Query psy4032
Match_columns 84
No_of_seqs 114 out of 1081
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 23:39:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4032.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4032hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1687|consensus 100.0 2.2E-33 4.7E-38 194.2 6.0 81 3-84 88-168 (168)
2 COG0377 NuoB NADH:ubiquinone o 100.0 4.9E-33 1.1E-37 198.6 7.9 80 2-82 91-170 (194)
3 PRK14818 NADH dehydrogenase su 100.0 9.1E-31 2E-35 185.2 8.3 75 2-77 86-160 (173)
4 TIGR01957 nuoB_fam NADH-quinon 100.0 8.7E-30 1.9E-34 176.0 7.7 73 2-75 73-145 (145)
5 PRK06411 NADH dehydrogenase su 100.0 1.3E-29 2.9E-34 180.6 8.1 77 2-79 90-166 (183)
6 PRK14813 NADH dehydrogenase su 100.0 2.7E-29 5.8E-34 179.8 8.3 79 2-81 83-162 (189)
7 CHL00023 ndhK NADH dehydrogena 100.0 7.8E-29 1.7E-33 181.0 8.2 76 2-78 87-163 (225)
8 PRK14816 NADH dehydrogenase su 100.0 8.8E-29 1.9E-33 176.3 8.0 74 2-76 97-170 (182)
9 COG3260 Ni,Fe-hydrogenase III 100.0 1.1E-28 2.4E-33 169.9 7.4 75 2-77 65-139 (148)
10 PRK14817 NADH dehydrogenase su 100.0 1.5E-28 3.3E-33 175.0 8.2 74 3-78 92-165 (181)
11 PRK14815 NADH dehydrogenase su 100.0 2.2E-28 4.8E-33 174.3 8.3 76 2-79 89-164 (183)
12 PRK14814 NADH dehydrogenase su 99.9 8.3E-28 1.8E-32 171.8 8.1 76 2-79 89-164 (186)
13 PRK14820 NADH dehydrogenase su 99.9 9.8E-28 2.1E-32 170.7 8.2 76 2-79 89-164 (180)
14 PRK14819 NADH dehydrogenase su 99.9 1.2E-27 2.7E-32 177.6 7.9 81 2-83 87-168 (264)
15 PRK13292 trifunctional NADH de 99.9 8E-25 1.7E-29 181.2 8.2 74 2-77 78-151 (788)
16 PF01058 Oxidored_q6: NADH ubi 99.9 4.6E-24 1E-28 143.6 2.5 66 2-68 61-131 (131)
17 TIGR03294 FrhG coenzyme F420 h 99.9 8.9E-23 1.9E-27 148.4 6.1 71 3-74 67-146 (228)
18 PRK10468 hydrogenase 2 small s 99.8 5.9E-20 1.3E-24 142.3 6.4 81 3-84 137-226 (371)
19 TIGR00391 hydA hydrogenase (Ni 99.8 2.1E-19 4.5E-24 139.0 6.5 81 3-84 139-228 (365)
20 COG1941 FrhG Coenzyme F420-red 99.8 3.2E-19 6.8E-24 131.9 4.8 71 3-74 66-156 (247)
21 COG1740 HyaA Ni,Fe-hydrogenase 99.7 6.3E-17 1.4E-21 124.3 6.8 78 5-83 139-225 (355)
22 cd00069 GHB Glycoprotein hormo 58.7 5.4 0.00012 26.3 1.1 16 44-59 54-69 (102)
23 PF02495 7kD_coat: 7kD viral c 57.0 12 0.00026 21.7 2.3 13 49-61 36-48 (59)
24 smart00068 GHB Glycoprotein ho 54.2 7 0.00015 26.0 1.1 14 46-59 60-73 (107)
25 KOG1111|consensus 53.7 12 0.00026 30.2 2.5 38 37-75 302-339 (426)
26 PF11029 DAZAP2: DAZ associate 45.9 16 0.00034 25.3 1.8 12 52-63 99-110 (137)
27 PF12403 Pax2_C: Paired-box pr 35.7 17 0.00037 24.5 0.7 9 49-57 35-43 (115)
28 cd01977 Nitrogenase_VFe_alpha 35.2 43 0.00094 26.0 3.0 23 2-24 77-99 (415)
29 cd00886 MogA_MoaB MogA_MoaB fa 33.8 39 0.00085 22.6 2.2 24 49-72 125-148 (152)
30 PF03167 UDG: Uracil DNA glyco 33.4 29 0.00063 21.9 1.5 20 4-24 78-97 (152)
31 TIGR00412 redox_disulf_2 small 32.9 24 0.00051 20.8 1.0 25 46-71 2-26 (76)
32 PF10941 DUF2620: Protein of u 32.1 67 0.0014 21.8 3.1 45 18-66 47-92 (117)
33 COG4401 AroH Chorismate mutase 29.4 71 0.0015 21.7 2.9 24 56-79 15-38 (125)
34 PF05025 RbsD_FucU: RbsD / Fuc 27.6 60 0.0013 22.1 2.3 24 6-30 111-134 (142)
35 COG0694 Thioredoxin-like prote 27.6 75 0.0016 20.5 2.7 20 51-70 53-72 (93)
36 PF07723 LRR_2: Leucine Rich R 27.4 25 0.00055 17.2 0.4 7 49-55 20-26 (26)
37 PRK00941 acetyl-CoA decarbonyl 27.4 63 0.0014 28.2 2.9 19 46-64 504-522 (781)
38 TIGR03562 osmo_induc_OsmC pero 27.3 80 0.0017 21.1 2.9 21 44-64 25-50 (135)
39 PF04718 ATP-synt_G: Mitochond 25.9 62 0.0013 20.9 2.1 20 54-73 31-50 (103)
40 TIGR01284 alt_nitrog_alph nitr 25.4 76 0.0016 25.2 2.9 23 2-24 114-136 (457)
41 cd01413 SIR2_Af2 SIR2_Af2: Arc 24.7 81 0.0018 22.5 2.7 22 3-24 161-182 (222)
42 cd03026 AhpF_NTD_C TRX-GRX-lik 23.9 1.5E+02 0.0032 18.1 3.5 20 41-60 10-30 (89)
43 COG3325 ChiA Chitinase [Carboh 23.5 2.1E+02 0.0046 23.5 5.0 29 3-32 116-144 (441)
44 PF07796 DUF1638: Protein of u 23.4 95 0.002 21.1 2.7 22 3-24 17-40 (166)
45 PF02146 SIR2: Sir2 family; I 23.2 64 0.0014 22.0 1.9 21 3-23 153-173 (178)
46 PF05655 AvrD: Pseudomonas avi 22.9 56 0.0012 25.4 1.6 26 59-84 227-252 (311)
47 PRK15420 fucU L-fucose mutarot 22.5 77 0.0017 21.7 2.1 24 6-30 109-132 (140)
48 COG1573 Uracil-DNA glycosylase 22.2 40 0.00086 24.0 0.7 19 6-24 117-135 (202)
49 cd01410 SIRT7 SIRT7: Eukaryoti 22.2 1E+02 0.0022 21.9 2.8 21 4-24 146-166 (206)
50 PRK06214 sulfite reductase; Pr 22.1 84 0.0018 25.9 2.6 57 4-74 80-137 (530)
51 PRK02842 light-independent pro 21.9 91 0.002 24.4 2.7 23 2-24 86-108 (427)
52 PF10621 FpoO: F420H2 dehydrog 21.7 92 0.002 21.1 2.3 24 2-25 42-65 (119)
53 TIGR01721 AMN-like AMP nucleos 20.3 3.3E+02 0.0072 20.4 5.3 14 11-24 84-97 (266)
54 cd03063 TRX_Fd_FDH_beta TRX-li 20.2 43 0.00093 21.3 0.5 17 54-70 63-79 (92)
No 1
>KOG1687|consensus
Probab=100.00 E-value=2.2e-33 Score=194.23 Aligned_cols=81 Identities=74% Similarity=1.289 Sum_probs=79.7
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhcccccccc
Q psy4032 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQSWY 82 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~~~~~ 82 (84)
+|+++|||||+||+||++|+|| .+||.|+.||++++++|++||||+++|||||++|+++++|++|++||++.+..|.||
T Consensus 88 alrkvYdQMPEpr~VisMGsCa-ngGGyyhysYSvvRGcDriiPVDiYvPGCPPtaEAllygilqLqkKi~R~r~~q~wy 166 (168)
T KOG1687|consen 88 ALRKVYDQMPEPRWVISMGSCA-NGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALLYGILQLQKKIKRIRPLQFWY 166 (168)
T ss_pred HHHHHHhhCCCCeeEEEecccc-cCCceEEEEehhhccccceeeeeeecCCCCCCHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence 7999999999999999999999 899999999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q psy4032 83 RR 84 (84)
Q Consensus 83 ~~ 84 (84)
|+
T Consensus 167 r~ 168 (168)
T KOG1687|consen 167 RK 168 (168)
T ss_pred cC
Confidence 96
No 2
>COG0377 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]
Probab=100.00 E-value=4.9e-33 Score=198.57 Aligned_cols=80 Identities=50% Similarity=0.830 Sum_probs=74.5
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhccccccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQSW 81 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~~~~ 81 (84)
-+|+++|||||+||+|||+|+|| ++||+|+.||++++++|.+||||+|||||||+||+++++|+.|+++|+++.....|
T Consensus 91 p~lr~~YdQMPePK~VIsMGsCa-~~GG~f~~sYsvV~g~D~~vPVDvyIPGCPPrPEAl~~gi~~Lq~KI~~~~~~~~~ 169 (194)
T COG0377 91 PALRRVYDQMPEPKWVISMGSCA-NSGGMYWNSYSVVQGVDRVVPVDVYIPGCPPRPEALLYGILLLQEKIRREGRPLRD 169 (194)
T ss_pred HHHHHHHHhCCCCcEEEEecccc-cCCCcccccceeeeccceeEeeeeecCCCCCCHHHHHHHHHHHHHHHHhccCcccc
Confidence 37999999999999999999999 89999999999999999999999999999999999999999999999986555544
Q ss_pred c
Q psy4032 82 Y 82 (84)
Q Consensus 82 ~ 82 (84)
+
T Consensus 170 ~ 170 (194)
T COG0377 170 K 170 (194)
T ss_pred c
Confidence 4
No 3
>PRK14818 NADH dehydrogenase subunit B; Provisional
Probab=99.97 E-value=9.1e-31 Score=185.16 Aligned_cols=75 Identities=48% Similarity=0.834 Sum_probs=71.8
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKI 77 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~ 77 (84)
.+|+++|||||+||+|||+|+|| ++||+|+++|+..+++++++|||++||||||+||+|+++|+.|++++++++.
