Psyllid ID: psy6642

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290--
Protein Sequence
MLAHSDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHcccEEEEccccccccEEEEEEccEEEEEEEccHHHHHHHHcccccccccccccccccccccEEEEEcccccccccccccccccccEEcccccccccccccccccccccccccccEEEccccEEEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHcccEEEEccccccccEEEEEEccEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEHHHcccccEEEEEEccEEEEEEEccHHHHHHHHcccHHHccccccHHHccccccEEEEEccccccccccEEcccccEEEEEccccEEEEccccEEEcccccccccccEEEccccEEEEEcccccccccccHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEHHHcccccEEEEEEccEEEEEEEc
Coil and Loop (DISEMBL)
mlahsdirtpdfskyrrdrnpdkgqeETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDlnlipegqsvtfkwrgkplfirhRTQKEidteqntnisqlrdpqadsdrvkdpswLVIIGICThlgcvpianagdwggyycpchgshydasgrirkgpaptnmevppyqfgdegILIRMLahsdirtpdfskyrrdrnpdkgqeETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDlnlipegqsvtfkwrgkplfirhr
Flexible Loop (DISEMBL)
mlahsdirtpdfskyrrdrnpdkgqeetqRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLnlipegqsvtfkwrgkpLFIRHRtqkeidteqntnisqlrdpqadsdrVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHsdirtpdfskyrrdrnpdkgqeetqRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDlnlipegqsvtfkwrgkplfirhr
Low Complexity Region (SEG)
MLAHSDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR
Disordered region (IsUnstruct)
*******************************AFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR****************************PSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRI**********VPPYQFGDEGILIRMLAHSDI************************AFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFI***
Disordered Region (DISOPRED)
*LAHSDIRTPDFS********************TYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQK**********************VKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPDF*********************TYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR
Disordered Region (DISEMBL)
MLAHSDIRTPDFSKYRR***********QRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQ**********VKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYR************QRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR
Disordered Region (DISPRO)
****SDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLAHSDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR
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	292	2.2.26 [Sep-21-2011]
Q69BJ7	274	Cytochrome b-c1 complex s	N/A	N/A	0.650	0.693	0.628	5e-73
Q69BJ8	274	Cytochrome b-c1 complex s	N/A	N/A	0.650	0.693	0.625	6e-73
Q69BK3	274	Cytochrome b-c1 complex s	N/A	N/A	0.650	0.693	0.623	2e-72
Q69BJ9	274	Cytochrome b-c1 complex s	N/A	N/A	0.650	0.693	0.618	3e-72
Q69BK1	274	Cytochrome b-c1 complex s	N/A	N/A	0.650	0.693	0.620	7e-72
P47985	274	Cytochrome b-c1 complex s	yes	N/A	0.650	0.693	0.613	2e-71
Q69BK4	274	Cytochrome b-c1 complex s	N/A	N/A	0.650	0.693	0.613	2e-71
Q9CR68	274	Cytochrome b-c1 complex s	yes	N/A	0.654	0.697	0.605	3e-71
Q69BK5	274	Cytochrome b-c1 complex s	yes	N/A	0.650	0.693	0.608	4e-71
Q69BK6	274	Cytochrome b-c1 complex s	N/A	N/A	0.650	0.693	0.608	4e-71

>sp|Q69BJ7|UCRI_SAISC Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Saimiri sciureus GN=UQCRFS1 PE=3 SV=1

 Score =  274 bits (701), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 122/194 (62%), Positives = 152/194 (78%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRRDRNPDKGQEETQ----RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+DI+ PDFS YRR    DK +   +    RK F+YM+   ++V     AKS+V QFIS
Sbjct: 79  SHTDIKVPDFSDYRRSEVLDKTKSSRESSDARKVFSYMVTATTAVGVTYAAKSIVTQFIS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 199 QHDLDRVKKPEWMILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 258

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + +++
Sbjct: 259 EVPTYEFLSDDMVV 272

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.
Saimiri sciureus (taxid: 9521)
EC: 1EC: .EC: 1EC: 0EC: .EC: 2EC: .EC: 2

>sp|Q69BJ8|UCRI_LAGLA Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Lagothrix lagotricha GN=UQCRFS1 PE=3 SV=1

 Score =  274 bits (700), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 122/195 (62%), Positives = 154/195 (78%), Gaps = 5/195 (2%)

Query: 3   AHSDIRTPDFSKYRRDRNPDKGQEETQ----RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+DI+ PDFS YRR    DK +   +    RK F+Y++   ++V     AKS+V QF+S
Sbjct: 79  SHTDIKVPDFSDYRRSEVLDKTKSSRESSDARKGFSYLVTAATAVGVTYAAKSIVTQFVS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 199 QHDLDRVKKPEWMILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 258

Query: 179 EVPPYQF-GDEGILI 192
           EVP Y+F GD+ +++
Sbjct: 259 EVPTYEFTGDDMVIV 273

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Lagothrix lagotricha (taxid: 9519)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

>sp|Q69BK3|UCRI_PONPY Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Pongo pygmaeus GN=UQCRFS1 PE=3 SV=1

 Score =  272 bits (696), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 121/194 (62%), Positives = 152/194 (78%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+D+R PDFS+YRR    D      +    RK F+Y++ G ++V     AK+VV QF+S
Sbjct: 79  SHTDVRVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNVVTQFVS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLA+A IE+ L+ IPEG+++TFKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLALAKIEIKLSDIPEGKNMTFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIR GPAP N+
Sbjct: 199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNL 258

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 259 EVPIYEFTSDDMVI 272

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Pongo pygmaeus (taxid: 9600)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

>sp|Q69BJ9|UCRI_AOTAZ Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Aotus azarae GN=UQCRFS1 PE=3 SV=1

 Score =  271 bits (694), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 120/194 (61%), Positives = 150/194 (77%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+DI+ PDFS YRR    D      +    RK F+Y++   ++V     AKS+V QF+S
Sbjct: 79  SHTDIKVPDFSDYRRSEVLDTTKSSRESSDARKGFSYLVTATTAVGVTYAAKSIVTQFVS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 199 QHDLDRVKKPEWMILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 258

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 259 EVPTYEFTSDDLVI 272

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Aotus azarae (taxid: 30591)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

>sp|Q69BK1|UCRI_CHLAE Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Chlorocebus aethiops GN=UQCRFS1 PE=3 SV=1

 Score =  270 bits (691), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 121/195 (62%), Positives = 152/195 (77%), Gaps = 5/195 (2%)

Query: 3   AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+D++ PDF  YRR    D      +    RK F+Y++   ++V     AK+VV QFIS
Sbjct: 79  SHTDVKVPDFYDYRRLEVLDSTKSSRESSEARKGFSYLVTAVTTVGVAYAAKNVVTQFIS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAMA IE++L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLAMAKIEINLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEEEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIR GPAP N+
Sbjct: 199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNL 258

Query: 179 EVPPYQF-GDEGILI 192
           EVPPY+F GD+ +++
Sbjct: 259 EVPPYEFTGDDVVVV 273

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Chlorocebus aethiops (taxid: 9534)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

>sp|P47985|UCRI_HUMAN Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Homo sapiens GN=UQCRFS1 PE=1 SV=2

 Score =  269 bits (687), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 119/194 (61%), Positives = 150/194 (77%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+DI+ PDFS+YRR    D      +    RK F+Y++ G ++V     AK+ V QF+S
Sbjct: 79  SHTDIKVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLA+A IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIR GPAP N+
Sbjct: 199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNL 258

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 259 EVPTYEFTSDDMVI 272

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Homo sapiens (taxid: 9606)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

>sp|Q69BK4|UCRI_GORGO Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Gorilla gorilla gorilla GN=UQCRFS1 PE=3 SV=1

 Score =  268 bits (686), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 119/194 (61%), Positives = 150/194 (77%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+DI+ PDFS+YRR    D      +    RK F+Y++ G ++V     AK+ V QF+S
Sbjct: 79  SHTDIKVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLA+A IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIR GPAP N+
Sbjct: 199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNL 258

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 259 EVPTYEFTSDDMVI 272

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Gorilla gorilla gorilla (taxid: 9595)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

>sp|Q9CR68|UCRI_MOUSE Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Mus musculus GN=Uqcrfs1 PE=1 SV=1

 Score =  268 bits (686), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 118/195 (60%), Positives = 151/195 (77%), Gaps = 4/195 (2%)

Query: 2   LAHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFI 57
            +H+D++ PDFS YRR    D      +    RK F+Y++   ++V     AK+VV+QF+
Sbjct: 78  FSHTDVKVPDFSDYRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFV 137

Query: 58  SSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRD 117
           SSMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRD
Sbjct: 138 SSMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRD 197

Query: 118 PQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTN 177
           PQ D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N
Sbjct: 198 PQHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLN 257

Query: 178 MEVPPYQFGDEGILI 192
           +EVP Y+F  + +++
Sbjct: 258 LEVPAYEFTSDDVVV 272

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Mus musculus (taxid: 10090)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

>sp|Q69BK5|UCRI_PANTR Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Pan troglodytes GN=UQCRFS1 PE=3 SV=1

 Score =  268 bits (685), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 118/194 (60%), Positives = 150/194 (77%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+D++ PDFS+YRR    D      +    RK F+Y++ G ++V     AK+ V QF+S
Sbjct: 79  SHTDVKVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLA+A IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIR GPAP N+
Sbjct: 199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNL 258

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 259 EVPTYEFTSDDMVI 272

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Pan troglodytes (taxid: 9598)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

>sp|Q69BK6|UCRI_PANPA Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Pan paniscus GN=UQCRFS1 PE=3 SV=1

 Score =  268 bits (685), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 118/194 (60%), Positives = 150/194 (77%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+D++ PDFS+YRR    D      +    RK F+Y++ G ++V     AK+ V QF+S
Sbjct: 79  SHTDVKVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVS 138

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLA+A IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct: 139 SMSASADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIR GPAP N+
Sbjct: 199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNL 258

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 259 EVPTYEFTSDDMVI 272

The transit peptide of the Rieske protein seems to form part of the bc1 complex and is considered to be the subunit 11/IX of that complex.

Pan paniscus (taxid: 9597)

EC: 1

EC: .

EC: 1

EC: 0

EC: .

EC: 2

EC: .

EC: 2

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	292
348519190	240	PREDICTED: cytochrome b-c1 complex subun	0.654	0.795	0.635	5e-75
288814596	272	ubiquinol-cytochrome c reductase [Locust	0.650	0.698	0.673	9e-75
209734266	273	Cytochrome b-c1 complex subunit Rieske,	0.654	0.699	0.646	1e-74
283046728	268	ubiquinol-cytochrome c reductase, Rieske	0.650	0.708	0.680	1e-74
37747939	273	Ubiquinol-cytochrome c reductase, Rieske	0.654	0.699	0.641	2e-74
157073897	273	cytochrome b-c1 complex subunit Rieske,	0.654	0.699	0.641	2e-74
158299624	265	AGAP008955-PA [Anopheles gambiae str. PE	0.650	0.716	0.663	4e-74
432862546	235	PREDICTED: cytochrome b-c1 complex subun	0.654	0.812	0.635	4e-74
289742957	258	ubiquinol cytochrome c reductase subunit	0.654	0.740	0.664	5e-74
289742955	248	ubiquinol cytochrome c reductase subunit	0.654	0.770	0.664	7e-74

>gi|348519190|ref|XP_003447114.1| PREDICTED: cytochrome b-c1 complex subunit Rieske, mitochondrial-like [Oreochromis niloticus]

 Score =  287 bits (734), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 124/195 (63%), Positives = 164/195 (84%), Gaps = 4/195 (2%)

Query: 2   LAHSDIRTPDFSKYRRDR--NPDKGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFI 57
           LAH+DI+ PDFS YRR    +P+K  +E+   R+AF+Y++ G ++VVG+  AK+VV QFI
Sbjct: 44  LAHTDIKIPDFSDYRRPEVMDPNKSSQESSEARRAFSYLVTGATTVVGVYAAKTVVTQFI 103

Query: 58  SSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRD 117
           SSMSASADVLA++ IE+ L+ IPEG+++TFKWRGKPLF+RHRT+KEI TEQ  N+++LRD
Sbjct: 104 SSMSASADVLALSKIEIKLSDIPEGKNMTFKWRGKPLFVRHRTEKEIATEQAVNLAELRD 163

Query: 118 PQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTN 177
           P+ D DRV +P W++++G+CTHLGCVPIANAG++GGYYCPCHGSHYDASGRIRKGPAP N
Sbjct: 164 PEHDKDRVTNPKWVIVLGVCTHLGCVPIANAGEYGGYYCPCHGSHYDASGRIRKGPAPLN 223

Query: 178 MEVPPYQFGDEGILI 192
           +EVP Y+F D+  ++
Sbjct: 224 LEVPYYEFQDDETVV 238

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|288814596|gb|ADC54384.1| ubiquinol-cytochrome c reductase [Locusta migratoria manilensis]

 Score =  286 bits (731), Expect = 9e-75,   Method: Compositional matrix adjust.
 Identities = 130/193 (67%), Positives = 153/193 (79%), Gaps = 3/193 (1%)

Query: 3   AHSDIRTPDFSKYRRDRNPD---KGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISS 59
           AH+DI+ PDFS YRR    D   K  E   RK+FTY++AG  ++ G   AK++V QF+SS
Sbjct: 78  AHTDIQVPDFSAYRRHSVTDPTTKNTEPEARKSFTYLVAGTGAIAGAYGAKALVTQFVSS 137

Query: 60  MSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQ 119
           MSASADVLA+A IEV L  IPEG+SVTFKWRGKPLFIRHRT  EI  EQ+ N+S LRDPQ
Sbjct: 138 MSASADVLALAKIEVKLAEIPEGKSVTFKWRGKPLFIRHRTAAEIQQEQSVNVSTLRDPQ 197

Query: 120 ADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNME 179
            D++RV+ P WLV++G+CTHLGCVPIANAGD+GGYYCPCHGSHYDAS RIRKGPAP N+E
Sbjct: 198 HDNERVQKPEWLVVLGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASRRIRKGPAPLNLE 257

Query: 180 VPPYQFGDEGILI 192
           VP Y F DEG L+
Sbjct: 258 VPAYVFQDEGTLV 270

Source: Locusta migratoria manilensis

Species: Locusta migratoria

Genus: Locusta

Family: Acrididae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|209734266|gb|ACI68002.1| Cytochrome b-c1 complex subunit Rieske, mitochondrial precursor [Salmo salar]

 Score =  286 bits (731), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 126/195 (64%), Positives = 159/195 (81%), Gaps = 4/195 (2%)

Query: 2   LAHSDIRTPDFSKYRRDR--NPDKGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFI 57
            AH+DI+ PDFS YRR    +P+K  +E+   RK F+Y++ G ++VVG+  AK+V  QFI
Sbjct: 77  FAHTDIKVPDFSDYRRPELLDPNKSSQESSESRKTFSYLVTGATAVVGVYTAKTVATQFI 136

Query: 58  SSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRD 117
           SSMSASADVLAM+ IEV L  IPEG+++TFKWRGKPLFIRHR++KEI  E+  ++++LRD
Sbjct: 137 SSMSASADVLAMSKIEVKLGEIPEGKNMTFKWRGKPLFIRHRSEKEIAAEEAVDMAELRD 196

Query: 118 PQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTN 177
           PQ D DRV +P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N
Sbjct: 197 PQHDKDRVANPKWIIVIGVCTHLGCVPIANAGDYGGYYCPCHGSHYDASGRIRKGPAPLN 256

Query: 178 MEVPPYQFGDEGILI 192
           +EVP Y+F DE  +I
Sbjct: 257 LEVPYYEFPDEDTVI 271

Source: Salmo salar

Species: Salmo salar

Genus: Salmo

Family: Salmonidae

Order: Salmoniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|283046728|ref|NP_001164310.1| ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 [Tribolium castaneum] gi|270004785|gb|EFA01233.1| hypothetical protein TcasGA2_TC000043 [Tribolium castaneum]

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 132/194 (68%), Positives = 156/194 (80%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRRD--RNPDKGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           AH+DI  PD+S YRRD  + P     +++  RK+FTY+IAG  +V     AK+VV QF+S
Sbjct: 73  AHTDINVPDWSHYRRDPVKAPTAKSTDSEEGRKSFTYLIAGAGTVTAAYAAKAVVGQFVS 132

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLA+A IE+ L  IPEG+SVTFKWRGKPLFIRHRT +EI TEQ  N+S LRDP
Sbjct: 133 SMSASADVLALAKIEIKLGEIPEGKSVTFKWRGKPLFIRHRTAEEIATEQGVNVSSLRDP 192

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D+DRVK P WLVI+G+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 193 QHDNDRVKKPEWLVILGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 252

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F D+  L+
Sbjct: 253 EVPYYEFPDDTTLV 266

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|37747939|gb|AAH59475.1| Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 [Danio rerio]

 Score =  285 bits (728), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 125/195 (64%), Positives = 162/195 (83%), Gaps = 4/195 (2%)

Query: 2   LAHSDIRTPDFSKYRRDR--NPDKGQEET--QRKAFTYMIAGGSSVVGMVCAKSVVNQFI 57
            AH+DI+ PDFS YRR    NP+K  +E+   R+AF+Y++ G + VVG+  AK+VV QF+
Sbjct: 77  FAHTDIKIPDFSDYRRPEVLNPNKQSQESGDARRAFSYLMTGSTLVVGVYTAKTVVTQFV 136

Query: 58  SSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRD 117
           SSMSASADVLA++ IE+ L  IPEG+++TFKWRGKPLF+RHRT+KEI+TE   N+++LRD
Sbjct: 137 SSMSASADVLALSKIEIKLADIPEGKNMTFKWRGKPLFVRHRTEKEIETEAGVNLAELRD 196

Query: 118 PQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTN 177
           PQ D DRV +PSW+++IG+CTHLGCVPIANAG++GGYYCPCHGSHYDASGRIRKGPAP N
Sbjct: 197 PQHDKDRVVNPSWVIVIGVCTHLGCVPIANAGEFGGYYCPCHGSHYDASGRIRKGPAPLN 256

Query: 178 MEVPPYQFGDEGILI 192
           +EVP Y+F D+  ++
Sbjct: 257 LEVPYYEFPDDDTVV 271

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|157073897|ref|NP_001096664.1| cytochrome b-c1 complex subunit Rieske, mitochondrial [Danio rerio] gi|292616189|ref|XP_002662916.1| PREDICTED: cytochrome b-c1 complex subunit Rieske, mitochondrial-like isoform 1 [Danio rerio] gi|326669539|ref|XP_003199036.1| PREDICTED: cytochrome b-c1 complex subunit Rieske, mitochondrial-like isoform 2 [Danio rerio] gi|156230934|gb|AAI52278.1| Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 [Danio rerio]

 Score =  285 bits (728), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 125/195 (64%), Positives = 162/195 (83%), Gaps = 4/195 (2%)

Query: 2   LAHSDIRTPDFSKYRRDR--NPDKGQEET--QRKAFTYMIAGGSSVVGMVCAKSVVNQFI 57
            AH+DI+ PDFS YRR    NP+K  +E+   R+AF+Y++ G + VVG+  AK+VV QF+
Sbjct: 77  FAHTDIKIPDFSDYRRPEVLNPNKQSQESGDARRAFSYLMTGSTLVVGVYTAKTVVTQFV 136

Query: 58  SSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRD 117
           SSMSASADVLA++ IE+ L  IPEG+++TFKWRGKPLF+RHRT+KEI+TE   N+++LRD
Sbjct: 137 SSMSASADVLALSKIEIKLADIPEGKNMTFKWRGKPLFVRHRTEKEIETEAGVNLAELRD 196

Query: 118 PQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTN 177
           PQ D DRV +PSW+++IG+CTHLGCVPIANAG++GGYYCPCHGSHYDASGRIRKGPAP N
Sbjct: 197 PQHDKDRVVNPSWVIVIGVCTHLGCVPIANAGEFGGYYCPCHGSHYDASGRIRKGPAPLN 256

Query: 178 MEVPPYQFGDEGILI 192
           +EVP Y+F D+  ++
Sbjct: 257 LEVPYYEFPDDDTVV 271

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|158299624|ref|XP_319708.4| AGAP008955-PA [Anopheles gambiae str. PEST] gi|157013606|gb|EAA14787.4| AGAP008955-PA [Anopheles gambiae str. PEST]

 Score =  284 bits (726), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 128/193 (66%), Positives = 157/193 (81%), Gaps = 3/193 (1%)

Query: 3   AHSDIRTPDFSKYRRD--RNPD-KGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISS 59
           AH+DIR PDFS YRRD  + P+ K      R AFTY++ GG++V     AKS+V+ F+SS
Sbjct: 71  AHTDIRVPDFSDYRRDQVKRPNAKNDSADDRAAFTYLLVGGAAVSTAYVAKSLVSTFVSS 130

Query: 60  MSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQ 119
           MSASADVLAM+ IE+ L  IPEG+S+TFKWRGKPLFIRHRT  EI+ EQ+  ++ LRDPQ
Sbjct: 131 MSASADVLAMSKIEIKLADIPEGKSMTFKWRGKPLFIRHRTSAEIEAEQSVAVATLRDPQ 190

Query: 120 ADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNME 179
            D++RV+ P WLV+IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+E
Sbjct: 191 NDAERVQKPEWLVVIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLE 250

Query: 180 VPPYQFGDEGILI 192
           VP Y+F ++G+LI
Sbjct: 251 VPHYEFPEDGLLI 263

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|432862546|ref|XP_004069909.1| PREDICTED: cytochrome b-c1 complex subunit Rieske, mitochondrial-like [Oryzias latipes]

 Score =  283 bits (725), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 124/195 (63%), Positives = 163/195 (83%), Gaps = 4/195 (2%)

Query: 2   LAHSDIRTPDFSKYRRDR--NPDKGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFI 57
           LAH+DI+ PDFS YRR    +P+K  +E+   R+AF+Y++ G ++VVG+  AK+VV QF+
Sbjct: 39  LAHTDIKIPDFSDYRRPEVLDPNKSSQESSEARRAFSYLLTGATTVVGVYAAKTVVTQFV 98

Query: 58  SSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRD 117
           SSMSASADVLA++ IE+ L  IPEG+++TFKWRGKPLF+RHRT+KEI TE+  N+++LRD
Sbjct: 99  SSMSASADVLALSQIEIKLGDIPEGKNMTFKWRGKPLFVRHRTEKEIATEEAVNLTELRD 158

Query: 118 PQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTN 177
           PQ D DRV +P W++++G+CTHLGCVPI+NAGD+GGYYCPCHGSHYDASGRIRKGPAP N
Sbjct: 159 PQHDKDRVINPKWVIVLGVCTHLGCVPISNAGDFGGYYCPCHGSHYDASGRIRKGPAPLN 218

Query: 178 MEVPPYQFGDEGILI 192
           +EVP Y+F DE  ++
Sbjct: 219 LEVPFYEFPDEETVV 233

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|289742957|gb|ADD20226.1| ubiquinol cytochrome c reductase subunit RIP1 [Glossina morsitans morsitans]

 Score =  283 bits (725), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 129/194 (66%), Positives = 154/194 (79%), Gaps = 3/194 (1%)

Query: 2   LAHSDIRTPDFSKYRRD--RNPDKGQEET-QRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           LAHSD+  PDF+ YRR+  +N ++  +   QRKAF+YM+ G ++V     AK +VN F+S
Sbjct: 63  LAHSDLEVPDFTPYRRENVKNANRRNDSAEQRKAFSYMLVGATAVGSAYAAKGLVNTFVS 122

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAMA IE+ L  IPEG+SVTFKWRGKPLFIRHRT  EI TE+N  ++ LRDP
Sbjct: 123 SMSASADVLAMAKIEIKLGDIPEGKSVTFKWRGKPLFIRHRTGAEIATERNVAVATLRDP 182

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q+D  RV  P WLV+IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 183 QSDDQRVTKPEWLVVIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 242

Query: 179 EVPPYQFGDEGILI 192
           EVP + F DEG L+
Sbjct: 243 EVPAHTFPDEGTLV 256

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289742955|gb|ADD20225.1| ubiquinol cytochrome c reductase subunit RIP1 [Glossina morsitans morsitans]

 Score =  283 bits (723), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 129/194 (66%), Positives = 154/194 (79%), Gaps = 3/194 (1%)

Query: 2   LAHSDIRTPDFSKYRRD--RNPDKGQEET-QRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           LAHSD+  PDF+ YRR+  +N ++  +   QRKAF+YM+ G ++V     AK +VN F+S
Sbjct: 53  LAHSDLEVPDFTPYRRENVKNANRRNDSAEQRKAFSYMLVGATAVGSAYAAKGLVNTFVS 112

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAMA IE+ L  IPEG+SVTFKWRGKPLFIRHRT  EI TE+N  ++ LRDP
Sbjct: 113 SMSASADVLAMAKIEIKLGDIPEGKSVTFKWRGKPLFIRHRTGAEIATERNVAVATLRDP 172

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q+D  RV  P WLV+IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 173 QSDDQRVTKPEWLVVIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 232

Query: 179 EVPPYQFGDEGILI 192
           EVP + F DEG L+
Sbjct: 233 EVPAHTFPDEGTLV 246

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

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	292
ZFIN|ZDB-GENE-040426-2060	273	uqcrfs1 "ubiquinol-cytochrome	0.650	0.695	0.644	1.4e-69
UNIPROTKB|E2R1A6	274	UQCRFS1 "Ubiquinol-cytochrome	0.650	0.693	0.635	2.2e-66
MGI|MGI:1913944	274	Uqcrfs1 "ubiquinol-cytochrome	0.650	0.693	0.618	1.2e-65
UNIPROTKB|G3MXD1	271	UQCRFS1 "Ubiquinol-cytochrome	0.650	0.701	0.623	2.5e-65
UNIPROTKB|P13272	274	UQCRFS1 "Cytochrome b-c1 compl	0.650	0.693	0.623	2.5e-65
UNIPROTKB|F1RNZ1	274	UQCRFS1 "Uncharacterized prote	0.650	0.693	0.628	2.5e-65
UNIPROTKB|P47985	274	UQCRFS1 "Cytochrome b-c1 compl	0.650	0.693	0.613	6.7e-65
RGD|628838	274	Uqcrfs1 "ubiquinol-cytochrome	0.650	0.693	0.613	1.8e-64
UNIPROTKB|Q5ZLR5	272	UQCRFS1 "Cytochrome b-c1 compl	0.647	0.694	0.608	4.7e-64
UNIPROTKB|P0C7P4	283	UQCRFS1P1 "Putative cytochrome	0.650	0.671	0.618	9.7e-64

ZFIN|ZDB-GENE-040426-2060 uqcrfs1 "ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1" [Danio rerio (taxid:7955)]

 Score = 705 (253.2 bits), Expect = 1.4e-69, P = 1.4e-69
 Identities = 125/194 (64%), Positives = 162/194 (83%)

Query:     3 AHSDIRTPDFSKYRRDR--NPDKGQEET--QRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             AH+DI+ PDFS YRR    NP+K  +E+   R+AF+Y++ G + VVG+  AK+VV QF+S
Sbjct:    78 AHTDIKIPDFSDYRRPEVLNPNKQSQESGDARRAFSYLMTGSTLVVGVYTAKTVVTQFVS 137

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLA++ IE+ L  IPEG+++TFKWRGKPLF+RHRT+KEI+TE   N+++LRDP
Sbjct:   138 SMSASADVLALSKIEIKLADIPEGKNMTFKWRGKPLFVRHRTEKEIETEAGVNLAELRDP 197

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D DRV +PSW+++IG+CTHLGCVPIANAG++GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct:   198 QHDKDRVVNPSWVIVIGVCTHLGCVPIANAGEFGGYYCPCHGSHYDASGRIRKGPAPLNL 257

Query:   179 EVPPYQFGDEGILI 192
             EVP Y+F D+  ++
Sbjct:   258 EVPYYEFPDDDTVV 271

GO:0016679 "oxidoreductase activity, acting on diphenols and related substances as donors" evidence=IEA

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

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

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

GO:0070469 "respiratory chain" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0006810 "transport" evidence=IEA

UNIPROTKB|E2R1A6 UQCRFS1 "Ubiquinol-cytochrome c reductase iron-sulfur subunit" [Canis lupus familiaris (taxid:9615)]

 Score = 675 (242.7 bits), Expect = 2.2e-66, P = 2.2e-66
 Identities = 124/195 (63%), Positives = 156/195 (80%)

Query:     3 AHSDIRTPDFSKYRRDRNPD--KGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             +H+DIR PDFS YRR    D  K  +E+   RK F+Y+I   +S+     AK+VV+QF+S
Sbjct:    79 SHTDIRVPDFSDYRRAEVLDGTKSSKESSEARKGFSYLITATTSIGVAYAAKNVVSQFVS 138

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEI+ E    +SQLRDP
Sbjct:   139 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIEQEAAVEVSQLRDP 198

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct:   199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 258

Query:   179 EVPPYQF-GDEGILI 192
             EVP Y+F GD+ +++
Sbjct:   259 EVPSYEFTGDDMVIV 273

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=IEA

GO:0070469 "respiratory chain" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

MGI|MGI:1913944 Uqcrfs1 "ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1" [Mus musculus (taxid:10090)]

 Score = 668 (240.2 bits), Expect = 1.2e-65, P = 1.2e-65
 Identities = 120/194 (61%), Positives = 154/194 (79%)

Query:     3 AHSDIRTPDFSKYRRDRNPD--KGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             +H+D++ PDFS YRR    D  K  +E+   RK F+Y++   ++V     AK+VV+QF+S
Sbjct:    79 SHTDVKVPDFSDYRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 138

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDP
Sbjct:   139 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP 198

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct:   199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 258

Query:   179 EVPPYQFGDEGILI 192
             EVP Y+F  + +++
Sbjct:   259 EVPAYEFTSDDVVV 272

GO:0005515 "protein binding" evidence=IPI

GO:0005739 "mitochondrion" evidence=IDA

GO:0005743 "mitochondrial inner membrane" evidence=IDA

GO:0005750 "mitochondrial respiratory chain complex III" evidence=ISO

GO:0006810 "transport" evidence=IEA

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=IEA

GO:0016679 "oxidoreductase activity, acting on diphenols and related substances as donors" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0031966 "mitochondrial membrane" evidence=ISO

GO:0032403 "protein complex binding" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

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

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

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

GO:0070469 "respiratory chain" evidence=IEA

UNIPROTKB|G3MXD1 UQCRFS1 "Ubiquinol-cytochrome c reductase iron-sulfur subunit" [Bos taurus (taxid:9913)]

 Score = 665 (239.2 bits), Expect = 2.5e-65, P = 2.5e-65
 Identities = 121/194 (62%), Positives = 154/194 (79%)

Query:     3 AHSDIRTPDFSKYRRDRNPD--KGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             +H+DI+ PDFS YRR    D  K  +E+   RK F+Y++   ++V     AK+VV+QF+S
Sbjct:    76 SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 135

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDP
Sbjct:   136 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP 195

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D +RVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct:   196 QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 255

Query:   179 EVPPYQFGDEGILI 192
             EVP Y+F  + ++I
Sbjct:   256 EVPSYEFTSDDMVI 269

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=IEA

GO:0070469 "respiratory chain" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

UNIPROTKB|P13272 UQCRFS1 "Cytochrome b-c1 complex subunit Rieske, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 665 (239.2 bits), Expect = 2.5e-65, P = 2.5e-65
 Identities = 121/194 (62%), Positives = 154/194 (79%)

Query:     3 AHSDIRTPDFSKYRRDRNPD--KGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             +H+DI+ PDFS YRR    D  K  +E+   RK F+Y++   ++V     AK+VV+QF+S
Sbjct:    79 SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 138

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDP
Sbjct:   139 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP 198

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D +RVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct:   199 QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 258

Query:   179 EVPPYQFGDEGILI 192
             EVP Y+F  + ++I
Sbjct:   259 EVPSYEFTSDDMVI 272

GO:0005739 "mitochondrion" evidence=ISS

GO:0005743 "mitochondrial inner membrane" evidence=ISS

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=IEA

GO:0070469 "respiratory chain" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|F1RNZ1 UQCRFS1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 665 (239.2 bits), Expect = 2.5e-65, P = 2.5e-65
 Identities = 122/194 (62%), Positives = 153/194 (78%)

Query:     3 AHSDIRTPDFSKYRRDRNPD--KGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             +H+DIR PDFS YRR    D  K  +E+   RK F+Y+I   ++V     AK+ V+QF+S
Sbjct:    79 SHTDIRVPDFSDYRRAEVLDSTKSSKESSDARKGFSYLITATTTVGVAYAAKNAVSQFVS 138

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDP
Sbjct:   139 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP 198

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D +RVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct:   199 QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 258

Query:   179 EVPPYQFGDEGILI 192
             EVP Y+F  + ++I
Sbjct:   259 EVPTYEFTSDDLVI 272

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=IEA

UNIPROTKB|P47985 UQCRFS1 "Cytochrome b-c1 complex subunit Rieske, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 661 (237.7 bits), Expect = 6.7e-65, P = 6.7e-65
 Identities = 119/194 (61%), Positives = 150/194 (77%)

Query:     3 AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             +H+DI+ PDFS+YRR    D      +    RK F+Y++ G ++V     AK+ V QF+S
Sbjct:    79 SHTDIKVPDFSEYRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVS 138

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLA+A IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI+ E    +SQLRDP
Sbjct:   139 SMSASADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDP 198

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIR GPAP N+
Sbjct:   199 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNL 258

Query:   179 EVPPYQFGDEGILI 192
             EVP Y+F  + ++I
Sbjct:   259 EVPTYEFTSDDMVI 272

GO:0016021 "integral to membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0009725 "response to hormone stimulus" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0042493 "response to drug" evidence=IEA

GO:0046677 "response to antibiotic" evidence=IEA

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=NAS

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

GO:0005750 "mitochondrial respiratory chain complex III" evidence=NAS

GO:0005743 "mitochondrial inner membrane" evidence=TAS

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

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

GO:0005739 "mitochondrion" evidence=IDA

RGD|628838 Uqcrfs1 "ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1" [Rattus norvegicus (taxid:10116)]

 Score = 657 (236.3 bits), Expect = 1.8e-64, P = 1.8e-64
 Identities = 119/194 (61%), Positives = 152/194 (78%)

Query:     3 AHSDIRTPDFSKYRRDRNPD--KGQEETQ--RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             +H+DI+ PDFS YRR    D  K  +E+   RK F+Y++   ++V     AK+ V+QF+S
Sbjct:    79 SHTDIKVPDFSDYRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNAVSQFVS 138

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDP
Sbjct:   139 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP 198

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D +RVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct:   199 QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 258

Query:   179 EVPPYQFGDEGILI 192
             EVP Y+F    +++
Sbjct:   259 EVPTYEFTSGDVVV 272

GO:0005739 "mitochondrion" evidence=ISO

GO:0005743 "mitochondrial inner membrane" evidence=ISO

GO:0005750 "mitochondrial respiratory chain complex III" evidence=IDA

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=TAS

GO:0009725 "response to hormone stimulus" evidence=IEP

GO:0016021 "integral to membrane" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0031966 "mitochondrial membrane" evidence=IDA

GO:0032403 "protein complex binding" evidence=IDA

GO:0042493 "response to drug" evidence=IEP

GO:0045275 "respiratory chain complex III" evidence=TAS

GO:0046677 "response to antibiotic" evidence=IEP

GO:0046872 "metal ion binding" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

UNIPROTKB|Q5ZLR5 UQCRFS1 "Cytochrome b-c1 complex subunit Rieske, mitochondrial" [Gallus gallus (taxid:9031)]

 Score = 653 (234.9 bits), Expect = 4.7e-64, P = 4.7e-64
 Identities = 118/194 (60%), Positives = 152/194 (78%)

Query:     4 HSDIRTPDFSKYRRDRNPD---KGQEETQ-RKAFTYMIAGGSSVVGMVCAKSVVNQFISS 59
             H+D+  PDFS YRR+   D     Q  ++ RK F+Y++   + V     AK+VV QFISS
Sbjct:    78 HNDVTVPDFSAYRREDVMDATTSSQTSSEDRKGFSYLVTATACVATAYAAKNVVTQFISS 137

Query:    60 MSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQ 119
             +SASADVLA++ IE+ L+ IPEG++V FKWRGKPLF+RHRTQ EI+ E   ++S+LRDPQ
Sbjct:   138 LSASADVLALSKIEIKLSDIPEGKNVAFKWRGKPLFVRHRTQAEINQEAEVDVSKLRDPQ 197

Query:   120 ADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNME 179
              D DRVK P W++++G+CTHLGCVPIAN+GD+GGYYCPCHGSHYDASGRIRKGPAP N+E
Sbjct:   198 HDLDRVKKPEWVILVGVCTHLGCVPIANSGDFGGYYCPCHGSHYDASGRIRKGPAPYNLE 257

Query:   180 VPPYQF-GDEGILI 192
             VP YQF GD+ +++
Sbjct:   258 VPTYQFVGDDLVVV 271

GO:0016021 "integral to membrane" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0070469 "respiratory chain" evidence=IEA

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=IEA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

UNIPROTKB|P0C7P4 UQCRFS1P1 "Putative cytochrome b-c1 complex subunit Rieske-like protein 1" [Homo sapiens (taxid:9606)]

 Score = 650 (233.9 bits), Expect = 9.7e-64, P = 9.7e-64
 Identities = 120/194 (61%), Positives = 151/194 (77%)

Query:     3 AHSDIRTPDFSKYRRDRNPDK---GQEETQ-RKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
             +H+DI+ PDFS+YRR    D     +E T+ RK F+Y++ G ++V     AK+ V QF+S
Sbjct:    88 SHTDIKVPDFSEYRRLEVLDSTKSSRESTEARKGFSYLVTGVTTVGVAYAAKNAVTQFVS 147

Query:    59 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
             SMSASADVLA+A IE+ L+ IPEG+++ FKWRGKPLF+RHRTQKEI  E    +SQLRDP
Sbjct:   148 SMSASADVLALAKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIKQEAAVELSQLRDP 207

Query:   119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
             Q D DRVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIR GPA  N+
Sbjct:   208 QHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPATLNL 267

Query:   179 EVPPYQFGDEGILI 192
             EVP Y+F  + ++I
Sbjct:   268 EVPTYEFTSDDMVI 281

GO:0008121 "ubiquinol-cytochrome-c reductase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

---

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)
P51130	UCRI_BRAJA	1, ., 1, 0, ., 2, ., 2	0.5864	0.4452	0.7386	yes	N/A
P13272	UCRI_BOVIN	1, ., 1, 0, ., 2, ., 2	0.6134	0.6506	0.6934	yes	N/A
P08067	UCRI_YEAST	1, ., 1, 0, ., 2, ., 2	0.5284	0.6369	0.8651	yes	N/A
Q9CR68	UCRI_MOUSE	1, ., 1, 0, ., 2, ., 2	0.6051	0.6541	0.6970	yes	N/A
Q9ZDQ5	UCRI_RICPR	1, ., 1, 0, ., 2, ., 2	0.5120	0.5513	0.9096	yes	N/A
Q4UKR6	UCRI_RICFE	1, ., 1, 0, ., 2, ., 2	0.5060	0.5513	0.9096	yes	N/A
Q92IR2	UCRI_RICCN	1, ., 1, 0, ., 2, ., 2	0.5060	0.5513	0.9096	yes	N/A
Q09154	UCRI_SCHPO	1, ., 1, 0, ., 2, ., 2	0.5409	0.6061	0.7763	yes	N/A
P0C7P4	UCRIL_HUMAN	No assigned EC number	0.6082	0.6506	0.6713	yes	N/A
P47985	UCRI_HUMAN	1, ., 1, 0, ., 2, ., 2	0.6134	0.6506	0.6934	yes	N/A
Q1RIA5	UCRI_RICBR	1, ., 1, 0, ., 2, ., 2	0.5214	0.5410	0.8494	yes	N/A
P20788	UCRI_RAT	1, ., 1, 0, ., 2, ., 2	0.6030	0.6506	0.6934	yes	N/A
Q69BK5	UCRI_PANTR	1, ., 1, 0, ., 2, ., 2	0.6082	0.6506	0.6934	yes	N/A
Q5ZLR5	UCRI_CHICK	1, ., 1, 0, ., 2, ., 2	0.6030	0.6472	0.6948	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	1.10.2.2	0.824
3rd Layer	1.10.2	0.766

---

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	292
cd03470	126	cd03470, Rieske_cytochrome_bc1, Iron-sulfur protei	5e-76
TIGR01416	174	TIGR01416, Rieske_proteo, ubiquinol-cytochrome c r	2e-67
COG0723	177	COG0723, QcrA, Rieske Fe-S protein [Energy product	2e-41
pfam02921	63	pfam02921, UCR_TM, Ubiquinol cytochrome reductase	2e-21
pfam02921	63	pfam02921, UCR_TM, Ubiquinol cytochrome reductase	2e-21
pfam00355	99	pfam00355, Rieske, Rieske [2Fe-2S] domain	1e-16
TIGR01416	174	TIGR01416, Rieske_proteo, ubiquinol-cytochrome c r	5e-16
PRK13474	178	PRK13474, PRK13474, cytochrome b6-f complex iron-s	2e-14
cd03471	126	cd03471, Rieske_cytochrome_b6f, Iron-sulfur protei	3e-14
cd03467	98	cd03467, Rieske, Rieske domain; a [2Fe-2S] cluster	4e-12
cd03470	126	cd03470, Rieske_cytochrome_bc1, Iron-sulfur protei	8e-11
COG0723	177	COG0723, QcrA, Rieske Fe-S protein [Energy product	3e-07
cd03477	91	cd03477, Rieske_YhfW_C, YhfW family, C-terminal Ri	9e-07
cd03476	126	cd03476, Rieske_ArOX_small, Small subunit of Arsen	5e-04
TIGR02694	129	TIGR02694, arsenite_ox_S, arsenite oxidase, small	0.002

>gnl|CDD|239552 cd03470, Rieske_cytochrome_bc1, Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer

 Score =  227 bits (581), Expect = 5e-76
 Identities = 74/124 (59%), Positives = 93/124 (75%), Gaps = 2/124 (1%)

Query: 71  TIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP--QADSDRVKDP 128
            +EVDL+ I EGQ +T +WRGKP+FIR RT +EI   +  ++S L DP   A+  R   P
Sbjct: 1   PVEVDLSKIEEGQLITVEWRGKPVFIRRRTPEEIAEAKAVDLSLLDDPDPAANRVRSGKP 60

Query: 129 SWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDE 188
            WLV+IGICTHLGCVP   AGD+GG++CPCHGSHYDASGRIRKGPAP N+EVPPY+F  +
Sbjct: 61  EWLVVIGICTHLGCVPTYRAGDYGGFFCPCHGSHYDASGRIRKGPAPLNLEVPPYKFLSD 120

Query: 189 GILI 192
             ++
Sbjct: 121 TTIV 124

The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. Length = 126

>gnl|CDD|233404 TIGR01416, Rieske_proteo, ubiquinol-cytochrome c reductase, iron-sulfur subunit

 Score =  207 bits (529), Expect = 2e-67
 Identities = 90/176 (51%), Positives = 112/176 (63%), Gaps = 15/176 (8%)

Query: 29  QRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAM-ATIEVDLNLIPEGQSVTF 87
            R+ F Y     +  VG V A +    FI SM+ SA V A  A  EVD++ I  GQ +T 
Sbjct: 1   TRRDFLYA---ATGAVGAVGAAAAAVPFIDSMNPSASVKAAGAPTEVDVSKIQPGQQLTV 57

Query: 88  KWRGKPLFIRHRTQKEIDTEQNTNISQLRDP-----QADSDRVKD---PSWLVIIGICTH 139
           +WRGKP+FIR RT+KEID  +  ++  L+DP     Q D  RVK    P WLV+IGICTH
Sbjct: 58  EWRGKPVFIRRRTKKEIDELKALDLGALKDPNSEAQQPDYARVKRSGKPEWLVVIGICTH 117

Query: 140 LGCVPI--ANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF-GDEGILI 192
           LGC+P      GD GG++CPCHGSHYD +GR+RKGPAP N+ VPPY+F  D  ILI
Sbjct: 118 LGCIPTYGPEEGDKGGFFCPCHGSHYDTAGRVRKGPAPLNLPVPPYKFLSDTTILI 173

This model represents the Proteobacterial and mitochondrial type of the Rieske [2Fe-2S] iron-sulfur as found in ubiquinol-cytochrome c reductase. The model excludes the Rieske iron-sulfur protein as found in the cytochrome b6-f complex of the Cyanobacteria and chloroplasts. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix [Energy metabolism, Electron transport]. Length = 174

>gnl|CDD|223795 COG0723, QcrA, Rieske Fe-S protein [Energy production and conversion]

 Score =  141 bits (356), Expect = 2e-41
 Identities = 57/166 (34%), Positives = 76/166 (45%), Gaps = 14/166 (8%)

Query: 30  RKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADV-LAMATIEVDLNLIPEGQSVTFK 88
           R+ F  ++  G   VG   A   +   + S+   A   LA A IEVD + I  G  VT  
Sbjct: 11  RRDFLVLLTTGVGAVGAGAA---LYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVP 67

Query: 89  WRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA 148
           WRGKP+F+  RT+        T                    +    ICTHLGC    N 
Sbjct: 68  WRGKPVFLLRRTEYAGPKGGVTRDGDGGVGN--------KEIVAYSAICTHLGCTVPWNN 119

Query: 149 GDW-GGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF-GDEGILI 192
               GG++CPCHGS YD  G + KGPAP  + +PP ++  D+  LI
Sbjct: 120 AGAEGGFFCPCHGSRYDPDGGVVKGPAPRPLPIPPLEYDSDKLYLI 165

Length = 177

>gnl|CDD|217287 pfam02921, UCR_TM, Ubiquinol cytochrome reductase transmembrane region

 Score = 85.1 bits (211), Expect = 2e-21
 Identities = 33/63 (52%), Positives = 44/63 (69%), Gaps = 1/63 (1%)

Query: 4  HSDIRTPDFSKYRRDRNPDKGQE-ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSA 62
          H+D+R PDFS YRR    DK +E +  R+AF+Y++ GG+ V+    AKS V  F+SSMSA
Sbjct: 1  HTDVRVPDFSDYRRKSTKDKSRESDDGRRAFSYLMVGGAGVLSAYAAKSTVTTFLSSMSA 60

Query: 63 SAD 65
          SAD
Sbjct: 61 SAD 63

Each subunit of the cytochrome bc1 complex provides a single helix (this family) to make up the transmembrane region of the complex. Length = 63

>gnl|CDD|217287 pfam02921, UCR_TM, Ubiquinol cytochrome reductase transmembrane region

 Score = 85.1 bits (211), Expect = 2e-21
 Identities = 33/63 (52%), Positives = 44/63 (69%), Gaps = 1/63 (1%)

Query: 197 HSDIRTPDFSKYRRDRNPDKGQE-ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSA 255
           H+D+R PDFS YRR    DK +E +  R+AF+Y++ GG+ V+    AKS V  F+SSMSA
Sbjct: 1   HTDVRVPDFSDYRRKSTKDKSRESDDGRRAFSYLMVGGAGVLSAYAAKSTVTTFLSSMSA 60

Query: 256 SAD 258
           SAD
Sbjct: 61  SAD 63

Each subunit of the cytochrome bc1 complex provides a single helix (this family) to make up the transmembrane region of the complex. Length = 63

>gnl|CDD|215875 pfam00355, Rieske, Rieske [2Fe-2S] domain

 Score = 73.3 bits (180), Expect = 1e-16
 Identities = 23/101 (22%), Positives = 37/101 (36%), Gaps = 12/101 (11%)

Query: 95  FIRHRTQKEIDTEQNTNISQLRDPQADSDRV----KDPSWLVIIGICTHLGCVPIANA-- 148
           ++    + E+         +  D   +   V    KD     +  +CTH G         
Sbjct: 2   WVPVCHESELP---EPGDFKTVDLDGEDPVVVRRDKDGEVRALSNVCTHRGAPLSRGGVG 58

Query: 149 GDWGGYYCPCHGSHYDAS-GRIRKGPAP--TNMEVPPYQFG 186
            + GG+ CP HG  +D S G++  GPAP          + G
Sbjct: 59  NEKGGFECPYHGWRFDLSTGKLVGGPAPRPLKTYPVLEEVG 99

The rieske domain has a [2Fe-2S] centre. Two conserved cysteines that one Fe ion while the other Fe ion is coordinated by two conserved histidines. Length = 99

>gnl|CDD|233404 TIGR01416, Rieske_proteo, ubiquinol-cytochrome c reductase, iron-sulfur subunit

 Score = 74.0 bits (182), Expect = 5e-16
 Identities = 32/72 (44%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 222 QRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAM-ATIEVDLNLIPEGQSVTF 280
            R+ F Y     +  VG V A +    FI SM+ SA V A  A  EVD++ I  GQ +T 
Sbjct: 1   TRRDFLYA---ATGAVGAVGAAAAAVPFIDSMNPSASVKAAGAPTEVDVSKIQPGQQLTV 57

Query: 281 KWRGKPLFIRHR 292
           +WRGKP+FIR R
Sbjct: 58  EWRGKPVFIRRR 69

This model represents the Proteobacterial and mitochondrial type of the Rieske [2Fe-2S] iron-sulfur as found in ubiquinol-cytochrome c reductase. The model excludes the Rieske iron-sulfur protein as found in the cytochrome b6-f complex of the Cyanobacteria and chloroplasts. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix [Energy metabolism, Electron transport]. Length = 174

