Query 014204
Match_columns 429
No_of_seqs 433 out of 1978
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 02:51:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014204.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014204hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00380 AP2 DNA-binding dom 99.8 1.4E-18 3.1E-23 136.0 7.0 63 108-179 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.8 1.5E-18 3.3E-23 134.3 6.9 61 107-176 1-61 (61)
3 smart00380 AP2 DNA-binding dom 99.7 6E-18 1.3E-22 132.5 6.8 63 210-273 1-63 (64)
4 cd00018 AP2 DNA-binding domain 99.7 8.6E-18 1.9E-22 130.1 6.6 61 209-270 1-61 (61)
5 PHA00280 putative NHN endonucl 99.5 2.9E-14 6.4E-19 125.3 8.7 105 153-264 11-119 (121)
6 PHA00280 putative NHN endonucl 99.3 5.3E-12 1.1E-16 111.1 7.3 56 104-170 64-119 (121)
7 PF00847 AP2: AP2 domain; Int 99.1 5.1E-10 1.1E-14 84.7 6.9 56 107-167 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 99.0 8.2E-10 1.8E-14 83.6 5.8 53 209-261 1-56 (56)
9 cd04518 TBP_archaea archaeal T 68.7 65 0.0014 30.3 10.7 132 107-259 34-172 (174)
10 PF14657 Integrase_AP2: AP2-li 67.2 16 0.00035 26.5 5.1 39 120-164 1-41 (46)
11 cd00652 TBP_TLF TATA box bindi 63.4 84 0.0018 29.4 10.3 132 107-258 34-172 (174)
12 cd04517 TLF TBP-like factors ( 61.2 87 0.0019 29.4 10.0 125 108-257 35-171 (174)
13 cd04516 TBP_eukaryotes eukaryo 54.1 1.6E+02 0.0036 27.6 10.6 132 107-255 34-168 (174)
14 PF14657 Integrase_AP2: AP2-li 52.2 38 0.00082 24.6 4.8 38 222-259 1-42 (46)
15 PRK00394 transcription factor; 51.9 1.4E+02 0.0031 28.1 9.9 135 107-259 33-173 (179)
16 PLN00062 TATA-box-binding prot 51.7 2E+02 0.0043 27.2 10.8 135 107-258 34-171 (179)
17 PF11879 DUF3399: Domain of un 34.8 43 0.00094 29.2 3.2 11 3-13 35-45 (104)
18 PF08471 Ribonuc_red_2_N: Clas 31.5 48 0.001 28.4 2.9 21 238-258 70-90 (93)
19 PF08471 Ribonuc_red_2_N: Clas 27.6 60 0.0013 27.8 2.8 20 145-164 71-90 (93)
20 PF05036 SPOR: Sporulation rel 26.9 45 0.00098 25.3 1.9 24 138-161 42-65 (76)
21 PRK10927 essential cell divisi 26.3 2.9E+02 0.0062 28.8 7.9 21 235-255 285-305 (319)
22 COG2823 OsmY Predicted peripla 25.9 2.6E+02 0.0057 27.0 7.2 105 136-265 78-189 (196)
23 PF12286 DUF3622: Protein of u 25.8 73 0.0016 26.0 2.9 31 218-248 13-47 (71)
24 PHA02601 int integrase; Provis 25.4 89 0.0019 30.9 4.1 45 111-164 2-46 (333)
25 PF00352 TBP: Transcription fa 23.9 2.4E+02 0.0052 23.0 5.7 46 108-164 37-82 (86)
26 PF00352 TBP: Transcription fa 23.6 1.7E+02 0.0038 23.8 4.9 47 210-259 37-83 (86)
27 PF10729 CedA: Cell division a 23.4 1.4E+02 0.0031 24.3 4.1 39 105-155 29-67 (80)
28 PF08846 DUF1816: Domain of un 22.8 1.2E+02 0.0025 24.6 3.5 39 222-260 9-47 (68)
29 COG3087 FtsN Cell division pro 20.7 2.3E+02 0.0051 28.6 5.9 20 235-254 230-249 (264)
30 PRK09692 integrase; Provisiona 20.6 1.9E+02 0.0042 29.8 5.6 32 222-253 42-77 (413)
31 cd00801 INT_P4 Bacteriophage P 20.4 1.7E+02 0.0036 28.6 4.9 38 221-258 10-49 (357)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.76 E-value=1.4e-18 Score=136.03 Aligned_cols=63 Identities=46% Similarity=0.942 Sum_probs=59.3
Q ss_pred ceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhccccccccCCCcchh
Q 014204 108 QYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGATTHINFPLSTYE 179 (429)
Q Consensus 108 ~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~~a~~NFp~~~ye 179 (429)
+|+||+++++ |||+|+|++ +.+|+++|||+|+|+||||+|||.|+++++|..+.+|||.+.|+
T Consensus 1 ~~kGV~~~~~-gkw~A~I~~--------~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPW-GKWVAEIRD--------PSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCC-CeEEEEEEe--------cCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 4999999887 999999987 55899999999999999999999999999999999999999986
No 2
