Query 019329
Match_columns 342
No_of_seqs 256 out of 605
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:34:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019329.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019329hhsearch_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 5.9E-29 1.3E-33 209.4 10.6 118 152-274 1-120 (120)
2 COG1661 Predicted DNA-binding 99.9 9.7E-25 2.1E-29 190.8 13.8 119 151-276 8-129 (141)
3 PF02178 AT_hook: AT hook moti 96.3 0.0014 3.1E-08 36.6 0.6 13 74-86 1-13 (13)
4 smart00384 AT_hook DNA binding 96.2 0.0023 4.9E-08 41.9 1.3 15 74-88 1-15 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 84.7 0.34 7.4E-06 45.2 0.4 12 72-83 66-77 (219)
6 COG1710 Uncharacterized protei 70.3 2 4.3E-05 38.0 0.9 17 70-86 80-97 (139)
7 PF13546 DDE_5: DDE superfamil 70.2 2.3 5E-05 39.9 1.4 15 72-86 229-243 (273)
8 COG1777 Predicted transcriptio 47.5 7.8 0.00017 37.0 0.7 21 72-92 62-83 (217)
9 PF03306 AAL_decarboxy: Alpha- 42.0 90 0.0019 29.7 6.8 108 156-269 83-201 (220)
10 PRK11675 LexA regulated protei 29.8 59 0.0013 27.2 3.1 53 124-178 16-74 (90)
11 KOG4565 E93 protein involved i 29.1 20 0.00044 33.5 0.3 17 70-86 109-125 (206)
12 TIGR01252 acetolac_decarb alph 27.3 3E+02 0.0065 26.5 7.8 88 176-268 104-202 (232)
13 PF13737 DDE_Tnp_1_5: Transpos 26.6 31 0.00068 29.6 1.0 18 71-89 21-38 (112)
14 TIGR03836 termin_org_HMW1 cyta 24.7 53 0.0011 26.8 1.9 19 19-37 31-49 (82)
15 PF14869 DUF4488: Domain of un 21.7 1.1E+02 0.0024 27.4 3.5 35 179-215 28-62 (133)
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=99.96 E-value=5.9e-29 Score=209.37 Aligned_cols=118 Identities=28% Similarity=0.380 Sum_probs=103.3
Q ss_pred ceeEEEEEcCCCCHHHHHHHHHHhCCccEEEEEeeceeeeEEEecccC--CCCeeeeecceEEEEeeeeeeccCCCCCCC
Q 019329 152 FTPHVITVKAGEDVSSKIMSFSQNGPRAVCILSANGAISNVTLRQAAT--SGGTVTYEGRFEILSLSGSFLLSESSGQRS 229 (342)
Q Consensus 152 f~phVIrV~~GEDIvekI~~Faq~~~~a~cILSAiGAVSnVTLrq~~~--sg~tvt~eG~FEILSLsGnis~~e~g~~~s 229 (342)
||+|++||++||||+++|++||++..+..|+|+++|+|++|+|++++. ....++|+|+|||+||+|||...+ + +
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~g~~Ei~sl~G~i~~~~-g---~ 76 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFEGPFEIISLSGTISPED-G---K 76 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEESEEEEEEEEEEEEEET-T---E
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEecccEEEEEeEEEEECCC-C---C
Confidence 799999999999999999999998889889999999999999999964 335789999999999999999833 3 2
Q ss_pred CCcceEEEEeCCCCceEeeeccCCcEEcccEEEEEEecccccccc
Q 019329 230 RTGGLSVSLSGPDGRVLGGSVAGLLTAATPVQVVVGSFLADGRKE 274 (342)
Q Consensus 230 ~~~HLHVSLAg~DGqViGGHL~g~lIAastVEVVV~sF~~~~~k~ 274 (342)
++.|||++|+|.||+|+||||..+.+ ..++||+|.++....++|
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 79999999999999999999996555 788999999998876654
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.92 E-value=9.7e-25 Score=190.78 Aligned_cols=119 Identities=20% Similarity=0.276 Sum_probs=107.5
Q ss_pred CceeEEEEEcCCCCHHHHHHHHHHhCCccEEEEEeeceeeeEEEecccCCC---CeeeeecceEEEEeeeeeeccCCCCC
Q 019329 151 GFTPHVITVKAGEDVSSKIMSFSQNGPRAVCILSANGAISNVTLRQAATSG---GTVTYEGRFEILSLSGSFLLSESSGQ 227 (342)
Q Consensus 151 ~f~phVIrV~~GEDIvekI~~Faq~~~~a~cILSAiGAVSnVTLrq~~~sg---~tvt~eG~FEILSLsGnis~~e~g~~ 227 (342)
.-+.+++||++|||+++.|.+||+++.+.+++++|||++++++|++++.++ .+++++|+||||||.|||..++
T Consensus 8 ~gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlSL~G~i~~~~---- 83 (141)
T COG1661 8 SGRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLSLLGNIALDD---- 83 (141)
T ss_pred cceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEEecceeecCC----
Confidence 348899999999999999999999999988999999999999999999654 5789999999999999998755
Q ss_pred CCCCcceEEEEeCCCCceEeeeccCCcEEcccEEEEEEecccccccccc
Q 019329 228 RSRTGGLSVSLSGPDGRVLGGSVAGLLTAATPVQVVVGSFLADGRKESK 276 (342)
Q Consensus 228 ~s~~~HLHVSLAg~DGqViGGHL~g~lIAastVEVVV~sF~~~~~k~~~ 276 (342)
|+.|||++|++.+|+++||||.++.+ ..|+||+|.++......|..
