Query 009943
Match_columns 522
No_of_seqs 325 out of 1764
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 19:10:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009943.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009943hhsearch_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 5.4E-17 1.2E-21 128.4 6.6 58 158-216 1-60 (61)
2 smart00380 AP2 DNA-binding dom 99.7 1.7E-16 3.6E-21 127.2 7.7 61 159-220 1-63 (64)
3 smart00380 AP2 DNA-binding dom 99.7 1.2E-16 2.6E-21 128.0 6.3 63 251-313 1-63 (64)
4 cd00018 AP2 DNA-binding domain 99.6 2.3E-16 5E-21 124.8 6.8 61 250-310 1-61 (61)
5 PHA00280 putative NHN endonucl 99.4 3.5E-13 7.7E-18 121.7 8.0 63 148-211 57-119 (121)
6 PHA00280 putative NHN endonucl 99.2 8.5E-11 1.8E-15 106.4 8.5 104 194-304 11-119 (121)
7 PF00847 AP2: AP2 domain; Int 99.0 4.4E-10 9.5E-15 86.9 5.9 50 158-207 1-55 (56)
8 PF00847 AP2: AP2 domain; Int 98.7 4E-08 8.6E-13 76.0 6.0 51 250-300 1-55 (56)
9 cd00652 TBP_TLF TATA box bindi 81.0 30 0.00066 33.4 12.1 134 158-298 34-172 (174)
10 cd04518 TBP_archaea archaeal T 80.8 37 0.00081 32.9 12.7 134 158-299 34-172 (174)
11 cd04517 TLF TBP-like factors ( 75.0 54 0.0012 31.7 11.9 133 159-298 35-172 (174)
12 PRK00394 transcription factor; 63.2 1.4E+02 0.0029 29.2 12.0 133 158-299 33-173 (179)
13 cd04516 TBP_eukaryotes eukaryo 53.7 2.2E+02 0.0048 27.7 12.3 131 158-295 34-168 (174)
14 PLN00062 TATA-box-binding prot 52.5 2.4E+02 0.0051 27.7 12.4 134 158-298 34-171 (179)
15 PF08846 DUF1816: Domain of un 50.3 23 0.00051 29.8 3.8 36 262-297 9-44 (68)
16 PF14657 Integrase_AP2: AP2-li 43.8 68 0.0015 24.2 5.2 36 171-206 1-42 (46)
17 PF14657 Integrase_AP2: AP2-li 30.3 1.4E+02 0.003 22.5 4.9 26 274-299 17-42 (46)
18 PF00352 TBP: Transcription fa 23.9 1.8E+02 0.0038 24.6 5.0 47 158-205 36-82 (86)
19 PRK10927 essential cell divisi 21.1 2.8E+02 0.006 29.9 6.8 21 275-295 285-305 (319)
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=99.68 E-value=5.4e-17 Score=128.40 Aligned_cols=58 Identities=53% Similarity=0.910 Sum_probs=55.0
Q ss_pred CCeEEeEEecCCCeEEEEEeeC--CeEEecCCCCCHHHHHHHHHHHHHHhccccccccccc
Q 009943 158 SQYRGVTFYRRTGRWESHIWDS--GKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSI 216 (522)
Q Consensus 158 SgYRGVt~~r~~GKW~A~I~~~--gK~i~LGtFdTeEeAArAYD~Aaikl~G~~A~~NFp~ 216 (522)
|+|+||++++. |||+|+|+++ +|+++||+|+|+||||+|||+|+++++|..+.+|||.
