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
P56726 UniProt NPD GO	SMO_MOUSE	Smoothened homolog precursor (SMO)	0.44	+	end	7	Membrane; multi-pass membrane protein				793
P01286 UniProt NPD GO	SLIB_HUMAN	Somatoliberin precursor (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) ( ...	0.44	-	nuc	0	Secreted protein		139190		108
P34006 UniProt NPD GO	SOMA_PRIGL	Somatotropin (Growth hormone)	0.44	-	nuc	0	Secreted protein				183
P34747 UniProt NPD GO	SOMA_THUAL	Somatotropin (Growth hormone)	0.44	-	nuc	0	Secreted protein				187
Q01283 UniProt NPD GO	SOMA_LATCA	Somatotropin precursor (Growth hormone)	0.44	-	exc	0	Secreted protein				204
Q9DEV3 UniProt NPD GO	SOMA_PERFV	Somatotropin precursor (Growth hormone)	0.44	-	exc	0	Secreted protein				204
Q9IB11 UniProt NPD GO	SOMA_SCIOC	Somatotropin precursor (Growth hormone)	0.44	-	exc	0	Secreted protein				204
P09113 UniProt NPD GO	SOMA_THUTH	Somatotropin precursor (Growth hormone)	0.44	-	exc	0	Secreted protein				204
P28220 UniProt NPD GO	SORB_PIG	Sorbin	0.44	-	nuc	0					153
Q6NYA0 UniProt NPD GO	SFRS1_BRARE	Splicing factor, arginine/serine-rich 1	0.44	+	nuc	0	Nucleus (By similarity)				245
Q8R4Y4 UniProt NPD GO	STAB1_MOUSE	Stabilin-1 precursor (FEEL-1 protein)	0.44	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [ISS]			2571
Q6PDS3 UniProt NPD GO	SARM1_MOUSE	Sterile alpha and TIR motif-containing protein 1 (Tir-1 homolog)	0.44	-	cyt	0	Cytoplasm (By similarity)				724
P16375 UniProt NPD GO	7UP1_DROME	Steroid receptor seven-up, isoforms B/C	0.44	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA]			543
P97260 UniProt NPD GO	SCAP_CRIGR	Sterol regulatory element-binding protein cleavage-activating protein (SREBP cleavage-activating pro ...	0.44	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to membrane [ISS]			1276
Q9Y7X6 UniProt NPD GO	ISH1_SCHPO	Stress response protein ish1	0.44	-	mit	1 *	Nucleus; nuclear membrane				684
Q8BGG7 UniProt NPD GO	STS1_MOUSE	Suppressor of T-cell receptor signaling 1 (Sts-1) (Cbl-interacting protein p70)	0.44	-	nuc	0	Cytoplasm (By similarity). Nucleus (Potential)				638
Q800L1 UniProt NPD GO	SURF1_CHICK	Surfeit locus protein 1	0.44	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				309
O57595 UniProt NPD GO	SURF5_FUGRU	Surfeit locus protein 5	0.44	-	nuc	0					200
P30233 UniProt NPD GO	2SS2_CAPMA	Sweet protein mabinlin-2 precursor (Mabinlin II) (MAB II) [Contains: Sweet protein mabinlin-2 chain ...	0.44	-	exc	1 *					155
Q96A49 UniProt NPD GO	SYAP1_HUMAN	Synapse-associated protein 1	0.44	-	exc	0				1X3A	352
Q5R8F5 UniProt NPD GO	RIC8A_PONPY	Synembryn-A (Protein Ric-8A)	0.44	-	nuc	0	Cytoplasm (By similarity)				530
Q9D3G5 UniProt NPD GO	STX11_MOUSE	Syntaxin-11	0.44	-	nuc	0	Membrane; peripheral membrane protein (Potential)				287
Q39233 UniProt NPD GO	SYP21_ARATH	Syntaxin-21 (AtSYP21) (PEP12 homolog) (AtPEP12) (aPEP12)	0.44	-	nuc	1	Prevacuolar compartment; prevacuolar compartment membrane; single-pass type IV membrane protein				279
O43752 UniProt NPD GO	STX6_HUMAN	Syntaxin-6	0.44	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)	clathrin-coated vesicle [TAS] early endosome [IDA] perinuclear region [IDA] plasma membrane [TAS]	603944		255
Q5R6Q2 UniProt NPD GO	STX6_PONPY	Syntaxin-6	0.44	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				255
Q9JKD8 UniProt NPD GO	TBX21_MOUSE	T-box transcription factor TBX21 (T-box protein 21) (Transcription factor TBLYM) (T-cell-specific T- ...	0.44	+	nuc	0	Nucleus				530
P27633 UniProt NPD GO	TBP_XENLA	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.44	+	nuc	0	Nucleus	transcription factor TFIID complex [NAS]			297
