Query 010002
Match_columns 520
No_of_seqs 336 out of 1932
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 19:52:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010002.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010002hhsearch_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 4.8E-17 1E-21 128.5 6.8 58 158-216 1-60 (61)
2 smart00380 AP2 DNA-binding dom 99.7 9.2E-17 2E-21 128.5 6.1 63 251-313 1-63 (64)
3 smart00380 AP2 DNA-binding dom 99.7 1.8E-16 3.9E-21 126.8 7.7 61 159-220 1-63 (64)
4 cd00018 AP2 DNA-binding domain 99.7 1.3E-16 2.9E-21 126.0 6.7 61 250-310 1-61 (61)
5 PHA00280 putative NHN endonucl 99.4 2.5E-13 5.5E-18 122.6 8.2 64 147-211 56-119 (121)
6 PHA00280 putative NHN endonucl 99.3 7.5E-12 1.6E-16 113.1 7.9 104 194-304 11-119 (121)
7 PF00847 AP2: AP2 domain; Int 99.1 3.1E-10 6.7E-15 87.7 6.1 51 158-208 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 98.8 1.6E-08 3.5E-13 78.1 6.2 52 250-301 1-56 (56)
9 cd00652 TBP_TLF TATA box bindi 83.5 18 0.0004 34.8 11.7 134 158-298 34-172 (174)
10 cd04518 TBP_archaea archaeal T 83.3 20 0.00044 34.7 11.9 134 157-298 33-171 (174)
11 cd04517 TLF TBP-like factors ( 77.1 34 0.00074 33.1 11.2 131 159-296 35-170 (174)
12 PRK00394 transcription factor; 70.5 60 0.0013 31.6 11.1 134 158-298 33-172 (179)
13 cd04516 TBP_eukaryotes eukaryo 67.6 77 0.0017 30.8 11.2 131 158-295 34-168 (174)
14 PLN00062 TATA-box-binding prot 67.4 81 0.0018 30.8 11.3 133 158-297 34-170 (179)
15 PF08846 DUF1816: Domain of un 48.6 24 0.00052 29.7 3.6 31 262-292 9-39 (68)
16 PRK10927 essential cell divisi 46.7 81 0.0017 33.8 7.9 21 275-295 285-305 (319)
17 PF14657 Integrase_AP2: AP2-li 44.8 68 0.0015 24.2 5.3 36 171-206 1-42 (46)
18 COG2101 SPT15 TATA-box binding 32.8 5.2E+02 0.011 25.9 11.7 136 155-298 37-179 (185)
19 PF14657 Integrase_AP2: AP2-li 27.7 1.4E+02 0.0031 22.4 4.6 26 274-299 17-42 (46)
20 PF00352 TBP: Transcription fa 27.4 1.6E+02 0.0034 24.9 5.4 47 158-205 36-82 (86)
21 COG3087 FtsN Cell division pro 27.3 1.3E+02 0.0028 31.5 5.6 26 183-210 193-218 (264)
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=4.8e-17 Score=128.52 Aligned_cols=58 Identities=53% Similarity=0.910 Sum_probs=55.1
Q ss_pred CCeEEeEEecCCCeEEEEEEeC--CeEEEeCCCCCHHHHHHHHHHHHHHhhcCccCccccc
Q 010002 158 SQYRGVTFYRRTGRWESHIWDS--GKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSI 216 (520)
Q Consensus 158 SgYRGVt~~kr~GKW~A~I~~~--GKri~LGtFdTeEEAArAYD~AAikl~G~~A~~NFp~ 216 (520)
|+|+||++++. |||+|+|+++ +|++|||+|+|+||||+|||.|+++++|..+.+|||.
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 78999997665 9999999999 9999999999999999999999999999999999995
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.66 E-value=9.2e-17 Score=128.51 Aligned_cols=63 Identities=52% Similarity=0.769 Sum_probs=59.3
Q ss_pred cccCeeeecCCceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCccCCCCcchH
Q 010002 251 KYRGVTLHKCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPSLYQ 313 (520)
Q Consensus 251 kYRGV~~~k~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAAikl~G~~A~tNFp~s~Y~ 313 (520)
+|+||+++++|||+|+|+...+++.++||+|+|+||||+|||.|+++++|..+.+|||.+.|.
