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
Q00006 UniProt NPD GO	2ABB_RABIT	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, B ...	0.70	-	nuc	0					413
Q6PD03 UniProt NPD GO	2A5A_MOUSE	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform (PP2A, B subunit, B' ...	0.70	-	cyt	0	Cytoplasm (By similarity)				486
O04421 UniProt NPD GO	SRP14_ARATH	Signal recognition particle 14 kDa protein (SRP14)	0.70	-	nuc	0	Cytoplasm				121
Q9Y6M7 UniProt NPD GO	S4A7_HUMAN	Sodium bicarbonate cotransporter 3 (Sodium bicarbonate cotransporter 2) (Sodium bicarbonate cotransp ...	0.70	+	end	11	Cell membrane; basolateral cell membrane; multi-pass membrane protein. Also described at the apical ...	integral to membrane [NAS]	603353		1214
Q3MPQ4 UniProt NPD GO	MVP1_CANAL	Sorting nexin MVP1	0.70	+	nuc	0	Cytoplasm (By similarity)				745
Q6FNH2 UniProt NPD GO	MVP1_CANGA	Sorting nexin MVP1	0.70	-	nuc	0	Cytoplasm (By similarity)				509
Q9Y5W9 UniProt NPD GO	SNX11_HUMAN	Sorting nexin-11	0.70	-	nuc	0					270
Q9Y5X3 UniProt NPD GO	SNX5_HUMAN	Sorting nexin-5	0.70	-	cyt	0			605937	1SYS	404
P83216 UniProt NPD GO	HSP4_OCTVU	Sperm protamine P4 (Po4)	0.70	+	nuc	0	Nucleus	nucleosome [NAS] nucleus [NAS]			28
Q9UM82 UniProt NPD GO	SPAT2_HUMAN	Spermatogenesis-associated protein 2 (Spermatogenesis-associated protein PD1)	0.70	-	nuc	0	Nucleus	cytoplasm [IDA]	607662		520
Q8K3V1 UniProt NPD GO	SPAT4_MOUSE	Spermatogenesis-associated protein 4 (Testis spermatocyte apoptosis-related gene 2 protein) (Testis ...	0.70	-	nuc	0					295
Q6C452 UniProt NPD GO	MAD1_YARLI	Spindle assembly checkpoint component MAD1 (Mitotic arrest deficient protein 1)	0.70	-	nuc	0	Nucleus (By similarity)				704
Q9USQ2 UniProt NPD GO	ALP6_SCHPO	Spindle pole body component alp6 (Altered polarity protein 6)	0.70	-	cyt	0	Spindle pole body. And the microtubule organizing center (MTOC)	equatorial microtubule organizing center [IDA] gamma-tubulin complex [TAS] spindle pole body [IDA]			832
O14132 UniProt NPD GO	PIT1_SCHPO	Sporulation protein kinase pit1 (EC 2.7.11.1)	0.70	-	nuc	0					650
Q64HA9 UniProt NPD GO	SPL11_ORYSA	Spotted leaf protein 11 (Spotted leaf11) (Cell death-related protein SPL11)	0.70	-	mit	0					694
P33242 UniProt NPD GO	STF1_MOUSE	Steroidogenic factor 1 (STF-1) (SF-1) (Adrenal 4-binding protein) (Steroid hormone receptor Ad4BP) ( ...	0.70	+	nuc	0	Nucleus	nucleus [IDA]		2FF0	462
P31948 UniProt NPD GO	STIP1_HUMAN	Stress-induced-phosphoprotein 1 (STI1) (Hsc70/Hsp90-organizing protein) (Hop) (Transformation-sensit ...	0.70	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	Golgi apparatus [TAS] nucleus [TAS]	605063	1ELW	543
O14512 UniProt NPD GO	SOCS7_HUMAN	Suppressor of cytokine signaling 7 (SOCS-7) (Nck, Ash and phospholipase C gamma-binding protein) (Nc ...	0.70	-	nuc	0			608788		485
O02019 UniProt NPD GO	SUH_HALRO	Suppressor of hairless homolog (RBP-Jkappa)	0.70	-	nuc	0					518
P40847 UniProt NPD GO	SAP1_SCHPO	Switch-activating protein 1	0.70	-	nuc	0	Nucleus (Probable)	nuclear chromatin [TAS]			254
Q13190 UniProt NPD GO	STX5_HUMAN	Syntaxin-5	0.70	-	gol	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...		603189		301
Q24509 UniProt NPD GO	STX5_DROME	Syntaxin-5 (Sed5 protein) (dSed5)	0.70	-	nuc	1	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; single-pass type IV membrane protein ...	endoplasmic reticulum [ISS] Golgi apparatus [IDA] Golgi cis-face [IDA] Golgi membrane [ISS]			467
P59277 UniProt NPD GO	SYP81_ARATH	Syntaxin-81 (AtSYP81)	0.70	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				310
P33705 UniProt NPD GO	CD4_CANFA	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.70	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			463
P42081 UniProt NPD GO	CD86_HUMAN	T-lymphocyte activation antigen CD86 precursor (Activation B7-2 antigen) (CTLA-4 counter-receptor B7 ...	0.70	-	nuc	2 *	Membrane; single-pass type I membrane protein	integral to membrane [IC] plasma membrane [NAS]	601020	1NCN	329
Q9NXG2 UniProt NPD GO	THUM1_HUMAN	THUMP domain-containing protein 1	0.70	-	nuc	0					353
