Query 038197
Match_columns 366
No_of_seqs 243 out of 602
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 08:34:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038197.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038197hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03479 DUF296: Domain of unk 100.0 1.6E-28 3.5E-33 208.4 10.6 118 148-270 1-120 (120)
2 COG1661 Predicted DNA-binding 99.9 8.9E-25 1.9E-29 192.6 14.2 122 146-274 7-131 (141)
3 PF02178 AT_hook: AT hook moti 96.4 0.0012 2.7E-08 37.2 0.6 12 71-82 1-12 (13)
4 smart00384 AT_hook DNA binding 96.4 0.0018 3.8E-08 42.8 1.4 15 71-85 1-15 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 84.3 0.35 7.7E-06 45.5 0.4 13 69-81 66-78 (219)
6 COG1710 Uncharacterized protei 73.1 1.5 3.2E-05 39.1 0.8 16 68-83 81-97 (139)
7 PF13546 DDE_5: DDE superfamil 67.8 3.2 6.8E-05 39.3 1.8 13 71-83 231-243 (273)
8 COG1777 Predicted transcriptio 53.8 6.3 0.00014 38.0 1.1 20 69-88 62-82 (217)
9 PF03306 AAL_decarboxy: Alpha- 51.3 79 0.0017 30.3 8.1 107 153-265 84-201 (220)
10 KOG4565 E93 protein involved i 29.6 18 0.00038 34.3 -0.0 14 70-83 112-125 (206)
11 TIGR01252 acetolac_decarb alph 27.0 2.4E+02 0.0051 27.5 7.1 90 172-266 104-204 (232)
12 PF13737 DDE_Tnp_1_5: Transpos 25.3 36 0.00077 29.6 1.1 14 69-82 22-35 (112)
13 PF15333 TAF1D: TATA box-bindi 20.8 42 0.00092 32.4 0.7 12 73-84 64-75 (217)
No 1
>PF03479 DUF296: Domain of unknown function (DUF296); InterPro: IPR005175 This putative conserved domain is found in proteins that contain AT-hook motifs IPR000637 from INTERPRO, suggesting a DNA-binding function for the proteins as a whole, however, the function of this domain is unknown. Overexpression of a protein containing this domain, Q9S7C9 from SWISSPROT, in Arabidopsis thaliana causes late flowering and modified leaf development []. ; PDB: 2DT4_A 2P6Y_A 3HWU_A 3HTN_A 2NMU_A 2H6L_A 2HX0_A.
Probab=99.95 E-value=1.6e-28 Score=208.43 Aligned_cols=118 Identities=29% Similarity=0.397 Sum_probs=104.1
Q ss_pred ceeEEEEEcCCCCHHHHHHHHHhhCCccEEEEEeeceeeeEEEecCCC--CCCceeeeeceeEEEeeeceeecCCCCCCC
Q 038197 148 FTPHVVTVNTGEDVAGKILSFSQKGPRGICVLSANGAVSNVTIRQPGS--SGGILTYEGRFEILSLSGSFTVTETGGARS 225 (366)
Q Consensus 148 ~~phVIrV~~GEDIvesI~~Faq~~~ra~cILSAiGAVsnVTLrq~~~--s~~~~t~eG~FEILSLSGnis~~~~gg~~~ 225 (366)
||+|++||++||||+++|.+||++..+.+|+|+++|+|++|+|++++. ....++|+|+|||+||+|||...++ +
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~g~~Ei~sl~G~i~~~~g----~ 76 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFEGPFEIISLSGTISPEDG----K 76 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEESEEEEEEEEEEEEEETT----E
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEecccEEEEEeEEEEECCCC----C
Confidence 689999999999999999999999889889999999999999999954 2347899999999999999998442 6
Q ss_pred CCCeeEEEEeCCCCcEEeeecCCccEEecceEEEEEEcCCCcccc
Q 038197 226 RTGGLSVSLAGPDGRVIGGGVAGLLMAASPIQIVVGSFMPNGFKV 270 (366)
Q Consensus 226 ~~~HLHVSLA~~dGqViGGHL~g~LIAasTVEVVV~sF~~~~~kr 270 (366)
++.|||++|++.||+++||||..+.+ ..++||+|..+....++|
T Consensus 77 ~~~HlHisl~~~~g~v~gGHl~~g~v-~~t~Ev~i~~~~~~~~~~ 120 (120)