T Consensus 84 --p~~HlHa~l~~~~G~~~GGHL~~~~V-~~t~Ev~I~el~~~~~~R~~ 129 (141)
T COG1661 84 --PFVHLHAALGDENGITLGGHLLEGEV-FPTAEVFIRELPGELFRREF 129 (141)
T ss_pred --CcEEEEEEEecCCCcEEeeeecccEE-eEEEEEEEEEccccceeEec
Confidence 79999999999999999999998665 45999999999998766543
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=96.29 E-value=0.0014 Score=36.57 Aligned_cols=13 Identities=69% Similarity=1.066 Sum_probs=4.6
Q ss_pred cccCCCCCCCCCC
Q 019329 74 KRKRGRPRKYGPD 86 (342)
Q Consensus 74 kkKRGRPRKY~~d 86 (342)
+|+||||||+..+
T Consensus 1 ~r~RGRP~k~~~~ 13 (13)
T PF02178_consen 1 KRKRGRPRKNAKK 13 (13)
T ss_dssp S--SS--TT----
T ss_pred CCcCCCCccccCC
Confidence 6899999998653
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=96.23 E-value=0.0023 Score=41.90 Aligned_cols=15 Identities=67% Similarity=0.855 Sum_probs=13.1
Q ss_pred cccCCCCCCCCCCCC
Q 019329 74 KRKRGRPRKYGPDGT 88 (342)
Q Consensus 74 kkKRGRPRKY~~dg~ 88 (342)
|||||||||+..+..
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=84.66 E-value=0.34 Score=45.20 Aligned_cols=12 Identities=75% Similarity=1.085 Sum_probs=10.6
Q ss_pred cccccCCCCCCC
Q 019329 72 PMKRKRGRPRKY 83 (342)
Q Consensus 72 ~~kkKRGRPRKY 83 (342)
.+|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 689999999964
No 6
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=70.32 E-value=2 Score=37.97 Aligned_cols=17 Identities=53% Similarity=0.999 Sum_probs=13.9
Q ss_pred CCccc-ccCCCCCCCCCC
Q 019329 70 SEPMK-RKRGRPRKYGPD 86 (342)
Q Consensus 70 ~~~~k-kKRGRPRKY~~d 86 (342)
.-++| |-|||||||+..
T Consensus 80 vIPvk~KgrGrprkyd~~ 97 (139)
T COG1710 80 VIPVKLKGRGRPRKYDRN 97 (139)
T ss_pred EeeeeecCCCCCcccchh
Confidence 44788 889999999864
No 7
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=70.15 E-value=2.3 Score=39.85 Aligned_cols=15 Identities=67% Similarity=1.145 Sum_probs=11.7
Q ss_pred cccccCCCCCCCCCC
Q 019329 72 PMKRKRGRPRKYGPD 86 (342)
Q Consensus 72 ~~kkKRGRPRKY~~d 86 (342)
...+|||||||||.-
T Consensus 229 ~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 229 PPPPKRGRPRKYGRR 243 (273)
T ss_pred ccCCCCCCCCCCCCc
Confidence 445569999999964
No 8
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=47.53 E-value=7.8 Score=37.01 Aligned_cols=21 Identities=43% Similarity=0.558 Sum_probs=14.6
Q ss_pred cccccCCCCCCCCC-CCCcccc
Q 019329 72 PMKRKRGRPRKYGP-DGTMSLA 92 (342)
Q Consensus 72 ~~kkKRGRPRKY~~-dg~~~l~ 92 (342)
-.|.+|||||||-- .++++|-
T Consensus 62 ie~~~Rg~~rKYY~Is~~~rle 83 (217)
T COG1777 62 IEKIPRGRPRKYYMISRNLRLE 83 (217)
T ss_pred ccccccCCCcceeeccCCeEEE
Confidence 45778899999864 4555553
