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Conserved domains on  [gi|2727058504|ref|WP_343032208|]
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tRNA dihydrouridine synthase DusB [Allochromatium palmeri]

Protein Classification

tRNA dihydrouridine synthase( domain architecture ID 11414563)

tRNA dihydrouridine synthase catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs

CATH:  3.20.20.70|1.10.1200.80
EC:  1.3.1.-
Gene Ontology:  GO:0017150|GO:0008033|GO:0050660|GO:0016491
PubMed:  30149704|34798057
SCOP:  4000080

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 7-318 1.64e-148

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 419.88  E-value: 1.64e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504   7 GPHRLANNLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEAA 86
Cdd:COG0042     1 GNLELPNPLILAPMAGVTDRPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  87 RLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARESGI 166
Cdd:COG0042    81 RIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWDDDDENALEFARIAEDAGA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 167 AALTVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADPVP 246
Cdd:COG0042   161 AALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREIDAYLAG 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2727058504 247 EPALPParaaSRDWIRDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRL 318
Cdd:COG0042   241 GEAPPP----SLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLEL 308
 
Name Accession Description Interval E-value
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 7-318 1.64e-148

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 419.88  E-value: 1.64e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504   7 GPHRLANNLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEAA 86
Cdd:COG0042     1 GNLELPNPLILAPMAGVTDRPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  87 RLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARESGI 166
Cdd:COG0042    81 RIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWDDDDENALEFARIAEDAGA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 167 AALTVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADPVP 246
Cdd:COG0042   161 AALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREIDAYLAG 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2727058504 247 EPALPParaaSRDWIRDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRL 318
Cdd:COG0042   241 GEAPPP----SLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLEL 308
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 6-322 9.00e-131

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 375.16  E-value: 9.00e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504   6 IGPHRLANNLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEA 85
Cdd:TIGR00737   1 IGNIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSDPDTMAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  86 ARLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARESG 165
Cdd:TIGR00737  81 AKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDAG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 166 IAALTVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADPV 245
Cdd:TIGR00737 161 AQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYLT 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2727058504 246 PEPALPPARAASRdwiRDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRLALAF 322
Cdd:TIGR00737 241 TGKYKPPPTFAEK---LDAILRHLQLLADYYGESKGLRIARKHIAWYLKGFPGNAALRQTLNHASSFQEVKQLLDDF 314
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 5-324 1.75e-127

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 366.99  E-value: 1.75e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504   5 QIGPHRLANNLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAE 84
Cdd:PRK10415    2 RIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMAD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  85 AARLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARES 164
Cdd:PRK10415   82 AARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDC 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 165 GIAALTVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADP 244
Cdd:PRK10415  162 GIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 245 VPEPALPPARAASrdwIRDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRLALAFLD 324
Cdd:PRK10415  242 DTGELLPPLPLAE---VKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQEHAPNDQFRRTFNAIEDASEQLEALEAYFE 318
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 16-324 6.13e-111

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.


Pssm-ID: 426126  Cd Length: 309  Bit Score: 324.66  E-value: 6.13e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  16 ILAPMAGITDRPFRTLCRRLGAG-LAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEAARLNVELGA 94
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAGdLVYTEMVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  95 HIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARESGIAALTVHGR 174
Cdd:pfam01207  81 DGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGWDDSHENAVEIAKIVEDAGAQALTVHGR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 175 TRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADP--VPEPALPP 252
Cdd:pfam01207 161 TRAQNYEGTADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFAEQHTVKtgEFGPSPPL 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2727058504 253 ARAAsrdwirDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRLALAFLD 324
Cdd:pfam01207 241 AEEA------EKVLRHLPYLEEFLGEDKGLRHARKHLAWYLKGFPGAAELRRELNDVFDPVEALINLDAALR 306
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 14-244 2.05e-97

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 287.08  E-value: 2.05e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  14 NLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEAARLNVELG 93
Cdd:cd02801     1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEELG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  94 AHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSpEERNAVRIARIARESGIAALTVHG 173
Cdd:cd02801    81 ADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWD-DEEETLELAKALEDAGASALTVHG 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2727058504 174 RTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADP 244
Cdd:cd02801   160 RTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELL 230
 
Name Accession Description Interval E-value
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 7-318 1.64e-148

