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
P83282 UniProt NPD GO	CICD_CICFL	Cicadin (Fragment)	0.41	+	nuc	0					55
P30383 UniProt NPD GO	1C01_GORGO	Class I histocompatibility antigen, GOGO-C0101/C0102 alpha chain precursor	0.41	-	end	1	Membrane; single-pass type I membrane protein				365
Q8C7E9 UniProt NPD GO	CSTFT_MOUSE	Cleavage stimulation factor 64 kDa subunit, tau variant (CSTF 64 kDa subunit, tau variant) (CF-1 64 ...	0.41	-	nuc	0	Nucleus				632
P14683 UniProt NPD GO	CLUS_MESAU	Clusterin (Sulfated glycoprotein 2) (SGP-2) [Contains: Clusterin beta chain; Clusterin alpha chain] ...	0.41	-	mit	0	Secreted protein				191
P00748 UniProt NPD GO	FA12_HUMAN	Coagulation factor XII precursor (EC 3.4.21.38) (Hageman factor) (HAF) [Contains: Coagulation factor ...	0.41	-	exc	0	Secreted protein	extracellular region [NAS]	234000		615
Q01833 UniProt NPD GO	CO3_NAJNA	Cobra venom factor precursor (CVF) (Complement C3 homolog) [Contains: Cobra venom factor alpha chain ...	0.41	-	nuc	1 *	Secreted protein				1651
Q8TAB7 UniProt NPD GO	CCD26_HUMAN	Coiled-coil domain-containing protein 26	0.41	-	nuc	0					109
P13942 UniProt NPD GO	COBA2_HUMAN	Collagen alpha-2(XI) chain precursor	0.41	-	exc	1 *		collagen type XI [NAS]	609706		1736
P06684 UniProt NPD GO	CO5_MOUSE	Complement C5 precursor (Hemolytic complement) [Contains: Complement C5 beta chain; Complement C5 al ...	0.41	-	cyt	0					1680
Q9H9E3 UniProt NPD GO	COG4_HUMAN	Conserved oligomeric Golgi complex component 4	0.41	-	cyt	0	Golgi apparatus		606976		785
P97527 UniProt NPD GO	CNTN5_RAT	Contactin-5 precursor (Neural recognition molecule NB-2)	0.41	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				1099
P11090 UniProt NPD GO	CRUA_BRANA	Cruciferin precursor (11S globulin) (12S storage protein) [Contains: Cruciferin alpha subunit; Cruci ...	0.41	-	gol	0	Endoplasmic reticulum; rough endoplasmic reticulum				488
Q9JLB4 UniProt NPD GO	CUBN_MOUSE	Cubilin precursor (Intrinsic factor-cobalamin receptor)	0.41	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysosomal membr ...	apical plasma membrane [IDA] brush border [IDA] coated pit [IDA] cytoplasm [IDA] endocytic vesicle [IDA] endoplasmic reticulum [IDA] endosome [IDA] Golgi apparatus [IDA]			3623
P17292 UniProt NPD GO	RR7_CYAPA	Cyanelle 30S ribosomal protein S7	0.41	-	mit	0	Plastid; cyanelle				156
P51959 UniProt NPD GO	CCNG1_HUMAN	Cyclin-G1 (Cyclin-G)	0.41	-	cyt	0	Nucleus. DNA replication foci after DNA damage		601578		295
P79153 UniProt NPD GO	CP11A_CAPHI	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.41	-	mit	0	Mitochondrion				520
Q29527 UniProt NPD GO	C11B1_PAPHU	Cytochrome P450 11B1, mitochondrial precursor (EC 1.14.15.4) (CYPXIB1) (P450C11) (Steroid 11-beta-hy ...	0.41	-	mit	0	Mitochondrion				503
Q8WNE1 UniProt NPD GO	CP2F5_GORGO	Cytochrome P450 2F5 (EC 1.14.14.1) (CYPIIF5) (CYP4502F5)	0.41	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
Q3MID2 UniProt NPD GO	CP4F3_RAT	Cytochrome P450 4F3 (EC 1.14.13.30) (CYPIVF3) (Leukotriene-B(4) omega-hydroxylase) (Leukotriene-B(4) ...	0.41	-	vac	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				524
Q5RE72 UniProt NPD GO	CP51A_PONPY	Cytochrome P450 51A1 (EC 1.14.13.70) (CYPLI) (P450LI) (Sterol 14-alpha demethylase) (Lanosterol 14-a ...	0.41	-	mit	1 *	Microsome (By similarity)				503
P37122 UniProt NPD GO	C76A2_SOLME	Cytochrome P450 76A2 (EC 1.14.-.-) (CYPLXXVIA2) (P-450EG7)	0.41	-	nuc	1 *					505
Q68DD2 UniProt NPD GO	PA24F_HUMAN	Cytosolic phospholipase A2 zeta (EC 3.1.1.4) (cPLA2-zeta) (Phospholipase A2 group IVF)	0.41	-	cyt	0	Cytoplasm; cytosol. Translocates to lysosomal membranes in a calcium-dependent fashion (By similarit ...				849
Q38732 UniProt NPD GO	DAG_ANTMA	DAG protein, chloroplast precursor	0.41	-	mit	0	Plastid; chloroplast				230
Q750P7 UniProt NPD GO	SPC19_ASHGO	DASH complex subunit SPC19 (Outer kinetochore protein SPC19)	0.41	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				148
