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
P28481 UniProt NPD GO	CO2A1_MOUSE	Collagen alpha-1(II) chain precursor [Contains: Chondrocalcin]	0.32	-	exc	0		cytoplasm [IDA] extracellular space [IDA]			1459
P13941 UniProt NPD GO	CO3A1_RAT	Collagen alpha-1(III) chain precursor	0.32	-	exc	0		collagen type III [TAS]			1463
Q01955 UniProt NPD GO	CO4A3_HUMAN	Collagen alpha-3(IV) chain precursor (Goodpasture antigen)	0.32	-	mit	0	Cell surface (Potential)	collagen type IV [IDA]	203780		1670
P55787 UniProt NPD GO	CO4A4_RABIT	Collagen alpha-4(IV) chain (Fragment)	0.32	-	nuc	0	Cell surface (Potential)				623
Q9HBJ8 UniProt NPD GO	TMM27_HUMAN	Collectrin precursor (Transmembrane protein 27)	0.32	-	end	1	Membrane; single-pass type I membrane protein (Potential)				222
Q9ET61 UniProt NPD GO	C1QR1_RAT	Complement component C1q receptor precursor (Complement component 1 q subcomponent receptor 1) (C1qR ...	0.32	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [ISS]			643
Q7Z7G2 UniProt NPD GO	CPLX4_HUMAN	Complexin-4 (Complexin IV) (CPX IV)	0.32	-	nuc	0	Membrane; lipid-anchor. Enriched at the synaptic terminal (By similarity)		609586		160
P53195 UniProt NPD GO	COG7_YEAST	Conserved oligomeric Golgi complex subunit 7 (COG complex subunit 7) (Complexed with DOR1 protein 5) ...	0.32	-	nuc	0		Golgi transport complex [IPI] mitochondrion [IDA]			279
Q7TPC1 UniProt NPD GO	CDSN_MOUSE	Corneodesmosin precursor	0.32	-	exc	1 *	Secreted protein. Found in corneodesmosomes, the intercellular structures that are involved in desqu ...				561
P01197 UniProt NPD GO	COLI_SQUAC	Corticotropin (Adrenocorticotropic hormone) (ACTH) [Contains: Melanotropin alpha (Alpha-MSH); Cortic ...	0.32	-	nuc	0					39
Q90Y50 UniProt NPD GO	CXAR_BRARE	Coxsackievirus and adenovirus receptor homolog precursor	0.32	-	exc	1 *	Membrane; single-pass type I membrane protein (By similarity)				372
P48139 UniProt NPD GO	RR16_CYAPA	Cyanelle 30S ribosomal protein S16	0.32	-	mit	0	Plastid; cyanelle				77
P23406 UniProt NPD GO	RK16_CYAPA	Cyanelle 50S ribosomal protein L16	0.32	-	mit	0	Plastid; cyanelle				136
P24863 UniProt NPD GO	CCNC_HUMAN	Cyclin-C	0.32	-	nuc	0	Nucleus		123838		303
P51945 UniProt NPD GO	CCNG1_MOUSE	Cyclin-G1 (Cyclin-G)	0.32	-	cyt	0	Nucleus				294
O14519 UniProt NPD GO	CDKA1_HUMAN	Cyclin-dependent kinase 2-associated protein 1 (CDK2-associated protein 1) (Putative oral cancer sup ...	0.32	-	nuc	0		cytoplasm [TAS] nucleus [TAS]	602198		115
Q9H112 UniProt NPD GO	CST11_HUMAN	Cystatin-11 precursor	0.32	-	nuc	1 *	Nucleus. Cytoplasm. Nuclear and cytoplasmic in the epididymis. Localized to the postacrosomal and ta ...		609731		138
Q9Y697 UniProt NPD GO	NFS1_HUMAN	Cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7)	0.32	-	mit	0	Mitochondrion. Cytoplasm	cytosol [TAS] mitochondrion [TAS] nucleus [TAS]	603485		457
P51663 UniProt NPD GO	C11B1_SHEEP	Cytochrome P450 11B1, mitochondrial precursor (EC 1.14.15.4) (CYPXIB1) (P450C11) (Steroid 11-beta-hy ...	0.32	-	mit	0	Mitochondrion				503
Q8HYN0 UniProt NPD GO	CP17A_PAPCY	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.32	-	end	0					508
Q9GLD2 UniProt NPD GO	CP17A_PAPHU	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.32	-	end	0					508
P05093 UniProt NPD GO	CP17A_HUMAN	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-monooxygenase) ...	0.32	-	end	0		endoplasmic reticulum [NAS]	202110	2C17	508
Q64562 UniProt NPD GO	CP21A_RAT	Cytochrome P450 21 (EC 1.14.99.10) (Cytochrome P450 XXI) (Steroid 21-hydroxylase) (21-OHase) (P450-C ...	0.32	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				493
P56593 UniProt NPD GO	CP2AC_MOUSE	Cytochrome P450 2A12 (EC 1.14.14.1) (CYPIIA12) (Steroid hormones 7-alpha-hydroxylase) (Testosterone ...	0.32	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				492
P33261 UniProt NPD GO	CP2CJ_HUMAN	Cytochrome P450 2C19 (EC 1.14.13.80) ((R)-limonene 6-monooxygenase) (EC 1.14.13.48) ((S)-limonene 6- ...	0.32	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [TAS]	609535		490
