Query 033164
Match_columns 126
No_of_seqs 51 out of 53
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 10:36:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033164.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033164hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00053 photosystem II subuni 100.0 8.8E-57 1.9E-61 334.7 9.1 103 24-126 1-117 (117)
2 PF04725 PsbR: Photosystem II 100.0 1.8E-50 3.9E-55 294.2 7.5 87 40-126 1-99 (99)
3 PLN00083 photosystem II subuni 100.0 5.9E-35 1.3E-39 213.3 6.5 83 39-124 3-101 (101)
4 PF11088 RL11D: Glycoprotein e 61.8 5.1 0.00011 29.9 1.5 26 69-94 69-94 (98)
5 COG4059 MtrE Tetrahydromethano 42.7 9.2 0.0002 33.0 0.3 43 75-120 224-280 (304)
6 PF13163 DUF3999: Protein of u 30.9 29 0.00064 30.0 1.5 22 97-118 406-427 (429)
7 PF13179 DUF4006: Family of un 26.9 62 0.0013 22.5 2.3 20 96-115 12-31 (66)
8 CHL00114 psbX photosystem II p 22.8 1E+02 0.0023 19.7 2.6 21 101-121 12-32 (39)
9 PF06195 DUF996: Protein of un 19.9 46 0.00099 25.0 0.6 23 96-118 112-134 (139)
10 COG4982 3-oxoacyl-[acyl-carrie 16.1 1.2E+02 0.0026 29.9 2.5 31 95-126 403-433 (866)
No 1
>PLN00053 photosystem II subunit R; Provisional
Probab=100.00 E-value=8.8e-57 Score=334.66 Aligned_cols=103 Identities=82% Similarity=1.338 Sum_probs=100.8
Q ss_pred ccCCCCCcc--ceeEEeecCc-eeecccccccCCCcccCCCcCCCCCCccCCeeEEecccccccccCCC-----------
Q 033164 24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYS----------- 89 (126)
Q Consensus 24 ~rglp~l~R--~~~~v~asgg-Kikt~kp~G~~ggm~~k~gvDasGRkgKg~gVYqf~~kyGANVDgYS----------- 89 (126)
+||||+++| ++|+|+||++ ||||++|||++|+|++|+|+||+|||+||||||||+|||||||||||
T Consensus 1 ~~glp~l~r~~ss~~v~as~~kkikt~~p~G~~G~m~~k~gvDasGRk~kGkGVYqFvdKYGANVDgYSPIY~~~ews~~ 80 (117)
T PLN00053 1 VRGLPPLSRTARSFKVTASGGKKIKTDQPYGPSGGMNLKDGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWSPS 80 (117)
T ss_pred CCccCcccccccceEEEecCCceeeecCCcccCCCcccccccCCCCccCCCcceEEehhhcCccccccCCCcChhhcCCC
Confidence 589999999 6899999988 89999999999999999999999999999999999999999999999
Q ss_pred CceeccchhHHHHHHHHHHHHhhhceeeeeecccccC
Q 033164 90 GDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ 126 (126)
Q Consensus 90 GD~Y~gG~~gL~~wA~tl~glL~~GallVy~TSaLa~ 126 (126)
||+|+|||+||+|||+||+|||++|||||||||||+|
T Consensus 81 Gd~Y~ggttgL~~wa~~l~gll~~gallvynTSaLa~ 117 (117)
T PLN00053 81 GDVYVGGTTGLLIWAVTLAGLLAGGALLVYNTSALAQ 117 (117)
T ss_pred CCeeeCChhhHHHHHHHHHHHHcccceeEEehhhhcC
Confidence 9999999999999999999999999999999999997
No 2
>PF04725 PsbR: Photosystem II 10 kDa polypeptide PsbR; InterPro: IPR006814 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight intrinsic protein PsbR found in PSII, which is also known as the 10 kDa polypeptide. The PsbR gene is found only in the nucleus of green algae and higher plants. PsbR may provide a binding site for the extrinsic oxygen-evolving complex protein PsbP to the thylakoid membrane. PsbR has a transmembrane domain to anchor it to the thylakoid membrane, and a charged N-terminal domain capable of forming ion bridges with extrinsic proteins, allowing PsbR to act as a docking protein. PsbR may be a pH-dependent stabilising protein that functions at both donor and acceptor sides of PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0042651 thylakoid membrane
