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Conserved domains on  [gi|1440106093|emb|STQ54268|]
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dihydropyrimidine dehydrogenase [Escherichia coli]

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;
4-408 0e+00

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


:

Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 710.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   4 KDLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGFFIANEVSPRFDHLVKEDTGFIGFKNMEQIAEH 83
Cdd:PRK08318    2 ADLSITFCGIKSPNPFWLASAPPTNKYYNVARAFEAGWGGVVWKTLGPPIVNVSSPRFGALVKEDRRFIGFNNIELITDR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  84 PLEENLAALRRLKEDYPDKVLIASIMGE-NEQQWEELARLVQEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYCR 161
Cdd:PRK08318   82 PLEVNLREIRRVKRDYPDRALIASIMVEcNEEEWKEIAPLVEETGADGIELNFGCPHgMSERGMGSAVGQVPELVEMYTR 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 162 AVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRF 241
Cdd:PRK08318  162 WVKRGSRLPVIVKLTPNITDIREPARAAKRGGADAVSLINTINSITGVDLDRMIPMPIVNGKSSHGGYCGPAVKPIALNM 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 242 IQQMRTHPELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFDSLQDMVGLANN 321
Cdd:PRK08318  242 VAEIARDPETRGLPISGIGGIETWRDAAEFILLGAGTVQVCTAAMQYGFRIVEDMISGLSHYMDEKGFASLEDMVGLAVP 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 322 NIVPAEDLDRSYIVYPHINLDKCVGCGRCYISCYDGGHQAMEWSE-KTRTPHCNTEKCVGCLLCGHVCPV-GCIDLGEVK 399
Cdd:PRK08318  322 NVTDWEDLDLNYIVYARIDQDKCIGCGRCYIACEDTSHQAIEWDEdGTRTPEVIEEECVGCNLCAHVCPVeGCITMGEVK 401

                         410
                  ....*....|..
gi 1440106093 400 FKKGE---KEHP 408
Cdd:PRK08318  402 FGKPYanwTTHP 413
 
Name Accession Description Interval E-value
PRK08318 PRK08318
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
4-408 0e+00

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 710.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   4 KDLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGFFIANEVSPRFDHLVKEDTGFIGFKNMEQIAEH 83
Cdd:PRK08318    2 ADLSITFCGIKSPNPFWLASAPPTNKYYNVARAFEAGWGGVVWKTLGPPIVNVSSPRFGALVKEDRRFIGFNNIELITDR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  84 PLEENLAALRRLKEDYPDKVLIASIMGE-NEQQWEELARLVQEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYCR 161
Cdd:PRK08318   82 PLEVNLREIRRVKRDYPDRALIASIMVEcNEEEWKEIAPLVEETGADGIELNFGCPHgMSERGMGSAVGQVPELVEMYTR 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 162 AVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRF 241
Cdd:PRK08318  162 WVKRGSRLPVIVKLTPNITDIREPARAAKRGGADAVSLINTINSITGVDLDRMIPMPIVNGKSSHGGYCGPAVKPIALNM 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 242 IQQMRTHPELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFDSLQDMVGLANN 321
Cdd:PRK08318  242 VAEIARDPETRGLPISGIGGIETWRDAAEFILLGAGTVQVCTAAMQYGFRIVEDMISGLSHYMDEKGFASLEDMVGLAVP 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 322 NIVPAEDLDRSYIVYPHINLDKCVGCGRCYISCYDGGHQAMEWSE-KTRTPHCNTEKCVGCLLCGHVCPV-GCIDLGEVK 399
Cdd:PRK08318  322 NVTDWEDLDLNYIVYARIDQDKCIGCGRCYIACEDTSHQAIEWDEdGTRTPEVIEEECVGCNLCAHVCPVeGCITMGEVK 401

                         410
                  ....*....|..
gi 1440106093 400 FKKGE---KEHP 408
Cdd:PRK08318  402 FGKPYanwTTHP 413
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: 512.60  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGF--FIANEVSPRFDHLVKEDTGFIGFKNMEQIAE 82
Cdd:cd02940     1 DLSVTFCGIKFPNPFGLASAPPTTSYPMIRRAFEAGWGGAVTKTLGLdkDIVTNVSPRIARLRTSGRGQIGFNNIELISE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  83 HPLEENLAALRRLKEDYPDKVLIASIMGE-NEQQWEELARLVQEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYC 160
Cdd:cd02940    81 KPLEYWLKEIRELKKDFPDKILIASIMCEyNKEDWTELAKLVEEAGADALELNFSCPHgMPERGMGAAVGQDPELVEEIC 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 161 RAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALR 240
Cdd:cd02940   161 RWVREAVKIPVIAKLTPNITDIREIARAAKEGGADGVSAINTVNSLMGVDLDGTPPAPGVEGKTTYGGYSGPAVKPIALR 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 241 FIQQMRTHPElRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGL 300
Cdd:cd02940   241 AVSQIARAPE-PGLPISGIGGIESWEDAAEFLLLGASVVQVCTAVMNQGFTIVDDMCTGL 299
PyrD COG0167
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ...
 5-312 1.46e-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: 318.56  E-value: 1.46e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGFF-IANEVSPRFDHLVKEDtgfiGFKNMEQIAEH 83
Cdd:COG0167     1 DLSVELAGLKFPNPVGLASGFFDKNAEYIDALDLLGFGAVEVKTVTPEpQPGNPRPRLFRLPEDS----GLINRMGLNNP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  84 PLEENLAALRRLKEdyPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQMtsHAMGSDVGQSPELVEKYCRAV 163
Cdd:COG0167    77 GVDAFLERLLPAKR--YDVPVIVNIGGNTVEDYVELARRLADAGADYLELNISCPNT--PGGGRALGQDPEALAELLAAV 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 164 KRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITnIDLnqKIGMPIVNGKssISGYSGKAVKPIALRFIQ 243
Cdd:COG0167   153 KAATDKPVLVKLAPDLTDIVEIARAAEEAGADGVIAINTTLGRA-IDL--ETRRPVLANE--AGGLSGPALKPIALRMVR 227

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 244 QMRTHPElRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFDSL 312
Cdd:COG0167   228 EVAQAVG-GDIPIIGVGGISTAEDALEFILAGASAVQVGTALFYEGPGLVRRIIRGLEAYLEEKGFSSI 295
pyrD_sub1_fam TIGR01037
dihydroorotate dehydrogenase (subfamily 1) family protein; This family includes subfamily 1 ...
 6-319 2.03e-63

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: 205.74  E-value: 2.03e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   6 LSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGffianeVSPRFDH---LVKEDTGfiGFKNMEQIAE 82
Cdd:TIGR01037   1 LEVELFGIRFKNPLILASGIMGSGVESLRRIDRSGAGAVVTKSIG------LEPRPGYrnpTIVETPC--GMLNAIGLQN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  83 HPLEENLAALRRLKEDYPdKVLIASIMGENEQQWEELARLVQEAG--ADMIECNFSCPqmtsHAM--GSDVGQSPELVEK 158
Cdd:TIGR01037  73 PGVEAFLEELKPVREEFP-TPLIASVYGSSVEEFAEVAEKLEKAPpyVDAYELNLSCP----HVKggGIAIGQDPELSAD 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 159 YCRAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITnIDLnqKIGMPIVNGKSsiSGYSGKAVKPIA 238
Cdd:TIGR01037 148 VVKAVKDKTDVPVFAKLSPNVTDITEIAKAAEEAGADGLTLINTLRGMK-IDI--KTGKPILANKT--GGLSGPAIKPIA 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 239 LRFIQQMRthpELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMqYGYRIVEDMASGLSHYLADQGFDSLQDMVGL 318
Cdd:TIGR01037 223 LRMVYDVY---KMVDIPIIGVGGITSFEDALEFLMAGASAVQVGTAVY-YRGFAFKKIIEGLIAFLKAEGFTSIEELIGI 298


                  .
gi 1440106093 319 A 319
Cdd:TIGR01037 299 A 299
DHO_dh pfam01180
Dihydroorotate dehydrogenase;
6-304 3.31e-40

Dihydroorotate dehydrogenase;


