Query 017799
Match_columns 365
No_of_seqs 187 out of 429
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:32:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017799.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017799hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03162 golden-2 like transcr 99.9 3.8E-24 8.3E-29 211.9 7.3 66 253-319 230-295 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.8 1.6E-21 3.5E-26 148.1 6.5 56 258-313 1-56 (57)
3 PF14379 Myb_CC_LHEQLE: MYB-CC 98.9 4E-10 8.6E-15 84.8 2.2 24 342-365 1-24 (51)
4 PF00249 Myb_DNA-binding: Myb- 97.4 0.00038 8.3E-09 50.1 5.1 48 260-311 1-48 (48)
5 smart00426 TEA TEA domain. 88.4 0.59 1.3E-05 37.6 3.5 47 262-309 5-67 (68)
6 smart00717 SANT SANT SWI3, AD 68.1 22 0.00048 23.7 5.6 44 261-310 2-46 (49)
7 PF01285 TEA: TEA/ATTS domain 67.8 5.3 0.00012 41.7 3.6 54 256-310 45-112 (431)
8 cd00167 SANT 'SWI3, ADA2, N-Co 63.0 29 0.00064 22.8 5.4 44 262-310 1-44 (45)
9 PF12776 Myb_DNA-bind_3: Myb/S 62.2 13 0.00028 29.4 4.1 50 262-311 1-62 (96)
10 PF07384 DUF1497: Protein of u 37.2 32 0.00068 26.7 2.4 21 262-282 37-57 (59)
11 smart00501 BRIGHT BRIGHT, ARID 36.0 36 0.00078 27.5 2.8 46 265-311 32-84 (93)
12 TIGR02894 DNA_bind_RsfA transc 29.5 35 0.00076 31.7 1.9 50 257-312 45-94 (161)
13 KOG3841 TEF-1 and related tran 28.7 42 0.0009 35.3 2.4 51 259-311 75-142 (455)
14 PF11888 DUF3408: Protein of u 23.6 63 0.0014 28.3 2.3 46 257-313 80-125 (136)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.90 E-value=3.8e-24 Score=211.89 Aligned_cols=66 Identities=47% Similarity=0.728 Sum_probs=61.1
Q ss_pred CCCCCCCCcccChHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCCCHHHHHHHhhhhhhcccCCCC
Q 017799 253 NNAPAKPRMRWTPELHEAFVEAVNQLGGSERATPKGVLKLMKVEGLTIYHVKSHLQKYRTARYRPDS 319 (365)
Q Consensus 253 ~~~~~K~RlrWT~eLH~rFV~Av~~LGG~~kAtPK~IL~lM~v~gLT~~hVkSHLQKYR~~~~~~~~ 319 (365)
+...+|+||+||+|||+|||+||++|| .+|||||+||++|+|+|||++||||||||||+.+++...
T Consensus 230 ~~g~KKpRLrWTpELH~rFVeAV~qLG-~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~ 295 (526)
T PLN03162 230 APGKKKAKVDWTPELHRRFVHAVEQLG-VEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAA 295 (526)
T ss_pred CCCCCCCcccCCHHHHHHHHHHHHHhC-cCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccc
Confidence 345689999999999999999999999 699999999999999999999999999999999886543
No 2
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=99.85 E-value=1.6e-21 Score=148.11 Aligned_cols=56 Identities=57% Similarity=0.952 Sum_probs=54.3
Q ss_pred CCCcccChHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCCCHHHHHHHhhhhhhc
Q 017799 258 KPRMRWTPELHEAFVEAVNQLGGSERATPKGVLKLMKVEGLTIYHVKSHLQKYRTA 313 (365)
Q Consensus 258 K~RlrWT~eLH~rFV~Av~~LGG~~kAtPK~IL~lM~v~gLT~~hVkSHLQKYR~~ 313 (365)
|+|++||+|+|++|++||++||+.+.|+||.|+++|++++||+.||+|||||||+.