>gnl|CDD|237392 PRK13474, PRK13474, cytochrome b6-f complex iron-sulfur subunit; Provisional

 Score = 69.3 bits (170), Expect = 2e-14
 Identities = 32/87 (36%), Positives = 49/87 (56%), Gaps = 12/87 (13%)

Query: 127 DPSWLVIIG-----------ICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAP 175
           DP++LV+             +CTHLGCV   N+G+   + CPCHGS YDA+G++ +GPAP
Sbjct: 86  DPTYLVVEEDGTIASYGINAVCTHLGCVVPWNSGE-NKFQCPCHGSQYDATGKVVRGPAP 144

Query: 176 TNMEVPPYQFGDEGILIRMLAHSDIRT 202
            ++ +      D+ +L      +D RT
Sbjct: 145 LSLALVHVTVEDDKVLFSPWTETDFRT 171

Length = 178

>gnl|CDD|239553 cd03471, Rieske_cytochrome_b6f, Iron-sulfur protein (ISP) component of the b6f complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer

 Score = 67.8 bits (166), Expect = 3e-14
 Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 12/87 (13%)

Query: 127 DPSWLVIIG-----------ICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAP 175
           DP++L++             +CTHLGCV   NA +   + CPCHGS YDA+G++ +GPAP
Sbjct: 34  DPTYLIVEEDKTIANYGINAVCTHLGCVVPWNAAE-NKFKCPCHGSQYDATGKVVRGPAP 92

Query: 176 TNMEVPPYQFGDEGILIRMLAHSDIRT 202
            ++ +      D+ +++     +D RT
Sbjct: 93  LSLALVHATVDDDKVVLSPWTETDFRT 119

The cytochrome b6f complex from Mastigocladus laminosus, a thermophilic cyanobacterium, contains four large subunits, including cytochrome f, cytochrome b6, the Rieske ISP, and subunit IV; as well as four small hydrophobic subunits, PetG, PetL, PetM, and PetN. Rieske ISP, one of the large subunits of the cytochrome bc-type complexes, is involved in respiratory and photosynthetic electron transfer. The core of the chloroplast b6f complex is similar to the analogous respiratory cytochrome bc(1) complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. Length = 126

>gnl|CDD|239550 cd03467, Rieske, Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes

 Score = 61.4 bits (149), Expect = 4e-12
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 124 RVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYD-ASGRIRKGPAPTNMEVPP 182
           R +      +   CTH GC      G+ G   CPCHGS +D  +G +  GPAP  +   P
Sbjct: 29  RREGGEVYALSNRCTHQGCPLSEGEGEDGCIVCPCHGSRFDLRTGEVVSGPAPRPLPKYP 88

Query: 183 YQFGDEGILI 192
            +   +G++ 
Sbjct: 89  VKVEGDGVVW 98

The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis. Length = 98

>gnl|CDD|239552 cd03470, Rieske_cytochrome_bc1, Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer

 Score = 58.3 bits (142), Expect = 8e-11
 Identities = 18/29 (62%), Positives = 23/29 (79%)

Query: 264 TIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
            +EVDL+ I EGQ +T +WRGKP+FIR R
Sbjct: 1   PVEVDLSKIEEGQLITVEWRGKPVFIRRR 29

The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. Length = 126

>gnl|CDD|223795 COG0723, QcrA, Rieske Fe-S protein [Energy production and conversion]

 Score = 49.4 bits (118), Expect = 3e-07
 Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 223 RKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADV-LAMATIEVDLNLIPEGQSVTFK 281
           R+ F  ++  G   VG   A   +   + S+   A   LA A IEVD + I  G  VT  
Sbjct: 11  RRDFLVLLTTGVGAVGAGAA---LYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVP 67

Query: 282 WRGKPLFIRHR 292
           WRGKP+F+  R
Sbjct: 68  WRGKPVFLLRR 78

Length = 177

>gnl|CDD|239559 cd03477, Rieske_YhfW_C, YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain

 Score = 45.8 bits (109), Expect = 9e-07
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 5/47 (10%)

Query: 136 ICTHLGCVPIANAGD--WGGYYCPCHGSHYDASGRIRKGPAPTNMEV 180
            CTHLGC+   N  +  W    CPCHGS +   G + +GPA + ++ 
Sbjct: 39  TCTHLGCIVHWNDAEKSWD---CPCHGSRFSYDGEVIEGPAVSGLKP 82

The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. It is commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. YhfW is found in bacteria, some eukaryotes and archaea. Length = 91

>gnl|CDD|239558 cd03476, Rieske_ArOX_small, Small subunit of Arsenite oxidase (ArOX) family, Rieske domain; ArOX is a molybdenum/iron protein involved in the detoxification of arsenic, oxidizing it to arsenate

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 135 GICTHLGCVPIANAGDWGGYYCPCHGSHYDAS 166
            +CTH+GC P+        + CPCH S +D +
Sbjct: 53  ALCTHMGC-PLTYDPSNKTFVCPCHFSQFDPA 83

It consists of two subunits, a large subunit similar to members of the DMSO reductase family of molybdenum enzymes and a small subunit with a Rieske-type [2Fe-2S] cluster. The large subunit of ArOX contains the molybdenum site at which the oxidation of arsenite occurs. The small subunit contains a domain homologous to the Rieske domains of the cytochrome bc(1) and cytochrome b6f complexes as well as naphthalene 1,2-dioxygenase. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Length = 126

>gnl|CDD|131741 TIGR02694, arsenite_ox_S, arsenite oxidase, small subunit

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 136 ICTHLGCVPIANAGDWGGYYCPCHGSHYDAS--GRIRKGPAPTNMEVPPYQFGDEG 189
           +CTH+GC P++ + D   + CPCH S +D    G+   G A  N+     +  D G
Sbjct: 57  LCTHMGC-PVSYSADNKTFNCPCHFSVFDPEKGGQQVWGQATQNLPQIVLRVADNG 111

This model represents the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance. Homologs to both large (TIGR02693) and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7 [Energy metabolism, Electron transport]. Length = 129

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	292
KOG1671|consensus	210		100.0
TIGR01416	174	Rieske_proteo ubiquinol-cytochrome c reductase, ir	100.0
cd03470	126	Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) co	99.96
COG0723	177	QcrA Rieske Fe-S protein [Energy production and co	99.95
PRK13474	178	cytochrome b6-f complex iron-sulfur subunit; Provi	99.95
KOG1671|consensus	210		99.87
TIGR03171	321	soxL2 Rieske iron-sulfur protein SoxL2. This iron-	99.86
TIGR02377	101	MocE_fam_FeS Rieske [2Fe-2S] domain protein, MocE	99.85
cd03528	98	Rieske_RO_ferredoxin Rieske non-heme iron oxygenas	99.85
cd03478	95	Rieske_AIFL_N AIFL (apoptosis-inducing factor like	99.84
cd03476	126	Rieske_ArOX_small Small subunit of Arsenite oxidas	99.84
PRK09965	106	3-phenylpropionate dioxygenase ferredoxin subunit;	99.82
cd03530	98	Rieske_NirD_small_Bacillus Small subunit of nitrit	99.82
PF00355	97	Rieske: Rieske [2Fe-2S] domain; InterPro: IPR01794	99.82
cd03469	118	Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (	99.81
cd03477	91	Rieske_YhfW_C YhfW family, C-terminal Rieske domai	99.81
cd04337	129	Rieske_RO_Alpha_Cao Cao (chlorophyll a oxygenase)	99.81
cd03471	126	Rieske_cytochrome_b6f Iron-sulfur protein (ISP) co	99.81
cd03474	108	Rieske_T4moC Toluene-4-monooxygenase effector prot	99.81
cd03479	144	Rieske_RO_Alpha_PhDO_like Rieske non-heme iron oxy	99.8
cd03531	115	Rieske_RO_Alpha_KSH The alignment model represents	99.8
TIGR02694	129	arsenite_ox_S arsenite oxidase, small subunit. Thi	99.77
cd04338	134	Rieske_RO_Alpha_Tic55 Tic55 is a 55kDa LLS1-relate	99.77
cd03532	116	Rieske_RO_Alpha_VanA_DdmC Rieske non-heme iron oxy	99.77
COG2146	106	{NirD} Ferredoxin subunits of nitrite reductase an	99.75
cd03548	136	Rieske_RO_Alpha_OMO_CARDO Rieske non-heme iron oxy	99.75
cd03467	98	Rieske Rieske domain; a [2Fe-2S] cluster binding d	99.74
cd03529	103	Rieske_NirD Assimilatory nitrite reductase (NirD)	99.74
TIGR02378	105	nirD_assim_sml nitrite reductase [NAD(P)H], small	99.74
PRK09511	108	nirD nitrite reductase small subunit; Provisional	99.73
cd03480	138	Rieske_RO_Alpha_PaO Rieske non-heme iron oxygenase	99.72
cd03536	123	Rieske_RO_Alpha_DTDO This alignment model represen	99.71
cd03475	171	Rieske_SoxF_SoxL SoxF and SoxL family, Rieske doma	99.69
cd03472	128	Rieske_RO_Alpha_BPDO_like Rieske non-heme iron oxy	99.69
cd03537	123	Rieske_RO_Alpha_PrnD This alignment model represen	99.66
PF13806	104	Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A	99.66
cd03473	107	Rieske_CMP_Neu5Ac_hydrolase_N Cytidine monophospha	99.66
PLN02281	536	chlorophyllide a oxygenase	99.65
cd03545	150	Rieske_RO_Alpha_OHBDO_like Rieske non-heme iron ox	99.65
cd03539	129	Rieske_RO_Alpha_S5H This alignment model represent	99.63
PLN00095	394	chlorophyllide a oxygenase; Provisional	99.62
cd03535	123	Rieske_RO_Alpha_NDO Rieske non-heme iron oxygenase	99.62
cd03541	118	Rieske_RO_Alpha_CMO Rieske non-heme iron oxygenase	99.62
cd03538	146	Rieske_RO_Alpha_AntDO Rieske non-heme iron oxygena	99.6
cd03542	123	Rieske_RO_Alpha_HBDO Rieske non-heme iron oxygenas	99.6
TIGR01416	174	Rieske_proteo ubiquinol-cytochrome c reductase, ir	99.53
PLN02518	539	pheophorbide a oxygenase	99.52
PF02921	64	UCR_TM: Ubiquinol cytochrome reductase transmembra	99.45
TIGR03228	438	anthran_1_2_A anthranilate 1,2-dioxygenase, large	99.42
TIGR03229	433	benzo_1_2_benA benzoate 1,2-dioxygenase, large sub	99.41
COG4638	367	HcaE Phenylpropionate dioxygenase and related ring	99.34
PF02921	64	UCR_TM: Ubiquinol cytochrome reductase transmembra	99.31
PF10399	41	UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-	98.93
COG0723	177	QcrA Rieske Fe-S protein [Energy production and co	98.59
PF10399	41	UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-	98.11
PRK13474	178	cytochrome b6-f complex iron-sulfur subunit; Provi	98.0
TIGR03171	321	soxL2 Rieske iron-sulfur protein SoxL2. This iron-	95.62
KOG1336|consensus	478		95.4
PF08802	39	CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit	91.15
PF08802	39	CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit	89.5
PF10518	26	TAT_signal: TAT (twin-arginine translocation) path	85.41
TIGR02811	66	formate_TAT formate dehydrogenase region TAT targe	85.36

>KOG1671|consensus

Probab=100.00  E-value=1.2e-43  Score=307.23  Aligned_cols=188  Identities=63%  Similarity=1.116  Sum_probs=176.1

Q ss_pred             CCCCCCCCCccccccCCCCC-CCCCCcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhhccccceeecCCCCC
Q psy6642           3 AHSDIRTPDFSKYRRDRNPD-KGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPE   81 (292)
Q Consensus         3 ~~~~~~~pd~~~yr~~~~~~-~~~~~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~a~~~~~v~~s~l~~   81 (292)
                      .|||+.+|||..||++.+++ ....+.+||-|.|..+|+.+++.+.+|+.++..|+.+|..++++++.+.+++++++|||
T Consensus        18 ~~t~~~~p~~~~~~~~~~~~~~~~~~~~k~~~sy~~~g~~~~~~a~~ak~~v~~fi~smsAsadvlA~akiei~l~~IPe   97 (210)
T KOG1671|consen   18 SHTDLMVPDFSDYRRESVKDHQDTGEERKGFRSYLMVGAGAAGRAYAAKNLVTTFISSMSASADVLAMAKIEIKLSDIPE   97 (210)
T ss_pred             ccccccCCCchhhhchhhhccccchhhhhceeeEEEecccceeehhhhhhhHHHHHHHhhhhhhhhhheeeeeeeecCCC
Confidence            49999999999999999888 22335555666999999999998999999999999999999999999999999999999


Q ss_pred             CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeEEcCCCCc
Q psy6642          82 GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGS  161 (292)
Q Consensus        82 g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs  161 (292)
                      |..++++|+|+|+|+.|+++.+|+.+..|..+.++|||.++.|..+.+|+++.++||||||.+.++.+++++|+||||||
T Consensus        98 Gk~~~~kwrGkpvfirhrt~~ei~~~r~V~~s~lrDPq~d~~rvk~~ewl~~igVCThLGCVp~~~AGd~gg~~CPCHGS  177 (210)
T KOG1671|consen   98 GKTVAFKWRGKPVFIRHRTKAEIEGERNVPQSTLRDPQDDVDRVKKPEWLVVIGVCTHLGCVPIANAGDYGGYYCPCHGS  177 (210)
T ss_pred             CCCcceeccCCceEEeeccccccccccccchhhccCchhhhhhccCcceEEEEeeeccccccccccccccCceecccccc
Confidence            99999999999999999999999999999999999999888899999999999999999999999999999999999999


Q ss_pred             EEcCCCceecCCCCCCCCCCceEeecCce
Q psy6642         162 HYDASGRIRKGPAPTNMEVPPYQFGDEGI  190 (292)
Q Consensus       162 ~FD~~G~v~~gPa~~~L~~~p~~~~~d~i  190 (292)
                      +||..|++.+||||.||+++.|.|.+++.
T Consensus       178 HYdasGRIrkGPAPlnlevP~y~F~~~d~  206 (210)
T KOG1671|consen  178 HYDASGRIRKGPAPLNLEVPTYEFTSEDK  206 (210)
T ss_pred             cccccCceecCCCCCccCCCceecccCce
Confidence            99999999999999999999999998443

>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit

Probab=100.00  E-value=7.8e-35  Score=253.28  Aligned_cols=160  Identities=49%  Similarity=0.979  Sum_probs=138.7

Q ss_pred             CchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhhcc-ccceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhc
Q psy6642          29 QRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAM-ATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTE  107 (292)
Q Consensus        29 ~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~a~-~~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~  107 (292)
                      +||+||++++++.+.+++   ..++.|++.++.|.++..+. +.++|++++|++|+.+.+.|+|++++|.++|++||...
T Consensus         1 ~RR~fl~~~~~~~~~~~~---~~~~~p~v~~~~P~~~~~a~~~~~~v~l~eL~pG~~~~v~~~GkpI~I~~~t~~~~~~~   77 (174)
T TIGR01416         1 TRRDFLYAATGAVGAVGA---AAAAVPFIDSMNPSASVKAAGAPTEVDVSKIQPGQQLTVEWRGKPVFIRRRTKKEIDAL   77 (174)
T ss_pred             ChHHHHHHHHHHHHHHHH---HHHHHHHHheeCcchhccccCCcEEEEHHHCCCCCeEEEEECCeEEEEEeCCHHHhhhh
Confidence            599999999986554443   35678999999999988877 68899999999999999999999999999999999999


Q ss_pred             ccccccccCCCCcc--------cccccCCCeEEEEecccCCCcccCCcCC-C-CCeEEcCCCCcEEcCCCceecCCCCCC
Q psy6642         108 QNTNISQLRDPQAD--------SDRVKDPSWLVIIGICTHLGCVPIANAG-D-WGGYYCPCHGSHYDASGRIRKGPAPTN  177 (292)
Q Consensus       108 ~~v~~~~l~dp~~~--------~~R~~~g~~~a~~~~CtHlGc~l~~~~~-~-~~~~~CPcHGs~FD~~G~v~~gPa~~~  177 (292)
                      +++....++||+..        .+|+.+++|+|++++|||+||.+.|... + ++.|+||||||+||++|+++.|||+++
T Consensus        78 ~~~~~~~l~Dp~~~~~~~~~~~~~r~~~~~~~a~~~~CtH~Gc~~~~~~~~~~~~~~~CPcHgs~Fd~~G~~~~gpa~~~  157 (174)
T TIGR01416        78 KALDLGALKDPNSEAQQPDYARVKRSGKPEWLVVIGICTHLGCIPTYGPEEGDKGGFFCPCHGSHYDTAGRVRKGPAPLN  157 (174)
T ss_pred             hccchhhcCCCcccccCcchhhhhhccCCcEEEEEeccCCCCCccccccCCCCCCEEEeCCCCCEECCCCcEecCCCCCC
Confidence            88888888888433        4466689999999999999999987632 2 468999999999999999999999999


Q ss_pred             CCCCceEeecCceE
Q psy6642         178 MEVPPYQFGDEGIL  191 (292)
Q Consensus       178 L~~~p~~~~~d~i~  191 (292)
                      |++||+++++|..+
T Consensus       158 L~~~~~~~~~~~~~  171 (174)
T TIGR01416       158 LPVPPYKFLSDTTI  171 (174)
T ss_pred             CCCCCEEEcCCCEE
Confidence            99999999988654

Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.

>cd03470 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer

Probab=99.96  E-value=7.3e-30  Score=211.29  Aligned_cols=119  Identities=61%  Similarity=1.204  Sum_probs=106.9

Q ss_pred             ceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCc--ccccccCCCeEEEEecccCCCcccCCcCC
Q psy6642          72 IEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQA--DSDRVKDPSWLVIIGICTHLGCVPIANAG  149 (292)
Q Consensus        72 ~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~--~~~R~~~g~~~a~~~~CtHlGc~l~~~~~  149 (292)
                      +++++++|++|+.++++|+|+|++|++++++||+...+.....+.||+.  ..+|..+++|+|++++|||+||.+.++..
T Consensus         2 ~~vdl~~l~~G~~~~v~w~Gkpv~I~~rt~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~CtH~gc~~~~~~~   81 (126)
T cd03470           2 VEVDLSKIEEGQLITVEWRGKPVFIRRRTPEEIAEAKAVDLSLLDDPDPAANRVRSGKPEWLVVIGICTHLGCVPTYRAG   81 (126)
T ss_pred             EEEEhhhCCCCCEEEEEECCeEEEEEECCHHHHhhhhhcchhhcCCccccccccccCCCcEEEEeCcCCCCCCeeccccC
Confidence            6889999999999999999999999999999999988776666666543  36788899999999999999999988865


Q ss_pred             CCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEeecCce
Q psy6642         150 DWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGI  190 (292)
Q Consensus       150 ~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~d~i  190 (292)
                      +++.|+||||||+||++|+++.|||+++|++||++++++..
T Consensus        82 ~~~~~~CPcHgs~Fdl~G~~~~gPa~~~L~~~p~~~~~~~~  122 (126)
T cd03470          82 DYGGFFCPCHGSHYDASGRIRKGPAPLNLEVPPYKFLSDTT  122 (126)
T ss_pred             CCCEEEecCcCCEECCCCeEecCCCCCCCCeeeEEEecCCE
Confidence            66899999999999999999999999999999999998643

The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.

>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]

Probab=99.95  E-value=2.1e-28  Score=213.13  Aligned_cols=155  Identities=36%  Similarity=0.636  Sum_probs=125.2

Q ss_pred             CcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhh-hccccceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhh
Q psy6642          27 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADV-LAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEID  105 (292)
Q Consensus        27 ~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~-~a~~~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~  105 (292)
                      ..+||+|+..+++..+..+   +..++.|+...++|.++. .+.+.++++...+.+++...+.|+++|+++.++++.++.
T Consensus         8 ~~~~~~~l~~~~~~~~~~~---~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~   84 (177)
T COG0723           8 GLSRRDFLVLLTTGVGAVG---AGAALYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVPWRGKPVFLLRRTEYAGP   84 (177)
T ss_pred             cccHHHhhhhhhccccccc---eeeeeeehhhcccCcccccccCCceeeeccCCccceEEEEecCCCCeeeEeecccccc
Confidence            6689999988877554333   335677888888887665 677888999998999999999999999998877665555


Q ss_pred             hcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCc-CCCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceE
Q psy6642         106 TEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIAN-AGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQ  184 (292)
Q Consensus       106 ~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~-~~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~  184 (292)
                      .........+.++        ..+|+|++.+||||||.+.|+ ..+.++|+||||||+||.+|++++|||+++|++++++
T Consensus        85 ~~~~~~~~~~~~~--------~~~~~a~~~iCtHlGC~~~~~~~~~~~~~~CPCHGS~yd~~g~vv~GPA~~~L~~~~~~  156 (177)
T COG0723          85 KGGVTRDGDGGVG--------NKEIVAYSAICTHLGCTVPWNNAGAEGGFFCPCHGSRYDPDGGVVKGPAPRPLPIPPLE  156 (177)
T ss_pred             cccceecccCCCC--------CccEEEEeeeccCCCCccCcccCCCCCeEEccCCCCeEcCCCCeeCCCCCCCcCCceEE
Confidence            5444444444442        268999999999999999994 4455999999999999999999999999999999999


Q ss_pred             eecCceEE
Q psy6642         185 FGDEGILI  192 (292)
Q Consensus       185 ~~~d~i~V  192 (292)
                      +++|++++
T Consensus       157 ~~~d~~~~  164 (177)
T COG0723         157 YDSDKLYL  164 (177)
T ss_pred             EeCCceEE
Confidence            99986543

>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional

Probab=99.95  E-value=3.6e-27  Score=205.89  Aligned_cols=146  Identities=27%  Similarity=0.521  Sum_probs=112.9

Q ss_pred             CcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhhccccc--------eeecCCC----CCCCeEEEE-EcCee
Q psy6642          27 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATI--------EVDLNLI----PEGQSVTFK-WRGKP   93 (292)
Q Consensus        27 ~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~a~~~~--------~v~~s~l----~~g~~~~~~-~~g~p   93 (292)
                      +++||+||..++++.+.++   |..++.|++.++.|.+...+....        .|+++++    ++|+...+. ..|++
T Consensus        11 d~~RR~FL~~~~~~~gg~~---a~~~~~P~v~~~~Pp~~~~~~g~~~a~d~~G~~I~~s~~~~~~~~g~~~~v~~~~g~~   87 (178)
T PRK13474         11 SMGRRQFMNLLTFGTVTGV---ALGALYPVVKYFIPPSAGGAGGGTTAKDELGNDIPASQFLATHPAGDRSLVQGLKGDP   87 (178)
T ss_pred             CccHHHHHHHHHHHHHHHH---HHHHHHHhhheeCChhHccCCCcceeecccCCeeehhhccccCCCCCcEEEEEcCCCe
Confidence            6799999998886544333   335678999999887765443221        2345565    567666655 45655


Q ss_pred             EEEEeCChhhhhhcccccccccCCCCcccccccCCCe--EEEEecccCCCcccCCcCCCCCeEEcCCCCcEEcCCCceec
Q psy6642          94 LFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSW--LVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRK  171 (292)
Q Consensus        94 v~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~--~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~v~~  171 (292)
                      .+++.                          ..+|++  +|++++|||+||++.++..+ +.|.||||||+||.+|+++.
T Consensus        88 ~~lv~--------------------------~~~g~~~~~a~~~~CtH~gc~l~~~~~~-~~~~CP~Hgs~Fd~tG~~~~  140 (178)
T PRK13474         88 TYLVV--------------------------EEDGTIASYGINAVCTHLGCVVPWNSGE-NKFQCPCHGSQYDATGKVVR  140 (178)
T ss_pred             EEEEE--------------------------eCCCEEEEEEecCCCCCCCCccccccCC-CEEEecCcCCEECCCCCCcc
Confidence            33321                          247888  67799999999999998765 69999999999999999999


Q ss_pred             CCCCCCCCCCceEeecCceEEEeecccCCCC
Q psy6642         172 GPAPTNMEVPPYQFGDEGILIRMLAHSDIRT  202 (292)
Q Consensus       172 gPa~~~L~~~p~~~~~d~i~V~I~ahtD~~~  202 (292)
                      ||++++|+.|++++++|.|+|.+|..+|++.
T Consensus       141 gPa~~~L~~y~v~v~~g~v~v~~~~e~~~~~  171 (178)
T PRK13474        141 GPAPLSLALVHVTVEDDKVLFSPWTETDFRT  171 (178)
T ss_pred             CCCCCCCCeEeEEEECCEEEEEEeeecCCcC
Confidence            9999999999999999999999999988774

>KOG1671|consensus

Probab=99.87  E-value=1.7e-23  Score=181.92  Aligned_cols=97  Identities=53%  Similarity=0.869  Sum_probs=89.9

Q ss_pred             cccCCCCCCccccccCCCCCCCcccccc-ceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhhhccceEEecCCCCC
Q psy6642         196 AHSDIRTPDFSKYRRDRNPDKGQEETQR-KAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPE  274 (292)
Q Consensus       196 ahtD~~~P~F~~yr~~~~~~~~~~~~~r-r~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~a~~~~evdls~i~~  274 (292)
                      .|+|+.+|+|++|++++++|.+....+| +.|.|++++++++.++++++..+..||.||..|++++|+|++||+|+.|||
T Consensus        18 ~~t~~~~p~~~~~~~~~~~~~~~~~~~~k~~~sy~~~g~~~~~~a~~ak~~v~~fi~smsAsadvlA~akiei~l~~IPe   97 (210)
T KOG1671|consen   18 SHTDLMVPDFSDYRRESVKDHQDTGEERKGFRSYLMVGAGAAGRAYAAKNLVTTFISSMSASADVLAMAKIEIKLSDIPE   97 (210)
T ss_pred             ccccccCCCchhhhchhhhccccchhhhhceeeEEEecccceeehhhhhhhHHHHHHHhhhhhhhhhheeeeeeeecCCC
Confidence            4999999999999999998855444455 555999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEECCeeeEEEcC
Q psy6642         275 GQSVTFKWRGKPLFIRHR  292 (292)
Q Consensus       275 G~~~~~~WrgkPvfv~~R  292 (292)
                      |++++|+|||||||||||
T Consensus        98 Gk~~~~kwrGkpvfirhr  115 (210)
T KOG1671|consen   98 GKTVAFKWRGKPVFIRHR  115 (210)
T ss_pred             CCCcceeccCCceEEeec
Confidence            999999999999999998

>TIGR03171 soxL2 Rieske iron-sulfur protein SoxL2

Probab=99.86  E-value=1.2e-21  Score=182.28  Aligned_cols=175  Identities=19%  Similarity=0.269  Sum_probs=105.8

Q ss_pred             CcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhhccc----------cceeecCCCCCCCeEEE--EE--cCe
Q psy6642          27 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMA----------TIEVDLNLIPEGQSVTF--KW--RGK   92 (292)
Q Consensus        27 ~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~a~~----------~~~v~~s~l~~g~~~~~--~~--~g~   92 (292)
                      +++||+||..+++.++.+ ++   +.+.|++..+.|.++..+.+          ...|++++|+.|+...+  ++  .+.
T Consensus        60 D~~RR~fL~~al~gAga~-a~---~~avPlv~~l~PP~~a~atG~pk~La~D~~GnPIKASdL~vnSp~~~lfeyPl~gd  135 (321)
T TIGR03171        60 DEGRRKFLKGLIFGIAAA-AV---VGIIPGLRVLVPPTVAAASGFPKSLLVDSSGNPIKASSIPVNSPIITIFEYPMTGE  135 (321)
T ss_pred             CccHHHHHHHHHHHHHHH-Hh---hhhhhheecccCchhhhccCCCceEEecCCCCeeeHHHccCCCcccccccCcCCCC
Confidence            789999999888766543 22   22459999999876655431          12356678888877743  32  233


Q ss_pred             eEEEEeCChhhhhhcccccccccCCCCcc-cccc-----cCCCeEEEEecccCCCcccCCc-------------------
Q psy6642          93 PLFIRHRTQKEIDTEQNTNISQLRDPQAD-SDRV-----KDPSWLVIIGICTHLGCVPIAN-------------------  147 (292)
Q Consensus        93 pv~i~~~t~~~i~~~~~v~~~~l~dp~~~-~~R~-----~~g~~~a~~~~CtHlGc~l~~~-------------------  147 (292)
                      |-++.+...+..... .+....++-|+.. .|+.     +++.++|||.+|||+||++.+-                   
T Consensus       136 P~fLIklgka~~~~v-~i~p~~v~~~~~g~~y~~pgGVGp~~~IVAyS~IC~H~GC~~~~~~~Ypp~~~~~~~~~~~~~~  214 (321)
T TIGR03171       136 PNFLLNLGDSSGKPV-EIPPTKVVVPQTGKTYTFPGGVGPNKSIVAYSAICQHLGCTPPYIHFYPPNYVNPSQLTAPEPD  214 (321)
T ss_pred             cHHHHHhhhhcCCce-ecCccccccCCCCcceeccCCcCCCCCEEEEecccCcCCCCcchhhccCccccccccccccccc
Confidence            433322111000000 1111112222111 1222     4689999999999999988331                   


Q ss_pred             ---------CCC---CCeEEcCCCCcEEcC-C-CceecCCCCCCCCCCceEeecC-ceEEEeecccCCCCCCcc
Q psy6642         148 ---------AGD---WGGYYCPCHGSHYDA-S-GRIRKGPAPTNMEVPPYQFGDE-GILIRMLAHSDIRTPDFS  206 (292)
Q Consensus       148 ---------~~~---~~~~~CPcHGs~FD~-~-G~v~~gPa~~~L~~~p~~~~~d-~i~V~I~ahtD~~~P~F~  206 (292)
                               ..+   .+.|.||||||+||+ + |+++.|||+++|+.++++++++ +-++.+....-..+|+|.
T Consensus       215 ~~~~~~~~~~~~~~~~~~~~CPCHgS~FD~~~gg~Vv~GPA~rpLp~i~l~~d~~~~~l~AvG~~g~~~~~~~~  288 (321)
T TIGR03171       215 QLTAQALLAAKQANVPALIHCDCHGSTYDPYHGAAVLTGPTVRPLPAVILEWDSSTDYLYAIGSIGVAVYPEGS  288 (321)
T ss_pred             ccchhhhhhhhccCCCCeEECCCCCCEECCCCCCceeCCCCCCCCCcceEEEeCCCCeEEEEecCCcccccccc
Confidence                     011   148999999999999 4 5899999999999999999864 334444433223344443

This iron-sulfur protein is found in a contiguous genomic region with subunits of cytochrome b558/566 in several archaeal species, and appears to be part of a cytochrome bc1-analogous system.

>TIGR02377 MocE_fam_FeS Rieske [2Fe-2S] domain protein, MocE subfamily

Probab=99.85  E-value=2.3e-21  Score=154.25  Aligned_cols=95  Identities=20%  Similarity=0.300  Sum_probs=84.1

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCe
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGG  153 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~  153 (292)
                      .++++|++|+...+...|.++.+.+                          ..+|+++|+++.|||+|++|..+..+++.
T Consensus         6 ~~~~dl~~g~~~~~~~~g~~i~l~r--------------------------~~~g~~~A~~~~CpH~g~~L~~G~~~~~~   59 (101)
T TIGR02377         6 CDADDIGREDVARFDHGGRTFAIYR--------------------------TPDDQYYATDGLCTHEYAHLADGLVMDTT   59 (101)
T ss_pred             EEHHHcCCCCEEEEEECCeEEEEEE--------------------------eCCCEEEEEcCcCCCCCCCCCCCEEcCCE
Confidence            3678899999999999998887753                          24789999999999999999988766689


Q ss_pred             EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         154 YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       154 ~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      +.||||||+||+ +|+++.+|+..+|+.||+++++|.++|.+
T Consensus        60 i~CP~Hg~~Fdl~tG~~~~~p~~~~l~~y~v~v~~g~v~V~~  101 (101)
T TIGR02377        60 VECPKHAGCFDYRTGEALNPPVCVNLKTYPVKVVDGAVYVDI  101 (101)
T ss_pred             EECCccCCEEECCCCcccCCCccCCcceEeEEEECCEEEEeC
Confidence            999999999998 99999999988999999999999988763

This model describes a subfamily of the Rieske-like [2Fe-2S] family of ferredoxins that includes MocE, part of the rhizopine (3-O-methyl-scyllo-inosamine) catabolic cluster in Rhizobium. Members of this family are related to, yet distinct from, the small subunit of nitrite reductase [NAD(P)H].

>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO)

Probab=99.85  E-value=3.9e-21  Score=151.03  Aligned_cols=91  Identities=22%  Similarity=0.430  Sum_probs=81.8

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .+++|++|+.+.+.+.|.++++.+                           .+++++|+++.|||+||+|..+..+++.+
T Consensus         6 ~~~~l~~g~~~~~~~~g~~~~v~r---------------------------~~~~~~a~~~~CpH~g~~L~~g~~~~~~i   58 (98)
T cd03528           6 AVDELPEGEPKRVDVGGRPIAVYR---------------------------VDGEFYATDDLCTHGDASLSEGYVEGGVI   58 (98)
T ss_pred             EhhhcCCCCEEEEEECCeEEEEEE---------------------------ECCEEEEECCcCCCCCCCCCCCeEeCCEE
Confidence            578899999999999999988754                           24699999999999999999876666899


Q ss_pred             EcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEE
Q psy6642         155 YCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILI  192 (292)
Q Consensus       155 ~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V  192 (292)
                      .||||||+||+ +|+++.+|+..+|+.|++++++|.++|
T Consensus        59 ~Cp~Hg~~fd~~~G~~~~~p~~~~L~~~~v~~~~g~v~v   97 (98)
T cd03528          59 ECPLHGGRFDLRTGKALSLPATEPLKTYPVKVEDGDVYV   97 (98)
T ss_pred             EeCCcCCEEECCCCcccCCCCCCCcceEeEEEECCEEEE
Confidence            99999999999 999999999999999999999998876

The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in

>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox)

Probab=99.84  E-value=4.6e-21  Score=150.33  Aligned_cols=89  Identities=18%  Similarity=0.302  Sum_probs=80.3

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .+++|++|+.+.+.+.|.++++.+                           .+|+++|++++|||+||+|.++..+++.+
T Consensus         5 ~~~~l~~g~~~~~~~~~~~v~v~r---------------------------~~g~~~A~~~~CpH~g~~L~~g~~~~~~i   57 (95)
T cd03478           5 RLSDLGDGEMKEVDVGDGKVLLVR---------------------------QGGEVHAIGAKCPHYGAPLAKGVLTDGRI   57 (95)
T ss_pred             ehhhCCCCCEEEEEeCCcEEEEEE---------------------------ECCEEEEEcCcCcCCCCccCCCeEeCCEE
Confidence            578899999999999999887753                           26899999999999999999887666899


Q ss_pred             EcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCce
Q psy6642         155 YCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGI  190 (292)
Q Consensus       155 ~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i  190 (292)
                      .||||||+||+ +|+++.+|+..+|+.|++++++|.|
T Consensus        58 ~CP~Hg~~Fdl~tG~~~~~p~~~~l~~~~v~~~~g~i   94 (95)
T cd03478          58 RCPWHGACFNLRTGDIEDAPALDSLPCYEVEVEDGRV   94 (95)
T ss_pred             EcCCCCCEEECCCCcCcCCCccCCcceEEEEEECCEE
Confidence            99999999999 9999999998899999999999865

The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.

>cd03476 Rieske_ArOX_small Small subunit of Arsenite oxidase (ArOX) family, Rieske domain; ArOX is a molybdenum/iron protein involved in the detoxification of arsenic, oxidizing it to arsenate

Probab=99.84  E-value=9.2e-21  Score=156.95  Aligned_cols=101  Identities=24%  Similarity=0.464  Sum_probs=82.8

Q ss_pred             ecCCCCCCCeEEEEEcC--eeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCC
Q psy6642          75 DLNLIPEGQSVTFKWRG--KPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWG  152 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g--~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~  152 (292)
                      ++++|++|+.+.+.+.+  .++++++..+...                 -.+..+++++|++++|||+||+|.++. +++
T Consensus         8 ~~~~l~~g~~~~~~~~~~~~~i~v~r~~~~~~-----------------~~~~~~g~~~A~~~~CpH~g~~L~~g~-~~~   69 (126)
T cd03476           8 NLSQLSPGQPVTFNYPDESSPCVLVKLGVPVP-----------------GGVGPDNDIVAFSALCTHMGCPLTYDP-SNK   69 (126)
T ss_pred             eHHHCCCCCeEEEEcCCCCCcEEEEECCcccc-----------------CccccCCEEEEEeCcCCCCCccccccc-cCC
Confidence            67999999999999987  6787765321110                 011247899999999999999999876 558


Q ss_pred             eEEcCCCCcEEcC--CCceecCCCCCCCCCCceEee--cCceEEE
Q psy6642         153 GYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPYQFG--DEGILIR  193 (292)
Q Consensus       153 ~~~CPcHGs~FD~--~G~v~~gPa~~~L~~~p~~~~--~d~i~V~  193 (292)
                      .|.||||||+||+  +|+++.+|+..+|++||++++  +|.|+|.
T Consensus        70 ~v~CP~Hg~~Fdl~tgG~~~~gPa~~~L~~ypv~ve~~~g~V~~~  114 (126)
T cd03476          70 TFVCPCHFSQFDPARGGQMVSGQATQNLPQIVLEYDEASGDIYAV  114 (126)
T ss_pred             EEEccCcCCEEeCCCCCeEEcCCCCCCCCeEEEEEECCCCEEEEE
Confidence            9999999999999  479999999999999999999  8877664

It consists of two subunits, a large subunit similar to members of the DMSO reductase family of molybdenum enzymes and a small subunit with a Rieske-type [2Fe-2S] cluster. The large subunit of ArOX contains the molybdenum site at which the oxidation of arsenite occurs. The small subunit contains a domain homologous to the Rieske domains of the cytochrome bc(1) and cytochrome b6f complexes as well as naphthalene 1,2-dioxygenase. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer.

>PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional

Probab=99.82  E-value=2.3e-20  Score=149.65  Aligned_cols=92  Identities=16%  Similarity=0.248  Sum_probs=79.1

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCC-Ce
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDW-GG  153 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~-~~  153 (292)
                      .+++|++|+.+.+... .++++.+                           .+|+++|+++.|||+||+|+.+..++ +.
T Consensus         8 ~~~~l~~g~~~~~~~~-~~i~v~~---------------------------~~g~~~A~~~~CpH~g~~L~~G~~~~~~~   59 (106)
T PRK09965          8 PVADLPEGEALRVDTS-PVIALFN---------------------------VGGEFYAIDDRCSHGNASLSEGYLEDDAT   59 (106)
T ss_pred             eHHHcCCCCeEEEeCC-CeEEEEE---------------------------ECCEEEEEeCcCCCCCCCCCceEECCCCE
Confidence            6788999988888765 5555543                           37899999999999999998766555 68


Q ss_pred             EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         154 YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       154 ~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      +.||||||+||+ +|+++.+|+..+|+.|++++++|.++|.+
T Consensus        60 i~Cp~Hg~~Fd~~tG~~~~~p~~~~l~~y~v~v~~g~v~v~~  101 (106)
T PRK09965         60 VECPLHAASFCLRTGKALCLPATDPLRTYPVHVEGGDIFIDL  101 (106)
T ss_pred             EEcCCCCCEEEcCCCCeeCCCCCCCcceEeEEEECCEEEEEc
Confidence            999999999999 99999989889999999999999998875

>cd03530 Rieske_NirD_small_Bacillus Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain

Probab=99.82  E-value=3.3e-20  Score=146.09  Aligned_cols=91  Identities=19%  Similarity=0.251  Sum_probs=80.0

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .+++|++|+.+.+...|.++++.+                          ..+|+++|+++.|||+||+|.++..+++.+
T Consensus         6 ~~~~l~~~~~~~~~~~g~~i~l~r--------------------------~~~g~~~A~~~~CpH~g~~L~~g~~~~~~i   59 (98)
T cd03530           6 ALEDIPPRGARKVQTGGGEIAVFR--------------------------TADDEVFALENRCPHKGGPLSEGIVHGEYV   59 (98)
T ss_pred             EHHHCCCCCcEEEEECCEEEEEEE--------------------------eCCCCEEEEcCcCCCCCCCccCCEEcCCEE
Confidence            568899999999999999887754                          346899999999999999999987767899


Q ss_pred             EcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEE
Q psy6642         155 YCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILI  192 (292)
Q Consensus       155 ~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V  192 (292)
                      .||||||+||+ +|++. +|+..+|+.||+++++|.++|
T Consensus        60 ~Cp~Hg~~Fdl~~G~~~-~p~~~~l~~y~v~v~~g~v~v   97 (98)
T cd03530          60 TCPLHNWVIDLETGEAQ-GPDEGCVRTFPVKVEDGRVYL   97 (98)
T ss_pred             ECCCCCCEEECCCCCCC-CCCCCccceEeEEEECCEEEE
Confidence            99999999999 89875 677788999999999998876

The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.

>PF00355 Rieske: Rieske [2Fe-2S] domain; InterPro: IPR017941 There are multiple types of iron-sulphur clusters which are grouped into three main categories based on their atomic content: [2Fe-2S], [3Fe-4S], [4Fe-4S] (see PDOC00176 from PROSITEDOC), and other hybrid or mixed metal types

Probab=99.82  E-value=3.5e-20  Score=145.17  Aligned_cols=87  Identities=29%  Similarity=0.567  Sum_probs=73.5

Q ss_pred             ecCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC--CCC
Q psy6642          75 DLNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA--GDW  151 (292)
Q Consensus        75 ~~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~--~~~  151 (292)
                      ..++|++ |....+...+..+++.+                           .+|+++|++++|||+||+|.++.  .++
T Consensus         7 ~~~el~~~~~~~~~~~~~~~v~~~~---------------------------~~g~~~A~~~~CpH~g~~l~~~~~~~~~   59 (97)
T PF00355_consen    7 RSSELPEPGDVKRVDVGGKLVLVRR---------------------------SDGEIYAFSNRCPHQGCPLSEGPFSEDG   59 (97)
T ss_dssp             EGGGSHSTTEEEEEEETTEEEEEEE---------------------------TTTEEEEEESB-TTTSBBGGCSSEETTT
T ss_pred             EHHHCCCCCCEEEEEcCCcEEEEEe---------------------------CCCCEEEEEccCCccceeEcceeccccc
Confidence            5678888 77888888655665532                           58999999999999999999983  445


Q ss_pred             CeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecC
Q psy6642         152 GGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDE  188 (292)
Q Consensus       152 ~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d  188 (292)
                      +.+.||||||+||+ +|+++.+|+..+|+.||+++++|
T Consensus        60 ~~i~Cp~Hg~~Fd~~tG~~~~~p~~~~l~~~~v~ve~~   97 (97)
T PF00355_consen   60 GVIVCPCHGWRFDLDTGECVGGPAPRPLPLYPVKVEGD   97 (97)
T ss_dssp             TEEEETTTTEEEETTTSBEEESTTCSBSTEEEEEEETT
T ss_pred             CEEEeCCcCCEEeCCCceEecCCCCCCcCCCCeEEeCC
Confidence            79999999999999 69999999999999999999886

Two general types of [2Fe-2S] clusters are known and they differ in their coordinating residues. The ferredoxin-type [2Fe-2S] clusters are coordinated to the protein by four cysteine residues (see PDOC00175 from PROSITEDOC). The Rieske-type [2Fe-2S] cluster is coordinated to its protein by two cysteine residues and two histidine residues [, ]. The structure of several Rieske domains has been solved []. It contains three layers of antiparallel beta sheets forming two beta sandwiches. Both beta sandwiches share the central sheet 2. The metal-binding site is at the top of the beta sandwich formed by the sheets 2 and 3. The Fe1 iron of the Rieske cluster is coordinated by two cysteines while the other iron Fe2 is coordinated by two histidines. Two inorganic sulphide ions bridge the two iron ions forming a flat, rhombic cluster. Rieske-type iron-sulphur clusters are common to electron transfer chains of mitochondria and chloroplast and to non-haem iron oxygenase systems: The Rieske protein of the Ubiquinol-cytochrome c reductase (1.10.2.2 from EC) (also known as the bc1 complex or complex III), a complex of the electron transport chains of mitochondria and of some aerobic prokaryotes; it catalyses the oxidoreduction of ubiquinol and cytochrome c. The Rieske protein of chloroplastic plastoquinone-plastocyanin reductase (1.10.99.1 from EC) (also known as the b6f complex). It is functionally similar to the bc1 complex and catalyses the oxidoreduction of plastoquinol and cytochrome f. Bacterial naphthalene 1,2-dioxygenase subunit alpha, a component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyses the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol. Bacterial 3-phenylpropionate dioxygenase ferredoxin subunit. Bacterial toluene monoxygenase. Bacterial biphenyl dioxygenase. ; GO: 0016491 oxidoreductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 2XRX_A 2XR8_O 2XSH_G 2XSO_I 2YFI_C 2YFL_A 2YFJ_K 1G8J_D 1G8K_D 1NYK_B ....

>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms

Probab=99.81  E-value=8.2e-20  Score=147.98  Aligned_cols=94  Identities=24%  Similarity=0.456  Sum_probs=82.5

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCC-CCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAG-DWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~-~~~  152 (292)
                      .+++|+ +|+.+.+.+.+.++++.+                          ..+|+++|+.+.|||+||+|.++.. +++
T Consensus         6 ~~~el~~~g~~~~~~~~~~~i~v~r--------------------------~~~g~~~a~~n~CpH~g~~L~~g~~~~~~   59 (118)
T cd03469           6 HSSELPEPGDYVTLELGGEPLVLVR--------------------------DRDGEVRAFHNVCPHRGARLCEGRGGNAG   59 (118)
T ss_pred             EHHHCCCCCCEEEEEECCccEEEEE--------------------------CCCCCEEEEEEeCCCCCCEeeeccCCCCC
Confidence            467888 999999999998887754                          3578999999999999999999876 678


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCC----------CCCCCceEeecCceEEEe
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPT----------NMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~----------~L~~~p~~~~~d~i~V~I  194 (292)
                      .+.||||||+||++|+++.+|+..          .|+.|++++++|.|+|.+
T Consensus        60 ~i~Cp~Hg~~Fd~~G~~~~~P~~~~~~~~~~~~~~L~~~~v~~~~g~v~v~~  111 (118)
T cd03469          60 RLVCPYHGWTYDLDGKLVGVPREEGFPGFDKEKLGLRTVPVEEWGGLIFVNL  111 (118)
T ss_pred             EEECCCCCCEECCCCcEEeCCcccccCCCCHHHCCCeEEEEEEECCEEEEEc
Confidence            999999999999999999998764          489999999999888765

These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i

>cd03477 Rieske_YhfW_C YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain

Probab=99.81  E-value=7.6e-20  Score=143.26  Aligned_cols=87  Identities=28%  Similarity=0.531  Sum_probs=76.0

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .+++|++|+.+.+.+.|.+++|.+                          ..+|+++|+++.|||+||+|.++..+ +.|
T Consensus         4 ~~~dl~~g~~~~~~~~g~~v~v~r--------------------------~~~g~~~A~~~~CpH~g~~l~~g~~~-~~i   56 (91)
T cd03477           4 DIEDLAPGEGGVVNIGGKRLAVYR--------------------------DEDGVLHTVSATCTHLGCIVHWNDAE-KSW   56 (91)
T ss_pred             chhhcCCCCeEEEEECCEEEEEEE--------------------------CCCCCEEEEcCcCCCCCCCCcccCCC-CEE
Confidence            357889999999999999987754                          35799999999999999999987653 799


Q ss_pred             EcCCCCcEEcCCCceecCCCCCCCCCCceEeecC
Q psy6642         155 YCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDE  188 (292)
Q Consensus       155 ~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~d  188 (292)
                      .||||||+||.+|+++++|+..+|+.|+++-.++
T Consensus        57 ~CP~Hg~~Fd~~G~~~~~Pa~~~l~~y~v~~~~~   90 (91)
T cd03477          57 DCPCHGSRFSYDGEVIEGPAVSGLKPADDAPIDN   90 (91)
T ss_pred             ECCCCCCEECCCCcEeeCCCCCCCCeeEeecccC
Confidence            9999999999999999999999999999875543

The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. It is commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. YhfW is found in bacteria, some eukaryotes and archaea.

