Query 042319
Match_columns 393
No_of_seqs 355 out of 1897
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 05:04:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042319.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042319hhsearch_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 3.8E-18 8.2E-23 130.5 7.0 61 70-139 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.7 5.6E-18 1.2E-22 131.1 7.6 63 71-142 1-63 (64)
3 smart00380 AP2 DNA-binding dom 99.7 6.1E-17 1.3E-21 125.3 6.6 63 173-236 1-63 (64)
4 cd00018 AP2 DNA-binding domain 99.7 6.2E-17 1.3E-21 123.8 6.6 61 172-233 1-61 (61)
5 PHA00280 putative NHN endonucl 99.5 1.6E-14 3.5E-19 125.5 8.9 104 117-227 12-119 (121)
6 PHA00280 putative NHN endonucl 99.5 1.1E-14 2.4E-19 126.4 7.6 72 49-134 49-120 (121)
7 PF00847 AP2: AP2 domain; Int 99.1 3.3E-10 7.3E-15 84.7 6.4 56 70-130 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 99.0 8.8E-10 1.9E-14 82.4 6.0 53 172-224 1-56 (56)
9 cd04518 TBP_archaea archaeal T 69.2 63 0.0014 30.0 10.6 137 68-222 32-172 (174)
10 cd00652 TBP_TLF TATA box bindi 64.8 81 0.0018 29.1 10.4 135 69-220 33-171 (174)
11 PF14657 Integrase_AP2: AP2-li 51.4 44 0.00095 23.9 5.0 27 101-127 15-41 (46)
12 PRK00394 transcription factor; 48.9 1.7E+02 0.0036 27.3 9.7 139 68-222 31-173 (179)
13 cd04517 TLF TBP-like factors ( 48.8 2.2E+02 0.0048 26.3 10.5 131 71-218 35-169 (174)
14 PF14657 Integrase_AP2: AP2-li 42.9 74 0.0016 22.7 5.1 38 185-222 1-42 (46)
15 cd04516 TBP_eukaryotes eukaryo 33.7 3.9E+02 0.0085 24.7 9.6 132 69-217 33-167 (174)
16 PF08846 DUF1816: Domain of un 31.2 75 0.0016 25.3 3.8 30 185-214 9-38 (68)
17 PRK10545 nucleotide excision r 26.0 95 0.0021 31.1 4.4 25 104-128 140-164 (286)
18 PF08471 Ribonuc_red_2_N: Clas 24.4 75 0.0016 26.9 2.8 20 108-127 71-90 (93)
19 PLN00062 TATA-box-binding prot 22.3 6.4E+02 0.014 23.5 10.3 137 68-221 32-171 (179)
20 PF05036 SPOR: Sporulation rel 21.7 61 0.0013 24.2 1.7 22 103-124 44-65 (76)
21 PF00352 TBP: Transcription fa 20.9 2.7E+02 0.0059 22.3 5.5 47 70-127 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=99.74 E-value=3.8e-18 Score=130.54 Aligned_cols=61 Identities=48% Similarity=0.863 Sum_probs=56.9
Q ss_pred CCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhcCCccccCCCCC
Q 042319 70 SRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYWGTSTFTNFPIS 139 (393)
Q Consensus 70 S~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~G~~a~~NFp~~ 139 (393)
|+|+||+++++ |||.|+|+.+. .|+++|||+|+|+||||.|||.|+++++|..+.+|||.+
T Consensus 1 s~~~GV~~~~~-gkw~A~I~~~~--------~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPW-GKWVAEIRDPS--------GGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCC-CcEEEEEEeCC--------CCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 78999999998 99999998762 489999999999999999999999999999999999964
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.74 E-value=5.6e-18 Score=131.07 Aligned_cols=63 Identities=49% Similarity=0.892 Sum_probs=59.0
Q ss_pred CeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhcCCccccCCCCCchh
Q 042319 71 RFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYWGTSTFTNFPISDYE 142 (393)
Q Consensus 71 ~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~G~~a~~NFp~~~yd 142 (393)
+|+||+++++ |||.|+|+++ .+|+++|||+|+|+||||.|||.|+++++|..+.+|||.++|+
T Consensus 1 ~~kGV~~~~~-gkw~A~I~~~--------~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPW-GKWVAEIRDP--------SKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCC-CeEEEEEEec--------CCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 5899999887 9999999885 2699999999999999999999999999999999999999986
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.68 E-value=6.1e-17 Score=125.27 Aligned_cols=63 Identities=49% Similarity=0.709 Sum_probs=58.0
Q ss_pred ccccceecccCCeeEEeeccccCCeEEecCCCCcHHHHHHHHHHHHHHhcCCCcccCCCCchhh
Q 042319 173 KYRGVARHHHNGRWEARIGRVFGNKYLYLGTYSTQEEAARAYDIAAIEYRGINAVTNFDLSSYI 236 (393)
Q Consensus 173 ~yrGV~~~~~~grW~A~I~~~~~~k~i~LG~f~t~EEAA~AYD~Aa~~l~G~~a~~NF~~~~y~ 236 (393)
+|+||+++ .+|+|+|+|+.+.+++.++||+|+|+||||.|||.++++++|..+.+|||.+.|.
