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Pden_0306 Pden_0306 Pden_0307 Pden_0307 Pden_0308 Pden_0308 Pden_0311 Pden_0311 Pden_0595 Pden_0595 Pden_0786 Pden_0786 Pden_1072 Pden_1072 Pden_1073 Pden_1073 Pden_1074 Pden_1074 Pden_1075 Pden_1075 Pden_1382 Pden_1382 Pden_1397 Pden_1397 Pden_1559 Pden_1559 Pden_1620 Pden_1620 Pden_1630 Pden_1630 Pden_1771 Pden_1771 Pden_1783 Pden_1783 Pden_1808 Pden_1808 ccoP ccoP Pden_1846 Pden_1846 Pden_1847 Pden_1847 Pden_1848 Pden_1848 Pden_1937 Pden_1937 Pden_2026 Pden_2026 Pden_2305 Pden_2305 Pden_2306 Pden_2306 Pden_2307 Pden_2307 Pden_2600 Pden_2600 Pden_2630 Pden_2630 Pden_2645 Pden_2645 Pden_2663 Pden_2663 Pden_2727 Pden_2727 Pden_2779 Pden_2779 Pden_2781 Pden_2781 dnaA dnaA Pden_2870 Pden_2870 Pden_2907 Pden_2907 Pden_2963 Pden_2963 Pden_2978 Pden_2978 Pden_3073 Pden_3073 Pden_3074 Pden_3074 Pden_3075 Pden_3075 Pden_3093 Pden_3093 Pden_3094 Pden_3094 Pden_3095 Pden_3095 Pden_3097 Pden_3097 Pden_3098 Pden_3098 Pden_3100 Pden_3100 Pden_3109 Pden_3109 Pden_3450 Pden_3450 ctaA ctaA Pden_3702 Pden_3702 Pden_3938 Pden_3938 glnD glnD Pden_3982 Pden_3982 Pden_4010 Pden_4010 Pden_4011 Pden_4011 Pden_4096 Pden_4096 Pden_4110 Pden_4110 Pden_4120 Pden_4120 Pden_4121 Pden_4121 Pden_4122 Pden_4122 Pden_4127 Pden_4127 Pden_4128 Pden_4128 Pden_4129 Pden_4129 Pden_4130 Pden_4130 Pden_4157 Pden_4157 Pden_4233 Pden_4233 Pden_4234 Pden_4234 Pden_4235 Pden_4235 Pden_4236 Pden_4236 Pden_4325 Pden_4325 Pden_4330 Pden_4330 Pden_4368 Pden_4368 Pden_4405 Pden_4405 Pden_4406 Pden_4406 Pden_4461 Pden_4461 Pden_4462 Pden_4462 Pden_4504 Pden_4504
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splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.
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query proteins and first shell of interactors
white nodes:
second shell of interactors
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empty nodes:
proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
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Edges represent protein-protein associations
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Known Interactions
from curated databases
experimentally determined
Predicted Interactions
gene neighborhood
gene fusions
gene co-occurrence
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textmining
co-expression
protein homology
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Pden_0306PFAM: protein of unknown function DUF112, transmembrane; KEGG: sme:SMb20726 conserved hypothetical membrane protein. (505 aa)
Pden_0307KEGG: atc:AGR_C_4484 putative tricarboxylic transport membrane protein. (164 aa)
Pden_0308PFAM: Uncharacterized protein UPF0065; KEGG: sme:SMb20724 putative tricarboxylic transport membrane protein. (313 aa)
Pden_0311Integral membrane sensor signal transduction histidine kinase; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; Two-component sensor kinase N-terminal domain protein; KEGG: ret:RHE_CH03588 probable two-component sensor histidine kinase protein. (476 aa)
Pden_0595Multi-sensor hybrid histidine kinase; PFAM: response regulator receiver; ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; KEGG: sit:TM1040_1228 multi-sensor hybrid histidine kinase. (680 aa)
Pden_0786Transcriptional regulator, LuxR family; PFAM: regulatory protein, LuxR; Autoinducer-binding domain protein; KEGG: jan:Jann_0619 transcriptional regulator, LuxR family. (203 aa)
Pden_1072L-glutamate-binding protein / L-aspartate-binding protein; PFAM: extracellular solute-binding protein, family 3; KEGG: bja:blr3096 ABC transporter substrate-binding protein. (295 aa)
Pden_1073TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bja:blr3097 ABC transporter permease protein. (253 aa)
Pden_1074TIGRFAM: polar amino acid ABC transporter, inner membrane subunit; PFAM: binding-protein-dependent transport systems inner membrane component; KEGG: bja:blr3098 ABC transporter permease protein. (230 aa)
