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
P69678 UniProt NPD GO	CUTA_BOVIN	Protein CutA precursor (Brain acetylcholinesterase putative membrane anchor)	0.09	-	mit	1 *					176
Q4KMX7 UniProt NPD GO	F106A_HUMAN	Protein FAM106A	0.09	-	mit	0					169
Q96G04 UniProt NPD GO	FA86A_HUMAN	Protein FAM86A	0.09	-	cyt	0					330
Q92537 UniProt NPD GO	K0247_HUMAN	Protein KIAA0247 precursor	0.09	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				303
Q84MM9 UniProt NPD GO	MOC_ORYSA	Protein MONOCULM 1	0.09	-	cyt	0	Nucleus				441
P46955 UniProt NPD GO	NCA3_YEAST	Protein NCA3, mitochondrial precursor	0.09	-	exc	0	Mitochondrion				337
Q9W5D4 UniProt NPD GO	POMT2_DROME	Protein O-mannosyl-transferase 2 (EC 2.4.1.109) (Dolichyl-phosphate-mannose--protein mannosyltransfe ...	0.09	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]			765
Q751U2 UniProt NPD GO	PBN1_ASHGO	Protein PBN1	0.09	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				413
Q6C5K1 UniProt NPD GO	PBN1_YARLI	Protein PBN1	0.09	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				523
P36139 UniProt NPD GO	PET10_YEAST	Protein PET10 (Petite colonies protein 10)	0.09	-	nuc	0	Lipid particle; lipid particle membrane; peripheral membrane protein	lipid particle [IDA]			282
P24479 UniProt NPD GO	S10AB_CHICK	Protein S100-A11 (S100 calcium-binding protein A11) (Calgizzarin)	0.09	-	cyt	0					101
P33763 UniProt NPD GO	S10A5_HUMAN	Protein S100-A5 (S100 calcium-binding protein A5) (Protein S-100D)	0.09	-	nuc	0			176991		92
P02632 UniProt NPD GO	S100G_PIG	Protein S100-G (S100 calcium-binding protein G) (Vitamin D-dependent calcium-binding protein, intest ...	0.09	-	nuc	0				1RSX	78
P82642 UniProt NPD GO	SCR23_ARATH	Protein SCRL23 precursor	0.09	-	exc	0					95
Q8IUB5 UniProt NPD GO	WFD13_HUMAN	Protein WFDC13 precursor	0.09	-	exc	0	Secreted protein (Potential)				93
P49337 UniProt NPD GO	WNT4_CHICK	Protein Wnt-4 precursor	0.09	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix				351
Q9BWQ6 UniProt NPD GO	YIPF2_HUMAN	Protein YIPF2 (YIP1 family member 2)	0.09	-	end	5	Membrane; multi-pass membrane protein (Potential)				316
Q4QQU5 UniProt NPD GO	YIPF6_RAT	Protein YIPF6 (YIP1 family member 6)	0.09	-	end	5	Membrane; multi-pass membrane protein (Potential)				236
Q13087 UniProt NPD GO	PDIA2_HUMAN	Protein disulfide-isomerase A2 precursor (EC 5.3.4.1) (PDIp)	0.09	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [IDA]	608012		525
Q6GNG3 UniProt NPD GO	TXD10_XENLA	Protein disulfide-isomerase TXNDC10 precursor (EC 5.3.4.1) (Thioredoxin domain-containing protein 10 ...	0.09	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				452
P34055 UniProt NPD GO	INC11_TRIAT	Protein indc11	0.09	-	cyt	0					339
Q616J1 UniProt NPD GO	ORAI_CAEBR	Protein orai	0.09	-	end	4	Membrane; multi-pass membrane protein (By similarity)				300
Q5EAU0 UniProt NPD GO	ORAI1_XENLA	Protein orai-1	0.09	-	end	4	Cell membrane; multi-pass membrane protein (By similarity)				258
Q96SN7 UniProt NPD GO	ORAI2_HUMAN	Protein orai-2 (CAP-binding protein complex-interacting protein 2)	0.09	-	end	4	Membrane; multi-pass membrane protein (By similarity)				254
Q6CGE1 UniProt NPD GO	PPME1_YARLI	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.09	-	cyt	0					419
O82569 UniProt NPD GO	SUI1_PIMBR	Protein translation factor SUI1 homolog	0.09	-	cyt	0					113
Q9SQF4 UniProt NPD GO	SUI1_BRAOL	Protein translation factor SUI1 homolog (Translation initiation factor nps45)	0.09	-	cyt	0					113
