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
Q5R6X7 UniProt NPD GO	CBX3_PONPY	Chromobox protein homolog 3 (Heterochromatin protein 1 homolog gamma) (HP1 gamma)	0.47	+	nuc	0	Nucleus (Probable). May be associated with microtubules and mitotic poles during mitosis (Potential) ...				183
Q13185 UniProt NPD GO	CBX3_HUMAN	Chromobox protein homolog 3 (Heterochromatin protein 1 homolog gamma) (HP1 gamma) (Modifier 2 protei ...	0.47	+	nuc	0	Nucleus (Potential). Associates with euchromatin and is largely excluded from constitutive heterochr ...	nucleus [TAS]	604477		183
P23198 UniProt NPD GO	CBX3_MOUSE	Chromobox protein homolog 3 (Heterochromatin protein 1 homolog gamma) (HP1 gamma) (Modifier 2 protei ...	0.47	+	nuc	0	Nucleus. May be associated with microtubules and mitotic poles during mitosis (Potential). Associate ...	polytene chromosome chromocenter [IDA]			183
P49299 UniProt NPD GO	CYSZ_CUCMA	Citrate synthase, glyoxysomal precursor (EC 2.3.3.1) (GCS)	0.47	-	nuc	0	Glyoxysome				516
P30375 UniProt NPD GO	1A01_GORGO	Class I histocompatibility antigen, GOGO-A0101 alpha chain precursor	0.47	-	end	1	Membrane; single-pass type I membrane protein				365
P42159 UniProt NPD GO	RTK2_GEOCY	Class II receptor tyrosine kinase (EC 2.7.10.1) (GCTK)	0.47	-	nuc	1	Membrane; single-pass membrane protein				605
Q7LZ61 UniProt NPD GO	RVVX_DABRU	Coagulation factor X-activating enzyme heavy chain (EC 3.4.24.58) (RVV-X heavy chain) (Coagulation f ...	0.47	-	nuc	0	Secreted protein				429
P23514 UniProt NPD GO	COPB_RAT	Coatomer subunit beta (Beta-coat protein) (Beta-COP)	0.47	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IDA] Golgi apparatus [IDA] Golgi-associated vesicle [IDA]			953
Q5U2X6 UniProt NPD GO	CCD47_RAT	Coiled-coil domain-containing protein 47 precursor	0.47	-	end	0	Membrane; single-pass membrane protein (Potential)				483
O88207 UniProt NPD GO	CO5A1_MOUSE	Collagen alpha-1(V) chain precursor	0.47	-	exc	1 *					1838
Q863A0 UniProt NPD GO	CO2_GORGO	Complement C2 precursor (EC 3.4.21.43) (C3/C5 convertase) [Contains: Complement C2b fragment; Comple ...	0.47	-	cyt	0	Secreted protein (By similarity)				752
P06681 UniProt NPD GO	CO2_HUMAN	Complement C2 precursor (EC 3.4.21.43) (C3/C5 convertase) [Contains: Complement C2b fragment; Comple ...	0.47	-	exc	0	Secreted protein	complement component C2 complex [TAS]	217000		752
Q8SQ75 UniProt NPD GO	CO2_PONPY	Complement C2 precursor (EC 3.4.21.43) (C3/C5 convertase) [Contains: Complement C2b fragment; Comple ...	0.47	-	exc	0	Secreted protein				752
P12387 UniProt NPD GO	CO3_CAVPO	Complement C3 precursor [Contains: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphyla ...	0.47	-	exc	0					1666
Q62930 UniProt NPD GO	CO9_RAT	Complement component C9 precursor	0.47	-	nuc	0	Secreted protein	membrane attack complex [TAS]			554
P11353 UniProt NPD GO	HEM6_YEAST	Coproporphyrinogen III oxidase (EC 1.3.3.3) (Coproporphyrinogenase) (Coprogen oxidase) (COX)	0.47	-	cyt	0	Cytoplasm			1TXN	328
Q92828 UniProt NPD GO	COR2A_HUMAN	Coronin-2A (WD repeat-containing protein 2) (IR10)	0.47	-	nuc	0			602159		525
P13241 UniProt NPD GO	CRF1_CATCO	Corticoliberin-1 precursor (Corticotropin-releasing factor 1) (CRF 1) (Corticotropin-releasing hormo ...	0.47	-	exc	0	Secreted protein				162
P01192 UniProt NPD GO	COLI_PIG	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.47	-	nuc	0					267
P01191 UniProt NPD GO	COLI_SHEEP	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.47	-	nuc	0					212
O77618 UniProt NPD GO	CD2A2_MONDO	Cyclin-dependent kinase inhibitor 2A, isoform 2 (p19ARF)	0.47	-	mit	0	Nucleus; nucleolus (By similarity)				155
Q5B7L0 UniProt NPD GO	ATG4_EMENI	Cysteine protease atg4 (EC 3.4.22.-) (Autophagy-related protein 4)	0.47	-	nuc	0	Cytoplasm (By similarity)				379
