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
P57078 UniProt NPD GO	RIPK4_HUMAN	Receptor-interacting serine/threonine-protein kinase 4 (EC 2.7.11.1) (Ankyrin repeat domain protein ...	0.19	-	cyt	0			605706		832
P47939 UniProt NPD GO	RES18_MOUSE	Regulated endocrine-specific protein 18 precursor [Contains: Regulated endocrine-specific protein 18 ...	0.19	-	exc	0	Secreted protein	endoplasmic reticulum [IDA]			175
Q3T0T8 UniProt NPD GO	RGS5_BOVIN	Regulator of G-protein signaling 5 (RGS5)	0.19	-	nuc	0					181
Q864Z2 UniProt NPD GO	RGS5_PIG	Regulator of G-protein signaling 5 (RGS5)	0.19	-	nuc	0					181
P38629 UniProt NPD GO	RFC3_YEAST	Replication factor C subunit 3 (Replication factor C3) (Activator 1 40 kDa subunit)	0.19	-	cyt	0	Nucleus (Probable)	DNA replication factor C complex [IDA] nucleus [IDA]		1SXJ	340
O74111 UniProt NPD GO	RFC3_ARXAD	Replication factor C subunit 3 (Replication factor C3) (Activator 1 subunit 3)	0.19	-	cyt	0	Nucleus (By similarity)				338
Q62193 UniProt NPD GO	RFA2_MOUSE	Replication protein A 32 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 2) (p32)	0.19	-	nuc	0	Nucleus. Also present in PML nuclear bodies. Redistributes to discrete nuclear foci upon DNA damage ...				270
Q5R7Q4 UniProt NPD GO	RFA1_PONPY	Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (p70 ...	0.19	-	cyt	0	Nucleus (By similarity)				616
P11528 UniProt NPD GO	GCY_ARBPU	Resact receptor precursor (Guanylate cyclase) (EC 4.6.1.2)	0.19	-	end	2 *	Membrane; single-pass type I membrane protein				986
Q62703 UniProt NPD GO	RCN2_RAT	Reticulocalbin-2 precursor (Calcium-binding protein ERC-55) (Taipoxin-associated calcium-binding pro ...	0.19	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				320
Q96D15 UniProt NPD GO	RCN3_HUMAN	Reticulocalbin-3 precursor (EF-hand calcium-binding protein RLP49)	0.19	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				328
P54827 UniProt NPD GO	CNRG_CANFA	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GMP ...	0.19	-	cyt	0					87
P61248 UniProt NPD GO	CNRG_FELCA	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GMP ...	0.19	-	cyt	0					87
P09174 UniProt NPD GO	CNRG_MOUSE	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase gamma-subunit (EC 3.1.4.17) (GMP ...	0.19	-	cyt	0					87
P81649 UniProt NPD GO	RNAS6_PIG	Ribonuclease K3 (EC 3.1.27.-) (RNase K3)	0.19	-	mit	0	Lysosome (Probable). Matrix of eosinophil's large specific granule (By similarity)				126
O46533 UniProt NPD GO	RNAS6_MACMU	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.19	-	nuc	1 *	Secreted protein				150
P00664 UniProt NPD GO	RNAS1_CAPCA	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.19	-	nuc	0	Secreted protein				124
P07201 UniProt NPD GO	RIR2_SPISO	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.19	-	cyt	0					384
P32101 UniProt NPD GO	RLP7_PICJA	Ribosome biogenesis protein RLP7 (Fragment)	0.19	-	mit	0	Nucleus; nucleolus (By similarity)				212
P26985 UniProt NPD GO	RBS_BATOE	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.19	-	mit	0	Plastid; chloroplast				175
O22077 UniProt NPD GO	RBS_FAGCR	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.19	-	mit	0	Plastid; chloroplast				182
Q41373 UniProt NPD GO	RBS_SACHY	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.19	-	mit	0	Plastid; chloroplast				168
Q5ENN5 UniProt NPD GO	RBL2_HETTR	Ribulose bisphosphate carboxylase, chloroplast precursor (EC 4.1.1.39) (RuBisCO)	0.19	-	mit	0	Plastid; chloroplast (Probable). In this organism the plastid is the result of a secondary endosymbi ...				740
Q42694 UniProt NPD GO	RUBA_CHLRE	RuBisCO large subunit-binding protein subunit alpha, chloroplast precursor (60 kDa chaperonin subuni ...	0.19	-	mit	0	Plastid; chloroplast				580
P21182 UniProt NPD GO	DCAM_YEAST	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.19	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			396
