Query 019401
Match_columns 341
No_of_seqs 222 out of 461
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:10:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019401hhsearch_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 99.9 6.6E-27 1.4E-31 196.6 9.6 113 154-272 1-116 (120)
2 COG1661 Predicted DNA-binding 99.9 2.2E-21 4.8E-26 169.7 13.9 118 153-277 8-128 (141)
3 PF02178 AT_hook: AT hook moti 96.1 0.0021 4.5E-08 36.0 0.5 12 89-100 1-12 (13)
4 smart00384 AT_hook DNA binding 96.0 0.0032 7E-08 41.3 1.4 15 89-103 1-15 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 82.0 0.5 1.1E-05 44.2 0.4 12 87-98 66-77 (219)
6 PF13546 DDE_5: DDE superfamil 73.9 1.9 4.1E-05 40.3 1.7 16 86-101 228-243 (273)
7 COG1710 Uncharacterized protei 71.0 1.9 4.1E-05 38.1 0.9 16 86-101 81-97 (139)
8 COG1777 Predicted transcriptio 45.0 9.1 0.0002 36.6 0.7 24 88-111 63-89 (217)
9 PF14869 DUF4488: Domain of un 40.0 35 0.00075 30.5 3.5 36 181-218 28-63 (133)
10 PF15333 TAF1D: TATA box-bindi 32.3 19 0.00042 34.3 0.7 12 91-102 64-75 (217)
11 PF03306 AAL_decarboxy: Alpha- 29.8 2.7E+02 0.0058 26.5 7.9 103 159-265 84-197 (220)
12 PF02196 RBD: Raf-like Ras-bin 27.0 1.6E+02 0.0035 22.9 5.0 36 154-189 10-47 (71)
13 PF13737 DDE_Tnp_1_5: Transpos 24.2 39 0.00084 29.1 1.1 19 86-105 21-39 (112)
14 cd01817 RGS12_RBD Ubiquitin do 23.8 1.7E+02 0.0037 23.6 4.6 44 156-199 11-56 (73)
15 KOG4565 E93 protein involved i 21.5 31 0.00067 32.4 -0.0 15 87-101 111-125 (206)
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=99.94 E-value=6.6e-27 Score=196.57 Aligned_cols=113 Identities=30% Similarity=0.391 Sum_probs=94.6
Q ss_pred ceEEEEEecCCchHHHHHHHHHHhCCccEEEEeeeceeeeEEEeCCCC--CCCceeeeeeeEEEEeeceeeeCCCCCCCC
Q 019401 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPSS--SGGSVTYEGRFEILCLSGSYLLSGNGGSRN 231 (341)
Q Consensus 154 f~phVIrV~~GEDV~~kI~~Faqq~~~aicILSa~GaVSnVTLRqp~s--~~~tvtyeG~FEILSLSGT~~~~~~~~~~~ 231 (341)
|++|++||++||||+++|.+||+++++..|+|+++|+|++|+|++++. .....+|+|+|||+||+|||...++ .
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 789999999999999999999999999889999999999999999843 3468899999999999999998443 2
Q ss_pred CCCceEEEEeCCCCeEEeeecC-cceEeecceEEEEEEccCC
Q 019401 232 RSGGLSVSLASPDGRVIGGGVG-GMLIAANNVQVIVGSFLWG 272 (341)
Q Consensus 232 ~~~hLhISLAg~dGqViGGhV~-G~LIAAtpVqVVvgSF~~~ 272 (341)
++.||||+|+|.||+|+||||. |.++++ +||+|-.+...