Pssm-ID: 426103  Cd Length: 291  Bit Score: 144.80  E-value: 3.31e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   6 LSITFCGVKFPNPFCLSSSPVGNCYEMcAKAYDTGwggvvfkTIGFFIANEVS--PRFDH----LVKEDTGFI---GFKN 76
Cdd:pfam01180   2 LATKIPGLDFKNPIGLASGFDKFGEEA-LKWLALG-------KFGAIEIKSVTpyPQPGNptprVFRLPEGVLnrmGLNN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  77 MEqiaehpLEENLAALRRLKEDYPDKVL--IASIMGENEQQWEELARLVQEAgADMIECNFSCPQMtshAMGSDVGQSPE 154
Cdd:pfam01180  74 PG------LDAVLAELLKRRKEYPRPDLgiNLSKAGMTVDDYVEVARKIGPF-ADYIELNVSCPNT---PGLRALQTDPE 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 155 LVEKYCRAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITN---IDLnqKIGMPIVngKSSISGYSG 231
Cdd:pfam01180 144 LAAILLKVVKEVSKVPVLVKLAPDLTDIVIIDIADVALGEDGLDGINATNTTVRgmrIDL--KTEKPIL--ANGTGGLSG 219

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 232 KAVKPIALRFIQQMRTHPELRdFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYL 304
Cdd:pfam01180 220 PPIKPIALKVIRELYQRTGPE-IPIIGVGGIESGEDALEKILAGASAVQIGTALIFGGPFIFPKIIDELPELL 291
ferrodoxin_EFR1 NF038196
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 332-403 7.47e-04

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: 41.00  E-value: 7.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 332 SYIVYPHINL-----------DKCVGCGRCY-------ISCYDGGhqaMEWSEKtrtphcntekCVGCLLCGHVCPVGCI 393
Cdd:NF038196  164 SKLVNPLFYKfkvkdkkfhvtDKCIGCGICAkvcpvnnIEMEDGK---PVWGHN----------CTHCLACIHRCPKEAI 230

                          90
                  ....*....|
gi 1440106093 394 DLGEVKFKKG 403
Cdd:NF038196  231 EYGKKTKKKG 240
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 83-131 2.28e-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: 39.31  E-value: 2.28e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1440106093   83 HPLEENLAALRRLKEDYPDKV---LIASIMGENEQQWEELARLVQEAGADMI 131
Cdd:smart00729 133 HTVEDVLEAVELLREAGPIKVstdLIVGLPGETEEDFEETLKLLKELGPDRV 184
 
Name Accession Description Interval E-value
PRK08318 PRK08318
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;
4-408 0e+00

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA;


Pssm-ID: 236237 [Multi-domain]  Cd Length: 420  Bit Score: 710.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   4 KDLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGFFIANEVSPRFDHLVKEDTGFIGFKNMEQIAEH 83
Cdd:PRK08318    2 ADLSITFCGIKSPNPFWLASAPPTNKYYNVARAFEAGWGGVVWKTLGPPIVNVSSPRFGALVKEDRRFIGFNNIELITDR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  84 PLEENLAALRRLKEDYPDKVLIASIMGE-NEQQWEELARLVQEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYCR 161
Cdd:PRK08318   82 PLEVNLREIRRVKRDYPDRALIASIMVEcNEEEWKEIAPLVEETGADGIELNFGCPHgMSERGMGSAVGQVPELVEMYTR 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 162 AVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRF 241
Cdd:PRK08318  162 WVKRGSRLPVIVKLTPNITDIREPARAAKRGGADAVSLINTINSITGVDLDRMIPMPIVNGKSSHGGYCGPAVKPIALNM 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 242 IQQMRTHPELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFDSLQDMVGLANN 321
Cdd:PRK08318  242 VAEIARDPETRGLPISGIGGIETWRDAAEFILLGAGTVQVCTAAMQYGFRIVEDMISGLSHYMDEKGFASLEDMVGLAVP 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 322 NIVPAEDLDRSYIVYPHINLDKCVGCGRCYISCYDGGHQAMEWSE-KTRTPHCNTEKCVGCLLCGHVCPV-GCIDLGEVK 399
Cdd:PRK08318  322 NVTDWEDLDLNYIVYARIDQDKCIGCGRCYIACEDTSHQAIEWDEdGTRTPEVIEEECVGCNLCAHVCPVeGCITMGEVK 401

                         410
                  ....*....|..
gi 1440106093 400 FKKGE---KEHP 408
Cdd:PRK08318  402 FGKPYanwTTHP 413
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: 512.60  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGF--FIANEVSPRFDHLVKEDTGFIGFKNMEQIAE 82
Cdd:cd02940     1 DLSVTFCGIKFPNPFGLASAPPTTSYPMIRRAFEAGWGGAVTKTLGLdkDIVTNVSPRIARLRTSGRGQIGFNNIELISE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  83 HPLEENLAALRRLKEDYPDKVLIASIMGE-NEQQWEELARLVQEAGADMIECNFSCPQ-MTSHAMGSDVGQSPELVEKYC 160
Cdd:cd02940    81 KPLEYWLKEIRELKKDFPDKILIASIMCEyNKEDWTELAKLVEEAGADALELNFSCPHgMPERGMGAAVGQDPELVEEIC 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 161 RAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALR 240
Cdd:cd02940   161 RWVREAVKIPVIAKLTPNITDIREIARAAKEGGADGVSAINTVNSLMGVDLDGTPPAPGVEGKTTYGGYSGPAVKPIALR 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 241 FIQQMRTHPElRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGL 300
Cdd:cd02940   241 AVSQIARAPE-PGLPISGIGGIESWEDAAEFLLLGASVVQVCTAVMNQGFTIVDDMCTGL 299
PyrD COG0167
Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Dihydroorotate ...
 5-312 1.46e-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: 318.56  E-value: 1.46e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGFF-IANEVSPRFDHLVKEDtgfiGFKNMEQIAEH 83
Cdd:COG0167     1 DLSVELAGLKFPNPVGLASGFFDKNAEYIDALDLLGFGAVEVKTVTPEpQPGNPRPRLFRLPEDS----GLINRMGLNNP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  84 PLEENLAALRRLKEdyPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQMtsHAMGSDVGQSPELVEKYCRAV 163
Cdd:COG0167    77 GVDAFLERLLPAKR--YDVPVIVNIGGNTVEDYVELARRLADAGADYLELNISCPNT--PGGGRALGQDPEALAELLAAV 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 164 KRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITnIDLnqKIGMPIVNGKssISGYSGKAVKPIALRFIQ 243
Cdd:COG0167   153 KAATDKPVLVKLAPDLTDIVEIARAAEEAGADGVIAINTTLGRA-IDL--ETRRPVLANE--AGGLSGPALKPIALRMVR 227

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 244 QMRTHPElRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFDSL 312
Cdd:COG0167   228 EVAQAVG-GDIPIIGVGGISTAEDALEFILAGASAVQVGTALFYEGPGLVRRIIRGLEAYLEEKGFSSI 295
PLN02495 PLN02495
oxidoreductase, acting on the CH-CH group of donors
 5-319 1.36e-102

oxidoreductase, acting on the CH-CH group of donors


Pssm-ID: 215273 [Multi-domain]  Cd Length: 385  Bit Score: 309.46  E-value: 1.36e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGFFIAN--EVSPRFDHLVKEDTG-----FIGFKNM 77
Cdd:PLN02495   10 DLSVTVNGLKMPNPFVIGSGPPGTNYTVMKRAFDEGWGGVIAKTVSLDASKviNVTPRYARLRAGANGsakgrVIGWQNI 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  78 EQIAEHPLEENLAALRRLKEDYPDKVLIASIMGE-NEQQWEELARLVQEAGADMIECNFSCPQ-MTSHAMGSDVGQSPEL 155
Cdd:PLN02495   90 ELISDRPFETMLAEFKQLKEEYPDRILIASIMEEyNKDAWEEIIERVEETGVDALEINFSCPHgMPERKMGAAVGQDCDL 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 156 VEKYCRAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVK 235
Cdd:PLN02495  170 LEEVCGWINAKATVPVWAKMTPNITDITQPARVALKSGCEGVAAINTIMSVMGINLDTLRPEPCVEGYSTPGGYSSKAVR 249

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 236 PIAL---RFIQQMRTHPELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFDSL 312
Cdd:PLN02495  250 PIALakvMAIAKMMKSEFPEDRSLSGIGGVETGGDAAEFILLGADTVQVCTGVMMHGYPLVKNLCAELQDFMKKHNFSSI 329