>cd04337 Rieske_RO_Alpha_Cao Cao (chlorophyll a oxygenase) is a rieske non-heme iron-sulfur protein located within the plastid-envelope inner and thylakoid membranes, that catalyzes the conversion of chlorophyllide a to chlorophyllide b

Probab=99.81  E-value=1.2e-19  Score=150.62  Aligned_cols=96  Identities=23%  Similarity=0.251  Sum_probs=84.5

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCe
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGG  153 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~  153 (292)
                      ..+++|++|+.+.+++.|.++++.+                          +.+|+++|+++.|||+||+|+.+..+.+.
T Consensus        22 ~~~~el~~g~~~~~~v~g~~l~l~r--------------------------~~~g~v~A~~n~CpH~g~~L~~G~~~~~~   75 (129)
T cd04337          22 EFSKDLKMDTMVPFELFGQPWVLFR--------------------------DEDGTPGCIRDECAHRACPLSLGKVIEGR   75 (129)
T ss_pred             EEHHHCCCCCeEEEEECCcEEEEEE--------------------------CCCCcEEEEeCcCCCCcCCcccCcEeCCE
Confidence            3678899999999999998887653                          35799999999999999999998877789


Q ss_pred             EEcCCCCcEEcCCCceecCCCCC----CCCCCceEeecCceEEEee
Q psy6642         154 YYCPCHGSHYDASGRIRKGPAPT----NMEVPPYQFGDEGILIRML  195 (292)
Q Consensus       154 ~~CPcHGs~FD~~G~v~~gPa~~----~L~~~p~~~~~d~i~V~I~  195 (292)
                      +.||||||+||.+|+++..|...    +|+.|++++++|.|+|.+.
T Consensus        76 i~CP~Hgw~Fd~tG~~~~~P~~~~~~~~l~~y~v~v~~g~V~V~~~  121 (129)
T cd04337          76 IQCPYHGWEYDGDGECTKMPSTKCLNVGIAALPCMEQDGMIWVWPG  121 (129)
T ss_pred             EEeCCCCCEECCCCCEEeCCcCCCccCCcceEeEEEECCEEEEEcC
Confidence            99999999999999999988653    7999999999998888764

CAO is found not only in plants but also in chlorophytes and prochlorophytes. This domain represents the N-terminal rieske domain of the oxygenase alpha subunit. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Cao is closely related to several other plant RO's including Tic 55, a 55 kDa protein associated with protein transport through the inner

>cd03471 Rieske_cytochrome_b6f Iron-sulfur protein (ISP) component of the b6f complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer

Probab=99.81  E-value=1.4e-19  Score=149.67  Aligned_cols=79  Identities=37%  Similarity=0.756  Sum_probs=68.0

Q ss_pred             cCCCe--EEEEecccCCCcccCCcCCCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEeecCceEEEeecccCCCCC
Q psy6642         126 KDPSW--LVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTP  203 (292)
Q Consensus       126 ~~g~~--~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~d~i~V~I~ahtD~~~P  203 (292)
                      .+|++  +|++++|||+||++.++..+ +.+.||||||+||.+|+++.+|++.+|++|++++++|.|+|.++-.+|...-
T Consensus        42 ~dg~i~~~A~~~~CpH~G~~l~~~~~~-~~i~CP~Hg~~Fd~tG~~~~gPa~~~L~~y~V~vedg~I~V~~~~~~~~~~~  120 (126)
T cd03471          42 EDKTIANYGINAVCTHLGCVVPWNAAE-NKFKCPCHGSQYDATGKVVRGPAPLSLALVHATVDDDKVVLSPWTETDFRTG  120 (126)
T ss_pred             CCCeEEEEEecCCCcCCCCCcCccCCC-CEEEcCCCCCEECCCCCEecCCCCCCCceEeEEEECCEEEEEECcccCcccC
Confidence            46766  89999999999999887653 7999999999999999999999999999999999999999998765554433


Q ss_pred             Cc
Q psy6642         204 DF  205 (292)
Q Consensus       204 ~F  205 (292)
                      +|
T Consensus       121 ~~  122 (126)
T cd03471         121 EK  122 (126)
T ss_pred             CC
Confidence            33

The cytochrome b6f complex from Mastigocladus laminosus, a thermophilic cyanobacterium, contains four large subunits, including cytochrome f, cytochrome b6, the Rieske ISP, and subunit IV; as well as four small hydrophobic subunits, PetG, PetL, PetM, and PetN. Rieske ISP, one of the large subunits of the cytochrome bc-type complexes, is involved in respiratory and photosynthetic electron transfer. The core of the chloroplast b6f complex is similar to the analogous respiratory cytochrome bc(1) complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.

>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer

Probab=99.81  E-value=1.5e-19  Score=144.88  Aligned_cols=93  Identities=20%  Similarity=0.284  Sum_probs=80.6

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .+++|++|+.+.+.+.++++++++                          ..+|+++|++++|||+||+|..+..+++.+
T Consensus         6 ~~~~l~~g~~~~~~~~~~~~~~~~--------------------------~~~g~~~A~~n~CpH~g~~L~~g~~~g~~i   59 (108)
T cd03474           6 SLDDVWEGEMELVDVDGEEVLLVA--------------------------PEGGEFRAFQGICPHQEIPLAEGGFDGGVL   59 (108)
T ss_pred             ehhccCCCceEEEEECCeEEEEEE--------------------------ccCCeEEEEcCcCCCCCCCcccCcccCCEE
Confidence            578899999999999887766543                          247899999999999999999887776799


Q ss_pred             EcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         155 YCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       155 ~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      .||||||+||+ +|++. +|+..+|+.|+++++++.|+|.+
T Consensus        60 ~CP~Hg~~Fdl~~G~~~-~~~~~~L~~~~v~v~~g~v~v~~   99 (108)
T cd03474          60 TCRAHLWQFDADTGEGL-NPRDCRLARYPVKVEGGDILVDT   99 (108)
T ss_pred             EeCCcCCEEECCCcccc-CCCCCccceEeEEEECCEEEEeC
Confidence            99999999999 77776 58888999999999999888775

T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.

>cd03479 Rieske_RO_Alpha_PhDO_like Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3,4-dioxygenase (CBDO), phenoxybenzoate dioxygenase (POB-dioxygenase) and 3-nitrobenzoate oxygenase (MnbA)

Probab=99.80  E-value=3.1e-19  Score=150.77  Aligned_cols=108  Identities=19%  Similarity=0.266  Sum_probs=88.3

Q ss_pred             eecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCC
Q psy6642          74 VDLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWG  152 (292)
Q Consensus        74 v~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~  152 (292)
                      ..+++|+ +|+.+.+.+.|.+++|.                          |..+|+++|++++|||+||+|+++..+.+
T Consensus        26 ~~~~eL~~~g~~~~~~~~g~~i~v~--------------------------r~~~G~v~A~~n~CpHrG~~L~~G~~~~~   79 (144)
T cd03479          26 ALSSELTEDGQPVRVRLLGEDLVAF--------------------------RDTSGRVGLLDEHCPHRGASLVFGRVEEC   79 (144)
T ss_pred             EEHHHCCCCCCEEEEEECCcEEEEE--------------------------EeCCCCEEEEcCcCCCCCCcccCCcccCC
Confidence            3678888 68888888888887664                          33588999999999999999999887778


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCC---------CCCCCceEeecCceEEEeecccCCCCCCccccc
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPT---------NMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYR  209 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~---------~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr  209 (292)
                      .|.||||||+||.+|+++..|+..         .|+.|+++++++.|+|.+.  .....|.+++|.
T Consensus        80 ~i~CP~Hgw~F~~~G~~~~~P~~~~~~~~~~~~~l~~~~v~~~~G~I~V~~~--~~~~~p~~~~~~  143 (144)
T cd03479          80 GLRCCYHGWKFDVDGQCLEMPSEPPDSQLKQKVRQPAYPVRERGGLVWAYMG--PAEEAPEFPRYD  143 (144)
T ss_pred             EEEccCCCcEECCCCCEEECCCCccccCCccccCcceEeEEEECCEEEEECC--CCCCCCCCCCCC
Confidence            999999999999999999988643         5899999999998887753  334566666653

ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PhDO and CBDO are two-component RO systems, containing oxygenase and reductase components. PhDO catalyzes the dihydroxylation of phthalate to form th

>cd03531 Rieske_RO_Alpha_KSH The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH)

Probab=99.80  E-value=3e-19  Score=145.42  Aligned_cols=101  Identities=16%  Similarity=0.190  Sum_probs=84.7

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .+++|++|+.+.++..|.+++|.+                          +.+|+++|++++|||+|++|..+..+++.+
T Consensus         7 ~~~dl~~g~~~~~~~~g~~i~l~r--------------------------~~~g~~~a~~n~CpH~ga~L~~G~~~~~~i   60 (115)
T cd03531           7 LARDFRDGKPHGVEAFGTKLVVFA--------------------------DSDGALNVLDAYCRHMGGDLSQGTVKGDEI   60 (115)
T ss_pred             EHHHCCCCCeEEEEECCeEEEEEE--------------------------CCCCCEEEEcCcCCCCCCCCccCcccCCEE
Confidence            467889999999999998887643                          458999999999999999999998887899


Q ss_pred             EcCCCCcEEcCCCceecCCC------CCCCCCCceEeecCceEEEeecccCCCCC
Q psy6642         155 YCPCHGSHYDASGRIRKGPA------PTNMEVPPYQFGDEGILIRMLAHSDIRTP  203 (292)
Q Consensus       155 ~CPcHGs~FD~~G~v~~gPa------~~~L~~~p~~~~~d~i~V~I~ahtD~~~P  203 (292)
                      .||||||+||.+|+++..|+      ...|+.||++++++.|+|.  .+.|.+.|
T Consensus        61 ~CP~Hg~~fd~~G~~~~~p~~~~~p~~~~l~~ypv~~~~g~v~v~--~~~~~~~p  113 (115)
T cd03531          61 ACPFHDWRWGGDGRCKAIPYARRVPPLARTRAWPTLERNGQLFVW--HDPEGNPP  113 (115)
T ss_pred             ECCCCCCEECCCCCEEECCcccCCCcccccceEeEEEECCEEEEE--CCCCCCCC
Confidence            99999999999999998764      3468899999999877655  45555444

The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia.

>TIGR02694 arsenite_ox_S arsenite oxidase, small subunit

Probab=99.77  E-value=1.5e-18  Score=144.16  Aligned_cols=103  Identities=21%  Similarity=0.362  Sum_probs=80.1

Q ss_pred             eecCCCCCCCeEEEEEcC--eeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCC
Q psy6642          74 VDLNLIPEGQSVTFKWRG--KPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDW  151 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g--~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~  151 (292)
                      .++++|++|+.+.+.+.+  .++++++....                ..... ..+|+++|++++|||+||+|.++. ++
T Consensus        10 ~~~~dl~~g~~~~~~~~~~~~~~~v~~~~~~----------------~~~~~-~~~G~~~A~~~~CpH~g~~L~~~~-~~   71 (129)
T TIGR02694        10 ANISELKLNEPLDFNYPDASSPGVLLKLGTP----------------VEGGV-GPDGDIVAFSTLCTHMGCPVSYSA-DN   71 (129)
T ss_pred             EeHHHCCCCCCEEEecCCCCCCEEEEecCCc----------------ccCcc-ccCCEEEEEeCcCCCCCccccccc-CC
Confidence            378999999999999865  36666542110                01111 147999999999999999999875 45


Q ss_pred             CeEEcCCCCcEEcC-C-CceecCCCCCCCCCCceEeec-CceEEEee
Q psy6642         152 GGYYCPCHGSHYDA-S-GRIRKGPAPTNMEVPPYQFGD-EGILIRML  195 (292)
Q Consensus       152 ~~~~CPcHGs~FD~-~-G~v~~gPa~~~L~~~p~~~~~-d~i~V~I~  195 (292)
                      +.|.||||||+||+ + |+++.+|+..+|+.|++++++ +.++ .+.
T Consensus        72 ~~i~CP~Hga~Fdl~tgG~~~~gP~~~~L~~y~v~v~~~G~V~-~~~  117 (129)
T TIGR02694        72 KTFNCPCHFSVFDPEKGGQQVWGQATQNLPQIVLRVADNGDIF-AEG  117 (129)
T ss_pred             CEEEcCCCCCEECCCCCCcEECCCCCCCCCeeEEEEECCCeEE-EEe
Confidence            89999999999999 4 699999999999999999975 5555 444

This model represents the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance. Homologs to both large (TIGR02693) and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7.

>cd04338 Rieske_RO_Alpha_Tic55 Tic55 is a 55kDa LLS1-related non-heme iron oxygenase associated with protein transport through the plant inner chloroplast membrane

Probab=99.77  E-value=1.9e-18  Score=144.30  Aligned_cols=98  Identities=13%  Similarity=0.113  Sum_probs=83.3

Q ss_pred             cceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCC
Q psy6642          71 TIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGD  150 (292)
Q Consensus        71 ~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~  150 (292)
                      .....+++|++|+.+.+.+.|++++|.+                          ..+|+++|+.|.|||+|++|+.+..+
T Consensus        19 ~~v~~~~el~~~~~~~~~v~g~~ivl~r--------------------------~~~G~v~A~~n~CpHrga~L~~G~~~   72 (134)
T cd04338          19 YPLYLLKDVPTDAPLGLSVYDEPFVLFR--------------------------DQNGQLRCLEDRCPHRLAKLSEGQLI   72 (134)
T ss_pred             EEEEEHHHCCCCCCEEEEECCceEEEEE--------------------------cCCCCEEEEcCcCCCCcCcccCCeec
Confidence            3345678899998888888888887643                          35899999999999999999998877


Q ss_pred             CCeEEcCCCCcEEcCCCceecCCC---------CCCCCCCceEeecCceEEEe
Q psy6642         151 WGGYYCPCHGSHYDASGRIRKGPA---------PTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       151 ~~~~~CPcHGs~FD~~G~v~~gPa---------~~~L~~~p~~~~~d~i~V~I  194 (292)
                      ++.+.||+|||+||.+|+++..|.         ...|+.|++++++|.|+|.+
T Consensus        73 ~~~i~CP~Hgw~Fd~~G~~~~~P~~~~~~~~~~~~~l~~y~v~~~~G~V~V~~  125 (134)
T cd04338          73 DGKLECLYHGWQFGGEGKCVKIPQLPADAKIPKNACVKSYEVRDSQGVVWMWM  125 (134)
T ss_pred             CCEEEccCCCCEECCCCCEEECCCCCccCCCCcccCcceEeEEEECCEEEEEc
Confidence            789999999999999999998763         24589999999999888775

This domain represents the N-terminal Rieske domain of the Tic55 oxygenase alpha subunit. Tic55 is closely related to the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO), Ptc52, and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis.

>cd03532 Rieske_RO_Alpha_VanA_DdmC Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth

Probab=99.77  E-value=1.9e-18  Score=140.68  Aligned_cols=93  Identities=20%  Similarity=0.292  Sum_probs=80.2

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      ..++|+ |+.+.+...|.+++|.+                          ..+|+++|++++|||+|++|+.+..+++.+
T Consensus        11 ~~~el~-~~~~~~~~~g~~i~l~r--------------------------~~~g~~~a~~n~CpH~g~~L~~G~~~~~~i   63 (116)
T cd03532          11 WADELG-DKPLARTLLGEPVVLYR--------------------------TQDGRVAALEDRCPHRSAPLSKGSVEGGGL   63 (116)
T ss_pred             EHHHcC-CCcEEEEECCceEEEEE--------------------------CCCCCEEEeCCcCCCCCCCccCCcccCCEE
Confidence            467777 88888888888877643                          358999999999999999999988777899


Q ss_pred             EcCCCCcEEcCCCceecCCCC------CCCCCCceEeecCceEEEe
Q psy6642         155 YCPCHGSHYDASGRIRKGPAP------TNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       155 ~CPcHGs~FD~~G~v~~gPa~------~~L~~~p~~~~~d~i~V~I  194 (292)
                      .||+|||+||.+|+++..|..      .+|+.|+++++++.|+|.+
T Consensus        64 ~Cp~Hg~~fd~~G~~~~~p~~~~~~~~~~l~~~~v~~~~g~v~v~~  109 (116)
T cd03532          64 VCGYHGLEFDSDGRCVHMPGQERVPAKACVRSYPVVERDALIWIWM  109 (116)
T ss_pred             EeCCCCcEEcCCCCEEeCCCCCCCCCccccccCCEEEECCEEEEEc
Confidence            999999999999999988764      3799999999999888876

The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degrad

>COG2146 {NirD} Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases [Inorganic ion transport and metabolism / General function prediction only]

Probab=99.75  E-value=3.4e-18  Score=137.61  Aligned_cols=94  Identities=20%  Similarity=0.370  Sum_probs=78.9

Q ss_pred             eecCCCCCCCeEEEEEcC-eeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCC
Q psy6642          74 VDLNLIPEGQSVTFKWRG-KPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWG  152 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g-~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~  152 (292)
                      ..+++|+++..+.+...+ ..++++                           ..+|++||+.|.|||.||+++.+..+++
T Consensus         9 c~~~dl~~~~~~~v~~~~~~~~~~~---------------------------~~~g~v~A~~n~CpH~~~~l~~g~v~~~   61 (106)
T COG2146           9 CKVDDLPEGGGVRVLVGGGRFALVV---------------------------RADGEVFAIDNRCPHAGAPLSRGLVEGD   61 (106)
T ss_pred             EehHhcCCCCceEEEecCCEEEEEE---------------------------ecCCEEEEEeCcCCCCCCcccccEeCCC
Confidence            467899999988888844 444443                           2589999999999999999998887765


Q ss_pred             -eEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         153 -GYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       153 -~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                       .+.||||+++||+ ||+++.+|+...|++||++++++.++|.+
T Consensus        62 ~~i~Cp~H~a~Fdl~tG~~~~~p~~~~l~~y~vrve~g~v~v~~  105 (106)
T COG2146          62 ETVVCPLHGARFDLRTGECLEPPAGKTLKTYPVRVEGGRVFVDL  105 (106)
T ss_pred             CEEECCccCCEEEcCCCceecCCCCCceeEEeEEEECCEEEEec
Confidence             5999999999999 99999998754499999999999888763

>cd03548 Rieske_RO_Alpha_OMO_CARDO Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth

Probab=99.75  E-value=7.3e-18  Score=141.08  Aligned_cols=106  Identities=19%  Similarity=0.275  Sum_probs=86.8

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC--CCC
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA--GDW  151 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~--~~~  151 (292)
                      ...++|++|+.+.+.+.|++++|.+                           .+|+++|+.|.|||+|++|..+.  .++
T Consensus        19 ~~~~el~~g~~~~~~~~g~~i~l~r---------------------------~~g~v~A~~n~CpHrg~~L~~g~~~~~~   71 (136)
T cd03548          19 LFSHELEEGEPKGIQLCGEPILLRR---------------------------VDGKVYALKDRCLHRGVPLSKKPECFTK   71 (136)
T ss_pred             EEHHHCCCCCeEEEEECCcEEEEEe---------------------------cCCEEEEEeCcCcCCCCccccCcccccC
Confidence            3578899999999999999887743                           37899999999999999999764  345


Q ss_pred             CeEEcCCCCcEEcC-CCceecC---CC-----CCCCCCCceEeecCceEEEeecccCCCCCCcc
Q psy6642         152 GGYYCPCHGSHYDA-SGRIRKG---PA-----PTNMEVPPYQFGDEGILIRMLAHSDIRTPDFS  206 (292)
Q Consensus       152 ~~~~CPcHGs~FD~-~G~v~~g---Pa-----~~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~  206 (292)
                      +.|.||+|||+||+ +|+++..   |.     ...|+.||+++.+|.|+|.+.....-..|.|+
T Consensus        72 ~~i~Cp~Hgw~Fdl~tG~~~~~~~~p~~~~~~~~~L~~ypv~~~~g~V~v~~~~~~~~~~~~~~  135 (136)
T cd03548          72 GTITCWYHGWTYRLDDGKLVTILANPDDPLIGRTGLKTYPVEEAKGMIFVFVGDGDYADPPPLA  135 (136)
T ss_pred             CEEEecCCccEEeCCCccEEEcccCCCccccccCCCceEeEEEECCEEEEEeCCcccCCCCCCC
Confidence            79999999999998 9999863   32     34699999999999999887655555666654

The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OMO catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline, the second step in the bacterial degradation of quinoline. OMO consists of a reductase component (OMR) and an oxygenase component (OMO) that together function to shuttle electrons from the

>cd03467 Rieske Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes

Probab=99.74  E-value=1e-17  Score=131.62  Aligned_cols=87  Identities=29%  Similarity=0.582  Sum_probs=76.8

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      ..++|++|..+.+...++.++|.+                          ..+++++|+++.|||+||+|..+..+++.+
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~v~~--------------------------~~~~~~~a~~~~CpH~g~~l~~~~~~~~~i   59 (98)
T cd03467           6 ALSELPPGGGRVVVVGGGPVVVVR--------------------------REGGEVYALSNRCTHQGCPLSEGEGEDGCI   59 (98)
T ss_pred             eccccCCCceEEEEECCeEEEEEE--------------------------eCCCEEEEEcCcCCCCCccCCcCccCCCEE
Confidence            456788999998888888887654                          246899999999999999999887666899


Q ss_pred             EcCCCCcEEcC-CCceecCCCCCCCCCCceEeec
Q psy6642         155 YCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGD  187 (292)
Q Consensus       155 ~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~  187 (292)
                      .||||||+||+ +|+++.+|+..+|+.|++++++
T Consensus        60 ~Cp~H~~~f~~~~G~~~~~p~~~~l~~~~v~~~~   93 (98)
T cd03467          60 VCPCHGSRFDLRTGEVVSGPAPRPLPKYPVKVEG   93 (98)
T ss_pred             EeCCCCCEEeCCCccCcCCCCCCCcCEEEEEEeC
Confidence            99999999999 9999999999999999999986

The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.

>cd03529 Rieske_NirD Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium

Probab=99.74  E-value=4.7e-18  Score=135.40  Aligned_cols=91  Identities=13%  Similarity=0.131  Sum_probs=76.3

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcc-cCCcCC----
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCV-PIANAG----  149 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~-l~~~~~----  149 (292)
                      .+++|++|+.+.+...|+++++.+                          ..+|+++|+.+.|||+|++ ++.+..    
T Consensus         6 ~~~~l~~g~~~~~~~~g~~i~l~r--------------------------~~~g~~~A~~~~CpH~g~~ll~~G~~~~~~   59 (103)
T cd03529           6 ALDDLPPGSGVAALVGDTQIAIFR--------------------------LPGREVYAVQNMDPHSRANVLSRGIVGDIG   59 (103)
T ss_pred             EHHHCCCCCcEEEEECCEEEEEEE--------------------------eCCCeEEEEeCcCCCCCCcccCCceEcccC
Confidence            578899999999999999987754                          2356999999999999997 555432    


Q ss_pred             CCCeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEE
Q psy6642         150 DWGGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILI  192 (292)
Q Consensus       150 ~~~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V  192 (292)
                      +.+.+.||+|||+||+ +|+++.+|. .+|+.||+++++|.++|
T Consensus        60 ~~~~i~Cp~Hg~~Fdl~tG~~~~~p~-~~l~~y~v~~~~g~v~v  102 (103)
T cd03529          60 GEPVVASPLYKQHFSLKTGRCLEDED-VSVATFPVRVEDGEVYV  102 (103)
T ss_pred             CCeEEECCCCCCEEEcCCCCccCCCC-ccEeeEeEEEECCEEEE
Confidence            1247999999999998 999999886 58999999999998876

Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.

>TIGR02378 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit

Probab=99.74  E-value=5.2e-18  Score=135.43  Aligned_cols=92  Identities=17%  Similarity=0.250  Sum_probs=77.5

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCC-CcccCCcCCCCCe
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHL-GCVPIANAGDWGG  153 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHl-Gc~l~~~~~~~~~  153 (292)
                      .+++|++|+...+...|.+++|.+                          ..+++++|+.+.|||+ +++|+.+..+.+.
T Consensus         7 ~~~el~~g~~~~~~v~g~~l~v~r--------------------------~~~~~~~a~~~~CpH~g~~~L~~g~~~~~~   60 (105)
T TIGR02378         7 AIDDIPEETGVCVLLGDTQIAIFR--------------------------VPGDQVFAIQNMCPHKRAFVLSRGIVGDAQ   60 (105)
T ss_pred             EHHHCCCCCcEEEEECCEEEEEEE--------------------------eCCCcEEEEeCcCCCCCCccccceEEccCC
Confidence            578899999999999999987754                          2367899999999999 7788876433333


Q ss_pred             ----EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEE
Q psy6642         154 ----YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIR  193 (292)
Q Consensus       154 ----~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~  193 (292)
                          +.||+|||+||+ +|+++.+|. .+|+.||+++++|.++|.
T Consensus        61 ~~~~i~Cp~Hg~~Fdl~tG~~~~~~~-~~L~~y~v~v~~g~v~v~  104 (105)
T TIGR02378        61 GELWVACPLHKRNFRLEDGRCLEDDS-GSVRTYEVRVEDGRVYVA  104 (105)
T ss_pred             CcEEEECCcCCCEEEcCCccccCCCC-ccEeeEeEEEECCEEEEe
Confidence                999999999999 999998765 689999999999988875

This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused.

>PRK09511 nirD nitrite reductase small subunit; Provisional

Probab=99.73  E-value=7e-18  Score=136.08  Aligned_cols=94  Identities=13%  Similarity=0.058  Sum_probs=78.2

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcc-cCCcCCC--
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCV-PIANAGD--  150 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~-l~~~~~~--  150 (292)
                      ..+++|++|+...+...|+.+.|.+.                         ..+|++||++|.|||.|++ |+.+...  
T Consensus         8 ~~~~dl~~g~~~~v~v~g~~i~l~~~-------------------------~~~g~~~A~~n~CpH~~~~~L~~G~~~~~   62 (108)
T PRK09511          8 CKIDDILPGTGVCALVGDEQVAIFRP-------------------------YHDEQVFAISNIDPFFQASVLSRGLIAEH   62 (108)
T ss_pred             eEHhHcCCCceEEEEECCEEEEEEEE-------------------------CCCCEEEEEeCcCCCCCCcccCCceEccC
Confidence            36799999999999999988877531                         1378999999999999996 8777542  


Q ss_pred             CC--eEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEE
Q psy6642         151 WG--GYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIR  193 (292)
Q Consensus       151 ~~--~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~  193 (292)
                      .+  .+.||+|||+||+ ||+++..|. .+|++||+++++|.|+|.
T Consensus        63 ~g~~~V~CP~H~~~Fdl~TG~~~~~~~-~~l~typV~ve~g~V~v~  107 (108)
T PRK09511         63 QGELWVASPLKKQRFRLSDGLCMEDEQ-FSVKHYDARVKDGVVQLR  107 (108)
T ss_pred             CCeEEEECCCCCCEEECCCcccCCCCC-ccEeeEeEEEECCEEEEe
Confidence            12  4999999999999 999997664 699999999999998874

>cd03480 Rieske_RO_Alpha_PaO Rieske non-heme iron oxygenase (RO) family, Pheophorbide a oxygenase (PaO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO) and ACD1 (accelerated cell death 1)

Probab=99.72  E-value=1.8e-17  Score=139.24  Aligned_cols=96  Identities=19%  Similarity=0.273  Sum_probs=80.9

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCccccccc-CCCeEEEEecccCCCcccCCcCCC-C
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVK-DPSWLVIIGICTHLGCVPIANAGD-W  151 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~-~g~~~a~~~~CtHlGc~l~~~~~~-~  151 (292)
                      ..+++|++|+.+.+++.|.+++|.+                          .. +|+++|+.|+|||+|++|+.+... .
T Consensus        22 ~~~~el~~g~~~~~~~~g~~i~v~r--------------------------~~~dG~~~A~~n~CpHrga~L~~G~~~~~   75 (138)
T cd03480          22 AYVEDLDPSRPTPFTLLGRDLVIWW--------------------------DRNSQQWRAFDDQCPHRLAPLSEGRIDEE   75 (138)
T ss_pred             EEHHHCCCCCcEEEEECCeeEEEEE--------------------------ECCCCEEEEEcCCCcCCcCccccceEcCC
Confidence            3678899999999999999887753                          33 899999999999999999988653 3


Q ss_pred             CeEEcCCCCcEEcCCCceecCCC-----------CCCCCCCceEeecCceEEEee
Q psy6642         152 GGYYCPCHGSHYDASGRIRKGPA-----------PTNMEVPPYQFGDEGILIRML  195 (292)
Q Consensus       152 ~~~~CPcHGs~FD~~G~v~~gPa-----------~~~L~~~p~~~~~d~i~V~I~  195 (292)
                      +.+.||+|||+||.+|+++..|.           ...|+.||++++++.|+|.+.
T Consensus        76 ~~i~CP~Hgw~Fd~tG~~~~~P~~~~~g~~~~~~~~~l~~ypv~v~~g~V~V~~~  130 (138)
T cd03480          76 GCLECPYHGWSFDGSGSCQRIPQAAEGGKAHTSPRACVASLPTAVRQGLLFVWPG  130 (138)
T ss_pred             CEEEeCCCCCEECCCCCEEECCCCccccccCCCcccccceEeEEEECCEEEEecC
Confidence            68999999999999999998763           256889999999998887753

ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PaO expression increases upon physical wounding of plant leaves and is thought to catalyze a key step in chlorophyll degradation. The

>cd03536 Rieske_RO_Alpha_DTDO This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit (DitA) of diterpenoid dioxygenase (DTDO)

Probab=99.71  E-value=5.2e-17  Score=133.71  Aligned_cols=102  Identities=19%  Similarity=0.279  Sum_probs=78.4

Q ss_pred             ecCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCC-CC
Q psy6642          75 DLNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGD-WG  152 (292)
Q Consensus        75 ~~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~-~~  152 (292)
                      .+++|++ |..+++...+.++++.+                          ..+|+++|+.|+|||+|++|.++... ..
T Consensus         6 ~~~el~~~g~~~~~~~~~~~i~v~r--------------------------~~~g~v~A~~n~CpH~g~~L~~~~~~~~~   59 (123)
T cd03536           6 HESEIPNKGDFMVRDMGSDSVIVAR--------------------------DKDGEIHVSLNVCPHRGMRISTTDGGNTQ   59 (123)
T ss_pred             EHHHCCCCCCEEEEEECCceEEEEE--------------------------CCCCCEEEEeeeCCCCCCCcccccCCCcC
Confidence            4677887 55566677888877643                          35799999999999999999876543 25


Q ss_pred             eEEcCCCCcEEcCCCceecCCCC-------------CCCCCCceEeecCceEEEeecccCCCCCCcc
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAP-------------TNMEVPPYQFGDEGILIRMLAHSDIRTPDFS  206 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~-------------~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~  206 (292)
                      .+.||||||+||.+|+++..|..             .+|..+++++.++-|+|.+    +...|.|.
T Consensus        60 ~i~Cp~Hgw~fd~~G~~~~~p~~~~~~~~~~~~~~~~~L~~~~v~~~~g~Ifv~~----~~~~~~~~  122 (123)
T cd03536          60 IHVCIYHGWAFRPNGDFIGAPVEKECMHGKMRTKAELGLHKARVTLYGGLIFATW----NIDGPSFE  122 (123)
T ss_pred             EEECCcCCCEECCCCcEEECCccccccccCCCCHHHCCCcceeEEEECCEEEEEe----CCCCCCCC
Confidence            78999999999999999988863             4588889999888776653    33455554

DTDO is a novel aromatic-ring-hydroxylating dioxygenase found in Pseudomonas and other proteobacteria that degrades dehydroabietic acid (DhA). Specifically, DitA hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8, 13-abietadien acid. The ditA1 and ditA2 genes encode the alpha and beta subunits of the oxygenase component of DTDO while the ditA3 gene encodes the ferredoxin component of DTDO. The organization of the genes encoding the various diterpenoid dioxygenase components, the phylogenetic distinctiveness of both the alpha subunit and the ferredoxin component, and the unusual iron-sulfur cluster of the ferredoxin all suggest that this enzyme belongs to a new class of aromatic ring-hydroxylating dioxygenases.

>cd03475 Rieske_SoxF_SoxL SoxF and SoxL family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer

Probab=99.69  E-value=1.1e-16  Score=138.30  Aligned_cols=61  Identities=34%  Similarity=0.673  Sum_probs=53.2

Q ss_pred             CCCeEEEEecccCCCcccCCc---------------CCCCCeEEcCCCCcEEcC-CC-ceecCCCCCCCCCCceEeec
Q psy6642         127 DPSWLVIIGICTHLGCVPIAN---------------AGDWGGYYCPCHGSHYDA-SG-RIRKGPAPTNMEVPPYQFGD  187 (292)
Q Consensus       127 ~g~~~a~~~~CtHlGc~l~~~---------------~~~~~~~~CPcHGs~FD~-~G-~v~~gPa~~~L~~~p~~~~~  187 (292)
                      +++++|++++|||+||++.+.               ..+.+.|.||||||+||+ +| .++.|||+++|+++++++++
T Consensus        74 ~g~IvA~S~iCpHlGc~l~~~~~y~~~~~~~~~~~g~~~~~~i~CPcHgS~FD~~tGg~v~~GPA~~pLp~~~L~~d~  151 (171)
T cd03475          74 NKSIVAFSAICQHLGCQPPPIVSYPSYYPPDKAPGLASKGAVIHCCCHGSTYDPYKGGVVLTGPAPRPLPAVILEYDS  151 (171)
T ss_pred             CCEEEEEeCcCCCCCCcccccccccccccccccccccccCCEEEcCCCCCEEeCCCCCeEcCCCCCCCcCEeEEEEeC
Confidence            789999999999999988641               123579999999999999 55 78889999999999999996

SoxF is a subunit of the terminal oxidase supercomplex SoxM in the plasma membrane of Sulfolobus acidocaldarius that combines features of a cytochrome bc(1) complex and a cytochrome. The Rieske domain of SoxF has a 12 residue insertion which is not found in eukaryotic and bacterial Rieske proteins and is thought to influence the redox properties of the iron-sulfur cluster. SoxL is a Rieske protein which may be part of an archaeal bc-complex homologue whose physiological function is still unknown. SoxL has two features not seen in other Rieske proteins; (i) a significantly greater distance between the two cluster-binding sites and (ii) an unexpected Pro - Asp substitution at one of the cluster binding sites. SoxF and SoxL are found in archaea and in bacteria.

>cd03472 Rieske_RO_Alpha_BPDO_like Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO), nitrobenzene dioxygenase (NBDO), alkylbenzene dioxygenase (AkbDO) and dibenzofuran 4,4a-dioxygenase (DFDO)

Probab=99.69  E-value=1.6e-16  Score=131.79  Aligned_cols=75  Identities=25%  Similarity=0.418  Sum_probs=61.1

Q ss_pred             ecCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCC-CCC
Q psy6642          75 DLNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAG-DWG  152 (292)
Q Consensus        75 ~~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~-~~~  152 (292)
                      .+++|++ |...++.+.++++++.+                          +.+|+++|+.|+|||+|++|+.+.. +.+
T Consensus        14 ~~~el~~~g~~~~~~~~~~~i~l~r--------------------------~~~g~i~A~~n~C~Hrg~~L~~g~~g~~~   67 (128)
T cd03472          14 HETHIPKAGDYLTTYMGEDPVIVVR--------------------------QKDGSIRVFLNQCRHRGMRICRSDAGNAK   67 (128)
T ss_pred             EHHHCCCCCCEEEEEECCceEEEEE--------------------------CCCCCEEEEhhhCcCCCCeeeccCCCCcC
Confidence            5677876 44456777888877643                          3589999999999999999988653 335


Q ss_pred             eEEcCCCCcEEcCCCceecCCCC
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAP  175 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~  175 (292)
                      .+.||||||+||.+|++++.|+.
T Consensus        68 ~i~CP~Hgw~fd~~G~~~~~P~~   90 (128)
T cd03472          68 AFTCTYHGWAYDTAGNLVNVPFE   90 (128)
T ss_pred             EEECCcCCeEECCCcCEEeccCc
Confidence            89999999999999999999884

ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. BPDO degrades biphenyls and polychlorinated biphenyls (PCB's) while CumDO degrades cumene (isopropylbenzene), an aromatic hydrocarbon that is i

>cd03537 Rieske_RO_Alpha_PrnD This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit of aminopyrrolnitrin oxygenase (PrnD)

Probab=99.66  E-value=3e-16  Score=129.44  Aligned_cols=92  Identities=17%  Similarity=0.187  Sum_probs=73.5

Q ss_pred             cCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeEE
Q psy6642          76 LNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYY  155 (292)
Q Consensus        76 ~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~~  155 (292)
                      .++|+ ++.+.+++.|.++++.                          |..+|+++|+.|.|||+|++|+.+..+++.+.
T Consensus        10 ~~~l~-~~~~~~~~~g~~ivl~--------------------------r~~~g~v~a~~n~CpHrg~~Ls~G~v~~~~l~   62 (123)
T cd03537          10 SDDLK-DKPTELTLFGRPCVAW--------------------------RGATGRAVVMDRHCSHLGANLADGRVKDGCIQ   62 (123)
T ss_pred             HHHcC-CCcEEEEECCeEEEEE--------------------------EccCCEEEEEcCCCCCCCCCccCCEEeCCEEE
Confidence            45554 5566777778877664                          44588999999999999999999887778999


Q ss_pred             cCCCCcEEcCCCceecCCC-------------CCCCCCCceEeecCceEEEe
Q psy6642         156 CPCHGSHYDASGRIRKGPA-------------PTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       156 CPcHGs~FD~~G~v~~gPa-------------~~~L~~~p~~~~~d~i~V~I  194 (292)
                      ||+|||+||.+|+++..|.             ...+..||++..+|-|+|.+
T Consensus        63 CpyHGw~Fd~~G~~~~iP~~~~~~~~~~~~p~~~~~~~~pv~e~~G~Vwv~~  114 (123)
T cd03537          63 CPFHHWRYDEQGQCVHIPGHSTAVRRLEPVPRGARQPTLVTAERYGYVWVWY  114 (123)
T ss_pred             CCCCCCEECCCCCEEECCCCcccccccccCCcccccccEeEEEECCEEEEEc
Confidence            9999999999999997764             13577888888888666654

PrnD is a novel Rieske N-oxygenase that catalyzes the final step in the pyrrolnitrin biosynthetic pathway, the oxidation of the amino group in aminopyrrolnitrin to a nitro group, forming the antibiotic pyrrolnitrin. The biosynthesis of pyrrolnitrin is one of the best examples of enzyme-catalyzed arylamine oxidation. Although arylamine oxygenases are widely distributed within the microbial world and used in a variety of metabolic reactions, PrnD represents one of only two known examples of arylamine oxygenases or N-oxygenases involved in arylnitro group formation, the other being AurF involved in aureothin biosynthesis.

>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A

Probab=99.66  E-value=2.6e-16  Score=126.22  Aligned_cols=93  Identities=18%  Similarity=0.299  Sum_probs=81.3

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccC-CCcccCCcCCCC-
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTH-LGCVPIANAGDW-  151 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtH-lGc~l~~~~~~~-  151 (292)
                      ..+++|++|+.+.+...|+.+.|.+                          ..++++||++|.||| .+.+|+.|..+. 
T Consensus         6 ~~~~~L~~~~~~~~~v~g~~Ialf~--------------------------~~~~~vyAi~n~Cph~~~~~Ls~G~i~~~   59 (104)
T PF13806_consen    6 CPLDDLPPGEGRAVEVDGRQIALFR--------------------------VRDGEVYAIDNRCPHSQAGPLSDGLIGDG   59 (104)
T ss_dssp             EETTTSCTTSEEEEEETTEEEEEEE--------------------------ESTTEEEEEESBETTTTSSCGCGSEEEEC
T ss_pred             ccHHHCCCCCcEEEEECCeEEEEEE--------------------------eCCCCEEEEeccCCccCCcccceeEEccC
Confidence            3789999999999999999998865                          247899999999999 799999875433 


Q ss_pred             ---CeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEE
Q psy6642         152 ---GGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIR  193 (292)
Q Consensus       152 ---~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~  193 (292)
                         ..+.||+|+++||+ +|+++..|. .+|++||++++++.|+|.
T Consensus        60 ~g~~~V~CPlH~~~f~L~tG~~~~~~~-~~l~~ypvrv~~g~V~V~  104 (104)
T PF13806_consen   60 NGEPCVACPLHKWRFDLRTGECLEDPD-VSLRTYPVRVEDGQVYVE  104 (104)
T ss_dssp             TTEEEEEETTTTEEEETTTTEESSECS-EBSBEEEEEECTTEEEEE
T ss_pred             CCCEEEECCCCCCeEECCCcCcCCCCC-CcEEeEEEEEECCEEEEC
Confidence               38999999999999 999998776 899999999999988874

>cd03473 Rieske_CMP_Neu5Ac_hydrolase_N Cytidine monophosphate-N-acetylneuraminic acid (CMP Neu5Ac) hydroxylase family, N-terminal Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer

Probab=99.66  E-value=2.3e-16  Score=126.42  Aligned_cols=84  Identities=17%  Similarity=0.175  Sum_probs=69.4

Q ss_pred             cCCCCCCCeEEEEE-cCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCc--CCCCC
Q psy6642          76 LNLIPEGQSVTFKW-RGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIAN--AGDWG  152 (292)
Q Consensus        76 ~s~l~~g~~~~~~~-~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~--~~~~~  152 (292)
                      +.+|++|..+.+++ .|+.+.|.+                           .+|+++|+.+.|||+|++|..+  ..+++
T Consensus        14 l~eL~~G~~~~v~v~~g~~I~V~~---------------------------~~G~~~A~~n~CpH~g~pL~~g~g~~~g~   66 (107)
T cd03473          14 VANLKEGINFFRNKEDGKKYIIYK---------------------------SKSELKACKNQCKHQGGLFIKDIEDLDGR   66 (107)
T ss_pred             HhcCCCCceEEEEecCCcEEEEEE---------------------------ECCEEEEEcCCCCCCCccccCCcceEeCC
Confidence            47899999999999 898887754                           3789999999999999999874  35668


Q ss_pred             eEEcCCCCcEEcC-CCceecCCCCCCCCCCceEee
Q psy6642         153 GYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFG  186 (292)
Q Consensus       153 ~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~  186 (292)
                      .+.||+|||+||+ +|+++..|+..+-+..-+++.
T Consensus        67 ~V~CP~Hg~~FDLrTG~~~~~p~~~~~~~~~~~~~  101 (107)
T cd03473          67 TVRCTKHNWKLDVSTMKYVNPPDSFCQDELVVEYD  101 (107)
T ss_pred             EEEeCCCCCEEEcCCCCCccCCcccccceeEEEEc
Confidence            8999999999999 999999887665544444443

CMP Neu5Ac hydroxylase is the key enzyme for the synthesis of N-glycolylneuraminic acid (NeuGc) from N-acetylneuraminic acid (Neu5Ac), NeuGc and Neu5Ac are members of a family of cell surface sugars called sialic acids. All mammals except humans have both NeuGc variants on their cell surfaces. In humans, the gene encoding CMP Neu5Ac hydroxylase has a mutation within its coding region that abolishes NeuGc production.

>PLN02281 chlorophyllide a oxygenase

Probab=99.65  E-value=6.3e-16  Score=153.57  Aligned_cols=88  Identities=20%  Similarity=0.254  Sum_probs=72.5

Q ss_pred             cccccccCCCeEEEEecccCCCcccCCcCCCCCeEEcCCCCcEEcCCCceecCCCC----CCCCCCceEeecCceEEEee
Q psy6642         120 ADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAP----TNMEVPPYQFGDEGILIRML  195 (292)
Q Consensus       120 ~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~v~~gPa~----~~L~~~p~~~~~d~i~V~I~  195 (292)
                      ..++|..+|+++|+.|.|||+|++|+.|..+++.+.||||||+||.+|+|+..|..    ..+..||+++.+|.|+|.+ 
T Consensus       245 IVL~R~~dG~v~A~~D~CPHRgaPLs~G~v~g~~L~CPYHGW~FD~dG~cv~iP~~~~~~~~l~sYPV~e~~GlVwV~l-  323 (536)
T PLN02281        245 WVIFRGEDGKPGCVRNTCAHRACPLDLGTVNEGRIQCPYHGWEYSTDGECKKMPSTKLLKVKIKSLPCLEQEGMIWIWP-  323 (536)
T ss_pred             EEEEECCCCeEEEEeCcCcCCCCccccceeeCCEEEeCCCCCEECCCCCEeeCCCCccccCCcceEeEEEECCEEEEEe-
Confidence            45677789999999999999999999998888999999999999999999998864    3578999999888777665 


Q ss_pred             cccCCCCCCccccc
Q psy6642         196 AHSDIRTPDFSKYR  209 (292)
Q Consensus       196 ahtD~~~P~F~~yr  209 (292)
                       ..+...|.++++.
T Consensus       324 -gd~~~aP~~p~ld  336 (536)
T PLN02281        324 -GDEPPAPILPSLQ  336 (536)
T ss_pred             -CCCCCCCCCcccc
Confidence             3333446666554

>cd03545 Rieske_RO_Alpha_OHBDO_like Rieske non-heme iron oxygenase (RO) family, Ortho-halobenzoate-1,2-dioxygenase (OHBDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of OHBDO, salicylate 5-hydroxylase (S5H), terephthalate 1,2-dioxygenase system (TERDOS) and similar proteins

Probab=99.65  E-value=7.7e-16  Score=131.07  Aligned_cols=96  Identities=19%  Similarity=0.245  Sum_probs=77.3

Q ss_pred             eeecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CC
Q psy6642          73 EVDLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GD  150 (292)
Q Consensus        73 ~v~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~  150 (292)
                      ....++|+ +|..+++.+.|+++++.+                          ..+|+++|+.|+|||+|++|+.+. ++
T Consensus        29 v~~~~el~~~g~~~~~~i~g~~iiv~r--------------------------~~~g~v~A~~n~CpHrg~~L~~g~~g~   82 (150)
T cd03545          29 VGLEAEIPNAGDFKSTFVGDTPVVVTR--------------------------AEDGSLHAWVNRCAHRGALVCRERRGN   82 (150)
T ss_pred             EEEHHHCCCCCCEEEEEECCceEEEEE--------------------------CCCCCEEEEcccCcCCCCEecccccCC
Confidence            34678888 588888989888887753                          357899999999999999998763 44


Q ss_pred             CCeEEcCCCCcEEcCCCceecCCCC-----------------CCCCCCceEeecCceEEEe
Q psy6642         151 WGGYYCPCHGSHYDASGRIRKGPAP-----------------TNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       151 ~~~~~CPcHGs~FD~~G~v~~gPa~-----------------~~L~~~p~~~~~d~i~V~I  194 (292)
                      .+.+.||||||+||++|+++..|+.                 ..|..+++++.++-|+|.+
T Consensus        83 ~~~i~CP~Hgw~Fdl~G~~~~ip~~~~~~~~~~~~~~~~~~~~~L~~~~v~~~~g~ifv~l  143 (150)
T cd03545          83 DGSLTCVYHQWAYDLKGNLKGVPFRRGLKGQGGMPKDFDMKQHGLEKLRVETVGGLVFASF  143 (150)
T ss_pred             CCEEECCCCCCEECCCCCEEECccccccccccccccCcCHHHCCCcceeEeEECCEEEEEe
Confidence            5789999999999999999998753                 3577777887778776654

ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OHBDO converts 2-chlorobenzoate (2-CBA) to catechol as well as 2,4-dCBA and 2,5-dCBA to 4-chlorocatechol, as part of the chlorobenzoate degradation pathway. Although ortho-substituted chlorobe

>cd03539 Rieske_RO_Alpha_S5H This alignment model represents the N-terminal rieske iron-sulfur domain of the oxygenase alpha subunit (NagG) of salicylate 5-hydroxylase (S5H)

Probab=99.63  E-value=1.6e-15  Score=126.00  Aligned_cols=92  Identities=16%  Similarity=0.245  Sum_probs=71.9

Q ss_pred             cCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CCCCe
Q psy6642          76 LNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GDWGG  153 (292)
Q Consensus        76 ~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~~~~  153 (292)
                      .++|+ +|...++.+.+.++++.+                          ..+|+++|+.|+|||+|++|..+. ++.+.
T Consensus         7 ~~~l~~~g~~~~~~~~~~~v~v~r--------------------------~~dg~v~A~~n~C~Hrg~~L~~g~~~~~~~   60 (129)
T cd03539           7 EAEIPNPGDFKRTLIGERSVIMTR--------------------------DPDGGINVVENVCAHRGMRFCRERNGNAKD   60 (129)
T ss_pred             HHHCCCCCCEEEEEECCcEEEEEE--------------------------CCCCCEEEEeccCcCCCCEeeeeccCccCE
Confidence            56777 478888888888877643                          357899999999999999998764 34468


Q ss_pred             EEcCCCCcEEcCCCceecCCCC---------------------CCCCCCceEeecCceEEE
Q psy6642         154 YYCPCHGSHYDASGRIRKGPAP---------------------TNMEVPPYQFGDEGILIR  193 (292)
Q Consensus       154 ~~CPcHGs~FD~~G~v~~gPa~---------------------~~L~~~p~~~~~d~i~V~  193 (292)
                      |.||||||+||++|+++..|..                     ..|..++++..++-|+|.
T Consensus        61 l~CPyHgw~fdl~G~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~v~~~~g~Ifv~  121 (129)
T cd03539          61 FVCPYHQWNYSLKGDLQGVPFRRGVKKDGKVNGGMPKDFKTKDHGLTKLKVATRGGVVFAS  121 (129)
T ss_pred             EECCCCCCEECCCCCEeeccccccccccccccccccCCcChHHCCCceeeEeEECCEEEEE
Confidence            9999999999999999987642                     346666777777755554

S5H converts salicylate (2-hydroxybenzoate), a metabolic intermediate of phenanthrene, to gentisate (2,5-dihydroxybenzoate) as part of an alternate pathway for naphthalene catabolism. S5H is a multicomponent enzyme made up of NagGH (the oxygenase components), NagAa (the ferredoxin reductase component), and NagAb (the ferredoxin component). The oxygenase component is made up of alpha (NagG) and beta (NagH) subunits.

