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
Q8BHD8 UniProt NPD GO	PCMD2_MOUSE	Protein-L-isoaspartate O-methyltransferase domain-containing protein 2	0.60	+	nuc	0	Cytoplasm (By similarity)				359
Q9DBQ7 UniProt NPD GO	PACE1_MOUSE	Protein-associating with the carboxyl-terminal domain of ezrin (Ezrin-binding protein PACE-1) (SCY1- ...	0.60	-	vac	0	Cytoplasm. Golgi apparatus. Colocalized with VIL2/ezrin, actin and CD44 in lamellipodia (By similari ...				734
P33072 UniProt NPD GO	LYOX_BOVIN	Protein-lysine 6-oxidase precursor (EC 1.4.3.13) (Lysyl oxidase)	0.60	-	exc	0	Secreted protein; extracellular space				418
O60063 UniProt NPD GO	YBB1_SCHPO	Putative 40S ribosomal protein S4-like	0.60	-	nuc	0	Mitochondrion (Potential)				327
Q9M1U2 UniProt NPD GO	GATA8_ARATH	Putative GATA transcription factor 8	0.60	-	nuc	0	Nucleus (Probable)				204
Q94045 UniProt NPD GO	TCP4_CAEEL	Putative RNA polymerase II transcriptional coactivator	0.60	-	nuc	0	Nucleus (By similarity)				124
Q95PX3 UniProt NPD GO	TBX7_CAEEL	Putative T-box protein 7	0.60	-	nuc	0	Nucleus (Potential)	nucleus [NAS]			327
Q9C8T1 UniProt NPD GO	CCMA_ARATH	Putative cytochrome c biogenesis ATP-binding export protein ccmA-like (EC 3.6.3.41) (AtNAP10)	0.60	-	mit	0	Membrane; peripheral membrane protein (By similarity)				229
P83103 UniProt NPD GO	HASP_DROME	Putative serine/threonine-protein kinase Haspin homolog (EC 2.7.11.1)	0.60	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			566
Q9C9F4 UniProt NPD GO	COLX_ARATH	Putative zinc finger protein At1g68190	0.60	+	nuc	0	Nucleus (Potential)				356
P04049 UniProt NPD GO	RAF1_HUMAN	RAF proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (Raf-1) (C-RAF) (cRaf)	0.60	-	nuc	0		mitochondrial outer membrane [TAS]	164760	1RFA	648
Q4R5T4 UniProt NPD GO	RNF32_MACFA	RING finger protein 32	0.60	-	nuc	0	Cytoplasm (By similarity)				362
Q4WYA1 UniProt NPD GO	REXO3_ASPFU	RNA exonuclease 3 (EC 3.1.-.-)	0.60	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				645
Q91560 UniProt NPD GO	REXO4_XENLA	RNA exonuclease 4 (EC 3.1.-.-) (Exonuclease XPMC2) (Prevents mitotic catastrophe 2 protein)	0.60	+	nuc	0	Nucleus				421
Q96T51 UniProt NPD GO	RUFY1_HUMAN	RUN and FYVE domain-containing protein 1 (FYVE-finger protein EIP1) (Zinc finger FYVE domain-contain ...	0.60	-	nuc	0	Cytoplasm. Early endosome; endosomal membrane; peripheral membrane protein				708
P46694 UniProt NPD GO	IEX1_MOUSE	Radiation-inducible immediate-early gene IEX-1 (Immediate early protein GLY96) (Immediate early resp ...	0.60	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				153
Q9GQN0 UniProt NPD GO	RBP16_DROME	Ran-binding protein 16	0.60	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Nucleus; nuclear envelope; nuclear pore complex ...	cytoplasm [ISS] nuclear pore [ISS] nucleus [ISS]			1098
Q4R4T9 UniProt NPD GO	RANB3_MACFA	Ran-binding protein 3 (RanBP3)	0.60	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				499
Q99MK9 UniProt NPD GO	RASF1_MOUSE	Ras association domain-containing protein 1 (Protein 123F2)	0.60	-	nuc	0	Isoform A: Cytoskeleton (By similarity). Centrosome (By similarity). Spindle (By similarity). Isofor ...	microtubule cytoskeleton [ISS] nucleus [ISS]			340
Q63475 UniProt NPD GO	PTPR2_RAT	Receptor-type tyrosine-protein phosphatase N2 precursor (EC 3.1.3.48) (R-PTP-N2) (PTP NE-6) (PTPNE6) ...	0.60	-	end	0	Membrane; single-pass type I membrane protein (Probable)				1004
Q06330 UniProt NPD GO	SUH_HUMAN	Recombining binding protein suppressor of hairless (J kappa-recombination signal-binding protein) (R ...	0.60	-	nuc	0	Nucleus	nucleolus [IDA] nucleus [IDA]	147183		500
Q8LDU4 UniProt NPD GO	RCCR_ARATH	Red chlorophyll catabolite reductase, chloroplast precursor (EC 1.-.-.-) (RCC reductase) (AtRCCR) (A ...	0.60	-	mit	0	Plastid; chloroplast; chloroplast stroma. And a low amount in mitochondria of 7-day-old seedlings				319
Q3S853 UniProt NPD GO	RGS2_PIG	Regulator of G-protein signaling 2 (RGS2)	0.60	-	nuc	0					212
Q6XPR3 UniProt NPD GO	RPTN_HUMAN	Repetin	0.60	+	nuc	0					784
