Citrus Sinensis ID: 027264

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220------
Protein Sequence
MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEcccccccccccccHHHHHccccccEEEEEEcccccccEEEEEcccccccccccccccccccccccccccccccccHHHHcccHHHHHHcccccHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHcccccHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEccccccccccccccHHHHHcccccHcccccccccccccccccEEEHHHccHHccccccccEEcccccccccHHHHccccccEEEccccEEccccHHHHHHcHHHHHHccccHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MASILARKSLSALRARHLAVSgqalqgsqhyglrfnahpyssyfpskkddeEKEQLLKEISKDWSSVFERSINMLFLTEMVRGLGLTLkyffdkkvtinypfekgplsprfrgehalrryptgeerciACKLCEAVCPAQAITIeaeeredgsrrttrydidmtkciycgfcqeacpvdaivegpnfeysteTHEELLYDKEKLLENGDRWETEIAENlrseslyr
Flexible Loop (DISEMBL)
MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYpfekgplsprfrgeHALRRYPTGEERCIACKLCEAVCPAQaitieaeeredgsrrttrydiDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKllengdrweteiaenlrseslyr
Low Complexity Region (SEG)
MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSkkddeekeqllkeISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHeellydkeklleNGDRWETEIAENLRSESLYR
Disordered region (IsUnstruct)
****************************QHYGLRFNAHPY*******************ISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEA*********TTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLE********************
Disordered Region (DISOPRED)
*****************************************************************SVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENL*****Y*
Disordered Region (DISEMBL)
MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAE********TTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR
Disordered Region (DISPRO)
*****************************************************EQLLKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEER*DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESL**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	226	2.2.26 [Sep-21-2011]
Q9FX83	222	NADH dehydrogenase [ubiqu	yes	no	0.982	1.0	0.876	1e-112
Q42599	222	NADH dehydrogenase [ubiqu	no	no	0.982	1.0	0.867	1e-111
P80269	229	NADH dehydrogenase [ubiqu	N/A	no	0.991	0.978	0.826	1e-109
O24143	230	NADH dehydrogenase [ubiqu	N/A	no	1.0	0.982	0.804	1e-106
P42028	212	NADH dehydrogenase [ubiqu	yes	no	0.752	0.801	0.788	3e-78
O21233	162	NADH-ubiquinone oxidoredu	N/A	no	0.712	0.993	0.826	3e-78
Q8K3J1	212	NADH dehydrogenase [ubiqu	yes	no	0.915	0.976	0.635	6e-78
P0CB97	210	NADH dehydrogenase [ubiqu	yes	no	0.752	0.809	0.776	3e-77
Q60HE3	210	NADH dehydrogenase [ubiqu	N/A	no	0.752	0.809	0.776	4e-77
P0CB98	210	NADH dehydrogenase [ubiqu	N/A	no	0.752	0.809	0.764	4e-76

>sp|Q9FX83|NDS8B_ARATH NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-B, mitochondrial OS=Arabidopsis thaliana GN=At1g16700 PE=1 SV=1

 Score =  404 bits (1038), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 198/226 (87%), Positives = 205/226 (90%), Gaps = 4/226 (1%)

Query: 1   MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEI 60
           MAS+LAR+S SALRARHLA SGQ LQGS   GL+  A  Y S     KDDEE EQL KEI
Sbjct: 1   MASLLARRSFSALRARHLAFSGQGLQGSHLCGLQSRAISYGS----NKDDEEAEQLAKEI 56

Query: 61  SKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRY 120
           SKDWS+VFERS+N LFLTEMVRGL LTLKYFFD KVTINYPFEKGPLSPRFRGEHALRRY
Sbjct: 57  SKDWSTVFERSMNTLFLTEMVRGLSLTLKYFFDPKVTINYPFEKGPLSPRFRGEHALRRY 116

Query: 121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
           PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA
Sbjct: 117 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 176

Query: 181 IVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           IVEGPNFE++TETHEELLYDKEKLLENGDRWETEIAENLRSESLYR
Sbjct: 177 IVEGPNFEFATETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 222

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). May donate electrons to ubiquinone.
Arabidopsis thaliana (taxid: 3702)
EC: 1EC: .EC: 6EC: .EC: 9EC: 9EC: .EC: 3

>sp|Q42599|NDS8A_ARATH NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial OS=Arabidopsis thaliana GN=At1g79010 PE=1 SV=1

 Score =  400 bits (1028), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 196/226 (86%), Positives = 204/226 (90%), Gaps = 4/226 (1%)

Query: 1   MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEI 60
           MASILAR+SL+ LRARHL +SGQALQGS    L+     Y S     KDDEE EQL KEI
Sbjct: 1   MASILARRSLNTLRARHLVLSGQALQGSHLSRLQSRGISYGS----NKDDEEAEQLSKEI 56

Query: 61  SKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRY 120
           SKDW++VFERSIN LFLTEMVRGL LTLKYFFD KVTINYPFEKGPLSPRFRGEHALRRY
Sbjct: 57  SKDWNTVFERSINTLFLTEMVRGLSLTLKYFFDPKVTINYPFEKGPLSPRFRGEHALRRY 116

Query: 121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
           PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA
Sbjct: 117 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 176

Query: 181 IVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           IVEGPNFE++TETHEELLYDKEKLLENGDRWETEIAENLRSESLYR
Sbjct: 177 IVEGPNFEFATETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 222

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). May donate electrons to ubiquinone.

Arabidopsis thaliana (taxid: 3702)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|P80269|NDUS8_SOLTU NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Solanum tuberosum PE=1 SV=2

 Score =  392 bits (1007), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 191/231 (82%), Positives = 207/231 (89%), Gaps = 7/231 (3%)

Query: 1   MASILARKSLSALRARHLAVSGQALQGSQHY-----GLRFNAHPYSSYFPSKKDDEEKEQ 55
           MA+ILARKSLSALR+R L ++G  ++G+  Y     G R  A  +S  F + KDDEE+EQ
Sbjct: 1   MAAILARKSLSALRSRQLVLAGHTIEGTNGYNRTLLGTRSFATKHS--FSTDKDDEEREQ 58

Query: 56  LLKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEH 115
           L KE+SKDW+SVFERSIN LFLTEMVRGL LTLKYFF+KKVTINYPFEKGPLSPRFRGEH
Sbjct: 59  LAKELSKDWNSVFERSINTLFLTEMVRGLMLTLKYFFEKKVTINYPFEKGPLSPRFRGEH 118

Query: 116 ALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEA 175
           ALRRY TGEERCIACKLCEA+CPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEA
Sbjct: 119 ALRRYATGEERCIACKLCEAICPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEA 178

Query: 176 CPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           CPVDAIVEGPNFE++TETHEELLYDKEKLLENGDRWETEIAENLRSESLYR
Sbjct: 179 CPVDAIVEGPNFEFATETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 229

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). May donate electrons to ubiquinone.

Solanum tuberosum (taxid: 4113)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|O24143|NDUS8_TOBAC NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Nicotiana tabacum PE=2 SV=1

 Score =  382 bits (982), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 185/230 (80%), Positives = 202/230 (87%), Gaps = 4/230 (1%)

Query: 1   MASILARKSLSALRARHLAVSGQALQ--GSQHYGLRFNAHPYSSY--FPSKKDDEEKEQL 56
           MA+ILARKSLSALR+R L ++GQA Q   +   G       +++   F + KDDEE+EQL
Sbjct: 1   MAAILARKSLSALRSRQLVLAGQAWQQGANTSNGTLLGTRTFATNDSFSTDKDDEEREQL 60

Query: 57  LKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHA 116
            KE+SKDW+SVFE+ IN LFLTEMVRGL LTLKYFF+KKVTINYPFEKGPLSPRFRGE  
Sbjct: 61  AKELSKDWNSVFEQQINTLFLTEMVRGLMLTLKYFFEKKVTINYPFEKGPLSPRFRGEQP 120

Query: 117 LRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEAC 176
           LRRYPTGEERCIACKLCEA+CPAQAITIEAE REDGSRRTTRYDIDMTKCIYCGFCQEAC
Sbjct: 121 LRRYPTGEERCIACKLCEAICPAQAITIEAEAREDGSRRTTRYDIDMTKCIYCGFCQEAC 180

Query: 177 PVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           PVDAIVEGPNFE++TETHEELLYDKEKLLENGDRWETEIAENLRSESLYR
Sbjct: 181 PVDAIVEGPNFEFATETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 230

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). May donate electrons to ubiquinone.

Nicotiana tabacum (taxid: 4097)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|P42028|NDUS8_BOVIN NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Bos taurus GN=NDUFS8 PE=1 SV=1

 Score =  291 bits (745), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 134/170 (78%), Positives = 149/170 (87%)

Query: 57  LKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHA 116
           L+E S D  SV +R+   L  TE++RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHA
Sbjct: 43  LREPSMDMKSVTDRAAQTLLWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHA 102

Query: 117 LRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEAC 176
           LRRYP+GEERCIACKLCEAVCPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEAC
Sbjct: 103 LRRYPSGEERCIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEAC 162

Query: 177 PVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           PVDAIVEGPNFE+STETHEELLY+KEKLL NGD+WE EIA N++++ LYR
Sbjct: 163 PVDAIVEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 212

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Bos taurus (taxid: 9913)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|O21233|NDUS8_RECAM NADH-ubiquinone oxidoreductase subunit 8 OS=Reclinomonas americana GN=NAD8 PE=3 SV=1

 Score =  291 bits (744), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 133/161 (82%), Positives = 148/161 (91%)

Query: 66  SVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEE 125
           ++  ++   LFLTE+V+G+ LTL YFF KKVT+NYPFEKGPLSPRFRGEHALRRY TGEE
Sbjct: 2   TIINKTAQTLFLTELVKGMSLTLDYFFRKKVTLNYPFEKGPLSPRFRGEHALRRYQTGEE 61

Query: 126 RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 185
           RCIACKLCEA+CPAQAITIE+E R DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP
Sbjct: 62  RCIACKLCEAICPAQAITIESEPRIDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 121

Query: 186 NFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           NFE++TETHEELLYDKEKLL+NGDRWETEIA NL +E+LYR
Sbjct: 122 NFEFATETHEELLYDKEKLLQNGDRWETEIAANLANEALYR 162

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone (By similarity). May donate electrons to ubiquinone.

Reclinomonas americana (taxid: 48483)

EC: 1

EC: .

EC: 6

EC: .

EC: 5

EC: .

EC: 3

>sp|Q8K3J1|NDUS8_MOUSE NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Mus musculus GN=Ndufs8 PE=1 SV=1

 Score =  290 bits (742), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 143/225 (63%), Positives = 169/225 (75%), Gaps = 18/225 (8%)

Query: 2   ASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEIS 61
           +S+L R    A+R  HL  +GQ+L  S        A   +  + +KK+ E +        
Sbjct: 6   SSMLPRALAQAMRTGHL--NGQSLHSS--------AVAATYKYVNKKEQESE-------- 47

Query: 62  KDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYP 121
            D  S  + +  +L  TE++RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHALRRYP
Sbjct: 48  VDMKSATDNAARILMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYP 107

Query: 122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           +GEERCIACKLCEA+CPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVDAI
Sbjct: 108 SGEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 167

Query: 182 VEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           VEGPNFE+STETHEELLY+KEKLL NGD+WE EIA N++++ LYR
Sbjct: 168 VEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 212

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Mus musculus (taxid: 10090)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|P0CB97|NDUS8_PONAB NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Pongo abelii GN=NDUFS8 PE=2 SV=1

 Score =  288 bits (736), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 132/170 (77%), Positives = 148/170 (87%)

Query: 57  LKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHA 116
           ++E   D  SV +R+   L LTE+ RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHA
Sbjct: 41  MQEPEMDMKSVTDRAARTLLLTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHA 100

Query: 117 LRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEAC 176
           LRRYP+GEERCIACKLCEA+CPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEAC
Sbjct: 101 LRRYPSGEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEAC 160

Query: 177 PVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           PVDAIVEGPNFE+STETHEELLY+KEKLL NGD+WE EIA N++++ LYR
Sbjct: 161 PVDAIVEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 210

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Pongo abelii (taxid: 9601)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|Q60HE3|NDUS8_MACFA NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Macaca fascicularis GN=NDUFS8 PE=2 SV=1

 Score =  287 bits (735), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 132/170 (77%), Positives = 147/170 (86%)

Query: 57  LKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHA 116
           ++E   D  SV +R+   L  TE+ RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHA
Sbjct: 41  MQESKTDMKSVTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHA 100

Query: 117 LRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEAC 176
           LRRYP+GEERCIACKLCEAVCPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEAC
Sbjct: 101 LRRYPSGEERCIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEAC 160

Query: 177 PVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           PVDAIVEGPNFE+STETHEELLY+KEKLL NGD+WE EIA N++++ LYR
Sbjct: 161 PVDAIVEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 210

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Macaca fascicularis (taxid: 9541)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|P0CB98|NDUS8_PONPY NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Pongo pygmaeus GN=NDUFS8 PE=2 SV=1

 Score =  284 bits (726), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 130/170 (76%), Positives = 147/170 (86%)

Query: 57  LKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHA 116
           +++   D  SV +R+   L  TE+ RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHA
Sbjct: 41  MQDPEMDMKSVTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHA 100

Query: 117 LRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEAC 176
           LRRYP+GEERCIACKLCEA+CPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEAC
Sbjct: 101 LRRYPSGEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEAC 160

Query: 177 PVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           PVDAIVEGPNFE+STETHEELLY+KEKLL NGD+WE EIA N++++ LYR
Sbjct: 161 PVDAIVEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 210

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.

Pongo pygmaeus (taxid: 9600)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	226
TAIR|locus:2015636	222	AT1G16700 [Arabidopsis thalian	0.982	1.0	0.778	1.7e-89
TAIR|locus:2207285	222	AT1G79010 [Arabidopsis thalian	0.982	1.0	0.774	1.6e-88
RGD|1309436	212	Ndufs8 "NADH dehydrogenase (ub	0.725	0.773	0.719	2.3e-66
ZFIN|ZDB-GENE-040426-2153	210	ndufs8a "NADH dehydrogenase (u	0.725	0.780	0.719	9.4e-66
UNIPROTKB|E2R5X8	210	NDUFS8 "Uncharacterized protei	0.734	0.790	0.734	1.5e-65
UNIPROTKB|P42028	212	NDUFS8 "NADH dehydrogenase [ub	0.734	0.783	0.734	2e-65
UNIPROTKB|P0CB97	210	NDUFS8 "NADH dehydrogenase [ub	0.725	0.780	0.737	3.2e-65
UNIPROTKB|Q60HE3	210	NDUFS8 "NADH dehydrogenase [ub	0.725	0.780	0.737	1.1e-64
ZFIN|ZDB-GENE-050522-131	210	ndufs8b "NADH dehydrogenase (u	0.738	0.795	0.724	1.1e-64
UNIPROTKB|O00217	210	NDUFS8 "NADH dehydrogenase [ub	0.725	0.780	0.731	1.4e-64

TAIR|locus:2015636 AT1G16700 [Arabidopsis thaliana (taxid:3702)]

 Score = 893 (319.4 bits), Expect = 1.7e-89, P = 1.7e-89
 Identities = 176/226 (77%), Positives = 183/226 (80%)

Query:     1 MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSXXXXXXXXXXXXXI 60
             MAS+LAR+S SALRARHLA SGQ LQGS   GL+  A  Y S                 I
Sbjct:     1 MASLLARRSFSALRARHLAFSGQGLQGSHLCGLQSRAISYGS----NKDDEEAEQLAKEI 56

Query:    61 SKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRY 120
             SKDWS+VFERS+N LFLTEMVRGL LTLKYFFD KVTINYPFEKGPLSPRFRGEHALRRY
Sbjct:    57 SKDWSTVFERSMNTLFLTEMVRGLSLTLKYFFDPKVTINYPFEKGPLSPRFRGEHALRRY 116

Query:   121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
             PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA
Sbjct:   117 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 176

Query:   181 IVEGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             IVEGPNFE++TETH            NGDRWETEIAENLRSESLYR
Sbjct:   177 IVEGPNFEFATETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 222

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=ISS

GO:0009055 "electron carrier activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016651 "oxidoreductase activity, acting on NAD(P)H" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0055114 "oxidation-reduction process" evidence=IEA

GO:0046872 "metal ion binding" evidence=IDA

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IDA

TAIR|locus:2207285 AT1G79010 [Arabidopsis thaliana (taxid:3702)]

 Score = 884 (316.2 bits), Expect = 1.6e-88, P = 1.6e-88
 Identities = 175/226 (77%), Positives = 184/226 (81%)

Query:     1 MASILARKSLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSXXXXXXXXXXXXXI 60
             MASILAR+SL+ LRARHL +SGQALQGS H   R  +   S  + S             I
Sbjct:     1 MASILARRSLNTLRARHLVLSGQALQGS-HLS-RLQSRGIS--YGSNKDDEEAEQLSKEI 56

Query:    61 SKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRY 120
             SKDW++VFERSIN LFLTEMVRGL LTLKYFFD KVTINYPFEKGPLSPRFRGEHALRRY
Sbjct:    57 SKDWNTVFERSINTLFLTEMVRGLSLTLKYFFDPKVTINYPFEKGPLSPRFRGEHALRRY 116

Query:   121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
             PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA
Sbjct:   117 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 176

Query:   181 IVEGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             IVEGPNFE++TETH            NGDRWETEIAENLRSESLYR
Sbjct:   177 IVEGPNFEFATETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 222

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=ISS

GO:0009055 "electron carrier activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016651 "oxidoreductase activity, acting on NAD(P)H" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0055114 "oxidation-reduction process" evidence=IEA

GO:0046872 "metal ion binding" evidence=IDA

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IDA

RGD|1309436 Ndufs8 "NADH dehydrogenase (ubiquinone) Fe-S protein 8" [Rattus norvegicus (taxid:10116)]

 Score = 650 (233.9 bits), Expect = 2.3e-66, Sum P(2) = 2.3e-66
 Identities = 118/164 (71%), Positives = 132/164 (80%)

Query:    63 DWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPT 122
             D  S  + +  +L  TE+ RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHALRRYP+
Sbjct:    49 DMKSATDSAARILMWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPS 108

Query:   123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
             GEERCIACKLCEA+CPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV
Sbjct:   109 GEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 168

Query:   183 EGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             EGPNFE+STETH            NGD+WE EIA N++++ LYR
Sbjct:   169 EGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 212

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005739 "mitochondrion" evidence=ISO

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IEA;ISO

GO:0006979 "response to oxidative stress" evidence=IEA;ISO

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=IEA;ISO

GO:0008150 "biological_process" evidence=ND

GO:0009055 "electron carrier activity" evidence=IEA

GO:0032981 "mitochondrial respiratory chain complex I assembly" evidence=IEA;ISO

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0003954 "NADH dehydrogenase activity" evidence=ISO

ZFIN|ZDB-GENE-040426-2153 ndufs8a "NADH dehydrogenase (ubiquinone) Fe-S protein 8a" [Danio rerio (taxid:7955)]

 Score = 669 (240.6 bits), Expect = 9.4e-66, P = 9.4e-66
 Identities = 118/164 (71%), Positives = 135/164 (82%)

Query:    63 DWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPT 122
             DW S+ +R+   L LTE++RG+G+ + Y F +  TINYPFEKGPLSPRFRGEHALRRYP+
Sbjct:    47 DWKSITDRAAQTLLLTELIRGMGMAVSYLFREPATINYPFEKGPLSPRFRGEHALRRYPS 106

Query:   123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
             GEERCIACKLCEA+CPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV
Sbjct:   107 GEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 166

Query:   183 EGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             EGPNFE+STETH            NGD+WE EIA N++++ LYR
Sbjct:   167 EGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADFLYR 210

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=IEA

GO:0055114 "oxidation-reduction process" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016651 "oxidoreductase activity, acting on NAD(P)H" evidence=IEA

UNIPROTKB|E2R5X8 NDUFS8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 667 (239.9 bits), Expect = 1.5e-65, P = 1.5e-65
 Identities = 122/166 (73%), Positives = 135/166 (81%)

Query:    61 SKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRY 120
             S D  SV +R+   L  TE++RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHALRRY
Sbjct:    45 SMDMKSVTDRAAQTLLWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRY 104

Query:   121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
             P+GEERCIACKLCEAVCPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVDA
Sbjct:   105 PSGEERCIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 164

Query:   181 IVEGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             IVEGPNFE+STETH            NGD+WE EIA N++++ LYR
Sbjct:   165 IVEGPNFEFSTETHEELLYNKEKLLSNGDKWEAEIAANIQADYLYR 210

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0016651 "oxidoreductase activity, acting on NAD(P)H" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

UNIPROTKB|P42028 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 666 (239.5 bits), Expect = 2.0e-65, P = 2.0e-65
 Identities = 122/166 (73%), Positives = 135/166 (81%)

Query:    61 SKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRY 120
             S D  SV +R+   L  TE++RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHALRRY
Sbjct:    47 SMDMKSVTDRAAQTLLWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRY 106

Query:   121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
             P+GEERCIACKLCEAVCPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVDA
Sbjct:   107 PSGEERCIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 166

Query:   181 IVEGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             IVEGPNFE+STETH            NGD+WE EIA N++++ LYR
Sbjct:   167 IVEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 212

GO:0006979 "response to oxidative stress" evidence=IDA

GO:0032981 "mitochondrial respiratory chain complex I assembly" evidence=IEA

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IEA

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

UNIPROTKB|P0CB97 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" [Pongo abelii (taxid:9601)]

 Score = 664 (238.8 bits), Expect = 3.2e-65, P = 3.2e-65
 Identities = 121/164 (73%), Positives = 134/164 (81%)

Query:    63 DWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPT 122
             D  SV +R+   L LTE+ RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHALRRYP+
Sbjct:    47 DMKSVTDRAARTLLLTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPS 106

Query:   123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
             GEERCIACKLCEA+CPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV
Sbjct:   107 GEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 166

Query:   183 EGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             EGPNFE+STETH            NGD+WE EIA N++++ LYR
Sbjct:   167 EGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 210

GO:0005739 "mitochondrion" evidence=ISS

GO:0005747 "mitochondrial respiratory chain complex I" evidence=ISS

GO:0006979 "response to oxidative stress" evidence=ISS

GO:0032981 "mitochondrial respiratory chain complex I assembly" evidence=ISS

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=ISS

UNIPROTKB|Q60HE3 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" [Macaca fascicularis (taxid:9541)]

 Score = 659 (237.0 bits), Expect = 1.1e-64, P = 1.1e-64
 Identities = 121/164 (73%), Positives = 133/164 (81%)

Query:    63 DWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPT 122
             D  SV +R+   L  TE+ RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHALRRYP+
Sbjct:    47 DMKSVTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPS 106

Query:   123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
             GEERCIACKLCEAVCPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV
Sbjct:   107 GEERCIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 166

Query:   183 EGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             EGPNFE+STETH            NGD+WE EIA N++++ LYR
Sbjct:   167 EGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 210

GO:0005739 "mitochondrion" evidence=ISS

GO:0005747 "mitochondrial respiratory chain complex I" evidence=ISS

GO:0006979 "response to oxidative stress" evidence=ISS

GO:0032981 "mitochondrial respiratory chain complex I assembly" evidence=ISS

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=ISS

ZFIN|ZDB-GENE-050522-131 ndufs8b "NADH dehydrogenase (ubiquinone) Fe-S protein 8b" [Danio rerio (taxid:7955)]

 Score = 659 (237.0 bits), Expect = 1.1e-64, P = 1.1e-64
 Identities = 121/167 (72%), Positives = 132/167 (79%)

Query:    60 ISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRR 119
             +  D  S+ +R+   L LTE+ RGL + L Y F +  TINYPFEKGPLSPRFRGEHALRR
Sbjct:    44 LPSDLKSITDRAAQTLLLTELCRGLAMALSYLFREPATINYPFEKGPLSPRFRGEHALRR 103

Query:   120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD 179
             YP GEERCIACKLCEAVCPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVD
Sbjct:   104 YPNGEERCIACKLCEAVCPAQAITIEAETRADGSRRTTRYDIDMTKCIYCGFCQEACPVD 163

Query:   180 AIVEGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             AIVEGPNFEYSTETH            NGDRWE EIA N++++ LYR
Sbjct:   164 AIVEGPNFEYSTETHEELLYNKEKLLNNGDRWEVEIAANIQADYLYR 210

GO:0016491 "oxidoreductase activity" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0055114 "oxidation-reduction process" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016651 "oxidoreductase activity, acting on NAD(P)H" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

UNIPROTKB|O00217 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 658 (236.7 bits), Expect = 1.4e-64, P = 1.4e-64
 Identities = 120/164 (73%), Positives = 133/164 (81%)

Query:    63 DWSSVFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPT 122
             D  SV +R+   L  TE+ RGLG+TL Y F +  TINYPFEKGPLSPRFRGEHALRRYP+
Sbjct:    47 DMKSVTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPS 106

Query:   123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
             GEERCIACKLCEA+CPAQAITIEAE R DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV
Sbjct:   107 GEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 166

Query:   183 EGPNFEYSTETHXXXXXXXXXXXXNGDRWETEIAENLRSESLYR 226
             EGPNFE+STETH            NGD+WE EIA N++++ LYR
Sbjct:   167 EGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 210

GO:0009055 "electron carrier activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0006120 "mitochondrial electron transport, NADH to ubiquinone" evidence=NAS

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IDA;IMP;NAS

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=IMP;NAS

GO:0032981 "mitochondrial respiratory chain complex I assembly" evidence=IMP

GO:0003954 "NADH dehydrogenase activity" evidence=IMP

GO:0005739 "mitochondrion" evidence=IDA

GO:0006979 "response to oxidative stress" evidence=IDA

GO:0005743 "mitochondrial inner membrane" evidence=TAS

GO:0022904 "respiratory electron transport chain" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q163R7	NUOI_ROSDO	1, ., 6, ., 9, 9, ., 5	0.7421	0.7035	0.9695	yes	no
Q2W3J2	NUOI_MAGSA	1, ., 6, ., 9, 9, ., 5	0.7267	0.7123	0.9938	yes	no
P29921	NQO9_PARDE	1, ., 6, ., 9, 9, ., 5	0.7547	0.7035	0.9754	yes	no
A1B486	NUOI_PARDP	1, ., 6, ., 9, 9, ., 5	0.7547	0.7035	0.9754	yes	no
Q42599	NDS8A_ARATH	1, ., 6, ., 9, 9, ., 3	0.8672	0.9823	1.0	no	no
Q1RKD0	NUOI_RICBR	1, ., 6, ., 9, 9, ., 5	0.7548	0.6858	0.9748	yes	no
B0BVB0	NUOI_RICRO	1, ., 6, ., 9, 9, ., 5	0.7483	0.6858	0.9748	yes	no
B9JVF4	NUOI_AGRVS	1, ., 6, ., 9, 9, ., 5	0.7341	0.6946	0.9631	yes	no
O00217	NDUS8_HUMAN	1, ., 6, ., 9, 9, ., 3	0.7647	0.7522	0.8095	yes	no
C3PLS5	NUOI_RICAE	1, ., 6, ., 9, 9, ., 5	0.7548	0.6858	0.9748	yes	no
Q28T58	NUOI_JANSC	1, ., 6, ., 9, 9, ., 5	0.7610	0.7035	0.9695	yes	no
Q92G94	NUOI_RICCN	1, ., 6, ., 9, 9, ., 5	0.7483	0.6858	0.9748	yes	no
A7IP99	NUOI_XANP2	1, ., 6, ., 9, 9, ., 5	0.7437	0.7035	0.9814	yes	no
Q1GIM9	NUOI_RUEST	1, ., 6, ., 9, 9, ., 5	0.7672	0.7035	0.9695	yes	no
A7HY41	NUOI_PARL1	1, ., 6, ., 9, 9, ., 5	0.7375	0.7035	0.9754	yes	no
Q1MIK6	NUOI_RHIL3	1, ., 6, ., 9, 9, ., 5	0.7515	0.6902	0.9570	yes	no
A8I407	NUOI_AZOC5	1, ., 6, ., 9, 9, ., 5	0.7437	0.7035	0.9814	yes	no
Q8K3J1	NDUS8_MOUSE	1, ., 6, ., 9, 9, ., 3	0.6355	0.9159	0.9764	yes	no
A8GY32	NUOI_RICB8	1, ., 6, ., 9, 9, ., 5	0.7548	0.6858	0.9748	yes	no
Q3J3F0	NUOI1_RHOS4	1, ., 6, ., 9, 9, ., 5	0.7610	0.7035	0.9520	yes	no
P0CB98	NDUS8_PONPY	1, ., 6, ., 9, 9, ., 3	0.7647	0.7522	0.8095	N/A	no
Q2RU32	NUOI_RHORT	1, ., 6, ., 9, 9, ., 5	0.7579	0.6946	0.9691	yes	no
Q0BSL0	NUOI_GRABC	1, ., 6, ., 9, 9, ., 5	0.7204	0.7123	0.9938	yes	no
P0CB97	NDUS8_PONAB	1, ., 6, ., 9, 9, ., 3	0.7764	0.7522	0.8095	yes	no
Q60HE3	NDUS8_MACFA	1, ., 6, ., 9, 9, ., 3	0.7764	0.7522	0.8095	N/A	no
Q2NA74	NUOI_ERYLH	1, ., 6, ., 9, 9, ., 5	0.82	0.6637	0.9259	yes	no
Q92QP4	NUOI1_RHIME	1, ., 6, ., 9, 9, ., 5	0.7579	0.6902	0.9512	yes	no
A8F2T4	NUOI_RICM5	1, ., 6, ., 9, 9, ., 5	0.7419	0.6858	0.9748	yes	no
Q4UK24	NUOI_RICFE	1, ., 6, ., 9, 9, ., 5	0.7419	0.6858	0.9748	yes	no
B6ISX3	NUOI_RHOCS	1, ., 6, ., 9, 9, ., 5	0.7421	0.7035	0.9814	yes	no
O21233	NDUS8_RECAM	1, ., 6, ., 5, ., 3	0.8260	0.7123	0.9938	N/A	no
P80269	NDUS8_SOLTU	1, ., 6, ., 9, 9, ., 3	0.8268	0.9911	0.9781	N/A	no
O24143	NDUS8_TOBAC	1, ., 6, ., 9, 9, ., 3	0.8043	1.0	0.9826	N/A	no
P42031	NUOI_RHOCA	1, ., 6, ., 9, 9, ., 5	0.7358	0.7035	0.9754	yes	no
C4K221	NUOI_RICPU	1, ., 6, ., 9, 9, ., 5	0.7483	0.6858	0.9748	yes	no
Q5LPS9	NUOI_RUEPO	1, ., 6, ., 9, 9, ., 5	0.7735	0.7035	0.9695	yes	no
A8GPY5	NUOI_RICAH	1, ., 6, ., 9, 9, ., 5	0.7354	0.6858	0.9748	yes	no
A8GTS0	NUOI_RICRS	1, ., 6, ., 9, 9, ., 5	0.7483	0.6858	0.9748	yes	no
Q2G5Z4	NUOI_NOVAD	1, ., 6, ., 9, 9, ., 5	0.8064	0.6858	0.9627	yes	no
Q2K9S4	NUOI1_RHIEC	1, ., 6, ., 9, 9, ., 5	0.7515	0.6902	0.9570	yes	no
Q22619	NDUS8_CAEEL	1, ., 6, ., 9, 9, ., 3	0.7948	0.6902	0.7358	yes	no
Q12644	NDUS8_NEUCR	1, ., 6, ., 9, 9, ., 3	0.6	0.8982	0.9269	N/A	no
Q9FX83	NDS8B_ARATH	1, ., 6, ., 9, 9, ., 3	0.8761	0.9823	1.0	yes	no
Q0MQI2	NDUS8_GORGO	1, ., 6, ., 9, 9, ., 3	0.7588	0.7522	0.8095	N/A	no
Q0MQI3	NDUS8_PANTR	1, ., 6, ., 9, 9, ., 3	0.7647	0.7522	0.8095	yes	no
A8LIV0	NUOI_DINSH	1, ., 6, ., 9, 9, ., 5	0.7484	0.7035	0.9695	yes	no
Q8UFW9	NUOI_AGRT5	1, ., 6, ., 9, 9, ., 5	0.7405	0.6946	0.9631	yes	no
A3PIX9	NUOI1_RHOS1	1, ., 6, ., 9, 9, ., 5	0.7610	0.7035	0.9520	yes	no
Q0APY2	NUOI_MARMM	1, ., 6, ., 9, 9, ., 5	0.7405	0.6991	0.9753	yes	no
P42028	NDUS8_BOVIN	1, ., 6, ., 9, 9, ., 3	0.7882	0.7522	0.8018	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	1.6.5.3	0.994
3rd Layer	1.6.99	0.998
3rd Layer	1.6.99.3	0.994
3rd Layer	1.6.5	0.998

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	AT1G16700	NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial, putative; NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial, putative; FUNCTIONS IN- NADH dehydrogenase (ubiquinone) activity, metal ion binding; LOCATED IN- mitochondrion, respiratory chain complex I; CONTAINS InterPro DOMAIN/s- 4Fe-4S ferredoxin, iron-sulphur binding, subgroup (InterPro-IPR001450), NADH-quinone oxidoreductase, chain I (InterPro-IPR010226), 4Fe-4S ferredoxin, iron-sulphur binding, conserved site (InterPro-IPR017900), 4Fe-4S ferredoxin, iron-sulpur binding domain (InterPro-IPR017896), Alpha-helica [...] (222 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	CI51	CI51 (51 kDa subunit of complex I); 4 iron, 4 sulfur cluster binding / FMN binding / NAD or NAD [...] (486 aa)	•		•	•	•	•	•		0.999
	EMB1467	EMB1467 (embryo defective 1467); NADH dehydrogenase (ubiquinone)/ NADH dehydrogenase/ electron [...] (748 aa)	•		•	•	•	•	•		0.998
	AT4G02580	NADH-ubiquinone oxidoreductase 24 kDa subunit, putative; NADH-ubiquinone oxidoreductase 24 kDa [...] (255 aa)	•		•	•	•	•	•		0.998
	AT5G11770	NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrial; NADH-ubiquinone oxidoreductase 20 [...] (218 aa)	•		•	•	•	•	•		0.997
	NAD9	unknown protein; NADH dehydrogenase subunit 9 ; Core subunit of the mitochondrial membrane resp [...] (190 aa)	•		•	•	•	•	•		0.985
	NAD7	unknown protein; NADH dehydrogenase subunit 7 ; Core subunit of the mitochondrial membrane resp [...] (394 aa)	•		•	•	•	•	•		0.975
	NDHE	unknown protein; NADH dehydrogenase ND4L ; NDH shuttles electrons from NAD(P)H-plastoquinone, v [...] (101 aa)	•			•		•	•		0.971
	AT2G20360	binding / catalytic/ coenzyme binding; binding / catalytic/ coenzyme binding; FUNCTIONS IN- coe [...] (402 aa)				•		•	•		0.963
	AT5G47890	NADH-ubiquinone oxidoreductase B8 subunit, putative; NADH-ubiquinone oxidoreductase B8 subunit, [...] (97 aa)				•	•	•	•		0.963
	AT5G67590.1-P	FRO1 (FROSTBITE1); NADH dehydrogenase (ubiquinone); Mutant leaves have a reduced capacity for c [...] (154 aa)				•	•	•	•		0.961

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	226
PRK05888	164	PRK05888, PRK05888, NADH dehydrogenase subunit I;	6e-95
COG1143	172	COG1143, NuoI, Formate hydrogenlyase subunit 6/NAD	9e-66
TIGR01971	122	TIGR01971, NuoI, NADH-quinone oxidoreductase, chai	8e-65
PRK08222	181	PRK08222, PRK08222, hydrogenase 4 subunit H; Valid	3e-17
PRK12387	180	PRK12387, PRK12387, formate hydrogenlyase complex	4e-17
TIGR00403	183	TIGR00403, ndhI, NADH-plastoquinone oxidoreductase	4e-17
CHL00014	167	CHL00014, ndhI, NADH dehydrogenase subunit I	7e-16
pfam12838	48	pfam12838, Fer4_7, 4Fe-4S dicluster domain	1e-12
PRK13984	604	PRK13984, PRK13984, putative oxidoreductase; Provi	6e-12
PRK07118	280	PRK07118, PRK07118, ferredoxin; Validated	4e-11
COG1145	99	COG1145, NapF, Ferredoxin [Energy production and c	7e-11
TIGR02512	374	TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, grou	1e-10
PRK08348	120	PRK08348, PRK08348, NADH-plastoquinone oxidoreduct	3e-10
pfam13187	44	pfam13187, Fer4_9, 4Fe-4S dicluster domain	1e-09
pfam13484	67	pfam13484, Fer4_16, 4Fe-4S double cluster binding	2e-09
TIGR02179	78	TIGR02179, PorD_KorD, 2-oxoacid:acceptor oxidoredu	2e-09
pfam13237	51	pfam13237, Fer4_10, 4Fe-4S dicluster domain	4e-09
COG3383	978	COG3383, COG3383, Uncharacterized anaerobic dehydr	6e-09
TIGR02700	234	TIGR02700, flavo_MJ0208, archaeoflavoprotein, MJ02	6e-09
COG1146	68	COG1146, COG1146, Ferredoxin [Energy production an	8e-09
PRK06273	165	PRK06273, PRK06273, ferredoxin; Provisional	2e-08
COG1144	91	COG1144, COG1144, Pyruvate:ferredoxin oxidoreducta	2e-08
COG1149	284	COG1149, COG1149, MinD superfamily P-loop ATPase c	3e-08
TIGR04105	462	TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, gro	3e-08
COG2221	317	COG2221, DsrA, Dissimilatory sulfite reductase (de	7e-08
TIGR04105	462	TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, gro	8e-08
TIGR02494	295	TIGR02494, PFLE_PFLC, glycyl-radical enzyme activa	2e-07
PRK12771	564	PRK12771, PRK12771, putative glutamate synthase (N	2e-07
PRK13795	636	PRK13795, PRK13795, hypothetical protein; Provisio	3e-07
PRK14028	312	PRK14028, PRK14028, pyruvate ferredoxin oxidoreduc	4e-07
COG2768	354	COG2768, COG2768, Uncharacterized Fe-S center prot	4e-07
pfam00037	24	pfam00037, Fer4, 4Fe-4S binding domain	1e-06
COG0437	203	COG0437, HybA, Fe-S-cluster-containing hydrogenase	1e-06
COG1142	165	COG1142, HycB, Fe-S-cluster-containing hydrogenase	2e-06
COG1142	165	COG1142, HycB, Fe-S-cluster-containing hydrogenase	2e-06
pfam13183	54	pfam13183, Fer4_8, 4Fe-4S dicluster domain	5e-06
PRK09623	105	PRK09623, vorD, 2-ketoisovalerate ferredoxin oxido	8e-06
PRK09898	208	PRK09898, PRK09898, hypothetical protein; Provisio	1e-05
TIGR01944	165	TIGR01944, rnfB, electron transport complex, RnfAB	1e-05
COG0437	203	COG0437, HybA, Fe-S-cluster-containing hydrogenase	2e-05
TIGR03336	595	TIGR03336, IOR_alpha, indolepyruvate ferredoxin ox	2e-05
PRK08318	420	PRK08318, PRK08318, dihydropyrimidine dehydrogenas	2e-05
PRK07118	280	PRK07118, PRK07118, ferredoxin; Validated	5e-05
COG4231	640	COG4231, COG4231, Indolepyruvate ferredoxin oxidor	8e-05
pfam00037	24	pfam00037, Fer4, 4Fe-4S binding domain	1e-04
COG1142	165	COG1142, HycB, Fe-S-cluster-containing hydrogenase	1e-04
TIGR04003	314	TIGR04003, rSAM_BssD, [benzylsuccinate synthase]-a	1e-04
TIGR03224	411	TIGR03224, benzo_boxA, benzoyl-CoA oxygenase/reduc	1e-04
TIGR01944	165	TIGR01944, rnfB, electron transport complex, RnfAB	2e-04
COG1148	622	COG1148, HdrA, Heterodisulfide reductase, subunit	2e-04
COG1148	622	COG1148, HdrA, Heterodisulfide reductase, subunit	2e-04
PRK14993	244	PRK14993, PRK14993, tetrathionate reductase subuni	2e-04
PRK12769	654	PRK12769, PRK12769, putative oxidoreductase Fe-S b	2e-04
pfam13534	61	pfam13534, Fer4_17, 4Fe-4S dicluster domain	2e-04
pfam12837	24	pfam12837, Fer4_6, 4Fe-4S binding domain	2e-04
TIGR03294	228	TIGR03294, FrhG, coenzyme F420 hydrogenase, subuni	3e-04
TIGR04041	276	TIGR04041, activase_YjjW, glycine radical enzyme a	4e-04
COG1600	337	COG1600, COG1600, Uncharacterized Fe-S protein [En	4e-04
PRK06991	270	PRK06991, PRK06991, ferredoxin; Provisional	4e-04
COG1146	68	COG1146, COG1146, Ferredoxin [Energy production an	5e-04
COG1149	284	COG1149, COG1149, MinD superfamily P-loop ATPase c	5e-04
TIGR03287	391	TIGR03287, methan_mark_16, putative methanogenesis	5e-04
PRK09898	208	PRK09898, PRK09898, hypothetical protein; Provisio	6e-04
pfam13459	60	pfam13459, Fer4_15, 4Fe-4S single cluster domain	6e-04
COG0348	386	COG0348, NapH, Polyferredoxin [Energy production a	6e-04
TIGR02163	255	TIGR02163, napH_, ferredoxin-type protein, NapH/Ma	6e-04
TIGR04270	535	TIGR04270, Rama_corrin_act, methylamine methyltran	7e-04
pfam12837	24	pfam12837, Fer4_6, 4Fe-4S binding domain	8e-04
PRK09624	105	PRK09624, porD, pyuvate ferredoxin oxidoreductase	8e-04
PRK05113	191	PRK05113, PRK05113, electron transport complex pro	0.001
TIGR02486	314	TIGR02486, RDH, reductive dehalogenase	0.001
PRK09326	341	PRK09326, PRK09326, F420H2 dehydrogenase subunit F	0.001
pfam13484	67	pfam13484, Fer4_16, 4Fe-4S double cluster binding	0.002
COG2878	198	COG2878, COG2878, Predicted NADH:ubiquinone oxidor	0.002
COG2878	198	COG2878, COG2878, Predicted NADH:ubiquinone oxidor	0.002
PRK10330	181	PRK10330, PRK10330, formate dehydrogenase-H ferred	0.002
PRK06259	486	PRK06259, PRK06259, succinate dehydrogenase/fumara	0.002
PRK00941	781	PRK00941, PRK00941, acetyl-CoA decarbonylase/synth	0.002
COG1150	195	COG1150, HdrC, Heterodisulfide reductase, subunit	0.002
PRK07118	280	PRK07118, PRK07118, ferredoxin; Validated	0.003
PRK06991	270	PRK06991, PRK06991, ferredoxin; Provisional	0.003
TIGR00397	213	TIGR00397, mauM_napG, MauM/NapG family ferredoxin-	0.003
TIGR02745	434	TIGR02745, ccoG_rdxA_fixG, cytochrome c oxidase ac	0.003
TIGR02176	1165	TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flav	0.003
TIGR02060	132	TIGR02060, aprB, adenosine phosphosulphate reducta	0.003
PRK00783	263	PRK00783, PRK00783, DNA-directed RNA polymerase su	0.003
COG1034	693	COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone	0.004
TIGR02936	91	TIGR02936, fdxN_nitrog, ferredoxin III, nif-specif	0.004
PRK08764	135	PRK08764, PRK08764, ferredoxin; Provisional	0.004

>gnl|CDD|235637 PRK05888, PRK05888, NADH dehydrogenase subunit I; Provisional

 Score =  274 bits (702), Expect = 6e-95
 Identities = 109/159 (68%), Positives = 128/159 (80%)

Query: 68  FERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERC 127
            ++ +  + L E+++GLG+TLKYFF KKVTI YP EK PLSPRFRG HALRR P GEERC
Sbjct: 1   IKQYLKSMLLKELLKGLGVTLKYFFKKKVTIQYPEEKLPLSPRFRGRHALRRDPNGEERC 60

Query: 128 IACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF 187
           IACKLC A+CPA AITIEA EREDG RRTTRYDI+  +CI+CGFC+EACP DAIVE P+F
Sbjct: 61  IACKLCAAICPADAITIEAAEREDGRRRTTRYDINFGRCIFCGFCEEACPTDAIVETPDF 120

Query: 188 EYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
           E +TET EEL+YDKEKLL NGDR E EIA    +++ YR
Sbjct: 121 ELATETREELIYDKEKLLANGDRVEREIAPGKAADANYR 159

Length = 164

>gnl|CDD|224066 COG1143, NuoI, Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]

 Score =  200 bits (510), Expect = 9e-66
 Identities = 69/147 (46%), Positives = 91/147 (61%), Gaps = 6/147 (4%)

Query: 67  VFERSINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEER 126
             + +  + FL + ++GL  TLK  F K VTI YP EK PLSPRFRG H L R       
Sbjct: 2   KLKEAAKVKFLLDFLKGLWTTLKNLFKKPVTIEYPEEKIPLSPRFRGRHVLDRDK----- 56

Query: 127 CIACKLCEAVCPAQAITIEAEERE-DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 185
           CI C LC  +CPA AIT+E  ER+ DG ++  R DI++ +CI+CG C E CP  A+V  P
Sbjct: 57  CIGCGLCANICPANAITMETAERKVDGRKKPKRPDINLGRCIFCGLCVEVCPTGALVLTP 116

Query: 186 NFEYSTETHEELLYDKEKLLENGDRWE 212
            FE ++   E+L+YDKE+LL   D+ E
Sbjct: 117 EFELASYKREDLVYDKERLLAPPDKKE 143

Length = 172

>gnl|CDD|233661 TIGR01971, NuoI, NADH-quinone oxidoreductase, chain I

 Score =  196 bits (500), Expect = 8e-65
 Identities = 72/122 (59%), Positives = 82/122 (67%)

Query: 83  GLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAI 142
           GLGLTLKYFF K VT+ YP EK  L PRFRG   L R P GEE+CI C LC AVCPA AI
Sbjct: 1   GLGLTLKYFFSKPVTVQYPEEKLYLPPRFRGRIVLTRDPNGEEKCIGCTLCAAVCPADAI 60

Query: 143 TIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKE 202
            +   E EDG RR   Y I+  +CI+CG C+EACP DAIV  P FE +T T  +L+Y KE
Sbjct: 61  RVVPAEGEDGKRRLKFYQINFGRCIFCGLCEEACPTDAIVLTPEFELATYTRSDLVYGKE 120

Query: 203 KL 204
            L
Sbjct: 121 DL 122

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]. Length = 122

>gnl|CDD|181301 PRK08222, PRK08222, hydrogenase 4 subunit H; Validated

 Score = 75.9 bits (187), Expect = 3e-17
 Identities = 41/106 (38%), Positives = 58/106 (54%), Gaps = 10/106 (9%)

Query: 96  VTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRR 155
            T+ YPF    +SP FRG+  L        +CIAC  C   CPA A+TI+ ++ +  SR 
Sbjct: 14  ATVKYPFAPLEVSPGFRGKPDL-----MPSQCIACGACTCACPANALTIQTDD-QQNSRT 67

Query: 156 TTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDK 201
              + + + +CIYCG C+E CP  AI    NFE  T T++  LY +
Sbjct: 68  ---WQLYLGRCIYCGRCEEVCPTRAIQLTNNFEL-TVTNKADLYTR 109

Length = 181

>gnl|CDD|183492 PRK12387, PRK12387, formate hydrogenlyase complex iron-sulfur subunit; Provisional

 Score = 75.8 bits (187), Expect = 4e-17
 Identities = 35/132 (26%), Positives = 60/132 (45%), Gaps = 23/132 (17%)

Query: 80  MVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRG--EHALRRYPTGEERCIACKLCEAVC 137
           M + +   +K       T +YP E   +   FRG  E+         ++CI C  C   C
Sbjct: 1   MFKLIKKVIKT---GTATSSYPLEPIAVDKNFRGKPEYNP-------QQCIGCAACVNAC 50

Query: 138 PAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEEL 197
           P+ A+T+E +     +     ++ ++ +CI+CG C+E CP  AI     FE +       
Sbjct: 51  PSNALTVETDL----ATGELAWEFNLGRCIFCGRCEEVCPTAAIKLSQEFELA------- 99

Query: 198 LYDKEKLLENGD 209
           ++ KE LL+  +
Sbjct: 100 VWKKEDLLQQSE 111

Length = 180

>gnl|CDD|129498 TIGR00403, ndhI, NADH-plastoquinone oxidoreductase subunit I protein

 Score = 75.7 bits (186), Expect = 4e-17
 Identities = 43/124 (34%), Positives = 63/124 (50%), Gaps = 6/124 (4%)

Query: 82  RGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQA 141
           +G  +TL +     +TI YP+EK   S RFRG     R     ++CIAC++C  VCP   
Sbjct: 24  QGFAVTLDHMNRLPITIQYPYEKLIPSERFRG-----RIHFEFDKCIACEVCVRVCPINL 78

Query: 142 ITIEAEEREDGSRRTTR-YDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYD 200
             ++ E  +   ++  + Y ID   CI+CG C E CP + +     +E ST    EL YD
Sbjct: 79  PVVDWEFNKAIKKKQLKNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYD 138

Query: 201 KEKL 204
           +  L
Sbjct: 139 QIAL 142

[Energy metabolism, Electron transport]. Length = 183

>gnl|CDD|214334 CHL00014, ndhI, NADH dehydrogenase subunit I

 Score = 72.1 bits (177), Expect = 7e-16
 Identities = 43/121 (35%), Positives = 62/121 (51%), Gaps = 6/121 (4%)

Query: 82  RGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQA 141
           +G  +TL +     VTI YP+EK   S RFRG     R     ++CIAC++C  VCP   
Sbjct: 21  QGFMITLSHANRLPVTIQYPYEKLITSERFRG-----RIHFEFDKCIACEVCVRVCPIDL 75

Query: 142 ITIEAE-EREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYD 200
             ++ + E +   +R   Y ID   CI+CG C E CP + +     +E ST    EL Y+
Sbjct: 76  PVVDWKLETDIRKKRLLNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYN 135

Query: 201 K 201
           +
Sbjct: 136 Q 136

Length = 167

>gnl|CDD|221801 pfam12838, Fer4_7, 4Fe-4S dicluster domain

 Score = 60.3 bits (146), Expect = 1e-12
 Identities = 20/53 (37%), Positives = 24/53 (45%), Gaps = 5/53 (9%)

Query: 127 CIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD 179
           CI C  C   CP  AIT++ E  + G       +ID  KC  CG C   CP  
Sbjct: 1   CIGCGACVRACPYGAITLDEEGGKKG-----TVEIDPDKCTGCGACVAVCPTG 48

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. Length = 48

>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional

 Score = 64.0 bits (156), Expect = 6e-12
 Identities = 32/91 (35%), Positives = 44/91 (48%), Gaps = 9/91 (9%)

Query: 89  KYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAIT-IEAE 147
           K+ F K VTI  P  K   + R+RG H         E+CI C  C  +CP  AIT +E  
Sbjct: 14  KFLFRKPVTIKVPNVKREAAERYRGFHI-----NDWEKCIGCGTCSKICPTDAITMVEVP 68

Query: 148 E--REDGSRRTTRYDIDMTKCIYCGFCQEAC 176
           +  +E G  +  R  ID  +C +C  C + C
Sbjct: 69  DLPQEYGK-KPQRPVIDYGRCSFCALCVDIC 98

Length = 604

>gnl|CDD|235941 PRK07118, PRK07118, ferredoxin; Validated

 Score = 60.7 bits (148), Expect = 4e-11
 Identities = 24/60 (40%), Positives = 25/60 (41%), Gaps = 16/60 (26%)

Query: 127 CIACKLCEAVCPAQAITIE---AEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
           CI C  C   CPA AIT+E   A              ID  KC  CG C E CP  AI  
Sbjct: 215 CIGCGKCVKACPAGAITMENNLAV-------------IDQEKCTSCGKCVEKCPTKAIRI 261

Length = 280

>gnl|CDD|224068 COG1145, NapF, Ferredoxin [Energy production and conversion]

 Score = 56.8 bits (136), Expect = 7e-11
 Identities = 23/58 (39%), Positives = 28/58 (48%), Gaps = 5/58 (8%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            E+CI C LC  VCP  AI +  E             ID   C+ CG C + CPVDA+
Sbjct: 28  AEKCIGCGLCVKVCPTGAIELIEEGLLLP-----EVVIDPDLCVLCGACLKVCPVDAL 80

Length = 99

>gnl|CDD|233903 TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A

 Score = 60.0 bits (146), Expect = 1e-10
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 126 RCIACKLCEAVCPAQAIT--IEAEEREDGSRRTTRYD--IDMTKCIYCGFCQEACPVDAI 181
           +CI C  C   C    I   +    R   +    ++   +D + CI CG C   CPV AI
Sbjct: 8   KCIGCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLVCPVGAI 67

Query: 182 VEGPNFEYSTETHEELLYDKEKL 204
            E  +     +   + L D +K+
Sbjct: 68  TEKDH----VDRVLKALADPKKV 86

This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some heterogeneity in terms of periplasmic, cytosolic, or hydrogenosome location, NAD or NADP dependence, and overal protein protein length. Length = 374

>gnl|CDD|181399 PRK08348, PRK08348, NADH-plastoquinone oxidoreductase subunit; Provisional

 Score = 55.6 bits (134), Expect = 3e-10
 Identities = 27/106 (25%), Positives = 46/106 (43%), Gaps = 14/106 (13%)

Query: 88  LKYFFDKKVTINYP-FEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEA 146
           L+  F K  T  +P  E  P+   FRG+          ++C+ C++C  VCPA       
Sbjct: 9   LRNLFKKPATNLFPATEPVPVPEDFRGKILYDV-----DKCVGCRMCVTVCPAGVFVYLP 63

Query: 147 EEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTE 192
           E R        +  +   +C++CG C + CP  A+    +F  ++ 
Sbjct: 64  EIR--------KVALWTGRCVFCGQCVDVCPTGALQMSDDFLLASY 101

Length = 120

>gnl|CDD|221966 pfam13187, Fer4_9, 4Fe-4S dicluster domain

 Score = 51.9 bits (124), Expect = 1e-09
 Identities = 21/56 (37%), Positives = 25/56 (44%), Gaps = 12/56 (21%)

Query: 126 RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           +CI C  C  VCPA  I  +   +             + KCI CG C E CPV AI
Sbjct: 1   KCIGCGACVKVCPAGVIMRDNGGKV------------VVKCIGCGACVEVCPVGAI 44

Length = 44

>gnl|CDD|222168 pfam13484, Fer4_16, 4Fe-4S double cluster binding domain

 Score = 52.1 bits (125), Expect = 2e-09
 Identities = 22/65 (33%), Positives = 25/65 (38%), Gaps = 13/65 (20%)

Query: 126 RCIACKLCEAVCPAQAITIEAEEREDGSR-------RTTRYDIDMTKCI------YCGFC 172
            C  C  C   CP  AI+ E E   D  R           + ID  KC+       CG C
Sbjct: 1   FCGTCGKCADACPTGAISGEDEPTWDARRCISYNTIGKKGWIIDELKCLLGGRIYGCGIC 60

Query: 173 QEACP 177
           QE CP
Sbjct: 61  QEVCP 65

Length = 67

>gnl|CDD|131234 TIGR02179, PorD_KorD, 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 24/58 (41%), Positives = 27/58 (46%), Gaps = 9/58 (15%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           +E+CI CK C   CP  AI    +E E G        ID   C  CG C   CPV AI
Sbjct: 24  KEKCIKCKNCWLYCPEGAI----QEDEGGFVG-----IDYDYCKGCGICANVCPVKAI 72

A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of delta subunits, representing mostly pyruvate, 2-ketoisovalerate, and 2-oxoglutarate specific enzymes. The delta subunit is the smallest and resembles ferredoxins. Length = 78

>gnl|CDD|205417 pfam13237, Fer4_10, 4Fe-4S dicluster domain

 Score = 50.8 bits (121), Expect = 4e-09
 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 6/54 (11%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACP 177
            ++CI C  C A CPA+       +           +ID  +CI CG C E CP
Sbjct: 4   PDKCIGCGRCVAACPARVGAGAIRDEG------GAVEIDPDRCIGCGACVEVCP 51

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. Length = 51

>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]

 Score = 55.1 bits (133), Expect = 6e-09
 Identities = 42/160 (26%), Positives = 66/160 (41%), Gaps = 24/160 (15%)

Query: 77  LTEMVRGLGLT-LKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEA 135
           L  MV  LGLT  +Y +++K   N P+ K   +P +  +           +CI C  C  
Sbjct: 112 LHNMVMALGLTEQRYPYEEK---NPPYPKDESNPFYIYDPN---------QCILCGRCVE 159

Query: 136 VCP----AQAITIEAEEREDGSRRTTRYDIDMT--KCIYCGFCQEACPVDAIVEGP---N 186
            C      +A+TI+    ED  R     D+ +    C+ CG C   CPV+A++E      
Sbjct: 160 ACQEVQVNEALTID-WRGED-PRVIWDNDVPINESSCVSCGACVTVCPVNALMEKSMLGE 217

Query: 187 FEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
             Y T  +E+ L     L++  +     I      E+  R
Sbjct: 218 AGYLTGINEDTLEPMIDLVKKVEPEYGPIFAISEIEAAMR 257

Length = 978

>gnl|CDD|131747 TIGR02700, flavo_MJ0208, archaeoflavoprotein, MJ0208 family

 Score = 54.1 bits (130), Expect = 6e-09
 Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 10/69 (14%)

Query: 120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD 179
           Y    +RC  C +C   CP  AI               +  I + KC+ CG C+EACP +
Sbjct: 143 YMIDRKRCKGCGICVDACPRSAI----------DMVDGKAFIRLLKCVGCGKCKEACPYN 192

Query: 180 AIVEGPNFE 188
           AI  G  +E
Sbjct: 193 AIHGGLEYE 201

This model describes one of two paralogous families of archaealflavoprotein. The other, described by TIGR02699 and typified by the partially characterized AF1518 of Archaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown [Unknown function, General]. Length = 234

>gnl|CDD|224069 COG1146, COG1146, Ferredoxin [Energy production and conversion]

 Score = 50.2 bits (120), Expect = 8e-09
 Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            ++CI C +C  VCPA    +  +E                +CI CG C+ ACPV AI
Sbjct: 7   YDKCIGCGICVEVCPAGVFDLGEDEGGKP------VVARPEECIDCGLCELACPVGAI 58

Length = 68

>gnl|CDD|235764 PRK06273, PRK06273, ferredoxin; Provisional

 Score = 52.0 bits (125), Expect = 2e-08
 Identities = 31/86 (36%), Positives = 45/86 (52%), Gaps = 3/86 (3%)

Query: 124 EERCIACKLCEAVCPAQAIT---IEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
           EE CI C  C  VCP +AI    +E  +  +G  +T    ID  KC+YC +C + CPV A
Sbjct: 48  EELCIGCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCPVFA 107

Query: 181 IVEGPNFEYSTETHEELLYDKEKLLE 206
           +    +  +  +  E++  D  KLLE
Sbjct: 108 LFNEISPIHPRDVGEDIEVDVSKLLE 133

Length = 165

>gnl|CDD|224067 COG1144, COG1144, Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 25/59 (42%), Positives = 28/59 (47%), Gaps = 8/59 (13%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
           E++CI CKLC   CP  AI     E E G +    YD     C  CG C   CPV AI 
Sbjct: 34  EDKCINCKLCWLYCPEPAI----LEEEGGYKVRIDYD----YCKGCGICANVCPVKAIE 84

Length = 91

>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

 Score = 52.7 bits (127), Expect = 3e-08
 Identities = 19/72 (26%), Positives = 24/72 (33%), Gaps = 9/72 (12%)

Query: 114 EHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQ 173
                      E+CI C  C  VC   AI +    +           ++   C  CG C 
Sbjct: 58  VIRGEIPEIDPEKCIRCGKCAEVCRFGAIVVLPGGK---------PVLNPDLCEGCGACS 108

Query: 174 EACPVDAIVEGP 185
             CP  AI E P
Sbjct: 109 IVCPEPAIEEEP 120

Length = 284

>gnl|CDD|234472 TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3

 Score = 53.0 bits (128), Expect = 3e-08
 Identities = 24/57 (42%), Positives = 31/57 (54%), Gaps = 11/57 (19%)

Query: 127 CIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
           C+A   C  VCP  AI++        + R     ID  KCI CG C++ACP +AIVE
Sbjct: 116 CLA-HPCIEVCPKGAISM-------VNGRAY---IDQEKCIECGKCKKACPYNAIVE 161

See PMID:20395274 for descriptions of different groups. Length = 462

>gnl|CDD|225131 COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]

 Score = 51.6 bits (124), Expect = 7e-08
 Identities = 24/63 (38%), Positives = 28/63 (44%), Gaps = 11/63 (17%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
           EE C  C  C  VCP  AIT + ++            ID +KCI CG C  ACP  A   
Sbjct: 171 EELCRGCGKCVKVCPTGAITWDGKK----------LKIDGSKCIGCGKCIRACP-KAAFR 219

Query: 184 GPN 186
           G  
Sbjct: 220 GEK 222

Length = 317

>gnl|CDD|234472 TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3

 Score = 51.4 bits (124), Expect = 8e-08
 Identities = 22/51 (43%), Positives = 26/51 (50%), Gaps = 9/51 (17%)

Query: 133 CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
           CE  CP  AI+ +    E+G     R  ID  KCI CG C  ACP  AI +
Sbjct: 166 CEKACPVGAISSD----ENG-----RAVIDYDKCISCGACMVACPFGAISD 207

See PMID:20395274 for descriptions of different groups. Length = 462

>gnl|CDD|233895 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein family

 Score = 50.0 bits (120), Expect = 2e-07
 Identities = 24/58 (41%), Positives = 28/58 (48%), Gaps = 5/58 (8%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           E RC+ C  C  VCPA    +   E  DG     R  I   KC +CG C EACP  A+
Sbjct: 47  ENRCLGCGKCVEVCPAGTARLS--ELADGR---NRIIIRREKCTHCGKCTEACPSGAL 99

This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2,) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines. Length = 295

>gnl|CDD|237198 PRK12771, PRK12771, putative glutamate synthase (NADPH) small subunit; Provisional

 Score = 50.3 bits (121), Expect = 2e-07
 Identities = 21/59 (35%), Positives = 22/59 (37%), Gaps = 8/59 (13%)

Query: 127 CIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 185
           C  C  C   CP  AI      R        RY  D  KC  C  C + CP  AI  GP
Sbjct: 512 CFECDNCYGACPQDAIIKLGPGR--------RYHFDYDKCTGCHICADVCPCGAIEMGP 562

Length = 564

>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional

 Score = 50.0 bits (120), Expect = 3e-07
 Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 126 RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV 178
            C+ C +C   CP  AI IE  +R        +  +D  KCI+CG C E CPV
Sbjct: 582 ECVGCGVCVGACPTGAIRIEEGKR--------KISVDEEKCIHCGKCTEVCPV 626

Length = 636

>gnl|CDD|172522 PRK14028, PRK14028, pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional

 Score = 49.2 bits (117), Expect = 4e-07
 Identities = 25/60 (41%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 126 RCIACKLCEAVCPAQAITIEAEEREDGSR----RTTRYDIDMTKCIYCGFCQEACPVDAI 181
           +CI C+ C   CP  AI IEA    +G R    R    D D   C  CG C E CP  AI
Sbjct: 248 KCIMCRKCWLYCPDDAI-IEAWREAEGPRGRKFRMKMIDFDYQYCKGCGVCAEVCPTGAI 306

Length = 312

>gnl|CDD|225358 COG2768, COG2768, Uncharacterized Fe-S center protein [General function prediction only]

 Score = 49.4 bits (118), Expect = 4e-07
 Identities = 27/74 (36%), Positives = 34/74 (45%), Gaps = 14/74 (18%)

Query: 120 YPTG-EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV 178
            P   EE+C  C LC  +CP  AIT+         +      ID  KCI CG C EACP 
Sbjct: 187 KPVVVEEKCYDCGLCVKICPVGAITLT-----KVVK------IDYEKCIGCGQCMEACPY 235

Query: 179 DAIVEGPNFEYSTE 192
            A+    N+E  + 
Sbjct: 236 GAV--DQNWEEDSP 247

Length = 354

>gnl|CDD|215671 pfam00037, Fer4, 4Fe-4S binding domain

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 14/23 (60%), Positives = 14/23 (60%)

Query: 159 YDIDMTKCIYCGFCQEACPVDAI 181
             ID  KCI CG C E CPV AI
Sbjct: 1   VVIDEEKCIGCGACVEVCPVGAI 23

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. Length = 24

>gnl|CDD|223514 COG0437, HybA, Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]

 Score = 47.0 bits (112), Expect = 1e-06
 Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 21/71 (29%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQE 174
           ++ CI C  C A CP  A     ++              + KC +C           C E
Sbjct: 99  KDLCIGCGYCIAACPYGAPQFNPDKGV------------VDKCTFCVDRVAVGKLPACVE 146

Query: 175 ACPVDAIVEGP 185
           ACP  A++ G 
Sbjct: 147 ACPTGALIFGD 157

Length = 203

>gnl|CDD|224065 COG1142, HycB, Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 21/49 (42%), Positives = 25/49 (51%), Gaps = 10/49 (20%)

Query: 133 CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           C  VCP  AIT     R+DG+ +     +D  KCI C  C  ACP  AI
Sbjct: 61  CAEVCPVGAIT-----RDDGAVQ-----VDEEKCIGCKLCVVACPFGAI 99

Length = 165

>gnl|CDD|224065 COG1142, HycB, Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 22/65 (33%), Positives = 28/65 (43%), Gaps = 14/65 (21%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGF------CQEACP 177
           EE+CI CKLC   CP  AIT+        ++          KC  C        C EACP
Sbjct: 81  EEKCIGCKLCVVACPFGAITM--VSYPVAAKAV------AVKCDLCAGREVGPACVEACP 132

Query: 178 VDAIV 182
            +A+ 
Sbjct: 133 TEALE 137

Length = 165

>gnl|CDD|221963 pfam13183, Fer4_8, 4Fe-4S dicluster domain

 Score = 42.2 bits (99), Expect = 5e-06
 Identities = 20/55 (36%), Positives = 23/55 (41%), Gaps = 4/55 (7%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD 179
            +CI C  C AVCP       A  R  G  R      ++  C  CG C E CPV 
Sbjct: 3   SKCIRCGACRAVCPV----YRALGRFSGDPRGGALAAELWSCTSCGACTEVCPVG 53

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. Length = 54

>gnl|CDD|170016 PRK09623, vorD, 2-ketoisovalerate ferredoxin oxidoreductase subunit delta; Reviewed

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 22/58 (37%), Positives = 26/58 (44%), Gaps = 9/58 (15%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           E +C+ C +C   CP  AI I    +EDG        ID   C  CG C   CP  AI
Sbjct: 50  ESKCVKCYICWKFCPEPAIYI----KEDGY-----VAIDYDYCKGCGICANECPTKAI 98

Length = 105

>gnl|CDD|182135 PRK09898, PRK09898, hypothetical protein; Provisional

 Score = 44.4 bits (105), Expect = 1e-05
 Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 12/58 (20%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            +RCI C  C   CP    T+  E ++             +KC+ CG C  ACP  A+
Sbjct: 153 HKRCIGCSACTTACPWMMATVNTESKKS------------SKCVLCGECANACPTGAL 198

Length = 208

>gnl|CDD|233648 TIGR01944, rnfB, electron transport complex, RnfABCDGE type, B subunit

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 9/59 (15%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
           E+ CI C  C   CP  AI         G+ +     I   +C  C  C E CP D I 
Sbjct: 112 EDNCIGCTKCIQACPVDAIV--------GAAKAMHTVI-ADECTGCDLCVEPCPTDCIE 161

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]. Length = 165

>gnl|CDD|223514 COG0437, HybA, Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 21/59 (35%), Positives = 25/59 (42%), Gaps = 13/59 (22%)

Query: 128 IACKLCE-----AVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           I+C  CE      VCP  A+    E   DG        +D   CI CG+C  ACP  A 
Sbjct: 67  ISCMHCEDPPCVKVCPTGALFKREE---DGI-----VLVDKDLCIGCGYCIAACPYGAP 117

Length = 203

>gnl|CDD|234170 TIGR03336, IOR_alpha, indolepyruvate ferredoxin oxidoreductase, alpha subunit

 Score = 44.7 bits (106), Expect = 2e-05
 Identities = 26/76 (34%), Positives = 32/76 (42%), Gaps = 17/76 (22%)

Query: 110 RFRGEHALRRYP--TGEERCIACKLC--EAVCPAQAITIEAEEREDGSRRTTRYDIDMTK 165
                   R  P    +++CI CK C  E  CPA    IE E++E          ID   
Sbjct: 533 LSNKRAGKRAGPYKVDQDKCIGCKKCIKELGCPA----IEPEDKE--------AVIDPL- 579

Query: 166 CIYCGFCQEACPVDAI 181
           C  CG C + CP DAI
Sbjct: 580 CTGCGVCAQICPFDAI 595

Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase. Length = 595

>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B; Validated

 Score = 44.6 bits (106), Expect = 2e-05
 Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 10/63 (15%)

Query: 124 EERCIACKLCEAVC---PAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
           +++CI C  C   C     QAI  +    EDG+R     ++   +C+ C  C   CPV+ 
Sbjct: 341 QDKCIGCGRCYIACEDTSHQAIEWD----EDGTRT---PEVIEEECVGCNLCAHVCPVEG 393

Query: 181 IVE 183
            + 
Sbjct: 394 CIT 396

Length = 420

>gnl|CDD|235941 PRK07118, PRK07118, ferredoxin; Validated

 Score = 43.0 bits (102), Expect = 5e-05
 Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 124 EERCIACKLCEAVCPAQAIT-IEAEEREDGSRRTTRYDIDMTK-----CIYCGFCQEACP 177
           E++C  C  C   CP   I  I    R   +  +      + K     CI CG C +ACP
Sbjct: 167 EDKCTGCGACVKACPRNVIELIPKSARVFVACNSKDKGKAVKKVCEVGCIGCGKCVKACP 226

Query: 178 VDAIV 182
             AI 
Sbjct: 227 AGAIT 231

Length = 280

>gnl|CDD|226684 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]

 Score = 42.7 bits (101), Expect = 8e-05
 Identities = 25/75 (33%), Positives = 33/75 (44%), Gaps = 12/75 (16%)

Query: 112 RGEHALRRYPTGEERCIACKLC--EAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC 169
           RG     +Y   EE+C  C  C   + CP+  I  +   ++    R     ID + C  C
Sbjct: 564 RGGMKAPKYFVDEEKCTGCGDCIVLSGCPS--IEPDPTFKK---AR-----IDPSSCNGC 613

Query: 170 GFCQEACPVDAIVEG 184
           G C E CP  AI EG
Sbjct: 614 GSCVEVCPSFAIKEG 628

Length = 640

>gnl|CDD|215671 pfam00037, Fer4, 4Fe-4S binding domain

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 12/20 (60%), Positives = 13/20 (65%)

Query: 124 EERCIACKLCEAVCPAQAIT 143
           EE+CI C  C  VCP  AIT
Sbjct: 5   EEKCIGCGACVEVCPVGAIT 24

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. Length = 24

>gnl|CDD|224065 COG1142, HycB, Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 118 RRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMT--KCIYC--GFCQ 173
           R      E+CI C+ CE  C      I+++          + D +     C +C    C 
Sbjct: 3   RFIIADPEKCIGCRTCEVACVVAHEEIQSQSIFLPRIMVIKNDGESAPVVCHHCEDAPCA 62

Query: 174 EACPVDAIVEGPNF 187
           E CPV AI      
Sbjct: 63  EVCPVGAITRDDGA 76

Length = 165

>gnl|CDD|188518 TIGR04003, rSAM_BssD, [benzylsuccinate synthase]-activating enzyme

 Score = 41.8 bits (98), Expect = 1e-04
 Identities = 21/57 (36%), Positives = 25/57 (43%), Gaps = 5/57 (8%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
             RC+ C  C AVCPA    +      D S   T   +D TKC  C  C  AC  +A
Sbjct: 49  PNRCVGCGRCVAVCPAGTSRL-----VDNSDGRTIVVVDRTKCQRCMRCVAACLTEA 100

Members of this radical SAM protein family are [benzylsuccinate synthase]-activating enzyme, a glycyl radical active site-creating enzyme related to [pyruvate formate-lyase]-activating enzyme and additional uncharacterized homologs activating additional glycyl radical-containing enzymes [Protein fate, Protein modification and repair]. Length = 314

>gnl|CDD|132268 TIGR03224, benzo_boxA, benzoyl-CoA oxygenase/reductase, BoxA protein

 Score = 41.8 bits (98), Expect = 1e-04
 Identities = 19/57 (33%), Positives = 21/57 (36%), Gaps = 10/57 (17%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           E CI C  CE  CP  AIT +             Y +    C  C  C   CP  AI
Sbjct: 10  EICIRCNTCEETCPIDAITHD----------DRNYVVKADVCNGCMACVSPCPTGAI 56

Members of this protein family are BoxA, the A component of the BoxAB benzoyl-CoA oxygenase/reductase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. BoxA is a homodimeric iron-sulphur-flavoprotein and acts as an NADPH-dependent reductase for BoxB [Energy metabolism, Other]. Length = 411

>gnl|CDD|233648 TIGR01944, rnfB, electron transport complex, RnfABCDGE type, B subunit

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 161 IDMTKCIYCGFCQEACPVDAIVEGPNF 187
           ID   CI C  C +ACPVDAIV     
Sbjct: 110 IDEDNCIGCTKCIQACPVDAIVGAAKA 136

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]. Length = 165

>gnl|CDD|224070 COG1148, HdrA, Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 18/71 (25%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTR-------------YDIDMTKCIYCGF 171
           ++C  C  C  VCP     +E     +      +             Y+ID   CI CG 
Sbjct: 224 DKCTGCGACSEVCP-----VEVPNEFNEGLGKRKAIYIPFPQAVPLNYNIDPKHCIECGL 278

Query: 172 CQEACPVDAIV 182
           C++ACP +A+ 
Sbjct: 279 CEKACPNEAVD 289

Length = 622

>gnl|CDD|224070 COG1148, HdrA, Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]

 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 13/60 (21%)

Query: 122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
             E++C  C +C   CP  AI+++            + +++  +C  CG C  ACP  AI
Sbjct: 558 VDEDKCTGCGICAE-CPFGAISVD------------KAEVNPLRCKGCGICSAACPSGAI 604

Length = 622

>gnl|CDD|184955 PRK14993, PRK14993, tetrathionate reductase subunit B; Provisional

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 9/48 (18%)

Query: 133 CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
           C  VCP QA      +REDG        +D  +C+ C +C +ACP DA
Sbjct: 108 CVPVCPVQATF----QREDGI-----VVVDNKRCVGCAYCVQACPYDA 146

Length = 244

>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit; Reviewed

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 11/64 (17%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG------FCQEACP 177
           +++CI CK C   CP   + I       G  + T +     KC  C        C E CP
Sbjct: 84  QQKCIGCKSCVVACPFGTMQIVLTPVAAGKVKATAH-----KCDLCAGRENGPACVENCP 138

Query: 178 VDAI 181
            DA+
Sbjct: 139 ADAL 142

Length = 654

>gnl|CDD|222205 pfam13534, Fer4_17, 4Fe-4S dicluster domain

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 5/57 (8%)

Query: 126 RCIACKLCEAVCPAQAITIE-----AEEREDGSRRTTRYDIDMTKCIYCGFCQEACP 177
           RCI C  C  VCP+  +  +          +G       +     C  CG C+  CP
Sbjct: 1   RCIQCGYCVPVCPSYLLNGDEPKKLMRAAYNGDLEELLANEAADSCSECGLCEYVCP 57

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. Length = 61

>gnl|CDD|205098 pfam12837, Fer4_6, 4Fe-4S binding domain

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 12/21 (57%), Positives = 12/21 (57%)

Query: 161 IDMTKCIYCGFCQEACPVDAI 181
           ID  KCI CG C   CP  AI
Sbjct: 4   IDPDKCIGCGRCVAVCPEGAI 24

This 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. Length = 24

>gnl|CDD|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma

 Score = 40.2 bits (94), Expect = 3e-04
 Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 10/51 (19%)

Query: 127 CIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACP 177
           C+ C  C A CP +AI +     EDG     R +++  +CI CG C   CP
Sbjct: 176 CMGCGTCAAACPTRAIEM-----EDG-----RPNVNRDRCIKCGACYVQCP 216

This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (pfam00037) and scores above the trusted cutoff to model pfam01058 for the "NADH ubiquinone oxidoreductase, 20 Kd subunit" family. Length = 228

>gnl|CDD|188556 TIGR04041, activase_YjjW, glycine radical enzyme activase, YjjW family

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 10/52 (19%)

Query: 126 RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACP 177
            C  C  C A CPA A+++      DG      +D +  +CI C  C + CP
Sbjct: 42  HCDHCGDCVAGCPAGALSL-----VDGK---VVWDKE--RCIGCDTCIKVCP 83

Members of this family are radical SAM enzymes, designated YjjW in E. coli, that are paired with and appear to activate a glycyl radical enzyme of unknown function, designated YjjI. This activase and its target are found in Clostridial species as well as E. coli and cousins. Members of this family may be misannotated as pyruvate formate lyase activating enzyme [Protein fate, Protein modification and repair]. Length = 276

>gnl|CDD|224516 COG1600, COG1600, Uncharacterized Fe-S protein [Energy production and conversion]

 Score = 40.1 bits (94), Expect = 4e-04
 Identities = 19/69 (27%), Positives = 26/69 (37%), Gaps = 14/69 (20%)

Query: 121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDID-----------MTKCIY- 168
           P  E+ C +C  C   CP  A+   A    D  R  +   I+           +   IY 
Sbjct: 181 PEEEDHCGSCTRCLDACPTGALV--APYTVDARRCISYLTIEKGGAPEEFRPLIGNRIYG 238

Query: 169 CGFCQEACP 177
           C  CQ+ CP
Sbjct: 239 CDICQKVCP 247

Length = 337

>gnl|CDD|235903 PRK06991, PRK06991, ferredoxin; Provisional

 Score = 40.2 bits (94), Expect = 4e-04
 Identities = 26/75 (34%), Positives = 32/75 (42%), Gaps = 6/75 (8%)

Query: 112 RGEHALRRYPTGEERCIACKLCEAV-CPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG 170
            GE    R P G    IA +L   +  P   I ++     +  R      ID   CI C 
Sbjct: 37  AGEANYNRCPPGGAEGIA-RLAALLGKPV--IPLDPANGVERPRAVAV--IDEQLCIGCT 91

Query: 171 FCQEACPVDAIVEGP 185
            C +ACPVDAIV  P
Sbjct: 92  LCMQACPVDAIVGAP 106

Length = 270

>gnl|CDD|224069 COG1146, COG1146, Ferredoxin [Energy production and conversion]

 Score = 37.1 bits (86), Expect = 5e-04
 Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 2/39 (5%)

Query: 111 FRGEHALRRYPTG--EERCIACKLCEAVCPAQAITIEAE 147
           F         P     E CI C LCE  CP  AI ++  
Sbjct: 25  FDLGEDEGGKPVVARPEECIDCGLCELACPVGAIKVDIL 63

Length = 68

>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 18/42 (42%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 145 EAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 186
           E  E E+   R    +ID  KCI CG C E C   AIV  P 
Sbjct: 51  EVLEEEE-VIRGEIPEIDPEKCIRCGKCAEVCRFGAIVVLPG 91

Length = 284

>gnl|CDD|234157 TIGR03287, methan_mark_16, putative methanogenesis marker 16 metalloprotein

 Score = 40.1 bits (94), Expect = 5e-04
 Identities = 21/64 (32%), Positives = 26/64 (40%), Gaps = 15/64 (23%)

Query: 119 RYPTGEERCIACKLC--EAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEAC 176
           R     ERC  C  C  E  CP  AI      ++DG        ++   C  CG+C E C
Sbjct: 296 RPKYNPERCENCDPCLVEEACPVPAI------KKDG-------TLNTEDCFGCGYCAEIC 342

Query: 177 PVDA 180
           P  A
Sbjct: 343 PGGA 346

Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (pfam00037), with each copy having four Cys residues invariant across all members [Energy metabolism, Methanogenesis]. Length = 391

>gnl|CDD|182135 PRK09898, PRK09898, hypothetical protein; Provisional

 Score = 39.4 bits (92), Expect = 6e-04
 Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 10/55 (18%)

Query: 125 ERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACP 177
           + C  CK   C  VCP  AIT + +E   G        +D  +CI C  C  ACP
Sbjct: 121 DTCRQCKEPQCMNVCPIGAITWQQKE---GC-----ITVDHKRCIGCSACTTACP 167

Length = 208

>gnl|CDD|222145 pfam13459, Fer4_15, 4Fe-4S single cluster domain

 Score = 36.9 bits (86), Expect = 6e-04
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 15/65 (23%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRT---TRYDIDMTKCIYCGFCQEA---CP 177
            + CI C LC A+ P     +   + +  +R          D+ +       QEA   CP
Sbjct: 4   RDTCIGCGLCVALAP----DVFELDEDGKARVILDEGEVPDDLEEDA-----QEAADACP 54

Query: 178 VDAIV 182
           VDAI 
Sbjct: 55  VDAIH 59

Length = 60

>gnl|CDD|223425 COG0348, NapH, Polyferredoxin [Energy production and conversion]

 Score = 40.1 bits (94), Expect = 6e-04
 Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 13/63 (20%)

Query: 124 EERCIA-CKLCEAVCPAQ---AITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD 179
           ++R    CK C+ VCP      + +     +           D  +CI CG C +AC  D
Sbjct: 210 DKRGCPRCKRCKKVCPEPIPLWVQVCPAGIDIR---------DGLECIGCGRCIDACDDD 260

Query: 180 AIV 182
            + 
Sbjct: 261 MLK 263

Length = 386

>gnl|CDD|233754 TIGR02163, napH_, ferredoxin-type protein, NapH/MauN family

 Score = 39.3 bits (92), Expect = 6e-04
 Identities = 17/70 (24%), Positives = 26/70 (37%), Gaps = 12/70 (17%)

Query: 122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           +  E+C  C  C  VCP   + +    ++ GS      D     C  CG C + C  D  
Sbjct: 198 SDREKCTNCMDCFNVCPEPQV-LRMPLKKGGSTLVLSGD-----CTLCGRCIDVCHEDV- 250

Query: 182 VEGPNFEYST 191
                  ++T
Sbjct: 251 -----LGFTT 255

Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase. Length = 255

>gnl|CDD|211993 TIGR04270, Rama_corrin_act, methylamine methyltransferase corrinoid protein reductive activase

 Score = 39.7 bits (93), Expect = 7e-04
 Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 7/57 (12%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           E CIAC+ C   CP +A++I   E         R D D      C  C+  CP    
Sbjct: 479 EGCIACQKCVKECPGKALSILESEP-------PRIDTDRCLGTACRRCERVCPEKVF 528

Members of this family occur as paralogs in species capable of generating methane from mono-, di-, and tri-methylamine. Members include RamA (Reductive Activation of Methyltransfer, Amines) from Methanosarcina barkeri MS (DSM 800). Member proteins have two C-terminal motifs with four Cys each, likely to bind one 4Fe-4S cluster per motif. Length = 535

>gnl|CDD|205098 pfam12837, Fer4_6, 4Fe-4S binding domain

 Score = 35.3 bits (82), Expect = 8e-04
 Identities = 10/19 (52%), Positives = 12/19 (63%)

Query: 124 EERCIACKLCEAVCPAQAI 142
            ++CI C  C AVCP  AI
Sbjct: 6   PDKCIGCGRCVAVCPEGAI 24

This 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. Length = 24

>gnl|CDD|170017 PRK09624, porD, pyuvate ferredoxin oxidoreductase subunit delta; Reviewed

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 11/60 (18%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDI-DMTKCIYCGFCQEACPVDAIV 182
            ++C+ C LC   CP  AI ++ E           Y + D   C  CG C   CP  AI 
Sbjct: 50  RDKCVRCYLCYIYCPEPAIYLDEEG----------YPVFDYDYCKGCGICANECPTKAIE 99

Length = 105

>gnl|CDD|235347 PRK05113, PRK05113, electron transport complex protein RnfB; Provisional

