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
Q9TKX5 UniProt NPD GO	RR4_NEPOL	Chloroplast 30S ribosomal protein S4	0.75	-	nuc	0	Plastid; chloroplast				202
P56352 UniProt NPD GO	RK20_CHLVU	Chloroplast 50S ribosomal protein L20	0.75	+	mit	0	Plastid; chloroplast				114
Q9MTK0 UniProt NPD GO	RK20_OENHO	Chloroplast 50S ribosomal protein L20	0.75	+	nuc	0	Plastid; chloroplast				130
Q8W8J2 UniProt NPD GO	RK32_PSINU	Chloroplast 50S ribosomal protein L32	0.75	-	nuc	0	Plastid; chloroplast				60
P51190 UniProt NPD GO	RK34_PORPU	Chloroplast 50S ribosomal protein L34	0.75	-	nuc	0	Plastid; chloroplast				46
Q7SDW6 UniProt NPD GO	EAF6_NEUCR	Chromatin modification-related protein eaf-6	0.75	-	nuc	0	Nucleus (By similarity)				179
Q9WTK2 UniProt NPD GO	CDYL_MOUSE	Chromodomain Y-like protein (CDY-like)	0.75	-	end	0	Nucleus (By similarity)				593
Q7RTS1 UniProt NPD GO	BHLH8_HUMAN	Class B basic helix-loop-helix protein 8 (bHLHB8) (Muscle, intestine and stomach expression 1) (MIST ...	0.75	-	nuc	0	Nucleus (Probable)		608606		189
Q96M91 UniProt NPD GO	CCD11_HUMAN	Coiled-coil domain-containing protein 11	0.75	-	nuc	0					399
Q99089 UniProt NPD GO	CPRF1_PETCR	Common plant regulatory factor CPRF-1	0.75	+	nuc	0	Nucleus				411
P01030 UniProt NPD GO	CO4_BOVIN	Complement C4 precursor [Contains: Complement C4 alpha chain; C4a anaphylatoxin; Complement C4 gamma ...	0.75	+	mit	1					920
Q03702 UniProt NPD GO	CCE1_YEAST	Cruciform cutting endonuclease 1, mitochondrial precursor (EC 3.1.-.-)	0.75	-	nuc	0	Mitochondrion	mitochondrial inner membrane [IDA]			353
Q94AH6 UniProt NPD GO	CUL1_ARATH	Cullin-1	0.75	-	mit	0	Nucleus. Cytoplasm. Mainly nuclear during interphase and preprophase, but also weakly cytoplasmic du ...				738
P18847 UniProt NPD GO	ATF3_HUMAN	Cyclic AMP-dependent transcription factor ATF-3 (Activating transcription factor 3)	0.75	+	nuc	0	Nucleus		603148		181
Q60439 UniProt NPD GO	CDN1B_CRIGR	Cyclin-dependent kinase inhibitor 1B (Cyclin-dependent kinase inhibitor p27) (p27Kip1)	0.75	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear and cytoplasmic in quiescent cells. Upon ...				198
P46527 UniProt NPD GO	CDN1B_HUMAN	Cyclin-dependent kinase inhibitor 1B (Cyclin-dependent kinase inhibitor p27) (p27Kip1)	0.75	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear and cytoplasmic in quiescent cells. Upon ...	cytoplasm [IDA] nucleus [IDA]	600778	2AST	198
P46414 UniProt NPD GO	CDN1B_MOUSE	Cyclin-dependent kinase inhibitor 1B (Cyclin-dependent kinase inhibitor p27) (p27Kip1)	0.75	-	nuc	0	Nucleus. Cytoplasm. Nuclear and cytoplasmic in quiescent cells. Upon cell cycle progression, mostly ...	cytoplasm [IDA] nucleus [IDA]			197
Q9VL92 UniProt NPD GO	CP4E3_DROME	Cytochrome P450 4e3 (EC 1.14.-.-) (CYPIVE3)	0.75	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				526
Q6E3C9 UniProt NPD GO	CPB1_CAERE	Cytoplasmic polyadenylation element-binding protein 1	0.75	-	nuc	0					594
P11434 UniProt NPD GO	41_XENLA	Cytoskeletal protein 4.1 (Band 4.1)	0.75	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				801
P10582 UniProt NPD GO	DPOM_MAIZE	DNA polymerase (EC 2.7.7.7) (S-1 DNA ORF 3)	0.75	-	nuc	0					929
Q758V1 UniProt NPD GO	DPB2_ASHGO	DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)	0.75	-	nuc	0	Nucleus (By similarity)				677
Q6PB75 UniProt NPD GO	POLS_MOUSE	DNA polymerase sigma (EC 2.7.7.7)	0.75	-	nuc	0	Nucleus (Probable)				542
P38953 UniProt NPD GO	RAD55_YEAST	DNA repair protein RAD55	0.75	-	nuc	0	Nucleus (Potential)	nucleus [IPI]			406
P49736 UniProt NPD GO	MCM2_HUMAN	DNA replication licensing factor MCM2 (Minichromosome maintenance protein 2 homolog) (Nuclear protei ...	0.75	-	nuc	0	Nucleus (Probable)	chromatin [TAS] nucleus [TAS]	116945		904
P38207 UniProt NPD GO	APN2_YEAST	DNA-(apurinic or apyrimidinic site) lyase 2 (EC 4.2.99.18) (AP endonuclease 2) (Apurinic-apyrimidini ...	0.75	-	nuc	0	Nucleus	nucleus [IC]			520
