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
Q9V726 UniProt NPD GO	CPSF1_DROME	Cleavage and polyadenylation specificity factor 160 kDa subunit (CPSF 160 kDa subunit) (CPSF-160) (d ...	0.33	-	cyt	0	Nucleus (By similarity)				1455
Q8HXM1 UniProt NPD GO	CSTF2_BOVIN	Cleavage stimulation factor 64 kDa subunit (CSTF 64 kDa subunit) (CF-1 64 kDa subunit) (CstF-64)	0.33	-	nuc	0	Nucleus (By similarity)				572
Q9H0L4 UniProt NPD GO	CSTFT_HUMAN	Cleavage stimulation factor 64 kDa subunit, tau variant (CSTF 64 kDa subunit, tau variant) (CF-1 64 ...	0.33	-	nuc	0	Nucleus (By similarity)				616
Q8VBZ3 UniProt NPD GO	CLPT1_MOUSE	Cleft lip and palate transmembrane protein 1 homolog (Thymic epithelial cell surface antigen)	0.33	-	end	5	Membrane; multi-pass membrane protein (Potential)	aspartate carbamoyltransferase complex [RCA] integral to membrane [RCA]			664
Q4QXT9 UniProt NPD GO	FA10_TROCA	Coagulation factor X precursor (EC 3.4.21.6) [Contains: Factor X light chain; Factor X heavy chain; ...	0.33	-	exc	0					483
Q9XSJ7 UniProt NPD GO	CO1A1_CANFA	Collagen alpha-1(I) chain precursor	0.33	-	exc	0					1460
P05539 UniProt NPD GO	CO2A1_RAT	Collagen alpha-1(II) chain precursor [Contains: Chondrocalcin]	0.33	-	exc	0		collagen type II [TAS]			1419
Q9N281 UniProt NPD GO	COHA1_CANFA	Collagen alpha-1(XVII) chain (Bullous pemphigoid antigen 2) (180 kDa bullous pemphigoid antigen 2) ( ...	0.33	-	nuc	1	Membrane; single-pass type II membrane protein (By similarity)				709
O89103 UniProt NPD GO	C1QR1_MOUSE	Complement component C1q receptor precursor (Complement component 1 q subcomponent receptor 1) (C1qR ...	0.33	-	exc	1	Membrane; single-pass type I membrane protein	cytoplasmic membrane-bound vesicle [IDA] integral to membrane [ISS] plasma membrane [IDA]			644
Q03591 UniProt NPD GO	FHR1_HUMAN	Complement factor H-related protein 1 precursor (FHR-1) (H factor-like protein 1) (H-factor-like 1) ...	0.33	-	exc	0	Secreted protein	extracellular space [TAS]	134371		330
P84088 UniProt NPD GO	CPLX2_BOVIN	Complexin-2 (Complexin II) (CPX II) (Synaphin-1)	0.33	-	nuc	0	Cytoplasm; cytosol. Enriched at synaptic-releasing sites in mature neurons (By similarity)				134
Q6PUV4 UniProt NPD GO	CPLX2_HUMAN	Complexin-2 (Complexin II) (CPX II) (Synaphin-1)	0.33	-	nuc	0	Cytoplasm; cytosol. Enriched at synaptic-releasing sites in mature neurons (By similarity)		605033		134
P84087 UniProt NPD GO	CPLX2_RAT	Complexin-2 (Complexin II) (CPX II) (Synaphin-1)	0.33	-	nuc	0	Cytoplasm; cytosol. Enriched at synaptic-releasing sites in mature neurons. In mast cells, cytosol a ...				134
P84086 UniProt NPD GO	CPLX2_MOUSE	Complexin-2 (Complexin II) (CPX II) (Synaphin-1) (921-L)	0.33	-	nuc	0	Cytoplasm; cytosol. Enriched at synaptic-releasing sites in mature neurons				134
P07231 UniProt NPD GO	CXKG_CONGE	Conantokin-G precursor (Con-G) (Conotoxin GV) (Sleeper peptide) (CGX-1007)	0.33	-	exc	0	Secreted protein			1ONU	100
Q5K0D5 UniProt NPD GO	CXO15_CONST	Conotoxin-15 precursor	0.33	-	exc	1 *	Secreted protein (By similarity)				72
P59108 UniProt NPD GO	CPNE2_MOUSE	Copine-2 (Copine II)	0.33	-	cyt	0					548
Q8JZW4 UniProt NPD GO	CPNE5_MOUSE	Copine-5 (Copine V)	0.33	-	cyt	0					593
O13923 UniProt NPD GO	CORO_SCHPO	Coronin-like protein crn1	0.33	-	nuc	0		actin cortical patch [IDA] contractile ring (sensu Fungi) [IDA]			601
P48132 UniProt NPD GO	RR2_CYAPA	Cyanelle 30S ribosomal protein S2	0.33	-	cyt	0	Plastid; cyanelle				233
Q90980 UniProt NPD GO	CNG3_CHICK	Cyclic nucleotide-gated channel rod photoreceptor subunit alpha (CNG channel 3) (CNG-3) (CNG3)	0.33	+	nuc	4	Membrane; multi-pass membrane protein				645
P47827 UniProt NPD GO	CCNA2_XENLA	Cyclin-A2	0.33	-	mit	0					415
P55168 UniProt NPD GO	CCNC_CHICK	Cyclin-C	0.33	-	nuc	0	Nucleus (By similarity)				283
P49119 UniProt NPD GO	CDKA1_MESAU	Cyclin-dependent kinase 2-associated protein 1 (CDK2-associated protein 1) (Putative oral cancer sup ...	0.33	-	nuc	0					114
O35207 UniProt NPD GO	CDKA1_MOUSE	Cyclin-dependent kinase 2-associated protein 1 (CDK2-associated protein 1) (Putative oral cancer sup ...	0.33	-	nuc	0					114
P38675 UniProt NPD GO	MET7_NEUCR	Cystathionine gamma-synthase (EC 2.5.1.48) (O-succinylhomoserine (thiol)-lyase)	0.33	-	nuc	0					542
