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
Q86RB2 UniProt NPD GO	CXAC_CONGE	Alpha-conotoxin GIC precursor (Fragment)	0.12	-	nuc	0	Secreted protein			1UL2	40
Q09187 UniProt NPD GO	MEL_SACPA	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase) (MELp ...	0.12	-	cyt	0					471
Q9P4V4 UniProt NPD GO	MEL_ZYGMR	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase) (MELr ...	0.12	-	cyt	0					470
Q865F8 UniProt NPD GO	AHSP_BOVIN	Alpha-hemoglobin-stabilizing protein (Erythroid-associated factor)	0.12	-	nuc	0	Cytoplasm (By similarity)				92
Q9YGJ6 UniProt NPD GO	NXSA1_NAJSP	Alpha-neurotoxin NTX-1 precursor	0.12	-	nuc	0	Secreted protein				83
P28173 UniProt NPD GO	PUR1_CHICK	Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidot ...	0.12	-	cyt	0					510
P35433 UniProt NPD GO	PUR1_RAT	Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidot ...	0.12	-	cyt	0					517
P52419 UniProt NPD GO	PUR1_VIGAC	Amidophosphoribosyltransferase, chloroplast precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyropho ...	0.12	-	nuc	0	Plastid; chloroplast				485
Q708S7 UniProt NPD GO	ACC2B_BRARE	Amiloride-sensitive cation channel 2-B, neuronal (Acid-sensing ion channel 1.2) (ZASIC1.2)	0.12	-	cyt	1 *	Cell membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [IDA]			501
P21397 UniProt NPD GO	AOFA_HUMAN	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A)	0.12	-	cyt	0	Mitochondrion; mitochondrial outer membrane		309850	2BXS	527
Q9DAX9 UniProt NPD GO	APBP2_MOUSE	Amyloid protein-binding protein 2 (Amyloid beta precursor protein-binding protein 2) (APP-BP2)	0.12	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Associated with membranes and microtubules (By s ...				585
Q9NWX5 UniProt NPD GO	ASB6_HUMAN	Ankyrin repeat and SOCS box protein 6 (ASB-6)	0.12	-	cyt	0	Cytoplasm (By similarity)				421
Q5VYY1 UniProt NPD GO	ANR22_HUMAN	Ankyrin repeat domain-containing protein 22	0.12	-	cyt	1					191
Q2QLC6 UniProt NPD GO	ASZ1_CARPS	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.12	-	cyt	1	Cytoplasm (By similarity)				475
P17153 UniProt NPD GO	ANXA5_CHICK	Annexin A5 (Annexin V) (Lipocortin V) (Endonexin II) (Calphobindin I) (CBP-I) (Placental anticoagula ...	0.12	-	cyt	0				1YJ0	321
P22184 UniProt NPD GO	ASF2_HELAN	Anther-specific protein SF2 precursor	0.12	-	exc	1 *					121
P36371 UniProt NPD GO	TAP2_MOUSE	Antigen peptide transporter 2 (APT2) (Histocompatibility antigen modifier 2)	0.12	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. The transmembran ...	cytosol [ISS] endoplasmic reticulum lumen [ISS] integral to membrane [ISS] TAP complex [ISS]			702
P97430 UniProt NPD GO	ALK1_MOUSE	Antileukoproteinase 1 precursor (ALP) (Secretory leukocyte protease inhibitor)	0.12	-	nuc	0					131
P01008 UniProt NPD GO	ANT3_HUMAN	Antithrombin-III precursor (ATIII)	0.12	-	exc	0	Secreted protein; extracellular space	extracellular region [NAS]	107300	2BEH	464
Q5R5A3 UniProt NPD GO	ANT3_PONPY	Antithrombin-III precursor (ATIII)	0.12	-	exc	0	Secreted protein; extracellular space				464
Q85AR2 UniProt NPD GO	CYF_ANTFO	Apocytochrome f precursor	0.12	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				322
P23577 UniProt NPD GO	CYF_CHLRE	Apocytochrome f precursor	0.12	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein			1Q90	317
P06669 UniProt NPD GO	CYF_VICFA	Apocytochrome f precursor	0.12	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P13276 UniProt NPD GO	APL3_MANSE	Apolipophorin-3 precursor (Apolipophorin-III) (ApoLp-III)	0.12	-	exc	0	Secreted protein			1EQ1	189
