Query 033199
Match_columns 125
No_of_seqs 48 out of 50
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 11:02:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033199hhsearch_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 3.7E-60 7.9E-65 352.3 7.4 102 24-125 1-117 (117)
2 PF04725 PsbR: Photosystem II 100.0 6.1E-54 1.3E-58 311.9 5.4 86 40-125 1-99 (99)
3 PLN00083 photosystem II subuni 100.0 6.8E-38 1.5E-42 228.5 3.6 60 61-123 41-101 (101)
4 PF03918 CcmH: Cytochrome C bi 57.7 4.4 9.6E-05 30.7 0.6 40 64-118 82-121 (148)
5 cd03016 PRX_1cys Peroxiredoxin 55.4 17 0.00037 27.4 3.5 59 26-93 112-175 (203)
6 COG4678 Muramidase (phage lamb 54.4 6.3 0.00014 32.0 1.0 43 43-88 72-114 (180)
7 PF05430 Methyltransf_30: S-ad 46.2 6.6 0.00014 28.7 -0.0 16 73-88 56-71 (124)
8 CHL00082 psbZ photosystem II p 37.9 33 0.00072 23.5 2.4 23 81-106 29-51 (62)
9 TIGR03043 PS_II_psbZ photosyst 36.1 32 0.00068 23.3 2.0 23 81-106 26-48 (58)
10 PRK02576 psbZ photosystem II r 35.9 32 0.00069 23.6 2.0 23 81-106 29-51 (62)
11 PRK13190 putative peroxiredoxi 35.7 45 0.00098 25.3 3.0 53 32-93 118-175 (202)
12 PRK10144 formate-dependent nit 35.2 23 0.00051 26.8 1.4 38 63-115 81-118 (126)
13 PF08576 DUF1764: Eukaryotic p 34.5 11 0.00024 26.4 -0.3 23 72-96 69-91 (102)
14 COG4121 Uncharacterized conser 34.0 12 0.00026 31.1 -0.3 16 73-88 174-189 (252)
15 PF10417 1-cysPrx_C: C-termina 33.4 41 0.00089 20.4 2.1 22 63-92 2-23 (40)
16 TIGR03147 cyt_nit_nrfF cytochr 31.4 30 0.00064 26.3 1.5 38 63-115 81-118 (126)
17 PF13163 DUF3999: Protein of u 28.9 35 0.00077 29.3 1.7 22 96-117 406-427 (429)
18 PRK15006 thiosulfate reductase 26.1 46 0.001 26.9 1.8 16 71-86 12-27 (261)
19 PF13179 DUF4006: Family of un 24.1 75 0.0016 22.1 2.3 21 94-114 11-31 (66)
20 PF02388 FemAB: FemAB family; 22.1 28 0.00061 29.4 -0.2 31 50-80 356-389 (406)
21 PF01102 Glycophorin_A: Glycop 20.9 50 0.0011 24.8 1.0 34 84-118 53-86 (122)
No 1
>PLN00053 photosystem II subunit R; Provisional
Probab=100.00 E-value=3.7e-60 Score=352.28 Aligned_cols=102 Identities=79% Similarity=1.367 Sum_probs=99.4
Q ss_pred ccCCCCCCc--ceeEEEEecc-eeeeccccccCCCccccc------------chhhhhhhhcCCCCCccCcccCCCCCCC
Q 033199 24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLRE------------GVYQFVDKYGANVDGYSPIYNENDWSPS 88 (125)
Q Consensus 24 ~~glp~laR--~s~~v~Asg~-Kikt~~P~G~~Ggm~~k~------------Gvyqf~~KyGANVDgYSPIY~p~~ws~~ 88 (125)
+||||+++| ++|+|+||++ ||||++|||++|+|++|+ |||||+||||||||||||||+||||||+
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 6899999987 999999999999999997 9999999999999999999999999999
Q ss_pred CCeeccChhHHHHHHHHHHHHhhhceeeeeecccccC
Q 033199 89 GDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ 125 (125)