Probab=100.00 E-value=1.8e-50 Score=294.18 Aligned_cols=87 Identities=86% Similarity=1.388 Sum_probs=85.1
Q ss_pred cCc-eeecccccccCCCcccCCCcCCCCCCccCCeeEEecccccccccCCC-----------CceeccchhHHHHHHHHH
Q 033164 40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYS-----------GDVYTGGATGLAIWAVTL 107 (126)
Q Consensus 40 sgg-Kikt~kp~G~~ggm~~k~gvDasGRkgKg~gVYqf~~kyGANVDgYS-----------GD~Y~gG~~gL~~wA~tl 107 (126)
|++ ||||++|||++|+|++|+|+||+|||+||+|||||+||||||||||| ||+|+|||+||+|||+||
T Consensus 1 Sg~KKIkt~~p~G~~g~m~~k~gvDa~gRkgKg~gVYqf~~KyGANVDgYSPIY~p~~Ws~~GD~Y~gGt~gL~~WA~~l 80 (99)
T PF04725_consen 1 SGGKKIKTDKPYGPSGGMTLKDGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWSPSGDVYVGGTTGLLIWAVTL 80 (99)
T ss_pred CCCccccccCCccCCCCccccCCccCCCCCCCCceeEEehhhcCccccccCCCcChhhcCCCCCeecCChhhHHHHHHHH
Confidence 455 99999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred HHHhhhceeeeeecccccC
Q 033164 108 AGLLAGGALLVYNTSALAQ 126 (126)
Q Consensus 108 ~glL~~GallVy~TSaLa~ 126 (126)
+|||++||+||||||||+|
T Consensus 81 ~glL~~Gallvy~TSaL~q 99 (99)
T PF04725_consen 81 AGLLGGGALLVYNTSALAQ 99 (99)
T ss_pred HHHHcccceeEEehhhhcC
Confidence 9999999999999999998
No 3
>PLN00083 photosystem II subunit R; Provisional
Probab=100.00 E-value=5.9e-35 Score=213.32 Aligned_cols=83 Identities=37% Similarity=0.545 Sum_probs=78.3
Q ss_pred ecCceeecccccccCCCcccCC----CcCCCCCCccCCeeEEeccccc-ccccCCC-----------CceeccchhHHHH
Q 033164 39 AKGGKIKTDKPYGVNGGMDLRE----GLDASGRKAKGKGVYQFVDKYG-ANVDGYS-----------GDVYTGGATGLAI 102 (126)
Q Consensus 39 asggKikt~kp~G~~ggm~~k~----gvDasGRkgKg~gVYqf~~kyG-ANVDgYS-----------GD~Y~gG~~gL~~ 102 (126)
+|.++.+.+|.-+.+.++.+|+ |..|+|||+||+|||||+|||| ||||||| ||+|+| ||+|
T Consensus 3 nssgpkrgtk~a~~q~~vgykgst~agsapkgRk~Kg~gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~G---gL~~ 79 (101)
T PLN00083 3 NSSGPKRGTKAAGGQAGVGYKGSTEAGSAPKTRSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEG---DLKL 79 (101)
T ss_pred CCCCCCCccccCccccccccccccccCCCCCCccCCCceEEEehhccCcccccccCCccChhhcCCCcchhhc---cHHH
Confidence 4667788888899999999998 8889999999999999999999 9999999 999998 5999
Q ss_pred HHHHHHHHhhhceeeeeecccc
Q 033164 103 WAVTLAGLLAGGALLVYNTSAL 124 (126)
Q Consensus 103 wA~tl~glL~~GallVy~TSaL 124 (126)
||+||+|||++|||||||||||
T Consensus 80 WA~tlaglLg~GAllVy~TSaL 101 (101)
T PLN00083 80 AAAAVAGVIGTGALAILLTSAL 101 (101)
T ss_pred HHHHHHHHHccceeEEEecccC
Confidence 9999999999999999999997
No 4
>PF11088 RL11D: Glycoprotein encoding membrane proteins RL5A and RL6; InterPro: IPR024349 This entry represents RL5A and RL6 from human herpesvirus 5. RL5A and RL6 are members of the RL11 family, which are predicted to encode membrane glycoproteins [].