T Consensus 1 s~~~GV~~~~~-gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~ 60 (61)
T cd00018 1 SKYRGVRQRPW-GKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPD 60 (61)
T ss_pred CCccCEEECCC-CcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCC
Confidence 78999997654 9999999999 9999999999999999999999999999999999985
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.67 E-value=1.7e-16 Score=127.19 Aligned_cols=61 Identities=57% Similarity=0.945 Sum_probs=57.8
Q ss_pred CeEEeEEecCCCeEEEEEee--CCeEEecCCCCCHHHHHHHHHHHHHHhcccccccccccccch
Q 009943 159 QYRGVTFYRRTGRWESHIWD--SGKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSIEDYE 220 (522)
Q Consensus 159 gYRGVt~~r~~GKW~A~I~~--~gK~i~LGtFdTeEeAArAYD~Aaikl~G~~A~~NFp~sdYe 220 (522)
+|+||++ +++|||+|+|++ .+|+++||+|+|+||||+|||.|+++++|..+.+|||.++|+
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=1.2e-16 Score=128.04 Aligned_cols=63 Identities=52% Similarity=0.769 Sum_probs=59.4
Q ss_pred CccCceeeecccEEEEeccccCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCCccCCCCCcch
Q 009943 251 KYRGVTLHKCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPSLYQ 313 (522)
Q Consensus 251 kYRGV~~~k~GKW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAAikl~G~~A~tNFp~s~Y~ 313 (522)
+|+||+++++|+|+|+|+.+.+++.++||+|+|+||||+|||.|+++++|..+.+||+.+.|+
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 589999988999999997766899999999999999999999999999999999999999985
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=99.65 E-value=2.3e-16 Score=124.84 Aligned_cols=61 Identities=52% Similarity=0.797 Sum_probs=56.1
Q ss_pred CCccCceeeecccEEEEeccccCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCCccCCCCC
Q 009943 250 SKYRGVTLHKCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPS 310 (522)
Q Consensus 250 SkYRGV~~~k~GKW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAAikl~G~~A~tNFp~s 310 (522)
|+|+||+++++|||+|+|+....+++++||+|+|+||||+|||.|+++++|..+.+|||.+
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=99.42 E-value=3.5e-13 Score=121.71 Aligned_cols=63 Identities=21% Similarity=0.347 Sum_probs=56.6
Q ss_pred cCCCCCCCCCCCeEEeEEecCCCeEEEEEeeCCeEEecCCCCCHHHHHHHHHHHHHHhcccccc
Q 009943 148 KSRRGPRSRSSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEAD 211 (522)
Q Consensus 148 K~rr~~r~rsSgYRGVt~~r~~GKW~A~I~~~gK~i~LGtFdTeEeAArAYD~Aaikl~G~~A~ 211 (522)
++++.+++++|||+||+|++..+||+|+|+++||+++||.|+++|+|+.||+ ++.+++|.+|+
T Consensus 57 ~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 57 WNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred cccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 3445567899999999999999999999999999999999999999999997 77789997764
No 6
>PHA00280 putative NHN endonuclease
Probab=99.17 E-value=8.5e-11 Score=106.39 Aligned_cols=104 Identities=16% Similarity=0.111 Sum_probs=76.5
Q ss_pred HHHHHHHHHHHhcccccc---ccccc-ccchhhhhhhcccchhhhhhhhcccCCCCCCCCCCccCceeee-cccEEEEec
Q 009943 194 AARAYDRAAIKFRGAEAD---INFSI-EDYEDDLKQMSNLTKEEFVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMG 268 (522)
Q Consensus 194 AArAYD~Aaikl~G~~A~---~NFp~-sdYeeeL~qm~~lSkEE~V~aLRRQs~g~pr~sSkYRGV~~~k-~GKW~ArI~ 268 (522)
+-+++..+...++|.-.. +.+.- ......+..|..++..|.....+.. ..++|+|+||+|++ .|||.|+|
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 445677777788884331 22211 1223456667777777777665433 56789999999986 89999999
Q ss_pred cccCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCCc
Q 009943 269 QFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAV 304 (522)
Q Consensus 269 ~~~~~k~v~LGtFdTeEEAARAYDkAAikl~G~~A~ 304 (522)
..++|.++||+|+|+|+|+.||+ ++++++|..|.
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 57899999999999999999997 77889987553
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=99.03 E-value=4.4e-10 Score=86.95 Aligned_cols=50 Identities=34% Similarity=0.557 Sum_probs=46.9