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 78999999999999999999998899999999999999999999999999999985
No 3
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=98.93 E-value=4e-10 Score=84.80 Aligned_cols=24 Identities=83% Similarity=1.196 Sum_probs=22.8
Q ss_pred CcChHHHHHHHHHHhhhhhhhhcC
Q 017799 342 GIEITEALRLQMEVQKRLHEQLEV 365 (365)
Q Consensus 342 ~~~itEaLr~QmevQr~LhEQLEv 365 (365)
|++|+||||+||||||||||||||
T Consensus 1 g~~i~EALr~QmEvQrrLhEQLEv 24 (51)
T PF14379_consen 1 GMQITEALRMQMEVQRRLHEQLEV 24 (51)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999996
No 4
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=97.37 E-value=0.00038 Score=50.09 Aligned_cols=48 Identities=33% Similarity=0.418 Sum_probs=41.3
Q ss_pred CcccChHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCCCHHHHHHHhhhhh
Q 017799 260 RMRWTPELHEAFVEAVNQLGGSERATPKGVLKLMKVEGLTIYHVKSHLQKYR 311 (365)
Q Consensus 260 RlrWT~eLH~rFV~Av~~LGG~~kAtPK~IL~lM~v~gLT~~hVkSHLQKYR 311 (365)
|..||+|=+++|++||.++|. + .-+.|.+.|+ .|-|..++++|.++|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~-~--~W~~Ia~~~~-~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGK-D--NWKKIAKRMP-GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTT-T--HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCC-c--HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence 568999999999999999993 2 6788988888 7999999999999985
No 5
>smart00426 TEA TEA domain.
Probab=88.35 E-value=0.59 Score=37.62 Aligned_cols=47 Identities=28% Similarity=0.333 Sum_probs=29.8
Q ss_pred ccChHHHHHHHHHHHHhCCCCCCChHHHHhh--c-C-----------CCC--CCHHHHHHHhhh
Q 017799 262 RWTPELHEAFVEAVNQLGGSERATPKGVLKL--M-K-----------VEG--LTIYHVKSHLQK 309 (365)
Q Consensus 262 rWT~eLH~rFV~Av~~LGG~~kAtPK~IL~l--M-~-----------v~g--LT~~hVkSHLQK 309 (365)
.|.++|-..|++|+...- +....+-.+... | + ..| -|..+|.||||.
T Consensus 5 vWp~~lE~Af~~aL~~~~-~~g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsShIQv 67 (68)
T smart00426 5 VWSPDIEQAFQEALAIYP-PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQV 67 (68)
T ss_pred cCcHHHHHHHHHHHHHcC-ccCcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcchhee
Confidence 699999999999998776 222111122211 1 0 133 688889999984
No 6
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=68.06 E-value=22 Score=23.67 Aligned_cols=44 Identities=23% Similarity=0.349 Sum_probs=33.8
Q ss_pred cccChHHHHHHHHHHHHhC-CCCCCChHHHHhhcCCCCCCHHHHHHHhhhh
Q 017799 261 MRWTPELHEAFVEAVNQLG-GSERATPKGVLKLMKVEGLTIYHVKSHLQKY 310 (365)
Q Consensus 261 lrWT~eLH~rFV~Av~~LG-G~~kAtPK~IL~lM~v~gLT~~hVkSHLQKY 310 (365)
-.||++=...|+.++.++| + .=+.|-+.|+ +-|..+|+.+..++
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~----~w~~Ia~~~~--~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKN----NWEKIAKELP--GRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcC----CHHHHHHHcC--CCCHHHHHHHHHHH
Confidence 4699999999999999999 4 2455656654 78888888775543
No 7
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=67.83 E-value=5.3 Score=41.74 Aligned_cols=54 Identities=24% Similarity=0.270 Sum_probs=28.9
Q ss_pred CCCCCcccChHHHHHHHHHHHHhCCCCCCChHHHH-hhcC-------------CCCCCHHHHHHHhhhh
Q 017799 256 PAKPRMRWTPELHEAFVEAVNQLGGSERATPKGVL-KLMK-------------VEGLTIYHVKSHLQKY 310 (365)
Q Consensus 256 ~~K~RlrWT~eLH~rFV~Av~~LGG~~kAtPK~IL-~lM~-------------v~gLT~~hVkSHLQKY 310 (365)
..+..-+|.+++...|++|+...--..+++ -.+. +..| =.--|+.+|.||+|..
