Query 032020
Match_columns 148
No_of_seqs 107 out of 423
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 08:30:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032020.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032020hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3292 Predicted membrane pro 100.0 1.8E-39 4E-44 248.2 9.1 135 1-146 1-135 (196)
2 COG4539 Predicted membrane pro 100.0 4.7E-38 1E-42 239.1 7.6 126 7-146 2-127 (180)
3 PF06127 DUF962: Protein of un 99.9 2E-24 4.4E-29 153.1 7.2 69 7-146 2-70 (95)
4 COG4323 Predicted membrane pro 95.5 0.019 4.2E-07 40.5 3.6 27 120-146 52-78 (105)
5 COG2245 Predicted membrane pro 62.6 34 0.00074 27.0 6.3 23 122-145 101-123 (182)
6 PF00283 Cytochrom_B559: Cytoc 59.8 7.5 0.00016 21.8 1.6 14 26-39 15-28 (29)
7 PF14975 DUF4512: Domain of un 27.2 37 0.00079 23.8 1.2 15 31-45 1-15 (88)
8 PHA02554 13 neck protein; Prov 22.5 39 0.00085 28.9 0.8 26 9-34 37-62 (311)
9 PF05398 PufQ: PufQ cytochrome 22.2 1.8E+02 0.0038 19.8 3.8 29 119-147 28-56 (73)
10 PF04431 Pec_lyase_N: Pectate 20.1 48 0.001 21.3 0.7 16 14-29 19-34 (56)
No 1
>KOG3292 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=1.8e-39 Score=248.23 Aligned_cols=135 Identities=59% Similarity=1.069 Sum_probs=119.4
Q ss_pred CCCCCCCCHHHHHHHHhhhhcCcchhhhhhhhhhHHHHHHHHHHhcCCCccccCccccccccccccccccccHHHHHHHH
Q 032020 1 MGKSGLLDLEKHFAFYGAYHSNKINVLIHTLFVWPILFSTLMFLHFTPSVCDFSDKVSFLPCGLFGHALVFNLGFLFTLI 80 (148)
Q Consensus 1 m~~~~~~~L~~~l~fY~~yH~N~~N~~IH~i~VP~Il~s~~~ll~~~p~~~~~~~~~~~~~~~~~~~~~~~n~a~l~~~~ 80 (148)
|+. +++|||++++||++||+||+|+.||.+|||+|++|.++++.+++..... -.++...+|.|.++.+.
T Consensus 1 Ms~-~l~dL~k~~aFY~aYHsNPiNIlIH~ifvp~ilfs~l~lLh~l~f~qsl----------tl~~vLr~nv~~~~~v~ 69 (196)
T KOG3292|consen 1 MSE-GLLDLEKHFAFYGAYHSNPINILIHSIFVPPILFSGLLLLHSLGFYQSL----------TLDGVLRINVGFLVSVL 69 (196)
T ss_pred CCc-hhhhHHHhhhHHHHhccCCceEEEEeeehhHHHHHHHHHHHhcCceEEE----------EeeeEEEeehHHHHHHH
Confidence 443 4789999999999999999999999999999999999999988763221 01234678999999999
Q ss_pred HHHHHHhhchhhHHHHHHHHHHHHHHHHHHHhhhchhHHHHHHHHHHHHHHHHHHHhhcccccCCC
Q 032020 81 YASFYYCLDKKAGSLAALLCFACWVGASLLSNRLGFSLAWKVAVAAQLICWTGQFLGHGIFEGTSS 146 (148)
Q Consensus 81 ~~~yY~~Ld~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~al~i~vv~Wi~QFiGH~vfEgr~P 146 (148)
