Query 010040
Match_columns 519
No_of_seqs 329 out of 1918
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 20:19:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010040.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010040hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00018 AP2 DNA-binding domain 99.7 4.5E-17 9.7E-22 128.8 6.8 58 158-216 1-60 (61)
2 smart00380 AP2 DNA-binding dom 99.7 1.4E-16 3.1E-21 127.5 7.8 61 159-220 1-63 (64)
3 smart00380 AP2 DNA-binding dom 99.7 9.7E-17 2.1E-21 128.5 6.1 63 251-313 1-63 (64)
4 cd00018 AP2 DNA-binding domain 99.7 1.6E-16 3.4E-21 125.7 6.7 61 250-310 1-61 (61)
5 PHA00280 putative NHN endonucl 99.4 2.7E-13 5.8E-18 122.4 8.2 64 147-211 56-119 (121)
6 PHA00280 putative NHN endonucl 99.2 1.7E-11 3.7E-16 110.8 7.9 104 194-304 11-119 (121)
7 PF00847 AP2: AP2 domain; Int 99.0 3.7E-10 7.9E-15 87.4 6.1 51 158-208 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 98.7 2.3E-08 4.9E-13 77.3 6.3 52 250-301 1-56 (56)
9 cd04518 TBP_archaea archaeal T 82.9 22 0.00048 34.5 11.9 135 157-299 33-172 (174)
10 cd00652 TBP_TLF TATA box bindi 81.3 25 0.00054 33.9 11.7 134 158-298 34-172 (174)
11 cd04517 TLF TBP-like factors ( 74.7 44 0.00095 32.3 11.2 132 159-297 35-171 (174)
12 PRK00394 transcription factor; 68.0 76 0.0017 30.9 11.3 134 158-298 33-172 (179)
13 cd04516 TBP_eukaryotes eukaryo 62.5 1.1E+02 0.0024 29.7 11.2 131 158-295 34-168 (174)
14 PLN00062 TATA-box-binding prot 59.9 1.3E+02 0.0029 29.3 11.3 134 158-298 34-171 (179)
15 PF08846 DUF1816: Domain of un 48.7 25 0.00054 29.6 3.7 34 262-295 9-42 (68)
16 PRK10927 essential cell divisi 45.0 89 0.0019 33.4 7.9 21 275-295 285-305 (319)
17 PF14657 Integrase_AP2: AP2-li 44.7 68 0.0015 24.1 5.3 36 171-206 1-42 (46)
18 COG2101 SPT15 TATA-box binding 29.1 6E+02 0.013 25.4 11.7 130 156-298 38-179 (185)
19 PF14657 Integrase_AP2: AP2-li 28.8 1.4E+02 0.003 22.5 4.7 26 274-299 17-42 (46)
20 COG3087 FtsN Cell division pro 26.1 1.4E+02 0.003 31.2 5.7 26 183-210 193-218 (264)
21 PF00352 TBP: Transcription fa 23.8 2E+02 0.0042 24.3 5.3 47 158-205 36-82 (86)
No 1
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.69 E-value=4.5e-17 Score=128.82 Aligned_cols=58 Identities=53% Similarity=0.899 Sum_probs=55.1
Q ss_pred CCeEEEEEecCCCeEEEEEEeC--CeEEEeCCCCCHHHHHHHHHHHHHHhhcccCCccccc
Q 010040 158 SQYRGVTFYRRTGRWESHIWDS--GKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSI 216 (519)
Q Consensus 158 SgYRGV~~~k~~GKW~A~I~~~--gKri~LGtFdTeEEAArAYD~AAikl~G~~A~~NFp~ 216 (519)
|+|+||++++ +|||+|+|+++ +|++|||+|+|+||||+|||.|+++++|..+.+|||.