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 419.88  E-value: 1.64e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504   7 GPHRLANNLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEAA 86
Cdd:COG0042     1 GNLELPNPLILAPMAGVTDRPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  87 RLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARESGI 166
Cdd:COG0042    81 RIAEELGADEIDINMGCPVKKVTKGGAGAALLRDPELVAEIVKAVVEAVDVPVTVKIRLGWDDDDENALEFARIAEDAGA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 167 AALTVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADPVP 246
Cdd:COG0042   161 AALTVHGRTREQRYKGPADWDAIARVKEAVSIPVIGNGDIFSPEDAKRMLEETGCDGVMIGRGALGNPWLFREIDAYLAG 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2727058504 247 EPALPParaaSRDWIRDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRL 318
Cdd:COG0042   241 GEAPPP----SLEEVLELLLEHLELLLEFYGERRGLRRMRKHLLWYFKGLPGARELRRRLSKAKSLAELLEL 308
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
 6-322 9.00e-131

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 375.16  E-value: 9.00e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504   6 IGPHRLANNLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEA 85
Cdd:TIGR00737   1 IGNIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSDPDTMAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  86 ARLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARESG 165
Cdd:TIGR00737  81 AKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDAG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 166 IAALTVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADPV 245
Cdd:TIGR00737 161 AQAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYLT 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2727058504 246 PEPALPPARAASRdwiRDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRLALAF 322
Cdd:TIGR00737 241 TGKYKPPPTFAEK---LDAILRHLQLLADYYGESKGLRIARKHIAWYLKGFPGNAALRQTLNHASSFQEVKQLLDDF 314
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
 5-324 1.75e-127

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 366.99  E-value: 1.75e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504   5 QIGPHRLANNLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAE 84
Cdd:PRK10415    2 RIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMAD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  85 AARLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARES 164
Cdd:PRK10415   82 AARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDC 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 165 GIAALTVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADP 244
Cdd:PRK10415  162 GIQALTIHGRTRACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 245 VPEPALPPARAASrdwIRDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRLALAFLD 324
Cdd:PRK10415  242 DTGELLPPLPLAE---VKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQEHAPNDQFRRTFNAIEDASEQLEALEAYFE 318
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 16-324 6.13e-111

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.


Pssm-ID: 426126  Cd Length: 309  Bit Score: 324.66  E-value: 6.13e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  16 ILAPMAGITDRPFRTLCRRLGAG-LAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEAARLNVELGA 94
Cdd:pfam01207   1 LLAPMAGVTDLPFRRLVREYGAGdLVYTEMVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  95 HIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSPEERNAVRIARIARESGIAALTVHGR 174
Cdd:pfam01207  81 DGIDINMGCPSKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIGWDDSHENAVEIAKIVEDAGAQALTVHGR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 175 TRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADP--VPEPALPP 252
Cdd:pfam01207 161 TRAQNYEGTADWDAIKQVKQAVSIPVIANGDITDPEDAQRCLAYTGADGVMIGRGALGNPWLFAEQHTVKtgEFGPSPPL 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2727058504 253 ARAAsrdwirDILREHLEALYAFHGDYAGVRIARKHIAWYCRDLPGAASFRETINRTETASEQLRLALAFLD 324
Cdd:pfam01207 241 AEEA------EKVLRHLPYLEEFLGEDKGLRHARKHLAWYLKGFPGAAELRRELNDVFDPVEALINLDAALR 306
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 14-244 2.05e-97

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 287.08  E-value: 2.05e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  14 NLILAPMAGITDRPFRTLCRRLGAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSDPAQMAEAARLNVELG 93
Cdd:cd02801     1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEELG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  94 AHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWSpEERNAVRIARIARESGIAALTVHG 173
Cdd:cd02801    81 ADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKIRLGWD-DEEETLELAKALEDAGASALTVHG 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2727058504 174 RTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRPWIFGDIAADP 244
Cdd:cd02801   160 RTREQRYSGPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELL 230
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
15-234 5.96e-27