|+++|+.||++-|++++.++..||.....++...+.+...+.+++.|++||+.||+|||+||||||
T Consensus 70 yaiFYi~Ld~~sGlla~vl~l~~~i~~s~l~~r~~~sl~~k~g~~s~licWi~QFvGHGvFEKR~P 135 (196)
T KOG3292|consen 70 YAIFYILLDKKSGLLAAVLCLSCWIGSSFLAHRLGLSLKLKVGLASQLICWIGQFVGHGVFEKRAP 135 (196)
T ss_pred HHHHheeecccccHHHHHHHHHHHhhHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcccccccccch
Confidence 999999999999999999999999999999888775666788999999999999999999999999
No 2
>COG4539 Predicted membrane protein [Function unknown]
Probab=100.00 E-value=4.7e-38 Score=239.06 Aligned_cols=126 Identities=31% Similarity=0.433 Sum_probs=105.6
Q ss_pred CCHHHHHHHHhhhhcCcchhhhhhhhhhHHHHHHHHHHhcCCCccccCccccccccccccccccccHHHHHHHHHHHHHH
Q 032020 7 LDLEKHFAFYGAYHSNKINVLIHTLFVWPILFSTLMFLHFTPSVCDFSDKVSFLPCGLFGHALVFNLGFLFTLIYASFYY 86 (148)
Q Consensus 7 ~~L~~~l~fY~~yH~N~~N~~IH~i~VP~Il~s~~~ll~~~p~~~~~~~~~~~~~~~~~~~~~~~n~a~l~~~~~~~yY~ 86 (148)
.+|.|+++||++|||||+|+.||.+|||+|++|..+++++.-... .++...+|.+.++.+++.++|+
T Consensus 2 ~~Ls~~lsfYaaYH~nprNI~iH~i~IP~ills~avllhr~vi~l-------------~~~~l~is~a~ll~va~~iFYl 68 (180)
T COG4539 2 LDLSDHLSFYAAYHHNPRNILIHFIGIPTILLSGAVLLHRPVIGL-------------SNSKLQISPALLLSVAFSIFYL 68 (180)
T ss_pred ccHHHHHHHHHHHhcCCcceeeeeecchHHHHHHHHHhhcceeee-------------cCCcceecHHHHHHHHHHHHhe
Confidence 489999999999999999999999999999999999999854311 1234678999999999999999
Q ss_pred hhchhhHHHHHHHHHHHHHHHHHHHhhhchhHHHHHHHHHHHHHHHHHHHhhcccccCCC
Q 032020 87 CLDKKAGSLAALLCFACWVGASLLSNRLGFSLAWKVAVAAQLICWTGQFLGHGIFEGTSS 146 (148)
Q Consensus 87 ~Ld~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~al~i~vv~Wi~QFiGH~vfEgr~P 146 (148)
+||++.|++|++++....+....+++... +...+..+++|++|||.||+|||+||||||
T Consensus 69 ~Ldl~~Gll~~~ll~l~~wi~~~l~a~~t-~a~l~~~lglfvIgWI~QFVGHgvfEkRkP 127 (180)
T COG4539 69 RLDLPFGLLMGVLLLLLVWILLALAAHRT-DAWLKQGLGLFVIGWIFQFVGHGVFEKRKP 127 (180)
T ss_pred eeccchhHHHHHHHHHHHHHHHHHHHhhH-HHHHhcCceeeeehHHHHhccccccccCCc
Confidence 99999999999988774333344444322 233467899999999999999999999999
No 3
>PF06127 DUF962: Protein of unknown function (DUF962); InterPro: IPR009305 This family consists of several eukaryotic and prokaryotic proteins of unknown function. The yeast protein P25338 from SWISSPROT has been found to be non-essential for cell growth.