T Consensus 1 ~~kGV~~~-~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQR-PWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeC-CCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 58999874 5699999997555899999999999999999999999999999999999999985
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=99.68 E-value=6.2e-17 Score=123.81 Aligned_cols=61 Identities=52% Similarity=0.803 Sum_probs=55.0
Q ss_pred cccccceecccCCeeEEeeccccCCeEEecCCCCcHHHHHHHHHHHHHHhcCCCcccCCCCc
Q 042319 172 SKYRGVARHHHNGRWEARIGRVFGNKYLYLGTYSTQEEAARAYDIAAIEYRGINAVTNFDLS 233 (393)
Q Consensus 172 S~yrGV~~~~~~grW~A~I~~~~~~k~i~LG~f~t~EEAA~AYD~Aa~~l~G~~a~~NF~~~ 233 (393)
|+|+||++++. |+|+|+|+....++.++||+|+|+||||.|||.++++++|..+.+|||++
T Consensus 1 s~~~GV~~~~~-gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPW-GKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCC-CcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 68999998764 99999996433489999999999999999999999999999999999974
No 5
>PHA00280 putative NHN endonuclease
Probab=99.55 E-value=1.6e-14 Score=125.46 Aligned_cols=104 Identities=13% Similarity=0.103 Sum_probs=85.1
Q ss_pred HHHHHHHHHhhcCCcc----ccCCCCCchhHHHHHhhhhhHHHHHHhhhccCCCCcccccccccceecccCCeeEEeecc
Q 042319 117 ARAYDLAALKYWGTST----FTNFPISDYEKEIEFMQTVTKEEYLASLRRKSSGFSRGVSKYRGVARHHHNGRWEARIGR 192 (393)
Q Consensus 117 A~AYD~Aa~~~~G~~a----~~NFp~~~yd~Ei~~Lr~vS~eE~v~~LRrkssg~sr~~S~yrGV~~~~~~grW~A~I~~ 192 (393)
-+++..+...++|+-. ..-......++.+.+|+.++..++..+.+.. ++++|+|+||+|++..|||+|+|
T Consensus 12 ~~~Hrlvw~~~~G~~P~g~~VdHidg~~~dnri~NLr~~T~~eN~~N~~~~----~~N~SG~kGV~~~k~~~kw~A~I-- 85 (121)
T PHA00280 12 PRRHIQVWEAANGPIPKGYYIDHIDGNPLNDALDNLRLALPKENSWNMKTP----KSNTSGLKGLSWSKEREMWRGTV-- 85 (121)
T ss_pred hhHhHhhhHHHHCCCCCCCEEEcCCCCCCCCcHHHhhhcCHHHHhcccCCC----CCCCCCCCeeEEecCCCeEEEEE--
Confidence 3456677778888743 1122344567889999999999998886544 37789999999999999999999
Q ss_pred ccCCeEEecCCCCcHHHHHHHHHHHHHHhcCCCcc
Q 042319 193 VFGNKYLYLGTYSTQEEAARAYDIAAIEYRGINAV 227 (393)
Q Consensus 193 ~~~~k~i~LG~f~t~EEAA~AYD~Aa~~l~G~~a~ 227 (393)
..+||.++||.|+++|+|+.||+ ++.+|+|.+|.
