Query 032633
Match_columns 137
No_of_seqs 53 out of 55
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 03:57:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032633hhsearch_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 1.4E-68 3E-73 402.2 9.4 114 24-137 1-117 (117)
2 PF04725 PsbR: Photosystem II 100.0 3E-62 6.4E-67 359.8 7.4 98 40-137 1-99 (99)
3 PLN00083 photosystem II subuni 100.0 1.6E-44 3.5E-49 266.3 6.2 85 48-135 12-101 (101)
4 PF03918 CcmH: Cytochrome C bi 59.6 2.7 5.8E-05 32.4 -0.3 40 76-130 82-121 (148)
5 COG5659 FOG: Transposase [DNA 47.7 8.1 0.00017 34.9 0.7 50 62-112 98-171 (385)
6 COG4678 Muramidase (phage lamb 42.6 7.2 0.00016 32.1 -0.3 35 63-100 80-114 (180)
7 PF05430 Methyltransf_30: S-ad 41.9 7.9 0.00017 28.8 -0.2 16 85-100 56-71 (124)
8 CHL00082 psbZ photosystem II p 41.2 27 0.00059 24.3 2.4 23 93-118 29-51 (62)
9 TIGR03043 PS_II_psbZ photosyst 39.0 26 0.00057 24.1 2.0 23 93-118 26-48 (58)
10 PRK02576 psbZ photosystem II r 39.0 26 0.00057 24.4 2.0 23 93-118 29-51 (62)
11 PF08576 DUF1764: Eukaryotic p 36.2 10 0.00022 27.1 -0.4 22 85-108 70-91 (102)
12 PRK10144 formate-dependent nit 34.1 19 0.00042 27.7 0.9 37 76-127 82-118 (126)
13 PF13163 DUF3999: Protein of u 32.3 27 0.00059 30.6 1.6 22 108-129 406-427 (429)
14 COG4121 Uncharacterized conser 30.8 14 0.00031 31.1 -0.4 16 85-100 174-189 (252)
15 TIGR03147 cyt_nit_nrfF cytochr 30.3 25 0.00053 27.1 0.9 38 76-128 82-119 (126)
16 PRK15006 thiosulfate reductase 29.2 37 0.0008 27.9 1.8 16 83-98 12-27 (261)
17 PF13179 DUF4006: Family of un 28.7 55 0.0012 23.1 2.3 20 107-126 12-31 (66)
18 CHL00114 psbX photosystem II p 22.1 1E+02 0.0022 19.9 2.5 21 112-132 12-32 (39)
19 PF06195 DUF996: Protein of un 21.1 46 0.001 25.3 0.9 22 108-129 113-134 (139)
20 PF01737 Ycf9: YCF9; InterPro 21.0 32 0.00069 23.7 -0.0 23 93-118 26-48 (59)
21 PF01102 Glycophorin_A: Glycop 20.8 53 0.0012 25.0 1.1 34 96-130 53-86 (122)
22 PF10417 1-cysPrx_C: C-termina 20.2 44 0.00095 20.6 0.5 22 75-104 2-23 (40)
23 PF05283 MGC-24: Multi-glycosy 20.0 35 0.00076 27.7 0.0 22 100-128 159-180 (186)
No 1
>PLN00053 photosystem II subunit R; Provisional
Probab=100.00 E-value=1.4e-68 Score=402.19 Aligned_cols=114 Identities=80% Similarity=1.357 Sum_probs=111.8
Q ss_pred ccCCCCCCc--ceeEEEEccc-eeeeccccccCCCcccCccccCCCCCccCCcceeeehhcccCCCCccccccCCCCCCC
Q 032633 24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPS 100 (137)
Q Consensus 24 ~rglp~l~R--~s~~v~as~~-Kikt~kp~G~~g~m~~k~~vDa~gRk~kgkGvYqfv~KyGANVDgYSPIY~p~eWs~~ 100 (137)
+||||+++| ++|+|+||++ ||||++|||++|+|++|+|+||+|||+||||||||+||||||||||||||+||||||+
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 CCeeccChhHHHHHHHHHHHHhhhceeeeeecccccC
Q 032633 101 GDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ 137 (137)
Q Consensus 101 GD~Y~gG~~gL~~WA~tl~glL~~Gallvy~TSaLa~ 137 (137)
||+|+|||+||+|||+||+|||++|||||||||||+|
