Query 042221
Match_columns 305
No_of_seqs 239 out of 510
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 04:03:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042221hhsearch_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 5E-29 1.1E-33 206.2 11.2 120 88-219 1-120 (120)
2 COG1661 Predicted DNA-binding 99.9 5.1E-26 1.1E-30 196.0 15.0 126 86-224 7-132 (141)
3 PF02178 AT_hook: AT hook moti 90.8 0.097 2.1E-06 29.0 0.5 13 61-73 1-13 (13)
4 smart00384 AT_hook DNA binding 80.3 1.1 2.5E-05 29.2 1.5 15 61-75 1-15 (26)
5 TIGR01252 acetolac_decarb alph 29.3 2.7E+02 0.0058 26.4 7.7 96 113-221 105-209 (232)
6 cd01817 RGS12_RBD Ubiquitin do 25.5 1.2E+02 0.0025 24.2 3.9 43 91-133 12-56 (73)
7 PF03306 AAL_decarboxy: Alpha- 24.0 96 0.0021 29.0 3.7 116 92-221 83-207 (220)
8 PF02196 RBD: Raf-like Ras-bin 23.2 2.3E+02 0.0051 21.6 5.2 43 89-133 11-55 (71)
9 smart00455 RBD Raf-like Ras-bi 20.7 1.7E+02 0.0038 22.4 4.0 45 89-133 10-56 (70)
10 PF14869 DUF4488: Domain of un 19.7 1.2E+02 0.0027 26.7 3.3 35 115-163 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=5e-29 Score=206.17 Aligned_cols=120 Identities=29% Similarity=0.436 Sum_probs=104.2
Q ss_pred ceEEEEEeCCCChHHHHHHHHHHhcCceEEEEEEeeeeceEEEcCCCCCCCCCCcccccCcceeEeeeeeEEEEEeeecc
Q 042221 88 LRSHVLEISSGADIVDSVSTYARRRGRGVCILSGAGAVTNVTLRQPPAGAGGSSSASIAGGAVNITLHGRFEILSLTGTS 167 (305)
Q Consensus 88 mr~hVLrL~~GeDIvesI~~fArr~~~aicVLSaiGaVsnVTLRq~~~~~g~~~~a~l~g~y~~~tleGrFEILSLsGti 167 (305)
||+|++||++||||+++|.+||+++++..|+||++|+|++|+|++++. ++ .|.+.+++|+|||+||+|||
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~-~~---------~~~~~~~~g~~Ei~sl~G~i 70 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDP-PS---------YYEPLEFEGPFEIISLSGTI 70 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEET-TT---------EEEEEEEESEEEEEEEEEEE
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecc-cC---------CcceEEecccEEEEEeEEEE
Confidence 799999999999999999999999999999999999999999999975 32 58899999999999999999
Q ss_pred CCCCCCCCCCeEEEEEeCCCCcEEceecCCceeecceEEEEEeeeccceeee
Q 042221 168 LPPPAPPGAGGLTIYLAGGQGQVVGGSVVGPLTASGTVVLMAASFANAVYDR 219 (305)
Q Consensus 168 sp~~~~~~~~HLHISLAg~dGqViGGHL~G~LIAAt~VeVV~~SF~n~~yeR 219 (305)
.+.+ .+++.||||+|++.||+|+||||....+ ..++||++..+....++|
T Consensus 71 ~~~~-g~~~~HlHisl~~~~g~v~gGHl~~g~v-~~t~Ev~i~~~~~~~~~~ 120 (120)
T PF03479_consen 71 SPED-GKPFVHLHISLADPDGQVFGGHLLEGTV-FATAEVVITELSGINFTR 120 (120)