                  ....*..
gi 1440106093 313 QDMVGLA 319
Cdd:PLN02495  330 EDFRGAS 336
PRK07259 PRK07259
dihydroorotate dehydrogenase;
5-319 1.29e-70

dihydroorotate dehydrogenase;


Pssm-ID: 235982  Cd Length: 301  Bit Score: 224.26  E-value: 1.29e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSSPVGNCYEMcAKAYD-TGWGGVVFKTIGffianeVSPRFDH----LVKEDTGF---IGFKN 76
Cdd:PRK07259    1 RLSVELPGLKLKNPVMPASGTFGFGGEY-ARFYDlNGLGAIVTKSTT------LEPREGNptprIAETPGGMlnaIGLQN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  77 MEqiAEHPLEENLAALRRLkedypDKVLIASIMGENEQQWEELARLVQEAG-ADMIECNFSCPqmtsHAM--GSDVGQSP 153
Cdd:PRK07259   74 PG--VDAFIEEELPWLEEF-----DTPIIANVAGSTEEEYAEVAEKLSKAPnVDAIELNISCP----NVKhgGMAFGTDP 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 154 ELVEKYCRAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITnIDLnqKIGMPIVNGKssISGYSGKA 233
Cdd:PRK07259  143 ELAYEVVKAVKEVVKVPVIVKLTPNVTDIVEIAKAAEEAGADGLSLINTLKGMA-IDI--KTRKPILANV--TGGLSGPA 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 234 VKPIALRFIQQMRTHPELrdfPISGIGGIETWEDAAEFLLLGAATLQVTTGIMqYGYRIVEDMASGLSHYLADQGFDSLQ 313
Cdd:PRK07259  218 IKPIALRMVYQVYQAVDI---PIIGMGGISSAEDAIEFIMAGASAVQVGTANF-YDPYAFPKIIEGLEAYLDKYGIKSIE 293


                  ....*.
gi 1440106093 314 DMVGLA 319
Cdd:PRK07259  294 EIVGIA 299
DHOD_1B_like cd04740
Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation ...
 7-319 2.03e-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: 223.58  E-value: 2.03e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   7 SITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGffianeVSPRFDH----LVKEDTGF---IGFKNMEq 79
Cdd:cd04740     1 SVELAGLRLKNPVILASGTFGFGEELSRVADLGKLGAIVTKSIT------LEPREGNppprVVETPGGMlnaIGLQNPG- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  80 iAEHPLEENLAALRRlkedyPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPqmtsHAM--GSDVGQSPELVE 157
Cdd:cd04740    74 -VEAFLEELLPWLRE-----FGTPVIASIAGSTVEEFVEVAEKLADAGADAIELNISCP----NVKggGMAFGTDPEAVA 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 158 KYCRAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITnIDLnqKIGMPIVNGKssISGYSGKAVKPI 237
Cdd:cd04740   144 EIVKAVKKATDVPVIVKLTPNVTDIVEIARAAEEAGADGLTLINTLKGMA-IDI--ETRKPILGNV--TGGLSGPAIKPI 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 238 ALRFIQQMRTHPELrdfPISGIGGIETWEDAAEFLLLGAATLQVTTGIMqYGYRIVEDMASGLSHYLADQGFDSLQDMVG 317
Cdd:cd04740   219 ALRMVYQVYKAVEI---PIIGVGGIASGEDALEFLMAGASAVQVGTANF-VDPEAFKEIIEGLEAYLDEEGIKSIEELVG 294


                  ..
gi 1440106093 318 LA 319
Cdd:cd04740   295 LA 296
pyrD_sub1_fam TIGR01037
dihydroorotate dehydrogenase (subfamily 1) family protein; This family includes subfamily 1 ...
 6-319 2.03e-63

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: 205.74  E-value: 2.03e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   6 LSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIGffianeVSPRFDH---LVKEDTGfiGFKNMEQIAE 82
Cdd:TIGR01037   1 LEVELFGIRFKNPLILASGIMGSGVESLRRIDRSGAGAVVTKSIG------LEPRPGYrnpTIVETPC--GMLNAIGLQN 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  83 HPLEENLAALRRLKEDYPdKVLIASIMGENEQQWEELARLVQEAG--ADMIECNFSCPqmtsHAM--GSDVGQSPELVEK 158
Cdd:TIGR01037  73 PGVEAFLEELKPVREEFP-TPLIASVYGSSVEEFAEVAEKLEKAPpyVDAYELNLSCP----HVKggGIAIGQDPELSAD 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 159 YCRAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITnIDLnqKIGMPIVNGKSsiSGYSGKAVKPIA 238
Cdd:TIGR01037 148 VVKAVKDKTDVPVFAKLSPNVTDITEIAKAAEEAGADGLTLINTLRGMK-IDI--KTGKPILANKT--GGLSGPAIKPIA 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 239 LRFIQQMRthpELRDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMqYGYRIVEDMASGLSHYLADQGFDSLQDMVGL 318
Cdd:TIGR01037 223 LRMVYDVY---KMVDIPIIGVGGITSFEDALEFLMAGASAVQVGTAVY-YRGFAFKKIIEGLIAFLKAEGFTSIEELIGI 298


                  .
gi 1440106093 319 A 319
Cdd:TIGR01037 299 A 299
DHOD_DHPD_FMN cd02810
Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding ...
 8-295 2.75e-61

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: 199.89  E-value: 2.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   8 ITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIgfFI---ANEVSPRFDHLVKEDTGF---IGFKNMEQIA 81
Cdd:cd02810     1 VNFLGLKLKNPFGVAAGPLLKTGELIARAAAAGFGAVVYKTV--TLhprPGNPLPRVARLPPEGESYpeqLGILNSFGLP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  82 EHPLEENLAALRRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPqmtsHAMGSD-VGQSPELVEKYC 160
Cdd:cd02810    79 NLGLDVWLQDIAKAKKEFPGQPLIASVGGSSKEDYVELARKIERAGAKALELNLSCP----NVGGGRqLGQDPEAVANLL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 161 RAVKRGSTLPMLAKMTPN--IGDMCEVALAAKRGGADGIAAINTvksITNIDLNQKIGMPIvnGKSSISGYSGKAVKPIA 238
Cdd:cd02810   155 KAVKAAVDIPLLVKLSPYfdLEDIVELAKAAERAGADGLTAINT---ISGRVVDLKTVGPG--PKRGTGGLSGAPIRPLA 229

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1440106093 239 LRFIQQMRTHPELrDFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVED 295
Cdd:cd02810   230 LRWVARLAARLQL-DIPIIGVGGIDSGEDVLEMLMAGASAVQVATALMWDGPDVIRK 285
DHO_dh pfam01180
Dihydroorotate dehydrogenase;
6-304 3.31e-40

Dihydroorotate dehydrogenase;


Pssm-ID: 426103  Cd Length: 291  Bit Score: 144.80  E-value: 3.31e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   6 LSITFCGVKFPNPFCLSSSPVGNCYEMcAKAYDTGwggvvfkTIGFFIANEVS--PRFDH----LVKEDTGFI---GFKN 76
Cdd:pfam01180   2 LATKIPGLDFKNPIGLASGFDKFGEEA-LKWLALG-------KFGAIEIKSVTpyPQPGNptprVFRLPEGVLnrmGLNN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  77 MEqiaehpLEENLAALRRLKEDYPDKVL--IASIMGENEQQWEELARLVQEAgADMIECNFSCPQMtshAMGSDVGQSPE 154
Cdd:pfam01180  74 PG------LDAVLAELLKRRKEYPRPDLgiNLSKAGMTVDDYVEVARKIGPF-ADYIELNVSCPNT---PGLRALQTDPE 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 155 LVEKYCRAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSITN---IDLnqKIGMPIVngKSSISGYSG 231
Cdd:pfam01180 144 LAAILLKVVKEVSKVPVLVKLAPDLTDIVIIDIADVALGEDGLDGINATNTTVRgmrIDL--KTEKPIL--ANGTGGLSG 219

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 232 KAVKPIALRFIQQMRTHPELRdFPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYL 304
Cdd:pfam01180 220 PPIKPIALKVIRELYQRTGPE-IPIIGVGGIESGEDALEKILAGASAVQIGTALIFGGPFIFPKIIDELPELL 291
DHOD_like cd04739
Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S) ...
 5-317 1.10e-27

