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
O19113 UniProt NPD GO	CTGF_PIG	Connective tissue growth factor precursor	0.15	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity). Secreted protein (By si ...				349
P0C1N4 UniProt NPD GO	CXM35_CONMR	Conotoxin Mr3.5 precursor	0.15	-	exc	0	Secreted protein (By similarity)				64
Q9U6Z6 UniProt NPD GO	CX5A_CONPU	Conotoxin p5a precursor	0.15	-	exc	0	Secreted protein				63
O89053 UniProt NPD GO	COR1A_MOUSE	Coronin-1A (Coronin-like protein p57) (Coronin-like protein A) (CLIPINA) (Tryptophan aspartate-conta ...	0.15	-	mit	0	In non-infected macrophages, associated with the cortical microtubule network; in mycobacteria-infec ...			2B4E	460
P01377 UniProt NPD GO	DEF4_RABIT	Corticostatin-4 precursor (Corticostatin IV) (CS-IV) (Macrophage antibiotic peptide MCP-2) (NP-2) (A ...	0.15	-	exc	0	Secreted protein				95
Q13324 UniProt NPD GO	CRFR2_HUMAN	Corticotropin-releasing factor receptor 2 precursor (CRF-R 2) (CRF2) (Corticotropin-releasing hormon ...	0.15	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	602034		411
P04414 UniProt NPD GO	KCRM_TORCA	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK)	0.15	-	cyt	0	Cytoplasm			1VRP	381
P46109 UniProt NPD GO	CRKL_HUMAN	Crk-like protein	0.15	-	nuc	0			602007		303
Q9BUF7 UniProt NPD GO	CRUM3_HUMAN	Crumbs protein homolog 3 precursor	0.15	-	exc	2 *	Cell membrane; apical cell membrane; single-pass type I membrane protein. Cell membrane; cell-cell j ...		609737		120
O97386 UniProt NPD GO	CHH4_PENMO	Crustacean hyperglycemic hormones 4 precursor (Pm-SGP-IV) [Contains: CHH precursor-related peptide 4 ...	0.15	-	exc	0	Secreted protein				120
P35800 UniProt NPD GO	DPY10_CAEEL	Cuticle collagen dpy-10 precursor (Protein dumpy-10)	0.15	-	nuc	1 *		extracellular region [NAS]			372
P15766 UniProt NPD GO	RK3_CYAPA	Cyanelle 50S ribosomal protein L3	0.15	-	nuc	0	Plastid; cyanelle				209
P22549 UniProt NPD GO	IPDE_DICDI	Cyclic nucleotide phosphodiesterase inhibitor precursor (PDI)	0.15	-	nuc	1 *					237
Q64359 UniProt NPD GO	CGN2_RAT	Cyclic nucleotide-gated olfactory channel subunit OCNC2	0.15	-	end	3 *	Membrane; multi-pass membrane protein				575
P08935 UniProt NPD GO	CYT_BITAR	Cystatin	0.15	-	nuc	0	Secreted protein				111
P87131 UniProt NPD GO	CYSK2_SCHPO	Cysteine synthase 2 (EC 2.5.1.47) (O-acetylserine sulfhydrylase 2) (O-acetylserine (Thiol)-lyase 2) ...	0.15	-	cyt	0					395
Q9QYG5 UniProt NPD GO	CP2DK_MESAU	Cytochrome P450 2D20 (EC 1.14.14.-) (CYPIID20)	0.15	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				500
Q64148 UniProt NPD GO	CP3AA_MESAU	Cytochrome P450 3A10 (EC 1.14.13.94) (CYPIIIA10) (Lithocholate 6-beta-hydroxylase) (6 beta-hydroxyla ...	0.15	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				503
P23295 UniProt NPD GO	NOR_FUSOX	Cytochrome P450 55A1 (EC 1.14.-.-) (CYPLVA1) (P450 DNIR) (Nitric-oxide reductase) (P450nor)	0.15	-	nuc	0				2ROM	402
P13527 UniProt NPD GO	CP6A1_MUSDO	Cytochrome P450 6A1 (EC 1.14.14.1) (CYPVIA1)	0.15	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				509
P49264 UniProt NPD GO	C71B1_THLAR	Cytochrome P450 71B1 (EC 1.14.-.-) (CYPLXXIB1)	0.15	-	nuc	0					496
P03873 UniProt NPD GO	MBI2_YEAST	Cytochrome b mRNA maturase bI2	0.15	-	end	4 *		mitochondrion [TAS]			423
Q9ZZW7 UniProt NPD GO	MBI3_YEAST	Cytochrome b mRNA maturase bI3	0.15	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrion [TAS]		2AB5	517
Q95L73 UniProt NPD GO	CY24A_BISBI	Cytochrome b-245 light chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 22 kDa polypeptid ...	0.15	-	end	3 *					190
Q85FH6 UniProt NPD GO	CCSA_ADICA	Cytochrome c biogenesis protein ccsA	0.15	-	end	8 *	Plastid; chloroplast				316
Q7KZN9 UniProt NPD GO	COX15_HUMAN	Cytochrome c oxidase assembly protein COX15 homolog	0.15	-	end	8	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrial electron transport chain [TAS]	603646		410
