Citrus Sinensis ID: 041751

---

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---
Protein Sequence
MAVVSRTASRLALTSPATPRPTLLHSTRCFSSSSYSPSPSPSSSPQPRATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEHHHHHHHHHccccccccHHHHHHHHHHHHHccccccccccccccccccccccEEEEcccccHHHHHHHHHHHHccccccEEEEEcccccccccccccccEEccccEEccccEEcccccccHHHHHHHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccHHcccHHHHHHHccccccHHHHHHHHccccccccccccccccccccccccccccccccEEEEEcHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccHHccEEEEccccccccEEEEHHHHHHHHHHHHHHHHHccccccEEEEEccccccccEEEEEEEEEcccccEEEEEEEccccccHHHHHHHHHHHHHHHHHHcccEEEEEcc
Coil and Loop (DISEMBL)
MAVVSRtasrlaltspatprptllhstrcfssssyspspspssspqpratfgpvglskASEYVISKVDNLLnwvrrgslwpmTFGLACCAVEmmhtgaagydldrfgiifrpsprqsdvMIVAGTLTNKMAPALRKvydqmpeprwvismgsrangggyyhysysvvrgcdrivpvdiyvpgcpptAEALLYGILQLQKKINRRRDFLHWWTK
Flexible Loop (DISEMBL)
mavvsrtasrlaltspatprptllhSTRCFSSSSYSpspspssspqprATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK
Low Complexity Region (SEG)
MAVVSRTASRLALTSPATPRPTLLHSTRCFssssyspspspssspQPRATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANgggyyhysysvvrgCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK
Disordered region (IsUnstruct)
******************************************************GLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWW**
Disordered Region (DISOPRED)
*************************************************************YVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRD***WWTK
Disordered Region (DISEMBL)
***********ALTSPATPRPTLLHSTR**********************FGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK
Disordered Region (DISPRO)
*********RLA**SP*TPR*************************************KASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAVVSRTASRLALTSPATPRPTLLHSTRCFSSSSYSPSPSPSSSPQPRATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	213	2.2.26 [Sep-21-2011]
Q43844	213	NADH dehydrogenase [ubiqu	N/A	no	1.0	1.0	0.751	3e-91
P42027	215	NADH dehydrogenase [ubiqu	N/A	no	1.0	0.990	0.748	6e-89
Q42577	218	NADH dehydrogenase [ubiqu	yes	no	0.957	0.935	0.735	2e-88
O21272	182	NADH-ubiquinone oxidoredu	N/A	no	0.723	0.846	0.844	1e-76
P42026	216	NADH dehydrogenase [ubiqu	yes	no	0.859	0.847	0.729	8e-75
Q0MQI0	213	NADH dehydrogenase [ubiqu	yes	no	0.882	0.882	0.696	5e-74
O75251	213	NADH dehydrogenase [ubiqu	yes	no	0.882	0.882	0.696	7e-74
P0CB84	213	NADH dehydrogenase [ubiqu	N/A	no	0.882	0.882	0.696	8e-74
Q0MQH9	213	NADH dehydrogenase [ubiqu	N/A	no	0.882	0.882	0.696	8e-74
Q9DC70	224	NADH dehydrogenase [ubiqu	yes	no	0.723	0.687	0.798	9e-74

>sp|Q43844|NDUS7_SOLTU NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Solanum tuberosum PE=2 SV=1

 Score =  334 bits (856), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 160/213 (75%), Positives = 177/213 (83%)

Query: 1   MAVVSRTASRLALTSPATPRPTLLHSTRCFSSSSYSPSPSPSSSPQPRATFGPVGLSKAS 60
           MA+++R A  L  T+P   R   +H+T    S   + SP+ S   QP +   P G+SK +
Sbjct: 1   MALIARNAKLLTGTAPFLQRAATIHTTLPSLSQQPASSPATSGGAQPPSMNTPAGISKPA 60

Query: 61  EYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVM 120
           EYVISKVD+L+NW RRGS+WPMTFGLACCAVEMMH GAA YD DRFGIIFRPSPRQSDVM
Sbjct: 61  EYVISKVDDLMNWARRGSIWPMTFGLACCAVEMMHAGAARYDFDRFGIIFRPSPRQSDVM 120

Query: 121 IVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYV 180
           IVAGTLTNKMAPALRKVYDQMPEPRWVISMGS ANGGGYYHYSY+VVRGCDRIVPVDIYV
Sbjct: 121 IVAGTLTNKMAPALRKVYDQMPEPRWVISMGSCANGGGYYHYSYAVVRGCDRIVPVDIYV 180

Query: 181 PGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
           PGCPPTAEALLYGILQLQKKINRR+D L WWT+
Sbjct: 181 PGCPPTAEALLYGILQLQKKINRRKDLLMWWTQ 213

Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.
Solanum tuberosum (taxid: 4113)
EC: 1EC: .EC: 6EC: .EC: 9EC: 9EC: .EC: 3

>sp|P42027|NDUS7_BRAOL NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Brassica oleracea PE=2 SV=1

 Score =  326 bits (836), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 161/215 (74%), Positives = 180/215 (83%), Gaps = 2/215 (0%)

Query: 1   MAVVSR-TASRLALTSPATPRPTLLHSTRCFSSSSYSPSPSPSSSPQPRATFGPV-GLSK 58
           MA+++R TA+RL L   +     + H      + S + +P+  + P P +T  P  GLSK
Sbjct: 1   MAMITRNTATRLPLVLQSHRAAAVSHLHTSLPALSPATTPTSYTRPGPPSTSAPPPGLSK 60

Query: 59  ASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSD 118
            +E+VISKVD+L+NW RRGS+WPMTFGLACCAVEMMHTGAA YDLDRFGIIFRPSPRQSD
Sbjct: 61  TAEFVISKVDDLMNWARRGSIWPMTFGLACCAVEMMHTGAARYDLDRFGIIFRPSPRQSD 120

Query: 119 VMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDI 178
            MIVAGTLTNKMAPALRKVYDQMPEPRWVISMGS ANGGGYYHYSYSVVRGCDRIVPVDI
Sbjct: 121 CMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDI 180

Query: 179 YVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
           YVPGCPPTAEALLYG+LQLQKKINRR+DFLHWW K
Sbjct: 181 YVPGCPPTAEALLYGLLQLQKKINRRKDFLHWWNK 215

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

Brassica oleracea (taxid: 3712)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|Q42577|NDUS7_ARATH NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Arabidopsis thaliana GN=At5g11770 PE=1 SV=1

 Score =  325 bits (832), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 167/227 (73%), Positives = 184/227 (81%), Gaps = 23/227 (10%)

Query: 1   MAVVSR-TASRLALTSPATPRPTLLHSTRCFSSSSYS------PSPSPSSSPQP------ 47
           MA+++R TA+RL         P LL S R  +++S S      P+ SPS+SP        
Sbjct: 1   MAMITRNTATRL---------PLLLQSQRAVAAASVSHLHTSLPALSPSTSPTSYTRPGP 51

Query: 48  -RATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRF 106
              +  P GLSKA+E+VISKVD+L+NW R GS+WPMTFGLACCAVEMMHTGAA YDLDRF
Sbjct: 52  PSTSPPPPGLSKAAEFVISKVDDLMNWARTGSIWPMTFGLACCAVEMMHTGAARYDLDRF 111

Query: 107 GIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSV 166
           GIIFRPSPRQSD MIVAGTLTNKMAPALRKVYDQMPEPRWVISMGS ANGGGYYHYSYSV
Sbjct: 112 GIIFRPSPRQSDCMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSCANGGGYYHYSYSV 171

Query: 167 VRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
           VRGCDRIVPVDIYVPGCPPTAEALLYG+LQLQKKINRR+DFLHWW K
Sbjct: 172 VRGCDRIVPVDIYVPGCPPTAEALLYGLLQLQKKINRRKDFLHWWNK 218

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

Arabidopsis thaliana (taxid: 3702)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|O21272|NDUS7_RECAM NADH-ubiquinone oxidoreductase 20 kDa subunit OS=Reclinomonas americana GN=NAD10 PE=3 SV=1

 Score =  285 bits (730), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 130/154 (84%), Positives = 142/154 (92%)

Query: 60  SEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDV 119
           +E+++SK+D L+NW R+GSLWPMTFGLACCAVEMMH+ A+ YDLDRFGIIFRPSPRQSDV
Sbjct: 29  TEFIVSKMDELVNWARKGSLWPMTFGLACCAVEMMHSAASRYDLDRFGIIFRPSPRQSDV 88

Query: 120 MIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIY 179
           MIVAGTLTNKMAPALRKVYDQM EPRWV+SMGS ANGGGYYHYSYSVVRGCDRIVPVDIY
Sbjct: 89  MIVAGTLTNKMAPALRKVYDQMSEPRWVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIY 148

Query: 180 VPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
           VPGCPPTAEALLYG+LQLQKKI R R  L+W  K
Sbjct: 149 VPGCPPTAEALLYGLLQLQKKIKRSRKTLYWLQK 182

Reclinomonas americana (taxid: 48483)

EC: 1

EC: .

EC: 6

EC: .

EC: 5

EC: .

EC: 3

>sp|P42026|NDUS7_BOVIN NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Bos taurus GN=NDUFS7 PE=1 SV=1

 Score =  279 bits (714), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 135/185 (72%), Positives = 152/185 (82%), Gaps = 2/185 (1%)

Query: 31  SSSSYSPSPSPSSSPQPRATF-GPVGL-SKASEYVISKVDNLLNWVRRGSLWPMTFGLAC 88
           S ++ SPS +  +  Q RA    P  L S   EYV++K+D+L+NW RR SLWPMTFGLAC
Sbjct: 32  SMAADSPSSTQPAVSQARAVVPKPAALPSSRGEYVVAKLDDLINWARRSSLWPMTFGLAC 91

Query: 89  CAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVI 148
           CAVEMMH  A  YD+DRFG++FR SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+
Sbjct: 92  CAVEMMHMAAPRYDMDRFGVVFRASPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRYVV 151

Query: 149 SMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFL 208
           SMGS ANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKI R +   
Sbjct: 152 SMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKIKREKRLR 211

Query: 209 HWWTK 213
            W+ +
Sbjct: 212 IWYRR 216

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

Bos taurus (taxid: 9913)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|Q0MQI0|NDUS7_PANTR NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Pan troglodytes GN=NDUFS7 PE=2 SV=1

 Score =  277 bits (708), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 131/188 (69%), Positives = 148/188 (78%)

Query: 26  STRCFSSSSYSPSPSPSSSPQPRATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFG 85
             R    S  +  PS +    P+A       S   EYV++K+D+L+NW RR SLWPMTFG
Sbjct: 26  QARSVHQSVATDGPSSTQPALPKARAVAPKPSSRGEYVVAKLDDLVNWARRSSLWPMTFG 85

Query: 86  LACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR 145
           LACCAVEMMH  A  YD+DRFG++FR SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR
Sbjct: 86  LACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR 145

Query: 146 WVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRR 205
           +V+SMGS ANGGGYYHYSYSVVRGCDRIVPVDIY+PGCPPTAEALLYGILQLQ+KI R R
Sbjct: 146 YVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIYIPGCPPTAEALLYGILQLQRKIKRER 205

Query: 206 DFLHWWTK 213
               W+ +
Sbjct: 206 RLQIWYRR 213

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

Pan troglodytes (taxid: 9598)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|O75251|NDUS7_HUMAN NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Homo sapiens GN=NDUFS7 PE=1 SV=3

 Score =  276 bits (706), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 131/188 (69%), Positives = 148/188 (78%)

Query: 26  STRCFSSSSYSPSPSPSSSPQPRATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFG 85
             R    S  +  PS +    P+A       S   EYV++K+D+L+NW RR SLWPMTFG
Sbjct: 26  QARGVHQSVATDGPSSTQPALPKARAVAPKPSSRGEYVVAKLDDLVNWARRSSLWPMTFG 85

Query: 86  LACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR 145
           LACCAVEMMH  A  YD+DRFG++FR SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR
Sbjct: 86  LACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR 145

Query: 146 WVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRR 205
           +V+SMGS ANGGGYYHYSYSVVRGCDRIVPVDIY+PGCPPTAEALLYGILQLQ+KI R R
Sbjct: 146 YVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIYIPGCPPTAEALLYGILQLQRKIKRER 205

Query: 206 DFLHWWTK 213
               W+ +
Sbjct: 206 RLQIWYRR 213

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

Homo sapiens (taxid: 9606)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|P0CB84|NDUS7_PONPY NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Pongo pygmaeus GN=NDUFS7 PE=2 SV=1

 Score =  276 bits (706), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 131/188 (69%), Positives = 148/188 (78%)

Query: 26  STRCFSSSSYSPSPSPSSSPQPRATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFG 85
             R    S  +  PS +    P+A       S   EYV++K+D+L+NW RR SLWPMTFG
Sbjct: 26  QARGVHQSVATDGPSSTQPALPKARAVAPKPSSRGEYVVAKLDDLVNWARRSSLWPMTFG 85

Query: 86  LACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR 145
           LACCAVEMMH  A  YD+DRFG++FR SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR
Sbjct: 86  LACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR 145

Query: 146 WVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRR 205
           +V+SMGS ANGGGYYHYSYSVVRGCDRIVPVDIY+PGCPPTAEALLYGILQLQ+KI R R
Sbjct: 146 YVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIYIPGCPPTAEALLYGILQLQRKIKRER 205

Query: 206 DFLHWWTK 213
               W+ +
Sbjct: 206 RLQIWYRR 213

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

Pongo pygmaeus (taxid: 9600)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|Q0MQH9|NDUS7_GORGO NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Gorilla gorilla gorilla GN=NDUFS7 PE=2 SV=1

 Score =  276 bits (706), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 131/188 (69%), Positives = 148/188 (78%)

Query: 26  STRCFSSSSYSPSPSPSSSPQPRATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFG 85
             R    S  +  PS +    P+A       S   EYV++K+D+L+NW RR SLWPMTFG
Sbjct: 26  QARGVHQSVATDGPSSTQPALPKARAVAPKPSSRGEYVVAKLDDLVNWARRSSLWPMTFG 85

Query: 86  LACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR 145
           LACCAVEMMH  A  YD+DRFG++FR SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR
Sbjct: 86  LACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR 145

Query: 146 WVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRR 205
           +V+SMGS ANGGGYYHYSYSVVRGCDRIVPVDIY+PGCPPTAEALLYGILQLQ+KI R R
Sbjct: 146 YVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIYIPGCPPTAEALLYGILQLQRKIKRER 205

Query: 206 DFLHWWTK 213
               W+ +
Sbjct: 206 RLQIWYRR 213

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

Gorilla gorilla gorilla (taxid: 9595)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

>sp|Q9DC70|NDUS7_MOUSE NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Mus musculus GN=Ndufs7 PE=1 SV=1

 Score =  276 bits (705), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 123/154 (79%), Positives = 139/154 (90%)

Query: 60  SEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDV 119
           +EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+DRFG++FR SPRQ+DV
Sbjct: 71  AEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQADV 130

Query: 120 MIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIY 179
           MIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS ANGGGYYHYSYSVVRGCDRIVPVDIY
Sbjct: 131 MIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIY 190

Query: 180 VPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
           VPGCPPTAEALLYGILQLQ+KI R +    W+ +
Sbjct: 191 VPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR 224

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

Mus musculus (taxid: 10090)

EC: 1

EC: .

EC: 6

EC: .

EC: 9

EC: 9

EC: .

EC: 3

---

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	213
TAIR|locus:2181885	218	AT5G11770 [Arabidopsis thalian	1.0	0.977	0.665	1.4e-71
UNIPROTKB|A8WFQ0	179	NDUFS7 "NDUFS7 protein" [Bos t	0.788	0.938	0.688	3.5e-59
UNIPROTKB|P42026	216	NDUFS7 "NADH dehydrogenase [ub	0.788	0.777	0.688	3.5e-59
UNIPROTKB|P0CB83	213	NDUFS7 "NADH dehydrogenase [ub	0.737	0.737	0.707	9.3e-59
UNIPROTKB|E2R6E2	216	NDUFS7 "Uncharacterized protei	0.737	0.726	0.707	1.2e-58
UNIPROTKB|O75251	213	NDUFS7 "NADH dehydrogenase [ub	0.737	0.737	0.707	1.2e-58
UNIPROTKB|P0CB84	213	NDUFS7 "NADH dehydrogenase [ub	0.737	0.737	0.707	1.2e-58
UNIPROTKB|Q0MQH9	213	NDUFS7 "NADH dehydrogenase [ub	0.737	0.737	0.707	1.2e-58
UNIPROTKB|Q0MQI0	213	NDUFS7 "NADH dehydrogenase [ub	0.737	0.737	0.707	1.2e-58
UNIPROTKB|I3LHL4	218	NDUFS7 "Uncharacterized protei	0.737	0.720	0.707	1.9e-58

TAIR|locus:2181885 AT5G11770 [Arabidopsis thaliana (taxid:3702)]

 Score = 724 (259.9 bits), Expect = 1.4e-71, P = 1.4e-71
 Identities = 145/218 (66%), Positives = 160/218 (73%)

Query:     1 MAVVSR-TASRLAL---TSPATPRPTLLHSTRCFXXXXXXXXXXXXXXXQPRATFGPV-G 55
             MA+++R TA+RL L   +  A    ++ H                     P +T  P  G
Sbjct:     1 MAMITRNTATRLPLLLQSQRAVAAASVSHLHTSLPALSPSTSPTSYTRPGPPSTSPPPPG 60

Query:    56 LSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPR 115
             LSKA+E+VISKVD+L+NW R GS+WPMTFGLACCAVEMMHTGAA YDLDRFGIIFRPSPR
Sbjct:    61 LSKAAEFVISKVDDLMNWARTGSIWPMTFGLACCAVEMMHTGAARYDLDRFGIIFRPSPR 120

Query:   116 QSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVP 175
             QSD MIVAGTLTNKMAPALRKVYDQMPEPRWVISMGS AN              CDRIVP
Sbjct:   121 QSDCMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSCANGGGYYHYSYSVVRGCDRIVP 180

Query:   176 VDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
             VDIYVPGCPPTAEALLYG+LQLQKKINRR+DFLHWW K
Sbjct:   181 VDIYVPGCPPTAEALLYGLLQLQKKINRRKDFLHWWNK 218

GO:0005739 "mitochondrion" evidence=ISM;IDA

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

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

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

GO:0048038 "quinone binding" evidence=IEA

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

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

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

GO:0008270 "zinc ion binding" evidence=IDA

GO:0006486 "protein glycosylation" evidence=RCA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=RCA

GO:0009853 "photorespiration" evidence=RCA

GO:0051788 "response to misfolded protein" evidence=RCA

GO:0080129 "proteasome core complex assembly" evidence=RCA

UNIPROTKB|A8WFQ0 NDUFS7 "NDUFS7 protein" [Bos taurus (taxid:9913)]

 Score = 607 (218.7 bits), Expect = 3.5e-59, P = 3.5e-59
 Identities = 117/170 (68%), Positives = 130/170 (76%)

Query:    46 QPRATFG-PVGL-SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDL 103
             Q RA    P  L S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+
Sbjct:    10 QARAVVPKPAALPSSRGEYVVAKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDM 69

Query:   104 DRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXX 163
             DRFG++FR SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN        
Sbjct:    70 DRFGVVFRASPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYS 129

Query:   164 XXXXXXCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
                   CDRIVPVDIYVPGCPPTAEALLYGILQLQKKI R +    W+ +
Sbjct:   130 YSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKIKREKRLRIWYRR 179

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0048038 "quinone binding" evidence=IEA

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

UNIPROTKB|P42026 NDUFS7 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 607 (218.7 bits), Expect = 3.5e-59, P = 3.5e-59
 Identities = 117/170 (68%), Positives = 130/170 (76%)

Query:    46 QPRATFG-PVGL-SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDL 103
             Q RA    P  L S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+
Sbjct:    47 QARAVVPKPAALPSSRGEYVVAKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDM 106

Query:   104 DRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXX 163
             DRFG++FR SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN        
Sbjct:   107 DRFGVVFRASPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYS 166

Query:   164 XXXXXXCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
                   CDRIVPVDIYVPGCPPTAEALLYGILQLQKKI R +    W+ +
Sbjct:   167 YSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKIKREKRLRIWYRR 216

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

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

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0022900 "electron transport chain" evidence=IEA

GO:0048038 "quinone binding" evidence=IEA

UNIPROTKB|P0CB83 NDUFS7 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial" [Pongo abelii (taxid:9601)]

 Score = 603 (217.3 bits), Expect = 9.3e-59, P = 9.3e-59
 Identities = 111/157 (70%), Positives = 125/157 (79%)

Query:    57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQ 116
             S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+DRFG++FR SPRQ
Sbjct:    57 SSRGEYVVAKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQ 116

Query:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVPV 176
             SDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN              CDRIVPV
Sbjct:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPV 176

Query:   177 DIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
             DIY+PGCPPTAEALLYGILQLQ+KI R R    W+ +
Sbjct:   177 DIYIPGCPPTAEALLYGILQLQRKIKRERRLQIWYRR 213

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

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

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

UNIPROTKB|E2R6E2 NDUFS7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 111/157 (70%), Positives = 125/157 (79%)

Query:    57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQ 116
             S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+DRFG++FR SPRQ
Sbjct:    60 SSRGEYVVAKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQ 119

Query:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVPV 176
             SDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN              CDRIVPV
Sbjct:   120 SDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPV 179

Query:   177 DIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
             DIYVPGCPPTAEALLYGILQLQ+KI R +    W+ +
Sbjct:   180 DIYVPGCPPTAEALLYGILQLQRKIKREKKLRIWYRR 216

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0048038 "quinone binding" evidence=IEA

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

UNIPROTKB|O75251 NDUFS7 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 111/157 (70%), Positives = 125/157 (79%)

Query:    57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQ 116
             S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+DRFG++FR SPRQ
Sbjct:    57 SSRGEYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQ 116

Query:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVPV 176
             SDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN              CDRIVPV
Sbjct:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPV 176

Query:   177 DIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
             DIY+PGCPPTAEALLYGILQLQ+KI R R    W+ +
Sbjct:   177 DIYIPGCPPTAEALLYGILQLQRKIKRERRLQIWYRR 213

GO:0048038 "quinone binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

GO:0002020 "protease binding" evidence=IEA

GO:0043005 "neuron projection" evidence=IEA

GO:0043025 "neuronal cell body" evidence=IEA

GO:0097060 "synaptic membrane" evidence=IEA

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

GO:0016655 "oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor" evidence=NAS

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

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

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

GO:0003954 "NADH dehydrogenase activity" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005743 "mitochondrial inner membrane" evidence=TAS

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

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

UNIPROTKB|P0CB84 NDUFS7 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial" [Pongo pygmaeus (taxid:9600)]

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 111/157 (70%), Positives = 125/157 (79%)

Query:    57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQ 116
             S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+DRFG++FR SPRQ
Sbjct:    57 SSRGEYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQ 116