T PF03479_consen 77 PFVHLHISLADPDGQVFGGHLLEGTV-FATAEVVITELSGINFTR 120 (120)
T ss_dssp EEEEEEEEEE-TTSEEEEEEEEEEEE-EEEEEEEEEEETTEEEEE
T ss_pred CcceEEEEEECCCCeEEeeEeCCCEE-eEEEEEEEEEecCccccC
Confidence 88999999999999999999997766 678999999998876665
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.92 E-value=8.9e-25 Score=192.61 Aligned_cols=122 Identities=16% Similarity=0.249 Sum_probs=112.1
Q ss_pred CCceeEEEEEcCCCCHHHHHHHHHhhCCccEEEEEeeceeeeEEEecCCCCC---CceeeeeceeEEEeeeceeecCCCC
Q 038197 146 GDFTPHVVTVNTGEDVAGKILSFSQKGPRGICVLSANGAVSNVTIRQPGSSG---GILTYEGRFEILSLSGSFTVTETGG 222 (366)
Q Consensus 146 ~~~~phVIrV~~GEDIvesI~~Faq~~~ra~cILSAiGAVsnVTLrq~~~s~---~~~t~eG~FEILSLSGnis~~~~gg 222 (366)
..-+.|++||++|||+++.|.+||+++.+.+++++|+|++++++|+|++... .++++.|+||||||.|||..++
T Consensus 7 ~~gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlSL~G~i~~~~--- 83 (141)
T COG1661 7 SSGRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLSLLGNIALDD--- 83 (141)
T ss_pred ccceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEEecceeecCC---
Confidence 3457899999999999999999999999988999999999999999999665 3789999999999999999986
Q ss_pred CCCCCCeeEEEEeCCCCcEEeeecCCccEEecceEEEEEEcCCCcccccccc
Q 038197 223 ARSRTGGLSVSLAGPDGRVIGGGVAGLLMAASPIQIVVGSFMPNGFKVHKRK 274 (366)
Q Consensus 223 ~~~~~~HLHVSLA~~dGqViGGHL~g~LIAasTVEVVV~sF~~~~~kr~~~k 274 (366)
|+.|||++|++++|+++||||.++.+.. ++||+|.++....+.|..+.
T Consensus 84 ---p~~HlHa~l~~~~G~~~GGHL~~~~V~~-t~Ev~I~el~~~~~~R~~d~ 131 (141)
T COG1661 84 ---PFVHLHAALGDENGITLGGHLLEGEVFP-TAEVFIRELPGELFRREFDP 131 (141)
T ss_pred ---CcEEEEEEEecCCCcEEeeeecccEEeE-EEEEEEEEccccceeEecCC
Confidence 6899999999999999999999997655 99999999999988887765
No 3
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=96.37 E-value=0.0012 Score=37.21 Aligned_cols=12 Identities=67% Similarity=1.082 Sum_probs=4.6
Q ss_pred cccCCCCCCCCC
Q 038197 71 KKKRGRPRKYDS 82 (366)
Q Consensus 71 KKKRGRPRKY~p 82 (366)
+|+||||+|+..
T Consensus 1 ~r~RGRP~k~~~ 12 (13)
T PF02178_consen 1 KRKRGRPRKNAK 12 (13)
T ss_dssp S--SS--TT---
T ss_pred CCcCCCCccccC
Confidence 689999999865
No 4
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=96.37 E-value=0.0018 Score=42.84 Aligned_cols=15 Identities=60% Similarity=0.920 Sum_probs=13.2
Q ss_pred cccCCCCCCCCCCCC
Q 038197 71 KKKRGRPRKYDSDGN 85 (366)
Q Consensus 71 KKKRGRPRKY~pDg~ 85 (366)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999998754
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=84.26 E-value=0.35 Score=45.49 Aligned_cols=13 Identities=62% Similarity=0.897 Sum_probs=10.5
Q ss_pred cCcccCCCCCCCC
Q 038197 69 FGKKKRGRPRKYD 81 (366)
Q Consensus 69 ~~KKKRGRPRKY~ 81 (366)
..|||||||||-.
T Consensus 66 dAKRKRGRPRKKs 78 (219)
T PF14621_consen 66 DAKRKRGRPRKKS 78 (219)
T ss_pred hhhhhcCCCccCC
Confidence 3699999999643
No 6
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=73.10 E-value=1.5 Score=39.08 Aligned_cols=16 Identities=69% Similarity=1.003 Sum_probs=12.9
Q ss_pred ccCc-ccCCCCCCCCCC
Q 038197 68 IFGK-KKRGRPRKYDSD 83 (366)
Q Consensus 68 ~~~K-KKRGRPRKY~pD 83 (366)
.+.| |-|||||||+..
