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
Q04359 UniProt NPD GO	SPO20_YEAST	Sporulation-specific protein 20	0.89	-	nuc	0	Membrane-associated to the plasma during vegetative growth and prospore membrane associated during s ...	prospore membrane [IMP]			397
Q7Z699 UniProt NPD GO	SPRE1_HUMAN	Sprouty-related, EVH1 domain-containing protein 1 (Spred-1)	0.89	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				444
Q924S8 UniProt NPD GO	SPRE1_MOUSE	Sprouty-related, EVH1 domain-containing protein 1 (Spred-1)	0.89	-	nuc	0	Membrane; peripheral membrane protein				444
Q38741 UniProt NPD GO	SBP1_ANTMA	Squamosa promoter-binding protein 1	0.89	-	nuc	0	Nucleus				131
Q9M2Q6 UniProt NPD GO	SPL15_ARATH	Squamosa promoter-binding-like protein 15	0.89	-	nuc	0	Nucleus (Probable)				354
Q9S840 UniProt NPD GO	SPL2_ARATH	Squamosa promoter-binding-like protein 2	0.89	+	nuc	0	Nucleus (Probable)				419
O70166 UniProt NPD GO	STMN3_MOUSE	Stathmin-3 (SCG10-like protein) (SCG10-related protein HiAT3) (Hippocampus abundant transcript 3)	0.89	-	nuc	0					180
Q5K651 UniProt NPD GO	SAMD9_HUMAN	Sterile alpha motif domain-containing protein 9	0.89	-	nuc	0					1589
Q12286 UniProt NPD GO	SUT2_YEAST	Sterol uptake protein 2	0.89	+	nuc	0	Nucleus	nucleus [IDA]			268
Q03088 UniProt NPD GO	SVL3_YEAST	Styryl dye vacuolar localization protein 3	0.89	-	nuc	0	Cytoplasm. Bud. Bud neck. Cytoplasm; cell cortex. And cell periphery	bud neck [IDA] cytoplasm [IDA]			825
Q8WXH5 UniProt NPD GO	SOCS4_HUMAN	Suppressor of cytokine signaling 4 (SOCS-4) (Suppressor of cytokine signaling 7) (SOCS-7)	0.89	-	nuc	0					440
P87164 UniProt NPD GO	SEF1_KLULA	Suppressor protein SEF1	0.89	-	nuc	0	Nucleus (Probable)				1087
P70281 UniProt NPD GO	SYCP3_MOUSE	Synaptonemal complex protein 3 (SCP-3)	0.89	-	nuc	0	Nucleus (By similarity). In tripartite segments of synaptonemal complexes, irrespective of whether t ...	condensed chromosome [IDA] lateral element [IDA] transverse filament [IDA]			254
Q9EPZ6 UniProt NPD GO	TBX18_MOUSE	T-box transcription factor TBX18 (T-box protein 18)	0.89	+	nuc	0	Nucleus (Potential)				613
Q9H0W7 UniProt NPD GO	THAP2_HUMAN	THAP domain-containing protein 2	0.89	-	nuc	0					228
Q8WY91 UniProt NPD GO	THAP4_HUMAN	THAP domain-containing protein 4	0.89	-	nuc	0					577
Q642B6 UniProt NPD GO	THAP4_RAT	THAP domain-containing protein 4	0.89	-	nuc	0					569
Q9H2D6 UniProt NPD GO	TARA_HUMAN	TRIO and F-actin-binding protein (Protein Tara) (Trio-associated repeat on actin)	0.89	-	nuc	0	Nucleus. Cytoplasm; localized to F-actin in a periodic pattern	actin cytoskeleton [NAS]	609823		2365
Q9ULW0 UniProt NPD GO	TPX2_HUMAN	Targeting protein for Xklp2 (Restricted expression proliferation-associated protein 100) (p100) (Dif ...	0.89	-	nuc	0	Nucleus. During mitosis it is strictly associated with the spindle pole and with the mitotic spindle ...	nucleus [TAS] spindle [TAS]	605917	1OL5	747
Q5TCY1 UniProt NPD GO	TTBK1_HUMAN	Tau-tubulin kinase 1 (EC 2.7.11.1) (Brain-derived tau kinase)	0.89	-	nuc	0					1321
O42450 UniProt NPD GO	THA_PYGAD	Thyroid hormone receptor alpha (Fragment)	0.89	+	nuc	0	Nucleus				402
Q9Z1J1 UniProt NPD GO	TF7L1_MOUSE	Transcription factor 7-like 1 (HMG box transcription factor 3) (TCF-3) (mTCF-3)	0.89	+	nuc	0	Nucleus				584
P52167 UniProt NPD GO	GATB_BOMMO	Transcription factor BCFI (GATA-beta) (BmGATA-beta)	0.89	+	nuc	1	Nucleus				508
Q14188 UniProt NPD GO	TDP2_HUMAN	Transcription factor Dp-2 (E2F dimerization partner 2)	0.89	-	nuc	0	Nucleus		602160	1CF7	446
