Query 021228
Match_columns 315
No_of_seqs 226 out of 599
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:36:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021228.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021228hhsearch_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 1.4E-28 3.1E-33 204.8 10.4 113 113-230 1-115 (120)
2 COG1661 Predicted DNA-binding 99.9 1.9E-24 4.2E-29 187.0 14.0 115 110-231 6-123 (141)
3 PF02178 AT_hook: AT hook moti 96.1 0.0019 4.1E-08 35.7 0.5 12 55-66 1-12 (13)
4 smart00384 AT_hook DNA binding 96.1 0.0029 6.3E-08 41.0 1.3 15 55-69 1-15 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 83.7 0.41 8.8E-06 44.2 0.5 19 52-70 65-84 (219)
6 COG1710 Uncharacterized protei 69.4 2.2 4.7E-05 37.3 0.9 20 48-67 77-97 (139)
7 PF13546 DDE_5: DDE superfamil 67.7 2.9 6.3E-05 38.7 1.5 14 54-67 230-243 (273)
8 PF03306 AAL_decarboxy: Alpha- 61.0 42 0.00091 31.5 7.8 101 119-223 85-196 (220)
9 COG1777 Predicted transcriptio 47.6 7.7 0.00017 36.6 0.6 17 53-69 62-79 (217)
10 TIGR01252 acetolac_decarb alph 36.3 1.7E+02 0.0038 27.7 7.8 87 137-228 104-201 (232)
11 KOG4565 E93 protein involved i 27.0 21 0.00045 33.2 -0.1 15 53-67 111-125 (206)
12 PF13737 DDE_Tnp_1_5: Transpos 23.9 36 0.00078 28.9 0.8 15 52-66 21-35 (112)
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=1.4e-28 Score=204.78 Aligned_cols=113 Identities=32% Similarity=0.436 Sum_probs=100.3
Q ss_pred ceeEEEEecCCChHHHHHHHHHHhCCccEEEEEeeeeeeeEEEeCCCC--CCCceeeccceeEEEeeeeeeccCCCCCcC
Q 021228 113 FTPHVITINAGEDVMMKVISFSQQGPRAICILSANGVISNVTLRQPDS--SGGTLTYEGRFEILSLSGSFMLTESQGTRS 190 (315)
Q Consensus 113 f~phVIrL~pGEDIv~kI~~Faq~~~ra~cILSAiGAVSnVTLr~~~~--s~~~~tyeG~fEILSLsGsis~~e~gg~~~ 190 (315)
||+|++||++||||+++|++||++..+.+|+++++|+|++|+|++++. ....++|+|+|||+||+|||...++ +
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 799999999999999999999998888888889999999999999954 3368899999999999999998444 3
Q ss_pred CCCceEEEEeCCCCcEEeeeccCccEEecceEEEEEEecC
Q 021228 191 RSGGMSVSLASPDGRVVGGAVAGLLVAAGPVQVVVGSFLP 230 (315)
Q Consensus 191 ~~~HLHVSLA~~DGrV~GGHL~g~lIAastVEVVVgsF~~ 230 (315)
++.|||++|++.||+++||||..+.+ ..++||+|.++..
T Consensus 77 ~~~HlHisl~~~~g~v~gGHl~~g~v-~~t~Ev~i~~~~~ 115 (120)
T PF03479_consen 77 PFVHLHISLADPDGQVFGGHLLEGTV-FATAEVVITELSG 115 (120)
T ss_dssp EEEEEEEEEE-TTSEEEEEEEEEEEE-EEEEEEEEEEETT
T ss_pred CcceEEEEEECCCCeEEeeEeCCCEE-eEEEEEEEEEecC
Confidence 89999999999999999999997776 6799999998843
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.92 E-value=1.9e-24 Score=186.98 Aligned_cols=115 Identities=20% Similarity=0.309 Sum_probs=105.5
Q ss_pred CCCceeEEEEecCCChHHHHHHHHHHhCCccEEEEEeeeeeeeEEEeCCCCCC---CceeeccceeEEEeeeeeeccCCC
Q 021228 110 GTNFTPHVITINAGEDVMMKVISFSQQGPRAICILSANGVISNVTLRQPDSSG---GTLTYEGRFEILSLSGSFMLTESQ 186 (315)
Q Consensus 110 g~~f~phVIrL~pGEDIv~kI~~Faq~~~ra~cILSAiGAVSnVTLr~~~~s~---~~~tyeG~fEILSLsGsis~~e~g 186 (315)
...-+.+++||++|||+++.|.+||+++.+.+++++|+|++++++|++++.++ .+++++|+||||||.|||..++
T Consensus 6 ~~~gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlSL~G~i~~~~-- 83 (141)
T COG1661 6 SSSGRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLSLLGNIALDD-- 83 (141)
T ss_pred cccceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEEecceeecCC--
Confidence 34568899999999999999999999999988999999999999999999654 5888999999999999999887
Q ss_pred CCcCCCCceEEEEeCCCCcEEeeeccCccEEecceEEEEEEecCC
Q 021228 187 GTRSRSGGMSVSLASPDGRVVGGAVAGLLVAAGPVQVVVGSFLPG 231 (315)
Q Consensus 187 g~~~~~~HLHVSLA~~DGrV~GGHL~g~lIAastVEVVVgsF~~~ 231 (315)
|+.|||++|++++|+++||||.++++.. ++||+|.++...
