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
P16042 UniProt NPD GO	NEU4_ONCKE	Vasotocin-neurophysin VT 2 precursor [Contains: Vasotocin (VT); Neurophysin VT 2]	0.29	-	exc	1 *	Secreted protein				158
P14330 UniProt NPD GO	VSV4_DICDI	Vegetative-specific protein V4	0.29	+	nuc	0					160
Q9C111 UniProt NPD GO	YIPK_SCHPO	Very hypothetical protein C343.20 in chromosome I	0.29	-	nuc	0					113
P53097 UniProt NPD GO	YGU3_YEAST	Very hypothetical protein YGL193C	0.29	-	nuc	0					103
Q04897 UniProt NPD GO	YM98_YEAST	Very hypothetical protein YMR320W	0.29	-	mit	0					101
Q75CY3 UniProt NPD GO	BOS1_ASHGO	Vesicular transport protein BOS1	0.29	-	nuc	1	Secretory vesicle; secretory vesicle membrane; peripheral membrane protein (By similarity). Secretor ...				220
Q9P4D0 UniProt NPD GO	SEC17_PICPA	Vesicular-fusion protein SEC17	0.29	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				294
Q92093 UniProt NPD GO	VIT_ONCMY	Vitellogenin precursor (VTG) [Contains: Lipovitellin I (LVI); Phosvitin (PV); Lipovitellin II (LVII) ...	0.29	-	mit	0					1659
Q02485 UniProt NPD GO	CAC1S_RAT	Voltage-dependent L-type calcium channel subunit alpha-1S (Voltage-gated calcium channel subunit alp ...	0.29	-	end	9	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [IDA]			1146
Q9BTV6 UniProt NPD GO	WDR85_HUMAN	WD repeat protein 85	0.29	-	cyt	0					452
Q9Z0G4 UniProt NPD GO	WISP2_MOUSE	WNT1-inducible signaling pathway protein 2 precursor (WISP-2) (Connective tissue growth factor-like ...	0.29	-	nuc	0	Secreted protein (Probable)	plasma membrane [IDA]			251
Q5GH67 UniProt NPD GO	XKR4_MOUSE	XK-related protein 4	0.29	-	end	10	Membrane; multi-pass membrane protein (Potential)				647
P47990 UniProt NPD GO	XDH_CHICK	Xanthine dehydrogenase/oxidase [Includes: Xanthine dehydrogenase (EC 1.17.1.4) (XD); Xanthine oxidas ...	0.29	-	cyt	0	Peroxisome				1358
Q14590 UniProt NPD GO	ZN235_HUMAN	Zinc finger protein 235 (Zinc finger protein 93 homolog) (Zfp-93) (Zinc finger protein HZF6) (Fragme ...	0.29	-	nuc	0	Nucleus (Probable)		604749		209
Q9BS34 UniProt NPD GO	ZN670_HUMAN	Zinc finger protein 670	0.29	-	nuc	0	Nucleus (Probable)				389
P60852 UniProt NPD GO	ZP1_HUMAN	Zona pellucida sperm-binding protein 1 precursor (Zona pellucida glycoprotein 1) (Zp-1)	0.29	-	end	2 *	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...		195000		638
Q7TSY4 UniProt NPD GO	ZP3R_RAT	Zona pellucida sperm-binding protein 3 receptor precursor (Sperm fertilization protein 56) (sp56)	0.29	-	exc	0	Acrosome; acrosomal lumen. Sperm acrosomal matrix	acrosomal matrix [IDA]			577
Q00972 UniProt NPD GO	BCKD_RAT	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (EC 2.7.11.4) (B ...	0.29	-	nuc	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [ISS] mitochondrion [ISS]		1GKZ	412
Q15120 UniProt NPD GO	PDK3_HUMAN	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.29	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	602526	1Y8P	406
Q922H2 UniProt NPD GO	PDK3_MOUSE	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.29	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				415
P35816 UniProt NPD GO	PDP1_BOVIN	[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1, mitochondrial precursor (EC 3.1.3.43) (PDP 1) (P ...	0.29	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]			538
Q3UV70 UniProt NPD GO	PDP1_MOUSE	[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1, mitochondrial precursor (EC 3.1.3.43) (PDP 1) (P ...	0.29	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [ISS]			538