T Consensus 77 ~~~HlHisl~~~~g~v~gGHl~~g~v~~t--~Ev~i~~~~~~ 116 (120)
T PF03479_consen 77 PFVHLHISLADPDGQVFGGHLLEGTVFAT--AEVVITELSGI 116 (120)
T ss_dssp EEEEEEEEEE-TTSEEEEEEEEEEEEEEE--EEEEEEEETTE
T ss_pred CcceEEEEEECCCCeEEeeEeCCCEEeEE--EEEEEEEecCc
Confidence 6789999999999999999999 555444 55555554443
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.87 E-value=2.2e-21 Score=169.68 Aligned_cols=118 Identities=20% Similarity=0.229 Sum_probs=107.7
Q ss_pred CceEEEEEecCCchHHHHHHHHHHhCCccEEEEeeeceeeeEEEeCCCCCC---CceeeeeeeEEEEeeceeeeCCCCCC
Q 019401 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPSSSG---GSVTYEGRFEILCLSGSYLLSGNGGS 229 (341)
Q Consensus 153 ~f~phVIrV~~GEDV~~kI~~Faqq~~~aicILSa~GaVSnVTLRqp~s~~---~tvtyeG~FEILSLSGT~~~~~~~~~ 229 (341)
.=+-+++||++|||+.+.|.+||+++.+..++++|+|++++++|++++..+ .++++.++||||||.|+|..++
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 346789999999999999999999999988999999999999999999543 5789999999999999999998
Q ss_pred CCCCCceEEEEeCCCCeEEeeecCcceEeecceEEEEEEccCCCCCcc
Q 019401 230 RNRSGGLSVSLASPDGRVIGGGVGGMLIAANNVQVIVGSFLWGGPKMK 277 (341)
Q Consensus 230 ~~~~~hLhISLAg~dGqViGGhV~G~LIAAtpVqVVvgSF~~~~~k~~ 277 (341)
++.|||++|++++|+++||||.++++.. ++||+|..+....+.++
T Consensus 84 --p~~HlHa~l~~~~G~~~GGHL~~~~V~~-t~Ev~I~el~~~~~~R~ 128 (141)
T COG1661 84 --PFVHLHAALGDENGITLGGHLLEGEVFP-TAEVFIRELPGELFRRE 128 (141)
T ss_pred --CcEEEEEEEecCCCcEEeeeecccEEeE-EEEEEEEEccccceeEe
Confidence 5679999999999999999999999888 79999999988766654
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=96.07 E-value=0.0021 Score=36.02 Aligned_cols=12 Identities=75% Similarity=1.140 Sum_probs=4.3
Q ss_pred cccCCCCCCCCC
Q 019401 89 KRKRGRPRKYGP 100 (341)
Q Consensus 89 KkKRGRPRKY~~ 100 (341)
+|+||||+|+..
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 589999999864
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=96.04 E-value=0.0032 Score=41.31 Aligned_cols=15 Identities=67% Similarity=0.948 Sum_probs=12.9
Q ss_pred cccCCCCCCCCCCCC
Q 019401 89 KRKRGRPRKYGPDGS 103 (341)
Q Consensus 89 KkKRGRPRKY~~dg~ 103 (341)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999988754
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=82.02 E-value=0.5 Score=44.18 Aligned_cols=12 Identities=75% Similarity=1.107 Sum_probs=10.5
Q ss_pred cccccCCCCCCC
Q 019401 87 PVKRKRGRPRKY 98 (341)
Q Consensus 87 ~~KkKRGRPRKY 98 (341)
..|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 489999999965
No 6
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=73.91 E-value=1.9 Score=40.35 Aligned_cols=16 Identities=63% Similarity=1.076 Sum_probs=12.1
Q ss_pred ccccccCCCCCCCCCC
Q 019401 86 EPVKRKRGRPRKYGPD 101 (341)
Q Consensus 86 ~~~KkKRGRPRKY~~d 101 (341)
.+..+|||||||||.-
T Consensus 228 ~~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 228 PPPPPKRGRPRKYGRR 243 (273)
T ss_pred cccCCCCCCCCCCCCc
Confidence 3455559999999965
No 7
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=70.96 E-value=1.9 Score=38.14 Aligned_cols=16 Identities=63% Similarity=1.120 Sum_probs=13.2
Q ss_pred cccc-ccCCCCCCCCCC
Q 019401 86 EPVK-RKRGRPRKYGPD 101 (341)
Q Consensus 86 ~~~K-kKRGRPRKY~~d 101 (341)
-|+| |-|||||||.-.
