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
Q9URZ8 UniProt NPD GO	VATL2_SCHPO	Vacuolar ATP synthase 16 kDa proteolipid subunit 2 (EC 3.6.3.14) (Proteolipid protein vma11)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				162
Q91V37 UniProt NPD GO	VATO_MOUSE	Vacuolar ATP synthase 21 kDa proteolipid subunit (EC 3.6.3.14) (23 kDa subunit of V-ATPase)	0.00	-	end	5 *	Vacuole; vacuolar membrane; multi-pass membrane protein	endosome [IDA] integral to membrane [IDA]			205
Q99437 UniProt NPD GO	VATO_HUMAN	Vacuolar ATP synthase 21 kDa proteolipid subunit (EC 3.6.3.14) (HATPL)	0.00	-	end	5 *	Vacuole; vacuolar membrane; multi-pass membrane protein	integral to membrane [TAS]	603717		205
P54642 UniProt NPD GO	VATL_DICDI	Vacuolar ATP synthase proteolipid subunit (EC 3.6.3.14)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				196
Q20591 UniProt NPD GO	VA0H_CAEEL	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump H subunit)	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				86
P81103 UniProt NPD GO	VA0H_BOVIN	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump H subunit) ...	0.00	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				80
Q9BDP4 UniProt NPD GO	VA0H_CANFA	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump H subunit) ...	0.00	-	vac	2 *	Membrane; multi-pass membrane protein (Potential)				80
O15342 UniProt NPD GO	VA0H_HUMAN	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump H subunit) ...	0.00	-	vac	2 *	Membrane; multi-pass membrane protein (Potential)	membrane fraction [TAS]	603931		80
Q9R1Q9 UniProt NPD GO	VAS1_MOUSE	Vacuolar ATP synthase subunit S1 precursor (EC 3.6.3.14) (V-ATPase S1 subunit) (V-ATPase S1 accessor ...	0.00	-	mit	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				463
P25515 UniProt NPD GO	VATL1_YEAST	Vacuolar ATP synthase subunit c (EC 3.6.3.14) (V-ATPase c subunit) (Vacuolar proton pump c subunit) ...	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein	hydrogen-transporting ATPase V0 domain [TAS] integral to membrane [IDA]			160
P32842 UniProt NPD GO	VATL2_YEAST	Vacuolar ATP synthase subunit c' (EC 3.6.3.14) (V-ATPase c' subunit) (Vacuolar proton pump c' subuni ...	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein	hydrogen-transporting ATPase V0 domain [TAS] integral to membrane [IDA]			164
P41806 UniProt NPD GO	VMA21_YEAST	Vacuolar ATPase assembly integral membrane protein VMA21	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] endoplasmic reticulum membrane [IDA]			77
P40074 UniProt NPD GO	AVT6_YEAST	Vacuolar amino acid transporter 6	0.00	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuole [IMP]			448
Q12016 UniProt NPD GO	VPS68_YEAST	Vacuolar protein sorting protein 68	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Mitochondrion (Potential)	integral to membrane [NAS] mitochondrion [IDA] vacuolar membrane (sensu Fungi) [IDA]			184
P36017 UniProt NPD GO	VPS21_YEAST	Vacuolar protein sorting-associated protein 21 (GTP-binding protein YPT51)	0.00	-	cyt	0	Endosome; endosomal membrane; lipid-anchor. Mitochondrion; mitochondrial membrane; lipid-anchor	late endosome [IMP] mitochondrial outer membrane [IDA] mitochondrion [IDA]		1EK0	210
P43000 UniProt NPD GO	OXYV_SQUAC	Valitocin	0.00	-		0	Secreted protein				9
P83835 UniProt NPD GO	CYO12_VIOAR	Varv peptide E	0.00	-	nuc	0					29
P84843 UniProt NPD GO	VASOT_HYBBI	Vasotab precursor	0.00	-	vac	0	Secreted protein	extracellular region [IDA]			76
Q10749 UniProt NPD GO	VMOC_NAJMO	Venom metalloproteinase mocarhagin (EC 3.4.24.-) (Fragment)	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			24
P01140 UniProt NPD GO	NGFV_NAJNA	Venom nerve growth factor (v-NGF)	0.00	-	cyt	0	Secreted protein				116
P84879 UniProt NPD GO	VPCP_POLPI	Venom protein CP	0.00	-		0	Secreted protein				12
P84011 UniProt NPD GO	T223_PHONI	Venom protein PNTx22C3	0.00	-	nuc	0	Secreted protein				58
P50161 UniProt NPD GO	VER1_ASPPA	Versicolorin reductase (EC 1.1.-.-) (VER-1)	0.00	-	cyt	0					262
