Query 029409
Match_columns 194
No_of_seqs 53 out of 55
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 12:27:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029409.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029409hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06549 DUF1118: Protein of u 100.0 8.2E-48 1.8E-52 302.8 10.3 114 81-194 1-116 (116)
2 PF06549 DUF1118: Protein of u 99.5 1.7E-14 3.8E-19 114.4 3.0 56 73-129 2-58 (116)
3 COG3413 Predicted DNA binding 55.1 5.7 0.00012 32.8 0.9 49 72-122 157-205 (215)
4 PRK15418 transcriptional regul 52.5 48 0.001 29.6 6.3 60 97-159 33-93 (318)
5 cd02433 Nodulin-21_like_2 Nodu 27.9 1.1E+02 0.0025 26.5 4.6 22 91-112 98-119 (234)
6 COG2390 DeoR Transcriptional r 27.8 3.7E+02 0.0079 24.7 8.0 68 88-158 21-89 (321)
7 smart00550 Zalpha Z-DNA-bindin 26.0 61 0.0013 22.6 2.2 31 95-127 24-54 (68)
8 PF01988 VIT1: VIT family; In 25.7 2.2E+02 0.0048 23.7 5.8 92 93-192 82-186 (213)
9 PF13412 HTH_24: Winged helix- 24.9 87 0.0019 19.7 2.6 25 99-125 23-47 (48)
10 PF09278 MerR-DNA-bind: MerR, 22.8 67 0.0014 21.3 1.8 22 92-113 2-23 (65)
11 PF10007 DUF2250: Uncharacteri 22.5 1.2E+02 0.0027 23.2 3.4 41 86-128 11-54 (92)
12 PF13309 HTH_22: HTH domain 21.5 1.3E+02 0.0028 21.0 3.1 36 75-110 17-59 (64)
13 PF13518 HTH_28: Helix-turn-he 20.3 1.5E+02 0.0032 18.4 3.0 37 95-133 14-50 (52)
No 1
>PF06549 DUF1118: Protein of unknown function (DUF1118); InterPro: IPR009500 This family consists of several hypothetical plant proteins of unknown function.
Probab=100.00 E-value=8.2e-48 Score=302.79 Aligned_cols=114 Identities=75% Similarity=1.032 Sum_probs=112.7
Q ss_pred HHHHhhhHHHHHHhchhhHHHHcCCchhhhhhhcchhhhhhcccccccCCCC--ChhhHHHHHHHHHhhcceeEEEecCC
Q 029409 81 RVEQLKLLSKAEKAGLLSAAEKFGLSLSSIEKLGLLSKAEEFGVLSAATDPA--TPGALLTLSLGLLLLGPSCVYLVPED 158 (194)
Q Consensus 81 ~vEk~~LLskaEkaGLLS~aE~~GlSLs~iE~LGlLS~aE~lg~Ls~a~~~~--tPgaL~slaL~LlvAg~a~v~lvPdd 158 (194)
|+||+|+|||+||+||||+||++|+|||+|||+|||||||++|+||+++|+. +||+|++++||++++||++||+||||
T Consensus 1 ~~Ek~KlLs~~EkaGLLS~AE~~GlsLS~iEkLgLlSkAE~LGlLs~a~~~~~~~P~~L~slaL~ll~ag~~~v~~vPdd 80 (116)
T PF06549_consen 1 RVEKLKLLSKAEKAGLLSKAEKAGLSLSSIEKLGLLSKAEELGLLSLAEDPASSSPGALASLALPLLVAGPAAVYLVPDD 80 (116)
T ss_pred ChHHHHHHHHHHHhhhHHHHHHcCCcHHHHHHhccccchHHhhhhHhccccccCChHHHHHHHHHHHHhhhheEEEecCC
Confidence 6899999999999999999999999999999999999999999999999987 99999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHhhhhhhhhhHHHHhhhhccCC
Q 029409 159 YPWEVALQGVVALVSVVGGSAAFAASNLVSNLQKSS 194 (194)
Q Consensus 159 s~~~Va~Q~vvA~~~vvg~~a~f~gS~~ls~LQ~s~ 194 (194)
|+|+|++|+|+|++|++|++++|+||+++++|||+|
T Consensus 81 s~~~va~Q~vvA~~~~vg~~a~f~gS~~l~~LQ~s~ 116 (116)
T PF06549_consen 81 STWLVALQAVVALVCVVGGSAAFAGSSLLSKLQESD 116 (116)
T ss_pred cHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhhcCC
Confidence 999999999999999999999999999999999998
No 2
>PF06549 DUF1118: Protein of unknown function (DUF1118); InterPro: IPR009500 This family consists of several hypothetical plant proteins of unknown function.
