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
P22727 UniProt NPD GO	WNT6_MOUSE	Protein Wnt-6 precursor	0.29	-	exc	0	Secreted protein; extracellular space; extracellular matrix				364
P29703 UniProt NPD GO	RAM2_YEAST	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.29	-	cyt	0		CAAX-protein geranylgeranyltransferase complex [IDA] protein farnesyltransferase complex [IDA]			316
Q62919 UniProt NPD GO	NELL1_RAT	Protein kinase C-binding protein NELL1 precursor (NEL-like protein 1)	0.29	-	nuc	0	Secreted protein	cytoplasm [IMP]			810
Q9U6B8 UniProt NPD GO	ORAI_DROME	Protein orai (dOrai)	0.29	-	mit	4	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]			351
O77237 UniProt NPD GO	PELI_DROME	Protein pellino	0.29	-	cyt	0					424
Q7ZWC4 UniProt NPD GO	PELO_BRARE	Protein pelota homolog	0.29	-	cyt	0	Nucleus (Potential)				385
Q8MIK9 UniProt NPD GO	PP14B_PIG	Protein phosphatase 1 regulatory subunit 14B (Phosphatase holoenzyme inhibitor 1) (PHI-1) (Ubiquitou ...	0.29	-	cyt	0	Cytoplasm (Probable)				147
Q96C90 UniProt NPD GO	PP14B_HUMAN	Protein phosphatase 1 regulatory subunit 14B (Phospholipase C beta 3 neighbouring gene protein)	0.29	-	cyt	0	Cytoplasm (Probable)		601140		147
Q9Z176 UniProt NPD GO	2A5R_MOUSE	Protein phosphatase 2A, 59 kDa regulatory subunit B (PP2A PR59) (PP2A B''-PR59)	0.29	-	mit	0					491
P39966 UniProt NPD GO	PP2C2_YEAST	Protein phosphatase 2C homolog 2 (EC 3.1.3.16) (PP2C-2)	0.29	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			464
P22214 UniProt NPD GO	SEC22_YEAST	Protein transport protein SEC22 (Protein SLY2)	0.29	-	nuc	1	Membrane; single-pass type IV membrane protein (Probable)	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to membrane [IDA]			214
Q9Y5E9 UniProt NPD GO	PCDBE_HUMAN	Protocadherin beta 14 precursor (PCDH-beta14)	0.29	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]	606340		798
Q5DRD3 UniProt NPD GO	PCDBF_PANTR	Protocadherin beta 15 precursor (PCDH-beta15)	0.29	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				787
Q5DRC3 UniProt NPD GO	PCDBG_PANTR	Protocadherin beta 16 precursor (PCDH-beta16)	0.29	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				795
Q5DRC0 UniProt NPD GO	PCDGB_PANTR	Protocadherin gamma A11 precursor (PCDH-gamma-A11)	0.29	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)				935
Q42536 UniProt NPD GO	PORA_ARATH	Protochlorophyllide reductase A, chloroplast precursor (EC 1.3.1.33) (PCR A) (NADPH-protochlorophyll ...	0.29	-	mit	0	Plastid; chloroplast				405
P60514 UniProt NPD GO	TXP1_PSACA	Psalmotoxin-1 (PcTx1)	0.29	-	nuc	0	Secreted protein			1LMM	40
Q5A0Y2 UniProt NPD GO	PUS5_CANAL	Pseudouridylate synthase PUS5 (EC 5.4.99.-) (Pseudouridine synthase 5) (Uracil hydrolyase PUS5)	0.29	-	mit	0	Mitochondrion (By similarity)				247
Q8IYL9 UniProt NPD GO	PSYR_HUMAN	Psychosine receptor (G-protein coupled receptor 65) (T cell death-associated protein 8)	0.29	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	604620		337
P14484 UniProt NPD GO	CUPP_DROME	Pupal cuticle protein precursor	0.29	-	nuc	0					184
Q09724 UniProt NPD GO	YA43_SCHPO	Putative 60S mitochondrial ribosomal protein C31A2.03	0.29	-	mit	0					216
Q8BG58 UniProt NPD GO	EGLX_MOUSE	Putative HIF-prolyl hydroxylase PH-4 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl 4-hydroxylase)	0.29	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				503
Q60E60 UniProt NPD GO	NADK3_ORYSA	Putative NAD kinase 3 (EC 2.7.1.23)	0.29	-	cyt	0					494
Q22180 UniProt NPD GO	UGT55_CAEEL	Putative UDP-glucuronosyltransferase ugt-55 precursor (EC 2.4.1.17) (UDPGT)	0.29	-	nuc	1 *					512
P26337 UniProt NPD GO	ESA8C_TRYEQ	Putative adenylate cyclase regulatory protein	0.29	-	nuc	0					630
Q539E5 UniProt NPD GO	APX1_CHLVR	Putative ascorbate peroxidase precursor (EC 1.11.1.11) (HvAPX1)	0.29	-	nuc	0					367
