Query 020999
Match_columns 318
No_of_seqs 269 out of 616
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 06:49:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020999.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020999hhsearch_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 1.3E-28 2.7E-33 205.6 9.1 111 134-249 1-113 (120)
2 COG1661 Predicted DNA-binding 99.9 2.4E-24 5.3E-29 186.5 13.1 121 132-260 7-130 (141)
3 PF02178 AT_hook: AT hook moti 96.4 0.0011 2.4E-08 36.5 0.5 12 62-73 1-12 (13)
4 smart00384 AT_hook DNA binding 96.3 0.0019 4.2E-08 41.7 1.3 15 62-76 1-15 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 83.5 0.41 8.9E-06 44.2 0.4 17 59-75 65-82 (219)
6 PF13546 DDE_5: DDE superfamil 74.6 1.7 3.7E-05 40.4 1.6 14 61-74 230-243 (273)
7 COG1710 Uncharacterized protei 72.7 1.6 3.5E-05 38.1 0.9 17 58-74 80-97 (139)
8 COG1777 Predicted transcriptio 47.9 7.6 0.00016 36.7 0.6 25 60-84 62-89 (217)
9 PF03306 AAL_decarboxy: Alpha- 37.0 61 0.0013 30.5 4.8 102 139-244 84-196 (220)
10 KOG4565 E93 protein involved i 28.5 19 0.00041 33.4 -0.0 15 59-73 110-124 (206)
11 TIGR01252 acetolac_decarb alph 26.4 2.4E+02 0.0052 26.8 6.9 86 158-248 104-200 (232)
12 PF14869 DUF4488: Domain of un 26.4 72 0.0016 28.2 3.2 35 161-197 28-62 (133)
13 PF13737 DDE_Tnp_1_5: Transpos 24.5 36 0.00079 28.9 1.0 13 60-72 22-34 (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=1.3e-28 Score=205.64 Aligned_cols=111 Identities=32% Similarity=0.469 Sum_probs=98.9
Q ss_pred ceeEEEEecCCCcHHHHHHHHHHcCCccEEEEEeeceeeEEEEecCCC--CCCceeeecceeEEEeeeccccCCCCCCCC
Q 020999 134 FTPHIITVNTGEDVTMKIISFSQQGPRAICILSANGVISSVTLRQPDS--SGGTLTYEGRFEILSLSGSFMPSDSGGTRS 211 (318)
Q Consensus 134 f~phVIrV~~GEDIve~I~~Faq~~~raicILSaiGaVsnVTLrq~~~--~~~~vt~eG~FEILSLSGsis~~e~g~~~~ 211 (318)
||+|++||++||||+++|++||+++.+..|+++++|+|++|+|++++. ....++|+|+|||+||+|||...++ +
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 789999999999999999999999889899999999999999999954 3468899999999999999998444 5
Q ss_pred CCCceEEEEeCCCCcEEeeecCCcceeecceEEEEEEc
Q 020999 212 RSGGMSVSLASPDGRVVGGGVAGLLVAASPVQVVVGSF 249 (318)
Q Consensus 212 ~~~HLHVSLA~~dGqViGGHV~g~lIAastVEVVv~sF 249 (318)
++.|||++|++.||+|+||||..+.+ ..++||+|..+
T Consensus 77 ~~~HlHisl~~~~g~v~gGHl~~g~v-~~t~Ev~i~~~ 113 (120)
T PF03479_consen 77 PFVHLHISLADPDGQVFGGHLLEGTV-FATAEVVITEL 113 (120)
T ss_dssp EEEEEEEEEE-TTSEEEEEEEEEEEE-EEEEEEEEEEE
T ss_pred CcceEEEEEECCCCeEEeeEeCCCEE-eEEEEEEEEEe
Confidence 89999999999999999999996666 67999999984
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.92 E-value=2.4e-24 Score=186.52 Aligned_cols=121 Identities=21% Similarity=0.306 Sum_probs=108.4
