Query 014824
Match_columns 418
No_of_seqs 162 out of 441
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 08:52:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014824hhsearch_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 1.3E-23 2.7E-28 210.2 6.6 64 241-305 229-292 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.8 1.9E-21 4.2E-26 148.7 6.4 56 247-302 1-56 (57)
3 PF00249 Myb_DNA-binding: Myb- 97.2 0.00083 1.8E-08 48.5 5.3 48 249-300 1-48 (48)
4 PF14379 Myb_CC_LHEQLE: MYB-CC 96.8 3.3E-05 7.1E-10 59.6 -5.5 34 325-358 3-45 (51)
5 smart00426 TEA TEA domain. 86.8 0.69 1.5E-05 38.0 3.1 46 251-298 5-67 (68)
6 smart00717 SANT SANT SWI3, AD 58.9 43 0.00093 22.3 5.6 45 250-299 2-46 (49)
7 PF01285 TEA: TEA/ATTS domain 58.2 9.8 0.00021 40.0 3.4 54 245-299 45-112 (431)
8 PF12776 Myb_DNA-bind_3: Myb/S 56.0 14 0.0003 29.2 3.2 51 251-301 1-63 (96)
9 cd00167 SANT 'SWI3, ADA2, N-Co 53.1 57 0.0012 21.4 5.4 44 251-299 1-44 (45)
10 smart00501 BRIGHT BRIGHT, ARID 44.2 22 0.00047 28.9 2.7 44 255-299 33-83 (93)
11 PF11888 DUF3408: Protein of u 41.0 33 0.00072 30.2 3.5 60 229-301 65-124 (136)
12 TIGR02894 DNA_bind_RsfA transc 40.6 16 0.00035 34.4 1.6 54 242-301 41-94 (161)
13 PF07384 DUF1497: Protein of u 35.6 33 0.00071 27.5 2.3 22 250-271 36-57 (59)
14 KOG3841 TEF-1 and related tran 27.8 33 0.00072 36.5 1.6 56 247-304 74-146 (455)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.89 E-value=1.3e-23 Score=210.19 Aligned_cols=64 Identities=47% Similarity=0.730 Sum_probs=59.9
Q ss_pred cccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHhhhhhhccccC
Q 014824 241 AKRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTVKTT 305 (418)
Q Consensus 241 ~krs~kKpRlrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl~k~t 305 (418)
.....||+||+||+|||+|||+||++|| .++||||+||++|+|+|||++||||||||||+.++.
T Consensus 229 ~~~g~KKpRLrWTpELH~rFVeAV~qLG-~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~ 292 (526)
T PLN03162 229 AAPGKKKAKVDWTPELHRRFVHAVEQLG-VEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRH 292 (526)
T ss_pred cCCCCCCCcccCCHHHHHHHHHHHHHhC-cCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhccc
Confidence 3455899999999999999999999999 799999999999999999999999999999998774
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=1.9e-21 Score=148.72 Aligned_cols=56 Identities=55% Similarity=0.844 Sum_probs=54.1
Q ss_pred CCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHhhhhhhcc
Q 014824 247 APRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTV 302 (418)
Q Consensus 247 KpRlrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl~ 302 (418)
|+|++||+|+|++||+||+.||+.+.|+||+|+++|++++||+.+|+|||||||+.
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 68999999999999999999998789999999999999999999999999999985
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=97.21 E-value=0.00083 Score=48.52 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=41.5
Q ss_pred CcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHhhhhhh
Q 014824 249 RMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYR 300 (418)
Q Consensus 249 RlrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYR 300 (418)
|..||+|=+.+|++||.++|. -.-+.|.+.|+ .+-|..+|++|.++|+
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 25899999998 8999999999999985
No 4
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=96.77 E-value=3.3e-05 Score=59.56 Aligned_cols=34 Identities=21% Similarity=0.328 Sum_probs=29.3
Q ss_pred CCccccccccCCCCCC-C-C-------cchhccCccccccccC
Q 014824 325 DTSEDIMFGIQHPRRP-E-T-------SSIQQQGRASNGLWSN 358 (418)
Q Consensus 325 d~SEALrlQiEvQRRl-E-l-------~~IeqQGk~~qsLWSN 358 (418)
.++|||++|||||||| | + ++||+||||+++|+..