>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=99.75 E-value=1.5e-18 Score=134.34 Aligned_cols=61 Identities=48% Similarity=0.893 Sum_probs=56.6
Q ss_pred cceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhccccccccCCCc
Q 014204 107 SQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGATTHINFPLS 176 (429)
Q Consensus 107 S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~~a~~NFp~~ 176 (429)
|+|+||+++++ |||+|+|++ ...|+++|||+|+|+||||+|||.|+++++|..+.+|||.+
T Consensus 1 s~~~GV~~~~~-gkw~A~I~~--------~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPW-GKWVAEIRD--------PSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCC-CcEEEEEEe--------CCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 68999999998 999999987 33499999999999999999999999999999999999964
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.73 E-value=6e-18 Score=132.49 Aligned_cols=63 Identities=54% Similarity=0.807 Sum_probs=58.7
Q ss_pred ccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHhhCCCCCCCCCCCccc
Q 014204 210 VYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGTSAVTNFDISRYD 273 (429)
Q Consensus 210 ~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l~G~~a~~NFp~s~y~ 273 (429)
+|+||++ +++|||+|+|+.+.+++.++||+|+|+||||+|||.++++++|..+++|||.++|+
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 4899997 56799999998666999999999999999999999999999999999999999885
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=99.72 E-value=8.6e-18 Score=130.12 Aligned_cols=61 Identities=54% Similarity=0.845 Sum_probs=55.3
Q ss_pred cccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHhhCCCCCCCCCCC
Q 014204 209 SVYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGTSAVTNFDIS 270 (429)
Q Consensus 209 S~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l~G~~a~~NFp~s 270 (429)
|+|+||++++ +|||+|+|+....+++++||+|+|+||||+|||.++++++|..+.+|||.+
T Consensus 1 s~~~GV~~~~-~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRP-WGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECC-CCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 5899999764 699999997554599999999999999999999999999999999999964
No 5
>PHA00280 putative NHN endonuclease
Probab=99.53 E-value=2.9e-14 Score=125.30 Aligned_cols=105 Identities=16% Similarity=0.158 Sum_probs=84.6
Q ss_pred HHHHHHHHHHHhccccc---cccCCC-cchhhhHHHhhhhhhhhhhhhhhcccCCCCCCCcccccceeeccCceEEeeec
Q 014204 153 AARAYDLAALKYWGATT---HINFPL-STYEKELEEMKHMTRQEFVANLRRKSSGFSRGASVYRGVTRHHQHGRWQARIG 228 (429)
Q Consensus 153 AArAYD~Aal~~~G~~a---~~NFp~-~~yenEIeeLR~mTkeE~va~lRr~ssg~s~~~S~yrGV~r~~~~gkW~A~Ir 228 (429)
+-+++..+.+..+|.-. .+.+-. ....+.+++|+.++..|+..+.+..+ +++|+|+||+|++..|||+|+|
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 APRRHIQVWEAANGPIPKGYYIDHIDGNPLNDALDNLRLALPKENSWNMKTPK----SNTSGLKGLSWSKEREMWRGTV- 85 (121)
T ss_pred hhhHhHhhhHHHHCCCCCCCEEEcCCCCCCCCcHHHhhhcCHHHHhcccCCCC----CCCCCCCeeEEecCCCeEEEEE-
Confidence 34567777777888542 122221 23457899999999999998876543 7899999999999999999999
Q ss_pred cccCCceeecCCCCcHHHHHHHHHHHHHHhhCCCCC
Q 014204 229 RVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGTSAV 264 (429)
Q Consensus 229 ~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l~G~~a~ 264 (429)
.++||+++||.|+++|+|+.||+ ++++|+|.+|.
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 48999999999999999999997 77889998875
No 6
>PHA00280 putative NHN endonuclease
Probab=99.30 E-value=5.3e-12 Score=111.10 Aligned_cols=56 Identities=18% Similarity=0.243 Sum_probs=51.5
Q ss_pred CCCcceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhcccccc
Q 014204 104 QRTSQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGATTH 170 (429)
Q Consensus 104 ~~~S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~~a~ 170 (429)
..+|+|+||+|++.+|||+|+| ..+||+++||.|+++|+|+.||+ ++.+|+|.++.