>PLN00095 chlorophyllide a oxygenase; Provisional

Probab=99.62  E-value=1.2e-15  Score=146.07  Aligned_cols=95  Identities=22%  Similarity=0.233  Sum_probs=78.9

Q ss_pred             ecCCC-CCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCe
Q psy6642          75 DLNLI-PEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGG  153 (292)
Q Consensus        75 ~~s~l-~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~  153 (292)
                      .+++| ++|+.+.+.+.|.+++|.                          |+.+|+++|+.|.|||+||+|+.|..+++.
T Consensus        78 ~ssdL~~~g~~~~f~L~GepIVL~--------------------------Rd~dGqv~Af~N~CPHRGapLSeG~v~~g~  131 (394)
T PLN00095         78 FAAGLRDEDALIAFDLFNVPWVLF--------------------------RDADGEAGCIKDECAHRACPLSLGKLVDGK  131 (394)
T ss_pred             EHHHCCCCCceEEEEECCEEEEEE--------------------------ECCCCCEEEEeccCCCCCCccccCcccCCE
Confidence            46677 567777777777777664                          446899999999999999999999887799


Q ss_pred             EEcCCCCcEEcCCCceecCCCCCC------CCCCceEeecCceEEEee
Q psy6642         154 YYCPCHGSHYDASGRIRKGPAPTN------MEVPPYQFGDEGILIRML  195 (292)
Q Consensus       154 ~~CPcHGs~FD~~G~v~~gPa~~~------L~~~p~~~~~d~i~V~I~  195 (292)
                      +.||||||+||.+|+|+..|....      +..||+++.+|.|+|...
T Consensus       132 L~CPYHGW~FD~~G~C~~iP~~~~~~~~~~v~tYPV~e~dGlVwVw~G  179 (394)
T PLN00095        132 AQCPYHGWEYETGGECAKMPSCKKFLKGVFADAAPVIERDGFIFLWAG  179 (394)
T ss_pred             EEecCCCcEECCCCCEeeCCCccccccccccceEEEEEECCEEEEEeC
Confidence            999999999999999999886432      468999999998877654

>cd03535 Rieske_RO_Alpha_NDO Rieske non-heme iron oxygenase (RO) family, Nathphalene 1,2-dioxygenase (NDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth

Probab=99.62  E-value=2.7e-15  Score=123.49  Aligned_cols=75  Identities=23%  Similarity=0.352  Sum_probs=61.1

Q ss_pred             ecCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCC-C
Q psy6642          75 DLNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDW-G  152 (292)
Q Consensus        75 ~~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~-~  152 (292)
                      .+++|++ |..+.+.+.+.+++|.+                          ..+|+++|+.|+|||+|++|..+..+. +
T Consensus         8 ~~~el~~~g~~~~~~~~~~~iiv~r--------------------------~~~g~~~A~~n~CpHrg~~L~~g~~~~~~   61 (123)
T cd03535           8 HESEIPNAGDYVVRYIGDDSFIVCR--------------------------DEDGEIRAMFNSCRHRGMQVCRAEMGNTS   61 (123)
T ss_pred             EHHHCCCCCCEEEEEECCeEEEEEE--------------------------CCCCCEEEEcccCccCCCEeeccccCCCC
Confidence            5678887 55555667777877653                          357999999999999999999876543 5


Q ss_pred             eEEcCCCCcEEcCCCceecCCCC
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAP  175 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~  175 (292)
                      .+.||||||+||.+|+++..|+.
T Consensus        62 ~i~Cp~Hgw~Fd~tG~~~~~p~~   84 (123)
T cd03535          62 HFRCPYHGWTYRNTGRLVGVPAQ   84 (123)
T ss_pred             EEECCcCCCEECCCcCEeeCCCc
Confidence            89999999999999999998863

The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. NDO is a three-component RO system consisting of a reductase, a ferredoxin, and a hetero-hexameric alpha-beta subunit oxygenase component. NDO catalyzes the oxidation of naphthalene to cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene (naphthalene cis-dihydrodiol) with the consumption of O2 and NAD(P)H. NDO has a relaxed substrate specificity and can oxidize almost 1

>cd03541 Rieske_RO_Alpha_CMO Rieske non-heme iron oxygenase (RO) family, Choline monooxygenase (CMO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth

Probab=99.62  E-value=2e-15  Score=123.66  Aligned_cols=78  Identities=19%  Similarity=0.343  Sum_probs=64.8

Q ss_pred             cCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          76 LNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        76 ~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .++|++ |..+++.+.|.++++.+                          ..+|+++|+.|+|||+|++|..+.++.+.|
T Consensus         8 ~~el~~~g~~~~~~~~g~~i~v~r--------------------------~~dg~v~A~~n~C~Hrg~~L~~g~~~~~~i   61 (118)
T cd03541           8 SDQVKEKNQYFTGRLGNVEYVVCR--------------------------DGNGKLHAFHNVCTHRASILACGSGKKSCF   61 (118)
T ss_pred             HHHCCCCCCeEEEEECCeEEEEEE--------------------------CCCCCEEEEeCCCCCCcCCccCCccccCEE
Confidence            466775 44568888888887753                          357899999999999999999888777899


Q ss_pred             EcCCCCcEEcCCCceecCCCCCCCC
Q psy6642         155 YCPCHGSHYDASGRIRKGPAPTNME  179 (292)
Q Consensus       155 ~CPcHGs~FD~~G~v~~gPa~~~L~  179 (292)
                      .||||||+||.+|+++..|....++
T Consensus        62 ~CP~Hgw~f~l~G~l~~~P~~~~~~   86 (118)
T cd03541          62 VCPYHGWVYGLDGSLTKATQATGIQ   86 (118)
T ss_pred             EeCCCCCEEcCCCeEEeCCCccccc
Confidence            9999999999999999988765443

The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. CMO is a novel RO found in certain plants which catalyzes the first step in betaine synthesis. CMO is not found in animals or bacteria. In these organisms, the first step in betaine synthesis is catalyzed by either the membrane-bound choline dehydrogenase (CDH) or the soluble choline oxidase (COX).

>cd03538 Rieske_RO_Alpha_AntDO Rieske non-heme iron oxygenase (RO) family, Anthranilate 1,2-dioxygenase (AntDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth

Probab=99.60  E-value=6.6e-15  Score=124.77  Aligned_cols=76  Identities=21%  Similarity=0.409  Sum_probs=63.6

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CC-C
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GD-W  151 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~-~  151 (292)
                      .+++|+ +|..+++++.|.+++|.+                          ..+|+++|+.|+|||+|++|..+. +. +
T Consensus        28 ~~~elp~~G~~~~~~i~g~~i~v~r--------------------------~~~g~v~A~~n~CpHrg~~L~~~~~g~~~   81 (146)
T cd03538          28 HESQVPNPGDYITTRIGDQPVVMVR--------------------------HTDGSVHVLYNRCPHKGTKIVSDGCGNTG   81 (146)
T ss_pred             EHHHCCCCCCEEEEEECCeeEEEEE--------------------------CCCCCEEEEeccCcCCCCEeecccccccC
Confidence            568888 688999999999987754                          357999999999999999997543 32 3


Q ss_pred             CeEEcCCCCcEEcCCCceecCCCCC
Q psy6642         152 GGYYCPCHGSHYDASGRIRKGPAPT  176 (292)
Q Consensus       152 ~~~~CPcHGs~FD~~G~v~~gPa~~  176 (292)
                      +.+.||+|||+||.+|++++.|+.+
T Consensus        82 ~~i~CP~Hgw~Fd~~G~~~~~p~~~  106 (146)
T cd03538          82 KFFRCPYHAWSFKTDGSLLAIPLKK  106 (146)
T ss_pred             CEEECCCCCCEECCCCCEEECCchh
Confidence            5799999999999999999988643

The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. AntDO converts anthranilate to catechol, a naturally occurring compound formed through tryptophan degradation and an important intermediate in the metabolism of many N-heterocyclic compounds such as indole, o-nitrobenzoate, carbazole, and quinaldine.

>cd03542 Rieske_RO_Alpha_HBDO Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth

Probab=99.60  E-value=1.8e-15  Score=124.71  Aligned_cols=86  Identities=24%  Similarity=0.410  Sum_probs=66.8

Q ss_pred             ecCCCCCC-CeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CCCC
Q psy6642          75 DLNLIPEG-QSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GDWG  152 (292)
Q Consensus        75 ~~s~l~~g-~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~~~  152 (292)
                      .+++|+++ ..+.++..+.++++.+                          ..+|+++|+.|+|||+|++|..+. ++.+
T Consensus         6 ~~~elp~~g~~~~~~~~~~~i~l~r--------------------------~~~g~v~A~~n~C~Hrg~~L~~g~~~~~~   59 (123)
T cd03542           6 HESQIPNNNDYFTTTIGRQPVVITR--------------------------DKDGELNAFINACSHRGAMLCRRKQGNKG   59 (123)
T ss_pred             EHHHCCCCCCEEEEEECCcEEEEEE--------------------------CCCCCEEEEcccCcCCCCccccccccCCC
Confidence            46788874 5677788888887654                          358999999999999999998764 3446


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCCCCCCCceEeec
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGD  187 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~  187 (292)
                      .|.||||||+||.+|+++..| ..++..|+..++.
T Consensus        60 ~i~CP~Hg~~Fd~~G~~~~~p-~~~~~~y~~~~~~   93 (123)
T cd03542          60 TFTCPFHGWTFSNTGKLLKVK-DPKTAGYPEGFNC   93 (123)
T ss_pred             EEECcCCCCEecCCccEEECC-cccccCcCcccCh
Confidence            899999999999999999655 3456666655543

The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. HBDO catalyzes the double hydroxylation of 2-halobenzoates with concomitant release of halogenide and carbon dioxide, yielding catechol.

>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit

Probab=99.53  E-value=7.9e-15  Score=127.79  Aligned_cols=68  Identities=46%  Similarity=0.750  Sum_probs=61.5

Q ss_pred             ccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhhhc-cceEEecCCCCCCceEEEEECCeeeEEEcC
Q psy6642         222 QRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAM-ATIEVDLNLIPEGQSVTFKWRGKPLFIRHR  292 (292)
Q Consensus       222 ~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~a~-~~~evdls~i~~G~~~~~~WrgkPvfv~~R  292 (292)
                      +||+||++++++++++++   +++++||+++|+|+++++|. +++||++++|+||+.++|+|+||||||+||
T Consensus         1 ~RR~fl~~~~~~~~~~~~---~~~~~p~v~~~~P~~~~~a~~~~~~v~l~eL~pG~~~~v~~~GkpI~I~~~   69 (174)
T TIGR01416         1 TRRDFLYAATGAVGAVGA---AAAAVPFIDSMNPSASVKAAGAPTEVDVSKIQPGQQLTVEWRGKPVFIRRR   69 (174)
T ss_pred             ChHHHHHHHHHHHHHHHH---HHHHHHHHheeCcchhccccCCcEEEEHHHCCCCCeEEEEECCeEEEEEeC
Confidence            499999888877666665   46789999999999999998 899999999999999999999999999986

Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.

>PLN02518 pheophorbide a oxygenase

Probab=99.52  E-value=3.3e-14  Score=142.74  Aligned_cols=76  Identities=16%  Similarity=0.169  Sum_probs=63.1

Q ss_pred             cccccc-cCCCeEEEEecccCCCcccCCcCCC-CCeEEcCCCCcEEcCCCceecCCCC--------------CCCCCCce
Q psy6642         120 ADSDRV-KDPSWLVIIGICTHLGCVPIANAGD-WGGYYCPCHGSHYDASGRIRKGPAP--------------TNMEVPPY  183 (292)
Q Consensus       120 ~~~~R~-~~g~~~a~~~~CtHlGc~l~~~~~~-~~~~~CPcHGs~FD~~G~v~~gPa~--------------~~L~~~p~  183 (292)
                      ..++|+ .+|+++|+.|.|||+|++|+.|..+ ++.+.||||||+||.+|+|+..|..              ..+..||+
T Consensus       115 lVl~Rd~~~G~~~A~~d~CPHRgapLS~G~v~~~g~L~CpYHGW~Fd~~G~c~~IP~~~~~~~~~~~~~~~~a~v~sypv  194 (539)
T PLN02518        115 LVLWKDPNQGEWVAFDDKCPHRLAPLSEGRIDENGHLQCSYHGWSFDGCGSCTRIPQAAPEGPEARAVKSPRACAIKFPT  194 (539)
T ss_pred             EEEEEECCCCeEEEEcccCcCcCCCcccceecCCCEEEcCCCCCEEcCCCCeeecccccccccccccccCcccccceEeE
Confidence            445676 7899999999999999999998764 5799999999999999999876531              24778999


Q ss_pred             EeecCceEEEee
Q psy6642         184 QFGDEGILIRML  195 (292)
Q Consensus       184 ~~~~d~i~V~I~  195 (292)
                      ++.+|-|+|.+.
T Consensus       195 ~e~~GlIwV~~~  206 (539)
T PLN02518        195 MVSQGLLFVWPD  206 (539)
T ss_pred             EEECCEEEEEeC
Confidence            999987777654

>PF02921 UCR_TM: Ubiquinol cytochrome reductase transmembrane region; InterPro: IPR004192 The ubiquinol cytochrome c reductase (cytochrome bc1) complex is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis

Probab=99.45  E-value=2.1e-14  Score=105.36  Aligned_cols=63  Identities=49%  Similarity=0.831  Sum_probs=51.6

Q ss_pred             cccCCCCCCccccccCC-CCCCCccccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHH
Q psy6642         196 AHSDIRTPDFSKYRRDR-NPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASAD  258 (292)
Q Consensus       196 ahtD~~~P~F~~yr~~~-~~~~~~~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~  258 (292)
                      +|||+++|||++||+++ .+...+++.+||.|.|+++|+++++++++|+.+|..||.+|+||+|
T Consensus         1 Ahtdi~~PdF~~Yr~~~~~~~~~~~~~~rr~fsY~~~g~~~~~~a~~AK~~V~~fv~~mSaSAD   64 (64)
T PF02921_consen    1 AHTDIKVPDFSDYRRKSPSKRSRESDDSRRAFSYFMVGGGGVASAYAAKSTVQDFVSSMSASAD   64 (64)
T ss_dssp             -GGGTS----TTTBSGGTTS-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSHH
T ss_pred             CCCCCCCCCchhhcccccccccCCCCcccceeeehhhhhHHHHHHHHHHHHHHHHHHhcCccCC
Confidence            69999999999999997 2222356678999999999999999999999999999999999997

The bc1 complex contains 11 subunits, 3 respiratory subunits (cytochrome B, cytochrome C1, Rieske protein), 2 core proteins and 6 low-molecular weight proteins. Each subunit of the cytochrome bc1 complex provides a single helix (this domain) to make up the transmembrane region of the complex.; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1NU1_E 1L0L_E 1BCC_E 1SQB_E 1SQQ_E 1SQP_E 1PPJ_E 2A06_R 1BE3_E 1BGY_E ....

>TIGR03228 anthran_1_2_A anthranilate 1,2-dioxygenase, large subunit

Probab=99.42  E-value=4.6e-13  Score=131.68  Aligned_cols=106  Identities=20%  Similarity=0.368  Sum_probs=77.4

Q ss_pred             cCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCC-cCCCCCe
Q psy6642          76 LNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIA-NAGDWGG  153 (292)
Q Consensus        76 ~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~-~~~~~~~  153 (292)
                      .++|++ |.-+++.+.++||+|.                          |+.+|+++|+.|.|+|+|+.|+. +.++.+.
T Consensus        45 ~selp~~GDy~t~~ig~~pviv~--------------------------R~~dG~i~a~~N~C~HRGa~L~~~~~Gn~~~   98 (438)
T TIGR03228        45 ESELPNNHDFVTVRAGRQPMIVT--------------------------RDGKGELHALVNACQHRGATLTRVGKGNQST   98 (438)
T ss_pred             HHHCCCCCCeEEEEECCeEEEEE--------------------------ECCCCCEEEEcccCCCCCCccccCCccccCE
Confidence            467774 7778888888888764                          44689999999999999999986 5666678


Q ss_pred             EEcCCCCcEEcCCCceecCCCC-----------CCCCCCceEeecCceEEEeecccCCC-CCCccccccC
Q psy6642         154 YYCPCHGSHYDASGRIRKGPAP-----------TNMEVPPYQFGDEGILIRMLAHSDIR-TPDFSKYRRD  211 (292)
Q Consensus       154 ~~CPcHGs~FD~~G~v~~gPa~-----------~~L~~~p~~~~~d~i~V~I~ahtD~~-~P~F~~yr~~  211 (292)
                      |.||||||+||.+|+++..|.+           ..|...+++.-.+-|++.    .|.. .|++.+|..+
T Consensus        99 ~~CPYHgW~y~~dG~L~~vp~~~~y~~~fd~~~~~L~~~rv~~y~GfIFv~----l~~~a~~~l~e~lg~  164 (438)
T TIGR03228        99 FTCPFHAWCYKSDGRLVKVKAPGEYCEGFDKATRGLKKARIASYRGFVFVS----LDVAATDSLEDFLGD  164 (438)
T ss_pred             EEcCCCCCcccCCCceeecCcccccCCCCChhhCCCcceeEEEECCEEEEE----eCCCCCCCHHHHhhh
Confidence            9999999999999999987643           224444455555544433    2333 2567777643

Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation. Members of this family are the large subunit of anthranilate 1,2-dioxygenase, which acts in Trp degradation by converting anthranilate to catechol. Closely related paralogs typically are the benzoate 1,2-dioxygenase large subunit, among the larger set of ring-hydroxylating dioxygenases.

>TIGR03229 benzo_1_2_benA benzoate 1,2-dioxygenase, large subunit

Probab=99.41  E-value=4.8e-13  Score=131.51  Aligned_cols=107  Identities=21%  Similarity=0.370  Sum_probs=77.6

Q ss_pred             ecCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CCCC
Q psy6642          75 DLNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GDWG  152 (292)
Q Consensus        75 ~~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~~~  152 (292)
                      ..++|++ |.-+++.+.++||+|.+                          +.+|+++|+.|+|+|.|+.|+.+. ++.+
T Consensus        44 ~~selp~~gd~~t~~~~~~~vvv~R--------------------------~~dG~i~af~N~C~HRga~L~~~~~g~~~   97 (433)
T TIGR03229        44 HESQIPNNNDYYTTYMGRQPIFIAR--------------------------NKDGELNAFINACSHRGAMLCRHKRGNKT   97 (433)
T ss_pred             EHHHCCCCCCeEEEEECCeEEEEEE--------------------------CCCCcEEEEeCcCCCCCCCcccccccCCC
Confidence            5678885 45567888888887753                          468999999999999999998764 4557


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCC------------CCCCCce-Eee--cCceEEEeecccCCCCCCccccccC
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPT------------NMEVPPY-QFG--DEGILIRMLAHSDIRTPDFSKYRRD  211 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~------------~L~~~p~-~~~--~d~i~V~I~ahtD~~~P~F~~yr~~  211 (292)
                      .|.||||||+||.+|+++..|.+.            .+...++ +++  .+-|    |...|...|++++|..+
T Consensus        98 ~~~CPyHgW~f~~~G~l~~vP~~~~~~~~~~fd~~~~~~L~~v~rve~y~GfI----Fv~l~~~~~~l~e~Lg~  167 (433)
T TIGR03229        98 TYTCPFHGWTFNNSGKLLKVKDPEDAGYPECFNKDGSHDLKKVARFESYRGFL----FGSLNPDVLPLEEHLGE  167 (433)
T ss_pred             EEEcCCCCCEecCCcceEeCCCcccccCccccCcHhhcCCccceEEEEECCEE----EEEcCCCCCCHHHHhhh
Confidence            899999999999999999887631            1223344 233  3433    34455566778888654

Benzoate 1,2-dioxygenase (EC 1.14.12.10) belongs to the larger family of aromatic ring-hydroxylating dioxygenases. Members of this family all act on benzoate, but may have additional activities on various benozate analogs. This model describes the large subunit. Between the trusted and noise cutoffs are similar enzymes, likely to act on benzoate but perhaps best identified according to some other activity, such as 2-chlorobenzoate 1,2-dioxygenase (1.14.12.13).

>COG4638 HcaE Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]

Probab=99.34  E-value=2.8e-12  Score=122.96  Aligned_cols=93  Identities=28%  Similarity=0.428  Sum_probs=75.2

Q ss_pred             cCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCC-CeE
Q psy6642          76 LNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDW-GGY  154 (292)
Q Consensus        76 ~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~-~~~  154 (292)
                      .++|+.+..+++...|+++.|.                          |+.+|+++|+.|.|+|.|..|+.+...+ +.|
T Consensus        34 ~~el~~~~~~~~~i~g~~lvi~--------------------------R~~dg~~~al~d~C~HRga~Ls~g~~~~~~~l   87 (367)
T COG4638          34 SSELPKPDPLTVRIGGEPLVVV--------------------------RDKDGQVHALADVCPHRGARLSEGRVGGKGRL   87 (367)
T ss_pred             HHHCCCCCceeEEEcCeEEEEE--------------------------ECCCCCEEEEeccCCCCCchhccccCCCCceE
Confidence            5677777778888888887663                          5679999999999999999999998776 799


Q ss_pred             EcCCCCcEEcCCCceecCCC-----C-----CCCCCCceEeecCceEEEe
Q psy6642         155 YCPCHGSHYDASGRIRKGPA-----P-----TNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       155 ~CPcHGs~FD~~G~v~~gPa-----~-----~~L~~~p~~~~~d~i~V~I  194 (292)
                      .||+|||+||.+|+|+.-|.     .     ..|..+|++...|-|+|..
T Consensus        88 ~CpyHgW~y~~~G~~~~ip~~~~~~~~~~~~~~l~~~~~~~~~G~Iwi~~  137 (367)
T COG4638          88 TCPYHGWTYDLDGRLRGVPARGYPLDFDKSEHGLKRYPVEERYGFIWIWL  137 (367)
T ss_pred             ecCCCceEECCCCcEecCCccccCCCCCHhhCCccccceEEEccEEEEec
Confidence            99999999999999998772     1     2466777777777555543

>PF02921 UCR_TM: Ubiquinol cytochrome reductase transmembrane region; InterPro: IPR004192 The ubiquinol cytochrome c reductase (cytochrome bc1) complex is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis

Probab=99.31  E-value=1.1e-12  Score=96.30  Aligned_cols=62  Identities=53%  Similarity=0.897  Sum_probs=50.6

Q ss_pred             CCCCCCCCCccccccCCCCCCCCC--CcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchh
Q psy6642           3 AHSDIRTPDFSKYRRDRNPDKGQE--ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASAD   65 (292)
Q Consensus         3 ~~~~~~~pd~~~yr~~~~~~~~~~--~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~   65 (292)
                      |||||.+|||++||+++ ..++++  +.+||.|.|+++|.++++++.+|+.++..|+..|.+++|
T Consensus         1 Ahtdi~~PdF~~Yr~~~-~~~~~~~~~~~rr~fsY~~~g~~~~~~a~~AK~~V~~fv~~mSaSAD   64 (64)
T PF02921_consen    1 AHTDIKVPDFSDYRRKS-PSKRSRESDDSRRAFSYFMVGGGGVASAYAAKSTVQDFVSSMSASAD   64 (64)
T ss_dssp             -GGGTS----TTTBSGG-TTS-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSHH
T ss_pred             CCCCCCCCCchhhcccc-cccccCCCCcccceeeehhhhhHHHHHHHHHHHHHHHHHHhcCccCC
Confidence            79999999999999998 444443  779999999999999999999999999999999998875

The bc1 complex contains 11 subunits, 3 respiratory subunits (cytochrome B, cytochrome C1, Rieske protein), 2 core proteins and 6 low-molecular weight proteins. Each subunit of the cytochrome bc1 complex provides a single helix (this domain) to make up the transmembrane region of the complex.; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1NU1_E 1L0L_E 1BCC_E 1SQB_E 1SQQ_E 1SQP_E 1PPJ_E 2A06_R 1BE3_E 1BGY_E ....

>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex)

Probab=98.93  E-value=2.9e-10  Score=76.13  Aligned_cols=36  Identities=25%  Similarity=0.398  Sum_probs=26.7

Q ss_pred             ccccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCC
Q psy6642         218 QEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSAS  256 (292)
Q Consensus       218 ~~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~  256 (292)
                      ..+.+||+||++++++++++|+   ++++||||+||+||
T Consensus         6 ~~~~~RRdFL~~at~~~gavG~---~~~a~Pfv~s~~Ps   41 (41)
T PF10399_consen    6 PVDPTRRDFLTIATSAVGAVGA---AAAAWPFVSSMNPS   41 (41)
T ss_dssp             ----HHHHHHHHHHHHHHHHHH---HHHHHHHHHTTSS-
T ss_pred             CCCchHHHHHHHHHHHHHHHHH---HHHHHHHHhccCCC
Confidence            3456799999888777776665   58899999999997

This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.

>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]

Probab=98.59  E-value=1.4e-08  Score=88.55  Aligned_cols=71  Identities=35%  Similarity=0.526  Sum_probs=61.2

Q ss_pred             cccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHh-hhccceEEecCCCCCCceEEEEECCeeeEEEcC
Q psy6642         219 EETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADV-LAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR  292 (292)
Q Consensus       219 ~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~-~a~~~~evdls~i~~G~~~~~~WrgkPvfv~~R  292 (292)
                      ....||+|+.++++..+++++   ..+++|++.+++|+++. .+.+++|+|++.+.+++..+++|||+|+|+++|
T Consensus         7 ~~~~~~~~l~~~~~~~~~~~~---~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~   78 (177)
T COG0723           7 TGLSRRDFLVLLTTGVGAVGA---GAALYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVPWRGKPVFLLRR   78 (177)
T ss_pred             ccccHHHhhhhhhccccccce---eeeeeehhhcccCcccccccCCceeeeccCCccceEEEEecCCCCeeeEee
Confidence            345699999877777666654   47889999999999988 566999999999999999999999999999865

>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex)

Probab=98.11  E-value=2.5e-06  Score=57.13  Aligned_cols=35  Identities=26%  Similarity=0.416  Sum_probs=26.7

Q ss_pred             CCcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcc
Q psy6642          26 EETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSAS   63 (292)
Q Consensus        26 ~~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~   63 (292)
                      .+.+||+||+++|++.+.+|++   .+++||+.+++|+
T Consensus         7 ~~~~RRdFL~~at~~~gavG~~---~~a~Pfv~s~~Ps   41 (41)
T PF10399_consen    7 VDPTRRDFLTIATSAVGAVGAA---AAAWPFVSSMNPS   41 (41)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHH---HHHHHHHHTTSS-
T ss_pred             CCchHHHHHHHHHHHHHHHHHH---HHHHHHHhccCCC
Confidence            4789999999999987766654   5789999999985

This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.

>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional

Probab=98.00  E-value=1.1e-05  Score=70.75  Aligned_cols=67  Identities=15%  Similarity=0.239  Sum_probs=49.3

Q ss_pred             cccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhhhcc-ce-------EEecCCC----CCCceEEEE-ECCee-
Q psy6642         221 TQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMA-TI-------EVDLNLI----PEGQSVTFK-WRGKP-  286 (292)
Q Consensus       221 ~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~a~~-~~-------evdls~i----~~G~~~~~~-WrgkP-  286 (292)
                      .+||.||..+++++++++   ++++++|||++|.|+++..+.. ++       +|.++++    ++|+...+. -.|++ 
T Consensus        12 ~~RR~FL~~~~~~~gg~~---a~~~~~P~v~~~~Pp~~~~~~g~~~a~d~~G~~I~~s~~~~~~~~g~~~~v~~~~g~~~   88 (178)
T PRK13474         12 MGRRQFMNLLTFGTVTGV---ALGALYPVVKYFIPPSAGGAGGGTTAKDELGNDIPASQFLATHPAGDRSLVQGLKGDPT   88 (178)
T ss_pred             ccHHHHHHHHHHHHHHHH---HHHHHHHhhheeCChhHccCCCcceeecccCCeeehhhccccCCCCCcEEEEEcCCCeE
Confidence            479999977665554444   4578899999999999887652 21       4577788    899888877 57888 


Q ss_pred             eEEE
Q psy6642         287 LFIR  290 (292)
Q Consensus       287 vfv~  290 (292)
                      ++|+
T Consensus        89 ~lv~   92 (178)
T PRK13474         89 YLVV   92 (178)
T ss_pred             EEEE
Confidence            4444

>TIGR03171 soxL2 Rieske iron-sulfur protein SoxL2

Probab=95.62  E-value=0.0062  Score=57.74  Aligned_cols=57  Identities=12%  Similarity=0.111  Sum_probs=39.9

Q ss_pred             cccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhhhc-c--c-e------EEecCCCCCCceEE
Q psy6642         219 EETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAM-A--T-I------EVDLNLIPEGQSVT  279 (292)
Q Consensus       219 ~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~a~-~--~-~------evdls~i~~G~~~~  279 (292)
                      -+..||.||..++++++++    +.+.++||+++|.|++++++. +  . +      .|..|+|++|+...
T Consensus        59 vD~~RR~fL~~al~gAga~----a~~~avPlv~~l~PP~~a~atG~pk~La~D~~GnPIKASdL~vnSp~~  125 (321)
T TIGR03171        59 VDEGRRKFLKGLIFGIAAA----AVVGIIPGLRVLVPPTVAAASGFPKSLLVDSSGNPIKASSIPVNSPII  125 (321)
T ss_pred             CCccHHHHHHHHHHHHHHH----HhhhhhhheecccCchhhhccCCCceEEecCCCCeeeHHHccCCCccc
Confidence            3557999998766665552    234478999999999888755 2  1 2      26678888887664

This iron-sulfur protein is found in a contiguous genomic region with subunits of cytochrome b558/566 in several archaeal species, and appears to be part of a cytochrome bc1-analogous system.

>KOG1336|consensus

Probab=95.40  E-value=0.013  Score=58.35  Aligned_cols=47  Identities=21%  Similarity=0.415  Sum_probs=38.6

Q ss_pred             CCCcccCCcCCCCCeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeec
Q psy6642         139 HLGCVPIANAGDWGGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGD  187 (292)
Q Consensus       139 HlGc~l~~~~~~~~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~  187 (292)
                      |.|.+|..+....+.+.|||||..|+. +|.+..-|+...|  ..+..++
T Consensus         1 hygapl~~g~~s~g~v~cpwhgacfn~~~gdiedfP~~~sl--~~v~~~~   48 (478)
T KOG1336|consen    1 HYGAPLAKGVLSRGRVRCPWHGACFNLSTGDIEDFPGLDSL--SRVVVDN   48 (478)
T ss_pred             CCCcchhhccccCCcccccccceeecCCcCchhhCcCccce--eeEEecC
Confidence            889999888655589999999999999 9999999998888  3444433

>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions

Probab=91.15  E-value=0.07  Score=35.35  Aligned_cols=34  Identities=12%  Similarity=0.357  Sum_probs=24.8

Q ss_pred             ccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCC
Q psy6642         220 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSAS  256 (292)
Q Consensus       220 ~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~  256 (292)
                      +.+||.|+.+++++++++-+   ...++|+++.+-|.
T Consensus         5 dm~RR~lmN~ll~Gava~~a---~~~lyP~~~ffvPP   38 (39)
T PF08802_consen    5 DMSRRQLMNLLLGGAVAVPA---GGMLYPYVKFFVPP   38 (39)
T ss_dssp             -HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHS--
T ss_pred             ChhHHHHHHHHHHhhHHHHH---HHHhhhheeEecCC
Confidence            35799999998887766654   46789999988775

The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.

>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions

Probab=89.50  E-value=0.48  Score=31.38  Aligned_cols=20  Identities=20%  Similarity=0.474  Sum_probs=15.2

Q ss_pred             CcCchhhHHHHHHhHHHHHH
Q psy6642          27 ETQRKAFTYMIAGGSSVVGM   46 (292)
Q Consensus        27 ~~~RR~fl~~atG~~~~~g~   46 (292)
                      +++||+|+...+++++.+.+
T Consensus         5 dm~RR~lmN~ll~Gava~~a   24 (39)
T PF08802_consen    5 DMSRRQLMNLLLGGAVAVPA   24 (39)
T ss_dssp             -HHHHHHHHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHhhHHHHH
Confidence            67899999999987765543

The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.

>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []

Probab=85.41  E-value=0.76  Score=27.61  Aligned_cols=16  Identities=19%  Similarity=0.156  Sum_probs=11.8

Q ss_pred             cCchhhHHHHHHhHHH
Q psy6642          28 TQRKAFTYMIAGGSSV   43 (292)
Q Consensus        28 ~~RR~fl~~atG~~~~   43 (292)
                      .+||+||+...+.++.
T Consensus         2 ~sRR~fLk~~~a~~a~   17 (26)
T PF10518_consen    2 LSRRQFLKGGAAAAAA   17 (26)
T ss_pred             CcHHHHHHHHHHHHHH
Confidence            6899999877665543

Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].

>TIGR02811 formate_TAT formate dehydrogenase region TAT target

Probab=85.36  E-value=1.1  Score=33.12  Aligned_cols=15  Identities=13%  Similarity=0.288  Sum_probs=11.2

Q ss_pred             CcCchhhHHHHHHhH
Q psy6642          27 ETQRKAFTYMIAGGS   41 (292)
Q Consensus        27 ~~~RR~fl~~atG~~   41 (292)
                      +.+||+||..+.+++
T Consensus         8 ~~sRR~Flk~lg~~a   22 (66)
T TIGR02811         8 DPSRRDLLKGLGVGA   22 (66)
T ss_pred             CccHHHHHHHHHHHH
Confidence            679999998655433

Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	292
1qcr_E	196	Crystal Structure Of Bovine Mitochondrial Cytochrom		2e-71
1qcr_E	196	Crystal Structure Of Bovine Mitochondrial Cytochrom		7e-25
3cwb_E	196	Chicken Cytochrome Bc1 Complex Inhibited By An Iodi		1e-70
3cwb_E	196	Chicken Cytochrome Bc1 Complex Inhibited By An Iodi		1e-24
1bcc_E	196	Cytochrome Bc1 Complex From Chicken Length = 196		1e-70
1bcc_E	196	Cytochrome Bc1 Complex From Chicken Length = 196		4e-24
1ezv_E	185	Structure Of The Yeast Cytochrome Bc1 Complex Co- C		5e-60
1ezv_E	185	Structure Of The Yeast Cytochrome Bc1 Complex Co- C		8e-18
1rie_A	129	Structure Of A Water Soluble Fragment Of The Rieske		2e-54
1rie_A	129	Structure Of A Water Soluble Fragment Of The Rieske		2e-08
1zrt_E	191	Rhodobacter Capsulatus Cytochrome Bc1 Complex With		4e-39
1zrt_E	191	Rhodobacter Capsulatus Cytochrome Bc1 Complex With		2e-09
2yiu_C	190	X-Ray Structure Of The Dimeric Cytochrome Bc1 Compl		6e-38
2yiu_C	190	X-Ray Structure Of The Dimeric Cytochrome Bc1 Compl		2e-06
2qjp_C	179	Crystal Structure Of Wild Type Rhodobacter Sphaeroi		3e-34
2qjp_C	179	Crystal Structure Of Wild Type Rhodobacter Sphaeroi		1e-04
2fyn_C	187	Crystal Structure Analysis Of The Double Mutant Rho		1e-33
2fyn_C	187	Crystal Structure Analysis Of The Double Mutant Rho		1e-04
2qjk_C	179	Crystal Structure Analysis Of Mutant Rhodobacter Sp		1e-33
2qjk_C	179	Crystal Structure Analysis Of Mutant Rhodobacter Sp		1e-04
2nuk_A	141	Soluble Domain Of The Rieske Iron-Sulfur Protein Fr		7e-31
2nvg_A	141	Soluble Domain Of Rieske Iron Sulfur Protein Length		1e-30
2nve_A	141	Soluble Domain Of Rieske Iron Sulfur Protein Length		1e-30
2num_A	141	Soluble Domain Of Rieske Iron-Sulfur Protein Length		2e-30
2nvf_A	141	Soluble Domain Of Rieske Iron-Sulfur Protein Length		2e-30
2nwf_A	141	Soluble Domain Of Rieske Iron Sulfur Protein Length		3e-30
1vf5_D	179	Crystal Structure Of Cytochrome B6f Complex From M.		1e-11
2e74_D	179	Crystal Structure Of The Cytochrome B6f Complex Fro		3e-11
2zt9_D	179	Crystal Structure Of The Cytochrome B6f Complex Fro		6e-11
1rfs_A	139	Rieske Soluble Fragment From Spinach Length = 139		3e-09
1q90_C	127	Structure Of The Cytochrome B6f (Plastohydroquinone		2e-08
3azc_A	133	Crystal Structure Of The Soluble Part Of Cytochrome		6e-08

>pdb|1QCR|E Chain E, Crystal Structure Of Bovine Mitochondrial Cytochrome Bc1 Complex, Alpha Carbon Atoms Only Length = 196

Iteration: 1
 Score =  265 bits (678), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 119/194 (61%), Positives = 151/194 (77%), Gaps = 4/194 (2%)
Query: 3   AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+DI+ PDFS YRR    D      +    RK F+Y++   ++V     AK+VV+QF+S
Sbjct: 1   SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 60
Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDP
Sbjct: 61  SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP 120
Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D +RVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 121 QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 180
Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 181 EVPSYEFTSDDMVI 194

>pdb|1QCR|E Chain E, Crystal Structure Of Bovine Mitochondrial Cytochrome Bc1 Complex, Alpha Carbon Atoms Only Length = 196

Iteration: 1
 Score =  110 bits (276), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 53/101 (52%), Positives = 72/101 (71%), Gaps = 4/101 (3%)
Query: 196 AHSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 251
           +H+DI+ PDFS YRR    D      +    RK F+Y++   ++V     AK+VV+QF+S
Sbjct: 1   SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 60
Query: 252 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHR
Sbjct: 61  SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHR 101

>pdb|3CWB|E Chain E, Chicken Cytochrome Bc1 Complex Inhibited By An Iodinated Analogue Of The Polyketide Crocacin-d Length = 196

Iteration: 1
 Score =  263 bits (671), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 117/194 (60%), Positives = 148/194 (76%), Gaps = 5/194 (2%)
Query: 4   HSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISS 59
           H+D+  PDFS YRR    D           RK F+Y++   + V     AK+VV QFISS
Sbjct: 2   HNDVTVPDFSAYRREDVMDATTSSQTSSEDRKGFSYLVTATACVATAYAAKNVVTQFISS 61
Query: 60  MSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQ 119
           +SASADVLA++ IE+ L+ IPEG++V FKWRGKPLF+RHRTQ EI+ E   ++S+LRDPQ
Sbjct: 62  LSASADVLALSKIEIKLSDIPEGKNVAFKWRGKPLFVRHRTQAEINQEAEVDVSKLRDPQ 121
Query: 120 ADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNME 179
            D DRVK P W++++G+CTHLGCVPIAN+GD+GGYYCPCHGSHYDASGRIRKGPAP N+E
Sbjct: 122 HDLDRVKKPEWVILVGVCTHLGCVPIANSGDFGGYYCPCHGSHYDASGRIRKGPAPYNLE 181
Query: 180 VPPYQF-GDEGILI 192
           VP YQF GD+ +++
Sbjct: 182 VPTYQFVGDDLVVV 195

>pdb|3CWB|E Chain E, Chicken Cytochrome Bc1 Complex Inhibited By An Iodinated Analogue Of The Polyketide Crocacin-d Length = 196

Iteration: 1
 Score =  109 bits (273), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 52/100 (52%), Positives = 67/100 (67%), Gaps = 4/100 (4%)
Query: 197 HSDIRTPDFSKYRR----DRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISS 252
           H+D+  PDFS YRR    D           RK F+Y++   + V     AK+VV QFISS
Sbjct: 2   HNDVTVPDFSAYRREDVMDATTSSQTSSEDRKGFSYLVTATACVATAYAAKNVVTQFISS 61
Query: 253 MSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           +SASADVLA++ IE+ L+ IPEG++V FKWRGKPLF+RHR
Sbjct: 62  LSASADVLALSKIEIKLSDIPEGKNVAFKWRGKPLFVRHR 101

>pdb|1BCC|E Chain E, Cytochrome Bc1 Complex From Chicken Length = 196

Iteration: 1
 Score =  263 bits (671), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 119/194 (61%), Positives = 152/194 (78%), Gaps = 4/194 (2%)
Query: 3   AHSDIRTPDFSKYRR--DRNPDKGQEET--QRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+DI+ P+FS YRR  D    K   E+   RK F+Y++   +++     AK+VV QF+S
Sbjct: 1   SHTDIKVPNFSDYRRPPDDYSTKSSRESDPSRKGFSYLVTAVTTLGVAYAAKNVVTQFVS 60
Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDP
Sbjct: 61  SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP 120
Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D +RVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 121 QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 180
Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 181 EVPSYEFTSDDMVI 194

>pdb|1BCC|E Chain E, Cytochrome Bc1 Complex From Chicken Length = 196

Iteration: 1
 Score =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 53/101 (52%), Positives = 73/101 (72%), Gaps = 4/101 (3%)
Query: 196 AHSDIRTPDFSKYRR--DRNPDKGQEET--QRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 251
           +H+DI+ P+FS YRR  D    K   E+   RK F+Y++   +++     AK+VV QF+S
Sbjct: 1   SHTDIKVPNFSDYRRPPDDYSTKSSRESDPSRKGFSYLVTAVTTLGVAYAAKNVVTQFVS 60
Query: 252 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHR
Sbjct: 61  SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHR 101

>pdb|1EZV|E Chain E, Structure Of The Yeast Cytochrome Bc1 Complex Co- Crystallized With An Antibody Fv-Fragment Length = 185

Iteration: 1
 Score =  227 bits (579), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 102/189 (53%), Positives = 137/189 (72%), Gaps = 7/189 (3%)
Query: 5   SDIRTPDFSKYRRDRN-PDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSAS 63
           S  RTP+F    ++ N  DKG      +++ Y + G   ++    AKS V  FISSM+A+
Sbjct: 2   STYRTPNFDDVLKENNDADKG------RSYAYFMVGAMGLLSSAGAKSTVETFISSMTAT 55
Query: 64  ADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSD 123
           ADVLAMA +EV+L  IP G++V  KW+GKP+FIRHRT  EI    + ++S L+DPQ D+D
Sbjct: 56  ADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDAD 115
Query: 124 RVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPY 183
           RVKDP WL+++GICTHLGCVPI  AGD+GG++CPCHGSHYD SGRIRKGPAP N+E+P Y
Sbjct: 116 RVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAY 175
Query: 184 QFGDEGILI 192
           +F  + +++
Sbjct: 176 EFDGDKVIV 184

>pdb|1EZV|E Chain E, Structure Of The Yeast Cytochrome Bc1 Complex Co- Crystallized With An Antibody Fv-Fragment Length = 185

Iteration: 1
 Score = 87.4 bits (215), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 45/96 (46%), Positives = 62/96 (64%), Gaps = 7/96 (7%)
Query: 198 SDIRTPDFSKYRRDRN-PDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSAS 256
           S  RTP+F    ++ N  DKG      +++ Y + G   ++    AKS V  FISSM+A+
Sbjct: 2   STYRTPNFDDVLKENNDADKG------RSYAYFMVGAMGLLSSAGAKSTVETFISSMTAT 55
Query: 257 ADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           ADVLAMA +EV+L  IP G++V  KW+GKP+FIRHR
Sbjct: 56  ADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHR 91

>pdb|1RIE|A Chain A, Structure Of A Water Soluble Fragment Of The Rieske Iron- Sulfur Protein Of The Bovine Heart Mitochondrial Cytochrome Bc1-complex Length = 129

Iteration: 1
 Score =  208 bits (530), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 89/127 (70%), Positives = 109/127 (85%)
Query: 66  VLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRV 125
           VLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDPQ D +RV
Sbjct: 1   VLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERV 60
Query: 126 KDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF 185
           K P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+EVP Y+F
Sbjct: 61  KKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPSYEF 120
Query: 186 GDEGILI 192
             + ++I
Sbjct: 121 TSDDMVI 127

>pdb|1RIE|A Chain A, Structure Of A Water Soluble Fragment Of The Rieske Iron- Sulfur Protein Of The Bovine Heart Mitochondrial Cytochrome Bc1-complex Length = 129

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/34 (67%), Positives = 30/34 (88%)
Query: 259 VLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           VLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHR
Sbjct: 1   VLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHR 34

>pdb|1ZRT|E Chain E, Rhodobacter Capsulatus Cytochrome Bc1 Complex With Stigmatellin Bound Length = 191

Iteration: 1
 Score =  158 bits (399), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 77/178 (43%), Positives = 112/178 (62%), Gaps = 22/178 (12%)
Query: 30  RKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKW 89
           R+ F Y     ++  G+V   + V   I+ M+ASADV AMA+I VD++ +  G  +T KW
Sbjct: 11  RRDFLYH---ATAATGVVVTGAAVWPLINQMNASADVKAMASIFVDVSAVEVGTQLTVKW 67
Query: 90  RGKPLFIRHRTQKEIDTEQNTNISQLRDPQADS------------------DRVKDPSWL 131
           RGKP+FIR R +K+I+  ++  +  LRD  A++                  D      WL
Sbjct: 68  RGKPVFIRRRDEKDIELARSVPLGALRDTSAENANKPGAEATDENRTLPAFDGTNTGEWL 127
Query: 132 VIIGICTHLGCVPIAN-AGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDE 188
           V++G+CTHLGCVP+ + +GD+GG++CPCHGSHYD++GRIRKGPAP N+++P   F DE
Sbjct: 128 VMLGVCTHLGCVPMGDKSGDFGGWFCPCHGSHYDSAGRIRKGPAPRNLDIPVAAFVDE 185

>pdb|1ZRT|E Chain E, Rhodobacter Capsulatus Cytochrome Bc1 Complex With Stigmatellin Bound Length = 191

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 44/70 (62%), Gaps = 3/70 (4%)
Query: 223 RKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKW 282
           R+ F Y     ++  G+V   + V   I+ M+ASADV AMA+I VD++ +  G  +T KW
Sbjct: 11  RRDFLYH---ATAATGVVVTGAAVWPLINQMNASADVKAMASIFVDVSAVEVGTQLTVKW 67
Query: 283 RGKPLFIRHR 292
           RGKP+FIR R
Sbjct: 68  RGKPVFIRRR 77

>pdb|2YIU|C Chain C, X-Ray Structure Of The Dimeric Cytochrome Bc1 Complex From The Soil Bacterium Paracoccus Denitrificans At 2.7 Angstrom Resolution Length = 190

Iteration: 1
 Score =  154 bits (388), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 72/147 (48%), Positives = 100/147 (68%), Gaps = 14/147 (9%)
Query: 56  FISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQL 115
            ++ M+ SADV A+A+I+VD++ +  G  +T KW GKP+FIR RT+ EI   +  ++ QL
Sbjct: 38  LVNQMNPSADVQALASIQVDVSGVETGTQLTVKWLGKPVFIRRRTEDEIQAGREVDLGQL 97
Query: 116 RD-----------PQADSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHGS 161
            D           P  D +R  D +  WLV+IG+CTHLGCVPI + AGD+GG++CPCHGS
Sbjct: 98  IDRSAQNSNKPDAPATDENRTMDEAGEWLVMIGVCTHLGCVPIGDGAGDFGGWFCPCHGS 157
Query: 162 HYDASGRIRKGPAPTNMEVPPYQFGDE 188
           HYD SGRIR+GPAP N+ +P  +F D+
Sbjct: 158 HYDTSGRIRRGPAPQNLHIPVAEFLDD 184

>pdb|2YIU|C Chain C, X-Ray Structure Of The Dimeric Cytochrome Bc1 Complex From The Soil Bacterium Paracoccus Denitrificans At 2.7 Angstrom Resolution Length = 190

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 32/44 (72%)
Query: 249 FISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
            ++ M+ SADV A+A+I+VD++ +  G  +T KW GKP+FIR R
Sbjct: 38  LVNQMNPSADVQALASIQVDVSGVETGTQLTVKWLGKPVFIRRR 81

>pdb|2QJP|C Chain C, Crystal Structure Of Wild Type Rhodobacter Sphaeroides With Stigmatellin And Antimycin Inhibited Length = 179

Iteration: 1
 Score =  142 bits (357), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 70/148 (47%), Positives = 99/148 (66%), Gaps = 15/148 (10%)
Query: 56  FISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQL 115
            I+ M+ SADV A+A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL
Sbjct: 26  LINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQL 85
Query: 116 RDPQA------------DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHG 160
            D  A            D +R  D +  WLV+ G+CTHLGCVPI   +GD+GG++CPCHG
Sbjct: 86  VDTNARNANIDAGAEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHG 145
Query: 161 SHYDASGRIRKGPAPTNMEVPPYQFGDE 188
           SHYD++GRIRKGPAP N+ +P  +F DE
Sbjct: 146 SHYDSAGRIRKGPAPENLPIPLAKFIDE 173

>pdb|2QJP|C Chain C, Crystal Structure Of Wild Type Rhodobacter Sphaeroides With Stigmatellin And Antimycin Inhibited Length = 179

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 31/44 (70%)
Query: 249 FISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
            I+ M+ SADV A+A+I VD++ +  G  +T K+ GKP+FIR R
Sbjct: 26  LINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRR 69

>pdb|2FYN|C Chain C, Crystal Structure Analysis Of The Double Mutant Rhodobacter Sphaeroides Bc1 Complex Length = 187