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: 111.55  E-value: 1.10e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTIgfF---IANEvSPRFDHLVKEDTGFIGFKNM--EQ 79
Cdd:cd04739     1 DLSTTYLGLSLKNPLVASASPLSRNLDNIRRLEDAGAGAIVLPSL--FeeqIERE-AQELDRFLTYGSSFAEALSYfpEY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  80 IAEHP-LEENLAALRRLKE--DYPdkvLIASIMGENEQQWEELARLVQEAGADMIECNFscpqmtsHAMGSDVGQSPELV 156
Cdd:cd04739    78 GRYNLgPEEYLELIRRAKRavSIP---VIASLNGVSAGGWVDYARQIEEAGADALELNI-------YALPTDPDISGAEV 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 157 EK-YC---RAVKRGSTLPMLAKMTP---NIGDMCEVALAAkrgGADGIAAINTVKSiTNIDLNQkigMPIVNGkSSISgY 229
Cdd:cd04739   148 EQrYLdilRAVKSAVTIPVAVKLSPffsALAHMAKQLDAA---GADGLVLFNRFYQ-PDIDLET---LEVVPN-LLLS-S 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 230 SGKAVKPiaLRFIQQMRTHPELrDFPISgiGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGF 309
Cdd:cd04739   219 PAEIRLP--LRWIAILSGRVKA-SLAAS--GGVHDAEDVVKYLLAGADVVMTTSALLRHGPDYIGTLLAGLEAWMEEHGY 293


                  ....*...
gi 1440106093 310 DSLQDMVG 317
Cdd:cd04739   294 ESVQQLRG 301
PRK07565 PRK07565
dihydroorotate dehydrogenase-like protein;
5-327 4.62e-26

dihydroorotate dehydrogenase-like protein;


Pssm-ID: 236051  Cd Length: 334  Bit Score: 107.26  E-value: 4.62e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSSPVGNCYEMCAKAYDTGWGGVVFKTigFF---IANEVSPRFDHLVKEDTGFI---GFKNME 78
Cdd:PRK07565    2 DLSTTYLGLTLRNPLVASASPLSESVDNVKRLEDAGAGAVVLKS--LFeeqIRHEAAELDRHLTHGTESFAealDYFPEP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  79 QIAEHPLEENLAALRRLKE--DYPdkvLIASIMGENEQQWEELARLVQEAGADMIECNFscpqmtsHAMGSDVGQSPELV 156
Cdd:PRK07565   80 AKFYVGPEEYLELIRRAKEavDIP---VIASLNGSSAGGWVDYARQIEQAGADALELNI-------YYLPTDPDISGAEV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 157 EK-YC---RAVKRGSTLPMLAKMTPNIGDMCEVALAAKRGGADGIAAINTVKSiTNIDLNQkigMPIVNGK--SSisgyS 230
Cdd:PRK07565  150 EQrYLdilRAVKSAVSIPVAVKLSPYFSNLANMAKRLDAAGADGLVLFNRFYQ-PDIDLET---LEVVPGLvlST----P 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 231 GKAVKPiaLRFIQQMRTHPELrDFPISgiGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFD 310
Cdd:PRK07565  222 AELRLP--LRWIAILSGRVGA-DLAAT--TGVHDAEDVIKMLLAGADVVMIASALLRHGPDYIGTILRGLEDWMERHGYE 296

                         330
                  ....*....|....*..
gi 1440106093 311 SLQDMVGLANNNIVPAE 327
Cdd:PRK07565  297 SLQQFRGSMSQKNVPDP 313
DHOD_2_like cd04738
Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S) ...
 5-300 1.78e-18

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: 85.63  E-value: 1.78e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   5 DLSITFCGVKFPNPFCLSSspvG---NcyemcAKAYDtGWGGvvfktIGF-FIanEV------------SPRFDHLVkED 68
Cdd:cd04738    38 RLEVEVFGLTFPNPVGLAA---GfdkN-----AEAID-ALLA-----LGFgFV--EVgtvtprpqpgnpKPRLFRLP-ED 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  69 TGFI---GFKN--MEQIAEhpleeNLAALRrlkedYPDKVLIASI----MGENEQQWEELARLVQEAG--ADMIECNFSC 137
Cdd:cd04738   101 EALInrmGFNNdgADAVAK-----RLKKRR-----PRGGPLGVNIgknkDTPLEDAVEDYVIGVRKLGpyADYLVVNVSS 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 138 P------QMtshamgsdvgQSPELVEKYCRAVKR-----GSTLPMLAKMTPNI--GDMCEVALAAKRGGADGIAAINTVK 204
Cdd:cd04738   171 PntpglrDL----------QGKEALRELLTAVKEernklGKKVPLLVKIAPDLsdEELEDIADVALEHGVDGIIATNTTI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 205 S---ITNIDLNQKIGmpivngkssisGYSGKAVKPIALRFIQQMRTHPElRDFPISGIGGIETWEDAAEFLLLGAATLQV 281
Cdd:cd04738   241 SrpgLLRSPLANETG-----------GLSGAPLKERSTEVLRELYKLTG-GKIPIIGVGGISSGEDAYEKIRAGASLVQL 308

                         330
                  ....*....|....*....
gi 1440106093 282 TTGIMQYGYRIVEDMASGL 300
Cdd:cd04738   309 YTGLVYEGPGLVKRIKREL 327
PRK05286 PRK05286
quinone-dependent dihydroorotate dehydrogenase;
6-308 2.11e-17

quinone-dependent dihydroorotate dehydrogenase;


Pssm-ID: 235388  Cd Length: 344  Bit Score: 82.52  E-value: 2.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093   6 LSITFCGVKFPNPFCLSSspvG---NcyemcAKAYDtGWGGvvfktIGF-FIanEV------------SPRFDHLVkEDT 69
Cdd:PRK05286   49 LPVTVMGLTFPNPVGLAA---GfdkN-----GEAID-ALGA-----LGFgFV--EVgtvtprpqpgnpKPRLFRLP-EDE 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  70 GFI---GFKN--MEqiaehpleenlAALRRLKEDYPDKVLIASI----MGENEQQWEELARLVQEAG--ADMIECNFSCP 138
Cdd:PRK05286  112 ALInrmGFNNdgAD-----------ALAERLKKAYRGIPLGINIgknkDTPLEDAVDDYLICLEKLYpyADYFTVNISSP 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 139 ------QMtshamgsdvgQSPELVEKYCRAVKR-----GSTLPMLAKMTPNI--GDMCEVALAAKRGGADGIAAINTVKS 205
Cdd:PRK05286  181 ntpglrDL----------QYGEALDELLAALKEaqaelHGYVPLLVKIAPDLsdEELDDIADLALEHGIDGVIATNTTLS 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 206 ---ITNIDLNQKIGmpivngkssisGYSGKAVKPIALRFIQQMRTHpeLRD-FPISGIGGIETWEDAAEFLLLGAATLQV 281
Cdd:PRK05286  251 rdgLKGLPNADEAG-----------GLSGRPLFERSTEVIRRLYKE--LGGrLPIIGVGGIDSAEDAYEKIRAGASLVQI 317

                         330       340
                  ....*....|....*....|....*..
gi 1440106093 282 TTGIMQYGYRIVEDMASGLSHYLADQG 308
Cdd:PRK05286  318 YSGLIYEGPGLVKEIVRGLARLLRRDG 344
DHOD_1A_like cd04741
Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation ...
 102-300 1.18e-15

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: 76.98  E-value: 1.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 102 KVLIASIMGENEQQWEELARLV--QEAGADMIECNFSCPQMTSHamgSDVGQSPELVEKYCRAVKRGSTLPMLAKMTP-- 177
Cdd:cd04741    92 KPFFISVTGSAEDIAAMYKKIAahQKQFPLAMELNLSCPNVPGK---PPPAYDFDATLEYLTAVKAAYSIPVGVKTPPyt 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 178 ---NIGDMCEVALAAkrggADGIAAINTVKSITN---IDLNQKigMPIVNGKSSISGYSGKAVKPIALRFIQQMRT--HP 249
Cdd:cd04741   169 dpaQFDTLAEALNAF----ACPISFITATNTLGNglvLDPERE--TVVLKPKTGFGGLAGAYLHPLALGNVRTFRRllPS 242