T Consensus 1 s~~~GV~~~~-~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~ 60 (61)
T cd00018 1 SKYRGVRQRP-WGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPD 60 (61)
T ss_pred CCccCEEECC-CCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCC
Confidence 7899999765 49999999999 9999999999999999999999999999999999985
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.67 E-value=1.4e-16 Score=127.53 Aligned_cols=61 Identities=57% Similarity=0.945 Sum_probs=57.8
Q ss_pred CeEEEEEecCCCeEEEEEEe--CCeEEEeCCCCCHHHHHHHHHHHHHHhhcccCCccccccccc
Q 010040 159 QYRGVTFYRRTGRWESHIWD--SGKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSIEDYE 220 (519)
Q Consensus 159 gYRGV~~~k~~GKW~A~I~~--~gKri~LGtFdTeEEAArAYD~AAikl~G~~A~~NFp~sdYe 220 (519)
+|+||++ +++|||+|+|++ .+|+++||+|+|+||||+|||.|+++++|..+.+|||.++|+
T Consensus 1 ~~kGV~~-~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQ-RPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEe-CCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 5999997 567999999999 899999999999999999999999999999999999999986
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.66 E-value=9.7e-17 Score=128.49 Aligned_cols=63 Identities=52% Similarity=0.769 Sum_probs=59.3
Q ss_pred cccCeeeecCcceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCcCCCCCcchH
Q 010040 251 KYRGVTLHKCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPSLYQ 313 (519)
Q Consensus 251 kYRGV~~~k~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AAikl~G~~A~tNFp~s~Y~ 313 (519)
+|+||+++++|+|+|+|+...+++.++||+|+|+||||+|||.|+++++|..+.+|||++.|+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 589999988899999997666899999999999999999999999999999999999999985
No 4
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.66 E-value=1.6e-16 Score=125.73 Aligned_cols=61 Identities=52% Similarity=0.797 Sum_probs=56.1
Q ss_pred CcccCeeeecCcceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCcCCCCCc
Q 010040 250 SKYRGVTLHKCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPS 310 (519)
Q Consensus 250 SkYRGV~~~k~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AAikl~G~~A~tNFp~s 310 (519)
|+|+||+++++|||+|+|+....++.++||+|+|+||||+|||.|+++++|..+.+|||.+
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 6899999988999999996544489999999999999999999999999999999999864
No 5
>PHA00280 putative NHN endonuclease
Probab=99.44 E-value=2.7e-13 Score=122.43 Aligned_cols=64 Identities=20% Similarity=0.342 Sum_probs=58.1
Q ss_pred ccCCCCCCCCCCCeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcccCC
Q 010040 147 KKSRRGPRSRSSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEAD 211 (519)
Q Consensus 147 kk~rr~~r~~tSgYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~A~ 211 (519)
.++++.+++++|||+||+|++..+||+|+|+++||+++||.|+++|+|+.||+ ++.+++|.+|+
T Consensus 56 ~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 56 SWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred hcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 44556677899999999999999999999999999999999999999999997 77889998874
No 6
>PHA00280 putative NHN endonuclease
Probab=99.24 E-value=1.7e-11 Score=110.80 Aligned_cols=104 Identities=16% Similarity=0.109 Sum_probs=80.2
Q ss_pred HHHHHHHHHHHhhcccCC---cccc-ccccchhhhhhccccccceeeeecccccCcCCCCCcccCeeeec-CcceEEeec
Q 010040 194 AARAYDRAAIKFRGAEAD---INFS-IEDYEDDLKQMSNLTKEEFVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMG 268 (519)
Q Consensus 194 AArAYD~AAikl~G~~A~---~NFp-~sdYeeELkqL~~LSKEE~V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~ 268 (519)
+-+++..+...++|.-.. +.+. -...+..+..|+.++..|...+.+.. ..++|+|+||++++ .|||+|+|
T Consensus 11 ~~~~Hrlvw~~~~G~~P~g~~VdHidg~~~dnri~NLr~~T~~eN~~N~~~~----~~N~SG~kGV~~~k~~~kw~A~I- 85 (121)
T PHA00280 11 APRRHIQVWEAANGPIPKGYYIDHIDGNPLNDALDNLRLALPKENSWNMKTP----KSNTSGLKGLSWSKEREMWRGTV- 85 (121)
T ss_pred hhhHhHhhhHHHHCCCCCCCEEEcCCCCCCCCcHHHhhhcCHHHHhcccCCC----CCCCCCCCeeEEecCCCeEEEEE-
Confidence 345667777788885431 2221 12334667888888888888776544 57789999999986 79999999
Q ss_pred cccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCc
Q 010040 269 QFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAV 304 (519)
Q Consensus 269 ~~~~~K~v~LGtFdTeEEAArAYD~AAikl~G~~A~ 304 (519)
.+++|.++||.|+|+|+|+.||+ ++.+++|..|.
