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Conserved domains on  [gi|323130514|gb|ADX17944|]
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dihydropyrimidine dehydrogenase [Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74]

Protein Classification

dihydropyrimidine dehydrogenase subunit B( domain architecture ID 11483255)

dihydropyrimidine dehydrogenase subunit B catalyzes the first step in pyrimidine degradation by conversion to their corresponding 5,6-dihydropyrimidines

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08318 PRK08318
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
4-403 0e+00

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


:

Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 708.63  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   4 KDLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGFFIANEVSPRFDHLTKEDTGFIGFKNMEQIAEH 83
Cdd:PRK08318   2 ADLSITFCGIKSPNPFWLASAPPTNKYYNVARAFEAGWGGVVWKTLGPPIVNVSSPRFGALVKEDRRFIGFNNIELITDR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  84 PLEENLAAIRRLKQDYPDKVLIASIMGE-NEQQWQELARLVEEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYCR 161
Cdd:PRK08318  82 PLEVNLREIRRVKRDYPDRALIASIMVEcNEEEWKEIAPLVEETGADGIELNFGCPHgMSERGMGSAVGQVPELVEMYTR 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 162 AVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRF 241
Cdd:PRK08318 162 WVKRGSRLPVIVKLTPNITDIREPARAAKRGGADAVSLINTINSITGVDLDRMIPMPIVNGKSSHGGYCGPAVKPIALNM 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 242 IQQLRMHPELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFASLQEMIGLANG 321
Cdd:PRK08318 242 VAEIARDPETRGLPISGIGGIETWRDAAEFILLGAGTVQVCTAAMQYGFRIVEDMISGLSHYMDEKGFASLEDMVGLAVP 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 322 NIIPAEDLDRSYIVYPRINQEKCVGCGRCYISCYDGGHQAMEWDEH-SRTPHCNTEKCVGCLLCGHVCPVA-CIDLGEVK 399
Cdd:PRK08318 322 NVTDWEDLDLNYIVYARIDQDKCIGCGRCYIACEDTSHQAIEWDEDgTRTPEVIEEECVGCNLCAHVCPVEgCITMGEVK 401


                 ....
gi 323130514 400 FKKG 403
Cdd:PRK08318 402 FGKP 405
 
Name Accession Description Interval E-value
PRK08318 PRK08318
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
4-403 0e+00

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 708.63  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   4 KDLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGFFIANEVSPRFDHLTKEDTGFIGFKNMEQIAEH 83
Cdd:PRK08318   2 ADLSITFCGIKSPNPFWLASAPPTNKYYNVARAFEAGWGGVVWKTLGPPIVNVSSPRFGALVKEDRRFIGFNNIELITDR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  84 PLEENLAAIRRLKQDYPDKVLIASIMGE-NEQQWQELARLVEEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYCR 161
Cdd:PRK08318  82 PLEVNLREIRRVKRDYPDRALIASIMVEcNEEEWKEIAPLVEETGADGIELNFGCPHgMSERGMGSAVGQVPELVEMYTR 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 162 AVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRF 241
Cdd:PRK08318 162 WVKRGSRLPVIVKLTPNITDIREPARAAKRGGADAVSLINTINSITGVDLDRMIPMPIVNGKSSHGGYCGPAVKPIALNM 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 242 IQQLRMHPELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFASLQEMIGLANG 321
Cdd:PRK08318 242 VAEIARDPETRGLPISGIGGIETWRDAAEFILLGAGTVQVCTAAMQYGFRIVEDMISGLSHYMDEKGFASLEDMVGLAVP 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 322 NIIPAEDLDRSYIVYPRINQEKCVGCGRCYISCYDGGHQAMEWDEH-SRTPHCNTEKCVGCLLCGHVCPVA-CIDLGEVK 399
Cdd:PRK08318 322 NVTDWEDLDLNYIVYARIDQDKCIGCGRCYIACEDTSHQAIEWDEDgTRTPEVIEEECVGCNLCAHVCPVEgCITMGEVK 401


                 ....
gi 323130514 400 FKKG 403
Cdd:PRK08318 402 FGKP 405
DHPD_FMN cd02940
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in ...
 5-300 0e+00

Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. 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 the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.


Pssm-ID: 239244  Cd Length: 299  Bit Score: 507.59  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGF--FIANEVSPRFDHLTKEDTGFIGFKNMEQIAE 82
Cdd:cd02940    1 DLSVTFCGIKFPNPFGLASAPPTTSYPMIRRAFEAGWGGAVTKTLGLdkDIVTNVSPRIARLRTSGRGQIGFNNIELISE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  83 HPLEENLAAIRRLKQDYPDKVLIASIMGE-NEQQWQELARLVEEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYC 160
Cdd:cd02940   81 KPLEYWLKEIRELKKDFPDKILIASIMCEyNKEDWTELAKLVEEAGADALELNFSCPHgMPERGMGAAVGQDPELVEEIC 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 161 RAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALR 240
Cdd:cd02940  161 RWVREAVKIPVIAKLTPNITDIREIARAAKEGGADGVSAINTVNSLMGVDLDGTPPAPGVEGKTTYGGYSGPAVKPIALR 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 241 FIQQLRMHPElRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGL 300
Cdd:cd02940  241 AVSQIARAPE-PGLPISGIGGIESWEDAAEFLLLGASVVQVCTAVMNQGFTIVDDMCTGL 299
PyrD COG0167
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ...
 5-312 8.85e-107

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: 316.63  E-value: 8.85e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGFF-IANEVSPRFdHLTKEDTGFIgfkNMEQIAEH 83
Cdd:COG0167    1 DLSVELAGLKFPNPVGLASGFFDKNAEYIDALDLLGFGAVEVKTVTPEpQPGNPRPRL-FRLPEDSGLI---NRMGLNNP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  84 PLEENLAAIRRLKQdyPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMtsHAMGSDVGQSPELVEKYCRAV 163
Cdd:COG0167   77 GVDAFLERLLPAKR--YDVPVIVNIGGNTVEDYVELARRLADAGADYLELNISCPNT--PGGGRALGQDPEALAELLAAV 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 164 KRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITnIDLNRkiGMPVVNGKssISGYSGKAVKPIALRFIQ 243
Cdd:COG0167  153 KAATDKPVLVKLAPDLTDIVEIARAAEEAGADGVIAINTTLGRA-IDLET--RRPVLANE--AGGLSGPALKPIALRMVR 227

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514 244 QLRMHPElRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFASL 312
Cdd:COG0167  228 EVAQAVG-GDIPIIGVGGISTAEDALEFILAGASAVQVGTALFYEGPGLVRRIIRGLEAYLEEKGFSSI 295
pyrD_sub1_fam TIGR01037
dihydroorotate dehydrogenase (subfamily 1) family protein; This family includes subfamily 1 ...
 6-319 4.30e-64

dihydroorotate dehydrogenase (subfamily 1) family protein; This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase.


Pssm-ID: 130109 [Multi-domain]  Cd Length: 300  Bit Score: 207.67  E-value: 4.30e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514    6 LSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGffianeVSPRFDHLTK---EDTGfiGFKNMEQIAE 82
Cdd:TIGR01037   1 LEVELFGIRFKNPLILASGIMGSGVESLRRIDRSGAGAVVTKSIG------LEPRPGYRNPtivETPC--GMLNAIGLQN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   83 HPLEENLAAIRRLKQDYPdKVLIASIMGENEQQWQELARLVEEAG--ADMIECNFSCPqmtsHAM--GSDVGQSPELVEK 158
Cdd:TIGR01037  73 PGVEAFLEELKPVREEFP-TPLIASVYGSSVEEFAEVAEKLEKAPpyVDAYELNLSCP----HVKggGIAIGQDPELSAD 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITnIDLnrKIGMPVVNGKSsiSGYSGKAVKPIA 238
Cdd:TIGR01037 148 VVKAVKDKTDVPVFAKLSPNVTDITEIAKAAEEAGADGLTLINTLRGMK-IDI--KTGKPILANKT--GGLSGPAIKPIA 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  239 LRFIQQLRmhpELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMqYGYRIVEDMASGLSHYLADQGFASLQEMIGL 318
Cdd:TIGR01037 223 LRMVYDVY---KMVDIPIIGVGGITSFEDALEFLMAGASAVQVGTAVY-YRGFAFKKIIEGLIAFLKAEGFTSIEELIGI 298


