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
Q864V9 UniProt NPD GO	CFAB_GORGO	Complement factor B precursor (EC 3.4.21.47) (C3/C5 convertase) [Contains: Complement factor B Ba fr ...	0.46	-	mit	0	Secreted protein				764
P06909 UniProt NPD GO	CFAH_MOUSE	Complement factor H precursor (Protein beta-1-H)	0.46	-	exc	0	Secreted protein				1234
P05156 UniProt NPD GO	CFAI_HUMAN	Complement factor I precursor (EC 3.4.21.45) (C3B/C4B inactivator) [Contains: Complement factor I he ...	0.46	-	exc	0	Secreted protein; extracellular space		217030		583
Q03149 UniProt NPD GO	WA_EMENI	Conidial yellow pigment biosynthesis polyketide synthase (EC 2.3.1.-) (PKS)	0.46	+	end	0					2157
Q9JJA2 UniProt NPD GO	COG8_MOUSE	Conserved oligomeric Golgi complex component 8	0.46	-	cyt	0	Golgi apparatus (By similarity)				640
Q7ZW34 UniProt NPD GO	CNTN5_BRARE	Contactin-5 precursor	0.46	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				1056
Q9P0M6 UniProt NPD GO	H2AW_HUMAN	Core histone macro-H2A.2 (Histone macroH2A2) (mH2A2)	0.46	-	mit	0	Nucleus. Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin	Barr body [IDA]			371
P80365 UniProt NPD GO	DHI2_HUMAN	Corticosteroid 11-beta-dehydrogenase isozyme 2 (EC 1.1.1.-) (11-DH2) (11-beta-hydroxysteroid dehydro ...	0.46	-	mit	0	Microsome		218030		405
Q62949 UniProt NPD GO	CORT_RAT	Cortistatin precursor [Contains: Cortistatin-29; Cortistatin-14]	0.46	-	exc	1 *	Secreted protein				112
P97792 UniProt NPD GO	CXAR_MOUSE	Coxsackievirus and adenovirus receptor homolog precursor (CAR) (mCAR)	0.46	-	exc	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein. Isoform 3: Secreted protei ...				365
P17294 UniProt NPD GO	RR12_CYAPA	Cyanelle 30S ribosomal protein S12	0.46	-	nuc	0	Plastid; cyanelle				124
Q9TTK0 UniProt NPD GO	CDKL2_RABIT	Cyclin-dependent kinase-like 2 (EC 2.7.11.22) (Serine/threonine-protein kinase KKIAMRE)	0.46	-	nuc	0	Cytoplasm. Nucleus				566
Q59UG3 UniProt NPD GO	ATG4_CANAL	Cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.46	-	nuc	0	Cytoplasm (By similarity)				446
O43174 UniProt NPD GO	CP26A_HUMAN	Cytochrome P450 26A1 (EC 1.14.-.-) (Retinoic acid-metabolizing cytochrome) (P450 retinoic acid-inact ...	0.46	-	vac	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein		602239		497
Q64406 UniProt NPD GO	CP3AF_CAVPO	Cytochrome P450 3A15 (EC 1.14.14.1) (CYPIIIA15)	0.46	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				503
P19516 UniProt NPD GO	COX11_YEAST	Cytochrome c oxidase assembly protein COX11, mitochondrial precursor	0.46	-	mit	1	Mitochondrion; mitochondrial inner membrane. Intrinsic component of the inner-membrane	mitochondrial envelope [IDA] mitochondrial inner membrane [IDA] mitochondrial ribosome [IDA]			300
P31785 UniProt NPD GO	IL2RG_HUMAN	Cytokine receptor common gamma chain precursor (Gamma-C) (Interleukin-2 receptor gamma chain) (IL-2R ...	0.46	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [ISS] integral to plasma membrane [TAS]	300400	2ERJ	369
O22213 UniProt NPD GO	CKX1_ARATH	Cytokinin dehydrogenase 1 precursor (EC 1.5.99.12) (Cytokinin oxidase 1) (CKO 1) (AtCKX1)	0.46	-	nuc	0	Vacuole	vacuole [IDA]			575
P24628 UniProt NPD GO	DRD2A_XENLA	D(2) dopamine receptor A (D2R-A) (D2R 1)	0.46	-	end	7 *	Membrane; multi-pass membrane protein				442
Q6FIN2 UniProt NPD GO	ASK1_CANGA	DASH complex subunit ASK1 (Outer kinetochore protein ASK1) (Associated with spindles and kinetochore ...	0.46	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				204
P36162 UniProt NPD GO	DAD2_YEAST	DASH complex subunit DAD2 (Outer kinetochore protein DAD2) (DUO1 and DAM1-interacting protein 2) (He ...	0.46	-	nuc	0	Nucleus. Associates with the mitotic spindle and the kinetochore	DASH complex [IDA] spindle [IDA]			133
Q6FU23 UniProt NPD GO	DUO1_CANGA	DASH complex subunit DUO1 (Outer kinetochore protein DUO1)	0.46	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				212
Q59QH6 UniProt NPD GO	SPC19_CANAL	DASH complex subunit SPC19 (Outer kinetochore protein SPC19)	0.46	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				175