Q03402 UniProt NPD GO	CRIS3_MOUSE	Cysteine-rich secretory protein 3 precursor (CRISP-3) (Acidic epididymal glycoprotein 2) (Sperm-coat ...	0.47	-	exc	0	Stored in secretory granules of granular convoluted tubules cells				241
P70091 UniProt NPD GO	CP19A_ORENI	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.47	-	end	0	Membrane; peripheral membrane protein				522
P05177 UniProt NPD GO	CP1A2_HUMAN	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2) (P450-P3) (P(3)450) (P450 4)	0.47	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [NAS]	124060		514
O55127 UniProt NPD GO	CP26A_MOUSE	Cytochrome P450 26A1 (EC 1.14.-.-) (Retinoic acid-metabolizing cytochrome) (P450RAI) (Retinoic acid ...	0.47	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				497
O65790 UniProt NPD GO	C81F1_ARATH	Cytochrome P450 81F1 (EC 1.14.-.-)	0.47	-	nuc	0					500
Q42600 UniProt NPD GO	C84A1_ARATH	Cytochrome P450 84A1 (EC 1.14.-.-) (Ferulate-5-hydroxylase) (F5H)	0.47	+	nuc	1 *					520
P30728 UniProt NPD GO	DRD3_MOUSE	D(3) dopamine receptor	0.47	-	end	7 *	Membrane; multi-pass membrane protein				446
Q944I4 UniProt NPD GO	GLYK_ARATH	D-glycerate 3-kinase, chloroplast precursor (EC 2.7.1.31) (AtGLYK)	0.47	-	mit	0	Plastid; chloroplast				456
Q753W8 UniProt NPD GO	HSK3_ASHGO	DASH complex subunit HSK3 (Outer kinetochore protein HSK3)	0.47	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				68
Q694C5 UniProt NPD GO	ABC3G_ERYPA	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.47	-	mit	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				383
Q750A4 UniProt NPD GO	DPB4_ASHGO	DNA polymerase epsilon subunit D (EC 2.7.7.7) (DNA polymerase II subunit D)	0.47	-	nuc	0	Nucleus (By similarity)				204
O02334 UniProt NPD GO	PRI2_CAEEL	DNA primase large subunit (EC 2.7.7.-)	0.47	-	nuc	0					503
O42905 UniProt NPD GO	RTI1_SCHPO	DNA repair and recombination protein rti1 (Rad twenty-two isogene 1) (Rad22 homolog)	0.47	-	nuc	0					371
Q3ZBH9 UniProt NPD GO	MCM7_BOVIN	DNA replication licensing factor MCM7	0.47	-	cyt	0	Nucleus (By similarity)				719
Q7Q0Q1 UniProt NPD GO	MCM6_ANOGA	DNA replication licensing factor Mcm6	0.47	-	cyt	0	Nucleus. Associated with chromatin during cell cycles (By similarity)				814
P30190 UniProt NPD GO	TOP2_TRYCR	DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.47	-	cyt	0	Nucleus				1232
P35084 UniProt NPD GO	RPB1_DICDI	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (Fragment)	0.47	-	nuc	0	Nucleus				902
O14802 UniProt NPD GO	RPC1_HUMAN	DNA-directed RNA polymerase III largest subunit (EC 2.7.7.6) (RPC155) (RPC1)	0.47	-	nuc	0	Nucleus	DNA-directed RNA polymerase III complex [NAS]			1391
Q7GED9 UniProt NPD GO	RPOA_AEGCM	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
P92892 UniProt NPD GO	RPOA_AEGSP	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
Q8MAJ0 UniProt NPD GO	RPOA_AEGUN	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	mit	0	Plastid; chloroplast				339
P93993 UniProt NPD GO	RPOA_AUSVE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
Q7YJU6 UniProt NPD GO	RPOA_CALFE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	nuc	0	Plastid; chloroplast				340
Q7H6I5 UniProt NPD GO	RPOA_ELYCA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
Q8MAI8 UniProt NPD GO	RPOA_ELYHY	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
P93968 UniProt NPD GO	RPOA_FESFE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
P92392 UniProt NPD GO	RPOA_HORVU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339
P92418 UniProt NPD GO	RPOA_PSAFR	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.47	-	cyt	0	Plastid; chloroplast				339

You are viewing entries 26851 to 26900 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.