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 589999988999999997666899999999999999999999999999999999999999985
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.66 E-value=1.8e-16 Score=126.82 Aligned_cols=61 Identities=57% Similarity=0.945 Sum_probs=57.8
Q ss_pred CeEEeEEecCCCeEEEEEEe--CCeEEEeCCCCCHHHHHHHHHHHHHHhhcCccCccccccccc
Q 010002 159 QYRGVTFYRRTGRWESHIWD--SGKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSIEDYE 220 (520)
Q Consensus 159 gYRGVt~~kr~GKW~A~I~~--~GKri~LGtFdTeEEAArAYD~AAikl~G~~A~~NFp~sdYe 220 (520)
+|+||++ +.+|||+|+|++ .+|+++||+|+|+||||+|||.|+++++|..+.+|||.++|+
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 566999999999 899999999999999999999999999999999999999886
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=1.3e-16 Score=126.04 Aligned_cols=61 Identities=52% Similarity=0.797 Sum_probs=56.1
Q ss_pred ccccCeeeecCCceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCccCCCCc
Q 010002 250 SKYRGVTLHKCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPS 310 (520)
Q Consensus 250 SkYRGV~~~k~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAAikl~G~~A~tNFp~s 310 (520)
|+|+||+++++|||+|+|+....++.++||+|+|+||||+|||.|+++++|..+.+|||.+
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=2.5e-13 Score=122.58 Aligned_cols=64 Identities=20% Similarity=0.342 Sum_probs=57.8
Q ss_pred ccCCCCCCCCCCCeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcCccC
Q 010002 147 KKSRRGPRSRSSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEAD 211 (520)
Q Consensus 147 kk~rr~~r~~tSgYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl~G~~A~ 211 (520)
.++++.+++++|||+||+|++..+||+|.|+++||+++||+|+++|+|+.||+ ++.+++|.+|+
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 44555677899999999999999999999999999999999999999999997 77889998874
No 6
>PHA00280 putative NHN endonuclease
Probab=99.29 E-value=7.5e-12 Score=113.10 Aligned_cols=104 Identities=16% Similarity=0.109 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHhhcCccC---cccc-ccccchhhhhhccccccceeeeecccccCcCCCCccccCeeeec-CCceEEeec
Q 010002 194 AARAYDRAAIKFRGAEAD---INFS-IEDYEDDLKQMSNLTKEEFVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMG 268 (520)
Q Consensus 194 AArAYD~AAikl~G~~A~---~NFp-~sdYeeELkqL~eLSKEE~V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~ 268 (520)
+-+++..+...++|.-.. +.+. -...+..+..|+.++..|.....+.. ..++|+|+||+|++ .|||+|+|
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 345666777788885331 2221 12334667888889988888876544 57789999999987 89999999
Q ss_pred cccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCc
Q 010002 269 QFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAV 304 (520)
Q Consensus 269 ~~~~gK~v~LGtFdTeEEAARAYDkAAikl~G~~A~ 304 (520)
.+++|.++||.|+|+|+|+.||+ ++++++|..|.
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 77889998764
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=99.06 E-value=3.1e-10 Score=87.66 Aligned_cols=51 Identities=33% Similarity=0.546 Sum_probs=47.0
Q ss_pred CCeEEeEEecCCCeEEEEEEeC-----CeEEEeCCCCCHHHHHHHHHHHHHHhhcC
Q 010002 158 SQYRGVTFYRRTGRWESHIWDS-----GKQVYLGGFDTAHAAARAYDRAAIKFRGA 208 (520)
Q Consensus 158 SgYRGVt~~kr~GKW~A~I~~~-----GKri~LGtFdTeEEAArAYD~AAikl~G~ 208 (520)
|+|+||+|++..++|+|.|++. +|.++||.|+++++|++||+.++++++|.