P21136 UniProt NPD GO	KGP1B_BOVIN	cGMP-dependent protein kinase 1, beta isozyme (EC 2.7.11.12) (cGK 1 beta) (cGKI-beta)	0.29	-	cyt	0					686
P39707 UniProt NPD GO	SEN34_YEAST	tRNA-splicing endonuclease subunit SEN34 (EC 3.1.27.9) (tRNA-intron endonuclease SEN34) (Splicing en ...	0.29	-	cyt	0	Nucleus. Intracellular membrane; peripheral membrane protein. Mitochondrion; mitochondrial outer mem ...	mitochondrial outer membrane [IDA] nuclear inner membrane [TAS] tRNA-intron endonuclease complex [TAS]			275
Q9STR4 UniProt NPD GO	1A17_ARATH	1-aminocyclopropane-1-carboxylate synthase 7 (EC 4.4.1.14) (ACC synthase 7) (S-adenosyl-L-methionine ...	0.28	+	nuc	0					447
P42652 UniProt NPD GO	14334_LYCES	14-3-3 protein 4 (PBLT4)	0.28	-	nuc	0					260
Q6NRY9 UniProt NPD GO	143GB_XENLA	14-3-3 protein gamma-B	0.28	-	nuc	0	Cytoplasm (By similarity)				247
P29361 UniProt NPD GO	1433Z_SHEEP	14-3-3 protein zeta/delta (Protein kinase C inhibitor protein 1) (KCIP-1)	0.28	-	nuc	0	Cytoplasm				245
Q39757 UniProt NPD GO	1433_FUCVE	14-3-3-like protein	0.28	-	cyt	0					251
P46266 UniProt NPD GO	1433_PEA	14-3-3-like protein	0.28	-	nuc	0					260
P41932 UniProt NPD GO	14331_CAEEL	14-3-3-like protein 1 (Partitioning defective protein 5)	0.28	-	cyt	0					248
Q2R2W2 UniProt NPD GO	14334_ORYSA	14-3-3-like protein GF14-D (G-box factor 14-3-3 homolog D)	0.28	-	nuc	0					265
Q12723 UniProt NPD GO	2NPD_WILMR	2-nitropropane dioxygenase (EC 1.13.11.32) (Nitroalkane oxidase) (2-NPD)	0.28	-	mit	0					374
Q3T0B2 UniProt NPD GO	PSD6_BOVIN	26S proteasome non-ATPase regulatory subunit 6	0.28	-	cyt	0					389
Q9CR00 UniProt NPD GO	PSD9_MOUSE	26S proteasome non-ATPase regulatory subunit 9 (26S proteasome regulatory subunit p27)	0.28	-	nuc	0					222
Q8WZY4 UniProt NPD GO	RPN8_NEUCR	26S proteasome regulatory subunit rpn-8	0.28	-	mit	0					352
O94444 UniProt NPD GO	RPN10_SCHPO	26S proteasome regulatory subunit rpn10	0.28	-	nuc	0	Nucleus				243
P82278 UniProt NPD GO	RR9_SPIOL	30S ribosomal protein S9, chloroplast precursor (Fragment)	0.28	-	mit	0	Plastid; chloroplast				197
P19683 UniProt NPD GO	ROC4_NICSY	31 kDa ribonucleoprotein, chloroplast precursor	0.28	-	mit	0	Plastid; chloroplast				315
Q9VJ38 UniProt NPD GO	RM13_DROME	39S ribosomal protein L13, mitochondrial (L13mt)	0.28	-	cyt	0	Mitochondrion (By similarity)	mitochondrial large ribosomal subunit [ISS]			178
Q9D0Q7 UniProt NPD GO	RM45_MOUSE	39S ribosomal protein L45, mitochondrial precursor (L45mt) (MRP-L45)	0.28	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			306
O23920 UniProt NPD GO	HPPD_DAUCA	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.28	-	cyt	0	Cytoplasm				442
Q9FY66 UniProt NPD GO	RS152_ARATH	40S ribosomal protein S15-2	0.28	-	cyt	0	Cytoplasm				152
P62251 UniProt NPD GO	RS16_AEDAE	40S ribosomal protein S16	0.28	-	cyt	0					148
Q9U9L1 UniProt NPD GO	RS17_ANOGA	40S ribosomal protein S17	0.28	-	nuc	0					130
Q90YQ5 UniProt NPD GO	RS18_ICTPU	40S ribosomal protein S18	0.28	-	mit	0	Cytoplasm				152
Q75DJ1 UniProt NPD GO	RS25_ASHGO	40S ribosomal protein S25	0.28	-	nuc	0					108
Q56JX5 UniProt NPD GO	RS25_BOVIN	40S ribosomal protein S25	0.28	+	nuc	0					125
Q8ISN9 UniProt NPD GO	RS25_BRABE	40S ribosomal protein S25	0.28	-	nuc	0					123
Q6FPX5 UniProt NPD GO	RS25_CANGA	40S ribosomal protein S25	0.28	-	nuc	0					107

You are viewing entries 41901 to 41950 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.