Psyllid ID: psy4925

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160
Protein Sequence
MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHccccccEEEEEEcccccccEEEEEcccccccccccccccccccccccccccccccccHHHHcccHHHHcccccccHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEccccccccccccccHHHHHcccccHcccccccccccccccccEEEHHHccHHccccccccEEccccccccccHHHHcccccEEEccccEEccccHHHHHHcHHHHHHccccHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MVDRGIHAAFLTEIFRGFFvatghifkepatinypfekgplsprfrgehalrrypsgeerciACKLCEAICPAQAITIEAeeradgsrrttrydidmtkciycgfcqeacpvdaivegpnfefsteSHEELLYNKEKLLSNGDKWESEIAsnihadhlyr
Flexible Loop (DISEMBL)
MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPfekgplsprfrgEHALRRYPSGEERCIACKLCEAICPAQAitieaeeradgsrrttrydiDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLlsngdkweseiasnihadhlyr
Low Complexity Region (SEG)
MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR
Disordered region (IsUnstruct)
****GIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEE*****RRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNK*************************
Disordered Region (DISOPRED)
**DRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNI**DHLYR
Disordered Region (DISEMBL)
MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR
Disordered Region (DISPRO)
MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER**GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHL**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR
Positional Conservation
no confident homologs detected

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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	160	2.2.26 [Sep-21-2011]
P0CB97	210	NADH dehydrogenase [ubiqu	yes	N/A	1.0	0.761	0.843	9e-79
Q60HE3	210	NADH dehydrogenase [ubiqu	N/A	N/A	1.0	0.761	0.831	2e-78
P0CB98	210	NADH dehydrogenase [ubiqu	N/A	N/A	1.0	0.761	0.837	4e-78
Q0MQI3	210	NADH dehydrogenase [ubiqu	yes	N/A	1.0	0.761	0.837	4e-78
O00217	210	NADH dehydrogenase [ubiqu	yes	N/A	1.0	0.761	0.837	4e-78
Q22619	212	Probable NADH dehydrogena	yes	N/A	0.993	0.75	0.830	1e-77
P42028	212	NADH dehydrogenase [ubiqu	yes	N/A	1.0	0.754	0.825	1e-77
Q0MQI2	210	NADH dehydrogenase [ubiqu	N/A	N/A	1.0	0.761	0.831	1e-77
Q8K3J1	212	NADH dehydrogenase [ubiqu	yes	N/A	0.993	0.75	0.830	3e-77
P80269	229	NADH dehydrogenase [ubiqu	N/A	N/A	1.0	0.698	0.775	2e-73

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

 Score =  291 bits (746), Expect = 9e-79,   Method: Compositional matrix adjust.
 Identities = 135/160 (84%), Positives = 146/160 (91%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR      LTE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 51  VTDRAARTLLLTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct: 171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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: 1EC: .EC: 6EC: .EC: 9EC: 9EC: .EC: 3

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

 Score =  290 bits (743), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 133/160 (83%), Positives = 145/160 (90%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 51  VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEA+CPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 111 CIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct: 171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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 =  289 bits (740), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 134/160 (83%), Positives = 145/160 (90%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 51  VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct: 171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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

>sp|Q0MQI3|NDUS8_PANTR NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Pan troglodytes GN=NDUFS8 PE=2 SV=1

 Score =  289 bits (740), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 134/160 (83%), Positives = 145/160 (90%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 51  VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct: 171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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.

Pan troglodytes (taxid: 9598)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|O00217|NDUS8_HUMAN NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Homo sapiens GN=NDUFS8 PE=1 SV=1

 Score =  289 bits (740), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 134/160 (83%), Positives = 145/160 (90%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 51  VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct: 171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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 (By similarity). May donate electrons to ubiquinone.

Homo sapiens (taxid: 9606)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|Q22619|NDUS8_CAEEL Probable NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Caenorhabditis elegans GN=T20H4.5 PE=2 SV=1

 Score =  288 bits (737), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 132/159 (83%), Positives = 144/159 (90%)

Query: 2   VDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERC 61
           ++ G+H  F TE+FRGF V  GH+F EPATINYPFEKGPLS RFRGEHALRRYPSGEERC
Sbjct: 54  LNYGLHNVFFTELFRGFGVMLGHVFMEPATINYPFEKGPLSSRFRGEHALRRYPSGEERC 113

Query: 62  IACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF 121
           IACKLCEAICPAQAITIEAE R DGSRRTTRYDIDMTKCIYCG CQEACPVDAIVEGPNF
Sbjct: 114 IACKLCEAICPAQAITIEAETRPDGSRRTTRYDIDMTKCIYCGLCQEACPVDAIVEGPNF 173

Query: 122 EFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           E+STE+HEELLYNKEKLL NGD+WE E+ASN+ A++LYR
Sbjct: 174 EYSTETHEELLYNKEKLLLNGDRWEPELASNLQAEYLYR 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.

Caenorhabditis elegans (taxid: 6239)

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 =  288 bits (736), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 132/160 (82%), Positives = 144/160 (90%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR       TE+ RG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 53  VTDRAAQTLLWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 112

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEA+CPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 113 CIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 172

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct: 173 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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|Q0MQI2|NDUS8_GORGO NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Gorilla gorilla gorilla GN=NDUFS8 PE=2 SV=1

 Score =  288 bits (736), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 133/160 (83%), Positives = 144/160 (90%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 51  VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWE+EI +NI AD+LYR
Sbjct: 171 FEFSTETHEELLYNKEKLLNNGDKWEAEITANIQADYLYR 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.

Gorilla gorilla gorilla (taxid: 9595)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

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 =  286 bits (733), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 132/159 (83%), Positives = 142/159 (89%)

Query: 2   VDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERC 61
            D        TE+ RG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEERC
Sbjct: 54  TDNAARILMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERC 113

Query: 62  IACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF 121
           IACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF
Sbjct: 114 IACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF 173

Query: 122 EFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           EFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct: 174 EFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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|P80269|NDUS8_SOLTU NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial OS=Solanum tuberosum PE=1 SV=2

 Score =  274 bits (701), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 124/160 (77%), Positives = 141/160 (88%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + +R I+  FLTE+ RG  +   + F++  TINYPFEKGPLSPRFRGEHALRRY +GEER
Sbjct: 70  VFERSINTLFLTEMVRGLMLTLKYFFEKKVTINYPFEKGPLSPRFRGEHALRRYATGEER 129

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEER DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 130 CIACKLCEAICPAQAITIEAEEREDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 189

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEF+TE+HEELLY+KEKLL NGD+WE+EIA N+ ++ LYR
Sbjct: 190 FEFATETHEELLYDKEKLLENGDRWETEIAENLRSESLYR 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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	160
114051372	221	NADH dehydrogenase ubiquinone Fe-S 8 [Bo	1.0	0.723	0.893	3e-81
283046736	212	NADH:ubiquinone reductase 23kD subunit [	1.0	0.754	0.893	4e-81
288856257	201	NADH dehydrogenase [ubiquinone] iron-sul	1.0	0.796	0.881	7e-81
289743757	215	NADH-ubiquinone oxidoreductase NDUFS8/23	1.0	0.744	0.887	1e-80
347966427	218	AGAP001711-PA [Anopheles gambiae str. PE	1.0	0.733	0.887	1e-80
195108159	216	GI24093 [Drosophila mojavensis] gi|19391	1.0	0.740	0.887	2e-80
240849392	206	NADH dehydrogenase [ubiquinone] iron-sul	1.0	0.776	0.887	2e-80
170068344	213	NADH dehydrogenase iron-sulfur protein 8	1.0	0.751	0.887	2e-80
195395498	217	GJ10912 [Drosophila virilis] gi|19414308	1.0	0.737	0.887	2e-80
195454170	217	GK14477 [Drosophila willistoni] gi|19417	1.0	0.737	0.887	3e-80

>gi|114051372|ref|NP_001040316.1| NADH dehydrogenase ubiquinone Fe-S 8 [Bombyx mori] gi|87248369|gb|ABD36237.1| NADH dehydrogenase (ubiquinone) Fe-S protein 8 [Bombyx mori]

 Score =  305 bits (782), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 143/160 (89%), Positives = 146/160 (91%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           M DR     F TE+ RGF V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 62  MSDRAAQTMFWTELARGFAVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 121

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEER DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 122 CIACKLCEAICPAQAITIEAEERKDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 181

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEF+TE+HEELLYNKEKLLSNGDKWESEIASNI ADHLYR
Sbjct: 182 FEFTTETHEELLYNKEKLLSNGDKWESEIASNIRADHLYR 221

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|283046736|ref|NP_001164315.1| NADH:ubiquinone reductase 23kD subunit [Tribolium castaneum] gi|270009224|gb|EFA05672.1| hypothetical protein TcasGA2_TC015022 [Tribolium castaneum]

 Score =  305 bits (781), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 143/160 (89%), Positives = 148/160 (92%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR     F TE+ RGF V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 53  VTDRAAEKVFFTELVRGFAVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 112

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 113 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 172

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWESEIA+NIHADHLYR
Sbjct: 173 FEFSTETHEELLYNKEKLLNNGDKWESEIAANIHADHLYR 212

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|288856257|ref|NP_001165784.1| NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial [Nasonia vitripennis]

 Score =  304 bits (779), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 141/160 (88%), Positives = 149/160 (93%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           +  R ++  FL E+FRG  VA  H FKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 42  IASRAVNTMFLQELFRGMGVALAHFFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 101

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 102 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 161

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEE+LYNKEKLL+NGDKWESEIASN+HADHLYR
Sbjct: 162 FEFSTETHEEMLYNKEKLLNNGDKWESEIASNLHADHLYR 201

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

>gi|289743757|gb|ADD20626.1| NADH-ubiquinone oxidoreductase NDUFS8/23 kDa subunit [Glossina morsitans morsitans]

 Score =  304 bits (778), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 142/160 (88%), Positives = 148/160 (92%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR     FL+E+ RGF V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 56  LTDRAASTIFLSELARGFAVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 115

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 116 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 175

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL+NGDKWESEIASN+ ADHLYR
Sbjct: 176 FEFSTETHEELLYNKEKLLNNGDKWESEIASNLQADHLYR 215

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347966427|ref|XP_321378.5| AGAP001711-PA [Anopheles gambiae str. PEST] gi|333470064|gb|EAA00878.5| AGAP001711-PA [Anopheles gambiae str. PEST]

 Score =  303 bits (777), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 142/160 (88%), Positives = 148/160 (92%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR     F TE+FRG  V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 59  ITDRAAQTIFWTELFRGAAVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 118

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 119 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 178

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLLSNGDKWESEIA+NI+AD+LYR
Sbjct: 179 FEFSTETHEELLYNKEKLLSNGDKWESEIATNINADYLYR 218

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195108159|ref|XP_001998660.1| GI24093 [Drosophila mojavensis] gi|193915254|gb|EDW14121.1| GI24093 [Drosophila mojavensis]

 Score =  303 bits (775), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 142/160 (88%), Positives = 147/160 (91%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR   + F  E+FRGF V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 57  ITDRAATSMFFGELFRGFAVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 116

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 117 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 176

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL NGDKWESEIASN+ ADHLYR
Sbjct: 177 FEFSTETHEELLYNKEKLLCNGDKWESEIASNLQADHLYR 216

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|240849392|ref|NP_001155795.1| NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondri [Acyrthosiphon pisum] gi|239789288|dbj|BAH71275.1| ACYPI009382 [Acyrthosiphon pisum]

 Score =  303 bits (775), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 142/160 (88%), Positives = 150/160 (93%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           M D+ I  AF+TE+ RG  V+  H FKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 47  MTDQAISYAFVTELCRGAAVSLAHFFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 106

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 107 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 166

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FE+STE+HEELLYNKEKLL+NGDKWESEIA+NIHADHLYR
Sbjct: 167 FEYSTETHEELLYNKEKLLNNGDKWESEIAANIHADHLYR 206

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

>gi|170068344|ref|XP_001868829.1| NADH dehydrogenase iron-sulfur protein 8, mitochondrial [Culex quinquefasciatus] gi|167864397|gb|EDS27780.1| NADH dehydrogenase iron-sulfur protein 8, mitochondrial [Culex quinquefasciatus]

 Score =  303 bits (775), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 142/160 (88%), Positives = 147/160 (91%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR     F TE+FRG  V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 54  ITDRAAQTIFWTELFRGAAVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 113

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEER DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 114 CIACKLCEAICPAQAITIEAEERTDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 173

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLLSNGDKWESEIASNI+AD+LYR
Sbjct: 174 FEFSTETHEELLYNKEKLLSNGDKWESEIASNINADYLYR 213

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195395498|ref|XP_002056373.1| GJ10912 [Drosophila virilis] gi|194143082|gb|EDW59485.1| GJ10912 [Drosophila virilis]

 Score =  302 bits (774), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 142/160 (88%), Positives = 146/160 (91%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR     F  E+FRGF V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 58  ITDRAATTMFFGELFRGFAVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 117

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 118 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 177

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL NGDKWESEIASN+ ADHLYR
Sbjct: 178 FEFSTETHEELLYNKEKLLCNGDKWESEIASNLQADHLYR 217

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195454170|ref|XP_002074119.1| GK14477 [Drosophila willistoni] gi|194170204|gb|EDW85105.1| GK14477 [Drosophila willistoni]

 Score =  302 bits (774), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 142/160 (88%), Positives = 146/160 (91%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
           + DR     F  E+FRGF V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct: 58  ITDRAATTMFFGELFRGFGVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 117

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct: 118 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 177

Query: 121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           FEFSTE+HEELLYNKEKLL NGDKWESEIASN+ ADHLYR
Sbjct: 178 FEFSTETHEELLYNKEKLLCNGDKWESEIASNLQADHLYR 217

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

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	160
FB|FBgn0017567	217	ND23 "NADH:ubiquinone reductas	1.0	0.737	0.875	1.3e-75
UNIPROTKB|P0CB97	210	NDUFS8 "NADH dehydrogenase [ub	1.0	0.761	0.843	6.5e-74
ZFIN|ZDB-GENE-040426-2153	210	ndufs8a "NADH dehydrogenase (u	1.0	0.761	0.843	1.7e-73
UNIPROTKB|F1NAF3	210	NDUFS8 "Uncharacterized protei	1.0	0.761	0.837	2.2e-73
UNIPROTKB|O00217	210	NDUFS8 "NADH dehydrogenase [ub	1.0	0.761	0.837	2.8e-73
UNIPROTKB|P0CB98	210	NDUFS8 "NADH dehydrogenase [ub	1.0	0.761	0.837	2.8e-73
UNIPROTKB|Q0MQI3	210	NDUFS8 "NADH dehydrogenase [ub	1.0	0.761	0.837	2.8e-73
UNIPROTKB|Q60HE3	210	NDUFS8 "NADH dehydrogenase [ub	1.0	0.761	0.831	3.6e-73
UNIPROTKB|E2R5X8	210	NDUFS8 "Uncharacterized protei	1.0	0.761	0.831	7.5e-73
UNIPROTKB|Q0MQI2	210	NDUFS8 "NADH dehydrogenase [ub	1.0	0.761	0.831	7.5e-73

FB|FBgn0017567 ND23 "NADH:ubiquinone reductase 23kD subunit precursor" [Drosophila melanogaster (taxid:7227)]

 Score = 762 (273.3 bits), Expect = 1.3e-75, P = 1.3e-75
 Identities = 140/160 (87%), Positives = 144/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR     F  E+ RGF V   HIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    58 ITDRAASTMFFGELLRGFAVTLAHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 117

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV AIVEGPN
Sbjct:   118 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVGAIVEGPN 177

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL NGDKWESEIASN+ ADHLYR
Sbjct:   178 FEFSTETHEELLYNKEKLLCNGDKWESEIASNLQADHLYR 217

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

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

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

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

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

GO:0009055 "electron carrier activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

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

 Score = 746 (267.7 bits), Expect = 6.5e-74, P = 6.5e-74
 Identities = 135/160 (84%), Positives = 146/160 (91%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR      LTE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 VTDRAARTLLLTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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-040426-2153 ndufs8a "NADH dehydrogenase (ubiquinone) Fe-S protein 8a" [Danio rerio (taxid:7955)]

 Score = 742 (266.3 bits), Expect = 1.7e-73, P = 1.7e-73
 Identities = 135/160 (84%), Positives = 145/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR      LTE+ RG  +A  ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 ITDRAAQTLLLTELIRGMGMAVSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADFLYR 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|F1NAF3 NDUFS8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 741 (265.9 bits), Expect = 2.2e-73, P = 2.2e-73
 Identities = 134/160 (83%), Positives = 145/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 ITDRAAQTLLWTELFRGLAMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 210

GO:0009055 "electron carrier activity" evidence=IEA

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

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

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

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

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

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

 Score = 740 (265.6 bits), Expect = 2.8e-73, P = 2.8e-73
 Identities = 134/160 (83%), Positives = 145/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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

UNIPROTKB|P0CB98 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" [Pongo pygmaeus (taxid:9600)]

 Score = 740 (265.6 bits), Expect = 2.8e-73, P = 2.8e-73
 Identities = 134/160 (83%), Positives = 145/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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|Q0MQI3 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" [Pan troglodytes (taxid:9598)]

 Score = 740 (265.6 bits), Expect = 2.8e-73, P = 2.8e-73
 Identities = 134/160 (83%), Positives = 145/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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 = 739 (265.2 bits), Expect = 3.6e-73, P = 3.6e-73
 Identities = 133/160 (83%), Positives = 145/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEA+CPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL+NGDKWE+EIA+NI AD+LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR 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|E2R5X8 NDUFS8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 736 (264.1 bits), Expect = 7.5e-73, P = 7.5e-73
 Identities = 133/160 (83%), Positives = 144/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR       TE+ RG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 VTDRAAQTLLWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEA+CPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLLSNGDKWE+EIA+NI AD+LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLSNGDKWEAEIAANIQADYLYR 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|Q0MQI2 NDUFS8 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial" [Gorilla gorilla gorilla (taxid:9595)]

 Score = 736 (264.1 bits), Expect = 7.5e-73, P = 7.5e-73
 Identities = 133/160 (83%), Positives = 144/160 (90%)

Query:     1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
             + DR       TE+FRG  +   ++F+EPATINYPFEKGPLSPRFRGEHALRRYPSGEER
Sbjct:    51 VTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEER 110

Query:    61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
             CIACKLCEAICPAQAITIEAE RADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN
Sbjct:   111 CIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 170

Query:   121 FEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
             FEFSTE+HEELLYNKEKLL+NGDKWE+EI +NI AD+LYR
Sbjct:   171 FEFSTETHEELLYNKEKLLNNGDKWEAEITANIQADYLYR 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

---

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	0.7070	0.9812	0.9573	yes	N/A
Q2W3J2	NUOI_MAGSA	1, ., 6, ., 9, 9, ., 5	0.7106	0.9937	0.9814	yes	N/A
B0ULL2	NUOI_METS4	1, ., 6, ., 9, 9, ., 5	0.7187	0.9937	0.9814	yes	N/A
Q42599	NDS8A_ARATH	1, ., 6, ., 9, 9, ., 3	0.775	1.0	0.7207	yes	N/A
Q1RKD0	NUOI_RICBR	1, ., 6, ., 9, 9, ., 5	0.7032	0.9687	0.9748	yes	N/A
B0BVB0	NUOI_RICRO	1, ., 6, ., 9, 9, ., 5	0.7032	0.9687	0.9748	yes	N/A
B9JVF4	NUOI_AGRVS	1, ., 6, ., 9, 9, ., 5	0.725	0.9937	0.9754	yes	N/A
A8I407	NUOI_AZOC5	1, ., 6, ., 9, 9, ., 5	0.7625	0.9937	0.9814	yes	N/A
Q68VV4	NUOI_RICTY	1, ., 6, ., 9, 9, ., 5	0.6903	0.9687	0.9748	yes	N/A
Q28T58	NUOI_JANSC	1, ., 6, ., 9, 9, ., 5	0.7388	0.9812	0.9573	yes	N/A
Q92G94	NUOI_RICCN	1, ., 6, ., 9, 9, ., 5	0.7032	0.9687	0.9748	yes	N/A
A7IP99	NUOI_XANP2	1, ., 6, ., 9, 9, ., 5	0.75	0.9937	0.9814	yes	N/A
Q1GIM9	NUOI_RUEST	1, ., 6, ., 9, 9, ., 5	0.7261	0.9812	0.9573	yes	N/A
A7HY41	NUOI_PARL1	1, ., 6, ., 9, 9, ., 5	0.7187	0.9937	0.9754	yes	N/A
Q1MIK6	NUOI_RHIL3	1, ., 6, ., 9, 9, ., 5	0.7307	0.9687	0.9509	yes	N/A
O00217	NDUS8_HUMAN	1, ., 6, ., 9, 9, ., 3	0.8375	1.0	0.7619	yes	N/A
Q8K3J1	NDUS8_MOUSE	1, ., 6, ., 9, 9, ., 3	0.8301	0.9937	0.75	yes	N/A
A8GY32	NUOI_RICB8	1, ., 6, ., 9, 9, ., 5	0.7032	0.9687	0.9748	yes	N/A
Q3J3F0	NUOI1_RHOS4	1, ., 6, ., 9, 9, ., 5	0.7142	0.9937	0.9520	yes	N/A
P0CB98	NDUS8_PONPY	1, ., 6, ., 9, 9, ., 3	0.8375	1.0	0.7619	N/A	N/A
Q2RU32	NUOI_RHORT	1, ., 6, ., 9, 9, ., 5	0.7106	0.9937	0.9814	yes	N/A
Q0BSL0	NUOI_GRABC	1, ., 6, ., 9, 9, ., 5	0.7	1.0	0.9876	yes	N/A
P0CB97	NDUS8_PONAB	1, ., 6, ., 9, 9, ., 3	0.8437	1.0	0.7619	yes	N/A
Q60HE3	NDUS8_MACFA	1, ., 6, ., 9, 9, ., 3	0.8312	1.0	0.7619	N/A	N/A
Q2NA74	NUOI_ERYLH	1, ., 6, ., 9, 9, ., 5	0.7733	0.9375	0.9259	yes	N/A
Q92QP4	NUOI1_RHIME	1, ., 6, ., 9, 9, ., 5	0.7187	0.9937	0.9695	yes	N/A
Q4UK24	NUOI_RICFE	1, ., 6, ., 9, 9, ., 5	0.7032	0.9687	0.9748	yes	N/A
B6ISX3	NUOI_RHOCS	1, ., 6, ., 9, 9, ., 5	0.7232	0.9937	0.9814	yes	N/A
O21233	NDUS8_RECAM	1, ., 6, ., 5, ., 3	0.7375	1.0	0.9876	N/A	N/A
P80269	NDUS8_SOLTU	1, ., 6, ., 9, 9, ., 3	0.775	1.0	0.6986	N/A	N/A
O24143	NDUS8_TOBAC	1, ., 6, ., 9, 9, ., 3	0.7562	1.0	0.6956	N/A	N/A
C4K221	NUOI_RICPU	1, ., 6, ., 9, 9, ., 5	0.7032	0.9687	0.9748	yes	N/A
Q5LPS9	NUOI_RUEPO	1, ., 6, ., 9, 9, ., 5	0.7452	0.9812	0.9573	yes	N/A
Q4FM83	NUOI_PELUB	1, ., 6, ., 9, 9, ., 5	0.7106	0.9937	0.9875	yes	N/A
A8GTS0	NUOI_RICRS	1, ., 6, ., 9, 9, ., 5	0.7032	0.9687	0.9748	yes	N/A
Q2G5Z4	NUOI_NOVAD	1, ., 6, ., 9, 9, ., 5	0.7421	0.9937	0.9875	yes	N/A
Q2K9S4	NUOI1_RHIEC	1, ., 6, ., 9, 9, ., 5	0.7187	0.9937	0.9754	yes	N/A
B8IUV4	NUOI_METNO	1, ., 6, ., 9, 9, ., 5	0.7312	0.9937	0.9814	yes	N/A
Q22619	NDUS8_CAEEL	1, ., 6, ., 9, 9, ., 3	0.8301	0.9937	0.75	yes	N/A
Q0C1D6	NUOI_HYPNA	1, ., 6, ., 9, 9, ., 5	0.7290	0.9687	0.9627	yes	N/A
Q12644	NDUS8_NEUCR	1, ., 6, ., 9, 9, ., 3	0.775	1.0	0.7305	N/A	N/A
Q9FX83	NDS8B_ARATH	1, ., 6, ., 9, 9, ., 3	0.7687	1.0	0.7207	no	N/A
Q0MQI2	NDUS8_GORGO	1, ., 6, ., 9, 9, ., 3	0.8312	1.0	0.7619	N/A	N/A
Q0MQI3	NDUS8_PANTR	1, ., 6, ., 9, 9, ., 3	0.8375	1.0	0.7619	yes	N/A
A8LIV0	NUOI_DINSH	1, ., 6, ., 9, 9, ., 5	0.7388	0.9812	0.9573	yes	N/A
Q8UFW9	NUOI_AGRT5	1, ., 6, ., 9, 9, ., 5	0.7062	0.9937	0.9754	yes	N/A
A3PIX9	NUOI1_RHOS1	1, ., 6, ., 9, 9, ., 5	0.7142	0.9937	0.9520	yes	N/A
Q0APY2	NUOI_MARMM	1, ., 6, ., 9, 9, ., 5	0.7044	0.9937	0.9814	yes	N/A
P42028	NDUS8_BOVIN	1, ., 6, ., 9, 9, ., 3	0.825	1.0	0.7547	yes	N/A
Q9ZCF8	NUOI_RICPR	1, ., 6, ., 9, 9, ., 5	0.6967	0.9687	0.9748	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	1.6.5.3	LOW CONFIDENCE prediction!
3rd Layer	1.6.99	0.983
3rd Layer	1.6.99.3	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	160
PRK05888	164	PRK05888, PRK05888, NADH dehydrogenase subunit I;	2e-88
COG1143	172	COG1143, NuoI, Formate hydrogenlyase subunit 6/NAD	1e-62
TIGR01971	122	TIGR01971, NuoI, NADH-quinone oxidoreductase, chai	2e-58
TIGR00403	183	TIGR00403, ndhI, NADH-plastoquinone oxidoreductase	4e-19
CHL00014	167	CHL00014, ndhI, NADH dehydrogenase subunit I	6e-18
PRK12387	180	PRK12387, PRK12387, formate hydrogenlyase complex	6e-17
PRK08222	181	PRK08222, PRK08222, hydrogenase 4 subunit H; Valid	1e-16
PRK13984	604	PRK13984, PRK13984, putative oxidoreductase; Provi	3e-12
PRK08348	120	PRK08348, PRK08348, NADH-plastoquinone oxidoreduct	2e-11
pfam12838	48	pfam12838, Fer4_7, 4Fe-4S dicluster domain	2e-10
TIGR02512	374	TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, grou	4e-10
PRK07118	280	PRK07118, PRK07118, ferredoxin; Validated	6e-10
COG1145	99	COG1145, NapF, Ferredoxin [Energy production and c	3e-09
TIGR02700	234	TIGR02700, flavo_MJ0208, archaeoflavoprotein, MJ02	1e-08
COG2768	354	COG2768, COG2768, Uncharacterized Fe-S center prot	2e-08
pfam13484	67	pfam13484, Fer4_16, 4Fe-4S double cluster binding	7e-08
PRK06273	165	PRK06273, PRK06273, ferredoxin; Provisional	1e-07
PRK14028	312	PRK14028, PRK14028, pyruvate ferredoxin oxidoreduc	1e-07
TIGR02494	295	TIGR02494, PFLE_PFLC, glycyl-radical enzyme activa	2e-07
TIGR04105	462	TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, gro	2e-07
PRK13795	636	PRK13795, PRK13795, hypothetical protein; Provisio	2e-07
pfam13237	51	pfam13237, Fer4_10, 4Fe-4S dicluster domain	2e-07
pfam13187	44	pfam13187, Fer4_9, 4Fe-4S dicluster domain	2e-07
TIGR04105	462	TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, gro	3e-07
COG1149	284	COG1149, COG1149, MinD superfamily P-loop ATPase c	3e-07
COG2221	317	COG2221, DsrA, Dissimilatory sulfite reductase (de	3e-07
TIGR02179	78	TIGR02179, PorD_KorD, 2-oxoacid:acceptor oxidoredu	4e-07
COG1146	68	COG1146, COG1146, Ferredoxin [Energy production an	6e-07
PRK12771	564	PRK12771, PRK12771, putative glutamate synthase (N	1e-06
COG1144	91	COG1144, COG1144, Pyruvate:ferredoxin oxidoreducta	2e-06
COG3383	978	COG3383, COG3383, Uncharacterized anaerobic dehydr	6e-06
pfam00037	24	pfam00037, Fer4, 4Fe-4S binding domain	1e-05
COG0437	203	COG0437, HybA, Fe-S-cluster-containing hydrogenase	2e-05
COG1142	165	COG1142, HycB, Fe-S-cluster-containing hydrogenase	3e-05
PRK07118	280	PRK07118, PRK07118, ferredoxin; Validated	4e-05
PRK09898	208	PRK09898, PRK09898, hypothetical protein; Provisio	4e-05
TIGR03224	411	TIGR03224, benzo_boxA, benzoyl-CoA oxygenase/reduc	6e-05
PRK09623	105	PRK09623, vorD, 2-ketoisovalerate ferredoxin oxido	7e-05
PRK12769	654	PRK12769, PRK12769, putative oxidoreductase Fe-S b	9e-05
COG1142	165	COG1142, HycB, Fe-S-cluster-containing hydrogenase	1e-04
PRK08318	420	PRK08318, PRK08318, dihydropyrimidine dehydrogenas	1e-04
TIGR03336	595	TIGR03336, IOR_alpha, indolepyruvate ferredoxin ox	1e-04
TIGR04003	314	TIGR04003, rSAM_BssD, [benzylsuccinate synthase]-a	1e-04
COG4231	640	COG4231, COG4231, Indolepyruvate ferredoxin oxidor	2e-04
TIGR01944	165	TIGR01944, rnfB, electron transport complex, RnfAB	2e-04
pfam13183	54	pfam13183, Fer4_8, 4Fe-4S dicluster domain	2e-04
COG1148	622	COG1148, HdrA, Heterodisulfide reductase, subunit	3e-04
COG1148	622	COG1148, HdrA, Heterodisulfide reductase, subunit	4e-04
COG1600	337	COG1600, COG1600, Uncharacterized Fe-S protein [En	4e-04
TIGR04270	535	TIGR04270, Rama_corrin_act, methylamine methyltran	5e-04
PRK09898	208	PRK09898, PRK09898, hypothetical protein; Provisio	6e-04
TIGR01944	165	TIGR01944, rnfB, electron transport complex, RnfAB	6e-04
TIGR03294	228	TIGR03294, FrhG, coenzyme F420 hydrogenase, subuni	7e-04
COG0437	203	COG0437, HybA, Fe-S-cluster-containing hydrogenase	8e-04
COG0348	386	COG0348, NapH, Polyferredoxin [Energy production a	8e-04
COG1142	165	COG1142, HycB, Fe-S-cluster-containing hydrogenase	0.001
TIGR02163	255	TIGR02163, napH_, ferredoxin-type protein, NapH/Ma	0.001
PRK06991	270	PRK06991, PRK06991, ferredoxin; Provisional	0.001
PRK09624	105	PRK09624, porD, pyuvate ferredoxin oxidoreductase	0.001
PRK14993	244	PRK14993, PRK14993, tetrathionate reductase subuni	0.001
COG4656	529	COG4656, RnfC, Predicted NADH:ubiquinone oxidoredu	0.001
COG1149	284	COG1149, COG1149, MinD superfamily P-loop ATPase c	0.002
pfam00037	24	pfam00037, Fer4, 4Fe-4S binding domain	0.002
PRK00941	781	PRK00941, PRK00941, acetyl-CoA decarbonylase/synth	0.002
TIGR04041	276	TIGR04041, activase_YjjW, glycine radical enzyme a	0.002
PRK05113	191	PRK05113, PRK05113, electron transport complex pro	0.002
pfam12837	24	pfam12837, Fer4_6, 4Fe-4S binding domain	0.002
pfam13459	60	pfam13459, Fer4_15, 4Fe-4S single cluster domain	0.002
TIGR02060	132	TIGR02060, aprB, adenosine phosphosulphate reducta	0.002
pfam13534	61	pfam13534, Fer4_17, 4Fe-4S dicluster domain	0.002
cd07030	259	cd07030, RNAP_D, D subunit of Archaeal RNA polymer	0.003
TIGR03287	391	TIGR03287, methan_mark_16, putative methanogenesis	0.003
COG2878	198	COG2878, COG2878, Predicted NADH:ubiquinone oxidor	0.003
PRK00783	263	PRK00783, PRK00783, DNA-directed RNA polymerase su	0.004

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

 Score =  254 bits (652), Expect = 2e-88
 Identities = 100/159 (62%), Positives = 120/159 (75%)

Query: 2   VDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERC 61
           + + + +  L E+ +G  V   + FK+  TI YP EK PLSPRFRG HALRR P+GEERC
Sbjct: 1   IKQYLKSMLLKELLKGLGVTLKYFFKKKVTIQYPEEKLPLSPRFRGRHALRRDPNGEERC 60

Query: 62  IACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF 121
           IACKLC AICPA AITIEA ER DG RRTTRYDI+  +CI+CGFC+EACP DAIVE P+F
Sbjct: 61  IACKLCAAICPADAITIEAAEREDGRRRTTRYDINFGRCIFCGFCEEACPTDAIVETPDF 120

Query: 122 EFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           E +TE+ EEL+Y+KEKLL+NGD+ E EIA    AD  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 =  189 bits (483), Expect = 1e-62
 Identities = 71/165 (43%), Positives = 94/165 (56%), Gaps = 10/165 (6%)

Query: 1   MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
            +       FL +  +G +    ++FK+P TI YP EK PLSPRFRG H L R       
Sbjct: 2   KLKEAAKVKFLLDFLKGLWTTLKNLFKKPVTIEYPEEKIPLSPRFRGRHVLDRDK----- 56

Query: 61  CIACKLCEAICPAQAITIEAEER-ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 119
           CI C LC  ICPA AIT+E  ER  DG ++  R DI++ +CI+CG C E CP  A+V  P
Sbjct: 57  CIGCGLCANICPANAITMETAERKVDGRKKPKRPDINLGRCIFCGLCVEVCPTGALVLTP 116

Query: 120 NFEFSTESHEELLYNKEKLLSNGDKWE----SEIASNIHADHLYR 160
            FE ++   E+L+Y+KE+LL+  DK E     EIA  +  D  Y 
Sbjct: 117 EFELASYKREDLVYDKERLLAPPDKKEEDKPFEIARLLALDAKYL 161

Length = 172

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

 Score =  177 bits (451), Expect = 2e-58
 Identities = 60/122 (49%), Positives = 76/122 (62%)

Query: 17  GFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAI 76
           G  +   + F +P T+ YP EK  L PRFRG   L R P+GEE+CI C LC A+CPA AI
Sbjct: 1   GLGLTLKYFFSKPVTVQYPEEKLYLPPRFRGRIVLTRDPNGEEKCIGCTLCAAVCPADAI 60

Query: 77  TIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKE 136
            +   E  DG RR   Y I+  +CI+CG C+EACP DAIV  P FE +T +  +L+Y KE
Sbjct: 61  RVVPAEGEDGKRRLKFYQINFGRCIFCGLCEEACPTDAIVLTPEFELATYTRSDLVYGKE 120

Query: 137 KL 138
            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|129498 TIGR00403, ndhI, NADH-plastoquinone oxidoreductase subunit I protein

 Score = 79.2 bits (195), Expect = 4e-19
 Identities = 45/126 (35%), Positives = 65/126 (51%), Gaps = 6/126 (4%)

Query: 14  IFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPA 73
           I +GF V   H+ + P TI YP+EK   S RFRG     R     ++CIAC++C  +CP 
Sbjct: 22  IGQGFAVTLDHMNRLPITIQYPYEKLIPSERFRG-----RIHFEFDKCIACEVCVRVCPI 76

Query: 74  QAITIEAE-ERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELL 132
               ++ E  +A   ++   Y ID   CI+CG C E CP + +     +E ST    EL 
Sbjct: 77  NLPVVDWEFNKAIKKKQLKNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELN 136

Query: 133 YNKEKL 138
           Y++  L
Sbjct: 137 YDQIAL 142

[Energy metabolism, Electron transport]. Length = 183

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

 Score = 75.6 bits (186), Expect = 6e-18
 Identities = 44/123 (35%), Positives = 62/123 (50%), Gaps = 6/123 (4%)

Query: 14  IFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPA 73
           I +GF +   H  + P TI YP+EK   S RFRG     R     ++CIAC++C  +CP 
Sbjct: 19  IGQGFMITLSHANRLPVTIQYPYEKLITSERFRG-----RIHFEFDKCIACEVCVRVCPI 73

Query: 74  QAITIEAEERAD-GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELL 132
               ++ +   D   +R   Y ID   CI+CG C E CP + +     +E ST    EL 
Sbjct: 74  DLPVVDWKLETDIRKKRLLNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELN 133

Query: 133 YNK 135
           YN+
Sbjct: 134 YNQ 136

Length = 167

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

 Score = 73.1 bits (180), Expect = 6e-17
 Identities = 34/110 (30%), Positives = 52/110 (47%), Gaps = 13/110 (11%)

Query: 29  PATINYPFEKGPLSPRFRG--EHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADG 86
            AT +YP E   +   FRG  E+         ++CI C  C   CP+ A+T+E +     
Sbjct: 13  TATSSYPLEPIAVDKNFRGKPEYNP-------QQCIGCAACVNACPSNALTVETDLATG- 64

Query: 87  SRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKE 136
                 ++ ++ +CI+CG C+E CP  AI     FE +    E+LL   E
Sbjct: 65  ---ELAWEFNLGRCIFCGRCEEVCPTAAIKLSQEFELAVWKKEDLLQQSE 111

Length = 180

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

 Score = 72.5 bits (178), Expect = 1e-16
 Identities = 37/102 (36%), Positives = 56/102 (54%), Gaps = 9/102 (8%)

Query: 30  ATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRR 89
           AT+ YPF    +SP FRG+  L        +CIAC  C   CPA A+TI+ +++ +    
Sbjct: 14  ATVKYPFAPLEVSPGFRGKPDL-----MPSQCIACGACTCACPANALTIQTDDQQN---- 64

Query: 90  TTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEEL 131
           +  + + + +CIYCG C+E CP  AI    NFE +  +  +L
Sbjct: 65  SRTWQLYLGRCIYCGRCEEVCPTRAIQLTNNFELTVTNKADL 106

Length = 181

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

 Score = 62.9 bits (153), Expect = 3e-12
 Identities = 31/98 (31%), Positives = 45/98 (45%), Gaps = 7/98 (7%)

Query: 15  FRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQ 74
           F     A   +F++P TI  P  K   + R+RG H      +  E+CI C  C  ICP  
Sbjct: 6   FFAPLKAWKFLFRKPVTIKVPNVKREAAERYRGFHI-----NDWEKCIGCGTCSKICPTD 60

Query: 75  AIT-IEAEERADG-SRRTTRYDIDMTKCIYCGFCQEAC 110
           AIT +E  +      ++  R  ID  +C +C  C + C
Sbjct: 61  AITMVEVPDLPQEYGKKPQRPVIDYGRCSFCALCVDIC 98

Length = 604

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

 Score = 57.2 bits (138), Expect = 2e-11
 Identities = 27/103 (26%), Positives = 48/103 (46%), Gaps = 14/103 (13%)

Query: 25  IFKEPATINYP-FEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER 83
           +FK+PAT  +P  E  P+   FRG+          ++C+ C++C  +CPA       E R
Sbjct: 12  LFKKPATNLFPATEPVPVPEDFRGKILYDV-----DKCVGCRMCVTVCPAGVFVYLPEIR 66

Query: 84  ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTE 126
                   +  +   +C++CG C + CP  A+    +F  ++ 
Sbjct: 67  --------KVALWTGRCVFCGQCVDVCPTGALQMSDDFLLASY 101

Length = 120

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

 Score = 52.9 bits (127), Expect = 2e-10
 Identities = 20/53 (37%), Positives = 23/53 (43%), Gaps = 5/53 (9%)

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
           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|233903 TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A

 Score = 56.6 bits (137), Expect = 4e-10
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 60  RCIACKLCEAICPAQAIT--IEAEERADGSRRTTRYD--IDMTKCIYCGFCQEACPVDAI 115
           +CI C  C   C    I   +    R   +    ++   +D + CI CG C   CPV AI
Sbjct: 8   KCIGCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLVCPVGAI 67

Query: 116 VEGPNFEFSTESHEELLYNKEKL 138
            E  +     +   + L + +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|235941 PRK07118, PRK07118, ferredoxin; Validated

 Score = 55.7 bits (135), Expect = 6e-10
 Identities = 23/57 (40%), Positives = 24/57 (42%), Gaps = 10/57 (17%)

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
           CI C  C   CPA AIT+E               ID  KC  CG C E CP  AI  
Sbjct: 215 CIGCGKCVKACPAGAITME----------NNLAVIDQEKCTSCGKCVEKCPTKAIRI 261

Length = 280

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

 Score = 51.1 bits (121), Expect = 3e-09
 Identities = 22/58 (37%), Positives = 28/58 (48%), Gaps = 5/58 (8%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            E+CI C LC  +CP  AI +  E             ID   C+ CG C + CPVDA+
Sbjct: 28  AEKCIGCGLCVKVCPTGAIELIEEGLLLP-----EVVIDPDLCVLCGACLKVCPVDAL 80

Length = 99

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

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 10/69 (14%)

Query: 54  YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
           Y    +RC  C +C   CP  AI               +  I + KC+ CG C+EACP +
Sbjct: 143 YMIDRKRCKGCGICVDACPRSAI----------DMVDGKAFIRLLKCVGCGKCKEACPYN 192

Query: 114 AIVEGPNFE 122
           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|225358 COG2768, COG2768, Uncharacterized Fe-S center protein [General function prediction only]

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 37/118 (31%), Positives = 47/118 (39%), Gaps = 20/118 (16%)

Query: 23  GHIFKE--PATINYPFEKGPLSPRFRGEHALRRYPSG-EERCIACKLCEAICPAQAITIE 79
           GH          N       L+ +   +H L   P   EE+C  C LC  ICP  AIT+ 
Sbjct: 156 GHGMTGFGGTIKNVGMGCASLAGKV-DQH-LDEKPVVVEEKCYDCGLCVKICPVGAITLT 213

Query: 80  AEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELL--YNK 135
                   +      ID  KCI CG C EACP  A+    N+E  +    E +  Y K
Sbjct: 214 -----KVVK------IDYEKCIGCGQCMEACPYGAV--DQNWEEDSPEFLERMAEYAK 258

Length = 354

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

 Score = 46.8 bits (111), Expect = 7e-08
 Identities = 22/65 (33%), Positives = 25/65 (38%), Gaps = 13/65 (20%)

Query: 60  RCIACKLCEAICPAQAITIEAEERADGSR-------RTTRYDIDMTKCI------YCGFC 106
            C  C  C   CP  AI+ E E   D  R           + ID  KC+       CG C
Sbjct: 1   FCGTCGKCADACPTGAISGEDEPTWDARRCISYNTIGKKGWIIDELKCLLGGRIYGCGIC 60

Query: 107 QEACP 111
           QE CP
Sbjct: 61  QEVCP 65

Length = 67

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

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 58  EERCIACKLCEAICPAQAIT---IEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
           EE CI C  C  +CP +AI    +E  +  +G  +T    ID  KC+YC +C + CPV
Sbjct: 48  EELCIGCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCPV 105

Length = 165

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

 Score = 49.2 bits (117), Expect = 1e-07
 Identities = 26/60 (43%), Positives = 29/60 (48%), Gaps = 5/60 (8%)

Query: 60  RCIACKLCEAICPAQAITIEAEERADGSR----RTTRYDIDMTKCIYCGFCQEACPVDAI 115
           +CI C+ C   CP  AI IEA   A+G R    R    D D   C  CG C E CP  AI
Sbjct: 248 KCIMCRKCWLYCPDDAI-IEAWREAEGPRGRKFRMKMIDFDYQYCKGCGVCAEVCPTGAI 306

Length = 312

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

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 24/58 (41%), Positives = 29/58 (50%), Gaps = 5/58 (8%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           E RC+ C  C  +CPA    +   E ADG     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|234472 TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3

 Score = 49.1 bits (118), Expect = 2e-07
 Identities = 21/51 (41%), Positives = 24/51 (47%), Gaps = 9/51 (17%)

Query: 67  CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
           CE  CP  AI+ +   RA          ID  KCI CG C  ACP  AI +
Sbjct: 166 CEKACPVGAISSDENGRAV---------IDYDKCISCGACMVACPFGAISD 207

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

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

 Score = 49.2 bits (118), Expect = 2e-07
 Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 60  RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
            C+ C +C   CP  AI IE  +R        +  +D  KCI+CG C E CPV
Sbjct: 582 ECVGCGVCVGACPTGAIRIEEGKR--------KISVDEEKCIHCGKCTEVCPV 626

Length = 636

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

 Score = 45.1 bits (106), Expect = 2e-07
 Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 6/54 (11%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
            ++CI C  C A CPA                    +ID  +CI CG C E CP
Sbjct: 4   PDKCIGCGRCVAACPA------RVGAGAIRDEGGAVEIDPDRCIGCGACVEVCP 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|221966 pfam13187, Fer4_9, 4Fe-4S dicluster domain

 Score = 44.9 bits (106), Expect = 2e-07
 Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 12/56 (21%)

Query: 60  RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           +CI C  C  +CPA  I  +   +             + KCI CG C E CPV AI
Sbjct: 1   KCIGCGACVKVCPAGVIMRDNGGKV------------VVKCIGCGACVEVCPVGAI 44

Length = 44

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

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 11/57 (19%)

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
           C+A   C  +CP  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|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 18/72 (25%), Positives = 24/72 (33%), Gaps = 9/72 (12%)

Query: 48  EHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQ 107
                      E+CI C  C  +C   AI +    +           ++   C  CG C 
Sbjct: 58  VIRGEIPEIDPEKCIRCGKCAEVCRFGAIVVLPGGK---------PVLNPDLCEGCGACS 108

Query: 108 EACPVDAIVEGP 119
             CP  AI E P
Sbjct: 109 IVCPEPAIEEEP 120

Length = 284

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

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 23/63 (36%), Positives = 28/63 (44%), Gaps = 11/63 (17%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
           EE C  C  C  +CP  AIT + ++            ID +KCI CG C  ACP  A   
Sbjct: 171 EELCRGCGKCVKVCPTGAITWDGKK----------LKIDGSKCIGCGKCIRACP-KAAFR 219

Query: 118 GPN 120
           G  
Sbjct: 220 GEK 222

Length = 317

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

 Score = 45.0 bits (107), Expect = 4e-07
 Identities = 23/58 (39%), Positives = 26/58 (44%), Gaps = 9/58 (15%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           +E+CI CK C   CP  AI    +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|224069 COG1146, COG1146, Ferredoxin [Energy production and conversion]

 Score = 44.4 bits (105), Expect = 6e-07
 Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 6/58 (10%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            ++CI C +C  +CPA    +                    +CI CG C+ ACPV AI
Sbjct: 7   YDKCIGCGICVEVCPAGVFDL------GEDEGGKPVVARPEECIDCGLCELACPVGAI 58

Length = 68

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

 Score = 46.8 bits (112), Expect = 1e-06
 Identities = 21/59 (35%), Positives = 22/59 (37%), Gaps = 8/59 (13%)

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 119
           C  C  C   CP  AI      R        RY  D  KC  C  C + CP  AI  GP
Sbjct: 512 CFECDNCYGACPQDAIIKLGPGR--------RYHFDYDKCTGCHICADVCPCGAIEMGP 562

Length = 564

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

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 24/59 (40%), Positives = 27/59 (45%), Gaps = 8/59 (13%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
           E++CI CKLC   CP  AI     E   G +    YD     C  CG C   CPV AI 
Sbjct: 34  EDKCINCKLCWLYCPEPAI----LEEEGGYKVRIDYD----YCKGCGICANVCPVKAIE 84

Length = 91

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

 Score = 44.7 bits (106), Expect = 6e-06
 Identities = 24/95 (25%), Positives = 37/95 (38%), Gaps = 25/95 (26%)

Query: 33  NYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICP----AQAITIEAEERADGSR 88
           N P+ K   +P +  +           +CI C  C   C      +A+TI      D   
Sbjct: 132 NPPYPKDESNPFYIYDPN---------QCILCGRCVEACQEVQVNEALTI------DWRG 176

Query: 89  RTTR------YDIDMTKCIYCGFCQEACPVDAIVE 117
              R        I+ + C+ CG C   CPV+A++E
Sbjct: 177 EDPRVIWDNDVPINESSCVSCGACVTVCPVNALME 211

Length = 978

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

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 14/23 (60%), Positives = 14/23 (60%)

Query: 93  YDIDMTKCIYCGFCQEACPVDAI 115
             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 = 42.4 bits (100), Expect = 2e-05
 Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 21/71 (29%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQE 108
           ++ CI C  C A CP  A     ++              + KC +C           C E
Sbjct: 99  KDLCIGCGYCIAACPYGAPQFNPDKGV------------VDKCTFCVDRVAVGKLPACVE 146

Query: 109 ACPVDAIVEGP 119
           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 = 41.3 bits (97), Expect = 3e-05
 Identities = 22/65 (33%), Positives = 28/65 (43%), Gaps = 14/65 (21%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGF------CQEACP 111
           EE+CI CKLC   CP  AIT+        ++          KC  C        C EACP
Sbjct: 81  EEKCIGCKLCVVACPFGAITM--VSYPVAAKAV------AVKCDLCAGREVGPACVEACP 132

Query: 112 VDAIV 116
            +A+ 
Sbjct: 133 TEALE 137

Length = 165

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

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 58  EERCIACKLCEAICPAQAIT-IEAEERADGSRRTTRYDIDMTK-----CIYCGFCQEACP 111
           E++C  C  C   CP   I  I    R   +  +      + K     CI CG C +ACP
Sbjct: 167 EDKCTGCGACVKACPRNVIELIPKSARVFVACNSKDKGKAVKKVCEVGCIGCGKCVKACP 226

Query: 112 VDAIV 116
             AI 
Sbjct: 227 AGAIT 231

Length = 280

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

 Score = 41.7 bits (98), Expect = 4e-05
 Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 12/58 (20%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            +RCI C  C   CP    T+  E +              +KC+ CG C  ACP  A+
Sbjct: 153 HKRCIGCSACTTACPWMMATVNTESKKS------------SKCVLCGECANACPTGAL 198

Length = 208

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

 Score = 41.8 bits (98), Expect = 6e-05
 Identities = 19/57 (33%), Positives = 21/57 (36%), Gaps = 10/57 (17%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           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|170016 PRK09623, vorD, 2-ketoisovalerate ferredoxin oxidoreductase subunit delta; Reviewed

 Score = 39.5 bits (92), Expect = 7e-05
 Identities = 21/58 (36%), Positives = 25/58 (43%), Gaps = 9/58 (15%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           E +C+ C +C   CP  AI I    + DG        ID   C  CG C   CP  AI
Sbjct: 50  ESKCVKCYICWKFCPEPAIYI----KEDGY-----VAIDYDYCKGCGICANECPTKAI 98

Length = 105

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

 Score = 41.3 bits (97), Expect = 9e-05
 Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 11/64 (17%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG------FCQEACP 111
           +++CI CK C   CP   + I     A G  + T +     KC  C        C E CP
Sbjct: 84  QQKCIGCKSCVVACPFGTMQIVLTPVAAGKVKATAH-----KCDLCAGRENGPACVENCP 138

Query: 112 VDAI 115
            DA+
Sbjct: 139 ADAL 142

Length = 654

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 10/49 (20%)

Query: 67  CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           C  +CP  AIT     R DG+ +     +D  KCI C  C  ACP  AI
Sbjct: 61  CAEVCPVGAIT-----RDDGAVQ-----VDEEKCIGCKLCVVACPFGAI 99

Length = 165

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

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 10/63 (15%)

Query: 58  EERCIACKLCEAIC---PAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
           +++CI C  C   C     QAI  +     DG+R     ++   +C+ C  C   CPV+ 
Sbjct: 341 QDKCIGCGRCYIACEDTSHQAIEWDE----DGTRT---PEVIEEECVGCNLCAHVCPVEG 393

Query: 115 IVE 117
            + 
Sbjct: 394 CIT 396

Length = 420

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

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 25/76 (32%), Positives = 30/76 (39%), Gaps = 17/76 (22%)

Query: 44  RFRGEHALRRYP--SGEERCIACKLC--EAICPAQAITIEAEERADGSRRTTRYDIDMTK 99
                   R  P    +++CI CK C  E  CPA  I  E +E            ID   
Sbjct: 533 LSNKRAGKRAGPYKVDQDKCIGCKKCIKELGCPA--IEPEDKEAV----------IDPL- 579

Query: 100 CIYCGFCQEACPVDAI 115
           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|188518 TIGR04003, rSAM_BssD, [benzylsuccinate synthase]-activating enzyme

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 5/57 (8%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
             RC+ C  C A+CPA    +      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|226684 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 12/63 (19%)

Query: 58  EERCIACKLC--EAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           EE+C  C  C   + CP+  I  +   +        +  ID + C  CG C E CP  AI
Sbjct: 576 EEKCTGCGDCIVLSGCPS--IEPDPTFK--------KARIDPSSCNGCGSCVEVCPSFAI 625

Query: 116 VEG 118
            EG
Sbjct: 626 KEG 628

Length = 640

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 9/59 (15%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
           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|221963 pfam13183, Fer4_8, 4Fe-4S dicluster domain

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 4/55 (7%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
            +CI C  C A+CP       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|224070 COG1148, HdrA, Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 13/58 (22%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           E++C  C +C   CP  AI+++            + +++  +C  CG C  ACP  AI
Sbjct: 560 EDKCTGCGICAE-CPFGAISVD------------KAEVNPLRCKGCGICSAACPSGAI 604

Length = 622

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

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 18/71 (25%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTR-------------YDIDMTKCIYCGF 105
           ++C  C  C  +CP     +E     +      +             Y+ID   CI CG 
Sbjct: 224 DKCTGCGACSEVCP-----VEVPNEFNEGLGKRKAIYIPFPQAVPLNYNIDPKHCIECGL 278

Query: 106 CQEACPVDAIV 116
           C++ACP +A+ 
Sbjct: 279 CEKACPNEAVD 289

Length = 622

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

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 19/69 (27%), Positives = 26/69 (37%), Gaps = 14/69 (20%)

Query: 55  PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDID-----------MTKCIY- 102
           P  E+ C +C  C   CP  A+   A    D  R  +   I+           +   IY 
Sbjct: 181 PEEEDHCGSCTRCLDACPTGALV--APYTVDARRCISYLTIEKGGAPEEFRPLIGNRIYG 238

Query: 103 CGFCQEACP 111
           C  CQ+ CP
Sbjct: 239 CDICQKVCP 247

Length = 337

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

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 7/57 (12%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           E CIAC+ C   CP +A++I   E         R D D      C  C+  CP    
Sbjct: 479 EGCIACQKCVKECPGKALSILESEPP-------RIDTDRCLGTACRRCERVCPEKVF 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|182135 PRK09898, PRK09898, hypothetical protein; Provisional

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 10/55 (18%)

Query: 59  ERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
           + C  CK   C  +CP  AIT + +E            +D  +CI C  C  ACP
Sbjct: 121 DTCRQCKEPQCMNVCPIGAITWQQKEGC--------ITVDHKRCIGCSACTTACP 167

Length = 208

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

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 95  IDMTKCIYCGFCQEACPVDAIVEGPNF 121
           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|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 10/51 (19%)

Query: 61  CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
           C+ C  C A CP +AI +E     DG     R +++  +CI CG C   CP
Sbjct: 176 CMGCGTCAAACPTRAIEME-----DG-----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|223514 COG0437, HybA, Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 13/59 (22%)

Query: 62  IACKLCE-----AICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           I+C  CE      +CP  A+    E   DG        +D   CI CG+C  ACP  A 
Sbjct: 67  ISCMHCEDPPCVKVCPTGALFKREE---DGI-----VLVDKDLCIGCGYCIAACPYGAP 117

Length = 203

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

 Score = 38.2 bits (89), Expect = 8e-04
 Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 17/65 (26%)

Query: 58  EERCIA-CKLCEAICPAQA-----ITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
           ++R    CK C+ +CP        +     +  DG            +CI CG C +AC 
Sbjct: 210 DKRGCPRCKRCKKVCPEPIPLWVQVCPAGIDIRDGL-----------ECIGCGRCIDACD 258

Query: 112 VDAIV 116
            D + 
Sbjct: 259 DDMLK 263

Length = 386

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 4/74 (5%)

Query: 52  RRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMT--KCIYC--GFCQ 107
           R   +  E+CI C+ CE  C      I+++          + D +     C +C    C 
Sbjct: 3   RFIIADPEKCIGCRTCEVACVVAHEEIQSQSIFLPRIMVIKNDGESAPVVCHHCEDAPCA 62

Query: 108 EACPVDAIVEGPNF 121
           E CPV AI      
Sbjct: 63  EVCPVGAITRDDGA 76

Length = 165

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 18/70 (25%), Positives = 25/70 (35%), Gaps = 12/70 (17%)

Query: 56  SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           S  E+C  C  C  +CP   + +    +  GS      D     C  CG C + C  D  
Sbjct: 198 SDREKCTNCMDCFNVCPEPQV-LRMPLKKGGSTLVLSGD-----CTLCGRCIDVCHEDV- 250

Query: 116 VEGPNFEFST 125
                  F+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|235903 PRK06991, PRK06991, ferredoxin; Provisional

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 15/25 (60%), Positives = 16/25 (64%)

Query: 95  IDMTKCIYCGFCQEACPVDAIVEGP 119
           ID   CI C  C +ACPVDAIV  P
Sbjct: 82  IDEQLCIGCTLCMQACPVDAIVGAP 106

Length = 270

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

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 11/60 (18%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDI-DMTKCIYCGFCQEACPVDAIV 116
            ++C+ C LC   CP  AI ++ E           Y + D   C  CG C   CP  AI 
Sbjct: 50  RDKCVRCYLCYIYCPEPAIYLDEEG----------YPVFDYDYCKGCGICANECPTKAIE 99

Length = 105

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

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 9/48 (18%)

Query: 67  CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
           C  +CP QA      +R DG        +D  +C+ C +C +ACP DA
Sbjct: 108 CVPVCPVQATF----QREDGI-----VVVDNKRCVGCAYCVQACPYDA 146

Length = 244

>gnl|CDD|227003 COG4656, RnfC, Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion]

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 18/58 (31%), Positives = 25/58 (43%)

Query: 55  PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
           P  E+ CI C LC   CP   +  +    A G +     + ++  CI CG C   CP 
Sbjct: 361 PIKEQSCIRCSLCADACPVNLLPQQLYWFAKGEQHDEEEEHNLLDCIECGACAYVCPS 418

Length = 529

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 17/42 (40%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 79  EAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           E  E  +   R    +ID  KCI CG C E C   AIV  P 
Sbjct: 51  EVLEEEE-VIRGEIPEIDPEKCIRCGKCAEVCRFGAIVVLPG 91

Length = 284

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

 Score = 33.8 bits (78), Expect = 0.002
 Identities = 11/20 (55%), Positives = 13/20 (65%)

Query: 58 EERCIACKLCEAICPAQAIT 77
          EE+CI C  C  +CP  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|179174 PRK00941, PRK00941, acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 13/75 (17%)

Query: 46  RGEHALRRYPSGEE------RCIACKLCEAICPAQAITIEAEERA---DGSRRTTRYDID 96
           R    ++  P+ EE      +C  C  C  +CP +    EA E A   D S+    YD  
Sbjct: 385 RKAKGIKALPTDEELKELAKKCTECGWCVRVCPNELPIPEAMEAAAKGDLSKLEDLYD-- 442

Query: 97  MTKCIYCGFCQEACP 111
             KCI CG C++ CP
Sbjct: 443 --KCIGCGRCEQVCP 455

Length = 781

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

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 10/52 (19%)

Query: 60  RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
            C  C  C A CPA A+++      DG      +D +  +CI C  C + CP
Sbjct: 42  HCDHCGDCVAGCPAGALSLV-----DGK---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|235347 PRK05113, PRK05113, electron transport complex protein RnfB; Provisional

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 14/22 (63%), Positives = 15/22 (68%)

Query: 95  IDMTKCIYCGFCQEACPVDAIV 116
           ID   CI C  C +ACPVDAIV
Sbjct: 111 IDEDNCIGCTKCIQACPVDAIV 132

Length = 191

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

 Score = 33.7 bits (78), Expect = 0.002
 Identities = 12/21 (57%), Positives = 12/21 (57%)

Query: 95  IDMTKCIYCGFCQEACPVDAI 115
           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|222145 pfam13459, Fer4_15, 4Fe-4S single cluster domain

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 9/62 (14%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEA---CPVDA 114
            + CI C LC A+ P     ++ + +A           D+ +       QEA   CPVDA
Sbjct: 4   RDTCIGCGLCVALAPD-VFELDEDGKARVILDEGEVPDDLEEDA-----QEAADACPVDA 57

Query: 115 IV 116
           I 
Sbjct: 58  IH 59

Length = 60

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 12/75 (16%)

Query: 59  ERCIACKL-----CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
            +C  CK      C  ICP   + ++ E           Y+I+   C  C  C +ACP  
Sbjct: 8   TKCDGCKAGEKTACVYICPNDLMHLDTEIM-------KAYNIEPDMCWECYSCVKACPQG 60

Query: 114 AIVEGPNFEFSTESH 128
           AI      +F+    
Sbjct: 61  AIDVRGYADFAPLGG 75

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|222205 pfam13534, Fer4_17, 4Fe-4S dicluster domain

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 5/57 (8%)

Query: 60  RCIACKLCEAICPAQAITIE-----AEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
           RCI C  C  +CP+  +  +          +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|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 26/94 (27%), Positives = 32/94 (34%), Gaps = 23/94 (24%)

Query: 48  EHA---------LRRYPSGE--ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDID 96
           EHA          + YP  E  E C  C  C   CP   + +E  +             D
Sbjct: 147 EHAKWQPTTACGYKYYPVIEIDEDCDGCGKCVEECPRGVLELEEGKVVVE---------D 197

Query: 97  MTKCIYCGFCQEACPVDAIVEGP---NFEFSTES 127
           +  C  C  C+ AC   AI  G     F F  ES
Sbjct: 198 LEDCSLCKLCERACDAGAIRVGWDEDRFIFEVES 231

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 which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer. Length = 259

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

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 20/58 (34%), Positives = 24/58 (41%), Gaps = 15/58 (25%)

Query: 59  ERCIACKLC--EAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
           ERC  C  C  E  CP  AI      + DG        ++   C  CG+C E CP  A
Sbjct: 302 ERCENCDPCLVEEACPVPAI------KKDG-------TLNTEDCFGCGYCAEICPGGA 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|225433 COG2878, COG2878, Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 95  IDMTKCIYCGFCQEACPVDAIVEGPNF 121
           ID   CI C  C +ACPVDAIV     
Sbjct: 112 IDEANCIGCTKCIQACPVDAIVGATKA 138

Length = 198

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 12/73 (16%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
            E C  C+ C   CP   + ++  +             D+  C  C  C+ ACP  AI  
Sbjct: 168 SEDCDECEKCVEACPRGVLELKEGKLVVT---------DLLNCSLCKLCERACPGKAIRV 218

Query: 118 G--PN-FEFSTES 127
               N F F+ ES
Sbjct: 219 SDDENKFIFTVES 231