T Consensus 86 ~~l~~~yeqmPePK~VIA~G~CA-~sGGif~~sY~~~~gvd~vIpVDvyIPGCPP~PeaIl~gil~L~~~i~~~~~ 160 (173)
T PRK14818 86 ERARLLYDQMPEPKYVISMGSCS-NCGGLFQLGYSVCKGVDKVIPVDVYVPGCPPRPEALTEGLLRLQEIVRSEPW 160 (173)
T ss_pred HHHHHHHHhCCCCCEEEEecccc-ccCCcccCCcccccCCCCccCCcEEccCCCCCHHHHHHHHHHHHHHHhcccc
Confidence 57999999999999999999999 8999999999999999999999999999999999999999999999987643
No 4
>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit. 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.
Probab=99.96 E-value=8.7e-30 Score=176.01 Aligned_cols=73 Identities=58% Similarity=1.021 Sum_probs=70.1
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRM 75 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~ 75 (84)
.+|+++|||||+||+|||+|+|| ++||+|+++|+..+++++++|||++||||||+|++|+++|++|+++++++
T Consensus 73 ~~l~~~~e~~p~pk~VIA~GsCA-~~GGi~~~~y~~~~~v~~~ipVDi~IPGCPp~Pe~i~~~l~~l~~~~~~~ 145 (145)
T TIGR01957 73 PALRRLYDQMPEPKWVISMGACA-NSGGMFHTSYSVVQGVDRIVPVDVYIPGCPPRPEALIYGLIKLQKKIKRE 145 (145)
T ss_pred HHHHHHHHhccCCceEEEeccee-ecCCCccCCCccccCcccccccceEeCCCCCCHHHHHHHHHHHHHHhhcC
Confidence 57999999999999999999999 99999999999999999999999999999999999999999999999853
No 5
>PRK06411 NADH dehydrogenase subunit B; Validated
Probab=99.96 E-value=1.3e-29 Score=180.63 Aligned_cols=77 Identities=58% Similarity=1.010 Sum_probs=73.2
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhccccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQ 79 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~~ 79 (84)
.+|+++|||||+||+|||+|+|| ++||+|+++|+...++++++|||++||||||+|++|+++|++++++++++....
T Consensus 90 ~~l~~~~e~mp~pk~VIA~GaCA-~~GGif~~sy~~~~gv~~~ipVDv~IPGCPP~Pe~il~~l~~l~~~i~~~~~~~ 166 (183)
T PRK06411 90 PALRRLYDQMPEPKWVISMGSCA-NSGGMYHYSYSVVQGVDRIVPVDVYVPGCPPRPEALLYGILKLQKKIRQSERER 166 (183)
T ss_pred HHHHHHHHHcCcCCeEEEEeccc-ccCCcccCCCccccCcccccccceEeCCCCCCHHHHHHHHHHHHHHHhcccccc
Confidence 57999999999999999999999 999999999999999999999999999999999999999999999999876654
No 6
>PRK14813 NADH dehydrogenase subunit B; Provisional
Probab=99.96 E-value=2.7e-29 Score=179.75 Aligned_cols=79 Identities=46% Similarity=0.759 Sum_probs=72.0
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCC-CCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhcccccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYH-YSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQS 80 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~-~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~~~ 80 (84)
++|+++|+|||+||+|||+|+|| ++||+|. ++|+..+|++++||||++||||||+||+|+++|+.+++++++++....
T Consensus 83 ~~l~~~y~qmPePK~VIA~GaCA-~sGG~~~~~sY~~~~gvd~vIpVDv~IPGCPP~PeaIl~gl~~l~~~i~~~~~~~~ 161 (189)
T PRK14813 83 ERVVRLYEQMPEPRYVLSMGSCS-NCGGPYWEHGYHVLKGVDRIIPVDVYVPGCPPRPEALIGGLMKVQELIRMEQIGIS 161 (189)
T ss_pred HHHHHHHHhCCCCCEEEEecccc-cCCCCcccCCcccccCCCCccCCcEEccCCCCCHHHHHHHHHHHHHHHHhcccccc
Confidence 57999999999999999999999 7777765 599999999999999999999999999999999999999999876544
Q ss_pred c
Q psy4032 81 W 81 (84)
Q Consensus 81 ~ 81 (84)
|
T Consensus 162 ~ 162 (189)
T PRK14813 162 R 162 (189)
T ss_pred h
Confidence 4
No 7
>CHL00023 ndhK NADH dehydrogenase subunit K
Probab=99.95 E-value=7.8e-29 Score=181.03 Aligned_cols=76 Identities=43% Similarity=0.747 Sum_probs=71.7
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCC-CCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhcccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYH-YSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 78 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~-~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~ 78 (84)
.+|+++|||||+||+|||+|+|| ++||+|+ ++|++++|++++||||++||||||+||+|+++|+.|+++++++...
