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
O48741 UniProt NPD GO	PORC_ARATH	Protochlorophyllide reductase C, chloroplast precursor (EC 1.3.1.33) (PCR C) (NADPH-protochlorophyll ...	0.37	-	nuc	0	Plastid; chloroplast. Prolamellar body of etiolated seedling				401
Q9Y5Y4 UniProt NPD GO	GPR44_HUMAN	Putative G-protein coupled receptor 44 (Chemoattractant receptor-homologous molecule expressed on Th ...	0.37	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	604837		395
Q9SCS4 UniProt NPD GO	LBD28_ARATH	Putative LOB domain-containing protein 28	0.37	-	nuc	0					198
O49691 UniProt NPD GO	ATL4I_ARATH	Putative RING-H2 finger protein ATL4I	0.37	-	nuc	1 *					289
Q09456 UniProt NPD GO	COL80_CAEEL	Putative cuticle collagen 80	0.37	-	nuc	1 *					317
Q06417 UniProt NPD GO	YL426_YEAST	Putative oxidoreductase YLR426W (EC 1.-.-.-)	0.37	-	mit	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			326
Q9XIE6 UniProt NPD GO	ALA3_ARATH	Putative phospholipid-transporting ATPase 3 (EC 3.6.3.1) (Aminophospholipid flippase 3)	0.37	-	end	8	Membrane; multi-pass membrane protein				1213
Q21950 UniProt NPD GO	SBP_CAEEL	Putative selenium-binding protein	0.37	-	cyt	0					576
Q9UFM2 UniProt NPD GO	CU030_HUMAN	Putative uncharacterized protein C21orf30	0.37	-	nuc	0					244
O22755 UniProt NPD GO	ATL2A_ARATH	RING-H2 finger protein ATL2A (RING-H2 zinc finger protein RHA3a)	0.37	-	nuc	1 *					185
Q6Q7J2 UniProt NPD GO	GDIB_PIG	Rab GDP dissociation inhibitor beta (Rab GDI beta) (Guanosine diphosphate dissociation inhibitor 2) ...	0.37	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				445
Q15404 UniProt NPD GO	RSU1_HUMAN	Ras suppressor protein 1 (Rsu-1) (RSP-1)	0.37	-	nuc	0			179555		276
P04388 UniProt NPD GO	RAS2_DROME	Ras-like protein 2	0.37	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				192
P01120 UniProt NPD GO	RAS2_YEAST	Ras-like protein 2 precursor	0.37	-	nuc	0	Cell membrane; lipid-anchor	plasma membrane [IDA]			321
P59025 UniProt NPD GO	RTP1_HUMAN	Receptor-transporting protein 1	0.37	-	cyt	1	Cell membrane; single-pass type III membrane protein (By similarity). Effective cell surface express ...	cell surface [IDA]	609137		263
Q6NY74 UniProt NPD GO	RFA1_BRARE	Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (p70 ...	0.37	-	nuc	0	Nucleus (By similarity)				601
Q9H063 UniProt NPD GO	MAF1_HUMAN	Repressor of RNA polymerase III transcription MAF1 homolog	0.37	-	nuc	0	Nucleus (By similarity)				256
Q64548 UniProt NPD GO	RTN1_RAT	Reticulon-1 (Neuroendocrine-specific protein) (S-rex)	0.37	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				777
O75298 UniProt NPD GO	RTN2_HUMAN	Reticulon-2 (Neuroendocrine-specific protein-like 1) (NSP-like protein 1) (NSPLI)	0.37	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	integral to endoplasmic reticulum membrane [NAS]	603183		545
P51841 UniProt NPD GO	GUC2F_HUMAN	Retinal guanylyl cyclase 2 precursor (EC 4.6.1.2) (Guanylate cyclase 2F, retinal) (RETGC-2) (Rod out ...	0.37	-	end	2	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] nuclear outer membrane [TAS]	300041		1108
P84618 UniProt NPD GO	RCAL2_RHEAM	Rheacalcin-2 (RCA-2)	0.37	-	cyt	0	Eggshell matrix				143
Q07960 UniProt NPD GO	RHG01_HUMAN	Rho-GTPase-activating protein 1 (GTPase-activating protein rhoOGAP) (Rho-related small GTPase protei ...	0.37	-	cyt	0	Cytoplasm		602732	2NGR	439
Q9CXP4 UniProt NPD GO	RHG08_MOUSE	Rho-GTPase-activating protein 8	0.37	-	nuc	0					425
Q9WVL4 UniProt NPD GO	RK_MOUSE	Rhodopsin kinase precursor (EC 2.7.11.14) (RK) (G protein-coupled receptor kinase 1)	0.37	+	cyt	0	Membrane; lipid-anchor				564
Q8BWR8 UniProt NPD GO	RHPN2_MOUSE	Rhophilin-2 (GTP-Rho-binding protein 2)	0.37	-	cyt	0	Cytoplasm; perinuclear region (By similarity)			1VAE	686