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1440106093 250 ELRdfpISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGL 300
Cdd:cd04741   243 EIQ---IIGVGGVLDGRGAFRMRLAGASAVQVGTALGKEGPKVFARIEKEL 290
PRK02506 PRK02506
dihydroorotate dehydrogenase 1A; Reviewed
 92-317 4.62e-15

dihydroorotate dehydrogenase 1A; Reviewed


Pssm-ID: 235045  Cd Length: 310  Bit Score: 75.38  E-value: 4.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  92 LRRLKEDYPDKVLIASIMGENEQQWEELARLVQEAG-ADMIECNFSCPQMTSHAmgsDVGQSPELVEKYCRAVKRGSTLP 170
Cdd:PRK02506   83 VLELQKKGPNKPHFLSVVGLSPEETHTILKKIQASDfNGLVELNLSCPNVPGKP---QIAYDFETTEQILEEVFTYFTKP 159

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 171 MLAKMTPNIgDMCEVALAAKRGGADGIAAINTVKSITN---IDLNQKigMPIVNGKSSISGYSGKAVKPIALRFIQQMRT 247
Cdd:PRK02506  160 LGVKLPPYF-DIVHFDQAAAIFNKFPLAFVNCINSIGNglvIDPEDE--TVVIKPKNGFGGIGGDYIKPTALANVRAFYQ 236

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1440106093 248 --HPELrdfPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFDSLQDMVG 317
Cdd:PRK02506  237 rlNPSI---QIIGTGGVKTGRDAFEHILCGASMVQVGTALHKEGPAVFERLTKELKAIMAEKGYQSLEDFRG 305
PorD COG1144
Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta ...
 336-395 1.36e-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: 68.54  E-value: 1.36e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 336 YPHINLDKCVGCGRCYISCYDGghqAMEWSEKTRtPHCNTEKCVGCLLCGHVCPVGCIDL 395
Cdd:COG1144    24 RPVVDEDKCIGCGLCWIVCPDG---AIRVDDGKY-YGIDYDYCKGCGICAEVCPVKAIEM 79
Fer4_21 pfam14697
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 338-395 2.69e-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: 66.92  E-value: 2.69e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 338 HINLDKCVGCGRCYISCYDGGHQAMEWSEKTRTPHcNTEKCVGCLLCGHVCPV-GCIDL 395
Cdd:pfam14697   2 RIDEDTCIGCGKCYIACPDTSHQAIVGDGKRHHTV-IEDECTGCNLCVSVCPVdDCITM 59
PreA COG1146
NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and ...
 335-403 1.65e-12

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


Pssm-ID: 440761 [Multi-domain]  Cd Length: 67  Bit Score: 62.03  E-value: 1.65e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 335 VYPHINLDKCVGCGRCYISCydgGHQAMEWSEKTRTPHC-NTEKCVGCLLCGHVCPVGCIDLGEVKFKKG 403
Cdd:COG1146     1 MMPVIDTDKCIGCGACVEVC---PVDVLELDEEGKKALViNPEECIGCGACELVCPVGAITVEDDEPEEQ 67
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 336-399 3.50e-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: 58.59  E-value: 3.50e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1440106093 336 YPHINLDKCVGCGRCYISCydgGHQAMEWsEKTRTPHCNTEKCVGCLLCGHVCPVGCIDLGEVK 399
Cdd:COG1149     5 IPVIDEEKCIGCGLCVEVC---PEGAIKL-DDGGAPVVDPDLCTGCGACVGVCPTGAITLEERE 64
PLN02826 PLN02826
dihydroorotate dehydrogenase
 169-317 4.50e-11

dihydroorotate dehydrogenase


Pssm-ID: 178421  Cd Length: 409  Bit Score: 63.99  E-value: 4.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 169 LPMLAKMTPNI--GDMCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGmpivngkSSISGYSGKAVKPIALRFIQQM- 245
Cdd:PLN02826  263 PPLLVKIAPDLskEDLEDIAAVALALGIDGLIISNTTISRPDSVLGHPHA-------DEAGGLSGKPLFDLSTEVLREMy 335

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 246 -RTHPELrdfPISGIGGIETWEDAAEFLLLGAATLQVTTGIMQYGYRIVEDMASGLSHYLADQGFDSLQDMVG 317
Cdd:PLN02826  336 rLTRGKI---PLVGCGGVSSGEDAYKKIRAGASLVQLYTAFAYEGPALIPRIKAELAACLERDGFKSIQEAVG 405
NapF COG1145
Ferredoxin [Energy production and conversion];
339-401 7.64e-11

Ferredoxin [Energy production and conversion];


Pssm-ID: 440760 [Multi-domain]  Cd Length: 238  Bit Score: 62.05  E-value: 7.64e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 339 INLDKCVGCGRCYISCydgGHQAMEWSEKTRTPHCNTEKCVGCLLCGHVCPVGCIDLGEVKFK 401
Cdd:COG1145   179 IDAEKCIGCGLCVKVC---PTGAIRLKDGKPQIVVDPDKCIGCGACVKVCPVGAISLEPKEIE 238
NuoI COG1143
Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy ...
 342-407 3.84e-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: 55.52  E-value: 3.84e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1440106093 342 DKCVGCGRCYISCYdggHQA--MEWSEKTRTPHCNTEKCVGCLLCGHVCPVGCIDLGEVKFKKGEKEH 407
Cdd:COG1143     2 DKCIGCGLCVRVCP---VDAitIEDGEPGKVYVIDPDKCIGCGLCVEVCPTGAISMTPFELAVEDREE 66
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
 85-272 4.31e-10

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: 59.43  E-value: 4.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  85 LEENLAALRRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQM--TSHAMGSDVGQSPELVEKYCRA 162
Cdd:cd02801    38 LRGNRKRLRLLTRNPEERPLIVQLGGSDPETLAEAAKIVEELGADGIDLNMGCPSPkvTKGGAGAALLKDPELVAEIVRA 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 163 VKRGSTLPMLAKM----TPNIgDMCEVALAAKRGGADGIaaintvksitnidlnqkigmpIVNGKSSISGYSGKAVkpia 238
Cdd:cd02801   118 VREAVPIPVTVKIrlgwDDEE-ETLELAKALEDAGASAL---------------------TVHGRTREQRYSGPAD---- 171

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1440106093 239 LRFIQQMRTHPELrdfPISGIGGIETWEDAAEFL 272
Cdd:cd02801   172 WDYIAEIKEAVSI---PVIANGDIFSLEDALRCL 202
COG2768 COG2768
Uncharacterized Fe-S cluster protein [Function unknown];
335-401 1.23e-09

Uncharacterized Fe-S cluster protein [Function unknown];


Pssm-ID: 442050 [Multi-domain]  Cd Length: 74  Bit Score: 54.35  E-value: 1.23e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1440106093 335 VYPHINLDKCVGCGRCYISCYdggHQAMEWSEKTrtPHCNTEKCVGCLLCGHVCPVGCIDLGEVKFK 401
Cdd:COG2768     4 GKPYVDEEKCIGCGACVKVCP---VGAISIEDGK--AVIDPEKCIGCGACIEVCPVGAIKIEWEEDE 65
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 338-393 1.73e-09

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


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 53.89  E-value: 1.73e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1440106093 338 HINLDKCVGCGRCYISCydgghQAMEWSEKTRTPHCNTEKCVGCLLCGHVCPVGCI 393
Cdd:COG4231    18 VIDEDKCTGCGACVKVC-----PADAIEEGDGKAVIDPDLCIGCGSCVQVCPVDAI 68
DsrA COG2221
Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion ...
 334-399 4.49e-09

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


Pssm-ID: 441823 [Multi-domain]  Cd Length: 69  Bit Score: 52.36  E-value: 4.49e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1440106093 334 IVYPHINLDKCVGCGRCYISCydgGHQAMEWSEKTrtPHCNTEKCVGCLLCGHVCPVGCIDLGEVK 399
Cdd:COG2221     7 TWPPKIDEEKCIGCGLCVAVC---PTGAISLDDGK--LVIDEEKCIGCGACIRVCPTGAIKGEKPK 67
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
 85-272 3.16e-08

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: 54.71  E-value: 3.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  85 LEENLAALRRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCP--QMTSHAMGSDVGQSPELVEKYCRA 162
Cdd:COG0042    45 LHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAARIAEELGADEIDINMGCPvkKVTKGGAGAALLRDPELVAEIVKA 124

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 163 VKRGSTLPMLAKM-------TPNIGDMCEVALAAkrggadGIAAInTV----KSitnidlnQkigmpivngkssisGYSG 231
Cdd:COG0042   125 VVEAVDVPVTVKIrlgwdddDENALEFARIAEDA------GAAAL-TVhgrtRE-------Q--------------RYKG 176