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=3e-62 Score=359.75 Aligned_cols=98 Identities=84% Similarity=1.404 Sum_probs=96.1
Q ss_pred ccc-eeeeccccccCCCcccCccccCCCCCccCCcceeeehhcccCCCCccccccCCCCCCCCCeeccChhHHHHHHHHH
Q 032633 40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTL 118 (137)
Q Consensus 40 s~~-Kikt~kp~G~~g~m~~k~~vDa~gRk~kgkGvYqfv~KyGANVDgYSPIY~p~eWs~~GD~Y~gG~~gL~~WA~tl 118 (137)
|++ |||||+|||++|+|++|+|+||+|||+||+|||||+||||||||||||||+||||||+||+|+|||+||+|||+||
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 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhceeeeeecccccC
Q 032633 119 AGLLAGGALLVYNTSALAQ 137 (137)
Q Consensus 119 ~glL~~Gallvy~TSaLa~ 137 (137)
+|||++|||||||||||+|
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=1.6e-44 Score=266.31 Aligned_cols=85 Identities=39% Similarity=0.615 Sum_probs=80.5
Q ss_pred cccccCCCcccCccccC----CCCCccCCcceeeehhcc-cCCCCccccccCCCCCCCCCeeccChhHHHHHHHHHHHHh
Q 032633 48 KPYGVNGGMDLREGLDA----SGRKAKGKGVYQFVDKYG-ANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLL 122 (137)
Q Consensus 48 kp~G~~g~m~~k~~vDa----~gRk~kgkGvYqfv~KyG-ANVDgYSPIY~p~eWs~~GD~Y~gG~~gL~~WA~tl~glL 122 (137)
|.-+.+.++.+|+.+|| +|||+||+|||||+|||| ||||||||||+||||+|+||+|+| ||+|||+||+|||
T Consensus 12 k~a~~q~~vgykgst~agsapkgRk~Kg~gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~G---gL~~WA~tlaglL 88 (101)
T PLN00083 12 KAAGGQAGVGYKGSTEAGSAPKTRSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEG---DLKLAAAAVAGVI 88 (101)
T ss_pred ccCccccccccccccccCCCCCCccCCCceEEEehhccCcccccccCCccChhhcCCCcchhhc---cHHHHHHHHHHHH
Confidence 45577889999999997 589999999999999999 999999999999999999999998 6999999999999
Q ss_pred hhceeeeeecccc
Q 032633 123 AGGALLVYNTSAL 135 (137)
Q Consensus 123 ~~Gallvy~TSaL 135 (137)
++|||||||||||
T Consensus 89 g~GAllVy~TSaL 101 (101)
T PLN00083 89 GTGALAILLTSAL 101 (101)
T ss_pred ccceeEEEecccC
Confidence 9999999999997
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=59.62 E-value=2.7 Score=32.39 Aligned_cols=40 Identities=38% Similarity=0.693 Sum_probs=8.8
Q ss_pred eeehhcccCCCCccccccCCCCCCCCCeeccChhHHHHHHHHHHHHhhhceeeee
Q 032633 76 QFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVY 130 (137)
Q Consensus 76 qfv~KyGANVDgYSPIY~p~eWs~~GD~Y~gG~~gL~~WA~tl~glL~~Gallvy 130 (137)
-|+++||--| .|+|. ..| .++++|++-++.++++++++++
T Consensus 82 ~~v~rYG~~V-----l~~Pp--------~~~--~~~~lW~~P~~~l~~g~~~~~~ 121 (148)
T PF03918_consen 82 YFVERYGEFV-----LYEPP--------FKG--FTWLLWLGPFLLLLLGGALLFR 121 (148)
T ss_dssp HHHHHHTTT------EES----------S--------------------------
T ss_pred HHHHhcCcce-----eecCC--------CCc--cHHHHHHHHHHHHHHHHHHHHH
Confidence 3789999766 44443 122 2589999999988888877664
No 5
>COG5659 FOG: Transposase [DNA replication, recombination, and repair]
Probab=47.68 E-value=8.1 Score=34.89 Aligned_cols=50 Identities=34% Similarity=0.696 Sum_probs=39.1