Probab=99.48 E-value=1.7e-14 Score=114.39 Aligned_cols=56 Identities=55% Similarity=0.681 Sum_probs=51.4
Q ss_pred CCchhhhhHHHHhhhHHHHHHhch-hhHHHHcCCchhhhhhhcchhhhhhcccccccC
Q 029409 73 SPPVKLLTRVEQLKLLSKAEKAGL-LSAAEKFGLSLSSIEKLGLLSKAEEFGVLSAAT 129 (194)
Q Consensus 73 ~~~~~vL~~vEk~~LLskaEkaGL-LS~aE~~GlSLs~iE~LGlLS~aE~lg~Ls~a~ 129 (194)
.|+.|+|+|+||.||||+|||+|+ ||++||+|+ |||.|++|+||.+|+++..++..
T Consensus 2 ~Ek~KlLs~~EkaGLLS~AE~~GlsLS~iEkLgL-lSkAE~LGlLs~a~~~~~~~P~~ 58 (116)
T PF06549_consen 2 VEKLKLLSKAEKAGLLSKAEKAGLSLSSIEKLGL-LSKAEELGLLSLAEDPASSSPGA 58 (116)
T ss_pred hHHHHHHHHHHHhhhHHHHHHcCCcHHHHHHhcc-ccchHHhhhhHhccccccCChHH
Confidence 578999999999999999999999 999999999 99999999999999998544433
No 3
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=55.08 E-value=5.7 Score=32.77 Aligned_cols=49 Identities=20% Similarity=0.316 Sum_probs=41.5
Q ss_pred CCCchhhhhHHHHhhhHHHHHHhchhhHHHHcCCchhhhhhhcchhhhhhc
Q 029409 72 TSPPVKLLTRVEQLKLLSKAEKAGLLSAAEKFGLSLSSIEKLGLLSKAEEF 122 (194)
Q Consensus 72 ~~~~~~vL~~vEk~~LLskaEkaGLLS~aE~~GlSLs~iE~LGlLS~aE~l 122 (194)
++-++++|+.+=+.|...-=.+.++-..||++|+|-+.+++ -|.+||+-
T Consensus 157 TdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e--hLRrAe~K 205 (215)
T COG3413 157 TDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE--HLRRAERK 205 (215)
T ss_pred CHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH--HHHHHHHH
Confidence 44457888888888888888888888999999999999999 69999874
No 4
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=52.52 E-value=48 Score=29.59 Aligned_cols=60 Identities=20% Similarity=0.338 Sum_probs=42.3
Q ss_pred hhHHHHcCCchhhhhhhcchhhhhhcccccccCCCCChhhHHHHHHHH-HhhcceeEEEecCCC
Q 029409 97 LSAAEKFGLSLSSIEKLGLLSKAEEFGVLSAATDPATPGALLTLSLGL-LLLGPSCVYLVPEDY 159 (194)
Q Consensus 97 LS~aE~~GlSLs~iE~LGlLS~aE~lg~Ls~a~~~~tPgaL~slaL~L-lvAg~a~v~lvPdds 159 (194)
--.|+++|+|-.++=+ +|..|.+.|++..--+...... .-|.=-| =-.|+--+++||++.
T Consensus 33 ~eIA~~lgiSR~~VsR--lL~~Ar~~GiV~I~I~~~~~~~-~~Le~~L~~~fgLk~~iVvp~~~ 93 (318)
T PRK15418 33 SEIGERLGLTRLKVSR--LLEKGRQSGIIRVQINSRFEGC-LELENALRQHFSLQHIRVLPALA 93 (318)
T ss_pred HHHHHHhCCCHHHHHH--HHHHHHHcCcEEEEEeCCCccH-HHHHHHHHHHhCCCEEEEEeCCC
Confidence 5689999999999999 6999999999987766432221 1121111 125888889999754
No 5
>cd02433 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=27.86 E-value=1.1e+02 Score=26.47 Aligned_cols=22 Identities=23% Similarity=0.169 Sum_probs=16.4
Q ss_pred HHHhchhhHHHHcCCchhhhhh
Q 029409 91 AEKAGLLSAAEKFGLSLSSIEK 112 (194)
Q Consensus 91 aEkaGLLS~aE~~GlSLs~iE~ 112 (194)
-|+.-+...-++.|++.+++++
T Consensus 98 ~e~~el~~iy~~~G~~~~~a~~ 119 (234)
T cd02433 98 EEAAELALIYRAKGLDEEEAKR 119 (234)
T ss_pred HHHHHHHHHHHHcCCCHHHHHH
Confidence 5666677777888888887765
No 6
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=27.83 E-value=3.7e+02 Score=24.66 Aligned_cols=68 Identities=29% Similarity=0.406 Sum_probs=45.7