Iteration: 1
 Score =  140 bits (352), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 69/148 (46%), Positives = 98/148 (66%), Gaps = 15/148 (10%)
Query: 56  FISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQL 115
            I+ M+ SADV A+A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL
Sbjct: 34  LINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQL 93
Query: 116 RDPQA------------DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHG 160
            D  A            D +R  D +  WLV+ G+CTHLGC PI   +GD+GG++CPCHG
Sbjct: 94  VDTNARNANIDAGAEATDQNRTLDEAGEWLVMWGVCTHLGCSPIGGVSGDFGGWFCPCHG 153
Query: 161 SHYDASGRIRKGPAPTNMEVPPYQFGDE 188
           SHYD++GRIRKGPAP N+ +P  +F DE
Sbjct: 154 SHYDSAGRIRKGPAPENLPIPLAKFIDE 181

>pdb|2FYN|C Chain C, Crystal Structure Analysis Of The Double Mutant Rhodobacter Sphaeroides Bc1 Complex Length = 187

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 31/44 (70%)
Query: 249 FISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
            I+ M+ SADV A+A+I VD++ +  G  +T K+ GKP+FIR R
Sbjct: 34  LINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRR 77

>pdb|2QJK|C Chain C, Crystal Structure Analysis Of Mutant Rhodobacter Sphaeroides Bc1 With Stigmatellin And Antimycin Length = 179

Iteration: 1
 Score =  139 bits (351), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 69/148 (46%), Positives = 98/148 (66%), Gaps = 15/148 (10%)
Query: 56  FISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQL 115
            I+ M+ SADV A+A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL
Sbjct: 26  LINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQL 85
Query: 116 RDPQA------------DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHG 160
            D  A            D +R  D +  WLV+ G+CTHLGC PI   +GD+GG++CPCHG
Sbjct: 86  VDTNARNANIDAGAEATDQNRTLDEAGEWLVMWGVCTHLGCSPIGGVSGDFGGWFCPCHG 145
Query: 161 SHYDASGRIRKGPAPTNMEVPPYQFGDE 188
           SHYD++GRIRKGPAP N+ +P  +F DE
Sbjct: 146 SHYDSAGRIRKGPAPENLPIPLAKFIDE 173

>pdb|2QJK|C Chain C, Crystal Structure Analysis Of Mutant Rhodobacter Sphaeroides Bc1 With Stigmatellin And Antimycin Length = 179

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 31/44 (70%)
Query: 249 FISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
            I+ M+ SADV A+A+I VD++ +  G  +T K+ GKP+FIR R
Sbjct: 26  LINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRR 69

>pdb|2NUK|A Chain A, Soluble Domain Of The Rieske Iron-Sulfur Protein From Rhodobacter Sphaeroides Length = 141

Iteration: 1
 Score =  130 bits (328), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 63/135 (46%), Positives = 90/135 (66%), Gaps = 15/135 (11%)
Query: 69  MATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQA-------- 120
           +A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL D  A        
Sbjct: 1   LASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAG 60
Query: 121 ----DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHGSHYDASGRIRKGP 173
               D +R  D +  WLV+ G+CTHLGCVPI   +GD+GG++CPCHGSHYD++GRIRKGP
Sbjct: 61  AEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGSHYDSAGRIRKGP 120
Query: 174 APTNMEVPPYQFGDE 188
           AP N+ +P  +F DE
Sbjct: 121 APENLPIPLAKFIDE 135

>pdb|2NVG|A Chain A, Soluble Domain Of Rieske Iron Sulfur Protein Length = 141

Iteration: 1
 Score =  129 bits (325), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 62/135 (45%), Positives = 90/135 (66%), Gaps = 15/135 (11%)
Query: 69  MATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQA-------- 120
           +A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL D  A        
Sbjct: 1   LASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAG 60
Query: 121 ----DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHGSHYDASGRIRKGP 173
               D +R  D +  WLV+ G+CTHLGCVPI   +GD+GG++CPCHG+HYD++GRIRKGP
Sbjct: 61  AEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGAHYDSAGRIRKGP 120
Query: 174 APTNMEVPPYQFGDE 188
           AP N+ +P  +F DE
Sbjct: 121 APENLPIPLAKFIDE 135

>pdb|2NVE|A Chain A, Soluble Domain Of Rieske Iron Sulfur Protein Length = 141

Iteration: 1
 Score =  129 bits (325), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 62/135 (45%), Positives = 90/135 (66%), Gaps = 15/135 (11%)
Query: 69  MATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQA-------- 120
           +A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL D  A        
Sbjct: 1   LASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAG 60
Query: 121 ----DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHGSHYDASGRIRKGP 173
               D +R  D +  WLV+ G+CTHLGCVPI   +GD+GG++CPCHG+HYD++GRIRKGP
Sbjct: 61  AEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGTHYDSAGRIRKGP 120
Query: 174 APTNMEVPPYQFGDE 188
           AP N+ +P  +F DE
Sbjct: 121 APENLPIPLAKFIDE 135

>pdb|2NUM|A Chain A, Soluble Domain Of Rieske Iron-Sulfur Protein Length = 141

Iteration: 1
 Score =  129 bits (325), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 62/135 (45%), Positives = 90/135 (66%), Gaps = 15/135 (11%)
Query: 69  MATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQA-------- 120
           +A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL D  A        
Sbjct: 1   LASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAG 60
Query: 121 ----DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHGSHYDASGRIRKGP 173
               D +R  D +  WLV+ G+CTHLGCVPI   +GD+GG++CPCHGSH+D++GRIRKGP
Sbjct: 61  AEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGSHFDSAGRIRKGP 120
Query: 174 APTNMEVPPYQFGDE 188
           AP N+ +P  +F DE
Sbjct: 121 APENLPIPLAKFIDE 135

>pdb|2NVF|A Chain A, Soluble Domain Of Rieske Iron-Sulfur Protein Length = 141

Iteration: 1
 Score =  129 bits (323), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 62/135 (45%), Positives = 89/135 (65%), Gaps = 15/135 (11%)
Query: 69  MATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQA-------- 120
           +A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL D  A        
Sbjct: 1   LASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAG 60
Query: 121 ----DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHGSHYDASGRIRKGP 173
               D +R  D +  WLV+ G+CTHLGCVPI   +GD+GG++CPCHG HYD++GRIRKGP
Sbjct: 61  AEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGCHYDSAGRIRKGP 120
Query: 174 APTNMEVPPYQFGDE 188
           AP N+ +P  +F DE
Sbjct: 121 APENLPIPLAKFIDE 135

>pdb|2NWF|A Chain A, Soluble Domain Of Rieske Iron Sulfur Protein Length = 141

Iteration: 1
 Score =  129 bits (323), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 62/135 (45%), Positives = 90/135 (66%), Gaps = 15/135 (11%)
Query: 69  MATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQA-------- 120
           +A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL D  A        
Sbjct: 1   LASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAG 60
Query: 121 ----DSDRVKDPS--WLVIIGICTHLGCVPIAN-AGDWGGYYCPCHGSHYDASGRIRKGP 173
               D +R  D +  WLV+ G+CTHLGCVPI   +GD+GG++CPCHGSH+D++GRIRKGP
Sbjct: 61  AEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGSHWDSAGRIRKGP 120
Query: 174 APTNMEVPPYQFGDE 188
           AP N+ +P  +F DE
Sbjct: 121 APENLPIPLAKFIDE 135

>pdb|1VF5|D Chain D, Crystal Structure Of Cytochrome B6f Complex From M.Laminosus Length = 179

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 56/112 (50%), Gaps = 18/112 (16%)
Query: 108 QNTNISQLRDPQADSDRV------KDPSWLV-----------IIGICTHLGCVPIANAGD 150
            N  +S+  +     DRV       DP+++V           I  +CTHLGCV   NA +
Sbjct: 62  NNVKVSKFLESHNAGDRVLVQGLKGDPTYIVVESKEAIRDYGINAVCTHLGCVVPWNAAE 121
Query: 151 WGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRT 202
              + CPCHGS YD +GR+ +GPAP ++ +      D+ I++     +D RT
Sbjct: 122 -NKFKCPCHGSQYDETGRVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRT 172

>pdb|2E74|D Chain D, Crystal Structure Of The Cytochrome B6f Complex From M.Laminosus Length = 179

Iteration: 1
 Score = 65.9 bits (159), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 56/112 (50%), Gaps = 18/112 (16%)
Query: 108 QNTNISQLRDPQADSDRV------KDPSWLV-----------IIGICTHLGCVPIANAGD 150
            N  +S+  +     DRV       DP+++V           I  +CTHLGCV   NA +
Sbjct: 62  NNVKVSKFLESHNAGDRVLVQGLKGDPTYIVVESKEAIRDYGINAVCTHLGCVVPWNAAE 121
Query: 151 WGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRT 202
              + CPCHGS YD +G++ +GPAP ++ +      D+ I++     +D RT
Sbjct: 122 -NKFKCPCHGSQYDETGKVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRT 172

>pdb|2ZT9|D Chain D, Crystal Structure Of The Cytochrome B6f Complex From Nostoc Sp. Pcc 7120 Length = 179

Iteration: 1
 Score = 64.7 bits (156), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 133 IIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILI 192
           I  +CTHLGCV   NA +   + CPCHGS YDA+G++ +GPAP ++ +   +  ++ I++
Sbjct: 104 INAVCTHLGCVVPWNAAE-NKFKCPCHGSQYDATGKVVRGPAPKSLALSHAKTENDKIVL 162
Query: 193 RMLAHSDIRT 202
                +D RT
Sbjct: 163 TSWTETDFRT 172

>pdb|1RFS|A Chain A, Rieske Soluble Fragment From Spinach Length = 139

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 45/87 (51%), Gaps = 12/87 (13%)
Query: 127 DPSWLV-----------IIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAP 175
           DP++LV           I  +CTHLGCV   NA +   + CPCHGS Y+  GR+ +GPAP
Sbjct: 46  DPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAE-NKFICPCHGSQYNNQGRVVRGPAP 104
Query: 176 TNMEVPPYQFGDEGILIRMLAHSDIRT 202
            ++ +      D  ++      +D RT
Sbjct: 105 LSLALAHCDVDDGKVVFVPWTETDFRT 131

>pdb|1Q90|C Chain C, Structure Of The Cytochrome B6f (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii Length = 127

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 13/88 (14%)
Query: 127 DPSWLVIIG-----------ICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAP 175
           DP++L++             +CTHLGCV    A +   + CPCHGS Y+A G++ +GPAP
Sbjct: 34  DPTYLIVTADSTIEKYGLNAVCTHLGCVVPWVAAE-NKFKCPCHGSQYNAEGKVVRGPAP 92
Query: 176 TNMEVPPYQFGDEGIL-IRMLAHSDIRT 202
            ++ +      + G++       +D RT
Sbjct: 93  LSLALAHCDVAESGLVTFSTWTETDFRT 120

>pdb|3AZC|A Chain A, Crystal Structure Of The Soluble Part Of Cytochrome B6f Complex Iron- Sulfur Subunit From Thermosynechococcus Elongatus Bp-1 Length = 133

Iteration: 1
 Score = 54.7 bits (130), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 32/46 (69%), Gaps = 1/46 (2%)
Query: 135 GICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEV 180
            +CTHLGCV   N  +   + CPCHGS YD++G++ +GPAP ++ +
Sbjct: 59  AVCTHLGCVVPWNVSE-NKFICPCHGSQYDSTGKVVRGPAPLSLAL 103

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	292
1pp9_E	196	Ubiquinol-cytochrome C reductase iron-sulfur SUBU	2e-82
1pp9_E	196	Ubiquinol-cytochrome C reductase iron-sulfur SUBU	2e-34
3cx5_E	185	Cytochrome B-C1 complex subunit rieske, mitochondr	4e-77
3cx5_E	185	Cytochrome B-C1 complex subunit rieske, mitochondr	4e-27
2qjy_C	187	Ubiquinol-cytochrome C reductase iron-sulfur SUBU;	3e-65
2qjy_C	187	Ubiquinol-cytochrome C reductase iron-sulfur SUBU;	3e-19
1rie_A	129	Rieske iron-sulfur protein; oxidoreductase, cytoch	1e-62
1rie_A	129	Rieske iron-sulfur protein; oxidoreductase, cytoch	3e-13
2nwf_A	141	Ubiquinol-cytochrome C reductase iron-sulfur SUBU;	3e-61
2nwf_A	141	Ubiquinol-cytochrome C reductase iron-sulfur SUBU;	2e-12
3azc_A	133	Cytochrome B6-F complex iron-sulfur subunit; riesk	3e-51
3azc_A	133	Cytochrome B6-F complex iron-sulfur subunit; riesk	7e-05
1vf5_D	179	Rieske iron-sulfur protein; photosynthesis, membra	4e-46
1nyk_A	165	Rieske iron-sulfur protein; beta barrel, iron sulf	5e-40
1rfs_A	139	Rieske protein; iron-sulfur protein, electron tran	1e-31
1jm1_A	204	Rieske iron-sulfur protein SOXF; electron transpor	3e-17
1g8k_B	133	Arsenite oxidase; molybdopterin, [3Fe-4S] cluster,	1e-11

>1pp9_E Ubiquinol-cytochrome C reductase iron-sulfur SUBU mitochondrial; cytochrome BC1, membrane protein, heme protein, rieske iron protein, cytochrome B, complex III; HET: BHG HEM HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: b.33.1.1 f.23.12.1 PDB: 1bgy_E* 1be3_E* 1l0n_E* 1ntk_E* 1ntm_E* 1ntz_E* 1nu1_E* 1l0l_E* 1ppj_E* 1qcr_E* 1sqb_E* 1sqp_E* 1sqq_E* 1sqv_E* 1sqx_E* 2a06_E* 2fyu_E* 2ybb_E* 1bcc_E* 2bcc_E* ... Length = 196

 Score =  245 bits (627), Expect = 2e-82
 Identities = 119/194 (61%), Positives = 151/194 (77%), Gaps = 4/194 (2%)

Query: 3   AHSDIRTPDFSKYRRDRNPD----KGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
           +H+DI+ PDFS YRR    D      +    RK F+Y++   ++V     AK+VV+QF+S
Sbjct: 1   SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 60

Query: 59  SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDP 118
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDP
Sbjct: 61  SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP 120

Query: 119 QADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNM 178
           Q D +RVK P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+
Sbjct: 121 QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL 180

Query: 179 EVPPYQFGDEGILI 192
           EVP Y+F  + ++I
Sbjct: 181 EVPSYEFTSDDMVI 194

>1pp9_E Ubiquinol-cytochrome C reductase iron-sulfur SUBU mitochondrial; cytochrome BC1, membrane protein, heme protein, rieske iron protein, cytochrome B, complex III; HET: BHG HEM HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: b.33.1.1 f.23.12.1 PDB: 1bgy_E* 1be3_E* 1l0n_E* 1ntk_E* 1ntm_E* 1ntz_E* 1nu1_E* 1l0l_E* 1ppj_E* 1qcr_E* 1sqb_E* 1sqp_E* 1sqq_E* 1sqv_E* 1sqx_E* 2a06_E* 2fyu_E* 2ybb_E* 1bcc_E* 2bcc_E* ... Length = 196

 Score =  122 bits (308), Expect = 2e-34
 Identities = 53/101 (52%), Positives = 72/101 (71%), Gaps = 4/101 (3%)

Query: 196 AHSDIRTPDFSKYRRDRNPD----KGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 251
           +H+DI+ PDFS YRR    D      +    RK F+Y++   ++V     AK+VV+QF+S
Sbjct: 1   SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 60

Query: 252 SMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           SMSASADVLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHR
Sbjct: 61  SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHR 101

>3cx5_E Cytochrome B-C1 complex subunit rieske, mitochondrial; complex III, electron transfer complex, cytochrome BC1 complex, mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces cerevisiae} SCOP: b.33.1.1 f.23.12.1 PDB: 1kb9_E* 1kyo_E* 1p84_E* 2ibz_E* 1ezv_E* 3cxh_E* Length = 185

 Score =  232 bits (592), Expect = 4e-77
 Identities = 99/188 (52%), Positives = 136/188 (72%), Gaps = 5/188 (2%)

Query: 5   SDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASA 64
           S  RTP+F    ++ N     +  + +++ Y + G   ++    AKS V  FISSM+A+A
Sbjct: 2   STYRTPNFDDVLKENN-----DADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATA 56

Query: 65  DVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDR 124
           DVLAMA +EV+L  IP G++V  KW+GKP+FIRHRT  EI    + ++S L+DPQ D+DR
Sbjct: 57  DVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADR 116

Query: 125 VKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQ 184
           VKDP WL+++GICTHLGCVPI  AGD+GG++CPCHGSHYD SGRIRKGPAP N+E+P Y+
Sbjct: 117 VKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYE 176

Query: 185 FGDEGILI 192
           F  + +++
Sbjct: 177 FDGDKVIV 184

>3cx5_E Cytochrome B-C1 complex subunit rieske, mitochondrial; complex III, electron transfer complex, cytochrome BC1 complex, mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces cerevisiae} SCOP: b.33.1.1 f.23.12.1 PDB: 1kb9_E* 1kyo_E* 1p84_E* 2ibz_E* 1ezv_E* 3cxh_E* Length = 185

 Score =  103 bits (257), Expect = 4e-27
 Identities = 42/95 (44%), Positives = 61/95 (64%), Gaps = 5/95 (5%)

Query: 198 SDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASA 257
           S  RTP+F    ++ N     +  + +++ Y + G   ++    AKS V  FISSM+A+A
Sbjct: 2   STYRTPNFDDVLKENN-----DADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATA 56

Query: 258 DVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           DVLAMA +EV+L  IP G++V  KW+GKP+FIRHR
Sbjct: 57  DVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHR 91

>2qjy_C Ubiquinol-cytochrome C reductase iron-sulfur SUBU; cytochrome B, 8 TM helixces cytochrome C1, 1 C-TERM TM helix 1 N-TERM TM helix; HET: BGL HEM SMA LOP UQ2; 2.40A {Rhodobacter sphaeroides} PDB: 2fyn_C* 2qjk_C* 2qjp_C* 1zrt_E* 2yiu_C* Length = 187

 Score =  201 bits (513), Expect = 3e-65
 Identities = 70/186 (37%), Positives = 102/186 (54%), Gaps = 18/186 (9%)

Query: 22  DKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPE 81
           +       R+ F Y    G+  V      + V   I+ M+ SADV A+A+I VD++ +  
Sbjct: 3   NAEDHAGTRRDFLYYATAGAGAVA---TGAAVWPLINQMNPSADVQALASIFVDVSSVEP 59

Query: 82  GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSD--------------RVKD 127
           G  +T K+ GKP+FIR RT+ +I+  ++  + QL D  A +                 + 
Sbjct: 60  GVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAGAEATDQNRTLDEA 119

Query: 128 PSWLVIIGICTHLGCVPIANAGDW-GGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFG 186
             WLV+ G+CTHLGC PI       GG++CPCHGSHYD++GRIRKGPAP N+ +P  +F 
Sbjct: 120 GEWLVMWGVCTHLGCSPIGGVSGDFGGWFCPCHGSHYDSAGRIRKGPAPENLPIPLAKFI 179

Query: 187 DEGILI 192
           DE  + 
Sbjct: 180 DETTIQ 185

>2qjy_C Ubiquinol-cytochrome C reductase iron-sulfur SUBU; cytochrome B, 8 TM helixces cytochrome C1, 1 C-TERM TM helix 1 N-TERM TM helix; HET: BGL HEM SMA LOP UQ2; 2.40A {Rhodobacter sphaeroides} PDB: 2fyn_C* 2qjk_C* 2qjp_C* 1zrt_E* 2yiu_C* Length = 187

 Score = 82.5 bits (203), Expect = 3e-19
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 3/78 (3%)

Query: 215 DKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPE 274
           +       R+ F Y    G+  V      + V   I+ M+ SADV A+A+I VD++ +  
Sbjct: 3   NAEDHAGTRRDFLYYATAGAGAVA---TGAAVWPLINQMNPSADVQALASIFVDVSSVEP 59

Query: 275 GQSVTFKWRGKPLFIRHR 292
           G  +T K+ GKP+FIR R
Sbjct: 60  GVQLTVKFLGKPIFIRRR 77

>1rie_A Rieske iron-sulfur protein; oxidoreductase, cytochrome BC1 complex, histidine ligands, rieske iron-sulfur cluster, electron transport; 1.50A {Bos taurus} SCOP: b.33.1.1 Length = 129

 Score =  193 bits (491), Expect = 1e-62
 Identities = 89/127 (70%), Positives = 109/127 (85%)

Query: 66  VLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRV 125
           VLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDPQ D +RV
Sbjct: 1   VLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERV 60

Query: 126 KDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF 185
           K P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+EVP Y+F
Sbjct: 61  KKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPSYEF 120

Query: 186 GDEGILI 192
             + ++I
Sbjct: 121 TSDDMVI 127

>1rie_A Rieske iron-sulfur protein; oxidoreductase, cytochrome BC1 complex, histidine ligands, rieske iron-sulfur cluster, electron transport; 1.50A {Bos taurus} SCOP: b.33.1.1 Length = 129

 Score = 64.6 bits (157), Expect = 3e-13
 Identities = 23/34 (67%), Positives = 30/34 (88%)

Query: 259 VLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           VLAM+ IE+ L+ IPEG+++ FKWRGKPLF+RHR
Sbjct: 1   VLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHR 34

>2nwf_A Ubiquinol-cytochrome C reductase iron-sulfur SUBU; rieske [2Fe-2S] ISP, oxidoreductase; HET: GOL; 1.10A {Rhodobacter sphaeroides} PDB: 2nuk_A 2nve_A 2num_A 2nvg_A 2nvf_A Length = 141

 Score =  189 bits (482), Expect = 3e-61
 Identities = 57/139 (41%), Positives = 85/139 (61%), Gaps = 15/139 (10%)

Query: 69  MATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRV--- 125
           +A+I VD++ +  G  +T K+ GKP+FIR RT+ +I+  ++  + QL D  A +  +   
Sbjct: 1   LASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAG 60

Query: 126 -----------KDPSWLVIIGICTHLGCVPIANAGDW-GGYYCPCHGSHYDASGRIRKGP 173
                      +   WLV+ G+CTHLGCVPI       GG++CPCHGSH+D++GRIRKGP
Sbjct: 61  AEATDQNRTLDEAGEWLVMWGVCTHLGCVPIGGVSGDFGGWFCPCHGSHWDSAGRIRKGP 120

Query: 174 APTNMEVPPYQFGDEGILI 192
           AP N+ +P  +F DE  + 
Sbjct: 121 APENLPIPLAKFIDETTIQ 139

>2nwf_A Ubiquinol-cytochrome C reductase iron-sulfur SUBU; rieske [2Fe-2S] ISP, oxidoreductase; HET: GOL; 1.10A {Rhodobacter sphaeroides} PDB: 2nuk_A 2nve_A 2num_A 2nvg_A 2nvf_A Length = 141

 Score = 62.2 bits (151), Expect = 2e-12
 Identities = 14/31 (45%), Positives = 22/31 (70%)

Query: 262 MATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           +A+I VD++ +  G  +T K+ GKP+FIR R
Sbjct: 1   LASIFVDVSSVEPGVQLTVKFLGKPIFIRRR 31

>3azc_A Cytochrome B6-F complex iron-sulfur subunit; rieske, thermosynechococcus elongatu photosynthesis, electron transport; 2.00A {Thermosynechococcus elongatus} Length = 133

 Score =  163 bits (415), Expect = 3e-51
 Identities = 29/113 (25%), Positives = 53/113 (46%), Gaps = 2/113 (1%)

Query: 81  EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADS-DRVKDPSWLVIIGICTH 139
           EG++V     G  + +     K +  +++       DP           +   +  +CTH
Sbjct: 4   EGRAVAKDALGNDIKVSEYLAKHLPGDRSLAQGIKGDPTYVIVTEDHQIANYGLNAVCTH 63

Query: 140 LGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILI 192
           LGCV   N  +   + CPCHGS YD++G++ +GPAP ++ +      ++  L+
Sbjct: 64  LGCVVPWNVSE-NKFICPCHGSQYDSTGKVVRGPAPLSLALVKATVTEDDKLV 115

>3azc_A Cytochrome B6-F complex iron-sulfur subunit; rieske, thermosynechococcus elongatu photosynthesis, electron transport; 2.00A {Thermosynechococcus elongatus} Length = 133

 Score = 40.9 bits (96), Expect = 7e-05
 Identities = 4/19 (21%), Positives = 8/19 (42%)

Query: 274 EGQSVTFKWRGKPLFIRHR 292
           EG++V     G  + +   
Sbjct: 4   EGRAVAKDALGNDIKVSEY 22

>1vf5_D Rieske iron-sulfur protein; photosynthesis, membrane protein complex, electron transfer complex; HET: HEM TDS PL9 OPC CLA BCR; 3.00A {Mastigocladus laminosus} SCOP: b.33.1.1 f.23.12.1 PDB: 2d2c_D* 2e74_D* 2e75_D* 2e76_D* 2zt9_D* Length = 179

 Score =  152 bits (386), Expect = 4e-46
 Identities = 41/183 (22%), Positives = 71/183 (38%), Gaps = 20/183 (10%)

Query: 22  DKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDL--NLI 79
               +  +R+    +  G  + V +     +V  FI     S   +   T   D   N +
Sbjct: 8   MDVPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPP---SGGAVGGGTTAKDKLGNNV 64

Query: 80  PEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTH 139
              + +     G  + ++                 +     ++ R        I  +CTH
Sbjct: 65  KVSKFLESHNAGDRVLVQGLKGDPTY---------IVVESKEAIR-----DYGINAVCTH 110

Query: 140 LGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSD 199
           LGCV   NA +   + CPCHGS YD +GR+ +GPAP ++ +      D+ I++     +D
Sbjct: 111 LGCVVPWNAAE-NKFKCPCHGSQYDETGRVIRGPAPLSLALCHATVQDDNIVLTPWTETD 169

Query: 200 IRT 202
            RT
Sbjct: 170 FRT 172

>1nyk_A Rieske iron-sulfur protein; beta barrel, iron sulfur cluster, electron transport; 1.31A {Thermus thermophilus} SCOP: b.33.1.1 PDB: 3fou_A Length = 165

 Score =  136 bits (343), Expect = 5e-40
 Identities = 27/129 (20%), Positives = 45/129 (34%), Gaps = 9/129 (6%)

Query: 70  ATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPS 129
               + L  +  G      +   P         +    +NT +    DP+  +  V   +
Sbjct: 21  EPKPIRLEELKPGDPFVLAYPMDP----KTKVVKSGEAKNTLLVARFDPEELAPEVAQHA 76

Query: 130 ---WLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPYQ 184
               +    +CTHLGC+      D     CPCHG  YD     ++  GP P  +   P +
Sbjct: 77  AEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVR 136

Query: 185 FGDEGILIR 193
             D  ++  
Sbjct: 137 VEDGVLVAA 145

>1rfs_A Rieske protein; iron-sulfur protein, electron transport; 1.83A {Spinacia oleracea} SCOP: b.33.1.1 PDB: 1q90_C* Length = 139

 Score =  113 bits (285), Expect = 1e-31
 Identities = 32/121 (26%), Positives = 51/121 (42%), Gaps = 12/121 (9%)

Query: 95  FIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLV-----------IIGICTHLGCV 143
             +     ++   +        D         DP++LV           I  +CTHLGCV
Sbjct: 14  IAKDALGNDVIAAEWLKTHAPGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCV 73

Query: 144 PIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTP 203
              NA +   + CPCHGS Y+  GR+ +GPAP ++ +      D  ++      +D RT 
Sbjct: 74  VPFNAAE-NKFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRTG 132

Query: 204 D 204
           +
Sbjct: 133 E 133

>1jm1_A Rieske iron-sulfur protein SOXF; electron transport, respiratory chain, oxidoreductase; 1.11A {Sulfolobus acidocaldarius} SCOP: b.33.1.1 Length = 204

 Score = 77.5 bits (190), Expect = 3e-17
 Identities = 23/130 (17%), Positives = 38/130 (29%), Gaps = 31/130 (23%)

Query: 89  WRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVK------------DPSWLVIIGI 136
              +P F+               I+++ +P                    + +      +
Sbjct: 39  LTDEPCFLVDLQ-----ALTGQQITEIPNPYYGKYAGPLGQIQTIKGVGPNGTIFAFSDV 93

Query: 137 CTHLGCVPIANAGDW-----------GGYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPY 183
           C HLGC   A                   +CPCHGS Y     G +  GPAP  + +   
Sbjct: 94  CVHLGCQLPAQVIVSSESDPGLYAKGADLHCPCHGSIYALKDGGVVVSGPAPRPLPIVIL 153

Query: 184 QF-GDEGILI 192
            +    G + 
Sbjct: 154 DYDSSTGDIY 163

>1g8k_B Arsenite oxidase; molybdopterin, [3Fe-4S] cluster, [2Fe-2S] rieske, oxidoreductase; HET: MGD; 1.64A {Alcaligenes faecalis} SCOP: b.33.1.1 PDB: 1g8j_B* Length = 133

 Score = 60.3 bits (146), Expect = 1e-11
 Identities = 18/122 (14%), Positives = 38/122 (31%), Gaps = 22/122 (18%)

Query: 75  DLNLIPEGQSVTFKWR--GKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLV 132
               +   + V+F +     P                                 D   + 
Sbjct: 13  VAKNLAANEPVSFTYPDTSSPCVAVKLGAPVPGG-----------------VGPDDDIVA 55

Query: 133 IIGICTHLGCVPIANAGDWGGYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPYQFGDEGI 190
              +CTH+GC    ++     + CPCH + +DA  +G++  G A  ++     ++     
Sbjct: 56  YSVLCTHMGCPTSYDSSS-KTFSCPCHFTEFDAEKAGQMICGEATADLPRVLLRYDAASD 114

Query: 191 LI 192
            +
Sbjct: 115 AL 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	292
1pp9_E	196	Ubiquinol-cytochrome C reductase iron-sulfur SUBU	100.0
3cx5_E	185	Cytochrome B-C1 complex subunit rieske, mitochondr	100.0
2qjy_C	187	Ubiquinol-cytochrome C reductase iron-sulfur SUBU;	100.0
2nwf_A	141	Ubiquinol-cytochrome C reductase iron-sulfur SUBU;	100.0
1rie_A	129	Rieske iron-sulfur protein; oxidoreductase, cytoch	99.97
1vf5_D	179	Rieske iron-sulfur protein; photosynthesis, membra	99.95
4aay_B	175	AROB; oxidoreductase, rieske, iron sulfur, molybdo	99.91
1pp9_E	196	Ubiquinol-cytochrome C reductase iron-sulfur SUBU	99.91
1nyk_A	165	Rieske iron-sulfur protein; beta barrel, iron sulf	99.9
3gce_A	121	Ferredoxin component of carbazole 1,9A- dioxygenas	99.87
3cx5_E	185	Cytochrome B-C1 complex subunit rieske, mitochondr	99.87
2qpz_A	103	Naphthalene 1,2-dioxygenase system ferredoxin subu	99.87
3dqy_A	106	Toluene 1,2-dioxygenase system ferredoxin subunit;	99.86
1fqt_A	112	Rieske-type ferredoxin of biphenyl dioxygenase; 2F	99.86
2i7f_A	108	Ferredoxin component of dioxygenase; rieske ferred	99.85
1g8k_B	133	Arsenite oxidase; molybdopterin, [3Fe-4S] cluster,	99.85
1vm9_A	111	Toluene-4-monooxygenase system protein C; structur	99.85
2de6_D	115	Ferredoxin component of carbazole; electron transf	99.84
1rfs_A	139	Rieske protein; iron-sulfur protein, electron tran	99.83
1jm1_A	204	Rieske iron-sulfur protein SOXF; electron transpor	99.82
3c0d_A	119	Putative nitrite reductase NADPH (small subunit) o	99.8
2jo6_A	113	Nitrite reductase [NAD(P)H] small subunit; all bet	99.8
2jza_A	130	Nitrite reductase [NAD(P)H] small subunit; ISP dom	99.79
3azc_A	133	Cytochrome B6-F complex iron-sulfur subunit; riesk	99.63
4aiv_A	119	Probable nitrite reductase [NAD(P)H] small subuni;	99.75
3d89_A	157	Rieske domain-containing protein; CAsp target, rie	99.69
2qjy_C	187	Ubiquinol-cytochrome C reductase iron-sulfur SUBU;	99.69
2zyl_A	386	Possible oxidoreductase; KSHA, cholesterol, rieske	99.69
3gke_A	349	DDMC; rieske cluster, non-heme mononuclear iron, o	99.68
3gkq_A	389	Terminal oxygenase component of carbazole 1,9A- di	99.65
3gcf_A	394	Terminal oxygenase component of carbazole 1,9A- di	99.64
3vca_A	412	Ring-hydroxylating dioxygenase; rieske-type, monon	99.63
3n0q_A	409	Putative aromatic-ring hydroxylating dioxygenase;	99.62
2gbw_A	454	Biphenyl 2,3-dioxygenase alpha subunit; rieske oxy	99.62
2bmo_A	447	Oxygenase-alpha NBDO; nitrobenzene dioxygenase, ni	99.61
2de6_A	392	Terminal oxygenase component of carbazole; electro	99.59
1z01_A	446	2-OXO-1,2-dihydroquinoline 8-monooxygenase, oxygen	99.58
2b1x_A	470	Naphthalene dioxygenase large subunit; rieske non-	99.58
1uli_A	460	Biphenyl dioxygenase large subunit; alpha3 BETA3 h	99.58
3gzx_A	457	Biphenyl dioxygenase subunit alpha; rieskie, non-h	99.52
1vf5_D	179	Rieske iron-sulfur protein; photosynthesis, membra	98.52
4aay_B	175	AROB; oxidoreductase, rieske, iron sulfur, molybdo	95.6
1q90_R	49	Cytochrome B6-F complex iron-sulfur subunit; membr	85.66
1q90_R	49	Cytochrome B6-F complex iron-sulfur subunit; membr	83.39

>1pp9_E Ubiquinol-cytochrome C reductase iron-sulfur SUBU mitochondrial; cytochrome BC1, membrane protein, heme protein, rieske iron protein, cytochrome B, complex III; HET: BHG HEM HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: b.33.1.1 f.23.12.1 PDB: 1bgy_E* 1be3_E* 1l0n_E* 1ntk_E* 1ntm_E* 1ntz_E* 1nu1_E* 1l0l_E* 1ppj_E* 1qcr_E* 1sqb_E* 1sqp_E* 1sqq_E* 1sqv_E* 1sqx_E* 2a06_E* 2fyu_E* 2ybb_E* 1bcc_E* 2bcc_E* ...

Probab=100.00  E-value=1.5e-48  Score=343.97  Aligned_cols=190  Identities=63%  Similarity=1.161  Sum_probs=176.7

Q ss_pred             CCCCCCCCCccccccCCCCC--CCCC--CcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhhccccceeecCC
Q psy6642           3 AHSDIRTPDFSKYRRDRNPD--KGQE--ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNL   78 (292)
Q Consensus         3 ~~~~~~~pd~~~yr~~~~~~--~~~~--~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~a~~~~~v~~s~   78 (292)
                      +|||+.+|||++||+.+++|  ++++  +.+||+|+|+++|+++++|++++..++.+|+.+++|+++.++.+.+++++++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~RR~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~a~~~v~v~ls~   80 (196)
T 1pp9_E            1 SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMSKIEIKLSD   80 (196)
T ss_dssp             CGGGCCCCCCTTTBCGGGCCTTSCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCHHHHCCCCEEEEGGG
T ss_pred             CCCCcCCCCchHhhcccccCcccccccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcccccccccEEEHHH
Confidence            79999999999999999888  3332  6789999999999988888888888999999999999999988899999999


Q ss_pred             CCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeEEcCC
Q psy6642          79 IPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPC  158 (292)
Q Consensus        79 l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~~CPc  158 (292)
                      |++|+.++++|+|+|++|+++++++|+...++....++||+...+|..+++|+|++++|||+||+|.++.++++.|+|||
T Consensus        81 l~~G~~~~v~~~G~pV~V~r~t~~~i~~~~~~~~~~l~dp~~~~~r~~~ge~~a~~~~CtH~G~~l~~~~~~~~~~~CP~  160 (196)
T 1pp9_E           81 IPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPC  160 (196)
T ss_dssp             SCTTCEEEEEETTEEEEEEECCHHHHHHHHHSCTTTCSSCCCGGGTCSSTTEEEEECCCTTTSCCCEETCSTTSSEEETT
T ss_pred             CCCCCeEEEEECCEEEEEEECCHHHHhhhhccccccccCcccccccccCCeEEEEECccCCCCeeccccCCCCCEEEeCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999887778999999


Q ss_pred             CCcEEcCCCceecCCCCCCCCCCceEe-ecCceEE
Q psy6642         159 HGSHYDASGRIRKGPAPTNMEVPPYQF-GDEGILI  192 (292)
Q Consensus       159 HGs~FD~~G~v~~gPa~~~L~~~p~~~-~~d~i~V  192 (292)
                      |||+||++|+++.||++.+|++||+++ +++.|+|
T Consensus       161 HGs~FD~~G~v~~gPa~~~L~~~p~~v~~d~~I~v  195 (196)
T 1pp9_E          161 HGSHYDASGRIRKGPAPLNLEVPSYEFTSDDMVIV  195 (196)
T ss_dssp             TTEEECTTCCEEESSCCSCCCCCCEEEETTTEEEE
T ss_pred             CCCEECCCCCCccCCCCCCCcceeEEEEECCEEEE
Confidence            999999999999999999999999999 6776654

>3cx5_E Cytochrome B-C1 complex subunit rieske, mitochondrial; complex III, electron transfer complex, cytochrome BC1 complex, mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces cerevisiae} SCOP: b.33.1.1 f.23.12.1 PDB: 1kb9_E* 1kyo_E* 1p84_E* 2ibz_E* 1ezv_E* 3cxh_E*

Probab=100.00  E-value=1.1e-45  Score=323.09  Aligned_cols=184  Identities=53%  Similarity=1.076  Sum_probs=169.3

Q ss_pred             CCCCCCCCccccccCCCCCCCCCCcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhhccccceeecCCCCCCC
Q psy6642           4 HSDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQ   83 (292)
Q Consensus         4 ~~~~~~pd~~~yr~~~~~~~~~~~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~a~~~~~v~~s~l~~g~   83 (292)
                      .+|+.+|||++||+.+     ..+++||+|||+++|++++++++++.+.+.+|+.+++|.+++++.+.+++++++|++|+
T Consensus         1 ~~~~~~~~~~~~~~~~-----~~~~~RR~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~a~~~v~V~~s~l~~G~   75 (185)
T 3cx5_E            1 KSTYRTPNFDDVLKEN-----NDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGK   75 (185)
T ss_dssp             CCTTSCCCCTTTBCCT-----TCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCGGGCCCCCEEEEGGGCCTTC
T ss_pred             CCCccCCCchhhccCC-----CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcCCCcchhccCcEEEEHHHCCCCC
Confidence            4899999999999754     34778999999999998888888888889999999999999998888999999999999


Q ss_pred             eEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeEEcCCCCcEE
Q psy6642          84 SVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHY  163 (292)
Q Consensus        84 ~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs~F  163 (292)
                      .++++|+|+|++|++++.+||....++....++||+...+|..+++|+|++++|||+||.+.++.++++.|+||||||+|
T Consensus        76 ~~~v~~~g~pv~v~r~~~~~i~~~~~~~~~~l~dp~~~~~r~~~g~~~a~~~iCtHlGc~p~~~~~~~~~~~CPcHGs~F  155 (185)
T 3cx5_E           76 NVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHY  155 (185)
T ss_dssp             EEEEEETTEEEEEEECCHHHHHHHHCSCGGGCSSCCCSTTTCSSTTEEEEECCCTTTSCCCEEEETTTTEEEETTTTEEE
T ss_pred             eEEEEECCeEEEEEECCHHHhhhhhhcchhhhcCcccccccccCCeEEEEecccCCCCceeccCCCCCCEEEcCCCCCEE
Confidence            99999999999999999999999999999999999999999999999999999999999776665566899999999999


Q ss_pred             cCCCceecCCCCCCCCCCceEeecCceEE
Q psy6642         164 DASGRIRKGPAPTNMEVPPYQFGDEGILI  192 (292)
Q Consensus       164 D~~G~v~~gPa~~~L~~~p~~~~~d~i~V  192 (292)
                      |++|+++.||++++|++++++++++.++|
T Consensus       156 D~~G~v~~gPa~~~L~v~p~~v~~~~I~v  184 (185)
T 3cx5_E          156 DISGRIRKGPAPLNLEIPAYEFDGDKVIV  184 (185)
T ss_dssp             CTTCCEEESSCCSCCCCCCEEEETTEEEE
T ss_pred             CCCCCEecCCCCCCcceEEEEEECCEEEE
Confidence            99999999999999999999998877765

>2qjy_C Ubiquinol-cytochrome C reductase iron-sulfur SUBU; cytochrome B, 8 TM helixces cytochrome C1, 1 C-TERM TM helix 1 N-TERM TM helix; HET: BGL HEM SMA LOP UQ2; 2.40A {Rhodobacter sphaeroides} PDB: 2fyn_C* 2qjk_C* 2qjp_C* 1zrt_E* 2yiu_C*

Probab=100.00  E-value=2.9e-37  Score=270.16  Aligned_cols=163  Identities=45%  Similarity=0.873  Sum_probs=143.2

Q ss_pred             CcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhhccccceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhh
Q psy6642          27 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDT  106 (292)
Q Consensus        27 ~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~a~~~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~  106 (292)
                      +++||+||+++|++.+.++   +..++.||+.+++|.++..+.+.+++++++|++|+.++++|+|+|++|+++++++|..
T Consensus         8 ~~~RR~Fl~~~~~~~~~~~---a~~~~~p~v~~~~p~~~~~a~~~v~v~ls~l~~G~~~~v~~~g~pv~i~rrt~~~i~~   84 (187)
T 2qjy_C            8 AGTRRDFLYYATAGAGAVA---TGAAVWPLINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIEL   84 (187)
T ss_dssp             -CHHHHHHHHHHHHHHHHH---HHHHHHHHHHTTSCCTTTSCCCCEEEECTTCCTTEEEEEEETTEEEEEEECCHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHH---HHHHHHHHHHhcCCchhhcccccEEEEHHHCCCCCeEEEEECCEEEEEEECCHHHhhh
Confidence            6789999999988655443   4467899999999999988888889999999999999999999999999999999999


Q ss_pred             cccccccccCCCC------------ccccccc--CCCeEEEEecccCCCcccCC-cCCCCCeEEcCCCCcEEcCCCceec
Q psy6642         107 EQNTNISQLRDPQ------------ADSDRVK--DPSWLVIIGICTHLGCVPIA-NAGDWGGYYCPCHGSHYDASGRIRK  171 (292)
Q Consensus       107 ~~~v~~~~l~dp~------------~~~~R~~--~g~~~a~~~~CtHlGc~l~~-~~~~~~~~~CPcHGs~FD~~G~v~~  171 (292)
                      ...+....++||+            ....|..  +|+|+|++++|||+||+|.+ +.++.+.|+||||||+||++|+++.
T Consensus        85 ~~~~~~~~l~dp~~~~~~~p~~~~~~~~~r~~~~~g~~~a~~~~C~H~G~~l~~~~~g~~~~~~CP~Hg~~Fd~~G~~~~  164 (187)
T 2qjy_C           85 GRSVQLGQLVDTNARNANIDAGAEATDQNRTLDEAGEWLVMWGVCTHLGCSPIGGVSGDFGGWFCPCHGSHYDSAGRIRK  164 (187)
T ss_dssp             HHTCCGGGCSCCBCCBTTSCTTCBCCGGGGSSSTTCCEEEEECCCTTTSCCCEEEEETTTTEEEETTTTEEECTTSCEEE
T ss_pred             hhccchhhccCcccccccccccccccccccccCCCCeEEEEeCccCCCCeECccCcCCCcCEEEeCCCCCEECCCCeEeC
Confidence            9988888999997            6666654  89999999999999999988 4455579999999999999999999


Q ss_pred             CCCCCCCCCCceEeec-CceEE
Q psy6642         172 GPAPTNMEVPPYQFGD-EGILI  192 (292)
Q Consensus       172 gPa~~~L~~~p~~~~~-d~i~V  192 (292)
                      ||++.+|++|++++++ +.|+|
T Consensus       165 gPa~~~L~~~~~~v~~d~~i~i  186 (187)
T 2qjy_C          165 GPAPENLPIPLAKFIDETTIQL  186 (187)
T ss_dssp             SSCCSCCCBCSEEEEETTEEEE
T ss_pred             CCCCCCCceEEEEEEeCCEEEE
Confidence            9999999999999975 55544

>2nwf_A Ubiquinol-cytochrome C reductase iron-sulfur SUBU; rieske [2Fe-2S] ISP, oxidoreductase; HET: GOL; 1.10A {Rhodobacter sphaeroides} PDB: 2nuk_A 2nve_A 2num_A 2nvg_A 2nvf_A

Probab=100.00  E-value=5.2e-33  Score=233.08  Aligned_cols=123  Identities=48%  Similarity=1.001  Sum_probs=112.8

Q ss_pred             ccceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCC------------ccccccc--CCCeEEEEe
Q psy6642          70 ATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQ------------ADSDRVK--DPSWLVIIG  135 (292)
Q Consensus        70 ~~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~------------~~~~R~~--~g~~~a~~~  135 (292)
                      +.+++|+++|++|++++++|+|+|+||++||++||+....+.+..|+||+            ...+|..  +|+|+|+++
T Consensus         2 ~~~~vd~s~l~~g~~~~v~wrgkPv~i~~rt~~~~~~~~~~~~~~l~Dp~~~~~~~p~~~y~~~~~R~~~~~g~~~a~~~   81 (141)
T 2nwf_A            2 ASIFVDVSSVEPGVQLTVKFLGKPIFIRRRTEADIELGRSVQLGQLVDTNARNANIDAGAEATDQNRTLDEAGEWLVMWG   81 (141)
T ss_dssp             CCEEEECTTCCTTEEEEEEETTEEEEEEECCHHHHHHHHTCCGGGCSCCBCCBTTSCTTCBCCGGGGSSSTTSCEEEEEC
T ss_pred             CCEEEecccCCCCCEEEEEECCEEEEEEECCHHHHhhhhcccccccCCcccccccCCccccccchhccccCCCcEEEEeC
Confidence            46799999999999999999999999999999999999999989999998            5567765  899999999


Q ss_pred             cccCCCcccCC-cCCCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEe-ecCceEE
Q psy6642         136 ICTHLGCVPIA-NAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF-GDEGILI  192 (292)
Q Consensus       136 ~CtHlGc~l~~-~~~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~-~~d~i~V  192 (292)
                      +|||+||+|.+ +.++.+.|+||||||+||++|+++.||++.+|++||+++ +++.|+|
T Consensus        82 ~C~H~G~~l~~~~~~~~~~~~CP~Hgs~Fd~~G~~~~gPa~~~L~~~pv~v~~d~~i~v  140 (141)
T 2nwf_A           82 VCTHLGCVPIGGVSGDFGGWFCPCHGSHWDSAGRIRKGPAPENLPIPLAKFIDETTIQL  140 (141)
T ss_dssp             CCTTTCCCCEEEEETTTTEEEETTTTEEECTTSCEEESSCCSCCCBCSEEESSSSEEEE
T ss_pred             cCCCCCeEccccCccCCCEEEcCCCCCEECCCCCCccCCCCCCCCceeEEEEECCEEEE
Confidence            99999999998 666668999999999999999999999999999999999 6777664

>1rie_A Rieske iron-sulfur protein; oxidoreductase, cytochrome BC1 complex, histidine ligands, rieske iron-sulfur cluster, electron transport; 1.50A {Bos taurus} SCOP: b.33.1.1

Probab=99.97  E-value=6.7e-31  Score=216.87  Aligned_cols=125  Identities=70%  Similarity=1.365  Sum_probs=116.8

Q ss_pred             ccccceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCc
Q psy6642          68 AMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIAN  147 (292)
Q Consensus        68 a~~~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~  147 (292)
                      +.+.+++++++|++|+.+++.|+|+|++|+++++++|....++....++||+...+|..+|+++|++++|||+||+|.++
T Consensus         3 a~~~~~v~~s~l~~G~~~~v~~~g~pv~v~r~~~~~~~~~~~~~~~~l~dp~~~~~r~~~g~~~a~~~~C~H~g~~l~~g   82 (129)
T 1rie_A            3 AMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERVKKPEWVILIGVCTHLGCVPIAN   82 (129)
T ss_dssp             CCSSEEEEGGGSCTTCEEEEEETTEEEEEEECCHHHHHHHHTCCGGGCSSCCCGGGTCSSTTEEEEECCCTTTSCCCEET
T ss_pred             ccCceEeeHHHCCCCCEEEEEECCeEEEEEECCHHHHhhhhccccceecCcccccccccCCeEEEEECccCCCCeecccc
Confidence            45677889999999999999999999999999999999988888899999999999999999999999999999999998


