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
P09006 UniProt NPD GO	CPI6_RAT	Contrapsin-like protease inhibitor 6 precursor (CPI-26) (Serine protease inhibitor 3) (SPI-3) (SPI-2 ...	0.26	-	end	0	Secreted protein (By similarity)				418
Q8C166 UniProt NPD GO	CPNE1_MOUSE	Copine-1 (Copine I)	0.26	-	mit	0					536
P35055 UniProt NPD GO	HEM6_SOYBN	Coproporphyrinogen III oxidase, chloroplast precursor (EC 1.3.3.3) (Coproporphyrinogenase) (Coprogen ...	0.26	-	mit	0	Plastid; chloroplast (Probable)				385
Q9LR75 UniProt NPD GO	HEM6_ARATH	Coproporphyrinogen III oxidase, chloroplast precursor (EC 1.3.3.3) (Coproporphyrinogenase) (Coprogen ...	0.26	-	mit	0	Plastid; chloroplast (Probable)				386
P07468 UniProt NPD GO	DEF2_RABIT	Corticostatin-2 (Corticostatin II) (CS-II) (Neutrophil antibiotic peptide NP-3B) (Microbicidal pepti ...	0.26	-	nuc	0	Secreted protein				34
P50233 UniProt NPD GO	DHI2_RAT	Corticosteroid 11-beta-dehydrogenase isozyme 2 (EC 1.1.1.-) (11-DH2) (11-beta-hydroxysteroid dehydro ...	0.26	-	mit	0	Microsome				400
Q75WS4 UniProt NPD GO	CRYD_XENLA	Cryptochrome DASH	0.26	-	cyt	0					523
Q9GSA4 UniProt NPD GO	CORZ_GALME	Crz precursor [Contains: Corazonin; Corazonin-precursor-related peptide (CPRP)]	0.26	-	nuc	0	Secreted protein	extracellular region [ISS]			113
P18834 UniProt NPD GO	COL14_CAEEL	Cuticle collagen 14	0.26	-	nuc	1 *		extracellular region [NAS]			345
P55934 UniProt NPD GO	CNG_ICTPU	Cyclic nucleotide-gated cation channel	0.26	-	end	4	Membrane; multi-pass membrane protein (Potential)				682
Q61456 UniProt NPD GO	CCNA1_MOUSE	Cyclin-A1	0.26	-	cyt	0	Spindle. In oocytes at least, it associates with the spindle during metaphase				421
Q8WYN0 UniProt NPD GO	ATG4A_HUMAN	Cysteine protease ATG4A (EC 3.4.22.-) (Autophagy-related protein 4 homolog A) (hAPG4A) (Autophagin-2 ...	0.26	-	cyt	0	Cytoplasm (Probable)	cytoplasm [ISS] cytosol [ISS] microtubule associated complex [ISS]			398
Q8MJC6 UniProt NPD GO	CMAH_PONPY	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.26	-	cyt	0	Cytoplasm (By similarity)				585
Q9Y471 UniProt NPD GO	CMAH_HUMAN	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase-like protein (CMP-NeuAc hydroxylase-like ...	0.26	-	cyt	0		cytoplasm [TAS]	603209		486
P98181 UniProt NPD GO	CP1A1_PAGMA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.26	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				515
Q9VWR5 UniProt NPD GO	CP306_DROME	Cytochrome P450 306a1 (EC 1.14.-.-) (CYPCCCVIA1) (Phantom protein) (Dmphm)	0.26	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [IDA]			574
Q9UVC3 UniProt NPD GO	CP51_CUNEL	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Lanosterol 14- ...	0.26	-	mit	1 *					512
P10614 UniProt NPD GO	CP51_YEAST	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Lanosterol 14- ...	0.26	-	nuc	2 *		endoplasmic reticulum [IDA]			530
Q9LTM3 UniProt NPD GO	C71BK_ARATH	Cytochrome P450 71B20 (EC 1.14.-.-)	0.26	-	mit	1 *					502
Q6FR37 UniProt NPD GO	CTM1_CANGA	Cytochrome c lysine N-methyltransferase 1 (EC 2.1.1.59)	0.26	-	nuc	0	Cytoplasm; cytosol (By similarity)				551
Q3E731 UniProt NPD GO	COX19_YEAST	Cytochrome c oxidase assembly protein COX19	0.26	-	nuc	0	Cytoplasm. Mitochondrion; mitochondrial intermembrane space	cytosol [IDA] mitochondrial intermembrane space [IDA]			98
P29873 UniProt NPD GO	COX2_EXERO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.26	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				224
Q96KJ9 UniProt NPD GO	COX42_HUMAN	Cytochrome c oxidase subunit 4 isoform 2, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.26	-	mit	1	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [IC]	607976		171
P00125 UniProt NPD GO	CY1_BOVIN	Cytochrome c1, heme protein, mitochondrial precursor (Cytochrome c-1)	0.26	-	mit	1	Mitochondrion; mitochondrial intermembrane space			3BCC	325