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 107.59  E-value: 5.96e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  15 LILAPMAGITDRPFRTLCRRLGA-GLAVAEMVAANTALWgSRKSLRRL------DYRDEPG-PISAQIVGSDPAQMAEAA 86
Cdd:PRK10550    3 VLLAPMEGVLDSLVRELLTEVNDyDLCITEFLRVVDQLL-PVKVFHRLcpelhnASRTPSGtLVRIQLLGQYPQWLAENA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  87 RLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVP--VTLKIRTGWSPEERNaVRIARIARES 164
Cdd:PRK10550   82 ARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHlpVTVKVRLGWDSGERK-FEIADAVQQA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2727058504 165 GIAALTVHGRTRACTYGAPA-EYDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIGRAAQGRP 234
Cdd:PRK10550  161 GATELVVHGRTKEDGYRAEHiNWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIP 231
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
8-326 1.65e-23

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 98.67  E-value: 1.65e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504   8 PHRLAnnliLAPMAGITDRPFRTLCRRLGAG-LAVAEMVAANTALWGSRKslRRLDYRDEPGPISAQIVGSDPAQMAEAA 86
Cdd:PRK11815   10 SRRFS----VAPMMDWTDRHCRYFHRLLSRHaLLYTEMVTTGAIIHGDRE--RLLAFDPEEHPVALQLGGSDPADLAEAA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  87 RLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIRTGWS--PEERNAVRIARIARES 164
Cdd:PRK11815   84 KLAEDWGYDEINLNVGCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIGIDdqDSYEFLCDFVDTVAEA 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 165 GIAALTVHGRTractygA------PAE--------YDTIRAIRASV-DIPLIANGDIASPEDARHVLHYtgADAIMIGRA 229
Cdd:PRK11815  164 GCDTFIVHARK------AwlkglsPKEnreippldYDRVYRLKRDFpHLTIEINGGIKTLEEAKEHLQH--VDGVMIGRA 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 230 AQGRPWIFGDIAADPVPEPALPPARAASRDWIRDILREHLEalyafHGDYAGvRIARkHIAWYCRDLPGAASFR----ET 305
Cdd:PRK11815  236 AYHNPYLLAEVDRELFGEPAPPLSRSEVLEAMLPYIERHLA-----QGGRLN-HITR-HMLGLFQGLPGARAWRrylsEN 308

                         330       340
                  ....*....|....*....|.
gi 2727058504 306 INRTETASEQLRLALAFLDQD 326
Cdd:PRK11815  309 AHKPGAGIEVLEEALALVEEA 329
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 68-243 5.55e-11

Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.


Pssm-ID: 239204 [Multi-domain]  Cd Length: 289  Bit Score: 62.37  E-value: 5.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  68 GPISAQIVGSDPAQMAEAARLNVELGAHIVDINMGCPakkvcKVAAGSALLRDETRVARILEAVVAAVEVPVTLKIrtGW 147
Cdd:cd02810    99 QPLIASVGGSSKEDYVELARKIERAGAKALELNLSCP-----NVGGGRQLGQDPEAVANLLKAVKAAVDIPLLVKL--SP 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 148 SPEERNAVRIARIARESGIAALTVHGRTRAC-------------TYGA-------PAEYDTIRAIRASV--DIPLIANGD 205
Cdd:cd02810   172 YFDLEDIVELAKAAERAGADGLTAINTISGRvvdlktvgpgpkrGTGGlsgapirPLALRWVARLAARLqlDIPIIGVGG 251

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2727058504 206 IASPEDARHVLHyTGADAIMIGRAAQGR-PWIFGDIAAD 243
Cdd:cd02810   252 IDSGEDVLEMLM-AGASAVQVATALMWDgPDVIRKIKKE 289
FadH COG1902
2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family ...
 143-230 4.33e-09

2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family [Energy production and conversion];


Pssm-ID: 441506 [Multi-domain]  Cd Length: 365  Bit Score: 57.10  E-value: 4.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 143 IRTGWSPEErnAVRIARIARESGIAALTV----HGRTRACTYGAPAEYDT--IRAIRASVDIPLIANGDIASPEDARHVL 216
Cdd:COG1902   229 VEGGLTLEE--SVELAKALEEAGVDYLHVssggYEPDAMIPTIVPEGYQLpfAARIRKAVGIPVIAVGGITTPEQAEAAL 306

                          90
                  ....*....|....
gi 2727058504 217 HYTGADAIMIGRAA 230
Cdd:COG1902   307 ASGDADLVALGRPL 320
arch_FMN cd02911
Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent ...
 15-240 4.58e-09

Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent flavin oxidoreductase (oxidored) FMN-binding family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. The specific function of this group is unknown.