O13018 UniProt NPD GO	OPSO_SALSA	Vertebrate ancient opsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				323
Q9Y7J2 UniProt NPD GO	YOI5_SCHPO	Very hypothetical protein C1778.05c in chromosome II	0.00	-	cyt	0					98
Q10345 UniProt NPD GO	YDA3_SCHPO	Very hypothetical protein C1F12.03c in chromosome I	0.00	-	cyt	1 *					37
Q9UUI9 UniProt NPD GO	YIY3_SCHPO	Very hypothetical protein C22F8.03c in chromosome I	0.00	-	cyt	0					133
Q10493 UniProt NPD GO	YDG5_SCHPO	Very hypothetical protein C26F1.05 in chromosome I	0.00	-	mit	2 *					115
Q2YDE3 UniProt NPD GO	GOT1B_BOVIN	Vesicle transport protein GOT1B (Golgi transport 1 homolog B)	0.00	-	end	3 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				138
Q9CR60 UniProt NPD GO	GOT1B_MOUSE	Vesicle transport protein GOT1B (Golgi transport 1 homolog B)	0.00	-	end	3 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				138
Q9Y3E0 UniProt NPD GO	GOT1B_HUMAN	Vesicle transport protein GOT1B (Golgi transport 1 homolog B) (hGOT1a) (Putative NF-kappa-B-activati ...	0.00	-	end	3 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				138
Q8WV19 UniProt NPD GO	SFT2A_HUMAN	Vesicle transport protein SFT2A (SFT2 domain-containing protein 1) (pRGR1)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				159
P0C1M1 UniProt NPD GO	CRBLE_VESMG	Vespid chemotactic peptide 5e	0.00	-		0	Secreted protein				13
P0C1M3 UniProt NPD GO	CRBLG_VESMG	Vespid chemotactic peptide 5g	0.00	-		0	Secreted protein				13
P17233 UniProt NPD GO	CRBL_VESAN	Vespid chemotactic peptide A (VESCP-A)	0.00	-		0	Secreted protein				13
P17235 UniProt NPD GO	CRBL_VESLE	Vespid chemotactic peptide L (VESCP-L) (Ves-CP-L)	0.00	-		0	Secreted protein				13
P17232 UniProt NPD GO	CRBL_VESMA	Vespid chemotactic peptide M (VESCP-M) (Ves-CP-M)	0.00	-		0	Secreted protein				13
P17231 UniProt NPD GO	CRBL_VESTR	Vespid chemotactic peptide T (VESCP-T) (Ves-CP-T)	0.00	-		0	Secreted protein				13
P17234 UniProt NPD GO	CRBL_VESXA	Vespid chemotactic peptide X (VESCP-X) (Ves-CP-X)	0.00	-		0	Secreted protein				13
Q6B4J2 UniProt NPD GO	VKOR1_BOVIN	Vitamin K epoxide reductase complex subunit 1 (EC 1.1.4.1) (Vitamin K1 2,3-epoxide reductase subunit ...	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				163
Q9BQB6 UniProt NPD GO	VKOR1_HUMAN	Vitamin K epoxide reductase complex subunit 1 (EC 1.1.4.1) (Vitamin K1 2,3-epoxide reductase subunit ...	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		608547		163
Q9CRC0 UniProt NPD GO	VKOR1_MOUSE	Vitamin K epoxide reductase complex subunit 1 (EC 1.1.4.1) (Vitamin K1 2,3-epoxide reductase subunit ...	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				161
Q6TEK4 UniProt NPD GO	VKOR1_RAT	Vitamin K epoxide reductase complex subunit 1 (EC 1.1.4.1) (Vitamin K1 2,3-epoxide reductase subunit ...	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				161
O73707 UniProt NPD GO	CAC1C_CHICK	Voltage-dependent L-type calcium channel subunit alpha-1C (Voltage-gated calcium channel subunit alp ...	0.00	-	end	2	Membrane; multi-pass membrane protein				177
Q8WWY7 UniProt NPD GO	WFD12_HUMAN	WAP four-disulfide core domain protein 12 precursor (Putative protease inhibitor WAP12) (Whey acidic ...	0.00	-	mit	0	Secreted protein (Potential)	extracellular space [ISS]	609872		111
Q32LN7 UniProt NPD GO	WDR61_BOVIN	WD repeat protein 61	0.00	-	nuc	0					305
Q5ZJH5 UniProt NPD GO	WDR61_CHICK	WD repeat protein 61	0.00	-	nuc	0					305
Q9GZS3 UniProt NPD GO	WDR61_HUMAN	WD repeat protein 61 (Meiotic recombination REC14 protein homolog)	0.00	-	nuc	0					305
P83195 UniProt NPD GO	WP1_PEROL	Wall protein 1 (PWP-1) (Fragment)	0.00	-		0	Cell wall. Disulfide-linked to other cell wall components				8
P16231 UniProt NPD GO	ICI1_LYCPE	Wound-induced proteinase inhibitor 1 precursor (Wound-induced proteinase inhibitor I)	0.00	-	exc	0	Secreted protein (Potential)				111

You are viewing entries 98651 to 98700 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.