T Consensus 87 ~~L~rlyeqmPePK~VIA~GaCA-~sGGif~~dsy~~v~gvd~vIPVDv~IPGCPP~PeaIi~~l~~L~~ki~~~~~~ 163 (225)
T CHL00023 87 PSLVRLYEQMPEPKYVIAMGACT-ITGGMFSTDSYSTVRGVDKLIPVDVYLPGCPPKPEAVIDAITKLRKKISREIYE 163 (225)
T ss_pred HHHHHHHHhcCCCCeEEEEcccc-ccCCcccCCCcccccCccccceeeEEecCCCCCHHHHHHHHHHHHHHHhccccc
Confidence 47999999999999999999999 8999997 8999999999999999999999999999999999999999876543
No 8
>PRK14816 NADH dehydrogenase subunit B; Provisional
Probab=99.95 E-value=8.8e-29 Score=176.29 Aligned_cols=74 Identities=49% Similarity=0.877 Sum_probs=71.1
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhcc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMK 76 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~ 76 (84)
.+|+++|||||+||+|||+|+|| ++||+|+++|+...++++++|||++||||||+||+|+++|++|++++++++
T Consensus 97 ~~l~~~~e~~p~pK~VIAvGsCA-~~GGif~~sy~~~~gvd~vIpVDv~IPGCPP~Pe~Il~~l~~L~~ki~~~~ 170 (182)
T PRK14816 97 PVLKRLYDQMADPKYVIAVGGCA-VSGGPFKKSYHVLNGVDKILPVDVYIPGCPPRPEAFYYGMMQLQRKVKIEK 170 (182)
T ss_pred HHHHHHHHhcCCCCEEEEecccc-ccCCccccCCccCCCccccccccEEeeCcCCCHHHHHHHHHHHHHHhcccc
Confidence 58999999999999999999999 899999999999999999999999999999999999999999999998764
No 9
>COG3260 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]
Probab=99.95 E-value=1.1e-28 Score=169.88 Aligned_cols=75 Identities=36% Similarity=0.610 Sum_probs=71.0
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKI 77 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~ 77 (84)
|+|+++||+||+||+|||+|+|| ++||+|.++|.+..|+|+++|||++||||||+|++|+++|++++.++.+..+
T Consensus 65 e~lkk~Yea~PePKiViA~GaCa-~~GGIf~~~~~v~gpvd~viPVDv~IPGCPP~P~~il~g~~~al~~~~k~~~ 139 (148)
T COG3260 65 EPLKKAYEAMPEPKIVIAVGACA-LSGGIFKDSYSVWGPVDKVIPVDVEIPGCPPRPEAILAGLVAALGKLEKKIH 139 (148)
T ss_pred HHHHHHHHhCCCCcEEEEEcccc-cCCceecccccccccccceeEeeeEcCCCCCCHHHHHHHHHHHHHHHHHhhh
Confidence 68999999999999999999999 8999999999999999999999999999999999999999999988766443
No 10
>PRK14817 NADH dehydrogenase subunit B; Provisional
Probab=99.95 E-value=1.5e-28 Score=174.96 Aligned_cols=74 Identities=43% Similarity=0.807 Sum_probs=70.0
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhcccc
Q psy4032 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKIL 78 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~ 78 (84)
+|+++|||||+||+|||+|+|| ++||+| ++|++.+++++++|||++||||||+|++|+++|++|+++++++++.
T Consensus 92 ~l~~~~e~~p~pK~VIAvGaCA-~~GGi~-~~y~~~~gv~~vvpVDv~IPGCPP~Pe~il~~l~~l~~ki~~~~~~ 165 (181)
T PRK14817 92 ILQRVYEQMADPKWVMAFGVCA-SSGGFY-DNYATVQGIDRIIPVDVYVPGCPPRPEQVLDGIMLLQKKIQNQSHK 165 (181)
T ss_pred HHHHHHHHcccCCEEEEecccc-ccCCcC-CCcccccCccccceeeEEecCCCCCHHHHHHHHHHHHHHhhcCCcc
Confidence 5899999999999999999999 899988 7999999999999999999999999999999999999999876554
No 11
>PRK14815 NADH dehydrogenase subunit B; Provisional
Probab=99.95 E-value=2.2e-28 Score=174.32 Aligned_cols=76 Identities=43% Similarity=0.844 Sum_probs=71.5
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhccccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQ 79 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~~ 79 (84)
++|+++|||||+||+|||+|+|| ++||+|+ +|++.+|+++++|||++||||||+|++|+++|+.|++++++++..+
T Consensus 89 ~~l~r~ye~~p~pK~VIAvGsCA-~~GGi~~-sy~~~~gv~~~ipVDv~IPGCPP~Pe~il~~l~~l~~~i~~~~~~~ 164 (183)
T PRK14815 89 LAVRRIYDQMPEPKWVIAMGACA-SSGGMYR-SYSVLQGVDRILPVDVYISGCPPRPEAILDALIKLQKKIDTERAAR 164 (183)
T ss_pred HHHHHHHHhCCCCCEEEEecccc-ccCCCcc-ccccccCccccccccEEecCCCCCHHHHHHHHHHHHHHHhhccccc
Confidence 57999999999999999999999 8999995 8999999999999999999999999999999999999999876554
No 12
>PRK14814 NADH dehydrogenase subunit B; Provisional
Probab=99.95 E-value=8.3e-28 Score=171.78 Aligned_cols=76 Identities=42% Similarity=0.804 Sum_probs=71.2
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhccccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQ 79 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~~ 79 (84)
++|+++|||||+||+|||+|+|| ++||+|+ +|+...++++++|||++||||||+|++|+++|++|+++++++....
T Consensus 89 ~~l~~~yeqmp~pk~VIAvGsCA-~~GGi~~-~y~~~~gv~~vvpVDv~IPGCPP~Pe~il~~l~~L~~~i~~~~~~~ 164 (186)
T PRK14814 89 PVLRQIYDQMAEPKFVISVGACA-SSGGMFH-TYGVLQGVDRILPVDVYVPGCPPRPEAILDALVKLQTKLKTQGLEA 164 (186)
T ss_pred HHHHHHHHhcCCCCeEEEecccc-ccCCccC-cCCCCcCccccccccEEecCCCCCHHHHHHHHHHHHHHHhcccccc
Confidence 58999999999999999999999 9999996 7999999999999999999999999999999999999998865544
No 13
>PRK14820 NADH dehydrogenase subunit B; Provisional
Probab=99.95 E-value=9.8e-28 Score=170.70 Aligned_cols=76 Identities=39% Similarity=0.764 Sum_probs=71.2
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhccccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKILQ 79 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~~~ 79 (84)
.+|+++|||||+||+|||+|+|| ++||+| ++|+...++++++|||++||||||+|++|+++|+++++++++++..+
T Consensus 89 ~~l~~~~e~~p~pk~VIAvGaCA-~~GGi~-~~y~~~~~v~~~ipVDv~IPGCPP~Pe~il~~l~~l~~~i~~~~~~~ 164 (180)
T PRK14820 89 PVLKQVYLQMAEPRWVVAVGACA-SSGGIF-DTYSVLQGIDRIIPVDVYVPGCPPRPEQIIDGVMRVQELVKNESLRR 164 (180)
T ss_pred HHHHHHHHhcCCCCeEEEEeccc-ccCCcc-ccccccccccccccccEEecCCCCCHHHHHHHHHHHHHHHhhccccc
Confidence 47999999999999999999999 999999 68999999999999999999999999999999999999998875444
No 14
>PRK14819 NADH dehydrogenase subunit B; Provisional
Probab=99.94 E-value=1.2e-27 Score=177.62 Aligned_cols=81 Identities=43% Similarity=0.769 Sum_probs=73.3
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhcc-cccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMK-ILQS 80 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~-~~~~ 80 (84)
.+|+++|+|||+||+|||+|+|| ++||+|+++|+..++++++|+||++||||||+|++|+++|++|+++++..+ ..-.
T Consensus 87 ~~L~rlyeqmP~PK~VIAvGaCA-~~GGIf~~sY~v~~gId~vIPVDv~IPGCPP~Pe~Il~gLl~L~~ki~~d~~~Rp~ 165 (264)
T PRK14819 87 PQVVRLYNQMPEPRYVISMGACA-TSGGPFRDGYNVLRGIDLLIPVDVYIPGCPPRPEALLHALMTLQKQIDAQSLGRVR 165 (264)
T ss_pred HHHHHHHHhccCCCeEEEEcccc-ccCCccccCCCccCCccccccccEEecCCCCCHHHHHHHHHHHHhhcccccccCcc
Confidence 47899999999999999999999 999999999999999999999999999999999999999999999886543 1336
Q ss_pred ccc
Q psy4032 81 WYR 83 (84)
Q Consensus 81 ~~~ 83 (84)
||+
T Consensus 166 ~~~ 168 (264)
T PRK14819 166 WYG 168 (264)
T ss_pred ccc
Confidence 765
No 15
>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional
Probab=99.91 E-value=8e-25 Score=181.22 Aligned_cols=74 Identities=47% Similarity=0.871 Sum_probs=70.5
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhccc
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRMKI 77 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~~~ 77 (84)
.+|+++|||||+||+|||+|+|| ++||+| ++|+++.+++++||||++||||||+|++|+++|++|+++++.++.
T Consensus 78 ~~l~~~~~~~p~pk~via~G~Ca-~~GG~~-~~y~~~~g~~~~ipVDv~iPGCPP~Pe~i~~~i~~l~~~~~~~~~ 151 (788)
T PRK13292 78 PSILRLYEQMAEPKWVISMGSCA-NSGGMY-DVYSVVQGVNQILPVDVYIPGCPPRPEAFLQGLMLLQEKIRREER 151 (788)
T ss_pred HHHHHHHHhCCCCCEEEEecccc-cCCCCc-CccccccCcCCcccccEEccCCCCCHHHHHHHHHHHHHHhhcCcc
Confidence 57999999999999999999999 999999 799999999999999999999999999999999999999987664
No 16
>PF01058 Oxidored_q6: NADH ubiquinone oxidoreductase, 20 Kd subunit; InterPro: IPR006137 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 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 ....
