Query 045254
Match_columns 444
No_of_seqs 129 out of 667
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 11:22:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045254.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045254hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03140 DUF247: Plant protein 100.0 1E-105 2E-110 827.0 33.6 375 50-428 1-391 (391)
2 PF14770 TMEM18: Transmembrane 60.4 13 0.00029 32.4 4.1 44 392-438 56-104 (123)
3 PHA02103 hypothetical protein 51.7 29 0.00063 29.4 4.5 77 281-360 11-104 (135)
4 PF14579 HHH_6: Helix-hairpin- 46.5 75 0.0016 25.7 6.3 83 278-365 1-87 (90)
5 PF12911 OppC_N: N-terminal TM 28.6 70 0.0015 23.1 3.1 33 400-434 3-38 (56)
6 PF02468 PsbN: Photosystem II 27.5 61 0.0013 23.0 2.4 28 417-444 4-31 (43)
7 PF13172 PepSY_TM_1: PepSY-ass 26.9 72 0.0016 20.9 2.6 20 416-435 12-31 (34)
8 KOG3110 Riboflavin kinase [Coe 26.6 45 0.00098 29.5 2.0 63 65-127 65-138 (153)
9 KOG4134 DNA-dependent RNA poly 23.9 67 0.0014 30.9 2.7 37 44-91 21-57 (253)
10 PF15103 G0-G1_switch_2: G0/G1 23.6 73 0.0016 26.8 2.5 24 416-439 29-52 (102)
11 PF04531 Phage_holin_1: Bacter 23.5 90 0.0019 25.2 3.1 31 405-439 4-34 (84)
No 1
>PF03140 DUF247: Plant protein of unknown function; InterPro: IPR004158 The function of the plant proteins constituting this family is unknown.
Probab=100.00 E-value=1.1e-105 Score=826.96 Aligned_cols=375 Identities=41% Similarity=0.689 Sum_probs=335.5
Q ss_pred eeecCccccccCCCCccceEEEeccCCCCCchhhhHHHHHHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHHHHHhccccC
Q 045254 50 IFRVPQSFVEVHGKSYEPHIVSIGPYHHGEDHVKMIQEHKWRYLGNLLNRLKNAKGLGLEDFLKAVEPLEMKARECYSET 129 (444)
Q Consensus 50 I~rVP~~lr~~n~~aY~P~vVSIGPyHhg~~~L~~mE~~K~~~~~~~l~r~~~~~~~~l~~~~~~i~~~e~~~R~~Y~e~ 129 (444)
|||||+++|++|++||+|++|||||||||+++|+.||++|++|++.|++|.+ ..+.++++++++|+++|++||+||+++
T Consensus 1 I~rVP~~lr~~~~~~Y~P~~VsIGPyH~g~~~L~~mE~~K~~~l~~~l~~~~-~~~~~l~~~~~~i~~~e~~~R~~Y~~~ 79 (391)
T PF03140_consen 1 IYRVPESLRDVNPKAYTPQVVSIGPYHHGKPDLQEMEEHKLRYLHRFLKRSG-APAESLEDYVEAIRSLEEEARACYAED 79 (391)
T ss_pred CcCCCHHHccCCchhcCCceEEeCCCCCCchhhhhhHHHHHHHHHHHHHHhC-CCcccHHHHHHHHHHHHHHHHHHhccc
Confidence 8999999999999999999999999999999999999999999999999943 224899999999999999999999999
Q ss_pred CC-CChHHHHHHHHHHHHHHHHHHHHHhhcccccCCCC-ccccchhhhhhhhhhhhhccCCchHHHHHhhhccCCCCCCc
Q 045254 130 IH-LDTDEFVELLVLDGIFLIELFRLVAGLVAVEANDP-LISVTWILSSFYKDFLRLENQIPYFVLECLFDLSKLPGEES 207 (444)
Q Consensus 130 ~~-~~~~ef~~MmllDgcFiLe~~~~~~~~~~~~~~d~-~~~~~~~~~~i~~DllLLENQIPffVL~~L~~~~~~~~~~~ 207 (444)
+. +++++|++||++|||||||+|+.+.. ..+.+|| ++..+|....|++||+|||||||||||++||++...+....