Pssm-ID: 239237 [Multi-domain]  Cd Length: 233  Bit Score: 55.80  E-value: 4.58e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  15 LILAPMAGITDRPFrtlCRRLG--AGLAVAEMVAANTAlwgSRKSLRRLDYRDE----PGPISAQIVG------------ 76
Cdd:cd02911     2 VALASMAGITDGDF---CRKRAdhAGLVFLGGYNLDER---TIEAARKLVKRGRkeflPDDPLEFIEGeikalkdsnvlv 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  77 ------SDPAQMAEAARLNVELGAhIVDINMGCPAKKVCKVAAGSALLRDETRVARILeAVVAAVEVPVTLKIRTGWSPe 150
Cdd:cd02911    76 gvnvrsSSLEPLLNAAALVAKNAA-ILEINAHCRQPEMVEAGAGEALLKDPERLSEFI-KALKETGVPVSVKIRAGVDV- 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 151 erNAVRIARIARESGIAALTVHgrtrACTYGAPAEYDTIRaiRASVDIPLIANGDIASPEDARHVLHYtGADAIMIGRAA 230
Cdd:cd02911   153 --DDEELARLIEKAGADIIHVD----AMDPGNHADLKKIR--DISTELFIIGNNSVTTIESAKEMFSY-GADMVSVARAS 223

                         250
                  ....*....|
gi 2727058504 231 qgRPWIFGDI 240
Cdd:cd02911   224 --LPENIEWL 231
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 146-230 6.45e-08

Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.


Pssm-ID: 239201 [Multi-domain]  Cd Length: 327  Bit Score: 53.34  E-value: 6.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 146 GWSPEErnAVRIARIARESGIAALTVHGRT--------RACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLH 217
Cdd:cd02803   224 GLTLEE--AIEIAKALEEAGVDALHVSGGSyespppiiPPPYVPEGYFLELAEKIKKAVKIPVIAVGGIRDPEVAEEILA 301

                          90
                  ....*....|...
gi 2727058504 218 YTGADAIMIGRAA 230
Cdd:cd02803   302 EGKADLVALGRAL 314
PyrD COG0167
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ...
 59-243 4.85e-06

Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate dehydrogenase is part of the Pathway/BioSystem: Pyrimidine biosynthesis


Pssm-ID: 439937 [Multi-domain]  Cd Length: 296  Bit Score: 47.37  E-value: 4.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  59 RRLDYRDEPGPISAQIVGSDPAQMAEAARLNVELGAHIVDINMGCP-AKKvckvaAGSALLRDETRVARILEAVVAAVEV 137
Cdd:COG0167    84 RLLPAKRYDVPVIVNIGGNTVEDYVELARRLADAGADYLELNISCPnTPG-----GGRALGQDPEALAELLAAVKAATDK 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 138 PVTLKIrtgwSPEERNAVRIARIARESGIAAL----TVHGRTRACTYGAPAEYDT----------------IRAIRASV- 196
Cdd:COG0167   159 PVLVKL----APDLTDIVEIARAAEEAGADGViainTTLGRAIDLETRRPVLANEagglsgpalkpialrmVREVAQAVg 234

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2727058504 197 -DIPLIANGDIASPEDA-RHVLHytGADAIMIGRAA-QGRPWIFGDIAAD 243
Cdd:COG0167   235 gDIPIIGVGGISTAEDAlEFILA--GASAVQVGTALfYEGPGLVRRIIRG 282
NanE cd04729
N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to ...
 170-229 1.21e-05

N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.


Pssm-ID: 240080 [Multi-domain]  Cd Length: 219  Bit Score: 45.64  E-value: 1.21e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 170 TVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHyTGADAIMIGRA 229
Cdd:cd04729   150 TLSGYTEETAKTEDPDFELLKELRKALGIPVIAEGRINSPEQAAKALE-LGADAVVVGSA 208
OYE_YqiM_FMN cd02932
Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress ...
 146-231 3.47e-05

Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.


