Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database
ID Alignment Graph Length
Definition
E-value Query 113
PRK06411 183
PRK06411, PRK06411, NADH dehydrogenase subunit B;
9e-46 COG0377 194
COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 k
4e-42 TIGR01957 145
TIGR01957, nuoB_fam, NADH-quinone oxidoreductase,
6e-41 PRK13292 788
PRK13292, PRK13292, trifunctional NADH dehydrogena
1e-26 PRK14818 173
PRK14818, PRK14818, NADH dehydrogenase subunit B;
6e-26 PRK14819 264
PRK14819, PRK14819, NADH dehydrogenase subunit B;
6e-25 PRK14813 189
PRK14813, PRK14813, NADH dehydrogenase subunit B;
2e-24 PRK14816 182
PRK14816, PRK14816, NADH dehydrogenase subunit B;
4e-24 PRK14815 183
PRK14815, PRK14815, NADH dehydrogenase subunit B;
9e-24 PRK14820 180
PRK14820, PRK14820, NADH dehydrogenase subunit B;
2e-22 COG3260 148
COG3260, COG3260, Ni,Fe-hydrogenase III small subu
3e-22 PRK14817 181
PRK14817, PRK14817, NADH dehydrogenase subunit B;
5e-22 PRK14814 186
PRK14814, PRK14814, NADH dehydrogenase subunit B;
2e-21 CHL00023 225
CHL00023, ndhK, NADH dehydrogenase subunit K
3e-21 pfam01058 122
pfam01058, Oxidored_q6, NADH ubiquinone oxidoreduc
2e-19 COG1941 247
COG1941, FrhG, Coenzyme F420-reducing hydrogenase,
1e-05 TIGR03294 228
TIGR03294, FrhG, coenzyme F420 hydrogenase, subuni
5e-04
>gnl|CDD|235797 PRK06411, PRK06411, NADH dehydrogenase subunit B; Validated
Back Hide alignment and domain information
Score = 145 bits (368), Expect = 9e-46
Identities = 49/73 (67%), Positives = 60/73 (82%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M EP+WVISMGSCAN GG YHYSYSVV+G DRI+PVD+YVPGCPP EAL+YGIL+LQKK
Sbjct: 99 MPEPKWVISMGSCANSGGMYHYSYSVVQGVDRIVPVDVYVPGCPPRPEALLYGILKLQKK 158
Query: 101 VKRMKILQSWYRR 113
+++ + + R
Sbjct: 159 IRQSERERKRGER 171
>gnl|CDD|223454 COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]
Back Show alignment and domain information
Score = 136 bits (345), Expect = 4e-42
Identities = 44/73 (60%), Positives = 54/73 (73%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M EP+WVISMGSCAN GG Y SYSVV+G DR++PVD+Y+PGCPP EAL+YGIL LQ+K
Sbjct: 100 MPEPKWVISMGSCANSGGMYWNSYSVVQGVDRVVPVDVYIPGCPPRPEALLYGILLLQEK 159
Query: 101 VKRMKILQSWYRR 113
++R
Sbjct: 160 IRREGRPLRDKPG 172
>gnl|CDD|233656 TIGR01957, nuoB_fam, NADH-quinone oxidoreductase, B subunit
Back Show alignment and domain information
Score = 132 bits (333), Expect = 6e-41
Identities = 48/83 (57%), Positives = 63/83 (75%), Gaps = 2/83 (2%)
Query: 23 IEPGSTTCKASAVTTTSW--MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYV 80
I G+ T K + + M EP+WVISMG+CAN GG +H SYSVV+G DRI+PVD+Y+
Sbjct: 62 IVAGTVTKKMAPALRRLYDQMPEPKWVISMGACANSGGMFHTSYSVVQGVDRIVPVDVYI 121
Query: 81 PGCPPTAEALMYGILQLQKKVKR 103
PGCPP EAL+YG+++LQKK+KR
Sbjct: 122 PGCPPRPEALIYGLIKLQKKIKR 144
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|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit B/C/D; Provisional
Back Show alignment and domain information
Score = 102 bits (256), Expect = 1e-26
Identities = 38/63 (60%), Positives = 51/63 (80%), Gaps = 1/63 (1%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M EP+WVISMGSCAN GG Y YSVV+G ++I+PVD+Y+PGCPP EA + G++ LQ+K
Sbjct: 87 MAEPKWVISMGSCANSGGMYDV-YSVVQGVNQILPVDVYIPGCPPRPEAFLQGLMLLQEK 145
Query: 101 VKR 103
++R
Sbjct: 146 IRR 148
>gnl|CDD|173279 PRK14818, PRK14818, NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Score = 95.0 bits (236), Expect = 6e-26
Identities = 37/62 (59%), Positives = 49/62 (79%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M EP++VISMGSC+N GG + YSV +G D++IPVD+YVPGCPP EAL G+L+LQ+
Sbjct: 95 MPEPKYVISMGSCSNCGGLFQLGYSVCKGVDKVIPVDVYVPGCPPRPEALTEGLLRLQEI 154
Query: 101 VK 102
V+
Sbjct: 155 VR 156
>gnl|CDD|237822 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Score = 94.3 bits (234), Expect = 6e-25
Identities = 36/73 (49%), Positives = 52/73 (71%), Gaps = 1/73 (1%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M EPR+VISMG+CA GG + Y+V+RG D +IPVD+Y+PGCPP EAL++ ++ LQK+
Sbjct: 96 MPEPRYVISMGACATSGGPFRDGYNVLRGIDLLIPVDVYIPGCPPRPEALLHALMTLQKQ 155
Query: 101 VKRMKILQS-WYR 112
+ + + WY
Sbjct: 156 IDAQSLGRVRWYG 168
>gnl|CDD|173274 PRK14813, PRK14813, NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Score = 91.5 bits (227), Expect = 2e-24
Identities = 42/87 (48%), Positives = 61/87 (70%), Gaps = 3/87 (3%)
Query: 23 IEPGSTTCKAS--AVTTTSWMLEPRWVISMGSCANGGG-YYHYSYSVVRGCDRIIPVDIY 79
I G+ T K + V M EPR+V+SMGSC+N GG Y+ + Y V++G DRIIPVD+Y
Sbjct: 72 IVAGTVTMKMAERVVRLYEQMPEPRYVLSMGSCSNCGGPYWEHGYHVLKGVDRIIPVDVY 131
Query: 80 VPGCPPTAEALMYGILQLQKKVKRMKI 106
VPGCPP EAL+ G++++Q+ ++ +I
Sbjct: 132 VPGCPPRPEALIGGLMKVQELIRMEQI 158
>gnl|CDD|173277 PRK14816, PRK14816, NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Score = 90.4 bits (224), Expect = 4e-24
Identities = 34/62 (54%), Positives = 48/62 (77%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M +P++VI++G CA GG + SY V+ G D+I+PVD+Y+PGCPP EA YG++QLQ+K
Sbjct: 106 MADPKYVIAVGGCAVSGGPFKKSYHVLNGVDKILPVDVYIPGCPPRPEAFYYGMMQLQRK 165
Query: 101 VK 102
VK
Sbjct: 166 VK 167
>gnl|CDD|237821 PRK14815, PRK14815, NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Score = 89.2 bits (221), Expect = 9e-24
Identities = 39/93 (41%), Positives = 63/93 (67%), Gaps = 3/93 (3%)
Query: 23 IEPGSTTCKASAVTTTSW--MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYV 80
I G+ T K + + M EP+WVI+MG+CA+ GG Y SYSV++G DRI+PVD+Y+
Sbjct: 78 IVAGTVTYKMALAVRRIYDQMPEPKWVIAMGACASSGGMYR-SYSVLQGVDRILPVDVYI 136
Query: 81 PGCPPTAEALMYGILQLQKKVKRMKILQSWYRR 113
GCPP EA++ +++LQKK+ + ++ +++
Sbjct: 137 SGCPPRPEAILDALIKLQKKIDTERAARTLFKK 169
>gnl|CDD|184833 PRK14820, PRK14820, NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Score = 86.0 bits (213), Expect = 2e-22
Identities = 34/62 (54%), Positives = 51/62 (82%), Gaps = 1/62 (1%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M EPRWV+++G+CA+ GG + +YSV++G DRIIPVD+YVPGCPP E ++ G++++Q+
Sbjct: 98 MAEPRWVVAVGACASSGGIFD-TYSVLQGIDRIIPVDVYVPGCPPRPEQIIDGVMRVQEL 156
Query: 101 VK 102
VK
Sbjct: 157 VK 158
>gnl|CDD|225799 COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [Energy production and conversion]
