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
P28124 UniProt NPD GO	WNT9_EPTST	Protein Wnt-9 (Fragment)	0.49	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				130
P33205 UniProt NPD GO	XFD1_XENLA	Protein XFD-1 (Protein pintallavis)	0.49	+	nuc	0	Nucleus (Probable)				399
Q93249 UniProt NPD GO	CAB1_CAEEL	Protein cab-1	0.49	-	nuc	1 *		cell [IDA]			425
P54353 UniProt NPD GO	DOD_DROME	Protein dodo	0.49	-	nuc	0		nucleus [IDA]			166
O46250 UniProt NPD GO	HUNB_DROMU	Protein hunchback (Fragments)	0.49	-	nuc	0	Nucleus (By similarity)				174
Q8R4S0 UniProt NPD GO	PP14C_MOUSE	Protein phosphatase 1 regulatory subunit 14C (PKC-potentiated PP1 inhibitory protein) (Kinase-enhanc ...	0.49	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein				164
Q5RFS7 UniProt NPD GO	PP1R7_PONPY	Protein phosphatase 1 regulatory subunit 7 (Protein phosphatase 1 regulatory subunit 22)	0.49	-	nuc	0	Nucleus (By similarity)				360
P48607 UniProt NPD GO	SPZ_DROME	Protein spaetzle precursor [Contains: Protein spaetzle C-106]	0.49	-	exc	0	Isoform 8.19, isoform 8.29, isoform 11.15, isoform 11.6, isoform 11.7: Secreted protein. These isofo ...	extracellular region [IDA]			326
Q15436 UniProt NPD GO	SC23A_HUMAN	Protein transport protein Sec23A (SEC23-related protein A)	0.49	-	cyt	0	Endoplasmic reticulum; smooth endoplasmic reticulum; smooth endoplasmic reticulum membrane; peripher ...	cytosol [TAS] endoplasmic reticulum [TAS]			765
Q8IZE3 UniProt NPD GO	PACE1_HUMAN	Protein-associating with the carboxyl-terminal domain of ezrin (Ezrin-binding protein PACE-1) (SCY1- ...	0.49	-	vac	0	Cytoplasm. Golgi apparatus. Colocalized with VIL2/ezrin, actin and CD44 in lamellipodia	cytoplasm [IDA] Golgi apparatus [IDA] lamellipodium [IDA]	608192		741
P70339 UniProt NPD GO	FRAT1_MOUSE	Proto-oncogene FRAT1 (Frequently rearranged in advanced T-cell lymphomas) (Frat-1)	0.49	-	nuc	0	Cytoplasm				274
Q5DRA6 UniProt NPD GO	PCDGI_PANTR	Protocadherin gamma B6 precursor (PCDH-gamma-B6)	0.49	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				930
Q9Y5F6 UniProt NPD GO	PCDGM_HUMAN	Protocadherin gamma C5 precursor (PCDH-gamma-C5)	0.49	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606306		944
Q6WXV7 UniProt NPD GO	PC11X_PONPY	Protocadherin-11 X-linked precursor (Protocadherin-11) (Protocadherin on the X chromosome)	0.49	+	nuc	0	Membrane; single-pass type I membrane protein (Potential)				1347
P47150 UniProt NPD GO	YJ83_YEAST	Putative 40S ribosomal protein YJR113C	0.49	+	nuc	0		mitochondrial small ribosomal subunit [IDA]			247
Q09466 UniProt NPD GO	YQ5C_CAEEL	Putative ABC transporter C16C10.12 in chromosome III	0.49	-	end	6	Membrane; multi-pass membrane protein (Potential)				610
Q9LQM2 UniProt NPD GO	ATL1F_ARATH	Putative RING-H2 finger protein ATL1F precursor	0.49	-	nuc	1					332
P52893 UniProt NPD GO	ALAM_YEAST	Putative alanine aminotransferase, mitochondrial precursor (EC 2.6.1.2) (Glutamic--pyruvic transamin ...	0.49	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			592
Q5G8B3 UniProt NPD GO	AP6_TITCO	Putative antimicrobial peptide clone 6 precursor	0.49	-	exc	1 *	Secreted protein				73
Q9SA65 UniProt NPD GO	CAP4_ARATH	Putative clathrin assembly protein At1g03050	0.49	-	nuc	0					599
Q8LBH2 UniProt NPD GO	CAP8_ARATH	Putative clathrin assembly protein At2g01600	0.49	-	nuc	0					571
O04093 UniProt NPD GO	RP8L1_ARATH	Putative disease resistance protein RPP8-like protein 1	0.49	-	cyt	0					821
Q10179 UniProt NPD GO	SYG_SCHPO	Putative glycyl-tRNA synthetase (EC 6.1.1.14) (Glycine--tRNA ligase) (GlyRS)	0.49	+	cyt	0					652
P83297 UniProt NPD GO	GR64F_DROME	Putative gustatory receptor 64f	0.49	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			469
Q09891 UniProt NPD GO	ATCX_SCHPO	Putative phospholipid-transporting ATPase 1 (EC 3.6.3.1)	0.49	+	end	10	Membrane; multi-pass membrane protein				1402
Q9SLK6 UniProt NPD GO	ALA6_ARATH	Putative phospholipid-transporting ATPase 6 (EC 3.6.3.1) (Aminophospholipid flippase 6)	0.49	-	end	10	Membrane; multi-pass membrane protein				1244