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 14/22 (63%), Positives = 15/22 (68%)

Query: 161 IDMTKCIYCGFCQEACPVDAIV 182
           ID   CI C  C +ACPVDAIV
Sbjct: 111 IDEDNCIGCTKCIQACPVDAIV 132

Length = 191

>gnl|CDD|233890 TIGR02486, RDH, reductive dehalogenase

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 17/71 (23%), Positives = 20/71 (28%), Gaps = 20/71 (28%)

Query: 127 CIACKLCEAVCPAQAITIEAEEREDGSRRTTRYD----------IDMTKC---------- 166
           C  C  C   CP+ AI+   E   D                    D  +C          
Sbjct: 207 CETCGKCADECPSGAISKGGEPTWDPEDSNGDPPGENNPGLKWQYDGWRCLLFRCYNEGG 266

Query: 167 IYCGFCQEACP 177
             CG CQ  CP
Sbjct: 267 GGCGVCQAVCP 277

This model represents a family of corrin and 8-iron Fe-S cluster-containing reductive dehalogenases found primarily in halorespiring microorganisms such as dehalococcoides ethenogenes which contains as many as 17 enzymes of this type with varying substrate ranges. One example of a characterized species is the tetrachloroethene reductive dehalogenase (1.97.1.8) which also acts on trichloroethene converting it to dichloroethene. Length = 314

>gnl|CDD|181779 PRK09326, PRK09326, F420H2 dehydrogenase subunit F; Provisional

 Score = 38.7 bits (90), Expect = 0.001
 Identities = 23/60 (38%), Positives = 27/60 (45%), Gaps = 3/60 (5%)

Query: 127 CIACKLCEAVCPAQAITIE--AEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVE 183
           C AC  CEAVCP  AIT++  AE R+               C  C  C   CPV D  +E
Sbjct: 14  CTACGACEAVCPIGAITVDKKAEIRDPNDLELYEKGAAPNVCEGCLTCSRICPVVDGYIE 73

Length = 341

>gnl|CDD|222168 pfam13484, Fer4_16, 4Fe-4S double cluster binding domain

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 9/25 (36%), Positives = 11/25 (44%)

Query: 165 KCIYCGFCQEACPVDAIVEGPNFEY 189
            C  CG C +ACP  AI       +
Sbjct: 1   FCGTCGKCADACPTGAISGEDEPTW 25

Length = 67

>gnl|CDD|225433 COG2878, COG2878, Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 161 IDMTKCIYCGFCQEACPVDAIVEGPNF 187
           ID   CI C  C +ACPVDAIV     
Sbjct: 112 IDEANCIGCTKCIQACPVDAIVGATKA 138

Length = 198

>gnl|CDD|225433 COG2878, COG2878, Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 21/80 (26%), Positives = 24/80 (30%), Gaps = 29/80 (36%)

Query: 124 EERCIACKLCEAVCPAQAI--------TIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEA 175
           E  CI C  C   CP  AI        T+ A+                  C  C  C   
Sbjct: 114 EANCIGCTKCIQACPVDAIVGATKAMHTVIADL-----------------CTGCDLCVAP 156

Query: 176 CPVDAIVEGPNFEYSTETHE 195
           CP D I   P      ET +
Sbjct: 157 CPTDCIEMQP----VAETPD 172

Length = 198

>gnl|CDD|182382 PRK10330, PRK10330, formate dehydrogenase-H ferredoxin subunit; Provisional

 Score = 37.9 bits (88), Expect = 0.002
 Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 9/68 (13%)

Query: 124 EERCIACKLCEAVCP--AQAITIEAEEREDGSRRTTR-YDIDMTKCIYCGF------CQE 174
           +ERCI CK C   CP  A  + +    R  G+    R    +  KC  C        C  
Sbjct: 86  QERCIGCKTCVVACPYGAMEVVVRPVIRNSGAGLNVRAEKAEANKCDLCNHREDGPACMA 145

Query: 175 ACPVDAIV 182
           ACP  A++
Sbjct: 146 ACPTHALI 153

Length = 181

>gnl|CDD|235756 PRK06259, PRK06259, succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Provisional

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 13/64 (20%)

Query: 127 CIACKLCEAVCPAQAIT-------------IEAEEREDGSRRTTRYDIDMTKCIYCGFCQ 173
           CI C  C + CPA+ ++                + R++G R    +D  +  C  CG C 
Sbjct: 135 CIECLSCVSTCPARKVSDYPGPTFMRQLARFAFDPRDEGDREKEAFDEGLYNCTTCGKCV 194

Query: 174 EACP 177
           E CP
Sbjct: 195 EVCP 198

Length = 486

>gnl|CDD|179174 PRK00941, PRK00941, acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 26/77 (33%), Positives = 35/77 (45%), Gaps = 17/77 (22%)

Query: 112 RGEHALRRYPTGEE------RCIACKLCEAVCPA-----QAITIEAEEREDGSRRTTRYD 160
           R    ++  PT EE      +C  C  C  VCP      +A+  EA  + D S+    YD
Sbjct: 385 RKAKGIKALPTDEELKELAKKCTECGWCVRVCPNELPIPEAM--EAAAKGDLSKLEDLYD 442

Query: 161 IDMTKCIYCGFCQEACP 177
               KCI CG C++ CP
Sbjct: 443 ----KCIGCGRCEQVCP 455

Length = 781

>gnl|CDD|224072 COG1150, HdrC, Heterodisulfide reductase, subunit C [Energy production and conversion]

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 27/121 (22%), Positives = 38/121 (31%), Gaps = 37/121 (30%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEERED-GSRRTTRY-----------DIDMTKCIYCGFC 172
           E C  C  C   CP+           D   R+  R               +  C+ C  C
Sbjct: 39  EGCYQCGTCTGSCPSG-------RFTDYSPRKIIRKARLGLVDLILSSESLWACVTCYTC 91

Query: 173 QEACPVD-------------AIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENL 219
            E CP               A+ EG   E   + H E+L   E ++  G+     I + L
Sbjct: 92  TERCPRGVKIVEVVKALRNIAVKEG-LIEPMLKAHREVL---ETVITTGNHA-VPINKEL 146

Query: 220 R 220
           R
Sbjct: 147 R 147

Length = 195

>gnl|CDD|235941 PRK07118, PRK07118, ferredoxin; Validated

 Score = 37.6 bits (88), Expect = 0.003
 Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 10/56 (17%)

Query: 127 CIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
           C+    C A CP  AI IE     +G        +D  KC  CG C +ACP + I 
Sbjct: 141 CLGLGSCVAACPFDAIHIE-----NGLPV-----VDEDKCTGCGACVKACPRNVIE 186

Length = 280

>gnl|CDD|235903 PRK06991, PRK06991, ferredoxin; Provisional

 Score = 37.5 bits (87), Expect = 0.003
 Identities = 20/66 (30%), Positives = 23/66 (34%), Gaps = 25/66 (37%)

Query: 124 EERCIACKLCEAVCPAQAI--------TIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEA 175
           E+ CI C LC   CP  AI        T+ A+                  C  C  C   
Sbjct: 84  EQLCIGCTLCMQACPVDAIVGAPKQMHTVLADL-----------------CTGCDLCVPP 126

Query: 176 CPVDAI 181
           CPVD I
Sbjct: 127 CPVDCI 132

Length = 270

>gnl|CDD|129492 TIGR00397, mauM_napG, MauM/NapG family ferredoxin-type protein

 Score = 37.2 bits (86), Expect = 0.003
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 123 GEERCI-----ACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEAC 176
           G E C+      C +C  VCP +   I  +  E+   R     +D  KC  CG C++ C
Sbjct: 129 GHETCLNYKGLNCSICVRVCPIRGEAISLKPIENERGRLQIPTVDSAKCTGCGTCEKHC 187

MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar [Energy metabolism, Electron transport]. Length = 213

>gnl|CDD|233993 TIGR02745, ccoG_rdxA_fixG, cytochrome c oxidase accessory protein FixG

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 29/87 (33%), Positives = 38/87 (43%), Gaps = 19/87 (21%)

Query: 92  FDKK-VTINYPFEKG-PLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEER 149
           FDK  + + Y  ++G P  PR   +      P G+  CI C LC  VCP   I I     
Sbjct: 198 FDKDTLIVVYDEKRGEPRGPRKGKKDPKAPGPLGD--CIDCNLCVQVCPT-GIDI----- 249

Query: 150 EDGSRRTTRYDIDMTKCIYCGFCQEAC 176
            DG +          +CI CG C +AC
Sbjct: 250 RDGLQ---------LECINCGLCIDAC 267

Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum. Length = 434

>gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 20/70 (28%), Positives = 24/70 (34%), Gaps = 17/70 (24%)

Query: 125 ERCIACKLCEAVCPAQAITI---EAEEREDGSRRTT--------------RYDIDMTKCI 167
           + CI C  C  VCP  AI     + EE E+                    R  I    C 
Sbjct: 683 DNCIQCNQCAFVCPHAAIRPKLADEEELENAPAGFKSLDAKGKELEGMKFRIQISPLDCT 742

Query: 168 YCGFCQEACP 177
            CG C + CP
Sbjct: 743 GCGNCVDICP 752

This model represents a single chain form of pyruvate:ferredoxin (or flavodoxin) oxidoreductase. This enzyme may transfer electrons to nitrogenase in nitrogen-fixing species. Portions of this protein are homologous to gamma subunit of the four subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase. Length = 1165

>gnl|CDD|131115 TIGR02060, aprB, adenosine phosphosulphate reductase, beta subunit

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 12/71 (16%)

Query: 125 ERCIACKL-----CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD 179
            +C  CK      C  +CP   + ++ E  +        Y+I+   C  C  C +ACP  
Sbjct: 8   TKCDGCKAGEKTACVYICPNDLMHLDTEIMK-------AYNIEPDMCWECYSCVKACPQG 60

Query: 180 AIVEGPNFEYS 190
           AI      +++
Sbjct: 61  AIDVRGYADFA 71

During dissimilatory sulfate reduction and sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the beta subunit of APS reductase, sharing common evolutionary origin with other iron-sulfur cluster-binding proteins [Central intermediary metabolism, Sulfur metabolism]. Length = 132

>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D; Provisional

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 20/82 (24%), Positives = 28/82 (34%), Gaps = 20/82 (24%)

Query: 114 EHA---------LRRYP--TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDID 162
           EHA          + YP     E C  C+ C   CP   + ++  +             D
Sbjct: 147 EHAKWQPGSACGYKYYPRIEVSEDCDECEKCVEACPRGVLELKEGKLVVT---------D 197

Query: 163 MTKCIYCGFCQEACPVDAIVEG 184
           +  C  C  C+ ACP  AI   
Sbjct: 198 LLNCSLCKLCERACPGKAIRVS 219

Length = 263

>gnl|CDD|223965 COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 18/67 (26%), Positives = 25/67 (37%), Gaps = 4/67 (5%)

Query: 125 ERCIACKLCEAVCP--AQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
            RCI C  C   C   A    +   +R   +     Y     +   CG C + CPV A+ 
Sbjct: 144 NRCILCTRCVRFCKEIAGTHELGVIKR-GENSEIGTYLDQPLESELCGNCVDVCPVGALT 202

Query: 183 EGPNFEY 189
             P F +
Sbjct: 203 SKP-FAF 208

Length = 693

>gnl|CDD|234064 TIGR02936, fdxN_nitrog, ferredoxin III, nif-specific

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 10/67 (14%)

Query: 124 EERCIACKLCEAVCPAQAITIEA----------EEREDGSRRTTRYDIDMTKCIYCGFCQ 173
           +E+CI C  C  VC    +T++           ++ +D   R      +   CI CG C 
Sbjct: 20  QEKCIGCGRCYKVCGRDVLTLKGINEEGELVASDDDDDEIERKVMVVANPGNCIGCGACA 79

Query: 174 EACPVDA 180
             CP   
Sbjct: 80  RVCPKKC 86

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]. Length = 91

>gnl|CDD|181550 PRK08764, PRK08764, ferredoxin; Provisional

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 24/74 (32%), Positives = 28/74 (37%), Gaps = 10/74 (13%)

Query: 110 RFRGEHALRRYP-TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIY 168
           R RG H L +     E  CI C  C   CP  AI   A+           + +    C  
Sbjct: 69  RSRGTHKLPQVAWIVEADCIGCTKCIQACPVDAIVGGAKHM---------HTVIAPLCTG 119

Query: 169 CGFCQEACPVDAIV 182
           C  C  ACPVD I 
Sbjct: 120 CELCVPACPVDCIE 133

Length = 135

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	226
KOG3256	212	consensus NADH:ubiquinone oxidoreductase, NDUFS8/2	100.0
COG1143	172	NuoI Formate hydrogenlyase subunit 6/NADH:ubiquino	99.93
PRK05888	164	NADH dehydrogenase subunit I; Provisional	99.79
TIGR00403	183	ndhI NADH-plastoquinone oxidoreductase subunit I p	99.78
TIGR01971	122	NuoI NADH-quinone oxidoreductase, chain I. This mo	99.7
CHL00014	167	ndhI NADH dehydrogenase subunit I	99.66
PRK08348	120	NADH-plastoquinone oxidoreductase subunit; Provisi	99.54
PRK08222	181	hydrogenase 4 subunit H; Validated	99.47
PRK12387	180	formate hydrogenlyase complex iron-sulfur subunit;	99.44
PF14697	59	Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE	99.37
COG1148	622	HdrA Heterodisulfide reductase, subunit A and rela	99.31
PF13187	55	Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_	99.31
PF12838	52	Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR0014	99.27
COG4231	640	Indolepyruvate ferredoxin oxidoreductase, alpha an	99.25
PRK13984	604	putative oxidoreductase; Provisional	99.19
COG1144	91	Pyruvate:ferredoxin oxidoreductase and related 2-o	99.18
PRK09624	105	porD pyuvate ferredoxin oxidoreductase subunit del	99.15
PRK06273	165	ferredoxin; Provisional	99.15
TIGR02936	91	fdxN_nitrog ferredoxin III, nif-specific. Members	99.14
TIGR02179	78	PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta	99.14
PRK06991	270	ferredoxin; Provisional	99.09
PF13237	52	Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A.	99.06
CHL00065	81	psaC photosystem I subunit VII	99.05
PLN00071	81	photosystem I subunit VII; Provisional	99.04
PRK09623	105	vorD 2-ketoisovalerate ferredoxin oxidoreductase s	99.04
PRK09626	103	oorD 2-oxoglutarate-acceptor oxidoreductase subuni	99.03
PRK09625	133	porD pyruvate flavodoxin oxidoreductase subunit de	99.0
COG1146	68	Ferredoxin [Energy production and conversion]	99.0
TIGR03048	80	PS_I_psaC photosystem I iron-sulfur protein PsaC.	99.0
TIGR02060	132	aprB adenosine phosphosulphate reductase, beta sub	98.99
TIGR02163	255	napH_ ferredoxin-type protein, NapH/MauN family. M	98.97
COG1145	99	NapF Ferredoxin [Energy production and conversion]	98.96
PRK02651	81	photosystem I subunit VII; Provisional	98.96
PRK05113	191	electron transport complex protein RnfB; Provision	98.96
PRK09477	271	napH quinol dehydrogenase membrane component; Prov	98.96
TIGR01944	165	rnfB electron transport complex, RnfABCDGE type, B	98.94
TIGR02494	295	PFLE_PFLC glycyl-radical enzyme activating protein	98.91
COG1149	284	MinD superfamily P-loop ATPase containing an inser	98.9
PRK05035	695	electron transport complex protein RnfC; Provision	98.88
TIGR02700	234	flavo_MJ0208 archaeoflavoprotein, MJ0208 family. T	98.87
PRK14028	312	pyruvate ferredoxin oxidoreductase subunit gamma/d	98.85
TIGR00402	101	napF ferredoxin-type protein NapF. The gene codes	98.85
COG3383	978	Uncharacterized anaerobic dehydrogenase [General f	98.84
PRK08764	135	ferredoxin; Provisional	98.82
PRK07569	234	bidirectional hydrogenase complex protein HoxU; Va	98.8
COG2768	354	Uncharacterized Fe-S center protein [General funct	98.77
PF13247	98	Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX	98.74
TIGR03149	225	cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S	98.72
TIGR02512	374	Fe_only_hydrog hydrogenases, Fe-only. This model d	98.72
TIGR02912	314	sulfite_red_C sulfite reductase, subunit C. Member	98.72
PRK10194	163	ferredoxin-type protein; Provisional	98.71
PRK09898	208	hypothetical protein; Provisional	98.7
COG0437	203	HybA Fe-S-cluster-containing hydrogenase component	98.7
TIGR03224	411	benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA p	98.69
PRK10194	163	ferredoxin-type protein; Provisional	98.69
PF13484	67	Fer4_16: 4Fe-4S double cluster binding domain	98.68
PRK14993	244	tetrathionate reductase subunit B; Provisional	98.68
PF13247	98	Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX	98.68
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	98.67
TIGR02176	1165	pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxid	98.66
TIGR01660	492	narH nitrate reductase, beta subunit. The Nitrate	98.65
COG1142	165	HycB Fe-S-cluster-containing hydrogenase component	98.64
COG4656	529	RnfC Predicted NADH:ubiquinone oxidoreductase, sub	98.61
PRK08493	819	NADH dehydrogenase subunit G; Validated	98.61
PRK07118	280	ferredoxin; Validated	98.61
TIGR03478	321	DMSO_red_II_bet DMSO reductase family type II enzy	98.61
PF13183	57	Fer4_8: 4Fe-4S dicluster domain; PDB: 2BS4_B 1E7P_	98.6
TIGR03478	321	DMSO_red_II_bet DMSO reductase family type II enzy	98.6
COG1148	622	HdrA Heterodisulfide reductase, subunit A and rela	98.59
PRK10882	328	hydrogenase 2 protein HybA; Provisional	98.57
COG2221	317	DsrA Dissimilatory sulfite reductase (desulfovirid	98.57
TIGR03149	225	cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S	98.57
PRK10330	181	formate dehydrogenase-H ferredoxin subunit; Provis	98.56
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	98.55
TIGR03287	391	methan_mark_16 putative methanogenesis marker 16 m	98.53
COG2878	198	Predicted NADH:ubiquinone oxidoreductase, subunit	98.52
PRK08318	420	dihydropyrimidine dehydrogenase subunit B; Validat	98.52
TIGR00397	213	mauM_napG MauM/NapG family ferredoxin-type protein	98.51
COG0437	203	HybA Fe-S-cluster-containing hydrogenase component	98.51
TIGR02951	161	DMSO_dmsB DMSO reductase, iron-sulfur subunit. Thi	98.49
PRK07118	280	ferredoxin; Validated	98.49
TIGR00397	213	mauM_napG MauM/NapG family ferredoxin-type protein	98.49
TIGR01582	283	FDH-beta formate dehydrogenase, beta subunit, Fe-S	98.48
TIGR00384	220	dhsB succinate dehydrogenase and fumarate reductas	98.46
PRK14993	244	tetrathionate reductase subunit B; Provisional	98.44
TIGR01973	603	NuoG NADH-quinone oxidoreductase, chain G. This mo	98.44
TIGR01582	283	FDH-beta formate dehydrogenase, beta subunit, Fe-S	98.44
COG0479	234	FrdB Succinate dehydrogenase/fumarate reductase, F	98.43
PRK09476	254	napG quinol dehydrogenase periplasmic component; P	98.42
PRK09898	208	hypothetical protein; Provisional	98.42
PRK09129	776	NADH dehydrogenase subunit G; Validated	98.41
TIGR03294	228	FrhG coenzyme F420 hydrogenase, subunit gamma. Thi	98.4
TIGR01660	492	narH nitrate reductase, beta subunit. The Nitrate	98.39
PLN00129	276	succinate dehydrogenase [ubiquinone] iron-sulfur s	98.39
PRK12575	235	succinate dehydrogenase iron-sulfur subunit; Provi	98.39
TIGR03315	1012	Se_ygfK putative selenate reductase, YgfK subunit.	98.38
PRK09326	341	F420H2 dehydrogenase subunit F; Provisional	98.37
PRK12576	279	succinate dehydrogenase iron-sulfur subunit; Provi	98.36
PF12837	24	Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450	98.36
PRK13795	636	hypothetical protein; Provisional	98.35
TIGR02951	161	DMSO_dmsB DMSO reductase, iron-sulfur subunit. Thi	98.33
PRK09476	254	napG quinol dehydrogenase periplasmic component; P	98.33
PRK08640	249	sdhB succinate dehydrogenase iron-sulfur subunit;	98.33
PRK13552	239	frdB fumarate reductase iron-sulfur subunit; Provi	98.32
PRK10882	328	hydrogenase 2 protein HybA; Provisional	98.32
PRK10330	181	formate dehydrogenase-H ferredoxin subunit; Provis	98.31
PRK12386	251	fumarate reductase iron-sulfur subunit; Provisiona	98.31
PTZ00305	297	NADH:ubiquinone oxidoreductase; Provisional	98.31
PRK07570	250	succinate dehydrogenase/fumarate reductase iron-su	98.31
PF00037	24	Fer4: 4Fe-4S binding domain; InterPro: IPR001450 T	98.3
PRK12769	654	putative oxidoreductase Fe-S binding subunit; Revi	98.3
PRK07860	797	NADH dehydrogenase subunit G; Validated	98.3
PRK08166	847	NADH dehydrogenase subunit G; Validated	98.29
PRK09853	1019	putative selenate reductase subunit YgfK; Provisio	98.29
PRK12771	564	putative glutamate synthase (NADPH) small subunit;	98.29
PRK09130	687	NADH dehydrogenase subunit G; Validated	98.29
PRK12385	244	fumarate reductase iron-sulfur subunit; Provisiona	98.28
PRK15449	95	ferredoxin-like protein FixX; Provisional	98.28
PF12837	24	Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450	98.26
PRK12577	329	succinate dehydrogenase iron-sulfur subunit; Provi	98.26
TIGR02066	341	dsrB sulfite reductase, dissimilatory-type beta su	98.25
COG1142	165	HycB Fe-S-cluster-containing hydrogenase component	98.24
TIGR03290	144	CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, s	98.24
TIGR01945	435	rnfC electron transport complex, RnfABCDGE type, C	98.22
TIGR03336	595	IOR_alpha indolepyruvate ferredoxin oxidoreductase	98.19
PRK12809	639	putative oxidoreductase Fe-S binding subunit; Revi	98.16
PRK05950	232	sdhB succinate dehydrogenase iron-sulfur subunit;	98.15
COG1034	693	NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreduc	98.1
PRK12769	654	putative oxidoreductase Fe-S binding subunit; Revi	98.1
PF00037	24	Fer4: 4Fe-4S binding domain; InterPro: IPR001450 T	98.07
PRK12809	639	putative oxidoreductase Fe-S binding subunit; Revi	98.06
PF13534	61	Fer4_17: 4Fe-4S dicluster domain; PDB: 1ZOY_B 3AE9	98.06
TIGR02745	434	ccoG_rdxA_fixG cytochrome c oxidase accessory prot	98.02
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	98.01
TIGR00314	784	cdhA CO dehydrogenase/acetyl-CoA synthase complex,	97.97
PRK00941	781	acetyl-CoA decarbonylase/synthase complex subunit	97.93
TIGR00276	282	iron-sulfur cluster binding protein, putative. Thi	97.93
cd01916	731	ACS_1 Acetyl-CoA synthase (ACS), also known as ace	97.9
PRK13409	590	putative ATPase RIL; Provisional	97.89
TIGR02486	314	RDH reductive dehalogenase. This model represents	97.86
PF12798	15	Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450	97.86
PRK11168	396	glpC sn-glycerol-3-phosphate dehydrogenase subunit	97.86
TIGR00273	432	iron-sulfur cluster-binding protein. Members of th	97.77
PRK09193	1165	indolepyruvate ferredoxin oxidoreductase; Validate	97.71
TIGR01936	447	nqrA NADH:ubiquinone oxidoreductase, Na(+)-translo	97.71
TIGR03379	397	glycerol3P_GlpC glycerol-3-phosphate dehydrogenase	97.68
PRK11274	407	glcF glycolate oxidase iron-sulfur subunit; Provis	97.68
PRK06259	486	succinate dehydrogenase/fumarate reductase iron-su	97.66
PRK05352	448	Na(+)-translocating NADH-quinone reductase subunit	97.64
TIGR02910	334	sulfite_red_A sulfite reductase, subunit A. Member	97.63
PRK13030	1159	2-oxoacid ferredoxin oxidoreductase; Provisional	97.62
COG1150	195	HdrC Heterodisulfide reductase, subunit C [Energy	97.59
COG0247	388	GlpC Fe-S oxidoreductase [Energy production and co	97.58
PF12797	22	Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450	97.57
COG1139	459	Uncharacterized conserved protein containing a fer	97.56
COG2440	99	FixX Ferredoxin-like protein [Energy production an	97.55
PF12797	22	Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450	97.51
PF12798	15	Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450	97.5
PRK15055	344	anaerobic sulfite reductase subunit A; Provisional	97.46
PRK13029	1186	2-oxoacid ferredoxin oxidoreductase; Provisional	97.4
COG1600	337	Uncharacterized Fe-S protein [Energy production an	97.35
COG1152	772	CdhA CO dehydrogenase/acetyl-CoA synthase alpha su	97.33
PF14697	59	Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE	97.3
TIGR02064	402	dsrA sulfite reductase, dissimilatory-type alpha s	97.3
PF12800	17	Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450	97.27
COG1143	172	NuoI Formate hydrogenlyase subunit 6/NADH:ubiquino	97.24
PRK13984	604	putative oxidoreductase; Provisional	97.23
PRK12387	180	formate hydrogenlyase complex iron-sulfur subunit;	97.14
PF12800	17	Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450	97.07
TIGR02163	255	napH_ ferredoxin-type protein, NapH/MauN family. M	97.05
PRK09477	271	napH quinol dehydrogenase membrane component; Prov	97.03
PF13187	55	Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_	97.01
TIGR02484	372	CitB CitB domain protein. CobZ is essential for co	96.98
PF13484	67	Fer4_16: 4Fe-4S double cluster binding domain	96.96
COG1141	68	Fer Ferredoxin [Energy production and conversion]	96.82
KOG3256	212	consensus NADH:ubiquinone oxidoreductase, NDUFS8/2	96.82
PF13370	58	Fer4_13: 4Fe-4S single cluster domain; PDB: 1FXR_A	96.79
PF12838	52	Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR0014	96.77
PRK08222	181	hydrogenase 4 subunit H; Validated	96.66
PF13459	65	Fer4_15: 4Fe-4S single cluster domain	96.65
TIGR02745	434	ccoG_rdxA_fixG cytochrome c oxidase accessory prot	96.63
PRK15033	389	tricarballylate utilization protein B; Provisional	96.62
COG1145	99	NapF Ferredoxin [Energy production and conversion]	96.57
TIGR02936	91	fdxN_nitrog ferredoxin III, nif-specific. Members	96.41
COG1144	91	Pyruvate:ferredoxin oxidoreductase and related 2-o	96.35
PRK09626	103	oorD 2-oxoglutarate-acceptor oxidoreductase subuni	96.33
COG1146	68	Ferredoxin [Energy production and conversion]	96.33
PRK08348	120	NADH-plastoquinone oxidoreductase subunit; Provisi	96.23
PF13237	52	Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A.	96.22
KOG0063	592	consensus RNAse L inhibitor, ABC superfamily [RNA	96.14
PF13746	69	Fer4_18: 4Fe-4S dicluster domain	96.09
PLN00071	81	photosystem I subunit VII; Provisional	96.05
PRK09623	105	vorD 2-ketoisovalerate ferredoxin oxidoreductase s	96.0
PRK06273	165	ferredoxin; Provisional	95.99
TIGR02179	78	PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta	95.92
CHL00065	81	psaC photosystem I subunit VII	95.91
COG1035	332	FrhB Coenzyme F420-reducing hydrogenase, beta subu	95.88
COG2221	317	DsrA Dissimilatory sulfite reductase (desulfovirid	95.86
TIGR02494	295	PFLE_PFLC glycyl-radical enzyme activating protein	95.78
COG1453	391	Predicted oxidoreductases of the aldo/keto reducta	95.75
PRK08493	819	NADH dehydrogenase subunit G; Validated	95.72
COG0348	386	NapH Polyferredoxin [Energy production and convers	95.65
TIGR00403	183	ndhI NADH-plastoquinone oxidoreductase subunit I p	95.62
TIGR03048	80	PS_I_psaC photosystem I iron-sulfur protein PsaC.	95.58
COG1140	513	NarY Nitrate reductase beta subunit [Energy produc	95.34
COG1941	247	FrhG Coenzyme F420-reducing hydrogenase, gamma sub	95.27
PF13746	69	Fer4_18: 4Fe-4S dicluster domain	95.25
PRK06991	270	ferredoxin; Provisional	95.23
PRK05888	164	NADH dehydrogenase subunit I; Provisional	95.21
CHL00014	167	ndhI NADH dehydrogenase subunit I	95.17
TIGR01971	122	NuoI NADH-quinone oxidoreductase, chain I. This mo	94.98
PRK09625	133	porD pyruvate flavodoxin oxidoreductase subunit de	94.97
TIGR02060	132	aprB adenosine phosphosulphate reductase, beta sub	94.93
PRK09624	105	porD pyuvate ferredoxin oxidoreductase subunit del	94.9
PRK13409	590	putative ATPase RIL; Provisional	94.83
PRK02651	81	photosystem I subunit VII; Provisional	94.82
TIGR01944	165	rnfB electron transport complex, RnfABCDGE type, B	94.67
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	94.65
KOG0063	592	consensus RNAse L inhibitor, ABC superfamily [RNA	94.63
PRK09326	341	F420H2 dehydrogenase subunit F; Provisional	94.39
PRK05113	191	electron transport complex protein RnfB; Provision	94.34
PRK08764	135	ferredoxin; Provisional	94.11
COG1149	284	MinD superfamily P-loop ATPase containing an inser	94.09
TIGR02512	374	Fe_only_hydrog hydrogenases, Fe-only. This model d	94.09
TIGR02066	341	dsrB sulfite reductase, dissimilatory-type beta su	93.84
PRK12814	652	putative NADPH-dependent glutamate synthase small	93.68
TIGR02700	234	flavo_MJ0208 archaeoflavoprotein, MJ0208 family. T	93.64
TIGR00402	101	napF ferredoxin-type protein NapF. The gene codes	93.63
PRK15449	95	ferredoxin-like protein FixX; Provisional	93.45
TIGR03294	228	FrhG coenzyme F420 hydrogenase, subunit gamma. Thi	93.39
TIGR03224	411	benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA p	93.33
COG1141	68	Fer Ferredoxin [Energy production and conversion]	93.31
TIGR02486	314	RDH reductive dehalogenase. This model represents	93.25
PLN02805	555	D-lactate dehydrogenase [cytochrome]	93.05
COG2878	198	Predicted NADH:ubiquinone oxidoreductase, subunit	92.99
TIGR02912	314	sulfite_red_C sulfite reductase, subunit C. Member	92.99
PRK14028	312	pyruvate ferredoxin oxidoreductase subunit gamma/d	92.91
PF13459	65	Fer4_15: 4Fe-4S single cluster domain	92.73
TIGR00276	282	iron-sulfur cluster binding protein, putative. Thi	92.7
PF02913	248	FAD-oxidase_C: FAD linked oxidases, C-terminal dom	92.6
TIGR00387	413	glcD glycolate oxidase, subunit GlcD. This protein	92.47
COG3383	978	Uncharacterized anaerobic dehydrogenase [General f	92.44
PF13370	58	Fer4_13: 4Fe-4S single cluster domain; PDB: 1FXR_A	92.19
COG1140	513	NarY Nitrate reductase beta subunit [Energy produc	92.12
PRK08318	420	dihydropyrimidine dehydrogenase subunit B; Validat	92.01
PRK07569	234	bidirectional hydrogenase complex protein HoxU; Va	91.91
COG2768	354	Uncharacterized Fe-S center protein [General funct	91.74
TIGR03287	391	methan_mark_16 putative methanogenesis marker 16 m	91.42
TIGR01973	603	NuoG NADH-quinone oxidoreductase, chain G. This mo	91.34
PF13183	57	Fer4_8: 4Fe-4S dicluster domain; PDB: 2BS4_B 1E7P_	91.19
COG4231	640	Indolepyruvate ferredoxin oxidoreductase, alpha an	91.17
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	90.96
TIGR02176	1165	pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxid	90.85
PRK12771	564	putative glutamate synthase (NADPH) small subunit;	90.68
PF13534	61	Fer4_17: 4Fe-4S dicluster domain; PDB: 1ZOY_B 3AE9	90.62
PRK13795	636	hypothetical protein; Provisional	90.47
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	90.27
COG1600	337	Uncharacterized Fe-S protein [Energy production an	89.59
PRK07860	797	NADH dehydrogenase subunit G; Validated	89.41
PRK09129	776	NADH dehydrogenase subunit G; Validated	88.49
PRK09130	687	NADH dehydrogenase subunit G; Validated	88.26
PRK08166	847	NADH dehydrogenase subunit G; Validated	87.97
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	87.65
PRK05035	695	electron transport complex protein RnfC; Provision	86.85
COG1035	332	FrhB Coenzyme F420-reducing hydrogenase, beta subu	86.46
PRK07570	250	succinate dehydrogenase/fumarate reductase iron-su	86.45
TIGR03290	144	CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, s	86.45
TIGR03315	1012	Se_ygfK putative selenate reductase, YgfK subunit.	85.99
PRK11230	499	glycolate oxidase subunit GlcD; Provisional	85.68
TIGR02910	334	sulfite_red_A sulfite reductase, subunit A. Member	85.14
PRK12814	652	putative NADPH-dependent glutamate synthase small	85.11
TIGR03336	595	IOR_alpha indolepyruvate ferredoxin oxidoreductase	84.66
PRK09853	1019	putative selenate reductase subunit YgfK; Provisio	83.14
PRK15055	344	anaerobic sulfite reductase subunit A; Provisional	82.69
PRK12576	279	succinate dehydrogenase iron-sulfur subunit; Provi	82.27
TIGR01945	435	rnfC electron transport complex, RnfABCDGE type, C	82.2
TIGR00384	220	dhsB succinate dehydrogenase and fumarate reductas	81.96
PRK08640	249	sdhB succinate dehydrogenase iron-sulfur subunit;	81.9
TIGR02064	402	dsrA sulfite reductase, dissimilatory-type alpha s	81.33
KOG3049	288	consensus Succinate dehydrogenase, Fe-S protein su	80.93
TIGR00273	432	iron-sulfur cluster-binding protein. Members of th	80.56
COG1453	391	Predicted oxidoreductases of the aldo/keto reducta	80.2

>KOG3256 consensus NADH:ubiquinone oxidoreductase, NDUFS8/23 kDa subunit [Energy production and conversion]

Probab=100.00  E-value=5.5e-38  Score=239.47  Aligned_cols=205  Identities=74%  Similarity=1.197  Sum_probs=177.5

Q ss_pred             HhhhhHhhhhccCCcccCcccccCCCCCCCCCchhHHHHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCC
Q 027264           15 ARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEISKDWSSVFERSINMLFLTEMVRGLGLTLKYFFDK   94 (226)
Q Consensus        15 ~~~~~i~Gha~~gn~~~~~~~~~H~~~~~~~~~~p~~~~~~~~~~~~~~v~~~~~~~i~~~~~~~~~~~l~~~~~~~f~~   94 (226)
                      ..+.+++|.++.|.  +|.+. +|+   .....+.+.++. -++++...+...++.......+.+++++++++++++|+.
T Consensus         8 ~~~~~~~gq~~~g~--~~~r~-~~~---~~~~~~~~y~~v-~~~e~~~~~~~~~n~~~~tl~~te~~rGf~itLsh~f~~   80 (212)
T KOG3256|consen    8 ALTLALSGQRLQGS--HGVRL-LSS---NYGSVKDDYKYV-NMKEMSPDITGVMNRGQQTLFATELIRGFMITLSHTFRE   80 (212)
T ss_pred             HHHHHhccCcccCC--ccccc-chh---hhccccccceee-chhccchHHHHHHHHHHHHHHHHHHHHHHHhhHHhhcCC
Confidence            33788899998888  22222 122   122223333332 236666666677777777888999999999999999999


Q ss_pred             cceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhh
Q 027264           95 KVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQE  174 (226)
Q Consensus        95 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~  174 (226)
                      ++++|||+++++++++|+|.|.+.+++...++||.|..|+.+||..+|+++...+..+++....+.+|...|+.||.|+.
T Consensus        81 p~TInYPfEKgplS~RFRGehalrRyp~geerCIACklCeavCPaqaitieae~r~dgsrRttrYdIDmtkCIyCG~CqE  160 (212)
T KOG3256|consen   81 PVTINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAVCPAQAITIEAEERTDGSRRTTRYDIDMTKCIYCGFCQE  160 (212)
T ss_pred             CeeecCccccCCCCcccccchhhhcCCCcchhhhhHHHHHHhCCcccceeeceecCCccccceeecccceeeeeecchhh
Confidence            99999999999999999999999999999999999999999999999999998888888888899999999999999999


Q ss_pred             cCcccccccCCCcccchhcHHHhhcCHHHHhhcCCCchHHHHHHhhhhcccC
Q 027264          175 ACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR  226 (226)
Q Consensus       175 ~CP~~Ai~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (226)
                      +||++||..++.|+++++++++++|+++.+...|+.|+..++.|+|.|-|||
T Consensus       161 aCPvdaivegpnfEfsTetheELlYnkekLl~ngd~Wese~a~N~~~~~lyr  212 (212)
T KOG3256|consen  161 ACPVDAIVEGPNFEFSTETHEELLYNKEKLLTNGDRWESEIAKNLQAELLYR  212 (212)
T ss_pred             hCCccceeccCCceeccccHHHHhhhHHHHhhccccccchhhhcccchhhcC
Confidence            9999999999999999999999999999999999999999999999999997

>COG1143 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]

Probab=99.93  E-value=1.6e-26  Score=182.35  Aligned_cols=130  Identities=51%  Similarity=0.999  Sum_probs=119.6

Q ss_pred             HHHHHHHHHHHHhcCCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhc-cCCcccc
Q 027264           79 EMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEERE-DGSRRTT  157 (226)
Q Consensus        79 ~~~~~l~~~~~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~-~~~~~~~  157 (226)
                      +++.++...++++|++..+..||+++...+++|+|.+.+.     .++||+|+.|+.+||++||.+....+. .+.+...
T Consensus        14 ~~~~~l~~~~K~~fk~~vT~~YP~e~~~~~~rfRG~~~l~-----~~~CIgC~lCa~iCP~~aI~m~~~~~~~~g~~~~~   88 (172)
T COG1143          14 DFLKGLWTTLKNLFKKPVTIEYPEEKIPLSPRFRGRHVLD-----RDKCIGCGLCANICPANAITMETAERKVDGRKKPK   88 (172)
T ss_pred             HHHHHHHHHHHHHhCCCchhhCccccCCCCCCccceeecc-----ccCCcchhHHHhhCCcCceEEEEcccCCCCccccc
Confidence            7889999999999999999999999999999999998754     456999999999999999999877665 4666777


Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCCCcccchhcHHHhhcCHHHHhhcCCCchH
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWET  213 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~  213 (226)
                      .+.+|...|++||.|+++||++||.+++.|+++++++++++++...++..+.+|..
T Consensus        89 ~~~In~grCIfCg~C~e~CPt~Al~~t~~~e~a~~~~~dl~~~~~~ll~~~~~~~~  144 (172)
T COG1143          89 RPDINLGRCIFCGLCVEVCPTGALVLTPEFELASYKREDLVYDKERLLAPPDKKEE  144 (172)
T ss_pred             cceeccccccccCchhhhCchhhhcCCcceeecccchHhhhccHHHhccCcccccc
Confidence            88999999999999999999999999999999999999999999999999998876

>PRK05888 NADH dehydrogenase subunit I; Provisional

Probab=99.79  E-value=6.6e-19  Score=139.36  Aligned_cols=140  Identities=76%  Similarity=1.314  Sum_probs=109.5

Q ss_pred             hhHHHHHHHHHHHHHhcCCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhccCCcc
Q 027264           76 FLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRR  155 (226)
Q Consensus        76 ~~~~~~~~l~~~~~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~  155 (226)
                      .+..++.++..+++++|++..+.+||+.....++++++...+.....+.++|++|+.|+.+||.+++.........+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~t~~yp~~~~~~~~~~~g~~~l~~~~~~~~~Ci~C~~C~~~CP~~ai~~~~~~~~~g~~~   88 (164)
T PRK05888          9 LLKELLKGLGVTLKYFFKKKVTIQYPEEKLPLSPRFRGRHALRRDPNGEERCIACKLCAAICPADAITIEAAEREDGRRR   88 (164)
T ss_pred             HHHHHHHHHHHHHHHHcCCCcccCCCCCCCCCCCCcCCEEeecCCCCCCccCCcccChHHHcCccccccccccCCCCccc
Confidence            45577889999999999999999999988777777777654332223345999999999999999887654321111111


Q ss_pred             ccccccCCCCCCcchhhhhcCcccccccCCCcccchhcHHHhhcCHHHHhhcCCCchHHH
Q 027264          156 TTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEI  215 (226)
Q Consensus       156 ~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~  215 (226)
                      ...+.++...|++||.|+.+||++||.+...+++.+.++.++.++...+.+.+..+..-.
T Consensus        89 ~~~~~i~~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~  148 (164)
T PRK05888         89 TTRYDINFGRCIFCGFCEEACPTDAIVETPDFELATETREELIYDKEKLLANGDRVEREI  148 (164)
T ss_pred             ceeeecCCCcCcccCcchhhcCcCcceecCcceeccCCHHHHccCHHHHhcccccccccc
Confidence            223457888999999999999999999999999999999999999999988866655443

>TIGR00403 ndhI NADH-plastoquinone oxidoreductase subunit I protein

Probab=99.78  E-value=9.2e-19  Score=140.62  Aligned_cols=124  Identities=34%  Similarity=0.621  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHHHHhcCCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhc-cCCccc
Q 027264           78 TEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEERE-DGSRRT  156 (226)
Q Consensus        78 ~~~~~~l~~~~~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~-~~~~~~  156 (226)
                      ..+..++.++++++|++..+.+||+.+...++++++...     ++.++|++||.|+.+||.+++........ ...+..
T Consensus        20 ~~i~~g~~vt~~~~~~~p~T~~YP~~~~~~~~~~rG~i~-----~~~~kCi~Cg~C~~aCP~~ai~~~~~~~~~~~~~~~   94 (183)
T TIGR00403        20 RYIGQGFAVTLDHMNRLPITIQYPYEKLIPSERFRGRIH-----FEFDKCIACEVCVRVCPINLPVVDWEFNKAIKKKQL   94 (183)
T ss_pred             HHHHHHHHHHHHHhcCCCccccCCCCCCCCCccccceEE-----eCcccCcCcCChhhhCCCCccccccccccccccccc
Confidence            346779999999999999999999998888888887543     55789999999999999987644221110 011112


Q ss_pred             cccccCCCCCCcchhhhhcCcccccccCCCcccchhcHHHhhcCHHHHhh
Q 027264          157 TRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLE  206 (226)
Q Consensus       157 ~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~~~~~  206 (226)
                      ..+.++.+.|++||.|+.+||++||.++.+|++.+.++.++.+|...+.+
T Consensus        95 ~~~~id~~~Ci~Cg~Cv~aCP~~AI~~~~~~e~~~~~r~~l~~~~~~l~~  144 (183)
T TIGR00403        95 KNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYDQIALGR  144 (183)
T ss_pred             ceeecCcccccCcCchhhhcCCCCeecccccccccccHHHHhccHHHhcC
Confidence            24567788999999999999999999999999999999999999888754

>TIGR01971 NuoI NADH-quinone oxidoreductase, chain I

Probab=99.70  E-value=6.3e-18  Score=127.36  Aligned_cols=119  Identities=59%  Similarity=1.089  Sum_probs=92.8

Q ss_pred             HHHHHHHhcCCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhccCCccccccccCC
Q 027264           84 LGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDM  163 (226)
Q Consensus        84 l~~~~~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~  163 (226)
                      +.+.++++|.+..+..||+.+...+.++++...+.......++|++|+.|+.+||++++.........+......+.++.
T Consensus         2 ~~~~~~~~~~~~~t~~~p~~~~~~~~~~~g~~~~~~~~~~~~~Ci~C~~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~   81 (122)
T TIGR01971         2 LGLTLKYFFSKPVTVQYPEEKLYLPPRFRGRIVLTRDPNGEEKCIGCTLCAAVCPADAIRVVPAEGEDGKRRLKFYQINF   81 (122)
T ss_pred             cEeeHHHHcCCCceeECCCcCCCCCcccCCeEeeccCCCCcCcCcCcchhhhhcCHhHeeeeeeccCCCceecccceECc
Confidence            34578999999999999998888888888876554433455899999999999999888765322111111112345677


Q ss_pred             CCCCcchhhhhcCcccccccCCCcccchhcHHHhhcCHH
Q 027264          164 TKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKE  202 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~  202 (226)
                      ..|.+||.|+.+||.+||.+...++..+.++.++.++.+
T Consensus        82 ~~C~~Cg~Cv~~CP~~al~~~~~~~~~~~~~~~~~~~~~  120 (122)
T TIGR01971        82 GRCIFCGLCEEACPTDAIVLTPEFELATYTRSDLVYGKE  120 (122)
T ss_pred             ccCCCCCchhhhCCCccccccceeeeccccHHHheechh
Confidence            899999999999999999999999999999999988765

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.

>CHL00014 ndhI NADH dehydrogenase subunit I

Probab=99.66  E-value=3.5e-16  Score=124.08  Aligned_cols=134  Identities=32%  Similarity=0.560  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHHhcCCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhh-ccCCcccc
Q 027264           79 EMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEER-EDGSRRTT  157 (226)
Q Consensus        79 ~~~~~l~~~~~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~-~~~~~~~~  157 (226)
                      .+..++...+++++....+..||+.......++++...     ++.++|++||.|+.+||++++....... ........
T Consensus        18 ~i~~~~~~~~~~~~~~~~t~~yp~~~~~~~~~~rg~i~-----~~~~~Ci~Cg~C~~aCP~~~~~~~~~~~~~~~~~~~~   92 (167)
T CHL00014         18 YIGQGFMITLSHANRLPVTIQYPYEKLITSERFRGRIH-----FEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLL   92 (167)
T ss_pred             HHHHHHHHHHHHHcCCCcceeCCCCCCCCCcCcCCeEE-----eccccCCCcCcHHHhCCCCCccccccccccccccccc
Confidence            44567888899999999999999877666667776432     4568999999999999998764422110 00011112


Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCCCcccchhcHHHhhcCHHHHh----hcCCCchHHHHH
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLL----ENGDRWETEIAE  217 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~~~~----~~~~~~~~~~~~  217 (226)
                      .+.+|...|++||.|+.+||++||.+...|++...++..+++++..+.    ..+++|....+.
T Consensus        93 ~~~id~~~C~~Cg~C~~~CP~~AI~~~~~~~~~~~~r~~l~~~~~~~~~~~~~~~~~~~~~~~~  156 (167)
T CHL00014         93 NYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIALGRLPMSVIDDYTIRTIS  156 (167)
T ss_pred             cccCCCCcCcCccchHhhcCcCceecCCccccccccHHHHhcCHHHHhCCCCccccccchhhhh
Confidence            345677889999999999999999999999999999999999988873    335555544443

>PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional

Probab=99.54  E-value=5.1e-15  Score=111.24  Aligned_cols=100  Identities=27%  Similarity=0.643  Sum_probs=76.4

Q ss_pred             HHHHHHHhcCCcceecCccc-cCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhccCCccccccccC
Q 027264           84 LGLTLKYFFDKKVTINYPFE-KGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDID  162 (226)
Q Consensus        84 l~~~~~~~f~~~~~~~~p~~-~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d  162 (226)
                      +...++++|.+..+..||+. ....+..+++.     +.++.++|++||.|+.+||.+++.......        ...++
T Consensus         5 ~~~~~k~~~~~~~t~~~p~~~~~~~~~~~~g~-----i~i~~~~Ci~C~~C~~~CP~~ai~~~~~~~--------~~~i~   71 (120)
T PRK08348          5 LPTVLRNLFKKPATNLFPATEPVPVPEDFRGK-----ILYDVDKCVGCRMCVTVCPAGVFVYLPEIR--------KVALW   71 (120)
T ss_pred             HHHHHHHhcCCCccccCCccCCCCCCccccce-----EEECcccCcCcccHHHHCCccceEcccccc--------ceEec
Confidence            45667899999999999985 44555566553     346678999999999999999886643210        23456


Q ss_pred             CCCCCcchhhhhcCcccccccCCCcccchhcHHH
Q 027264          163 MTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEE  196 (226)
Q Consensus       163 ~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~  196 (226)
                      ...|+.||.|+.+||++||.+...+.+....+.+
T Consensus        72 ~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~r~~  105 (120)
T PRK08348         72 TGRCVFCGQCVDVCPTGALQMSDDFLLASYDRFD  105 (120)
T ss_pred             CCcCcChhhhHHhCCcCcEEeccceeeehhhhhh
Confidence            7889999999999999999998887766555533

>PRK08222 hydrogenase 4 subunit H; Validated

Probab=99.47  E-value=3.2e-14  Score=114.15  Aligned_cols=96  Identities=36%  Similarity=0.832  Sum_probs=74.8

Q ss_pred             CCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhh
Q 027264           93 DKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFC  172 (226)
Q Consensus        93 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~C  172 (226)
                      ....+..||+.+...++.|+|...     ++.++|++||.|+.+||+++|........ +   ...+.++...|++||.|
T Consensus        11 ~g~~T~~yP~~~~~~p~~~rG~~~-----~d~~~Ci~Cg~Cv~aCP~~Ai~~~~~~~~-~---~~~~~~~~~~C~~Cg~C   81 (181)
T PRK08222         11 AGTATVKYPFAPLEVSPGFRGKPD-----LMPSQCIACGACTCACPANALTIQTDDQQ-N---SRTWQLYLGRCIYCGRC   81 (181)
T ss_pred             CCCccccCCCcccCCCCCccCceE-----eChhhCcchhHHHHhCCccceEccccccc-C---ccceeeccCcCcCCCCc
Confidence            467899999988888888888643     56789999999999999999987543210 1   11245667899999999


Q ss_pred             hhcCcccccccCCCcccchhcHHHh
Q 027264          173 QEACPVDAIVEGPNFEYSTETHEEL  197 (226)
Q Consensus       173 v~~CP~~Ai~~~~~~~~~~~~~~~~  197 (226)
                      +.+||++||.+.+.++.....+.++
T Consensus        82 ~~~CPt~AI~~~~~~~~~~~~~~~l  106 (181)
T PRK08222         82 EEVCPTRAIQLTNNFELTVTNKADL  106 (181)
T ss_pred             ccccCcCeEEeccceeeeccchhhh
Confidence            9999999999998887776555443

>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional

Probab=99.44  E-value=9.3e-14  Score=111.52  Aligned_cols=96  Identities=32%  Similarity=0.764  Sum_probs=74.8

Q ss_pred             CCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhh
Q 027264           93 DKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFC  172 (226)
Q Consensus        93 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~C  172 (226)
                      .+..+..||+.+.....+|++..     .++.++|++||.|+.+||+++|........ +   ...+.++...|++||.|
T Consensus        11 ~g~~T~~yP~~~~~~~~~~rg~p-----~~d~~~C~~C~~Cv~~CP~~ai~~~~~~~~-~---~~~~~i~~~~C~~Cg~C   81 (180)
T PRK12387         11 TGTATSSYPLEPIAVDKNFRGKP-----EYNPQQCIGCAACVNACPSNALTVETDLAT-G---ELAWEFNLGRCIFCGRC   81 (180)
T ss_pred             cCCccccCCCCCCCCCCCCCCce-----EEChhhCcChhHHHHhcCccCeEeeccccC-C---cccceeccccCcCccch
Confidence            46788999988777777777754     356889999999999999999877543211 1   11345778899999999


Q ss_pred             hhcCcccccccCCCcccchhcHHHh
Q 027264          173 QEACPVDAIVEGPNFEYSTETHEEL  197 (226)
Q Consensus       173 v~~CP~~Ai~~~~~~~~~~~~~~~~  197 (226)
                      +.+||.+||.+...++....++.++
T Consensus        82 ~~vCP~~AI~~~~~~~~~~~~~~~l  106 (180)
T PRK12387         82 EEVCPTAAIKLSQEFELAVWKKEDL  106 (180)
T ss_pred             hhhcCcCceEccCccchhhccHHHh
Confidence            9999999999988888777666655

>PF14697 Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B

Probab=99.37  E-value=9.4e-14  Score=91.16  Aligned_cols=56  Identities=38%  Similarity=0.860  Sum_probs=33.0

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcc-ccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVE  183 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~-~Ai~~  183 (226)
                      ++.++|++||.|+.+||.+++........      ..+.++.+.|++||.|+.+||+ +||++
T Consensus         3 Id~~~Ci~Cg~C~~~Cp~~~~~~i~~~~~------~~~~v~~~~C~GCg~C~~~CPv~~AI~m   59 (59)
T PF14697_consen    3 IDEDKCIGCGKCVRACPDGAIDAIEVDEG------KKVPVNPDKCIGCGLCVKVCPVKDAITM   59 (59)
T ss_dssp             E-TTT----SCCCHHCCCCS-S-ECCTTT------TSSECE-TT--S-SCCCCCSSSTTSEEE
T ss_pred             ECcccccChhhHHhHcCccceeeEEecCC------eeEEeccccCcCcCcccccCCCccCCCC
Confidence            56789999999999999865544322111      1234567899999999999997 99975

...

>COG1148 HdrA Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]

Probab=99.31  E-value=5.1e-13  Score=119.00  Aligned_cols=101  Identities=27%  Similarity=0.531  Sum_probs=81.9

Q ss_pred             CccccccccccchhccccccccchhhhhccCCc----------cccccccCCCCCCcchhhhhcCcccccccCCCcccch
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSR----------RTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYST  191 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~----------~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~  191 (226)
                      ++ ++|++||.|.++||..+-.  +.+.+-+.+          ....+.+|.+.|+.||.|..+||.+|+.+.++-+...
T Consensus       222 Vd-d~CtgCg~C~~vCPve~~n--efn~Gl~~~kAiy~p~~qaVp~~~~Id~~~c~~c~~C~~ac~~~av~~~q~~e~ve  298 (622)
T COG1148         222 VD-DKCTGCGACSEVCPVEVPN--EFNEGLGKRKAIYIPFPQAVPLNYNIDPKHCIECGLCEKACPNEAVDLNQEPEEVE  298 (622)
T ss_pred             cc-ccccccccccccCCcccCc--ccccccccceeeeccchhhcccccccChhhhccchhhhhcCCccccccCCCCcEEE
Confidence            45 8999999999999985321  111111111          1234568889999999999999999999999988888


Q ss_pred             hcHHHh-------hcCHHHHhhcCCCchHHHHHHhhhhccc
Q 027264          192 ETHEEL-------LYDKEKLLENGDRWETEIAENLRSESLY  225 (226)
Q Consensus       192 ~~~~~~-------~~d~~~~~~~~~~~~~~~~~~~~~~~~~  225 (226)
                      .+.+.+       .||.+...++|-+.+.+|+|++++||+.
T Consensus       299 ~~vGaIIvAtGy~~~Da~~k~EyGYG~~~nVIT~lElErml  339 (622)
T COG1148         299 LEVGAIIVATGYKPFDATRKEEYGYGKYPNVITNLELERML  339 (622)
T ss_pred             EEeceEEEEccccccCcchhhhcCCCCCcchhhHHHHHHHh
Confidence            888887       6799999999999999999999999985

>PF13187 Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 2VKR_C 1KQG_B 1KQF_B 3GYX_J

Probab=99.31  E-value=3.9e-13  Score=86.94  Aligned_cols=55  Identities=33%  Similarity=0.783  Sum_probs=34.3

Q ss_pred             cccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccc
Q 027264          126 RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      +|++||.|+.+||.+++.+........... .....+.+.|++||.|+.+||++||
T Consensus         1 kCi~Cg~C~~~CP~~~~~~~~~~~~~~~~~-~~~~~~~~~C~~Cg~C~~~CP~~AI   55 (55)
T PF13187_consen    1 KCIGCGRCVEACPVGVIEFDEDGGKKVVDK-DNERRNAEKCIGCGACVKACPTGAI   55 (55)
T ss_dssp             C--TTTHHHHHSTTT-EEEETTTTCEECSE-CCESTTGGG--TTCHHHHHSTTT-E
T ss_pred             CCCCcchHHHHCCccCeEccCccccccccc-cccCCCCCccccHhHHHHHcchhhC
Confidence            699999999999999988766543221110 0111144689999999999999997

>PF12838 Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=99.27  E-value=5.9e-13  Score=85.17  Aligned_cols=52  Identities=44%  Similarity=0.997  Sum_probs=33.7

Q ss_pred             cccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccc
Q 027264          126 RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      +|++||.|+.+||+++|.+.......+.   ..+.++.+.|++||.|+.+||++|
T Consensus         1 ~C~~C~~C~~~CP~~~i~~~~~~~~~~~---~~~~~~~~~C~~C~~C~~~CP~~A   52 (52)
T PF12838_consen    1 KCIGCGACVEACPTGAIRLDEEENEEGK---PKMVIDPDKCTGCGACVEVCPTGA   52 (52)
T ss_dssp             C-SS--HHHHH-TTHHCEEEETTT-SSS---TTSEETGGG----SHHHHHTTTS-
T ss_pred             CCCCcCchHHhcCccccCcccccccCCc---eEEEEechhCcCcChhhhhCcCcC
Confidence            5999999999999999988765432222   345678899999999999999987

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3CF4_A 1K0T_A 2VKR_C 1JB0_C 3PCQ_C.

>COG4231 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]

Probab=99.25  E-value=8.2e-13  Score=120.76  Aligned_cols=151  Identities=23%  Similarity=0.338  Sum_probs=97.6

Q ss_pred             HHHHHHHhhhhHhhhhccCCcccCcccccCCCCCCCCCchhHHHHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHHH
Q 027264            9 SLSALRARHLAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDDEEKEQLLKEISKDWSSVFERSINMLFLTEMVRGLGLTL   88 (226)
Q Consensus         9 ~~~~l~~~~~~i~Gha~~gn~~~~~~~~~H~~~~~~~~~~p~~~~~~~~~~~~~~v~~~~~~~i~~~~~~~~~~~l~~~~   88 (226)
                      ...+|+++.+++|||+            .|+.++.-+.+.+..+..  ++++.+.++..+...++++.+.++...+...+
T Consensus       476 ~~vvLdN~~tAMTGgQ------------p~pg~~~~~~g~~~~~i~--iee~~r~~Gv~~v~~vdp~~~~~~~~~~keal  541 (640)
T COG4231         476 LVVVLDNRTTAMTGGQ------------PHPGTGVAAEGTKSTAIV--IEEVVRAMGVEDVETVDPYDVKELSEAIKEAL  541 (640)
T ss_pred             EEEEEeccchhccCCC------------CCCCcccccCCCccceeE--hhHhhhhcCceeeeccCCcchHHHHHHHHHHh
Confidence            3457899999999999            777777666666666544  77777777777777777666665555544444


Q ss_pred             HHhcCCcc-eecCccccCCCCCCccCccccccCCCccccccccccchh--ccccccccchhhhhccCCccccccccCCCC
Q 027264           89 KYFFDKKV-TINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEA--VCPAQAITIEAEEREDGSRRTTRYDIDMTK  165 (226)
Q Consensus        89 ~~~f~~~~-~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~--~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~  165 (226)
                      +.-- +.+ ..+.++.... ..+-++....+++.+|.++|++|+.|..  .||+-  ...+..        ....+|...
T Consensus       542 e~~g-psViiak~~Cal~~-~r~k~~~~~~~~~~Vd~~~CtGC~~C~~~~~Cpsi--~~~~~~--------~k~~id~~~  609 (640)
T COG4231         542 EVPG-PSVIIAKRECALEK-RRRKRGGMKAPKYFVDEEKCTGCGDCIVLSGCPSI--EPDPTF--------KKARIDPSS  609 (640)
T ss_pred             cCCC-ceEEEEcCcchhhh-hhhccccccCCCceechhhcCCcHHHHhhcCCceE--eecCCC--------Cceeecccc
Confidence            3211 222 2223332211 1111221233446688999999999984  79963  332211        145788888


Q ss_pred             CCcchhhhhcCcccccccCC
Q 027264          166 CIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       166 C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      |++||.|+++||.+|+..+.
T Consensus       610 C~GCg~C~~iCP~~a~~~~~  629 (640)
T COG4231         610 CNGCGSCVEVCPSFAIKEGG  629 (640)
T ss_pred             cccchhhhhcCchhheeccc
Confidence            99999999999999998654

>PRK13984 putative oxidoreductase; Provisional

Probab=99.19  E-value=1.7e-11  Score=115.37  Aligned_cols=112  Identities=27%  Similarity=0.563  Sum_probs=84.6

Q ss_pred             HHHHHHHhcCCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhccC--Ccccccccc
Q 027264           84 LGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDG--SRRTTRYDI  161 (226)
Q Consensus        84 l~~~~~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~--~~~~~~~~~  161 (226)
                      ....++.+++..++..||+.+..+.++|++.+.     .+.++|++|+.|+.+||.+++..........  ........+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~d~~~Ci~C~~C~~~Cp~~ai~~~~~~~~~~~~g~~~~~~~i   83 (604)
T PRK13984          9 PLKAWKFLFRKPVTIKVPNVKREAAERYRGFHI-----NDWEKCIGCGTCSKICPTDAITMVEVPDLPQEYGKKPQRPVI   83 (604)
T ss_pred             HHHHHHHhcCCCcceECCCCCCCCCccccCccc-----cChhhCcCccchhhhCCccceEeecccccccccccccccccc
Confidence            344567888999999999999999999998642     5778999999999999999886543210000  000113456


Q ss_pred             CCCCCCcchhhhhcCcccccccCCCcccchhcHHHhhcC
Q 027264          162 DMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYD  200 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d  200 (226)
                      +...|..|+.|+.+||++||.+..++...+...+++++-
T Consensus        84 ~~~~c~~c~~c~~~Cp~~Ai~~~~~~~~~~~~~~~~~~~  122 (604)
T PRK13984         84 DYGRCSFCALCVDICTTGSLKMTREYIHISPDPEDFIFM  122 (604)
T ss_pred             CcccCcCcchHHhhCCcCcEEecceEEEeecChhhEEEe
Confidence            778899999999999999999988877777777766553

>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]

Probab=99.18  E-value=5.3e-12  Score=87.86  Aligned_cols=67  Identities=37%  Similarity=0.645  Sum_probs=52.5

Q ss_pred             CccCccccccCCCccccccccccchhccccccccchhhhhccCCccccccc-cCCCCCCcchhhhhcCcccccccCC
Q 027264          110 RFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYD-IDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       110 ~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~-~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...+.-...++.++.++|+.|+.|...||-++|....+..         .. +|.+.|-+||.|+++||++||.+..
T Consensus        20 ~kTg~Wrv~rPv~d~~kCi~C~~C~~yCPe~~i~~~~~~~---------~~~idYdyCKGCGICa~vCP~kaI~Mv~   87 (91)
T COG1144          20 NKTGSWRVFRPVVDEDKCINCKLCWLYCPEPAILEEEGGY---------KVRIDYDYCKGCGICANVCPVKAIEMVR   87 (91)
T ss_pred             cccceeEEEeeEEcccccccCceeEEECCchheeeccCCc---------cceeEcccccCceechhhCChhheEeEe
Confidence            3344444445567889999999999999999887765431         12 7888999999999999999998754

>PRK09624 porD pyuvate ferredoxin oxidoreductase subunit delta; Reviewed

Probab=99.15  E-value=1.3e-11  Score=90.46  Aligned_cols=56  Identities=32%  Similarity=0.713  Sum_probs=46.0

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .++.++|++|+.|+.+||.+++..+...         ...++...|++|+.|+.+||.+||.+..
T Consensus        47 ~~d~~~Ci~C~~C~~~CP~~ai~~~~~~---------~~~id~~~C~~Cg~Cv~~CP~~AI~~~~  102 (105)
T PRK09624         47 EFNRDKCVRCYLCYIYCPEPAIYLDEEG---------YPVFDYDYCKGCGICANECPTKAIEMVR  102 (105)
T ss_pred             EEChhHCcChhhHHhhCCHhhEEecCCC---------cEEECchhCCCcCchhhhcCcCcEEEec
Confidence            4678899999999999999988765321         2346778999999999999999998764

>PRK06273 ferredoxin; Provisional

Probab=99.15  E-value=2e-11  Score=96.29  Aligned_cols=83  Identities=35%  Similarity=0.624  Sum_probs=55.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCc---cccccccCCCCCCcchhhhhcCcccccccCCCcccchhcHHH-h
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSR---RTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEE-L  197 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~---~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~-~  197 (226)
                      ++.++|++||.|+.+||+++|.+..........   ....+.++...|++||.|+.+||++||..... .++...++. .
T Consensus        46 id~~~CigCg~C~~aCP~~AI~~~~~ep~~~~~~~~~~~~~~Id~~kCi~Cg~C~~aCP~~AI~~~~~-~~~~~~~~~~~  124 (165)
T PRK06273         46 VFEELCIGCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCPVFALFNEIS-PIHPRDVGEDI  124 (165)
T ss_pred             ECchhCcChhHHHHhcCccceeeecccccchhcccccccceecccccCcCCCCcchhCCHhheecccc-cCChhhhhhHh
Confidence            567899999999999999999875421110000   01234678889999999999999999954322 233344454 5


Q ss_pred             hcCHHHHh
Q 027264          198 LYDKEKLL  205 (226)
Q Consensus       198 ~~d~~~~~  205 (226)
                      +.|...+.
T Consensus       125 ~~~~~~ll  132 (165)
T PRK06273        125 EVDVSKLL  132 (165)
T ss_pred             hccHHHHh
Confidence            55555543

>TIGR02936 fdxN_nitrog ferredoxin III, nif-specific

Probab=99.14  E-value=1.1e-11  Score=88.52  Aligned_cols=64  Identities=27%  Similarity=0.618  Sum_probs=46.0

Q ss_pred             CCccccccccccchhccccccccchhhhhcc---------CCc-cccccccCCCCCCcchhhhhcCcccccccC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEERED---------GSR-RTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~---------~~~-~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++.++|++||.|+.+||.++|.+.......         +.. ......++...|++||.|+.+||++||.+.
T Consensus        17 ~i~~~~Ci~C~~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~C~~Cg~C~~~CP~~AI~~~   90 (91)
T TIGR02936        17 SIDQEKCIGCGRCYKVCGRDVLTLKGINEEGELVASDDDDDEIERKVMVVANPGNCIGCGACARVCPKKCQTHA   90 (91)
T ss_pred             EECHhHCCCcchHHHHcChhhceeeccccccccccccccccccccceeeecCCccCcChhhhhhhCCHhHEecC
Confidence            3677899999999999999988765311000         000 001224678899999999999999999753

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.

>TIGR02179 PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family

Probab=99.14  E-value=1.6e-11  Score=85.07  Aligned_cols=57  Identities=37%  Similarity=0.688  Sum_probs=45.8

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ..++.++|++|+.|+.+||.+++......         ...++...|..|+.|+.+||++||.+..
T Consensus        20 ~~i~~~~C~~C~~C~~~Cp~~ai~~~~~~---------~~~i~~~~C~~C~~C~~~CP~~Ai~~~~   76 (78)
T TIGR02179        20 PVVDKEKCIKCKNCWLYCPEGAIQEDEGG---------FVGIDYDYCKGCGICANVCPVKAIEMVR   76 (78)
T ss_pred             EEEcCCcCcChhHHHhhcCccceEecCCC---------cEEecCccCcCccchhhhCCccccEecc
Confidence            34667899999999999999988764321         2356667899999999999999998654

A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of delta subunits, representing mostly pyruvate, 2-ketoisovalerate, and 2-oxoglutarate specific enzymes. The delta subunit is the smallest and resembles ferredoxins.

>PRK06991 ferredoxin; Provisional

Probab=99.09  E-value=3e-11  Score=102.33  Aligned_cols=57  Identities=33%  Similarity=0.691  Sum_probs=46.1

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF  187 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~  187 (226)
                      ++.++|++||.|+.+||+++|......         ...++...|++||.|+.+||++||.+.+..
T Consensus        82 id~~~CigCg~Cv~aCP~~AI~~~~~~---------~~~v~~~~CigCg~Cv~vCP~~AI~~~~~~  138 (270)
T PRK06991         82 IDEQLCIGCTLCMQACPVDAIVGAPKQ---------MHTVLADLCTGCDLCVPPCPVDCIDMVPVT  138 (270)
T ss_pred             EccccCCCCcHHHHhCCHhheeccccc---------ceeeCHhhCCCchHHHhhCCcCCeEeecCc
Confidence            567899999999999999998654321         124566789999999999999999877654

>PF13237 Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A

Probab=99.06  E-value=4.2e-11  Score=76.50  Aligned_cols=49  Identities=45%  Similarity=1.030  Sum_probs=23.3

Q ss_pred             CCccccccccccchhcccc-ccccchhhhhccCCccccccccCCCCCCcchhhhhcCc
Q 027264          121 PTGEERCIACKLCEAVCPA-QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACP  177 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~-~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP  177 (226)
                      .++.++|++||.|+++||+ .+......        ...+.++.+.|++||.|+.+||
T Consensus         3 ~id~~~C~~C~~C~~~CP~~~~~~~~~~--------~~~~~~~~~~C~~Cg~C~~~CP   52 (52)
T PF13237_consen    3 VIDEDKCIGCGRCVKVCPADNAIAIDDG--------EKKVEIDPERCIGCGACVEVCP   52 (52)
T ss_dssp             ---TT------TTGGG-TT-----EEE---------SSSEEE-TTT--TTSHHHHH-T
T ss_pred             ccCcccCcCCcChHHHccchhHHHhhcc--------CCCeEeCcccccccChhhhhCc
Confidence            4678999999999999998 22222111        1135668899999999999999

>CHL00065 psaC photosystem I subunit VII

Probab=99.05  E-value=7.7e-11  Score=82.33  Aligned_cols=62  Identities=21%  Similarity=0.521  Sum_probs=44.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+.++|++||.|+.+||++++.+..........  ....++.+.|++|+.|+.+||++||.+..
T Consensus         6 ~~~~~Ci~Cg~C~~~CP~~~i~~~~~~~~~~~~--~~~~~~~~~C~~C~~C~~~CP~~Ai~~~~   67 (81)
T CHL00065          6 KIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQ--IASAPRTEDCVGCKRCESACPTDFLSVRV   67 (81)
T ss_pred             CccccCCChhHHHHHCCccchhheecccccccc--ccccCCCCcCCChhhhhhhcCccccEEEE
Confidence            346799999999999999988765422100100  11234567899999999999999998543

>PLN00071 photosystem I subunit VII; Provisional

Probab=99.04  E-value=8.2e-11  Score=82.15  Aligned_cols=62  Identities=21%  Similarity=0.521  Sum_probs=44.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++||.|+.+||++++............  .....+.+.|++||.|+.+||++||.+..
T Consensus         6 ~~~~~C~~C~~C~~~CP~~~i~~~~~~~~~~~~--~~~~~~~~~C~~Cg~C~~~CP~~Ai~~~~   67 (81)
T PLN00071          6 KIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQ--IASAPRTEDCVGCKRCESACPTDFLSVRV   67 (81)
T ss_pred             EcCCcCcChhHHHHHCCccceeeeccccccccc--ccCcCCCCcCcChhhHHhhcCCccceEee
Confidence            456899999999999999988765321100000  01124567899999999999999998643

>PRK09623 vorD 2-ketoisovalerate ferredoxin oxidoreductase subunit delta; Reviewed

Probab=99.04  E-value=7.5e-11  Score=86.48  Aligned_cols=58  Identities=33%  Similarity=0.727  Sum_probs=46.8

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ..++.++|++|+.|+.+||.+++......         ...++...|.+||.|+.+||.+||.+...
T Consensus        46 p~i~~~~Ci~C~~C~~~CP~~ai~~~~~~---------~~~id~~~C~~Cg~Cv~~CP~~AI~~~~~  103 (105)
T PRK09623         46 PVVDESKCVKCYICWKFCPEPAIYIKEDG---------YVAIDYDYCKGCGICANECPTKAITMVKE  103 (105)
T ss_pred             EEECcccCccccchhhhCCHhheEecCCC---------cEEeCchhCcCcchhhhhcCcCcEEeccc
Confidence            34678899999999999999988654221         23577789999999999999999987654

>PRK09626 oorD 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed

Probab=99.03  E-value=1e-10  Score=85.44  Aligned_cols=64  Identities=28%  Similarity=0.527  Sum_probs=47.0

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      .++.++|++||.|+.+||++++..........  ......++...|++|+.|+.+||++||...+.
T Consensus        12 ~id~~~Ci~C~~Cv~aCP~~ai~~~~~~~~~~--~~~~~~i~~~~C~~C~~C~~~CP~~AI~~~~~   75 (103)
T PRK09626         12 WVDESRCKACDICVSVCPAGVLAMRIDPHAVL--GKMIKVVHPESCIGCRECELHCPDFAIYVADR   75 (103)
T ss_pred             EECcccccCCcchhhhcChhhhcccccccccc--CceeeEeCCccCCCcCcchhhCChhhEEEecc
Confidence            35678999999999999999887654321100  00123456678999999999999999987654

>PRK09625 porD pyruvate flavodoxin oxidoreductase subunit delta; Reviewed

Probab=99.00  E-value=1.3e-10  Score=88.71  Aligned_cols=54  Identities=31%  Similarity=0.677  Sum_probs=42.9

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      +.++.++|++|+.|+.+||.+++......         ...++...|++||.|+.+||++|+.
T Consensus        54 p~~d~~~Ci~C~~C~~~CP~~ai~~~~~~---------~~~i~~~~C~~Cg~Cv~vCP~~a~~  107 (133)
T PRK09625         54 PVHNNEICINCFNCWVYCPDAAILSRDKK---------LKGVDYSHCKGCGVCVEVCPTNPKS  107 (133)
T ss_pred             EEEehhHCcChhhHHHhCCHhheEecCCc---------eEEeCcCcCcChhHHHHHCCcCceE
Confidence            34667999999999999999987643211         2346678899999999999999964

>COG1146 Ferredoxin [Energy production and conversion]

Probab=99.00  E-value=1e-10  Score=78.93  Aligned_cols=58  Identities=34%  Similarity=0.767  Sum_probs=47.1

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++|+.|+.+||.+.+......      ....+..+.+.|++||.|+.+||++||....
T Consensus         5 Id~~~C~~c~~C~~~CP~~~~~~~~~~------~~~~~~~~~e~C~~C~~C~~~CP~~aI~~~~   62 (68)
T COG1146           5 IDYDKCIGCGICVEVCPAGVFDLGEDE------GGKPVVARPEECIDCGLCELACPVGAIKVDI   62 (68)
T ss_pred             ECchhcCCCChheeccChhhEEecccc------CcceeEeccccCccchhhhhhCCcceEEEec
Confidence            567899999999999999988776432      1114567889999999999999999998654

>TIGR03048 PS_I_psaC photosystem I iron-sulfur protein PsaC

Probab=99.00  E-value=1.7e-10  Score=80.37  Aligned_cols=60  Identities=22%  Similarity=0.560  Sum_probs=43.5

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      .+.++|++|+.|+.+||++++.+..........  .....+...|++||.|+++||++||.+
T Consensus         5 ~~~~~Ci~C~~Cv~~CP~~~i~~~~~~~~~~~~--~~~~~~~~~C~~Cg~C~~~CP~~ai~~   64 (80)
T TIGR03048         5 KIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQ--IASAPRTEDCVGCKRCESACPTDFLSV   64 (80)
T ss_pred             ecCCcCcCcchHHHHCCccceeeeccccccccc--ccCcCCCCcCcChhHHHHhcCcccCEE
Confidence            346799999999999999988765421100000  012345678999999999999999986

Members of this family are PsaC, an essential component of photosystem I (PS-I) reaction center in Cyanobacteria and chloroplasts. This small protein, about 80 amino acids in length, contains two copies of the ferredoxin-like 4Fe-4S binding site (pfam00037) and therefore eight conserved Cys residues. This protein is also called photosystem I subunit VII.

>TIGR02060 aprB adenosine phosphosulphate reductase, beta subunit

Probab=98.99  E-value=1.3e-10  Score=88.35  Aligned_cols=62  Identities=27%  Similarity=0.629  Sum_probs=49.3

Q ss_pred             Cccccccccc-----cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcccc
Q 027264          122 TGEERCIACK-----LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYS  190 (226)
Q Consensus       122 ~~~~~Ci~Cg-----~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~  190 (226)
                      ++.++|++||     .|+.+||.+++.++...       ...+.++...|++|+.|+.+||.+||.+....++.
T Consensus         5 v~~~~C~gC~~~~~~~Cv~~CP~~ai~~~~~~-------~~~~~id~~~C~~Cg~Cv~~CP~~AI~~~~~~~~~   71 (132)
T TIGR02060         5 VYPTKCDGCKAGEKTACVYICPNDLMHLDTEI-------MKAYNIEPDMCWECYSCVKACPQGAIDVRGYADFA   71 (132)
T ss_pred             EccccccCccCCchhcCHhhcCccceEecCCC-------ceeeecCchhCccHHHHHHhCCcCceEEECccccc
Confidence            5678999999     99999999998765321       01235677899999999999999999987765544

During dissimilatory sulfate reduction and sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the beta subunit of APS reductase, sharing common evolutionary origin with other iron-sulfur cluster-binding proteins.

>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family

Probab=98.97  E-value=3e-10  Score=96.03  Aligned_cols=89  Identities=17%  Similarity=0.368  Sum_probs=57.9

Q ss_pred             HHHhcCCcceecCccccCCCCCCccCccccccCCC-ccccccccccchhccccccc-cchhhhhccCCccccccccCCCC
Q 027264           88 LKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPT-GEERCIACKLCEAVCPAQAI-TIEAEEREDGSRRTTRYDIDMTK  165 (226)
Q Consensus        88 ~~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~-~~~~Ci~Cg~C~~~CP~~ai-~~~~~~~~~~~~~~~~~~~d~~~  165 (226)
                      +..++.++.+..+-++.+.....+..... .+... +.++|++|+.|+++||++++ ......  .     ....++...
T Consensus       164 ~~~~~~~r~~C~~~CP~Ga~~~~~~~~~~-~~i~~~~~~~C~~C~~C~~vCP~~~vl~~~~~~--~-----~~~~i~~~~  235 (255)
T TIGR02163       164 FDLLFSERGWCGHLCPLGAFYGLIGRKSL-IKIAASDREKCTNCMDCFNVCPEPQVLRMPLKK--G-----GSTLVLSGD  235 (255)
T ss_pred             HHHHhcCCchhhCcCCCcchhhhhhccCc-eEEEeeccccCeEcCCccCcCCCCceeeccccC--C-----CceEecccc
Confidence            34566677788876666654332221111 12223 37899999999999999863 221110  0     123456778


Q ss_pred             CCcchhhhhcCcccccccC
Q 027264          166 CIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       166 C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      |+.||.|+++||++|+.++
T Consensus       236 C~~Cg~Cv~~CP~~Ai~f~  254 (255)
T TIGR02163       236 CTLCGRCIDVCHEDVLGFT  254 (255)
T ss_pred             ccchhHHHHhCCccccccc
Confidence            9999999999999999864

Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.

>COG1145 NapF Ferredoxin [Energy production and conversion]

Probab=98.96  E-value=1.8e-10  Score=82.84  Aligned_cols=59  Identities=39%  Similarity=0.799  Sum_probs=46.1

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+.++|++||.|+.+||+++|........     .....++...|+.|+.|+.+||++|+.+..
T Consensus        26 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~-----~~~~~~~~~~C~~C~~C~~~Cp~~a~~~~~   84 (99)
T COG1145          26 IDAEKCIGCGLCVKVCPTGAIELIEEGLL-----LPEVVIDPDLCVLCGACLKVCPVDALSIAE   84 (99)
T ss_pred             eCccccCCCCCchhhCCHHHhhcccccCc-----cceEEEccccCccccchHhhCCcCCeehhh
Confidence            55788999999999999999987322100     124567788999999999999999987544

>PRK02651 photosystem I subunit VII; Provisional

Probab=98.96  E-value=2.9e-10  Score=79.32  Aligned_cols=63  Identities=21%  Similarity=0.514  Sum_probs=45.0

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFE  188 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~  188 (226)
                      .++|++|+.|+.+||.+++..........  .......+...|.+|+.|+.+||++||.++..+.
T Consensus         8 ~~~Ci~C~~C~~~CP~~~i~~~~~~~~~~--~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~   70 (81)
T PRK02651          8 YDTCIGCTQCVRACPLDVLEMVPWDGCKA--GQIASSPRTEDCVGCKRCETACPTDFLSIRVYLG   70 (81)
T ss_pred             cccCCCcchHHHHCCccceeccccccccc--CcccccCCCCcCCChhhhhhhcCCCceEEEEEec
Confidence            58999999999999998876643211110  0011234667899999999999999998755433

>PRK05113 electron transport complex protein RnfB; Provisional

Probab=98.96  E-value=1.7e-10  Score=93.36  Aligned_cols=56  Identities=30%  Similarity=0.658  Sum_probs=45.4

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .++.++|++||.|+++||++++....+.         ...++.+.|++||.|+.+||++||.+.+
T Consensus       110 ~id~~~Ci~Cg~Cv~aCp~~ai~~~~~~---------~~~v~~~~C~~Cg~Cv~vCP~~AI~~~~  165 (191)
T PRK05113        110 FIDEDNCIGCTKCIQACPVDAIVGATKA---------MHTVISDLCTGCDLCVAPCPTDCIEMIP  165 (191)
T ss_pred             EEeCCcCCCCChhhhhCCHhhhecccCC---------ceeecCCcCCchHHHHHHcCcCceEEee
Confidence            3567899999999999999988654321         1245678999999999999999998765

>PRK09477 napH quinol dehydrogenase membrane component; Provisional

Probab=98.96  E-value=4e-10  Score=96.08  Aligned_cols=94  Identities=19%  Similarity=0.370  Sum_probs=58.5

Q ss_pred             HHhcCCcceecCccccCCCCCCccCccccccCC-CccccccccccchhccccccccchhhhhccCCccccccccCCCCCC
Q 027264           89 KYFFDKKVTINYPFEKGPLSPRFRGEHALRRYP-TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCI  167 (226)
Q Consensus        89 ~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~-~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~  167 (226)
                      ..++.++.+..|-++.+.....+. ..+..++. ++.++|++|+.|+++||++++...... +..    ....++...|+
T Consensus       172 ~~~~~~r~wC~~lCP~Ga~~~~~~-~~~~~~i~~~d~~~C~~C~~C~~~CP~~~i~~~~~~-~~~----~~~~i~~~~C~  245 (271)
T PRK09477        172 DLFVVEHGWCGHLCPLGAFYGLIG-KKSLIRVKAHDRQKCTRCMDCFHVCPEPQVLRPPLK-GKQ----SPSQVTSGDCI  245 (271)
T ss_pred             HHHHcCCchhhccCCHHHHHHhcc-cccccccccCCcccCcccCCcCCcCCCcceeccccc-CCC----ccceeCcccCc
Confidence            345556667776555443322211 11222334 678899999999999999864321100 000    01135667899


Q ss_pred             cchhhhhcCcccccccCCCcc
Q 027264          168 YCGFCQEACPVDAIVEGPNFE  188 (226)
Q Consensus       168 ~Cg~Cv~~CP~~Ai~~~~~~~  188 (226)
                      .||.|+++||++||.++..+.
T Consensus       246 ~Cg~Cv~~CP~~Ai~~~~r~~  266 (271)
T PRK09477        246 TCGRCIDVCSEDVFNFTIRFK  266 (271)
T ss_pred             ChhHHHhhcCccceeeccccc
Confidence            999999999999999876543

>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit

Probab=98.94  E-value=2.5e-10  Score=90.42  Aligned_cols=56  Identities=34%  Similarity=0.723  Sum_probs=45.3

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .++.++|++|+.|+++||++++......         ...++.+.|++||.|+.+||++||.+.+
T Consensus       109 ~id~~~Ci~Cg~C~~aCp~~ai~~~~~~---------~~~i~~~~C~~Cg~Cv~~CP~~AI~~~~  164 (165)
T TIGR01944       109 LIDEDNCIGCTKCIQACPVDAIVGAAKA---------MHTVIADECTGCDLCVEPCPTDCIEMIP  164 (165)
T ss_pred             EEECCcCCChhHHHHhCCccceEecCCC---------ceEeecccccChhHHHHhcCcCceEeeC
Confidence            3567899999999999999988654321         2345668899999999999999998654

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.

