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
Q5HZ97 UniProt NPD GO	SPT4H_XENLA	Transcription elongation factor SPT4 (DRB sensitivity-inducing factor small subunit) (DSIF small sub ...	0.02	-	mit	0	Nucleus (By similarity)				117
Q94HL5 UniProt NPD GO	T2AG_ORYSA	Transcription initiation factor IIA gamma chain (TFIIA-gamma)	0.02	-	cyt	0	Nucleus (By similarity)				106
Q03010 UniProt NPD GO	UME1_YEAST	Transcriptional regulatory protein UME1 (WD repeat-containing transcriptional modulator 3)	0.02	-	cyt	0	Cytoplasm. Nucleus	nucleus [IDA]			460
Q90997 UniProt NPD GO	TFR1_CHICK	Transferrin receptor protein 1 (TfR1) (TR) (TfR) (Trfr)	0.02	-	mit	1	Membrane; single-pass type II membrane protein (By similarity)				776
Q42677 UniProt NPD GO	TKT7_CRAPL	Transketolase 7 (EC 2.2.1.1) (TK)	0.02	-	cyt	0					676
Q42676 UniProt NPD GO	TKTC_CRAPL	Transketolase, chloroplast (EC 2.2.1.1) (TK) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast (Potential)				519
Q93573 UniProt NPD GO	TCTP_CAEEL	Translationally-controlled tumor protein homolog (TCTP)	0.02	-	cyt	0	Cytoplasm (By similarity)				181
Q9M5I8 UniProt NPD GO	TCTP_CUCME	Translationally-controlled tumor protein homolog (TCTP)	0.02	-	cyt	0	Cytoplasm (By similarity)				168
O03992 UniProt NPD GO	TCTP_FRAAN	Translationally-controlled tumor protein homolog (TCTP)	0.02	-	cyt	0	Cytoplasm (By similarity)				170
Q9ZSW9 UniProt NPD GO	TCTP_HEVBR	Translationally-controlled tumor protein homolog (TCTP)	0.02	-	cyt	0	Cytoplasm (By similarity)				168
Q4YZC6 UniProt NPD GO	TCTP_PLABA	Translationally-controlled tumor protein homolog (TCTP)	0.02	-	cyt	0	Cytoplasm (By similarity)				171
P84152 UniProt NPD GO	TCTP_PLAKN	Translationally-controlled tumor protein homolog (TCTP)	0.02	-	cyt	0	Cytoplasm (By similarity)			1TXJ	171
Q944T2 UniProt NPD GO	TCTP_SOYBN	Translationally-controlled tumor protein homolog (TCTP)	0.02	-	cyt	0	Cytoplasm (By similarity)				168
Q9M5G3 UniProt NPD GO	TCTP_HORVU	Translationally-controlled tumor protein homolog (TCTP) (HTP)	0.02	-	cyt	0	Cytoplasm (By similarity)				168
P43349 UniProt NPD GO	TCTP_SOLTU	Translationally-controlled tumor protein homolog (TCTP) (p23)	0.02	-	cyt	0	Cytoplasm (By similarity)				168
Q96CE8 UniProt NPD GO	T4S18_HUMAN	Transmembrane 4 L6 family 18	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				201
Q5RE43 UniProt NPD GO	T4S1_PONPY	Transmembrane 4 L6 family member 1	0.02	-	end	4 *	Membrane; multi-pass membrane protein				202
Q5FVF4 UniProt NPD GO	TM7S3_RAT	Transmembrane 7 superfamily member 3 precursor	0.02	-	end	7	Cell membrane; multi-pass membrane protein (By similarity)				565
Q9CRG1 UniProt NPD GO	TM7S3_MOUSE	Transmembrane 7 superfamily member 3 precursor (NARP1)	0.02	-	end	7	Cell membrane; multi-pass membrane protein (By similarity)				565
P57727 UniProt NPD GO	TMPS3_HUMAN	Transmembrane protease, serine 3 (EC 3.4.21.-) (Serine protease TADG-12) (Tumor-associated different ...	0.02	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum membrane [IDA] integral to membrane [NAS]	605511		454
P83748 UniProt NPD GO	TMSP8_RAT	Transmembrane serine protease 8 precursor (EC 3.4.21.-) (Distal intestinal serine protease) (Transme ...	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Probable)	anchored to plasma membrane [NAS]			304
P38334 UniProt NPD GO	TRS20_YEAST	Transport protein particle 20 kDa subunit (TRAPP 20 kDa subunit)	0.02	-	nuc	0		TRAPP complex [IDA]			175
Q5U7I5 UniProt NPD GO	TTHY_PANTR	Transthyretin precursor (Prealbumin)	0.02	-	end	0	Secreted protein (By similarity)				147
