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
Q754J2 UniProt NPD GO	DBP7_ASHGO	ATP-dependent RNA helicase DBP7 (EC 3.6.1.-)	0.55	-	nuc	0	Nucleus; nucleolus (By similarity)				710
Q6CDS6 UniProt NPD GO	ROK1_YARLI	ATP-dependent RNA helicase ROK1 (EC 3.6.1.-)	0.55	+	cyt	0	Nucleus; nucleolus (By similarity)				547
Q7RV88 UniProt NPD GO	IF4A_NEUCR	ATP-dependent RNA helicase eIF4A (EC 3.6.1.-) (Eukaryotic initiation factor 4A) (eIF-4A) (Translatio ...	0.55	-	cyt	0	Cytoplasm (By similarity)				425
P30771 UniProt NPD GO	NAM7_YEAST	ATP-dependent helicase NAM7 (EC 3.6.1.-) (Nuclear accomodation of mitochondria 7 protein) (Nonsense- ...	0.55	-	nuc	0	Cytoplasm. Nucleus. Present predominantly in the cytoplasm, but is also found in small quantities in ...	cytoplasm [IDA] polysome [TAS]			971
P15108 UniProt NPD GO	HSC82_YEAST	ATP-dependent molecular chaperone HSC82 (Heat shock protein Hsp90 constitutive isoform) (82 kDa heat ...	0.55	-	cyt	0	Cytoplasm. Mitochondrion	cytoplasm [IDA] mitochondrion [IDA]			704
Q9N077 UniProt NPD GO	ATRIP_MACFA	ATR-interacting protein (ATM and Rad3-related-interacting protein) (Fragment)	0.55	-	nuc	0	Nucleus (By similarity). Redistributes to discrete nuclear foci upon DNA damage (By similarity)				655
Q6AY33 UniProt NPD GO	ACRBP_RAT	Acrosin-binding protein precursor (Proacrosin-binding protein sp32)	0.55	-	nuc	0	Secreted protein (By similarity). Acrosome (By similarity). Colocalizes with proacrosin in the acros ...				316
P30803 UniProt NPD GO	ADCY5_CANFA	Adenylate cyclase type 5 (EC 4.6.1.1) (Adenylate cyclase type V) (ATP pyrophosphate-lyase 5) (Adenyl ...	0.55	-	end	10	Membrane; multi-pass membrane protein			1U0H	1265
P98999 UniProt NPD GO	ADCY9_XENLA	Adenylate cyclase type 9 (EC 4.6.1.1) (Adenylate cyclase type IX) (ATP pyrophosphate-lyase 9) (Adeny ...	0.55	-	end	10	Membrane; multi-pass membrane protein (By similarity)				1305
Q16186 UniProt NPD GO	ADRM1_HUMAN	Adhesion-regulating molecule 1 precursor (110 kDa cell membrane glycoprotein) (Gp110)	0.55	-	nuc	0		integral to plasma membrane [TAS] membrane fraction [TAS]			407
P84407 UniProt NPD GO	FETA_CHICK	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.55	-	nuc	0	Secreted protein				615
Q16352 UniProt NPD GO	AINX_HUMAN	Alpha-internexin (Alpha-Inx) (66 kDa neurofilament protein) (Neurofilament-66) (NF-66)	0.55	-	nuc	0		neurofilament [TAS]	605338		499
P39193 UniProt NPD GO	ALU6_HUMAN	Alu subfamily SP sequence contamination warning entry	0.55	-	exc	0					593
Q96FT7 UniProt NPD GO	ACCN4_HUMAN	Amiloride-sensitive cation channel 4 (Amiloride-sensitive cation channel 4, pituitary) (Acid-sensing ...	0.55	-	nuc	0	Membrane; multi-pass membrane protein (By similarity)		606715		647
Q24049 UniProt NPD GO	AMN_DROME	Amnesiac neuropeptides precursor [Contains: Amnesiac peptide 24; Amnesiac peptide 30; Amnesiac pepti ...	0.55	-	mit	1 *	Secreted protein (Potential)				180