Q Consensus 89 GD~Y~gg~~gL~~wA~tl~glL~~Gallvy~TSaLa~ 125 (125)
||+|+|||+||+|||+||+|||++|||||||||||+|
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=6.1e-54 Score=311.94 Aligned_cols=86 Identities=84% Similarity=1.423 Sum_probs=83.8
Q ss_pred ecc-eeeeccccccCCCccccc------------chhhhhhhhcCCCCCccCcccCCCCCCCCCeeccChhHHHHHHHHH
Q 033199 40 KGG-KIKTDKPYGVNGGMDLRE------------GVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTL 106 (125)
Q Consensus 40 sg~-Kikt~~P~G~~Ggm~~k~------------Gvyqf~~KyGANVDgYSPIY~p~~ws~~GD~Y~gg~~gL~~wA~tl 106 (125)
|++ |||||+|||++|+|++|+ |||||+||||||||||||||+||||||+||+|+||++||++||+||
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 445 999999999999999998 9999999999999999999999999999999999999999999999
Q ss_pred HHHhhhceeeeeecccccC
Q 033199 107 AGLLAGGALLVYNTSALAQ 125 (125)
Q Consensus 107 ~glL~~Gallvy~TSaLa~ 125 (125)
+|||++|||||||||||+|
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=6.8e-38 Score=228.50 Aligned_cols=60 Identities=45% Similarity=0.720 Sum_probs=59.1
Q ss_pred chhhhhhhhc-CCCCCccCcccCCCCCCCCCeeccChhHHHHHHHHHHHHhhhceeeeeecccc
Q 033199 61 GVYQFVDKYG-ANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSAL 123 (125)
Q Consensus 61 Gvyqf~~KyG-ANVDgYSPIY~p~~ws~~GD~Y~gg~~gL~~wA~tl~glL~~Gallvy~TSaL 123 (125)
|||||+|||| ||||||||||+||||+|+||+|+| ||++||+||+|||++|||||||||||
T Consensus 41 gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~G---gL~~WA~tlaglLg~GAllVy~TSaL 101 (101)
T PLN00083 41 YVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEG---DLKLAAAAVAGVIGTGALAILLTSAL 101 (101)
T ss_pred eEEEehhccCcccccccCCccChhhcCCCcchhhc---cHHHHHHHHHHHHccceeEEEecccC
Confidence 9999999999 999999999999999999999998 69999999999999999999999997
No 4
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=57.74 E-value=4.4 Score=30.68 Aligned_cols=40 Identities=40% Similarity=0.687 Sum_probs=8.8
Q ss_pred hhhhhhcCCCCCccCcccCCCCCCCCCeeccChhHHHHHHHHHHHHhhhceeeee
Q 033199 64 QFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVY 118 (125)
Q Consensus 64 qf~~KyGANVDgYSPIY~p~~ws~~GD~Y~gg~~gL~~wA~tl~glL~~Gallvy 118 (125)
-|+++||--| =|.|-.+ | .++++|++-++.++++++++++
T Consensus 82 ~~v~rYG~~V-l~~Pp~~------------~--~~~~lW~~P~~~l~~g~~~~~~ 121 (148)
T PF03918_consen 82 YFVERYGEFV-LYEPPFK------------G--FTWLLWLGPFLLLLLGGALLFR 121 (148)
T ss_dssp HHHHHHTTT--EES--S--------------------------------------
T ss_pred HHHHhcCcce-eecCCCC------------c--cHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999766 2444322 2 2588999999888888777664
No 5
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=55.42 E-value=17 Score=27.38 Aligned_cols=59 Identities=25% Similarity=0.428 Sum_probs=36.3