Query:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVPV 176
             SDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN              CDRIVPV
Sbjct:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPV 176

Query:   177 DIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
             DIY+PGCPPTAEALLYGILQLQ+KI R R    W+ +
Sbjct:   177 DIYIPGCPPTAEALLYGILQLQRKIKRERRLQIWYRR 213

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

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

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

UNIPROTKB|Q0MQH9 NDUFS7 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial" [Gorilla gorilla gorilla (taxid:9595)]

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 111/157 (70%), Positives = 125/157 (79%)

Query:    57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQ 116
             S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+DRFG++FR SPRQ
Sbjct:    57 SSRGEYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQ 116

Query:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVPV 176
             SDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN              CDRIVPV
Sbjct:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPV 176

Query:   177 DIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
             DIY+PGCPPTAEALLYGILQLQ+KI R R    W+ +
Sbjct:   177 DIYIPGCPPTAEALLYGILQLQRKIKRERRLQIWYRR 213

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

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

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

UNIPROTKB|Q0MQI0 NDUFS7 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial" [Pan troglodytes (taxid:9598)]

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 111/157 (70%), Positives = 125/157 (79%)

Query:    57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQ 116
             S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+DRFG++FR SPRQ
Sbjct:    57 SSRGEYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQ 116

Query:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVPV 176
             SDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN              CDRIVPV
Sbjct:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPV 176

Query:   177 DIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
             DIY+PGCPPTAEALLYGILQLQ+KI R R    W+ +
Sbjct:   177 DIYIPGCPPTAEALLYGILQLQRKIKRERRLQIWYRR 213

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

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

GO:0003954 "NADH dehydrogenase activity" evidence=ISS

UNIPROTKB|I3LHL4 NDUFS7 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 600 (216.3 bits), Expect = 1.9e-58, P = 1.9e-58
 Identities = 111/157 (70%), Positives = 125/157 (79%)

Query:    57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQ 116
             S   EYV++K+D+L+NW RR SLWPMTFGLACCAVEMMH  A  YD+DRFG++FR SPRQ
Sbjct:    62 SSRGEYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQ 121

Query:   117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVPV 176
             SDVMIVAGTLTNKMAPALRKVYDQMPEPR+V+SMGS AN              CDRIVPV
Sbjct:   122 SDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPV 181

Query:   177 DIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
             DIYVPGCPPTAEALLYGILQLQ+KI R +    W+ +
Sbjct:   182 DIYVPGCPPTAEALLYGILQLQRKIKREKRLRIWYRR 218

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0048038 "quinone binding" evidence=IEA

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

---

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)
B0RR99	NUOB_XANCB	1, ., 6, ., 9, 9, ., 5	0.8661	0.6666	0.7717	yes	no
Q1LPW2	NUOB_RALME	1, ., 6, ., 9, 9, ., 5	0.8521	0.6666	0.8875	yes	no
Q9DC70	NDUS7_MOUSE	1, ., 6, ., 9, 9, ., 3	0.7987	0.7230	0.6875	yes	no
Q54NI6	NDUS7_DICDI	No assigned EC number	0.7908	0.7183	0.8595	yes	no
B2JDM7	NUOB_BURP8	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8930	yes	no
B2I785	NUOB_XYLF2	1, ., 6, ., 9, 9, ., 5	0.8541	0.6760	0.7826	yes	no
Q42577	NDUS7_ARATH	1, ., 6, ., 9, 9, ., 3	0.7356	0.9577	0.9357	yes	no
Q87EQ4	NUOB_XYLFT	1, ., 6, ., 9, 9, ., 5	0.8541	0.6760	0.7826	yes	no
Q0MQH9	NDUS7_GORGO	1, ., 6, ., 9, 9, ., 3	0.6968	0.8826	0.8826	N/A	no
B8GNY6	NUOB_THISH	1, ., 6, ., 9, 9, ., 5	0.8591	0.6666	0.8987	yes	no
Q0KCS9	NUOB_CUPNH	1, ., 6, ., 9, 9, ., 5	0.8521	0.6666	0.8875	yes	no
Q8XXQ2	NUOB_RALSO	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8875	yes	no
Q8P7T3	NUOB_XANCP	1, ., 6, ., 9, 9, ., 5	0.8661	0.6666	0.7717	yes	no
Q3JUA8	NUOB1_BURP1	1, ., 6, ., 9, 9, ., 5	0.8380	0.6666	0.8930	yes	no
B2U7R0	NUOB_RALPJ	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8875	yes	no
A3N7L8	NUOB1_BURP6	1, ., 6, ., 9, 9, ., 5	0.8380	0.6666	0.8930	yes	no
Q2RU39	NUOB_RHORT	1, ., 6, ., 9, 9, ., 5	0.8591	0.6666	0.7675	yes	no
B3R3W8	NUOB_CUPTR	1, ., 6, ., 9, 9, ., 5	0.8521	0.6666	0.8875	yes	no
O75251	NDUS7_HUMAN	1, ., 6, ., 9, 9, ., 3	0.6968	0.8826	0.8826	yes	no
Q82TU4	NUOB_NITEU	1, ., 6, ., 9, 9, ., 5	0.8591	0.6666	0.8987	yes	no
A4SXQ2	NUOB_POLSQ	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8875	yes	no
Q473U2	NUOB_CUPPJ	1, ., 6, ., 9, 9, ., 5	0.8521	0.6666	0.8875	yes	no
O21272	NDUS7_RECAM	1, ., 6, ., 5, ., 3	0.8441	0.7230	0.8461	N/A	no
Q43844	NDUS7_SOLTU	1, ., 6, ., 9, 9, ., 3	0.7511	1.0	1.0	N/A	no
B2T2E8	NUOB_BURPP	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8930	yes	no
A5IHW2	NUOB_LEGPC	1, ., 6, ., 9, 9, ., 5	0.8531	0.6713	0.9050	yes	no
Q1GZL0	NUOB_METFK	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8987	yes	no
Q9PGJ4	NUOB_XYLFA	1, ., 6, ., 9, 9, ., 5	0.8541	0.6760	0.7826	yes	no
Q142H2	NUOB_BURXL	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8930	yes	no
Q3J829	NUOB2_NITOC	1, ., 6, ., 9, 9, ., 5	0.8652	0.6619	0.8924	yes	no
Q5X1A8	NUOB_LEGPA	1, ., 6, ., 9, 9, ., 5	0.8531	0.6713	0.9050	yes	no
B5EN70	NUOB2_ACIF5	1, ., 6, ., 9, 9, ., 5	0.8521	0.6666	0.8987	yes	no
Q5WT21	NUOB_LEGPL	1, ., 6, ., 9, 9, ., 5	0.8531	0.6713	0.9050	yes	no
Q2W3I5	NUOB_MAGSA	1, ., 6, ., 9, 9, ., 5	0.8163	0.6901	0.7903	yes	no
Q5ZRT9	NUOB_LEGPH	1, ., 6, ., 9, 9, ., 5	0.8531	0.6713	0.9050	yes	no
Q2SZN4	NUOB_BURTA	1, ., 6, ., 9, 9, ., 5	0.8380	0.6666	0.8930	yes	no
B1XUJ9	NUOB_POLNS	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8875	yes	no
Q4UWB7	NUOB_XANC8	1, ., 6, ., 9, 9, ., 5	0.8661	0.6666	0.7717	yes	no
A6SY06	NUOB_JANMA	1, ., 6, ., 9, 9, ., 5	0.8450	0.6666	0.8987	yes	no
Q0MQI0	NDUS7_PANTR	1, ., 6, ., 9, 9, ., 3	0.6968	0.8826	0.8826	yes	no
B0U1W6	NUOB_XYLFM	1, ., 6, ., 9, 9, ., 5	0.8541	0.6760	0.7826	yes	no
P42026	NDUS7_BOVIN	1, ., 6, ., 9, 9, ., 3	0.7297	0.8591	0.8472	yes	no
P42027	NDUS7_BRAOL	1, ., 6, ., 9, 9, ., 3	0.7488	1.0	0.9906	N/A	no
Q63VN2	NUOB1_BURPS	1, ., 6, ., 9, 9, ., 5	0.8380	0.6666	0.8930	yes	no
P0CB84	NDUS7_PONPY	1, ., 6, ., 9, 9, ., 3	0.6968	0.8826	0.8826	N/A	no
Q31HF9	NUOB_THICR	1, ., 6, ., 9, 9, ., 5	0.8723	0.6619	0.8924	yes	no
Q2GDX9	NUOB_NEOSM	1, ., 6, ., 9, 9, ., 5	0.8299	0.6901	0.8802	yes	no
P0CB83	NDUS7_PONAB	1, ., 6, ., 9, 9, ., 3	0.7371	0.8215	0.8215	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	1.6.5.3	0.979
3rd Layer	1.6.99	0.983
3rd Layer	1.6.99.3	0.979
3rd Layer	1.6.5	0.983

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	213
PRK06411	183	PRK06411, PRK06411, NADH dehydrogenase subunit B;	1e-106
COG0377	194	COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 k	1e-101
TIGR01957	145	TIGR01957, nuoB_fam, NADH-quinone oxidoreductase,	2e-96
PRK14813	189	PRK14813, PRK14813, NADH dehydrogenase subunit B;	1e-67
PRK14818	173	PRK14818, PRK14818, NADH dehydrogenase subunit B;	2e-64
PRK14815	183	PRK14815, PRK14815, NADH dehydrogenase subunit B;	2e-64
PRK14819	264	PRK14819, PRK14819, NADH dehydrogenase subunit B;	3e-64
PRK14816	182	PRK14816, PRK14816, NADH dehydrogenase subunit B;	1e-60
PRK13292	788	PRK13292, PRK13292, trifunctional NADH dehydrogena	7e-58
CHL00023	225	CHL00023, ndhK, NADH dehydrogenase subunit K	3e-50
PRK14814	186	PRK14814, PRK14814, NADH dehydrogenase subunit B;	6e-50
PRK14820	180	PRK14820, PRK14820, NADH dehydrogenase subunit B;	2e-49
PRK14817	181	PRK14817, PRK14817, NADH dehydrogenase subunit B;	2e-46
COG3260	148	COG3260, COG3260, Ni,Fe-hydrogenase III small subu	8e-41
pfam01058	122	pfam01058, Oxidored_q6, NADH ubiquinone oxidoreduc	1e-34
COG1941	247	COG1941, FrhG, Coenzyme F420-reducing hydrogenase,	0.002

>gnl|CDD|235797 PRK06411, PRK06411, NADH dehydrogenase subunit B; Validated

 Score =  303 bits (778), Expect = e-106
 Identities = 106/148 (71%), Positives = 126/148 (85%)

Query: 63  VISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIV 122
           V++ +D+L+NW R+ SLWP+TFGLACCA+EMM  G + YDLDRFG++FR SPRQ+D+MIV
Sbjct: 21  VLTTLDDLVNWARKNSLWPLTFGLACCAIEMMAAGTSRYDLDRFGMVFRASPRQADLMIV 80

Query: 123 AGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPG 182
           AGTLTNKMAPALR++YDQMPEP+WVISMGS AN GG YHYSYSVV+G DRIVPVD+YVPG
Sbjct: 81  AGTLTNKMAPALRRLYDQMPEPKWVISMGSCANSGGMYHYSYSVVQGVDRIVPVDVYVPG 140

Query: 183 CPPTAEALLYGILQLQKKINRRRDFLHW 210
           CPP  EALLYGIL+LQKKI +       
Sbjct: 141 CPPRPEALLYGILKLQKKIRQSERERKR 168

Length = 183

>gnl|CDD|223454 COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]

 Score =  290 bits (743), Expect = e-101
 Identities = 105/149 (70%), Positives = 123/149 (82%)

Query: 62  YVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMI 121
            +++KVD L+NW R+ SLWP+TFGLACCAVEMM T A+ YDL+RFG + R SPRQ+D+MI
Sbjct: 21  VLLTKVDKLINWGRKNSLWPVTFGLACCAVEMMATFASRYDLERFGEVPRASPRQADLMI 80

Query: 122 VAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVP 181
           VAGTLTNKMAPALR+VYDQMPEP+WVISMGS AN GG Y  SYSVV+G DR+VPVD+Y+P
Sbjct: 81  VAGTLTNKMAPALRRVYDQMPEPKWVISMGSCANSGGMYWNSYSVVQGVDRVVPVDVYIP 140

Query: 182 GCPPTAEALLYGILQLQKKINRRRDFLHW 210
           GCPP  EALLYGIL LQ+KI R    L  
Sbjct: 141 GCPPRPEALLYGILLLQEKIRREGRPLRD 169

Length = 194

>gnl|CDD|233656 TIGR01957, nuoB_fam, NADH-quinone oxidoreductase, B subunit

 Score =  276 bits (709), Expect = 2e-96
 Identities = 102/143 (71%), Positives = 123/143 (86%), Gaps = 1/143 (0%)

Query: 63  VISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFG-IIFRPSPRQSDVMI 121
           +++ VD LLNW R  SLWP+TFGLACCA+EMM TGA+ YDLDRFG  +FR SPRQ+DVMI
Sbjct: 3   LLTTVDKLLNWGRSNSLWPLTFGLACCAIEMMATGASRYDLDRFGSEVFRASPRQADVMI 62

Query: 122 VAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVP 181
           VAGT+T KMAPALR++YDQMPEP+WVISMG+ AN GG +H SYSVV+G DRIVPVD+Y+P
Sbjct: 63  VAGTVTKKMAPALRRLYDQMPEPKWVISMGACANSGGMFHTSYSVVQGVDRIVPVDVYIP 122

Query: 182 GCPPTAEALLYGILQLQKKINRR 204
           GCPP  EAL+YG+++LQKKI R 
Sbjct: 123 GCPPRPEALIYGLIKLQKKIKRE 145

This model describes the B chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. The quinone is plastoquinone in Synechocystis (where the chain is designated K) and in chloroplast, where NADH may be replaced by NADPH. In the methanogenic archaeal genus Methanosarcina, NADH is replaced by F420H2 [Energy metabolism, Electron transport]. Length = 145

>gnl|CDD|173274 PRK14813, PRK14813, NADH dehydrogenase subunit B; Provisional

 Score =  205 bits (522), Expect = 1e-67
 Identities = 86/140 (61%), Positives = 114/140 (81%), Gaps = 1/140 (0%)

Query: 63  VISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIV 122
           +++ VDN+LNW R  SLWPM FGLACCA+EMM T A+ YDL+RFGI  R SPRQSD+MIV
Sbjct: 14  LVTSVDNVLNWARLSSLWPMGFGLACCAIEMMATNASNYDLERFGIFPRSSPRQSDLMIV 73

Query: 123 AGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGG-YYHYSYSVVRGCDRIVPVDIYVP 181
           AGT+T KMA  + ++Y+QMPEPR+V+SMGS +N GG Y+ + Y V++G DRI+PVD+YVP
Sbjct: 74  AGTVTMKMAERVVRLYEQMPEPRYVLSMGSCSNCGGPYWEHGYHVLKGVDRIIPVDVYVP 133

Query: 182 GCPPTAEALLYGILQLQKKI 201
           GCPP  EAL+ G++++Q+ I
Sbjct: 134 GCPPRPEALIGGLMKVQELI 153

Length = 189

>gnl|CDD|173279 PRK14818, PRK14818, NADH dehydrogenase subunit B; Provisional

 Score =  197 bits (501), Expect = 2e-64
 Identities = 85/165 (51%), Positives = 109/165 (66%), Gaps = 4/165 (2%)

Query: 49  ATFGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI 108
           A   P      +    S++DNL+N  R  SL+ +TFGLACC +E+M TG    D+ RFG 
Sbjct: 3   ARMDPGIGGDVTLLHTSQLDNLINLARASSLYYLTFGLACCGIELMQTGGPRADVMRFGA 62

Query: 109 IFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVR 168
           I R SPRQ+D MIVAGTLT KMA   R +YDQMPEP++VISMGS +N GG +   YSV +
Sbjct: 63  IPRASPRQADFMIVAGTLTYKMAERARLLYDQMPEPKYVISMGSCSNCGGLFQLGYSVCK 122

Query: 169 GCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK 213
           G D+++PVD+YVPGCPP  EAL  G+L+LQ+ +        W TK
Sbjct: 123 GVDKVIPVDVYVPGCPPRPEALTEGLLRLQEIVRSEP----WSTK 163

Length = 173

>gnl|CDD|237821 PRK14815, PRK14815, NADH dehydrogenase subunit B; Provisional

 Score =  197 bits (501), Expect = 2e-64
 Identities = 82/148 (55%), Positives = 113/148 (76%), Gaps = 2/148 (1%)

Query: 61  EYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDV 119
             V++ +D  +NW+R+ SLWPM  GLACCA+E+M    + +D+ RFG  + R SPRQ+DV
Sbjct: 17  NVVVTTLDAAINWIRKNSLWPMPMGLACCAIELMAVACSRFDISRFGAEVMRFSPRQADV 76

Query: 120 MIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIY 179
           MIVAGT+T KMA A+R++YDQMPEP+WVI+MG+ A+ GG Y  SYSV++G DRI+PVD+Y
Sbjct: 77  MIVAGTVTYKMALAVRRIYDQMPEPKWVIAMGACASSGGMYR-SYSVLQGVDRILPVDVY 135

Query: 180 VPGCPPTAEALLYGILQLQKKINRRRDF 207
           + GCPP  EA+L  +++LQKKI+  R  
Sbjct: 136 ISGCPPRPEAILDALIKLQKKIDTERAA 163

Length = 183

>gnl|CDD|237822 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provisional

 Score =  199 bits (507), Expect = 3e-64
 Identities = 82/143 (57%), Positives = 111/143 (77%), Gaps = 1/143 (0%)

Query: 64  ISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMIV 122
           ++ V+   NW RR S+WPM FGLACCA+EMM TG + YDL RFG  +FR SPRQ+D+MIV
Sbjct: 18  LTTVNRFYNWGRRSSVWPMAFGLACCAIEMMATGLSRYDLARFGAELFRASPRQADLMIV 77

Query: 123 AGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPG 182
           AGT+T KMAP + ++Y+QMPEPR+VISMG+ A  GG +   Y+V+RG D ++PVD+Y+PG
Sbjct: 78  AGTVTKKMAPQVVRLYNQMPEPRYVISMGACATSGGPFRDGYNVLRGIDLLIPVDVYIPG 137

Query: 183 CPPTAEALLYGILQLQKKINRRR 205
           CPP  EALL+ ++ LQK+I+ + 
Sbjct: 138 CPPRPEALLHALMTLQKQIDAQS 160

Length = 264

>gnl|CDD|173277 PRK14816, PRK14816, NADH dehydrogenase subunit B; Provisional

 Score =  187 bits (476), Expect = 1e-60
 Identities = 74/145 (51%), Positives = 107/145 (73%), Gaps = 1/145 (0%)

Query: 64  ISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMIV 122
           +  +D+L+NW R  SLWP+TF  +CC +E M  GAA YD+ RFG  + R SPRQ+D+++V
Sbjct: 28  VGVLDDLINWGRSNSLWPLTFATSCCGIEFMALGAARYDMARFGFEVARASPRQADMIMV 87

Query: 123 AGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPG 182
            GT+TNKMAP L+++YDQM +P++VI++G  A  GG +  SY V+ G D+I+PVD+Y+PG
Sbjct: 88  CGTITNKMAPVLKRLYDQMADPKYVIAVGGCAVSGGPFKKSYHVLNGVDKILPVDVYIPG 147

Query: 183 CPPTAEALLYGILQLQKKINRRRDF 207
           CPP  EA  YG++QLQ+K+   + F
Sbjct: 148 CPPRPEAFYYGMMQLQRKVKIEKFF 172

Length = 182

>gnl|CDD|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit B/C/D; Provisional

 Score =  194 bits (495), Expect = 7e-58
 Identities = 80/158 (50%), Positives = 114/158 (72%), Gaps = 6/158 (3%)

Query: 57  SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPR 115
           +     +++ +D+L+NW R  SLWPM FGL+CC VEMM +  + YD+ RFG  + R +PR
Sbjct: 2   TIPENILLASLDDLINWGRANSLWPMFFGLSCCFVEMMTSFTSRYDISRFGAEVLRGTPR 61

Query: 116 QSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVP 175
           ++D+M++AGT+  KMAP++ ++Y+QM EP+WVISMGS AN GG Y   YSVV+G ++I+P
Sbjct: 62  EADLMVIAGTVFKKMAPSILRLYEQMAEPKWVISMGSCANSGGMYDV-YSVVQGVNQILP 120

Query: 176 VDIYVPGCPPTAEALLYGILQLQKKINRR----RDFLH 209
           VD+Y+PGCPP  EA L G++ LQ+KI R     R  LH
Sbjct: 121 VDVYIPGCPPRPEAFLQGLMLLQEKIRREERPARPVLH 158

Length = 788

>gnl|CDD|214337 CHL00023, ndhK, NADH dehydrogenase subunit K

 Score =  162 bits (411), Expect = 3e-50
 Identities = 71/143 (49%), Positives = 104/143 (72%), Gaps = 2/143 (1%)

Query: 63  VISKVDN-LLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMI 121
           VIS   N L NW R  SLWP+ +G +CC +E      + +D DR+G++ R SPRQ+D+++
Sbjct: 17  VISTTLNDLSNWSRLSSLWPLLYGTSCCFIEFASLIGSRFDFDRYGLVPRSSPRQADLIL 76

Query: 122 VAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHY-SYSVVRGCDRIVPVDIYV 180
            AGT+T KMAP+L ++Y+QMPEP++VI+MG+    GG +   SYS VRG D+++PVD+Y+
Sbjct: 77  TAGTVTMKMAPSLVRLYEQMPEPKYVIAMGACTITGGMFSTDSYSTVRGVDKLIPVDVYL 136

Query: 181 PGCPPTAEALLYGILQLQKKINR 203
           PGCPP  EA++  I +L+KKI+R
Sbjct: 137 PGCPPKPEAVIDAITKLRKKISR 159

Length = 225

>gnl|CDD|173275 PRK14814, PRK14814, NADH dehydrogenase subunit B; Provisional

 Score =  160 bits (406), Expect = 6e-50
 Identities = 71/140 (50%), Positives = 103/140 (73%), Gaps = 4/140 (2%)

Query: 64  ISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPS--PRQSDVMI 121
           +  +++++ W R  SLWP  F  ACC +E M T  + YD+ RFG   RPS  PRQ+D+++
Sbjct: 20  LGNLESVIQWGRSFSLWPYPFATACCGIEYMSTACSDYDIARFGAE-RPSFSPRQADMIL 78

Query: 122 VAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVP 181
           V GT+T KMAP LR++YDQM EP++VIS+G+ A+ GG +H +Y V++G DRI+PVD+YVP
Sbjct: 79  VLGTITYKMAPVLRQIYDQMAEPKFVISVGACASSGGMFH-TYGVLQGVDRILPVDVYVP 137

