Query 033756
Match_columns 112
No_of_seqs 53 out of 55
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 05:57:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033756.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033756hhsearch_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 1.6E-51 3.5E-56 301.8 6.4 86 24-109 1-89 (117)
2 PF04725 PsbR: Photosystem II 100.0 1.4E-44 3.1E-49 259.2 4.4 70 40-109 1-71 (99)
3 PLN00083 photosystem II subuni 100.0 2.2E-30 4.9E-35 186.4 3.1 62 48-109 12-78 (101)
4 PF08576 DUF1764: Eukaryotic p 65.2 1.9 4.2E-05 29.8 -0.1 24 85-110 70-93 (102)
5 COG5659 FOG: Transposase [DNA 45.4 8.4 0.00018 33.7 0.5 42 62-103 98-160 (385)
6 PF05430 Methyltransf_30: S-ad 44.2 7.3 0.00016 28.0 -0.0 15 85-99 56-70 (124)
7 COG4678 Muramidase (phage lamb 39.2 7.4 0.00016 31.1 -0.7 35 63-100 80-114 (180)
8 COG4121 Uncharacterized conser 32.2 13 0.00028 30.4 -0.4 16 85-100 174-189 (252)
9 COG5007 Predicted transcriptio 19.4 25 0.00053 25.0 -0.9 9 92-100 70-78 (80)
10 PF10417 1-cysPrx_C: C-termina 17.8 44 0.00096 20.0 0.1 21 75-103 2-22 (40)
No 1
>PLN00053 photosystem II subunit R; Provisional
Probab=100.00 E-value=1.6e-51 Score=301.76 Aligned_cols=86 Identities=73% Similarity=1.349 Sum_probs=83.9
Q ss_pred ccCCCCCcc--ceEEEEecCc-eeeeccccccCCCcccCccccCCCCcccCCcceeeeeccccCCCCccccccCCCCCCC
Q 033756 24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPS 100 (112)
Q Consensus 24 ~rglp~l~R--~s~~V~as~~-Kikt~kp~G~~g~m~~k~~vDa~gRk~kgkGVYqfv~KyGANVDgYSPIY~p~eWs~s 100 (112)
+||||+++| ++|+|+||++ ||||++|||++|+|++|+|+||+|||+||||||||+||||||||||||||+||||||+
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 9999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeccCcc
Q 033756 101 GDVYTGGNA 109 (112)
Q Consensus 101 GD~Y~gG~~ 109 (112)
||+|+||++
T Consensus 81 Gd~Y~ggtt 89 (117)
T PLN00053 81 GDVYVGGTT 89 (117)
T ss_pred CCeeeCChh
Confidence 999999987
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=1.4e-44 Score=259.24 Aligned_cols=70 Identities=79% Similarity=1.422 Sum_probs=68.0
Q ss_pred cCc-eeeeccccccCCCcccCccccCCCCcccCCcceeeeeccccCCCCccccccCCCCCCCCCeeccCcc
Q 033756 40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGNA 109 (112)
Q Consensus 40 s~~-Kikt~kp~G~~g~m~~k~~vDa~gRk~kgkGVYqfv~KyGANVDgYSPIY~p~eWs~sGD~Y~gG~~ 109 (112)
|++ ||||++|+|++|+|++|+|+||+||++||+|||||++|||||||||||||+||||||+||+|+||++
T Consensus 1 Sg~KKIkt~~p~G~~g~m~~k~gvDa~gRkgKg~gVYqf~~KyGANVDgYSPIY~p~~Ws~~GD~Y~gGt~ 71 (99)
T PF04725_consen 1 SGGKKIKTDKPYGPSGGMTLKDGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWSPSGDVYVGGTT 71 (99)
T ss_pred CCCccccccCCccCCCCccccCCccCCCCCCCCceeEEehhhcCccccccCCCcChhhcCCCCCeecCChh