Pssm-ID: 239242 [Multi-domain]  Cd Length: 336  Bit Score: 44.79  E-value: 3.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 146 GWSPEErnAVRIARIARESGIAALTVhgrtraCTYG-APAEYDTI---------RAIRASVDIPLIANGDIASPEDARHV 215
Cdd:cd02932   237 GWDLED--SVELAKALKELGVDLIDV------SSGGnSPAQKIPVgpgyqvpfaERIRQEAGIPVIAVGLITDPEQAEAI 308

                          90
                  ....*....|....*.
gi 2727058504 216 LHYTGADAIMIGRAAQ 231
Cdd:cd02932   309 LESGRADLVALGRELL 324
HisF cd04731
The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol ...
 186-223 7.65e-05

The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.


Pssm-ID: 240082  Cd Length: 243  Bit Score: 43.22  E-value: 7.65e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2727058504 186 YDT--IRAIRASVDIPLIANGDIASPEDARHVLHYTGADA 223
Cdd:cd04731   180 YDLelIRAVSSAVNIPVIASGGAGKPEHFVEAFEEGGADA 219
PRK01130 PRK01130
putative N-acetylmannosamine-6-phosphate 2-epimerase;
170-229 1.08e-04

putative N-acetylmannosamine-6-phosphate 2-epimerase;


Pssm-ID: 234907  Cd Length: 221  Bit Score: 42.83  E-value: 1.08e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 170 TVHGRTRACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYtGADAIMIGRA 229
Cdd:PRK01130  146 TLSGYTEETKKPEEPDFALLKELLKAVGCPVIAEGRINTPEQAKKALEL-GAHAVVVGGA 204
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 61-243 1.60e-04

Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.


Pssm-ID: 240091 [Multi-domain]  Cd Length: 296  Bit Score: 42.54  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  61 LDYRDEPG-PISAQIVGSDPAQMAEAARLNVELGAHIVDINMGCPAKKvckvAAGSALLRDETRVARILEAVVAAVEVPV 139
Cdd:cd04740    82 LPWLREFGtPVIASIAGSTVEEFVEVAEKLADAGADAIELNISCPNVK----GGGMAFGTDPEAVAEIVKAVKKATDVPV 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 140 TLKIrtgwSPEERNAVRIARIARESGIAAL----TVHG-----RTR----ACTYG---APAeydtIR--AIRA------S 195
Cdd:cd04740   158 IVKL----TPNVTDIVEIARAAEEAGADGLtlinTLKGmaidiETRkpilGNVTGglsGPA----IKpiALRMvyqvykA 229

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2727058504 196 VDIPLIANGDIASPEDARHVLhYTGADAIMIGRAAQGRPWIFGDIAAD 243
Cdd:cd04740   230 VEIPIIGVGGIASGEDALEFL-MAGASAVQVGTANFVDPEAFKEIIEG 276
OYE_like_4_FMN cd04735
Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN ...
 198-229 3.02e-04

Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.


Pssm-ID: 240086 [Multi-domain]  Cd Length: 353  Bit Score: 42.20  E-value: 3.02e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2727058504 198 IPLIANGDIASPEDARHVLHyTGADAIMIGRA 229
Cdd:cd04735   285 LPLIAVGSINTPDDALEALE-TGADLVAIGRG 315
PRK13585 PRK13585
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide ...
 187-229 5.47e-04

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase;


Pssm-ID: 184165  Cd Length: 241  Bit Score: 40.66  E-value: 5.47e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2727058504 187 DTIRAIRASVDIPLIANGDIASPEDARhVLHYTGADAIMIGRA 229
Cdd:PRK13585  183 EPVKELVDSVDIPVIASGGVTTLDDLR-ALKEAGAAGVVVGSA 224
HisF COG0107
Imidazole glycerol phosphate synthase subunit HisF [Amino acid transport and metabolism]; ...
 186-227 5.48e-04

Imidazole glycerol phosphate synthase subunit HisF [Amino acid transport and metabolism]; Imidazole glycerol phosphate synthase subunit HisF is part of the Pathway/BioSystem: Histidine biosynthesis


Pssm-ID: 439877  Cd Length: 251  Bit Score: 40.78  E-value: 5.48e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2727058504 186 YDT--IRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMIG 227
Cdd:COG0107   182 YDLelTRAVSEAVSIPVIASGGAGTLEHFVEVFTEGGADAALAA 225
PcrB_like cd02812
PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been ...
 142-227 5.57e-04

PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown.