T Consensus 80 ~~~~~~~~f~~MmllDgCFlLe~~~~~~~--~~~~~d~~~~~~~~~~~~i~~Dl~LLENQIPffVL~~L~~l~~~~~~~~ 157 (391)
T PF03140_consen 80 IDDMSSDEFVEMMLLDGCFLLEFFLRYSR--SDGENDPGIFSRPWLLSAIRRDLLLLENQIPFFVLEKLFELLFGSKSDV 157 (391)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHhhhh--ccccccccccccccccccchhheeeecccchHHHHHHHHHHhcccccCc
Confidence 98 99999999999999999999999875 2345788 88889999999999999999999999999999998555567
Q ss_pred chhHHHHHHHhcccCCCCCCCccccCCCCCCcChHHHHHHhcCCCCC---CCCCccc-----CCccccccCHHHHHhcCc
Q 045254 208 GHTLATLALGFFNNTMLRPCDDIANYKYHEGVHLLDLVRSSFIPSDL---AEPRRDV-----ISVTHTILPISKLLYAGI 279 (444)
Q Consensus 208 ~~~l~~l~~~~f~~~~~~~~~~~~~~~~~~~~HlLdL~~~~~~p~~~---~~~~~~~-----~~~~~~~~sAteL~~aGV 279 (444)
..++.+++.+||........+. ......+++|||||+|++++|+.. +.+.... ...+..|||||||++|||
T Consensus 158 ~~~l~~l~~~~~~~~~~~~~~~-~~~~~~~~~HlL~L~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~sA~eL~~aGV 236 (391)
T PF03140_consen 158 DESLIDLVLKFFYKHWPSWPPD-EPISNPEPHHLLDLLRMSLLPSPPSSSPTPPRPPRSNGEKPPPKRIRSATELREAGV 236 (391)
T ss_pred cchHHHHHHhHhcccccccccc-ccccCCCCCChHHHHHHHhccccCCcccCCCCcccccccccccccCCCHHHHHhCCc
Confidence 8899999999994321111111 125566799999999999999321 1111110 112578999999999999
Q ss_pred EEEeCCCC-CceeEEEecceeecCeEEEecchhhhhhhHHHHhhhcCCCCCccchHHHHHhhhcCChhhHHHHHhCCcee
Q 045254 280 NFNAAPAD-SFLAVKFRNGAFEMPSITIDDFMTCFLVNSVAYEQCHSSCSKHFSVYASLLGSLVNTSTDVEHLCDRNIIT 358 (444)
Q Consensus 280 ~Fk~~~~~-~llDI~F~~G~L~IP~L~id~~Te~llrNLiA~Eq~~~~~~~~vtsYv~fM~~LI~t~eDV~lL~~~GII~ 358 (444)
+||++++. +++||+|++|+|+||+|.||++|+++||||||||||+...+.+|||||.||++||+|++||++|+++|||+
T Consensus 237 ~fk~~~~~~~~lDv~F~~G~L~IP~L~id~~T~~~lrNLiA~Eq~~~~~~~~vtsY~~fm~~Li~t~~DV~lL~~kgIi~ 316 (391)
T PF03140_consen 237 KFKPSETDRSLLDVKFKKGVLEIPPLYIDDNTESLLRNLIAFEQCHPPTGSYVTSYVFFMDSLINTPEDVELLRRKGIIV 316 (391)
T ss_pred EEeeccCccccccceecCCEEEeCeEEECCcchHHHhHHHHHHHHhccCCchHhHHHHHHHHHhCcHhhHHHHHhCCeEe
Confidence 99999876 59999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCChHHHHHHHHhhhcccccCCCCcchHHHHHHHHhHhcCchhhhhHhhhccccc-----hHHHHHHHHHHHH
Q 045254 359 NYLGKPAEVERFIYNLEKDVAFDVDRCYLSSLFKDVHDYYCYSWRVQWAAFKYSYRA-----RLQCGAVILLFLT 428 (444)
Q Consensus 359 n~lgsdeeva~lfn~L~~~~~~~~~~~y~~~v~~~ln~~~~~rw~~~~a~l~~~yf~-----~s~vaA~ill~lT 428 (444)
|++|+|+||++|||+||+++.++.+++||.+++++||+||++||++|+|+++++||+ +|++||+++|+||
T Consensus 317 ~~l~~d~eva~~F~~L~~~v~~~~~~~~~~~v~~~l~~~~~~~~~~~~a~l~~~yf~~pw~~is~~aa~~ll~lT 391 (391)
T PF03140_consen 317 NWLGSDEEVAKLFNGLCKGVVFDVDDSYYSDVCEDLNKYYQSRWNRWWAWLRRKYFSNPWTFISLVAAIILLLLT 391 (391)
T ss_pred cCCCCcHHHHHHHHHHhccCCCCCccHHHHHHHHHHHHHhcChHHHHHHHHhhhhcCCcHHHHHHHHHHHHHHhC
Confidence 999999999999999999999987788999999999999999999999999999999 9999999999987
No 2
>PF14770 TMEM18: Transmembrane protein 18
Probab=60.43 E-value=13 Score=32.37 Aligned_cols=44 Identities=18% Similarity=0.215 Sum_probs=31.9