Query: 182 GCPPTAEALLYGILQLQKKI 201
           GCPP  EA+L  +++LQ K+
Sbjct: 138 GCPPRPEAILDALVKLQTKL 157

Length = 186

>gnl|CDD|184833 PRK14820, PRK14820, NADH dehydrogenase subunit B; Provisional

 Score =  158 bits (402), Expect = 2e-49
 Identities = 72/160 (45%), Positives = 110/160 (68%), Gaps = 9/160 (5%)

Query: 53  PVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRP 112
           P G      +  + +D+++   R+ SLWP+ F  +CC +E M T A+ YDL RFG   RP
Sbjct: 10  PEGYE-GEGFFATSLDSVIGLARKNSLWPLPFATSCCGIEFMATMASHYDLARFGS-ERP 67

Query: 113 --SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGC 170
             SPRQ+D+++V GT+  KMAP L++VY QM EPRWV+++G+ A+ GG +  +YSV++G 
Sbjct: 68  SFSPRQADMLMVMGTIAKKMAPVLKQVYLQMAEPRWVVAVGACASSGGIFD-TYSVLQGI 126

Query: 171 DRIVPVDIYVPGCPPTAEALLYGILQLQKKIN----RRRD 206
           DRI+PVD+YVPGCPP  E ++ G++++Q+ +     RRR+
Sbjct: 127 DRIIPVDVYVPGCPPRPEQIIDGVMRVQELVKNESLRRRN 166

Length = 180

>gnl|CDD|173278 PRK14817, PRK14817, NADH dehydrogenase subunit B; Provisional

 Score =  151 bits (382), Expect = 2e-46
 Identities = 70/145 (48%), Positives = 98/145 (67%), Gaps = 2/145 (1%)

Query: 58  KASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIF-RPSPRQ 116
           +A  ++   V   L W R+ SL+   F  ACC +E M   +A YD DRFG    R SPRQ
Sbjct: 16  EAEGFLQGLVSKSLGWARKYSLFTYPFVTACCGMEYMTMASARYDSDRFGAAMPRFSPRQ 75

Query: 117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPV 176
           +D+++V GT+  K AP L++VY+QM +P+WV++ G  A+ GG+Y  +Y+ V+G DRI+PV
Sbjct: 76  ADLLMVVGTVNCKQAPILQRVYEQMADPKWVMAFGVCASSGGFYD-NYATVQGIDRIIPV 134

Query: 177 DIYVPGCPPTAEALLYGILQLQKKI 201
           D+YVPGCPP  E +L GI+ LQKKI
Sbjct: 135 DVYVPGCPPRPEQVLDGIMLLQKKI 159

Length = 181

>gnl|CDD|225799 COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [Energy production and conversion]

 Score =  135 bits (342), Expect = 8e-41
 Identities = 47/119 (39%), Positives = 76/119 (63%)

Query: 89  CAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVI 148
           C +E++   +  YD +RFGI    SPR +D+++V G +T +M   L+K Y+ MPEP+ VI
Sbjct: 22  CDIEILAALSPRYDAERFGIKVVNSPRHADILLVTGAVTRQMREPLKKAYEAMPEPKIVI 81

Query: 149 SMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDF 207
           ++G+ A  GG +  SYSV    D+++PVD+ +PGCPP  EA+L G++    K+ ++   
Sbjct: 82  AVGACALSGGIFKDSYSVWGPVDKVIPVDVEIPGCPPRPEAILAGLVAALGKLEKKIHA 140

Length = 148

>gnl|CDD|216271 pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 20 Kd subunit

 Score =  118 bits (299), Expect = 1e-34
 Identities = 42/119 (35%), Positives = 64/119 (53%), Gaps = 10/119 (8%)

Query: 89  CAVEMMHTGAAGYDL----DRFGIIFRPSPR--QSDVMIVAGTLTNKMAPALRKVYDQMP 142
           C++ ++       DL     R+ I     PR   +DV++V G +T K   AL ++Y+  P
Sbjct: 4   CSISLLALHPPLLDLLDISLRYHITLMADPREEHADVLLVEGAVTRKPKEALERLYELAP 63

Query: 143 EPRWVISMGSRANGGG---YYHYSYSV-VRGCDRIVPVDIYVPGCPPTAEALLYGILQL 197
           + + VI++G+ A  GG     + SY V V     +VPVDI +PGCPP  EA+L  +L L
Sbjct: 64  KAKAVIAVGTCAAYGGIPAAGNNSYGVGVGPVLEVVPVDINIPGCPPHPEAILGTLLAL 122

Length = 122

>gnl|CDD|224852 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 9/26 (34%), Positives = 14/26 (53%)

Query: 167 VRGCDRIVPVDIYVPGCPPTAEALLY 192
           V     ++ VD  +PGCPP+ E +  
Sbjct: 120 VVPLGEVIDVDYAIPGCPPSPEEIAR 145

Length = 247

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
KOG1687	168	consensus NADH-ubiquinone oxidoreductase, NUFS7/PS	100.0
COG0377	194	NuoB NADH:ubiquinone oxidoreductase 20 kD subunit	100.0
PRK14818	173	NADH dehydrogenase subunit B; Provisional	100.0
PRK14813	189	NADH dehydrogenase subunit B; Provisional	100.0
CHL00023	225	ndhK NADH dehydrogenase subunit K	100.0
PRK06411	183	NADH dehydrogenase subunit B; Validated	100.0
PRK14817	181	NADH dehydrogenase subunit B; Provisional	100.0
PRK14816	182	NADH dehydrogenase subunit B; Provisional	100.0
TIGR01957	145	nuoB_fam NADH-quinone oxidoreductase, B subunit. T	100.0
PRK14814	186	NADH dehydrogenase subunit B; Provisional	100.0
PRK14815	183	NADH dehydrogenase subunit B; Provisional	100.0
PRK14820	180	NADH dehydrogenase subunit B; Provisional	100.0
PRK14819	264	NADH dehydrogenase subunit B; Provisional	100.0
PRK13292	788	trifunctional NADH dehydrogenase I subunit B/C/D;	100.0
COG3260	148	Ni,Fe-hydrogenase III small subunit [Energy produc	100.0
TIGR03294	228	FrhG coenzyme F420 hydrogenase, subunit gamma. Thi	99.98
PF01058	131	Oxidored_q6: NADH ubiquinone oxidoreductase, 20 Kd	99.97
TIGR00391	365	hydA hydrogenase (NiFe) small subunit (hydA). Call	99.97
PRK10468	371	hydrogenase 2 small subunit; Provisional	99.96
COG1740	355	HyaA Ni,Fe-hydrogenase I small subunit [Energy pro	99.95
COG1941	247	FrhG Coenzyme F420-reducing hydrogenase, gamma sub	99.94
PF00919	98	UPF0004: Uncharacterized protein family UPF0004; I	88.17
cd00886	152	MogA_MoaB MogA_MoaB family. Members of this family	84.6
TIGR01125	430	MiaB-like tRNA modifying enzyme YliG, TIGR01125. T	80.88

>KOG1687 consensus NADH-ubiquinone oxidoreductase, NUFS7/PSST/20 kDa subunit [Energy production and conversion]

Probab=100.00  E-value=7.2e-65  Score=413.20  Aligned_cols=160  Identities=78%  Similarity=1.405  Sum_probs=157.0

Q ss_pred             CcCCCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEecccCCCChHH
Q 041751           54 VGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPA  133 (213)
Q Consensus        54 ~~~~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG~Vt~km~~~  133 (213)
                      ..+++.++|++++||||+||+|..||||++||.+||.+|||++..++||++|||++|++||||+|++||.|++|+||+|+
T Consensus         9 ~~~s~~~e~~~a~ldDl~Nwar~~SlWPltfGlaCCavEmmh~~a~RyD~DRyGvvfRaSPRQaD~iivAGTlTnKMAPa   88 (168)
T KOG1687|consen    9 LNPSSKAEYVLARLDDLLNWARRGSLWPLTFGLACCAVEMMHLAAPRYDMDRYGVVFRASPRQADLIIVAGTLTNKMAPA   88 (168)
T ss_pred             CCccchhhhhhhhHHHHhhhhhhcCccchhhhhHHHHHHHHHhccccccccccceeecCCCccccEEEEeccchhhhcHH
Confidence            45577899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCccccccC
Q 041751          134 LRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWTK  213 (213)
Q Consensus       134 l~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~~~~y~~  213 (213)
                      ++++|||||||||||+||+||++||+|+++|++++|+|++||||||||||||++|+++++|++||+||++.+..++||||
T Consensus        89 lrkvYdQMPEpr~VisMGsCangGGyyhysYSvvRGcDriiPVDiYvPGCPPtaEAllygilqLqkKi~R~r~~q~wyr~  168 (168)
T KOG1687|consen   89 LRKVYDQMPEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALLYGILQLQKKIKRIRPLQFWYRK  168 (168)
T ss_pred             HHHHHhhCCCCeeEEEecccccCCceEEEEehhhccccceeeeeeecCCCCCCHHHHHHHHHHHHHHHHHhhhhhhhhcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999996

>COG0377 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]

Probab=100.00  E-value=4.9e-61  Score=405.04  Aligned_cols=156  Identities=67%  Similarity=1.126  Sum_probs=150.3

Q ss_pred             CCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEecccCCCChHHHHH
Q 041751           57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRK  136 (213)
Q Consensus        57 ~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG~Vt~km~~~l~~  136 (213)
                      ....++++|++|+++||+|++||||++||.+||++||+++..++||+||||+++++||||+|++||+|++++||++++++
T Consensus        16 ~~~~~~~~t~~~~l~~W~r~~SLWp~~fg~aCC~iEm~~~~~~r~D~~RfG~~~r~SPRQaDvmIvaGt~t~Kmap~lr~   95 (194)
T COG0377          16 LLSKGVLLTKVDKLINWGRKNSLWPVTFGLACCAVEMMATFASRYDLERFGEVPRASPRQADLMIVAGTLTNKMAPALRR   95 (194)
T ss_pred             hhccCeeeechHHHHhhhhhcccchhhhcchhHHHHHHhhccccccHHHhCcCCCCCcccccEEEEeccchHHHHHHHHH
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCcccccc
Q 041751          137 VYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWWT  212 (213)
Q Consensus       137 l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~~~~y~  212 (213)
                      +|||||+||||||||+||+.||+|+++|++++|+|++||||||||||||+||+++++|++||+||++++++.-|++
T Consensus        96 ~YdQMPePK~VIsMGsCa~~GG~f~~sYsvV~g~D~~vPVDvyIPGCPPrPEAl~~gi~~Lq~KI~~~~~~~~~~~  171 (194)
T COG0377          96 VYDQMPEPKWVISMGSCANSGGMYWNSYSVVQGVDRVVPVDVYIPGCPPRPEALLYGILLLQEKIRREGRPLRDKP  171 (194)
T ss_pred             HHHhCCCCcEEEEecccccCCCcccccceeeeccceeEeeeeecCCCCCCHHHHHHHHHHHHHHHHhccCcccccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999777766554

>PRK14818 NADH dehydrogenase subunit B; Provisional

Probab=100.00  E-value=2.3e-55  Score=368.09  Aligned_cols=152  Identities=53%  Similarity=0.885  Sum_probs=146.2

Q ss_pred             cCCCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEecccCCCChHHH
Q 041751           55 GLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPAL  134 (213)
Q Consensus        55 ~~~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG~Vt~km~~~l  134 (213)
                      -..+...++.+++|+++||+|++|+|+.++|++||++||+++..++||++|||+.|++||||+||++|+|+||.+|++.+
T Consensus         9 ~~~~~~~~~~~~~~~~~~w~r~~Slw~~~~~t~cC~iEi~a~~~p~yD~eRfGi~~~aSPRhADvLlVtG~vT~km~~~l   88 (173)
T PRK14818          9 IGGDVTLLHTSQLDNLINLARASSLYYLTFGLACCGIELMQTGGPRADVMRFGAIPRASPRQADFMIVAGTLTYKMAERA   88 (173)
T ss_pred             CCceEEeeehhhHHHHHHHHhhCCceeeEeCCccHHHHHHHhcCCccCHHHcCCeecCCcccccEEEEeCcCccccHHHH
Confidence            34555678899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCC
Q 041751          135 RKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRD  206 (213)
Q Consensus       135 ~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~  206 (213)
                      +++|||||+||+|||+|+||++||+|+++|+++++++++||||+|||||||+||+|+++|++|+++|++++.
T Consensus        89 ~~~yeqmPePK~VIA~G~CA~sGGif~~sY~~~~gvd~vIpVDvyIPGCPP~PeaIl~gil~L~~~i~~~~~  160 (173)
T PRK14818         89 RLLYDQMPEPKYVISMGSCSNCGGLFQLGYSVCKGVDKVIPVDVYVPGCPPRPEALTEGLLRLQEIVRSEPW  160 (173)
T ss_pred             HHHHHhCCCCCEEEEeccccccCCcccCCcccccCCCCccCCcEEccCCCCCHHHHHHHHHHHHHHHhcccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999987753

>PRK14813 NADH dehydrogenase subunit B; Provisional

Probab=100.00  E-value=1.7e-54  Score=367.48  Aligned_cols=151  Identities=57%  Similarity=1.027  Sum_probs=144.6

Q ss_pred             cceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEecccCCCChHHHHHHHH
Q 041751           60 SEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYD  139 (213)
Q Consensus        60 ~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG~Vt~km~~~l~~l~e  139 (213)
                      .+++++++|+++||+|++|+|+.+++++||++||+++.+++||++|||+.|+++|||+||+||+|+||++|+++++++|+
T Consensus        11 ~~~~~~~~~~~~~w~r~~Slw~~~~~t~cC~iE~~a~~~p~yD~eRfGi~~~asPR~ADvllVtG~Vt~km~~~l~~~y~   90 (189)
T PRK14813         11 HNVLVTSVDNVLNWARLSSLWPMGFGLACCAIEMMATNASNYDLERFGIFPRSSPRQSDLMIVAGTVTMKMAERVVRLYE   90 (189)
T ss_pred             CCeEeeeHHHHHHHHHhCCCceeeeCcccHHHHHHHhcccCCCHHHcCCeecCCcccceEEEEeccCchhhHHHHHHHHH
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HCCCCceEEEecCccCcCCCCC-CCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCcccc
Q 041751          140 QMPEPRWVISMGSRANGGGYYH-YSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHW  210 (213)
Q Consensus       140 ~~~~pk~VIA~GsCA~~GGi~~-~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~~~~  210 (213)
                      |||+||+|||+|+||++||+|. ++|++++|+|++||||+|||||||+||+|+++|++|+++|++++....+
T Consensus        91 qmPePK~VIA~GaCA~sGG~~~~~sY~~~~gvd~vIpVDv~IPGCPP~PeaIl~gl~~l~~~i~~~~~~~~~  162 (189)
T PRK14813         91 QMPEPRYVLSMGSCSNCGGPYWEHGYHVLKGVDRIIPVDVYVPGCPPRPEALIGGLMKVQELIRMEQIGISR  162 (189)
T ss_pred             hCCCCCEEEEecccccCCCCcccCCcccccCCCCccCCcEEccCCCCCHHHHHHHHHHHHHHHHhcccccch
Confidence            9999999999999999988886 5999999999999999999999999999999999999999988754433

>CHL00023 ndhK NADH dehydrogenase subunit K

Probab=100.00  E-value=2.6e-54  Score=373.89  Aligned_cols=151  Identities=44%  Similarity=0.925  Sum_probs=145.2

Q ss_pred             cCCCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEecccCCCChHHH
Q 041751           55 GLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPAL  134 (213)
Q Consensus        55 ~~~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG~Vt~km~~~l  134 (213)
                      ......++++|++|+++||+|++|+|+.++|++||++||+++..++||++|||+.|++|||||||+||+|+||++|++++
T Consensus        10 ~~~~~~~~~~~~~~~~~~w~r~~Slw~~~~g~sCC~iE~~a~~~p~yDleRfGi~~~aSPRhADvliVtG~VT~km~~~L   89 (225)
T CHL00023         10 DRTTSNSVISTTLNDLSNWSRLSSLWPLLYGTSCCFIEFASLIGSRFDFDRYGLVPRSSPRQADLILTAGTVTMKMAPSL   89 (225)
T ss_pred             ccccCCCeEeeeHHHHHHHHHhCCcccccCCcchHHHHHHHhCCCccCHHHcCCeecCCcccceEEEEecCCccccHHHH
Confidence            34455789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHCCCCceEEEecCccCcCCCCC-CCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcC
Q 041751          135 RKVYDQMPEPRWVISMGSRANGGGYYH-YSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRR  205 (213)
Q Consensus       135 ~~l~e~~~~pk~VIA~GsCA~~GGi~~-~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~  205 (213)
                      +++|||||+||+|||||+||++||+|+ ++|++++|++++||||+|||||||+||+|+++|+.|+++|+++.
T Consensus        90 ~rlyeqmPePK~VIA~GaCA~sGGif~~dsy~~v~gvd~vIPVDv~IPGCPP~PeaIi~~l~~L~~ki~~~~  161 (225)
T CHL00023         90 VRLYEQMPEPKYVIAMGACTITGGMFSTDSYSTVRGVDKLIPVDVYLPGCPPKPEAVIDAITKLRKKISREI  161 (225)
T ss_pred             HHHHHhcCCCCeEEEEccccccCCcccCCCcccccCccccceeeEEecCCCCCHHHHHHHHHHHHHHHhccc
Confidence            999999999999999999999999997 89999999999999999999999999999999999999998765

>PRK06411 NADH dehydrogenase subunit B; Validated

Probab=100.00  E-value=2.2e-53  Score=359.68  Aligned_cols=152  Identities=70%  Similarity=1.262  Sum_probs=146.5

Q ss_pred             CCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEecccCCCChHHHHH
Q 041751           57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRK  136 (213)
Q Consensus        57 ~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG~Vt~km~~~l~~  136 (213)
                      ....+++.+++|+++||+|++|+|+.+++++||++|++++..++||++|||+.++++|||+||+||||+||++|.+.+++
T Consensus        15 ~~~~~~~~~~~~~~~~w~r~~Slw~~~~~~~CC~iE~~~~~~~~yDieRfGi~~~~sPr~aDvllV~G~vt~~~~~~l~~   94 (183)
T PRK06411         15 ELNKGVVLTTLDDLVNWARKNSLWPLTFGLACCAIEMMAAGTSRYDLDRFGMVFRASPRQADLMIVAGTLTNKMAPALRR   94 (183)
T ss_pred             cccCCeeeeeHHHHHHHHHhCCccceeeCccHhHHHHHHccCccccHHHhCccccCCCCceeEEEEEeCCCccchHHHHH
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCcc
Q 041751          137 VYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFL  208 (213)
Q Consensus       137 l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~~  208 (213)
                      +||||++||+|||+|+||++||+|+++|++++|++++||||+|||||||+||+|+++|++|+++|++++...
T Consensus        95 ~~e~mp~pk~VIA~GaCA~~GGif~~sy~~~~gv~~~ipVDv~IPGCPP~Pe~il~~l~~l~~~i~~~~~~~  166 (183)
T PRK06411         95 LYDQMPEPKWVISMGSCANSGGMYHYSYSVVQGVDRIVPVDVYVPGCPPRPEALLYGILKLQKKIRQSERER  166 (183)
T ss_pred             HHHHcCcCCeEEEEecccccCCcccCCCccccCcccccccceEeCCCCCCHHHHHHHHHHHHHHHhcccccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999876654

>PRK14817 NADH dehydrogenase subunit B; Provisional

Probab=100.00  E-value=1.1e-52  Score=354.63  Aligned_cols=150  Identities=47%  Similarity=0.905  Sum_probs=142.7

Q ss_pred             CCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhccee-cCCCCCeeEEEEecccCCCChHHHH
Q 041751           57 SKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIF-RPSPRQSDVMIVAGTLTNKMAPALR  135 (213)
Q Consensus        57 ~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~-~~sPr~aDIliVeG~Vt~km~~~l~  135 (213)
                      ....+++.+++|+++||+|++|+|+.+|+++||++||+++.+++||++|||+.+ +++|||+||+||||+||++|.+.++
T Consensus        15 ~~~~~~~~~~~~~~~~w~r~~Slw~~~~~~~CC~iE~~a~~~~~yDleRfGi~~~~~sPR~ADillVeG~VT~~m~~~l~   94 (181)
T PRK14817         15 EEAEGFLQGLVSKSLGWARKYSLFTYPFVTACCGMEYMTMASARYDSDRFGAAMPRFSPRQADLLMVVGTVNCKQAPILQ   94 (181)
T ss_pred             ccCCCeehhhHHHHHHHHhhCCccccccccchHHHHHHHhcCccccHHHhceeeccCCCcceeEEEEEecCCccchHHHH
Confidence            344578999999999999999999999999999999999999999999999977 6999999999999999999999999


Q ss_pred             HHHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCc
Q 041751          136 KVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDF  207 (213)
Q Consensus       136 ~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~  207 (213)
                      ++||||++||+|||+|+||++||++ ++|++++|++++||||+|||||||+||+|+++|++|++||++++..
T Consensus        95 ~~~e~~p~pK~VIAvGaCA~~GGi~-~~y~~~~gv~~vvpVDv~IPGCPP~Pe~il~~l~~l~~ki~~~~~~  165 (181)
T PRK14817         95 RVYEQMADPKWVMAFGVCASSGGFY-DNYATVQGIDRIIPVDVYVPGCPPRPEQVLDGIMLLQKKIQNQSHK  165 (181)
T ss_pred             HHHHHcccCCEEEEeccccccCCcC-CCcccccCccccceeeEEecCCCCCHHHHHHHHHHHHHHhhcCCcc
Confidence            9999999999999999999999988 6899999999999999999999999999999999999999876543

>PRK14816 NADH dehydrogenase subunit B; Provisional

Probab=100.00  E-value=1.1e-52  Score=354.87  Aligned_cols=148  Identities=49%  Similarity=1.033  Sum_probs=142.9

Q ss_pred             CCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhccee-cCCCCCeeEEEEecccCCCChHHHHH
Q 041751           58 KASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIF-RPSPRQSDVMIVAGTLTNKMAPALRK  136 (213)
Q Consensus        58 ~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~-~~sPr~aDIliVeG~Vt~km~~~l~~  136 (213)
                      .+.+++++++|+++||+|++|+|+++++.+||++||+++.+++||++|||+.+ +++|||+||+||+|+||++|++++++
T Consensus        22 ~~~~~~~~~~~~~~~w~r~~slw~~~~~~~CC~iE~~a~~~p~yD~eRfGi~~~~~sPRhADvllVtG~VT~~m~~~l~~  101 (182)
T PRK14816         22 GGANVFVGVLDDLINWGRSNSLWPLTFATSCCGIEFMALGAARYDMARFGFEVARASPRQADMIMVCGTITNKMAPVLKR  101 (182)
T ss_pred             ccCceeeeeHHHHHhhhhcCccceeeeCcchHHHHHHHhcCccccHHHhCccccCCCCCcceEEEEecCCcchhHHHHHH
Confidence            35678999999999999999999999999999999999999999999999966 59999999999999999999999999


Q ss_pred             HHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcC
Q 041751          137 VYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRR  205 (213)
Q Consensus       137 l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~  205 (213)
                      +|+||++||+|||+|+||++||+|+++|+++.|++++||||+|||||||+||+|+++|++|+++|++++
T Consensus       102 ~~e~~p~pK~VIAvGsCA~~GGif~~sy~~~~gvd~vIpVDv~IPGCPP~Pe~Il~~l~~L~~ki~~~~  170 (182)
T PRK14816        102 LYDQMADPKYVIAVGGCAVSGGPFKKSYHVLNGVDKILPVDVYIPGCPPRPEAFYYGMMQLQRKVKIEK  170 (182)
T ss_pred             HHHhcCCCCEEEEeccccccCCccccCCccCCCccccccccEEeeCcCCCHHHHHHHHHHHHHHhcccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999775

>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit

Probab=100.00  E-value=1.3e-52  Score=343.96  Aligned_cols=144  Identities=71%  Similarity=1.296  Sum_probs=140.0

Q ss_pred             ceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhc-ceecCCCCCeeEEEEecccCCCChHHHHHHHH
Q 041751           61 EYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFG-IIFRPSPRQSDVMIVAGTLTNKMAPALRKVYD  139 (213)
Q Consensus        61 ~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfg-i~~~~sPr~aDIliVeG~Vt~km~~~l~~l~e  139 (213)
                      +++++++|+++||+|++|+|+.+++++||++|++++..++||++||| +.++++|||+||++|||+||++|.+.++++||
T Consensus         1 ~~~~~~~~~~~~~~r~~s~w~~~~~t~cC~iE~~~~~~~~~D~erfG~i~~~~sPr~aDvllVtG~vt~~~~~~l~~~~e   80 (145)
T TIGR01957         1 GVLLTTVDKLLNWGRSNSLWPLTFGLACCAIEMMATGASRYDLDRFGSEVFRASPRQADVMIVAGTVTKKMAPALRRLYD   80 (145)
T ss_pred             CcccccHHHHHhhhhcCCceeeeeCccHHHHHHHHccCccccHHHhCCceecCCCCcceEEEEecCCcHHHHHHHHHHHH
Confidence            35679999999999999999999999999999999999999999999 89999999999999999999999999999999


Q ss_pred             HCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhc
Q 041751          140 QMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRR  204 (213)
Q Consensus       140 ~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~  204 (213)
                      ||++||+|||+|+||++||+|+++|+.++|++++||||+|||||||+||+|+++|++|+++|+++
T Consensus        81 ~~p~pk~VIA~GsCA~~GGi~~~~y~~~~~v~~~ipVDi~IPGCPp~Pe~i~~~l~~l~~~~~~~  145 (145)
T TIGR01957        81 QMPEPKWVISMGACANSGGMFHTSYSVVQGVDRIVPVDVYIPGCPPRPEALIYGLIKLQKKIKRE  145 (145)
T ss_pred             hccCCceEEEecceeecCCCccCCCccccCcccccccceEeCCCCCCHHHHHHHHHHHHHHhhcC
Confidence            99999999999999999999999999999999999999999999999999999999999999864

This model describes the B chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. The quinone is plastoquinone in Synechocystis (where the chain is designated K) and in chloroplast, where NADH may be replaced by NADPH. In the methanogenic archaeal genus Methanosarcina, NADH is replaced by F420H2.