Length = 263

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	160
KOG3256|consensus	212		100.0
COG1143	172	NuoI Formate hydrogenlyase subunit 6/NADH:ubiquino	99.96
PRK05888	164	NADH dehydrogenase subunit I; Provisional	99.88
TIGR00403	183	ndhI NADH-plastoquinone oxidoreductase subunit I p	99.82
TIGR01971	122	NuoI NADH-quinone oxidoreductase, chain I. This mo	99.78
CHL00014	167	ndhI NADH dehydrogenase subunit I	99.71
PRK08348	120	NADH-plastoquinone oxidoreductase subunit; Provisi	99.62
PRK08222	181	hydrogenase 4 subunit H; Validated	99.57
PRK12387	180	formate hydrogenlyase complex iron-sulfur subunit;	99.53
PF14697	59	Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE	99.42
PF13187	55	Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_	99.42
PF12838	52	Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR0014	99.36
PRK13984	604	putative oxidoreductase; Provisional	99.28
PRK06273	165	ferredoxin; Provisional	99.25
TIGR02936	91	fdxN_nitrog ferredoxin III, nif-specific. Members	99.25
COG1144	91	Pyruvate:ferredoxin oxidoreductase and related 2-o	99.23
TIGR02179	78	PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta	99.22
PF13237	52	Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A.	99.19
PRK09624	105	porD pyuvate ferredoxin oxidoreductase subunit del	99.18
PRK09623	105	vorD 2-ketoisovalerate ferredoxin oxidoreductase s	99.18
CHL00065	81	psaC photosystem I subunit VII	99.17
COG3383	978	Uncharacterized anaerobic dehydrogenase [General f	99.16
PRK09626	103	oorD 2-oxoglutarate-acceptor oxidoreductase subuni	99.14
PRK09625	133	porD pyruvate flavodoxin oxidoreductase subunit de	99.14
PLN00071	81	photosystem I subunit VII; Provisional	99.13
PRK06991	270	ferredoxin; Provisional	99.1
PRK02651	81	photosystem I subunit VII; Provisional	99.1
TIGR03048	80	PS_I_psaC photosystem I iron-sulfur protein PsaC.	99.1
TIGR02060	132	aprB adenosine phosphosulphate reductase, beta sub	99.09
TIGR01944	165	rnfB electron transport complex, RnfABCDGE type, B	99.08
TIGR00397	213	mauM_napG MauM/NapG family ferredoxin-type protein	99.08
PRK05113	191	electron transport complex protein RnfB; Provision	99.08
TIGR02494	295	PFLE_PFLC glycyl-radical enzyme activating protein	99.07
TIGR02163	255	napH_ ferredoxin-type protein, NapH/MauN family. M	99.05
COG1145	99	NapF Ferredoxin [Energy production and conversion]	99.05
PRK09477	271	napH quinol dehydrogenase membrane component; Prov	99.04
COG1146	68	Ferredoxin [Energy production and conversion]	99.04
COG1149	284	MinD superfamily P-loop ATPase containing an inser	99.0
PRK08764	135	ferredoxin; Provisional	99.0
TIGR00402	101	napF ferredoxin-type protein NapF. The gene codes	98.99
PRK07569	234	bidirectional hydrogenase complex protein HoxU; Va	98.98
PF13247	98	Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX	98.97
PF13247	98	Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX	98.96
PF13484	67	Fer4_16: 4Fe-4S double cluster binding domain	98.95
PRK09476	254	napG quinol dehydrogenase periplasmic component; P	98.95
TIGR02700	234	flavo_MJ0208 archaeoflavoprotein, MJ0208 family. T	98.95
PRK14028	312	pyruvate ferredoxin oxidoreductase subunit gamma/d	98.93
COG0437	203	HybA Fe-S-cluster-containing hydrogenase component	98.92
PRK05035	695	electron transport complex protein RnfC; Provision	98.91
TIGR02512	374	Fe_only_hydrog hydrogenases, Fe-only. This model d	98.89
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	98.88
TIGR01660	492	narH nitrate reductase, beta subunit. The Nitrate	98.88
PRK10194	163	ferredoxin-type protein; Provisional	98.88
PRK08493	819	NADH dehydrogenase subunit G; Validated	98.87
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	98.86
COG1142	165	HycB Fe-S-cluster-containing hydrogenase component	98.85
TIGR03478	321	DMSO_red_II_bet DMSO reductase family type II enzy	98.85
TIGR02912	314	sulfite_red_C sulfite reductase, subunit C. Member	98.84
PRK09898	208	hypothetical protein; Provisional	98.83
COG4656	529	RnfC Predicted NADH:ubiquinone oxidoreductase, sub	98.83
COG0437	203	HybA Fe-S-cluster-containing hydrogenase component	98.82
TIGR03149	225	cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S	98.82
COG1142	165	HycB Fe-S-cluster-containing hydrogenase component	98.82
TIGR03224	411	benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA p	98.82
COG2768	354	Uncharacterized Fe-S center protein [General funct	98.81
PRK14993	244	tetrathionate reductase subunit B; Provisional	98.81
PRK10194	163	ferredoxin-type protein; Provisional	98.78
PRK10882	328	hydrogenase 2 protein HybA; Provisional	98.78
TIGR03149	225	cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S	98.77
COG2878	198	Predicted NADH:ubiquinone oxidoreductase, subunit	98.77
PRK07118	280	ferredoxin; Validated	98.77
TIGR02176	1165	pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxid	98.75
PRK10330	181	formate dehydrogenase-H ferredoxin subunit; Provis	98.74
TIGR01973	603	NuoG NADH-quinone oxidoreductase, chain G. This mo	98.74
TIGR03478	321	DMSO_red_II_bet DMSO reductase family type II enzy	98.72
PF13183	57	Fer4_8: 4Fe-4S dicluster domain; PDB: 2BS4_B 1E7P_	98.71
PRK09129	776	NADH dehydrogenase subunit G; Validated	98.69
COG2221	317	DsrA Dissimilatory sulfite reductase (desulfovirid	98.68
TIGR01582	283	FDH-beta formate dehydrogenase, beta subunit, Fe-S	98.68
COG1148	622	HdrA Heterodisulfide reductase, subunit A and rela	98.67
TIGR02951	161	DMSO_dmsB DMSO reductase, iron-sulfur subunit. Thi	98.66
PRK14993	244	tetrathionate reductase subunit B; Provisional	98.66
PRK09898	208	hypothetical protein; Provisional	98.65
TIGR01582	283	FDH-beta formate dehydrogenase, beta subunit, Fe-S	98.64
PRK15449	95	ferredoxin-like protein FixX; Provisional	98.64
PRK07118	280	ferredoxin; Validated	98.63
PRK08166	847	NADH dehydrogenase subunit G; Validated	98.63
TIGR03294	228	FrhG coenzyme F420 hydrogenase, subunit gamma. Thi	98.63
PRK07860	797	NADH dehydrogenase subunit G; Validated	98.61
PRK12576	279	succinate dehydrogenase iron-sulfur subunit; Provi	98.61
COG1148	622	HdrA Heterodisulfide reductase, subunit A and rela	98.6
PRK09130	687	NADH dehydrogenase subunit G; Validated	98.6
TIGR00397	213	mauM_napG MauM/NapG family ferredoxin-type protein	98.6
PRK09476	254	napG quinol dehydrogenase periplasmic component; P	98.59
PRK08318	420	dihydropyrimidine dehydrogenase subunit B; Validat	98.59
TIGR02951	161	DMSO_dmsB DMSO reductase, iron-sulfur subunit. Thi	98.58
PTZ00305	297	NADH:ubiquinone oxidoreductase; Provisional	98.58
TIGR03287	391	methan_mark_16 putative methanogenesis marker 16 m	98.58
PRK10882	328	hydrogenase 2 protein HybA; Provisional	98.58
PRK10330	181	formate dehydrogenase-H ferredoxin subunit; Provis	98.57
COG1034	693	NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreduc	98.57
PRK12771	564	putative glutamate synthase (NADPH) small subunit;	98.55
PRK13795	636	hypothetical protein; Provisional	98.55
PF12837	24	Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450	98.54
PRK07570	250	succinate dehydrogenase/fumarate reductase iron-su	98.54
TIGR00384	220	dhsB succinate dehydrogenase and fumarate reductas	98.53
PRK09326	341	F420H2 dehydrogenase subunit F; Provisional	98.52
PRK12769	654	putative oxidoreductase Fe-S binding subunit; Revi	98.51
TIGR01660	492	narH nitrate reductase, beta subunit. The Nitrate	98.44
TIGR01945	435	rnfC electron transport complex, RnfABCDGE type, C	98.38
PRK13552	239	frdB fumarate reductase iron-sulfur subunit; Provi	98.38
COG0479	234	FrdB Succinate dehydrogenase/fumarate reductase, F	98.37
PF12837	24	Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450	98.36
PRK12809	639	putative oxidoreductase Fe-S binding subunit; Revi	98.36
TIGR03315	1012	Se_ygfK putative selenate reductase, YgfK subunit.	98.36
PRK12575	235	succinate dehydrogenase iron-sulfur subunit; Provi	98.35
PRK08640	249	sdhB succinate dehydrogenase iron-sulfur subunit;	98.34
TIGR02486	314	RDH reductive dehalogenase. This model represents	98.34
PRK12769	654	putative oxidoreductase Fe-S binding subunit; Revi	98.33
PRK09853	1019	putative selenate reductase subunit YgfK; Provisio	98.32
PF00037	24	Fer4: 4Fe-4S binding domain; InterPro: IPR001450 T	98.32
PF00037	24	Fer4: 4Fe-4S binding domain; InterPro: IPR001450 T	98.31
TIGR02066	341	dsrB sulfite reductase, dissimilatory-type beta su	98.31
TIGR02745	434	ccoG_rdxA_fixG cytochrome c oxidase accessory prot	98.3
PLN00129	276	succinate dehydrogenase [ubiquinone] iron-sulfur s	98.3
PRK12809	639	putative oxidoreductase Fe-S binding subunit; Revi	98.29
COG2440	99	FixX Ferredoxin-like protein [Energy production an	98.26
TIGR03336	595	IOR_alpha indolepyruvate ferredoxin oxidoreductase	98.25
PRK05950	232	sdhB succinate dehydrogenase iron-sulfur subunit;	98.25
PRK12385	244	fumarate reductase iron-sulfur subunit; Provisiona	98.24
PRK12577	329	succinate dehydrogenase iron-sulfur subunit; Provi	98.22
TIGR00276	282	iron-sulfur cluster binding protein, putative. Thi	98.22
TIGR03290	144	CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, s	98.19
PRK12386	251	fumarate reductase iron-sulfur subunit; Provisiona	98.15
TIGR00314	784	cdhA CO dehydrogenase/acetyl-CoA synthase complex,	98.13
PF13534	61	Fer4_17: 4Fe-4S dicluster domain; PDB: 1ZOY_B 3AE9	98.12
PRK00941	781	acetyl-CoA decarbonylase/synthase complex subunit	98.12
cd01916	731	ACS_1 Acetyl-CoA synthase (ACS), also known as ace	98.08
COG4231	640	Indolepyruvate ferredoxin oxidoreductase, alpha an	98.04
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	97.97
PRK11168	396	glpC sn-glycerol-3-phosphate dehydrogenase subunit	97.96
TIGR01936	447	nqrA NADH:ubiquinone oxidoreductase, Na(+)-translo	97.92
PF12798	15	Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450	97.91
PF12797	22	Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450	97.91
PRK05352	448	Na(+)-translocating NADH-quinone reductase subunit	97.89
PF12798	15	Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450	97.87
TIGR00273	432	iron-sulfur cluster-binding protein. Members of th	97.85
PRK13409	590	putative ATPase RIL; Provisional	97.83
TIGR03379	397	glycerol3P_GlpC glycerol-3-phosphate dehydrogenase	97.74
PRK06259	486	succinate dehydrogenase/fumarate reductase iron-su	97.72
PRK11274	407	glcF glycolate oxidase iron-sulfur subunit; Provis	97.67
COG1139	459	Uncharacterized conserved protein containing a fer	97.61
PRK15055	344	anaerobic sulfite reductase subunit A; Provisional	97.6
PF12797	22	Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450	97.6
COG1600	337	Uncharacterized Fe-S protein [Energy production an	97.59
PF13370	58	Fer4_13: 4Fe-4S single cluster domain; PDB: 1FXR_A	97.57
PRK13984	604	putative oxidoreductase; Provisional	97.52
COG1150	195	HdrC Heterodisulfide reductase, subunit C [Energy	97.51
COG1152	772	CdhA CO dehydrogenase/acetyl-CoA synthase alpha su	97.47
PF12800	17	Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450	97.46
PF13187	55	Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_	97.46
PF14697	59	Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE	97.45
TIGR02910	334	sulfite_red_A sulfite reductase, subunit A. Member	97.45
TIGR02064	402	dsrA sulfite reductase, dissimilatory-type alpha s	97.42
COG1143	172	NuoI Formate hydrogenlyase subunit 6/NADH:ubiquino	97.4
PF13459	65	Fer4_15: 4Fe-4S single cluster domain	97.35
PF12800	17	Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450	97.29
COG1140	513	NarY Nitrate reductase beta subunit [Energy produc	97.2
COG0247	388	GlpC Fe-S oxidoreductase [Energy production and co	97.18
PRK08222	181	hydrogenase 4 subunit H; Validated	97.15
PRK09477	271	napH quinol dehydrogenase membrane component; Prov	97.13
PRK12387	180	formate hydrogenlyase complex iron-sulfur subunit;	97.13
PF13484	67	Fer4_16: 4Fe-4S double cluster binding domain	97.11
COG1141	68	Fer Ferredoxin [Energy production and conversion]	97.1
COG1453	391	Predicted oxidoreductases of the aldo/keto reducta	97.09
PRK15033	389	tricarballylate utilization protein B; Provisional	97.05
PF12838	52	Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR0014	97.02
TIGR02484	372	CitB CitB domain protein. CobZ is essential for co	97.01
KOG3256|consensus	212		97.0
TIGR02163	255	napH_ ferredoxin-type protein, NapH/MauN family. M	96.99
TIGR02936	91	fdxN_nitrog ferredoxin III, nif-specific. Members	96.87
PF13746	69	Fer4_18: 4Fe-4S dicluster domain	96.83
TIGR02745	434	ccoG_rdxA_fixG cytochrome c oxidase accessory prot	96.75
COG1146	68	Ferredoxin [Energy production and conversion]	96.75
COG1144	91	Pyruvate:ferredoxin oxidoreductase and related 2-o	96.72
PF13746	69	Fer4_18: 4Fe-4S dicluster domain	96.71
COG1145	99	NapF Ferredoxin [Energy production and conversion]	96.69
CHL00065	81	psaC photosystem I subunit VII	96.47
PRK09626	103	oorD 2-oxoglutarate-acceptor oxidoreductase subuni	96.4
PRK08348	120	NADH-plastoquinone oxidoreductase subunit; Provisi	96.39
TIGR00403	183	ndhI NADH-plastoquinone oxidoreductase subunit I p	96.38
PRK09623	105	vorD 2-ketoisovalerate ferredoxin oxidoreductase s	96.37
PLN00071	81	photosystem I subunit VII; Provisional	96.35
PRK13030	1159	2-oxoacid ferredoxin oxidoreductase; Provisional	96.32
CHL00014	167	ndhI NADH dehydrogenase subunit I	96.2
PF13237	52	Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A.	96.17
COG1035	332	FrhB Coenzyme F420-reducing hydrogenase, beta subu	96.15
TIGR03048	80	PS_I_psaC photosystem I iron-sulfur protein PsaC.	96.14
COG0348	386	NapH Polyferredoxin [Energy production and convers	96.14
PRK09193	1165	indolepyruvate ferredoxin oxidoreductase; Validate	96.09
TIGR02060	132	aprB adenosine phosphosulphate reductase, beta sub	96.01
PRK06273	165	ferredoxin; Provisional	96.01
PRK13029	1186	2-oxoacid ferredoxin oxidoreductase; Provisional	96.01
PRK09624	105	porD pyuvate ferredoxin oxidoreductase subunit del	95.97
PRK09625	133	porD pyruvate flavodoxin oxidoreductase subunit de	95.96
PRK12814	652	putative NADPH-dependent glutamate synthase small	95.94
PRK05888	164	NADH dehydrogenase subunit I; Provisional	95.94
TIGR01971	122	NuoI NADH-quinone oxidoreductase, chain I. This mo	95.91
PRK02651	81	photosystem I subunit VII; Provisional	95.82
PRK05113	191	electron transport complex protein RnfB; Provision	95.76
TIGR02179	78	PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta	95.73
PRK08493	819	NADH dehydrogenase subunit G; Validated	95.68
COG3383	978	Uncharacterized anaerobic dehydrogenase [General f	95.67
TIGR01944	165	rnfB electron transport complex, RnfABCDGE type, B	95.64
TIGR02494	295	PFLE_PFLC glycyl-radical enzyme activating protein	95.62
PRK08764	135	ferredoxin; Provisional	95.46
KOG0063|consensus	592		95.41
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	95.38
PRK13409	590	putative ATPase RIL; Provisional	95.37
TIGR02066	341	dsrB sulfite reductase, dissimilatory-type beta su	95.35
COG2221	317	DsrA Dissimilatory sulfite reductase (desulfovirid	95.32
TIGR00402	101	napF ferredoxin-type protein NapF. The gene codes	95.27
TIGR02912	314	sulfite_red_C sulfite reductase, subunit C. Member	94.99
PRK06991	270	ferredoxin; Provisional	94.99
PRK15449	95	ferredoxin-like protein FixX; Provisional	94.94
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	94.9
PRK14028	312	pyruvate ferredoxin oxidoreductase subunit gamma/d	94.7
PRK07569	234	bidirectional hydrogenase complex protein HoxU; Va	94.56
COG1941	247	FrhG Coenzyme F420-reducing hydrogenase, gamma sub	94.54
TIGR02512	374	Fe_only_hydrog hydrogenases, Fe-only. This model d	94.43
PRK09326	341	F420H2 dehydrogenase subunit F; Provisional	94.39
TIGR03287	391	methan_mark_16 putative methanogenesis marker 16 m	94.19
KOG0063|consensus	592		94.17
PF13183	57	Fer4_8: 4Fe-4S dicluster domain; PDB: 2BS4_B 1E7P_	94.06
TIGR02486	314	RDH reductive dehalogenase. This model represents	93.98
PRK08318	420	dihydropyrimidine dehydrogenase subunit B; Validat	93.8
TIGR02700	234	flavo_MJ0208 archaeoflavoprotein, MJ0208 family. T	93.58
PRK12771	564	putative glutamate synthase (NADPH) small subunit;	93.49
COG1149	284	MinD superfamily P-loop ATPase containing an inser	93.29
PF13534	61	Fer4_17: 4Fe-4S dicluster domain; PDB: 1ZOY_B 3AE9	93.17
TIGR00276	282	iron-sulfur cluster binding protein, putative. Thi	93.03
TIGR03294	228	FrhG coenzyme F420 hydrogenase, subunit gamma. Thi	92.97
TIGR01973	603	NuoG NADH-quinone oxidoreductase, chain G. This mo	92.91
TIGR03224	411	benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA p	92.72
COG4231	640	Indolepyruvate ferredoxin oxidoreductase, alpha an	92.59
COG2768	354	Uncharacterized Fe-S center protein [General funct	92.42
PF13459	65	Fer4_15: 4Fe-4S single cluster domain	92.4
PRK07860	797	NADH dehydrogenase subunit G; Validated	92.3
COG1141	68	Fer Ferredoxin [Energy production and conversion]	91.94
TIGR02176	1165	pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxid	91.83
PRK13795	636	hypothetical protein; Provisional	91.17
TIGR03336	595	IOR_alpha indolepyruvate ferredoxin oxidoreductase	91.13
COG2878	198	Predicted NADH:ubiquinone oxidoreductase, subunit	90.74
COG1600	337	Uncharacterized Fe-S protein [Energy production an	90.61
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	90.28
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	90.12
PRK09130	687	NADH dehydrogenase subunit G; Validated	90.01
TIGR02910	334	sulfite_red_A sulfite reductase, subunit A. Member	89.94
PRK08166	847	NADH dehydrogenase subunit G; Validated	89.86
PRK09129	776	NADH dehydrogenase subunit G; Validated	89.66
PF13370	58	Fer4_13: 4Fe-4S single cluster domain; PDB: 1FXR_A	89.5
PRK07570	250	succinate dehydrogenase/fumarate reductase iron-su	88.77
TIGR03315	1012	Se_ygfK putative selenate reductase, YgfK subunit.	88.53
TIGR03290	144	CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, s	88.41
COG1035	332	FrhB Coenzyme F420-reducing hydrogenase, beta subu	88.12
PF06902	64	Fer4_19: Divergent 4Fe-4S mono-cluster; InterPro:	87.86
PRK15055	344	anaerobic sulfite reductase subunit A; Provisional	87.83
TIGR00384	220	dhsB succinate dehydrogenase and fumarate reductas	86.52
PRK05035	695	electron transport complex protein RnfC; Provision	86.03
PRK08640	249	sdhB succinate dehydrogenase iron-sulfur subunit;	86.0
COG1140	513	NarY Nitrate reductase beta subunit [Energy produc	85.79
PRK12576	279	succinate dehydrogenase iron-sulfur subunit; Provi	85.54
PRK12386	251	fumarate reductase iron-sulfur subunit; Provisiona	85.21
PRK12575	235	succinate dehydrogenase iron-sulfur subunit; Provi	84.33
PRK12814	652	putative NADPH-dependent glutamate synthase small	83.41
TIGR01945	435	rnfC electron transport complex, RnfABCDGE type, C	83.35
PRK11168	396	glpC sn-glycerol-3-phosphate dehydrogenase subunit	82.72
PRK09853	1019	putative selenate reductase subunit YgfK; Provisio	82.61
PRK12385	244	fumarate reductase iron-sulfur subunit; Provisiona	82.6
PRK13552	239	frdB fumarate reductase iron-sulfur subunit; Provi	82.44
TIGR00273	432	iron-sulfur cluster-binding protein. Members of th	82.42
PLN00129	276	succinate dehydrogenase [ubiquinone] iron-sulfur s	81.9
PRK05950	232	sdhB succinate dehydrogenase iron-sulfur subunit;	81.25
PTZ00305	297	NADH:ubiquinone oxidoreductase; Provisional	81.11
TIGR02064	402	dsrA sulfite reductase, dissimilatory-type alpha s	81.03
COG1941	247	FrhG Coenzyme F420-reducing hydrogenase, gamma sub	80.68
COG1150	195	HdrC Heterodisulfide reductase, subunit C [Energy	80.19
PRK12577	329	succinate dehydrogenase iron-sulfur subunit; Provi	80.18

>KOG3256|consensus

Probab=100.00  E-value=6.7e-38  Score=220.41  Aligned_cols=157  Identities=84%  Similarity=1.453  Sum_probs=152.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhh
Q psy4925           4 RGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER   83 (160)
Q Consensus         4 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~   83 (160)
                      .+.+.+++..+++|+.+++.|.|+.+.+++||.++++.+++|+|.+++.+++...++||.|..|+.+||.++|.++...+
T Consensus        56 ~~~~tl~~te~~rGf~itLsh~f~~p~TInYPfEKgplS~RFRGehalrRyp~geerCIACklCeavCPaqaitieae~r  135 (212)
T KOG3256|consen   56 RGQQTLFATELIRGFMITLSHTFREPVTINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAVCPAQAITIEAEER  135 (212)
T ss_pred             HHHHHHHHHHHHHHHHhhHHhhcCCCeeecCccccCCCCcccccchhhhcCCCcchhhhhHHHHHHhCCcccceeeceec
Confidence            45677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCccccccccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHHHhccCCcchHHHhhhhhhhhccC
Q psy4925          84 ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR  160 (160)
Q Consensus        84 ~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (160)
                      .+++++...+.+|+..|+.||.|+++||++||.++++|+|+++++.|+.|+..+++.+|..|++++.++..++..||
T Consensus       136 ~dgsrRttrYdIDmtkCIyCG~CqEaCPvdaivegpnfEfsTetheELlYnkekLl~ngd~Wese~a~N~~~~~lyr  212 (212)
T KOG3256|consen  136 TDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETHEELLYNKEKLLTNGDRWESEIAKNLQAELLYR  212 (212)
T ss_pred             CCccccceeecccceeeeeecchhhhCCccceeccCCceeccccHHHHhhhHHHHhhccccccchhhhcccchhhcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998

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

Probab=99.96  E-value=7.9e-29  Score=179.34  Aligned_cols=140  Identities=46%  Similarity=0.964  Sum_probs=126.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhh
Q psy4925           3 DRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEE   82 (160)
Q Consensus         3 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~   82 (160)
                      +..+...++.+++.|+..+++++|+++.+..||.+....+++|+|.+.+.     ..+||+|+.|+.+||++||.+....
T Consensus         4 ~~~~~~~~~~~~~~~l~~~~K~~fk~~vT~~YP~e~~~~~~rfRG~~~l~-----~~~CIgC~lCa~iCP~~aI~m~~~~   78 (172)
T COG1143           4 KEAAKVKFLLDFLKGLWTTLKNLFKKPVTIEYPEEKIPLSPRFRGRHVLD-----RDKCIGCGLCANICPANAITMETAE   78 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCchhhCccccCCCCCCccceeecc-----ccCCcchhHHHhhCCcCceEEEEcc
Confidence            44554555559999999999999999999999999999999999988774     5569999999999999999988776


Q ss_pred             hc-CCCccccccccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHHHhccCCcchH
Q psy4925          83 RA-DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWES  147 (160)
Q Consensus        83 ~~-~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (160)
                      .. ++++....+.+|.+.|+.||.|+++||++||.++..|+++.++++++.++...++..+..|++
T Consensus        79 ~~~~g~~~~~~~~In~grCIfCg~C~e~CPt~Al~~t~~~e~a~~~~~dl~~~~~~ll~~~~~~~~  144 (172)
T COG1143          79 RKVDGRKKPKRPDINLGRCIFCGLCVEVCPTGALVLTPEFELASYKREDLVYDKERLLAPPDKKEE  144 (172)
T ss_pred             cCCCCccccccceeccccccccCchhhhCchhhhcCCcceeecccchHhhhccHHHhccCcccccc
Confidence            55 577777888999999999999999999999999999999999999999999999999999987

>PRK05888 NADH dehydrogenase subunit I; Provisional

Probab=99.88  E-value=1.7e-22  Score=146.58  Aligned_cols=156  Identities=64%  Similarity=1.105  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhc
Q psy4925           5 GIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERA   84 (160)
Q Consensus         5 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~   84 (160)
                      ..++.++..+++|+.+++.++|+.+.+..||........++++...+.....+.++|++|+.|+.+||.+++.+......
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~t~~yp~~~~~~~~~~~g~~~l~~~~~~~~~Ci~C~~C~~~CP~~ai~~~~~~~~   83 (164)
T PRK05888          4 YLKSMLLKELLKGLGVTLKYFFKKKVTIQYPEEKLPLSPRFRGRHALRRDPNGEERCIACKLCAAICPADAITIEAAERE   83 (164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCCCCCCCCCCCcCCEEeecCCCCCCccCCcccChHHHcCccccccccccCC
Confidence            46778888999999999999999999999998887777777766555433334559999999999999998876543222


Q ss_pred             CCCccccccccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHHHhccCCcchHHHhhhhhhhhccC
Q psy4925          85 DGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR  160 (160)
Q Consensus        85 ~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (160)
                      .+......+.++...|++||.|+++||++||.+...+.....++.++.++...+...+..|......-...+..|+
T Consensus        84 ~g~~~~~~~~i~~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (164)
T PRK05888         84 DGRRRTTRYDINFGRCIFCGFCEEACPTDAIVETPDFELATETREELIYDKEKLLANGDRVEREIAPGKAADANYR  159 (164)
T ss_pred             CCcccceeeecCCCcCcccCcchhhcCcCcceecCcceeccCCHHHHccCHHHHhccccccccccccccccccccc
Confidence            2222222345788899999999999999999999999999999999999999999988888777766666666654

>TIGR00403 ndhI NADH-plastoquinone oxidoreductase subunit I protein

Probab=99.82  E-value=5.4e-20  Score=135.39  Aligned_cols=125  Identities=34%  Similarity=0.638  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhcC-CCc
Q psy4925          10 FLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERAD-GSR   88 (160)
Q Consensus        10 ~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~-~~~   88 (160)
                      ....++.|+.++++++++.+.+.+||.+.....+++++...     ++.++|++|+.|+.+||.+++......... ...
T Consensus        18 ~~~~i~~g~~vt~~~~~~~p~T~~YP~~~~~~~~~~rG~i~-----~~~~kCi~Cg~C~~aCP~~ai~~~~~~~~~~~~~   92 (183)
T TIGR00403        18 AARYIGQGFAVTLDHMNRLPITIQYPYEKLIPSERFRGRIH-----FEFDKCIACEVCVRVCPINLPVVDWEFNKAIKKK   92 (183)
T ss_pred             HHHHHHHHHHHHHHHhcCCCccccCCCCCCCCCccccceEE-----eCcccCcCcCChhhhCCCCccccccccccccccc
Confidence            34567789999999999999999999999888888887543     357899999999999999876543221111 111


Q ss_pred             cccccccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHHHh
Q psy4925          89 RTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLL  139 (160)
Q Consensus        89 ~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~  139 (160)
                      ....+.++...|+.||.|+++||++||.++..++....++..+.++...+.
T Consensus        93 ~~~~~~id~~~Ci~Cg~Cv~aCP~~AI~~~~~~e~~~~~r~~l~~~~~~l~  143 (183)
T TIGR00403        93 QLKNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYDQIALG  143 (183)
T ss_pred             ccceeecCcccccCcCchhhhcCCCCeecccccccccccHHHHhccHHHhc
Confidence            112345788899999999999999999999999999999999999887663

>TIGR01971 NuoI NADH-quinone oxidoreductase, chain I

Probab=99.78  E-value=1.1e-19  Score=125.71  Aligned_cols=121  Identities=49%  Similarity=0.972  Sum_probs=95.1

Q ss_pred             HHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccC
Q psy4925          17 GFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDID   96 (160)
Q Consensus        17 g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~   96 (160)
                      |++++++++|+++.+..||........++++...+.......++|++|+.|+.+||.+++.+.......+......+..+
T Consensus         1 ~~~~~~~~~~~~~~t~~~p~~~~~~~~~~~g~~~~~~~~~~~~~Ci~C~~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~   80 (122)
T TIGR01971         1 GLGLTLKYFFSKPVTVQYPEEKLYLPPRFRGRIVLTRDPNGEEKCIGCTLCAAVCPADAIRVVPAEGEDGKRRLKFYQIN   80 (122)
T ss_pred             CcEeeHHHHcCCCceeECCCcCCCCCcccCCeEeeccCCCCcCcCcCcchhhhhcCHhHeeeeeeccCCCceecccceEC
Confidence            45678899999999999998887788888887666554445689999999999999988875432211122222234567


Q ss_pred             ccCCcCcccchhcccccccccCCcccccccchhhhhccHHH
Q psy4925          97 MTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEK  137 (160)
Q Consensus        97 ~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~  137 (160)
                      ...|+.||.|+++||++||.+...+......+.++.+..++
T Consensus        81 ~~~C~~Cg~Cv~~CP~~al~~~~~~~~~~~~~~~~~~~~~~  121 (122)
T TIGR01971        81 FGRCIFCGLCEEACPTDAIVLTPEFELATYTRSDLVYGKED  121 (122)
T ss_pred             cccCCCCCchhhhCCCccccccceeeeccccHHHheechhh
Confidence            88999999999999999999999999999999888887654

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=99.71  E-value=7.2e-17  Score=117.32  Aligned_cols=125  Identities=35%  Similarity=0.678  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhcC-CC
Q psy4925           9 AFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERAD-GS   87 (160)
Q Consensus         9 ~~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~-~~   87 (160)
                      .+...++.|+.+++.++++.+.+..||.........+++...     ++.++|++|+.|+.+||.+++.+....... ..
T Consensus        14 ~~~~~i~~~~~~~~~~~~~~~~t~~yp~~~~~~~~~~rg~i~-----~~~~~Ci~Cg~C~~aCP~~~~~~~~~~~~~~~~   88 (167)
T CHL00014         14 RAARYIGQGFMITLSHANRLPVTIQYPYEKLITSERFRGRIH-----FEFDKCIACEVCVRVCPIDLPVVDWKLETDIRK   88 (167)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCcceeCCCCCCCCCcCcCCeEE-----eccccCCCcCcHHHhCCCCCccccccccccccc
Confidence            345667889999999999999999999877666667765433     356889999999999999876543221100 11


Q ss_pred             ccccccccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHHH
Q psy4925          88 RRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKL  138 (160)
Q Consensus        88 ~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~  138 (160)
                      .....+.++...|+.||.|+++||++||.+...+++....+..+.++...+
T Consensus        89 ~~~~~~~id~~~C~~Cg~C~~~CP~~AI~~~~~~~~~~~~r~~l~~~~~~~  139 (167)
T CHL00014         89 KRLLNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYNQIAL  139 (167)
T ss_pred             cccccccCCCCcCcCccchHhhcCcCceecCCccccccccHHHHhcCHHHH
Confidence            111234567788999999999999999999999999999999999988766

>PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional

Probab=99.62  E-value=5e-16  Score=107.15  Aligned_cols=99  Identities=26%  Similarity=0.655  Sum_probs=75.0

Q ss_pred             HHHHHHHhhcCCCCcccCCCc-cCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhcCCCcccccccc
Q psy4925          17 GFFVATGHIFKEPATINYPFE-KGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDI   95 (160)
Q Consensus        17 g~~~~~~~~~~~~~~~~~p~~-~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~   95 (160)
                      .++..++++|+.+.+..||.. .......+++.     +.++.++|++|+.|+.+||.+++.......        ...+
T Consensus         4 ~~~~~~k~~~~~~~t~~~p~~~~~~~~~~~~g~-----i~i~~~~Ci~C~~C~~~CP~~ai~~~~~~~--------~~~i   70 (120)
T PRK08348          4 LLPTVLRNLFKKPATNLFPATEPVPVPEDFRGK-----ILYDVDKCVGCRMCVTVCPAGVFVYLPEIR--------KVAL   70 (120)
T ss_pred             hHHHHHHHhcCCCccccCCccCCCCCCccccce-----EEECcccCcCcccHHHHCCccceEcccccc--------ceEe
Confidence            456778899999999999975 34445555543     345688999999999999999886543210        2346


Q ss_pred             CccCCcCcccchhcccccccccCCcccccccch
Q psy4925          96 DMTKCIYCGFCQEACPVDAIVEGPNFEFSTESH  128 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~  128 (160)
                      +...|+.||.|+++||++||.+...+.+....+
T Consensus        71 ~~~~C~~Cg~Cv~~CP~~Ai~~~~~~~~~~~~r  103 (120)
T PRK08348         71 WTGRCVFCGQCVDVCPTGALQMSDDFLLASYDR  103 (120)
T ss_pred             cCCcCcChhhhHHhCCcCcEEeccceeeehhhh
Confidence            678899999999999999999988766554444

>PRK08222 hydrogenase 4 subunit H; Validated

Probab=99.57  E-value=3.1e-15  Score=110.00  Aligned_cols=90  Identities=40%  Similarity=0.890  Sum_probs=70.5

Q ss_pred             CCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccc
Q psy4925          27 KEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFC  106 (160)
Q Consensus        27 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C  106 (160)
                      ..+.+..||.......+.++|...+     +.++|++|+.|+.+||++++.+.....    .....+.++...|+.||.|
T Consensus        11 ~g~~T~~yP~~~~~~p~~~rG~~~~-----d~~~Ci~Cg~Cv~aCP~~Ai~~~~~~~----~~~~~~~~~~~~C~~Cg~C   81 (181)
T PRK08222         11 AGTATVKYPFAPLEVSPGFRGKPDL-----MPSQCIACGACTCACPANALTIQTDDQ----QNSRTWQLYLGRCIYCGRC   81 (181)
T ss_pred             CCCccccCCCcccCCCCCccCceEe-----ChhhCcchhHHHHhCCccceEcccccc----cCccceeeccCcCcCCCCc
Confidence            5678999999888888888876543     688999999999999999987654321    0112345677899999999


Q ss_pred             hhcccccccccCCcccccc
Q psy4925         107 QEACPVDAIVEGPNFEFST  125 (160)
Q Consensus       107 ~~~CP~~ai~~~~~~~~~~  125 (160)
                      +++||++||.+...++...
T Consensus        82 ~~~CPt~AI~~~~~~~~~~  100 (181)
T PRK08222         82 EEVCPTRAIQLTNNFELTV  100 (181)
T ss_pred             ccccCcCeEEeccceeeec
Confidence            9999999999988766544

>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional

Probab=99.53  E-value=9.6e-15  Score=107.39  Aligned_cols=96  Identities=32%  Similarity=0.755  Sum_probs=71.9

Q ss_pred             CCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccc
Q psy4925          27 KEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFC  106 (160)
Q Consensus        27 ~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C  106 (160)
                      .++.+..||.+....++.+++...     ++.++|++|+.|+.+||++++.+......    ....+.++...|++||.|
T Consensus        11 ~g~~T~~yP~~~~~~~~~~rg~p~-----~d~~~C~~C~~Cv~~CP~~ai~~~~~~~~----~~~~~~i~~~~C~~Cg~C   81 (180)
T PRK12387         11 TGTATSSYPLEPIAVDKNFRGKPE-----YNPQQCIGCAACVNACPSNALTVETDLAT----GELAWEFNLGRCIFCGRC   81 (180)
T ss_pred             cCCccccCCCCCCCCCCCCCCceE-----EChhhCcChhHHHHhcCccCeEeeccccC----CcccceeccccCcCccch
Confidence            457899999887777777776543     46889999999999999999876543211    111345788899999999


Q ss_pred             hhcccccccccCCcccccccchhhh
Q psy4925         107 QEACPVDAIVEGPNFEFSTESHEEL  131 (160)
Q Consensus       107 ~~~CP~~ai~~~~~~~~~~~~~~~~  131 (160)
                      +++||++||.++..++.......++
T Consensus        82 ~~vCP~~AI~~~~~~~~~~~~~~~l  106 (180)
T PRK12387         82 EEVCPTAAIKLSQEFELAVWKKEDL  106 (180)
T ss_pred             hhhcCcCceEccCccchhhccHHHh
Confidence            9999999999988776554444333

>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=99.42  E-value=2.9e-14  Score=86.22  Aligned_cols=56  Identities=38%  Similarity=0.856  Sum_probs=32.4

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccc-ccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVE  117 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~-~ai~~  117 (160)
                      +|.++||+||+|+.+||.+++........  .    .+.++.+.|++||.|+.+||+ +||++
T Consensus         3 Id~~~Ci~Cg~C~~~Cp~~~~~~i~~~~~--~----~~~v~~~~C~GCg~C~~~CPv~~AI~m   59 (59)
T PF14697_consen    3 IDEDKCIGCGKCVRACPDGAIDAIEVDEG--K----KVPVNPDKCIGCGLCVKVCPVKDAITM   59 (59)
T ss_dssp             E-TTT----SCCCHHCCCCS-S-ECCTTT--T----SSECE-TT--S-SCCCCCSSSTTSEEE
T ss_pred             ECcccccChhhHHhHcCccceeeEEecCC--e----eEEeccccCcCcCcccccCCCccCCCC
Confidence            46789999999999999865543221110  0    234557899999999999996 99975

...

>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=99.42  E-value=4.1e-14  Score=84.33  Aligned_cols=55  Identities=33%  Similarity=0.752  Sum_probs=34.0

Q ss_pred             cccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccc
Q psy4925          60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      +||+||.|+.+||++++.+.......... ......+...|++||.|+++||++||
T Consensus         1 kCi~Cg~C~~~CP~~~~~~~~~~~~~~~~-~~~~~~~~~~C~~Cg~C~~~CP~~AI   55 (55)
T PF13187_consen    1 KCIGCGRCVEACPVGVIEFDEDGGKKVVD-KDNERRNAEKCIGCGACVKACPTGAI   55 (55)
T ss_dssp             C--TTTHHHHHSTTT-EEEETTTTCEECS-ECCESTTGGG--TTCHHHHHSTTT-E
T ss_pred             CCCCcchHHHHCCccCeEccCcccccccc-ccccCCCCCccccHhHHHHHcchhhC
Confidence            69999999999999998776544221110 00111245689999999999999997

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

Probab=99.36  E-value=1.6e-13  Score=80.98  Aligned_cols=52  Identities=42%  Similarity=0.968  Sum_probs=33.6

Q ss_pred             cccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccc
Q psy4925          60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      +|++||.|+.+||+++|.+.......+.   ..+.++.+.|++||.|+.+||++|
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   345678999999999999999986

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.

>PRK13984 putative oxidoreductase; Provisional

Probab=99.28  E-value=2.4e-12  Score=110.25  Aligned_cols=110  Identities=27%  Similarity=0.606  Sum_probs=83.1

Q ss_pred             HHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhcCC--CccccccccCcc
Q psy4925          21 ATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADG--SRRTTRYDIDMT   98 (160)
Q Consensus        21 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~--~~~~~~~~~~~~   98 (160)
                      .+..+++.+.++.||..+..+.++|++...     +|.++|++|+.|+.+||.+++..........  ........++..
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~d~~~Ci~C~~C~~~Cp~~ai~~~~~~~~~~~~g~~~~~~~i~~~   86 (604)
T PRK13984         12 AWKFLFRKPVTIKVPNVKREAAERYRGFHI-----NDWEKCIGCGTCSKICPTDAITMVEVPDLPQEYGKKPQRPVIDYG   86 (604)
T ss_pred             HHHHhcCCCcceECCCCCCCCCccccCccc-----cChhhCcCccchhhhCCccceEeeccccccccccccccccccCcc
Confidence            456788999999999999999999987533     4788999999999999999876543311100  001112456778


Q ss_pred             CCcCcccchhcccccccccCCcccccccchhhhhccH
Q psy4925          99 KCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNK  135 (160)
Q Consensus        99 ~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~  135 (160)
                      .|..|+.|+++||++||.+...+......++.+++.+
T Consensus        87 ~c~~c~~c~~~Cp~~Ai~~~~~~~~~~~~~~~~~~~~  123 (604)
T PRK13984         87 RCSFCALCVDICTTGSLKMTREYIHISPDPEDFIFMP  123 (604)
T ss_pred             cCcCcchHHhhCCcCcEEecceEEEeecChhhEEEec
Confidence            8999999999999999999888777666777666654

>PRK06273 ferredoxin; Provisional

Probab=99.25  E-value=4e-12  Score=92.04  Aligned_cols=84  Identities=32%  Similarity=0.587  Sum_probs=55.3

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCC-c--cccccccCccCCcCcccchhcccccccccCCcccccccchhh-h
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGS-R--RTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEE-L  131 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~-~--~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~-~  131 (160)
                      ++.+.|++|+.|+.+||.+++.+......... .  ....+.++...|+.|+.|+++||++||......... ..+++ +
T Consensus        46 id~~~CigCg~C~~aCP~~AI~~~~~ep~~~~~~~~~~~~~~Id~~kCi~Cg~C~~aCP~~AI~~~~~~~~~-~~~~~~~  124 (165)
T PRK06273         46 VFEELCIGCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCPVFALFNEISPIHP-RDVGEDI  124 (165)
T ss_pred             ECchhCcChhHHHHhcCccceeeecccccchhcccccccceecccccCcCCCCcchhCCHhheecccccCCh-hhhhhHh
Confidence            46789999999999999999876532111000 0  012345788899999999999999998553332222 33444 5


Q ss_pred             hccHHHHhc
Q psy4925         132 LYNKEKLLS  140 (160)
Q Consensus       132 ~~~~~~~~~  140 (160)
                      .++...++.
T Consensus       125 ~~~~~~ll~  133 (165)
T PRK06273        125 EVDVSKLLE  133 (165)
T ss_pred             hccHHHHhh
Confidence            665555554

>TIGR02936 fdxN_nitrog ferredoxin III, nif-specific

Probab=99.25  E-value=1.4e-12  Score=85.58  Aligned_cols=64  Identities=23%  Similarity=0.591  Sum_probs=45.9

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcC---------CCc-cccccccCccCCcCcccchhcccccccccC
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERAD---------GSR-RTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~---------~~~-~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      .++.++|++|+.|+.+||.+++.+.......         +.. ......++...|++||.|+++||++||.+.
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            3578899999999999999988765311000         000 011124678899999999999999999863

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=99.23  E-value=1.4e-12  Score=83.69  Aligned_cols=64  Identities=39%  Similarity=0.688  Sum_probs=52.0

Q ss_pred             CccccccCCCccccccchhhcHHhchhccccchhhhhcCCCccccccc-cCccCCcCcccchhcccccccccCC
Q psy4925          47 GEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYD-IDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        47 ~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~-~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.....+..++.++|+.|+.|...||.++|...+++         ... +|.+.|.+||.|+++||++||.+-.
T Consensus        23 g~Wrv~rPv~d~~kCi~C~~C~~yCPe~~i~~~~~~---------~~~~idYdyCKGCGICa~vCP~kaI~Mv~   87 (91)
T COG1144          23 GSWRVFRPVVDEDKCINCKLCWLYCPEPAILEEEGG---------YKVRIDYDYCKGCGICANVCPVKAIEMVR   87 (91)
T ss_pred             ceeEEEeeEEcccccccCceeEEECCchheeeccCC---------ccceeEcccccCceechhhCChhheEeEe
Confidence            444555666788999999999999999988776654         222 7889999999999999999998744

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

Probab=99.22  E-value=4.7e-12  Score=80.71  Aligned_cols=56  Identities=38%  Similarity=0.715  Sum_probs=45.7

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .++.++|++|+.|+.+||.+++.....+         ...++...|..|+.|+.+||++||.+..
T Consensus        21 ~i~~~~C~~C~~C~~~Cp~~ai~~~~~~---------~~~i~~~~C~~C~~C~~~CP~~Ai~~~~   76 (78)
T TIGR02179        21 VVDKEKCIKCKNCWLYCPEGAIQEDEGG---------FVGIDYDYCKGCGICANVCPVKAIEMVR   76 (78)
T ss_pred             EEcCCcCcChhHHHhhcCccceEecCCC---------cEEecCccCcCccchhhhCCccccEecc
Confidence            4567899999999999999988764321         2346677899999999999999998754

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.

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

Probab=99.19  E-value=4e-12  Score=74.84  Aligned_cols=50  Identities=44%  Similarity=1.020  Sum_probs=23.4

Q ss_pred             CCCccccccchhhcHHhchh-ccccchhhhhcCCCccccccccCccCCcCcccchhccc
Q psy4925          54 YPSGEERCIACKLCEAICPA-QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP  111 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~-~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP  111 (160)
                      +.+|.++|++||.|+++||+ .+.......        ..+.++...|++||.|+++||
T Consensus         2 i~id~~~C~~C~~C~~~CP~~~~~~~~~~~--------~~~~~~~~~C~~Cg~C~~~CP   52 (52)
T PF13237_consen    2 IVIDEDKCIGCGRCVKVCPADNAIAIDDGE--------KKVEIDPERCIGCGACVEVCP   52 (52)
T ss_dssp             ----TT------TTGGG-TT-----EEE-S--------SSEEE-TTT--TTSHHHHH-T
T ss_pred             CccCcccCcCCcChHHHccchhHHHhhccC--------CCeEeCcccccccChhhhhCc
Confidence            45678999999999999998 222222111        145678899999999999998

>PRK09624 porD pyuvate ferredoxin oxidoreductase subunit delta; Reviewed

Probab=99.18  E-value=5.5e-12  Score=84.96  Aligned_cols=57  Identities=32%  Similarity=0.704  Sum_probs=46.6

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .++.++|++|+.|+.+||.+++..+..+         ...++...|+.|+.|+.+||++||.+..+
T Consensus        47 ~~d~~~Ci~C~~C~~~CP~~ai~~~~~~---------~~~id~~~C~~Cg~Cv~~CP~~AI~~~~~  103 (105)
T PRK09624         47 EFNRDKCVRCYLCYIYCPEPAIYLDEEG---------YPVFDYDYCKGCGICANECPTKAIEMVRE  103 (105)
T ss_pred             EEChhHCcChhhHHhhCCHhhEEecCCC---------cEEECchhCCCcCchhhhcCcCcEEEecc
Confidence            4578899999999999999988765322         23467789999999999999999987654

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

Probab=99.18  E-value=1e-11  Score=83.71  Aligned_cols=58  Identities=33%  Similarity=0.726  Sum_probs=47.0

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..++.++|++|+.|+.+||.+++.....+         ...++...|..||.|+.+||++||.+...
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            44678899999999999999887654321         23577888999999999999999987653

>CHL00065 psaC photosystem I subunit VII

Probab=99.17  E-value=1.3e-11  Score=79.31  Aligned_cols=61  Identities=21%  Similarity=0.545  Sum_probs=43.9

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      .+.++|++|+.|+.+||.+++.+.........  ......+...|+.|+.|+.+||++||.+.
T Consensus         6 ~~~~~Ci~Cg~C~~~CP~~~i~~~~~~~~~~~--~~~~~~~~~~C~~C~~C~~~CP~~Ai~~~   66 (81)
T CHL00065          6 KIYDTCIGCTQCVRACPTDVLEMIPWDGCKAK--QIASAPRTEDCVGCKRCESACPTDFLSVR   66 (81)
T ss_pred             CccccCCChhHHHHHCCccchhheeccccccc--cccccCCCCcCCChhhhhhhcCccccEEE
Confidence            34678999999999999998876532110000  01123456789999999999999999863

>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]

Probab=99.16  E-value=1.4e-11  Score=105.05  Aligned_cols=97  Identities=24%  Similarity=0.420  Sum_probs=61.7

Q ss_pred             ccccCCCccccccchhhcHHhch----hccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCccccc-
Q psy4925          50 ALRRYPSGEERCIACKLCEAICP----AQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFS-  124 (160)
Q Consensus        50 ~~~~~~~~~~~Ci~Cg~Cv~~CP----~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~-  124 (160)
                      ..+.+.+|.++||.||+||++|.    +.++.++..+..-.........++.++|++||+|+.+||.+|+..++....+ 
T Consensus       140 s~Pfy~ydp~qCIlCgRCVeaCqevqv~eaL~i~w~~~~pRV~wd~~~~i~~SSCVsCG~CvtVCP~nALmek~m~g~ag  219 (978)
T COG3383         140 SNPFYIYDPNQCILCGRCVEACQEVQVNEALTIDWRGEDPRVIWDNDVPINESSCVSCGACVTVCPVNALMEKSMLGEAG  219 (978)
T ss_pred             CCCeEEecchheeehhHHHHHHHhhhceeEEEeecccCCcceecCCCCccccccccccCccceecchhhhhhhhhhcccc
Confidence            34556678999999999999998    2455555443222222222334677899999999999999999887764211 


Q ss_pred             --ccchhhhhccHHHHhccCCcch
Q psy4925         125 --TESHEELLYNKEKLLSNGDKWE  146 (160)
Q Consensus       125 --~~~~~~~~~~~~~~~~~~~~~~  146 (160)
                        +-...+.......+-+.-++|-
T Consensus       220 ~~t~~~~~~~~~mid~~k~~eP~~  243 (978)
T COG3383         220 YLTGINEDTLEPMIDLVKKVEPEY  243 (978)
T ss_pred             ccccccchhhhhhhhhhhccCCCc
Confidence              1222333344444555555655

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

Probab=99.14  E-value=1.5e-11  Score=82.62  Aligned_cols=65  Identities=28%  Similarity=0.519  Sum_probs=47.7

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.++.++|++|+.|+.+||++++.+........  ......++...|+.|+.|+.+||++||.+...
T Consensus        11 v~id~~~Ci~C~~Cv~aCP~~ai~~~~~~~~~~--~~~~~~i~~~~C~~C~~C~~~CP~~AI~~~~~   75 (103)
T PRK09626         11 VWVDESRCKACDICVSVCPAGVLAMRIDPHAVL--GKMIKVVHPESCIGCRECELHCPDFAIYVADR   75 (103)
T ss_pred             eEECcccccCCcchhhhcChhhhcccccccccc--CceeeEeCCccCCCcCcchhhCChhhEEEecc
Confidence            445788999999999999999886543221110  01122456778999999999999999998664

>PRK09625 porD pyruvate flavodoxin oxidoreductase subunit delta; Reviewed

Probab=99.14  E-value=1.2e-11  Score=86.78  Aligned_cols=56  Identities=30%  Similarity=0.655  Sum_probs=44.3

Q ss_pred             cCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ...++.++|++|+.|+.+||.+++......         ...++...|+.||.|+++||++|+.+
T Consensus        53 ~p~~d~~~Ci~C~~C~~~CP~~ai~~~~~~---------~~~i~~~~C~~Cg~Cv~vCP~~a~~l  108 (133)
T PRK09625         53 KPVHNNEICINCFNCWVYCPDAAILSRDKK---------LKGVDYSHCKGCGVCVEVCPTNPKSL  108 (133)
T ss_pred             eEEEehhHCcChhhHHHhCCHhheEecCCc---------eEEeCcCcCcChhHHHHHCCcCceEE
Confidence            344678999999999999999987643221         23467788999999999999999654

>PLN00071 photosystem I subunit VII; Provisional

Probab=99.13  E-value=2.4e-11  Score=78.06  Aligned_cols=62  Identities=21%  Similarity=0.527  Sum_probs=44.4

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ++.++|++|+.|+.+||.+++.+.........  ......+...|+.|+.|+++||++||.+..
T Consensus         6 ~~~~~C~~C~~C~~~CP~~~i~~~~~~~~~~~--~~~~~~~~~~C~~Cg~C~~~CP~~Ai~~~~   67 (81)
T PLN00071          6 KIYDTCIGCTQCVRACPTDVLEMIPWDGCKAK--QIASAPRTEDCVGCKRCESACPTDFLSVRV   67 (81)
T ss_pred             EcCCcCcChhHHHHHCCccceeeecccccccc--cccCcCCCCcCcChhhHHhhcCCccceEee
Confidence            35679999999999999998876532110000  011234667899999999999999998743

>PRK06991 ferredoxin; Provisional

Probab=99.10  E-value=1.8e-11  Score=94.96  Aligned_cols=58  Identities=33%  Similarity=0.657  Sum_probs=46.6

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCcc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF  121 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~  121 (160)
                      .++.+.|++|+.|+.+||+++|.+....         ...++...|++||.|+.+||+++|.+....
T Consensus        81 ~id~~~CigCg~Cv~aCP~~AI~~~~~~---------~~~v~~~~CigCg~Cv~vCP~~AI~~~~~~  138 (270)
T PRK06991         81 VIDEQLCIGCTLCMQACPVDAIVGAPKQ---------MHTVLADLCTGCDLCVPPCPVDCIDMVPVT  138 (270)
T ss_pred             EEccccCCCCcHHHHhCCHhheeccccc---------ceeeCHhhCCCchHHHhhCCcCCeEeecCc
Confidence            3567899999999999999998654321         234567789999999999999999886543

>PRK02651 photosystem I subunit VII; Provisional

Probab=99.10  E-value=3.9e-11  Score=77.00  Aligned_cols=61  Identities=21%  Similarity=0.513  Sum_probs=44.0

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++|++|+.|+.+||.+++........  .........+...|+.|+.|+.+||++||.+..
T Consensus         7 ~~~~Ci~C~~C~~~CP~~~i~~~~~~~~--~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~   67 (81)
T PRK02651          7 IYDTCIGCTQCVRACPLDVLEMVPWDGC--KAGQIASSPRTEDCVGCKRCETACPTDFLSIRV   67 (81)
T ss_pred             ccccCCCcchHHHHCCccceeccccccc--ccCcccccCCCCcCCChhhhhhhcCCCceEEEE
Confidence            3588999999999999988765432111  101111234667899999999999999999744

>TIGR03048 PS_I_psaC photosystem I iron-sulfur protein PsaC

Probab=99.10  E-value=3.6e-11  Score=77.05  Aligned_cols=60  Identities=22%  Similarity=0.550  Sum_probs=43.6

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      .+.++|++|+.|+.+||.+++.+......  .........+...|++||.|+++||++||.+
T Consensus         5 ~~~~~Ci~C~~Cv~~CP~~~i~~~~~~~~--~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~   64 (80)
T TIGR03048         5 KIYDTCIGCTQCVRACPTDVLEMVPWDGC--KAGQIASAPRTEDCVGCKRCESACPTDFLSV   64 (80)
T ss_pred             ecCCcCcCcchHHHHCCccceeeeccccc--ccccccCcCCCCcCcChhHHHHhcCcccCEE
Confidence            45688999999999999998876532110  0000112346678999999999999999986

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=99.09  E-value=2.4e-11  Score=84.93  Aligned_cols=61  Identities=31%  Similarity=0.643  Sum_probs=48.6

Q ss_pred             Cccccccchh-----hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCcccc
Q psy4925          56 SGEERCIACK-----LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEF  123 (160)
Q Consensus        56 ~~~~~Ci~Cg-----~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~  123 (160)
                      ++.++|++|+     .|+.+||.+++.++...       ...+.++...|++|+.|+.+||++||.+....++
T Consensus         5 v~~~~C~gC~~~~~~~Cv~~CP~~ai~~~~~~-------~~~~~id~~~C~~Cg~Cv~~CP~~AI~~~~~~~~   70 (132)
T TIGR02060         5 VYPTKCDGCKAGEKTACVYICPNDLMHLDTEI-------MKAYNIEPDMCWECYSCVKACPQGAIDVRGYADF   70 (132)
T ss_pred             EccccccCccCCchhcCHhhcCccceEecCCC-------ceeeecCchhCccHHHHHHhCCcCceEEECcccc
Confidence            4678999999     99999999998765321       0123467889999999999999999998776443

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.

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

Probab=99.08  E-value=3.1e-11  Score=87.60  Aligned_cols=56  Identities=34%  Similarity=0.710  Sum_probs=45.1

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .++.++|++|+.|+++||.+++......         ...++...|+.||.|+.+||++||.+..
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            3578899999999999999987654321         2345678899999999999999998753

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.

>TIGR00397 mauM_napG MauM/NapG family ferredoxin-type protein

Probab=99.08  E-value=1.5e-10  Score=87.23  Aligned_cols=58  Identities=24%  Similarity=0.604  Sum_probs=42.7

Q ss_pred             ccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc--cchhccccccccc
Q psy4925          59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG--FCQEACPVDAIVE  117 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg--~C~~~CP~~ai~~  117 (160)
                      ++|++||.|+.+||++++.+...... .....+.+..+...|++|+  .|+.+||++||..
T Consensus        53 ~~Ci~Cg~Cv~aCP~~ai~~~~~~~~-~~~g~p~~~~~~~~C~~C~d~~Cv~~CP~~Ai~~  112 (213)
T TIGR00397        53 AACVRCGLCVEACPYDILSLASWSDP-APLGTPFFTPREVPCRMCKDIPCARACPTGALDP  112 (213)
T ss_pred             ccccchhHHHHhCCcccccccccccc-cccCCccccccCCcCCCCCCchHHhHcCHhhhch
Confidence            78999999999999999976532211 1112223345567899998  6999999999974

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

>PRK05113 electron transport complex protein RnfB; Provisional

Probab=99.08  E-value=2.7e-11  Score=89.79  Aligned_cols=57  Identities=30%  Similarity=0.621  Sum_probs=45.7

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++.++|++|+.|+++||.+++.....+         ....+...|+.||.|+.+||++||.+.+
T Consensus       109 ~~id~~~Ci~Cg~Cv~aCp~~ai~~~~~~---------~~~v~~~~C~~Cg~Cv~vCP~~AI~~~~  165 (191)
T PRK05113        109 AFIDEDNCIGCTKCIQACPVDAIVGATKA---------MHTVISDLCTGCDLCVAPCPTDCIEMIP  165 (191)
T ss_pred             eEEeCCcCCCCChhhhhCCHhhhecccCC---------ceeecCCcCCchHHHHHHcCcCceEEee
Confidence            34578899999999999999987654321         2245678899999999999999999855

>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family

Probab=99.07  E-value=3.3e-11  Score=94.80  Aligned_cols=63  Identities=33%  Similarity=0.678  Sum_probs=48.2

Q ss_pred             cCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .+.++.++|++||.|+.+||.+++.+.....  +   ......+...|.+||.|+.+||++||.+...
T Consensus        42 ~~~~~~~~C~~C~~C~~~Cp~~a~~~~~~~~--~---~~~~~~~~~~C~~Cg~C~~~CP~~Ai~~~g~  104 (295)
T TIGR02494        42 ELLFKENRCLGCGKCVEVCPAGTARLSELAD--G---RNRIIIRREKCTHCGKCTEACPSGALSIVGE  104 (295)
T ss_pred             eEEEccccCCCCchhhhhCcccccccccccC--C---CcceeechhhcCchhHhhccCcHhHHhhhcc
Confidence            3456789999999999999999986321110  0   1134678889999999999999999998654

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

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

Probab=99.05  E-value=9.6e-11  Score=90.59  Aligned_cols=87  Identities=18%  Similarity=0.395  Sum_probs=55.7

Q ss_pred             hhcCCCCcccCCCccCCCCCCccCccccccCCC-ccccccchhhcHHhchhccc-cchhhhhcCCCccccccccCccCCc
Q psy4925          24 HIFKEPATINYPFEKGPLSPRFRGEHALRRYPS-GEERCIACKLCEAICPAQAI-TIEAEERADGSRRTTRYDIDMTKCI  101 (160)
Q Consensus        24 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~-~~~~Ci~Cg~Cv~~CP~~~i-~~~~~~~~~~~~~~~~~~~~~~~C~  101 (160)
                      .++..+.+..+-.+.+.....+. .....++.. +.++|++|+.|+++||++++ ......       ......+...|+
T Consensus       166 ~~~~~r~~C~~~CP~Ga~~~~~~-~~~~~~i~~~~~~~C~~C~~C~~vCP~~~vl~~~~~~-------~~~~~i~~~~C~  237 (255)
T TIGR02163       166 LLFSERGWCGHLCPLGAFYGLIG-RKSLIKIAASDREKCTNCMDCFNVCPEPQVLRMPLKK-------GGSTLVLSGDCT  237 (255)
T ss_pred             HHhcCCchhhCcCCCcchhhhhh-ccCceEEEeeccccCeEcCCccCcCCCCceeeccccC-------CCceEecccccc
Confidence            45566677776655554432221 111222333 37899999999999998753 221110       002345777899


Q ss_pred             CcccchhcccccccccC
Q psy4925         102 YCGFCQEACPVDAIVEG  118 (160)
Q Consensus       102 ~Cg~C~~~CP~~ai~~~  118 (160)
                      .||+|+++||++|+.++
T Consensus       238 ~Cg~Cv~~CP~~Ai~f~  254 (255)
T TIGR02163       238 LCGRCIDVCHEDVLGFT  254 (255)
T ss_pred             chhHHHHhCCccccccc
Confidence            99999999999999874

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=99.05  E-value=5.1e-11  Score=78.69  Aligned_cols=61  Identities=36%  Similarity=0.768  Sum_probs=46.8

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..+.++|++||.|+.+||+++|........     .....++...|+.|+.|+.+||.+|+.+...
T Consensus        25 ~~~~~~Ci~Cg~C~~~CP~~ai~~~~~~~~-----~~~~~~~~~~C~~C~~C~~~Cp~~a~~~~~~   85 (99)
T COG1145          25 VIDAEKCIGCGLCVKVCPTGAIELIEEGLL-----LPEVVIDPDLCVLCGACLKVCPVDALSIAEE   85 (99)
T ss_pred             EeCccccCCCCCchhhCCHHHhhcccccCc-----cceEEEccccCccccchHhhCCcCCeehhhc
Confidence            345778999999999999999876322100     1245678889999999999999999776443

>PRK09477 napH quinol dehydrogenase membrane component; Provisional

Probab=99.04  E-value=8.8e-11  Score=91.57  Aligned_cols=90  Identities=19%  Similarity=0.386  Sum_probs=56.4

Q ss_pred             hcCCCCcccCCCccCCCCCCccCccccccCC-CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc
Q psy4925          25 IFKEPATINYPFEKGPLSPRFRGEHALRRYP-SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC  103 (160)
Q Consensus        25 ~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~-~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C  103 (160)
                      ++.++.+..|-.+.+.....+ +.....++. ++.++|++|+.|+++||.+++...... +..    .....+...|+.|
T Consensus       174 ~~~~r~wC~~lCP~Ga~~~~~-~~~~~~~i~~~d~~~C~~C~~C~~~CP~~~i~~~~~~-~~~----~~~~i~~~~C~~C  247 (271)
T PRK09477        174 FVVEHGWCGHLCPLGAFYGLI-GKKSLIRVKAHDRQKCTRCMDCFHVCPEPQVLRPPLK-GKQ----SPSQVTSGDCITC  247 (271)
T ss_pred             HHcCCchhhccCCHHHHHHhc-ccccccccccCCcccCcccCCcCCcCCCcceeccccc-CCC----ccceeCcccCcCh
Confidence            345556666655444332221 122233344 678999999999999998764321000 000    0112566789999


Q ss_pred             ccchhcccccccccCCc
Q psy4925         104 GFCQEACPVDAIVEGPN  120 (160)
Q Consensus       104 g~C~~~CP~~ai~~~~~  120 (160)
                      |.|+++||++||.++..
T Consensus       248 g~Cv~~CP~~Ai~~~~r  264 (271)
T PRK09477        248 GRCIDVCSEDVFNFTIR  264 (271)
T ss_pred             hHHHhhcCccceeeccc
Confidence            99999999999998765

>COG1146 Ferredoxin [Energy production and conversion]

Probab=99.04  E-value=4e-11  Score=74.53  Aligned_cols=59  Identities=32%  Similarity=0.729  Sum_probs=47.3

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++.++|++|+.|+.+||.+.+......      ....+..+.+.|+.||.|+.+||.+||.+...
T Consensus         5 Id~~~C~~c~~C~~~CP~~~~~~~~~~------~~~~~~~~~e~C~~C~~C~~~CP~~aI~~~~~   63 (68)
T COG1146           5 IDYDKCIGCGICVEVCPAGVFDLGEDE------GGKPVVARPEECIDCGLCELACPVGAIKVDIL   63 (68)
T ss_pred             ECchhcCCCChheeccChhhEEecccc------CcceeEeccccCccchhhhhhCCcceEEEecc
Confidence            467789999999999999988765431      11145678899999999999999999987554

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

Probab=99.00  E-value=1.2e-10  Score=89.40  Aligned_cols=58  Identities=31%  Similarity=0.616  Sum_probs=49.5

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..++.++|+.||.|..+|+.+|+.....+         .+.++...|.+||.|.-+||.+||.+.+.
T Consensus        64 p~i~~e~C~~CG~C~~vC~f~Ai~~~~~~---------~~~~~~~lC~GCgaC~~~CP~~AI~~~~~  121 (284)
T COG1149          64 PEIDPEKCIRCGKCAEVCRFGAIVVLPGG---------KPVLNPDLCEGCGACSIVCPEPAIEEEPV  121 (284)
T ss_pred             cccChhhccccCcHHHhCCCCeEEEcCCC---------ceecCcccccCcccceeeCCCcccccccc
Confidence            34678889999999999999999764433         56788899999999999999999998765

>PRK08764 ferredoxin; Provisional

Probab=99.00  E-value=1.3e-10  Score=81.65  Aligned_cols=52  Identities=37%  Similarity=0.703  Sum_probs=41.8

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ..++|++|++|+++||.++|......         ...++...|+.||.|+.+||++||.+
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            35789999999999999988653221         12356678999999999999999875

>TIGR00402 napF ferredoxin-type protein NapF

Probab=98.99  E-value=2e-10  Score=76.80  Aligned_cols=57  Identities=25%  Similarity=0.626  Sum_probs=44.4

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..++|++|+.|+.+||.+++.+...+       ...+.++...|+.||.|+.+||++||.....
T Consensus        32 ~~~~C~~C~~C~~~CP~~~i~~~~~g-------~~~~~i~~~~C~~Cg~C~~~CP~~Ai~~~~~   88 (101)
T TIGR00402        32 FSAVCTRCGECASACENNILQLGQQG-------QPTVEFDNAECDFCGKCAEACPTNAFHPRFP   88 (101)
T ss_pred             CcCcCcChhHHHHHcCcccceeccCC-------ceeeEecCccCcCccChhhHCCccccCcCCC
Confidence            45789999999999999988765321       0124567788999999999999999976443

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.

