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
Q6CQ91 UniProt NPD GO	PP4R3_KLULA	Serine/threonine-protein phosphatase 4 regulatory subunit 3 (PP4R3)	0.62	-	cyt	0	Nucleus (By similarity)				749
Q90718 UniProt NPD GO	SRF_CHICK	Serum response factor (SRF) (Fragment)	0.62	-	nuc	0	Nucleus (By similarity)				375
O88892 UniProt NPD GO	SERF1_MOUSE	Small EDRK-rich factor 1 (4F5) (m4F5)	0.62	-	nuc	0					62
Q15858 UniProt NPD GO	SCN9A_HUMAN	Sodium channel protein type 9 subunit alpha (Sodium channel protein type IX subunit alpha) (Voltage- ...	0.62	-	end	21	Membrane; multi-pass membrane protein. In neurite terminals (By similarity)		603415		1988
Q98930 UniProt NPD GO	SORL_CHICK	Sortilin-related receptor (Sorting protein-related receptor containing LDLR class A repeats) (SorLA) ...	0.62	-	nuc	0	Membrane; single-pass type I membrane protein (Potential)				1592
Q6C9X0 UniProt NPD GO	SNX41_YARLI	Sorting nexin-41	0.62	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				570
O62479 UniProt NPD GO	SAS6_CAEEL	Spindle assembly abnormal protein 6	0.62	-	nuc	0	Cytoplasm. Centriole. Localizes to centrioles; zyg-1 and sas-5 are required for centriole localizati ...	centriole [IDA] cytoplasm [IDA]			492
Q07798 UniProt NPD GO	SPO75_YEAST	Sporulation-specific protein 75	0.62	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				868
P18410 UniProt NPD GO	SPO7_YEAST	Sporulation-specific protein SPO7	0.62	-	nuc	2		integral to membrane [IDA] nuclear envelope-endoplasmic reticulum network [IDA]			259
P63042 UniProt NPD GO	STMN4_MOUSE	Stathmin-4 (Stathmin-like protein B3) (RB3)	0.62	-	nuc	0					189
P63043 UniProt NPD GO	STMN4_RAT	Stathmin-4 (Stathmin-like protein B3) (RB3)	0.62	-	nuc	0				1Z2B	189
P41830 UniProt NPD GO	CNR14_CAEEL	Steroid hormone receptor family member cnr14	0.62	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			534
P56720 UniProt NPD GO	SRBP1_RAT	Sterol regulatory element-binding protein 1 (SREBP-1) (Sterol regulatory element-binding transcripti ...	0.62	-	mit	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				1024
Q24546 UniProt NPD GO	SYN_DROME	Synapsin [Contains: Synapsin-1 (Syn1) (Syn1-S); Synapsin-2 (Syn2)]	0.62	-	nuc	0	Synapse	terminal button [IDA]			1025
Q5RCK6 UniProt NPD GO	SYT10_PONPY	Synaptotagmin-10 (Synaptotagmin X) (SytX)	0.62	+	nuc	1	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				523
Q9D0I4 UniProt NPD GO	STX17_MOUSE	Syntaxin-17	0.62	-	mit	2	Membrane; single-pass type IV membrane protein. Appears to be associated with a membrane compartment ...				301
Q9Y2K9 UniProt NPD GO	STB5L_HUMAN	Syntaxin-binding protein 5-like (Tomosyn-2) (Lethal(2) giant larvae protein homolog 4)	0.62	-	end	0	Cytoplasm (Potential). Cell membrane; peripheral membrane protein (Potential). Membrane; peripheral ...		609381		1186
Q8WUA7 UniProt NPD GO	TB22A_HUMAN	TBC1 domain family member 22A	0.62	-	nuc	0					517
Q96EK4 UniProt NPD GO	THA11_HUMAN	THAP domain-containing protein 11	0.62	+	nuc	0	Nucleus		609119		313
Q9Y3Q8 UniProt NPD GO	T22D4_HUMAN	TSC22 domain family protein 4 (TSC22-related-inducible leucine zipper protein 2) (Tsc-22-like protei ...	0.62	-	nuc	0	Nucleus (Potential)				395
Q00546 UniProt NPD GO	TENR_CHICK	Tenascin-R precursor (TN-R) (Restrictin)	0.62	-	nuc	0	Secreted protein; extracellular space; extracellular matrix. May be attach to the cell surface of ne ...				1353
Q61241 UniProt NPD GO	TSSK1_MOUSE	Testis-specific serine/threonine-protein kinase 1 (EC 2.7.11.1) (TSSK-1) (Testis-specific kinase 1) ...	0.62	-	nuc	0	Cytoplasm				364
P48307 UniProt NPD GO	TFPI2_HUMAN	Tissue factor pathway inhibitor 2 precursor (TFPI-2) (Placental protein 5) (PP5)	0.62	+	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]	600033	1ZR0	235
P19761 UniProt NPD GO	TFPI1_RABIT	Tissue factor pathway inhibitor precursor (TFPI) (Lipoprotein-associated coagulation inhibitor) (LAC ...	0.62	-	exc	0	Secreted protein				300