>PRK14814 NADH dehydrogenase subunit B; Provisional

Probab=100.00  E-value=7.7e-52  Score=350.79  Aligned_cols=157  Identities=45%  Similarity=0.873  Sum_probs=148.3

Q ss_pred             CCCCcCCCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcc-eecCCCCCeeEEEEecccCCC
Q 041751           51 FGPVGLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMIVAGTLTNK  129 (213)
Q Consensus        51 ~~~~~~~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi-~~~~sPr~aDIliVeG~Vt~k  129 (213)
                      +.......+..++++++|+++||+|++|+|+++++++||++||+++..++||++|||+ .|+++|||+||+||||+||++
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~w~r~~Slw~~~~~~~CC~iE~~~~~~~~yD~eRfGi~~~~~sPR~ADvllVtG~VT~~   86 (186)
T PRK14814          7 SKKPGQALGDMFQLGNLESVIQWGRSFSLWPYPFATACCGIEYMSTACSDYDIARFGAERPSFSPRQADMILVLGTITYK   86 (186)
T ss_pred             hhchhhhccCCeeeeeHHHHHHHHHhCCCceeeeCCccHHHHHHHhcCccccHHHhCccccCCCcccceEEEEeccCchh
Confidence            4555666778999999999999999999999999999999999999999999999999 479999999999999999999


Q ss_pred             ChHHHHHHHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCcc
Q 041751          130 MAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFL  208 (213)
Q Consensus       130 m~~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~~  208 (213)
                      |.++++++||||++||+|||+|+||++||+|+ +|++.+|++++||||+|||||||+||+|+++|++|+++|++++...
T Consensus        87 m~~~l~~~yeqmp~pk~VIAvGsCA~~GGi~~-~y~~~~gv~~vvpVDv~IPGCPP~Pe~il~~l~~L~~~i~~~~~~~  164 (186)
T PRK14814         87 MAPVLRQIYDQMAEPKFVISVGACASSGGMFH-TYGVLQGVDRILPVDVYVPGCPPRPEAILDALVKLQTKLKTQGLEA  164 (186)
T ss_pred             hHHHHHHHHHhcCCCCeEEEeccccccCCccC-cCCCCcCccccccccEEecCCCCCHHHHHHHHHHHHHHHhcccccc
Confidence            99999999999999999999999999999996 6999999999999999999999999999999999999999876544

>PRK14815 NADH dehydrogenase subunit B; Provisional

Probab=100.00  E-value=1.7e-51  Score=347.58  Aligned_cols=149  Identities=55%  Similarity=1.062  Sum_probs=142.0

Q ss_pred             CcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhccee-cCCCCCeeEEEEecccCCCChHHHHHH
Q 041751           59 ASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGIIF-RPSPRQSDVMIVAGTLTNKMAPALRKV  137 (213)
Q Consensus        59 ~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~-~~sPr~aDIliVeG~Vt~km~~~l~~l  137 (213)
                      ..+++++++|+++||+|++|+|+.+++++||++||+++..++||++|||+.+ +++|||+||++|||+||++|.+.++++
T Consensus        15 ~~~~~~~~~~~~~~w~r~~Slw~~~~~~sCC~iE~~a~~~~~yDieRfGi~~~~~SPR~ADillVtG~VT~~m~~~l~r~   94 (183)
T PRK14815         15 EGNVVVTTLDAAINWIRKNSLWPMPMGLACCAIELMAVACSRFDISRFGAEVMRFSPRQADVMIVAGTVTYKMALAVRRI   94 (183)
T ss_pred             ccCeehhhHHHHHHHHHhCCccceeEccchHHHHHHHhcCccccHHHhCcccCCCCCccccEEEEeCcCchhhHHHHHHH
Confidence            3568899999999999999999999999999999999999999999999865 699999999999999999999999999


Q ss_pred             HHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCcc
Q 041751          138 YDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFL  208 (213)
Q Consensus       138 ~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~~  208 (213)
                      |||||+||+|||+|+||++||+|+ +|++.+|++++||||+|||||||+||+|+++|++|+++|++++...
T Consensus        95 ye~~p~pK~VIAvGsCA~~GGi~~-sy~~~~gv~~~ipVDv~IPGCPP~Pe~il~~l~~l~~~i~~~~~~~  164 (183)
T PRK14815         95 YDQMPEPKWVIAMGACASSGGMYR-SYSVLQGVDRILPVDVYISGCPPRPEAILDALIKLQKKIDTERAAR  164 (183)
T ss_pred             HHhCCCCCEEEEeccccccCCCcc-ccccccCccccccccEEecCCCCCHHHHHHHHHHHHHHHhhccccc
Confidence            999999999999999999999995 8999999999999999999999999999999999999999876543

>PRK14820 NADH dehydrogenase subunit B; Provisional

Probab=100.00  E-value=8e-51  Score=343.20  Aligned_cols=149  Identities=44%  Similarity=0.909  Sum_probs=142.9

Q ss_pred             CCCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcc-eecCCCCCeeEEEEecccCCCChHHH
Q 041751           56 LSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMIVAGTLTNKMAPAL  134 (213)
Q Consensus        56 ~~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi-~~~~sPr~aDIliVeG~Vt~km~~~l  134 (213)
                      .....+++.+++|+++||+|++|+|+.+++.+||++||+++..++||++|||+ .++++|||+||++|||+||++|.+.+
T Consensus        12 ~~~~~~~~~~~~~~~~~w~r~~Slw~~~~~~sCC~iE~~a~~~~~yDi~RfGi~~~~~sPR~aDillVeG~VT~~m~~~l   91 (180)
T PRK14820         12 GYEGEGFFATSLDSVIGLARKNSLWPLPFATSCCGIEFMATMASHYDLARFGSERPSFSPRQADMLMVMGTIAKKMAPVL   91 (180)
T ss_pred             ccccCceEeeeHHHHHHHHhhCCCceeeecccHHHHHHHHhcCccccHHHhCccccCCCCccceEEEEEecCCcccHHHH
Confidence            35567899999999999999999999999999999999999999999999999 47899999999999999999999999


Q ss_pred             HHHHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcC
Q 041751          135 RKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRR  205 (213)
Q Consensus       135 ~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~  205 (213)
                      +++||||++||+|||+|+||++||+| ++|++++|+++++|||+|||||||+||+|+++|++|+++|++++
T Consensus        92 ~~~~e~~p~pk~VIAvGaCA~~GGi~-~~y~~~~~v~~~ipVDv~IPGCPP~Pe~il~~l~~l~~~i~~~~  161 (180)
T PRK14820         92 KQVYLQMAEPRWVVAVGACASSGGIF-DTYSVLQGIDRIIPVDVYVPGCPPRPEQIIDGVMRVQELVKNES  161 (180)
T ss_pred             HHHHHhcCCCCeEEEEecccccCCcc-ccccccccccccccccEEecCCCCCHHHHHHHHHHHHHHHhhcc
Confidence            99999999999999999999999999 58999999999999999999999999999999999999998764

>PRK14819 NADH dehydrogenase subunit B; Provisional

Probab=100.00  E-value=2.3e-50  Score=354.92  Aligned_cols=154  Identities=54%  Similarity=1.073  Sum_probs=146.0

Q ss_pred             CCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcc-eecCCCCCeeEEEEecccCCCChHHHHH
Q 041751           58 KASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMIVAGTLTNKMAPALRK  136 (213)
Q Consensus        58 ~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi-~~~~sPr~aDIliVeG~Vt~km~~~l~~  136 (213)
                      ...+++.+++|+++||+|++|+|+.++||+||++|++++..++||++|||+ .|+++|||+||+||||+||++|.+.+++
T Consensus        12 ~~~~~~~~~~~~~~~W~r~~Slw~~~~gt~CC~iEila~l~p~yDieRFGi~~~~~sPRhADIlLVtG~VT~km~~~L~r   91 (264)
T PRK14819         12 EKQGVLLTTVNRFYNWGRRSSVWPMAFGLACCAIEMMATGLSRYDLARFGAELFRASPRQADLMIVAGTVTKKMAPQVVR   91 (264)
T ss_pred             ccCceeeeeHHHHHHHHHhCCcceeeeCCcccHHHHHHhccccccHHHhCcccccCCCCcceEEEEecCCchhhHHHHHH
Confidence            456799999999999999999999999999999999999999999999999 5899999999999999999999999999


Q ss_pred             HHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhc--CCcccccc
Q 041751          137 VYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRR--RDFLHWWT  212 (213)
Q Consensus       137 l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~--~~~~~~y~  212 (213)
                      +|+||++||+|||+|+||++||+|+++|++++|++++||||+|||||||+||+|+++|++|+++++..  +|+ .||+
T Consensus        92 lyeqmP~PK~VIAvGaCA~~GGIf~~sY~v~~gId~vIPVDv~IPGCPP~Pe~Il~gLl~L~~ki~~d~~~Rp-~~~~  168 (264)
T PRK14819         92 LYNQMPEPRYVISMGACATSGGPFRDGYNVLRGIDLLIPVDVYIPGCPPRPEALLHALMTLQKQIDAQSLGRV-RWYG  168 (264)
T ss_pred             HHHhccCCCeEEEEccccccCCccccCCCccCCccccccccEEecCCCCCHHHHHHHHHHHHhhcccccccCc-cccc
Confidence            99999999999999999999999999999999999999999999999999999999999999988643  355 6775

>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional

Probab=100.00  E-value=5.2e-46  Score=368.63  Aligned_cols=147  Identities=52%  Similarity=1.056  Sum_probs=142.6

Q ss_pred             cceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcc-eecCCCCCeeEEEEecccCCCChHHHHHHH
Q 041751           60 SEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMIVAGTLTNKMAPALRKVY  138 (213)
Q Consensus        60 ~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi-~~~~sPr~aDIliVeG~Vt~km~~~l~~l~  138 (213)
                      .+++++++|+++||+|++|+|+.+++|+||++||+++.+++||++|||+ .|++||||+|++||+|+||.+|+++++++|
T Consensus         5 ~~~~~~~~~~~~~~~r~~s~w~~~~~~~cc~~E~~~~~~~~~D~~r~G~~~~~~sPr~aD~llv~G~vt~~~~~~l~~~~   84 (788)
T PRK13292          5 ENILLASLDDLINWGRANSLWPMFFGLSCCFVEMMTSFTSRYDISRFGAEVLRGTPREADLMVIAGTVFKKMAPSILRLY   84 (788)
T ss_pred             CceeeeeHHHHHHHHhhCCCcceecCCccHHHHHHHhcCCcCCHHHcCCCccCCCcccceEEEEecCCcHhhHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999 589999999999999999999999999999


Q ss_pred             HHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCc
Q 041751          139 DQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDF  207 (213)
Q Consensus       139 e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~  207 (213)
                      ||||+||+|||+|+||++||+| ++|++++|++++||||+|||||||+||+|+++|++|++||+.+++.
T Consensus        85 ~~~p~pk~via~G~Ca~~GG~~-~~y~~~~g~~~~ipVDv~iPGCPP~Pe~i~~~i~~l~~~~~~~~~~  152 (788)
T PRK13292         85 EQMAEPKWVISMGSCANSGGMY-DVYSVVQGVNQILPVDVYIPGCPPRPEAFLQGLMLLQEKIRREERP  152 (788)
T ss_pred             HhCCCCCEEEEecccccCCCCc-CccccccCcCCcccccEEccCCCCCHHHHHHHHHHHHHHhhcCccc
Confidence            9999999999999999999999 7999999999999999999999999999999999999999987754

>COG3260 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]

Probab=100.00  E-value=1e-44  Score=294.37  Aligned_cols=128  Identities=39%  Similarity=0.756  Sum_probs=122.4

Q ss_pred             cCCcceec---ccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEecccCCCChHHHHHHHHHCCCCceEEEecC
Q 041751           76 RGSLWPMT---FGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGS  152 (213)
Q Consensus        76 ~~siW~~~---~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG~Vt~km~~~l~~l~e~~~~pk~VIA~Gs  152 (213)
                      ++|+|..+   .||+||++|++++..|+||.|||||.++++|||||+|+|+|.+|.+|++.++++||+||+||+|||+|+
T Consensus         6 ~rS~~v~~VdsG~CNgCdIEi~a~~sP~YDaErfgI~~v~sPRhADiLlVTG~vT~~~~e~lkk~Yea~PePKiViA~Ga   85 (148)
T COG3260           6 KRSLHVYHVDSGGCNGCDIEILAALSPRYDAERFGIKVVNSPRHADILLVTGAVTRQMREPLKKAYEAMPEPKIVIAVGA   85 (148)
T ss_pred             ccceEEEEeccCCcCceeEEEeeccCcccchHHheeEEeCCCccccEEEEeccccHHHHHHHHHHHHhCCCCcEEEEEcc
Confidence            67888765   589999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhh
Q 041751          153 RANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINR  203 (213)
Q Consensus       153 CA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~  203 (213)
                      ||++||||+++|.+..|+|++||||++||||||+|++|+++|.++++++.+
T Consensus        86 Ca~~GGIf~~~~~v~gpvd~viPVDv~IPGCPP~P~~il~g~~~al~~~~k  136 (148)
T COG3260          86 CALSGGIFKDSYSVWGPVDKVIPVDVEIPGCPPRPEAILAGLVAALGKLEK  136 (148)
T ss_pred             cccCCceecccccccccccceeEeeeEcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999998876644

>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma

Probab=99.98  E-value=5.4e-33  Score=241.34  Aligned_cols=124  Identities=21%  Similarity=0.385  Sum_probs=111.0

Q ss_pred             cCCcceecccCCccHHHHHhcCCCCcch-hhh-cceecCC------CCCeeEEEEecccCCCChHHHHHHHHHCCCCceE
Q 041751           76 RGSLWPMTFGLACCAVEMMHTGAAGYDL-DRF-GIIFRPS------PRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWV  147 (213)
Q Consensus        76 ~~siW~~~~gc~GC~iE~l~~~~~~~Dl-~rf-gi~~~~s------Pr~aDIliVeG~Vt~km~~~l~~l~e~~~~pk~V  147 (213)
                      .+.+|++..+|+||+++|+++.++.+|+ +.+ ++.|+++      ..++||++|||+|++++.+.++++++++++||+|
T Consensus         2 ~~v~~~~~~~C~GC~~s~l~~~~~~~~ll~~~i~~~y~~~~~~~~~~~~~dil~VeG~i~~~~~~~~~~~~~~~~~ak~v   81 (228)
T TIGR03294         2 ITVGYVHLSGCTGCLVSLTDNYEGLLDILDNIADLVYCQTLADAREIPEMDVALVEGSVCLQDEHSLEEIKELREKAKVV   81 (228)
T ss_pred             ceEEEEECCCCCChHHHHHccCCcHHHHHHHhhHheecHhhhhhccCCCccEEEEeCCCCCCccHHHHHHHHHhccCCEE
Confidence            5679999999999999999999888887 455 7888762      2458999999999999999999999999999999


Q ss_pred             EEecCccCcCCCCCCCCc---------cccCCCccccceEEccCCCCCHHHHHHHHHHHHH
Q 041751          148 ISMGSRANGGGYYHYSYS---------VVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQK  199 (213)
Q Consensus       148 IA~GsCA~~GGi~~~sy~---------~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~  199 (213)
                      ||+|+||++||+++.+++         .++|++++|+||||||||||+|++|+++|.+|+.
T Consensus        82 VA~GtCA~~GGi~~~~~~~~~~~~~~~~~~~~~~~V~vdi~IpGCPp~p~~i~~~l~~ll~  142 (228)
T TIGR03294        82 VALGACAATGNFTRYSRGGQQAQPQHESFVPITDVIDVDLAIPGCPPSPEAIRNVCVALLN  142 (228)
T ss_pred             EEeecccccCCcccccCCcccCCCCCCCCcCHHHcccCCEEeeCCCCCHHHHHHHHHHHHc
Confidence            999999999999876543         4788899999999999999999999999999875

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

>PF01058 Oxidored_q6: NADH ubiquinone oxidoreductase, 20 Kd subunit; InterPro: IPR006137 NADH:ubiquinone oxidoreductase (complex I) (1

Probab=99.97  E-value=8.2e-34  Score=227.22  Aligned_cols=112  Identities=33%  Similarity=0.573  Sum_probs=92.9

Q ss_pred             CCccHHHHHhcCCCCcch-hhhcceecC----CCC---------CeeEEEEecccCCCChHHHHHHHHHCCCCceEEEec
Q 041751           86 LACCAVEMMHTGAAGYDL-DRFGIIFRP----SPR---------QSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMG  151 (213)
Q Consensus        86 c~GC~iE~l~~~~~~~Dl-~rfgi~~~~----sPr---------~aDIliVeG~Vt~km~~~l~~l~e~~~~pk~VIA~G  151 (213)
                      |+||++||++...+.+|+ +.+++.|++    +++         ++||+||||+|++++.+.+++++++|+++|+|||+|
T Consensus         1 C~GC~~s~~~~~~~~~dll~~i~~~~~~~l~~~~~~~~~~~~~~~~diliVeG~v~~~~~~~~e~~~~~~~~a~~vIAvG   80 (131)
T PF01058_consen    1 CTGCTISFLALEPSLLDLLELIEIRYHPSLMASPGEQDEENGEEEADILIVEGSVPRNMEEALEWLKELRPKAKAVIAVG   80 (131)
T ss_dssp             -SHHHHHHTTTTTTHHHHHHTEEEEEETTT-SS-HHHHHHHHTTTTEEEEEESBEETGGEEHHHHHHHHHGCSSEEEEEH
T ss_pred             CCCcHHHHhhCCCCHHHHHhhhHHHhCCEehhhcCCccccccccCceEEEEEeeccCCchHHHHHHHHHccCCceeEcCC
Confidence            999999998888899997 556666643    444         999999999999999999999999999999999999


Q ss_pred             CccCcCCCCC--CCCcc---ccCCCccccceEEccCCCCCHHHHHHHHHHH
Q 041751          152 SRANGGGYYH--YSYSV---VRGCDRIVPVDIYVPGCPPTAEALLYGILQL  197 (213)
Q Consensus       152 sCA~~GGi~~--~sy~~---~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~L  197 (213)
                      +||++|||++  .+++.   ++++++++|||||||||||+||+|+++|.+|
T Consensus        81 tCA~~GGi~~~~~~~~~~~~~~~~~~~~~VDi~IpGCPp~pd~i~~~l~~L  131 (131)
T PF01058_consen   81 TCASFGGIPAARNNPSVGDSVGPLLEVVPVDINIPGCPPHPDWILETLLAL  131 (131)
T ss_dssp             HHHHH-TGGGSTTSTTEEE-HHHHHGCS-ECEEE-SSS--HHHHHHHHHHH
T ss_pred             CccccCCcccccccccccccccCcCCCccEEEEeeCCCCCHHHHHHHHhhC
Confidence            9999999994  44543   4678889999999999999999999999986

6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 20 kDa (in mammals) [], which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 4Fe-4S iron-sulphur cluster. The 20 kDa subunit has been found to be nuclear encoded, as a precursor form with a transit peptide in mammals, and in Neurospora crassa. It is and chloroplast encoded in various higher plants (gene ndhK or psbG).; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0048038 quinone binding, 0051539 4 iron, 4 sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 3MYR_E 3RGW_S 2FUG_F 3IAS_6 3I9V_F 3IAM_F 2YBB_6 3M9S_F 2FRV_G 1YQ9_B ....