>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated

Probab=98.98  E-value=1.9e-10  Score=87.94  Aligned_cols=81  Identities=30%  Similarity=0.546  Sum_probs=51.3

Q ss_pred             ccCCCccccccchhhcHHhchh--ccccchhhhhcCCCccccc---cccCccCCcCcccchhcccccccccCCccccccc
Q psy4925          52 RRYPSGEERCIACKLCEAICPA--QAITIEAEERADGSRRTTR---YDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTE  126 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~---~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~  126 (160)
                      +.+.++.++||+|++|+.+||.  ++..+.....+........   ...+...|++||.|+++||++||.....      
T Consensus       139 ~~i~~d~~kCi~Cg~Cv~aC~~i~~~~~~~~~~~g~~~~i~~~~~~~~~~~~~C~~Cg~Cv~vCP~gAL~~~~~------  212 (234)
T PRK07569        139 PRFGIDHNRCVLCTRCVRVCDEIEGAHTWDVAGRGAKSRVITDLNQPWGTSETCTSCGKCVQACPTGAIFRKGS------  212 (234)
T ss_pred             CcEEeehhhCcCccHHHHHHHHhcCCceeeecccCCcceEeecCCccccccccccchHHHHHhCCCCcEEecCC------
Confidence            4445678999999999999994  3333222211111100000   1123458999999999999999988754      


Q ss_pred             chhhhhccHHHH
Q psy4925         127 SHEELLYNKEKL  138 (160)
Q Consensus       127 ~~~~~~~~~~~~  138 (160)
                      ..+++.++...+
T Consensus       213 ~~~~~~~~~~~~  224 (234)
T PRK07569        213 TVGEMEKDRDKL  224 (234)
T ss_pred             cHHHhhcCcccc
Confidence            566666665544

>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=98.97  E-value=7.1e-11  Score=78.42  Aligned_cols=55  Identities=42%  Similarity=0.840  Sum_probs=31.8

Q ss_pred             cccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          58 EERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        58 ~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ...|.+|.  .|+++||++||..+...+        .+.++...|++|+.|+.+||+++|.+...
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            34577776  677777777776554211        45667777777777777777777776554

...

>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=98.96  E-value=1e-10  Score=77.62  Aligned_cols=56  Identities=34%  Similarity=0.720  Sum_probs=37.9

Q ss_pred             ccCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc---------ccchhcccccccccCC
Q psy4925          52 RRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC---------GFCQEACPVDAIVEGP  119 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C---------g~C~~~CP~~ai~~~~  119 (160)
                      ..+.++.++|++|+.|+.+||.+++.++...            ....+|.+|         .+|+++||++||.+.+
T Consensus        33 G~V~id~~~CigC~~C~~aCP~~ai~~~~~~------------~~~~KCdlC~~r~~~G~~PaCv~~Cp~~Al~~g~   97 (98)
T PF13247_consen   33 GIVVIDEDKCIGCGYCVEACPYGAIRFDPDT------------GKARKCDLCIDRIEEGEEPACVEACPTGALTFGD   97 (98)
T ss_dssp             S-EEE-TTTCCTHHHHHHH-TTS-EEEETTT------------TCEEE--TTHHHHTTT-S-HHHHH-TTS-EEEEE
T ss_pred             CeEEechhhccCchhhhhhhccCcceeeccc------------ccCCcCceehhhhhcCCCChhHHhccccceEEec
Confidence            3445678999999999999999999876532            244569898         5899999999998753

...

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

Probab=98.95  E-value=1.9e-10  Score=71.06  Aligned_cols=54  Identities=37%  Similarity=0.863  Sum_probs=36.3

Q ss_pred             cccchhhcHHhchhccccchhhhhcCCC-------ccccccccCccCCc------Ccccchhccccc
Q psy4925          60 RCIACKLCEAICPAQAITIEAEERADGS-------RRTTRYDIDMTKCI------YCGFCQEACPVD  113 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~-------~~~~~~~~~~~~C~------~Cg~C~~~CP~~  113 (160)
                      +|+.|++|+.+||++||..+.....+..       .....+..+...|.      +||.|+.+||.+
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            4999999999999999988722211110       11122334444555      999999999985

>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional

Probab=98.95  E-value=7.1e-10  Score=85.64  Aligned_cols=61  Identities=26%  Similarity=0.537  Sum_probs=43.1

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc--cchhcccccccccCC
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG--FCQEACPVDAIVEGP  119 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg--~C~~~CP~~ai~~~~  119 (160)
                      .++|++|+.|+.+||+++|.+....... ....+.+..+...|..|+  .|+.+||++||.+..
T Consensus        58 ~~~Ci~Cg~Cv~aCP~~aI~~~~~~~~~-~~g~p~~~~~~~~C~~C~~~~Cv~aCPtgAL~~~~  120 (254)
T PRK09476         58 LSACIRCGLCVQACPYDTLKLATLASGL-SAGTPYFVARDIPCEMCEDIPCVKACPSGALDREL  120 (254)
T ss_pred             hhhCcCchHHHHhCCccccCcccccccc-ccCCceeeecCCcCcCCCCCchhhccCccceEeec
Confidence            3789999999999999999765322110 011122334446799999  599999999998643

>TIGR02700 flavo_MJ0208 archaeoflavoprotein, MJ0208 family

Probab=98.95  E-value=2e-10  Score=87.80  Aligned_cols=60  Identities=37%  Similarity=0.812  Sum_probs=49.3

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCccccc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFS  124 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~  124 (160)
                      .++.++|++|+.|+.+||.+++.....          ...++...|..|+.|+++||++||.+..+++..
T Consensus       144 ~id~~~C~~C~~C~~~CP~~ai~~~~~----------~~~i~~~~C~~Cg~C~~~CP~~AI~~~~~~~~~  203 (234)
T TIGR02700       144 MIDRKRCKGCGICVDACPRSAIDMVDG----------KAFIRLLKCVGCGKCKEACPYNAIHGGLEYEMR  203 (234)
T ss_pred             EEChhHCcCcchHHHhCCcccEEecCC----------ceEEchhhCCccchHHhhCCCCceecCCceEEe
Confidence            356789999999999999998876432          235677889999999999999999998776644

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=98.93  E-value=3.5e-10  Score=89.81  Aligned_cols=66  Identities=33%  Similarity=0.640  Sum_probs=46.0

Q ss_pred             CCCccccccchhhcHHhchhccccchhhh--hcCCCc-cccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEE--RADGSR-RTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~--~~~~~~-~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++.++|++|+.|+.+||.+++......  ...+.. .......+...|.+|+.|+++||++||.+..
T Consensus       242 p~id~~~Ci~C~~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~d~~~C~gCg~C~~~CP~~AI~~~~  310 (312)
T PRK14028        242 PVIDHSKCIMCRKCWLYCPDDAIIEAWREAEGPRGRKFRMKMIDFDYQYCKGCGVCAEVCPTGAIQMVR  310 (312)
T ss_pred             eEECcccCcCcccccccCChhhhhcccccccCcccccccceeecCCcccCcCcCchhhhCCHhheEecc
Confidence            34578899999999999999887532111  001110 1112345677899999999999999998754

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

Probab=98.92  E-value=4.9e-10  Score=83.20  Aligned_cols=60  Identities=32%  Similarity=0.688  Sum_probs=41.2

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc------c---cchhcccccccccCCccccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------G---FCQEACPVDAIVEGPNFEFS  124 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C------g---~C~~~CP~~ai~~~~~~~~~  124 (160)
                      +.+|.+.||+|+.|+.+||.+|..+....            .....|++|      |   +|+++||++|+.+.+.-+..
T Consensus        95 V~vd~d~CIGC~yCi~ACPyga~~~~~~~------------~~~~KCt~C~~ri~~g~~PaCV~~CP~~A~~fG~~~d~~  162 (203)
T COG0437          95 VLVDKDLCIGCGYCIAACPYGAPQFNPDK------------GVVDKCTFCVDRVAVGKLPACVEACPTGALIFGDIDDPK  162 (203)
T ss_pred             EEecCCcccCchHHHhhCCCCCceeCccc------------CcccccCcchhhHhcCCCCcccccCCcccccccchhhcc
Confidence            34567778888888888888777655421            125677777      6   78888888888877765554


Q ss_pred             c
Q psy4925         125 T  125 (160)
Q Consensus       125 ~  125 (160)
                      +
T Consensus       163 ~  163 (203)
T COG0437         163 S  163 (203)
T ss_pred             h
Confidence            4

>PRK05035 electron transport complex protein RnfC; Provisional

Probab=98.91  E-value=6.9e-11  Score=102.19  Aligned_cols=121  Identities=21%  Similarity=0.323  Sum_probs=64.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHH-HhhcCCCCc------ccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhc
Q psy4925           2 VDRGIHAAFLTEIFRGFFVAT-GHIFKEPAT------INYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQ   74 (160)
Q Consensus         2 ~~~~~~~~~~~~~~~g~~~~~-~~~~~~~~~------~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~   74 (160)
                      +|+|++...+++..++..... ..+...++.      +..|.-+......+.....+. ...+...||.||.|+.+||.+
T Consensus       307 v~iGTpv~~Ll~~~G~~~~~~~rvI~GGPmmG~~~~~~d~pv~K~t~~il~~~~~~~~-~~~~e~~CI~CG~Cv~aCP~~  385 (695)
T PRK05035        307 ARLGTPVRHLLNQAGFKPDADQRVIMGGPMMGFTLPSLDVPVVKTTNCLLAPSATELP-PPPPEQPCIRCGACADACPAS  385 (695)
T ss_pred             EeCCCCHHHHHHhcCCCCCCCceEEECCCCcCcccccCCCCeecceeEEEeccccccc-CCCchhhcCCcccHHHHCCcc
Confidence            577888888887665443221 122233321      222222222111111111111 123567899999999999998


Q ss_pred             cccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCccccc
Q psy4925          75 AITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFS  124 (160)
Q Consensus        75 ~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~  124 (160)
                      ++............+.....++...|+.||.|..+||.+ |.+...+...
T Consensus       386 llP~~l~~~~~~~d~~~~~~~~~~~CieCG~C~~vCPs~-Iplv~~~r~a  434 (695)
T PRK05035        386 LLPQQLYWFAKAEEHDKAQEYNLFDCIECGACAYVCPSN-IPLVQYYRQA  434 (695)
T ss_pred             chhhhHHHhhhccccchhhhcChhhccccCcccccCCCC-CcHHHHHHHH
Confidence            875432211111111112235667899999999999999 5554444333

>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only

Probab=98.89  E-value=4.8e-10  Score=91.12  Aligned_cols=65  Identities=29%  Similarity=0.561  Sum_probs=45.4

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCc----cccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSR----RTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~----~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++.++|++||.|+++||.+++.........+..    ......++...|+.||.|+.+||++||.....
T Consensus         4 id~~kCi~Cg~Cv~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~id~~~C~~Cg~Cv~~CP~~Ai~~~~~   72 (374)
T TIGR02512         4 RDMSKCIGCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLVCPVGAITEKDH   72 (374)
T ss_pred             echhhCCcChHhhhhCCHhhccccccccccCCccccccccccccCcccCcCccCHHHhCCCChhhhhcc
Confidence            567899999999999999987632111000100    00113467789999999999999999987643

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.

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=98.88  E-value=4.9e-10  Score=87.04  Aligned_cols=73  Identities=29%  Similarity=0.616  Sum_probs=54.4

Q ss_pred             cccCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc---ccccccc
Q psy4925          51 LRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN---FEFSTES  127 (160)
Q Consensus        51 ~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~---~~~~~~~  127 (160)
                      .+.+.+ .++|++|+.|+.+||.+++.++...         ....+...|+.|+.|+.+||.+||.+...   +.+..++
T Consensus       162 ~p~I~i-~~~C~~C~~C~~~CP~~vi~~~~~~---------~~v~~~~~C~~C~~Ci~~CP~~AI~i~~~~~~~if~vEs  231 (263)
T PRK00783        162 YPRIEV-SEDCDECEKCVEACPRGVLELKEGK---------LVVTDLLNCSLCKLCERACPGKAIRVSDDENKFIFTVES  231 (263)
T ss_pred             cccccc-cccCCchHHHHHhCCccccEecCCe---------EEEeChhhCCCchHHHHhCCCCceEEEEcCCeEEEEecc
Confidence            344555 6889999999999999998875421         22346678999999999999999987654   4566666


Q ss_pred             hhhhhc
Q psy4925         128 HEELLY  133 (160)
Q Consensus       128 ~~~~~~  133 (160)
                      .|.+..
T Consensus       232 ~G~l~p  237 (263)
T PRK00783        232 DGSLPV  237 (263)
T ss_pred             CCCCCH
Confidence            554433

>TIGR01660 narH nitrate reductase, beta subunit

Probab=98.88  E-value=3.8e-10  Score=92.19  Aligned_cols=57  Identities=30%  Similarity=0.450  Sum_probs=46.4

Q ss_pred             Cccccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +....|++|+  .|+.+||++||.......        .+.++.+.|++|+.|+.+||++||.+...
T Consensus       178 y~p~~C~HC~nP~CV~ACPtGAI~k~eedG--------iV~ID~dkCiGCg~CV~ACPygAI~~n~~  236 (492)
T TIGR01660       178 YLPRLCEHCLNPACVASCPSGAIYKREEDG--------IVLIDQDKCRGWRMCISGCPYKKIYFNWK  236 (492)
T ss_pred             ECCCcCcCCCcccchhhCccCCeEEecCCC--------eEEEehhhccChHHHHHhCCCCCcEecCC
Confidence            4567999998  999999999997543211        44578899999999999999999987754

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.

>PRK10194 ferredoxin-type protein; Provisional

Probab=98.88  E-value=5.1e-10  Score=81.05  Aligned_cols=55  Identities=20%  Similarity=0.527  Sum_probs=41.5

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .++|++||.|+.+||.+++.....+       ...+.++...|++|+.|+.+||++||....
T Consensus        33 ~~~C~~Cg~C~~aCp~~~i~~~~~~-------~~~~~~~~~~C~~C~~C~~~CP~~ai~~~~   87 (163)
T PRK10194         33 LTHCTRCDACINACENNILQRGAGG-------YPSVNFKNNECSFCYACAQACPESLFSPRH   87 (163)
T ss_pred             hhhCcChhHHHHHcChhhcccCCCC-------ceeeeecCCCCCCchhhHhhCcchheeccc
Confidence            5679999999999999888654321       113446677899999999999999887643

>PRK08493 NADH dehydrogenase subunit G; Validated

Probab=98.87  E-value=9.4e-10  Score=96.66  Aligned_cols=67  Identities=22%  Similarity=0.555  Sum_probs=44.4

Q ss_pred             cccCCCccccccchhhcHHhchh----ccccchhhhhcCCCcc------------------c-c---ccccCccCCcCcc
Q psy4925          51 LRRYPSGEERCIACKLCEAICPA----QAITIEAEERADGSRR------------------T-T---RYDIDMTKCIYCG  104 (160)
Q Consensus        51 ~~~~~~~~~~Ci~Cg~Cv~~CP~----~~i~~~~~~~~~~~~~------------------~-~---~~~~~~~~C~~Cg  104 (160)
                      .+.+.+|.++||.|++||++|+.    +++.+..  ++.....                  . .   ....+...|+.||
T Consensus       133 ~~~I~~D~~rCI~C~RCVr~C~ev~g~~al~~~~--RG~~~~~~~~~~~~~~da~~~~~~~~~~~i~~~~~~~~~C~~CG  210 (819)
T PRK08493        133 WGKINYDPSLCIVCERCVTVCKDKIGESALKTVP--RGLDAPDKSFKESMPKDAYAVWSKKQKSLIGPVGGETLDCSFCG  210 (819)
T ss_pred             CCcEEechhhcccccHHHhhCcccccchhhhhcc--CCcccccccccccccccchhhhhhcccceecccCCCcccccccC
Confidence            35567899999999999999994    2332221  1111100                  0 0   0011346899999


Q ss_pred             cchhcccccccccCC
Q psy4925         105 FCQEACPVDAIVEGP  119 (160)
Q Consensus       105 ~C~~~CP~~ai~~~~  119 (160)
                      +|+++||+|||..+.
T Consensus       211 ~Cv~VCPvGAL~~k~  225 (819)
T PRK08493        211 ECIAVCPVGALSSSD  225 (819)
T ss_pred             cHHHhCCCCccccCc
Confidence            999999999998864

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=98.86  E-value=4.9e-10  Score=86.85  Aligned_cols=65  Identities=32%  Similarity=0.653  Sum_probs=50.0

Q ss_pred             ccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc---ccccccchhhhh
Q psy4925          59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN---FEFSTESHEELL  132 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~---~~~~~~~~~~~~  132 (160)
                      ++|++|+.|+.+||.+++.++...         ....+...|+.|+.|+.+||.+||.+...   +.+..++.|.+.
T Consensus       169 ~~C~~C~~C~~~CP~~vi~~d~~~---------~~v~~~~~C~~C~~C~~~Cp~~AI~~~~~~~~~if~vEs~Gsl~  236 (259)
T cd07030         169 EDCDGCGKCVEECPRGVLELEEGK---------VVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSLP  236 (259)
T ss_pred             hhCCChHHHHHhCCccceEccCCe---------eEEeChhhCcCchHHHHhCCCCcEEEEecCCEEEEEEeCCCCCC
Confidence            789999999999999999775431         33456779999999999999999987654   445556654443

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

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

Probab=98.85  E-value=6.7e-10  Score=79.91  Aligned_cols=51  Identities=37%  Similarity=0.782  Sum_probs=35.6

Q ss_pred             cccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          60 RCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        60 ~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .|.+|.  -|+.+||++||..+++          ....+.++|++||.|+.+||+|||.+.+.
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            466654  6788888887776632          45667777888888888888887776553

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

Probab=98.85  E-value=5.5e-10  Score=87.79  Aligned_cols=54  Identities=30%  Similarity=0.568  Sum_probs=27.8

Q ss_pred             ccccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          57 GEERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        57 ~~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      ....|++|+  .|+.+||++||.......        .+.++...|++|+.|+.+||++|+.+.
T Consensus       127 ~p~~C~hC~nP~Cv~aCPtgAI~k~eedG--------iV~ID~ekCiGCg~Cv~ACPygAi~~n  182 (321)
T TIGR03478       127 LPRICNHCTNPACLAACPTGAIYKREEDG--------IVLVDQERCKGYRYCVEACPYKKVYFN  182 (321)
T ss_pred             ecccCCCCCCccchhhCCcCcEEEecCCC--------eEEECHHHCcchHHHHHhCCCCCcEec
Confidence            345566666  566666666664321110        233455555555555555555555543

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.

>TIGR02912 sulfite_red_C sulfite reductase, subunit C

Probab=98.84  E-value=1.2e-09  Score=86.95  Aligned_cols=57  Identities=32%  Similarity=0.690  Sum_probs=45.1

Q ss_pred             CCCccccccchhhcHHhchhc---cccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPAQ---AITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~---~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..++.++|++|+.|+++||..   ++...+.          ...++...|+.||.|+.+||++|+.....
T Consensus       164 ~~~d~~~C~~Cg~C~~~Cp~~a~~ai~~~~~----------~~~id~~~C~~Cg~Cv~~CP~~Al~~~~~  223 (314)
T TIGR02912       164 PQYDADRCIGCGACVKVCKKKAVGALSFENY----------KVVRDHSKCIGCGECVLKCPTGAWTRSEE  223 (314)
T ss_pred             CceeCccCCcchHHHHhcChhhcCceeccCC----------eEEeCCCcCcCcchhhhhCCHhhcccCcC
Confidence            346788999999999999964   4443221          45678889999999999999999987654

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.

>PRK09898 hypothetical protein; Provisional

Probab=98.83  E-value=6.7e-10  Score=83.45  Aligned_cols=57  Identities=33%  Similarity=0.725  Sum_probs=43.8

Q ss_pred             Cccccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++...|++|+  .|+.+||++++......   +     .+.++...|++|+.|+.+||++++.+...
T Consensus       118 ~~~~~C~~C~~~~C~~~CP~gAi~~~~~~---g-----~v~vd~~~CigC~~C~~aCP~~ai~~~~~  176 (208)
T PRK09898        118 YTADTCRQCKEPQCMNVCPIGAITWQQKE---G-----CITVDHKRCIGCSACTTACPWMMATVNTE  176 (208)
T ss_pred             EeCccCCCccCcchhhhCCcceEEeeccC---C-----eEEeccccCCCcCcccccCCCCCCEecCC
Confidence            4577899998  89999999998754321   1     34567788999999999999998876543

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

Probab=98.83  E-value=1.5e-10  Score=95.46  Aligned_cols=150  Identities=21%  Similarity=0.299  Sum_probs=85.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhc-CCC------CcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhc
Q psy4925           2 VDRGIHAAFLTEIFRGFFVATGHIF-KEP------ATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQ   74 (160)
Q Consensus         2 ~~~~~~~~~~~~~~~g~~~~~~~~~-~~~------~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~   74 (160)
                      +++|++...+++..+|......+++ ..+      .+++.|.-+....-......+.... .....||.|+.|+.+||++
T Consensus       302 VrIGTP~~~lL~~~G~~~~~~~~vi~gGPmmG~~l~~ld~PVtK~t~~Ll~~~~~e~~~~-~~~~sCi~C~~C~d~CP~~  380 (529)
T COG4656         302 VRIGTPVSQLLNEAGGIDTKPYRVIMGGPMMGFKLPTLDAPVTKTTNGLLALTKKELLEP-IKEQSCIRCSLCADACPVN  380 (529)
T ss_pred             EECCCcHHHHHHHcCCCCCCCceEEeCCCcccccccccCCceecccceEEecCccccccc-hhhhccccHHHHHHhCccc
Confidence            5677788887777766555544443 222      2344443333333222222222111 1123799999999999998


Q ss_pred             cccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHHHhccCCcchHHHhhhh
Q psy4925          75 AITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNI  153 (160)
Q Consensus        75 ~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (160)
                      .+...-.....+..++.....+...|++||.|..+||.+ |.+...+.........+.....+.+....+++....++.
T Consensus       381 Llp~ql~~~a~~~~~~e~~~~~l~dCIECg~Ca~vCPs~-iplvq~~r~~Ka~i~~~~~~~~~~~~~~~rf~~~~~rl~  458 (529)
T COG4656         381 LLPQQLYWFAKGEQHDEEEEHNLLDCIECGACAYVCPSN-IPLVQYFRQEKAEILAQRQELKKAEEAKTRFEARTARLE  458 (529)
T ss_pred             cCHHHhhHHhhhhhhhHHHHHHhhhhhhhCcchhcCCCC-CCHHHHHHHHHHHHHHhchhhhccccccchhhhhhhhhh
Confidence            776655555455555555567778999999999999988 444333333333333334444444444444444444443

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

Probab=98.82  E-value=1e-09  Score=81.51  Aligned_cols=54  Identities=31%  Similarity=0.749  Sum_probs=47.1

Q ss_pred             cccccchh--hcHHhchhccccchh-hhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          58 EERCIACK--LCEAICPAQAITIEA-EERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        58 ~~~Ci~Cg--~Cv~~CP~~~i~~~~-~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ...|.+|.  -|+.+||++|+.... ++         .+.+|.+.|++|+.|+.+||++|..+...
T Consensus        66 ~~~C~HC~~ppCv~vCPtgA~~k~~~dG---------iV~vd~d~CIGC~yCi~ACPyga~~~~~~  122 (203)
T COG0437          66 SISCMHCEDPPCVKVCPTGALFKREEDG---------IVLVDKDLCIGCGYCIAACPYGAPQFNPD  122 (203)
T ss_pred             cccccCCCCCcccccCCCcceEEecCCC---------EEEecCCcccCchHHHhhCCCCCceeCcc
Confidence            46799998  799999999998774 43         67889999999999999999999998774

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

Probab=98.82  E-value=1.5e-09  Score=82.52  Aligned_cols=24  Identities=29%  Similarity=0.611  Sum_probs=19.0

Q ss_pred             Cccccccchhh--cHHhchhccccch
Q psy4925          56 SGEERCIACKL--CEAICPAQAITIE   79 (160)
Q Consensus        56 ~~~~~Ci~Cg~--Cv~~CP~~~i~~~   79 (160)
                      ++...|++|+.  |+.+||++||...
T Consensus        89 ~~~~~C~~C~~~~Cv~~CP~gAi~~~  114 (225)
T TIGR03149        89 FFRKSCQHCDNAPCVAVCPTGASFKD  114 (225)
T ss_pred             ECchhccCCcCcChHhhCCCCcEEEe
Confidence            45678999985  9999999888654

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.

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

Probab=98.82  E-value=6.4e-10  Score=80.02  Aligned_cols=61  Identities=36%  Similarity=0.674  Sum_probs=43.8

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc------ccchhcccccccccCCccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GFCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C------g~C~~~CP~~ai~~~~~~~  122 (160)
                      ...+.++||+||.|+.+||.|+|.+... ....       .-....|..|      .+|+++||++|+.+.+..+
T Consensus        77 v~V~~ekCiGC~~C~~aCPfGai~~~~~-~~~~-------~~~a~KCdlC~~~e~gpaCVe~CP~~AL~lv~~~~  143 (165)
T COG1142          77 VQVDEEKCIGCKLCVVACPFGAITMVSY-PVAA-------KAVAVKCDLCAGREVGPACVEACPTEALELVDEIV  143 (165)
T ss_pred             eEEchhhccCcchhhhcCCcceEEEEee-cCcc-------hhhhhhcccccCccCCCceeeeCCHHHhhcccHHH
Confidence            3457899999999999999999987664 1111       1222345555      4699999999999866533

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

Probab=98.82  E-value=1.3e-09  Score=89.69  Aligned_cols=55  Identities=35%  Similarity=0.670  Sum_probs=45.3

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      ..++.++|++|+.|+.+||.+++..+..          ...++...|..|+.|+.+||++||...
T Consensus         5 ~~id~~~Ci~C~~C~~~CP~~ai~~~~~----------~~~i~~~~C~~C~~C~~~CP~~AI~~~   59 (411)
T TIGR03224         5 HLIDPEICIRCNTCEETCPIDAITHDDR----------NYVVKADVCNGCMACVSPCPTGAIDNW   59 (411)
T ss_pred             eeeCcccCcCccchhhhCCcccEeccCC----------ceEeCcccCcCHHHHHhhcCcccceec
Confidence            3457889999999999999998865432          234677889999999999999999853

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.

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

Probab=98.81  E-value=1.3e-09  Score=84.62  Aligned_cols=56  Identities=45%  Similarity=0.829  Sum_probs=48.1

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +...+.+|+.|+.|++.||.+|+...+           ...++...|++|++|.++||++|+...+.
T Consensus       188 p~v~e~kc~~c~~cv~~cp~~Ai~~~~-----------~~~I~~~~ci~c~~c~~ac~~gav~~~W~  243 (354)
T COG2768         188 PVVVEEKCYDCGLCVKICPVGAITLTK-----------VVKIDYEKCIGCGQCMEACPYGAVDQNWE  243 (354)
T ss_pred             ceeeeecccccchhhhhCCCcceeccc-----------ceeechhhccchhhhhhhccCcccccchh
Confidence            346678999999999999999997653           56799999999999999999999876553

>PRK14993 tetrathionate reductase subunit B; Provisional

Probab=98.81  E-value=7.7e-10  Score=84.99  Aligned_cols=21  Identities=33%  Similarity=0.749  Sum_probs=13.4

Q ss_pred             cccccchhh--cHHhchhccccc
Q psy4925          58 EERCIACKL--CEAICPAQAITI   78 (160)
Q Consensus        58 ~~~Ci~Cg~--Cv~~CP~~~i~~   78 (160)
                      ...|++|+.  |+.+||++++..
T Consensus        97 ~~~C~~C~~p~Cv~~CP~~Ai~~  119 (244)
T PRK14993         97 PRLCNHCDNPPCVPVCPVQATFQ  119 (244)
T ss_pred             chhcCCcCCccCccccCCCCEEE
Confidence            456777774  777777666643

>PRK10194 ferredoxin-type protein; Provisional

Probab=98.78  E-value=2e-09  Score=77.89  Aligned_cols=24  Identities=21%  Similarity=0.595  Sum_probs=16.9

Q ss_pred             CccccccchhhcHHhchhccccch
Q psy4925          56 SGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      ++.+.|+.|+.|+.+||++++...
T Consensus        63 ~~~~~C~~C~~C~~~CP~~ai~~~   86 (163)
T PRK10194         63 FKNNECSFCYACAQACPESLFSPR   86 (163)
T ss_pred             ecCCCCCCchhhHhhCcchheecc
Confidence            455678888888888887776543

>PRK10882 hydrogenase 2 protein HybA; Provisional

Probab=98.78  E-value=1.2e-09  Score=86.99  Aligned_cols=23  Identities=30%  Similarity=0.882  Sum_probs=15.3

Q ss_pred             ccccccchh--hcHHhchhccccch
Q psy4925          57 GEERCIACK--LCEAICPAQAITIE   79 (160)
Q Consensus        57 ~~~~Ci~Cg--~Cv~~CP~~~i~~~   79 (160)
                      ....|++|+  .|+.+||.+++..+
T Consensus       108 ~~~~C~hC~~p~Cv~aCP~gAi~k~  132 (328)
T PRK10882        108 IKKQCMHCVDPNCVSVCPVSALTKD  132 (328)
T ss_pred             ccccCCCcCchhhHhhCCCCCEEec
Confidence            345677776  67777777776654

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

Probab=98.77  E-value=1.8e-09  Score=82.03  Aligned_cols=56  Identities=29%  Similarity=0.661  Sum_probs=45.3

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc----------cchhcccccccccCCcc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG----------FCQEACPVDAIVEGPNF  121 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg----------~C~~~CP~~ai~~~~~~  121 (160)
                      +.++.++|++|+.|+.+||.+++.....            ..+...|++|+          +|+++||++||.+...-
T Consensus       120 v~id~~~C~~C~~C~~aCP~~A~~~~~~------------~~~~~kC~~C~~~~~~~g~~P~Cv~~Cp~~Ai~f~~~~  185 (225)
T TIGR03149       120 VDVHKDLCVGCQYCIAACPYRVRFIHPV------------TKSADKCNFCRDTNLAEGKLPACVESCPTKALTFGDLN  185 (225)
T ss_pred             EEechhhCCcchHHHHhCCCCCcEecCC------------CCccccCCCCCcchhhCCCCCcccccCccCCEEEeccc
Confidence            3467889999999999999999754321            23567899998          89999999999987653

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.

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

Probab=98.77  E-value=1.2e-09  Score=78.95  Aligned_cols=56  Identities=30%  Similarity=0.664  Sum_probs=45.8

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++.+.||+|-+|+++||++||......         -.....+.|++|+.|+..||+++|.+...
T Consensus       112 i~e~~ciGCtkCiqaCpvdAivg~~~~---------mhtv~~dlCTGC~lCva~CPtdci~m~~~  167 (198)
T COG2878         112 IDEANCIGCTKCIQACPVDAIVGATKA---------MHTVIADLCTGCDLCVAPCPTDCIEMQPV  167 (198)
T ss_pred             ecchhccccHHHHHhCChhhhhccchh---------HHHHHHHHhcCCCcccCCCCCCceeeeec
Confidence            578899999999999999999754432         12345567999999999999999998765

>PRK07118 ferredoxin; Validated

Probab=98.77  E-value=2.3e-09  Score=83.88  Aligned_cols=53  Identities=45%  Similarity=0.797  Sum_probs=46.1

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ...|++|+.|+++||.++|.+...          ...++...|+.||.|+++||++||.+...
T Consensus       212 ~~~Ci~Cg~Cv~~CP~~AI~~~~~----------~~vId~~~C~~Cg~C~~~CP~~AI~~~~~  264 (280)
T PRK07118        212 EVGCIGCGKCVKACPAGAITMENN----------LAVIDQEKCTSCGKCVEKCPTKAIRILNK  264 (280)
T ss_pred             ccccccchHHHhhCCcCcEEEeCC----------cEEEcCCcCCCHHHHHHhCCccccEeecc
Confidence            567999999999999999987543          34678899999999999999999998655

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

Probab=98.75  E-value=3.7e-09  Score=96.24  Aligned_cols=67  Identities=30%  Similarity=0.630  Sum_probs=47.2

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhc--------------CC---CccccccccCccCCcCcccchhccccc--c
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERA--------------DG---SRRTTRYDIDMTKCIYCGFCQEACPVD--A  114 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~--------------~~---~~~~~~~~~~~~~C~~Cg~C~~~CP~~--a  114 (160)
                      +.++.++|++|+.|+.+||+++|........              .+   ......+.++...|++||.|+++||.+  |
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            4467889999999999999999875311000              00   001112356788999999999999995  8


Q ss_pred             cccCCc
Q psy4925         115 IVEGPN  120 (160)
Q Consensus       115 i~~~~~  120 (160)
                      |.+...
T Consensus       758 l~m~~~  763 (1165)
T TIGR02176       758 LVMQPL  763 (1165)
T ss_pred             ccccch
Confidence            887654

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.

>PRK10330 formate dehydrogenase-H ferredoxin subunit; Provisional

Probab=98.74  E-value=2e-09  Score=79.15  Aligned_cols=66  Identities=29%  Similarity=0.589  Sum_probs=44.7

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCc---cccccccCccCCcCcc------cchhcccccccccCCc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSR---RTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPN  120 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~---~~~~~~~~~~~C~~Cg------~C~~~CP~~ai~~~~~  120 (160)
                      .++.++|++|+.|+.+||.+++.+..........   .......+...|..|+      +|+++||++||.+.+.
T Consensus        83 ~i~~~~C~~C~~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~kC~~C~~~~~~paCv~~CP~~Al~~~~~  157 (181)
T PRK10330         83 HVMQERCIGCKTCVVACPYGAMEVVVRPVIRNSGAGLNVRAEKAEANKCDLCNHREDGPACMAACPTHALICVDR  157 (181)
T ss_pred             EeChhhCCCcchhhhhCCccCeEeeccccccccccccccccCCceeeeCcCCCCCCCCccchhhCchhhEEEeCH
Confidence            3567889999999999999988765322110000   0001134556899998      8999999999997654

>TIGR01973 NuoG NADH-quinone oxidoreductase, chain G

Probab=98.74  E-value=4.5e-09  Score=90.29  Aligned_cols=68  Identities=21%  Similarity=0.355  Sum_probs=44.0

Q ss_pred             ccCCCccccccchhhcHHhchh--ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          52 RRYPSGEERCIACKLCEAICPA--QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.+..|.++||.|++||++|-.  +.-.+...+++....... .......|..||+|+++||+|||..+..
T Consensus       135 p~i~~d~~rCI~C~rCvr~c~e~~g~~~l~~~~rg~~~~i~~-~~~~~~~~~~cg~cv~vCP~GAl~~k~~  204 (603)
T TIGR01973       135 PLIKTEMTRCIHCTRCVRFANEVAGVEDLGVIGRGNNVEIGT-YEGKTLESELSGNLIDICPVGALTSKPY  204 (603)
T ss_pred             CCeEecCCcCccccHHHHHHHHhhCCceEEEeccCCCCEEec-CCCCCCCCcccCChHhhCCccccccccc
Confidence            4456789999999999999973  222222222222221111 1123336889999999999999997653

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.

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

Probab=98.72  E-value=2.6e-09  Score=84.02  Aligned_cols=55  Identities=25%  Similarity=0.556  Sum_probs=46.1

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc---------ccchhcccccccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC---------GFCQEACPVDAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C---------g~C~~~CP~~ai~~~~~  120 (160)
                      +.++.++|++|+.|+.+||.+|+.+...            ......|++|         .+|+++||++|+.+...
T Consensus       157 V~ID~ekCiGCg~Cv~ACPygAi~~n~~------------~~~~eKC~~C~~Rie~G~~PaCv~aCP~~A~~fGdl  220 (321)
T TIGR03478       157 VLVDQERCKGYRYCVEACPYKKVYFNPQ------------SQKSEKCIGCYPRIEKGIAPACVKQCPGRIRFVGYL  220 (321)
T ss_pred             EEECHHHCcchHHHHHhCCCCCcEecCC------------CCchhhCCCchhhhccCCCCHHHhhcCcccEEEEeC
Confidence            3467889999999999999999876432            2566789999         79999999999998665

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=98.71  E-value=7.7e-10  Score=66.11  Aligned_cols=55  Identities=29%  Similarity=0.684  Sum_probs=24.4

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      .++|++||.|+.+||+.............. .......+.+.|+.||+|..+||.+
T Consensus         2 ~~~Ci~Cg~C~~~CP~~~~~~~~~~~~~~~-~~~~~~~~~~~C~~C~~C~~~CP~~   56 (57)
T PF13183_consen    2 LSKCIRCGACTSVCPVYRNTGRFSHPPRDR-RSAVLREEAWSCTTCGACSEVCPVG   56 (57)
T ss_dssp             HHC--S-SHHHHCSHHHHHHHHHHTSTTS---HHHHHHHHGG-----HHHHH-TT-
T ss_pred             HHHccCccChHHHChhhhcccccccCcchh-HHHhhcccccCCcCcCCccCcCccc
Confidence            467999999999999643221111111111 1111122237899999999999987

...

>PRK09129 NADH dehydrogenase subunit G; Validated

Probab=98.69  E-value=6.5e-09  Score=91.60  Aligned_cols=67  Identities=22%  Similarity=0.353  Sum_probs=44.7

Q ss_pred             ccCCCccccccchhhcHHhchh--ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          52 RRYPSGEERCIACKLCEAICPA--QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.+..|.++||.||+||++|-.  +.-.+...+++......... .....|..||+|+++||+|||..+.
T Consensus       137 p~i~~d~~rCi~C~rCvr~c~ev~g~~~l~~~~rg~~~~i~~~~-~~~~~~~~cg~cv~~CP~GAl~~k~  205 (776)
T PRK09129        137 PLISTEMTRCIHCTRCVRFGQEIAGVMELGMMGRGEHSEITTYV-GKTVDSELSGNMIDLCPVGALTSKP  205 (776)
T ss_pred             cceeecccccccCcHHHHHHHHhcCCceeeeeccCCCCEEcCCC-CCCccCcccCCchhhCCcccccccc
Confidence            4456789999999999999973  33333333333333222211 2334688899999999999999764

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

Probab=98.68  E-value=5.8e-09  Score=81.66  Aligned_cols=49  Identities=43%  Similarity=0.914  Sum_probs=43.5

Q ss_pred             cCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccc
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP  111 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP  111 (160)
                      .+.++++.|.+|++|+++||++|+..+..          ...++.+.|+.||.|+.+||
T Consensus       166 ~P~~~~E~c~gc~~cv~~C~~gAI~~~~~----------~l~id~~~Ci~Cg~Ci~~Cp  214 (317)
T COG2221         166 KPKVDEELCRGCGKCVKVCPTGAITWDGK----------KLKIDGSKCIGCGKCIRACP  214 (317)
T ss_pred             cCccCHHHhchhHhHHHhCCCCceeeccc----------eEEEehhhccCccHHhhhCC
Confidence            35678899999999999999999987752          56789999999999999999

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

Probab=98.68  E-value=3.1e-09  Score=83.15  Aligned_cols=52  Identities=35%  Similarity=0.790  Sum_probs=27.1

Q ss_pred             cccccchhh--cHHhchh-ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          58 EERCIACKL--CEAICPA-QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        58 ~~~Ci~Cg~--Cv~~CP~-~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      ..+|++|+.  |+.+||+ +++.....+         .+.++.+.|++|+.|+.+||++|+.+.
T Consensus        90 ~~~C~hC~~p~Cv~aCP~~gA~~~~~~G---------~V~id~dkCigC~~Cv~aCP~~a~~~~  144 (283)
T TIGR01582        90 KDGCMHCREPGCLKACPAPGAIIQYQNG---------IVDFDHSKCIGCGYCIVGCPFNIPRYD  144 (283)
T ss_pred             CccCCCCCCccccCCCCcCCeEEEcCCC---------cEEEeHHHCCcchHHHhhCCCCCcEEc
Confidence            345666665  6666665 444333221         234455555555555555555555543

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.

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

Probab=98.67  E-value=4.6e-09  Score=86.51  Aligned_cols=51  Identities=33%  Similarity=0.879  Sum_probs=45.0

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .|.+.|++|+.|++ ||.+||+++.            ...+...|.+||.|..+||.+|+.+..
T Consensus       558 vde~~C~gC~~C~~-Cpf~ais~~k------------a~v~~~~C~gCG~C~~aCp~gai~~~~  608 (622)
T COG1148         558 VDEDKCTGCGICAE-CPFGAISVDK------------AEVNPLRCKGCGICSAACPSGAIDLAG  608 (622)
T ss_pred             cchhhhcCCcceee-CCCCceeccc------------cccChhhhCcccchhhhCCcccchhcc
Confidence            57889999999999 9999998762            357888999999999999999998754

>TIGR02951 DMSO_dmsB DMSO reductase, iron-sulfur subunit

Probab=98.66  E-value=5.2e-09  Score=75.58  Aligned_cols=55  Identities=33%  Similarity=0.648  Sum_probs=33.4

Q ss_pred             cccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          58 EERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        58 ~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ...|++|+  .|+.+||+++|.......        .+.++...|++|+.|+.+||++||.+...
T Consensus        61 ~~~C~~C~~~~C~~~CP~~ai~~~~~~~--------~~~i~~~~C~~C~~C~~aCP~~ai~~~~~  117 (161)
T TIGR02951        61 SISCNHCADPACVKNCPTGAMYKREEDG--------LVLVDQDKCIGCRYCVWACPYGAPQYDPQ  117 (161)
T ss_pred             CccCCCcCCcchHHhCCCCCEEeecCCC--------cEEECHHhCCCchHHHhhCCCCCcEEcCC
Confidence            45677777  777777777765431110        23455666777777777777776665443

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.

>PRK14993 tetrathionate reductase subunit B; Provisional

Probab=98.66  E-value=4.5e-09  Score=80.79  Aligned_cols=58  Identities=29%  Similarity=0.603  Sum_probs=47.5

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCCccccc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPNFEFS  124 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~~~~~~  124 (160)
                      .++.++|++|+.|+.+||.+++.+...            ......|++|+         +|+++||++|+.+.+.-+..
T Consensus       126 ~id~~~CigC~~Cv~aCP~~Ai~~~~~------------~~~~~KC~~C~~r~~~G~~PaCv~~CP~~Al~~g~~~~~~  192 (244)
T PRK14993        126 VVDNKRCVGCAYCVQACPYDARFINHE------------TQTADKCTFCVHRLEAGLLPACVESCVGGARIIGDIKDPH  192 (244)
T ss_pred             EEcHHHCCCHHHHHHhcCCCCCEEeCC------------CCCcccCcCCcchhhCCCCcccchhcccCCEEEcccccch
Confidence            467889999999999999999986542            23567899997         89999999999987764433

>PRK09898 hypothetical protein; Provisional

Probab=98.65  E-value=8.6e-09  Score=77.46  Aligned_cols=55  Identities=33%  Similarity=0.746  Sum_probs=44.8

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.++.++|++|+.|+.+||.+++.++..            ..+...|+.|+.|+++||++||.+.+.
T Consensus       149 v~vd~~~CigC~~C~~aCP~~ai~~~~~------------~~~~~kC~~Cg~Cv~~CP~~Ai~~~~~  203 (208)
T PRK09898        149 ITVDHKRCIGCSACTTACPWMMATVNTE------------SKKSSKCVLCGECANACPTGALKIIEW  203 (208)
T ss_pred             EEeccccCCCcCcccccCCCCCCEecCC------------CCcCCcCcChHHHHHhCCcccEEEecH
Confidence            3467889999999999999998875432            124568999999999999999987553

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

Probab=98.64  E-value=2.8e-09  Score=83.43  Aligned_cols=59  Identities=25%  Similarity=0.543  Sum_probs=46.4

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCCccccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPNFEFS  124 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~~~~~~  124 (160)
                      +.++.++|++|+.|+.+||.+++.++...            .....|.+|.         +|+.+||++||.+....++.
T Consensus       119 V~id~dkCigC~~Cv~aCP~~a~~~~~~~------------~~~~KC~~C~dr~~~G~~PaCv~aCP~gAi~fg~~~~~~  186 (283)
T TIGR01582       119 VDFDHSKCIGCGYCIVGCPFNIPRYDKVD------------NRPYKCTLCIDRVSVGQEPACVKTCPTNAISFGFKEDMK  186 (283)
T ss_pred             EEEeHHHCCcchHHHhhCCCCCcEEcCCC------------CChhhhcccccccccCCCChHhCcccHhhEEECCHHHHH
Confidence            34678999999999999999998765421            2345788884         89999999999998764443

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.

>PRK15449 ferredoxin-like protein FixX; Provisional

Probab=98.64  E-value=1.2e-08  Score=67.08  Aligned_cols=43  Identities=23%  Similarity=0.441  Sum_probs=36.9

Q ss_pred             hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccc
Q psy4925          65 KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        65 g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      ..|+.+||++|+..+..+         .+.++.+.|++||.|+.+||.+++.
T Consensus        37 k~C~~aCPagA~~~~e~G---------~V~vd~e~CigCg~C~~~C~~~~~~   79 (95)
T PRK15449         37 ELLVKACPAGLYKKQDDG---------SVRFDYAGCLECGTCRILGLGSALE   79 (95)
T ss_pred             hHHHHHCCHhhcEeCCCC---------CEEEcCCCCCcchhhhhhcCCCCcc
Confidence            489999999999765433         6788999999999999999999764

>PRK07118 ferredoxin; Validated

Probab=98.63  E-value=9.3e-09  Score=80.50  Aligned_cols=52  Identities=38%  Similarity=0.690  Sum_probs=44.4

Q ss_pred             ccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..|++||.|+.+||+++|.+.+.          ...++.+.|+.|+.|+.+||+++|.+...
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            36999999999999999876541          45678899999999999999999988654

>PRK08166 NADH dehydrogenase subunit G; Validated

Probab=98.63  E-value=9.5e-09  Score=91.36  Aligned_cols=67  Identities=18%  Similarity=0.265  Sum_probs=42.6

Q ss_pred             ccCCCccccccchhhcHHhchh--ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          52 RRYPSGEERCIACKLCEAICPA--QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.+..|.++||.|++||++|..  +.-.+...+++...... ........|.+||+|+++||+|||..+.
T Consensus       142 ~~i~~d~~rCi~C~rCVr~c~e~~g~~~l~~~~~~~~~~~~-~~~~~~~~~~~~G~cv~vCP~GAl~~k~  210 (847)
T PRK08166        142 PFISHEMNRCIACYRCVRYYKDYAGGTDLGVYGAHDNVYFG-RPEDGTLESEFSGNLVEVCPTGVFTDKT  210 (847)
T ss_pred             CceEecCCcCccccHHHHHHHhhcCcceEEEeecCceeEec-CCCCCcccChhhCChHhhCCchhccccc
Confidence            4456789999999999999983  21112111211111111 1122334688999999999999998765

>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma

Probab=98.63  E-value=7.5e-09  Score=78.80  Aligned_cols=55  Identities=33%  Similarity=0.742  Sum_probs=45.1

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .++.++|++|+.|+.+||.+++.....          ...++...|+.|+.|+++||++.+....
T Consensus       170 ~id~~~C~~C~~C~~aCP~~ai~~~~~----------~~~i~~~~C~~C~~C~~~CP~~~~~~~~  224 (228)
T TIGR03294       170 VVNQGLCMGCGTCAAACPTRAIEMEDG----------RPNVNRDRCIKCGACYVQCPRAFWPEYE  224 (228)
T ss_pred             EEChhhCcChhHHHHhCCHhhEEEeCC----------cEEEChhhccCHHHHHHHcCCCCcchhh
Confidence            356789999999999999999876432          2346778899999999999999887644

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.

>PRK07860 NADH dehydrogenase subunit G; Validated

Probab=98.61  E-value=1.5e-08  Score=89.60  Aligned_cols=66  Identities=21%  Similarity=0.414  Sum_probs=42.3

Q ss_pred             cCCCccccccchhhcHHhchh--ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          53 RYPSGEERCIACKLCEAICPA--QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .+..|.++||.|++||++|-.  +.-.+...+++....... .......|..||+|+++||+|||..+.
T Consensus       144 ~i~~d~~rCI~C~rCvr~c~ev~g~~~l~~~~rg~~~~i~~-~~~~~~~~~~cG~cv~vCP~GAl~~k~  211 (797)
T PRK07860        144 QVLLDRERCVLCARCTRFSDQIAGDPFIDLQERGALQQVGI-YEGEPFQSYFSGNTVQICPVGALTGAA  211 (797)
T ss_pred             ceeecccccccCcHHHHHHHhhcCCcEEEeeecCCCCEEec-CCCCCcCccccCCchhhCCcccccccc
Confidence            355789999999999999973  221222222222221111 112334678999999999999998654

>PRK12576 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=98.61  E-value=8.6e-09  Score=80.66  Aligned_cols=106  Identities=21%  Similarity=0.284  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhh-----
Q psy4925           9 AFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER-----   83 (160)
Q Consensus         9 ~~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~-----   83 (160)
                      ..+++|+.++...+..+-+...++....+.......+...++......+...||.||.|+.+||+.....+..+.     
T Consensus       102 ~vikDLvvD~~~~~~k~~~~~~~l~~~~~~~~~~~~~~~~p~~~~~~~~~~~CI~CG~C~~~CP~~~~~~~flgP~~l~~  181 (279)
T PRK12576        102 KVVKDLIVDFDEFYERMFKVKPRLYRAKEVLEGKAEHRLKPEDQKELWKFAQCIWCGLCVSACPVVAIDPEFLGPAAHAK  181 (279)
T ss_pred             ceeecceechHHHHHHHHhccceeccCccCCCCccccccCHHHHHHhhcchhCcccCcccccCCCccccCCcCCHHHHHH
Confidence            345566666666655554444444321111111122332233333334678999999999999975432111100     


Q ss_pred             -------cCCCcc---ccccccCccCCcCcccchhcccccc
Q psy4925          84 -------ADGSRR---TTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        84 -------~~~~~~---~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                             ......   ........+.|+.||.|..+||.+.
T Consensus       182 a~r~~~d~rd~~~~~rl~~~~~~i~~C~~Cg~C~~~CP~~I  222 (279)
T PRK12576        182 GYRFLADPRDTITEERMKILIDSSWRCTYCYSCSNVCPRDI  222 (279)
T ss_pred             HHHHhcCccccchHHHHHHHcCcCCcccCcccchhhCCCCC
Confidence                   000000   0011234578999999999999874

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

Probab=98.60  E-value=7.3e-09  Score=85.35  Aligned_cols=84  Identities=23%  Similarity=0.489  Sum_probs=64.2

Q ss_pred             ccccchhhcHHhchhccccchhhhhcCCCcc--------ccccccCccCCcCcccchhcccccccccCCcccccccchhh
Q psy4925          59 ERCIACKLCEAICPAQAITIEAEERADGSRR--------TTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEE  130 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~--------~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~  130 (160)
                      ++|++||.|+.+||..+.+..+.+.+..+..        +....+|...|+.||.|..+||.+|+.++..-+.....++.
T Consensus       224 d~CtgCg~C~~vCPve~~nefn~Gl~~~kAiy~p~~qaVp~~~~Id~~~c~~c~~C~~ac~~~av~~~q~~e~ve~~vGa  303 (622)
T COG1148         224 DKCTGCGACSEVCPVEVPNEFNEGLGKRKAIYIPFPQAVPLNYNIDPKHCIECGLCEKACPNEAVDLNQEPEEVELEVGA  303 (622)
T ss_pred             ccccccccccccCCcccCcccccccccceeeeccchhhcccccccChhhhccchhhhhcCCccccccCCCCcEEEEEece
Confidence            8999999999999987665444443333211        22345788899999999999999999999998888888898


Q ss_pred             hhccHHHHhccC
Q psy4925         131 LLYNKEKLLSNG  142 (160)
Q Consensus       131 ~~~~~~~~~~~~  142 (160)
                      |+..++.-..+.
T Consensus       304 IIvAtGy~~~Da  315 (622)
T COG1148         304 IIVATGYKPFDA  315 (622)
T ss_pred             EEEEccccccCc
Confidence            888766554443

>PRK09130 NADH dehydrogenase subunit G; Validated

Probab=98.60  E-value=1.4e-08  Score=88.32  Aligned_cols=65  Identities=25%  Similarity=0.390  Sum_probs=42.4

Q ss_pred             CCCccccccchhhcHHhchh--ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPA--QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +..+.++||+|++||++|-.  |.-.+...+++....... +......|..||+|+++||+|||+.+.
T Consensus       140 i~~~~~rCI~C~rCvr~c~ev~g~~~l~~~~rg~~~~i~~-~~~~~~~~~~~G~cv~~CPvgAl~~k~  206 (687)
T PRK09130        140 VKTVMTRCIHCTRCVRFATEVAGVPELGAIGRGEDMEITT-YLEQALTSELSGNVIDLCPVGALTSKP  206 (687)
T ss_pred             EEEecccCCcccHHHHHHHhhcCCceEEeeecCCCCEEcc-CCCCCccccccccHHhhCCCccccccc
Confidence            45678999999999999973  222222222222222211 122333578999999999999999765

>TIGR00397 mauM_napG MauM/NapG family ferredoxin-type protein

Probab=98.60  E-value=1.5e-08  Score=76.39  Aligned_cols=62  Identities=35%  Similarity=0.816  Sum_probs=44.7

Q ss_pred             Ccccccc-----chhhcHHhchh--ccccchhhhhcCCCccccccccCccCCcCcccchhccccc--ccccCC
Q psy4925          56 SGEERCI-----ACKLCEAICPA--QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD--AIVEGP  119 (160)
Q Consensus        56 ~~~~~Ci-----~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~--ai~~~~  119 (160)
                      ++.++|+     .|+.|+++||+  +||.+.......+  ......++.+.|++||.|+.+||++  ||.+..
T Consensus       128 id~~~C~~~~g~~C~~C~~~CP~~~~AI~~~~~~~~~~--~~~~p~Vd~~~C~gCG~C~~~CP~~~~AI~v~~  198 (213)
T TIGR00397       128 VGHETCLNYKGLNCSICVRVCPIRGEAISLKPIENERG--RLQIPTVDSAKCTGCGTCEKHCVLSEAAIRVLP  198 (213)
T ss_pred             ECCCCcccCCCCCcccchhhCCCCcceEEEecccccCC--cccceEEecccCCCcchhhHhCCCCCCeEEEee
Confidence            4677898     99999999998  6887654221111  1113456888999999999999987  776644

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

>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional

Probab=98.59  E-value=1.4e-08  Score=78.48  Aligned_cols=62  Identities=32%  Similarity=0.727  Sum_probs=44.6

Q ss_pred             Ccccccc-----chhhcHHhchh--ccccchhhhhcC-CCccccccccCccCCcCcccchhccccc--cccc
Q psy4925          56 SGEERCI-----ACKLCEAICPA--QAITIEAEERAD-GSRRTTRYDIDMTKCIYCGFCQEACPVD--AIVE  117 (160)
Q Consensus        56 ~~~~~Ci-----~Cg~Cv~~CP~--~~i~~~~~~~~~-~~~~~~~~~~~~~~C~~Cg~C~~~CP~~--ai~~  117 (160)
                      ++.++|+     .|+.|+.+||.  +||.++...... +........++.+.|++||.|+.+||++  ||.+
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            6778999     89999999996  788765432111 1111112356778999999999999998  7765

>PRK08318 dihydropyrimidine dehydrogenase subunit B; Validated

Probab=98.59  E-value=1e-08  Score=84.60  Aligned_cols=58  Identities=26%  Similarity=0.693  Sum_probs=43.9

Q ss_pred             CCccccccchhhcHHhchhc---cccchhhhhcCCCccccccccCccCCcCcccchhcccc-cccccCC
Q psy4925          55 PSGEERCIACKLCEAICPAQ---AITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVEGP  119 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~---~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~-~ai~~~~  119 (160)
                      .++.++|++|+.|+.+||.+   ++.+...+.       ....++...|+.|+.|+.+||. +||.+..
T Consensus       338 ~~~~~~C~~C~~C~~~Cp~~~~~ai~~~~~~~-------~~~~i~~~~C~~Cg~C~~~CP~~~Ai~~~~  399 (420)
T PRK08318        338 RIDQDKCIGCGRCYIACEDTSHQAIEWDEDGT-------RTPEVIEEECVGCNLCAHVCPVEGCITMGE  399 (420)
T ss_pred             EECHHHCCCCCcccccCCCcchhheeeccCCC-------ceEEechhhCcccchHHhhCCCCCCEEEec
Confidence            35778999999999999964   454422110       1235677889999999999999 9998755

>TIGR02951 DMSO_dmsB DMSO reductase, iron-sulfur subunit

Probab=98.58  E-value=1.7e-08  Score=72.85  Aligned_cols=56  Identities=32%  Similarity=0.654  Sum_probs=45.7

Q ss_pred             cCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCCc
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPN  120 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~~  120 (160)
                      .+.++.++|++|+.|+.+||.+++.+...            ......|++|+         +|+.+||++||.+.+.
T Consensus        89 ~~~i~~~~C~~C~~C~~aCP~~ai~~~~~------------~~~~~kC~~C~~r~~~g~~p~Cv~~Cp~~Ai~~~~~  153 (161)
T TIGR02951        89 LVLVDQDKCIGCRYCVWACPYGAPQYDPQ------------QGVMGKCDGCYDRVEKGLRPACVDACPMRALDFGPI  153 (161)
T ss_pred             cEEECHHhCCCchHHHhhCCCCCcEEcCC------------CCccccCCCCHHHHHCCCCCcchhhccccceEEecH
Confidence            44578899999999999999999876532            12356899997         8999999999998654

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.

>PTZ00305 NADH:ubiquinone oxidoreductase; Provisional

Probab=98.58  E-value=2.2e-08  Score=77.90  Aligned_cols=67  Identities=21%  Similarity=0.253  Sum_probs=41.0

Q ss_pred             ccCCCccccccchhhcHHhchh--ccccchhhhhcCCCccccccccCccCCc--CcccchhcccccccccCCc
Q psy4925          52 RRYPSGEERCIACKLCEAICPA--QAITIEAEERADGSRRTTRYDIDMTKCI--YCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~~~~~~~~C~--~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.+.+|.++||.|++||++|-.  +.-.+...+++.......  ..+...|.  +||+|+++||+|||..++.
T Consensus       205 p~i~~D~nKCIlCgRCVRaC~EVqg~~aL~~~~RG~~t~I~t--~~d~~~~~~~~~g~cvdvCPvGAL~~~d~  275 (297)
T PTZ00305        205 PQTRVVLNRCIHCTRCVRFLNEHAQDFNLGMIGRGGLSEIST--FLDELEVKTDNNMPVSQLCPVGKLYLGDA  275 (297)
T ss_pred             CceeecCCcCcCccHHHHHHHHhhCCcEEEEeecCCCCEEee--cCCCcccccCCCCceeeECCCcccccCCc
Confidence            3345678999999999999984  222222223332222211  12222243  4677999999999988765

>TIGR03287 methan_mark_16 putative methanogenesis marker 16 metalloprotein

Probab=98.58  E-value=7.9e-09  Score=83.58  Aligned_cols=55  Identities=31%  Similarity=0.690  Sum_probs=44.9

Q ss_pred             CCccccccchhhcH--HhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCccc
Q psy4925          55 PSGEERCIACKLCE--AICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv--~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~  122 (160)
                      .++.++|++|+.|.  .+||++++..+             ..++...|+.|+.|+++||++|+.+.....
T Consensus       298 ~id~dkCi~Cg~C~~~~aCPt~AI~~~-------------~~Id~~~Ci~CGaCV~aCP~~AI~~~~~~i  354 (391)
T TIGR03287       298 KYNPERCENCDPCLVEEACPVPAIKKD-------------GTLNTEDCFGCGYCAEICPGGAFEVNLGSV  354 (391)
T ss_pred             EEchhhCcCCCCCcCCcCCCHhhEecc-------------ceeChHhCcChHHHHhhCCccceEEeCCeE
Confidence            35678999999995  89999988632             136777899999999999999999876544

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.