T ss_dssp EEET-TEEEEEEEEEEE-TTSEEEEEEEEEEEE-EEEEEEEEEEETTEEEEE
T ss_pred ECCC-CCCcceEEEEEECCCCeEEeeEeCCCEE-eEEEEEEEEEecCccccC
Confidence 9843 3568999999999999999999995555 346888888887777766
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.94 E-value=5.1e-26 Score=195.97 Aligned_cols=126 Identities=17% Similarity=0.234 Sum_probs=118.5
Q ss_pred CCceEEEEEeCCCChHHHHHHHHHHhcCceEEEEEEeeeeceEEEcCCCCCCCCCCcccccCcceeEeeeeeEEEEEeee
Q 042221 86 NALRSHVLEISSGADIVDSVSTYARRRGRGVCILSGAGAVTNVTLRQPPAGAGGSSSASIAGGAVNITLHGRFEILSLTG 165 (305)
Q Consensus 86 ~~mr~hVLrL~~GeDIvesI~~fArr~~~aicVLSaiGaVsnVTLRq~~~~~g~~~~a~l~g~y~~~tleGrFEILSLsG 165 (305)
..-|.+++||++|+|++++|.+||+++.+..++++|+|+|++++||+++.+.+ +|.++++.++||||||.|
T Consensus 7 ~~gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~---------~y~~~~~~e~~EvlSL~G 77 (141)
T COG1661 7 SSGRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEK---------EYETIPVNEPLEVLSLLG 77 (141)
T ss_pred ccceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCC---------ceEEEecCCcEEEEEecc
Confidence 44588999999999999999999999999889999999999999999998765 699999999999999999
Q ss_pred ccCCCCCCCCCCeEEEEEeCCCCcEEceecCCceeecceEEEEEeeeccceeeeccccc
Q 042221 166 TSLPPPAPPGAGGLTIYLAGGQGQVVGGSVVGPLTASGTVVLMAASFANAVYDRLPLEL 224 (305)
Q Consensus 166 tisp~~~~~~~~HLHISLAg~dGqViGGHL~G~LIAAt~VeVV~~SF~n~~yeRlp~e~ 224 (305)
||...+ ++.|||++|++++|.++||||+++++.. ++||+|..+....++|.+++.
T Consensus 78 ~i~~~~---p~~HlHa~l~~~~G~~~GGHL~~~~V~~-t~Ev~I~el~~~~~~R~~d~~ 132 (141)
T COG1661 78 NIALDD---PFVHLHAALGDENGITLGGHLLEGEVFP-TAEVFIRELPGELFRREFDPT 132 (141)
T ss_pred eeecCC---CcEEEEEEEecCCCcEEeeeecccEEeE-EEEEEEEEccccceeEecCCC
Confidence 999986 6999999999999999999999999988 899999999999999988873
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=90.81 E-value=0.097 Score=29.00 Aligned_cols=13 Identities=46% Similarity=0.846 Sum_probs=4.2
Q ss_pred CCCCCCCCCCCCC
Q 042221 61 RRPRGRPAGSRNK 73 (305)
Q Consensus 61 kr~RGRP~GSknK 73 (305)
+|+||||+.+.+|
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 5899999987654
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=80.28 E-value=1.1 Score=29.17 Aligned_cols=15 Identities=33% Similarity=0.680 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCCCC
Q 042221 61 RRPRGRPAGSRNKPK 75 (305)
Q Consensus 61 kr~RGRP~GSknKpk 75 (305)
+|+||||+..++...
