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
P93004 UniProt NPD GO	PIP27_ARATH	Aquaporin PIP2.7 (Plasma membrane intrinsic protein 3) (Salt stress-induced major intrinsic protein) ...	0.09	-	end	6 *	Cell membrane; multi-pass membrane protein				280
Q923J4 UniProt NPD GO	AQP4_DIPME	Aquaporin-4 (AQP-4)	0.09	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				324
P05487 UniProt NPD GO	CONO_CONST	Arg-conopressin S	0.09	-		0	Secreted protein				9
P05089 UniProt NPD GO	ARGI1_HUMAN	Arginase-1 (EC 3.5.3.1) (Type I arginase) (Liver-type arginase)	0.09	-	cyt	0	Cytoplasm	cytoplasm [TAS]	207800	2AEB	322
Q5B058 UniProt NPD GO	RMT2_EMENI	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				426
O23141 UniProt NPD GO	SPE2_ARATH	Arginine decarboxylase 2 (EC 4.1.1.19) (ARGDC 2) (ADC 2) (ADC-N)	0.09	-	cyt	0					711
O15989 UniProt NPD GO	KARG_TURCO	Arginine kinase (EC 2.7.3.3) (AK)	0.09	-	cyt	0					358
Q95PM9 UniProt NPD GO	KARG_PLOIN	Arginine kinase (EC 2.7.3.3) (AK) (Allergen Plo i 1)	0.09	-	cyt	0					355
P41906 UniProt NPD GO	ARLY_SACDO	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.09	-	cyt	0					463
Q9SZX3 UniProt NPD GO	ASSY_ARATH	Argininosuccinate synthase, chloroplast precursor (EC 6.3.4.5) (Citrulline--aspartate ligase)	0.09	-	mit	0	Plastid; chloroplast (Potential)				494
P36575 UniProt NPD GO	ARRC_HUMAN	Arrestin-C (Cone arrestin) (Retinal cone arrestin-3) (X-arrestin) (C-arrestin)	0.09	-	mit	0		cytoplasm [TAS] soluble fraction [TAS]	301770		388
Q9HBK9 UniProt NPD GO	AS3MT_HUMAN	Arsenite methyltransferase (EC 2.1.1.137) (S-adenosyl-L-methionine:arsenic(III) methyltransferase) ( ...	0.09	-	mit	0	Cytoplasm (By similarity)	cytosol [ISS]			375
Q7Z1F8 UniProt NPD GO	ARY_ANTPE	Arylphorin precursor	0.09	-	end	0	Secreted protein; extracellular space (By similarity)				704
P14297 UniProt NPD GO	ARYB_MANSE	Arylphorin subunit beta precursor	0.09	-	exc	0	Secreted protein; extracellular space				703
P55956 UniProt NPD GO	ASP3_CAEEL	Aspartic protease 3 precursor (EC 3.4.23.-)	0.09	-	end	0	Secreted protein				398
Q96HD9 UniProt NPD GO	ACY3_HUMAN	Aspartoacylase-2 (EC 3.5.1.15) (Aminoacylase-3) (ACY-3) (Acylase III) (Hepatitis C virus core-bindin ...	0.09	-	mit	0					319
Q26431 UniProt NPD GO	ATT_BOMMO	Attacin precursor (Nuecin)	0.09	-	nuc	0	Secreted protein				214
O13332 UniProt NPD GO	AUR1_CANAL	Aureobasidin A resistance protein homolog	0.09	-	ves	6	Membrane; multi-pass membrane protein (Potential)				471
Q6CKE2 UniProt NPD GO	ATG5_KLULA	Autophagy protein 5	0.09	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				271
Q9W3R7 UniProt NPD GO	ATG5_DROME	Autophagy protein 5 (APG5-like)	0.09	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			269
Q9CQY1 UniProt NPD GO	ATG12_MOUSE	Autophagy-related protein 12 (APG12-like)	0.09	-	mit	0	Cytoplasm (By similarity)	cytoplasm [ISS]			141
Q5A5S7 UniProt NPD GO	ATG27_CANAL	Autophagy-related protein 27 precursor	0.09	-	end	1	Intracytoplasmic membrane; single-pass type I membrane protein (By similarity). Perivacuolar punctat ...				252
Q5AWA2 UniProt NPD GO	ATG7_EMENI	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme atg7)	0.09	-	cyt	0	Cytoplasm (By similarity)				617
Q68FE2 UniProt NPD GO	ATG9A_MOUSE	Autophagy-related protein 9A (APG9-like 1)	0.09	-	end	5	Membrane; multi-pass membrane protein (Potential)	autophagic vacuole [IDA] cytoplasm [IDA]			551
P32293 UniProt NPD GO	AX22A_PHAAU	Auxin-induced protein 22A (Indole-3-acetic acid-induced protein ARG3)	0.09	-	cyt	0	Nucleus (By similarity)				194