T Consensus 86 -~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 86 -TAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred -EECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 68999999999999999999997 77889997764
No 7
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=99.05 E-value=3.7e-10 Score=87.35 Aligned_cols=51 Identities=33% Similarity=0.546 Sum_probs=47.0
Q ss_pred CCeEEEEEecCCCeEEEEEEeC-----CeEEEeCCCCCHHHHHHHHHHHHHHhhcc
Q 010040 158 SQYRGVTFYRRTGRWESHIWDS-----GKQVYLGGFDTAHAAARAYDRAAIKFRGA 208 (519)
Q Consensus 158 SgYRGV~~~k~~GKW~A~I~~~-----gKri~LGtFdTeEEAArAYD~AAikl~G~ 208 (519)
|+|+||+|++..++|+|.|++. +|.++||.|+++++|++||+.++++++|.
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 7899999999999999999984 48999999999999999999999998873
No 8
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=98.74 E-value=2.3e-08 Score=77.33 Aligned_cols=52 Identities=37% Similarity=0.554 Sum_probs=44.9
Q ss_pred CcccCeeeec-CcceEEeecccc-C--ceeeeccCCCCHHHHHHHHHHHHHHhcCC
Q 010040 250 SKYRGVTLHK-CGRWEARMGQFL-G--KKYVYLGLFDTEVEAARAYDRAAVKCNGK 301 (519)
Q Consensus 250 SkYRGV~~~k-~GKW~ArI~~~~-~--~K~v~LGtFdTeEEAArAYD~AAikl~G~ 301 (519)
|+|+||++++ .++|+|.|+... + ++.++||.|++++||++||+.+.+++.|.
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 6899999986 899999996532 1 49999999999999999999999998763
No 9
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=82.89 E-value=22 Score=34.45 Aligned_cols=135 Identities=16% Similarity=0.222 Sum_probs=80.5
Q ss_pred CCCeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcccC----Cccccccccchhhhhhcccccc
Q 010040 157 SSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEA----DINFSIEDYEDDLKQMSNLTKE 232 (519)
Q Consensus 157 tSgYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~A----~~NFp~sdYeeELkqL~~LSKE 232 (519)
..+|.||.++-+.-+=.+.|+..||-+--|. .++++|..|-++.+..+....- ..+|.....-.....-..+..+
T Consensus 33 P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGa-ks~~~a~~a~~~~~~~L~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~ 111 (174)
T cd04518 33 PDQFPGLVYRLEDPKIAALIFRSGKMVCTGA-KSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVASADLGREVNLD 111 (174)
T ss_pred CCcCcEEEEEccCCcEEEEEECCCeEEEEcc-CCHHHHHHHHHHHHHHHHhcCCCccCCCceEEEEEEEEEEcCCccCHH
Confidence 3688999987777788899999998877775 6788888888887776654221 1222221100000000011111
Q ss_pred ceeeeecccccCcCCCCCcccCeeeec-CcceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHhc
Q 010040 233 EFVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCN 299 (519)
Q Consensus 233 E~V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AAikl~ 299 (519)
.+...++ .. .=...+|-|+.++- .-|=.+-| +..||-+..|. .+++|+.+|.++-...+.
T Consensus 112 ~la~~~~-~~---~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 112 AIAIGLP-NA---EYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred HHHhhCC-CC---ccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 1111111 11 11335788988763 44555666 77889888886 568889999888776653
No 10
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=81.33 E-value=25 Score=33.92 Aligned_cols=134 Identities=16% Similarity=0.154 Sum_probs=77.9
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhccc--C--Cccccccccchhhhhhccccccc
Q 010040 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAE--A--DINFSIEDYEDDLKQMSNLTKEE 233 (519)
Q Consensus 158 SgYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~--A--~~NFp~sdYeeELkqL~~LSKEE 233 (519)
.+|.||.++-..-+=.+.|+..||-+--|. .++|+|..|.++.+..+.... . ..||....-......-..+..++
T Consensus 34 e~fpgli~R~~~P~~t~lIf~sGKivitGa-ks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v~NIvas~~l~~~i~L~~ 112 (174)
T cd00652 34 KRFPGVIMRLREPKTTALIFSSGKMVITGA-KSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCDLGFPIRLEE 112 (174)
T ss_pred CccceEEEEcCCCcEEEEEECCCEEEEEec-CCHHHHHHHHHHHHHHHHHcCCCccccCceEEEEEEEEEECCCcccHHH
Confidence 588999987777788899999999877776 467788888888776663321 1 22333211000000000111111
Q ss_pred eeeeecccccCcCCCCCcccCeeeec-CcceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 010040 234 FVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (519)
Q Consensus 234 ~V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AAikl 298 (519)
+....+.... =...+|-|+.++- ..+=..-| +..||-+..|. .+++|+.+|+++-.-.+
T Consensus 113 la~~~~~~~~---YePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~i~~~L 172 (174)
T cd00652 113 LALKHPENAS---YEPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEKIYPIL 172 (174)
T ss_pred HHhhhhcccE---ECCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 1111111111 1234688888774 34555566 77888888876 56888999987765443
No 11