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 48999999999999999999999999873
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=98.77 E-value=1.6e-08 Score=78.09 Aligned_cols=52 Identities=37% Similarity=0.554 Sum_probs=45.0
Q ss_pred ccccCeeeec-CCceEEeecccc-C--ceeeeccCCCCHHHHHHHHHHHHHHhcCC
Q 010002 250 SKYRGVTLHK-CGRWEARMGQFL-G--KKYVYLGLFDTEVEAARAYDRAAVKCNGK 301 (520)
Q Consensus 250 SkYRGV~~~k-~GKW~ArI~~~~-~--gK~v~LGtFdTeEEAARAYDkAAikl~G~ 301 (520)
|+|+||++++ .++|+|+|+... + ++.++||.|++++||++||+.+++++.|+
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 6899999987 899999996531 1 49999999999999999999999999763
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=83.48 E-value=18 Score=34.81 Aligned_cols=134 Identities=16% Similarity=0.154 Sum_probs=78.9
Q ss_pred CCeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcCc--c--Cccccccccchhhhhhccccccc
Q 010002 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAE--A--DINFSIEDYEDDLKQMSNLTKEE 233 (520)
Q Consensus 158 SgYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl~G~~--A--~~NFp~sdYeeELkqL~eLSKEE 233 (520)
.+|.||.++...-+=.+.|+..||-+--|. .++|+|..|.++.+..+.... . ..||....-......--.+..++
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 688999987777888899999998877776 567788888888777663322 1 23333211110000000111111
Q ss_pred eeeeecccccCcCCCCccccCeeeec-CCceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 010002 234 FVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (520)
Q Consensus 234 ~V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAAikl 298 (520)
+....+.... =...+|-|+.++- ..+=..-| +..||-+..|. .+++|+.+|+++-.-.+
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 2111111111 1234688888764 34555666 77888888886 56888999887755443
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=83.33 E-value=20 Score=34.66 Aligned_cols=134 Identities=16% Similarity=0.221 Sum_probs=80.9
Q ss_pred CCCeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcCcc----Cccccccccchhhhhhcccccc
Q 010002 157 SSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEA----DINFSIEDYEDDLKQMSNLTKE 232 (520)
Q Consensus 157 tSgYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl~G~~A----~~NFp~sdYeeELkqL~eLSKE 232 (520)
..+|.||.++-+.-+=.+.|+..||-+--|. .++++|..|-++.+..+..... ..+|.....-....--..+..+
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 3689999987777788899999998776665 7888899888888776654221 1222221110000000011111
Q ss_pred ceeeeecccccCcCCCCccccCeeeec-CCceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 010002 233 EFVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (520)
Q Consensus 233 E~V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAAikl 298 (520)
.+...++ .. .=...+|-|+.++- .-|=.+-| +..||-+..|. .++||+.+|.++-...+
T Consensus 112 ~la~~~~-~~---~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l 171 (174)
T cd04518 112 AIAIGLP-NA---EYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRL 171 (174)
T ss_pred HHHhhCC-CC---ccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 1211111 11 11345788987764 44556666 78889888886 56888999988876655
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=77.12 E-value=34 Score=33.09 Aligned_cols=131 Identities=19% Similarity=0.179 Sum_probs=76.7
Q ss_pred CeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhc--Ccc--Cccccccccchhhhhhccccccce
Q 010002 159 QYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRG--AEA--DINFSIEDYEDDLKQMSNLTKEEF 234 (520)
Q Consensus 159 gYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl~G--~~A--~~NFp~sdYeeELkqL~eLSKEE~ 234 (520)
+|-||.++-+.-+=.+.|+..||-+--| ..++|+|.+|.++.+..+.. ... ..||....-......--.+..+++
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 8899998777788889999999876665 57889999999888776633 221 233432211000000001111111
Q ss_pred eeeecccccCcCCCCccccCeeeec-CCceEEeeccccCceeeeccCCCCHHHHHHHHHHHHH
Q 010002 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAV 296 (520)
Q Consensus 235 V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAAi 296 (520)
...-.+... =....|-|+.++- .-+=.+.| +..||-+..|. .+++|+.+|+++-.-
T Consensus 114 a~~~~~~~~---YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~p 170 (174)
T cd04517 114 AAKNRSSAS---YEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIYP 170 (174)
T ss_pred HHhchhhcE---eCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHH
Confidence 111011111 1234688988764 33455555 78888888886 567888888876543
No 12
>PRK00394 transcription factor; Reviewed
Probab=70.53 E-value=60 Score=31.61 Aligned_cols=134 Identities=16% Similarity=0.186 Sum_probs=79.4
Q ss_pred CCeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcCc--c--Cccccccccchhhhhhccccccc
Q 010002 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAE--A--DINFSIEDYEDDLKQMSNLTKEE 233 (520)
Q Consensus 158 SgYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl~G~~--A--~~NFp~sdYeeELkqL~eLSKEE 233 (520)
.+|-||.++-+.-+=.+.|+..||-+--|.. ++++|..|-++.+..+.... . ..+|.....-....--..+..++
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 5788999877788889999999998888875 56788888877766653321 1 12232211000000000111111
Q ss_pred eeeeec-ccccCcCCCCccccCeeeec-CCceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 010002 234 FVHVLR-RQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (520)
Q Consensus 234 ~V~aLR-Rqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAAikl 298 (520)
+...+. +.. .=...+|-|+.++- .-|=..-| +..||-+..|. .+++|+.+|.++-...+
T Consensus 112 la~~~~~~~~---~YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l 172 (179)
T PRK00394 112 IAIGLGLENI---EYEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKL 172 (179)
T ss_pred HHHhcCcCCc---EECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 111110 111 11235788988764 44566666 78889888886 56888999988876555
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=67.63 E-value=77 Score=30.77 Aligned_cols=131 Identities=17% Similarity=0.198 Sum_probs=75.1
Q ss_pred CCeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcCcc---Cccccccccchhhhhhccccccce
Q 010002 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEA---DINFSIEDYEDDLKQMSNLTKEEF 234 (520)
Q Consensus 158 SgYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl~G~~A---~~NFp~sdYeeELkqL~eLSKEE~ 234 (520)
.+|-||.++-+.-+=.+.|+..||-+--|. .++|+|..|.++.+..+....- ..||...........-..+..+++
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 578899987777888899999999877776 5678888888887776633221 123332111111000001111111
Q ss_pred eeeecccccCcCCCCccccCeeeec-CCceEEeeccccCceeeeccCCCCHHHHHHHHHHHH
Q 010002 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAA 295 (520)
Q Consensus 235 V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAA 295 (520)
....+... .=....|-|+.++- .-|-...| +..||-+.+|. .+++|+.+|++.-.