Q5NB25 UniProt NPD GO	IAA3_ORYSA	Auxin-responsive protein IAA3 (Indoleacetic acid-induced protein 3)	0.09	-	nuc	0	Nucleus (By similarity)				263
Q8RYC6 UniProt NPD GO	IAA32_ARATH	Auxin-responsive protein IAA32 (Indoleacetic acid-induced protein 32)	0.09	-	cyt	0	Nucleus (By similarity)				191
P02701 UniProt NPD GO	AVID_CHICK	Avidin precursor	0.09	-	end	1 *				2CAM	152
Q62896 UniProt NPD GO	BET1_RAT	BET1 homolog (Golgi vesicular membrane-trafficking protein p18) (rBET1)	0.09	-	cyt	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein	Golgi apparatus [IMP] integral to membrane [IPI] SNARE complex [TAS]			118
Q68EL3 UniProt NPD GO	BET1L_BRARE	BET1-like protein	0.09	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				110
Q9XV51 UniProt NPD GO	BAT45_CAEEL	BTB and MATH domain-containing protein 45	0.09	-	nuc	0					468
Q8NFQ6 UniProt NPD GO	BPIL2_HUMAN	Bactericidal/permeability-increasing protein-like 2 precursor	0.09	-	end	0	Secreted protein (By similarity)	extracellular region [NAS]			507
Q8NFQ5 UniProt NPD GO	BPIL3_HUMAN	Bactericidal/permeability-increasing protein-like 3 precursor	0.09	-	end	0	Secreted protein (By similarity)				453
Q99MH9 UniProt NPD GO	BBS2_RAT	Bardet-Biedl syndrome 2 protein homolog	0.09	-	nuc	0					721
Q09117 UniProt NPD GO	BSPB_POPDE	Bark storage protein B precursor	0.09	-	nuc	0					312
Q9FYZ9 UniProt NPD GO	BAMT_ANTMA	Benzoate carboxyl methyltransferase (EC 2.1.1.-) (S-adenosyl-L-methionine:benzoic acid carboxyl meth ...	0.09	-	cyt	0					364
Q9HAY6 UniProt NPD GO	BCDO1_HUMAN	Beta,beta-carotene 15,15'-monooxygenase (EC 1.14.99.36) (Beta-carotene dioxygenase 1)	0.09	-	cyt	0			605748		547
Q91XT5 UniProt NPD GO	BCDO1_RAT	Beta,beta-carotene 15,15'-monooxygenase (EC 1.14.99.36) (Beta-carotene dioxygenase 1)	0.09	-	cyt	0					566
Q920V1 UniProt NPD GO	B3GT3_MOUSE	Beta-1,3-galactosyltransferase 3 (EC 2.4.1.79) (Beta-1,3-GalTase 3) (Beta3Gal-T3) (b3Gal-T3) (Galact ...	0.09	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				331
Q793U7 UniProt NPD GO	B3GT3_MUSSI	Beta-1,3-galactosyltransferase 3 (EC 2.4.1.79) (Beta-1,3-GalTase 3) (Beta3Gal-T3) (b3Gal-T3) (Galact ...	0.09	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				331
O88178 UniProt NPD GO	B3GT4_RAT	Beta-1,3-galactosyltransferase 4 (EC 2.4.1.62) (Beta-1,3-GalTase 4) (Beta3Gal-T4) (b3Gal-T4) (Gangli ...	0.09	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				371
P55078 UniProt NPD GO	B2MG_MUSCE	Beta-2-microglobulin (Fragment)	0.09	-	nuc	0	Secreted protein				92
P55077 UniProt NPD GO	B2MG_MUSCR	Beta-2-microglobulin (Fragment)	0.09	-	nuc	0	Secreted protein				92
Q9WV24 UniProt NPD GO	B2MG_CRIGR	Beta-2-microglobulin precursor	0.09	-	exc	0	Secreted protein				119
P49407 UniProt NPD GO	ARRB1_HUMAN	Beta-arrestin-1 (Arrestin, beta 1)	0.09	-	mit	0		cytoplasm [IDA] membrane fraction [IDA] plasma membrane [TAS] soluble fraction [TAS]	107940		418
P46159 UniProt NPD GO	BD01_BOVIN	Beta-defensin 1 (BNDB-1) (BNBD-1)	0.09	-	nuc	0	Secreted protein				38
O62697 UniProt NPD GO	BD01_PIG	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.09	-	mit	0	Secreted protein (Potential)				64
Q30KK4 UniProt NPD GO	DB124_PANTR	Beta-defensin 124 precursor (Defensin, beta 124)	0.09	-	end	0	Secreted protein (Potential)				71
P46161 UniProt NPD GO	BD03_BOVIN	Beta-defensin 3 precursor (BNDB-3) (BNBD-3) (Fragment)	0.09	-	vac	0	Secreted protein				57
O88514 UniProt NPD GO	BD04_RAT	Beta-defensin 4 precursor (Defensin, beta 4) (BD-4) (RBD-4) (BD-2) (RBD-2)	0.09	-	gol	0	Secreted protein (By similarity)				63

You are viewing entries 65751 to 65800 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.