Q ss_pred CCeEEeEEecCCCeEEEEEeeC-----CeEEecCCCCCHHHHHHHHHHHHHHhcc
Q 009943 158 SQYRGVTFYRRTGRWESHIWDS-----GKQVYLGGFDTAHAAARAYDRAAIKFRG 207 (522)
Q Consensus 158 SgYRGVt~~r~~GKW~A~I~~~-----gK~i~LGtFdTeEeAArAYD~Aaikl~G 207 (522)
|+|+||+|++..++|+|.|++. +|.++||.|+++++|++||+.++++++|
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~ 55 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEG 55 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcC
Confidence 7899999999999999999983 4899999999999999999999999987
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=98.68 E-value=4e-08 Score=76.02 Aligned_cols=51 Identities=37% Similarity=0.549 Sum_probs=44.8
Q ss_pred CCccCceeee-cccEEEEeccccC---CeeeecCCCCCHHHHHHHHHHHHHHhcC
Q 009943 250 SKYRGVTLHK-CGRWEARMGQFLG---KKYVYLGLFDTEVEAARAYDRAAVKCNG 300 (522)
Q Consensus 250 SkYRGV~~~k-~GKW~ArI~~~~~---~k~v~LGtFdTeEEAARAYDkAAikl~G 300 (522)
|+|+||++++ .++|+|.|+.... ++.++||.|++++||++||+.+.++++|
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~ 55 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEG 55 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcC
Confidence 6899999986 8999999975311 4899999999999999999999999976
No 9
>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=80.97 E-value=30 Score=33.36 Aligned_cols=134 Identities=16% Similarity=0.149 Sum_probs=79.8
Q ss_pred CCeEEeEEecCCCeEEEEEeeCCeEEecCCCCCHHHHHHHHHHHHHHhcccc--c--ccccccccchhhhhhhcccchhh
Q 009943 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAE--A--DINFSIEDYEDDLKQMSNLTKEE 233 (522)
Q Consensus 158 SgYRGVt~~r~~GKW~A~I~~~gK~i~LGtFdTeEeAArAYD~Aaikl~G~~--A--~~NFp~sdYeeeL~qm~~lSkEE 233 (522)
.+|.||.++...-+-.+.|+..||-+--|. .++|+|.+|.++.+..+.-.. . ..||....-......--.+..++
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 578899987777888899999999876675 577888888888877763221 1 23443221111100011122233
Q ss_pred hhhhhcccCCCCCCCCCCccCceeee-cccEEEEeccccCCeeeecCCCCCHHHHHHHHHHHHHHh
Q 009943 234 FVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (522)
Q Consensus 234 ~V~aLRRQs~g~pr~sSkYRGV~~~k-~GKW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAAikl 298 (522)
+....+..... ...+|-|+..+- ..+=..-| +..||-+..|. .+++|+.+|+++-.-.|
T Consensus 113 la~~~~~~~~Y---ePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~i~~~L 172 (174)
T cd00652 113 LALKHPENASY---EPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEKIYPIL 172 (174)
T ss_pred HHhhhhcccEE---CCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 33333222111 234688888764 34455555 67777776765 56888999987765544
No 10
>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=80.76 E-value=37 Score=32.90 Aligned_cols=134 Identities=16% Similarity=0.225 Sum_probs=81.2
Q ss_pred CCeEEeEEecCCCeEEEEEeeCCeEEecCCCCCHHHHHHHHHHHHHHhcccc--c--ccccccccchhhhhhhcccchhh
Q 009943 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAE--A--DINFSIEDYEDDLKQMSNLTKEE 233 (522)
Q Consensus 158 SgYRGVt~~r~~GKW~A~I~~~gK~i~LGtFdTeEeAArAYD~Aaikl~G~~--A--~~NFp~sdYeeeL~qm~~lSkEE 233 (522)
.+|.||.++-+.-+-.+.|+..||-+--|. .++|+|..|-++.+..+.... . ..+|....-.....--..+..++
T Consensus 34 ~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGa-ks~~~a~~a~~~~~~~L~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~ 112 (174)
T cd04518 34 DQFPGLVYRLEDPKIAALIFRSGKMVCTGA-KSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVASADLGREVNLDA 112 (174)
T ss_pred CcCcEEEEEccCCcEEEEEECCCeEEEEcc-CCHHHHHHHHHHHHHHHHhcCCCccCCCceEEEEEEEEEEcCCccCHHH
Confidence 678999987777788899999998876664 788999999988877764322 1 12232221111000001122222
Q ss_pred hhhhhcccCCCCCCCCCCccCceeee-cccEEEEeccccCCeeeecCCCCCHHHHHHHHHHHHHHhc
Q 009943 234 FVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCN 299 (522)
Q Consensus 234 ~V~aLRRQs~g~pr~sSkYRGV~~~k-~GKW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAAikl~ 299 (522)
+...++ .. .=...+|-|+..+- .-|=.+-| +..||-+..|. .+++|+.+|.++....+.