T Consensus 81 IPvk~KgrGrprkyd~~ 97 (139)
T COG1710 81 IPVKLKGRGRPRKYDRN 97 (139)
T ss_pred eeeeecCCCCCcccchh
Confidence 3556 889999999984
No 7
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=67.75 E-value=3.2 Score=39.32 Aligned_cols=13 Identities=62% Similarity=1.048 Sum_probs=10.6
Q ss_pred cccCCCCCCCCCC
Q 038197 71 KKKRGRPRKYDSD 83 (366)
Q Consensus 71 KKKRGRPRKY~pD 83 (366)
.+||||||||+.-
T Consensus 231 ~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 231 PPKRGRPRKYGRR 243 (273)
T ss_pred CCCCCCCCCCCCc
Confidence 4559999999973
No 8
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=53.82 E-value=6.3 Score=38.01 Aligned_cols=20 Identities=55% Similarity=0.755 Sum_probs=14.4
Q ss_pred cCcccCCCCCCCCCC-CCccc
Q 038197 69 FGKKKRGRPRKYDSD-GNLRV 88 (366)
Q Consensus 69 ~~KKKRGRPRKY~pD-g~~~~ 88 (366)
..|.+|||||||..= +++++
T Consensus 62 ie~~~Rg~~rKYY~Is~~~rl 82 (217)
T COG1777 62 IEKIPRGRPRKYYMISRNLRL 82 (217)
T ss_pred ccccccCCCcceeeccCCeEE
Confidence 458899999999863 44444
No 9
>PF03306 AAL_decarboxy: Alpha-acetolactate decarboxylase; InterPro: IPR005128 Alpha-acetolactate decarboxylase plays a dual role in the cell: (i) it catalyzes the second step of the acetoin pathway, (S)-2-hydroxy-2-methyl-3-oxobutanoate = (R)-2-acetoin + CO2 and thus potentially the internal pH of cells and (ii) it controls the pool of alpha-acetolactate during leucine and valine synthesis.; GO: 0047605 acetolactate decarboxylase activity, 0019751 polyol metabolic process, 0005789 endoplasmic reticulum membrane; PDB: 1XV2_B.
Probab=51.31 E-value=79 Score=30.34 Aligned_cols=107 Identities=15% Similarity=0.186 Sum_probs=55.7
Q ss_pred EEEcCCCCHHHHHHHHHhhCCccEEEEEeeceeeeEEEecCCCCCC-------ceeeeeceeEEEeeecee----ecCCC
Q 038197 153 VTVNTGEDVAGKILSFSQKGPRGICVLSANGAVSNVTIRQPGSSGG-------ILTYEGRFEILSLSGSFT----VTETG 221 (366)
Q Consensus 153 IrV~~GEDIvesI~~Faq~~~ra~cILSAiGAVsnVTLrq~~~s~~-------~~t~eG~FEILSLSGnis----~~~~g 221 (366)
.....-++|-+.|.+.... ......+-.-|..+.|++|-...... .+.-+-.||.=.+.|++. +.--.
T Consensus 84 ~~~~~~~~l~~~l~~~~~~-~N~f~airi~G~F~~v~~Rsv~~qe~Py~~l~e~~~~Q~~f~~~ni~GTlVGf~sP~~~~ 162 (220)
T PF03306_consen 84 DSPMSKEELEAKLDELLPS-KNLFYAIRIDGTFSSVKTRSVPKQEKPYPPLAEVAKNQPEFTFENIEGTLVGFYSPEYMG 162 (220)
T ss_dssp EEEEEHHHHHHHHHHHSS--TTS-EEEEEEEEEEEEEEE------SS---THHHHTT--EEEEEEEEEEEEEEEE-GGGB
T ss_pred CCCCCHHHHHHHHHHhcCC-CceEEEEEEEEEECeEEEEeccCccCCCCChhHHhccCceEEecCcEEEEEEEEcchhcc
Confidence 4445566777778777663 34577778899999999996543221 111123456666666654 43222
Q ss_pred CCCCCCCeeEEEEeCCCCcEEeeecCCccEEecceEEEEEEcCC
Q 038197 222 GARSRTGGLSVSLAGPDGRVIGGGVAGLLMAASPIQIVVGSFMP 265 (366)
Q Consensus 222 g~~~~~~HLHVSLA~~dGqViGGHL~g~LIAasTVEVVV~sF~~ 265 (366)
+..-+-.|||..=. -+.+||||.+-.+- .++|-+..+..