Q ss_pred ccCCCCCccCC---cce-eeehhcc-------------cCCCCcccc----ccCCCCCCCCCe---eccChhHHH
Q 032633 62 LDASGRKAKGK---GVY-QFVDKYG-------------ANVDGYSPI----YNENDWSPSGDV---YTGGATGLA 112 (137)
Q Consensus 62 vDa~gRk~kgk---GvY-qfv~KyG-------------ANVDgYSPI----Y~p~eWs~~GD~---Y~gG~~gL~ 112 (137)
+|.-|=++||| ||+ ||+-.|| +|.+++-|| |-|++|-+.||. |+- .++|+
T Consensus 98 idetg~~kkgk~s~~v~rqy~G~Lgkidn~~v~v~~~~~~~~~~~~i~~~~~kp~~~l~e~~k~~~f~t-kP~ia 171 (385)
T COG5659 98 IDETGFPKKGKHSDGVARQYIGNLGKIDNCQVAVSLYGITEGGTLPIASQLYKPEEWLDEGDKRAKFAT-KPEIA 171 (385)
T ss_pred ccccCCCcccccccchhhhhhhhhhhhhhhHHHHHHhhhhcceeEeechhccCChhhccccchhhhhcc-CchHH
Confidence 57788889999 888 5555554 788999999 999999999999 743 34454
No 6
>COG4678 Muramidase (phage lambda lysozyme) [Carbohydrate transport and metabolism]
Probab=42.57 E-value=7.2 Score=32.15 Aligned_cols=35 Identities=29% Similarity=0.576 Sum_probs=30.0
Q ss_pred cCCCCCccCCcceeeehhcccCCCCccccccCCCCCCC
Q 032633 63 DASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPS 100 (137)
Q Consensus 63 Da~gRk~kgkGvYqfv~KyGANVDgYSPIY~p~eWs~~ 100 (137)
+..|-+.+.-|.|||.+++ -|.|.|-|.|.+|+|.
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 3346778889999999998 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=41.91 E-value=7.9 Score=28.75 Aligned_cols=16 Identities=44% Similarity=0.862 Sum_probs=12.6
Q ss_pred CCCccccccCCCCCCC
Q 032633 85 VDGYSPIYNENDWSPS 100 (137)
Q Consensus 85 VDgYSPIY~p~eWs~~ 100 (137)
-||+||-=|||-|++.
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=41.17 E-value=27 Score=24.30 Aligned_cols=23 Identities=22% Similarity=0.606 Sum_probs=16.4
Q ss_pred cCCCCCCCCCeeccChhHHHHHHHHH
Q 032633 93 NENDWSPSGDVYTGGATGLAIWAVTL 118 (137)
Q Consensus 93 ~p~eWs~~GD~Y~gG~~gL~~WA~tl 118 (137)
+||+|+++-+..--| ..+|..++
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 699999987765553 66786554
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=39.01 E-value=26 Score=24.05 Aligned_cols=23 Identities=22% Similarity=0.534 Sum_probs=17.2
Q ss_pred cCCCCCCCCCeeccChhHHHHHHHHH
Q 032633 93 NENDWSPSGDVYTGGATGLAIWAVTL 118 (137)
Q Consensus 93 ~p~eWs~~GD~Y~gG~~gL~~WA~tl 118 (137)
+||+|+++-+..--| ..+|..++
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 899999998766553 67886554
No 10
>PRK02576 psbZ photosystem II reaction center protein Z; Provisional
Probab=38.96 E-value=26 Score=24.37 Aligned_cols=23 Identities=17% Similarity=0.536 Sum_probs=17.0
Q ss_pred cCCCCCCCCCeeccChhHHHHHHHHH
Q 032633 93 NENDWSPSGDVYTGGATGLAIWAVTL 118 (137)
Q Consensus 93 ~p~eWs~~GD~Y~gG~~gL~~WA~tl 118 (137)
+||+|+++-+..--| ..+|..++
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 799999987776554 66787654
No 11
>PF08576 DUF1764: Eukaryotic protein of unknown function (DUF1764); InterPro: IPR013885 This entry consists of eukaryotic proteins of unknown function, including many hypothetical proteins.