Q ss_pred CCCCCCcceeEEEEecceeeeccccccCCCccccc-----chhhhhhhhcCCCCCccCcccCCCCCCCCCeec
Q 033199 26 GLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLRE-----GVYQFVDKYGANVDGYSPIYNENDWSPSGDVYT 93 (125)
Q Consensus 26 glp~laR~s~~v~Asg~Kikt~~P~G~~Ggm~~k~-----Gvyqf~~KyGANVDgYSPIY~p~~ws~~GD~Y~ 93 (125)
+.|...|..| |+...+||.-...+-..-|.++.+ -.+|+.+|+| .-+|-+|.++.|+-+
T Consensus 112 ~~~~~~r~~f-iID~~G~I~~~~~~~~~~gr~~~ell~~l~~lq~~~~~~--------~~~p~~w~~g~~~~~ 175 (203)
T cd03016 112 GSTLTVRAVF-IIDPDKKIRLILYYPATTGRNFDEILRVVDALQLTDKHK--------VATPANWKPGDDVIV 175 (203)
T ss_pred CCCceeeEEE-EECCCCeEEEEEecCCCCCCCHHHHHHHHHHHhhHhhcC--------cCcCCCCCCCCceec
Confidence 3343456666 666667777666444444544444 4467777663 568999999766543
No 6
>COG4678 Muramidase (phage lambda lysozyme) [Carbohydrate transport and metabolism]
Probab=54.38 E-value=6.3 Score=32.02 Aligned_cols=43 Identities=30% Similarity=0.513 Sum_probs=31.8
Q ss_pred eeeeccccccCCCcccccchhhhhhhhcCCCCCccCcccCCCCCCC
Q 033199 43 KIKTDKPYGVNGGMDLREGVYQFVDKYGANVDGYSPIYNENDWSPS 88 (125)
Q Consensus 43 Kikt~~P~G~~Ggm~~k~Gvyqf~~KyGANVDgYSPIY~p~~ws~~ 88 (125)
.++..-|-++||--.--.|.|||.+++ -|.|.|-|.|.+|+|.
T Consensus 72 ~~~v~i~~~~ng~cSTAAGrYQ~L~~t---W~~~~~~l~l~dF~P~ 114 (180)
T COG4678 72 RKCVTIPTGPNGLCSTAAGRYQLLNRT---WDDYAPQLHLKDFSPE 114 (180)
T ss_pred hhhEEeecCCCCccccchhhHHHHHhH---HHHhhhhcCcccCChh
Confidence 344455566664333334999999998 7899999999999984
No 7
>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=46.18 E-value=6.6 Score=28.66 Aligned_cols=16 Identities=44% Similarity=0.862 Sum_probs=12.6
Q ss_pred CCCccCcccCCCCCCC
Q 033199 73 VDGYSPIYNENDWSPS 88 (125)
Q Consensus 73 VDgYSPIY~p~~ws~~ 88 (125)
-||+||-=|||-|++.
T Consensus 56 lDgFsP~~nPelWs~e 71 (124)
T PF05430_consen 56 LDGFSPAKNPELWSEE 71 (124)
T ss_dssp E-SS-TTTSGGGSSHH
T ss_pred ecCCCCcCCcccCCHH
Confidence 4899999999999975
No 8
>CHL00082 psbZ photosystem II protein Z
Probab=37.92 E-value=33 Score=23.52 Aligned_cols=23 Identities=22% Similarity=0.606 Sum_probs=16.1
Q ss_pred cCCCCCCCCCeeccChhHHHHHHHHH
Q 033199 81 NENDWSPSGDVYTGGATGLAIWAVTL 106 (125)
Q Consensus 81 ~p~~ws~~GD~Y~gg~~gL~~wA~tl 106 (125)
+||+|+++-+..--| ..+|..++
T Consensus 29 sp~~W~~sK~~v~~g---~~~W~~LV 51 (62)
T CHL00082 29 SPDGWSSNKNVVFSG---TSLWIGLV 51 (62)
T ss_pred CCCcchhhcceeeeH---HHHHHHHH
Confidence 699999887765553 66776543
No 9
>TIGR03043 PS_II_psbZ photosystem II core protein PsbZ. PsbZ is a core protein of photosystem II in thylakoid-containing Cyanobacteria and plant chloroplasts. The original Chlamydomonas gene symbol, ycf9, is a synonym. PsbZ controls the interaction of the reaction center core with the light-harvesting antenna.