                  .
gi 323130514  319 A 319
Cdd:TIGR01037 299 A 299
DHO_dh pfam01180
Dihydroorotate dehydrogenase;
6-304 1.25e-38

Dihydroorotate dehydrogenase;


Pssm-ID: 426103  Cd Length: 291  Bit Score: 140.56  E-value: 1.25e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514    6 LSVTFCGVKFPNPFCLSSSPVGNCYEMcAKAYDTGW-GGIVFKTIGFFiANEVSPR---FDhlTKEDT-GFIGFKNMEqi 80
Cdd:pfam01180   2 LATKIPGLDFKNPIGLASGFDKFGEEA-LKWLALGKfGAIEIKSVTPY-PQPGNPTprvFR--LPEGVlNRMGLNNPG-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   81 aehpLEENLAAIRRLKQDYPDKVL--IASIMGENEQQWQELARLVEEAgADMIECNFSCPQMtshAMGSDVGQSPELVEK 158
Cdd:pfam01180  76 ----LDAVLAELLKRRKEYPRPDLgiNLSKAGMTVDDYVEVARKIGPF-ADYIELNVSCPNT---PGLRALQTDPELAAI 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITN---IDLnrKIGMPVVngKSSISGYSGKAVK 235
Cdd:pfam01180 148 LLKVVKEVSKVPVLVKLAPDLTDIVIIDIADVALGEDGLDGINATNTTVRgmrIDL--KTEKPIL--ANGTGGLSGPPIK 223

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514  236 PIALRFIQQLRMHPELRdFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYL 304
Cdd:pfam01180 224 PIALKVIRELYQRTGPE-IPIIGVGGIESGEDALEKILAGASAVQIGTALIFGGPFIFPKIIDELPELL 291
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 83-131 1.15e-03

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 40.08  E-value: 1.15e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 323130514    83 HPLEENLAAIRRLKQDYPDKV---LIASIMGENEQQWQELARLVEEAGADMI 131
Cdd:smart00729 133 HTVEDVLEAVELLREAGPIKVstdLIVGLPGETEEDFEETLKLLKELGPDRV 184
ferrodoxin_EFR1 NF038196
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 342-403 1.81e-03

EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1).


Pssm-ID: 468407 [Multi-domain]  Cd Length: 243  Bit Score: 39.84  E-value: 1.81e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514 342 EKCVGCGRCY-------ISCYDGGhqaMEWDEHsrtphcntekCVGCLLCGHVCPVACIDLGEVKFKKG 403
Cdd:NF038196 185 DKCIGCGICAkvcpvnnIEMEDGK---PVWGHN----------CTHCLACIHRCPKEAIEYGKKTKKKG 240
 
Name Accession Description Interval E-value
PRK08318 PRK08318
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
4-403 0e+00

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 708.63  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   4 KDLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGFFIANEVSPRFDHLTKEDTGFIGFKNMEQIAEH 83
Cdd:PRK08318   2 ADLSITFCGIKSPNPFWLASAPPTNKYYNVARAFEAGWGGVVWKTLGPPIVNVSSPRFGALVKEDRRFIGFNNIELITDR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  84 PLEENLAAIRRLKQDYPDKVLIASIMGE-NEQQWQELARLVEEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYCR 161
Cdd:PRK08318  82 PLEVNLREIRRVKRDYPDRALIASIMVEcNEEEWKEIAPLVEETGADGIELNFGCPHgMSERGMGSAVGQVPELVEMYTR 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 162 AVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRF 241
Cdd:PRK08318 162 WVKRGSRLPVIVKLTPNITDIREPARAAKRGGADAVSLINTINSITGVDLDRMIPMPIVNGKSSHGGYCGPAVKPIALNM 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 242 IQQLRMHPELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFASLQEMIGLANG 321
Cdd:PRK08318 242 VAEIARDPETRGLPISGIGGIETWRDAAEFILLGAGTVQVCTAAMQYGFRIVEDMISGLSHYMDEKGFASLEDMVGLAVP 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 322 NIIPAEDLDRSYIVYPRINQEKCVGCGRCYISCYDGGHQAMEWDEH-SRTPHCNTEKCVGCLLCGHVCPVA-CIDLGEVK 399
Cdd:PRK08318 322 NVTDWEDLDLNYIVYARIDQDKCIGCGRCYIACEDTSHQAIEWDEDgTRTPEVIEEECVGCNLCAHVCPVEgCITMGEVK 401


                 ....
gi 323130514 400 FKKG 403
Cdd:PRK08318 402 FGKP 405
DHPD_FMN cd02940
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in ...
 5-300 0e+00

Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. 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 the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.


Pssm-ID: 239244  Cd Length: 299  Bit Score: 507.59  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGF--FIANEVSPRFDHLTKEDTGFIGFKNMEQIAE 82
Cdd:cd02940    1 DLSVTFCGIKFPNPFGLASAPPTTSYPMIRRAFEAGWGGAVTKTLGLdkDIVTNVSPRIARLRTSGRGQIGFNNIELISE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  83 HPLEENLAAIRRLKQDYPDKVLIASIMGE-NEQQWQELARLVEEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYC 160
Cdd:cd02940   81 KPLEYWLKEIRELKKDFPDKILIASIMCEyNKEDWTELAKLVEEAGADALELNFSCPHgMPERGMGAAVGQDPELVEEIC 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 161 RAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALR 240
Cdd:cd02940  161 RWVREAVKIPVIAKLTPNITDIREIARAAKEGGADGVSAINTVNSLMGVDLDGTPPAPGVEGKTTYGGYSGPAVKPIALR 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 241 FIQQLRMHPElRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGL 300
Cdd:cd02940  241 AVSQIARAPE-PGLPISGIGGIESWEDAAEFLLLGASVVQVCTAVMNQGFTIVDDMCTGL 299
PyrD COG0167
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ...
 5-312 8.85e-107

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: 316.63  E-value: 8.85e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGFF-IANEVSPRFdHLTKEDTGFIgfkNMEQIAEH 83
Cdd:COG0167    1 DLSVELAGLKFPNPVGLASGFFDKNAEYIDALDLLGFGAVEVKTVTPEpQPGNPRPRL-FRLPEDSGLI---NRMGLNNP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  84 PLEENLAAIRRLKQdyPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMtsHAMGSDVGQSPELVEKYCRAV 163
Cdd:COG0167   77 GVDAFLERLLPAKR--YDVPVIVNIGGNTVEDYVELARRLADAGADYLELNISCPNT--PGGGRALGQDPEALAELLAAV 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 164 KRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITnIDLNRkiGMPVVNGKssISGYSGKAVKPIALRFIQ 243
Cdd:COG0167  153 KAATDKPVLVKLAPDLTDIVEIARAAEEAGADGVIAINTTLGRA-IDLET--RRPVLANE--AGGLSGPALKPIALRMVR 227

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514 244 QLRMHPElRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFASL 312
Cdd:COG0167  228 EVAQAVG-GDIPIIGVGGISTAEDALEFILAGASAVQVGTALFYEGPGLVRRIIRGLEAYLEEKGFSSI 295
PLN02495 PLN02495
oxidoreductase, acting on the CH-CH group of donors
 5-319 1.69e-99

oxidoreductase, acting on the CH-CH group of donors


Pssm-ID: 215273 [Multi-domain]  Cd Length: 385  Bit Score: 301.37  E-value: 1.69e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGFFIAN--EVSPRFDHLTKEDTG-----FIGFKNM 77
Cdd:PLN02495  10 DLSVTVNGLKMPNPFVIGSGPPGTNYTVMKRAFDEGWGGVIAKTVSLDASKviNVTPRYARLRAGANGsakgrVIGWQNI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  78 EQIAEHPLEENLAAIRRLKQDYPDKVLIASIMGE-NEQQWQELARLVEEAGADMIECNFSCPQ-MTSHAMGSDVGQSPEL 155
Cdd:PLN02495  90 ELISDRPFETMLAEFKQLKEEYPDRILIASIMEEyNKDAWEEIIERVEETGVDALEINFSCPHgMPERKMGAAVGQDCDL 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 156 VEKYCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMPVVNGKSSISGYSGKAVK 235
Cdd:PLN02495 170 LEEVCGWINAKATVPVWAKMTPNITDITQPARVALKSGCEGVAAINTIMSVMGINLDTLRPEPCVEGYSTPGGYSSKAVR 249