P38454 UniProt NPD GO	CCMB_MARPO	Putative cytochrome c biogenesis ccmB-like mitochondrial protein (ORF 277)	0.29	-	end	6	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				277
O13962 UniProt NPD GO	YE42_SCHPO	Putative cytochrome c1 heme lyase (EC 4.4.1.-) (CC1HL)	0.29	-	nuc	0	Mitochondrion; mitochondrial inner membrane. Partially exposed to the intermembrane space (By simila ...				216
Q9FJ70 UniProt NPD GO	FIMB3_ARATH	Putative fimbrin-like protein 3	0.29	-	cyt	0	Cytoplasm (By similarity)				714
Q9C102 UniProt NPD GO	GLT1_SCHPO	Putative glutamate synthase [NADPH] (EC 1.4.1.13) (NADPH-GOGAT)	0.29	-	nuc	0					2111
Q9M1X9 UniProt NPD GO	ASHH4_ARATH	Putative histone-lysine N-methyltransferase ASHH4 (EC 2.1.1.43) (ASH1-homolog protein 4) (Protein SE ...	0.29	+	nuc	0	Nucleus (By similarity). Associates with centromeric constitutive heterochromatin (By similarity)				352
P82717 UniProt NPD GO	LCR2_ARATH	Putative low-molecular-weight cysteine-rich protein LCR2 precursor	0.29	-	mit	1 *					89
Q4FZG7 UniProt NPD GO	TI8AB_MOUSE	Putative mitochondrial import inner membrane translocase subunit Tim8 A-B	0.29	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				97
Q615B0 UniProt NPD GO	RT10_CAEBR	Putative mitochondrial ribosomal protein S10	0.29	-	mit	0	Mitochondrion (By similarity)				158
Q9C7F8 UniProt NPD GO	MDR15_ARATH	Putative multidrug resistance protein 15 (P-glycoprotein 13)	0.29	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1245
Q8GU88 UniProt NPD GO	PDR7_ORYSA	Putative pleiotropic drug resistance protein 7	0.29	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1444
Q9VDD9 UniProt NPD GO	RRMJ2_DROME	Putative ribosomal RNA methyltransferase CG7009 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase ...	0.29	-	mit	0		endoplasmic reticulum [NAS]			320
Q8MTI2 UniProt NPD GO	BSL1_TRIVA	Putative surface protein bspA-like (TvBspA-like-625)	0.29	-	nuc	1	Cell membrane; single-pass membrane protein (Probable). Surface membrane (Probable)				625
P53087 UniProt NPD GO	YGW4_YEAST	Putative uncharacterized protein YGL214W	0.29	-	nuc	0					162
P38898 UniProt NPD GO	YH17_YEAST	Putative uncharacterized protein YHR217C	0.29	-	nuc	0					153
Q6P0D0 UniProt NPD GO	QKIA_BRARE	Quaking protein A (zqk)	0.29	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				341
Q96A37 UniProt NPD GO	RN166_HUMAN	RING finger protein 166	0.29	-	nuc	0					237
Q64LC9 UniProt NPD GO	RBM4B_RAT	RNA-binding protein 4B (RNA-binding motif protein 4B) (RNA-binding protein 30) (RNA-binding motif pr ...	0.29	-	nuc	0	Nucleus; nucleolus (By similarity)				357
P06341 UniProt NPD GO	HB2A_RAT	RT1 class II histocompatibility antigen, A beta chain (Fragment)	0.29	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				233
Q8WUD1 UniProt NPD GO	RAB2B_HUMAN	Ras-related protein Rab-2B	0.29	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		607466	2A5J	216
Q20365 UniProt NPD GO	RAB33_CAEEL	Ras-related protein Rab-33	0.29	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				307
Q8WXH6 UniProt NPD GO	RB40A_HUMAN	Ras-related protein Rab-40A (SOCS box containing protein RAR2A) (Rar-2 protein)	0.29	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				277
Q8C8C1 UniProt NPD GO	RTP1_MOUSE	Receptor-transporting protein 1	0.29	-	nuc	1	Cell membrane; single-pass type III membrane protein. Effective cell surface expression depends upon ...				263
P70289 UniProt NPD GO	PTPRV_MOUSE	Receptor-type tyrosine-protein phosphatase V precursor (EC 3.1.3.48) (Embryonic stem cell protein-ty ...	0.29	-	end	1	Membrane; single-pass type I membrane protein				1705
P18052 UniProt NPD GO	PTPRA_MOUSE	Receptor-type tyrosine-protein phosphatase alpha precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.29	-	nuc	2	Membrane; single-pass type I membrane protein			1YFO	829

You are viewing entries 41701 to 41750 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.