Back Show alignment and domain information
Score = 84.3 bits (209), Expect = 3e-22
Identities = 28/65 (43%), Positives = 44/65 (67%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M EP+ VI++G+CA GG + SYSV D++IPVD+ +PGCPP EA++ G++ K
Sbjct: 74 MPEPKIVIAVGACALSGGIFKDSYSVWGPVDKVIPVDVEIPGCPPRPEAILAGLVAALGK 133
Query: 101 VKRMK 105
+++
Sbjct: 134 LEKKI 138
>gnl|CDD|173278 PRK14817, PRK14817, NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Score = 84.6 bits (209), Expect = 5e-22
Identities = 40/93 (43%), Positives = 59/93 (63%), Gaps = 12/93 (12%)
Query: 21 PRIEP---------GSTTCKASAVTTTSW--MLEPRWVISMGSCANGGGYYHYSYSVVRG 69
PR P G+ CK + + + M +P+WV++ G CA+ GG+Y +Y+ V+G
Sbjct: 69 PRFSPRQADLLMVVGTVNCKQAPILQRVYEQMADPKWVMAFGVCASSGGFYD-NYATVQG 127
Query: 70 CDRIIPVDIYVPGCPPTAEALMYGILQLQKKVK 102
DRIIPVD+YVPGCPP E ++ GI+ LQKK++
Sbjct: 128 IDRIIPVDVYVPGCPPRPEQVLDGIMLLQKKIQ 160
>gnl|CDD|173275 PRK14814, PRK14814, NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Score = 83.2 bits (205), Expect = 2e-21
Identities = 34/62 (54%), Positives = 51/62 (82%), Gaps = 1/62 (1%)
Query: 41 MLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKK 100
M EP++VIS+G+CA+ GG +H +Y V++G DRI+PVD+YVPGCPP EA++ +++LQ K
Sbjct: 98 MAEPKFVISVGACASSGGMFH-TYGVLQGVDRILPVDVYVPGCPPRPEAILDALVKLQTK 156
Query: 101 VK 102
+K
Sbjct: 157 LK 158
>gnl|CDD|214337 CHL00023, ndhK, NADH dehydrogenase subunit K
Back Show alignment and domain information
Score = 84.0 bits (208), Expect = 3e-21
Identities = 34/64 (53%), Positives = 48/64 (75%), Gaps = 1/64 (1%)
Query: 41 MLEPRWVISMGSCANGGGYYHY-SYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQK 99
M EP++VI+MG+C GG + SYS VRG D++IPVD+Y+PGCPP EA++ I +L+K
Sbjct: 96 MPEPKYVIAMGACTITGGMFSTDSYSTVRGVDKLIPVDVYLPGCPPKPEAVIDAITKLRK 155
Query: 100 KVKR 103
K+ R
Sbjct: 156 KISR 159
>gnl|CDD|216271 pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 20 Kd subunit
Back Show alignment and domain information
Score = 76.4 bits (189), Expect = 2e-19
Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 41 MLEPRWVISMGSCANGGG---YYHYSYSV-VRGCDRIIPVDIYVPGCPPTAEALMYGILQ 96
+ + VI++G+CA GG + SY V V ++PVDI +PGCPP EA++ +L
Sbjct: 62 APKAKAVIAVGTCAAYGGIPAAGNNSYGVGVGPVLEVVPVDINIPGCPPHPEAILGTLLA 121
Query: 97 L 97
L
Sbjct: 122 L 122
>gnl|CDD|224852 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Back Show alignment and domain information
Score = 42.0 bits (99), Expect = 1e-05
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 20/63 (31%)
Query: 47 VISMGSCANGGG--------------YYHYSYSVVRGCDR------IIPVDIYVPGCPPT 86
V+++GSCA GG + + +I VD +PGCPP+
Sbjct: 80 VVALGSCAVTGGVQGLRNKSGEELLRPVYGDAKSTFNEESVVPLGEVIDVDYAIPGCPPS 139
Query: 87 AEA 89
E
Sbjct: 140 PEE 142
>gnl|CDD|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma
Back Show alignment and domain information
Score = 37.5 bits (87), Expect = 5e-04
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 47 VISMGSCANGGGYYHYS---------YSVVRGCDRIIPVDIYVPGCPPTAEAL 90
V+++G+CA G + YS + +I VD+ +PGCPP+ EA+
Sbjct: 81 VVALGACAATGNFTRYSRGGQQAQPQHESFVPITDVIDVDLAIPGCPPSPEAI 133
This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (pfam00037) and scores above the trusted cutoff to model pfam01058 for the "NADH ubiquinone oxidoreductase, 20 Kd subunit" family. Length = 228
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
ID Alignment Graph Length
Definition
Probability Query
113
COG0377 194
NuoB NADH:ubiquinone oxidoreductase 20 kD subunit
100.0 KOG1687|consensus 168
100.0 PRK14818 173
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 PRK06411 183
NADH dehydrogenase subunit B; Validated
100.0 COG3260 148
Ni,Fe-hydrogenase III small subunit [Energy produc
100.0 PRK14817 181
NADH dehydrogenase subunit B; Provisional
100.0 CHL00023 225
ndhK NADH dehydrogenase subunit K
100.0 PRK14813 189
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 PRK14814 186
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;
99.96 PF01058 131
Oxidored_q6: NADH ubiquinone oxidoreductase, 20 Kd
99.93 TIGR03294 228
FrhG coenzyme F420 hydrogenase, subunit gamma. Thi
99.92 COG1941 247
FrhG Coenzyme F420-reducing hydrogenase, gamma sub
99.89 PRK10468 371
hydrogenase 2 small subunit; Provisional
99.86 TIGR00391 365
hydA hydrogenase (NiFe) small subunit (hydA). Call
99.85 COG1740 355
HyaA Ni,Fe-hydrogenase I small subunit [Energy pro
99.8
>COG0377 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]
Back Hide alignment and domain information
Probab=100.00 E-value=4.7e-37 Score=230.03 Aligned_cols=109 Identities=48% Similarity=0.793 Sum_probs=99.7
Q ss_pred eecCcccchhhcCCcc-CCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 3 FIYRPFTASLQLTNFL-TPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 3 ~~~~p~~d~~r~~~~~-~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
-++.+.||.+|+|... +||| ||+|++++| .++ +++|+||++||+|||+|+||.+||+|..+|+++.++|.+|
T Consensus 54 ~~~~~r~D~~RfG~~~r~SPRQaDvmIvaGt~t~Kmap~lr~~YdQMPePK~VIsMGsCa~~GG~f~~sYsvV~g~D~~v 133 (194)
T COG0377 54 ATFASRYDLERFGEVPRASPRQADLMIVAGTLTNKMAPALRRVYDQMPEPKWVISMGSCANSGGMYWNSYSVVQGVDRVV 133 (194)
T ss_pred hhccccccHHHhCcCCCCCcccccEEEEeccchHHHHHHHHHHHHhCCCCcEEEEecccccCCCcccccceeeeccceeE
Confidence 3578899999999655 6899 999999999 787 9999999999999999999999999999999999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhcccccccc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQSWY 111 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~~~~~ 111 (113)
|||+|||||||+||+++++|++|++||+++.....|+
T Consensus 134 PVDvyIPGCPPrPEAl~~gi~~Lq~KI~~~~~~~~~~ 170 (194)
T COG0377 134 PVDVYIPGCPPRPEALLYGILLLQEKIRREGRPLRDK 170 (194)
T ss_pred eeeeecCCCCCCHHHHHHHHHHHHHHHHhccCccccc
Confidence 9999999999999999999999999999855444333
>KOG1687|consensus
Back Show alignment and domain information
Probab=100.00 E-value=8e-37 Score=220.97 Aligned_cols=110 Identities=67% Similarity=1.145 Sum_probs=105.9
Q ss_pred ecCcccchhhcCCcc-CCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCcccc
Q psy5271 4 IYRPFTASLQLTNFL-TPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIP 75 (113)