Probab=99.89 E-value=4.6e-24 Score=143.59 Aligned_cols=66 Identities=32% Similarity=0.498 Sum_probs=53.4
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCCCCCCCCC--CCCcc---ccCcccccccceeccCCCCCHHHHHHHHHHH
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAPNGGGYYH--YSYSV---VRGCDRIIPVDIYVPGCPPTAEALMYGILQL 68 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~--~~~~~---~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l 68 (84)
..++.++++++++|+|||+|+|| ++||+++ .+++. +++++++++||++||||||+||+|+++|.+|
T Consensus 61 ~~~e~~~~~~~~a~~vIAvGtCA-~~GGi~~~~~~~~~~~~~~~~~~~~~VDi~IpGCPp~pd~i~~~l~~L 131 (131)
T PF01058_consen 61 EALEWLKELRPKAKAVIAVGTCA-SFGGIPAARNNPSVGDSVGPLLEVVPVDINIPGCPPHPDWILETLLAL 131 (131)
T ss_dssp EHHHHHHHHHGCSSEEEEEHHHH-HH-TGGGSTTSTTEEE-HHHHHGCS-ECEEE-SSS--HHHHHHHHHHH
T ss_pred HHHHHHHHHccCCceeEcCCCcc-ccCCcccccccccccccccCcCCCccEEEEeeCCCCCHHHHHHHHhhC
Confidence 46789999999999999999999 9999994 44443 4678889999999999999999999999876
No 17
>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma. 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.
Probab=99.87 E-value=8.9e-23 Score=148.42 Aligned_cols=71 Identities=24% Similarity=0.408 Sum_probs=63.0
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCc---------cccCcccccccceeccCCCCCHHHHHHHHHHHHHHHh
Q psy4032 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYS---------VVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVK 73 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~---------~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~ 73 (84)
.++++++++++||+|||+|||| ++||+|+.+++ ..+|++++|+||++||||||+|++|+++|.+++.+..
T Consensus 67 ~~~~~~~~~~~ak~vVA~GtCA-~~GGi~~~~~~~~~~~~~~~~~~~~~~~V~vdi~IpGCPp~p~~i~~~l~~ll~g~~ 145 (228)
T TIGR03294 67 SLEEIKELREKAKVVVALGACA-ATGNFTRYSRGGQQAQPQHESFVPITDVIDVDLAIPGCPPSPEAIRNVCVALLNGDM 145 (228)
T ss_pred HHHHHHHHhccCCEEEEeeccc-ccCCcccccCCcccCCCCCCCCcCHHHcccCCEEeeCCCCCHHHHHHHHHHHHcCCC
Confidence 6889999999999999999999 99999876543 4678899999999999999999999999999986544
Q ss_pred h
Q psy4032 74 R 74 (84)
Q Consensus 74 ~ 74 (84)
+
T Consensus 146 ~ 146 (228)
T TIGR03294 146 E 146 (228)
T ss_pred c
Confidence 3
No 18
>PRK10468 hydrogenase 2 small subunit; Provisional
Probab=99.80 E-value=5.9e-20 Score=142.26 Aligned_cols=81 Identities=21% Similarity=0.383 Sum_probs=70.8
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCcc--ccCcccccccc--eeccCCCCCHHHHHHHHHHHH-H----HHh
Q psy4032 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSV--VRGCDRIIPVD--IYVPGCPPTAEALMYGILQLQ-K----KVK 73 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~--~~~v~~~v~VD--~~IPGCPP~p~~i~~~l~~l~-~----~i~ 73 (84)
.++.++++++++|+|||+|||| ++|||++.+++. ..+++++++.+ ++||||||+|++|+.+|++++ . .++
T Consensus 137 ~~e~l~~~a~~A~aVVAvGtCA-s~GGI~aa~pnptga~gv~~~l~~~PVINIPGCPp~P~~i~~tL~~l~~~g~lp~LD 215 (371)
T PRK10468 137 IVDHIRKAAEGAAAIIAIGSCS-AWGGVAAAGVNPTGAVSLQEVLPGKTVINIPGCPPNPHNFLATVAHIITYGKPPKLD 215 (371)
T ss_pred HHHHHHHHhccCCEEEEEeccc-ccCCcccCCCCCCCCccHHHhcCCCCeEEcCCCCCCHHHHHHHHHHHHhcCCCcccc
Confidence 5788999999999999999999 999999886664 55788887554 999999999999999999998 2 489
Q ss_pred hcccccccccC
Q psy4032 74 RMKILQSWYRR 84 (84)
Q Consensus 74 ~~~~~~~~~~~ 84 (84)
+.+||+.||.+
T Consensus 216 ~~gRPk~fyg~ 226 (371)
T PRK10468 216 DKNRPTFAYGR 226 (371)
T ss_pred ccCCcHHHhcC
Confidence 99999999863
No 19
>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA). 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.
Probab=99.78 E-value=2.1e-19 Score=139.01 Aligned_cols=81 Identities=22% Similarity=0.317 Sum_probs=69.7
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCc--cccCccccc--ccceeccCCCCCHHHHHHHHHHHH-H----HHh
Q psy4032 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYS--VVRGCDRII--PVDIYVPGCPPTAEALMYGILQLQ-K----KVK 73 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~--~~~~v~~~v--~VD~~IPGCPP~p~~i~~~l~~l~-~----~i~ 73 (84)
.++.+.+.++++|+|||+|||| ++|||++..++ ...|+++++ +.+++||||||+|++|+.+|++++ . .++
T Consensus 139 ~~e~l~~~a~~A~aVIAvGtCA-s~GGI~aa~pnptga~~v~~vi~~~pvinIPGCPp~Pe~i~~tl~~~ll~G~lP~LD 217 (365)
T TIGR00391 139 IVEHIRKAAEGAAAIIAIGTCS-SWGGVQAAGPNPTGAVPLQKVIPDKPVINVPGCPPNPHNFLATVAYIITFGKLPKLD 217 (365)
T ss_pred HHHHHHHHhhcCCEEEEEeccc-cccCccCCCCCCCCCcchhHhcCCCCeEEeCCCCCCHHHHHHHHHHHHHcCCCCCCC
Confidence 5788999999999999999999 99999987655 456889888 334999999999999999999975 3 478
Q ss_pred hcccccccccC
Q psy4032 74 RMKILQSWYRR 84 (84)
Q Consensus 74 ~~~~~~~~~~~ 84 (84)
+++||..||.+
T Consensus 218 ~~~RP~~fyg~ 228 (365)
T TIGR00391 218 DKNRPTFAYGR 228 (365)
T ss_pred CCCCchhhhcC
Confidence 89999988863
No 20
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=99.77 E-value=3.2e-19 Score=131.86 Aligned_cols=71 Identities=25% Similarity=0.425 Sum_probs=61.8
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCCCCCC-----------CC---------ccccCcccccccceeccCCCCCHHHHH
Q psy4032 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYYHY-----------SY---------SVVRGCDRIIPVDIYVPGCPPTAEALM 62 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~-----------~~---------~~~~~v~~~v~VD~~IPGCPP~p~~i~ 62 (84)
-|+.+-|.+.++|+|||+|+|| ++||+.+. .| ..+.|++++|+||++||||||+|+.|.
T Consensus 66 ~lE~v~ElRekakivVA~GsCA-~~Ggv~~~~~~s~~e~l~~~y~~~~~~~~~~~v~Pl~evI~VD~~IpGCPP~~e~I~ 144 (247)
T COG1941 66 ELELVKELREKAKIVVALGSCA-VTGGVQGLRNKSGEELLRPVYGDAKSTFNEESVVPLGEVIDVDYAIPGCPPSPEEIA 144 (247)
T ss_pred HHHHHHHHHHhCcEEEEEecch-hcCCchhhhhccccccchhhhhcccCCCCccceEEchheeeeeeecCCCCcCHHHHH
Confidence 4677889999999999999999 89999642 13 357899999999999999999999999
Q ss_pred HHHHHHHHHHhh
Q psy4032 63 YGILQLQKKVKR 74 (84)
Q Consensus 63 ~~l~~l~~~i~~ 74 (84)
++|.+++++-++
T Consensus 145 ~al~all~ge~p 156 (247)
T COG1941 145 RALTALLEGEEP 156 (247)
T ss_pred HHHHHHHcCCCc
Confidence 999999876554
No 21
>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]
Probab=99.68 E-value=6.3e-17 Score=124.27 Aligned_cols=78 Identities=22% Similarity=0.406 Sum_probs=66.4
Q ss_pred HHHHHHhcCCCEEEEeccCCCCCCCCCCC--CCccccCcccccc--cceeccCCCCCHHHHHHHHHHHHHH-----Hhhc
Q psy4032 5 SLLAQAMLGPVGVISMGGAAPNGGGYYHY--SYSVVRGCDRIIP--VDIYVPGCPPTAEALMYGILQLQKK-----VKRM 75 (84)
Q Consensus 5 ~~~~e~~~~~k~vIA~G~CAv~~GGi~~~--~~~~~~~v~~~v~--VD~~IPGCPP~p~~i~~~l~~l~~~-----i~~~ 75 (84)
+.+-++...+++|||+|+|| ++|||++. +.+...+++++++ --++||||||+||+|+.+|.+++-. +++.