Pden_1075PFAM: ABC transporter related; SMART: AAA ATPase; KEGG: psp:PSPPH_1133 amino acid ABC transporter, ATP-binding protein; TC 3.A.1.3.-. (250 aa)
Pden_1382TIGRFAM: protease Do; PFAM: peptidase S1 and S6, chymotrypsin/Hap; PDZ/DHR/GLGF domain protein; KEGG: rsp:RSP_0355 possible serine protease; Belongs to the peptidase S1C family. (514 aa)
Pden_1397PFAM: glutamine synthetase, catalytic region; KEGG: rsp:RSP_0377 probable glutamine synthetase. (452 aa)
Pden_1559PFAM: polysaccharide export protein; KEGG: sit:TM1040_2133 polysaccharide export protein. (392 aa)
Pden_1620Flagellin domain protein; Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella. (284 aa)
Pden_1630PFAM: FecR protein; KEGG: nwi:Nwi_2882 FecR protein. (324 aa)
Pden_1771Integral membrane sensor signal transduction histidine kinase; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; KEGG: sil:SPO2173 sensor histidine kinase. (445 aa)
Pden_1783Signal transduction histidine kinase, glucose-6-phosphate specific; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase, dimerisation and phosphoacceptor region; KEGG: rpe:RPE_2819 signal transduction histidine kinase, glucose-6-phosphate specific. (468 aa)
Pden_1808PFAM: cytochrome c, class I; KEGG: sil:SPO3538 cytochrome c552. (176 aa)
ccoPCytochrome c oxidase, cbb3-type, subunit III; C-type cytochrome. Part of the cbb3-type cytochrome c oxidase complex. CcoP subunit is required for transferring electrons from donor cytochrome c via its heme groups to CcoO subunit. From there, electrons are shuttled to the catalytic binuclear center of CcoN subunit where oxygen reduction takes place. The complex also functions as a proton pump. (349 aa)
Pden_1846PFAM: Cbb3-type cytochrome oxidase component; KEGG: sit:TM1040_2543 Cbb3-type cytochrome oxidase component. (62 aa)
Pden_1847TIGRFAM: cytochrome c oxidase, cbb3-type, subunit II; PFAM: cytochrome C oxidase, mono-heme subunit/FixO; KEGG: rde:RD1_1271 cytochrome c oxidase, cbb3-type, subunit II. (241 aa)
Pden_1848TIGRFAM: cytochrome c oxidase, cbb3-type, subunit I; PFAM: cytochrome c oxidase, subunit I; KEGG: rsp:RSP_0696 Cbb3-type cytochrome oxidase CcoN subunit; Belongs to the heme-copper respiratory oxidase family. (539 aa)
Pden_1937PFAM: cytochrome c, class I; KEGG: sil:SPO0130 cytochrome c family protein. (155 aa)
Pden_2026KEGG: rsp:RSP_0745 acetyl-CoA acetyltransferase; TIGRFAM: acetyl-CoA acetyltransferases; PFAM: Thiolase; Belongs to the thiolase-like superfamily. Thiolase family. (391 aa)
Pden_2305Ubiquinol-cytochrome c reductase, iron-sulfur subunit; Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis. (195 aa)
Pden_2306Cytochrome b/b6, N-terminal domain; Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis. (440 aa)
Pden_2307PFAM: cytochrome c1; KEGG: rde:RD1_0565 cytochrome c1. (450 aa)
Pden_2600Two component transcriptional regulator, winged helix family; PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: rsp:RSP_1138 two component transcriptional regulator, winged helix family. (239 aa)
Pden_2630KEGG: rsp:RSP_1316 flagellar motor protein. (166 aa)
Pden_2645KEGG: sit:TM1040_2951 chemotaxis protein MotA. (148 aa)
Pden_2663KEGG: sil:SPO0142 beta-ketothiolase; TIGRFAM: acetyl-CoA acetyltransferases; PFAM: Thiolase; Belongs to the thiolase-like superfamily. Thiolase family. (393 aa)
Pden_2727TIGRFAM: type I secretion outer membrane protein, TolC family; PFAM: outer membrane efflux protein; KEGG: rsp:RSP_0251 outer membrane efflux protein. (464 aa)
Pden_2779Integral membrane sensor signal transduction histidine kinase; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_1520 sensor histidine kinase PrrB (RegB). (462 aa)
Pden_2781Two component transcriptional regulator, Fis family; PFAM: response regulator receiver; KEGG: sit:TM1040_2838 response regulator receiver protein. (182 aa)
dnaAHypothetical protein; Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'- TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids. Belongs to the DnaA family. (448 aa)