Q12627 UniProt NPD GO	DLD1_KLULA	D-lactate dehydrogenase [cytochrome], mitochondrial precursor (EC 1.1.2.4) (D-lactate ferricytochrom ...	0.26	-	mit	0	Mitochondrion; mitochondrial matrix				576
Q9JII5 UniProt NPD GO	DAZP1_MOUSE	DAZ-associated protein 1 (Deleted in azoospermia-associated protein 1)	0.26	-	nuc	0	Cytoplasm. Predominantly. Nucleus. Nuclear at some stages of spermatozoides development. In midpachy ...	cytoplasm [IDA]			406
Q8BZJ7 UniProt NPD GO	DCNL2_MOUSE	DCN1-like protein 2 (Defective in cullin neddylation protein 1-like protein 2) (DCUN1 domain-contain ...	0.26	-	cyt	0					258
Q944S1 UniProt NPD GO	RH22_ARATH	DEAD-box ATP-dependent RNA helicase 22 (EC 3.6.1.-)	0.26	-	mit	0					581
Q9SLH3 UniProt NPD GO	RGA_ARATH	DELLA protein RGA (Repressor on the ga1-3 mutant) (GAI-related sequence) (Restoration of growth on a ...	0.26	-	mit	0	Nucleus	nucleus [TAS]			587
Q9LF53 UniProt NPD GO	RGL3_ARATH	DELLA protein RGL3 (RGA-like protein 3)	0.26	-	cyt	0	Nucleus (By similarity)	nucleus [TAS]			523
Q06624 UniProt NPD GO	RHC31_YEAST	DNA damage tolerance protein RHC31 (RAD31 homolog)	0.26	-	cyt	0		nucleus [IDA]			347
Q5XXB5 UniProt NPD GO	MSH2_CERAE	DNA mismatch repair protein Msh2 (MutS protein homolog 2)	0.26	-	nuc	0	Nucleus (Potential)				933
Q6FXJ8 UniProt NPD GO	DPB3_CANGA	DNA polymerase epsilon subunit C (EC 2.7.7.7) (DNA polymerase II subunit C)	0.26	-	nuc	0	Nucleus (By similarity)				255
P49005 UniProt NPD GO	DPOD2_HUMAN	DNA polymerase subunit delta 2 (EC 2.7.7.7) (DNA polymerase subunit delta p50)	0.26	-	mit	0	Nucleus	nucleus [TAS]	600815		469
P20664 UniProt NPD GO	PRI1_MOUSE	DNA primase small subunit (EC 2.7.7.-) (DNA primase 49 kDa subunit) (p49)	0.26	-	cyt	0					417
Q67EU8 UniProt NPD GO	R51A1_MAIZE	DNA repair protein RAD51 homolog A (Rad51-like protein A) (RAD51A) (ZmRAD51a)	0.26	-	cyt	0	Nucleus				340
Q9Y248 UniProt NPD GO	PSF2_HUMAN	DNA replication complex GINS protein PSF2	0.26	-	cyt	0	Nucleus (By similarity)				185
P42552 UniProt NPD GO	S1FA_SPIOL	DNA-binding protein S1FA	0.26	-	nuc	1 *	Nucleus (Probable)				70
P42551 UniProt NPD GO	S1FA1_ARATH	DNA-binding protein S1FA1	0.26	-	nuc	1 *	Nucleus (Probable)				76
P36958 UniProt NPD GO	RPB9_DROME	DNA-directed RNA polymerase II 15.1 kDa polypeptide (EC 2.7.7.6)	0.26	-	nuc	0	Nucleus				129
Q64029 UniProt NPD GO	XPA_CRIGR	DNA-repair protein complementing XP-A cells homolog (Xeroderma pigmentosum group A complementing pro ...	0.26	-	nuc	0	Nucleus (By similarity)				97
P17534 UniProt NPD GO	DEFR2_MOUSE	Defensin-related cryptdin, related sequence 2 precursor (Cryptdin-related protein 4C-1) (CRS4C) (CRS ...	0.26	-	exc	0	Secreted protein				91
P22912 UniProt NPD GO	DH16C_ORYSA	Dehydrin Rab16C	0.26	-	nuc	0					164
O80458 UniProt NPD GO	DDPS1_ARATH	Dehydrodolichyl diphosphate synthase 1 (EC 2.5.1.-) (Dedol-PP synthase 1)	0.26	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				303
Q4JK73 UniProt NPD GO	DHRS8_MACFA	Dehydrogenase/reductase SDR family member 8 precursor (EC 1.1.1.-) (17-beta-hydroxysteroid dehydroge ...	0.26	-	mit	0	Secreted protein (Potential)				300
Q13117 UniProt NPD GO	DAZ2_HUMAN	Deleted in azoospermia protein 2	0.26	-	cyt	0	Cytoplasm. Predominantly. Nucleus. Nuclear at some stages of spermatozoide development. Localizes bo ...		415000		558
Q6DFN7 UniProt NPD GO	DENR_XENTR	Density-regulated protein (DRP)	0.26	-	cyt	0					200
P49184 UniProt NPD GO	DNSL1_HUMAN	Deoxyribonuclease I-like 1 precursor (EC 3.1.21.-) (DNase I-like 1) (Muscle-specific DNase I-like) ( ...	0.26	-	exc	0	Endoplasmic reticulum		300081		302
Q5E9D5 UniProt NPD GO	DEST_BOVIN	Destrin (Actin-depolymerizing factor) (ADF)	0.26	+	cyt	0					164
P60981 UniProt NPD GO	DEST_HUMAN	Destrin (Actin-depolymerizing factor) (ADF)	0.26	+	cyt	0			609114		164

You are viewing entries 44101 to 44150 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.)

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