>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA)

Probab=99.97  E-value=1.9e-30  Score=239.04  Aligned_cols=142  Identities=14%  Similarity=0.297  Sum_probs=122.6

Q ss_pred             hhhhcCCcceecccCCccHHHHHhcCCCCcc--hhh-hcceecCC-------------------CCCeeEEEEecccCCC
Q 041751           72 NWVRRGSLWPMTFGLACCAVEMMHTGAAGYD--LDR-FGIIFRPS-------------------PRQSDVMIVAGTLTNK  129 (213)
Q Consensus        72 ~w~R~~siW~~~~gc~GC~iE~l~~~~~~~D--l~r-fgi~~~~s-------------------Pr~aDIliVeG~Vt~k  129 (213)
                      +-.|.+.+|++..+|+||+++|+++..|.+|  +.. ..++|+++                   ....||++|||+|+++
T Consensus        47 ~~~~~~viWL~~~~CtGCs~SlL~s~~P~~~~~ll~~isl~yhptlmaa~G~~ae~~l~~~~~~~~g~~ILvVEGaIp~~  126 (365)
T TIGR00391        47 NPQRPPVIWIHAQECTGCTESLLRSAHPTVENLILETISLEYHETLMAAFGHQAEENKHDAIEKYKGQYILVVEGSIPLG  126 (365)
T ss_pred             cCCCCCEEEEeCCCCCCcHHHHhccCCCCHHHHHhcCceEEechHhHHhhHHHHHHHHHHHHhccCCCeEEEEeCCCCCC
Confidence            3477899999999999999999999999888  433 47788763                   1236999999999998


Q ss_pred             C---------hHHHHHHHHHCCCCceEEEecCccCcCCCCCCCCcc--ccCCCccc--cceEEccCCCCCHHHHHHHHHH
Q 041751          130 M---------APALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSV--VRGCDRIV--PVDIYVPGCPPTAEALLYGILQ  196 (213)
Q Consensus       130 m---------~~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~--~~gv~~vV--pVDi~IPGCPP~Pe~il~~L~~  196 (213)
                      +         .+.++.++++++++|+|||+|+||++|||++..++.  ..||++++  ..+||||||||+||+|+++|++
T Consensus       127 ~~G~y~~~~g~~~~e~l~~~a~~A~aVIAvGtCAs~GGI~aa~pnptga~~v~~vi~~~pvinIPGCPp~Pe~i~~tl~~  206 (365)
T TIGR00391       127 DNGIYCMVAGEPIVEHIRKAAEGAAAIIAIGTCSSWGGVQAAGPNPTGAVPLQKVIPDKPVINVPGCPPNPHNFLATVAY  206 (365)
T ss_pred             CCceeeeeCCcHHHHHHHHHhhcCCEEEEEeccccccCccCCCCCCCCCcchhHhcCCCCeEEeCCCCCCHHHHHHHHHH
Confidence            7         468999999999999999999999999999876654  56899998  3459999999999999999999


Q ss_pred             HH-----HHHhhcCCccccccC
Q 041751          197 LQ-----KKINRRRDFLHWWTK  213 (213)
Q Consensus       197 Ll-----~ki~~~~~~~~~y~~  213 (213)
                      ++     .++++.+||++||++
T Consensus       207 ~ll~G~lP~LD~~~RP~~fyg~  228 (365)
T TIGR00391       207 IITFGKLPKLDDKNRPTFAYGR  228 (365)
T ss_pred             HHHcCCCCCCCCCCCchhhhcC
Confidence            75     268999999999974

Called (hupA/hydA/hupS/hoxK/vhtG) Involved in hydrogenase reactions performing different specific functions in different species eg (EC 1.12.2.1) in Desulfovibrio gigas,(EC 1.12.99.3) in Wolinella succinogenes and (EC 1.18.99.1) in E.coli and a number of other species and (EC 1.12.99.-) in the archea.

>PRK10468 hydrogenase 2 small subunit; Provisional

Probab=99.96  E-value=3e-30  Score=237.98  Aligned_cols=142  Identities=16%  Similarity=0.311  Sum_probs=121.8

Q ss_pred             hhhhcCCcceecccCCccHHHHHhcCCCCcc--hhh-hcceecCC-------------------CCCeeEEEEecccCCC
Q 041751           72 NWVRRGSLWPMTFGLACCAVEMMHTGAAGYD--LDR-FGIIFRPS-------------------PRQSDVMIVAGTLTNK  129 (213)
Q Consensus        72 ~w~R~~siW~~~~gc~GC~iE~l~~~~~~~D--l~r-fgi~~~~s-------------------Pr~aDIliVeG~Vt~k  129 (213)
                      .-.|.+.||++..+|+||+++|+++..|.++  +.. ..+.||++                   ...-|||+|||+|+.+
T Consensus        45 ~~~r~~viWLq~~~CtGcs~SlL~a~~P~~~~ll~~~i~l~yH~tl~aa~G~~a~~~l~~~~~~~~~~~ILvVEGaIp~~  124 (371)
T PRK10468         45 NPQRPPVIWIGAQECTGCTESLLRATHPTVENLVLETISLEYHEVLSAAFGHQVEENKHNALEKYKGQYVLVVDGSIPLK  124 (371)
T ss_pred             cCCCCcEEEEeCCCCCCcHHHHhccCCCCHHHHHhcCceeeeccHHHHHhHHHHHHHHHHHHhcCCCCeEEEEeCCCCCC
Confidence            3467899999999999999999999998776  233 36788773                   1346999999999998


Q ss_pred             C---------hHHHHHHHHHCCCCceEEEecCccCcCCCCCCCCcc--ccCCCccccce--EEccCCCCCHHHHHHHHHH
Q 041751          130 M---------APALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSV--VRGCDRIVPVD--IYVPGCPPTAEALLYGILQ  196 (213)
Q Consensus       130 m---------~~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~--~~gv~~vVpVD--i~IPGCPP~Pe~il~~L~~  196 (213)
                      +         .+.++.+++++++||+|||+|+||++|||++..++.  ..|++++++.+  ||||||||+||+|+++|++
T Consensus       125 ~~G~y~~~gg~~~~e~l~~~a~~A~aVVAvGtCAs~GGI~aa~pnptga~gv~~~l~~~PVINIPGCPp~P~~i~~tL~~  204 (371)
T PRK10468        125 DNGIYCMVAGEPIVDHIRKAAEGAAAIIAIGSCSAWGGVAAAGVNPTGAVSLQEVLPGKTVINIPGCPPNPHNFLATVAH  204 (371)
T ss_pred             CCcceeeECCchHHHHHHHHhccCCEEEEEecccccCCcccCCCCCCCCccHHHhcCCCCeEEcCCCCCCHHHHHHHHHH
Confidence            5         478999999999999999999999999999987765  55888887433  9999999999999999999


Q ss_pred             HH-H----HHhhcCCccccccC
Q 041751          197 LQ-K----KINRRRDFLHWWTK  213 (213)
Q Consensus       197 Ll-~----ki~~~~~~~~~y~~  213 (213)
                      |+ .    ++|+.+||++||.+
T Consensus       205 l~~~g~lp~LD~~gRPk~fyg~  226 (371)
T PRK10468        205 IITYGKPPKLDDKNRPTFAYGR  226 (371)
T ss_pred             HHhcCCCccccccCCcHHHhcC
Confidence            98 2    59999999999974

>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]

Probab=99.95  E-value=1.1e-27  Score=217.68  Aligned_cols=151  Identities=15%  Similarity=0.292  Sum_probs=124.4

Q ss_pred             eeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcch--hhh-cceecCC-------------------CCCeeE
Q 041751           62 YVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDL--DRF-GIIFRPS-------------------PRQSDV  119 (213)
Q Consensus        62 ~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl--~rf-gi~~~~s-------------------Pr~aDI  119 (213)
                      |.......+=+--|.+.||++...|+||+++|++...|..+.  ..| .+.|+++                   -+.-||
T Consensus        35 ~~~~~~~a~e~~~~~~viWLhg~eCTGcteSfLrs~~P~~~~li~~~IsL~Yhetlmaa~G~~aee~l~~~i~~~kg~yI  114 (355)
T COG1740          35 YAPEIAKALENKPRTPVIWLHGLECTGCTESFLRSEHPTANDLILELISLEYHETLMAASGTQAEELLEDAILKYKGKYI  114 (355)
T ss_pred             chHHHHHHHhcCCCCceEEEecccccCchHHHhccCCCCHHHHHHHHHhhhhhhhhhhhcchhHHHHHHHHHHhcCCceE
Confidence            333344444445555899999999999999999999998874  233 4567652                   234689


Q ss_pred             EEEecccCCCC---------hHHHHHHHHHCCCCceEEEecCccCcCCCCCCC--CccccCCCccc---cceEEccCCCC
Q 041751          120 MIVAGTLTNKM---------APALRKVYDQMPEPRWVISMGSRANGGGYYHYS--YSVVRGCDRIV---PVDIYVPGCPP  185 (213)
Q Consensus       120 liVeG~Vt~km---------~~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~s--y~~~~gv~~vV---pVDi~IPGCPP  185 (213)
                      |+|||+|++.+         .+..+.++++.+.+++|||+|+||++|||++..  ++...++++++   || ||||||||
T Consensus       115 LvVEG~v~~~~~G~y~~vgg~~~~e~l~~aA~~A~aIiAvGtCAs~GgI~AA~pnps~a~~i~ev~~~kpV-INiPGCPp  193 (355)
T COG1740         115 LVVEGAVPLGENGMYCIVGGEPFKEILRKAAEGASAIIAVGTCASWGGIQAAKPNPTGAGPLSEVIKDKPV-INIPGCPP  193 (355)
T ss_pred             EEEeCCccCCCCceEEEEcChhHHHHHHHHhhcCceEEEEecccccCCeeccCCCCCCcccceecccCCce-eeCCCCCC
Confidence            99999999994         578889999999999999999999999999874  56778999988   56 99999999


Q ss_pred             CHHHHHHHHHHHHH-----HHhhcCCccccccC
Q 041751          186 TAEALLYGILQLQK-----KINRRRDFLHWWTK  213 (213)
Q Consensus       186 ~Pe~il~~L~~Ll~-----ki~~~~~~~~~y~~  213 (213)
                      +||+|+.+|.+++-     +||+.+||++||.+
T Consensus       194 ~pd~iv~tl~~~~~~gk~P~LD~~~RPk~fyg~  226 (355)
T COG1740         194 NPDWIVATLLHIVTFGKLPDLDELGRPKMFYGN  226 (355)
T ss_pred             CchhHHHHHHHHHHcCCCcchhhcCCchhhhcc
Confidence            99999999998764     59999999999973

>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]

Probab=99.94  E-value=1e-27  Score=209.92  Aligned_cols=116  Identities=26%  Similarity=0.470  Sum_probs=101.2

Q ss_pred             ecccCCccHHHHHhcCCCCcch-hhhcceecC-------CCCCeeEEEEecccCCCChHHHHHHHHHCCCCceEEEecCc
Q 041751           82 MTFGLACCAVEMMHTGAAGYDL-DRFGIIFRP-------SPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSR  153 (213)
Q Consensus        82 ~~~gc~GC~iE~l~~~~~~~Dl-~rfgi~~~~-------sPr~aDIliVeG~Vt~km~~~l~~l~e~~~~pk~VIA~GsC  153 (213)
                      +..||+||.++|+++....+|+ ++.+++|.+       .|+ .||++|||+|.+++.  ++.++|+|+++|+|||+|+|
T Consensus        10 ~L~gC~GC~~slldl~E~L~dll~~~div~~~~l~D~keiPE-vDValVEGsV~~ee~--lE~v~ElRekakivVA~GsC   86 (247)
T COG1941          10 WLTGCSGCHMSLLDLYEKLLDLLEDADIVYCPTLVDEKEIPE-VDVALVEGSVCDEEE--LELVKELREKAKIVVALGSC   86 (247)
T ss_pred             EeccccchHHHHHhHHHHHHHhhhhhcEEEeecccccccCCc-ccEEEEecccCcHHH--HHHHHHHHHhCcEEEEEecc
Confidence            4469999999999999999997 557888765       355 999999999995544  99999999999999999999


Q ss_pred             cCcCCCCCC-----------CC---------ccccCCCccccceEEccCCCCCHHHHHHHHHHHHHH
Q 041751          154 ANGGGYYHY-----------SY---------SVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKK  200 (213)
Q Consensus       154 A~~GGi~~~-----------sy---------~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~k  200 (213)
                      |++||+++.           .|         ..++|+.++|+||++||||||+||.|.++|..|+++
T Consensus        87 A~~Ggv~~~~~~s~~e~l~~~y~~~~~~~~~~~v~Pl~evI~VD~~IpGCPP~~e~I~~al~all~g  153 (247)
T COG1941          87 AVTGGVQGLRNKSGEELLRPVYGDAKSTFNEESVVPLGEVIDVDYAIPGCPPSPEEIARALTALLEG  153 (247)
T ss_pred             hhcCCchhhhhccccccchhhhhcccCCCCccceEEchheeeeeeecCCCCcCHHHHHHHHHHHHcC
Confidence            999999842           23         357899999999999999999999999999999763

>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA

Probab=88.17  E-value=0.61  Score=35.85  Aligned_cols=70  Identities=19%  Similarity=0.245  Sum_probs=40.4

Q ss_pred             ceecccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEec-ccCCCCh-H---HHHHHHHHCCCCceEEEecCc
Q 041751           80 WPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAG-TLTNKMA-P---ALRKVYDQMPEPRWVISMGSR  153 (213)
Q Consensus        80 W~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG-~Vt~km~-~---~l~~l~e~~~~pk~VIA~GsC  153 (213)
                      +..++||   .++..++..-.-.+.+.|......+.+||++||.- +|+.+-. +   .++++.+.- +++..|.+.-|
T Consensus         3 ~i~T~GC---~~N~~Dse~i~~~l~~~G~~~~~~~e~AD~iiiNTC~V~~~Ae~k~~~~i~~l~~~~-~~~~~ivv~GC   77 (98)
T PF00919_consen    3 YIETLGC---QMNQYDSERIASILQAAGYEIVDDPEEADVIIINTCTVRESAEQKSRNRIRKLKKLK-KPGAKIVVTGC   77 (98)
T ss_pred             EEEECCC---cccHHHHHHHHHHHHhcCCeeecccccCCEEEEEcCCCCcHHHHHHHHHHHHHHHhc-CCCCEEEEEeC
Confidence            4556654   45544444333445677888888899999888754 4444332 2   344444443 45566666556

A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification

>cd00886 MogA_MoaB MogA_MoaB family

Probab=84.60  E-value=3.1  Score=33.76  Aligned_cols=26  Identities=23%  Similarity=0.355  Sum_probs=19.0

Q ss_pred             cceEEccCCCCCHHHHHHHHHHHHHHH
Q 041751          175 PVDIYVPGCPPTAEALLYGILQLQKKI  201 (213)
Q Consensus       175 pVDi~IPGCPP~Pe~il~~L~~Ll~ki  201 (213)
                      +| +.+||||......++.++-+++++
T Consensus       123 ~v-~~LPG~P~aa~~~~~~v~P~l~~~  148 (152)
T cd00886         123 LI-FNLPGSPKAVREALEVILPELPHL  148 (152)
T ss_pred             EE-EECCCCHHHHHHHHHHHHHHHHHH
Confidence            45 899999997777776666566554

Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.

>TIGR01125 MiaB-like tRNA modifying enzyme YliG, TIGR01125

Probab=80.88  E-value=0.82  Score=43.00  Aligned_cols=74  Identities=11%  Similarity=0.023  Sum_probs=44.0

Q ss_pred             cceecccCCccHHHHHhcCCCCcchhhhcceecCCCCCeeEEEEec-ccCCCChH-HHHHHHHHCCCCceEEEecCccCc
Q 041751           79 LWPMTFGLACCAVEMMHTGAAGYDLDRFGIIFRPSPRQSDVMIVAG-TLTNKMAP-ALRKVYDQMPEPRWVISMGSRANG  156 (213)
Q Consensus        79 iW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi~~~~sPr~aDIliVeG-~Vt~km~~-~l~~l~e~~~~pk~VIA~GsCA~~  156 (213)
                      ++..++||.=...|--.+   .-.+...|......+.+|||++|.- +|+.+-.. +.+.+.+.+.. +..|.+|-|...
T Consensus         2 ~~i~t~GC~~N~~ds~~~---~~~l~~~g~~~~~~~~~aD~viinTC~v~~~a~~~~~~~i~~~~~~-~~~vvvgGc~a~   77 (430)
T TIGR01125         2 IGFISLGCPKNLVDSEVM---LGILREAGYEVTPNYEDADYVIVNTCGFIEDARQESIDTIGELADA-GKKVIVTGCLVQ   77 (430)
T ss_pred             EEEEECCCCCcHHHHHHH---HHHHHHCcCEECCCcccCCEEEEeCCCccchHHHHHHHHHHHHHhc-CCCEEEECCccc
Confidence            567777775444332222   2234556766667778999999997 67766543 45555554422 234677777544

This clade spans alpha and gamma proteobacteria, cyano bacteria, deinococcus, porphyromonas, aquifex, helicobacter, campylobacter, thermotoga, chlamydia, streptococcus coelicolor and clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	213
2fug_6	181	Crystal Structure Of The Hydrophilic Domain Of Resp		2e-39

>pdb|2FUG|6 Chain 6, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 181

Iteration: 1
 Score =  158 bits (400), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 76/140 (54%), Positives = 100/140 (71%), Gaps = 2/140 (1%)
Query: 63  VISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMI 121
           + + ++ L+ W R  SLWP TFGLACCA+EMM +  A  DL RFG  +FR SPRQ+DVMI
Sbjct: 20  LFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVMI 79
Query: 122 VAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANXXXXXXXXXXXXXXCDRIVPVDIYVP 181
           VAG L+ KMAP +R+V++QMP+P+WVISMG+ A+               D +VPVD+YVP
Sbjct: 80  VAGRLSKKMAPVMRRVWEQMPDPKWVISMGACAS-SGGMFNNYAIVQNVDSVVPVDVYVP 138
Query: 182 GCPPTAEALLYGILQLQKKI 201
           GCPP  EAL+Y ++QLQKK+
Sbjct: 139 GCPPRPEALIYAVMQLQKKV 158

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
3i9v_6	181	NADH-quinone oxidoreductase subunit 6; electron tr	3e-99
1cc1_S	283	Hydrogenase (small subunit); NI-Fe-Se hydrogenase,	3e-09
2wpn_A	317	Periplasmic [nifese] hydrogenase, small subunit; m	7e-09
3ayx_B	283	Membrane-bound hydrogenase small subunit; oxidored	1e-07
1h2a_S	317	Hydrogenase; SO ligand, hydrogen metabolism, Mg ce	2e-07
3rgw_S	339	Membrane-bound hydrogenase (NIFE) small subunit H;	8e-07
3uqy_S	335	Hydrogenase-1 small chain; membrane-bound hydrogen	2e-06
1wui_S	267	Periplasmic [NIFE] hydrogenase small subunit; high	4e-06
1yqw_A	264	Periplasmic [NIFE] hydrogenase small subunit; NI-F	1e-05
1yq9_A	264	Periplasmic [NIFE] hydrogenase small subunit; oxid	3e-05
3myr_A	269	Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydr	4e-04

>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_6* 2fug_6* 3iam_6* 3ias_6* 3m9s_6* Length = 181

 Score =  284 bits (729), Expect = 3e-99
 Identities = 80/150 (53%), Positives = 111/150 (74%), Gaps = 2/150 (1%)

Query: 62  YVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVM 120
            + + ++ L+ W R  SLWP TFGLACCA+EMM +  A  DL RFG  +FR SPRQ+DVM
Sbjct: 19  ILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVM 78

Query: 121 IVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYV 180
           IVAG L+ KMAP +R+V++QMP+P+WVISMG+ A+ GG ++ +Y++V+  D +VPVD+YV
Sbjct: 79  IVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-NYAIVQNVDSVVPVDVYV 137

Query: 181 PGCPPTAEALLYGILQLQKKINRRRDFLHW 210
           PGCPP  EAL+Y ++QLQKK+  +      
Sbjct: 138 PGCPPRPEALIYAVMQLQKKVRGQAYNERG 167

>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.19.1.1 Length = 283

 Score = 54.7 bits (131), Expect = 3e-09
 Identities = 13/86 (15%), Positives = 33/86 (38%), Gaps = 8/86 (9%)

Query: 124 GTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSV--------VRGCDRIVP 175
               +     +  + D  P+    +++G+ +  GG      +V            ++I  
Sbjct: 97  AKAHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEK 156

Query: 176 VDIYVPGCPPTAEALLYGILQLQKKI 201
           + + VPGCPP  + ++  ++     +
Sbjct: 157 LLVNVPGCPPHPDWMVGTLVAAWSHV 182

>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} Length = 317

 Score = 53.6 bits (128), Expect = 7e-09
 Identities = 15/122 (12%), Positives = 39/122 (31%), Gaps = 22/122 (18%)

Query: 98  AAGYDLDRFGIIFRPSPRQSDVMIVAGTL--------------TNKMAPALRKVYDQMPE 143
             G              +    +++ G++               +     +  + +  P 
Sbjct: 86  WEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPN 145

Query: 144 PRWVISMGSRANGGG----YYHYSYSV----VRGCDRIVPVDIYVPGCPPTAEALLYGIL 195
              V+++G+ A  GG        + +       G + I    + +PGCPP  + ++  ++
Sbjct: 146 AAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVV 205

Query: 196 QL 197
             
Sbjct: 206 LA 207

>3ayx_B Membrane-bound hydrogenase small subunit; oxidoreductase, membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio marinus} PDB: 3ayy_B 3ayz_B Length = 283

 Score = 50.0 bits (119), Expect = 1e-07
 Identities = 21/116 (18%), Positives = 41/116 (35%), Gaps = 16/116 (13%)

Query: 98  AAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKM---------APALRKVYDQMPEPRWVI 148
           A+G+  +      +   + + ++ V G                P   ++     + + +I
Sbjct: 57  ASGHAAEAILDEIKEKYKGNYILAVEGNPPLNQDGMSCIIGGRPFSEQLKRMADDAKAII 116

Query: 149 SMGSRANGGGYY--HYSYSVVRGCDRIVPVD-----IYVPGCPPTAEALLYGILQL 197
           S GS A+ G       + +      + +        I VPGCPP AE +   I  +
Sbjct: 117 SWGSCASWGCVQAAKPNPTQATPVHKFLGGGYDKPIIKVPGCPPIAEVMTGVITYM 172

>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 Length = 317

 Score = 49.3 bits (117), Expect = 2e-07
 Identities = 25/178 (14%), Positives = 53/178 (29%), Gaps = 38/178 (21%)

Query: 55  GLSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYD---LDRFGIIFR 111
           G+  A    +++        R   ++        C+  ++       D   LD   + + 
Sbjct: 38  GMGPAFAPEVARALM--GPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYH 95

Query: 112 PSP------------------RQSDVMIVAGTLTNKMA---------PALRKVYDQMPEP 144
            +                       + +V G +                L      +P+ 
Sbjct: 96  ETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKA 155