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 236 PIALRFIQQL--RMHPEL-RDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFASL 312
Cdd:PLN02495 250 PIALAKVMAIakMMKSEFpEDRSLSGIGGVETGGDAAEFILLGADTVQVCTGVMMHGYPLVKNLCAELQDFMKKHNFSSI 329


                 ....*..
gi 323130514 313 QEMIGLA 319
Cdd:PLN02495 330 EDFRGAS 336
PRK07259 PRK07259
dihydroorotate dehydrogenase;
5-319 6.92e-71

dihydroorotate dehydrogenase;


Pssm-ID: 235982  Cd Length: 301  Bit Score: 225.03  E-value: 6.92e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSSPVGNCYEMcAKAYD-TGWGGIVFKTIGffianeVSPRFDH----LTKEDTGF---IGFKN 76
Cdd:PRK07259   1 RLSVELPGLKLKNPVMPASGTFGFGGEY-ARFYDlNGLGAIVTKSTT------LEPREGNptprIAETPGGMlnaIGLQN 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  77 MEqiAEHPLEENLAAIRRLkqdypDKVLIASIMGENEQQWQELARLVEEAG-ADMIECNFSCPqmtsHAM--GSDVGQSP 153
Cdd:PRK07259  74 PG--VDAFIEEELPWLEEF-----DTPIIANVAGSTEEEYAEVAEKLSKAPnVDAIELNISCP----NVKhgGMAFGTDP 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 154 ELVEKYCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITnIDLNRKigMPVVNGKssISGYSGKA 233
Cdd:PRK07259 143 ELAYEVVKAVKEVVKVPVIVKLTPNVTDIVEIAKAAEEAGADGLSLINTLKGMA-IDIKTR--KPILANV--TGGLSGPA 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 234 VKPIALRFIQQLRmhpELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMqYGYRIVEDMASGLSHYLADQGFASLQ 313
Cdd:PRK07259 218 IKPIALRMVYQVY---QAVDIPIIGMGGISSAEDAIEFIMAGASAVQVGTANF-YDPYAFPKIIEGLEAYLDKYGIKSIE 293


                 ....*.
gi 323130514 314 EMIGLA 319
Cdd:PRK07259 294 EIVGIA 299
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 7-319 3.99e-70

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: 222.81  E-value: 3.99e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   7 SVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGffianeVSPRFDHLT----KEDTGF---IGFKN--M 77
Cdd:cd04740    1 SVELAGLRLKNPVILASGTFGFGEELSRVADLGKLGAIVTKSIT------LEPREGNPPprvvETPGGMlnaIGLQNpgV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  78 EQIAEHPLEENlaairrlkqDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPqmtsHAM--GSDVGQSPEL 155
Cdd:cd04740   75 EAFLEELLPWL---------REFGTPVIASIAGSTVEEFVEVAEKLADAGADAIELNISCP----NVKggGMAFGTDPEA 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 156 VEKYCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITnIDLNRkiGMPVVNGKssISGYSGKAVK 235
Cdd:cd04740  142 VAEIVKAVKKATDVPVIVKLTPNVTDIVEIARAAEEAGADGLTLINTLKGMA-IDIET--RKPILGNV--TGGLSGPAIK 216

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 236 PIALRFIQQLRmhpELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMqYGYRIVEDMASGLSHYLADQGFASLQEM 315
Cdd:cd04740  217 PIALRMVYQVY---KAVEIPIIGVGGIASGEDALEFLMAGASAVQVGTANF-VDPEAFKEIIEGLEAYLDEEGIKSIEEL 292


                 ....
gi 323130514 316 IGLA 319
Cdd:cd04740  293 VGLA 296
pyrD_sub1_fam TIGR01037
dihydroorotate dehydrogenase (subfamily 1) family protein; This family includes subfamily 1 ...
 6-319 4.30e-64

dihydroorotate dehydrogenase (subfamily 1) family protein; This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase.


Pssm-ID: 130109 [Multi-domain]  Cd Length: 300  Bit Score: 207.67  E-value: 4.30e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514    6 LSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIGffianeVSPRFDHLTK---EDTGfiGFKNMEQIAE 82
Cdd:TIGR01037   1 LEVELFGIRFKNPLILASGIMGSGVESLRRIDRSGAGAVVTKSIG------LEPRPGYRNPtivETPC--GMLNAIGLQN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   83 HPLEENLAAIRRLKQDYPdKVLIASIMGENEQQWQELARLVEEAG--ADMIECNFSCPqmtsHAM--GSDVGQSPELVEK 158
Cdd:TIGR01037  73 PGVEAFLEELKPVREEFP-TPLIASVYGSSVEEFAEVAEKLEKAPpyVDAYELNLSCP----HVKggGIAIGQDPELSAD 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITnIDLnrKIGMPVVNGKSsiSGYSGKAVKPIA 238
Cdd:TIGR01037 148 VVKAVKDKTDVPVFAKLSPNVTDITEIAKAAEEAGADGLTLINTLRGMK-IDI--KTGKPILANKT--GGLSGPAIKPIA 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  239 LRFIQQLRmhpELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMqYGYRIVEDMASGLSHYLADQGFASLQEMIGL 318
Cdd:TIGR01037 223 LRMVYDVY---KMVDIPIIGVGGITSFEDALEFLMAGASAVQVGTAVY-YRGFAFKKIIEGLIAFLKAEGFTSIEELIGI 298


                  .
gi 323130514  319 A 319
Cdd:TIGR01037 299 A 299
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 8-295 6.84e-62

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: 201.43  E-value: 6.84e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   8 VTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIgfFI---ANEVSPRFDHLTKEDTGF---IGFKNMEQIA 81
Cdd:cd02810    1 VNFLGLKLKNPFGVAAGPLLKTGELIARAAAAGFGAVVYKTV--TLhprPGNPLPRVARLPPEGESYpeqLGILNSFGLP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  82 EHPLEENLAAIRRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPqmtsHAMGSD-VGQSPELVEKYC 160
Cdd:cd02810   79 NLGLDVWLQDIAKAKKEFPGQPLIASVGGSSKEDYVELARKIERAGAKALELNLSCP----NVGGGRqLGQDPEAVANLL 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 161 RAVKRGSSLPMLAKMTPN--IGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMpvvngKSSISGYSGKAVKPIA 238
Cdd:cd02810  155 KAVKAAVDIPLLVKLSPYfdLEDIVELAKAAERAGADGLTAINTISGRVVDLKTVGPGP-----KRGTGGLSGAPIRPLA 229

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 323130514 239 LRFIQQLRMHPELrDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVED 295
Cdd:cd02810  230 LRWVARLAARLQL-DIPIIGVGGIDSGEDVLEMLMAGASAVQVATALMWDGPDVIRK 285
DHO_dh pfam01180
Dihydroorotate dehydrogenase;
6-304 1.25e-38

Dihydroorotate dehydrogenase;


Pssm-ID: 426103  Cd Length: 291  Bit Score: 140.56  E-value: 1.25e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514    6 LSVTFCGVKFPNPFCLSSSPVGNCYEMcAKAYDTGW-GGIVFKTIGFFiANEVSPR---FDhlTKEDT-GFIGFKNMEqi 80
Cdd:pfam01180   2 LATKIPGLDFKNPIGLASGFDKFGEEA-LKWLALGKfGAIEIKSVTPY-PQPGNPTprvFR--LPEGVlNRMGLNNPG-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   81 aehpLEENLAAIRRLKQDYPDKVL--IASIMGENEQQWQELARLVEEAgADMIECNFSCPQMtshAMGSDVGQSPELVEK 158
Cdd:pfam01180  76 ----LDAVLAELLKRRKEYPRPDLgiNLSKAGMTVDDYVEVARKIGPF-ADYIELNVSCPNT---PGLRALQTDPELAAI 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITN---IDLnrKIGMPVVngKSSISGYSGKAVK 235
Cdd:pfam01180 148 LLKVVKEVSKVPVLVKLAPDLTDIVIIDIADVALGEDGLDGINATNTTVRgmrIDL--KTEKPIL--ANGTGGLSGPPIK 223

