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
Q61923 UniProt NPD GO	KCNA6_MOUSE	Potassium voltage-gated channel subfamily A member 6 (Voltage-gated potassium channel subunit Kv1.6) ...	0.23	-	end	4	Membrane; multi-pass membrane protein				529
Q8R523 UniProt NPD GO	KCNG3_RAT	Potassium voltage-gated channel subfamily G member 3 (Voltage-gated potassium channel subunit Kv6.3) ...	0.23	+	end	7	Cell membrane; multi-pass membrane protein. Has to be associated with KCNB1 or possibly another part ...				433
Q4WT34 UniProt NPD GO	PRP46_ASPFU	Pre-mRNA-splicing factor prp46 (Pre-mRNA-processing protein 46)	0.23	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				453
Q9CWM4 UniProt NPD GO	PFD1_MOUSE	Prefoldin subunit 1	0.23	-	nuc	0					122
Q9UQ72 UniProt NPD GO	PSG11_HUMAN	Pregnancy-specific beta-1-glycoprotein 11 precursor (PSBG-11) (PSBG-13)	0.23	-	nuc	0	Secreted protein (Potential)		176401		332
P05226 UniProt NPD GO	CAER4_XENBO	Preprocaerulein type-4 precursor (Preprocaerulein type IV) [Contains: Caerulein]	0.23	-	exc	0	Secreted protein				234
P01357 UniProt NPD GO	CAER4_XENLA	Preprocaerulein type-4 precursor (Preprocaerulein type IV) [Contains: Caerulein]	0.23	-	exc	0	Secreted protein				233
Q5XXR2 UniProt NPD GO	MCH_CANFA	Pro-MCH precursor [Contains: Neuropeptide-glycine-glutamic acid (NGE) (Neuropeptide G-E); Neuropepti ...	0.23	-	exc	1 *	Secreted protein (By similarity)				165
Q9BQD1 UniProt NPD GO	MCHL2_HUMAN	Pro-MCH-like protein 2 (Pro-melanin-concentrating hormone-like protein 2)	0.23	-	nuc	0			176794		86
P37262 UniProt NPD GO	SOL2_YEAST	Probable 6-phosphogluconolactonase 2 (EC 3.1.1.31) (6PGL) (Suppressor of LOS1)	0.23	-	cyt	0	Cytoplasm	cytoplasm [IDA] cytosol [IDA]			315
Q9STT5 UniProt NPD GO	ATH6_ARATH	Probable ABC2 homolog 6	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				935
Q9Y2T5 UniProt NPD GO	GPR52_HUMAN	Probable G-protein coupled receptor 52	0.23	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604106		361
Q7XJ02 UniProt NPD GO	APX7_ORYSA	Probable L-ascorbate peroxidase 7, chloroplast precursor (EC 1.11.1.11)	0.23	-	mit	0	Plastid; chloroplast; chloroplast stroma (Probable)				359
Q7XKQ8 UniProt NPD GO	ILV2_ORYSA	Probable acetolactate synthase 2, chloroplast precursor (EC 2.2.1.6) (Acetohydroxy-acid synthase 2)	0.23	-	cyt	0	Plastid; chloroplast (By similarity)				663
Q8WTM6 UniProt NPD GO	ARPC2_CAEEL	Probable actin-related protein 2/3 complex subunit 2 (ARP2/3 complex 34 kDa subunit) (p34-ARC)	0.23	-	cyt	0					301
Q9JHX6 UniProt NPD GO	ALLC_MOUSE	Probable allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.23	-	nuc	0					414
Q6AYP0 UniProt NPD GO	ALLC_RAT	Probable allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.23	-	nuc	0					413
Q9S6Z8 UniProt NPD GO	KCO5_ARATH	Probable calcium-activated outward-rectifying potassium channel 5, chloroplast precursor (AtKCO5)	0.23	-	end	5	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Potential)				408
Q9VYT8 UniProt NPD GO	C28C1_DROME	Probable cytochrome P450 28c1 (EC 1.14.-.-) (CYPXXVIIIC1)	0.23	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				505
Q2HU68 UniProt NPD GO	H2A1_MEDTR	Probable histone H2A.1	0.23	-	nuc	0	Nucleus (By similarity)				148
Q91695 UniProt NPD GO	HDA1A_XENLA	Probable histone deacetylase 1-A (HD1) (Maternally-expressed histone deacetylase) (HDM) (AB21)	0.23	-	cyt	0	Nucleus				480
P83506 UniProt NPD GO	NLTP2_MAIZE	Probable nonspecific lipid-transfer protein 2 (LTP 2)	0.23	-	nuc	0					70
Q9T034 UniProt NPD GO	SYFA_ARATH	Probable phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase alpha ch ...	0.23	-	cyt	0	Cytoplasm (By similarity)				485
Q9W3J5 UniProt NPD GO	SYFA_DROME	Probable phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase alpha ch ...	0.23	-	cyt	0	Cytoplasm (By similarity)				498