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=74.72 E-value=44 Score=32.35 Aligned_cols=132 Identities=19% Similarity=0.172 Sum_probs=76.2
Q ss_pred CeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhc--ccC--Cccccccccchhhhhhccccccce
Q 010040 159 QYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRG--AEA--DINFSIEDYEDDLKQMSNLTKEEF 234 (519)
Q Consensus 159 gYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl~G--~~A--~~NFp~sdYeeELkqL~~LSKEE~ 234 (519)
+|-||.++-+.-+=.+.|+..||-+--| ..++|+|.+|.++.+..+.. ... ..||....--.....-..+..+++
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~sGKiviTG-aks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~l 113 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSSGKITITG-ATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCSMPFPIRLDEL 113 (174)
T ss_pred CCCEEEEEecCCcEEEEEECCCeEEEEc-cCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEeCCCcccHHHH
Confidence 8899998777778889999999876666 47889999999887776633 211 233332110000000000111111
Q ss_pred eeeecccccCcCCCCCcccCeeeec-CcceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHH
Q 010040 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVK 297 (519)
Q Consensus 235 V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AAik 297 (519)
...-.+... =...+|-|+.++- ..+=.+.| +..||-+..|. .+++|+.+|+++-.-.
T Consensus 114 a~~~~~~~~---YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~pi 171 (174)
T cd04517 114 AAKNRSSAS---YEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIYPI 171 (174)
T ss_pred HHhchhhcE---eCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHH
Confidence 110011111 1234688888774 33455555 77888888876 5678888888765433
No 12
>PRK00394 transcription factor; Reviewed
Probab=67.96 E-value=76 Score=30.88 Aligned_cols=134 Identities=16% Similarity=0.191 Sum_probs=78.5
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcc--cC--Cccccccccchhhhhhccccccc
Q 010040 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGA--EA--DINFSIEDYEDDLKQMSNLTKEE 233 (519)
Q Consensus 158 SgYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl~G~--~A--~~NFp~sdYeeELkqL~~LSKEE 233 (519)
.+|-||.++-+.-+=.+.|+..||-+--|.. ++++|..|-++.+..+... .. ..+|.....-....--..+..++
T Consensus 33 e~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~-S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVas~~l~~~i~L~~ 111 (179)
T PRK00394 33 EQFPGLVYRLEDPKIAALIFRSGKVVCTGAK-SVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASADLGVELNLNA 111 (179)
T ss_pred ccCceEEEEecCCceEEEEEcCCcEEEEccC-CHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEEEEEcCCeEcHHH
Confidence 4788999877777888999999998888875 5668888877776655332 11 12222211000000000011111
Q ss_pred eeeeec-ccccCcCCCCCcccCeeeec-CcceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 010040 234 FVHVLR-RQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (519)
Q Consensus 234 ~V~aLR-Rqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AAikl 298 (519)
+...+. +... =...+|-|+.++- ..|=..-| +..||-+..|. .+++|+.+|.++-...+
T Consensus 112 la~~~~~~~~~---YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l 172 (179)
T PRK00394 112 IAIGLGLENIE---YEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKL 172 (179)
T ss_pred HHHhcCcCCcE---ECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 111110 1111 1235788988773 44556666 77888888886 56888999988876655
No 13
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=62.49 E-value=1.1e+02 Score=29.69 Aligned_cols=131 Identities=17% Similarity=0.198 Sum_probs=73.8
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcccC---Cccccccccchhhhhhccccccce
Q 010040 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEA---DINFSIEDYEDDLKQMSNLTKEEF 234 (519)
Q Consensus 158 SgYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~A---~~NFp~sdYeeELkqL~~LSKEE~ 234 (519)
.+|-||.++-+.-+=.+.|+..||-+--|. .++|+|..|.++.+..+....- ..||.....-.....-..+..+++
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~SGKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~~~v~Nivat~~l~~~i~L~~l 112 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFSSGKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGL 112 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEECCCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEEEEEECCCcccHHHH
Confidence 578899987777788899999999887776 5677888888887766633221 123322111100000001111111
Q ss_pred eeeecccccCcCCCCCcccCeeeec-CcceEEeeccccCceeeeccCCCCHHHHHHHHHHHH
Q 010040 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAA 295 (519)
Q Consensus 235 V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AA 295 (519)
....+... .=....|-|+.++- .-|-..-| +..||-+.+|. .+++|+.+|++.-.
