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
O24011 UniProt NPD GO	VATL_LYCES	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.02	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				164
Q40585 UniProt NPD GO	VATL_TOBAC	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.02	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				165
P31400 UniProt NPD GO	VATA_MANSE	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.02	-	nuc	0					617
Q27331 UniProt NPD GO	VATA2_DROME	Vacuolar ATP synthase catalytic subunit A isoform 2 (EC 3.6.3.14) (V-ATPase subunit A 2) (Vacuolar p ...	0.02	-	cyt	0		hydrogen-transporting ATPase V1 domain [ISS]			614
P38607 UniProt NPD GO	VATA2_HUMAN	Vacuolar ATP synthase catalytic subunit A, osteoclast isoform (EC 3.6.3.14) (V-ATPase subunit A 2) ( ...	0.02	-	cyt	0		plasma membrane [TAS] proton-transporting two-sector ATPase complex [TAS]			615
P31404 UniProt NPD GO	VATA1_BOVIN	Vacuolar ATP synthase catalytic subunit A, ubiquitous isoform (EC 3.6.3.14) (V-ATPase subunit A 1) ( ...	0.02	-	nuc	0					617
P50516 UniProt NPD GO	VATA1_MOUSE	Vacuolar ATP synthase catalytic subunit A, ubiquitous isoform (EC 3.6.3.14) (V-ATPase subunit A 1) ( ...	0.02	-	nuc	0		mitochondrion [IDA]			617
Q29048 UniProt NPD GO	VATA1_PIG	Vacuolar ATP synthase catalytic subunit A, ubiquitous isoform (EC 3.6.3.14) (V-ATPase subunit A 1) ( ...	0.02	-	nuc	0					617
Q5R5H2 UniProt NPD GO	VATA1_PONPY	Vacuolar ATP synthase catalytic subunit A, ubiquitous isoform (EC 3.6.3.14) (V-ATPase subunit A 1) ( ...	0.02	-	nuc	0					617
P38606 UniProt NPD GO	VATA1_HUMAN	Vacuolar ATP synthase catalytic subunit A, ubiquitous isoform (EC 3.6.3.14) (V-ATPase subunit A 1) ( ...	0.02	-	nuc	0		integral to plasma membrane [TAS] proton-transporting two-sector ATPase complex [TAS]	607027		617
Q24583 UniProt NPD GO	VATF1_DROME	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.02	-	cyt	0					124
P31478 UniProt NPD GO	VATF_MANSE	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.02	-	cyt	0					124
P40682 UniProt NPD GO	VAS1_BOVIN	Vacuolar ATP synthase subunit S1 precursor (EC 3.6.3.14) (V-ATPase S1 subunit) (V-ATPase S1 accessor ...	0.02	-	nuc	1	Vacuole; vacuolar membrane; multi-pass membrane protein				468
P14904 UniProt NPD GO	AMPL_YEAST	Vacuolar aminopeptidase 1 precursor (EC 3.4.11.22) (Vacuolar aminopeptidase I) (Polypeptidase) (Leuc ...	0.02	-	cyt	0	Vacuole	vacuole (sensu Fungi) [IDA]			514
Q99385 UniProt NPD GO	VCX1_YEAST	Vacuolar calcium ion transporter (Vacuolar Ca(2+)/H(+) exchanger) (High copy number undoes manganese ...	0.02	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuole (sensu Fungi) [IDA]			411
Q5KQN0 UniProt NPD GO	CAX2_ORYSA	Vacuolar cation/proton exchanger 2 (Ca(2+)/H(+) exchanger 2) (OsCAX2)	0.02	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein (Probable). Tonoplast				437
P47111 UniProt NPD GO	VPS55_YEAST	Vacuolar protein sorting protein 55	0.02	-	end	4 *	Endosome; endosomal membrane; multi-pass membrane protein (Potential)	late endosome [IDA]			140
P93484 UniProt NPD GO	VSR1_PEA	Vacuolar sorting receptor 1 precursor (BP-80) (80 kDa proaleurein-binding protein)	0.02	-	end	2 *	Membrane; single-pass type I membrane protein. Associated to the Golgi apparatus, mostly on the tran ...				623
Q86WA6 UniProt NPD GO	BPHL_HUMAN	Valacyclovir hydrolase precursor (EC 3.1.-.-) (VACVase) (Biphenyl hydrolase-like protein) (Biphenyl ...	0.02	-	mit	0		mitochondrion [ISS]	603156		291
P07209 UniProt NPD GO	VSM0_TRYBB	Variant surface glycoprotein MITAT 1.1000BC precursor (VSG) (Fragment)	0.02	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				72
P58446 UniProt NPD GO	VARA_VIOAR	Varv peptide A	0.02	-	nuc	0					29
P58448 UniProt NPD GO	VARC_VIOAR	Varv peptide C	0.02	-	nuc	0					29
O49195 UniProt NPD GO	VSP1_ARATH	Vegetative storage protein 1 precursor	0.02	-	vac	0					270
P30894 UniProt NPD GO	NGFV_DABRR	Venom nerve growth factor (v-NGF)	0.02	-	cyt	0	Secreted protein				117
P49265 UniProt NPD GO	TXP1_BRASM	Venom protein 1 (TXP1)	0.02	-	nuc	0	Secreted protein				39
O13059 UniProt NPD GO	VSP1_TRIGA	Venom serine proteinase 1 precursor (EC 3.4.21.-)	0.02	-	exc	0	Secreted protein				258