T Consensus 3 ~i~EALr~QmEvQrrLhEQLEvQr~Lqlrieaqgkyl~~ilek 45 (51)
T PF14379_consen 3 QITEALRMQMEVQRRLHEQLEVQRHLQLRIEAQGKYLQSILEK 45 (51)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 5789999999999998 3 2 6899999999998865
No 5
>smart00426 TEA TEA domain.
Probab=86.83 E-value=0.69 Score=37.96 Aligned_cols=46 Identities=24% Similarity=0.323 Sum_probs=30.1
Q ss_pred ccCHHHHHHHHHHHHHhCCCCCCChH-HHHhh--c------------CC--CCccHHHHHHhhhh
Q 014824 251 RWTTTLHARFVHAVELLGGHERATPK-SVLEL--M------------DV--KDLTLAHVKSHLQM 298 (418)
Q Consensus 251 rWT~ELH~rFV~AVeqLGG~dkAtPK-~ILel--M------------nV--~GLTr~hVkSHLQK 298 (418)
+|.++|-..|++|++..- ...+=| +++.. | .. .-=|+.+|+||||.
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 799999999999999875 222222 22221 0 01 23577889999885
No 6
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=58.91 E-value=43 Score=22.25 Aligned_cols=45 Identities=11% Similarity=0.175 Sum_probs=33.8
Q ss_pred cccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHhhhhh
Q 014824 250 MRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMY 299 (418)
Q Consensus 250 lrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKY 299 (418)
-.||++=...|+.+|.++| . ..=+.|.+.|+ +=|...|+.+..++
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g-~--~~w~~Ia~~~~--~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYG-K--NNWEKIAKELP--GRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHC-c--CCHHHHHHHcC--CCCHHHHHHHHHHH
Confidence 4699999999999999999 1 23466777765 77888887765443
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=58.17 E-value=9.8 Score=39.98 Aligned_cols=54 Identities=19% Similarity=0.187 Sum_probs=29.3
Q ss_pred CCCCCcccCHHHHHHHHHHHHHhCCCCCCChH--------------HHHhhcCCCCccHHHHHHhhhhh
Q 014824 245 MRAPRMRWTTTLHARFVHAVELLGGHERATPK--------------SVLELMDVKDLTLAHVKSHLQMY 299 (418)
Q Consensus 245 ~kKpRlrWT~ELH~rFV~AVeqLGG~dkAtPK--------------~ILelMnV~GLTr~hVkSHLQKY 299 (418)
.....-+|.+++...|++|+...-=-.++.-+ .|...-| +.=|+.+|+||+|..
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 45678899999999999999887311112211 1111112 346889999999998
No 8
>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=55.97 E-value=14 Score=29.22 Aligned_cols=51 Identities=14% Similarity=0.236 Sum_probs=34.4
Q ss_pred ccCHHHHHHHHHHHHHh---CCC-CCCChH-----HHHhhcCC---CCccHHHHHHhhhhhhc
Q 014824 251 RWTTTLHARFVHAVELL---GGH-ERATPK-----SVLELMDV---KDLTLAHVKSHLQMYRT 301 (418)
Q Consensus 251 rWT~ELH~rFV~AVeqL---GG~-dkAtPK-----~ILelMnV---~GLTr~hVkSHLQKYRl 301 (418)
+||++..+.||+++-+. |.. .....| .|.+.|+- ..+|..+|++|+...|.