Q ss_pred             CCCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEe-ecCceEE
Q psy6642         148 AGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF-GDEGILI  192 (292)
Q Consensus       148 ~~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~-~~d~i~V  192 (292)
                      ..+++.|.||||||+||++|+++.+|++.+|++||+++ +++.++|
T Consensus        83 ~~~~~~i~CP~Hg~~fd~~G~~~~~P~~~~l~~~~v~v~~~~~v~v  128 (129)
T 1rie_A           83 AGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPSYEFTSDDMVIV  128 (129)
T ss_dssp             CTTTEEEEETTTTEEEETTCCEEESSCCSCCCCCCEEESSSSEEEE
T ss_pred             cCCCCEEEcCCCCCEEcCCCCEeeCCCCCCCCceeEEEEeCCEEEE
Confidence            77778999999999999999999999999999999999 7887765

>1vf5_D Rieske iron-sulfur protein; photosynthesis, membrane protein complex, electron transfer complex; HET: HEM TDS PL9 OPC CLA BCR; 3.00A {Mastigocladus laminosus} SCOP: b.33.1.1 f.23.12.1 PDB: 2d2c_D* 2e74_D* 2e75_D* 2e76_D* 2zt9_D*

Probab=99.95  E-value=2.3e-29  Score=218.48  Aligned_cols=145  Identities=28%  Similarity=0.480  Sum_probs=106.0

Q ss_pred             CcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhhccc-cceee-----------cCCCCCCCeEEEE-EcCee
Q psy6642          27 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMA-TIEVD-----------LNLIPEGQSVTFK-WRGKP   93 (292)
Q Consensus        27 ~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~a~~-~~~v~-----------~s~l~~g~~~~~~-~~g~p   93 (292)
                      +++||+||+.++++++.++   +..++.|++..++|.+...+.+ .+.++           ++++++|+...+. +.|++
T Consensus        12 ~~~RR~Fl~~~~~~~~~~~---~~~~~~p~~~~~~p~~~~~~~~~~v~~d~~g~~i~~~~~~~~l~~g~~~~~~~~~g~~   88 (179)
T 1vf5_D           12 DMGRRQFMNLLAFGTVTGV---ALGALYPLVKYFIPPSGGAVGGGTTAKDKLGNNVKVSKFLESHNAGDRVLVQGLKGDP   88 (179)
T ss_dssp             CCCCCTTSCTTHHHHHHHH---HHHHHHHHHHHHSCCCCSSCCCCCCCCBTTSSCCCHHHHHHCCCTTCCCEESCSSSSC
T ss_pred             CCcHHHHHHHHHHHHHHHH---HHHHHHHHHHHhCCchhhcccCCcEEEccCCCeEehhhcccccCCCceEEEeccCCCe
Confidence            6799999998887554333   3356778888777766543322 11111           2234444443332 33333


Q ss_pred             EEEEeCChhhhhhcccccccccCCCCcccccccCCCe--EEEEecccCCCcccCCcCCCCCeEEcCCCCcEEcCCCceec
Q psy6642          94 LFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSW--LVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRK  171 (292)
Q Consensus        94 v~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~--~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~v~~  171 (292)
                      ++                          ++|..+|++  +|++++|||+||+|.++.. .+.|.||||||+||.+|+++.
T Consensus        89 ~~--------------------------lv~~~~g~~~~~a~~~~CtH~G~~l~~~~~-~~~~~CP~Hgs~Fd~~G~~~~  141 (179)
T 1vf5_D           89 TY--------------------------IVVESKEAIRDYGINAVCTHLGCVVPWNAA-ENKFKCPCHGSQYDETGRVIR  141 (179)
T ss_dssp             EE--------------------------CCBCTTCCBCSCCCBCBCTTTSCBCCBCSS-SSSEECTTTCCEECSSSCCCS
T ss_pred             EE--------------------------EEEECCCcEEEEEEeCccCCCCCCCcccCC-CCEEECCCCCCEECCCCcEec
Confidence            32                          345567876  9999999999999999875 489999999999999999999


Q ss_pred             CCCCCCCCCCceEeecCceEEEeecccCCC
Q psy6642         172 GPAPTNMEVPPYQFGDEGILIRMLAHSDIR  201 (292)
Q Consensus       172 gPa~~~L~~~p~~~~~d~i~V~I~ahtD~~  201 (292)
                      ||++++|++|+++++++.|+|.+|..+|++
T Consensus       142 gPa~~~L~~~~v~v~~g~v~v~~~~~~~~r  171 (179)
T 1vf5_D          142 GPAPLSLALCHATVQDDNIVLTPWTETDFR  171 (179)
T ss_dssp             SSCCSCCBCCCCCCSSSSCCCCCCCCCCTT
T ss_pred             CCCCCCCCeEEEEEECCEEEEEeecCCCCc
Confidence            999999999999999999998888777765

>4aay_B AROB; oxidoreductase, rieske, iron sulfur, molybdopterin; HET: MGD; 2.70A {Rhizobium species}

Probab=99.91  E-value=4.3e-25  Score=191.11  Aligned_cols=105  Identities=15%  Similarity=0.224  Sum_probs=87.5

Q ss_pred             ccccee-ecCCCCCCCeEEEEEcC--eeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccC
Q psy6642          69 MATIEV-DLNLIPEGQSVTFKWRG--KPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPI  145 (292)
Q Consensus        69 ~~~~~v-~~s~l~~g~~~~~~~~g--~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~  145 (292)
                      ..++.+ ++++|++|+.+.+.+.+  .|+++++.++                 ....+|+.+|+++|++++|||+||+|.
T Consensus        49 ~p~~~v~~~~dL~~g~~~~v~~~~~~~pv~v~R~g~-----------------~~~~~r~~~G~v~A~~n~CpH~G~~L~  111 (175)
T 4aay_B           49 YPANRLANISELTLNEPLDVAYPDEDAAGVLLKLGT-----------------RVEGGVGPDGDIVGFSTICPHKGFPLS  111 (175)
T ss_dssp             CCCEEEEEGGGCBBTBCEEEESSSTTSEEEEEECSS-----------------CCTTCBTTTTCEEEEECBCTTTCCBCE
T ss_pred             CCcceEEEHHHCCCCCEEEEEECCCCCEEEEEEccc-----------------ccccccCCCCEEEEEeCCCCCCCCCCc
Confidence            344455 88999999999999964  5888876421                 134577789999999999999999999


Q ss_pred             CcCCCCCeEEcCCCCcEEcCC--CceecCCCCCCCCCCceEee-cCceE
Q psy6642         146 ANAGDWGGYYCPCHGSHYDAS--GRIRKGPAPTNMEVPPYQFG-DEGIL  191 (292)
Q Consensus       146 ~~~~~~~~~~CPcHGs~FD~~--G~v~~gPa~~~L~~~p~~~~-~d~i~  191 (292)
                      ++ .+.+.|.||||||+||++  |+++.+|+.++|+.|+++++ ++.|+
T Consensus       112 ~g-~~~~~i~CP~Hg~~Fd~~~tG~~~~gPa~~~L~~y~v~vd~dG~V~  159 (175)
T 4aay_B          112 YS-ADNKTFNCPGHFSVFDPEKGGQQVWGQATQNLPQYVLRVADNGDIF  159 (175)
T ss_dssp             EE-TTTTEEECTTTCCEEEGGGTTEEEECSCSSCCCBEEEEECTTSEEE
T ss_pred             cC-CCCCEEEcCCCCCEECCCCCceEecCCCCCCcCEEEEEEEcCCEEE
Confidence            98 455899999999999995  99999999999999999994 66654

>1pp9_E Ubiquinol-cytochrome C reductase iron-sulfur SUBU mitochondrial; cytochrome BC1, membrane protein, heme protein, rieske iron protein, cytochrome B, complex III; HET: BHG HEM HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: b.33.1.1 f.23.12.1 PDB: 1bgy_E* 1be3_E* 1l0n_E* 1ntk_E* 1ntm_E* 1ntz_E* 1nu1_E* 1l0l_E* 1ppj_E* 1qcr_E* 1sqb_E* 1sqp_E* 1sqq_E* 1sqv_E* 1sqx_E* 2a06_E* 2fyu_E* 2ybb_E* 1bcc_E* 2bcc_E* ...

Probab=99.91  E-value=3.6e-25  Score=194.84  Aligned_cols=97  Identities=55%  Similarity=0.921  Sum_probs=90.4

Q ss_pred             cccCCCCCCccccccCCCCCCCc----cccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhhhccceEEecCC
Q psy6642         196 AHSDIRTPDFSKYRRDRNPDKGQ----EETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNL  271 (292)
Q Consensus       196 ahtD~~~P~F~~yr~~~~~~~~~----~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~a~~~~evdls~  271 (292)
                      +|||+++|||++||.++++|++.    .+.+||+|+|+++++++++|+++++.+++||+++|+|+++++|++++|+|+++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~RR~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~a~~~v~v~ls~   80 (196)
T 1pp9_E            1 SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMSKIEIKLSD   80 (196)
T ss_dssp             CGGGCCCCCCTTTBCGGGCCTTSCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCHHHHCCCCEEEEGGG
T ss_pred             CCCCcCCCCchHhhcccccCcccccccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcccccccccEEEHHH
Confidence            69999999999999999877642    24569999999999999999999999999999999999999999999999999


Q ss_pred             CCCCceEEEEECCeeeEEEcC
Q psy6642         272 IPEGQSVTFKWRGKPLFIRHR  292 (292)
Q Consensus       272 i~~G~~~~~~WrgkPvfv~~R  292 (292)
                      |+|||.++|+|+||||||+||
T Consensus        81 l~~G~~~~v~~~G~pV~V~r~  101 (196)
T 1pp9_E           81 IPEGKNMAFKWRGKPLFVRHR  101 (196)
T ss_dssp             SCTTCEEEEEETTEEEEEEEC
T ss_pred             CCCCCeEEEEECCEEEEEEEC
Confidence            999999999999999999986

>1nyk_A Rieske iron-sulfur protein; beta barrel, iron sulfur cluster, electron transport; 1.31A {Thermus thermophilus} SCOP: b.33.1.1 PDB: 3fou_A

Probab=99.90  E-value=1.5e-24  Score=186.04  Aligned_cols=121  Identities=21%  Similarity=0.439  Sum_probs=90.4

Q ss_pred             ccceeecCCCCCCCeEEEEEcCeeE--EEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCc
Q psy6642          70 ATIEVDLNLIPEGQSVTFKWRGKPL--FIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIAN  147 (292)
Q Consensus        70 ~~~~v~~s~l~~g~~~~~~~~g~pv--~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~  147 (292)
                      +.+++++++|++|+.+++.|+|+|+  ++.+++..++.....+....+ +|+... |..++ ++|++++|||+||+|+.+
T Consensus        21 ~~~~v~~sdl~~G~~~~~~~~g~p~~~~~r~~~~~~~~~~~~~~p~~~-~~~~~~-~~~~g-v~A~~~~CpH~G~~L~~g   97 (165)
T 1nyk_A           21 EPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEEL-APEVAQ-HAAEG-VVAYSAVCTHLGCIVSQW   97 (165)
T ss_dssp             SCCBCBGGGCCTTSCCEEEEEECTTTCCBCTTSGGGCEEEEECCGGGS-CHHHHT-TCBTT-EEEEECBCTTTCCBCCEE
T ss_pred             CCcEecHHHCCCCCEEEEEeCCCcchhhccCcchhcchheeccChhhc-Cccccc-cccCC-EEEEEeecCCCCeEcccc
Confidence            5678999999999999999999986  333322222111112222223 333322 44454 999999999999999876


Q ss_pred             CCCCCeEEcCCCCcEEcC-CCc-eecCCCCCCCCCCceEeecCceEEE
Q psy6642         148 AGDWGGYYCPCHGSHYDA-SGR-IRKGPAPTNMEVPPYQFGDEGILIR  193 (292)
Q Consensus       148 ~~~~~~~~CPcHGs~FD~-~G~-v~~gPa~~~L~~~p~~~~~d~i~V~  193 (292)
                      ..+.+.|.||||||+||+ +|. ++.||++.+|+.|+++++++.++|.
T Consensus        98 ~~~~~~i~CP~Hgs~Fd~~tG~~~~~gPa~~~L~~~~v~v~~g~V~v~  145 (165)
T 1nyk_A           98 VADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVRVEDGVLVAA  145 (165)
T ss_dssp             EGGGTEEECTTTCCEEEGGGTTEEEESSCSSCCCEECEEEETTEEEEC
T ss_pred             cCCCCEEECCCCCCEEcCCCCCeeecCCCCCCCcEEEEEEECCEEEEE
Confidence            666689999999999999 686 9999999999999999999877664

>3gce_A Ferredoxin component of carbazole 1,9A- dioxygenase; rieske ferredoxin, 2Fe-2S, electron transfer, oxidoreductase; 2.00A {Nocardioides aromaticivorans}

Probab=99.87  E-value=3e-22  Score=162.98  Aligned_cols=94  Identities=17%  Similarity=0.259  Sum_probs=84.8

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCc--CCCC
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIAN--AGDW  151 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~--~~~~  151 (292)
                      ..+++|++|+.+.+.+.|++++|.+                           .+|+++|+++.|||+||+|+++  ..++
T Consensus        15 ~~~~el~~g~~~~~~~~g~~v~v~r---------------------------~~g~~~A~~n~CpH~g~~L~~G~~~~~~   67 (121)
T 3gce_A           15 ATLDQLKPGVPTAFDVDGDEVMVVR---------------------------DGDSVYAISNLCSHAEAYLDMGVFHAES   67 (121)
T ss_dssp             EEGGGSCTTCCEEEEETTEEEEEEE---------------------------ETTEEEEEESBCSSSSCBGGGSEEETTT
T ss_pred             EEHHHCCCCCEEEEEECCEEEEEEE---------------------------ECCEEEEEeCcCCCCCCCCCCCceeecC
Confidence            3689999999999999999988754                           2789999999999999999988  6666


Q ss_pred             CeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         152 GGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       152 ~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      +.|.||||||+||+ +|+++.+|+..+|+.|++++++|.|+|.+
T Consensus        68 ~~i~CP~Hg~~Fdl~tG~~~~~P~~~~L~~~~v~v~~g~V~v~~  111 (121)
T 3gce_A           68 LEIECPLHVGRFDVRTGAPTALPCVLPVRAYDVVVDGTEILVAP  111 (121)
T ss_dssp             TEEECTTTCCEEETTTCCEEETTCCSCCCBCCEEEETTEEEECC
T ss_pred             CEEEcCCCCCEEcCCCccEeCCCCcCCcceEEEEEECCEEEEEE
Confidence            89999999999997 99999999999999999999999887653

>3cx5_E Cytochrome B-C1 complex subunit rieske, mitochondrial; complex III, electron transfer complex, cytochrome BC1 complex, mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces cerevisiae} SCOP: b.33.1.1 f.23.12.1 PDB: 1kb9_E* 1kyo_E* 1p84_E* 2ibz_E* 1ezv_E* 3cxh_E*

Probab=99.87  E-value=1.1e-22  Score=177.54  Aligned_cols=90  Identities=47%  Similarity=0.836  Sum_probs=83.8

Q ss_pred             cCCCCCCccccccCCCCCCCccccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhhhccceEEecCCCCCCce
Q psy6642         198 SDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQS  277 (292)
Q Consensus       198 tD~~~P~F~~yr~~~~~~~~~~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~a~~~~evdls~i~~G~~  277 (292)
                      +|+++|||++||+++.     .+.+||+|||+++++++++|+++++++++||+++|+|+++++|++.++||+++|+||+.
T Consensus         2 ~~~~~~~~~~~~~~~~-----~~~~RR~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~a~~~v~V~~s~l~~G~~   76 (185)
T 3cx5_E            2 STYRTPNFDDVLKENN-----DADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKN   76 (185)
T ss_dssp             CTTSCCCCTTTBCCTT-----CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCGGGCCCCCEEEEGGGCCTTCE
T ss_pred             CCccCCCchhhccCCC-----CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcCCCcchhccCcEEEEHHHCCCCCe
Confidence            7899999999997432     34579999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEECCeeeEEEcC
Q psy6642         278 VTFKWRGKPLFIRHR  292 (292)
Q Consensus       278 ~~~~WrgkPvfv~~R  292 (292)
                      ++|+|+||||||+||
T Consensus        77 ~~v~~~g~pv~v~r~   91 (185)
T 3cx5_E           77 VVVKWQGKPVFIRHR   91 (185)
T ss_dssp             EEEEETTEEEEEEEC
T ss_pred             EEEEECCeEEEEEEC
Confidence            999999999999986

>2qpz_A Naphthalene 1,2-dioxygenase system ferredoxin subunit; rieske ferredoxin, 2Fe-2S, aromatic hydrocarbons catabolism, electron transport, iron; 1.85A {Pseudomonas putida}

Probab=99.87  E-value=5e-22  Score=156.60  Aligned_cols=93  Identities=20%  Similarity=0.316  Sum_probs=84.0

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .+++|++|+.+.+.+.|++++|.+                           .+|+++|+++.|||+||+|+++..+++.+
T Consensus         9 ~~~~l~~g~~~~~~~~g~~i~v~r---------------------------~~g~~~A~~~~CpH~g~~L~~g~~~~~~i   61 (103)
T 2qpz_A            9 ALSDILEGDVLGVTVEGKELALYE---------------------------VEGEIYATDNLCTHGSARMSDGYLEGREI   61 (103)
T ss_dssp             ETTSCCTTCEEEEEETTEEEEEEE---------------------------ETTEEEEEESBCSSSSCBGGGSEEETTEE
T ss_pred             EHHHcCCCCEEEEEECCEEEEEEE---------------------------ECCEEEEECCcCCCCCCCCCCCeEeCCEE
Confidence            679999999999999999987753                           47899999999999999999886566899


Q ss_pred             EcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         155 YCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       155 ~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      .||||||+||+ +|+++.+|+..+|+.|+++++++.++|.+
T Consensus        62 ~Cp~Hg~~Fd~~~G~~~~~P~~~~L~~~~v~~~~g~v~v~~  102 (103)
T 2qpz_A           62 ECPLHQGRFDVCTGKALCAPVTQNIKTYPVKIENLRVMIDL  102 (103)
T ss_dssp             ECTTTTCEEETTTCCEEETTCCSCCCEECEEEETTEEEEEC
T ss_pred             ECCCCCCEEeCCCCCEeCCCCCCCCCEEeEEEECCEEEEEc
Confidence            99999999999 99999999999999999999999888753

>3dqy_A Toluene 1,2-dioxygenase system ferredoxin subunit; rieske, iron-sulfur cluster, 2Fe-2S, aromatic hydrocarbons catabolism, electron transport; 1.20A {Pseudomonas putida} SCOP: b.33.1.0 PDB: 4emj_B*

Probab=99.86  E-value=2.5e-22  Score=159.27  Aligned_cols=93  Identities=16%  Similarity=0.288  Sum_probs=83.8

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      .+++|++|+.+.+.+.|++++|.+                           .+|+++|+++.|||+||+|+++..+++.+
T Consensus         7 ~~~~l~~g~~~~~~~~g~~i~v~r---------------------------~~g~~~A~~~~CpH~g~~L~~g~~~~~~i   59 (106)
T 3dqy_A            7 RQGDLPPGEMQRYEGGPEPVMVCN---------------------------VDGEFFAVQDTCTHGDWALSDGYLDGDIV   59 (106)
T ss_dssp             EGGGSCTTCEEEECCSSSCEEEEE---------------------------ETTEEEEEESBCSSSSCBGGGSEEETTEE
T ss_pred             EHHHCCCCCEEEEEECCEEEEEEE---------------------------ECCEEEEEeCcCCCCCCCCcCcEEeCCEE
Confidence            678999999999999999988753                           37899999999999999999876666899


Q ss_pred             EcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         155 YCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       155 ~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      .||||||+||+ +|+++.+|++.+|+.|++++++|.|+|.+
T Consensus        60 ~Cp~Hg~~Fdl~~G~~~~~P~~~~L~~~~v~~~~g~v~v~~  100 (106)
T 3dqy_A           60 ECTLHFGKFCVRTGKVKALPACKPIKVFPIKVEGDEVHVDL  100 (106)
T ss_dssp             ECTTTCCEEETTTCCEEETTCCSCCCEECEEEETTEEEECG
T ss_pred             ECCCCCCEEeCCCCCEeCCCCCCCccEEEEEEECCEEEEEc
Confidence            99999999997 99999999999999999999999887753

>1fqt_A Rieske-type ferredoxin of biphenyl dioxygenase; 2Fe-2S cluster, beta sandwich, oxido; 1.60A {Burkholderia xenovorans} SCOP: b.33.1.1 PDB: 2e4q_A 2e4p_A 2yvj_B*

Probab=99.86  E-value=1.3e-21  Score=156.62  Aligned_cols=93  Identities=19%  Similarity=0.333  Sum_probs=83.2

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCc-CCCCCe
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIAN-AGDWGG  153 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~-~~~~~~  153 (292)
                      .+++|++|+.+.+.+.|++++|.+                          . +|+++|+++.|||+||+|+.+ ..+++.
T Consensus        11 ~~~~l~~g~~~~~~~~g~~i~v~r--------------------------~-~g~~~A~~n~CpH~g~~L~~g~~~~~~~   63 (112)
T 1fqt_A           11 DRRDVPEGEALKVESGGTSVAIFN--------------------------V-DGELFATQDRCTHGDWSLSDGGYLEGDV   63 (112)
T ss_dssp             EGGGSCTTCEEEEEETTEEEEEEE--------------------------E-TTEEEEEESBCTTSSCBSSTTCCEETTE
T ss_pred             eHHHCCCCCeEEEEECCEEEEEEE--------------------------E-CCEEEEEECCCCCCCcCCCCCCEEcCCE
Confidence            688999999999999999988754                          2 789999999999999999887 555689


Q ss_pred             EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         154 YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       154 ~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      |.||||||+||+ +|+++.+|+..+|+.|+++++++.|+|.+
T Consensus        64 i~CP~Hg~~Fd~~tG~~~~~P~~~~L~~~~v~~~~g~v~v~~  105 (112)
T 1fqt_A           64 VECSLHMGKFCVRTGKVKSPPPCEALKIFPIRIEDNDVLVDF  105 (112)
T ss_dssp             EECTTTCCEEETTTCCEEESSCCSCCCBCCEEEETTEEEECT
T ss_pred             EECCCCCCEEeCCCCcEeCCCCCCCccEEEEEEECCEEEEEe
Confidence            999999999999 99999999999999999999999777653

>2i7f_A Ferredoxin component of dioxygenase; rieske ferredoxin, oxidoreductase; HET: CIT; 1.90A {Sphingobium yanoikuyae}

Probab=99.85  E-value=9.7e-22  Score=156.33  Aligned_cols=93  Identities=23%  Similarity=0.349  Sum_probs=83.0

Q ss_pred             ecCCCCCCCeEEEEEcCee-EEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCe
Q psy6642          75 DLNLIPEGQSVTFKWRGKP-LFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGG  153 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~p-v~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~  153 (292)
                      .+++|++|+.+.+.+.|++ ++|.+                          . +|+++|+++.|||+||+|+++..+++.
T Consensus         9 ~~~~l~~g~~~~~~~~g~~~v~v~r--------------------------~-~g~~~A~~~~CpH~g~~L~~g~~~~~~   61 (108)
T 2i7f_A            9 QVASVKDGEPVAVYQEKMPALAVYN--------------------------V-DGEVFVTDNLCTHGNAMLTDGYQDGTI   61 (108)
T ss_dssp             EGGGCBTTBCEEECCTTSSCEEEEE--------------------------E-TTEEEEEESBCSSSSCBGGGSEEETTE
T ss_pred             EHhHcCCCCeEEEEECCeeEEEEEE--------------------------E-CCEEEEEeCcCCCCCCCCCCCEEeCCE
Confidence            6788999999999888888 87753                          3 789999999999999999987665689


Q ss_pred             EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         154 YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       154 ~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      |.||||||+||+ +|+++.+|+..+|+.|++++++|.|+|.+
T Consensus        62 i~Cp~Hg~~Fdl~tG~~~~~P~~~~L~~~~v~~~~g~v~v~~  103 (108)
T 2i7f_A           62 IECPFHGGSFDIATGAAKAFPCQIPIKTYPVTIEDGWVCIDQ  103 (108)
T ss_dssp             EECSSTTCEEETTTCCBCSTTCCSCCCEECEEEETTEEEEEC
T ss_pred             EEcCCCCCEEeCCCcCEeCCCCCCCccEEeEEEECCEEEEeC
Confidence            999999999998 99999999999999999999999888764

>1g8k_B Arsenite oxidase; molybdopterin, [3Fe-4S] cluster, [2Fe-2S] rieske, oxidoreductase; HET: MGD; 1.64A {Alcaligenes faecalis} SCOP: b.33.1.1 PDB: 1g8j_B*

Probab=99.85  E-value=2.3e-21  Score=160.48  Aligned_cols=105  Identities=18%  Similarity=0.365  Sum_probs=85.0

Q ss_pred             ccee-ecCCCCCCCeEEEEEc--CeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCc
Q psy6642          71 TIEV-DLNLIPEGQSVTFKWR--GKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIAN  147 (292)
Q Consensus        71 ~~~v-~~s~l~~g~~~~~~~~--g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~  147 (292)
                      ++.+ .+++|++|+.+.+.|.  ++++++++.+..+.                 ..+..+|+++|++++|||+||+|++.
T Consensus         8 ~~~v~~~~dl~~g~~~~~~~~~~g~~v~v~r~~~~~~-----------------~~~~~~g~~~A~~n~CpH~g~~L~~~   70 (133)
T 1g8k_B            8 ATAVSVAKNLAANEPVSFTYPDTSSPCVAVKLGAPVP-----------------GGVGPDDDIVAYSVLCTHMGCPTSYD   70 (133)
T ss_dssp             CEEEEEGGGCCBTCCEEEECSSTTSEEEEEECSSCCT-----------------TCBTTTTCEEEEECBCTTTCCBCEEE
T ss_pred             ceeEEEHHHCCCCCeEEEEecCCCceEEEEEcccccc-----------------ccccCCCEEEEEeCcCCCCCCCCCcc
Confidence            3444 7899999999999996  88998876432110                 11235899999999999999999985


Q ss_pred             CCCCCeEEcCCCCcEEcC--CCceecCCCCCCCCCCceEee--cCceEEE
Q psy6642         148 AGDWGGYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPYQFG--DEGILIR  193 (292)
Q Consensus       148 ~~~~~~~~CPcHGs~FD~--~G~v~~gPa~~~L~~~p~~~~--~d~i~V~  193 (292)
                       .+++.|.||||||+||+  +|+++.+|++.+|+.|+++++  ++.++|.
T Consensus        71 -~~~~~i~CP~Hg~~Fd~~~~G~~~~gP~~~~L~~~~v~v~~~g~~V~v~  119 (133)
T 1g8k_B           71 -SSSKTFSCPCHFTEFDAEKAGQMICGEATADLPRVLLRYDAASDALTAV  119 (133)
T ss_dssp             -TTTTEEECTTTCCEEEGGGTTEEEESSCSSCCCEEEEEEETTTTEEEEE
T ss_pred             -cCCCEEECCCCCCEECCCCCCCEEcCCCCCCCCEEEEEEECCCCEEEEE
Confidence             34589999999999999  899999999999999999998  4546554

>1vm9_A Toluene-4-monooxygenase system protein C; structural genomics, CESG, protein structure initiative, PSI, ferredoxin, FES, [2Fe-2S] cluster; 1.48A {Pseudomonas mendocina} SCOP: b.33.1.1 PDB: 2q3w_A 1sjg_A

Probab=99.85  E-value=1.9e-21  Score=155.39  Aligned_cols=101  Identities=17%  Similarity=0.237  Sum_probs=85.7

Q ss_pred             ecCCCCCCCeEEEEE-cCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCe
Q psy6642          75 DLNLIPEGQSVTFKW-RGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGG  153 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~-~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~  153 (292)
                      .+++|++|+.+.+.+ .|++++|.+                          ..+|+++|+++.|||+||+|.++..+++.
T Consensus         7 ~~~~l~~g~~~~~~~~~g~~v~v~r--------------------------~~~g~~~A~~~~CpH~g~~L~~g~~~~~~   60 (111)
T 1vm9_A            7 SLDDIWVGEMETFETSDGTEVLIVN--------------------------SEEHGVKAYQAMCPHQEILLSEGSYEGGV   60 (111)
T ss_dssp             EGGGSCTTCEEEEECTTCCEEEEEE--------------------------ETTTEEEEEESBCSSSSCBGGGSEEETTE
T ss_pred             EHHHCCCCCeEEEEEcCCCEEEEEE--------------------------eCCCeEEEEeCcCCCCCcCCCCceEcCCE
Confidence            578999999999999 888887754                          34799999999999999999987655689


Q ss_pred             EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEeecccCCCCCCcc
Q psy6642         154 YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPDFS  206 (292)
Q Consensus       154 ~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~  206 (292)
                      |.||||||+||+ +|+++. |+..+|+.|+++++++.|+|.+    +...|.|+
T Consensus        61 i~Cp~Hg~~Fd~~tG~~~~-p~~~~L~~~~v~~~~g~v~v~~----~~~~~~~~  109 (111)
T 1vm9_A           61 ITCRAHLWTFNDGTGHGIN-PDDAALAEYPVEVKGDDIYVST----KGILPNKA  109 (111)
T ss_dssp             EECTTTCCEEETTTCBBSS-SSSCBCCEECEEEETTEEEECC----TTCCCCCC
T ss_pred             EEcCCCCCEEeCCCccCCC-CCcCCcCEEEEEEECCEEEEec----cCcCCCcc
Confidence            999999999999 699998 9999999999999998777653    33445554

>2de6_D Ferredoxin component of carbazole; electron transfer complex, rieske non-heme iron oxygenase system, terminal oxygenase; 1.80A {Pseudomonas resinovorans} PDB: 2de5_D 1vck_A 2de7_D*

Probab=99.84  E-value=3.7e-21  Score=155.05  Aligned_cols=93  Identities=17%  Similarity=0.243  Sum_probs=84.0

Q ss_pred             ecCCCCCCCeEEEEEcCe-eEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCe
Q psy6642          75 DLNLIPEGQSVTFKWRGK-PLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGG  153 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~-pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~  153 (292)
                      .+++|++|+.+.+.+.|+ +++|.+                          . +|+++|+++.|||+||+|+++..+++.
T Consensus        10 ~~~el~~g~~~~~~~~g~~~v~v~r--------------------------~-~g~~~A~~n~CpH~g~~L~~g~~~~~~   62 (115)
T 2de6_D           10 AASDMQPGTIRRVNRVGAAPLAVYR--------------------------V-GDQFYATEDTCTHGIASLSEGTLDGDV   62 (115)
T ss_dssp             EGGGCCTTEEEEEEETTEEEEEEEE--------------------------E-TTEEEEEESBCTTSSCBGGGSEEETTE
T ss_pred             EHHHCCCCCeEEEEECCccEEEEEE--------------------------E-CCEEEEEeCCCCCCCCCCcCCEEeCCE
Confidence            678999999999999999 888754                          2 789999999999999999987665689


Q ss_pred             EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         154 YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       154 ~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      |.||||||+||+ +|+++.+|+..+|+.|++++++|.|+|.+
T Consensus        63 i~CP~Hg~~Fdl~tG~~~~~P~~~~L~~~~v~~~~g~V~v~~  104 (115)
T 2de6_D           63 IECPFHGGAFNVCTGMPASSPCTVPLGVFEVEVKEGEVYVAG  104 (115)
T ss_dssp             EECTTTCCEEETTTCCEEETTCCSCCCEEEEEESSSEEEEEE
T ss_pred             EECCCCCCEEcCCCcCEeCCCCcCCCCEEEEEEECCEEEEec
Confidence            999999999998 99999999999999999999999888775

>1rfs_A Rieske protein; iron-sulfur protein, electron transport; 1.83A {Spinacia oleracea} SCOP: b.33.1.1 PDB: 1q90_C*

Probab=99.83  E-value=7.4e-21  Score=158.69  Aligned_cols=97  Identities=31%  Similarity=0.646  Sum_probs=81.1

Q ss_pred             cCCCCCCCeEEEE-EcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCe--EEEEecccCCCcccCCcCCCCC
Q psy6642          76 LNLIPEGQSVTFK-WRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSW--LVIIGICTHLGCVPIANAGDWG  152 (292)
Q Consensus        76 ~s~l~~g~~~~~~-~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~--~a~~~~CtHlGc~l~~~~~~~~  152 (292)
                      +++|++|+.+.+. +.+.++++++                          ..+|++  +|++++|||+||+|.++.. .+
T Consensus        29 ~~dlp~g~~~~~~~~~g~~~ilv~--------------------------~~~G~i~~~A~~n~CpH~g~~L~~g~~-~~   81 (139)
T 1rfs_A           29 LKTHAPGDRTLTQGLKGDPTYLVV--------------------------ESDKTLATFGINAVCTHLGCVVPFNAA-EN   81 (139)
T ss_dssp             HHHSCTTCEEEEECGGGCEEEEEB--------------------------CTTSSBCSEEEECBCTTTCCBCCEETT-TT
T ss_pred             HhhCCCCccEEEEecCCCeEEEEE--------------------------eCCCcEEEEEEeCcCCCCCCCCccCCC-CC
Confidence            5678999888776 3566655433                          247888  9999999999999998764 48


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCCCCCCCceEeecCceEEEeecccC
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSD  199 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~d~i~V~I~ahtD  199 (292)
                      .|.||||||+||.+|+++.+|++++|+.|+++++++.|+|.++...+
T Consensus        82 ~i~CP~Hg~~Fd~tG~~~~~P~~~~L~~~~v~v~~g~V~V~~~~~~~  128 (139)
T 1rfs_A           82 KFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETD  128 (139)
T ss_dssp             EEECTTTCCEEETTCCEEESSCCSCCCEEEEEEETTEEEEEECCSCC
T ss_pred             EEEcCCCCCEECCCCCCccCCCCCCCCEEEEEEECCEEEEEeCCccc
Confidence            99999999999999999999999999999999999999888654433

>1jm1_A Rieske iron-sulfur protein SOXF; electron transport, respiratory chain, oxidoreductase; 1.11A {Sulfolobus acidocaldarius} SCOP: b.33.1.1

Probab=99.82  E-value=2.3e-21  Score=171.44  Aligned_cols=91  Identities=25%  Similarity=0.474  Sum_probs=72.8

Q ss_pred             ccCCCCccccccc------------CCCeEEEEecccCCCcccCCcC-----------CCCCeEEcCCCCcEEcCC--Cc
Q psy6642         114 QLRDPQADSDRVK------------DPSWLVIIGICTHLGCVPIANA-----------GDWGGYYCPCHGSHYDAS--GR  168 (292)
Q Consensus       114 ~l~dp~~~~~R~~------------~g~~~a~~~~CtHlGc~l~~~~-----------~~~~~~~CPcHGs~FD~~--G~  168 (292)
                      .+.++++.++|..            +|+++|++++|||+||+|+++.           .+.+.|.||||||+||++  |+
T Consensus        59 ~v~~~~i~v~r~~~~~~r~~ggvg~~g~i~A~~n~CpH~G~~L~~g~~~p~~~~~~~~~~~~~i~CP~Hgs~FDl~tGG~  138 (204)
T 1jm1_A           59 EIPNPYYGKYAGPLGQIQTIKGVGPNGTIFAFSDVCVHLGCQLPAQVIVSSESDPGLYAKGADLHCPCHGSIYALKDGGV  138 (204)
T ss_dssp             EEECTTTTSSCTTGGGCCEEECBTTTTCEEEEESBCTTTCCBCCTTEEESSTTSSEEETTTTEEECTTTCCEEEGGGTSE
T ss_pred             eeCCceEEEEecCccccccccccccCCEEEEEeCcCCCCCcCccccccccccccccccCCCCEEECCCCCCEEeCCCCCe
Confidence            3556666666665            7999999999999999998762           345899999999999995  69


Q ss_pred             eecCCCCCCCCCCceEee--cCceEEEeecccCCCCCCccccc
Q psy6642         169 IRKGPAPTNMEVPPYQFG--DEGILIRMLAHSDIRTPDFSKYR  209 (292)
Q Consensus       169 v~~gPa~~~L~~~p~~~~--~d~i~V~I~ahtD~~~P~F~~yr  209 (292)
                      ++.+|++.+|+.++++++  +|.+++.-     ..-|+|.+..
T Consensus       139 v~~gPa~~~L~~~~v~v~~~~g~v~v~g-----~~~p~~~~~~  176 (204)
T 1jm1_A          139 VVSGPAPRPLPIVILDYDSSTGDIYAVG-----TNAPYFSAGI  176 (204)
T ss_dssp             EEESSCCSCCCBEEEEECTTTCEEEEEE-----ESSCCCCSSS
T ss_pred             EecCCCCCCCCeEeeEEEecCCEEEEEe-----CCCCChhhcc
Confidence            999999999999999998  67666542     1246777755

>3c0d_A Putative nitrite reductase NADPH (small subunit) oxidoreductase protein; NESG, VPR162, Q87HB1, XRAY, structure; 2.40A {Vibrio parahaemolyticus rimd 2210633} SCOP: b.33.1.3

Probab=99.80  E-value=4.4e-20  Score=149.61  Aligned_cols=93  Identities=12%  Similarity=-0.010  Sum_probs=80.7

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCc-ccCCcCCCC--
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGC-VPIANAGDW--  151 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc-~l~~~~~~~--  151 (292)
                      .+++|++|+.+.+.+.|.+++|.+                          ..+|+++|+++.|||+|| +|+.+..++  
T Consensus        11 ~~~el~~g~~~~~~~~g~~v~v~r--------------------------~~~G~~~A~~n~CpH~g~~~L~~G~~~~~~   64 (119)
T 3c0d_A           11 QLDDLMPFIGATVLIEGERVALFY--------------------------IPDSGVYAVQDWDPIGKAYVMSRGIVGDIN   64 (119)
T ss_dssp             EGGGSCBTCCEEEEETTEEEEEEE--------------------------ETTTEEEEEESEETTTTEECGGGSEEEESS
T ss_pred             EHHHCCCCCeEEEEECCeEEEEEE--------------------------ecCCeEEEEeCCCCCCCCccCCCeEEcCCC
Confidence            678999999999999999987754                          347899999999999999 798765332  


Q ss_pred             --CeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         152 --GGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       152 --~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                        ..|.||||||+||+ +|+++.+|+ .+|+.|++++++|.|+|.+
T Consensus        65 g~~~i~CP~Hg~~Fdl~tG~~~~~P~-~~l~~~~v~v~~g~V~v~~  109 (119)
T 3c0d_A           65 GEMCVASPLYKQHFSLKSGQCLEDEA-HCLKTWRVTVDDNQVCYLA  109 (119)
T ss_dssp             SSEEEECTTTCCEEETTTCBBSSCTT-CBCCEECEEESSSEEEEEC
T ss_pred             CCeEEECCCCCCEEECCCCcCCCCCC-ceeeEEEEEEECCEEEEEe
Confidence              28999999999999 999999998 7999999999999888764

>2jo6_A Nitrite reductase [NAD(P)H] small subunit; all beta, ISP domain, rieske iron-sulfur protein, 3-layer sandwich, structural genomics, PSI-2; NMR {Escherichia coli} SCOP: b.33.1.3

Probab=99.80  E-value=9.1e-20  Score=146.02  Aligned_cols=93  Identities=11%  Similarity=-0.010  Sum_probs=80.3

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCC-CeEEEEecccCCCc-ccCCcCCC--
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDP-SWLVIIGICTHLGC-VPIANAGD--  150 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g-~~~a~~~~CtHlGc-~l~~~~~~--  150 (292)
                      .+++|++|+.+.+.+.|.+++|.+                          ..+| +++|++|.|||+|| +|+.+..+  
T Consensus        12 ~~~el~~g~~~~~~~~g~~i~v~r--------------------------~~~g~~~~A~~n~CpH~g~~~L~~G~~~~~   65 (113)
T 2jo6_A           12 KIDDILPETGVCALLGDEQVAIFR--------------------------PYHSDQVFAISNIDPFFESSVLSRGLIAEH   65 (113)
T ss_dssp             ETTTSCTTEEEEEEETTEEEEEEE--------------------------CSSSSCCEEEESSCSSSCCSCSTTSEEEEE
T ss_pred             eHHHCCCCCeEEEEECCEEEEEEE--------------------------ECCCCEEEEEeCcCCCCCCcccCCeEEecc
Confidence            679999999999999999987754                          3478 59999999999999 79876532  


Q ss_pred             -CC-eEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         151 -WG-GYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       151 -~~-~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                       +. .+.||||||+||+ +|+++.+|+ .+|+.||++++++.|+|.+
T Consensus        66 ~g~~~i~CP~Hg~~Fd~~tG~~~~~P~-~~l~~~~v~v~~g~V~v~~  111 (113)
T 2jo6_A           66 QGELWVASPLKKQRFRLSDGLCMEDEQ-FSVKHYEARVKDGVVQLRG  111 (113)
T ss_dssp             TTEEEEEETTTTEEEETTTTEETTTTT-TCCCEEEEEEETTEEEEEC
T ss_pred             CCCcEEECCCCCCEEeCCCccCCCCCc-ccccEEeEEEECCEEEEEc
Confidence             22 7999999999999 999999998 8899999999999888764

>2jza_A Nitrite reductase [NAD(P)H] small subunit; ISP domain, rieske iron-sulfur protein, 3-layer beta- sandwich; NMR {Pectobacterium atrosepticum SCRI1043} SCOP: b.33.1.3

Probab=99.79  E-value=2.3e-19  Score=147.69  Aligned_cols=105  Identities=11%  Similarity=0.009  Sum_probs=85.9

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCC-CeEEEEecccCCCcc-cCCcCCC--
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDP-SWLVIIGICTHLGCV-PIANAGD--  150 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g-~~~a~~~~CtHlGc~-l~~~~~~--  150 (292)
                      .+++|++|+.+.+.+.|++++|.+                          ..+| +++|++|.|||+||. |+.+..+  
T Consensus         9 ~~~el~~g~~~~~~~~g~~i~v~r--------------------------~~~g~~v~A~~n~CpH~g~~~L~~G~~~~~   62 (130)
T 2jza_A            9 KLDDILPGTGVCALVEQQQIAVFR--------------------------PRNDEQVYAISNIDPFAQASVLSRGIVAEH   62 (130)
T ss_dssp             ETTTSCTTBCCEEEETTEEEEEEB--------------------------CSSSSCCEEEBCCCTTTSSGGGTSSEEEES
T ss_pred             EHHHCCCCCeEEEEECCcEEEEEE--------------------------ECCCCEEEEEeCcCCCCCCCcCCCccCccc
Confidence            678999999999999999887753                          3356 899999999999995 9877432  


Q ss_pred             -C-CeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEeecccCCCCCCcccccc
Q psy6642         151 -W-GGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRR  210 (292)
Q Consensus       151 -~-~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr~  210 (292)
                       + ..|.||||||+||+ +|+++.+|+ .+|+.|+++++++.|+|.+    +...+.+++|..
T Consensus        63 ~g~~~i~CP~Hg~~Fdl~tG~~~~~P~-~~L~~~~v~v~~g~V~V~~----~~~~~~~~~~~~  120 (130)
T 2jza_A           63 QDDLWVASPLKKQHFRLYDGFCLEDGA-YSVAAYDTQVTNGNVQISI----ADSDVAVDNSQP  120 (130)
T ss_dssp             SSSEEEECSSSCCEEETTTCCBSSCCS-SCCBCCCEEESSSEEEEEC----CCCCCCCCCCCC
T ss_pred             CCCeEEECCCCCCEEeCCCcCCCCCCc-CcceEEEEEEECCEEEEEe----CCCCCCcccccc
Confidence             2 38999999999999 999999998 8899999999999888764    333455666654

>3azc_A Cytochrome B6-F complex iron-sulfur subunit; rieske, thermosynechococcus elongatu photosynthesis, electron transport; 2.00A {Thermosynechococcus elongatus}

Probab=99.63  E-value=2.8e-20  Score=154.18  Aligned_cols=75  Identities=33%  Similarity=0.707  Sum_probs=66.9

Q ss_pred             cCCC--eEEEEecccCCCcccCCcCCCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEe-ecCceEEEeecccCCC
Q psy6642         126 KDPS--WLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQF-GDEGILIRMLAHSDIR  201 (292)
Q Consensus       126 ~~g~--~~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~-~~d~i~V~I~ahtD~~  201 (292)
                      .+|+  ++|+++.|||+||+|.++. +.+.|.||||||+||.+|+++.+|+..+|+.|++++ +++.|+|..+...|++
T Consensus        48 ~~G~~~v~A~~n~CpH~g~~L~~g~-~~~~i~CP~Hg~~Fd~tG~~~~~P~~~~L~~ypv~v~~~g~V~V~~~~e~d~~  125 (133)
T 3azc_A           48 EDHQIANYGLNAVCTHLGCVVPWNV-SENKFICPCHGSQYDSTGKVVRGPAPLSLALVKATVTEDDKLVFTPWTEIDFR  125 (133)
Confidence            4677  9999999999999999886 457899999999999999999999999999999999 9999998876665544

>4aiv_A Probable nitrite reductase [NAD(P)H] small subuni; oxidoreductase, nitrite metabolism; 2.00A {Mycobacterium tuberculosis}

Probab=99.75  E-value=1.8e-18  Score=140.55  Aligned_cols=94  Identities=14%  Similarity=0.153  Sum_probs=75.7

Q ss_pred             eecCCCCCCCeEEEEE-cCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCC---
Q psy6642          74 VDLNLIPEGQSVTFKW-RGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAG---  149 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~-~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~---  149 (292)
                      ..+++|++|+.+.+.. .|+++.|.                          |..+|+++|++|.|||+|++|..+..   
T Consensus        14 c~~~dL~~g~~~~~~~~~G~~v~l~--------------------------r~~dG~v~A~~n~CpH~ga~L~~~~~~~~   67 (119)
T 4aiv_A           14 CAYDHLIPGRGVGVLLDDGSQVALF--------------------------RLDDGSVHAVGNVDPFSGAAVMSRGIVGD   67 (119)
T ss_dssp             EEGGGSCTTCCEEEECTTSCEEEEE--------------------------ECTTSCEEEEESBCTTTCCBCGGGSEEEE
T ss_pred             eEHHHcCCCCceEEEEcCCcEEEEE--------------------------EcCCCeEEEEECCCCCCCCccccCceecc
Confidence            3678999998887776 46777664                          34579999999999999999876542   


Q ss_pred             --CCCeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeec-CceEEEe
Q psy6642         150 --DWGGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGD-EGILIRM  194 (292)
Q Consensus       150 --~~~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~-d~i~V~I  194 (292)
                        +...+.||+|||+||+ +|+|+.+|+ .+|+.||+++++ +.|+|..
T Consensus        68 ~~~~~~i~CP~Hg~~Fdl~tG~~~~~p~-~~l~~ypv~ve~dG~V~V~~  115 (119)
T 4aiv_A           68 RGGRAMVQSPILKQAFALDDGSCLDDPR-VSVPVYPARVTPEGRIQVAR  115 (119)
T ss_dssp             ETTEEEEECTTTCCEEETTTCBBSSCTT-CBCCEECEEECTTSEEEEEE
T ss_pred             ccCCCEEECCCCCCEEeCCCCcCcCCCC-CccceEEEEEEeCCEEEEec
Confidence              1235899999999998 999999887 589999999984 5677653

>3d89_A Rieske domain-containing protein; CAsp target, rieske ferredoxin, [2Fe-2S] cluster, protein ST initiative, PSI; 2.07A {Mus musculus}

Probab=99.69  E-value=8e-18  Score=142.50  Aligned_cols=93  Identities=14%  Similarity=0.142  Sum_probs=76.0

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCC---
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDW---  151 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~---  151 (292)
                      .+++|++|+.+.+.+.|.+++|.+                           .+|+++|++|.|||+||+|+++..++   
T Consensus        22 ~~~el~~g~~~~~~~~g~~i~v~r---------------------------~~G~v~A~~n~CpH~g~~L~~G~~~~~~g   74 (157)
T 3d89_A           22 REEDIRKSERMTAVVHDREVVIFY---------------------------HKGEYHAMDIRCYHSGGPLHLGEIEDFNG   74 (157)
T ss_dssp             EHHHHHHHSEEEEEETTEEEEEEE---------------------------ETTEEEEEESBCTTTCCBGGGSEEEEETT
T ss_pred             EHHHCCCCCeEEEEECCEEEEEEE---------------------------ECCEEEEEeCCCCCCCCCCcCCEecCcCC
Confidence            567888888888888888887653                           37899999999999999999875432   


Q ss_pred             -CeEEcCCCCcEEcC-CCceec---CC----CC-------CCCCCCceEeecCceEEEe
Q psy6642         152 -GGYYCPCHGSHYDA-SGRIRK---GP----AP-------TNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       152 -~~~~CPcHGs~FD~-~G~v~~---gP----a~-------~~L~~~p~~~~~d~i~V~I  194 (292)
                       +.|.||||||+||+ +|+++.   +|    +.       ..|+.|++++++|.|+|.+
T Consensus        75 ~~~i~CP~Hgw~Fdl~tG~~~~~~i~P~~~~~~~~~~~~~~~L~~~~v~v~~G~V~V~~  133 (157)
T 3d89_A           75 QSCIVCPWHKYKITLATGEGLYQSINPKDPSAKPKWCSKGVKQRIHTVKVDNGNIYVTL  133 (157)
T ss_dssp             EEEEECTTTCCEEETTTCEEEEEECCCC-----CEEEEEEECSCEEEEEEETTEEEEEC
T ss_pred             CCEEECCCCCCEEecCCcCEEEeccCCCccccccccccccCcceEEEEEEECCEEEEEe
Confidence             58999999999999 999985   24    21       4789999999999888765