Q ss_pred HHHHhHhcCchhhhhHhhhccccc-----hHHHHHHHHHHHHHHHHHHHHhc
Q 045254 392 KDVHDYYCYSWRVQWAAFKYSYRA-----RLQCGAVILLFLTVAQTFFTIYS 438 (444)
Q Consensus 392 ~~ln~~~~~rw~~~~a~l~~~yf~-----~s~vaA~ill~lT~~QT~~sv~~ 438 (444)
+.+|++..+.|+ ..-+++||. +|++.++=+|+.+++..+..+++
T Consensus 56 E~iN~~~a~nW~---~Fs~qnYFDs~G~Fisvv~s~PlLl~~~ii~~~~l~~ 104 (123)
T PF14770_consen 56 EYINEYAARNWR---SFSKQNYFDSSGVFISVVFSAPLLLNCLIILVNWLYQ 104 (123)
T ss_pred HHHHHHHHHHHH---HHhhccCcCCCCeeehHHHHHhHHHHHHHHHHHHHHH
Confidence 688999988774 444579999 88888876666666666655543
No 3
>PHA02103 hypothetical protein
Probab=51.74 E-value=29 Score=29.36 Aligned_cols=77 Identities=17% Similarity=0.285 Sum_probs=51.9
Q ss_pred EEeCCCCCceeEE--Ee----cce--eecCeEEEecchhhhhhhHHHHhhhcCCC--C-------CccchHHHHHhhhcC
Q 045254 281 FNAAPADSFLAVK--FR----NGA--FEMPSITIDDFMTCFLVNSVAYEQCHSSC--S-------KHFSVYASLLGSLVN 343 (444)
Q Consensus 281 Fk~~~~~~llDI~--F~----~G~--L~IP~L~id~~Te~llrNLiA~Eq~~~~~--~-------~~vtsYv~fM~~LI~ 343 (444)
||+.+.++.+-|+ |+ ..+ -+||.+..|....-+.|=.+-+|.|...- + .++-.|-.. .-.
T Consensus 11 fk~kd~rn~f~v~~~fsdkf~d~t~~~e~pai~~~~~~~ei~rl~~f~~kck~~yp~gkgg~~df~~ipdyyry---f~e 87 (135)
T PHA02103 11 FKPKDDRNTFMVKMHFSDKFSDATLEYEIPAIDADRTKAEIVRLITFMDKCKAEYPRGKGGQADFNHIPDYYRY---FGE 87 (135)
T ss_pred cCCccCcceEEEEEecccccCcceeEEeccccccchhhHHHHHHHHHHHHHHhhCCCCCCCccccccChHHHHH---hcc
Confidence 3444455554443 43 344 58999999999999999999999998532 1 245555443 335
Q ss_pred ChhhHHHHHhCCceecC
Q 045254 344 TSTDVEHLCDRNIITNY 360 (444)
Q Consensus 344 t~eDV~lL~~~GII~n~ 360 (444)
.+|-|++-.+-||=.-|
T Consensus 88 e~e~ie~we~ygve~l~ 104 (135)
T PHA02103 88 EAEGVELWEEYGVEGLC 104 (135)
T ss_pred cchhhhHHHHhCcceee
Confidence 67788888888875443
No 4
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=46.48 E-value=75 Score=25.68 Aligned_cols=83 Identities=12% Similarity=0.104 Sum_probs=56.5
Q ss_pred CcEEEeCC-CCCceeEEEec--ceeecCeEEEecchhhhhhhHHHHhhhcCCCCCccchHHHHHhhh-cCChhhHHHHHh
Q 045254 278 GINFNAAP-ADSFLAVKFRN--GAFEMPSITIDDFMTCFLVNSVAYEQCHSSCSKHFSVYASLLGSL-VNTSTDVEHLCD 353 (444)
Q Consensus 278 GV~Fk~~~-~~~llDI~F~~--G~L~IP~L~id~~Te~llrNLiA~Eq~~~~~~~~vtsYv~fM~~L-I~t~eDV~lL~~ 353 (444)
||++.+.. ..|-.+-+..+ |.+.+|=-.|..-.+.....+++-=+ ...++|+..|...+ --+..+++.|.+
T Consensus 1 Gi~v~ppdIn~S~~~~~~~~~~~~Ir~gl~~Ikglg~~~a~~I~~~R~-----~g~f~s~~df~~R~~~i~~~~le~Li~ 75 (90)
T PF14579_consen 1 GIKVLPPDINKSDADFTVEDKNNAIRLGLSAIKGLGEEVAEKIVEERE-----NGPFKSLEDFIQRLPKINKRQLEALIK 75 (90)
T ss_dssp T-EEE---TTT-BSS-EEETT-TEEE-BGGGSTTS-HHHHHHHHHHHH-----CSS-SSHHHHHHHS-TS-HHHHHHHHH
T ss_pred CCEEeCCeecccCCCeEEECCCCEEeehHhhcCCCCHHHHHHHHHhHh-----cCCCCCHHHHHHHHhcCCHHHHHHHHH
Confidence 67777653 23444555565 79999999999998888777776544 35588999999999 888999999999
Q ss_pred CCceecCCCChH
Q 045254 354 RNIITNYLGKPA 365 (444)
Q Consensus 354 ~GII~n~lgsde 365 (444)
.|.+...-+++.