>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family

Probab=98.91  E-value=4.1e-10  Score=96.97  Aligned_cols=62  Identities=34%  Similarity=0.652  Sum_probs=47.3

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      +.++.++|++||.|+.+||.+++.+......     .....++...|.+||.|+.+||++||.+...
T Consensus        43 ~~~~~~~C~~C~~C~~~Cp~~a~~~~~~~~~-----~~~~~~~~~~C~~Cg~C~~~CP~~Ai~~~g~  104 (295)
T TIGR02494        43 LLFKENRCLGCGKCVEVCPAGTARLSELADG-----RNRIIIRREKCTHCGKCTEACPSGALSIVGE  104 (295)
T ss_pred             EEEccccCCCCchhhhhCcccccccccccCC-----CcceeechhhcCchhHhhccCcHhHHhhhcc
Confidence            3467889999999999999999863221100     1134677789999999999999999987543

This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0

>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

Probab=98.90  E-value=4.3e-10  Score=94.09  Aligned_cols=57  Identities=33%  Similarity=0.648  Sum_probs=47.9

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.++|+.||.|.++|+.+||...+..         .+.+++..|.+||.|..+||.+||.+++
T Consensus        64 p~i~~e~C~~CG~C~~vC~f~Ai~~~~~~---------~~~~~~~lC~GCgaC~~~CP~~AI~~~~  120 (284)
T COG1149          64 PEIDPEKCIRCGKCAEVCRFGAIVVLPGG---------KPVLNPDLCEGCGACSIVCPEPAIEEEP  120 (284)
T ss_pred             cccChhhccccCcHHHhCCCCeEEEcCCC---------ceecCcccccCcccceeeCCCccccccc
Confidence            44677889999999999999999764332         4677889999999999999999998654

>PRK05035 electron transport complex protein RnfC; Provisional

Probab=98.88  E-value=5e-11  Score=112.83  Aligned_cols=98  Identities=23%  Similarity=0.443  Sum_probs=60.1

Q ss_pred             ccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcccchhcHHHhhcCHH
Q 027264          123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKE  202 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~  202 (226)
                      ....|+.||.|+.+||.+.+...................+...|+.||.|..+||.+ |.+...+..........-.+..
T Consensus       368 ~e~~CI~CG~Cv~aCP~~llP~~l~~~~~~~d~~~~~~~~~~~CieCG~C~~vCPs~-Iplv~~~r~aK~~i~~~~~~~~  446 (695)
T PRK05035        368 PEQPCIRCGACADACPASLLPQQLYWFAKAEEHDKAQEYNLFDCIECGACAYVCPSN-IPLVQYYRQAKAEIRAIEQEKK  446 (695)
T ss_pred             chhhcCCcccHHHHCCccchhhhHHHhhhccccchhhhcChhhccccCcccccCCCC-CcHHHHHHHHHHHHHHhhhhhh
Confidence            457899999999999999876432211111111111234567899999999999999 6655544444433333333344


Q ss_pred             HHhhcCCCchHHHHHHhhh
Q 027264          203 KLLENGDRWETEIAENLRS  221 (226)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~  221 (226)
                      +......+++++.+++.+.
T Consensus       447 ~a~~ar~r~e~r~~R~~r~  465 (695)
T PRK05035        447 KAEEAKARFEARQARLERE  465 (695)
T ss_pred             hHHHHHHHHHHHHHHHHHH
Confidence            4445566666666666543

>TIGR02700 flavo_MJ0208 archaeoflavoprotein, MJ0208 family

Probab=98.87  E-value=5.4e-10  Score=93.32  Aligned_cols=63  Identities=35%  Similarity=0.785  Sum_probs=50.8

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcccchhc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTET  193 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~  193 (226)
                      .++.++|++|+.|+++||.+++.....          ...++...|..||.|+.+||.+||...++++.....
T Consensus       144 ~id~~~C~~C~~C~~~CP~~ai~~~~~----------~~~i~~~~C~~Cg~C~~~CP~~AI~~~~~~~~~~~~  206 (234)
T TIGR02700       144 MIDRKRCKGCGICVDACPRSAIDMVDG----------KAFIRLLKCVGCGKCKEACPYNAIHGGLEYEMRVRS  206 (234)
T ss_pred             EEChhHCcCcchHHHhCCcccEEecCC----------ceEEchhhCCccchHHhhCCCCceecCCceEEeeee
Confidence            356789999999999999998876432          235677899999999999999999988776655433

This model describes one of two paralogous families of archaealflavoprotein. The other, described by TIGR02699 and typified by the partially characterized AF1518 of Archaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown.

>PRK14028 pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional

Probab=98.85  E-value=1.1e-09  Score=95.16  Aligned_cols=67  Identities=33%  Similarity=0.637  Sum_probs=46.2

Q ss_pred             CCCccccccccccchhccccccccchhhhh--ccCCc-cccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEER--EDGSR-RTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~--~~~~~-~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ..++.++|+.|+.|..+||..++.......  ..+.. .......+...|.+|+.|+.+||++||.+..+
T Consensus       242 p~id~~~Ci~C~~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~d~~~C~gCg~C~~~CP~~AI~~~~e  311 (312)
T PRK14028        242 PVIDHSKCIMCRKCWLYCPDDAIIEAWREAEGPRGRKFRMKMIDFDYQYCKGCGVCAEVCPTGAIQMVRE  311 (312)
T ss_pred             eEECcccCcCcccccccCChhhhhcccccccCcccccccceeecCCcccCcCcCchhhhCCHhheEeccc
Confidence            345788999999999999998875321110  00000 11123456678999999999999999987653

>TIGR00402 napF ferredoxin-type protein NapF

Probab=98.85  E-value=1.2e-09  Score=79.45  Aligned_cols=57  Identities=25%  Similarity=0.638  Sum_probs=44.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...++|++|+.|+.+||.+++.......       ..+.++...|++||.|+.+||++||....
T Consensus        31 ~~~~~C~~C~~C~~~CP~~~i~~~~~g~-------~~~~i~~~~C~~Cg~C~~~CP~~Ai~~~~   87 (101)
T TIGR00402        31 LFSAVCTRCGECASACENNILQLGQQGQ-------PTVEFDNAECDFCGKCAEACPTNAFHPRF   87 (101)
T ss_pred             cCcCcCcChhHHHHHcCcccceeccCCc-------eeeEecCccCcCccChhhHCCccccCcCC
Confidence            3457999999999999999887653210       12456778999999999999999997543

The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation.

>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]

Probab=98.84  E-value=1.4e-09  Score=101.28  Aligned_cols=66  Identities=30%  Similarity=0.703  Sum_probs=45.0

Q ss_pred             ccCCCccccccccccchhcccc----ccccchhhhhccCCccc--cccccCCCCCCcchhhhhcCcccccccCC
Q 027264          118 RRYPTGEERCIACKLCEAVCPA----QAITIEAEEREDGSRRT--TRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       118 ~~~~~~~~~Ci~Cg~C~~~CP~----~ai~~~~~~~~~~~~~~--~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      |.+..+.++||.||.|+++|-.    .+|.++.+.  ...+..  ....++...|..||.|+++||++|+..++
T Consensus       142 Pfy~ydp~qCIlCgRCVeaCqevqv~eaL~i~w~~--~~pRV~wd~~~~i~~SSCVsCG~CvtVCP~nALmek~  213 (978)
T COG3383         142 PFYIYDPNQCILCGRCVEACQEVQVNEALTIDWRG--EDPRVIWDNDVPINESSCVSCGACVTVCPVNALMEKS  213 (978)
T ss_pred             CeEEecchheeehhHHHHHHHhhhceeEEEeeccc--CCcceecCCCCccccccccccCccceecchhhhhhhh
Confidence            4455788999999999999983    344443321  111111  11234567899999999999999997554

>PRK08764 ferredoxin; Provisional

Probab=98.82  E-value=1.2e-09  Score=83.68  Aligned_cols=52  Identities=37%  Similarity=0.709  Sum_probs=41.6

Q ss_pred             ccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ..++|++|+.|+++||+++|......         ...++.+.|++||.|+.+||++||.+
T Consensus        83 ~~~~Ci~C~~Cv~aCp~~ai~~~~~~---------~~~v~~~~C~~Cg~Cv~~CP~~Ai~~  134 (135)
T PRK08764         83 VEADCIGCTKCIQACPVDAIVGGAKH---------MHTVIAPLCTGCELCVPACPVDCIEL  134 (135)
T ss_pred             CcccCcCcchHHHhCChhhcCccCCC---------ceeecCCcCcCccchhhhcCccceEe
Confidence            35799999999999999988653211         12356678999999999999999975

>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated

Probab=98.80  E-value=1.7e-09  Score=90.26  Aligned_cols=79  Identities=33%  Similarity=0.567  Sum_probs=50.3

Q ss_pred             CCCccccccccccchhcccc--ccccchhhhhccCCcccc---ccccCCCCCCcchhhhhcCcccccccCCCcccchhcH
Q 027264          120 YPTGEERCIACKLCEAVCPA--QAITIEAEEREDGSRRTT---RYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETH  194 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~--~ai~~~~~~~~~~~~~~~---~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~  194 (226)
                      +.++.++|+.||.|+.+||.  +...+....+........   ....+...|++||.|+.+||++||..+..      ..
T Consensus       141 i~~d~~kCi~Cg~Cv~aC~~i~~~~~~~~~~~g~~~~i~~~~~~~~~~~~~C~~Cg~Cv~vCP~gAL~~~~~------~~  214 (234)
T PRK07569        141 FGIDHNRCVLCTRCVRVCDEIEGAHTWDVAGRGAKSRVITDLNQPWGTSETCTSCGKCVQACPTGAIFRKGS------TV  214 (234)
T ss_pred             EEeehhhCcCccHHHHHHHHhcCCceeeecccCCcceEeecCCccccccccccchHHHHHhCCCCcEEecCC------cH
Confidence            44678999999999999994  333332221111111100   01123458999999999999999987754      46


Q ss_pred             HHhhcCHHHH
Q 027264          195 EELLYDKEKL  204 (226)
Q Consensus       195 ~~~~~d~~~~  204 (226)
                      +++.+|...+
T Consensus       215 ~~~~~~~~~~  224 (234)
T PRK07569        215 GEMEKDRDKL  224 (234)
T ss_pred             HHhhcCcccc
Confidence            6666665533

>COG2768 Uncharacterized Fe-S center protein [General function prediction only]

Probab=98.77  E-value=1.2e-09  Score=92.22  Aligned_cols=58  Identities=41%  Similarity=0.801  Sum_probs=49.0

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEY  189 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~  189 (226)
                      .....+|+.||.|++.||++|+....           ...|+.+.|++|+.|..+||++|+...+.+..
T Consensus       189 ~v~e~kc~~c~~cv~~cp~~Ai~~~~-----------~~~I~~~~ci~c~~c~~ac~~gav~~~W~~~~  246 (354)
T COG2768         189 VVVEEKCYDCGLCVKICPVGAITLTK-----------VVKIDYEKCIGCGQCMEACPYGAVDQNWEEDS  246 (354)
T ss_pred             eeeeecccccchhhhhCCCcceeccc-----------ceeechhhccchhhhhhhccCcccccchhhcc
Confidence            35678999999999999999998763           34788899999999999999999987665443

>PF13247 Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX_B 2VPZ_B 2VPW_F 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B

Probab=98.74  E-value=2.1e-09  Score=77.64  Aligned_cols=55  Identities=42%  Similarity=0.846  Sum_probs=36.3

Q ss_pred             cccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          124 EERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       124 ~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ...|..|.  .|+++||++||..++..+        .+.+|.+.|++|+.|+.+||++||.+.+.
T Consensus         6 ~~~C~hC~~ppC~~~CP~~Ai~~~~~~G--------~V~id~~~CigC~~C~~aCP~~ai~~~~~   62 (98)
T PF13247_consen    6 PVQCRHCEDPPCVEACPTGAIYKDPEDG--------IVVIDEDKCIGCGYCVEACPYGAIRFDPD   62 (98)
T ss_dssp             EEC---BSS-HHHHHCTTTSEEEETTTS---------EEE-TTTCCTHHHHHHH-TTS-EEEETT
T ss_pred             CCcCcCcCCCchhhhCCccceEEEcCCC--------eEEechhhccCchhhhhhhccCcceeecc
Confidence            45688886  888889988887765221        45678888888988999999888876654

...

>TIGR03149 cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S protein

Probab=98.72  E-value=2.4e-09  Score=88.88  Aligned_cols=55  Identities=29%  Similarity=0.712  Sum_probs=35.8

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch----------hhhhcCcccccccCCCcc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG----------FCQEACPVDAIVEGPNFE  188 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg----------~Cv~~CP~~Ai~~~~~~~  188 (226)
                      ++.++|++|+.|+.+||.+++.....            ..+...|++|+          .|+.+||++||.+.+.-+
T Consensus       122 id~~~C~~C~~C~~aCP~~A~~~~~~------------~~~~~kC~~C~~~~~~~g~~P~Cv~~Cp~~Ai~f~~~~~  186 (225)
T TIGR03149       122 VHKDLCVGCQYCIAACPYRVRFIHPV------------TKSADKCNFCRDTNLAEGKLPACVESCPTKALTFGDLND  186 (225)
T ss_pred             echhhCCcchHHHHhCCCCCcEecCC------------CCccccCCCCCcchhhCCCCCcccccCccCCEEEecccc
Confidence            44566777777777777666543221            12346788887          788888888888766433

Members of this protein family are the Fe-S protein, NrfC, of a cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family TIGR03146) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of a polysulfide reductase.

>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only

Probab=98.72  E-value=3.4e-09  Score=94.30  Aligned_cols=64  Identities=30%  Similarity=0.566  Sum_probs=44.7

Q ss_pred             Cccccccccccchhccccccccch--hhhhccCCc--cccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIE--AEEREDGSR--RTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~--~~~~~~~~~--~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++||.|+++||.+++...  ...+.....  ......++...|+.||.|+.+||++||....
T Consensus         4 id~~kCi~Cg~Cv~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~id~~~C~~Cg~Cv~~CP~~Ai~~~~   71 (374)
T TIGR02512         4 RDMSKCIGCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLVCPVGAITEKD   71 (374)
T ss_pred             echhhCCcChHhhhhCCHhhccccccccccCCccccccccccccCcccCcCccCHHHhCCCChhhhhc
Confidence            567899999999999999988632  111110000  0012346778999999999999999997653

This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than Pfam model pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some heterogeneity in terms of periplasmic, cytosolic, or hydrogenosome location, NAD or NADP dependence, and overal protein protein length.

>TIGR02912 sulfite_red_C sulfite reductase, subunit C

Probab=98.72  E-value=4.8e-09  Score=91.31  Aligned_cols=56  Identities=34%  Similarity=0.723  Sum_probs=44.4

Q ss_pred             CCccccccccccchhccccc---cccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          121 PTGEERCIACKLCEAVCPAQ---AITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~---ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      .++.++|+.||.|+++||..   ++.....          ...++...|++||.|+.+||++|+..+..
T Consensus       165 ~~d~~~C~~Cg~C~~~Cp~~a~~ai~~~~~----------~~~id~~~C~~Cg~Cv~~CP~~Al~~~~~  223 (314)
T TIGR02912       165 QYDADRCIGCGACVKVCKKKAVGALSFENY----------KVVRDHSKCIGCGECVLKCPTGAWTRSEE  223 (314)
T ss_pred             ceeCccCCcchHHHHhcChhhcCceeccCC----------eEEeCCCcCcCcchhhhhCCHhhcccCcC
Confidence            46788999999999999974   4443221          34678889999999999999999976653

Members of this protein family include the C subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite.

>PRK10194 ferredoxin-type protein; Provisional

Probab=98.71  E-value=5.1e-09  Score=82.71  Aligned_cols=53  Identities=26%  Similarity=0.614  Sum_probs=40.1

Q ss_pred             cccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          128 IACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       128 i~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.|+.|+.+||+++|.+.....+     .....++.+.|++||.|+.+||++||.+++
T Consensus       107 ~~C~~C~~~CP~~Ai~~~~~~~~-----~~~~~i~~~~C~gCg~C~~~CP~~AI~~~~  159 (163)
T PRK10194        107 VECRRCQDSCEPMAIIFRPTLSG-----IYQPQLNSQLCNGCGACAASCPVSAITAEY  159 (163)
T ss_pred             CCcCcchhhCCHhHeEeeecCCC-----cccceeCcccCcCcchhhhhCCccceEecc
Confidence            68999999999988877532110     012356778999999999999999998765

>PRK09898 hypothetical protein; Provisional

Probab=98.70  E-value=5e-09  Score=86.00  Aligned_cols=21  Identities=48%  Similarity=0.975  Sum_probs=10.9

Q ss_pred             cccccccc--cchhccccccccc
Q 027264          124 EERCIACK--LCEAVCPAQAITI  144 (226)
Q Consensus       124 ~~~Ci~Cg--~C~~~CP~~ai~~  144 (226)
                      ...|+.|+  .|+.+||+++|..
T Consensus       120 ~~~C~~C~~~~C~~~CP~gAi~~  142 (208)
T PRK09898        120 ADTCRQCKEPQCMNVCPIGAITW  142 (208)
T ss_pred             CccCCCccCcchhhhCCcceEEe
Confidence            34455554  5555555555443

>COG0437 HybA Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]

Probab=98.70  E-value=6.1e-09  Score=84.27  Aligned_cols=59  Identities=32%  Similarity=0.741  Sum_probs=42.8

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc------h---hhhhcCcccccccCCCcccch
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------G---FCQEACPVDAIVEGPNFEYST  191 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C------g---~Cv~~CP~~Ai~~~~~~~~~~  191 (226)
                      .++.++||+|+.|+.+||.+|..+....+            ..++|++|      |   .|+.+||++|+.+++.-+..+
T Consensus        96 ~vd~d~CIGC~yCi~ACPyga~~~~~~~~------------~~~KCt~C~~ri~~g~~PaCV~~CP~~A~~fG~~~d~~~  163 (203)
T COG0437          96 LVDKDLCIGCGYCIAACPYGAPQFNPDKG------------VVDKCTFCVDRVAVGKLPACVEACPTGALIFGDIDDPKS  163 (203)
T ss_pred             EecCCcccCchHHHhhCCCCCceeCcccC------------cccccCcchhhHhcCCCCcccccCCcccccccchhhcch
Confidence            35678888888888888888877665221            13678888      7   788888888888777655544

>TIGR03224 benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA protein

Probab=98.69  E-value=5.4e-09  Score=94.13  Aligned_cols=54  Identities=35%  Similarity=0.718  Sum_probs=44.8

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ..++.++|++|+.|+.+||.+++.....          .+.++...|.+|+.|+.+||.+||..
T Consensus         5 ~~id~~~Ci~C~~C~~~CP~~ai~~~~~----------~~~i~~~~C~~C~~C~~~CP~~AI~~   58 (411)
T TIGR03224         5 HLIDPEICIRCNTCEETCPIDAITHDDR----------NYVVKADVCNGCMACVSPCPTGAIDN   58 (411)
T ss_pred             eeeCcccCcCccchhhhCCcccEeccCC----------ceEeCcccCcCHHHHHhhcCccccee
Confidence            3467889999999999999998876432          23567789999999999999999973

Members of this protein family are BoxA, the A component of the BoxAB benzoyl-CoA oxygenase/reductase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. BoxA is a homodimeric iron-sulphur-flavoprotein and acts as an NADPH-dependent reductase for BoxB.

>PRK10194 ferredoxin-type protein; Provisional

Probab=98.69  E-value=5e-09  Score=82.77  Aligned_cols=54  Identities=20%  Similarity=0.550  Sum_probs=40.8

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++|++||.|+++||.++|.......       ..+.++.+.|++|+.|+.+||++||...
T Consensus        33 ~~~C~~Cg~C~~aCp~~~i~~~~~~~-------~~~~~~~~~C~~C~~C~~~CP~~ai~~~   86 (163)
T PRK10194         33 LTHCTRCDACINACENNILQRGAGGY-------PSVNFKNNECSFCYACAQACPESLFSPR   86 (163)
T ss_pred             hhhCcChhHHHHHcChhhcccCCCCc-------eeeeecCCCCCCchhhHhhCcchheecc
Confidence            56899999999999999886543210       1234566789999999999999998654

>PF13484 Fer4_16: 4Fe-4S double cluster binding domain

Probab=98.68  E-value=3.6e-09  Score=71.01  Aligned_cols=54  Identities=39%  Similarity=0.868  Sum_probs=36.1

Q ss_pred             cccccccchhccccccccchhh-hhccCC------ccccccccCCCCC------CcchhhhhcCccc
Q 027264          126 RCIACKLCEAVCPAQAITIEAE-EREDGS------RRTTRYDIDMTKC------IYCGFCQEACPVD  179 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~~-~~~~~~------~~~~~~~~d~~~C------~~Cg~Cv~~CP~~  179 (226)
                      .|+.|++|+++||++||..... ......      .....+..+...|      .+||.|+.+||.+
T Consensus         1 ~C~~C~~C~~~CP~~AI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~C~~C~~vCP~N   67 (67)
T PF13484_consen    1 FCITCGKCAEACPTGAISGEDEPTWEPKGCWSYNNPGVKKWRIDWEKCVSYWDCYGCGICQKVCPFN   67 (67)
T ss_pred             CCcchhHHHHhCcHhhccCCCcCeeecCcchhccCccccCccchHHhhhcCCCccccchhhccCCCC
Confidence            4999999999999999988721 111100      1112334444445      4999999999975

>PRK14993 tetrathionate reductase subunit B; Provisional

Probab=98.68  E-value=6e-09  Score=87.44  Aligned_cols=60  Identities=28%  Similarity=0.608  Sum_probs=46.1

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccCCCcccch
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPNFEYST  191 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~~~~~~~~  191 (226)
                      .++.++|++|+.|+.+||.+++.+...            ..+.+.|++|+         .|+.+||++||.+.+.-+..+
T Consensus       126 ~id~~~CigC~~Cv~aCP~~Ai~~~~~------------~~~~~KC~~C~~r~~~G~~PaCv~~CP~~Al~~g~~~~~~s  193 (244)
T PRK14993        126 VVDNKRCVGCAYCVQACPYDARFINHE------------TQTADKCTFCVHRLEAGLLPACVESCVGGARIIGDIKDPHS  193 (244)
T ss_pred             EEcHHHCCCHHHHHHhcCCCCCEEeCC------------CCCcccCcCCcchhhCCCCcccchhcccCCEEEcccccchH
Confidence            356788999999999999998876542            23457899998         899999999998876554443


Q ss_pred             h
Q 027264          192 E  192 (226)
Q Consensus       192 ~  192 (226)
                      +
T Consensus       194 ~  194 (244)
T PRK14993        194 R  194 (244)
T ss_pred             H
Confidence            3

>PF13247 Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX_B 2VPZ_B 2VPW_F 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B

Probab=98.68  E-value=1.8e-09  Score=77.99  Aligned_cols=53  Identities=36%  Similarity=0.824  Sum_probs=36.2

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc---------hhhhhcCcccccccCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC---------GFCQEACPVDAIVEGP  185 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C---------g~Cv~~CP~~Ai~~~~  185 (226)
                      .++.++|++|+.|+.+||.+++.+.....            ...+|..|         ..|+++||++||.+++
T Consensus        36 ~id~~~CigC~~C~~aCP~~ai~~~~~~~------------~~~KCdlC~~r~~~G~~PaCv~~Cp~~Al~~g~   97 (98)
T PF13247_consen   36 VIDEDKCIGCGYCVEACPYGAIRFDPDTG------------KARKCDLCIDRIEEGEEPACVEACPTGALTFGD   97 (98)
T ss_dssp             EE-TTTCCTHHHHHHH-TTS-EEEETTTT------------CEEE--TTHHHHTTT-S-HHHHH-TTS-EEEEE
T ss_pred             EechhhccCchhhhhhhccCcceeecccc------------cCCcCceehhhhhcCCCChhHHhccccceEEec
Confidence            46789999999999999999998865421            22468888         6899999999998753

...

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=98.67  E-value=4.9e-09  Score=89.02  Aligned_cols=70  Identities=26%  Similarity=0.608  Sum_probs=53.4

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc---CCCcccchhcHHH
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE---GPNFEYSTETHEE  196 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~---~~~~~~~~~~~~~  196 (226)
                      +.+ .++|++|+.|+.+||.+++.+++..         ....+...|+.|+.|+.+||.+||.+   ++.|.+..++.+.
T Consensus       165 I~i-~~~C~~C~~C~~~CP~~vi~~~~~~---------~~v~~~~~C~~C~~Ci~~CP~~AI~i~~~~~~~if~vEs~G~  234 (263)
T PRK00783        165 IEV-SEDCDECEKCVEACPRGVLELKEGK---------LVVTDLLNCSLCKLCERACPGKAIRVSDDENKFIFTVESDGS  234 (263)
T ss_pred             ccc-cccCCchHHHHHhCCccccEecCCe---------EEEeChhhCCCchHHHHhCCCCceEEEEcCCeEEEEeccCCC
Confidence            434 6899999999999999998875421         12336678999999999999999964   4556677777777


Q ss_pred             hhc
Q 027264          197 LLY  199 (226)
Q Consensus       197 ~~~  199 (226)
                      +..
T Consensus       235 l~p  237 (263)
T PRK00783        235 LPV  237 (263)
T ss_pred             CCH
Confidence            644

>TIGR02176 pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric

Probab=98.66  E-value=8.8e-09  Score=102.90  Aligned_cols=67  Identities=31%  Similarity=0.626  Sum_probs=47.4

Q ss_pred             CCCccccccccccchhccccccccchhhh-----h---c------cC---CccccccccCCCCCCcchhhhhcCccc--c
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEE-----R---E------DG---SRRTTRYDIDMTKCIYCGFCQEACPVD--A  180 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~-----~---~------~~---~~~~~~~~~d~~~C~~Cg~Cv~~CP~~--A  180 (226)
                      +.++.++|+.||.|+.+||+++|......     .   .      .+   ........++.+.|++||.|+.+||.+  |
T Consensus       678 p~~~~~~Ci~Cg~C~~vCP~~ai~~~~~~~~~~~~ap~~~~~~~~~~~~~~~~~~~i~i~~~~C~gCg~Cv~~CP~~~~A  757 (1165)
T TIGR02176       678 PVWVPDNCIQCNQCAFVCPHAAIRPKLADEEELENAPAGFKSLDAKGKELEGMKFRIQISPLDCTGCGNCVDICPAKEKA  757 (1165)
T ss_pred             ceeccccCCCccchHHhcChhhccccccchhhhhcCcccchhhhhhcccccccceeEEeccccCcCccchhhhcCCCCcc
Confidence            44678899999999999999998753110     0   0      00   001112457788999999999999995  8


Q ss_pred             cccCCC
Q 027264          181 IVEGPN  186 (226)
Q Consensus       181 i~~~~~  186 (226)
                      |.+++.
T Consensus       758 l~m~~~  763 (1165)
T TIGR02176       758 LVMQPL  763 (1165)
T ss_pred             ccccch
Confidence            987764

This model represents a single chain form of pyruvate:ferredoxin (or flavodoxin) oxidoreductase. This enzyme may transfer electrons to nitrogenase in nitrogen-fixing species. Portions of this protein are homologous to gamma subunit of the four subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.

>TIGR01660 narH nitrate reductase, beta subunit

Probab=98.65  E-value=8.4e-09  Score=92.02  Aligned_cols=55  Identities=31%  Similarity=0.478  Sum_probs=41.0

Q ss_pred             ccccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          123 GEERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       123 ~~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ....|++|+  .|+.+||++||......+        .+.++.+.|++|+.|+.+||++||.+..
T Consensus       179 ~p~~C~HC~nP~CV~ACPtGAI~k~eedG--------iV~ID~dkCiGCg~CV~ACPygAI~~n~  235 (492)
T TIGR01660       179 LPRLCEHCLNPACVASCPSGAIYKREEDG--------IVLIDQDKCRGWRMCISGCPYKKIYFNW  235 (492)
T ss_pred             CCCcCcCCCcccchhhCccCCeEEecCCC--------eEEEehhhccChHHHHHhCCCCCcEecC
Confidence            456899998  899999998886432211        2356778899999999999999887654

The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model.The seed members used in this model are all experimentally characterized and include the following: NarH and NarY, both E.Coli, sequences from B. Subtilis, Pseudomonas fluorescens, Paracoccus denitrificans, and Halomonas halodenitrificans. This model also matches PFAM pfam00037 for 4Fe-4S binding domain.

>COG1142 HycB Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]

Probab=98.64  E-value=7.8e-09  Score=81.00  Aligned_cols=51  Identities=39%  Similarity=0.774  Sum_probs=40.1

Q ss_pred             ccccc--ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          126 RCIAC--KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       126 ~Ci~C--g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      .|..|  .-|+++||++||..+++          ...++.+.|++||.|+.+||+|||.+...
T Consensus        52 ~C~qCedaPC~~vCP~~AI~~~~~----------~v~V~~ekCiGC~~C~~aCPfGai~~~~~  104 (165)
T COG1142          52 VCHHCEDAPCAEVCPVGAITRDDG----------AVQVDEEKCIGCKLCVVACPFGAITMVSY  104 (165)
T ss_pred             cCCCCCCcchhhhCchhheeecCC----------ceEEchhhccCcchhhhcCCcceEEEEee
Confidence            35555  68999999999987743          35677889999999999999999986553

>COG4656 RnfC Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion]

Probab=98.61  E-value=7.5e-10  Score=99.70  Aligned_cols=96  Identities=24%  Similarity=0.450  Sum_probs=60.9

Q ss_pred             cccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcccchhcHHHhhcCHHHHh
Q 027264          126 RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLL  205 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~~~~  205 (226)
                      .|+.|+.|+.+||++.+...-..................+|+.||.|..+||.+ |.+...|+.....-...-.......
T Consensus       366 sCi~C~~C~d~CP~~Llp~ql~~~a~~~~~~e~~~~~l~dCIECg~Ca~vCPs~-iplvq~~r~~Ka~i~~~~~~~~~~~  444 (529)
T COG4656         366 SCIRCSLCADACPVNLLPQQLYWFAKGEQHDEEEEHNLLDCIECGACAYVCPSN-IPLVQYFRQEKAEILAQRQELKKAE  444 (529)
T ss_pred             ccccHHHHHHhCccccCHHHhhHHhhhhhhhHHHHHHhhhhhhhCcchhcCCCC-CCHHHHHHHHHHHHHHhchhhhccc
Confidence            799999999999998766544332222222223344567899999999999998 5555555554444444434444444


Q ss_pred             hcCCCchHHHHHHhhhh
Q 027264          206 ENGDRWETEIAENLRSE  222 (226)
Q Consensus       206 ~~~~~~~~~~~~~~~~~  222 (226)
                      ....++.+..+++...+
T Consensus       445 ~~~~rf~~~~~rl~~~~  461 (529)
T COG4656         445 EAKTRFEARTARLEREK  461 (529)
T ss_pred             cccchhhhhhhhhhhhh
Confidence            55666666655555443

>PRK08493 NADH dehydrogenase subunit G; Validated

Probab=98.61  E-value=1.3e-08  Score=98.15  Aligned_cols=66  Identities=23%  Similarity=0.524  Sum_probs=43.9

Q ss_pred             ccCCCccccccccccchhcccc----ccccchhhhhccCCcc----------------------ccccccCCCCCCcchh
Q 027264          118 RRYPTGEERCIACKLCEAVCPA----QAITIEAEEREDGSRR----------------------TTRYDIDMTKCIYCGF  171 (226)
Q Consensus       118 ~~~~~~~~~Ci~Cg~C~~~CP~----~ai~~~~~~~~~~~~~----------------------~~~~~~d~~~C~~Cg~  171 (226)
                      +.+..+.++||.|++|+++|+.    .+|.+..+  +.....                      .....-+...|+.||.
T Consensus       134 ~~I~~D~~rCI~C~RCVr~C~ev~g~~al~~~~R--G~~~~~~~~~~~~~~da~~~~~~~~~~~i~~~~~~~~~C~~CG~  211 (819)
T PRK08493        134 GKINYDPSLCIVCERCVTVCKDKIGESALKTVPR--GLDAPDKSFKESMPKDAYAVWSKKQKSLIGPVGGETLDCSFCGE  211 (819)
T ss_pred             CcEEechhhcccccHHHhhCcccccchhhhhccC--CcccccccccccccccchhhhhhcccceecccCCCcccccccCc
Confidence            3456788999999999999995    34443322  211100                      0000112468999999


Q ss_pred             hhhcCcccccccCC
Q 027264          172 CQEACPVDAIVEGP  185 (226)
Q Consensus       172 Cv~~CP~~Ai~~~~  185 (226)
                      |+.+||+|||..++
T Consensus       212 Cv~VCPvGAL~~k~  225 (819)
T PRK08493        212 CIAVCPVGALSSSD  225 (819)
T ss_pred             HHHhCCCCccccCc
Confidence            99999999998764

>PRK07118 ferredoxin; Validated

Probab=98.61  E-value=1.4e-08  Score=86.80  Aligned_cols=52  Identities=46%  Similarity=0.813  Sum_probs=45.0

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...|+.|+.|+++||.++|.++..          ...+|.+.|++||.|+.+||++||.+..
T Consensus       212 ~~~Ci~Cg~Cv~~CP~~AI~~~~~----------~~vId~~~C~~Cg~C~~~CP~~AI~~~~  263 (280)
T PRK07118        212 EVGCIGCGKCVKACPAGAITMENN----------LAVIDQEKCTSCGKCVEKCPTKAIRILN  263 (280)
T ss_pred             ccccccchHHHhhCCcCcEEEeCC----------cEEEcCCcCCCHHHHHHhCCccccEeec
Confidence            467999999999999999988543          3467889999999999999999998654

>TIGR03478 DMSO_red_II_bet DMSO reductase family type II enzyme, iron-sulfur subunit

Probab=98.61  E-value=1.2e-08  Score=87.60  Aligned_cols=53  Identities=26%  Similarity=0.610  Sum_probs=40.1

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc---------hhhhhcCcccccccCCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC---------GFCQEACPVDAIVEGPN  186 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C---------g~Cv~~CP~~Ai~~~~~  186 (226)
                      ++.++|++|+.|+.+||.+++.+...            ....++|++|         ..|+.+||.+|+.++..
T Consensus       159 ID~ekCiGCg~Cv~ACPygAi~~n~~------------~~~~eKC~~C~~Rie~G~~PaCv~aCP~~A~~fGdl  220 (321)
T TIGR03478       159 VDQERCKGYRYCVEACPYKKVYFNPQ------------SQKSEKCIGCYPRIEKGIAPACVKQCPGRIRFVGYL  220 (321)
T ss_pred             ECHHHCcchHHHHHhCCCCCcEecCC------------CCchhhCCCchhhhccCCCCHHHhhcCcccEEEEeC
Confidence            56678888888888888888776432            2345689999         78999999999887654

This model represents the iron-sulfur subunit, typically called the beta subunit, of various proteins that also contain a molybdopterin subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase.

>PF13183 Fer4_8: 4Fe-4S dicluster domain; PDB: 2BS4_B 1E7P_B 2BS3_B 1QLB_B 2BS2_B 3P4Q_N 1KFY_N 3CIR_N 3P4R_B 2B76_N

Probab=98.60  E-value=2.2e-09  Score=69.67  Aligned_cols=55  Identities=31%  Similarity=0.681  Sum_probs=23.9

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~  179 (226)
                      .++|++||.|..+||+............... ........+.|+.||.|+.+||++
T Consensus         2 ~~~Ci~Cg~C~~~CP~~~~~~~~~~~~~~~~-~~~~~~~~~~C~~C~~C~~~CP~~   56 (57)
T PF13183_consen    2 LSKCIRCGACTSVCPVYRNTGRFSHPPRDRR-SAVLREEAWSCTTCGACSEVCPVG   56 (57)
T ss_dssp             HHC--S-SHHHHCSHHHHHHHHHHTSTTS---HHHHHHHHGG-----HHHHH-TT-
T ss_pred             HHHccCccChHHHChhhhcccccccCcchhH-HHhhcccccCCcCcCCccCcCccc
Confidence            4689999999999996432221111111110 001111127899999999999997

...

>TIGR03478 DMSO_red_II_bet DMSO reductase family type II enzyme, iron-sulfur subunit

Probab=98.60  E-value=1.1e-08  Score=87.74  Aligned_cols=56  Identities=30%  Similarity=0.587  Sum_probs=45.3

Q ss_pred             Cccccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ....+|..|+  .|+.+||++||......+        .+.+|.+.|++|+.|+.+||.+|+.+..
T Consensus       126 y~p~~C~hC~nP~Cv~aCPtgAI~k~eedG--------iV~ID~ekCiGCg~Cv~ACPygAi~~n~  183 (321)
T TIGR03478       126 YLPRICNHCTNPACLAACPTGAIYKREEDG--------IVLVDQERCKGYRYCVEACPYKKVYFNP  183 (321)
T ss_pred             EecccCCCCCCccchhhCCcCcEEEecCCC--------eEEECHHHCcchHHHHHhCCCCCcEecC
Confidence            4467999999  899999999996533211        3457888999999999999999998654

This model represents the iron-sulfur subunit, typically called the beta subunit, of various proteins that also contain a molybdopterin subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase.

>COG1148 HdrA Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]

Probab=98.59  E-value=1.3e-08  Score=91.23  Aligned_cols=51  Identities=33%  Similarity=0.896  Sum_probs=44.8

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+.|++||.|++ ||.+||+.+ .           ...|+-.|.+||.|..+||.+|+.+..
T Consensus       558 vde~~C~gC~~C~~-Cpf~ais~~-k-----------a~v~~~~C~gCG~C~~aCp~gai~~~~  608 (622)
T COG1148         558 VDEDKCTGCGICAE-CPFGAISVD-K-----------AEVNPLRCKGCGICSAACPSGAIDLAG  608 (622)
T ss_pred             cchhhhcCCcceee-CCCCceecc-c-----------cccChhhhCcccchhhhCCcccchhcc
Confidence            67889999999999 999999876 2           356778899999999999999998754

>PRK10882 hydrogenase 2 protein HybA; Provisional

Probab=98.57  E-value=1.4e-08  Score=88.44  Aligned_cols=55  Identities=25%  Similarity=0.654  Sum_probs=36.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchh-------------hhhcCcccccccCCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGF-------------CQEACPVDAIVEGPN  186 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~-------------Cv~~CP~~Ai~~~~~  186 (226)
                      ++.++|++|+.|+.+||.+++.+....          .......|..|+.             |+.+||++||.+++.
T Consensus       140 id~dkCigCg~Cv~aCP~gai~~~~~~----------~~~~~~KC~~C~~~~~~R~~~G~~PACv~aCP~gAi~fG~~  207 (328)
T PRK10882        140 YDKDVCTGCRYCMVACPFNVPKYDYNN----------PFGAIHKCELCNQKGVERLDKGGLPGCVEVCPTGAVIFGTR  207 (328)
T ss_pred             CCHHHcCcccHHHHhCCccceeccccc----------cccceeecccccccchhhhhcCCCChhhhhccccceEeccH
Confidence            456677777777777777776554321          1123357888887             888888888876653

>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]

Probab=98.57  E-value=1.7e-08  Score=86.08  Aligned_cols=50  Identities=44%  Similarity=0.893  Sum_probs=43.3

Q ss_pred             ccCCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCc
Q 027264          118 RRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACP  177 (226)
Q Consensus       118 ~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP  177 (226)
                      ..+.++++.|.+|+.|+++||++||.....          ...++.+.|+.||.|+.+||
T Consensus       165 ~~P~~~~E~c~gc~~cv~~C~~gAI~~~~~----------~l~id~~~Ci~Cg~Ci~~Cp  214 (317)
T COG2221         165 WKPKVDEELCRGCGKCVKVCPTGAITWDGK----------KLKIDGSKCIGCGKCIRACP  214 (317)
T ss_pred             ecCccCHHHhchhHhHHHhCCCCceeeccc----------eEEEehhhccCccHHhhhCC
Confidence            335678899999999999999999987652          45778899999999999999

>TIGR03149 cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S protein

Probab=98.57  E-value=2e-08  Score=83.31  Aligned_cols=56  Identities=32%  Similarity=0.675  Sum_probs=44.5

Q ss_pred             Ccccccccccc--chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~--C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+.|+.|+.  |+.+||++||......   +     .+.+|.+.|++|+.|+.+||++|+.+.+
T Consensus        89 ~~~~~C~~C~~~~Cv~~CP~gAi~~~~~~---g-----~v~id~~~C~~C~~C~~aCP~~A~~~~~  146 (225)
T TIGR03149        89 FFRKSCQHCDNAPCVAVCPTGASFKDEET---G-----IVDVHKDLCVGCQYCIAACPYRVRFIHP  146 (225)
T ss_pred             ECchhccCCcCcChHhhCCCCcEEEeCCC---C-----eEEechhhCCcchHHHHhCCCCCcEecC
Confidence            34678999996  9999999999764321   1     3457778999999999999999986543

Members of this protein family are the Fe-S protein, NrfC, of a cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family TIGR03146) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of a polysulfide reductase.

>PRK10330 formate dehydrogenase-H ferredoxin subunit; Provisional

Probab=98.56  E-value=1.7e-08  Score=80.99  Aligned_cols=65  Identities=29%  Similarity=0.604  Sum_probs=45.7

Q ss_pred             CccccccccccchhccccccccchhhhhccCCc---cccccccCCCCCCcch------hhhhcCcccccccCCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSR---RTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPN  186 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~---~~~~~~~d~~~C~~Cg------~Cv~~CP~~Ai~~~~~  186 (226)
                      ++.++|++|+.|+.+||.+++.+..........   .......+...|..|+      .|+.+||++||.+.+.
T Consensus        84 i~~~~C~~C~~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~kC~~C~~~~~~paCv~~CP~~Al~~~~~  157 (181)
T PRK10330         84 VMQERCIGCKTCVVACPYGAMEVVVRPVIRNSGAGLNVRAEKAEANKCDLCNHREDGPACMAACPTHALICVDR  157 (181)
T ss_pred             eChhhCCCcchhhhhCCccCeEeeccccccccccccccccCCceeeeCcCCCCCCCCccchhhCchhhEEEeCH
Confidence            567899999999999999999775322100000   0001234456899998      9999999999987653

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=98.55  E-value=1.3e-08  Score=86.29  Aligned_cols=65  Identities=29%  Similarity=0.681  Sum_probs=50.2

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC---CCcccchhcHHHh
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG---PNFEYSTETHEEL  197 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~---~~~~~~~~~~~~~  197 (226)
                      .++|++|+.|+++||.+++..+...         ....+...|+.|+.|+.+||.+||...   +.|.+..++.+.+
T Consensus       168 ~~~C~~C~~C~~~CP~~vi~~d~~~---------~~v~~~~~C~~C~~C~~~Cp~~AI~~~~~~~~~if~vEs~Gsl  235 (259)
T cd07030         168 DEDCDGCGKCVEECPRGVLELEEGK---------VVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSL  235 (259)
T ss_pred             hhhCCChHHHHHhCCccceEccCCe---------eEEeChhhCcCchHHHHhCCCCcEEEEecCCEEEEEEeCCCCC
Confidence            3789999999999999999775431         223566789999999999999999644   4456666666665

The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w

>TIGR03287 methan_mark_16 putative methanogenesis marker 16 metalloprotein

Probab=98.53  E-value=1.7e-08  Score=89.14  Aligned_cols=52  Identities=33%  Similarity=0.769  Sum_probs=43.1

Q ss_pred             Cccccccccccch--hccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          122 TGEERCIACKLCE--AVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~--~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ++.++|++|+.|.  .+||++++...             ..++...|+.|+.|+.+||.+|+.+...
T Consensus       299 id~dkCi~Cg~C~~~~aCPt~AI~~~-------------~~Id~~~Ci~CGaCV~aCP~~AI~~~~~  352 (391)
T TIGR03287       299 YNPERCENCDPCLVEEACPVPAIKKD-------------GTLNTEDCFGCGYCAEICPGGAFEVNLG  352 (391)
T ss_pred             EchhhCcCCCCCcCCcCCCHhhEecc-------------ceeChHhCcChHHHHhhCCccceEEeCC
Confidence            5678999999995  89999988632             1356678999999999999999987654

Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (pfam00037), with each copy having four Cys residues invariant across all members.

>COG2878 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]

Probab=98.52  E-value=1.1e-08  Score=80.47  Aligned_cols=59  Identities=31%  Similarity=0.639  Sum_probs=46.7

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEY  189 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~  189 (226)
                      ++.+.|++|.+|+.+||++||.-..+.         -..+..+.|++|++|+..||+++|.+...-++
T Consensus       112 i~e~~ciGCtkCiqaCpvdAivg~~~~---------mhtv~~dlCTGC~lCva~CPtdci~m~~~~~~  170 (198)
T COG2878         112 IDEANCIGCTKCIQACPVDAIVGATKA---------MHTVIADLCTGCDLCVAPCPTDCIEMQPVAET  170 (198)
T ss_pred             ecchhccccHHHHHhCChhhhhccchh---------HHHHHHHHhcCCCcccCCCCCCceeeeecccc
Confidence            667899999999999999998754432         12344567999999999999999987765443

>PRK08318 dihydropyrimidine dehydrogenase subunit B; Validated

Probab=98.52  E-value=2.6e-08  Score=89.97  Aligned_cols=59  Identities=25%  Similarity=0.691  Sum_probs=44.1

Q ss_pred             CCccccccccccchhccccc---cccchhhhhccCCccccccccCCCCCCcchhhhhcCcc-cccccCCC
Q 027264          121 PTGEERCIACKLCEAVCPAQ---AITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVEGPN  186 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~---ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~-~Ai~~~~~  186 (226)
                      .++.++|++|+.|+.+||..   ++......    .   ..+.++...|++||.|+.+||. +||.+...
T Consensus       338 ~~~~~~C~~C~~C~~~Cp~~~~~ai~~~~~~----~---~~~~i~~~~C~~Cg~C~~~CP~~~Ai~~~~~  400 (420)
T PRK08318        338 RIDQDKCIGCGRCYIACEDTSHQAIEWDEDG----T---RTPEVIEEECVGCNLCAHVCPVEGCITMGEV  400 (420)
T ss_pred             EECHHHCCCCCcccccCCCcchhheeeccCC----C---ceEEechhhCcccchHHhhCCCCCCEEEecc
Confidence            35678999999999999974   55442210    0   1245677899999999999999 99976553

>TIGR00397 mauM_napG MauM/NapG family ferredoxin-type protein

Probab=98.51  E-value=1.2e-07  Score=78.03  Aligned_cols=59  Identities=24%  Similarity=0.563  Sum_probs=41.5

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch--hhhhcCccccccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG--FCQEACPVDAIVE  183 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg--~Cv~~CP~~Ai~~  183 (226)
                      .++|++||.|+++||+++|.+........ .....+..+...|.+|+  .|+++||++||..
T Consensus        52 ~~~Ci~Cg~Cv~aCP~~ai~~~~~~~~~~-~g~p~~~~~~~~C~~C~d~~Cv~~CP~~Ai~~  112 (213)
T TIGR00397        52 LAACVRCGLCVEACPYDILSLASWSDPAP-LGTPFFTPREVPCRMCKDIPCARACPTGALDP  112 (213)
T ss_pred             cccccchhHHHHhCCcccccccccccccc-cCCccccccCCcCCCCCCchHHhHcCHhhhch
Confidence            37999999999999999997653221100 00112223446799998  6999999999974

MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar.

>COG0437 HybA Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]

Probab=98.51  E-value=4.4e-08  Score=79.33  Aligned_cols=54  Identities=35%  Similarity=0.758  Sum_probs=45.3

Q ss_pred             cccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          124 EERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       124 ~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...|..|.  -|+++||++|+.....++        -+.+|.+.|++|+.|+.+||++|+.+.+
T Consensus        66 ~~~C~HC~~ppCv~vCPtgA~~k~~~dG--------iV~vd~d~CIGC~yCi~ACPyga~~~~~  121 (203)
T COG0437          66 SISCMHCEDPPCVKVCPTGALFKREEDG--------IVLVDKDLCIGCGYCIAACPYGAPQFNP  121 (203)
T ss_pred             cccccCCCCCcccccCCCcceEEecCCC--------EEEecCCcccCchHHHhhCCCCCceeCc
Confidence            45799995  899999999998764222        4578889999999999999999998776

>TIGR02951 DMSO_dmsB DMSO reductase, iron-sulfur subunit

Probab=98.49  E-value=2.5e-08  Score=78.55  Aligned_cols=22  Identities=32%  Similarity=0.886  Sum_probs=11.6

Q ss_pred             ccccccccccchhccccccccc
Q 027264          123 GEERCIACKLCEAVCPAQAITI  144 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~  144 (226)
                      +.++|++|+.|+.+||.+++.+
T Consensus        93 ~~~~C~~C~~C~~aCP~~ai~~  114 (161)
T TIGR02951        93 DQDKCIGCRYCVWACPYGAPQY  114 (161)
T ss_pred             CHHhCCCchHHHhhCCCCCcEE
Confidence            3445555555555555555543

This family consists of the iron-sulfur subunit, or chain B, of an enzyme called the anaerobic dimethyl sulfoxide reductase. Chains A and B are catalytic, while chain C is a membrane anchor.

>PRK07118 ferredoxin; Validated

Probab=98.49  E-value=3.6e-08  Score=84.35  Aligned_cols=52  Identities=38%  Similarity=0.696  Sum_probs=44.2

Q ss_pred             ccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ..|++||.|+++||+++|...+.          ...+|.+.|++|+.|+.+||.++|.+.+.
T Consensus       139 ~~CigCg~C~~aCp~~AI~~~~g----------~~~id~~~C~~Cg~Cv~aCP~~ai~~~~~  190 (280)
T PRK07118        139 YGCLGLGSCVAACPFDAIHIENG----------LPVVDEDKCTGCGACVKACPRNVIELIPK  190 (280)
T ss_pred             CCCcChhHHHHhCCccCeEccCC----------eEEEChhhCcChhHHHHhcCccceeeecc
Confidence            47999999999999999986541          35678899999999999999999987643

>TIGR00397 mauM_napG MauM/NapG family ferredoxin-type protein

Probab=98.49  E-value=4.4e-08  Score=80.65  Aligned_cols=60  Identities=38%  Similarity=0.852  Sum_probs=44.2

Q ss_pred             Ccccccc-----ccccchhcccc--ccccchhhhhccCCccccccccCCCCCCcchhhhhcCccc--cccc
Q 027264          122 TGEERCI-----ACKLCEAVCPA--QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD--AIVE  183 (226)
Q Consensus       122 ~~~~~Ci-----~Cg~C~~~CP~--~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~--Ai~~  183 (226)
                      ++.++|+     .|+.|+++||+  .||.+.......+  ......++.+.|++||.|+.+||++  ||..
T Consensus       128 id~~~C~~~~g~~C~~C~~~CP~~~~AI~~~~~~~~~~--~~~~p~Vd~~~C~gCG~C~~~CP~~~~AI~v  196 (213)
T TIGR00397       128 VGHETCLNYKGLNCSICVRVCPIRGEAISLKPIENERG--RLQIPTVDSAKCTGCGTCEKHCVLSEAAIRV  196 (213)
T ss_pred             ECCCCcccCCCCCcccchhhCCCCcceEEEecccccCC--cccceEEecccCCCcchhhHhCCCCCCeEEE
Confidence            5678898     99999999998  6887654321111  1113467888999999999999987  6654

MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar.

>TIGR01582 FDH-beta formate dehydrogenase, beta subunit, Fe-S containing

Probab=98.48  E-value=2.9e-08  Score=84.84  Aligned_cols=53  Identities=28%  Similarity=0.624  Sum_probs=31.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccCCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPN  186 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~~~  186 (226)
                      ++.++|++|+.|+.+||.+++.++...            .....|..|.         .|+.+||++||.+++.
T Consensus       121 id~dkCigC~~Cv~aCP~~a~~~~~~~------------~~~~KC~~C~dr~~~G~~PaCv~aCP~gAi~fg~~  182 (283)
T TIGR01582       121 FDHSKCIGCGYCIVGCPFNIPRYDKVD------------NRPYKCTLCIDRVSVGQEPACVKTCPTNAISFGFK  182 (283)
T ss_pred             EeHHHCCcchHHHhhCCCCCcEEcCCC------------CChhhhcccccccccCCCChHhCcccHhhEEECCH
Confidence            455667777777777776666553311            1123566663         6777777777766554

In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within the scope of this model. This appears to be the case for the alpha, gamma and epsilon (accessory protein TIGR01562) chains as well.

>TIGR00384 dhsB succinate dehydrogenase and fumarate reductase iron-sulfur protein

Probab=98.46  E-value=5.6e-09  Score=86.40  Aligned_cols=108  Identities=21%  Similarity=0.351  Sum_probs=56.0

Q ss_pred             HHHhhhHHHHHHHHHHHHHhcCCcceecCccccCC---CCCCccCccccccCCCccccccccccchhccccccccchh--
Q 027264           72 INMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGP---LSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEA--  146 (226)
Q Consensus        72 i~~~~~~~~~~~l~~~~~~~f~~~~~~~~p~~~~~---~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~--  146 (226)
                      +.++..+.++++|.+++..+|++.....-......   .....+.............+|+.||.|..+||+.....+.  
T Consensus        82 iepl~~~pvikDLvvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ci~CG~C~~~CP~~~~~~~~~g  161 (220)
T TIGR00384        82 IEPLPNLPVIKDLVVDMGPFYAKLEAIKPYLIRKSQPEPEGEFLQTPEQREKLDQLSGCILCGCCYSSCPAFWWNPEFLG  161 (220)
T ss_pred             EeeCCCCceeeeeeechHHHHHHHHhcCCeecCCCCCCccccccCCHHHHHHHhhhhhccccccccccCCCCccCCCCcC
Confidence            44555667788888888877764332221000100   0001111110001112457899999999999985332110  


Q ss_pred             ------------hhhccCCccc-c-cc-ccCCCCCCcchhhhhcCccc
Q 027264          147 ------------EEREDGSRRT-T-RY-DIDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       147 ------------~~~~~~~~~~-~-~~-~~d~~~C~~Cg~Cv~~CP~~  179 (226)
                                  +.+....... . .. ....+.|+.||.|+.+||++
T Consensus       162 p~~~~~~~r~~~d~~~~~~~~r~~~~~~~~~~~~C~~Cg~C~~~CP~~  209 (220)
T TIGR00384       162 PAALTAAYRFLIDSRDHATKDRLEGLNDKNGVWRCTTCMNCSEVCPKG  209 (220)
T ss_pred             HHHHHHHHHHhcCCCccchHHHHHHhhccCCCccCccccccccccCCC
Confidence                        0000000000 0 01 23467899999999999998

Succinate dehydrogenase and fumarate reductase are reverse directions of the same enzymatic interconversion, succinate + FAD+ = fumarate + FADH2 (EC 1.3.11.1). In E. coli, the forward and reverse reactions are catalyzed by distinct complexes: fumarate reductase operates under anaerobic conditions and succinate dehydrogenase operates under aerobic conditions. This model also describes a region of the B subunit of a cytosolic archaeal fumarate reductase.

>PRK14993 tetrathionate reductase subunit B; Provisional

Probab=98.44  E-value=5.4e-08  Score=81.67  Aligned_cols=54  Identities=31%  Similarity=0.703  Sum_probs=44.1

Q ss_pred             ccccccccc--chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          124 EERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       124 ~~~Ci~Cg~--C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ...|+.|+.  |+.+||++++......         .+.++.+.|++|+.|+.+||++||.+...
T Consensus        97 ~~~C~~C~~p~Cv~~CP~~Ai~~~~~G---------~v~id~~~CigC~~Cv~aCP~~Ai~~~~~  152 (244)
T PRK14993         97 PRLCNHCDNPPCVPVCPVQATFQREDG---------IVVVDNKRCVGCAYCVQACPYDARFINHE  152 (244)
T ss_pred             chhcCCcCCccCccccCCCCEEECCCC---------CEEEcHHHCCCHHHHHHhcCCCCCEEeCC
Confidence            568999996  9999999998654321         34677789999999999999999986553

>TIGR01973 NuoG NADH-quinone oxidoreductase, chain G

Probab=98.44  E-value=6.1e-08  Score=91.43  Aligned_cols=64  Identities=23%  Similarity=0.430  Sum_probs=43.0

Q ss_pred             cCCCccccccccccchhcccc----ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          119 RYPTGEERCIACKLCEAVCPA----QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~~CP~----~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+..+.++||.||+|+++|-.    .+|.+..  |+....... ..-....|..||.|+++||+|||..+.
T Consensus       136 ~i~~d~~rCI~C~rCvr~c~e~~g~~~l~~~~--rg~~~~i~~-~~~~~~~~~~cg~cv~vCP~GAl~~k~  203 (603)
T TIGR01973       136 LIKTEMTRCIHCTRCVRFANEVAGVEDLGVIG--RGNNVEIGT-YEGKTLESELSGNLIDICPVGALTSKP  203 (603)
T ss_pred             CeEecCCcCccccHHHHHHHHhhCCceEEEec--cCCCCEEec-CCCCCCCCcccCChHhhCCcccccccc
Confidence            355788999999999999973    3444433  332222111 111223688999999999999998664

This model represents the G 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 while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes related subunits from formate dehydrogenase complexes.

>TIGR01582 FDH-beta formate dehydrogenase, beta subunit, Fe-S containing

Probab=98.44  E-value=5.3e-08  Score=83.24  Aligned_cols=54  Identities=33%  Similarity=0.756  Sum_probs=43.6

Q ss_pred             cccccccccc--chhcccc-ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          123 GEERCIACKL--CEAVCPA-QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       123 ~~~~Ci~Cg~--C~~~CP~-~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ..++|+.|+.  |+++||+ +++......         .+.++.+.|++|+.|+.+||.+|+.+..
T Consensus        89 ~~~~C~hC~~p~Cv~aCP~~gA~~~~~~G---------~V~id~dkCigC~~Cv~aCP~~a~~~~~  145 (283)
T TIGR01582        89 RKDGCMHCREPGCLKACPAPGAIIQYQNG---------IVDFDHSKCIGCGYCIVGCPFNIPRYDK  145 (283)
T ss_pred             CCccCCCCCCccccCCCCcCCeEEEcCCC---------cEEEeHHHCCcchHHHhhCCCCCcEEcC
Confidence            4578999998  9999998 677554321         3467788999999999999999998754

In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within the scope of this model. This appears to be the case for the alpha, gamma and epsilon (accessory protein TIGR01562) chains as well.

>COG0479 FrdB Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]

Probab=98.43  E-value=7.2e-09  Score=85.68  Aligned_cols=105  Identities=25%  Similarity=0.458  Sum_probs=58.8

Q ss_pred             HhhhHHHHHHHHHHHHHhcCCcceecCcccc---CCCCCCccCccccccCCCccccccccccchhccccccccc------
Q 027264           74 MLFLTEMVRGLGLTLKYFFDKKVTINYPFEK---GPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITI------  144 (226)
Q Consensus        74 ~~~~~~~~~~l~~~~~~~f~~~~~~~~p~~~---~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~------  144 (226)
                      ++..+.++++|.+++..||+....+. |+-.   ......+...+.-.........||.||.|..+||+.....      
T Consensus        89 PL~~fpVIkDLVVD~~~f~~~~~~ik-p~~~~~~~~~~~~~~q~pe~~~~~~~~~~CI~Cg~C~s~CP~~~~~~~f~GPa  167 (234)
T COG0479          89 PLPNFPVIRDLVVDMEEFYEKLRKIK-PYLIRDDEPDPGERLQSPEEREKLDELSECILCGCCTAACPSIWWNPDFLGPA  167 (234)
T ss_pred             ECCCCCceeeeeeccHHHHHhhhccc-cceecCCcCCCccccCCHHHHHHHHhhhhccccchhhhhCCccccccCCcCHH
Confidence            44556789999999999998643332 1111   1111112222211112234568999999999999743322      


Q ss_pred             --------hhhhhccCCccc-cccc--cCCCCCCcchhhhhcCccc
Q 027264          145 --------EAEEREDGSRRT-TRYD--IDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       145 --------~~~~~~~~~~~~-~~~~--~d~~~C~~Cg~Cv~~CP~~  179 (226)
                              ..+.|+.++... ....  ...+.|..|+.|+++||++
T Consensus       168 ~l~~a~R~~~D~rd~~~~~R~~~~~~~~gv~~C~~~~~C~~vCPK~  213 (234)
T COG0479         168 ALRQAYRFLADSRDEGTAERLKILEDPDGVWRCTTCGNCTEVCPKG  213 (234)
T ss_pred             HHHHHHHHhcCCcccchHHHHHhccCCCCEecccccccccccCCCC
Confidence                    111121111111 1111  1247899999999999998

>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional

Probab=98.42  E-value=6.3e-08  Score=81.74  Aligned_cols=62  Identities=35%  Similarity=0.755  Sum_probs=44.8

Q ss_pred             Ccccccc-----ccccchhcccc--ccccchhhhhc-cCCccccccccCCCCCCcchhhhhcCccc--cccc
Q 027264          122 TGEERCI-----ACKLCEAVCPA--QAITIEAEERE-DGSRRTTRYDIDMTKCIYCGFCQEACPVD--AIVE  183 (226)
Q Consensus       122 ~~~~~Ci-----~Cg~C~~~CP~--~ai~~~~~~~~-~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~--Ai~~  183 (226)
                      ++.++|+     .|+.|+.+||+  +||.++..... .+........++.+.|++||.|+.+||++  ||..
T Consensus       134 id~~~Ci~~~~~~C~~C~~~CP~~~~AI~~~~~~~~r~g~~~~~~p~Id~d~C~gCG~C~~aCP~~~~AI~v  205 (254)
T PRK09476        134 VDQENCLNFQGLRCDVCYRVCPLIDKAITLELERNERTGKHAFFLPTVHSDACTGCGKCEKACVLEKAAIKV  205 (254)
T ss_pred             cchhhccccCCCchHHHhhhCCCccCeEEEEcccccccccccccceEEeHHHCcCcChhhHhcCCCcceEEE
Confidence            6788999     89999999996  78877543211 01111123457778999999999999998  7763

>PRK09898 hypothetical protein; Provisional

Probab=98.42  E-value=8.4e-08  Score=78.72  Aligned_cols=54  Identities=33%  Similarity=0.794  Sum_probs=44.1

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.++|++|+.|+.+||.+++.++..            ..+...|++||.|+.+||++||.+.+
T Consensus       149 v~vd~~~CigC~~C~~aCP~~ai~~~~~------------~~~~~kC~~Cg~Cv~~CP~~Ai~~~~  202 (208)
T PRK09898        149 ITVDHKRCIGCSACTTACPWMMATVNTE------------SKKSSKCVLCGECANACPTGALKIIE  202 (208)
T ss_pred             EEeccccCCCcCcccccCCCCCCEecCC------------CCcCCcCcChHHHHHhCCcccEEEec
Confidence            3467789999999999999998876432            12356899999999999999998654

>PRK09129 NADH dehydrogenase subunit G; Validated

Probab=98.41  E-value=8.5e-08  Score=92.91  Aligned_cols=66  Identities=24%  Similarity=0.348  Sum_probs=43.1

Q ss_pred             cCCCccccccccccchhcccc--ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          119 RYPTGEERCIACKLCEAVCPA--QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~~CP~--~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+..+.++||.||+|+++|-.  +.-.+....|+...+.... .-....|..||.|+++||+|||..+.
T Consensus       138 ~i~~d~~rCi~C~rCvr~c~ev~g~~~l~~~~rg~~~~i~~~-~~~~~~~~~cg~cv~~CP~GAl~~k~  205 (776)
T PRK09129        138 LISTEMTRCIHCTRCVRFGQEIAGVMELGMMGRGEHSEITTY-VGKTVDSELSGNMIDLCPVGALTSKP  205 (776)
T ss_pred             ceeecccccccCcHHHHHHHHhcCCceeeeeccCCCCEEcCC-CCCCccCcccCCchhhCCcccccccc
Confidence            345678999999999999973  3222222333333222111 11233588899999999999998764

>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma

Probab=98.40  E-value=6.4e-08  Score=80.48  Aligned_cols=54  Identities=33%  Similarity=0.771  Sum_probs=44.2

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++.++|++|+.|+.+||.+++.....          ...++...|+.|+.|+.+||.+.+...
T Consensus       170 ~id~~~C~~C~~C~~aCP~~ai~~~~~----------~~~i~~~~C~~C~~C~~~CP~~~~~~~  223 (228)
T TIGR03294       170 VVNQGLCMGCGTCAAACPTRAIEMEDG----------RPNVNRDRCIKCGACYVQCPRAFWPEY  223 (228)
T ss_pred             EEChhhCcChhHHHHhCCHhhEEEeCC----------cEEEChhhccCHHHHHHHcCCCCcchh
Confidence            366789999999999999999876432          134677889999999999999977653

This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (pfam00037) and scores above the trusted cutoff to model pfam01058 for the "NADH ubiquinone oxidoreductase, 20 Kd subunit" family.

>TIGR01660 narH nitrate reductase, beta subunit

Probab=98.39  E-value=1e-07  Score=85.16  Aligned_cols=54  Identities=24%  Similarity=0.538  Sum_probs=43.8

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccCCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPN  186 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~~~  186 (226)
                      .++.++|++|+.|+.+||.+++.+....            ....+|.+|.         .|+.+||.+|+.++..
T Consensus       210 ~ID~dkCiGCg~CV~ACPygAI~~n~~~------------g~~~KCd~C~~Rie~G~pPaCVeaCP~~Ar~fG~l  272 (492)
T TIGR01660       210 LIDQDKCRGWRMCISGCPYKKIYFNWKT------------GKSEKCIFCYPRIEAGQPTVCSETCVGRIRYLGVL  272 (492)
T ss_pred             EEehhhccChHHHHHhCCCCCcEecCCC------------CccccCCCChhHHhCCCCCcchhhcChhhhhhhhh
Confidence            3678999999999999999999876431            1236899995         6999999999887753

The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model.The seed members used in this model are all experimentally characterized and include the following: NarH and NarY, both E.Coli, sequences from B. Subtilis, Pseudomonas fluorescens, Paracoccus denitrificans, and Halomonas halodenitrificans. This model also matches PFAM pfam00037 for 4Fe-4S binding domain.

>PLN00129 succinate dehydrogenase [ubiquinone] iron-sulfur subunit

Probab=98.39  E-value=9.7e-09  Score=87.25  Aligned_cols=109  Identities=18%  Similarity=0.352  Sum_probs=57.2

Q ss_pred             HHHhhhHHHHHHHHHHHHHhcCCcceecCccccCCCCC----CccCccccccCCCccccccccccchhccccccccchh-
Q 027264           72 INMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSP----RFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEA-  146 (226)
Q Consensus        72 i~~~~~~~~~~~l~~~~~~~f~~~~~~~~p~~~~~~~~----~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~-  146 (226)
                      +.++..++++++|.+++..||+......-.........    .....+...........||.||.|..+||+.....+. 
T Consensus       130 iePl~~fpVirDLvVD~~~f~~klk~v~p~l~~~~~~~~~~~~~~q~pe~~~~~~~~~~CI~CG~C~saCPv~~~~~~~f  209 (276)
T PLN00129        130 ITPLPHMFVIKDLVVDMTNFYQQYKSIEPWLKTKKPPEDGQKEHLQSKEDRAKLDGMYECILCACCSTSCPSYWWNPEKF  209 (276)
T ss_pred             EEECCCCCeeeecccccHHHHHHHHhccccccCCCCCCCCccccCCCHHHHHHHhhhhhCccccccccccCCCcccCccc
Confidence            33555567899999999998885443331111111100    1111111001112235799999999999964221110 


Q ss_pred             --------------hhhccCCccccc-c--ccCCCCCCcchhhhhcCcccc
Q 027264          147 --------------EEREDGSRRTTR-Y--DIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       147 --------------~~~~~~~~~~~~-~--~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                                    +.+......... .  ....+.|+.|+.|..+||.+.
T Consensus       210 lGP~~l~~a~R~~~D~RD~~~~erl~~l~~~~gl~~C~~C~~C~~vCPkgI  260 (276)
T PLN00129        210 LGPAALLHAYRWISDSRDEYTKERLEALDDEFKLYRCHTIRNCSNACPKGL  260 (276)
T ss_pred             ccHHHHHHHHHhcCCccccchHHHHHHHHhcCCCCcCcChhhccccCCCCC
Confidence                          001100000001 1  114589999999999999984

>PRK12575 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=98.39  E-value=9.6e-09  Score=85.64  Aligned_cols=109  Identities=19%  Similarity=0.319  Sum_probs=58.2

Q ss_pred             HHHhhhHHHHHHHHHHHHHhcCCcceecCccccCC--CCCCccCccccccCCCccccccccccchhccccccccch----
Q 027264           72 INMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGP--LSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIE----  145 (226)
Q Consensus        72 i~~~~~~~~~~~l~~~~~~~f~~~~~~~~p~~~~~--~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~----  145 (226)
                      +.++..+.++++|.+++..+|+......-......  ...+.+..+...........|+.||.|..+||+.....+    
T Consensus        89 iePl~~~pvikDLvvD~~~~~~~~~~~~p~l~~~~~~~~~~~~~~p~~~~~~~~~~~CI~CG~C~s~CP~~~~~~~~f~G  168 (235)
T PRK12575         89 LRPLPGLPVVRDLIVDMTDFFNQYHSIRPYLINDTVPPERERLQTPQEREQLDGLYECILCACCSTACPSYWWNPDKFVG  168 (235)
T ss_pred             EeECCCCCccccceecCHHHHHHHHhccCccccCCCCccccccCCHHHHHHHHhhhhCcccccccccccCccccCCCcCC
Confidence            33555667899999999888875444331111110  001111111111111245689999999999997533211    


Q ss_pred             hh-----------hhccCCccccc-cc--cCCCCCCcchhhhhcCcccc
Q 027264          146 AE-----------EREDGSRRTTR-YD--IDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       146 ~~-----------~~~~~~~~~~~-~~--~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      +.           .+......... +.  ...+.|+.||.|..+||.+.
T Consensus       169 P~~~~~a~r~~~D~rd~~~~~rl~~l~~~~gl~~C~~C~~C~~vCPkgI  217 (235)
T PRK12575        169 PAGLLQAYRFIADSRDDATAARLDDLEDPYRLFRCRTIMNCVDVCPKGL  217 (235)
T ss_pred             HHHHHHHHHHHhCCCCCCcHHHHHhhhcCCCcccccCcchhccccCCCC
Confidence            10           00000000001 11  13578999999999999983

>TIGR03315 Se_ygfK putative selenate reductase, YgfK subunit

Probab=98.38  E-value=1.2e-07  Score=93.26  Aligned_cols=59  Identities=29%  Similarity=0.603  Sum_probs=40.3

Q ss_pred             ccccccc----cccchhcccccccc-chhhhhccCCccccccccCCC-CCCcchhhhhcCcccccccCCC
Q 027264          123 GEERCIA----CKLCEAVCPAQAIT-IEAEEREDGSRRTTRYDIDMT-KCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       123 ~~~~Ci~----Cg~C~~~CP~~ai~-~~~~~~~~~~~~~~~~~~d~~-~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      +.++|.+    ||.|+.+||.+|+. +........     ...++.+ .|+.||.|+.+||++|+.+...
T Consensus       879 ~~~rC~~c~~~Cg~Cv~vCP~~Aii~i~~~~~~~~-----~~~i~~d~~C~~CG~C~~vCP~~a~~~~gk  943 (1012)
T TIGR03315       879 ESQRCLECSYVCEKCVDVCPNRANIVIYVPGFRDQ-----FQIVHLDGMCNECGNCATFCPYDGAPYKDK  943 (1012)
T ss_pred             ccccccCCCCCCCChhhhCChhhhhccccccccCC-----ceeeecCccccccchHHHhCCCCcccceee
Confidence            4479996    99999999999752 211000000     1112223 4999999999999999988776

Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase.

>PRK09326 F420H2 dehydrogenase subunit F; Provisional

Probab=98.37  E-value=1.4e-07  Score=82.95  Aligned_cols=61  Identities=30%  Similarity=0.529  Sum_probs=42.7

Q ss_pred             CccccccccccchhccccccccchhhhhccCCc--cccccccCCCCCCcchhhhhcCcccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSR--RTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~--~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      ++.++|++||.|+.+||+++|.+..........  ......++.+.|+.||.|..+||..++.
T Consensus         9 i~~~~C~gCg~C~~~CP~~aI~~~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~C~~vCP~~~~~   71 (341)
T PRK09326          9 IEYDVCTACGACEAVCPIGAITVDKKAEIRDPNDLELYEKGAAPNVCEGCLTCSRICPVVDGY   71 (341)
T ss_pred             ECcccCcChHHHHHhCCHhhhecccCcccccccchhhhccCCCcCcCcCcCchhhhCCCCccc
Confidence            567899999999999999998875432210000  0011124667899999999999986653

>PRK12576 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=98.36  E-value=2.3e-08  Score=85.56  Aligned_cols=110  Identities=22%  Similarity=0.410  Sum_probs=58.7

Q ss_pred             HHHHhhhHHHHHHHHHHHHHhcCCcceec-CccccCC-C--CCCccCccccccCCCccccccccccchhccccccccchh
Q 027264           71 SINMLFLTEMVRGLGLTLKYFFDKKVTIN-YPFEKGP-L--SPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus        71 ~i~~~~~~~~~~~l~~~~~~~f~~~~~~~-~p~~~~~-~--~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .+.++..+.++++|.+++..+|++..... |-..... .  .......+.......+.+.|+.||.|..+||+.....+.
T Consensus        94 tiePl~~~~vikDLvvD~~~~~~k~~~~~~~l~~~~~~~~~~~~~~~~p~~~~~~~~~~~CI~CG~C~~~CP~~~~~~~f  173 (279)
T PRK12576         94 TIEPMDYFKVVKDLIVDFDEFYERMFKVKPRLYRAKEVLEGKAEHRLKPEDQKELWKFAQCIWCGLCVSACPVVAIDPEF  173 (279)
T ss_pred             EEEECCCCceeecceechHHHHHHHHhccceeccCccCCCCccccccCHHHHHHhhcchhCcccCcccccCCCccccCCc
Confidence            34455566788999999888886433322 1110110 0  011111111111223567999999999999986432110


Q ss_pred             --------------hhhccCCcccc-ccccCCCCCCcchhhhhcCcccc
Q 027264          147 --------------EEREDGSRRTT-RYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       147 --------------~~~~~~~~~~~-~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                                    +.+..+..... ......+.|+.||.|+.+||.+.
T Consensus       174 lgP~~l~~a~r~~~d~rd~~~~~rl~~~~~~i~~C~~Cg~C~~~CP~~I  222 (279)
T PRK12576        174 LGPAAHAKGYRFLADPRDTITEERMKILIDSSWRCTYCYSCSNVCPRDI  222 (279)
T ss_pred             CCHHHHHHHHHHhcCccccchHHHHHHHcCcCCcccCcccchhhCCCCC
Confidence                          00110000000 11224579999999999999874

>PF12837 Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=98.36  E-value=1e-07  Score=50.76  Aligned_cols=22  Identities=55%  Similarity=0.997  Sum_probs=14.6

Q ss_pred             ccCCCCCCcchhhhhcCccccc
Q 027264          160 DIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      .+|.+.|++||.|+.+||.+||
T Consensus         3 ~id~~~C~~Cg~C~~~Cp~~ai   24 (24)
T PF12837_consen    3 VIDPDKCIGCGDCVRVCPEGAI   24 (24)
T ss_pred             EEChhhCcChhHHHHhcchhcC
Confidence            3555667777777777776665

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding

>PRK13795 hypothetical protein; Provisional

Probab=98.35  E-value=1e-07  Score=90.23  Aligned_cols=54  Identities=39%  Similarity=0.916  Sum_probs=44.0

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      .+.+.|++||.|+.+||++++.......        .+.++...|+.||.|+.+||.+++..
T Consensus       578 ~~~~~C~~Cg~C~~~CP~~ai~~~~~~~--------~~~id~~~C~~Cg~C~~aCP~~a~~~  631 (636)
T PRK13795        578 RRAAECVGCGVCVGACPTGAIRIEEGKR--------KISVDEEKCIHCGKCTEVCPVVKYKD  631 (636)
T ss_pred             EccccCCCHhHHHHhCCcccEEeecCCc--------eEEechhhcCChhHHHhhcCCCeeEe
Confidence            4567999999999999999987754211        24567789999999999999999864

>TIGR02951 DMSO_dmsB DMSO reductase, iron-sulfur subunit

Probab=98.33  E-value=1.8e-07  Score=73.67  Aligned_cols=55  Identities=33%  Similarity=0.619  Sum_probs=42.8

Q ss_pred             ccccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          123 GEERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       123 ~~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ....|+.|+  .|+++||+++|......        ..+.++.+.|++|+.|+.+||.+||.+..
T Consensus        60 ~~~~C~~C~~~~C~~~CP~~ai~~~~~~--------~~~~i~~~~C~~C~~C~~aCP~~ai~~~~  116 (161)
T TIGR02951        60 ISISCNHCADPACVKNCPTGAMYKREED--------GLVLVDQDKCIGCRYCVWACPYGAPQYDP  116 (161)
T ss_pred             cCccCCCcCCcchHHhCCCCCEEeecCC--------CcEEECHHhCCCchHHHhhCCCCCcEEcC
Confidence            357899999  99999999998654211        13456778899999999999999987654

This family consists of the iron-sulfur subunit, or chain B, of an enzyme called the anaerobic dimethyl sulfoxide reductase. Chains A and B are catalytic, while chain C is a membrane anchor.

>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional

Probab=98.33  E-value=1.9e-07  Score=78.78  Aligned_cols=60  Identities=25%  Similarity=0.556  Sum_probs=41.4

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch--hhhhcCcccccccC
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG--FCQEACPVDAIVEG  184 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg--~Cv~~CP~~Ai~~~  184 (226)
                      .++|++||.|+.+||+++|.+......... ....+......|..|+  .|+.+||++||.+.
T Consensus        58 ~~~Ci~Cg~Cv~aCP~~aI~~~~~~~~~~~-g~p~~~~~~~~C~~C~~~~Cv~aCPtgAL~~~  119 (254)
T PRK09476         58 LSACIRCGLCVQACPYDTLKLATLASGLSA-GTPYFVARDIPCEMCEDIPCVKACPSGALDRE  119 (254)
T ss_pred             hhhCcCchHHHHhCCccccCcccccccccc-CCceeeecCCcCcCCCCCchhhccCccceEee
Confidence            378999999999999999976532211000 0001222335799999  59999999999764

>PRK08640 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed

Probab=98.33  E-value=1.7e-08  Score=84.93  Aligned_cols=109  Identities=18%  Similarity=0.305  Sum_probs=56.9

Q ss_pred             HHHhhhHHHHHHHHHHHHHhcCCcceecCccccCC---CCCCccCccccccCCCccccccccccchhccccccccchhh-
Q 027264           72 INMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGP---LSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAE-  147 (226)
Q Consensus        72 i~~~~~~~~~~~l~~~~~~~f~~~~~~~~p~~~~~---~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~-  147 (226)
                      +.|+..+.++++|.+++..+|+....+.-......   ........+...........||.||.|.++||+....-+.. 
T Consensus        96 iePl~~fpVikDLvVD~~~~~~~~~~~~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~CI~CG~C~saCP~~~~~~~f~G  175 (249)
T PRK08640         96 LEPMSTFPVVRDLQVDRSRMFDNLKRVKAWIPIDGTYDLGPGPRMPEEKRQWAYELSKCMTCGCCLEACPNVNEKSDFIG  175 (249)
T ss_pred             EEECCCCCccccCcEEChHHHHHHHhhCCccccCCCCCCCcccCCCHHHHHHHhhhhhccCcCcccccCCCCccCCCccC
Confidence            34555567899999998888774333221111110   01111111111111234578999999999999754311000 


Q ss_pred             -------------h-hccCCccc-ccc--ccCCCCCCcchhhhhcCcccc
Q 027264          148 -------------E-REDGSRRT-TRY--DIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       148 -------------~-~~~~~~~~-~~~--~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                                   . +....... ...  ....+.|+.||.|..+||.+.
T Consensus       176 P~~l~ka~r~~~d~~rd~~~~~rl~~l~~~~g~~~C~~Cg~C~~vCPkgI  225 (249)
T PRK08640        176 PAAISQVRLFNAHPTGEMHKEERLRALMGDGGIADCGNAQNCVRVCPKGI  225 (249)
T ss_pred             hHHHHHHHHHhcCcCcCccHHHHHHHhhcCCCeeCCcCcCcccccCCCCC
Confidence                         0 00000000 011  123478999999999999983

>PRK13552 frdB fumarate reductase iron-sulfur subunit; Provisional

Probab=98.32  E-value=2e-08  Score=84.04  Aligned_cols=108  Identities=18%  Similarity=0.339  Sum_probs=57.5

Q ss_pred             HHHhhhHHHHHHHHHHHHHhcCCc-ceec-CccccCCCC---CCccCccccccCCCccccccccccchhccccccccchh
Q 027264           72 INMLFLTEMVRGLGLTLKYFFDKK-VTIN-YPFEKGPLS---PRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus        72 i~~~~~~~~~~~l~~~~~~~f~~~-~~~~-~p~~~~~~~---~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      +.++..+.++++|.+++..+|+.. .... |........   ......+...........|+.||.|.++||+....-+.
T Consensus        91 iePl~~fpVirDLvVD~~~~~~~~~~~v~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~CI~Cg~C~saCP~~~~~~~f  170 (239)
T PRK13552         91 LMPLPVFKLIGDLSVNTGKWFREMSERVESWIHTDKEFDIHRLEERMEPEEADEIYELDRCIECGCCVAACGTKQMREDF  170 (239)
T ss_pred             EEECCCCCcceeCccccHHHHHHHHHhhcCccccCCCCCCcccccCCCHHHHHHhhchhhccccchhHhhCCCCccCCCc
Confidence            345556678999999998888754 2222 111110100   01111111111223457899999999999964321110


Q ss_pred             --------------hhhccCCcccc-cc---ccCCCCCCcchhhhhcCccc
Q 027264          147 --------------EEREDGSRRTT-RY---DIDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       147 --------------~~~~~~~~~~~-~~---~~d~~~C~~Cg~Cv~~CP~~  179 (226)
                                    +.+........ ..   ....+.|+.||.|..+||.+
T Consensus       171 ~GP~~~~~a~r~~~d~rd~~~~~~~~~~l~~~~gi~~C~~C~~C~~vCPk~  221 (239)
T PRK13552        171 VGAVGLNRIARFELDPRDERTDEDFYELIGNDDGVFGCMSLLGCEDNCPKD  221 (239)
T ss_pred             cChHHHHHHHHHhhCCCcchhHHHHHHHhccCCCcCCCcCcCccchhCCCC
Confidence                          00110000000 11   12457999999999999987

>PRK10882 hydrogenase 2 protein HybA; Provisional

Probab=98.32  E-value=2.1e-07  Score=81.19  Aligned_cols=54  Identities=28%  Similarity=0.663  Sum_probs=44.2

Q ss_pred             ccccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          123 GEERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       123 ~~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ....|+.|+  .|+.+||++++..+...        ..+.++.+.|++|+.|+.+||.++|.+.
T Consensus       108 ~~~~C~hC~~p~Cv~aCP~gAi~k~~~~--------g~V~id~dkCigCg~Cv~aCP~gai~~~  163 (328)
T PRK10882        108 IKKQCMHCVDPNCVSVCPVSALTKDPKT--------GIVHYDKDVCTGCRYCMVACPFNVPKYD  163 (328)
T ss_pred             ccccCCCcCchhhHhhCCCCCEEecccC--------CcccCCHHHcCcccHHHHhCCccceecc
Confidence            457899998  89999999999875421        1345777899999999999999999754

>PRK10330 formate dehydrogenase-H ferredoxin subunit; Provisional

Probab=98.31  E-value=1.8e-07  Score=75.11  Aligned_cols=52  Identities=31%  Similarity=0.633  Sum_probs=42.8

Q ss_pred             cccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          124 EERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       124 ~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...|+.|+  .|+.+||++++.....          ...++.+.|++|+.|+.+||.+||.+..
T Consensus        55 ~~~C~~C~~~~C~~~Cp~~ai~~~~~----------~v~i~~~~C~~C~~C~~~CP~~ai~~~~  108 (181)
T PRK10330         55 ATVCRQCEDAPCANVCPNGAISRDKG----------FVHVMQERCIGCKTCVVACPYGAMEVVV  108 (181)
T ss_pred             CCcCcCcCCcHHHHHcCcccEEccCC----------eEEeChhhCCCcchhhhhCCccCeEeec
Confidence            35899999  8999999999876421          2456778999999999999999997654

>PRK12386 fumarate reductase iron-sulfur subunit; Provisional

Probab=98.31  E-value=1.9e-08  Score=84.49  Aligned_cols=110  Identities=19%  Similarity=0.324  Sum_probs=58.4

Q ss_pred             HHHHhhhHHHHHHHHHHHHHhcCCcceecCccccCCCC-CCccCccccccCCCccccccccccchhccccccccchh---
Q 027264           71 SINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLS-PRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEA---  146 (226)
Q Consensus        71 ~i~~~~~~~~~~~l~~~~~~~f~~~~~~~~p~~~~~~~-~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~---  146 (226)
                      .+.++..+.++++|.+++..+|+....+.-........ ...+..+...........||.||.|.++||+....-..   
T Consensus        87 tiepl~~fpVikDLvVD~~~~~~~l~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~CI~CG~C~s~CPv~~~~~~~~~~  166 (251)
T PRK12386         87 TVTPMRTFPVIRDLVTDVSFNYEKAREIPSFTPPKDLQPGEYRMQQVDVERSQEFRKCIECFLCQNVCHVVRDHEENKPA  166 (251)
T ss_pred             EEccCCCCCccccceEEcHHHHHHHHhcCCcccCCCCCccccCCCHHHHHHHhchhhcccCCcccCcCCcccccCCCccc
Confidence            34455566789999999888887544332111111100 11111111111123457899999999999975332100   


Q ss_pred             hhhc---------------cCCcccc-ccccCCCCCCcchhhhhcCcccc
Q 027264          147 EERE---------------DGSRRTT-RYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       147 ~~~~---------------~~~~~~~-~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ..+.               ...+... ......+.|..|+.|..+||.+.
T Consensus       167 f~GP~~~~~a~r~~~D~Rd~~~rl~~~~~~~gl~~C~~C~~C~~vCPkgI  216 (251)
T PRK12386        167 FAGPRFLMRIAELEMHPLDTADRRAEAQEEHGLGYCNITKCCTEVCPEHI  216 (251)
T ss_pred             ccCHHHHHHHHHhhcCccchHHHHHHhhcccCcccCcCCCCcCCcCCCCc
Confidence            0000               0000000 01123577999999999999983

>PTZ00305 NADH:ubiquinone oxidoreductase; Provisional

Probab=98.31  E-value=2.3e-07  Score=78.72  Aligned_cols=63  Identities=21%  Similarity=0.246  Sum_probs=40.2

Q ss_pred             CCCccccccccccchhcccc----ccccchhhhhccCCccccccccCCCCCC--cchhhhhcCcccccccCCC
Q 027264          120 YPTGEERCIACKLCEAVCPA----QAITIEAEEREDGSRRTTRYDIDMTKCI--YCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~----~ai~~~~~~~~~~~~~~~~~~~d~~~C~--~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      +..+.++||.||+|+++|-.    ++|.+..  |+.......  ..+...|.  +||.|+++||+|||..++.
T Consensus       207 i~~D~nKCIlCgRCVRaC~EVqg~~aL~~~~--RG~~t~I~t--~~d~~~~~~~~~g~cvdvCPvGAL~~~d~  275 (297)
T PTZ00305        207 TRVVLNRCIHCTRCVRFLNEHAQDFNLGMIG--RGGLSEIST--FLDELEVKTDNNMPVSQLCPVGKLYLGDA  275 (297)
T ss_pred             eeecCCcCcCccHHHHHHHHhhCCcEEEEee--cCCCCEEee--cCCCcccccCCCCceeeECCCcccccCCc
Confidence            44668999999999999994    4454433  332222111  11222243  3567999999999987764

>PRK07570 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated

Probab=98.31  E-value=2.7e-08  Score=83.66  Aligned_cols=59  Identities=24%  Similarity=0.604  Sum_probs=36.0

Q ss_pred             Cccccccccccchhcccccccc-----------chhhhhcc-CCccc---cccc-cCCCCCCcchhhhhcCcccc
Q 027264          122 TGEERCIACKLCEAVCPAQAIT-----------IEAEERED-GSRRT---TRYD-IDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~-----------~~~~~~~~-~~~~~---~~~~-~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      .....||.||.|+++||+....           +.+..... ..+..   .... ...+.|+.||.|+.+||.+.
T Consensus       154 ~~~~~CI~CG~C~saCP~~~~~~f~Gp~~~~~~l~p~~~~~r~~~~~~~~~~~~~~gv~~C~~Cg~Cs~VCPk~I  228 (250)
T PRK07570        154 FDAAACIGCGACVAACPNGSAMLFTGAKVSHLALLPQGQPERARRVRAMVAQMDEEGFGNCTNTGECEAVCPKGI  228 (250)
T ss_pred             hCccccCCCcccccccCCcccccccchhhhhhhhCcccchhHHHHHHHHHHHHhccCcccCcccCccccccCCCC
Confidence            4467899999999999986432           00000000 00000   0111 23578999999999999984

>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=98.30  E-value=2.1e-07  Score=49.61  Aligned_cols=22  Identities=68%  Similarity=1.244  Sum_probs=15.1

Q ss_pred             cCCCCCCcchhhhhcCcccccc
Q 027264          161 IDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      +|.+.|++||.|+.+||++||+
T Consensus         3 id~~~C~~Cg~C~~~CP~~ai~   24 (24)
T PF00037_consen    3 IDPDKCIGCGRCVEACPFDAIT   24 (24)
T ss_dssp             EETTTSSS-THHHHHSTTSSEE
T ss_pred             EchHHCCCcchhhhhcccccCC
Confidence            4556777777777777777763

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1DUR_A 1H98_A 1BD6_A 1BQX_A 1BWE_A 1BC6_A 3BK7_A 1FCA_A 1FDN_A 2FDN_A ....