O35293 UniProt NPD GO	CP2F2_RAT	Cytochrome P450 2F2 (EC 1.14.14.-) (CYPIIF2) (Naphthalene dehydrogenase) (Naphthalene hydroxylase) ( ...	0.32	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
P14263 UniProt NPD GO	CP51_CANTR	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Lanosterol 14- ...	0.32	-	cyt	2 *					528
Q9LTL0 UniProt NPD GO	C71BQ_ARATH	Cytochrome P450 71B26 (EC 1.14.-.-)	0.32	-	nuc	2 *					500
P37121 UniProt NPD GO	C76A1_SOLME	Cytochrome P450 76A1 (EC 1.14.-.-) (CYPLXXVIA1) (P-450EG8) (Fragment)	0.32	-	cyt	0					467
O93980 UniProt NPD GO	COX5_ASPNG	Cytochrome c oxidase polypeptide V, mitochondrial precursor (EC 1.9.3.1)	0.32	-	mit	1	Mitochondrion; mitochondrial inner membrane (By similarity)				197
Q62225 UniProt NPD GO	CISH_MOUSE	Cytokine-inducible SH2-containing protein (CIS) (CIS-1) (Suppressor of cytokine signaling) (SOCS)	0.32	-	nuc	0		plasma membrane [IDA]			257
Q9NSE2 UniProt NPD GO	CISH_HUMAN	Cytokine-inducible SH2-containing protein (CIS) (CIS-1) (Suppressor of cytokine signaling) (SOCS) (P ...	0.32	-	nuc	0			602441		258
P21917 UniProt NPD GO	DRD4_HUMAN	D(4) dopamine receptor (Dopamine D4 receptor) (D(2C) dopamine receptor)	0.32	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	126452		467
P94102 UniProt NPD GO	RAD51_ARATH	DNA repair protein RAD51 homolog 1 (Rad51-like protein 1) (AtRAD51)	0.32	-	cyt	0	Nucleus (By similarity)				342
P43138 UniProt NPD GO	APEX1_RAT	DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP endonuclease 1) (APEX nuclease) (APEN)	0.32	-	nuc	0	Nucleus	cytoplasm [IDA] endoplasmic reticulum [ISS] nucleus [ISS] perinuclear region [ISS] ribosome [ISS]			316
Q9UBZ4 UniProt NPD GO	APEX2_HUMAN	DNA-(apurinic or apyrimidinic site) lyase 2 (EC 4.2.99.18) (Apurinic-apyrimidinic endonuclease 2) (A ...	0.32	-	nuc	0	Nucleus (Probable). Mitochondrion (Probable). Co-localizated partly with PCNA in nuclear foci				518
P19387 UniProt NPD GO	RPB3_HUMAN	DNA-directed RNA polymerase II 33 kDa polypeptide (EC 2.7.7.6) (RPB3) (RNA polymerase II subunit 3) ...	0.32	-	nuc	0	Nucleus		180663		275
P04051 UniProt NPD GO	RPC1_YEAST	DNA-directed RNA polymerase III largest subunit (EC 2.7.7.6) (C160)	0.32	-	cyt	0	Nucleus	DNA-directed RNA polymerase III complex [TAS]			1460
P41629 UniProt NPD GO	RPOA_PINTH	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.32	-	cyt	0	Plastid; chloroplast				335
Q01569 UniProt NPD GO	RPOA_PYRSA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.32	-	cyt	0	Plastid; chloroplast				314
P06505 UniProt NPD GO	RPOA_SPIOL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.32	-	mit	0	Plastid; chloroplast				335
P20435 UniProt NPD GO	RPB6_YEAST	DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide (EC 2.7.7.6) (ABC23)	0.32	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase II, core complex [TAS] DNA-directed RNA polymerase III complex [TAS]		2B8K	155
Q9CX47 UniProt NPD GO	XRCC2_MOUSE	DNA-repair protein XRCC2 (X-ray repair cross-complementing protein 2)	0.32	-	nuc	0	Nucleus (By similarity)				278
O88843 UniProt NPD GO	CRADD_MOUSE	Death domain-containing protein CRADD (Caspase and RIP adapter with death domain) (RIP-associated pr ...	0.32	-	cyt	0					199
Q33DR3 UniProt NPD GO	DLP1_MOUSE	Decaprenyl-diphosphate synthase subunit 2 (EC 2.5.1.-) (Decaprenyl pyrophosphate synthetase subunit ...	0.32	-	mit	0					401
P24057 UniProt NPD GO	ARLY1_ANAPL	Delta-1 crystallin (Delta crystallin I)	0.32	-	nuc	0				1U16	466
Q9LND8 UniProt NPD GO	ADSL2_ARATH	Delta-9 desaturase-like 2 protein (EC 1.14.19.-)	0.32	-	nuc	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				299
Q07828 UniProt NPD GO	GRA5_TOXGO	Dense granule protein 5 precursor (Protein GRA 5) (p21)	0.32	+	end	2 *	Secreted protein. Located in dense granules of tachyzoites. Upon infection, secreted into the cyst a ...				120
Q9H4B8 UniProt NPD GO	DPEP3_HUMAN	Dipeptidase 3 precursor (EC 3.4.13.19)	0.32	-	mit	0	Membrane; lipid-anchor; GPI-anchor (By similarity)		609926		488
Q6BPC1 UniProt NPD GO	DPH4_DEBHA	Diphthamide biosynthesis protein 4	0.32	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				168

You are viewing entries 38401 to 38450 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.