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=42.03 E-value=90 Score=29.68 Aligned_cols=108 Identities=16% Similarity=0.208 Sum_probs=55.0
Q ss_pred EEEEcCCCCHHHHHHHHHHhCCccEEEEEeeceeeeEEEecccCCCC-------eeeeecceEEEEeeeeee----ccCC
Q 019329 156 VITVKAGEDVSSKIMSFSQNGPRAVCILSANGAISNVTLRQAATSGG-------TVTYEGRFEILSLSGSFL----LSES 224 (342)
Q Consensus 156 VIrV~~GEDIvekI~~Faq~~~~a~cILSAiGAVSnVTLrq~~~sg~-------tvt~eG~FEILSLsGnis----~~e~ 224 (342)
+.....-++|-+.|.+.... ......+-.-|..+.|++|-...... .+.-+-.||.=-+.|++. +.--
T Consensus 83 ~~~~~~~~~l~~~l~~~~~~-~N~f~airi~G~F~~v~~Rsv~~qe~Py~~l~e~~~~Q~~f~~~ni~GTlVGf~sP~~~ 161 (220)
T PF03306_consen 83 LDSPMSKEELEAKLDELLPS-KNLFYAIRIDGTFSSVKTRSVPKQEKPYPPLAEVAKNQPEFTFENIEGTLVGFYSPEYM 161 (220)
T ss_dssp -EEEEEHHHHHHHHHHHSS--TTS-EEEEEEEEEEEEEEE------SS---THHHHTT--EEEEEEEEEEEEEEEE-GGG
T ss_pred cCCCCCHHHHHHHHHHhcCC-CceEEEEEEEEEECeEEEEeccCccCCCCChhHHhccCceEEecCcEEEEEEEEcchhc
Confidence 34444556777777777653 34466777899999999996543221 111133466666677664 3221
Q ss_pred CCCCCCCcceEEEEeCCCCceEeeeccCCcEEcccEEEEEEeccc
Q 019329 225 SGQRSRTGGLSVSLSGPDGRVLGGSVAGLLTAATPVQVVVGSFLA 269 (342)
Q Consensus 225 g~~~s~~~HLHVSLAg~DGqViGGHL~g~lIAastVEVVV~sF~~ 269 (342)
.+-.-+--|||.. + |-+.+||||.+-.+ ..++|-+..+..
T Consensus 162 ~gi~v~G~HlHFl--s-~Dr~~GGHvld~~~--~~~~v~~~~~~~ 201 (220)
T PF03306_consen 162 GGINVPGFHLHFL--S-DDRTFGGHVLDFEL--DNGTVEIDVFDD 201 (220)
T ss_dssp BTTB-CEEEEEEE--E-TTSS-EEEEEEEEE--EEEEEEEEE-SE
T ss_pred cccCCceEEEEEe--c-CCCCCCCCeEEEEe--ceEEEEEEecCC
Confidence 2221234455554 3 34678999996333 445555555443
No 10
>PRK11675 LexA regulated protein; Provisional
Probab=29.79 E-value=59 Score=27.23 Aligned_cols=53 Identities=15% Similarity=0.186 Sum_probs=33.1
Q ss_pred ccCCCCCCCCCCCCCccccccc------ccCCCCceeEEEEEcCCCCHHHHHHHHHHhCCc
Q 019329 124 IKKSRGRPPGSGSGKKHQLEAL------GSAGVGFTPHVITVKAGEDVSSKIMSFSQNGPR 178 (342)
Q Consensus 124 ~kk~RGRP~GS~~~nK~k~~~~------g~~g~~f~phVIrV~~GEDIvekI~~Faq~~~~ 178 (342)
..|++|||.-.-..++.|+-+- ..-..+++.+- |.-.+|++++|.++|++..+
T Consensus 16 ~~~~~grp~tnpl~r~~ql~inkrnq~~rdk~~glKRve--VKldedl~ekL~eyAe~~ni 74 (90)
T PRK11675 16 DERRPGRPKTNPLSRDEQLRINKRNQLKRDKVRGLKRVE--LKLNADLVDALNELAEARNI 74 (90)
T ss_pred cCCCCCCCCCCCCChHHHHHhhHHHHHHHHHHcCceeEE--EEECHHHHHHHHHHHHHcCC
Confidence 3466899876543344444321 13345566554 44567999999999977654
No 11
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=29.07 E-value=20 Score=33.54 Aligned_cols=17 Identities=41% Similarity=0.755 Sum_probs=14.1
Q ss_pred CCcccccCCCCCCCCCC
Q 019329 70 SEPMKRKRGRPRKYGPD 86 (342)
Q Consensus 70 ~~~~kkKRGRPRKY~~d 86 (342)
...-+|||||=|+|...