Probab=36.06 E-value=32 Score=23.32 Aligned_cols=23 Identities=22% Similarity=0.534 Sum_probs=16.9
Q ss_pred cCCCCCCCCCeeccChhHHHHHHHHH
Q 033199 81 NENDWSPSGDVYTGGATGLAIWAVTL 106 (125)
Q Consensus 81 ~p~~ws~~GD~Y~gg~~gL~~wA~tl 106 (125)
+||+|+++-+..--| ..+|..++
T Consensus 26 sp~~W~~sK~~i~~g---~~~W~~LV 48 (58)
T TIGR03043 26 SPGGWSRSKNLIFSG---AGLWFGLV 48 (58)
T ss_pred CCCcchhccceeeeH---HHHHHHHH
Confidence 799999987766553 67786554
No 10
>PRK02576 psbZ photosystem II reaction center protein Z; Provisional
Probab=35.89 E-value=32 Score=23.61 Aligned_cols=23 Identities=17% Similarity=0.536 Sum_probs=16.6
Q ss_pred cCCCCCCCCCeeccChhHHHHHHHHH
Q 033199 81 NENDWSPSGDVYTGGATGLAIWAVTL 106 (125)
Q Consensus 81 ~p~~ws~~GD~Y~gg~~gL~~wA~tl 106 (125)
+||+|+++-+..--| ..+|..++
T Consensus 29 sp~gW~~sK~~v~~g---~~lW~~LV 51 (62)
T PRK02576 29 SPQNWGQSKRLILLG---SGVWVALV 51 (62)
T ss_pred CCCccccccceeeeH---HHHHHHHH
Confidence 699999887766553 66776554
No 11
>PRK13190 putative peroxiredoxin; Provisional
Probab=35.66 E-value=45 Score=25.25 Aligned_cols=53 Identities=17% Similarity=0.266 Sum_probs=36.4
Q ss_pred cceeEEEEecceeeeccccccCCCccccc-----chhhhhhhhcCCCCCccCcccCCCCCCCCCeec
Q 033199 32 KTSFKIVAKGGKIKTDKPYGVNGGMDLRE-----GVYQFVDKYGANVDGYSPIYNENDWSPSGDVYT 93 (125)
Q Consensus 32 R~s~~v~Asg~Kikt~~P~G~~Ggm~~k~-----Gvyqf~~KyGANVDgYSPIY~p~~ws~~GD~Y~ 93 (125)
|..| |+...+||+-...+-..+|.+..+ -.+|+++|+| .-+|-+|.|..|+-.
T Consensus 118 p~~f-iId~~G~I~~~~~~~~~~gr~~~ellr~l~~l~~~~~~~--------~~~p~~w~~g~~~~~ 175 (202)
T PRK13190 118 RGVF-IIDPNQIVRWMIYYPAETGRNIDEIIRITKALQVNWKRK--------VATPANWQPGQEGIV 175 (202)
T ss_pred eEEE-EECCCCEEEEEEEeCCCCCCCHHHHHHHHHHhhhHHhcC--------CCcCCCCCcCCceec
Confidence 5555 556666887666566666766555 5578888875 457999999777644
No 12
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=35.16 E-value=23 Score=26.84 Aligned_cols=38 Identities=26% Similarity=0.483 Sum_probs=25.2
Q ss_pred hhhhhhhcCCCCCccCcccCCCCCCCCCeeccChhHHHHHHHHHHHHhhhcee
Q 033199 63 YQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGAL 115 (125)
Q Consensus 63 yqf~~KyGANVDgYSPIY~p~~ws~~GD~Y~gg~~gL~~wA~tl~glL~~Gal 115 (125)
=-|+++||--| =|.|-+++. .+++|++-++.++++|++
T Consensus 81 ~~~v~RYG~~V-l~~Pp~~~~--------------t~~LW~~P~~lll~g~~~ 118 (126)
T PRK10144 81 GWMTERYGDFV-RYNPPLTGQ--------------TLVLWALPVVLLLLMALI 118 (126)
T ss_pred HHHHHhcCCeE-EecCCCCcc--------------hHHHHHHHHHHHHHHHHH
Confidence 34789998655 366655543 478998877766665543
No 13
>PF08576 DUF1764: Eukaryotic protein of unknown function (DUF1764); InterPro: IPR013885 This entry consists of eukaryotic proteins of unknown function, including many hypothetical proteins.
