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
Q23126 UniProt NPD GO	TRMB_CAEEL	Probable tRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) (tRNA(m7G46)-methyltransferase)	0.12	-	cyt	0					256
Q7LKV3 UniProt NPD GO	SEN15_SCHPO	Probable tRNA-splicing endonuclease subunit sen15 (tRNA-intron endonuclease sen15)	0.12	-	cyt	0					143
P56288 UniProt NPD GO	EI2BG_SCHPO	Probable translation initiation factor eIF-2B subunit gamma (eIF-2B GDP-GTP exchange factor subunit ...	0.12	-	cyt	0					468
Q9NAE2 UniProt NPD GO	HUTU_CAEEL	Probable urocanate hydratase (EC 4.2.1.49) (Urocanase) (Imidazolonepropionate hydrolase)	0.12	-	nuc	0					731
Q38911 UniProt NPD GO	XTH15_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 15 precursor (EC 2.4.1.207) (At-XTH15) (X ...	0.12	-	end	1 *	Secreted protein; extracellular space; apoplast (Probable)				289
Q9ZV40 UniProt NPD GO	XTH21_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 21 precursor (EC 2.4.1.207) (At-XTH21) (X ...	0.12	-	exc	1 *	Secreted protein; extracellular space; apoplast (Probable)				305
Q9UKZ9 UniProt NPD GO	PCOC2_HUMAN	Procollagen C-endopeptidase enhancer 2 precursor (Procollagen COOH-terminal proteinase enhancer 2) ( ...	0.12	-	mit	0	Secreted protein (Probable)		607064		415
Q6TCG5 UniProt NPD GO	PAQR6_MOUSE	Progestin and adipoQ receptor family member 6 (Progestin and adipoQ receptor family member VI)	0.12	-	end	4	Membrane; multi-pass membrane protein (Potential)				343
Q8UW80 UniProt NPD GO	GON1_VERMO	Progonadoliberin-1 precursor (Progonadoliberin I) (Seabream-type gonadotropin-releasing hormone) (Sb ...	0.12	-	mit	0	Secreted protein	extracellular region [ISS]			96
Q90Y63 UniProt NPD GO	GON1_RANCA	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (LHRH ...	0.12	-	gol	1 *	Secreted protein	extracellular region [NAS]			90
P13562 UniProt NPD GO	GON1_MOUSE	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.12	-	exc	0	Secreted protein				90
O61667 UniProt NPD GO	EGL1_CAEEL	Programmed cell death activator egl-1 (Egg-laying defective protein 1)	0.12	-	nuc	0				1TY4	106
P46718 UniProt NPD GO	PDCD2_MOUSE	Programmed cell death protein 2 (Zinc finger protein Rp-8)	0.12	-	cyt	0	Nucleus (Potential)				343
P58366 UniProt NPD GO	ANKH_RAT	Progressive ankylosis protein homolog (ANK)	0.12	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [ISS] outer membrane [ISS]			492
P58367 UniProt NPD GO	ANKH_XENLA	Progressive ankylosis protein homolog (ANK)	0.12	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [ISS] outer membrane [ISS]			492
Q9WUQ2 UniProt NPD GO	PREB_MOUSE	Prolactin regulatory element-binding protein (Mammalian guanine nucleotide exchange factor mSec12)	0.12	-	cyt	2	Nucleus (By similarity). Membrane; single-pass membrane protein. Endoplasmic reticulum				417
Q9WTV0 UniProt NPD GO	PREB_RAT	Prolactin regulatory element-binding protein (Mammalian guanine nucleotide exchange factor mSec12)	0.12	-	cyt	2	Nucleus. Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				417
P55751 UniProt NPD GO	PRL1_ALLMI	Prolactin-1 (Prolactin I) (PRL-I)	0.12	-	cyt	0	Secreted protein				199
P55753 UniProt NPD GO	PRL1_CRONO	Prolactin-1 (Prolactin I) (PRL-I)	0.12	-	cyt	0	Secreted protein				199
P55754 UniProt NPD GO	PRL2_CRONO	Prolactin-2 (Prolactin II) (PRL-II)	0.12	-	cyt	0	Secreted protein				199
P18248 UniProt NPD GO	PCNA_XENLA	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.12	-	cyt	0	Nucleus				261
Q20065 UniProt NPD GO	P4HA2_CAEEL	Prolyl 4-hydroxylase alpha-2 subunit precursor (EC 1.14.11.2) (4-PH alpha-2) (Procollagen-proline,2- ...	0.12	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				539