Q9P8E3 UniProt NPD GO	SC61A_CANAL	Protein transport protein SEC61 subunit alpha	0.09	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				479
Q6BN08 UniProt NPD GO	SC61A_DEBHA	Protein transport protein SEC61 subunit alpha	0.09	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				479
Q9ULW8 UniProt NPD GO	PADI3_HUMAN	Protein-arginine deiminase type-3 (EC 3.5.3.15) (Protein-arginine deiminase type III) (Peptidylargin ...	0.09	-	cyt	0	Cytoplasm		606755		664
O60704 UniProt NPD GO	TPS2_HUMAN	Protein-tyrosine sulfotransferase 2 (EC 2.8.2.20) (Tyrosylprotein sulfotransferase-2) (TPST-2)	0.09	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	membrane fraction [TAS]	603126		377
P26350 UniProt NPD GO	PTMA_MOUSE	Prothymosin alpha [Contains: Thymosin alpha]	0.09	-	nuc	0	Nucleus				110
P13653 UniProt NPD GO	PORA_HORVU	Protochlorophyllide reductase A, chloroplast precursor (EC 1.3.1.33) (PCR A) (NADPH-protochlorophyll ...	0.09	-	cyt	0	Plastid; chloroplast				388
Q6KF81 UniProt NPD GO	PHCY2_HOMAM	Pseudohemocyanin-2 precursor (Fragment)	0.09	-	exc	0					681
P08938 UniProt NPD GO	PURP_CHICK	Purpurin precursor	0.09	-	vac	0	Interphotoreceptor cell matrix				196
Q9VZ64 UniProt NPD GO	6PGL_DROME	Putative 6-phosphogluconolactonase (EC 3.1.1.31) (6PGL)	0.09	-	cyt	0					243
Q9STT6 UniProt NPD GO	ATH5_ARATH	Putative ABC2 homolog 5	0.09	-	end	4	Membrane; multi-pass membrane protein (Potential)				722
Q9M0Y6 UniProt NPD GO	DPNPM_ARATH	Putative PAP-specific phosphatase, mitochondrial precursor (3'(2'),5'-bisphosphate nucleotidase) (EC ...	0.09	-	nuc	0	Mitochondrion (Potential)				397
Q20086 UniProt NPD GO	UGT58_CAEEL	Putative UDP-glucuronosyltransferase ugt-58 precursor (EC 2.4.1.17) (UDPGT)	0.09	-	end	2 *					533
P83401 UniProt NPD GO	AL7A1_DICDI	Putative aldehyde dehydrogenase family 7 member A1 homolog (EC 1.2.1.3) (Antiquitin-1)	0.09	-	nuc	0					509
Q5BLE8 UniProt NPD GO	RETST_BRARE	Putative all-trans-retinol 13,14-reductase precursor (EC 1.3.99.23) (All-trans-13,14-dihydroretinol ...	0.09	-	end	1 *	Membrane; peripheral membrane protein (By similarity)				607
Q09887 UniProt NPD GO	YC9D_SCHPO	Putative amino-acid permease C584.13	0.09	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				544
P36029 UniProt NPD GO	YKR4_YEAST	Putative amino-acid permease YKL174C	0.09	-	end	12	Membrane; multi-pass membrane protein (Probable)	Golgi apparatus [IDA]			618
P38821 UniProt NPD GO	DNPEP_YEAST	Putative aspartyl aminopeptidase (EC 3.4.11.21)	0.09	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA]			490
Q9SH30 UniProt NPD GO	AHM7_ARATH	Putative copper-transporting ATPase 3 (EC 3.6.3.4)	0.09	-	end	8	Membrane; multi-pass membrane protein				995
Q9SZC9 UniProt NPD GO	AHM6_ARATH	Putative copper-transporting ATPase PAA1 (EC 3.6.3.4)	0.09	-	mit	5	Membrane; multi-pass membrane protein				949
Q60TI7 UniProt NPD GO	CDO_CAEBR	Putative cysteine dioxygenase (EC 1.13.11.20) (CDO)	0.09	-	cyt	0					190
P53206 UniProt NPD GO	CYSK_YEAST	Putative cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyas ...	0.09	-	mit	1 *		mitochondrial outer membrane [IDA] mitochondrion [IDA]			393
Q9LVT1 UniProt NPD GO	DRL39_ARATH	Putative disease resistance protein At5g47280	0.09	-	cyt	0					623
P35894 UniProt NPD GO	GU01_RAT	Putative gustatory receptor clone PTE01 (Fragment)	0.09	-	end	3 *	Membrane; multi-pass membrane protein				185

You are viewing entries 66901 to 66950 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.