P29056 UniProt NPD GO	TF3B_YEAST	Transcription factor IIIB 70 kDa subunit (TFIIIB) (B-related factor) (BRF)	0.89	+	nuc	0	Nucleus	transcription factor TFIIIB complex [TAS]		1NGM	596
P52954 UniProt NPD GO	LBX1_HUMAN	Transcription factor LBX1	0.89	+	nuc	0	Nucleus (Probable)				280
O94993 UniProt NPD GO	SOX30_HUMAN	Transcription factor SOX-30	0.89	-	nuc	0	Nucleus		606698		753
Q6EJB7 UniProt NPD GO	SOX3_BRARE	Transcription factor Sox-3	0.89	+	nuc	0	Nucleus				300
Q10280 UniProt NPD GO	GAF1_SCHPO	Transcription factor gaf1 (Gaf-1)	0.89	-	nuc	0	Nucleus (Probable)				855
Q9D902 UniProt NPD GO	T2EB_MOUSE	Transcription initiation factor IIE subunit beta (TFIIE-beta)	0.89	+	nuc	0	Nucleus (By similarity)				292
O13701 UniProt NPD GO	TAF7_SCHPO	Transcription initiation factor TFIID subunit 7 (Transcription initiation factor TFIID 55 kDa subuni ...	0.89	-	nuc	0	Nucleus	transcription factor TFIID complex [TAS]			393
P21657 UniProt NPD GO	DAL81_YEAST	Transcriptional activator protein DAL81 (Regulatory protein UGA35)	0.89	-	nuc	0	Nucleus	nucleus [IC]			970
Q3SZP8 UniProt NPD GO	TAD2L_BOVIN	Transcriptional adapter 2-like (ADA2-like protein)	0.89	+	nuc	0	Nucleus (By similarity)				443
P34257 UniProt NPD GO	TC3A_CAEEL	Transposable element Tc3 transposase	0.89	-	nuc	0	Nucleus			1U78	329
O08784 UniProt NPD GO	TCOF_MOUSE	Treacle protein (Treacher Collins syndrome protein homolog)	0.89	+	nuc	0	Nucleus; nucleolus (Potential)				1320
P50753 UniProt NPD GO	TNNT2_RAT	Troponin T, cardiac muscle (TnTc) (Cardiac muscle troponin T) (cTnT)	0.89	+	nuc	0					298
Q80UG8 UniProt NPD GO	TTLL4_MOUSE	Tubulin--tyrosine ligase-like protein 4	0.89	-	nuc	0					1193
Q940D0 UniProt NPD GO	ARR1_ARATH	Two-component response regulator ARR1	0.89	-	nuc	0	Nucleus				690
O49397 UniProt NPD GO	ARR10_ARATH	Two-component response regulator ARR10 (Receiver-like protein 4)	0.89	-	nuc	0	Nucleus			1IRZ	552
Q689G9 UniProt NPD GO	PRR1_ORYSA	Two-component response regulator-like PRR1 (Pseudo-response regulator 1) (OsPRR1)	0.89	-	nuc	0	Nucleus (Probable)				518
P52332 UniProt NPD GO	JAK1_MOUSE	Tyrosine-protein kinase JAK1 (EC 2.7.10.2) (Janus kinase 1) (JAK-1)	0.89	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...				1153
P40048 UniProt NPD GO	PTP3_YEAST	Tyrosine-protein phosphatase 3 (EC 3.1.3.48) (Protein-tyrosine phosphatase 3) (PTPase 3)	0.89	-	nuc	0		cytoplasm [IDA]			928
Q15678 UniProt NPD GO	PTN14_HUMAN	Tyrosine-protein phosphatase non-receptor type 14 (EC 3.1.3.48) (Protein-tyrosine phosphatase pez)	0.89	-	nuc	0			603155	2BZL	1187
Q6DH74 UniProt NPD GO	SNUT3_BRARE	U4/U6.U5 tri-snRNP-associated protein 3	0.89	+	nuc	0	Nucleus (Potential)				158
Q8K194 UniProt NPD GO	SNUT3_MOUSE	U4/U6.U5 tri-snRNP-associated protein 3	0.89	+	nuc	0	Nucleus (Potential)				155
Q6DDA4 UniProt NPD GO	SNUT3_XENTR	U4/U6.U5 tri-snRNP-associated protein 3	0.89	+	nuc	0	Nucleus (Potential)				156
Q3TDN2 UniProt NPD GO	UBXD8_MOUSE	UBX domain-containing protein 8	0.89	+	nuc	0	Cytoplasm (By similarity)				445
O01757 UniProt NPD GO	YIL8_CAEEL	UPF0202 protein F55A12.8	0.89	-	nuc	0	Nucleus (By similarity)				1043
Q92560 UniProt NPD GO	BAP1_HUMAN	Ubiquitin carboxyl-terminal hydrolase BAP1 (EC 3.4.19.12) (BRCA1-associated protein 1) (Cerebral pro ...	0.89	+	nuc	0	Nucleus	nucleus [TAS]	603089		729
Q9ES00 UniProt NPD GO	UBE4B_MOUSE	Ubiquitin conjugation factor E4 B (Ubiquitin fusion degradation protein 2) (Ufd2a)	0.89	-	nuc	0	Cytoplasm	cytoplasm [IDA] ubiquitin ligase complex [TAS]			1173

You are viewing entries 4901 to 4950 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.