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514  236 PIALRFIQQLRMHPELRdFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYL 304
Cdd:pfam01180 224 PIALKVIRELYQRTGPE-IPIIGVGGIESGEDALEKILAGASAVQIGTALIFGGPFIFPKIIDELPELL 291
PRK07565 PRK07565
dihydroorotate dehydrogenase-like protein;
5-317 2.28e-29

dihydroorotate dehydrogenase-like protein;


Pssm-ID: 236051  Cd Length: 334  Bit Score: 116.50  E-value: 2.28e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTigFF---IANEVSPRFDHLTKEDTGFI---GFKNME 78
Cdd:PRK07565   2 DLSTTYLGLTLRNPLVASASPLSESVDNVKRLEDAGAGAVVLKS--LFeeqIRHEAAELDRHLTHGTESFAealDYFPEP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  79 QIAEHPLEENLAAIRRLKQ--DYPdkvLIASIMGENEQQWQELARLVEEAGADMIECNFscpqmtsHAMGSDVGQSPELV 156
Cdd:PRK07565  80 AKFYVGPEEYLELIRRAKEavDIP---VIASLNGSSAGGWVDYARQIEQAGADALELNI-------YYLPTDPDISGAEV 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 157 EK-YC---RAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSiTNIDLNRkigMPVVNGK--SSisgyS 230
Cdd:PRK07565 150 EQrYLdilRAVKSAVSIPVAVKLSPYFSNLANMAKRLDAAGADGLVLFNRFYQ-PDIDLET---LEVVPGLvlST----P 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 231 GKAVKPiaLRFIQQLRMHPELrDFPISgiGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFA 310
Cdd:PRK07565 222 AELRLP--LRWIAILSGRVGA-DLAAT--TGVHDAEDVIKMLLAGADVVMIASALLRHGPDYIGTILRGLEDWMERHGYE 296


                 ....*..
gi 323130514 311 SLQEMIG 317
Cdd:PRK07565 297 SLQQFRG 303
DHOD_like cd04739
Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S) ...
 5-317 5.14e-29

Dihydroorotate dehydrogenase (DHOD) like proteins. 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. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive.


Pssm-ID: 240090  Cd Length: 325  Bit Score: 115.40  E-value: 5.14e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGIVFKTIgfF---IANEvSPRFDHLTKEDTGFIGFKNM--EQ 79
Cdd:cd04739    1 DLSTTYLGLSLKNPLVASASPLSRNLDNIRRLEDAGAGAIVLPSL--FeeqIERE-AQELDRFLTYGSSFAEALSYfpEY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  80 IAEHP-LEENLAAIRRLKQ--DYPdkvLIASIMGENEQQWQELARLVEEAGADMIECNFscpqmtsHAMGSDVGQSPELV 156
Cdd:cd04739   78 GRYNLgPEEYLELIRRAKRavSIP---VIASLNGVSAGGWVDYARQIEEAGADALELNI-------YALPTDPDISGAEV 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 157 EK-YC---RAVKRGSSLPMLAKMTP---NIGDMCEVALAAkrgGADGIATINTVKSiTNIDLNRkigMPVVNGkSSISgY 229
Cdd:cd04739  148 EQrYLdilRAVKSAVTIPVAVKLSPffsALAHMAKQLDAA---GADGLVLFNRFYQ-PDIDLET---LEVVPN-LLLS-S 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 230 SGKAVKPiaLRFIQQLRMHPELrDFPISgiGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGF 309
Cdd:cd04739  219 PAEIRLP--LRWIAILSGRVKA-SLAAS--GGVHDAEDVVKYLLAGADVVMTTSALLRHGPDYIGTLLAGLEAWMEEHGY 293


                 ....*...
gi 323130514 310 ASLQEMIG 317
Cdd:cd04739  294 ESVQQLRG 301
DHOD_1A_like cd04741
Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation ...
 84-300 1.31e-17

Dihydroorotate dehydrogenase (DHOD) class 1A 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: 240092  Cd Length: 294  Bit Score: 82.76  E-value: 1.31e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  84 PLEENLAAIRRLKQDYPD--KVLIASIMGENEQQWQELARLVEEA--GADMIECNFSCPQMTSHamgSDVGQSPELVEKY 159
Cdd:cd04741   72 GLDYYLEYIRTISDGLPGsaKPFFISVTGSAEDIAAMYKKIAAHQkqFPLAMELNLSCPNVPGK---PPPAYDFDATLEY 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 160 CRAVKRGSSLPMLAKMTP-----NIGDMCEVALAAkrggADGIATINTVKSITN---IDLNRKigMPVVNGKSSISGYSG 231
Cdd:cd04741  149 LTAVKAAYSIPVGVKTPPytdpaQFDTLAEALNAF----ACPISFITATNTLGNglvLDPERE--TVVLKPKTGFGGLAG 222

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 232 KAVKPIALRFIQQLR-MHPELRDfpISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGL 300
Cdd:cd04741  223 AYLHPLALGNVRTFRrLLPSEIQ--IIGVGGVLDGRGAFRMRLAGASAVQVGTALGKEGPKVFARIEKEL 290
PRK05286 PRK05286
quinone-dependent dihydroorotate dehydrogenase;
6-308 1.46e-17

quinone-dependent dihydroorotate dehydrogenase;


Pssm-ID: 235388  Cd Length: 344  Bit Score: 83.29  E-value: 1.46e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   6 LSVTFCGVKFPNPFCLSSspvG---NcyemcAKAYDtGWGGIvfktiGF-FIanEV------------SPRFDHLtKEDT 69
Cdd:PRK05286  49 LPVTVMGLTFPNPVGLAA---GfdkN-----GEAID-ALGAL-----GFgFV--EVgtvtprpqpgnpKPRLFRL-PEDE 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  70 GFI---GFKN--MEqiaehpleenlAAIRRLKQDYPDKVLIASI----MGENEQQWQELARLVEEAG--ADMIECNFSCP 138
Cdd:PRK05286 112 ALInrmGFNNdgAD-----------ALAERLKKAYRGIPLGINIgknkDTPLEDAVDDYLICLEKLYpyADYFTVNISSP 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 139 ------QMtshamgsdvgQSPELVEKYCRAVKR-----GSSLPMLAKMTPNI--GDMCEVALAAKRGGADG-IATiNTVK 204
Cdd:PRK05286 181 ntpglrDL----------QYGEALDELLAALKEaqaelHGYVPLLVKIAPDLsdEELDDIADLALEHGIDGvIAT-NTTL 249

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 205 S---ITNIDLNRKIGmpvvngkssisGYSGKAVKPIALRFIQQLRMHpeLRD-FPISGIGGIETWEDAAEFLLLGAATLQ 280
Cdd:PRK05286 250 SrdgLKGLPNADEAG-----------GLSGRPLFERSTEVIRRLYKE--LGGrLPIIGVGGIDSAEDAYEKIRAGASLVQ 316

                        330       340
                 ....*....|....*....|....*...
gi 323130514 281 VTTGIMQYGYRIVEDMASGLSHYLADQG 308
Cdd:PRK05286 317 IYSGLIYEGPGLVKEIVRGLARLLRRDG 344
DHOD_2_like cd04738
Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S) ...
 5-300 2.04e-17

Dihydroorotate dehydrogenase (DHOD) class 2. 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, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors.


Pssm-ID: 240089  Cd Length: 327  Bit Score: 82.55  E-value: 2.04e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514   5 DLSVTFCGVKFPNPFCLSSspvG---NcyemcAKAYDtGWGGIvfktiGF-FIanEV------------SPRFDHLTkED 68
Cdd:cd04738   38 RLEVEVFGLTFPNPVGLAA---GfdkN-----AEAID-ALLAL-----GFgFV--EVgtvtprpqpgnpKPRLFRLP-ED 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  69 TGFI---GFKNmeqiaeHPLEenlAAIRRLKQDYPDKVLI-ASI----MGENEQQWQELARLVEEAG--ADMIECNFSCP 138
Cdd:cd04738  101 EALInrmGFNN------DGAD---AVAKRLKKRRPRGGPLgVNIgknkDTPLEDAVEDYVIGVRKLGpyADYLVVNVSSP 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 139 ------QMtshamgsdvgQSPELVEKYCRAVKR-----GSSLPMLAKMTPNI--GDMCEVALAAKRGGADG-IATiNTVK 204
Cdd:cd04738  172 ntpglrDL----------QGKEALRELLTAVKEernklGKKVPLLVKIAPDLsdEELEDIADVALEHGVDGiIAT-NTTI 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 205 SITNIDLNRKIGMPvvnGkssisGYSGKAVKPIALRFIQqlRMHPELRD-FPISGIGGIETWEDAAEFLLLGAATLQVTT 283
Cdd:cd04738  241 SRPGLLRSPLANET---G-----GLSGAPLKERSTEVLR--ELYKLTGGkIPIIGVGGISSGEDAYEKIRAGASLVQLYT 310