Q Consensus 4 ~~~p~~d~~r~~~~~-~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v~ 75 (113)
+..|.||..|||.++ +||| ||.|++|++ .|+ +++|+||++||+||++|+||..||.+..+|++++++|.+||
T Consensus 51 ~~a~RyD~DRyGvvfRaSPRQaD~iivAGTlTnKMAPalrkvYdQMPEpr~VisMGsCangGGyyhysYSvvRGcDriiP 130 (168)
T KOG1687|consen 51 LAAPRYDMDRYGVVFRASPRQADLIIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIP 130 (168)
T ss_pred hccccccccccceeecCCCccccEEEEeccchhhhcHHHHHHHhhCCCCeeEEEecccccCCceEEEEehhhccccceee
Confidence 568999999999876 6899 999999999 888 99999999999999999999999999999999999999999
Q ss_pred cceEecCCCCCHHHHHHHHHHHHHHHHhcccccccccC
Q psy5271 76 VDIYVPGCPPTAEALMYGILQLQKKVKRMKILQSWYRR 113 (113)
Q Consensus 76 vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~~~~~~~ 113 (113)
||+|||||||++|+++++|++|++||++....|.|||+
T Consensus 131 VDiYvPGCPPtaEAllygilqLqkKi~R~r~~q~wyr~ 168 (168)
T KOG1687|consen 131 VDIYVPGCPPTAEALLYGILQLQKKIKRIRPLQFWYRK 168 (168)
T ss_pred eeeecCCCCCCHHHHHHHHHHHHHHHHHhhhhhhhhcC
Confidence 99999999999999999999999999999999999996
>PRK14818 NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=5e-36 Score=222.79 Aligned_cols=102 Identities=44% Similarity=0.780 Sum_probs=96.2
Q ss_pred ecCcccchhhcCCc-cCCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCcccc
Q psy5271 4 IYRPFTASLQLTNF-LTPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIP 75 (113)
Q Consensus 4 ~~~p~~d~~r~~~~-~~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v~ 75 (113)
+.+|.||.+|+|.. ++||| +|||++|.+ .+. +++|++|++||+|||+|+||++||+|+++|+...++++++|
T Consensus 50 ~~~p~yD~eRfGi~~~aSPRhADvLlVtG~vT~km~~~l~~~yeqmPePK~VIA~G~CA~sGGif~~sY~~~~gvd~vIp 129 (173)
T PRK14818 50 TGGPRADVMRFGAIPRASPRQADFMIVAGTLTYKMAERARLLYDQMPEPKYVISMGSCSNCGGLFQLGYSVCKGVDKVIP 129 (173)
T ss_pred hcCCccCHHHcCCeecCCcccccEEEEeCcCccccHHHHHHHHHhCCCCCEEEEeccccccCCcccCCcccccCCCCccC
Confidence 57899999999975 56999 999999999 665 99999999999999999999999999999999999999999
Q ss_pred cceEecCCCCCHHHHHHHHHHHHHHHHhcc
Q psy5271 76 VDIYVPGCPPTAEALMYGILQLQKKVKRMK 105 (113)
Q Consensus 76 vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~ 105 (113)
||++||||||+||+|+++|++|++++++++
T Consensus 130 VDvyIPGCPP~PeaIl~gil~L~~~i~~~~ 159 (173)
T PRK14818 130 VDVYVPGCPPRPEALTEGLLRLQEIVRSEP 159 (173)
T ss_pred CcEEccCCCCCHHHHHHHHHHHHHHHhccc
Confidence 999999999999999999999999998764
>PRK14816 NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=2.4e-35 Score=220.88 Aligned_cols=102 Identities=40% Similarity=0.734 Sum_probs=95.9
Q ss_pred ecCcccchhhcCC-cc-CCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 4 IYRPFTASLQLTN-FL-TPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~~-~~-~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+|. ++ +||| +|||++|++ .+. ++++++|++||+|||+|+||++||+|+++|+.+.++++++
T Consensus 60 ~~~p~yD~eRfGi~~~~~sPRhADvllVtG~VT~~m~~~l~~~~e~~p~pK~VIAvGsCA~~GGif~~sy~~~~gvd~vI 139 (182)
T PRK14816 60 LGAARYDMARFGFEVARASPRQADMIMVCGTITNKMAPVLKRLYDQMADPKYVIAVGGCAVSGGPFKKSYHVLNGVDKIL 139 (182)
T ss_pred hcCccccHHHhCccccCCCCCcceEEEEecCCcchhHHHHHHHHHhcCCCCEEEEeccccccCCccccCCccCCCccccc
Confidence 5789999999996 55 7999 999999999 555 9999999999999999999999999999999999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhcc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMK 105 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~ 105 (113)
|||++||||||+||+|+++|++|++++++++
T Consensus 140 pVDv~IPGCPP~Pe~Il~~l~~L~~ki~~~~ 170 (182)
T PRK14816 140 PVDVYIPGCPPRPEAFYYGMMQLQRKVKIEK 170 (182)
T ss_pred cccEEeeCcCCCHHHHHHHHHHHHHHhcccc
Confidence 9999999999999999999999999998764
>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit
Back Show alignment and domain information
Probab=100.00 E-value=2.9e-35 Score=214.10 Aligned_cols=101 Identities=52% Similarity=0.919 Sum_probs=94.2
Q ss_pred ecCcccchhhcC-C-ccCCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 4 IYRPFTASLQLT-N-FLTPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~-~-~~~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+| . +++||| +|||++|++ .+. +++|++|++||+|||+|+||++||+|+++|+.+.++++++
T Consensus 36 ~~~~~~D~erfG~i~~~~sPr~aDvllVtG~vt~~~~~~l~~~~e~~p~pk~VIA~GsCA~~GGi~~~~y~~~~~v~~~i 115 (145)
T TIGR01957 36 TGASRYDLDRFGSEVFRASPRQADVMIVAGTVTKKMAPALRRLYDQMPEPKWVISMGACANSGGMFHTSYSVVQGVDRIV 115 (145)
T ss_pred ccCccccHHHhCCceecCCCCcceEEEEecCCcHHHHHHHHHHHHhccCCceEEEecceeecCCCccCCCccccCccccc
Confidence 568999999999 4 457999 999999999 554 9999999999999999999999999999999999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRM 104 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~ 104 (113)
|||++||||||+||+|+++|++|+++++++
T Consensus 116 pVDi~IPGCPp~Pe~i~~~l~~l~~~~~~~ 145 (145)
T TIGR01957 116 PVDVYIPGCPPRPEALIYGLIKLQKKIKRE 145 (145)
T ss_pred ccceEeCCCCCCHHHHHHHHHHHHHHhhcC
Confidence 999999999999999999999999999864
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.
>PRK06411 NADH dehydrogenase subunit B; Validated
Back Show alignment and domain information
Probab=100.00 E-value=7.7e-35 Score=218.57 Aligned_cols=104 Identities=54% Similarity=0.890 Sum_probs=97.0
Q ss_pred ecCcccchhhcCCc-cCCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCcccc
Q psy5271 4 IYRPFTASLQLTNF-LTPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIP 75 (113)
Q Consensus 4 ~~~p~~d~~r~~~~-~~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v~ 75 (113)
..+|.||.+|+|.. .+||| +|||++|++ .+. ++++++|++||+|||+|+||++||+|+++|+.+.++++++|
T Consensus 54 ~~~~~yDieRfGi~~~~sPr~aDvllV~G~vt~~~~~~l~~~~e~mp~pk~VIA~GaCA~~GGif~~sy~~~~gv~~~ip 133 (183)
T PRK06411 54 AGTSRYDLDRFGMVFRASPRQADLMIVAGTLTNKMAPALRRLYDQMPEPKWVISMGSCANSGGMYHYSYSVVQGVDRIVP 133 (183)
T ss_pred ccCccccHHHhCccccCCCCceeEEEEEeCCCccchHHHHHHHHHcCcCCeEEEEecccccCCcccCCCccccCcccccc
Confidence 56899999999975 46899 999999999 555 99999999999999999999999999999999999999999
Q ss_pred cceEecCCCCCHHHHHHHHHHHHHHHHhcccc
Q psy5271 76 VDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 107 (113)
Q Consensus 76 vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~ 107 (113)
||++||||||+||+|+++|++|+++|+++...
