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
P82419 UniProt NPD GO	PCG6_PACGO	Ponericin-G6	0.00	-		0	Secreted protein				18
P82420 UniProt NPD GO	PCG7_PACGO	Ponericin-G7	0.00	-		0	Secreted protein				19
P82421 UniProt NPD GO	PCL1_PACGO	Ponericin-L1	0.00	-	cyt	0	Secreted protein				24
P82422 UniProt NPD GO	PCL2_PACGO	Ponericin-L2	0.00	-	cyt	0	Secreted protein				24
P82428 UniProt NPD GO	PCW6_PACGO	Ponericin-W6	0.00	-		0	Secreted protein				20
P34095 UniProt NPD GO	PFPA_ENTHI	Pore-forming peptide ameobapore A precursor (EH-APP)	0.00	-	exc	0	Cytoplasmic granule			1OF9	98
Q24824 UniProt NPD GO	PFPB_ENTHI	Pore-forming peptide ameobapore B precursor (EH-APP)	0.00	-	end	0	Cytoplasmic granule				96
Q24825 UniProt NPD GO	PFPC_ENTHI	Pore-forming peptide ameobapore C precursor (EH-APP)	0.00	-	exc	0	Cytoplasmic granule				101
Q9Y257 UniProt NPD GO	KCNK6_HUMAN	Potassium channel subfamily K member 6 (Inward rectifying potassium channel protein TWIK-2) (TWIK-or ...	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	voltage-gated potassium channel complex [TAS]	603939		313
Q9NII6 UniProt NPD GO	KAX15_MESMA	Potassium channel toxin alpha-KTx 1.5 precursor (Neurotoxin TX1) (BmTX1)	0.00	-	exc	0	Secreted protein			1BIG	57
Q9NII5 UniProt NPD GO	KAX16_MESMA	Potassium channel toxin alpha-KTx 1.6 precursor (Neurotoxin TX2) (BmTX2)	0.00	-	exc	0	Secreted protein			2BMT	58
P60165 UniProt NPD GO	KA112_PARVI	Potassium channel toxin alpha-KTx 11.2 (Parabutoxin-2) (PBTx2)	0.00	-	nuc	0	Secreted protein	extracellular region [IDA]			37
Q967F9 UniProt NPD GO	KA141_MESMA	Potassium channel toxin alpha-KTx 14.1 precursor (Toxin Kk1) (BmKK1)	0.00	-	vac	1 *	Secreted protein				54
Q9BJX2 UniProt NPD GO	KA143_MESMA	Potassium channel toxin alpha-KTx 14.3 precursor (Toxin Kk3) (BmKK3) (Neurotoxin SKTx2)	0.00	-	vac	1 *	Secreted protein				54
Q8I0L5 UniProt NPD GO	KA152_MESMA	Potassium channel toxin alpha-KTx 15.2 precursor (Toxin BmTX3) (Neurotoxin TX3) (BmTX3A)	0.00	-	exc	0	Secreted protein				59
Q867F4 UniProt NPD GO	KA154_ANDAU	Potassium channel toxin alpha-KTx 15.4 precursor (Toxin AaTX1) (Toxin Aa1)	0.00	-	exc	0	Secreted protein				59
Q86SD8 UniProt NPD GO	KA155_ANDAU	Potassium channel toxin alpha-KTx 15.5 precursor (Toxin AaTX2)	0.00	-	exc	0	Secreted protein (By similarity)				59
Q5K0E0 UniProt NPD GO	KA157_ANDAM	Potassium channel toxin alpha-KTx 15.7 precursor (Neurotoxin AamTX)	0.00	-	nuc	1 *	Secreted protein				59
P45696 UniProt NPD GO	KAX35_ANDAU	Potassium channel toxin alpha-KTx 3.5 precursor (Kaliotoxin-2) (KTX-2)	0.00	-	vac	1 *	Secreted protein				59
Q9NII7 UniProt NPD GO	KAX36_MESMA	Potassium channel toxin alpha-KTx 3.6 precursor (Kaliotoxin) (BmKTX)	0.00	-	mit	1 *	Secreted protein			1BKT	60
Q5G8B6 UniProt NPD GO	KAX45_TITCO	Potassium channel toxin alpha-KTx 4.5 precursor	0.00	-	mit	1 *	Secreted protein				59
Q9U8D2 UniProt NPD GO	KAX82_MESMA	Potassium channel toxin alpha-KTx 8.2 precursor (Neurotoxin BmP01) (Potassium ion channel blocker P0 ...	0.00	-	mit	1 *	Secreted protein			1WM7	57
P69940 UniProt NPD GO	KBX1_TITSE	Potassium channel toxin beta-KTx 1 precursor (Tityustoxin K-beta) (TsTX-K beta) (TsTX K beta) (TSK2) ...	0.00	-	exc	0	Secreted protein				85
P69939 UniProt NPD GO	KBX2_ANDAU	Potassium channel toxin beta-KTx 2 precursor (Toxin AaTX K-beta)	0.00	-	end	0	Secreted protein (By similarity)				91
Q9N661 UniProt NPD GO	KBX4_MESMA	Potassium channel toxin beta-KTx 4 precursor (Toxin BmTX K-beta2) (BmTXKbeta2) (BmTX K beta2')	0.00	-	end	0	Secreted protein (By similarity)				91
Q86QT3 UniProt NPD GO	KGX11_CENNO	Potassium channel toxin gamma-KTx 1.1 precursor (Ergtoxin) (ErgTx) (Ergtoxin-like protein 1) (ErgTx1 ...	0.00	-	mit	0	Secreted protein			1PX9	62