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 59999999999988333 433 233333 35555544 45889999999885543
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=53.14 E-value=57 Score=21.43 Aligned_cols=44 Identities=14% Similarity=0.195 Sum_probs=33.8
Q ss_pred ccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHhhhhh
Q 014824 251 RWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMY 299 (418)
Q Consensus 251 rWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKY 299 (418)
.||.|=...|+.++..+|- ..=+.|.+.|+ +=|..+|+.+.+++
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 33567777774 46888888776543
No 10
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=44.21 E-value=22 Score=28.90 Aligned_cols=44 Identities=20% Similarity=0.336 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhCCCCCCC----hHHHHhhcCCCCc---cHHHHHHhhhhh
Q 014824 255 TLHARFVHAVELLGGHERAT----PKSVLELMDVKDL---TLAHVKSHLQMY 299 (418)
Q Consensus 255 ELH~rFV~AVeqLGG~dkAt----PK~ILelMnV~GL---Tr~hVkSHLQKY 299 (418)
+|++.|. +|..+||.++.+ =+.|.+.|+++.- ....++++-+||
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 7999998 588999977543 3578889999752 245566666666
No 11
>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=41.00 E-value=33 Score=30.23 Aligned_cols=60 Identities=23% Similarity=0.374 Sum_probs=42.2
Q ss_pred ccchhhccccCccccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHhhhhhhc
Q 014824 229 GLMRSRFMSRFPAKRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRT 301 (418)
Q Consensus 229 g~~r~~~~~~~p~krs~kKpRlrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl 301 (418)
.-.+++|+.. .+-..|++ +-=..|+|++....|..+|+. -|.|.|+--.=++-||..|+.
T Consensus 65 ~~Y~~~FL~~--~~~~~R~~-vyI~~e~h~~l~~Iv~~ig~~----------~~si~~yidNIL~~Hle~~~e 124 (136)
T PF11888_consen 65 EDYRETFLKR--PKIKARKG-VYISRETHERLSRIVRVIGER----------KMSISGYIDNILRHHLEEYRE 124 (136)
T ss_pred HHHHHHhCCC--CCCCCCee-eEECHHHHHHHHHHHHHHCCC----------CCcHHHHHHHHHHHHHHHHHH
Confidence 4567788732 23334444 888999999999999999963 344555544456789999975
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=40.60 E-value=16 Score=34.37 Aligned_cols=54 Identities=31% Similarity=0.434 Sum_probs=41.7
Q ss_pred ccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHhhhhhhc
Q 014824 242 KRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRT 301 (418)
Q Consensus 242 krs~kKpRlrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl 301 (418)
.|+.-++.+||...+-.++.+||+..- .++-.+|.. ...||++.|-+-||.|..
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 567788999999999999999999765 222222221 367999999999999974
No 13
>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=35.57 E-value=33 Score=27.51 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=19.2
Q ss_pred cccCHHHHHHHHHHHHHhCCCC
Q 014824 250 MRWTTTLHARFVHAVELLGGHE 271 (418)
Q Consensus 250 lrWT~ELH~rFV~AVeqLGG~d 271 (418)
-.+..|+|..|-+-|+.|||.+
T Consensus 36 ~kfnqem~aefheri~klggk~ 57 (59)
T PF07384_consen 36 NKFNQEMQAEFHERIKKLGGKN 57 (59)
T ss_pred hHhhHHHHHHHHHHHHHhcccc
Confidence 3578999999999999999854
No 14
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=27.75 E-value=33 Score=36.54 Aligned_cols=56 Identities=21% Similarity=0.275 Sum_probs=36.7
Q ss_pred CCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhh--------------cC---CCCccHHHHHHhhhhhhcccc
Q 014824 247 APRMRWTTTLHARFVHAVELLGGHERATPKSVLEL--------------MD---VKDLTLAHVKSHLQMYRTVKT 304 (418)
Q Consensus 247 KpRlrWT~ELH~rFV~AVeqLGG~dkAtPK~ILel--------------Mn---V~GLTr~hVkSHLQKYRl~k~ 304 (418)
-.-=+|+++.-+.|.+|+...- .--+=|-||.- .. =+-=||.+|.||.|.....|.
T Consensus 74 daegvWSpdIEqsFqEALaiyp--pcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~ 146 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYP--PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKL 146 (455)
T ss_pred ccccccChhHHHHHHHHHhhcC--CCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHH
Confidence 3445899999999999998763 11222333321 11 145789999999998754433
Done!