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
P02466 UniProt NPD GO	CO1A2_RAT	Collagen alpha-2(I) chain precursor	0.25	-	exc	0				1YGV	1372
P15988 UniProt NPD GO	CO6A2_CHICK	Collagen alpha-2(VI) chain precursor	0.25	-	exc	0					1022
P53420 UniProt NPD GO	CO4A4_HUMAN	Collagen alpha-4(IV) chain precursor	0.25	-	nuc	0	Cell surface (Potential)	collagen type IV [IDA]	203780		1690
P00976 UniProt NPD GO	IBPC_BOVIN	Colostrum trypsin inhibitor (Colostrum BPI)	0.25	-	nuc	0	Secreted protein				67
Q8WVH0 UniProt NPD GO	CPLX3_HUMAN	Complexin-3 (Complexin III) (CPX III)	0.25	-	nuc	0	Membrane; lipid-anchor. Enriched at the synaptic terminal (By similarity)		609585		158
Q9Z140 UniProt NPD GO	CPNE6_MOUSE	Copine-6 (Copine VI) (Neuronal-copine) (N-copine)	0.25	-	cyt	0		axon [IDA] dendrite [IDA] membrane fraction [IDA]			557
O94722 UniProt NPD GO	CTR4_SCHPO	Copper transport protein ctr4 (Copper transporter 4)	0.25	-	mit	3	Membrane; multi-pass membrane protein				289
Q9XT50 UniProt NPD GO	ATP7B_SHEEP	Copper-transporting ATPase 2 (EC 3.6.3.4) (Copper pump 2) (Wilson disease-associated protein homolog ...	0.25	-	end	7	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein (By ...				1505
Q63532 UniProt NPD GO	SPR1A_RAT	Cornifin A (Small proline-rich protein 1A) (SPR1A) (SPRR1)	0.25	-	nuc	0	Cytoplasm				152
P35324 UniProt NPD GO	SPRR1_RABIT	Cornifin alpha (Small proline-rich protein I) (SPR-I)	0.25	-	nuc	0	Cytoplasm				126
P50168 UniProt NPD GO	DHI2_SHEEP	Corticosteroid 11-beta-dehydrogenase isozyme 2 (EC 1.1.1.-) (11-DH2) (11-beta-hydroxysteroid dehydro ...	0.25	-	nuc	0	Microsome				427
Q91653 UniProt NPD GO	CRHBP_XENLA	Corticotropin-releasing factor-binding protein precursor (CRF-binding protein) (CRF-BP) (Corticotrop ...	0.25	-	end	0					321
Q9TTK8 UniProt NPD GO	KCRU_BOVIN	Creatine kinase, ubiquitous mitochondrial precursor (EC 2.7.3.2) (U-MtCK) (Mia-CK) (Acidic-type mito ...	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane. Outer side (By similarity)				416
Q94676 UniProt NPD GO	CHH3_PENJP	Crustacean hyperglycemic hormones 3 precursor (Pej-SGP-III) [Contains: CHH precursor-related peptide ...	0.25	-	exc	0	Secreted protein				117
O60676 UniProt NPD GO	CST8_HUMAN	Cystatin-related epididymal spermatogenic protein precursor (Cystatin-8)	0.25	-	nuc	0	Secreted protein				142
P22497 UniProt NPD GO	CYSP_THEPA	Cysteine proteinase precursor (EC 3.4.22.-)	0.25	-	cyt	1 *					440
O42196 UniProt NPD GO	CSP_XENLA	Cysteine string protein (CSP) (Xcsp)	0.25	-	nuc	0	Membrane; lipid-anchor (By similarity)				197
P16562 UniProt NPD GO	CRIS2_HUMAN	Cysteine-rich secretory protein 2 precursor (CRISP-2) (Testis-specific protein TPX-1)	0.25	-	exc	0	Secreted protein (Probable)	extracellular space [TAS]	187430	2CQ7	243
P79845 UniProt NPD GO	CRVP_TRIMU	Cysteine-rich venom protein precursor (TM-CRVP)	0.25	-	exc	0	Secreted protein				240
Q61419 UniProt NPD GO	CMAH_MOUSE	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase precursor (EC 1.14.18.2) (CMP-N-acetylneu ...	0.25	-	cyt	0	Cytoplasm. Isoform 2: Endoplasmic reticulum (Probable)	cytoplasm [IDA]			577
Q07217 UniProt NPD GO	CP11A_ONCMY	Cytochrome P450 11A1, mitochondrial precursor (EC 1.14.15.6) (CYPXIA1) (P450(SCC)) (Cholesterol side ...	0.25	-	mit	0	Mitochondrion				514
Q9N0U7 UniProt NPD GO	CP17A_CAPHI	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.25	-	mit	0					509
Q29497 UniProt NPD GO	CP17A_SHEEP	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.25	-	mit	0					509
Q3LFT9 UniProt NPD GO	CP1A2_BALAC	Cytochrome P450 1A2 (EC 1.14.14.1) (CYPIA2)	0.25	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				515
Q9NR63 UniProt NPD GO	CP26B_HUMAN	Cytochrome P450 26B1 (EC 1.14.-.-) (P450 26A2) (P450 retinoic acid-inactivating 2) (P450RAI-2) (Reti ...	0.25	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)	endoplasmic reticulum [NAS] microsome [NAS]	605207		512