Query: 145 RWVISMGSRANGGG--YYHYSYSVVRGCDRIVP----VDIYVPGCPPTAEALLYGILQ 196
           + VI+ G+ A  GG      + +  +G +  +       I + GCPP    L+  I+ 
Sbjct: 156 QAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVY 213

>3rgw_S Membrane-bound hydrogenase (NIFE) small subunit H; [NIFE] hydrogenase, high-resolution knallgasbacteria, proteobacteria; 1.50A {Ralstonia eutropha} Length = 339

 Score = 47.4 bits (112), Expect = 8e-07
 Identities = 22/113 (19%), Positives = 42/113 (37%), Gaps = 13/113 (11%)

Query: 98  AAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNK---------MAPALRKVYDQMPEPRWVI 148
           AAG+  +          + + ++ V G                P + ++     + + +I
Sbjct: 51  AAGHQAEAILEEIMTKYKGNYILAVEGNPPLNQDGMSCIIGGRPFIEQLKYVAKDAKAII 110

Query: 149 SMGSRANGGGYY--HYSYSVVRGCDRIVPVD--IYVPGCPPTAEALLYGILQL 197
           S GS A+ G       + +      +++     I VPGCPP AE +   I  +
Sbjct: 111 SWGSCASWGCVQAAKPNPTQATPVHKVITDKPIIKVPGCPPIAEVMTGVITYM 163

>3uqy_S Hydrogenase-1 small chain; membrane-bound hydrogenase, oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB: 3usc_S* 3use_S* Length = 335

 Score = 46.2 bits (109), Expect = 2e-06
 Identities = 20/113 (17%), Positives = 37/113 (32%), Gaps = 13/113 (11%)

Query: 98  AAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMA---------PALRKVYDQMPEPRWVI 148
           AAG   +              ++ V G                P + K+         +I
Sbjct: 51  AAGTQAEEVFEDIITQYNGKYILAVEGNPPLGEQGMFCISSGRPFIEKLKRAAAGASAII 110

Query: 149 SMGSRANGGG--YYHYSYSVVRGCDRIVP--VDIYVPGCPPTAEALLYGILQL 197
           + G+ A+ G       + +     D+++     I VPGCPP  + +   I  +
Sbjct: 111 AWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIPDVMSAIITYM 163

>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S 1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S 1wuk_S 1wul_S 1e3d_A* Length = 267

 Score = 45.0 bits (106), Expect = 4e-06
 Identities = 18/99 (18%), Positives = 35/99 (35%), Gaps = 15/99 (15%)

Query: 113 SPRQSDVMIVAGTLTNKMA---------PALRKVYDQMPEPRWVISMGSRANGGG--YYH 161
           +     + +V G +                L      +P+ + VI+ G+ A  GG     
Sbjct: 65  NSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAK 124

Query: 162 YSYSVVRGCDRIVP----VDIYVPGCPPTAEALLYGILQ 196
            + +  +G +  +       I + GCPP    L+  I+ 
Sbjct: 125 PNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVY 163

>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S Length = 264

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 16/95 (16%), Positives = 34/95 (35%), Gaps = 12/95 (12%)

Query: 115 RQSDVMIVAGTLTNKMA---------PALRKVYDQMPEPRWVISMGSRANGGG--YYHYS 163
           +    ++V G L              P +        + + +I +G+ +  GG      +
Sbjct: 67  KDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPN 126

Query: 164 YSVVRGCDRIVPVDIY-VPGCPPTAEALLYGILQL 197
            S  +G    + V    +PGCPP     +  ++ +
Sbjct: 127 PSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHV 161

>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A Length = 264

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 18/115 (15%), Positives = 40/115 (34%), Gaps = 18/115 (15%)

Query: 98  AAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNK---------MAPALRKVYDQMPEPRWVI 148
            AG+ ++        + +   V ++ G +                     +  P+ + VI
Sbjct: 51  GAGHAVEE---ALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVI 107

Query: 149 SMGSRANGGG--YYHYSYSVVRGCDRIVPV----DIYVPGCPPTAEALLYGILQL 197
           ++G+ A  GG      + +   G +  +       I + GCPP     +  ++ L
Sbjct: 108 AIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHL 162

>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} Length = 269

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 22/117 (18%), Positives = 39/117 (33%), Gaps = 14/117 (11%)

Query: 95  HTGAAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKMA----------PALRKVYDQMPEP 144
              A+G   +   +      R   ++IV G++    A               + + +   
Sbjct: 45  LQAASGEAAEAARLQAMDENRGQYLVIVDGSIPGPDANPGFSTVAGHSNYSILMETVEHA 104

Query: 145 RWVISMGSRANGGGYY--HYSYSVVRGCDRIVPVD--IYVPGCPPTAEALLYGILQL 197
             VI++G+ A  GG      + +       +V     I VPGCPP    +   I   
Sbjct: 105 AAVIAVGTCAAFGGLPQARPNPTGAMSVMDLVRDKPVINVPGCPPIPMVITGVIAHY 161

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
3i9v_6	181	NADH-quinone oxidoreductase subunit 6; electron tr	100.0
1yq9_A	264	Periplasmic [NIFE] hydrogenase small subunit; oxid	100.0
1wui_S	267	Periplasmic [NIFE] hydrogenase small subunit; high	100.0
1h2a_S	317	Hydrogenase; SO ligand, hydrogen metabolism, Mg ce	100.0
2wpn_A	317	Periplasmic [nifese] hydrogenase, small subunit; m	100.0
1cc1_S	283	Hydrogenase (small subunit); NI-Fe-Se hydrogenase,	100.0
3ayx_B	283	Membrane-bound hydrogenase small subunit; oxidored	100.0
1yqw_A	264	Periplasmic [NIFE] hydrogenase small subunit; NI-F	100.0
3myr_A	269	Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydr	100.0
3uqy_S	335	Hydrogenase-1 small chain; membrane-bound hydrogen	100.0
3rgw_S	339	Membrane-bound hydrogenase (NIFE) small subunit H;	100.0

>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_6* 2fug_6* 3iam_6* 3ias_6* 3m9s_6*

Probab=100.00  E-value=2.3e-55  Score=370.12  Aligned_cols=155  Identities=52%  Similarity=0.984  Sum_probs=132.6

Q ss_pred             CCCCcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcc-eecCCCCCeeEEEEecccCCCChHHH
Q 041751           56 LSKASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMIVAGTLTNKMAPAL  134 (213)
Q Consensus        56 ~~~~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi-~~~~sPr~aDIliVeG~Vt~km~~~l  134 (213)
                      .....+++.+++|+++||+|++|+|++++||+||++||+++..|+||++|||+ .|+++|||+||++|||+|+++|++.+
T Consensus        13 ~~~~~~~~~~~~~~l~~w~R~~slW~~~~gc~cC~iEll~~~~p~yDl~rfGi~~~~aSPrqaDiliVeG~Vt~~m~~~l   92 (181)
T 3i9v_6           13 ELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVMIVAGRLSKKMAPVM   92 (181)
T ss_dssp             --CTTSHHHHHHHHHHHHHHTTSCCCEEEECSTHHHHHTTTTTTC----------------CCCCEEEESCCBTTTHHHH
T ss_pred             HhccCCchHHHHHHHHhhcccCCcccccCCCCchHHHHHHhhhchhhHHHcCcccccCCCCCceEEEEeccCCcccHHHH
Confidence            34457899999999999999999999999999999999999999999999999 89999999999999999999999999


Q ss_pred             HHHHHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCCccccc
Q 041751          135 RKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRDFLHWW  211 (213)
Q Consensus       135 ~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~~~~~y  211 (213)
                      +++||+|++||+|||+|+||++||+| ++|++++|++++||||+|||||||+||+|+++|++|++||++++....|.
T Consensus        93 ~~~~e~~p~pk~VIAvGsCA~~GGi~-~~y~~~~gvd~iipVDv~IPGCPP~Pe~il~~l~~l~~ki~~~~~~~~~~  168 (181)
T 3i9v_6           93 RRVWEQMPDPKWVISMGACASSGGMF-NNYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGE  168 (181)
T ss_dssp             HHHHHSSCSSCCEEEEHHHHHSCTTC-CSTTBCSCGGGTSCCSEEECCSSCCHHHHHHHHHHHHHHHTTCCBCTTSC
T ss_pred             HHHHHHcCCCceEEEeecccccCCCC-CCCcccCCcccCCCccEEeeCCCCCHHHHHHHHHHHHHHHhhcccccccc
Confidence            99999999999999999999999999 89999999999999999999999999999999999999999888765554

>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A

Probab=100.00  E-value=9e-41  Score=295.06  Aligned_cols=139  Identities=16%  Similarity=0.288  Sum_probs=130.7

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCcc---hhhhcceecCCC----------------CCeeEEEEecccCCCCh----
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGYD---LDRFGIIFRPSP----------------RQSDVMIVAGTLTNKMA----  131 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~D---l~rfgi~~~~sP----------------r~aDIliVeG~Vt~km~----  131 (213)
                      |.+++|++.++|+||++||+++.+|.+|   +++|+++|++++                +|+||+||||+|+++|+    
T Consensus         6 ~~~v~wl~~~~C~GC~isll~~~~p~~~~ll~~~i~i~~~~s~~~~~g~~a~~~~~~~~~~~diliVeGsV~~~~~g~~~   85 (264)
T 1yq9_A            6 RPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKGDFVCVIEGGIPMGDGGYWG   85 (264)
T ss_dssp             SCEEEEEECBCCSHHHHHHHTCTTTTHHHHHHHTCEEEECTTTCSSCTHHHHHHHHHHTTSSEEEEEESBEECGGGSTTB
T ss_pred             CCcEEEEeCCccCchHHHHHhcCCcCHHHHHhhheeeEecCChhhhcchhHHHHHhhhccCCeEEEEeCCcccCCCccee
Confidence            6789999999999999999999999888   389999999987                89999999999999995    


Q ss_pred             -----HHHHHHHHHCCCCceEEEecCccCcCCCCCC--CCccccCCCcccc----ceEEccCCCCCHHHHHHHHHHHHH-
Q 041751          132 -----PALRKVYDQMPEPRWVISMGSRANGGGYYHY--SYSVVRGCDRIVP----VDIYVPGCPPTAEALLYGILQLQK-  199 (213)
Q Consensus       132 -----~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~--sy~~~~gv~~vVp----VDi~IPGCPP~Pe~il~~L~~Ll~-  199 (213)
                           +.++++||+|++||+|||+|+||++||||+.  +|+++.|++++|+    +|||||||||+||+|+++|++|++ 
T Consensus        86 ~~~~~~~~~~l~~~~~~~k~VIA~GsCA~~GGi~a~~~n~~~~~gv~~~l~~~~~~di~IPGCPP~Pe~i~~~l~~ll~~  165 (264)
T 1yq9_A           86 KVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTK  165 (264)
T ss_dssp             EETTEEHHHHHHHHGGGSSEEEEEHHHHHHCCGGGSTTCTTCEECHHHHHGGGTCCCEEECSSSCCHHHHHHHHHHHHHT
T ss_pred             ecCcHHHHHHHHHHhccCCEEEEeccccccCCCCCCCCCCccccChhHhccCCCCeEEEEECCCCCHHHHHHHHHHHHhC
Confidence                 8899999999999999999999999999976  6788899999998    899999999999999999999998 


Q ss_pred             ---HHhhcCCccccccC
Q 041751          200 ---KINRRRDFLHWWTK  213 (213)
Q Consensus       200 ---ki~~~~~~~~~y~~  213 (213)
                         ++++.+||++||++
T Consensus       166 ~~p~Ld~~~RP~~~~~~  182 (264)
T 1yq9_A          166 GMPELDKQGRPVMFFGE  182 (264)
T ss_dssp             CSCCBCTTSCBHHHHSS
T ss_pred             CCCCccccCCchhhhCC
Confidence               67999999999975

>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S 1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S 1wuk_S 1wul_S 1e3d_A*

Probab=100.00  E-value=2.4e-40  Score=292.69  Aligned_cols=139  Identities=19%  Similarity=0.306  Sum_probs=126.8

Q ss_pred             hhcCCcceecccCCccHHHHHhcCCCCcc---hhhhcceec-------------------CCCCCeeEEEEecccCCCCh
Q 041751           74 VRRGSLWPMTFGLACCAVEMMHTGAAGYD---LDRFGIIFR-------------------PSPRQSDVMIVAGTLTNKMA  131 (213)
Q Consensus        74 ~R~~siW~~~~gc~GC~iE~l~~~~~~~D---l~rfgi~~~-------------------~sPr~aDIliVeG~Vt~km~  131 (213)
                      .|.+++|++.++|+||++||+++.+|.||   +++++++|+                   ++|+| ||++|||+|+++|+
T Consensus         5 ~r~~v~wl~~~~C~GC~isll~~~~p~~d~lll~~i~l~y~~~l~~~~g~~~e~~~~~~~~~p~~-Dil~VeG~V~~~~~   83 (267)
T 1wui_S            5 RRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHG-FIAVVEGGIPTAAN   83 (267)
T ss_dssp             SSCEEEEEECBCCSHHHHHHHTCTTTTHHHHHHTTCEEEECTTTCSCCHHHHHHHHHHHHTCTTC-EEEEEESBEECGGG
T ss_pred             CCccEEEEecCccCcHHHHHHhcCCCCHHHHHhhheeeeecchhhhhhhHHHHHHHHHHhcCCCC-eEEEEeCCCccCCC
Confidence            46789999999999999999999999998   567777775                   36899 99999999999998


Q ss_pred             ---------HHHHHHHHHCCCCceEEEecCccCcCCCCCCCCc--cccCCCcccc---c-eEEccCCCCCHHHHHHHHHH
Q 041751          132 ---------PALRKVYDQMPEPRWVISMGSRANGGGYYHYSYS--VVRGCDRIVP---V-DIYVPGCPPTAEALLYGILQ  196 (213)
Q Consensus       132 ---------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy~--~~~gv~~vVp---V-Di~IPGCPP~Pe~il~~L~~  196 (213)
                               +.++++||+|++||+|||+|+||++||||+.+|+  .+.||+++|+   | |||||||||+||+|+++|++
T Consensus        84 g~~~~~~g~~~l~~~~e~~~~ak~VIAvGsCA~~GGi~a~~~n~t~~~gv~~vv~~~~vpdi~IPGCPP~Pe~i~~~l~~  163 (267)
T 1wui_S           84 GIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVY  163 (267)
T ss_dssp             GTTBEETTEEHHHHHHHHGGGSSEEEEESHHHHHCCGGGSTTCTTCEECHHHHHGGGTCCCEEECSSSCCHHHHHHHHHH
T ss_pred             cceeecCChHHHHHHHHHhccCCEEEEeeeccccCCCCCCcCCCcCCCCHHHhcCcCCceEEEEeCCCCCHHHHHHHHHH
Confidence                     8899999999999999999999999999988665  6789999999   7 99999999999999999999


Q ss_pred             HH-H----HHhhcCCccccccC
Q 041751          197 LQ-K----KINRRRDFLHWWTK  213 (213)
Q Consensus       197 Ll-~----ki~~~~~~~~~y~~  213 (213)
                      |+ .    ++++.+||++||++
T Consensus       164 ll~~g~~p~ld~~~RP~~~~~~  185 (267)
T 1wui_S          164 YLKNKAAPELDSLNRPTMFFGQ  185 (267)
T ss_dssp             HHHHSSCCCBCTTSCBHHHHSS
T ss_pred             HHHcCCCcCccccCCchhhhCC
Confidence            75 3    47899999999975

>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP: e.19.1.1

Probab=100.00  E-value=1.5e-40  Score=300.20  Aligned_cols=140  Identities=19%  Similarity=0.295  Sum_probs=129.1

Q ss_pred             hhhcCCcceecccCCccHHHHHhcCCCCcc---hhhhcceecC-------------------CCCCeeEEEEecccCCCC
Q 041751           73 WVRRGSLWPMTFGLACCAVEMMHTGAAGYD---LDRFGIIFRP-------------------SPRQSDVMIVAGTLTNKM  130 (213)
Q Consensus        73 w~R~~siW~~~~gc~GC~iE~l~~~~~~~D---l~rfgi~~~~-------------------sPr~aDIliVeG~Vt~km  130 (213)
                      ..|.+++|++.+||+||++||+++.+|.||   +++++++|++                   +|+| ||++|||+|+++|
T Consensus        54 ~~r~~v~Wl~~~~C~GC~is~l~~~~p~~d~lll~~i~l~y~~~lm~~~G~~ae~~~~~~~~~pr~-DIliVeGsV~~~~  132 (317)
T 1h2a_S           54 PRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHG-FIAVVEGGIPTAA  132 (317)
T ss_dssp             SSSCEEEEEECBCCSHHHHHHTTCTTTTHHHHHHTTCEEEECTTTCSCCHHHHHHHHHHHHSCTTC-CEEEEESBEECGG
T ss_pred             CCCCeEEEeeCCccCcHHHHHHhcCCCCHHHHHhhceeeeecchhhhhchhHHHHHHHHHhcCCCC-eEEEEeCCCcCCC
Confidence            468899999999999999999999999999   5788888876                   6899 9999999999999


Q ss_pred             ---------hHHHHHHHHHCCCCceEEEecCccCcCCCCCC--CCccccCCCcccc---c-eEEccCCCCCHHHHHHHHH
Q 041751          131 ---------APALRKVYDQMPEPRWVISMGSRANGGGYYHY--SYSVVRGCDRIVP---V-DIYVPGCPPTAEALLYGIL  195 (213)
Q Consensus       131 ---------~~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~--sy~~~~gv~~vVp---V-Di~IPGCPP~Pe~il~~L~  195 (213)
                               .+.++++||+|++||+|||+|+||++||||+.  +|+++.||+++||   | |||||||||+||+|+++|+
T Consensus       133 ~g~~~~~~g~~~l~~l~e~~~~ak~VIAvGsCA~~GGi~a~~~npt~~~gv~~vvp~~~vpdi~IPGCPP~Pe~i~~~l~  212 (317)
T 1h2a_S          133 NGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIV  212 (317)
T ss_dssp             GGTTBEETTEEHHHHHHHHGGGCSEEEEESHHHHHCCGGGSTTCTTCEECHHHHHGGGTCCCBCCCCSSCCHHHHHHHHH
T ss_pred             CCcceeeCChHHHHHHHHHhccCCEEEEeccccccCCcCCCCCCCccCcCHHHhcCcCCceEEEEeCCCCCHHHHHHHHH
Confidence                     68999999999999999999999999999987  4558999999999   8 9999999999999999999


Q ss_pred             HHH-H----HHhhcCCccccccC
Q 041751          196 QLQ-K----KINRRRDFLHWWTK  213 (213)
Q Consensus       196 ~Ll-~----ki~~~~~~~~~y~~  213 (213)
                      +|+ .    ++++.+||++||++
T Consensus       213 ~lL~~g~~p~Ld~~~RP~~~~~~  235 (317)
T 1h2a_S          213 YYLKNKAAPELDSLNRPTMFFGQ  235 (317)
T ss_dssp             HHHTTSSCCCBCTTSCBHHHHSS
T ss_pred             HHHHcCCCCCccccCCchhhhcC
Confidence            985 2    48999999999975

>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris}

Probab=100.00  E-value=9.6e-40  Score=294.96  Aligned_cols=139  Identities=15%  Similarity=0.315  Sum_probs=129.2

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCcch---hhhcceecCCC-------------------CCeeEEEEecccCCCCh-
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGYDL---DRFGIIFRPSP-------------------RQSDVMIVAGTLTNKMA-  131 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~Dl---~rfgi~~~~sP-------------------r~aDIliVeG~Vt~km~-  131 (213)
                      |.+++|++.++|+||++||+++..|.||.   +++++.|++++                   +|+||+||||+|+++|+ 
T Consensus        41 ~~~v~wl~~~~C~GC~isll~~~~p~~d~ll~~~i~l~~~~slm~~~g~~a~~~l~~~~~~~~~~DIliVEGsV~~~~~g  120 (317)
T 2wpn_A           41 RPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADG  120 (317)
T ss_dssp             CCEEEEEESBCCSHHHHHHHTCCCTTHHHHHHHTCEEEECTTTCSCCHHHHHHHHHHHHHHTTTTEEEEEESBEECTGGG
T ss_pred             CceEEEEeCCcCCcHHHHHHhcCCCCHHHHHhhceeeEecCchhhhcchHHHHHHHHHhccCCCCeEEEEeCCcccCCCc
Confidence            56899999999999999999999999997   89999999865                   89999999999999998 


Q ss_pred             -------------HHHHHHHHHCCCCceEEEecCccCcCCCCC--CCCccccCCCccc-----cc-eEEccCCCCCHHHH
Q 041751          132 -------------PALRKVYDQMPEPRWVISMGSRANGGGYYH--YSYSVVRGCDRIV-----PV-DIYVPGCPPTAEAL  190 (213)
Q Consensus       132 -------------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~--~sy~~~~gv~~vV-----pV-Di~IPGCPP~Pe~i  190 (213)
                                   +.++++|++|++||+|||+|+||++||||+  .+|+.+.||+++|     +| |||||||||+||+|
T Consensus       121 ~~~~~~~~~~~~~~~~e~l~e~~~~ak~VIAvGsCA~~GGI~a~~~n~t~~~gv~~il~~~~~~vp~I~IPGCPP~Pe~i  200 (317)
T 2wpn_A          121 KYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWI  200 (317)
T ss_dssp             TTBEEEEETTEEEEHHHHHHHHGGGEEEEEEEHHHHHHCTGGGSTTCCSCEECHHHHHHHTTCCCCEEEECSSSCCHHHH
T ss_pred             ceeeecccccCCcCHHHHHHHHhccCCEEEEeccccccCCCCCCCCCCccccCHHHHhhccCCCCCeEEeeCCCCCHHHH
Confidence                         889999999999999999999999999997  4788899999999     67 99999999999999


Q ss_pred             HHHHHHHHHHH----------------hhcCCccccccC
Q 041751          191 LYGILQLQKKI----------------NRRRDFLHWWTK  213 (213)
Q Consensus       191 l~~L~~Ll~ki----------------~~~~~~~~~y~~  213 (213)
                      +++|++|++++                ++.+||++||++
T Consensus       201 ~~~L~~ll~~~~~~~~~~g~~~~~p~Ld~~~RP~~~~~~  239 (317)
T 2wpn_A          201 VGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGR  239 (317)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTBCTTSCBHHHHSS
T ss_pred             HHHHHHHHhcccccccccccccCCCCccccCCchhhcCC
Confidence            99999998765                678899999974

>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.19.1.1

Probab=100.00  E-value=4.7e-39  Score=286.56  Aligned_cols=139  Identities=15%  Similarity=0.322  Sum_probs=128.2