Probab=36.22 E-value=10 Score=27.10 Aligned_cols=22 Identities=41% Similarity=0.776 Sum_probs=14.5
Q ss_pred CCCccccccCCCCCCCCCeeccCh
Q 032633 85 VDGYSPIYNENDWSPSGDVYTGGA 108 (137)
Q Consensus 85 VDgYSPIY~p~eWs~~GD~Y~gG~ 108 (137)
+||| |||+.||-.- |....|+|
T Consensus 70 eDGl-~IYt~eEL~i-g~~~gG~T 91 (102)
T PF08576_consen 70 EDGL-PIYTEEELGI-GNPKGGGT 91 (102)
T ss_pred CCCc-eEecHHHhCC-CCCCCCCC
Confidence 6776 8999998773 33334443
No 12
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=34.06 E-value=19 Score=27.71 Aligned_cols=37 Identities=27% Similarity=0.532 Sum_probs=24.1
Q ss_pred eeehhcccCCCCccccccCCCCCCCCCeeccChhHHHHHHHHHHHHhhhcee
Q 032633 76 QFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGAL 127 (137)
Q Consensus 76 qfv~KyGANVDgYSPIY~p~eWs~~GD~Y~gG~~gL~~WA~tl~glL~~Gal 127 (137)
-|+++||--| =|.|-+++. .+++|++-++.++++|++
T Consensus 82 ~~v~RYG~~V-l~~Pp~~~~--------------t~~LW~~P~~lll~g~~~ 118 (126)
T PRK10144 82 WMTERYGDFV-RYNPPLTGQ--------------TLVLWALPVVLLLLMALI 118 (126)
T ss_pred HHHHhcCCeE-EecCCCCcc--------------hHHHHHHHHHHHHHHHHH
Confidence 3788998655 355555443 478999877766665543
No 13
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=32.28 E-value=27 Score=30.57 Aligned_cols=22 Identities=14% Similarity=0.297 Sum_probs=18.7
Q ss_pred hhHHHHHHHHHHHHhhhceeee
Q 032633 108 ATGLAIWAVTLAGLLAGGALLV 129 (137)
Q Consensus 108 ~~gL~~WA~tl~glL~~Gallv 129 (137)
.+-+++|+++++|++..|.+..