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1440106093 232 KAvkpiALRFIQQMRthpELRDFPISGIGGIETWEDAAEFL 272
Cdd:COG0042   177 PA----DWDAIARVK---EAVSIPVIGNGDIFSPEDAKRML 210
Fer4_7 pfam12838
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 344-392 1.46e-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: 47.91  E-value: 1.46e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1440106093 344 CVGCGRCYISCYdggHQAMEWSEK-----TRTPHCNTEKCVGCLLCGHVCPVGC 392
Cdd:pfam12838   1 CIGCGACVAACP---VGAITLDEVgekkgTKTVVIDPERCVGCGACVAVCPTGA 51
TIM_phosphate_binding cd04722
TIM barrel proteins share a structurally conserved phosphate binding motif and in general ...
 64-283 1.48e-07

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: 51.43  E-value: 1.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  64 LVKEDTGFIGFKNMEQIAEHPLEENLAALRRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIEcnfscpqmtsh 143
Cdd:cd04722    21 AAEAGADAIIVGTRSSDPEEAETDDKEVLKEVAAETDLPLGVQLAINDAAAAVDIAAAAARAAGADGVE----------- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 144 aMGSDVGQSPELVEKYCRAVK-RGSTLPMLAKMTPNIGDmceVALAAKRGGADgiaaintvksitnidlnqkigmpIVNG 222
Cdd:cd04722    90 -IHGAVGYLAREDLELIRELReAVPDVKVVVKLSPTGEL---AAAAAEEAGVD-----------------------EVGL 142

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1440106093 223 KSSISGYSGKAVKPIALRFIQQMRthpELRDFPISGIGGIETWEDAAEFLLLGAATLQVTT 283
Cdd:cd04722   143 GNGGGGGGGRDAVPIADLLLILAK---RGSKVPVIAGGGINDPEDAAEALALGADGVIVGS 200
HdrA COG1148
Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];
335-395 1.59e-07

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


Pssm-ID: 440762 [Multi-domain]  Cd Length: 563  Bit Score: 53.33  E-value: 1.59e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1440106093 335 VYPHINLDKCVGCGRCYISCydgGHQAMEWSEKtRTPHCNTEKCVGCLLCGHVCPVGCIDL 395
Cdd:COG1148   489 SVAEVDPEKCTGCGRCVEVC---PYGAISIDEK-GVAEVNPALCKGCGTCAAACPSGAISL 545
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
 85-268 2.27e-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: 51.94  E-value: 2.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  85 LEENLAALRRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVGQSPELVEKYCRA 162
Cdd:pfam01207  37 LRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDRGADGIDINMGCPSkkVTRGGGGAALLRNPDLVAQIVKA 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 163 VKRGSTLPMLAKMTPNIGDMCEVAL-AAKRGGADGIAAIntvksitnidlnqkigmpIVNGKSSISGYSGkavkPIALRF 241
Cdd:pfam01207 117 VVKAVGIPVTVKIRIGWDDSHENAVeIAKIVEDAGAQAL------------------TVHGRTRAQNYEG----TADWDA 174

                         170       180
                  ....*....|....*....|....*....
gi 1440106093 242 IQQMRthpelRDFPISGI--GGIETWEDA 268
Cdd:pfam01207 175 IKQVK-----QAVSIPVIanGDITDPEDA 198
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 330-395 3.00e-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: 48.93  E-value: 3.00e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 330 DRSYIVYPHINLDKCVGCGRCYISC-------YDGGHQAMEWSEKTrtpHCNTEKCVGCLLCGHVCPVGCIDL 395
Cdd:cd10549    28 NGAIARGPEIDEDKCVFCGACVEVCptgaielTPEGKEYVPKEKEA---EIDEEKCIGCGLCVKVCPVDAITL 97
fdxN_nitrog TIGR02936
ferredoxin III, nif-specific; Members of this family are homodimeric ferredoxins from nitrogen ...
 338-392 5.94e-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: 47.02  E-value: 5.94e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 338 HINLDKCVGCGRCYISCydgGHQAM------------------EWSEKTRTPHCNTEKCVGCLLCGHVCPVGC 392
Cdd:TIGR02936  17 SIDQEKCIGCGRCYKVC---GRDVLtlkgineegelvasddddDEIERKVMVVANPGNCIGCGACARVCPKKC 86
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 339-406 1.03e-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: 1.03e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1440106093 339 INLDKCVGCGRCYISC-------YDGGhqamewsEKTRTPHCNTEKCVGCLLCGHVCPVGCIDLGEVKFKKGEKE 406
Cdd:cd10549     3 YDPEKCIGCGICVKACptdaielGPNG-------AIARGPEIDEDKCVFCGACVEVCPTGAIELTPEGKEYVPKE 70
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 339-395 1.69e-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: 47.01  E-value: 1.69e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1440106093 339 INLDKCVGCGRCYISC-YDgghqAMEwSEKTRTPHCNTEKCVGCLLCGHVCPVGCIDL 395
Cdd:cd10549    75 IDEEKCIGCGLCVKVCpVD----AIT-LEDELEIVIDKEKCIGCGICAEVCPVNAIKL 127
PRK08348 PRK08348
NADH-plastoquinone oxidoreductase subunit; Provisional
 324-395 1.84e-06

NADH-plastoquinone oxidoreductase subunit; Provisional


Pssm-ID: 181399 [Multi-domain]  Cd Length: 120  Bit Score: 46.75  E-value: 1.84e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1440106093 324 VPAEDLDRSYIVYphiNLDKCVGCGRCYISCYDGghqAMEWSEKTRTPHCNTEKCVGCLLCGHVCPVGCIDL 395
Cdd:PRK08348   27 VPVPEDFRGKILY---DVDKCVGCRMCVTVCPAG---VFVYLPEIRKVALWTGRCVFCGQCVDVCPTGALQM 92
Fer4_10 pfam13237
4Fe-4S dicluster domain; This family includes proteins containing domains which bind to ...
 337-389 1.09e-05

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: 42.62  E-value: 1.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1440106093 337 PHINLDKCVGCGRCYISC--YDGGHQAMEWSEKTRTPHCNTEKCVGCLLCGHVCP 389
Cdd:pfam13237   2 VVIDPDKCIGCGRCTAACpaGLTRVGAIVERLEGEAVRIGVWKCIGCGACVEACP 56
RnfB COG2878
Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and ...
 344-395 1.26e-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: 46.53  E-value: 1.26e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 344 CVGCGRCYISC-YDgghqAMEWSEKtRTPHCNTEKCVGCLLCGHVCPVGCIDL 395
Cdd:COG2878   139 CIGCGDCIKACpFD----AIVGAAK-GMHTVDEDKCTGCGLCVEACPVDCIEM 186
PRK13795 PRK13795
hypothetical protein; Provisional
 343-401 2.25e-05

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 46.53  E-value: 2.25e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 343 KCVGCGRCYISCydgGHQAMEWSEKTRTPHCNTEKCVGCLLCGHVCPVgcidlgeVKFK 401
Cdd:PRK13795  582 ECVGCGVCVGAC---PTGAIRIEEGKRKISVDEEKCIHCGKCTEVCPV-------VKYK 630
DMSOR_beta-like cd04410
Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta ...
 339-393 4.69e-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: 42.76  E-value: 4.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 339 INLDKCVGCGRCYISC-YDGGHQAMEWSEKTRT--------------------PHC-------------------NTEKC 378
Cdd:cd04410     3 VDLDRCIGCGTCEVACkQEHGLRPGPDWSRIKViegggleraflpvscmhcedPPCvkacptgaiykdedgivliDEDKC 82

                          90
                  ....*....|....*
gi 1440106093 379 VGCLLCGHVCPVGCI 393
Cdd:cd04410    83 IGCGSCVEACPYGAI 97
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 374-399 5.52e-05

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


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 41.18  E-value: 5.52e-05
                          10        20
                  ....*....|....*....|....*.
gi 1440106093 374 NTEKCVGCLLCGHVCPVGCIDLGEVK 399
Cdd:COG4231    20 DEDKCTGCGACVKVCPADAIEEGDGK 45
NuoI TIGR01971
NADH-quinone oxidoreductase, chain I; This model represents the I subunit (one of 14: A->N) of ...
 341-398 8.00e-05