Pden_2870KEGG: sil:SPO2918 acetyl-CoA acyltransferase/thiolase; TIGRFAM: acetyl-CoA acetyltransferases; PFAM: Thiolase; Belongs to the thiolase-like superfamily. Thiolase family. (403 aa)
Pden_2907KEGG: bms:BRA0448 acetyl-CoA acetyltransferase; TIGRFAM: acetyl-CoA acetyltransferases; PFAM: Thiolase; Belongs to the thiolase-like superfamily. Thiolase family. (393 aa)
Pden_2963Integral membrane sensor signal transduction histidine kinase; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_2129 sensor histidine kinase. (597 aa)
Pden_2978PFAM: FecR protein; KEGG: nwi:Nwi_2050 probable FecR, iron siderophore sensor protein. (328 aa)
Pden_3073PFAM: protein of unknown function DUF112, transmembrane; KEGG: bja:blr3163 hypothetical protein. (499 aa)
Pden_3074KEGG: bja:blr3162 putative tricarboxylic transport membrane protein. (156 aa)
Pden_3075PFAM: Uncharacterized protein UPF0065; KEGG: bja:blr3161 putative tricarboxylic transport membrane protein. (323 aa)
Pden_3093KEGG: rsp:RSP_0491 hydrogen uptake histidine-kinase; TIGRFAM: PAS sensor protein; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; PAS fold domain protein; SMART: PAS domain containing protein. (444 aa)
Pden_3094PFAM: NADH ubiquinone oxidoreductase, 20 kDa subunit; KEGG: rsp:RSP_0492 hydrogenase small subunit. (329 aa)
Pden_3095PFAM: nickel-dependent hydrogenase, large subunit; KEGG: rsp:RSP_0493 hydrogenase large subunit. (477 aa)
Pden_3097KEGG: rsp:RSP_0495 hydrogenase protein small subunit; TIGRFAM: hydrogenase (NiFe) small subunit HydA; PFAM: NADH ubiquinone oxidoreductase, 20 kDa subunit; Nickel-iron dehydrogenase small subunit, N-terminal domain protein. (361 aa)
Pden_3098PFAM: nickel-dependent hydrogenase, large subunit; KEGG: rsp:RSP_0496 hydrogenase protein large subunit; Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit family. (597 aa)
Pden_3100TIGRFAM: Ni/Fe-hydrogenase, b-type cytochrome subunit; PFAM: cytochrome B561; KEGG: aeh:Mlg_2027 Ni/Fe-hydrogenase, b-type cytochrome subunit. (248 aa)
Pden_3109Two component, sigma54 specific, transcriptional regulator, Fis family; PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; KEGG: rsp:RSP_0507 HupR response regulator. (493 aa)
Pden_3450PFAM: beta-lactamase; KEGG: rsp:RSP_3749 putative beta-lactamase precursor. (401 aa)
ctaACytochrome oxidase assembly; Catalyzes the oxidation of the C8 methyl side group on heme O porphyrin ring into a formyl group; Belongs to the COX15/CtaA family. Type 2 subfamily. (391 aa)
Pden_3702Glutamate--putrescine ligase; PFAM: glutamine synthetase, catalytic region; KEGG: rsp:RSP_0375 probable glutamine synthetase. (443 aa)
Pden_3938PAS/PAC sensor signal transduction histidine kinase; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; PAS fold domain protein; SMART: PAS domain containing protein; KEGG: sil:SPO1947 phosphate regulon sensor histidine kinase, putative. (350 aa)
glnDMetal dependent phosphohydrolase; Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen assimilation and metabolism. (936 aa)
Pden_3982TIGRFAM: diguanylate cyclase; PFAM: GGDEF domain containing protein; response regulator receiver; KEGG: jan:Jann_3131 diguanylate cyclase. (464 aa)
Pden_4010PFAM: cytochrome bd ubiquinol oxidase, subunit I; KEGG: nar:Saro_1025 cytochrome bd ubiquinol oxidase, subunit I. (467 aa)
Pden_4011TIGRFAM: cytochrome d ubiquinol oxidase, subunit II; PFAM: cytochrome bd ubiquinol oxidase, subunit II; KEGG: nar:Saro_1026 cytochrome d ubiquinol oxidase, subunit II. (334 aa)
Pden_4096Two component transcriptional regulator, winged helix family; PFAM: response regulator receiver; KEGG: sil:SPO1679 DNA-binding response regulator CtrA. (184 aa)
Pden_4110PFAM: HpcH/HpaI aldolase; KEGG: bmb:BruAb2_0163 hypothetical citrate lyase, beta subunit. (266 aa)
Pden_4120TIGRFAM: TRAP dicarboxylate transporter, DctM subunit; PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit; KEGG: rsp:RSP_0912 TRAP-T family C4-dicarboxylate transporter, DctM (12TMs) subunit. (440 aa)
