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
Q8VHV8 UniProt NPD GO	SELS_RAT	Selenoprotein S (VCP-interacting membrane protein) (Sg2)	0.66	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				190
Q9WTL3 UniProt NPD GO	SEM6C_RAT	Semaphorin-6C precursor (Semaphorin Y) (Sema Y)	0.66	-	exc	1	Membrane; single-pass type I membrane protein				960
Q5U7N2 UniProt NPD GO	SEMG2_PONPY	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.66	-	nuc	0	Secreted protein (By similarity)				581
Q6Q137 UniProt NPD GO	SEPT7_BOVIN	Septin-7 (CDC10 protein homolog)	0.66	-	nuc	0					437
Q16181 UniProt NPD GO	SEPT7_HUMAN	Septin-7 (CDC10 protein homolog)	0.66	-	nuc	0		nucleus [IDA] stress fiber [IDA]	603151		437
Q9WVC0 UniProt NPD GO	SEPT7_RAT	Septin-7 (CDC10 protein homolog)	0.66	-	nuc	0		membrane fraction [IDA]			436
Q5R1W1 UniProt NPD GO	SEPT7_PANTR	Septin-7 (CDC10 protein homolog) (Fragment)	0.66	-	nuc	0					434
Q9UEE5 UniProt NPD GO	ST17A_HUMAN	Serine/threonine-protein kinase 17A (EC 2.7.11.1) (DAP kinase-related apoptosis-inducing protein kin ...	0.66	-	cyt	0	Nucleus	nucleus [IEP]	604726		414
Q64702 UniProt NPD GO	PLK4_MOUSE	Serine/threonine-protein kinase PLK4 (EC 2.7.11.21) (Polo-like kinase 4) (PLK-4) (Serine/threonine-p ...	0.66	-	nuc	0				1MBY	925
Q66LE6 UniProt NPD GO	2ABD_HUMAN	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform (PP2A, subunit B, ...	0.66	-	nuc	0	Cytoplasm (By similarity)				453
Q8BG02 UniProt NPD GO	2ABG_MOUSE	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform (PP2A, subunit B, ...	0.66	-	nuc	0					447
Q9VIQ0 UniProt NPD GO	SNPF_DROME	Short neuropeptide F precursor [Contains: sNPF-associated peptide (sNPF-AP); sNPF peptide 2 (sNPF-2) ...	0.66	-	exc	0	Secreted protein	extracellular region [NAS]			300
P42229 UniProt NPD GO	STA5A_HUMAN	Signal transducer and activator of transcription 5A	0.66	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation		601511		794
Q9R053 UniProt NPD GO	SC11A_MOUSE	Sodium channel protein type 11 subunit alpha (Sodium channel protein type XI subunit alpha) (Voltage ...	0.66	-	end	22	Membrane; multi-pass membrane protein (By similarity)				1765
P83211 UniProt NPD GO	HSP1_MURBR	Sperm protamine P1 precursor	0.66	+	nuc	0	Nucleus				107
P36084 UniProt NPD GO	MUD2_YEAST	Splicing factor MUD2	0.66	-	nuc	0		commitment complex [IPI]			527
Q5Y171 UniProt NPD GO	SPRE2_XENTR	Sprouty-related, EVH1 domain-containing protein 2 (Spred-2)	0.66	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				409
Q9HD15 UniProt NPD GO	SRA1_HUMAN	Steroid receptor RNA activator 1 (Steroid receptor RNA activator protein) (SRAP)	0.66	-	nuc	0	Nucleus. Cytoplasm	nucleus [IDA] ribonucleoprotein complex [IPI]	603819		236
P31928 UniProt NPD GO	SPS_SPIOL	Sucrose-phosphate synthase (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferase)	0.66	-	cyt	0					1056
Q01277 UniProt NPD GO	SCON2_NEUCR	Sulfur controller 2 (SCON2)	0.66	-	nuc	0					650
O65359 UniProt NPD GO	SYP41_ARATH	Syntaxin-41 (AtSYP41) (AtTLG2a)	0.66	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				322
Q08851 UniProt NPD GO	STX5_RAT	Syntaxin-5	0.66	-	nuc	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...	endoplasmic reticulum [IMP] Golgi membrane [IMP]			301
Q9WV89 UniProt NPD GO	STXB4_MOUSE	Syntaxin-binding protein 4 (Syntaxin 4-interacting protein) (Synip)	0.66	-	nuc	0	Cytoplasm			1WI4	557
Q16650 UniProt NPD GO	TBR1_HUMAN	T-brain-1 protein (T-box brain protein 1) (TBR-1) (TES-56)	0.66	+	nuc	0	Nucleus (Potential)		604616		682