O75817 UniProt NPD GO	POP7_HUMAN	Ribonuclease P protein subunit p20 (EC 3.1.26.5) (RNaseP protein p20) (hPOP7)	0.37	-	nuc	0	Nucleus; nucleolus (Potential)	nucleolar ribonuclease P complex [TAS] nucleus [TAS]	606113		140
Q9WUR3 UniProt NPD GO	RNAS1_AKOJE	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.37	-	exc	0	Secreted protein				149
P61821 UniProt NPD GO	RNAS1_CERAE	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.37	-	nuc	1 *	Secreted protein (By similarity)				152
P61822 UniProt NPD GO	RNAS1_MIOTA	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.37	-	nuc	1 *	Secreted protein (By similarity)				152
Q7YRH0 UniProt NPD GO	RNAS9_CERPY	Ribonuclease-like protein 9 precursor	0.37	-	exc	0	Secreted protein (Probable)				204
P58145 UniProt NPD GO	ROAA_ASTLO	Ribosomal operon-associated A protein (RoaA)	0.37	-	cyt	2	Plastid				519
Q5ZIZ2 UniProt NPD GO	SMYD5_CHICK	SET and MYND domain-containing protein 5	0.37	-	nuc	0					420
P13729 UniProt NPD GO	SGS3_DROSI	Salivary glue protein Sgs-3 precursor	0.37	-	exc	0					217
P81489 UniProt NPD GO	PRPP_HUMAN	Salivary proline-rich protein II-1 (Fragment)	0.37	-	nuc	0		extracellular region [NAS]			174
Q86VB7 UniProt NPD GO	C163A_HUMAN	Scavenger receptor cysteine-rich type 1 protein M130 precursor (CD163 antigen) (Hemoglobin scavenger ...	0.37	-	end	2 *	Cell membrane; single-pass type I membrane protein. Soluble CD163: Secreted protein. A soluble form ...		605545		1156
Q9BQB4 UniProt NPD GO	SOST_HUMAN	Sclerostin precursor	0.37	-	exc	0	Secreted protein (Potential)		605740		213
Q9Z2E9 UniProt NPD GO	BSCL2_MOUSE	Seipin (Bernardinelli-Seip congenital lipodystrophy type 2 protein homolog)	0.37	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			383
Q64356 UniProt NPD GO	SVS6_MOUSE	Seminal vesicle secretory protein 6 precursor (Seminal vesicle secretory protein VI) (SVS VI) (Semin ...	0.37	+	exc	0	Secreted protein; extracellular space				99
Q5FVJ8 UniProt NPD GO	SENP8_RAT	Sentrin-specific protease 8 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP8) (NEDD8-specific pro ...	0.37	-	nuc	0					217
Q9BXU1 UniProt NPD GO	STK31_HUMAN	Serine/threonine-protein kinase 31 (EC 2.7.11.1) (Serine/threonine-protein kinase NYD-SPK)	0.37	-	cyt	0			605790		1019
Q91ZN7 UniProt NPD GO	CHK1_RAT	Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)	0.37	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear export is mediated at least in part by X ...				476
O08875 UniProt NPD GO	DCAK1_RAT	Serine/threonine-protein kinase DCAMKL1 (EC 2.7.11.1) (Doublecortin-like and CAM kinase-like 1) (Cal ...	0.37	-	nuc	0					433
Q4KTY1 UniProt NPD GO	KPSH1_PINFU	Serine/threonine-protein kinase H1 homolog (EC 2.7.11.1)	0.37	-	nuc	0					415
Q6NU98 UniProt NPD GO	PDK1B_XENLA	Serine/threonine-protein kinase pdik1l-B (EC 2.7.11.1)	0.37	-	nuc	0	Nucleus (By similarity)				339
P97497 UniProt NPD GO	SHBG_MOUSE	Sex hormone-binding globulin precursor (SHBG) (Sex steroid-binding protein) (SBP) (Testis-specific a ...	0.37	-	mit	0	Secreted protein (By similarity). In testis, it is synthesized by the Sertoli cells, secreted into t ...				403
P10460 UniProt NPD GO	NXSC_LATLA	Short neurotoxin C	0.37	-	nuc	0	Secreted protein				62
Q9R283 UniProt NPD GO	TRPC2_RAT	Short transient receptor potential channel 2 (TrpC2) (rTRP2)	0.37	-	end	5	Membrane; multi-pass membrane protein (Probable)				885
Q8VD33 UniProt NPD GO	SGTB_MOUSE	Small glutamine-rich tetratricopeptide repeat-containing protein B	0.37	-	nuc	0					304
P11890 UniProt NPD GO	HS23C_CHERU	Small heat shock protein, chloroplast precursor	0.37	-	mit	0	Plastid; chloroplast; chloroplast stroma				204
Q8HYP8 UniProt NPD GO	CCL18_MACMU	Small inducible cytokine A18 precursor (CCL18)	0.37	-	exc	0	Secreted protein (By similarity)				88

You are viewing entries 34501 to 34550 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.