T Consensus 76 aGafd~~~~~~R 87 (90)
T PF14579_consen 76 AGAFDSFGKSRR 87 (90)
T ss_dssp TTTTTTCSSCHH
T ss_pred CCCccccChhhh
Confidence 999987655443
No 5
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=28.55 E-value=70 Score=23.14 Aligned_cols=33 Identities=24% Similarity=0.602 Sum_probs=14.8
Q ss_pred CchhhhhHhhhccccchHHHHHHH---HHHHHHHHHHH
Q 045254 400 YSWRVQWAAFKYSYRARLQCGAVI---LLFLTVAQTFF 434 (444)
Q Consensus 400 ~rw~~~~a~l~~~yf~~s~vaA~i---ll~lT~~QT~~ 434 (444)
+.|+..+..++++- .|+++.++ +++++++.-++
T Consensus 3 s~~~~~~~~f~~nk--~a~~gl~il~~~vl~ai~~p~~ 38 (56)
T PF12911_consen 3 SPWKDAWRRFRRNK--LAVIGLIILLILVLLAIFAPFI 38 (56)
T ss_pred CHHHHHHHHHHhCc--hHHHHHHHHHHHHHHHHHHHHc
Confidence 45654444444433 44444444 44444444443
No 6
>PF02468 PsbN: Photosystem II reaction centre N protein (psbN); InterPro: IPR003398 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 transmembrane protein PsbN found in PSII. PsbN may have a role in PSII stability, however its actual function unknown. PsbN does not appear to be essential for photoautotrophic growth or normal PSII function.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane
Probab=27.51 E-value=61 Score=22.95 Aligned_cols=28 Identities=29% Similarity=0.384 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccCCCC
Q 045254 417 LQCGAVILLFLTVAQTFFTIYSAVRPQN 444 (444)
Q Consensus 417 s~vaA~ill~lT~~QT~~sv~~~~~~~~ 444 (444)
|++.++.+.++.+-=|.|++|..+-||+
T Consensus 4 a~~~~i~i~~~lv~~Tgy~iYtaFGppS 31 (43)
T PF02468_consen 4 ATVLAIFISCLLVSITGYAIYTAFGPPS 31 (43)
T ss_pred eeeHHHHHHHHHHHHHhhhhhheeCCCc
Confidence 4556666666666677899998887653
No 7
>PF13172 PepSY_TM_1: PepSY-associated TM helix
Probab=26.86 E-value=72 Score=20.94 Aligned_cols=20 Identities=20% Similarity=0.315 Sum_probs=15.3
Q ss_pred hHHHHHHHHHHHHHHHHHHH
Q 045254 416 RLQCGAVILLFLTVAQTFFT 435 (444)
Q Consensus 416 ~s~vaA~ill~lT~~QT~~s 435 (444)
+|++++++++++++-.++++
T Consensus 12 ~g~~~~~~ll~~~lTG~~l~ 31 (34)
T PF13172_consen 12 LGLIAAIFLLLLALTGALLN 31 (34)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 77888888888887776654
No 8
>KOG3110 consensus Riboflavin kinase [Coenzyme transport and metabolism]
Probab=26.59 E-value=45 Score=29.51 Aligned_cols=63 Identities=19% Similarity=0.295 Sum_probs=40.6
Q ss_pred ccceEEEec--cCCCCCc---hhhhHHHHHHHHHHHHHHhhh------hhcCCCHHHHHHHHHHHHHHHHhccc
Q 045254 65 YEPHIVSIG--PYHHGED---HVKMIQEHKWRYLGNLLNRLK------NAKGLGLEDFLKAVEPLEMKARECYS 127 (444)
Q Consensus 65 Y~P~vVSIG--PyHhg~~---~L~~mE~~K~~~~~~~l~r~~------~~~~~~l~~~~~~i~~~e~~~R~~Y~ 127 (444)
