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
O13370 UniProt NPD GO	DED1_SCHPO	ATP-dependent RNA helicase ded1 (EC 3.6.1.-)	0.50	-	nuc	0	Cytoplasm (By similarity)				636
Q75EW9 UniProt NPD GO	RRP3_ASHGO	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.50	-	nuc	0	Nucleus (Probable)				487
Q42807 UniProt NPD GO	STAD_SOYBN	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.50	-	mit	0	Plastid; chloroplast (By similarity). In green tissue, found in chloroplasts. Plastid (By similarity ...				411
P26231 UniProt NPD GO	CTN1_MOUSE	Alpha-1 catenin (102 kDa cadherin-associated protein) (CAP102) (Alpha E-catenin)	0.50	+	nuc	0	Cell membrane; cell-cell junction. Cell membrane; cell-matrix junction. Found at cell-cell boundarie ...	adherens junction [IDA] lamellipodium [IDA] zonula adherens [IDA]		1DOW	906
P28800 UniProt NPD GO	A2AP_BOVIN	Alpha-2-antiplasmin precursor (Alpha-2-plasmin inhibitor) (Alpha-2-PI) (Alpha-2-AP)	0.50	-	exc	0	Secreted protein				492
O19091 UniProt NPD GO	ADA2B_TALEU	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.50	-	end	6 *	Membrane; multi-pass membrane protein				397
Q01337 UniProt NPD GO	ADA2C_MOUSE	Alpha-2C adrenergic receptor (Alpha-2C adrenoceptor) (Alpha-2C adrenoreceptor) (Alpha-2 adrenergic r ...	0.50	+	end	7	Membrane; multi-pass membrane protein				458
Q9NVD7 UniProt NPD GO	PARVA_HUMAN	Alpha-parvin (Calponin-like integrin-linked kinase-binding protein) (CH-ILKBP)	0.50	+	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...		608120		372
P39188 UniProt NPD GO	ALU1_HUMAN	Alu subfamily J sequence contamination warning entry	0.50	-	exc	0					591
P39190 UniProt NPD GO	ALU3_HUMAN	Alu subfamily SB1 sequence contamination warning entry	0.50	-	exc	0					587
P31955 UniProt NPD GO	AREG_MOUSE	Amphiregulin precursor (AR) (Schwannoma-derived growth factor) (SDGF)	0.50	+	exc	1					248
O88888 UniProt NPD GO	APBA3_MOUSE	Amyloid beta A4 precursor protein-binding family A member 3 (Neuron-specific X11L2 protein) (Neurona ...	0.50	-	nuc	0					571
P15943 UniProt NPD GO	APLP2_RAT	Amyloid-like protein 2 precursor (Sperm membrane protein YWK-II)	0.50	-	end	2 *	Membrane; single-pass type I membrane protein				765
Q6RUG5 UniProt NPD GO	AL2SE_RAT	Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 15 protein homolog (Ica69-related ...	0.50	-	nuc	0					435
O42839 UniProt NPD GO	APC4_SCHPO	Anaphase-promoting complex subunit 4 (20S cyclosome/APC complex protein apc4) (Cell untimely torn pr ...	0.50	-	nuc	0		anaphase-promoting complex [IDA]			719
Q91W96 UniProt NPD GO	ANC4_MOUSE	Anaphase-promoting complex subunit 4 (APC4) (Cyclosome subunit 4)	0.50	-	mit	0					807
Q60FC1 UniProt NPD GO	ANGP1_CANFA	Angiopoietin-1 precursor (ANG-1)	0.50	-	exc	0	Secreted protein (By similarity)				497
O35608 UniProt NPD GO	ANGP2_MOUSE	Angiopoietin-2 precursor (ANG-2)	0.50	-	nuc	0	Secreted protein				496
Q640P2 UniProt NPD GO	ANGL1_MOUSE	Angiopoietin-related protein 1 precursor (Angiopoietin-like 1)	0.50	-	mit	0	Secreted protein (By similarity)				490
O95841 UniProt NPD GO	ANGL1_HUMAN	Angiopoietin-related protein 1 precursor (Angiopoietin-like 1) (Angiopoietin-3) (ANG-3)	0.50	-	exc	0	Secreted protein	extracellular space [IDA]	603874		491
Q8R0Z6 UniProt NPD GO	ANGL6_MOUSE	Angiopoietin-related protein 6 precursor (Angiopoietin-like 6) (Angiopoietin-related growth factor)	0.50	-	nuc	0	Secreted protein (Probable)	secretory granule [IDA]			457
Q10751 UniProt NPD GO	ACE_CHICK	Angiotensin-converting enzyme (EC 3.4.15.1) (Dipeptidyl carboxypeptidase I) (Kininase II) (Fragment) ...	0.50	-	nuc	1	Membrane; single-pass type I membrane protein				1193
Q86SG2 UniProt NPD GO	ANR23_HUMAN	Ankyrin repeat domain-containing protein 23 (Diabetes-related ankyrin repeat protein) (Muscle ankyri ...	0.50	-	cyt	0	Nucleus. Sarcomeric I-band and some intercalated disks (By similarity)				305
Q9D2J7 UniProt NPD GO	ANKR5_MOUSE	Ankyrin repeat domain-containing protein 5	0.50	-	cyt	0					775
