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
Q96CH1 UniProt NPD GO	GP146_HUMAN	Probable G-protein-coupled receptor 146 (G-protein coupled receptor PGR8)	0.01	-	end	5 *	Membrane; multi-pass membrane protein				333
Q61Z75 UniProt NPD GO	NDUB2_CAEBR	Probable NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial precursor (EC 1. ...	0.01	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				160
P0C0Y4 UniProt NPD GO	MTDH_ALTAL	Probable NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) (MtDH) (Mannitol 2-dehydrogenase [NADP ...	0.01	-	cyt	0					266
P0C0Y5 UniProt NPD GO	MTDH_CLAHE	Probable NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) (MtDH) (Mannitol 2-dehydrogenase [NADP ...	0.01	-	cyt	0					267
O00058 UniProt NPD GO	MTDH_UROFA	Probable NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) (MtDH) (Mannitol 2-dehydrogenase [NADP ...	0.01	-	mit	0					256
Q9WVS2 UniProt NPD GO	GCP_RAT	Probable O-sialoglycoprotein endopeptidase (EC 3.4.24.57) (Pasteurella haemolytica metalloprotease h ...	0.01	-	cyt	0					322
Q9NPF4 UniProt NPD GO	GCP_HUMAN	Probable O-sialoglycoprotein endopeptidase (EC 3.4.24.57) (hOSGEP)	0.01	-	cyt	0					335
Q8BWU5 UniProt NPD GO	GCP_MOUSE	Probable O-sialoglycoprotein endopeptidase (EC 3.4.24.57) (mOsgep)	0.01	-	cyt	0					335
Q8SQH7 UniProt NPD GO	LSMH_ENCCU	Probable U6 snRNA-associated Sm-like protein	0.01	-	nuc	0	Nucleus (By similarity)				70
Q9Y7M4 UniProt NPD GO	LSM3_SCHPO	Probable U6 snRNA-associated Sm-like protein LSm3	0.01	-	nuc	0	Nucleus (By similarity)				93
Q03598 UniProt NPD GO	UFC1_CAEEL	Probable Ufm1-conjugating enzyme (Ubiquitin-fold modifier-conjugating enzyme)	0.01	-	cyt	0					162
P08540 UniProt NPD GO	PHOX_KLULA	Probable acid phosphatase (EC 3.1.3.2)	0.01	-	cyt	0					421
O15604 UniProt NPD GO	ARPC3_ENTHI	Probable actin-related protein 2/3 complex subunit 3 (ARP2/3 complex 21 kDa subunit) (p21-ARC) (Frag ...	0.01	-	cyt	0					128
P49173 UniProt NPD GO	NIP1_NICAL	Probable aquaporin NIP-type (Pollen-specific membrane integral protein)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				270
Q9SAI4 UniProt NPD GO	NIP61_ARATH	Probable aquaporin NIP6.1 (NOD26-like intrinsic protein 6.1)	0.01	-	end	6	Membrane; multi-pass membrane protein (Probable)				305
Q8LAI1 UniProt NPD GO	NIP71_ARATH	Probable aquaporin NIP7.1 (NOD26-like intrinsic protein 7.1)	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				275
P33560 UniProt NPD GO	TIP_ANTMA	Probable aquaporin TIP-type (Tonoplast intrinsic protein DiP) (Dark intrinsic protein)	0.01	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (Probable). Tonoplast				250
Q94CS9 UniProt NPD GO	TIP12_ORYSA	Probable aquaporin TIP1.2 (Tonoplast intrinsic protein 1.2) (OsTIP1.2)	0.01	-	end	7 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				252
Q9FWV6 UniProt NPD GO	TIP31_ORYSA	Probable aquaporin TIP3.1 (Tonoplast intrinsic protein 3.1) (OsTIP3.1)	0.01	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				264
O22588 UniProt NPD GO	TIP32_ARATH	Probable aquaporin TIP3.2 (Tonoplast intrinsic protein 3.2) (Beta-tonoplast intrinsic protein) (Beta ...	0.01	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				267
Q75GA5 UniProt NPD GO	TIP41_ORYSA	Probable aquaporin TIP4.1 (Tonoplast intrinsic protein 4.1) (OsTIP4.1)	0.01	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				251
Q6ZIB5 UniProt NPD GO	PIN4_ORYSA	Probable auxin efflux carrier component 4 (OsPIN4)	0.01	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				370
Q5VQY3 UniProt NPD GO	PIN5_ORYSA	Probable auxin efflux carrier component 5 (OsPIN5)	0.01	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				426