T Consensus 84 ----p~~HlHa~l~~~~G~~~GGHL~~~~V~~-t~Ev~I~el~~~ 123 (141)
T COG1661 84 ----PFVHLHAALGDENGITLGGHLLEGEVFP-TAEVFIRELPGE 123 (141)
T ss_pred ----CcEEEEEEEecCCCcEEeeeecccEEeE-EEEEEEEEcccc
Confidence 6899999999999999999999989865 999999999554
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=96.14 E-value=0.0019 Score=35.69 Aligned_cols=12 Identities=67% Similarity=1.085 Sum_probs=4.5
Q ss_pred cccCCCCCCCCC
Q 021228 55 KKKRGRPRKYGP 66 (315)
Q Consensus 55 kkkRGRPrky~~ 66 (315)
+|+||||+|+..
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 689999999864
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=96.08 E-value=0.0029 Score=40.98 Aligned_cols=15 Identities=60% Similarity=0.811 Sum_probs=13.1
Q ss_pred cccCCCCCCCCCCCC
Q 021228 55 KKKRGRPRKYGPDGT 69 (315)
Q Consensus 55 kkkRGRPrky~~dg~ 69 (315)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999988764
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=83.66 E-value=0.41 Score=44.24 Aligned_cols=19 Identities=53% Similarity=0.898 Sum_probs=13.8
Q ss_pred ccccccCCCCCCC-CCCCCc
Q 021228 52 TQEKKKRGRPRKY-GPDGTM 70 (315)
Q Consensus 52 ~~~kkkRGRPrky-~~dg~~ 70 (315)
..+|||||||||- +-.|..
T Consensus 65 sdAKRKRGRPRKKsggsgEr 84 (219)
T PF14621_consen 65 SDAKRKRGRPRKKSGGSGER 84 (219)
T ss_pred chhhhhcCCCccCCCCCccc
Confidence 4789999999964 444443
No 6
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=69.35 E-value=2.2 Score=37.33 Aligned_cols=20 Identities=50% Similarity=0.825 Sum_probs=15.8
Q ss_pred CCCCcccc-ccCCCCCCCCCC
Q 021228 48 GLTGTQEK-KKRGRPRKYGPD 67 (315)
Q Consensus 48 ~~~~~~~k-kkRGRPrky~~d 67 (315)
+..-.++| |-|||||||...
T Consensus 77 gI~vIPvk~KgrGrprkyd~~ 97 (139)
T COG1710 77 GIKVIPVKLKGRGRPRKYDRN 97 (139)
T ss_pred CceEeeeeecCCCCCcccchh
Confidence 44456888 889999999874
No 7
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=67.69 E-value=2.9 Score=38.73 Aligned_cols=14 Identities=64% Similarity=1.099 Sum_probs=10.9
Q ss_pred ccccCCCCCCCCCC
Q 021228 54 EKKKRGRPRKYGPD 67 (315)
Q Consensus 54 ~kkkRGRPrky~~d 67 (315)
..+|||||||||.-
T Consensus 230 ~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 230 PPPKRGRPRKYGRR 243 (273)
T ss_pred cCCCCCCCCCCCCc
Confidence 34459999999964
No 8
>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=60.97 E-value=42 Score=31.48 Aligned_cols=101 Identities=15% Similarity=0.208 Sum_probs=52.5
Q ss_pred EecCCChHHHHHHHHHHhCCccEEEEEeeeeeeeEEEeCCCCCCCc-------eeeccceeEEEeeeeee----ccCCCC
Q 021228 119 TINAGEDVMMKVISFSQQGPRAICILSANGVISNVTLRQPDSSGGT-------LTYEGRFEILSLSGSFM----LTESQG 187 (315)
Q Consensus 119 rL~pGEDIv~kI~~Faq~~~ra~cILSAiGAVSnVTLr~~~~s~~~-------~tyeG~fEILSLsGsis----~~e~gg 187 (315)
....-++|-+.|.+... .......+-.-|..+.+++|-....... +.-+-.||.=-+.|++. +.--++
T Consensus 85 ~~~~~~~l~~~l~~~~~-~~N~f~airi~G~F~~v~~Rsv~~qe~Py~~l~e~~~~Q~~f~~~ni~GTlVGf~sP~~~~g 163 (220)
T PF03306_consen 85 SPMSKEELEAKLDELLP-SKNLFYAIRIDGTFSSVKTRSVPKQEKPYPPLAEVAKNQPEFTFENIEGTLVGFYSPEYMGG 163 (220)
T ss_dssp EEEEHHHHHHHHHHHSS--TTS-EEEEEEEEEEEEEEE------SS---THHHHTT--EEEEEEEEEEEEEEEE-GGGBT
T ss_pred CCCCHHHHHHHHHHhcC-CCceEEEEEEEEEECeEEEEeccCccCCCCChhHHhccCceEEecCcEEEEEEEEcchhccc