T Consensus 406 ~~~~~LW~~Lv~gV~vL~~mA~ 427 (429)
T PF13163_consen 406 WKRWLLWGALVLGVAVLGGMAW 427 (429)
T ss_pred hhhhHHHHHHHHHHHHHHHHhe
Confidence 5668999999999999887654
No 14
>COG4121 Uncharacterized conserved protein [Function unknown]
Probab=30.81 E-value=14 Score=31.10 Aligned_cols=16 Identities=31% Similarity=0.868 Sum_probs=14.2
Q ss_pred CCCccccccCCCCCCC
Q 032633 85 VDGYSPIYNENDWSPS 100 (137)
Q Consensus 85 VDgYSPIY~p~eWs~~ 100 (137)
-||+||.-|||-|+++
T Consensus 174 lDgFsP~kNP~mW~~e 189 (252)
T COG4121 174 LDGFRPVKNPEMWEDE 189 (252)
T ss_pred cCCccccCChhhccHH
Confidence 4999999999999874
No 15
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=30.26 E-value=25 Score=27.11 Aligned_cols=38 Identities=26% Similarity=0.444 Sum_probs=24.9
Q ss_pred eeehhcccCCCCccccccCCCCCCCCCeeccChhHHHHHHHHHHHHhhhceee
Q 032633 76 QFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALL 128 (137)
Q Consensus 76 qfv~KyGANVDgYSPIY~p~eWs~~GD~Y~gG~~gL~~WA~tl~glL~~Gall 128 (137)
-|+++||--| =|.|-+++. .+++|.+-++.++.+++++
T Consensus 82 ~~v~RYG~~V-ly~Pp~~~~--------------t~~LW~~P~lll~~G~~~~ 119 (126)
T TIGR03147 82 FMTARFGDFV-LYNPPFKWQ--------------TLLLWLLPVLLLLLAFVLL 119 (126)
T ss_pred HHHHhcCCeE-EecCCCCcc--------------hHHHHHHHHHHHHHHHHHH
Confidence 3789998655 355555443 4789988777776655443
No 16
>PRK15006 thiosulfate reductase cytochrome B subunit; Provisional
Probab=29.20 E-value=37 Score=27.93 Aligned_cols=16 Identities=25% Similarity=0.792 Sum_probs=13.0
Q ss_pred cCCCCccccccCCCCC
Q 032633 83 ANVDGYSPIYNENDWS 98 (137)
Q Consensus 83 ANVDgYSPIY~p~eWs 98 (137)
+..-+|-|.|+||-|-
T Consensus 12 ~~~~~~~~~~~~~~~~ 27 (261)
T PRK15006 12 SQLANYVPQYTPDYWP 27 (261)
T ss_pred HHHhcccccCCccccH
Confidence 3456899999999995
No 17
>PF13179 DUF4006: Family of unknown function (DUF4006)
Probab=28.66 E-value=55 Score=23.11 Aligned_cols=20 Identities=40% Similarity=0.376 Sum_probs=16.9
Q ss_pred ChhHHHHHHHHHHHHhhhce
Q 032633 107 GATGLAIWAVTLAGLLAGGA 126 (137)
Q Consensus 107 G~~gL~~WA~tl~glL~~Ga 126 (137)
|.+|.+|--++|+.+|++..
T Consensus 12 Gi~G~LIAvvLLLsIl~~lt 31 (66)
T PF13179_consen 12 GITGMLIAVVLLLSILAFLT 31 (66)
T ss_pred chHhHHHHHHHHHHHHHHHH
Confidence 78899999999998887754
No 18
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=22.10 E-value=1e+02 Score=19.93 Aligned_cols=21 Identities=14% Similarity=0.082 Sum_probs=15.5
Q ss_pred HHHHHHHHHHhhhceeeeeec
Q 032633 112 AIWAVTLAGLLAGGALLVYNT 132 (137)
Q Consensus 112 ~~WA~tl~glL~~Gallvy~T 132 (137)
++|...++++-.++||+..+.
T Consensus 12 L~~Ga~ivvipi~~aLifvSq 32 (39)
T CHL00114 12 LLLGAIIVVIPITLALLFVSQ 32 (39)
T ss_pred HHHHHHHhHHHhhhheEEEec
Confidence 467777777777888877764
No 19
>PF06195 DUF996: Protein of unknown function (DUF996); InterPro: IPR010397 This is a family of uncharacterised bacterial and archaeal proteins.