                        330
                 ....*....|....*..
gi 323130514 284 GIMQYGYRIVEDMASGL 300
Cdd:cd04738  311 GLVYEGPGLVKRIKREL 327
PRK02506 PRK02506
dihydroorotate dehydrogenase 1A; Reviewed
 92-317 2.20e-14

dihydroorotate dehydrogenase 1A; Reviewed


Pssm-ID: 235045  Cd Length: 310  Bit Score: 73.45  E-value: 2.20e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  92 IRRLKQDYPDKVLIASIMGENEQQWQELARLVEEAG-ADMIECNFSCPQMTSHAmgsDVGQSPELVEKYCRAVKRGSSLP 170
Cdd:PRK02506  83 VLELQKKGPNKPHFLSVVGLSPEETHTILKKIQASDfNGLVELNLSCPNVPGKP---QIAYDFETTEQILEEVFTYFTKP 159

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 171 MLAKMTPNIgDMCEVALAAKRGGADGIATINTVKSITN---IDLNRKigMPVVNGKSSISGYSGKAVKPIALRFIQQL-- 245
Cdd:PRK02506 160 LGVKLPPYF-DIVHFDQAAAIFNKFPLAFVNCINSIGNglvIDPEDE--TVVIKPKNGFGGIGGDYIKPTALANVRAFyq 236

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 323130514 246 RMHPELrdfPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFASLQEMIG 317
Cdd:PRK02506 237 RLNPSI---QIIGTGGVKTGRDAFEHILCGASMVQVGTALHKEGPAVFERLTKELKAIMAEKGYQSLEDFRG 305
PorD COG1144
Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta ...
 336-395 2.76e-14

Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit [Energy production and conversion]; Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 440759 [Multi-domain]  Cd Length: 84  Bit Score: 67.77  E-value: 2.76e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 336 YPRINQEKCVGCGRCYISCYDGghqAMEWDEhSRTPHCNTEKCVGCLLCGHVCPVACIDL 395
Cdd:COG1144   24 RPVVDEDKCIGCGLCWIVCPDG---AIRVDD-GKYYGIDYDYCKGCGICAEVCPVKAIEM 79
Fer4_21 pfam14697
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 338-395 9.47e-14

4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.


Pssm-ID: 434137 [Multi-domain]  Cd Length: 59  Bit Score: 65.38  E-value: 9.47e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514  338 RINQEKCVGCGRCYISCYDGGHQAMEWDEhSRTPHCNTEKCVGCLLCGHVCPVA-CIDL 395
Cdd:pfam14697   2 RIDEDTCIGCGKCYIACPDTSHQAIVGDG-KRHHTVIEDECTGCNLCVSVCPVDdCITM 59
PreA COG1146
NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and ...
 335-403 3.68e-12

NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and metabolism];


Pssm-ID: 440761 [Multi-domain]  Cd Length: 67  Bit Score: 61.26  E-value: 3.68e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 335 VYPRINQEKCVGCGRCYISCydgGHQAMEWDEHSRTPHC-NTEKCVGCLLCGHVCPVACIDLGEVKFKKG 403
Cdd:COG1146    1 MMPVIDTDKCIGCGACVEVC---PVDVLELDEEGKKALViNPEECIGCGACELVCPVGAITVEDDEPEEQ 67
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 336-399 1.33e-11

MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function prediction only];


Pssm-ID: 440763 [Multi-domain]  Cd Length: 68  Bit Score: 59.74  E-value: 1.33e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 323130514 336 YPRINQEKCVGCGRCYISCydgGHQAMEWDEhSRTPHCNTEKCVGCLLCGHVCPVACIDLGEVK 399
Cdd:COG1149    5 IPVIDEEKCIGCGLCVEVC---PEGAIKLDD-GGAPVVDPDLCTGCGACVGVCPTGAITLEERE 64
NapF COG1145
Ferredoxin [Energy production and conversion];
339-401 1.87e-10

Ferredoxin [Energy production and conversion];


Pssm-ID: 440760 [Multi-domain]  Cd Length: 238  Bit Score: 60.89  E-value: 1.87e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 323130514 339 INQEKCVGCGRCYISCydgGHQAMEWDEHSRTPHCNTEKCVGCLLCGHVCPVACIDLGEVKFK 401
Cdd:COG1145  179 IDAEKCIGCGLCVKVC---PTGAIRLKDGKPQIVVDPDKCIGCGACVKVCPVGAISLEPKEIE 238
DsrA COG2221
Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion ...
 334-399 3.20e-10

Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion transport and metabolism];


Pssm-ID: 441823 [Multi-domain]  Cd Length: 69  Bit Score: 55.83  E-value: 3.20e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 323130514 334 IVYPRINQEKCVGCGRCYISCydgGHQAMEWDEHsrTPHCNTEKCVGCLLCGHVCPVACIDLGEVK 399
Cdd:COG2221    7 TWPPKIDEEKCIGCGLCVAVC---PTGAISLDDG--KLVIDEEKCIGCGACIRVCPTGAIKGEKPK 67
PLN02826 PLN02826
dihydroorotate dehydrogenase
 169-317 3.52e-10

dihydroorotate dehydrogenase


Pssm-ID: 178421  Cd Length: 409  Bit Score: 61.29  E-value: 3.52e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 169 LPMLAKMTPNI--GDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGmpvvngkSSISGYSGKAVKPIALRFIQQlr 246
Cdd:PLN02826 263 PPLLVKIAPDLskEDLEDIAAVALALGIDGLIISNTTISRPDSVLGHPHA-------DEAGGLSGKPLFDLSTEVLRE-- 333

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 323130514 247 MHPELR-DFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFASLQEMIG 317
Cdd:PLN02826 334 MYRLTRgKIPLVGCGGVSSGEDAYKKIRAGASLVQLYTAFAYEGPALIPRIKAELAACLERDGFKSIQEAVG 405
NuoI COG1143
Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy ...
 341-407 8.81e-10

Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]; Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) is part of the Pathway/BioSystem: NADH dehydrogenase


Pssm-ID: 440758 [Multi-domain]  Cd Length: 66  Bit Score: 54.37  E-value: 8.81e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514 341 QEKCVGCGRCYISCYdggHQA--MEWDEHSRTPHCNTEKCVGCLLCGHVCPVACIDLGEVKFKKGEKEH 407
Cdd:COG1143    1 EDKCIGCGLCVRVCP---VDAitIEDGEPGKVYVIDPDKCIGCGLCVEVCPTGAISMTPFELAVEDREE 66
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 85-272 1.11e-09

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: 58.27  E-value: 1.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  85 LEENLAAIRRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQM--TSHAMGSDVGQSPELVEKYCRA 162
Cdd:cd02801   38 LRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEELGADGIDLNMGCPSPkvTKGGAGAALLKDPELVAEIVRA 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 163 VKRGSSLPMLAKM----TPNIgDMCEVALAAKRGGADGIAtintvksitnidlnrkigmpvVNGKSSISGYSGKAVkpia 238
Cdd:cd02801  118 VREAVPIPVTVKIrlgwDDEE-ETLELAKALEDAGASALT---------------------VHGRTREQRYSGPAD---- 171

                        170       180       190
                 ....*....|....*....|....*....|....
gi 323130514 239 LRFIQQLRmhpELRDFPISGIGGIETWEDAAEFL 272
Cdd:cd02801  172 WDYIAEIK---EAVSIPVIANGDIFSLEDALRCL 202
COG2768 COG2768
Uncharacterized Fe-S cluster protein [Function unknown];
335-401 2.25e-09

Uncharacterized Fe-S cluster protein [Function unknown];


Pssm-ID: 442050 [Multi-domain]  Cd Length: 74  Bit Score: 53.58  E-value: 2.25e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 323130514 335 VYPRINQEKCVGCGRCYISCYdggHQAMEWDEHsrTPHCNTEKCVGCLLCGHVCPVACIDLGEVKFK 401
Cdd:COG2768    4 GKPYVDEEKCIGCGACVKVCP---VGAISIEDG--KAVIDPEKCIGCGACIEVCPVGAIKIEWEEDE 65
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 338-393 2.56e-09

TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and conversion];


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 53.51  E-value: 2.56e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 323130514 338 RINQEKCVGCGRCYISCydgghQAMEWDEHSRTPHCNTEKCVGCLLCGHVCPVACI 393
Cdd:COG4231   18 VIDEDKCTGCGACVKVC-----PADAIEEGDGKAVIDPDLCIGCGSCVQVCPVDAI 68
TIM_phosphate_binding cd04722
TIM barrel proteins share a structurally conserved phosphate binding motif and in general ...
 64-283 2.02e-08

TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.