Q9P4W7 UniProt NPD GO	APC5_SCHPO	Anaphase-promoting complex subunit 5 (20S cyclosome/APC complex protein apc5)	0.55	-	nuc	0		anaphase-promoting complex [IDA]			737
Q9UJX4 UniProt NPD GO	ANC5_HUMAN	Anaphase-promoting complex subunit 5 (APC5) (Cyclosome subunit 5)	0.55	-	cyt	0		anaphase-promoting complex [TAS]	606948		755
Q9UNK9 UniProt NPD GO	ANGE1_HUMAN	Angel homolog 1	0.55	-	mit	0					670
Q9Y5C1 UniProt NPD GO	ANGL3_HUMAN	Angiopoietin-related protein 3 precursor (Angiopoietin-like 3) (Angiopoietin-5) (ANG-5)	0.55	-	exc	0	Secreted protein (By similarity)	extracellular region [IEP]	604774		460
Q9Z1P8 UniProt NPD GO	ANGL4_MOUSE	Angiopoietin-related protein 4 precursor (Angiopoietin-like 4) (Hepatic fibrinogen/angiopoietin-rela ...	0.55	-	nuc	0	Secreted protein	extracellular region [IEP] extracellular space [IDA]			410
Q75F26 UniProt NPD GO	ATG29_ASHGO	Autophagy-related protein 29	0.55	-	nuc	0	Pre-autophagosomal and other perivacuolar punctate structures (By similarity)				172
Q8L7G0 UniProt NPD GO	ARFA_ARATH	Auxin response factor 1	0.55	+	nuc	0	Nucleus				665
Q6DEV7 UniProt NPD GO	BCL7A_XENTR	B-cell CLL/lymphoma 7 protein family member A	0.55	+	nuc	0					231
P35329 UniProt NPD GO	CD22_MOUSE	B-cell receptor CD22 precursor (Leu-14) (B-lymphocyte cell adhesion molecule) (BL-CAM) (Siglec-2)	0.55	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [IPI]			862
Q9JIB6 UniProt NPD GO	BIR1F_MOUSE	Baculoviral IAP repeat-containing protein 1f (Neuronal apoptosis inhibitory protein 6)	0.55	-	nuc	0					1403
Q9JIB3 UniProt NPD GO	BIR1G_MOUSE	Baculoviral IAP repeat-containing protein 1g (Neuronal apoptosis inhibitory protein 7)	0.55	-	nuc	0					1402
Q9BXH1 UniProt NPD GO	BBC3_HUMAN	Bcl-2-binding component 3 (p53 up-regulated modulator of apoptosis) (JFY-1)	0.55	-	nuc	0	Mitochondrion. Localized to the mitochondria in order to induce cytochrome c release	mitochondrion [IDA]	605854		193
Q4A1L4 UniProt NPD GO	BCN1_BOVIN	Beclin-1	0.55	-	cyt	0	Cytoplasm (Potential). Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				448
P87024 UniProt NPD GO	SKN1_CANAL	Beta-glucan synthesis-associated protein SKN1	0.55	-	nuc	1	Membrane; single-pass type II membrane protein				737
P01139 UniProt NPD GO	NGF_MOUSE	Beta-nerve growth factor precursor (Beta-NGF)	0.55	-	exc	0	Secreted protein			1SGF	241
Q9UK28 UniProt NPD GO	BSMAP_HUMAN	Brain-specific membrane-anchored protein precursor	0.55	-	end	1	Membrane (Potential). Could be associated with an intracellular organelle or membrane (Potential)	integral to membrane [TAS] membrane fraction [TAS]			342
Q6UX41 UniProt NPD GO	BTNL8_HUMAN	Butyrophilin-like protein 8 precursor	0.55	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				500
Q9EQP0 UniProt NPD GO	ABEC1_MESAU	C->U-editing enzyme APOBEC-1 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme 1)	0.55	-	cyt	0					229