Probab=21.13 E-value=46 Score=25.28 Aligned_cols=22 Identities=14% Similarity=0.372 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHHHhhhceeee
Q 032633 108 ATGLAIWAVTLAGLLAGGALLV 129 (137)
Q Consensus 108 ~~gL~~WA~tl~glL~~Gallv 129 (137)
|.|+++|.++++-++..|.+++
T Consensus 113 tag~ly~iGAiL~IIlIG~ii~ 134 (139)
T PF06195_consen 113 TAGLLYFIGAILTIILIGLIII 134 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5689999999988888887764
No 20
>PF01737 Ycf9: YCF9; InterPro: IPR002644 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 PsbZ (Ycf9), which is a core low molecular weight transmembrane protein of photosystem II in thylakoid-containing chloroplasts of cyanobacteria and plants. It is thought to be located at the interface of PSII and LHCII (light-harvesting complex II) complexes, the latter containing the light-harvesting antenna. PsbZ appears to act as a structural factor, or linker, that stabilises the PSII-LHCII supercomplexes, which fail to form in PsbZ-deficient mutants. This may in part be due to the marked decrease in two LHCII antenna proteins, CP26 and CP29, found in PsbZ-deficient mutants, which result in structural changes, as well as functional modifications in PSII []. PsbZ may also be involved in photo-protective processes under sub-optimal growth conditions.; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009539 photosystem II reaction center; PDB: 3A0B_Z 3ARC_Z 3A0H_Z 3PRQ_Z 4FBY_l 2AXT_z 3PRR_Z 3BZ1_Z 3KZI_Z 1S5L_Z ....
Probab=20.95 E-value=32 Score=23.74 Aligned_cols=23 Identities=22% Similarity=0.601 Sum_probs=16.1
Q ss_pred cCCCCCCCCCeeccChhHHHHHHHHH
Q 032633 93 NENDWSPSGDVYTGGATGLAIWAVTL 118 (137)
Q Consensus 93 ~p~eWs~~GD~Y~gG~~gL~~WA~tl 118 (137)
+||+|+++-+.--- |..+|..++
T Consensus 26 sp~~W~~sK~~i~~---g~~lW~~LV 48 (59)
T PF01737_consen 26 SPDGWSSSKNLIFS---GAGLWIGLV 48 (59)
T ss_dssp STSCCCCHHHHHHH---HHHHHHHHH
T ss_pred CCcchhhhccchhh---HHHHHHHHH
Confidence 69999998765433 366887654
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=20.79 E-value=53 Score=25.03 Aligned_cols=34 Identities=24% Similarity=0.239 Sum_probs=19.3
Q ss_pred CCCCCCCeeccChhHHHHHHHHHHHHhhhceeeee
Q 032633 96 DWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVY 130 (137)
Q Consensus 96 eWs~~GD~Y~gG~~gL~~WA~tl~glL~~Gallvy 130 (137)
+.++.-..+.++...++++.+ ++|+++.-+|+.|
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 445555567777777777765 4566666666655
No 22
>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=20.23 E-value=44 Score=20.62 Aligned_cols=22 Identities=41% Similarity=0.782 Sum_probs=16.0
Q ss_pred eeeehhcccCCCCccccccCCCCCCCCCee
Q 032633 75 YQFVDKYGANVDGYSPIYNENDWSPSGDVY 104 (137)
Q Consensus 75 Yqfv~KyGANVDgYSPIY~p~eWs~~GD~Y 104 (137)
+||+||+|. -+|..|.|.-|+-
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 478888853 5899999865554
No 23
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=20.01 E-value=35 Score=27.73 Aligned_cols=22 Identities=32% Similarity=0.391 Sum_probs=16.7
Q ss_pred CCCeeccChhHHHHHHHHHHHHhhhceee
Q 032633 100 SGDVYTGGATGLAIWAVTLAGLLAGGALL 128 (137)
Q Consensus 100 ~GD~Y~gG~~gL~~WA~tl~glL~~Gall 128 (137)
|+-+|.|| .|+.+|||+++.++
T Consensus 159 D~~SFiGG-------IVL~LGv~aI~ff~ 180 (186)
T PF05283_consen 159 DAASFIGG-------IVLTLGVLAIIFFL 180 (186)
T ss_pred chhhhhhH-------HHHHHHHHHHHHHH
Confidence 44567888 78888999887665
Done!