Query 016225
Match_columns 393
No_of_seqs 160 out of 437
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 04:56:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016225.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016225hhsearch_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 1.1E-23 2.3E-28 209.3 5.8 63 242-305 230-292 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.8 1.7E-21 3.6E-26 147.8 5.5 56 247-302 1-56 (57)
3 PF00249 Myb_DNA-binding: Myb- 97.1 0.00072 1.6E-08 48.4 4.1 48 249-300 1-48 (48)
4 PF14379 Myb_CC_LHEQLE: MYB-CC 96.7 4.2E-05 9E-10 58.6 -5.5 35 321-355 2-45 (51)
5 smart00426 TEA TEA domain. 85.7 0.91 2E-05 37.0 3.3 46 251-298 5-67 (68)
6 PF01285 TEA: TEA/ATTS domain 58.1 8.8 0.00019 39.9 3.0 54 245-299 45-112 (431)
7 PF12776 Myb_DNA-bind_3: Myb/S 54.4 12 0.00026 29.3 2.6 51 251-301 1-63 (96)
8 smart00717 SANT SANT SWI3, AD 54.2 41 0.0009 22.1 4.9 43 250-297 2-44 (49)
9 cd00167 SANT 'SWI3, ADA2, N-Co 47.0 59 0.0013 21.1 4.7 43 251-298 1-43 (45)
10 PF11888 DUF3408: Protein of u 45.3 20 0.00043 31.3 2.8 62 228-302 64-125 (136)
11 smart00501 BRIGHT BRIGHT, ARID 36.8 27 0.00059 28.0 2.1 44 255-299 33-83 (93)
12 PF07384 DUF1497: Protein of u 34.7 34 0.00073 27.2 2.2 22 250-271 36-57 (59)
13 TIGR02894 DNA_bind_RsfA transc 28.7 29 0.00063 32.4 1.2 54 242-301 41-94 (161)
14 KOG3841 TEF-1 and related tran 27.4 43 0.00093 35.5 2.3 54 248-303 75-145 (455)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.88 E-value=1.1e-23 Score=209.28 Aligned_cols=63 Identities=46% Similarity=0.729 Sum_probs=59.2
Q ss_pred ccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChhHHHhhcCCCcccHHHHHHhhccccccccc
Q 016225 242 KRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTVKTT 305 (393)
Q Consensus 242 krs~kKpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl~K~t 305 (393)
....||+||+||+|||+|||+||++|| .++||||+||++|+|+|||++||||||||||+.++.
T Consensus 230 ~~g~KKpRLrWTpELH~rFVeAV~qLG-~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~ 292 (526)
T PLN03162 230 APGKKKAKVDWTPELHRRFVHAVEQLG-VEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRH 292 (526)
T ss_pred CCCCCCCcccCCHHHHHHHHHHHHHhC-cCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhccc
Confidence 445789999999999999999999999 799999999999999999999999999999998763
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=99.84 E-value=1.7e-21 Score=147.83 Aligned_cols=56 Identities=55% Similarity=0.844 Sum_probs=54.0
Q ss_pred CCCcccCHHHHHHHHHHHHHhCCCCCCChhHHHhhcCCCcccHHHHHHhhcccccc
Q 016225 247 APRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTV 302 (393)
Q Consensus 247 KpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl~ 302 (393)
|+|++||+|+|++||+||+.||+.+.|+||.|+++|++++||+.+|+|||||||+.
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 68999999999999999999997789999999999999999999999999999975
No 3
>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=97.11 E-value=0.00072 Score=48.38 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=41.2
Q ss_pred CcccCHHHHHHHHHHHHHhCCCCCCChhHHHhhcCCCcccHHHHHHhhcccc
Q 016225 249 RMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYR 300 (393)
Q Consensus 249 RLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYR 300 (393)
|..||+|=+.+|++||.++|. -.-+.|.+.|+ .+-|..+|++|.++|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~---~~W~~Ia~~~~-~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGK---DNWKKIAKRMP-GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTT---THHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCC---cHHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence 568999999999999999992 25889999998 8999999999999885
No 4
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=96.67 E-value=4.2e-05 Score=58.56 Aligned_cols=35 Identities=20% Similarity=0.298 Sum_probs=29.3
Q ss_pred CCCchhhhccCCCCCCC-CC--------cchhhcCCcccccccC
Q 016225 321 GDTSEDIMFGIQHPRRP-ET--------SSIQQQGRASNGLWSN 355 (393)
Q Consensus 321 g~~SEAL~mQmEvQrRL-E~--------~sIE~QGr~lq~lWsn 355 (393)
..++|||++|||||+|| |+ ++|+++|||+++|.+.