Q99JA4 UniProt NPD GO	CLTR1_MOUSE	Cysteinyl leukotriene receptor 1 (CysLTR1) (Cysteinyl leukotriene D4 receptor) (LTD4 receptor)	0.33	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			352
Q6GML1 UniProt NPD GO	CMAH_BRARE	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.33	-	nuc	0	Cytoplasm (By similarity)				591
P10612 UniProt NPD GO	CP11A_PIG	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(scc)) (Cholesterol side ...	0.33	-	mit	0	Mitochondrion				520
Q8HYN1 UniProt NPD GO	CP17A_PANTR	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.33	-	end	0					508
Q00557 UniProt NPD GO	CP1A1_MESAU	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1) (P-450MC)	0.33	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				524
P00184 UniProt NPD GO	CP1A1_MOUSE	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1) (P450-P1)	0.33	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			524
P56592 UniProt NPD GO	CP1A2_CANFA	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2) (DAH2) (Cytochrome P450-D2)	0.33	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				511
Q8WNW0 UniProt NPD GO	CP21A_CANFA	Cytochrome P450 21 (EC 1.14.99.10) (Cytochrome P450 XXI) (Steroid 21-hydroxylase) (21-OHase) (P450-C ...	0.33	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				492
P03940 UniProt NPD GO	CP21A_MOUSE	Cytochrome P450 21 (EC 1.14.99.10) (Cytochrome P450 XXI) (Steroid 21-hydroxylase) (21-OHase) (P450-C ...	0.33	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				487
P17178 UniProt NPD GO	CP27A_RAT	Cytochrome P450 27, mitochondrial precursor (EC 1.14.13.15) (Cytochrome P-450C27/25) (Sterol 26-hydr ...	0.33	-	nuc	0	Mitochondrion				533
P24454 UniProt NPD GO	CP2A8_MESAU	Cytochrome P450 2A8 (EC 1.14.14.1) (CYPIIA8) (P450-MC1) (P450-AFB)	0.33	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				494
P11510 UniProt NPD GO	CP2CC_RAT	Cytochrome P450 2C12, female-specific (EC 1.14.14.1) (CYPIIC12) (P450I) (15-beta) (P450-UT-I) (UT-1) ...	0.33	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P33267 UniProt NPD GO	CP2F2_MOUSE	Cytochrome P450 2F2 (EC 1.14.14.-) (CYPIIF2) (Naphthalene dehydrogenase) (Naphthalene hydroxylase) ( ...	0.33	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				491
Q9PVE8 UniProt NPD GO	C330_FUNHE	Cytochrome P450 3A30 (EC 1.14.14.1) (CYPIIIA30)	0.33	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				496
P11707 UniProt NPD GO	CP3A6_RABIT	Cytochrome P450 3A6 (EC 1.14.14.1) (CYPIIIA6) (P450-3C)	0.33	+	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]			501
Q64462 UniProt NPD GO	CP4B1_MOUSE	Cytochrome P450 4B1 (EC 1.14.14.1) (CYPIVB1)	0.33	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				511
P15129 UniProt NPD GO	CP4B1_RAT	Cytochrome P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-isozyme 5) (P450 L-2)	0.33	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				510
P29981 UniProt NPD GO	CP4C1_BLADI	Cytochrome P450 4C1 (EC 1.14.14.1) (CYPIVC1)	0.33	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				511
P30611 UniProt NPD GO	CP52N_CANTR	Cytochrome P450 52B1 (EC 1.14.14.-) (CYPLIIB1) (Alkane-inducible P450-ALK6)	0.33	-	cyt	0					506
Q9T0K0 UniProt NPD GO	C71AJ_ARATH	Cytochrome P450 71A19 (EC 1.14.-.-)	0.33	-	nuc	2 *					490
P37123 UniProt NPD GO	C77A1_SOLME	Cytochrome P450 77A1 (EC 1.14.-.-) (CYPLXXVIIA1) (P-450EG6) (Fragment)	0.33	-	mit	0					499
Q9Y6N1 UniProt NPD GO	COX11_HUMAN	Cytochrome c oxidase assembly protein COX11, mitochondrial precursor	0.33	-	cyt	1	Mitochondrion	mitochondrion [TAS]	603648		276
Q4P821 UniProt NPD GO	COX19_USTMA	Cytochrome c oxidase assembly protein COX19	0.33	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial intermembrane space (By similarity)				197
Q5R686 UniProt NPD GO	CLR59_PONPY	Cytoplasmic linker protein 170-related 59 kDa protein (CLIPR-59) (CLIP-170-related 59 kDa protein)	0.33	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi stack. Localized to Golgi stacks as well as on tubulovesicular ele ...				547

You are viewing entries 37451 to 37500 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.