T Consensus 113 a~~~~~~~---~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~a~~~i~ 168 (174)
T cd04516 113 AHAHKQFS---SYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KSREEIYQAFENIY 168 (174)
T ss_pred HHhChhcc---EeCCccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHH
Confidence 11001110 11235788888764 33333444 78888888875 56777888876543
No 14
>PLN00062 TATA-box-binding protein; Provisional
Probab=59.90 E-value=1.3e+02 Score=29.32 Aligned_cols=134 Identities=16% Similarity=0.156 Sum_probs=75.5
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcccCC---ccccccccchhhhhhccccccce
Q 010040 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEAD---INFSIEDYEDDLKQMSNLTKEEF 234 (519)
Q Consensus 158 SgYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~A~---~NFp~sdYeeELkqL~~LSKEE~ 234 (519)
..|-||.++-+.-+=.+.|+..||-+--|. .++|+|..|.++.+..+....-. .||.....-.....-..+..+.+
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~SGKiviTGa-ks~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~l 112 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFASGKMVCTGA-KSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGL 112 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEECCCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEEEECCCcccHHHH
Confidence 478899987777788899999998876664 67888888888877766432212 23322111100000001111111
Q ss_pred eeeecccccCcCCCCCcccCeeeec-CcceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 010040 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (519)
Q Consensus 235 V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AAikl 298 (519)
...-++.. .-...+|-|+.++- .-+-..-| +..||-+..|. .+++|+.+|++.-.-.+
T Consensus 113 a~~~~~~~---~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~ai~~i~p~L 171 (179)
T PLN00062 113 AYAHGAFS---SYEPELFPGLIYRMKQPKIVLLI--FVSGKIVITGA-KVREEIYTAFENIYPVL 171 (179)
T ss_pred HHhchhhc---ccCcccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 11101111 11335788887764 23344445 78888888886 45777777776554333
No 15
>PF08846 DUF1816: Domain of unknown function (DUF1816); InterPro: IPR014945 Q4C9H3 from SWISSPROT is associated with the IPR008213 from INTERPRO domain suggesting this protein could have a role in phycobilisomes.
Probab=48.72 E-value=25 Score=29.60 Aligned_cols=34 Identities=24% Similarity=0.278 Sum_probs=27.3
Q ss_pred ceEEeeccccCceeeeccCCCCHHHHHHHHHHHH
Q 010040 262 RWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAA 295 (519)
Q Consensus 262 KW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AA 295 (519)
.|.++|.-.......|.|-|+|.+||..+..-.+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyi 42 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYI 42 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHH
Confidence 5999997656678999999999999988754333
No 16
>PRK10927 essential cell division protein FtsN; Provisional
Probab=44.96 E-value=89 Score=33.41 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=17.9
Q ss_pred eeeccCCCCHHHHHHHHHHHH
Q 010040 275 YVYLGLFDTEVEAARAYDRAA 295 (519)
Q Consensus 275 ~v~LGtFdTeEEAArAYD~AA 295 (519)
+|.||-|.+.++|.++.++..
T Consensus 285 RVrVGPf~sr~eAe~a~~rLk 305 (319)
T PRK10927 285 RVVIGPVKGKENADSTLNRLK 305 (319)
T ss_pred EEEeCCCCCHHHHHHHHHHHH
Confidence 568999999999999988754
No 17
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=44.75 E-value=68 Score=24.14 Aligned_cols=36 Identities=25% Similarity=0.468 Sum_probs=27.0
Q ss_pred eEEEEEE-e---CC--eEEEeCCCCCHHHHHHHHHHHHHHhh
Q 010040 171 RWESHIW-D---SG--KQVYLGGFDTAHAAARAYDRAAIKFR 206 (519)
Q Consensus 171 KW~A~I~-~---~g--Kri~LGtFdTeEEAArAYD~AAikl~ 206 (519)
+|...|. . .| ++++-+.|.|..||-.+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 4777773 2 23 57889999999999999888766553
No 18
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=29.07 E-value=6e+02 Score=25.43 Aligned_cols=130 Identities=22% Similarity=0.326 Sum_probs=81.1
Q ss_pred CCCCeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcccCCccccccccchhhhhhcccccccee
Q 010040 156 RSSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSIEDYEDDLKQMSNLTKEEFV 235 (519)
Q Consensus 156 ~tSgYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~A~~NFp~sdYeeELkqL~~LSKEE~V 235 (519)
+..+|-|+-++-..-|=.+-|...||-+-.|. .+.|++.+|-.+-+..++.......|.+. -..+++...
