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
Q9Y818 UniProt NPD GO	UBC15_SCHPO	Ubiquitin-conjugating enzyme E2 15 (EC 6.3.2.19) (Ubiquitin-protein ligase 15) (Ubiquitin carrier pr ...	0.23	-	nuc	0					167
Q07629 UniProt NPD GO	YD218_YEAST	Uncharacterized protein YDL218W	0.23	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			317
P40496 UniProt NPD GO	YIJ3_YEAST	Uncharacterized protein YIL093C	0.23	-	cyt	0		mitochondrial small ribosomal subunit [IDA]			264
Q06170 UniProt NPD GO	YL326_YEAST	Uncharacterized protein YLR326W	0.23	-	mit	2	Membrane; multi-pass membrane protein (Potential)				240
P54074 UniProt NPD GO	YM08_YEAST	Uncharacterized protein YMR119W	0.23	-	end	5	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum membrane [IGI]			624
Q765I1 UniProt NPD GO	UTS2B_MOUSE	Urotensin-2B precursor (Urotensin-IIB) (U-IIB) (UIIB) (Urotensin II-related peptide) (Urotensin 2 do ...	0.23	-	mit	0	Secreted protein (By similarity)				113
Q9H0V9 UniProt NPD GO	LMA2L_HUMAN	VIP36-like protein precursor (Lectin, mannose-binding 2-like) (LMAN2-like protein)	0.23	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein. Predomin ...	endoplasmic reticulum membrane [IDA] ER to Golgi transport vesicle [NAS] Golgi apparatus [IDA] integral to membrane [TAS]	609552		348
Q9NA26 UniProt NPD GO	VPS28_CAEEL	VPS28 protein homolog	0.23	-	cyt	0					210
O23948 UniProt NPD GO	VATE_GOSHI	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit)	0.23	-	cyt	0					237
Q6DFU4 UniProt NPD GO	V26AB_XENLA	Vacuolar protein sorting 26A-B (Vesicle protein sorting 26A-B)	0.23	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein (By similarity)				326
Q9Y1I2 UniProt NPD GO	VP33A_DROME	Vacuolar protein sorting 33A (Protein carnation)	0.23	-	nuc	0	Late endosome; late endosomal membrane; peripheral membrane protein. Lysosome; lysosomal membrane; p ...	lysosome [IDA]			617
P41588 UniProt NPD GO	VIPR2_MOUSE	Vasoactive intestinal polypeptide receptor 2 precursor (VIP-R-2) (Pituitary adenylate cyclase-activa ...	0.23	-	end	7	Membrane; multi-pass membrane protein				437
P41587 UniProt NPD GO	VIPR2_HUMAN	Vasoactive intestinal polypeptide receptor 2 precursor (VIP-R-2) (Pituitary adenylate cyclase-activa ...	0.23	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601970		438
Q62463 UniProt NPD GO	V1AR_MOUSE	Vasopressin V1a receptor (V1aR) (Vascular/hepatic-type arginine vasopressin receptor) (Antidiuretic ...	0.23	-	end	7	Membrane; multi-pass membrane protein				423
Q9C116 UniProt NPD GO	YKO4_SCHPO	Very hypothetical protein C1786.04 in chromosome I	0.23	-	mit	0					111
P38303 UniProt NPD GO	YB40_YEAST	Very hypothetical protein YBR190W	0.23	-	nuc	0					103
P38225 UniProt NPD GO	FAT1_YEAST	Very long-chain fatty acid transport protein	0.23	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)	lipid particle [IDA] microsome [IDA] peroxisome [IDA] plasma membrane [IMP]			669
Q8VY69 UniProt NPD GO	VA723_ARATH	Vesicle-associated membrane protein 723 (AtVAMP723)	0.23	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				217
O17444 UniProt NPD GO	VACHT_DROME	Vesicular acetylcholine transporter (VAChT)	0.23	-	end	10 *	Membrane; multi-pass membrane protein				578
P78603 UniProt NPD GO	SEC17_COPCI	Vesicular-fusion protein SEC17	0.23	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				285
P42661 UniProt NPD GO	NF314_NAEFO	Virulence-related protein Nf314 (EC 3.4.16.-)	0.23	-	cyt	0					482
P07224 UniProt NPD GO	PROS_BOVIN	Vitamin K-dependent protein S precursor	0.23	-	mit	0	Secreted protein				675
Q9XT31 UniProt NPD GO	KCAB1_RABIT	Voltage-gated potassium channel subunit beta-1 (K(+) channel subunit beta-1) (Kv-beta-1)	0.23	-	nuc	0	Cytoplasm (Potential)				419
Q9PTM4 UniProt NPD GO	KCAB3_XENLA	Voltage-gated potassium channel subunit beta-3 (K(+) channel subunit beta-3) (Kv-beta-3)	0.23	-	nuc	0	Cytoplasm (Potential)				401