>2qjy_C Ubiquinol-cytochrome C reductase iron-sulfur SUBU; cytochrome B, 8 TM helixces cytochrome C1, 1 C-TERM TM helix 1 N-TERM TM helix; HET: BGL HEM SMA LOP UQ2; 2.40A {Rhodobacter sphaeroides} PDB: 2fyn_C* 2qjk_C* 2qjp_C* 1zrt_E* 2yiu_C*

Probab=99.69  E-value=1.4e-17  Score=145.35  Aligned_cols=70  Identities=39%  Similarity=0.625  Sum_probs=62.8

Q ss_pred             ccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhhhccceEEecCCCCCCceEEEEECCeeeEEEcC
Q psy6642         220 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR  292 (292)
Q Consensus       220 ~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~a~~~~evdls~i~~G~~~~~~WrgkPvfv~~R  292 (292)
                      +.+||+|||++++++++++   ++++++||+++|+|+++++|+++++||+++|++||.++|+|+||||||+||
T Consensus         8 ~~~RR~Fl~~~~~~~~~~~---a~~~~~p~v~~~~p~~~~~a~~~v~v~ls~l~~G~~~~v~~~g~pv~i~rr   77 (187)
T 2qjy_C            8 AGTRRDFLYYATAGAGAVA---TGAAVWPLINQMNPSADVQALASIFVDVSSVEPGVQLTVKFLGKPIFIRRR   77 (187)
T ss_dssp             -CHHHHHHHHHHHHHHHHH---HHHHHHHHHHTTSCCTTTSCCCCEEEECTTCCTTEEEEEEETTEEEEEEEC
T ss_pred             CCcHHHHHHHHHHHHHHHH---HHHHHHHHHHhcCCchhhcccccEEEEHHHCCCCCeEEEEECCEEEEEEEC
Confidence            4579999999887766555   457899999999999999999999999999999999999999999999986

>2zyl_A Possible oxidoreductase; KSHA, cholesterol, rieske; 2.30A {Mycobacterium tuberculosis}

Probab=99.69  E-value=9.1e-17  Score=154.17  Aligned_cols=112  Identities=16%  Similarity=0.199  Sum_probs=90.0

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      ..++|++|+.+.+.+.|.+++|.                          |+.+|+++|+.+.|||+||+|+.+.++++.|
T Consensus        31 ~~~el~~g~~~~~~~~g~~vvl~--------------------------R~~~G~v~a~~n~CpHrga~L~~g~~~~~~i   84 (386)
T 2zyl_A           31 VAKDYLEGKPHGVEAFGTKLVVF--------------------------ADSHGDLKVLDGYCRHMGGDLSEGTVKGDEV   84 (386)
T ss_dssp             EGGGGCSSSCEEEEETTEEEEEE--------------------------ECTTSCEEEEESBCTTTCCBGGGSEEETTEE
T ss_pred             EHHHCCCCCeEEEEECCeEEEEE--------------------------ECCCCCEEEEcCcCCCCCCCCCCCcccCCEE
Confidence            56888889999999999988764                          3458999999999999999999887767899


Q ss_pred             EcCCCCcEEcCCCceecCCCC------CCCCCCceEeecCceEEEeecccC-----CCCCCccccccCC
Q psy6642         155 YCPCHGSHYDASGRIRKGPAP------TNMEVPPYQFGDEGILIRMLAHSD-----IRTPDFSKYRRDR  212 (292)
Q Consensus       155 ~CPcHGs~FD~~G~v~~gPa~------~~L~~~p~~~~~d~i~V~I~ahtD-----~~~P~F~~yr~~~  212 (292)
                      .||||||+||.+|+|+.+|+.      ..|+.||+++.+|.|+|.+-....     ...|+++.|..+.
T Consensus        85 ~CpyHgw~f~~~G~~~~~P~~~~~~~~~~l~~~~v~~~~G~v~v~~~~~~~~~~~~~~~p~~~~~~~~~  153 (386)
T 2zyl_A           85 ACPFHDWRWGGDGRCKLVPYARRTPRMARTRSWTTDVRSGLLFVWHDHEGNPPDPAVRIPEIPEAASDE  153 (386)
T ss_dssp             ECTTTCCEEETTSBEEECTTCSSCCTTCBCCEECEEEETTEEEEEECTTCCCCCGGGCCCCCGGGGCTT
T ss_pred             EeCCCCCEECCCCCccccCcccccCcccCcceEeEEEECCEEEEEECCccCCCcccccCcccccccCCC
Confidence            999999999999999999873      468899999999988877632211     2356666665443

>3gke_A DDMC; rieske cluster, non-heme mononuclear iron, oxygenase, oxidoreductase; 1.75A {Stenotrophomonas maltophilia} PDB: 3gb4_A 3gl0_A* 3gl2_A* 3gob_A* 3gte_A 3gts_A*

Probab=99.68  E-value=6.7e-17  Score=153.10  Aligned_cols=109  Identities=21%  Similarity=0.213  Sum_probs=88.0

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCeE
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGGY  154 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~  154 (292)
                      ..++| +|+.+.+.+.|.+++|.+                          ..+|+++|+.|.|||+||+|+.+.++++.|
T Consensus        14 ~~~el-~g~~~~~~~~g~~vvv~R--------------------------~~~G~v~a~~n~CpHrg~~L~~G~~~~~~i   66 (349)
T 3gke_A           14 LPEEL-SEKPLGRTILDTPLALYR--------------------------QPDGVVAALLDICPHRFAPLSDGILVNGHL   66 (349)
T ss_dssp             CGGGC-CSSCEEEEETTEEEEEEE--------------------------CTTSCEEEEESSCTTTCCCGGGCEEETTEE
T ss_pred             EHHHC-CCCeEEEEECCEEEEEEE--------------------------cCCCcEEEEeCcCCCCCcCCccCCccceEE
Confidence            46788 899999999999987753                          458999999999999999999987777899


Q ss_pred             EcCCCCcEEcCCCceecCCC-------CCCCCCCceEeecCceEEEeeccc--CC-CCCCcccccc
Q psy6642         155 YCPCHGSHYDASGRIRKGPA-------PTNMEVPPYQFGDEGILIRMLAHS--DI-RTPDFSKYRR  210 (292)
Q Consensus       155 ~CPcHGs~FD~~G~v~~gPa-------~~~L~~~p~~~~~d~i~V~I~aht--D~-~~P~F~~yr~  210 (292)
                      .||||||+||.+|+|+.+|.       ...|+.||+++.+|.|+|.+....  +. ..|+|+.+..
T Consensus        67 ~CpyHgw~fd~~G~~~~~P~~~~~~~~~~~l~~~~v~~~~G~V~v~~~~~~~~~~~~~p~~~~~~~  132 (349)
T 3gke_A           67 QCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVD  132 (349)
T ss_dssp             ECTTTCCEECTTCCEEECCSTTCCCCGGGCCCBCCEEEETTEEEECCSCGGGCCGGGSCCCGGGGC
T ss_pred             EECCCCCEEcCCCCccccCccccccccccccceeeEEEECCEEEEeeCCCCCCcccccCCccccCC
Confidence            99999999999999999983       457899999999987776653322  11 2577765443

>3gkq_A Terminal oxygenase component of carbazole 1,9A- dioxygenase; rieske nonheme iron oxygenase, electron transfer, putidaredoxin-type ferredoxin; 2.10A {Sphingomonas}

Probab=99.65  E-value=5.6e-16  Score=148.56  Aligned_cols=109  Identities=16%  Similarity=0.154  Sum_probs=88.7

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC--CCC
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA--GDW  151 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~--~~~  151 (292)
                      ...++|++|+.+.+.+.|.+++|.                          | .+|+++|+.|.|||+||+|+.+.  +++
T Consensus        36 ~~~~ELp~G~~~~v~i~G~~VvV~--------------------------R-~dG~v~A~~N~CpHRGa~Ls~G~~~~~~   88 (389)
T 3gkq_A           36 RLSAEVAEASPVPVQLLGEKVLLN--------------------------R-VDGVVHAIADRCLHRGVTLSDKVECYSK   88 (389)
T ss_dssp             EEGGGSCBTCCEEEEETTEEEEEE--------------------------E-ETTEEEEEESSCTTTCCCGGGGCCCSBT
T ss_pred             EEHHHCCCCCeEEEEECCEEEEEE--------------------------E-eCCeEEEeCCcCCCCCCCccCCcccCcC
Confidence            367899999999999999998764                          3 47999999999999999999885  356


Q ss_pred             CeEEcCCCCcEEcC-CCceecCCC--------CCCCCCCceEeecCceEEEeecccCCCCCCccccccCC
Q psy6642         152 GGYYCPCHGSHYDA-SGRIRKGPA--------PTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRRDR  212 (292)
Q Consensus       152 ~~~~CPcHGs~FD~-~G~v~~gPa--------~~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr~~~  212 (292)
                      +.|.||||||+||+ +|+|+..|+        ..+|..|++++.+|.|+|.+.   |...|.+.++..+.
T Consensus        89 ~~I~CPyHGW~Fdl~dG~cv~iP~~P~~~~~~~~~L~~ypV~e~~G~VfV~lg---d~~~ppL~e~l~~~  155 (389)
T 3gkq_A           89 ATISCWYHGWTYRWDNGKLVDILTNPTSVQIGRHALKTYPVREEKGLVFLFVG---DQEPHDLAEDVPPG  155 (389)
T ss_dssp             TEEECTTTCEEEETTTCBEEEETTCTTCTTTTSCBCCBCCEEEETTEEEEEES---SSCCCCGGGGSCTT
T ss_pred             CEEECCCCCCEEECCCCCeecccCCcccccccccCCcEEEEEEECCeEEEecC---CCCCCCchhhcchh
Confidence            89999999999999 999998664        357899999999998877652   33346677665543

>3gcf_A Terminal oxygenase component of carbazole 1,9A- dioxygenase; rieske oxygenase, 2Fe-2S, electron transfer, oxidoreductase; 2.30A {Nocardioides aromaticivorans}

Probab=99.64  E-value=6.4e-16  Score=148.45  Aligned_cols=107  Identities=21%  Similarity=0.225  Sum_probs=87.3

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC--CCCC
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA--GDWG  152 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~--~~~~  152 (292)
                      ..++|++|+.+.+.+.|.+++|.                          | .+|+++|+.|.|||+||+|+.+.  ++++
T Consensus        40 ~~~ELp~G~~~~v~i~G~~VvV~--------------------------R-~dG~v~A~~N~CpHRGa~Ls~G~~~~~~~   92 (394)
T 3gcf_A           40 FDHELAEGEFVAVTMLGEKVLLT--------------------------R-AKGEVKAIADGCAHRGVPFSKEPLCFKAG   92 (394)
T ss_dssp             EGGGCCBTCEEEEEETTEEEEEE--------------------------E-ETTEEEEEESSCTTTCCCGGGSCBCSSTT
T ss_pred             EHHHCCCCCeEEEEECCEEEEEE--------------------------E-eCCeEEEeeCcCCCCCCCCcCCcccCcCC
Confidence            67899999999999999998764                          3 47999999999999999999875  3568


Q ss_pred             eEEcCCCCcEEcC-CCceecCCC--------CCCCCCCceEeecCceEEEeecccCCCCCCccccccC
Q psy6642         153 GYYCPCHGSHYDA-SGRIRKGPA--------PTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRRD  211 (292)
Q Consensus       153 ~~~CPcHGs~FD~-~G~v~~gPa--------~~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr~~  211 (292)
                      .|.||||||+||+ +|+|+.+|+        ...|+.|++++.+|.|+|.+.   |...|.+.++..+
T Consensus        93 ~I~CPyHGW~Fdl~dG~cv~iP~~p~~~~~~~~~L~~ypV~e~~G~VfV~lg---d~~~ppL~e~L~~  157 (394)
T 3gcf_A           93 TVSCWYHGWTYDLDDGRLVDVLTSPGSPVIGKIGIKVYPVQVAQGVVFVFIG---DEEPHALSEDLPP  157 (394)
T ss_dssp             EEECTTTCEEEETTTCBEEEETTSTTCTTTTSCBCCEECEEEETTEEEEEES---SSCCCCGGGGSCT
T ss_pred             EEECCCCCcEEECCCCceeccCCCcccccccccCceEEEEEEECCcEEEecC---CCCCCCchhhcch
Confidence            9999999999999 999998764        456889999999998877652   2233666665543

>3vca_A Ring-hydroxylating dioxygenase; rieske-type, mononuclear non-heme iron, N-demethylase, oxido; 1.59A {Sinorhizobium meliloti} PDB: 3vcp_A

Probab=99.63  E-value=4.3e-16  Score=150.84  Aligned_cols=105  Identities=19%  Similarity=0.283  Sum_probs=85.8

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccC-CcCCCCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPI-ANAGDWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~-~~~~~~~  152 (292)
                      ..++|+ +|+.+.+.+.|.+++|.+                          +.+|+++|+.|+|||+|++|+ .+.++.+
T Consensus        49 ~~~elp~~G~~~~~~i~g~~vvv~R--------------------------~~dG~v~A~~n~CpHrga~L~~~g~~~~~  102 (412)
T 3vca_A           49 PVCQLAKAGSYTTLRVGAYEVVIVR--------------------------SRDGEVRAFHNSCRHRGSLICKARQGQVA  102 (412)
T ss_dssp             EGGGGCSTTEEEEEEETTEEEEEEE--------------------------CTTSCEEEEESSCTTTCCCSCCSSEEECS
T ss_pred             EHHHCCCCCCeEEEEECCEEEEEEE--------------------------cCCCCEEEecccCCCCCCEeecccccCCC
Confidence            568888 588889999999987753                          458999999999999999998 5656668


Q ss_pred             eEEcCCCCcEEcCCCceecCCCC--------CCCCCCceEeecCceEEEeecccCCCCCCccccc
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAP--------TNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYR  209 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~--------~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr  209 (292)
                      .|.||||||+||++|+|+.+|+.        .+|+.+++++.+|.|+|.+    +...|+|++|.
T Consensus       103 ~i~CPyHgw~fdldG~~~~~P~~~~~~~~~~~~L~~~~v~~~~G~V~v~~----~~~~p~l~~~l  163 (412)
T 3vca_A          103 KLVCPYHQWTYELDGKLIWANDMGPDFDASKYGLKPVNLRNLDGLIYICL----SDTPPDFQTFA  163 (412)
T ss_dssp             SEECTTTCCEECTTSCEEECTTCCTTCCGGGCSCCEEEEEEETTEEEEEC----SSSCCCCHHHH
T ss_pred             EEEcCCCCCEEcCCCccccCCccccccCcccCCCcEEEEEEECCEEEEEe----cCCCCCHHHHh
Confidence            99999999999999999999863        4688899999888777664    23346777665

>3n0q_A Putative aromatic-ring hydroxylating dioxygenase; rieske [2Fe-2S] domain, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.80A {Ruegeria SP}

Probab=99.62  E-value=6.6e-16  Score=149.44  Aligned_cols=105  Identities=20%  Similarity=0.252  Sum_probs=85.6

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCC-cCCCCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIA-NAGDWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~-~~~~~~  152 (292)
                      ..++|+ +|+.+++.+.|.+++|.+                          +.+|+++|+.|+|||+|++|+. +.++.+
T Consensus        47 ~~~elp~~G~~~~~~i~g~~vvv~R--------------------------~~dG~v~A~~n~C~Hrga~L~~~g~~~~~  100 (409)
T 3n0q_A           47 PACELDKPGSYVTHQVGNYNVIIVR--------------------------GADNVIRAFHNACRHRGSVICKAKKGNNP  100 (409)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEEE--------------------------CTTSCEEEEESCCTTTCCCSCCSSEEECS
T ss_pred             EHHHCCCCCCeEEEEECCEEEEEEE--------------------------cCCCCEEeecCcCCcCcCCccCcCccCCC
Confidence            578897 588899999999988753                          4689999999999999999986 556668


Q ss_pred             eEEcCCCCcEEcCCCceecCCCC--------CCCCCCceEeecCceEEEeecccCCCCCCccccc
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAP--------TNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYR  209 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~--------~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr  209 (292)
                      .|.||||||+||.+|+|+.+|+.        .+|+.+++++.+|.|+|.+    +...|+|++|.
T Consensus       101 ~i~CpyHgw~fd~dG~~~~~P~~~~~~~~~~~~L~~~~v~~~~G~Vfv~~----~~~~~~l~~~l  161 (409)
T 3n0q_A          101 KLVCPYHQWTYELDGRLLWARDMGPDFEPSRHGLKTVHCRELAGLIYICL----ADEAPDFERFA  161 (409)
T ss_dssp             SEECTTTCCEECTTSCEEECTTCCTTCCGGGCSCCEEEEEEETTEEEEEC----SSSCCCCHHHH
T ss_pred             EEEECCCCCEEeCCCCcccCCcCCcccCcccCCCceEEEEEECCEEEEEe----CCCCCChHHhh
Confidence            99999999999999999998852        4788888988888777654    33346676664

>2gbw_A Biphenyl 2,3-dioxygenase alpha subunit; rieske oxygenase, oxidoreductase, non heme iron; 1.70A {Sphingobium yanoikuyae} PDB: 2gbx_A* 2ckf_A

Probab=99.62  E-value=7.8e-16  Score=150.39  Aligned_cols=106  Identities=17%  Similarity=0.267  Sum_probs=84.2

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCC-CCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAG-DWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~-~~~  152 (292)
                      ..++|+ +|..+++.+.+.+|+|.                          |+.+|+++|+.|.|||+||+|+.+.. +.+
T Consensus        43 ~~~el~~~g~~~~~~~~~~~vvv~--------------------------R~~~G~v~a~~n~CpHrga~L~~g~~g~~~   96 (454)
T 2gbw_A           43 HESLVPKPGDFITTYMAEDKVILS--------------------------HQSDGTFRAFINSCSHRGNQICHADSGNAK   96 (454)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEE--------------------------ECTTSCEEEEESSCTTTCCCSCCCSEEECS
T ss_pred             EHHHCCCCCCeEEEEECCeEEEEE--------------------------EcCCCCEEEEeccCCCCCCCCcccccCCcC
Confidence            568888 58888888888888764                          34689999999999999999998653 457


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCC------------CCCCCceEeecCceEEEeecccCCCCCCcccccc
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPT------------NMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRR  210 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~------------~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr~  210 (292)
                      .|.||||||+||.+|+|+.+|+..            .|..+++++.+|.|+|.+    +...|+|++|..
T Consensus        97 ~i~CpyHgw~f~~~G~~~~~P~~~~~~~~~~~~~~~~l~~~~v~~~~G~v~v~~----~~~~p~~~~~l~  162 (454)
T 2gbw_A           97 AFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCH----DPEAPSLEDYLG  162 (454)
T ss_dssp             EEECTTTCCEEETTSCEEECTTTTTTTTTCCCGGGCCCCEEEEEEETTEEEEEC----CTTCCCHHHHHG
T ss_pred             EEEeCCCCCEecCCCCcccCCcccccccccCCHhhCCCeeEEEEEECCEEEEEe----CCCCCCHHHHhh
Confidence            899999999999999999998743            366778888888776653    333577887754

>2bmo_A Oxygenase-alpha NBDO; nitrobenzene dioxygenase, nitroarene, rieske non-heme dioxygenase, substrate specificity iron- sulfur, metal-binding, NAD; 1.2A {Comamonas SP} SCOP: b.33.1.2 d.129.3.3 PDB: 2bmq_A 2bmr_A* 2hmj_A 2hml_A* 2hmn_A* 1o7n_A 1ndo_A 1o7g_A* 1o7h_A 1o7m_A 1eg9_A 1o7p_A* 1o7w_A 1uuv_A 1uuw_A 2hmk_A* 2hmm_A* 2hmo_A*

Probab=99.61  E-value=9.8e-16  Score=149.34  Aligned_cols=106  Identities=23%  Similarity=0.355  Sum_probs=85.3

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCC-CCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAG-DWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~-~~~  152 (292)
                      ..++|+ +|..+++.+.+.+++|.                          |+.+|+++|+.|.|||+|++|+.+.. +.+
T Consensus        42 ~~~el~~~g~~~~~~~~~~~vvv~--------------------------R~~~G~v~a~~n~CpHrga~L~~g~~g~~~   95 (447)
T 2bmo_A           42 HDSLIPSPGDYVKAKMGVDEVIVS--------------------------RQNDGSVRAFLNVCRHRGKTLVHAEAGNAK   95 (447)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEE--------------------------ECTTSCEEEEESBCTTTCCBCCCSSEEECS
T ss_pred             EHHHCCCCCCeEEEEECCeeEEEE--------------------------ECCCCCEEEEeccCcCCCCCccccccCCcC
Confidence            568888 58888888888888764                          34689999999999999999988753 447


Q ss_pred             eEEcCCCCcEEcCCCceecCCCC------------CCCCCCc-eEeecCceEEEeecccCCCCCCcccccc
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAP------------TNMEVPP-YQFGDEGILIRMLAHSDIRTPDFSKYRR  210 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~------------~~L~~~p-~~~~~d~i~V~I~ahtD~~~P~F~~yr~  210 (292)
                      .|.||||||+||.+|+|+..|+.            ..|..++ +++.+|.|+|.+    +...|.|++|..
T Consensus        96 ~l~CpyHgw~f~~~G~~~~~P~~~~~~~~~~~~~~~~l~~~~~v~~~~G~v~v~~----~~~~~~l~~~l~  162 (447)
T 2bmo_A           96 GFVCGYHGWGYGSNGELQSVPFEKELYGDAIKKKCLGLKEVPRIESFHGFIYGCF----DAEAPPLIDYLG  162 (447)
T ss_dssp             EEECTTTCCEEETTSCEEECTTHHHHTGGGCCGGGCCCCBCSEEEEETTEEEEES----CTTCCCHHHHHT
T ss_pred             eEECCCCcchhcCCCcccccCcccccccccCCHhHCCCcccceEEEECCEEEEEc----CCCCCCHHHHhc
Confidence            89999999999999999998863            3688887 988888776653    334577877754

>2de6_A Terminal oxygenase component of carbazole; electron transfer complex, rieske non-heme iron oxygenase system, terminal oxygenase; 1.80A {Janthinobacterium} SCOP: b.33.1.2 d.129.3.3 PDB: 1ww9_A 2de5_A 2de7_A*

Probab=99.59  E-value=5.6e-15  Score=141.73  Aligned_cols=105  Identities=19%  Similarity=0.210  Sum_probs=84.2

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCC--CCC
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAG--DWG  152 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~--~~~  152 (292)
                      ..++|++|+.+.+.+.|.+++|.                          | .+|+++|+.|.|||+||+|+.+..  +++
T Consensus        34 ~~~el~~g~~~~~~~~g~~vvl~--------------------------R-~~G~v~a~~n~CpHrga~L~~g~~~~~~~   86 (392)
T 2de6_A           34 FSKEINEGEPKTLKLLGENLLVN--------------------------R-IDGKLYCLKDRCLHRGVQLSVKVECKTKS   86 (392)
T ss_dssp             EGGGSCBTCCEEEEETTEEEEEE--------------------------E-ETTEEEEEESSCTTTCCCGGGGCCCCSTT
T ss_pred             EHHHCCCCCeEEEEECCEEEEEE--------------------------E-eCCEEEEEeCcCCCCCCCCcCCcccCCCC
Confidence            56889889999999999998764                          4 379999999999999999998753  458


Q ss_pred             eEEcCCCCcEEcC-CCceecCCC--------CCCCCCCceEeecCceEEEeecccCCCCCCccccc
Q psy6642         153 GYYCPCHGSHYDA-SGRIRKGPA--------PTNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYR  209 (292)
Q Consensus       153 ~~~CPcHGs~FD~-~G~v~~gPa--------~~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr  209 (292)
                      .|.||||||+||. +|+|+.+|+        ...|..|++++.+|.|+|.+..   ...|.+.++.
T Consensus        87 ~i~CpyHgw~f~~~~G~~~~~p~~p~~~~~~~~~l~~~~v~~~~G~v~v~~~~---~~~~~l~~~l  149 (392)
T 2de6_A           87 TITCWYHAWTYRWEDGVLCDILTNPTSAQIGRQKLKTYPVQEAKGCVFIYLGD---GDPPPLARDT  149 (392)
T ss_dssp             EEECTTTCEEEETTTCBEEEETTCTTCTTTTSCBCCBCCEEEETTEEEEEESS---SSCCCGGGGS
T ss_pred             EEEeCCCCCEEcCCCCccccccCCccccccccCCCceEeEEEECCEEEEEeCC---CCCCChhHhc
Confidence            9999999999998 999998754        2478899999999988776522   1235555544

>1z01_A 2-OXO-1,2-dihydroquinoline 8-monooxygenase, oxygenase component; rieske center, oxygen binding/activation, substrate bound complex; 1.80A {Pseudomonas putida} SCOP: b.33.1.2 d.129.3.3 PDB: 1z02_A 1z03_A*

Probab=99.58  E-value=3.7e-15  Score=145.38  Aligned_cols=94  Identities=19%  Similarity=0.221  Sum_probs=79.8

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC--CCCC
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA--GDWG  152 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~--~~~~  152 (292)
                      ..++|++|+.+.+.+.|.+++|.                          | .+|+++|+.|.|||+||+|+.+.  ++++
T Consensus        49 ~~~el~~g~~~~~~~~g~~vvl~--------------------------r-~~G~v~a~~n~CpHrga~L~~g~~~~~~~  101 (446)
T 1z01_A           49 FTHELEEDQVQGIQICGVPIVLR--------------------------R-VNGKVFALKDQCLHRGVRLSEKPTCFTKS  101 (446)
T ss_dssp             EGGGSCBTCEEEEEETTEEEEEE--------------------------E-ETTEEEEEESSCTTTCCCGGGSCCCSSTT
T ss_pred             EHHHCCCCCeEEEEECCEEEEEE--------------------------E-eCCEEEEEeCcCCCCcCCCCCCccCCCCC
Confidence            56888889999999999988764                          3 47999999999999999999885  4568


Q ss_pred             eEEcCCCCcEEcC-CCceecCCC--------CCCCCCCceEeecCceEEEee
Q psy6642         153 GYYCPCHGSHYDA-SGRIRKGPA--------PTNMEVPPYQFGDEGILIRML  195 (292)
Q Consensus       153 ~~~CPcHGs~FD~-~G~v~~gPa--------~~~L~~~p~~~~~d~i~V~I~  195 (292)
                      .|.||||||+||+ +|+|+.+|+        ...|..|++++.+|.|+|.+.
T Consensus       102 ~i~CpyHgw~fd~~~G~~~~~p~~p~~~~~~~~~l~~~~v~~~~G~V~v~~~  153 (446)
T 1z01_A          102 TISCWYHGFTFDLETGKLVTIVANPEDKLIGTTGVTTYPVHEVNGMIFVFVR  153 (446)
T ss_dssp             EEECTTTCEEEETTTCBEEEETTCTTCTTTTSCBCCEECEEEETTEEEEEEC
T ss_pred             EEEeCCCCeEEeCCCCCccccCCCccccCcccCCCcEEEEEEECCEEEEEeC
Confidence            9999999999998 999998764        246888999998988877653

>2b1x_A Naphthalene dioxygenase large subunit; rieske non-heme iron oxygenase, oxidoreductase; 2.00A {Rhodococcus SP} SCOP: b.33.1.2 d.129.3.3 PDB: 2b24_A

Probab=99.58  E-value=2.5e-15  Score=147.40  Aligned_cols=106  Identities=20%  Similarity=0.295  Sum_probs=80.5

Q ss_pred             ecCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCC-CC
Q psy6642          75 DLNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGD-WG  152 (292)
Q Consensus        75 ~~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~-~~  152 (292)
                      ..++|++ |..+++.+.|.+++|.                          |+.+|+++|+.|+|||+||+|+.+... .+
T Consensus        51 ~~~el~~~g~~~~~~~~g~~vvv~--------------------------R~~~G~v~a~~n~C~Hrga~L~~g~~~~~~  104 (470)
T 2b1x_A           51 HESEIPERGDYVVRYISEDQFIVC--------------------------RDEGGEIRGHLNACRHRGMQVCRAEMGNTS  104 (470)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEE--------------------------ECTTSCEEEEESSCTTTCCCSCCSSEEECS
T ss_pred             eHHHCCCCCCeEEEEECCeEEEEE--------------------------EcCCCCEEEEecccCCCCCEeeccCcCCCC
Confidence            5688885 6677888888888765                          345899999999999999999887543 36


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCCC----------CCCCce-Eee--cCceEEEeecccCCCCCCcccccc
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPTN----------MEVPPY-QFG--DEGILIRMLAHSDIRTPDFSKYRR  210 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~~----------L~~~p~-~~~--~d~i~V~I~ahtD~~~P~F~~yr~  210 (292)
                      .|.||||||+||.+|+|+.+|+...          +..+++ +++  +|.|+|.+    |...|.|++|..
T Consensus       105 ~i~CpyHgw~f~~~G~~~~~P~~~~~~~~~~~~~~~~l~~~p~ve~~~G~Vfv~~----~~~~~~~~~~l~  171 (470)
T 2b1x_A          105 HFRCPYHGWTYSNTGSLVGVPAGKDAYGNQLKKSDWNLRPMPNLASYKGLIFGSL----DPHADSLEDYLG  171 (470)
T ss_dssp             EEECTTTCCEEETTSCEEECTTTTTTTTTCCCGGGGSCCBCSEEEEETTEEEEES----CTTCCCHHHHHG
T ss_pred             EEEECCCCCeecCCCceeecCcccccccccCCHhhCCCcccceEEEECCEEEEEe----CCCCCCHHHHhc
Confidence            8999999999999999999997421          345566 555  67666553    333567777754

>1uli_A Biphenyl dioxygenase large subunit; alpha3 BETA3 hetero hexamer, oxidoreductase; 2.20A {Rhodococcus SP} SCOP: b.33.1.2 d.129.3.3 PDB: 1ulj_A* 3en1_A* 3eqq_A

Probab=99.58  E-value=1.6e-15  Score=148.53  Aligned_cols=106  Identities=23%  Similarity=0.327  Sum_probs=82.1

Q ss_pred             ecCCCCC-CCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCC-CCC
Q psy6642          75 DLNLIPE-GQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAG-DWG  152 (292)
Q Consensus        75 ~~s~l~~-g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~-~~~  152 (292)
                      ..++|++ |..+++.+.+.+++|.                          |+.+|+++|+.|.|||+||+|+.+.. +.+
T Consensus        61 ~~~el~~~g~~~~~~i~~~~vvv~--------------------------R~~~G~v~a~~n~CpHrga~L~~g~~g~~~  114 (460)
T 1uli_A           61 HETQIPKAGDFMTNYMGEDPVMVV--------------------------RQKNGEIRVFLNQCRHRGMRICRADGGNAK  114 (460)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEE--------------------------ECTTSCEEEEESCCTTTCCCSCCSSEEECS
T ss_pred             EHHHCCCCCCeEEEEECCeEEEEE--------------------------EcCCCCEEEEeeeCCCCCCCCccccCCCCC
Confidence            5678885 6667788888887764                          34689999999999999999988753 347


Q ss_pred             eEEcCCCCcEEcCCCceecCCCC-----------CCCCCCceEeecCceEEEeecccCCCCCCcccccc
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAP-----------TNMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRR  210 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~-----------~~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr~  210 (292)
                      .|.||||||+||.+|+|+.+|+.           ..|..+++++.+|.|+|.+    +...|.|++|..
T Consensus       115 ~i~CpyHgw~fd~~G~~~~~P~~~~~~~~~~~~~~~L~~~~v~~~~G~V~v~~----~~~~p~l~~~l~  179 (460)
T 1uli_A          115 SFTCSYHGWAYDTGGNLVSVPFEEQAFPGLRKEDWGPLQARVETYKGLIFANW----DADAPDLDTYLG  179 (460)
T ss_dssp             CEECTTTCCEECTTCCEEECTTHHHHCTTCCGGGSSCCEEEEEEETTEEEEEC----CTTSCCHHHHHT
T ss_pred             EEEcCCCCCEEeCCCCEeeCCccccccCCCCHhHcCCceeeEEEECCEEEEEe----CCCCCCHHHHhc
Confidence            89999999999999999999863           2366778888888776653    334577777744

>3gzx_A Biphenyl dioxygenase subunit alpha; rieskie, non-heme iron, 2Fe-2S, aromatic hydroc catabolism, iron, iron-sulfur, metal-binding, NAD; HET: BNL MES; 1.58A {Comamonas testosteroni} PDB: 3gzy_A* 1wql_A 2xso_A 2xsh_A 2xrx_A* 2xr8_A* 2yfi_A 2yfj_A* 2yfl_A*

Probab=99.52  E-value=1.5e-14  Score=141.77  Aligned_cols=107  Identities=24%  Similarity=0.360  Sum_probs=80.9

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CCCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GDWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~~~  152 (292)
                      ..++|+ +|..+++.+.+.+|+|.                          |+.+|+++|+.|.|+|+|++|+.+. ++.+
T Consensus        63 ~~~elp~~G~~~~~~i~~~~vvv~--------------------------R~~dG~v~A~~n~C~Hrga~L~~g~~g~~~  116 (457)
T 3gzx_A           63 HETHIPKIGDYLTTYMGEDPVIMV--------------------------RQKDQSIKVFLNQCRHRGMRIVRSDGGNAK  116 (457)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEE--------------------------ECTTSCEEEEESCCTTTCCCSCCSSEEECS
T ss_pred             EHHHcCCCCCeEEEEECCEEEEEE--------------------------ECCCCeEEEEeCcCCCCCcCccCCCCCcCC
Confidence            567887 57788888888888764                          3468999999999999999999875 4558


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCC------------------CCCCCceEeecCceEEEeecccCCCCCCccccccC
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPT------------------NMEVPPYQFGDEGILIRMLAHSDIRTPDFSKYRRD  211 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~------------------~L~~~p~~~~~d~i~V~I~ahtD~~~P~F~~yr~~  211 (292)
                      .|.||||||+||.+|+|+..|+..                  .|..++++..++-|+|.  .  |...|+|++|..+
T Consensus       117 ~i~CpyHgw~fd~~G~~~~~P~~~~~~~~~~~~~~~~~~~~~~L~~~~v~e~~G~Vfv~--~--~~~ap~l~e~lg~  189 (457)
T 3gzx_A          117 AFTCTYHGWAYDIAGNLVNVPFEKEAFCDKKEGDCGFDKADWGPLQARVETYKGLVFAN--W--DPEAPDLKTYLSD  189 (457)
T ss_dssp             EEECTTTCCEEETTSCEEECTTHHHHTCSSSTTTTSCCGGGCCCCEEEEEEETTEEEEE--S--CTTSCCHHHHTTT
T ss_pred             EEEcCCCCCEecCCCcceecCccccccccccccccccChhhCCCceEeEEEECCEEEEe--c--CCCCCChHHHHhh
Confidence            999999999999999999988631                  23344555556655443  3  3345778888653

>1vf5_D Rieske iron-sulfur protein; photosynthesis, membrane protein complex, electron transfer complex; HET: HEM TDS PL9 OPC CLA BCR; 3.00A {Mastigocladus laminosus} SCOP: b.33.1.1 f.23.12.1 PDB: 2d2c_D* 2e74_D* 2e75_D* 2e76_D* 2zt9_D*

Probab=98.52  E-value=1.5e-08  Score=87.29  Aligned_cols=69  Identities=17%  Similarity=0.235  Sum_probs=55.8

Q ss_pred             ccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhhhc-cceEEe-----------cCCCCCCceEEEE-ECCee
Q psy6642         220 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVLAM-ATIEVD-----------LNLIPEGQSVTFK-WRGKP  286 (292)
Q Consensus       220 ~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~a~-~~~evd-----------ls~i~~G~~~~~~-WrgkP  286 (292)
                      +.+||+||++++++++++++   .++++||+++|+|++...+. +.+++|           ++.|++|+...+. +.|+|
T Consensus        12 ~~~RR~Fl~~~~~~~~~~~~---~~~~~p~~~~~~p~~~~~~~~~~v~~d~~g~~i~~~~~~~~l~~g~~~~~~~~~g~~   88 (179)
T 1vf5_D           12 DMGRRQFMNLLAFGTVTGVA---LGALYPLVKYFIPPSGGAVGGGTTAKDKLGNNVKVSKFLESHNAGDRVLVQGLKGDP   88 (179)
T ss_dssp             CCCCCTTSCTTHHHHHHHHH---HHHHHHHHHHHSCCCCSSCCCCCCCCBTTSSCCCHHHHHHCCCTTCCCEESCSSSSC
T ss_pred             CCcHHHHHHHHHHHHHHHHH---HHHHHHHHHHhCCchhhcccCCcEEEccCCCeEehhhcccccCCCceEEEeccCCCe
Confidence            35799999998877665554   46789999999999987755 467777           6789999999997 99999


Q ss_pred             eEEEc
Q psy6642         287 LFIRH  291 (292)
Q Consensus       287 vfv~~  291 (292)
                      +++.+
T Consensus        89 ~~lv~   93 (179)
T 1vf5_D           89 TYIVV   93 (179)
T ss_dssp             EECCB
T ss_pred             EEEEE
Confidence            98755

>4aay_B AROB; oxidoreductase, rieske, iron sulfur, molybdopterin; HET: MGD; 2.70A {Rhizobium species}

Probab=95.60  E-value=0.0038  Score=53.32  Aligned_cols=68  Identities=9%  Similarity=0.130  Sum_probs=24.7

Q ss_pred             cccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCC---HHhhhccceEE-ecCCCCCCceEEEEEC--CeeeEEEc
Q psy6642         219 EETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSAS---ADVLAMATIEV-DLNLIPEGQSVTFKWR--GKPLFIRH  291 (292)
Q Consensus       219 ~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~---~~~~a~~~~ev-dls~i~~G~~~~~~Wr--gkPvfv~~  291 (292)
                      ...+||.||-   +++++++++  +.+.+|+-..+.++   ..++....+.| +++.|++|+.++|+|.  ++||+|.|
T Consensus         8 ~~~~rr~fl~---~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~~~p~~~v~~~~dL~~g~~~~v~~~~~~~pv~v~R   81 (175)
T 4aay_B            8 VDIGRRQFLR---GGALAAAGA--TAAVFGVGAPQARAATAAAGVEYPANRLANISELTLNEPLDVAYPDEDAAGVLLK   81 (175)
T ss_dssp             -----------------------------------------CCSCCCCCEEEEEGGGCBBTBCEEEESSSTTSEEEEEE
T ss_pred             ccccHHHHhh---hhHHhhhhe--eEeccccccccccccccCcccCCCcceEEEHHHCCCCCEEEEEECCCCCEEEEEE
Confidence            3568999996   322222221  12234443333332   11112223344 8999999999999996  57999986

>1q90_R Cytochrome B6-F complex iron-sulfur subunit; membrane protein complex, photosynthesis, electron transfer, oxydoreductase, chlorophyll; HET: HEM CL1 BCR TDS SQD LFA LMG; 3.10A {Chlamydomonas reinhardtii} SCOP: f.23.12.1

Probab=85.66  E-value=0.7  Score=31.18  Aligned_cols=16  Identities=13%  Similarity=0.441  Sum_probs=12.9

Q ss_pred             CcCchhhHHHHHHhHH
Q psy6642          27 ETQRKAFTYMIAGGSS   42 (292)
Q Consensus        27 ~~~RR~fl~~atG~~~   42 (292)
                      +++||+|+..++..++
T Consensus         8 dm~RRqfln~l~~G~~   23 (49)
T 1q90_R            8 DMNKRNIMNLILAGGA   23 (49)
T ss_dssp             CHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHH
Confidence            7899999998886443

>1q90_R Cytochrome B6-F complex iron-sulfur subunit; membrane protein complex, photosynthesis, electron transfer, oxydoreductase, chlorophyll; HET: HEM CL1 BCR TDS SQD LFA LMG; 3.10A {Chlamydomonas reinhardtii} SCOP: f.23.12.1

Probab=83.39  E-value=0.39  Score=32.45  Aligned_cols=36  Identities=6%  Similarity=0.173  Sum_probs=24.1

Q ss_pred             ccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHH
Q psy6642         220 ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASAD  258 (292)
Q Consensus       220 ~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~  258 (292)
                      +.+||.|+.+++.++++.-   +...++|++..+-|...
T Consensus         8 dm~RRqfln~l~~G~~a~~---a~~~~~P~v~ffvpP~~   43 (49)
T 1q90_R            8 DMNKRNIMNLILAGGAGLP---ITTLALGYGAFFVPPSS   43 (49)
T ss_dssp             CHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHSCC--
T ss_pred             ChHHHHHHHHHHHHHHHHH---HHHHHHhhheeecCCcc
Confidence            4679999988876443332   34678999998766543

---

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	292
d1riea_	127	b.33.1.1 (A:) ISP subunit of the mitochondrial cyt	2e-52
d1riea_	127	b.33.1.1 (A:) ISP subunit of the mitochondrial cyt	1e-10
d3cx5e1	129	b.33.1.1 (E:87-215) ISP subunit of the mitochondri	2e-49
d3cx5e1	129	b.33.1.1 (E:87-215) ISP subunit of the mitochondri	4e-12
d1ppje2	69	f.23.12.1 (E:1-69) Iron-sulfur subunit (ISP) of cy	2e-24
d1ppje2	69	f.23.12.1 (E:1-69) Iron-sulfur subunit (ISP) of cy	2e-24
d1nyka_	156	b.33.1.1 (A:) Soluble Rieske protein {Thermus ther	2e-21
d1nyka_	156	b.33.1.1 (A:) Soluble Rieske protein {Thermus ther	6e-05
d3cx5e2	56	f.23.12.1 (E:31-86) Iron-sulfur subunit (ISP) of c	1e-18
d3cx5e2	56	f.23.12.1 (E:31-86) Iron-sulfur subunit (ISP) of c	1e-18
d1rfsa_	127	b.33.1.1 (A:) ISP subunit from chloroplast cytochr	3e-16
d1jm1a_	202	b.33.1.1 (A:) Rieske protein II (SoxF) {Archaeon S	2e-15
d2e74d1	134	b.33.1.1 (D:46-179) ISP subunit from the cytochrom	2e-14
d1g8kb_	133	b.33.1.1 (B:) Arsenite oxidase Rieske subunit {Alc	8e-09
d1vm9a_	109	b.33.1.1 (A:) Toluene-4-monooxygenase system prote	0.002

>d1riea_ b.33.1.1 (A:) ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain {Cow (Bos taurus) [TaxId: 9913]} Length = 127

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  165 bits (419), Expect = 2e-52
 Identities = 87/125 (69%), Positives = 107/125 (85%)

Query: 68  AMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKD 127
           AM+ IE+ L+ IPEG+++ FKWRGKPLF+RHRT+KEID E    +SQLRDPQ D +RVK 
Sbjct: 1   AMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERVKK 60

Query: 128 PSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGD 187
           P W+++IG+CTHLGCVPIANAGD+GGYYCPCHGSHYDASGRIRKGPAP N+EVP Y+F  
Sbjct: 61  PEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPSYEFTS 120

Query: 188 EGILI 192
           + ++I
Sbjct: 121 DDMVI 125

>d1riea_ b.33.1.1 (A:) ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain {Cow (Bos taurus) [TaxId: 9913]} Length = 127

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 55.8 bits (134), Expect = 1e-10
 Identities = 21/32 (65%), Positives = 28/32 (87%)

Query: 261 AMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           AM+ IE+ L+ IPEG+++ FKWRGKPLF+RHR
Sbjct: 1   AMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHR 32

>d3cx5e1 b.33.1.1 (E:87-215) ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 129

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  157 bits (399), Expect = 2e-49
 Identities = 80/128 (62%), Positives = 104/128 (81%)

Query: 65  DVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDR 124
           DVLAMA +EV+L  IP G++V  KW+GKP+FIRHRT  EI    + ++S L+DPQ D+DR
Sbjct: 1   DVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADR 60

Query: 125 VKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQ 184
           VKDP WL+++GICTHLGCVPI  AGD+GG++CPCHGSHYD SGRIRKGPAP N+E+P Y+
Sbjct: 61  VKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYE 120

Query: 185 FGDEGILI 192
           F  + +++
Sbjct: 121 FDGDKVIV 128

>d3cx5e1 b.33.1.1 (E:87-215) ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 129

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 60.1 bits (145), Expect = 4e-12
 Identities = 23/35 (65%), Positives = 29/35 (82%)

Query: 258 DVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
           DVLAMA +EV+L  IP G++V  KW+GKP+FIRHR
Sbjct: 1   DVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHR 35

>d1ppje2 f.23.12.1 (E:1-69) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Cow (Bos taurus) [TaxId: 9913]} Length = 69

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 91.4 bits (227), Expect = 2e-24
 Identities = 33/69 (47%), Positives = 47/69 (68%), Gaps = 4/69 (5%)

Query: 3  AHSDIRTPDFSKYRRD--RNPDKGQEET--QRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 58
          +H+DI+ PDFS YRR    +  K  +E+   RK F+Y++   ++V     AK+VV+QF+S
Sbjct: 1  SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 60

Query: 59 SMSASADVL 67
          SMSASADVL
Sbjct: 61 SMSASADVL 69

>d1ppje2 f.23.12.1 (E:1-69) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Cow (Bos taurus) [TaxId: 9913]} Length = 69

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 91.4 bits (227), Expect = 2e-24
 Identities = 33/69 (47%), Positives = 47/69 (68%), Gaps = 4/69 (5%)

Query: 196 AHSDIRTPDFSKYRRD--RNPDKGQEET--QRKAFTYMIAGGSSVVGMVCAKSVVNQFIS 251
           +H+DI+ PDFS YRR    +  K  +E+   RK F+Y++   ++V     AK+VV+QF+S
Sbjct: 1   SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS 60

Query: 252 SMSASADVL 260
           SMSASADVL
Sbjct: 61  SMSASADVL 69

>d1nyka_ b.33.1.1 (A:) Soluble Rieske protein {Thermus thermophilus [TaxId: 274]} Length = 156

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Soluble Rieske protein
species: Thermus thermophilus [TaxId: 274]

 Score = 86.3 bits (213), Expect = 2e-21
 Identities = 23/130 (17%), Positives = 43/130 (33%), Gaps = 7/130 (5%)

Query: 68  AMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKD 127
                 + L  +  G      +   P     ++ +  +T            +   +  + 
Sbjct: 19  GGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVAR---FDPEELAPEVAQH 75

Query: 128 PS--WLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDAS--GRIRKGPAPTNMEVPPY 183
            +   +    +CTHLGC+      D     CPCHG  YD     ++  GP P  +   P 
Sbjct: 76  AAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPV 135

Query: 184 QFGDEGILIR 193
           +  D  ++  
Sbjct: 136 RVEDGVLVAA 145

>d1nyka_ b.33.1.1 (A:) Soluble Rieske protein {Thermus thermophilus [TaxId: 274]} Length = 156

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Soluble Rieske protein
species: Thermus thermophilus [TaxId: 274]

 Score = 40.4 bits (94), Expect = 6e-05
 Identities = 3/32 (9%), Positives = 7/32 (21%)

Query: 261 AMATIEVDLNLIPEGQSVTFKWRGKPLFIRHR 292
                 + L  +  G      +   P     +
Sbjct: 19  GGEPKPIRLEELKPGDPFVLAYPMDPKTKVVK 50

>d3cx5e2 f.23.12.1 (E:31-86) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 76.0 bits (187), Expect = 1e-18
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 5  SDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASA 64
          S  RTP+F    ++ N        + +++ Y + G   ++    AKS V  FISSM+A+A
Sbjct: 2  STYRTPNFDDVLKENNDA-----DKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATA 56

>d3cx5e2 f.23.12.1 (E:31-86) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 76.0 bits (187), Expect = 1e-18
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 198 SDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASA 257
           S  RTP+F    ++ N        + +++ Y + G   ++    AKS V  FISSM+A+A
Sbjct: 2   STYRTPNFDDVLKENNDA-----DKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATA 56

>d1rfsa_ b.33.1.1 (A:) ISP subunit from chloroplast cytochrome bf complex {Spinach (Spinacia oleracea) [TaxId: 3562]} Length = 127

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit from chloroplast cytochrome bf complex
species: Spinach (Spinacia oleracea) [TaxId: 3562]

 Score = 71.2 bits (174), Expect = 3e-16
 Identities = 26/69 (37%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 136 ICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRML 195
           +CTHLGCV   NA +   + CPCHGS Y+  GR+ +GPAP ++ +      D  ++    
Sbjct: 54  VCTHLGCVVPFNAAE-NKFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPW 112

Query: 196 AHSDIRTPD 204
             +D RT +
Sbjct: 113 TETDFRTGE 121

>d1jm1a_ b.33.1.1 (A:) Rieske protein II (SoxF) {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 202

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Rieske protein II (SoxF)
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score = 71.3 bits (174), Expect = 2e-15
 Identities = 26/141 (18%), Positives = 41/141 (29%), Gaps = 33/141 (23%)

Query: 74  VDLNLIPEGQSVTFKWRGKPLFIRHRTQK-------EIDTEQNTNISQLRDPQADSDRVK 126
             +  I + Q    K  G  ++              ++       I+++ +P        
Sbjct: 11  YKVANIQQVQ-QQIKSSGCAVYFFAYPLTDEPCFLVDLQALTGQQITEIPNPYYGKYAGP 69