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 11101110 11235788988764 33333444 78888888876 56777888876543
No 14
>PLN00062 TATA-box-binding protein; Provisional
Probab=67.37 E-value=81 Score=30.82 Aligned_cols=133 Identities=17% Similarity=0.161 Sum_probs=76.3
Q ss_pred CCeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcCccC---ccccccccchhhhhhccccccce
Q 010002 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEAD---INFSIEDYEDDLKQMSNLTKEEF 234 (520)
Q Consensus 158 SgYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl~G~~A~---~NFp~sdYeeELkqL~eLSKEE~ 234 (520)
..|-||.++-+.-+=.+.|+..||-+--|. .++|+|..|.++.+..+....-. .||...........-..+..+.+
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 578899987778888999999998776664 67888988888887776432212 23332111110000001111111
Q ss_pred eeeecccccCcCCCCccccCeeeec-CCceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHH
Q 010002 235 VHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVK 297 (520)
Q Consensus 235 V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAAik 297 (520)
...-++.. .-....|-|+.++- .-|-...| +..||-+..|. .+++|+.+|++.-.-.
T Consensus 113 a~~~~~~~---~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~ai~~i~p~ 170 (179)
T PLN00062 113 AYAHGAFS---SYEPELFPGLIYRMKQPKIVLLI--FVSGKIVITGA-KVREEIYTAFENIYPV 170 (179)
T ss_pred HHhchhhc---ccCcccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHH
Confidence 11101111 12335788887764 33444445 78888888886 4577777777654433
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=48.57 E-value=24 Score=29.74 Aligned_cols=31 Identities=26% Similarity=0.348 Sum_probs=26.0
Q ss_pred ceEEeeccccCceeeeccCCCCHHHHHHHHH
Q 010002 262 RWEARMGQFLGKKYVYLGLFDTEVEAARAYD 292 (520)
Q Consensus 262 KW~ArI~~~~~gK~v~LGtFdTeEEAARAYD 292 (520)
.|.++|.-......+|.|-|+|.+||..+..
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~ 39 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALP 39 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhc
Confidence 5999996556678999999999999988743
No 16
>PRK10927 essential cell division protein FtsN; Provisional
Probab=46.65 E-value=81 Score=33.75 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=17.6
Q ss_pred eeeccCCCCHHHHHHHHHHHH
Q 010002 275 YVYLGLFDTEVEAARAYDRAA 295 (520)
Q Consensus 275 ~v~LGtFdTeEEAARAYDkAA 295 (520)
+|.||-|.+.++|.++.++..
T Consensus 285 RVrVGPf~sr~eAe~a~~rLk 305 (319)
T PRK10927 285 RVVIGPVKGKENADSTLNRLK 305 (319)
T ss_pred EEEeCCCCCHHHHHHHHHHHH
Confidence 578999999999999977643
No 17
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=44.82 E-value=68 Score=24.16 Aligned_cols=36 Identities=25% Similarity=0.468 Sum_probs=27.2
Q ss_pred eEEEEEE-e---CC--eEEEeCCCCCHHHHHHHHHHHHHHhh
Q 010002 171 RWESHIW-D---SG--KQVYLGGFDTAHAAARAYDRAAIKFR 206 (520)
Q Consensus 171 KW~A~I~-~---~G--Kri~LGtFdTeEEAArAYD~AAikl~ 206 (520)
+|...|. . .| ++++-+.|.|..||-.+...+...+.