>PRK10882 hydrogenase 2 protein HybA; Provisional

Probab=98.58  E-value=1.9e-08  Score=80.22  Aligned_cols=22  Identities=32%  Similarity=0.782  Sum_probs=10.7

Q ss_pred             cCccCCcCcccchhcccccccc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      ++...|++|+.|+.+||+++|.
T Consensus       140 id~dkCigCg~Cv~aCP~gai~  161 (328)
T PRK10882        140 YDKDVCTGCRYCMVACPFNVPK  161 (328)
T ss_pred             CCHHHcCcccHHHHhCCcccee
Confidence            3444455555555555555444

>PRK10330 formate dehydrogenase-H ferredoxin subunit; Provisional

Probab=98.57  E-value=1.8e-08  Score=74.13  Aligned_cols=52  Identities=29%  Similarity=0.631  Sum_probs=43.4

Q ss_pred             cccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          58 EERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        58 ~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ...|++|+  .|+.+||++++.....          ...++...|++|+.|+.+||++||.+..
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            45799999  8999999999876431          3456888999999999999999998754

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

Probab=98.57  E-value=2.7e-08  Score=85.84  Aligned_cols=64  Identities=28%  Similarity=0.593  Sum_probs=42.7

Q ss_pred             CccccccchhhcHHhchh--ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPA--QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~--~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .|+++||+|++||++|-.  |.-.+...+++.+.........-... ..||+|+++||+|||+.++.
T Consensus       141 ~dm~RCI~C~RCVR~c~eiaG~~~l~~~~rg~~~~i~t~~~~~l~s-e~cGncv~vCPvGALt~K~~  206 (693)
T COG1034         141 YDMNRCILCTRCVRFCKEIAGTHELGVIKRGENSEIGTYLDQPLES-ELCGNCVDVCPVGALTSKPF  206 (693)
T ss_pred             cccccceechhhHHhhhhhcCccccceeecCCCceeeccccccccc-ccccceeeeccccccccChH
Confidence            689999999999999984  32233333333333332222222222 78999999999999998775

>PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional

Probab=98.55  E-value=2.1e-08  Score=85.50  Aligned_cols=56  Identities=39%  Similarity=0.899  Sum_probs=44.0

Q ss_pred             Cccccccch------hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          56 SGEERCIAC------KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        56 ~~~~~Ci~C------g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .+..+|+.|      +.|+.+||.+++.....+.        ...++...|+.|+.|+.+||++||.+..
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            356677777      8999999999887543211        2457888999999999999999998754

>PRK13795 hypothetical protein; Provisional

Probab=98.55  E-value=2e-08  Score=86.74  Aligned_cols=55  Identities=36%  Similarity=0.850  Sum_probs=44.7

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      .++.+.|++|+.|+.+||.+++......        ..+.++...|+.|+.|+++||.+++..
T Consensus       577 v~~~~~C~~Cg~C~~~CP~~ai~~~~~~--------~~~~id~~~C~~Cg~C~~aCP~~a~~~  631 (636)
T PRK13795        577 LRRAAECVGCGVCVGACPTGAIRIEEGK--------RKISVDEEKCIHCGKCTEVCPVVKYKD  631 (636)
T ss_pred             EEccccCCCHhHHHHhCCcccEEeecCC--------ceEEechhhcCChhHHHhhcCCCeeEe
Confidence            3457899999999999999998765421        124567789999999999999999875

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

Probab=98.54  E-value=1.9e-08  Score=49.57  Aligned_cols=21  Identities=38%  Similarity=0.986  Sum_probs=14.4

Q ss_pred             CccccccchhhcHHhchhccc
Q psy4925          56 SGEERCIACKLCEAICPAQAI   76 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i   76 (160)
                      +|.++|++||.|+.+||.+||
T Consensus         4 id~~~C~~Cg~C~~~Cp~~ai   24 (24)
T PF12837_consen    4 IDPDKCIGCGDCVRVCPEGAI   24 (24)
T ss_pred             EChhhCcChhHHHHhcchhcC
Confidence            456677777777777776654

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

>PRK07570 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated

Probab=98.54  E-value=1.2e-08  Score=78.64  Aligned_cols=60  Identities=25%  Similarity=0.583  Sum_probs=36.8

Q ss_pred             CCccccccchhhcHHhchhccccchh-------hhhcCCCc-cc-------cccc-cCccCCcCcccchhcccccc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA-------EERADGSR-RT-------TRYD-IDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~-------~~~~~~~~-~~-------~~~~-~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ..+...||.||.|+++||+.......       ........ ..       .... ...+.|+.||.|.++||.+.
T Consensus       153 ~~~~~~CI~CG~C~saCP~~~~~~f~Gp~~~~~~l~p~~~~~r~~~~~~~~~~~~~~gv~~C~~Cg~Cs~VCPk~I  228 (250)
T PRK07570        153 AFDAAACIGCGACVAACPNGSAMLFTGAKVSHLALLPQGQPERARRVRAMVAQMDEEGFGNCTNTGECEAVCPKGI  228 (250)
T ss_pred             hhCccccCCCcccccccCCcccccccchhhhhhhhCcccchhHHHHHHHHHHHHhccCcccCcccCccccccCCCC
Confidence            45678999999999999986432000       00000000 00       0011 34568999999999999984

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

Probab=98.53  E-value=1.2e-08  Score=77.32  Aligned_cols=58  Identities=28%  Similarity=0.491  Sum_probs=35.8

Q ss_pred             ccccccchhhcHHhchhccccchhhh----------hcCCC-----cccccc--ccCccCCcCcccchhcccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEE----------RADGS-----RRTTRY--DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~----------~~~~~-----~~~~~~--~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      +..+||+||.|+.+||+.....+..+          ..+..     ......  ....+.|+.||.|.++||.+.
T Consensus       136 ~~~~Ci~CG~C~~~CP~~~~~~~~~gp~~~~~~~r~~~d~~~~~~~~r~~~~~~~~~~~~C~~Cg~C~~~CP~~I  210 (220)
T TIGR00384       136 QLSGCILCGCCYSSCPAFWWNPEFLGPAALTAAYRFLIDSRDHATKDRLEGLNDKNGVWRCTTCMNCSEVCPKGV  210 (220)
T ss_pred             hhhhccccccccccCCCCccCCCCcCHHHHHHHHHHhcCCCccchHHHHHHhhccCCCccCccccccccccCCCC
Confidence            46789999999999997532211100          00000     000011  235678999999999999983

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.

>PRK09326 F420H2 dehydrogenase subunit F; Provisional

Probab=98.52  E-value=4.2e-08  Score=78.92  Aligned_cols=61  Identities=28%  Similarity=0.531  Sum_probs=41.7

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCc--cccccccCccCCcCcccchhcccccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSR--RTTRYDIDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~--~~~~~~~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      ++.+.|++|+.|+.+||++++.+..........  .......+...|+.||.|..+||..++.
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            467899999999999999998875432100000  0001124667899999999999986643

>PRK12769 putative oxidoreductase Fe-S binding subunit; Reviewed

Probab=98.51  E-value=2.9e-08  Score=86.06  Aligned_cols=64  Identities=28%  Similarity=0.601  Sum_probs=47.0

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc------cchhcccccccccCCccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg------~C~~~CP~~ai~~~~~~~  122 (160)
                      +.++.++|++|+.|+.+||.+++.+......     ......+...|..|+      .|+++||++||.+.+..+
T Consensus        80 ~~id~~~C~~C~~C~~~CP~~ai~~~~~~~~-----~~~~~~~~~~C~~C~~~~~~p~Cv~~CP~~Ai~~~~~~~  149 (654)
T PRK12769         80 IQVNQQKCIGCKSCVVACPFGTMQIVLTPVA-----AGKVKATAHKCDLCAGRENGPACVENCPADALQLVTEQA  149 (654)
T ss_pred             EEEecccccCcChhcccCCccCeeecccCCc-----ccceeeecCcCcCCCCCCCCCceeccCCcCcEEEecHHH
Confidence            3457789999999999999998876533210     012234567899998      899999999999876533

>TIGR01660 narH nitrate reductase, beta subunit

Probab=98.44  E-value=5.3e-08  Score=79.86  Aligned_cols=54  Identities=24%  Similarity=0.524  Sum_probs=43.6

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCCc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPN  120 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~~  120 (160)
                      .++.++|++|+.|+.+||.+++.+....            ....+|.+|.         +|+++||++|+.+...
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            4678999999999999999998765421            2456899994         6999999999887644

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.

>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit

Probab=98.38  E-value=1.5e-07  Score=78.06  Aligned_cols=58  Identities=28%  Similarity=0.645  Sum_probs=38.5

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      .+...|+.||.|+.+||.+.+...................+...|+.||.|..+||.+
T Consensus       360 ~~~~~Ci~Cg~C~~vCP~~l~p~~l~~~~~~~~~~~~~~~~~~~C~~Cg~C~~vCP~~  417 (435)
T TIGR01945       360 SPEKPCIRCGKCVQVCPMNLLPQQLNWLALADEFDEAEEHNLMDCIECGCCSYVCPSN  417 (435)
T ss_pred             ccCCcCcCccchhhhCccchhhHHHHHHhhhcccchhhcCCCCcCCcCCCcccccCCC
Confidence            4567999999999999987553321110000111112245667899999999999998

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.

>PRK13552 frdB fumarate reductase iron-sulfur subunit; Provisional

Probab=98.38  E-value=1e-07  Score=73.11  Aligned_cols=106  Identities=17%  Similarity=0.184  Sum_probs=53.8

Q ss_pred             HHHHHHHHHHHHHHHhh-cCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhh----
Q psy4925           9 AFLTEIFRGFFVATGHI-FKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER----   83 (160)
Q Consensus         9 ~~~~~~~~g~~~~~~~~-~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~----   83 (160)
                      ..+.+|+.++...+..+ -+-..++.-.....+........++..........||.||.|..+||+.....+..+.    
T Consensus        98 pVirDLvVD~~~~~~~~~~~v~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~CI~Cg~C~saCP~~~~~~~f~GP~~~~  177 (239)
T PRK13552         98 KLIGDLSVNTGKWFREMSERVESWIHTDKEFDIHRLEERMEPEEADEIYELDRCIECGCCVAACGTKQMREDFVGAVGLN  177 (239)
T ss_pred             CcceeCccccHHHHHHHHHhhcCccccCCCCCCcccccCCCHHHHHHhhchhhccccchhHhhCCCCccCCCccChHHHH
Confidence            34566666766666655 3333343311011101011222222222334567899999999999964322111100    


Q ss_pred             ------cCCCc--ccccc------ccCccCCcCcccchhcccccc
Q psy4925          84 ------ADGSR--RTTRY------DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        84 ------~~~~~--~~~~~------~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                            .+.+.  .....      ....+.|+.|+.|.++||.+.
T Consensus       178 ~a~r~~~d~rd~~~~~~~~~~l~~~~gi~~C~~C~~C~~vCPk~I  222 (239)
T PRK13552        178 RIARFELDPRDERTDEDFYELIGNDDGVFGCMSLLGCEDNCPKDL  222 (239)
T ss_pred             HHHHHhhCCCcchhHHHHHHHhccCCCcCCCcCcCccchhCCCCC
Confidence                  01110  00001      134679999999999999873

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

Probab=98.37  E-value=3e-08  Score=75.29  Aligned_cols=103  Identities=20%  Similarity=0.323  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhh-------
Q psy4925          10 FLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEE-------   82 (160)
Q Consensus        10 ~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~-------   82 (160)
                      .+.+++.++...+..+-+.+.++....+..+..  +.+.++......+...||.||.|+.+||......+..+       
T Consensus        95 VIkDLVVD~~~f~~~~~~ikp~~~~~~~~~~~~--~~q~pe~~~~~~~~~~CI~Cg~C~s~CP~~~~~~~f~GPa~l~~a  172 (234)
T COG0479          95 VIRDLVVDMEEFYEKLRKIKPYLIRDDEPDPGE--RLQSPEEREKLDELSECILCGCCTAACPSIWWNPDFLGPAALRQA  172 (234)
T ss_pred             ceeeeeeccHHHHHhhhccccceecCCcCCCcc--ccCCHHHHHHHHhhhhccccchhhhhCCccccccCCcCHHHHHHH
Confidence            456667777777776655554544422222222  44334443344456789999999999996433321111       


Q ss_pred             -------hcCCC-ccccccc--cCccCCcCcccchhcccccc
Q psy4925          83 -------RADGS-RRTTRYD--IDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        83 -------~~~~~-~~~~~~~--~~~~~C~~Cg~C~~~CP~~a  114 (160)
                             +..++ .+.....  ...+.|..|++|.++||.+.
T Consensus       173 ~R~~~D~rd~~~~~R~~~~~~~~gv~~C~~~~~C~~vCPK~i  214 (234)
T COG0479         173 YRFLADSRDEGTAERLKILEDPDGVWRCTTCGNCTEVCPKGI  214 (234)
T ss_pred             HHHhcCCcccchHHHHHhccCCCCEecccccccccccCCCCC
Confidence                   10110 0000111  13478999999999999984

>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=7.8e-08  Score=47.36  Aligned_cols=22  Identities=55%  Similarity=0.997  Sum_probs=20.1

Q ss_pred             ccCccCCcCcccchhccccccc
Q psy4925          94 DIDMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      .+|.+.|++||.|+.+||.+||
T Consensus         3 ~id~~~C~~Cg~C~~~Cp~~ai   24 (24)
T PF12837_consen    3 VIDPDKCIGCGDCVRVCPEGAI   24 (24)
T ss_pred             EEChhhCcChhHHHHhcchhcC
Confidence            5788899999999999999986

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

>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed

Probab=98.36  E-value=1.5e-07  Score=81.50  Aligned_cols=24  Identities=33%  Similarity=0.861  Sum_probs=12.7

Q ss_pred             CCCccccccchhhcHHhchhcccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAIT   77 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~   77 (160)
                      +.++.++|++|+.|+.+||.+++.
T Consensus        80 v~~d~~~C~gC~~C~~~CP~~ai~  103 (639)
T PRK12809         80 VQLDEQKCIGCKRCAIACPFGVVE  103 (639)
T ss_pred             eecChhhCcchhhHhhhcCCCCEE
Confidence            334455555555555555555543

>TIGR03315 Se_ygfK putative selenate reductase, YgfK subunit

Probab=98.36  E-value=1.3e-07  Score=84.98  Aligned_cols=60  Identities=28%  Similarity=0.605  Sum_probs=40.4

Q ss_pred             ccccccc----hhhcHHhchhcccc-chhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          57 GEERCIA----CKLCEAICPAQAIT-IEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci~----Cg~Cv~~CP~~~i~-~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.++|.+    ||.|+.+||.+|+. +...+....   ...+..+ ..|+.||.|+++||++|+.+...
T Consensus       879 ~~~rC~~c~~~Cg~Cv~vCP~~Aii~i~~~~~~~~---~~~i~~d-~~C~~CG~C~~vCP~~a~~~~gk  943 (1012)
T TIGR03315       879 ESQRCLECSYVCEKCVDVCPNRANIVIYVPGFRDQ---FQIVHLD-GMCNECGNCATFCPYDGAPYKDK  943 (1012)
T ss_pred             ccccccCCCCCCCChhhhCChhhhhccccccccCC---ceeeecC-ccccccchHHHhCCCCcccceee
Confidence            4579996    99999999999752 221000000   0011222 24999999999999999998776

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.

>PRK12575 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=98.35  E-value=3e-08  Score=75.77  Aligned_cols=104  Identities=14%  Similarity=0.228  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhc----
Q psy4925           9 AFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERA----   84 (160)
Q Consensus         9 ~~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~----   84 (160)
                      ..+++++.++...+..+-+...++.-. .. .........++......+...||.||.|..+||+-....+....+    
T Consensus        96 pvikDLvvD~~~~~~~~~~~~p~l~~~-~~-~~~~~~~~~p~~~~~~~~~~~CI~CG~C~s~CP~~~~~~~~f~GP~~~~  173 (235)
T PRK12575         96 PVVRDLIVDMTDFFNQYHSIRPYLIND-TV-PPERERLQTPQEREQLDGLYECILCACCSTACPSYWWNPDKFVGPAGLL  173 (235)
T ss_pred             CccccceecCHHHHHHHHhccCccccC-CC-CccccccCCHHHHHHHHhhhhCcccccccccccCccccCCCcCCHHHHH
Confidence            345566666666655554444444321 11 111122222222222235678999999999999743321111100    


Q ss_pred             -------CCCc--ccccc-----ccCccCCcCcccchhcccccc
Q psy4925          85 -------DGSR--RTTRY-----DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        85 -------~~~~--~~~~~-----~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                             +++.  .....     ....+.|+.|++|.++||.+.
T Consensus       174 ~a~r~~~D~rd~~~~~rl~~l~~~~gl~~C~~C~~C~~vCPkgI  217 (235)
T PRK12575        174 QAYRFIADSRDDATAARLDDLEDPYRLFRCRTIMNCVDVCPKGL  217 (235)
T ss_pred             HHHHHHhCCCCCCcHHHHHhhhcCCCcccccCcchhccccCCCC
Confidence                   0110  00011     123578999999999999984

>PRK08640 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed

Probab=98.34  E-value=4e-08  Score=75.73  Aligned_cols=59  Identities=22%  Similarity=0.490  Sum_probs=35.8

Q ss_pred             CccccccchhhcHHhchhccccchhhh--------h--cC--CC-ccccc---c--ccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEE--------R--AD--GS-RRTTR---Y--DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~--------~--~~--~~-~~~~~---~--~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      .+...||.||.|+.+||+....-+..+        +  .+  +. .....   .  ....+.|+.||.|.++||.+.
T Consensus       149 ~~~~~CI~CG~C~saCP~~~~~~~f~GP~~l~ka~r~~~d~~rd~~~~~rl~~l~~~~g~~~C~~Cg~C~~vCPkgI  225 (249)
T PRK08640        149 YELSKCMTCGCCLEACPNVNEKSDFIGPAAISQVRLFNAHPTGEMHKEERLRALMGDGGIADCGNAQNCVRVCPKGI  225 (249)
T ss_pred             hhhhhccCcCcccccCCCCccCCCccChHHHHHHHHHhcCcCcCccHHHHHHHhhcCCCeeCCcCcCcccccCCCCC
Confidence            346789999999999996543211111        0  00  00 00001   1  123478999999999999884

>TIGR02486 RDH reductive dehalogenase

Probab=98.34  E-value=1.9e-07  Score=74.24  Aligned_cols=56  Identities=30%  Similarity=0.696  Sum_probs=36.4

Q ss_pred             ccccchhhcHHhchhccccchhhhhcCC----------CccccccccCcc-----CCc-----Ccccchhcccccc
Q psy4925          59 ERCIACKLCEAICPAQAITIEAEERADG----------SRRTTRYDIDMT-----KCI-----YCGFCQEACPVDA  114 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~----------~~~~~~~~~~~~-----~C~-----~Cg~C~~~CP~~a  114 (160)
                      +.|..|++|+.+||++||..+.....+.          ........++..     .|.     .|+.|+.+||.+.
T Consensus       205 ~fC~~C~~C~~~CP~~Ai~~~~~psw~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~C~~C~~~CPf~~  280 (314)
T TIGR02486       205 KFCETCGKCADECPSGAISKGGEPTWDPEDSNGDPPGENNPGLKWQYDGWRCLLFRCYNEGGGGCGVCQAVCPFNK  280 (314)
T ss_pred             ccCcchhHHHhhCCccccCCCCCCcccccccccccccccCCCcccccchhhcccccccCCCCCCCCCCeeECCCCC
Confidence            5799999999999999998764321111          000011122333     354     5999999999984

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.

>PRK12769 putative oxidoreductase Fe-S binding subunit; Reviewed

Probab=98.33  E-value=2e-07  Score=80.85  Aligned_cols=54  Identities=28%  Similarity=0.610  Sum_probs=44.8

Q ss_pred             ccccccchhh--cHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          57 GEERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci~Cg~--Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ....|++|+.  |+.+||++++.....          .+.++...|++|+.|+.+||++||.+...
T Consensus        52 ~~~~C~~C~~~~C~~~CP~~ai~~~~~----------~~~id~~~C~~C~~C~~~CP~~ai~~~~~  107 (654)
T PRK12769         52 SAVTCHHCEDAPCARSCPNGAISHVDD----------SIQVNQQKCIGCKSCVVACPFGTMQIVLT  107 (654)
T ss_pred             CCccCCCCCChhHhhhCCccceeccCC----------eEEEecccccCcChhcccCCccCeeeccc
Confidence            3578999996  999999999876432          35678889999999999999999987543

>PRK09853 putative selenate reductase subunit YgfK; Provisional

Probab=98.32  E-value=2.3e-07  Score=83.28  Aligned_cols=61  Identities=25%  Similarity=0.561  Sum_probs=42.1

Q ss_pred             Cccccccch----hhcHHhchhccc-cchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIAC----KLCEAICPAQAI-TIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~C----g~Cv~~CP~~~i-~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .+.++|.+|    |.|+.+||.+|+ .+...+   .......+.+ ...|++||.|+.+||+++-.+.+.
T Consensus       883 ~~~~rC~~C~~~C~~C~~vCP~~A~~~i~~~g---~~~~~~~~~~-~~~C~~CG~C~~~CP~~~~py~dk  948 (1019)
T PRK09853        883 QEAARCLECNYVCEKCVDVCPNRANVSIAVPG---FQNRFQIVHL-DAMCNECGNCAQFCPWNGKPYKDK  948 (1019)
T ss_pred             ccccccCCcccccchhhhhCCcccccccccCC---cccCCceEEc-CccCccccchhhhCCCCCCccccc
Confidence            356799999    999999999983 222111   0000112333 488999999999999998766665

>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=98.32  E-value=1.5e-07  Score=46.35  Aligned_cols=20  Identities=70%  Similarity=1.301  Sum_probs=9.3

Q ss_pred             CccCCcCcccchhccccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      +.+.|++||.|+.+||++||
T Consensus         4 d~~~C~~Cg~C~~~CP~~ai   23 (24)
T PF00037_consen    4 DPDKCIGCGRCVEACPFDAI   23 (24)
T ss_dssp             ETTTSSS-THHHHHSTTSSE
T ss_pred             chHHCCCcchhhhhcccccC
Confidence            33445555555555555544

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 ....

>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=98.31  E-value=1.3e-07  Score=46.59  Aligned_cols=22  Identities=41%  Similarity=0.951  Sum_probs=18.5

Q ss_pred             CccccccchhhcHHhchhcccc
Q psy4925          56 SGEERCIACKLCEAICPAQAIT   77 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~   77 (160)
                      ++.++|++||.|+.+||.+||.
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            4678999999999999999873

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 ....

>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit

Probab=98.31  E-value=1.3e-07  Score=76.02  Aligned_cols=52  Identities=29%  Similarity=0.655  Sum_probs=40.6

Q ss_pred             ccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        61 Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      |..|+.|+.+||++|+.+.... .     ...+.++...|+.||.|+.+||++|+...
T Consensus       183 ~c~~~~Cv~~CP~~Ai~~~~~~-~-----~~~~~id~~~Ci~Cg~Ci~~CP~~a~~~~  234 (341)
T TIGR02066       183 VCEIPSVVAACPTGALKPRRDG-K-----NKSLEVDVEKCIYCGNCYTMCPAMPIFDP  234 (341)
T ss_pred             hcCCCceEeeCchhhceecccC-C-----CCceeeccccCCcCCchHHhCchhhccCC
Confidence            4566899999999999874221 0     11467899999999999999999998633

This model describes the beta subunit of sulfite reductase.

>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG

Probab=98.30  E-value=4.9e-07  Score=74.74  Aligned_cols=43  Identities=37%  Similarity=0.889  Sum_probs=33.2

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      .++|++|+.|+.+||++ +...+              .....|+.|+.|+++||. ++.
T Consensus       230 ~~~Ci~C~~Cv~vCP~g-i~~~~--------------~~~~~Ci~Cg~CidaCp~-a~~  272 (434)
T TIGR02745       230 LGDCIDCNLCVQVCPTG-IDIRD--------------GLQLECINCGLCIDACDD-VME  272 (434)
T ss_pred             CCCCCChhhhHHhCCCC-CEeCC--------------CCchhChhhhHHHHhCCC-hHH
Confidence            46899999999999998 43221              123579999999999997 443

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.

>PLN00129 succinate dehydrogenase [ubiquinone] iron-sulfur subunit

Probab=98.30  E-value=6.4e-08  Score=75.42  Aligned_cols=105  Identities=16%  Similarity=0.224  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccch-hhhhc----
Q psy4925          10 FLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIE-AEERA----   84 (160)
Q Consensus        10 ~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~-~~~~~----   84 (160)
                      .+.+++.++...+..+-+...++.-..............++..........||.||.|..+||+-....+ ..+..    
T Consensus       138 VirDLvVD~~~f~~klk~v~p~l~~~~~~~~~~~~~~q~pe~~~~~~~~~~CI~CG~C~saCPv~~~~~~~flGP~~l~~  217 (276)
T PLN00129        138 VIKDLVVDMTNFYQQYKSIEPWLKTKKPPEDGQKEHLQSKEDRAKLDGMYECILCACCSTSCPSYWWNPEKFLGPAALLH  217 (276)
T ss_pred             eeeecccccHHHHHHHHhccccccCCCCCCCCccccCCCHHHHHHHhhhhhCccccccccccCCCcccCcccccHHHHHH
Confidence            4556666666666555444444432111111101222222222222345689999999999995322111 00000    


Q ss_pred             ------C--CCcccccc-----ccCccCCcCcccchhcccccc
Q psy4925          85 ------D--GSRRTTRY-----DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        85 ------~--~~~~~~~~-----~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                            +  ......+.     ....+.|+.|+.|.++||.+.
T Consensus       218 a~R~~~D~RD~~~~erl~~l~~~~gl~~C~~C~~C~~vCPkgI  260 (276)
T PLN00129        218 AYRWISDSRDEYTKERLEALDDEFKLYRCHTIRNCSNACPKGL  260 (276)
T ss_pred             HHHhcCCccccchHHHHHHHHhcCCCCcCcChhhccccCCCCC
Confidence                  0  00000011     124588999999999999984

>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed

Probab=98.29  E-value=2.5e-07  Score=80.12  Aligned_cols=54  Identities=30%  Similarity=0.690  Sum_probs=40.8

Q ss_pred             ccccccchhh--cHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          57 GEERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci~Cg~--Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ....|++|+.  |+.+||++++.....          ...++...|++|+.|+.+||++||.+...
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  999999999876432          34566677888888888888877766543

>COG2440 FixX Ferredoxin-like protein [Energy production and conversion]

Probab=98.26  E-value=2.3e-07  Score=60.52  Aligned_cols=60  Identities=22%  Similarity=0.549  Sum_probs=46.5

Q ss_pred             ccccccCC-Cccccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccc-cccc
Q psy4925          48 EHALRRYP-SGEERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIV  116 (160)
Q Consensus        48 ~~~~~~~~-~~~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~-~ai~  116 (160)
                      +...+.+. .+...|..|.  .|+.+||++.....+.+         .+.++...|.+||.|--+||. +.|.
T Consensus        21 De~~pHI~v~~~~~~~~~~~~~l~~aCPA~~Y~~~~~g---------~l~~~yegClECGTCRvlc~~~~~i~   84 (99)
T COG2440          21 DEDHPHIIVKDPDDCQECEDKPLIKACPAGCYKLIDDG---------KLRFDYEGCLECGTCRVLCPHSGLIQ   84 (99)
T ss_pred             cCCCCcEecCCchhhhhccchhhhhcCCHHHeeECCCC---------cEEEeecCeeeccceeEecCCCcceE
Confidence            33334443 3477899999  99999999988876644         678899999999999999999 4443

>TIGR03336 IOR_alpha indolepyruvate ferredoxin oxidoreductase, alpha subunit

Probab=98.25  E-value=2.4e-07  Score=79.60  Aligned_cols=51  Identities=41%  Similarity=0.866  Sum_probs=38.7

Q ss_pred             ccCCCccccccchhhcHH--hchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccc
Q psy4925          52 RRYPSGEERCIACKLCEA--ICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~--~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      ..+.++.++|++|+.|+.  +||...  .++.          ...++. .|+.||.|+++||++||
T Consensus       543 ~~~~id~~~C~~C~~C~~~~~CP~~~--~~~~----------~~~i~~-~C~~Cg~C~~~CP~~Ai  595 (595)
T TIGR03336       543 GPYKVDQDKCIGCKKCIKELGCPAIE--PEDK----------EAVIDP-LCTGCGVCAQICPFDAI  595 (595)
T ss_pred             ceEEEcCCcCCCccccccccCCCCcc--ccCC----------cceeCC-CCcCHHHHHhhCccccC
Confidence            345567889999999999  999532  2111          234555 69999999999999986

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.

>PRK05950 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed

Probab=98.25  E-value=8.4e-08  Score=73.25  Aligned_cols=103  Identities=16%  Similarity=0.191  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccch-hhhhc----
Q psy4925          10 FLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIE-AEERA----   84 (160)
Q Consensus        10 ~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~-~~~~~----   84 (160)
                      .+++|+.++...+..+-....++. +.... .........+......+...|+.||.|..+||+.....+ ..+..    
T Consensus        94 vikDLvvD~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~~~Ci~Cg~C~~~CP~~~~~~~~~~gp~~l~~  171 (232)
T PRK05950         94 VIKDLVVDMTQFYAQYRSIKPYLI-NDTPP-PARERLQSPEDREKLDGLYECILCACCSTSCPSFWWNPDKFLGPAALLQ  171 (232)
T ss_pred             eeeeceeehHHHHHHHHhccCeec-CCCCC-CchhccCCHHHHHHHHhHHhccccccccccCCccccCCCCCCCHHHHHH
Confidence            345555555555555444433333 11111 111222222222222346789999999999996432211 00000    


Q ss_pred             ------CCCc--cccc---c--ccCccCCcCcccchhcccccc
Q psy4925          85 ------DGSR--RTTR---Y--DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        85 ------~~~~--~~~~---~--~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                            +...  ....   .  ....+.|+.||.|..+||.+.
T Consensus       172 ~~r~~~d~rd~~~~~~~~~~~~~~~i~~C~~Cg~C~~~CP~gi  214 (232)
T PRK05950        172 AYRFIADSRDEATGERLDILDDPFGVFRCHTIMNCVEVCPKGL  214 (232)
T ss_pred             HHHHhhCCccchhHHHHHHhhcccccccCcCcCCcCccccCCC
Confidence                  0000  0000   0  114578999999999999873

>PRK12385 fumarate reductase iron-sulfur subunit; Provisional

Probab=98.24  E-value=6.8e-08  Score=74.28  Aligned_cols=57  Identities=32%  Similarity=0.701  Sum_probs=34.5

Q ss_pred             ccccccchhhcHHhchhccccchhhhhc--------------CCCc-cccc--cccCccCCcCcccchhccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERA--------------DGSR-RTTR--YDIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~--------------~~~~-~~~~--~~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      ....||+||.|+.+||+-....+..+..              .+.. ....  .....+.|+.||.|..+||.+
T Consensus       145 ~~~~CI~Cg~C~saCP~~~~~~~y~GP~~l~~a~r~~~d~rd~~~~~rl~~~~~~~gl~~C~~C~~C~~vCP~~  218 (244)
T PRK12385        145 QFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNLDSRDHGKKERMKQLNGQNGVWSCTFVGYCSEVCPKH  218 (244)
T ss_pred             HHHhcCcCccccCcCcCcccCCCCCCHHHHHHHHHHhhcCCccchHHHHHhhcccchhhhCcCcccccccCCCC
Confidence            3568999999999999743221111100              0000 0000  123446899999999999997

>PRK12577 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=98.22  E-value=1.3e-07  Score=75.80  Aligned_cols=105  Identities=16%  Similarity=0.317  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhh-----
Q psy4925           9 AFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER-----   83 (160)
Q Consensus         9 ~~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~-----   83 (160)
                      ..+++++.++...+..+.+...++.-... ......+...++..........||.||.|+.+||+....-+..+.     
T Consensus       103 pvikDLvVD~~~~~~k~~~v~p~~~~~~~-~~~~~e~~~~p~~~~~~~~~~~Ci~CG~C~s~CP~~~~~~~f~GP~~~~~  181 (329)
T PRK12577        103 PVIKDLVVDMSSFWQNLEAVDPYVSTAAR-QVPEREFLQTPEERSKLDQTGNCILCGACYSECNAREVNPEFVGPHALAK  181 (329)
T ss_pred             CccccceeccHHHHHHHHhccCccccCCC-CCCcccccCCHHHHHHHHHhhhCcccCcccccCCCCCcCcCcCCHHHHHH
Confidence            34566666776666666554434332111 111122222222222222356799999999999964322111100     


Q ss_pred             -----cCCCc--cccccc------cCccCCcCcccchhcccccc
Q psy4925          84 -----ADGSR--RTTRYD------IDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        84 -----~~~~~--~~~~~~------~~~~~C~~Cg~C~~~CP~~a  114 (160)
                           .++..  ......      ...+.|+.|+.|..+||.+.
T Consensus       182 a~r~~~d~rd~~~~~~l~~~~~~~~giw~C~~C~~C~~~CPk~I  225 (329)
T PRK12577        182 AQRMVADSRDTATEQRLELYNQGTAGVWGCTRCYYCNSVCPMEV  225 (329)
T ss_pred             HHHHhhCCcchhHHHHHHHHhcCCCccccCcChhhhhhhCCCCC
Confidence                 00000  000111      12578999999999999874

>TIGR00276 iron-sulfur cluster binding protein, putative

Probab=98.22  E-value=7.4e-07  Score=69.91  Aligned_cols=60  Identities=27%  Similarity=0.492  Sum_probs=38.0

Q ss_pred             cccccchhhcHHhchhccccchhhhhc----------CCCccccccccCccCCc-Ccccchhccccccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERA----------DGSRRTTRYDIDMTKCI-YCGFCQEACPVDAIVE  117 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~----------~~~~~~~~~~~~~~~C~-~Cg~C~~~CP~~ai~~  117 (160)
                      .+.|..|+.|+.+||++||........          .+......+..+...|+ +|+.|+.+||.+....
T Consensus       158 ~~~C~~C~~C~~aCPt~AI~~~~~~d~~~C~sy~ti~~~~~~~~~~~~~~~~~~~gCd~Cq~vCP~n~~~~  228 (282)
T TIGR00276       158 EEYCGRCTKCIDACPTQALVEPEFVDAPRCISYLTIEKDAALPKEFASNCGGRSYGCDICQEVCPWNKKGQ  228 (282)
T ss_pred             CCCCccHHHHHHhcCcccccCCCccCHHHHHHHhcccCCCcCCHHHHHHhcCcccCCCCccccCCCCCCCC
Confidence            568999999999999999863211000          00001111223345675 6999999999996433

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.

>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C

Probab=98.19  E-value=4.5e-07  Score=64.31  Aligned_cols=56  Identities=32%  Similarity=0.608  Sum_probs=33.2

Q ss_pred             ccccchhhcHHhchhcccc---chhhhhc--CCCccccccccCccCCcCcccchhcccccc
Q psy4925          59 ERCIACKLCEAICPAQAIT---IEAEERA--DGSRRTTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~i~---~~~~~~~--~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      +.|+.||.|..+||+....   .......  .+...........+.|+.||.|..+||.+.
T Consensus         2 ~~Ci~CG~C~~~CP~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~C~~Cg~C~~~CP~~i   62 (144)
T TIGR03290         2 KACYQCGTCTGSCPSGRRTSYRTRLIIRKALLGLKDEVISDDDLWMCTTCYTCQERCPRDV   62 (144)
T ss_pred             ccccCCCCCcCcCCCccccCCCHHHHHHHHHccchhhhccCCCCCcCcCcCchhhhcCCCC
Confidence            4699999999999974211   0000000  000000011124568999999999999884

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.

>PRK12386 fumarate reductase iron-sulfur subunit; Provisional

Probab=98.15  E-value=2.1e-07  Score=71.73  Aligned_cols=59  Identities=24%  Similarity=0.452  Sum_probs=35.5

Q ss_pred             CccccccchhhcHHhchhccccch---hhhhcCC-C-------------cc--ccccccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIE---AEERADG-S-------------RR--TTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~---~~~~~~~-~-------------~~--~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      .....||.||.|+.+||+-.....   +...+.+ .             .+  ........+.|..|+.|.++||.+.
T Consensus       139 ~~~~~CI~CG~C~s~CPv~~~~~~~~~~f~GP~~~~~a~r~~~D~Rd~~~rl~~~~~~~gl~~C~~C~~C~~vCPkgI  216 (251)
T PRK12386        139 QEFRKCIECFLCQNVCHVVRDHEENKPAFAGPRFLMRIAELEMHPLDTADRRAEAQEEHGLGYCNITKCCTEVCPEHI  216 (251)
T ss_pred             hchhhcccCCcccCcCCcccccCCCcccccCHHHHHHHHHhhcCccchHHHHHHhhcccCcccCcCCCCcCCcCCCCc
Confidence            356789999999999996432100   0000000 0             00  0011234677999999999999984

>TIGR00314 cdhA CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit

Probab=98.13  E-value=5.4e-07  Score=78.45  Aligned_cols=58  Identities=21%  Similarity=0.557  Sum_probs=36.3

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ...++|++||.|+.+||.+... ..............+......|+.||.|+++||.+.
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 ELANKCTQCGNCVRTCPNSLRV-DEAMAHAQKGDLSKLEQLEEQCYACGRCEQACPKNI  453 (784)
T ss_pred             hhcccCCCcccchhhCCCCcch-HHHHHHHhcCCccccccCHhhhhhhhHHhccCCCCC
Confidence            3468999999999999986321 111000000000112234568999999999999983

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.

>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=98.12  E-value=4e-07  Score=55.00  Aligned_cols=54  Identities=26%  Similarity=0.648  Sum_probs=24.4

Q ss_pred             cccchhhcHHhchhccccchhhhhc-----CCCccccccccCccCCcCcccchhccccc
Q psy4925          60 RCIACKLCEAICPAQAITIEAEERA-----DGSRRTTRYDIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~~~~~~-----~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      +|+.||.|+.+||.+..........     .+...........+.|+.||.|..+||.+
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            4999999999999864421111000     00000111125667899999999999987

...

>PRK00941 acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated

Probab=98.12  E-value=5.7e-07  Score=78.36  Aligned_cols=58  Identities=29%  Similarity=0.660  Sum_probs=37.0

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ...++|++|+.|+.+||.+........... ...........+.|+.||.|.++||++.
T Consensus       401 ~eadrCI~CG~Cv~aCP~~l~i~~~I~~a~-~G~~~~l~~l~~~Ct~CG~CeeVCPtgI  458 (781)
T PRK00941        401 ELAKKCTECGWCVRVCPNELPIPEAMEAAA-KGDLSKLEDLYDKCIGCGRCEQVCPKNI  458 (781)
T ss_pred             HhhhhCcCCCCccccCCCCcchhHHHHHHh-cCChhhhhhhhhhccchhHHhhhCCCCC
Confidence            356889999999999998642211110000 0000112234578999999999999984

>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=98.08  E-value=5e-07  Score=78.52  Aligned_cols=57  Identities=26%  Similarity=0.649  Sum_probs=36.7

Q ss_pred             CccccccchhhcHHhchhccccchhhh-hcCCCccccccccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEE-RADGSRRTTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~-~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ...++|++||.|+.+||++........ ...+.  ..........|+.||.|+++||+++
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            346789999999999998733111110 00010  0112223578999999999999986

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.

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

Probab=98.04  E-value=1.7e-06  Score=73.32  Aligned_cols=59  Identities=36%  Similarity=0.706  Sum_probs=44.7

Q ss_pred             ccCCCccccccchhhcH--HhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          52 RRYPSGEERCIACKLCE--AICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv--~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..+.+|.++|.+|+.|.  ..||.-  .......        +..+|...|.+||.|+++||..||....+
T Consensus       570 ~~~~Vd~~~CtGC~~C~~~~~Cpsi--~~~~~~~--------k~~id~~~C~GCg~C~~iCP~~a~~~~~~  630 (640)
T COG4231         570 PKYFVDEEKCTGCGDCIVLSGCPSI--EPDPTFK--------KARIDPSSCNGCGSCVEVCPSFAIKEGGE  630 (640)
T ss_pred             CCceechhhcCCcHHHHhhcCCceE--eecCCCC--------ceeecccccccchhhhhcCchhheecccc
Confidence            33567899999999998  459963  3222111        56788888999999999999999887543

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=97.97  E-value=1.7e-06  Score=71.37  Aligned_cols=56  Identities=34%  Similarity=0.719  Sum_probs=39.2

Q ss_pred             cccccc--chh-hcHHhchh-----ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          57 GEERCI--ACK-LCEAICPA-----QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci--~Cg-~Cv~~CP~-----~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      |.++|.  .|+ .|.+.||.     .+|.+++..        ....+....|++||.|+..||.+||.+-.-
T Consensus         9 d~D~C~PkkC~~eC~~yCP~vrtg~~~I~i~~~~--------gkpvIsE~lCiGCGICvkkCPF~AI~IvnL   72 (591)
T COG1245           9 DYDRCQPKKCGYECIKYCPVVRTGKETIEIDEDT--------GKPVISEELCIGCGICVKKCPFDAISIVNL   72 (591)
T ss_pred             ehhccCccccchhhhhcCCCccCCCeeEEecCCC--------CCceeEhhhhccchhhhccCCcceEEEecC
Confidence            445565  455 89999995     244443321        134677788999999999999999986443

>PRK11168 glpC sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional

Probab=97.96  E-value=2.1e-06  Score=70.13  Aligned_cols=57  Identities=25%  Similarity=0.624  Sum_probs=36.0

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCcc--------ccccccCccCCcCcccchhcccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRR--------TTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~--------~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ...||+||.|..+||+........+.......        ........+.|++|+.|..+||.+.
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            46799999999999986543111000000000        0112235578999999999999984

>TIGR01936 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit

Probab=97.92  E-value=3.1e-06  Score=70.26  Aligned_cols=57  Identities=12%  Similarity=0.088  Sum_probs=39.6

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcC--cccchhccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIY--CGFCQEACPVD  113 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~--Cg~C~~~CP~~  113 (160)
                      ....||.||.|+++||.+.+...-...............+...|+.  ||.|..+||.+
T Consensus       371 ~~~aCI~CG~C~~vCPm~L~P~~L~~a~~~~d~d~a~~lg~~ecieedCG~CsyVCPSk  429 (447)
T TIGR01936       371 GERAMIPIGIYERVMPLDIPPTLLLKALIAGDFDKAQRLGALEVDEEDFALCTFVDPSK  429 (447)
T ss_pred             CccceeECChHhhcCCCCCCHHHHHHHHHcCCHHHHHHCCCcccCccccccCceECCCC
Confidence            3456999999999999986654432222222222233466678988  99999999998

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.

>PF12798 Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.91  E-value=3e-06  Score=36.93  Aligned_cols=14  Identities=36%  Similarity=1.236  Sum_probs=6.8

Q ss_pred             ccchhhcHHhchhc
Q psy4925          61 CIACKLCEAICPAQ   74 (160)
Q Consensus        61 Ci~Cg~Cv~~CP~~   74 (160)
                      |++|+.|+.+||++
T Consensus         1 C~~C~~C~~~Cp~~   14 (15)
T PF12798_consen    1 CTGCGACVEVCPTG   14 (15)
T ss_pred             CCCchHHHHHhcCC
Confidence            44455555555544

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

>PF12797 Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.91  E-value=2.9e-06  Score=40.49  Aligned_cols=18  Identities=50%  Similarity=1.158  Sum_probs=13.6

Q ss_pred             CccccccchhhcHHhchh
Q psy4925          56 SGEERCIACKLCEAICPA   73 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~   73 (160)
                      +|.++||+|+.|+.+||+
T Consensus         5 iD~~rCiGC~~C~~AC~~   22 (22)
T PF12797_consen    5 IDLERCIGCGACEVACPV   22 (22)
T ss_pred             EccccccCchhHHHhhCc
Confidence            567778888888888873

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

>PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional

Probab=97.89  E-value=3.9e-06  Score=69.77  Aligned_cols=60  Identities=10%  Similarity=0.084  Sum_probs=40.2

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcC--cccchhccccccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIY--CGFCQEACPVDAIVE  117 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~--Cg~C~~~CP~~ai~~  117 (160)
                      ....||.||.|+.+||.+.....-...............+...|+.  ||.|.-+||.+ |.+
T Consensus       372 ~~~~CI~Cg~C~~vCP~~L~P~~l~ra~~~~d~~~~e~~~~~~C~EedCG~CsyVCPsk-ipL  433 (448)
T PRK05352        372 SERAMVPIGNYERVMPLDILPTQLLRALIVGDTDEAQALGALELDEEDLALCTFVCPGK-YEY  433 (448)
T ss_pred             CCcceeecCcHhhcCCCCCCHHHHHHHHHcCCHHHHHHcCchhcCccccCCCccCCCCC-chH
Confidence            3568999999999999875543322211111111123467778999  99999999998 443

>PF12798 Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.87  E-value=4.9e-06  Score=36.24  Aligned_cols=15  Identities=53%  Similarity=1.287  Sum_probs=14.0

Q ss_pred             CcCcccchhcccccc
Q psy4925         100 CIYCGFCQEACPVDA  114 (160)
Q Consensus       100 C~~Cg~C~~~CP~~a  114 (160)
                      |++|+.|+++||++|
T Consensus         1 C~~C~~C~~~Cp~~A   15 (15)
T PF12798_consen    1 CTGCGACVEVCPTGA   15 (15)
T ss_pred             CCCchHHHHHhcCCC
Confidence            789999999999987

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

>TIGR00273 iron-sulfur cluster-binding protein

Probab=97.85  E-value=4.4e-06  Score=69.20  Aligned_cols=59  Identities=27%  Similarity=0.461  Sum_probs=35.1

Q ss_pred             CccccccchhhcHHhchhccccchh-----hhhcCCCcc------ccccccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA-----EERADGSRR------TTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~-----~~~~~~~~~------~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      .+..+||.||.|..+||+-...-..     .....+...      ..........|..||.|.++||.+.
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            3567999999999999964221100     000000000      0011123468999999999999983

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.

>PRK13409 putative ATPase RIL; Provisional

Probab=97.83  E-value=5.2e-06  Score=71.39  Aligned_cols=55  Identities=35%  Similarity=0.759  Sum_probs=38.8

Q ss_pred             cccccc--chh-hcHHhchhc-----cccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          57 GEERCI--ACK-LCEAICPAQ-----AITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        57 ~~~~Ci--~Cg-~Cv~~CP~~-----~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.++|.  .|+ .|.+.||..     +|.++...        ....+....|++||.|+..||.+||.+-.
T Consensus         8 ~~~~c~~~~c~~~c~~~cp~~~~~~~~~~~~~~~--------~~~~~~e~~c~~c~~c~~~cp~~a~~i~~   70 (590)
T PRK13409          8 DYDRCQPKKCNYECIKYCPVVRTGEETIEIDEDD--------GKPVISEELCIGCGICVKKCPFDAISIVN   70 (590)
T ss_pred             eccccCcchhhhhHHhhCCCcccCCeEEEEcCCC--------CCceeeHhhccccccccccCCcceEEEee
Confidence            456665  577 799999952     33332111        14567778899999999999999988644

>TIGR03379 glycerol3P_GlpC glycerol-3-phosphate dehydrogenase, anaerobic, C subunit

Probab=97.74  E-value=8.9e-06  Score=66.62  Aligned_cols=57  Identities=33%  Similarity=0.730  Sum_probs=34.7

Q ss_pred             cccccchhhcHHhchhccccchhhhhc----CCCc----cccccccCccCCcCcccchhcccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERA----DGSR----RTTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~----~~~~----~~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      .+.||.||.|..+||+-...-...+..    .+..    ....+....+.|..|+.|..+||.+.
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            467999999999999743321100000    0000    00011234678999999999999984

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.

>PRK06259 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Provisional

Probab=97.72  E-value=8e-06  Score=68.62  Aligned_cols=58  Identities=28%  Similarity=0.690  Sum_probs=35.6

Q ss_pred             CccccccchhhcHHhchhccccchhhh----------hcCCCcc----ccccccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEE----------RADGSRR----TTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~----------~~~~~~~----~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      .+...|+.||.|..+||+.... +..+          .......    ........+.|+.||.|..+||.+.
T Consensus       130 ~~~~~Ci~CG~C~~~CP~~~~~-~~~gp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP~gi  201 (486)
T PRK06259        130 KKLRGCIECLSCVSTCPARKVS-DYPGPTFMRQLARFAFDPRDEGDREKEAFDEGLYNCTTCGKCVEVCPKEI  201 (486)
T ss_pred             hCchhcccCccccccCCCCccc-cCcCHHHHHHHHHHhhCCcchhhHHHHHhcCCCcCCCCcCcccCcCCCCC
Confidence            3467899999999999975321 0000          0000000    0012234578999999999999873

>PRK11274 glcF glycolate oxidase iron-sulfur subunit; Provisional

Probab=97.67  E-value=6.4e-06  Score=67.63  Aligned_cols=57  Identities=23%  Similarity=0.742  Sum_probs=34.3

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCC-----------CccccccccCccCCcCcccchhcccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADG-----------SRRTTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~-----------~~~~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      .+.|++||.|..+||+-...-.......+           ...........+.|+.|+.|..+||.+.
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            35799999999999964222111111101           0000111223568999999999999973

>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]

Probab=97.61  E-value=2.1e-05  Score=64.26  Aligned_cols=56  Identities=29%  Similarity=0.506  Sum_probs=33.1

Q ss_pred             ccccchhhcHHhchhcccc-----chhhhhcCCCcccc------ccccCccCCcCcccchhcccccc
Q psy4925          59 ERCIACKLCEAICPAQAIT-----IEAEERADGSRRTT------RYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~i~-----~~~~~~~~~~~~~~------~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      -.||.||.|..+||+-...     ......+.+....+      ........|..||.|.++||.+.
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            4799999999999963111     00011111111111      11223456999999999999883

>PRK15055 anaerobic sulfite reductase subunit A; Provisional

Probab=97.60  E-value=1.4e-05  Score=64.32  Aligned_cols=20  Identities=35%  Similarity=0.859  Sum_probs=16.8

Q ss_pred             ccCCcCcccchhccccccccc
Q psy4925          97 MTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        97 ~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ...|++||.|.++||.+ |.+
T Consensus       306 ~~~CvgCGrC~~~CP~~-I~i  325 (344)
T PRK15055        306 YHMCVGCGRCDDRCPEY-ISF  325 (344)
T ss_pred             hhhCcCcCccccccCCC-CCH
Confidence            35799999999999998 444

>PF12797 Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.60  E-value=2.1e-05  Score=37.56  Aligned_cols=20  Identities=55%  Similarity=1.240  Sum_probs=17.6

Q ss_pred             cccCccCCcCcccchhcccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPV  112 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~  112 (160)
                      +.+|.+.|++|+.|+.+||.
T Consensus         3 ~~iD~~rCiGC~~C~~AC~~   22 (22)
T PF12797_consen    3 MVIDLERCIGCGACEVACPV   22 (22)
T ss_pred             eEEccccccCchhHHHhhCc
Confidence            35788999999999999984

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

>COG1600 Uncharacterized Fe-S protein [Energy production and conversion]

Probab=97.59  E-value=2.9e-05  Score=62.11  Aligned_cols=56  Identities=23%  Similarity=0.539  Sum_probs=34.7

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCC--------Cccc-cccccCccCC-cCcccchhccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADG--------SRRT-TRYDIDMTKC-IYCGFCQEACPVD  113 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~--------~~~~-~~~~~~~~~C-~~Cg~C~~~CP~~  113 (160)
                      .+.|-.|.+|+.+||++|++.........        .... ..+-.....+ .+|+.|+.+||.+
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            38899999999999999997543221100        0000 1111122223 3799999999998

>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=97.57  E-value=5.8e-06  Score=49.60  Aligned_cols=52  Identities=25%  Similarity=0.514  Sum_probs=26.6

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCcc----CCcCcccchhcccccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMT----KCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~----~C~~Cg~C~~~CP~~ai~  116 (160)
                      |.++||+||.|+..+|. .+.+++.+..       .+..+..    .=..+...++.||++||+
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            46789999999999995 3554443211       1111111    112357899999999986

...

>PRK13984 putative oxidoreductase; Provisional

Probab=97.52  E-value=3.3e-05  Score=66.55  Aligned_cols=27  Identities=26%  Similarity=0.586  Sum_probs=22.2

Q ss_pred             CCCccccccchhhcHHhchhccccchh
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ..++...|+.|+.|+.+||++++.+..
T Consensus        81 ~~i~~~~c~~c~~c~~~Cp~~Ai~~~~  107 (604)
T PRK13984         81 PVIDYGRCSFCALCVDICTTGSLKMTR  107 (604)
T ss_pred             cccCcccCcCcchHHhhCCcCcEEecc
Confidence            345678899999999999999877643

>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]

Probab=97.51  E-value=2e-05  Score=57.98  Aligned_cols=58  Identities=24%  Similarity=0.538  Sum_probs=37.6

Q ss_pred             cccccchhhcHHhchhccccchhhhhcC------CCccccccccCccCCcCcccchhcccccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERAD------GSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~------~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      ...|.+||.|...||++-. .+...+..      +.........+.+.|+.|..|..-||.+...
T Consensus        38 l~~C~QCG~CT~sCPs~r~-t~y~pR~ii~~~~~g~~d~il~~~~lW~C~tCytC~eRCPr~v~i  101 (195)
T COG1150          38 LEGCYQCGTCTGSCPSGRF-TDYSPRKIIRKARLGLVDLILSSESLWACVTCYTCTERCPRGVKI  101 (195)
T ss_pred             HhHhhccCcccCCCCCccc-CCCCHHHHHHHHHcccHHHHhcCCcceeeeechhhhhhCCCCCCH
Confidence            3459999999999998644 22211110      0000112345778999999999999988633

>COG1152 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]

Probab=97.47  E-value=2e-05  Score=66.37  Aligned_cols=57  Identities=23%  Similarity=0.590  Sum_probs=37.1

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      ..+|..||-|..+||.. +.+.+.-..........+..-.+.|++|+.|..+||.+..
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-LDIPEAMEYAAKGDFSKLEDLHDVCIGCGRCEQVCPKNIP  455 (772)
T ss_pred             HHhcccccchhccCCcc-cchHHHHHHhhcCChHHHHHHHHHhhhhhhhhhhCcccCc
Confidence            46899999999999975 3333211111111112333445689999999999999843

>PF12800 Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.46  E-value=3e-05  Score=34.87  Aligned_cols=14  Identities=50%  Similarity=1.452  Sum_probs=7.4

Q ss_pred             cccchhhcHHhchh
Q psy4925          60 RCIACKLCEAICPA   73 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~   73 (160)
                      +|++|+.|+.+||+
T Consensus         3 ~C~~C~~C~~~Cp~   16 (17)
T PF12800_consen    3 RCIGCGSCVDVCPT   16 (17)
T ss_dssp             CCTTSSSSTTTSTT
T ss_pred             cCCCCchHHhhccC
Confidence            45555555555553

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.

>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=97.46  E-value=4.3e-05  Score=44.94  Aligned_cols=20  Identities=45%  Similarity=1.089  Sum_probs=15.1

Q ss_pred             ccccccchhhcHHhchhccc
Q psy4925          57 GEERCIACKLCEAICPAQAI   76 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i   76 (160)
                      +.++|++||.|+.+||++||
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

>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=97.45  E-value=2e-05  Score=47.41  Aligned_cols=23  Identities=43%  Similarity=1.136  Sum_probs=16.1

Q ss_pred             CccccccchhhcHHhchh-ccccc
Q psy4925          56 SGEERCIACKLCEAICPA-QAITI   78 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~-~~i~~   78 (160)
                      ++.+.|++||.|+.+||+ +||.+
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            456899999999999996 99864

...

>TIGR02910 sulfite_red_A sulfite reductase, subunit A

Probab=97.45  E-value=4.3e-05  Score=61.20  Aligned_cols=21  Identities=33%  Similarity=0.817  Sum_probs=17.4

Q ss_pred             CccCCcCcccchhccccccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ....|++||.|+++||.+ |.+
T Consensus       299 G~~~CvgCGrC~~~CP~~-idi  319 (334)
T TIGR02910       299 GYHMCVGCGRCDDICPEY-ISF  319 (334)
T ss_pred             CccccCCcCchhhhCCCC-CCH
Confidence            455799999999999999 444

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.

>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit

Probab=97.42  E-value=5.9e-05  Score=61.96  Aligned_cols=44  Identities=27%  Similarity=0.597  Sum_probs=36.2

Q ss_pred             hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          65 KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        65 g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      ..|+.+||++|+.++...         ...++...|+.|+.|+.+||. |+...
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            359999999999886421         467899999999999999997 66655

This model describes the alpha subunit of sulfite reductase.

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

Probab=97.40  E-value=5.1e-05  Score=55.31  Aligned_cols=33  Identities=33%  Similarity=0.682  Sum_probs=26.9

Q ss_pred             ccccCCCccccccchhhcHHhchhccccchhhh
Q psy4925          50 ALRRYPSGEERCIACKLCEAICPAQAITIEAEE   82 (160)
Q Consensus        50 ~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~   82 (160)
                      ....+.+|..+||-||.|+.+||++||.+....
T Consensus        86 ~~~~~~In~grCIfCg~C~e~CPt~Al~~t~~~  118 (172)
T COG1143          86 KPKRPDINLGRCIFCGLCVEVCPTGALVLTPEF  118 (172)
T ss_pred             ccccceeccccccccCchhhhCchhhhcCCcce
Confidence            344556788999999999999999999876543

>PF13459 Fer4_15: 4Fe-4S single cluster domain

Probab=97.35  E-value=2.3e-05  Score=48.00  Aligned_cols=61  Identities=25%  Similarity=0.417  Sum_probs=32.8

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCcccc--ccccCccCCcCcccchhccccccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTT--RYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~--~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      +|.++|++||.|+..||. ...++..+.........  ........=..-...++.||++||+.
T Consensus         3 vD~~~C~gcg~C~~~aP~-vF~~d~~g~a~~~~~~~~~~~~v~~~~~~~~~~Aa~~CP~~aI~v   65 (65)
T PF13459_consen    3 VDRDRCIGCGLCVELAPE-VFELDDDGKAVVLVDGGEGEGEVPEEDEEDVREAAEACPVGAIHV   65 (65)
T ss_pred             EecccCcCccHHHhhCCc-cEEECCCCCEEEEecCcccccCCCchhHHHHHHHHHhCCHhhEEC
Confidence            567899999999999994 24443332110000000  00011111112356799999999863

>PF12800 Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters

Probab=97.29  E-value=0.00012  Score=32.83  Aligned_cols=16  Identities=44%  Similarity=1.294  Sum_probs=13.7

Q ss_pred             cCCcCcccchhccccc
Q psy4925          98 TKCIYCGFCQEACPVD  113 (160)
Q Consensus        98 ~~C~~Cg~C~~~CP~~  113 (160)
                      ..|++|+.|+.+||++
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            4699999999999974

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.

>COG1140 NarY Nitrate reductase beta subunit [Energy production and conversion]

Probab=97.20  E-value=0.00011  Score=59.19  Aligned_cols=54  Identities=30%  Similarity=0.508  Sum_probs=44.4

Q ss_pred             ccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          59 ERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        59 ~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      --|.+|-  .||.+||.||+-..+...        .+.+|.+.|.+...|+..||++.+.+...
T Consensus       181 RiCeHCLNPsCvasCPsgaiYKReEDG--------IVLiDQd~CRGwR~CvsgCPYKKvYfNwk  236 (513)
T COG1140         181 RLCEHCLNPSCVASCPSGAIYKREEDG--------IVLIDQDKCRGWRMCVSGCPYKKVYFNWK  236 (513)
T ss_pred             HHHhhcCCcHHhhcCCcccccccccCc--------eEEeecccccchhhhhcCCCcceeEeecc
Confidence            3588885  899999999997654432        56789999999999999999999887665

>COG0247 GlpC Fe-S oxidoreductase [Energy production and conversion]

Probab=97.18  E-value=3.9e-05  Score=62.34  Aligned_cols=55  Identities=25%  Similarity=0.708  Sum_probs=36.0

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCcc------------ccccccCccCCcCcccchhcccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRR------------TTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~------------~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ...|++||.|..+||+-...  ....+.+...            ........+.|+.|+.|+.+||.+.
T Consensus         8 ~~~Cv~Cg~C~~~CP~~~~~--~~~sPrgr~~~~r~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP~~i   74 (388)
T COG0247           8 LDKCVHCGFCTNVCPSYRAT--EALSPRGRIVLVREVLRGKAPGDEEVYEALDTCLACGACATACPSGI   74 (388)
T ss_pred             HHhcCCCCcccCcCCCcccc--CCCCCchHHHHHHHHHhCCCcchhhhHHHHHhCcCccchHhhCCCCC
Confidence            46799999999999975443  1111111100            1112234468999999999999985

>PRK08222 hydrogenase 4 subunit H; Validated

Probab=97.15  E-value=0.00013  Score=53.68  Aligned_cols=26  Identities=38%  Similarity=0.827  Sum_probs=22.3

Q ss_pred             CCccccccchhhcHHhchhccccchh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .++...|+.||.|+.+||++||.+..
T Consensus        69 ~~~~~~C~~Cg~C~~~CPt~AI~~~~   94 (181)
T PRK08222         69 QLYLGRCIYCGRCEEVCPTRAIQLTN   94 (181)
T ss_pred             eeccCcCcCCCCcccccCcCeEEecc
Confidence            34567899999999999999998764

>PRK09477 napH quinol dehydrogenase membrane component; Provisional

Probab=97.13  E-value=0.00013  Score=56.98  Aligned_cols=49  Identities=24%  Similarity=0.485  Sum_probs=34.5

Q ss_pred             chhhcHHhchhccccchhhhhcCCCccccccc-cCccCCcCcccchhcccccccc
Q psy4925          63 ACKLCEAICPAQAITIEAEERADGSRRTTRYD-IDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        63 ~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~-~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      ..+-|...||.|++.....     +....+.. .+.+.|+.|+.|+++||.+++.
T Consensus       177 ~r~wC~~lCP~Ga~~~~~~-----~~~~~~i~~~d~~~C~~C~~C~~~CP~~~i~  226 (271)
T PRK09477        177 EHGWCGHLCPLGAFYGLIG-----KKSLIRVKAHDRQKCTRCMDCFHVCPEPQVL  226 (271)
T ss_pred             CCchhhccCCHHHHHHhcc-----cccccccccCCcccCcccCCcCCcCCCccee
Confidence            4567899999998753221     11111334 7788999999999999998653

>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional

Probab=97.13  E-value=0.00012  Score=53.87  Aligned_cols=52  Identities=23%  Similarity=0.508  Sum_probs=39.4

Q ss_pred             ccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        61 Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ....|.+...+|...+......+       ....++...|+.|+.|+.+||++||.+..
T Consensus         8 ~~~~g~~T~~yP~~~~~~~~~~r-------g~p~~d~~~C~~C~~Cv~~CP~~ai~~~~   59 (180)
T PRK12387          8 VIKTGTATSSYPLEPIAVDKNFR-------GKPEYNPQQCIGCAACVNACPSNALTVET   59 (180)
T ss_pred             HHhcCCccccCCCCCCCCCCCCC-------CceEEChhhCcChhHHHHhcCccCeEeec
Confidence            44568888899987766544322       14567889999999999999999988653

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

Probab=97.11  E-value=0.00014  Score=44.50  Aligned_cols=21  Identities=52%  Similarity=1.092  Sum_probs=19.1

Q ss_pred             CcCcccchhcccccccccCCc
Q psy4925         100 CIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus       100 C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      |..|+.|+++||++||.....
T Consensus         2 C~~C~~C~~~CP~~AI~~~~~   22 (67)
T PF13484_consen    2 CITCGKCAEACPTGAISGEDE   22 (67)
T ss_pred             CcchhHHHHhCcHhhccCCCc
Confidence            899999999999999998733

>COG1141 Fer Ferredoxin [Energy production and conversion]

Probab=97.10  E-value=7.8e-05  Score=45.99  Aligned_cols=61  Identities=25%  Similarity=0.331  Sum_probs=33.9

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCC-CccccccccCccCCcCcccchhccccccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADG-SRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~-~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      +|.++||+||.|..+||.- ...++.+.... ........+..+.=...-..+..||++||+.
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            5678999999999999952 44443332200 0000001111111011256889999999986

>COG1453 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]

Probab=97.09  E-value=0.00022  Score=57.37  Aligned_cols=52  Identities=35%  Similarity=0.773  Sum_probs=32.7

Q ss_pred             cccchhhcHHhchhccccchhhhh------c---------------CCCccccccccCccCCcCcccchhccccc
Q psy4925          60 RCIACKLCEAICPAQAITIEAEER------A---------------DGSRRTTRYDIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~~~~~------~---------------~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      .|+.|+.|+. ||.+ |.+.....      .               .+..+.+...-+...|++||+|.+.||.+
T Consensus       294 ~Ct~C~yC~P-CP~g-InIP~~f~lyN~~~~~~~~~~~~~~Y~~l~~~~~~~~~~~g~as~CieCgqCl~~CPq~  366 (391)
T COG1453         294 PCTGCRYCLP-CPSG-INIPEIFRLYNLAVAFDDVDYAKFRYNMLENGGHWFPGPKGKASDCIECGQCLEKCPQH  366 (391)
T ss_pred             CCccccccCc-CCCC-CChHHHHHHHHHHHhhccchhhHHHHHHHhccCccCCCCcccccccchhhhhhhcCCCc
Confidence            4999999998 9976 33321110      0               00011111223467899999999999998

>PRK15033 tricarballylate utilization protein B; Provisional

Probab=97.05  E-value=0.00025  Score=57.66  Aligned_cols=83  Identities=19%  Similarity=0.419  Sum_probs=46.3

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHH
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEK  137 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~  137 (160)
                      .+.|..|..|...||.- ..+.+..    +.....+..-.+.|..||.|...||+ +..    .++....+..+...+..
T Consensus        32 ~~iC~~Cr~C~~~Cpvf-P~l~~r~----~~~~~d~~~~a~~C~~Cg~C~~~CP~-apP----hef~i~ip~~l~~~r~~  101 (389)
T PRK15033         32 MQICNACRYCEGFCAVF-PAMTRRL----EFGKADIHYLANLCHNCGACLHACQY-APP----HEFAVNVPKAMAQVRLE  101 (389)
T ss_pred             hHhCCCCCCccccCCCc-hhhhhhh----cCChhhhHHHHHhCcCcccccccCcC-CCC----cccCCCHHHHHHHHHHH
Confidence            46899999999999963 2211110    00111122334589999999999999 322    23333444444444433


Q ss_pred             HhccCCcchHHHhh
Q psy4925         138 LLSNGDKWESEIAS  151 (160)
Q Consensus       138 ~~~~~~~~~~~~~~  151 (160)
                      +.. ...|..-..+
T Consensus       102 sy~-~yawP~~lgk  114 (389)
T PRK15033        102 TYQ-EYAWPAALGA  114 (389)
T ss_pred             HHH-HccCcHHHHH
Confidence            333 4555554444

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

Probab=97.02  E-value=0.00021  Score=41.55  Aligned_cols=21  Identities=29%  Similarity=0.885  Sum_probs=13.9

Q ss_pred             CCccccccchhhcHHhchhcc
Q psy4925          55 PSGEERCIACKLCEAICPAQA   75 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~   75 (160)
                      .++.++|++|+.|+.+||++|
T Consensus        32 ~~~~~~C~~C~~C~~~CP~~A   52 (52)
T PF12838_consen   32 VIDPDKCTGCGACVEVCPTGA   52 (52)
T ss_dssp             EETGGG----SHHHHHTTTS-
T ss_pred             EEechhCcCcChhhhhCcCcC
Confidence            456889999999999999985

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.