O59808 UniProt NPD GO	BADH_SCHPO	Probable betaine aldehyde dehydrogenase (EC 1.2.1.8) (BADH) (Meiotic expression up-regulated protein ...	0.01	-	cyt	0					500
P81081 UniProt NPD GO	CAMT_PINPS	Probable caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) ...	0.01	-	cyt	0					24
P34575 UniProt NPD GO	CISY_CAEEL	Probable citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				468
Q9SUS9 UniProt NPD GO	CPR4_ARATH	Probable cysteine proteinase At4g11320 precursor (EC 3.4.22.-)	0.01	-	exc	1 *					371
Q9USM6 UniProt NPD GO	CYB52_SCHPO	Probable cytochrome b5 2	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				129
O94337 UniProt NPD GO	DHYS_SCHPO	Probable deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.01	-	cyt	0					350
Q10479 UniProt NPD GO	ALG8_SCHPO	Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl ...	0.01	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				501
Q23361 UniProt NPD GO	ALG12_CAEEL	Probable dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl-alpha-1,6-mannosyltransferase (EC 2.4.1.-) (Mann ...	0.01	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [ISS]			492
P45971 UniProt NPD GO	OST48_CAEEL	Probable dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit precursor (EC ...	0.01	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Potentia ...				445
Q93615 UniProt NPD GO	ETFA_CAEEL	Probable electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				332
Q5Y223 UniProt NPD GO	ETFA_CRYGA	Probable electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				346
Q8J112 UniProt NPD GO	ETFA_CRYNV	Probable electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				346
Q40708 UniProt NPD GO	PIR7A_ORYSA	Probable esterase PIR7A (EC 3.1.-.-)	0.01	-	cyt	0					263
P56538 UniProt NPD GO	IF6_DROME	Probable eukaryotic translation initiation factor 6 (eIF-6)	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				245
Q9SID0 UniProt NPD GO	SCRK1_ARATH	Probable fructokinase-1 (EC 2.7.1.4)	0.01	-	cyt	0					325
Q9M1B9 UniProt NPD GO	SCRK4_ARATH	Probable fructokinase-4 (EC 2.7.1.4)	0.01	-	cyt	0					326
O65252 UniProt NPD GO	GL25_ARATH	Probable germin-like protein subfamily 2 member 5 precursor	0.01	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				213
Q9XVJ2 UniProt NPD GO	GNPI_CAEEL	Probable glucosamine-6-phosphate isomerase (EC 3.5.99.6) (Glucosamine-6-phosphate deaminase) (GNPDA) ...	0.01	-	cyt	0					267
Q9S7A0 UniProt NPD GO	DHE3_ARATH	Probable glutamate dehydrogenase 3 (EC 1.4.1.3) (GDH 3)	0.01	-	mit	0					411
Q03666 UniProt NPD GO	GSTX4_TOBAC	Probable glutathione S-transferase (EC 2.5.1.18) (Auxin-induced protein PCNT107)	0.01	-	cyt	0					221
Q03663 UniProt NPD GO	GSTX2_TOBAC	Probable glutathione S-transferase (EC 2.5.1.18) (Auxin-induced protein PGNT35/PCNT111)	0.01	-	cyt	0					223
P91253 UniProt NPD GO	GST7_CAEEL	Probable glutathione S-transferase 7 (EC 2.5.1.18) (GST class-sigma)	0.01	-	cyt	0					206
O82451 UniProt NPD GO	GSTH2_ORYSA	Probable glutathione S-transferase GSTF2 (EC 2.5.1.18) (GST-II)	0.01	-	cyt	0					214
Q06398 UniProt NPD GO	GSTU6_ORYSA	Probable glutathione S-transferase GSTU6 (EC 2.5.1.18) (28 kDa cold-induced protein)	0.01	-	cyt	0					236
Q09607 UniProt NPD GO	GST36_CAEEL	Probable glutathione S-transferase gst-36 (EC 2.5.1.18) (GST class-sigma)	0.01	-	cyt	0					210
O62327 UniProt NPD GO	GPX2_CAEEL	Probable glutathione peroxidase R05H10.5 (EC 1.11.1.9)	0.01	-	pox	0	Cytoplasm (Potential)				163
Q6ZLA3 UniProt NPD GO	GH39_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.9 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.01	-	cyt	0					441

You are viewing entries 90701 to 90750 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.