P58753 UniProt NPD GO	TIRAP_HUMAN	Toll-interleukin 1 receptor domain-containing adapter protein (TIR domain-containing adapter protein ...	0.62	+	nuc	0	Cytoplasm (By similarity)		606252		221
Q9H4I3 UniProt NPD GO	TRABD_HUMAN	TraB domain-containing protein	0.62	-	cyt	0					376
Q5BCN2 UniProt NPD GO	SPT5_EMENI	Transcription elongation factor spt5 (Chromatin elongation factor spt5)	0.62	+	nuc	0	Nucleus (By similarity)				1016
Q7YR48 UniProt NPD GO	TCF19_PANTR	Transcription factor 19 (Transcription factor SC1)	0.62	+	nuc	0	Nucleus (Potential)				345
Q61313 UniProt NPD GO	AP2B_MOUSE	Transcription factor AP-2 beta (AP2-beta) (Activating enhancer-binding protein 2 beta)	0.62	-	nuc	0	Nucleus (Probable)				448
P14164 UniProt NPD GO	BAF1_YEAST	Transcription factor BAF1 (ARS-binding factor 1) (Protein ABF1) (Bidirectionally acting factor) (SFB ...	0.62	-	nuc	0	Nucleus	nuclear chromatin [TAS] nucleotide-excision repair factor 4 complex [IPI] nucleus [IDA]			731
P15923 UniProt NPD GO	TFE2_HUMAN	Transcription factor E2-alpha (Immunoglobulin enhancer-binding factor E12/E47) (Transcription factor ...	0.62	-	nuc	0	Nucleus	nucleus [NAS]	147141	1HLH	654
Q92908 UniProt NPD GO	GATA6_HUMAN	Transcription factor GATA-6 (GATA-binding factor 6)	0.62	-	nuc	0	Nucleus		601656		449
P03001 UniProt NPD GO	TF3A_XENLA	Transcription factor IIIA (Factor A) (TFIIIA) (S-TFIIIA/O-TFIIIA)	0.62	-	nuc	0	Nucleus			1UN6	366
Q9M0K4 UniProt NPD GO	LAF1_ARATH	Transcription factor LAF1 (Long after far-red light protein 1) (Myb-related protein 18) (AtMYB18)	0.62	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle				283
Q8LPH6 UniProt NPD GO	MYB86_ARATH	Transcription factor MYB86 (Myb-related protein 86) (AtMYB86) (Myb homolog 4) (AtMyb4)	0.62	-	nuc	0	Nucleus (Probable)				352
O75444 UniProt NPD GO	MAF_HUMAN	Transcription factor Maf (Proto-oncogene c-maf)	0.62	-	nuc	0	Nucleus (By similarity)	chromatin [TAS]	177075		403
Q9BRP0 UniProt NPD GO	OVOL2_HUMAN	Transcription factor Ovo-like 2 (hOvo2) (Zinc finger protein 339)	0.62	-	nuc	0	Nucleus (Probable)				275
Q6BDS1 UniProt NPD GO	SPI1_RAT	Transcription factor PU.1	0.62	+	nuc	0	Nucleus (By similarity)				271
P17275 UniProt NPD GO	JUNB_HUMAN	Transcription factor jun-B	0.62	+	nuc	0	Nucleus	chromatin [TAS]	165161		347
Q62318 UniProt NPD GO	TIF1B_MOUSE	Transcription intermediary factor 1-beta (TIF1-beta) (Tripartite motif-containing protein 28) (KRAB- ...	0.62	-	nuc	0	Nucleus. Associated with centromeric heterochromatin during cell differentiation through CBX1	chromatin [IDA]			833
Q12060 UniProt NPD GO	HFI1_YEAST	Transcriptional coactivator HFI1/ADA1	0.62	-	nuc	0	Nucleus (Probable)	Ada2/Gcn5/Ada3 transcription activator complex [IDA] SAGA complex [IDA] SLIK (SAGA-like) complex [IPI]			488
P81270 UniProt NPD GO	ERG_MOUSE	Transcriptional regulator ERG	0.62	-	nuc	0	Nucleus				486
Q6CVS3 UniProt NPD GO	LGE1_KLULA	Transcriptional regulatory protein LGE1	0.62	-	nuc	0	Nucleus (By similarity)				230
Q99161 UniProt NPD GO	SEC62_YARLI	Translocation protein SEC62	0.62	+	vac	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				396
Q5F3A1 UniProt NPD GO	SEC62_CHICK	Translocation protein SEC62 (Translocation protein 1) (TP-1)	0.62	+	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				398
Q99PN3 UniProt NPD GO	TRI26_MOUSE	Tripartite motif-containing protein 26 (Zinc finger protein 173)	0.62	-	cyt	0		cytoplasm [IDA]			545
P02643 UniProt NPD GO	TNNI2_RABIT	Troponin I, fast skeletal muscle (Troponin I, fast-twitch isoform)	0.62	-	nuc	0				1NPQ	181
Q8NAT2 UniProt NPD GO	TDRD5_HUMAN	Tudor domain-containing protein 5	0.62	-	nuc	0					682
P50555 UniProt NPD GO	TNR1A_PIG	Tumor necrosis factor receptor superfamily member 1A precursor (p60) (TNF-R1) (TNF-RI) (TNFR-I) (p55 ...	0.62	-	exc	1	Membrane; single-pass type I membrane protein				461
O60674 UniProt NPD GO	JAK2_HUMAN	Tyrosine-protein kinase JAK2 (EC 2.7.10.2) (Janus kinase 2) (JAK-2)	0.62	-	cyt	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...		147796	2B7A	1132

You are viewing entries 18201 to 18250 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.