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
Q2TBV1 UniProt NPD GO	RFC3_BOVIN	Replication factor C subunit 3 (Replication factor C 38 kDa subunit) (RFC38) (Activator 1 38 kDa sub ...	0.51	-	cyt	0	Nucleus (Probable)				356
P51128 UniProt NPD GO	RXRA_XENLA	Retinoic acid receptor RXR-alpha (Retinoid X receptor alpha)	0.51	+	nuc	0	Nucleus				488
P51129 UniProt NPD GO	RXRG_XENLA	Retinoic acid receptor RXR-gamma (Retinoid X receptor gamma)	0.51	+	nuc	0	Nucleus				470
Q9QVY8 UniProt NPD GO	RAI2_MOUSE	Retinoic acid-induced protein 2 (3f8)	0.51	-	nuc	0					529
Q60924 UniProt NPD GO	STRAD_MOUSE	Retinoic acid-inducible E3 protein (Hematopoietic-specific protein E3)	0.51	-	nuc	0					215
Q8HXG3 UniProt NPD GO	RHPN2_CANFA	Rhophilin-2 (GTP-Rho-binding protein 2) (76 kDa RhoB effector protein) (p76RBE)	0.51	-	cyt	0	Cytoplasm; perinuclear region (By similarity)				686
Q9JJH1 UniProt NPD GO	RNAS4_MOUSE	Ribonuclease 4 precursor (EC 3.1.27.-) (RNase 4)	0.51	-	exc	1 *	Secreted protein				148
Q4WXZ5 UniProt NPD GO	RNY1_ASPFU	Ribonuclease T2-like precursor (EC 3.1.27.1) (RNase T2-like)	0.51	-	cyt	0	Secreted protein (By similarity)				414
Q10155 UniProt NPD GO	RNZ_SCHPO	Ribonuclease Z (EC 3.1.26.11) (RNase Z) (tRNase Z) (tRNA 3 endonuclease)	0.51	-	mit	0	Nucleus (Probable)				809
Q9XGA0 UniProt NPD GO	KPRS3_SPIOL	Ribose-phosphate pyrophosphokinase 3, mitochondrial precursor (EC 2.7.6.1) (Phosphoribosyl pyrophosp ...	0.51	-	mit	0	Mitochondrion (Potential)				406
Q9Z2I4 UniProt NPD GO	ROBO3_MOUSE	Roundabout homolog 3 precursor (Retinoblastoma-inhibiting gene 1) (Rig-1)	0.51	+	nuc	0	Membrane; single-pass type I membrane protein				1366
Q09512 UniProt NPD GO	YLN9_CAEEL	SET and TTL domain-containing protein D2013.9	0.51	-	cyt	0					662
Q99962 UniProt NPD GO	SH3G2_HUMAN	SH3-containing GRB2-like protein 2 (EC 2.3.1.-) (SH3 domain protein 2A) (Endophilin 1) (EEN-B1)	0.51	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Concentrated in presynaptic nerve terminals in neu ...		604465	1X04	352
P70663 UniProt NPD GO	SPRL1_MOUSE	SPARC-like protein 1 precursor (Matrix glycoprotein Sc1) (Extracellular matrix protein 2)	0.51	-	exc	0	Secreted protein; extracellular space; extracellular matrix				650
P40638 UniProt NPD GO	AES2_ALLMI	SRY-related protein AES2 (Fragment)	0.51	-	nuc	0	Nucleus (Potential)				72
Q9P3W2 UniProt NPD GO	HSV2_SCHPO	SVP1-like protein 2	0.51	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				364
Q9UBV2 UniProt NPD GO	SEL1L_HUMAN	Sel-1 homolog precursor (Suppressor of lin-12-like protein) (Sel-1L)	0.51	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]	602329		794
Q13214 UniProt NPD GO	SEM3B_HUMAN	Semaphorin-3B precursor (Semaphorin V) (Sema V) (Sema A(V))	0.51	-	exc	1 *	Secreted protein (By similarity). Endoplasmic reticulum. Accumulates in the endoplasmic reticulum	endoplasmic reticulum [TAS]	601281		749
P70275 UniProt NPD GO	SEM3E_MOUSE	Semaphorin-3E precursor (Semaphorin H) (Sema H)	0.51	+	nuc	0	Secreted protein				775
Q99JT2 UniProt NPD GO	MST4_MOUSE	Serine/threonine-protein kinase MST4 (EC 2.7.11.1) (STE20-like kinase MST4) (MST-4) (Mammalian STE20 ...	0.51	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus (By similarity). Localizes to the Golgi apparatus (By sim ...	Golgi apparatus [ISS]			416
Q63433 UniProt NPD GO	PKN1_RAT	Serine/threonine-protein kinase N1 (EC 2.7.11.13) (Protein kinase C-like 1) (Protein-kinase C-relate ...	0.51	-	nuc	0	Cytoplasm				946
P38622 UniProt NPD GO	RCK1_YEAST	Serine/threonine-protein kinase RCK1 (EC 2.7.11.1)	0.51	-	nuc	0					512
P40160 UniProt NPD GO	RIO2_YEAST	Serine/threonine-protein kinase RIO2 (EC 2.7.11.1)	0.51	+	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] cytosol [IDA] nucleus [IDA]			425
Q61RA2 UniProt NPD GO	CHK1_CAEBR	Serine/threonine-protein kinase chk-1 (EC 2.7.11.1)	0.51	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				493
Q09488 UniProt NPD GO	SMA6_CAEEL	Serine/threonine-protein kinase sma-6 precursor (EC 2.7.11.30)	0.51	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				636
Q7S6M5 UniProt NPD GO	PTPA1_NEUCR	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.51	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				617
Q9NP81 UniProt NPD GO	SYSM_HUMAN	Seryl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.11) (Serine--tRNA ligase) (SerRSmt)	0.51	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			518