T Consensus 134 VDv~IPGCPP~Pe~il~~l~~l~~~i~~~~~~ 165 (183)
T PRK06411 134 VDVYVPGCPPRPEALLYGILKLQKKIRQSERE 165 (183)
T ss_pred cceEeCCCCCCHHHHHHHHHHHHHHHhccccc
Confidence 99999999999999999999999999976655
>COG3260 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]
Back Show alignment and domain information
Probab=100.00 E-value=7.7e-35 Score=209.87 Aligned_cols=101 Identities=33% Similarity=0.598 Sum_probs=95.0
Q ss_pred eecCcccchhhcCCcc-CCCe-----EEeecCCCC--chHHHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 3 FIYRPFTASLQLTNFL-TPPR-----IEPGSTTCK--ASAVTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 3 ~~~~p~~d~~r~~~~~-~sP~-----iVeG~v~~~--~~~~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
-+.+|.||.|||+.++ .||| +|||.+|.+ ++++++||++|+||+|||+|+||++||||.++|....|+|+++
T Consensus 28 a~~sP~YDaErfgI~~v~sPRhADiLlVTG~vT~~~~e~lkk~Yea~PePKiViA~GaCa~~GGIf~~~~~v~gpvd~vi 107 (148)
T COG3260 28 AALSPRYDAERFGIKVVNSPRHADILLVTGAVTRQMREPLKKAYEAMPEPKIVIAVGACALSGGIFKDSYSVWGPVDKVI 107 (148)
T ss_pred eccCcccchHHheeEEeCCCccccEEEEeccccHHHHHHHHHHHHhCCCCcEEEEEcccccCCceeccccccccccccee
Confidence 4689999999999876 5899 999999999 5559999999999999999999999999999999999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHh
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKR 103 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~ 103 (113)
|||++||||||+|++|+++|.+++.+..+
T Consensus 108 PVDv~IPGCPP~P~~il~g~~~al~~~~k 136 (148)
T COG3260 108 PVDVEIPGCPPRPEAILAGLVAALGKLEK 136 (148)
T ss_pred EeeeEcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999888765
>PRK14817 NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=2.5e-34 Score=215.29 Aligned_cols=103 Identities=40% Similarity=0.791 Sum_probs=95.2
Q ss_pred ecCcccchhhcCC-cc-CCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 4 IYRPFTASLQLTN-FL-TPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~~-~~-~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+|. ++ .||| +|||++|++ .+. +++|++|++||+|||+|+||++||++ ++|+...++++++
T Consensus 54 ~~~~~yDleRfGi~~~~~sPR~ADillVeG~VT~~m~~~l~~~~e~~p~pK~VIAvGaCA~~GGi~-~~y~~~~gv~~vv 132 (181)
T PRK14817 54 MASARYDSDRFGAAMPRFSPRQADLLMVVGTVNCKQAPILQRVYEQMADPKWVMAFGVCASSGGFY-DNYATVQGIDRII 132 (181)
T ss_pred hcCccccHHHhceeeccCCCcceeEEEEEecCCccchHHHHHHHHHcccCCEEEEeccccccCCcC-CCcccccCccccc
Confidence 5789999999997 44 6999 999999999 555 99999999999999999999999988 7899999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhcccc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 107 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~ 107 (113)
|||++||||||+||+|+++|++|++++++++..
T Consensus 133 pVDv~IPGCPP~Pe~il~~l~~l~~ki~~~~~~ 165 (181)
T PRK14817 133 PVDVYVPGCPPRPEQVLDGIMLLQKKIQNQSHK 165 (181)
T ss_pred eeeEEecCCCCCHHHHHHHHHHHHHHhhcCCcc
Confidence 999999999999999999999999999876543
>CHL00023 ndhK NADH dehydrogenase subunit K
Back Show alignment and domain information
Probab=100.00 E-value=2.3e-34 Score=221.02 Aligned_cols=104 Identities=39% Similarity=0.689 Sum_probs=96.3
Q ss_pred ecCcccchhhcCCc-cCCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCC-CCCccccCCCccc
Q psy5271 4 IYRPFTASLQLTNF-LTPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYH-YSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~~~-~~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~-~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+|.+ ++||| ||||++|.+ .+. +++|++|++||+|||+|+||++||+|+ ++|+.+.|++++|
T Consensus 51 ~~~p~yDleRfGi~~~aSPRhADvliVtG~VT~km~~~L~rlyeqmPePK~VIA~GaCA~sGGif~~dsy~~v~gvd~vI 130 (225)
T CHL00023 51 LIGSRFDFDRYGLVPRSSPRQADLILTAGTVTMKMAPSLVRLYEQMPEPKYVIAMGACTITGGMFSTDSYSTVRGVDKLI 130 (225)
T ss_pred hCCCccCHHHcCCeecCCcccceEEEEecCCccccHHHHHHHHHhcCCCCeEEEEccccccCCcccCCCcccccCccccc
Confidence 57899999999975 46999 999999999 555 999999999999999999999999997 8999999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhcccc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 107 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~ 107 (113)
|||++||||||+||+|+++|++|+++++++...
T Consensus 131 PVDv~IPGCPP~PeaIi~~l~~L~~ki~~~~~~ 163 (225)
T CHL00023 131 PVDVYLPGCPPKPEAVIDAITKLRKKISREIYE 163 (225)
T ss_pred eeeEEecCCCCCHHHHHHHHHHHHHHHhccccc
Confidence 999999999999999999999999999876443
>PRK14813 NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=2.3e-34 Score=216.53 Aligned_cols=106 Identities=44% Similarity=0.736 Sum_probs=96.5
Q ss_pred ecCcccchhhcCCc-cCCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCC-CCCccccCCCccc
Q psy5271 4 IYRPFTASLQLTNF-LTPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYH-YSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~~~-~~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~-~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+|.. ++||| +|+|++|++ .+. +++|++|++||+|||+|+||++||++. ++|+.+.+++++|
T Consensus 47 ~~~p~yD~eRfGi~~~asPR~ADvllVtG~Vt~km~~~l~~~y~qmPePK~VIA~GaCA~sGG~~~~~sY~~~~gvd~vI 126 (189)
T PRK14813 47 TNASNYDLERFGIFPRSSPRQSDLMIVAGTVTMKMAERVVRLYEQMPEPRYVLSMGSCSNCGGPYWEHGYHVLKGVDRII 126 (189)
T ss_pred hcccCCCHHHcCCeecCCcccceEEEEeccCchhhHHHHHHHHHhCCCCCEEEEecccccCCCCcccCCcccccCCCCcc
Confidence 57899999999975 47999 999999999 555 999999999999999999999988886 5999999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhcccccc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQS 109 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~~~ 109 (113)
|||++||||||+||+|+++|++|+++|++++....
T Consensus 127 pVDv~IPGCPP~PeaIl~gl~~l~~~i~~~~~~~~ 161 (189)
T PRK14813 127 PVDVYVPGCPPRPEALIGGLMKVQELIRMEQIGIS 161 (189)
T ss_pred CCcEEccCCCCCHHHHHHHHHHHHHHHHhcccccc
Confidence 99999999999999999999999999998765433
>PRK14815 NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=5.3e-34 Score=213.69 Aligned_cols=104 Identities=41% Similarity=0.776 Sum_probs=95.3
Q ss_pred ecCcccchhhcCC-cc-CCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 4 IYRPFTASLQLTN-FL-TPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~~-~~-~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+|. ++ +||| +|||++|++ .+. +++|++|++||+|||+|+||++||+|+ +|+...++++++
T Consensus 52 ~~~~~yDieRfGi~~~~~SPR~ADillVtG~VT~~m~~~l~r~ye~~p~pK~VIAvGsCA~~GGi~~-sy~~~~gv~~~i 130 (183)
T PRK14815 52 VACSRFDISRFGAEVMRFSPRQADVMIVAGTVTYKMALAVRRIYDQMPEPKWVIAMGACASSGGMYR-SYSVLQGVDRIL 130 (183)
T ss_pred hcCccccHHHhCcccCCCCCccccEEEEeCcCchhhHHHHHHHHHhCCCCCEEEEeccccccCCCcc-ccccccCccccc
Confidence 5789999999995 54 6999 999999999 444 999999999999999999999999995 899999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhccccc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQ 108 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~~ 108 (113)
|||++||||||+||+|+++|++|++++++++..+
T Consensus 131 pVDv~IPGCPP~Pe~il~~l~~l~~~i~~~~~~~ 164 (183)
T PRK14815 131 PVDVYISGCPPRPEAILDALIKLQKKIDTERAAR 164 (183)
T ss_pred cccEEecCCCCCHHHHHHHHHHHHHHHhhccccc
Confidence 9999999999999999999999999999865443
>PRK14820 NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=2.2e-33 Score=210.19 Aligned_cols=103 Identities=38% Similarity=0.724 Sum_probs=94.8
Q ss_pred eecCcccchhhcCC--ccCCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCcc
Q psy5271 3 FIYRPFTASLQLTN--FLTPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRI 73 (113)
Q Consensus 3 ~~~~p~~d~~r~~~--~~~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~ 73 (113)
-+.+|.||.+|+|. +++||| +|||++|++ .+. +++|+++++||+|||+|+||++||+| ++|+.+.+++++
T Consensus 51 a~~~~~yDi~RfGi~~~~~sPR~aDillVeG~VT~~m~~~l~~~~e~~p~pk~VIAvGaCA~~GGi~-~~y~~~~~v~~~ 129 (180)
T PRK14820 51 ATMASHYDLARFGSERPSFSPRQADMLMVMGTIAKKMAPVLKQVYLQMAEPRWVVAVGACASSGGIF-DTYSVLQGIDRI 129 (180)
T ss_pred HhcCccccHHHhCccccCCCCccceEEEEEecCCcccHHHHHHHHHhcCCCCeEEEEecccccCCcc-cccccccccccc
Confidence 35789999999997 357999 999999999 666 99999999999999999999999999 589999999999
Q ss_pred cccceEecCCCCCHHHHHHHHHHHHHHHHhccc
Q psy5271 74 IPVDIYVPGCPPTAEALMYGILQLQKKVKRMKI 106 (113)
Q Consensus 74 v~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~ 106 (113)
+|||++||||||+||+|+++|++|++++++++-
T Consensus 130 ipVDv~IPGCPP~Pe~il~~l~~l~~~i~~~~~ 162 (180)
T PRK14820 130 IPVDVYVPGCPPRPEQIIDGVMRVQELVKNESL 162 (180)
T ss_pred ccccEEecCCCCCHHHHHHHHHHHHHHHhhccc
Confidence 999999999999999999999999999987643
>PRK14814 NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=1.9e-33 Score=211.29 Aligned_cols=103 Identities=39% Similarity=0.702 Sum_probs=94.6
Q ss_pred ecCcccchhhcCC--ccCCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 4 IYRPFTASLQLTN--FLTPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~~--~~~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+|. +++||| ||||+||++ .+. +++|++|++||+|||+|+||++||+|+ +|+...++++++
T Consensus 52 ~~~~~yD~eRfGi~~~~~sPR~ADvllVtG~VT~~m~~~l~~~yeqmp~pk~VIAvGsCA~~GGi~~-~y~~~~gv~~vv 130 (186)
T PRK14814 52 TACSDYDIARFGAERPSFSPRQADMILVLGTITYKMAPVLRQIYDQMAEPKFVISVGACASSGGMFH-TYGVLQGVDRIL 130 (186)
T ss_pred hcCccccHHHhCccccCCCcccceEEEEeccCchhhHHHHHHHHHhcCCCCeEEEeccccccCCccC-cCCCCcCccccc
Confidence 5679999999997 367999 999999999 555 999999999999999999999999996 688899999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhcccc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 107 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~ 107 (113)
|||++||||||+||+|+++|++|+++++++...
