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
Q38882 UniProt NPD GO	PLDA1_ARATH	Phospholipase D alpha 1 (EC 3.1.4.4) (AtPLDalpha1) (PLD alpha 1) (Choline phosphatase 1) (Phosphatid ...	0.20	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Found in vacuoles and also associated with plasma, ...				810
O23078 UniProt NPD GO	PLDB2_ARATH	Phospholipase D beta 2 (EC 3.1.4.4) (AtPLDbeta2) (PLD beta 2) (PLDdelta1)	0.20	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				915
P56531 UniProt NPD GO	VIT_MELGA	Phosvitin (PV) (Fragment)	0.20	-	nuc	0					40
Q8S9F2 UniProt NPD GO	PCYAA_EUGGR	Photoactivated adenylate cyclase subunit alpha (EC 4.6.1.1) (Photoactivated adenylyl cyclase subunit ...	0.20	-	mit	0	Paraflagellar body, flagellum and paraxonemal bodies (PABs)	flagellum [IDA]			1019
Q5IBL2 UniProt NPD GO	YCF3_PLALA	Photosystem I assembly protein ycf3	0.20	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
P12204 UniProt NPD GO	YCF3_TOBAC	Photosystem I assembly protein ycf3	0.20	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
P58257 UniProt NPD GO	YCF3_WHEAT	Photosystem I assembly protein ycf3	0.20	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
Q6YXR4 UniProt NPD GO	YCF4_PHYPA	Photosystem I assembly protein ycf4	0.20	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
P29130 UniProt NPD GO	PHYB_TOBAC	Phytochrome B	0.20	-	cyt	0					1132
P37273 UniProt NPD GO	PSY2_LYCES	Phytoene synthase 2, chloroplast precursor (EC 2.5.1.-) (Fragment)	0.20	-	cyt	0	Plastid; chloroplast				310
Q9NZF1 UniProt NPD GO	PLAC8_HUMAN	Placenta-specific gene 8 protein (C15 protein)	0.20	-	exc	0			607515		115
P24800 UniProt NPD GO	PRLPB_RAT	Placental prolactin-like protein B precursor (PRL-like protein B) (PLP-B)	0.20	-	mit	0	Secreted protein				234
P33580 UniProt NPD GO	PRLPH_RAT	Placental prolactin-like protein H precursor (PRL-like protein H) (PLP-H) (Growth hormone-related pl ...	0.20	-	end	0	Secreted protein				239
Q8CJ42 UniProt NPD GO	PRLPN_RAT	Placental prolactin-like protein N precursor (PRL-like protein N) (PLP-N)	0.20	-	vac	0	Secreted protein (By similarity)				251
Q9CRB5 UniProt NPD GO	PRLPO_MOUSE	Placental prolactin-like protein O precursor (PRL-like protein O) (PLP-O)	0.20	-	cyt	0	Secreted protein (By similarity)				251
Q08435 UniProt NPD GO	PMA1_NICPL	Plasma membrane ATPase 1 (EC 3.6.3.6) (Proton pump 1)	0.20	-	end	8	Cell membrane; multi-pass membrane protein				957
Q00804 UniProt NPD GO	AT2B1_RABIT	Plasma membrane calcium-transporting ATPase 1 (EC 3.6.3.8) (PMCA1) (Plasma membrane calcium pump iso ...	0.20	-	end	7	Cell membrane; multi-pass membrane protein				1249
O24381 UniProt NPD GO	TLC1_SOLTU	Plastidic ATP/ADP-transporter	0.20	-	end	10	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				631
Q9ZP40 UniProt NPD GO	PG1_PEA	Plastoglobulin-1, chloroplast precursor	0.20	-	mit	0	Plastid; chloroplast. Localized to the plastoglobules periphery				358
P10720 UniProt NPD GO	PF4V_HUMAN	Platelet factor 4 variant precursor (PF4var1) (PF4alt) (CXCL4L1) [Contains: Platelet factor 4 varian ...	0.20	-	mit	0	Secreted protein		173461		104
Q9H7M9 UniProt NPD GO	GI24_HUMAN	Platelet receptor Gi24 precursor	0.20	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)				311
Q60963 UniProt NPD GO	PAFA_MOUSE	Platelet-activating factor acetylhydrolase precursor (EC 3.1.1.47) (PAF acetylhydrolase) (PAF 2-acyl ...	0.20	-	end	0	Secreted protein; extracellular space				440
Q15223 UniProt NPD GO	PVRL1_HUMAN	Poliovirus receptor-related protein 1 precursor (Herpes virus entry mediator C) (HveC) (Nectin-1) (H ...	0.20	-	end	2 *	Isoform alpha, isoform delta: Cell membrane; single-pass type I membrane protein. Isoform gamma: Sec ...	adherens junction [NAS] integral to membrane [NAS] membrane [TAS]	600644		517
Q6FJS0 UniProt NPD GO	PFS2_CANGA	Polyadenylation factor subunit 2	0.20	-	nuc	0	Nucleus (By similarity)				455
P50264 UniProt NPD GO	FMS1_YEAST	Polyamine oxidase FMS1 (EC 1.5.3.11) (Fenpropimorph resistance multicopy suppressor 1)	0.20	-	cyt	0		cytoplasm [IDA]		1Z6L	508
Q40161 UniProt NPD GO	GP1_LYCES	Polygalacturonase-1 non-catalytic subunit beta precursor (AroGP1) (Polygalacturonase converter) (PG ...	0.20	-	exc	0	Secreted protein; extracellular space; apoplast. Cell wall. Associated to the cell wall				630
