Query 016012
Match_columns 397
No_of_seqs 161 out of 447
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 02:59:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016012.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016012hhsearch_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 1.2E-23 2.7E-28 209.0 6.6 63 242-305 230-292 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.8 1.5E-21 3.2E-26 148.3 6.2 56 247-302 1-56 (57)
3 PF14379 Myb_CC_LHEQLE: MYB-CC 97.6 1.4E-06 3.1E-11 66.5 -5.4 35 324-358 2-45 (51)
4 PF00249 Myb_DNA-binding: Myb- 97.2 0.00088 1.9E-08 48.0 5.3 48 249-300 1-48 (48)
5 smart00426 TEA TEA domain. 84.4 1.3 2.9E-05 36.1 3.7 18 251-268 5-22 (68)
6 smart00717 SANT SANT SWI3, AD 58.2 46 0.00099 21.9 5.6 45 250-299 2-46 (49)
7 PF01285 TEA: TEA/ATTS domain 56.1 11 0.00025 39.2 3.4 54 245-299 45-112 (431)
8 cd00167 SANT 'SWI3, ADA2, N-Co 51.0 66 0.0014 20.9 5.4 44 251-299 1-44 (45)
9 smart00501 BRIGHT BRIGHT, ARID 50.2 16 0.00034 29.4 2.7 45 254-299 32-83 (93)
10 PF12776 Myb_DNA-bind_3: Myb/S 49.6 19 0.00042 28.1 3.1 50 251-300 1-62 (96)
11 PF11888 DUF3408: Protein of u 45.7 23 0.00049 31.0 3.2 60 229-301 65-124 (136)
12 TIGR02894 DNA_bind_RsfA transc 39.0 18 0.00038 33.8 1.5 54 242-301 41-94 (161)
13 PF07384 DUF1497: Protein of u 37.6 29 0.00063 27.6 2.3 22 250-271 36-57 (59)
14 KOG3841 TEF-1 and related tran 20.9 50 0.0011 35.1 1.3 72 229-304 58-146 (455)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.89 E-value=1.2e-23 Score=208.98 Aligned_cols=63 Identities=46% Similarity=0.729 Sum_probs=59.4
Q ss_pred ccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHHhhhccccccC
Q 016012 242 KRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTVKTT 305 (397)
Q Consensus 242 krs~kKpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl~k~t 305 (397)
....||+||+||+|||+|||+||++|| .+|||||+||++|+|+|||++||||||||||+.++.
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 799999999999999999999999999999998773
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=1.5e-21 Score=148.26 Aligned_cols=56 Identities=55% Similarity=0.844 Sum_probs=54.2
Q ss_pred CCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHHhhhcccc
Q 016012 247 APRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRTV 302 (397)
Q Consensus 247 KpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl~ 302 (397)
|+|++||+|+|++||+||+.||+.+.|+||.|+++|++.+||+.+|+|||||||+.
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
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=97.59 E-value=1.4e-06 Score=66.52 Aligned_cols=35 Identities=20% Similarity=0.298 Sum_probs=30.7
Q ss_pred CCCcchhhccCCCCCCC-CC--------cchhhcCccccccccC
Q 016012 324 GDTSEDIMFGIQHPRRP-ET--------SSIQQQGRASNGLWSN 358 (397)
Q Consensus 324 gdiSEALr~QIEvQrRL-El--------~rIEqQGkylqsLwsn 358 (397)
..++|||++|||||||| |+ ++||++|||+++|+++
T Consensus 2 ~~i~EALr~QmEvQrrLhEQLEvQr~Lqlrieaqgkyl~~ilek 45 (51)
T PF14379_consen 2 MQITEALRMQMEVQRRLHEQLEVQRHLQLRIEAQGKYLQSILEK 45 (51)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 36789999999999998 32 7899999999999987
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=97.20 E-value=0.00088 Score=47.98 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=41.5
Q ss_pred CcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHHhhhcc
Q 016012 249 RMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYR 300 (397)
Q Consensus 249 RLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYR 300 (397)
|..||+|=+.+|++||.++|. -.-+.|.+.|+ .+-|..+|++|.++|+
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 8999999999999985
No 5
>smart00426 TEA TEA domain.