Q ss_pred HHHHHHhchhhHHHHcCCchhhhhhhcchhhhhhcccccccCCCCChhhHHHHHHHH-HhhcceeEEEecCC
Q 029409 88 LSKAEKAGLLSAAEKFGLSLSSIEKLGLLSKAEEFGVLSAATDPATPGALLTLSLGL-LLLGPSCVYLVPED 158 (194)
Q Consensus 88 LskaEkaGLLS~aE~~GlSLs~iE~LGlLS~aE~lg~Ls~a~~~~tPgaL~slaL~L-lvAg~a~v~lvPdd 158 (194)
|-..+..+-=..||++|+|-.++-+ +|.+|.+.|++..-.++.....+. |.=-| =-.|+==+++||+|
T Consensus 21 lYY~~gltQ~eIA~~LgiSR~~v~r--lL~~Ar~~GiV~I~i~~~~~~~~~-Le~~L~~~fgL~~a~VVp~~ 89 (321)
T COG2390 21 LYYVEGLTQSEIAERLGISRATVSR--LLAKAREEGIVKISINSPVEGCLE-LEQQLKERFGLKEAIVVPSD 89 (321)
T ss_pred HHHhcCCCHHHHHHHhCCCHHHHHH--HHHHHHHCCeEEEEeCCCCcchHH-HHHHHHHhcCCCeEEEEcCC
Confidence 3334444557889999999999999 699999999998877743333322 11111 11566677888854
No 7
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=26.00 E-value=61 Score=22.61 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=24.5
Q ss_pred chhhHHHHcCCchhhhhhhcchhhhhhcccccc
Q 029409 95 GLLSAAEKFGLSLSSIEKLGLLSKAEEFGVLSA 127 (194)
Q Consensus 95 GLLS~aE~~GlSLs~iE~LGlLS~aE~lg~Ls~ 127 (194)
..--.++++|++-+.+.+ .|...++.|++.-
T Consensus 24 ta~eLa~~lgl~~~~v~r--~L~~L~~~G~V~~ 54 (68)
T smart00550 24 TALQLAKNLGLPKKEVNR--VLYSLEKKGKVCK 54 (68)
T ss_pred CHHHHHHHHCCCHHHHHH--HHHHHHHCCCEEe
Confidence 346678899999998888 6888888887643
No 8
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=25.70 E-value=2.2e+02 Score=23.69 Aligned_cols=92 Identities=24% Similarity=0.166 Sum_probs=49.1
Q ss_pred HhchhhHHHHcCCchhhhhhh-cchhh---------hhhcccccccCCCCChhh---HHHHHHHHHhhcceeEEEecCCC
Q 029409 93 KAGLLSAAEKFGLSLSSIEKL-GLLSK---------AEEFGVLSAATDPATPGA---LLTLSLGLLLLGPSCVYLVPEDY 159 (194)
Q Consensus 93 kaGLLS~aE~~GlSLs~iE~L-GlLS~---------aE~lg~Ls~a~~~~tPga---L~slaL~LlvAg~a~v~lvPdds 159 (194)
+.=+....++.|++-.++|+. ..+++ .|++|+.. ++...|-. ...++..+...-|...|++.+ +
T Consensus 82 ~~el~~iy~~~Gl~~~~a~~i~~~l~~~~~~~~~m~~ee~g~~~--~~~~~p~~~al~~~~sf~lg~liPllp~~~~~-~ 158 (213)
T PF01988_consen 82 KEELVEIYRAKGLSEEDAEEIAEELSKDKDALDFMMREELGLSP--EEEESPWKAALATFLSFILGGLIPLLPYFFLP-S 158 (213)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHhCchHHHHHHhhhccCCc--cccchHHHHHHHHHHHHHHHHHHHHHHHHHhh-h
Confidence 334455666668877777763 12222 45566655 44455543 333566666666777776655 2
Q ss_pred hHHHHHHHHHHHHHhhhhhhhhhHHHHhhhhcc
Q 029409 160 PWEVALQGVVALVSVVGGSAAFAASNLVSNLQK 192 (194)
Q Consensus 160 ~~~Va~Q~vvA~~~vvg~~a~f~gS~~ls~LQ~ 192 (194)
.. ..+...+++...++|.-+.+.+++.+
T Consensus 159 -~~----~a~~~s~~~~~~~L~~~G~~~a~~~~ 186 (213)
T PF01988_consen 159 -VS----EAFIASIAVTILALFILGYFKARISG 186 (213)
T ss_pred -HH----HHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 11 33334444555555655555555543
No 9
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=24.89 E-value=87 Score=19.73 Aligned_cols=25 Identities=44% Similarity=0.680 Sum_probs=18.7