Pssm-ID: 240073 [Multi-domain]  Cd Length: 200  Bit Score: 54.13  E-value: 2.02e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  64 LTKEDTGFIGFKNMEQIAEHPLEENLAAIRRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIEcnfscpqmtsh 143
Cdd:cd04722   21 AAEAGADAIIVGTRSSDPEEAETDDKEVLKEVAAETDLPLGVQLAINDAAAAVDIAAAAARAAGADGVE----------- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 144 aMGSDVGQSPELVEKYCRAVK-RGSSLPMLAKMTPNIGDmceVALAAKRGGADGiatintvksitnidlnrkigmpvVNG 222
Cdd:cd04722   90 -IHGAVGYLAREDLELIRELReAVPDVKVVVKLSPTGEL---AAAAAEEAGVDE-----------------------VGL 142

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 323130514 223 KSSISGYSGKAVKPIALRFIQQLRmhpELRDFPISGIGGIETWEDAAEFLLLGAATLQVTT 283
Cdd:cd04722  143 GNGGGGGGGRDAVPIADLLLILAK---RGSKVPVIAGGGINDPEDAAEALALGADGVIVGS 200
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 101-268 1.28e-07

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: 52.71  E-value: 1.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVGQSPELVEKYCRAVKRGSSLPMLAKMTPN 178
Cdd:pfam01207  53 PTPLAVQLGGSDPALLAEAAKLVEDRGADGIDINMGCPSkkVTRGGGGAALLRNPDLVAQIVKAVVKAVGIPVTVKIRIG 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  179 IGDMCEVAL-AAKRGGADGIATIntvksitnidlnrkigmpVVNGKSSISGYSGkavkPIALRFIQQLRmhpelRDFPIS 257
Cdd:pfam01207 133 WDDSHENAVeIAKIVEDAGAQAL------------------TVHGRTRAQNYEG----TADWDAIKQVK-----QAVSIP 185

                         170
                  ....*....|...
gi 323130514  258 GI--GGIETWEDA 268
Cdd:pfam01207 186 VIanGDITDPEDA 198
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 85-272 1.36e-07

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: 52.79  E-value: 1.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  85 LEENLAAIRRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCP--QMTSHAMGSDVGQSPELVEKYCRA 162
Cdd:COG0042   45 LHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAARIAEELGADEIDINMGCPvkKVTKGGAGAALLRDPELVAEIVKA 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 163 VKRGSSLPMLAKMtpNIG------DMCEVALAAKRGGADGIatinTV----KSitnidlNRkigmpvvngkssisgYSGK 232
Cdd:COG0042  125 VVEAVDVPVTVKI--RLGwddddeNALEFARIAEDAGAAAL----TVhgrtRE------QR---------------YKGP 177

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 323130514 233 AvkpiALRFIQQLRmhpELRDFPISGIGGIETWEDAAEFL 272
Cdd:COG0042  178 A----DWDAIARVK---EAVSIPVIGNGDIFSPEDAKRML 210
HdrA COG1148
Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];
335-395 2.26e-07

Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];


Pssm-ID: 440762 [Multi-domain]  Cd Length: 563  Bit Score: 52.94  E-value: 2.26e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 323130514 335 VYPRINQEKCVGCGRCYISCydgGHQAMEWDEhSRTPHCNTEKCVGCLLCGHVCPVACIDL 395
Cdd:COG1148  489 SVAEVDPEKCTGCGRCVEVC---PYGAISIDE-KGVAEVNPALCKGCGTCAAACPSGAISL 545
fdxN_nitrog TIGR02936
ferredoxin III, nif-specific; Members of this family are homodimeric ferredoxins from nitrogen ...
 339-392 2.51e-07

ferredoxin III, nif-specific; Members of this family are homodimeric ferredoxins from nitrogen fixation regions of many nitrogen-fixing bacteria. As characterized in Rhodobacter capsulatus, these proteins are homodimeric, with two 4Fe-4S clusters bound per monomer. Although nif-specific, this protein family is not usiveral, as other nitrogenase systems may substitute flavodoxins, or different types of ferredoxin. [Central intermediary metabolism, Nitrogen fixation]


Pssm-ID: 274356 [Multi-domain]  Cd Length: 91  Bit Score: 48.17  E-value: 2.51e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 323130514  339 INQEKCVGCGRCYISCydgGHQAMEW----------------DEHSRTPHC--NTEKCVGCLLCGHVCPVAC 392
Cdd:TIGR02936  18 IDQEKCIGCGRCYKVC---GRDVLTLkgineegelvasddddDEIERKVMVvaNPGNCIGCGACARVCPKKC 86
Fer4_7 pfam12838
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 344-392 2.91e-07

4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.


Pssm-ID: 463724 [Multi-domain]  Cd Length: 51  Bit Score: 46.75  E-value: 2.91e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 323130514  344 CVGCGRCYISCYdggHQAMEWDEHS-----RTPHCNTEKCVGCLLCGHVCPVAC 392
Cdd:pfam12838   1 CIGCGACVAACP---VGAITLDEVGekkgtKTVVIDPERCVGCGACVAVCPTGA 51
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 337-406 6.75e-07

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 48.16  E-value: 6.75e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 337 PRINQEKCVGCGRCYISCYDGGHQAMEWDEHSRTPHCNTEKCVGCLLCGHVCPVACIDLGEVKFKKGEKE 406
Cdd:cd10549    1 LKYDPEKCIGCGICVKACPTDAIELGPNGAIARGPEIDEDKCVFCGACVEVCPTGAIELTPEGKEYVPKE 70
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 322-395 1.02e-06

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 47.39  E-value: 1.02e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 323130514 322 NIIPAEDLDRSYIVYPR---INQEKCVGCGRCYISC-YDGGHqaMEWDEHSRTphcNTEKCVGCLLCGHVCPVACIDL 395
Cdd:cd10549   55 GAIELTPEGKEYVPKEKeaeIDEEKCIGCGLCVKVCpVDAIT--LEDELEIVI---DKEKCIGCGICAEVCPVNAIKL 127
DMSOR_beta_like cd16373
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 338-390 3.14e-06

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319895 [Multi-domain]  Cd Length: 154  Bit Score: 46.86  E-value: 3.14e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 338 RINQEKCV------GCGRCYISC-YDGGhqAMEWDEHSRTPHCNTEKCVGCLLCGHVCPV 390
Cdd:cd16373   87 VIDKDRCLawqggtDCGVCVEACpTEAI--AIVLEDDVLRPVVDEDKCVGCGLCEYVCPV 144
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 330-395 3.91e-06

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 45.85  E-value: 3.91e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 323130514 330 DRSYIVYPRINQEKCVGCGRCYISC-------YDGGHQAMEWDEHSrtpHCNTEKCVGCLLCGHVCPVACIDL 395
Cdd:cd10549   28 NGAIARGPEIDEDKCVFCGACVEVCptgaielTPEGKEYVPKEKEA---EIDEEKCIGCGLCVKVCPVDAITL 97
PRK13795 PRK13795
hypothetical protein; Provisional
 343-391 4.52e-06

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 48.84  E-value: 4.52e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 323130514 343 KCVGCGRCYISCydgGHQAMEWDEHSRTPHCNTEKCVGCLLCGHVCPVA 391
Cdd:PRK13795 582 ECVGCGVCVGAC---PTGAIRIEEGKRKISVDEEKCIHCGKCTEVCPVV 627
Fer4_10 pfam13237
4Fe-4S dicluster domain; This family includes proteins containing domains which bind to ...
 337-389 5.18e-06