Confidence 445 9999999999999999999999999999999999999999999999999999999999999999987
No 3
>PLN00083 photosystem II subunit R; Provisional
Probab=99.96 E-value=2.2e-30 Score=186.39 Aligned_cols=62 Identities=35% Similarity=0.590 Sum_probs=57.3
Q ss_pred cccccCCCcccCccccC----CCCcccCCcceeeeeccc-cCCCCccccccCCCCCCCCCeeccCcc
Q 033756 48 KPYGVNGGMDLREGLDA----SGRKAKGKGVYQFVDKYG-ANVDGYSPIYNENDWSPSGDVYTGGNA 109 (112)
Q Consensus 48 kp~G~~g~m~~k~~vDa----~gRk~kgkGVYqfv~KyG-ANVDgYSPIY~p~eWs~sGD~Y~gG~~ 109 (112)
|.-+.+.++.+|+.+|| +||++||+|||||+|||| ||||||||||+||||+|+||+|+||+-
T Consensus 12 k~a~~q~~vgykgst~agsapkgRk~Kg~gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~GgL~ 78 (101)
T PLN00083 12 KAAGGQAGVGYKGSTEAGSAPKTRSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEGDLK 78 (101)
T ss_pred ccCccccccccccccccCCCCCCccCCCceEEEehhccCcccccccCCccChhhcCCCcchhhccHH
Confidence 45577889999999997 589999999999999999 999999999999999999999999864
No 4
>PF08576 DUF1764: Eukaryotic protein of unknown function (DUF1764); InterPro: IPR013885 This entry consists of eukaryotic proteins of unknown function, including many hypothetical proteins.
Probab=65.20 E-value=1.9 Score=29.82 Aligned_cols=24 Identities=42% Similarity=0.781 Sum_probs=17.2
Q ss_pred CCCccccccCCCCCCCCCeeccCccc
Q 033756 85 VDGYSPIYNENDWSPSGDVYTGGNAL 110 (112)
Q Consensus 85 VDgYSPIY~p~eWs~sGD~Y~gG~~~ 110 (112)
+||| |||+.||-. -|....|+|.+
T Consensus 70 eDGl-~IYt~eEL~-ig~~~gG~T~~ 93 (102)
T PF08576_consen 70 EDGL-PIYTEEELG-IGNPKGGGTPL 93 (102)
T ss_pred CCCc-eEecHHHhC-CCCCCCCCCCC
Confidence 6777 899999988 44445566654
No 5
>COG5659 FOG: Transposase [DNA replication, recombination, and repair]
Probab=45.36 E-value=8.4 Score=33.75 Aligned_cols=42 Identities=38% Similarity=0.759 Sum_probs=35.0
Q ss_pred ccCCCCcccCC---cce-eeeeccc-------------cCCCCcccc----ccCCCCCCCCCe
Q 033756 62 LDASGRKAKGK---GVY-QFVDKYG-------------ANVDGYSPI----YNENDWSPSGDV 103 (112)
Q Consensus 62 vDa~gRk~kgk---GVY-qfv~KyG-------------ANVDgYSPI----Y~p~eWs~sGD~ 103 (112)
+|.-|=++||+ ||+ ||+-.|| +|.+++-|| |-|++|-..||.
T Consensus 98 idetg~~kkgk~s~~v~rqy~G~Lgkidn~~v~v~~~~~~~~~~~~i~~~~~kp~~~l~e~~k 160 (385)
T COG5659 98 IDETGFPKKGKHSDGVARQYIGNLGKIDNCQVAVSLYGITEGGTLPIASQLYKPEEWLDEGDK 160 (385)
T ss_pred ccccCCCcccccccchhhhhhhhhhhhhhhHHHHHHhhhhcceeEeechhccCChhhccccch
Confidence 57788888888 888 5555554 789999999 999999999998
No 6
>PF05430 Methyltransf_30: S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR008471 This entry contains several uncharacterised bacterial proteins with no known function.; GO: 0016645 oxidoreductase activity, acting on the CH-NH group of donors, 0055114 oxidation-reduction process; PDB: 2E58_D 3SGL_A 3PVC_A 3AWI_D 3PS9_A 2QY6_A.