>PRK12769 putative oxidoreductase Fe-S binding subunit; Reviewed

Probab=98.30  E-value=2.7e-07  Score=87.82  Aligned_cols=64  Identities=27%  Similarity=0.597  Sum_probs=47.7

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch------hhhhcCcccccccCCCccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPNFEY  189 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg------~Cv~~CP~~Ai~~~~~~~~  189 (226)
                      .++.++|++|+.|+.+||.+++.+.......     .....+...|..|+      .|+.+||++||.+.+..++
T Consensus        81 ~id~~~C~~C~~C~~~CP~~ai~~~~~~~~~-----~~~~~~~~~C~~C~~~~~~p~Cv~~CP~~Ai~~~~~~~~  150 (654)
T PRK12769         81 QVNQQKCIGCKSCVVACPFGTMQIVLTPVAA-----GKVKATAHKCDLCAGRENGPACVENCPADALQLVTEQAL  150 (654)
T ss_pred             EEecccccCcChhcccCCccCeeecccCCcc-----cceeeecCcCcCCCCCCCCCceeccCCcCcEEEecHHHH
Confidence            3567899999999999999998775432110     12234567899998      9999999999987765433

>PRK07860 NADH dehydrogenase subunit G; Validated

Probab=98.30  E-value=2.2e-07  Score=90.17  Aligned_cols=63  Identities=21%  Similarity=0.415  Sum_probs=42.0

Q ss_pred             CCCccccccccccchhcccc----ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPA----QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~----~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +..+.++||.|++|+++|-.    .+|.+..  |+...... ........|..||.|+++||+|||..++
T Consensus       145 i~~d~~rCI~C~rCvr~c~ev~g~~~l~~~~--rg~~~~i~-~~~~~~~~~~~cG~cv~vCP~GAl~~k~  211 (797)
T PRK07860        145 VLLDRERCVLCARCTRFSDQIAGDPFIDLQE--RGALQQVG-IYEGEPFQSYFSGNTVQICPVGALTGAA  211 (797)
T ss_pred             eeecccccccCcHHHHHHHhhcCCcEEEeee--cCCCCEEe-cCCCCCcCccccCCchhhCCcccccccc
Confidence            44678999999999999973    3343332  22222211 1111234688999999999999998663

>PRK08166 NADH dehydrogenase subunit G; Validated

Probab=98.29  E-value=1.9e-07  Score=91.38  Aligned_cols=64  Identities=19%  Similarity=0.309  Sum_probs=41.7

Q ss_pred             cCCCccccccccccchhcccc----ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          119 RYPTGEERCIACKLCEAVCPA----QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~~CP~----~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+..+.++||.|++|+++|-.    .++.+.  .++.... ...+......|.+||+|+++||+|||..+.
T Consensus       143 ~i~~d~~rCi~C~rCVr~c~e~~g~~~l~~~--~~~~~~~-~~~~~~~~~~~~~~G~cv~vCP~GAl~~k~  210 (847)
T PRK08166        143 FISHEMNRCIACYRCVRYYKDYAGGTDLGVY--GAHDNVY-FGRPEDGTLESEFSGNLVEVCPTGVFTDKT  210 (847)
T ss_pred             ceEecCCcCccccHHHHHHHhhcCcceEEEe--ecCceeE-ecCCCCCcccChhhCChHhhCCchhccccc
Confidence            355778999999999999984    333332  1111110 001111234688999999999999998764

>PRK09853 putative selenate reductase subunit YgfK; Provisional

Probab=98.29  E-value=2.9e-07  Score=90.39  Aligned_cols=65  Identities=23%  Similarity=0.471  Sum_probs=45.0

Q ss_pred             Ccccccccc----ccchhccccccc-cchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcccc
Q 027264          122 TGEERCIAC----KLCEAVCPAQAI-TIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYS  190 (226)
Q Consensus       122 ~~~~~Ci~C----g~C~~~CP~~ai-~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~  190 (226)
                      .+.++|.+|    |.|+.+||.+|+ +++...    .+....+....+.|++||.|+.+||+++-..++.|...
T Consensus       883 ~~~~rC~~C~~~C~~C~~vCP~~A~~~i~~~g----~~~~~~~~~~~~~C~~CG~C~~~CP~~~~py~dk~t~f  952 (1019)
T PRK09853        883 QEAARCLECNYVCEKCVDVCPNRANVSIAVPG----FQNRFQIVHLDAMCNECGNCAQFCPWNGKPYKDKITLF  952 (1019)
T ss_pred             ccccccCCcccccchhhhhCCcccccccccCC----cccCCceEEcCccCccccchhhhCCCCCCcccccceEE
Confidence            356799999    999999999983 222111    00001222234899999999999999998877766544

>PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional

Probab=98.29  E-value=2.2e-07  Score=86.91  Aligned_cols=56  Identities=39%  Similarity=0.904  Sum_probs=43.8

Q ss_pred             Ccccccccc------ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIAC------KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~C------g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+.++|+.|      +.|+.+||.+++.......        .+.++.+.|++|+.|+.+||.+||.+..
T Consensus       501 ~~~~rCl~C~~c~~C~~C~~~Cp~~ai~~~~~~~--------~~~i~~~~C~~Cg~C~~~CP~~Ai~~~~  562 (564)
T PRK12771        501 QEAARCLSCGNCFECDNCYGACPQDAIIKLGPGR--------RYHFDYDKCTGCHICADVCPCGAIEMGP  562 (564)
T ss_pred             hhcccCcccccccccchhhhhCChhheeeecCCc--------eEEEecccCcChhHHHhhcCcCceEecc
Confidence            346677777      8999999999887643210        2457788999999999999999998754

>PRK09130 NADH dehydrogenase subunit G; Validated

Probab=98.29  E-value=2.2e-07  Score=88.73  Aligned_cols=63  Identities=24%  Similarity=0.382  Sum_probs=41.6

Q ss_pred             CCCccccccccccchhcccc----ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPA----QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~----~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +..+.++||.|++|+++|-.    .++.+.  .|+...... .+.-....|..||.|+++||+|||+.++
T Consensus       140 i~~~~~rCI~C~rCvr~c~ev~g~~~l~~~--~rg~~~~i~-~~~~~~~~~~~~G~cv~~CPvgAl~~k~  206 (687)
T PRK09130        140 VKTVMTRCIHCTRCVRFATEVAGVPELGAI--GRGEDMEIT-TYLEQALTSELSGNVIDLCPVGALTSKP  206 (687)
T ss_pred             EEEecccCCcccHHHHHHHhhcCCceEEee--ecCCCCEEc-cCCCCCccccccccHHhhCCCccccccc
Confidence            44678999999999999974    333332  232222211 1111233588999999999999998764

>PRK12385 fumarate reductase iron-sulfur subunit; Provisional

Probab=98.28  E-value=1.7e-08  Score=84.71  Aligned_cols=109  Identities=21%  Similarity=0.392  Sum_probs=55.9

Q ss_pred             HHHHhhhHHHHHHHHHHHHHhcCCcceecCccccCC--CC-CCccCccccccCCCccccccccccchhccccccccch--
Q 027264           71 SINMLFLTEMVRGLGLTLKYFFDKKVTINYPFEKGP--LS-PRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIE--  145 (226)
Q Consensus        71 ~i~~~~~~~~~~~l~~~~~~~f~~~~~~~~p~~~~~--~~-~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~--  145 (226)
                      .+.++..+.++++|.+++..+|++.....-......  .. ................+.|+.||.|..+||+.....+  
T Consensus        90 ~iePl~~fpvikDLvvD~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CI~Cg~C~saCP~~~~~~~y~  169 (244)
T PRK12385         90 KVEALANFPIERDLVVDMTHFIESLEAIKPYIIGNDRTPDDGPNKQTPAQMAKYHQFSGCINCGLCYAACPQFGLNPEFI  169 (244)
T ss_pred             EEeeCCCCCeeeeCeeecHHHHHHHHHhcCeeeCCCCCCCcccccCCHHHHHHHHHHHhcCcCccccCcCcCcccCCCCC
Confidence            344556677888888888777764333221100000  00 0011111000011235689999999999998432111  


Q ss_pred             ------------hhhhccCCccccc---cccCCCCCCcchhhhhcCccc
Q 027264          146 ------------AEEREDGSRRTTR---YDIDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       146 ------------~~~~~~~~~~~~~---~~~d~~~C~~Cg~Cv~~CP~~  179 (226)
                                  .+.+.........   .....+.|+.||.|..+||.+
T Consensus       170 GP~~l~~a~r~~~d~rd~~~~~rl~~~~~~~gl~~C~~C~~C~~vCP~~  218 (244)
T PRK12385        170 GPAAITLAHRYNLDSRDHGKKERMKQLNGQNGVWSCTFVGYCSEVCPKH  218 (244)
T ss_pred             CHHHHHHHHHHhhcCCccchHHHHHhhcccchhhhCcCcccccccCCCC
Confidence                        0111111111001   113446899999999999997

>PRK15449 ferredoxin-like protein FixX; Provisional

Probab=98.28  E-value=2.9e-07  Score=65.74  Aligned_cols=42  Identities=24%  Similarity=0.473  Sum_probs=35.6

Q ss_pred             ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccc
Q 027264          131 KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       131 g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      ..|+.+||++|+..+...         .+.++.+.|++||.|+.+||.+++
T Consensus        37 k~C~~aCPagA~~~~e~G---------~V~vd~e~CigCg~C~~~C~~~~~   78 (95)
T PRK15449         37 ELLVKACPAGLYKKQDDG---------SVRFDYAGCLECGTCRILGLGSAL   78 (95)
T ss_pred             hHHHHHCCHhhcEeCCCC---------CEEEcCCCCCcchhhhhhcCCCCc
Confidence            689999999999764322         467888999999999999999986

>PF12837 Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=98.26  E-value=1.7e-07  Score=49.86  Aligned_cols=22  Identities=41%  Similarity=0.937  Sum_probs=19.6

Q ss_pred             CCccccccccccchhccccccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAI  142 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai  142 (226)
                      .++.++|++||.|+.+||.+||
T Consensus         3 ~id~~~C~~Cg~C~~~Cp~~ai   24 (24)
T PF12837_consen    3 VIDPDKCIGCGDCVRVCPEGAI   24 (24)
T ss_pred             EEChhhCcChhHHHHhcchhcC
Confidence            3678999999999999999875

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding

>PRK12577 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=98.26  E-value=3.2e-08  Score=86.64  Aligned_cols=109  Identities=19%  Similarity=0.437  Sum_probs=57.0

Q ss_pred             HHHhhhHHHHHHHHHHHHHhcCCcceec-CccccCC--CCCCccCccccccCCCccccccccccchhccccccccchh--
Q 027264           72 INMLFLTEMVRGLGLTLKYFFDKKVTIN-YPFEKGP--LSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEA--  146 (226)
Q Consensus        72 i~~~~~~~~~~~l~~~~~~~f~~~~~~~-~p~~~~~--~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~--  146 (226)
                      +.|+..+.++++|.+++..|++...... |-.....  ....+...+...........|+.||.|..+||+.....+.  
T Consensus        96 iePl~~~pvikDLvVD~~~~~~k~~~v~p~~~~~~~~~~~~e~~~~p~~~~~~~~~~~Ci~CG~C~s~CP~~~~~~~f~G  175 (329)
T PRK12577         96 IAPLGNMPVIKDLVVDMSSFWQNLEAVDPYVSTAARQVPEREFLQTPEERSKLDQTGNCILCGACYSECNAREVNPEFVG  175 (329)
T ss_pred             EEECCCCCccccceeccHHHHHHHHhccCccccCCCCCCcccccCCHHHHHHHHHhhhCcccCcccccCCCCCcCcCcCC
Confidence            4455566789999999988886443322 1110100  0111211111111112246799999999999975332110  


Q ss_pred             ------------hhhccCCccccc-c---ccCCCCCCcchhhhhcCcccc
Q 027264          147 ------------EEREDGSRRTTR-Y---DIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       147 ------------~~~~~~~~~~~~-~---~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                                  +.+......... +   ....+.|+.|+.|..+||.+.
T Consensus       176 P~~~~~a~r~~~d~rd~~~~~~l~~~~~~~~giw~C~~C~~C~~~CPk~I  225 (329)
T PRK12577        176 PHALAKAQRMVADSRDTATEQRLELYNQGTAGVWGCTRCYYCNSVCPMEV  225 (329)
T ss_pred             HHHHHHHHHHhhCCcchhHHHHHHHHhcCCCccccCcChhhhhhhCCCCC
Confidence                        000000000001 1   112578999999999999984

>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit

Probab=98.25  E-value=3.5e-07  Score=80.31  Aligned_cols=50  Identities=30%  Similarity=0.690  Sum_probs=40.0

Q ss_pred             ccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          127 CIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       127 Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      |.+|+.|+.+||++||...... .     ...+.+|...|++||.|+.+||.+|+.
T Consensus       183 ~c~~~~Cv~~CP~~Ai~~~~~~-~-----~~~~~id~~~Ci~Cg~Ci~~CP~~a~~  232 (341)
T TIGR02066       183 VCEIPSVVAACPTGALKPRRDG-K-----NKSLEVDVEKCIYCGNCYTMCPAMPIF  232 (341)
T ss_pred             hcCCCceEeeCchhhceecccC-C-----CCceeeccccCCcCCchHHhCchhhcc
Confidence            5567999999999999874221 1     114678899999999999999999986

This model describes the beta subunit of sulfite reductase.

>COG1142 HycB Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]

Probab=98.24  E-value=2.3e-07  Score=72.78  Aligned_cols=61  Identities=33%  Similarity=0.609  Sum_probs=41.2

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc---hhhhhcCcccccccCCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC---GFCQEACPVDAIVEGPN  186 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C---g~Cv~~CP~~Ai~~~~~  186 (226)
                      .++.++|++||.|+.+||.++|.+... .. ..   ....+.-+.|.+-   .+|+.+||++|+.+.+.
T Consensus        78 ~V~~ekCiGC~~C~~aCPfGai~~~~~-~~-~~---~~~a~KCdlC~~~e~gpaCVe~CP~~AL~lv~~  141 (165)
T COG1142          78 QVDEEKCIGCKLCVVACPFGAITMVSY-PV-AA---KAVAVKCDLCAGREVGPACVEACPTEALELVDE  141 (165)
T ss_pred             EEchhhccCcchhhhcCCcceEEEEee-cC-cc---hhhhhhcccccCccCCCceeeeCCHHHhhcccH
Confidence            367899999999999999999988654 11 00   0111111224332   46999999999986653

>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C

Probab=98.24  E-value=4e-07  Score=70.42  Aligned_cols=57  Identities=32%  Similarity=0.598  Sum_probs=34.0

Q ss_pred             ccccccccchhcccccccc-ch--hhhhc--cCCccccccccCCCCCCcchhhhhcCccccc
Q 027264          125 ERCIACKLCEAVCPAQAIT-IE--AEERE--DGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~ai~-~~--~~~~~--~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      +.|+.||.|..+||+.... +.  ...+.  .+.+.........+.|+.||.|..+||.+..
T Consensus         2 ~~Ci~CG~C~~~CP~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~C~~Cg~C~~~CP~~i~   63 (144)
T TIGR03290         2 KACYQCGTCTGSCPSGRRTSYRTRLIIRKALLGLKDEVISDDDLWMCTTCYTCQERCPRDVK   63 (144)
T ss_pred             ccccCCCCCcCcCCCccccCCCHHHHHHHHHccchhhhccCCCCCcCcCcCchhhhcCCCCC
Confidence            5799999999999975211 00  00000  0100000011245689999999999999843

The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.

>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit

Probab=98.22  E-value=4.6e-07  Score=82.25  Aligned_cols=57  Identities=26%  Similarity=0.631  Sum_probs=38.0

Q ss_pred             ccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccc
Q 027264          123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~  179 (226)
                      ..+.|+.||.|+.+||++.+...........+.......+...|+.||.|..+||.+
T Consensus       361 ~~~~Ci~Cg~C~~vCP~~l~p~~l~~~~~~~~~~~~~~~~~~~C~~Cg~C~~vCP~~  417 (435)
T TIGR01945       361 PEKPCIRCGKCVQVCPMNLLPQQLNWLALADEFDEAEEHNLMDCIECGCCSYVCPSN  417 (435)
T ss_pred             cCCcCcCccchhhhCccchhhHHHHHHhhhcccchhhcCCCCcCCcCCCcccccCCC
Confidence            457899999999999997554322110001111112245667899999999999998

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 C subunit.

>TIGR03336 IOR_alpha indolepyruvate ferredoxin oxidoreductase, alpha subunit

Probab=98.19  E-value=5.8e-07  Score=84.66  Aligned_cols=50  Identities=42%  Similarity=0.905  Sum_probs=38.3

Q ss_pred             cCCCccccccccccchh--ccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccc
Q 027264          119 RYPTGEERCIACKLCEA--VCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~--~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      .+.++.++|++|+.|.+  .||...  ....          ...++. .|+.||.|+.+||.+||
T Consensus       544 ~~~id~~~C~~C~~C~~~~~CP~~~--~~~~----------~~~i~~-~C~~Cg~C~~~CP~~Ai  595 (595)
T TIGR03336       544 PYKVDQDKCIGCKKCIKELGCPAIE--PEDK----------EAVIDP-LCTGCGVCAQICPFDAI  595 (595)
T ss_pred             eEEEcCCcCCCccccccccCCCCcc--ccCC----------cceeCC-CCcCHHHHHhhCccccC
Confidence            45577889999999999  999532  2111          234555 79999999999999986

Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase.

>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed

Probab=98.16  E-value=8.1e-07  Score=84.40  Aligned_cols=50  Identities=32%  Similarity=0.738  Sum_probs=26.2

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch-------hhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG-------FCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg-------~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++|+.|+.+||.+++.....              ....|..|+       .|+.+||++||.+.+
T Consensus        82 ~d~~~C~gC~~C~~~CP~~ai~~~~~--------------~~~kC~~C~~~~~~~~~Cv~~CP~~Ai~~~~  138 (639)
T PRK12809         82 LDEQKCIGCKRCAIACPFGVVEMVDT--------------IAQKCDLCNQRSSGTQACIEVCPTQALRLMD  138 (639)
T ss_pred             cChhhCcchhhHhhhcCCCCEEccCC--------------CcccccCCcccCCCCChhhhhCccceEEEec
Confidence            44555555555555555555543221              123455554       466666666666544

>PRK05950 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed

Probab=98.15  E-value=4.9e-08  Score=81.41  Aligned_cols=109  Identities=19%  Similarity=0.321  Sum_probs=55.9

Q ss_pred             HHHHhhhHHHHHHHHHHHHHhcCCcceec-CccccCC-CCCCccCccccccCCCccccccccccchhccccccccch---
Q 027264           71 SINMLFLTEMVRGLGLTLKYFFDKKVTIN-YPFEKGP-LSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIE---  145 (226)
Q Consensus        71 ~i~~~~~~~~~~~l~~~~~~~f~~~~~~~-~p~~~~~-~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~---  145 (226)
                      .+.++..+.++++|.++...+|++..... |...... ....................|+.||.|..+||+.....+   
T Consensus        85 tiepl~~~~vikDLvvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~~~~~~~~~  164 (232)
T PRK05950         85 VIRPLPGLPVIKDLVVDMTQFYAQYRSIKPYLINDTPPPARERLQSPEDREKLDGLYECILCACCSTSCPSFWWNPDKFL  164 (232)
T ss_pred             EEEECCCCCeeeeceeehHHHHHHHHhccCeecCCCCCCchhccCCHHHHHHHHhHHhccccccccccCCccccCCCCCC
Confidence            34455556778888888888776433322 1110010 111111111111111245689999999999997532211   


Q ss_pred             -hhhhc-------cCC----ccccc-c--ccCCCCCCcchhhhhcCccc
Q 027264          146 -AEERE-------DGS----RRTTR-Y--DIDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       146 -~~~~~-------~~~----~~~~~-~--~~d~~~C~~Cg~Cv~~CP~~  179 (226)
                       +....       .+.    ..... .  ....+.|+.||.|..+||.+
T Consensus       165 gp~~l~~~~r~~~d~rd~~~~~~~~~~~~~~~i~~C~~Cg~C~~~CP~g  213 (232)
T PRK05950        165 GPAALLQAYRFIADSRDEATGERLDILDDPFGVFRCHTIMNCVEVCPKG  213 (232)
T ss_pred             CHHHHHHHHHHhhCCccchhHHHHHHhhcccccccCcCcCCcCccccCC
Confidence             10000       000    00000 1  11357899999999999997

>COG1034 NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]

Probab=98.10  E-value=7.7e-07  Score=84.17  Aligned_cols=72  Identities=29%  Similarity=0.529  Sum_probs=43.8

Q ss_pred             Cccccccccccchhccccccccchh--hhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcccchhcHH
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEA--EEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHE  195 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~--~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~  195 (226)
                      .+.++||.|++|+++|-.-+-....  ..|+...... .+......=..||+|+.+||+|||+.++. ++....++
T Consensus       141 ~dm~RCI~C~RCVR~c~eiaG~~~l~~~~rg~~~~i~-t~~~~~l~se~cGncv~vCPvGALt~K~~-~~~ar~wE  214 (693)
T COG1034         141 YDMNRCILCTRCVRFCKEIAGTHELGVIKRGENSEIG-TYLDQPLESELCGNCVDVCPVGALTSKPF-AFTARKWE  214 (693)
T ss_pred             cccccceechhhHHhhhhhcCccccceeecCCCceee-cccccccccccccceeeeccccccccChH-Hhhhccch
Confidence            6789999999999999964322222  1122211111 11111112278999999999999997774 55444443

>PRK12769 putative oxidoreductase Fe-S binding subunit; Reviewed

Probab=98.10  E-value=1.2e-06  Score=83.41  Aligned_cols=52  Identities=29%  Similarity=0.633  Sum_probs=43.6

Q ss_pred             ccccccccc--chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          124 EERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       124 ~~~Ci~Cg~--C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...|+.|+.  |+.+||+++|.....          .+.++.+.|++|+.|+.+||++||.+..
T Consensus        53 ~~~C~~C~~~~C~~~CP~~ai~~~~~----------~~~id~~~C~~C~~C~~~CP~~ai~~~~  106 (654)
T PRK12769         53 AVTCHHCEDAPCARSCPNGAISHVDD----------SIQVNQQKCIGCKSCVVACPFGTMQIVL  106 (654)
T ss_pred             CccCCCCCChhHhhhCCccceeccCC----------eEEEecccccCcChhcccCCccCeeecc
Confidence            568999986  999999999876432          3467888999999999999999997654

>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=98.07  E-value=7.3e-07  Score=47.52  Aligned_cols=22  Identities=41%  Similarity=0.982  Sum_probs=18.7

Q ss_pred             Cccccccccccchhcccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAIT  143 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~  143 (226)
                      ++.++|++||.|+.+||.+||.
T Consensus         3 id~~~C~~Cg~C~~~CP~~ai~   24 (24)
T PF00037_consen    3 IDPDKCIGCGRCVEACPFDAIT   24 (24)
T ss_dssp             EETTTSSS-THHHHHSTTSSEE
T ss_pred             EchHHCCCcchhhhhcccccCC
Confidence            5678999999999999999874

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1DUR_A 1H98_A 1BD6_A 1BQX_A 1BWE_A 1BC6_A 3BK7_A 1FCA_A 1FDN_A 2FDN_A ....

>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed

Probab=98.06  E-value=1.2e-06  Score=83.30  Aligned_cols=54  Identities=30%  Similarity=0.696  Sum_probs=44.7

Q ss_pred             cccccccccc--chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          123 GEERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       123 ~~~~Ci~Cg~--C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ....|..|+.  |+.+||++++.....          ...++.+.|++|+.|+.+||++||.+...
T Consensus        52 ~~~~C~~C~~~~C~~~CP~~ai~~~~~----------~v~~d~~~C~gC~~C~~~CP~~ai~~~~~  107 (639)
T PRK12809         52 NPVACHHCNNAPCVTACPVNALTFQSD----------SVQLDEQKCIGCKRCAIACPFGVVEMVDT  107 (639)
T ss_pred             cCCCCcCcCChhHHhhCCcCceecccc----------ceecChhhCcchhhHhhhcCCCCEEccCC
Confidence            4678999996  999999999976432          34577789999999999999999976543

>PF13534 Fer4_17: 4Fe-4S dicluster domain; PDB: 1ZOY_B 3AE9_B 3AED_B 3AEA_B 3AE1_B 3SFD_B 3ABV_B 3AEF_B 3AEB_B 3AE3_B

Probab=98.06  E-value=8.2e-07  Score=58.27  Aligned_cols=54  Identities=26%  Similarity=0.649  Sum_probs=24.5

Q ss_pred             cccccccchhccccccccchhhhhc-----cCCccccccccCCCCCCcchhhhhcCccc
Q 027264          126 RCIACKLCEAVCPAQAITIEAEERE-----DGSRRTTRYDIDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~~~~~-----~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~  179 (226)
                      +|+.||.|..+||++..........     .+...........+.|+.||.|..+||.+
T Consensus         1 ~C~~Cg~C~~~CP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~   59 (61)
T PF13534_consen    1 ACTQCGYCVPACPSYIATPDEPRSPMRAIYLGKIDEISESHAASLCIGCGLCESVCPQG   59 (61)
T ss_dssp             T----STTGGGSHHHHHCTTTHHHHHHHHHHCHCHTTHHHTTTTT--S--HHHHH-TT-
T ss_pred             CCCCCCcCcccCCCccccCccHHHHHHHHHHhcchhhhhCcccccCcCcCcCcccccCC
Confidence            5999999999999865422111100     00000001124567899999999999987

...

>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG

Probab=98.02  E-value=1.6e-06  Score=78.32  Aligned_cols=43  Identities=40%  Similarity=0.920  Sum_probs=33.1

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      .++|++|+.|+++||++ +.....              ....|+.|+.|+++||. ++.
T Consensus       230 ~~~Ci~C~~Cv~vCP~g-i~~~~~--------------~~~~Ci~Cg~CidaCp~-a~~  272 (434)
T TIGR02745       230 LGDCIDCNLCVQVCPTG-IDIRDG--------------LQLECINCGLCIDACDD-VME  272 (434)
T ss_pred             CCCCCChhhhHHhCCCC-CEeCCC--------------CchhChhhhHHHHhCCC-hHH
Confidence            46899999999999998 332211              12579999999999998 553

Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=98.01  E-value=1.4e-06  Score=78.05  Aligned_cols=55  Identities=35%  Similarity=0.747  Sum_probs=39.2

Q ss_pred             Ccccccc--cc-ccchhcccc-----ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          122 TGEERCI--AC-KLCEAVCPA-----QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       122 ~~~~~Ci--~C-g~C~~~CP~-----~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ++.|+|-  .| ..|.+.||.     .+|.+++..        ....|....|++||.|++.||++||..-
T Consensus         8 vd~D~C~PkkC~~eC~~yCP~vrtg~~~I~i~~~~--------gkpvIsE~lCiGCGICvkkCPF~AI~Iv   70 (591)
T COG1245           8 VDYDRCQPKKCGYECIKYCPVVRTGKETIEIDEDT--------GKPVISEELCIGCGICVKKCPFDAISIV   70 (591)
T ss_pred             eehhccCccccchhhhhcCCCccCCCeeEEecCCC--------CCceeEhhhhccchhhhccCCcceEEEe
Confidence            4556674  45 589999996     244444321        1335666789999999999999999743

>TIGR00314 cdhA CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit

Probab=97.97  E-value=2.1e-06  Score=81.69  Aligned_cols=58  Identities=21%  Similarity=0.583  Sum_probs=35.9

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ...++|++||.|+.+||.... ...............+....+.|++||.|+.+||.+.
T Consensus       396 ~~~~kCI~CG~Cv~aCP~~l~-i~e~i~~a~~G~l~~l~~~~d~C~~CG~C~evCP~gI  453 (784)
T TIGR00314       396 ELANKCTQCGNCVRTCPNSLR-VDEAMAHAQKGDLSKLEQLEEQCYACGRCEQACPKNI  453 (784)
T ss_pred             hhcccCCCcccchhhCCCCcc-hHHHHHHHhcCCccccccCHhhhhhhhHHhccCCCCC
Confidence            346899999999999998632 1111000000000112223468999999999999983

Acetyl-CoA decarbonylase/synthase (ACDS) is a multienzyme complex. Carbon monoxide dehydrogenase is a synonym. The ACDS complex carries out an unusual reaction involving the reversible cleavage and synthesis of acetyl-CoA in methanogens. The model contains the prosite signature for 4Fe-4S ferredoxins [C-x(2)-C-x(2)-C-x(3)-C-[PEG]] between residues 448-462 of the model.

>PRK00941 acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated

Probab=97.93  E-value=2.6e-06  Score=81.11  Aligned_cols=58  Identities=29%  Similarity=0.651  Sum_probs=36.7

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ...++|++||.|+.+||++.......... ............+.|++||.|..+||++.
T Consensus       401 ~eadrCI~CG~Cv~aCP~~l~i~~~I~~a-~~G~~~~l~~l~~~Ct~CG~CeeVCPtgI  458 (781)
T PRK00941        401 ELAKKCTECGWCVRVCPNELPIPEAMEAA-AKGDLSKLEDLYDKCIGCGRCEQVCPKNI  458 (781)
T ss_pred             HhhhhCcCCCCccccCCCCcchhHHHHHH-hcCChhhhhhhhhhccchhHHhhhCCCCC
Confidence            34689999999999999863211110000 00000012334578999999999999984

>TIGR00276 iron-sulfur cluster binding protein, putative

Probab=97.93  E-value=4.2e-06  Score=71.75  Aligned_cols=58  Identities=26%  Similarity=0.515  Sum_probs=37.3

Q ss_pred             cccccccccchhccccccccchhh--hh---c--c---CCccccccccCCCCCC-cchhhhhcCccccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAE--ER---E--D---GSRRTTRYDIDMTKCI-YCGFCQEACPVDAI  181 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~--~~---~--~---~~~~~~~~~~d~~~C~-~Cg~Cv~~CP~~Ai  181 (226)
                      .+.|..|+.|+.+||++||.....  ..   .  .   .......+..+...|+ +|+.|+.+||.+..
T Consensus       158 ~~~C~~C~~C~~aCPt~AI~~~~~~d~~~C~sy~ti~~~~~~~~~~~~~~~~~~~gCd~Cq~vCP~n~~  226 (282)
T TIGR00276       158 EEYCGRCTKCIDACPTQALVEPEFVDAPRCISYLTIEKDAALPKEFASNCGGRSYGCDICQEVCPWNKK  226 (282)
T ss_pred             CCCCccHHHHHHhcCcccccCCCccCHHHHHHHhcccCCCcCCHHHHHHhcCcccCCCCccccCCCCCC
Confidence            568999999999999999863110  00   0  0   0001112223345686 79999999999964

This series of proteins contain the prosite signature for 4Fe-4S ferredoxins iron-sulfur binding proteins (C-x(2)-C-x(2)-C-x(3)-C-[PEG]) between residues 175-188 of the model.

>cd01916 ACS_1 Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA

Probab=97.90  E-value=2.2e-06  Score=81.43  Aligned_cols=58  Identities=24%  Similarity=0.586  Sum_probs=36.3

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ...++|+.||.|..+||++.............. ...+....+.|+.||.|..+||+++
T Consensus       362 ~~~~kCI~CG~Cv~aCP~~l~i~e~i~~~~~G~-~~~l~~~~~~Ct~CG~C~evCP~gI  419 (731)
T cd01916         362 ELAAKCTDCGWCTRACPNSLRIKEAMEAAKEGD-FSGLADLFDQCVGCGRCEQECPKEI  419 (731)
T ss_pred             HhhhcCCCCCcccccCCCCCcHHHHHHHHhcCC-hhhhhhhHhhhhhhhHHhhhCCCCC
Confidence            446899999999999998632111000000000 0011223478999999999999996

ACS forms a heterotetramer with carbon monoxide dehydrogenase (CODH) consisting of two ACS and two CODH subunits. CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP). ACS has three structural domains, an N-terminal rossman fold domain with a helical region at its N-terminus which interacts with CODH, and two alpha + beta fold domains. A Ni-Fe-S center referred to as the A-cluster is located in the C-terminal domain. A large cavity exists between the three domains which may bind CoA.

>PRK13409 putative ATPase RIL; Provisional

Probab=97.89  E-value=2.9e-06  Score=79.81  Aligned_cols=54  Identities=35%  Similarity=0.796  Sum_probs=38.9

Q ss_pred             Ccccccc--ccc-cchhccccc-----cccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          122 TGEERCI--ACK-LCEAVCPAQ-----AITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       122 ~~~~~Ci--~Cg-~C~~~CP~~-----ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ++.|+|-  .|+ .|.+.||..     +|.++...        ....+..+.|++||.|++.||++||..
T Consensus         7 ~~~~~c~~~~c~~~c~~~cp~~~~~~~~~~~~~~~--------~~~~~~e~~c~~c~~c~~~cp~~a~~i   68 (590)
T PRK13409          7 VDYDRCQPKKCNYECIKYCPVVRTGEETIEIDEDD--------GKPVISEELCIGCGICVKKCPFDAISI   68 (590)
T ss_pred             eeccccCcchhhhhHHhhCCCcccCCeEEEEcCCC--------CCceeeHhhccccccccccCCcceEEE
Confidence            4567775  675 799999963     33332211        145677789999999999999999973

>TIGR02486 RDH reductive dehalogenase

Probab=97.86  E-value=1.1e-05  Score=70.26  Aligned_cols=55  Identities=29%  Similarity=0.723  Sum_probs=35.6

Q ss_pred             ccccccccchhccccccccchhhh-hcc-----C----CccccccccCCC-----CCC-----cchhhhhcCccc
Q 027264          125 ERCIACKLCEAVCPAQAITIEAEE-RED-----G----SRRTTRYDIDMT-----KCI-----YCGFCQEACPVD  179 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~ai~~~~~~-~~~-----~----~~~~~~~~~d~~-----~C~-----~Cg~Cv~~CP~~  179 (226)
                      +.|..|++|+++||++||..+... -+.     .    .+......++.+     .|.     .|+.|+.+||++
T Consensus       205 ~fC~~C~~C~~~CP~~Ai~~~~~psw~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~C~~C~~~CPf~  279 (314)
T TIGR02486       205 KFCETCGKCADECPSGAISKGGEPTWDPEDSNGDPPGENNPGLKWQYDGWRCLLFRCYNEGGGGCGVCQAVCPFN  279 (314)
T ss_pred             ccCcchhHHHhhCCccccCCCCCCcccccccccccccccCCCcccccchhhcccccccCCCCCCCCCCeeECCCC
Confidence            579999999999999999875332 000     0    000011223333     354     599999999998

This model represents a family of corrin and 8-iron Fe-S cluster-containing reductive dehalogenases found primarily in halorespiring microorganisms such as dehalococcoides ethenogenes which contains as many as 17 enzymes of this type with varying substrate ranges. One example of a characterized species is the tetrachloroethene reductive dehalogenase (1.97.1.8) which also acts on trichloroethene converting it to dichloroethene.

>PF12798 Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.86  E-value=4.8e-06  Score=39.16  Aligned_cols=15  Identities=53%  Similarity=1.287  Sum_probs=10.3

Q ss_pred             CCcchhhhhcCcccc
Q 027264          166 CIYCGFCQEACPVDA  180 (226)
Q Consensus       166 C~~Cg~Cv~~CP~~A  180 (226)
                      |++|+.|+++||++|
T Consensus         1 C~~C~~C~~~Cp~~A   15 (15)
T PF12798_consen    1 CTGCGACVEVCPTGA   15 (15)
T ss_pred             CCCchHHHHHhcCCC
Confidence            566777777777665

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding

>PRK11168 glpC sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional

Probab=97.86  E-value=5.6e-06  Score=74.12  Aligned_cols=57  Identities=30%  Similarity=0.735  Sum_probs=36.5

Q ss_pred             cccccccccchhccccccccchhh--hhc--cCCcc----ccccccCCCCCCcchhhhhcCcccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAE--ERE--DGSRR----TTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~--~~~--~~~~~----~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      .++|+.||.|..+||+........  ...  .+.+.    ........+.|+.|+.|..+||.+.
T Consensus         6 ~~~Ci~Cg~C~~~CP~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP~~i   70 (396)
T PRK11168          6 FDSCIKCTVCTTACPVARVNPLYPGPKQAGPDGERLRLKDGALYDESLKYCSNCKRCEVACPSGV   70 (396)
T ss_pred             hhhcCCCCCCCccCCCcccCCCCCChhhhccHHHHHhccchhhcCCCCCcCcCcCccCcccCCCC
Confidence            468999999999999975532100  000  00000    0112234578999999999999985

>TIGR00273 iron-sulfur cluster-binding protein

Probab=97.77  E-value=9.3e-06  Score=73.54  Aligned_cols=59  Identities=25%  Similarity=0.402  Sum_probs=35.0

Q ss_pred             Cccccccccccchhccccccccch------h-hhhccCC----ccccccccCCCCCCcchhhhhcCcccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIE------A-EEREDGS----RRTTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~------~-~~~~~~~----~~~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      .+..+|+.||.|..+||+....-.      . ..++...    .....+......|..||.|..+||++.
T Consensus       290 ~e~~~CIrCG~C~~~CPvy~~~g~~~~~~~~~Gp~G~v~~~~~~g~~~~~~~~~~C~~Cg~C~~vCP~gI  359 (432)
T TIGR00273       290 REVLACIRCGACQNECPVYRHIGGHWYGSIYPGPIGAVWSPLLGGYTDYKHLPYLSSLCGACREVCPVKI  359 (432)
T ss_pred             hhHhhCCCCCCccccCcchhccCccccccccCChHHHHHHHHhcccccccccCccchhhhhhhccCCCCC
Confidence            346799999999999997532110      0 0000000    000011112368999999999999984

Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters.

>PRK09193 indolepyruvate ferredoxin oxidoreductase; Validated

Probab=97.71  E-value=4.7e-06  Score=82.80  Aligned_cols=53  Identities=26%  Similarity=0.431  Sum_probs=38.5

Q ss_pred             cCCCccccccccccchh--ccccccccchhhhhccCCccccccccCCCCCCcchhhhh-cCccc
Q 027264          119 RYPTGEERCIACKLCEA--VCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQE-ACPVD  179 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~--~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~-~CP~~  179 (226)
                      ++.++.+.|.+||.|..  .||+  |...+..  .++    +..||...|.+|+.|++ .||.-
T Consensus       637 r~~In~~vCegCgdC~~~s~C~a--i~p~~t~--~gr----K~~Idqs~Cn~d~sC~~G~CPsF  692 (1165)
T PRK09193        637 RVFINEAVCEGCGDCSVKSNCLS--VEPVETE--FGR----KRRIDQSSCNKDFSCLKGFCPSF  692 (1165)
T ss_pred             eEEEcccccCCchhhhhccCCcc--eeecccc--CCc----cEEECHhHCCCccccccCCCCCc
Confidence            35578899999999976  6985  3332211  111    24688899999999999 99975

>TIGR01936 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit

Probab=97.71  E-value=9.5e-06  Score=73.65  Aligned_cols=56  Identities=13%  Similarity=0.043  Sum_probs=38.0

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCc--chhhhhcCccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIY--CGFCQEACPVD  179 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~--Cg~Cv~~CP~~  179 (226)
                      ...||.||.|+++||++.+...-............-..+...|+.  ||.|..+||.+
T Consensus       372 ~~aCI~CG~C~~vCPm~L~P~~L~~a~~~~d~d~a~~lg~~ecieedCG~CsyVCPSk  429 (447)
T TIGR01936       372 ERAMIPIGIYERVMPLDIPPTLLLKALIAGDFDKAQRLGALEVDEEDFALCTFVDPSK  429 (447)
T ss_pred             ccceeECChHhhcCCCCCCHHHHHHHHHcCCHHHHHHCCCcccCccccccCceECCCC
Confidence            456999999999999986654332211111111122345678998  99999999988

This model represents the NqrA subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump.

>TIGR03379 glycerol3P_GlpC glycerol-3-phosphate dehydrogenase, anaerobic, C subunit

Probab=97.68  E-value=1.5e-05  Score=71.42  Aligned_cols=57  Identities=33%  Similarity=0.744  Sum_probs=35.3

Q ss_pred             cccccccccchhccccccccchhh--hhc--cCCcc----ccccccCCCCCCcchhhhhcCcccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAE--ERE--DGSRR----TTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~--~~~--~~~~~----~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      .++|+.||.|..+||+........  ...  .+.+.    ...+....+.|..|+.|..+||.+.
T Consensus         4 ~~~Ci~Cg~C~~~Cp~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~C~~C~~C~~~CP~~i   68 (397)
T TIGR03379         4 FESCIKCTVCTVYCPVAKANPLYPGPKQAGPDGERLRLKSAELYDEALKYCTNCKRCEVACPSDV   68 (397)
T ss_pred             hhhCCCCCCCcccCcCccccCCccCcccCCcHHHHHhcccchhcccccccCcCcCccchhcCCCC
Confidence            468999999999999864321100  000  00000    0011123578999999999999984

Members of this protein family are the membrane-anchoring, non-catalytic C subunit, product of the glpC gene, of a three-subunit, FAD-dependent, anaerobic glycerol-3-phosphate dehydrogenase. GlpC lasks classical hydrophobic transmembrane helices; Cole, et al suggest interaction with the membrane may involve amphipathic helices. GlcC has conserved Cys-containing motifs suggestive of iron-sulfur binding. This complex is found mostly in Escherichia coli and closely related species.

>PRK11274 glcF glycolate oxidase iron-sulfur subunit; Provisional

Probab=97.68  E-value=8.4e-06  Score=73.34  Aligned_cols=57  Identities=25%  Similarity=0.726  Sum_probs=34.8

Q ss_pred             cccccccccchhccccccccc----hhhhhcc-------CCccccccccCCCCCCcchhhhhcCcccc
Q 027264          124 EERCIACKLCEAVCPAQAITI----EAEERED-------GSRRTTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~----~~~~~~~-------~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      .+.|++||.|..+||+....-    .+..+..       +...........+.|+.|+.|..+||.+.
T Consensus        22 ~~~C~~Cg~C~~~CP~~~~~~~~~~~p~g~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP~~v   89 (407)
T PRK11274         22 LRKCVHCGFCTATCPTYQLLGDELDGPRGRIYLIKQVLEGAEVTEKTQLHLDRCLTCRNCETTCPSGV   89 (407)
T ss_pred             HHhCccCCCccccCCcccccCCcccChhHHHHHHHHHhccCccchhhccccccCccccchhhhCCCCC
Confidence            468999999999999753321    1111110       00000011122568999999999999983

>PRK06259 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Provisional

Probab=97.66  E-value=1.2e-05  Score=73.97  Aligned_cols=59  Identities=31%  Similarity=0.789  Sum_probs=35.8

Q ss_pred             Cccccccccccchhccccccccchh-------------hhhccCCccccccccCCCCCCcchhhhhcCcccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEA-------------EEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~-------------~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ...+.|+.||.|..+||+....--.             ..+....+.........+.|+.||.|..+||.+.
T Consensus       130 ~~~~~Ci~CG~C~~~CP~~~~~~~~gp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP~gi  201 (486)
T PRK06259        130 KKLRGCIECLSCVSTCPARKVSDYPGPTFMRQLARFAFDPRDEGDREKEAFDEGLYNCTTCGKCVEVCPKEI  201 (486)
T ss_pred             hCchhcccCccccccCCCCccccCcCHHHHHHHHHHhhCCcchhhHHHHHhcCCCcCCCCcCcccCcCCCCC
Confidence            3457899999999999976431000             0000000000111234578999999999999883

>PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional

Probab=97.64  E-value=1.4e-05  Score=72.69  Aligned_cols=59  Identities=12%  Similarity=0.076  Sum_probs=38.5

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCc--chhhhhcCccccccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIY--CGFCQEACPVDAIVE  183 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~--Cg~Cv~~CP~~Ai~~  183 (226)
                      ...|+.||.|+++||.+.....-...............+...|+.  ||.|..+||.+ |.+
T Consensus       373 ~~~CI~Cg~C~~vCP~~L~P~~l~ra~~~~d~~~~e~~~~~~C~EedCG~CsyVCPsk-ipL  433 (448)
T PRK05352        373 ERAMVPIGNYERVMPLDILPTQLLRALIVGDTDEAQALGALELDEEDLALCTFVCPGK-YEY  433 (448)
T ss_pred             CcceeecCcHhhcCCCCCCHHHHHHHHHcCCHHHHHHcCchhcCccccCCCccCCCCC-chH
Confidence            457999999999999965443221111111111112356678999  99999999998 443

>TIGR02910 sulfite_red_A sulfite reductase, subunit A

Probab=97.63  E-value=1.7e-05  Score=69.24  Aligned_cols=18  Identities=33%  Similarity=0.969  Sum_probs=16.0

Q ss_pred             CCCCCCcchhhhhcCccc
Q 027264          162 DMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~  179 (226)
                      ....|++||.|+.+||++
T Consensus       299 G~~~CvgCGrC~~~CP~~  316 (334)
T TIGR02910       299 GYHMCVGCGRCDDICPEY  316 (334)
T ss_pred             CccccCCcCchhhhCCCC
Confidence            345799999999999999

Members of this protein family include the A subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite.

>PRK13030 2-oxoacid ferredoxin oxidoreductase; Provisional

Probab=97.62  E-value=8.3e-06  Score=81.25  Aligned_cols=53  Identities=25%  Similarity=0.405  Sum_probs=38.5

Q ss_pred             cCCCccccccccccchh--ccccccccchhhhhccCCccccccccCCCCCCcchhhhh-cCccc
Q 027264          119 RYPTGEERCIACKLCEA--VCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQE-ACPVD  179 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~--~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~-~CP~~  179 (226)
                      ++.++.+.|++||.|..  .||+  |...+..  .++    +..||...|.+|+.|++ +||.-
T Consensus       623 ~~~In~~vCegCg~C~~~s~C~a--i~~~~t~--~gr----K~~Id~s~Cn~~~~C~~G~CPsf  678 (1159)
T PRK13030        623 RLFINEAVCEGCGDCGVQSNCLS--VEPVETP--FGR----KRRIDQSSCNKDFSCVNGFCPSF  678 (1159)
T ss_pred             eEEEcccccCCchhhhhccCCcc--eeecccc--CCc----cEEECHHHCCCccccccCCCCCC
Confidence            35578899999999976  6884  3332211  111    34688899999999999 99964

>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]

Probab=97.59  E-value=1.7e-05  Score=63.50  Aligned_cols=56  Identities=25%  Similarity=0.570  Sum_probs=36.7

Q ss_pred             ccccccccchhccccccccchhhhhcc------CCccccccccCCCCCCcchhhhhcCccccc
Q 027264          125 ERCIACKLCEAVCPAQAITIEAEERED------GSRRTTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~ai~~~~~~~~~------~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      ..|..||.|..+||++-. .+.+.|..      +.+......-+.|.|+.|..|...||.+..
T Consensus        39 ~~C~QCG~CT~sCPs~r~-t~y~pR~ii~~~~~g~~d~il~~~~lW~C~tCytC~eRCPr~v~  100 (195)
T COG1150          39 EGCYQCGTCTGSCPSGRF-TDYSPRKIIRKARLGLVDLILSSESLWACVTCYTCTERCPRGVK  100 (195)
T ss_pred             hHhhccCcccCCCCCccc-CCCCHHHHHHHHHcccHHHHhcCCcceeeeechhhhhhCCCCCC
Confidence            569999999999999744 22222211      111011122356899999999999998854

>COG0247 GlpC Fe-S oxidoreductase [Energy production and conversion]

Probab=97.58  E-value=8.8e-06  Score=72.43  Aligned_cols=58  Identities=28%  Similarity=0.667  Sum_probs=37.9

Q ss_pred             cccccccccchhcccccccc--chhhhhccCCcc--------ccccccCCCCCCcchhhhhcCccccc
Q 027264          124 EERCIACKLCEAVCPAQAIT--IEAEEREDGSRR--------TTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~--~~~~~~~~~~~~--------~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      .++|++||.|..+||+....  .++..+....+.        ........+.|+.|++|+..||.+.-
T Consensus         8 ~~~Cv~Cg~C~~~CP~~~~~~~~sPrgr~~~~r~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP~~i~   75 (388)
T COG0247           8 LDKCVHCGFCTNVCPSYRATEALSPRGRIVLVREVLRGKAPGDEEVYEALDTCLACGACATACPSGID   75 (388)
T ss_pred             HHhcCCCCcccCcCCCccccCCCCCchHHHHHHHHHhCCCcchhhhHHHHHhCcCccchHhhCCCCCc
Confidence            47899999999999987665  222222211110        01111224789999999999999953

>PF12797 Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.57  E-value=2.6e-05  Score=40.23  Aligned_cols=18  Identities=56%  Similarity=1.318  Sum_probs=11.0

Q ss_pred             ccCCCCCCcchhhhhcCc
Q 027264          160 DIDMTKCIYCGFCQEACP  177 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP  177 (226)
                      .+|.+.|++|+.|+.+||
T Consensus         4 ~iD~~rCiGC~~C~~AC~   21 (22)
T PF12797_consen    4 VIDLERCIGCGACEVACP   21 (22)
T ss_pred             EEccccccCchhHHHhhC
Confidence            355566666666666665

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding

>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]

Probab=97.56  E-value=2.1e-05  Score=69.88  Aligned_cols=56  Identities=29%  Similarity=0.514  Sum_probs=33.0

Q ss_pred             ccccccccchhcccccccc----c-hhhhhccCC---c---cccccccCCCCCCcchhhhhcCcccc
Q 027264          125 ERCIACKLCEAVCPAQAIT----I-EAEEREDGS---R---RTTRYDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~ai~----~-~~~~~~~~~---~---~~~~~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      -.||.||.|..+||+....    . +.-.++-+.   -   ........+..|+.||.|..+||++.
T Consensus       308 L~CIRCGaC~n~CPvY~~iGgh~y~~~Y~GPiG~v~s~~~~g~~~~~~~~~~c~lcg~C~evCPv~I  374 (459)
T COG1139         308 LRCIRCGACLNHCPVYRHIGGHAYGSIYPGPIGVVWSPILGGYDAAGDLPYACSLCGACTEVCPVKI  374 (459)
T ss_pred             HHhhcchHhhhcChhhhhccCeecccccCCcccceecchhcchhhccccchhhccccCCCCcCCCCC
Confidence            4699999999999973110    0 000000000   0   00122233567999999999999993

>COG2440 FixX Ferredoxin-like protein [Energy production and conversion]

Probab=97.55  E-value=1.7e-05  Score=56.27  Aligned_cols=52  Identities=25%  Similarity=0.628  Sum_probs=42.9

Q ss_pred             ccccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcc-ccccc
Q 027264          123 GEERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVE  183 (226)
Q Consensus       123 ~~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~-~Ai~~  183 (226)
                      +.+.|..|.  .|+.+||.+.....+..         .+.++.+.|..||.|.-+||. +.+.+
T Consensus        31 ~~~~~~~~~~~~l~~aCPA~~Y~~~~~g---------~l~~~yegClECGTCRvlc~~~~~i~W   85 (99)
T COG2440          31 DPDDCQECEDKPLIKACPAGCYKLIDDG---------KLRFDYEGCLECGTCRVLCPHSGLIQW   85 (99)
T ss_pred             CchhhhhccchhhhhcCCHHHeeECCCC---------cEEEeecCeeeccceeEecCCCcceEE
Confidence            357899998  99999999988776633         467788899999999999999 66654

>PF12797 Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.51  E-value=2.7e-05  Score=40.19  Aligned_cols=19  Identities=47%  Similarity=1.102  Sum_probs=16.8

Q ss_pred             CCccccccccccchhcccc
Q 027264          121 PTGEERCIACKLCEAVCPA  139 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~  139 (226)
                      .+|.++|++|+.|+.+||.
T Consensus         4 ~iD~~rCiGC~~C~~AC~~   22 (22)
T PF12797_consen    4 VIDLERCIGCGACEVACPV   22 (22)
T ss_pred             EEccccccCchhHHHhhCc
Confidence            3678999999999999984

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding

>PF12798 Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.50  E-value=2.9e-05  Score=36.46  Aligned_cols=15  Identities=47%  Similarity=1.214  Sum_probs=13.8

Q ss_pred             ccccccchhcccccc
Q 027264          127 CIACKLCEAVCPAQA  141 (226)
Q Consensus       127 Ci~Cg~C~~~CP~~a  141 (226)
                      |+.|+.|+.+||++|
T Consensus         1 C~~C~~C~~~Cp~~A   15 (15)
T PF12798_consen    1 CTGCGACVEVCPTGA   15 (15)
T ss_pred             CCCchHHHHHhcCCC
Confidence            789999999999975

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding

>PRK15055 anaerobic sulfite reductase subunit A; Provisional

Probab=97.46  E-value=3.1e-05  Score=67.98  Aligned_cols=17  Identities=35%  Similarity=1.028  Sum_probs=15.4

Q ss_pred             CCCCCcchhhhhcCccc
Q 027264          163 MTKCIYCGFCQEACPVD  179 (226)
Q Consensus       163 ~~~C~~Cg~Cv~~CP~~  179 (226)
                      ...|++||.|..+||++
T Consensus       306 ~~~CvgCGrC~~~CP~~  322 (344)
T PRK15055        306 YHMCVGCGRCDDRCPEY  322 (344)
T ss_pred             hhhCcCcCccccccCCC
Confidence            35799999999999998

>PRK13029 2-oxoacid ferredoxin oxidoreductase; Provisional

Probab=97.40  E-value=2.9e-05  Score=77.32  Aligned_cols=52  Identities=27%  Similarity=0.449  Sum_probs=37.7

Q ss_pred             cCCCccccccccccchh--ccccccccchhhhhccCCccccccccCCCCCCcchhhhh-cCcc
Q 027264          119 RYPTGEERCIACKLCEA--VCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQE-ACPV  178 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~--~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~-~CP~  178 (226)
                      .+.++.+.|.+||.|..  .||+  |...+..  .++    +..||...|.+|+.|++ .||.
T Consensus       651 r~~In~~vCeGCgdC~~~snC~a--i~p~et~--~gr----K~~Idqs~Cn~d~sC~~G~CPs  705 (1186)
T PRK13029        651 RVFINELVCEGCGDCSVQSNCLA--VQPVETE--FGR----KRKINQSSCNKDFSCVKGFCPS  705 (1186)
T ss_pred             cEEEcccccCCchhhhhccCCce--eeecccc--CCc----cEEECHhHCCCccccccCCCCC
Confidence            34578899999999976  6885  3332211  111    24688889999999999 9998

>COG1600 Uncharacterized Fe-S protein [Energy production and conversion]

Probab=97.35  E-value=7.8e-05  Score=65.06  Aligned_cols=56  Identities=21%  Similarity=0.540  Sum_probs=34.3

Q ss_pred             cccccccccchhccccccccchhhhhcc-----CC--c--cccccccCCCCC-CcchhhhhcCccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEERED-----GS--R--RTTRYDIDMTKC-IYCGFCQEACPVD  179 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~-----~~--~--~~~~~~~d~~~C-~~Cg~Cv~~CP~~  179 (226)
                      .+.|-.|..|+.+||++|++.....-..     .+  +  ...++......+ .+|+.|+.+||.+
T Consensus       184 ~~~Cg~C~~CldaCPt~Al~~~~~~~~~~cis~lt~~~~~~p~e~r~~~~n~iygCd~C~~vCPwn  249 (337)
T COG1600         184 EDHCGSCTRCLDACPTGALVAPYTVDARRCISYLTIEKGGAPEEFRPLIGNRIYGCDICQKVCPWN  249 (337)
T ss_pred             CccChhhHHHHhhCCcccccCCCccchhHHhhhhhhhccCCcHHHHHhccCceecCchHHHhCCcc
Confidence            3889999999999999999754321100     00  0  000111111222 2899999999998

>COG1152 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]

Probab=97.33  E-value=4.4e-05  Score=69.95  Aligned_cols=56  Identities=23%  Similarity=0.604  Sum_probs=35.4

Q ss_pred             cccccccccchhccccccccchhhh-hccCCccccccccCCCCCCcchhhhhcCccccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEE-REDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~-~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      ..+|+.||-|..+||.. +.+.+.. +..... ...+..-.+.|++||.|.++||.+..
T Consensus       399 a~kc~~cG~C~~~CP~~-l~i~eam~~A~~Gd-~~~l~~l~d~C~~C~rCEq~Cpk~ip  455 (772)
T COG1152         399 ARKCTYCGNCMRACPNE-LDIPEAMEYAAKGD-FSKLEDLHDVCIGCGRCEQVCPKNIP  455 (772)
T ss_pred             HHhcccccchhccCCcc-cchHHHHHHhhcCC-hHHHHHHHHHhhhhhhhhhhCcccCc
Confidence            47899999999999974 3332221 111000 01112224679999999999999843

>PF14697 Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B

Probab=97.30  E-value=7.3e-05  Score=48.83  Aligned_cols=23  Identities=48%  Similarity=1.155  Sum_probs=16.3

Q ss_pred             Cccccccccccchhcccc-ccccc
Q 027264          122 TGEERCIACKLCEAVCPA-QAITI  144 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~-~ai~~  144 (226)
                      ++.+.|++||.|+.+||+ +||++
T Consensus        36 v~~~~C~GCg~C~~~CPv~~AI~m   59 (59)
T PF14697_consen   36 VNPDKCIGCGLCVKVCPVKDAITM   59 (59)
T ss_dssp             CE-TT--S-SCCCCCSSSTTSEEE
T ss_pred             eccccCcCcCcccccCCCccCCCC
Confidence            557899999999999997 99863

...

>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit

Probab=97.30  E-value=9.2e-05  Score=66.43  Aligned_cols=44  Identities=27%  Similarity=0.600  Sum_probs=35.7

Q ss_pred             ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          131 KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       131 g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ..|+..||++||..+...         .+.+|...|+.||.|+++||. |+..+
T Consensus       248 ~~~v~~Cp~~ai~~~~~~---------~~~id~~~C~~Cm~Ci~~~p~-a~~~g  291 (402)
T TIGR02064       248 NEVVNRCPTKAISWDGSK---------ELSIDNRECVRCMHCINKMPK-ALHPG  291 (402)
T ss_pred             hhHhhcCCccccccCCCc---------eEEEcchhcCcCccccccCcc-cccCC
Confidence            349999999999886421         467888999999999999997 66544

This model describes the alpha subunit of sulfite reductase.

>PF12800 Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.27  E-value=0.00011  Score=35.74  Aligned_cols=15  Identities=60%  Similarity=1.442  Sum_probs=8.5

Q ss_pred             ccccccccchhcccc
Q 027264          125 ERCIACKLCEAVCPA  139 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~  139 (226)
                      ++|++|+.|+.+||+
T Consensus         2 ~~C~~C~~C~~~Cp~   16 (17)
T PF12800_consen    2 ERCIGCGSCVDVCPT   16 (17)
T ss_dssp             CCCTTSSSSTTTSTT
T ss_pred             CcCCCCchHHhhccC
Confidence            345566666666654

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1BD6_A 1BQX_A 1BWE_A 1BC6_A.

>COG1143 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]

Probab=97.24  E-value=9.7e-05  Score=58.66  Aligned_cols=31  Identities=39%  Similarity=0.788  Sum_probs=26.0

Q ss_pred             cccCCCccccccccccchhccccccccchhh
Q 027264          117 LRRYPTGEERCIACKLCEAVCPAQAITIEAE  147 (226)
Q Consensus       117 ~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~  147 (226)
                      ...+.++..+||-||.|+.+||++||..+..
T Consensus        87 ~~~~~In~grCIfCg~C~e~CPt~Al~~t~~  117 (172)
T COG1143          87 PKRPDINLGRCIFCGLCVEVCPTGALVLTPE  117 (172)
T ss_pred             cccceeccccccccCchhhhCchhhhcCCcc
Confidence            3446678899999999999999999987653

>PRK13984 putative oxidoreductase; Provisional

Probab=97.23  E-value=0.0001  Score=69.67  Aligned_cols=26  Identities=23%  Similarity=0.652  Sum_probs=21.7

Q ss_pred             CCccccccccccchhccccccccchh
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .++.+.|+.|+.|+.+||++||....
T Consensus        82 ~i~~~~c~~c~~c~~~Cp~~Ai~~~~  107 (604)
T PRK13984         82 VIDYGRCSFCALCVDICTTGSLKMTR  107 (604)
T ss_pred             ccCcccCcCcchHHhhCCcCcEEecc
Confidence            45678899999999999999877643

>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional

Probab=97.14  E-value=0.00017  Score=57.87  Aligned_cols=53  Identities=23%  Similarity=0.523  Sum_probs=39.9

Q ss_pred             cccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          126 RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+...|.+...+|...+...++-++       ...++.+.|++|+.|+.+||++||.+..
T Consensus         7 ~~~~~g~~T~~yP~~~~~~~~~~rg-------~p~~d~~~C~~C~~Cv~~CP~~ai~~~~   59 (180)
T PRK12387          7 KVIKTGTATSSYPLEPIAVDKNFRG-------KPEYNPQQCIGCAACVNACPSNALTVET   59 (180)
T ss_pred             HHHhcCCccccCCCCCCCCCCCCCC-------ceEEChhhCcChhHHHHhcCccCeEeec
Confidence            3455788888999876665443222       4567888999999999999999997653

>PF12800 Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.07  E-value=0.00022  Score=34.61  Aligned_cols=16  Identities=44%  Similarity=1.294  Sum_probs=13.8

Q ss_pred             CCCCcchhhhhcCccc
Q 027264          164 TKCIYCGFCQEACPVD  179 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~  179 (226)
                      +.|++|+.|+.+||++
T Consensus         2 ~~C~~C~~C~~~Cp~~   17 (17)
T PF12800_consen    2 ERCIGCGSCVDVCPTQ   17 (17)
T ss_dssp             CCCTTSSSSTTTSTT-
T ss_pred             CcCCCCchHHhhccCC
Confidence            4799999999999974

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1BD6_A 1BQX_A 1BWE_A 1BC6_A.

>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family

Probab=97.05  E-value=0.0002  Score=60.57  Aligned_cols=50  Identities=22%  Similarity=0.434  Sum_probs=35.4

Q ss_pred             ccccccchhccccccccchhhhhccCCcccccccc-CCCCCCcchhhhhcCccccc
Q 027264          127 CIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDI-DMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       127 Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~-d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      -..++.|...||.+++.-.....     ...+... |.+.|+.|+.|+++||.+++
T Consensus       168 ~~~r~~C~~~CP~Ga~~~~~~~~-----~~~~i~~~~~~~C~~C~~C~~vCP~~~v  218 (255)
T TIGR02163       168 FSERGWCGHLCPLGAFYGLIGRK-----SLIKIAASDREKCTNCMDCFNVCPEPQV  218 (255)
T ss_pred             hcCCchhhCcCCCcchhhhhhcc-----CceEEEeeccccCeEcCCccCcCCCCce
Confidence            45789999999999885322111     1112333 37899999999999999974

Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.

>PRK09477 napH quinol dehydrogenase membrane component; Provisional

Probab=97.03  E-value=0.00018  Score=61.39  Aligned_cols=50  Identities=24%  Similarity=0.496  Sum_probs=35.9

Q ss_pred             cccccchhccccccccchhhhhccCCccccccc-cCCCCCCcchhhhhcCcccccc
Q 027264          128 IACKLCEAVCPAQAITIEAEEREDGSRRTTRYD-IDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       128 i~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~-~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      +..+-|...||.+++.-....     ....+.. +|.+.|++|+.|+++||.+++.
T Consensus       176 ~~r~wC~~lCP~Ga~~~~~~~-----~~~~~i~~~d~~~C~~C~~C~~~CP~~~i~  226 (271)
T PRK09477        176 VEHGWCGHLCPLGAFYGLIGK-----KSLIRVKAHDRQKCTRCMDCFHVCPEPQVL  226 (271)
T ss_pred             cCCchhhccCCHHHHHHhccc-----ccccccccCCcccCcccCCcCCcCCCccee
Confidence            457899999999987532211     1111334 6778999999999999998754

>PF13187 Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 2VKR_C 1KQG_B 1KQF_B 3GYX_J

Probab=97.01  E-value=0.00022  Score=45.48  Aligned_cols=20  Identities=45%  Similarity=1.104  Sum_probs=15.1

Q ss_pred             ccccccccccchhccccccc
Q 027264          123 GEERCIACKLCEAVCPAQAI  142 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai  142 (226)
                      +.++|++||.|+.+||++||
T Consensus        36 ~~~~C~~Cg~C~~~CP~~AI   55 (55)
T PF13187_consen   36 NAEKCIGCGACVKACPTGAI   55 (55)
T ss_dssp             TGGG--TTCHHHHHSTTT-E
T ss_pred             CCCccccHhHHHHHcchhhC
Confidence            45689999999999999986

>TIGR02484 CitB CitB domain protein

Probab=96.98  E-value=0.00016  Score=63.74  Aligned_cols=52  Identities=21%  Similarity=0.429  Sum_probs=34.5

Q ss_pred             cccccccccchhccccc-cccchhhhhccCCccccccccCCCCCCcchhhhhcCccccc
Q 027264          124 EERCIACKLCEAVCPAQ-AITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~-ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      .+.|..|+.|...||+- ++.  .  +....  ...+..-.+.|..||.|...||..+.
T Consensus        13 l~iC~~C~~C~~~CpvfPa~~--~--~~~~~--~~d~~~la~lChnC~~C~~~CPy~pP   65 (372)
T TIGR02484        13 LNLCNSCGYCTGLCAVFPAAQ--G--RPDLT--RGDLRHLAHLCHDCQSCWHDCQYAPP   65 (372)
T ss_pred             hHhCcCcCCccccCCCccccc--c--ccccC--HHHHHHHHHHCcCcccccccCcCCCC
Confidence            47899999999999974 111  1  11000  11122224679999999999999764

CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the C-terminal domain of the R. capsulatus CobZ, which, in most other species exists as a separate gene adjacent to CobZ.

>PF13484 Fer4_16: 4Fe-4S double cluster binding domain

Probab=96.96  E-value=0.00028  Score=46.93  Aligned_cols=21  Identities=52%  Similarity=1.026  Sum_probs=19.0

Q ss_pred             CCCcchhhhhcCcccccccCC
Q 027264          165 KCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       165 ~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .|..|+.|+++||++||..+.
T Consensus         1 ~C~~C~~C~~~CP~~AI~~~~   21 (67)
T PF13484_consen    1 FCITCGKCAEACPTGAISGED   21 (67)
T ss_pred             CCcchhHHHHhCcHhhccCCC
Confidence            389999999999999999873

>COG1141 Fer Ferredoxin [Energy production and conversion]

Probab=96.82  E-value=0.00026  Score=47.42  Aligned_cols=61  Identities=25%  Similarity=0.326  Sum_probs=32.8

Q ss_pred             CccccccccccchhccccccccchhhhhccC-CccccccccCCCCCCcchhhhhcCccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDG-SRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~-~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ++.++||+||.|..+||.- +.+.+...... ........+..+.=.....-+..||++||++
T Consensus         5 vDrd~Cigcg~C~~~aPdv-F~~~d~G~a~~~~~~~~~~~~~~e~~~~~~~A~~~CP~~aI~v   66 (68)
T COG1141           5 VDRDTCIGCGACLAVAPDV-FDYDDEGIAFVLDGNIGEGEVPEELEEDAEDAAEACPTDAIKV   66 (68)
T ss_pred             echhhccccchhhhcCCcc-eeeCCCcceEeccCccccccCChHHHHHHHHHHHhCCccceEe
Confidence            5678999999999999962 22222211100 0000011111111111246789999999975

>KOG3256 consensus NADH:ubiquinone oxidoreductase, NDUFS8/23 kDa subunit [Energy production and conversion]

Probab=96.82  E-value=0.00047  Score=53.69  Aligned_cols=32  Identities=31%  Similarity=0.757  Sum_probs=26.9

Q ss_pred             cccccCCCccccccccccchhccccccccchh
Q 027264          115 HALRRYPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       115 ~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .....+.+|..+||-||.|.++||+++|...+
T Consensus       140 rRttrYdIDmtkCIyCG~CqEaCPvdaivegp  171 (212)
T KOG3256|consen  140 RRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  171 (212)
T ss_pred             ccceeecccceeeeeecchhhhCCccceeccC
Confidence            34556778889999999999999999998654

>PF13370 Fer4_13: 4Fe-4S single cluster domain; PDB: 1FXR_A 1DAX_A 1DFD_A 1WTF_A 1IR0_A 1IQZ_A 1SIZ_A 1SJ1_A 3PNI_B 2Z8Q_A

Probab=96.79  E-value=0.00042  Score=45.06  Aligned_cols=52  Identities=23%  Similarity=0.517  Sum_probs=25.6

Q ss_pred             ccccccccccchhccccccccchhhhhccCCccccccccCC----CCCCcchhhhhcCcccccc
Q 027264          123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDM----TKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~----~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      +.++|++||.|+..+|. .+.+++..+.       .+..+.    ..=..+...+..||++||.
T Consensus         2 D~~~Ci~Cg~C~~~aP~-vF~~~d~~~~-------~~v~~~~~~~~~~~~~~~A~~~CP~~aI~   57 (58)
T PF13370_consen    2 DRDKCIGCGLCVEIAPD-VFDYDDDGGK-------AVVLDQPVPEEEEEAAREAAESCPTAAIR   57 (58)
T ss_dssp             -TTT--S-SHHHHH-TT-TEEEETTSTE-------EECTTCCCSHCHHHHHHHHHHHSTT--EE
T ss_pred             ChhhCcCCChHHHhCcH-heeEcCCCCe-------EEEeCCCcChHHHHHHHHHHHcCCHhhcC
Confidence            45799999999999996 2333332110       011110    1112367889999999985

...

>PF12838 Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=96.77  E-value=0.00034  Score=44.22  Aligned_cols=22  Identities=55%  Similarity=1.026  Sum_probs=15.4

Q ss_pred             CCCcchhhhhcCcccccccCCC
Q 027264          165 KCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       165 ~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      .|++||.|+.+||.++|.+...
T Consensus         1 ~C~~C~~C~~~CP~~~i~~~~~   22 (52)
T PF12838_consen    1 KCIGCGACVEACPTGAIRLDEE   22 (52)
T ss_dssp             C-SS--HHHHH-TTHHCEEEET
T ss_pred             CCCCcCchHHhcCccccCcccc
Confidence            4999999999999999986653

Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3CF4_A 1K0T_A 2VKR_C 1JB0_C 3PCQ_C.

>PRK08222 hydrogenase 4 subunit H; Validated

Probab=96.66  E-value=0.00074  Score=54.23  Aligned_cols=25  Identities=44%  Similarity=0.877  Sum_probs=21.8

Q ss_pred             Cccccccccccchhccccccccchh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .+..+|+.||.|+.+||++||.+..
T Consensus        70 ~~~~~C~~Cg~C~~~CPt~AI~~~~   94 (181)
T PRK08222         70 LYLGRCIYCGRCEEVCPTRAIQLTN   94 (181)
T ss_pred             eccCcCcCCCCcccccCcCeEEecc
Confidence            4457899999999999999998765

>PF13459 Fer4_15: 4Fe-4S single cluster domain

Probab=96.65  E-value=0.00042  Score=46.03  Aligned_cols=60  Identities=23%  Similarity=0.427  Sum_probs=31.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCcc--ccccccCCCCCCcchhhhhcCcccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRR--TTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~--~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      ++.++|++||.|+..||. .+.+++.........  .....+....=..-..-+..||++||.
T Consensus         3 vD~~~C~gcg~C~~~aP~-vF~~d~~g~a~~~~~~~~~~~~v~~~~~~~~~~Aa~~CP~~aI~   64 (65)
T PF13459_consen    3 VDRDRCIGCGLCVELAPE-VFELDDDGKAVVLVDGGEGEGEVPEEDEEDVREAAEACPVGAIH   64 (65)
T ss_pred             EecccCcCccHHHhhCCc-cEEECCCCCEEEEecCcccccCCCchhHHHHHHHHHhCCHhhEE
Confidence            567899999999999995 233332211100000  000011111111124568999999986

>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG

Probab=96.63  E-value=0.00076  Score=61.17  Aligned_cols=55  Identities=20%  Similarity=0.554  Sum_probs=33.0

Q ss_pred             cccccccchhccccccccc---hhh--------hhccCCc--cccc-c--ccCCCCCCcchhhhhcCcccc
Q 027264          126 RCIACKLCEAVCPAQAITI---EAE--------EREDGSR--RTTR-Y--DIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~---~~~--------~~~~~~~--~~~~-~--~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      -...+..|..+||.+++.-   +.+        .|+....  .... .  ..+.+.|++|+.|+++||.++
T Consensus       177 ~~~re~~C~~~CP~g~~qs~m~d~~tl~v~yd~~Rgepr~~~~~~~~~~~~~~~~~Ci~C~~Cv~vCP~gi  247 (434)
T TIGR02745       177 GWMREQFCIYMCPYARIQSVMFDKDTLIVVYDEKRGEPRGPRKGKKDPKAPGPLGDCIDCNLCVQVCPTGI  247 (434)
T ss_pred             HeeccchhhhhCCHHHHHHHhccCCcceEecccccCCcCccccccccccCCCCCCCCCChhhhHHhCCCCC
Confidence            3778899999999987652   111        0100000  0000 0  011468999999999999993

Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.

>PRK15033 tricarballylate utilization protein B; Provisional

Probab=96.62  E-value=0.00055  Score=60.67  Aligned_cols=50  Identities=28%  Similarity=0.603  Sum_probs=31.9

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV  178 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~  178 (226)
                      .+.|..|..|...||+- -.+.++. ...   ...+..-.+.|..||.|...||.
T Consensus        32 ~~iC~~Cr~C~~~Cpvf-P~l~~r~-~~~---~~d~~~~a~~C~~Cg~C~~~CP~   81 (389)
T PRK15033         32 MQICNACRYCEGFCAVF-PAMTRRL-EFG---KADIHYLANLCHNCGACLHACQY   81 (389)
T ss_pred             hHhCCCCCCccccCCCc-hhhhhhh-cCC---hhhhHHHHHhCcCcccccccCcC
Confidence            57899999999999974 1111110 000   00111123479999999999999

>COG1145 NapF Ferredoxin [Energy production and conversion]

Probab=96.57  E-value=0.00072  Score=48.06  Aligned_cols=24  Identities=50%  Similarity=0.999  Sum_probs=21.6

Q ss_pred             ccCCCCCCcchhhhhcCccccccc
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      .++.+.|++||.|+.+||++||..
T Consensus        25 ~~~~~~Ci~Cg~C~~~CP~~ai~~   48 (99)
T COG1145          25 VIDAEKCIGCGLCVKVCPTGAIEL   48 (99)
T ss_pred             EeCccccCCCCCchhhCCHHHhhc
Confidence            466778999999999999999987

>TIGR02936 fdxN_nitrog ferredoxin III, nif-specific

Probab=96.41  E-value=0.00089  Score=47.30  Aligned_cols=27  Identities=37%  Similarity=0.698  Sum_probs=23.3

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ...++.+.|++|+.|+.+||.++|.+.
T Consensus        15 ~~~i~~~~Ci~C~~Cv~~CP~~~i~~~   41 (91)
T TIGR02936        15 VTSIDQEKCIGCGRCYKVCGRDVLTLK   41 (91)
T ss_pred             eEEECHhHCCCcchHHHHcChhhceee
Confidence            345788899999999999999999765

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.