Probab=99.91 E-value=2e-24 Score=153.06 Aligned_cols=69 Identities=41% Similarity=0.635 Sum_probs=61.9
Q ss_pred CCHHHHHHHHhhhhcCcchhhhhhhhhhHHHHHHHHHHhcCCCccccCccccccccccccccccccHHHHHHHHHHHHHH
Q 032020 7 LDLEKHFAFYGAYHSNKINVLIHTLFVWPILFSTLMFLHFTPSVCDFSDKVSFLPCGLFGHALVFNLGFLFTLIYASFYY 86 (148)
Q Consensus 7 ~~L~~~l~fY~~yH~N~~N~~IH~i~VP~Il~s~~~ll~~~p~~~~~~~~~~~~~~~~~~~~~~~n~a~l~~~~~~~yY~ 86 (148)
.|+|||+++|++|||||+|+.+|++|||+|++|++.++... +
T Consensus 2 ~~~~~~~~~Y~~~H~~~~n~~lH~igvp~~~~~~~~~~~~~------------------------~-------------- 43 (95)
T PF06127_consen 2 KSLEEFFAFYLSYHRNPINRALHFIGVPLIIFSLLLLLARI------------------------P-------------- 43 (95)
T ss_pred cCHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHHHHHc------------------------c--------------
Confidence 48999999999999999999999999999999998776531 1
Q ss_pred hhchhhHHHHHHHHHHHHHHHHHHHhhhchhHHHHHHHHHHHHHHHHHHHhhcccccCCC
Q 032020 87 CLDKKAGSLAALLCFACWVGASLLSNRLGFSLAWKVAVAAQLICWTGQFLGHGIFEGTSS 146 (148)
Q Consensus 87 ~Ld~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~al~i~vv~Wi~QFiGH~vfEgr~P 146 (148)
|+.+++++++||+.|++||++||||||
T Consensus 44 ---------------------------------~~~~l~~~~~g~~~q~~GH~~~E~~~P 70 (95)
T PF06127_consen 44 ---------------------------------WWLALAVFVVGWGLQFIGHFFFEKNKP 70 (95)
T ss_pred ---------------------------------HHHHHHHHHHHHHHHHHhHHHHHcCCC
Confidence 455788999999999999999999999
No 4
>COG4323 Predicted membrane protein [Function unknown]
Probab=95.48 E-value=0.019 Score=40.49 Aligned_cols=27 Identities=30% Similarity=0.581 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccCCC
Q 032020 120 WKVAVAAQLICWTGQFLGHGIFEGTSS 146 (148)
Q Consensus 120 ~~~al~i~vv~Wi~QFiGH~vfEgr~P 146 (148)
|++-++.=+++...-.+||-+|||.+|
T Consensus 52 w~wllAapv~GYgFAWvGHFvFEKNRP 78 (105)
T COG4323 52 WRWLLAAPVIGYGFAWVGHFVFEKNRP 78 (105)
T ss_pred hHHHHHhhhhcccceeeeeeeeecCCC
Confidence 444556666777777789999999998
No 5
>COG2245 Predicted membrane protein [Function unknown]
Probab=62.63 E-value=34 Score=27.03 Aligned_cols=23 Identities=17% Similarity=0.322 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHhhcccccCC
Q 032020 122 VAVAAQLICWTGQFLGHGIFEGTS 145 (148)
Q Consensus 122 ~al~i~vv~Wi~QFiGH~vfEgr~ 145 (148)
..++-|++.|++|.+|- +||||.
T Consensus 101 ~~Lag~Vi~wIl~Iisa-yf~kka 123 (182)
T COG2245 101 SFLAGFVILWILYIISA-YFQKKA 123 (182)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHH
Confidence 45788999999999998 788874
No 6
>PF00283 Cytochrom_B559: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits; InterPro: IPR013081 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 []. Cytochrome b559, which forms part of the reaction centre core of PSII is a heterodimer composed of one alpha subunit (PsbE), one beta (PsbF) subunit, and a haem cofactor. Two histidine residues from each subunit coordinate the haem. Although cytochrome b559 is a redox-active protein, it is unlikely to be involved in the primary electron transport in PSII due to its very slow photo-oxidation and photo-reduction kinetics. Instead, cytochrome b559 could participate in a secondary electron transport pathway that helps protect PSII from photo-damage. Cytochrome b559 is essential for PSII assembly []. This domain occurs in both the alpha and beta subunits of cytochrome B559. In the alpha sbunit it occurs together with a lumenal domain (IPR013082 from INTERPRO), while in the beta subunit it occurs on its own.; GO: 0046872 metal ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009536 plastid, 0009579 thylakoid, 0016021 integral to membrane; PDB: 3ARC_f 3A0H_f 3A0B_f 1W5C_K 1S5L_e 3BZ2_E 3PRQ_E 1IZL_P 2AXT_E 4FBY_R ....
