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
Q5IBH7 UniProt NPD GO	SPDYA_MOUSE	Speedy protein A (Speedy-1) (Spy1) (Rapid inducer of G2/M progression in oocytes A) (RINGO A) (mSpy/ ...	0.54	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			310
Q6DMN8 UniProt NPD GO	SPAT4_PANTR	Spermatogenesis-associated protein 4	0.54	-	nuc	0					305
Q755C4 UniProt NPD GO	IPL1_ASHGO	Spindle assembly checkpoint kinase (EC 2.7.11.1) (Aurora kinase)	0.54	+	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and on elongated and disassembling spin ...				367
Q9C004 UniProt NPD GO	SPY4_HUMAN	Sprouty homolog 4 (Spry-4)	0.54	-	nuc	0	Cytoplasm		607984		299
Q13285 UniProt NPD GO	STF1_HUMAN	Steroidogenic factor 1 (STF-1) (SF-1) (Adrenal 4-binding protein) (Steroid hormone receptor Ad4BP) ( ...	0.54	+	nuc	0	Nucleus	nucleus [IDA]	184757	1ZDT	461
Q98989 UniProt NPD GO	STXA_SYNHO	Stonustoxin subunit alpha (SNTX subunit alpha)	0.54	-	cyt	0	Secreted protein. Secreted into the venom gland lumen. The secretion is proved by the fact that the ...				702
O14893 UniProt NPD GO	GEMI2_HUMAN	Survival of motor neuron protein-interacting protein 1 (SMN-interacting protein 1) (Component of gem ...	0.54	-	nuc	0	Nucleus; gem. Localized in subnuclear structures next to coiled bodies, called gems, which are highl ...	cytoplasm [TAS] nucleus [TAS] spliceosome complex [TAS]	602595		280
Q8NB59 UniProt NPD GO	SYT14_HUMAN	Synaptotagmin-14 (Synaptotagmin XIV) (SytXIV)	0.54	-	nuc	1 *	Membrane; single-pass type III membrane protein (Potential)				555
P59926 UniProt NPD GO	SYT15_RAT	Synaptotagmin-15 (Synaptotagmin XV) (SytXV)	0.54	-	mit	1 *	Membrane; single-pass type III membrane protein (By similarity)				422
Q4VBI7 UniProt NPD GO	STX18_BRARE	Syntaxin-18	0.54	+	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...				314
Q9GZC8 UniProt NPD GO	SID1_CAEEL	Systemic RNA interference defective protein 1 precursor (Systemic RNAi enabling protein)	0.54	-	end	11	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS] plasma membrane [IDA]			776
P70327 UniProt NPD GO	TBX6_MOUSE	T-box transcription factor TBX6 (T-box protein 6)	0.54	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			540
Q9XSJ9 UniProt NPD GO	CD3Z_PIG	T-cell surface glycoprotein CD3 zeta chain precursor (T-cell receptor T3 zeta chain)	0.54	+	nuc	1 *	Membrane; single-pass type I membrane protein				163
P58802 UniProt NPD GO	TBC10_MOUSE	TBC1 domain family member 10A (EBP50-PDX interactor of 64 kDa) (EPI64 protein)	0.54	-	nuc	0	Localizes to the microvilli-rich region of the syncytiotrophoblast (By similarity)				500
Q13888 UniProt NPD GO	TF2H2_HUMAN	TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) ( ...	0.54	-	nuc	0	Nucleus		601748	1Z60	395
P53038 UniProt NPD GO	TEL2_YEAST	Telomere length regulation protein TEL2	0.54	-	cyt	0	Nucleus (Potential)	nuclear telomere cap complex [IDA]			688
Q01534 UniProt NPD GO	TSPY1_HUMAN	Testis-specific Y-encoded protein 1	0.54	-	cyt	0	Cytoplasm. Predominantly. Nucleus. Also found in nucleus		480100		308
Q95LY5 UniProt NPD GO	TTC12_MACFA	Tetratricopeptide repeat protein 12 (TPR repeat protein 12) (Fragment)	0.54	+	cyt	0					577
Q8CC21 UniProt NPD GO	TTC19_MOUSE	Tetratricopeptide repeat protein 19 (TPR repeat protein 19)	0.54	-	mit	0					365
Q6R5P0 UniProt NPD GO	TLR11_MOUSE	Toll-like receptor 11 precursor	0.54	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				926
P83510 UniProt NPD GO	TNIK_MOUSE	Traf2 and NCK-interacting kinase (EC 2.7.11.1) (Fragments)	0.54	-	nuc	0					916
P20290 UniProt NPD GO	BTF3_HUMAN	Transcription factor BTF3 (RNA polymerase B transcription factor 3)	0.54	-	nuc	0	Nucleus		602542		206
O54790 UniProt NPD GO	MAFG_MOUSE	Transcription factor MafG (V-maf musculoaponeurotic fibrosarcoma oncogene homolog G)	0.54	-	nuc	0	Nucleus (By similarity)			1K1V	162
Q6P3D7 UniProt NPD GO	SPIC_MOUSE	Transcription factor Spi-C (Pu.1-related factor) (Prf)	0.54	+	nuc	0	Nucleus (Probable)				242
Q12030 UniProt NPD GO	TAF10_YEAST	Transcription initiation factor TFIID subunit 10 (TBP-associated factor 10) (TBP-associated factor 2 ...	0.54	-	nuc	0	Nucleus	SAGA complex [IDA] SLIK (SAGA-like) complex [IPI] transcription factor TFIID complex [IDA]			206