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 24 57889999999999999888776653
No 18
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=32.79 E-value=5.2e+02 Score=25.88 Aligned_cols=136 Identities=22% Similarity=0.296 Sum_probs=82.3
Q ss_pred CCCCCeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHhhcCccCcccccc----cc--chhhhhhcc
Q 010002 155 SRSSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSIE----DY--EDDLKQMSN 228 (520)
Q Consensus 155 ~~tSgYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl~G~~A~~NFp~s----dY--eeELkqL~e 228 (520)
=+..+|-|+-++-..-|=.+-|...||-+-.|. .+.|++.+|-.+.+..++.......|.+. .- ..++...-+
T Consensus 37 YnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGa-Ks~ed~~~av~~~~~~L~~~g~~~~~~p~i~iQNIVaSadL~~~ln 115 (185)
T COG2101 37 YNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGA-KSVEDVHRAVKKLAKKLKDGGIDIDFEPEIKVQNIVASADLGVELN 115 (185)
T ss_pred cCHhHCCeeEEEecCCcceEEEEecCcEEEecc-CcHHHHHHHHHHHHHHHHhcCcCcCCCCceEEEEEEEEeccCcccc
Confidence 355789999988889999999999999988886 77888888888887777763333332210 00 000000000
Q ss_pred ccccceeeeecccccCcCCCCccccCeeeec-CCceEEeeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 010002 229 LTKEEFVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (520)
Q Consensus 229 LSKEE~V~aLRRqs~g~~r~sSkYRGV~~~k-~GKW~ArI~~~~~gK~v~LGtFdTeEEAARAYDkAAikl 298 (520)
+ +.+.-.+.-.. .-=-.-+|-|+-++- .-|-..-| +..||-+.-|. .++|||.+|+.+-..++
T Consensus 116 L--~~iA~~lg~e~--~eYEPEqFPGLVYRl~~P~VV~Li--F~SGK~ViTGa-K~~ed~~~Av~~i~~~L 179 (185)
T COG2101 116 L--NAIAIGLGLEN--IEYEPEQFPGLVYRLDEPRVVLLL--FGSGKLVITGA-KSEEDAEQAVEKIQSRL 179 (185)
T ss_pred H--HHHHHhccccc--cccccccCCeeEEEcCCCCEEEEE--ecCCcEEEecC-CCHHHHHHHHHHHHHHH
Confidence 0 00000000000 000123677866653 55666666 77788887776 56889999998877665
No 19
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=27.70 E-value=1.4e+02 Score=22.42 Aligned_cols=26 Identities=23% Similarity=0.172 Sum_probs=21.9
Q ss_pred eeeeccCCCCHHHHHHHHHHHHHHhc
Q 010002 274 KYVYLGLFDTEVEAARAYDRAAVKCN 299 (520)
Q Consensus 274 K~v~LGtFdTeEEAARAYDkAAikl~ 299 (520)
+++.-+-|.|..||-.+..++...+.
T Consensus 17 k~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 17 KQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred EEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 67788889999999999988777653
No 20
>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=27.37 E-value=1.6e+02 Score=24.93 Aligned_cols=47 Identities=21% Similarity=0.361 Sum_probs=37.7
Q ss_pred CCeEEeEEecCCCeEEEEEEeCCeEEEeCCCCCHHHHHHHHHHHHHHh
Q 010002 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKF 205 (520)
Q Consensus 158 SgYRGVt~~kr~GKW~A~I~~~GKri~LGtFdTeEEAArAYD~AAikl 205 (520)
..|.||.++-..-+-.+.|+..||-+..|. .++++|..|.++....+
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 468888877777788999999998877775 67889999988776554
No 21
>COG3087 FtsN Cell division protein [Cell division and chromosome partitioning]
Probab=27.32 E-value=1.3e+02 Score=31.51 Aligned_cols=26 Identities=31% Similarity=0.468 Sum_probs=19.3
Q ss_pred EEeCCCCCHHHHHHHHHHHHHHhhcCcc
Q 010002 183 VYLGGFDTAHAAARAYDRAAIKFRGAEA 210 (520)
Q Consensus 183 i~LGtFdTeEEAArAYD~AAikl~G~~A 210 (520)
+-.|.|.+.++|-+. +|-+.|.|.++
T Consensus 193 LQcGaFk~~~qAE~~--rA~LAmlG~ss 218 (264)
T COG3087 193 LQCGAFKTAEQAESV--RAQLAMLGISS 218 (264)
T ss_pred EeecccccHHHHHHH--HHHHHhccccc
Confidence 566999999999876 46666777443
Done!