O13061 UniProt NPD GO	VSPB_TRIGA	Venom serine proteinase 2B precursor (EC 3.4.21.-)	0.02	-	exc	0	Secreted protein				260
Q9I8X0 UniProt NPD GO	VSP3_AGKAC	Venom serine proteinase Dav-KN precursor (EC 3.4.21.-)	0.02	-	exc	0	Secreted protein				257
Q9Y7I3 UniProt NPD GO	YD53_SCHPO	Very hypothetical protein C6C3.03c	0.02	-	mit	0					100
P38189 UniProt NPD GO	YBG2_YEAST	Very hypothetical protein YBL062W	0.02	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				126
P37265 UniProt NPD GO	YCT1_YEAST	Very hypothetical protein YCR041W	0.02	-	end	3 *					110
Q04501 UniProt NPD GO	YMJ0_YEAST	Very hypothetical protein YML090W	0.02	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				128
Q9WUF4 UniProt NPD GO	VAMP8_RAT	Vesicle-associated membrane protein 8 (VAMP-8) (Endobrevin) (EDB)	0.02	-	gol	1	Intracytoplasmic membrane; single-pass type IV membrane protein (Probable). Perinuclear vesicular st ...			1GL2	100
O70404 UniProt NPD GO	VAMP8_MOUSE	Vesicle-associated membrane protein 8 (VAMP-8) (Endobrevin) (Edb)	0.02	-	gol	1	Membrane; single-pass type IV membrane protein (Probable)	early endosome [TAS]			101
O35304 UniProt NPD GO	VACHT_MOUSE	Vesicular acetylcholine transporter (VAChT) (Solute carrier family 18 member 3)	0.02	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] membrane fraction [ISS]			530
Q62666 UniProt NPD GO	VACHT_RAT	Vesicular acetylcholine transporter (VAChT) (Solute carrier family 18 member 3) (rVAT)	0.02	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] membrane fraction [ISS]			530
O14718 UniProt NPD GO	OPSX_HUMAN	Visual pigment-like receptor peropsin	0.02	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	605224		337
Q28506 UniProt NPD GO	PROC_MACMU	Vitamin K-dependent protein C (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein C) (Blood ...	0.02	-	cyt	0					161
P83839 UniProt NPD GO	VODM_VIOOD	Vodo peptide M	0.02	-	nuc	0					29
P83838 UniProt NPD GO	VODN_VIOOD	Vodo peptide N	0.02	-	nuc	0				2GJ0	29
O42398 UniProt NPD GO	CAC1S_CHICK	Voltage-dependent L-type calcium channel subunit alpha-1S (Voltage-gated calcium channel subunit alp ...	0.02	-	end	4	Membrane; multi-pass membrane protein				281
Q9MZ16 UniProt NPD GO	VDAC1_PIG	Voltage-dependent anion-selective channel protein 1 (VDAC-1)	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity). Cell membrane (By similarity)				282
Q9TT15 UniProt NPD GO	VDAC1_RABIT	Voltage-dependent anion-selective channel protein 1 (VDAC-1) (Outer mitochondrial membrane protein p ...	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity). Cell membrane (By similarity)				282
P45879 UniProt NPD GO	VDAC1_BOVIN	Voltage-dependent anion-selective channel protein 1 (VDAC-1) (Plasmalemmal porin) (Brain-derived vol ...	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane. Cell membrane				282
Q60932 UniProt NPD GO	VDAC1_MOUSE	Voltage-dependent anion-selective channel protein 1 (VDAC-1) (mVDAC1) (mVDAC5) (Outer mitochondrial ...	0.02	-	mit	0	Isoform Mt-VDAC1: Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein. Isoform ...	mitochondrial inner membrane [IDA] mitochondrion [IDA]			296
Q9Z2L0 UniProt NPD GO	VDAC1_RAT	Voltage-dependent anion-selective channel protein 1 (VDAC-1) (rVDAC1) (Outer mitochondrial membrane ...	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity). Cell membrane (By similarity)	mitochondrial outer membrane [IDA]			282
Q60930 UniProt NPD GO	VDAC2_MOUSE	Voltage-dependent anion-selective channel protein 2 (VDAC-2) (mVDAC2) (mVDAC6) (Outer mitochondrial ...	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			295
Q9TT13 UniProt NPD GO	VDAC3_RABIT	Voltage-dependent anion-selective channel protein 3 (VDAC-3) (Outer mitochondrial membrane protein p ...	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane				283
Q9MZ13 UniProt NPD GO	VDAC3_BOVIN	Voltage-dependent anion-selective channel protein 3 (VDAC-3) (hVDAC3) (Outer mitochondrial membrane ...	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane				283
P41244 UniProt NPD GO	VEGP2_RAT	Von Ebner gland protein 2 precursor (VEG protein 2)	0.02	-	exc	0	Secreted protein				177

You are viewing entries 86201 to 86250 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.