Q ss_pred CCceeEEEEecCCCcHHHHHHHHHHcCCccEEEEEeeceeeEEEEecCCCCC---CceeeecceeEEEeeeccccCCCCC
Q 020999 132 ANFTPHIITVNTGEDVTMKIISFSQQGPRAICILSANGVISSVTLRQPDSSG---GTLTYEGRFEILSLSGSFMPSDSGG 208 (318)
Q Consensus 132 ~~f~phVIrV~~GEDIve~I~~Faq~~~raicILSaiGaVsnVTLrq~~~~~---~~vt~eG~FEILSLSGsis~~e~g~ 208 (318)
..-+.+++||++|||+++.|.+||+++.+..++++|+|++++++|++++.++ .++++.|+||||||.|||..++
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 4567899999999999999999999999988999999999999999999654 5899999999999999999877
Q ss_pred CCCCCCceEEEEeCCCCcEEeeecCCcceeecceEEEEEEccCCchhhhccc
Q 020999 209 TRSRSGGMSVSLASPDGRVVGGGVAGLLVAASPVQVVVGSFLAGNQHEQKHK 260 (318)
Q Consensus 209 ~~~~~~HLHVSLA~~dGqViGGHV~g~lIAastVEVVv~sF~~~~~~~~k~~ 260 (318)
|+.|||++|++++|+++||||.++++.. ++||+|.+ +......|++.
T Consensus 84 ---p~~HlHa~l~~~~G~~~GGHL~~~~V~~-t~Ev~I~e-l~~~~~~R~~d 130 (141)
T COG1661 84 ---PFVHLHAALGDENGITLGGHLLEGEVFP-TAEVFIRE-LPGELFRREFD 130 (141)
T ss_pred ---CcEEEEEEEecCCCcEEeeeecccEEeE-EEEEEEEE-ccccceeEecC
Confidence 6889999999999999999999988765 99999999 56555666554
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=96.39 E-value=0.0011 Score=36.50 Aligned_cols=12 Identities=67% Similarity=1.085 Sum_probs=4.4
Q ss_pred ccccCCCCCCCC
Q 020999 62 KKKRGRPRKYGP 73 (318)
Q Consensus 62 KkKRGRPRKY~~ 73 (318)
+|+||||+|+..
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=96.30 E-value=0.0019 Score=41.73 Aligned_cols=15 Identities=60% Similarity=0.811 Sum_probs=13.1
Q ss_pred ccccCCCCCCCCCCC
Q 020999 62 KKKRGRPRKYGPDGT 76 (318)
Q Consensus 62 KkKRGRPRKY~~dg~ 76 (318)
|||||||||+..+..
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=83.46 E-value=0.41 Score=44.19 Aligned_cols=17 Identities=59% Similarity=0.913 Sum_probs=12.5
Q ss_pred cccccccCCCCCC-CCCC
Q 020999 59 LPLKKKRGRPRKY-GPDG 75 (318)
Q Consensus 59 ~~~KkKRGRPRKY-~~dg 75 (318)
...|||||||||- |-.|
T Consensus 65 sdAKRKRGRPRKKsggsg 82 (219)
T PF14621_consen 65 SDAKRKRGRPRKKSGGSG 82 (219)
T ss_pred chhhhhcCCCccCCCCCc
Confidence 4689999999964 4433
No 6
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=74.61 E-value=1.7 Score=40.37 Aligned_cols=14 Identities=64% Similarity=1.056 Sum_probs=10.9
Q ss_pred cccccCCCCCCCCC
Q 020999 61 LKKKRGRPRKYGPD 74 (318)
Q Consensus 61 ~KkKRGRPRKY~~d 74 (318)
..+|||||||||.-
T Consensus 230 ~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 230 PPPKRGRPRKYGRR 243 (273)
T ss_pred cCCCCCCCCCCCCc
Confidence 34459999999965
No 7
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=72.69 E-value=1.6 Score=38.05 Aligned_cols=17 Identities=59% Similarity=1.142 Sum_probs=13.7
Q ss_pred Ccccc-cccCCCCCCCCC
Q 020999 58 ALPLK-KKRGRPRKYGPD 74 (318)
Q Consensus 58 ~~~~K-kKRGRPRKY~~d 74 (318)
.-++| |-|||||||.-.
