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
P58392 UniProt NPD GO	KCNN3_PIG	Small conductance calcium-activated potassium channel protein 3 (SK3)	0.94	+	nuc	5	Membrane; multi-pass membrane protein				724
Q9UGI6 UniProt NPD GO	KCNN3_HUMAN	Small conductance calcium-activated potassium channel protein 3 (SK3) (SKCa3)	0.94	+	end	5	Membrane; multi-pass membrane protein		602983		736
Q2UB56 UniProt NPD GO	MVP1_ASPOR	Sorting nexin mvp1	0.94	-	nuc	0	Cytoplasm (By similarity)				724
P13395 UniProt NPD GO	SPTCA_DROME	Spectrin alpha chain	0.94	-	nuc	0	Cytoskeleton. Golgi apparatus. Near the inner surface of the plasma membrane of nearly all cells. Lv ...	cell cortex [IDA] fusome [IDA] Golgi apparatus [IDA] plasma membrane [IDA] spectrosome [IDA]		2SPC	2415
Q62261 UniProt NPD GO	SPTB2_MOUSE	Spectrin beta chain, brain 1 (Spectrin, non-erythroid beta chain 1) (Beta-II spectrin) (Fodrin beta ...	0.94	+	nuc	0		nucleus [IDA] plasma membrane [IDA]		1MPH	2363
Q04621 UniProt NPD GO	PHI1_MYTED	Sperm-specific protein Phi-1	0.94	+	mit	0	Nucleus				91
Q754Z1 UniProt NPD GO	MAD1_ASHGO	Spindle assembly checkpoint component MAD1 (Mitotic arrest deficient protein 1)	0.94	-	nuc	0	Nucleus (By similarity)				659
Q874L7 UniProt NPD GO	MAD1_KLUDE	Spindle assembly checkpoint component MAD1 (Mitotic arrest deficient protein 1)	0.94	-	nuc	0	Nucleus (By similarity)				674
P40957 UniProt NPD GO	MAD1_YEAST	Spindle assembly checkpoint component MAD1 (Mitotic arrest deficient protein 1)	0.94	-	nuc	0	Nucleus	nuclear pore [IDA] nucleus [IDA]			749
Q63627 UniProt NPD GO	SFR15_RAT	Splicing factor, arginine/serine-rich 15 (CTD-binding SR-like protein RA4) (Fragment)	0.94	+	nuc	0					1048
Q8VE97 UniProt NPD GO	SFRS4_MOUSE	Splicing factor, arginine/serine-rich 4	0.94	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				489
P38871 UniProt NPD GO	SSP1_YEAST	Sporulation-specific protein 1	0.94	-	nuc	0	Localizes to prospore membrane. Localizes to precursors of the PSM and to the leading edge, which co ...	prospore membrane [IDA]			571
Q9SMX9 UniProt NPD GO	SPL1_ARATH	Squamosa promoter-binding-like protein 1	0.94	+	nuc	1	Nucleus (Probable)				881
Q94JW8 UniProt NPD GO	SPL6_ARATH	Squamosa promoter-binding-like protein 6	0.94	-	nuc	0	Nucleus (Probable)				405
Q8GXL3 UniProt NPD GO	SPL8_ARATH	Squamosa promoter-binding-like protein 8	0.94	-	nuc	0	Nucleus (Probable)				333
Q62407 UniProt NPD GO	SPEG_MOUSE	Striated muscle-specific serine/threonine protein kinase (EC 2.7.11.1) (Aortic preferentially expres ...	0.94	-	nuc	0	Isoform 3: Nucleus				3262
Q63638 UniProt NPD GO	SPEG_RAT	Striated muscle-specific serine/threonine protein kinase (EC 2.7.11.1) (Aortic preferentially expres ...	0.94	-	nuc	0	Isoform 2: Nucleus	nucleus [IMP]			3259
O97594 UniProt NPD GO	SMC3_BOVIN	Structural maintenance of chromosome 3 (Chondroitin sulfate proteoglycan 6)	0.94	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...	cohesin complex [ISS] cytoplasm [ISS] nuclear matrix [ISS] spindle pole [ISS]			1218
Q08204 UniProt NPD GO	SMC5_YEAST	Structural maintenance of chromosome 5	0.94	-	nuc	0	Nucleus (Potential)	nucleus [IDA] Smc5-Smc6 complex [IPI]			1093
P25648 UniProt NPD GO	SRB8_YEAST	Suppressor of RNA polymerase B SRB8	0.94	-	cyt	0	Nucleus (Probable)	transcription factor complex [TAS]			1427
P25623 UniProt NPD GO	SYP1_YEAST	Suppressor of yeast profilin deletion	0.94	-	nuc	0	Concentrates at the mother-bud neck and at the tip of the forming bud. As the bud grows, abundant in ...	bud neck [IDA] bud tip [IDA] mating projection base [IDA]			870
Q3T0E2 UniProt NPD GO	SYCP3_BOVIN	Synaptonemal complex protein 3 (SCP-3)	0.94	-	nuc	0	Nucleus (By similarity). In tripartite segments of synaptonemal complexes, irrespective of whether t ...				225
Q91YE8 UniProt NPD GO	SYNP2_MOUSE	Synaptopodin-2 (Myopodin)	0.94	+	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm in a differentiation-dependent an ...				1087
Q9P2M4 UniProt NPD GO	TBC14_HUMAN	TBC1 domain family member 14	0.94	-	nuc	0					678
Q96UP3 UniProt NPD GO	RIF1_SCHPO	Telomere length regulator protein rif1	0.94	+	nuc	0	Nucleus. Localized to telomeres. This interaction may be increased by perturbation of telomere struc ...	nuclear telomeric heterochromatin [IDA] nucleus [IDA] telomere cap complex [IDA]			1400