>TIGR02484 CitB CitB domain protein

Probab=97.01  E-value=0.00021  Score=57.81  Aligned_cols=54  Identities=17%  Similarity=0.361  Sum_probs=35.3

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      .+.|..|+.|..+||.- .....  .  .+.....+..-.+.|..|+.|..+||+.+.+
T Consensus        13 l~iC~~C~~C~~~Cpvf-Pa~~~--~--~~~~~~d~~~la~lChnC~~C~~~CPy~pPH   66 (372)
T TIGR02484        13 LNLCNSCGYCTGLCAVF-PAAQG--R--PDLTRGDLRHLAHLCHDCQSCWHDCQYAPPH   66 (372)
T ss_pred             hHhCcCcCCccccCCCc-ccccc--c--cccCHHHHHHHHHHCcCcccccccCcCCCCc
Confidence            46799999999999963 11110  0  0000111223456799999999999998864

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.

>KOG3256|consensus

Probab=97.00  E-value=0.00026  Score=50.79  Aligned_cols=37  Identities=32%  Similarity=0.717  Sum_probs=29.1

Q ss_pred             CccCccccccCCCccccccchhhcHHhchhccccchh
Q psy4925          44 RFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        44 ~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      +..+.....++.+|..+||-||-|+.+||+++|+...
T Consensus       135 r~dgsrRttrYdIDmtkCIyCG~CqEaCPvdaivegp  171 (212)
T KOG3256|consen  135 RTDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  171 (212)
T ss_pred             cCCccccceeecccceeeeeecchhhhCCccceeccC
Confidence            3334445566778999999999999999999998654

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

Probab=96.99  E-value=0.00024  Score=55.09  Aligned_cols=49  Identities=22%  Similarity=0.455  Sum_probs=33.8

Q ss_pred             cchhhcHHhchhccccchhhhhcCCCcccccccc-CccCCcCcccchhccccccc
Q psy4925          62 IACKLCEAICPAQAITIEAEERADGSRRTTRYDI-DMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        62 i~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~-~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      +..+-|...||.|++......     ....+... +.++|+.|+.|+++||.+++
T Consensus       169 ~~r~~C~~~CP~Ga~~~~~~~-----~~~~~i~~~~~~~C~~C~~C~~vCP~~~v  218 (255)
T TIGR02163       169 SERGWCGHLCPLGAFYGLIGR-----KSLIKIAASDREKCTNCMDCFNVCPEPQV  218 (255)
T ss_pred             cCCchhhCcCCCcchhhhhhc-----cCceEEEeeccccCeEcCCccCcCCCCce
Confidence            456778899999988533211     11112333 47899999999999999864

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.

>TIGR02936 fdxN_nitrog ferredoxin III, nif-specific

Probab=96.87  E-value=0.00037  Score=45.21  Aligned_cols=23  Identities=30%  Similarity=0.852  Sum_probs=20.5

Q ss_pred             CccccccchhhcHHhchhccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      ++...|++||.|+.+||++||.+
T Consensus        67 i~~~~C~~Cg~C~~~CP~~AI~~   89 (91)
T TIGR02936        67 ANPGNCIGCGACARVCPKKCQTH   89 (91)
T ss_pred             cCCccCcChhhhhhhCCHhHEec
Confidence            56789999999999999999864

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.

>PF13746 Fer4_18: 4Fe-4S dicluster domain

Probab=96.83  E-value=0.00044  Score=42.86  Aligned_cols=18  Identities=44%  Similarity=1.202  Sum_probs=16.0

Q ss_pred             ccccccchhhcHHhchhc
Q psy4925          57 GEERCIACKLCEAICPAQ   74 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~   74 (160)
                      ....|++||+|+.+||++
T Consensus        48 ~~~~CVgCgrCv~~CP~~   65 (69)
T PF13746_consen   48 GEGDCVGCGRCVRVCPAG   65 (69)
T ss_pred             CCccCCCcChHhhhcCCC
Confidence            466899999999999987

>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG

Probab=96.75  E-value=0.0005  Score=57.09  Aligned_cols=54  Identities=24%  Similarity=0.588  Sum_probs=32.1

Q ss_pred             ccchhhcHHhchhccccc---hhhhh------cCCCccccc-----c--ccCccCCcCcccchhcccccc
Q psy4925          61 CIACKLCEAICPAQAITI---EAEER------ADGSRRTTR-----Y--DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        61 Ci~Cg~Cv~~CP~~~i~~---~~~~~------~~~~~~~~~-----~--~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ...+.-|..+||.+++.-   +.+..      ..++.+...     .  ..+...|+.|+.|+++||++.
T Consensus       178 ~~re~~C~~~CP~g~~qs~m~d~~tl~v~yd~~Rgepr~~~~~~~~~~~~~~~~~Ci~C~~Cv~vCP~gi  247 (434)
T TIGR02745       178 WMREQFCIYMCPYARIQSVMFDKDTLIVVYDEKRGEPRGPRKGKKDPKAPGPLGDCIDCNLCVQVCPTGI  247 (434)
T ss_pred             eeccchhhhhCCHHHHHHHhccCCcceEecccccCCcCccccccccccCCCCCCCCCChhhhHHhCCCCC
Confidence            456779999999987752   21110      001100000     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.

>COG1146 Ferredoxin [Energy production and conversion]

Probab=96.75  E-value=0.00041  Score=42.73  Aligned_cols=26  Identities=42%  Similarity=0.951  Sum_probs=22.2

Q ss_pred             CCccccccchhhcHHhchhccccchh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ..+.+.|++|+.|+.+||++||.+..
T Consensus        37 ~~~~e~C~~C~~C~~~CP~~aI~~~~   62 (68)
T COG1146          37 VARPEECIDCGLCELACPVGAIKVDI   62 (68)
T ss_pred             EeccccCccchhhhhhCCcceEEEec
Confidence            35678899999999999999987654

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

Probab=96.72  E-value=0.0004  Score=44.86  Aligned_cols=25  Identities=28%  Similarity=0.812  Sum_probs=21.5

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      +|-+.|.+||.|+.+||+.||.+..
T Consensus        63 idYdyCKGCGICa~vCP~kaI~Mv~   87 (91)
T COG1144          63 IDYDYCKGCGICANVCPVKAIEMVR   87 (91)
T ss_pred             eEcccccCceechhhCChhheEeEe
Confidence            4567899999999999999998754

>PF13746 Fer4_18: 4Fe-4S dicluster domain

Probab=96.71  E-value=0.00075  Score=41.83  Aligned_cols=19  Identities=32%  Similarity=0.913  Sum_probs=16.9

Q ss_pred             cCccCCcCcccchhccccc
Q psy4925          95 IDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~  113 (160)
                      .....|++||.|+.+||++
T Consensus        47 ~~~~~CVgCgrCv~~CP~~   65 (69)
T PF13746_consen   47 YGEGDCVGCGRCVRVCPAG   65 (69)
T ss_pred             cCCccCCCcChHhhhcCCC
Confidence            4567899999999999998

>COG1145 NapF Ferredoxin [Energy production and conversion]

Probab=96.69  E-value=0.00055  Score=44.65  Aligned_cols=24  Identities=50%  Similarity=0.999  Sum_probs=21.8

Q ss_pred             ccCccCCcCcccchhccccccccc
Q psy4925          94 DIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ..+...|++||.|+.+||++||.+
T Consensus        25 ~~~~~~Ci~Cg~C~~~CP~~ai~~   48 (99)
T COG1145          25 VIDAEKCIGCGLCVKVCPTGAIEL   48 (99)
T ss_pred             EeCccccCCCCCchhhCCHHHhhc
Confidence            467778999999999999999998

>CHL00065 psaC photosystem I subunit VII

Probab=96.47  E-value=0.0012  Score=41.97  Aligned_cols=25  Identities=32%  Similarity=0.915  Sum_probs=21.4

Q ss_pred             ccccccchhhcHHhchhccccchhh
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      +.+.|+.|+.|+.+||++||.+...
T Consensus        44 ~~~~C~~C~~C~~~CP~~Ai~~~~~   68 (81)
T CHL00065         44 RTEDCVGCKRCESACPTDFLSVRVY   68 (81)
T ss_pred             CCCcCCChhhhhhhcCccccEEEEE
Confidence            4578999999999999999987644

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

Probab=96.40  E-value=0.0012  Score=43.99  Aligned_cols=28  Identities=21%  Similarity=0.591  Sum_probs=23.8

Q ss_pred             ccccCccCCcCcccchhcccccccccCC
Q psy4925          92 RYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        92 ~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .+.++...|++|+.|+.+||.++|.+..
T Consensus        10 ~v~id~~~Ci~C~~Cv~aCP~~ai~~~~   37 (103)
T PRK09626         10 PVWVDESRCKACDICVSVCPAGVLAMRI   37 (103)
T ss_pred             CeEECcccccCCcchhhhcChhhhcccc
Confidence            4556888999999999999999987654

>PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional

Probab=96.39  E-value=0.0015  Score=44.77  Aligned_cols=28  Identities=32%  Similarity=0.759  Sum_probs=23.8

Q ss_pred             ccccCccCCcCcccchhcccccccccCC
Q psy4925          92 RYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        92 ~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .+.++.+.|++|+.|+.+||.+|+.+..
T Consensus        36 ~i~i~~~~Ci~C~~C~~~CP~~ai~~~~   63 (120)
T PRK08348         36 KILYDVDKCVGCRMCVTVCPAGVFVYLP   63 (120)
T ss_pred             eEEECcccCcCcccHHHHCCccceEccc
Confidence            4567888999999999999999987653

>TIGR00403 ndhI NADH-plastoquinone oxidoreductase subunit I protein

Probab=96.38  E-value=0.0012  Score=48.64  Aligned_cols=27  Identities=26%  Similarity=0.703  Sum_probs=23.1

Q ss_pred             CCCccccccchhhcHHhchhccccchh
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      +.++...|+.||.|+.+||++|+.+..
T Consensus        97 ~~id~~~Ci~Cg~Cv~aCP~~AI~~~~  123 (183)
T TIGR00403        97 YSIDFGVCIFCGNCVEYCPTNCLSMTE  123 (183)
T ss_pred             eecCcccccCcCchhhhcCCCCeeccc
Confidence            346678899999999999999998754

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

Probab=96.37  E-value=0.0019  Score=43.32  Aligned_cols=51  Identities=27%  Similarity=0.426  Sum_probs=32.4

Q ss_pred             HHhchhccccchhhhh-cCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          68 EAICPAQAITIEAEER-ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        68 v~~CP~~~i~~~~~~~-~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      +..+|...+.+..... ..+........++...|+.|+.|+.+||.+++...
T Consensus        20 ~~~~p~~~~~~g~~~~n~e~~~~~~~p~i~~~~Ci~C~~C~~~CP~~ai~~~   71 (105)
T PRK09623         20 VDEYPEAPISLGTTLSNFTGDWRTFMPVVDESKCVKCYICWKFCPEPAIYIK   71 (105)
T ss_pred             hhcCCCccccccccccCccccccceeEEECcccCccccchhhhCCHhheEec
Confidence            3447876665543211 11111222445788899999999999999998653

>PLN00071 photosystem I subunit VII; Provisional

Probab=96.35  E-value=0.0015  Score=41.56  Aligned_cols=25  Identities=32%  Similarity=0.915  Sum_probs=21.4

Q ss_pred             ccccccchhhcHHhchhccccchhh
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      +.+.|++|+.|+.+||+++|.+...
T Consensus        44 ~~~~C~~Cg~C~~~CP~~Ai~~~~~   68 (81)
T PLN00071         44 RTEDCVGCKRCESACPTDFLSVRVY   68 (81)
T ss_pred             CCCcCcChhhHHhhcCCccceEeee
Confidence            4578999999999999999987543

>PRK13030 2-oxoacid ferredoxin oxidoreductase; Provisional

Probab=96.32  E-value=0.0012  Score=60.66  Aligned_cols=53  Identities=25%  Similarity=0.394  Sum_probs=38.6

Q ss_pred             cCCCccccccchhhcHH--hchhccccchhhhhcCCCccccccccCccCCcCcccchh-ccccc
Q psy4925          53 RYPSGEERCIACKLCEA--ICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQE-ACPVD  113 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~--~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~-~CP~~  113 (160)
                      ++.++.+.|++||.|..  -||.  +...+..  .++    +..+|...|..|+.|++ .||.=
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            45578899999999987  4985  3222210  111    45789999999999999 99965

>CHL00014 ndhI NADH dehydrogenase subunit I

Probab=96.20  E-value=0.002  Score=46.79  Aligned_cols=27  Identities=26%  Similarity=0.703  Sum_probs=22.8

Q ss_pred             CCCccccccchhhcHHhchhccccchh
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      +.++...|+.|+.|+.+||.+|+.+..
T Consensus        94 ~~id~~~C~~Cg~C~~~CP~~AI~~~~  120 (167)
T CHL00014         94 YSIDFGVCIFCGNCVEYCPTNCLSMTE  120 (167)
T ss_pred             ccCCCCcCcCccchHhhcCcCceecCC
Confidence            445668899999999999999998754

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

Probab=96.17  E-value=0.002  Score=37.24  Aligned_cols=20  Identities=50%  Similarity=1.052  Sum_probs=8.6

Q ss_pred             cccCccCCcCcccchhcccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPV  112 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~  112 (160)
                      +.+|.+.|++||.|+.+||.
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            35788899999999999999

>COG1035 FrhB Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]

Probab=96.15  E-value=0.0019  Score=51.68  Aligned_cols=46  Identities=33%  Similarity=0.586  Sum_probs=32.8

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV  112 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~  112 (160)
                      +..-|.+||.|+.+||. ++...+...         .....-.+.+|+.|..+||.
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            45679999999999999 776554321         12333345577899999993

>TIGR03048 PS_I_psaC photosystem I iron-sulfur protein PsaC

Probab=96.14  E-value=0.0026  Score=40.35  Aligned_cols=25  Identities=32%  Similarity=0.957  Sum_probs=21.2

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+.+.|+.|+.|+.+||++++.+..
T Consensus        42 ~~~~~C~~Cg~C~~~CP~~ai~~~~   66 (80)
T TIGR03048        42 PRTEDCVGCKRCESACPTDFLSVRV   66 (80)
T ss_pred             CCCCcCcChhHHHHhcCcccCEEEE
Confidence            3457899999999999999998654

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.

>COG0348 NapH Polyferredoxin [Energy production and conversion]

Probab=96.14  E-value=0.0017  Score=53.28  Aligned_cols=82  Identities=23%  Similarity=0.417  Sum_probs=44.9

Q ss_pred             CCCcccCCCccCCCCCCccCccccccCCCcccccc-chhhcHHhchhccc---cchhhhhcCCCccccccccCcc-CCcC
Q psy4925          28 EPATINYPFEKGPLSPRFRGEHALRRYPSGEERCI-ACKLCEAICPAQAI---TIEAEERADGSRRTTRYDIDMT-KCIY  102 (160)
Q Consensus        28 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci-~Cg~Cv~~CP~~~i---~~~~~~~~~~~~~~~~~~~~~~-~C~~  102 (160)
                      ++.+..|-.+.+..-... .......+..+...|. .|..|.+.||.+..   .+...          ....... .|+.
T Consensus       181 rr~~C~ylCP~g~~~~v~-~~~~~~~v~~~~~~~~~r~~~c~k~cp~~~~~~v~v~p~----------~~~~~~~~~CI~  249 (386)
T COG0348         181 RRFWCRYLCPYGAFQGVL-FDKSLLKVNYDDKRGCPRCKRCKKVCPEPIPLWVQVCPA----------GIDIRDGLECIG  249 (386)
T ss_pred             ccceeEEeCCHHHHHHHH-cccceEEEecccccCCcccccccccCCccccceeEeccc----------cccccccccccc
Confidence            456666654443221111 1222223333444444 68999999997642   11111          1111222 5999


Q ss_pred             cccchhcccccccccCCc
Q psy4925         103 CGFCQEACPVDAIVEGPN  120 (160)
Q Consensus       103 Cg~C~~~CP~~ai~~~~~  120 (160)
                      |+.|+++|+.....+...
T Consensus       250 C~~CidaCd~~~~~~~~~  267 (386)
T COG0348         250 CGRCIDACDDDMLKFNLP  267 (386)
T ss_pred             HhhHhhhCCHHhheeccc
Confidence            999999999887776544

>PRK09193 indolepyruvate ferredoxin oxidoreductase; Validated

Probab=96.09  E-value=0.0018  Score=59.42  Aligned_cols=53  Identities=23%  Similarity=0.322  Sum_probs=38.8

Q ss_pred             cCCCccccccchhhcHH--hchhccccchhhhhcCCCccccccccCccCCcCcccchh-ccccc
Q psy4925          53 RYPSGEERCIACKLCEA--ICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQE-ACPVD  113 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~--~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~-~CP~~  113 (160)
                      ++.++.+.|.+||.|..  .||.-.....+.+    +    +..+|...|..|+.|+. .||.=
T Consensus       637 r~~In~~vCegCgdC~~~s~C~ai~p~~t~~g----r----K~~Idqs~Cn~d~sC~~G~CPsF  692 (1165)
T PRK09193        637 RVFINEAVCEGCGDCSVKSNCLSVEPVETEFG----R----KRRIDQSSCNKDFSCLKGFCPSF  692 (1165)
T ss_pred             eEEEcccccCCchhhhhccCCcceeeccccCC----c----cEEECHhHCCCccccccCCCCCc
Confidence            45578999999999987  4996322111111    1    45689999999999999 99975

>TIGR02060 aprB adenosine phosphosulphate reductase, beta subunit

Probab=96.01  E-value=0.0023  Score=44.72  Aligned_cols=25  Identities=28%  Similarity=0.688  Sum_probs=22.0

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ++.+.|++|+.|+.+||.+||.+..
T Consensus        42 id~~~C~~Cg~Cv~~CP~~AI~~~~   66 (132)
T TIGR02060        42 IEPDMCWECYSCVKACPQGAIDVRG   66 (132)
T ss_pred             cCchhCccHHHHHHhCCcCceEEEC
Confidence            5678899999999999999998754

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.

>PRK06273 ferredoxin; Provisional

Probab=96.01  E-value=0.0021  Score=46.65  Aligned_cols=27  Identities=37%  Similarity=0.675  Sum_probs=23.3

Q ss_pred             cccCccCCcCcccchhcccccccccCC
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++...|++|+.|+.+||.+||.+..
T Consensus        44 ~~id~~~CigCg~C~~aCP~~AI~~~~   70 (165)
T PRK06273         44 KKVFEELCIGCGGCANVCPTKAIEMIP   70 (165)
T ss_pred             CeECchhCcChhHHHHhcCccceeeec
Confidence            356788899999999999999998754

>PRK13029 2-oxoacid ferredoxin oxidoreductase; Provisional

Probab=96.01  E-value=0.0021  Score=59.06  Aligned_cols=53  Identities=23%  Similarity=0.301  Sum_probs=38.2

Q ss_pred             cCCCccccccchhhcHH--hchhccccchhhhhcCCCccccccccCccCCcCcccchh-ccccc
Q psy4925          53 RYPSGEERCIACKLCEA--ICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQE-ACPVD  113 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~--~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~-~CP~~  113 (160)
                      ++.++.+.|.+||.|..  .||.-.....+.+    +    +..+|...|..|+.|++ .||.=
T Consensus       651 r~~In~~vCeGCgdC~~~snC~ai~p~et~~g----r----K~~Idqs~Cn~d~sC~~G~CPsF  706 (1186)
T PRK13029        651 RVFINELVCEGCGDCSVQSNCLAVQPVETEFG----R----KRKINQSSCNKDFSCVKGFCPSF  706 (1186)
T ss_pred             cEEEcccccCCchhhhhccCCceeeeccccCC----c----cEEECHhHCCCccccccCCCCCc
Confidence            44578899999999987  4985322111111    1    45689999999999999 99973

>PRK09624 porD pyuvate ferredoxin oxidoreductase subunit delta; Reviewed

Probab=95.97  E-value=0.0023  Score=42.96  Aligned_cols=24  Identities=29%  Similarity=0.767  Sum_probs=20.9

Q ss_pred             CccccccchhhcHHhchhccccch
Q psy4925          56 SGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      ++.+.|++|+.|+.+||.+||.+.
T Consensus        78 id~~~C~~Cg~Cv~~CP~~AI~~~  101 (105)
T PRK09624         78 FDYDYCKGCGICANECPTKAIEMV  101 (105)
T ss_pred             ECchhCCCcCchhhhcCcCcEEEe
Confidence            466789999999999999998754

>PRK09625 porD pyruvate flavodoxin oxidoreductase subunit delta; Reviewed

Probab=95.96  E-value=0.0028  Score=44.33  Aligned_cols=24  Identities=21%  Similarity=0.724  Sum_probs=20.1

Q ss_pred             CccccccchhhcHHhchhccccch
Q psy4925          56 SGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      ++.+.|++||.|+.+||++++.+.
T Consensus        86 i~~~~C~~Cg~Cv~vCP~~a~~l~  109 (133)
T PRK09625         86 VDYSHCKGCGVCVEVCPTNPKSLL  109 (133)
T ss_pred             eCcCcCcChhHHHHHCCcCceEEE
Confidence            456789999999999999986543

>PRK12814 putative NADPH-dependent glutamate synthase small subunit; Provisional

Probab=95.94  E-value=0.0027  Score=55.42  Aligned_cols=20  Identities=20%  Similarity=0.585  Sum_probs=15.2

Q ss_pred             cCCCccccccchhhcHHhch
Q psy4925          53 RYPSGEERCIACKLCEAICP   72 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP   72 (160)
                      .+..|.++||.||+|+++|.
T Consensus       610 ~i~~D~~kCI~CgrCv~~C~  629 (652)
T PRK12814        610 DIRFEREKCVDCGICVRTLE  629 (652)
T ss_pred             CeEeccccccCchHHHHHHH
Confidence            35567788888888888886

>PRK05888 NADH dehydrogenase subunit I; Provisional

Probab=95.94  E-value=0.0027  Score=45.92  Aligned_cols=27  Identities=37%  Similarity=0.802  Sum_probs=22.8

Q ss_pred             CCccccccchhhcHHhchhccccchhh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      .++...|+.|+.|+.+||+++|.+...
T Consensus        93 ~i~~~~C~~Cg~Cv~~CP~~Ai~~~~~  119 (164)
T PRK05888         93 DINFGRCIFCGFCEEACPTDAIVETPD  119 (164)
T ss_pred             ecCCCcCcccCcchhhcCcCcceecCc
Confidence            356789999999999999999986543

>TIGR01971 NuoI NADH-quinone oxidoreductase, chain I

Probab=95.91  E-value=0.003  Score=43.25  Aligned_cols=26  Identities=42%  Similarity=0.901  Sum_probs=22.1

Q ss_pred             CCccccccchhhcHHhchhccccchh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .++...|+.|+.|+.+||++++.+..
T Consensus        78 ~~~~~~C~~Cg~Cv~~CP~~al~~~~  103 (122)
T TIGR01971        78 QINFGRCIFCGLCEEACPTDAIVLTP  103 (122)
T ss_pred             eECcccCCCCCchhhhCCCccccccc
Confidence            35678899999999999999987654

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.

>PRK02651 photosystem I subunit VII; Provisional

Probab=95.82  E-value=0.0043  Score=39.32  Aligned_cols=25  Identities=36%  Similarity=0.921  Sum_probs=21.2

Q ss_pred             ccccccchhhcHHhchhccccchhh
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      +...|+.|+.|+.+||.++|.+...
T Consensus        44 ~~~~C~~Cg~C~~~CP~~ai~~~~~   68 (81)
T PRK02651         44 RTEDCVGCKRCETACPTDFLSIRVY   68 (81)
T ss_pred             CCCcCCChhhhhhhcCCCceEEEEE
Confidence            4578999999999999999986543

>PRK05113 electron transport complex protein RnfB; Provisional

Probab=95.76  E-value=0.0038  Score=46.34  Aligned_cols=25  Identities=32%  Similarity=0.761  Sum_probs=21.7

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+.++|+.||.|+.+||+++|.+..
T Consensus       141 v~~~~C~~Cg~Cv~vCP~~AI~~~~  165 (191)
T PRK05113        141 VISDLCTGCDLCVAPCPTDCIEMIP  165 (191)
T ss_pred             ecCCcCCchHHHHHHcCcCceEEee
Confidence            4568899999999999999998754

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

Probab=95.73  E-value=0.0044  Score=38.91  Aligned_cols=28  Identities=39%  Similarity=0.668  Sum_probs=23.4

Q ss_pred             ccccCccCCcCcccchhcccccccccCC
Q psy4925          92 RYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        92 ~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ...++.+.|+.|+.|+.+||.+++....
T Consensus        19 ~~~i~~~~C~~C~~C~~~Cp~~ai~~~~   46 (78)
T TIGR02179        19 KPVVDKEKCIKCKNCWLYCPEGAIQEDE   46 (78)
T ss_pred             EEEEcCCcCcChhHHHhhcCccceEecC
Confidence            3457788999999999999999987643

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.

>PRK08493 NADH dehydrogenase subunit G; Validated

Probab=95.68  E-value=0.0061  Score=54.44  Aligned_cols=23  Identities=30%  Similarity=0.712  Sum_probs=20.1

Q ss_pred             cccccchhhcHHhchhccccchh
Q psy4925          58 EERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ...|+.||.|+.+||+||+....
T Consensus       203 ~~~C~~CG~Cv~VCPvGAL~~k~  225 (819)
T PRK08493        203 TLDCSFCGECIAVCPVGALSSSD  225 (819)
T ss_pred             cccccccCcHHHhCCCCccccCc
Confidence            46899999999999999997643

>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]

Probab=95.67  E-value=0.0034  Score=54.97  Aligned_cols=25  Identities=32%  Similarity=0.946  Sum_probs=20.9

Q ss_pred             CCccccccchhhcHHhchhccccch
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      ++..+.|+.||.||.|||.+|+...
T Consensus       188 ~i~~SSCVsCG~CvtVCP~nALmek  212 (978)
T COG3383         188 PINESSCVSCGACVTVCPVNALMEK  212 (978)
T ss_pred             ccccccccccCccceecchhhhhhh
Confidence            3456799999999999999988644

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

Probab=95.64  E-value=0.0042  Score=45.03  Aligned_cols=24  Identities=29%  Similarity=0.789  Sum_probs=20.8

Q ss_pred             CccccccchhhcHHhchhccccch
Q psy4925          56 SGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .+.++|+.||.|+.+||+++|.+.
T Consensus       140 i~~~~C~~Cg~Cv~~CP~~AI~~~  163 (165)
T TIGR01944       140 VIADECTGCDLCVEPCPTDCIEMI  163 (165)
T ss_pred             eecccccChhHHHHhcCcCceEee
Confidence            456889999999999999998753

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=95.62  E-value=0.0045  Score=48.64  Aligned_cols=25  Identities=28%  Similarity=0.733  Sum_probs=22.5

Q ss_pred             ccccCccCCcCcccchhcccccccc
Q psy4925          92 RYDIDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        92 ~~~~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      .+.++...|++||.|+++||++|+.
T Consensus        42 ~~~~~~~~C~~C~~C~~~Cp~~a~~   66 (295)
T TIGR02494        42 ELLFKENRCLGCGKCVEVCPAGTAR   66 (295)
T ss_pred             eEEEccccCCCCchhhhhCcccccc
Confidence            4567889999999999999999987

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

>PRK08764 ferredoxin; Provisional

Probab=95.46  E-value=0.0053  Score=43.01  Aligned_cols=23  Identities=30%  Similarity=0.816  Sum_probs=20.1

Q ss_pred             CccccccchhhcHHhchhccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      ++.++|+.|+.|+.+||+++|.+
T Consensus       112 v~~~~C~~Cg~Cv~~CP~~Ai~~  134 (135)
T PRK08764        112 VIAPLCTGCELCVPACPVDCIEL  134 (135)
T ss_pred             ecCCcCcCccchhhhcCccceEe
Confidence            45678999999999999999864

>KOG0063|consensus

Probab=95.41  E-value=0.0045  Score=51.32  Aligned_cols=23  Identities=43%  Similarity=0.953  Sum_probs=16.2

Q ss_pred             cCccCCcCcccchhccccccccc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      +....|++||.|+.-||.+||..
T Consensus        47 ise~lCigcgicvkkcpf~ai~i   69 (592)
T KOG0063|consen   47 ISEELCIGCGICVKKCPFEAIQI   69 (592)
T ss_pred             hhHhhhccccceeeccCcceEEe
Confidence            44456777888888888777654

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=95.38  E-value=0.0041  Score=51.89  Aligned_cols=26  Identities=42%  Similarity=0.839  Sum_probs=22.4

Q ss_pred             CCccccccchhhcHHhchhccccchh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+.+..|++||.|++-||.+||.+..
T Consensus        46 vIsE~lCiGCGICvkkCPF~AI~Ivn   71 (591)
T COG1245          46 VISEELCIGCGICVKKCPFDAISIVN   71 (591)
T ss_pred             eeEhhhhccchhhhccCCcceEEEec
Confidence            45578899999999999999998754

>PRK13409 putative ATPase RIL; Provisional

Probab=95.37  E-value=0.0038  Score=53.91  Aligned_cols=26  Identities=42%  Similarity=0.839  Sum_probs=22.2

Q ss_pred             CCccccccchhhcHHhchhccccchh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+.++.||+||.||+-||.+||.+-+
T Consensus        45 ~~~e~~c~~c~~c~~~cp~~a~~i~~   70 (590)
T PRK13409         45 VISEELCIGCGICVKKCPFDAISIVN   70 (590)
T ss_pred             eeeHhhccccccccccCCcceEEEee
Confidence            35678899999999999999998753

>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit

Probab=95.35  E-value=0.0056  Score=49.42  Aligned_cols=26  Identities=35%  Similarity=0.778  Sum_probs=22.5

Q ss_pred             ccCCCccccccchhhcHHhchhcccc
Q psy4925          52 RRYPSGEERCIACKLCEAICPAQAIT   77 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~~~i~   77 (160)
                      ..+.+|.++|++||.|+.+||++++.
T Consensus       207 ~~~~id~~~Ci~Cg~Ci~~CP~~a~~  232 (341)
T TIGR02066       207 KSLEVDVEKCIYCGNCYTMCPAMPIF  232 (341)
T ss_pred             CceeeccccCCcCCchHHhCchhhcc
Confidence            34567889999999999999999885

This model describes the beta subunit of sulfite reductase.

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

Probab=95.32  E-value=0.0042  Score=49.20  Aligned_cols=27  Identities=33%  Similarity=0.642  Sum_probs=24.1

Q ss_pred             cccCccCCcCcccchhcccccccccCC
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++.+.|.+|+.|+++||++||....
T Consensus       167 P~~~~E~c~gc~~cv~~C~~gAI~~~~  193 (317)
T COG2221         167 PKVDEELCRGCGKCVKVCPTGAITWDG  193 (317)
T ss_pred             CccCHHHhchhHhHHHhCCCCceeecc
Confidence            457888999999999999999999875

>TIGR00402 napF ferredoxin-type protein NapF

Probab=95.27  E-value=0.0066  Score=40.35  Aligned_cols=24  Identities=25%  Similarity=0.603  Sum_probs=20.7

Q ss_pred             CCccccccchhhcHHhchhccccc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      .++...|+.|+.|+.+||+++|..
T Consensus        62 ~i~~~~C~~Cg~C~~~CP~~Ai~~   85 (101)
T TIGR00402        62 EFDNAECDFCGKCAEACPTNAFHP   85 (101)
T ss_pred             EecCccCcCccChhhHCCccccCc
Confidence            456678999999999999999864

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.

>TIGR02912 sulfite_red_C sulfite reductase, subunit C

Probab=94.99  E-value=0.009  Score=47.61  Aligned_cols=27  Identities=30%  Similarity=0.615  Sum_probs=22.6

Q ss_pred             CCCccccccchhhcHHhchhccccchh
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      +.++.+.|++|+.|+.+||++|+....
T Consensus       196 ~~id~~~C~~Cg~Cv~~CP~~Al~~~~  222 (314)
T TIGR02912       196 VVRDHSKCIGCGECVLKCPTGAWTRSE  222 (314)
T ss_pred             EEeCCCcCcCcchhhhhCCHhhcccCc
Confidence            345788999999999999999987543

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.

>PRK06991 ferredoxin; Provisional

Probab=94.99  E-value=0.0098  Score=46.51  Aligned_cols=27  Identities=56%  Similarity=1.015  Sum_probs=23.0

Q ss_pred             cccCccCCcCcccchhcccccccccCC
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++...|++|+.|+.+||+++|.+..
T Consensus        80 ~~id~~~CigCg~Cv~aCP~~AI~~~~  106 (270)
T PRK06991         80 AVIDEQLCIGCTLCMQACPVDAIVGAP  106 (270)
T ss_pred             eEEccccCCCCcHHHHhCCHhheeccc
Confidence            356778999999999999999997653

>PRK15449 ferredoxin-like protein FixX; Provisional

Probab=94.94  E-value=0.0083  Score=39.49  Aligned_cols=25  Identities=16%  Similarity=0.392  Sum_probs=20.8

Q ss_pred             ccCCCccccccchhhcHHhchhccc
Q psy4925          52 RRYPSGEERCIACKLCEAICPAQAI   76 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~~~i   76 (160)
                      ..+.++.++|++||.|+.+||.+++
T Consensus        54 G~V~vd~e~CigCg~C~~~C~~~~~   78 (95)
T PRK15449         54 GSVRFDYAGCLECGTCRILGLGSAL   78 (95)
T ss_pred             CCEEEcCCCCCcchhhhhhcCCCCc
Confidence            3455678999999999999998765

>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

Probab=94.90  E-value=0.009  Score=47.17  Aligned_cols=68  Identities=18%  Similarity=0.061  Sum_probs=46.8

Q ss_pred             chhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcc-ccccccc---CCcccccccchhhhhccH
Q psy4925          63 ACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEAC-PVDAIVE---GPNFEFSTESHEELLYNK  135 (160)
Q Consensus        63 ~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~C-P~~ai~~---~~~~~~~~~~~~~~~~~~  135 (160)
                      .+..|+..||.+++.++..+. .    ......+...|+.|..|+..+ -.+++.+   .++|.|..|+.|.+-...
T Consensus       201 ~~~~~~~~cP~~Vf~i~~~~~-~----~~~~V~~~~~ct~crec~~~~~~~~~V~v~~~~d~fiF~VES~G~l~p~~  272 (291)
T cd07032         201 DAEKLQKCFPPGVIDIEEVKG-K----KKAVVANPRKDTLSREVLRHEEFKDKVELGRVRDHFIFSIESTGALPPDV  272 (291)
T ss_pred             HHHHHHhhCCCccEEecccCC-C----ceEEEcccccCcccHhHhhhhccCCceeEEEeCCEEEEEEeCCCCCCHHH
Confidence            577899999999988753211 0    113456888999999999876 2344544   455888888887765433

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

>PRK14028 pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional

Probab=94.70  E-value=0.011  Score=46.95  Aligned_cols=24  Identities=29%  Similarity=0.790  Sum_probs=20.7

Q ss_pred             CccccccchhhcHHhchhccccch
Q psy4925          56 SGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .+...|.+|+.|+.+||++||.+.
T Consensus       286 ~d~~~C~gCg~C~~~CP~~AI~~~  309 (312)
T PRK14028        286 FDYQYCKGCGVCAEVCPTGAIQMV  309 (312)
T ss_pred             CCcccCcCcCchhhhCCHhheEec
Confidence            455789999999999999998764

>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated

Probab=94.56  E-value=0.015  Score=44.48  Aligned_cols=24  Identities=33%  Similarity=0.762  Sum_probs=20.4

Q ss_pred             cccccchhhcHHhchhccccchhh
Q psy4925          58 EERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      ...|++||.|+.+||++||.....
T Consensus       189 ~~~C~~Cg~Cv~vCP~gAL~~~~~  212 (234)
T PRK07569        189 SETCTSCGKCVQACPTGAIFRKGS  212 (234)
T ss_pred             cccccchHHHHHhCCCCcEEecCC
Confidence            458999999999999999976543

>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]

Probab=94.54  E-value=0.011  Score=45.12  Aligned_cols=46  Identities=33%  Similarity=0.866  Sum_probs=35.8

Q ss_pred             ccc-cccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccc
Q psy4925          57 GEE-RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        57 ~~~-~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      +.. .|.+|+.|...||+.++....            -......|+.||.|...||...
T Consensus       187 ~qg~~C~G~~TC~A~CP~~ai~c~G------------c~g~~~~~~~~Ga~~v~~~rs~  233 (247)
T COG1941         187 EQGLPCMGCGTCAASCPSRAIPCRG------------CRGNIPRCIKCGACFVSCPRSK  233 (247)
T ss_pred             cCCCcccCchhhhccCCccCCcccC------------CcCCcccchhhhHHHHHHhHHh
Confidence            344 799999999999998887652            1356667999999999998764

>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only

Probab=94.43  E-value=0.013  Score=47.91  Aligned_cols=23  Identities=52%  Similarity=0.888  Sum_probs=20.7

Q ss_pred             ccCccCCcCcccchhcccccccc
Q psy4925          94 DIDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      .++...|+.||.|+.+||++|+.
T Consensus         3 ~id~~kCi~Cg~Cv~~CP~~ai~   25 (374)
T TIGR02512         3 VRDMSKCIGCGRCVRACTNVQIV   25 (374)
T ss_pred             EechhhCCcChHhhhhCCHhhcc
Confidence            46778899999999999999986

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.

>PRK09326 F420H2 dehydrogenase subunit F; Provisional

Probab=94.39  E-value=0.014  Score=47.06  Aligned_cols=27  Identities=33%  Similarity=0.824  Sum_probs=23.5

Q ss_pred             ccCccCCcCcccchhcccccccccCCc
Q psy4925          94 DIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .++...|++||.|+.+||+++|.+...
T Consensus         8 vi~~~~C~gCg~C~~~CP~~aI~~~~~   34 (341)
T PRK09326          8 VIEYDVCTACGACEAVCPIGAITVDKK   34 (341)
T ss_pred             EECcccCcChHHHHHhCCHhhhecccC
Confidence            467789999999999999999988654

>TIGR03287 methan_mark_16 putative methanogenesis marker 16 metalloprotein

Probab=94.19  E-value=0.014  Score=47.73  Aligned_cols=25  Identities=32%  Similarity=0.868  Sum_probs=21.8

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ++.++|+.|+.|+.+||.+|+.+..
T Consensus       327 Id~~~Ci~CGaCV~aCP~~AI~~~~  351 (391)
T TIGR03287       327 LNTEDCFGCGYCAEICPGGAFEVNL  351 (391)
T ss_pred             eChHhCcChHHHHhhCCccceEEeC
Confidence            5678899999999999999987654

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.

>KOG0063|consensus

Probab=94.17  E-value=0.014  Score=48.59  Aligned_cols=55  Identities=25%  Similarity=0.325  Sum_probs=40.3

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .+.-||+||.||+-||.+|+.+-...         .-......|..|+.|..-|+-.+.+....
T Consensus        48 se~lCigcgicvkkcpf~ai~iinlp---------~nl~~etthry~~n~fKlhrlp~prpg~v  102 (592)
T KOG0063|consen   48 SEELCIGCGICVKKCPFEAIQIINLP---------TNLEKETTHRYSANSFKLHRLPIPRPGQV  102 (592)
T ss_pred             hHhhhccccceeeccCcceEEecCCc---------hhHhhhhhhhhcccceeeccCCCCCcchh
Confidence            45679999999999999998764432         11234446888999999998777665544

>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=94.06  E-value=0.019  Score=33.55  Aligned_cols=16  Identities=31%  Similarity=1.024  Sum_probs=8.1

Q ss_pred             ccccchhhcHHhchhc
Q psy4925          59 ERCIACKLCEAICPAQ   74 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~   74 (160)
                      ..|+.||.|+.+||.+
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            5799999999999986

...

>TIGR02486 RDH reductive dehalogenase

Probab=93.98  E-value=0.02  Score=45.71  Aligned_cols=23  Identities=39%  Similarity=0.915  Sum_probs=20.1

Q ss_pred             cCCcCcccchhcccccccccCCc
Q psy4925          98 TKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        98 ~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .-|..|+.|+++||++||.....
T Consensus       205 ~fC~~C~~C~~~CP~~Ai~~~~~  227 (314)
T TIGR02486       205 KFCETCGKCADECPSGAISKGGE  227 (314)
T ss_pred             ccCcchhHHHhhCCccccCCCCC
Confidence            46999999999999999987654

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.

>PRK08318 dihydropyrimidine dehydrogenase subunit B; Validated

Probab=93.80  E-value=0.021  Score=47.30  Aligned_cols=27  Identities=37%  Similarity=0.886  Sum_probs=22.9

Q ss_pred             CCccccccchhhcHHhchh-ccccchhh
Q psy4925          55 PSGEERCIACKLCEAICPA-QAITIEAE   81 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~-~~i~~~~~   81 (160)
                      .++.+.|++|+.|+.+||. ++|.+...
T Consensus       373 ~i~~~~C~~Cg~C~~~CP~~~Ai~~~~~  400 (420)
T PRK08318        373 EVIEEECVGCNLCAHVCPVEGCITMGEV  400 (420)
T ss_pred             EechhhCcccchHHhhCCCCCCEEEecc
Confidence            3567899999999999999 99976653

>TIGR02700 flavo_MJ0208 archaeoflavoprotein, MJ0208 family

Probab=93.58  E-value=0.026  Score=43.18  Aligned_cols=26  Identities=42%  Similarity=0.788  Sum_probs=22.3

Q ss_pred             ccCccCCcCcccchhcccccccccCC
Q psy4925          94 DIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .++...|+.|+.|+++||.+++....
T Consensus       144 ~id~~~C~~C~~C~~~CP~~ai~~~~  169 (234)
T TIGR02700       144 MIDRKRCKGCGICVDACPRSAIDMVD  169 (234)
T ss_pred             EEChhHCcCcchHHHhCCcccEEecC
Confidence            46778899999999999999988654

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.

>PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional

Probab=93.49  E-value=0.027  Score=48.38  Aligned_cols=25  Identities=28%  Similarity=0.881  Sum_probs=21.7

Q ss_pred             CCccccccchhhcHHhchhccccch
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .++.++|+.|+.|+.+||++||.+.
T Consensus       537 ~i~~~~C~~Cg~C~~~CP~~Ai~~~  561 (564)
T PRK12771        537 HFDYDKCTGCHICADVCPCGAIEMG  561 (564)
T ss_pred             EEecccCcChhHHHhhcCcCceEec
Confidence            3567899999999999999999764

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

Probab=93.29  E-value=0.028  Score=43.80  Aligned_cols=25  Identities=52%  Similarity=0.949  Sum_probs=21.6

Q ss_pred             cccCccCCcCcccchhccccccccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ..++.+.|..||.|.++|+.+||..
T Consensus        64 p~i~~e~C~~CG~C~~vC~f~Ai~~   88 (284)
T COG1149          64 PEIDPEKCIRCGKCAEVCRFGAIVV   88 (284)
T ss_pred             cccChhhccccCcHHHhCCCCeEEE
Confidence            3567778999999999999999964

>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=93.17  E-value=0.038  Score=32.82  Aligned_cols=18  Identities=44%  Similarity=1.191  Sum_probs=9.8

Q ss_pred             cccccchhhcHHhchhcc
Q psy4925          58 EERCIACKLCEAICPAQA   75 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~   75 (160)
                      ...|+.||.|..+||.+.
T Consensus        43 ~~~C~~Cg~C~~~CP~~l   60 (61)
T PF13534_consen   43 ASLCIGCGLCESVCPQGL   60 (61)
T ss_dssp             TTT--S--HHHHH-TT--
T ss_pred             cccCcCcCcCcccccCCC
Confidence            567999999999999873

...

>TIGR00276 iron-sulfur cluster binding protein, putative

Probab=93.03  E-value=0.032  Score=43.91  Aligned_cols=21  Identities=43%  Similarity=0.873  Sum_probs=18.6

Q ss_pred             ccCCcCcccchhccccccccc
Q psy4925          97 MTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        97 ~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ...|..|+.|+++||++||..
T Consensus       158 ~~~C~~C~~C~~aCPt~AI~~  178 (282)
T TIGR00276       158 EEYCGRCTKCIDACPTQALVE  178 (282)
T ss_pred             CCCCccHHHHHHhcCcccccC
Confidence            457999999999999999873

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.

>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma

Probab=92.97  E-value=0.029  Score=42.78  Aligned_cols=28  Identities=32%  Similarity=0.666  Sum_probs=23.5

Q ss_pred             cccCccCCcCcccchhcccccccccCCc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..++...|+.|+.|+.+||.+++.....
T Consensus       169 ~~id~~~C~~C~~C~~aCP~~ai~~~~~  196 (228)
T TIGR03294       169 KVVNQGLCMGCGTCAAACPTRAIEMEDG  196 (228)
T ss_pred             EEEChhhCcChhHHHHhCCHhhEEEeCC
Confidence            3567789999999999999999887543

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.

>TIGR01973 NuoG NADH-quinone oxidoreductase, chain G

Probab=92.91  E-value=0.051  Score=47.11  Aligned_cols=20  Identities=25%  Similarity=0.291  Sum_probs=17.3

Q ss_pred             cccchhhcHHhchhccccch
Q psy4925          60 RCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .|..||.|+.+||+||+...
T Consensus       183 ~~~~cg~cv~vCP~GAl~~k  202 (603)
T TIGR01973       183 ESELSGNLIDICPVGALTSK  202 (603)
T ss_pred             CCcccCChHhhCCccccccc
Confidence            57789999999999999743

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.

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

Probab=92.72  E-value=0.052  Score=44.95  Aligned_cols=28  Identities=43%  Similarity=0.858  Sum_probs=23.7

Q ss_pred             cccCccCCcCcccchhcccccccccCCc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..++...|+.|+.|+.+||.++|.....
T Consensus         5 ~~id~~~Ci~C~~C~~~CP~~ai~~~~~   32 (411)
T TIGR03224         5 HLIDPEICIRCNTCEETCPIDAITHDDR   32 (411)
T ss_pred             eeeCcccCcCccchhhhCCcccEeccCC
Confidence            4578889999999999999999876543

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.

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

Probab=92.59  E-value=0.041  Score=47.42  Aligned_cols=29  Identities=24%  Similarity=0.591  Sum_probs=23.1

Q ss_pred             ccCCCccccccchhhcHHhchhccccchh
Q psy4925          52 RRYPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+..+|...|++||.|+.+||..++....
T Consensus       601 ~k~~id~~~C~GCg~C~~iCP~~a~~~~~  629 (640)
T COG4231         601 KKARIDPSSCNGCGSCVEVCPSFAIKEGG  629 (640)
T ss_pred             CceeecccccccchhhhhcCchhheeccc
Confidence            33446777899999999999999887543

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

Probab=92.42  E-value=0.063  Score=42.53  Aligned_cols=59  Identities=24%  Similarity=0.364  Sum_probs=34.6

Q ss_pred             ccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHHHhcc--CCcchHHHhhh
Q psy4925          94 DIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSN--GDKWESEIASN  152 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~  152 (160)
                      ......|..||.|+..||.+||..........+..-.-.+.....-+.  ...|++...++
T Consensus       189 ~v~e~kc~~c~~cv~~cp~~Ai~~~~~~~I~~~~ci~c~~c~~ac~~gav~~~W~~~~~~f  249 (354)
T COG2768         189 VVVEEKCYDCGLCVKICPVGAITLTKVVKIDYEKCIGCGQCMEACPYGAVDQNWEEDSPEF  249 (354)
T ss_pred             eeeeecccccchhhhhCCCcceecccceeechhhccchhhhhhhccCcccccchhhccHHH
Confidence            356678999999999999999998744333333332222222222221  15666655443

>PF13459 Fer4_15: 4Fe-4S single cluster domain

Probab=92.40  E-value=0.047  Score=33.08  Aligned_cols=20  Identities=40%  Similarity=0.848  Sum_probs=16.8

Q ss_pred             ccCccCCcCcccchhccccc
Q psy4925          94 DIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      .++...|++||.|+..||.-
T Consensus         2 ~vD~~~C~gcg~C~~~aP~v   21 (65)
T PF13459_consen    2 WVDRDRCIGCGLCVELAPEV   21 (65)
T ss_pred             EEecccCcCccHHHhhCCcc
Confidence            35678899999999999853

>PRK07860 NADH dehydrogenase subunit G; Validated

Probab=92.30  E-value=0.066  Score=47.98  Aligned_cols=20  Identities=25%  Similarity=0.291  Sum_probs=17.2

Q ss_pred             cccchhhcHHhchhccccch
Q psy4925          60 RCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .|..||.|+.+||+||+...
T Consensus       191 ~~~~cG~cv~vCP~GAl~~k  210 (797)
T PRK07860        191 QSYFSGNTVQICPVGALTGA  210 (797)
T ss_pred             CccccCCchhhCCccccccc
Confidence            46789999999999999743

>COG1141 Fer Ferredoxin [Energy production and conversion]

Probab=91.94  E-value=0.056  Score=33.35  Aligned_cols=21  Identities=33%  Similarity=0.649  Sum_probs=18.0

Q ss_pred             cccCccCCcCcccchhccccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      ..++.+.|++||+|..+||.-
T Consensus         3 v~vDrd~Cigcg~C~~~aPdv   23 (68)
T COG1141           3 VIVDRDTCIGCGACLAVAPDV   23 (68)
T ss_pred             EEechhhccccchhhhcCCcc
Confidence            456778999999999999965

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

Probab=91.83  E-value=0.068  Score=49.79  Aligned_cols=25  Identities=32%  Similarity=0.521  Sum_probs=21.9

Q ss_pred             cccCccCCcCcccchhccccccccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ...+...|+.||.|+.+||++||..
T Consensus       678 p~~~~~~Ci~Cg~C~~vCP~~ai~~  702 (1165)
T TIGR02176       678 PVWVPDNCIQCNQCAFVCPHAAIRP  702 (1165)
T ss_pred             ceeccccCCCccchHHhcChhhccc
Confidence            3467788999999999999999975

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.

>PRK13795 hypothetical protein; Provisional

Probab=91.17  E-value=0.075  Score=46.44  Aligned_cols=27  Identities=33%  Similarity=0.677  Sum_probs=22.9

Q ss_pred             ccCccCCcCcccchhcccccccccCCc
Q psy4925          94 DIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .++...|..|+.|+.+||++||.....
T Consensus       577 v~~~~~C~~Cg~C~~~CP~~ai~~~~~  603 (636)
T PRK13795        577 LRRAAECVGCGVCVGACPTGAIRIEEG  603 (636)
T ss_pred             EEccccCCCHhHHHHhCCcccEEeecC
Confidence            456778999999999999999887543

>TIGR03336 IOR_alpha indolepyruvate ferredoxin oxidoreductase, alpha subunit

Probab=91.13  E-value=0.086  Score=45.70  Aligned_cols=20  Identities=40%  Similarity=0.976  Sum_probs=17.1

Q ss_pred             CccccccchhhcHHhchhccc
Q psy4925          56 SGEERCIACKLCEAICPAQAI   76 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i   76 (160)
                      ++. .|+.||.|+.+||.+|+
T Consensus       576 i~~-~C~~Cg~C~~~CP~~Ai  595 (595)
T TIGR03336       576 IDP-LCTGCGVCAQICPFDAI  595 (595)
T ss_pred             eCC-CCcCHHHHHhhCccccC
Confidence            444 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.

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

Probab=90.74  E-value=0.08  Score=38.86  Aligned_cols=30  Identities=47%  Similarity=0.750  Sum_probs=25.3

Q ss_pred             cccCccCCcCcccchhcccccccccCCccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~  122 (160)
                      ..++...|++|..|+++||.+||.-.....
T Consensus       110 a~i~e~~ciGCtkCiqaCpvdAivg~~~~m  139 (198)
T COG2878         110 ALIDEANCIGCTKCIQACPVDAIVGATKAM  139 (198)
T ss_pred             eEecchhccccHHHHHhCChhhhhccchhH
Confidence            346888999999999999999998777633

>COG1600 Uncharacterized Fe-S protein [Energy production and conversion]

Probab=90.61  E-value=0.084  Score=42.52  Aligned_cols=23  Identities=35%  Similarity=0.746  Sum_probs=19.8

Q ss_pred             cCCcCcccchhcccccccccCCc
Q psy4925          98 TKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        98 ~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.|-.|..|+++||++||.-...
T Consensus       185 ~~Cg~C~~CldaCPt~Al~~~~~  207 (337)
T COG1600         185 DHCGSCTRCLDACPTGALVAPYT  207 (337)
T ss_pred             ccChhhHHHHhhCCcccccCCCc
Confidence            67999999999999999886443

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=90.28  E-value=0.1  Score=40.46  Aligned_cols=25  Identities=44%  Similarity=0.784  Sum_probs=21.1

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+...|+.|+.|+.+||.+++.+..
T Consensus       196 ~~~~~C~~C~~C~~~Cp~~AI~~~~  220 (259)
T cd07030         196 EDLEDCSLCKLCERACDAGAIRVGW  220 (259)
T ss_pred             eChhhCcCchHHHHhCCCCcEEEEe
Confidence            3467899999999999999887654

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

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=90.12  E-value=0.12  Score=40.21  Aligned_cols=24  Identities=29%  Similarity=0.578  Sum_probs=21.1

Q ss_pred             ccCCcCcccchhcccccccccCCc
Q psy4925          97 MTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        97 ~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ...|..|+.|+.+||.+++.+...
T Consensus       168 ~~~C~~C~~C~~~CP~~vi~~~~~  191 (263)
T PRK00783        168 SEDCDECEKCVEACPRGVLELKEG  191 (263)
T ss_pred             cccCCchHHHHHhCCccccEecCC
Confidence            578999999999999999987654

>PRK09130 NADH dehydrogenase subunit G; Validated

Probab=90.01  E-value=0.17  Score=44.64  Aligned_cols=20  Identities=20%  Similarity=0.287  Sum_probs=17.2

Q ss_pred             cccchhhcHHhchhccccch
Q psy4925          60 RCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .|..||.|+.+||+||+...
T Consensus       186 ~~~~~G~cv~~CPvgAl~~k  205 (687)
T PRK09130        186 TSELSGNVIDLCPVGALTSK  205 (687)
T ss_pred             cccccccHHhhCCCcccccc
Confidence            46789999999999999744

>TIGR02910 sulfite_red_A sulfite reductase, subunit A

Probab=89.94  E-value=0.13  Score=41.53  Aligned_cols=22  Identities=36%  Similarity=1.038  Sum_probs=17.8

Q ss_pred             CccccccchhhcHHhchhccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      +....|++||+|+.+||++ |++
T Consensus       298 fG~~~CvgCGrC~~~CP~~-idi  319 (334)
T TIGR02910       298 NGYHMCVGCGRCDDICPEY-ISF  319 (334)
T ss_pred             cCccccCCcCchhhhCCCC-CCH
Confidence            3467799999999999987 443

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.

>PRK08166 NADH dehydrogenase subunit G; Validated

Probab=89.86  E-value=0.14  Score=46.13  Aligned_cols=20  Identities=15%  Similarity=0.184  Sum_probs=17.4

Q ss_pred             cccchhhcHHhchhccccch
Q psy4925          60 RCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .|..||.|+.+||+||+...
T Consensus       190 ~~~~~G~cv~vCP~GAl~~k  209 (847)
T PRK08166        190 ESEFSGNLVEVCPTGVFTDK  209 (847)
T ss_pred             cChhhCChHhhCCchhcccc
Confidence            57789999999999999754

>PRK09129 NADH dehydrogenase subunit G; Validated

Probab=89.66  E-value=0.19  Score=44.92  Aligned_cols=20  Identities=20%  Similarity=0.270  Sum_probs=17.0

Q ss_pred             cccchhhcHHhchhccccch
Q psy4925          60 RCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .|..||.|+.+||+||+...
T Consensus       185 ~~~~cg~cv~~CP~GAl~~k  204 (776)
T PRK09129        185 DSELSGNMIDLCPVGALTSK  204 (776)
T ss_pred             cCcccCCchhhCCccccccc
Confidence            46679999999999999744

>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=89.50  E-value=0.12  Score=30.71  Aligned_cols=18  Identities=50%  Similarity=0.979  Sum_probs=11.3

Q ss_pred             CccCCcCcccchhccccc
Q psy4925          96 DMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~  113 (160)
                      |...|+.||.|+..+|.-
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            456899999999999976

...

>PRK07570 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated

Probab=88.77  E-value=0.19  Score=38.93  Aligned_cols=21  Identities=43%  Similarity=0.986  Sum_probs=17.7

Q ss_pred             cCccCCcCcccchhccccccc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      .+...|+.||.|+.+||..++
T Consensus       154 ~~~~~CI~CG~C~saCP~~~~  174 (250)
T PRK07570        154 FDAAACIGCGACVAACPNGSA  174 (250)
T ss_pred             hCccccCCCcccccccCCccc
Confidence            456679999999999998863

>TIGR03315 Se_ygfK putative selenate reductase, YgfK subunit

Probab=88.53  E-value=0.18  Score=46.36  Aligned_cols=21  Identities=24%  Similarity=0.719  Sum_probs=18.2

Q ss_pred             cccchhhcHHhchhccccchh
Q psy4925          60 RCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .|++||.|+.+||++++.+..
T Consensus       922 ~C~~CG~C~~vCP~~a~~~~g  942 (1012)
T TIGR03315       922 MCNECGNCATFCPYDGAPYKD  942 (1012)
T ss_pred             cccccchHHHhCCCCccccee
Confidence            499999999999999887643

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.

>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C

Probab=88.41  E-value=0.2  Score=35.33  Aligned_cols=16  Identities=38%  Similarity=1.138  Sum_probs=14.4

Q ss_pred             cCCcCcccchhccccc
Q psy4925          98 TKCIYCGFCQEACPVD  113 (160)
Q Consensus        98 ~~C~~Cg~C~~~CP~~  113 (160)
                      ..|+.||.|..+||+.
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.

>COG1035 FrhB Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]

Probab=88.12  E-value=0.21  Score=40.19  Aligned_cols=24  Identities=42%  Similarity=0.863  Sum_probs=20.2

Q ss_pred             CccCCcCcccchhcccccccccCCc
Q psy4925          96 DMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +...|+.||.|+..||. +|++...
T Consensus         3 ~~~~c~~Cg~C~a~cp~-~i~~~~~   26 (332)
T COG1035           3 DAGLCTGCGTCAAVCPY-AITERDE   26 (332)
T ss_pred             cCcccccchhhHhhCCc-eEEEecc
Confidence            55679999999999999 8887554

>PF06902 Fer4_19: Divergent 4Fe-4S mono-cluster; InterPro: IPR010693 This entry represents bacterial ferredoxins such Ferredoxin-1, -2 and -soy from Streptomyces griseolus and Ferredoxin fas2 from Rhodococcus fascians, plus several bacterial hypothetical proteins that contain three highly conserved cysteine residues

Probab=87.86  E-value=0.11  Score=31.55  Aligned_cols=56  Identities=20%  Similarity=0.256  Sum_probs=33.1

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.++.+.|++=|.|+..-|. +......+         -+..+...=..-..-++.||.+||.+..
T Consensus         8 V~~d~~~C~hag~Cv~~~p~-VFd~~~~~---------~v~~d~a~~~~v~~~v~~CPSGAL~~~~   63 (64)
T PF06902_consen    8 VTWDRERCIHAGFCVRGAPE-VFDQDDEP---------WVSPDEASAEEVREAVDRCPSGALSYWD   63 (64)
T ss_pred             EEECcCcccchhhhhcCCCC-cccCCCCC---------cCCcCccCHHHHHHHHHcCCccCcEEee
Confidence            34577899999999998874 23222211         1111111112234678899999998743

These ferredoxins each bind a 3Fe-4S cluster. Ferredoxin-soy (SoyB) act as electron transport protein for the cytochrome P450-SOY system []. Ferredoxin-1 (SuaB) and Ferredoxin-2 (SubB) act as electron transport proteins for the herbicide-metabolising cytochrome P-450 SU1 and SU2 systems, respectively [, ]. Ferredoxin-fas2 also plays a role in electrontransfer, the fas operon encoding genes involved in cytokinin production and in host plant fasciation (leafy gall).

>PRK15055 anaerobic sulfite reductase subunit A; Provisional

Probab=87.83  E-value=0.17  Score=41.03  Aligned_cols=18  Identities=33%  Similarity=1.014  Sum_probs=15.7

Q ss_pred             ccccccchhhcHHhchhc
Q psy4925          57 GEERCIACKLCEAICPAQ   74 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~   74 (160)
                      ....|++||+|..+||.+
T Consensus       305 g~~~CvgCGrC~~~CP~~  322 (344)
T PRK15055        305 GYHMCVGCGRCDDRCPEY  322 (344)
T ss_pred             chhhCcCcCccccccCCC
Confidence            346799999999999986

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

Probab=86.52  E-value=0.22  Score=37.67  Aligned_cols=18  Identities=33%  Similarity=0.920  Sum_probs=15.7

Q ss_pred             cccccchhhcHHhchhcc
Q psy4925          58 EERCIACKLCEAICPAQA   75 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~   75 (160)
                      ...|+.||.|+.+||.+.
T Consensus       193 ~~~C~~Cg~C~~~CP~~I  210 (220)
T TIGR00384       193 VWRCTTCMNCSEVCPKGV  210 (220)
T ss_pred             CccCccccccccccCCCC
Confidence            457999999999999874

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.