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCcch---hhhcceecCCC-------------------CCeeEEEEecccCCCCh-
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGYDL---DRFGIIFRPSP-------------------RQSDVMIVAGTLTNKMA-  131 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~Dl---~rfgi~~~~sP-------------------r~aDIliVeG~Vt~km~-  131 (213)
                      +.+++|++.++|+||++||+++..|.+|.   +++++.|++++                   +|+||++|||+|+++|+ 
T Consensus         7 ~~~v~wl~~~~C~GC~isll~~~~p~~~~ll~~~i~l~~~~sl~~~~g~~a~~~l~~~~~~~~~~DilvVEGsV~~~~~g   86 (283)
T 1cc1_S            7 KAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEG   86 (283)
T ss_dssp             CEEEEEEESBCCSHHHHHHHTCBTTBHHHHHHHTEEEEECTTTCSCCHHHHHHHHHHHHHHTTTSSEEEEESBEECGGGG
T ss_pred             CccEEEEecCccCcHHHHHHhccCCCHHHHHhhceeEEeccchhhhcchHHHHHHHHHHhcCCCceEEEEeCCcccCCCc
Confidence            56889999999999999999999999986   89999999986                   89999999999999999 


Q ss_pred             ------------------HHHHHHHHHCCCCceEEEecCccCcCCCCCC--CCccccCCCccc-----cc-eEEccCCCC
Q 041751          132 ------------------PALRKVYDQMPEPRWVISMGSRANGGGYYHY--SYSVVRGCDRIV-----PV-DIYVPGCPP  185 (213)
Q Consensus       132 ------------------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~--sy~~~~gv~~vV-----pV-Di~IPGCPP  185 (213)
                                        +.++++|++|++||+|||+|+||++||||+.  +|+.+.++++++     ++ |||||||||
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~le~l~~~~~~ak~VIAvGtCA~~GGI~a~~~n~t~~~gv~~vl~~~~~~~p~i~IPGCPP  166 (283)
T 1cc1_S           87 RYCIVGETLDAKAHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPP  166 (283)
T ss_dssp             TTBEEEC---CCSSSCCEEHHHHHHHHGGGSSEEEEESHHHHHCTGGGSTTCCSCEECHHHHHHHHTCCCCEEEECCSSC
T ss_pred             eeeeecCccccccccccccHHHHHHHHhccCCEEEEEeeccccCCcCCCCCCCcccccHHHHhhcccCCCceEEeeCCCC
Confidence                              8999999999999999999999999999975  777889999997     77 899999999


Q ss_pred             CHHHHHHHHHHHHH-----------HHhhcCCccccccC
Q 041751          186 TAEALLYGILQLQK-----------KINRRRDFLHWWTK  213 (213)
Q Consensus       186 ~Pe~il~~L~~Ll~-----------ki~~~~~~~~~y~~  213 (213)
                      +||+|+++|++|+.           .+++.+||++||++
T Consensus       167 ~Pe~i~~~L~~l~~~~~~ll~~~~p~Ld~~~RP~~~~~~  205 (283)
T 1cc1_S          167 HPDWMVGTLVAAWSHVLNPTEHPLPELDDDGRPLLFFGD  205 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHSTTTSCCCCBCTTSCBHHHHSS
T ss_pred             CHHHHHHHHHHHhhhhhHHHhCCCCCccccCCchhhcCC
Confidence            99999999999543           46788899999974

>3ayx_B Membrane-bound hydrogenase small subunit; oxidoreductase, membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio marinus} PDB: 3ayy_B 3ayz_B

Probab=100.00  E-value=1.7e-38  Score=283.08  Aligned_cols=139  Identities=19%  Similarity=0.332  Sum_probs=127.7

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCc-ch--hhhcceecCC-------------------CCCeeEEEEecccCCCCh-
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGY-DL--DRFGIIFRPS-------------------PRQSDVMIVAGTLTNKMA-  131 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~-Dl--~rfgi~~~~s-------------------Pr~aDIliVeG~Vt~km~-  131 (213)
                      |.+.+|++..+|+||++||+++..|.+ |+  +.+++.|+++                   ++++||++|||+|+++|+ 
T Consensus        12 ~~~v~wl~~~~C~GC~islL~~~~P~~~d~l~~~i~l~~~~tl~~a~g~~a~~~l~~~~~~~~~~dilvVeG~V~~~~~g   91 (283)
T 3ayx_B           12 RTPVIWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAASGHAAEAILDEIKEKYKGNYILAVEGNPPLNQDG   91 (283)
T ss_dssp             CEEEEEEECBCCSHHHHHHHTCSSSCHHHHHHHTEEEEEETTTCSCCHHHHHHHHHHHHHHTTTTEEEEEESBCBCSGGG
T ss_pred             CceEEEEeCCccCcHHHHHHhcCCCcHHHHHhhceeEEEecchhhhcchhHHHHHHHHhccCCCCeEEEEeCCCccCCCc
Confidence            778999999999999999999999988 74  4578889875                   378999999999999998 


Q ss_pred             --------HHHHHHHHHCCCCceEEEecCccCcCCCCCC--CCccccCCCcccc--ce---EEccCCCCCHHHHHHHHHH
Q 041751          132 --------PALRKVYDQMPEPRWVISMGSRANGGGYYHY--SYSVVRGCDRIVP--VD---IYVPGCPPTAEALLYGILQ  196 (213)
Q Consensus       132 --------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~--sy~~~~gv~~vVp--VD---i~IPGCPP~Pe~il~~L~~  196 (213)
                              +.++++||+|++||+|||+|+||++||||+.  +|+.+.|++++|+  ||   ||||||||+||+|+++|++
T Consensus        92 ~~~~~~g~~~l~~~~~~~~~ak~VIA~GsCA~~GGi~a~~pn~~~~~gv~~~i~~~vd~pvi~IPGCPP~Pe~i~~~l~~  171 (283)
T 3ayx_B           92 MSCIIGGRPFSEQLKRMADDAKAIISWGSCASWGCVQAAKPNPTQATPVHKFLGGGYDKPIIKVPGCPPIAEVMTGVITY  171 (283)
T ss_dssp             TTBEETTEEHHHHHHHHHHTEEEEEEEHHHHHTCTGGGSTTCTTCBCCHHHHHCTTCCSCEEEECSSSCCHHHHHHHHHH
T ss_pred             ceeeeCCcHHHHHHHHHcccCCEEEEeeeccccCCCCCCCCCCccCcChhHhccccCCCceEEeeCCCCCHHHHHHHHHH
Confidence                    8999999999999999999999999999986  7889999999999  99   9999999999999999999


Q ss_pred             -HHH----HHhhcCCccccccC
Q 041751          197 -LQK----KINRRRDFLHWWTK  213 (213)
Q Consensus       197 -Ll~----ki~~~~~~~~~y~~  213 (213)
                       |+.    .+++.+||++||++
T Consensus       172 ~Ll~G~~p~Ld~~~RP~~~y~~  193 (283)
T 3ayx_B          172 MLTFDRIPELDRQGRPKMFYSQ  193 (283)
T ss_dssp             HHHHSSCCCBCTTSCBHHHHSS
T ss_pred             HHHcCCCCCcccccCchhhhCC
Confidence             444    48999999999975

>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S

Probab=100.00  E-value=3.2e-37  Score=272.41  Aligned_cols=137  Identities=18%  Similarity=0.339  Sum_probs=125.7

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCcc-h--hhhcceecCC-------------------CCCeeEEEEecccCCCCh-
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGYD-L--DRFGIIFRPS-------------------PRQSDVMIVAGTLTNKMA-  131 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~D-l--~rfgi~~~~s-------------------Pr~aDIliVeG~Vt~km~-  131 (213)
                      |.+.+|++..+|+||++||+++.+|.+| +  +++++.|+++                   +++ ||++|||+|+++|+ 
T Consensus         6 ~~~v~wl~~~~C~GC~isll~~~~P~~d~ll~~~i~l~~~~tlm~a~g~~a~~~~~~~~~~~~~-dil~VeG~V~~~~~g   84 (264)
T 1yqw_A            6 RPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDG-YYLVVEGGLPTIDGG   84 (264)
T ss_dssp             CCEEEEEECBCCSHHHHHHTTCBTTBHHHHHHHTCEEEEETTTCSCCHHHHHHHHHHHHTCTTC-EEEEEESBEECGGGG
T ss_pred             CceEEEEeCCccCcHHHHHHHcCCCCHHHHHhcceEEEEecchhhhchhhHHHHHHHHhccCCC-eEEEEeCCcccCCCc
Confidence            6688999999999999999999999998 4  6788888865                   367 99999999999998 


Q ss_pred             --------HHHHHHHHHCCCCceEEEecCccCcCCCCCC--CCccccCCCc--cccceEEccCCCCCHHHHHHHHHHHHH
Q 041751          132 --------PALRKVYDQMPEPRWVISMGSRANGGGYYHY--SYSVVRGCDR--IVPVDIYVPGCPPTAEALLYGILQLQK  199 (213)
Q Consensus       132 --------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~--sy~~~~gv~~--vVpVDi~IPGCPP~Pe~il~~L~~Ll~  199 (213)
                              +.++++||+|++||+|||+|+||++||||+.  +|+.+.|+++  ++|| ||||||||+||+|+++|++|++
T Consensus        85 ~~~~~~g~~~~~~~~~~~~~~k~VIA~GsCA~~GGi~a~~~n~~~~~gv~~v~~~PV-i~IPGCPP~Pe~i~~~l~~ll~  163 (264)
T 1yqw_A           85 QWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKT-INIPGCPPNPINFVGAVVHVLT  163 (264)
T ss_dssp             TTBEETTEEHHHHHHHHHHTCSCEEEESHHHHHCCGGGSTTCTTCEECHHHHHTSCC-EEECSSSCCHHHHHHHHHHHHH
T ss_pred             cceeeCChHHHHHHHHHhcCCCEEEEeccccccCCccCCCCCCcccccccccCCCCE-EEeeCCCCCHHHHHHHHHHHHh
Confidence                    8999999999999999999999999999987  5667889998  6899 9999999999999999999998


Q ss_pred             ----HHhhcCCccccccC
Q 041751          200 ----KINRRRDFLHWWTK  213 (213)
Q Consensus       200 ----ki~~~~~~~~~y~~  213 (213)
                          .+++.+||++||.+
T Consensus       164 ~~~p~Ld~~~RP~~~~~~  181 (264)
T 1yqw_A          164 KGIPDLDENGRPKLFYGE  181 (264)
T ss_dssp             TCCCCBCTTSCBHHHHSS
T ss_pred             CCCccccccCCchhhcCC
Confidence                78999999999974

>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} SCOP: e.19.1.0

Probab=100.00  E-value=1.6e-36  Score=268.79  Aligned_cols=139  Identities=18%  Similarity=0.282  Sum_probs=124.7

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCcc--h-hhhcceecCCC-------------------CCeeEEEEecccC--CCC
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGYD--L-DRFGIIFRPSP-------------------RQSDVMIVAGTLT--NKM  130 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~D--l-~rfgi~~~~sP-------------------r~aDIliVeG~Vt--~km  130 (213)
                      |.+.+|++..+|+||+++|+++..|.+|  + +.+.+.|+++-                   +++||++|||+|+  +++
T Consensus         3 r~~viWl~~~~C~GCt~SlL~~~~p~l~~ll~~~I~l~yhptl~~~~G~~a~~~l~~~~~~~~~~dilvVEGsV~~p~~~   82 (269)
T 3myr_A            3 RPSVIWLSFQECTGCTESLTRAHAPTLEDLILDFISLDYHHTLQAASGEAAEAARLQAMDENRGQYLVIVDGSIPGPDAN   82 (269)
T ss_dssp             SCEEEEEECBCCSHHHHHHHHCCSSCHHHHHHHTCEEEECTTTCSSCHHHHHHHHHHHHHHTTTTCEEEEESBEECTTSC
T ss_pred             CCeEEEEeCCccCchHHHHHCCCCCCHHHHHhCCeeEEechhhhhhhhHHHHHHHHHHHhcCCCCeEEEEeccCCCCcCC
Confidence            5688999999999999999999999998  3 55678888742                   5689999999999  777


Q ss_pred             --------hHHHHHHHHHCCCCceEEEecCccCcCCCCCCC--CccccCCCccc--cceEEccCCCCCHHHHHHHHHHHH
Q 041751          131 --------APALRKVYDQMPEPRWVISMGSRANGGGYYHYS--YSVVRGCDRIV--PVDIYVPGCPPTAEALLYGILQLQ  198 (213)
Q Consensus       131 --------~~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~s--y~~~~gv~~vV--pVDi~IPGCPP~Pe~il~~L~~Ll  198 (213)
                              .+.++.++|+|++||+|||+|+||++||||+.+  |+.+.|++++|  +||||||||||+||+|+++|++|+
T Consensus        83 ~g~~~~gg~~~~e~l~e~~~~~k~VIA~G~CA~~GGi~a~~~n~~~~~gv~~~i~~~vdi~IPGCPp~Pe~i~~~l~~ll  162 (269)
T 3myr_A           83 PGFSTVAGHSNYSILMETVEHAAAVIAVGTCAAFGGLPQARPNPTGAMSVMDLVRDKPVINVPGCPPIPMVITGVIAHYL  162 (269)
T ss_dssp             GGGBEETTEEHHHHHHHHHTTCSEEEEEHHHHHHCHHHHSTTCTTCEECHHHHCCSSCEEEECSSSCCHHHHHHHHHHHH
T ss_pred             CccceeCChHHHHHHHHHcccCCEEEEeccccccCCccCCCCCccccCCHHHhCCCCCEEEecCCCCCHHHHHHHHHHHH
Confidence                    488999999999999999999999999999765  45678999999  999999999999999999999988


Q ss_pred             H-----HHhhcCCccccccC
Q 041751          199 K-----KINRRRDFLHWWTK  213 (213)
Q Consensus       199 ~-----ki~~~~~~~~~y~~  213 (213)
                      .     .+++.+||++||.+
T Consensus       163 ~~G~~p~Ld~~~RP~~~y~~  182 (269)
T 3myr_A          163 VFGRLPELDGYGRPLAFYGQ  182 (269)
T ss_dssp             HHSSCCCBCTTSCBHHHHSS
T ss_pred             HcCCCCCCCcccCchHHhCC
Confidence            3     57899999999974

>3uqy_S Hydrogenase-1 small chain; membrane-bound hydrogenase, oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB: 3usc_S* 3use_S*

Probab=100.00  E-value=1.9e-36  Score=275.15  Aligned_cols=140  Identities=16%  Similarity=0.282  Sum_probs=125.5

Q ss_pred             hhcCCcceecccCCccHHHHHhcCCCCcc--h-hhhcceecCC-------------------CCCeeEEEEecccCCCCh
Q 041751           74 VRRGSLWPMTFGLACCAVEMMHTGAAGYD--L-DRFGIIFRPS-------------------PRQSDVMIVAGTLTNKMA  131 (213)
Q Consensus        74 ~R~~siW~~~~gc~GC~iE~l~~~~~~~D--l-~rfgi~~~~s-------------------Pr~aDIliVeG~Vt~km~  131 (213)
                      .|.+.+|++..+|+||+++|+++..|.+|  + +.+.+.|+++                   .+++||++|||+|+++|.
T Consensus         5 ~r~~ViWl~~~~CtGCs~SlL~~~~P~l~~lll~~I~L~yhptlm~~~G~~ae~~l~~~~~~~~~~dILlVeGsV~~~~~   84 (335)
T 3uqy_S            5 PRIPVVWIHGLECTCCTESFIRSAHPLAKDVILSLISLDYDDTLMAAAGTQAEEVFEDIITQYNGKYILAVEGNPPLGEQ   84 (335)
T ss_dssp             CCEEEEEEECBCCSHHHHHHHTCBTTBHHHHHHHTEEEEEETTTCSCCHHHHHHHHHHHHHHTTTTEEEEEESBCBCGGG
T ss_pred             CCCcEEEEeCCccCchHHHHHCCCCCCHHHHHhcCceEeechhhhhhhhHHHHHHHHHHHhcCCCCeEEEEeccCCCCCC
Confidence            46789999999999999999999999998  3 5567788873                   257899999999999998


Q ss_pred             ---------HHHHHHHHHCCCCceEEEecCccCcCCCCCCCC--ccccCCCcccc--ceEEccCCCCCHHHHHHHHHHHH
Q 041751          132 ---------PALRKVYDQMPEPRWVISMGSRANGGGYYHYSY--SVVRGCDRIVP--VDIYVPGCPPTAEALLYGILQLQ  198 (213)
Q Consensus       132 ---------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy--~~~~gv~~vVp--VDi~IPGCPP~Pe~il~~L~~Ll  198 (213)
                               +.++++||+|++||+|||+|+||++||||+.+|  +.+.||+++|+  ||||||||||+||+|+++|++|+
T Consensus        85 G~y~~~gg~~~l~~l~e~~~~ak~VIAvGsCA~~GGi~a~~~npt~~~gv~~vi~~~~di~IPGCPP~Pe~i~~~l~~ll  164 (335)
T 3uqy_S           85 GMFCISSGRPFIEKLKRAAAGASAIIAWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIPDVMSAIITYMV  164 (335)
T ss_dssp             GTTBEETTEEHHHHHHHHHHHEEEEEEEHHHHHTCHHHHSTTCTTCBCCGGGTCCSSCEEEECSSSCCHHHHHHHHHHHH
T ss_pred             cceeccCCcHHHHHHHHHccCCCEEEEeccccccCCccCCCCCcccCcCHHHhCCCCCEEEEeCCCCCHHHHHHHHHHHH
Confidence                     889999999999999999999999999998754  56889999998  79999999999999999999976


Q ss_pred             H-----HHhhcCCccccccC
Q 041751          199 K-----KINRRRDFLHWWTK  213 (213)
Q Consensus       199 ~-----ki~~~~~~~~~y~~  213 (213)
                      .     .+++.+||++||.+
T Consensus       165 ~~G~~p~LD~~~RP~~~y~~  184 (335)
T 3uqy_S          165 TFDRLPDVDRMGRPLMFYGQ  184 (335)
T ss_dssp             HHTSCCCBCTTSCBHHHHSS
T ss_pred             hCCCCCCCCccCCchhhhCC
Confidence            3     46899999999974

>3rgw_S Membrane-bound hydrogenase (NIFE) small subunit H; [NIFE] hydrogenase, high-resolution knallgasbacteria, proteobacteria; 1.50A {Ralstonia eutropha}

Probab=100.00  E-value=5.5e-36  Score=272.40  Aligned_cols=140  Identities=18%  Similarity=0.312  Sum_probs=125.3

Q ss_pred             hhcCCcceecccCCccHHHHHhcCCCCcc--h-hhhcceecCC-------------------CCCeeEEEEecccCCCC-
Q 041751           74 VRRGSLWPMTFGLACCAVEMMHTGAAGYD--L-DRFGIIFRPS-------------------PRQSDVMIVAGTLTNKM-  130 (213)
Q Consensus        74 ~R~~siW~~~~gc~GC~iE~l~~~~~~~D--l-~rfgi~~~~s-------------------Pr~aDIliVeG~Vt~km-  130 (213)
                      .|.+.+|++..+|+||+++|+++..|.+|  + +.+.+.|+++                   ++++||++|||+|+++| 
T Consensus         5 ~r~~ViWl~~~~CtGCt~SlL~~~~P~l~~ll~~~I~L~yhptlm~~~G~~a~~~l~~~~~~~~~~dILlVEGsV~~~~~   84 (339)
T 3rgw_S            5 PRTPVLWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAAAGHQAEAILEEIMTKYKGNYILAVEGNPPLNQD   84 (339)
T ss_dssp             CCEEEEEEECBCCSHHHHHHTTCBTTBHHHHHHHTEEEEEETTTCSCCHHHHHHHHHHHHHHTTTCSEEEEESBCBCSGG
T ss_pred             CCCcEEEEECCcCCchHHHHHcCCCCCHHHHHhCCeeEEecchhhhhhhHHHHHHHHHHHhccCCCcEEEEeeeccCCCC
Confidence            46789999999999999999999999887  2 5567788873                   36789999999999999 


Q ss_pred             --------hHHHHHHHHHCCCCceEEEecCccCcCCCCCCCC--ccccCCCcccc--ceEEccCCCCCHHHHHHHHHHHH
Q 041751          131 --------APALRKVYDQMPEPRWVISMGSRANGGGYYHYSY--SVVRGCDRIVP--VDIYVPGCPPTAEALLYGILQLQ  198 (213)
Q Consensus       131 --------~~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy--~~~~gv~~vVp--VDi~IPGCPP~Pe~il~~L~~Ll  198 (213)
                              .+.++++||+|++||+|||+|+||++||||+.+|  +...|++++|+  ||||||||||+||+|+++|++|+
T Consensus        85 g~y~~~gg~~~~e~l~e~~~~~k~VIAvGtCA~~GGi~a~~~n~~~~~gv~~~i~~~vdi~IPGCPP~Pe~i~~~l~~ll  164 (339)
T 3rgw_S           85 GMSCIIGGRPFIEQLKYVAKDAKAIISWGSCASWGCVQAAKPNPTQATPVHKVITDKPIIKVPGCPPIAEVMTGVITYML  164 (339)
T ss_dssp             GTTBEETTEEHHHHHHHHHTTCSEEEEEHHHHHTCTGGGSTTCTTCBCCGGGTCCSSCEEEECSSSCCHHHHHHHHHHHH
T ss_pred             cceeccCChHHHHHHHHHccCCCEEEEeccccccCCcCCCCCCccccCCHHHhCCCCCEEEeCCCCCCHHHHHHHHHHHH
Confidence                    4789999999999999999999999999998654  56789999998  99999999999999999999988


Q ss_pred             H-----HHhhcCCccccccC
Q 041751          199 K-----KINRRRDFLHWWTK  213 (213)
Q Consensus       199 ~-----ki~~~~~~~~~y~~  213 (213)
                      .     .|++.+||++||.+
T Consensus       165 ~~G~~p~LD~~~RP~~fy~~  184 (339)
T 3rgw_S          165 TFDRIPELDRQGRPKMFYSQ  184 (339)
T ss_dssp             HHSSCCCBCTTSCBHHHHSS
T ss_pred             hcCCCCCCCcccCchhhhCC
Confidence            3     57899999999974

---

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	213
d2fug61	161	e.19.1.2 (6:15-175) NAD-quinone oxidoreductase cha	1e-70
d1wuis1	267	e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small	1e-15
d1yq9a1	261	e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small	7e-14
d1cc1s_	278	e.19.1.1 (S:) Nickel-iron hydrogenase, small subun	2e-12
d1frfs_	261	e.19.1.1 (S:) Nickel-iron hydrogenase, small subun	5e-12

>d2fug61 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus thermophilus [TaxId: 274]} Length = 161

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nq06-like
domain: NAD-quinone oxidoreductase chain 6, Nqo6
species: Thermus thermophilus [TaxId: 274]

 Score =  210 bits (536), Expect = 1e-70
 Identities = 80/149 (53%), Positives = 112/149 (75%), Gaps = 2/149 (1%)