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 589999998777654
No 5
>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=29.29 E-value=2.7e+02 Score=26.41 Aligned_cols=96 Identities=19% Similarity=0.239 Sum_probs=56.6
Q ss_pred CceEEEEEEeeeeceEEEcCCCCCCCCCCcccccCccee----EeeeeeEEEEEeeeccC----CCCC-CCCCCeEEEEE
Q 042221 113 GRGVCILSGAGAVTNVTLRQPPAGAGGSSSASIAGGAVN----ITLHGRFEILSLTGTSL----PPPA-PPGAGGLTIYL 183 (305)
Q Consensus 113 ~~aicVLSaiGaVsnVTLRq~~~~~g~~~~a~l~g~y~~----~tleGrFEILSLsGtis----p~~~-~~~~~HLHISL 183 (305)
....+-+-.-|..++|+.|-....++ -|.. +.=.-.||+-.+.||+. |.-. .-...++|+-+
T Consensus 105 ~N~f~Airi~G~F~~v~~Rsvp~Q~k---------Py~~l~e~~~~Q~~f~~~nv~GTlvGF~sP~~~~gi~v~G~HlHF 175 (232)
T TIGR01252 105 KNVFYAIRITGEFPKVQTRTVPKQEK---------PYPPFVEVVKGQPEFHFDNVTGTIVGFWTPAYAKGINVAGYHLHF 175 (232)
T ss_pred CccEEEEEEEEEeceeEEEecCCCCC---------CCcCHHHHhcCCceEEEeccEEEEEEEecchhccccCCceEEEEE
Confidence 45688889999999999998654332 1221 12245577776666654 4321 11134566666
Q ss_pred eCCCCcEEceecCCceeecceEEEEEeeeccceeeecc
Q 042221 184 AGGQGQVVGGSVVGPLTASGTVVLMAASFANAVYDRLP 221 (305)
Q Consensus 184 Ag~dGqViGGHL~G~LIAAt~VeVV~~SF~n~~yeRlp 221 (305)
-+. -+.+||||....+... .|-+..+.+.. -+||
T Consensus 176 isd-Dr~~GGHVld~~~~~~--~~~i~~~~~~~-~~lP 209 (232)
T TIGR01252 176 ISE-DRTFGGHVLDYIIDNG--TLEIGQIQEFN-LQLP 209 (232)
T ss_pred ecC-CCCCCcceeEEEeeee--EEEEeecccEE-EeCC
Confidence 644 4567999998887654 44444444332 2466
No 6
>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=25.50 E-value=1.2e+02 Score=24.23 Aligned_cols=43 Identities=26% Similarity=0.278 Sum_probs=32.1
Q ss_pred EEEEeCCCChHHHHHHHHHHhcCc--eEEEEEEeeeeceEEEcCC
Q 042221 91 HVLEISSGADIVDSVSTYARRRGR--GVCILSGAGAVTNVTLRQP 133 (305)
Q Consensus 91 hVLrL~~GeDIvesI~~fArr~~~--aicVLSaiGaVsnVTLRq~ 133 (305)
=++.+.+|+-|.+.|+..|++++. ..|.+--.|.=.-+.+.+.
T Consensus 12 T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~~~qD 56 (73)
T cd01817 12 TVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLVLDQD 56 (73)
T ss_pred EEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCcccccCCc
Confidence 378999999999999999999954 5666666665444444444
No 7
>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=24.00 E-value=96 Score=28.98 Aligned_cols=116 Identities=16% Similarity=0.170 Sum_probs=57.0
Q ss_pred EEEeCCCChHHHHHHHHHHhcCceEEEEEEeeeeceEEEcCCCCCCCCCCcccccCcce----eEeeeeeEEEEEeeecc
Q 042221 92 VLEISSGADIVDSVSTYARRRGRGVCILSGAGAVTNVTLRQPPAGAGGSSSASIAGGAV----NITLHGRFEILSLTGTS 167 (305)
Q Consensus 92 VLrL~~GeDIvesI~~fArr~~~aicVLSaiGaVsnVTLRq~~~~~g~~~~a~l~g~y~----~~tleGrFEILSLsGti 167 (305)
+.....-++|.+.|.+..... .....+-.-|..+.|++|-....++ .|. ++.-.-.||.=-++||+
T Consensus 83 ~~~~~~~~~l~~~l~~~~~~~-N~f~airi~G~F~~v~~Rsv~~qe~---------Py~~l~e~~~~Q~~f~~~ni~GTl 152 (220)
T PF03306_consen 83 LDSPMSKEELEAKLDELLPSK-NLFYAIRIDGTFSSVKTRSVPKQEK---------PYPPLAEVAKNQPEFTFENIEGTL 152 (220)
T ss_dssp -EEEEEHHHHHHHHHHHSS-T-TS-EEEEEEEEEEEEEEE------S---------S---THHHHTT--EEEEEEEEEEE