>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]

Probab=96.35  E-value=0.0011  Score=46.49  Aligned_cols=25  Identities=32%  Similarity=0.832  Sum_probs=22.1

Q ss_pred             Cccccccccccchhccccccccchh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      ++.+.|-+||.|+.+||+.||.+..
T Consensus        63 idYdyCKGCGICa~vCP~kaI~Mv~   87 (91)
T COG1144          63 IDYDYCKGCGICANVCPVKAIEMVR   87 (91)
T ss_pred             eEcccccCceechhhCChhheEeEe
Confidence            6788999999999999999997653

>PRK09626 oorD 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed

Probab=96.33  E-value=0.0014  Score=47.70  Aligned_cols=28  Identities=21%  Similarity=0.591  Sum_probs=23.4

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+.++.+.|++|+.|+.+||++++.+..
T Consensus        10 ~v~id~~~Ci~C~~Cv~aCP~~ai~~~~   37 (103)
T PRK09626         10 PVWVDESRCKACDICVSVCPAGVLAMRI   37 (103)
T ss_pred             CeEECcccccCCcchhhhcChhhhcccc
Confidence            4456788999999999999999987543

>COG1146 Ferredoxin [Energy production and conversion]

Probab=96.33  E-value=0.0011  Score=44.34  Aligned_cols=27  Identities=41%  Similarity=0.907  Sum_probs=22.8

Q ss_pred             CCCccccccccccchhccccccccchh
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      +..+.+.|++||.|+.+||++||.+..
T Consensus        36 ~~~~~e~C~~C~~C~~~CP~~aI~~~~   62 (68)
T COG1146          36 VVARPEECIDCGLCELACPVGAIKVDI   62 (68)
T ss_pred             eEeccccCccchhhhhhCCcceEEEec
Confidence            345678999999999999999987654

>PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional

Probab=96.23  E-value=0.002  Score=48.08  Aligned_cols=27  Identities=30%  Similarity=0.694  Sum_probs=23.3

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .+.++.+.|++||.|+.+||.+|+...
T Consensus        36 ~i~i~~~~Ci~C~~C~~~CP~~ai~~~   62 (120)
T PRK08348         36 KILYDVDKCVGCRMCVTVCPAGVFVYL   62 (120)
T ss_pred             eEEECcccCcCcccHHHHCCccceEcc
Confidence            456778899999999999999998754

>PF13237 Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A

Probab=96.22  E-value=0.0019  Score=40.64  Aligned_cols=20  Identities=50%  Similarity=1.052  Sum_probs=8.6

Q ss_pred             cccCCCCCCcchhhhhcCcc
Q 027264          159 YDIDMTKCIYCGFCQEACPV  178 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~  178 (226)
                      +.+|.+.|++||.|+.+||.
T Consensus         2 i~id~~~C~~C~~C~~~CP~   21 (52)
T PF13237_consen    2 IVIDEDKCIGCGRCVKVCPA   21 (52)
T ss_dssp             ----TT------TTGGG-TT
T ss_pred             CccCcccCcCCcChHHHccc
Confidence            35678899999999999999

>KOG0063 consensus RNAse L inhibitor, ABC superfamily [RNA processing and modification]

Probab=96.14  E-value=0.0013  Score=59.01  Aligned_cols=21  Identities=43%  Similarity=1.023  Sum_probs=14.5

Q ss_pred             CCCCCCcchhhhhcCcccccc
Q 027264          162 DMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      ....|++||.|+.-||.+||.
T Consensus        48 se~lCigcgicvkkcpf~ai~   68 (592)
T KOG0063|consen   48 SEELCIGCGICVKKCPFEAIQ   68 (592)
T ss_pred             hHhhhccccceeeccCcceEE
Confidence            335677777777777777765

>PF13746 Fer4_18: 4Fe-4S dicluster domain

Probab=96.09  E-value=0.0025  Score=42.88  Aligned_cols=18  Identities=33%  Similarity=0.977  Sum_probs=15.6

Q ss_pred             CCCCCCcchhhhhcCccc
Q 027264          162 DMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~  179 (226)
                      ....|++||.|+.+||++
T Consensus        48 ~~~~CVgCgrCv~~CP~~   65 (69)
T PF13746_consen   48 GEGDCVGCGRCVRVCPAG   65 (69)
T ss_pred             CCccCCCcChHhhhcCCC
Confidence            456799999999999998

>PLN00071 photosystem I subunit VII; Provisional

Probab=96.05  E-value=0.0026  Score=43.94  Aligned_cols=25  Identities=32%  Similarity=0.554  Sum_probs=21.2

Q ss_pred             ccCCCCCCcchhhhhcCcccccccC
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++.+.|++|+.|+.+||+++|.+.
T Consensus         5 ~~~~~~C~~C~~C~~~CP~~~i~~~   29 (81)
T PLN00071          5 VKIYDTCIGCTQCVRACPTDVLEMI   29 (81)
T ss_pred             eEcCCcCcChhHHHHHCCccceeee
Confidence            3456789999999999999998764

>PRK09623 vorD 2-ketoisovalerate ferredoxin oxidoreductase subunit delta; Reviewed

Probab=96.00  E-value=0.004  Score=45.46  Aligned_cols=27  Identities=33%  Similarity=0.611  Sum_probs=22.9

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ...++.+.|++|+.|+.+||.+|+.+.
T Consensus        45 ~p~i~~~~Ci~C~~C~~~CP~~ai~~~   71 (105)
T PRK09623         45 MPVVDESKCVKCYICWKFCPEPAIYIK   71 (105)
T ss_pred             eEEECcccCccccchhhhCCHhheEec
Confidence            456778899999999999999998654

>PRK06273 ferredoxin; Provisional

Probab=95.99  E-value=0.0029  Score=49.99  Aligned_cols=28  Identities=36%  Similarity=0.641  Sum_probs=23.7

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...++...|++||.|+.+||.+||.+..
T Consensus        43 ~~~id~~~CigCg~C~~aCP~~AI~~~~   70 (165)
T PRK06273         43 PKKVFEELCIGCGGCANVCPTKAIEMIP   70 (165)
T ss_pred             CCeECchhCcChhHHHHhcCccceeeec
Confidence            3456778999999999999999997653

>TIGR02179 PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family

Probab=95.92  E-value=0.0038  Score=42.73  Aligned_cols=27  Identities=41%  Similarity=0.699  Sum_probs=23.0

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ...++.+.|++|+.|+.+||.+++.+.
T Consensus        19 ~~~i~~~~C~~C~~C~~~Cp~~ai~~~   45 (78)
T TIGR02179        19 KPVVDKEKCIKCKNCWLYCPEGAIQED   45 (78)
T ss_pred             EEEEcCCcCcChhHHHhhcCccceEec
Confidence            346777899999999999999998764

A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of delta subunits, representing mostly pyruvate, 2-ketoisovalerate, and 2-oxoglutarate specific enzymes. The delta subunit is the smallest and resembles ferredoxins.

>CHL00065 psaC photosystem I subunit VII

Probab=95.91  E-value=0.0034  Score=43.42  Aligned_cols=26  Identities=35%  Similarity=0.630  Sum_probs=21.5

Q ss_pred             ccCCCCCCcchhhhhcCcccccccCC
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .++.+.|++|+.|+.+||++++.+.+
T Consensus         5 ~~~~~~Ci~Cg~C~~~CP~~~i~~~~   30 (81)
T CHL00065          5 VKIYDTCIGCTQCVRACPTDVLEMIP   30 (81)
T ss_pred             cCccccCCChhHHHHHCCccchhhee
Confidence            34567899999999999999987644

>COG1035 FrhB Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]

Probab=95.88  E-value=0.0033  Score=54.89  Aligned_cols=46  Identities=35%  Similarity=0.588  Sum_probs=33.6

Q ss_pred             ccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcc
Q 027264          123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV  178 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~  178 (226)
                      +...|++||.|+.+||. +|...+...         ..+..-.|.+|+.|..+||.
T Consensus         3 ~~~~c~~Cg~C~a~cp~-~i~~~~~~~---------~~~~~c~~~~~~~~~~~cp~   48 (332)
T COG1035           3 DAGLCTGCGTCAAVCPY-AITERDEAP---------LLIEECMDNGHGTCLKVCPE   48 (332)
T ss_pred             cCcccccchhhHhhCCc-eEEEecccc---------hhhhhhhcccchHHhhhCcc
Confidence            45689999999999999 777654321         12333456678899999993

>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]

Probab=95.86  E-value=0.0024  Score=55.01  Aligned_cols=27  Identities=33%  Similarity=0.642  Sum_probs=24.0

Q ss_pred             cccCCCCCCcchhhhhcCcccccccCC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ..++.+.|.+||.|+++||++||....
T Consensus       167 P~~~~E~c~gc~~cv~~C~~gAI~~~~  193 (317)
T COG2221         167 PKVDEELCRGCGKCVKVCPTGAITWDG  193 (317)
T ss_pred             CccCHHHhchhHhHHHhCCCCceeecc
Confidence            567888999999999999999998765

>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family

Probab=95.78  E-value=0.0044  Score=53.27  Aligned_cols=25  Identities=28%  Similarity=0.733  Sum_probs=22.4

Q ss_pred             ccccCCCCCCcchhhhhcCcccccc
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      .+.++.+.|++||.|+.+||++|+.
T Consensus        42 ~~~~~~~~C~~C~~C~~~Cp~~a~~   66 (295)
T TIGR02494        42 ELLFKENRCLGCGKCVEVCPAGTAR   66 (295)
T ss_pred             eEEEccccCCCCchhhhhCcccccc
Confidence            4567888999999999999999986

This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0

>COG1453 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]

Probab=95.75  E-value=0.0025  Score=55.94  Aligned_cols=17  Identities=47%  Similarity=1.189  Sum_probs=15.5

Q ss_pred             CCCCCcchhhhhcCccc
Q 027264          163 MTKCIYCGFCQEACPVD  179 (226)
Q Consensus       163 ~~~C~~Cg~Cv~~CP~~  179 (226)
                      ...|+.||.|...||.+
T Consensus       350 as~CieCgqCl~~CPq~  366 (391)
T COG1453         350 ASDCIECGQCLEKCPQH  366 (391)
T ss_pred             ccccchhhhhhhcCCCc
Confidence            46799999999999998

>PRK08493 NADH dehydrogenase subunit G; Validated

Probab=95.72  E-value=0.0052  Score=59.95  Aligned_cols=23  Identities=35%  Similarity=0.716  Sum_probs=20.3

Q ss_pred             cccccccccchhccccccccchh
Q 027264          124 EERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      ...|+.||.|+.+||++||....
T Consensus       203 ~~~C~~CG~Cv~VCPvGAL~~k~  225 (819)
T PRK08493        203 TLDCSFCGECIAVCPVGALSSSD  225 (819)
T ss_pred             cccccccCcHHHhCCCCccccCc
Confidence            46899999999999999998754

>COG0348 NapH Polyferredoxin [Energy production and conversion]

Probab=95.65  E-value=0.0053  Score=55.05  Aligned_cols=93  Identities=23%  Similarity=0.393  Sum_probs=51.2

Q ss_pred             CcceecCccccCCCCCCccCccccccCCCcccccc-ccccchhccccccc---cchhhhhccCCccccccccCCC-CCCc
Q 027264           94 KKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCI-ACKLCEAVCPAQAI---TIEAEEREDGSRRTTRYDIDMT-KCIY  168 (226)
Q Consensus        94 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci-~Cg~C~~~CP~~ai---~~~~~~~~~~~~~~~~~~~d~~-~C~~  168 (226)
                      ++.+..|-++.+....... ..++..+..+..+|. +|..|.+.||....   .+.+.          ...+..+ .|+.
T Consensus       181 rr~~C~ylCP~g~~~~v~~-~~~~~~v~~~~~~~~~r~~~c~k~cp~~~~~~v~v~p~----------~~~~~~~~~CI~  249 (386)
T COG0348         181 RRFWCRYLCPYGAFQGVLF-DKSLLKVNYDDKRGCPRCKRCKKVCPEPIPLWVQVCPA----------GIDIRDGLECIG  249 (386)
T ss_pred             ccceeEEeCCHHHHHHHHc-ccceEEEecccccCCcccccccccCCccccceeEeccc----------cccccccccccc
Confidence            4666766554332211111 112222334444454 79999999997653   11111          1111112 5999


Q ss_pred             chhhhhcCcccccccCCCcccchhcHHHh
Q 027264          169 CGFCQEACPVDAIVEGPNFEYSTETHEEL  197 (226)
Q Consensus       169 Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~  197 (226)
                      |+.|+++||.....+.-.+....++....
T Consensus       250 C~~CidaCd~~~~~~~~~~~~i~~~~~~a  278 (386)
T COG0348         250 CGRCIDACDDDMLKFNLPFGLIAYSTFMA  278 (386)
T ss_pred             HhhHhhhCCHHhheecccccHHHHHHHHh
Confidence            99999999999887665545554444333

>TIGR00403 ndhI NADH-plastoquinone oxidoreductase subunit I protein

Probab=95.62  E-value=0.0048  Score=49.63  Aligned_cols=27  Identities=26%  Similarity=0.712  Sum_probs=23.1

Q ss_pred             CCCccccccccccchhccccccccchh
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      +.++.++|+.||.|+.+||++||.+..
T Consensus        97 ~~id~~~Ci~Cg~Cv~aCP~~AI~~~~  123 (183)
T TIGR00403        97 YSIDFGVCIFCGNCVEYCPTNCLSMTE  123 (183)
T ss_pred             eecCcccccCcCchhhhcCCCCeeccc
Confidence            345678999999999999999998764

>TIGR03048 PS_I_psaC photosystem I iron-sulfur protein PsaC

Probab=95.58  E-value=0.0055  Score=42.26  Aligned_cols=24  Identities=38%  Similarity=0.768  Sum_probs=20.4

Q ss_pred             CCCCCCcchhhhhcCcccccccCC
Q 027264          162 DMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ....|++|+.|+.+||++++.+..
T Consensus         6 ~~~~Ci~C~~Cv~~CP~~~i~~~~   29 (80)
T TIGR03048         6 IYDTCIGCTQCVRACPTDVLEMVP   29 (80)
T ss_pred             cCCcCcCcchHHHHCCccceeeec
Confidence            456899999999999999987643

Members of this family are PsaC, an essential component of photosystem I (PS-I) reaction center in Cyanobacteria and chloroplasts. This small protein, about 80 amino acids in length, contains two copies of the ferredoxin-like 4Fe-4S binding site (pfam00037) and therefore eight conserved Cys residues. This protein is also called photosystem I subunit VII.

>COG1140 NarY Nitrate reductase beta subunit [Energy production and conversion]

Probab=95.34  E-value=0.0069  Score=53.31  Aligned_cols=49  Identities=33%  Similarity=0.625  Sum_probs=30.7

Q ss_pred             ccccc--ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          126 RCIAC--KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       126 ~Ci~C--g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      -|..|  -.|+.+||++|+...+..+        -+.+|.+.|.+-..|+..||++-+.
T Consensus       182 iCeHCLNPsCvasCPsgaiYKReEDG--------IVLiDQd~CRGwR~CvsgCPYKKvY  232 (513)
T COG1140         182 LCEHCLNPSCVASCPSGAIYKREEDG--------IVLIDQDKCRGWRMCVSGCPYKKVY  232 (513)
T ss_pred             HHhhcCCcHHhhcCCcccccccccCc--------eEEeecccccchhhhhcCCCcceeE
Confidence            36666  3677777777775543322        2345666777777777777776664

>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]

Probab=95.27  E-value=0.0066  Score=50.23  Aligned_cols=48  Identities=31%  Similarity=0.778  Sum_probs=38.1

Q ss_pred             Cccc-cccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccc
Q 027264          122 TGEE-RCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       122 ~~~~-~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      +++. -|++|+.|...||+.+|.... -           ..+...|+.||.|...||.+..
T Consensus       186 l~qg~~C~G~~TC~A~CP~~ai~c~G-c-----------~g~~~~~~~~Ga~~v~~~rs~~  234 (247)
T COG1941         186 LEQGLPCMGCGTCAASCPSRAIPCRG-C-----------RGNIPRCIKCGACFVSCPRSKG  234 (247)
T ss_pred             ecCCCcccCchhhhccCCccCCcccC-C-----------cCCcccchhhhHHHHHHhHHhh
Confidence            3444 799999999999999998763 1           2345689999999999998743

>PF13746 Fer4_18: 4Fe-4S dicluster domain

Probab=95.25  E-value=0.0068  Score=40.78  Aligned_cols=18  Identities=50%  Similarity=1.208  Sum_probs=16.0

Q ss_pred             ccccccccccchhccccc
Q 027264          123 GEERCIACKLCEAVCPAQ  140 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~  140 (226)
                      ....|++||.|+.+||++
T Consensus        48 ~~~~CVgCgrCv~~CP~~   65 (69)
T PF13746_consen   48 GEGDCVGCGRCVRVCPAG   65 (69)
T ss_pred             CCccCCCcChHhhhcCCC
Confidence            456799999999999986

>PRK06991 ferredoxin; Provisional

Probab=95.23  E-value=0.0081  Score=51.22  Aligned_cols=26  Identities=54%  Similarity=0.957  Sum_probs=22.5

Q ss_pred             cccCCCCCCcchhhhhcCcccccccC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ..++.+.|++||.|+.+||+++|...
T Consensus        80 ~~id~~~CigCg~Cv~aCP~~AI~~~  105 (270)
T PRK06991         80 AVIDEQLCIGCTLCMQACPVDAIVGA  105 (270)
T ss_pred             eEEccccCCCCcHHHHhCCHhheecc
Confidence            35677899999999999999999754

>PRK05888 NADH dehydrogenase subunit I; Provisional

Probab=95.21  E-value=0.011  Score=46.49  Aligned_cols=22  Identities=41%  Similarity=0.998  Sum_probs=19.4

Q ss_pred             CCCCcchhhhhcCcccccccCC
Q 027264          164 TKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.|++|+.|+.+||.+||.+..
T Consensus        58 ~~Ci~C~~C~~~CP~~ai~~~~   79 (164)
T PRK05888         58 ERCIACKLCAAICPADAITIEA   79 (164)
T ss_pred             ccCCcccChHHHcCcccccccc
Confidence            4899999999999999987654

>CHL00014 ndhI NADH dehydrogenase subunit I

Probab=95.17  E-value=0.0086  Score=47.41  Aligned_cols=27  Identities=26%  Similarity=0.712  Sum_probs=22.7

Q ss_pred             CCCccccccccccchhccccccccchh
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      +.++.+.|+.||.|+.+||.+||.+..
T Consensus        94 ~~id~~~C~~Cg~C~~~CP~~AI~~~~  120 (167)
T CHL00014         94 YSIDFGVCIFCGNCVEYCPTNCLSMTE  120 (167)
T ss_pred             ccCCCCcCcCccchHhhcCcCceecCC
Confidence            345667899999999999999998754

>TIGR01971 NuoI NADH-quinone oxidoreductase, chain I

Probab=94.98  E-value=0.0099  Score=44.28  Aligned_cols=26  Identities=46%  Similarity=0.976  Sum_probs=22.1

Q ss_pred             Cccccccccccchhccccccccchhh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAE  147 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~  147 (226)
                      ++.++|+.||.|+.+||.+++.+...
T Consensus        79 ~~~~~C~~Cg~Cv~~CP~~al~~~~~  104 (122)
T TIGR01971        79 INFGRCIFCGLCEEACPTDAIVLTPE  104 (122)
T ss_pred             ECcccCCCCCchhhhCCCccccccce
Confidence            45678999999999999999987543

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.

>PRK09625 porD pyruvate flavodoxin oxidoreductase subunit delta; Reviewed

Probab=94.97  E-value=0.0083  Score=45.71  Aligned_cols=28  Identities=29%  Similarity=0.440  Sum_probs=23.0

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...++.+.|++|+.|+.+||.+||....
T Consensus        53 ~p~~d~~~Ci~C~~C~~~CP~~ai~~~~   80 (133)
T PRK09625         53 KPVHNNEICINCFNCWVYCPDAAILSRD   80 (133)
T ss_pred             eEEEehhHCcChhhHHHhCCHhheEecC
Confidence            3456778999999999999999986443

>TIGR02060 aprB adenosine phosphosulphate reductase, beta subunit

Probab=94.93  E-value=0.011  Score=45.07  Aligned_cols=26  Identities=31%  Similarity=0.459  Sum_probs=22.5

Q ss_pred             ccCCCCCCcch-----hhhhcCcccccccCC
Q 027264          160 DIDMTKCIYCG-----FCQEACPVDAIVEGP  185 (226)
Q Consensus       160 ~~d~~~C~~Cg-----~Cv~~CP~~Ai~~~~  185 (226)
                      .++...|++|+     .|+.+||.++|.++.
T Consensus         4 ~v~~~~C~gC~~~~~~~Cv~~CP~~ai~~~~   34 (132)
T TIGR02060         4 FVYPTKCDGCKAGEKTACVYICPNDLMHLDT   34 (132)
T ss_pred             EEccccccCccCCchhcCHhhcCccceEecC
Confidence            46778899999     999999999997654

During dissimilatory sulfate reduction and sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the beta subunit of APS reductase, sharing common evolutionary origin with other iron-sulfur cluster-binding proteins.

>PRK09624 porD pyuvate ferredoxin oxidoreductase subunit delta; Reviewed

Probab=94.90  E-value=0.0094  Score=43.52  Aligned_cols=24  Identities=29%  Similarity=0.786  Sum_probs=20.8

Q ss_pred             Cccccccccccchhccccccccch
Q 027264          122 TGEERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      ++.++|++|+.|+.+||.+||.+.
T Consensus        78 id~~~C~~Cg~Cv~~CP~~AI~~~  101 (105)
T PRK09624         78 FDYDYCKGCGICANECPTKAIEMV  101 (105)
T ss_pred             ECchhCCCcCchhhhcCcCcEEEe
Confidence            456799999999999999998764

>PRK13409 putative ATPase RIL; Provisional

Probab=94.83  E-value=0.0091  Score=56.49  Aligned_cols=25  Identities=44%  Similarity=0.898  Sum_probs=21.8

Q ss_pred             CCccccccccccchhccccccccch
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      .+.++.|++||.|++.||..||.+.
T Consensus        45 ~~~e~~c~~c~~c~~~cp~~a~~i~   69 (590)
T PRK13409         45 VISEELCIGCGICVKKCPFDAISIV   69 (590)
T ss_pred             eeeHhhccccccccccCCcceEEEe
Confidence            3567899999999999999998864

>PRK02651 photosystem I subunit VII; Provisional

Probab=94.82  E-value=0.012  Score=40.45  Aligned_cols=24  Identities=38%  Similarity=1.009  Sum_probs=20.6

Q ss_pred             ccccccccccchhccccccccchh
Q 027264          123 GEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      +..+|+.||.|+.+||.++|.+..
T Consensus        44 ~~~~C~~Cg~C~~~CP~~ai~~~~   67 (81)
T PRK02651         44 RTEDCVGCKRCETACPTDFLSIRV   67 (81)
T ss_pred             CCCcCCChhhhhhhcCCCceEEEE
Confidence            456899999999999999998643

>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit

Probab=94.67  E-value=0.014  Score=46.03  Aligned_cols=27  Identities=52%  Similarity=0.871  Sum_probs=22.9

Q ss_pred             cccCCCCCCcchhhhhcCcccccccCC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ..++.+.|++|+.|+++||++|+....
T Consensus       108 ~~id~~~Ci~Cg~C~~aCp~~ai~~~~  134 (165)
T TIGR01944       108 ALIDEDNCIGCTKCIQACPVDAIVGAA  134 (165)
T ss_pred             EEEECCcCCChhHHHHhCCccceEecC
Confidence            456778999999999999999987643

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.

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=94.65  E-value=0.01  Score=53.91  Aligned_cols=25  Identities=44%  Similarity=0.898  Sum_probs=21.6

Q ss_pred             CCccccccccccchhccccccccch
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      .+....|++||.|++.||.+||.+.
T Consensus        46 vIsE~lCiGCGICvkkCPF~AI~Iv   70 (591)
T COG1245          46 VISEELCIGCGICVKKCPFDAISIV   70 (591)
T ss_pred             eeEhhhhccchhhhccCCcceEEEe
Confidence            3557789999999999999999864

>KOG0063 consensus RNAse L inhibitor, ABC superfamily [RNA processing and modification]

Probab=94.63  E-value=0.0087  Score=53.93  Aligned_cols=55  Identities=25%  Similarity=0.337  Sum_probs=40.9

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +....|++||.|++.||..||.+..-..         -.....+|..|+.|...||..+...++
T Consensus        47 ise~lCigcgicvkkcpf~ai~iinlp~---------nl~~etthry~~n~fKlhrlp~prpg~  101 (592)
T KOG0063|consen   47 ISEELCIGCGICVKKCPFEAIQIINLPT---------NLEKETTHRYSANSFKLHRLPIPRPGQ  101 (592)
T ss_pred             hhHhhhccccceeeccCcceEEecCCch---------hHhhhhhhhhcccceeeccCCCCCcch
Confidence            4456899999999999999987643211         112235799999999999988776443

>PRK09326 F420H2 dehydrogenase subunit F; Provisional

Probab=94.39  E-value=0.017  Score=50.98  Aligned_cols=27  Identities=33%  Similarity=0.824  Sum_probs=23.3

Q ss_pred             ccCCCCCCcchhhhhcCcccccccCCC
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      .++.+.|++||.|+.+||+++|.+.+.
T Consensus         8 vi~~~~C~gCg~C~~~CP~~aI~~~~~   34 (341)
T PRK09326          8 VIEYDVCTACGACEAVCPIGAITVDKK   34 (341)
T ss_pred             EECcccCcChHHHHHhCCHhhhecccC
Confidence            466789999999999999999987654

>PRK05113 electron transport complex protein RnfB; Provisional

Probab=94.34  E-value=0.018  Score=46.62  Aligned_cols=27  Identities=52%  Similarity=0.862  Sum_probs=22.8

Q ss_pred             cccCCCCCCcchhhhhcCcccccccCC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ..++.+.|++||.|+++||+++|....
T Consensus       109 ~~id~~~Ci~Cg~Cv~aCp~~ai~~~~  135 (191)
T PRK05113        109 AFIDEDNCIGCTKCIQACPVDAIVGAT  135 (191)
T ss_pred             eEEeCCcCCCCChhhhhCCHhhheccc
Confidence            456788999999999999999987543

>PRK08764 ferredoxin; Provisional

Probab=94.11  E-value=0.02  Score=43.73  Aligned_cols=23  Identities=30%  Similarity=0.843  Sum_probs=20.0

Q ss_pred             Cccccccccccchhccccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITI  144 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~  144 (226)
                      ++.++|+.||.|+.+||+++|.+
T Consensus       112 v~~~~C~~Cg~Cv~~CP~~Ai~~  134 (135)
T PRK08764        112 VIAPLCTGCELCVPACPVDCIEL  134 (135)
T ss_pred             ecCCcCcCccchhhhcCccceEe
Confidence            45678999999999999999864

>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

Probab=94.09  E-value=0.015  Score=49.30  Aligned_cols=25  Identities=52%  Similarity=0.942  Sum_probs=22.2

Q ss_pred             ccccCCCCCCcchhhhhcCcccccc
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      .+.++.+.|+.||.|..+|+.+||.
T Consensus        63 ~p~i~~e~C~~CG~C~~vC~f~Ai~   87 (284)
T COG1149          63 IPEIDPEKCIRCGKCAEVCRFGAIV   87 (284)
T ss_pred             ccccChhhccccCcHHHhCCCCeEE
Confidence            4567788899999999999999996

>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only

Probab=94.09  E-value=0.018  Score=51.48  Aligned_cols=23  Identities=52%  Similarity=0.888  Sum_probs=20.5

Q ss_pred             ccCCCCCCcchhhhhcCcccccc
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      .+|...|++||.|+.+||++|+.
T Consensus         3 ~id~~kCi~Cg~Cv~~CP~~ai~   25 (374)
T TIGR02512         3 VRDMSKCIGCGRCVRACTNVQIV   25 (374)
T ss_pred             EechhhCCcChHhhhhCCHhhcc
Confidence            45678899999999999999986

This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than Pfam model pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some heterogeneity in terms of periplasmic, cytosolic, or hydrogenosome location, NAD or NADP dependence, and overal protein protein length.

>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit

Probab=93.84  E-value=0.021  Score=50.42  Aligned_cols=24  Identities=38%  Similarity=0.809  Sum_probs=21.5

Q ss_pred             CCCccccccccccchhcccccccc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAIT  143 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~  143 (226)
                      +.++.++|++||.|+.+||..++.
T Consensus       209 ~~id~~~Ci~Cg~Ci~~CP~~a~~  232 (341)
T TIGR02066       209 LEVDVEKCIYCGNCYTMCPAMPIF  232 (341)
T ss_pred             eeeccccCCcCCchHHhCchhhcc
Confidence            457789999999999999999886

This model describes the beta subunit of sulfite reductase.

>PRK12814 putative NADPH-dependent glutamate synthase small subunit; Provisional

Probab=93.68  E-value=0.022  Score=54.46  Aligned_cols=19  Identities=21%  Similarity=0.642  Sum_probs=13.5

Q ss_pred             CCCccccccccccchhccc
Q 027264          120 YPTGEERCIACKLCEAVCP  138 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP  138 (226)
                      +..|.++||.||.|+++|.
T Consensus       611 i~~D~~kCI~CgrCv~~C~  629 (652)
T PRK12814        611 IRFEREKCVDCGICVRTLE  629 (652)
T ss_pred             eEeccccccCchHHHHHHH
Confidence            4456777777777777776

>TIGR02700 flavo_MJ0208 archaeoflavoprotein, MJ0208 family

Probab=93.64  E-value=0.025  Score=47.17  Aligned_cols=27  Identities=44%  Similarity=0.855  Sum_probs=22.9

Q ss_pred             cccCCCCCCcchhhhhcCcccccccCC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.+.|++|+.|+.+||.+++...+
T Consensus       143 ~~id~~~C~~C~~C~~~CP~~ai~~~~  169 (234)
T TIGR02700       143 YMIDRKRCKGCGICVDACPRSAIDMVD  169 (234)
T ss_pred             eEEChhHCcCcchHHHhCCcccEEecC
Confidence            456778899999999999999997643

This model describes one of two paralogous families of archaealflavoprotein. The other, described by TIGR02699 and typified by the partially characterized AF1518 of Archaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown.

>TIGR00402 napF ferredoxin-type protein NapF

Probab=93.63  E-value=0.026  Score=40.81  Aligned_cols=23  Identities=26%  Similarity=0.658  Sum_probs=20.1

Q ss_pred             Cccccccccccchhccccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITI  144 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~  144 (226)
                      ++.+.|+.||.|+.+||+++|..
T Consensus        63 i~~~~C~~Cg~C~~~CP~~Ai~~   85 (101)
T TIGR00402        63 FDNAECDFCGKCAEACPTNAFHP   85 (101)
T ss_pred             ecCccCcCccChhhHCCccccCc
Confidence            45678999999999999999865

The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation.

>PRK15449 ferredoxin-like protein FixX; Provisional

Probab=93.45  E-value=0.027  Score=40.32  Aligned_cols=22  Identities=18%  Similarity=0.474  Sum_probs=19.0

Q ss_pred             CCccccccccccchhccccccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAI  142 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai  142 (226)
                      .++.++|++||.|+.+||..++
T Consensus        57 ~vd~e~CigCg~C~~~C~~~~~   78 (95)
T PRK15449         57 RFDYAGCLECGTCRILGLGSAL   78 (95)
T ss_pred             EEcCCCCCcchhhhhhcCCCCc
Confidence            3678999999999999998764

>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma

Probab=93.39  E-value=0.028  Score=46.74  Aligned_cols=27  Identities=33%  Similarity=0.685  Sum_probs=23.3

Q ss_pred             cccCCCCCCcchhhhhcCcccccccCC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ..++...|++|+.|+.+||.+|+....
T Consensus       169 ~~id~~~C~~C~~C~~aCP~~ai~~~~  195 (228)
T TIGR03294       169 KVVNQGLCMGCGTCAAACPTRAIEMED  195 (228)
T ss_pred             EEEChhhCcChhHHHHhCCHhhEEEeC
Confidence            457778999999999999999997654

This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (pfam00037) and scores above the trusted cutoff to model pfam01058 for the "NADH ubiquinone oxidoreductase, 20 Kd subunit" family.

>TIGR03224 benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA protein

Probab=93.33  E-value=0.038  Score=50.01  Aligned_cols=28  Identities=43%  Similarity=0.872  Sum_probs=23.9

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +..++.+.|++|+.|+.+||+++|...+
T Consensus         4 ~~~id~~~Ci~C~~C~~~CP~~ai~~~~   31 (411)
T TIGR03224         4 QHLIDPEICIRCNTCEETCPIDAITHDD   31 (411)
T ss_pred             eeeeCcccCcCccchhhhCCcccEeccC
Confidence            4567888999999999999999997644

Members of this protein family are BoxA, the A component of the BoxAB benzoyl-CoA oxygenase/reductase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. BoxA is a homodimeric iron-sulphur-flavoprotein and acts as an NADPH-dependent reductase for BoxB.

>COG1141 Fer Ferredoxin [Energy production and conversion]

Probab=93.31  E-value=0.027  Score=37.68  Aligned_cols=22  Identities=32%  Similarity=0.585  Sum_probs=18.3

Q ss_pred             cccCCCCCCcchhhhhcCcccc
Q 027264          159 YDIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ..+|.++|++||.|..+||.--
T Consensus         3 v~vDrd~Cigcg~C~~~aPdvF   24 (68)
T COG1141           3 VIVDRDTCIGCGACLAVAPDVF   24 (68)
T ss_pred             EEechhhccccchhhhcCCcce
Confidence            3567789999999999999653

>TIGR02486 RDH reductive dehalogenase

Probab=93.25  E-value=0.036  Score=48.31  Aligned_cols=22  Identities=41%  Similarity=0.943  Sum_probs=19.5

Q ss_pred             CCCCcchhhhhcCcccccccCC
Q 027264          164 TKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .-|..|+.|+++||++||....
T Consensus       205 ~fC~~C~~C~~~CP~~Ai~~~~  226 (314)
T TIGR02486       205 KFCETCGKCADECPSGAISKGG  226 (314)
T ss_pred             ccCcchhHHHhhCCccccCCCC
Confidence            4699999999999999998654

This model represents a family of corrin and 8-iron Fe-S cluster-containing reductive dehalogenases found primarily in halorespiring microorganisms such as dehalococcoides ethenogenes which contains as many as 17 enzymes of this type with varying substrate ranges. One example of a characterized species is the tetrachloroethene reductive dehalogenase (1.97.1.8) which also acts on trichloroethene converting it to dichloroethene.

>PLN02805 D-lactate dehydrogenase [cytochrome]

Probab=93.05  E-value=0.27  Score=46.23  Aligned_cols=73  Identities=18%  Similarity=0.046  Sum_probs=41.9

Q ss_pred             hhHhhhhccCCcccCcccccCCCCC-CCCCchhHHHHHHHHHHHhhhHHHHHHHHHH---------H----hhhHHHHHH
Q 027264           18 LAVSGQALQGSQHYGLRFNAHPYSS-YFPSKKDDEEKEQLLKEISKDWSSVFERSIN---------M----LFLTEMVRG   83 (226)
Q Consensus        18 ~~i~Gha~~gn~~~~~~~~~H~~~~-~~~~~~p~~~~~~~~~~~~~~v~~~~~~~i~---------~----~~~~~~~~~   83 (226)
                      .+++||+.+||        .|++.. ........++..+..+++.+.+ .++.+++.         .    ..+.+....
T Consensus       458 ~~~~gHaGdGn--------lH~~i~~~~~~~~~~~~~~~~~~~i~~~~-~~~gGsiSgEHGiG~~k~~~l~~~~g~~~~~  528 (555)
T PLN02805        458 CTVIAHAGDGN--------FHTIILFDPSQEDQRREAERLNHFMVHTA-LSMEGTCTGEHGVGTGKMKYLEKELGIEALQ  528 (555)
T ss_pred             EEEEEEcCCCc--------EEEEeccCCCCHHHHHHHHHHHHHHHHHH-HHcCCeEeEECCCChhHHHHHHHhcCHHHHH
Confidence            67889999999        999432 1111122223333333333332 12222111         1    122345788


Q ss_pred             HHHHHHHhcCCcceec
Q 027264           84 LGLTLKYFFDKKVTIN   99 (226)
Q Consensus        84 l~~~~~~~f~~~~~~~   99 (226)
                      ++..+|..|||...+|
T Consensus       529 lm~~IK~a~DP~gILN  544 (555)
T PLN02805        529 TMKRIKKALDPNNIMN  544 (555)
T ss_pred             HHHHHHHHhCcCcCCC
Confidence            8999999999999998

>COG2878 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]

Probab=92.99  E-value=0.032  Score=44.37  Aligned_cols=29  Identities=48%  Similarity=0.802  Sum_probs=24.4

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ...++...|++|..|+++||++||.-...
T Consensus       109 va~i~e~~ciGCtkCiqaCpvdAivg~~~  137 (198)
T COG2878         109 VALIDEANCIGCTKCIQACPVDAIVGATK  137 (198)
T ss_pred             eeEecchhccccHHHHHhCChhhhhccch
Confidence            34577789999999999999999986554

>TIGR02912 sulfite_red_C sulfite reductase, subunit C

Probab=92.99  E-value=0.035  Score=48.39  Aligned_cols=26  Identities=31%  Similarity=0.658  Sum_probs=22.1

Q ss_pred             CCccccccccccchhccccccccchh
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .++.++|+.||.|+.+||++|+....
T Consensus       197 ~id~~~C~~Cg~Cv~~CP~~Al~~~~  222 (314)
T TIGR02912       197 VRDHSKCIGCGECVLKCPTGAWTRSE  222 (314)
T ss_pred             EeCCCcCcCcchhhhhCCHhhcccCc
Confidence            35678999999999999999987543

Members of this protein family include the C subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite.

>PRK14028 pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional

Probab=92.91  E-value=0.038  Score=48.04  Aligned_cols=24  Identities=33%  Similarity=0.802  Sum_probs=20.5

Q ss_pred             Cccccccccccchhccccccccch
Q 027264          122 TGEERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      .+.+.|++|+.|+.+||++||.+.
T Consensus       286 ~d~~~C~gCg~C~~~CP~~AI~~~  309 (312)
T PRK14028        286 FDYQYCKGCGVCAEVCPTGAIQMV  309 (312)
T ss_pred             CCcccCcCcCchhhhCCHhheEec
Confidence            345789999999999999998764

>PF13459 Fer4_15: 4Fe-4S single cluster domain

Probab=92.73  E-value=0.044  Score=36.17  Aligned_cols=19  Identities=42%  Similarity=0.943  Sum_probs=16.3

Q ss_pred             ccCCCCCCcchhhhhcCcc
Q 027264          160 DIDMTKCIYCGFCQEACPV  178 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~  178 (226)
                      .+|.+.|++||.|+..||.
T Consensus         2 ~vD~~~C~gcg~C~~~aP~   20 (65)
T PF13459_consen    2 WVDRDRCIGCGLCVELAPE   20 (65)
T ss_pred             EEecccCcCccHHHhhCCc
Confidence            3566889999999999994

>TIGR00276 iron-sulfur cluster binding protein, putative

Probab=92.70  E-value=0.053  Score=46.58  Aligned_cols=21  Identities=43%  Similarity=0.873  Sum_probs=18.6

Q ss_pred             CCCCCcchhhhhcCccccccc
Q 027264          163 MTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       163 ~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ...|..|+.|+++||++||..
T Consensus       158 ~~~C~~C~~C~~aCPt~AI~~  178 (282)
T TIGR00276       158 EEYCGRCTKCIDACPTQALVE  178 (282)
T ss_pred             CCCCccHHHHHHhcCcccccC
Confidence            357999999999999999973

This series of proteins contain the prosite signature for 4Fe-4S ferredoxins iron-sulfur binding proteins (C-x(2)-C-x(2)-C-x(3)-C-[PEG]) between residues 175-188 of the model.

>PF02913 FAD-oxidase_C: FAD linked oxidases, C-terminal domain; InterPro: IPR004113 Some oxygen-dependent oxidoreductases are flavoproteins that contain a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage

Probab=92.60  E-value=0.16  Score=41.66  Aligned_cols=73  Identities=22%  Similarity=0.131  Sum_probs=43.5

Q ss_pred             hhHhhhhccCCcccCcccccCCCCC-CCCCchhHHHHHHHHHHHhhhHHHHHHHHHH-------------HhhhHHHHHH
Q 027264           18 LAVSGQALQGSQHYGLRFNAHPYSS-YFPSKKDDEEKEQLLKEISKDWSSVFERSIN-------------MLFLTEMVRG   83 (226)
Q Consensus        18 ~~i~Gha~~gn~~~~~~~~~H~~~~-~~~~~~p~~~~~~~~~~~~~~v~~~~~~~i~-------------~~~~~~~~~~   83 (226)
                      ..++||+.+||        .|.+.. ........+...+.++++.+.+. ++.+++.             .....+....
T Consensus       158 ~~~~gH~~~g~--------~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~gG~is~eHG~G~~k~~~~~~~~~~~~~~  228 (248)
T PF02913_consen  158 VCHFGHAGDGN--------LHLYILFDPRDPEEPERAEALWDELYELVL-ELGGSISAEHGIGKLKKPYLEEEYGPAALR  228 (248)
T ss_dssp             EEEEEEEEECE--------EEEEEEEETTSHHHHHHHHHHHHHHHHHHH-HTT-BBSSSSGGGHHHHHHHCHHCHHHHHH
T ss_pred             ccceEEccCCe--------EEEEeecccchHHHHHHHHHHHHHHHHHHH-hcccccccccchhhhhHHHHHHhcchHHHH
Confidence            78999999999        999433 23333444444555555544332 2222111             1223345788


Q ss_pred             HHHHHHHhcCCcceec
Q 027264           84 LGLTLKYFFDKKVTIN   99 (226)
Q Consensus        84 l~~~~~~~f~~~~~~~   99 (226)
                      ++..+|..|||..++|
T Consensus       229 ~~~~iK~~~DP~~ilN  244 (248)
T PF02913_consen  229 LMRAIKQAFDPNGILN  244 (248)
T ss_dssp             HHHHHHHHH-TTS-BS
T ss_pred             HHHHhhhccCCccCCC
Confidence            9999999999999988

The region around the histidine that binds the FAD group is conserved in these enzymes (see IPR006093 from INTERPRO).; GO: 0003824 catalytic activity, 0050660 flavin adenine dinucleotide binding; PDB: 1WVE_B 1DII_B 1WVF_A 1DIQ_A 2UUU_B 2UUV_A 1W1M_A 1E8H_B 1E0Y_B 1DZN_B ....

>TIGR00387 glcD glycolate oxidase, subunit GlcD

Probab=92.47  E-value=0.46  Score=42.97  Aligned_cols=72  Identities=21%  Similarity=0.092  Sum_probs=41.1

Q ss_pred             hhHhhhhccCCcccCcccccCCCCCCCCCchh--HHHHHHHHHHHhhhHHHHHHH-------------HHHHhhhHHHHH
Q 027264           18 LAVSGQALQGSQHYGLRFNAHPYSSYFPSKKD--DEEKEQLLKEISKDWSSVFER-------------SINMLFLTEMVR   82 (226)
Q Consensus        18 ~~i~Gha~~gn~~~~~~~~~H~~~~~~~~~~p--~~~~~~~~~~~~~~v~~~~~~-------------~i~~~~~~~~~~   82 (226)
                      .+++||+.+||        +|.+.. +....+  .++..+..+++.+.+.+ +.+             ......+.+...
T Consensus       324 ~~~~gH~g~g~--------lh~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~-~gG~is~eHG~G~~r~~~~~~~~~~~~~  393 (413)
T TIGR00387       324 IANFGHAGDGN--------LHPTIL-TDPEDKGEMERVEEAGGEIFELAIE-LGGTISGEHGIGVVKAEFMPYKFNEKEL  393 (413)
T ss_pred             EEEEEEecCCc--------cccccC-CCCCCHHHHHHHHHHHHHHHHHHHH-cCCEEEEeccCcHhHHHHHHHhcCHHHH
Confidence            56899999999        998433 222222  22333444444433221 111             111122234577


Q ss_pred             HHHHHHHHhcCCcceec
Q 027264           83 GLGLTLKYFFDKKVTIN   99 (226)
Q Consensus        83 ~l~~~~~~~f~~~~~~~   99 (226)
                      .++..+|..|||...+|
T Consensus       394 ~~~~~iK~~fDP~~ilN  410 (413)
T TIGR00387       394 ETMRAIKKAFDPDNILN  410 (413)
T ss_pred             HHHHHHHHHcCcCcCCC
Confidence            88999999999988887

This protein, the glycolate oxidase GlcD subunit, is similar in sequence to that of several D-lactate dehydrogenases, including that of E. coli. The glycolate oxidase has been found to have some D-lactate dehydrogenase activity.

>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]

Probab=92.44  E-value=0.044  Score=52.44  Aligned_cols=23  Identities=35%  Similarity=0.923  Sum_probs=19.8

Q ss_pred             Cccccccccccchhccccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITI  144 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~  144 (226)
                      ++.+.|+.||.|+.+||++|+.-
T Consensus       189 i~~SSCVsCG~CvtVCP~nALme  211 (978)
T COG3383         189 INESSCVSCGACVTVCPVNALME  211 (978)
T ss_pred             cccccccccCccceecchhhhhh
Confidence            45678999999999999998754

>PF13370 Fer4_13: 4Fe-4S single cluster domain; PDB: 1FXR_A 1DAX_A 1DFD_A 1WTF_A 1IR0_A 1IQZ_A 1SIZ_A 1SJ1_A 3PNI_B 2Z8Q_A

Probab=92.19  E-value=0.055  Score=34.98  Aligned_cols=18  Identities=50%  Similarity=0.979  Sum_probs=11.3

Q ss_pred             CCCCCCcchhhhhcCccc
Q 027264          162 DMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~  179 (226)
                      |.+.|++||.|...+|.-
T Consensus         2 D~~~Ci~Cg~C~~~aP~v   19 (58)
T PF13370_consen    2 DRDKCIGCGLCVEIAPDV   19 (58)
T ss_dssp             -TTT--S-SHHHHH-TTT
T ss_pred             ChhhCcCCChHHHhCcHh
Confidence            457899999999999965

...

>COG1140 NarY Nitrate reductase beta subunit [Energy production and conversion]

Probab=92.12  E-value=0.28  Score=43.53  Aligned_cols=48  Identities=27%  Similarity=0.749  Sum_probs=35.8

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc---------hhhhhcCccccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC---------GFCQEACPVDAI  181 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C---------g~Cv~~CP~~Ai  181 (226)
                      .+|+++|-+...|++.||..-+.+....            -..++|++|         -.|...| +|-|
T Consensus       210 LiDQd~CRGwR~CvsgCPYKKvYfNwks------------gKsEKCifCyPRiEaGqPtVCSeTC-VGri  266 (513)
T COG1140         210 LIDQDKCRGWRMCVSGCPYKKVYFNWKS------------GKSEKCIFCYPRIEAGQPTVCSETC-VGRI  266 (513)
T ss_pred             EeecccccchhhhhcCCCcceeEeeccC------------CCcceeEEeccccccCCCccchhhh-hcce
Confidence            3789999999999999999877664321            234689999         3588888 4444

>PRK08318 dihydropyrimidine dehydrogenase subunit B; Validated

Probab=92.01  E-value=0.05  Score=49.28  Aligned_cols=26  Identities=42%  Similarity=0.943  Sum_probs=22.6

Q ss_pred             Cccccccccccchhcccc-ccccchhh
Q 027264          122 TGEERCIACKLCEAVCPA-QAITIEAE  147 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~-~ai~~~~~  147 (226)
                      ++.++|++||.|+.+||. +||.+...
T Consensus       374 i~~~~C~~Cg~C~~~CP~~~Ai~~~~~  400 (420)
T PRK08318        374 VIEEECVGCNLCAHVCPVEGCITMGEV  400 (420)
T ss_pred             echhhCcccchHHhhCCCCCCEEEecc
Confidence            567899999999999999 99987654

>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated

Probab=91.91  E-value=0.06  Score=44.91  Aligned_cols=23  Identities=35%  Similarity=0.806  Sum_probs=20.0

Q ss_pred             cccccccccchhccccccccchh
Q 027264          124 EERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      ...|+.||.|+.+||++||....
T Consensus       189 ~~~C~~Cg~Cv~vCP~gAL~~~~  211 (234)
T PRK07569        189 SETCTSCGKCVQACPTGAIFRKG  211 (234)
T ss_pred             cccccchHHHHHhCCCCcEEecC
Confidence            45899999999999999997654

>COG2768 Uncharacterized Fe-S center protein [General function prediction only]

Probab=91.74  E-value=0.071  Score=45.86  Aligned_cols=26  Identities=38%  Similarity=0.755  Sum_probs=22.1

Q ss_pred             cccCCCCCCcchhhhhcCcccccccC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ..+....|..||.|+..||++||...
T Consensus       188 p~v~e~kc~~c~~cv~~cp~~Ai~~~  213 (354)
T COG2768         188 PVVVEEKCYDCGLCVKICPVGAITLT  213 (354)
T ss_pred             ceeeeecccccchhhhhCCCcceecc
Confidence            34566889999999999999999855

>TIGR03287 methan_mark_16 putative methanogenesis marker 16 metalloprotein

Probab=91.42  E-value=0.058  Score=48.23  Aligned_cols=26  Identities=27%  Similarity=0.823  Sum_probs=22.3

Q ss_pred             Cccccccccccchhccccccccchhh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAE  147 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~  147 (226)
                      ++.++|+.|+.|+.+||.+|+.+...
T Consensus       327 Id~~~Ci~CGaCV~aCP~~AI~~~~~  352 (391)
T TIGR03287       327 LNTEDCFGCGYCAEICPGGAFEVNLG  352 (391)
T ss_pred             eChHhCcChHHHHhhCCccceEEeCC
Confidence            56788999999999999999987543

Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (pfam00037), with each copy having four Cys residues invariant across all members.

>TIGR01973 NuoG NADH-quinone oxidoreductase, chain G

Probab=91.34  E-value=0.092  Score=49.81  Aligned_cols=21  Identities=19%  Similarity=0.268  Sum_probs=18.1

Q ss_pred             cccccccchhccccccccchh
Q 027264          126 RCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .|..||.|+.+||++||....
T Consensus       183 ~~~~cg~cv~vCP~GAl~~k~  203 (603)
T TIGR01973       183 ESELSGNLIDICPVGALTSKP  203 (603)
T ss_pred             CCcccCChHhhCCcccccccc
Confidence            578999999999999997543

This model represents the G 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 while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes related subunits from formate dehydrogenase complexes.

>PF13183 Fer4_8: 4Fe-4S dicluster domain; PDB: 2BS4_B 1E7P_B 2BS3_B 1QLB_B 2BS2_B 3P4Q_N 1KFY_N 3CIR_N 3P4R_B 2B76_N

Probab=91.19  E-value=0.064  Score=34.06  Aligned_cols=16  Identities=38%  Similarity=1.030  Sum_probs=8.2

Q ss_pred             ccccccccchhccccc
Q 027264          125 ERCIACKLCEAVCPAQ  140 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~  140 (226)
                      ..|+.||.|+.+||++
T Consensus        41 ~~C~~C~~C~~~CP~~   56 (57)
T PF13183_consen   41 WSCTTCGACSEVCPVG   56 (57)
T ss_dssp             GG-----HHHHH-TT-
T ss_pred             cCCcCcCCccCcCccc
Confidence            6799999999999986

...

>COG4231 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]

Probab=91.17  E-value=0.074  Score=49.90  Aligned_cols=28  Identities=29%  Similarity=0.598  Sum_probs=22.7

Q ss_pred             cCCCccccccccccchhccccccccchh
Q 027264          119 RYPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      +..+|+..|++||.|+++||+.++....
T Consensus       602 k~~id~~~C~GCg~C~~iCP~~a~~~~~  629 (640)
T COG4231         602 KARIDPSSCNGCGSCVEVCPSFAIKEGG  629 (640)
T ss_pred             ceeecccccccchhhhhcCchhheeccc
Confidence            3446777899999999999999887543

>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

Probab=90.96  E-value=0.064  Score=46.23  Aligned_cols=72  Identities=15%  Similarity=0.063  Sum_probs=50.0

Q ss_pred             cccc--ccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcC-cccccc---cCCCcccchhcHHHhh
Q 027264          125 ERCI--ACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEAC-PVDAIV---EGPNFEYSTETHEELL  198 (226)
Q Consensus       125 ~~Ci--~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~C-P~~Ai~---~~~~~~~~~~~~~~~~  198 (226)
                      +.+.  .|..|++.||.+.+.+++....     ......++..|+.|..|+..| -.+++.   .++.|.+..++.|++.
T Consensus       195 ~~~~~~~~~~~~~~cP~~Vf~i~~~~~~-----~~~~V~~~~~ct~crec~~~~~~~~~V~v~~~~d~fiF~VES~G~l~  269 (291)
T cd07032         195 KPITGEDAEKLQKCFPPGVIDIEEVKGK-----KKAVVANPRKDTLSREVLRHEEFKDKVELGRVRDHFIFSIESTGALP  269 (291)
T ss_pred             CcCCHHHHHHHHhhCCCccEEecccCCC-----ceEEEcccccCcccHhHhhhhccCCceeEEEeCCEEEEEEeCCCCCC
Confidence            3453  6778999999998877542110     012345778999999999876 234553   5677999999999885


Q ss_pred             cCH
Q 027264          199 YDK  201 (226)
Q Consensus       199 ~d~  201 (226)
                      .+.
T Consensus       270 p~~  272 (291)
T cd07032         270 PDV  272 (291)
T ss_pred             HHH
Confidence            433

The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun

>TIGR02176 pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric

Probab=90.85  E-value=0.091  Score=53.54  Aligned_cols=25  Identities=32%  Similarity=0.521  Sum_probs=21.8

Q ss_pred             cccCCCCCCcchhhhhcCccccccc
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ..++.+.|+.||.|+.+||++||..
T Consensus       678 p~~~~~~Ci~Cg~C~~vCP~~ai~~  702 (1165)
T TIGR02176       678 PVWVPDNCIQCNQCAFVCPHAAIRP  702 (1165)
T ss_pred             ceeccccCCCccchHHhcChhhccc
Confidence            4567789999999999999999974

This model represents a single chain form of pyruvate:ferredoxin (or flavodoxin) oxidoreductase. This enzyme may transfer electrons to nitrogenase in nitrogen-fixing species. Portions of this protein are homologous to gamma subunit of the four subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.

>PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional

Probab=90.68  E-value=0.085  Score=49.58  Aligned_cols=25  Identities=32%  Similarity=0.911  Sum_probs=21.8

Q ss_pred             Cccccccccccchhccccccccchh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      ++.++|+.||.|+.+||++||.+..
T Consensus       538 i~~~~C~~Cg~C~~~CP~~Ai~~~~  562 (564)
T PRK12771        538 FDYDKCTGCHICADVCPCGAIEMGP  562 (564)
T ss_pred             EecccCcChhHHHhhcCcCceEecc
Confidence            5678999999999999999997643

>PF13534 Fer4_17: 4Fe-4S dicluster domain; PDB: 1ZOY_B 3AE9_B 3AED_B 3AEA_B 3AE1_B 3SFD_B 3ABV_B 3AEF_B 3AEB_B 3AE3_B

Probab=90.62  E-value=0.09  Score=33.92  Aligned_cols=17  Identities=53%  Similarity=1.290  Sum_probs=9.8

Q ss_pred             cccccccccchhccccc
Q 027264          124 EERCIACKLCEAVCPAQ  140 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~  140 (226)
                      .+.|+.||.|..+||.+
T Consensus        43 ~~~C~~Cg~C~~~CP~~   59 (61)
T PF13534_consen   43 ASLCIGCGLCESVCPQG   59 (61)
T ss_dssp             TTT--S--HHHHH-TT-
T ss_pred             cccCcCcCcCcccccCC
Confidence            46899999999999986

...

>PRK13795 hypothetical protein; Provisional

Probab=90.47  E-value=0.11  Score=49.64  Aligned_cols=26  Identities=35%  Similarity=0.698  Sum_probs=22.3

Q ss_pred             ccCCCCCCcchhhhhcCcccccccCC
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .++...|++|+.|+.+||++||...+
T Consensus       577 v~~~~~C~~Cg~C~~~CP~~ai~~~~  602 (636)
T PRK13795        577 LRRAAECVGCGVCVGACPTGAIRIEE  602 (636)
T ss_pred             EEccccCCCHhHHHHhCCcccEEeec
Confidence            45677899999999999999997654

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=90.27  E-value=0.14  Score=43.54  Aligned_cols=24  Identities=29%  Similarity=0.578  Sum_probs=21.0

Q ss_pred             CCCCCcchhhhhcCcccccccCCC
Q 027264          163 MTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       163 ~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      .+.|.+|+.|+.+||.+++.+++.
T Consensus       168 ~~~C~~C~~C~~~CP~~vi~~~~~  191 (263)
T PRK00783        168 SEDCDECEKCVEACPRGVLELKEG  191 (263)
T ss_pred             cccCCchHHHHHhCCccccEecCC
Confidence            578999999999999999987653

>COG1600 Uncharacterized Fe-S protein [Energy production and conversion]

Probab=89.59  E-value=0.14  Score=45.02  Aligned_cols=21  Identities=38%  Similarity=0.858  Sum_probs=18.8

Q ss_pred             CCCCcchhhhhcCcccccccC
Q 027264          164 TKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      +.|-.|..|+++||++||.-.
T Consensus       185 ~~Cg~C~~CldaCPt~Al~~~  205 (337)
T COG1600         185 DHCGSCTRCLDACPTGALVAP  205 (337)
T ss_pred             ccChhhHHHHhhCCcccccCC
Confidence            689999999999999999743

>PRK07860 NADH dehydrogenase subunit G; Validated

Probab=89.41  E-value=0.17  Score=49.67  Aligned_cols=21  Identities=24%  Similarity=0.301  Sum_probs=17.9

Q ss_pred             cccccccchhccccccccchh
Q 027264          126 RCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .|..||.|+.+||++||....
T Consensus       191 ~~~~cG~cv~vCP~GAl~~k~  211 (797)
T PRK07860        191 QSYFSGNTVQICPVGALTGAA  211 (797)
T ss_pred             CccccCCchhhCCcccccccc
Confidence            478899999999999997543

>PRK09129 NADH dehydrogenase subunit G; Validated

Probab=88.49  E-value=0.25  Score=48.37  Aligned_cols=21  Identities=19%  Similarity=0.246  Sum_probs=17.8

Q ss_pred             cccccccchhccccccccchh
Q 027264          126 RCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .|.-||.|+.+||++||....
T Consensus       185 ~~~~cg~cv~~CP~GAl~~k~  205 (776)
T PRK09129        185 DSELSGNMIDLCPVGALTSKP  205 (776)
T ss_pred             cCcccCCchhhCCcccccccc
Confidence            467799999999999997553

>PRK09130 NADH dehydrogenase subunit G; Validated

Probab=88.26  E-value=0.25  Score=47.68  Aligned_cols=21  Identities=19%  Similarity=0.262  Sum_probs=17.9

Q ss_pred             cccccccchhccccccccchh
Q 027264          126 RCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .|..||.|+.+||++||...+
T Consensus       186 ~~~~~G~cv~~CPvgAl~~k~  206 (687)
T PRK09130        186 TSELSGNVIDLCPVGALTSKP  206 (687)
T ss_pred             cccccccHHhhCCCccccccc
Confidence            477899999999999998544

>PRK08166 NADH dehydrogenase subunit G; Validated

Probab=87.97  E-value=0.19  Score=49.61  Aligned_cols=21  Identities=19%  Similarity=0.189  Sum_probs=18.2

Q ss_pred             cccccccchhccccccccchh
Q 027264          126 RCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .|..||.|+.+||++||.-..
T Consensus       190 ~~~~~G~cv~vCP~GAl~~k~  210 (847)
T PRK08166        190 ESEFSGNLVEVCPTGVFTDKT  210 (847)
T ss_pred             cChhhCChHhhCCchhccccc
Confidence            578899999999999997654

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=87.65  E-value=0.24  Score=41.93  Aligned_cols=23  Identities=30%  Similarity=0.681  Sum_probs=20.2

Q ss_pred             CCCCcchhhhhcCcccccccCCC
Q 027264          164 TKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      +.|.+|+.|+.+||.+++..++.
T Consensus       169 ~~C~~C~~C~~~CP~~vi~~d~~  191 (259)
T cd07030         169 EDCDGCGKCVEECPRGVLELEEG  191 (259)
T ss_pred             hhCCChHHHHHhCCccceEccCC
Confidence            67999999999999999986553

The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w

>PRK05035 electron transport complex protein RnfC; Provisional

Probab=86.85  E-value=0.25  Score=47.71  Aligned_cols=21  Identities=38%  Similarity=0.985  Sum_probs=18.2

Q ss_pred             CCCCCCcchhhhhcCcccccc
Q 027264          162 DMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      ....|+.||.|+.+||.+.+.
T Consensus       368 ~e~~CI~CG~Cv~aCP~~llP  388 (695)
T PRK05035        368 PEQPCIRCGACADACPASLLP  388 (695)
T ss_pred             chhhcCCcccHHHHCCccchh
Confidence            346799999999999999874

>COG1035 FrhB Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]

Probab=86.46  E-value=0.33  Score=42.62  Aligned_cols=25  Identities=44%  Similarity=0.882  Sum_probs=20.3

Q ss_pred             cCCCCCCcchhhhhcCcccccccCCC
Q 027264          161 IDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ++.+.|+.||.|+.+||. +|.....
T Consensus         2 ~~~~~c~~Cg~C~a~cp~-~i~~~~~   26 (332)
T COG1035           2 IDAGLCTGCGTCAAVCPY-AITERDE   26 (332)
T ss_pred             CcCcccccchhhHhhCCc-eEEEecc
Confidence            345789999999999999 8875544

>PRK07570 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated

Probab=86.45  E-value=0.28  Score=41.40  Aligned_cols=21  Identities=43%  Similarity=0.986  Sum_probs=17.9

Q ss_pred             cCCCCCCcchhhhhcCccccc
Q 027264          161 IDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      .+...|+.||.|+.+||+...
T Consensus       154 ~~~~~CI~CG~C~saCP~~~~  174 (250)
T PRK07570        154 FDAAACIGCGACVAACPNGSA  174 (250)
T ss_pred             hCccccCCCcccccccCCccc
Confidence            456789999999999999863

>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C

Probab=86.45  E-value=0.26  Score=37.83  Aligned_cols=16  Identities=38%  Similarity=1.138  Sum_probs=14.5

Q ss_pred             CCCCcchhhhhcCccc
Q 027264          164 TKCIYCGFCQEACPVD  179 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~  179 (226)
                      ..|+.||.|..+||+.
T Consensus         2 ~~Ci~CG~C~~~CP~~   17 (144)
T TIGR03290         2 KACYQCGTCTGSCPSG   17 (144)
T ss_pred             ccccCCCCCcCcCCCc
Confidence            4699999999999985

The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.

>TIGR03315 Se_ygfK putative selenate reductase, YgfK subunit

Probab=85.99  E-value=0.3  Score=49.02  Aligned_cols=21  Identities=24%  Similarity=0.705  Sum_probs=18.6

Q ss_pred             cccccccchhccccccccchh
Q 027264          126 RCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .|++||.|+.+||++++.+..
T Consensus       922 ~C~~CG~C~~vCP~~a~~~~g  942 (1012)
T TIGR03315       922 MCNECGNCATFCPYDGAPYKD  942 (1012)
T ss_pred             cccccchHHHhCCCCccccee
Confidence            399999999999999887754

Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase.

>PRK11230 glycolate oxidase subunit GlcD; Provisional

Probab=85.68  E-value=1  Score=41.94  Aligned_cols=72  Identities=24%  Similarity=0.146  Sum_probs=41.4

Q ss_pred             hhHhhhhccCCcccCcccccCCCCCCCCCchhH--HHHHHHHHHHhhhHHHHHHHHH---------HHh----hhHHHHH
Q 027264           18 LAVSGQALQGSQHYGLRFNAHPYSSYFPSKKDD--EEKEQLLKEISKDWSSVFERSI---------NML----FLTEMVR   82 (226)
Q Consensus        18 ~~i~Gha~~gn~~~~~~~~~H~~~~~~~~~~p~--~~~~~~~~~~~~~v~~~~~~~i---------~~~----~~~~~~~   82 (226)
                      ..++||+++||        .|.+.. +....+.  ++..++.+++.+.+. ++.+++         +..    .+.+...
T Consensus       381 ~~~~gH~GdGn--------~H~~i~-~~~~~~~~~~~~~~~~~~l~~~~~-~~GG~is~EHGiG~~k~~~l~~~~g~~~~  450 (499)
T PRK11230        381 VANVFHAGDGN--------MHPLIL-FDANEPGELERAEALGGKILELCV-EVGGSITGEHGVGREKINQMCAQFNSDEI  450 (499)
T ss_pred             EEEEEEeCCCc--------ceeeec-CCCCCHHHHHHHHHHHHHHHHHHH-HcCCeEeeeccCchhhHHHHHHhcCHHHH
Confidence            78899999999        999532 2222221  233333334433322 222211         111    1123568


Q ss_pred             HHHHHHHHhcCCcceec
Q 027264           83 GLGLTLKYFFDKKVTIN   99 (226)
Q Consensus        83 ~l~~~~~~~f~~~~~~~   99 (226)
                      .++..+|..|||...+|
T Consensus       451 ~~m~~IK~~fDP~~iLN  467 (499)
T PRK11230        451 TLFHAVKAAFDPDGLLN  467 (499)
T ss_pred             HHHHHHHHHcCCCcCCC
Confidence            88999999999999998

>TIGR02910 sulfite_red_A sulfite reductase, subunit A

Probab=85.14  E-value=0.35  Score=42.51  Aligned_cols=18  Identities=33%  Similarity=1.115  Sum_probs=16.0

Q ss_pred             ccccccccccchhccccc
Q 027264          123 GEERCIACKLCEAVCPAQ  140 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~  140 (226)
                      ....|++||.|..+||++
T Consensus       299 G~~~CvgCGrC~~~CP~~  316 (334)
T TIGR02910       299 GYHMCVGCGRCDDICPEY  316 (334)
T ss_pred             CccccCCcCchhhhCCCC
Confidence            456799999999999986

Members of this protein family include the A subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite.

>PRK12814 putative NADPH-dependent glutamate synthase small subunit; Provisional

Probab=85.11  E-value=0.48  Score=45.46  Aligned_cols=20  Identities=25%  Similarity=0.728  Sum_probs=16.0

Q ss_pred             ccccCCCCCCcchhhhhcCc
Q 027264          158 RYDIDMTKCIYCGFCQEACP  177 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP  177 (226)
                      .+..|.++|+.||.|+.+|.
T Consensus       610 ~i~~D~~kCI~CgrCv~~C~  629 (652)
T PRK12814        610 DIRFEREKCVDCGICVRTLE  629 (652)
T ss_pred             CeEeccccccCchHHHHHHH
Confidence            35578899999999996664

>TIGR03336 IOR_alpha indolepyruvate ferredoxin oxidoreductase, alpha subunit

Probab=84.66  E-value=0.33  Score=46.08  Aligned_cols=20  Identities=35%  Similarity=0.981  Sum_probs=17.0

Q ss_pred             Cccccccccccchhccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAI  142 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai  142 (226)
                      ++. .|+.||.|+.+||.+||
T Consensus       576 i~~-~C~~Cg~C~~~CP~~Ai  595 (595)
T TIGR03336       576 IDP-LCTGCGVCAQICPFDAI  595 (595)
T ss_pred             eCC-CCcCHHHHHhhCccccC
Confidence            344 79999999999999875

Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase.

>PRK09853 putative selenate reductase subunit YgfK; Provisional

Probab=83.14  E-value=0.45  Score=47.74  Aligned_cols=22  Identities=23%  Similarity=0.662  Sum_probs=18.7

Q ss_pred             cccccccccchhccccccccch
Q 027264          124 EERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      .+.|++||.|+.+||+.+-++.
T Consensus       925 ~~~C~~CG~C~~~CP~~~~py~  946 (1019)
T PRK09853        925 DAMCNECGNCAQFCPWNGKPYK  946 (1019)
T ss_pred             CccCccccchhhhCCCCCCccc
Confidence            5899999999999999765543

>PRK15055 anaerobic sulfite reductase subunit A; Provisional

Probab=82.69  E-value=0.5  Score=41.74  Aligned_cols=17  Identities=29%  Similarity=0.952  Sum_probs=15.3

Q ss_pred             cccccccccchhccccc
Q 027264          124 EERCIACKLCEAVCPAQ  140 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~  140 (226)
                      ...|++||.|..+||++
T Consensus       306 ~~~CvgCGrC~~~CP~~  322 (344)
T PRK15055        306 YHMCVGCGRCDDRCPEY  322 (344)
T ss_pred             hhhCcCcCccccccCCC
Confidence            45799999999999986

>PRK12576 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=82.27  E-value=0.5  Score=40.57  Aligned_cols=20  Identities=55%  Similarity=1.373  Sum_probs=17.1

Q ss_pred             CCCCCCcchhhhhcCccccc
Q 027264          162 DMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      +...|+.||.|+.+||..+.
T Consensus       150 ~~~~CI~CG~C~~~CP~~~~  169 (279)
T PRK12576        150 KFAQCIWCGLCVSACPVVAI  169 (279)
T ss_pred             cchhCcccCcccccCCCccc
Confidence            44689999999999998755

>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit

Probab=82.20  E-value=0.59  Score=42.66  Aligned_cols=20  Identities=35%  Similarity=1.026  Sum_probs=17.2

Q ss_pred             CCCCCCcchhhhhcCccccc
Q 027264          162 DMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      ....|+.||.|+.+||.+.+
T Consensus       361 ~~~~Ci~Cg~C~~vCP~~l~  380 (435)
T TIGR01945       361 PEKPCIRCGKCVQVCPMNLL  380 (435)
T ss_pred             cCCcCcCccchhhhCccchh
Confidence            44689999999999999855

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 C subunit.

>TIGR00384 dhsB succinate dehydrogenase and fumarate reductase iron-sulfur protein

Probab=81.96  E-value=0.46  Score=39.17  Aligned_cols=20  Identities=35%  Similarity=0.954  Sum_probs=17.0

Q ss_pred             CCCCCCcchhhhhcCccccc
Q 027264          162 DMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      ....|+.||.|+.+||+...
T Consensus       136 ~~~~Ci~CG~C~~~CP~~~~  155 (220)
T TIGR00384       136 QLSGCILCGCCYSSCPAFWW  155 (220)
T ss_pred             hhhhccccccccccCCCCcc
Confidence            45789999999999998744

Succinate dehydrogenase and fumarate reductase are reverse directions of the same enzymatic interconversion, succinate + FAD+ = fumarate + FADH2 (EC 1.3.11.1). In E. coli, the forward and reverse reactions are catalyzed by distinct complexes: fumarate reductase operates under anaerobic conditions and succinate dehydrogenase operates under aerobic conditions. This model also describes a region of the B subunit of a cytosolic archaeal fumarate reductase.

>PRK08640 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed

Probab=81.90  E-value=0.5  Score=39.85  Aligned_cols=20  Identities=45%  Similarity=1.107  Sum_probs=16.8

Q ss_pred             CCCCCCcchhhhhcCccccc
Q 027264          162 DMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      ....|+.||.|..+||+...
T Consensus       150 ~~~~CI~CG~C~saCP~~~~  169 (249)
T PRK08640        150 ELSKCMTCGCCLEACPNVNE  169 (249)
T ss_pred             hhhhccCcCcccccCCCCcc
Confidence            45679999999999997753

>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit

Probab=81.33  E-value=0.54  Score=42.47  Aligned_cols=26  Identities=19%  Similarity=0.498  Sum_probs=21.2

Q ss_pred             cCCCccccccccccchhccccccccch
Q 027264          119 RYPTGEERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       119 ~~~~~~~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      .+.++.++|+.|+.|+++||. |+...
T Consensus       266 ~~~id~~~C~~Cm~Ci~~~p~-a~~~g  291 (402)
T TIGR02064       266 ELSIDNRECVRCMHCINKMPK-ALHPG  291 (402)
T ss_pred             eEEEcchhcCcCccccccCcc-cccCC
Confidence            345778899999999999997 66654

This model describes the alpha subunit of sulfite reductase.

>KOG3049 consensus Succinate dehydrogenase, Fe-S protein subunit [Energy production and conversion]

Probab=80.93  E-value=0.29  Score=40.06  Aligned_cols=55  Identities=22%  Similarity=0.562  Sum_probs=32.9

Q ss_pred             ccccccccchhccccccccchh---------------hhhccCCccccccc---cCCCCCCcchhhhhcCccc
Q 027264          125 ERCIACKLCEAVCPAQAITIEA---------------EEREDGSRRTTRYD---IDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~ai~~~~---------------~~~~~~~~~~~~~~---~d~~~C~~Cg~Cv~~CP~~  179 (226)
                      -.||.|..|...||+.....+.               +.|...........   .....|-.=.+|.+.||.|
T Consensus       192 YECILCACCsTSCPSYWWN~ekYLGPAvLmqAyRWiiDSRD~~t~eRl~~l~d~~slyrCHtImNCtrtCPKg  264 (288)
T KOG3049|consen  192 YECILCACCSTSCPSYWWNSEKYLGPAVLMQAYRWIIDSRDEATKERLAKLQDPFSLYRCHTIMNCTRTCPKG  264 (288)
T ss_pred             HHHHHHHHhcCCCcccccCcccccCHHHHHHHHhhhhcchhHHHHHHHHHhcCchhheehhhhhhhhhcCCCC
Confidence            3599999999999985443221               11110000111111   2235688889999999998

>TIGR00273 iron-sulfur cluster-binding protein

Probab=80.56  E-value=0.53  Score=42.96  Aligned_cols=19  Identities=47%  Similarity=1.162  Sum_probs=16.1

Q ss_pred             CCCCCCcchhhhhcCcccc
Q 027264          162 DMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      +...|+.||.|..+||+-.
T Consensus       291 e~~~CIrCG~C~~~CPvy~  309 (432)
T TIGR00273       291 EVLACIRCGACQNECPVYR  309 (432)
T ss_pred             hHhhCCCCCCccccCcchh
Confidence            4568999999999999754

Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters.

>COG1453 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]

Probab=80.20  E-value=0.88  Score=40.37  Aligned_cols=18  Identities=33%  Similarity=0.929  Sum_probs=15.8

Q ss_pred             ccccccccccchhccccc
Q 027264          123 GEERCIACKLCEAVCPAQ  140 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~  140 (226)
                      ....|++||.|.+.||..
T Consensus       349 ~as~CieCgqCl~~CPq~  366 (391)
T COG1453         349 KASDCIECGQCLEKCPQH  366 (391)
T ss_pred             cccccchhhhhhhcCCCc
Confidence            357899999999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	226
2fug_9	182	Crystal Structure Of The Hydrophilic Domain Of Resp		1e-27
1fca_A	55	Structure Of The Ferredoxin From Clostridium Acidur		1e-06
1fdn_A	55	Refined Crystal Structure Of The 2[4fe-4s] Ferredox		2e-06
1clf_A	55	Clostridium Pasteurianum Ferredoxin Length = 55		8e-04

>pdb|2FUG|9 Chain 9, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 182

Iteration: 1
 Score =  119 bits (298), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 57/122 (46%), Positives = 73/122 (59%), Gaps = 6/122 (4%)
Query: 75  LFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCE 134
           + L  + + LG+TLKY F K VT+ YP     L PRF G H L R+P G E+CI C LC 
Sbjct: 1   MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA 60
Query: 135 AVCPAQAITIEAEERED------GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFE 188
           A CPA AI +E  E +       G R    Y+I+M +CI+CG C+EACP  AIV G +FE
Sbjct: 61  AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE 120
Query: 189 YS 190
            +
Sbjct: 121 MA 122

>pdb|1FCA|A Chain A, Structure Of The Ferredoxin From Clostridium Acidurici: Model At 1.8 Angstroms Resolution Length = 55

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/60 (43%), Positives = 30/60 (50%), Gaps = 10/60 (16%)
Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 184
           E CI+C  CE  CP  AI          S+  +RY ID   CI CG C   CPVDA V+ 
Sbjct: 6   EACISCGACEPECPVDAI----------SQGGSRYVIDADTCIDCGACAGVCPVDAPVQA 55

>pdb|1FDN|A Chain A, Refined Crystal Structure Of The 2[4fe-4s] Ferredoxin From Clostridium Acidurici At 1.84 Angstroms Resolution Length = 55

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/60 (43%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 184
           E CI+C  CE  CP  AI          S    RY ID   CI CG C   CPVDA V+ 
Sbjct: 6   EACISCGACEPECPVNAI----------SSGDDRYVIDADTCIDCGACAGVCPVDAPVQA 55

>pdb|1CLF|A Chain A, Clostridium Pasteurianum Ferredoxin Length = 55

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
           + C++C  C + CP  AI          S+  + + ID   CI CG C   CPV A V+
Sbjct: 6   DSCVSCGACASECPVNAI----------SQGDSIFVIDADTCIDCGNCANVCPVGAPVQ 54

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	226
3i9v_9	182	NADH-quinone oxidoreductase subunit 9; electron tr	5e-89
1xer_A	103	Ferredoxin; electron transport, iron-sulfur, dupli	4e-23
2fgo_A	82	Ferredoxin; allochromatium vinosum, [4Fe-4S] clust	2e-18
2zvs_A	85	Uncharacterized ferredoxin-like protein YFHL; elec	6e-18
3eun_A	82	Ferredoxin; electron transport, [4Fe-4S] cluster,	9e-17
1rgv_A	80	Ferredoxin; electron transport; 2.90A {Thauera aro	1e-16
2fdn_A	55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	5e-16
2fdn_A	55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	3e-06
1jb0_C	80	Photosystem I iron-sulfur center; membrane protein	2e-15
1jb0_C	80	Photosystem I iron-sulfur center; membrane protein	5e-07
1hfe_L	421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	6e-12
1hfe_L	421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	2e-05
1jnr_B	150	Adenylylsulfate reductase; oxidoreductase; HET: FA	2e-11
3c8y_A	574	Iron hydrogenase 1; dithiomethylether, H-cluster,	2e-10
3gyx_B	166	Adenylylsulfate reductase; oxidoreductase; HET: FA	4e-10
1kqf_B	294	FDH-N beta S, formate dehydrogenase, nitrate-induc	4e-07
1kqf_B	294	FDH-N beta S, formate dehydrogenase, nitrate-induc	8e-05
2v2k_A	105	Ferredoxin; iron, transport, iron-sulfur, mycobact	6e-07
2v2k_A	105	Ferredoxin; iron, transport, iron-sulfur, mycobact	6e-04
1bc6_A	77	7-Fe ferredoxin; electron transport, iron-sulfur;	8e-07
2vpz_B	195	NRFC protein; oxidoreductase, molybdopterin guanin	1e-06
2vpz_B	195	NRFC protein; oxidoreductase, molybdopterin guanin	2e-06
1h98_A	78	Ferredoxin; electron transport, thermophilic, iron	1e-06
7fd1_A	106	FD1, protein (7-Fe ferredoxin I); electron transpo	2e-06
1dax_A	64	Ferredoxin I; electron transport, electron-transfe	1e-05
2ivf_B	352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	2e-05
2ivf_B	352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	2e-04
1q16_B	512	Respiratory nitrate reductase 1 beta chain; membra	2e-05
1q16_B	512	Respiratory nitrate reductase 1 beta chain; membra	5e-05
1gte_A	1025	Dihydropyrimidine dehydrogenase; electron transfer	2e-05
1dwl_A	59	Ferredoxin I; electron transfer, model, heteronucl	2e-05
1ti6_B	274	Pyrogallol hydroxytransferase small subunit; molyb	7e-05
1ti6_B	274	Pyrogallol hydroxytransferase small subunit; molyb	2e-04
1h0h_B	214	Formate dehydrogenase (small subunit); tungsten se	1e-04
1h0h_B	214	Formate dehydrogenase (small subunit); tungsten se	1e-04
1f2g_A	58	Ferredoxin II; electron transport, FDII desulfovib	1e-04
3or1_B	386	Sulfite reductase beta; dissimilatory sulfite redu	5e-04
2c42_A	1231	Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron,	8e-04

>3i9v_9 NADH-quinone oxidoreductase subunit 9; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_8* 2fug_9* 3iam_9* 3ias_9* 3m9s_9* Length = 182

 Score =  259 bits (663), Expect = 5e-89
 Identities = 64/158 (40%), Positives = 89/158 (56%), Gaps = 6/158 (3%)

Query: 75  LFLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCE 134
           + L  + + LG+TLKY F K VT+ YP     L PRF G H L R+P G E+CI C LC 
Sbjct: 1   MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA 60

Query: 135 AVCPAQAITIEAEERED------GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFE 188
           A CPA AI +E  E +       G R    Y+I+M +CI+CG C+EACP  AIV G +FE
Sbjct: 61  AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE 120

Query: 189 YSTETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 226
            +   + +L+Y KE +L +    + +  E  R+    +
Sbjct: 121 MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVK 158

>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A Length = 103

 Score = 88.8 bits (220), Expect = 4e-23
 Identities = 19/93 (20%), Positives = 29/93 (31%), Gaps = 7/93 (7%)

Query: 94  KKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGS 153
               +  P E   +         +       + CIA   C   CP        +     +
Sbjct: 17  SGHKVYGPVEPPXVLGIHGTIVGVD-----FDLCIADGSCINACPVNVFQWY-DTPGHPA 70

Query: 154 RRTTRYDIDMTKCIYCGFCQEACPVDAI-VEGP 185
                  ++   CI+C  C   CPV AI V+ P
Sbjct: 71  SEKKADPVNEQACIFCMACVNVCPVAAIDVKPP 103

>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction potential, iron binding protein electron transport; 1.32A {Pseudomonas aeruginosa} Length = 82

 Score = 75.9 bits (187), Expect = 2e-18
 Identities = 25/86 (29%), Positives = 34/86 (39%), Gaps = 19/86 (22%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GFCQEACPV 178
           + CI C +CE  CP  AI+   E           Y ID   C  C        CQ+ CPV
Sbjct: 6   DDCINCDVCEPECPNGAISQGEE----------IYVIDPNLCTECVGHYDEPQCQQVCPV 55

Query: 179 DAIVEGPNFEYSTETHEELLYDKEKL 204
           D I          E+ ++L+    K+
Sbjct: 56  DCIPLDDAN---VESKDQLMEKYRKI 78

>2zvs_A Uncharacterized ferredoxin-like protein YFHL; electron transport, [4Fe-4S] clusters, iron-SULF clusters, reduction potential; 1.65A {Escherichia coli} Length = 85

 Score = 74.8 bits (184), Expect = 6e-18
 Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 21/93 (22%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC-GF-----CQEACPV 178
           ++CI C +CE  CP +AI++              Y+I+  KC  C G      CQ+ CP+
Sbjct: 6   KKCINCDMCEPECPNEAISMGDH----------IYEINSDKCTECVGHYETPTCQKVCPI 55

Query: 179 -DAIVEGPNFEYSTETHEELLYDKEKLLENGDR 210
            + IV+ P      ET E+L   K  L+ + D+
Sbjct: 56  PNTIVKDPAH---VETEEQLWD-KFVLMHHADK 84

>3eun_A Ferredoxin; electron transport, [4Fe-4S] cluster, 4Fe-4S, iron, iron-sulfur, metal-binding, transport; 1.05A {Allochromatium vinosum} PDB: 1blu_A 3exy_A Length = 82

 Score = 71.3 bits (175), Expect = 9e-17
 Identities = 31/91 (34%), Positives = 42/91 (46%), Gaps = 19/91 (20%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC-GF-----CQEACP 177
            + CI C +CE  CP  AI+   E           Y I+ + C  C G      C E CP
Sbjct: 5   TDECINCDVCEPECPNGAISQGDE----------TYVIEPSLCTECVGHYETSQCVEVCP 54

Query: 178 VDAIVEGPNFEYSTETHEELLYDKEKLLENG 208
           VDAI++ P+ E   ET +EL    E++   G
Sbjct: 55  VDAIIKDPSHE---ETEDELRAKYERITGEG 82

>1rgv_A Ferredoxin; electron transport; 2.90A {Thauera aromatica} SCOP: d.58.1.1 Length = 80

 Score = 71.3 bits (175), Expect = 1e-16
 Identities = 28/86 (32%), Positives = 36/86 (41%), Gaps = 19/86 (22%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GFCQEACPV 178
           + C AC  C   CP +AIT               Y ID TKC  C        C+  CP 
Sbjct: 6   DDCTACDACVEECPNEAITPG----------DPIYVIDPTKCSECVGAFDEPQCRLVCPA 55

Query: 179 DAIVEGPNFEYSTETHEELLYDKEKL 204
           D I + P++    ET EEL    ++L
Sbjct: 56  DCIPDNPDY---RETREELQEKYDRL 78

>2fdn_A Ferredoxin; electron transport, iron-sulfur, 4Fe-4S; 0.94A {Clostridium acidurici} SCOP: d.58.1.1 PDB: 1fdn_A 1fca_A 1clf_A 1dur_A Length = 55

 Score = 68.8 bits (169), Expect = 5e-16
 Identities = 25/60 (41%), Positives = 30/60 (50%), Gaps = 10/60 (16%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 184
           E CI+C  CE  CP  AI+   ++R         Y ID   CI CG C   CPVDA V+ 
Sbjct: 6   EACISCGACEPECPVNAIS-SGDDR---------YVIDADTCIDCGACAGVCPVDAPVQA 55

>2fdn_A Ferredoxin; electron transport, iron-sulfur, 4Fe-4S; 0.94A {Clostridium acidurici} SCOP: d.58.1.1 PDB: 1fdn_A 1fca_A 1clf_A 1dur_A Length = 55

 Score = 42.3 bits (100), Expect = 3e-06
 Identities = 11/23 (47%), Positives = 14/23 (60%)

Query: 165 KCIYCGFCQEACPVDAIVEGPNF 187
            CI CG C+  CPV+AI  G + 
Sbjct: 7   ACISCGACEPECPVNAISSGDDR 29

>1jb0_C Photosystem I iron-sulfur center; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.58.1.2 PDB: 3pcq_C* 1k0t_A 2wsc_C* 2wse_C* 2wsf_C* 3lw5_C* 2o01_C* Length = 80

 Score = 68.0 bits (166), Expect = 2e-15
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 2/58 (3%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            + CI C  C   CP   + +   +     +  +    +   C+ C  C+ ACP D +
Sbjct: 7   YDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTE--DCVGCKRCETACPTDFL 62

>1jb0_C Photosystem I iron-sulfur center; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.58.1.2 PDB: 3pcq_C* 1k0t_A 2wsc_C* 2wse_C* 2wsf_C* 3lw5_C* 2o01_C* Length = 80

 Score = 45.2 bits (107), Expect = 5e-07
 Identities = 11/50 (22%), Positives = 18/50 (36%)

Query: 107 LSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRT 156
           + P    +          E C+ CK CE  CP   ++I      + +R  
Sbjct: 27  MVPWDGCKAGQIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSM 76