T Consensus 139 e~l~~aA~~A~aIiAvGtCA-s~GgI~AA~pnps~a~~i~ev~~~kpVINiPGCPp~pd~iv~tl~~~~~~gk~P~LD~~ 217 (355)
T COG1740 139 EILRKAAEGASAIIAVGTCA-SWGGIQAAKPNPTGAGPLSEVIKDKPVINIPGCPPNPDWIVATLLHIVTFGKLPDLDEL 217 (355)
T ss_pred HHHHHHhhcCceEEEEeccc-ccCCeeccCCCCCCcccceecccCCceeeCCCCCCCchhHHHHHHHHHHcCCCcchhhc
Confidence 44556788999999999999 99999976 4557788898873 2299999999999999999987754 8999
Q ss_pred cccccccc
Q psy4032 76 KILQSWYR 83 (84)
Q Consensus 76 ~~~~~~~~ 83 (84)
+||+-||.
T Consensus 218 ~RPk~fyg 225 (355)
T COG1740 218 GRPKMFYG 225 (355)
T ss_pred CCchhhhc
Confidence 99999985
No 22
>cd00069 GHB Glycoprotein hormone beta chain homologues. Gonadotropins; reproductive hormones consisting of two glycosylated chains (alpha and beta) of similar topology with Cysteine-knot motifs.
Probab=58.68 E-value=5.4 Score=26.30 Aligned_cols=16 Identities=31% Similarity=0.868 Sum_probs=11.5
Q ss_pred ccccceeccCCCCCHH
Q psy4032 44 IIPVDIYVPGCPPTAE 59 (84)
Q Consensus 44 ~v~VD~~IPGCPP~p~ 59 (84)
+.-..+.||||||+-+
T Consensus 54 ~~Y~tv~lpgCp~gvd 69 (102)
T cd00069 54 LSYETVRLPGCPPGVD 69 (102)
T ss_pred EEEEEEECCCCcCCCC
Confidence 3334589999999754
No 23
>PF02495 7kD_coat: 7kD viral coat protein; InterPro: IPR003411 This family consists of a 7 kDa coat protein from Carlavirus and Potexvirus [].
Probab=57.04 E-value=12 Score=21.73 Aligned_cols=13 Identities=31% Similarity=0.652 Sum_probs=11.0
Q ss_pred eeccCCCCCHHHH
Q psy4032 49 IYVPGCPPTAEAL 61 (84)
Q Consensus 49 ~~IPGCPP~p~~i 61 (84)
+.|.||+.+||-+
T Consensus 36 v~I~gC~~~~e~i 48 (59)
T PF02495_consen 36 VTISGCEFTPEFI 48 (59)
T ss_pred EEEECCCCCHHHH
Confidence 7899998888865
No 24
>smart00068 GHB Glycoprotein hormone beta chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=54.20 E-value=7 Score=25.99 Aligned_cols=14 Identities=36% Similarity=0.968 Sum_probs=10.8
Q ss_pred ccceeccCCCCCHH
Q psy4032 46 PVDIYVPGCPPTAE 59 (84)
Q Consensus 46 ~VD~~IPGCPP~p~ 59 (84)
-..+.||||||+-+
T Consensus 60 Y~tv~lpgCp~gvd 73 (107)
T smart00068 60 YETVRLPGCPPGVD 73 (107)
T ss_pred EEEEECCCccCCCC
Confidence 34589999999844
No 25
>KOG1111|consensus
Probab=53.65 E-value=12 Score=30.20 Aligned_cols=38 Identities=18% Similarity=0.338 Sum_probs=32.9
Q ss_pred cccCcccccccceeccCCCCCHHHHHHHHHHHHHHHhhc
Q psy4032 37 VVRGCDRIIPVDIYVPGCPPTAEALMYGILQLQKKVKRM 75 (84)
Q Consensus 37 ~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~~l~~~i~~~ 75 (84)
.++|+.+++|-| .+-=|.|.|+++.+++...+.+++..
T Consensus 302 rVGGIpeVLP~d-~i~~~~~~~~dl~~~v~~ai~~~~~~ 339 (426)
T KOG1111|consen 302 RVGGIPEVLPED-MITLGEPGPDDLVGAVEKAITKLRTL 339 (426)
T ss_pred ecCCccccCCcc-ceeccCCChHHHHHHHHHHHHHhccC
Confidence 578899999999 77789999999999999988877553
No 26
>PF11029 DAZAP2: DAZ associated protein 2 (DAZAP2); InterPro: IPR022730 DAZ associated protein 2 has a highly conserved sequence throughout evolution including a conserved polyproline region and several SH2/SH3 binding sites. It occurs as a single copy gene with a four-exon organisation and is located on chromosome 12. It encodes a ubiquitously expressed protein and binds to DAZ and DAZL1 through DAZ repeats [, ].
Probab=45.89 E-value=16 Score=25.35 Aligned_cols=12 Identities=58% Similarity=1.240 Sum_probs=10.3
Q ss_pred cCCCCCHHHHHH
Q psy4032 52 PGCPPTAEALMY 63 (84)
Q Consensus 52 PGCPP~p~~i~~ 63 (84)
|||+|++..+..
T Consensus 99 PGc~PnaAQlAA 110 (137)
T PF11029_consen 99 PGCPPNAAQLAA 110 (137)
T ss_pred CCCCCCHHHHHH
Confidence 799999999863
No 27
>PF12403 Pax2_C: Paired-box protein 2 C terminal; InterPro: IPR022130 This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with PF00292 from PFAM. This family is the C-terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.
Probab=35.68 E-value=17 Score=24.52 Aligned_cols=9 Identities=44% Similarity=1.032 Sum_probs=7.6
Q ss_pred eeccCCCCC
Q psy4032 49 IYVPGCPPT 57 (84)
Q Consensus 49 ~~IPGCPP~ 57 (84)
--|||||||
T Consensus 35 tTLPGYPPH 43 (115)
T PF12403_consen 35 TTLPGYPPH 43 (115)
T ss_pred cccCCCCCC
Confidence 459999998
No 28
>cd01977 Nitrogenase_VFe_alpha Nitrogenase_VFe_alpha -like: Nitrogenase VFe protein, alpha subunit like. This group contains proteins similar to the alpha subunits of, the VFe protein of the vanadium-dependent (V-) nitrogenase and the FeFe protein of the iron only (Fe-) nitrogenase Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V- and Fe- nitrogenases there is a molybdenum (Mo)-dependent nitrogenase which is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha sub
Probab=35.16 E-value=43 Score=26.01 Aligned_cols=23 Identities=0% Similarity=-0.166 Sum_probs=20.9
Q ss_pred hHHHHHHHHhcCCCEEEEeccCC
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAA 24 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CA 24 (84)
++++++.+..|+||++.-++||.
T Consensus 77 ~aI~~~~~~~p~p~~i~V~~tc~ 99 (415)
T cd01977 77 KNIIEAFKEFPDIKRMTVYTTCT 99 (415)
T ss_pred HHHHHHHHhCCCCcEEEEECCCc
Confidence 57888999888999999999999
No 29
>cd00886 MogA_MoaB MogA_MoaB family. 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.