O94130 UniProt NPD GO	CREA_BOTCI	DNA-binding protein creA (Carbon catabolite repressor)	0.75	-	nuc	0	Nucleus				435
P28363 UniProt NPD GO	RPA1_EUPOC	DNA-directed RNA polymerase I largest subunit (EC 2.7.7.6) (Fragment)	0.75	-	nuc	0	Nucleus				638
P16356 UniProt NPD GO	RPB1_CAEEL	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	0.75	-	nuc	0	Nucleus	nucleus [IDA]			1852
Q75A34 UniProt NPD GO	RPB1_ASHGO	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) (RNA polymerase II subunit 1)	0.75	-	nuc	0	Nucleus (By similarity)				1745
Q6FS48 UniProt NPD GO	RPB9_CANGA	DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6)	0.75	-	nuc	1	Nucleus (By similarity)				122
Q8HUH2 UniProt NPD GO	RPOA_CHLRE	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.75	-	nuc	0	Plastid; chloroplast				550
Q9TL04 UniProt NPD GO	RPOC2_NEPOL	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.75	-	cyt	0	Plastid; chloroplast				1463
Q6EW58 UniProt NPD GO	RPOC2_NYMAL	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.75	+	nuc	0	Plastid; chloroplast				1401
P38671 UniProt NPD GO	RPOM_NEUCR	DNA-directed RNA polymerase, mitochondrial precursor (EC 2.7.7.6)	0.75	-	mit	0	Mitochondrion				1423
O88764 UniProt NPD GO	DAPK3_RAT	Death-associated protein kinase 3 (EC 2.7.11.1) (DAP kinase 3) (DAP-like kinase) (Dlk) (ZIP-kinase)	0.75	-	cyt	0	Nucleus. Cytoplasm. Relocates to the cytoplasm on binding PAWR where the complex appears to interact ...	nucleus [IEP]			448
Q14185 UniProt NPD GO	DOCK1_HUMAN	Dedicator of cytokinesis protein 1 (180 kDa protein downstream of CRK) (DOCK180)	0.75	+	nuc	0	Cytoplasm (Probable). Membrane (Probable). Recruited to membranes via its interaction with phosphati ...	cytoplasm [TAS]	601403		1865
Q9UK85 UniProt NPD GO	DKKL1_HUMAN	Dickkopf-like protein 1 precursor (Soggy-1 protein) (SGY-1)	0.75	-	nuc	1 *	Secreted protein	extracellular space [TAS]	605418		242
Q9NUL3 UniProt NPD GO	STAU2_HUMAN	Double-stranded RNA-binding protein Staufen homolog 2	0.75	-	nuc	0	Cytoplasm. Nucleus. Nucleus; nucleolus. Shuttles between the nucleolus, nucleus and the cytoplasm. N ...		605920		570
Q86SG4 UniProt NPD GO	DPCA2_HUMAN	Dresden prostate carcinoma 2 protein (D-PCa-2)	0.75	-	nuc	0					172
Q9Y0H4 UniProt NPD GO	SUDX_DROME	E3 ubiquitin-protein ligase suppressor of deltex (EC 6.3.2.-)	0.75	-	cyt	0		ubiquitin ligase complex [ISS]		1TK7	949
P41164 UniProt NPD GO	ETV1_MOUSE	ETS translocation variant 1 (ER81 protein)	0.75	-	nuc	0	Nucleus	nucleus [IC]			477
P08046 UniProt NPD GO	EGR1_MOUSE	Early growth response protein 1 (EGR-1) (Krox-24 protein) (Transcription factor Zif268) (Nerve growt ...	0.75	-	nuc	0	Nucleus	nucleus [IMP]		1ZAA	533
P08154 UniProt NPD GO	EGR1_RAT	Early growth response protein 1 (EGR-1) (Krox-24 protein) (Transcription factor Zif268) (Nerve growt ...	0.75	-	nuc	0	Nucleus				508
P26632 UniProt NPD GO	EGR1_BRARE	Early growth response protein 1 (EGR-1) (Krox24)	0.75	-	nuc	0	Nucleus				511
Q08893 UniProt NPD GO	E75_MANSE	Ecdysone-inducible protein E75	0.75	-	nuc	0	Nucleus (Potential)				699
Q8K203 UniProt NPD GO	NEIL3_MOUSE	Endonuclease VIII-like 3 (Nei-like 3) (DNA glycosylase FPG2)	0.75	-	nuc	0	Nucleus (By similarity)				606
Q5E9D0 UniProt NPD GO	IF2B_BOVIN	Eukaryotic translation initiation factor 2 subunit 2 (Eukaryotic translation initiation factor 2 sub ...	0.75	+	nuc	0					333
O60645 UniProt NPD GO	EXOC3_HUMAN	Exocyst complex component 3 (Exocyst complex component Sec6)	0.75	-	cyt	0			608186		756
Q75B91 UniProt NPD GO	EXO84_ASHGO	Exocyst complex component EXO84	0.75	-	nuc	0	Secretory vesicle (By similarity). Cell periphery. The polarization of EXO84 requires actin cables ( ...				697

You are viewing entries 11251 to 11300 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.