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
Q5IS43 UniProt NPD GO	LIS1_PANTR	Platelet-activating factor acetylhydrolase IB subunit alpha (PAF acetylhydrolase 45 kDa subunit) (PA ...	0.03	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
Q9UF11 UniProt NPD GO	PKHB1_HUMAN	Pleckstrin homology domain-containing family B member 1 (Pleckstrin homology domain retinal protein ...	0.03	-	cyt	0	Membrane-associated. Highly expressed in the outer segments of photoreceptor cells, both in rods and ...	integral to membrane [IDA]	607651		243
Q86YL7 UniProt NPD GO	PDPN_HUMAN	Podoplanin precursor (Glycoprotein 36) (Gp36) (PA2.26 antigen) (T1A) (T1-alpha) (Aggrus)	0.03	-	end	1	Membrane; single-pass type I membrane protein. Localized to actin-rich microvilli and plasma membran ...	filopodium [ISS] lamellipodium [ISS] plasma membrane [ISS] ruffle [ISS]	608863		162
Q62011 UniProt NPD GO	PDPN_MOUSE	Podoplanin precursor (Glycoprotein 38) (Gp38) (OTS-8) (PA2.26 antigen) (Aggrus) (T1A) (T1-alpha) (Tr ...	0.03	-	cyt	1	Membrane; single-pass type I membrane protein. Localized to actin-rich microvilli and plasma membran ...	filopodium [IDA] lamellipodium [IDA] plasma membrane [IDA] ruffle [IDA]			172
Q8VWY6 UniProt NPD GO	POLC1_TOBAC	Polcalcin Nic t 1 (Calcium-binding pollen allergen Nic t 1)	0.03	-	cyt	0					84
P58171 UniProt NPD GO	POLC3_SYRVU	Polcalcin Syr v 3 (Calcium-binding pollen allergen Syr v 3)	0.03	-	cyt	0					81
P93124 UniProt NPD GO	MPAG3_DACGL	Pollen allergen Dac g 3 (Dac g III) (Fragment)	0.03	-	cyt	0	Secreted protein				96
Q08824 UniProt NPD GO	PARP1_ONCMA	Poly [ADP-ribose] polymerase (EC 2.4.2.30) (PARP) (ADPRT) (NAD(+) ADP-ribosyltransferase) (Poly[ADP- ...	0.03	-	cyt	0	Nucleus				135
Q9LT47 UniProt NPD GO	FIE_ARATH	Polycomb group protein FERTILIZATION-INDEPENDENT ENDOSPERM (Protein FERTILIZATION-INDEPENDENT SEED3) ...	0.03	-	cyt	0	Nucleus. Excluded from the nucleolus				369
Q40312 UniProt NPD GO	PGLR_MEDSA	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.03	-	exc	0					421
P82427 UniProt NPD GO	PCW5_PACGO	Ponericin-W5	0.03	-	mit	0	Secreted protein				24
P0C167 UniProt NPD GO	KAX14_CENLM	Potassium channel toxin alpha-KTx 1.4 (Limbatotoxin) (LbTx) (Limbatustoxin)	0.03	-	cyt	0	Secreted protein				37
P60208 UniProt NPD GO	KA153_ANDMA	Potassium channel toxin alpha-KTx 15.3 (Toxin AmmTX3)	0.03	-	nuc	0	Secreted protein				37
Q86BX0 UniProt NPD GO	KA158_MESMA	Potassium channel toxin alpha-KTx 15.8 precursor (Neurotoxin Kk4) (BmKKx1)	0.03	-	nuc	0	Secreted protein (Probable)				60
Q9TVX3 UniProt NPD GO	KAX53_MESMA	Potassium channel toxin alpha-KTx 5.3 precursor (Neurotoxin BmP05) (Potassium ion channel blocker P0 ...	0.03	-	cyt	1 *	Secreted protein				61
P59869 UniProt NPD GO	KAX54_MESTA	Potassium channel toxin alpha-KTx 5.4 (Tamapin)	0.03	-	nuc	0	Secreted protein				31
Q6XLL5 UniProt NPD GO	KAX6A_OPICA	Potassium channel toxin alpha-KTx 6.10 precursor (OcKTx5)	0.03	-	nuc	0	Secreted protein (By similarity)				60
Q9TT17 UniProt NPD GO	KCNS3_RABIT	Potassium voltage-gated channel subfamily S member 3 (Voltage-gated potassium channel subunit Kv9.3) ...	0.03	-	end	3	Cell membrane; multi-pass membrane protein (By similarity). Membrane; multi-pass membrane protein (B ...				491
P46367 UniProt NPD GO	ALDH4_YEAST	Potassium-activated aldehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.3) (K(+)-activated ace ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial nucleoid [IDA] mitochondrion [IDA]			519
Q28057 UniProt NPD GO	PAG2_BOVIN	Pregnancy-associated glycoprotein 2 precursor (EC 3.4.23.-) (PAG 2)	0.03	-	exc	0	Secreted protein; extracellular space				376
P80933 UniProt NPD GO	PAG62_CAPHI	Pregnancy-associated glycoprotein 62 (EC 3.4.23.-) (PAG 62) (Fragment)	0.03	-	cyt	0					27
Q95KC9 UniProt NPD GO	PCYOX_MACFA	Prenylcysteine oxidase precursor (EC 1.8.3.5)	0.03	-	end	0	Lysosome (By similarity)				505
Q5R748 UniProt NPD GO	PCYOX_PONPY	Prenylcysteine oxidase precursor (EC 1.8.3.5)	0.03	-	end	0	Lysosome (By similarity)				505
Q9UHG3 UniProt NPD GO	PCYOX_HUMAN	Prenylcysteine oxidase precursor (EC 1.8.3.5) (PCL1)	0.03	-	end	0	Lysosome	lysosome [NAS]			505