--|+++||| ||...+. ++..++..|--+..+-++-.- ..+=.++++++++|....+.|+..-+
T Consensus 65 v~kMvmSIGwNP~Y~N~~Kt~E~hlih~f~~DFYge~l~~~IvGyiRpe~nf~slesLi~~I~~Di~vA~~~l~ 138 (153)
T KOG3110|consen 65 VFKMVMSIGWNPYYKNKKKTMELHLIHDFGEDFYGETLKVIIVGYIRPELNFDSLESLIEAIHGDIEVAKKVLD 138 (153)
T ss_pred ceeEEEEcccCcccCCcccceeeeeehhcccchhhheeeEEEEEeeccccCcchHHHHHHHHHhhHHHHHHhhc
Confidence 458999999 8877653 344455555555444443211 01224799999999998888887654
No 9
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=23.90 E-value=67 Score=30.91 Aligned_cols=37 Identities=16% Similarity=0.365 Sum_probs=27.7
Q ss_pred CCCcceeeecCccccccCCCCccceEEEeccCCCCCchhhhHHHHHHH
Q 045254 44 GKKSCCIFRVPQSFVEVHGKSYEPHIVSIGPYHHGEDHVKMIQEHKWR 91 (444)
Q Consensus 44 ~~~~~~I~rVP~~lr~~n~~aY~P~vVSIGPyHhg~~~L~~mE~~K~~ 91 (444)
.++.-|++++|-.+ .+|+||||-.++.-..||+|=-.
T Consensus 21 nsp~sclv~~t~dl-----------hlalaP~yl~npl~~~i~ehld~ 57 (253)
T KOG4134|consen 21 NSPESCLVCITTDL-----------HLALAPYYLANPLHALIEEHLDT 57 (253)
T ss_pred cCCcceEEEeeehe-----------eeeecchhhcchhHHHHHHHhhH
Confidence 35567999999764 69999999988765567766443
No 10
>PF15103 G0-G1_switch_2: G0/G1 switch protein 2
Probab=23.56 E-value=73 Score=26.77 Aligned_cols=24 Identities=17% Similarity=0.084 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhcc
Q 045254 416 RLQCGAVILLFLTVAQTFFTIYSA 439 (444)
Q Consensus 416 ~s~vaA~ill~lT~~QT~~sv~~~ 439 (444)
++.+.|++..++.+++|+|+=++.
T Consensus 29 LGSvLA~~Gvv~GLVEtVCsPFs~ 52 (102)
T PF15103_consen 29 LGSVLAFFGVVIGLVETVCSPFSA 52 (102)
T ss_pred hhhHHHHHHHHHHHHHHHhCcccc
Confidence 677778888999999999987664
No 11
>PF04531 Phage_holin_1: Bacteriophage holin; InterPro: IPR006485 Phage proteins for bacterial lysis typically include a membrane-disrupting protein, or holin, and one or more cell wall degrading enzymes that reach the cell wall because of holin action. Holins are found in a large number of mutually non-homologous families. This entry is represented by the Bacteriophage phi-LC3, holin. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.53 E-value=90 Score=25.22 Aligned_cols=31 Identities=19% Similarity=0.054 Sum_probs=15.8
Q ss_pred hhHhhhccccchHHHHHHHHHHHHHHHHHHHHhcc
Q 045254 405 QWAAFKYSYRARLQCGAVILLFLTVAQTFFTIYSA 439 (444)
Q Consensus 405 ~~a~l~~~yf~~s~vaA~ill~lT~~QT~~sv~~~ 439 (444)
|+..|+..- +.+|++.+++.++|++..+.++
T Consensus 4 wKvR~kN~~----~w~ali~~i~l~vq~~~~~fg~ 34 (84)
T PF04531_consen 4 WKVRFKNKA----FWVALISAILLLVQQVGGLFGW 34 (84)
T ss_pred hhhcccCHH----HHHHHHHHHHHHHHHHHHHhcc
Confidence 455554433 4445555555556666554443
Done!