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: 42.02  E-value: 8.00e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 341 LDKCVGCGRCYISCYDGGHQAMEWSEKTRT-----PHCNTEKCVGCLLCGHVCPVGCIDLGEV 398
Cdd:TIGR01971  42 EEKCIGCTLCAAVCPADAIRVVPAEGEDGKrrlkfYEINFGRCIFCGLCEEACPTDAIVLTPE 104
DMSOR_beta-like cd04410
Beta subunit of the DMSO Reductase (DMSOR) family; This family consists of the small beta ...
 338-396 1.06e-04

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: 1.06e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 338 HINLDKCVGCGRCYISC-YDgghqAMEWSEKTRTPhcntEKCVGCL---------LCGHVCPVGCIDLG 396
Cdd:cd04410    76 LIDEDKCIGCGSCVEACpYG----AIVFDPEPGKA----VKCDLCGdrldeglepACVKACPTGALTFG 136
Fer4_9 pfam13187
4Fe-4S dicluster domain;
343-393 1.08e-04

4Fe-4S dicluster domain;


Pssm-ID: 463801 [Multi-domain]  Cd Length: 50  Bit Score: 39.46  E-value: 1.08e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1440106093 343 KCVGCGRCYISCyDGGHQAMEWSEKTRTPHCNTEKCVGCLLCGHVCPVGCI 393
Cdd:pfam13187   1 KCTGCGACVAAC-PAGAIVPDLVGQTIRGDIAGLACIGCGACVDACPRGAI 50
DMSOR_beta_like cd16373
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 339-390 1.45e-04

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: 41.86  E-value: 1.45e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 339 INLDKCV------GCGRCYISC-YDGGhqAMEWSEKTRTPHCNTEKCVGCLLCGHVCPV 390
Cdd:cd16373    88 IDKDRCLawqggtDCGVCVEACpTEAI--AIVLEDDVLRPVVDEDKCVGCGLCEYVCPV 144
PorD COG1144
Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta ...
 367-400 1.91e-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: 40.04  E-value: 1.91e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1440106093 367 KTRTPHCNTEKCVGCLLCGHVCPVGCIDLGEVKF 400
Cdd:COG1144    21 RVERPVVDEDKCIGCGLCWIVCPDGAIRVDDGKY 54
PRK12771 PRK12771
putative glutamate synthase (NADPH) small subunit; Provisional
 344-396 2.04e-04

putative glutamate synthase (NADPH) small subunit; Provisional


Pssm-ID: 237198 [Multi-domain]  Cd Length: 564  Bit Score: 43.33  E-value: 2.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 344 CVGCGRCYISCYDgghQAMEWSEKTRTPHCNTEKCVGCLLCGHVCPVGCIDLG 396
Cdd:PRK12771  512 CFECDNCYGACPQ---DAIIKLGPGRRYHFDYDKCTGCHICADVCPCGAIEMG 561
NuoI TIGR01971
NADH-quinone oxidoreductase, chain I; This model represents the I subunit (one of 14: A->N) of ...
 376-405 4.21e-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: 39.71  E-value: 4.21e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1440106093 376 EKCVGCLLCGHVCPVGCIDLGEVKFKKGEK 405
Cdd:TIGR01971  43 EKCIGCTLCAAVCPADAIRVVPAEGEDGKR 72
porD PRK09624
pyruvate ferredoxin oxidoreductase subunit delta; Reviewed
 337-395 5.17e-04

pyruvate ferredoxin oxidoreductase subunit delta; Reviewed


Pssm-ID: 170017 [Multi-domain]  Cd Length: 105  Bit Score: 39.24  E-value: 5.17e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 337 PHINLDKCVGCGRCYISCYDgghQAMEWSEKTrTPHCNTEKCVGCLLCGHVCPVGCIDL 395
Cdd:PRK09624   46 PEFNRDKCVRCYLCYIYCPE---PAIYLDEEG-YPVFDYDYCKGCGICANECPTKAIEM 100
HycB COG1142
Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];
336-398 6.82e-04

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


Pssm-ID: 440757 [Multi-domain]  Cd Length: 138  Bit Score: 39.64  E-value: 6.82e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 336 YPHINLDKCVGCGRCYISC-YdgghQAMEWSEKTRTPHCNteKCVGCL------LCGHVCPVGCIDLGEV 398
Cdd:COG1142    75 AVVVDEEKCIGCGLCVLACpF----GAITMVGEKSRAVAV--KCDLCGgreggpACVEACPTGALRLVDV 138
ferrodoxin_EFR1 NF038196
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 332-403 7.47e-04

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: 41.00  E-value: 7.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 332 SYIVYPHINL-----------DKCVGCGRCY-------ISCYDGGhqaMEWSEKtrtphcntekCVGCLLCGHVCPVGCI 393
Cdd:NF038196  164 SKLVNPLFYKfkvkdkkfhvtDKCIGCGICAkvcpvnnIEMEDGK---PVWGHN----------CTHCLACIHRCPKEAI 230

                          90
                  ....*....|
gi 1440106093 394 DLGEVKFKKG 403
Cdd:NF038196  231 EYGKKTKKKG 240
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
337-393 1.05e-03

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 40.69  E-value: 1.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 337 PHINLDKCVGCGRCYISCYDGGHQAMEWSEKTRTPhCNTEK------------CVGCLLCGHVCPVGCI 393
Cdd:PRK07118  163 PVVDEDKCTGCGACVKACPRNVIELIPKSARVFVA-CNSKDkgkavkkvcevgCIGCGKCVKACPAGAI 230
NuoI COG1143
Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy ...
 375-402 1.07e-03

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: 37.42  E-value: 1.07e-03
                          10        20
                  ....*....|....*....|....*...
gi 1440106093 375 TEKCVGCLLCGHVCPVGCIDLGEVKFKK 402
Cdd:COG1143     1 EDKCIGCGLCVRVCPVDAITIEDGEPGK 28
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 367-399 1.17e-03

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


Pssm-ID: 440763 [Multi-domain]  Cd Length: 68  Bit Score: 37.01  E-value: 1.17e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1440106093 367 KTRTPHCNTEKCVGCLLCGHVCPVGCIDLGEVK 399
Cdd:COG1149     2 KRKIPVIDEEKCIGCGLCVEVCPEGAIKLDDGG 34
ICL_PEPM cd00377
Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. ...
 38-178 1.46e-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: 1.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093  38 DTGWGGV--VFKTIGFFIAN-------EvsprfDHLVKEDTGFIGFKNMEQIAEHplEENLAALRRLKEDYPDKVLIASI 108
Cdd:cd00377    77 DTGYGNAlnVARTVRELEEAgaagihiE-----DQVGPKKCGHHGGKVLVPIEEF--VAKIKAARDARDDLPDFVIIART 149

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1440106093 109 --MGENEQQWEE-LARLV--QEAGADMIECnfscpqmtsHAMgsdvgQSPELVEKYCRAVKrgstLPMLAKMTPN 178
Cdd:cd00377   150 daLLAGEEGLDEaIERAKayAEAGADGIFV---------EGL-----KDPEEIRAFAEAPD----VPLNVNMTPG 206
HycB_like cd10554
HycB, HydN and similar proteins; This family includes HycB, the FeS subunit of a ...
 340-395 2.24e-03

HycB, HydN and similar proteins; This family includes HycB, the FeS subunit of a membrane-associated formate hydrogenlyase system (FHL-1) in Escherichia coli that breaks down formate, produced during anaerobic fermentation, to H2 and CO2. FHL-1 consists of formate dehydrogenase H (FDH-H) and the hydrogenase 3 complex (Hyd-3). HycB is thought to code for the [4Fe-4S] ferredoxin subunit of hydrogenase 3, which functions as an intermediate electron carrier protein between hydrogenase 3 and formate dehydrogenase. HydN codes for the [4Fe-4S] ferredoxin subunit of FDH-H; a hydN in-frame deletion mutation causes only weak reduction in hydrogenase activity, but loss of more than 60% of FDH-H activity. This pathway is only active at low pH and high formate concentrations, and is thought to provide a detoxification/de-acidification system countering the buildup of formate during fermentation.


