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
Q9QZC2 UniProt NPD GO	PLXC1_MOUSE	Plexin-C1 precursor (Virus-encoded semaphorin protein receptor) (CD232 antigen)	0.69	-	end	2	Membrane; single-pass type I membrane protein (Potential)				1574
Q9H074 UniProt NPD GO	PAIP1_HUMAN	Polyadenylate-binding protein-interacting protein 1 (Poly(A)-binding protein-interacting protein 1) ...	0.69	-	nuc	0	Cytoplasm (Probable)	cytoplasm [TAS]	605184	1JH4	479
P70419 UniProt NPD GO	GALT3_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 3 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.69	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				633
Q9TSZ3 UniProt NPD GO	KCNH2_CANFA	Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit Kv11.1 ...	0.69	-	ves	4	Membrane; multi-pass membrane protein				1158
O08962 UniProt NPD GO	KCNH2_RAT	Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit Kv11.1 ...	0.69	-	nuc	4	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			1163
Q12809 UniProt NPD GO	KCNH2_HUMAN	Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit Kv11.1 ...	0.69	-	nuc	4	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	152427	1UJL	1159
Q9P1Z3 UniProt NPD GO	HCN3_HUMAN	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3	0.69	-	end	1	Membrane; multi-pass membrane protein				774
P45976 UniProt NPD GO	FIP1_YEAST	Pre-mRNA polyadenylation factor FIP1	0.69	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI]			327
Q9JKB8 UniProt NPD GO	PRP18_RAT	Pre-mRNA-splicing factor 18 (PRP18 homolog) (Potassium channel regulatory factor)	0.69	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with spliceosomal snRNPs (By simi ...				342
Q6C0E6 UniProt NPD GO	CWC15_YARLI	Pre-mRNA-splicing factor CWC15	0.69	-	mit	0	Nucleus (Probable)				215
Q4IB70 UniProt NPD GO	CWC21_GIBZE	Pre-mRNA-splicing factor CWC21	0.69	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				182
Q59LQ5 UniProt NPD GO	CWC25_CANAL	Pre-mRNA-splicing factor CWC25	0.69	-	nuc	0	Nucleus (By similarity)				221
Q6FL63 UniProt NPD GO	CWC26_CANGA	Pre-mRNA-splicing factor CWC26	0.69	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				235
Q23670 UniProt NPD GO	TOP2_CAEEL	Probable DNA topoisomerase 2 (EC 5.99.1.3) (DNA topoisomerase II)	0.69	+	nuc	0	Nucleus (By similarity)				1520
O61394 UniProt NPD GO	GALT6_CAEEL	Probable N-acetylgalactosaminyltransferase 6 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransfera ...	0.69	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				618
O14369 UniProt NPD GO	SCE3_SCHPO	Probable RNA-binding protein sce3	0.69	-	nuc	0	Cytoplasm				388
P82712 UniProt NPD GO	CCD1P_DROME	Probable cytochrome P450 12d1 proximal, mitochondrial precursor (EC 1.14.-.-) (CYPXIID1)	0.69	-	nuc	0	Mitochondrion (Potential)				521
Q9V559 UniProt NPD GO	CP4P3_DROME	Probable cytochrome P450 4p3 (EC 1.14.-.-) (CYPIVP3)	0.69	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				515
Q19262 UniProt NPD GO	EXOC3_CAEEL	Probable exocyst complex component 3 (Exocyst complex component Sec6)	0.69	-	cyt	0					796
P34607 UniProt NPD GO	MUT7_CAEEL	Probable exonuclease mut-7 (EC 3.1.-.-)	0.69	-	nuc	0		cytosol [IDA] nucleus [IDA]			910
Q6CJ06 UniProt NPD GO	NUF2_KLULA	Probable kinetochore protein NUF2	0.69	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				451
O43520 UniProt NPD GO	AT8B1_HUMAN	Probable phospholipid-transporting ATPase IC (EC 3.6.3.1) (Familial intrahepatic cholestasis type 1) ...	0.69	-	end	10	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602397		1251