P54274 UniProt NPD GO	TERF1_HUMAN	Telomeric repeat-binding factor 1 (TTAGGG repeat-binding factor 1) (NIMA-interacting protein 2) (Tel ...	0.94	-	nuc	0	Nucleus. Colocalizes with telomeric DNA in interphase and metaphase cells and is located at chromoso ...	chromosome, telomeric region [TAS] nucleus [NAS]	600951	1W0T	439
Q9UHV7 UniProt NPD GO	TR240_HUMAN	Thyroid hormone receptor-associated protein complex 240 kDa component (Trap240) (Thyroid hormone rec ...	0.94	-	nuc	0	Nucleus	mediator complex [IDA] nucleus [IDA]	603808		2174
Q07157 UniProt NPD GO	ZO1_HUMAN	Tight junction protein ZO-1 (Zonula occludens 1 protein) (Zona occludens 1 protein) (Tight junction ...	0.94	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Movement of ZO-1 from the cytoplasm to ...	cell-cell adherens junction [TAS] tight junction [TAS]	601009		1748
P70064 UniProt NPD GO	T7L1D_XENLA	Transcription factor 7-like 1-D (HMG box transcription factor 3-D) (TCF-3-D) (xTcf-3d)	0.94	+	nuc	0	Nucleus (By similarity)				550
P56432 UniProt NPD GO	JUN_PIG	Transcription factor AP-1 (Activator protein 1) (AP1) (Proto-oncogene c-jun) (V-jun avian sarcoma vi ...	0.94	+	nuc	0	Nucleus				331
P17325 UniProt NPD GO	JUN_RAT	Transcription factor AP-1 (Activator protein 1) (AP1) (Proto-oncogene c-jun) (V-jun avian sarcoma vi ...	0.94	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IMP]			334
P05627 UniProt NPD GO	JUN_MOUSE	Transcription factor AP-1 (Activator protein 1) (AP1) (Proto-oncogene c-jun) (V-jun avian sarcoma vi ...	0.94	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			334
P18870 UniProt NPD GO	JUN_CHICK	Transcription factor AP-1 (Proto-oncogene c-jun)	0.94	+	nuc	0	Nucleus				314
P54864 UniProt NPD GO	JUN_SERCA	Transcription factor AP-1 (Proto-oncogene c-jun)	0.94	+	nuc	0	Nucleus				314
Q01664 UniProt NPD GO	TFAP4_HUMAN	Transcription factor AP-4 (Activating enhancer-binding protein 4)	0.94	-	nuc	0	Nucleus		600743		338
Q27368 UniProt NPD GO	E2F_DROME	Transcription factor E2f (dE2F)	0.94	-	mit	0	Nucleus	nucleus [IDA] Rb-E2F complex [IDA]			805
Q61657 UniProt NPD GO	HES3_MOUSE	Transcription factor HES-3 (Hairy and enhancer of split 3)	0.94	+	nuc	0	Nucleus				175
Q04667 UniProt NPD GO	HES3_RAT	Transcription factor HES-3 (Hairy and enhancer of split 3)	0.94	+	nuc	0	Nucleus				175
P43072 UniProt NPD GO	TF3B_CANAL	Transcription factor IIIB 70 kDa subunit (TFIIIB) (B-related factor) (BRF)	0.94	-	nuc	0	Nucleus				553
Q6FVX3 UniProt NPD GO	IWS1_CANGA	Transcription factor IWS1	0.94	-	nuc	0	Nucleus (By similarity)				382
Q6CVL1 UniProt NPD GO	IWS1_KLULA	Transcription factor IWS1	0.94	+	nuc	0	Nucleus (By similarity)				362
Q16621 UniProt NPD GO	NFE2_HUMAN	Transcription factor NF-E2 45 kDa subunit (Nuclear factor, erythroid-derived 2 45 kDa subunit) (p45 ...	0.94	+	nuc	0	Nucleus	nucleus [TAS]	601490	1LVX	373
Q02086 UniProt NPD GO	SP2_HUMAN	Transcription factor Sp2	0.94	-	nuc	0	Nucleus		601801		606
Q4WSM6 UniProt NPD GO	IWS1_ASPFU	Transcription factor iws1	0.94	+	nuc	0	Nucleus (By similarity)				460
P79703 UniProt NPD GO	JUNB_CYPCA	Transcription factor jun-B	0.94	+	nuc	0	Nucleus				308
P13528 UniProt NPD GO	UNC86_CAEEL	Transcription factor unc-86 (Uncoordinated protein 86)	0.94	+	nuc	1 *	Nucleus				467
P29084 UniProt NPD GO	T2EB_HUMAN	Transcription initiation factor IIE subunit beta (TFIIE-beta)	0.94	+	nuc	0	Nucleus		189964	1D8K	291
Q04870 UniProt NPD GO	T2FA_XENLA	Transcription initiation factor IIF alpha subunit (EC 2.7.11.1) (TFIIF-alpha) (Transcription initiat ...	0.94	+	nuc	0	Nucleus				524
P46677 UniProt NPD GO	TAF1_YEAST	Transcription initiation factor TFIID subunit 1 (EC 2.3.1.48) (TBP-associated factor 1) (TBP-associa ...	0.94	+	nuc	0	Nucleus	transcription factor TFIID complex [IDA]			1066
Q9UPN9 UniProt NPD GO	TIF1G_HUMAN	Transcription intermediary factor 1-gamma (TIF1-gamma) (Tripartite motif-containing protein 33) (RET ...	0.94	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	605769		1127

You are viewing entries 2551 to 2600 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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