Q8W4R3 UniProt NPD GO	RH30_ARATH	DEAD-box ATP-dependent RNA helicase 30 (EC 3.6.1.-)	0.41	-	nuc	0	Nucleus (By similarity)				591
O73770 UniProt NPD GO	DGCR6_CHICK	DGCR6 protein (DiGeorge syndrome critical region 6 homolog)	0.41	-	nuc	0					200
O55055 UniProt NPD GO	DNMT2_MOUSE	DNA (cytosine-5)-methyltransferase-like protein 2 (Dnmt2) (DNA methyltransferase homolog MmuIIP) (DN ...	0.41	-	mit	0	Nucleus (Probable)				415
P31378 UniProt NPD GO	NTG1_YEAST	DNA base excision repair N-glycosylase 1, mitochondrial precursor	0.41	-	mit	0	Mitochondrial transmembrane space or matrix	mitochondrion [IDA] nucleus [IDA]			399
Q08214 UniProt NPD GO	NTG2_YEAST	DNA base excision repair N-glycosylase 2	0.41	-	nuc	0	Nucleus	nucleus [IDA]			380
O57383 UniProt NPD GO	DPOLB_XENLA	DNA polymerase beta (EC 2.7.7.7) (EC 4.2.99.-)	0.41	-	nuc	0	Nucleus (By similarity)				333
Q6C030 UniProt NPD GO	DPB2_YARLI	DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)	0.41	-	nuc	0	Nucleus (By similarity)				652
P87174 UniProt NPD GO	DPB4_SCHPO	DNA polymerase epsilon subunit D (EC 2.7.7.7) (DNA polymerase II subunit D)	0.41	-	nuc	0	Nucleus	epsilon DNA polymerase complex [IPI] nucleus [IDA]			210
Q92076 UniProt NPD GO	DPOG1_CHICK	DNA polymerase subunit gamma 1 (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit) (Fragme ...	0.41	-	cyt	0	Mitochondrion				647
Q8W4M7 UniProt NPD GO	ERCC2_ARATH	DNA repair helicase UVH6 (EC 3.6.1.-) (UV hypersensitive protein 6) (XPD homolog) (ERCC2 homolog) (R ...	0.41	-	mit	0	Nucleus (Probable)				758
Q12488 UniProt NPD GO	PSF1_YEAST	DNA replication complex GINS protein PSF1 (Partner of Sld five 1)	0.41	-	cyt	0	Nucleus. Associates with autonomously replicating sequence (ARS) regions in S phase. This associatio ...	GINS complex [IPI]			208
P08266 UniProt NPD GO	RPB2_DROME	DNA-directed RNA polymerase II 140 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 2)	0.41	-	cyt	0	Nucleus	DNA-directed RNA polymerase II, core complex [NAS]			1176
P28364 UniProt NPD GO	RPB1_EUPOC	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (Fragment)	0.41	-	nuc	0	Nucleus				478
Q8SR75 UniProt NPD GO	RPB2_ENCCU	DNA-directed RNA polymerase II polypeptide 2 (EC 2.7.7.6) (RNA polymerase II subunit 2)	0.41	-	cyt	0	Nucleus (By similarity)				1141
P06270 UniProt NPD GO	RPOA_MARPO	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.41	-	cyt	0	Plastid; chloroplast				340
Q6EW20 UniProt NPD GO	RPOA_NYMAL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.41	-	cyt	0	Plastid; chloroplast				341
Q3BAK5 UniProt NPD GO	RPOA_PHAAO	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.41	-	nuc	0	Plastid; chloroplast				337
Q6EW57 UniProt NPD GO	RPOC1_NYMAL	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.41	-	nuc	0	Plastid; chloroplast				684
Q6BIJ0 UniProt NPD GO	RPB5_DEBHA	DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.41	-	nuc	0	Nucleus (By similarity)				214
Q62598 UniProt NPD GO	DSPP_RAT	Dentin sialophosphoprotein precursor [Contains: Dentin phosphoprotein (Dentin phosphophoryn) (DPP); ...	0.41	-	exc	1 *	Secreted protein				687
Q2QDE6 UniProt NPD GO	DNSL1_CRIGR	Deoxyribonuclease I-like 1 precursor (EC 3.1.21.-) (DNase I-like 1) (DNase X)	0.41	-	exc	1 *	Endoplasmic reticulum (By similarity)				304
Q6W3B0 UniProt NPD GO	DSG4_RAT	Desmoglein-4 precursor	0.41	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	extracellular region [IMP]			1040
P13806 UniProt NPD GO	CAC2D_RABIT	Dihydropyridine-sensitive L-type calcium channel subunits alpha-2/delta precursor [Contains: L-type ...	0.41	-	nuc	0	Membrane; multi-pass membrane protein				1106
Q8L3R3 UniProt NPD GO	RFL1_ARATH	Disease resistance protein RFL1 (RPS5-like protein 1) (pNd13/pNd14)	0.41	-	nuc	0					885
Q24114 UniProt NPD GO	DALY_DROME	Division abnormally delayed protein precursor (Dally protein)	0.41	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				626
Q02330 UniProt NPD GO	SMA2_CAEEL	Dwarfin sma-2 (MAD protein homolog 1)	0.41	-	nuc	0					418

You are viewing entries 31001 to 31050 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.