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
Q5ABD0 UniProt NPD GO	SNF7_CANAL	Vacuolar sorting protein SNF7 (Vacuolar protein sorting-associated protein VPS32)	0.57	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				226
P02898 UniProt NPD GO	VSG7_TRYBR	Variant surface glycoprotein 7 precursor (VSG 7) (Metacyclic variable antigen) (Fragments)	0.57	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				467
P97953 UniProt NPD GO	VEGFC_MOUSE	Vascular endothelial growth factor C precursor (VEGF-C) (Vascular endothelial growth factor-related ...	0.57	-	exc	0	Secreted protein				415
Q3HXX8 UniProt NPD GO	NGFV1_TROCA	Venom nerve growth factor 1 precursor (vNGF-1)	0.57	-	exc	0	Secreted protein				245
Q3HXY8 UniProt NPD GO	NGFV2_PSETE	Venom nerve growth factor 2 precursor (vNGF-2)	0.57	-	exc	0	Secreted protein				243
Q3HXX4 UniProt NPD GO	NGFV5_TROCA	Venom nerve growth factor 5 precursor (vNGF-5)	0.57	-	exc	0	Secreted protein				243
P84198 UniProt NPD GO	VIME_CERAE	Vimentin	0.57	-	mit	0		cytoplasm [ISS] intermediate filament [ISS]			465
Q4R4X4 UniProt NPD GO	VIME_MACFA	Vimentin	0.57	-	mit	0					465
P48670 UniProt NPD GO	VIME_CRIGR	Vimentin (Fragment)	0.57	-	mit	0					448
P48673 UniProt NPD GO	VIMB_CARAU	Vimentin beta	0.57	-	nuc	0					450
P04276 UniProt NPD GO	VTDB_RAT	Vitamin D-binding protein precursor (DBP) (Group-specific component) (Gc-globulin) (VDB)	0.57	-	exc	0	Secreted protein				476
Q9MZL3 UniProt NPD GO	CACB3_BOVIN	Voltage-dependent L-type calcium channel subunit beta-3 (CAB3) (Calcium channel voltage-dependent su ...	0.57	-	nuc	0					484
Q80ZK9 UniProt NPD GO	WDTC1_MOUSE	WD and tetratricopeptide repeats protein 1	0.57	-	nuc	0					677
Q8NI36 UniProt NPD GO	WDR36_HUMAN	WD repeat protein 36 (T-cell activation WD repeat-containing protein) (TA-WDRP)	0.57	-	nuc	0		small nucleolar ribonucleoprotein complex [ISS]	609887		951
P57081 UniProt NPD GO	WDR4_HUMAN	WD repeat protein 4	0.57	-	cyt	0			605924		412
Q920I9 UniProt NPD GO	WDR7_MOUSE	WD repeat protein 7 (TGF-beta resistance-associated protein TRAG)	0.57	-	mit	0					1489
Q9ERH3 UniProt NPD GO	WDR7_RAT	WD repeat protein 7 (TGF-beta resistance-associated protein TRAG)	0.57	-	cyt	0					1488
Q58D06 UniProt NPD GO	WDR74_BOVIN	WD repeat protein 74	0.57	+	cyt	0	Nucleus; nucleolus (By similarity)				385
Q8VCG3 UniProt NPD GO	WDR74_MOUSE	WD repeat protein 74	0.57	+	cyt	0	Nucleus; nucleolus (By similarity)				384
Q6RFH5 UniProt NPD GO	WDR74_HUMAN	WD repeat protein 74 (NOP seven-associated protein 1)	0.57	+	cyt	0	Nucleus; nucleolus				385
P78972 UniProt NPD GO	SLP1_SCHPO	WD repeat-containing protein slp1	0.57	-	mit	0					488
Q6X7K1 UniProt NPD GO	WOX2_ARATH	WUSCHEL-related homeobox 2	0.57	-	nuc	0	Nucleus (By similarity)				260
Q6X7J9 UniProt NPD GO	WOX4_ARATH	WUSCHEL-related homeobox 4	0.57	-	nuc	0	Nucleus (By similarity)				251
Q5GH72 UniProt NPD GO	XKR7_HUMAN	XK-related protein 7	0.57	-	end	6	Membrane; multi-pass membrane protein (Potential)				579
Q811B1 UniProt NPD GO	XYLT1_MOUSE	Xylosyltransferase 1 (EC 2.4.2.26) (Xylosyltransferase I) (Peptide O-xylosyltransferase 1)	0.57	+	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				953
Q5QQ52 UniProt NPD GO	XYLT_CAEBR	Xylosyltransferase sqv-6 (EC 2.4.2.26) (Peptide O-xylosyltransferase) (Squashed vulva protein 6)	0.57	-	cyt	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				803
Q96IU2 UniProt NPD GO	ZBED3_HUMAN	Zinc finger BED domain-containing protein 3	0.57	-	nuc	0					234