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 58999999999999999999997 77899998764
No 6
>PHA00280 putative NHN endonuclease
Probab=99.54 E-value=1.1e-14 Score=126.43 Aligned_cols=72 Identities=18% Similarity=0.162 Sum_probs=64.4
Q ss_pred hhhhhhhhcccCCCCCCCCCCCCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhc
Q 042319 49 QSQQQQNDHISGAAATTVKRSSRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYW 128 (393)
Q Consensus 49 ~~~~~~n~~~~~~~~~~~~~sS~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~ 128 (393)
.+++.+|..| ....++++|||+||+|++.+|||.|.|+ ++||+++||.|+++|+|+.||+ ++.+++
T Consensus 49 ~~T~~eN~~N---~~~~~~N~SG~kGV~~~k~~~kw~A~I~----------~~gK~~~lG~f~~~e~A~~a~~-~~~~lh 114 (121)
T PHA00280 49 LALPKENSWN---MKTPKSNTSGLKGLSWSKEREMWRGTVT----------AEGKQHNFRSRDLLEVVAWIYR-TRRELH 114 (121)
T ss_pred hcCHHHHhcc---cCCCCCCCCCCCeeEEecCCCeEEEEEE----------ECCEEEEcCCCCCHHHHHHHHH-HHHHHh
Confidence 5778889988 6678899999999999999999999995 4699999999999999999997 778999
Q ss_pred CCcccc
Q 042319 129 GTSTFT 134 (393)
Q Consensus 129 G~~a~~ 134 (393)
|.++..
T Consensus 115 GeFa~~ 120 (121)
T PHA00280 115 GQFARF 120 (121)
T ss_pred hccccC
Confidence 998753
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=99.07 E-value=3.3e-10 Score=84.67 Aligned_cols=56 Identities=32% Similarity=0.351 Sum_probs=47.6
Q ss_pred CCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhcCC
Q 042319 70 SRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYWGT 130 (393)
Q Consensus 70 S~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~G~ 130 (393)
|+|+||+|++..++|+|.|++... +. .++.++||.|+++++|++||+.++++++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~-~g----~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSE-NG----KRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCC-TT----EEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEccc-Cc----ccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 789999999999999999987421 11 139999999999999999999999999874
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=98.99 E-value=8.8e-10 Score=82.40 Aligned_cols=53 Identities=36% Similarity=0.500 Sum_probs=46.5
Q ss_pred cccccceecccCCeeEEeecccc-C--CeEEecCCCCcHHHHHHHHHHHHHHhcCC
Q 042319 172 SKYRGVARHHHNGRWEARIGRVF-G--NKYLYLGTYSTQEEAARAYDIAAIEYRGI 224 (393)
Q Consensus 172 S~yrGV~~~~~~grW~A~I~~~~-~--~k~i~LG~f~t~EEAA~AYD~Aa~~l~G~ 224 (393)
|+|+||++++..++|+|+|+... + +++++||.|++++||++||+.++++++|.