P35054 UniProt NPD GO	TGBR3_PIG	TGF-beta receptor type III precursor (TGFR-3) (Transforming growth factor beta receptor III) (Betagl ...	0.44	-	exc	1	Cell membrane; single-pass type I membrane protein. Secreted protein; serum. Secreted protein; extra ...				848
O75674 UniProt NPD GO	TM1L1_HUMAN	TOM1-like 1 protein (Target of myb-like 1 protein) (Src-activating and signaling molecule protein)	0.44	-	nuc	0	Golgi apparatus; Golgi stack. Endosome; endosomal membrane (Potential)	endosome [TAS] lysosome [TAS]	604701		476
Q969V4 UniProt NPD GO	TEKT1_HUMAN	Tektin-1	0.44	-	nuc	0			609002		418
P22105 UniProt NPD GO	TENX_HUMAN	Tenascin-X precursor (TN-X) (Hexabrachion-like protein)	0.44	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [NAS]	600985	2CUM	4289
Q8BGB2 UniProt NPD GO	TTC7A_MOUSE	Tetratricopeptide repeat protein 7A (TPR repeat protein 7)	0.44	-	cyt	0					858
Q92623 UniProt NPD GO	TTC9_HUMAN	Tetratricopeptide repeat protein 9 (TPR repeat protein 9) (Fragment)	0.44	-	mit	0					336
P47788 UniProt NPD GO	MEPD_PIG	Thimet oligopeptidase (EC 3.4.24.15) (Endopeptidase 24.15)	0.44	-	cyt	0	Cytoplasm				686
Q91XB0 UniProt NPD GO	TREX1_MOUSE	Three prime repair exonuclease 1 (EC 3.1.11.2) (3'-5' exonuclease TREX1)	0.44	-	cyt	1	Nucleus (By similarity)	nuclear envelope [ISS]			314
Q28178 UniProt NPD GO	TSP1_BOVIN	Thrombospondin-1 precursor	0.44	-	nuc	0					1170
P09933 UniProt NPD GO	PERT_PIG	Thyroid peroxidase precursor (EC 1.11.1.8) (TPO)	0.44	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				926
P19637 UniProt NPD GO	TPA_RAT	Tissue-type plasminogen activator precursor (EC 3.4.21.68) (tPA) (t-PA) (t-plasminogen activator) [C ...	0.44	-	end	0	Secreted protein; extracellular space				559
Q8SPE8 UniProt NPD GO	TLR4_GORGO	Toll-like receptor 4 precursor (CD284 antigen)	0.44	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	lipopolysaccharide receptor complex [ISS]			837
Q9TTN0 UniProt NPD GO	TLR4_PANPA	Toll-like receptor 4 precursor (CD284 antigen)	0.44	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	lipopolysaccharide receptor complex [ISS]			839
Q68Y56 UniProt NPD GO	TLR4_PIG	Toll-like receptor 4 precursor (CD284 antigen)	0.44	-	mit	1	Membrane; single-pass type I membrane protein (By similarity)				841
Q8BYU6 UniProt NPD GO	TOIP2_MOUSE	Torsin-1A-interacting protein 2	0.44	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				502
P13741 UniProt NPD GO	REP1_ZYGFE	Trans-acting factor B (REP1)	0.44	-	nuc	0					224
Q90683 UniProt NPD GO	ITF2_CHICK	Transcription factor 4 (Class A helix-loop-helix transcription factor GE2) (Fragment)	0.44	-	nuc	0	Nucleus (Probable)				85
Q8BMJ8 UniProt NPD GO	SP8_MOUSE	Transcription factor Sp8	0.44	-	nuc	0	Nucleus (Potential)				486
Q8IXZ3 UniProt NPD GO	SP8_HUMAN	Transcription factor Sp8 (Specificity protein 8)	0.44	-	nuc	0	Nucleus (Potential)		608306		508
Q8R0A0 UniProt NPD GO	T2FB_MOUSE	Transcription initiation factor IIF subunit beta (EC 3.6.1.-) (ATP-dependent helicase GTF2F2) (TFIIF ...	0.44	-	nuc	0	Nucleus (By similarity)				249
P13984 UniProt NPD GO	T2FB_HUMAN	Transcription initiation factor IIF subunit beta (EC 3.6.1.-) (ATP-dependent helicase GTF2F2) (TFIIF ...	0.44	-	cyt	0	Nucleus		189969	2BBY	249
Q91857 UniProt NPD GO	TAF6_XENLA	Transcription initiation factor TFIID subunit 6 (Transcription initiation factor TFIID 70 kDa subuni ...	0.44	-	nuc	0	Nucleus (By similarity)				618
P42669 UniProt NPD GO	PURA_MOUSE	Transcriptional activator protein Pur-alpha (Purine-rich single-stranded DNA-binding protein alpha)	0.44	-	cyt	0	Nucleus	cytoplasm [IDA] DNA replication factor A complex [IDA] nucleus [IDA]			321

You are viewing entries 29301 to 29350 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.