Q9M2E0 UniProt NPD GO	RH12_ARATH	DEAD-box ATP-dependent RNA helicase 12 (EC 3.6.1.-)	0.46	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				498
Q94A52 UniProt NPD GO	RH2_ARATH	DEAD-box ATP-dependent RNA helicase 2 (EC 3.6.1.-)	0.46	+	cyt	0	Nucleus; nucleolus (By similarity)				408
Q99J79 UniProt NPD GO	DDB2_MOUSE	DNA damage-binding protein 2 (Damage-specific DNA-binding protein 2)	0.46	-	nuc	0	Nucleus (By similarity)				432
O00273 UniProt NPD GO	DFFA_HUMAN	DNA fragmentation factor subunit alpha (DNA fragmentation factor 45 kDa subunit) (DFF-45) (Inhibitor ...	0.46	-	nuc	0	Cytoplasm	cytosol [TAS] nucleus [IDA]	601882	1KOY	331
Q6CHS6 UniProt NPD GO	DPB4_YARLI	DNA polymerase epsilon subunit D (EC 2.7.7.7) (DNA polymerase II subunit D)	0.46	-	nuc	0	Nucleus (By similarity)				163
Q9CWV1 UniProt NPD GO	MCM8_MOUSE	DNA replication licensing factor MCM8 (Minichromosome maintenance 8)	0.46	-	nuc	0	Nucleus (By similarity)				833
Q21902 UniProt NPD GO	MCM5_CAEEL	DNA replication licensing factor mcm-5	0.46	-	cyt	0	Nucleus (Potential)				759
P51173 UniProt NPD GO	APEA_DICDI	DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (Class II apurinic/apyrimidinic(AP)-endonuc ...	0.46	+	nuc	0	Nucleus (Potential)				361
Q75DS1 UniProt NPD GO	RPA2_ASHGO	DNA-directed RNA polymerase I polypeptide 2 (EC 2.7.7.6) (RNA polymerase I subunit 2)	0.46	-	nuc	0	Nucleus (By similarity)				1198
Q4G3A7 UniProt NPD GO	RPOB_EMIHU	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.46	-	cyt	0	Plastid; chloroplast				1093
P21422 UniProt NPD GO	RPOC_PLAFA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6)	0.46	-	cyt	3	Plastid; apicoplast				575
P12116 UniProt NPD GO	RPOC1_TOBAC	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.46	-	cyt	0	Plastid; chloroplast				680
Q6CJ62 UniProt NPD GO	RPB5_KLULA	DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.46	-	cyt	0	Nucleus (By similarity)				215
P28518 UniProt NPD GO	XPA_DROME	DNA-repair protein complementing XP-A cells homolog (Xeroderma pigmentosum group A complementing pro ...	0.46	-	nuc	0	Nucleus	nucleus [IDA]			296
P25863 UniProt NPD GO	XERO1_ARATH	Dehydrin Xero 1	0.46	-	nuc	0					128
P00979 UniProt NPD GO	IVBII_DENPO	Dendrotoxin-1 (Dendrotoxin I) (Venom basic protease inhibitor 1)	0.46	-	nuc	0	Secreted protein			1DEN	60
Q27002 UniProt NPD GO	GRA4_TOXGO	Dense granule protein 4 precursor (Protein GRA 4) (Antigen H11)	0.46	-	end	0	Secreted protein. Located in dense granules of tachyzoites. Upon infection, secreted into the parasi ...				345
Q9QZK9 UniProt NPD GO	DNS2B_RAT	Deoxyribonuclease-2-beta precursor (EC 3.1.22.1) (Deoxyribonuclease II beta) (DNase II beta) (DNase2 ...	0.46	-	exc	0	Lysosome (Probable)				356
P70186 UniProt NPD GO	PGLB_MOUSE	Dermatan sulfate proteoglycan 3 precursor (Epiphycan) (Small chondroitin/dermatan sulfate proteoglyc ...	0.46	-	exc	0	Secreted protein; extracellular space; extracellular matrix. Surrounding resting, proliferating, and ...				322
Q7TMD7 UniProt NPD GO	DSG4_MOUSE	Desmoglein-4 precursor	0.46	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	desmosome [IMP]			1041
Q4X0S7 UniProt NPD GO	DPH1_ASPFU	Diphthamide biosynthesis protein 1	0.46	-	nuc	0	Cytoplasm (By similarity)				445
Q9Y2E4 UniProt NPD GO	DIP2C_HUMAN	Disco-interacting protein 2 homolog C	0.46	-	nuc	0					1556
O76324 UniProt NPD GO	DCO_DROME	Discs overgrown protein kinase (EC 2.7.11.1) (Protein double-time)	0.46	-	cyt	0		cytoplasm [TAS] nucleus [TAS]			440
P23834 UniProt NPD GO	DIUH_ACHDO	Diuretic hormone (DH) (Diuretic peptide) (DP)	0.46	-	nuc	0	Secreted protein				46
P41538 UniProt NPD GO	DIUH_PERAM	Diuretic hormone (DH) (Diuretic peptide) (DP)	0.46	-	nuc	0	Secreted protein				46
Q5U458 UniProt NPD GO	DCJ11_MOUSE	DnaJ homolog subfamily C member 11	0.46	-	nuc	0		mitochondrial inner membrane [IDA]			559
Q5RC70 UniProt NPD GO	DCJ11_PONPY	DnaJ homolog subfamily C member 11	0.46	-	cyt	0					559

You are viewing entries 27551 to 27600 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.