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
Q24535 UniProt NPD GO	SRF_DROME	Serum response factor homolog (dSRF) (Protein blistered)	0.83	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			449
Q9XT60 UniProt NPD GO	SRY_CANFA	Sex-determining region Y protein (Testis-determining factor)	0.83	+	nuc	0	Nucleus				220
Q6TC30 UniProt NPD GO	SRY_ERIBA	Sex-determining region Y protein (Testis-determining factor)	0.83	+	nuc	0	Nucleus				221
Q864P4 UniProt NPD GO	SRY_GLOMA	Sex-determining region Y protein (Testis-determining factor)	0.83	+	nuc	0	Nucleus				201
Q6TC28 UniProt NPD GO	SRY_LUTLU	Sex-determining region Y protein (Testis-determining factor)	0.83	+	nuc	0	Nucleus				219
Q14765 UniProt NPD GO	STAT4_HUMAN	Signal transducer and activator of transcription 4	0.83	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation		600558		748
O88279 UniProt NPD GO	SLIT1_RAT	Slit homolog 1 protein precursor (Slit-1) (Multiple epidermal growth factor-like domains 4)	0.83	-	nuc	0	Secreted protein (By similarity)				1531
O88280 UniProt NPD GO	SLIT3_RAT	Slit homolog 3 protein precursor (Slit-3) (Multiple epidermal growth factor-like domains 5)	0.83	-	nuc	0	Secreted protein (By similarity)				1523
Q9WVB4 UniProt NPD GO	SLIT3_MOUSE	Slit homolog 3 protein precursor (Slit-3) (Slit3)	0.83	-	nuc	0	Secreted protein (By similarity)	extracellular space [IDA]			1523
P90895 UniProt NPD GO	GCY33_CAEEL	Soluble guanylate cyclase gcy-33 (EC 4.6.1.2)	0.83	+	nuc	0	Cytoplasm (By similarity)				945
Q9I7W5 UniProt NPD GO	SAS10_DROME	Something about silencing protein 10	0.83	-	nuc	0	Nucleus (Probable)	cytoplasm [NAS]			428
Q7SB97 UniProt NPD GO	MVP1_NEUCR	Sorting nexin mvp-1	0.83	-	nuc	0	Cytoplasm (By similarity)				780
P67837 UniProt NPD GO	HSP1_DIDMA	Sperm protamine P1	0.83	+	nuc	0	Nucleus				57
Q8WNZ8 UniProt NPD GO	HSP1_HIPCO	Sperm protamine P1	0.83	+	nuc	0	Nucleus (By similarity)				48
P67836 UniProt NPD GO	HSP1_MONDO	Sperm protamine P1	0.83	+	nuc	0	Nucleus				57
Q80ZX8 UniProt NPD GO	SPAG1_MOUSE	Sperm-associated antigen 1 (Infertility-related sperm protein Spag-1) (TPR-containing protein involv ...	0.83	-	nuc	0	Cytoplasm (By similarity)				901
Q9JLI8 UniProt NPD GO	SART3_MOUSE	Squamous cell carcinoma antigen recognized by T-cells 3 (SART-3) (mSART-3) (Tumor-rejection antigen ...	0.83	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized in speckles (By similarity)				962
Q92502 UniProt NPD GO	STAR8_HUMAN	StAR-related lipid transfer protein 8 (StARD8) (START domain-containing protein 8)	0.83	+	nuc	0					1023
Q09002 UniProt NPD GO	STM2B_XENLA	Stathmin-2-B (SCG10 protein homolog B)	0.83	-	nuc	0					178
Q13586 UniProt NPD GO	STIM1_HUMAN	Stromal interaction molecule 1 precursor	0.83	+	end	1	Cell membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	605921		685
O95347 UniProt NPD GO	SMC2_HUMAN	Structural maintenance of chromosome 2-like 1 protein (Chromosome-associated protein E) (hCAP-E) (XC ...	0.83	-	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensin complex [IDA] cytoplasm [IDA] nuclear chromosome [IDA]	605576		1197
P38931 UniProt NPD GO	SSN2_YEAST	Suppressor of RNA polymerase B SSN2 (SCA1 protein)	0.83	-	nuc	0	Nucleus (Potential)	transcription factor complex [TAS]			1420
Q91YU8 UniProt NPD GO	SSF1_MOUSE	Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan homolog)	0.83	-	nuc	0	Nucleus; nucleolus (By similarity)				470
O54928 UniProt NPD GO	SOCS5_MOUSE	Suppressor of cytokine signaling 5 (SOCS-5) (Cytokine-inducible SH2-containing protein 5)	0.83	-	nuc	0		cytoplasm [NAS]			536
O57589 UniProt NPD GO	SURF2_FUGRU	Surfeit locus protein 2 (Surf-2)	0.83	-	nuc	0					242
Q92797 UniProt NPD GO	SYMPK_HUMAN	Symplekin	0.83	+	nuc	0	Cytoskeleton. Cell membrane; cell-cell junction; adherens junction; cytoplasmic side. Cell membrane; ...	cytoplasm [IDA] nucleoplasm [IDA]	602388		1274