Q5J3M3 UniProt NPD GO	V1B13_RAT	Vomeronasal type-1 receptor B13 (Vomeronasal receptor 7) (Pheromone receptor VN7)	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q9EQ44 UniProt NPD GO	VN1B9_MOUSE	Vomeronasal type-1 receptor B9 (Vomeronasal type-1 receptor A12)	0.23	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
P40042 UniProt NPD GO	YEP6_YEAST	WD repeat protein YER066W	0.23	-	cyt	0					185
O95388 UniProt NPD GO	WISP1_HUMAN	WNT1-inducible signaling pathway protein 1 precursor (WISP-1) (Wnt-1-induced secreted protein)	0.23	-	mit	0	Secreted protein	soluble fraction [TAS]	603398		367
Q9JHC6 UniProt NPD GO	WISP2_RAT	WNT1-inducible signaling pathway protein 2 precursor (WISP-2) (Connective tissue growth factor-like ...	0.23	-	nuc	0	Secreted protein (Probable)	cell surface [IDA] cytoplasm [IDA]			250
P29182 UniProt NPD GO	TXW8_NAJNA	Weak neurotoxin 8	0.23	-	nuc	0	Secreted protein			1LMG	65
Q9ZU35 UniProt NPD GO	WBC7_ARATH	White-brown complex homolog protein 7	0.23	+	end	4 *	Membrane; multi-pass membrane protein (By similarity)				725
P91711 UniProt NPD GO	XDH_DROSU	Xanthine dehydrogenase (EC 1.17.1.4) (XD) (Protein rosy locus)	0.23	-	cyt	0	Peroxisome				1344
Q9BTP6 UniProt NPD GO	ZBED2_HUMAN	Zinc finger BED domain-containing protein 2	0.23	-	cyt	0					217
P10076 UniProt NPD GO	ZFP26_MOUSE	Zinc finger protein 26 (Zfp-26) (Protein mKR3) (Fragment)	0.23	-	nuc	0	Nucleus (Potential)				428
Q28151 UniProt NPD GO	OZF_BOVIN	Zinc finger protein OZF (Only zinc finger protein) (Zinc finger protein 146)	0.23	-	nuc	0	Nucleus (By similarity)				292
O55174 UniProt NPD GO	ZNT4_RAT	Zinc transporter 4 (ZnT-4) (Solute carrier family 30 member 4) (Dri 27 protein)	0.23	-	end	6	Endosome; endosomal membrane; multi-pass membrane protein (Probable). In the polarized enterocytes, ...	cytoplasmic membrane-bound vesicle [IDA]			430
O35149 UniProt NPD GO	ZNT4_MOUSE	Zinc transporter 4 (ZnT-4) (Solute carrier family 30 member 4) (Lethal milk protein)	0.23	-	end	6	Endosome; endosomal membrane; multi-pass membrane protein (Probable)				430
Q6TNS2 UniProt NPD GO	PK1IP_BRARE	p21-activated protein kinase-interacting protein 1-like (PAK1-interacting protein 1-like)	0.23	-	cyt	0	Nucleus; nucleolus (By similarity)				368
P43076 UniProt NPD GO	PHR1_CANAL	pH-responsive protein 1 precursor (pH-regulated protein 1)	0.23	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				548
Q8N0Z8 UniProt NPD GO	PUSL1_HUMAN	tRNA pseudouridine synthase-like 1 (EC 5.4.99.-) (tRNA-uridine isomerase-like 1) (tRNA pseudouridyla ...	0.23	-	mit	0					303
Q3B8C8 UniProt NPD GO	MTND_XENLA	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.22	-	cyt	0		cytoplasm [ISS] nucleus [ISS] plasma membrane [ISS]			179
Q9NUQ2 UniProt NPD GO	PLCE_HUMAN	1-acyl-sn-glycerol-3-phosphate acyltransferase epsilon (EC 2.3.1.51) (1-AGP acyltransferase 5) (1-AG ...	0.22	-	exc	3 *	Membrane; multi-pass membrane protein (Potential)				364
P15839 UniProt NPD GO	PRO1_ORYSA	10 kDa prolamin precursor	0.22	-	exc	2 *	In rice prolamin accumulates as type I protein body, which originates directly from the endoplasmic ...				134
P93207 UniProt NPD GO	14310_LYCES	14-3-3 protein 10	0.22	-	cyt	0					252
Q5QNB8 UniProt NPD GO	14337_ORYSA	14-3-3-like protein GF14-G (G-box factor 14-3-3 homolog G)	0.22	-	nuc	0					257
Q06103 UniProt NPD GO	RPN7_YEAST	26S proteasome regulatory subunit RPN7	0.22	-	cyt	0		proteasome regulatory particle, lid subcomp... [IPI]			428
Q08723 UniProt NPD GO	RPN8_YEAST	26S proteasome regulatory subunit RPN8	0.22	-	nuc	0		proteasome regulatory particle, lid subcomp... [IDA]			337
P87048 UniProt NPD GO	RPN1_SCHPO	26S proteasome regulatory subunit rpn1 (Proteasome non-ATPase subunit mts4) (19S regulatory cap regi ...	0.22	-	nuc	0		nucleus [TAS]			891
O74762 UniProt NPD GO	RPN2_SCHPO	26S proteasome regulatory subunit rpn2	0.22	-	nuc	0		nucleus [TAS]			965
Q29RU1 UniProt NPD GO	RT12_BOVIN	28S ribosomal protein S12, mitochondrial precursor (S12mt) (MRP-S12)	0.22	-	mit	0	Mitochondrion (By similarity)				139

You are viewing entries 48001 to 48050 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.