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
P04241 UniProt NPD GO	HBAD_RHEAM	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.00	-	cyt	0					141
P04242 UniProt NPD GO	HBAD_STRCA	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.00	-	cyt	0					141
P02006 UniProt NPD GO	HBAD_PHRHI	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin) (Component CII)	0.00	-	cyt	0					141
P02120 UniProt NPD GO	HBB_ANSSE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	cyt	0					146
P14526 UniProt NPD GO	HBB_BRATR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	cyt	0					146
P80271 UniProt NPD GO	HBB_CHEKU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	cyt	0					146
Q6H1U7 UniProt NPD GO	HBB_MACEU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	cyt	0					146
P02106 UniProt NPD GO	HBB_MACGI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	cyt	0					146
P02107 UniProt NPD GO	HBB_MACRU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	cyt	0					146
P02092 UniProt NPD GO	HBB_MICXA	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	mit	1 *					146
P02108 UniProt NPD GO	HBB_POTTR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	cyt	0					146
Q28932 UniProt NPD GO	HBB_SMICR	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.00	-	cyt	0					146
Q9TT33 UniProt NPD GO	HBB_COLGU	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) (Fragment)	0.00	-	cyt	0					41
P07420 UniProt NPD GO	HBB_DASVI	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) (Fragment)	0.00	-	cyt	0					87
Q9TSP1 UniProt NPD GO	HBB_PAPAN	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) (Fragment)	0.00	-	cyt	0					41
Q9TT34 UniProt NPD GO	HBB_PONPY	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin) (Fragment)	0.00	-	cyt	0					36
P0C0U9 UniProt NPD GO	HBB2_DRYCE	Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Hemoglobin beta-II chain) (Beta-2-globin) (Frag ...	0.00	-		0					10
P02080 UniProt NPD GO	HBBN_AMMLE	Hemoglobin subunit beta-C(NA) (Hemoglobin beta C(NA) chain) (Beta-C(NA)-globin)	0.00	-	cyt	0					141
P29627 UniProt NPD GO	HBBZ_MESAU	Hemoglobin subunit beta-Z (Hemoglobin beta-Z chain) (Beta-Z-globin) (Fragment)	0.00	-	cyt	0					102
P06347 UniProt NPD GO	HBAZ_PANTR	Hemoglobin subunit zeta (Hemoglobin zeta chain) (Zeta-globin)	0.00	-	cyt	0					141
P02008 UniProt NPD GO	HBAZ_HUMAN	Hemoglobin subunit zeta (Hemoglobin zeta chain) (Zeta-globin) (HBAZ)	0.00	-	cyt	0		hemoglobin complex [TAS]	142310	1JEB	141
P41260 UniProt NPD GO	GLB1_LUCPE	Hemoglobin-1 (Hemoglobin I) (Hb I) (HbI) (Sulfide-reactive hemoglobin)	0.00	-	cyt	0	Cytoplasm			1MOH	142
P23244 UniProt NPD GO	HBP2_CASGL	Hemoglobin-2 (Hemoglobin II)	0.00	-	cyt	0					160
P41261 UniProt NPD GO	GLB2_LUCPE	Hemoglobin-2 (Hemoglobin II) (Hb II) (HbII)	0.00	-	mit	0	Cytoplasm				150
P41262 UniProt NPD GO	GLB3_LUCPE	Hemoglobin-3 (Hemoglobin III) (Hb III)	0.00	-	cyt	0	Cytoplasm				152
P80743 UniProt NPD GO	LE04_BIOGL	Hemolymph 65 kDa lectin BG04 (Fragment)	0.00	-	cyt	0	Secreted protein				21
P80744 UniProt NPD GO	LE05_BIOGL	Hemolymph 65 kDa lectin BG05 (Fragment)	0.00	-		0	Secreted protein				16
P26226 UniProt NPD GO	HTIA_MANSE	Hemolymph trypsin inhibitor A (BPI-type) (Fragment)	0.00	-	mit	0					56
P32416 UniProt NPD GO	HPB9_RANES	Hemolytic protein B9 (Fragment)	0.00	-		0	Secreted protein				13