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 68999999999999999997421 1 49999999999999999999999999873
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=69.17 E-value=63 Score=29.98 Aligned_cols=137 Identities=15% Similarity=0.170 Sum_probs=80.8
Q ss_pred CCCCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhcCCc--c--ccCCCCCchhH
Q 042319 68 RSSRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYWGTS--T--FTNFPISDYEK 143 (393)
Q Consensus 68 ~sS~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~G~~--a--~~NFp~~~yd~ 143 (393)
+..+|.||..+-..-+-.+.|+.. ||-+--|+ .++++|..|-++.+..+.... . ..+|-....-.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~S----------GKiv~tGa-ks~~~a~~a~~~~~~~L~~~g~~~~~~~~~~i~NIVa 100 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFRS----------GKMVCTGA-KSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVA 100 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEECC----------CeEEEEcc-CCHHHHHHHHHHHHHHHHhcCCCccCCCceEEEEEEE
Confidence 347899999998877888888764 88877775 678888888888777664221 1 11111111000
Q ss_pred HHHHhhhhhHHHHHHhhhccCCCCcccccccccceecccCCeeEEeeccccCCeEEecCCCCcHHHHHHHHHHHHHHhc
Q 042319 144 EIEFMQTVTKEEYLASLRRKSSGFSRGVSKYRGVARHHHNGRWEARIGRVFGNKYLYLGTYSTQEEAARAYDIAAIEYR 222 (393)
Q Consensus 144 Ei~~Lr~vS~eE~v~~LRrkssg~sr~~S~yrGV~~~~~~grW~A~I~~~~~~k~i~LG~f~t~EEAA~AYD~Aa~~l~ 222 (393)
-...-..+..+.....++ ...=....|.|+.+.-..-+=..-| ...||-+-.|. .+.||+.+|.++....+.
T Consensus 101 s~~l~~~i~L~~la~~~~----~~~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 101 SADLGREVNLDAIAIGLP----NAEYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred EEEcCCccCHHHHHhhCC----CCccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 000001112222222222 1122346789997655555666666 56788777776 577999999887665543
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=64.82 E-value=81 Score=29.12 Aligned_cols=135 Identities=20% Similarity=0.190 Sum_probs=78.4
Q ss_pred CCCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhh--cCCcc--ccCCCCCchhHH
Q 042319 69 SSRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKY--WGTST--FTNFPISDYEKE 144 (393)
Q Consensus 69 sS~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~--~G~~a--~~NFp~~~yd~E 144 (393)
..+|.||..+...-+-.+.|+.. ||-+--|. .++|+|..|.++.+..+ .|-.. ..||-......-
T Consensus 33 Pe~fpgli~R~~~P~~t~lIf~s----------GKivitGa-ks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v~NIvas 101 (174)
T cd00652 33 PKRFPGVIMRLREPKTTALIFSS----------GKMVITGA-KSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVAS 101 (174)
T ss_pred CCccceEEEEcCCCcEEEEEECC----------CEEEEEec-CCHHHHHHHHHHHHHHHHHcCCCccccCceEEEEEEEE
Confidence 47899999999877888888764 88877776 46778888888877766 33221 122221110000
Q ss_pred HHHhhhhhHHHHHHhhhccCCCCcccccccccceecccCCeeEEeeccccCCeEEecCCCCcHHHHHHHHHHHHHH
Q 042319 145 IEFMQTVTKEEYLASLRRKSSGFSRGVSKYRGVARHHHNGRWEARIGRVFGNKYLYLGTYSTQEEAARAYDIAAIE 220 (393)
Q Consensus 145 i~~Lr~vS~eE~v~~LRrkssg~sr~~S~yrGV~~~~~~grW~A~I~~~~~~k~i~LG~f~t~EEAA~AYD~Aa~~ 220 (393)
...-..+..+......+. ...=....|.|+.+.-..-+=..-| ...||-+-.|. .+++|+.+|++.....
T Consensus 102 ~~l~~~i~L~~la~~~~~---~~~YePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~i~~~ 171 (174)
T cd00652 102 CDLGFPIRLEELALKHPE---NASYEPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEKIYPI 171 (174)
T ss_pred EECCCcccHHHHHhhhhc---ccEECCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHH
Confidence 000001122222222221 1112345688987665555666666 56788777776 5779999998775443
No 11
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=51.39 E-value=44 Score=23.87 Aligned_cols=27 Identities=19% Similarity=0.176 Sum_probs=21.9
Q ss_pred CCeEEEccCCCCHHHHHHHHHHHHHhh
Q 042319 101 KGKQVYLGAYDEEEAAARAYDLAALKY 127 (393)
Q Consensus 101 ~gk~~~LG~F~teEeAA~AYD~Aa~~~ 127 (393)
+.++++-+-|.|..||-.+...+...+
T Consensus 15 krk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 15 KRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 346788899999999999988776554
No 12
>PRK00394 transcription factor; Reviewed
Probab=48.86 E-value=1.7e+02 Score=27.27 Aligned_cols=139 Identities=14% Similarity=0.159 Sum_probs=81.1
Q ss_pred CCCCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhc--CCcc--ccCCCCCchhH
Q 042319 68 RSSRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYW--GTST--FTNFPISDYEK 143 (393)
Q Consensus 68 ~sS~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~--G~~a--~~NFp~~~yd~ 143 (393)
+..+|-||..+...-+-.+.||.. ||-+--|+. ++++|..|-+..+..+. |-.. ..+|.......