Q ss_pred HHHHcCCchhhhhhhcchhhhhhcccc
Q 029409 99 AAEKFGLSLSSIEKLGLLSKAEEFGVL 125 (194)
Q Consensus 99 ~aE~~GlSLs~iE~LGlLS~aE~lg~L 125 (194)
.+++.|+|.+.+-+ .+.+.++.|++
T Consensus 23 la~~~~is~~tv~~--~l~~L~~~g~I 47 (48)
T PF13412_consen 23 LAEKLGISRSTVNR--YLKKLEEKGLI 47 (48)
T ss_dssp HHHHHTS-HHHHHH--HHHHHHHTTSE
T ss_pred HHHHhCCCHHHHHH--HHHHHHHCcCc
Confidence 57888999888887 57777777764
No 10
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=22.85 E-value=67 Score=21.32 Aligned_cols=22 Identities=27% Similarity=0.536 Sum_probs=15.4
Q ss_pred HHhchhhHHHHcCCchhhhhhh
Q 029409 92 EKAGLLSAAEKFGLSLSSIEKL 113 (194)
Q Consensus 92 EkaGLLS~aE~~GlSLs~iE~L 113 (194)
++.-++-.+..+|+||.+|-++
T Consensus 2 ~rL~~I~~~r~lGfsL~eI~~~ 23 (65)
T PF09278_consen 2 ERLQFIRRLRELGFSLEEIREL 23 (65)
T ss_dssp HHHHHHHHHHHTT--HHHHHHH
T ss_pred hHHHHHHHHHHcCCCHHHHHHH
Confidence 4455677888999999999883
No 11
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.53 E-value=1.2e+02 Score=23.25 Aligned_cols=41 Identities=34% Similarity=0.526 Sum_probs=28.7
Q ss_pred hhHHHHHHhch---hhHHHHcCCchhhhhhhcchhhhhhccccccc
Q 029409 86 KLLSKAEKAGL---LSAAEKFGLSLSSIEKLGLLSKAEEFGVLSAA 128 (194)
Q Consensus 86 ~LLskaEkaGL---LS~aE~~GlSLs~iE~LGlLS~aE~lg~Ls~a 128 (194)
++|--..++|- -+.|...++++..+++ ++-+.|+.|++-=.
T Consensus 11 ~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~--~l~~Le~~GLler~ 54 (92)
T PF10007_consen 11 KILQHLKKAGPDYAKSIARRLKIPLEEVRE--ALEKLEEMGLLERV 54 (92)
T ss_pred HHHHHHHHHCCCcHHHHHHHHCCCHHHHHH--HHHHHHHCCCeEEe
Confidence 34444455555 5677788999998888 58888888877543
No 12
>PF13309 HTH_22: HTH domain
Probab=21.51 E-value=1.3e+02 Score=21.02 Aligned_cols=36 Identities=25% Similarity=0.489 Sum_probs=26.5
Q ss_pred chhhhhHHHHhhhHHHHHHhchhh-------HHHHcCCchhhh
Q 029409 75 PVKLLTRVEQLKLLSKAEKAGLLS-------AAEKFGLSLSSI 110 (194)
Q Consensus 75 ~~~vL~~vEk~~LLskaEkaGLLS-------~aE~~GlSLs~i 110 (194)
+++.+++-|+..++....+.|+.. .|+++|+|-.++
T Consensus 17 ~~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TV 59 (64)
T PF13309_consen 17 PPSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATV 59 (64)
T ss_pred ChhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHH
Confidence 457788888888888888888832 477788775544
No 13
>PF13518 HTH_28: Helix-turn-helix domain
Probab=20.28 E-value=1.5e+02 Score=18.38 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=27.0
Q ss_pred chhhHHHHcCCchhhhhhhcchhhhhhcccccccCCCCC
Q 029409 95 GLLSAAEKFGLSLSSIEKLGLLSKAEEFGVLSAATDPAT 133 (194)
Q Consensus 95 GLLS~aE~~GlSLs~iE~LGlLS~aE~lg~Ls~a~~~~t 133 (194)
.+-..|++.|+|.+.+.. .+..-++-|.-.+...+..
T Consensus 14 s~~~~a~~~gis~~tv~~--w~~~y~~~G~~~l~~~~~r 50 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYR--WIKRYREGGIEGLKPKKRR 50 (52)
T ss_pred CHHHHHHHHCCCHhHHHH--HHHHHHhcCHHHhccCCCC
Confidence 345578999999999987 6888888776555554443
Done!