P39088 UniProt NPD GO	ACTPH_RADMG	Hemolytic toxin (Cytolysin) (Fragment)	0.00	-	cyt	0	Secreted protein. Found in nematocyst				54
O43504 UniProt NPD GO	XIP_HUMAN	Hepatitis B virus X-interacting protein (HBX-interacting protein) (HBV X-interacting protein)	0.00	-	cyt	0	Cytoplasm		608521		91
P80350 UniProt NPD GO	ROAB_ARTSA	Heterogeneous nuclear ribonucleoprotein A/B (P38) (Fragments)	0.00	-	cyt	0	Cytoplasm. Nucleus. At the onset of the cryptoblastic phase, when transcription is blocked, it accum ...				195
Q09135 UniProt NPD GO	RO40_ARTSA	Heterogeneous nuclear ribonucleoprotein-like protein HD40 (Fragments)	0.00	-	cyt	0	Cytoplasm. Nucleus. Accumulates in the nucleus during cyst development, presumably concomitant with ...				109
P80581 UniProt NPD GO	HXK_EMENI	Hexokinase (EC 2.7.1.1) (Fragment)	0.00	-	cyt	0					122
Q9NFT7 UniProt NPD GO	HXK2_DROME	Hexokinase type 2 (EC 2.7.1.1)	0.00	-	pox	0					486
P20490 UniProt NPD GO	FCERB_MOUSE	High affinity immunoglobulin epsilon receptor beta-subunit (FcERI) (IgE Fc receptor, beta-subunit) ( ...	0.00	-	end	4	Membrane; multi-pass membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [IDA] lipid raft [TAS]			235
Q28003 UniProt NPD GO	CXCR2_BOVIN	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (CD182 antigen)	0.00	-	vac	6	Membrane; multi-pass membrane protein				360
Q8K211 UniProt NPD GO	COPT1_MOUSE	High-affinity copper uptake protein 1 (CTR1) (Copper transporter 1) (Solute carrier family 31 member ...	0.00	-	end	3	Membrane; multi-pass membrane protein (Probable)				196
O15431 UniProt NPD GO	COPT1_HUMAN	High-affinity copper uptake protein 1 (hCTR1) (Copper transporter 1) (Solute carrier family 31 membe ...	0.00	-	end	2	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	603085		190
P84590 UniProt NPD GO	ITH1_POEVI	Hirudin	0.00	-	nuc	0	Secreted protein				63
P13231 UniProt NPD GO	HATA_DICDI	Hisactophilin-1 (Histidine-rich actin-binding protein 1) (HS I)	0.00	-	cyt	0	Or: Cytoplasm. Or: Cell membrane; lipid-anchor; cytoplasmic side			1HCE	117
P42526 UniProt NPD GO	HATB_DICDI	Hisactophilin-2 (Histidine-rich actin-binding protein 2) (HS II)	0.00	-	cyt	0	Or: Cytoplasm. Or: Cell membrane; lipid-anchor; cytoplasmic side				117
P17236 UniProt NPD GO	CRBL_VESOR	Histamine-releasing peptide 2 (Histamine-releasing peptide II) (HR-II)	0.00	-		0	Secreted protein				14
P35492 UniProt NPD GO	HUTH_MOUSE	Histidine ammonia-lyase (EC 4.3.1.3) (Histidase)	0.00	-	cyt	0					657
P15872 UniProt NPD GO	H13_WHEAT	Histone H1.3 (Fragments)	0.00	-	cyt	0	Nucleus				31
P56520 UniProt NPD GO	HDAC3_CHICK	Histone deacetylase 3 (HD3)	0.00	-	cyt	0	Nucleus	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			428
O15379 UniProt NPD GO	HDAC3_HUMAN	Histone deacetylase 3 (HD3) (RPD3-2) (SMAP45)	0.00	-	cyt	0	Nucleus	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]	605166		428
Q8VHL1 UniProt NPD GO	SETD7_MOUSE	Histone-lysine N-methyltransferase, H3 lysine-4 specific SET7 (EC 2.1.1.43) (Histone H3-K4 methyltra ...	0.00	-	cyt	0	Nucleus (Probable)	nucleus [ISS]			366
Q8WTS6 UniProt NPD GO	SETD7_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-4 specific SET7 (EC 2.1.1.43) (Histone H3-K4 methyltra ...	0.00	-	cyt	0	Nucleus (Probable)	nucleus [NAS]	606594	2F69	366
Q8AYB8 UniProt NPD GO	HOP_BRARE	Homeodomain-only protein	0.00	-	cyt	0	Nucleus (By similarity)				77

You are viewing entries 95101 to 95150 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.