T Consensus 31 ePe~fpgli~Rl~~Pk~t~lIf~s----------GKiv~tGa~-S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVa 99 (179)
T PRK00394 31 NPEQFPGLVYRLEDPKIAALIFRS----------GKVVCTGAK-SVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVA 99 (179)
T ss_pred CcccCceEEEEecCCceEEEEEcC----------CcEEEEccC-CHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEE
Confidence 346899999999877888888764 888888885 56688888777766553 2211 11111111000
Q ss_pred HHHHhhhhhHHHHHHhhhccCCCCcccccccccceecccCCeeEEeeccccCCeEEecCCCCcHHHHHHHHHHHHHHhc
Q 042319 144 EIEFMQTVTKEEYLASLRRKSSGFSRGVSKYRGVARHHHNGRWEARIGRVFGNKYLYLGTYSTQEEAARAYDIAAIEYR 222 (393)
Q Consensus 144 Ei~~Lr~vS~eE~v~~LRrkssg~sr~~S~yrGV~~~~~~grW~A~I~~~~~~k~i~LG~f~t~EEAA~AYD~Aa~~l~ 222 (393)
-...-..+..+.....+.. ....=....|.|+.+.-..-+=..-| ...||-+-.|. .+++|+.+|.+.....+.
T Consensus 100 s~~l~~~i~L~~la~~~~~--~~~~YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 173 (179)
T PRK00394 100 SADLGVELNLNAIAIGLGL--ENIEYEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKLE 173 (179)
T ss_pred EEEcCCeEcHHHHHHhcCc--CCcEECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 0000011122222222200 01112346789997666666667777 56788877776 578999999888665553
No 13
>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=48.82 E-value=2.2e+02 Score=26.29 Aligned_cols=131 Identities=22% Similarity=0.197 Sum_probs=75.0
Q ss_pred CeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhc--CCcc--ccCCCCCchhHHHH
Q 042319 71 RFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYW--GTST--FTNFPISDYEKEIE 146 (393)
Q Consensus 71 ~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~--G~~a--~~NFp~~~yd~Ei~ 146 (393)
+|.||..+-..-+-.+-||.. ||-+--| ..++++|..|.+..+..+. |-.. ..||-......-..
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~s----------GKiviTG-aks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~ 103 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSS----------GKITITG-ATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCS 103 (174)
T ss_pred CCCEEEEEecCCcEEEEEECC----------CeEEEEc-cCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEe
Confidence 899999998877888888764 7776666 4789999999988877663 3211 12222111000000
Q ss_pred HhhhhhHHHHHHhhhccCCCCcccccccccceecccCCeeEEeeccccCCeEEecCCCCcHHHHHHHHHHHH
Q 042319 147 FMQTVTKEEYLASLRRKSSGFSRGVSKYRGVARHHHNGRWEARIGRVFGNKYLYLGTYSTQEEAARAYDIAA 218 (393)
Q Consensus 147 ~Lr~vS~eE~v~~LRrkssg~sr~~S~yrGV~~~~~~grW~A~I~~~~~~k~i~LG~f~t~EEAA~AYD~Aa 218 (393)
.-..+..++....-.. ...=....|.|+.+.-..-+=.+.| ...||-+-.|. .+++|+..|++...
