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
Q7M323 UniProt NPD GO	PLMN_CAPHI	Plasminogen (EC 3.4.21.7) (Fragment)	0.51	-	nuc	0	Secreted protein				123
Q6Q7I7 UniProt NPD GO	PDGFB_CANFA	Platelet-derived growth factor B chain precursor (PDGF B-chain) (Platelet-derived growth factor beta ...	0.51	-	exc	0					242
Q8GZ52 UniProt NPD GO	PDR2_ARATH	Pleiotropic drug resistance protein 2	0.51	-	end	11	Membrane; multi-pass membrane protein (By similarity)				1400
P31669 UniProt NPD GO	PARP1_XENLA	Poly [ADP-ribose] polymerase (EC 2.4.2.30) (PARP) (ADPRT) (NAD(+) ADP-ribosyltransferase) (Poly[ADP- ...	0.51	+	nuc	0	Nucleus				998
Q460N5 UniProt NPD GO	PRP14_HUMAN	Poly [ADP-ribose] polymerase 14 (EC 2.4.2.30) (PARP-14) (B aggressive lymphoma protein 2)	0.51	-	cyt	0	Nucleus. Cytoplasm. In steady state cells the protein is mostly nuclear. A minor proportion is detec ...		610028		1720
Q8CAS9 UniProt NPD GO	PARP9_MOUSE	Poly [ADP-ribose] polymerase 9 (EC 2.4.2.30) (PARP-9) (B aggressive lymphoma protein homolog)	0.51	-	cyt	0	Nucleus (By similarity)				866
P61286 UniProt NPD GO	PABP1_BOVIN	Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)	0.51	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the cytoplasm and the nucleus ( ...				636
P11940 UniProt NPD GO	PABP1_HUMAN	Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)	0.51	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the cytoplasm and the nucleus	cytoplasm [TAS]	604679	1JH4	636
P20965 UniProt NPD GO	PABPA_XENLA	Polyadenylate-binding protein 1-A (Poly(A)-binding protein 1-A) (Cytoplasmic poly(A)-binding protein ...	0.51	-	nuc	0	Cytoplasm. Associated with polysomes	cytoplasm [ISS] polysome [IDA]			633
Q6IP09 UniProt NPD GO	PABPB_XENLA	Polyadenylate-binding protein 1-B (Poly(A)-binding protein 1-B) (Cytoplasmic poly(A)-binding protein ...	0.51	-	nuc	0	Cytoplasm. Associated with polysomes (By similarity)	polysome [ISS]			633
Q2TZG4 UniProt NPD GO	PFS2_ASPOR	Polyadenylation factor subunit 2	0.51	-	nuc	0	Nucleus (By similarity)				610
Q8TCZ9 UniProt NPD GO	PKHD1_HUMAN	Polycystic kidney and hepatic disease 1 precursor (Fibrocystin) (Polyductin) (Tigmin)	0.51	-	end	1	Membrane; single-pass type I membrane protein (Probable)	anchored to external side of plasma membrane [TAS] apical plasma membrane [IDA] basal body [IDA]	606702		4074
Q91VJ5 UniProt NPD GO	PQBP1_MOUSE	Polyglutamine-binding protein 1 (Polyglutamine tract-binding protein 1) (PQBP-1) (38 kDa nuclear pro ...	0.51	+	nuc	0	Nucleus. Co-localized with POU3F2 (By similarity)				263
Q9Z0N7 UniProt NPD GO	KCNQ1_RAT	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.51	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			669
P08798 UniProt NPD GO	PSV_DICDI	Prespore vesicle protein precursor (PSV)	0.51	-	exc	0					513
Q4R5S7 UniProt NPD GO	DDX4_MACFA	Probable ATP-dependent RNA helicase DDX4 (EC 3.6.1.-) (DEAD box protein 4) (VASA homolog)	0.51	-	nuc	0	Cytoplasm (By similarity)				725
P25371 UniProt NPD GO	ADP1_YEAST	Probable ATP-dependent permease precursor	0.51	+	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	cytoplasm [IDA] endoplasmic reticulum [IDA]			1049
Q7XZF7 UniProt NPD GO	GYRA_ORYSA	Probable DNA gyrase subunit A, chloroplast/mitochondrial precursor (EC 5.99.1.3)	0.51	-	mit	0	Plastid; chloroplast (Potential). Mitochondrial (Potential)				939
P33538 UniProt NPD GO	DPOM_NEUIN	Probable DNA polymerase (EC 2.7.7.7)	0.51	-	mit	0					969
Q19196 UniProt NPD GO	DPOE2_CAEEL	Probable DNA polymerase epsilon subunit 2 (EC 2.7.7.7) (DNA polymerase II subunit 2) (DNA polymerase ...	0.51	-	cyt	0	Nucleus (By similarity)				534
Q8IHI1 UniProt NPD GO	PSF2_BRUMA	Probable DNA replication complex GINS protein PSF2	0.51	-	cyt	0	Nucleus (By similarity)				190