Q9Z1J8 UniProt NPD GO	S14L3_RAT	SEC14-like protein 3 (45 kDa secretory protein) (rsec45)	0.19	-	cyt	0					400
Q9NQ25 UniProt NPD GO	SLAF7_HUMAN	SLAM family member 7 precursor (CD2-like receptor activating cytotoxic cells) (CRACC) (Protein 19A) ...	0.19	-	end	1	Membrane; single-pass type I membrane protein	membrane [NAS]	606625		335
P40641 UniProt NPD GO	AMA1_ALLMI	SRY-related protein AMA1 (Fragment)	0.19	-	nuc	0	Nucleus (Potential)				54
P40642 UniProt NPD GO	AMA2_ALLMI	SRY-related protein AMA2 (Fragment)	0.19	-	nuc	0	Nucleus (Potential)				54
P40670 UniProt NPD GO	CH31_CHICK	SRY-related protein CH31 (Fragment)	0.19	-	nuc	0	Nucleus (Potential)				54
Q95017 UniProt NPD GO	UBC9_CAEEL	SUMO-conjugating enzyme UBC9 (EC 6.3.2.19) (Ubiquitin-conjugating enzyme E2 9) (Ubiquitin-protein li ...	0.19	-	nuc	0					166
Q6FRX6 UniProt NPD GO	SWC7_CANGA	SWR1-complex protein 7	0.19	-	nuc	0	Nucleus (By similarity)				129
P09910 UniProt NPD GO	SECR_CANFA	Secretin	0.19	-	nuc	0	Secreted protein				27
P09186 UniProt NPD GO	LOX3_SOYBN	Seed lipoxygenase-3 (EC 1.13.11.12) (L-3)	0.19	-	cyt	0	Cytoplasm			1RRL	857
Q64151 UniProt NPD GO	SEM4C_MOUSE	Semaphorin-4C precursor (Semaphorin I) (Sema I) (Semaphorin C-like 1) (M-Sema F)	0.19	-	end	2 *	Membrane; single-pass type I membrane protein				834
P81019 UniProt NPD GO	SFP4_BOVIN	Seminal plasma protein BSP-30 kDa precursor (BSP-30K)	0.19	-	vac	0	Secreted protein			2CEB	183
P18297 UniProt NPD GO	SPRE_RAT	Sepiapterin reductase (EC 1.1.1.153) (SPR)	0.19	-	mit	0	Cytoplasm				262
P50431 UniProt NPD GO	GLYC_MOUSE	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.19	-	cyt	0	Cytoplasm	mitochondrion [IDA]		1EJI	478
O15270 UniProt NPD GO	LCB2_HUMAN	Serine palmitoyltransferase 2 (EC 2.3.1.50) (Long chain base biosynthesis protein 2) (LCB 2) (Serine ...	0.19	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)		605713		562
Q7Y0B9 UniProt NPD GO	SAPK8_ORYSA	Serine/threonine-protein kinase SAPK8 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.19	-	cyt	0					371
Q03785 UniProt NPD GO	VHS1_YEAST	Serine/threonine-protein kinase VHS1 (EC 2.7.11.1) (Viable in a HAL3 SIT4 background protein 1)	0.19	-	nuc	0	Cytoplasm	cytoplasm [IDA]			461
Q38950 UniProt NPD GO	2AAB_ARATH	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform (PP2A, subunit A, b ...	0.19	-	cyt	0					587
Q5ADP9 UniProt NPD GO	PTPA1_CANAL	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.19	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				424
P48452 UniProt NPD GO	PP2BA_BOVIN	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform (EC 3.1.3.16) (Calmodulin-de ...	0.19	-	cyt	0	Nucleus (By similarity). Colocalizes with ACTN1 and MYOZ2 at the Z line in heart and skeletal muscle ...			1TCO	521
P63328 UniProt NPD GO	PP2BA_MOUSE	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform (EC 3.1.3.16) (Calmodulin-de ...	0.19	-	cyt	0	Nucleus. Colocalizes with ACTN1 and MYOZ2 at the Z line in heart and skeletal muscle	Z disc [IDA]			521
P63329 UniProt NPD GO	PP2BA_RAT	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform (EC 3.1.3.16) (Calmodulin-de ...	0.19	-	cyt	0	Nucleus (By similarity). Colocalizes with ACTN1 and MYOZ2 at the Z line in heart and skeletal muscle ...				521
P16298 UniProt NPD GO	PP2BB_HUMAN	Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform (EC 3.1.3.16) (Calmodulin-dep ...	0.19	-	cyt	0		calcineurin complex [IDA]	114106		524
P22198 UniProt NPD GO	PP1_MAIZE	Serine/threonine-protein phosphatase PP1 (EC 3.1.3.16)	0.19	-	cyt	0					316
P48485 UniProt NPD GO	PP15_ARATH	Serine/threonine-protein phosphatase PP1 isozyme 5 (EC 3.1.3.16)	0.19	-	cyt	0					312
Q9HFQ2 UniProt NPD GO	PP2A1_EMENI	Serine/threonine-protein phosphatase PP2A catalytic subunit (EC 3.1.3.16) (Protein phosphatase 2a)	0.19	-	cyt	0					329

You are viewing entries 52401 to 52450 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.