Q9FJA2 UniProt NPD GO	TT2_ARATH	TRANSPARENT TESTA 2 protein (Myb-related protein 123) (AtMYB123) (Myb-related transcription factor L ...	0.70	-	nuc	0	Nucleus				258
O75157 UniProt NPD GO	T22D2_HUMAN	TSC22 domain family protein 2 (TSC22-related-inducible leucine zipper protein 4)	0.70	-	nuc	0					780
Q94819 UniProt NPD GO	TE95_TETTH	Telomerase component p95 (EC 2.7.7.49)	0.70	-	nuc	0	Nucleus (Potential)				872
Q27ID4 UniProt NPD GO	TERT_BOVIN	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit)	0.70	-	mit	0	Nucleus (By similarity)				1125
Q6A548 UniProt NPD GO	TERT_CANFA	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit)	0.70	-	mit	0	Nucleus				1123
P37244 UniProt NPD GO	THB2_MOUSE	Thyroid hormone receptor beta-2	0.70	+	cyt	0	Nucleus	nucleus [TAS]			475
O60603 UniProt NPD GO	TLR2_HUMAN	Toll-like receptor 2 precursor (Toll/interleukin 1 receptor-like protein 4) (CD282 antigen)	0.70	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	cell surface [IDA] integral to plasma membrane [TAS] plasma membrane [TAS]	603028	1O77	784
Q9NYK1 UniProt NPD GO	TLR7_HUMAN	Toll-like receptor 7 precursor	0.70	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)		300365		1049
Q5I2M4 UniProt NPD GO	TLR9_SHEEP	Toll-like receptor 9 precursor (CD289 antigen)	0.70	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				1029
Q9UPV9 UniProt NPD GO	TRAK1_HUMAN	Trafficking kinesin-binding protein 1 (106 kDa O-GlcNAc transferase-interacting protein)	0.70	-	nuc	0	Nucleus	mitochondrion [IDA] nucleus [ISS]	608112		953
P13780 UniProt NPD GO	REP2_ZYGBA	Trans-acting factor C (REP2)	0.70	-	nuc	0					249
Q7S3C4 UniProt NPD GO	SPT5_NEUCR	Transcription elongation factor spt-5 (Chromatin elongation factor spt-5)	0.70	+	nuc	0	Nucleus (By similarity)				1054
Q4WP96 UniProt NPD GO	SPT5_ASPFU	Transcription elongation factor spt5 (Chromatin elongation factor spt5)	0.70	+	nuc	0	Nucleus (By similarity)				1058
Q01094 UniProt NPD GO	E2F1_HUMAN	Transcription factor E2F1 (E2F-1) (Retinoblastoma-binding protein 3) (RBBP-3) (PRB-binding protein E ...	0.70	+	nuc	0	Nucleus		189971	2AZE	437
Q61502 UniProt NPD GO	E2F5_MOUSE	Transcription factor E2F5 (E2F-5)	0.70	-	nuc	0	Nucleus	cytoplasm [IDA] nuclear envelope [TAS] nucleus [IDA]			335
Q00492 UniProt NPD GO	SUM1_LYTVA	Transcription factor SUM-1 (Sea urchin myogenic factor 1)	0.70	+	nuc	0	Nucleus				260
P36100 UniProt NPD GO	T2EA_YEAST	Transcription initiation factor IIE subunit alpha (TFIIE-alpha) (Transcription factor A large subuni ...	0.70	-	nuc	1 *	Nucleus (Probable)	transcription factor TFIIE complex [TAS]			482
Q15561 UniProt NPD GO	TEAD4_HUMAN	Transcriptional enhancer factor TEF-3 (TEA domain family member 4) (TEAD-4) (Transcription factor RT ...	0.70	-	nuc	0	Nucleus		601714		427
P48301 UniProt NPD GO	TEAD2_MOUSE	Transcriptional enhancer factor TEF-4 (TEA domain family member 2) (TEAD-2) (Embryonic TEA domain-co ...	0.70	-	nuc	0	Nucleus	transcription factor complex [IDA]			445
Q03125 UniProt NPD GO	NRG1_YEAST	Transcriptional regulator NRG1 (Zinc finger protein MSS1)	0.70	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			231
Q07458 UniProt NPD GO	RXT3_YEAST	Transcriptional regulatory protein RXT3	0.70	-	nuc	0	Nucleus	nucleus [IDA]			294
P21957 UniProt NPD GO	OPI1_YEAST	Transcriptional repressor OPI1 (Negative regulator of phospholipid biosynthesis) (Overproducer of in ...	0.70	-	nuc	0	Endoplasmic reticulum. Maintained at the endoplasmic reticulum by SCS2. Nucleus. In response to elev ...	nucleus [IC]			404
Q8BXJ2 UniProt NPD GO	TREF1_MOUSE	Transcriptional-regulating factor 1 (Transcriptional-regulating protein 132) (Zinc finger transcript ...	0.70	-	nuc	0	Nucleus (By similarity)				1205
Q96PN7 UniProt NPD GO	TREF1_HUMAN	Transcriptional-regulating factor 1 (Transcriptional-regulating protein 132) (Zinc finger transcript ...	0.70	-	nuc	0	Nucleus	nucleus [IDA]			1200

You are viewing entries 14001 to 14050 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.