T Consensus 64 ~N~SG~kGV~~~k~~~kw~A~I----------~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 64 SNTSGLKGLSWSKEREMWRGTV----------TAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCeeEEecCCCeEEEEE----------EECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 5789999999999999999999 55999999999999999999997 77899998874
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=5.1e-10 Score=84.73 Aligned_cols=56 Identities=30% Similarity=0.409 Sum_probs=47.4
Q ss_pred cceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhccc
Q 014204 107 SQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGA 167 (429)
Q Consensus 107 S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~ 167 (429)
|+|+||++++..++|+|.|++... .| .+|.++||.|++++||++|++.++++++|.
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 689999999999999999987311 11 249999999999999999999999999873
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=8.2e-10 Score=83.57 Aligned_cols=53 Identities=34% Similarity=0.535 Sum_probs=46.6
Q ss_pred cccccceeeccCceEEeeecccc-C--CceeecCCCCcHHHHHHHHHHHHHHhhCC
Q 014204 209 SVYRGVTRHHQHGRWQARIGRVA-G--NKDLYLGTFSTQEEAAEAYDIAAIKFRGT 261 (429)
Q Consensus 209 S~yrGV~r~~~~gkW~A~Ir~~~-~--~k~i~LGtF~t~EeAArAYD~Aa~~l~G~ 261 (429)
|+|+||++++..++|+|+|+... + ++.++||.|.++|||++||+.++++++|+
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 68999999999999999997532 1 49999999999999999999999999874
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=68.73 E-value=65 Score=30.27 Aligned_cols=132 Identities=12% Similarity=0.161 Sum_probs=79.9
Q ss_pred cceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhcccccc----ccCCCcchhhhH
Q 014204 107 SQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGATTH----INFPLSTYEKEL 182 (429)
Q Consensus 107 S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~~a~----~NFp~~~yenEI 182 (429)
.+|.||..|-..-+=.+.|+. .||-+--| ..++|+|..|-++.+..+....-. .+|-. .+.+
T Consensus 34 ~~fpgli~Rl~~Pk~t~lIF~----------SGKiv~tG-aks~~~a~~a~~~~~~~L~~~g~~~~~~~~~~i---~NIV 99 (174)
T cd04518 34 DQFPGLVYRLEDPKIAALIFR----------SGKMVCTG-AKSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKV---QNIV 99 (174)
T ss_pred CcCcEEEEEccCCcEEEEEEC----------CCeEEEEc-cCCHHHHHHHHHHHHHHHHhcCCCccCCCceEE---EEEE
Confidence 469999999887787888865 77776655 478899999988887776532211 11111 1100
Q ss_pred HH--hh-hhhhhhhhhhhhcccCCCCCCCcccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHhh
Q 014204 183 EE--MK-HMTRQEFVANLRRKSSGFSRGASVYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFR 259 (429)
Q Consensus 183 ee--LR-~mTkeE~va~lRr~ssg~s~~~S~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l~ 259 (429)
.. |. .+..+.....++. ..=.-..|-|+.++-..-|=.+-| ...||-+..|. .++||+.+|.+.....|.
T Consensus 100 as~~l~~~i~L~~la~~~~~----~~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 100 ASADLGREVNLDAIAIGLPN----AEYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred EEEEcCCccCHHHHHhhCCC----CccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 00 00 1111111111221 111225688998665555667777 57888888886 789999999988776654
No 10
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=67.19 E-value=16 Score=26.52 Aligned_cols=39 Identities=18% Similarity=0.296 Sum_probs=27.9
Q ss_pred eEEEEE--ecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 014204 120 RYEAHL--WDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKY 164 (429)
Q Consensus 120 rW~A~I--~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~ 164 (429)
+|...| +++. ..+.++++-+.|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~------~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDE------TGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECC------CCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 577777 2311 22346788899999999999988776655
No 11
>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=63.35 E-value=84 Score=29.44 Aligned_cols=132 Identities=16% Similarity=0.187 Sum_probs=77.5
Q ss_pred cceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhc--cccc--cccCCCcchhhhH
Q 014204 107 SQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYW--GATT--HINFPLSTYEKEL 182 (429)
Q Consensus 107 S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~--G~~a--~~NFp~~~yenEI 182 (429)
.+|.||..|...-+=.+.|+. .||-+--|. .++|+|.+|.++.+..+. |-.. ..||-. .+..