T Consensus 2 ~~i~EALr~QmEvQrrLhEQLEvQr~Lqlrieaqgkyl~~ilek 45 (51)
T PF14379_consen 2 MQITEALRMQMEVQRRLHEQLEVQRHLQLRIEAQGKYLQSILEK 45 (51)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 35789999999999998 32 6799999999988753
No 5
>smart00426 TEA TEA domain.
Probab=85.75 E-value=0.91 Score=36.98 Aligned_cols=46 Identities=24% Similarity=0.353 Sum_probs=29.8
Q ss_pred ccCHHHHHHHHHHHHHhCCCCCCChh-HHHhh--c-C-----------C--CcccHHHHHHhhcc
Q 016225 251 RWTTTLHARFVHAVELLGGHERATPK-SVLEL--M-D-----------V--KDLTLAHVKSHLQM 298 (393)
Q Consensus 251 rWT~ELH~rFV~AVeqLGG~dkAtPK-~ILel--M-n-----------V--~GLTr~hVkSHLQK 298 (393)
+|.++|-..|++|++..= ...+=| +++.. | | . .-=|+.+|+||||.
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 799999999999998774 122222 22211 0 0 1 23578899999995
No 6
>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=58.06 E-value=8.8 Score=39.93 Aligned_cols=54 Identities=19% Similarity=0.268 Sum_probs=29.1
Q ss_pred CCCCCcccCHHHHHHHHHHHHHhC--CCCCCC------------hhHHHhhcCCCcccHHHHHHhhccc
Q 016225 245 MRAPRMRWTTTLHARFVHAVELLG--GHERAT------------PKSVLELMDVKDLTLAHVKSHLQMY 299 (393)
Q Consensus 245 ~kKpRLrWT~ELH~rFV~AVeqLG--G~dkAt------------PK~ILelMnV~GLTr~hVkSHLQKY 299 (393)
..+..-+|.++|...|++|+...- |-.|-. -..|...-| ..=|+.+|+||||..
T Consensus 45 ~~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg-~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 45 DGDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTG-KTRTRKQVSSHIQVL 112 (431)
T ss_dssp -GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS-----SHHHHHHHHHH
T ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhC-cccchhHHHHHHHHH
Confidence 356788999999999999998763 222200 011111112 346788999999998
No 7
>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=54.41 E-value=12 Score=29.27 Aligned_cols=51 Identities=14% Similarity=0.232 Sum_probs=34.3
Q ss_pred ccCHHHHHHHHHHHHH---hCCC-CCCChh-----HHHhhcCC---CcccHHHHHHhhccccc
Q 016225 251 RWTTTLHARFVHAVEL---LGGH-ERATPK-----SVLELMDV---KDLTLAHVKSHLQMYRT 301 (393)
Q Consensus 251 rWT~ELH~rFV~AVeq---LGG~-dkAtPK-----~ILelMnV---~GLTr~hVkSHLQKYRl 301 (393)
+||++..+-||+++-+ .|.. .....| .|.+.|+- -.+|..+|++|+...|.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 5999999999998843 3433 233333 35555554 45889999999875443
No 8
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=54.23 E-value=41 Score=22.07 Aligned_cols=43 Identities=12% Similarity=0.200 Sum_probs=31.9
Q ss_pred cccCHHHHHHHHHHHHHhCCCCCCChhHHHhhcCCCcccHHHHHHhhc
Q 016225 250 MRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQ 297 (393)
Q Consensus 250 LrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQ 297 (393)
-.||++=...|+.+|.++| . ..=+.|.+.|+ +=|...|+.+-.
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g-~--~~w~~Ia~~~~--~rt~~~~~~~~~ 44 (49)
T smart00717 2 GEWTEEEDELLIELVKKYG-K--NNWEKIAKELP--GRTAEQCRERWN 44 (49)
T ss_pred CCCCHHHHHHHHHHHHHHC-c--CCHHHHHHHcC--CCCHHHHHHHHH
Confidence 4699999999999999998 1 22456666665 667777776644
No 9
>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=46.97 E-value=59 Score=21.12 Aligned_cols=43 Identities=14% Similarity=0.200 Sum_probs=32.2
Q ss_pred ccCHHHHHHHHHHHHHhCCCCCCChhHHHhhcCCCcccHHHHHHhhcc
Q 016225 251 RWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQM 298 (393)
Q Consensus 251 rWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQK 298 (393)
.||.|=...|+.+|.++|- ..=+.|.+.|+ +=|..+|+.+.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~--~rs~~~~~~~~~~ 43 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELP--GRTPKQCRERWRN 43 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcC--CCCHHHHHHHHHH
Confidence 4999999999999999992 23466777764 3677788776543
No 10
>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=45.31 E-value=20 Score=31.30 Aligned_cols=62 Identities=21% Similarity=0.313 Sum_probs=43.8
Q ss_pred ccchhhhccccCccccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChhHHHhhcCCCcccHHHHHHhhcccccc
Q 016225 228 QGLMRSRFMSRFPAKRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTV 302 (393)
Q Consensus 228 ~g~~r~~~~~~~p~krs~kKpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl~ 302 (393)
-.-.+++|+. +.+-..|++ +-=..|+|++....|..+||. -|.|.|+--.=+.-||..|+..