T ss_pred cCCCCCHHHHHHHHHHhcCCC-ceEEEEEEEEEECeEEEEeccCccC---------CCCChhHHhccCceEEecCcEEEE
Confidence 445555677777777776533 3467788899999999998765433 121 11123455555555555
Q ss_pred ----CCCCCC-CCCCeEEEEEeCCCCcEEceecCCceeecceEEEEEeeeccceeeecc
Q 042221 168 ----LPPPAP-PGAGGLTIYLAGGQGQVVGGSVVGPLTASGTVVLMAASFANAVYDRLP 221 (305)
Q Consensus 168 ----sp~~~~-~~~~HLHISLAg~dGqViGGHL~G~LIAAt~VeVV~~SF~n~~yeRlp 221 (305)
+|.--. -...++|+-+-+ +-+.+||||...-+...+| -+..+.+.. -+||
T Consensus 153 VGf~sP~~~~gi~v~G~HlHFls-~Dr~~GGHvld~~~~~~~v--~~~~~~~~~-l~lP 207 (220)
T PF03306_consen 153 VGFYSPEYMGGINVPGFHLHFLS-DDRTFGGHVLDFELDNGTV--EIDVFDDFE-LELP 207 (220)
T ss_dssp EEEEE-GGGBTTB-CEEEEEEEE-TTSS-EEEEEEEEEEEEEE--EEEE-SEEE-EE--
T ss_pred EEEEcchhccccCCceEEEEEec-CCCCCCCCeEEEEeceEEE--EEEecCCEE-EECc
Confidence 443110 012345555553 3467899999887755444 444444332 2456
No 8
>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=23.22 E-value=2.3e+02 Score=21.63 Aligned_cols=43 Identities=23% Similarity=0.414 Sum_probs=32.4
Q ss_pred eEEEEEeCCCChHHHHHHHHHHhcC--ceEEEEEEeeeeceEEEcCC
Q 042221 89 RSHVLEISSGADIVDSVSTYARRRG--RGVCILSGAGAVTNVTLRQP 133 (305)
Q Consensus 89 r~hVLrL~~GeDIvesI~~fArr~~--~aicVLSaiGaVsnVTLRq~ 133 (305)
++-++.+.+|+-|-+.|...|++++ ...|.+--.| .+-.|-+-
T Consensus 11 q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~--~~k~l~~~ 55 (71)
T PF02196_consen 11 QRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVG--EKKPLDWD 55 (71)
T ss_dssp EEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEE--EEEEE-TT
T ss_pred CEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcC--CCccccCC
Confidence 5668999999999999999999995 4678888777 44444443
No 9
>smart00455 RBD Raf-like Ras-binding domain.
Probab=20.72 E-value=1.7e+02 Score=22.38 Aligned_cols=45 Identities=22% Similarity=0.510 Sum_probs=33.1
Q ss_pred eEEEEEeCCCChHHHHHHHHHHhcCc--eEEEEEEeeeeceEEEcCC
Q 042221 89 RSHVLEISSGADIVDSVSTYARRRGR--GVCILSGAGAVTNVTLRQP 133 (305)
Q Consensus 89 r~hVLrL~~GeDIvesI~~fArr~~~--aicVLSaiGaVsnVTLRq~ 133 (305)
+...+.+.||.-|.+.|...|++++. ..|.|.-.|.=.-+.+.++
T Consensus 10 ~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~ldl~~~ 56 (70)
T smart00455 10 QRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLDLNQP 56 (70)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCcceecCCc
Confidence 56789999999999999999999964 5677766663233333433
No 10
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=19.70 E-value=1.2e+02 Score=26.67 Aligned_cols=35 Identities=37% Similarity=0.422 Sum_probs=27.7
Q ss_pred eEEEEEEeeeeceEEEcCCCCCCCCCCcccccCcceeEeeeeeEEEEEe
Q 042221 115 GVCILSGAGAVTNVTLRQPPAGAGGSSSASIAGGAVNITLHGRFEILSL 163 (305)
Q Consensus 115 aicVLSaiGaVsnVTLRq~~~~~g~~~~a~l~g~y~~~tleGrFEILSL 163 (305)
.+=|||.-|...|+++. +.. ++ +++..|.||+.|=
T Consensus 28 ~lKilS~Dgtf~Ni~~~-~~~--~a-----------iIt~~GtY~~~sD 62 (133)
T PF14869_consen 28 VLKILSDDGTFVNITMI-PKS--GA-----------IITGYGTYEQPSD 62 (133)
T ss_pred cEEEEcCCCcEEEEEEe-CCC--Cc-----------EEEEeEEEEEcCC
Confidence 46799999999999993 322 22 8999999999873
Done!