Q62565 UniProt NPD GO	SRY_MUSSI	Sex-determining region Y protein (Testis-determining factor)	0.51	-	nuc	0	Nucleus				311
O15266 UniProt NPD GO	SHOX_HUMAN	Short stature homeobox protein (Short stature homeobox-containing protein) (Pseudoautosomal homeobox ...	0.51	+	nuc	0	Nucleus (By similarity)		400020		292
Q8SRC3 UniProt NPD GO	SEC65_ENCCU	Signal recognition particle SEC65 subunit	0.51	-	nuc	0	Cytoplasm (By similarity)				137
P32342 UniProt NPD GO	SRP21_YEAST	Signal recognition particle subunit SRP21 (Signal recognition particle 21 kDa protein)	0.51	+	nuc	0	Cytoplasm (By similarity). Nucleus	nucleus [IDA] signal recognition particle (sensu Eukaryota) [IDA]			166
Q9JM90 UniProt NPD GO	STAP1_MOUSE	Signal-transducing adaptor protein 1 (STAP-1) (Stem cell adaptor protein 1)	0.51	-	mit	0	Cytoplasm (Potential)				297
Q9NS25 UniProt NPD GO	SPNXB_HUMAN	Sperm protein associated with the nucleus on the X chromosome B/F (Nuclear-associated protein SPAN-X ...	0.51	+	nuc	0	Cytoplasm. Nucleus. Associated with nuclear craters	nucleus [TAS]			103
Q6PDM2 UniProt NPD GO	SFRS1_MOUSE	Splicing factor, arginine/serine-rich 1	0.51	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the nucleus and the cytoplasm ( ...	nucleus [IDA]		1X4C	247
Q5R7H2 UniProt NPD GO	SFRS1_PONPY	Splicing factor, arginine/serine-rich 1	0.51	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the nucleus and the cytoplasm ( ...				247
Q07955 UniProt NPD GO	SFRS1_HUMAN	Splicing factor, arginine/serine-rich 1 (pre-mRNA-splicing factor SF2, P33 subunit) (Alternative-spl ...	0.51	+	nuc	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm		600812	1X4A	247
O43609 UniProt NPD GO	SPY1_HUMAN	Sprouty homolog 1 (Spry-1)	0.51	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in the cytoplasm in unstimulated cells but i ...	cytoplasm [NAS] lamellipodium [NAS]	602465		319
Q9NY15 UniProt NPD GO	STAB1_HUMAN	Stabilin-1 precursor (FEEL-1 protein) (MS-1 antigen)	0.51	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [IDA]	608560		2570
Q8WWQ8 UniProt NPD GO	STAB2_HUMAN	Stabilin-2 precursor (FEEL-2 protein) (Fasciclin EGF-like laminin-type EGF-like and link domain-cont ...	0.51	-	nuc	1	Cell membrane; single-pass type I membrane protein	external side of plasma membrane [ISS] integral to plasma membrane [IDA]	608561		2551
Q9N0T1 UniProt NPD GO	STC1_BOVIN	Stanniocalcin-1 precursor (STC-1)	0.51	-	exc	0	Secreted protein (By similarity)				247
P79387 UniProt NPD GO	STF1_PIG	Steroidogenic factor 1 (STF-1) (SF-1) (Adrenal 4-binding protein) (Steroid hormone receptor Ad4BP) ( ...	0.51	+	mit	0	Nucleus (By similarity)				461
Q751Z4 UniProt NPD GO	ATG26_ASHGO	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26)	0.51	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				1227
Q8WU79 UniProt NPD GO	SMP1L_HUMAN	Stromal membrane-associated protein 1-like	0.51	-	nuc	0	Cytoplasm. Detected in multiple foci throughout the cytoplasm and in juxtanuclear structures (By sim ...				429
P14410 UniProt NPD GO	SUIS_HUMAN	Sucrase-isomaltase, intestinal [Contains: Sucrase (EC 3.2.1.48); Isomaltase (EC 3.2.1.10)]	0.51	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Brush border	brush border [TAS] Golgi apparatus [TAS]	609845		1826
O88583 UniProt NPD GO	SOCS3_RAT	Suppressor of cytokine signaling 3 (SOCS-3) (Cytokine-inducible SH2 protein 3)	0.51	-	nuc	0					225
P56962 UniProt NPD GO	STX17_HUMAN	Syntaxin-17 (KAT01814)	0.51	-	cyt	2	Membrane; single-pass type IV membrane protein. Appears to be associated with a membrane compartment ...		604204		302
Q810F8 UniProt NPD GO	TBX10_MOUSE	T-box transcription factor TBX10 (T-box protein 10) (T-box protein 13) (MmTBX7)	0.51	-	nuc	0	Nucleus (Potential)				385
P43345 UniProt NPD GO	TLX1_MOUSE	T-cell leukemia homeobox protein 1 (Homeobox protein Hox-11) (Homeobox TLX-1)	0.51	+	nuc	0	Nucleus (Probable)				332
Q08338 UniProt NPD GO	CD4_CERAE	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.51	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			458
P79185 UniProt NPD GO	CD4_MACFA	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.51	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			458

You are viewing entries 24601 to 24650 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.