T Consensus 80 vIPvk~KgrGrprkyd~~ 97 (139)
T COG1710 80 VIPVKLKGRGRPRKYDRN 97 (139)
T ss_pred EeeeeecCCCCCcccchh
Confidence 45778 889999999763
No 8
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=47.90 E-value=7.6 Score=36.70 Aligned_cols=25 Identities=44% Similarity=0.632 Sum_probs=16.7
Q ss_pred ccccccCCCCCCC-CCCCcee--ccCCC
Q 020999 60 PLKKKRGRPRKYG-PDGTVTM--ALSPK 84 (318)
Q Consensus 60 ~~KkKRGRPRKY~-~dg~~~~--~l~~~ 84 (318)
-.|.+|||||||- ..+++++ .|+|.
T Consensus 62 ie~~~Rg~~rKYY~Is~~~rleV~lsp~ 89 (217)
T COG1777 62 IEKIPRGRPRKYYMISRNLRLEVTLSPN 89 (217)
T ss_pred ccccccCCCcceeeccCCeEEEEEecCc
Confidence 3578889999996 4555544 45554
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=37.02 E-value=61 Score=30.46 Aligned_cols=102 Identities=20% Similarity=0.325 Sum_probs=53.9
Q ss_pred EEecCCCcHHHHHHHHHHcCCccEEEEEeeceeeEEEEecCCCCCC-------ceeeecceeEEEeeeccc----cCCCC
Q 020999 139 ITVNTGEDVTMKIISFSQQGPRAICILSANGVISSVTLRQPDSSGG-------TLTYEGRFEILSLSGSFM----PSDSG 207 (318)
Q Consensus 139 IrV~~GEDIve~I~~Faq~~~raicILSaiGaVsnVTLrq~~~~~~-------~vt~eG~FEILSLSGsis----~~e~g 207 (318)
.....-++|-+.|.+... .......+-.-|..+.|++|-...... .+.-+-.||.=.+.|++. +.--+
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 DSPMSKEELEAKLDELLP-SKNLFYAIRIDGTFSSVKTRSVPKQEKPYPPLAEVAKNQPEFTFENIEGTLVGFYSPEYMG 162 (220)
T ss_dssp EEEEEHHHHHHHHHHHSS--TTS-EEEEEEEEEEEEEEE------SS---THHHHTT--EEEEEEEEEEEEEEEE-GGGB
T ss_pred CCCCCHHHHHHHHHHhcC-CCceEEEEEEEEEECeEEEEeccCccCCCCChhHHhccCceEEecCcEEEEEEEEcchhcc
Confidence 344456677777777765 334577778899999999996543221 111233467777777664 43322
Q ss_pred CCCCCCCceEEEEeCCCCcEEeeecCCcceeecceEE
Q 020999 208 GTRSRSGGMSVSLASPDGRVVGGGVAGLLVAASPVQV 244 (318)
Q Consensus 208 ~~~~~~~HLHVSLA~~dGqViGGHV~g~lIAastVEV 244 (318)
+..- .++|+-+-+ |-+.+||||.+-.+-..++||
T Consensus 163 gi~v--~G~HlHFls-~Dr~~GGHvld~~~~~~~v~~ 196 (220)
T PF03306_consen 163 GINV--PGFHLHFLS-DDRTFGGHVLDFELDNGTVEI 196 (220)
T ss_dssp TTB---CEEEEEEEE-TTSS-EEEEEEEEEEEEEEEE
T ss_pred ccCC--ceEEEEEec-CCCCCCCCeEEEEeceEEEEE
Confidence 2222 344444444 336799999985544444444
No 10
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=28.49 E-value=19 Score=33.40 Aligned_cols=15 Identities=47% Similarity=0.687 Sum_probs=12.6
Q ss_pred cccccccCCCCCCCC
Q 020999 59 LPLKKKRGRPRKYGP 73 (318)
Q Consensus 59 ~~~KkKRGRPRKY~~ 73 (318)
-.-+|||||=|+|.-