T Consensus 163 gi~v~G~HlHFls~---Dr~~GGHvld~~~~--~~~v~~~~~~~ 201 (220)
T PF03306_consen 163 GINVPGFHLHFLSD---DRTFGGHVLDFELD--NGTVEIDVFDD 201 (220)
T ss_dssp TTB-CEEEEEEEET---TSS-EEEEEEEEEE--EEEEEEEE-SE
T ss_pred ccCCceEEEEEecC---CCCCCCCeEEEEec--eEEEEEEecCC
Confidence 22222245555433 36899999985543 45555555543
No 10
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=29.59 E-value=18 Score=34.26 Aligned_cols=14 Identities=57% Similarity=0.997 Sum_probs=12.2
Q ss_pred CcccCCCCCCCCCC
Q 038197 70 GKKKRGRPRKYDSD 83 (366)
Q Consensus 70 ~KKKRGRPRKY~pD 83 (366)
-+|||||=|+|+..
T Consensus 112 pRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 112 PRKKRGRYRQYDKE 125 (206)
T ss_pred ccccccchhhhhHH
Confidence 37999999999974
No 11
>TIGR01252 acetolac_decarb alpha-acetolactate decarboxylase. Puruvate can be fermented to 2,3-butanediol. It is first converted to alpha-acetolactate by alpha-acetolactate synthase, then decarboxylated to acetoin by this enzyme. Acetoin can be reduced in some species to 2,3-butanediol by acetoin reductase.
Probab=26.96 E-value=2.4e+02 Score=27.46 Aligned_cols=90 Identities=14% Similarity=0.272 Sum_probs=52.3
Q ss_pred CCccEEEEEeeceeeeEEEecCCCCC-C------ceeeeeceeEEEeeecee----ecCCCCCCCCCCeeEEEEeCCCCc
Q 038197 172 GPRGICVLSANGAVSNVTIRQPGSSG-G------ILTYEGRFEILSLSGSFT----VTETGGARSRTGGLSVSLAGPDGR 240 (366)
Q Consensus 172 ~~ra~cILSAiGAVsnVTLrq~~~s~-~------~~t~eG~FEILSLSGnis----~~~~gg~~~~~~HLHVSLA~~dGq 240 (366)
.....+-+-.-|..+.|+.|-.-... . .+.=+-.||+-.+.|++. +.--.|. -..++|+.+-+. -+
T Consensus 104 ~~N~f~Airi~G~F~~v~~Rsvp~Q~kPy~~l~e~~~~Q~~f~~~nv~GTlvGF~sP~~~~gi--~v~G~HlHFisd-Dr 180 (232)
T TIGR01252 104 GKNVFYAIRITGEFPKVQTRTVPKQEKPYPPFVEVVKGQPEFHFDNVTGTIVGFWTPAYAKGI--NVAGYHLHFISE-DR 180 (232)
T ss_pred CCccEEEEEEEEEeceeEEEecCCCCCCCcCHHHHhcCCceEEEeccEEEEEEEecchhcccc--CCceEEEEEecC-CC
Confidence 45568888899999999999643221 1 111133477777777765 3221122 134455555543 36
Q ss_pred EEeeecCCccEEecceEEEEEEcCCC
Q 038197 241 VIGGGVAGLLMAASPIQIVVGSFMPN 266 (366)
Q Consensus 241 ViGGHL~g~LIAasTVEVVV~sF~~~ 266 (366)
-+||||.+-.+. .+.|-|..+...
T Consensus 181 ~~GGHVld~~~~--~~~~~i~~~~~~ 204 (232)
T TIGR01252 181 TFGGHVLDYIID--NGTLEIGQIQEF 204 (232)
T ss_pred CCCcceeEEEee--eeEEEEeecccE
Confidence 789999985443 455555555443
No 12
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=25.31 E-value=36 Score=29.60 Aligned_cols=14 Identities=43% Similarity=0.800 Sum_probs=11.5
Q ss_pred cCcccCCCCCCCCC
Q 038197 69 FGKKKRGRPRKYDS 82 (366)
Q Consensus 69 ~~KKKRGRPRKY~p 82 (366)
....|||||++|..
T Consensus 22 ~~~~kRGr~~~ySD 35 (112)
T PF13737_consen 22 PPRGKRGRPPRYSD 35 (112)
T ss_pred CCCCCCCCCcccch
Confidence 44689999999974
No 13
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=20.83 E-value=42 Score=32.42 Aligned_cols=12 Identities=42% Similarity=0.839 Sum_probs=8.5
Q ss_pred cCCCCCCCCCCC
Q 038197 73 KRGRPRKYDSDG 84 (366)
Q Consensus 73 KRGRPRKY~pDg 84 (366)
|+-+-|||-+-|
T Consensus 64 KkrkkrKYk~tg 75 (217)
T PF15333_consen 64 KKRKKRKYKPTG 75 (217)
T ss_pred HHhhhhccCccC
Confidence 555668998854
Done!