T Consensus 38 nP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGa-Ks~ed~~~av~~~~~~L~~~g~~~~~~p~------i~iQNIVaS--- 107 (185)
T COG2101 38 NPEQFPGLVYRLEEPKTAALIFRSGKVVCTGA-KSVEDVHRAVKKLAKKLKDGGIDIDFEPE------IKVQNIVAS--- 107 (185)
T ss_pred CHhHCCeeEEEecCCcceEEEEecCcEEEecc-CcHHHHHHHHHHHHHHHHhcCcCcCCCCc------eEEEEEEEE---
Confidence 55789999987888899999999999988886 67788888888877777763332222210 000110000
Q ss_pred eeeccc------ccCcCC-----CCCcccCeeee-cCcceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 010040 236 HVLRRQ------STGFPR-----GSSKYRGVTLH-KCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (519)
Q Consensus 236 ~aLRRq------s~g~~r-----~sSkYRGV~~~-k~GKW~ArI~~~~~~K~v~LGtFdTeEEAArAYD~AAikl 298 (519)
..|+.. .-+... -.-+|-|+-++ ..-|-+.-| +..||-+.-|. .+++||.+|+.+-..++
T Consensus 108 adL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~Li--F~SGK~ViTGa-K~~ed~~~Av~~i~~~L 179 (185)
T COG2101 108 ADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLL--FGSGKLVITGA-KSEEDAEQAVEKIQSRL 179 (185)
T ss_pred eccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEE--ecCCcEEEecC-CCHHHHHHHHHHHHHHH
Confidence 000000 000000 12367786665 355666666 67788877776 56889999999877666
No 19
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=28.77 E-value=1.4e+02 Score=22.47 Aligned_cols=26 Identities=23% Similarity=0.172 Sum_probs=22.1
Q ss_pred eeeeccCCCCHHHHHHHHHHHHHHhc
Q 010040 274 KYVYLGLFDTEVEAARAYDRAAVKCN 299 (519)
Q Consensus 274 K~v~LGtFdTeEEAArAYD~AAikl~ 299 (519)
++++-+-|.|..||-.+..++...+.
T Consensus 17 k~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 17 KQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred EEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 67778889999999999998877663
No 20
>COG3087 FtsN Cell division protein [Cell division and chromosome partitioning]
Probab=26.10 E-value=1.4e+02 Score=31.21 Aligned_cols=26 Identities=31% Similarity=0.468 Sum_probs=19.6
Q ss_pred EEeCCCCCHHHHHHHHHHHHHHhhcccC
Q 010040 183 VYLGGFDTAHAAARAYDRAAIKFRGAEA 210 (519)
Q Consensus 183 i~LGtFdTeEEAArAYD~AAikl~G~~A 210 (519)
+-.|.|.+.++|-.. +|-+.|.|.++
T Consensus 193 LQcGaFk~~~qAE~~--rA~LAmlG~ss 218 (264)
T COG3087 193 LQCGAFKTAEQAESV--RAQLAMLGISS 218 (264)
T ss_pred EeecccccHHHHHHH--HHHHHhccccc
Confidence 566999999999876 56666777444
No 21
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=23.83 E-value=2e+02 Score=24.33 Aligned_cols=47 Identities=21% Similarity=0.361 Sum_probs=37.3
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHh
Q 010040 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKF 205 (519)
Q Consensus 158 SgYRGV~~~k~~GKW~A~I~~~gKri~LGtFdTeEEAArAYD~AAikl 205 (519)
..|-||.+.-..-+-.+.|+..||-+..|. .++|+|..|.++....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFSSGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEETTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 367888876677788899999999887775 67888998888776554
Done!