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
O88544 UniProt NPD GO	CSN4_MOUSE	COP9 signalosome complex subunit 4 (Signalosome subunit 4) (SGN4) (JAB1-containing signalosome subun ...	0.47	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	signalosome complex [IDA]		1UFM	406
Q68FS2 UniProt NPD GO	CSN4_RAT	COP9 signalosome complex subunit 4 (Signalosome subunit 4) (SGN4) (JAB1-containing signalosome subun ...	0.47	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				406
Q60632 UniProt NPD GO	COT1_MOUSE	COUP transcription factor 1 (COUP-TF1) (COUP-TF I)	0.47	-	nuc	0	Nucleus	nucleus [IDA]			422
Q01066 UniProt NPD GO	PDE1B_RAT	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17) (Cam-PDE 1B) ...	0.47	-	mit	0	Cytoplasm				535
P53238 UniProt NPD GO	CPNSH_YEAST	Calpain small subunit homolog protein YGR058W	0.47	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			335
O15484 UniProt NPD GO	CAN5_HUMAN	Calpain-5 (EC 3.4.22.-) (nCL-3) (htra-3)	0.47	-	cyt	0			602537		640
Q805E5 UniProt NPD GO	CHSTE_BRARE	Carbohydrate sulfotransferase D4ST1 (EC 2.8.2.-) (Dermatan 4-sulfotransferase 1) (D4ST-1) (zD4ST-1)	0.47	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [ISS]			367
P19784 UniProt NPD GO	CSK22_HUMAN	Casein kinase II subunit alpha' (EC 2.7.11.1) (CK II)	0.47	-	cyt	0			115442		350
Q8TG12 UniProt NPD GO	CSK2B_NEUCR	Casein kinase II subunit beta-1 (CK II beta-1)	0.47	-	nuc	0					333
P29466 UniProt NPD GO	CASP1_HUMAN	Caspase-1 precursor (EC 3.4.22.36) (CASP-1) (Interleukin-1 beta convertase) (IL-1BC) (IL-1 beta-conv ...	0.47	-	nuc	0	Cytoplasm		147678	2HBZ	404
P49662 UniProt NPD GO	CASP4_HUMAN	Caspase-4 precursor (EC 3.4.22.-) (CASP-4) (ICH-2 protease) (TX protease) (ICE(rel)-II) [Contains: C ...	0.47	-	nuc	0			602664		377
O35116 UniProt NPD GO	CTND2_RAT	Catenin delta-2 (Fragment)	0.47	+	nuc	0	Nucleus (By similarity). Cell membrane; cell-cell junction; adherens junction (By similarity)				264
Q9MBA3 UniProt NPD GO	RAD17_ARATH	Cell cycle checkpoint protein RAD17 (AtRAD17) (Radiation sensitive 17)	0.47	-	nuc	0	Nucleus (Probable)				599
O54692 UniProt NPD GO	ZW10_MOUSE	Centromere/kinetochore protein zw10 homolog	0.47	-	cyt	0	Cytoplasm (By similarity). Dynamic pattern of localization during the cell cycle. In most cells at i ...	endoplasmic reticulum [ISS] kinetochore [ISS] kinetochore microtubule [ISS] nucleus [ISS] spindle pole [ISS]			778
Q4V8C2 UniProt NPD GO	ZW10_RAT	Centromere/kinetochore protein zw10 homolog	0.47	-	cyt	0	Cytoplasm (By similarity). Dynamic pattern of localization during the cell cycle. In most cells at i ...				776
P30572 UniProt NPD GO	CHS2_CANAL	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2)	0.47	-	end	7	Cell membrane; multi-pass membrane protein				1009
O78506 UniProt NPD GO	RR14_GUITH	Chloroplast 30S ribosomal protein S14	0.47	-	nuc	0	Plastid; chloroplast				100
Q332S0 UniProt NPD GO	RR15_LACSA	Chloroplast 30S ribosomal protein S15	0.47	-	nuc	0	Plastid; chloroplast				92
Q9MUK9 UniProt NPD GO	RR15_MESVI	Chloroplast 30S ribosomal protein S15	0.47	-	mit	0	Plastid; chloroplast				90
Q9TKX8 UniProt NPD GO	RR18_NEPOL	Chloroplast 30S ribosomal protein S18	0.47	-	mit	0	Plastid; chloroplast				73
Q9FTC7 UniProt NPD GO	RR4_ANTPU	Chloroplast 30S ribosomal protein S4	0.47	-	mit	0	Plastid; chloroplast				202
Q6H9K2 UniProt NPD GO	RR4_EQUVA	Chloroplast 30S ribosomal protein S4	0.47	-	nuc	0	Plastid; chloroplast				207