Probab=61.84 E-value=5.1 Score=29.90 Aligned_cols=26 Identities=31% Similarity=0.625 Sum_probs=22.4
Q ss_pred ccCCeeEEecccccccccCCCCceec
Q 033164 69 AKGKGVYQFVDKYGANVDGYSGDVYT 94 (126)
Q Consensus 69 gKg~gVYqf~~kyGANVDgYSGD~Y~ 94 (126)
.+-.|+|....+||-|-|+|+||.+-
T Consensus 69 ~g~eg~ydl~r~~~~N~dee~ge~W~ 94 (98)
T PF11088_consen 69 QGNEGVYDLGRRFGENGDEESGELWF 94 (98)
T ss_pred ccCcccEeeeeeecCCCCcccCcEEE
Confidence 34568999999999999999999863
No 5
>COG4059 MtrE Tetrahydromethanopterin S-methyltransferase, subunit E [Coenzyme metabolism]
Probab=42.68 E-value=9.2 Score=33.02 Aligned_cols=43 Identities=28% Similarity=0.479 Sum_probs=35.3
Q ss_pred EEecccccccccCCC--------------CceeccchhHHHHHHHHHHHHhhhceeeeee
Q 033164 75 YQFVDKYGANVDGYS--------------GDVYTGGATGLAIWAVTLAGLLAGGALLVYN 120 (126)
Q Consensus 75 Yqf~~kyGANVDgYS--------------GD~Y~gG~~gL~~wA~tl~glL~~GallVy~ 120 (126)
--|+.|||--+.|.- +|.-++++-| |+..+.||+-...|.|.|
T Consensus 224 ~~FCak~GgplTGl~FGliVFl~~W~~~~~d~~~~i~~G---~isiv~Gliiv~iLii~N 280 (304)
T COG4059 224 SYFCAKFGGPLTGLAFGLIVFLSSWVTTVFDPAVSIQGG---WISIVAGLIIVLILIIWN 280 (304)
T ss_pred hhhHHHhCCcchhhhhhhhhhhhhhhhhhcCcccccccc---hhhhHHHHHHHHHHHHhc
Confidence 359999998888765 7777777777 899999999998888877
No 6
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=30.91 E-value=29 Score=29.96 Aligned_cols=22 Identities=14% Similarity=0.297 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHHHhhhceeee
Q 033164 97 ATGLAIWAVTLAGLLAGGALLV 118 (126)
Q Consensus 97 ~~gL~~wA~tl~glL~~GallV 118 (126)
.+-+++|+++++|++..|.+..
T Consensus 406 ~~~~~LW~~Lv~gV~vL~~mA~ 427 (429)
T PF13163_consen 406 WKRWLLWGALVLGVAVLGGMAW 427 (429)
T ss_pred hhhhHHHHHHHHHHHHHHHHhe
Confidence 5668999999999999887654
No 7
>PF13179 DUF4006: Family of unknown function (DUF4006)
Probab=26.92 E-value=62 Score=22.55 Aligned_cols=20 Identities=40% Similarity=0.376 Sum_probs=16.8
Q ss_pred chhHHHHHHHHHHHHhhhce
Q 033164 96 GATGLAIWAVTLAGLLAGGA 115 (126)
Q Consensus 96 G~~gL~~wA~tl~glL~~Ga 115 (126)
|.+|.+|--++|+.+|++..
T Consensus 12 Gi~G~LIAvvLLLsIl~~lt 31 (66)
T PF13179_consen 12 GITGMLIAVVLLLSILAFLT 31 (66)
T ss_pred chHhHHHHHHHHHHHHHHHH
Confidence 78999999999998887654
No 8
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=22.82 E-value=1e+02 Score=19.67 Aligned_cols=21 Identities=14% Similarity=0.082 Sum_probs=15.5
Q ss_pred HHHHHHHHHHhhhceeeeeec
Q 033164 101 AIWAVTLAGLLAGGALLVYNT 121 (126)
Q Consensus 101 ~~wA~tl~glL~~GallVy~T 121 (126)
++|...++++-.++||+..+.
T Consensus 12 L~~Ga~ivvipi~~aLifvSq 32 (39)
T CHL00114 12 LLLGAIIVVIPITLALLFVSQ 32 (39)
T ss_pred HHHHHHHhHHHhhhheEEEec
Confidence 477777777777788877764
No 9
>PF06195 DUF996: Protein of unknown function (DUF996); InterPro: IPR010397 This is a family of uncharacterised bacterial and archaeal proteins.
Probab=19.89 E-value=46 Score=24.95 Aligned_cols=23 Identities=13% Similarity=0.340 Sum_probs=18.8
Q ss_pred chhHHHHHHHHHHHHhhhceeee
Q 033164 96 GATGLAIWAVTLAGLLAGGALLV 118 (126)
Q Consensus 96 G~~gL~~wA~tl~glL~~GallV 118 (126)
.|.|++.|.++++-++.+|.+++
T Consensus 112 ~tag~ly~iGAiL~IIlIG~ii~ 134 (139)
T PF06195_consen 112 KTAGLLYFIGAILTIILIGLIII 134 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999888887764
No 10
>COG4982 3-oxoacyl-[acyl-carrier protein]
Probab=16.13 E-value=1.2e+02 Score=29.85 Aligned_cols=31 Identities=45% Similarity=0.621 Sum_probs=24.2
Q ss_pred cchhHHHHHHHHHHHHhhhceeeeeecccccC
Q 033164 95 GGATGLAIWAVTLAGLLAGGALLVYNTSALAQ 126 (126)
Q Consensus 95 gG~~gL~~wA~tl~glL~~GallVy~TSaLa~ 126 (126)
|.-+|- |-|-.+.+||.+||..|.-||-|++
T Consensus 403 GA~~gS-Iaa~Vv~~LL~gGAtVI~TTS~~s~ 433 (866)
T COG4982 403 GASKGS-IAAAVVARLLAGGATVIATTSRLSE 433 (866)
T ss_pred cCCCcc-hHHHHHHHHHhCCcEEEEEcccccH
Confidence 444444 4466789999999999999998763
Done!