Probab=33.76 E-value=39 Score=22.61 Aligned_cols=24 Identities=21% Similarity=0.343 Sum_probs=17.6
Q ss_pred eeccCCCCCHHHHHHHHHHHHHHH
Q psy4032 49 IYVPGCPPTAEALMYGILQLQKKV 72 (84)
Q Consensus 49 ~~IPGCPP~p~~i~~~l~~l~~~i 72 (84)
+.+||+|......+..++.+++.+
T Consensus 125 ~~LPG~P~aa~~~~~~v~P~l~~~ 148 (152)
T cd00886 125 FNLPGSPKAVREALEVILPELPHL 148 (152)
T ss_pred EECCCCHHHHHHHHHHHHHHHHHH
Confidence 899999997766666666555544
No 30
>PF03167 UDG: Uracil DNA glycosylase superfamily; InterPro: IPR005122 This entry represents various uracil-DNA glycosylases and related DNA glycosylases (3.2.2 from EC), such as uracil-DNA glycosylase [], thermophilic uracil-DNA glycosylase [], G:T/U mismatch-specific DNA glycosylase (Mug) [], and single-strand selective monofunctional uracil-DNA glycosylase (SMUG1) []. These proteins have a 3-layer alpha/beta/alpha structure. Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosylic bond, initiating the base excision repair pathway. Uracil in DNA can arise either through the deamination of cytosine to form mutagenic U:G mispairs, or through the incorporation of dUMP by DNA polymerase to form U:A pairs []. These aberrant uracil residues are genotoxic []. The sequence of uracil-DNA glycosylase is extremely well conserved [] in bacteria and eukaryotes as well as in herpes viruses. More distantly related uracil-DNA glycosylases are also found in poxviruses []. In eukaryotic cells, UNG activity is found in both the nucleus and the mitochondria. Human UNG1 protein is transported to both the mitochondria and the nucleus []. The N-terminal 77 amino acids of UNG1 seem to be required for mitochondrial localization, but the presence of a mitochondrial transit peptide has not been directly demonstrated. The most N-terminal conserved region contains an aspartic acid residue which has been proposed, based on X-ray structures [] to act as a general base in the catalytic mechanism. ; PDB: 1UI0_A 1UI1_A 2C2P_A 2C2Q_A 1MTL_B 1MWI_A 1MUG_A 1MWJ_A 1OKB_B 1OE6_A ....
Probab=33.42 E-value=29 Score=21.89 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=15.9
Q ss_pred HHHHHHHhcCCCEEEEeccCC
Q psy4032 4 VSLLAQAMLGPVGVISMGGAA 24 (84)
Q Consensus 4 l~~~~e~~~~~k~vIA~G~CA 24 (84)
|.+..+..+ |++||++|..|
T Consensus 78 l~~~l~~~~-p~iii~lG~~a 97 (152)
T PF03167_consen 78 LEEELEIIK-PKIIICLGKEA 97 (152)
T ss_dssp HHHHHHHHS-SSEEEEESHHH
T ss_pred HHHHHHhcC-CCEEEEEchHH
Confidence 455566666 99999999988
No 31
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=32.93 E-value=24 Score=20.84 Aligned_cols=25 Identities=16% Similarity=0.336 Sum_probs=16.2
Q ss_pred ccceeccCCCCCHHHHHHHHHHHHHH
Q psy4032 46 PVDIYVPGCPPTAEALMYGILQLQKK 71 (84)
Q Consensus 46 ~VD~~IPGCPP~p~~i~~~l~~l~~~ 71 (84)
.|+++-++|||-...- ..+..+++.
T Consensus 2 ~i~~~a~~C~~C~~~~-~~~~~~~~e 26 (76)
T TIGR00412 2 KIQIYGTGCANCQMTE-KNVKKAVEE 26 (76)
T ss_pred EEEEECCCCcCHHHHH-HHHHHHHHH
Confidence 3678899999986543 344444443
No 32
>PF10941 DUF2620: Protein of unknown function DUF2620; InterPro: IPR021238 This is a bacterial family of proteins with unknown function.
Probab=32.07 E-value=67 Score=21.75 Aligned_cols=45 Identities=20% Similarity=0.395 Sum_probs=26.4
Q ss_pred EEeccCCCCCCCC-CCCCCccccCcccccccceeccCCCCCHHHHHHHHH
Q psy4032 18 ISMGGAAPNGGGY-YHYSYSVVRGCDRIIPVDIYVPGCPPTAEALMYGIL 66 (84)
Q Consensus 18 IA~G~CAv~~GGi-~~~~~~~~~~v~~~v~VD~~IPGCPP~p~~i~~~l~ 66 (84)
.=+|+|. ++||= .+-.. ..-+-++ -..+..||=+|++|+|...+.
T Consensus 47 YY~GACn-TGgGgALamAI-allG~~~--C~Tvs~pg~~~~eeeI~~~v~ 92 (117)
T PF10941_consen 47 YYLGACN-TGGGGALAMAI-ALLGYGK--CATVSMPGKIPSEEEIRKEVA 92 (117)
T ss_pred EeEeecC-CCccHHHHHHH-HHhCccc--eeEeecCCCCCCHHHHHHHHH
Confidence 3479999 77662 11000 0011122 245789999999999976553
No 33
>COG4401 AroH Chorismate mutase [Amino acid transport and metabolism]
Probab=29.43 E-value=71 Score=21.75 Aligned_cols=24 Identities=17% Similarity=0.271 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHHHHHHHhhccccc
Q psy4032 56 PTAEALMYGILQLQKKVKRMKILQ 79 (84)
Q Consensus 56 P~p~~i~~~l~~l~~~i~~~~~~~ 79 (84)
.++|+|+++...|++.|.++++.+
T Consensus 15 nt~eeI~~at~eLl~~i~~~N~~~ 38 (125)
T COG4401 15 NTEEEILDATKELLEEIEEENITD 38 (125)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCC
Confidence 478999999999999999888654
No 34
>PF05025 RbsD_FucU: RbsD / FucU transport protein family; InterPro: IPR007721 RbsD is a component of the ribose operon. It was originally thought to be a high affinity ribose transport protein, but further analysis [] shows that it is a D-ribose pyranase 5.5.1.n1 from EC. It catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. It also catalyzes the conversion between beta-allofuranose and beta-allopyranose. FucU is a component of the fucose operon and is a L-fucose mutarotase 5.1.3.n2 from EC, involved in the anomeric conversion of L-fucose. It also exhibits a pyranase activity for D-ribose []. Both have been classified in the RbsD/FucU family of proteins. Members of this family are ubiquitous having been found in organisms from eubacteria to mammals.; GO: 0016853 isomerase activity, 0048029 monosaccharide binding, 0005996 monosaccharide metabolic process; PDB: 2WCV_B 3E7N_N 4A34_I 1OGF_B 1OGE_A 1OGC_A 1OGD_E 3P12_C 3P13_A 3MVK_E ....
Probab=27.64 E-value=60 Score=22.07 Aligned_cols=24 Identities=8% Similarity=0.021 Sum_probs=17.2
Q ss_pred HHHHHhcCCCEEEEeccCCCCCCCC
Q psy4032 6 LLAQAMLGPVGVISMGGAAPNGGGY 30 (84)
Q Consensus 6 ~~~e~~~~~k~vIA~G~CAv~~GGi 30 (84)
..|++..+++.+|.-|.|+ -+|-+
T Consensus 111 ~Fy~~~~~a~~vVrTGE~~-pYaNi 134 (142)
T PF05025_consen 111 EFYERAKKAKAVVRTGETT-PYANI 134 (142)
T ss_dssp HHHHHHHTSSEEEEES--S-TT--E
T ss_pred HHHHHHhccEEEEEeCCCC-ceeEE
Confidence 4689999999999999999 56643
No 35
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=27.64 E-value=75 Score=20.47 Aligned_cols=20 Identities=35% Similarity=0.630 Sum_probs=17.0
Q ss_pred ccCCCCCHHHHHHHHHHHHH
Q psy4032 51 VPGCPPTAEALMYGILQLQK 70 (84)
Q Consensus 51 IPGCPP~p~~i~~~l~~l~~ 70 (84)
=.|||.++-.+.++|-+.+.
T Consensus 53 C~gC~sS~~TLk~gIE~~L~ 72 (93)
T COG0694 53 CSGCPSSTVTLKNGIERQLK 72 (93)
T ss_pred CCCCcccHHHHHHHHHHHHH
Confidence 37999999999999987664
No 36
>PF07723 LRR_2: Leucine Rich Repeat; InterPro: IPR013101 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by IPR001611 from INTERPRO [, ].