P49848 UniProt NPD GO	TAF6_HUMAN	Transcription initiation factor TFIID subunit 6 (Transcription initiation factor TFIID 70 kDa subuni ...	0.54	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA] transcription factor TFIIE complex [TAS]	602955		677
Q63801 UniProt NPD GO	TAF6_RAT	Transcription initiation factor TFIID subunit 6 (Transcription initiation factor TFIID 70 kDa subuni ...	0.54	-	nuc	0	Nucleus				678
P56093 UniProt NPD GO	TUP1_CANAL	Transcriptional repressor TUP1	0.54	-	nuc	0					514
Q6RI86 UniProt NPD GO	TRPA1_RAT	Transient receptor potential cation channel subfamily A member 1 (Ankyrin-like with transmembrane do ...	0.54	-	end	5	Membrane; multi-pass membrane protein (Probable)				1125
P23787 UniProt NPD GO	TERA_XENLA	Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)-ATPase p97 subunit)	0.54	+	cyt	0	Cytoplasm. Nucleus				805
P54812 UniProt NPD GO	TERA2_CAEEL	Transitional endoplasmic reticulum ATPase homolog 2 (p97/CDC48 homolog 2) (Cell division cycle-relat ...	0.54	+	nuc	0					810
Q4KMQ2 UniProt NPD GO	TM16F_HUMAN	Transmembrane protein 16F	0.54	-	end	8	Membrane; multi-pass membrane protein (Probable)		608663		910
Q04706 UniProt NPD GO	YME5_YEAST	Transposon Ty1 protein A	0.54	-	nuc	0					440
Q12231 UniProt NPD GO	YMU1_YEAST	Transposon Ty1 protein A	0.54	-	nuc	0					440
Q99PQ1 UniProt NPD GO	TRI12_MOUSE	Tripartite motif-containing protein 12	0.54	-	nuc	0	Cytoplasm	cytoplasm [IDA]			284
Q9TSW0 UniProt NPD GO	TRI15_PIG	Tripartite motif-containing protein 15 (Zinc finger protein B7)	0.54	-	cyt	0					461
Q7YR34 UniProt NPD GO	TRI26_PANTR	Tripartite motif-containing protein 26 (Zinc finger protein 173)	0.54	-	cyt	0					539
O77666 UniProt NPD GO	TRI26_PIG	Tripartite motif-containing protein 26 (Zinc finger protein 173)	0.54	-	cyt	0					545
Q14134 UniProt NPD GO	TRI29_HUMAN	Tripartite motif-containing protein 29 (Ataxia-telangiectasia group D-associated protein)	0.54	+	nuc	0	Cytoplasm. Colocalizes with intermediate filaments			2CSV	588
Q9C037 UniProt NPD GO	TRIM4_HUMAN	Tripartite motif-containing protein 4 (RING finger protein 87)	0.54	-	cyt	0					500
Q9NZQ9 UniProt NPD GO	TMOD4_HUMAN	Tropomodulin-4 (Skeletal muscle tropomodulin) (Sk-Tmod)	0.54	-	nuc	0			605834		345
O08970 UniProt NPD GO	TUFT1_MOUSE	Tuftelin	0.54	-	nuc	0	Secreted protein (By similarity). Secreted at a very early stage of enamel formation, concentrated a ...	extracellular region [ISS]			390
O00300 UniProt NPD GO	TR11B_HUMAN	Tumor necrosis factor receptor superfamily member 11B precursor (Osteoprotegerin) (Osteoclastogenesi ...	0.54	-	nuc	0	Secreted protein	extracellular region [TAS]	602643		401
Q07011 UniProt NPD GO	TNR9_HUMAN	Tumor necrosis factor receptor superfamily member 9 precursor (4-1BB ligand receptor) (T-cell antige ...	0.54	+	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	602250		255
P42680 UniProt NPD GO	TEC_HUMAN	Tyrosine-protein kinase Tec (EC 2.7.10.2)	0.54	-	cyt	0	Cytoplasm (Probable)		600583		631
Q01974 UniProt NPD GO	ROR2_HUMAN	Tyrosine-protein kinase transmembrane receptor ROR2 precursor (EC 2.7.10.1) (Neurotrophic tyrosine k ...	0.54	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	602337		943
P29351 UniProt NPD GO	PTN6_MOUSE	Tyrosine-protein phosphatase non-receptor type 6 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1C) (PT ...	0.54	-	nuc	0	Cytoplasm	cytoplasm [TAS]			595
P81718 UniProt NPD GO	PTN6_RAT	Tyrosine-protein phosphatase non-receptor type 6 (EC 3.1.3.48) (Protein-tyrosine phosphatase SHP-1)	0.54	-	nuc	0	Cytoplasm (By similarity)				613
Q06682 UniProt NPD GO	UBX5_YEAST	UBX domain-containing protein 5	0.54	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			500
Q09332 UniProt NPD GO	UGGG_DROME	UDP-glucose:glycoprotein glucosyltransferase precursor (EC 2.4.1.-) (UDP--Glc:glycoprotein glucosylt ...	0.54	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen	cytoplasm [TAS] nuclear envelope [IDA] rough endoplasmic reticulum [IDA]			1548

You are viewing entries 22801 to 22850 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.