T Consensus 131 pVDv~IPGCPP~Pe~il~~l~~L~~~i~~~~~~ 163 (186)
T PRK14814 131 PVDVYVPGCPPRPEAILDALVKLQTKLKTQGLE 163 (186)
T ss_pred cccEEecCCCCCHHHHHHHHHHHHHHHhccccc
Confidence 999999999999999999999999999876543
>PRK14819 NADH dehydrogenase subunit B; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=4.8e-33 Score=217.22 Aligned_cols=109 Identities=41% Similarity=0.728 Sum_probs=98.2
Q ss_pred ecCcccchhhcCC--ccCCCe-----EEeecCCCC-c-hHHHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 4 IYRPFTASLQLTN--FLTPPR-----IEPGSTTCK-A-SAVTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~~--~~~sP~-----iVeG~v~~~-~-~~~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+|. +++||| ||||+||++ . .++++|++|++||+|||+|+||++||+|+++|+.+.+++++|
T Consensus 50 ~l~p~yDieRFGi~~~~~sPRhADIlLVtG~VT~km~~~L~rlyeqmP~PK~VIAvGaCA~~GGIf~~sY~v~~gId~vI 129 (264)
T PRK14819 50 TGLSRYDLARFGAELFRASPRQADLMIVAGTVTKKMAPQVVRLYNQMPEPRYVISMGACATSGGPFRDGYNVLRGIDLLI 129 (264)
T ss_pred hccccccHHHhCcccccCCCCcceEEEEecCCchhhHHHHHHHHHhccCCCeEEEEccccccCCccccCCCccCCccccc
Confidence 5689999999997 457999 999999999 4 449999999999999999999999999999999999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhcc-ccccccc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMK-ILQSWYR 112 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~-~~~~~~~ 112 (113)
+||++||||||+|++|+++|++|+++++..+ ..-.||+
T Consensus 130 PVDv~IPGCPP~Pe~Il~gLl~L~~ki~~d~~~Rp~~~~ 168 (264)
T PRK14819 130 PVDVYIPGCPPRPEALLHALMTLQKQIDAQSLGRVRWYG 168 (264)
T ss_pred cccEEecCCCCCHHHHHHHHHHHHhhcccccccCccccc
Confidence 9999999999999999999999999886433 2346775
>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional
Back Show alignment and domain information
Probab=99.96 E-value=1.1e-29 Score=222.61 Aligned_cols=103 Identities=42% Similarity=0.793 Sum_probs=96.3
Q ss_pred ecCcccchhhcCC--ccCCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCccc
Q psy5271 4 IYRPFTASLQLTN--FLTPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRII 74 (113)
Q Consensus 4 ~~~p~~d~~r~~~--~~~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~v 74 (113)
+.+|.||.+|+|. +++||| +|||++|.+ .+. +++|++|++||+|||+|+||++||+| ++|+.+.+++++|
T Consensus 41 ~~~~~~D~~r~G~~~~~~sPr~aD~llv~G~vt~~~~~~l~~~~~~~p~pk~via~G~Ca~~GG~~-~~y~~~~g~~~~i 119 (788)
T PRK13292 41 SFTSRYDISRFGAEVLRGTPREADLMVIAGTVFKKMAPSILRLYEQMAEPKWVISMGSCANSGGMY-DVYSVVQGVNQIL 119 (788)
T ss_pred hcCCcCCHHHcCCCccCCCcccceEEEEecCCcHhhHHHHHHHHHhCCCCCEEEEecccccCCCCc-CccccccCcCCcc
Confidence 5789999999997 358999 999999999 665 99999999999999999999999999 7999999999999
Q ss_pred ccceEecCCCCCHHHHHHHHHHHHHHHHhcccc
Q psy5271 75 PVDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 107 (113)
Q Consensus 75 ~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~ 107 (113)
|||+|||||||+|++|+++|++|+++++++++.
T Consensus 120 pVDv~iPGCPP~Pe~i~~~i~~l~~~~~~~~~~ 152 (788)
T PRK13292 120 PVDVYIPGCPPRPEAFLQGLMLLQEKIRREERP 152 (788)
T ss_pred cccEEccCCCCCHHHHHHHHHHHHHHhhcCccc
Confidence 999999999999999999999999999977654
>PF01058 Oxidored_q6: NADH ubiquinone oxidoreductase, 20 Kd subunit; InterPro: IPR006137 NADH:ubiquinone oxidoreductase (complex I) (1
Back Show alignment and domain information
Probab=99.93 E-value=9.8e-27 Score=165.51 Aligned_cols=75 Identities=33% Similarity=0.510 Sum_probs=61.8
Q ss_pred EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCC--CCcc---ccCCCcccccceEecCCCCCHHHHHHHHH
Q psy5271 23 IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHY--SYSV---VRGCDRIIPVDIYVPGCPPTAEALMYGIL 95 (113)
Q Consensus 23 iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~--~~~~---~~~v~~~v~vdi~IpGCPP~Pe~i~~~l~ 95 (113)
+|||+|+++ ++. +.+++++++||+|||+|+||++||+++. .++. +.+++++++||++||||||+||+|+++|.
T Consensus 50 iVeG~v~~~~~~~~e~~~~~~~~a~~vIAvGtCA~~GGi~~~~~~~~~~~~~~~~~~~~~VDi~IpGCPp~pd~i~~~l~ 129 (131)
T PF01058_consen 50 IVEGSVPRNMEEALEWLKELRPKAKAVIAVGTCASFGGIPAARNNPSVGDSVGPLLEVVPVDINIPGCPPHPDWILETLL 129 (131)
T ss_dssp EEESBEETGGEEHHHHHHHHHGCSSEEEEEHHHHHH-TGGGSTTSTTEEE-HHHHHGCS-ECEEE-SSS--HHHHHHHHH
T ss_pred EEEeeccCCchHHHHHHHHHccCCceeEcCCCccccCCcccccccccccccccCcCCCccEEEEeeCCCCCHHHHHHHHh
Confidence 999999888 555 9999999999999999999999999954 3443 45788889999999999999999999999
Q ss_pred HH
Q psy5271 96 QL 97 (113)
Q Consensus 96 ~l 97 (113)
+|
T Consensus 130 ~L 131 (131)
T PF01058_consen 130 AL 131 (131)
T ss_dssp HH
T ss_pred hC
Confidence 86
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 ....