Q01317 UniProt NPD GO	NUC2_NEUCR	Ankyrin repeat protein nuc-2	0.50	-	nuc	0					1066
Q16671 UniProt NPD GO	AMHR2_HUMAN	Anti-Muellerian hormone type-2 receptor precursor (EC 2.7.11.30) (Anti-Muellerian hormone type II re ...	0.50	-	exc	1	Membrane; single-pass type I membrane protein		600956		573
P50492 UniProt NPD GO	AMA1_PLAF8	Apical membrane antigen 1 precursor (Merozoite surface antigen)	0.50	-	nuc	1	Membrane; single-pass type I membrane protein				622
P10517 UniProt NPD GO	APOE_MACFA	Apolipoprotein E precursor (Apo-E)	0.50	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			317
P08226 UniProt NPD GO	APOE_MOUSE	Apolipoprotein E precursor (Apo-E)	0.50	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]		1YA9	311
P05770 UniProt NPD GO	APOE_PAPAN	Apolipoprotein E precursor (Apo-E)	0.50	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			317
P02650 UniProt NPD GO	APOE_RAT	Apolipoprotein E precursor (Apo-E)	0.50	-	exc	0	Secreted protein	cytoplasm [ISS] extracellular region [ISS]			312
Q7M2U7 UniProt NPD GO	APOE_ZALCA	Apolipoprotein E precursor (Apo-E)	0.50	-	exc	0	Secreted protein				329
P41957 UniProt NPD GO	CED9_CAEBR	Apoptosis regulator ced-9 (Cell death protein 9)	0.50	-	nuc	1	Intracytoplasmic membrane; peripheral membrane protein (By similarity). Mitochondrion; mitochondrial ...				266
Q9SJK3 UniProt NPD GO	AGOL_ARATH	Argonaute-like protein At2g27880	0.50	-	nuc	0					997
Q60XN1 UniProt NPD GO	ATX3_CAEBR	Ataxin-3 homolog (EC 3.4.22.-) (Machado-Joseph disease-like protein)	0.50	-	nuc	0	Nucleus (By similarity)				319
Q6BSK5 UniProt NPD GO	ATG17_DEBHA	Autophagy-related protein 17	0.50	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				487
Q93YR9 UniProt NPD GO	ARFP_ARATH	Auxin response factor 16	0.50	-	nuc	0	Nucleus	nucleus [IDA]			670
Q9XED8 UniProt NPD GO	ARFI_ARATH	Auxin response factor 9	0.50	-	nuc	0	Nucleus				638
Q9XFB0 UniProt NPD GO	YAB2_ARATH	Axial regulator YABBY2	0.50	-	nuc	1 *	Nucleus (By similarity)				184
O01395 UniProt NPD GO	MST3_DROHY	Axoneme-associated protein mst101(3)	0.50	+	nuc	0	Cytoplasm (By similarity)				275
Q9CXE2 UniProt NPD GO	BCL7A_MOUSE	B-cell CLL/lymphoma 7 protein family member A	0.50	-	nuc	0					210
Q7Z569 UniProt NPD GO	BRAP_HUMAN	BRCA1-associated protein (EC 6.3.2.-) (BRAP2) (Impedes mitogenic signal propagation) (IMP) (RING fin ...	0.50	-	nuc	0	Cytoplasm	cytoplasm [IEP]	604986		592
P34371 UniProt NPD GO	BAT42_CAEEL	BTB and MATH domain-containing protein 42	0.50	-	mit	0					410
Q9HCM4 UniProt NPD GO	E41L5_HUMAN	Band 4.1-like protein 5	0.50	-	nuc	0					732
Q06561 UniProt NPD GO	UNC52_CAEEL	Basement membrane proteoglycan precursor (Perlecan homolog) (Uncoordinated protein 52)	0.50	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	basement membrane [IDA]			3375
Q05793 UniProt NPD GO	PGBM_MOUSE	Basement membrane-specific heparan sulfate proteoglycan core protein precursor (HSPG) (Perlecan) (PL ...	0.50	-	nuc	0	Secreted protein; extracellular space	basement membrane [IDA]		1GL4	3707
P10162 UniProt NPD GO	PRB4L_HUMAN	Basic salivary proline-rich protein 4 allele L (Salivary proline-rich protein Po) (Parotid o protein ...	0.50	-	nuc	0		extracellular region [NAS]	180990		276
Q61337 UniProt NPD GO	BAD_MOUSE	Bcl2 antagonist of cell death (BAD) (Bcl-2-binding component 6) (Bcl-xL/Bcl-2-associated death promo ...	0.50	-	nuc	0	Mitochondrion; mitochondrial outer membrane. Cytoplasm. Upon phosphorylation, locates to the cytopla ...	mitochondrion [IDA]			204
Q8N1D0 UniProt NPD GO	BWR1B_HUMAN	Beckwith-Wiedemann syndrome chromosome region 1 candidate protein B (p27-Beckwith-Wiedemann region 1 ...	0.50	-	nuc	0			603240		253
O88597 UniProt NPD GO	BCN1_MOUSE	Beclin-1 (Coiled-coil myosin-like BCL2-interacting protein)	0.50	-	mit	0	Cytoplasm (Potential). Golgi apparatus; Golgi membrane; peripheral membrane protein. Expressed in de ...	cytoplasmic membrane-bound vesicle [IDA] Golgi trans face [IDA]			448

You are viewing entries 24801 to 24850 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.