Pssm-ID: 239206  Cd Length: 219  Bit Score: 40.69  E-value: 5.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 142 KIRTGWSPEErnAVRIARIARESGIAALTVHGRtractyGAPAEYDTIRAIRASV-DIPLIANGDIASPEDARHVLhYTG 220
Cdd:cd02812   127 GAKTDLKPED--AAAYALAAEYLGMPIVYLEYS------GAYGPPEVVRAVKKVLgDTPLIVGGGIRSGEQAKEMA-EAG 197


                  ....*..
gi 2727058504 221 ADAIMIG 227
Cdd:cd02812   198 ADTIVVG 204
NPD_like cd04730
2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes ...
 155-227 1.71e-03

2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN.


Pssm-ID: 240081 [Multi-domain]  Cd Length: 236  Bit Score: 39.39  E-value: 1.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504 155 VRIARIARESGIAALTV-------HGRTRACTYGAPaeydtIRAIRASVDIPLIANGDIASPEDARHVLHYtGADAIMIG 227
Cdd:cd04730   112 VEEARKAEAAGADALVAqgaeaggHRGTFDIGTFAL-----VPEVRDAVDIPVIAAGGIADGRGIAAALAL-GADGVQMG 185
His_biosynth pfam00977
Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine ...
 186-229 2.95e-03

Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalyzed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family.


Pssm-ID: 425971  Cd Length: 228  Bit Score: 38.61  E-value: 2.95e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2727058504 186 YDTIRAIRASVDIPLIANGDIASPEDARHVLhYTGADAIMIGRA 229
Cdd:pfam00977 179 LELTRELAEAVNIPVIASGGVGSLEDLKELF-TEGVDGVIAGSA 221
MLE_like cd03315
Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this ...
 78-226 3.56e-03

Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and residues that can function as general acid/base catalysts, a Lys-X-Lys motif and another conserved lysine. Despite these conserved residues, the members of the MLE subgroup, like muconate lactonizing enzyme, o-succinylbenzoate synthase (OSBS) and N-acylamino acid racemase (NAAAR), catalyze different reactions.


Pssm-ID: 239431 [Multi-domain]  Cd Length: 265  Bit Score: 38.48  E-value: 3.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058504  78 DPAQMAEAARLNVELGAHivdinmgcpakkVCKVAAGSALLRDETRVARILEAVVAAVEVpvTLKIRTGWSPEErnAVRI 157
Cdd:cd03315    85 EPAEVAEEARRALEAGFR------------TFKLKVGRDPARDVAVVAALREAVGDDAEL--RVDANRGWTPKQ--AIRA 148

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2727058504 158 ARIARESGIAALT--VHGRTRactygapaeyDTIRAIRASVDIPLIANGDIASPEDARHVLHYTGADAIMI 226
Cdd:cd03315   149 LRALEDLGLDYVEqpLPADDL----------EGRAALARATDTPIMADESAFTPHDAFRELALGAADAVNI 209
His_biosynth pfam00977
Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine ...
 181-241 4.13e-03

Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalyzed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family.


Pssm-ID: 425971  Cd Length: 228  Bit Score: 37.84  E-value: 4.13e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2727058504 181 GAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYtGADAIMIGRAAQGRPWIFGDIA 241
Cdd:pfam00977  57 GRPVNLDVVEEIAEEVFIPVQVGGGIRSLEDVERLLSA-GADRVIIGTAAVKNPELIKEAA 116
HisF cd04731
The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol ...
 177-242 5.67e-03

The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.


Pssm-ID: 240082  Cd Length: 243  Bit Score: 37.83  E-value: 5.67e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2727058504 177 ACTYGAPAEYDTIRAIRASVDIPLIANGDIASPEDARHVLHYtGADAIMIGRAAQGRPWIFGDIAA 242
Cdd:cd04731    51 ASSEGRETMLDVVERVAEEVFIPLTVGGGIRSLEDARRLLRA-GADKVSINSAAVENPELIREIAK 115
PRK13585 PRK13585
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide ...
 187-247 8.98e-03

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase;


Pssm-ID: 184165  Cd Length: 241  Bit Score: 37.19  E-value: 8.98e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2727058504 187 DTIRAIRASVDIPLIANGDIASPEDARHVLHyTGADAIMIGRAAQGRPWIFGDIAADPVPE 247
Cdd:PRK13585   66 EAIEKIIEAVGVPVQLGGGIRSAEDAASLLD-LGVDRVILGTAAVENPEIVRELSEEFGSE 125
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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