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
Q5XLR4 UniProt NPD GO	BOREA_BRARE	Borealin (Cell division cycle-associated protein 8)	0.87	-	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...				276
Q8TDN6 UniProt NPD GO	BXDC2_HUMAN	Brix domain-containing protein 2 (Ribosome biogenesis protein Brix)	0.87	+	nuc	0	Nucleus; nucleolus				353
Q8UVY2 UniProt NPD GO	BXDC2_XENLA	Brix domain-containing protein 2 (Ribosome biogenesis protein Brix) (Bx24)	0.87	+	nuc	0	Nucleus; nucleolus				339
P25558 UniProt NPD GO	BUD3_YEAST	Bud site selection protein BUD3	0.87	-	nuc	0		contractile ring (sensu Saccharomyces) [TAS]			1636
P32870 UniProt NPD GO	CYA1_DROME	Ca(2+)/calmodulin-responsive adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Protein rutab ...	0.87	-	end	11 *	Membrane; multi-pass membrane protein				2248
Q9ULU8 UniProt NPD GO	CAPS1_HUMAN	Calcium-dependent secretion activator 1 (Calcium-dependent activator protein for secretion 1) (CAPS- ...	0.87	-	nuc	0	Cytoplasmic vesicle (By similarity). Membrane-associated to vesicles. Strongly enriched in synaptic ...		604667	1WI1	1353
Q62717 UniProt NPD GO	CAPS1_RAT	Calcium-dependent secretion activator 1 (Calcium-dependent activator protein for secretion 1) (CAPS- ...	0.87	-	nuc	0	Cytoplasmic vesicle. Membrane-associated to vesicles. Strongly enriched in synaptic fractions. Prefe ...				1289
Q9BXY5 UniProt NPD GO	CAYP2_HUMAN	Calcyphosin-2 (Calcyphosine-2)	0.87	-	nuc	0			607724		557
P13505 UniProt NPD GO	CALD1_MELGA	Caldesmon, smooth muscle (CDM) (Fragment)	0.87	+	nuc	0	On thin filaments in smooth muscle and on stress fibers in fibroblasts (nonmuscle)				274
P08855 UniProt NPD GO	ICAL_RABIT	Calpastatin (Calpain inhibitor) [Contains: Erythrocyte calpastatin]	0.87	-	nuc	0					718
Q8WXE0 UniProt NPD GO	CSKI2_HUMAN	Caskin-2	0.87	+	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			1202
Q08032 UniProt NPD GO	CDC45_YEAST	Cell division control protein 45	0.87	-	nuc	0	Nucleus	pre-replicative complex [IDA] replication fork [IDA]			650
Q5U4F0 UniProt NPD GO	HUCE1_RAT	Cerebral protein 1 homolog	0.87	+	nuc	0	Nucleus; nucleolus (By similarity)				457
Q9D7F7 UniProt NPD GO	CHM4C_MOUSE	Charged multivesicular body protein 4c (Chromatin-modifying protein 4c) (CHMP4c)	0.87	-	nuc	0	Cytoplasm (By similarity)				232
Q6ENH6 UniProt NPD GO	RR14_ORYNI	Chloroplast 30S ribosomal protein S14	0.87	+	nuc	0	Plastid; chloroplast				103
P09096 UniProt NPD GO	RR14_ORYSA	Chloroplast 30S ribosomal protein S14	0.87	+	nuc	0	Plastid; chloroplast				103
P27418 UniProt NPD GO	RR4_EUGGR	Chloroplast 30S ribosomal protein S4	0.87	+	nuc	0	Plastid; chloroplast				205
Q6CF40 UniProt NPD GO	EAF7_YARLI	Chromatin modification-related protein EAF7	0.87	-	nuc	0	Nucleus (By similarity)				354
Q8TE73 UniProt NPD GO	DYH5_HUMAN	Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1)	0.87	-	nuc	0			608644		4624
Q01306 UniProt NPD GO	CCG8_NEUCR	Clock-controlled protein 8	0.87	-	nuc	0					661
P12259 UniProt NPD GO	FA5_HUMAN	Coagulation factor V precursor (Activated protein C cofactor) [Contains: Coagulation factor V heavy ...	0.87	+	nuc	0		extracellular region [NAS]	188055	1FV4	2224
Q9D439 UniProt NPD GO	CCD11_MOUSE	Coiled-coil domain-containing protein 11	0.87	-	nuc	0					399
Q4R8V8 UniProt NPD GO	CCD37_MACFA	Coiled-coil domain-containing protein 37	0.87	-	nuc	0					608
P98137 UniProt NPD GO	CO8B_RABIT	Complement component C8 beta chain precursor (Complement component 8 subunit beta)	0.87	-	nuc	0	Secreted protein				590
Q921L5 UniProt NPD GO	COG2_MOUSE	Conserved oligomeric Golgi complex component 2 (Low density lipoprotein receptor defect C-complement ...	0.87	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity)				731
Q9BZJ0 UniProt NPD GO	CRNL1_HUMAN	Crooked neck-like protein 1 (Crooked neck homolog) (hCrn)	0.87	+	cyt	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes with core spliceosomal snRNP proteins. Cytoplasm. ...	nucleus [NAS]			848
Q9VWW0 UniProt NPD GO	CREBB_DROME	Cyclic AMP response element-binding protein B (dCREB-B)	0.87	+	nuc	0	Nucleus	nucleus [IDA]			359
