Query 033939
Match_columns 108
No_of_seqs 53 out of 55
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 08:00:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033939.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033939hhsearch_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 5.1E-51 1.1E-55 297.7 6.5 85 24-108 1-88 (117)
2 PF04725 PsbR: Photosystem II 100.0 1.4E-44 3E-49 258.1 4.7 69 40-108 1-70 (99)
3 PLN00083 photosystem II subuni 100.0 1.1E-32 2.4E-37 197.3 3.7 70 38-107 2-76 (101)
4 PF08576 DUF1764: Eukaryotic p 52.4 4.8 0.0001 27.7 0.0 13 85-98 70-82 (102)
5 PF05430 Methyltransf_30: S-ad 50.3 5.5 0.00012 28.5 0.1 15 85-99 56-70 (124)
6 COG4121 Uncharacterized conser 35.8 11 0.00023 30.7 -0.4 15 85-99 174-188 (252)
7 COG5659 FOG: Transposase [DNA 28.0 24 0.00053 30.8 0.6 42 62-103 98-160 (385)
8 COG5007 Predicted transcriptio 21.7 21 0.00045 25.2 -0.8 9 92-100 70-78 (80)
9 PF10417 1-cysPrx_C: C-termina 20.9 25 0.00054 20.9 -0.5 22 75-104 2-23 (40)
10 PRK01747 mnmC bifunctional tRN 17.3 49 0.0011 28.6 0.3 14 86-99 173-186 (662)
No 1
>PLN00053 photosystem II subunit R; Provisional
Probab=100.00 E-value=5.1e-51 Score=297.65 Aligned_cols=85 Identities=74% Similarity=1.361 Sum_probs=82.7
Q ss_pred ccCCCCCcc--ceEEEeecCc-eeeeccccccCCCcccCcccCCCCCCccCCeeEEeccccccCCCCccccccCCCCCCC
Q 033939 24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPS 100 (108)
Q Consensus 24 ~rglp~l~R--~s~~v~asgg-Kikt~kp~G~~ggm~~k~gvDasgRk~Kg~gVYqf~~kyGANVDgYSPIY~p~ews~~ 100 (108)
+||||+++| ++|+|+||++ ||||++|||++|+|++|+|+||+|||+||||||||+||||||||||||||+||||||+
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 8999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCC
Q 033939 101 GDVYTGGK 108 (108)
Q Consensus 101 GD~Y~ggt 108 (108)
||+|+|||
T Consensus 81 Gd~Y~ggt 88 (117)
T PLN00053 81 GDVYVGGT 88 (117)
T ss_pred CCeeeCCh
Confidence 99999996
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=258.07 Aligned_cols=69 Identities=80% Similarity=1.438 Sum_probs=67.0
Q ss_pred cCc-eeeeccccccCCCcccCcccCCCCCCccCCeeEEeccccccCCCCccccccCCCCCCCCCcccCCC
Q 033939 40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK 108 (108)
Q Consensus 40 sgg-Kikt~kp~G~~ggm~~k~gvDasgRk~Kg~gVYqf~~kyGANVDgYSPIY~p~ews~~GD~Y~ggt 108 (108)
|++ ||||++|+|++|+|++|+|+||+|||+||+|||||+||||||||||||||+||||||+||+|+|||
T Consensus 1 Sg~KKIkt~~p~G~~g~m~~k~gvDa~gRkgKg~gVYqf~~KyGANVDgYSPIY~p~~Ws~~GD~Y~gGt 70 (99)
T PF04725_consen 1 SGGKKIKTDKPYGPSGGMTLKDGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWSPSGDVYVGGT 70 (99)
T ss_pred CCCccccccCCccCCCCccccCCccCCCCCCCCceeEEehhhcCccccccCCCcChhhcCCCCCeecCCh
Confidence 455 999999999999999999999999999999999999999999999999999999999999999986
No 3
>PLN00083 photosystem II subunit R; Provisional
Probab=99.97 E-value=1.1e-32 Score=197.33 Aligned_cols=70 Identities=33% Similarity=0.568 Sum_probs=65.5
Q ss_pred eecCceeeeccccccCCCcccCc----ccCCCCCCccCCeeEEeccccc-cCCCCccccccCCCCCCCCCcccCC
Q 033939 38 VAKGGKIKTDKPYGVNGGMDLRE----GLDASGRKAKGKGVYQFVDKYG-ANVDGYSPIYNENDWSPSGDVYTGG 107 (108)
Q Consensus 38 ~asggKikt~kp~G~~ggm~~k~----gvDasgRk~Kg~gVYqf~~kyG-ANVDgYSPIY~p~ews~~GD~Y~gg 107 (108)
.+|.|+.+.+|.-+.+.++.+|+ |..++||++||+|||||+|||| ||||||||||+||||+|+||+|+||
T Consensus 2 ~nssgpkrgtk~a~~q~~vgykgst~agsapkgRk~Kg~gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~Gg 76 (101)
T PLN00083 2 ANSSGPKRGTKAAGGQAGVGYKGSTEAGSAPKTRSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEGD 76 (101)
T ss_pred CCCCCCCCccccCccccccccccccccCCCCCCccCCCceEEEehhccCcccccccCCccChhhcCCCcchhhcc
Confidence 35677888889999999999998 8889999999999999999999 9999999999999999999999986
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=52.40 E-value=4.8 Score=27.72 Aligned_cols=13 Identities=46% Similarity=0.928 Sum_probs=10.8
Q ss_pred CCCccccccCCCCC
Q 033939 85 VDGYSPIYNENDWS 98 (108)
Q Consensus 85 VDgYSPIY~p~ews 98 (108)
+||| |||+.||-.