P38483 UniProt NPD GO	ABEC1_RAT	C->U-editing enzyme APOBEC-1 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme 1)	0.55	-	nuc	0		nucleus [NAS]			229
Q9R0Q8 UniProt NPD GO	CLC4E_MOUSE	C-type lectin domain family 4 member E (C-type lectin superfamily member 9) (Macrophage-inducible C- ...	0.55	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)				214
Q00322 UniProt NPD GO	CEBPD_MOUSE	CCAAT/enhancer-binding protein delta (C/EBP delta) (C/EBP-related protein 3)	0.55	+	nuc	0	Nucleus	nucleus [IDA]			268
P49716 UniProt NPD GO	CEBPD_HUMAN	CCAAT/enhancer-binding protein delta (C/EBP delta) (Nuclear factor NF-IL6-beta) (NF-IL6-beta)	0.55	+	nuc	0	Nucleus		116898		269
Q15744 UniProt NPD GO	CEBPE_HUMAN	CCAAT/enhancer-binding protein epsilon (C/EBP epsilon)	0.55	+	nuc	0	Nucleus		600749		281
Q6PZD9 UniProt NPD GO	CEBPE_MOUSE	CCAAT/enhancer-binding protein epsilon (C/EBP epsilon)	0.55	+	nuc	0	Nucleus (By similarity)				281
P56261 UniProt NPD GO	CEBPE_RAT	CCAAT/enhancer-binding protein epsilon (C/EBP epsilon) (C/EBP-related protein 1)	0.55	+	nuc	0	Nucleus				281
Q13495 UniProt NPD GO	CG1_HUMAN	CG1 protein (F18)	0.55	-	nuc	0			300120		701
Q75E19 UniProt NPD GO	CSN5_ASHGO	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.55	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				420
Q5U462 UniProt NPD GO	CDCP1_MOUSE	CUB domain-containing protein 1 precursor (Transmembrane and associated with src kinases) (Membrane ...	0.55	-	end	1 *	Cell membrane; single-pass membrane protein (Potential). Its shedding may lead to a soluble peptide ...				833
Q8IXH8 UniProt NPD GO	CAD26_HUMAN	Cadherin-like protein 26 precursor (Cadherin-like protein VR20)	0.55	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				847
Q9N0T3 UniProt NPD GO	CALCB_HORSE	Calcitonin gene-related peptide 2 precursor (Calcitonin gene-related peptide II) (CGRP-II) (Beta-typ ...	0.55	-	exc	0	Secreted protein				129
Q7RAV5 UniProt NPD GO	CDPK3_PLAYO	Calcium-dependent protein kinase 3 (EC 2.7.11.1)	0.55	+	cyt	0					538
Q9EP78 UniProt NPD GO	CHST7_MOUSE	Carbohydrate sulfotransferase 7 (EC 2.8.2.17) (EC 2.8.2.-) (Chondroitin 6-sulfotransferase 2) (C6ST- ...	0.55	+	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				484
Q9WVT6 UniProt NPD GO	CAH14_MOUSE	Carbonic anhydrase 14 precursor (EC 4.2.1.1) (Carbonic anhydrase XIV) (Carbonate dehydratase XIV) (C ...	0.55	-	end	1	Membrane; single-pass type I membrane protein (Potential)			1RJ6	337
Q06486 UniProt NPD GO	KC1D_RAT	Casein kinase I isoform delta (EC 2.7.11.1) (CKI-delta)	0.55	-	nuc	0	Cytoplasm	centrosome [TAS] spindle [TAS]		1CKJ	415
Q9DC28 UniProt NPD GO	KC1D_MOUSE	Casein kinase I isoform delta (EC 2.7.11.1) (CKI-delta) (CKId)	0.55	-	nuc	0	Cytoplasm (By similarity)				415

You are viewing entries 21801 to 21850 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.