O93367 UniProt NPD GO	TLX3_CHICK	T-cell leukemia homeobox protein 3 (Homeobox protein Hox-11L2) (Homeobox TLX-3)	0.83	+	nuc	0	Nucleus (By similarity)				297
Q8TBP0 UniProt NPD GO	TBC16_HUMAN	TBC1 domain family member 16	0.83	-	nuc	0					767
Q92759 UniProt NPD GO	TF2H4_HUMAN	TFIIH basal transcription factor complex p52 subunit (Basic transcription factor 52 kDa subunit) (BT ...	0.83	+	cyt	0	Nucleus	transcription factor TFIIH complex [TAS]	601760		462
P60027 UniProt NPD GO	TF2H4_PANTR	TFIIH basal transcription factor complex p52 subunit (Basic transcription factor 52 kDa subunit) (BT ...	0.83	+	cyt	0	Nucleus (By similarity)				462
Q8WYN3 UniProt NPD GO	TAIP2_HUMAN	TGF-beta-induced apoptosis protein 2 (TAIP-2)	0.83	-	nuc	0	Nucleus (Potential)				585
Q96FV9 UniProt NPD GO	THOC1_HUMAN	THO complex subunit 1 (Tho1) (Nuclear matrix protein p84)	0.83	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nucleus; nucleoplasm; nuclear matrix	nucleus [TAS]	606930	1WXP	657
Q9Y2B4 UniProt NPD GO	T53G5_HUMAN	TP53-target gene 5 protein (TP53-inducible gene 5 protein)	0.83	-	nuc	0	Cell cycle dependent intracellular localization				290
Q9GLM4 UniProt NPD GO	TENS1_BOVIN	Tensin-1	0.83	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion				1715
Q9HBL0 UniProt NPD GO	TENS1_HUMAN	Tensin-1	0.83	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion		600076		1735
P23441 UniProt NPD GO	TITF1_RAT	Thyroid transcription factor 1 (Thyroid nuclear factor 1) (TTF-1) (Homeobox protein Nkx-2.1)	0.83	-	nuc	0	Nucleus	nucleus [TAS]		1FTT	372
P27692 UniProt NPD GO	SPT5_YEAST	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.83	+	nuc	0	Nucleus. Mitochondrion	DSIF complex [IPI] mitochondrion [IDA] nucleus [IDA]			1063
P43079 UniProt NPD GO	CPH1_CANAL	Transcription factor CPH1	0.83	-	nuc	0	Nucleus				656
P19484 UniProt NPD GO	TFEB_HUMAN	Transcription factor EB	0.83	+	nuc	0	Nucleus	nucleus [NAS]	600744		476
Q9R210 UniProt NPD GO	TFEB_MOUSE	Transcription factor EB	0.83	+	nuc	0	Nucleus (By similarity)	transcription factor complex [IDA]			475
P43691 UniProt NPD GO	GATA4_CHICK	Transcription factor GATA-4 (GATA-binding factor 4) (Fragment)	0.83	-	nuc	0	Nucleus				380
Q9P6R0 UniProt NPD GO	TF3B_SCHPO	Transcription factor IIIB 60 kDa subunit (TFIIIB) (B-related factor) (BRF) (TFIIB-related factor)	0.83	+	cyt	0	Nucleus (By similarity)	transcription factor TFIIIB complex [IDA]			500
Q4P7X6 UniProt NPD GO	IWS1_USTMA	Transcription factor IWS1	0.83	+	nuc	0	Nucleus (By similarity)				380
P31364 UniProt NPD GO	POU2_XENLA	Transcription factor POU2 (XLPOU2)	0.83	+	nuc	0	Nucleus				218
Q12224 UniProt NPD GO	RLM1_YEAST	Transcription factor RLM1	0.83	-	nuc	0	Nucleus (Potential)	nucleus [TAS]			676
Q9W757 UniProt NPD GO	SOX10_CHICK	Transcription factor SOX-10 (cSOX10)	0.83	+	nuc	0	Nucleus (By similarity)				461
Q04206 UniProt NPD GO	TF65_HUMAN	Transcription factor p65 (Nuclear factor NF-kappa-B p65 subunit)	0.83	+	nuc	0	Nucleus. Cytoplasm. Nuclear, but also found in the cytoplasm in an inactive form complexed to an inh ...	cytoplasm [IDA] nucleus [IDA] transcription factor complex [IDA]	164014	1NFI	551
P79011 UniProt NPD GO	T2EB_SCHPO	Transcription initiation factor IIE subunit beta (TFIIE-beta)	0.83	-	nuc	0	Nucleus (Probable)	transcription factor TFIIE complex [IDA]			285
Q9R1C0 UniProt NPD GO	TAF7_MOUSE	Transcription initiation factor TFIID subunit 7 (Transcription initiation factor TFIID 55 kDa subuni ...	0.83	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]			341
P53628 UniProt NPD GO	SNF12_YEAST	Transcription regulatory protein SNF12 (SWI/SNF complex component SWP73)	0.83	-	nuc	0	Nucleus	SWI/SNF complex [IMP]			566

You are viewing entries 7601 to 7650 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.