>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A* 1gx7_A* Length = 421

 Score = 63.2 bits (154), Expect = 6e-12
 Identities = 23/80 (28%), Positives = 30/80 (37%), Gaps = 11/80 (13%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
           E +CI C  C   CP  AI         G          +  CI CG C   CP +AI E
Sbjct: 32  EAKCIGCDTCSQYCPTAAIF--------GEMGEPHSIPHIEACINCGQCLTHCPENAIYE 83

Query: 184 GPNFEYSTETHEELLYDKEK 203
             ++       E+ L D + 
Sbjct: 84  AQSW---VPEVEKKLKDGKV 100

>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A* 1gx7_A* Length = 421

 Score = 43.9 bits (104), Expect = 2e-05
 Identities = 13/35 (37%), Positives = 15/35 (42%)

Query: 161 IDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHE 195
           ID  KCI C  C + CP  AI       +S    E
Sbjct: 30  IDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIE 64

>1jnr_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 1.60A {Archaeoglobus fulgidus dsm 4304} SCOP: d.58.1.5 PDB: 1jnz_B* 2fja_B* 2fjb_B* 2fjd_B* 2fje_B* Length = 150

 Score = 59.4 bits (143), Expect = 2e-11
 Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 12/78 (15%)

Query: 124 EERCIACK-----LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV 178
            E+C  CK      CE +CP   +T++ E+ +        Y+ +   C  C  C + CP 
Sbjct: 7   PEKCDGCKALERTACEYICPNDLMTLDKEKMK-------AYNREPDMCWECYSCVKMCPQ 59

Query: 179 DAIVEGPNFEYSTETHEE 196
            AI      +YS      
Sbjct: 60  GAIDVRGYVDYSPLGGAC 77

>3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, iron-sulfur binding, oxidoreductase; HET: HCN; 1.39A {Clostridium pasteurianum} SCOP: c.96.1.1 d.15.4.2 d.58.1.5 PDB: 1c4c_A* 1c4a_A* 1feh_A* Length = 574

 Score = 59.0 bits (143), Expect = 2e-10
 Identities = 23/116 (19%), Positives = 38/116 (32%), Gaps = 16/116 (13%)

Query: 77  LTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAV 136
             ++V          F  K    Y  E+           +L        +C+ C  C   
Sbjct: 109 FLKLVIKYKARASKPFLPKDKTEYVDERSK---------SLTVDR---TKCLLCGRCVNA 156

Query: 137 CPAQAIT--IEAEEREDGSRRTTRYD--IDMTKCIYCGFCQEACPVDAIVEGPNFE 188
           C     T  ++   +   +      +   D T C+ CG C  ACPV A+ E  + +
Sbjct: 157 CGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMD 212

>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas} Length = 166

 Score = 56.0 bits (134), Expect = 4e-10
 Identities = 16/103 (15%), Positives = 36/103 (34%), Gaps = 12/103 (11%)

Query: 124 EERCIACK-----LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV 178
             +C  CK      C  +CP   + ++ EE +        ++ +   C  C  C + CP 
Sbjct: 6   PSKCDGCKGGEKTACMYICPNDLMILDPEEMK-------AFNQEPEACWECYSCIKICPQ 58

Query: 179 DAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIAENLRS 221
            AI   P  +++      +     + +    ++     +  + 
Sbjct: 59  GAITARPYADFAPMGGTCIPLRGSEDIMWTIKFRNGSVKRFKF 101

>1kqf_B FDH-N beta S, formate dehydrogenase, nitrate-inducible, iron-SU subunit; oxidoreductase, selenium, selenocysteine, seCys, molybdenum; HET: MGD HEM CDL; 1.60A {Escherichia coli} SCOP: d.58.1.5 f.23.22.1 PDB: 1kqg_B* Length = 294

 Score = 48.7 bits (116), Expect = 4e-07
 Identities = 25/106 (23%), Positives = 35/106 (33%), Gaps = 26/106 (24%)

Query: 116 ALRRYPTG-----EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC- 169
           A+ +Y  G      E CI C  C A CP     +  E+              + KC  C 
Sbjct: 117 AIIQYANGIVDFQSENCIGCGYCIAGCPFNIPRLNKEDNR------------VYKCTLCV 164

Query: 170 -----GF---CQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLEN 207
                G    C + CP  AI  G   E      + +   K +  E+
Sbjct: 165 DRVSVGQEPACVKTCPTGAIHFGTKKEMLELAEQRVAKLKARGYEH 210

>1kqf_B FDH-N beta S, formate dehydrogenase, nitrate-inducible, iron-SU subunit; oxidoreductase, selenium, selenocysteine, seCys, molybdenum; HET: MGD HEM CDL; 1.60A {Escherichia coli} SCOP: d.58.1.5 f.23.22.1 PDB: 1kqg_B* Length = 294

 Score = 41.8 bits (98), Expect = 8e-05
 Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 8/49 (16%)

Query: 133 CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           C   CP+    I+     +G      +  +   CI CG+C   CP +  
Sbjct: 108 CLKACPSAGAIIQ---YANG---IVDFQSE--NCIGCGYCIAGCPFNIP 148

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis} Length = 105

 Score = 45.4 bits (108), Expect = 6e-07
 Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 12/60 (20%)

Query: 125 ERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
           E C+  K   C   CP   I        +G+R      I   +C+ CG C+  CPV+AI 
Sbjct: 6   EPCVDVKDKACIEECPVDCI-------YEGARM---LYIHPDECVDCGACEPVCPVEAIY 55

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis} Length = 105

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 10/27 (37%), Positives = 15/27 (55%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEERED 151
           + C+ C  CE VCP +AI  E +  + 
Sbjct: 37  DECVDCGACEPVCPVEAIYYEDDVPDQ 63

>1bc6_A 7-Fe ferredoxin; electron transport, iron-sulfur; NMR {Bacillus schlegelii} SCOP: d.58.1.2 PDB: 1bd6_A 1bqx_A 1bwe_A Length = 77

 Score = 44.5 bits (106), Expect = 8e-07
 Identities = 23/60 (38%), Positives = 26/60 (43%), Gaps = 12/60 (20%)

Query: 125 ERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
           E CI  K   C  VCP   I        +G  +   Y ID   CI CG C+  CPV AI 
Sbjct: 6   EPCIGTKDASCVEVCPVDCI-------HEGEDQ---YYIDPDVCIDCGACEAVCPVSAIY 55

>2vpz_B NRFC protein; oxidoreductase, molybdopterin guanine dinucleotide, iron-sulfur, metal-binding, molybdopterin; HET: MGD; 2.40A {Thermus thermophilus} PDB: 2vpx_B* 2vpw_B* 2vpy_B* Length = 195

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 19/49 (38%), Positives = 21/49 (42%), Gaps = 9/49 (18%)

Query: 133 CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           C  VCP  A        +DG        +D  KCI CG C  ACP DA 
Sbjct: 66  CVPVCPTGASYQ----TKDG-----LVLVDPKKCIACGACIAACPYDAR 105

>2vpz_B NRFC protein; oxidoreductase, molybdopterin guanine dinucleotide, iron-sulfur, metal-binding, molybdopterin; HET: MGD; 2.40A {Thermus thermophilus} PDB: 2vpx_B* 2vpw_B* 2vpy_B* Length = 195

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 18/81 (22%), Positives = 25/81 (30%), Gaps = 27/81 (33%)

Query: 116 ALRRYPTG-----EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG 170
           A  +   G      ++CIAC  C A CP  A  +                  ++KC +C 
Sbjct: 74  ASYQTKDGLVLVDPKKCIACGACIAACPYDARYLHPAGY-------------VSKCTFCA 120

Query: 171 ---------FCQEACPVDAIV 182
                     C E CP     
Sbjct: 121 HRLEKGKVPACVETCPTYCRT 141

>1h98_A Ferredoxin; electron transport, thermophilic, iron-sulfur, azotobacter, hydrogen bonds, stability, high resolution; 1.64A {Thermus aquaticus} SCOP: d.58.1.2 Length = 78

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 23/60 (38%), Positives = 27/60 (45%), Gaps = 12/60 (20%)

Query: 125 ERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
           E CI  K   C  VCP + I        DG  +     I   +CI CG C  ACPV+AI 
Sbjct: 6   EPCIGVKDQSCVEVCPVECI-------YDGGDQFY---IHPEECIDCGACVPACPVNAIY 55

>7fd1_A FD1, protein (7-Fe ferredoxin I); electron transport, iron-sulfur; 1.30A {Azotobacter vinelandii} SCOP: d.58.1.2 PDB: 1fda_A 1fdb_A 1fer_A 1axq_A 5fd1_A 6fdr_A 6fd1_A 7fdr_A 1frh_A 1fri_A 1fdd_A 1frl_A 1d3w_A 1frm_A 1frx_A 1g6b_A 1pc4_A 1frj_A 2fd2_A 1fd2_A ... Length = 106

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 18/61 (29%), Positives = 22/61 (36%), Gaps = 12/61 (19%)

Query: 125 ERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 182
           + CI CK   C  VCP           E  +       I   +CI C  C+  CP  AI 
Sbjct: 6   DNCIKCKYTDCVEVCPVDCF------YEGPNF----LVIHPDECIDCALCEPECPAQAIF 55

Query: 183 E 183
            
Sbjct: 56  S 56

>1dax_A Ferredoxin I; electron transport, electron-transfer protein, 4Fe-4S cluster; NMR {Desulfovibrio africanus} SCOP: d.58.1.4 PDB: 1dfd_A 1fxr_A Length = 64

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 12/61 (19%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEA---CPVDA 180
           ++ CIAC+ C  + P       A + E         +    + +     +EA   CPV  
Sbjct: 8   QDECIACESCVEIAPGAF----AMDPEIEKAYVKDVEGASQEEV-----EEAMDTCPVQC 58

Query: 181 I 181
           I
Sbjct: 59  I 59

>2ivf_B Ethylbenzene dehydrogenase beta-subunit; anaerobic hydrocarbon degradation, MOCO, Fe/S cluster, MO- B enzyme, DMSO reductase family; HET: MES MGD MD1 HEM; 1.88A {Aromatoleum aromaticum} Length = 352

 Score = 43.8 bits (103), Expect = 2e-05
 Identities = 17/70 (24%), Positives = 21/70 (30%), Gaps = 21/70 (30%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GF---CQE 174
           +ERC   + C   CP +AI      +               KCI C      G    C  
Sbjct: 181 QERCKGHRHCVEACPYKAIYFNPVSQT------------SEKCILCYPRIEKGIANACNR 228

Query: 175 ACPVDAIVEG 184
            CP      G
Sbjct: 229 QCPGRVRAFG 238

>2ivf_B Ethylbenzene dehydrogenase beta-subunit; anaerobic hydrocarbon degradation, MOCO, Fe/S cluster, MO- B enzyme, DMSO reductase family; HET: MES MGD MD1 HEM; 1.88A {Aromatoleum aromaticum} Length = 352

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 8/49 (16%)

Query: 133 CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           C A CP  AI    +   +G        +D  +C     C EACP  AI
Sbjct: 159 CLAACPTGAIYKRED---NG-----IVLVDQERCKGHRHCVEACPYKAI 199

>1q16_B Respiratory nitrate reductase 1 beta chain; membrane protein, electron-transfer, oxidoreductase; HET: FME MD1 HEM AGA 3PH; 1.90A {Escherichia coli} SCOP: d.58.1.5 PDB: 1r27_B* 1siw_B* 1y5i_B* 1y5l_B* 1y5n_B* 3ir5_B* 3ir6_B* 3ir7_B* 1y4z_B* 3egw_B* Length = 512

 Score = 43.9 bits (103), Expect = 2e-05
 Identities = 22/92 (23%), Positives = 28/92 (30%), Gaps = 23/92 (25%)

Query: 102 FEKGPLSPRFRGEHALRRYPTGE----------ERCIACKL--CEAVCPAQAITIEAEER 149
           F+K      F     +++    +            C  C    C A CP+ AI    E  
Sbjct: 152 FDKLAKDKNFDN---IQKAMYSQFENTFMMYLPRLCEHCLNPACVATCPSGAIYKREE-- 206

Query: 150 EDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            DG        ID  KC     C   CP   I
Sbjct: 207 -DG-----IVLIDQDKCRGWRMCITGCPYKKI 232

>1q16_B Respiratory nitrate reductase 1 beta chain; membrane protein, electron-transfer, oxidoreductase; HET: FME MD1 HEM AGA 3PH; 1.90A {Escherichia coli} SCOP: d.58.1.5 PDB: 1r27_B* 1siw_B* 1y5i_B* 1y5l_B* 1y5n_B* 3ir5_B* 3ir6_B* 3ir7_B* 1y4z_B* 3egw_B* Length = 512

 Score = 42.7 bits (100), Expect = 5e-05
 Identities = 14/71 (19%), Positives = 23/71 (32%), Gaps = 21/71 (29%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GF---CQE 174
           +++C   ++C   CP + I    +  +              KCI+C      G    C E
Sbjct: 214 QDKCRGWRMCITGCPYKKIYFNWKSGK------------SEKCIFCYPRIEAGQPTVCSE 261

Query: 175 ACPVDAIVEGP 185
            C       G 
Sbjct: 262 TCVGRIRYLGV 272

>1gte_A Dihydropyrimidine dehydrogenase; electron transfer, flavin, iron-sulfur clusters, pyrimidine catabolism, 5-fluorouracil degradation, oxidoreductase; HET: FMN FAD; 1.65A {Sus scrofa} SCOP: a.1.2.2 c.1.4.1 c.3.1.1 c.4.1.1 d.58.1.5 PDB: 1gt8_A* 1gth_A* 1h7w_A* 1h7x_A* Length = 1025

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 17/63 (26%), Positives = 20/63 (31%), Gaps = 12/63 (19%)

Query: 124  EERCIACKLCEAVCPA---QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
            EE CI C  C   C     QAI  + E         T        C  C  C   CP+  
Sbjct: 950  EEMCINCGKCYMTCNDSGYQAIQFDPE---------THLPTVTDTCTGCTLCLSVCPIID 1000

Query: 181  IVE 183
             + 
Sbjct: 1001 CIR 1003

>1dwl_A Ferredoxin I; electron transfer, model, heteronuclear docking; HET: HEC; NMR {Desulfomicrobium norvegicum} SCOP: i.4.1.1 Length = 59

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 13/61 (21%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEA---CPVDA 180
            E CI C+ C  +CP         +  +     T  D    +C      Q+A   CPV+A
Sbjct: 6   HEECIGCESCVELCPE---VFAMID-GEEKAMVTAPDST-AECA-----QDAIDACPVEA 55

Query: 181 I 181
           I
Sbjct: 56  I 56

>1ti6_B Pyrogallol hydroxytransferase small subunit; molybdenum binding enzyme, MGD-cofactors, DMSO-reductase family, 4Fe-4S-cluster; HET: MGD BTT; 2.00A {Pelobacter acidigallici} SCOP: b.3.5.1 d.58.1.5 PDB: 1ti2_B* 1ti4_B* 1vld_N* 1vle_N* 1vlf_N* Length = 274

 Score = 41.8 bits (98), Expect = 7e-05
 Identities = 11/71 (15%), Positives = 13/71 (18%), Gaps = 25/71 (35%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG------------- 170
            E+    K     CP   +    EE                KC  C              
Sbjct: 96  PEKAKGKKELLDTCPYGVMYWNEEENV------------AQKCTMCAHLLDDESWAPKMP 143

Query: 171 FCQEACPVDAI 181
            C   C     
Sbjct: 144 RCAHNCGSFVY 154

>1ti6_B Pyrogallol hydroxytransferase small subunit; molybdenum binding enzyme, MGD-cofactors, DMSO-reductase family, 4Fe-4S-cluster; HET: MGD BTT; 2.00A {Pelobacter acidigallici} SCOP: b.3.5.1 d.58.1.5 PDB: 1ti2_B* 1ti4_B* 1vld_N* 1vle_N* 1vlf_N* Length = 274

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 13/58 (22%), Positives = 16/58 (27%), Gaps = 13/58 (22%)

Query: 128 IACKLCE----AVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
             C  CE          A+      REDG        ID  K        + CP   +
Sbjct: 66  TPCMHCENAPCVAKGNGAVYQ----REDG-----IVLIDPEKAKGKKELLDTCPYGVM 114

>1h0h_B Formate dehydrogenase (small subunit); tungsten selenium formate dehydrogenase, selenocysteine, molybdopterin, MGD, iron-sulphur cluster; HET: 2MD MGD EPE; 1.8A {Desulfovibrio gigas} SCOP: d.58.1.5 Length = 214

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 14/71 (19%), Positives = 20/71 (28%), Gaps = 21/71 (29%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GF---CQE 174
            +     +   + CP       AE  +            M KC  C      G    C  
Sbjct: 107 TKDLEDYESVISACPYDVPRKVAESNQ------------MAKCDMCIDRITNGLRPACVT 154

Query: 175 ACPVDAIVEGP 185
           +CP  A+  G 
Sbjct: 155 SCPTGAMNFGD 165

>1h0h_B Formate dehydrogenase (small subunit); tungsten selenium formate dehydrogenase, selenocysteine, molybdopterin, MGD, iron-sulphur cluster; HET: 2MD MGD EPE; 1.8A {Desulfovibrio gigas} SCOP: d.58.1.5 Length = 214

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 7/49 (14%), Positives = 12/49 (24%), Gaps = 3/49 (6%)

Query: 133 CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           C+A    +  +    +   G      +               ACP D  
Sbjct: 80  CKATADMEDESAIIHDDATG---CVLFTPKTKDLEDYESVISACPYDVP 125

>1f2g_A Ferredoxin II; electron transport, FDII desulfovibrio gigas; NMR {Desulfovibrio gigas} SCOP: d.58.1.4 PDB: 1fxd_A Length = 58

 Score = 37.9 bits (88), Expect = 1e-04
 Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 13/61 (21%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEA---CPVDA 180
            + C+AC+ C  +CP      E  E E         D D   C+     +EA   CP +A
Sbjct: 5   NDDCMACEACVEICPD---VFEMNE-EGDKAVVINPDSD-LDCV-----EEAIDSCPAEA 54

Query: 181 I 181
           I
Sbjct: 55  I 55

>3or1_B Sulfite reductase beta; dissimilatory sulfite reductase, sulfate reduction, oxidored sulfite reduction; HET: SRM; 1.76A {Desulfovibrio gigas} PDB: 3or2_B* 2v4j_B* 2xsj_B* Length = 386

 Score = 39.3 bits (92), Expect = 5e-04
 Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 7/62 (11%)

Query: 130 CKLCE-----AVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 184
            +LCE     A CP  A+     E      ++    I+  +C+YCG C   CP   + +G
Sbjct: 219 AELCEIPLAVAACPTAAVKPITAEVNGQKVKSVA--INNDRCMYCGNCYTMCPALPLSDG 276

Query: 185 PN 186
             
Sbjct: 277 TG 278

>2c42_A Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron, iron-sulfur, iron-sulfur cluster, pyruvate catabolism, TPP-dependent enzyme; HET: TPP; 1.78A {Desulfovibrio africanus} SCOP: c.36.1.8 c.36.1.12 c.48.1.3 c.64.1.1 d.58.1.5 PDB: 1b0p_A* 1kek_A* 2c3o_A* 2c3p_A* 2c3u_A* 2c3y_A* 2c3m_A* 2pda_A* 2uza_A* Length = 1231

 Score = 39.1 bits (91), Expect = 8e-04
 Identities = 29/110 (26%), Positives = 36/110 (32%), Gaps = 33/110 (30%)

Query: 124 EERCIACKLCEAVCPAQAI---TIEAEEREDGSRRTT--------------RYDIDMTKC 166
            E CI C  C  VCP  AI     + EE        T              R  I+   C
Sbjct: 685 PENCIQCNQCAFVCPHSAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDC 744

Query: 167 IYCGFCQEACPV--DAIV----------EGPNFEYSTETHEELLYDKEKL 204
           + CG C + CP    A+V          + PN EY       +    E L
Sbjct: 745 MGCGNCADICPPKEKALVMQPLDTQRDAQVPNLEY----AARIPVKSEVL 790

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	226
3i9v_9	182	NADH-quinone oxidoreductase subunit 9; electron tr	99.78
3eun_A	82	Ferredoxin; electron transport, [4Fe-4S] cluster,	99.29
2fgo_A	82	Ferredoxin; allochromatium vinosum, [4Fe-4S] clust	99.29
1rgv_A	80	Ferredoxin; electron transport; 2.90A {Thauera aro	99.29
2fdn_A	55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	99.27
7fd1_A	106	FD1, protein (7-Fe ferredoxin I); electron transpo	99.25
1bc6_A	77	7-Fe ferredoxin; electron transport, iron-sulfur;	99.23
2zvs_A	85	Uncharacterized ferredoxin-like protein YFHL; elec	99.22
1xer_A	103	Ferredoxin; electron transport, iron-sulfur, dupli	99.22
1dax_A	64	Ferredoxin I; electron transport, electron-transfe	99.21
1h98_A	78	Ferredoxin; electron transport, thermophilic, iron	99.2
1f2g_A	58	Ferredoxin II; electron transport, FDII desulfovib	99.2
1rof_A	60	Ferredoxin; electron transport, iron-sulfur; NMR {	99.15
1jb0_C	80	Photosystem I iron-sulfur center; membrane protein	99.15
1dwl_A	59	Ferredoxin I; electron transfer, model, heteronucl	99.15
3gyx_B	166	Adenylylsulfate reductase; oxidoreductase; HET: FA	99.14
1jnr_B	150	Adenylylsulfate reductase; oxidoreductase; HET: FA	99.13
2v2k_A	105	Ferredoxin; iron, transport, iron-sulfur, mycobact	99.12
1iqz_A	81	Ferredoxin; iron-sulfer protein, ultlahigh resolut	99.03
1hfe_L	421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	98.96
1sj1_A	66	Ferredoxin; thermostability, iron-sulfur cluster,	98.9
3c8y_A	574	Iron hydrogenase 1; dithiomethylether, H-cluster,	98.85
2vpz_B	195	NRFC protein; oxidoreductase, molybdopterin guanin	98.8
2c42_A	1231	Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron,	98.76
2ivf_B	352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	98.74
1ti6_B	274	Pyrogallol hydroxytransferase small subunit; molyb	98.72
2ivf_B	352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	98.72
2vpz_B	195	NRFC protein; oxidoreductase, molybdopterin guanin	98.68
3i9v_3	783	NADH-quinone oxidoreductase subunit 3; electron tr	98.63
1q16_B	512	Respiratory nitrate reductase 1 beta chain; membra	98.61
1h0h_B	214	Formate dehydrogenase (small subunit); tungsten se	98.61
1gte_A	1025	Dihydropyrimidine dehydrogenase; electron transfer	98.58
1kqf_B	294	FDH-N beta S, formate dehydrogenase, nitrate-induc	98.58
3mm5_B	366	Sulfite reductase, dissimilatory-type subunit BET;	98.57
1kqf_B	294	FDH-N beta S, formate dehydrogenase, nitrate-induc	98.57
1ti6_B	274	Pyrogallol hydroxytransferase small subunit; molyb	98.55
1q16_B	512	Respiratory nitrate reductase 1 beta chain; membra	98.51
3or1_B	386	Sulfite reductase beta; dissimilatory sulfite redu	98.46
2wdq_B	238	Succinate dehydrogenase iron-sulfur subunit; succi	98.42
3vr8_B	282	Iron-sulfur subunit of succinate dehydrogenase; me	98.38
1h0h_B	214	Formate dehydrogenase (small subunit); tungsten se	98.37
1kf6_B	243	Fumarate reductase iron-sulfur protein; respiratio	98.28
3mm5_A	418	Sulfite reductase, dissimilatory-type subunit ALP;	98.26
2h88_B	252	Succinate dehydrogenase IP subunit; complex II, me	98.26
2bs2_B	241	Quinol-fumarate reductase iron-sulfur subunit B; 2	98.12
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	97.98
2gmh_A	584	Electron transfer flavoprotein-ubiquinone oxidored	97.96
3or1_A	437	Sulfite reductase alpha; dissimilatory sulfite red	97.9
3cf4_A	807	Acetyl-COA decarboxylase/synthase alpha subunit; m	97.86
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	97.79
2v2k_A	105	Ferredoxin; iron, transport, iron-sulfur, mycobact	97.19
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	97.14
1dax_A	64	Ferredoxin I; electron transport, electron-transfe	97.11
1rgv_A	80	Ferredoxin; electron transport; 2.90A {Thauera aro	97.07
2fgo_A	82	Ferredoxin; allochromatium vinosum, [4Fe-4S] clust	97.05
3eun_A	82	Ferredoxin; electron transport, [4Fe-4S] cluster,	97.02
2zvs_A	85	Uncharacterized ferredoxin-like protein YFHL; elec	96.96
2fdn_A	55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	96.85
1iqz_A	81	Ferredoxin; iron-sulfer protein, ultlahigh resolut	96.8
1jb0_C	80	Photosystem I iron-sulfur center; membrane protein	96.67
1xer_A	103	Ferredoxin; electron transport, iron-sulfur, dupli	96.66
1rof_A	60	Ferredoxin; electron transport, iron-sulfur; NMR {	96.56
7fd1_A	106	FD1, protein (7-Fe ferredoxin I); electron transpo	96.53
1f2g_A	58	Ferredoxin II; electron transport, FDII desulfovib	96.48
1sj1_A	66	Ferredoxin; thermostability, iron-sulfur cluster,	96.46
1dwl_A	59	Ferredoxin I; electron transfer, model, heteronucl	96.39
1bc6_A	77	7-Fe ferredoxin; electron transport, iron-sulfur;	96.34
1h98_A	78	Ferredoxin; electron transport, thermophilic, iron	96.21
3i9v_9	182	NADH-quinone oxidoreductase subunit 9; electron tr	96.11
1jnr_B	150	Adenylylsulfate reductase; oxidoreductase; HET: FA	95.89
3gyx_B	166	Adenylylsulfate reductase; oxidoreductase; HET: FA	95.84
1hfe_L	421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	95.49
2c42_A	1231	Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron,	95.08
3or1_B	386	Sulfite reductase beta; dissimilatory sulfite redu	94.57
3pm9_A	476	Putative oxidoreductase; putative D-2-hydroxygluta	94.48
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	94.2
3i9v_3	783	NADH-quinone oxidoreductase subunit 3; electron tr	93.92
3mm5_B	366	Sulfite reductase, dissimilatory-type subunit BET;	93.91
3c8y_A	574	Iron hydrogenase 1; dithiomethylether, H-cluster,	93.81
2gmh_A	584	Electron transfer flavoprotein-ubiquinone oxidored	92.9
2wdq_B	238	Succinate dehydrogenase iron-sulfur subunit; succi	90.88
3mm5_A	418	Sulfite reductase, dissimilatory-type subunit ALP;	90.81
1kf6_B	243	Fumarate reductase iron-sulfur protein; respiratio	90.58
2h88_B	252	Succinate dehydrogenase IP subunit; complex II, me	89.92
1gte_A	1025	Dihydropyrimidine dehydrogenase; electron transfer	89.76
2bs2_B	241	Quinol-fumarate reductase iron-sulfur subunit B; 2	89.32
1e8g_A	560	Vanillyl-alcohol oxidase; oxidoreductase, flavoenz	88.86
3or1_A	437	Sulfite reductase alpha; dissimilatory sulfite red	87.79
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	86.04
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	84.21
1wvf_A	520	4-cresol dehydrogenase [hydroxylating] flavoprote	84.01

>3i9v_9 NADH-quinone oxidoreductase subunit 9; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_8* 2fug_9* 3iam_9* 3ias_9* 3m9s_9*

Probab=99.78  E-value=8.6e-20  Score=144.88  Aligned_cols=141  Identities=43%  Similarity=0.831  Sum_probs=93.8

Q ss_pred             hhHHHHHHHHHHHHHhcCCcceecCccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhccC---
Q 027264           76 FLTEMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDG---  152 (226)
Q Consensus        76 ~~~~~~~~l~~~~~~~f~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~---  152 (226)
                      .+.++++++..+++++|.+..+..||..+....+++++.+.+.....+.++|++||.|+.+||++++.+........   
T Consensus         2 ~l~~~~~~l~~~~~~~~~~~~t~~yp~~~~~~~~~~~g~~~~~~~~~d~~~Ci~C~~C~~~CP~~ai~~~~~~~~~~~~~   81 (182)
T 3i9v_9            2 TLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAAACPAYAIYVEPAENDPENPV   81 (182)
T ss_dssp             ------------------------CCSSCEECCTTCCCSEEECBCTTSCBSCCCCCHHHHHCTTCCEEEEEECCCSSSCS
T ss_pred             CHHHHHHHHHHHHHHHcCCCcceECCCCCCCCCcccCCeEeeccCCCCCccCcccccchhhCCcccEEeecccccccccc
Confidence            35678899999999999999999999888788888998887776666788999999999999999987654321110   


Q ss_pred             ---CccccccccCCCCCCcchhhhhcCcccccccCCCcccchhcHHHhhcCHHHHhhcCCCchHHHH
Q 027264          153 ---SRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWETEIA  216 (226)
Q Consensus       153 ---~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~  216 (226)
                         ........++.+.|++||.|+.+||++||.++..++.....+..++++...+.....++...+.
T Consensus        82 ~~~~~~~~~~~~~~~~C~~C~~C~~~CP~~Ai~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~  148 (182)
T 3i9v_9           82 SAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTKPQRR  148 (182)
T ss_dssp             SSSSCEEEEEEEETTTCCCCCHHHHHCSSSCEEECSCCCCCBSSGGGGEECHHHHBTTCCSCHHHHH
T ss_pred             cccccccceeecCCCcCcChhChhhhCCccceEecCccccccccHHHHhcCHHHHhhcccCCCCCeE
Confidence               1111234567789999999999999999999999999999999999999888888888776654

>3eun_A Ferredoxin; electron transport, [4Fe-4S] cluster, 4Fe-4S, iron, iron-sulfur, metal-binding, transport; 1.05A {Allochromatium vinosum} SCOP: d.58.1.1 PDB: 1blu_A 3exy_A

Probab=99.29  E-value=6.4e-13  Score=91.87  Aligned_cols=56  Identities=41%  Similarity=0.886  Sum_probs=46.8

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch------hhhhcCcccccccCCCc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPNF  187 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg------~Cv~~CP~~Ai~~~~~~  187 (226)
                      ++.++|++||.|+.+||.++|.+...          .+.++...|++|+      .|+.+||++||.+...+
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~----------~~~i~~~~C~~C~~~~~~~~C~~~CP~~Ai~~~~~~   64 (82)
T 3eun_A            3 MITDECINCDVCEPECPNGAISQGDE----------TYVIEPSLCTECVGHYETSQCVEVCPVDAIIKDPSH   64 (82)
T ss_dssp             EECTTCCCCCTTGGGCTTCCEEECSS----------SEEECGGGCCTTTTTCSSCHHHHHCTTCCEEECGGG
T ss_pred             EeCCCCcCccchHHHCChhheEcCCC----------ceEEchhhcCCCCCCCCccHHHHhCCccceEEcCCC
Confidence            45689999999999999999987442          2456778899999      99999999999987653

>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction potential, iron binding protein electron transport; 1.32A {Pseudomonas aeruginosa}

Probab=99.29  E-value=1.5e-12  Score=89.85  Aligned_cols=56  Identities=39%  Similarity=0.756  Sum_probs=46.6

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch------hhhhcCcccccccCCCc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPNF  187 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg------~Cv~~CP~~Ai~~~~~~  187 (226)
                      ++.++|++||.|+.+||+++|.+...          .+.++...|++||      .|+.+||++||.+....
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~C~~~~~~~~C~~~CP~~Ai~~~~~~   64 (82)
T 2fgo_A            3 KITDDCINCDVCEPECPNGAISQGEE----------IYVIDPNLCTECVGHYDEPQCQQVCPVDCIPLDDAN   64 (82)
T ss_dssp             CCCTTCCCCCTTGGGCTTCCEEECSS----------SEEECTTTCCTTTTTCSSCHHHHHCTTCCCCBCTTS
T ss_pred             eeCCCCCChhhHHHHCChhccCCCCC----------eEEEEchhCccCCCcCCCCHhHhhCCcccEEccCCC
Confidence            34679999999999999999986532          2456778999999      99999999999987643

>1rgv_A Ferredoxin; electron transport; 2.90A {Thauera aromatica} SCOP: d.58.1.1

Probab=99.29  E-value=1.2e-12  Score=89.91  Aligned_cols=56  Identities=39%  Similarity=0.809  Sum_probs=46.6

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch------hhhhcCcccccccCCCc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPNF  187 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg------~Cv~~CP~~Ai~~~~~~  187 (226)
                      ++.++|++||.|+.+||+++|.+...          .+.++...|++|+      .|+.+||++||.+....
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~C~~~~~~~~C~~~CP~~Ai~~~~~~   64 (80)
T 1rgv_A            3 YINDDCTACDACVEECPNEAITPGDP----------IYVIDPTKCSECVGAFDEPQCRLVCPADCIPDNPDY   64 (80)
T ss_dssp             CCCSCCCCCCTTTTTCTTCCEECCSS----------SCEECTTTCCTTTTTCSSCHHHHHCSSCCCCBCGGG
T ss_pred             EeCCCCcChhhHHHHcChhccCcCCC----------eeEEcchhCcCCCCcCCccHHHHhcCcccEEecCCc
Confidence            45679999999999999999986532          2456778999999      99999999999976543

>2fdn_A Ferredoxin; electron transport, iron-sulfur, 4Fe-4S; 0.94A {Clostridium acidurici} SCOP: d.58.1.1 PDB: 1fdn_A 1fca_A 1clf_A 1dur_A

Probab=99.27  E-value=1.4e-12  Score=83.07  Aligned_cols=50  Identities=50%  Similarity=1.064  Sum_probs=42.5

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      .++|++||.|+++||.+++....+          .+.++.+.|++||.|+.+||++||.+
T Consensus         5 ~~~C~~C~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~C~~C~~~CP~~ai~~   54 (55)
T 2fdn_A            5 NEACISCGACEPECPVNAISSGDD----------RYVIDADTCIDCGACAGVCPVDAPVQ   54 (55)
T ss_dssp             CTTCCCCCTTGGGCTTCCEECCSS----------SCEECTTTCCCCCHHHHTCTTCCEEE
T ss_pred             cccCcChhhHHHHCCccccCcCCC----------EEEeccccCcChhChHHHccccceec
Confidence            578999999999999999876532          23567789999999999999999874

>7fd1_A FD1, protein (7-Fe ferredoxin I); electron transport, iron-sulfur; 1.30A {Azotobacter vinelandii} SCOP: d.58.1.2 PDB: 1fda_A 1fdb_A 1fer_A 1axq_A 5fd1_A 6fdr_A 6fd1_A 7fdr_A 1frh_A 1fri_A 1fdd_A 1frl_A 1d3w_A 1frm_A 1frx_A 1g6b_A 1pc4_A 1frj_A 2fd2_A 1fd2_A ...

Probab=99.25  E-value=1.7e-12  Score=94.07  Aligned_cols=56  Identities=30%  Similarity=0.706  Sum_probs=46.8

Q ss_pred             Cccccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCc
Q 027264          122 TGEERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF  187 (226)
Q Consensus       122 ~~~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~  187 (226)
                      ++.++|++||  .|+.+||.++|.....          ...++...|++||.|+.+||++||.+...+
T Consensus         3 ~~~~~C~~C~~~~C~~~CP~~ai~~~~~----------~~~i~~~~C~~Cg~C~~~CP~~ai~~~~~~   60 (106)
T 7fd1_A            3 VVTDNCIKCKYTDCVEVCPVDCFYEGPN----------FLVIHPDECIDCALCEPECPAQAIFSEDEV   60 (106)
T ss_dssp             EECGGGTTTCCCHHHHHCTTCCEEECSS----------CEEECTTTCCCCCTTGGGCTTCCEEEGGGC
T ss_pred             ECccccCCccCcHHHHHcCccceEcCCC----------cEEECcccCCChhhhHHhCCChhhhccccC
Confidence            4568999999  9999999999876542          245777899999999999999999877653

>1bc6_A 7-Fe ferredoxin; electron transport, iron-sulfur; NMR {Bacillus schlegelii} SCOP: d.58.1.2 PDB: 1bd6_A 1bqx_A 1bwe_A

Probab=99.23  E-value=2.7e-12  Score=87.55  Aligned_cols=54  Identities=39%  Similarity=0.771  Sum_probs=45.0

Q ss_pred             Cccccccc--cccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIA--CKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~--Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++  ||.|+++||+++|.+...          ...++.+.|++||.|+.+||++||.+..
T Consensus         3 i~~~~C~~c~C~~C~~~Cp~~ai~~~~~----------~~~~~~~~C~~Cg~C~~~CP~~ai~~~~   58 (77)
T 1bc6_A            3 VITEPCIGTKDASCVEVCPVDCIHEGED----------QYYIDPDVCIDCGACEAVCPVSAIYHED   58 (77)
T ss_dssp             ECCSTTTTCCCCSSTTTCTTCCEEECSS----------SEEECTTTCCSCCSHHHHSGGGSSEETT
T ss_pred             EeCccCCCCCcchhHHhcccccEEeCCC----------cEEECcccCcCccCCHhhcCccceEecC
Confidence            35678999  999999999999976431          2456788999999999999999998654

>2zvs_A Uncharacterized ferredoxin-like protein YFHL; electron transport, [4Fe-4S] clusters, iron-SULF clusters, reduction potential; 1.65A {Escherichia coli}

Probab=99.22  E-value=2.5e-12  Score=89.47  Aligned_cols=56  Identities=38%  Similarity=0.942  Sum_probs=46.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch------hhhhcCcc-cccccCCCc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG------FCQEACPV-DAIVEGPNF  187 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg------~Cv~~CP~-~Ai~~~~~~  187 (226)
                      ++.++|++||.|+.+||+++|.+...          .+.++...|++||      .|+.+||+ +||.+....
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~C~~~~~~~~C~~~CP~~~Ai~~~~~~   65 (85)
T 2zvs_A            3 LITKKCINCDMCEPECPNEAISMGDH----------IYEINSDKCTECVGHYETPTCQKVCPIPNTIVKDPAH   65 (85)
T ss_dssp             EECTTCCCCCTTTTTCTTCCEECCSS----------SCEECGGGCCTTTTTCSSCHHHHHCSSCCEEECTTSC
T ss_pred             EeCCcCcChhHHHHHCchhccCcCCC----------ceEEeChhccCCCCcCCccHhhHhCcCCCCEEecCCC
Confidence            34578999999999999999987532          2356778899999      99999999 999987653

>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A

Probab=99.22  E-value=1.9e-12  Score=93.07  Aligned_cols=65  Identities=25%  Similarity=0.492  Sum_probs=47.2

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.++|++||.|+.+||.+++.......... .......++.+.|++||.|+.+||++||.+..
T Consensus        38 ~~id~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~-~~~~~~~~~~~~C~~Cg~C~~~CP~~Ai~~~~  102 (103)
T 1xer_A           38 VGVDFDLCIADGSCINACPVNVFQWYDTPGHPA-SEKKADPVNEQACIFCMACVNVCPVAAIDVKP  102 (103)
T ss_dssp             EEEETTTCCCCCHHHHHCTTCCCEEEECTTCSS-CSEEEECTTGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             EEEehhhCCChhhHHHHcCccCeecccccCccc-cccceeecCcccccChhhHHHhccccceEecC
Confidence            346778999999999999999987654211100 00112345677899999999999999998654

>1dax_A Ferredoxin I; electron transport, electron-transfer protein, 4Fe-4S cluster; NMR {Desulfovibrio africanus} SCOP: d.58.1.4 PDB: 1dfd_A 1fxr_A

Probab=99.21  E-value=1.7e-12  Score=85.18  Aligned_cols=59  Identities=22%  Similarity=0.404  Sum_probs=43.0

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .++.++|++||.|+.+|| +++.+....   +..  .....+...|++|+.|+.+||++||.+.+
T Consensus         5 ~id~~~C~~Cg~C~~~CP-~~~~~~~~~---~~~--~~~~~~~~~C~~C~~C~~~CP~~Ai~~~~   63 (64)
T 1dax_A            5 YVDQDECIACESCVEIAP-GAFAMDPEI---EKA--YVKDVEGASQEEVEEAMDTCPVQCIHWED   63 (64)
T ss_dssp             EECSTTCCSCCHHHHHCT-TTEEECSSS---SSE--EECCGGGSCHHHHHHHHHHSSSCCEECCC
T ss_pred             EEccccCCCchHHHHhCC-ccEeEcCCC---CEE--EEecCCCcchhHHHHHHHhCCHhhEeeec
Confidence            356789999999999999 887664320   000  01112357899999999999999998754

>1h98_A Ferredoxin; electron transport, thermophilic, iron-sulfur, azotobacter, hydrogen bonds, stability, high resolution; 1.64A {Thermus aquaticus} SCOP: d.58.1.2

Probab=99.20  E-value=2.5e-12  Score=88.00  Aligned_cols=54  Identities=37%  Similarity=0.728  Sum_probs=45.1

Q ss_pred             Cccccccc--cccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIA--CKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~--Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++  ||.|+++||+++|.+...          .+.++...|++||.|+.+||++||.+..
T Consensus         3 i~~~~C~~c~C~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~C~~C~~~CP~~Ai~~~~   58 (78)
T 1h98_A            3 VICEPCIGVKDQSCVEVCPVECIYDGGD----------QFYIHPEECIDCGACVPACPVNAIYPEE   58 (78)
T ss_dssp             EECGGGTTTCCCHHHHHCTTCCEEECSS----------SEEECTTTCCCCCTHHHHCTTCCEEEGG
T ss_pred             EEchhCCCCCcChhhhhcCccceEcCCC----------EEEECcccCCcHhHHHHhCCccceEecc
Confidence            45689999  999999999999987531          2456778999999999999999998644

>1f2g_A Ferredoxin II; electron transport, FDII desulfovibrio gigas; NMR {Desulfovibrio gigas} SCOP: d.58.1.4 PDB: 1fxd_A

Probab=99.20  E-value=4.4e-12  Score=81.46  Aligned_cols=53  Identities=23%  Similarity=0.557  Sum_probs=40.8

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccC--CCCCCcchhhhhcCccccccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDID--MTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d--~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      .++ ++|++||.|+++||. ++.+.....        ...++  ...|++||.|+.+||++||.+
T Consensus         3 ~id-~~C~~C~~C~~~CP~-~~~~~~~~~--------~~~~~~~~~~C~~C~~C~~~CP~~Ai~~   57 (58)
T 1f2g_A            3 EVN-DDCMACEACVEICPD-VFEMNEEGD--------KAVVINPDSDLDCVEEAIDSCPAEAIVR   57 (58)
T ss_dssp             BCT-TTCCCCCHHHHHCTT-TEEECSSSS--------SEEESCTTCCSTHHHHHHHTCSSCCCBC
T ss_pred             EEC-CcCccchHHHHhCCc-cEEECCCCc--------EEEeCCCccchHHHHHHHhhCChhhEEe
Confidence            467 899999999999998 665432110        12344  678999999999999999975

>1rof_A Ferredoxin; electron transport, iron-sulfur; NMR {Thermotoga maritima} SCOP: d.58.1.4 PDB: 1vjw_A

Probab=99.15  E-value=1.3e-11  Score=79.57  Aligned_cols=54  Identities=22%  Similarity=0.538  Sum_probs=40.8

Q ss_pred             CccccccccccchhccccccccchhhhhccCCcccccccc-CCCCCCcchhhhhcCcccccccC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDI-DMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~-d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      ++.++|++||.|+.+||. ++.+.....        .... +.+.|..||.|+.+||++||.+.
T Consensus         5 i~~~~C~~C~~C~~~Cp~-~~~~~~~~~--------~~~~~~~~~c~~C~~C~~~CP~~Ai~~~   59 (60)
T 1rof_A            5 VDADACIGCGVCENLCPD-VFQLGDDGK--------AKVLQPETDLPCAKDAADSCPTGAISVE   59 (60)
T ss_dssp             ECTTTCCSCCSSTTTCTT-TBCCCSSSC--------CCBSCSSCCSTTHHHHHHHCTTCCEECC
T ss_pred             EchhhCCCChHHHHhCcH-HHeECCCCC--------EeecCchhhHHHHHHHHHhCCHhHEEEe
Confidence            567899999999999996 565432211        1122 36789999999999999999864

>1jb0_C Photosystem I iron-sulfur center; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.58.1.2 PDB: 3pcq_C* 1k0t_A 2wsc_C* 2wse_C* 2wsf_C* 3lw5_C* 2o01_C*

Probab=99.15  E-value=4.5e-12  Score=86.68  Aligned_cols=62  Identities=21%  Similarity=0.504  Sum_probs=44.5

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++||.|+.+||++++.+.......  ........+.+.|++||.|+.+||++||.+..
T Consensus         5 ~~~~~C~~Cg~C~~~CP~~a~~~~~~~~~~--~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~   66 (80)
T 1jb0_C            5 KIYDTCIGCTQCVRACPTDVLEMVPWDGCK--AGQIASSPRTEDCVGCKRCETACPTDFLSIRV   66 (80)
T ss_dssp             EEETTCCCCCHHHHHCTTCCCEEEECSSST--TSEEEECTTGGGCCCCCHHHHHCCSSSCSEEE
T ss_pred             ccCCcCcChhHHHHHCCccccccccccccc--ccccccCCCCCcCcCcCChhhhCCCCccEeee
Confidence            456899999999999999998765421100  00001234567899999999999999998643

>1dwl_A Ferredoxin I; electron transfer, model, heteronuclear docking; HET: HEC; NMR {Desulfomicrobium norvegicum} SCOP: i.4.1.1

Probab=99.15  E-value=1.3e-11  Score=79.25  Aligned_cols=54  Identities=26%  Similarity=0.528  Sum_probs=40.4

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccc-cCCCCCCcchhhhhcCccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYD-IDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~-~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ++.++|++||.|+.+||. ++.+....   +.    ... ++.+.|+.||.|+.+||++||.+
T Consensus         4 i~~~~C~~C~~C~~~Cp~-~~~~~~~~---~~----~~~~~~~~~c~~C~~C~~~CP~~Ai~~   58 (59)
T 1dwl_A            4 IDHEECIGCESCVELCPE-VFAMIDGE---EK----AMVTAPDSTAECAQDAIDACPVEAISK   58 (59)
T ss_dssp             ESSCCCSSCCGGGGTSTT-TEEEEECS---SC----EEESCTTCCCGGGGTGGGGSTTCCEEE
T ss_pred             EChhhCcChhHHHHHCCH-HheecCCC---Cc----EEEecChhhhhHHHHHHHhCCHhhEEc
Confidence            566899999999999994 66551111   10    111 46788999999999999999975

>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas}

Probab=99.14  E-value=8e-12  Score=97.89  Aligned_cols=60  Identities=27%  Similarity=0.680  Sum_probs=48.5

Q ss_pred             Cccccccccc-----cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcc
Q 027264          122 TGEERCIACK-----LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFE  188 (226)
Q Consensus       122 ~~~~~Ci~Cg-----~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~  188 (226)
                      ++.++|++||     .|+.+||.++|.+.....       ..+.++.+.|++||.|+.+||++||.+....+
T Consensus         4 id~~~C~gC~~c~~~~C~~~CP~~ai~~~~~~~-------~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~   68 (166)
T 3gyx_B            4 VDPSKCDGCKGGEKTACMYICPNDLMILDPEEM-------KAFNQEPEACWECYSCIKICPQGAITARPYAD   68 (166)
T ss_dssp             ECTTTCCCCCSSSCCHHHHHCTTSCEEEETTTT-------EEEESCGGGCCCCCHHHHHCSSCCEEECCCTT
T ss_pred             EcchhcCCCCCCCcchhHHhCCccccEEecCCc-------eeEecCcccCcccChHhHhCCccceEEecccc
Confidence            5678999999     999999999998765321       12346778999999999999999998776544

>1jnr_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 1.60A {Archaeoglobus fulgidus dsm 4304} SCOP: d.58.1.5 PDB: 1jnz_B* 2fja_B* 2fjb_B* 2fjd_B* 2fje_B*

Probab=99.13  E-value=9.1e-12  Score=95.99  Aligned_cols=62  Identities=32%  Similarity=0.709  Sum_probs=49.1

Q ss_pred             Cccccccccc-----cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcccc
Q 027264          122 TGEERCIACK-----LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYS  190 (226)
Q Consensus       122 ~~~~~Ci~Cg-----~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~  190 (226)
                      ++.++|++||     .|+.+||.++|.+.....       ..+.++.+.|++||.|+.+||++||.+....++.
T Consensus         5 vd~~~C~~C~~~~~~~C~~~CP~~ai~~~~~~~-------~~~~id~~~C~~Cg~Cv~~CP~~AI~~~~~~~~~   71 (150)
T 1jnr_B            5 VNPEKCDGCKALERTACEYICPNDLMTLDKEKM-------KAYNREPDMCWECYSCVKMCPQGAIDVRGYVDYS   71 (150)
T ss_dssp             ECTTTCCSCCSSSSCHHHHHCTTSCEEEETTTT-------EEEESCGGGCCCCCHHHHHCTTCCEEECCCTTTC
T ss_pred             ECcccCCCCCCcccccchhhcCccCeEEecCCc-------eeeeeCcccCcCHhHHHHhCCccceEecCcchhh
Confidence            5678999999     999999999998754321       1235677889999999999999999877654433

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis}

Probab=99.12  E-value=1.2e-11  Score=89.33  Aligned_cols=54  Identities=33%  Similarity=0.672  Sum_probs=44.9

Q ss_pred             Ccccccccc--ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIAC--KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~C--g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++|  |.|+.+||+++|.....          ...++.+.|++||.|+.+||++||.+..
T Consensus         3 i~~~~C~~C~c~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~Cg~C~~~CP~~Ai~~~~   58 (105)
T 2v2k_A            3 VIAEPCVDVKDKACIEECPVDCIYEGAR----------MLYIHPDECVDCGACEPVCPVEAIYYED   58 (105)
T ss_dssp             EECGGGTTTCCCHHHHHCTTCCEEECSS----------CEEECTTTCCCCCCSGGGCTTCCEEEGG
T ss_pred             EecccCCCCCcChhhhhcCccccCcCCC----------cEEEeCCcCcchhhHHHhCCccCEEecC
Confidence            456899988  99999999999976432          2456788999999999999999998654

>1iqz_A Ferredoxin; iron-sulfer protein, ultlahigh resolution analysis, geometry of [4Fe-4S] cluster, electron transport; 0.92A {Bacillus thermoproteolyticus} SCOP: d.58.1.4 PDB: 1ir0_A 1wtf_A*

Probab=99.03  E-value=2.2e-11  Score=83.75  Aligned_cols=64  Identities=20%  Similarity=0.263  Sum_probs=42.5

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCc--cccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSR--RTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~--~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .++.++|++||.|+.+|| +++.++.........  ......++.+.|..|+.|+.+||++||.+..
T Consensus         5 ~vd~~~CigCg~C~~~CP-~~~~~~~~g~~~~~~~~~~~~~~~~~~~c~~C~~C~~~CP~~AI~~~~   70 (81)
T 1iqz_A            5 IVDKETCIACGACGAAAP-DIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVAD   70 (81)
T ss_dssp             EECTTTCCCCSHHHHHCT-TTEEECTTSCEEETTTTTSSCSCCCGGGHHHHHHHHHHCTTCCEEEES
T ss_pred             EEecccCcccChhhHhCc-hheeeCCCCeEEEeccCccccCCCCHHHHHHHHHHHHhCCHhHEEEec
Confidence            467789999999999999 676654221100000  0000123346799999999999999998654

>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A* 1gx7_A*

Probab=98.96  E-value=2.1e-10  Score=102.26  Aligned_cols=55  Identities=40%  Similarity=0.831  Sum_probs=45.0

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCcccccccc-CCCCCCcchhhhhcCccccccc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDI-DMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~-d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      +.++.++|++||.|+.+||.++|......         ...+ +...|+.||.|+.+||++||..
T Consensus        28 i~~d~~kCi~Cg~C~~~CP~~ai~~~~~~---------~~~i~~~~~C~~Cg~C~~~CP~~Ai~~   83 (421)
T 1hfe_L           28 VQIDEAKCIGCDTCSQYCPTAAIFGEMGE---------PHSIPHIEACINCGQCLTHCPENAIYE   83 (421)
T ss_dssp             EEECTTTCCCCCHHHHHCTTCCCBCCTTS---------CCBCCCGGGCCCCCTTGGGCTTCCEEE
T ss_pred             EEECcccCCCccHHHHhcCcCceeccccc---------ceeecChhhCCchhhHHHhhCcCCccc
Confidence            44678899999999999999998754321         1234 6788999999999999999987

>1sj1_A Ferredoxin; thermostability, iron-sulfur cluster, hexammine cobalt(III), electron transport; HET: NCO; 1.50A {Pyrococcus furiosus} SCOP: d.58.1.4 PDB: 1siz_A* 2z8q_A 3pni_A

Probab=98.90  E-value=6.4e-11  Score=77.69  Aligned_cols=55  Identities=24%  Similarity=0.448  Sum_probs=39.6

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccC---CC--CCCcchhhhhcCcccccccC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDID---MT--KCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d---~~--~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++.++|++||.|+.+||. ++.+.....        ...++   ..  .|..|+.|+.+||++||.+.
T Consensus         5 ~id~~~C~~C~~C~~~Cp~-~~~~~~~~~--------~~~~~~~~~~~~~c~~c~~C~~~CP~~Ai~~~   64 (66)
T 1sj1_A            5 SVDQDTCIGDAICASLCPD-VFEMNDEGK--------AQPKVEVIEDEELYNCAKEAMEACPVSAITIE   64 (66)
T ss_dssp             EECTTTCCCCCHHHHHCTT-TEEECTTSC--------EEESCSCBCCHHHHHHHHHHHHHCTTCCEEEE
T ss_pred             EECcccCcCchHHHHhCCc-eEEECCCCc--------eeecccCCCcHHHHHHHHHHHhhCCHhhEEEe
Confidence            3567899999999999995 776542211        11122   23  47899999999999999864

>3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, iron-sulfur binding, oxidoreductase; HET: HCN; 1.39A {Clostridium pasteurianum} SCOP: c.96.1.1 d.15.4.2 d.58.1.5 PDB: 1c4c_A* 1c4a_A* 1feh_A*

Probab=98.85  E-value=2.9e-10  Score=105.10  Aligned_cols=67  Identities=25%  Similarity=0.546  Sum_probs=48.2

Q ss_pred             CCCccccccccccchhcccc----ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          120 YPTGEERCIACKLCEAVCPA----QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~----~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      +.++.++|++||.|+++||.    ++|.+..+.....-.......++...|++||.|+.+||++||.++..
T Consensus       140 i~~d~~kCi~Cg~Cv~~CP~~~~~~ai~~~~~g~~~~i~~~~~~~i~~~~Ci~Cg~Cv~~CP~gAi~~~~~  210 (574)
T 3c8y_A          140 LTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSH  210 (574)
T ss_dssp             EEEEGGGCCCCCHHHHHHHHHHSCCCSEEEEETTEEEEESGGGCCGGGSSCCCCCHHHHHCSSTTEEECCC
T ss_pred             ceeCcccCcCCCCccchhCchhcCCceeeccCCccceecccccceechhhCCcchhHHHhhccCCcccccc
Confidence            44678999999999999997    78876543211000000123467789999999999999999987653

>2vpz_B NRFC protein; oxidoreductase, molybdopterin guanine dinucleotide, iron-sulfur, metal-binding, molybdopterin; HET: MGD; 2.40A {Thermus thermophilus} PDB: 2vpx_B* 2vpw_B* 2vpy_B*

Probab=98.80  E-value=1.2e-09  Score=87.67  Aligned_cols=52  Identities=38%  Similarity=0.760  Sum_probs=26.4

Q ss_pred             cccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          124 EERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       124 ~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++|+.|+  .|+++||++||......         .+.++.+.|++||.|+.+||++||.+.
T Consensus        55 ~~~C~~C~~p~C~~~CP~gAi~~~~~g---------~~~id~~~CigC~~C~~~CP~~Ai~~~  108 (195)
T 2vpz_B           55 PEQCLHCENPPCVPVCPTGASYQTKDG---------LVLVDPKKCIACGACIAACPYDARYLH  108 (195)
T ss_dssp             EEECCCCSSCTTTTTCSSSCEEECTTS---------CEEECTTTCCCCCHHHHHCTTCCCEEC
T ss_pred             cccCcCccCcHHHHhcCCCceeccccc---------ceeecCCCCCCcChhHhhCCCCCeEEC
Confidence            45566666  46666666655443210         223444555555555555555555443

>2c42_A Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron, iron-sulfur, iron-sulfur cluster, pyruvate catabolism, TPP-dependent enzyme; HET: TPP; 1.78A {Desulfovibrio africanus} SCOP: c.36.1.8 c.36.1.12 c.48.1.3 c.64.1.1 d.58.1.5 PDB: 1b0p_A* 1kek_A* 2c3o_A* 2c3p_A* 2c3u_A* 2c3y_A* 2c3m_A* 2pda_A* 2uza_A*

Probab=98.76  E-value=1.5e-09  Score=107.83  Aligned_cols=68  Identities=34%  Similarity=0.624  Sum_probs=48.9

Q ss_pred             CCccccccccccchhccccccccch---hhh-----hccCC-----c----cccccccCCCCCCcchhhhhcCcc--ccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIE---AEE-----REDGS-----R----RTTRYDIDMTKCIYCGFCQEACPV--DAI  181 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~---~~~-----~~~~~-----~----~~~~~~~d~~~C~~Cg~Cv~~CP~--~Ai  181 (226)
                      .++.++|+.||.|+.+||.++|...   ...     +....     +    ......++...|++||.|+.+||+  +||
T Consensus       682 ~~d~~kCi~Cg~Cv~vCP~~AI~~~~~~~~e~~~ap~g~~~~~~~~k~~~g~~~~~~v~~~~C~gCG~Cv~vCP~~~~AI  761 (1231)
T 2c42_A          682 QWVPENCIQCNQCAFVCPHSAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDCMGCGNCADICPPKEKAL  761 (1231)
T ss_dssp             EECTTTCCCCCHHHHHCSSCCEEEEEECGGGGTTCCTTCCCEECCSGGGTTCEEEEEECTTTCCCCCHHHHHCSSSSCSE
T ss_pred             EEeCccCCchhhHHHhCCcccccccccchHHHhhCcccccccccccccccccccceeechhhCCChhHHHhhCCCCccCe
Confidence            3678999999999999999998753   110     00000     0    001245778899999999999999  999


Q ss_pred             ccCCCcc
Q 027264          182 VEGPNFE  188 (226)
Q Consensus       182 ~~~~~~~  188 (226)
                      .+.+...
T Consensus       762 ~~~~~~~  768 (1231)
T 2c42_A          762 VMQPLDT  768 (1231)
T ss_dssp             EEEEGGG
T ss_pred             EEecchh
Confidence            8877544

>2ivf_B Ethylbenzene dehydrogenase beta-subunit; anaerobic hydrocarbon degradation, MOCO, Fe/S cluster, MO- B enzyme, DMSO reductase family; HET: MES MGD MD1 HEM; 1.88A {Aromatoleum aromaticum}

Probab=98.74  E-value=1.7e-09  Score=93.97  Aligned_cols=23  Identities=35%  Similarity=0.624  Sum_probs=14.2

Q ss_pred             Cccccccccc--cchhccccccccc
Q 027264          122 TGEERCIACK--LCEAVCPAQAITI  144 (226)
Q Consensus       122 ~~~~~Ci~Cg--~C~~~CP~~ai~~  144 (226)
                      ++.++|++|+  .|+.+||++|+..
T Consensus       146 ~~~~~C~~C~~~~Cv~~CP~gAi~~  170 (352)
T 2ivf_B          146 YLARMCNHCTNPACLAACPTGAIYK  170 (352)
T ss_dssp             EEEECCCCCSSCHHHHHCTTCCEEE
T ss_pred             ECCCCCcCcCCccccccCCCCceee
Confidence            3345666666  6666666666654

>1ti6_B Pyrogallol hydroxytransferase small subunit; molybdenum binding enzyme, MGD-cofactors, DMSO-reductase family, 4Fe-4S-cluster; HET: MGD BTT; 2.00A {Pelobacter acidigallici} SCOP: b.3.5.1 d.58.1.5 PDB: 1ti2_B* 1ti4_B* 1vld_N* 1vle_N* 1vlf_N*

Probab=98.72  E-value=2e-09  Score=90.69  Aligned_cols=54  Identities=20%  Similarity=0.229  Sum_probs=43.3

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc----------h---hhhhcCcccccccCCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC----------G---FCQEACPVDAIVEGPN  186 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C----------g---~Cv~~CP~~Ai~~~~~  186 (226)
                      .++.++|++|+.|+.+||.++|.+....            .+...|++|          |   .|+.+||++||.+.+.
T Consensus        93 ~id~~~CigC~~C~~~CP~~Ai~~~~~~------------~~~~kC~~C~~r~~~~~~~G~~P~Cv~~CP~~Ai~~~~~  159 (274)
T 1ti6_B           93 LIDPEKAKGKKELLDTCPYGVMYWNEEE------------NVAQKCTMCAHLLDDESWAPKMPRCAHNCGSFVYEFLKT  159 (274)
T ss_dssp             EECTTTTTTCGGGGGGCSSCCCEEETTT------------TEEECCCTTHHHHTCTTCTTCSCHHHHHCSSCCEEEEEE
T ss_pred             EechhhccchHHHHhhCccCCeEEEccc------------CccccCCCchhhhhhhccCCCCcchhhhCCcCceEEcCC
Confidence            3667899999999999999998875421            234679999          8   9999999999987664

>2ivf_B Ethylbenzene dehydrogenase beta-subunit; anaerobic hydrocarbon degradation, MOCO, Fe/S cluster, MO- B enzyme, DMSO reductase family; HET: MES MGD MD1 HEM; 1.88A {Aromatoleum aromaticum}

Probab=98.72  E-value=1.9e-09  Score=93.73  Aligned_cols=56  Identities=29%  Similarity=0.546  Sum_probs=45.4

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccCCCcc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPNFE  188 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~~~~~  188 (226)
                      .++.++|++|+.|+.+||.+|+.+...            ......|++|+         .|+.+||++||.+++..+
T Consensus       178 ~id~~kCigCg~Cv~aCP~~Ai~~~~~------------~~~~~kC~~C~~r~~~g~~paCv~~CP~~Ai~~g~~~d  242 (352)
T 2ivf_B          178 LVDQERCKGHRHCVEACPYKAIYFNPV------------SQTSEKCILCYPRIEKGIANACNRQCPGRVRAFGYLDD  242 (352)
T ss_dssp             EECTTTCCCCCHHHHHCTTCCEEEETT------------TTEEEECCTTHHHHTTTBCCHHHHTCTTCCEEEEETTC
T ss_pred             EechhhcCCchHHHhhcCccceecccc------------cccccccCCCcchhhcCCCChHHHhcCccceeccccch
Confidence            356789999999999999999987542            22346899997         999999999998866444

>2vpz_B NRFC protein; oxidoreductase, molybdopterin guanine dinucleotide, iron-sulfur, metal-binding, molybdopterin; HET: MGD; 2.40A {Thermus thermophilus} PDB: 2vpx_B* 2vpw_B* 2vpy_B*

Probab=98.68  E-value=4.1e-09  Score=84.47  Aligned_cols=59  Identities=29%  Similarity=0.633  Sum_probs=47.0

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccCCCcccch
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPNFEYST  191 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~~~~~~~~  191 (226)
                      .++.++|++||.|+.+||++||.+....           .  ...|++|+         .|+.+||++||.+++..+..+
T Consensus        84 ~id~~~CigC~~C~~~CP~~Ai~~~~~~-----------~--~~kC~~C~~~~~~g~~p~Cv~~CP~~Ai~~g~~~~~~~  150 (195)
T 2vpz_B           84 LVDPKKCIACGACIAACPYDARYLHPAG-----------Y--VSKCTFCAHRLEKGKVPACVETCPTYCRTFGDLEDPES  150 (195)
T ss_dssp             EECTTTCCCCCHHHHHCTTCCCEECTTS-----------S--EECCCTTHHHHHTTCCCHHHHSCTTCCEEEEETTCTTS
T ss_pred             eecCCCCCCcChhHhhCCCCCeEECCCC-----------C--CccCcCcchHHhCCCCchhHhhCCcccEEEecccCchH
Confidence            3567899999999999999999876431           1  36799999         799999999999876544443


Q ss_pred             h
Q 027264          192 E  192 (226)
Q Consensus       192 ~  192 (226)
                      +
T Consensus       151 ~  151 (195)
T 2vpz_B          151 P  151 (195)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3i9v_3 NADH-quinone oxidoreductase subunit 3; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_3* 2fug_3* 3iam_3* 3ias_3* 3m9s_3*

Probab=98.63  E-value=5.9e-09  Score=99.60  Aligned_cols=62  Identities=19%  Similarity=0.242  Sum_probs=42.7

Q ss_pred             CCCccccccccccchhcc----ccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVC----PAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~C----P~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.++||.||.|+++|    |.++|.+..+..  ....  ....+...|++||.|+.+||++||..++
T Consensus       174 i~~d~~~CI~C~~Cv~~C~~~~~~~~i~~~~~g~--~~~i--~~~~~~~~C~~CG~Cv~vCP~gAl~~~~  239 (783)
T 3i9v_3          174 VILDRERCIHCKRCVRYFEEVPGDEVLDFIERGV--HTFI--GTMDFGLPSGFSGNITDICPVGALLDLT  239 (783)
T ss_dssp             EEECTTTCCCCCHHHHHHHHTTCCCCCEECSCTT--SCCE--ECSSTTCCSTTTTTHHHHCSSSSEEEGG
T ss_pred             EEEchhhCCCccHHHHHhhhhcCCceeeeecCCC--ccEE--ccCCCCCCCccchhHHhhcccCceeccc
Confidence            446789999999999999    556665543221  1110  0011234799999999999999998654

>1q16_B Respiratory nitrate reductase 1 beta chain; membrane protein, electron-transfer, oxidoreductase; HET: FME MD1 HEM AGA 3PH; 1.90A {Escherichia coli} SCOP: d.58.1.5 PDB: 1r27_B* 1siw_B* 1y5i_B* 1y5l_B* 1y5n_B* 3ir5_B* 3ir6_B* 3ir7_B* 1y4z_B* 3egw_B*

Probab=98.61  E-value=7.2e-09  Score=93.82  Aligned_cols=56  Identities=30%  Similarity=0.462  Sum_probs=40.0

Q ss_pred             Cccccccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++|+  .|+.+||++||.......        ...++.+.|++||.|+.+||++||.+.+
T Consensus       179 ~~~~~C~~C~~~~Cv~aCP~gAI~~~~~~g--------~v~id~~kCigCg~Cv~~CP~~AI~~~~  236 (512)
T 1q16_B          179 YLPRLCEHCLNPACVATCPSGAIYKREEDG--------IVLIDQDKCRGWRMCITGCPYKKIYFNW  236 (512)
T ss_dssp             EEEECCCCCSSCHHHHTCTTCCEEEETTTC--------CEEECTTTCCCCCCHHHHCTTCCEEEET
T ss_pred             ecCccCcCCCCchhhhhCCcCcEEeecCCC--------eEEECHHHCCCchHHHhhCCccceeccc
Confidence            4567899998  699999988887632110        2456677788888888888888876543

>1h0h_B Formate dehydrogenase (small subunit); tungsten selenium formate dehydrogenase, selenocysteine, molybdopterin, MGD, iron-sulphur cluster; HET: 2MD MGD EPE; 1.8A {Desulfovibrio gigas} SCOP: d.58.1.5

Probab=98.61  E-value=3.3e-09  Score=86.20  Aligned_cols=56  Identities=27%  Similarity=0.386  Sum_probs=43.1

Q ss_pred             CCcccccc--ccccchhccccccccchhhhhccCCccccccccCCCCCCcc------h---hhhhcCcccccccCCCcc
Q 027264          121 PTGEERCI--ACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------G---FCQEACPVDAIVEGPNFE  188 (226)
Q Consensus       121 ~~~~~~Ci--~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C------g---~Cv~~CP~~Ai~~~~~~~  188 (226)
                      .++.++|+  +|+.|+.+||++||.+....            .+...|++|      |   .|+.+||++||.+.+..+
T Consensus       102 ~id~~~C~~~~C~~C~~~CP~~Ai~~~~~~------------~~~~kC~~C~~~~~~G~~p~Cv~~CP~~Ai~~~~~~~  168 (214)
T 1h0h_B          102 LFTPKTKDLEDYESVISACPYDVPRKVAES------------NQMAKCDMCIDRITNGLRPACVTSCPTGAMNFGDLSE  168 (214)
T ss_dssp             EECGGGGGCSCHHHHHHHCTTCCCEECTTS------------SCEECCCTTHHHHTTTCCCHHHHHCSSSCEEEEEHHH
T ss_pred             EEeHHHCccccccHHHHhcCCCCeEecCCC------------cccCcCCCCcchhhcCCChhHHHhcCcccEEEccHHH
Confidence            35678899  99999999999988765421            134679999      5   999999999998765433

>1gte_A Dihydropyrimidine dehydrogenase; electron transfer, flavin, iron-sulfur clusters, pyrimidine catabolism, 5-fluorouracil degradation, oxidoreductase; HET: FMN FAD; 1.65A {Sus scrofa} SCOP: a.1.2.2 c.1.4.1 c.3.1.1 c.4.1.1 d.58.1.5 PDB: 1gt8_A* 1gth_A* 1h7w_A* 1h7x_A*

Probab=98.58  E-value=5.6e-09  Score=102.46  Aligned_cols=59  Identities=31%  Similarity=0.622  Sum_probs=46.1

Q ss_pred             CCCccccccccccchhcccc---ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcc-cccccCCCc
Q 027264          120 YPTGEERCIACKLCEAVCPA---QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVEGPNF  187 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~---~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~-~Ai~~~~~~  187 (226)
                      +.++.++|++||.|+.+||+   ++|.+.....        ...++ +.|++||.|+.+||+ +||.+....
T Consensus       946 ~~id~~~C~~Cg~C~~~CP~~~~~ai~~~~~~~--------~~~~~-~~C~~Cg~C~~~CP~~~Ai~~~~~~ 1008 (1025)
T 1gte_A          946 AVIDEEMCINCGKCYMTCNDSGYQAIQFDPETH--------LPTVT-DTCTGCTLCLSVCPIIDCIRMVSRT 1008 (1025)
T ss_dssp             EEECTTTCCCCCHHHHHHHHHSCSCEEECTTTC--------CEEEC-TTCCCCCHHHHHCSSTTTEEEEECC
T ss_pred             EEEEcccCcccCHHHHhcCccccCCEEEeCCCc--------eEEeC-ccCCChhHHHhhCCCCCCEEEecCc
Confidence            34677899999999999997   8887654311        13445 789999999999999 999876543

>1kqf_B FDH-N beta S, formate dehydrogenase, nitrate-inducible, iron-SU subunit; oxidoreductase, selenium, selenocysteine, seCys, molybdenum; HET: MGD HEM CDL; 1.60A {Escherichia coli} SCOP: d.58.1.5 f.23.22.1 PDB: 1kqg_B*

Probab=98.58  E-value=4.9e-09  Score=89.17  Aligned_cols=52  Identities=35%  Similarity=0.728  Sum_probs=27.8

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++||.|+.+||.+++.+....            .....|+.|+         .|+.+||++||.+.+
T Consensus       128 id~~~CigCg~C~~~CP~~ai~~~~~~------------~~~~kC~~C~~r~~~g~~p~Cv~~CP~~Ai~~~~  188 (294)
T 1kqf_B          128 FQSENCIGCGYCIAGCPFNIPRLNKED------------NRVYKCTLCVDRVSVGQEPACVKTCPTGAIHFGT  188 (294)
T ss_dssp             ECGGGCCCCCHHHHHCTTCCCEEETTT------------TEEECCCTTHHHHTTTCCCHHHHHCTTSCEEEEE
T ss_pred             eCcccCCCcchhhhcCCCCCcEecCCC------------CCeeeCCCccchhhcCccHHHHHhCCcCcEEEec
Confidence            344556666666666666555543211            1113466665         666666666665543

>3mm5_B Sulfite reductase, dissimilatory-type subunit BET; alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A {Archaeoglobus fulgidus} PDB: 3c7b_B* 3mm6_B* 3mm7_B* 3mm8_B* 3mm9_B* 3mma_B* 3mmb_B* 3mmc_B*

Probab=98.57  E-value=8.6e-09  Score=90.25  Aligned_cols=57  Identities=26%  Similarity=0.628  Sum_probs=45.2

Q ss_pred             CCCccccc-ccc--ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          120 YPTGEERC-IAC--KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       120 ~~~~~~~C-i~C--g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      +.++.++| ..|  +.|+.+||++||..+...        ..+.++.+.|++||.|+.+||.+||...
T Consensus       200 p~id~~~c~~~Ce~~~Cv~~CP~~AI~~~~~~--------~~~~id~~~C~~Cg~C~~~CP~~Ai~~~  259 (366)
T 3mm5_B          200 PIPNDEAIRKTCEIPSTVAACPTGALKPDMKN--------KTIKVDVEKCMYCGNCYTMCPGMPLFDP  259 (366)
T ss_dssp             CCCCHHHHHHHCCHHHHHHTCTTCCEEEETTT--------TEEEECGGGCCCCCHHHHHCTTCCCCCT
T ss_pred             eEEcchhccccccccchhccCCccceEecCCC--------CeEEEehhhCCCcchHHHhCCHhhcccc
Confidence            44666777 466  999999999999876421        1467888999999999999999998643

>1kqf_B FDH-N beta S, formate dehydrogenase, nitrate-inducible, iron-SU subunit; oxidoreductase, selenium, selenocysteine, seCys, molybdenum; HET: MGD HEM CDL; 1.60A {Escherichia coli} SCOP: d.58.1.5 f.23.22.1 PDB: 1kqg_B*

Probab=98.57  E-value=9.1e-09  Score=87.53  Aligned_cols=55  Identities=29%  Similarity=0.693  Sum_probs=44.9

Q ss_pred             Cccccccccc--cchhcccc-ccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACK--LCEAVCPA-QAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg--~C~~~CP~-~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+.|+.|+  .|+.+||+ +||......         .+.++.+.|++||.|+.+||++||.+..
T Consensus        95 ~~~~~C~~C~~~~C~~~CP~~gAi~~~~~g---------~v~id~~~CigCg~C~~~CP~~ai~~~~  152 (294)
T 1kqf_B           95 IRKDGCMHCEDPGCLKACPSAGAIIQYANG---------IVDFQSENCIGCGYCIAGCPFNIPRLNK  152 (294)
T ss_dssp             EEEESCCCBSSCHHHHHCCSTTSEEEETTS---------CEEECGGGCCCCCHHHHHCTTCCCEEET
T ss_pred             ECcccCCCcCChhhhhhCCccCcccccccc---------ceEeCcccCCCcchhhhcCCCCCcEecC
Confidence            3467899999  89999999 999754221         3567778999999999999999998654

>1ti6_B Pyrogallol hydroxytransferase small subunit; molybdenum binding enzyme, MGD-cofactors, DMSO-reductase family, 4Fe-4S-cluster; HET: MGD BTT; 2.00A {Pelobacter acidigallici} SCOP: b.3.5.1 d.58.1.5 PDB: 1ti2_B* 1ti4_B* 1vld_N* 1vle_N* 1vlf_N*

Probab=98.55  E-value=1.9e-08  Score=84.75  Aligned_cols=54  Identities=19%  Similarity=0.214  Sum_probs=44.3

Q ss_pred             Ccccccccccc--chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~--C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .....|+.|+.  |+++||+ |+......         ...++.+.|++|+.|+.+||++||.+.+
T Consensus        63 ~~~~~C~~C~~p~C~~~CP~-Ai~~~~~g---------~v~id~~~CigC~~C~~~CP~~Ai~~~~  118 (274)
T 1ti6_B           63 YRPTPCMHCENAPCVAKGNG-AVYQREDG---------IVLIDPEKAKGKKELLDTCPYGVMYWNE  118 (274)
T ss_dssp             EEEECCCCCTTCHHHHHTTT-SEEECTTS---------CEEECTTTTTTCGGGGGGCSSCCCEEET
T ss_pred             EcCCcCCCCCChHHHhhChH-HhhhccCC---------cEEechhhccchHHHHhhCccCCeEEEc
Confidence            34578999998  9999999 98764211         3567889999999999999999998654

>1q16_B Respiratory nitrate reductase 1 beta chain; membrane protein, electron-transfer, oxidoreductase; HET: FME MD1 HEM AGA 3PH; 1.90A {Escherichia coli} SCOP: d.58.1.5 PDB: 1r27_B* 1siw_B* 1y5i_B* 1y5l_B* 1y5n_B* 3ir5_B* 3ir6_B* 3ir7_B* 1y4z_B* 3egw_B*

Probab=98.51  E-value=1.3e-08  Score=92.06  Aligned_cols=52  Identities=25%  Similarity=0.588  Sum_probs=43.4

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEG  184 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~  184 (226)
                      .++.++|++||.|+.+||.+||.+....            .....|++|+         .|+.+||++||.++
T Consensus       211 ~id~~kCigCg~Cv~~CP~~AI~~~~~~------------~~~~kC~~Cg~ri~~G~~P~Cv~~CP~~Ai~~g  271 (512)
T 1q16_B          211 LIDQDKCRGWRMCITGCPYKKIYFNWKS------------GKSEKCIFCYPRIEAGQPTVCSETCVGRIRYLG  271 (512)
T ss_dssp             EECTTTCCCCCCHHHHCTTCCEEEETTT------------TEEEECCTTHHHHTTTCCCHHHHTCTTCCEEEE
T ss_pred             EECHHHCCCchHHHhhCCccceecccCC------------CCcccCcCCCchhhcCCCCceEeeCchhhhhcc
Confidence            3667899999999999999999875431            1246799999         99999999999876

>3or1_B Sulfite reductase beta; dissimilatory sulfite reductase, sulfate reduction, oxidored sulfite reduction; HET: SRM; 1.76A {Desulfovibrio gigas} PDB: 3or2_B* 2v4j_B* 2xsj_B*

Probab=98.46  E-value=3.5e-08  Score=86.96  Aligned_cols=63  Identities=27%  Similarity=0.593  Sum_probs=45.0

Q ss_pred             CCCcccccc---ccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          120 YPTGEERCI---ACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       120 ~~~~~~~Ci---~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      +.++.++|.   +|+.|+.+||++||....... .+ .....+.+|.+.|++||.|+.+||.+||..+
T Consensus       211 p~id~e~~~~~Ce~~~cv~~CPt~AI~~~~~~~-~g-~~~~~v~id~~~Ci~Cg~C~~~CP~~Ai~~~  276 (386)
T 3or1_B          211 PMIDHENLAELCEIPLAVAACPTAAVKPITAEV-NG-QKVKSVAINNDRCMYCGNCYTMCPALPLSDG  276 (386)
T ss_dssp             CCCCTTTHHHHCCHHHHHHHCTTCCEEEEEEEE-TT-EEEEEEEECTTTCCCCCHHHHHCTTCCCCCT
T ss_pred             ceechhhhcccccchhhhhhCchhhcccccccc-CC-ccccccccCCCcCCccccHHHhCcHhhCcCC
Confidence            345666665   459999999999998753100 00 0012467889999999999999999998653

>2wdq_B Succinate dehydrogenase iron-sulfur subunit; succinate dehydrogenase activity, cell inner membrane, trica acid cycle; HET: FAD HEM CBE; 2.40A {Escherichia coli} PDB: 1nen_B* 2acz_B* 1nek_B* 2wdr_B* 2wdv_B* 2ws3_B* 2wu2_B* 2wu5_B* 2wp9_B*

Probab=98.42  E-value=2.3e-08  Score=82.31  Aligned_cols=63  Identities=25%  Similarity=0.416  Sum_probs=40.0

Q ss_pred             CCCccccccccccchhccccccccc----hhhh-----hc-cCCccc---ccc-----ccCCCCCCcchhhhhcCccccc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITI----EAEE-----RE-DGSRRT---TRY-----DIDMTKCIYCGFCQEACPVDAI  181 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~----~~~~-----~~-~~~~~~---~~~-----~~d~~~C~~Cg~Cv~~CP~~Ai  181 (226)
                      ...+.++|+.||.|+.+||+..+..    .+..     +. ...+..   ..+     ..+.+.|+.||.|+.+||+++.
T Consensus       142 ~~~~~~~Ci~Cg~C~~~CP~~~~~~~~~~~p~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~vCP~gi~  221 (238)
T 2wdq_B          142 KLDGLYECILCACCSTSCPSFWWNPDKFIGPAGLLAAYRFLIDSRDTETDSRLDGLSDAFSVFRCHSIMNCVSVCPKGLN  221 (238)
T ss_dssp             TTTTTTTCCCCCTTGGGCHHHHHCTTTSCCHHHHHHHHHHHTCTTCCCHHHHHHTTCSTTTTTTCCCCCHHHHHCTTCCC
T ss_pred             HHhccccccccCCchhhCcCCccCCCCCCCHHHHHHHHHHHhCCcccchHHHHHHHhccCCCCcCcccchhhhhcCCCCC
Confidence            3456789999999999999876421    1100     00 000000   011     1356789999999999999965


Q ss_pred             c
Q 027264          182 V  182 (226)
Q Consensus       182 ~  182 (226)
                      .
T Consensus       222 ~  222 (238)
T 2wdq_B          222 P  222 (238)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3vr8_B Iron-sulfur subunit of succinate dehydrogenase; membrane protein, reductase, mitochondria MEMB oxidoreductase; HET: FAD HEM RQX EPH; 2.81A {Ascaris suum} PDB: 3vrb_B*

Probab=98.38  E-value=5.5e-09  Score=88.13  Aligned_cols=108  Identities=19%  Similarity=0.294  Sum_probs=57.5

Q ss_pred             HHHhhhHHHHHHHHHHHHHhcCCcceecCccc-cCCC--CC-CccCccccccCCCccccccccccchhcccccccc----
Q 027264           72 INMLFLTEMVRGLGLTLKYFFDKKVTINYPFE-KGPL--SP-RFRGEHALRRYPTGEERCIACKLCEAVCPAQAIT----  143 (226)
Q Consensus        72 i~~~~~~~~~~~l~~~~~~~f~~~~~~~~p~~-~~~~--~~-~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~----  143 (226)
                      +.++..+.++++|.+++..||+....+.-... ....  .. .................||.||.|..+||+....    
T Consensus       123 IepL~~~pVikDLvvD~~~f~~~~~~v~p~l~~~~~~~~~~~~~~qs~~~~~~~~~~~~CI~CG~C~~aCP~~~~~~~~~  202 (282)
T 3vr8_B          123 IYPLPHMFVIKDLVPDMNLFYAQYASIQPWLQKKTKINLGEKQQYQSIKEQEKLDGLYECILCACCSASCPSYWWNADKY  202 (282)
T ss_pred             eccCCCCceeeccccccHHHHHHHHHHhhhcCCCCCCCCCchhcccCHHHHHHHHhhhhCcccCcCcccCCceeccCCcC
Confidence            34555667899999999998875433221110 1100  00 1111111111112346799999999999986542    


Q ss_pred             chhhhhcc-------CC----cc-cccc--ccCCCCCCcchhhhhcCccc
Q 027264          144 IEAEERED-------GS----RR-TTRY--DIDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       144 ~~~~~~~~-------~~----~~-~~~~--~~d~~~C~~Cg~Cv~~CP~~  179 (226)
                      +.+.....       ..    .. ...+  ....+.|+.||.|..+||.+
T Consensus       203 lGP~~li~a~r~~~d~rd~~~~erl~~l~~~~~l~~C~~Cg~C~~vCP~g  252 (282)
T 3vr8_B          203 LGPAVLMQAYRWIIDSRDDSAAERLARMQDGFSAFKCHTIMNCTKTCPKH  252 (282)
T ss_pred             CCHHHHHHHHHHHhCCcccchHHHHHHHhhcCCcccChhhCCccccCcCC
Confidence            11111000       00    00 0011  12467899999999999998

>1h0h_B Formate dehydrogenase (small subunit); tungsten selenium formate dehydrogenase, selenocysteine, molybdopterin, MGD, iron-sulphur cluster; HET: 2MD MGD EPE; 1.8A {Desulfovibrio gigas} SCOP: d.58.1.5

Probab=98.37  E-value=5.1e-08  Score=79.19  Aligned_cols=56  Identities=18%  Similarity=0.167  Sum_probs=45.2

Q ss_pred             Ccccccccccc--chhccc---cccccchhhhhccCCccccccccCCCCCC--cchhhhhcCcccccccCC
Q 027264          122 TGEERCIACKL--CEAVCP---AQAITIEAEEREDGSRRTTRYDIDMTKCI--YCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~--C~~~CP---~~ai~~~~~~~~~~~~~~~~~~~d~~~C~--~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ....+|+.|+.  |+++||   ++||......        ..+.++.+.|+  +|+.|+.+||++||.+..
T Consensus        67 ~~~~~C~~C~~p~C~~~CP~~~~gAi~~~~~~--------g~v~id~~~C~~~~C~~C~~~CP~~Ai~~~~  129 (214)
T 1h0h_B           67 FFPDQCRHCIAPPCKATADMEDESAIIHDDAT--------GCVLFTPKTKDLEDYESVISACPYDVPRKVA  129 (214)
T ss_dssp             EEEECCCCCSSCHHHHHHTTTCTTSEEECTTT--------CCEEECGGGGGCSCHHHHHHHCTTCCCEECT
T ss_pred             ecCCcCcCcCCchhhccCCccccccEEecCCC--------CeEEEeHHHCccccccHHHHhcCCCCeEecC
Confidence            34678999996  999999   9998764311        13567778999  999999999999998754

>1kf6_B Fumarate reductase iron-sulfur protein; respiration, fumarate reductace, succinate dehydrogenase, CO quinol, quinone, oxidoreductase; HET: FAD HQO CE1 1PE; 2.70A {Escherichia coli} SCOP: a.1.2.1 d.15.4.2 PDB: 1kfy_B* 1l0v_B* 2b76_B* 3cir_B* 3p4p_B* 3p4q_B* 3p4r_B* 3p4s_B*

Probab=98.28  E-value=8.8e-08  Score=79.04  Aligned_cols=60  Identities=28%  Similarity=0.721  Sum_probs=38.1

Q ss_pred             CCccccccccccchhccccccccc---hhh-----------hhccCCc-ccccc--ccCCCCCCcchhhhhcCcccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITI---EAE-----------EREDGSR-RTTRY--DIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~---~~~-----------~~~~~~~-~~~~~--~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ..+.++|+.||.|+.+||..++..   .+.           .+..+.. ....+  ..+.+.|++||.|+.+||++.
T Consensus       142 ~~~~~~Ci~Cg~C~~~CP~~~~~~~~~gP~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~vCP~gi  218 (243)
T 1kf6_B          142 YHQFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHV  218 (243)
T ss_dssp             TGGGGCCCCCCHHHHHCHHHHHCTTSCCHHHHHHHHHHHTCTTCCCTHHHHHHHHSTTTGGGCCCCCHHHHHCTTCC
T ss_pred             hhhhhhccccCccccccCCCcccCCCCCHHHHHHHHHHhhCccccchHHHHHHHhccCCcccCcccCCcchhCCCCC
Confidence            366789999999999999876531   110           0000000 00011  134578999999999999983

>3mm5_A Sulfite reductase, dissimilatory-type subunit ALP; alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A {Archaeoglobus fulgidus} PDB: 3mm6_A* 3mm7_A* 3mm8_A* 3mm9_A* 3mma_A* 3mmb_A* 3mmc_A* 3c7b_A*

Probab=98.26  E-value=1.4e-07  Score=83.77  Aligned_cols=43  Identities=23%  Similarity=0.471  Sum_probs=36.9

Q ss_pred             cccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          130 CKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       130 Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      |+.|+.+||++||..+..          .+.+|.+.|++||.|+.+||++++.
T Consensus       260 ~~~cv~~CPt~Ai~~~~~----------~~~id~~~Ci~Cg~Ci~~CP~~~~~  302 (418)
T 3mm5_A          260 ENEVVKLCPTGAIKWDGK----------ELTIDNRECVRCMHCINKMPKALKP  302 (418)
T ss_dssp             HHHTGGGCTTCCEEECSS----------CEEECTTTCCCCCHHHHHCTTTEEC
T ss_pred             CccccccCCccccccCCc----------eeEEChhhcCccChhHHhCcHhhcc
Confidence            488999999999988532          4678899999999999999998765

>2h88_B Succinate dehydrogenase IP subunit; complex II, membrane protein, heme protein, iron sulfur PROT cytochrome B, oxidoreductase; HET: FAD BHG HEM UNL; 1.74A {Gallus gallus} PDB: 1yq4_B* 1yq3_B* 2fbw_B* 2h89_B* 2wqy_B* 3aef_B* 3abv_B* 3ae1_B* 3ae3_B* 3ae2_B* 3ae5_B* 3ae6_B* 3ae7_B* 3ae8_B* 3ae9_B* 3aea_B* 3aeb_B* 3aec_B* 3aed_B* 3aee_B* ...