Q96PE6 UniProt NPD GO	ZIM3_HUMAN	Zinc finger imprinted 3	0.57	-	nuc	0	Nucleus (Probable)				472
Q5RC79 UniProt NPD GO	ZFP1_PONPY	Zinc finger protein 1 homolog (Zfp-1)	0.57	-	nuc	0	Nucleus (Probable)				407
Q9Y2Q1 UniProt NPD GO	ZN257_HUMAN	Zinc finger protein 257 (Bone marrow zinc finger 4) (BMZF-4)	0.57	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	606957		535
Q9EQB9 UniProt NPD GO	ZN287_MOUSE	Zinc finger protein 287 (Zfp-287) (Zinc finger protein SKAT-2)	0.57	-	nuc	0	Nucleus (Probable)	nucleus [IC]			759
Q9BRR0 UniProt NPD GO	ZN306_HUMAN	Zinc finger protein 306 (Zinc finger protein 47 homolog) (Zfp-47) (Zf47) (Zinc finger and SCAN domai ...	0.57	-	nuc	0	Nucleus (Probable)				538
Q9DCK4 UniProt NPD GO	ZN414_MOUSE	Zinc finger protein 414	0.57	-	nuc	0	Nucleus (Probable)				299
Q8TBZ5 UniProt NPD GO	ZN502_HUMAN	Zinc finger protein 502	0.57	-	nuc	0	Nucleus (Potential)				544
Q9P0T4 UniProt NPD GO	ZN581_HUMAN	Zinc finger protein 581	0.57	-	nuc	0	Nucleus (Probable)				197
P16373 UniProt NPD GO	ZFP59_MOUSE	Zinc finger protein 59 (Zfp-59) (Zinc finger protein Mfg-2)	0.57	-	nuc	0	Nucleus				634
Q62396 UniProt NPD GO	ZFP92_MOUSE	Zinc finger protein 92 (Zfp-92)	0.57	-	nuc	0	Nucleus (Probable)				488
Q9UPG8 UniProt NPD GO	PLAL2_HUMAN	Zinc finger protein PLAGL2 (Pleiomorphic adenoma-like protein 2)	0.57	-	nuc	0	Nucleus (Probable)		604866		496
Q9UBL0 UniProt NPD GO	ARP21_HUMAN	cAMP-regulated phosphoprotein 21 (ARPP-21)	0.57	-	nuc	0	Cytoplasm (By similarity)		605488		89
Q5R6X9 UniProt NPD GO	ARP21_PONPY	cAMP-regulated phosphoprotein 21 (ARPP-21)	0.57	-	nuc	0	Cytoplasm (By similarity)				89
Q5R413 UniProt NPD GO	DCP1B_PONPY	mRNA decapping enzyme 1B (EC 3.-.-.-)	0.57	-	nuc	0	Cytoplasm. In discrete foci (By similarity)				609
Q9SJF3 UniProt NPD GO	DCP1_ARATH	mRNA decapping enzyme-like protein (EC 3.-.-.-) (DCP1 homolog)	0.57	-	nuc	0					367
P31115 UniProt NPD GO	PUS3_YEAST	tRNA pseudouridine synthase 3 (EC 5.4.99.-) (tRNA-uridine isomerase 3) (tRNA pseudouridylate synthas ...	0.57	+	mit	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			442
Q8I5D2 UniProt NPD GO	ABRA_PLAF7	101 kDa malaria antigen (p101) (Acidic basic repeat antigen)	0.56	-	nuc	0	Cell surface. Parasitophorous vacuole. At the merozoite surface and within the parasitophorous vacuo ...				743
P22620 UniProt NPD GO	ABRA_PLAFC	101 kDa malaria antigen (p101) (Acidic basic repeat antigen)	0.56	-	nuc	0	Cell surface. Parasitophorous vacuole. At the merozoite surface and within the parasitophorous vacuo ...				743
P19084 UniProt NPD GO	11S3_HELAN	11S globulin seed storage protein G3 precursor (Helianthinin G3) [Contains: 11S globulin seed storag ...	0.56	+	nuc	0					493
Q90732 UniProt NPD GO	PRS4_CHICK	26S protease regulatory subunit 4 (P26s4) (Proteasome 26S subunit ATPase 1)	0.56	+	cyt	0	Cytoplasm. Nucleus				440
P62191 UniProt NPD GO	PRS4_HUMAN	26S protease regulatory subunit 4 (P26s4) (Proteasome 26S subunit ATPase 1)	0.56	+	cyt	0	Cytoplasm. Nucleus		602706		440
P62192 UniProt NPD GO	PRS4_MOUSE	26S protease regulatory subunit 4 (P26s4) (Proteasome 26S subunit ATPase 1)	0.56	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				440
P62193 UniProt NPD GO	PRS4_RAT	26S protease regulatory subunit 4 (P26s4) (Proteasome 26S subunit ATPase 1)	0.56	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				440

You are viewing entries 21101 to 21150 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.