>PRK05035 electron transport complex protein RnfC; Provisional

Probab=86.03  E-value=0.28  Score=43.35  Aligned_cols=21  Identities=38%  Similarity=0.985  Sum_probs=18.3

Q ss_pred             CccCCcCcccchhcccccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      ....|+.||.|+.+||.+.+.
T Consensus       368 ~e~~CI~CG~Cv~aCP~~llP  388 (695)
T PRK05035        368 PEQPCIRCGACADACPASLLP  388 (695)
T ss_pred             chhhcCCcccHHHHCCccchh
Confidence            456799999999999999774

>PRK08640 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed

Probab=86.00  E-value=0.29  Score=37.82  Aligned_cols=19  Identities=47%  Similarity=1.212  Sum_probs=16.2

Q ss_pred             CccCCcCcccchhcccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~a  114 (160)
                      +...|+.||.|..+||...
T Consensus       150 ~~~~CI~CG~C~saCP~~~  168 (249)
T PRK08640        150 ELSKCMTCGCCLEACPNVN  168 (249)
T ss_pred             hhhhccCcCcccccCCCCc
Confidence            4567999999999999774

>COG1140 NarY Nitrate reductase beta subunit [Energy production and conversion]

Probab=85.79  E-value=0.3  Score=39.97  Aligned_cols=55  Identities=20%  Similarity=0.513  Sum_probs=37.6

Q ss_pred             ccCccccccCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhccc
Q psy4925          45 FRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACP  111 (160)
Q Consensus        45 ~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP  111 (160)
                      ...+.+..-+.+|.++|.+...|++.||..-+-+...            ......|+.|.         .|.+.|-
T Consensus       200 iYKReEDGIVLiDQd~CRGwR~CvsgCPYKKvYfNwk------------sgKsEKCifCyPRiEaGqPtVCSeTCV  263 (513)
T COG1140         200 IYKREEDGIVLIDQDKCRGWRMCVSGCPYKKVYFNWK------------SGKSEKCIFCYPRIEAGQPTVCSETCV  263 (513)
T ss_pred             ccccccCceEEeecccccchhhhhcCCCcceeEeecc------------CCCcceeEEeccccccCCCccchhhhh
Confidence            3334455556689999999999999999876544332            13456799884         4666664

>PRK12576 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=85.54  E-value=0.34  Score=38.08  Aligned_cols=20  Identities=55%  Similarity=1.373  Sum_probs=16.9

Q ss_pred             CccCCcCcccchhccccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      +...|+.||.|..+||..+.
T Consensus       150 ~~~~CI~CG~C~~~CP~~~~  169 (279)
T PRK12576        150 KFAQCIWCGLCVSACPVVAI  169 (279)
T ss_pred             cchhCcccCcccccCCCccc
Confidence            44689999999999998754

>PRK12386 fumarate reductase iron-sulfur subunit; Provisional

Probab=85.21  E-value=0.34  Score=37.53  Aligned_cols=20  Identities=40%  Similarity=0.835  Sum_probs=16.3

Q ss_pred             CccCCcCcccchhccccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      ....|+.||.|.++||.-..
T Consensus       140 ~~~~CI~CG~C~s~CPv~~~  159 (251)
T PRK12386        140 EFRKCIECFLCQNVCHVVRD  159 (251)
T ss_pred             chhhcccCCcccCcCCcccc
Confidence            44569999999999996643

>PRK12575 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=84.33  E-value=1  Score=34.60  Aligned_cols=20  Identities=35%  Similarity=0.879  Sum_probs=16.3

Q ss_pred             CccCCcCcccchhccccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      ....|+.||.|..+||+-..
T Consensus       142 ~~~~CI~CG~C~s~CP~~~~  161 (235)
T PRK12575        142 GLYECILCACCSTACPSYWW  161 (235)
T ss_pred             hhhhCcccccccccccCccc
Confidence            44569999999999997644

>PRK12814 putative NADPH-dependent glutamate synthase small subunit; Provisional

Probab=83.41  E-value=0.59  Score=41.03  Aligned_cols=19  Identities=26%  Similarity=0.772  Sum_probs=15.8

Q ss_pred             cccCccCCcCcccchhccc
Q psy4925          93 YDIDMTKCIYCGFCQEACP  111 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP  111 (160)
                      +..|.++|+.||.|+.+|.
T Consensus       611 i~~D~~kCI~CgrCv~~C~  629 (652)
T PRK12814        611 IRFEREKCVDCGICVRTLE  629 (652)
T ss_pred             eEeccccccCchHHHHHHH
Confidence            5568999999999996663

>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit

Probab=83.35  E-value=0.51  Score=39.44  Aligned_cols=21  Identities=33%  Similarity=0.948  Sum_probs=17.7

Q ss_pred             cCccCCcCcccchhccccccc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      .....|+.||.|.++||.+.+
T Consensus       360 ~~~~~Ci~Cg~C~~vCP~~l~  380 (435)
T TIGR01945       360 SPEKPCIRCGKCVQVCPMNLL  380 (435)
T ss_pred             ccCCcCcCccchhhhCccchh
Confidence            355789999999999999854

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.

>PRK11168 glpC sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional

Probab=82.72  E-value=0.52  Score=38.54  Aligned_cols=22  Identities=36%  Similarity=0.936  Sum_probs=18.0

Q ss_pred             cCccCCcCcccchhcccccccc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      .....|+.||.|..+||+-.+.
T Consensus         4 ~~~~~Ci~Cg~C~~~CP~~~~~   25 (396)
T PRK11168          4 TSFDSCIKCTVCTTACPVARVN   25 (396)
T ss_pred             cchhhcCCCCCCCccCCCcccC
Confidence            3456799999999999988653

>PRK09853 putative selenate reductase subunit YgfK; Provisional

Probab=82.61  E-value=0.57  Score=43.15  Aligned_cols=20  Identities=30%  Similarity=0.903  Sum_probs=17.5

Q ss_pred             cCccCCcCc----ccchhcccccc
Q psy4925          95 IDMTKCIYC----GFCQEACPVDA  114 (160)
Q Consensus        95 ~~~~~C~~C----g~C~~~CP~~a  114 (160)
                      .+..+|.+|    |.|+++||.+|
T Consensus       883 ~~~~rC~~C~~~C~~C~~vCP~~A  906 (1019)
T PRK09853        883 QEAARCLECNYVCEKCVDVCPNRA  906 (1019)
T ss_pred             ccccccCCcccccchhhhhCCccc
Confidence            355689999    99999999999

>PRK12385 fumarate reductase iron-sulfur subunit; Provisional

Probab=82.60  E-value=0.4  Score=36.93  Aligned_cols=17  Identities=24%  Similarity=0.741  Sum_probs=15.1

Q ss_pred             ccccchhhcHHhchhcc
Q psy4925          59 ERCIACKLCEAICPAQA   75 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~   75 (160)
                      ..|+.|+.|..+||.+.
T Consensus       203 ~~C~~C~~C~~vCP~~I  219 (244)
T PRK12385        203 WSCTFVGYCSEVCPKHV  219 (244)
T ss_pred             hhCcCcccccccCCCCC
Confidence            48999999999999873

>PRK13552 frdB fumarate reductase iron-sulfur subunit; Provisional

Probab=82.44  E-value=0.48  Score=36.41  Aligned_cols=19  Identities=37%  Similarity=1.067  Sum_probs=15.5

Q ss_pred             CccCCcCcccchhcccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ....|+.||.|..+||.-.
T Consensus       147 ~~~~CI~Cg~C~saCP~~~  165 (239)
T PRK13552        147 ELDRCIECGCCVAACGTKQ  165 (239)
T ss_pred             chhhccccchhHhhCCCCc
Confidence            4456999999999999653

>TIGR00273 iron-sulfur cluster-binding protein

Probab=82.42  E-value=0.47  Score=39.64  Aligned_cols=19  Identities=47%  Similarity=1.130  Sum_probs=16.1

Q ss_pred             cCccCCcCcccchhccccc
Q psy4925          95 IDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~  113 (160)
                      .+...|+.||.|..+||+-
T Consensus       290 ~e~~~CIrCG~C~~~CPvy  308 (432)
T TIGR00273       290 REVLACIRCGACQNECPVY  308 (432)
T ss_pred             hhHhhCCCCCCccccCcch
Confidence            3567899999999999964

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.

>PLN00129 succinate dehydrogenase [ubiquinone] iron-sulfur subunit

Probab=81.90  E-value=0.54  Score=36.97  Aligned_cols=17  Identities=35%  Similarity=0.987  Sum_probs=14.5

Q ss_pred             cCCcCcccchhcccccc
Q psy4925          98 TKCIYCGFCQEACPVDA  114 (160)
Q Consensus        98 ~~C~~Cg~C~~~CP~~a  114 (160)
                      ..|+.||.|..+||.-.
T Consensus       187 ~~CI~CG~C~saCPv~~  203 (276)
T PLN00129        187 YECILCACCSTSCPSYW  203 (276)
T ss_pred             hhCccccccccccCCCc
Confidence            36999999999999653

>PRK05950 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed

Probab=81.25  E-value=0.48  Score=36.13  Aligned_cols=17  Identities=29%  Similarity=0.675  Sum_probs=15.1

Q ss_pred             ccccchhhcHHhchhcc
Q psy4925          59 ERCIACKLCEAICPAQA   75 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~   75 (160)
                      ..|+.||.|..+||.+.
T Consensus       198 ~~C~~Cg~C~~~CP~gi  214 (232)
T PRK05950        198 FRCHTIMNCVEVCPKGL  214 (232)
T ss_pred             ccCcCcCCcCccccCCC
Confidence            57999999999999864

>PTZ00305 NADH:ubiquinone oxidoreductase; Provisional

Probab=81.11  E-value=0.55  Score=37.14  Aligned_cols=20  Identities=20%  Similarity=0.472  Sum_probs=16.7

Q ss_pred             cccCccCCcCcccchhcccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPV  112 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~  112 (160)
                      +..+..+|+.|+.|+.+|..
T Consensus       207 i~~D~nKCIlCgRCVRaC~E  226 (297)
T PTZ00305        207 TRVVLNRCIHCTRCVRFLNE  226 (297)
T ss_pred             eeecCCcCcCccHHHHHHHH
Confidence            34578899999999999963

>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit

Probab=81.03  E-value=0.44  Score=39.44  Aligned_cols=26  Identities=19%  Similarity=0.478  Sum_probs=20.8

Q ss_pred             cCCCccccccchhhcHHhchhccccch
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .+.++.++|+.|+.|+.+||. |+...
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            455678899999999999997 56543

This model describes the alpha subunit of sulfite reductase.

>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]

Probab=80.68  E-value=0.81  Score=35.08  Aligned_cols=25  Identities=32%  Similarity=0.772  Sum_probs=21.2

Q ss_pred             cCcc-CCcCcccchhcccccccccCC
Q psy4925          95 IDMT-KCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        95 ~~~~-~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ++.+ .|++|+.|.+.||+.||....
T Consensus       186 l~qg~~C~G~~TC~A~CP~~ai~c~G  211 (247)
T COG1941         186 LEQGLPCMGCGTCAASCPSRAIPCRG  211 (247)
T ss_pred             ecCCCcccCchhhhccCCccCCcccC
Confidence            3444 799999999999999999874

>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]

Probab=80.19  E-value=0.99  Score=33.54  Aligned_cols=20  Identities=30%  Similarity=0.903  Sum_probs=17.0

Q ss_pred             CccCCcCcccchhccccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      ....|..||.|...||.+-.
T Consensus        37 ~l~~C~QCG~CT~sCPs~r~   56 (195)
T COG1150          37 YLEGCYQCGTCTGSCPSGRF   56 (195)
T ss_pred             hHhHhhccCcccCCCCCccc
Confidence            35669999999999999954

>PRK12577 succinate dehydrogenase iron-sulfur subunit; Provisional

Probab=80.18  E-value=0.6  Score=37.59  Aligned_cols=19  Identities=32%  Similarity=0.945  Sum_probs=15.7

Q ss_pred             ccCCcCcccchhccccccc
Q psy4925          97 MTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        97 ~~~C~~Cg~C~~~CP~~ai  115 (160)
                      ...|+.||.|..+||.-..
T Consensus       151 ~~~Ci~CG~C~s~CP~~~~  169 (329)
T PRK12577        151 TGNCILCGACYSECNAREV  169 (329)
T ss_pred             hhhCcccCcccccCCCCCc
Confidence            3469999999999997643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	160
2fug_9	182	Crystal Structure Of The Hydrophilic Domain Of Resp		7e-27
1fca_A	55	Structure Of The Ferredoxin From Clostridium Acidur		5e-05
1fdn_A	55	Refined Crystal Structure Of The 2[4fe-4s] Ferredox		1e-04

>pdb|2FUG|9 Chain 9, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 182

Iteration: 1
 Score =  115 bits (289), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 55/137 (40%), Positives = 79/137 (57%), Gaps = 6/137 (4%)
Query: 11  LTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAI 70
           L  + +   +   ++F +P T+ YP     L PRF G H L R+P+G E+CI C LC A 
Sbjct: 3   LKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAAA 62
Query: 71  CPAQAITIEAEER------ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFS 124
           CPA AI +E  E       + G R    Y+I+M +CI+CG C+EACP  AIV G +FE +
Sbjct: 63  CPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEMA 122
Query: 125 TESHEELLYNKEKLLSN 141
              + +L+Y KE +L +
Sbjct: 123 DYEYSDLVYGKEDMLVD 139

>pdb|1FCA|A Chain A, Structure Of The Ferredoxin From Clostridium Acidurici: Model At 1.8 Angstroms Resolution Length = 55

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 30/59 (50%), Gaps = 10/59 (16%)
Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
           E CI+C  CE  CP  AI          S+  +RY ID   CI CG C   CPVDA V+
Sbjct: 6   EACISCGACEPECPVDAI----------SQGGSRYVIDADTCIDCGACAGVCPVDAPVQ 54

>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 = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
            E CI+C  CE  CP  AI          S    RY ID   CI CG C   CPVDA V+
Sbjct: 5   NEACISCGACEPECPVNAI----------SSGDDRYVIDADTCIDCGACAGVCPVDAPVQ 54

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	160
3i9v_9	182	NADH-quinone oxidoreductase subunit 9; electron tr	1e-82
1xer_A	103	Ferredoxin; electron transport, iron-sulfur, dupli	1e-19
1xer_A	103	Ferredoxin; electron transport, iron-sulfur, dupli	2e-04
2fgo_A	82	Ferredoxin; allochromatium vinosum, [4Fe-4S] clust	2e-15
2zvs_A	85	Uncharacterized ferredoxin-like protein YFHL; elec	2e-15
3eun_A	82	Ferredoxin; electron transport, [4Fe-4S] cluster,	7e-15
1rgv_A	80	Ferredoxin; electron transport; 2.90A {Thauera aro	1e-14
1jb0_C	80	Photosystem I iron-sulfur center; membrane protein	2e-13
1jb0_C	80	Photosystem I iron-sulfur center; membrane protein	2e-05
2fdn_A	55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	4e-13
2fdn_A	55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	4e-05
1hfe_L	421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	3e-11
1hfe_L	421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	1e-05
1jnr_B	150	Adenylylsulfate reductase; oxidoreductase; HET: FA	3e-10
3c8y_A	574	Iron hydrogenase 1; dithiomethylether, H-cluster,	2e-09
3c8y_A	574	Iron hydrogenase 1; dithiomethylether, H-cluster,	7e-05
3gyx_B	166	Adenylylsulfate reductase; oxidoreductase; HET: FA	6e-09
1kqf_B	294	FDH-N beta S, formate dehydrogenase, nitrate-induc	1e-05
2ivf_B	352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	3e-05
1gte_A	1025	Dihydropyrimidine dehydrogenase; electron transfer	3e-05
2vpz_B	195	NRFC protein; oxidoreductase, molybdopterin guanin	4e-05
2vpz_B	195	NRFC protein; oxidoreductase, molybdopterin guanin	7e-05
7fd1_A	106	FD1, protein (7-Fe ferredoxin I); electron transpo	5e-05
2v2k_A	105	Ferredoxin; iron, transport, iron-sulfur, mycobact	6e-05
1q16_B	512	Respiratory nitrate reductase 1 beta chain; membra	7e-05
1q16_B	512	Respiratory nitrate reductase 1 beta chain; membra	1e-04
1h98_A	78	Ferredoxin; electron transport, thermophilic, iron	1e-04
1bc6_A	77	7-Fe ferredoxin; electron transport, iron-sulfur;	2e-04
2c42_A	1231	Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron,	3e-04
1dax_A	64	Ferredoxin I; electron transport, electron-transfe	3e-04
1ti6_B	274	Pyrogallol hydroxytransferase small subunit; molyb	3e-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 =  240 bits (614), Expect = 1e-82
 Identities = 55/157 (35%), Positives = 81/157 (51%), Gaps = 6/157 (3%)

Query: 10  FLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEA 69
            L  + +   +   ++F +P T+ YP     L PRF G H L R+P+G E+CI C LC A
Sbjct: 2   TLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAA 61

Query: 70  ICPAQAITIEAEERAD------GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEF 123
            CPA AI +E  E         G R    Y+I+M +CI+CG C+EACP  AIV G +FE 
Sbjct: 62  ACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEM 121

Query: 124 STESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
           +   + +L+Y KE +L +    + +           +
Sbjct: 122 ADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVK 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 = 77.6 bits (191), Expect = 1e-19
 Identities = 19/94 (20%), Positives = 29/94 (30%), Gaps = 7/94 (7%)

Query: 27  KEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADG 86
                +  P E   +         +       + CIA   C   CP        +     
Sbjct: 16  HSGHKVYGPVEPPXVLGIHGTIVGVD-----FDLCIADGSCINACPVNVFQWY-DTPGHP 69

Query: 87  SRRTTRYDIDMTKCIYCGFCQEACPVDAI-VEGP 119
           +       ++   CI+C  C   CPV AI V+ P
Sbjct: 70  ASEKKADPVNEQACIFCMACVNVCPVAAIDVKPP 103

>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A Length = 103

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 10/30 (33%), Positives = 12/30 (40%)

Query: 91  TRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
           T   +D   CI  G C  ACPV+       
Sbjct: 36  TIVGVDFDLCIADGSCINACPVNVFQWYDT 65

>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction potential, iron binding protein electron transport; 1.32A {Pseudomonas aeruginosa} Length = 82

 Score = 66.2 bits (162), Expect = 2e-15
 Identities = 26/86 (30%), Positives = 34/86 (39%), Gaps = 19/86 (22%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GFCQEACPV 112
           + CI C +CE  CP  AI+   E           Y ID   C  C        CQ+ CPV
Sbjct: 6   DDCINCDVCEPECPNGAISQGEE----------IYVIDPNLCTECVGHYDEPQCQQVCPV 55

Query: 113 DAIVEGPNFEFSTESHEELLYNKEKL 138
           D I          ES ++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 = 66.3 bits (162), Expect = 2e-15
 Identities = 28/93 (30%), Positives = 44/93 (47%), Gaps = 21/93 (22%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GFCQEACPV 112
           ++CI C +CE  CP +AI++              Y+I+  KC  C        CQ+ CP+
Sbjct: 6   KKCINCDMCEPECPNEAISMGDH----------IYEINSDKCTECVGHYETPTCQKVCPI 55

Query: 113 -DAIVEGPNFEFSTESHEELLYNKEKLLSNGDK 144
            + IV+ P      E+ E+L   K  L+ + DK
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 = 64.7 bits (158), Expect = 7e-15
 Identities = 30/91 (32%), Positives = 42/91 (46%), Gaps = 19/91 (20%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC-GF-----CQEACP 111
            + CI C +CE  CP  AI+   E           Y I+ + C  C G      C E CP
Sbjct: 5   TDECINCDVCEPECPNGAISQGDE----------TYVIEPSLCTECVGHYETSQCVEVCP 54

Query: 112 VDAIVEGPNFEFSTESHEELLYNKEKLLSNG 142
           VDAI++ P+ E   E+ +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 = 64.0 bits (156), Expect = 1e-14
 Identities = 27/86 (31%), Positives = 36/86 (41%), Gaps = 19/86 (22%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GFCQEACPV 112
           + C AC  C   CP +AIT               Y ID TKC  C        C+  CP 
Sbjct: 6   DDCTACDACVEECPNEAITPG----------DPIYVIDPTKCSECVGAFDEPQCRLVCPA 55

Query: 113 DAIVEGPNFEFSTESHEELLYNKEKL 138
           D I + P++    E+ EEL    ++L
Sbjct: 56  DCIPDNPDY---RETREELQEKYDRL 78

>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 = 61.0 bits (148), Expect = 2e-13
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 2/58 (3%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            + 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 = 40.2 bits (94), Expect = 2e-05
 Identities = 12/50 (24%), Positives = 19/50 (38%)

Query: 41 LSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRT 90
          + P    +          E C+ CK CE  CP   ++I     A+ +R  
Sbjct: 27 MVPWDGCKAGQIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSM 76

>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 = 59.2 bits (144), Expect = 4e-13
 Identities = 25/60 (41%), Positives = 29/60 (48%), Gaps = 10/60 (16%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 118
           E CI+C  CE  CP  AI+   +          RY ID   CI CG C   CPVDA V+ 
Sbjct: 6   EACISCGACEPECPVNAISSGDD----------RYVIDADTCIDCGACAGVCPVDAPVQA 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 = 38.4 bits (90), Expect = 4e-05
 Identities = 11/23 (47%), Positives = 14/23 (60%)

Query: 99  KCIYCGFCQEACPVDAIVEGPNF 121
            CI CG C+  CPV+AI  G + 
Sbjct: 7   ACISCGACEPECPVNAISSGDDR 29

>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 = 59.3 bits (144), Expect = 3e-11
 Identities = 24/87 (27%), Positives = 31/87 (35%), Gaps = 18/87 (20%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
           E +CI C  C   CP  AI         G          +  CI CG C   CP +AI E
Sbjct: 32  EAKCIGCDTCSQYCPTAAIF--------GEMGEPHSIPHIEACINCGQCLTHCPENAIYE 83

Query: 118 GPNFEFSTESHEELLYNKEKLLSNGDK 144
             ++        E+     K L +G  
Sbjct: 84  AQSW------VPEVE----KKLKDGKV 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 = 43.2 bits (102), Expect = 1e-05
 Identities = 13/35 (37%), Positives = 14/35 (40%)

Query: 95  IDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHE 129
           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 = 54.7 bits (131), Expect = 3e-10
 Identities = 21/101 (20%), Positives = 35/101 (34%), Gaps = 12/101 (11%)

Query: 58  EERCIACK-----LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
            E+C  CK      CE ICP   +T++ E+          Y+ +   C  C  C + CP 
Sbjct: 7   PEKCDGCKALERTACEYICPNDLMTLDKEKM-------KAYNREPDMCWECYSCVKMCPQ 59

Query: 113 DAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEIASNI 153
            AI      ++S      +       +    K+ +      
Sbjct: 60  GAIDVRGYVDYSPLGGACVPMRGTSDIMWTVKYRNGKVLRF 100

>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 = 54.3 bits (131), Expect = 2e-09
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 58  EERCIACKLCEAICPAQAIT--IEAEERADGSRRTTRYD--IDMTKCIYCGFCQEACPVD 113
             +C+ C  C   C     T  ++   +   +      +   D T C+ CG C  ACPV 
Sbjct: 144 RTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVA 203

Query: 114 AIVEGPNFEF 123
           A+ E  + + 
Sbjct: 204 ALSEKSHMDR 213

>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 = 40.9 bits (96), Expect = 7e-05
 Identities = 13/58 (22%), Positives = 19/58 (32%), Gaps = 7/58 (12%)

Query: 64  CKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF 121
            +  +   P        E       R+    +D TKC+ CG C  AC  +       F
Sbjct: 118 ARASKPFLPKDKTEYVDE-------RSKSLTVDRTKCLLCGRCVNACGKNTETYAMKF 168

>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas} Length = 166

 Score = 51.4 bits (122), Expect = 6e-09
 Identities = 19/94 (20%), Positives = 33/94 (35%), Gaps = 12/94 (12%)

Query: 58  EERCIACK-----LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
             +C  CK      C  ICP   + ++ EE          ++ +   C  C  C + CP 
Sbjct: 6   PSKCDGCKGGEKTACMYICPNDLMILDPEEMK-------AFNQEPEACWECYSCIKICPQ 58

Query: 113 DAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWE 146
            AI   P  +F+      +     + +    K+ 
Sbjct: 59  GAITARPYADFAPMGGTCIPLRGSEDIMWTIKFR 92

>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 = 42.9 bits (101), Expect = 1e-05
 Identities = 24/102 (23%), Positives = 35/102 (34%), Gaps = 26/102 (25%)

Query: 50  ALRRYPSG-----EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC- 103
           A+ +Y +G      E CI C  C A CP     +  E+              + KC  C 
Sbjct: 117 AIIQYANGIVDFQSENCIGCGYCIAGCPFNIPRLNKEDNR------------VYKCTLCV 164

Query: 104 -----GF---CQEACPVDAIVEGPNFEFSTESHEELLYNKEK 137
                G    C + CP  AI  G   E    + + +   K +
Sbjct: 165 DRVSVGQEPACVKTCPTGAIHFGTKKEMLELAEQRVAKLKAR 206

>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 = 41.9 bits (98), Expect = 3e-05
 Identities = 17/70 (24%), Positives = 21/70 (30%), Gaps = 21/70 (30%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GF---CQE 108
           +ERC   + C   CP +AI      +               KCI C      G    C  
Sbjct: 181 QERCKGHRHCVEACPYKAIYFNPVSQT------------SEKCILCYPRIEKGIANACNR 228

Query: 109 ACPVDAIVEG 118
            CP      G
Sbjct: 229 QCPGRVRAFG 238

>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 = 42.1 bits (99), Expect = 3e-05
 Identities = 17/63 (26%), Positives = 20/63 (31%), Gaps = 12/63 (19%)

Query: 58   EERCIACKLCEAICPA---QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
            EE CI C  C   C     QAI  + E         T        C  C  C   CP+  
Sbjct: 950  EEMCINCGKCYMTCNDSGYQAIQFDPE---------THLPTVTDTCTGCTLCLSVCPIID 1000

Query: 115  IVE 117
             + 
Sbjct: 1001 CIR 1003

>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 = 40.8 bits (96), Expect = 4e-05
 Identities = 16/68 (23%), Positives = 20/68 (29%), Gaps = 22/68 (32%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQE 108
            ++CIAC  C A CP  A  +                    KC +C           C E
Sbjct: 87  PKKCIACGACIAACPYDARYLHPAGYVS-------------KCTFCAHRLEKGKVPACVE 133

Query: 109 ACPVDAIV 116
            CP     
Sbjct: 134 TCPTYCRT 141

>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 = 40.0 bits (94), Expect = 7e-05
 Identities = 18/49 (36%), Positives = 20/49 (40%), Gaps = 9/49 (18%)

Query: 67  CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           C  +CP  A         DG        +D  KCI CG C  ACP DA 
Sbjct: 66  CVPVCPTGASYQ----TKDG-----LVLVDPKKCIACGACIAACPYDAR 105

>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 = 39.2 bits (92), Expect = 5e-05
 Identities = 17/61 (27%), Positives = 21/61 (34%), Gaps = 12/61 (19%)

Query: 59  ERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
           + CI CK   C  +CP      E               I   +CI C  C+  CP  AI 
Sbjct: 6   DNCIKCKYTDCVEVCPVDCFY-EGPNF---------LVIHPDECIDCALCEPECPAQAIF 55

Query: 117 E 117
            
Sbjct: 56  S 56

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis} Length = 105

 Score = 39.3 bits (92), Expect = 6e-05
 Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 12/60 (20%)

Query: 59  ERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
           E C+  K   C   CP   I        +G+R      I   +C+ CG C+  CPV+AI 
Sbjct: 6   EPCVDVKDKACIEECPVDCI-------YEGARM---LYIHPDECVDCGACEPVCPVEAIY 55

>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 = 40.8 bits (95), Expect = 7e-05
 Identities = 13/71 (18%), Positives = 21/71 (29%), Gaps = 21/71 (29%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQE 108
           +++C   ++C   CP + I    +                 KCI+C           C E
Sbjct: 214 QDKCRGWRMCITGCPYKKIYFNWKSGK------------SEKCIFCYPRIEAGQPTVCSE 261

Query: 109 ACPVDAIVEGP 119
            C       G 
Sbjct: 262 TCVGRIRYLGV 272

>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 = 40.0 bits (93), Expect = 1e-04
 Identities = 17/49 (34%), Positives = 18/49 (36%), Gaps = 8/49 (16%)

Query: 67  CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           C A CP+ AI    E   DG        ID  KC     C   CP   I
Sbjct: 192 CVATCPSGAIYKREE---DG-----IVLIDQDKCRGWRMCITGCPYKKI 232

>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 = 37.6 bits (88), Expect = 1e-04
 Identities = 22/60 (36%), Positives = 27/60 (45%), Gaps = 12/60 (20%)

Query: 59  ERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
           E CI  K   C  +CP + I        DG  +     I   +CI CG C  ACPV+AI 
Sbjct: 6   EPCIGVKDQSCVEVCPVECI-------YDGGDQFY---IHPEECIDCGACVPACPVNAIY 55

>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 = 37.6 bits (88), Expect = 2e-04
 Identities = 23/60 (38%), Positives = 27/60 (45%), Gaps = 12/60 (20%)

Query: 59  ERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
           E CI  K   C  +CP   I  E E++         Y ID   CI CG C+  CPV AI 
Sbjct: 6   EPCIGTKDASCVEVCPVDCIH-EGEDQ---------YYIDPDVCIDCGACEAVCPVSAIY 55

>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 = 39.4 bits (92), Expect = 3e-04
 Identities = 24/98 (24%), Positives = 33/98 (33%), Gaps = 29/98 (29%)

Query: 58  EERCIACKLCEAICPAQAI-----TIEAEERADGSRRTT------------RYDIDMTKC 100
            E CI C  C  +CP  AI       E    A  +                R  I+   C
Sbjct: 685 PENCIQCNQCAFVCPHSAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDC 744

Query: 101 IYCGFCQEACPV--DAIV----------EGPNFEFSTE 126
           + CG C + CP    A+V          + PN E++  
Sbjct: 745 MGCGNCADICPPKEKALVMQPLDTQRDAQVPNLEYAAR 782

>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 = 36.2 bits (84), Expect = 3e-04
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 6/58 (10%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           ++ CIAC+ C  I P  A  ++ E            +    + +      + CPV  I
Sbjct: 8   QDECIACESCVEIAP-GAFAMDPE---IEKAYVKDVEGASQEEVEE--AMDTCPVQCI 59

>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 = 38.7 bits (90), Expect = 3e-04
 Identities = 11/71 (15%), Positives = 13/71 (18%), Gaps = 25/71 (35%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG------------- 104
            E+    K     CP   +    EE                KC  C              
Sbjct: 96  PEKAKGKKELLDTCPYGVMYWNEEENV------------AQKCTMCAHLLDDESWAPKMP 143

Query: 105 FCQEACPVDAI 115
            C   C     
Sbjct: 144 RCAHNCGSFVY 154

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	160
3i9v_9	182	NADH-quinone oxidoreductase subunit 9; electron tr	99.83
3eun_A	82	Ferredoxin; electron transport, [4Fe-4S] cluster,	99.42
2fgo_A	82	Ferredoxin; allochromatium vinosum, [4Fe-4S] clust	99.39
1rgv_A	80	Ferredoxin; electron transport; 2.90A {Thauera aro	99.37
7fd1_A	106	FD1, protein (7-Fe ferredoxin I); electron transpo	99.36
2fdn_A	55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	99.35
1xer_A	103	Ferredoxin; electron transport, iron-sulfur, dupli	99.33
2zvs_A	85	Uncharacterized ferredoxin-like protein YFHL; elec	99.31
1dax_A	64	Ferredoxin I; electron transport, electron-transfe	99.31
1f2g_A	58	Ferredoxin II; electron transport, FDII desulfovib	99.31
1h98_A	78	Ferredoxin; electron transport, thermophilic, iron	99.31
1bc6_A	77	7-Fe ferredoxin; electron transport, iron-sulfur;	99.31
1jb0_C	80	Photosystem I iron-sulfur center; membrane protein	99.28
1dwl_A	59	Ferredoxin I; electron transfer, model, heteronucl	99.26
1rof_A	60	Ferredoxin; electron transport, iron-sulfur; NMR {	99.25
2v2k_A	105	Ferredoxin; iron, transport, iron-sulfur, mycobact	99.25
3gyx_B	166	Adenylylsulfate reductase; oxidoreductase; HET: FA	99.24
1jnr_B	150	Adenylylsulfate reductase; oxidoreductase; HET: FA	99.24
1iqz_A	81	Ferredoxin; iron-sulfer protein, ultlahigh resolut	99.16
1hfe_L	421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	99.15
1sj1_A	66	Ferredoxin; thermostability, iron-sulfur cluster,	99.06
3c8y_A	574	Iron hydrogenase 1; dithiomethylether, H-cluster,	99.02
2vpz_B	195	NRFC protein; oxidoreductase, molybdopterin guanin	98.96
2ivf_B	352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	98.93
2c42_A	1231	Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron,	98.86
1ti6_B	274	Pyrogallol hydroxytransferase small subunit; molyb	98.85
3i9v_3	783	NADH-quinone oxidoreductase subunit 3; electron tr	98.84
2ivf_B	352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	98.84
2vpz_B	195	NRFC protein; oxidoreductase, molybdopterin guanin	98.84
1q16_B	512	Respiratory nitrate reductase 1 beta chain; membra	98.81
1kqf_B	294	FDH-N beta S, formate dehydrogenase, nitrate-induc	98.79
1h0h_B	214	Formate dehydrogenase (small subunit); tungsten se	98.78
1gte_A	1025	Dihydropyrimidine dehydrogenase; electron transfer	98.76
1kqf_B	294	FDH-N beta S, formate dehydrogenase, nitrate-induc	98.74
1ti6_B	274	Pyrogallol hydroxytransferase small subunit; molyb	98.74
3mm5_B	366	Sulfite reductase, dissimilatory-type subunit BET;	98.72
1q16_B	512	Respiratory nitrate reductase 1 beta chain; membra	98.66
2wdq_B	238	Succinate dehydrogenase iron-sulfur subunit; succi	98.61
3or1_B	386	Sulfite reductase beta; dissimilatory sulfite redu	98.58
1h0h_B	214	Formate dehydrogenase (small subunit); tungsten se	98.58
1kf6_B	243	Fumarate reductase iron-sulfur protein; respiratio	98.48
3vr8_B	282	Iron-sulfur subunit of succinate dehydrogenase; me	98.45
2bs2_B	241	Quinol-fumarate reductase iron-sulfur subunit B; 2	98.4
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	98.38
2h88_B	252	Succinate dehydrogenase IP subunit; complex II, me	98.38
3mm5_A	418	Sulfite reductase, dissimilatory-type subunit ALP;	98.28
2gmh_A	584	Electron transfer flavoprotein-ubiquinone oxidored	98.25
3cf4_A	807	Acetyl-COA decarboxylase/synthase alpha subunit; m	98.11
3or1_A	437	Sulfite reductase alpha; dissimilatory sulfite red	97.95
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	97.74
2v2k_A	105	Ferredoxin; iron, transport, iron-sulfur, mycobact	97.36
1rgv_A	80	Ferredoxin; electron transport; 2.90A {Thauera aro	97.18
2fgo_A	82	Ferredoxin; allochromatium vinosum, [4Fe-4S] clust	97.15
2fdn_A	55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	97.13
3eun_A	82	Ferredoxin; electron transport, [4Fe-4S] cluster,	97.12
1bc6_A	77	7-Fe ferredoxin; electron transport, iron-sulfur;	97.08
2zvs_A	85	Uncharacterized ferredoxin-like protein YFHL; elec	97.06
1jb0_C	80	Photosystem I iron-sulfur center; membrane protein	97.04
1h98_A	78	Ferredoxin; electron transport, thermophilic, iron	97.04
1xer_A	103	Ferredoxin; electron transport, iron-sulfur, dupli	97.03
1dax_A	64	Ferredoxin I; electron transport, electron-transfe	97.02
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	97.01
7fd1_A	106	FD1, protein (7-Fe ferredoxin I); electron transpo	96.97
1dwl_A	59	Ferredoxin I; electron transfer, model, heteronucl	96.96
1f2g_A	58	Ferredoxin II; electron transport, FDII desulfovib	96.89
1rof_A	60	Ferredoxin; electron transport, iron-sulfur; NMR {	96.85
1iqz_A	81	Ferredoxin; iron-sulfer protein, ultlahigh resolut	96.68
1jnr_B	150	Adenylylsulfate reductase; oxidoreductase; HET: FA	96.63
3i9v_9	182	NADH-quinone oxidoreductase subunit 9; electron tr	96.49
1sj1_A	66	Ferredoxin; thermostability, iron-sulfur cluster,	96.34
3gyx_B	166	Adenylylsulfate reductase; oxidoreductase; HET: FA	95.97
1hfe_L	421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	95.48
3c8y_A	574	Iron hydrogenase 1; dithiomethylether, H-cluster,	95.41
3or1_B	386	Sulfite reductase beta; dissimilatory sulfite redu	95.4
3mm5_B	366	Sulfite reductase, dissimilatory-type subunit BET;	95.14
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	95.11
3i9v_3	783	NADH-quinone oxidoreductase subunit 3; electron tr	94.97
2c42_A	1231	Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron,	94.74
2gmh_A	584	Electron transfer flavoprotein-ubiquinone oxidored	94.46
3mm5_A	418	Sulfite reductase, dissimilatory-type subunit ALP;	93.26
2wdq_B	238	Succinate dehydrogenase iron-sulfur subunit; succi	92.8
1kf6_B	243	Fumarate reductase iron-sulfur protein; respiratio	92.11
2h88_B	252	Succinate dehydrogenase IP subunit; complex II, me	91.07
2bs2_B	241	Quinol-fumarate reductase iron-sulfur subunit B; 2	90.21
3or1_A	437	Sulfite reductase alpha; dissimilatory sulfite red	90.0
1gte_A	1025	Dihydropyrimidine dehydrogenase; electron transfer	89.95
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	88.87
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	88.09
3cf4_A	807	Acetyl-COA decarboxylase/synthase alpha subunit; m	83.14
3vr8_B	282	Iron-sulfur subunit of succinate dehydrogenase; me	81.82

>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=99.83  E-value=4e-21  Score=139.66  Aligned_cols=140  Identities=39%  Similarity=0.757  Sum_probs=90.7

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhcCC---
Q psy4925          10 FLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADG---   86 (160)
Q Consensus        10 ~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~---   86 (160)
                      -+.+++.|++++++++|+.+.+..||.......+++++...+.....+.++|++|+.|+.+||++++.+........   
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            35778999999999999999999999988888889988888877777889999999999999999987654321110   


Q ss_pred             ---CccccccccCccCCcCcccchhcccccccccCCcccccccchhhhhccHHHHhccCCcchHHH
Q psy4925          87 ---SRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESEI  149 (160)
Q Consensus        87 ---~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (160)
                         ........++...|++||.|+++||++||.+...++........+.+....++.....|....
T Consensus        82 ~~~~~~~~~~~~~~~~C~~C~~C~~~CP~~Ai~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~  147 (182)
T 3i9v_9           82 SAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTKPQR  147 (182)
T ss_dssp             SSSSCEEEEEEEETTTCCCCCHHHHHCSSSCEEECSCCCCCBSSGGGGEECHHHHBTTCCSCHHHH
T ss_pred             cccccccceeecCCCcCcChhChhhhCCccceEecCccccccccHHHHhcCHHHHhhcccCCCCCe
Confidence               111123356788999999999999999999999999988889888888887777666655443

>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=99.42  E-value=4.2e-14  Score=89.98  Aligned_cols=55  Identities=42%  Similarity=0.893  Sum_probs=46.6

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc------cchhcccccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg------~C~~~CP~~ai~~~~~  120 (160)
                      ++.++|++|+.|+.+||.+++.+.+.          ...++...|++|+      .|+.+||++||.+...
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~----------~~~i~~~~C~~C~~~~~~~~C~~~CP~~Ai~~~~~   63 (82)
T 3eun_A            3 MITDECINCDVCEPECPNGAISQGDE----------TYVIEPSLCTECVGHYETSQCVEVCPVDAIIKDPS   63 (82)
T ss_dssp             EECTTCCCCCTTGGGCTTCCEEECSS----------SEEECGGGCCTTTTTCSSCHHHHHCTTCCEEECGG
T ss_pred             EeCCCCcCccchHHHCChhheEcCCC----------ceEEchhhcCCCCCCCCccHHHHhCCccceEEcCC
Confidence            35688999999999999999976432          3457788999999      9999999999998765

>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction potential, iron binding protein electron transport; 1.32A {Pseudomonas aeruginosa}

Probab=99.39  E-value=1.5e-13  Score=87.34  Aligned_cols=67  Identities=37%  Similarity=0.687  Sum_probs=51.3

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc------cchhcccccccccCCcccccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPNFEFSTESHE  129 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg------~C~~~CP~~ai~~~~~~~~~~~~~~  129 (160)
                      ++.++|++|+.|+.+||+++|.+...          ...++...|++|+      .|+.+||++||.+.....   .+..
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~C~~~~~~~~C~~~CP~~Ai~~~~~~~---~~~~   69 (82)
T 2fgo_A            3 KITDDCINCDVCEPECPNGAISQGEE----------IYVIDPNLCTECVGHYDEPQCQQVCPVDCIPLDDANV---ESKD   69 (82)
T ss_dssp             CCCTTCCCCCTTGGGCTTCCEEECSS----------SEEECTTTCCTTTTTCSSCHHHHHCTTCCCCBCTTSC---CCHH
T ss_pred             eeCCCCCChhhHHHHCChhccCCCCC----------eEEEEchhCccCCCcCCCCHhHhhCCcccEEccCCCc---cCHH
Confidence            35678999999999999999986432          3457888999999      999999999999866432   3445


Q ss_pred             hhhccH
Q psy4925         130 ELLYNK  135 (160)
Q Consensus       130 ~~~~~~  135 (160)
                      +++...
T Consensus        70 ~~~~~~   75 (82)
T 2fgo_A           70 QLMEKY   75 (82)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            554433

>1rgv_A Ferredoxin; electron transport; 2.90A {Thauera aromatica} SCOP: d.58.1.1

Probab=99.37  E-value=1.3e-13  Score=87.28  Aligned_cols=55  Identities=40%  Similarity=0.788  Sum_probs=46.3

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc------cchhcccccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG------FCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg------~C~~~CP~~ai~~~~~  120 (160)
                      ++.++|++|+.|+.+||.++|.+...          ...++...|++|+      .|+++||++||.+...
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~C~~~~~~~~C~~~CP~~Ai~~~~~   63 (80)
T 1rgv_A            3 YINDDCTACDACVEECPNEAITPGDP----------IYVIDPTKCSECVGAFDEPQCRLVCPADCIPDNPD   63 (80)
T ss_dssp             CCCSCCCCCCTTTTTCTTCCEECCSS----------SCEECTTTCCTTTTTCSSCHHHHHCSSCCCCBCGG
T ss_pred             EeCCCCcChhhHHHHcChhccCcCCC----------eeEEcchhCcCCCCcCCccHHHHhcCcccEEecCC
Confidence            35678999999999999999986532          2456788999999      9999999999998664

>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=99.36  E-value=2.1e-13  Score=90.81  Aligned_cols=55  Identities=29%  Similarity=0.710  Sum_probs=46.6

Q ss_pred             Cccccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++.++|++|+  .|+.+||.+++.....          ...++...|++||.|+.+||++||.+...
T Consensus         3 ~~~~~C~~C~~~~C~~~CP~~ai~~~~~----------~~~i~~~~C~~Cg~C~~~CP~~ai~~~~~   59 (106)
T 7fd1_A            3 VVTDNCIKCKYTDCVEVCPVDCFYEGPN----------FLVIHPDECIDCALCEPECPAQAIFSEDE   59 (106)
T ss_dssp             EECGGGTTTCCCHHHHHCTTCCEEECSS----------CEEECTTTCCCCCTTGGGCTTCCEEEGGG
T ss_pred             ECccccCCccCcHHHHHcCccceEcCCC----------cEEECcccCCChhhhHHhCCChhhhcccc
Confidence            3568899999  9999999999876542          34577888999999999999999998765

>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=99.35  E-value=1.9e-13  Score=80.28  Aligned_cols=50  Identities=50%  Similarity=1.058  Sum_probs=42.4

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      .++|++||.|+.+||.+++.+.+.          ...++...|++||.|+.+||++||.+
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            467999999999999999876532          23567889999999999999999875

>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A

Probab=99.33  E-value=2.4e-13  Score=89.84  Aligned_cols=65  Identities=25%  Similarity=0.479  Sum_probs=47.6

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.++.++|++||.|+.+||.+++.+....... ........++...|++||.|+.+||++||.+..
T Consensus        38 ~~id~~~C~~Cg~C~~~CP~~ai~~~~~~~~~-~~~~~~~~~~~~~C~~Cg~C~~~CP~~Ai~~~~  102 (103)
T 1xer_A           38 VGVDFDLCIADGSCINACPVNVFQWYDTPGHP-ASEKKADPVNEQACIFCMACVNVCPVAAIDVKP  102 (103)
T ss_dssp             EEEETTTCCCCCHHHHHCTTCCCEEEECTTCS-SCSEEEECTTGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             EEEehhhCCChhhHHHHcCccCeecccccCcc-ccccceeecCcccccChhhHHHhccccceEecC
Confidence            44678899999999999999998765421110 011112346778899999999999999998743

>2zvs_A Uncharacterized ferredoxin-like protein YFHL; electron transport, [4Fe-4S] clusters, iron-SULF clusters, reduction potential; 1.65A {Escherichia coli}

Probab=99.31  E-value=2.3e-13  Score=87.13  Aligned_cols=54  Identities=39%  Similarity=0.981  Sum_probs=45.9

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc------cchhcccc-cccccCCc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG------FCQEACPV-DAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg------~C~~~CP~-~ai~~~~~  120 (160)
                      +.++|++|+.|+.+||++++.+...          ...++...|++||      .|+.+||+ +||.+...
T Consensus         4 ~~~~C~~C~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~C~~~~~~~~C~~~CP~~~Ai~~~~~   64 (85)
T 2zvs_A            4 ITKKCINCDMCEPECPNEAISMGDH----------IYEINSDKCTECVGHYETPTCQKVCPIPNTIVKDPA   64 (85)
T ss_dssp             ECTTCCCCCTTTTTCTTCCEECCSS----------SCEECGGGCCTTTTTCSSCHHHHHCSSCCEEECTTS
T ss_pred             eCCcCcChhHHHHHCchhccCcCCC----------ceEEeChhccCCCCcCCccHhhHhCcCCCCEEecCC
Confidence            4678999999999999999986532          3456788999999      99999999 99998765

>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=99.31  E-value=1.6e-13  Score=83.06  Aligned_cols=59  Identities=24%  Similarity=0.410  Sum_probs=43.1

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .++.++|++||.|+.+|| +++.++...   +.  ......+...|+.|+.|+++||++||.+..
T Consensus         5 ~id~~~C~~Cg~C~~~CP-~~~~~~~~~---~~--~~~~~~~~~~C~~C~~C~~~CP~~Ai~~~~   63 (64)
T 1dax_A            5 YVDQDECIACESCVEIAP-GAFAMDPEI---EK--AYVKDVEGASQEEVEEAMDTCPVQCIHWED   63 (64)
T ss_dssp             EECSTTCCSCCHHHHHCT-TTEEECSSS---SS--EEECCGGGSCHHHHHHHHHHSSSCCEECCC
T ss_pred             EEccccCCCchHHHHhCC-ccEeEcCCC---CE--EEEecCCCcchhHHHHHHHhCCHhhEeeec
Confidence            356789999999999999 887654320   11  001123367899999999999999998753

>1f2g_A Ferredoxin II; electron transport, FDII desulfovibrio gigas; NMR {Desulfovibrio gigas} SCOP: d.58.1.4 PDB: 1fxd_A

Probab=99.31  E-value=4.2e-13  Score=79.51  Aligned_cols=54  Identities=24%  Similarity=0.547  Sum_probs=41.3

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccC--ccCCcCcccchhccccccccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDID--MTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~--~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      +.++ ++|++||.|+.+||. ++.+++.+    .    ...++  ...|+.|+.|+++||++||.+
T Consensus         2 v~id-~~C~~C~~C~~~CP~-~~~~~~~~----~----~~~~~~~~~~C~~C~~C~~~CP~~Ai~~   57 (58)
T 1f2g_A            2 IEVN-DDCMACEACVEICPD-VFEMNEEG----D----KAVVINPDSDLDCVEEAIDSCPAEAIVR   57 (58)
T ss_dssp             CBCT-TTCCCCCHHHHHCTT-TEEECSSS----S----SEEESCTTCCSTHHHHHHHTCSSCCCBC
T ss_pred             cEEC-CcCccchHHHHhCCc-cEEECCCC----c----EEEeCCCccchHHHHHHHhhCChhhEEe
Confidence            3467 899999999999998 56543221    0    12344  678999999999999999986

>1h98_A Ferredoxin; electron transport, thermophilic, iron-sulfur, azotobacter, hydrogen bonds, stability, high resolution; 1.64A {Thermus aquaticus} SCOP: d.58.1.2

Probab=99.31  E-value=3.6e-13  Score=84.79  Aligned_cols=54  Identities=35%  Similarity=0.720  Sum_probs=45.2

Q ss_pred             Cccccccc--hhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          56 SGEERCIA--CKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        56 ~~~~~Ci~--Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ++.++|++  ||.|+.+||.++|.+...          ...++...|++||.|+.+||++||.+..
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            35678999  999999999999976531          3456788999999999999999999644

>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=99.31  E-value=3.7e-13  Score=84.46  Aligned_cols=53  Identities=38%  Similarity=0.784  Sum_probs=44.7

Q ss_pred             ccccccc--hhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          57 GEERCIA--CKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        57 ~~~~Ci~--Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.++|++  ||.|+.+||+++|.+...          ...++...|++||.|+.+||++||.+..
T Consensus         4 ~~~~C~~c~C~~C~~~Cp~~ai~~~~~----------~~~~~~~~C~~Cg~C~~~CP~~ai~~~~   58 (77)
T 1bc6_A            4 ITEPCIGTKDASCVEVCPVDCIHEGED----------QYYIDPDVCIDCGACEAVCPVSAIYHED   58 (77)
T ss_dssp             CCSTTTTCCCCSSTTTCTTCCEEECSS----------SEEECTTTCCSCCSHHHHSGGGSSEETT
T ss_pred             eCccCCCCCcchhHHhcccccEEeCCC----------cEEECcccCcCccCCHhhcCccceEecC
Confidence            5678999  899999999999976431          3456888999999999999999999753

>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=99.28  E-value=4.6e-13  Score=84.30  Aligned_cols=62  Identities=21%  Similarity=0.515  Sum_probs=44.9

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ++.++|++||.|+.+||++++.+......  .........+...|++||.|+.+||++||.+..
T Consensus         5 ~~~~~C~~Cg~C~~~CP~~a~~~~~~~~~--~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~   66 (80)
T 1jb0_C            5 KIYDTCIGCTQCVRACPTDVLEMVPWDGC--KAGQIASSPRTEDCVGCKRCETACPTDFLSIRV   66 (80)
T ss_dssp             EEETTCCCCCHHHHHCTTCCCEEEECSSS--TTSEEEECTTGGGCCCCCHHHHHCCSSSCSEEE
T ss_pred             ccCCcCcChhHHHHHCCcccccccccccc--cccccccCCCCCcCcCcCChhhhCCCCccEeee
Confidence            45678999999999999999876542110  000111235677899999999999999998744

>1dwl_A Ferredoxin I; electron transfer, model, heteronuclear docking; HET: HEC; NMR {Desulfomicrobium norvegicum} SCOP: i.4.1.1

Probab=99.26  E-value=9.3e-13  Score=77.98  Aligned_cols=53  Identities=28%  Similarity=0.609  Sum_probs=40.6

Q ss_pred             CccccccchhhcHHhchhccccc-hhhhhcCCCccccccc-cCccCCcCcccchhccccccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITI-EAEERADGSRRTTRYD-IDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~-~~~~~~~~~~~~~~~~-~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ++.++|++||.|+.+||. ++.+ ...+    .    ... ++...|+.|+.|+.+||++||.+
T Consensus         4 i~~~~C~~C~~C~~~Cp~-~~~~~~~~~----~----~~~~~~~~~c~~C~~C~~~CP~~Ai~~   58 (59)
T 1dwl_A            4 IDHEECIGCESCVELCPE-VFAMIDGEE----K----AMVTAPDSTAECAQDAIDACPVEAISK   58 (59)
T ss_dssp             ESSCCCSSCCGGGGTSTT-TEEEEECSS----C----EEESCTTCCCGGGGTGGGGSTTCCEEE
T ss_pred             EChhhCcChhHHHHHCCH-HheecCCCC----c----EEEecChhhhhHHHHHHHhCCHhhEEc
Confidence            467889999999999994 6655 2211    0    112 47788999999999999999975

>1rof_A Ferredoxin; electron transport, iron-sulfur; NMR {Thermotoga maritima} SCOP: d.58.1.4 PDB: 1vjw_A

Probab=99.25  E-value=9.4e-13  Score=78.23  Aligned_cols=55  Identities=22%  Similarity=0.523  Sum_probs=41.3

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCcccccccc-CccCCcCcccchhcccccccccC
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDI-DMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~-~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      .++.++|++||.|+.+||. ++.++..+.        .... +...|..|+.|+.+||++||.+.
T Consensus         4 ~i~~~~C~~C~~C~~~Cp~-~~~~~~~~~--------~~~~~~~~~c~~C~~C~~~CP~~Ai~~~   59 (60)
T 1rof_A            4 RVDADACIGCGVCENLCPD-VFQLGDDGK--------AKVLQPETDLPCAKDAADSCPTGAISVE   59 (60)
T ss_dssp             EECTTTCCSCCSSTTTCTT-TBCCCSSSC--------CCBSCSSCCSTTHHHHHHHCTTCCEECC
T ss_pred             EEchhhCCCChHHHHhCcH-HHeECCCCC--------EeecCchhhHHHHHHHHHhCCHhHEEEe
Confidence            3567889999999999996 565432210        1122 36789999999999999999874

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis}

Probab=99.25  E-value=1.5e-12  Score=86.39  Aligned_cols=55  Identities=33%  Similarity=0.662  Sum_probs=45.6

Q ss_pred             Cccccccch--hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIAC--KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~C--g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++.++|++|  +.|+.+||.++|.+...          ...++...|++||.|+.+||++||.+...
T Consensus         3 i~~~~C~~C~c~~C~~~CP~~ai~~~~~----------~~~~~~~~C~~Cg~C~~~CP~~Ai~~~~~   59 (105)
T 2v2k_A            3 VIAEPCVDVKDKACIEECPVDCIYEGAR----------MLYIHPDECVDCGACEPVCPVEAIYYEDD   59 (105)
T ss_dssp             EECGGGTTTCCCHHHHHCTTCCEEECSS----------CEEECTTTCCCCCCSGGGCTTCCEEEGGG
T ss_pred             EecccCCCCCcChhhhhcCccccCcCCC----------cEEEeCCcCcchhhHHHhCCccCEEecCC
Confidence            356789988  99999999999976432          24568889999999999999999997643

>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas}

Probab=99.24  E-value=1.4e-12  Score=93.66  Aligned_cols=60  Identities=28%  Similarity=0.680  Sum_probs=48.9

Q ss_pred             Cccccccchh-----hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCccc
Q psy4925          56 SGEERCIACK-----LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        56 ~~~~~Ci~Cg-----~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~  122 (160)
                      ++.++|++|+     .|+.+||.+++.++....       ..+.++...|++||.|+.+||++||.+.....
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     999999999998765421       12346778999999999999999999876643

>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=99.24  E-value=1.9e-12  Score=91.55  Aligned_cols=60  Identities=32%  Similarity=0.677  Sum_probs=48.6

Q ss_pred             Cccccccchh-----hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCccc
Q psy4925          56 SGEERCIACK-----LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        56 ~~~~~Ci~Cg-----~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~  122 (160)
                      ++.++|++|+     .|+.+||.++|.++..+.       ..+.++...|++||.|+.+||++||.+....+
T Consensus         5 vd~~~C~~C~~~~~~~C~~~CP~~ai~~~~~~~-------~~~~id~~~C~~Cg~Cv~~CP~~AI~~~~~~~   69 (150)
T 1jnr_B            5 VNPEKCDGCKALERTACEYICPNDLMTLDKEKM-------KAYNREPDMCWECYSCVKMCPQGAIDVRGYVD   69 (150)
T ss_dssp             ECTTTCCSCCSSSSCHHHHHCTTSCEEEETTTT-------EEEESCGGGCCCCCHHHHHCTTCCEEECCCTT
T ss_pred             ECcccCCCCCCcccccchhhcCccCeEEecCCc-------eeeeeCcccCcCHhHHHHhCCccceEecCcch
Confidence            4678999999     999999999998754321       02457788999999999999999999876543

>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=99.16  E-value=1.7e-12  Score=82.18  Aligned_cols=65  Identities=22%  Similarity=0.276  Sum_probs=43.2

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCC--ccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGS--RRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~--~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .++.++|++||.|+.+|| +++.++..+.....  .......++...|..|+.|+++||++||.+...
T Consensus         5 ~vd~~~CigCg~C~~~CP-~~~~~~~~g~~~~~~~~~~~~~~~~~~~c~~C~~C~~~CP~~AI~~~~~   71 (81)
T 1iqz_A            5 IVDKETCIACGACGAAAP-DIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADE   71 (81)
T ss_dssp             EECTTTCCCCSHHHHHCT-TTEEECTTSCEEETTTTTSSCSCCCGGGHHHHHHHHHHCTTCCEEEESS
T ss_pred             EEecccCcccChhhHhCc-hheeeCCCCeEEEeccCccccCCCCHHHHHHHHHHHHhCCHhHEEEecC
Confidence            457889999999999999 67665422110000  000001223567999999999999999998653

>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=99.15  E-value=1.6e-11  Score=100.01  Aligned_cols=59  Identities=37%  Similarity=0.729  Sum_probs=47.2

Q ss_pred             cCCCccccccchhhcHHhchhccccchhhhhcCCCcccccccc-CccCCcCcccchhccccccccc-CCc
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDI-DMTKCIYCGFCQEACPVDAIVE-GPN  120 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~-~~~~C~~Cg~C~~~CP~~ai~~-~~~  120 (160)
                      .+.++.++|++|+.|+.+||.++|......         ...+ +...|+.||.|+.+||++||.. ...
T Consensus        27 ~i~~d~~kCi~Cg~C~~~CP~~ai~~~~~~---------~~~i~~~~~C~~Cg~C~~~CP~~Ai~~~~~~   87 (421)
T 1hfe_L           27 FVQIDEAKCIGCDTCSQYCPTAAIFGEMGE---------PHSIPHIEACINCGQCLTHCPENAIYEAQSW   87 (421)
T ss_dssp             SEEECTTTCCCCCHHHHHCTTCCCBCCTTS---------CCBCCCGGGCCCCCTTGGGCTTCCEEESCCC
T ss_pred             eEEECcccCCCccHHHHhcCcCceeccccc---------ceeecChhhCCchhhHHHhhCcCCccccccc
Confidence            345678899999999999999998754321         1234 7889999999999999999998 443

>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=99.06  E-value=5.4e-12  Score=76.30  Aligned_cols=55  Identities=24%  Similarity=0.425  Sum_probs=39.6

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccC----c-cCCcCcccchhcccccccccC
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDID----M-TKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~----~-~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      .++.++|++||.|+.+||. ++.++..+    .    ....+    . ..|..|+.|+++||++||.+.
T Consensus         5 ~id~~~C~~C~~C~~~Cp~-~~~~~~~~----~----~~~~~~~~~~~~~c~~c~~C~~~CP~~Ai~~~   64 (66)
T 1sj1_A            5 SVDQDTCIGDAICASLCPD-VFEMNDEG----K----AQPKVEVIEDEELYNCAKEAMEACPVSAITIE   64 (66)
T ss_dssp             EECTTTCCCCCHHHHHCTT-TEEECTTS----C----EEESCSCBCCHHHHHHHHHHHHHCTTCCEEEE
T ss_pred             EECcccCcCchHHHHhCCc-eEEECCCC----c----eeecccCCCcHHHHHHHHHHHhhCCHhhEEEe
Confidence            3567899999999999995 77654221    1    11122    2 347889999999999999864

>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=99.02  E-value=2.8e-11  Score=101.98  Aligned_cols=68  Identities=25%  Similarity=0.520  Sum_probs=49.2

Q ss_pred             cCCCccccccchhhcHHhchh----ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          53 RYPSGEERCIACKLCEAICPA----QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~----~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .+.+|.++|++|+.|+.+||.    +++.+...+............++...|++||.|+.+||++||.+...
T Consensus       139 ~i~~d~~kCi~Cg~Cv~~CP~~~~~~ai~~~~~g~~~~i~~~~~~~i~~~~Ci~Cg~Cv~~CP~gAi~~~~~  210 (574)
T 3c8y_A          139 SLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSH  210 (574)
T ss_dssp             SEEEEGGGCCCCCHHHHHHHHHHSCCCSEEEEETTEEEEESGGGCCGGGSSCCCCCHHHHHCSSTTEEECCC
T ss_pred             cceeCcccCcCCCCccchhCchhcCCceeeccCCccceecccccceechhhCCcchhHHHhhccCCcccccc
Confidence            445678999999999999998    78876543211000001123467789999999999999999998764

>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=98.96  E-value=8.8e-11  Score=86.34  Aligned_cols=51  Identities=33%  Similarity=0.787  Sum_probs=27.5

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCC
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGP  119 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~  119 (160)
                      ++.++|++|+.|+.+||.+|+.+....            . ...|++|+         +|+++||++||.+..
T Consensus        85 id~~~CigC~~C~~~CP~~Ai~~~~~~------------~-~~kC~~C~~~~~~g~~p~Cv~~CP~~Ai~~g~  144 (195)
T 2vpz_B           85 VDPKKCIACGACIAACPYDARYLHPAG------------Y-VSKCTFCAHRLEKGKVPACVETCPTYCRTFGD  144 (195)
T ss_dssp             ECTTTCCCCCHHHHHCTTCCCEECTTS------------S-EECCCTTHHHHHTTCCCHHHHSCTTCCEEEEE
T ss_pred             ecCCCCCCcChhHhhCCCCCeEECCCC------------C-CccCcCcchHHhCCCCchhHhhCCcccEEEec
Confidence            345556666666666665555443211            0 34566665         466666666666543

>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=98.93  E-value=1.5e-10  Score=92.01  Aligned_cols=57  Identities=32%  Similarity=0.528  Sum_probs=38.7

Q ss_pred             CCccccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          55 PSGEERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        55 ~~~~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .++...|++|+  .|+.+||++|+.......        .+.++...|++|+.|+.+||++||.+..
T Consensus       145 ~~~~~~C~~C~~~~Cv~~CP~gAi~~~~~~g--------~v~id~~kCigCg~Cv~aCP~~Ai~~~~  203 (352)
T 2ivf_B          145 FYLARMCNHCTNPACLAACPTGAIYKREDNG--------IVLVDQERCKGHRHCVEACPYKAIYFNP  203 (352)
T ss_dssp             EEEEECCCCCSSCHHHHHCTTCCEEECTTTC--------CEEECTTTCCCCCHHHHHCTTCCEEEET
T ss_pred             EECCCCCcCcCCccccccCCCCceeecCCCC--------eEEechhhcCCchHHHhhcCccceeccc
Confidence            35567899999  899999999886543211        2345666677777777777777766543