Probab=98.26  E-value=1.5e-07  Score=78.15  Aligned_cols=60  Identities=20%  Similarity=0.464  Sum_probs=37.7

Q ss_pred             CCccccccccccchhcccccccc----chhhhh-------ccCCc----cc-ccc--ccCCCCCCcchhhhhcCcccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAIT----IEAEER-------EDGSR----RT-TRY--DIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~----~~~~~~-------~~~~~----~~-~~~--~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ..+.++|++||.|+.+||+.++.    +.+...       ..+..    .. ..+  ....+.|+.||.|+.+||++.
T Consensus       152 ~~~~~~Ci~CG~C~~~CP~~~~~~~~~lgP~~~~~~~r~~~~~r~~~~~~r~~~~~~~~~~~~C~~Cg~C~~~CP~~i  229 (252)
T 2h88_B          152 LDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWMIDSRDDYTEERLAQLQDPFSLYRCHTIMNCTRTCPKGL  229 (252)
T ss_dssp             TTTTTTCCCCCTTGGGCHHHHHHTTTCCHHHHHHHHHHHHTCTTCCCHHHHHHTTCSTTTTTTCCCCCHHHHHCTTCC
T ss_pred             hHhHHhchhhCcchhhCCCCccCCCCcCCHHHHHHHHHHhhCCcccchHHHHHHHhcccCCCcCccccchhhhcCCCC
Confidence            34578999999999999987542    111100       00100    00 011  124578999999999999993

>2bs2_B Quinol-fumarate reductase iron-sulfur subunit B; 2Fe-2S, 3Fe-4S, 4Fe-4S, citric acid cycle, dihaem cytochrome B; HET: FAD HEM LMT; 1.78A {Wolinella succinogenes} SCOP: a.1.2.1 d.15.4.2 PDB: 2bs3_B* 1e7p_B* 1qlb_B* 2bs4_B*

Probab=98.12  E-value=1.8e-07  Score=77.03  Aligned_cols=58  Identities=24%  Similarity=0.527  Sum_probs=37.0

Q ss_pred             ccccccccccchhcccccccc---chhhh------------hccCCcc-cccc--ccCCCCCCcchhhhhcCcccc
Q 027264          123 GEERCIACKLCEAVCPAQAIT---IEAEE------------REDGSRR-TTRY--DIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~---~~~~~------------~~~~~~~-~~~~--~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      +.++|+.||.|+.+||+.++.   +.+..            +...... ...+  ....+.|+.||.|+.+||++.
T Consensus       147 ~~~~Ci~Cg~C~~~CP~~~~~~~~~~p~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~C~~Cg~C~~vCP~~i  222 (241)
T 2bs2_B          147 ELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMIDPHDERTDEDYYELIGDDDGVFGCMTLLACHDVCPKNL  222 (241)
T ss_dssp             HHHTCCCCCHHHHTCHHHHHCTTCCHHHHHHHHHHHHTCTTCCCCHHHHHHHHCSTTTGGGCCCCCHHHHHCTTCC
T ss_pred             hhhhhhccCcCcccCCCCccCCCCCCHHHHHHHHHHhhCccccccHHHHHHHHhcccCcccCcccChhhHhcCCCC
Confidence            467899999999999998653   11110            0000000 0001  234578999999999999993

>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D

Probab=97.98  E-value=7.5e-07  Score=74.56  Aligned_cols=60  Identities=18%  Similarity=0.391  Sum_probs=45.2

Q ss_pred             cccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC---CCcccchhcHHHh
Q 027264          128 IACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG---PNFEYSTETHEEL  197 (226)
Q Consensus       128 i~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~---~~~~~~~~~~~~~  197 (226)
                      .+||.|++.||.++|.++...         ....+...|++||.|+.+|| +|+...   +.|.+..++.+.+
T Consensus       174 ~~C~~C~~~CP~g~I~id~~~---------~v~~d~~~C~~C~~C~~vCp-~aI~~~~~~d~~i~~VEt~Gsl  236 (265)
T 2pa8_D          174 ANCEKAVNVCPEGVFELKDGK---------LSVKNELSCTLCEECLRYCN-GSIRISFVEDKYILEIESVGSL  236 (265)
T ss_dssp             SCCTTHHHHCTTCCEEEETTE---------EEESCGGGCCCCCHHHHHHT-TSEEEEEEEEEEEEEEEECSSS
T ss_pred             hhHHHHHHhCcccCeEecCCe---------eEEeccccCCCchHHHHhCC-CceEEEecCCeEEEEeccCCCC
Confidence            889999999999999876421         12346678999999999999 998644   3455665665554

>2gmh_A Electron transfer flavoprotein-ubiquinone oxidoreductase; HET: BHG FAD UQ5; 2.50A {Sus scrofa} SCOP: c.3.1.2 d.16.1.8 d.58.1.6 PDB: 2gmj_A*

Probab=97.96  E-value=1.1e-06  Score=81.22  Aligned_cols=57  Identities=21%  Similarity=0.318  Sum_probs=44.2

Q ss_pred             ccccc------cccccchhccccccccc-hhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          123 GEERC------IACKLCEAVCPAQAITI-EAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       123 ~~~~C------i~Cg~C~~~CP~~ai~~-~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      +.+.|      ..||.|+.+||.+++.. +.....     ...+.++.+.|+.||.|..+||+++|.+.
T Consensus       508 d~~~~~~~~~~~~~~~c~~~CPa~~~~~~~~~~~~-----~~~~~i~~~~Ci~C~~C~~~cp~~~i~~~  571 (584)
T 2gmh_A          508 DDSVPVNRNLSIYDGPEQRFCPAGVYEFVPLEQGD-----GFRLQINAQNCVHCKTCDIKDPSQNINWV  571 (584)
T ss_dssp             STTHHHHTHHHHHCCTHHHHCTTCCEEEEECSSTT-----CEEEEECGGGCCCCCHHHHHCTTCCEEEC
T ss_pred             CcccchhhchhhhcchhhhcCChhhEEEeecCCCC-----ceEEEEeCCCCcCCCCchhhCCCCCceeE
Confidence            45678      78999999999999976 311110     01367888999999999999999999754

>3or1_A Sulfite reductase alpha; dissimilatory sulfite reductase, sulfate reduction, oxidored sulfite reduction; HET: SRM; 1.76A {Desulfovibrio gigas} PDB: 3or2_A* 2v4j_A* 2xsj_A*

Probab=97.90  E-value=1.4e-06  Score=77.54  Aligned_cols=42  Identities=24%  Similarity=0.513  Sum_probs=35.5

Q ss_pred             ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          131 KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       131 g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      +.|+..||++||..+..          .+.+|...|+.||.|+.+||+.++.
T Consensus       278 ~~vv~~CPt~ai~~~~~----------~l~Id~~~C~~Cg~Ci~~CP~al~~  319 (437)
T 3or1_A          278 AEVVGLCPTGCMTYESG----------TLSIDNKNCTRCMHCINTMPRALKI  319 (437)
T ss_dssp             HHTTTTCTTCCEEEETT----------EEEECGGGCCCCSHHHHHCTTTEEC
T ss_pred             hhhhccCcHHheeecCC----------EEEEccccCCchhhhHhhCcHhhcc
Confidence            57999999999998632          4678889999999999999986653

>3cf4_A Acetyl-COA decarboxylase/synthase alpha subunit; methanomicrobia, iron-nikel-sulfur, 4Fe-NI-4S, oxidoreductas; 2.00A {Methanosarcina barkeri}

Probab=97.86  E-value=8.2e-07  Score=84.79  Aligned_cols=58  Identities=22%  Similarity=0.505  Sum_probs=38.2

Q ss_pred             ccccccccccchhccccccccchhh-hhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          123 GEERCIACKLCEAVCPAQAITIEAE-EREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~~-~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      +.++|++||.|+.+||+.+...... ....+..  ..+..+.+.|+.||.|+.+||++++.
T Consensus       413 ~~~~Ci~CG~C~~~CP~~~~~~~il~~~~~G~~--~~~~~~~~~Ci~Cg~C~~vCP~ga~~  471 (807)
T 3cf4_A          413 MVAKCADCGACLLACPEEIDIPEAMGFAKKGDF--SYFEEIHDTCIGCRRCEQVCKKEIPI  471 (807)
T ss_dssp             HHHHCCCCCHHHHHCTTCCCHHHHHHHHHTTCT--HHHHHHHHHCCCCCHHHHHCTTCCCH
T ss_pred             hHHhCCCCCchhhhCCCCCchHHHHHHHHcCCh--hhhhhchhhccchhhHHHhCCCCCCh
Confidence            4678999999999999975321100 0000100  01223346799999999999999875

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=97.79  E-value=3.6e-06  Score=78.21  Aligned_cols=54  Identities=31%  Similarity=0.748  Sum_probs=39.6

Q ss_pred             Ccccccc--ccc-cchhccccc-----cccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          122 TGEERCI--ACK-LCEAVCPAQ-----AITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       122 ~~~~~Ci--~Cg-~C~~~CP~~-----ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ++.|+|-  .|+ .|.+.||..     +|.++...        ....+..+.|++||.|++.||++||..
T Consensus        11 ~~~~~c~~~~~~~~c~~~cp~~~~~~~~~~~~~~~--------~~~~i~~~~c~~~~~~~~~cp~~~i~i   72 (608)
T 3j16_B           11 VSADKCKPKKCRQECKRSCPVVKTGKLCIEVTPTS--------KIAFISEILCIGCGICVKKCPFDAIQI   72 (608)
T ss_dssp             ECSSSCCHHHHCSHHHHHCHHHHHTCCSEEEETTT--------TEEEECTTTCCCCCHHHHHCSSCCEEE
T ss_pred             EeccccCccccccchhhcCCCccCCceEEEEcCCC--------CceEEehhhccccccccccCCccceEE
Confidence            5667885  575 899999962     34332211        145677789999999999999999964

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis}

Probab=97.19  E-value=0.00013  Score=51.85  Aligned_cols=58  Identities=26%  Similarity=0.436  Sum_probs=35.7

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF  187 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~  187 (226)
                      ++.++|++||.|+.+||++||.+..........   ....+..     -.....||.+|+.+++.-
T Consensus        34 ~~~~~C~~Cg~C~~~CP~~Ai~~~~~~~~~~~~---~~~~d~~-----~~~~~~~~~ga~~~g~~~   91 (105)
T 2v2k_A           34 IHPDECVDCGACEPVCPVEAIYYEDDVPDQWSS---YAQANAD-----FFAELGSPGGASKVGQTD   91 (105)
T ss_dssp             ECTTTCCCCCCSGGGCTTCCEEEGGGCCGGGTT---HHHHHHH-----TTTTTCCCSCHHHHCSCS
T ss_pred             EeCCcCcchhhHHHhCCccCEEecCCChHHHHH---HHHhchH-----HHhhcCCCcceEEeecCC
Confidence            457899999999999999999876432111000   0011100     012367999999877543

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=97.14  E-value=0.00013  Score=67.79  Aligned_cols=54  Identities=39%  Similarity=0.847  Sum_probs=40.6

Q ss_pred             Ccccccc--ccc--cchhccccc-----cccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          122 TGEERCI--ACK--LCEAVCPAQ-----AITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       122 ~~~~~Ci--~Cg--~C~~~CP~~-----ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ++.|+|-  .|+  .|.+.||..     +|.+++..        ....+....|++||.|+..||..||..
T Consensus        24 ~~~~~c~p~~c~~~~c~~~cp~~~~~~~~~~~~~~~--------~~~~i~e~~c~gc~~~~~~~p~~~i~i   86 (607)
T 3bk7_A           24 IDYDKCNPDKCGHFLCERVCPVNRMGGEAIIIDEEN--------YKPIIQEASCTGCGICVHKCPFNAISI   86 (607)
T ss_dssp             CCGGGCCTTTSSSCHHHHHCHHHHTTCCSEEEETTT--------TEEEECTTTCCCCCHHHHHCSSCCCEE
T ss_pred             eeccccCCCCCChhhHhhhCCCCcCCceEEEEcCCC--------CcceeeecccCccccccCCCCcceEEE
Confidence            6678995  796  999999962     33333221        134567789999999999999999876

>1dax_A Ferredoxin I; electron transport, electron-transfer protein, 4Fe-4S cluster; NMR {Desulfovibrio africanus} SCOP: d.58.1.4 PDB: 1dfd_A 1fxr_A

Probab=97.11  E-value=0.00014  Score=46.58  Aligned_cols=27  Identities=33%  Similarity=0.795  Sum_probs=22.4

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+.+|.+.|++||.|+.+|| +++.+.+
T Consensus         3 ~~~id~~~C~~Cg~C~~~CP-~~~~~~~   29 (64)
T 1dax_A            3 KFYVDQDECIACESCVEIAP-GAFAMDP   29 (64)
T ss_dssp             CCEECSTTCCSCCHHHHHCT-TTEEECS
T ss_pred             EEEEccccCCCchHHHHhCC-ccEeEcC
Confidence            34677789999999999999 9887654

>1rgv_A Ferredoxin; electron transport; 2.90A {Thauera aromatica} SCOP: d.58.1.1

Probab=97.07  E-value=0.0002  Score=48.23  Aligned_cols=25  Identities=36%  Similarity=0.757  Sum_probs=21.6

Q ss_pred             cCCCCCCcchhhhhcCcccccccCC
Q 027264          161 IDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+.|++||.|+.+||++||.+.+
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~   27 (80)
T 1rgv_A            3 YINDDCTACDACVEECPNEAITPGD   27 (80)
T ss_dssp             CCCSCCCCCCTTTTTCTTCCEECCS
T ss_pred             EeCCCCcChhhHHHHcChhccCcCC
Confidence            4557899999999999999998654

>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction potential, iron binding protein electron transport; 1.32A {Pseudomonas aeruginosa}

Probab=97.05  E-value=0.00021  Score=48.34  Aligned_cols=25  Identities=36%  Similarity=0.836  Sum_probs=21.5

Q ss_pred             cCCCCCCcchhhhhcCcccccccCC
Q 027264          161 IDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+.|++||.|+.+||++||.+.+
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~   27 (82)
T 2fgo_A            3 KITDDCINCDVCEPECPNGAISQGE   27 (82)
T ss_dssp             CCCTTCCCCCTTGGGCTTCCEEECS
T ss_pred             eeCCCCCChhhHHHHCChhccCCCC
Confidence            4557899999999999999998654

>3eun_A Ferredoxin; electron transport, [4Fe-4S] cluster, 4Fe-4S, iron, iron-sulfur, metal-binding, transport; 1.05A {Allochromatium vinosum} SCOP: d.58.1.1 PDB: 1blu_A 3exy_A

Probab=97.02  E-value=0.00019  Score=48.65  Aligned_cols=26  Identities=35%  Similarity=0.880  Sum_probs=22.0

Q ss_pred             cCCCCCCcchhhhhcCcccccccCCC
Q 027264          161 IDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ++.+.|++||.|+.+||++||.+.+.
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~   28 (82)
T 3eun_A            3 MITDECINCDVCEPECPNGAISQGDE   28 (82)
T ss_dssp             EECTTCCCCCTTGGGCTTCCEEECSS
T ss_pred             EeCCCCcCccchHHHCChhheEcCCC
Confidence            45578999999999999999987543

>2zvs_A Uncharacterized ferredoxin-like protein YFHL; electron transport, [4Fe-4S] clusters, iron-SULF clusters, reduction potential; 1.65A {Escherichia coli}

Probab=96.96  E-value=0.0002  Score=48.81  Aligned_cols=25  Identities=40%  Similarity=0.941  Sum_probs=21.4

Q ss_pred             cCCCCCCcchhhhhcCcccccccCC
Q 027264          161 IDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+.|++||.|+.+||++||.+.+
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~   27 (85)
T 2zvs_A            3 LITKKCINCDMCEPECPNEAISMGD   27 (85)
T ss_dssp             EECTTCCCCCTTTTTCTTCCEECCS
T ss_pred             EeCCcCcChhHHHHHCchhccCcCC
Confidence            3457899999999999999998754

>2fdn_A Ferredoxin; electron transport, iron-sulfur, 4Fe-4S; 0.94A {Clostridium acidurici} SCOP: d.58.1.1 PDB: 1fdn_A 1fca_A 1clf_A 1dur_A

Probab=96.85  E-value=0.00038  Score=43.16  Aligned_cols=23  Identities=48%  Similarity=1.094  Sum_probs=20.3

Q ss_pred             CCCCCcchhhhhcCcccccccCC
Q 027264          163 MTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       163 ~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      .+.|++||.|+.+||.+||.+.+
T Consensus         5 ~~~C~~C~~C~~~CP~~ai~~~~   27 (55)
T 2fdn_A            5 NEACISCGACEPECPVNAISSGD   27 (55)
T ss_dssp             CTTCCCCCTTGGGCTTCCEECCS
T ss_pred             cccCcChhhHHHHCCccccCcCC
Confidence            46899999999999999997654

>1iqz_A Ferredoxin; iron-sulfer protein, ultlahigh resolution analysis, geometry of [4Fe-4S] cluster, electron transport; 0.92A {Bacillus thermoproteolyticus} SCOP: d.58.1.4 PDB: 1ir0_A 1wtf_A*

Probab=96.80  E-value=0.00037  Score=46.99  Aligned_cols=26  Identities=35%  Similarity=0.599  Sum_probs=21.6

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .+.+|.+.|++||.|+.+|| +++.++
T Consensus         3 ~v~vd~~~CigCg~C~~~CP-~~~~~~   28 (81)
T 1iqz_A            3 YTIVDKETCIACGACGAAAP-DIYDYD   28 (81)
T ss_dssp             EEEECTTTCCCCSHHHHHCT-TTEEEC
T ss_pred             EEEEecccCcccChhhHhCc-hheeeC
Confidence            35678889999999999999 777654

>1jb0_C Photosystem I iron-sulfur center; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.58.1.2 PDB: 3pcq_C* 1k0t_A 2wsc_C* 2wse_C* 2wsf_C* 3lw5_C* 2o01_C*

Probab=96.67  E-value=0.00026  Score=47.30  Aligned_cols=25  Identities=32%  Similarity=0.570  Sum_probs=21.0

Q ss_pred             ccCCCCCCcchhhhhcCcccccccC
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++.+.|++||.|+.+||++|+.+.
T Consensus         4 ~~~~~~C~~Cg~C~~~CP~~a~~~~   28 (80)
T 1jb0_C            4 VKIYDTCIGCTQCVRACPTDVLEMV   28 (80)
T ss_dssp             EEEETTCCCCCHHHHHCTTCCCEEE
T ss_pred             cccCCcCcChhHHHHHCCccccccc
Confidence            3455789999999999999999754

>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A

Probab=96.66  E-value=0.0004  Score=48.89  Aligned_cols=27  Identities=33%  Similarity=0.577  Sum_probs=23.1

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .+.++.+.|++||.|+.+||.+||.+.
T Consensus        37 ~~~id~~~C~~Cg~C~~~CP~~ai~~~   63 (103)
T 1xer_A           37 IVGVDFDLCIADGSCINACPVNVFQWY   63 (103)
T ss_dssp             SEEEETTTCCCCCHHHHHCTTCCCEEE
T ss_pred             eEEEehhhCCChhhHHHHcCccCeecc
Confidence            356777899999999999999999754

>1rof_A Ferredoxin; electron transport, iron-sulfur; NMR {Thermotoga maritima} SCOP: d.58.1.4 PDB: 1vjw_A

Probab=96.56  E-value=0.00083  Score=42.00  Aligned_cols=25  Identities=36%  Similarity=0.899  Sum_probs=20.2

Q ss_pred             cccCCCCCCcchhhhhcCcccccccC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      +.++.+.|++||.|+.+||. ++.+.
T Consensus         3 ~~i~~~~C~~C~~C~~~Cp~-~~~~~   27 (60)
T 1rof_A            3 VRVDADACIGCGVCENLCPD-VFQLG   27 (60)
T ss_dssp             SEECTTTCCSCCSSTTTCTT-TBCCC
T ss_pred             EEEchhhCCCChHHHHhCcH-HHeEC
Confidence            45677899999999999997 66543

>7fd1_A FD1, protein (7-Fe ferredoxin I); electron transport, iron-sulfur; 1.30A {Azotobacter vinelandii} SCOP: d.58.1.2 PDB: 1fda_A 1fdb_A 1fer_A 1axq_A 5fd1_A 6fdr_A 6fd1_A 7fdr_A 1frh_A 1fri_A 1fdd_A 1frl_A 1d3w_A 1frm_A 1frx_A 1g6b_A 1pc4_A 1frj_A 2fd2_A 1fd2_A ...

Probab=96.53  E-value=0.00083  Score=47.69  Aligned_cols=26  Identities=54%  Similarity=0.998  Sum_probs=22.6

Q ss_pred             Cccccccccccchhccccccccchhh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAE  147 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~  147 (226)
                      ++.++|++||.|+.+||++||.+...
T Consensus        34 i~~~~C~~Cg~C~~~CP~~ai~~~~~   59 (106)
T 7fd1_A           34 IHPDECIDCALCEPECPAQAIFSEDE   59 (106)
T ss_dssp             ECTTTCCCCCTTGGGCTTCCEEEGGG
T ss_pred             ECcccCCChhhhHHhCCChhhhcccc
Confidence            55678999999999999999987654

>1f2g_A Ferredoxin II; electron transport, FDII desulfovibrio gigas; NMR {Desulfovibrio gigas} SCOP: d.58.1.4 PDB: 1fxd_A

Probab=96.48  E-value=0.00092  Score=41.70  Aligned_cols=23  Identities=26%  Similarity=0.801  Sum_probs=19.1

Q ss_pred             ccCCCCCCcchhhhhcCcccccccC
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++ +.|++||.|+.+||. ++.+.
T Consensus         3 ~id-~~C~~C~~C~~~CP~-~~~~~   25 (58)
T 1f2g_A            3 EVN-DDCMACEACVEICPD-VFEMN   25 (58)
T ss_dssp             BCT-TTCCCCCHHHHHCTT-TEEEC
T ss_pred             EEC-CcCccchHHHHhCCc-cEEEC
Confidence            567 889999999999998 66543

>1sj1_A Ferredoxin; thermostability, iron-sulfur cluster, hexammine cobalt(III), electron transport; HET: NCO; 1.50A {Pyrococcus furiosus} SCOP: d.58.1.4 PDB: 1siz_A* 2z8q_A 3pni_A

Probab=96.46  E-value=0.00088  Score=42.76  Aligned_cols=26  Identities=23%  Similarity=0.551  Sum_probs=21.4

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .+.+|.+.|++||.|+.+||. ++.+.
T Consensus         3 ~~~id~~~C~~C~~C~~~Cp~-~~~~~   28 (66)
T 1sj1_A            3 KVSVDQDTCIGDAICASLCPD-VFEMN   28 (66)
T ss_dssp             EEEECTTTCCCCCHHHHHCTT-TEEEC
T ss_pred             EEEECcccCcCchHHHHhCCc-eEEEC
Confidence            356777899999999999995 87653

>1dwl_A Ferredoxin I; electron transfer, model, heteronuclear docking; HET: HEC; NMR {Desulfomicrobium norvegicum} SCOP: i.4.1.1

Probab=96.39  E-value=0.0012  Score=41.10  Aligned_cols=22  Identities=18%  Similarity=0.330  Sum_probs=19.6

Q ss_pred             ccccccccccchhccccccccc
Q 027264          123 GEERCIACKLCEAVCPAQAITI  144 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~  144 (226)
                      +.+.|+.||.|+.+||++||.+
T Consensus        37 ~~~~c~~C~~C~~~CP~~Ai~~   58 (59)
T 1dwl_A           37 PDSTAECAQDAIDACPVEAISK   58 (59)
T ss_dssp             TTCCCGGGGTGGGGSTTCCEEE
T ss_pred             ChhhhhHHHHHHHhCCHhhEEc
Confidence            5678999999999999999864

>1bc6_A 7-Fe ferredoxin; electron transport, iron-sulfur; NMR {Bacillus schlegelii} SCOP: d.58.1.2 PDB: 1bd6_A 1bqx_A 1bwe_A

Probab=96.34  E-value=0.001  Score=44.20  Aligned_cols=25  Identities=44%  Similarity=0.761  Sum_probs=21.4

Q ss_pred             cCCCCCCc--chhhhhcCcccccccCC
Q 027264          161 IDMTKCIY--CGFCQEACPVDAIVEGP  185 (226)
Q Consensus       161 ~d~~~C~~--Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+.|++  ||.|+.+||.+||.+.+
T Consensus         3 i~~~~C~~c~C~~C~~~Cp~~ai~~~~   29 (77)
T 1bc6_A            3 VITEPCIGTKDASCVEVCPVDCIHEGE   29 (77)
T ss_dssp             ECCSTTTTCCCCSSTTTCTTCCEEECS
T ss_pred             EeCccCCCCCcchhHHhcccccEEeCC
Confidence            45678999  99999999999998654

>1h98_A Ferredoxin; electron transport, thermophilic, iron-sulfur, azotobacter, hydrogen bonds, stability, high resolution; 1.64A {Thermus aquaticus} SCOP: d.58.1.2

Probab=96.21  E-value=0.00089  Score=44.71  Aligned_cols=25  Identities=36%  Similarity=0.696  Sum_probs=21.2

Q ss_pred             cCCCCCCc--chhhhhcCcccccccCC
Q 027264          161 IDMTKCIY--CGFCQEACPVDAIVEGP  185 (226)
Q Consensus       161 ~d~~~C~~--Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+.|++  ||.|+.+||.+||.+.+
T Consensus         3 i~~~~C~~c~C~~C~~~CP~~ai~~~~   29 (78)
T 1h98_A            3 VICEPCIGVKDQSCVEVCPVECIYDGG   29 (78)
T ss_dssp             EECGGGTTTCCCHHHHHCTTCCEEECS
T ss_pred             EEchhCCCCCcChhhhhcCccceEcCC
Confidence            45568999  99999999999998654

>3i9v_9 NADH-quinone oxidoreductase subunit 9; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_8* 2fug_9* 3iam_9* 3ias_9* 3m9s_9*

Probab=96.11  E-value=0.0011  Score=51.35  Aligned_cols=24  Identities=42%  Similarity=0.851  Sum_probs=20.6

Q ss_pred             cCCCCCCcchhhhhcCcccccccC
Q 027264          161 IDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .+.+.|++||.|+.+||++||.+.
T Consensus        48 ~d~~~Ci~C~~C~~~CP~~ai~~~   71 (182)
T 3i9v_9           48 NGLEKCIGCSLCAAACPAYAIYVE   71 (182)
T ss_dssp             TSCBSCCCCCHHHHHCTTCCEEEE
T ss_pred             CCCccCcccccchhhCCcccEEee
Confidence            356789999999999999999654

>1jnr_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 1.60A {Archaeoglobus fulgidus dsm 4304} SCOP: d.58.1.5 PDB: 1jnz_B* 2fja_B* 2fjb_B* 2fjd_B* 2fje_B*

Probab=95.89  E-value=0.0021  Score=48.80  Aligned_cols=26  Identities=27%  Similarity=0.547  Sum_probs=22.6

Q ss_pred             ccCCCCCCcch-----hhhhcCcccccccCC
Q 027264          160 DIDMTKCIYCG-----FCQEACPVDAIVEGP  185 (226)
Q Consensus       160 ~~d~~~C~~Cg-----~Cv~~CP~~Ai~~~~  185 (226)
                      .++.+.|++||     .|+.+||.+||.+..
T Consensus         4 ~vd~~~C~~C~~~~~~~C~~~CP~~ai~~~~   34 (150)
T 1jnr_B            4 FVNPEKCDGCKALERTACEYICPNDLMTLDK   34 (150)
T ss_dssp             EECTTTCCSCCSSSSCHHHHHCTTSCEEEET
T ss_pred             EECcccCCCCCCcccccchhhcCccCeEEec
Confidence            46778999999     999999999997654

>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas}

Probab=95.84  E-value=0.0022  Score=49.51  Aligned_cols=26  Identities=35%  Similarity=0.731  Sum_probs=22.7

Q ss_pred             ccCCCCCCcch-----hhhhcCcccccccCC
Q 027264          160 DIDMTKCIYCG-----FCQEACPVDAIVEGP  185 (226)
Q Consensus       160 ~~d~~~C~~Cg-----~Cv~~CP~~Ai~~~~  185 (226)
                      .+|.+.|++||     .|+.+||.+||.+.+
T Consensus         3 ~id~~~C~gC~~c~~~~C~~~CP~~ai~~~~   33 (166)
T 3gyx_B            3 YVDPSKCDGCKGGEKTACMYICPNDLMILDP   33 (166)
T ss_dssp             EECTTTCCCCCSSSCCHHHHHCTTSCEEEET
T ss_pred             EEcchhcCCCCCCCcchhHHhCCccccEEec
Confidence            46778999999     999999999998654

>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A* 1gx7_A*

Probab=95.49  E-value=0.0042  Score=55.00  Aligned_cols=27  Identities=41%  Similarity=0.786  Sum_probs=23.3

Q ss_pred             cccCCCCCCcchhhhhcCcccccccCC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.+.|++||.|+.+||.+||....
T Consensus        28 i~~d~~kCi~Cg~C~~~CP~~ai~~~~   54 (421)
T 1hfe_L           28 VQIDEAKCIGCDTCSQYCPTAAIFGEM   54 (421)
T ss_dssp             EEECTTTCCCCCHHHHHCTTCCCBCCT
T ss_pred             EEECcccCCCccHHHHhcCcCceeccc
Confidence            457778999999999999999997654

>2c42_A Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron, iron-sulfur, iron-sulfur cluster, pyruvate catabolism, TPP-dependent enzyme; HET: TPP; 1.78A {Desulfovibrio africanus} SCOP: c.36.1.8 c.36.1.12 c.48.1.3 c.64.1.1 d.58.1.5 PDB: 1b0p_A* 1kek_A* 2c3o_A* 2c3p_A* 2c3u_A* 2c3y_A* 2c3m_A* 2pda_A* 2uza_A*

Probab=95.08  E-value=0.0074  Score=60.25  Aligned_cols=54  Identities=19%  Similarity=0.333  Sum_probs=33.6

Q ss_pred             cccccccc-chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          125 ERCIACKL-CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       125 ~~Ci~Cg~-C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      +.|.-|.. .--.||.+......+  ..   ......++.+.|+.||.|+.+||.+||..
T Consensus       651 ~~~pv~~~~~dG~~p~G~~~~~k~--~i---~~~~p~~d~~kCi~Cg~Cv~vCP~~AI~~  705 (1231)
T 2c42_A          651 DKLPVSAFEADGRFPLGTSQFEKR--GV---AINVPQWVPENCIQCNQCAFVCPHSAILP  705 (1231)
T ss_dssp             GGSCGGGSCTTCCBCTTGGGGTCC--CC---CSEEEEECTTTCCCCCHHHHHCSSCCEEE
T ss_pred             CCCCccccCCCCcccCCccccccc--CC---CccceEEeCccCCchhhHHHhCCcccccc
Confidence            44544433 234677764333221  10   11234678899999999999999999974

>3or1_B Sulfite reductase beta; dissimilatory sulfite reductase, sulfate reduction, oxidored sulfite reduction; HET: SRM; 1.76A {Desulfovibrio gigas} PDB: 3or2_B* 2v4j_B* 2xsj_B*

Probab=94.57  E-value=0.007  Score=53.03  Aligned_cols=27  Identities=26%  Similarity=0.716  Sum_probs=23.3

Q ss_pred             CCCccccccccccchhccccccccchh
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      +.++.++|+.||.|+.+||.+||....
T Consensus       251 v~id~~~Ci~Cg~C~~~CP~~Ai~~~~  277 (386)
T 3or1_B          251 VAINNDRCMYCGNCYTMCPALPLSDGT  277 (386)
T ss_dssp             EEECTTTCCCCCHHHHHCTTCCCCCTT
T ss_pred             cccCCCcCCccccHHHhCcHhhCcCCC
Confidence            457789999999999999999997644

>3pm9_A Putative oxidoreductase; putative D-2-hydroxyglutarate dehydrogenase, putative D-LACT dehydrogenase; HET: FAD; 2.57A {Rhodopseudomonas palustris}

Probab=94.48  E-value=0.039  Score=49.54  Aligned_cols=73  Identities=15%  Similarity=0.061  Sum_probs=42.0

Q ss_pred             hhHhhhhccCCcccCcccccCCC-CCCCCCchhH--HHHHHHHHHHhhhHHHHHHHHHH-------------HhhhHHHH
Q 027264           18 LAVSGQALQGSQHYGLRFNAHPY-SSYFPSKKDD--EEKEQLLKEISKDWSSVFERSIN-------------MLFLTEMV   81 (226)
Q Consensus        18 ~~i~Gha~~gn~~~~~~~~~H~~-~~~~~~~~p~--~~~~~~~~~~~~~v~~~~~~~i~-------------~~~~~~~~   81 (226)
                      ..+|||++|||        +|+. ........+.  ++..++.+++.+.+. ++.+++.             .....+..
T Consensus       383 ~~~~gH~gdGn--------lH~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~gGsis~EHGiG~~k~~~l~~~~~~~~  453 (476)
T 3pm9_A          383 PVPFGHLGDGN--------IHYNVSQPVGADKAEFLARWHDVSQVVFEVVL-RLGGSISAEHGIGVMKRDELAEVKDKTA  453 (476)
T ss_dssp             EEEEEEGGGTE--------EEEEEECCTTCCHHHHHTTHHHHHHHHHHHHH-HTTCBSCSSSCCTTTTHHHHHHHSCHHH
T ss_pred             EEEEEEeCCCc--------eEEEEecCCcCChHHHHHHHHHHHHHHHHHHH-HcCCEEEEcccCchhHHHHHHHhcCHHH
Confidence            67899999999        9983 2222111111  123334444443321 2222111             12223457


Q ss_pred             HHHHHHHHHhcCCcceec
Q 027264           82 RGLGLTLKYFFDKKVTIN   99 (226)
Q Consensus        82 ~~l~~~~~~~f~~~~~~~   99 (226)
                      ..++..+|..|||...+|
T Consensus       454 ~~~m~~iK~~~DP~~ilN  471 (476)
T 3pm9_A          454 IELMRSIKALLDPHGIMN  471 (476)
T ss_dssp             HHHHHHHHHHHCTTSCBS
T ss_pred             HHHHHHHHHHhCcccCCC
Confidence            889999999999999998

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=94.20  E-value=0.011  Score=54.90  Aligned_cols=25  Identities=40%  Similarity=0.804  Sum_probs=21.7

Q ss_pred             Cccccccccccchhccccccccchh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      +.++.|++||.|++.||.+||.+..
T Consensus        50 i~~~~c~~~~~~~~~cp~~~i~i~n   74 (608)
T 3j16_B           50 ISEILCIGCGICVKKCPFDAIQIIN   74 (608)
T ss_dssp             ECTTTCCCCCHHHHHCSSCCEEEEE
T ss_pred             EehhhccccccccccCCccceEEec
Confidence            5578999999999999999988743

>3i9v_3 NADH-quinone oxidoreductase subunit 3; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_3* 2fug_3* 3iam_3* 3ias_3* 3m9s_3*

Probab=93.92  E-value=0.013  Score=55.81  Aligned_cols=22  Identities=14%  Similarity=0.095  Sum_probs=19.6

Q ss_pred             cccccccchhccccccccchhh
Q 027264          126 RCIACKLCEAVCPAQAITIEAE  147 (226)
Q Consensus       126 ~Ci~Cg~C~~~CP~~ai~~~~~  147 (226)
                      .|+.||.|+.+||++||.....
T Consensus       219 ~C~~CG~Cv~vCP~gAl~~~~~  240 (783)
T 3i9v_3          219 PSGFSGNITDICPVGALLDLTA  240 (783)
T ss_dssp             CSTTTTTHHHHCSSSSEEEGGG
T ss_pred             CCccchhHHhhcccCceecccc
Confidence            6999999999999999987653

>3mm5_B Sulfite reductase, dissimilatory-type subunit BET; alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A {Archaeoglobus fulgidus} PDB: 3c7b_B* 3mm6_B* 3mm7_B* 3mm8_B* 3mm9_B* 3mma_B* 3mmb_B* 3mmc_B*

Probab=93.91  E-value=0.015  Score=50.55  Aligned_cols=26  Identities=23%  Similarity=0.623  Sum_probs=22.4

Q ss_pred             CCCccccccccccchhccccccccch
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      +.++.++|+.||.|+.+||.+||...
T Consensus       234 ~~id~~~C~~Cg~C~~~CP~~Ai~~~  259 (366)
T 3mm5_B          234 IKVDVEKCMYCGNCYTMCPGMPLFDP  259 (366)
T ss_dssp             EEECGGGCCCCCHHHHHCTTCCCCCT
T ss_pred             EEEehhhCCCcchHHHhCCHhhcccc
Confidence            45778999999999999999998654

>3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, iron-sulfur binding, oxidoreductase; HET: HCN; 1.39A {Clostridium pasteurianum} SCOP: c.96.1.1 d.15.4.2 d.58.1.5 PDB: 1c4c_A* 1c4a_A* 1feh_A*

Probab=93.81  E-value=0.015  Score=53.47  Aligned_cols=26  Identities=23%  Similarity=0.680  Sum_probs=22.6

Q ss_pred             CCccccccccccchhccccccccchh
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .++.++|+.||.|+.+||++||....
T Consensus       184 ~i~~~~Ci~Cg~Cv~~CP~gAi~~~~  209 (574)
T 3c8y_A          184 CFDDTNCLLCGQCIIACPVAALSEKS  209 (574)
T ss_dssp             CGGGSSCCCCCHHHHHCSSTTEEECC
T ss_pred             eechhhCCcchhHHHhhccCCccccc
Confidence            45678999999999999999998754

>2gmh_A Electron transfer flavoprotein-ubiquinone oxidoreductase; HET: BHG FAD UQ5; 2.50A {Sus scrofa} SCOP: c.3.1.2 d.16.1.8 d.58.1.6 PDB: 2gmj_A*

Probab=92.90  E-value=0.021  Score=52.45  Aligned_cols=31  Identities=26%  Similarity=0.545  Sum_probs=25.0

Q ss_pred             CCCccccccccccchhccccccccchhhhhc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEERE  150 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~  150 (226)
                      +.++.++|++||.|..+||+++|......++
T Consensus       546 ~~i~~~~Ci~C~~C~~~cp~~~i~~~~p~gg  576 (584)
T 2gmh_A          546 LQINAQNCVHCKTCDIKDPSQNINWVVPEGG  576 (584)
T ss_dssp             EEECGGGCCCCCHHHHHCTTCCEEECCCSTT
T ss_pred             EEEeCCCCcCCCCchhhCCCCCceeECCCCC
Confidence            3467789999999999999999987655443

>2wdq_B Succinate dehydrogenase iron-sulfur subunit; succinate dehydrogenase activity, cell inner membrane, trica acid cycle; HET: FAD HEM CBE; 2.40A {Escherichia coli} PDB: 1nen_B* 2acz_B* 1nek_B* 2wdr_B* 2wdv_B* 2ws3_B* 2wu2_B* 2wu5_B* 2wp9_B*

Probab=90.88  E-value=0.06  Score=43.56  Aligned_cols=23  Identities=26%  Similarity=0.577  Sum_probs=19.7

Q ss_pred             ccCCCCCCcchhhhhcCcccccc
Q 027264          160 DIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       160 ~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      ..+...|+.||.|+.+||..++.
T Consensus       143 ~~~~~~Ci~Cg~C~~~CP~~~~~  165 (238)
T 2wdq_B          143 LDGLYECILCACCSTSCPSFWWN  165 (238)
T ss_dssp             TTTTTTCCCCCTTGGGCHHHHHC
T ss_pred             HhccccccccCCchhhCcCCccC
Confidence            45678899999999999998764

>3mm5_A Sulfite reductase, dissimilatory-type subunit ALP; alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A {Archaeoglobus fulgidus} PDB: 3mm6_A* 3mm7_A* 3mm8_A* 3mm9_A* 3mma_A* 3mmb_A* 3mmc_A* 3c7b_A*

Probab=90.81  E-value=0.048  Score=48.19  Aligned_cols=24  Identities=17%  Similarity=0.462  Sum_probs=19.9

Q ss_pred             CCCccccccccccchhcccccccc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAIT  143 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~  143 (226)
                      +.++.++|+.||.|+.+||..+..
T Consensus       279 ~~id~~~Ci~Cg~Ci~~CP~~~~~  302 (418)
T 3mm5_A          279 LTIDNRECVRCMHCINKMPKALKP  302 (418)
T ss_dssp             EEECTTTCCCCCHHHHHCTTTEEC
T ss_pred             eEEChhhcCccChhHHhCcHhhcc
Confidence            345788999999999999997554

>1kf6_B Fumarate reductase iron-sulfur protein; respiration, fumarate reductace, succinate dehydrogenase, CO quinol, quinone, oxidoreductase; HET: FAD HQO CE1 1PE; 2.70A {Escherichia coli} SCOP: a.1.2.1 d.15.4.2 PDB: 1kfy_B* 1l0v_B* 2b76_B* 3cir_B* 3p4p_B* 3p4q_B* 3p4r_B* 3p4s_B*

Probab=90.58  E-value=0.043  Score=44.56  Aligned_cols=22  Identities=36%  Similarity=0.928  Sum_probs=19.2

Q ss_pred             cCCCCCCcchhhhhcCcccccc
Q 027264          161 IDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      .+...|+.||.|+.+||..++.
T Consensus       143 ~~~~~Ci~Cg~C~~~CP~~~~~  164 (243)
T 1kf6_B          143 HQFSGCINCGLCYAACPQFGLN  164 (243)
T ss_dssp             GGGGCCCCCCHHHHHCHHHHHC
T ss_pred             hhhhhccccCccccccCCCccc
Confidence            5667899999999999999874

>2h88_B Succinate dehydrogenase IP subunit; complex II, membrane protein, heme protein, iron sulfur PROT cytochrome B, oxidoreductase; HET: FAD BHG HEM UNL; 1.74A {Gallus gallus} PDB: 1yq4_B* 1yq3_B* 2fbw_B* 2h89_B* 2wqy_B* 3aef_B* 3abv_B* 3ae1_B* 3ae3_B* 3ae2_B* 3ae5_B* 3ae6_B* 3ae7_B* 3ae8_B* 3ae9_B* 3aea_B* 3aeb_B* 3aec_B* 3aed_B* 3aee_B* ...

Probab=89.92  E-value=0.081  Score=43.30  Aligned_cols=22  Identities=27%  Similarity=0.690  Sum_probs=18.7

Q ss_pred             cCCCCCCcchhhhhcCcccccc
Q 027264          161 IDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      .+...|+.||.|+.+||..++.
T Consensus       153 ~~~~~Ci~CG~C~~~CP~~~~~  174 (252)
T 2h88_B          153 DGLYECILCACCSTSCPSYWWN  174 (252)
T ss_dssp             TTTTTCCCCCTTGGGCHHHHHH
T ss_pred             HhHHhchhhCcchhhCCCCccC
Confidence            4567899999999999998753

>1gte_A Dihydropyrimidine dehydrogenase; electron transfer, flavin, iron-sulfur clusters, pyrimidine catabolism, 5-fluorouracil degradation, oxidoreductase; HET: FMN FAD; 1.65A {Sus scrofa} SCOP: a.1.2.2 c.1.4.1 c.3.1.1 c.4.1.1 d.58.1.5 PDB: 1gt8_A* 1gth_A* 1h7w_A* 1h7x_A*

Probab=89.76  E-value=0.085  Score=51.69  Aligned_cols=28  Identities=39%  Similarity=0.628  Sum_probs=23.8

Q ss_pred             ccccCCCCCCcchhhhhcCcc---cccccCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPV---DAIVEGP  185 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~---~Ai~~~~  185 (226)
                      ...+|.+.|++||.|+.+||.   +||.+.+
T Consensus       945 ~~~id~~~C~~Cg~C~~~CP~~~~~ai~~~~  975 (1025)
T 1gte_A          945 VAVIDEEMCINCGKCYMTCNDSGYQAIQFDP  975 (1025)
T ss_dssp             EEEECTTTCCCCCHHHHHHHHHSCSCEEECT
T ss_pred             eEEEEcccCcccCHHHHhcCccccCCEEEeC
Confidence            456788899999999999997   8997655

>2bs2_B Quinol-fumarate reductase iron-sulfur subunit B; 2Fe-2S, 3Fe-4S, 4Fe-4S, citric acid cycle, dihaem cytochrome B; HET: FAD HEM LMT; 1.78A {Wolinella succinogenes} SCOP: a.1.2.1 d.15.4.2 PDB: 2bs3_B* 1e7p_B* 1qlb_B* 2bs4_B*

Probab=89.32  E-value=0.077  Score=43.01  Aligned_cols=21  Identities=33%  Similarity=0.958  Sum_probs=18.1

Q ss_pred             CCCCCCcchhhhhcCcccccc
Q 027264          162 DMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      +...|+.||.|+.+||+.++.
T Consensus       147 ~~~~Ci~Cg~C~~~CP~~~~~  167 (241)
T 2bs2_B          147 ELDRCIECGCCIAACGTKIMR  167 (241)
T ss_dssp             HHHTCCCCCHHHHTCHHHHHC
T ss_pred             hhhhhhccCcCcccCCCCccC
Confidence            346799999999999999874

>1e8g_A Vanillyl-alcohol oxidase; oxidoreductase, flavoenzyme, specificity; HET: FAD FCR; 2.1A {Penicillium simplicissimum} SCOP: d.58.32.1 d.145.1.1 PDB: 1e8f_A* 1e8h_A* 1qlt_A* 1qlu_A* 1vao_A* 1ahv_A* 1ahz_A* 1ahu_A* 2vao_A* 1w1j_A* 1dzn_A* 1w1l_A* 1e0y_A* 1w1k_A* 1w1m_A*

Probab=88.86  E-value=0.11  Score=47.46  Aligned_cols=74  Identities=11%  Similarity=-0.059  Sum_probs=41.7

Q ss_pred             hhHhhhhccCCcccCcccccCCCC---CCCCCchhHHHHHHHHHHHhhhHHHHHHHHHH---------Hhhh---HHHHH
Q 027264           18 LAVSGQALQGSQHYGLRFNAHPYS---SYFPSKKDDEEKEQLLKEISKDWSSVFERSIN---------MLFL---TEMVR   82 (226)
Q Consensus        18 ~~i~Gha~~gn~~~~~~~~~H~~~---~~~~~~~p~~~~~~~~~~~~~~v~~~~~~~i~---------~~~~---~~~~~   82 (226)
                      ..++||+.+||        +|++.   .........++..++++++.+.+..-=.+..+         ...+   .+...
T Consensus       454 ~~~~gH~gdGn--------lH~~i~~~~~~~~~~~~~~~~~~~~~l~~~~~eHGiG~~k~~~~~l~~~~~~~~~~g~~~~  525 (560)
T 1e8g_A          454 FIGTFTVGMRE--------MHHIVCIVFNKKDLIQKRKVQWLMRTLIDDCAANGWGEYRTHLAFMDQIMETYNWNNSSFL  525 (560)
T ss_dssp             CCEEEEECSSC--------EEEEEEEEEETTCHHHHHHHHHHHHHHHHHHHHTTCCBSCCCGGGHHHHHHHTCHHHHHHH
T ss_pred             eEEEEEecCCe--------EEEEecccCCCCCHHHHHHHHHHHHHHHHHHHHcCCcccccchhHHHHHHHHhccCCHHHH
Confidence            67999999999        99943   22222222223344444444433110000000         1111   34567


Q ss_pred             HHHHHHHHhcCCcceec
Q 027264           83 GLGLTLKYFFDKKVTIN   99 (226)
Q Consensus        83 ~l~~~~~~~f~~~~~~~   99 (226)
                      .++..+|..|||..++|
T Consensus       526 ~lm~~iK~~~DP~gILN  542 (560)
T 1e8g_A          526 RFNEVLKNAVDPNGIIA  542 (560)
T ss_dssp             HHHHHHHHHHCTTCCBC
T ss_pred             HHHHHHHHHcCccCCCC
Confidence            88999999999999998

>3or1_A Sulfite reductase alpha; dissimilatory sulfite reductase, sulfate reduction, oxidored sulfite reduction; HET: SRM; 1.76A {Desulfovibrio gigas} PDB: 3or2_A* 2v4j_A* 2xsj_A*

Probab=87.79  E-value=0.11  Score=46.20  Aligned_cols=23  Identities=17%  Similarity=0.463  Sum_probs=19.4

Q ss_pred             CCCccccccccccchhccccccc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAI  142 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai  142 (226)
                      +.++.++|+.||.|+.+||..+.
T Consensus       296 l~Id~~~C~~Cg~Ci~~CP~al~  318 (437)
T 3or1_A          296 LSIDNKNCTRCMHCINTMPRALK  318 (437)
T ss_dssp             EEECGGGCCCCSHHHHHCTTTEE
T ss_pred             EEEccccCCchhhhHhhCcHhhc
Confidence            44678899999999999999554

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=86.04  E-value=0.19  Score=46.47  Aligned_cols=23  Identities=39%  Similarity=0.911  Sum_probs=20.2

Q ss_pred             Cccccccccccchhccccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITI  144 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~  144 (226)
                      +..+.|++||.|++.||..+|.+
T Consensus        64 i~e~~c~gc~~~~~~~p~~~i~i   86 (607)
T 3bk7_A           64 IQEASCTGCGICVHKCPFNAISI   86 (607)
T ss_dssp             ECTTTCCCCCHHHHHCSSCCCEE
T ss_pred             eeecccCccccccCCCCcceEEE
Confidence            45678999999999999988776

>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D

Probab=84.21  E-value=0.24  Score=40.85  Aligned_cols=24  Identities=29%  Similarity=0.613  Sum_probs=19.7

Q ss_pred             Cccccccccccchhccccccccchh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .+..+|+.||.|+.+|| +++.+..
T Consensus       198 ~d~~~C~~C~~C~~vCp-~aI~~~~  221 (265)
T 2pa8_D          198 KNELSCTLCEECLRYCN-GSIRISF  221 (265)
T ss_dssp             SCGGGCCCCCHHHHHHT-TSEEEEE
T ss_pred             eccccCCCchHHHHhCC-CceEEEe
Confidence            34579999999999999 8887643

>1wvf_A 4-cresol dehydrogenase [hydroxylating] flavoprote subunit; flavoprotein, electron-transfer, FAD, oxidoreductase; HET: FAD; 1.30A {Pseudomonas putida} SCOP: d.58.32.1 d.145.1.1 PDB: 1wve_A* 1dii_A* 1diq_A*

Probab=84.01  E-value=0.27  Score=44.44  Aligned_cols=74  Identities=8%  Similarity=0.042  Sum_probs=42.2

Q ss_pred             hhHhhhhccCCcccCcccccCCCC-CCCCCchhH--HHHHHHHHHHhhhHHHHHHHHHH---------HhhhHHHHHHHH
Q 027264           18 LAVSGQALQGSQHYGLRFNAHPYS-SYFPSKKDD--EEKEQLLKEISKDWSSVFERSIN---------MLFLTEMVRGLG   85 (226)
Q Consensus        18 ~~i~Gha~~gn~~~~~~~~~H~~~-~~~~~~~p~--~~~~~~~~~~~~~v~~~~~~~i~---------~~~~~~~~~~l~   85 (226)
                      ..++||+.+||        +|++. +.+....+.  ++..+.++++.+.+...=.+..+         ...+.+....++
T Consensus       423 ~~~~gh~gdGn--------lH~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ehG~G~~k~~~~~~~~~~~~~g~~~~~lm  494 (520)
T 1wvf_A          423 YVAEFIVAPRD--------MHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLE  494 (520)
T ss_dssp             CCEEEEECSSE--------EEEEEEEEEETTCHHHHHHHHHHHHHHHHHHHHTTCCBSCCCGGGHHHHHHHTCHHHHHHH
T ss_pred             eeEeecccCcc--------eeeeeccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCccccChhHhhhhhhhcCHHHHHHH
Confidence            56899999999        99842 223222222  23344444444433210000110         112224577899


Q ss_pred             HHHHHhcCCcceec
Q 027264           86 LTLKYFFDKKVTIN   99 (226)
Q Consensus        86 ~~~~~~f~~~~~~~   99 (226)
                      ..+|..|||...+|
T Consensus       495 r~IK~a~DP~~IlN  508 (520)
T 1wvf_A          495 HAIKRAVDPNNILA  508 (520)
T ss_dssp             HHHHHHHCTTCCBC
T ss_pred             HHHHHHcCCCCCCC
Confidence            99999999999998

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	226
d2fug91	154	d.58.1.5 (9:26-179) NADH-quinone oxidoreductase ch	6e-41
d2fdna_	55	d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici	3e-17
d2fdna_	55	d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici	3e-04
d1jb0c_	80	d.58.1.2 (C:) Photosystem I iron-sulfur protein Ps	5e-17
d1jb0c_	80	d.58.1.2 (C:) Photosystem I iron-sulfur protein Ps	6e-06
d1blua_	80	d.58.1.1 (A:) Ferredoxin II {Chromatium vinosum [T	7e-16
d1xera_	103	d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp.	5e-15
d1xera_	103	d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp.	1e-05
d1xera_	103	d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp.	2e-04
d1dura_	55	d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus as	1e-14
d1dura_	55	d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus as	3e-04
d1dura_	55	d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus as	3e-04
d1rgva_	80	d.58.1.1 (A:) Ferredoxin II {Thauera aromatica [Ta	3e-14
d1hfel2	85	d.58.1.5 (L:2-86) Fe-only hydrogenase larger subun	4e-14
d1hfel2	85	d.58.1.5 (L:2-86) Fe-only hydrogenase larger subun	2e-04
d1fxda_	58	d.58.1.4 (A:) Ferredoxin I {Desulfovibrio gigas [T	6e-14
d1gtea5	173	d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogen	2e-13
d1gtea5	173	d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogen	4e-04
d3c8ya3	83	d.58.1.5 (A:127-209) Fe-only hydrogenase, second d	6e-12
d3c8ya3	83	d.58.1.5 (A:127-209) Fe-only hydrogenase, second d	5e-04
d1sj1a_	66	d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus	1e-11
d1sj1a_	66	d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus	6e-04
d1sj1a_	66	d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus	7e-04
d2c42a5	117	d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoredu	2e-10
d2c42a5	117	d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoredu	0.003
d1vjwa_	59	d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [T	3e-10
d1vjwa_	59	d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [T	0.002
d1vjwa_	59	d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [T	0.003
d1jnrb_	149	d.58.1.5 (B:) Adenylylsulfate reductase B subunit	3e-10
d1jnrb_	149	d.58.1.5 (B:) Adenylylsulfate reductase B subunit	0.002
d1bc6a_	77	d.58.1.2 (A:) Ferredoxin {Bacillus schlegelii [Tax	1e-09
d1fxra_	64	d.58.1.4 (A:) Ferredoxin I {Sulfate-reducing bacte	4e-09
d1h98a_	77	d.58.1.2 (A:) Ferredoxin {Thermus thermophilus [Ta	6e-09
d3c7bb1	65	d.58.1.5 (B:197-261) DsrB insert domain {Archaeogl	1e-08
d1iqza_	81	d.58.1.4 (A:) Ferredoxin {Bacillus thermoproteolyt	1e-08
d7fd1a_	106	d.58.1.2 (A:) Ferredoxin {Azotobacter vinelandii [	2e-06
d1kqfb1	244	d.58.1.5 (B:2-245) Formate dehydrogenase N, iron-s	5e-06
d1y5ib1	509	d.58.1.5 (B:1-509) Respiratory nitrate reductase 1	8e-06
d1y5ib1	509	d.58.1.5 (B:1-509) Respiratory nitrate reductase 1	2e-05
d2fug34	151	d.58.1.5 (3:96-246) NADH-quinone oxidoreductase ch	1e-05
d2bs2b1	133	a.1.2.1 (B:107-239) Fumarate reductase {Wolinella	0.001

>d2fug91 d.58.1.5 (9:26-179) NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus thermophilus [TaxId: 274]} Length = 154

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: NADH-quinone oxidoreductase chain 9, Nqo9
species: Thermus thermophilus [TaxId: 274]

 Score =  134 bits (339), Expect = 6e-41
 Identities = 52/128 (40%), Positives = 70/128 (54%), Gaps = 8/128 (6%)

Query: 100 YPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIE------AEEREDGS 153
           YP     L PRF G H L R+P G E+CI C LC A CPA AI +E            G 
Sbjct: 1   YPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAAACPAYAIYVEPAENDPENPVSAGE 60

Query: 154 RRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLEN--GDRW 211
           R    Y+I+M +CI+CG C+EACP  AIV G +FE +   + +L+Y KE +L +  G + 
Sbjct: 61  RYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTKP 120

Query: 212 ETEIAENL 219
           +   A+  
Sbjct: 121 QRREAKRT 128

>d2fdna_ d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici [TaxId: 1556]} Length = 55

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Clostridium acidurici [TaxId: 1556]

 Score = 70.8 bits (173), Expect = 3e-17
 Identities = 25/60 (41%), Positives = 28/60 (46%), Gaps = 10/60 (16%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
            E CI+C  CE  CP  AI+              RY ID   CI CG C   CPVDA V+
Sbjct: 5   NEACISCGACEPECPVNAISSG----------DDRYVIDADTCIDCGACAGVCPVDAPVQ 54

>d2fdna_ d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici [TaxId: 1556]} Length = 55

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Clostridium acidurici [TaxId: 1556]

 Score = 35.7 bits (82), Expect = 3e-04
 Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 165 KCIYCGFCQEACPVDAIVEGPN 186
            CI CG C+  CPV+AI  G +
Sbjct: 7   ACISCGACEPECPVNAISSGDD 28

>d1jb0c_ d.58.1.2 (C:) Photosystem I iron-sulfur protein PsaC {Synechococcus elongatus [TaxId: 32046]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Photosystem I iron-sulfur protein PsaC
species: Synechococcus elongatus [TaxId: 32046]

 Score = 70.9 bits (173), Expect = 5e-17
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 6/67 (8%)

Query: 115 HALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQE 174
           H ++ Y    + CI C  C   CP   + +   +     +           C+ C  C+ 
Sbjct: 2   HTVKIY----DTCIGCTQCVRACPTDVLEMVPWDGCKAGQI--ASSPRTEDCVGCKRCET 55

Query: 175 ACPVDAI 181
           ACP D +
Sbjct: 56  ACPTDFL 62

>d1jb0c_ d.58.1.2 (C:) Photosystem I iron-sulfur protein PsaC {Synechococcus elongatus [TaxId: 32046]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Photosystem I iron-sulfur protein PsaC
species: Synechococcus elongatus [TaxId: 32046]

 Score = 40.9 bits (95), Expect = 6e-06
 Identities = 12/56 (21%), Positives = 20/56 (35%)

Query: 101 PFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRT 156
           P +   + P    +          E C+ CK CE  CP   ++I      + +R  
Sbjct: 21  PTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSM 76

>d1blua_ d.58.1.1 (A:) Ferredoxin II {Chromatium vinosum [TaxId: 1049]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Chromatium vinosum [TaxId: 1049]

 Score = 67.9 bits (165), Expect = 7e-16
 Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 19/87 (21%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GFCQEACP 177
            + CI C +CE  CP  AI+          +    Y I+ + C  C        C E CP
Sbjct: 5   TDECINCDVCEPECPNGAIS----------QGDETYVIEPSLCTECVGHYETSQCVEVCP 54

Query: 178 VDAIVEGPNFEYSTETHEELLYDKEKL 204
           VD I++ P+ E   ET +EL    E++
Sbjct: 55  VDCIIKDPSHE---ETEDELRAKYERI 78

>d1xera_ d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Archaeal ferredoxins
domain: Ferredoxin
species: Archaeon Sulfolobus sp. [TaxId: 2288]

 Score = 66.3 bits (161), Expect = 5e-15
 Identities = 17/63 (26%), Positives = 24/63 (38%), Gaps = 2/63 (3%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI-V 182
            + CIA   C   CP        +     +       ++   CI+C  C   CPV AI V
Sbjct: 42  FDLCIADGSCINACPVNVFQWY-DTPGHPASEKKADPVNEQACIFCMACVNVCPVAAIDV 100

Query: 183 EGP 185
           + P
Sbjct: 101 KPP 103

>d1xera_ d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Archaeal ferredoxins
domain: Ferredoxin
species: Archaeon Sulfolobus sp. [TaxId: 2288]

 Score = 40.5 bits (94), Expect = 1e-05
 Identities = 11/59 (18%), Positives = 19/59 (32%)

Query: 145 EAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEK 203
             E  +      T   +D   CI  G C  ACPV+         +     +    +++ 
Sbjct: 24  PVEPPKVLGIHGTIVGVDFDLCIADGSCINACPVNVFQWYDTPGHPASEKKADPVNEQA 82

>d1xera_ d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Archaeal ferredoxins
domain: Ferredoxin
species: Archaeon Sulfolobus sp. [TaxId: 2288]

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 11/28 (39%), Positives = 15/28 (53%)

Query: 118 RRYPTGEERCIACKLCEAVCPAQAITIE 145
           +  P  E+ CI C  C  VCP  AI ++
Sbjct: 74  KADPVNEQACIFCMACVNVCPVAAIDVK 101

>d1dura_ d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus asaccharolyticus [TaxId: 1258]} Length = 55

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Peptostreptococcus asaccharolyticus [TaxId: 1258]

 Score = 63.9 bits (155), Expect = 1e-14
 Identities = 20/58 (34%), Positives = 23/58 (39%), Gaps = 11/58 (18%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            + CIAC  C+  CP   I              + Y ID   CI CG C   CPV A 
Sbjct: 5   NDSCIACGACKPECPVNCIQEG-----------SIYAIDADSCIDCGSCASVCPVGAP 51

>d1dura_ d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus asaccharolyticus [TaxId: 1258]} Length = 55

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Peptostreptococcus asaccharolyticus [TaxId: 1258]

 Score = 35.7 bits (82), Expect = 3e-04
 Identities = 9/22 (40%), Positives = 11/22 (50%)

Query: 124 EERCIACKLCEAVCPAQAITIE 145
            + CI C  C +VCP  A   E
Sbjct: 33  ADSCIDCGSCASVCPVGAPNPE 54

>d1dura_ d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus asaccharolyticus [TaxId: 1258]} Length = 55

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Peptostreptococcus asaccharolyticus [TaxId: 1258]

 Score = 35.3 bits (81), Expect = 3e-04
 Identities = 11/32 (34%), Positives = 16/32 (50%)

Query: 161 IDMTKCIYCGFCQEACPVDAIVEGPNFEYSTE 192
           +    CI CG C+  CPV+ I EG  +    +
Sbjct: 3   VINDSCIACGACKPECPVNCIQEGSIYAIDAD 34

>d1rgva_ d.58.1.1 (A:) Ferredoxin II {Thauera aromatica [TaxId: 59405]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Thauera aromatica [TaxId: 59405]

 Score = 63.3 bits (153), Expect = 3e-14
 Identities = 27/87 (31%), Positives = 36/87 (41%), Gaps = 19/87 (21%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GFCQEACP 177
            + C AC  C   CP +AI          +     Y ID TKC  C        C+  CP
Sbjct: 5   NDDCTACDACVEECPNEAI----------TPGDPIYVIDPTKCSECVGAFDEPQCRLVCP 54

Query: 178 VDAIVEGPNFEYSTETHEELLYDKEKL 204
            D I + P++    ET EEL    ++L
Sbjct: 55  ADCIPDNPDYR---ETREELQEKYDRL 78

>d1hfel2 d.58.1.5 (L:2-86) Fe-only hydrogenase larger subunit, N-domain {Desulfovibrio desulfuricans [TaxId: 876]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Fe-only hydrogenase larger subunit, N-domain
species: Desulfovibrio desulfuricans [TaxId: 876]

 Score = 63.2 bits (153), Expect = 4e-14
 Identities = 21/60 (35%), Positives = 24/60 (40%), Gaps = 8/60 (13%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
           E +CI C  C   CP  AI  E  E              +  CI CG C   CP +AI E
Sbjct: 31  EAKCIGCDTCSQYCPTAAIFGEMGEP--------HSIPHIEACINCGQCLTHCPENAIYE 82

>d1hfel2 d.58.1.5 (L:2-86) Fe-only hydrogenase larger subunit, N-domain {Desulfovibrio desulfuricans [TaxId: 876]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Fe-only hydrogenase larger subunit, N-domain
species: Desulfovibrio desulfuricans [TaxId: 876]

 Score = 37.0 bits (85), Expect = 2e-04
 Identities = 11/21 (52%), Positives = 12/21 (57%)

Query: 161 IDMTKCIYCGFCQEACPVDAI 181
           ID  KCI C  C + CP  AI
Sbjct: 29  IDEAKCIGCDTCSQYCPTAAI 49

>d1fxda_ d.58.1.4 (A:) Ferredoxin I {Desulfovibrio gigas [TaxId: 879]} Length = 58

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin I
species: Desulfovibrio gigas [TaxId: 879]

 Score = 62.3 bits (151), Expect = 6e-14
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 7/60 (11%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
            + C+AC+ C  +CP           E+G +           C+      ++CP +AIV 
Sbjct: 5   NDDCMACEACVEICPDVFEMN-----EEGDKAVVINPDSDLDCVEE--AIDSCPAEAIVR 57

>d1gtea5 d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogenase, C-terminal domain {Pig (Sus scrofa) [TaxId: 9823]} Length = 173

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Dihydropyrimidine dehydrogenase, C-terminal domain
species: Pig (Sus scrofa) [TaxId: 9823]

 Score = 64.0 bits (155), Expect = 2e-13
 Identities = 16/59 (27%), Positives = 18/59 (30%), Gaps = 7/59 (11%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV-DAI 181
           EE CI C  C   C          + E      T        C  C  C   CP+ D I
Sbjct: 106 EEMCINCGKCYMTCNDSGYQAIQFDPE------THLPTVTDTCTGCTLCLSVCPIIDCI 158

>d1gtea5 d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogenase, C-terminal domain {Pig (Sus scrofa) [TaxId: 9823]} Length = 173

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Dihydropyrimidine dehydrogenase, C-terminal domain
species: Pig (Sus scrofa) [TaxId: 9823]

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 1/40 (2%)

Query: 118 RRYPTGEERCIACKLCEAVCPAQ-AITIEAEEREDGSRRT 156
              PT  + C  C LC +VCP    I + +       +R 
Sbjct: 133 THLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKRG 172

>d3c8ya3 d.58.1.5 (A:127-209) Fe-only hydrogenase, second domain {Clostridium pasteurianum [TaxId: 1501]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Fe-only hydrogenase, second domain
species: Clostridium pasteurianum [TaxId: 1501]

 Score = 57.5 bits (138), Expect = 6e-12
 Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 124 EERCIACKLCEAVCPAQAIT--IEAEEREDGSRRTT--RYDIDMTKCIYCGFCQEACPVD 179
             +C+ C  C   C     T  ++   +   +          D T C+ CG C  ACPV 
Sbjct: 18  RTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVA 77

Query: 180 AIVE 183
           A+ E
Sbjct: 78  ALSE 81

>d3c8ya3 d.58.1.5 (A:127-209) Fe-only hydrogenase, second domain {Clostridium pasteurianum [TaxId: 1501]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Fe-only hydrogenase, second domain
species: Clostridium pasteurianum [TaxId: 1501]

 Score = 35.6 bits (81), Expect = 5e-04
 Identities = 11/47 (23%), Positives = 17/47 (36%)

Query: 161 IDMTKCIYCGFCQEACPVDAIVEGPNFEYSTETHEELLYDKEKLLEN 207
           +D TKC+ CG C  AC  +       F            D++   + 
Sbjct: 16  VDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDT 62

>d1sj1a_ d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxId: 2261]} Length = 66

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Fe3S4-ferredoxin PF1909
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 56.3 bits (135), Expect = 1e-11
 Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 4/58 (6%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
           ++ CI   +C ++CP      +    E  ++       D           EACPV AI
Sbjct: 8   QDTCIGDAICASLCPDVFEMND----EGKAQPKVEVIEDEELYNCAKEAMEACPVSAI 61

>d1sj1a_ d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxId: 2261]} Length = 66

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Fe3S4-ferredoxin PF1909
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 35.1 bits (80), Expect = 6e-04
 Identities = 6/26 (23%), Positives = 9/26 (34%)

Query: 158 RYDIDMTKCIYCGFCQEACPVDAIVE 183
           +  +D   CI    C   CP    + 
Sbjct: 3   KVSVDQDTCIGDAICASLCPDVFEMN 28

>d1sj1a_ d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxId: 2261]} Length = 66

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Fe3S4-ferredoxin PF1909
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 34.8 bits (79), Expect = 7e-04
 Identities = 10/31 (32%), Positives = 10/31 (32%)

Query: 115 HALRRYPTGEERCIACKLCEAVCPAQAITIE 145
                    EE     K     CP  AITIE
Sbjct: 34  QPKVEVIEDEELYNCAKEAMEACPVSAITIE 64

>d2c42a5 d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoreductase, PFOR, domain V {Desulfovibrio africanus [TaxId: 873]} Length = 117

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Pyruvate-ferredoxin oxidoreductase, PFOR, domain V
species: Desulfovibrio africanus [TaxId: 873]

 Score = 54.5 bits (130), Expect = 2e-10
 Identities = 25/95 (26%), Positives = 32/95 (33%), Gaps = 29/95 (30%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTT-----------------RYDIDMTKC 166
            E CI C  C  VCP  AI     + E+                       R  I+   C
Sbjct: 18  PENCIQCNQCAFVCPHSAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDC 77

Query: 167 IYCGFCQEACPV--DAIV----------EGPNFEY 189
           + CG C + CP    A+V          + PN EY
Sbjct: 78  MGCGNCADICPPKEKALVMQPLDTQRDAQVPNLEY 112

>d2c42a5 d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoreductase, PFOR, domain V {Desulfovibrio africanus [TaxId: 873]} Length = 117

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Pyruvate-ferredoxin oxidoreductase, PFOR, domain V
species: Desulfovibrio africanus [TaxId: 873]

 Score = 34.1 bits (77), Expect = 0.003
 Identities = 8/21 (38%), Positives = 8/21 (38%)

Query: 161 IDMTKCIYCGFCQEACPVDAI 181
                CI C  C   CP  AI
Sbjct: 16  WVPENCIQCNQCAFVCPHSAI 36

>d1vjwa_ d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [TaxId: 2336]} Length = 59

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin A
species: Thermotoga maritima [TaxId: 2336]

 Score = 52.2 bits (124), Expect = 3e-10
 Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 8/58 (13%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            + CI C +CE +CP      +            +     T         ++CP  AI
Sbjct: 7   ADACIGCGVCENLCPDVFQLGD--------DGKAKVLQPETDLPCAKDAADSCPTGAI 56

>d1vjwa_ d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [TaxId: 2336]} Length = 59

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin A
species: Thermotoga maritima [TaxId: 2336]

 Score = 33.7 bits (76), Expect = 0.002
 Identities = 8/26 (30%), Positives = 12/26 (46%)

Query: 158 RYDIDMTKCIYCGFCQEACPVDAIVE 183
           +  +D   CI CG C+  CP    + 
Sbjct: 2   KVRVDADACIGCGVCENLCPDVFQLG 27

>d1vjwa_ d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [TaxId: 2336]} Length = 59

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin A
species: Thermotoga maritima [TaxId: 2336]

 Score = 33.3 bits (75), Expect = 0.003
 Identities = 8/34 (23%), Positives = 12/34 (35%)

Query: 112 RGEHALRRYPTGEERCIACKLCEAVCPAQAITIE 145
            G+    +    E      K     CP  AI++E
Sbjct: 26  LGDDGKAKVLQPETDLPCAKDAADSCPTGAISVE 59

>d1jnrb_ d.58.1.5 (B:) Adenylylsulfate reductase B subunit {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Adenylylsulfate reductase B subunit
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 54.5 bits (130), Expect = 3e-10
 Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 12/76 (15%)

Query: 124 EERCIACK-----LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV 178
            E+C  CK      CE +CP   +T++ E+ +        Y+ +   C  C  C + CP 
Sbjct: 6   PEKCDGCKALERTACEYICPNDLMTLDKEKMK-------AYNREPDMCWECYSCVKMCPQ 58

Query: 179 DAIVEGPNFEYSTETH 194
            AI      +YS    
Sbjct: 59  GAIDVRGYVDYSPLGG 74

>d1jnrb_ d.58.1.5 (B:) Adenylylsulfate reductase B subunit {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Adenylylsulfate reductase B subunit
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 35.2 bits (80), Expect = 0.002
 Identities = 7/31 (22%), Positives = 11/31 (35%), Gaps = 5/31 (16%)

Query: 161 IDMTKCIYCGF-----CQEACPVDAIVEGPN 186
           ++  KC  C       C+  CP D +     
Sbjct: 4   VNPEKCDGCKALERTACEYICPNDLMTLDKE 34

>d1bc6a_ d.58.1.2 (A:) Ferredoxin {Bacillus schlegelii [TaxId: 1484]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Bacillus schlegelii [TaxId: 1484]

 Score = 51.2 bits (122), Expect = 1e-09
 Identities = 25/82 (30%), Positives = 30/82 (36%), Gaps = 18/82 (21%)

Query: 124 EERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            E CI  K   C  VCP   I    +          +Y ID   CI CG C+  CPV AI
Sbjct: 5   TEPCIGTKDASCVEVCPVDCIHEGED----------QYYIDPDVCIDCGACEAVCPVSAI 54

Query: 182 VEGPNFEYSTETHEELLYDKEK 203
                  +     EE     +K
Sbjct: 55  Y------HEDFVPEEWKSYIQK 70

>d1fxra_ d.58.1.4 (A:) Ferredoxin I {Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873]} Length = 64

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin I
species: Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873]

 Score = 49.4 bits (117), Expect = 4e-09
 Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 6/64 (9%)

Query: 118 RRYPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACP 177
           R++   ++ CIAC+ C  + P           +    +    D++           + CP
Sbjct: 2   RKFYVDQDECIACESCVEIAPGAFA------MDPEIEKAYVKDVEGASQEEVEEAMDTCP 55

Query: 178 VDAI 181
           V  I
Sbjct: 56  VQCI 59

>d1h98a_ d.58.1.2 (A:) Ferredoxin {Thermus thermophilus [TaxId: 274]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Thermus thermophilus [TaxId: 274]

 Score = 49.3 bits (117), Expect = 6e-09
 Identities = 21/62 (33%), Positives = 26/62 (41%), Gaps = 12/62 (19%)

Query: 124 EERCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            E CI  K   C  VCP + I               ++ I   +CI CG C  ACPV+AI
Sbjct: 5   CEPCIGVKDQSCVEVCPVECIYDG----------GDQFYIHPEECIDCGACVPACPVNAI 54

Query: 182 VE 183
             
Sbjct: 55  YP 56

>d3c7bb1 d.58.1.5 (B:197-261) DsrB insert domain {Archaeoglobus fulgidus [TaxId: 2234]} Length = 65

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: DsrB insert domain
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 48.1 bits (114), Expect = 1e-08
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 13/62 (20%)

Query: 130 CKLCE-----AVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 184
            K CE     A CP  A+  +    ++ + +     +D+ KC+YCG C   CP   + + 
Sbjct: 12  RKTCEIPSTVAACPTGALKPD---MKNKTIK-----VDVEKCMYCGNCYTMCPGMPLFDP 63

Query: 185 PN 186
            N
Sbjct: 64  EN 65

>d1iqza_ d.58.1.4 (A:) Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1427]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin
species: Bacillus thermoproteolyticus [TaxId: 1427]

 Score = 48.6 bits (115), Expect = 1e-08
 Identities = 16/61 (26%), Positives = 21/61 (34%), Gaps = 5/61 (8%)

Query: 124 EERCIACKLCEAVCPAQAITIE---AEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
           +E CIAC  C A  P      E   A    D ++        +          E CP D+
Sbjct: 8   KETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDIL--IDDMMDAFEGCPTDS 65

Query: 181 I 181
           I
Sbjct: 66  I 66

>d7fd1a_ d.58.1.2 (A:) Ferredoxin {Azotobacter vinelandii [TaxId: 354]} Length = 106

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Azotobacter vinelandii [TaxId: 354]

 Score = 43.1 bits (101), Expect = 2e-06
 Identities = 17/61 (27%), Positives = 20/61 (32%), Gaps = 12/61 (19%)

Query: 124 EERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 181
            + CI CK   C  VCP                      I   +CI C  C+  CP  AI
Sbjct: 5   TDNCIKCKYTDCVEVCPVDCFYEGPN----------FLVIHPDECIDCALCEPECPAQAI 54

Query: 182 V 182
            
Sbjct: 55  F 55

>d1kqfb1 d.58.1.5 (B:2-245) Formate dehydrogenase N, iron-sulfur (beta) subunit {Escherichia coli [TaxId: 562]} Length = 244

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Formate dehydrogenase N, iron-sulfur (beta) subunit
species: Escherichia coli [TaxId: 562]

 Score = 43.7 bits (102), Expect = 5e-06
 Identities = 20/83 (24%), Positives = 28/83 (33%), Gaps = 3/83 (3%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 184
           E CI C  C A CP     +    +ED         +D         C + CP  AI  G
Sbjct: 130 ENCIGCGYCIAGCPFNIPRLN---KEDNRVYKCTLCVDRVSVGQEPACVKTCPTGAIHFG 186

Query: 185 PNFEYSTETHEELLYDKEKLLEN 207
              E      + +   K +  E+
Sbjct: 187 TKKEMLELAEQRVAKLKARGYEH 209

>d1y5ib1 d.58.1.5 (B:1-509) Respiratory nitrate reductase 1 beta chain {Escherichia coli [TaxId: 562]} Length = 509

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Respiratory nitrate reductase 1 beta chain
species: Escherichia coli [TaxId: 562]

 Score = 43.6 bits (102), Expect = 8e-06
 Identities = 20/61 (32%), Positives = 22/61 (36%), Gaps = 9/61 (14%)

Query: 121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDA 180
           P   E C+    C A CP+ AI       EDG        ID  KC     C   CP   
Sbjct: 181 PRLCEHCLN-PACVATCPSGAIYKR---EEDG-----IVLIDQDKCRGWRMCITGCPYKK 231

Query: 181 I 181
           I
Sbjct: 232 I 232

>d1y5ib1 d.58.1.5 (B:1-509) Respiratory nitrate reductase 1 beta chain {Escherichia coli [TaxId: 562]} Length = 509

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Respiratory nitrate reductase 1 beta chain
species: Escherichia coli [TaxId: 562]

 Score = 42.8 bits (100), Expect = 2e-05
 Identities = 10/61 (16%), Positives = 19/61 (31%), Gaps = 3/61 (4%)

Query: 124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 183
           +++C   ++C   CP + I    +    G      +     +      C E C       
Sbjct: 214 QDKCRGWRMCITGCPYKKIYFNWK---SGKSEKCIFCYPRIEAGQPTVCSETCVGRIRYL 270

Query: 184 G 184
           G
Sbjct: 271 G 271

>d2fug34 d.58.1.5 (3:96-246) NADH-quinone oxidoreductase chain 3, Nqo3, domain 2 {Thermus thermophilus [TaxId: 274]} Length = 151

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: NADH-quinone oxidoreductase chain 3, Nqo3, domain 2
species: Thermus thermophilus [TaxId: 274]

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 14/61 (22%), Positives = 20/61 (32%)

Query: 125 ERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 184
           ERCI CK C             +  E G               + G   + CPV A+++ 
Sbjct: 84  ERCIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSGFSGNITDICPVGALLDL 143

Query: 185 P 185
            
Sbjct: 144 T 144

>d2bs2b1 a.1.2.1 (B:107-239) Fumarate reductase {Wolinella succinogenes [TaxId: 844]} Length = 133

class: All alpha proteins
fold: Globin-like
superfamily: alpha-helical ferredoxin
family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
domain: Fumarate reductase
species: Wolinella succinogenes [TaxId: 844]

 Score = 35.7 bits (81), Expect = 0.001
 Identities = 16/97 (16%), Positives = 29/97 (29%), Gaps = 20/97 (20%)