Probab=27.43 E-value=25 Score=17.20 Aligned_cols=7 Identities=43% Similarity=1.213 Sum_probs=5.3
Q ss_pred eeccCCC
Q psy4032 49 IYVPGCP 55 (84)
Q Consensus 49 ~~IPGCP 55 (84)
-.|.|||
T Consensus 20 ~LlS~CP 26 (26)
T PF07723_consen 20 RLLSGCP 26 (26)
T ss_pred HhhccCc
Confidence 4678888
No 37
>PRK00941 acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated
Probab=27.36 E-value=63 Score=28.19 Aligned_cols=19 Identities=21% Similarity=0.181 Sum_probs=14.0
Q ss_pred ccceeccCCCCCHHHHHHH
Q psy4032 46 PVDIYVPGCPPTAEALMYG 64 (84)
Q Consensus 46 ~VD~~IPGCPP~p~~i~~~ 64 (84)
|=-+++|||+++|+.+.++
T Consensus 504 PG~~af~GCa~~P~~~e~v 522 (781)
T PRK00941 504 PGVIAFVGCSNYPNGTKEV 522 (781)
T ss_pred CCeEEEeCCCCCcchHHHH
Confidence 3349999999999655433
No 38
>TIGR03562 osmo_induc_OsmC peroxiredoxin, OsmC subfamily. Pfam model pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein OsmC, or osmotically induced protein C. The member from Thermus thermophilus was shown to have hydroperoxide peroxidase activity. In many species, this protein is induced by stress and helps resist oxidative stress.
Probab=27.26 E-value=80 Score=21.08 Aligned_cols=21 Identities=14% Similarity=0.127 Sum_probs=15.6
Q ss_pred ccccceecc-----CCCCCHHHHHHH
Q psy4032 44 IIPVDIYVP-----GCPPTAEALMYG 64 (84)
Q Consensus 44 ~v~VD~~IP-----GCPP~p~~i~~~ 64 (84)
++.+++.+| +.=|+|++++-+
T Consensus 25 ~~~~~~s~p~~~~~~~G~nPeeLLla 50 (135)
T TIGR03562 25 LSETPYSFKTRFEDGPGTNPEELIAA 50 (135)
T ss_pred eeccccccCcccCCCCCCCHHHHHHH
Confidence 337888888 555999998743
No 39
>PF04718 ATP-synt_G: Mitochondrial ATP synthase g subunit; InterPro: IPR006808 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents the G subunit found in the F0 complex of F-ATPases in mitochondria. The function of subunit G is currently unknown. There is no counterpart in chloroplast or bacterial F-ATPases identified so far []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
Probab=25.89 E-value=62 Score=20.90 Aligned_cols=20 Identities=40% Similarity=0.434 Sum_probs=16.3
Q ss_pred CCCCHHHHHHHHHHHHHHHh
Q psy4032 54 CPPTAEALMYGILQLQKKVK 73 (84)
Q Consensus 54 CPP~p~~i~~~l~~l~~~i~ 73 (84)
=||+|+++-+....+...++
T Consensus 31 ~PPt~~~~~~~~~~l~~~~~ 50 (103)
T PF04718_consen 31 APPTPAEFQSVYQQLFKTVK 50 (103)
T ss_pred CCcCHHHHHHHHHHHHHHHH
Confidence 38999999888888877666
No 40
>TIGR01284 alt_nitrog_alph nitrogenase alpha chain. This model represents the alpha chains of various forms of the nitrogen-fixing enzyme nitrogenase: vanadium-iron, iron-iron, and molybdenum-iron. Most examples of NifD, the molybdenum-iron type nitrogenase alpha chain, are excluded from this model and described instead by equivalog model TIGR01282. It appears by phylogenetic and UPGMA trees that this model represents a distinct clade of NifD homologs, in which arose several molybdenum-independent forms.
Probab=25.39 E-value=76 Score=25.25 Aligned_cols=23 Identities=0% Similarity=-0.165 Sum_probs=20.1
Q ss_pred hHHHHHHHHhcCCCEEEEeccCC
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAA 24 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CA 24 (84)
.+++++.+..|+|+.+.-+++|.
T Consensus 114 ~aI~e~~~~~p~p~~I~V~stC~ 136 (457)
T TIGR01284 114 RCILEAFREFPEIKRMYTYATCT 136 (457)
T ss_pred HHHHHHHHhCCCCceEEEECCCh
Confidence 46788888888999999999999
No 41
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=24.66 E-value=81 Score=22.54 Aligned_cols=22 Identities=14% Similarity=-0.017 Sum_probs=19.3
Q ss_pred HHHHHHHHhcCCCEEEEeccCC
Q psy4032 3 GVSLLAQAMLGPVGVISMGGAA 24 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~CA 24 (84)
.++++.+++.++..++.+||-.
T Consensus 161 ~~~~a~~~~~~~Dl~lvvGTSl 182 (222)
T cd01413 161 LLREAIEAAKEADLFIVLGSSL 182 (222)
T ss_pred HHHHHHHHHhcCCEEEEEccCC
Confidence 4678899999999999999875
No 42
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=23.85 E-value=1.5e+02 Score=18.11 Aligned_cols=20 Identities=20% Similarity=0.398 Sum_probs=13.9
Q ss_pred cccccccceec-cCCCCCHHH
Q psy4032 41 CDRIIPVDIYV-PGCPPTAEA 60 (84)
Q Consensus 41 v~~~v~VD~~I-PGCPP~p~~ 60 (84)
+.+-|.+.+++ |+||+-|+.
T Consensus 10 l~~pv~i~~F~~~~C~~C~~~ 30 (89)
T cd03026 10 LNGPINFETYVSLSCHNCPDV 30 (89)
T ss_pred cCCCEEEEEEECCCCCCcHHH
Confidence 44555666666 999999864
No 43
>COG3325 ChiA Chitinase [Carbohydrate transport and metabolism]
Probab=23.53 E-value=2.1e+02 Score=23.47 Aligned_cols=29 Identities=24% Similarity=0.376 Sum_probs=24.6
Q ss_pred HHHHHHHHhcCCCEEEEeccCCCCCCCCCC
Q psy4032 3 GVSLLAQAMLGPVGVISMGGAAPNGGGYYH 32 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~CAv~~GGi~~ 32 (84)
+|..+-++-|+.|++|++|.=+ -+||++.
T Consensus 116 ~L~~lk~~~~d~k~l~SIGGWs-~S~~F~~ 144 (441)
T COG3325 116 ALFDLKATYPDLKTLISIGGWS-DSGGFSD 144 (441)
T ss_pred HHHHHhhhCCCceEEEeecccc-cCCCcch
Confidence 5677777888889999999999 8999863
No 44
>PF07796 DUF1638: Protein of unknown function (DUF1638); InterPro: IPR012437 This entry contains sequences covering an approximately 270 amino acid stretch of a group of hypothetical proteins and are confined to Bacteria and Archaea.
Probab=23.38 E-value=95 Score=21.08 Aligned_cols=22 Identities=5% Similarity=-0.227 Sum_probs=18.2
Q ss_pred HHHHHHHHhc--CCCEEEEeccCC
Q psy4032 3 GVSLLAQAML--GPVGVISMGGAA 24 (84)
Q Consensus 3 ~l~~~~e~~~--~~k~vIA~G~CA 24 (84)
.|.+..+++. .-+++++.|.|-
T Consensus 17 ~lq~~id~~~~~~d~Ill~YG~Cg 40 (166)
T PF07796_consen 17 ELQEEIDKASKDYDGILLFYGLCG 40 (166)
T ss_pred HHHHHHHHhhccCCeEEEEEeCCC
Confidence 4667777776 688999999999
No 45
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=23.23 E-value=64 Score=21.96 Aligned_cols=21 Identities=5% Similarity=0.011 Sum_probs=16.6
Q ss_pred HHHHHHHHhcCCCEEEEeccC
Q psy4032 3 GVSLLAQAMLGPVGVISMGGA 23 (84)
Q Consensus 3 ~l~~~~e~~~~~k~vIA~G~C 23 (84)
.+.++.+.+.++.++|.+||-
T Consensus 153 ~~~~~~~~~~~~Dl~lviGTS 173 (178)
T PF02146_consen 153 EIEEAIEDAEEADLLLVIGTS 173 (178)
T ss_dssp HHHHHHHHHHH-SEEEEESS-
T ss_pred HHHHHHHHHHcCCEEEEEccC
Confidence 467788899999999999974
No 46
>PF05655 AvrD: Pseudomonas avirulence D protein (AvrD); InterPro: IPR008799 This family consists of several avirulence D (AvrD) proteins primarily found in Pseudomonas syringae [].