T Consensus 104 ~~~~i~L~~la~~~~~---~~~YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~ 169 (174)
T cd04517 104 MPFPIRLDELAAKNRS---SASYEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIY 169 (174)
T ss_pred CCCcccHHHHHHhchh---hcEeCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHH
Confidence 0001111111110000 0011235688987655554556666 66788777775 57789998887644
No 14
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=42.95 E-value=74 Score=22.67 Aligned_cols=38 Identities=21% Similarity=0.177 Sum_probs=27.4
Q ss_pred eeEEeec--cccCC--eEEecCCCCcHHHHHHHHHHHHHHhc
Q 042319 185 RWEARIG--RVFGN--KYLYLGTYSTQEEAARAYDIAAIEYR 222 (393)
Q Consensus 185 rW~A~I~--~~~~~--k~i~LG~f~t~EEAA~AYD~Aa~~l~ 222 (393)
+|..+|. ....| ++++-+-|.|..||-.+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 4767762 22234 66888999999999999888776653
No 15
>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=33.70 E-value=3.9e+02 Score=24.74 Aligned_cols=132 Identities=17% Similarity=0.142 Sum_probs=73.8
Q ss_pred CCCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhcCCccccCCC---CCchhHHH
Q 042319 69 SSRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYWGTSTFTNFP---ISDYEKEI 145 (393)
Q Consensus 69 sS~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~G~~a~~NFp---~~~yd~Ei 145 (393)
..+|.||..+...-+-.+.|+.. ||-+--|. .++|+|..|.++.+..+..-.-..+|+ ......-.
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~S----------GKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~~~v~Nivat~ 101 (174)
T cd04516 33 PKRFAAVIMRIREPKTTALIFSS----------GKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSC 101 (174)
T ss_pred CccCcEEEEEeCCCcEEEEEECC----------CeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEEEEE
Confidence 46889999999877888888764 88877786 567888888888877663221111222 11100000
Q ss_pred HHhhhhhHHHHHHhhhccCCCCcccccccccceecccCCeeEEeeccccCCeEEecCCCCcHHHHHHHHHHH
Q 042319 146 EFMQTVTKEEYLASLRRKSSGFSRGVSKYRGVARHHHNGRWEARIGRVFGNKYLYLGTYSTQEEAARAYDIA 217 (393)
Q Consensus 146 ~~Lr~vS~eE~v~~LRrkssg~sr~~S~yrGV~~~~~~grW~A~I~~~~~~k~i~LG~f~t~EEAA~AYD~A 217 (393)
..-..+..+.+....+ ....=....|-|+.+.-..-+=...| ...||-+-.|. .+.+|+..|++..
T Consensus 102 ~l~~~i~L~~la~~~~---~~~~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~a~~~i 167 (174)
T cd04516 102 DVKFPIRLEGLAHAHK---QFSSYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KSREEIYQAFENI 167 (174)
T ss_pred ECCCcccHHHHHHhCh---hccEeCCccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHH
Confidence 0000111111111000 01112346688987654443444455 66788776765 5778888887653
No 16
>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=31.24 E-value=75 Score=25.34 Aligned_cols=30 Identities=30% Similarity=0.470 Sum_probs=23.7
Q ss_pred eeEEeeccccCCeEEecCCCCcHHHHHHHH
Q 042319 185 RWEARIGRVFGNKYLYLGTYSTQEEAARAY 214 (393)
Q Consensus 185 rW~A~I~~~~~~k~i~LG~f~t~EEAA~AY 214 (393)
.|-++|.-..-...+|.|=|.|.+||..+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~ 38 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAAL 38 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHh
Confidence 577888544445789999999999999863
No 17
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=26.01 E-value=95 Score=31.15 Aligned_cols=25 Identities=20% Similarity=0.154 Sum_probs=21.7
Q ss_pred EEEccCCCCHHHHHHHHHHHHHhhc
Q 042319 104 QVYLGAYDEEEAAARAYDLAALKYW 128 (393)
Q Consensus 104 ~~~LG~F~teEeAA~AYD~Aa~~~~ 128 (393)
..++|.|.+..+|-.+-...+..+.