Query: 101 PFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPA--------------QAITIEA 146
             +   L  R   E A   +    +RCI C  C A C                + +    
Sbjct: 21  EHDISKLEERIEPEVAQEVF--ELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMI 78

Query: 147 EEREDGSRRTTRYDID----MTKCIYCGFCQEACPVD 179
           +  ++ +       I     +  C+    C + CP +
Sbjct: 79  DPHDERTDEDYYELIGDDDGVFGCMTLLACHDVCPKN 115

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	226
d2fug91	154	NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus	99.81
d2fdna_	55	Ferredoxin II {Clostridium acidurici [TaxId: 1556]	99.48
d1hfel2	85	Fe-only hydrogenase larger subunit, N-domain {Desu	99.48
d1dura_	55	Ferredoxin II {Peptostreptococcus asaccharolyticus	99.47
d1bc6a_	77	Ferredoxin {Bacillus schlegelii [TaxId: 1484]}	99.47
d1rgva_	80	Ferredoxin II {Thauera aromatica [TaxId: 59405]}	99.46
d1blua_	80	Ferredoxin II {Chromatium vinosum [TaxId: 1049]}	99.45
d1h98a_	77	Ferredoxin {Thermus thermophilus [TaxId: 274]}	99.45
d1jb0c_	80	Photosystem I iron-sulfur protein PsaC {Synechococ	99.43
d1xera_	103	Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}	99.39
d3c8ya3	83	Fe-only hydrogenase, second domain {Clostridium pa	99.38
d7fd1a_	106	Ferredoxin {Azotobacter vinelandii [TaxId: 354]}	99.35
d2c42a5	117	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	99.33
d1jnrb_	149	Adenylylsulfate reductase B subunit {Archaeon Arch	99.27
d1vjwa_	59	Ferredoxin A {Thermotoga maritima [TaxId: 2336]}	99.17
d1gtea5	173	Dihydropyrimidine dehydrogenase, C-terminal domain	99.16
d1fxra_	64	Ferredoxin I {Sulfate-reducing bacteria (Desulfovi	99.16
d1fxda_	58	Ferredoxin I {Desulfovibrio gigas [TaxId: 879]}	99.09
d1sj1a_	66	Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxI	99.08
d3c7bb1	65	DsrB insert domain {Archaeoglobus fulgidus [TaxId:	99.08
d2fug34	151	NADH-quinone oxidoreductase chain 3, Nqo3, domain	99.04
d1iqza_	81	Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1	98.77
d1kqfb1	244	Formate dehydrogenase N, iron-sulfur (beta) subuni	98.65
d1kqfb1	244	Formate dehydrogenase N, iron-sulfur (beta) subuni	98.59
d1vlfn2	195	Transhydroxylase beta subunit, BthL, N-terminal do	98.55
d1nekb1	132	Succinate dehydogenase {Escherichia coli [TaxId: 5	98.54
d1y5ib1	509	Respiratory nitrate reductase 1 beta chain {Escher	98.5
d1y5ib1	509	Respiratory nitrate reductase 1 beta chain {Escher	98.49
d1kf6b1	138	Fumarate reductase {Escherichia coli [TaxId: 562]}	98.37
d2bs2b1	133	Fumarate reductase {Wolinella succinogenes [TaxId:	98.33
d1vlfn2	195	Transhydroxylase beta subunit, BthL, N-terminal do	98.33
d1h0hb_	214	Tungsten containing formate dehydrogenase, small s	98.17
d1hfel2	85	Fe-only hydrogenase larger subunit, N-domain {Desu	97.54
d1dura_	55	Ferredoxin II {Peptostreptococcus asaccharolyticus	97.53
d1blua_	80	Ferredoxin II {Chromatium vinosum [TaxId: 1049]}	97.42
d2v4jb1	69	DsrB insert domain {Desulfovibrio vulgaris [TaxId:	97.4
d1bc6a_	77	Ferredoxin {Bacillus schlegelii [TaxId: 1484]}	97.37
d2fdna_	55	Ferredoxin II {Clostridium acidurici [TaxId: 1556]	97.37
d1h98a_	77	Ferredoxin {Thermus thermophilus [TaxId: 274]}	97.36
d1rgva_	80	Ferredoxin II {Thauera aromatica [TaxId: 59405]}	97.26
d1xera_	103	Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}	97.2
d1jb0c_	80	Photosystem I iron-sulfur protein PsaC {Synechococ	97.19
d7fd1a_	106	Ferredoxin {Azotobacter vinelandii [TaxId: 354]}	97.13
d1vjwa_	59	Ferredoxin A {Thermotoga maritima [TaxId: 2336]}	97.09
d2fug91	154	NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus	97.07
d3c8ya3	83	Fe-only hydrogenase, second domain {Clostridium pa	97.03
d3c7bb1	65	DsrB insert domain {Archaeoglobus fulgidus [TaxId:	97.03
d2gmha3	102	Electron transfer flavoprotein-ubiquinone oxidored	96.98
d1h0hb_	214	Tungsten containing formate dehydrogenase, small s	96.7
d1sj1a_	66	Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxI	96.56
d2c42a5	117	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	96.55
d1jnrb_	149	Adenylylsulfate reductase B subunit {Archaeon Arch	96.45
d1fxra_	64	Ferredoxin I {Sulfate-reducing bacteria (Desulfovi	96.33
d1gtea5	173	Dihydropyrimidine dehydrogenase, C-terminal domain	96.04
d1fxda_	58	Ferredoxin I {Desulfovibrio gigas [TaxId: 879]}	95.97
d3c7ba1	66	DsrA insert domain {Archaeoglobus fulgidus [TaxId:	95.76
d2fug34	151	NADH-quinone oxidoreductase chain 3, Nqo3, domain	95.72
d1iqza_	81	Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1	95.24
d2v4ja1	81	DsrA insert domain {Desulfovibrio vulgaris [TaxId:	95.02
d1e8ga1	287	Vanillyl-alcohol oxidase {Fungus (Penicillium simp	93.68
d1nekb1	132	Succinate dehydogenase {Escherichia coli [TaxId: 5	91.67
d2bs2b1	133	Fumarate reductase {Wolinella succinogenes [TaxId:	91.33
d2gmha3	102	Electron transfer flavoprotein-ubiquinone oxidored	90.94
d1wvfa1	279	Flavoprotein subunit of p-cresol methylhydroxylase	90.04
d2v4jb1	69	DsrB insert domain {Desulfovibrio vulgaris [TaxId:	89.7
d1kf6b1	138	Fumarate reductase {Escherichia coli [TaxId: 562]}	89.19
d1gtea1	182	Dihydropyrimidine dehydrogenase, N-terminal domain	81.1

>d2fug91 d.58.1.5 (9:26-179) NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: NADH-quinone oxidoreductase chain 9, Nqo9
species: Thermus thermophilus [TaxId: 274]

Probab=99.81  E-value=3.5e-21  Score=147.86  Aligned_cols=113  Identities=45%  Similarity=0.892  Sum_probs=91.3

Q ss_pred             CccccCCCCCCccCccccccCCCccccccccccchhccccccccchhhhhc------cCCccccccccCCCCCCcchhhh
Q 027264          100 YPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAVCPAQAITIEAEERE------DGSRRTTRYDIDMTKCIYCGFCQ  173 (226)
Q Consensus       100 ~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~------~~~~~~~~~~~d~~~C~~Cg~Cv  173 (226)
                      ||+.+..++++|+|.+.+...+.+.++||+|+.|+.+||+.++........      .+.+....+.++...|++||.|+
T Consensus         1 YP~e~~~~~~r~RG~~~l~~~~~~~ekCI~C~~C~~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~~id~~~C~~CG~Cv   80 (154)
T d2fug91           1 YPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAAACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCE   80 (154)
T ss_dssp             CCSSCEECCTTCCCSEEECBCTTSCBSCCCCTHHHHHCSSCCEEEEEEECCSSSCSBSSSEEEEEEEEETTTCCCCTHHH
T ss_pred             CCCCCCCCCCCcCCceecccCCCCcccCcCCCcHHhhcCCcceeccccccccccccccccccceeEEeccccCCCCCCch
Confidence            788888888999999988777777889999999999999998876443211      11223344678889999999999


Q ss_pred             hcCcccccccCCCcccchhcHHHhhcCHHHHhhcCCCch
Q 027264          174 EACPVDAIVEGPNFEYSTETHEELLYDKEKLLENGDRWE  212 (226)
Q Consensus       174 ~~CP~~Ai~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~  212 (226)
                      .+||++||.++++|++++.++.+++++...++....++.
T Consensus        81 e~CPt~AI~~~~~~e~~~~~r~~l~~~k~~ll~~~~~~~  119 (154)
T d2fug91          81 EACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTK  119 (154)
T ss_dssp             HHCSSSCEEECSCCCCCBSCGGGSEECSTTTBTTCCSCH
T ss_pred             hhCCCCeEeccCccccccCCHHHhccCHHHhhhcccCCc
Confidence            999999999999999999999999998887765544433

>d2fdna_ d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici [TaxId: 1556]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Clostridium acidurici [TaxId: 1556]

Probab=99.48  E-value=4.3e-15  Score=93.78  Aligned_cols=50  Identities=50%  Similarity=1.022  Sum_probs=43.7

Q ss_pred             ccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      ..++|++||.|+++||+++|...+.          .+.++.+.|++||.|+.+||++||.
T Consensus         4 i~e~C~~Cg~C~~~Cp~~ai~~~~~----------~~~i~~~~C~~Cg~C~~~CP~~AI~   53 (55)
T d2fdna_           4 INEACISCGACEPECPVNAISSGDD----------RYVIDADTCIDCGACAGVCPVDAPV   53 (55)
T ss_dssp             ECTTCCCCCTTGGGCTTCCEECCSS----------SCEECTTTCCCCCHHHHTCTTCCEE
T ss_pred             eCcCCCChhhHHHhcCccceEcCCc----------eEEECHHHCCCCCChhcccCCCCcC
Confidence            4579999999999999999987653          3467888999999999999999986

>d1hfel2 d.58.1.5 (L:2-86) Fe-only hydrogenase larger subunit, N-domain {Desulfovibrio desulfuricans [TaxId: 876]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Fe-only hydrogenase larger subunit, N-domain
species: Desulfovibrio desulfuricans [TaxId: 876]

Probab=99.48  E-value=6.9e-15  Score=101.17  Aligned_cols=57  Identities=37%  Similarity=0.747  Sum_probs=46.5

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      +.+|.++|++||.|+.+||+++|..+....        ...++.+.|++||.|+.+||++||...
T Consensus        27 ~~id~~~Ci~C~~Cv~~Cp~~ai~~~~~~~--------~~~~~~~~C~~Cg~C~~~CP~~AI~~~   83 (85)
T d1hfel2          27 VQIDEAKCIGCDTCSQYCPTAAIFGEMGEP--------HSIPHIEACINCGQCLTHCPENAIYEA   83 (85)
T ss_dssp             EEECTTTCCCCCHHHHHCTTCCCBCCTTSC--------CBCCCGGGCCCCCTTGGGCTTCCEEES
T ss_pred             EEEcHHHCCCchhHHHHCCccCEEeecCCc--------eEeCChhHCCCcChhhhhCCccceEec
Confidence            346789999999999999999997755321        234567789999999999999999754

>d1dura_ d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus asaccharolyticus [TaxId: 1258]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Peptostreptococcus asaccharolyticus [TaxId: 1258]

Probab=99.47  E-value=4.9e-15  Score=93.50  Aligned_cols=50  Identities=40%  Similarity=0.901  Sum_probs=43.0

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .++|++||.|+.+||+++|....           .+.++.+.|++||.|+.+||++||.++
T Consensus         5 ~d~C~~C~~C~~~CP~~ai~~~~-----------~~~i~~~~C~~Cg~C~~~CP~~AI~~e   54 (55)
T d1dura_           5 NDSCIACGACKPECPVNCIQEGS-----------IYAIDADSCIDCGSCASVCPVGAPNPE   54 (55)
T ss_dssp             CTTCCCCCCSGGGCTTCCEECSS-----------SCEECTTTCCCCCHHHHHCTTCCEEEC
T ss_pred             CccCcChhHHHhhCCcCeEeCCc-----------eeEEChhHCcCCCChhhhCCcCcCCCc
Confidence            57899999999999999986432           346788899999999999999999864

>d1bc6a_ d.58.1.2 (A:) Ferredoxin {Bacillus schlegelii [TaxId: 1484]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Bacillus schlegelii [TaxId: 1484]

Probab=99.47  E-value=6e-15  Score=99.56  Aligned_cols=53  Identities=40%  Similarity=0.803  Sum_probs=45.8

Q ss_pred             cccccccc--ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          123 GEERCIAC--KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       123 ~~~~Ci~C--g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ..++|++|  |.|+++||++||...++          .+.++.+.|++||.|+.+||++||.+..
T Consensus         4 v~~~C~~C~~g~C~~~CP~~Ai~~~~~----------~~~id~~~C~~Cg~C~~~CP~~AI~~~~   58 (77)
T d1bc6a_           4 ITEPCIGTKDASCVEVCPVDCIHEGED----------QYYIDPDVCIDCGACEAVCPVSAIYHED   58 (77)
T ss_dssp             CCSTTTTCCCCSSTTTCTTCCEEECSS----------SEEECTTTCCSCCSHHHHSGGGSSEETT
T ss_pred             cCccCCCccCcchhhhCCCCCeeccCC----------EEEEChhHCcCcCccchhCCccccCCCc
Confidence            46899999  89999999999987543          3567889999999999999999997654

>d1rgva_ d.58.1.1 (A:) Ferredoxin II {Thauera aromatica [TaxId: 59405]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Thauera aromatica [TaxId: 59405]

Probab=99.46  E-value=1.1e-14  Score=98.95  Aligned_cols=53  Identities=42%  Similarity=0.873  Sum_probs=45.7

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc------hhhhhcCcccccccCCC
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GFCQEACPVDAIVEGPN  186 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C------g~Cv~~CP~~Ai~~~~~  186 (226)
                      .++|++||.|+.+||++||.....          .+.++.+.|++|      |.|+.+||++||.+.+.
T Consensus         5 td~Ci~Cg~C~~~CP~~AI~~~~~----------~~~id~~~C~~C~~~~~~G~C~~vCP~~AI~~~~~   63 (80)
T d1rgva_           5 NDDCTACDACVEECPNEAITPGDP----------IYVIDPTKCSECVGAFDEPQCRLVCPADCIPDNPD   63 (80)
T ss_dssp             CSCCCCCCTTTTTCTTCCEECCSS----------SCEECTTTCCTTTTTCSSCHHHHHCSSCCCCBCGG
T ss_pred             cccCcCCcCHHHHHHhCccccccc----------cccccCCCCcCCCCcCCCCcchhhccccCeeCCCC
Confidence            579999999999999999986543          356788999999      89999999999987653

>d1blua_ d.58.1.1 (A:) Ferredoxin II {Chromatium vinosum [TaxId: 1049]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Chromatium vinosum [TaxId: 1049]

Probab=99.45  E-value=7.9e-15  Score=99.66  Aligned_cols=56  Identities=39%  Similarity=0.897  Sum_probs=47.0

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc------hhhhhcCcccccccCCCc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC------GFCQEACPVDAIVEGPNF  187 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C------g~Cv~~CP~~Ai~~~~~~  187 (226)
                      +..++|++||.|+.+||++||.....          .+.++.+.|++|      |.|+.+||++||.+.+.+
T Consensus         3 iitd~Ci~Cg~C~~~CP~~AI~~~~~----------~~~id~~~C~~C~~~~~~G~C~~vCP~~AI~~~~~~   64 (80)
T d1blua_           3 MITDECINCDVCEPECPNGAISQGDE----------TYVIEPSLCTECVGHYETSQCVEVCPVDCIIKDPSH   64 (80)
T ss_dssp             EECTTCCCCCTTGGGCTTCCEEECSS----------SEEECGGGCCTTTTTCSSCHHHHHCTTCCEEECTTS
T ss_pred             EeCcCCCChHHHHHHChhcchhhcCc----------ceEEccccccCCCCCCCCCccccccCCCCccCCCCC
Confidence            34689999999999999999986543          356788899999      899999999999876543

>d1h98a_ d.58.1.2 (A:) Ferredoxin {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Thermus thermophilus [TaxId: 274]

Probab=99.45  E-value=7.3e-15  Score=99.09  Aligned_cols=55  Identities=36%  Similarity=0.748  Sum_probs=46.9

Q ss_pred             Ccccccccc--ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          122 TGEERCIAC--KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       122 ~~~~~Ci~C--g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ++.++|++|  |.|+++||++||...++          .+.++.+.|++||.|+.+||++||.+..+
T Consensus         3 vv~d~C~~C~~~~C~~~CP~~AI~~~~~----------~~~id~~~Ci~Cg~C~~~CP~~AI~~~~~   59 (77)
T d1h98a_           3 VICEPCIGVKDQSCVEVCPVECIYDGGD----------QFYIHPEECIDCGACVPACPVNAIYPEED   59 (77)
T ss_dssp             EECGGGTTTCCCHHHHHCTTCCEEECSS----------SEEECTTTCCCCCTHHHHCTTCCEEEGGG
T ss_pred             EeCccCCCcCCchhHHHCCCCceEccCc----------EEEEcHHHCCCcCcCccccCcCccCCCcc
Confidence            446899999  88999999999987653          35678899999999999999999986553

>d1jb0c_ d.58.1.2 (C:) Photosystem I iron-sulfur protein PsaC {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Photosystem I iron-sulfur protein PsaC
species: Synechococcus elongatus [TaxId: 32046]

Probab=99.43  E-value=4.9e-15  Score=100.79  Aligned_cols=61  Identities=21%  Similarity=0.517  Sum_probs=46.8

Q ss_pred             ccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          123 GEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++|++||.|+++||.+++.........+  ......++.+.|++||.|+.+||++||.++.
T Consensus         6 ~~d~Ci~Cg~Cv~~Cp~~~i~~~~~~~~~~--~~~~~~~~~~~C~~Cg~C~~~CP~~Ai~~~~   66 (80)
T d1jb0c_           6 IYDTCIGCTQCVRACPTDVLEMVPWDGCKA--GQIASSPRTEDCVGCKRCETACPTDFLSIRV   66 (80)
T ss_dssp             EETTCCCCCHHHHHCTTCCCEEEECSSSTT--SEEEECTTGGGCCCCCHHHHHCCSSSCSEEE
T ss_pred             cCCCCcCccCHHHhCCccceEeeccccccc--cccceecchhhCcCCCCccccCCCCCceeEe
Confidence            368999999999999999998755432211  1223446677899999999999999998654

>d1xera_ d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Archaeal ferredoxins
domain: Ferredoxin
species: Archaeon Sulfolobus sp. [TaxId: 2288]

Probab=99.39  E-value=2.5e-14  Score=101.85  Aligned_cols=65  Identities=25%  Similarity=0.495  Sum_probs=49.5

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.++|++||.|+.+||++++.+....... ........++...|++||+|+.+||++||++.+
T Consensus        38 ~~iD~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~-~~~~~~~~i~~~~C~~Cg~C~~~CP~~AI~~~~  102 (103)
T d1xera_          38 VGVDFDLCIADGSCINACPVNVFQWYDTPGHP-ASEKKADPVNEQACIFCMACVNVCPVAAIDVKP  102 (103)
T ss_dssp             EEEETTTCCCCCHHHHHCTTCCCEEEECTTCS-SCSEEEECTTGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             EEECHHHCcCcCcccccCcccceeeecccccc-ccccceeEeccccCCCcChHHhhcCccceEeeC
Confidence            34678999999999999999999765432211 112224456778999999999999999998754

>d3c8ya3 d.58.1.5 (A:127-209) Fe-only hydrogenase, second domain {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Fe-only hydrogenase, second domain
species: Clostridium pasteurianum [TaxId: 1501]

Probab=99.38  E-value=1.4e-14  Score=99.05  Aligned_cols=65  Identities=26%  Similarity=0.567  Sum_probs=44.9

Q ss_pred             CCCccccccccccchhccccccccchhhh--hccCCc--cccccccCCCCCCcchhhhhcCcccccccC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEE--REDGSR--RTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~--~~~~~~--~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      +.+|.++||+||.|+.+||..++......  +.....  ......++...|++||.|+++||+|||+.+
T Consensus        14 i~iD~~kCI~C~~Cv~aCp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~Cv~vCP~gAi~~k   82 (83)
T d3c8ya3          14 LTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEK   82 (83)
T ss_dssp             EEEEGGGCCCCCHHHHHHHHHHSCCCSEEEEETTEEEEESGGGCCGGGSSCCCCCHHHHHCSSTTEEEC
T ss_pred             EEEchhHCCCCchHHHhhcccccccceeeeccccceEEcccccccccccccccCCHHHhhCCCCccccc
Confidence            45788999999999999997655432211  111100  112334566789999999999999999875

>d7fd1a_ d.58.1.2 (A:) Ferredoxin {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Azotobacter vinelandii [TaxId: 354]

Probab=99.35  E-value=1.2e-13  Score=98.62  Aligned_cols=54  Identities=30%  Similarity=0.712  Sum_probs=46.5

Q ss_pred             cccccccc--ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          123 GEERCIAC--KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       123 ~~~~Ci~C--g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ..++|++|  |.|+.+||++||...++          .+.+|.+.|++||.|+.+||++||...+.
T Consensus         4 i~~~C~~C~~~~C~~~CP~~ai~~~~~----------~~~id~~~Ci~Cg~C~~~CP~~ai~~~~~   59 (106)
T d7fd1a_           4 VTDNCIKCKYTDCVEVCPVDCFYEGPN----------FLVIHPDECIDCALCEPECPAQAIFSEDE   59 (106)
T ss_dssp             ECGGGTTTCCCHHHHHCTTCCEEECSS----------CEEECTTTCCCCCTTGGGCTTCCEEEGGG
T ss_pred             cCccCCCCCCCccccccCCCcccccCC----------EEEEchHHCCCCCCccccCCCCCcccccc
Confidence            45799999  89999999999987543          35689999999999999999999986554

>d2c42a5 d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoreductase, PFOR, domain V {Desulfovibrio africanus [TaxId: 873]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Pyruvate-ferredoxin oxidoreductase, PFOR, domain V
species: Desulfovibrio africanus [TaxId: 873]

Probab=99.33  E-value=1.1e-13  Score=100.55  Aligned_cols=70  Identities=30%  Similarity=0.562  Sum_probs=47.4

Q ss_pred             CCccccccccccchhccccccccchhhhh---ccC--------------CccccccccCCCCCCcchhhhhcCccc--cc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEER---EDG--------------SRRTTRYDIDMTKCIYCGFCQEACPVD--AI  181 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~---~~~--------------~~~~~~~~~d~~~C~~Cg~Cv~~CP~~--Ai  181 (226)
                      .++.++||+||.|+.+||..++.......   ...              ......+.++.+.|++||+|+.+||++  ||
T Consensus        15 v~d~~~Ci~Cg~C~~vCP~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~C~~CG~C~~~CP~~~~ai   94 (117)
T d2c42a5          15 QWVPENCIQCNQCAFVCPHSAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDCMGCGNCADICPPKEKAL   94 (117)
T ss_dssp             EECTTTCCCCCHHHHHCSSCCEEEEEECGGGGTTCCTTCCCEECCSGGGTTCEEEEEECTTTCCCCCHHHHHCSSSSCSE
T ss_pred             EeCchhcCCCcChhhhCchhheeeeecCHHHhhhhhhhccccccccccccccceeeeeccccCCccCchhhhcCCCcCcc
Confidence            36789999999999999998774311100   000              001123446778899999999999988  78


Q ss_pred             ccCCCcccc
Q 027264          182 VEGPNFEYS  190 (226)
Q Consensus       182 ~~~~~~~~~  190 (226)
                      .+.......
T Consensus        95 ~m~~~~~~~  103 (117)
T d2c42a5          95 VMQPLDTQR  103 (117)
T ss_dssp             EEEEGGGTH
T ss_pred             ccccccchH
Confidence            876644433

>d1jnrb_ d.58.1.5 (B:) Adenylylsulfate reductase B subunit {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Adenylylsulfate reductase B subunit
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.27  E-value=3.6e-13  Score=101.92  Aligned_cols=62  Identities=32%  Similarity=0.709  Sum_probs=50.2

Q ss_pred             Cccccccccc-----cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCCcccc
Q 027264          122 TGEERCIACK-----LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEYS  190 (226)
Q Consensus       122 ~~~~~Ci~Cg-----~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~  190 (226)
                      ++.++|++||     .|+++||++||.++...+       ..+.+|.+.|++||.|+.+||++||.+...+++.
T Consensus         4 id~~~C~gCg~c~~~~C~~~CP~~ai~~~~~~~-------~~~~~d~~~C~~C~~C~~~CP~~Ai~~~~~~d~~   70 (149)
T d1jnrb_           4 VNPEKCDGCKALERTACEYICPNDLMTLDKEKM-------KAYNREPDMCWECYSCVKMCPQGAIDVRGYVDYS   70 (149)
T ss_dssp             ECTTTCCSCCSSSSCHHHHHCTTSCEEEETTTT-------EEEESCGGGCCCCCHHHHHCTTCCEEECCCTTTC
T ss_pred             EcchhCCCCCCCCcchHHHhCCcccEEecCCCc-------EEEEeccccCCCCccccCcCchheeeeccccccc
Confidence            5789999999     599999999998865421       1345677899999999999999999877665544

>d1vjwa_ d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin A
species: Thermotoga maritima [TaxId: 2336]

Probab=99.17  E-value=2.2e-12  Score=82.22  Aligned_cols=55  Identities=22%  Similarity=0.456  Sum_probs=41.0

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      .++.++|++||.|+.+||...+. .++..       ..+..+...|..|+.|+.+||++||++
T Consensus         4 ~iD~~~C~~Cg~C~~~cP~~~~~-~~~g~-------~~~~~~~~~c~~c~~c~~~CP~~AI~i   58 (59)
T d1vjwa_           4 RVDADACIGCGVCENLCPDVFQL-GDDGK-------AKVLQPETDLPCAKDAADSCPTGAISV   58 (59)
T ss_dssp             EECTTTCCCCCHHHHHCTTTEEE-CTTSS-------EEESCSBCCCTHHHHHHHHCTTCCEEC
T ss_pred             EEeHHHCCCCCCChHhCchheEE-cccee-------eEEecChHHCcCcCcccCccCcccEEe
Confidence            46789999999999999975443 32211       122334467999999999999999975

>d1gtea5 d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogenase, C-terminal domain {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Dihydropyrimidine dehydrogenase, C-terminal domain
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=99.16  E-value=1.2e-12  Score=101.44  Aligned_cols=59  Identities=27%  Similarity=0.551  Sum_probs=45.6

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcc-cccccCCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVEGPN  186 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~-~Ai~~~~~  186 (226)
                      ++.++|++||.|+.+||.+++........      ....++.+.|++||.|+.+||+ +||++.+.
T Consensus       104 id~~~Ci~C~~C~~~Cp~~ai~~i~~~~~------~~~~v~~~~C~gCg~C~~vCP~~~aI~mv~~  163 (173)
T d1gtea5         104 IDEEMCINCGKCYMTCNDSGYQAIQFDPE------THLPTVTDTCTGCTLCLSVCPIIDCIRMVSR  163 (173)
T ss_dssp             ECTTTCCCCCHHHHHHHHHSCSCEEECTT------TCCEEECTTCCCCCHHHHHCSSTTTEEEEEC
T ss_pred             EEchhCCCchHHHHhhhhCCEEEEEecCC------CceEechhhCCCcChhHhhCCCCCcEEEEeC
Confidence            67899999999999999988764322111      1345677899999999999995 89987553

>d1fxra_ d.58.1.4 (A:) Ferredoxin I {Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin I
species: Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873]

Probab=99.16  E-value=1.5e-12  Score=84.42  Aligned_cols=60  Identities=20%  Similarity=0.361  Sum_probs=43.8

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.++|++||.|+.+||...........      ......+...|..|+.|+.+||++||.+.+
T Consensus         4 ~~VD~~~CigCg~C~~~cP~~f~~~~~~~~------~~~~~~~~~~c~~c~~c~~~CP~~aI~~~e   63 (64)
T d1fxra_           4 FYVDQDECIACESCVEIAPGAFAMDPEIEK------AYVKDVEGASQEEVEEAMDTCPVQCIHWED   63 (64)
T ss_dssp             EEECTTTCCCCCHHHHHCTTTEEEETTTTE------EEESCTTSSCHHHHHHHHHHCTTCCEEEEC
T ss_pred             EEEchhhCccCCCccccCcCeEEEecCCCe------eeeeccCCCcchhHHHHHhcCCcccEEEEe
Confidence            447789999999999999975332222111      112345678899999999999999998754

>d1fxda_ d.58.1.4 (A:) Ferredoxin I {Desulfovibrio gigas [TaxId: 879]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin I
species: Desulfovibrio gigas [TaxId: 879]

Probab=99.09  E-value=5.8e-12  Score=79.92  Aligned_cols=53  Identities=23%  Similarity=0.468  Sum_probs=39.7

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      .++||+||.|+.+||...+..++...       ..+..+.+.|..|+.|+++||++||+.
T Consensus         5 ~e~CigCg~C~~~CP~~~~~~~~g~~-------~~~~~~~~~~~~c~~c~~~CP~~AIs~   57 (58)
T d1fxda_           5 NDDCMACEACVEICPDVFEMNEEGDK-------AVVINPDSDLDCVEEAIDSCPAEAIVR   57 (58)
T ss_dssp             CTTCCCCCHHHHHCTTTEEECSSSSS-------EEESCTTCCCHHHHHHHHHCTTCCEEE
T ss_pred             CccCcChhhHHHHcChhheEcCCCCE-------EEEecCCCCcHHHHHHhhcCChhcEEC
Confidence            47899999999999986554332211       123345678999999999999999975

>d1sj1a_ d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Fe3S4-ferredoxin PF1909
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.08  E-value=1.6e-12  Score=84.67  Aligned_cols=62  Identities=21%  Similarity=0.342  Sum_probs=43.1

Q ss_pred             CCCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.++.++|++||.|+.+||......++ ...   .......++...|..|+.|+.+||++||++.+
T Consensus         4 i~vD~~~Ci~Cg~C~~~CP~~~~~~~~-~~~---~~~~~~~~~~~~c~~c~~c~~~CP~~AI~i~e   65 (66)
T d1sj1a_           4 VSVDQDTCIGDAICASLCPDVFEMNDE-GKA---QPKVEVIEDEELYNCAKEAMEACPVSAITIEE   65 (66)
T ss_dssp             EEECTTTCCCCCHHHHHCTTTEEECTT-SCE---EESCSCBCCHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             EEEeHHHCCCcChhhhhCCceEEEccc-Cce---EeeccccCChHHHhhhCHhhccCCcccEEEEe
Confidence            457789999999999999975332221 111   11112334555799999999999999998653

>d3c7bb1 d.58.1.5 (B:197-261) DsrB insert domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: DsrB insert domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.08  E-value=1e-11  Score=80.41  Aligned_cols=51  Identities=27%  Similarity=0.705  Sum_probs=42.1

Q ss_pred             cccccc--cchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccC
Q 027264          126 RCIACK--LCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  184 (226)
Q Consensus       126 ~Ci~Cg--~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~  184 (226)
                      .|..|+  .|+.+||++||..+...+        ...++.+.|++||.|+.+||++||...
T Consensus        11 ~c~~C~~~~Cv~~CP~~Ai~~~~~~g--------~v~id~~~CigCg~C~~aCP~~ai~d~   63 (65)
T d3c7bb1          11 IRKTCEIPSTVAACPTGALKPDMKNK--------TIKVDVEKCMYCGNCYTMCPGMPLFDP   63 (65)
T ss_dssp             HHHHCCHHHHHHTCTTCCEEEETTTT--------EEEECTTTCCCCCHHHHHCTTCCCCCT
T ss_pred             hhCCCCChHHHHhCcCCCccccccCC--------cEEEeCCcCcccChhhhhCCcccccCC
Confidence            499998  699999999998764321        356788999999999999999999643

>d2fug34 d.58.1.5 (3:96-246) NADH-quinone oxidoreductase chain 3, Nqo3, domain 2 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: NADH-quinone oxidoreductase chain 3, Nqo3, domain 2
species: Thermus thermophilus [TaxId: 274]

Probab=99.04  E-value=2.4e-11  Score=91.73  Aligned_cols=64  Identities=20%  Similarity=0.245  Sum_probs=44.0

Q ss_pred             ccCCCccccccccccchhccc----cccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          118 RRYPTGEERCIACKLCEAVCP----AQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       118 ~~~~~~~~~Ci~Cg~C~~~CP----~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.+..+.++||.||.|+++|+    .+++.+..  ++...... . ......|..||.|+.+||+|||..++
T Consensus        77 p~i~~d~~kCI~C~rCvr~C~ev~g~~~l~~~~--rG~~~~i~-~-~~~~~~c~~cG~Cv~vCPtGAL~ek~  144 (151)
T d2fug34          77 PFVILDRERCIHCKRCVRYFEEVPGDEVLDFIE--RGVHTFIG-T-MDFGLPSGFSGNITDICPVGALLDLT  144 (151)
T ss_dssp             SSSCEECSCCCCCCHHHHHHHHTTCCCCCCCBS--CGGGCBCC-C-SSTTCCSSCCTHHHHHCSSSSSBCGG
T ss_pred             CeEEecCCCCCcCchHHhhhhhccCCceEEEec--cccceEEc-c-CCCCCCChhhcCHHhcCcccccccCC
Confidence            345678899999999999998    34555433  22222211 1 11234699999999999999998544

>d1iqza_ d.58.1.4 (A:) Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1427]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin
species: Bacillus thermoproteolyticus [TaxId: 1427]

Probab=98.77  E-value=3.1e-10  Score=76.66  Aligned_cols=65  Identities=20%  Similarity=0.224  Sum_probs=43.3

Q ss_pred             CCccccccccccchhccccccccchhhhhcc--CCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEERED--GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~--~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      .++.++||+||.|+.+||.... ........  .........++...|..|+.|+.+||++||++.+.
T Consensus         5 ~VD~~~CigCg~C~~~cP~~f~-~~~dg~~~~~~~~~~~~~~v~~~~~~~~~~aa~~CP~~AI~v~d~   71 (81)
T d1iqza_           5 IVDKETCIACGACGAAAPDIYD-YDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADE   71 (81)
T ss_dssp             EECTTTCCCCSHHHHHCTTTEE-ECTTSCEEETTTTTSSCSCCCGGGHHHHHHHHHHCTTCCEEEESS
T ss_pred             EEeHHHCcCcChHhHhCchhee-EcCCCeEEEeecCCcCcccCCHHHHHHHHHHHHhCCcccEEEEeC
Confidence            3677999999999999996432 22211110  00111123455678999999999999999986653

>d1kqfb1 d.58.1.5 (B:2-245) Formate dehydrogenase N, iron-sulfur (beta) subunit {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Formate dehydrogenase N, iron-sulfur (beta) subunit
species: Escherichia coli [TaxId: 562]

Probab=98.65  E-value=1.1e-09  Score=88.80  Aligned_cols=52  Identities=35%  Similarity=0.747  Sum_probs=30.7

Q ss_pred             CccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccCC
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGP  185 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~~  185 (226)
                      ++.++|++|+.|+.+||.+++.+.....            ...+|++|.         +|+++||++||.+++
T Consensus       127 id~~~CiGC~~C~~ACPyga~~~~~~~~------------~~~KC~~C~~r~~~G~~PaCv~~CP~~Al~fG~  187 (244)
T d1kqfb1         127 FQSENCIGCGYCIAGCPFNIPRLNKEDN------------RVYKCTLCVDRVSVGQEPACVKTCPTGAIHFGT  187 (244)
T ss_dssp             ECGGGCCCCCHHHHHCTTCCCEEETTTT------------EEECCCTTHHHHTTTCCCHHHHHCTTSCEEEEE
T ss_pred             EccccccchhhHhhcCCCCCcEeccccC------------cceecccchhhhcCCCCcchHHhcccCCEEEec
Confidence            4556677777777777766665543211            113566662         577777777776655

>d1kqfb1 d.58.1.5 (B:2-245) Formate dehydrogenase N, iron-sulfur (beta) subunit {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Formate dehydrogenase N, iron-sulfur (beta) subunit
species: Escherichia coli [TaxId: 562]

Probab=98.59  E-value=3.6e-09  Score=85.65  Aligned_cols=54  Identities=26%  Similarity=0.716  Sum_probs=43.2

Q ss_pred             ccccccccc--chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          124 EERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       124 ~~~Ci~Cg~--C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ...|..|+.  |+++||++++......+        .+.+|.+.|++|+.|+.+||++|+.+..
T Consensus        96 ~~~C~HC~~p~Cv~vCPt~Aa~~~~e~G--------~V~id~~~CiGC~~C~~ACPyga~~~~~  151 (244)
T d1kqfb1          96 KDGCMHCEDPGCLKACPSAGAIIQYANG--------IVDFQSENCIGCGYCIAGCPFNIPRLNK  151 (244)
T ss_dssp             EESCCCBSSCHHHHHCCSTTSEEEETTS--------CEEECGGGCCCCCHHHHHCTTCCCEEET
T ss_pred             chhhccccCCcccccccccceeEEcCCC--------cEEEccccccchhhHhhcCCCCCcEecc
Confidence            346999997  99999997765543221        4578889999999999999999997654

>d1vlfn2 d.58.1.5 (N:1-195) Transhydroxylase beta subunit, BthL, N-terminal domain {Pelobacter acidigallici [TaxId: 35816]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Transhydroxylase beta subunit, BthL, N-terminal domain
species: Pelobacter acidigallici [TaxId: 35816]

Probab=98.55  E-value=6.8e-09  Score=81.26  Aligned_cols=52  Identities=21%  Similarity=0.272  Sum_probs=40.1

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch-------------hhhhcCcccccccC
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG-------------FCQEACPVDAIVEG  184 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg-------------~Cv~~CP~~Ai~~~  184 (226)
                      .++.++|++||.|+.+||.+++.+.....            ...+|.+|.             +|+.+||++||.+.
T Consensus        93 ~id~~kCiGC~~C~~aCPy~a~~~~~~~~------------~~~KC~~C~~r~~~~~~~g~~PaCv~~Cp~~a~~f~  157 (195)
T d1vlfn2          93 LIDPEKAKGKKELLDTCPYGVMYWNEEEN------------VAQKCTMCAHLLDDESWAPKMPRCAHNCGSFVYEFL  157 (195)
T ss_dssp             EECTTTTTTCGGGGGGCSSCCCEEETTTT------------EEECCCTTHHHHTCTTCTTCSCHHHHHCSSCCEEEE
T ss_pred             eeehhhccccchhhcCCCCCCeEcccccC------------CccccCcchhhhhccccccchhhhhhhCcHhheecC
Confidence            46788999999999999999988764321            124688883             69999999999763

>d1nekb1 a.1.2.1 (B:107-238) Succinate dehydogenase {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Globin-like
superfamily: alpha-helical ferredoxin
family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
domain: Succinate dehydogenase
species: Escherichia coli [TaxId: 562]

Probab=98.54  E-value=7.3e-09  Score=76.04  Aligned_cols=59  Identities=20%  Similarity=0.435  Sum_probs=35.3

Q ss_pred             Cccccccccccchhccccccccchhh---------------hhccCCcccccc---ccCCCCCCcchhhhhcCcccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEAE---------------EREDGSRRTTRY---DIDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~~---------------~~~~~~~~~~~~---~~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ....+||.||.|..+||+....-...               .+..........   ....+.|+.||.|+.+||+|.
T Consensus        38 ~~~~~CI~CG~C~~~CP~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~~C~~C~~C~~vCP~gI  114 (132)
T d1nekb1          38 DGLYECILCACCSTSCPSFWWNPDKFIGPAGLLAAYRFLIDSRDTETDSRLDGLSDAFSVFRCHSIMNCVSVCPKGL  114 (132)
T ss_dssp             TTTSCCCCCCHHHHTCHHHHHCTTTSCCHHHHHHHHHHHTCTTCCCHHHHHHTTCSSSTTTTCCCCCHHHHHCTTCC
T ss_pred             HhhHHHhHhhhhhhhCccccccCccccchhHHHHHHHHHhcccccccccchhhhhccchhhhCcCcccccccCcCCC
Confidence            44678999999999999742211100               000000000011   123578999999999999993

>d1y5ib1 d.58.1.5 (B:1-509) Respiratory nitrate reductase 1 beta chain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Respiratory nitrate reductase 1 beta chain
species: Escherichia coli [TaxId: 562]

Probab=98.50  E-value=1.1e-08  Score=90.54  Aligned_cols=51  Identities=33%  Similarity=0.570  Sum_probs=26.1

Q ss_pred             cccccccc--chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          125 ERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       125 ~~Ci~Cg~--C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      ..|.+|..  |+++||++||......+        .+.+|.+.|++|+.|+.+||++++.+
T Consensus       182 ~~C~hC~~~~C~~~CP~gAi~~~~e~G--------~v~id~~~CigC~~C~~aCPy~~~~~  234 (509)
T d1y5ib1         182 RLCEHCLNPACVATCPSGAIYKREEDG--------IVLIDQDKCRGWRMCITGCPYKKIYF  234 (509)
T ss_dssp             ECCCCCSSCHHHHHCTTCCEEEETTTC--------CEEECTTTCCCCCCHHHHCTTCCEEE
T ss_pred             ccccCCCCchhhhhcCcCceEEecCCC--------cEEEchhhccchHHHHhhCCCCCeEe
Confidence            45666654  66666666654322111        23445555555555555555555543

>d1y5ib1 d.58.1.5 (B:1-509) Respiratory nitrate reductase 1 beta chain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Respiratory nitrate reductase 1 beta chain
species: Escherichia coli [TaxId: 562]

Probab=98.49  E-value=7.9e-09  Score=91.57  Aligned_cols=60  Identities=22%  Similarity=0.490  Sum_probs=46.4

Q ss_pred             CCccccccccccchhccccccccchhhhhccCCccccccccCCCCCCcch---------hhhhcCcccccccCCCcccch
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPNFEYST  191 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg---------~Cv~~CP~~Ai~~~~~~~~~~  191 (226)
                      .++.++|++||.|+.+||.+++.+.....            ..++|++|.         +|+.+||++||.+++..+...
T Consensus       211 ~id~~~CigC~~C~~aCPy~~~~~~~~~~------------~~~KC~~C~~r~~~G~~paCv~~Cp~~A~~~g~~~d~~~  278 (509)
T d1y5ib1         211 LIDQDKCRGWRMCITGCPYKKIYFNWKSG------------KSEKCIFCYPRIEAGQPTVCSETCVGRIRYLGVLLYDAD  278 (509)
T ss_dssp             EECTTTCCCCCCHHHHCTTCCEEEETTTT------------EEEECCTTHHHHTTTCCCHHHHTCTTCCEEEEEEEEEGG
T ss_pred             EEchhhccchHHHHhhCCCCCeEecCCCC------------ceeecccchhHHhcCCCChhhhhCcHhhhhhchhcchHH
Confidence            46789999999999999999987754321            125799993         399999999998876655443


Q ss_pred             h
Q 027264          192 E  192 (226)
Q Consensus       192 ~  192 (226)
                      .
T Consensus       279 ~  279 (509)
T d1y5ib1         279 A  279 (509)
T ss_dssp             G
T ss_pred             H
Confidence            3

>d1kf6b1 a.1.2.1 (B:106-243) Fumarate reductase {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Globin-like
superfamily: alpha-helical ferredoxin
family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
domain: Fumarate reductase
species: Escherichia coli [TaxId: 562]

Probab=98.37  E-value=2.1e-08  Score=74.14  Aligned_cols=58  Identities=29%  Similarity=0.787  Sum_probs=34.3

Q ss_pred             ccccccccccchhccccccccch--------------hhhhccCCcc-ccccc--cCCCCCCcchhhhhcCcccc
Q 027264          123 GEERCIACKLCEAVCPAQAITIE--------------AEEREDGSRR-TTRYD--IDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~--------------~~~~~~~~~~-~~~~~--~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      ...+||.||.|..+||+....-+              .+.+...... ...+.  ...+.|+.||.|+.+||.|.
T Consensus        39 ~~~~CI~Cg~C~~~CP~~~~~~~~~gp~~~~~~~r~~~d~rd~~~~~rl~~l~~~~g~~~C~~C~~C~~~CP~gI  113 (138)
T d1kf6b1          39 QFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHV  113 (138)
T ss_dssp             GGGCCCCCCHHHHHCHHHHHCTTSCCHHHHHHHHHHHTCTTCCCTHHHHHHHHSTTTGGGCCCCCHHHHHCTTCC
T ss_pred             HHHHHHHhChhhccCccchhhhhhhhHHHHHHHHHhccCcchhhhhhhHHHhhcccccccCchhCcccccCCCCC
Confidence            45689999999999997432211              0011111110 01111  11356999999999999983

>d2bs2b1 a.1.2.1 (B:107-239) Fumarate reductase {Wolinella succinogenes [TaxId: 844]}

class: All alpha proteins
fold: Globin-like
superfamily: alpha-helical ferredoxin
family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
domain: Fumarate reductase
species: Wolinella succinogenes [TaxId: 844]

Probab=98.33  E-value=2.8e-08  Score=72.87  Aligned_cols=57  Identities=19%  Similarity=0.503  Sum_probs=34.1

Q ss_pred             ccccccccccchhccccccccchh--------------hhhccCCcc-ccccc---cCCCCCCcchhhhhcCccc
Q 027264          123 GEERCIACKLCEAVCPAQAITIEA--------------EEREDGSRR-TTRYD---IDMTKCIYCGFCQEACPVD  179 (226)
Q Consensus       123 ~~~~Ci~Cg~C~~~CP~~ai~~~~--------------~~~~~~~~~-~~~~~---~d~~~C~~Cg~Cv~~CP~~  179 (226)
                      +.++|+.||.|..+||+....-..              ..+..+... .....   ...+.|+.||.|+.+||++
T Consensus        41 ~~~~Ci~CG~C~~~CP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ct~Cg~C~~vCP~g  115 (133)
T d2bs2b1          41 ELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMIDPHDERTDEDYYELIGDDDGVFGCMTLLACHDVCPKN  115 (133)
T ss_dssp             HHHTCCCCCHHHHTCHHHHHCTTCCHHHHHHHHHHHHTCTTCCCCHHHHHHHHCSTTTGGGCCCCCHHHHHCTTC
T ss_pred             hHHHHhhhhhHHHhCCccccCCCccchHHHHHHHHHhhcchhhhhHHHHHHHhhccccchhChhhCCCcccCcCC
Confidence            356899999999999974322110              000111100 00111   1235699999999999998

>d1vlfn2 d.58.1.5 (N:1-195) Transhydroxylase beta subunit, BthL, N-terminal domain {Pelobacter acidigallici [TaxId: 35816]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Transhydroxylase beta subunit, BthL, N-terminal domain
species: Pelobacter acidigallici [TaxId: 35816]

Probab=98.33  E-value=8.1e-08  Score=74.98  Aligned_cols=53  Identities=17%  Similarity=0.217  Sum_probs=41.7

Q ss_pred             ccccccccc--chhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCCC
Q 027264          124 EERCIACKL--CEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       124 ~~~Ci~Cg~--C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ...|..|..  |+ +||++|+..++..         .+.+|.+.|++|+.|+.+||++||.+.+.
T Consensus        65 ~~~C~hC~~p~Cv-~~p~~A~~~~e~G---------~V~id~~kCiGC~~C~~aCPy~a~~~~~~  119 (195)
T d1vlfn2          65 PTPCMHCENAPCV-AKGNGAVYQREDG---------IVLIDPEKAKGKKELLDTCPYGVMYWNEE  119 (195)
T ss_dssp             EECCCCCTTCHHH-HTTTTSEEECTTS---------CEEECTTTTTTCGGGGGGCSSCCCEEETT
T ss_pred             hhhccCCcCcccc-ccccceEEeeccc---------ceeeehhhccccchhhcCCCCCCeEcccc
Confidence            456999986  98 4677777654321         46788999999999999999999987654

>d1h0hb_ d.58.1.5 (B:) Tungsten containing formate dehydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Tungsten containing formate dehydrogenase, small subunit
species: Desulfovibrio gigas [TaxId: 879]

Probab=98.17  E-value=8.1e-08  Score=76.03  Aligned_cols=51  Identities=25%  Similarity=0.439  Sum_probs=40.3

Q ss_pred             cccccccccchhccccccccchhhhhccCCccccccccCCCCCCcc---------hhhhhcCcccccccCCC
Q 027264          124 EERCIACKLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYC---------GFCQEACPVDAIVEGPN  186 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~C---------g~Cv~~CP~~Ai~~~~~  186 (226)
                      ..+|++|+.|+.+||.+++.+.....            ...+|.+|         -+|+++||++||.+++.
T Consensus       107 ~~~c~gc~~C~~aCPy~~~~~~~~~~------------~~~KCd~C~~R~~~G~~PaCV~~CP~~Al~fGd~  166 (214)
T d1h0hb_         107 TKDLEDYESVISACPYDVPRKVAESN------------QMAKCDMCIDRITNGLRPACVTSCPTGAMNFGDL  166 (214)
T ss_dssp             GGGCSCHHHHHHHCTTCCCEECTTSS------------CEECCCTTHHHHTTTCCCHHHHHCSSSCEEEEEH
T ss_pred             cccccCcceecccCCCCCceecccCC------------ccEeCcccHHHHhCCCCCCceeecccCCEEEeeh
Confidence            44799999999999999887644321            12579999         36999999999998774

>d1hfel2 d.58.1.5 (L:2-86) Fe-only hydrogenase larger subunit, N-domain {Desulfovibrio desulfuricans [TaxId: 876]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Fe-only hydrogenase larger subunit, N-domain
species: Desulfovibrio desulfuricans [TaxId: 876]

Probab=97.54  E-value=1.4e-05  Score=53.44  Aligned_cols=28  Identities=39%  Similarity=0.763  Sum_probs=24.1

Q ss_pred             cccCCCCCCcchhhhhcCcccccccCCC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      +.+|.+.|++||.|+.+||++||.....
T Consensus        27 ~~id~~~Ci~C~~Cv~~Cp~~ai~~~~~   54 (85)
T d1hfel2          27 VQIDEAKCIGCDTCSQYCPTAAIFGEMG   54 (85)
T ss_dssp             EEECTTTCCCCCHHHHHCTTCCCBCCTT
T ss_pred             EEEcHHHCCCchhHHHHCCccCEEeecC
Confidence            4578889999999999999999986554

>d1dura_ d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus asaccharolyticus [TaxId: 1258]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Peptostreptococcus asaccharolyticus [TaxId: 1258]

Probab=97.53  E-value=7.6e-06  Score=50.25  Aligned_cols=25  Identities=36%  Similarity=0.817  Sum_probs=21.8

Q ss_pred             CCccccccccccchhccccccccch
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      .++.++|++||.|+.+||++||.++
T Consensus        30 ~i~~~~C~~Cg~C~~~CP~~AI~~e   54 (55)
T d1dura_          30 AIDADSCIDCGSCASVCPVGAPNPE   54 (55)
T ss_dssp             EECTTTCCCCCHHHHHCTTCCEEEC
T ss_pred             EEChhHCcCCCChhhhCCcCcCCCc
Confidence            3567899999999999999999764

>d1blua_ d.58.1.1 (A:) Ferredoxin II {Chromatium vinosum [TaxId: 1049]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Chromatium vinosum [TaxId: 1049]

Probab=97.42  E-value=1.8e-05  Score=52.31  Aligned_cols=25  Identities=36%  Similarity=0.882  Sum_probs=21.2

Q ss_pred             CCCCCCcchhhhhcCcccccccCCC
Q 027264          162 DMTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       162 d~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      +.+.|++||.|+.+||++||.+.+.
T Consensus         4 itd~Ci~Cg~C~~~CP~~AI~~~~~   28 (80)
T d1blua_           4 ITDECINCDVCEPECPNGAISQGDE   28 (80)
T ss_dssp             ECTTCCCCCTTGGGCTTCCEEECSS
T ss_pred             eCcCCCChHHHHHHChhcchhhcCc
Confidence            3578999999999999999976543

>d2v4jb1 d.58.1.5 (B:209-277) DsrB insert domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: DsrB insert domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=97.40  E-value=1.2e-05  Score=50.83  Aligned_cols=47  Identities=32%  Similarity=0.714  Sum_probs=33.4

Q ss_pred             hhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccc
Q 027264          134 EAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       134 ~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      +.+||++||+......  +......+.++.+.|.+||+|-..||.--|.
T Consensus        20 iAaCPT~AIrP~k~~~--~~~~~ksV~V~~eRCMyCGNCYT~cp~~~i~   66 (69)
T d2v4jb1          20 VASCPTAAVRPTKLEI--GDKKVNTIAIKNERCMYCGNCYTMCPALPIS   66 (69)
T ss_dssp             HHTCTTCCEEEEEEEE--TTEEEEEEEECGGGCCCCCHHHHHCTTCCCC
T ss_pred             hhcCCccccccccccc--CCcccceEEEcCCcceecCCccccCCCcccC
Confidence            5789999998744221  1122335678889999999999999965443

>d1bc6a_ d.58.1.2 (A:) Ferredoxin {Bacillus schlegelii [TaxId: 1484]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Bacillus schlegelii [TaxId: 1484]

Probab=97.37  E-value=2e-05  Score=51.77  Aligned_cols=26  Identities=46%  Similarity=0.857  Sum_probs=22.4

Q ss_pred             CCccccccccccchhccccccccchh
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .++.++|++||.|+.+||++||....
T Consensus        33 ~id~~~C~~Cg~C~~~CP~~AI~~~~   58 (77)
T d1bc6a_          33 YIDPDVCIDCGACEAVCPVSAIYHED   58 (77)
T ss_dssp             EECTTTCCSCCSHHHHSGGGSSEETT
T ss_pred             EEChhHCcCcCccchhCCccccCCCc
Confidence            35678999999999999999997654

>d2fdna_ d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici [TaxId: 1556]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Clostridium acidurici [TaxId: 1556]

Probab=97.37  E-value=2.6e-05  Score=47.70  Aligned_cols=24  Identities=46%  Similarity=1.079  Sum_probs=21.0

Q ss_pred             CCCCCcchhhhhcCcccccccCCC
Q 027264          163 MTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       163 ~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      .+.|++||.|+.+||++||.+++.
T Consensus         5 ~e~C~~Cg~C~~~Cp~~ai~~~~~   28 (55)
T d2fdna_           5 NEACISCGACEPECPVNAISSGDD   28 (55)
T ss_dssp             CTTCCCCCTTGGGCTTCCEECCSS
T ss_pred             CcCCCChhhHHHhcCccceEcCCc
Confidence            468999999999999999987653

>d1h98a_ d.58.1.2 (A:) Ferredoxin {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Thermus thermophilus [TaxId: 274]

Probab=97.36  E-value=2.2e-05  Score=51.55  Aligned_cols=27  Identities=37%  Similarity=0.752  Sum_probs=23.3

Q ss_pred             CCccccccccccchhccccccccchhh
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAE  147 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~  147 (226)
                      .++.++|++||.|+.+||++||.....
T Consensus        33 ~id~~~Ci~Cg~C~~~CP~~AI~~~~~   59 (77)
T d1h98a_          33 YIHPEECIDCGACVPACPVNAIYPEED   59 (77)
T ss_dssp             EECTTTCCCCCTHHHHCTTCCEEEGGG
T ss_pred             EEcHHHCCCcCcCccccCcCccCCCcc
Confidence            357889999999999999999987553

>d1rgva_ d.58.1.1 (A:) Ferredoxin II {Thauera aromatica [TaxId: 59405]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Short-chain ferredoxins
domain: Ferredoxin II
species: Thauera aromatica [TaxId: 59405]

Probab=97.26  E-value=4.5e-05  Score=50.33  Aligned_cols=23  Identities=39%  Similarity=0.907  Sum_probs=20.1

Q ss_pred             CCCCcchhhhhcCcccccccCCC
Q 027264          164 TKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      +.|++||.|+.+||++||.+.+.
T Consensus         6 d~Ci~Cg~C~~~CP~~AI~~~~~   28 (80)
T d1rgva_           6 DDCTACDACVEECPNEAITPGDP   28 (80)
T ss_dssp             SCCCCCCTTTTTCTTCCEECCSS
T ss_pred             ccCcCCcCHHHHHHhCccccccc
Confidence            57999999999999999986543

>d1xera_ d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Archaeal ferredoxins
domain: Ferredoxin
species: Archaeon Sulfolobus sp. [TaxId: 2288]

Probab=97.20  E-value=3.9e-05  Score=53.07  Aligned_cols=27  Identities=41%  Similarity=0.922  Sum_probs=23.0

Q ss_pred             CCCccccccccccchhccccccccchh
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      ..++.++|++||.|+.+||++||+++.
T Consensus        76 ~~i~~~~C~~Cg~C~~~CP~~AI~~~~  102 (103)
T d1xera_          76 DPVNEQACIFCMACVNVCPVAAIDVKP  102 (103)
T ss_dssp             ECTTGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             eEeccccCCCcChHHhhcCccceEeeC
Confidence            346678999999999999999998753

>d1jb0c_ d.58.1.2 (C:) Photosystem I iron-sulfur protein PsaC {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Photosystem I iron-sulfur protein PsaC
species: Synechococcus elongatus [TaxId: 32046]

Probab=97.19  E-value=3.8e-05  Score=50.63  Aligned_cols=25  Identities=36%  Similarity=0.970  Sum_probs=21.8

Q ss_pred             Cccccccccccchhccccccccchh
Q 027264          122 TGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      ++.+.|++||.|+.+||++||.+..
T Consensus        42 ~~~~~C~~Cg~C~~~CP~~Ai~~~~   66 (80)
T d1jb0c_          42 PRTEDCVGCKRCETACPTDFLSIRV   66 (80)
T ss_dssp             TTGGGCCCCCHHHHHCCSSSCSEEE
T ss_pred             cchhhCcCCCCccccCCCCCceeEe
Confidence            5667899999999999999998753

>d7fd1a_ d.58.1.2 (A:) Ferredoxin {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: 7-Fe ferredoxin
domain: Ferredoxin
species: Azotobacter vinelandii [TaxId: 354]

Probab=97.13  E-value=5.7e-05  Score=52.57  Aligned_cols=27  Identities=52%  Similarity=0.939  Sum_probs=23.5

Q ss_pred             CCccccccccccchhccccccccchhh
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEAE  147 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~  147 (226)
                      .++.++|++||.|+.+||++||..++.
T Consensus        33 ~id~~~Ci~Cg~C~~~CP~~ai~~~~~   59 (106)
T d7fd1a_          33 VIHPDECIDCALCEPECPAQAIFSEDE   59 (106)
T ss_dssp             EECTTTCCCCCTTGGGCTTCCEEEGGG
T ss_pred             EEchHHCCCCCCccccCCCCCcccccc
Confidence            367899999999999999999987653

>d1vjwa_ d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin A
species: Thermotoga maritima [TaxId: 2336]

Probab=97.09  E-value=8.6e-05  Score=45.84  Aligned_cols=28  Identities=29%  Similarity=0.716  Sum_probs=23.0

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+|.+.|++||.|+.+||..++..++
T Consensus         2 rv~iD~~~C~~Cg~C~~~cP~~~~~~~~   29 (59)
T d1vjwa_           2 KVRVDADACIGCGVCENLCPDVFQLGDD   29 (59)
T ss_dssp             BCEECTTTCCCCCHHHHHCTTTEEECTT
T ss_pred             EEEEeHHHCCCCCCChHhCchheEEccc
Confidence            4567889999999999999987665444

>d2fug91 d.58.1.5 (9:26-179) NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: NADH-quinone oxidoreductase chain 9, Nqo9
species: Thermus thermophilus [TaxId: 274]

Probab=97.07  E-value=4.6e-05  Score=56.52  Aligned_cols=26  Identities=42%  Similarity=0.857  Sum_probs=23.0

Q ss_pred             CCccccccccccchhccccccccchh
Q 027264          121 PTGEERCIACKLCEAVCPAQAITIEA  146 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~  146 (226)
                      .++..+|+.||.|+.+||++||.++.
T Consensus        67 ~id~~~C~~CG~Cve~CPt~AI~~~~   92 (154)
T d2fug91          67 EINMLRCIFCGLCEEACPTGAIVLGY   92 (154)
T ss_dssp             EEETTTCCCCTHHHHHCSSSCEEECS
T ss_pred             EeccccCCCCCCchhhCCCCeEeccC
Confidence            45678999999999999999999865

>d3c8ya3 d.58.1.5 (A:127-209) Fe-only hydrogenase, second domain {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Fe-only hydrogenase, second domain
species: Clostridium pasteurianum [TaxId: 1501]

Probab=97.03  E-value=7.3e-05  Score=49.42  Aligned_cols=23  Identities=26%  Similarity=0.780  Sum_probs=19.9

Q ss_pred             Cccccccccccchhccccccccc
Q 027264          122 TGEERCIACKLCEAVCPAQAITI  144 (226)
Q Consensus       122 ~~~~~Ci~Cg~C~~~CP~~ai~~  144 (226)
                      ++...|+.||.|+.+||++||..
T Consensus        59 ~~~~~C~~Cg~Cv~vCP~gAi~~   81 (83)
T d3c8ya3          59 FDDTNCLLCGQCIIACPVAALSE   81 (83)
T ss_dssp             GGGSSCCCCCHHHHHCSSTTEEE
T ss_pred             ccccccccCCHHHhhCCCCcccc
Confidence            45567999999999999999964

>d3c7bb1 d.58.1.5 (B:197-261) DsrB insert domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: DsrB insert domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.03  E-value=7.1e-05  Score=47.33  Aligned_cols=23  Identities=26%  Similarity=0.777  Sum_probs=20.1

Q ss_pred             CCccccccccccchhcccccccc
Q 027264          121 PTGEERCIACKLCEAVCPAQAIT  143 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~~ai~  143 (226)
                      .++.++|++||.|+.+||..+|.
T Consensus        39 ~id~~~CigCg~C~~aCP~~ai~   61 (65)
T d3c7bb1          39 KVDVEKCMYCGNCYTMCPGMPLF   61 (65)
T ss_dssp             EECTTTCCCCCHHHHHCTTCCCC
T ss_pred             EEeCCcCcccChhhhhCCccccc
Confidence            36789999999999999998774

>d2gmha3 d.58.1.6 (A:483-584) Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: ETF-QO domain-like
domain: Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=96.98  E-value=6.5e-05  Score=51.62  Aligned_cols=57  Identities=21%  Similarity=0.333  Sum_probs=41.9

Q ss_pred             cccccc--ccchhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCcccccccCC
Q 027264          125 ERCIAC--KLCEAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       125 ~~Ci~C--g~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.|..|  +-|...||.+...+.+.+..    ...++.++.+.|+.||.|--.||.++|.+..
T Consensus        32 ~~~~~~y~~Pc~r~CPAgVYE~~~~~~~----~~~~l~In~~nCleC~tC~i~~p~~nI~W~~   90 (102)
T d2gmha3          32 NRNLSIYDGPEQRFCPAGVYEFVPLEQG----DGFRLQINAQNCVHCKTCDIKDPSQNINWVV   90 (102)
T ss_dssp             HTHHHHHCCTHHHHCTTCCEEEEECSST----TCEEEEECGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             hcccccccchheeeccceEEEEeecCCC----CccEEEEEeCCceeeccceeeCCCCceEEEC
Confidence            345555  57999999987766543211    1125778889999999999999999997653

>d1h0hb_ d.58.1.5 (B:) Tungsten containing formate dehydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Tungsten containing formate dehydrogenase, small subunit
species: Desulfovibrio gigas [TaxId: 879]

Probab=96.70  E-value=0.00018  Score=56.12  Aligned_cols=54  Identities=19%  Similarity=0.246  Sum_probs=36.9

Q ss_pred             ccccccc--cchhcccc---ccccchhhhhccCCccccccccC--CCCCCcchhhhhcCcccccccCCC
Q 027264          125 ERCIACK--LCEAVCPA---QAITIEAEEREDGSRRTTRYDID--MTKCIYCGFCQEACPVDAIVEGPN  186 (226)
Q Consensus       125 ~~Ci~Cg--~C~~~CP~---~ai~~~~~~~~~~~~~~~~~~~d--~~~C~~Cg~Cv~~CP~~Ai~~~~~  186 (226)
                      ..|..|.  .|+.+||+   +++...+..+        -..++  ...|++|+.|+.+||++++.+...
T Consensus        70 ~~C~HC~~ppC~~~Cp~~~~~~~v~~~~~G--------~v~~~~~~~~c~gc~~C~~aCPy~~~~~~~~  130 (214)
T d1h0hb_          70 DQCRHCIAPPCKATADMEDESAIIHDDATG--------CVLFTPKTKDLEDYESVISACPYDVPRKVAE  130 (214)
T ss_dssp             ECCCCCSSCHHHHHHTTTCTTSEEECTTTC--------CEEECGGGGGCSCHHHHHHHCTTCCCEECTT
T ss_pred             cccccCCCCcccccccccCCceEEEEeCCC--------eEEEecccccccCcceecccCCCCCceeccc
Confidence            4599996  49999998   3444433211        12233  336999999999999999976543

>d1sj1a_ d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Fe3S4-ferredoxin PF1909
species: Pyrococcus furiosus [TaxId: 2261]

Probab=96.56  E-value=0.00037  Score=43.75  Aligned_cols=28  Identities=21%  Similarity=0.471  Sum_probs=22.6

Q ss_pred             ccccCCCCCCcchhhhhcCcccccccCC
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ++.+|.+.|++||.|+.+||.......+
T Consensus         3 ki~vD~~~Ci~Cg~C~~~CP~~~~~~~~   30 (66)
T d1sj1a_           3 KVSVDQDTCIGDAICASLCPDVFEMNDE   30 (66)
T ss_dssp             EEEECTTTCCCCCHHHHHCTTTEEECTT
T ss_pred             EEEEeHHHCCCcChhhhhCCceEEEccc
Confidence            4578889999999999999987665433

>d2c42a5 d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoreductase, PFOR, domain V {Desulfovibrio africanus [TaxId: 873]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Pyruvate-ferredoxin oxidoreductase, PFOR, domain V
species: Desulfovibrio africanus [TaxId: 873]

Probab=96.55  E-value=0.00028  Score=49.59  Aligned_cols=24  Identities=33%  Similarity=0.664  Sum_probs=21.3

Q ss_pred             cccCCCCCCcchhhhhcCcccccc
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      ..+|.+.|++||.|+.+||.+++.
T Consensus        14 pv~d~~~Ci~Cg~C~~vCP~~~i~   37 (117)
T d2c42a5          14 PQWVPENCIQCNQCAFVCPHSAIL   37 (117)
T ss_dssp             EEECTTTCCCCCHHHHHCSSCCEE
T ss_pred             CEeCchhcCCCcChhhhCchhhee
Confidence            456888999999999999999985

>d1jnrb_ d.58.1.5 (B:) Adenylylsulfate reductase B subunit {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Adenylylsulfate reductase B subunit
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.45  E-value=0.00034  Score=51.37  Aligned_cols=27  Identities=26%  Similarity=0.538  Sum_probs=22.9

Q ss_pred             ccCCCCCCcch-----hhhhcCcccccccCCC
Q 027264          160 DIDMTKCIYCG-----FCQEACPVDAIVEGPN  186 (226)
Q Consensus       160 ~~d~~~C~~Cg-----~Cv~~CP~~Ai~~~~~  186 (226)
                      .+|.+.|++||     .|+.+||++||.++.+
T Consensus         3 ~id~~~C~gCg~c~~~~C~~~CP~~ai~~~~~   34 (149)
T d1jnrb_           3 FVNPEKCDGCKALERTACEYICPNDLMTLDKE   34 (149)
T ss_dssp             EECTTTCCSCCSSSSCHHHHHCTTSCEEEETT
T ss_pred             EEcchhCCCCCCCCcchHHHhCCcccEEecCC
Confidence            46778999999     6999999999987543

>d1fxra_ d.58.1.4 (A:) Ferredoxin I {Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin I
species: Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873]

Probab=96.33  E-value=0.00052  Score=42.85  Aligned_cols=25  Identities=28%  Similarity=0.667  Sum_probs=21.2

Q ss_pred             ccccCCCCCCcchhhhhcCcccccc
Q 027264          158 RYDIDMTKCIYCGFCQEACPVDAIV  182 (226)
Q Consensus       158 ~~~~d~~~C~~Cg~Cv~~CP~~Ai~  182 (226)
                      ++.+|.+.|++||.|+.+||.....
T Consensus         3 ~~~VD~~~CigCg~C~~~cP~~f~~   27 (64)
T d1fxra_           3 KFYVDQDECIACESCVEIAPGAFAM   27 (64)
T ss_dssp             EEEECTTTCCCCCHHHHHCTTTEEE
T ss_pred             eEEEchhhCccCCCccccCcCeEEE
Confidence            4568889999999999999987554

>d1gtea5 d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogenase, C-terminal domain {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: Dihydropyrimidine dehydrogenase, C-terminal domain
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=96.04  E-value=0.00051  Score=51.70  Aligned_cols=27  Identities=37%  Similarity=0.925  Sum_probs=22.6

Q ss_pred             CCccccccccccchhcccc-ccccchhh
Q 027264          121 PTGEERCIACKLCEAVCPA-QAITIEAE  147 (226)
Q Consensus       121 ~~~~~~Ci~Cg~C~~~CP~-~ai~~~~~  147 (226)
                      .++.++|++||.|+.+||+ +||.+.+.
T Consensus       136 ~v~~~~C~gCg~C~~vCP~~~aI~mv~~  163 (173)
T d1gtea5         136 PTVTDTCTGCTLCLSVCPIIDCIRMVSR  163 (173)
T ss_dssp             EEECTTCCCCCHHHHHCSSTTTEEEEEC
T ss_pred             EechhhCCCcChhHhhCCCCCcEEEEeC
Confidence            3567899999999999995 89988654

>d1fxda_ d.58.1.4 (A:) Ferredoxin I {Desulfovibrio gigas [TaxId: 879]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin I
species: Desulfovibrio gigas [TaxId: 879]

Probab=95.97  E-value=0.00099  Score=40.70  Aligned_cols=22  Identities=27%  Similarity=0.652  Sum_probs=18.4

Q ss_pred             CCCCcchhhhhcCcccccccCC
Q 027264          164 TKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       164 ~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      +.|++||.|+.+||..++..++
T Consensus         6 e~CigCg~C~~~CP~~~~~~~~   27 (58)
T d1fxda_           6 DDCMACEACVEICPDVFEMNEE   27 (58)
T ss_dssp             TTCCCCCHHHHHCTTTEEECSS
T ss_pred             ccCcChhhHHHHcChhheEcCC
Confidence            6799999999999988775444

>d3c7ba1 d.58.1.5 (A:239-304) DsrA insert domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: DsrA insert domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.76  E-value=0.0018  Score=40.32  Aligned_cols=39  Identities=28%  Similarity=0.633  Sum_probs=30.9

Q ss_pred             hhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          134 EAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       134 ~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      +..||++++..+..          .+.++...|..|+.|+++-|. ||..
T Consensus        25 v~~CPT~cm~~dg~----------~L~Idn~~CvRCMHCIN~Mpk-AL~p   63 (66)
T d3c7ba1          25 VKLCPTGAIKWDGK----------ELTIDNRECVRCMHCINKMPK-ALKP   63 (66)
T ss_dssp             GGGCTTCCEEECSS----------CEEECTTTCCCCCHHHHHCTT-TEEC
T ss_pred             hccCccccccccCC----------EEEEcCcccCccccchhcCcc-ccCC
Confidence            44689999988642          467888999999999999986 3543

>d2fug34 d.58.1.5 (3:96-246) NADH-quinone oxidoreductase chain 3, Nqo3, domain 2 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: NADH-quinone oxidoreductase chain 3, Nqo3, domain 2
species: Thermus thermophilus [TaxId: 274]

Probab=95.72  E-value=0.0029  Score=46.37  Aligned_cols=21  Identities=14%  Similarity=0.045  Sum_probs=18.5

Q ss_pred             ccccccccchhccccccccch
Q 027264          125 ERCIACKLCEAVCPAQAITIE  145 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~ai~~~  145 (226)
                      ..|+.||.|+.+||++||...
T Consensus       123 ~~c~~cG~Cv~vCPtGAL~ek  143 (151)
T d2fug34         123 LPSGFSGNITDICPVGALLDL  143 (151)
T ss_dssp             CCSSCCTHHHHHCSSSSSBCG
T ss_pred             CCChhhcCHHhcCcccccccC
Confidence            469999999999999999743

>d1iqza_ d.58.1.4 (A:) Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1427]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Single 4Fe-4S cluster ferredoxin
domain: Ferredoxin
species: Bacillus thermoproteolyticus [TaxId: 1427]

Probab=95.24  E-value=0.003  Score=41.15  Aligned_cols=27  Identities=30%  Similarity=0.473  Sum_probs=21.4

Q ss_pred             cccCCCCCCcchhhhhcCcccccccCC
Q 027264          159 YDIDMTKCIYCGFCQEACPVDAIVEGP  185 (226)
Q Consensus       159 ~~~d~~~C~~Cg~Cv~~CP~~Ai~~~~  185 (226)
                      ..+|.+.|++||.|+.+||......++
T Consensus         4 v~VD~~~CigCg~C~~~cP~~f~~~~d   30 (81)
T d1iqza_           4 TIVDKETCIACGACGAAAPDIYDYDED   30 (81)
T ss_dssp             EEECTTTCCCCSHHHHHCTTTEEECTT
T ss_pred             EEEeHHHCcCcChHhHhCchheeEcCC
Confidence            457788999999999999976554443

>d2v4ja1 d.58.1.5 (A:242-322) DsrA insert domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: DsrA insert domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=95.02  E-value=0.003  Score=40.91  Aligned_cols=39  Identities=21%  Similarity=0.577  Sum_probs=30.7

Q ss_pred             hhccccccccchhhhhccCCccccccccCCCCCCcchhhhhcCccccccc
Q 027264          134 EAVCPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  183 (226)
Q Consensus       134 ~~~CP~~ai~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP~~Ai~~  183 (226)
                      +.-||++++..+..          .+.++...|+.|+.|+++-|.- |..
T Consensus        40 v~~CPT~cm~~d~~----------~L~Idn~~C~RCMHCINvMPkA-Lrp   78 (81)
T d2v4ja1          40 VNRCPSKCMKWDGS----------KLSIDNKECVRCMHCINTMPRA-LHI   78 (81)
T ss_dssp             GGGCTTCCEEECSS----------CEEECGGGCCCCSHHHHHCTTT-EEC
T ss_pred             hccCCHhhccccCC----------eeEEeCcccccCcCchhhCccc-cCC
Confidence            45689999988642          4678888999999999999863 543

>d1e8ga1 d.58.32.1 (A:274-560) Vanillyl-alcohol oxidase {Fungus (Penicillium simplicissimum) [TaxId: 69488]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: FAD-linked oxidases, C-terminal domain
family: Vanillyl-alcohol oxidase-like
domain: Vanillyl-alcohol oxidase
species: Fungus (Penicillium simplicissimum) [TaxId: 69488]

Probab=93.68  E-value=0.043  Score=43.44  Aligned_cols=32  Identities=19%  Similarity=0.198  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHhcCCcceecCccccCCCCCCc
Q 027264           79 EMVRGLGLTLKYFFDKKVTINYPFEKGPLSPRF  111 (226)
Q Consensus        79 ~~~~~l~~~~~~~f~~~~~~~~p~~~~~~~~~~  111 (226)
                      +....++..+|..|||..++| |-..++.+.++
T Consensus       249 ~~~~~l~~~iK~a~DP~gIlN-PGK~gi~p~~~  280 (287)
T d1e8ga1         249 SSFLRFNEVLKNAVDPNGIIA-PGKSGVWPSQY  280 (287)
T ss_dssp             HHHHHHHHHHHHHHCTTCCBC-TTGGGCCCTTS
T ss_pred             HHHHHHHHHHHHHhCCCcCCC-CCCCCCCCccc
Confidence            456688999999999999999 33233444443

>d1nekb1 a.1.2.1 (B:107-238) Succinate dehydogenase {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Globin-like
superfamily: alpha-helical ferredoxin
family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
domain: Succinate dehydogenase
species: Escherichia coli [TaxId: 562]

Probab=91.67  E-value=0.023  Score=40.07  Aligned_cols=20  Identities=30%  Similarity=0.796  Sum_probs=16.8

Q ss_pred             cCCCCCCcchhhhhcCcccc
Q 027264          161 IDMTKCIYCGFCQEACPVDA  180 (226)
Q Consensus       161 ~d~~~C~~Cg~Cv~~CP~~A  180 (226)
                      .+...|+.||.|..+||+-.
T Consensus        38 ~~~~~CI~CG~C~~~CP~~~   57 (132)
T d1nekb1          38 DGLYECILCACCSTSCPSFW   57 (132)
T ss_dssp             TTTSCCCCCCHHHHTCHHHH
T ss_pred             HhhHHHhHhhhhhhhCcccc
Confidence            34578999999999999854

>d2bs2b1 a.1.2.1 (B:107-239) Fumarate reductase {Wolinella succinogenes [TaxId: 844]}

class: All alpha proteins
fold: Globin-like
superfamily: alpha-helical ferredoxin
family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
domain: Fumarate reductase
species: Wolinella succinogenes [TaxId: 844]

Probab=91.33  E-value=0.023  Score=40.06  Aligned_cols=18  Identities=28%  Similarity=0.670  Sum_probs=15.5

Q ss_pred             cccccccccchhcccccc
Q 027264          124 EERCIACKLCEAVCPAQA  141 (226)
Q Consensus       124 ~~~Ci~Cg~C~~~CP~~a  141 (226)
                      ...|+.||.|..+||++.
T Consensus        99 ~~~Ct~Cg~C~~vCP~gI  116 (133)
T d2bs2b1          99 VFGCMTLLACHDVCPKNL  116 (133)
T ss_dssp             GGGCCCCCHHHHHCTTCC
T ss_pred             chhChhhCCCcccCcCCC
Confidence            347999999999999873

>d2gmha3 d.58.1.6 (A:483-584) Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: ETF-QO domain-like
domain: Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=90.94  E-value=0.023  Score=38.41  Aligned_cols=32  Identities=25%  Similarity=0.529  Sum_probs=26.0

Q ss_pred             CCCccccccccccchhccccccccchhhhhcc
Q 027264          120 YPTGEERCIACKLCEAVCPAQAITIEAEERED  151 (226)
Q Consensus       120 ~~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~~  151 (226)
                      +.++.+.|++||.|--.||.++|..+...++.
T Consensus        64 l~In~~nCleC~tC~i~~p~~nI~W~~P~GG~   95 (102)
T d2gmha3          64 LQINAQNCVHCKTCDIKDPSQNINWVVPEGGG   95 (102)
T ss_dssp             EEECGGGCCCCCHHHHHCTTCCEEECCCSTTC
T ss_pred             EEEEeCCceeeccceeeCCCCceEEECCCCCC
Confidence            44678899999999999999999876655443

>d1wvfa1 d.58.32.1 (A:243-521) Flavoprotein subunit of p-cresol methylhydroxylase {Pseudomonas putida [TaxId: 303]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: FAD-linked oxidases, C-terminal domain
family: Vanillyl-alcohol oxidase-like
domain: Flavoprotein subunit of p-cresol methylhydroxylase
species: Pseudomonas putida [TaxId: 303]

Probab=90.04  E-value=0.12  Score=40.68  Aligned_cols=74  Identities=9%  Similarity=0.051  Sum_probs=41.8

Q ss_pred             hhHhhhhccCCcccCcccccCCC-CCCCCCchhHH--HHHHHHHHHhhhHHHHHHH-----HHH----HhhhHHHHHHHH
Q 027264           18 LAVSGQALQGSQHYGLRFNAHPY-SSYFPSKKDDE--EKEQLLKEISKDWSSVFER-----SIN----MLFLTEMVRGLG   85 (226)
Q Consensus        18 ~~i~Gha~~gn~~~~~~~~~H~~-~~~~~~~~p~~--~~~~~~~~~~~~v~~~~~~-----~i~----~~~~~~~~~~l~   85 (226)
                      ..++||+.+||        +|+. ...+....|.+  +..+..+++.+.+.+.-.+     ..+    ...+.+....++
T Consensus       182 ~~~~~H~gdgn--------lh~~v~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Gg~eHGiG~~~~~~l~~~~g~~~~~lm  253 (279)
T d1wvfa1         182 YVAEFIVAPRD--------MHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLE  253 (279)
T ss_dssp             CCEEEEECSSE--------EEEEEEEEEETTCHHHHHHHHHHHHHHHHHHHHTTCCBSCCCGGGHHHHHHHTCHHHHHHH
T ss_pred             eEEEEecCCce--------EEEEeecccCCCCHHHHHHHHHHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHhCHHHHHHH
Confidence            78899999999        9983 22232222322  3333333333332110000     001    122334577889


Q ss_pred             HHHHHhcCCcceec
Q 027264           86 LTLKYFFDKKVTIN   99 (226)
Q Consensus        86 ~~~~~~f~~~~~~~   99 (226)
                      ..+|..|||..++|
T Consensus       254 ~~iK~alDP~~IlN  267 (279)
T d1wvfa1         254 HAIKRAVDPNNILA  267 (279)
T ss_dssp             HHHHHHHCTTCCBC
T ss_pred             HHHHHHhCCCcCCC
Confidence            99999999999999

>d2v4jb1 d.58.1.5 (B:209-277) DsrB insert domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: 4Fe-4S ferredoxins
family: Ferredoxin domains from multidomain proteins
domain: DsrB insert domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=89.70  E-value=0.031  Score=34.76  Aligned_cols=23  Identities=35%  Similarity=0.830  Sum_probs=19.2

Q ss_pred             ccCCCccccccccccchhccccc
Q 027264          118 RRYPTGEERCIACKLCEAVCPAQ  140 (226)
Q Consensus       118 ~~~~~~~~~Ci~Cg~C~~~CP~~  140 (226)
                      +.+.++.++|+-||.|...||.-
T Consensus        41 ksV~V~~eRCMyCGNCYT~cp~~   63 (69)
T d2v4jb1          41 NTIAIKNERCMYCGNCYTMCPAL   63 (69)
T ss_dssp             EEEEECGGGCCCCCHHHHHCTTC
T ss_pred             ceEEEcCCcceecCCccccCCCc
Confidence            34557789999999999999964

>d1kf6b1 a.1.2.1 (B:106-243) Fumarate reductase {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Globin-like
superfamily: alpha-helical ferredoxin
family: Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
domain: Fumarate reductase
species: Escherichia coli [TaxId: 562]

Probab=89.19  E-value=0.044  Score=38.99  Aligned_cols=17  Identities=29%  Similarity=0.747  Sum_probs=15.0

Q ss_pred             ccccccccchhcccccc
Q 027264          125 ERCIACKLCEAVCPAQA  141 (226)
Q Consensus       125 ~~Ci~Cg~C~~~CP~~a  141 (226)
                      ..|+.||.|+.+||.+.
T Consensus        97 ~~C~~C~~C~~~CP~gI  113 (138)
T d1kf6b1          97 WSCTFVGYCSEVCPKHV  113 (138)
T ss_dssp             GGCCCCCHHHHHCTTCC
T ss_pred             ccCchhCcccccCCCCC
Confidence            46999999999999873

>d1gtea1 a.1.2.2 (A:2-183) Dihydropyrimidine dehydrogenase, N-terminal domain {Pig (Sus scrofa) [TaxId: 9823]}

class: All alpha proteins
fold: Globin-like
superfamily: alpha-helical ferredoxin
family: Dihydropyrimidine dehydrogenase, N-terminal domain
domain: Dihydropyrimidine dehydrogenase, N-terminal domain
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=81.10  E-value=0.069  Score=39.76  Aligned_cols=19  Identities=32%  Similarity=0.983  Sum_probs=16.2

Q ss_pred             ccccccccc--cchhcccccc
Q 027264          123 GEERCIACK--LCEAVCPAQA  141 (226)
Q Consensus       123 ~~~~Ci~Cg--~C~~~CP~~a  141 (226)
                      ..++|+.|+  .|...||++.
T Consensus        74 EA~RCl~C~~ppC~~aCP~~~   94 (182)
T d1gtea1          74 EAMRCLKCADAPCQKSCPTHL   94 (182)
T ss_dssp             HHHHSCCCTTCHHHHTSTTCC
T ss_pred             HHHHhhCCCCCCcCCCCCCCC
Confidence            467999998  8999999863