T Consensus 81 IPvk~KgrGrprkyd~~ 97 (139)
T COG1710 81 IPVKLKGRGRPRKYDRN 97 (139)
T ss_pred eeeeecCCCCCcccchh
Confidence 3677 889999999764
No 8
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=44.97 E-value=9.1 Score=36.59 Aligned_cols=24 Identities=50% Similarity=0.729 Sum_probs=15.9
Q ss_pred ccccCCCCCCCCC-CCCccc--ccCCC
Q 019401 88 VKRKRGRPRKYGP-DGSVSL--ALSPS 111 (341)
Q Consensus 88 ~KkKRGRPRKY~~-dg~~~l--~l~p~ 111 (341)
.|.+|||||||-- .++++| .++|.
T Consensus 63 e~~~Rg~~rKYY~Is~~~rleV~lsp~ 89 (217)
T COG1777 63 EKIPRGRPRKYYMISRNLRLEVTLSPN 89 (217)
T ss_pred cccccCCCcceeeccCCeEEEEEecCc
Confidence 5777899999964 355443 45553
No 9
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=40.03 E-value=35 Score=30.52 Aligned_cols=36 Identities=28% Similarity=0.400 Sum_probs=29.7
Q ss_pred cEEEEeeeceeeeEEEeCCCCCCCceeeeeeeEEEEee
Q 019401 181 AICVLSANGAISTATLRQPSSSGGSVTYEGRFEILCLS 218 (341)
Q Consensus 181 aicILSa~GaVSnVTLRqp~s~~~tvtyeG~FEILSLS 218 (341)
.+=|||.-|+..|+++. +. ++..++++|.||+.|=+
T Consensus 28 ~lKilS~Dgtf~Ni~~~-~~-~~aiIt~~GtY~~~sD~ 63 (133)
T PF14869_consen 28 VLKILSDDGTFVNITMI-PK-SGAIITGYGTYEQPSDN 63 (133)
T ss_pred cEEEEcCCCcEEEEEEe-CC-CCcEEEEeEEEEEcCCc
Confidence 47799999999999993 33 24799999999999843
No 10
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=32.29 E-value=19 Score=34.34 Aligned_cols=12 Identities=50% Similarity=0.994 Sum_probs=9.3
Q ss_pred cCCCCCCCCCCC
Q 019401 91 KRGRPRKYGPDG 102 (341)
Q Consensus 91 KRGRPRKY~~dg 102 (341)
|+-+.|||-+-|
T Consensus 64 KkrkkrKYk~tg 75 (217)
T PF15333_consen 64 KKRKKRKYKPTG 75 (217)
T ss_pred HHhhhhccCccC
Confidence 566779999876
No 11
>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=29.85 E-value=2.7e+02 Score=26.52 Aligned_cols=103 Identities=17% Similarity=0.218 Sum_probs=57.1
Q ss_pred EEecCCchHHHHHHHHHHhCCccEEEEeeeceeeeEEEeCCCCCCC-------ceeeeeeeEEEEeecee----eeCCCC
Q 019401 159 ITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPSSSGG-------SVTYEGRFEILCLSGSY----LLSGNG 227 (341)
Q Consensus 159 IrV~~GEDV~~kI~~Faqq~~~aicILSa~GaVSnVTLRqp~s~~~-------tvtyeG~FEILSLSGT~----~~~~~~ 227 (341)
...-.-+++.+.|.+..... .....+-..|..+.|++|-...... .+.=+-.||.=-++||+ +|.--.