T Consensus 113 la~~~~-~~---~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 113 IAIGLP-NA---EYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred HHhhCC-CC---ccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 322222 11 11335788887763 34555566 77788777775 578889999888776653
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=74.98 E-value=54 Score=31.73 Aligned_cols=133 Identities=20% Similarity=0.185 Sum_probs=77.8
Q ss_pred CeEEeEEecCCCeEEEEEeeCCeEEecCCCCCHHHHHHHHHHHHHHhc--cccc--ccccccccchhhhhhhcccchhhh
Q 009943 159 QYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFR--GAEA--DINFSIEDYEDDLKQMSNLTKEEF 234 (522)
Q Consensus 159 gYRGVt~~r~~GKW~A~I~~~gK~i~LGtFdTeEeAArAYD~Aaikl~--G~~A--~~NFp~sdYeeeL~qm~~lSkEE~ 234 (522)
+|-||.++-+.-+-.+.|+..||-+--| ..++|+|.+|.++.+..+. |-.. ..||....-......--.+..+++
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 8889998777788899999999876555 5889999999998877763 2211 234433221111000011222222
Q ss_pred hhhhcccCCCCCCCCCCccCceeee-cccEEEEeccccCCeeeecCCCCCHHHHHHHHHHHHHHh
Q 009943 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (522)
Q Consensus 235 V~aLRRQs~g~pr~sSkYRGV~~~k-~GKW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAAikl 298 (522)
...-.+.... ...+|-|+..+- .-+=.+.| +..||-+..|. .+++|+.+|+++-.-.+
T Consensus 114 a~~~~~~~~Y---ePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~pil 172 (174)
T cd04517 114 AAKNRSSASY---EPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIYPIV 172 (174)
T ss_pred HHhchhhcEe---CCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 2211111111 234688888764 33445555 77777777765 56788888887655433
No 12
>PRK00394 transcription factor; Reviewed
Probab=63.24 E-value=1.4e+02 Score=29.20 Aligned_cols=133 Identities=17% Similarity=0.238 Sum_probs=80.4
Q ss_pred CCeEEeEEecCCCeEEEEEeeCCeEEecCCCCCHHHHHHHHHHHHHHhcc--ccc--ccccccccchh--hhhhhcccch
Q 009943 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRG--AEA--DINFSIEDYED--DLKQMSNLTK 231 (522)
Q Consensus 158 SgYRGVt~~r~~GKW~A~I~~~gK~i~LGtFdTeEeAArAYD~Aaikl~G--~~A--~~NFp~sdYee--eL~qm~~lSk 231 (522)
.+|-||.++-+.-+-.+.|+..||-+--|. .++|+|..|-++.+..+.. ... ..+|....... ++. ..+..
T Consensus 33 e~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa-~S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVas~~l~--~~i~L 109 (179)
T PRK00394 33 EQFPGLVYRLEDPKIAALIFRSGKVVCTGA-KSVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASADLG--VELNL 109 (179)
T ss_pred ccCceEEEEecCCceEEEEEcCCcEEEEcc-CCHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEEEEEcC--CeEcH
Confidence 478899987778888999999999887777 4677888888887766633 211 12332221110 111 11222
Q ss_pred hhhhhhhc-ccCCCCCCCCCCccCceeee-cccEEEEeccccCCeeeecCCCCCHHHHHHHHHHHHHHhc
Q 009943 232 EEFVHVLR-RQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCN 299 (522)
Q Consensus 232 EE~V~aLR-RQs~g~pr~sSkYRGV~~~k-~GKW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAAikl~ 299 (522)
+++...+. +... =...+|-|+..+- ..|=..-| +..||-+..|. .+++|+.+|.++....+.
T Consensus 110 ~~la~~~~~~~~~---YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 173 (179)
T PRK00394 110 NAIAIGLGLENIE---YEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKLE 173 (179)
T ss_pred HHHHHhcCcCCcE---ECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 22322221 1111 1235788887763 44555666 77788777775 578899999888776663
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=53.74 E-value=2.2e+02 Score=27.68 Aligned_cols=131 Identities=18% Similarity=0.210 Sum_probs=75.2
Q ss_pred CCeEEeEEecCCCeEEEEEeeCCeEEecCCCCCHHHHHHHHHHHHHHhcccc--c-ccccccccchhhhhhhcccchhhh
Q 009943 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAE--A-DINFSIEDYEDDLKQMSNLTKEEF 234 (522)
Q Consensus 158 SgYRGVt~~r~~GKW~A~I~~~gK~i~LGtFdTeEeAArAYD~Aaikl~G~~--A-~~NFp~sdYeeeL~qm~~lSkEE~ 234 (522)
.+|-||.++-+.-+-.+.|+..||-+--|. .++|+|..|.++.+..+.... . ..||...........-..+..+++
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 578899987777888899999999876676 577888888888877763321 1 133332221111101111222222
Q ss_pred hhhhcccCCCCCCCCCCccCceeee-cccEEEEeccccCCeeeecCCCCCHHHHHHHHHHHH
Q 009943 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAA 295 (522)
Q Consensus 235 V~aLRRQs~g~pr~sSkYRGV~~~k-~GKW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAA 295 (522)
....+... .=....|-|+..+- .-|-...| +..||-+.+|. .+++|+.+|++.-.