P59147 UniProt NPD GO	RR4_LOPCO	Chloroplast 30S ribosomal protein S4	0.47	-	mit	0	Plastid; chloroplast				203
Q2MI98 UniProt NPD GO	RR4_LYCES	Chloroplast 30S ribosomal protein S4	0.47	-	mit	0	Plastid; chloroplast				201
Q2MII5 UniProt NPD GO	RR4_SOLBU	Chloroplast 30S ribosomal protein S4	0.47	-	mit	0	Plastid; chloroplast				201
Q2VEH5 UniProt NPD GO	RR4_SOLTU	Chloroplast 30S ribosomal protein S4	0.47	-	mit	0	Plastid; chloroplast				201
P69632 UniProt NPD GO	RR4_ARICA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.47	-	nuc	0	Plastid; chloroplast				183
P69633 UniProt NPD GO	RR4_ARIPL	Chloroplast 30S ribosomal protein S4 (Fragment)	0.47	-	nuc	0	Plastid; chloroplast				183
O20208 UniProt NPD GO	RR4_DIEGR	Chloroplast 30S ribosomal protein S4 (Fragment)	0.47	-	mit	0	Plastid; chloroplast				182
O20273 UniProt NPD GO	RR4_PATFR	Chloroplast 30S ribosomal protein S4 (Fragment)	0.47	-	nuc	0	Plastid; chloroplast				184
P36473 UniProt NPD GO	RR4_TRARA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.47	-	mit	0	Plastid; chloroplast				196
O19917 UniProt NPD GO	RR6_CYACA	Chloroplast 30S ribosomal protein S6	0.47	-	nuc	0	Plastid; chloroplast				103
Q67IC5 UniProt NPD GO	RR7_ASPOF	Chloroplast 30S ribosomal protein S7	0.47	-	nuc	0	Plastid; chloroplast				155
Q9GFM9 UniProt NPD GO	RR7_CABCA	Chloroplast 30S ribosomal protein S7	0.47	-	nuc	0	Plastid; chloroplast				155
Q9GFM3 UniProt NPD GO	RR7_CERDE	Chloroplast 30S ribosomal protein S7	0.47	-	nuc	0	Plastid; chloroplast				155
P07135 UniProt NPD GO	RR7_SOYBN	Chloroplast 30S ribosomal protein S7	0.47	-	nuc	0	Plastid; chloroplast				155
Q9GFK0 UniProt NPD GO	RR7_TROAR	Chloroplast 30S ribosomal protein S7	0.47	-	nuc	0	Plastid; chloroplast				155
P56801 UniProt NPD GO	RR8_ARATH	Chloroplast 30S ribosomal protein S8	0.47	-	nuc	0	Plastid; chloroplast				134
Q9BBQ1 UniProt NPD GO	RR8_LOTJA	Chloroplast 30S ribosomal protein S8	0.47	-	cyt	0	Plastid; chloroplast				134
Q6L366 UniProt NPD GO	RR8_SACHY	Chloroplast 30S ribosomal protein S8	0.47	-	cyt	0	Plastid; chloroplast				136
Q9TLT5 UniProt NPD GO	RK2_CYACA	Chloroplast 50S ribosomal protein L2	0.47	-	nuc	0	Plastid; chloroplast				275
P19165 UniProt NPD GO	RK2_EUGGR	Chloroplast 50S ribosomal protein L2	0.47	-	mit	0	Plastid; chloroplast				277
P31163 UniProt NPD GO	RK2_PEA	Chloroplast 50S ribosomal protein L2	0.47	-	mit	0	Plastid; chloroplast				273
Q85FV2 UniProt NPD GO	RK24_CYAME	Chloroplast 50S ribosomal protein L24	0.47	-	nuc	0	Plastid; chloroplast				75
Q85G82 UniProt NPD GO	RK28_CYAME	Chloroplast 50S ribosomal protein L28	0.47	-	mit	0	Plastid; chloroplast				75
Q70XW5 UniProt NPD GO	RK32_AMBTC	Chloroplast 50S ribosomal protein L32	0.47	-	mit	0	Plastid; chloroplast				57
O78434 UniProt NPD GO	RK32_GUITH	Chloroplast 50S ribosomal protein L32	0.47	-	mit	0	Plastid; chloroplast				52
Q85WV0 UniProt NPD GO	RK32_PINKO	Chloroplast 50S ribosomal protein L32	0.47	-	nuc	0	Plastid; chloroplast				71
P32738 UniProt NPD GO	CLAT_RAT	Choline O-acetyltransferase (EC 2.3.1.6) (CHOACTase) (Choline acetylase) (ChAT)	0.47	-	nuc	0				1T1U	639
P82600 UniProt NPD GO	PERC_AEDAE	Chorion peroxidase precursor (EC 1.11.1.7) [Contains: Chorion peroxidase light chain; Chorion peroxi ...	0.47	-	exc	1 *	Secreted protein. In the chorion layer of the mature eggs	extracellular region [IC]			791

You are viewing entries 26801 to 26850 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.