Q8ND76 UniProt NPD GO	CFP1_HUMAN	Cyclin fold protein 1 (Cyclin box protein 1)	0.87	-	nuc	0					341
P39689 UniProt NPD GO	CDN1A_MOUSE	Cyclin-dependent kinase inhibitor 1 (p21) (CDK-interacting protein 1) (Melanoma differentiation-asso ...	0.87	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cyclin-dependent protein kinase holoenzyme ... [IPI] nucleus [IDA]			158
P38909 UniProt NPD GO	CYC2_YEAST	Cytochrome c mitochondrial import factor CYC2	0.87	-	nuc	0	Mitochondrion	extrinsic to mitochondrial inner membrane [IDA] mitochondrion [IDA]			404
Q9UDT6 UniProt NPD GO	CYLN2_HUMAN	Cytoplasmic linker protein 2 (Cytoplasmic linker protein 115) (CLIP-115) (Williams-Beuren syndrome c ...	0.87	-	nuc	0	Cytoplasm (By similarity). Associated with the cytoskeleton (By similarity)		194050	2CP3	1046
Q2KN93 UniProt NPD GO	CYTSA_BRARE	Cytospin-A	0.87	-	nuc	0					1132
Q2KN99 UniProt NPD GO	CYTSA_RAT	Cytospin-A	0.87	+	nuc	0					1118
Q6FLB2 UniProt NPD GO	DAM1_CANGA	DASH complex subunit DAM1 (Outer kinetochore protein DAM1)	0.87	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				307
Q758R8 UniProt NPD GO	SPC34_ASHGO	DASH complex subunit SPC34 (Outer kinetochore protein SPC34)	0.87	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				290
Q8K3G9 UniProt NPD GO	DP13B_MOUSE	DCC-interacting protein 13 beta (Dip13 beta) (Adapter protein containing PH domain, PTB domain and l ...	0.87	-	cyt	0	Endosome; early endosome; early endosomal membrane; peripheral membrane protein (By similarity). Nuc ...	cytoplasm [ISS] endosome membrane [ISS] nucleus [ISS]			662
Q84TG1 UniProt NPD GO	RH57_ARATH	DEAD-box ATP-dependent RNA helicase 57 (EC 3.6.1.-)	0.87	+	nuc	0					541
O88509 UniProt NPD GO	DNM3B_MOUSE	DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) (Dnmt3b) (DNA methyltransferase MmuIIIB) (DNA MT ...	0.87	-	nuc	0	Nucleus (Probable)	nuclear heterochromatin [IDA]		1KHC	859
O54788 UniProt NPD GO	DFFB_MOUSE	DNA fragmentation factor subunit beta (EC 3.-.-.-) (DNA fragmentation factor 40 kDa subunit) (DFF-40 ...	0.87	-	nuc	0	Cytoplasm. Nucleus			1V0D	344
Q99N34 UniProt NPD GO	DFFB_RAT	DNA fragmentation factor subunit beta (EC 3.-.-.-) (DNA fragmentation factor 40 kDa subunit) (DFF-40 ...	0.87	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IDA]			349
Q9LL84 UniProt NPD GO	DNL4_ARATH	DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4)	0.87	-	nuc	0	Nucleus (By similarity)				1219
Q9NPF5 UniProt NPD GO	DMAP1_HUMAN	DNA methyltransferase 1-associated protein 1 (DNMT1-associated protein 1) (DNMAP1)	0.87	-	nuc	0	Nucleus. Targeted to replication foci throughout S phase by DNMT1	nucleus [NAS]	605077		467
Q9QXE2 UniProt NPD GO	DPOLL_MOUSE	DNA polymerase lambda (EC 2.7.7.7) (EC 4.2.99.-) (Pol Lambda) (DNA polymerase kappa)	0.87	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			573
Q92889 UniProt NPD GO	ERCC4_HUMAN	DNA repair endonuclease XPF (EC 3.1.-.-) (DNA excision repair protein ERCC-4) (DNA-repair protein co ...	0.87	+	nuc	0	Nucleus (Probable)	nucleotide-excision repair complex [IDA]	133520	2A1J	905
P12753 UniProt NPD GO	RAD50_YEAST	DNA repair protein RAD50 (EC 3.6.-.-) (153 kDa protein)	0.87	-	nuc	0		mitochondrion [IDA] Mre11 complex [IPI] nucleus [IDA]			1312
P87074 UniProt NPD GO	RHP9_SCHPO	DNA repair protein rhp9 (RAD9 homolog)	0.87	-	nuc	0	Nucleus				778
P29458 UniProt NPD GO	MCM4_SCHPO	DNA replication licensing factor mcm4 (Minichromosome maintenance protein 4) (Cell division control ...	0.87	+	nuc	0	Nucleus	MCM complex [IDA]			931
P11387 UniProt NPD GO	TOP1_HUMAN	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.87	+	nuc	0			126420	1TL8	765
Q9WUL0 UniProt NPD GO	TOP1_RAT	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.87	+	nuc	0					767
Q85FM9 UniProt NPD GO	RPOC2_ADICA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.87	-	nuc	0	Plastid; chloroplast				1420

You are viewing entries 5501 to 5550 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.