Probab=34.55 E-value=11 Score=26.40 Aligned_cols=23 Identities=39% Similarity=0.749 Sum_probs=14.9
Q ss_pred CCCCccCcccCCCCCCCCCeeccCh
Q 033199 72 NVDGYSPIYNENDWSPSGDVYTGGA 96 (125)
Q Consensus 72 NVDgYSPIY~p~~ws~~GD~Y~gg~ 96 (125)
-+||| |||+.||-.- |....|+|
T Consensus 69 teDGl-~IYt~eEL~i-g~~~gG~T 91 (102)
T PF08576_consen 69 TEDGL-PIYTEEELGI-GNPKGGGT 91 (102)
T ss_pred cCCCc-eEecHHHhCC-CCCCCCCC
Confidence 36787 8999998773 33333443
No 14
>COG4121 Uncharacterized conserved protein [Function unknown]
Probab=34.00 E-value=12 Score=31.05 Aligned_cols=16 Identities=31% Similarity=0.868 Sum_probs=14.3
Q ss_pred CCCccCcccCCCCCCC
Q 033199 73 VDGYSPIYNENDWSPS 88 (125)
Q Consensus 73 VDgYSPIY~p~~ws~~ 88 (125)
-||+||.-|||-|+++
T Consensus 174 lDgFsP~kNP~mW~~e 189 (252)
T COG4121 174 LDGFRPVKNPEMWEDE 189 (252)
T ss_pred cCCccccCChhhccHH
Confidence 4999999999999874
No 15
>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=33.42 E-value=41 Score=20.42 Aligned_cols=22 Identities=41% Similarity=0.782 Sum_probs=16.9
Q ss_pred hhhhhhhcCCCCCccCcccCCCCCCCCCee
Q 033199 63 YQFVDKYGANVDGYSPIYNENDWSPSGDVY 92 (125)
Q Consensus 63 yqf~~KyGANVDgYSPIY~p~~ws~~GD~Y 92 (125)
+||.||+|. -+|..|.|.-|+-
T Consensus 2 LQ~~d~~~v--------~tPanW~pGd~~i 23 (40)
T PF10417_consen 2 LQFTDKHGV--------ATPANWKPGDDVI 23 (40)
T ss_dssp HHHHHHHSS--------BBCTTTCTTSGEB
T ss_pred ceehhhhCc--------ccCcCCCCCCCeE
Confidence 689999963 5899999866654
No 16
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=31.44 E-value=30 Score=26.25 Aligned_cols=38 Identities=24% Similarity=0.385 Sum_probs=25.6
Q ss_pred hhhhhhhcCCCCCccCcccCCCCCCCCCeeccChhHHHHHHHHHHHHhhhcee
Q 033199 63 YQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGAL 115 (125)
Q Consensus 63 yqf~~KyGANVDgYSPIY~p~~ws~~GD~Y~gg~~gL~~wA~tl~glL~~Gal 115 (125)
=-|+++||--| =|.|-+++. .+++|.+-++.++.++++
T Consensus 81 ~~~v~RYG~~V-ly~Pp~~~~--------------t~~LW~~P~lll~~G~~~ 118 (126)
T TIGR03147 81 DFMTARFGDFV-LYNPPFKWQ--------------TLLLWLLPVLLLLLAFVL 118 (126)
T ss_pred HHHHHhcCCeE-EecCCCCcc--------------hHHHHHHHHHHHHHHHHH
Confidence 34799998655 366665543 478998877776665544
No 17
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=28.86 E-value=35 Score=29.33 Aligned_cols=22 Identities=14% Similarity=0.297 Sum_probs=18.6
Q ss_pred hhHHHHHHHHHHHHhhhceeee
Q 033199 96 ATGLAIWAVTLAGLLAGGALLV 117 (125)
Q Consensus 96 ~~gL~~wA~tl~glL~~Gallv 117 (125)
.+-+++|+++++|++..|.+..