Probab=59.81 E-value=7.5 Score=21.84 Aligned_cols=14 Identities=29% Similarity=0.401 Sum_probs=12.1
Q ss_pred hhhhhhhhhHHHHH
Q 032020 26 VLIHTLFVWPILFS 39 (148)
Q Consensus 26 ~~IH~i~VP~Il~s 39 (148)
-+||.+.||.+++.
T Consensus 15 ~~IH~l~iPtvf~~ 28 (29)
T PF00283_consen 15 WAIHALTIPTVFFL 28 (29)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred eeeeecccceEEec
Confidence 47999999999875
No 7
>PF14975 DUF4512: Domain of unknown function (DUF4512)
Probab=27.21 E-value=37 Score=23.83 Aligned_cols=15 Identities=13% Similarity=0.317 Sum_probs=12.2
Q ss_pred hhhhHHHHHHHHHHh
Q 032020 31 LFVWPILFSTLMFLH 45 (148)
Q Consensus 31 i~VP~Il~s~~~ll~ 45 (148)
||||.|++=++..++
T Consensus 1 VCIPCivIPvLLwIy 15 (88)
T PF14975_consen 1 VCIPCIVIPVLLWIY 15 (88)
T ss_pred CccchhHHHHHHHHH
Confidence 689999888887776
No 8
>PHA02554 13 neck protein; Provisional
Probab=22.54 E-value=39 Score=28.86 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=20.8
Q ss_pred HHHHHHHHhhhhcCcchhhhhhhhhh
Q 032020 9 LEKHFAFYGAYHSNKINVLIHTLFVW 34 (148)
Q Consensus 9 L~~~l~fY~~yH~N~~N~~IH~i~VP 34 (148)
.++-+..|++||.|=+||.-+.+-|-
T Consensus 37 I~rALely~EYH~dG~~k~y~~~~~t 62 (311)
T PHA02554 37 IQRALELYGEYHYDGVNKGYLKFKVT 62 (311)
T ss_pred HHHHHHHHHHHhccchhceeEEEEcc
Confidence 46788999999999999986655443
No 9
>PF05398 PufQ: PufQ cytochrome subunit; InterPro: IPR008800 This family consists of bacterial PufQ proteins. PufQ is required for bacteriochlorophyll biosynthesis serving a regulatory function in the formation of photosynthetic complexes [].; GO: 0015979 photosynthesis, 0030494 bacteriochlorophyll biosynthetic process
Probab=22.20 E-value=1.8e+02 Score=19.76 Aligned_cols=29 Identities=10% Similarity=0.277 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccCCCC
Q 032020 119 AWKVAVAAQLICWTGQFLGHGIFEGTSSF 147 (148)
Q Consensus 119 ~~~~al~i~vv~Wi~QFiGH~vfEgr~P~ 147 (148)
.+..++.+..++|+.+.+=|+-+-.|-|+
T Consensus 28 IflaAlP~a~l~W~~~~ir~~~lp~~GPi 56 (73)
T PF05398_consen 28 IFLAALPFATLTWAYALIRHRSLPEKGPI 56 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcCcccChh
Confidence 34456777788888888888877777775
No 10
>PF04431 Pec_lyase_N: Pectate lyase, N terminus; InterPro: IPR007524 This region is found N-terminal to the pectate lyase domain (IPR002022 from INTERPRO) in some plant pectate lyase enzymes.; GO: 0030570 pectate lyase activity
Probab=20.09 E-value=48 Score=21.27 Aligned_cols=16 Identities=31% Similarity=0.243 Sum_probs=12.7
Q ss_pred HHHhhhhcCcchhhhh
Q 032020 14 AFYGAYHSNKINVLIH 29 (148)
Q Consensus 14 ~fY~~yH~N~~N~~IH 29 (148)
.--.+||.||.|+.=|
T Consensus 19 ~a~~aY~pdP~~Vt~~ 34 (56)
T PF04431_consen 19 AALAAYVPDPENVTNE 34 (56)
T ss_pred HHHHhcCCCHHHHHHH
Confidence 4467999999988765
Done!