P14215 UniProt NPD GO	PPM1_LIMPO	Polyphemusin-1 (Polyphemusin I)	0.20	-		0	Secreted protein			2B5K	18
Q9ES82 UniProt NPD GO	POPD2_MOUSE	Popeye domain-containing protein 2 (Popeye protein 2)	0.20	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	membrane [IDA]			367
Q8N131 UniProt NPD GO	PORIM_HUMAN	Porimin precursor (Transmembrane protein 123) (Pro-oncosis receptor inducing membrane injury) (Kerat ...	0.20	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)		606356		208
Q8GXE6 UniProt NPD GO	AKT6_ARATH	Potassium channel AKT6 (Shaker pollen inward rectifier K(+) channel) (Potassium channel SPIK)	0.20	-	end	5	Membrane; multi-pass membrane protein				888
Q8R1P5 UniProt NPD GO	KCNKD_MOUSE	Potassium channel subfamily K member 13 (Tandem pore domain halothane-inhibited potassium channel 1) ...	0.20	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				405
P48547 UniProt NPD GO	KCNC1_HUMAN	Potassium voltage-gated channel subfamily C member 1 (Voltage-gated potassium channel subunit Kv3.1) ...	0.20	-	end	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176258		511
P15388 UniProt NPD GO	KCNC1_MOUSE	Potassium voltage-gated channel subfamily C member 1 (Voltage-gated potassium channel subunit Kv3.1) ...	0.20	-	end	6	Membrane; multi-pass membrane protein				511
P25122 UniProt NPD GO	KCNC1_RAT	Potassium voltage-gated channel subfamily C member 1 (Voltage-gated potassium channel subunit Kv3.1) ...	0.20	-	end	6	Membrane; multi-pass membrane protein				585
Q63959 UniProt NPD GO	KCNC3_MOUSE	Potassium voltage-gated channel subfamily C member 3 (Voltage-gated potassium channel subunit Kv3.3) ...	0.20	-	end	4	Membrane; multi-pass membrane protein				769
Q96KK3 UniProt NPD GO	KCNS1_HUMAN	Potassium voltage-gated channel subfamily S member 1 (Voltage-gated potassium channel subunit Kv9.1) ...	0.20	-	end	3	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. May not reach the ...	plasma membrane [IDA] voltage-gated potassium channel complex [IDA]	602905		526
P05225 UniProt NPD GO	CAER5_XENLA	Preprocaerulein clone PXC202 precursor [Contains: Caerulein] (Fragment)	0.20	-	mit	0	Secreted protein				187
Q90X07 UniProt NPD GO	PSN2_CHICK	Presenilin-2 (EC 3.4.23.-) (PS-2) [Contains: Presenilin-2 NTF subunit; Presenilin-2 CTF subunit]	0.20	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				451
Q16048 UniProt NPD GO	MCHL1_HUMAN	Pro-MCH-like protein 1 (Pro-melanin-concentrating hormone-like protein 1) (Pro-MCH variant)	0.20	-	nuc	0		extracellular region [NAS]	176793		86
P53585 UniProt NPD GO	ACLY_CAEEL	Probable ATP-citrate synthase (EC 2.3.3.8) (ATP-citrate (pro-S-)-lyase) (Citrate cleavage enzyme)	0.20	-	cyt	0	Cytoplasm (By similarity)				1106
Q9SS38 UniProt NPD GO	GYRBP_ARATH	Probable DNA gyrase subunit B, chloroplast precursor (EC 5.99.1.3)	0.20	-	cyt	0	Plastid; chloroplast				657
Q61IX2 UniProt NPD GO	RPO1D_CAEBR	Probable DNA-directed RNA polymerase I subunit D (EC 2.7.7.6)	0.20	-	nuc	0	Nucleus (By similarity)				145
Q7Z601 UniProt NPD GO	GP142_HUMAN	Probable G-protein coupled receptor 142 (G-protein coupled receptor PGR2)	0.20	+	end	7	Membrane; multi-pass membrane protein		609046		462
Q9UJ42 UniProt NPD GO	GP160_HUMAN	Probable G-protein coupled receptor 160	0.20	-	end	7 *	Membrane; multi-pass membrane protein				338
Q8N6U8 UniProt NPD GO	GP161_HUMAN	Probable G-protein coupled receptor 161 (G-protein coupled receptor RE2)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				529
Q8SQI6 UniProt NPD GO	AMP11_ENCCU	Probable M1-family aminopeptidase 1 (EC 3.4.11.-)	0.20	-	cyt	0					864
O94523 UniProt NPD GO	ACO1_SCHPO	Probable acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta ...	0.20	-	end	3	Membrane; multi-pass membrane protein				479
Q7XH05 UniProt NPD GO	ALDO1_ORYSA	Probable aldehyde oxidase 1 (EC 1.2.3.1) (AO-1)	0.20	-	cyt	0					1358
Q09681 UniProt NPD GO	GMH2_SCHPO	Probable alpha-1,2-galactosyltransferase gmh2 (EC 2.4.1.-)	0.20	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				346
Q9UTE2 UniProt NPD GO	HEM6_SCHPO	Probable coproporphyrinogen III oxidase (EC 1.3.3.3) (Coproporphyrinogenase) (Coprogen oxidase) (COX ...	0.20	-	cyt	0	Cytoplasm (By similarity)				312

You are viewing entries 51001 to 51050 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.