T Consensus 45 ~~~~~~vw~~~~e~af~~al~~~~~~g~~k-~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 45 DGDGEGVWPPDIEQAFQEALAIYPPCGRRK-LSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp -GGGS--S-HHHHHHHHHHHHHS-SSS----HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCCcc-cccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 457888999999999999997765222222 1111 1111 1347899999999988
No 8
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=62.97 E-value=29 Score=22.76 Aligned_cols=44 Identities=25% Similarity=0.367 Sum_probs=33.8
Q ss_pred ccChHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCCCHHHHHHHhhhh
Q 017799 262 RWTPELHEAFVEAVNQLGGSERATPKGVLKLMKVEGLTIYHVKSHLQKY 310 (365)
Q Consensus 262 rWT~eLH~rFV~Av~~LGG~~kAtPK~IL~lM~v~gLT~~hVkSHLQKY 310 (365)
.||.+=+..|+.++.++|- ..=+.|-+.|+ +-|..+|+.|..++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~--~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELP--GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcC--CCCHHHHHHHHHHh
Confidence 4999999999999999992 23456666664 47888898886654
No 9
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=62.17 E-value=13 Score=29.44 Aligned_cols=50 Identities=16% Similarity=0.312 Sum_probs=33.0
Q ss_pred ccChHHHHHHHHHHHH---hCCC-CCCChH-----HHHhhcC-C--CCCCHHHHHHHhhhhh
Q 017799 262 RWTPELHEAFVEAVNQ---LGGS-ERATPK-----GVLKLMK-V--EGLTIYHVKSHLQKYR 311 (365)
Q Consensus 262 rWT~eLH~rFV~Av~~---LGG~-~kAtPK-----~IL~lM~-v--~gLT~~hVkSHLQKYR 311 (365)
+||++..+.||+++-+ .|+- .....| .|.+.|+ . -.+|..|||+|+...|
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk 62 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLK 62 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHH
Confidence 5999999999999833 3432 123332 3445555 2 4488999999988544
No 10
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=37.23 E-value=32 Score=26.74 Aligned_cols=21 Identities=29% Similarity=0.727 Sum_probs=18.7
Q ss_pred ccChHHHHHHHHHHHHhCCCC
Q 017799 262 RWTPELHEAFVEAVNQLGGSE 282 (365)
Q Consensus 262 rWT~eLH~rFV~Av~~LGG~~ 282 (365)
.+..|+|..|-+-|++|||-+
T Consensus 37 kfnqem~aefheri~klggk~ 57 (59)
T PF07384_consen 37 KFNQEMQAEFHERIKKLGGKN 57 (59)
T ss_pred HhhHHHHHHHHHHHHHhcccc
Confidence 578999999999999999854
No 11
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=36.02 E-value=36 Score=27.50 Aligned_cols=46 Identities=17% Similarity=0.332 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHHHhCCCCCCC----hHHHHhhcCCCCC---CHHHHHHHhhhhh
Q 017799 265 PELHEAFVEAVNQLGGSERAT----PKGVLKLMKVEGL---TIYHVKSHLQKYR 311 (365)
Q Consensus 265 ~eLH~rFV~Av~~LGG~~kAt----PK~IL~lM~v~gL---T~~hVkSHLQKYR 311 (365)
-+|+.-|. +|..+||.++.+ =+.|.+.|+++.- ...++|+|-+||=
T Consensus 32 vdL~~Ly~-~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L 84 (93)
T smart00501 32 LDLYRLYR-LVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYL 84 (93)
T ss_pred CcHHHHHH-HHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHh
Confidence 37888888 589999976533 3567788998742 2456788777773
No 12
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=29.52 E-value=35 Score=31.69 Aligned_cols=50 Identities=28% Similarity=0.381 Sum_probs=36.9
Q ss_pred CCCCcccChHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCCCHHHHHHHhhhhhh
Q 017799 257 AKPRMRWTPELHEAFVEAVNQLGGSERATPKGVLKLMKVEGLTIYHVKSHLQKYRT 312 (365)
Q Consensus 257 ~K~RlrWT~eLH~rFV~Av~~LGG~~kAtPK~IL~lM~v~gLT~~hVkSHLQKYR~ 312 (365)
....|||...+-.++.+||..-- -.+-.++.. ...||+..|=+-||.|..