Q64336 UniProt NPD GO	TBR1_MOUSE	T-brain-1 protein (T-box brain protein 1) (TBR-1) (TES-56)	0.66	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			681
Q80XJ3 UniProt NPD GO	K1043_MOUSE	TPR repeat-containing protein KIAA1043	0.66	-	nuc	0					1691
P30974 UniProt NPD GO	TLR1_DROME	Tachykinin-like peptides receptor 86C (NKD)	0.66	-	end	7	Membrane; multi-pass membrane protein				504
O60784 UniProt NPD GO	TOM1_HUMAN	Target of Myb protein 1	0.66	-	nuc	0	Cytoplasm (Probable)	cytosol [IDA] early endosome [IDA] membrane [IDA]	604700	1WRD	492
Q06163 UniProt NPD GO	TERT_YEAST	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit)	0.66	-	nuc	0	Nucleus	nucleolus [IDA] nucleus [IDA] telomerase catalytic core complex [IDA]			884
P29550 UniProt NPD GO	TEBA_STYMY	Telomere-binding protein alpha subunit	0.66	-	mit	0	Nucleus				493
P06882 UniProt NPD GO	THYG_RAT	Thyroglobulin precursor	0.66	-	nuc	0	Secreted protein	extracellular space [TAS]			2768
P10828 UniProt NPD GO	THB1_HUMAN	Thyroid hormone receptor beta-1	0.66	+	cyt	0	Nucleus	nucleus [TAS]	188570	2NLL	461
P37826 UniProt NPD GO	THB2_RAT	Thyroid hormone receptor beta-2	0.66	+	cyt	0	Nucleus				514
Q6ZXC3 UniProt NPD GO	TRH_CHICK	Thyroliberin precursor [Contains: Prothyroliberin; Thyroliberin (Thyrotropin-releasing hormone) (TRH ...	0.66	-	exc	0	Secreted protein				260
Q9R1F8 UniProt NPD GO	TLR2_CRIGR	Toll-like receptor 2 precursor (CD282 antigen)	0.66	-	mit	1	Membrane; single-pass type I membrane protein (By similarity)				784
P58682 UniProt NPD GO	TLR8_MOUSE	Toll-like receptor 8 precursor	0.66	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [ISS]			1032
Q4I5I4 UniProt NPD GO	SPT5_GIBZE	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.66	+	nuc	0	Nucleus (By similarity)				1042
Q7T2U9 UniProt NPD GO	TFCP2_CHICK	Transcription factor CP2	0.66	-	nuc	0	Nucleus (By similarity)				496
Q15329 UniProt NPD GO	E2F5_HUMAN	Transcription factor E2F5 (E2F-5)	0.66	-	nuc	0	Nucleus		600967		346
Q04666 UniProt NPD GO	HES1_RAT	Transcription factor HES-1 (Hairy and enhancer of split 1) (Hairy-like) (RHL)	0.66	-	nuc	0	Nucleus				281
Q9LX82 UniProt NPD GO	MYB48_ARATH	Transcription factor MYB48 (Myb-related protein 48) (AtMYB48)	0.66	-	nuc	0	Nucleus. Isoform MYB48-2 and isoform MYB48-3 (harboring both NLS1 and NLS2) are nuclear, werheas iso ...				256
Q61473 UniProt NPD GO	SOX17_MOUSE	Transcription factor SOX-17	0.66	+	nuc	0	Nucleus (Potential)				419
P08047 UniProt NPD GO	SP1_HUMAN	Transcription factor Sp1	0.66	-	nuc	0	Nucleus	nucleus [NAS]	189906	1VA3	785
O89090 UniProt NPD GO	SP1_MOUSE	Transcription factor Sp1	0.66	-	nuc	0	Nucleus	nucleus [IDA]			784
Q01714 UniProt NPD GO	SP1_RAT	Transcription factor Sp1	0.66	-	nuc	0	Nucleus				786
O35906 UniProt NPD GO	SPIB_MOUSE	Transcription factor Spi-B	0.66	+	nuc	0	Nucleus (Probable)	transcription factor complex [IC]			267
Q9VWY6 UniProt NPD GO	TAF8_DROME	Transcription initiation factor TFIID subunit 8 (Protein prodos)	0.66	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]			328
Q02516 UniProt NPD GO	HAP5_YEAST	Transcriptional activator HAP5	0.66	-	nuc	0	Nucleus	CCAAT-binding factor complex [TAS] nucleus [IC]			242
P38429 UniProt NPD GO	SAP30_YEAST	Transcriptional regulatory protein SAP30	0.66	-	nuc	0	Nucleus	histone deacetylase complex [IPI]			201
Q9Y4A5 UniProt NPD GO	TRRAP_HUMAN	Transformation/transcription domain-associated protein (350/400 kDa PCAF-associated factor) (PAF350/ ...	0.66	-	end	0	Nucleus	nucleus [IDA] PCAF complex [NAS] TIP60 histone acetyltransferase complex [IDA]	603015		3859

You are viewing entries 16051 to 16100 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.