Pden_4121PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component; KEGG: rsp:RSP_0911 TRAP-T family C4-dicarboxylate transporter, DctQ (4TMs) subunit. (210 aa)
Pden_4122TIGRFAM: TRAP dicarboxylate transporter, DctP subunit; PFAM: TRAP dicarboxylate transporter- DctP subunit; KEGG: rsp:RSP_0910 TRAP-T family transporter, C4-dicarboxylate-binding protein DctP. (335 aa)
Pden_4127Two component, sigma54 specific, transcriptional regulator, Fis family; PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: rsp:RSP_2840 nitrogen assimilation transcriptional regulator, NtrX. (462 aa)
Pden_4128KEGG: rsp:RSP_2839 nitrogen regulation protein, NtrY, signal transduction histidine kinase; TIGRFAM: PAS sensor protein; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase, HAMP region domain protein; histidine kinase A domain protein domain protein; PAS fold-4 domain protein; PAS fold domain protein; SMART: PAS domain containing protein. (752 aa)
Pden_4129Two component, sigma54 specific, transcriptional regulator, Fis family; PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: rde:RD1_2763 nitrogen regulation protein. (485 aa)
Pden_4130Signal transduction histidine kinase, nitrogen specific, NtrB; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: rsp:RSP_2837 nitrogen regulation protein, NtrB signal transduction histidine kinase. (385 aa)
Pden_4157Sulfide dehydrogenase (flavocytochrome), cytochrome c subunit; PFAM: cytochrome c, class I; KEGG: rde:RD1_1518 cytochrome c2. (236 aa)
Pden_4233TIGRFAM: respiratory nitrate reductase, gamma subunit; PFAM: Nitrate reductase, gamma subunit; KEGG: mmr:Mmar10_2703 respiratory nitrate reductase, gamma subunit. (233 aa)
Pden_4234TIGRFAM: nitrate reductase molybdenum cofactor assembly chaperone; PFAM: Nitrate reductase, delta subunit; KEGG: rde:RD1_2444 nitrate reductase, delta subunit. (229 aa)
Pden_4235TIGRFAM: nitrate reductase, beta subunit; PFAM: 4Fe-4S ferredoxin, iron-sulfur binding domain protein; KEGG: rde:RD1_2443 nitrate reductase, beta subunit. (505 aa)
Pden_4236TIGRFAM: nitrate reductase, alpha subunit; PFAM: molybdopterin oxidoreductase; molydopterin dinucleotide-binding region; KEGG: rde:RD1_2442 nitrate reductase, alpha subunit; Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. (1254 aa)
Pden_4325Two component transcriptional regulator, winged helix family; TIGRFAM: phosphate regulon transcriptional regulatory protein PhoB; PFAM: response regulator receiver; transcriptional regulator domain protein; KEGG: sil:SPO1953 phosphate regulon transcriptional regulatory protein PhoB. (229 aa)
Pden_4330Phosphate ABC transporter substrate-binding protein, PhoT family; KEGG: sit:TM1040_1262 phosphate ABC transporter, periplasmic phosphate-binding protein; TC 3.A.1.7.1. (342 aa)
Pden_4368PFAM: sodium:dicarboxylate symporter; KEGG: pol:Bpro_1420 sodium:dicarboxylate symporter; Belongs to the dicarboxylate/amino acid:cation symporter (DAACS) (TC 2.A.23) family. (441 aa)
Pden_4405Two component, sigma54 specific, transcriptional regulator, Fis family; PFAM: response regulator receiver; sigma-54 factor, interaction domain-containing protein; helix-turn-helix, Fis-type; SMART: AAA ATPase; KEGG: ret:RHE_CH03433 probable two-component response regulator protein. (448 aa)
Pden_4406Histidine kinase; PFAM: ATP-binding region, ATPase domain protein domain protein; histidine kinase A domain protein domain protein; KEGG: ret:RHE_CH03434 probable two-component sensor histidine kinase protein. (622 aa)
Pden_4461PFAM: nitrogen regulatory protein P-II; KEGG: rsp:RSP_0146 nitrogen regulatory protein P-II; Belongs to the P(II) protein family. (112 aa)
Pden_4462KEGG: rsp:RSP_0147 glutamine synthetase class-I; TIGRFAM: glutamine synthetase, type I; PFAM: glutamine synthetase, catalytic region; glutamine synthetase, beta-Grasp. (468 aa)
Pden_4504KEGG: rsp:RSP_3825 hypothetical protein. (218 aa)
Your Current Organism:
Paracoccus denitrificans
NCBI taxonomy Id: 318586
Other names: P. denitrificans PD1222, Paracoccus denitrificans PD1222
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