Confidence 33445677777777655 3345777888999999999965443211 11122366666666654 443322
Q ss_pred CcCCCCceEEEEeCCCCcEEeeeccCccEEecceEE
Q 021228 188 TRSRSGGMSVSLASPDGRVVGGAVAGLLVAAGPVQV 223 (315)
Q Consensus 188 ~~~~~~HLHVSLA~~DGrV~GGHL~g~lIAastVEV 223 (315)
..-+--|||..=.| |.+||||.+-.+-..++||
T Consensus 164 i~v~G~HlHFls~D---r~~GGHvld~~~~~~~v~~ 196 (220)
T PF03306_consen 164 INVPGFHLHFLSDD---RTFGGHVLDFELDNGTVEI 196 (220)
T ss_dssp TB-CEEEEEEEETT---SS-EEEEEEEEEEEEEEEE
T ss_pred cCCceEEEEEecCC---CCCCCCeEEEEeceEEEEE
Confidence 22233466655433 7899999985554444443
No 9
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=47.60 E-value=7.7 Score=36.64 Aligned_cols=17 Identities=53% Similarity=0.685 Sum_probs=13.0
Q ss_pred cccccCCCCCCCC-CCCC
Q 021228 53 QEKKKRGRPRKYG-PDGT 69 (315)
Q Consensus 53 ~~kkkRGRPrky~-~dg~ 69 (315)
-.|.+|||||||- ..++
T Consensus 62 ie~~~Rg~~rKYY~Is~~ 79 (217)
T COG1777 62 IEKIPRGRPRKYYMISRN 79 (217)
T ss_pred ccccccCCCcceeeccCC
Confidence 4688889999996 4454
No 10
>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=36.32 E-value=1.7e+02 Score=27.75 Aligned_cols=87 Identities=15% Similarity=0.266 Sum_probs=49.6
Q ss_pred CCccEEEEEeeeeeeeEEEeCCCCCCC-------ceeeccceeEEEeeeeee----ccCCCCCcCCCCceEEEEeCCCCc
Q 021228 137 GPRAICILSANGVISNVTLRQPDSSGG-------TLTYEGRFEILSLSGSFM----LTESQGTRSRSGGMSVSLASPDGR 205 (315)
Q Consensus 137 ~~ra~cILSAiGAVSnVTLr~~~~s~~-------~~tyeG~fEILSLsGsis----~~e~gg~~~~~~HLHVSLA~~DGr 205 (315)
.....+-+-.-|..+.++.|-.-.... ...=.-.||+-...|++. +.--++..-+--|||. -+. -|
T Consensus 104 ~~N~f~Airi~G~F~~v~~Rsvp~Q~kPy~~l~e~~~~Q~~f~~~nv~GTlvGF~sP~~~~gi~v~G~HlHF--isd-Dr 180 (232)
T TIGR01252 104 GKNVFYAIRITGEFPKVQTRTVPKQEKPYPPFVEVVKGQPEFHFDNVTGTIVGFWTPAYAKGINVAGYHLHF--ISE-DR 180 (232)
T ss_pred CCccEEEEEEEEEeceeEEEecCCCCCCCcCHHHHhcCCceEEEeccEEEEEEEecchhccccCCceEEEEE--ecC-CC
Confidence 455688889999999999996432211 111123377777777665 3332222223335554 443 36
Q ss_pred EEeeeccCccEEecceEEEEEEe
Q 021228 206 VVGGAVAGLLVAAGPVQVVVGSF 228 (315)
Q Consensus 206 V~GGHL~g~lIAastVEVVVgsF 228 (315)
-+||||.+-.+. .+.|-|..+
T Consensus 181 ~~GGHVld~~~~--~~~~~i~~~ 201 (232)
T TIGR01252 181 TFGGHVLDYIID--NGTLEIGQI 201 (232)
T ss_pred CCCcceeEEEee--eeEEEEeec
Confidence 789999885544 344444443
No 11
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=27.01 E-value=21 Score=33.16 Aligned_cols=15 Identities=53% Similarity=0.897 Sum_probs=12.6
Q ss_pred cccccCCCCCCCCCC
Q 021228 53 QEKKKRGRPRKYGPD 67 (315)
Q Consensus 53 ~~kkkRGRPrky~~d 67 (315)
.-+|||||=|+|.-.
T Consensus 111 qpRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDKE 125 (206)
T ss_pred CccccccchhhhhHH
Confidence 568999999999754
No 12
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=23.93 E-value=36 Score=28.93 Aligned_cols=15 Identities=40% Similarity=0.835 Sum_probs=11.7
Q ss_pred ccccccCCCCCCCCC
Q 021228 52 TQEKKKRGRPRKYGP 66 (315)
Q Consensus 52 ~~~kkkRGRPrky~~ 66 (315)
.+...|||||++|..
T Consensus 21 ~~~~~kRGr~~~ySD 35 (112)
T PF13737_consen 21 APPRGKRGRPPRYSD 35 (112)
T ss_pred cCCCCCCCCCcccch
Confidence 355689999999953
Done!