>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma
Back Show alignment and domain information
Probab=99.92 E-value=8.2e-26 Score=173.96 Aligned_cols=80 Identities=26% Similarity=0.457 Sum_probs=70.8
Q ss_pred EEeecCCCC-c-hHHHHHHHhcCCCeEEEeeccCCcCCCCCCCCc---------cccCCCcccccceEecCCCCCHHHHH
Q psy5271 23 IEPGSTTCK-A-SAVTTTSWMLEPRWVISMGSCANGGGYYHYSYS---------VVRGCDRIIPVDIYVPGCPPTAEALM 91 (113)
Q Consensus 23 iVeG~v~~~-~-~~~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~---------~~~~v~~~v~vdi~IpGCPP~Pe~i~ 91 (113)
+|||+|+++ . .++.+++++++||+|||+||||++||+++.+++ .+.+++++|+||+|||||||+|++|+
T Consensus 55 ~VeG~i~~~~~~~~~~~~~~~~~ak~vVA~GtCA~~GGi~~~~~~~~~~~~~~~~~~~~~~~V~vdi~IpGCPp~p~~i~ 134 (228)
T TIGR03294 55 LVEGSVCLQDEHSLEEIKELREKAKVVVALGACAATGNFTRYSRGGQQAQPQHESFVPITDVIDVDLAIPGCPPSPEAIR 134 (228)
T ss_pred EEeCCCCCCccHHHHHHHHHhccCCEEEEeecccccCCcccccCCcccCCCCCCCCcCHHHcccCCEEeeCCCCCHHHHH
Confidence 999999987 3 349999999999999999999999999876543 46788999999999999999999999
Q ss_pred HHHHHHHHHHH
Q psy5271 92 YGILQLQKKVK 102 (113)
Q Consensus 92 ~~l~~l~~~i~ 102 (113)
++|.+|+.+-.
T Consensus 135 ~~l~~ll~g~~ 145 (228)
T TIGR03294 135 NVCVALLNGDM 145 (228)
T ss_pred HHHHHHHcCCC
Confidence 99999986543
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.
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Back Show alignment and domain information
Probab=99.89 E-value=8.2e-24 Score=164.18 Aligned_cols=81 Identities=26% Similarity=0.444 Sum_probs=72.8
Q ss_pred EEeecCCCCchHHHHHHHhcCCCeEEEeeccCCcCCCCCC-----------CC---------ccccCCCcccccceEecC
Q psy5271 23 IEPGSTTCKASAVTTTSWMLEPRWVISMGSCANGGGYYHY-----------SY---------SVVRGCDRIIPVDIYVPG 82 (113)
Q Consensus 23 iVeG~v~~~~~~~~~~~~~~~~k~vIA~GtCA~~GGi~~~-----------~~---------~~~~~v~~~v~vdi~IpG 82 (113)
+|||+|+++++++.+.|+|+++|+|||+||||++||+++- .| ..+.|++++|+||++|||
T Consensus 56 lVEGsV~~ee~lE~v~ElRekakivVA~GsCA~~Ggv~~~~~~s~~e~l~~~y~~~~~~~~~~~v~Pl~evI~VD~~IpG 135 (247)
T COG1941 56 LVEGSVCDEEELELVKELREKAKIVVALGSCAVTGGVQGLRNKSGEELLRPVYGDAKSTFNEESVVPLGEVIDVDYAIPG 135 (247)
T ss_pred EEecccCcHHHHHHHHHHHHhCcEEEEEecchhcCCchhhhhccccccchhhhhcccCCCCccceEEchheeeeeeecCC
Confidence 9999999778889999999999999999999999999842 13 347899999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHh
Q psy5271 83 CPPTAEALMYGILQLQKKVKR 103 (113)
Q Consensus 83 CPP~Pe~i~~~l~~l~~~i~~ 103 (113)
|||+||.|.++|.+|+++-+.
T Consensus 136 CPP~~e~I~~al~all~ge~p 156 (247)
T COG1941 136 CPPSPEEIARALTALLEGEEP 156 (247)
T ss_pred CCcCHHHHHHHHHHHHcCCCc
Confidence 999999999999999876544
>PRK10468 hydrogenase 2 small subunit; Provisional
Back Show alignment and domain information
Probab=99.86 E-value=4.7e-22 Score=162.43 Aligned_cols=90 Identities=20% Similarity=0.314 Sum_probs=77.6
Q ss_pred EEeecCCCC----------chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCcc--ccCCCccccc--ceEecCCCCCH
Q psy5271 23 IEPGSTTCK----------ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSV--VRGCDRIIPV--DIYVPGCPPTA 87 (113)
Q Consensus 23 iVeG~v~~~----------~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~--~~~v~~~v~v--di~IpGCPP~P 87 (113)
+|||+|+.+ ++. +.+++++++||+|||+||||++|||++..++. +.+++++++. .||||||||||
T Consensus 116 vVEGaIp~~~~G~y~~~gg~~~~e~l~~~a~~A~aVVAvGtCAs~GGI~aa~pnptga~gv~~~l~~~PVINIPGCPp~P 195 (371)
T PRK10468 116 VVDGSIPLKDNGIYCMVAGEPIVDHIRKAAEGAAAIIAIGSCSAWGGVAAAGVNPTGAVSLQEVLPGKTVINIPGCPPNP 195 (371)
T ss_pred EEeCCCCCCCCcceeeECCchHHHHHHHHhccCCEEEEEecccccCCcccCCCCCCCCccHHHhcCCCCeEEcCCCCCCH
Confidence 899999987 234 88999999999999999999999999987776 5578887743 39999999999
Q ss_pred HHHHHHHHHHH-H----HHHhccccccccc
Q psy5271 88 EALMYGILQLQ-K----KVKRMKILQSWYR 112 (113)
Q Consensus 88 e~i~~~l~~l~-~----~i~~~~~~~~~~~ 112 (113)
|+|+++|++++ . .+.+.++++.||-
T Consensus 196 ~~i~~tL~~l~~~g~lp~LD~~gRPk~fyg 225 (371)
T PRK10468 196 HNFLATVAHIITYGKPPKLDDKNRPTFAYG 225 (371)
T ss_pred HHHHHHHHHHHhcCCCccccccCCcHHHhc
Confidence 99999999998 2 3777888888885
>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA)
Back Show alignment and domain information
Probab=99.85 E-value=1.1e-21 Score=160.07 Aligned_cols=90 Identities=19% Similarity=0.264 Sum_probs=76.7
Q ss_pred EEeecCCCCc----------hH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCcc--ccCCCccc--ccceEecCCCCCH
Q psy5271 23 IEPGSTTCKA----------SA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSV--VRGCDRII--PVDIYVPGCPPTA 87 (113)
Q Consensus 23 iVeG~v~~~~----------~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~--~~~v~~~v--~vdi~IpGCPP~P 87 (113)
+|||+|++++ +. +.+++++++|++|||+||||++|||++..++. ..++++++ +.+++||||||+|
T Consensus 118 vVEGaIp~~~~G~y~~~~g~~~~e~l~~~a~~A~aVIAvGtCAs~GGI~aa~pnptga~~v~~vi~~~pvinIPGCPp~P 197 (365)
T TIGR00391 118 VVEGSIPLGDNGIYCMVAGEPIVEHIRKAAEGAAAIIAIGTCSSWGGVQAAGPNPTGAVPLQKVIPDKPVINVPGCPPNP 197 (365)
T ss_pred EEeCCCCCCCCceeeeeCCcHHHHHHHHHhhcCCEEEEEeccccccCccCCCCCCCCCcchhHhcCCCCeEEeCCCCCCH
Confidence 8999999973 24 89999999999999999999999999987665 56889888 3459999999999
Q ss_pred HHHHHHHHHHH-H----HHHhccccccccc
Q psy5271 88 EALMYGILQLQ-K----KVKRMKILQSWYR 112 (113)
Q Consensus 88 e~i~~~l~~l~-~----~i~~~~~~~~~~~ 112 (113)
++|+++|++++ . .+.+.++++.||.
T Consensus 198 e~i~~tl~~~ll~G~lP~LD~~~RP~~fyg 227 (365)
T TIGR00391 198 HNFLATVAYIITFGKLPKLDDKNRPTFAYG 227 (365)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCchhhhc
Confidence 99999999975 3 3467788887775
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.
