C11B2_RAT	Cytochrome P450 11B2, mitochondrial precursor (EC 1.14.15.4) (EC 1.14.15.5) (CYPXIB2) (P450-Aldo-1) ...	0.56	-	cyt	0	Mitochondrion				510
P30100 UniProt NPD GO	C11B3_RAT	Cytochrome P450 11B3, mitochondrial precursor (EC 1.14.15.4) (EC 1.14.15.5) (CYPXIB3) (P450-Aldo-2) ...	0.56	-	mit	0	Mitochondrion				500
P00187 UniProt NPD GO	CP1A2_RABIT	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2) (P450 isozyme 4) (P450-PM4) (P450 LM4)	0.56	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				515
Q27589 UniProt NPD GO	CP4D2_DROME	Cytochrome P450 4d2 (EC 1.14.-.-) (CYPIVD2)	0.56	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				501
P46634 UniProt NPD GO	CP7A1_CRIGR	Cytochrome P450 7A1 (EC 1.14.13.17) (Cholesterol 7-alpha-monooxygenase) (CYPVII) (Cholesterol 7-alph ...	0.56	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				504
Q94IW5 UniProt NPD GO	C90D2_ORYSA	Cytochrome P450 90D2 (EC 1.14.-.-) (C6-oxidase)	0.56	-	mit	1 *					490
O22907 UniProt NPD GO	RH24_ARATH	DEAD-box ATP-dependent RNA helicase 24 (EC 3.6.1.-)	0.56	+	cyt	0					760
Q10264 UniProt NPD GO	PSO2_SCHPO	DNA cross-link repair protein pso2/snm1 (EC 3.1.-.-)	0.56	-	nuc	0	Nucleus (By similarity)				560
Q01454 UniProt NPD GO	CTF4_YEAST	DNA polymerase alpha-binding protein (Protein CTF4) (Protein POB1) (Chromosome replication protein C ...	0.56	-	cyt	0	Nucleus	nuclear chromosome [IDA] nucleus [IPI]			926

You are viewing entries 21251 to 21300 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.