Pssm-ID: 319876 [Multi-domain]  Cd Length: 149  Bit Score: 38.39  E-value: 2.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 340 NLDKCVGCGRCYISCYDGgHQAMEW------------------SEKTRTP----HC-----------------------N 374
Cdd:cd10554     5 DPDKCIGCRTCEVACAAA-HSGKGIfeagtdglpflprlrvvkTGEVTAPvqcrQCedapcanvcpvgaisqedgvvqvD 83

                          90       100
                  ....*....|....*....|.
gi 1440106093 375 TEKCVGCLLCGHVCPVGCIDL 395
Cdd:cd10554    84 EERCIGCKLCVLACPFGAIEM 104
GlpC COG0247
Fe-S cluster-containing oxidoreductase, includes glycolate oxidase subunit GlcF [Energy ...
 341-399 2.24e-03

Fe-S cluster-containing oxidoreductase, includes glycolate oxidase subunit GlcF [Energy production and conversion];


Pssm-ID: 440017 [Multi-domain]  Cd Length: 420  Bit Score: 40.06  E-value: 2.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1440106093 341 LDKCVGCGRCYISC--YD----------GGHQAM-EWSEKTRTPHCNTE------KCVGCLLCGHVCPVGcIDLGEVK 399
Cdd:COG0247    77 LDACVGCGFCRAMCpsYKatgdekdsprGRINLLrEVLEGELPLDLSEEvyevldLCLTCKACETACPSG-VDIADLI 153
PRK06273 PRK06273
ferredoxin; Provisional
 342-390 2.24e-03

ferredoxin; Provisional


Pssm-ID: 235764 [Multi-domain]  Cd Length: 165  Bit Score: 38.54  E-value: 2.24e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 342 DKCVGCGRCYISCYDGghqAMEWSE-----------KTRTPHCNTEKCVGCLLCGHVCPV 390
Cdd:PRK06273   49 ELCIGCGGCANVCPTK---AIEMIPvepvkitegyvKTKIPKIDYEKCVYCLYCHDFCPV 105
PRK05888 PRK05888
NADH-quinone oxidoreductase subunit NuoI;
376-406 2.27e-03

NADH-quinone oxidoreductase subunit NuoI;


Pssm-ID: 235637 [Multi-domain]  Cd Length: 164  Bit Score: 38.71  E-value: 2.27e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1440106093 376 EKCVGCLLCGHVCPVGCIDLGEVKFKKGEKE 406
Cdd:PRK05888   58 ERCIACKLCAAICPADAITIEAAEREDGRRR 88
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 83-131 2.28e-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: 39.31  E-value: 2.28e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1440106093   83 HPLEENLAALRRLKEDYPDKV---LIASIMGENEQQWEELARLVQEAGADMI 131
Cdd:smart00729 133 HTVEDVLEAVELLREAGPIKVstdLIVGLPGETEEDFEETLKLLKELGPDRV 184
DMSOR_beta_like cd16372
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 339-397 2.37e-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: 37.70  E-value: 2.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 339 INLDKCVGCGRCYISCYDGghqAMEWSEKTRTPHcnteKCVGCLLCGHVCPVGCIDLGE 397
Cdd:cd16372    74 INKKLCVGCLMCVGFCPEG---AMFKHEDYPEPF----KCIACGICVKACPTGALELVE 125
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
338-405 2.53e-03

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


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 40.01  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 338 HINLDKCVGCGRCYISC------YDGGHQAMewsektrtphcNTEKCVGCLLCGHVCPVGCI----DLGEVK--FKKGEK 405
Cdd:COG4624    87 IRDKEKCKNCYPCVRACpvkaikVDDGKAEI-----------DEEKCISCGQCVAVCPFGAIteksDIEKVKkaLKDPEK 155
DMSOR_beta_like cd16371
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 334-396 2.59e-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: 37.93  E-value: 2.59e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 334 IVYphINLDKCVGCGRCYISC-YDgghqAMEWSEKTRTphcnTEKCVGCL---------LCGHVCPVGCIDLG 396
Cdd:cd16371    78 IVV--VDQDKCIGCGYCVWACpYG----APQYNPETGK----MDKCDMCVdrldegekpACVAACPTRALDFG 140
PRK14028 PRK14028
pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional
 337-395 2.72e-03

pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional


Pssm-ID: 172522 [Multi-domain]  Cd Length: 312  Bit Score: 39.60  E-value: 2.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1440106093 337 PHINLDKCVGCGRCYISCYDGGhqAME-WSE---------KTRTPHCNTEKCVGCLLCGHVCPVGCIDL 395
Cdd:PRK14028  242 PVIDHSKCIMCRKCWLYCPDDA--IIEaWREaegprgrkfRMKMIDFDYQYCKGCGVCAEVCPTGAIQM 308
HycB COG1142
Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];
339-402 3.17e-03

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


Pssm-ID: 440757 [Multi-domain]  Cd Length: 138  Bit Score: 37.71  E-value: 3.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 339 INLDKCVGCGRCYISCYDGGHQAMEWSEKTRT--------------PHC-----------------------NTEKCVGC 381
Cdd:COG1142     7 ADPEKCIGCRTCEAACAVAHEGEEGEPFLPRIrvvrkagvsapvqcRHCedapcaevcpvgaitrddgavvvDEEKCIGC 86

                          90       100
                  ....*....|....*....|.
gi 1440106093 382 LLCGHVCPVGCIDLGEVKFKK 402
Cdd:COG1142    87 GLCVLACPFGAITMVGEKSRA 107
DMSOR_beta_like cd16374
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 338-395 3.49e-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: 319896 [Multi-domain]  Cd Length: 139  Bit Score: 37.64  E-value: 3.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 338 HINLDKCVGCGRCYISCydgghqAMEWSEKTRT-----------P----HCNT------------------------EKC 378
Cdd:cd16374     2 YVDPERCIGCRACEIAC------AREHSGKPRIsvevvedlasvPvrcrHCEDapcmevcptgaiyrdedgavlvdpDKC 75

                          90
                  ....*....|....*..
gi 1440106093 379 VGCLLCGHVCPVGCIDL 395
Cdd:cd16374    76 IGCGMCAMACPFGVPRF 92
rnfB TIGR01944
electron transport complex, RnfABCDGE type, B subunit; The six subunit complex RnfABCDGE in ...
 311-398 5.60e-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: 37.47  E-value: 5.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440106093 311 SLQDMVGLANnnivPAEDLDRSYIVYP-----HINLDKCVGCGRCYISC-YD---GGHQAMewsektrtpHCNTEK-CVG 380
Cdd:TIGR01944  81 ALAELLGVEP----IPQPLDADAGTIQppmvaLIDEDNCIGCTKCIQACpVDaivGAAKAM---------HTVIADeCTG 147

                          90
                  ....*....|....*...
gi 1440106093 381 CLLCGHVCPVGCIDLGEV 398
Cdd:TIGR01944 148 CDLCVEPCPTDCIEMIPV 165
Fer4 pfam00037
4Fe-4S binding domain; Superfamily includes proteins containing domains which bind to ...
 374-394 6.56e-03

4Fe-4S binding 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.


Pssm-ID: 459642 [Multi-domain]  Cd Length: 24  Bit Score: 33.76  E-value: 6.56e-03
                          10        20
                  ....*....|....*....|.
gi 1440106093 374 NTEKCVGCLLCGHVCPVGCID 394
Cdd:pfam00037   4 DEEKCIGCGACVEVCPVGAIT 24
Fer4_8 pfam13183
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 343-391 8.66e-03

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: 433017 [Multi-domain]  Cd Length: 64  Bit Score: 34.59  E-value: 8.66e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1440106093 343 KCVGCGRCYISC--------------YDGGHQAMEWSEKTRTPHCNTEKCVGCLLCGHVCPVG 391
Cdd:pfam13183   1 RCIRCGACLAACpvylvtggrfpgdpRGGAAALLGRLEALEGLAEGLWLCTLCGACTEVCPVG 63
PRK05888 PRK05888
NADH-quinone oxidoreductase subunit NuoI;
343-398 9.38e-03

NADH-quinone oxidoreductase subunit NuoI;


Pssm-ID: 235637 [Multi-domain]  Cd Length: 164  Bit Score: 36.78  E-value: 9.38e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1440106093 343 KCVGCGRCYISC-----YdgghqaMEWSE------KTRTPHCNTEKCVGCLLCGHVCPVGCIDLGEV 398
Cdd:PRK05888   59 RCIACKLCAAICpadaiT------IEAAEredgrrRTTRYDINFGRCIFCGFCEEACPTDAIVETPD 119
 
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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