T Consensus 406 ~~~~~LW~~Lv~gV~vL~~mA~ 427 (429)
T PF13163_consen 406 WKRWLLWGALVLGVAVLGGMAW 427 (429)
T ss_pred hhhhHHHHHHHHHHHHHHHHhe
Confidence 5678999999999999887654
No 18
>PRK15006 thiosulfate reductase cytochrome B subunit; Provisional
Probab=26.06 E-value=46 Score=26.87 Aligned_cols=16 Identities=25% Similarity=0.792 Sum_probs=12.9
Q ss_pred CCCCCccCcccCCCCC
Q 033199 71 ANVDGYSPIYNENDWS 86 (125)
Q Consensus 71 ANVDgYSPIY~p~~ws 86 (125)
+..-+|-|.|+||-|-
T Consensus 12 ~~~~~~~~~~~~~~~~ 27 (261)
T PRK15006 12 SQLANYVPQYTPDYWP 27 (261)
T ss_pred HHHhcccccCCccccH
Confidence 3456899999999995
No 19
>PF13179 DUF4006: Family of unknown function (DUF4006)
Probab=24.14 E-value=75 Score=22.10 Aligned_cols=21 Identities=38% Similarity=0.365 Sum_probs=17.1
Q ss_pred cChhHHHHHHHHHHHHhhhce
Q 033199 94 GGATGLAIWAVTLAGLLAGGA 114 (125)
Q Consensus 94 gg~~gL~~wA~tl~glL~~Ga 114 (125)
-|.+|.+|--++|+.+|++..
T Consensus 11 nGi~G~LIAvvLLLsIl~~lt 31 (66)
T PF13179_consen 11 NGITGMLIAVVLLLSILAFLT 31 (66)
T ss_pred cchHhHHHHHHHHHHHHHHHH
Confidence 378899999999988887654
No 20
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=22.11 E-value=28 Score=29.38 Aligned_cols=31 Identities=26% Similarity=0.637 Sum_probs=22.6
Q ss_pred cccCCCccccc---chhhhhhhhcCCCCCccCcc
Q 033199 50 YGVNGGMDLRE---GVYQFVDKYGANVDGYSPIY 80 (125)
Q Consensus 50 ~G~~Ggm~~k~---Gvyqf~~KyGANVDgYSPIY 80 (125)
+|+.|..+-.+ |+|+|=.++|.++..|-+-|
T Consensus 356 ~Gi~~~~~~~~~~~Gl~~FK~~F~g~~~e~~G~f 389 (406)
T PF02388_consen 356 GGISGDFDGSDPDYGLYKFKKGFGGQIVEYIGEF 389 (406)
T ss_dssp EE-SSSSTTTHTTHHHHHHHHCCT-CEEEE--EE
T ss_pred eCCCCCCCCCcccchHHHHhhcCCCcEEEeeeeE
Confidence 68888776655 99999999999998887644
No 21
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=20.86 E-value=50 Score=24.77 Aligned_cols=34 Identities=24% Similarity=0.239 Sum_probs=19.0
Q ss_pred CCCCCCCeeccChhHHHHHHHHHHHHhhhceeeee
Q 033199 84 DWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVY 118 (125)
Q Consensus 84 ~ws~~GD~Y~gg~~gL~~wA~tl~glL~~Gallvy 118 (125)
+.++.-..+.+|...++++.+ ++|+++.-+|+.|
T Consensus 53 ~~~ql~h~fs~~~i~~Ii~gv-~aGvIg~Illi~y 86 (122)
T PF01102_consen 53 ERSQLVHRFSEPAIIGIIFGV-MAGVIGIILLISY 86 (122)
T ss_dssp ---SSSSSSS-TCHHHHHHHH-HHHHHHHHHHHHH
T ss_pred CCcccccCccccceeehhHHH-HHHHHHHHHHHHH
Confidence 445555567777777777665 4566666666555
Done!