Q6P9A2 UniProt NPD GO	GLTL4_HUMAN	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 4 (EC 2.4.1.41) (Protein-UDP ace ...	0.49	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				607
Q93380 UniProt NPD GO	UNC93_CAEEL	Putative potassium channel regulatory protein unc-93 (Uncoordinated protein 93)	0.49	+	end	12	Membrane; multi-pass membrane protein (Potential). Associated with dense bodies	integral to plasma membrane [NAS]			705
Q17426 UniProt NPD GO	YQ4B_CAEEL	Putative pseudouridine synthase B0024.11 (EC 5.4.99.-)	0.49	-	cyt	0					577
Q00668 UniProt NPD GO	STCC_EMENI	Putative sterigmatocystin biosynthesis peroxidase stcC precursor (EC 1.11.-.-)	0.49	-	cyt	0					311
Q8N290 UniProt NPD GO	CC053_HUMAN	Putative uncharacterized protein C3orf53	0.49	-	nuc	0					218
Q9D9R0 UniProt NPD GO	RN125_MOUSE	RING finger protein 125 (EC 6.3.2.-)	0.49	-	nuc	0					232
Q9SLC3 UniProt NPD GO	ATL2L_ARATH	RING-H2 finger protein ATL2L	0.49	-	nuc	1 *					236
Q6BGW8 UniProt NPD GO	TFB2_DEBHA	RNA polymerase II transcription factor B subunit 2 (RNA polymerase II transcription factor B p52 sub ...	0.49	-	nuc	0	Nucleus (By similarity)				515
Q3MHY8 UniProt NPD GO	RBM7_BOVIN	RNA-binding protein 7 (RNA-binding motif protein 7)	0.49	-	nuc	0					262
Q86UA6 UniProt NPD GO	RIP_HUMAN	RPA-interacting protein (hRIP)	0.49	-	nuc	0	Isoform 1: Cytoplasm. Isoform 1, isoform 2: Nucleus. Isoform 2 is only nuclear; localizes to PML bod ...				219
P01119 UniProt NPD GO	RAS1_YEAST	Ras-like protein 1 precursor	0.49	-	nuc	0	Cell membrane; lipid-anchor	plasma membrane [IDA]			309
Q5R598 UniProt NPD GO	REEP4_PONPY	Receptor expression-enhancing protein 4	0.49	-	end	2 *	Membrane; multi-pass membrane protein (By similarity)				257
O18735 UniProt NPD GO	ERBB2_CANFA	Receptor tyrosine-protein kinase erbB-2 precursor (EC 2.7.10.1) (p185erbB2) (C-erbB-2)	0.49	-	end	2	Membrane; single-pass type I membrane protein				1259
Q60553 UniProt NPD GO	ERBB2_MESAU	Receptor tyrosine-protein kinase erbB-2 precursor (EC 2.7.10.1) (p185erbB2) (C-erbB-2) (NEU proto-on ...	0.49	-	nuc	2	Membrane; single-pass type I membrane protein				1254
P93194 UniProt NPD GO	RPK1_IPONI	Receptor-like protein kinase precursor (EC 2.7.11.1)	0.49	-	end	1 *	Isoform INRPK1: Cell membrane; single-pass membrane protein. Isoform INRPK1b: Secreted protein. Isof ...	extracellular region [NAS] plasma membrane [NAS]			1109
P93002 UniProt NPD GO	NPR1_ARATH	Regulatory protein NPR1 (Nonexpresser of PR genes 1) (Noninducible immunity 1) (Nim1) (Salicylic aci ...	0.49	-	nuc	0					593
Q8N122 UniProt NPD GO	RPTOR_HUMAN	Regulatory-associated protein of mTOR (Raptor) (P150 target of rapamycin (TOR)-scaffold protein)	0.49	-	nuc	0			607130		1335
P38251 UniProt NPD GO	RFC5_YEAST	Replication factor C subunit 5 (Replication factor C5) (Activator 1 40 kDa subunit)	0.49	-	nuc	0	Nucleus (Probable)	DNA replication factor C complex [IDA]		1SXJ	354
Q80WD0 UniProt NPD GO	R4RL1_RAT	Reticulon-4 receptor-like 1 precursor (Nogo-66 receptor homolog 2) (Nogo-66 receptor-related protein ...	0.49	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential). Localized to the surface of neurons, including ...	anchored to plasma membrane [ISS] external side of plasma membrane [IDA] lipid raft [IDA]			445
P49743 UniProt NPD GO	RXRB_RAT	Retinoic acid receptor RXR-beta (Retinoid X receptor beta) (Nuclear receptor coregulator 1) (Fragmen ...	0.49	+	nuc	0	Nucleus				458
P48443 UniProt NPD GO	RXRG_HUMAN	Retinoic acid receptor RXR-gamma (Retinoid X receptor gamma)	0.49	+	nuc	0	Nucleus		180247	2GL8	463
Q8HDG8 UniProt NPD GO	TIG2_CRIGR	Retinoic acid receptor responder protein 2 precursor (Tazarotene-induced gene 2 protein) (RAR-respon ...	0.49	-	end	0	Secreted protein (Potential)				163
P32607 UniProt NPD GO	RTG1_YEAST	Retrograde regulation protein 1	0.49	+	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			177
Q8I7Q0 UniProt NPD GO	GAGO_DROME	Retrovirus-related Gag polyprotein from transposon opus	0.49	-	nuc	0		nucleus [NAS]			417

You are viewing entries 25851 to 25900 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.