Q86SQ6 UniProt NPD GO	GP123_HUMAN	Probable G-protein coupled receptor 123	0.51	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			1280
Q8NGU9 UniProt NPD GO	GP150_HUMAN	Probable G-protein coupled receptor 150	0.51	-	end	5 *	Membrane; multi-pass membrane protein				434
Q5BB41 UniProt NPD GO	TAH18_EMENI	Probable NADPH reductase tah18 (EC 1.-.-.-)	0.51	-	nuc	0					626
P25328 UniProt NPD GO	RRPW_YEAST	Probable RNA-directed RNA polymerase in W dsRNA (EC 2.7.7.48)	0.51	-	cyt	0					829
Q96SM3 UniProt NPD GO	CPXM_HUMAN	Probable carboxypeptidase X precursor (EC 3.4.17.-) (Metallocarboxypeptidase CPX-1)	0.51	+	exc	0	Secreted protein (By similarity)		609555		734
Q6BYP8 UniProt NPD GO	ATG4_DEBHA	Probable cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.51	-	nuc	0	Cytoplasm (By similarity)				492
P82713 UniProt NPD GO	CP392_DROME	Probable cytochrome P450 309a2 (EC 1.14.-.-) (CYPCCCIXA2)	0.51	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				538
Q9VVN6 UniProt NPD GO	CP312_DROME	Probable cytochrome P450 312a1 (EC 1.14.-.-) (CYPCCCXIIA1)	0.51	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				510
Q9UTI6 UniProt NPD GO	ECT1_SCHPO	Probable ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) (Phosphorylethanolamine transfera ...	0.51	+	cyt	0					365
Q9VYA0 UniProt NPD GO	NADE1_DROME	Probable glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing] ...	0.51	-	cyt	0					787
Q08882 UniProt NPD GO	HR3_MANSE	Probable nuclear hormone receptor HR3 (MHR3)	0.51	-	nuc	0	Nucleus (Potential)				548
Q9LFH0 UniProt NPD GO	PDR9_ARATH	Probable pleiotropic drug resistance protein 9	0.51	-	end	11	Membrane; multi-pass membrane protein (By similarity)				1450
Q7SC91 UniProt NPD GO	SEN54_NEUCR	Probable tRNA-splicing endonuclease subunit sen-54 (tRNA-intron endonuclease sen-54)	0.51	+	nuc	0					566
Q8T3Y0 UniProt NPD GO	SINAL_DROME	Probable ubiquitin ligase sina-like protein CG13030 (EC 6.3.2.-)	0.51	-	nuc	0		nucleus [ISS]			351
Q8VDW4 UniProt NPD GO	UBE2W_MOUSE	Probable ubiquitin-conjugating enzyme E2 W (EC 6.3.2.19) (Ubiquitin-protein ligase W) (Ubiquitin car ...	0.51	-	nuc	0					151
Q9MAH4 UniProt NPD GO	WBC10_ARATH	Probable white-brown complex homolog protein 10	0.51	-	end	6	Membrane; multi-pass membrane protein (By similarity)				590
Q2HJH9 UniProt NPD GO	PDCD5_BOVIN	Programmed cell death protein 5	0.51	-	nuc	0					124
P56812 UniProt NPD GO	PDCD5_MOUSE	Programmed cell death protein 5 (Protein TFAR19) (TF-1 cell apoptosis-related gene 19 protein)	0.51	-	nuc	0					125
Q06338 UniProt NPD GO	BCP1_YEAST	Protein BCP1	0.51	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			283
P59089 UniProt NPD GO	CU086_HUMAN	Protein C21orf86	0.51	+	nuc	0					165
O74779 UniProt NPD GO	YGB7_SCHPO	Protein C25B2.07c	0.51	-	nuc	0	Cytoplasm. Cytoplasm and microtubule	microtubule cytoskeleton [IDA]			501
Q9UK00 UniProt NPD GO	CC018_HUMAN	Protein C3orf18 (Protein G20)	0.51	-	nuc	1	Membrane; single-pass membrane protein (Potential)				162
Q9P6L4 UniProt NPD GO	YKQC_SCHPO	Protein C688.12c in chromosome I	0.51	+	end	2 *	Membrane; multi-pass membrane protein				167
Q8R043 UniProt NPD GO	CF001_MOUSE	Protein C6orf1 homolog precursor	0.51	-	mit	1 *					75
O95873 UniProt NPD GO	CF047_HUMAN	Protein C6orf47 (Protein G4)	0.51	-	end	0					294
Q8C3F2 UniProt NPD GO	CX017_MOUSE	Protein CXorf17 homolog	0.51	-	nuc	0					1091
Q5RCB7 UniProt NPD GO	FA60A_PONPY	Protein FAM60A	0.51	+	nuc	0					221
Q08559 UniProt NPD GO	FYV12_YEAST	Protein FYV12	0.51	-	nuc	1	Membrane; single-pass membrane protein (Potential)				129
Q66VE5 UniProt NPD GO	G10_GECJA	Protein G10 homolog	0.51	-	nuc	0	Nucleus (Potential)				144

You are viewing entries 24501 to 24550 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.