Q9JK11 UniProt NPD GO	RTN4_RAT	Reticulon-4 (Neurite outgrowth inhibitor) (Nogo protein) (Foocen) (Glut4 vesicle 20 kDa protein)	0.60	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	integral to endoplasmic reticulum membrane [IDA] integral to membrane [TAS] nuclear envelope [ISS]			1163
P41157 UniProt NPD GO	FLI1_XENLA	Retroviral integration site protein Fli-1 homolog	0.60	-	nuc	0	Nucleus				453
P04282 UniProt NPD GO	GAG17_DROME	Retrovirus-related Gag polyprotein from copia-like transposable element 17.6	0.60	-	nuc	0					439
O78453 UniProt NPD GO	RNE_GUITH	Ribonuclease E homolog (EC 3.1.4.-) (RNase E)	0.60	-	end	0	Plastid; chloroplast				429
Q5RAH8 UniProt NPD GO	RL7L_PONPY	Ribosomal protein L7-like 1	0.60	+	cyt	0					246
P67998 UniProt NPD GO	KS6B1_RABIT	Ribosomal protein S6 kinase beta-1 (EC 2.7.11.1) (Ribosomal protein S6 kinase I) (S6K) (p70-S6K)	0.60	+	mit	0	Cytoplasm. Synaptosome (By similarity). Also found in the soluble synaptosomal fractions (By similar ...				525
Q07915 UniProt NPD GO	RLP24_YEAST	Ribosome biogenesis protein RLP24 (Ribosomal protein L24-like)	0.60	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm	nucleolus [TAS]			199
Q07381 UniProt NPD GO	TSR1_YEAST	Ribosome biogenesis protein TSR1 (20S rRNA accumulation protein 1)	0.60	-	nuc	0	Nucleus; nucleolus	cytoplasm [IDA] nucleolus [IDA]			788
Q70JS2 UniProt NPD GO	KELC_ANOST	Ring canal kelch homolog (Kelch-like protein 1) [Contains: Kelch short protein]	0.60	-	nuc	0					1499
P83571 UniProt NPD GO	RUVB2_BRARE	RuvB-like 2 (EC 3.6.1.-) (Reptin) (zReptin)	0.60	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			463
Q6CT29 UniProt NPD GO	RUVB2_KLULA	RuvB-like helicase 2 (EC 3.6.1.-)	0.60	-	cyt	0	Nucleus (By similarity)				467
P21817 UniProt NPD GO	RYR1_HUMAN	Ryanodine receptor 1 (Skeletal muscle-type ryanodine receptor) (RyR1) (RYR-1) (Skeletal muscle calci ...	0.60	+	end	6	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS] smooth endoplasmic reticulum [TAS]	180901		5038
P27015 UniProt NPD GO	SCRY4_OMMSL	S-crystallin SL4 (Fragment)	0.60	-	nuc	0					302
Q06649 UniProt NPD GO	3BP2_MOUSE	SH3 domain-binding protein 2 (3BP-2)	0.60	-	nuc	0					559
P40856 UniProt NPD GO	SA185_YEAST	SIT4-associating protein SAP185	0.60	-	nuc	0		cytoplasm [IPI] mitochondrion [IDA]			1058
O60093 UniProt NPD GO	SRR1L_SCHPO	SRR1-like protein	0.60	-	nuc	0	Cytoplasm (By similarity)				251
O15041 UniProt NPD GO	SEM3E_HUMAN	Semaphorin-3E precursor	0.60	+	cyt	0	Secreted protein (By similarity)	extracellular space [TAS]	608166		775
Q76KF0 UniProt NPD GO	SEM6D_MOUSE	Semaphorin-6D precursor	0.60	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1073
O43236 UniProt NPD GO	SEPT4_HUMAN	Septin-4 (Peanut-like protein 2) (Brain protein H5) (Cell division control-related protein 2) (hCDCR ...	0.60	-	nuc	0			603696		478
Q6CRA9 UniProt NPD GO	BUR1_KLULA	Serine/threonine-protein kinase BUR1 (EC 2.7.11.22) (EC 2.7.11.23)	0.60	-	nuc	0	Nucleus (By similarity)				645
Q91820 UniProt NPD GO	STK6_XENLA	Serine/threonine-protein kinase Eg2 (EC 2.7.11.1) (pEg2) (p46Eg265)	0.60	-	nuc	0	Spindle. Centrosome. Localizes to the spindle pole during mitosis especially from prophase through a ...				407
Q6P5Z2 UniProt NPD GO	PKN3_HUMAN	Serine/threonine-protein kinase N3 (EC 2.7.11.13) (Protein kinase PKN-beta) (Protein-kinase C-relate ...	0.60	-	cyt	0	Nucleus. Cytoplasm; perinuclear region. Nuclear and perinuclear Golgi region				889
P57059 UniProt NPD GO	SN1L1_HUMAN	Serine/threonine-protein kinase SNF1-like kinase 1 (EC 2.7.11.1) (Serine/threonine-protein kinase SN ...	0.60	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). May translocate to the nucleus on activation (By ...	cytoplasm [ISS]	605705		783
P56932 UniProt NPD GO	2ABD_RAT	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform (PP2A, subunit B, ...	0.60	-	nuc	0	Cytoplasm	cytosol [TAS]			453
Q95LP0 UniProt NPD GO	2ABG_MACFA	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform (PP2A, subunit B, ...	0.60	-	nuc	0					447
O42773 UniProt NPD GO	PP2B1_CRYNV	Serine/threonine-protein phosphatase 2B catalytic subunit A1 (EC 3.1.3.16) (Calcineurin A1)	0.60	-	nuc	0					639

You are viewing entries 19251 to 19300 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.