>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=98.86  E-value=3.8e-10  Score=101.98  Aligned_cols=67  Identities=33%  Similarity=0.639  Sum_probs=48.1

Q ss_pred             CCccccccchhhcHHhchhccccch---hhhh---cCC--C------c---cccccccCccCCcCcccchhcccc--ccc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIE---AEER---ADG--S------R---RTTRYDIDMTKCIYCGFCQEACPV--DAI  115 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~---~~~~---~~~--~------~---~~~~~~~~~~~C~~Cg~C~~~CP~--~ai  115 (160)
                      .++.++||+|+.|+.+||.++|...   ....   ..+  .      .   ......++...|++||.|+.+||+  +||
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            4678999999999999999998753   1100   000  0      0   001234678899999999999999  999


Q ss_pred             ccCCcc
Q psy4925         116 VEGPNF  121 (160)
Q Consensus       116 ~~~~~~  121 (160)
                      .+....
T Consensus       762 ~~~~~~  767 (1231)
T 2c42_A          762 VMQPLD  767 (1231)
T ss_dssp             EEEEGG
T ss_pred             EEecch
Confidence            987653

>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=98.85  E-value=3.9e-10  Score=86.95  Aligned_cols=54  Identities=19%  Similarity=0.213  Sum_probs=38.7

Q ss_pred             CCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc----------c---cchhcccccccccCCc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC----------G---FCQEACPVDAIVEGPN  120 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C----------g---~C~~~CP~~ai~~~~~  120 (160)
                      .++.++|++|+.|+.+||.+++.+...            ......|++|          |   +|+++||++||.+...
T Consensus        93 ~id~~~CigC~~C~~~CP~~Ai~~~~~------------~~~~~kC~~C~~r~~~~~~~G~~P~Cv~~CP~~Ai~~~~~  159 (274)
T 1ti6_B           93 LIDPEKAKGKKELLDTCPYGVMYWNEE------------ENVAQKCTMCAHLLDDESWAPKMPRCAHNCGSFVYEFLKT  159 (274)
T ss_dssp             EECTTTTTTCGGGGGGCSSCCCEEETT------------TTEEECCCTTHHHHTCTTCTTCSCHHHHHCSSCCEEEEEE
T ss_pred             EechhhccchHHHHhhCccCCeEEEcc------------cCccccCCCchhhhhhhccCCCCcchhhhCCcCceEEcCC
Confidence            456677888888888888887765432            1245678888          7   8888888888887554

>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=98.84  E-value=5.2e-10  Score=97.33  Aligned_cols=65  Identities=18%  Similarity=0.209  Sum_probs=43.3

Q ss_pred             ccCCCccccccchhhcHHhchh----ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          52 RRYPSGEERCIACKLCEAICPA----QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~----~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.+.+|.++||+|++|+++||.    +++.+...+  .....  ........|++||+|+++||++||..+..
T Consensus       172 p~i~~d~~~CI~C~~Cv~~C~~~~~~~~i~~~~~g--~~~~i--~~~~~~~~C~~CG~Cv~vCP~gAl~~~~~  240 (783)
T 3i9v_3          172 PFVILDRERCIHCKRCVRYFEEVPGDEVLDFIERG--VHTFI--GTMDFGLPSGFSGNITDICPVGALLDLTA  240 (783)
T ss_dssp             TTEEECTTTCCCCCHHHHHHHHTTCCCCCEECSCT--TSCCE--ECSSTTCCSTTTTTHHHHCSSSSEEEGGG
T ss_pred             ccEEEchhhCCCccHHHHHhhhhcCCceeeeecCC--CccEE--ccCCCCCCCccchhHHhhcccCceecccc
Confidence            3455688999999999999954    455433221  11100  11122347999999999999999987653

>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=98.84  E-value=4.2e-10  Score=89.51  Aligned_cols=57  Identities=28%  Similarity=0.519  Sum_probs=46.4

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCCccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~~~~  122 (160)
                      +.++.++|++|+.|+.+||.+|+.+...            ......|++|+         +|+++||++||.+....+
T Consensus       177 v~id~~kCigCg~Cv~aCP~~Ai~~~~~------------~~~~~kC~~C~~r~~~g~~paCv~~CP~~Ai~~g~~~d  242 (352)
T 2ivf_B          177 VLVDQERCKGHRHCVEACPYKAIYFNPV------------SQTSEKCILCYPRIEKGIANACNRQCPGRVRAFGYLDD  242 (352)
T ss_dssp             EEECTTTCCCCCHHHHHCTTCCEEEETT------------TTEEEECCTTHHHHTTTBCCHHHHTCTTCCEEEEETTC
T ss_pred             EEechhhcCCchHHHhhcCccceecccc------------cccccccCCCcchhhcCCCChHHHhcCccceeccccch
Confidence            3456789999999999999999976542            24567899996         999999999999876533

>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=98.84  E-value=5.6e-10  Score=81.99  Aligned_cols=57  Identities=35%  Similarity=0.709  Sum_probs=47.7

Q ss_pred             CCccccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          55 PSGEERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        55 ~~~~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .++...|++|+  .|+.+||++|+.....+         .+.++...|++|+.|+.+||++||.+...
T Consensus        52 ~~~~~~C~~C~~p~C~~~CP~gAi~~~~~g---------~~~id~~~CigC~~C~~~CP~~Ai~~~~~  110 (195)
T 2vpz_B           52 EFRPEQCLHCENPPCVPVCPTGASYQTKDG---------LVLVDPKKCIACGACIAACPYDARYLHPA  110 (195)
T ss_dssp             EEEEEECCCCSSCTTTTTCSSSCEEECTTS---------CEEECTTTCCCCCHHHHHCTTCCCEECTT
T ss_pred             EECcccCcCccCcHHHHhcCCCceeccccc---------ceeecCCCCCCcChhHhhCCCCCeEECCC
Confidence            34578999999  79999999999765322         45678899999999999999999988665

>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=98.81  E-value=1e-09  Score=90.91  Aligned_cols=58  Identities=29%  Similarity=0.428  Sum_probs=43.2

Q ss_pred             CCCccccccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.++.+.|++|+  .|+.+||.+||.......        ...++...|++|+.|+.+||++||.+..
T Consensus       177 i~~~~~~C~~C~~~~Cv~aCP~gAI~~~~~~g--------~v~id~~kCigCg~Cv~~CP~~AI~~~~  236 (512)
T 1q16_B          177 MMYLPRLCEHCLNPACVATCPSGAIYKREEDG--------IVLIDQDKCRGWRMCITGCPYKKIYFNW  236 (512)
T ss_dssp             CEEEEECCCCCSSCHHHHTCTTCCEEEETTTC--------CEEECTTTCCCCCCHHHHCTTCCEEEET
T ss_pred             EEecCccCcCCCCchhhhhCCcCcEEeecCCC--------eEEECHHHCCCchHHHhhCCccceeccc
Confidence            335678899999  699999999887642110        3457778888888888888888887654

>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=98.79  E-value=8.4e-10  Score=85.89  Aligned_cols=53  Identities=30%  Similarity=0.721  Sum_probs=33.9

Q ss_pred             ccccccchh--hcHHhchh-ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          57 GEERCIACK--LCEAICPA-QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        57 ~~~~Ci~Cg--~Cv~~CP~-~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      +.+.|++|+  .|+.+||+ +|+.....+         .+.++.+.|++||.|+.+||++||.+.
T Consensus        96 ~~~~C~~C~~~~C~~~CP~~gAi~~~~~g---------~v~id~~~CigCg~C~~~CP~~ai~~~  151 (294)
T 1kqf_B           96 RKDGCMHCEDPGCLKACPSAGAIIQYANG---------IVDFQSENCIGCGYCIAGCPFNIPRLN  151 (294)
T ss_dssp             EEESCCCBSSCHHHHHCCSTTSEEEETTS---------CEEECGGGCCCCCHHHHHCTTCCCEEE
T ss_pred             CcccCCCcCChhhhhhCCccCcccccccc---------ceEeCcccCCCcchhhhcCCCCCcEec
Confidence            356677777  67777777 777543221         344566667777777777777766653

>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=98.78  E-value=7e-10  Score=82.61  Aligned_cols=57  Identities=26%  Similarity=0.366  Sum_probs=42.2

Q ss_pred             CCCcccccc--chhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc------c---cchhcccccccccCCccc
Q psy4925          54 YPSGEERCI--ACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------G---FCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        54 ~~~~~~~Ci--~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C------g---~C~~~CP~~ai~~~~~~~  122 (160)
                      +.++.++|+  +|+.|+.+||.+|+.+...            ..+...|++|      |   .|+++||++||.+....+
T Consensus       101 v~id~~~C~~~~C~~C~~~CP~~Ai~~~~~------------~~~~~kC~~C~~~~~~G~~p~Cv~~CP~~Ai~~~~~~~  168 (214)
T 1h0h_B          101 VLFTPKTKDLEDYESVISACPYDVPRKVAE------------SNQMAKCDMCIDRITNGLRPACVTSCPTGAMNFGDLSE  168 (214)
T ss_dssp             EEECGGGGGCSCHHHHHHHCTTCCCEECTT------------SSCEECCCTTHHHHTTTCCCHHHHHCSSSCEEEEEHHH
T ss_pred             EEEeHHHCccccccHHHHhcCCCCeEecCC------------CcccCcCCCCcchhhcCCChhHHHhcCcccEEEccHHH
Confidence            345677888  8888888888888876432            1245679999      5   899999999998865433

>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=98.76  E-value=1.1e-09  Score=97.77  Aligned_cols=58  Identities=31%  Similarity=0.635  Sum_probs=46.0

Q ss_pred             CCCccccccchhhcHHhchh---ccccchhhhhcCCCccccccccCccCCcCcccchhcccc-cccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPA---QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~---~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~-~ai~~~~~  120 (160)
                      +.++.++|++||.|+.+||.   +++.++....        ...++ ..|++||.|+.+||+ +||.+...
T Consensus       946 ~~id~~~C~~Cg~C~~~CP~~~~~ai~~~~~~~--------~~~~~-~~C~~Cg~C~~~CP~~~Ai~~~~~ 1007 (1025)
T 1gte_A          946 AVIDEEMCINCGKCYMTCNDSGYQAIQFDPETH--------LPTVT-DTCTGCTLCLSVCPIIDCIRMVSR 1007 (1025)
T ss_dssp             EEECTTTCCCCCHHHHHHHHHSCSCEEECTTTC--------CEEEC-TTCCCCCHHHHHCSSTTTEEEEEC
T ss_pred             EEEEcccCcccCHHHHhcCccccCCEEEeCCCc--------eEEeC-ccCCChhHHHhhCCCCCCEEEecC
Confidence            34678899999999999997   8887654321        22345 789999999999999 99998665

>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=98.74  E-value=1.2e-09  Score=84.95  Aligned_cols=55  Identities=33%  Similarity=0.671  Sum_probs=44.6

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCCc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPN  120 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~~  120 (160)
                      +.++.++|++|+.|+.+||.+++.++...            .....|+.|+         .|+.+||++||.+.+.
T Consensus       126 v~id~~~CigCg~C~~~CP~~ai~~~~~~------------~~~~kC~~C~~r~~~g~~p~Cv~~CP~~Ai~~~~~  189 (294)
T 1kqf_B          126 VDFQSENCIGCGYCIAGCPFNIPRLNKED------------NRVYKCTLCVDRVSVGQEPACVKTCPTGAIHFGTK  189 (294)
T ss_dssp             EEECGGGCCCCCHHHHHCTTCCCEEETTT------------TEEECCCTTHHHHTTTCCCHHHHHCTTSCEEEEEH
T ss_pred             eEeCcccCCCcchhhhcCCCCCcEecCCC------------CCeeeCCCccchhhcCccHHHHHhCCcCcEEEecH
Confidence            34578899999999999999999865421            2235799998         9999999999998654

>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=98.74  E-value=2.7e-09  Score=82.23  Aligned_cols=54  Identities=19%  Similarity=0.211  Sum_probs=44.8

Q ss_pred             Cccccccchhh--cHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          56 SGEERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        56 ~~~~~Ci~Cg~--Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +....|++|+.  |+.+||+ |+.....+         .+.++...|++|+.|+.+||++||.+..
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            34678999998  9999999 98754322         4568889999999999999999998754

>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=98.72  E-value=2.2e-09  Score=85.88  Aligned_cols=57  Identities=26%  Similarity=0.625  Sum_probs=45.5

Q ss_pred             CCCccccc-cch--hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          54 YPSGEERC-IAC--KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        54 ~~~~~~~C-i~C--g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      +.+|.+.| ..|  +.|+.+||++||..+...        ..+.++...|+.||.|+.+||++||...
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            34566666 456  999999999999876321        1567899999999999999999998754

>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=98.66  E-value=3.1e-09  Score=87.99  Aligned_cols=54  Identities=24%  Similarity=0.534  Sum_probs=44.6

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~  119 (160)
                      ..++.++|++|+.|+.+||.+||.+....            .....|++|+         +|+++||++||.+..
T Consensus       210 v~id~~kCigCg~Cv~~CP~~AI~~~~~~------------~~~~kC~~Cg~ri~~G~~P~Cv~~CP~~Ai~~g~  272 (512)
T 1q16_B          210 VLIDQDKCRGWRMCITGCPYKKIYFNWKS------------GKSEKCIFCYPRIEAGQPTVCSETCVGRIRYLGV  272 (512)
T ss_dssp             EEECTTTCCCCCCHHHHCTTCCEEEETTT------------TEEEECCTTHHHHTTTCCCHHHHTCTTCCEEEEE
T ss_pred             EEECHHHCCCchHHHhhCCccceecccCC------------CCcccCcCCCchhhcCCCCceEeeCchhhhhccc
Confidence            34678899999999999999999765421            2367899999         999999999988763

>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=98.61  E-value=3.2e-09  Score=80.01  Aligned_cols=65  Identities=22%  Similarity=0.360  Sum_probs=41.2

Q ss_pred             ccCCCccccccchhhcHHhchhccccch-hh----------hhcCCCc-----ccccc--ccCccCCcCcccchhccccc
Q psy4925          52 RRYPSGEERCIACKLCEAICPAQAITIE-AE----------ERADGSR-----RTTRY--DIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~-~~----------~~~~~~~-----~~~~~--~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      ..+..+.++||+||.|+.+||..++... ..          .......     ....+  ..+.+.|+.||+|+++||++
T Consensus       140 ~~~~~~~~~Ci~Cg~C~~~CP~~~~~~~~~~~p~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~vCP~g  219 (238)
T 2wdq_B          140 REKLDGLYECILCACCSTSCPSFWWNPDKFIGPAGLLAAYRFLIDSRDTETDSRLDGLSDAFSVFRCHSIMNCVSVCPKG  219 (238)
T ss_dssp             HHTTTTTTTCCCCCTTGGGCHHHHHCTTTSCCHHHHHHHHHHHTCTTCCCHHHHHHTTCSTTTTTTCCCCCHHHHHCTTC
T ss_pred             HHHHhccccccccCCchhhCcCCccCCCCCCCHHHHHHHHHHHhCCcccchHHHHHHHhccCCCCcCcccchhhhhcCCC
Confidence            3455678899999999999998754211 00          0001100     00011  13667899999999999999


Q ss_pred             ccc
Q psy4925         114 AIV  116 (160)
Q Consensus       114 ai~  116 (160)
                      +..
T Consensus       220 i~~  222 (238)
T 2wdq_B          220 LNP  222 (238)
T ss_dssp             CCH
T ss_pred             CCH
Confidence            654

>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=98.58  E-value=1.6e-08  Score=81.47  Aligned_cols=64  Identities=27%  Similarity=0.567  Sum_probs=45.5

Q ss_pred             CCCcccccc---chhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCI---ACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci---~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.+|.+.|.   .|+.|+.+||++||....... ++. ....+.++...|+.||.|+.+||++||....
T Consensus       211 p~id~e~~~~~Ce~~~cv~~CPt~AI~~~~~~~-~g~-~~~~v~id~~~Ci~Cg~C~~~CP~~Ai~~~~  277 (386)
T 3or1_B          211 PMIDHENLAELCEIPLAVAACPTAAVKPITAEV-NGQ-KVKSVAINNDRCMYCGNCYTMCPALPLSDGT  277 (386)
T ss_dssp             CCCCTTTHHHHCCHHHHHHHCTTCCEEEEEEEE-TTE-EEEEEEECTTTCCCCCHHHHHCTTCCCCCTT
T ss_pred             ceechhhhcccccchhhhhhCchhhcccccccc-CCc-cccccccCCCcCCccccHHHhCcHhhCcCCC
Confidence            345666665   358999999999998743100 000 0114678999999999999999999987654

>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=98.58  E-value=6.9e-09  Score=77.21  Aligned_cols=57  Identities=18%  Similarity=0.163  Sum_probs=46.0

Q ss_pred             Cccccccchhh--cHHhch---hccccchhhhhcCCCccccccccCccCCc--CcccchhcccccccccCCc
Q psy4925          56 SGEERCIACKL--CEAICP---AQAITIEAEERADGSRRTTRYDIDMTKCI--YCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~--Cv~~CP---~~~i~~~~~~~~~~~~~~~~~~~~~~~C~--~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +....|++|+.  |+.+||   ++|+......        ..+.++...|+  +|+.|+.+||++||.+...
T Consensus        67 ~~~~~C~~C~~p~C~~~CP~~~~gAi~~~~~~--------g~v~id~~~C~~~~C~~C~~~CP~~Ai~~~~~  130 (214)
T 1h0h_B           67 FFPDQCRHCIAPPCKATADMEDESAIIHDDAT--------GCVLFTPKTKDLEDYESVISACPYDVPRKVAE  130 (214)
T ss_dssp             EEEECCCCCSSCHHHHHHTTTCTTSEEECTTT--------CCEEECGGGGGCSCHHHHHHHCTTCCCEECTT
T ss_pred             ecCCcCcCcCCchhhccCCccccccEEecCCC--------CeEEEeHHHCccccccHHHHhcCCCCeEecCC
Confidence            45678999996  999999   9998764311        14567888999  9999999999999987643

>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=98.48  E-value=2.2e-08  Score=75.61  Aligned_cols=61  Identities=30%  Similarity=0.644  Sum_probs=39.3

Q ss_pred             CCCccccccchhhcHHhchhccccchhhh--------h--cCCC-----cccccc--ccCccCCcCcccchhcccccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEE--------R--ADGS-----RRTTRY--DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~--------~--~~~~-----~~~~~~--~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ...+.++||+||.|+.+||..++.....+        +  .+..     .....+  ..+.+.|+.||+|+++||++.
T Consensus       141 ~~~~~~~Ci~Cg~C~~~CP~~~~~~~~~gP~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~vCP~gi  218 (243)
T 1kf6_B          141 KYHQFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHV  218 (243)
T ss_dssp             TTGGGGCCCCCCHHHHHCHHHHHCTTSCCHHHHHHHHHHHTCTTCCCTHHHHHHHHSTTTGGGCCCCCHHHHHCTTCC
T ss_pred             HhhhhhhccccCccccccCCCcccCCCCCHHHHHHHHHHhhCccccchHHHHHHHhccCCcccCcccCCcchhCCCCC
Confidence            44678899999999999998765311000        0  0000     001111  135678999999999999984

>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=98.45  E-value=5.7e-09  Score=80.59  Aligned_cols=104  Identities=15%  Similarity=0.223  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCcccCCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhhc-----
Q psy4925          10 FLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERA-----   84 (160)
Q Consensus        10 ~~~~~~~g~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~-----   84 (160)
                      .+++|+.++..++..+-+-..|+.................+......+...||.||.|..+||+....-+....+     
T Consensus       131 VikDLvvD~~~f~~~~~~v~p~l~~~~~~~~~~~~~~qs~~~~~~~~~~~~CI~CG~C~~aCP~~~~~~~~~lGP~~li~  210 (282)
T 3vr8_B          131 VIKDLVPDMNLFYAQYASIQPWLQKKTKINLGEKQQYQSIKEQEKLDGLYECILCACCSASCPSYWWNADKYLGPAVLMQ  210 (282)
T ss_pred             eeeccccccHHHHHHHHHHhhhcCCCCCCCCCchhcccCHHHHHHHHhhhhCcccCcCcccCCceeccCCcCCCHHHHHH
Confidence            455666666666655444333433221111111111111221112223567999999999999754321100000     


Q ss_pred             ------CCCc-----ccccc--ccCccCCcCcccchhccccc
Q psy4925          85 ------DGSR-----RTTRY--DIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        85 ------~~~~-----~~~~~--~~~~~~C~~Cg~C~~~CP~~  113 (160)
                            +...     +...+  ....+.|+.||.|..+||.+
T Consensus       211 a~r~~~d~rd~~~~erl~~l~~~~~l~~C~~Cg~C~~vCP~g  252 (282)
T 3vr8_B          211 AYRWIIDSRDDSAAERLARMQDGFSAFKCHTIMNCTKTCPKH  252 (282)
T ss_pred             HHHHHhCCcccchHHHHHHHhhcCCcccChhhCCccccCcCC
Confidence                  0000     00001  13567899999999999988

>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=98.40  E-value=3.2e-08  Score=74.65  Aligned_cols=59  Identities=24%  Similarity=0.456  Sum_probs=37.8

Q ss_pred             CccccccchhhcHHhchhccccchhhhhc----------CC-Cc-----ccccc--ccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERA----------DG-SR-----RTTRY--DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~----------~~-~~-----~~~~~--~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      .+.++||+||.|+.+||+.++.....+..          +. ..     +....  ....+.|+.||.|+++||.+.
T Consensus       146 ~~~~~Ci~Cg~C~~~CP~~~~~~~~~~p~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~C~~Cg~C~~vCP~~i  222 (241)
T 2bs2_B          146 FELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMIDPHDERTDEDYYELIGDDDGVFGCMTLLACHDVCPKNL  222 (241)
T ss_dssp             HHHHTCCCCCHHHHTCHHHHHCTTCCHHHHHHHHHHHHTCTTCCCCHHHHHHHHCSTTTGGGCCCCCHHHHHCTTCC
T ss_pred             hhhhhhhccCcCcccCCCCccCCCCCCHHHHHHHHHHhhCccccccHHHHHHHHhcccCcccCcccChhhHhcCCCC
Confidence            35678999999999999986531110000          00 00     00011  345678999999999999994

>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=98.38  E-value=3.6e-08  Score=75.57  Aligned_cols=60  Identities=18%  Similarity=0.371  Sum_probs=45.2

Q ss_pred             cchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc---ccccccchhhh
Q psy4925          62 IACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN---FEFSTESHEEL  131 (160)
Q Consensus        62 i~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~---~~~~~~~~~~~  131 (160)
                      ++|+.|+.+||.++|.++...         ....+...|++|+.|+.+|| +||.+...   +.+..++.|.+
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            789999999999999876521         23457788999999999999 88876554   44555554443

>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=98.38  E-value=2.6e-08  Score=75.80  Aligned_cols=63  Identities=22%  Similarity=0.459  Sum_probs=39.1

Q ss_pred             ccCCCccccccchhhcHHhchhccccchhh-h----------hcCCCc-----ccccc--ccCccCCcCcccchhccccc
Q psy4925          52 RRYPSGEERCIACKLCEAICPAQAITIEAE-E----------RADGSR-----RTTRY--DIDMTKCIYCGFCQEACPVD  113 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~-~----------~~~~~~-----~~~~~--~~~~~~C~~Cg~C~~~CP~~  113 (160)
                      .....+...||+||.|+.+||+.++.-+.. +          ..++..     +...+  ....+.|+.||.|+++||.+
T Consensus       149 ~~~~~~~~~Ci~CG~C~~~CP~~~~~~~~~lgP~~~~~~~r~~~~~r~~~~~~r~~~~~~~~~~~~C~~Cg~C~~~CP~~  228 (252)
T 2h88_B          149 RQKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWMIDSRDDYTEERLAQLQDPFSLYRCHTIMNCTRTCPKG  228 (252)
T ss_dssp             HHTTTTTTTCCCCCTTGGGCHHHHHHTTTCCHHHHHHHHHHHHTCTTCCCHHHHHHTTCSTTTTTTCCCCCHHHHHCTTC
T ss_pred             HHHhHhHHhchhhCcchhhCCCCccCCCCcCCHHHHHHHHHHhhCCcccchHHHHHHHhcccCCCcCccccchhhhcCCC
Confidence            334456789999999999999875321000 0          001100     00111  13567899999999999999


Q ss_pred             c
Q psy4925         114 A  114 (160)
Q Consensus       114 a  114 (160)
                      .
T Consensus       229 i  229 (252)
T 2h88_B          229 L  229 (252)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=98.28  E-value=1.8e-07  Score=75.92  Aligned_cols=44  Identities=23%  Similarity=0.462  Sum_probs=37.4

Q ss_pred             hhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          64 CKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        64 Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      |+.|+.+||++||..+..          .+.++...|+.||.|+.+||++++..
T Consensus       260 ~~~cv~~CPt~Ai~~~~~----------~~~id~~~Ci~Cg~Ci~~CP~~~~~~  303 (418)
T 3mm5_A          260 ENEVVKLCPTGAIKWDGK----------ELTIDNRECVRCMHCINKMPKALKPG  303 (418)
T ss_dssp             HHHTGGGCTTCCEEECSS----------CEEECTTTCCCCCHHHHHCTTTEECC
T ss_pred             CccccccCCccccccCCc----------eeEEChhhcCccChhHHhCcHhhccC
Confidence            589999999999987632          56789999999999999999976543

>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=98.25  E-value=1.7e-07  Score=79.02  Aligned_cols=57  Identities=23%  Similarity=0.355  Sum_probs=43.9

Q ss_pred             ccccc------cchhhcHHhchhccccc-hhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          57 GEERC------IACKLCEAICPAQAITI-EAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        57 ~~~~C------i~Cg~Cv~~CP~~~i~~-~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      |.+.|      ..|+.|+.+||++++.+ +...   +.  ...+.++...|++||.|..+||+++|...
T Consensus       508 d~~~~~~~~~~~~~~~c~~~CPa~~~~~~~~~~---~~--~~~~~i~~~~Ci~C~~C~~~cp~~~i~~~  571 (584)
T 2gmh_A          508 DDSVPVNRNLSIYDGPEQRFCPAGVYEFVPLEQ---GD--GFRLQINAQNCVHCKTCDIKDPSQNINWV  571 (584)
T ss_dssp             STTHHHHTHHHHHCCTHHHHCTTCCEEEEECSS---TT--CEEEEECGGGCCCCCHHHHHCTTCCEEEC
T ss_pred             CcccchhhchhhhcchhhhcCChhhEEEeecCC---CC--ceEEEEeCCCCcCCCCchhhCCCCCceeE
Confidence            55678      77899999999999976 3111   00  01467899999999999999999999653

>3cf4_A Acetyl-COA decarboxylase/synthase alpha subunit; methanomicrobia, iron-nikel-sulfur, 4Fe-NI-4S, oxidoreductas; 2.00A {Methanosarcina barkeri}

Probab=98.11  E-value=1.6e-07  Score=81.79  Aligned_cols=59  Identities=22%  Similarity=0.473  Sum_probs=39.1

Q ss_pred             ccccccchhhcHHhchhccccchhh-hhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAE-ERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~-~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      +.++|++||.|+.+||+++...... ....+.  ...+..+.+.|+.||+|+.+||++++..
T Consensus       413 ~~~~Ci~CG~C~~~CP~~~~~~~il~~~~~G~--~~~~~~~~~~Ci~Cg~C~~vCP~ga~~~  472 (807)
T 3cf4_A          413 MVAKCADCGACLLACPEEIDIPEAMGFAKKGD--FSYFEEIHDTCIGCRRCEQVCKKEIPIL  472 (807)
T ss_dssp             HHHHCCCCCHHHHHCTTCCCHHHHHHHHHTTC--THHHHHHHHHCCCCCHHHHHCTTCCCHH
T ss_pred             hHHhCCCCCchhhhCCCCCchHHHHHHHHcCC--hhhhhhchhhccchhhHHHhCCCCCChH
Confidence            4678999999999999875321110 000111  0112334578999999999999998664

>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=97.95  E-value=9.5e-07  Score=71.89  Aligned_cols=41  Identities=24%  Similarity=0.509  Sum_probs=35.4

Q ss_pred             hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccc
Q psy4925          65 KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        65 g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai  115 (160)
                      +.|+.+||++||..+..          .+.++...|+.||.|+.+||+.+.
T Consensus       278 ~~vv~~CPt~ai~~~~~----------~l~Id~~~C~~Cg~Ci~~CP~al~  318 (437)
T 3or1_A          278 AEVVGLCPTGCMTYESG----------TLSIDNKNCTRCMHCINTMPRALK  318 (437)
T ss_dssp             HHTTTTCTTCCEEEETT----------EEEECGGGCCCCSHHHHHCTTTEE
T ss_pred             hhhhccCcHHheeecCC----------EEEEccccCCchhhhHhhCcHhhc
Confidence            57999999999998642          577899999999999999998654

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=97.74  E-value=7.1e-06  Score=69.58  Aligned_cols=55  Identities=31%  Similarity=0.696  Sum_probs=39.9

Q ss_pred             Ccccccc--chh-hcHHhchhc-----cccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          56 SGEERCI--ACK-LCEAICPAQ-----AITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        56 ~~~~~Ci--~Cg-~Cv~~CP~~-----~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      ++.++|.  .|+ .|.+.||..     +|.++...        ....+....|++||.|+..||.+||.+.
T Consensus        11 ~~~~~c~~~~~~~~c~~~cp~~~~~~~~~~~~~~~--------~~~~i~~~~c~~~~~~~~~cp~~~i~i~   73 (608)
T 3j16_B           11 VSADKCKPKKCRQECKRSCPVVKTGKLCIEVTPTS--------KIAFISEILCIGCGICVKKCPFDAIQII   73 (608)
T ss_dssp             ECSSSCCHHHHCSHHHHHCHHHHHTCCSEEEETTT--------TEEEECTTTCCCCCHHHHHCSSCCEEEE
T ss_pred             EeccccCccccccchhhcCCCccCCceEEEEcCCC--------CceEEehhhccccccccccCCccceEEe
Confidence            4567786  587 799999952     33332111        1456788899999999999999998763

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis}

Probab=97.36  E-value=3.5e-05  Score=50.34  Aligned_cols=57  Identities=25%  Similarity=0.453  Sum_probs=34.8

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++.+.|++||.|+.+||++||.+.........   .....+..     ......||.+|+.+.+.
T Consensus        34 ~~~~~C~~Cg~C~~~CP~~Ai~~~~~~~~~~~---~~~~~d~~-----~~~~~~~~~ga~~~g~~   90 (105)
T 2v2k_A           34 IHPDECVDCGACEPVCPVEAIYYEDDVPDQWS---SYAQANAD-----FFAELGSPGGASKVGQT   90 (105)
T ss_dssp             ECTTTCCCCCCSGGGCTTCCEEEGGGCCGGGT---THHHHHHH-----TTTTTCCCSCHHHHCSC
T ss_pred             EeCCcCcchhhHHHhCCccCEEecCCChHHHH---HHHHhchH-----HHhhcCCCcceEEeecC
Confidence            46788999999999999999987643211100   00001111     01236789999888654

>1rgv_A Ferredoxin; electron transport; 2.90A {Thauera aromatica} SCOP: d.58.1.1

Probab=97.18  E-value=0.00016  Score=44.75  Aligned_cols=26  Identities=35%  Similarity=0.717  Sum_probs=22.1

Q ss_pred             cCccCCcCcccchhcccccccccCCc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++...|++||.|+.+||++||.+...
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~   28 (80)
T 1rgv_A            3 YINDDCTACDACVEECPNEAITPGDP   28 (80)
T ss_dssp             CCCSCCCCCCTTTTTCTTCCEECCSS
T ss_pred             EeCCCCcChhhHHHHcChhccCcCCC
Confidence            45678999999999999999987553

>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction potential, iron binding protein electron transport; 1.32A {Pseudomonas aeruginosa}

Probab=97.15  E-value=0.00018  Score=44.73  Aligned_cols=26  Identities=35%  Similarity=0.815  Sum_probs=22.0

Q ss_pred             cCccCCcCcccchhcccccccccCCc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++...|++||.|+.+||++||.+...
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~   28 (82)
T 2fgo_A            3 KITDDCINCDVCEPECPNGAISQGEE   28 (82)
T ss_dssp             CCCTTCCCCCTTGGGCTTCCEEECSS
T ss_pred             eeCCCCCChhhHHHHCChhccCCCCC
Confidence            45678999999999999999987543

>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=97.13  E-value=8.8e-05  Score=42.46  Aligned_cols=23  Identities=30%  Similarity=0.845  Sum_probs=20.2

Q ss_pred             CccccccchhhcHHhchhccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      ++.+.|++||.|+.+||++||.+
T Consensus        32 ~~~~~C~~C~~C~~~CP~~ai~~   54 (55)
T 2fdn_A           32 IDADTCIDCGACAGVCPVDAPVQ   54 (55)
T ss_dssp             ECTTTCCCCCHHHHTCTTCCEEE
T ss_pred             eccccCcChhChHHHccccceec
Confidence            46788999999999999999864

>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=97.12  E-value=0.00015  Score=45.09  Aligned_cols=26  Identities=35%  Similarity=0.880  Sum_probs=22.2

Q ss_pred             cCccCCcCcccchhcccccccccCCc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++...|++|+.|+.+||++||.+...
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            45678999999999999999987554

>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=97.08  E-value=0.00014  Score=44.70  Aligned_cols=24  Identities=46%  Similarity=0.955  Sum_probs=21.2

Q ss_pred             CccccccchhhcHHhchhccccch
Q psy4925          56 SGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      ++.+.|++||.|+.+||++||.+.
T Consensus        34 ~~~~~C~~Cg~C~~~CP~~ai~~~   57 (77)
T 1bc6_A           34 IDPDVCIDCGACEAVCPVSAIYHE   57 (77)
T ss_dssp             ECTTTCCSCCSHHHHSGGGSSEET
T ss_pred             ECcccCcCccCCHhhcCccceEec
Confidence            467889999999999999999764

>2zvs_A Uncharacterized ferredoxin-like protein YFHL; electron transport, [4Fe-4S] clusters, iron-SULF clusters, reduction potential; 1.65A {Escherichia coli}

Probab=97.06  E-value=0.00018  Score=45.12  Aligned_cols=26  Identities=38%  Similarity=0.920  Sum_probs=21.9

Q ss_pred             cCccCCcCcccchhcccccccccCCc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ++...|++||.|+.+||++||.+...
T Consensus         3 ~~~~~C~~C~~C~~~CP~~ai~~~~~   28 (85)
T 2zvs_A            3 LITKKCINCDMCEPECPNEAISMGDH   28 (85)
T ss_dssp             EECTTCCCCCTTTTTCTTCCEECCSS
T ss_pred             EeCCcCcChhHHHHHCchhccCcCCC
Confidence            34568999999999999999987553

>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=97.04  E-value=0.00017  Score=44.32  Aligned_cols=26  Identities=35%  Similarity=0.890  Sum_probs=21.9

Q ss_pred             CccccccchhhcHHhchhccccchhh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      .+.+.|++||.|+.+||++||.+...
T Consensus        42 ~~~~~C~~Cg~C~~~CP~~ai~~~~~   67 (80)
T 1jb0_C           42 PRTEDCVGCKRCETACPTDFLSIRVY   67 (80)
T ss_dssp             TTGGGCCCCCHHHHHCCSSSCSEEEE
T ss_pred             CCCCcCcCcCChhhhCCCCccEeeee
Confidence            35678999999999999999987543

>1h98_A Ferredoxin; electron transport, thermophilic, iron-sulfur, azotobacter, hydrogen bonds, stability, high resolution; 1.64A {Thermus aquaticus} SCOP: d.58.1.2

Probab=97.04  E-value=0.00017  Score=44.39  Aligned_cols=25  Identities=40%  Similarity=0.789  Sum_probs=21.7

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ++.+.|++||.|+.+||++||.+..
T Consensus        34 ~~~~~C~~C~~C~~~CP~~Ai~~~~   58 (78)
T 1h98_A           34 IHPEECIDCGACVPACPVNAIYPEE   58 (78)
T ss_dssp             ECTTTCCCCCTHHHHCTTCCEEEGG
T ss_pred             ECcccCCcHhHHHHhCCccceEecc
Confidence            4578899999999999999998654

>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A

Probab=97.03  E-value=0.00016  Score=46.84  Aligned_cols=25  Identities=40%  Similarity=1.011  Sum_probs=21.5

Q ss_pred             CCccccccchhhcHHhchhccccch
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .++...|++||.|+.+||++||.+.
T Consensus        77 ~~~~~~C~~Cg~C~~~CP~~Ai~~~  101 (103)
T 1xer_A           77 PVNEQACIFCMACVNVCPVAAIDVK  101 (103)
T ss_dssp             CTTGGGCCCCCHHHHHCTTCCEEEC
T ss_pred             ecCcccccChhhHHHhccccceEec
Confidence            3567889999999999999999754

>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=97.02  E-value=0.0002  Score=42.18  Aligned_cols=26  Identities=35%  Similarity=0.791  Sum_probs=22.0

Q ss_pred             cccCccCCcCcccchhcccccccccCC
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.++...|++||.|+.+|| +++.+..
T Consensus         4 ~~id~~~C~~Cg~C~~~CP-~~~~~~~   29 (64)
T 1dax_A            4 FYVDQDECIACESCVEIAP-GAFAMDP   29 (64)
T ss_dssp             CEECSTTCCSCCHHHHHCT-TTEEECS
T ss_pred             EEEccccCCCchHHHHhCC-ccEeEcC
Confidence            4577889999999999999 8887654

>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=97.01  E-value=0.00023  Score=60.36  Aligned_cols=54  Identities=37%  Similarity=0.838  Sum_probs=39.8

Q ss_pred             Ccccccc--chh--hcHHhchhc-----cccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          56 SGEERCI--ACK--LCEAICPAQ-----AITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        56 ~~~~~Ci--~Cg--~Cv~~CP~~-----~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ++.++|.  .|+  .|.+.||..     +|.++...        ....+....|++||.|+..||..||.+
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            4667787  686  899999952     23333221        144577889999999999999998877

>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=96.97  E-value=0.0002  Score=46.82  Aligned_cols=26  Identities=54%  Similarity=0.972  Sum_probs=22.5

Q ss_pred             CccccccchhhcHHhchhccccchhh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      ++.+.|++||.|+.+||++||.+...
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            45678999999999999999987654

>1dwl_A Ferredoxin I; electron transfer, model, heteronuclear docking; HET: HEC; NMR {Desulfomicrobium norvegicum} SCOP: i.4.1.1

Probab=96.96  E-value=0.00027  Score=40.62  Aligned_cols=23  Identities=17%  Similarity=0.319  Sum_probs=20.0

Q ss_pred             CccccccchhhcHHhchhccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      ++.+.|+.|+.|+.+||++||.+
T Consensus        36 ~~~~~c~~C~~C~~~CP~~Ai~~   58 (59)
T 1dwl_A           36 APDSTAECAQDAIDACPVEAISK   58 (59)
T ss_dssp             CTTCCCGGGGTGGGGSTTCCEEE
T ss_pred             cChhhhhHHHHHHHhCCHhhEEc
Confidence            35678999999999999999864

>1f2g_A Ferredoxin II; electron transport, FDII desulfovibrio gigas; NMR {Desulfovibrio gigas} SCOP: d.58.1.4 PDB: 1fxd_A

Probab=96.89  E-value=0.00025  Score=40.82  Aligned_cols=21  Identities=24%  Similarity=0.305  Sum_probs=18.9

Q ss_pred             cccccchhhcHHhchhccccc
Q psy4925          58 EERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      .+.|+.|+.|+.+||++||.+
T Consensus        37 ~~~C~~C~~C~~~CP~~Ai~~   57 (58)
T 1f2g_A           37 DSDLDCVEEAIDSCPAEAIVR   57 (58)
T ss_dssp             TCCSTHHHHHHHTCSSCCCBC
T ss_pred             ccchHHHHHHHhhCChhhEEe
Confidence            578999999999999999864

>1rof_A Ferredoxin; electron transport, iron-sulfur; NMR {Thermotoga maritima} SCOP: d.58.1.4 PDB: 1vjw_A

Probab=96.85  E-value=0.0003  Score=40.57  Aligned_cols=22  Identities=32%  Similarity=0.471  Sum_probs=19.4

Q ss_pred             cccccchhhcHHhchhccccch
Q psy4925          58 EERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .+.|+.|+.|+.+||++||.+.
T Consensus        38 ~~~c~~C~~C~~~CP~~Ai~~~   59 (60)
T 1rof_A           38 ETDLPCAKDAADSCPTGAISVE   59 (60)
T ss_dssp             SCCSTTHHHHHHHCTTCCEECC
T ss_pred             hhhHHHHHHHHHhCCHhHEEEe
Confidence            5789999999999999998753

>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=96.68  E-value=0.00048  Score=42.62  Aligned_cols=26  Identities=35%  Similarity=0.599  Sum_probs=21.6

Q ss_pred             ccccCccCCcCcccchhcccccccccC
Q psy4925          92 RYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        92 ~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      .+.++...|++||.|+.+|| +++.+.
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            34678889999999999999 777654

>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=96.63  E-value=0.0005  Score=48.01  Aligned_cols=25  Identities=28%  Similarity=0.753  Sum_probs=21.9

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ++.++|++||.|+.+||++||.+..
T Consensus        42 id~~~C~~Cg~Cv~~CP~~AI~~~~   66 (150)
T 1jnr_B           42 REPDMCWECYSCVKMCPQGAIDVRG   66 (150)
T ss_dssp             SCGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             eCcccCcCHhHHHHhCCccceEecC
Confidence            5678899999999999999998754

>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=96.49  E-value=0.00081  Score=47.77  Aligned_cols=25  Identities=44%  Similarity=0.918  Sum_probs=21.3

Q ss_pred             cCccCCcCcccchhcccccccccCC
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      .+...|++|+.|+.+||++||.+..
T Consensus        48 ~d~~~Ci~C~~C~~~CP~~ai~~~~   72 (182)
T 3i9v_9           48 NGLEKCIGCSLCAAACPAYAIYVEP   72 (182)
T ss_dssp             TSCBSCCCCCHHHHHCTTCCEEEEE
T ss_pred             CCCccCcccccchhhCCcccEEeec
Confidence            4567899999999999999987644

>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=96.34  E-value=0.001  Score=38.96  Aligned_cols=26  Identities=23%  Similarity=0.551  Sum_probs=21.3

Q ss_pred             ccccCccCCcCcccchhcccccccccC
Q psy4925          92 RYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        92 ~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      .+.++...|++||.|+.+||. ++.+.
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            345778899999999999995 77764

>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas}

Probab=95.97  E-value=0.0017  Score=45.99  Aligned_cols=27  Identities=33%  Similarity=0.715  Sum_probs=23.3

Q ss_pred             ccCccCCcCcc-----cchhcccccccccCCc
Q psy4925          94 DIDMTKCIYCG-----FCQEACPVDAIVEGPN  120 (160)
Q Consensus        94 ~~~~~~C~~Cg-----~C~~~CP~~ai~~~~~  120 (160)
                      .++...|++|+     .|+.+||++||.+...
T Consensus         3 ~id~~~C~gC~~c~~~~C~~~CP~~ai~~~~~   34 (166)
T 3gyx_B            3 YVDPSKCDGCKGGEKTACMYICPNDLMILDPE   34 (166)
T ss_dssp             EECTTTCCCCCSSSCCHHHHHCTTSCEEEETT
T ss_pred             EEcchhcCCCCCCCcchhHHhCCccccEEecC
Confidence            46778899999     9999999999987654

>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=95.48  E-value=0.0042  Score=50.33  Aligned_cols=27  Identities=41%  Similarity=0.786  Sum_probs=23.4

Q ss_pred             cccCccCCcCcccchhcccccccccCC
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.++...|++||.|+.+||++||....
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            457888999999999999999998654

>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=95.41  E-value=0.0037  Score=52.61  Aligned_cols=27  Identities=22%  Similarity=0.610  Sum_probs=23.0

Q ss_pred             CCCccccccchhhcHHhchhccccchh
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ..++.++|+.||.|+.+||++||....
T Consensus       183 ~~i~~~~Ci~Cg~Cv~~CP~gAi~~~~  209 (574)
T 3c8y_A          183 KCFDDTNCLLCGQCIIACPVAALSEKS  209 (574)
T ss_dssp             CCGGGSSCCCCCHHHHHCSSTTEEECC
T ss_pred             ceechhhCCcchhHHHhhccCCccccc
Confidence            346778999999999999999997653

>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=95.40  E-value=0.004  Score=49.90  Aligned_cols=26  Identities=27%  Similarity=0.732  Sum_probs=22.7

Q ss_pred             CCCccccccchhhcHHhchhccccch
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      +.++.++|+.||.|+.+||.+|+...
T Consensus       251 v~id~~~Ci~Cg~C~~~CP~~Ai~~~  276 (386)
T 3or1_B          251 VAINNDRCMYCGNCYTMCPALPLSDG  276 (386)
T ss_dssp             EEECTTTCCCCCHHHHHCTTCCCCCT
T ss_pred             cccCCCcCCccccHHHhCcHhhCcCC
Confidence            55678899999999999999998754

>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=95.14  E-value=0.0054  Score=48.78  Aligned_cols=27  Identities=22%  Similarity=0.597  Sum_probs=22.7

Q ss_pred             cCCCccccccchhhcHHhchhccccch
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      ...++.++|++||.|+.+||.+||...
T Consensus       233 ~~~id~~~C~~Cg~C~~~CP~~Ai~~~  259 (366)
T 3mm5_B          233 TIKVDVEKCMYCGNCYTMCPGMPLFDP  259 (366)
T ss_dssp             EEEECGGGCCCCCHHHHHCTTCCCCCT
T ss_pred             eEEEehhhCCCcchHHHhCCHhhcccc
Confidence            345678899999999999999988643

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=95.11  E-value=0.0046  Score=52.37  Aligned_cols=25  Identities=40%  Similarity=0.782  Sum_probs=21.6

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      +.++.||+||.||+-||.+||.+.+
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            4577899999999999999998753

>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=94.97  E-value=0.0089  Score=52.03  Aligned_cols=22  Identities=18%  Similarity=0.108  Sum_probs=19.4

Q ss_pred             cccchhhcHHhchhccccchhh
Q psy4925          60 RCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        60 ~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      .|+.||.|+.+||++||.....
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            6999999999999999986543

>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=94.74  E-value=0.0076  Score=54.94  Aligned_cols=25  Identities=32%  Similarity=0.631  Sum_probs=22.4

Q ss_pred             cccCccCCcCcccchhccccccccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ...+...|+.||.|+.+||.+||..
T Consensus       681 p~~d~~kCi~Cg~Cv~vCP~~AI~~  705 (1231)
T 2c42_A          681 PQWVPENCIQCNQCAFVCPHSAILP  705 (1231)
T ss_dssp             EEECTTTCCCCCHHHHHCSSCCEEE
T ss_pred             eEEeCccCCchhhHHHhCCcccccc
Confidence            4568899999999999999999975

>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=94.46  E-value=0.0077  Score=50.59  Aligned_cols=28  Identities=29%  Similarity=0.624  Sum_probs=23.7

Q ss_pred             cCCCccccccchhhcHHhchhccccchh
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+.++.+.|++||.|..+||+++|....
T Consensus       545 ~~~i~~~~Ci~C~~C~~~cp~~~i~~~~  572 (584)
T 2gmh_A          545 RLQINAQNCVHCKTCDIKDPSQNINWVV  572 (584)
T ss_dssp             EEEECGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             EEEEeCCCCcCCCCchhhCCCCCceeEC
Confidence            3456788999999999999999997654

>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=93.26  E-value=0.015  Score=47.10  Aligned_cols=24  Identities=17%  Similarity=0.440  Sum_probs=20.2

Q ss_pred             CCCccccccchhhcHHhchhcccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAIT   77 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~   77 (160)
                      +.++.++|++|+.|+.+||.++..
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            446788999999999999997654

>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=92.80  E-value=0.033  Score=41.28  Aligned_cols=21  Identities=24%  Similarity=0.505  Sum_probs=17.9

Q ss_pred             ccccccchhhcHHhchhcccc
Q psy4925          57 GEERCIACKLCEAICPAQAIT   77 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~   77 (160)
                      +...|+.||.|+.+||+++..
T Consensus       202 ~~~~C~~Cg~C~~vCP~gi~~  222 (238)
T 2wdq_B          202 SVFRCHSIMNCVSVCPKGLNP  222 (238)
T ss_dssp             TTTTCCCCCHHHHHCTTCCCH
T ss_pred             CCCcCcccchhhhhcCCCCCH
Confidence            456899999999999998654

>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=92.11  E-value=0.043  Score=40.78  Aligned_cols=19  Identities=26%  Similarity=0.746  Sum_probs=16.5

Q ss_pred             ccccccchhhcHHhchhcc
Q psy4925          57 GEERCIACKLCEAICPAQA   75 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~   75 (160)
                      +...|+.||.|+.+||+++
T Consensus       200 ~~~~C~~Cg~C~~vCP~gi  218 (243)
T 1kf6_B          200 GVWSCTFVGYCSEVCPKHV  218 (243)
T ss_dssp             TGGGCCCCCHHHHHCTTCC
T ss_pred             CcccCcccCCcchhCCCCC
Confidence            4568999999999999974

>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=91.07  E-value=0.051  Score=40.75  Aligned_cols=22  Identities=27%  Similarity=0.690  Sum_probs=18.8

Q ss_pred             cCccCCcCcccchhcccccccc
Q psy4925          95 IDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        95 ~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      .+...|+.||.|+.+||..++.
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            4667899999999999998753

>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=90.21  E-value=0.048  Score=40.54  Aligned_cols=21  Identities=33%  Similarity=0.958  Sum_probs=18.3

Q ss_pred             CccCCcCcccchhcccccccc
Q psy4925          96 DMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        96 ~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      +...|+.||.|+.+||+.++.
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            456799999999999999864

>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=90.00  E-value=0.067  Score=43.49  Aligned_cols=24  Identities=17%  Similarity=0.411  Sum_probs=19.8

Q ss_pred             CCCccccccchhhcHHhchhcccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAIT   77 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~   77 (160)
                      +.++.++|+.|+.|+.+||..+..
T Consensus       296 l~Id~~~C~~Cg~Ci~~CP~al~~  319 (437)
T 3or1_A          296 LSIDNKNCTRCMHCINTMPRALKI  319 (437)
T ss_dssp             EEECGGGCCCCSHHHHHCTTTEEC
T ss_pred             EEEccccCCchhhhHhhCcHhhcc
Confidence            446788999999999999986543

>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=89.95  E-value=0.074  Score=47.57  Aligned_cols=29  Identities=38%  Similarity=0.617  Sum_probs=24.1

Q ss_pred             ccccCccCCcCcccchhcccc---cccccCCc
Q psy4925          92 RYDIDMTKCIYCGFCQEACPV---DAIVEGPN  120 (160)
Q Consensus        92 ~~~~~~~~C~~Cg~C~~~CP~---~ai~~~~~  120 (160)
                      ...++...|+.||.|+.+||.   +||.+...
T Consensus       945 ~~~id~~~C~~Cg~C~~~CP~~~~~ai~~~~~  976 (1025)
T 1gte_A          945 VAVIDEEMCINCGKCYMTCNDSGYQAIQFDPE  976 (1025)
T ss_dssp             EEEECTTTCCCCCHHHHHHHHHSCSCEEECTT
T ss_pred             eEEEEcccCcccCHHHHhcCccccCCEEEeCC
Confidence            345788899999999999996   89887553

>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=88.87  E-value=0.1  Score=39.57  Aligned_cols=24  Identities=29%  Similarity=0.618  Sum_probs=19.6

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+..+|+.|+.|+.+|| +++....
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            35578999999999999 8876543

>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=88.09  E-value=0.12  Score=43.66  Aligned_cols=23  Identities=39%  Similarity=0.888  Sum_probs=20.1

Q ss_pred             CccccccchhhcHHhchhccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      +.+..|++||.|++.||..+|.+
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            45678999999999999988876

>3cf4_A Acetyl-COA decarboxylase/synthase alpha subunit; methanomicrobia, iron-nikel-sulfur, 4Fe-NI-4S, oxidoreductas; 2.00A {Methanosarcina barkeri}

Probab=83.14  E-value=0.26  Score=43.07  Aligned_cols=21  Identities=29%  Similarity=0.950  Sum_probs=18.1

Q ss_pred             cccccchhhcHHhchhccccc
Q psy4925          58 EERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      .+.|+.||.|+.+||+++...
T Consensus       452 ~~~Ci~Cg~C~~vCP~ga~~~  472 (807)
T 3cf4_A          452 HDTCIGCRRCEQVCKKEIPIL  472 (807)
T ss_dssp             HHHCCCCCHHHHHCTTCCCHH
T ss_pred             hhhccchhhHHHhCCCCCChH
Confidence            468999999999999987654

>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=81.82  E-value=0.32  Score=37.25  Aligned_cols=18  Identities=33%  Similarity=0.901  Sum_probs=15.6

Q ss_pred             cCCcCcccchhccccccc
Q psy4925          98 TKCIYCGFCQEACPVDAI  115 (160)
Q Consensus        98 ~~C~~Cg~C~~~CP~~ai  115 (160)
                      ..|+.||.|..+||.-..
T Consensus       180 ~~CI~CG~C~~aCP~~~~  197 (282)
T 3vr8_B          180 YECILCACCSASCPSYWW  197 (282)
T ss_pred             hhCcccCcCcccCCceec
Confidence            469999999999998754

---

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	160
d2fug91	154	d.58.1.5 (9:26-179) NADH-quinone oxidoreductase ch	3e-38
d1jb0c_	80	d.58.1.2 (C:) Photosystem I iron-sulfur protein Ps	2e-14
d1jb0c_	80	d.58.1.2 (C:) Photosystem I iron-sulfur protein Ps	3e-04
d2fdna_	55	d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici	3e-14
d2fdna_	55	d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici	0.003
d1blua_	80	d.58.1.1 (A:) Ferredoxin II {Chromatium vinosum [T	2e-13
d1xera_	103	d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp.	7e-13
d1xera_	103	d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp.	2e-04
d1hfel2	85	d.58.1.5 (L:2-86) Fe-only hydrogenase larger subun	2e-12
d1hfel2	85	d.58.1.5 (L:2-86) Fe-only hydrogenase larger subun	9e-04
d1rgva_	80	d.58.1.1 (A:) Ferredoxin II {Thauera aromatica [Ta	6e-12
d1dura_	55	d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus as	7e-12
d1dura_	55	d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus as	0.003
d1gtea5	173	d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogen	8e-12
d1fxda_	58	d.58.1.4 (A:) Ferredoxin I {Desulfovibrio gigas [T	1e-11
d3c8ya3	83	d.58.1.5 (A:127-209) Fe-only hydrogenase, second d	4e-10
d1sj1a_	66	d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus	1e-09
d1jnrb_	149	d.58.1.5 (B:) Adenylylsulfate reductase B subunit	9e-09
d2c42a5	117	d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoredu	1e-08
d1vjwa_	59	d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [T	3e-08
d1bc6a_	77	d.58.1.2 (A:) Ferredoxin {Bacillus schlegelii [Tax	6e-08
d1iqza_	81	d.58.1.4 (A:) Ferredoxin {Bacillus thermoproteolyt	6e-08
d1h98a_	77	d.58.1.2 (A:) Ferredoxin {Thermus thermophilus [Ta	2e-07
d1fxra_	64	d.58.1.4 (A:) Ferredoxin I {Sulfate-reducing bacte	5e-07
d3c7bb1	65	d.58.1.5 (B:197-261) DsrB insert domain {Archaeogl	1e-06
d1kqfb1	244	d.58.1.5 (B:2-245) Formate dehydrogenase N, iron-s	1e-05
d7fd1a_	106	d.58.1.2 (A:) Ferredoxin {Azotobacter vinelandii [	2e-05
d2fug34	151	d.58.1.5 (3:96-246) NADH-quinone oxidoreductase ch	5e-05
d1y5ib1	509	d.58.1.5 (B:1-509) Respiratory nitrate reductase 1	5e-05
d1y5ib1	509	d.58.1.5 (B:1-509) Respiratory nitrate reductase 1	8e-05

>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 =  125 bits (315), Expect = 3e-38
 Identities = 50/121 (41%), Positives = 69/121 (57%), Gaps = 6/121 (4%)

Query: 34  YPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIE------AEERADGS 87
           YP     L PRF G H L R+P+G E+CI C LC A CPA AI +E          + G 
Sbjct: 1   YPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAAACPAYAIYVEPAENDPENPVSAGE 60

Query: 88  RRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWES 147
           R    Y+I+M +CI+CG C+EACP  AIV G +FE +   + +L+Y KE +L +    + 
Sbjct: 61  RYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTKP 120

Query: 148 E 148
           +
Sbjct: 121 Q 121

>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 = 62.8 bits (152), Expect = 2e-14
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 6/67 (8%)

Query: 49  HALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQE 108
           H ++ Y    + CI C  C   CP   + +   +     +           C+ C  C+ 
Sbjct: 2   HTVKIY----DTCIGCTQCVRACPTDVLEMVPWDGCKAGQI--ASSPRTEDCVGCKRCET 55

Query: 109 ACPVDAI 115
           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 = 35.5 bits (81), Expect = 3e-04
 Identities = 13/56 (23%), Positives = 21/56 (37%)

Query: 35 PFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRT 90
          P +   + P    +          E C+ CK CE  CP   ++I     A+ +R  
Sbjct: 21 PTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSM 76

>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 = 61.1 bits (148), Expect = 3e-14
 Identities = 25/60 (41%), Positives = 28/60 (46%), Gaps = 10/60 (16%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
            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 = 32.2 bits (73), Expect = 0.003
 Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 99  KCIYCGFCQEACPVDAIVEGPN 120
            CI CG C+  CPV+AI  G +
Sbjct: 7   ACISCGACEPECPVNAISSGDD 28

>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 = 60.1 bits (145), Expect = 2e-13
 Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 19/87 (21%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GFCQEACP 111
            + CI C +CE  CP  AI+          +    Y I+ + C  C        C E CP
Sbjct: 5   TDECINCDVCEPECPNGAIS----------QGDETYVIEPSLCTECVGHYETSQCVEVCP 54

Query: 112 VDAIVEGPNFEFSTESHEELLYNKEKL 138
           VD I++ P+ E   E+ +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 = 59.0 bits (142), Expect = 7e-13
 Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            + CIA   C   CP        +     +       ++   CI+C  C   CPV AI
Sbjct: 42  FDLCIADGSCINACPVNVFQWY-DTPGHPASEKKADPVNEQACIFCMACVNVCPVAAI 98

>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 = 36.7 bits (84), Expect = 2e-04
 Identities = 10/43 (23%), Positives = 15/43 (34%)

Query: 95  IDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEK 137
           +D   CI  G C  ACPV+               +    N++ 
Sbjct: 40  VDFDLCIADGSCINACPVNVFQWYDTPGHPASEKKADPVNEQA 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 = 57.4 bits (138), Expect = 2e-12
 Identities = 21/60 (35%), Positives = 24/60 (40%), Gaps = 8/60 (13%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
           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 = 34.3 bits (78), Expect = 9e-04
 Identities = 11/21 (52%), Positives = 12/21 (57%)

Query: 95  IDMTKCIYCGFCQEACPVDAI 115
           ID  KCI C  C + CP  AI
Sbjct: 29  IDEAKCIGCDTCSQYCPTAAI 49

>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 = 56.0 bits (134), Expect = 6e-12
 Identities = 26/87 (29%), Positives = 36/87 (41%), Gaps = 19/87 (21%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GFCQEACP 111
            + C AC  C   CP +AI          +     Y ID TKC  C        C+  CP
Sbjct: 5   NDDCTACDACVEECPNEAI----------TPGDPIYVIDPTKCSECVGAFDEPQCRLVCP 54

Query: 112 VDAIVEGPNFEFSTESHEELLYNKEKL 138
            D I + P++    E+ EEL    ++L
Sbjct: 55  ADCIPDNPDYR---ETREELQEKYDRL 78

>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 = 55.4 bits (133), Expect = 7e-12
 Identities = 20/58 (34%), Positives = 23/58 (39%), Gaps = 11/58 (18%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            + 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 = 32.3 bits (73), Expect = 0.003
 Identities = 11/32 (34%), Positives = 16/32 (50%)

Query: 95  IDMTKCIYCGFCQEACPVDAIVEGPNFEFSTE 126
           +    CI CG C+  CPV+ I EG  +    +
Sbjct: 3   VINDSCIACGACKPECPVNCIQEGSIYAIDAD 34

>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 = 57.8 bits (139), Expect = 8e-12
 Identities = 15/59 (25%), Positives = 17/59 (28%), Gaps = 7/59 (11%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV-DAI 115
           EE CI C  C   C          +        T        C  C  C   CP+ D I
Sbjct: 106 EEMCINCGKCYMTCNDSGYQAIQFDP------ETHLPTVTDTCTGCTLCLSVCPIIDCI 158

>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 = 54.6 bits (131), Expect = 1e-11
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 7/60 (11%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
            + C+AC+ C  ICP      E     +G +           C+      ++CP +AIV 
Sbjct: 5   NDDCMACEACVEICPDVFEMNE-----EGDKAVVINPDSDLDCVEE--AIDSCPAEAIVR 57

>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 = 51.4 bits (122), Expect = 4e-10
 Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 58  EERCIACKLCEAICPAQAIT--IEAEERADGSRRTT--RYDIDMTKCIYCGFCQEACPVD 113
             +C+ C  C   C     T  ++   +   +          D T C+ CG C  ACPV 
Sbjct: 18  RTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVA 77

Query: 114 AIVE 117
           A+ E
Sbjct: 78  ALSE 81

>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 = 49.4 bits (117), Expect = 1e-09
 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 4/58 (6%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           ++ CI   +C ++CP      +       ++       D           EACPV AI
Sbjct: 8   QDTCIGDAICASLCPDVFEMNDE----GKAQPKVEVIEDEELYNCAKEAMEACPVSAI 61

>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 = 49.5 bits (117), Expect = 9e-09
 Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 12/76 (15%)

Query: 58  EERCIACK-----LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
            E+C  CK      CE ICP   +T++ E+          Y+ +   C  C  C + CP 
Sbjct: 6   PEKCDGCKALERTACEYICPNDLMTLDKEKM-------KAYNREPDMCWECYSCVKMCPQ 58

Query: 113 DAIVEGPNFEFSTESH 128
            AI      ++S    
Sbjct: 59  GAIDVRGYVDYSPLGG 74

>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 = 48.3 bits (114), Expect = 1e-08
 Identities = 22/95 (23%), Positives = 29/95 (30%), Gaps = 19/95 (20%)

Query: 58  EERCIACKLCEAICPAQAITIEAEER-----------------ADGSRRTTRYDIDMTKC 100
            E CI C  C  +CP  AI     +                   +      R  I+   C
Sbjct: 18  PENCIQCNQCAFVCPHSAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDC 77

Query: 101 IYCGFCQEACPV--DAIVEGPNFEFSTESHEELLY 133
           + CG C + CP    A+V  P           L Y
Sbjct: 78  MGCGNCADICPPKEKALVMQPLDTQRDAQVPNLEY 112

>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 = 45.6 bits (107), Expect = 3e-08
 Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 8/58 (13%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            + CI C +CE +CP      +            +     T         ++CP  AI
Sbjct: 7   ADACIGCGVCENLCPDVFQLGD--------DGKAKVLQPETDLPCAKDAADSCPTGAI 56

>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 = 45.5 bits (107), Expect = 6e-08
 Identities = 21/61 (34%), Positives = 25/61 (40%), Gaps = 12/61 (19%)

Query: 58  EERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            E CI  K   C  +CP   I    +          +Y ID   CI CG C+  CPV AI
Sbjct: 5   TEPCIGTKDASCVEVCPVDCIHEGED----------QYYIDPDVCIDCGACEAVCPVSAI 54

Query: 116 V 116
            
Sbjct: 55  Y 55

>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 = 45.5 bits (107), Expect = 6e-08
 Identities = 14/59 (23%), Positives = 18/59 (30%), Gaps = 1/59 (1%)

Query: 58  EERCIACKLCEAICPAQAITIE-AEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           +E CIAC  C A  P      E               ++            E CP D+I
Sbjct: 8   KETCIACGACGAAAPDIYDYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSI 66