P50390 UniProt NPD GO	TTHY_PIG	Transthyretin precursor (Prealbumin)	0.02	-	end	0	Secreted protein				150
P30623 UniProt NPD GO	TTHY_TILRU	Transthyretin precursor (Prealbumin) (TBPA)	0.02	-	exc	0	Secreted protein				150
P02766 UniProt NPD GO	TTHY_HUMAN	Transthyretin precursor (Prealbumin) (TBPA) (TTR) (ATTR)	0.02	-	end	0	Secreted protein	extracellular region [NAS]	105210	5TTR	147
Q863T4 UniProt NPD GO	TFF1_CANFA	Trefoil factor 1 precursor	0.02	-	exc	0	Secreted protein (By similarity)				81
Q71DJ5 UniProt NPD GO	LIP1_ARATH	Triacylglycerol lipase 1 precursor (EC 3.1.1.3)	0.02	-	exc	0	Secreted protein (Probable)				393
P38152 UniProt NPD GO	TXTP_YEAST	Tricarboxylate transport protein (Citrate transport protein) (CTP)	0.02	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				299
Q27174 UniProt NPD GO	T2B_PARTE	Trichocyst matrix protein T2-B (Secretory granule protein T2-B) (TMP 2-B) (Fragment)	0.02	-	cyt	0	Trichocyst. These are architecturally complex secretory storage granules-docked at the plasma membra ...				23
P52177 UniProt NPD GO	TPT1_BRAOB	Triose phosphate/phosphate translocator, chloroplast precursor (cTPT)	0.02	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein. Located in zones of contact ...				407
P49131 UniProt NPD GO	TPT_FLAPR	Triose phosphate/phosphate translocator, chloroplast precursor (cTPT)	0.02	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein. Located in zones of contact ...				408
P29463 UniProt NPD GO	TPT_SOLTU	Triose phosphate/phosphate translocator, chloroplast precursor (cTPT) (E29)	0.02	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein. Located in zones of contact ...				414
P54714 UniProt NPD GO	TPIS_CANFA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
Q6FRI3 UniProt NPD GO	TPIS_CANGA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
O02611 UniProt NPD GO	TPIS_ENTHI	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0				1M6J	261
Q70JN8 UniProt NPD GO	TPIS_KLUMA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
Q60HC9 UniProt NPD GO	TPIS_MACFA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
P15426 UniProt NPD GO	TPIS_MACMU	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
P17751 UniProt NPD GO	TPIS_MOUSE	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
Q7S2Z9 UniProt NPD GO	TPIS_NEUCR	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
P00939 UniProt NPD GO	TPIS_RABIT	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0				1R2T	248
P48500 UniProt NPD GO	TPIS_RAT	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
P07669 UniProt NPD GO	TPIS_SCHPO	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0					248
P00942 UniProt NPD GO	TPIS_YEAST	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	cyt	0		cytoplasm [IDA]		7TIM	247
P82204 UniProt NPD GO	TPIS_BOMMO	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragment)	0.02	-	cyt	0					24
P91919 UniProt NPD GO	TPIS_CULPI	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragment)	0.02	-	cyt	0					206
P48496 UniProt NPD GO	TPIC_SPIOL	Triosephosphate isomerase, chloroplast precursor (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	mit	0	Plastid; chloroplast				322
P48491 UniProt NPD GO	TPIS_ARATH	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.02	-	mit	0	Cytoplasm (Probable)				254
P48492 UniProt NPD GO	TPIS_GRAVE	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragment)	0.02	-	cyt	0	Cytoplasm (Probable)				250

You are viewing entries 86001 to 86050 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.