4Fe-4S dicluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 404174 [Multi-domain]  Cd Length: 56  Bit Score: 43.39  E-value: 5.18e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 323130514  337 PRINQEKCVGCGRCYISC--YDGGHQAMEWDEHSRTPHCNTEKCVGCLLCGHVCP 389
Cdd:pfam13237   2 VVIDPDKCIGCGRCTAACpaGLTRVGAIVERLEGEAVRIGVWKCIGCGACVEACP 56
porD PRK09624
pyruvate ferredoxin oxidoreductase subunit delta; Reviewed
 337-395 4.29e-05

pyruvate ferredoxin oxidoreductase subunit delta; Reviewed


Pssm-ID: 170017 [Multi-domain]  Cd Length: 105  Bit Score: 42.32  E-value: 4.29e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514 337 PRINQEKCVGCGRCYISCYDgghQAMEWDEHSrTPHCNTEKCVGCLLCGHVCPVACIDL 395
Cdd:PRK09624  46 PEFNRDKCVRCYLCYIYCPE---PAIYLDEEG-YPVFDYDYCKGCGICANECPTKAIEM 100
RnfB COG2878
Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and ...
 344-395 7.71e-05

Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and conversion]; Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase


Pssm-ID: 442125 [Multi-domain]  Cd Length: 254  Bit Score: 43.83  E-value: 7.71e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 323130514 344 CVGCGRCYISC-YD---GGHQAMewdehsrtPHCNTEKCVGCLLCGHVCPVACIDL 395
Cdd:COG2878  139 CIGCGDCIKACpFDaivGAAKGM--------HTVDEDKCTGCGLCVEACPVDCIEM 186
DMSOR_beta-like cd04410
Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta ...
 338-396 9.27e-05

Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319870 [Multi-domain]  Cd Length: 136  Bit Score: 41.99  E-value: 9.27e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514 338 RINQEKCVGCGRCYISC-YDgghqAMEWDEHSRTPhcntEKCVGCL---------LCGHVCPVACIDLG 396
Cdd:cd04410   76 LIDEDKCIGCGSCVEACpYG----AIVFDPEPGKA----VKCDLCGdrldeglepACVKACPTGALTFG 136
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 374-399 1.95e-04

TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and conversion];


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 39.64  E-value: 1.95e-04
                         10        20
                 ....*....|....*....|....*.
gi 323130514 374 NTEKCVGCLLCGHVCPVACIDLGEVK 399
Cdd:COG4231   20 DEDKCTGCGACVKVCPADAIEEGDGK 45
PRK08348 PRK08348
NADH-plastoquinone oxidoreductase subunit; Provisional
 324-395 1.96e-04

NADH-plastoquinone oxidoreductase subunit; Provisional


Pssm-ID: 181399 [Multi-domain]  Cd Length: 120  Bit Score: 40.97  E-value: 1.96e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 323130514 324 IPAEDLDRSYIVYpriNQEKCVGCGRCYISCYDGghqAMEWDEHSRTPHCNTEKCVGCLLCGHVCPVACIDL 395
Cdd:PRK08348  27 VPVPEDFRGKILY---DVDKCVGCRMCVTVCPAG---VFVYLPEIRKVALWTGRCVFCGQCVDVCPTGALQM 92
PRK06991 PRK06991
electron transport complex subunit RsxB;
294-395 2.12e-04

electron transport complex subunit RsxB;


Pssm-ID: 235903 [Multi-domain]  Cd Length: 270  Bit Score: 42.86  E-value: 2.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 294 EDMASGLSHYL-----ADQGFASLQEMIGLangniiPAEDLDRSYIV-YPR----INQEKCVGCGRCYISC-YD---GGH 359
Cdd:PRK06991  33 EAIAAGEANYNrcppgGAEGIARLAALLGK------PVIPLDPANGVeRPRavavIDEQLCIGCTLCMQACpVDaivGAP 106

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 323130514 360 QAMewdeHSRTPhcntEKCVGCLLCGHVCPVACIDL 395
Cdd:PRK06991 107 KQM----HTVLA----DLCTGCDLCVPPCPVDCIDM 134
NuoI TIGR01971
NADH-quinone oxidoreductase, chain I; This model represents the I subunit (one of 14: A->N) of ...
 342-398 2.48e-04

NADH-quinone oxidoreductase, chain I; This model represents the I subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes "I" subunits from the closely related F420H2 dehydrogenase and formate hydrogenlyase complexes. [Energy metabolism, Electron transport]


Pssm-ID: 273902 [Multi-domain]  Cd Length: 122  Bit Score: 40.48  E-value: 2.48e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 323130514  342 EKCVGCGRCYISCydgGHQAMEWDEHSR--------TPHCNTEKCVGCLLCGHVCPVACIDLGEV 398
Cdd:TIGR01971  43 EKCIGCTLCAAVC---PADAIRVVPAEGedgkrrlkFYEINFGRCIFCGLCEEACPTDAIVLTPE 104
HycB COG1142
Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];
336-398 3.59e-04

Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];


Pssm-ID: 440757 [Multi-domain]  Cd Length: 138  Bit Score: 40.41  E-value: 3.59e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 336 YPRINQEKCVGCGRCYISC-YdgghQAMEWDEHSRTPHCNteKCVGCL------LCGHVCPVACIDLGEV 398
Cdd:COG1142   75 AVVVDEEKCIGCGLCVLACpF----GAITMVGEKSRAVAV--KCDLCGgreggpACVEACPTGALRLVDV 138
PorD COG1144
Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta ...
 371-400 6.75e-04

Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit [Energy production and conversion]; Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 440759 [Multi-domain]  Cd Length: 84  Bit Score: 38.49  E-value: 6.75e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 323130514 371 PHCNTEKCVGCLLCGHVCPVACIDLGEVKF 400
Cdd:COG1144   25 PVVDEDKCIGCGLCWIVCPDGAIRVDDGKY 54
OYE_like_FMN_family cd02803
Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme ...
 85-198 9.10e-04

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: 41.02  E-value: 9.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  85 LEENLAAIR-RLKQDYPdkVLI------ASIMGENEQQWQELARLVEEAGADMIECnfSCPQMTSHAMGSDVGQSPELVE 157
Cdd:cd02803  194 LLEIVAAVReAVGPDFP--VGVrlsaddFVPGGLTLEEAIEIAKALEEAGVDALHV--SGGSYESPPPIIPPPYVPEGYF 269

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 323130514 158 KY-CRAVKRGSSLPMLAkmTPNI--GDMCEVALAAkrGGADGIA 198
Cdd:cd02803  270 LElAEKIKKAVKIPVIA--VGGIrdPEVAEEILAE--GKADLVA 309
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 83-131 1.15e-03

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 40.08  E-value: 1.15e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 323130514    83 HPLEENLAAIRRLKQDYPDKV---LIASIMGENEQQWQELARLVEEAGADMI 131
Cdd:smart00729 133 HTVEDVLEAVELLREAGPIKVstdLIVGLPGETEEDFEETLKLLKELGPDRV 184
NuoI TIGR01971
NADH-quinone oxidoreductase, chain I; This model represents the I subunit (one of 14: A->N) of ...
 376-405 1.22e-03

NADH-quinone oxidoreductase, chain I; This model represents the I subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes "I" subunits from the closely related F420H2 dehydrogenase and formate hydrogenlyase complexes. [Energy metabolism, Electron transport]


Pssm-ID: 273902 [Multi-domain]  Cd Length: 122  Bit Score: 38.55  E-value: 1.22e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 323130514  376 EKCVGCLLCGHVCPVACIDLGEVKFKKGEK 405
Cdd:TIGR01971  43 EKCIGCTLCAAVCPADAIRVVPAEGEDGKR 72
ICL_PEPM cd00377
Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. ...
 38-178 1.60e-03

Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), and 2-methylisocitrate lyase (MICL). Isocitrate lyase (ICL) catalyzes the conversion of isocitrate to succinate and glyoxylate, the first committed step in the glyoxylate pathway. This carbon-conserving pathway is present in most prokaryotes, lower eukaryotes and plants, but has not been observed in vertebrates. PEP mutase (PEPM) turns phosphoenolpyruvate (PEP) into phosphonopyruvate (P-pyr), an important intermediate in the formation of organophosphonates, which function as antibiotics or play a role in pathogenesis or signaling. P-pyr can be hydrolyzed by phosphonopyruvate hydrolase (PPH) to from pyruvate and phosphate. Oxaloacetate acetylhydrolase (OAH) catalyzes the hydrolytic cleavage of oxaloacetate to form acetate and oxalate, an important pathway to produce oxalate in filamentous fungi. 2-methylisocitrate lyase (MICL) cleaves 2-methylisocitrate to pyruvate and succinate, part of the methylcitrate cycle for the alpha-oxidation of propionate.