Q9BKB7 UniProt NPD GO	KGX21_BUTEU	Potassium channel toxin gamma-KTx 2.1 precursor (Neurotoxin BeKm-1)	0.00	-	exc	0	Secreted protein			1LGL	57
P59938 UniProt NPD GO	KGX22_MESMA	Potassium channel toxin gamma-KTx 2.2 precursor (Neurotoxin Kk7) (BmKK7) (BmKKx2)	0.00	-	vac	0	Secreted protein				57
Q9TUI4 UniProt NPD GO	KCNH2_PIG	Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit Kv11.1 ...	0.00	-	end	0	Membrane; multi-pass membrane protein				97
O08703 UniProt NPD GO	KCNH2_CAVPO	Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit Kv11.1 ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein				162
O70344 UniProt NPD GO	KCNQ1_CAVPO	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.00	-	cyt	3 *	Membrane; multi-pass membrane protein				169
Q9TTJ7 UniProt NPD GO	KCNQ1_PIG	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.00	-	mit	2 *	Membrane; multi-pass membrane protein				123
Q9MYS6 UniProt NPD GO	KCNQ1_RABIT	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.00	-	mit	3 *	Membrane; multi-pass membrane protein				155
P83764 UniProt NPD GO	PB1_PROTR	Preblooming protein 1 (PB1) (Fragment)	0.00	-		0					15
P83765 UniProt NPD GO	PB2_PROTR	Preblooming protein 2 (PB2) (Fragment)	0.00	-	cyt	0					21
P83766 UniProt NPD GO	PB3_PROTR	Preblooming protein 3 (PB3) (Fragment)	0.00	-		0					15
P53633 UniProt NPD GO	PRA1_YEAST	Prenylated Rab acceptor 1	0.00	-	end	2	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] ER to Golgi transport vesicle [IDA] Golgi apparatus [IDA]			176
O13666 UniProt NPD GO	ERG32_SCHPO	Probable C-5 sterol desaturase 2 (EC 1.3.3.-) (Sterol-C5-desaturase 2) (Ergosterol delta 5,6 desatur ...	0.00	-	nuc	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				329
P87113 UniProt NPD GO	ERG2_SCHPO	Probable C-8 sterol isomerase (Delta-8--delta-7 sterol isomerase)	0.00	-	mit	0	Endoplasmic reticulum (By similarity)				219
Q19826 UniProt NPD GO	RPB8_CAEEL	Probable DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide (EC 2.7.7.6) (RPB17) (RPB8 ...	0.00	-	cyt	0	Nucleus (By similarity)				148
P46089 UniProt NPD GO	GPR3_HUMAN	Probable G-protein coupled receptor 3 (ACCA orphan receptor)	0.00	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600241		330
P35413 UniProt NPD GO	GPR3_MOUSE	Probable G-protein coupled receptor 3 (GPCR21)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				330
Q6P7G9 UniProt NPD GO	GP146_XENLA	Probable G-protein-coupled receptor 146	0.00	-	end	7 *	Membrane; multi-pass membrane protein				333
Q9W1X8 UniProt NPD GO	FCL_DROME	Probable GDP-L-fucose synthetase (EC 1.1.1.271) (Protein FX) (GDP-4-keto-6-deoxy-D-mannose-3,5-epime ...	0.00	-	cyt	0		cytoplasm [ISS]			321
Q20263 UniProt NPD GO	GOT1_CAEEL	Probable Golgi transport protein 1	0.00	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				141
Q56W64 UniProt NPD GO	ASPG3_ARATH	Probable L-asparaginase 3 precursor (EC 3.5.1.1) (L-asparagine amidohydrolase 3) [Contains: L-aspara ...	0.00	-	exc	1 *					359
Q20412 UniProt NPD GO	NDUB2_CAEEL	Probable NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial precursor (EC 1. ...	0.00	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)				160
P78870 UniProt NPD GO	FADH1_SCHPO	Probable S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284) (Glutathione-dependent formaldehy ...	0.00	-	cyt	0					378
O17680 UniProt NPD GO	METM_CAEEL	Probable S-adenosylmethionine synthetase C49F5.1 (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoM ...	0.00	-	cyt	0					403
Q84VY5 UniProt NPD GO	DPNP4_ARATH	Probable SAL4 phosphatase (3'(2'),5'-bisphosphate nucleotidase 4) (EC 3.1.3.7) (3'(2'),5'-bisphospho ...	0.00	-	nuc	0					345

You are viewing entries 97101 to 97150 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.