Query: 127 DPSWLVIIG------------ICTHLGCVPIAN-----------AGDWGGYYCPCHGSHY 163
                 I G            +C HLGC   A                   +CPCHGS Y
Sbjct: 70  LGQIQTIKGVGPNGTIFAFSDVCVHLGCQLPAQVIVSSESDPGLYAKGADLHCPCHGSIY 129

Query: 164 DAS--GRIRKGPAPTNMEVPP 182
                G +  GPAP  + +  
Sbjct: 130 ALKDGGVVVSGPAPRPLPIVI 150

>d2e74d1 b.33.1.1 (D:46-179) ISP subunit from the cytochrome b6f complex, soluble domain {Mastigocladus laminosus [TaxId: 83541]} Length = 134

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit from the cytochrome b6f complex, soluble domain
species: Mastigocladus laminosus [TaxId: 83541]

 Score = 66.7 bits (162), Expect = 2e-14
 Identities = 34/110 (30%), Positives = 56/110 (50%), Gaps = 18/110 (16%)

Query: 112 ISQLRDPQADSDRV------KDPSWLVIIG-----------ICTHLGCVPIANAGDWGGY 154
           +S+  +     DRV       DP+++V+             +CTHLGCV   NA +   +
Sbjct: 21  VSKFLESHNAGDRVLVQGLKGDPTYIVVESKEAIRDYGINAVCTHLGCVVPWNAAE-NKF 79

Query: 155 YCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTPD 204
            CPCHGS YD +G++ +GPAP ++ +      D+ I++     +D RT +
Sbjct: 80  KCPCHGSQYDETGKVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRTGE 129

>d1g8kb_ b.33.1.1 (B:) Arsenite oxidase Rieske subunit {Alcaligenes faecalis [TaxId: 511]} Length = 133

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Arsenite oxidase Rieske subunit
species: Alcaligenes faecalis [TaxId: 511]

 Score = 50.8 bits (121), Expect = 8e-09
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 126 KDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPY 183
            D   +    +CTH+GC P +       + CPCH + +DA  +G++  G A  ++     
Sbjct: 49  PDDDIVAYSVLCTHMGC-PTSYDSSSKTFSCPCHFTEFDAEKAGQMICGEATADLPRVLL 107

Query: 184 QFGDEGILIR 193
           ++      + 
Sbjct: 108 RYDAASDALT 117

>d1vm9a_ b.33.1.1 (A:) Toluene-4-monooxygenase system protein C, TmoC {Pseudomonas mendocina [TaxId: 300]} Length = 109

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Toluene-4-monooxygenase system protein C, TmoC
species: Pseudomonas mendocina [TaxId: 300]

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 8/71 (11%), Positives = 20/71 (28%)

Query: 124 RVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPY 183
             ++        +C H   +    + + G   C  H   ++        P    +   P 
Sbjct: 31  NSEEHGVKAYQAMCPHQEILLSEGSYEGGVITCRAHLWTFNDGTGHGINPDDAALAEYPV 90

Query: 184 QFGDEGILIRM 194
           +   + I +  
Sbjct: 91  EVKGDDIYVST 101

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	292
d3cx5e1	129	ISP subunit of the mitochondrial cytochrome bc1-co	100.0
d1riea_	127	ISP subunit of the mitochondrial cytochrome bc1-co	100.0
d1nyka_	156	Soluble Rieske protein {Thermus thermophilus [TaxI	99.88
d1rfsa_	127	ISP subunit from chloroplast cytochrome bf complex	99.85
d2e74d1	134	ISP subunit from the cytochrome b6f complex, solub	99.85
d1g8kb_	133	Arsenite oxidase Rieske subunit {Alcaligenes faeca	99.82
d1fqta_	109	Rieske-type ferredoxin associated with biphenyl di	99.82
d3c0da1	108	NADH-nitrite reductase small subunit NirD {Vibrio	99.81
d1vm9a_	109	Toluene-4-monooxygenase system protein C, TmoC {Ps	99.8
d1jm1a_	202	Rieske protein II (SoxF) {Archaeon Sulfolobus acid	99.78
d2jo6a1	108	NADH-nitrite reductase small subunit NirD {Escheri	99.76
d2jzaa1	122	NADH-nitrite reductase small subunit NirD {Erwinia	99.75
d1z01a1	148	2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygen	99.73
d2de6a1	142	Terminal oxygenase component of carbazole CarAa {J	99.71
d1ppje2	69	Iron-sulfur subunit (ISP) of cytochrome bc1 comple	99.64
d2b1xa1	162	Naphthalene 1,2-dioxygenase alpha subunit, N-domai	99.55
d2bmoa1	150	Nitrobenzene dioxygenase alpha subunit, NBDO-alpha	99.54
d1ulia1	154	Biphenyl dioxygenase large subunit BphA1, N-termin	99.53
d1ppje2	69	Iron-sulfur subunit (ISP) of cytochrome bc1 comple	99.49
d3cx5e2	56	Iron-sulfur subunit (ISP) of cytochrome bc1 comple	99.17
d3cx5e2	56	Iron-sulfur subunit (ISP) of cytochrome bc1 comple	98.87
d2e74d2	34	ISP subunit from the cytochrome b6f complex, trans	85.75
d2e74d2	34	ISP subunit from the cytochrome b6f complex, trans	83.08

>d3cx5e1 b.33.1.1 (E:87-215) ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.5e-37  Score=252.45  Aligned_cols=128  Identities=63%  Similarity=1.283  Sum_probs=121.5

Q ss_pred             hhhccccceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCccc
Q psy6642          65 DVLAMATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVP  144 (292)
Q Consensus        65 ~~~a~~~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l  144 (292)
                      |++|.+.++||+++|++|++++++|+|+|+||++||+++|+....+....+.+|+....|+.+++|++++++|||+||.+
T Consensus         1 dv~A~a~veVDis~l~pG~~~~V~WrGkPVfI~~Rt~e~i~~~~~~~~~~l~dp~~~~~r~~~~~~~v~~~~CtHlGC~~   80 (129)
T d3cx5e1           1 DVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVP   80 (129)
T ss_dssp             GGCCCCCEEEEGGGCCTTCEEEEEETTEEEEEEECCHHHHHHHHCSCGGGCSSCCCSTTTCSSTTEEEEECCCTTTSCCC
T ss_pred             CccccCceEEehhhCCCCCeEEEEeCCceEEEEecCHHHhhhccccccccccccccchhccccccEEEEEeeccCcceee
Confidence            56788999999999999999999999999999999999999988888889999999999999999999999999999999


Q ss_pred             CCcCCCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEeecCceEE
Q psy6642         145 IANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILI  192 (292)
Q Consensus       145 ~~~~~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~d~i~V  192 (292)
                      .+..++.++|+||||||+||.+|++++|||++||++||+++++++++|
T Consensus        81 ~~~~~~~~~~~CPCHgs~fd~~G~v~~GPA~~~L~~~~~~~~~~~i~i  128 (129)
T d3cx5e1          81 IGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGDKVIV  128 (129)
T ss_dssp             EEEETTTTEEEETTTTEEECTTCCEEESSCCSCCCCCCEEEETTEEEE
T ss_pred             eeccCcCCeEEEcCcCCCCCCCCCEEeCCCCCCCCCCcEEEECCEEEE
Confidence            988777789999999999999999999999999999999999998764

>d1riea_ b.33.1.1 (A:) ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain {Cow (Bos taurus) [TaxId: 9913]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=2.6e-36  Score=246.28  Aligned_cols=124  Identities=69%  Similarity=1.362  Sum_probs=116.7

Q ss_pred             cccceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC
Q psy6642          69 MATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA  148 (292)
Q Consensus        69 ~~~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~  148 (292)
                      .+.++||+++|++|++++++|+|+|+||++||++||+....+....++||+....|..++++++++++|||+||.+.+..
T Consensus         2 ~A~veVDlS~lepG~~~~V~WrGkPvfV~rRt~e~i~~~~~~~~~~l~dp~~~~~r~~~~~~~~~~~~CtHlGC~~~~~~   81 (127)
T d1riea_           2 MSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERVKKPEWVILIGVCTHLGCVPIANA   81 (127)
T ss_dssp             CSSEEEEGGGSCTTCEEEEEETTEEEEEEECCHHHHHHHHTCCGGGCSSCCCGGGTCSSTTEEEEECCCTTTSCCCEETC
T ss_pred             CCCEEEehhhCCCCCEEEEEECCceeEEEecCHHHhhhhhccchhhhcCccccccccccceEEEEEeccCCCCceeeccc
Confidence            46789999999999999999999999999999999999888888899999999999999999999999999999998887


Q ss_pred             CCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEeecCceEE
Q psy6642         149 GDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILI  192 (292)
Q Consensus       149 ~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~d~i~V  192 (292)
                      ++.++|+||||||+||.+|++++|||++||++||+++++|.+++
T Consensus        82 ~~~~~f~CPCHgs~fd~~Grv~~GPAp~~L~~p~~~~~~d~~v~  125 (127)
T d1riea_          82 GDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPSYEFTSDDMVI  125 (127)
T ss_dssp             TTTEEEEETTTTEEEETTCCEEESSCCSCCCCCCEEESSSSEEE
T ss_pred             ccCCeEEecCcCCcCCCCCCEEcCCCCCCCCCCcEEEeCCCEEE
Confidence            77689999999999999999999999999999999999987654

>d1nyka_ b.33.1.1 (A:) Soluble Rieske protein {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Soluble Rieske protein
species: Thermus thermophilus [TaxId: 274]

Probab=99.88  E-value=3.1e-24  Score=180.47  Aligned_cols=122  Identities=20%  Similarity=0.375  Sum_probs=92.8

Q ss_pred             ccceeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhccccccccc-CCCCcccccccCCCeEEEEecccCCCcccCCcC
Q psy6642          70 ATIEVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQL-RDPQADSDRVKDPSWLVIIGICTHLGCVPIANA  148 (292)
Q Consensus        70 ~~~~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l-~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~  148 (292)
                      ...++++++|++|+..++.|+++|.++++++...+.....+..... .+| ....| ..++++||+++|||+||+|+++.
T Consensus        21 ~~~pv~~s~l~~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~r~~~~~~~~-~~~~~-~~d~i~A~~~~CtH~g~~l~~~~   98 (156)
T d1nyka_          21 EPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAP-EVAQH-AAEGVVAYSAVCTHLGCIVSQWV   98 (156)
T ss_dssp             SCCBCBGGGCCTTSCCEEEEEECTTTCCBCTTSGGGCEEEEECCGGGSCH-HHHTT-CBTTEEEEECBCTTTCCBCCEEE
T ss_pred             CCCcccHHHCCCCCeeEeecCCCccceEecChhhccccceeecCccccCc-hhhcc-cCCcEEEEcccCccccccccccc
Confidence            3467899999999999999999988776665544433211111000 001 11233 35679999999999999998877


Q ss_pred             CCCCeEEcCCCCcEEcC--CCceecCCCCCCCCCCceEeecCceEEE
Q psy6642         149 GDWGGYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPYQFGDEGILIR  193 (292)
Q Consensus       149 ~~~~~~~CPcHGs~FD~--~G~v~~gPa~~~L~~~p~~~~~d~i~V~  193 (292)
                      .+++.|.||||||+||+  .|+++.|||+++|+.|++++++|.++|.
T Consensus        99 ~~~~~~~Cp~Hgs~FD~~~gg~v~~gPa~~~L~~~~~~~~~g~i~v~  145 (156)
T d1nyka_          99 ADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVRVEDGVLVAA  145 (156)
T ss_dssp             GGGTEEECTTTCCEEEGGGTTEEEESSCSSCCCEECEEEETTEEEEC
T ss_pred             ccCCeeeccccceEEecCCCceEeCCCCCCCCCEEEEEEECCEEEEe
Confidence            77789999999999998  5899999999999999999999877654

>d1rfsa_ b.33.1.1 (A:) ISP subunit from chloroplast cytochrome bf complex {Spinach (Spinacia oleracea) [TaxId: 3562]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit from chloroplast cytochrome bf complex
species: Spinach (Spinacia oleracea) [TaxId: 3562]

Probab=99.85  E-value=9.1e-22  Score=160.00  Aligned_cols=78  Identities=36%  Similarity=0.725  Sum_probs=70.4

Q ss_pred             cccCCCeEEEEecccCCCcccCCcCCCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEeecCceEEEeecccCCCC
Q psy6642         124 RVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRT  202 (292)
Q Consensus       124 R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~d~i~V~I~ahtD~~~  202 (292)
                      |+.+++++|++++|||+||++.++..+ +.|.||||||+||.+|+++.||++++|+.|++++++|.|+|..+...|.+.
T Consensus        42 ~d~~~~v~A~~~~C~H~g~~l~~~~~~-~~~~Cp~Hg~~Fd~~G~~~~~Pa~~~L~~~~v~v~~g~i~v~~~~~~~~r~  119 (127)
T d1rfsa_          42 SDKTLATFGINAVCTHLGCVVPFNAAE-NKFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRT  119 (127)
T ss_dssp             TTSSBCSEEEECBCTTTCCBCCEETTT-TEEECTTTCCEEETTCCEEESSCCSCCCEEEEEEETTEEEEEECCSCCTTT
T ss_pred             eCCCCEEEEEcCCCCCCCCCccCcccC-CeEEcCCCCeEECCCCCCCcCCCCCCcceEeEEEECCEEEEEcCCccCCcC
Confidence            445778999999999999999988655 799999999999999999999999999999999999999998777777654

>d2e74d1 b.33.1.1 (D:46-179) ISP subunit from the cytochrome b6f complex, soluble domain {Mastigocladus laminosus [TaxId: 83541]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: ISP subunit from the cytochrome b6f complex, soluble domain
species: Mastigocladus laminosus [TaxId: 83541]

Probab=99.85  E-value=1e-21  Score=161.01  Aligned_cols=79  Identities=35%  Similarity=0.688  Sum_probs=70.2

Q ss_pred             cccCCCeEEEEecccCCCcccCCcCCCCCeEEcCCCCcEEcCCCceecCCCCCCCCCCceEeecCceEEEeecccCCCCC
Q psy6642         124 RVKDPSWLVIIGICTHLGCVPIANAGDWGGYYCPCHGSHYDASGRIRKGPAPTNMEVPPYQFGDEGILIRMLAHSDIRTP  203 (292)
Q Consensus       124 R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~~~CPcHGs~FD~~G~v~~gPa~~~L~~~p~~~~~d~i~V~I~ahtD~~~P  203 (292)
                      |+..++++|++++|||+||+|.++..+ +.|+||||||+||++|+++.||++.+|+.|+++++++.++|..|.++|.+.+
T Consensus        50 ~~~~g~~~A~~~~C~H~G~~l~~g~~~-~~~~Cp~Hg~~Fd~~G~~~~gPa~~~L~~y~v~v~~~~i~V~p~~~~~~~~g  128 (134)
T d2e74d1          50 SKEAIRDYGINAVCTHLGCVVPWNAAE-NKFKCPCHGSQYDETGKVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRTG  128 (134)
T ss_dssp             ---CCCSEEEECBCTTTCCBCCBCTTT-SCEEETTTTEEECSSSCBCSSSCCSCCCEEEEECCTTSCEEEECCSCCTTTS
T ss_pred             eCCCCcEEEEeccccCCEEEccccccC-CccCCCCCCcEECCCCCEEeCCCCCCcceeeEEEECCEEEEeCCcccCCCCC
Confidence            446789999999999999999998765 7899999999999999999999999999999999999999988888876543

>d1g8kb_ b.33.1.1 (B:) Arsenite oxidase Rieske subunit {Alcaligenes faecalis [TaxId: 511]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Arsenite oxidase Rieske subunit
species: Alcaligenes faecalis [TaxId: 511]

Probab=99.82  E-value=1.1e-20  Score=154.65  Aligned_cols=100  Identities=18%  Similarity=0.375  Sum_probs=82.4

Q ss_pred             ecCCCCCCCeEEEEE--cCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCC
Q psy6642          75 DLNLIPEGQSVTFKW--RGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWG  152 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~--~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~  152 (292)
                      .+++|++|+.+.|.+  .+.|+++++....                 ....+..+++++||+++|||+||+|.++.. .+
T Consensus        13 ~~~~l~~~~p~~f~yp~~~~p~~lVr~g~~-----------------v~~~~g~~g~i~A~~~~CpH~g~~l~~~~~-~~   74 (133)
T d1g8kb_          13 VAKNLAANEPVSFTYPDTSSPCVAVKLGAP-----------------VPGGVGPDDDIVAYSVLCTHMGCPTSYDSS-SK   74 (133)
T ss_dssp             EGGGCCBTCCEEEECSSTTSEEEEEECSSC-----------------CTTCBTTTTCEEEEECBCTTTCCBCEEETT-TT
T ss_pred             EHHHCCCCCCEEEeccCCCCCEEEEEcCCc-----------------eeEEECCCCEEEEEehhcCCCCcccccCcc-cC
Confidence            688999999999997  6678887764211                 111233589999999999999999998764 47


Q ss_pred             eEEcCCCCcEEcC--CCceecCCCCCCCCCCceEeecCceEE
Q psy6642         153 GYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPYQFGDEGILI  192 (292)
Q Consensus       153 ~~~CPcHGs~FD~--~G~v~~gPa~~~L~~~p~~~~~d~i~V  192 (292)
                      .|.||||||+||+  +|+++.||++++|+.++++++++...|
T Consensus        75 ~i~Cp~Hg~~Fd~~~~G~~~~gPa~~~L~~~~v~ve~~~~~I  116 (133)
T d1g8kb_          75 TFSCPCHFTEFDAEKAGQMICGEATADLPRVLLRYDAASDAL  116 (133)
T ss_dssp             EEECTTTCCEEEGGGTTEEEESSCSSCCCEEEEEEETTTTEE
T ss_pred             EEECCCCCeEEecCCCceEeCCCCCCCCCeEeEEEECCCCEE
Confidence            8999999999997  699999999999999999999865443

>d1fqta_ b.33.1.1 (A:) Rieske-type ferredoxin associated with biphenyl dioxygenase {Burkholderia cepacia [TaxId: 292]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Rieske-type ferredoxin associated with biphenyl dioxygenase
species: Burkholderia cepacia [TaxId: 292]

Probab=99.82  E-value=3e-20  Score=146.52  Aligned_cols=93  Identities=18%  Similarity=0.325  Sum_probs=83.4

Q ss_pred             ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CCCCe
Q psy6642          75 DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GDWGG  153 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~~~~  153 (292)
                      ++++|++|+.+.+...+++++|.+                           .+++++|+++.|||+|++|..+. .+++.
T Consensus         8 ~~~dl~~g~~~~~~~~~~~i~v~r---------------------------~~~~~~A~~~~CpH~g~~l~~g~~~~~~~   60 (109)
T d1fqta_           8 DRRDVPEGEALKVESGGTSVAIFN---------------------------VDGELFATQDRCTHGDWSLSDGGYLEGDV   60 (109)
T ss_dssp             EGGGSCTTCEEEEEETTEEEEEEE---------------------------ETTEEEEEESBCTTSSCBSSTTCCEETTE
T ss_pred             EHHHCCCCCEEEEEECCEEEEEEE---------------------------ECCEEEEEEeeccccCcccccceeecCCE
Confidence            789999999999999999988765                           25789999999999999998764 34578


Q ss_pred             EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         154 YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       154 ~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      +.||+|||+||+ +|+++.+|+..+|++|++++++|.|+|.+
T Consensus        61 i~Cp~H~~~F~l~tG~~~~~p~~~~l~~~~v~~~~g~i~v~~  102 (109)
T d1fqta_          61 VECSLHMGKFCVRTGKVKSPPPCEALKIFPIRIEDNDVLVDF  102 (109)
T ss_dssp             EECTTTCCEEETTTCCEEESSCCSCCCBCCEEEETTEEEECT
T ss_pred             EEccccCCEEECCCccCccCCCCCCCCEEeEEEECCEEEEEe
Confidence            999999999998 99999999999999999999999888764

>d3c0da1 b.33.1.3 (A:4-111) NADH-nitrite reductase small subunit NirD {Vibrio parahaemolyticus [TaxId: 670]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: NirD-like
domain: NADH-nitrite reductase small subunit NirD
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=99.81  E-value=1.2e-20  Score=148.55  Aligned_cols=97  Identities=10%  Similarity=0.038  Sum_probs=81.7

Q ss_pred             ccee-ecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-
Q psy6642          71 TIEV-DLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-  148 (292)
Q Consensus        71 ~~~v-~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-  148 (292)
                      ++.+ .+++|++|+.+.+.+.|++++|.+                          ..+|+++|+++.|||+|++|.++. 
T Consensus         3 ~v~vc~~~dl~~g~~~~~~~~g~~i~v~r--------------------------~~~g~~~A~~~~CpH~g~~L~~~g~   56 (108)
T d3c0da1           3 KVKLCQLDDLMPFIGATVLIEGERVALFY--------------------------IPDSGVYAVQDWDPIGKAYVMSRGI   56 (108)
T ss_dssp             EEEEEEGGGSCBTCCEEEEETTEEEEEEE--------------------------ETTTEEEEEESEETTTTEECGGGSE
T ss_pred             cEEEEEHHHCCCCCEEEEEECCEEEEEEE--------------------------eCCCCEEEEEccCCCCCcccccccE
Confidence            3455 789999999999999999988754                          347899999999999999986643 


Q ss_pred             ----CCCCeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         149 ----GDWGGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       149 ----~~~~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                          .+...+.||||||+||+ +|+++.+|+ .+|+.||+++++|.|+|.+
T Consensus        57 ~~~~~~~~~i~Cp~Hg~~Fdl~tG~~~~~p~-~~l~~y~v~v~~g~V~V~~  106 (108)
T d3c0da1          57 VGDINGEMCVASPLYKQHFSLKSGQCLEDEA-HCLKTWRVTVDDNQVCYLA  106 (108)
T ss_dssp             EEESSSSEEEECTTTCCEEETTTCBBSSCTT-CBCCEECEEESSSEEEEEC
T ss_pred             EEecCCceEEeccccccEEeccCCccccCCC-CcccEEeEEEECCEEEEEe
Confidence                12246899999999998 999998886 4799999999999998764

>d1vm9a_ b.33.1.1 (A:) Toluene-4-monooxygenase system protein C, TmoC {Pseudomonas mendocina [TaxId: 300]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Toluene-4-monooxygenase system protein C, TmoC
species: Pseudomonas mendocina [TaxId: 300]

Probab=99.80  E-value=3.3e-20  Score=146.19  Aligned_cols=93  Identities=17%  Similarity=0.256  Sum_probs=81.5

Q ss_pred             ecCCCCCCCeEEEEE-cCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcCCCCCe
Q psy6642          75 DLNLIPEGQSVTFKW-RGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANAGDWGG  153 (292)
Q Consensus        75 ~~s~l~~g~~~~~~~-~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~~~~~~  153 (292)
                      ++++|++|+...+.+ .|++++|++                          ..+|+++|+++.|||+|++|.++..+++.
T Consensus         7 ~~~dl~~g~~~~~~~~~g~~v~v~r--------------------------~~~g~~~A~~~~CpH~g~~l~~g~~~~~~   60 (109)
T d1vm9a_           7 SLDDIWVGEMETFETSDGTEVLIVN--------------------------SEEHGVKAYQAMCPHQEILLSEGSYEGGV   60 (109)
T ss_dssp             EGGGSCTTCEEEEECTTCCEEEEEE--------------------------ETTTEEEEEESBCSSSSCBGGGSEEETTE
T ss_pred             EHHHCCCCCeEEEEecCCeEEEEEE--------------------------eCCCeEEEEEeeCCCCCccceeEeccCCE
Confidence            789999999999998 467877653                          35789999999999999999988766789


Q ss_pred             EEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         154 YYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       154 ~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      |.||||||+||+ +|+++ +|+..+|+.|++++++|.|+|.+
T Consensus        61 i~Cp~Hg~~F~l~~G~~~-~p~~~~L~~~~v~v~~g~v~V~~  101 (109)
T d1vm9a_          61 ITCRAHLWTFNDGTGHGI-NPDDAALAEYPVEVKGDDIYVST  101 (109)
T ss_dssp             EECTTTCCEEETTTCBBS-SSSSCBCCEECEEEETTEEEECC
T ss_pred             EEcccCCceEECCCccCC-CCCCCCccEEeEEEECCEEEEEe
Confidence            999999999999 89997 57788999999999999888764

>d1jm1a_ b.33.1.1 (A:) Rieske protein II (SoxF) {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Rieske protein II (SoxF)
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=99.78  E-value=1.4e-19  Score=157.58  Aligned_cols=61  Identities=30%  Similarity=0.660  Sum_probs=54.6

Q ss_pred             CCCeEEEEecccCCCcccCCc-----------CCCCCeEEcCCCCcEEcC--CCceecCCCCCCCCCCceEeec
Q psy6642         127 DPSWLVIIGICTHLGCVPIAN-----------AGDWGGYYCPCHGSHYDA--SGRIRKGPAPTNMEVPPYQFGD  187 (292)
Q Consensus       127 ~g~~~a~~~~CtHlGc~l~~~-----------~~~~~~~~CPcHGs~FD~--~G~v~~gPa~~~L~~~p~~~~~  187 (292)
                      +++++||+++|||+||++.+.           ..+.+.|+||||||+||+  +|+|+.|||+++|+++++++++
T Consensus        82 ~~~ivA~s~iCtHlGC~~~~~~~~~~~~~~~~~~~~~~i~CpcHgS~FD~~~gG~v~~GPA~~pLp~v~Le~d~  155 (202)
T d1jm1a_          82 NGTIFAFSDVCVHLGCQLPAQVIVSSESDPGLYAKGADLHCPCHGSIYALKDGGVVVSGPAPRPLPIVILDYDS  155 (202)
T ss_dssp             TTCEEEEESBCTTTCCBCCTTEEESSTTSSEEETTTTEEECTTTCCEEEGGGTSEEEESSCCSCCCBEEEEECT
T ss_pred             CCeEEEEeCcCCCCCCcccccccccccccccccCCCCEEEccCcCCEEcCCCCCeEeCCCCCCCcCccEEEEeC
Confidence            679999999999999999763           124578999999999998  5999999999999999999986

>d2jo6a1 b.33.1.3 (A:1-108) NADH-nitrite reductase small subunit NirD {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: NirD-like
domain: NADH-nitrite reductase small subunit NirD
species: Escherichia coli [TaxId: 562]

Probab=99.76  E-value=7.4e-19  Score=138.22  Aligned_cols=94  Identities=10%  Similarity=-0.006  Sum_probs=78.3

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCccc-CCcC----
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVP-IANA----  148 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l-~~~~----  148 (292)
                      ..+++|++|+.+.+...|+++.|.+.                         ..+|+++|+.+.|||+|+++ +.+.    
T Consensus         8 c~~~dl~~g~~~~~~~~g~~i~l~r~-------------------------~~~g~v~A~~~~CpH~g~~ll~~G~~~~~   62 (108)
T d2jo6a1           8 CKIDDILPETGVCALLGDEQVAIFRP-------------------------YHSDQVFAISNIDPFFESSVLSRGLIAEH   62 (108)
T ss_dssp             EETTTSCTTEEEEEEETTEEEEEEEC-------------------------SSSSCCEEEESSCSSSCCSCSTTSEEEEE
T ss_pred             eEHHHCCCCCeEEEEECCEEEEEEEE-------------------------CcCCEEEEEECcCCCCCCccccceeEecc
Confidence            37899999999999999999877541                         14789999999999999984 4332    


Q ss_pred             CCCCeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEE
Q psy6642         149 GDWGGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIR  193 (292)
Q Consensus       149 ~~~~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~  193 (292)
                      .+...+.||+|||+||+ +|+++.+|+ .+|+.||+++++|.|+|+
T Consensus        63 ~~~~~i~Cp~Hg~~F~l~tG~~~~~p~-~~l~~y~v~v~~g~V~V~  107 (108)
T d2jo6a1          63 QGELWVASPLKKQRFRLSDGLCMEDEQ-FSVKHYEARVKDGVVQLR  107 (108)
T ss_dssp             TTEEEEEETTTTEEEETTTTEETTTTT-TCCCEEEEEEETTEEEEE
T ss_pred             ccCCEEECCCCCceEECCCccCCCCCC-CcccEEeEEEECCEEEEe
Confidence            12246899999999998 999999886 589999999999988875

>d2jzaa1 b.33.1.3 (A:1-122) NADH-nitrite reductase small subunit NirD {Erwinia carotovora [TaxId: 554]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: NirD-like
domain: NADH-nitrite reductase small subunit NirD
species: Erwinia carotovora [TaxId: 554]

Probab=99.75  E-value=1.4e-18  Score=139.68  Aligned_cols=95  Identities=15%  Similarity=0.056  Sum_probs=79.9

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcc-cCCcC----
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCV-PIANA----  148 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~-l~~~~----  148 (292)
                      ..+++|++|+.+.+.+.|+++.|.+.                         ..+|+++|+.+.|||+|++ ++.+.    
T Consensus         8 c~~~dl~~g~~~~v~v~g~~v~l~~~-------------------------~~~g~v~A~~~~CpH~g~~ll~~G~v~~~   62 (122)
T d2jzaa1           8 CKLDDILPGTGVCALVEQQQIAVFRP-------------------------RNDEQVYAISNIDPFAQASVLSRGIVAEH   62 (122)
T ss_dssp             EETTTSCTTBCCEEEETTEEEEEEBC-------------------------SSSSCCEEEBCCCTTTSSGGGTSSEEEES
T ss_pred             EEHHHcCCCCeEEEEECCEEEEEEEE-------------------------cCCCEEEEEecCCCcccccccccceeeec
Confidence            47899999999999999999877541                         1378999999999999998 44442    


Q ss_pred             CCCCeEEcCCCCcEEcC-CCceecCCCCCCCCCCceEeecCceEEEe
Q psy6642         149 GDWGGYYCPCHGSHYDA-SGRIRKGPAPTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       149 ~~~~~~~CPcHGs~FD~-~G~v~~gPa~~~L~~~p~~~~~d~i~V~I  194 (292)
                      .+...+.||+|||+||+ +|+++.+|+ .+|+.|++++++|.|+|.+
T Consensus        63 ~~~~~i~Cp~Hg~~F~l~tG~~~~~p~-~~l~~~~v~v~~g~V~v~~  108 (122)
T d2jzaa1          63 QDDLWVASPLKKQHFRLYDGFCLEDGA-YSVAAYDTQVTNGNVQISI  108 (122)
T ss_dssp             SSSEEEECSSSCCEEETTTCCBSSCCS-SCCBCCCEEESSSEEEEEC
T ss_pred             cCCCEEECCCCCCeeecccceeeeccc-cCCCccceEEECCEEEEEe
Confidence            23357999999999998 899999887 6899999999999998875

>d1z01a1 b.33.1.2 (A:16-163) 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component OxoO {Pseudomonas putida [TaxId: 303]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Ring hydroxylating alpha subunit ISP domain
domain: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component OxoO
species: Pseudomonas putida [TaxId: 303]

Probab=99.73  E-value=5.1e-18  Score=140.42  Aligned_cols=95  Identities=18%  Similarity=0.218  Sum_probs=79.9

Q ss_pred             eeecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC--CC
Q psy6642          73 EVDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA--GD  150 (292)
Q Consensus        73 ~v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~--~~  150 (292)
                      ....++|++|+.+.+.+.|++|++.+                           .+|+++|+.|.|||+|++|+.+.  .+
T Consensus        32 v~~~~el~~g~~~~~~i~g~~vvl~~---------------------------~~g~i~A~~n~CpHrg~~L~~g~~~~~   84 (148)
T d1z01a1          32 ALFTHELEEDQVQGIQICGVPIVLRR---------------------------VNGKVFALKDQCLHRGVRLSEKPTCFT   84 (148)
T ss_dssp             EEEGGGSCBTCEEEEEETTEEEEEEE---------------------------ETTEEEEEESSCTTTCCCGGGSCCCSS
T ss_pred             EEEHHHCCCCCeEEEEECCEEEEEEE---------------------------ECCEEEEEEeecCccccEeEccccccc
Confidence            34678999999999999999986643                           47899999999999999998874  34


Q ss_pred             CCeEEcCCCCcEEcC-CCceecCCC--------CCCCCCCceEeecCceEEEe
Q psy6642         151 WGGYYCPCHGSHYDA-SGRIRKGPA--------PTNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       151 ~~~~~CPcHGs~FD~-~G~v~~gPa--------~~~L~~~p~~~~~d~i~V~I  194 (292)
                      ++.|.||||||+||+ +|++...|+        ...|+.|++++.+|.|+|.+
T Consensus        85 ~~~i~Cp~Hgw~fd~~~G~~~~~p~~~~~~~~~~~~l~~y~v~~~~g~I~v~l  137 (148)
T d1z01a1          85 KSTISCWYHGFTFDLETGKLVTIVANPEDKLIGTTGVTTYPVHEVNGMIFVFV  137 (148)
T ss_dssp             TTEEECTTTCEEEETTTCBEEEETTCTTCTTTTSCBCCEECEEEETTEEEEEE
T ss_pred             cCEEEecccCCEEecCcceEecccccccccCCccCCcceEEEEEECCEEEEEe
Confidence            578999999999999 799988765        35688999999999777765

>d2de6a1 b.33.1.2 (A:1-142) Terminal oxygenase component of carbazole CarAa {Janthinobacterium sp. j3 [TaxId: 213804]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Ring hydroxylating alpha subunit ISP domain
domain: Terminal oxygenase component of carbazole CarAa
species: Janthinobacterium sp. j3 [TaxId: 213804]

Probab=99.71  E-value=2.1e-17  Score=135.76  Aligned_cols=94  Identities=19%  Similarity=0.223  Sum_probs=79.1

Q ss_pred             eecCCCCCCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC--CCC
Q psy6642          74 VDLNLIPEGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA--GDW  151 (292)
Q Consensus        74 v~~s~l~~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~--~~~  151 (292)
                      ...++|++|+.+.+.+.|++++|.+                           .+|+++|+.|.|||+|++|+.+.  .+.
T Consensus        33 ~~~~el~~g~~~~~~i~g~~ivv~r---------------------------~~g~v~a~~n~CpHrga~L~~g~~~~~~   85 (142)
T d2de6a1          33 MFSKEINEGEPKTLKLLGENLLVNR---------------------------IDGKLYCLKDRCLHRGVQLSVKVECKTK   85 (142)
T ss_dssp             EEGGGSCBTCCEEEEETTEEEEEEE---------------------------ETTEEEEEESSCTTTCCCGGGGCCCCST
T ss_pred             EEHHHCCCCCeEEEEECCEEEEEEE---------------------------cCCEEEEEeCccCCCCccCCcccccccc
Confidence            4678999999999999999987753                           37899999999999999998764  334


Q ss_pred             CeEEcCCCCcEEcC-CCceecCCCC--------CCCCCCceEeecCceEEEe
Q psy6642         152 GGYYCPCHGSHYDA-SGRIRKGPAP--------TNMEVPPYQFGDEGILIRM  194 (292)
Q Consensus       152 ~~~~CPcHGs~FD~-~G~v~~gPa~--------~~L~~~p~~~~~d~i~V~I  194 (292)
                      +.|.||+|||+||+ +|+++..|+.        ..|..||+++.+|.|+|.+
T Consensus        86 ~~i~Cp~Hgw~fdl~~G~~~~~p~~~~~~~~~~~~l~~y~v~e~~G~I~v~l  137 (142)
T d2de6a1          86 STITCWYHAWTYRWEDGVLCDILTNPTSAQIGRQKLKTYPVQEAKGCVFIYL  137 (142)
T ss_dssp             TEEECTTTCEEEETTTCBEEEETTCTTCTTTTSCBCCBCCEEEETTEEEEEE
T ss_pred             CEEeccceeeEEeccCCceEecCCCcccCCccccCCCEEeEEEECCEEEEEe
Confidence            68999999999998 8999877653        3588999999998777765

>d1ppje2 f.23.12.1 (E:1-69) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Cow (Bos taurus) [TaxId: 9913]}

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.64  E-value=1.6e-17  Score=119.89  Aligned_cols=65  Identities=49%  Similarity=0.749  Sum_probs=60.1

Q ss_pred             cccCCCCCCccccccCCCCCCC----ccccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCHHhh
Q psy6642         196 AHSDIRTPDFSKYRRDRNPDKG----QEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVL  260 (292)
Q Consensus       196 ahtD~~~P~F~~yr~~~~~~~~----~~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~~~~  260 (292)
                      +|||+++|||++||+++++|++    +++.+||.|.|+++|+++++++++|+.+|..||++|+||+|+|
T Consensus         1 aHTDi~vPDFs~YRr~~~~d~~~~~~~s~~~Rk~fsYl~~g~~~v~~ay~AK~~V~~fvssmSaSADVL   69 (69)
T d1ppje2           1 SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVL   69 (69)
T ss_dssp             CGGGCCCCCCTTTBCGGGCCTTSCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCTTGG
T ss_pred             CCCCcCCCCchhhccccccCcccccccCcchhceehhhhhhhHHHHHHHHHHHHHHHHHHhcCcccccC
Confidence            6999999999999999988864    3456799999999999999999999999999999999999986

>d2b1xa1 b.33.1.2 (A:1-162) Naphthalene 1,2-dioxygenase alpha subunit, N-domain {Rhodococcus sp. ncimb12038 [TaxId: 92694]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Ring hydroxylating alpha subunit ISP domain
domain: Naphthalene 1,2-dioxygenase alpha subunit, N-domain
species: Rhodococcus sp. ncimb12038 [TaxId: 92694]

Probab=99.55  E-value=7.9e-15  Score=123.09  Aligned_cols=76  Identities=21%  Similarity=0.329  Sum_probs=64.6

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CCCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GDWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~~~  152 (292)
                      ..++|+ +|..+++.+.|.++++.+                          +.+|++.|+.|+|+|+|+.+..+. ++.+
T Consensus        51 ~~~el~~~g~~~~~~~~~~~~vv~R--------------------------~~dG~i~a~~N~C~HRG~~l~~~~~g~~~  104 (162)
T d2b1xa1          51 HESEIPERGDYVVRYISEDQFIVCR--------------------------DEGGEIRGHLNACRHRGMQVCRAEMGNTS  104 (162)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEEE--------------------------CTTSCEEEEESSCTTTCCCSCCSSEEECS
T ss_pred             EHHHcCCccceeeEeecCCceEEEe--------------------------cCCcceEEeecccccCcccccccccCccc
Confidence            568887 688888999999987753                          468999999999999999988765 4557


Q ss_pred             eEEcCCCCcEEcCCCceecCCCCC
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPAPT  176 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa~~  176 (292)
                      .|.||+|||+||.+|++...|...
T Consensus       105 ~i~CpYHgW~yd~~G~l~~~P~~~  128 (162)
T d2b1xa1         105 HFRCPYHGWTYSNTGSLVGVPAGK  128 (162)
T ss_dssp             EEECTTTCCEEETTSCEEECTTTT
T ss_pred             cccCCCceeEEcCCCCeEECCCcc
Confidence            899999999999999999988643

>d2bmoa1 b.33.1.2 (A:3-152) Nitrobenzene dioxygenase alpha subunit, NBDO-alpha {Comamonas sp. JS765 [TaxId: 58226]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Ring hydroxylating alpha subunit ISP domain
domain: Nitrobenzene dioxygenase alpha subunit, NBDO-alpha
species: Comamonas sp. JS765 [TaxId: 58226]

Probab=99.54  E-value=1.1e-14  Score=120.85  Aligned_cols=74  Identities=26%  Similarity=0.472  Sum_probs=63.5

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CCCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GDWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~~~  152 (292)
                      -.++|+ +|.-+++.+.+.++++.+                          +.+|++.|+.|+|+|+|+.|..+. +..+
T Consensus        40 ~~~elp~~Gd~~~~~i~~~~~vv~R--------------------------~~dg~i~af~N~C~HRG~~L~~~~~g~~~   93 (150)
T d2bmoa1          40 HDSLIPSPGDYVKAKMGVDEVIVSR--------------------------QNDGSVRAFLNVCRHRGKTLVHAEAGNAK   93 (150)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEEE--------------------------CTTSCEEEEESBCTTTCCBCCCSSEEECS
T ss_pred             hHHHcCCCcceeeeeecCceeEEEe--------------------------cCCCchhhhhhhccccccccccccccccc
Confidence            467786 688888999999988753                          468999999999999999999886 3557


Q ss_pred             eEEcCCCCcEEcCCCceecCCC
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPA  174 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa  174 (292)
                      .+.||+|||+||.+|+++..|.
T Consensus        94 ~i~CpYHgW~yd~~G~l~~~P~  115 (150)
T d2bmoa1          94 GFVCGYHGWGYGSNGELQSVPF  115 (150)
T ss_dssp             EEECTTTCCEEETTSCEEECTT
T ss_pred             ceEecccceeeccccchhcCCC
Confidence            8999999999999999998774

>d1ulia1 b.33.1.2 (A:17-170) Biphenyl dioxygenase large subunit BphA1, N-terminal domain {Rhodococcus sp. (strain RHA1) [TaxId: 101510]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Ring hydroxylating alpha subunit ISP domain
domain: Biphenyl dioxygenase large subunit BphA1, N-terminal domain
species: Rhodococcus sp. (strain RHA1) [TaxId: 101510]

Probab=99.53  E-value=1.1e-14  Score=121.10  Aligned_cols=74  Identities=24%  Similarity=0.412  Sum_probs=62.6

Q ss_pred             ecCCCC-CCCeEEEEEcCeeEEEEeCChhhhhhcccccccccCCCCcccccccCCCeEEEEecccCCCcccCCcC-CCCC
Q psy6642          75 DLNLIP-EGQSVTFKWRGKPLFIRHRTQKEIDTEQNTNISQLRDPQADSDRVKDPSWLVIIGICTHLGCVPIANA-GDWG  152 (292)
Q Consensus        75 ~~s~l~-~g~~~~~~~~g~pv~i~~~t~~~i~~~~~v~~~~l~dp~~~~~R~~~g~~~a~~~~CtHlGc~l~~~~-~~~~  152 (292)
                      -.++|+ +|..+++.+.+.|++|.+                          +.+|++.|+.|+|+|+|+.|..+. ++.+
T Consensus        45 ~~~el~~~g~~~~~~i~~~~ilv~R--------------------------~~~g~i~af~N~C~HRG~~L~~~~~g~~~   98 (154)
T d1ulia1          45 HETQIPKAGDFMTNYMGEDPVMVVR--------------------------QKNGEIRVFLNQCRHRGMRICRADGGNAK   98 (154)
T ss_dssp             EGGGSCSTTEEEEEEETTEEEEEEE--------------------------CTTSCEEEEESCCTTTCCCSCCSSEEECS
T ss_pred             EhhhCCCCcceeeeecCCcceeEEe--------------------------ecccceeeeecccccCCceeeecCCCccc
Confidence            467886 588888999999987753                          468999999999999999998754 4557


Q ss_pred             eEEcCCCCcEEcCCCceecCCC
Q psy6642         153 GYYCPCHGSHYDASGRIRKGPA  174 (292)
Q Consensus       153 ~~~CPcHGs~FD~~G~v~~gPa  174 (292)
                      .+.||+|||+||.+|+++..|.
T Consensus        99 ~l~CpYHgW~f~~~G~~~~iP~  120 (154)
T d1ulia1          99 SFTCSYHGWAYDTGGNLVSVPF  120 (154)
T ss_dssp             CEECTTTCCEECTTCCEEECTT
T ss_pred             eEEeeeceeEEecCCccccCCc
Confidence            8999999999999999998773

>d1ppje2 f.23.12.1 (E:1-69) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Cow (Bos taurus) [TaxId: 9913]}

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.49  E-value=5.5e-15  Score=106.45  Aligned_cols=65  Identities=51%  Similarity=0.770  Sum_probs=60.1

Q ss_pred             CCCCCCCCCccccccCCCCC--CCCC--CcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcchhhh
Q psy6642           3 AHSDIRTPDFSKYRRDRNPD--KGQE--ETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASADVL   67 (292)
Q Consensus         3 ~~~~~~~pd~~~yr~~~~~~--~~~~--~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a~~~   67 (292)
                      |||||..|||++||+...+|  ++++  +.+||.|.|+++|.++++++.+|+.++..|+.+|.+++|++
T Consensus         1 aHTDi~vPDFs~YRr~~~~d~~~~~~~s~~~Rk~fsYl~~g~~~v~~ay~AK~~V~~fvssmSaSADVL   69 (69)
T d1ppje2           1 SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVL   69 (69)
T ss_dssp             CGGGCCCCCCTTTBCGGGCCTTSCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCTTGG
T ss_pred             CCCCcCCCCchhhccccccCcccccccCcchhceehhhhhhhHHHHHHHHHHHHHHHHHHhcCcccccC
Confidence            79999999999999999888  5554  77999999999999999999999999999999999999975

>d3cx5e2 f.23.12.1 (E:31-86) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.17  E-value=5.3e-12  Score=86.64  Aligned_cols=55  Identities=35%  Similarity=0.609  Sum_probs=49.2

Q ss_pred             cCCCCCCccccccCCCCCCCccccccceeeehhHHHHHHHHHHhhhHhhhhhhhccCCCH
Q psy6642         198 SDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASA  257 (292)
Q Consensus       198 tD~~~P~F~~yr~~~~~~~~~~~~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p~~  257 (292)
                      ++.++|||++||+++..     ...||.|.|+++|++++++++||+.+|..||++|++||
T Consensus         2 s~~~vPDFs~Yr~~~~~-----~~~~r~fsY~mvGs~g~~~a~~AKstV~~FlssMSASA   56 (56)
T d3cx5e2           2 STYRTPNFDDVLKENND-----ADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATA   56 (56)
T ss_dssp             CTTSCCCCTTTBCCTTC-----TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCG
T ss_pred             CCCcCCCcHHhcCCCCC-----CcccceEEEEeeehhHHHHHHHHHHHHHHHHHhccccC
Confidence            57899999999986542     23589999999999999999999999999999999986

>d3cx5e2 f.23.12.1 (E:31-86) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.87  E-value=1.5e-09  Score=74.21  Aligned_cols=55  Identities=33%  Similarity=0.611  Sum_probs=48.4

Q ss_pred             CCCCCCCccccccCCCCCCCCCCcCchhhHHHHHHhHHHHHHHHHHHHHHHhhcCCCcch
Q psy6642           5 SDIRTPDFSKYRRDRNPDKGQEETQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSASA   64 (292)
Q Consensus         5 ~~~~~pd~~~yr~~~~~~~~~~~~~RR~fl~~atG~~~~~g~~aA~~~~~~~i~~~~p~a   64 (292)
                      +|+..|||.+||+.+     +...+||.|-|+.+|..+++++.+|+..+..|+.+|.+++
T Consensus         2 s~~~vPDFs~Yr~~~-----~~~~~~r~fsY~mvGs~g~~~a~~AKstV~~FlssMSASA   56 (56)
T d3cx5e2           2 STYRTPNFDDVLKEN-----NDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATA   56 (56)
T ss_dssp             CTTSCCCCTTTBCCT-----TCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCG
T ss_pred             CCCcCCCcHHhcCCC-----CCCcccceEEEEeeehhHHHHHHHHHHHHHHHHHhccccC
Confidence            689999999999864     2355799999999999999999999999999999998764

>d2e74d2 f.23.12.1 (D:12-45) ISP subunit from the cytochrome b6f complex, transmembrane anchor {Mastigocladus laminosus [TaxId: 83541]}

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: ISP subunit from the cytochrome b6f complex, transmembrane anchor
species: Mastigocladus laminosus [TaxId: 83541]

Probab=85.75  E-value=0.39  Score=27.79  Aligned_cols=22  Identities=18%  Similarity=0.240  Sum_probs=15.5

Q ss_pred             CcCchhhHHHHHHhHHHHHHHH
Q psy6642          27 ETQRKAFTYMIAGGSSVVGMVC   48 (292)
Q Consensus        27 ~~~RR~fl~~atG~~~~~g~~a   48 (292)
                      ++.||+|+...|-.+..+.+++
T Consensus         1 dmgrrqfmnlltfgt~tg~alg   22 (34)
T d2e74d2           1 DMGRRQFMNLLAFGTVTGVALG   22 (34)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHhhHHHHHHh
Confidence            4679999999987665444433

>d2e74d2 f.23.12.1 (D:12-45) ISP subunit from the cytochrome b6f complex, transmembrane anchor {Mastigocladus laminosus [TaxId: 83541]}

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: ISP transmembrane anchor
family: ISP transmembrane anchor
domain: ISP subunit from the cytochrome b6f complex, transmembrane anchor
species: Mastigocladus laminosus [TaxId: 83541]

Probab=83.08  E-value=0.15  Score=29.66  Aligned_cols=32  Identities=13%  Similarity=0.201  Sum_probs=23.7

Q ss_pred             cccceeeehhHHHHHHHHHHhhhHhhhhhhhccCC
Q psy6642         221 TQRKAFTYMIAGGSSVVGMVCAKSVVNQFISSMSA  255 (292)
Q Consensus       221 ~~rr~f~~~~~~~~~~~g~~~~~~~~~~~v~~~~p  255 (292)
                      ..||.|+.+++.+++...++   .+++|+++.+-|
T Consensus         2 mgrrqfmnlltfgt~tg~al---g~lypvvkyfip   33 (34)
T d2e74d2           2 MGRRQFMNLLAFGTVTGVAL---GALYPLVKYFIP   33 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHSC
T ss_pred             ccHHHHHHHHHHhhHHHHHH---hhhhhHHhhcCC
Confidence            35899999998776554443   567999988766