>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]
Back Show alignment and domain information
Probab=99.80 E-value=9.5e-20 Score=147.01 Aligned_cols=90 Identities=18% Similarity=0.309 Sum_probs=77.1
Q ss_pred EEeecCCCC----------chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCC--ccccCCCccc--ccceEecCCCCCH
Q psy5271 23 IEPGSTTCK----------ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSY--SVVRGCDRII--PVDIYVPGCPPTA 87 (113)
Q Consensus 23 iVeG~v~~~----------~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~--~~~~~v~~~v--~vdi~IpGCPP~P 87 (113)
+|||++++. ++. +.+.++.++|++|||+|+||++|||++..+ +...++++++ +..||||||||+|
T Consensus 116 vVEG~v~~~~~G~y~~vgg~~~~e~l~~aA~~A~aIiAvGtCAs~GgI~AA~pnps~a~~i~ev~~~kpVINiPGCPp~p 195 (355)
T COG1740 116 VVEGAVPLGENGMYCIVGGEPFKEILRKAAEGASAIIAVGTCASWGGIQAAKPNPTGAGPLSEVIKDKPVINIPGCPPNP 195 (355)
T ss_pred EEeCCccCCCCceEEEEcChhHHHHHHHHhhcCceEEEEecccccCCeeccCCCCCCcccceecccCCceeeCCCCCCCc
Confidence 899999997 244 777888999999999999999999998864 4568889887 3349999999999
Q ss_pred HHHHHHHHHHHHH-----HHhccccccccc
Q psy5271 88 EALMYGILQLQKK-----VKRMKILQSWYR 112 (113)
Q Consensus 88 e~i~~~l~~l~~~-----i~~~~~~~~~~~ 112 (113)
|+|+.+|.+++-. +.+.+|++.+|-
T Consensus 196 d~iv~tl~~~~~~gk~P~LD~~~RPk~fyg 225 (355)
T COG1740 196 DWIVATLLHIVTFGKLPDLDELGRPKMFYG 225 (355)
T ss_pred hhHHHHHHHHHHcCCCcchhhcCCchhhhc
Confidence 9999999987664 788999988884
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
ID Alignment Graph Length
Definition
E-value Query 113
d2fug61 161
e.19.1.2 (6:15-175) NAD-quinone oxidoreductase cha
8e-29 d1wuis1 267
e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small
7e-12 d1cc1s_ 278
e.19.1.1 (S:) Nickel-iron hydrogenase, small subun
3e-11 d1yq9a1 261
e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small
4e-11 d1frfs_ 261
e.19.1.1 (S:) Nickel-iron hydrogenase, small subun
1e-10
>d2fug61 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus thermophilus [TaxId: 274]} Length = 161
Back Hide information, alignment and structure
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 = 100 bits (249), Expect = 8e-29
Identities = 45/112 (40%), Positives = 68/112 (60%), Gaps = 7/112 (6%)
Query: 3 FIYRPFTASLQLTNFLTPPRIEPGSTTCKASAVTTTSW--MLEPRWVISMGSCANGGGYY 60
F F AS + + + I G + K + V W M +P+WVISMG+CA+ GG +
Sbjct: 49 FGSEVFRASPRQADVM----IVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMF 104
Query: 61 HYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQSWYR 112
+ +Y++V+ D ++PVD+YVPGCPP EAL+Y ++QLQKKV+ + R
Sbjct: 105 N-NYAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGER 155
>d1wuis1 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 267
Back Show information, alignment and structure
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 = 57.6 bits (139), Expect = 7e-12
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 41 MLEPRWVISMGSCANGGGYYH--YSYSVVRGCDRIIP----VDIYVPGCPPTAEALMYGI 94
+ + + VI+ G+CA GG + + +G + + I + GCPP L+ I
Sbjct: 102 LPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTI 161
Query: 95 LQLQKKVK 102
+ K
Sbjct: 162 VYYLKNKA 169
>d1cc1s_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfomicrobium baculatum [TaxId: 899]} Length = 278
Back Show information, alignment and structure
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 = 56.2 bits (135), Expect = 3e-11
Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 8/69 (11%)
Query: 43 EPRWVISMGSCANGGGYYHYSYSV--------VRGCDRIIPVDIYVPGCPPTAEALMYGI 94
+ +++G+C+ GG +V ++I + + VPGCPP + ++ +
Sbjct: 111 KSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTL 170
Query: 95 LQLQKKVKR 103
+ V
Sbjct: 171 VAAWSHVLN 179
>d1yq9a1 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]} Length = 261
Back Show information, alignment and structure
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 = 55.3 bits (133), Expect = 4e-11
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 41 MLEPRWVISMGSCANGGGYY--HYSYSVVRGCDRIIP----VDIYVPGCPPTAEALMYGI 94
+ + VI++G+CA GG + + G + + I + GCPP + +
Sbjct: 97 APKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTV 156
Query: 95 LQL 97
+ L
Sbjct: 157 VHL 159
>d1frfs_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfovibrio fructosovorans [TaxId: 878]} Length = 261
Back Show information, alignment and structure
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 = 54.2 bits (130), Expect = 1e-10
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 43 EPRWVISMGSCANGGGYYH--YSYSVVRGCDRIIPVD-IYVPGCPPTAEALMYGILQLQK 99
+ + +I +G+C+ GG + S +G + V I +PGCPP + ++ +
Sbjct: 101 KAKGIICIGTCSPYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHV-- 158
Query: 100 KVKRMKILQSWYR 112
K + L R
Sbjct: 159 LTKGIPDLDENGR 171
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
ID Alignment Graph Length
Definition
Probability Query 113
d2fug61 161
NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus
100.0 d1wuis1 267
Nickel-iron hydrogenase, small subunit {Desulfovib
99.89 d1frfs_ 261
Nickel-iron hydrogenase, small subunit {Desulfovib
99.88 d1yq9a1 261
Nickel-iron hydrogenase, small subunit {Desulfovib
99.88 d1cc1s_ 278
Nickel-iron hydrogenase, small subunit {Desulfomic
99.86
>d2fug61 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus thermophilus [TaxId: 274]}
Back Hide information, alignment and structure
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=8.6e-36 Score=216.95 Aligned_cols=104 Identities=39% Similarity=0.755 Sum_probs=82.8
Q ss_pred eecCcccchhhcCC-cc-CCCe-----EEeecCCCC-chH-HHHHHHhcCCCeEEEeeccCCcCCCCCCCCccccCCCcc
Q psy5271 3 FIYRPFTASLQLTN-FL-TPPR-----IEPGSTTCK-ASA-VTTTSWMLEPRWVISMGSCANGGGYYHYSYSVVRGCDRI 73 (113)
Q Consensus 3 ~~~~p~~d~~r~~~-~~-~sP~-----iVeG~v~~~-~~~-~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~~~~~v~~~ 73 (113)
-+.+|.||.+|+|. ++ +||| +|+|++|++ .+. +++|++|++||+|||+|+||++||+| ++|+...++|++
T Consensus 38 a~~~p~yD~eRfG~~~~~~sPR~ADvllVtG~vT~km~~~l~~~y~qmPePK~VIA~GaCa~sGG~f-~~y~v~~gvd~~ 116 (161)
T d2fug61 38 ASTDARNDLARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMF-NNYAIVQNVDSV 116 (161)
T ss_dssp GGCCC-----------------CCCCEEEESCCBTTTHHHHHHHHHTSCSSCCEEEEHHHHHSCTTC-CSTTBCSCGGGT
T ss_pred hccCCccchhhhcccccCCCcccCcEEEEeccchHHHHHHHHHHHHhCCCCceEEEecccccCCCcc-CCccccCCcCcc
Confidence 35689999999997 44 7999 999999999 666 99999999999999999999999999 589999999999
Q ss_pred cccceEecCCCCCHHHHHHHHHHHHHHHHhcccc
Q psy5271 74 IPVDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 107 (113)
Q Consensus 74 v~vdi~IpGCPP~Pe~i~~~l~~l~~~i~~~~~~ 107 (113)
+|||+|||||||+||+|+++|++|+++|+++...
T Consensus 117 iPVDvyIPGCPPrPeail~gl~~l~~ki~~~~~~ 150 (161)
T d2fug61 117 VPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYN 150 (161)
T ss_dssp SCCSEEECCSSCCHHHHHHHHHHHHHHHHSSCCC
T ss_pred CcCceeCCCCCcCHHHHHHHHHHHHHHHhhhcch
Confidence 9999999999999999999999999999876554
>d1wuis1 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subunit {Desulfovibrio vulgaris [TaxId: 881]}
Back Show information, alignment and structure
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=99.89 E-value=7.6e-25 Score=169.26 Aligned_cols=90 Identities=20% Similarity=0.316 Sum_probs=72.2
Q ss_pred EEeecCCCCch-----------HHHHHHHhcCCCeEEEeeccCCcCCCCCCCC--ccccCC----CcccccceEecCCCC
Q psy5271 23 IEPGSTTCKAS-----------AVTTTSWMLEPRWVISMGSCANGGGYYHYSY--SVVRGC----DRIIPVDIYVPGCPP 85 (113)
Q Consensus 23 iVeG~v~~~~~-----------~~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~--~~~~~v----~~~v~vdi~IpGCPP 85 (113)
+|||+|+++.. .+.+++++++||+|||+||||++|||++... +...++ +++++||+|||||||
T Consensus 73 vVEGsI~~~~~~~~~~~~~~~~~e~v~~~r~~ak~vVAvGtCA~~GGI~a~~~~~t~~~~~~~~l~~~~~vdi~IpGCPp 152 (267)
T d1wuis1 73 VVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPP 152 (267)
T ss_dssp EEESBEECGGGGTTBEETTEEHHHHHHHHGGGSSEEEEESHHHHHCCGGGSTTCTTCEECHHHHHGGGTCCCEEECSSSC
T ss_pred EEecccCcccccceeeeCCchHHHHHHHHhhcCCEEEEeechhccCCccccCCCCcccccccccccccCCCeEEeCCCCC
Confidence 89999998732 4899999999999999999999999997644 344444 456679999999999
Q ss_pred CHHHHHHHHHHHHHHH-----Hhccccccccc
Q psy5271 86 TAEALMYGILQLQKKV-----KRMKILQSWYR 112 (113)
Q Consensus 86 ~Pe~i~~~l~~l~~~i-----~~~~~~~~~~~ 112 (113)
||++|+++|.+++..- .+.+++..+|.
