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
Q9Y3S1 UniProt NPD GO	WNK2_HUMAN	Serine/threonine-protein kinase WNK2 (EC 2.7.11.1) (Protein kinase with no lysine 2) (Protein kinase ...	0.88	-	nuc	0			606249		2297
P38938 UniProt NPD GO	CEK1_SCHPO	Serine/threonine-protein kinase cek1 (EC 2.7.11.1)	0.88	-	nuc	0					1338
Q8I8U6 UniProt NPD GO	FEM3_CAEBR	Sex-determination protein fem-3 (Cb-FEM-3)	0.88	+	nuc	0					409
Q8SPQ2 UniProt NPD GO	SRY_BISBI	Sex-determining region Y protein (Testis-determining factor)	0.88	-	nuc	0	Nucleus				229
Q9XS37 UniProt NPD GO	SRY_BOSMU	Sex-determining region Y protein (Testis-determining factor)	0.88	-	nuc	0	Nucleus				229
Q03255 UniProt NPD GO	SRY_BOVIN	Sex-determining region Y protein (Testis-determining factor)	0.88	-	nuc	0	Nucleus				229
Q69FB1 UniProt NPD GO	SRY_BUBBU	Sex-determining region Y protein (Testis-determining factor)	0.88	+	nuc	0	Nucleus				229
Q864Q4 UniProt NPD GO	SRY_MESST	Sex-determining region Y protein (Testis-determining factor)	0.88	+	nuc	0	Nucleus				216
Q67EX7 UniProt NPD GO	SRY_MOSBE	Sex-determining region Y protein (Testis-determining factor)	0.88	+	nuc	0	Nucleus				227
O02799 UniProt NPD GO	STAT2_PIG	Signal transducer and activator of transcription 2	0.88	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus upon activation by ...				864
Q5JCS6 UniProt NPD GO	SI1L2_RAT	Signal-induced proliferation-associated 1-like protein 2 (Serine-rich synapse-associated protein)	0.88	-	nuc	0					1722
Q5XG71 UniProt NPD GO	UTP20_MOUSE	Small subunit processome component 20 homolog (Down-regulated in metastasis protein)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			2788
O75691 UniProt NPD GO	UTP20_HUMAN	Small subunit processome component 20 homolog (Down-regulated in metastasis protein) (Protein Key-1A ...	0.88	+	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [ISS]			2785
Q9NQZ2 UniProt NPD GO	SAS10_HUMAN	Something about silencing protein 10 (Disrupter of silencing SAS10) (Charged amino acid-rich leucine ...	0.88	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			479
Q6AXX4 UniProt NPD GO	SAS10_RAT	Something about silencing protein 10 (Disrupter of silencing SAS10) (Charged amino acid-rich leucine ...	0.88	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			470
Q62417 UniProt NPD GO	SRBS1_MOUSE	Sorbin and SH3 domain-containing protein 1 (Ponsin) (c-Cbl-associated protein) (CAP) (SH3 domain pro ...	0.88	-	nuc	0	Cell membrane; cell-cell junction; adherens junction. Cell membrane; cell-matrix junction; adherens ...	cell-cell adherens junction [IDA] cell-substrate adherens junction [IDA] lipid raft [IDA] nucleus [ISS] stress fiber [IDA]			1290
Q75CC3 UniProt NPD GO	MVP1_ASHGO	Sorting nexin MVP1	0.88	-	nuc	0	Cytoplasm (By similarity)				524
Q5RFP8 UniProt NPD GO	SNX1_PONPY	Sorting nexin-1	0.88	-	nuc	0					522
Q5KKB9 UniProt NPD GO	SNX41_CRYNE	Sorting nexin-41	0.88	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				638
Q5AZC9 UniProt NPD GO	SNX41_EMENI	Sorting nexin-41	0.88	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				615
Q9QYY8 UniProt NPD GO	SPAST_MOUSE	Spastin	0.88	-	nuc	1	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity)	nucleus [IDA]			614
O15020 UniProt NPD GO	SPTN2_HUMAN	Spectrin beta chain, brain 2 (Spectrin, non-erythroid beta chain 2) (Beta-III spectrin)	0.88	-	nuc	0		spectrin [IEP]	600224	1WYQ	2390
Q9NRC6 UniProt NPD GO	SPTN5_HUMAN	Spectrin beta chain, brain 4 (Spectrin, non-erythroid beta chain 4) (Beta-V spectrin) (BSPECV)	0.88	-	nuc	0	Cytoplasm. Detected prominently in the outer segments of photoreceptor rods and cones and in the bas ...	membrane [NAS] spectrin [NAS]	605916		3674
P22974 UniProt NPD GO	H1L_MYTCA	Sperm-specific protein PHI-2B (PL-II*) (Sperm-specific linker histone H1-like protein)	0.88	+	mit	0	Nucleus				148
P11020 UniProt NPD GO	SSS2_SCYCA	Spermatid-specific protein S2 (Basic nuclear protein S2)	0.88	+	nuc	0	Nucleus				80