Q5KAH3 UniProt NPD GO	COX19_CRYNE	Cytochrome c oxidase assembly protein COX19	0.15	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial intermembrane space (By similarity)				115
P35171 UniProt NPD GO	CX7A2_RAT	Cytochrome c oxidase polypeptide VIIa-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.15	-	mit	1	Mitochondrion; mitochondrial inner membrane				83
P24311 UniProt NPD GO	COX7B_HUMAN	Cytochrome c oxidase polypeptide VIIb, mitochondrial precursor (EC 1.9.3.1)	0.15	-	mit	0			603792		80
Q00988 UniProt NPD GO	CY1_KLULA	Cytochrome c1, heme protein, mitochondrial precursor	0.15	-	mit	1 *					292
Q4R5P6 UniProt NPD GO	DC1L2_MACFA	Cytoplasmic dynein 1 light intermediate chain 2 (Dynein light intermediate chain 2, cytosolic)	0.15	-	nuc	0					492
Q9D020 UniProt NPD GO	5NT3_MOUSE	Cytosolic 5'-nucleotidase III (EC 3.1.3.5) (cN-III) (Pyrimidine 5'-nucleotidase 1) (P5'N-1) (P5N-1) ...	0.15	-	cyt	0	Cytoplasm (Potential)	cytoplasm [ISS] endoplasmic reticulum [ISS]		2G0A	297
P09793 UniProt NPD GO	CTLA4_MOUSE	Cytotoxic T-lymphocyte protein 4 precursor (Cytotoxic T-lymphocyte-associated antigen 4) (CTLA-4) (C ...	0.15	-	mit	2 *	Membrane; single-pass type I membrane protein			1DQT	223
P19003 UniProt NPD GO	CXH32_ASPSC	Cytotoxin homolog S3C2	0.15	-	nuc	0	Secreted protein				63
P51436 UniProt NPD GO	DRD4_MOUSE	D(4) dopamine receptor (Dopamine D4 receptor) (D(2C) dopamine receptor)	0.15	-	end	7 *	Membrane; multi-pass membrane protein				387
Q6BL27 UniProt NPD GO	DAD1_DEBHA	DASH complex subunit DAD1 (Outer kinetochore protein DAD1)	0.15	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				104
Q6CER3 UniProt NPD GO	DAD1_YARLI	DASH complex subunit DAD1 (Outer kinetochore protein DAD1)	0.15	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				88
Q6FRP0 UniProt NPD GO	DAD4_CANGA	DASH complex subunit DAD4 (Outer kinetochore protein DAD4)	0.15	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				73
P79064 UniProt NPD GO	RAD31_SCHPO	DNA damage tolerance protein rad31	0.15	-	cyt	0		SUMO activating enzyme complex [TAS]			307
Q5BIM8 UniProt NPD GO	ERCC8_BOVIN	DNA excision repair protein ERCC-8	0.15	-	nuc	0	Nucleus (By similarity)				397
P37383 UniProt NPD GO	RAD51_CHICK	DNA repair protein RAD51 homolog	0.15	-	cyt	0	Nucleus (Probable)	nucleus [ISS] synaptonemal complex [ISS]			339
P48013 UniProt NPD GO	RAD9_SCHOT	DNA repair protein rad9	0.15	-	mit	0					432
O96651 UniProt NPD GO	TOP3B_DROME	DNA topoisomerase 3-beta (EC 5.99.1.2) (DNA topoisomerase III beta)	0.15	+	cyt	0					875
O94703 UniProt NPD GO	RPA9_SCHPO	DNA-directed RNA polymerase I 13.1 kDa polypeptide (EC 2.7.7.6)	0.15	-	nuc	0	Nucleus (Potential)	DNA-directed RNA polymerase I complex [TAS]			119
Q791N7 UniProt NPD GO	RPA12_MOUSE	DNA-directed RNA polymerase I subunit 12 (EC 2.7.7.6) (Nuclear RNA polymerase I small-specific subun ...	0.15	-	nuc	0	Nucleus (Potential)				123
Q9H1D9 UniProt NPD GO	RPO3F_HUMAN	DNA-directed RNA polymerase III subunit F (EC 2.7.7.6) (DNA-directed RNA polymerase III 39 kDa polyp ...	0.15	-	nuc	0	Nucleus (Potential)	DNA-directed RNA polymerase III complex [NAS]			316
P08036 UniProt NPD GO	RPOB_SAPOF	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.15	-	cyt	0	Plastid; chloroplast				417
Q9DE68 UniProt NPD GO	PGS2_COTJA	Decorin precursor (Bone proteoglycan II) (PG-S2)	0.15	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				356
Q8WZK4 UniProt NPD GO	DCN1_SCHPO	Defective in cullin neddylation protein 1	0.15	-	cyt	0					251
P84757 UniProt NPD GO	DEF1_PAPHA	Defensin-1 (PhD1) [Contains: Defensin-2 (PhD2)]	0.15	-	mit	0	Secreted protein				33

You are viewing entries 56801 to 56850 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.