T Consensus 64 ~~~Y~~~FL~--~~~~~~R~~-vyI~~e~h~~l~~Iv~~ig~~----------~~si~~yidNIL~~Hle~~~ee 125 (136)
T PF11888_consen 64 LEDYRETFLK--RPKIKARKG-VYISRETHERLSRIVRVIGER----------KMSISGYIDNILRHHLEEYREE 125 (136)
T ss_pred HHHHHHHhCC--CCCCCCCee-eEECHHHHHHHHHHHHHHCCC----------CCcHHHHHHHHHHHHHHHHHHH
Confidence 3456778883 333344555 888999999999999999963 3455555444567899998864
No 11
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=36.79 E-value=27 Score=28.04 Aligned_cols=44 Identities=20% Similarity=0.336 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCCCCCCC----hhHHHhhcCCCcc---cHHHHHHhhccc
Q 016225 255 TLHARFVHAVELLGGHERAT----PKSVLELMDVKDL---TLAHVKSHLQMY 299 (393)
Q Consensus 255 ELH~rFV~AVeqLGG~dkAt----PK~ILelMnV~GL---Tr~hVkSHLQKY 299 (393)
+|++.|. +|..+||.++.+ =+.|.+.||++.- ....++++-+||
T Consensus 33 dL~~Ly~-~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~ 83 (93)
T smart00501 33 DLYRLYR-LVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERY 83 (93)
T ss_pred cHHHHHH-HHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHH
Confidence 7999898 588999977543 3568889999742 234566666555
No 12
>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=34.66 E-value=34 Score=27.25 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=19.3
Q ss_pred cccCHHHHHHHHHHHHHhCCCC
Q 016225 250 MRWTTTLHARFVHAVELLGGHE 271 (393)
Q Consensus 250 LrWT~ELH~rFV~AVeqLGG~d 271 (393)
-.+..|+|..|-+-|+.|||.+
T Consensus 36 ~kfnqem~aefheri~klggk~ 57 (59)
T PF07384_consen 36 NKFNQEMQAEFHERIKKLGGKN 57 (59)
T ss_pred hHhhHHHHHHHHHHHHHhcccc
Confidence 3578999999999999999854
No 13
>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=28.67 E-value=29 Score=32.43 Aligned_cols=54 Identities=31% Similarity=0.434 Sum_probs=40.7
Q ss_pred ccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChhHHHhhcCCCcccHHHHHHhhccccc
Q 016225 242 KRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRT 301 (393)
Q Consensus 242 krs~kKpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl 301 (393)
.|..-.+.+||...+-.++.+||+..- ..+-.+++. ...||++.|-+-||.|..
T Consensus 41 ~RTsAACGFRWNs~VRkqY~~~i~~AK-kqRk~~~~~-----~~~ltl~~vI~fLq~l~~ 94 (161)
T TIGR02894 41 NRTAAACGFRWNAYVRKQYEEAIELAK-KQRKELKRE-----AGSLTLQDVISFLQNLKT 94 (161)
T ss_pred cccHHHhcchHHHHHHHHHHHHHHHHH-HHHhccccC-----cccCCHHHHHHHHHHHHh
Confidence 456667899999999999999998764 222222221 267999999999999985
No 14
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=27.35 E-value=43 Score=35.48 Aligned_cols=54 Identities=22% Similarity=0.326 Sum_probs=35.3
Q ss_pred CCcccCHHHHHHHHHHHHHhCCCCCCChhHHHhh--------------cCC---CcccHHHHHHhhccccccc
Q 016225 248 PRMRWTTTLHARFVHAVELLGGHERATPKSVLEL--------------MDV---KDLTLAHVKSHLQMYRTVK 303 (393)
Q Consensus 248 pRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILel--------------MnV---~GLTr~hVkSHLQKYRl~K 303 (393)
.-=+|+++.-+.|.||+...- .--+=|-||.- ... +-=||.+|.||.|.....|
T Consensus 75 aegvWSpdIEqsFqEALaiyp--pcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk 145 (455)
T KOG3841|consen 75 AEGVWSPDIEQSFQEALAIYP--PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRK 145 (455)
T ss_pred cccccChhHHHHHHHHHhhcC--CCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHH
Confidence 445899999999999998763 11122333321 111 4568999999999765443
Done!