Probab=84.40 E-value=1.3 Score=36.06 Aligned_cols=18 Identities=17% Similarity=0.510 Sum_probs=16.6
Q ss_pred ccCHHHHHHHHHHHHHhC
Q 016012 251 RWTTTLHARFVHAVELLG 268 (397)
Q Consensus 251 rWT~ELH~rFV~AVeqLG 268 (397)
+|.++|-..|++|++..-
T Consensus 5 vWp~~lE~Af~~aL~~~~ 22 (68)
T smart00426 5 VWSPDIEQAFQEALAIYP 22 (68)
T ss_pred cCcHHHHHHHHHHHHHcC
Confidence 799999999999999875
No 6
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=58.23 E-value=46 Score=21.88 Aligned_cols=45 Identities=11% Similarity=0.175 Sum_probs=33.3
Q ss_pred cccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHHhhhc
Q 016012 250 MRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMY 299 (397)
Q Consensus 250 LrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKY 299 (397)
-.||++=...|+.+|.++| . ..=+.|.+.|+ +=|...|+.+..++
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 23466766665 67777777665443
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=56.15 E-value=11 Score=39.20 Aligned_cols=54 Identities=19% Similarity=0.255 Sum_probs=29.1
Q ss_pred CCCCCcccCHHHHHHHHHHHHHhC--CCCCC------------ChHHHHhhcCCCCccHHHHHHHhhhc
Q 016012 245 MRAPRMRWTTTLHARFVHAVELLG--GHERA------------TPKSVLELMDVKDLTLAHVKSHLQMY 299 (397)
Q Consensus 245 ~kKpRLrWT~ELH~rFV~AVeqLG--G~dkA------------tPK~ILelMnV~GLTr~hVkSHLQKY 299 (397)
..+..-+|.++|...|++|+...- |-.|- .-..|...-| +.=|+.+|+||+|..
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 457788999999999999998773 22220 0011111112 335778999999998
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=51.01 E-value=66 Score=20.89 Aligned_cols=44 Identities=14% Similarity=0.195 Sum_probs=33.3
Q ss_pred ccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHHhhhc
Q 016012 251 RWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMY 299 (397)
Q Consensus 251 rWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKY 299 (397)
.||.+=...|+.++.++|- ..=+.|.+.|+ +=|..+|+.+.+++
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 33567777764 46777888776543
No 9
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=50.19 E-value=16 Score=29.44 Aligned_cols=45 Identities=20% Similarity=0.319 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhCCCCCCC----hHHHHhhcCCCCc---cHHHHHHHhhhc
Q 016012 254 TTLHARFVHAVELLGGHERAT----PKSVLELMDVKDL---TLAHVKSHLQMY 299 (397)
Q Consensus 254 ~ELH~rFV~AVeqLGG~dkAt----PK~ILelMnV~GL---Tr~hVkSHLQKY 299 (397)
-+|++.|. +|..+||.++.+ =+.|.+.||++.- ....++++-+||
T Consensus 32 vdL~~Ly~-~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~ 83 (93)
T smart00501 32 LDLYRLYR-LVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERY 83 (93)
T ss_pred CcHHHHHH-HHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHH
Confidence 37999998 599999977543 3568889999752 244677776666
No 10
>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=49.59 E-value=19 Score=28.13 Aligned_cols=50 Identities=14% Similarity=0.240 Sum_probs=33.1
Q ss_pred ccCHHHHHHHHHHHHHh---CCC-CCCChH-----HHHhhcCC---CCccHHHHHHHhhhcc
Q 016012 251 RWTTTLHARFVHAVELL---GGH-ERATPK-----SVLELMDV---KDLTLAHVKSHLQMYR 300 (397)
Q Consensus 251 rWT~ELH~rFV~AVeqL---GG~-dkAtPK-----~ILelMnV---~GLTr~hVkSHLQKYR 300 (397)
+||++..+.||+++-+. |.- .....| .|.+.|+- -.+|..+|++|+...|
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 59999999999988333 433 123333 35555544 4578899999987543
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=45.71 E-value=23 Score=31.00 Aligned_cols=60 Identities=23% Similarity=0.351 Sum_probs=43.2
Q ss_pred cccccccccCCcCccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHHhhhccc
Q 016012 229 GLMRSRFMSRFPAKRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRT 301 (397)
Q Consensus 229 g~~rs~~~~~~p~krs~kKpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl 301 (397)
.-.+++||... +-..|++ +-=..|+|++....|..+|+. -|.|.|+.-.=+.-||..|+.