Q9GKS6 UniProt NPD GO	AT10D_MACFA	Probable phospholipid-transporting ATPase VD (EC 3.6.3.1) (Fragment)	0.23	-	end	6	Membrane; multi-pass membrane protein (By similarity)				653
O74416 UniProt NPD GO	UMP1_SCHPO	Probable proteasome maturation factor ump1	0.23	-	nuc	0					129
P49595 UniProt NPD GO	PP2C1_CAEEL	Probable protein phosphatase 2C F42G9.1 (EC 3.1.3.16) (PP2C)	0.23	-	cyt	0					491
O13947 UniProt NPD GO	TRMU_SCHPO	Probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61)	0.23	-	mit	0					415
P30628 UniProt NPD GO	VPP1_CAEEL	Probable vacuolar proton translocating ATPase 116 kDa subunit a (Uncoordinated protein 32)	0.23	-	end	7	Membrane; multi-pass membrane protein (Probable)	integral to membrane [NAS]			905
P08116 UniProt NPD GO	PVA_PLAFA	Processed variable antigen (Fragment)	0.23	-	nuc	0					224
P45652 UniProt NPD GO	GON3_HAPBU	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.23	-	exc	0	Secreted protein				90
Q9BQ51 UniProt NPD GO	PDL2_HUMAN	Programmed cell death 1 ligand 2 precursor (Programmed death ligand 2) (PD-L2) (PD-1-ligand 2) (PDCD ...	0.23	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Intracellular membrane; si ...		605723		273
Q6DF07 UniProt NPD GO	PDC10_XENTR	Programmed cell death protein 10	0.23	-	cyt	0					212
P33090 UniProt NPD GO	PRL_CHEMY	Prolactin (PRL)	0.23	-	nuc	0	Secreted protein				198
P01240 UniProt NPD GO	PRL_SHEEP	Prolactin precursor (PRL)	0.23	-	nuc	0	Secreted protein				229
Q03392 UniProt NPD GO	PCNA_SCHPO	Proliferating cell nuclear antigen (PCNA)	0.23	-	cyt	0	Nucleus	PCNA complex [IMP]			260
P54001 UniProt NPD GO	P4HA1_RAT	Prolyl 4-hydroxylase alpha-1 subunit precursor (EC 1.14.11.2) (4-PH alpha-1) (Procollagen-proline,2- ...	0.23	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				534
Q8BWM0 UniProt NPD GO	PGES2_MOUSE	Prostaglandin E synthase 2 (EC 5.3.99.3) (Microsomal prostaglandin E synthase 2) (mPGES-2) (GATE-bin ...	0.23	-	mit	0	Golgi apparatus; Golgi membrane; single-pass membrane protein. Processed form: Cytoplasm. Synthetize ...	cytosol [IDA] nucleus [IDA]			384
Q8WNM1 UniProt NPD GO	PTGDS_GORGO	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.23	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...				190
Q9TUI1 UniProt NPD GO	PTGDS_MACFU	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.23	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...				190
Q8WNM0 UniProt NPD GO	PTGDS_PONPY	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.23	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...				190
Q4U5R3 UniProt NPD GO	PSME1_BOVIN	Proteasome activator complex subunit 1 (Proteasome activator 28-alpha subunit) (PA28alpha) (PA28a)	0.23	-	cyt	0					249
Q7RZK7 UniProt NPD GO	AF9_NEUCR	Protein AF-9 homolog	0.23	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				309
O60756 UniProt NPD GO	BCE1_HUMAN	Protein BCE-1	0.23	-	mit	1					84
Q9H0R1 UniProt NPD GO	CN108_HUMAN	Protein C14orf108 (Putative HIV-1 infection-related protein)	0.23	-	mit	0					490
Q9NPU4 UniProt NPD GO	CN132_HUMAN	Protein C14orf132	0.23	-	end	1					173
Q9Y224 UniProt NPD GO	CN166_HUMAN	Protein C14orf166	0.23	-	mit	0	Or: Nucleus. Or: Cytoplasm; perinuclear region. May localize at the spindle body during mitosis				244
Q5R8I2 UniProt NPD GO	CN166_PONPY	Protein C14orf166 homolog	0.23	-	mit	0	Or: Nucleus (By similarity). Or: Cytoplasm; perinuclear region (By similarity). May localize at the ...				244
Q8NFU9 UniProt NPD GO	CU081_HUMAN	Protein C21orf81	0.23	-	nuc	0					89
Q580R0 UniProt NPD GO	CB027_HUMAN	Protein C2orf27	0.23	-	nuc	0					203

You are viewing entries 47751 to 47800 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.