>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 = 44.3 bits (104), Expect = 2e-07
 Identities = 22/81 (27%), Positives = 33/81 (40%), Gaps = 14/81 (17%)

Query: 58  EERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            E CI  K   C  +CP + I               ++ I   +CI CG C  ACPV+AI
Sbjct: 5   CEPCIGVKDQSCVEVCPVECIYDG----------GDQFYIHPEECIDCGACVPACPVNAI 54

Query: 116 VEGPNFEFSTESHEELLYNKE 136
              P  +   +    +  N++
Sbjct: 55  Y--PEEDVPEQWKSYIEKNRK 73

>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 = 42.8 bits (100), Expect = 5e-07
 Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 6/58 (10%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           ++ CIAC+ C  I P         E+A         D++           + CPV  I
Sbjct: 8   QDECIACESCVEIAPGAFAMDPEIEKAY------VKDVEGASQEEVEEAMDTCPVQCI 59

>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 = 41.9 bits (98), Expect = 1e-06
 Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 13/62 (20%)

Query: 64  CKLCE-----AICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 118
            K CE     A CP  A+  +         +     +D+ KC+YCG C   CP   + + 
Sbjct: 12  RKTCEIPSTVAACPTGALKPD--------MKNKTIKVDVEKCMYCGNCYTMCPGMPLFDP 63

Query: 119 PN 120
            N
Sbjct: 64  EN 65

>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 = 41.4 bits (96), Expect = 1e-05
 Identities = 19/79 (24%), Positives = 26/79 (32%), Gaps = 3/79 (3%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 118
           E CI C  C A CP     +  E   D         +D         C + CP  AI  G
Sbjct: 130 ENCIGCGYCIAGCPFNIPRLNKE---DNRVYKCTLCVDRVSVGQEPACVKTCPTGAIHFG 186

Query: 119 PNFEFSTESHEELLYNKEK 137
              E    + + +   K +
Sbjct: 187 TKKEMLELAEQRVAKLKAR 205

>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 = 39.3 bits (91), Expect = 2e-05
 Identities = 16/61 (26%), Positives = 20/61 (32%), Gaps = 12/61 (19%)

Query: 58  EERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
            + CI CK   C  +CP                      I   +CI C  C+  CP  AI
Sbjct: 5   TDNCIKCKYTDCVEVCPVDCFYEGPN----------FLVIHPDECIDCALCEPECPAQAI 54

Query: 116 V 116
            
Sbjct: 55  F 55

>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 = 38.9 bits (90), Expect = 5e-05
 Identities = 13/61 (21%), Positives = 19/61 (31%)

Query: 59  ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG 118
           ERCI CK C             +    G               + G   + CPV A+++ 
Sbjct: 84  ERCIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSGFSGNITDICPVGALLDL 143

Query: 119 P 119
            
Sbjct: 144 T 144

>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 = 40.1 bits (93), Expect = 5e-05
 Identities = 10/61 (16%), Positives = 19/61 (31%), Gaps = 3/61 (4%)

Query: 58  EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
           +++C   ++C   CP + I    +    G      +     +      C E C       
Sbjct: 214 QDKCRGWRMCITGCPYKKIYFNWK---SGKSEKCIFCYPRIEAGQPTVCSETCVGRIRYL 270

Query: 118 G 118
           G
Sbjct: 271 G 271

>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 = 39.3 bits (91), Expect = 8e-05
 Identities = 17/49 (34%), Positives = 18/49 (36%), Gaps = 8/49 (16%)

Query: 67  CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
           C A CP+ AI    E   DG        ID  KC     C   CP   I
Sbjct: 192 CVATCPSGAIYKREE---DG-----IVLIDQDKCRGWRMCITGCPYKKI 232

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	160
d2fug91	154	NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus	99.85
d1hfel2	85	Fe-only hydrogenase larger subunit, N-domain {Desu	99.57
d1rgva_	80	Ferredoxin II {Thauera aromatica [TaxId: 59405]}	99.51
d1dura_	55	Ferredoxin II {Peptostreptococcus asaccharolyticus	99.51
d2fdna_	55	Ferredoxin II {Clostridium acidurici [TaxId: 1556]	99.51
d1blua_	80	Ferredoxin II {Chromatium vinosum [TaxId: 1049]}	99.5
d3c8ya3	83	Fe-only hydrogenase, second domain {Clostridium pa	99.5
d1xera_	103	Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}	99.49
d1bc6a_	77	Ferredoxin {Bacillus schlegelii [TaxId: 1484]}	99.49
d1h98a_	77	Ferredoxin {Thermus thermophilus [TaxId: 274]}	99.49
d1jb0c_	80	Photosystem I iron-sulfur protein PsaC {Synechococ	99.49
d7fd1a_	106	Ferredoxin {Azotobacter vinelandii [TaxId: 354]}	99.38
d1jnrb_	149	Adenylylsulfate reductase B subunit {Archaeon Arch	99.36
d2c42a5	117	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	99.33
d1vjwa_	59	Ferredoxin A {Thermotoga maritima [TaxId: 2336]}	99.29
d1fxra_	64	Ferredoxin I {Sulfate-reducing bacteria (Desulfovi	99.26
d1gtea5	173	Dihydropyrimidine dehydrogenase, C-terminal domain	99.25
d2fug34	151	NADH-quinone oxidoreductase chain 3, Nqo3, domain	99.24
d1sj1a_	66	Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxI	99.2
d1fxda_	58	Ferredoxin I {Desulfovibrio gigas [TaxId: 879]}	99.19
d3c7bb1	65	DsrB insert domain {Archaeoglobus fulgidus [TaxId:	99.18
d1kqfb1	244	Formate dehydrogenase N, iron-sulfur (beta) subuni	98.86
d1iqza_	81	Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1	98.82
d1kqfb1	244	Formate dehydrogenase N, iron-sulfur (beta) subuni	98.82
d1vlfn2	195	Transhydroxylase beta subunit, BthL, N-terminal do	98.78
d1y5ib1	509	Respiratory nitrate reductase 1 beta chain {Escher	98.76
d1nekb1	132	Succinate dehydogenase {Escherichia coli [TaxId: 5	98.74
d1y5ib1	509	Respiratory nitrate reductase 1 beta chain {Escher	98.7
d1vlfn2	195	Transhydroxylase beta subunit, BthL, N-terminal do	98.62
d2bs2b1	133	Fumarate reductase {Wolinella succinogenes [TaxId:	98.61
d1kf6b1	138	Fumarate reductase {Escherichia coli [TaxId: 562]}	98.57
d1h0hb_	214	Tungsten containing formate dehydrogenase, small s	98.51
d2gmha3	102	Electron transfer flavoprotein-ubiquinone oxidored	97.87
d1dura_	55	Ferredoxin II {Peptostreptococcus asaccharolyticus	97.83
d1bc6a_	77	Ferredoxin {Bacillus schlegelii [TaxId: 1484]}	97.69
d1h98a_	77	Ferredoxin {Thermus thermophilus [TaxId: 274]}	97.69
d1hfel2	85	Fe-only hydrogenase larger subunit, N-domain {Desu	97.61
d1jb0c_	80	Photosystem I iron-sulfur protein PsaC {Synechococ	97.59
d2fdna_	55	Ferredoxin II {Clostridium acidurici [TaxId: 1556]	97.58
d3c7bb1	65	DsrB insert domain {Archaeoglobus fulgidus [TaxId:	97.55
d1xera_	103	Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}	97.54
d3c8ya3	83	Fe-only hydrogenase, second domain {Clostridium pa	97.54
d2fug91	154	NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus	97.49
d1blua_	80	Ferredoxin II {Chromatium vinosum [TaxId: 1049]}	97.43
d1h0hb_	214	Tungsten containing formate dehydrogenase, small s	97.4
d7fd1a_	106	Ferredoxin {Azotobacter vinelandii [TaxId: 354]}	97.4
d1rgva_	80	Ferredoxin II {Thauera aromatica [TaxId: 59405]}	97.39
d2v4jb1	69	DsrB insert domain {Desulfovibrio vulgaris [TaxId:	97.23
d1jnrb_	149	Adenylylsulfate reductase B subunit {Archaeon Arch	96.91
d1sj1a_	66	Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxI	96.81
d2c42a5	117	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	96.71
d1vjwa_	59	Ferredoxin A {Thermotoga maritima [TaxId: 2336]}	96.71
d1gtea5	173	Dihydropyrimidine dehydrogenase, C-terminal domain	96.65
d1fxra_	64	Ferredoxin I {Sulfate-reducing bacteria (Desulfovi	96.6
d2fug34	151	NADH-quinone oxidoreductase chain 3, Nqo3, domain	96.46
d1fxda_	58	Ferredoxin I {Desulfovibrio gigas [TaxId: 879]}	95.66
d1iqza_	81	Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1	95.25
d3c7ba1	66	DsrA insert domain {Archaeoglobus fulgidus [TaxId:	94.13
d2bs2b1	133	Fumarate reductase {Wolinella succinogenes [TaxId:	93.8
d1nekb1	132	Succinate dehydogenase {Escherichia coli [TaxId: 5	93.09
d2gmha3	102	Electron transfer flavoprotein-ubiquinone oxidored	93.05
d2v4ja1	81	DsrA insert domain {Desulfovibrio vulgaris [TaxId:	92.92
d1kf6b1	138	Fumarate reductase {Escherichia coli [TaxId: 562]}	92.85
d2v4jb1	69	DsrB insert domain {Desulfovibrio vulgaris [TaxId:	88.19
d1gtea1	182	Dihydropyrimidine dehydrogenase, N-terminal domain	80.07

>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=99.85  E-value=2.2e-22  Score=141.77  Aligned_cols=115  Identities=44%  Similarity=0.886  Sum_probs=94.0

Q ss_pred             CCCccCCCCCCccCccccccCCCccccccchhhcHHhchhccccchhhhh------cCCCccccccccCccCCcCcccch
Q psy4925          34 YPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER------ADGSRRTTRYDIDMTKCIYCGFCQ  107 (160)
Q Consensus        34 ~p~~~~~~~~~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~------~~~~~~~~~~~~~~~~C~~Cg~C~  107 (160)
                      ||.+....+++|+|.+.+.+.+.+.++||+|+.|+.+||..++.......      ..+......+.++...|++||.|+
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            67777888899999998888888889999999999999999887643321      122233444568899999999999


Q ss_pred             hcccccccccCCcccccccchhhhhccHHHHhccCCcchHH
Q psy4925         108 EACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKWESE  148 (160)
Q Consensus       108 ~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (160)
                      ++||++||.++..++++.+++.+++++...++.+...+...
T Consensus        81 e~CPt~AI~~~~~~e~~~~~r~~l~~~k~~ll~~~~~~~~~  121 (154)
T d2fug91          81 EACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTKPQ  121 (154)
T ss_dssp             HHCSSSCEEECSCCCCCBSCGGGSEECSTTTBTTCCSCHHH
T ss_pred             hhCCCCeEeccCccccccCCHHHhccCHHHhhhcccCCccc
Confidence            99999999999999999999999999988888765544443

>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=99.57  E-value=5e-16  Score=98.40  Aligned_cols=57  Identities=37%  Similarity=0.742  Sum_probs=47.3

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      +.+|.++|++||.|+.+||.++|..+....        ...++...|++||.|+.+||++||...
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            345789999999999999999987655431        345678889999999999999999864

>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=99.51  E-value=1.7e-15  Score=94.84  Aligned_cols=65  Identities=40%  Similarity=0.791  Sum_probs=50.2

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc------ccchhcccccccccCCcccccccchhhh
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GFCQEACPVDAIVEGPNFEFSTESHEEL  131 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C------g~C~~~CP~~ai~~~~~~~~~~~~~~~~  131 (160)
                      .++|++||.|+.+||++||.+...          ...++...|++|      |+|+.+||++||.+....   .++..++
T Consensus         5 td~Ci~Cg~C~~~CP~~AI~~~~~----------~~~id~~~C~~C~~~~~~G~C~~vCP~~AI~~~~~~---~e~~~~l   71 (80)
T d1rgva_           5 NDDCTACDACVEECPNEAITPGDP----------IYVIDPTKCSECVGAFDEPQCRLVCPADCIPDNPDY---RETREEL   71 (80)
T ss_dssp             CSCCCCCCTTTTTCTTCCEECCSS----------SCEECTTTCCTTTTTCSSCHHHHHCSSCCCCBCGGG---CCCHHHH
T ss_pred             cccCcCCcCHHHHHHhCccccccc----------cccccCCCCcCCCCcCCCCcchhhccccCeeCCCCC---cccHHHH
Confidence            578999999999999999986543          346788899999      899999999999876532   2344444


Q ss_pred             hccH
Q psy4925         132 LYNK  135 (160)
Q Consensus       132 ~~~~  135 (160)
                      ....
T Consensus        72 ~~k~   75 (80)
T d1rgva_          72 QEKY   75 (80)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>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=99.51  E-value=1.1e-15  Score=89.05  Aligned_cols=50  Identities=40%  Similarity=0.896  Sum_probs=43.0

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      .++|++||.|+.+||+++|....           ...++...|++||.|+++||++||.+.
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            56899999999999999986432           345788899999999999999999864

>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=99.51  E-value=1.3e-15  Score=88.75  Aligned_cols=50  Identities=50%  Similarity=1.058  Sum_probs=43.6

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      .++|++||.|+++||+++|.+++.          .+.++...|++||.|+++||++||..
T Consensus         5 ~e~C~~Cg~C~~~Cp~~ai~~~~~----------~~~i~~~~C~~Cg~C~~~CP~~AI~~   54 (55)
T d2fdna_           5 NEACISCGACEPECPVNAISSGDD----------RYVIDADTCIDCGACAGVCPVDAPVQ   54 (55)
T ss_dssp             CTTCCCCCTTGGGCTTCCEECCSS----------SCEECTTTCCCCCHHHHTCTTCCEEE
T ss_pred             CcCCCChhhHHHhcCccceEcCCc----------eEEECHHHCCCCCChhcccCCCCcCC
Confidence            578999999999999999987653          34678889999999999999999864

>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=99.50  E-value=1.3e-15  Score=95.29  Aligned_cols=54  Identities=41%  Similarity=0.930  Sum_probs=46.2

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc------ccchhcccccccccCCc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC------GFCQEACPVDAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C------g~C~~~CP~~ai~~~~~  120 (160)
                      ..++|++||.|+.+||++||.+...          ...++...|++|      |+|+.+||++||.+...
T Consensus         4 itd~Ci~Cg~C~~~CP~~AI~~~~~----------~~~id~~~C~~C~~~~~~G~C~~vCP~~AI~~~~~   63 (80)
T d1blua_           4 ITDECINCDVCEPECPNGAISQGDE----------TYVIEPSLCTECVGHYETSQCVEVCPVDCIIKDPS   63 (80)
T ss_dssp             ECTTCCCCCTTGGGCTTCCEEECSS----------SEEECGGGCCTTTTTCSSCHHHHHCTTCCEEECTT
T ss_pred             eCcCCCChHHHHHHChhcchhhcCc----------ceEEccccccCCCCCCCCCccccccCCCCccCCCC
Confidence            4688999999999999999976543          456788999999      89999999999987654

>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=99.50  E-value=9.4e-16  Score=96.65  Aligned_cols=66  Identities=26%  Similarity=0.550  Sum_probs=46.1

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCc----cccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSR----RTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~----~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.+|.++||+||+|+.+||..++.........+..    ......++...|++||.|+++||+|||+.++
T Consensus        14 i~iD~~kCI~C~~Cv~aCp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~Cv~vCP~gAi~~k~   83 (83)
T d3c8ya3          14 LTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKS   83 (83)
T ss_dssp             EEEEGGGCCCCCHHHHHHHHHHSCCCSEEEEETTEEEEESGGGCCGGGSSCCCCCHHHHHCSSTTEEECC
T ss_pred             EEEchhHCCCCchHHHhhcccccccceeeeccccceEEcccccccccccccccCCHHHhhCCCCcccccC
Confidence            45689999999999999997655433221111111    1122345667899999999999999998753

>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=99.49  E-value=2.2e-15  Score=98.65  Aligned_cols=65  Identities=25%  Similarity=0.480  Sum_probs=50.0

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.+|.++|++||.|+.+||++++.+..... ..........++...|++||+|+++||++||++..
T Consensus        38 ~~iD~~~Ci~Cg~C~~~CP~~ai~~~~~~~-~~~~~~~~~~i~~~~C~~Cg~C~~~CP~~AI~~~~  102 (103)
T d1xera_          38 VGVDFDLCIADGSCINACPVNVFQWYDTPG-HPASEKKADPVNEQACIFCMACVNVCPVAAIDVKP  102 (103)
T ss_dssp             EEEETTTCCCCCHHHHHCTTCCCEEEECTT-CSSCSEEEECTTGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             EEECHHHCcCcCcccccCcccceeeecccc-ccccccceeEeccccCCCcChHHhhcCccceEeeC
Confidence            346789999999999999999997654321 12222334567888999999999999999999853

>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=99.49  E-value=1.9e-15  Score=93.91  Aligned_cols=53  Identities=38%  Similarity=0.801  Sum_probs=45.4

Q ss_pred             ccccccch--hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          57 GEERCIAC--KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        57 ~~~~Ci~C--g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++|++|  |.|+.+||++||...+.          .+.++...|++||.|+.+||++||.+..
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            36789999  89999999999976543          4567889999999999999999997644

>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=99.49  E-value=2.5e-15  Score=93.30  Aligned_cols=53  Identities=36%  Similarity=0.760  Sum_probs=45.9

Q ss_pred             ccccccch--hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          57 GEERCIAC--KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        57 ~~~~Ci~C--g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++|++|  |.|+.+||++||..+.+          .+.++...|++||.|+.+||++||.+..
T Consensus         4 v~d~C~~C~~~~C~~~CP~~AI~~~~~----------~~~id~~~Ci~Cg~C~~~CP~~AI~~~~   58 (77)
T d1h98a_           4 ICEPCIGVKDQSCVEVCPVECIYDGGD----------QFYIHPEECIDCGACVPACPVNAIYPEE   58 (77)
T ss_dssp             ECGGGTTTCCCHHHHHCTTCCEEECSS----------SEEECTTTCCCCCTHHHHCTTCCEEEGG
T ss_pred             eCccCCCcCCchhHHHCCCCceEccCc----------EEEEcHHHCCCcCcCccccCcCccCCCc
Confidence            46789999  88999999999986653          4567899999999999999999998754

>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=99.49  E-value=2.7e-15  Score=93.92  Aligned_cols=61  Identities=21%  Similarity=0.510  Sum_probs=47.1

Q ss_pred             ccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ..++||+||.|+.+||.+++.+.....  .........++...|++||.|+++||++||.+..
T Consensus         6 ~~d~Ci~Cg~Cv~~Cp~~~i~~~~~~~--~~~~~~~~~~~~~~C~~Cg~C~~~CP~~Ai~~~~   66 (80)
T d1jb0c_           6 IYDTCIGCTQCVRACPTDVLEMVPWDG--CKAGQIASSPRTEDCVGCKRCETACPTDFLSIRV   66 (80)
T ss_dssp             EETTCCCCCHHHHHCTTCCCEEEECSS--STTSEEEECTTGGGCCCCCHHHHHCCSSSCSEEE
T ss_pred             cCCCCcCccCHHHhCCccceEeecccc--ccccccceecchhhCcCCCCccccCCCCCceeEe
Confidence            367899999999999999987654332  2222233456778899999999999999998754

>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=99.38  E-value=5.2e-14  Score=92.38  Aligned_cols=53  Identities=28%  Similarity=0.745  Sum_probs=45.9

Q ss_pred             cccccch--hhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          58 EERCIAC--KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        58 ~~~Ci~C--g~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .++|++|  |.|+.+||++||...+.          .+.++...|++||.|+.+||++||.+.+.
T Consensus         5 ~~~C~~C~~~~C~~~CP~~ai~~~~~----------~~~id~~~Ci~Cg~C~~~CP~~ai~~~~~   59 (106)
T d7fd1a_           5 TDNCIKCKYTDCVEVCPVDCFYEGPN----------FLVIHPDECIDCALCEPECPAQAIFSEDE   59 (106)
T ss_dssp             CGGGTTTCCCHHHHHCTTCCEEECSS----------CEEECTTTCCCCCTTGGGCTTCCEEEGGG
T ss_pred             CccCCCCCCCccccccCCCcccccCC----------EEEEchHHCCCCCCccccCCCCCcccccc
Confidence            5789999  79999999999986543          45689999999999999999999987554

>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=99.36  E-value=6.9e-14  Score=97.17  Aligned_cols=60  Identities=32%  Similarity=0.677  Sum_probs=49.5

Q ss_pred             Cccccccchh-----hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCccc
Q psy4925          56 SGEERCIACK-----LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFE  122 (160)
Q Consensus        56 ~~~~~Ci~Cg-----~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~~~  122 (160)
                      +|.++|++||     .|+.+||++||.++..+.       ..+.++...|++||.|+.+||++||.+....+
T Consensus         4 id~~~C~gCg~c~~~~C~~~CP~~ai~~~~~~~-------~~~~~d~~~C~~C~~C~~~CP~~Ai~~~~~~d   68 (149)
T d1jnrb_           4 VNPEKCDGCKALERTACEYICPNDLMTLDKEKM-------KAYNREPDMCWECYSCVKMCPQGAIDVRGYVD   68 (149)
T ss_dssp             ECTTTCCSCCSSSSCHHHHHCTTSCEEEETTTT-------EEEESCGGGCCCCCHHHHHCTTCCEEECCCTT
T ss_pred             EcchhCCCCCCCCcchHHHhCCcccEEecCCCc-------EEEEeccccCCCCccccCcCchheeeeccccc
Confidence            4688999999     699999999998765431       13457888999999999999999999876544

>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=6.3e-14  Score=93.56  Aligned_cols=66  Identities=30%  Similarity=0.637  Sum_probs=44.4

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhh---cCC--------------CccccccccCccCCcCcccchhccccc--c
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEER---ADG--------------SRRTTRYDIDMTKCIYCGFCQEACPVD--A  114 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~---~~~--------------~~~~~~~~~~~~~C~~Cg~C~~~CP~~--a  114 (160)
                      ..+|.++||+||.|+.+||..++.......   ...              ......+.++.+.|++||+|+++||++  |
T Consensus        14 pv~d~~~Ci~Cg~C~~vCP~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~C~~CG~C~~~CP~~~~a   93 (117)
T d2c42a5          14 PQWVPENCIQCNQCAFVCPHSAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDCMGCGNCADICPPKEKA   93 (117)
T ss_dssp             EEECTTTCCCCCHHHHHCSSCCEEEEEECGGGGTTCCTTCCCEECCSGGGTTCEEEEEECTTTCCCCCHHHHHCSSSSCS
T ss_pred             CEeCchhcCCCcChhhhCchhheeeeecCHHHhhhhhhhccccccccccccccceeeeeccccCCccCchhhhcCCCcCc
Confidence            346789999999999999988774321100   000              001112335677899999999999988  6


Q ss_pred             cccCC
Q psy4925         115 IVEGP  119 (160)
Q Consensus       115 i~~~~  119 (160)
                      |.+..
T Consensus        94 i~m~~   98 (117)
T d2c42a5          94 LVMQP   98 (117)
T ss_dssp             EEEEE
T ss_pred             ccccc
Confidence            77654

>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=99.29  E-value=1.7e-13  Score=80.60  Aligned_cols=56  Identities=21%  Similarity=0.442  Sum_probs=41.9

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      +.+|.++|++||.|+.+||...+. .+++.       ..+..+...|..|+.|+++||++||++
T Consensus         3 v~iD~~~C~~Cg~C~~~cP~~~~~-~~~g~-------~~~~~~~~~c~~c~~c~~~CP~~AI~i   58 (59)
T d1vjwa_           3 VRVDADACIGCGVCENLCPDVFQL-GDDGK-------AKVLQPETDLPCAKDAADSCPTGAISV   58 (59)
T ss_dssp             CEECTTTCCCCCHHHHHCTTTEEE-CTTSS-------EEESCSBCCCTHHHHHHHHCTTCCEEC
T ss_pred             EEEeHHHCCCCCCChHhCchheEE-cccee-------eEEecChHHCcCcCcccCccCcccEEe
Confidence            346789999999999999975443 33221       123344567999999999999999986

>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=99.26  E-value=1.4e-13  Score=82.33  Aligned_cols=60  Identities=22%  Similarity=0.361  Sum_probs=44.2

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.+|.++||+||.|+.+||......++.+.      ......+...|..|+.|+++||++||++.+
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            456889999999999999975333222211      113345678899999999999999999743

>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=99.25  E-value=3.3e-13  Score=95.89  Aligned_cols=59  Identities=25%  Similarity=0.520  Sum_probs=45.4

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccc-ccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP-VDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP-~~ai~~~~~  120 (160)
                      +|.++|++|+.|+.+||.+++.......      .....++...|++||.|+++|| .+||++.+.
T Consensus       104 id~~~Ci~C~~C~~~Cp~~ai~~i~~~~------~~~~~v~~~~C~gCg~C~~vCP~~~aI~mv~~  163 (173)
T d1gtea5         104 IDEEMCINCGKCYMTCNDSGYQAIQFDP------ETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSR  163 (173)
T ss_dssp             ECTTTCCCCCHHHHHHHHHSCSCEEECT------TTCCEEECTTCCCCCHHHHHCSSTTTEEEEEC
T ss_pred             EEchhCCCchHHHHhhhhCCEEEEEecC------CCceEechhhCCCcChhHhhCCCCCcEEEEeC
Confidence            6889999999999999998875322110      0134567788999999999999 589998554

>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=99.24  E-value=8.4e-13  Score=91.64  Aligned_cols=64  Identities=22%  Similarity=0.270  Sum_probs=43.8

Q ss_pred             ccCCCccccccchhhcHHhchh----ccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCC
Q psy4925          52 RRYPSGEERCIACKLCEAICPA----QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~----~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.+.+|.++||.||+||++|+.    +++.+.  +++...... . ......|..||+|+++||+|||..++
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 PFVILDRERCIHCKRCVRYFEEVPGDEVLDFI--ERGVHTFIG-T-MDFGLPSGFSGNITDICPVGALLDLT  144 (151)
T ss_dssp             SSSCEECSCCCCCCHHHHHHHHTTCCCCCCCB--SCGGGCBCC-C-SSTTCCSSCCTHHHHHCSSSSSBCGG
T ss_pred             CeEEecCCCCCcCchHHhhhhhccCCceEEEe--ccccceEEc-c-CCCCCCChhhcCHHhcCcccccccCC
Confidence            5567789999999999999983    344332  222222111 1 12334699999999999999998644

>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=99.20  E-value=2.1e-13  Score=81.94  Aligned_cols=61  Identities=25%  Similarity=0.386  Sum_probs=42.9

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccC
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEG  118 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~  118 (160)
                      +.+|.++|++||.|+.+||..... +..+..   ........+...|..|+.|+.+||++||++.
T Consensus         4 i~vD~~~Ci~Cg~C~~~CP~~~~~-~~~~~~---~~~~~~~~~~~~c~~c~~c~~~CP~~AI~i~   64 (66)
T d1sj1a_           4 VSVDQDTCIGDAICASLCPDVFEM-NDEGKA---QPKVEVIEDEELYNCAKEAMEACPVSAITIE   64 (66)
T ss_dssp             EEECTTTCCCCCHHHHHCTTTEEE-CTTSCE---EESCSCBCCHHHHHHHHHHHHHCTTCCEEEE
T ss_pred             EEEeHHHCCCcChhhhhCCceEEE-cccCce---EeeccccCChHHHhhhCHhhccCCcccEEEE
Confidence            456789999999999999975332 222211   0111223455679999999999999999874

>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=99.19  E-value=7.1e-13  Score=77.63  Aligned_cols=53  Identities=25%  Similarity=0.457  Sum_probs=39.9

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      .++||+||.|+.+||...+..++..       ...+..+...|..|+.|+++||++||+.
T Consensus         5 ~e~CigCg~C~~~CP~~~~~~~~g~-------~~~~~~~~~~~~~c~~c~~~CP~~AIs~   57 (58)
T d1fxda_           5 NDDCMACEACVEICPDVFEMNEEGD-------KAVVINPDSDLDCVEEAIDSCPAEAIVR   57 (58)
T ss_dssp             CTTCCCCCHHHHHCTTTEEECSSSS-------SEEESCTTCCCHHHHHHHHHCTTCCEEE
T ss_pred             CccCcChhhHHHHcChhheEcCCCC-------EEEEecCCCCcHHHHHHhhcCChhcEEC
Confidence            4689999999999997655433221       1123446678999999999999999986

>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=99.18  E-value=1.6e-12  Score=77.63  Aligned_cols=50  Identities=28%  Similarity=0.723  Sum_probs=41.8

Q ss_pred             cccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          60 RCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        60 ~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      .|.+|+  .|+.+||++||..+....        .+.++.+.|++||.|+.+||++||..
T Consensus        11 ~c~~C~~~~Cv~~CP~~Ai~~~~~~g--------~v~id~~~CigCg~C~~aCP~~ai~d   62 (65)
T d3c7bb1          11 IRKTCEIPSTVAACPTGALKPDMKNK--------TIKVDVEKCMYCGNCYTMCPGMPLFD   62 (65)
T ss_dssp             HHHHCCHHHHHHTCTTCCEEEETTTT--------EEEECTTTCCCCCHHHHHCTTCCCCC
T ss_pred             hhCCCCChHHHHhCcCCCccccccCC--------cEEEeCCcCcccChhhhhCCcccccC
Confidence            489998  699999999998664321        45688999999999999999999854

>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=98.86  E-value=4.7e-11  Score=88.81  Aligned_cols=23  Identities=35%  Similarity=0.726  Sum_probs=11.2

Q ss_pred             CccccccchhhcHHhchhccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      +|.++||+|+.|+.+||.+++.+
T Consensus       127 id~~~CiGC~~C~~ACPyga~~~  149 (244)
T d1kqfb1         127 FQSENCIGCGYCIAGCPFNIPRL  149 (244)
T ss_dssp             ECGGGCCCCCHHHHHCTTCCCEE
T ss_pred             EccccccchhhHhhcCCCCCcEe
Confidence            34444555555555555554443

>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=98.82  E-value=1.9e-10  Score=71.43  Aligned_cols=64  Identities=22%  Similarity=0.274  Sum_probs=43.5

Q ss_pred             CccccccchhhcHHhchhccccchhhhhcCCC--ccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEERADGS--RRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~--~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +|.++||+||.|+.+||... .+++.+.....  .......++...|..|+.|+++||++||++...
T Consensus         6 VD~~~CigCg~C~~~cP~~f-~~~~dg~~~~~~~~~~~~~~v~~~~~~~~~~aa~~CP~~AI~v~d~   71 (81)
T d1iqza_           6 VDKETCIACGACGAAAPDIY-DYDEDGIAYVTLDDNQGIVEVPDILIDDMMDAFEGCPTDSIKVADE   71 (81)
T ss_dssp             ECTTTCCCCSHHHHHCTTTE-EECTTSCEEETTTTTSSCSCCCGGGHHHHHHHHHHCTTCCEEEESS
T ss_pred             EeHHHCcCcChHhHhCchhe-eEcCCCeEEEeecCCcCcccCCHHHHHHHHHHHHhCCcccEEEEeC
Confidence            57889999999999999543 23322211100  111122355677899999999999999998664

>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=98.82  E-value=3.4e-10  Score=84.10  Aligned_cols=55  Identities=25%  Similarity=0.703  Sum_probs=43.2

Q ss_pred             cccccchhh--cHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          58 EERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        58 ~~~Ci~Cg~--Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ...|.+|+.  |+.+||++++.......        .+.+|.+.|++|+.|+.+||++|+.+...
T Consensus        96 ~~~C~HC~~p~Cv~vCPt~Aa~~~~e~G--------~V~id~~~CiGC~~C~~ACPyga~~~~~~  152 (244)
T d1kqfb1          96 KDGCMHCEDPGCLKACPSAGAIIQYANG--------IVDFQSENCIGCGYCIAGCPFNIPRLNKE  152 (244)
T ss_dssp             EESCCCBSSCHHHHHCCSTTSEEEETTS--------CEEECGGGCCCCCHHHHHCTTCCCEEETT
T ss_pred             chhhccccCCcccccccccceeEEcCCC--------cEEEccccccchhhHhhcCCCCCcEeccc
Confidence            346999996  99999987655432211        56789999999999999999999987544

>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=98.78  E-value=4.8e-10  Score=80.64  Aligned_cols=52  Identities=21%  Similarity=0.262  Sum_probs=34.4

Q ss_pred             CCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc-------------cchhccccccccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG-------------FCQEACPVDAIVE  117 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg-------------~C~~~CP~~ai~~  117 (160)
                      ..+|.++||+|+.|+.+||.+++.++...            ....+|.+|.             +|+++||++||.+
T Consensus        92 V~id~~kCiGC~~C~~aCPy~a~~~~~~~------------~~~~KC~~C~~r~~~~~~~g~~PaCv~~Cp~~a~~f  156 (195)
T d1vlfn2          92 VLIDPEKAKGKKELLDTCPYGVMYWNEEE------------NVAQKCTMCAHLLDDESWAPKMPRCAHNCGSFVYEF  156 (195)
T ss_dssp             EEECTTTTTTCGGGGGGCSSCCCEEETTT------------TEEECCCTTHHHHTCTTCTTCSCHHHHHCSSCCEEE
T ss_pred             eeeehhhccccchhhcCCCCCCeEccccc------------CCccccCcchhhhhccccccchhhhhhhCcHhheec
Confidence            44567778888888888887777654321            1224677772             5778888777776

>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=98.76  E-value=8.5e-10  Score=89.47  Aligned_cols=56  Identities=30%  Similarity=0.464  Sum_probs=41.9

Q ss_pred             ccccccchhh--cHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          57 GEERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        57 ~~~~Ci~Cg~--Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ....|.+|..  |+.+||++|+..+....        .+.+|.+.|++|+.|+.+||++++.+...
T Consensus       180 ~~~~C~hC~~~~C~~~CP~gAi~~~~e~G--------~v~id~~~CigC~~C~~aCPy~~~~~~~~  237 (509)
T d1y5ib1         180 LPRLCEHCLNPACVATCPSGAIYKREEDG--------IVLIDQDKCRGWRMCITGCPYKKIYFNWK  237 (509)
T ss_dssp             EEECCCCCSSCHHHHHCTTCCEEEETTTC--------CEEECTTTCCCCCCHHHHCTTCCEEEETT
T ss_pred             ecccccCCCCchhhhhcCcCceEEecCCC--------cEEEchhhccchHHHHhhCCCCCeEecCC
Confidence            3457999985  99999999886543211        56678888999988888888888776544

>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=98.74  E-value=7.3e-10  Score=74.82  Aligned_cols=71  Identities=17%  Similarity=0.294  Sum_probs=40.4

Q ss_pred             CccCccccccCCCccccccchhhcHHhchhccccchhhhh-------------cCCCccc-----cccccCccCCcCccc
Q psy4925          44 RFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER-------------ADGSRRT-----TRYDIDMTKCIYCGF  105 (160)
Q Consensus        44 ~~~~~~~~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~-------------~~~~~~~-----~~~~~~~~~C~~Cg~  105 (160)
                      .....++......+...||.||.|+.+||+-...-.....             .......     .......+.|+.|++
T Consensus        26 e~~~~~~~~~~~~~~~~CI~CG~C~~~CP~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~~C~~C~~  105 (132)
T d1nekb1          26 EHLQMPEQREKLDGLYECILCACCSTSCPSFWWNPDKFIGPAGLLAAYRFLIDSRDTETDSRLDGLSDAFSVFRCHSIMN  105 (132)
T ss_dssp             SCCCCHHHHHTTTTTSCCCCCCHHHHTCHHHHHCTTTSCCHHHHHHHHHHHTCTTCCCHHHHHHTTCSSSTTTTCCCCCH
T ss_pred             ccccCHHHHHHHHhhHHHhHhhhhhhhCccccccCccccchhHHHHHHHHHhcccccccccchhhhhccchhhhCcCccc
Confidence            3333333334445678999999999999963211110000             0000000     011123567999999


Q ss_pred             chhcccccc
Q psy4925         106 CQEACPVDA  114 (160)
Q Consensus       106 C~~~CP~~a  114 (160)
                      |.++||.+.
T Consensus       106 C~~vCP~gI  114 (132)
T d1nekb1         106 CVSVCPKGL  114 (132)
T ss_dssp             HHHHCTTCC
T ss_pred             ccccCcCCC
Confidence            999999994

>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=98.70  E-value=8.2e-10  Score=89.58  Aligned_cols=62  Identities=21%  Similarity=0.388  Sum_probs=47.9

Q ss_pred             cccCCCccccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCcc---------cchhcccccccccCCcc
Q psy4925          51 LRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEACPVDAIVEGPNF  121 (160)
Q Consensus        51 ~~~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg---------~C~~~CP~~ai~~~~~~  121 (160)
                      ...+.+|.++||+|+.|+.+||.+++.+....            ....+|++|.         +|+.+||++||.+....
T Consensus       207 ~G~v~id~~~CigC~~C~~aCPy~~~~~~~~~------------~~~~KC~~C~~r~~~G~~paCv~~Cp~~A~~~g~~~  274 (509)
T d1y5ib1         207 DGIVLIDQDKCRGWRMCITGCPYKKIYFNWKS------------GKSEKCIFCYPRIEAGQPTVCSETCVGRIRYLGVLL  274 (509)
T ss_dssp             TCCEEECTTTCCCCCCHHHHCTTCCEEEETTT------------TEEEECCTTHHHHTTTCCCHHHHTCTTCCEEEEEEE
T ss_pred             CCcEEEchhhccchHHHHhhCCCCCeEecCCC------------CceeecccchhHHhcCCCChhhhhCcHhhhhhchhc
Confidence            34455789999999999999999998765432            2235799993         39999999999988765


Q ss_pred             ccc
Q psy4925         122 EFS  124 (160)
Q Consensus       122 ~~~  124 (160)
                      +..
T Consensus       275 d~~  277 (509)
T d1y5ib1         275 YDA  277 (509)
T ss_dssp             EEG
T ss_pred             chH
Confidence            443

>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=98.62  E-value=5.7e-09  Score=74.88  Aligned_cols=53  Identities=19%  Similarity=0.231  Sum_probs=43.0

Q ss_pred             cccccchhh--cHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccccCCc
Q psy4925          58 EERCIACKL--CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        58 ~~~Ci~Cg~--Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ...|.+|..  |+. ||.+|+..++.+         .+.+|.+.|++|+.|+.+||++||.+...
T Consensus        65 ~~~C~hC~~p~Cv~-~p~~A~~~~e~G---------~V~id~~kCiGC~~C~~aCPy~a~~~~~~  119 (195)
T d1vlfn2          65 PTPCMHCENAPCVA-KGNGAVYQREDG---------IVLIDPEKAKGKKELLDTCPYGVMYWNEE  119 (195)
T ss_dssp             EECCCCCTTCHHHH-TTTTSEEECTTS---------CEEECTTTTTTCGGGGGGCSSCCCEEETT
T ss_pred             hhhccCCcCccccc-cccceEEeeccc---------ceeeehhhccccchhhcCCCCCCeEcccc
Confidence            456999985  994 667777655443         67889999999999999999999998665

>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=98.61  E-value=9.7e-10  Score=74.20  Aligned_cols=59  Identities=20%  Similarity=0.450  Sum_probs=35.1

Q ss_pred             CccccccchhhcHHhchhccccchhhh--------------hcCCCc-c-cccc--ccCccCCcCcccchhcccccc
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEAEE--------------RADGSR-R-TTRY--DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~~~--------------~~~~~~-~-~~~~--~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ++.++||.||.|..+||+....-...+              +..+.. . ...+  ......|+.||.|.++||.+.
T Consensus        40 ~~~~~Ci~CG~C~~~CP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ct~Cg~C~~vCP~gI  116 (133)
T d2bs2b1          40 FELDRCIECGCCIAACGTKIMREDFVGAAGLNRVVRFMIDPHDERTDEDYYELIGDDDGVFGCMTLLACHDVCPKNL  116 (133)
T ss_dssp             HHHHTCCCCCHHHHTCHHHHHCTTCCHHHHHHHHHHHHTCTTCCCCHHHHHHHHCSTTTGGGCCCCCHHHHHCTTCC
T ss_pred             HhHHHHhhhhhHHHhCCccccCCCccchHHHHHHHHHhhcchhhhhHHHHHHHhhccccchhChhhCCCcccCcCCC
Confidence            356789999999999997432211000              000000 0 0011  123457999999999999883

>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=98.57  E-value=4.1e-09  Score=71.66  Aligned_cols=58  Identities=31%  Similarity=0.732  Sum_probs=34.2

Q ss_pred             ccccccchhhcHHhchhccccchhhh--------------hcCCCc-ccccc--ccCccCCcCcccchhcccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITIEAEE--------------RADGSR-RTTRY--DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~~~~~--------------~~~~~~-~~~~~--~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ...+||+||.|..+||+....-+..+              +..... +...+  ....+.|+.||.|.++||.+.
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            45789999999999997322111000              000000 00011  122457999999999999883

>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=98.51  E-value=1.3e-08  Score=73.93  Aligned_cols=51  Identities=25%  Similarity=0.413  Sum_probs=40.4

Q ss_pred             cccccchhhcHHhchhccccchhhhhcCCCccccccccCccCCcCc---------ccchhcccccccccCCc
Q psy4925          58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC---------GFCQEACPVDAIVEGPN  120 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~C---------g~C~~~CP~~ai~~~~~  120 (160)
                      ..+|++|+.|+.+||.+++.+....            ....+|.+|         -+|+++||++||.+.+.
T Consensus       107 ~~~c~gc~~C~~aCPy~~~~~~~~~------------~~~~KCd~C~~R~~~G~~PaCV~~CP~~Al~fGd~  166 (214)
T d1h0hb_         107 TKDLEDYESVISACPYDVPRKVAES------------NQMAKCDMCIDRITNGLRPACVTSCPTGAMNFGDL  166 (214)
T ss_dssp             GGGCSCHHHHHHHCTTCCCEECTTS------------SCEECCCTTHHHHTTTCCCHHHHHCSSSCEEEEEH
T ss_pred             cccccCcceecccCCCCCceecccC------------CccEeCcccHHHHhCCCCCCceeecccCCEEEeeh
Confidence            3479999999999999988664321            234579999         27999999999999775

>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=97.87  E-value=1.3e-06  Score=55.56  Aligned_cols=54  Identities=22%  Similarity=0.385  Sum_probs=40.3

Q ss_pred             cccchh--hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          60 RCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        60 ~Ci~Cg--~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      .|..|.  -|.++||+++..+......    ...++.++...|+.||.|.-+||.++|.-
T Consensus        33 ~~~~~y~~Pc~r~CPAgVYE~~~~~~~----~~~~l~In~~nCleC~tC~i~~p~~nI~W   88 (102)
T d2gmha3          33 RNLSIYDGPEQRFCPAGVYEFVPLEQG----DGFRLQINAQNCVHCKTCDIKDPSQNINW   88 (102)
T ss_dssp             THHHHHCCTHHHHCTTCCEEEEECSST----TCEEEEECGGGCCCCCHHHHHCTTCCEEE
T ss_pred             cccccccchheeeccceEEEEeecCCC----CccEEEEEeCCceeeccceeeCCCCceEE
Confidence            344453  6999999998876543211    12257889999999999999999999864

>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=97.83  E-value=1.4e-06  Score=49.39  Aligned_cols=25  Identities=32%  Similarity=0.797  Sum_probs=21.7

Q ss_pred             CCccccccchhhcHHhchhccccch
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .++.++|++||.|+.+||++||..+
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

>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=97.69  E-value=4.2e-06  Score=50.69  Aligned_cols=26  Identities=42%  Similarity=0.838  Sum_probs=22.3

Q ss_pred             CCccccccchhhcHHhchhccccchh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .++.++|++||.|+.+||++||....
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            35778999999999999999997653

>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=97.69  E-value=4.7e-06  Score=50.47  Aligned_cols=27  Identities=37%  Similarity=0.726  Sum_probs=23.2

Q ss_pred             CCccccccchhhcHHhchhccccchhh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      .++.++|++||.|+.+||++||..+..
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            357889999999999999999987654

>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=97.61  E-value=1.2e-05  Score=49.43  Aligned_cols=28  Identities=39%  Similarity=0.763  Sum_probs=24.1

Q ss_pred             cccCccCCcCcccchhcccccccccCCc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.+|.+.|++||.|+++||++||.....
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            3568899999999999999999987554

>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=97.59  E-value=6.2e-06  Score=50.17  Aligned_cols=26  Identities=35%  Similarity=0.930  Sum_probs=22.1

Q ss_pred             CCccccccchhhcHHhchhccccchh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .++.+.|++||.|+.+||++||.+..
T Consensus        41 ~~~~~~C~~Cg~C~~~CP~~Ai~~~~   66 (80)
T d1jb0c_          41 SPRTEDCVGCKRCETACPTDFLSIRV   66 (80)
T ss_dssp             CTTGGGCCCCCHHHHHCCSSSCSEEE
T ss_pred             ecchhhCcCCCCccccCCCCCceeEe
Confidence            35677899999999999999998753

>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=97.58  E-value=6.3e-06  Score=46.60  Aligned_cols=23  Identities=30%  Similarity=0.846  Sum_probs=20.3

Q ss_pred             CCccccccchhhcHHhchhcccc
Q psy4925          55 PSGEERCIACKLCEAICPAQAIT   77 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~   77 (160)
                      .++.++|++||.|+.+||++||.
T Consensus        31 ~i~~~~C~~Cg~C~~~CP~~AI~   53 (55)
T d2fdna_          31 VIDADTCIDCGACAGVCPVDAPV   53 (55)
T ss_dssp             EECTTTCCCCCHHHHTCTTCCEE
T ss_pred             EECHHHCCCCCChhcccCCCCcC
Confidence            35678899999999999999985

>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=97.55  E-value=7.1e-06  Score=48.03  Aligned_cols=24  Identities=25%  Similarity=0.733  Sum_probs=20.4

Q ss_pred             CCCccccccchhhcHHhchhcccc
Q psy4925          54 YPSGEERCIACKLCEAICPAQAIT   77 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~   77 (160)
                      ..++.++|++||.|+.+||.++|.
T Consensus        38 v~id~~~CigCg~C~~aCP~~ai~   61 (65)
T d3c7bb1          38 IKVDVEKCMYCGNCYTMCPGMPLF   61 (65)
T ss_dssp             EEECTTTCCCCCHHHHHCTTCCCC
T ss_pred             EEEeCCcCcccChhhhhCCccccc
Confidence            345788999999999999998773

>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=97.54  E-value=9.6e-06  Score=51.71  Aligned_cols=26  Identities=38%  Similarity=0.936  Sum_probs=22.2

Q ss_pred             CCCccccccchhhcHHhchhccccch
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      ..++.+.|++||.|+.+||++||.++
T Consensus        76 ~~i~~~~C~~Cg~C~~~CP~~AI~~~  101 (103)
T d1xera_          76 DPVNEQACIFCMACVNVCPVAAIDVK  101 (103)
T ss_dssp             ECTTGGGCCCCCHHHHHCTTCCEEEC
T ss_pred             eEeccccCCCcChHHhhcCccceEee
Confidence            34567899999999999999999864

>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=97.54  E-value=9.6e-06  Score=49.56  Aligned_cols=24  Identities=25%  Similarity=0.683  Sum_probs=20.6

Q ss_pred             CCccccccchhhcHHhchhccccc
Q psy4925          55 PSGEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      .++...|++||.|+.+||+|||..
T Consensus        58 ~~~~~~C~~Cg~Cv~vCP~gAi~~   81 (83)
T d3c8ya3          58 CFDDTNCLLCGQCIIACPVAALSE   81 (83)
T ss_dssp             CGGGSSCCCCCHHHHHCSSTTEEE
T ss_pred             cccccccccCCHHHhhCCCCcccc
Confidence            356678999999999999999864

>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=97.49  E-value=7e-06  Score=56.07  Aligned_cols=28  Identities=43%  Similarity=0.896  Sum_probs=23.8

Q ss_pred             CCCccccccchhhcHHhchhccccchhh
Q psy4925          54 YPSGEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      +.++..+|+.||.|+.+||++||.+...
T Consensus        66 ~~id~~~C~~CG~Cve~CPt~AI~~~~~   93 (154)
T d2fug91          66 YEINMLRCIFCGLCEEACPTGAIVLGYD   93 (154)
T ss_dssp             EEEETTTCCCCTHHHHHCSSSCEEECSC
T ss_pred             EEeccccCCCCCCchhhCCCCeEeccCc
Confidence            3467789999999999999999987643

>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=97.43  E-value=2.4e-05  Score=47.55  Aligned_cols=24  Identities=38%  Similarity=0.971  Sum_probs=21.1

Q ss_pred             ccCCcCcccchhcccccccccCCc
Q psy4925          97 MTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        97 ~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      .+.|++||.|+.+||++||.+...
T Consensus         5 td~Ci~Cg~C~~~CP~~AI~~~~~   28 (80)
T d1blua_           5 TDECINCDVCEPECPNGAISQGDE   28 (80)
T ss_dssp             CTTCCCCCTTGGGCTTCCEEECSS
T ss_pred             CcCCCChHHHHHHChhcchhhcCc
Confidence            467999999999999999987655

>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=97.40  E-value=1.6e-05  Score=57.09  Aligned_cols=54  Identities=20%  Similarity=0.292  Sum_probs=38.1

Q ss_pred             ccccchh--hcHHhchh---ccccchhhhhcCCCcccccccc--CccCCcCcccchhcccccccccCCc
Q psy4925          59 ERCIACK--LCEAICPA---QAITIEAEERADGSRRTTRYDI--DMTKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        59 ~~Ci~Cg--~Cv~~CP~---~~i~~~~~~~~~~~~~~~~~~~--~~~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      ..|.+|.  .|+.+||+   +++..++..   +     .+..  +...|++|+.|+.+||++++.+...
T Consensus        70 ~~C~HC~~ppC~~~Cp~~~~~~~v~~~~~---G-----~v~~~~~~~~c~gc~~C~~aCPy~~~~~~~~  130 (214)
T d1h0hb_          70 DQCRHCIAPPCKATADMEDESAIIHDDAT---G-----CVLFTPKTKDLEDYESVISACPYDVPRKVAE  130 (214)
T ss_dssp             ECCCCCSSCHHHHHHTTTCTTSEEECTTT---C-----CEEECGGGGGCSCHHHHHHHCTTCCCEECTT
T ss_pred             cccccCCCCcccccccccCCceEEEEeCC---C-----eEEEecccccccCcceecccCCCCCceeccc
Confidence            4699998  59999997   344433221   1     2223  4447999999999999999887554

>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=97.40  E-value=1.5e-05  Score=51.18  Aligned_cols=27  Identities=52%  Similarity=0.914  Sum_probs=23.4

Q ss_pred             CCccccccchhhcHHhchhccccchhh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEAE   81 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~~   81 (160)
                      .++.+.||+||.|+.+||++||..+..
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            367889999999999999999987654

>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=97.39  E-value=2.9e-05  Score=47.18  Aligned_cols=23  Identities=39%  Similarity=0.907  Sum_probs=20.4

Q ss_pred             cCCcCcccchhcccccccccCCc
Q psy4925          98 TKCIYCGFCQEACPVDAIVEGPN  120 (160)
Q Consensus        98 ~~C~~Cg~C~~~CP~~ai~~~~~  120 (160)
                      +.|++||.|+.+||++||.+...
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            46999999999999999987655

>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=97.23  E-value=3.9e-05  Score=44.64  Aligned_cols=49  Identities=33%  Similarity=0.710  Sum_probs=34.0

Q ss_pred             hcHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhcccccccc
Q psy4925          66 LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV  116 (160)
Q Consensus        66 ~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~  116 (160)
                      .=+.+||++||+-.....  +......+.++.++|..||+|-..||.--|.
T Consensus        18 l~iAaCPT~AIrP~k~~~--~~~~~ksV~V~~eRCMyCGNCYT~cp~~~i~   66 (69)
T d2v4jb1          18 LAVASCPTAAVRPTKLEI--GDKKVNTIAIKNERCMYCGNCYTMCPALPIS   66 (69)
T ss_dssp             HHHHTCTTCCEEEEEEEE--TTEEEEEEEECGGGCCCCCHHHHHCTTCCCC
T ss_pred             chhhcCCccccccccccc--CCcccceEEEcCCcceecCCccccCCCcccC
Confidence            456889999998533211  1122235668899999999999999975443

>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=96.91  E-value=0.00011  Score=49.60  Aligned_cols=26  Identities=27%  Similarity=0.713  Sum_probs=22.5

Q ss_pred             CCccccccchhhcHHhchhccccchh
Q psy4925          55 PSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        55 ~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .++.+.|++||.|+.+||++||.+..
T Consensus        40 ~~d~~~C~~C~~C~~~CP~~Ai~~~~   65 (149)
T d1jnrb_          40 NREPDMCWECYSCVKMCPQGAIDVRG   65 (149)
T ss_dssp             ESCGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             EeccccCCCCccccCcCchheeeecc
Confidence            35678999999999999999998754

>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=96.81  E-value=7.4e-05  Score=43.35  Aligned_cols=25  Identities=40%  Similarity=0.494  Sum_probs=21.5

Q ss_pred             CccccccchhhcHHhchhccccchh
Q psy4925          56 SGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      .+.+.|+.|+.|+.+||++||.+++
T Consensus        41 ~~~~~c~~c~~c~~~CP~~AI~i~e   65 (66)
T d1sj1a_          41 EDEELYNCAKEAMEACPVSAITIEE   65 (66)
T ss_dssp             CCHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             CChHHHhhhCHhhccCCcccEEEEe
Confidence            4567899999999999999998754

>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=96.71  E-value=0.00029  Score=45.45  Aligned_cols=25  Identities=32%  Similarity=0.631  Sum_probs=21.7

Q ss_pred             cccCccCCcCcccchhccccccccc
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      ...+.+.|++||.|+.+||.++|..
T Consensus        14 pv~d~~~Ci~Cg~C~~vCP~~~i~~   38 (117)
T d2c42a5          14 PQWVPENCIQCNQCAFVCPHSAILP   38 (117)
T ss_dssp             EEECTTTCCCCCHHHHHCSSCCEEE
T ss_pred             CEeCchhcCCCcChhhhCchhheee
Confidence            4568889999999999999998864

>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=96.71  E-value=0.00025  Score=40.13  Aligned_cols=28  Identities=29%  Similarity=0.716  Sum_probs=22.5

Q ss_pred             ccccCccCCcCcccchhcccccccccCC
Q psy4925          92 RYDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        92 ~~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      ++.+|.+.|++||.|+.+||..++....
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            3467889999999999999977665443

>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=96.65  E-value=0.00016  Score=50.04  Aligned_cols=27  Identities=30%  Similarity=0.904  Sum_probs=22.3

Q ss_pred             CCCccccccchhhcHHhchh-ccccchh
Q psy4925          54 YPSGEERCIACKLCEAICPA-QAITIEA   80 (160)
Q Consensus        54 ~~~~~~~Ci~Cg~Cv~~CP~-~~i~~~~   80 (160)
                      ..++.+.|++||.|+.+||+ +||.+..
T Consensus       135 ~~v~~~~C~gCg~C~~vCP~~~aI~mv~  162 (173)
T d1gtea5         135 LPTVTDTCTGCTLCLSVCPIIDCIRMVS  162 (173)
T ss_dssp             CEEECTTCCCCCHHHHHCSSTTTEEEEE
T ss_pred             eEechhhCCCcChhHhhCCCCCcEEEEe
Confidence            34567899999999999995 8998764

>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=96.60  E-value=0.00022  Score=41.05  Aligned_cols=24  Identities=21%  Similarity=0.224  Sum_probs=21.0

Q ss_pred             CccccccchhhcHHhchhccccch
Q psy4925          56 SGEERCIACKLCEAICPAQAITIE   79 (160)
Q Consensus        56 ~~~~~Ci~Cg~Cv~~CP~~~i~~~   79 (160)
                      .+.+.|..|+.|+.+||++||.+.
T Consensus        39 ~~~~~c~~c~~c~~~CP~~aI~~~   62 (64)
T d1fxra_          39 VEGASQEEVEEAMDTCPVQCIHWE   62 (64)
T ss_dssp             TTSSCHHHHHHHHHHCTTCCEEEE
T ss_pred             cCCCcchhHHHHHhcCCcccEEEE
Confidence            456789999999999999999864

>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=96.46  E-value=0.0009  Score=45.14  Aligned_cols=21  Identities=19%  Similarity=0.091  Sum_probs=18.4

Q ss_pred             cccccchhhcHHhchhccccc
Q psy4925          58 EERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        58 ~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      ...|+.||.|+.+||+|||..
T Consensus       122 ~~~c~~cG~Cv~vCPtGAL~e  142 (151)
T d2fug34         122 GLPSGFSGNITDICPVGALLD  142 (151)
T ss_dssp             TCCSSCCTHHHHHCSSSSSBC
T ss_pred             CCCChhhcCHHhcCccccccc
Confidence            346999999999999999964

>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=95.66  E-value=0.0014  Score=36.80  Aligned_cols=22  Identities=23%  Similarity=0.267  Sum_probs=19.0

Q ss_pred             ccccccchhhcHHhchhccccc
Q psy4925          57 GEERCIACKLCEAICPAQAITI   78 (160)
Q Consensus        57 ~~~~Ci~Cg~Cv~~CP~~~i~~   78 (160)
                      +.+.|..|+.|+.+||++||..
T Consensus        36 ~~~~~~~c~~c~~~CP~~AIs~   57 (58)
T d1fxda_          36 PDSDLDCVEEAIDSCPAEAIVR   57 (58)
T ss_dssp             TTCCCHHHHHHHHHCTTCCEEE
T ss_pred             CCCCcHHHHHHhhcCChhcEEC
Confidence            4567999999999999999864

>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=95.25  E-value=0.0029  Score=37.87  Aligned_cols=27  Identities=30%  Similarity=0.473  Sum_probs=21.5

Q ss_pred             cccCccCCcCcccchhcccccccccCC
Q psy4925          93 YDIDMTKCIYCGFCQEACPVDAIVEGP  119 (160)
Q Consensus        93 ~~~~~~~C~~Cg~C~~~CP~~ai~~~~  119 (160)
                      +.+|.+.|++||.|+.+||........
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            457888999999999999977554433

>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=94.13  E-value=0.0072  Score=34.58  Aligned_cols=40  Identities=28%  Similarity=0.625  Sum_probs=31.4

Q ss_pred             cHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          67 CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        67 Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      -+..||++++.++..          .+.++...|+-|.-|+.+-|. ||+.
T Consensus        24 Vv~~CPT~cm~~dg~----------~L~Idn~~CvRCMHCIN~Mpk-AL~p   63 (66)
T d3c7ba1          24 VVKLCPTGAIKWDGK----------ELTIDNRECVRCMHCINKMPK-ALKP   63 (66)
T ss_dssp             TGGGCTTCCEEECSS----------CEEECTTTCCCCCHHHHHCTT-TEEC
T ss_pred             hhccCccccccccCC----------EEEEcCcccCccccchhcCcc-ccCC
Confidence            456799999988643          467888999999999999874 4543

>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=93.80  E-value=0.0074  Score=39.23  Aligned_cols=17  Identities=24%  Similarity=0.741  Sum_probs=15.1

Q ss_pred             ccccchhhcHHhchhcc
Q psy4925          59 ERCIACKLCEAICPAQA   75 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~   75 (160)
                      ..|+.||.|+.+||.+.
T Consensus       100 ~~Ct~Cg~C~~vCP~gI  116 (133)
T d2bs2b1         100 FGCMTLLACHDVCPKNL  116 (133)
T ss_dssp             GGCCCCCHHHHHCTTCC
T ss_pred             hhChhhCCCcccCcCCC
Confidence            46999999999999874

>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=93.09  E-value=0.023  Score=36.78  Aligned_cols=21  Identities=29%  Similarity=0.695  Sum_probs=17.7

Q ss_pred             ccCccCCcCcccchhcccccc
Q psy4925          94 DIDMTKCIYCGFCQEACPVDA  114 (160)
Q Consensus        94 ~~~~~~C~~Cg~C~~~CP~~a  114 (160)
                      ..+...|+.||.|..+||.-.
T Consensus        37 ~~~~~~CI~CG~C~~~CP~~~   57 (132)
T d1nekb1          37 LDGLYECILCACCSTSCPSFW   57 (132)
T ss_dssp             TTTTSCCCCCCHHHHTCHHHH
T ss_pred             HHhhHHHhHhhhhhhhCcccc
Confidence            356778999999999999753

>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=93.05  E-value=0.0082  Score=37.51  Aligned_cols=28  Identities=29%  Similarity=0.624  Sum_probs=23.3

Q ss_pred             cCCCccccccchhhcHHhchhccccchh
Q psy4925          53 RYPSGEERCIACKLCEAICPAQAITIEA   80 (160)
Q Consensus        53 ~~~~~~~~Ci~Cg~Cv~~CP~~~i~~~~   80 (160)
                      ++.++.+.|++||.|-.+||.++|...-
T Consensus        63 ~l~In~~nCleC~tC~i~~p~~nI~W~~   90 (102)
T d2gmha3          63 RLQINAQNCVHCKTCDIKDPSQNINWVV   90 (102)
T ss_dssp             EEEECGGGCCCCCHHHHHCTTCCEEECC
T ss_pred             EEEEEeCCceeeccceeeCCCCceEEEC
Confidence            3456778999999999999999987654

>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=92.92  E-value=0.013  Score=34.75  Aligned_cols=40  Identities=23%  Similarity=0.582  Sum_probs=31.4

Q ss_pred             cHHhchhccccchhhhhcCCCccccccccCccCCcCcccchhccccccccc
Q psy4925          67 CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE  117 (160)
Q Consensus        67 Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~~ai~~  117 (160)
                      -+.-||++++.++..          .+.++...|+-|.-|+.+-|. ||+.
T Consensus        39 Vv~~CPT~cm~~d~~----------~L~Idn~~C~RCMHCINvMPk-ALrp   78 (81)
T d2v4ja1          39 VVNRCPSKCMKWDGS----------KLSIDNKECVRCMHCINTMPR-ALHI   78 (81)
T ss_dssp             TGGGCTTCCEEECSS----------CEEECGGGCCCCSHHHHHCTT-TEEC
T ss_pred             hhccCCHhhccccCC----------eeEEeCcccccCcCchhhCcc-ccCC
Confidence            457789999988643          567888999999999999885 3543

>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=92.85  E-value=0.013  Score=38.53  Aligned_cols=17  Identities=24%  Similarity=0.741  Sum_probs=15.0

Q ss_pred             ccccchhhcHHhchhcc
Q psy4925          59 ERCIACKLCEAICPAQA   75 (160)
Q Consensus        59 ~~Ci~Cg~Cv~~CP~~~   75 (160)
                      -.|+.||.|+.+||.++
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            36999999999999874

>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=88.19  E-value=0.048  Score=31.19  Aligned_cols=22  Identities=36%  Similarity=0.887  Sum_probs=18.5

Q ss_pred             ccCCCccccccchhhcHHhchh
Q psy4925          52 RRYPSGEERCIACKLCEAICPA   73 (160)
Q Consensus        52 ~~~~~~~~~Ci~Cg~Cv~~CP~   73 (160)
                      ..+.++.++|.-||.|...||.
T Consensus        41 ksV~V~~eRCMyCGNCYT~cp~   62 (69)
T d2v4jb1          41 NTIAIKNERCMYCGNCYTMCPA   62 (69)
T ss_dssp             EEEEECGGGCCCCCHHHHHCTT
T ss_pred             ceEEEcCCcceecCCccccCCC
Confidence            3455678999999999999996

>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=80.07  E-value=0.064  Score=36.74  Aligned_cols=19  Identities=32%  Similarity=0.969  Sum_probs=16.0

Q ss_pred             ccccccchh--hcHHhchhcc
Q psy4925          57 GEERCIACK--LCEAICPAQA   75 (160)
Q Consensus        57 ~~~~Ci~Cg--~Cv~~CP~~~   75 (160)
                      +.++|+.|+  -|+.+||++.
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            457999998  7999999863