Probab=22.90 E-value=56 Score=25.39 Aligned_cols=26 Identities=19% Similarity=0.218 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHhhcccccccccC
Q psy4032 59 EALMYGILQLQKKVKRMKILQSWYRR 84 (84)
Q Consensus 59 ~~i~~~l~~l~~~i~~~~~~~~~~~~ 84 (84)
.++.++|+.-+++|.+++....|-|+
T Consensus 227 aQl~Q~L~Y~lD~i~Re~SnTLWMRk 252 (311)
T PF05655_consen 227 AQLGQVLLYRLDGIPREESNTLWMRK 252 (311)
T ss_pred HHHHHHHHHHhcCCCcccCcchhhee
Confidence 68889999999999999999999885
No 47
>PRK15420 fucU L-fucose mutarotase; Provisional
Probab=22.53 E-value=77 Score=21.67 Aligned_cols=24 Identities=13% Similarity=0.164 Sum_probs=20.0
Q ss_pred HHHHHhcCCCEEEEeccCCCCCCCC
Q psy4032 6 LLAQAMLGPVGVISMGGAAPNGGGY 30 (84)
Q Consensus 6 ~~~e~~~~~k~vIA~G~CAv~~GGi 30 (84)
..|++..+++.+|.-|-|+ -||-+
T Consensus 109 ~Fy~~~~~a~avIrTGE~~-pYaNi 132 (140)
T PRK15420 109 AFYERAQKAFAIVITGERA-KYGNI 132 (140)
T ss_pred HHHHHHhcCeEEEEcCCCC-ceeEE
Confidence 4588899999999999999 66643
No 48
>COG1573 Uracil-DNA glycosylase [DNA replication, recombination, and repair]
Probab=22.19 E-value=40 Score=23.96 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=15.7
Q ss_pred HHHHHhcCCCEEEEeccCC
Q psy4032 6 LLAQAMLGPVGVISMGGAA 24 (84)
Q Consensus 6 ~~~e~~~~~k~vIA~G~CA 24 (84)
..--+|.++|++|++|.-|
T Consensus 117 ~~~i~l~~pkviv~LG~~A 135 (202)
T COG1573 117 EAEIALIRPKVILLLGEYA 135 (202)
T ss_pred HHHHhcCCCCEEEEcCHHH
Confidence 3445678999999999998
No 49
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=22.16 E-value=1e+02 Score=21.91 Aligned_cols=21 Identities=14% Similarity=-0.061 Sum_probs=18.8
Q ss_pred HHHHHHHhcCCCEEEEeccCC
Q psy4032 4 VSLLAQAMLGPVGVISMGGAA 24 (84)
Q Consensus 4 l~~~~e~~~~~k~vIA~G~CA 24 (84)
+.++++.+.++..+|.+||-.
T Consensus 146 ~~~a~~~~~~aDlllviGTSl 166 (206)
T cd01410 146 WMGAAAAACRADLFLCLGTSL 166 (206)
T ss_pred HHHHHHHHhcCCEEEEECcCc
Confidence 678899999999999999875
No 50
>PRK06214 sulfite reductase; Provisional
Probab=22.12 E-value=84 Score=25.88 Aligned_cols=57 Identities=16% Similarity=0.170 Sum_probs=38.9
Q ss_pred HHHHHHHhcCCCEEEEeccCCCCCCCCCCCCCccccCccccccc-ceeccCCCCCHHHHHHHHHHHHHHHhh
Q psy4032 4 VSLLAQAMLGPVGVISMGGAAPNGGGYYHYSYSVVRGCDRIIPV-DIYVPGCPPTAEALMYGILQLQKKVKR 74 (84)
Q Consensus 4 l~~~~e~~~~~k~vIA~G~CAv~~GGi~~~~~~~~~~v~~~v~V-D~~IPGCPP~p~~i~~~l~~l~~~i~~ 74 (84)
.+++.+.+|+.. +|.|. - | -..|. ..++.= +..+-.|||--++....|.+|++.+..
T Consensus 80 ~~~~~~~lp~~~----Cg~CG-y-~---C~~~a-----~a~~~~~~~~~~~C~~gg~~~~~~~~~~~~~~~~ 137 (530)
T PRK06214 80 PRKLMAAMAQQD----CGQCG-Y-N---CQDYA-----EAIASGEEKRLNLCAPGGKETARMLKKLAEEFGA 137 (530)
T ss_pred HHHHHHhCCCCC----cccCC-C-C---CHHHH-----HHHhCCCCCCCCCCCCCCHHHHHHHHHHHHhhcc
Confidence 467788888876 67777 2 2 11221 122322 256678999999999999999998654
No 51
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=21.92 E-value=91 Score=24.42 Aligned_cols=23 Identities=13% Similarity=-0.005 Sum_probs=19.1
Q ss_pred hHHHHHHHHhcCCCEEEEeccCC
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAA 24 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CA 24 (84)
.+++++.++.++|++++-+.||.
T Consensus 86 ~ai~ei~~~~~~P~~I~V~tTC~ 108 (427)
T PRK02842 86 RVVEELIKRRPNISVLFLVGSCP 108 (427)
T ss_pred HHHHHHHhccCCCCEEEEECCCh
Confidence 35667677778999999999999
No 52
>PF10621 FpoO: F420H2 dehydrogenase subunit FpoO ; InterPro: IPR018288 This entry represents the FpoO subunit of membrane-bound multi-subunit F420H2 dehydrogenase, which oxidises the reduced coenzyme F420H2 to coenzyme F420 and feeds the electrons via an FeS cluster into an energy-conserving electron transport chain [, ]. This enzyme plays a role in the methanogenic pathway in methanogenic archaea. Reduced coenzyme F420H2 is the major cytoplasmic electron carrier of methanogens and a reversible hydride donor, much like NADH []. F420H2 + COB-S-S-CoM = F420 + CoM-SH + CoB-SH Where CoB-S-S-CoM (the heterosulphide of 2-mercaptoethanesulphonate and 7-mercaptoheptanoylthreonine phosphate) is the terminal electron acceptor of the methanogenic pathway, and is reduced with the concomitant generation of a transmembrane proton potential and ATP synthesis. The FpoO subunit of F420H2 dehydrogenase probably participates in the reduction of methanophenazine, where it acts as a special mechanism for the reduction of the methanogenic cofactor [].
Probab=21.74 E-value=92 Score=21.10 Aligned_cols=24 Identities=8% Similarity=-0.137 Sum_probs=20.5
Q ss_pred hHHHHHHHHhcCCCEEEEeccCCC
Q psy4032 2 MGVSLLAQAMLGPVGVISMGGAAP 25 (84)
Q Consensus 2 ~~l~~~~e~~~~~k~vIA~G~CAv 25 (84)
...+.+|++..+.+.-...|.|..
T Consensus 42 ~sa~~ty~e~~~~~~s~~~gKC~L 65 (119)
T PF10621_consen 42 DSAEKTYQEVNENESSCRSGKCDL 65 (119)
T ss_pred HHHHHHHHHHhcccccccccceec
Confidence 356789999999998899999993
No 53
>TIGR01721 AMN-like AMP nucleosidase, putative. The sequences in the clade represented by this model are most closely related to the AMP nucleosidase found in TIGR01717. These sequences are found only in Chlamydia and Porphyromonas and differ sufficiently from the characterized AMP nucleosidase to put some doubt on assignment of this name.
Probab=20.32 E-value=3.3e+02 Score=20.44 Aligned_cols=14 Identities=21% Similarity=0.361 Sum_probs=12.6
Q ss_pred hcCCCEEEEeccCC
Q psy4032 11 MLGPVGVISMGGAA 24 (84)
Q Consensus 11 ~~~~k~vIA~G~CA 24 (84)
+-++|.+|-+|+|.
T Consensus 84 ~~G~k~iIriGtcG 97 (266)
T TIGR01721 84 LPHPKAAIMLGMCG 97 (266)
T ss_pred hcCCCEEEEEEecc
Confidence 45899999999998
No 54
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=20.25 E-value=43 Score=21.34 Aligned_cols=17 Identities=12% Similarity=-0.134 Sum_probs=12.9
Q ss_pred CCCCHHHHHHHHHHHHH
Q psy4032 54 CPPTAEALMYGILQLQK 70 (84)
Q Consensus 54 CPP~p~~i~~~l~~l~~ 70 (84)
+..+|+++-+.+.+.+.
T Consensus 63 ~~V~~edv~~Iv~~~~~ 79 (92)
T cd03063 63 GPVTPADVASLLDAGAL 79 (92)
T ss_pred EeCCHHHHHHHHHHHhh
Confidence 78899998877776554
Done!