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 22111111 11234788887764 33333444 77788777765 56777888876544
No 14
>PLN00062 TATA-box-binding protein; Provisional
Probab=52.47 E-value=2.4e+02 Score=27.66 Aligned_cols=134 Identities=16% Similarity=0.149 Sum_probs=77.0
Q ss_pred CCeEEeEEecCCCeEEEEEeeCCeEEecCCCCCHHHHHHHHHHHHHHhcccccc---cccccccchhhhhhhcccchhhh
Q 009943 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEAD---INFSIEDYEDDLKQMSNLTKEEF 234 (522)
Q Consensus 158 SgYRGVt~~r~~GKW~A~I~~~gK~i~LGtFdTeEeAArAYD~Aaikl~G~~A~---~NFp~sdYeeeL~qm~~lSkEE~ 234 (522)
..|-||.++-+.-+=.+.|+..||-+--| ..++|+|..|.++.+..+....-. .||...........--.+..+.+
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~SGKiviTG-aks~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~l 112 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFASGKMVCTG-AKSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGL 112 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEECCCeEEEEe-cCCHHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEEEECCCcccHHHH
Confidence 47889998777888899999999877555 478889999998887776332211 23332221111100011222222
Q ss_pred hhhhcccCCCCCCCCCCccCceeee-cccEEEEeccccCCeeeecCCCCCHHHHHHHHHHHHHHh
Q 009943 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (522)
Q Consensus 235 V~aLRRQs~g~pr~sSkYRGV~~~k-~GKW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAAikl 298 (522)
...-++.. .=...+|-|+..+- .-+-...| +..||-+-.|. .+++|+.+|++.-.-.|
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 22111111 11234788887764 23444444 77788777775 56777888876655444
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=50.34 E-value=23 Score=29.80 Aligned_cols=36 Identities=22% Similarity=0.250 Sum_probs=28.3
Q ss_pred cEEEEeccccCCeeeecCCCCCHHHHHHHHHHHHHH
Q 009943 262 RWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVK 297 (522)
Q Consensus 262 KW~ArI~~~~~~k~v~LGtFdTeEEAARAYDkAAik 297 (522)
.|.++|.-.......|.|-|+|.+||..+..-.+.-
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieD 44 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIED 44 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHH
Confidence 588999766667889999999999999885444433
No 16
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=43.78 E-value=68 Score=24.17 Aligned_cols=36 Identities=25% Similarity=0.468 Sum_probs=27.7
Q ss_pred eEEEEEe-e---CC--eEEecCCCCCHHHHHHHHHHHHHHhc
Q 009943 171 RWESHIW-D---SG--KQVYLGGFDTAHAAARAYDRAAIKFR 206 (522)
Q Consensus 171 KW~A~I~-~---~g--K~i~LGtFdTeEeAArAYD~Aaikl~ 206 (522)
+|...|. . .| ++++-+.|.|..||-.+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 4677773 2 24 57889999999999999988877663
No 17
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=30.31 E-value=1.4e+02 Score=22.51 Aligned_cols=26 Identities=23% Similarity=0.172 Sum_probs=22.0
Q ss_pred eeeecCCCCCHHHHHHHHHHHHHHhc
Q 009943 274 KYVYLGLFDTEVEAARAYDRAAVKCN 299 (522)
Q Consensus 274 k~v~LGtFdTeEEAARAYDkAAikl~ 299 (522)
++++-+-|.|..||-.+..++...+.
T Consensus 17 k~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 17 KQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred EEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 67888899999999999988877663
No 18
>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=23.88 E-value=1.8e+02 Score=24.64 Aligned_cols=47 Identities=21% Similarity=0.361 Sum_probs=38.1
Q ss_pred CCeEEeEEecCCCeEEEEEeeCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 009943 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKF 205 (522)
Q Consensus 158 SgYRGVt~~r~~GKW~A~I~~~gK~i~LGtFdTeEeAArAYD~Aaikl 205 (522)
..|-||.+.-+.-+-.+.|+..||-+-.|. .++|+|..|.++....+
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 467888877777788999999999877775 78899999998877665
No 19
>PRK10927 essential cell division protein FtsN; Provisional
Probab=21.06 E-value=2.8e+02 Score=29.87 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=17.4
Q ss_pred eeecCCCCCHHHHHHHHHHHH
Q 009943 275 YVYLGLFDTEVEAARAYDRAA 295 (522)
Q Consensus 275 ~v~LGtFdTeEEAARAYDkAA 295 (522)
+|.||-|.+.++|.++.++..
T Consensus 285 RVrVGPf~sr~eAe~a~~rLk 305 (319)
T PRK10927 285 RVVIGPVKGKENADSTLNRLK 305 (319)
T ss_pred EEEeCCCCCHHHHHHHHHHHH
Confidence 577999999999999876644
Done!