Pssm-ID: 119340 [Multi-domain]  Cd Length: 243  Bit Score: 39.78  E-value: 1.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514  38 DTGWGGI--VFKTIGFFIAN-------EvsprfDHLTKEDTGFIGFKNMEQIAEHplEENLAAIRRLKQDYPDKVLIASI 108
Cdd:cd00377   77 DTGYGNAlnVARTVRELEEAgaagihiE-----DQVGPKKCGHHGGKVLVPIEEF--VAKIKAARDARDDLPDFVIIART 149

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 323130514 109 --MGENEQQWQE-LARLV--EEAGADMIECnfscpqmtsHAMgsdvgQSPELVEKYCRAVkrgsSLPMLAKMTPN 178
Cdd:cd00377  150 daLLAGEEGLDEaIERAKayAEAGADGIFV---------EGL-----KDPEEIRAFAEAP----DVPLNVNMTPG 206
ferrodoxin_EFR1 NF038196
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 342-403 1.81e-03

EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1).


Pssm-ID: 468407 [Multi-domain]  Cd Length: 243  Bit Score: 39.84  E-value: 1.81e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514 342 EKCVGCGRCY-------ISCYDGGhqaMEWDEHsrtphcntekCVGCLLCGHVCPVACIDLGEVKFKKG 403
Cdd:NF038196 185 DKCIGCGICAkvcpvnnIEMEDGK---PVWGHN----------CTHCLACIHRCPKEAIEYGKKTKKKG 240
rnfB TIGR01944
electron transport complex, RnfABCDGE type, B subunit; The six subunit complex RnfABCDGE in ...
 339-398 1.92e-03

electron transport complex, RnfABCDGE type, B subunit; The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit. [Energy metabolism, Electron transport]


Pssm-ID: 273887 [Multi-domain]  Cd Length: 165  Bit Score: 38.63  E-value: 1.92e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 323130514  339 INQEKCVGCGRCYISC-YD---GGHQAMewdehsrtpHCNTEK-CVGCLLCGHVCPVACIDLGEV 398
Cdd:TIGR01944 110 IDEDNCIGCTKCIQACpVDaivGAAKAM---------HTVIADeCTGCDLCVEPCPTDCIEMIPV 165
DMSOR_beta-like cd04410
Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta ...
 339-393 2.67e-03

Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319870 [Multi-domain]  Cd Length: 136  Bit Score: 37.75  E-value: 2.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 339 INQEKCVGCGRCYISC-YDGGHQAMEWD--------------------EHSRTPHC-------------------NTEKC 378
Cdd:cd04410    3 VDLDRCIGCGTCEVACkQEHGLRPGPDWsrikviegggleraflpvscMHCEDPPCvkacptgaiykdedgivliDEDKC 82

                         90
                 ....*....|....*
gi 323130514 379 VGCLLCGHVCPVACI 393
Cdd:cd04410   83 IGCGSCVEACPYGAI 97
HycB COG1142
Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];
339-402 3.88e-03

Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];


Pssm-ID: 440757 [Multi-domain]  Cd Length: 138  Bit Score: 37.33  E-value: 3.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 339 INQEKCVGCGRCYISCYDGGHQAMEWDEHSRT--------------PHC-----------------------NTEKCVGC 381
Cdd:COG1142    7 ADPEKCIGCRTCEAACAVAHEGEEGEPFLPRIrvvrkagvsapvqcRHCedapcaevcpvgaitrddgavvvDEEKCIGC 86

                         90       100
                 ....*....|....*....|.
gi 323130514 382 LLCGHVCPVACIDLGEVKFKK 402
Cdd:COG1142   87 GLCVLACPFGAITMVGEKSRA 107
PRK05888 PRK05888
NADH-quinone oxidoreductase subunit NuoI;
376-406 5.50e-03

NADH-quinone oxidoreductase subunit NuoI;


Pssm-ID: 235637 [Multi-domain]  Cd Length: 164  Bit Score: 37.55  E-value: 5.50e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 323130514 376 EKCVGCLLCGHVCPVACIDLGEVKFKKGEKE 406
Cdd:PRK05888  58 ERCIACKLCAAICPADAITIEAAEREDGRRR 88
PRK12771 PRK12771
putative glutamate synthase (NADPH) small subunit; Provisional
 344-396 5.57e-03

putative glutamate synthase (NADPH) small subunit; Provisional


Pssm-ID: 237198 [Multi-domain]  Cd Length: 564  Bit Score: 38.70  E-value: 5.57e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 323130514 344 CVGCGRCYISCYDgghQAMEWDEHSRTPHCNTEKCVGCLLCGHVCPVACIDLG 396
Cdd:PRK12771 512 CFECDNCYGACPQ---DAIIKLGPGRRYHFDYDKCTGCHICADVCPCGAIEMG 561
DMSOR_beta_like cd16372
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 338-397 6.13e-03

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319894 [Multi-domain]  Cd Length: 125  Bit Score: 36.54  E-value: 6.13e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 323130514 338 RINQEKCVGCGRCYISCYDGghqAMEWDEHSRTPHcnteKCVGCLLCGHVCPVACIDLGE 397
Cdd:cd16372   73 MINKKLCVGCLMCVGFCPEG---AMFKHEDYPEPF----KCIACGICVKACPTGALELVE 125
DMSOR_beta_like cd16371
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 334-396 6.17e-03

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319893 [Multi-domain]  Cd Length: 140  Bit Score: 36.77  E-value: 6.17e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 323130514 334 IVYprINQEKCVGCGRCYISC-YDgghqAMEWDEHSRTphcnTEKCVGCL---------LCGHVCPVACIDLG 396
Cdd:cd16371   78 IVV--VDQDKCIGCGYCVWACpYG----APQYNPETGK----MDKCDMCVdrldegekpACVAACPTRALDFG 140
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
339-405 7.80e-03

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 38.47  E-value: 7.80e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 323130514 339 INQEKCVGCGRCYISCydgGHQAMEWDEHSRTPhcNTEKCVGCLLCGHVCPVACI----DLGEVK--FKKGEK 405
Cdd:COG4624   88 RDKEKCKNCYPCVRAC---PVKAIKVDDGKAEI--DEEKCISCGQCVAVCPFGAIteksDIEKVKkaLKDPEK 155
PRK05888 PRK05888
NADH-quinone oxidoreductase subunit NuoI;
341-398 8.23e-03

NADH-quinone oxidoreductase subunit NuoI;


Pssm-ID: 235637 [Multi-domain]  Cd Length: 164  Bit Score: 36.78  E-value: 8.23e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 323130514 341 QEKCVGCGRCYISC-----YdgghqaMEWDEHS------RTPHCNTEKCVGCLLCGHVCPVACIDLGEV 398
Cdd:PRK05888  57 EERCIACKLCAAICpadaiT------IEAAEREdgrrrtTRYDINFGRCIFCGFCEEACPTDAIVETPD 119
PRK06273 PRK06273
ferredoxin; Provisional
 337-390 8.90e-03

ferredoxin; Provisional


Pssm-ID: 235764 [Multi-domain]  Cd Length: 165  Bit Score: 37.00  E-value: 8.90e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 323130514 337 PRINQEKCVGCGRCYISCYDGghqAMEW---------DEHSRT--PHCNTEKCVGCLLCGHVCPV 390
Cdd:PRK06273  44 KKVFEELCIGCGGCANVCPTK---AIEMipvepvkitEGYVKTkiPKIDYEKCVYCLYCHDFCPV 105
PRK05113 PRK05113
electron transport complex protein RnfB; Provisional
 339-399 9.39e-03

electron transport complex protein RnfB; Provisional


Pssm-ID: 235347 [Multi-domain]  Cd Length: 191  Bit Score: 37.23  E-value: 9.39e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 323130514 339 INQEKCVGCGRCYISC-YD---GGHQAMewdeHSRTPhcntEKCVGCLLCGHVCPVACIDLGEVK 399
Cdd:PRK05113 111 IDEDNCIGCTKCIQACpVDaivGATKAM----HTVIS----DLCTGCDLCVAPCPTDCIEMIPVA 167
 
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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