T Consensus 45 AACGFRWNs~VRkqY~~~i~~AK-kqRk~~~~~-----~~~ltl~~vI~fLq~l~~ 94 (161)
T TIGR02894 45 AACGFRWNAYVRKQYEEAIELAK-KQRKELKRE-----AGSLTLQDVISFLQNLKT 94 (161)
T ss_pred HHhcchHHHHHHHHHHHHHHHHH-HHHhccccC-----cccCCHHHHHHHHHHHHh
Confidence 46789999999999999997643 122111111 256999999999999984
No 13
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=28.66 E-value=42 Score=35.34 Aligned_cols=51 Identities=27% Similarity=0.351 Sum_probs=34.0
Q ss_pred CCcccChHHHHHHHHHHHHhCCCCCCChHHHH-----------------hhcCCCCCCHHHHHHHhhhhh
Q 017799 259 PRMRWTPELHEAFVEAVNQLGGSERATPKGVL-----------------KLMKVEGLTIYHVKSHLQKYR 311 (365)
Q Consensus 259 ~RlrWT~eLH~rFV~Av~~LGG~~kAtPK~IL-----------------~lM~v~gLT~~hVkSHLQKYR 311 (365)
..=+|+++.-+.|.+|+...- ..-+-|-|| |+=-=+--|+.+|.||.|..-
T Consensus 75 aegvWSpdIEqsFqEALaiyp--pcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVla 142 (455)
T KOG3841|consen 75 AEGVWSPDIEQSFQEALAIYP--PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLA 142 (455)
T ss_pred cccccChhHHHHHHHHHhhcC--CCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHH
Confidence 445899999999999998764 122223333 111124589999999999543
No 14
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=23.64 E-value=63 Score=28.35 Aligned_cols=46 Identities=24% Similarity=0.369 Sum_probs=31.9
Q ss_pred CCCCcccChHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCCCHHHHHHHhhhhhhc
Q 017799 257 AKPRMRWTPELHEAFVEAVNQLGGSERATPKGVLKLMKVEGLTIYHVKSHLQKYRTA 313 (365)
Q Consensus 257 ~K~RlrWT~eLH~rFV~Av~~LGG~~kAtPK~IL~lM~v~gLT~~hVkSHLQKYR~~ 313 (365)
+++ +.=..|+|++.-..|..+|| .+.|--++ --.=++-||..|+.-
T Consensus 80 R~~-vyI~~e~h~~l~~Iv~~ig~-~~~si~~y---------idNIL~~Hle~~~ee 125 (136)
T PF11888_consen 80 RKG-VYISRETHERLSRIVRVIGE-RKMSISGY---------IDNILRHHLEEYREE 125 (136)
T ss_pred Cee-eEECHHHHHHHHHHHHHHCC-CCCcHHHH---------HHHHHHHHHHHHHHH
Confidence 444 88899999999999999996 33333322 222258899999853
Done!