T Consensus 70 eDGl-~IYt~eEL~ 82 (102)
T PF08576_consen 70 EDGL-PIYTEEELG 82 (102)
T ss_pred CCCc-eEecHHHhC
Confidence 6787 899998876
No 5
>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=50.26 E-value=5.5 Score=28.51 Aligned_cols=15 Identities=47% Similarity=0.915 Sum_probs=11.7
Q ss_pred CCCccccccCCCCCC
Q 033939 85 VDGYSPIYNENDWSP 99 (108)
Q Consensus 85 VDgYSPIY~p~ews~ 99 (108)
-||+||-=+||-|++
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 389999999999986
No 6
>COG4121 Uncharacterized conserved protein [Function unknown]
Probab=35.84 E-value=11 Score=30.72 Aligned_cols=15 Identities=33% Similarity=0.922 Sum_probs=13.7
Q ss_pred CCCccccccCCCCCC
Q 033939 85 VDGYSPIYNENDWSP 99 (108)
Q Consensus 85 VDgYSPIY~p~ews~ 99 (108)
-||+||.-|||-|++
T Consensus 174 lDgFsP~kNP~mW~~ 188 (252)
T COG4121 174 LDGFRPVKNPEMWED 188 (252)
T ss_pred cCCccccCChhhccH
Confidence 499999999999986
No 7
>COG5659 FOG: Transposase [DNA replication, recombination, and repair]
Probab=28.05 E-value=24 Score=30.82 Aligned_cols=42 Identities=40% Similarity=0.801 Sum_probs=31.5
Q ss_pred cCCCCCCccCC---eeE-Eec-------------cccccCCCCcccc----ccCCCCCCCCCc
Q 033939 62 LDASGRKAKGK---GVY-QFV-------------DKYGANVDGYSPI----YNENDWSPSGDV 103 (108)
Q Consensus 62 vDasgRk~Kg~---gVY-qf~-------------~kyGANVDgYSPI----Y~p~ews~~GD~ 103 (108)
+|.-|=..||+ ||+ |++ --|++|.+++-|| |-|++|-+.||.
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 45556666777 676 333 3455889999999 999999999998
No 8
>COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription]
Probab=21.70 E-value=21 Score=25.24 Aligned_cols=9 Identities=22% Similarity=0.929 Sum_probs=6.4
Q ss_pred ccCCCCCCC
Q 033939 92 YNENDWSPS 100 (108)
Q Consensus 92 Y~p~ews~~ 100 (108)
|||+||.++
T Consensus 70 ~Tp~eW~~~ 78 (80)
T COG5007 70 YTPAEWARD 78 (80)
T ss_pred cCHHHhhhc
Confidence 777888653
No 9
>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=20.93 E-value=25 Score=20.93 Aligned_cols=22 Identities=41% Similarity=0.827 Sum_probs=15.1
Q ss_pred EEeccccccCCCCccccccCCCCCCCCCcc
Q 033939 75 YQFVDKYGANVDGYSPIYNENDWSPSGDVY 104 (108)
Q Consensus 75 Yqf~~kyGANVDgYSPIY~p~ews~~GD~Y 104 (108)
+||.+|+| +-+|..|.+.-|+-
T Consensus 2 LQ~~d~~~--------v~tPanW~pGd~~i 23 (40)
T PF10417_consen 2 LQFTDKHG--------VATPANWKPGDDVI 23 (40)
T ss_dssp HHHHHHHS--------SBBCTTTCTTSGEB
T ss_pred ceehhhhC--------cccCcCCCCCCCeE
Confidence 36777776 35899998865543
No 10
>PRK01747 mnmC bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed
Probab=17.32 E-value=49 Score=28.60 Aligned_cols=14 Identities=50% Similarity=1.158 Sum_probs=0.0
Q ss_pred CCccccccCCCCCC
Q 033939 86 DGYSPIYNENDWSP 99 (108)
Q Consensus 86 DgYSPIY~p~ews~ 99 (108)
||+||-=|||-|++
T Consensus 173 D~FsP~~np~~W~~ 186 (662)
T PRK01747 173 DGFAPAKNPDMWSP 186 (662)
T ss_pred CCCCCccChhhccH
Done!