P36094 UniProt NPD GO	SPC42_YEAST	Spindle pole body component SPC42	0.88	-	nuc	0	Nucleus	central plaque of spindle pole body [IDA] intermediate layer of spindle pole body [IDA]			363
Q9S758 UniProt NPD GO	SPL5_ARATH	Squamosa promoter-binding-like protein 5	0.88	-	nuc	0	Nucleus (Probable)				181
Q9JHU6 UniProt NPD GO	STMN3_RAT	Stathmin-3 (SCG10-like protein)	0.88	-	nuc	0					180
O93388 UniProt NPD GO	STMN3_CHICK	Stathmin-3 (SCG10-like protein) (Neuroplasticin-2)	0.88	-	nuc	0					180
P53032 UniProt NPD GO	SUT1_YEAST	Sterol uptake protein 1	0.88	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			299
P38989 UniProt NPD GO	SMC2_YEAST	Structural maintenance of chromosome 2 (DA-box protein SMC2)	0.88	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	mitochondrion [IDA] nuclear condensin complex [IPI]			1170
Q9UH65 UniProt NPD GO	SWP70_HUMAN	Switch-associated protein 70 (SWAP-70)	0.88	-	nuc	0	Cytoplasm. Cell membrane. Nucleus. In resting B-cells it is localized mainly in the cytoplasm and up ...		604762		585
Q9Z327 UniProt NPD GO	SYNPO_RAT	Synaptopodin	0.88	-	nuc	0	Cytoplasm. Cell membrane; cell-cell junction; tight junction. Localized at the tight junction of cel ...				931
Q60949 UniProt NPD GO	TBCD1_MOUSE	TBC1 domain family member 1	0.88	-	nuc	0	Nucleus				1255
Q99KW3 UniProt NPD GO	TARA_MOUSE	TRIO and F-actin-binding protein (Protein Tara) (Trio-associated repeat on actin)	0.88	-	nuc	0	Nucleus. Cytoplasm; localized to F-actin in a periodic pattern (By similarity)	actin cytoskeleton [ISS]			2014
P97499 UniProt NPD GO	TEP1_MOUSE	Telomerase protein component 1 (Telomerase-associated protein 1) (Telomerase protein 1) (p240) (p80 ...	0.88	-	end	0		soluble fraction [IDA]			2629
O75764 UniProt NPD GO	TCEA3_HUMAN	Transcription elongation factor A protein 3 (Transcription elongation factor S-II protein 3) (Transc ...	0.88	-	nuc	0	Nucleus (By similarity)		604128		348
Q6BVE1 UniProt NPD GO	SPT6_DEBHA	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.88	+	nuc	0	Nucleus (By similarity)				1439
Q60542 UniProt NPD GO	TCF8_MESAU	Transcription factor 8 (Zinc finger protein BZP)	0.88	+	nuc	0	Nucleus				1043
Q8W191 UniProt NPD GO	HYH_ARATH	Transcription factor HY5-like (HY5 homolog)	0.88	-	nuc	0	Nucleus				149
Q5KJR1 UniProt NPD GO	IWS1_CRYNE	Transcription factor IWS1	0.88	+	nuc	0	Nucleus (By similarity)				475
O42569 UniProt NPD GO	SOX2_XENLA	Transcription factor SOX-2 (XLSOX-2)	0.88	+	nuc	0	Nucleus				311
P35712 UniProt NPD GO	SOX6_HUMAN	Transcription factor SOX-6	0.88	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	607257		828
P40645 UniProt NPD GO	SOX6_MOUSE	Transcription factor SOX-6 (SOX-LZ)	0.88	-	nuc	0	Nucleus (Potential)	nucleus [IC] transcription factor complex [IC]			827
P41895 UniProt NPD GO	T2FA_YEAST	Transcription initiation factor IIF subunit alpha (EC 2.7.11.1) (TFIIF-alpha) (TFIIF large subunit) ...	0.88	-	nuc	0	Nucleus	transcription factor TFIIF complex [TAS]			735
Q5VWG9 UniProt NPD GO	TAF3_HUMAN	Transcription initiation factor TFIID subunit 3 (TBP-associated factor 3) (Transcription initiation ...	0.88	+	nuc	0	Nucleus		606576		929
P32389 UniProt NPD GO	MET4_YEAST	Transcriptional activator of sulfur metabolism MET4 (Methionine-requiring protein 4)	0.88	-	nuc	0	Nucleus	nucleus [IPI]			672
P41546 UniProt NPD GO	HAC1_YEAST	Transcriptional activatory protein HAC1	0.88	+	nuc	0	Nucleus (Probable)	nucleus [TAS]			230
Q02336 UniProt NPD GO	ADA2_YEAST	Transcriptional adapter 2	0.88	-	nuc	0	Nucleus	Ada2/Gcn5/Ada3 transcription activator complex [IPI] SAGA complex [IDA] SLIK (SAGA-like) complex [IPI]			434
P49711 UniProt NPD GO	CTCF_HUMAN	Transcriptional repressor CTCF (CCCTC-binding factor) (CTCFL paralog) (11-zinc finger protein)	0.88	+	nuc	0	Nucleus	nucleus [IDA]	604167	2CT1	727

You are viewing entries 5351 to 5400 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.