P15392 UniProt NPD GO	CP2A4_MOUSE	Cytochrome P450 2A4 (EC 1.14.14.1) (CYPIIA4) (Testosterone 15-alpha-hydroxylase) (P450-15-alpha) (P4 ...	0.25	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			494
P24455 UniProt NPD GO	CP2A9_MESAU	Cytochrome P450 2A9 (EC 1.14.14.1) (CYPIIA9) (P450-MC1-R) (Testosterone 7-alpha-hydroxylase)	0.25	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				493
P00178 UniProt NPD GO	CP2B4_RABIT	Cytochrome P450 2B4 (EC 1.14.14.1) (CYPIIB4) (P450-LM2) (Isozyme 2) (P450 types B0 and B1)	0.25	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein			2BDM	491
P00180 UniProt NPD GO	CP2C1_RABIT	Cytochrome P450 2C1 (EC 1.14.14.1) (CYPIIC1) (P-450 IIC1) (P450 PBC1)	0.25	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
Q08078 UniProt NPD GO	CP2CP_MESAU	Cytochrome P450 2C25 (EC 1.14.14.1) (CYPIIC25) (P450 HSM1)	0.25	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
Q9QUJ1 UniProt NPD GO	CP2DS_MESAU	Cytochrome P450 2D28 (EC 1.14.14.-) (CYPIID28)	0.25	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				500
P13108 UniProt NPD GO	CP2D4_RAT	Cytochrome P450 2D4 (EC 1.14.14.1) (CYPIID4) (P450-DB4) (P450-CMF3) (Debrisoquine 4-hydroxylase)	0.25	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
Q98T91 UniProt NPD GO	C340_ORYLA	Cytochrome P450 3A40 (EC 1.14.14.1)	0.25	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				502
P33269 UniProt NPD GO	CP4D1_DROME	Cytochrome P450 4d1 (EC 1.14.-.-) (CYPIVD1)	0.25	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				512
O16805 UniProt NPD GO	CP4D1_DROSI	Cytochrome P450 4d1 (EC 1.14.-.-) (CYPIVD1)	0.25	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				512
Q12589 UniProt NPD GO	CP52K_CANMA	Cytochrome P450 52A11 (EC 1.14.14.-) (CYPLIIA11) (Alkane-inducible P450-ALK8)	0.25	-	cyt	1 *					519
Q9SAE3 UniProt NPD GO	C71BS_ARATH	Cytochrome P450 71B28 (EC 1.14.-.-)	0.25	-	end	0					490
Q43250 UniProt NPD GO	C71C1_MAIZE	Cytochrome P450 71C1 (EC 1.14.-.-) (Benzoxazineless 4)	0.25	-	vac	0					535
P30815 UniProt NPD GO	COX4_DICDI	Cytochrome c oxidase subunit 4, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase polypepti ...	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane				148
Q4PBY6 UniProt NPD GO	CCPR_USTMA	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.25	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				398
P53701 UniProt NPD GO	CCHL_HUMAN	Cytochrome c-type heme lyase (EC 4.4.1.17) (CCHL) (Holocytochrome c-type synthase)	0.25	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)	mitochondrial inner membrane [TAS] mitochondrion [IDA]	300056		268
Q8R1Q8 UniProt NPD GO	DC1L1_MOUSE	Cytoplasmic dynein 1 light intermediate chain 1 (Dynein light intermediate chain 1, cytosolic) (Dyne ...	0.25	-	cyt	0					523
Q5NBJ3 UniProt NPD GO	GYRB_ORYSA	DNA gyrase subunit B, chloroplast/mitochondrial precursor (EC 5.99.1.3)	0.25	-	mit	0	Plastid; chloroplast (Potential). Mitochondrion (Potential)				729
P42553 UniProt NPD GO	S1FA1_ORYSA	DNA-binding protein S1FA1	0.25	-	nuc	1 *	Nucleus (Probable)				76
Q42337 UniProt NPD GO	S1FA2_ARATH	DNA-binding protein S1FA2	0.25	-	nuc	1 *	Nucleus (Probable)				76
Q38859 UniProt NPD GO	RPO2J_ARATH	DNA-directed RNA polymerase II subunit J (EC 2.7.7.6) (DNA-directed RNA polymerase II 13.6 kDa polyp ...	0.25	-	cyt	0	Nucleus				116
P56298 UniProt NPD GO	RPOA_CHLVU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.25	-	cyt	0	Plastid; chloroplast				278
Q01523 UniProt NPD GO	DEF5_HUMAN	Defensin 5 precursor (Defensin, alpha 5)	0.25	-	exc	0	Secreted protein		600472		94
P50709 UniProt NPD GO	DEF11_MOUSE	Defensin-related cryptdin 11 precursor (Fragment)	0.25	-	exc	0	Secreted protein				85
P12949 UniProt NPD GO	DHN4_HORVU	Dehydrin DHN4 (B18)	0.25	-	cyt	0					225

You are viewing entries 45101 to 45150 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.