Query: 58  KASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQ 116
           +    + + ++ L+ W R  SLWP TFGLACCA+EMM +  A  DL RFG  +FR SPRQ
Sbjct: 1   EREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQ 60

Query: 117 SDVMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPV 176
           +DVMIVAG L+ KMAP +R+V++QMP+P+WVISMG+ A+ GG ++ +Y++V+  D +VPV
Sbjct: 61  ADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-NYAIVQNVDSVVPV 119

Query: 177 DIYVPGCPPTAEALLYGILQLQKKINRRR 205
           D+YVPGCPP  EAL+Y ++QLQKK+  + 
Sbjct: 120 DVYVPGCPPRPEALIYAVMQLQKKVRGQA 148

>d1wuis1 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 267

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nickel-iron hydrogenase, small subunit
domain: Nickel-iron hydrogenase, small subunit
species: Desulfovibrio vulgaris [TaxId: 881]

 Score = 71.1 bits (174), Expect = 1e-15
 Identities = 23/157 (14%), Positives = 47/157 (29%), Gaps = 36/157 (22%)

Query: 79  LWPMTFGLACCAVEMMHTGAAGYD---LDRFGIIFRPS------------------PRQS 117
           ++        C+  ++       D   LD   + +  +                      
Sbjct: 10  VYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHG 69

Query: 118 DVMIVAGTLTNKMA---------PALRKVYDQMPEPRWVISMGSRANGGGYYH--YSYSV 166
            + +V G +                L      +P+ + VI+ G+ A  GG      + + 
Sbjct: 70  FIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTG 129

Query: 167 VRGCDRIVP----VDIYVPGCPPTAEALLYGILQLQK 199
            +G +  +       I + GCPP    L+  I+   K
Sbjct: 130 AKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLK 166

>d1yq9a1 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]} Length = 261

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nickel-iron hydrogenase, small subunit
domain: Nickel-iron hydrogenase, small subunit
species: Desulfovibrio gigas [TaxId: 879]

 Score = 66.1 bits (161), Expect = 7e-14
 Identities = 16/104 (15%), Positives = 34/104 (32%), Gaps = 15/104 (14%)

Query: 109 IFRPSPRQSDVMIVAGTLTNKMA---------PALRKVYDQMPEPRWVISMGSRANGGGY 159
               + +   V ++ G +                     +  P+ + VI++G+ A  GG 
Sbjct: 56  ALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGV 115

Query: 160 Y--HYSYSVVRGCDRI----VPVDIYVPGCPPTAEALLYGILQL 197
                + +   G +          I + GCPP     +  ++ L
Sbjct: 116 QAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHL 159

>d1cc1s_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfomicrobium baculatum [TaxId: 899]} Length = 278

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nickel-iron hydrogenase, small subunit
domain: Nickel-iron hydrogenase, small subunit
species: Desulfomicrobium baculatum [TaxId: 899]

 Score = 62.4 bits (151), Expect = 2e-12
 Identities = 16/127 (12%), Positives = 39/127 (30%), Gaps = 27/127 (21%)

Query: 98  AAGYDLDRFGIIFRPSPRQSDVMIVAGTLTNKM-------------------APALRKVY 138
           + G                +  ++V G +                          +  + 
Sbjct: 47  SEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKAHHHEVTMMELIR 106

Query: 139 DQMPEPRWVISMGSRANGGGYYHYSYSV--------VRGCDRIVPVDIYVPGCPPTAEAL 190
           D  P+    +++G+ +  GG      +V            ++I  + + VPGCPP  + +
Sbjct: 107 DLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWM 166

Query: 191 LYGILQL 197
           +  ++  
Sbjct: 167 VGTLVAA 173

>d1frfs_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfovibrio fructosovorans [TaxId: 878]} Length = 261

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nickel-iron hydrogenase, small subunit
domain: Nickel-iron hydrogenase, small subunit
species: Desulfovibrio fructosovorans [TaxId: 878]

 Score = 61.1 bits (148), Expect = 5e-12
 Identities = 17/97 (17%), Positives = 35/97 (36%), Gaps = 12/97 (12%)

Query: 113 SPRQSDVMIVAGTLTNKM---------APALRKVYDQMPEPRWVISMGSRANGGGYYH-- 161
             +    ++V G L              P +        + + +I +G+ +  GG     
Sbjct: 62  EGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETCKKAAAKAKGIICIGTCSPYGGVQKAK 121

Query: 162 YSYSVVRGCDRIVPVD-IYVPGCPPTAEALLYGILQL 197
            + S  +G    + V  I +PGCPP     +  ++ +
Sbjct: 122 PNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHV 158

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	213
d2fug61	161	NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus	100.0
d1wuis1	267	Nickel-iron hydrogenase, small subunit {Desulfovib	100.0
d1frfs_	261	Nickel-iron hydrogenase, small subunit {Desulfovib	99.98
d1yq9a1	261	Nickel-iron hydrogenase, small subunit {Desulfovib	99.97
d1cc1s_	278	Nickel-iron hydrogenase, small subunit {Desulfomic	99.97

>d2fug61 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus thermophilus [TaxId: 274]}

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nq06-like
domain: NAD-quinone oxidoreductase chain 6, Nqo6
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=1e-57  Score=376.08  Aligned_cols=147  Identities=54%  Similarity=1.076  Sum_probs=126.8

Q ss_pred             CcceeehhhHHHHhhhhcCCcceecccCCccHHHHHhcCCCCcchhhhcc-eecCCCCCeeEEEEecccCCCChHHHHHH
Q 041751           59 ASEYVISKVDNLLNWVRRGSLWPMTFGLACCAVEMMHTGAAGYDLDRFGI-IFRPSPRQSDVMIVAGTLTNKMAPALRKV  137 (213)
Q Consensus        59 ~~~~~~~~~d~~~~w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl~rfgi-~~~~sPr~aDIliVeG~Vt~km~~~l~~l  137 (213)
                      +.+++.|++|+++||+|++|+|++++||+||++||+++..|+||++|||+ .|++||||+|+|+|+|+||++|+++++++
T Consensus         2 ~~~~i~t~~~~~~nw~r~~Slw~~~~g~~cC~iE~~a~~~p~yD~eRfG~~~~~~sPR~ADvllVtG~vT~km~~~l~~~   81 (161)
T d2fug61           2 REGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRV   81 (161)
T ss_dssp             TTSHHHHHHHHHHHHHHHHCCCCCCEECSHHHHHTGGGCCC-----------------CCCCEEEESCCBTTTHHHHHHH
T ss_pred             CCceEEeeHHHHHHHHHhCCCceeeccccccHHHHhhccCCccchhhhcccccCCCcccCcEEEEeccchHHHHHHHHHH
Confidence            56899999999999999999999999999999999999999999999999 58899999999999999999999999999


Q ss_pred             HHHCCCCceEEEecCccCcCCCCCCCCccccCCCccccceEEccCCCCCHHHHHHHHHHHHHHHhhcCC
Q 041751          138 YDQMPEPRWVISMGSRANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQKKINRRRD  206 (213)
Q Consensus       138 ~e~~~~pk~VIA~GsCA~~GGi~~~sy~~~~gv~~vVpVDi~IPGCPP~Pe~il~~L~~Ll~ki~~~~~  206 (213)
                      |||||+||+|||+|+||++||+| ++|++++|+|++||||+|||||||+||+|+++|++|++||+++..
T Consensus        82 y~qmPePK~VIA~GaCa~sGG~f-~~y~v~~gvd~~iPVDvyIPGCPPrPeail~gl~~l~~ki~~~~~  149 (161)
T d2fug61          82 WEQMPDPKWVISMGACASSGGMF-NNYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAY  149 (161)
T ss_dssp             HHTSCSSCCEEEEHHHHHSCTTC-CSTTBCSCGGGTSCCSEEECCSSCCHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHhCCCCceEEEecccccCCCcc-CCccccCCcCccCcCceeCCCCCcCHHHHHHHHHHHHHHHhhhcc
Confidence            99999999999999999999999 589999999999999999999999999999999999999987653

>d1wuis1 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subunit {Desulfovibrio vulgaris [TaxId: 881]}

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nickel-iron hydrogenase, small subunit
domain: Nickel-iron hydrogenase, small subunit
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=100.00  E-value=1.2e-34  Score=253.94  Aligned_cols=141  Identities=16%  Similarity=0.255  Sum_probs=120.9

Q ss_pred             hhhcCCcceecccCCccHHHHHhcCCCCcch---hhhcceecCC------------------CCCeeEEEEecccCCCCh
Q 041751           73 WVRRGSLWPMTFGLACCAVEMMHTGAAGYDL---DRFGIIFRPS------------------PRQSDVMIVAGTLTNKMA  131 (213)
Q Consensus        73 w~R~~siW~~~~gc~GC~iE~l~~~~~~~Dl---~rfgi~~~~s------------------Pr~aDIliVeG~Vt~km~  131 (213)
                      -.|.+++|++..+|+||++||+++.++.+|.   +.++++|+|+                  +++.||+||||+|++++.
T Consensus         4 ~~rp~v~Wl~~~~C~GC~iSlL~~~~p~~d~~~~~~i~l~y~p~lm~~~g~~~~~~~~~~~~~~~~dilvVEGsI~~~~~   83 (267)
T d1wuis1           4 PRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAAN   83 (267)
T ss_dssp             SSSCEEEEEECBCCSHHHHHHHTCTTTTHHHHHHTTCEEEECTTTCSCCHHHHHHHHHHHHTCTTCEEEEEESBEECGGG
T ss_pred             CCCCcEEEEeCCcCCChHHHHHccCCCCHHHHHhCCeeEEeccccchhhhHHHHHHHHHHhcccCCeEEEEecccCcccc
Confidence            3577899999999999999999999999983   5566788873                  467899999999999886


Q ss_pred             ---------HHHHHHHHHCCCCceEEEecCccCcCCCCCC--CCccccCCC----ccccceEEccCCCCCHHHHHHHHHH
Q 041751          132 ---------PALRKVYDQMPEPRWVISMGSRANGGGYYHY--SYSVVRGCD----RIVPVDIYVPGCPPTAEALLYGILQ  196 (213)
Q Consensus       132 ---------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~--sy~~~~gv~----~vVpVDi~IPGCPP~Pe~il~~L~~  196 (213)
                               +.++.++++++++|+|||+|+||++|||++.  +++...+++    ++++||||||||||+||+|+++|.+
T Consensus        84 ~~~~~~~~~~~~e~v~~~r~~ak~vVAvGtCA~~GGI~a~~~~~t~~~~~~~~l~~~~~vdi~IpGCPp~p~~i~~~l~~  163 (267)
T d1wuis1          84 GIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVY  163 (267)
T ss_dssp             GTTBEETTEEHHHHHHHHGGGSSEEEEESHHHHHCCGGGSTTCTTCEECHHHHHGGGTCCCEEECSSSCCHHHHHHHHHH
T ss_pred             cceeeeCCchHHHHHHHHhhcCCEEEEeechhccCCccccCCCCcccccccccccccCCCeEEeCCCCCCHHHHHHHHHH
Confidence                     5689999999999999999999999999975  444555554    5567999999999999999999999


Q ss_pred             HHH-----HHhhcCCccccccC
Q 041751          197 LQK-----KINRRRDFLHWWTK  213 (213)
Q Consensus       197 Ll~-----ki~~~~~~~~~y~~  213 (213)
                      ++.     ++++.+||+.||.+
T Consensus       164 ~l~~~~~p~ld~~~RP~~~~~~  185 (267)
T d1wuis1         164 YLKNKAAPELDSLNRPTMFFGQ  185 (267)
T ss_dssp             HHHHSSCCCBCTTSCBHHHHSS
T ss_pred             HHhcCCCCcccccCCCccccCC
Confidence            886     56788899999874

>d1frfs_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfovibrio fructosovorans [TaxId: 878]}

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nickel-iron hydrogenase, small subunit
domain: Nickel-iron hydrogenase, small subunit
species: Desulfovibrio fructosovorans [TaxId: 878]

Probab=99.98  E-value=3.6e-34  Score=250.25  Aligned_cols=139  Identities=17%  Similarity=0.355  Sum_probs=124.0

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCcc---hhhhcceecCC------------------CCCeeEEEEecccCCCCh--
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGYD---LDRFGIIFRPS------------------PRQSDVMIVAGTLTNKMA--  131 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~D---l~rfgi~~~~s------------------Pr~aDIliVeG~Vt~km~--  131 (213)
                      |.+.+|++..+|+||++||+++.+|.+|   ++.++++|+|+                  +++.||+||||+|++++.  
T Consensus         3 kp~ViWl~~~~C~GCs~S~l~~~~p~l~~~l~~~i~l~y~p~lm~~~g~~~~~~l~~~~~~~~~~vl~VEGsV~~~~~g~   82 (261)
T d1frfs_           3 RPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGETSEAALHEALEGKDGYYLVVEGGLPTIDGGQ   82 (261)
T ss_dssp             SCEEEEEECBCCSHHHHHHTTCTTTTHHHHHHHTCEEEECTTTCSCCHHHHHHHHHHHHHCSSCCEEEEESBEECHHHHT
T ss_pred             CCeEEEEeCCcCCchHHHHHccCCCcHHHHHhCCeeEEeccccchhcchHHHHHHHHHhcccCCcEEEEecCCccCCCce
Confidence            6789999999999999999999999998   37788899873                  356799999999999864  


Q ss_pred             -------HHHHHHHHHCCCCceEEEecCccCcCCCCCC--CCccccCCCccccce-EEccCCCCCHHHHHHHHHHHHH--
Q 041751          132 -------PALRKVYDQMPEPRWVISMGSRANGGGYYHY--SYSVVRGCDRIVPVD-IYVPGCPPTAEALLYGILQLQK--  199 (213)
Q Consensus       132 -------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~--sy~~~~gv~~vVpVD-i~IPGCPP~Pe~il~~L~~Ll~--  199 (213)
                             +.++.++++++++|+|||+|+||++|||++.  +++...|+++++++| ||||||||+||+|+++|.+++.  
T Consensus        83 ~~~~~~~~~~e~~~~~~~~ak~vIAvGtCA~~GGI~a~~~n~t~~~~v~~~i~~~vinIpGCPp~p~~i~~~l~~ll~g~  162 (261)
T d1frfs_          83 WGMVAGHPMIETCKKAAAKAKGIICIGTCSPYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKG  162 (261)
T ss_dssp             TBEETTEEHHHHHHHHHHHCSEEEEETTHHHHCCSTTSTTCTTCEECHHHHHTSCCEEECSSSCCHHHHHHHHHHHHTTC
T ss_pred             eeeecCchHHHHHHHhccCCCEEEEEecccccCCccccCCCCccccChhhhcCCceEEecCCCCCHHHHHHHHHHHHhCC
Confidence                   4589999999999999999999999999965  566788999999999 5999999999999999999986  


Q ss_pred             --HHhhcCCccccccC
Q 041751          200 --KINRRRDFLHWWTK  213 (213)
Q Consensus       200 --ki~~~~~~~~~y~~  213 (213)
                        ++++.+||++||.+
T Consensus       163 ~p~ld~~~RP~~~~~~  178 (261)
T d1frfs_         163 IPDLDENGRPKLFYGE  178 (261)
T ss_dssp             SCCBCTTSCBHHHHSS
T ss_pred             CccccccCCcccccCC
Confidence              57889999999864

>d1yq9a1 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]}

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nickel-iron hydrogenase, small subunit
domain: Nickel-iron hydrogenase, small subunit
species: Desulfovibrio gigas [TaxId: 879]

Probab=99.97  E-value=5.5e-33  Score=242.64  Aligned_cols=139  Identities=15%  Similarity=0.272  Sum_probs=119.7

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCcc--h-hhhcceecCC----------------CCCeeEEEEecccCCCCh----
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGYD--L-DRFGIIFRPS----------------PRQSDVMIVAGTLTNKMA----  131 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~D--l-~rfgi~~~~s----------------Pr~aDIliVeG~Vt~km~----  131 (213)
                      |.+.+|++..+|+||+++|+++.++.+|  + +.++++|+|+                .++.||+||||+|++++.    
T Consensus         3 kp~v~Wl~~~~C~GC~~S~L~~~~p~l~~~l~~~i~l~y~p~l~~~~g~~~~~~~~~~~~~~dvlvVEGsV~~~~~g~~~   82 (261)
T d1yq9a1           3 RPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKGDFVCVIEGGIPMGDGGYWG   82 (261)
T ss_dssp             SCEEEEEECBCCSHHHHHHHTCTTTTHHHHHHHTCEEEECTTTCSSCTHHHHHHHHHHTTSSEEEEEESBEECGGGSTTB
T ss_pred             CCeEEEEeCCcCCChHHHHHccCCCCHHHHHhCceEEEeccccchhhhHHHHHHHHhcccCCeEEEeeccccCCCCccee
Confidence            5678999999999999999999999887  3 6678888873                366799999999998864    


Q ss_pred             -----HHHHHHHHHCCCCceEEEecCccCcCCCCCC--CCccccCCCcc----ccceEEccCCCCCHHHHHHHHHHHHH-
Q 041751          132 -----PALRKVYDQMPEPRWVISMGSRANGGGYYHY--SYSVVRGCDRI----VPVDIYVPGCPPTAEALLYGILQLQK-  199 (213)
Q Consensus       132 -----~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~--sy~~~~gv~~v----VpVDi~IPGCPP~Pe~il~~L~~Ll~-  199 (213)
                           +.++.++++++++|+|||+|+||++|||++.  +++...+++++    +++|||||||||+||+|+++|.+|+. 
T Consensus        83 ~~~~~~~~e~v~~lr~~ak~vVAvGtCA~~GGI~a~~~~~t~~~~~~~~~~~~~~~~i~IpGCPp~p~~i~~~l~~ll~g  162 (261)
T d1yq9a1          83 KVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTK  162 (261)
T ss_dssp             EETTEEHHHHHHHHGGGSSEEEEEHHHHHHCCGGGSTTCTTCEECHHHHHGGGTCCCEEECSSSCCHHHHHHHHHHHHHT
T ss_pred             eccCchHHHHHHHHhhcCCEEEEecchhhcCCccccCCCccCcccccccccccCCCeEEeCCCCCCHHHHHHHHHHHHhC
Confidence                 4689999999999999999999999999965  45556666554    46889999999999999999999986 


Q ss_pred             ---HHhhcCCccccccC
Q 041751          200 ---KINRRRDFLHWWTK  213 (213)
Q Consensus       200 ---ki~~~~~~~~~y~~  213 (213)
                         .+++.+||++||.+
T Consensus       163 ~~p~ld~~~RP~~~~~~  179 (261)
T d1yq9a1         163 GMPELDKQGRPVMFFGE  179 (261)
T ss_dssp             CSCCBCTTSCBHHHHSS
T ss_pred             CCcccccccCcccccCC
Confidence               56788999999974

>d1cc1s_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfomicrobium baculatum [TaxId: 899]}

class: Multi-domain proteins (alpha and beta)
fold: HydA/Nqo6-like
superfamily: HydA/Nqo6-like
family: Nickel-iron hydrogenase, small subunit
domain: Nickel-iron hydrogenase, small subunit
species: Desulfomicrobium baculatum [TaxId: 899]

Probab=99.97  E-value=1.3e-32  Score=241.96  Aligned_cols=139  Identities=17%  Similarity=0.349  Sum_probs=118.4

Q ss_pred             hcCCcceecccCCccHHHHHhcCCCCcc--h-hhhcceecCC-------------------CCCeeEEEEecccCCCCh-
Q 041751           75 RRGSLWPMTFGLACCAVEMMHTGAAGYD--L-DRFGIIFRPS-------------------PRQSDVMIVAGTLTNKMA-  131 (213)
Q Consensus        75 R~~siW~~~~gc~GC~iE~l~~~~~~~D--l-~rfgi~~~~s-------------------Pr~aDIliVeG~Vt~km~-  131 (213)
                      |.+.+|++..+|+||+++|+++.+|.+|  + +.++++|+|+                   +++.||+||||+|++++. 
T Consensus         2 kp~vvWl~~~sC~GC~iS~ln~~~p~l~~~ll~~i~l~yhp~l~~~~g~~~~~~~~~~~~~~~~~dillVEGsI~~~~~~   81 (278)
T d1cc1s_           2 KAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEG   81 (278)
T ss_dssp             CEEEEEEESBCCSHHHHHHHTCBTTBHHHHHHHTEEEEECTTTCSCCHHHHHHHHHHHHHHTTTSSEEEEESBEECGGGG
T ss_pred             CCcEEEecCCCCCchHHHHHcCCCCCHHHHHhccEEEeecchhhhhhhHHHHHHHHHHhhccCCCeEEEeccCcCCCccc
Confidence            5678999999999999999999999887  3 6678888873                   467899999999998875 


Q ss_pred             ------------------HHHHHHHHHCCCCceEEEecCccCcCCCCCCCC--ccccCC------CccccceEEccCCCC
Q 041751          132 ------------------PALRKVYDQMPEPRWVISMGSRANGGGYYHYSY--SVVRGC------DRIVPVDIYVPGCPP  185 (213)
Q Consensus       132 ------------------~~l~~l~e~~~~pk~VIA~GsCA~~GGi~~~sy--~~~~gv------~~vVpVDi~IPGCPP  185 (213)
                                        +.++.++++++++|+|||+|+||++|||++..+  +...++      ++++++|||||||||
T Consensus        82 ~~~~~g~~~~~~~~~~~~~~~e~~~~l~~kak~vVAvGtCA~~GGI~a~~~n~t~~~~~~~~~~~~~~~~~~i~IpGCPp  161 (278)
T d1cc1s_          82 RYCIVGETLDAKAHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPP  161 (278)
T ss_dssp             TTBEEEC---CCSSSCCEEHHHHHHHHGGGSSEEEEESHHHHHCTGGGSTTCCSCEECHHHHHHHHTCCCCEEEECCSSC
T ss_pred             eeeeecccccccccccCccHHHHHHHHHhcCCEEEEEecccccCCcccccCCCccchhhheecCcCCcCCcccccCCCCC
Confidence                              458999999999999999999999999997643  333443      456789999999999


Q ss_pred             CHHHHHHHHHHHHH-----------HHhhcCCccccccC
Q 041751          186 TAEALLYGILQLQK-----------KINRRRDFLHWWTK  213 (213)
Q Consensus       186 ~Pe~il~~L~~Ll~-----------ki~~~~~~~~~y~~  213 (213)
                      +||+|+++|.+++.           .+++.+||++||.+
T Consensus       162 ~pd~i~~tl~~~l~~~~~~~~~~lp~lD~~gRP~~~~~~  200 (278)
T d1cc1s_         162 HPDWMVGTLVAAWSHVLNPTEHPLPELDDDGRPLLFFGD  200 (278)
T ss_dssp             CHHHHHHHHHHHHHHHHSTTTSCCCCBCTTSCBHHHHSS
T ss_pred             CHHHHHHHHHHHHHhhhccccccchhhHhcCCccccCCC
Confidence            99999999999985           36778999999874