T Consensus 140 ~~~~GpF~s~~~a~~~L~~l~~~fr 164 (286)
T PRK10545 140 PNLFGLFANRRAALQALQSIADEQK 164 (286)
T ss_pred CcEEEEECCHHHHHHHHHHHHHHHc
Confidence 4589999999999999998888873
No 18
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=24.41 E-value=75 Score=26.88 Aligned_cols=20 Identities=30% Similarity=0.388 Sum_probs=17.3
Q ss_pred cCCCCHHHHHHHHHHHHHhh
Q 042319 108 GAYDEEEAAARAYDLAALKY 127 (393)
Q Consensus 108 G~F~teEeAA~AYD~Aa~~~ 127 (393)
|+|+|+|+|..=||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999876543
No 19
>PLN00062 TATA-box-binding protein; Provisional
Probab=22.27 E-value=6.4e+02 Score=23.47 Aligned_cols=137 Identities=17% Similarity=0.103 Sum_probs=76.4
Q ss_pred CCCCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhhcCCcccc---CCCCCchhHH
Q 042319 68 RSSRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKYWGTSTFT---NFPISDYEKE 144 (393)
Q Consensus 68 ~sS~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~~G~~a~~---NFp~~~yd~E 144 (393)
+..+|.||..+...-+-.+.|+.. ||-+--|. .++|+|..|.++.+..+..-.-.. ||-......-
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~S----------GKiviTGa-ks~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas 100 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFAS----------GKMVCTGA-KSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGS 100 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEECC----------CeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEE
Confidence 346899999998877888888764 78776664 678889888888877773221112 2221110000
Q ss_pred HHHhhhhhHHHHHHhhhccCCCCcccccccccceecccCCeeEEeeccccCCeEEecCCCCcHHHHHHHHHHHHHHh
Q 042319 145 IEFMQTVTKEEYLASLRRKSSGFSRGVSKYRGVARHHHNGRWEARIGRVFGNKYLYLGTYSTQEEAARAYDIAAIEY 221 (393)
Q Consensus 145 i~~Lr~vS~eE~v~~LRrkssg~sr~~S~yrGV~~~~~~grW~A~I~~~~~~k~i~LG~f~t~EEAA~AYD~Aa~~l 221 (393)
...-..+..+.... +.. ....=....|.|+.+.-..-+=..-| ...||-+-.|. .+.+|+..|.+...-.|
T Consensus 101 ~~l~~~i~L~~la~-~~~--~~~~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~ai~~i~p~L 171 (179)
T PLN00062 101 CDVKFPIRLEGLAY-AHG--AFSSYEPELFPGLIYRMKQPKIVLLI--FVSGKIVITGA-KVREEIYTAFENIYPVL 171 (179)
T ss_pred EECCCcccHHHHHH-hch--hhcccCcccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 00000111111111 100 01112346788886654444445555 67888777776 56788888877644333
No 20
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=21.67 E-value=61 Score=24.22 Aligned_cols=22 Identities=23% Similarity=0.300 Sum_probs=16.5
Q ss_pred eEEEccCCCCHHHHHHHHHHHH
Q 042319 103 KQVYLGAYDEEEAAARAYDLAA 124 (393)
Q Consensus 103 k~~~LG~F~teEeAA~AYD~Aa 124 (393)
-+|.+|.|++.++|..+-....
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 4677788888888877766554
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=20.89 E-value=2.7e+02 Score=22.30 Aligned_cols=47 Identities=26% Similarity=0.313 Sum_probs=36.3
Q ss_pred CCeeeeeEeCCCCeeEEEEecccccchhhccCCeEEEccCCCCHHHHHHHHHHHHHhh
Q 042319 70 SRFRGVSRHRWTGRYEAHLWDKLSWNVTQKKKGKQVYLGAYDEEEAAARAYDLAALKY 127 (393)
Q Consensus 70 S~yrGV~~~~~~grw~A~I~~~~~w~~~~~~~gk~~~LG~F~teEeAA~AYD~Aa~~~ 127 (393)
.+|.||..+...-+-.+.|+.. ||-+..|+ .++++|..|.+.....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~s----------Gki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFSS----------GKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEETT----------SEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEcC----------CEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 5788998887766788888654 88888886 67888888888776544
Done!