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
P23957 UniProt NPD GO	VATL_AVESA	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				165
P68162 UniProt NPD GO	VATL_BETVU	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				165
P23956 UniProt NPD GO	VATL_BOVIN	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				155
Q43434 UniProt NPD GO	VATL_GOSHI	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				165
P31403 UniProt NPD GO	VATL_MANSE	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				156
P68161 UniProt NPD GO	VATL_MESCR	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				165
Q40635 UniProt NPD GO	VATL_ORYSA	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				165
O22552 UniProt NPD GO	VATL_PHAAU	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				164
P63081 UniProt NPD GO	VATL_RAT	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				155
P50515 UniProt NPD GO	VATL_SCHPO	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane [TAS]			161
O18882 UniProt NPD GO	VATL_SHEEP	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				155
P23380 UniProt NPD GO	VATL_DROME	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (Ductin) (VHA16K)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				159
P63082 UniProt NPD GO	VATL_MOUSE	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (PL16)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein	hydrogen-translocating V-type ATPase complex [TAS]			155
Q24808 UniProt NPD GO	VATL_ENTDI	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid subunit) ...	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				176
Q24810 UniProt NPD GO	VATL_ENTHI	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid subunit) ...	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				177
Q43362 UniProt NPD GO	VATL_PLECA	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid subunit) ...	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				164
O16110 UniProt NPD GO	VATL_AEDAE	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (V-ATPase C-subunit)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				157
Q96473 UniProt NPD GO	VATL_KALDA	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (V-type H+-ATPase 16 kDa subunit)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				165
P59227 UniProt NPD GO	VATL1_ARATH	Vacuolar ATP synthase 16 kDa proteolipid subunit 1/3/5 (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid su ...	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				164
Q9Y874 UniProt NPD GO	VATL2_NEUCR	Vacuolar ATP synthase 16 kDa proteolipid subunit 2 (EC 3.6.3.14) (Proteolipid protein vma-11)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				167
P59228 UniProt NPD GO	VATL2_ARATH	Vacuolar ATP synthase 16 kDa proteolipid subunit 2 (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid subuni ...	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				165
P34546 UniProt NPD GO	VATL2_CAEEL	Vacuolar ATP synthase 16 kDa proteolipid subunit 2/3 (EC 3.6.3.14)	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein	integral to membrane [NAS]			161
P59229 UniProt NPD GO	VATL4_ARATH	Vacuolar ATP synthase 16 kDa proteolipid subunit 4 (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid subuni ...	0.01	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				166
Q76NM6 UniProt NPD GO	VATA_PLAF7	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.01	-	cyt	0					611
Q03498 UniProt NPD GO	VATA_PLAFA	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.01	-	cyt	0					611
O54715 UniProt NPD GO	VAS1_RAT	Vacuolar ATP synthase subunit S1 precursor (EC 3.6.3.14) (V-ATPase S1 subunit) (V-ATPase S1 accessor ...	0.01	-	end	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				463
P23968 UniProt NPD GO	VATO_YEAST	Vacuolar ATP synthase subunit c'' (EC 3.6.3.14) (V-ATPase c'' subunit) (Vacuolar proton pump c'' sub ...	0.01	-	end	5 *	Membrane; multi-pass membrane protein	hydrogen-transporting ATPase V0 domain [TAS] integral to membrane [IDA]			213
Q69Z14 UniProt NPD GO	VA0E_SCHPO	Vacuolar ATP synthase subunit e (EC 3.6.3.14) (V-ATPase e subunit) (Vacuolar proton pump e subunit)	0.01	-	end	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				67
Q6K1C4 UniProt NPD GO	CAX3_ORYSA	Vacuolar cation/proton exchanger 3 (Ca(2+)/H(+) exchanger 3) (OsCAX3)	0.01	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein (Probable). Tonoplast				417
Q9QZ88 UniProt NPD GO	VPS29_MOUSE	Vacuolar protein sorting 29 (Vesicle protein sorting 29)	0.01	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)			1Z2X	182
Q9UBQ0 UniProt NPD GO	VPS29_HUMAN	Vacuolar protein sorting 29 (Vesicle protein sorting 29) (hVPS29) (PEP11)	0.01	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein		606932	1W24	182
P83853 UniProt NPD GO	VAM6L_MOUSE	Vam6-like protein (Fragment)	0.01	-		0	Cytoplasm (By similarity). Lysosome; lysosomal membrane; peripheral membrane protein (By similarity) ...				8
P06017 UniProt NPD GO	VSA8_TRYBB	Variant surface glycoprotein ANTAT 1.8 precursor (VSG) (Fragment)	0.01	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				115
P58447 UniProt NPD GO	VARB_VIOAR	Varv peptide B	0.01	-	nuc	0					30
P58449 UniProt NPD GO	VARD_VIOAR	Varv peptide D	0.01	-	nuc	0					29
P58451 UniProt NPD GO	VARF_VIOAR	Varv peptide F	0.01	-	nuc	0					29
P58453 UniProt NPD GO	VARH_VIOAR	Varv peptide H	0.01	-	nuc	0					30
P48142 UniProt NPD GO	VIP_ALLMI	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.01	-	nuc	0	Secreted protein				28
P81016 UniProt NPD GO	VIP_RANRI	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.01	-	nuc	0	Secreted protein				28
O82122 UniProt NPD GO	VSP2_ARATH	Vegetative storage protein 2 precursor	0.01	-	exc	0					265
P35786 UniProt NPD GO	VA5_VESSQ	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Ves s 5) (Ves s V)	0.01	-	cyt	0	Secreted protein. Venom reservoirs				205
P82807 UniProt NPD GO	FA10V_NOTSC	Venom coagulation factor Xa-like protease (EC 3.4.21.6) [Contains: Venom coagulation factor Xa-like ...	0.01	-	cyt	0	Secreted protein				98
Q91516 UniProt NPD GO	VSP1_TRIST	Venom plasminogen activator precursor (EC 3.4.21.-) (TSV-PA)	0.01	-	exc	0	Secreted protein			1BQY	258
P84878 UniProt NPD GO	MAST1_POLPI	Venom protein MP-1 (MP-I) (MPI)	0.01	-		0	Secreted protein				14
Q9I8X1 UniProt NPD GO	VSP2_AGKAC	Venom serine proteinase Dav-PA precursor (EC 3.4.21.-)	0.01	-	exc	0	Secreted protein			1OP2	258
P21800 UniProt NPD GO	VAO_PLEOS	Veratryl alcohol oxidase (VAO) (EC 1.1.3.-) (Fragments)	0.01	-	cyt	0					28
P83233 UniProt NPD GO	VTIN_ALOVR	Verectin (Fragment)	0.01	-		0					8
Q00791 UniProt NPD GO	STCU_EMENI	Versicolorin reductase (EC 1.1.-.-)	0.01	-	cyt	0					264
O14067 UniProt NPD GO	YFF8_SCHPO	Very hypothetical protein C1687.08 in chromosome I	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				96
Q09310 UniProt NPD GO	YQS2_CAEEL	Very hypothetical protein F21H12.2	0.01	-	nuc	1 *					64

You are viewing entries 92051 to 92100 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.