T Consensus 109 sKqpRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 109 SKQPRKKRGRYRQYDKE 125 (206)
T ss_pred ccCccccccchhhhhHH
Confidence 45678999999999864
No 12
>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=27.25 E-value=3e+02 Score=26.48 Aligned_cols=88 Identities=16% Similarity=0.322 Sum_probs=50.0
Q ss_pred CCccEEEEEeeceeeeEEEecccCCCC-------eeeeecceEEEEeeeeee----ccCCCCCCCCCcceEEEEeCCCCc
Q 019329 176 GPRAVCILSANGAISNVTLRQAATSGG-------TVTYEGRFEILSLSGSFL----LSESSGQRSRTGGLSVSLSGPDGR 244 (342)
Q Consensus 176 ~~~a~cILSAiGAVSnVTLrq~~~sg~-------tvt~eG~FEILSLsGnis----~~e~g~~~s~~~HLHVSLAg~DGq 244 (342)
.....+-+-.-|..++|..|-...... .+.=+-.||+-...|++. +.--.+. -..++|+-+-+ |-+
T Consensus 104 ~~N~f~Airi~G~F~~v~~Rsvp~Q~kPy~~l~e~~~~Q~~f~~~nv~GTlvGF~sP~~~~gi--~v~G~HlHFis-dDr 180 (232)
T TIGR01252 104 GKNVFYAIRITGEFPKVQTRTVPKQEKPYPPFVEVVKGQPEFHFDNVTGTIVGFWTPAYAKGI--NVAGYHLHFIS-EDR 180 (232)
T ss_pred CCccEEEEEEEEEeceeEEEecCCCCCCCcCHHHHhcCCceEEEeccEEEEEEEecchhcccc--CCceEEEEEec-CCC
Confidence 345678888899999999996432211 111234488888777775 2211111 23444544444 336
Q ss_pred eEeeeccCCcEEcccEEEEEEecc
Q 019329 245 VLGGSVAGLLTAATPVQVVVGSFL 268 (342)
Q Consensus 245 ViGGHL~g~lIAastVEVVV~sF~ 268 (342)
.+||||.+--+. .+.|-|..+.
T Consensus 181 ~~GGHVld~~~~--~~~~~i~~~~ 202 (232)
T TIGR01252 181 TFGGHVLDYIID--NGTLEIGQIQ 202 (232)
T ss_pred CCCcceeEEEee--eeEEEEeecc
Confidence 689999863333 4445444443
No 13
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=26.63 E-value=31 Score=29.64 Aligned_cols=18 Identities=44% Similarity=0.962 Sum_probs=13.6
Q ss_pred CcccccCCCCCCCCCCCCc
Q 019329 71 EPMKRKRGRPRKYGPDGTM 89 (342)
Q Consensus 71 ~~~kkKRGRPRKY~~dg~~ 89 (342)
++...|||||++|- |-.|
T Consensus 21 ~~~~~kRGr~~~yS-D~aI 38 (112)
T PF13737_consen 21 APPRGKRGRPPRYS-DAAI 38 (112)
T ss_pred cCCCCCCCCCcccc-hHHH
Confidence 46678999999994 6433
No 14
>TIGR03836 termin_org_HMW1 cytadherence high molecular weight protein 1 N-terminal region. This model describes the N-terminal region of the Mycoplasma cytadherence protein HMW1, up to but not including the first EAGR box domain. The apparent orthologs in different Mycoplasma species differ profoundly in archictecture C-terminally to the region described here.
Probab=24.71 E-value=53 Score=26.82 Aligned_cols=19 Identities=32% Similarity=0.579 Sum_probs=16.4
Q ss_pred ccceeeEeccCCceeeccC
Q 019329 19 IQSMRLAFSADGTAVYKPI 37 (342)
Q Consensus 19 ~~~~~~~~~~dg~~~~~~~ 37 (342)
-+++.+||.+||..+|-.-
T Consensus 31 Dg~ikvAyDaDgNgYYIaf 49 (82)
T TIGR03836 31 DGSIKVAYDADGNGYYIAF 49 (82)
T ss_pred CCcEEEEEecCCCEEEEEe
Confidence 5789999999999999643
No 15
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=21.73 E-value=1.1e+02 Score=27.35 Aligned_cols=35 Identities=34% Similarity=0.423 Sum_probs=28.1
Q ss_pred cEEEEEeeceeeeEEEecccCCCCeeeeecceEEEEe
Q 019329 179 AVCILSANGAISNVTLRQAATSGGTVTYEGRFEILSL 215 (342)
Q Consensus 179 a~cILSAiGAVSnVTLrq~~~sg~tvt~eG~FEILSL 215 (342)
..=|||.-|.+.|+++.. . ++..+++.|.||+.|=
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 467999999999999932 2 3368999999999874
Done!