T Consensus 153 ~p~~i~~~l~~~l~~~~~p~ld~~~RP~~~~~ 184 (267)
T d1wuis1 153 NPYNLVGTIVYYLKNKAAPELDSLNRPTMFFG 184 (267)
T ss_dssp CHHHHHHHHHHHHHHSSCCCBCTTSCBHHHHS
T ss_pred CHHHHHHHHHHHHhcCCCCcccccCCCccccC
Confidence 9999999999988753 23445555553
>d1frfs_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfovibrio fructosovorans [TaxId: 878]}
Back Show information, alignment and structure
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=99.88 E-value=1.2e-24 Score=167.66 Aligned_cols=89 Identities=20% Similarity=0.373 Sum_probs=74.6
Q ss_pred EEeecCCCCch-----------HHHHHHHhcCCCeEEEeeccCCcCCCCCCC--CccccCCCcccccc-eEecCCCCCHH
Q psy5271 23 IEPGSTTCKAS-----------AVTTTSWMLEPRWVISMGSCANGGGYYHYS--YSVVRGCDRIIPVD-IYVPGCPPTAE 88 (113)
Q Consensus 23 iVeG~v~~~~~-----------~~~~~~~~~~~k~vIA~GtCA~~GGi~~~~--~~~~~~v~~~v~vd-i~IpGCPP~Pe 88 (113)
+|||+|+++++ .+.+++++++||+|||+||||++|||++.. ++...++++++++| ++||||||||+
T Consensus 70 ~VEGsV~~~~~g~~~~~~~~~~~e~~~~~~~~ak~vIAvGtCA~~GGI~a~~~n~t~~~~v~~~i~~~vinIpGCPp~p~ 149 (261)
T d1frfs_ 70 VVEGGLPTIDGGQWGMVAGHPMIETCKKAAAKAKGIICIGTCSPYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPI 149 (261)
T ss_dssp EEESBEECHHHHTTBEETTEEHHHHHHHHHHHCSEEEEETTHHHHCCSTTSTTCTTCEECHHHHHTSCCEEECSSSCCHH
T ss_pred EEecCCccCCCceeeeecCchHHHHHHHhccCCCEEEEEecccccCCccccCCCCccccChhhhcCCceEEecCCCCCHH
Confidence 89999998632 388999999999999999999999999764 56778999999999 59999999999
Q ss_pred HHHHHHHHHHHHH----Hhcccccccc
Q psy5271 89 ALMYGILQLQKKV----KRMKILQSWY 111 (113)
Q Consensus 89 ~i~~~l~~l~~~i----~~~~~~~~~~ 111 (113)
+|+++|.+++.+- .+.++++.||
T Consensus 150 ~i~~~l~~ll~g~~p~ld~~~RP~~~~ 176 (261)
T d1frfs_ 150 NFVGAVVHVLTKGIPDLDENGRPKLFY 176 (261)
T ss_dssp HHHHHHHHHHTTCSCCBCTTSCBHHHH
T ss_pred HHHHHHHHHHhCCCccccccCCccccc
Confidence 9999999998753 2344454444
>d1yq9a1 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]}
Back Show information, alignment and structure
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=99.88 E-value=3.7e-24 Score=164.93 Aligned_cols=79 Identities=20% Similarity=0.318 Sum_probs=66.7
Q ss_pred EEeecCCCCch-----------HHHHHHHhcCCCeEEEeeccCCcCCCCCCC--CccccCCC----cccccceEecCCCC
Q psy5271 23 IEPGSTTCKAS-----------AVTTTSWMLEPRWVISMGSCANGGGYYHYS--YSVVRGCD----RIIPVDIYVPGCPP 85 (113)
Q Consensus 23 iVeG~v~~~~~-----------~~~~~~~~~~~k~vIA~GtCA~~GGi~~~~--~~~~~~v~----~~v~vdi~IpGCPP 85 (113)
+|||+|+++++ .+.+++++++||+|||+||||++|||++.. ++...+++ +..++|++||||||
T Consensus 68 vVEGsV~~~~~g~~~~~~~~~~~e~v~~lr~~ak~vVAvGtCA~~GGI~a~~~~~t~~~~~~~~~~~~~~~~i~IpGCPp 147 (261)
T d1yq9a1 68 VIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPP 147 (261)
T ss_dssp EEESBEECGGGSTTBEETTEEHHHHHHHHGGGSSEEEEEHHHHHHCCGGGSTTCTTCEECHHHHHGGGTCCCEEECSSSC
T ss_pred EeeccccCCCCcceeeccCchHHHHHHHHhhcCCEEEEecchhhcCCccccCCCccCcccccccccccCCCeEEeCCCCC
Confidence 89999988633 488999999999999999999999999764 44455554 44568899999999
Q ss_pred CHHHHHHHHHHHHHHH
Q psy5271 86 TAEALMYGILQLQKKV 101 (113)
Q Consensus 86 ~Pe~i~~~l~~l~~~i 101 (113)
||++|+++|.+++.+-
T Consensus 148 ~p~~i~~~l~~ll~g~ 163 (261)
T d1yq9a1 148 NPMNFVGTVVHLLTKG 163 (261)
T ss_dssp CHHHHHHHHHHHHHTC
T ss_pred CHHHHHHHHHHHHhCC
Confidence 9999999999998753
>d1cc1s_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfomicrobium baculatum [TaxId: 899]}
Back Show information, alignment and structure
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=99.86 E-value=3.4e-23 Score=160.59 Aligned_cols=79 Identities=16% Similarity=0.304 Sum_probs=66.9
Q ss_pred EEeecCCCCch---------------------HHHHHHHhcCCCeEEEeeccCCcCCCCCCCCc--cccCC------Ccc
Q psy5271 23 IEPGSTTCKAS---------------------AVTTTSWMLEPRWVISMGSCANGGGYYHYSYS--VVRGC------DRI 73 (113)
Q Consensus 23 iVeG~v~~~~~---------------------~~~~~~~~~~~k~vIA~GtCA~~GGi~~~~~~--~~~~v------~~~ 73 (113)
+|||+|+++++ ++.+++++++||+|||+||||++|||++..++ ...++ +++
T Consensus 70 lVEGsI~~~~~~~~~~~g~~~~~~~~~~~~~~~e~~~~l~~kak~vVAvGtCA~~GGI~a~~~n~t~~~~~~~~~~~~~~ 149 (278)
T d1cc1s_ 70 LVEGAIPTAKEGRYCIVGETLDAKAHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKI 149 (278)
T ss_dssp EEESBEECGGGGTTBEEEC---CCSSSCCEEHHHHHHHHGGGSSEEEEESHHHHHCTGGGSTTCCSCEECHHHHHHHHTC
T ss_pred EeccCcCCCccceeeeecccccccccccCccHHHHHHHHHhcCCEEEEEecccccCCcccccCCCccchhhheecCcCCc
Confidence 89999988732 48999999999999999999999999986543 33333 456
Q ss_pred cccceEecCCCCCHHHHHHHHHHHHHHH
Q psy5271 74 IPVDIYVPGCPPTAEALMYGILQLQKKV 101 (113)
Q Consensus 74 v~vdi~IpGCPP~Pe~i~~~l~~l~~~i 101 (113)
+++|++|||||||||+|+++|.+++...
T Consensus 150 ~~~~i~IpGCPp~pd~i~~tl~~~l~~~ 177 (278)
T d1cc1s_ 150 EKLLVNVPGCPPHPDWMVGTLVAAWSHV 177 (278)
T ss_dssp CCCEEEECCSSCCHHHHHHHHHHHHHHH
T ss_pred CCcccccCCCCCCHHHHHHHHHHHHHhh
Confidence 7899999999999999999999998754