T Consensus 110 KqpRkKRGrYRqYd~ 124 (206)
T KOG4565|consen 110 KQPRKKRGRYRQYDK 124 (206)
T ss_pred cCccccccchhhhhH
Confidence 356899999999975
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=26.39 E-value=2.4e+02 Score=26.83 Aligned_cols=86 Identities=19% Similarity=0.359 Sum_probs=50.9
Q ss_pred CCccEEEEEeeceeeEEEEecCCCCCC-------ceeeecceeEEEeeeccc----cCCCCCCCCCCCceEEEEeCCCCc
Q 020999 158 GPRAICILSANGVISSVTLRQPDSSGG-------TLTYEGRFEILSLSGSFM----PSDSGGTRSRSGGMSVSLASPDGR 226 (318)
Q Consensus 158 ~~raicILSaiGaVsnVTLrq~~~~~~-------~vt~eG~FEILSLSGsis----~~e~g~~~~~~~HLHVSLA~~dGq 226 (318)
.....+-+-.-|..+.|+.|-.-.... .+.=+-.||+-...|++. +.--.+. -..++|+-+-+.| +
T Consensus 104 ~~N~f~Airi~G~F~~v~~Rsvp~Q~kPy~~l~e~~~~Q~~f~~~nv~GTlvGF~sP~~~~gi--~v~G~HlHFisdD-r 180 (232)
T TIGR01252 104 GKNVFYAIRITGEFPKVQTRTVPKQEKPYPPFVEVVKGQPEFHFDNVTGTIVGFWTPAYAKGI--NVAGYHLHFISED-R 180 (232)
T ss_pred CCccEEEEEEEEEeceeEEEecCCCCCCCcCHHHHhcCCceEEEeccEEEEEEEecchhcccc--CCceEEEEEecCC-C
Confidence 456788888999999999996432211 111133478877777765 3332222 2345555555533 5
Q ss_pred EEeeecCCcceeecceEEEEEE
Q 020999 227 VVGGGVAGLLVAASPVQVVVGS 248 (318)
Q Consensus 227 ViGGHV~g~lIAastVEVVv~s 248 (318)
-+||||.+-.+. .+.|-+..
T Consensus 181 ~~GGHVld~~~~--~~~~~i~~ 200 (232)
T TIGR01252 181 TFGGHVLDYIID--NGTLEIGQ 200 (232)
T ss_pred CCCcceeEEEee--eeEEEEee
Confidence 689999974443 44444444
No 12
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=26.38 E-value=72 Score=28.20 Aligned_cols=35 Identities=31% Similarity=0.405 Sum_probs=28.5
Q ss_pred cEEEEEeeceeeEEEEecCCCCCCceeeecceeEEEe
Q 020999 161 AICILSANGVISSVTLRQPDSSGGTLTYEGRFEILSL 197 (318)
Q Consensus 161 aicILSaiGaVsnVTLrq~~~~~~~vt~eG~FEILSL 197 (318)
..=|||.-|...|+++.. . ++..+++.|.||+.|=
T Consensus 28 ~lKilS~Dgtf~Ni~~~~-~-~~aiIt~~GtY~~~sD 62 (133)
T PF14869_consen 28 VLKILSDDGTFVNITMIP-K-SGAIITGYGTYEQPSD 62 (133)
T ss_pred cEEEEcCCCcEEEEEEeC-C-CCcEEEEeEEEEEcCC
Confidence 477999999999999933 2 2369999999999873
No 13
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=24.46 E-value=36 Score=28.92 Aligned_cols=13 Identities=54% Similarity=1.119 Sum_probs=10.9
Q ss_pred ccccccCCCCCCC
Q 020999 60 PLKKKRGRPRKYG 72 (318)
Q Consensus 60 ~~KkKRGRPRKY~ 72 (318)
+...|||||++|-
T Consensus 22 ~~~~kRGr~~~yS 34 (112)
T PF13737_consen 22 PPRGKRGRPPRYS 34 (112)
T ss_pred CCCCCCCCCcccc
Confidence 4568999999995
Done!