Q9XT96 UniProt NPD GO	PSN2_BOVIN	Presenilin-2 (EC 3.4.23.-) (PS-2) [Contains: Presenilin-2 NTF subunit; Presenilin-2 CTF subunit]	0.03	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				449
Q61144 UniProt NPD GO	PSN2_MOUSE	Presenilin-2 (EC 3.4.23.-) (PS-2) [Contains: Presenilin-2 NTF subunit; Presenilin-2 CTF subunit]	0.03	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to plasma membrane [ISS]			448
O88777 UniProt NPD GO	PSN2_RAT	Presenilin-2 (EC 3.4.23.-) (PS-2) [Contains: Presenilin-2 NTF subunit; Presenilin-2 CTF subunit]	0.03	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				448
P79801 UniProt NPD GO	PSN2_MICMU	Presenilin-2 (EC 3.4.23.-) (PS-2) [Contains: Presenilin-2 NTF subunit; Presenilin-2 CTF subunit] (Fr ...	0.03	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				445
O12977 UniProt NPD GO	PSN2_XENLA	Presenilin-2 (EC 3.4.23.-) (Presenilin beta) (PS-beta)	0.03	-	end	8	Membrane; multi-pass membrane protein (By similarity)				449
O64668 UniProt NPD GO	PSNA_ARATH	Presenilin-like protein At1g08700	0.03	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				453
Q9SIK7 UniProt NPD GO	PSNB_ARATH	Presenilin-like protein At2g29900	0.03	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				397
Q6FJJ0 UniProt NPD GO	PAM17_CANGA	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.03	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				186
P14200 UniProt NPD GO	MCH_RAT	Pro-MCH precursor [Contains: Neuropeptide-glycine-glutamic acid (NGE) (Neuropeptide G-E); Neuropepti ...	0.03	-	mit	0	Secreted protein				165
O62694 UniProt NPD GO	MCHL1_HYLLA	Pro-MCH variant (Fragment)	0.03	-	cyt	0					62
P33333 UniProt NPD GO	PLSC_YEAST	Probable 1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) (1-AGP acyltransferase) (1-AGP ...	0.03	-	mit	1 *	Membrane; multi-pass membrane protein (Potential)	lipid particle [IDA]			303
Q9XIR8 UniProt NPD GO	SEM11_ARATH	Probable 26 proteasome complex subunit sem1-1	0.03	-	cyt	0					74
O74455 UniProt NPD GO	6PGL_SCHPO	Probable 6-phosphogluconolactonase (EC 3.1.1.31) (6PGL)	0.03	-	mit	0					257
P38328 UniProt NPD GO	ARPC1_YEAST	Probable ARP2/3 complex 41 kDa subunit (p41-ARC)	0.03	-	cyt	0		Arp2/3 protein complex [IDA]			384
O94448 UniProt NPD GO	RCE1_SCHPO	Probable CAAX prenyl protease 2 (EC 3.4.22.-) (Prenyl protein-specific endoprotease 2) (PPSEP 2)	0.03	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				271
P47775 UniProt NPD GO	GPR12_HUMAN	Probable G-protein coupled receptor 12	0.03	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600752		334
P30951 UniProt NPD GO	GPR12_RAT	Probable G-protein coupled receptor 12 (R334)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				334
Q7Z602 UniProt NPD GO	GP141_HUMAN	Probable G-protein coupled receptor 141 (G-protein coupled receptor PGR13)	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	609045		305
Q5FVG1 UniProt NPD GO	GP157_RAT	Probable G-protein coupled receptor 157	0.03	-	end	7 *	Membrane; multi-pass membrane protein				330
O00270 UniProt NPD GO	GPR31_HUMAN	Probable G-protein coupled receptor 31	0.03	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602043		319
O88416 UniProt NPD GO	GPR33_MOUSE	Probable G-protein coupled receptor 33	0.03	-	end	7 *	Membrane; multi-pass membrane protein				339
Q9HC97 UniProt NPD GO	GPR35_HUMAN	Probable G-protein coupled receptor 35	0.03	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	602646		309
Q2KI97 UniProt NPD GO	GPR84_BOVIN	Probable G-protein coupled receptor 84	0.03	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				396
Q8R0T6 UniProt NPD GO	GPR97_MOUSE	Probable G-protein coupled receptor 97 precursor	0.03	-	end	7	Membrane; multi-pass membrane protein				542
Q9W0V7 UniProt NPD GO	MTH8_DROME	Probable G-protein coupled receptor Mth-like 8 precursor (Protein methuselah-like 8)	0.03	-	end	7	Membrane; multi-pass membrane protein (Potential)				492
Q67WR2 UniProt NPD GO	FCL1_ORYSA	Probable GDP-L-fucose synthase 1 (EC 1.1.1.271) (GDP-4-keto-6-deoxy-D-mannose-3, 5-epimerase-4-reduc ...	0.03	-	cyt	0					328

You are viewing entries 81151 to 81200 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.