P49726 UniProt NPD GO	SPE1_LYCES	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC)	0.12	-	mit	0					502
Q9NH48 UniProt NPD GO	KARG_ERISI	Arginine kinase (EC 2.7.3.3) (AK)	0.12	-	cyt	0					357
P14208 UniProt NPD GO	KARG_HOMGA	Arginine kinase (EC 2.7.3.3) (AK)	0.12	-	cyt	0					355
Q9GYX1 UniProt NPD GO	KARG_PACMR	Arginine kinase (EC 2.7.3.3) (AK)	0.12	-	cyt	0					357
Q8N5I2 UniProt NPD GO	ARRD1_HUMAN	Arrestin domain-containing protein 1	0.12	-	cyt	0					433
P19891 UniProt NPD GO	ASNS_CRIGR	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.12	-	cyt	0					560
P08906 UniProt NPD GO	AATC_HORSE	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transa ...	0.12	-	cyt	0	Cytoplasm				412
P08907 UniProt NPD GO	AATM_HORSE	Aspartate aminotransferase, mitochondrial (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate tran ...	0.12	-	nuc	0	Mitochondrion; mitochondrial matrix				401
P17342 UniProt NPD GO	ANPRC_HUMAN	Atrial natriuretic peptide clearance receptor precursor (ANP-C) (ANPRC) (NPR-C) (Atrial natriuretic ...	0.12	-	end	1 *	Membrane; single-pass type I membrane protein		108962	1JDP	541
Q75BY9 UniProt NPD GO	ATG5_ASHGO	Autophagy protein 5	0.12	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				293
Q6BVI8 UniProt NPD GO	ATG5_DEBHA	Autophagy protein 5	0.12	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				292
Q2TBJ5 UniProt NPD GO	ATG12_RAT	Autophagy-related protein 12 (APG12-like)	0.12	-	mit	0	Cytoplasm (By similarity)				141
Q5KC57 UniProt NPD GO	ATG7_CRYNE	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7)	0.12	-	cyt	0	Cytoplasm (By similarity)				675
Q8RWZ6 UniProt NPD GO	PIN4_ARATH	Auxin efflux carrier component 4 (AtPIN4)	0.12	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				616
P78543 UniProt NPD GO	BTG2_HUMAN	BTG2 protein (NGF-inducible anti-proliferative protein PC3)	0.12	-	nuc	0			601597		158
Q9GLN5 UniProt NPD GO	BIRC5_PIG	Baculoviral IAP repeat-containing protein 5 (Apoptosis inhibitor survivin)	0.12	-	nuc	0	Cytoplasm. Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metapha ...	cytoplasm [NAS]			142
Q06209 UniProt NPD GO	CHI4_BRANA	Basic endochitinase CHB4 precursor (EC 3.2.1.14)	0.12	-	exc	0	Secreted protein; extracellular space				268
Q8NFU1 UniProt NPD GO	VMDL1_HUMAN	Bestrophin-2 (Vitelliform macular dystrophy 2-like protein 1)	0.12	-	cyt	5 *	Cell membrane; multi-pass membrane protein		607335		509
P10042 UniProt NPD GO	CRBA1_CHICK	Beta crystallin A3 (Beta crystallin A1)	0.12	-	cyt	0					215
Q9I993 UniProt NPD GO	BCDO1_CHICK	Beta,beta-carotene 15,15'-monooxygenase (EC 1.14.99.36) (Beta-carotene dioxygenase 1)	0.12	-	cyt	0					526
Q99NF1 UniProt NPD GO	BCDO2_MOUSE	Beta,beta-carotene 9',10'-dioxygenase (EC 1.14.99.-) (Beta-carotene dioxygenase 2) (B-diox-II)	0.12	-	cyt	0		intracellular [IC]			532
Q28927 UniProt NPD GO	ADRB1_SHEEP	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor) (BETA1AR)	0.12	-	end	7	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...				467
Q8UUY8 UniProt NPD GO	ADRB2_ONCMY	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.12	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			409
Q9XT58 UniProt NPD GO	ADRB3_SHEEP	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				405
Q60483 UniProt NPD GO	ADRB3_CAVPO	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor) (Fragment)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				351
P61261 UniProt NPD GO	BD01_MACFA	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.12	-	exc	0	Secreted protein (Potential)				68

You are viewing entries 60851 to 60900 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.