T Consensus 65 ~~Y~~~FL~~~--~~~~R~~-vyI~~e~h~~l~~Iv~~ig~~----------~~si~~yidNIL~~Hle~~~e 124 (136)
T PF11888_consen 65 EDYRETFLKRP--KIKARKG-VYISRETHERLSRIVRVIGER----------KMSISGYIDNILRHHLEEYRE 124 (136)
T ss_pred HHHHHHhCCCC--CCCCCee-eEECHHHHHHHHHHHHHHCCC----------CCcHHHHHHHHHHHHHHHHHH
Confidence 45677888433 3334555 888999999999999999963 355555555557789999875
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=38.96 E-value=18 Score=33.84 Aligned_cols=54 Identities=31% Similarity=0.434 Sum_probs=41.0
Q ss_pred ccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHhhcCCCCccHHHHHHHhhhccc
Q 016012 242 KRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLELMDVKDLTLAHVKSHLQMYRT 301 (397)
Q Consensus 242 krs~kKpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILelMnV~GLTr~hVkSHLQKYRl 301 (397)
.|..-++.+||...+-.++.+||+..- -++-.+++. ...||++.|-+-||.|..
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 455678999999999999999998765 222222221 267999999999999974
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=37.56 E-value=29 Score=27.62 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=19.3
Q ss_pred cccCHHHHHHHHHHHHHhCCCC
Q 016012 250 MRWTTTLHARFVHAVELLGGHE 271 (397)
Q Consensus 250 LrWT~ELH~rFV~AVeqLGG~d 271 (397)
-.+..|+|..|-+-|++|||.+
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=20.92 E-value=50 Score=35.08 Aligned_cols=72 Identities=21% Similarity=0.318 Sum_probs=42.5
Q ss_pred cccccccccCCcCccCCCCCCcccCHHHHHHHHHHHHHhCCCCCCChHHHHh--------------hcCC---CCccHHH
Q 016012 229 GLMRSRFMSRFPAKRSMRAPRMRWTTTLHARFVHAVELLGGHERATPKSVLE--------------LMDV---KDLTLAH 291 (397)
Q Consensus 229 g~~rs~~~~~~p~krs~kKpRLrWT~ELH~rFV~AVeqLGG~dkAtPK~ILe--------------lMnV---~GLTr~h 291 (397)
|.+.++-.+.+-.+ .+-.-=+|.++.-+.|.+|+...- .--+=|-||. .... +-=|+.+
T Consensus 58 ~~~~p~~~~~~~D~--~~daegvWSpdIEqsFqEALaiyp--pcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQ 133 (455)
T KOG3841|consen 58 DLKGPEAKDKFTDN--QRDAEGVWSPDIEQSFQEALAIYP--PCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQ 133 (455)
T ss_pred ccCCccccccCCcc--ccccccccChhHHHHHHHHHhhcC--CCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHH
Confidence 44444444433332 124456899999999999998763 1112233332 1111 4568899
Q ss_pred HHHHhhhcccccc
Q 016012 292 VKSHLQMYRTVKT 304 (397)
Q Consensus 292 VkSHLQKYRl~k~ 304 (397)
|.||.|.....|.
T Consensus 134 VSSHIQVlarrk~ 146 (455)
T KOG3841|consen 134 VSSHIQVLARRKL 146 (455)
T ss_pred HHHHHHHHHHHHH
Confidence 9999997754443
Done!