Q12398 UniProt NPD GO	HMS1_YEAST	Probable transcription factor HMS1 (High-copy MEP suppressor protein 1)	0.69	-	nuc	0	Nucleus (Potential)				434
Q7YR36 UniProt NPD GO	PRR3_PANTR	Proline-rich protein 3 (MHC class I region proline-rich protein CAT56)	0.69	-	nuc	0					188
Q9NJ15 UniProt NPD GO	PCSK5_BRACL	Proprotein convertase subtilisin/kexin type 5 precursor (EC 3.4.21.-) (Proprotein convertase PC6-lik ...	0.69	+	exc	1	Isoform A, isoform C: Secreted protein. Isoform B: Cell membrane; single-pass type I membrane protei ...				1696
Q9N179 UniProt NPD GO	41_BOVIN	Protein 4.1 (Band 4.1) (P4.1) (4.1R)	0.69	+	nuc	0	Cytoplasm. Nucleus				617
Q9V8R9 UniProt NPD GO	41_DROME	Protein 4.1 homolog (Protein coracle)	0.69	+	nuc	0	Septate junction in the apical-lateral domain of epithelial cells during embryonic and imaginal disk ...	septate junction [IDA]			1698
Q96IL0 UniProt NPD GO	CN153_HUMAN	Protein C14orf153 precursor	0.69	-	nuc	0					193
Q12102 UniProt NPD GO	CFT2_YEAST	Protein CFT2 (Cleavage factor two protein 2) (105 kDa protein associated with polyadenylation factor ...	0.69	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI]			859
Q8C9H6 UniProt NPD GO	FA40B_MOUSE	Protein FAM40B	0.69	-	mit	0					844
Q8N2R8 UniProt NPD GO	FA43A_HUMAN	Protein FAM43A	0.69	-	nuc	0					423
Q562C7 UniProt NPD GO	K0020_RAT	Protein KIAA0020 homolog	0.69	+	nuc	0	Nucleus; nucleolus (By similarity)				647
Q92628 UniProt NPD GO	K0232_HUMAN	Protein KIAA0232 (Fragment)	0.69	-	exc	0					1402
P32488 UniProt NPD GO	MBR3_YEAST	Protein MBR3 (Increasing suppression factor 1) (Protein ISF1)	0.69	-	nuc	0					338
Q13438 UniProt NPD GO	OS9_HUMAN	Protein OS-9 precursor (Amplified in osteosarcoma 9)	0.69	-	nuc	1 *		soluble fraction [TAS]	609677		667
P42519 UniProt NPD GO	STAR_DROME	Protein Star	0.69	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to membrane [TAS] plasma membrane [IDA]			597
Q08465 UniProt NPD GO	YNG1_YEAST	Protein YNG1 (ING1 homolog 1)	0.69	-	nuc	0	Nucleus	histone acetyltransferase complex [IDA] nuclear nucleosome [TAS]			219
Q5R6Y2 UniProt NPD GO	CRBN_PONPY	Protein cereblon	0.69	-	nuc	0					429
Q56AP7 UniProt NPD GO	CRBN_RAT	Protein cereblon	0.69	-	nuc	0					445
P20480 UniProt NPD GO	NCD_DROME	Protein claret segregational	0.69	-	nuc	0		spindle [IDA]		2NCD	700
Q5TM51 UniProt NPD GO	PP1RB_MACMU	Protein phosphatase 1 regulatory subunit 11	0.69	+	nuc	0					126
Q7YR30 UniProt NPD GO	PP1RB_PANTR	Protein phosphatase 1 regulatory subunit 11	0.69	+	nuc	0					126
O60927 UniProt NPD GO	PP1RB_HUMAN	Protein phosphatase 1 regulatory subunit 11 (Protein phosphatase inhibitor 3) (Hemochromatosis candi ...	0.69	+	nuc	0		soluble fraction [TAS]	606670		126
P14199 UniProt NPD GO	REF2P_DROME	Protein ref(2)P (Refractory to sigma P)	0.69	-	nuc	0	Nucleus (Potential)				599
P14906 UniProt NPD GO	SEC63_YEAST	Protein translocation protein SEC63 (Sec62/63 complex 73 kDa subunit) (Protein NPL1)	0.69	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Nucleus; nuclear ...	endoplasmic reticulum membrane [TAS] mitochondrion [IDA] Sec62/Sec63 complex [IPI]			663
Q6BKU3 UniProt NPD GO	SEC9_DEBHA	Protein transport protein SEC9	0.69	-	nuc	0					490
P54779 UniProt NPD GO	USP_MANSE	Protein ultraspiracle homolog	0.69	+	nuc	0	Nucleus				461
P52735 UniProt NPD GO	VAV2_HUMAN	Protein vav-2	0.69	-	cyt	0			600428		878
P12841 UniProt NPD GO	FOS_RAT	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.69	+	nuc	0	Nucleus				380
P54100 UniProt NPD GO	VAV_RAT	Proto-oncogene vav (p95)	0.69	-	mit	0					843

You are viewing entries 14401 to 14450 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.