Probab=44.17 E-value=7.3 Score=28.03 Aligned_cols=15 Identities=47% Similarity=0.915 Sum_probs=11.8
Q ss_pred CCCccccccCCCCCC
Q 033756 85 VDGYSPIYNENDWSP 99 (112)
Q Consensus 85 VDgYSPIY~p~eWs~ 99 (112)
-||+||-=+||-|++
T Consensus 56 lDgFsP~~nPelWs~ 70 (124)
T PF05430_consen 56 LDGFSPAKNPELWSE 70 (124)
T ss_dssp E-SS-TTTSGGGSSH
T ss_pred ecCCCCcCCcccCCH
Confidence 489999999999986
No 7
>COG4678 Muramidase (phage lambda lysozyme) [Carbohydrate transport and metabolism]
Probab=39.25 E-value=7.4 Score=31.14 Aligned_cols=35 Identities=29% Similarity=0.576 Sum_probs=29.8
Q ss_pred cCCCCcccCCcceeeeeccccCCCCccccccCCCCCCC
Q 033756 63 DASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPS 100 (112)
Q Consensus 63 Da~gRk~kgkGVYqfv~KyGANVDgYSPIY~p~eWs~s 100 (112)
+.+|-+.+.-|-|||.+++ -|.|.|-|.|.+|+|.
T Consensus 80 ~~ng~cSTAAGrYQ~L~~t---W~~~~~~l~l~dF~P~ 114 (180)
T COG4678 80 GPNGLCSTAAGRYQLLNRT---WDDYAPQLHLKDFSPE 114 (180)
T ss_pred CCCCccccchhhHHHHHhH---HHHhhhhcCcccCChh
Confidence 3446778889999999998 7899999999999874
No 8
>COG4121 Uncharacterized conserved protein [Function unknown]
Probab=32.22 E-value=13 Score=30.38 Aligned_cols=16 Identities=31% Similarity=0.868 Sum_probs=14.0
Q ss_pred CCCccccccCCCCCCC
Q 033756 85 VDGYSPIYNENDWSPS 100 (112)
Q Consensus 85 VDgYSPIY~p~eWs~s 100 (112)
-||+||.=|||-|+++
T Consensus 174 lDgFsP~kNP~mW~~e 189 (252)
T COG4121 174 LDGFRPVKNPEMWEDE 189 (252)
T ss_pred cCCccccCChhhccHH
Confidence 4999999999999863
No 9
>COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription]
Probab=19.37 E-value=25 Score=25.02 Aligned_cols=9 Identities=22% Similarity=0.929 Sum_probs=6.3
Q ss_pred ccCCCCCCC
Q 033756 92 YNENDWSPS 100 (112)
Q Consensus 92 Y~p~eWs~s 100 (112)
|||+||.++
T Consensus 70 ~Tp~eW~~~ 78 (80)
T COG5007 70 YTPAEWARD 78 (80)
T ss_pred cCHHHhhhc
Confidence 777777653
No 10
>PF10417 1-cysPrx_C: C-terminal domain of 1-Cys peroxiredoxin; InterPro: IPR019479 This entry represents the C-terminal domain of 1-Cys peroxiredoxin, a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols []. The C-terminal domain is crucial for providing the extra cysteine necessary for dimerisation of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine found upstream of this domain. Glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulphide to the sulphydryl and consequent activation of the enzyme []. The domain is associated with IPR000866 from INTERPRO, which carries the catalytic cysteine. ; GO: 0051920 peroxiredoxin activity, 0055114 oxidation-reduction process; PDB: 1ZOF_E 2H01_A 3EMP_D 1YF1_G 1YF0_D 1N8J_C 1YEP_D 1YEX_D 2V41_H 2V32_C ....
Probab=17.84 E-value=44 Score=19.96 Aligned_cols=21 Identities=38% Similarity=0.748 Sum_probs=0.0
Q ss_pred eeeeeccccCCCCccccccCCCCCCCCCe
Q 033756 75 YQFVDKYGANVDGYSPIYNENDWSPSGDV 103 (112)
Q Consensus 75 Yqfv~KyGANVDgYSPIY~p~eWs~sGD~ 103 (112)
+||++|+ .+-+|..|.+.-|+
T Consensus 2 LQ~~d~~--------~v~tPanW~pGd~~ 22 (40)
T PF10417_consen 2 LQFTDKH--------GVATPANWKPGDDV 22 (40)
T ss_dssp HHHHHHH--------SSBBCTTTCTTSGE
T ss_pred ceehhhh--------CcccCcCCCCCCCe
Done!