Q60716 UniProt NPD GO	P4HA2_MOUSE	Prolyl 4-hydroxylase alpha-2 subunit precursor (EC 1.14.11.2) (4-PH alpha-2) (Procollagen-proline,2- ...	0.12	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				537
Q61139 UniProt NPD GO	PCSK7_MOUSE	Proprotein convertase subtilisin/kexin type 7 precursor (EC 3.4.21.-) (Proprotein convertase PC7) (S ...	0.12	-	end	1 *	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...				770
P52897 UniProt NPD GO	PGFS2_BOVIN	Prostaglandin-F synthase 2 (EC 1.1.1.188) (PGF synthase 2) (PGF 2) (Prostaglandin-D2 11 reductase 2) ...	0.12	-	cyt	0	Cytoplasm				323
Q9NPD0 UniProt NPD GO	PART1_HUMAN	Prostate-specific and androgen-regulated protein 1 (PART-1)	0.12	-	cyt	0			604991		59
P80060 UniProt NPD GO	LCM_LOCMI	Protease inhibitors precursor [Contains: Protease inhibitor LCMI-I (PARS intercerebralis major pepti ...	0.12	-	exc	0	Secreted protein			1PMC	92
Q6BEA2 UniProt NPD GO	PRS27_RAT	Protease serine 27 precursor (EC 3.4.21.-) (Marapsin) (Pancreasin)	0.12	-	exc	0	Secreted protein (By similarity)				328
Q9LSU2 UniProt NPD GO	PSA2_ORYSA	Proteasome subunit alpha type 2 (EC 3.4.25.1) (20S proteasome alpha subunit B) (20S proteasome subun ...	0.12	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				235
Q9PTW9 UniProt NPD GO	PSA7_CARAU	Proteasome subunit alpha type 7 (EC 3.4.25.1) (Proteasome subunit alpha 4)	0.12	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				251
P22769 UniProt NPD GO	PSA71_DROME	Proteasome subunit alpha type 7-1 (EC 3.4.25.1) (Proteasome 28 kDa subunit 1) (PROS-Dm28.1)	0.12	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
P42742 UniProt NPD GO	PSB1_ARATH	Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome subunit beta type 6) (20S proteasome beta s ...	0.12	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				223
Q5E9K0 UniProt NPD GO	PSB2_BOVIN	Proteasome subunit beta type 2 (EC 3.4.25.1)	0.12	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				201
Q3T108 UniProt NPD GO	PSB4_BOVIN	Proteasome subunit beta type 4 precursor (EC 3.4.25.1)	0.12	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				264
P62597 UniProt NPD GO	POTE1_CHICK	Protection of telomeres 1 (cPot1) (POT1-like telomere end-binding protein)	0.12	-	nuc	0	Nucleus. Colocalizes with telomeric DNA				778
P49933 UniProt NPD GO	PG4_PIG	Protegrin-4 precursor (PG-4)	0.12	-	mit	1 *	Secreted protein			1N5P	149
Q9D0U9 UniProt NPD GO	ARV1_MOUSE	Protein ARV1	0.12	-	end	3	Membrane; multi-pass membrane protein (Potential)				266
P15063 UniProt NPD GO	MYCB_RAT	Protein B-Myc	0.12	-	nuc	0	Nucleus (By similarity)				168
Q9NQ88 UniProt NPD GO	CL005_HUMAN	Protein C12orf5	0.12	-	nuc	0					270
Q8TD88 UniProt NPD GO	CU109_HUMAN	Protein C21orf109	0.12	-	nuc	0					51
Q8NBI6 UniProt NPD GO	CC021_HUMAN	Protein C3orf21	0.12	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				393
O76042 UniProt NPD GO	CC051_HUMAN	Protein C3orf51 (PO42)	0.12	-	cyt	0					201
Q99440 UniProt NPD GO	CD006_HUMAN	Protein C4orf6 (AC1 protein)	0.12	-	nuc	0					93
Q5F3N9 UniProt NPD GO	CF106_CHICK	Protein C6orf106 homolog	0.12	-	nuc	0					291
Q9Y6Z4 UniProt NPD GO	CF054_HUMAN	Protein C6orf54 (HGC6.1 protein)	0.12	-	nuc	0					181
Q9H2N8 UniProt NPD GO	CI045_HUMAN	Protein C9orf45	0.12	-	mit	0					167
Q6GNP0 UniProt NPD GO	CQ10B_XENLA	Protein COQ10 B, mitochondrial precursor	0.12	-	mit	0	Mitochondrion (Potential)				244
Q9D8T4 UniProt NPD GO	FA18B_MOUSE	Protein FAM18B	0.12	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				205
O14524 UniProt NPD GO	K0286_HUMAN	Protein KIAA0286	0.12	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			444
P35200 UniProt NPD GO	MSF1_YEAST	Protein MSF1	0.12	-	cyt	0		mitochondrion [IDA]			230

You are viewing entries 61701 to 61750 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.