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 DSPMSKEELEAKLDELLPSK-NLFYAIRIDGTFSSVKTRSVPKQEKPYPPLAEVAKNQPEFTFENIEGTLVGFYSPEYMG 162 (220)
T ss_dssp EEEEEHHHHHHHHHHHSS-T-TS-EEEEEEEEEEEEEEE------SS---THHHHTT--EEEEEEEEEEEEEEEE-GGGB
T ss_pred CCCCCHHHHHHHHHHhcCCC-ceEEEEEEEEEECeEEEEeccCccCCCCChhHHhccCceEEecCcEEEEEEEEcchhcc
Confidence 34445678888888876633 3467778899999999998654322 11113345555555554 554322
Q ss_pred CCCCCCCceEEEEeCCCCeEEeeecCcceEeecceEEE
Q 019401 228 GSRNRSGGLSVSLASPDGRVIGGGVGGMLIAANNVQVI 265 (341)
Q Consensus 228 ~~~~~~~hLhISLAg~dGqViGGhV~G~LIAAtpVqVV 265 (341)
+- .-.++|+-+-+. -+-+||||.+--+....|+|-
T Consensus 163 gi--~v~G~HlHFls~-Dr~~GGHvld~~~~~~~v~~~ 197 (220)
T PF03306_consen 163 GI--NVPGFHLHFLSD-DRTFGGHVLDFELDNGTVEID 197 (220)
T ss_dssp TT--B-CEEEEEEEET-TSS-EEEEEEEEEEEEEEEEE
T ss_pred cc--CCceEEEEEecC-CCCCCCCeEEEEeceEEEEEE
Confidence 21 113566666654 478899999888866666553
No 12
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=27.04 E-value=1.6e+02 Score=22.87 Aligned_cols=36 Identities=19% Similarity=0.150 Sum_probs=29.9
Q ss_pred ceEEEEEecCCchHHHHHHHHHHhCCc--cEEEEeeec
Q 019401 154 FTPHVITVAVGEDIAMKLLSFSQQGPR--AICVLSANG 189 (341)
Q Consensus 154 f~phVIrV~~GEDV~~kI~~Faqq~~~--aicILSa~G 189 (341)
-++-++.+.+|+-|.+.|...|++++. ..|.+--.|
T Consensus 10 ~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~ 47 (71)
T PF02196_consen 10 GQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVG 47 (71)
T ss_dssp TEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEE
T ss_pred CCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcC
Confidence 357799999999999999999999984 678777777
No 13
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=24.24 E-value=39 Score=29.08 Aligned_cols=19 Identities=42% Similarity=0.945 Sum_probs=14.3
Q ss_pred ccccccCCCCCCCCCCCCcc
Q 019401 86 EPVKRKRGRPRKYGPDGSVS 105 (341)
Q Consensus 86 ~~~KkKRGRPRKY~~dg~~~ 105 (341)
++...|||||++| +|-.|.
T Consensus 21 ~~~~~kRGr~~~y-SD~aI~ 39 (112)
T PF13737_consen 21 APPRGKRGRPPRY-SDAAIQ 39 (112)
T ss_pred cCCCCCCCCCccc-chHHHH
Confidence 3557899999999 575554
No 14
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=23.83 E-value=1.7e+02 Score=23.65 Aligned_cols=44 Identities=23% Similarity=0.154 Sum_probs=33.2
Q ss_pred EEEEEecCCchHHHHHHHHHHhCCc--cEEEEeeeceeeeEEEeCC
Q 019401 156 PHVITVAVGEDIAMKLLSFSQQGPR--AICVLSANGAISTATLRQP 199 (341)
Q Consensus 156 phVIrV~~GEDV~~kI~~Faqq~~~--aicILSa~GaVSnVTLRqp 199 (341)
--++.+.+|+-|.+.|+..+++++. +.|.+--.|.=.-+.+.|.
T Consensus 11 ~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~~~qD 56 (73)
T cd01817 11 TTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLVLDQD 56 (73)
T ss_pred eEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCcccccCCc
Confidence 3489999999999999999999984 5666655565455555554
No 15
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=21.48 E-value=31 Score=32.41 Aligned_cols=15 Identities=40% Similarity=0.793 Sum_probs=12.8
Q ss_pred cccccCCCCCCCCCC
Q 019401 87 PVKRKRGRPRKYGPD 101 (341)
Q Consensus 87 ~~KkKRGRPRKY~~d 101 (341)
.-+|||||=|+|...
T Consensus 111 qpRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDKE 125 (206)
T ss_pred CccccccchhhhhHH
Confidence 578999999999764
Done!