T Consensus 34 e~fpgli~R~~~P~~t~lIf~----------sGKivitGa-ks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v---~NIv 99 (174)
T cd00652 34 KRFPGVIMRLREPKTTALIFS----------SGKMVITGA-KSEEDAKLAARKYARILQKLGFPVEKFPEFKV---QNIV 99 (174)
T ss_pred CccceEEEEcCCCcEEEEEEC----------CCEEEEEec-CCHHHHHHHHHHHHHHHHHcCCCccccCceEE---EEEE
Confidence 469999999887788888865 787776665 578888888888877663 3111 112211 0000
Q ss_pred HH--h-hhhhhhhhhhhhhcccCCCCCCCcccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHh
Q 014204 183 EE--M-KHMTRQEFVANLRRKSSGFSRGASVYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 258 (429)
Q Consensus 183 ee--L-R~mTkeE~va~lRr~ssg~s~~~S~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l 258 (429)
.. | -.+..++.....+... .=.-..|-|+.++-...+=..-| ...||-+..|. .+++|+.+|++.-...|
T Consensus 100 as~~l~~~i~L~~la~~~~~~~---~YePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~i~~~L 172 (174)
T cd00652 100 ASCDLGFPIRLEELALKHPENA---SYEPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEKIYPIL 172 (174)
T ss_pred EEEECCCcccHHHHHhhhhccc---EECCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 00 0 0011111111111000 01124688988665555666677 56788888887 78999999998765443
No 12
>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=61.20 E-value=87 Score=29.40 Aligned_cols=125 Identities=22% Similarity=0.224 Sum_probs=75.1
Q ss_pred ceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhc--cccc--cccCCCcc------
Q 014204 108 QYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYW--GATT--HINFPLST------ 177 (429)
Q Consensus 108 ~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~--G~~a--~~NFp~~~------ 177 (429)
+|.||..|-..-+=.+-||. .||-+--| ..++|+|.+|.++.+..+. |-.. ..||-...
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~----------sGKiviTG-aks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~ 103 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS----------SGKITITG-ATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCS 103 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC----------CCeEEEEc-cCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEe
Confidence 79999999887788888866 67765544 5889999999998877763 3111 11222100
Q ss_pred --hhhhHHHhhhhhhhhhhhhhhcccCCCCCCCcccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHH
Q 014204 178 --YEKELEEMKHMTRQEFVANLRRKSSGFSRGASVYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAA 255 (429)
Q Consensus 178 --yenEIeeLR~mTkeE~va~lRr~ssg~s~~~S~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa 255 (429)
..-.++.+... ..+.-. =.-..|-|+.++-..-+=.+.| ...||-+..|. .++||+.+|++.-.
T Consensus 104 ~~~~i~L~~la~~-------~~~~~~----YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~ 169 (174)
T cd04517 104 MPFPIRLDELAAK-------NRSSAS----YEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIY 169 (174)
T ss_pred CCCcccHHHHHHh-------chhhcE----eCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHH
Confidence 00011111110 001000 1124688988665544556666 56788888886 78899999987654
Q ss_pred HH
Q 014204 256 IK 257 (429)
Q Consensus 256 ~~ 257 (429)
-.
T Consensus 170 pi 171 (174)
T cd04517 170 PI 171 (174)
T ss_pred HH
Confidence 43
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=54.13 E-value=1.6e+02 Score=27.61 Aligned_cols=132 Identities=14% Similarity=0.129 Sum_probs=74.7
Q ss_pred cceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhccccccccCCCcchhhhHHH--
Q 014204 107 SQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGATTHINFPLSTYEKELEE-- 184 (429)
Q Consensus 107 S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~~a~~NFp~~~yenEIee-- 184 (429)
.+|.||..|-..-+=.+.|+. .||-+--|. .++|+|..|.++.+..+..-.-...|+.-...+....
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~----------SGKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~~~v~Nivat~~ 102 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFS----------SGKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCD 102 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEEC----------CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEEEEEE
Confidence 468999999887788888866 788776676 5778889898888777643221123321111111000
Q ss_pred hh-hhhhhhhhhhhhcccCCCCCCCcccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHH
Q 014204 185 MK-HMTRQEFVANLRRKSSGFSRGASVYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAA 255 (429)
Q Consensus 185 LR-~mTkeE~va~lRr~ssg~s~~~S~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa 255 (429)
|. .+..++.....+. ...=.-..|-|+.++-..-|=...| ...||-+..|. .++||+.+|++.-.
T Consensus 103 l~~~i~L~~la~~~~~---~~~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~a~~~i~ 168 (174)
T cd04516 103 VKFPIRLEGLAHAHKQ---FSSYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KSREEIYQAFENIY 168 (174)
T ss_pred CCCcccHHHHHHhChh---ccEeCCccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHH
Confidence 00 0011111100000 0001124688988654444445555 56888888876 78889998886543
No 14
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=52.17 E-value=38 Score=24.56 Aligned_cols=38 Identities=21% Similarity=0.242 Sum_probs=27.6
Q ss_pred eEEeeec--cccCC--ceeecCCCCcHHHHHHHHHHHHHHhh
Q 014204 222 RWQARIG--RVAGN--KDLYLGTFSTQEEAAEAYDIAAIKFR 259 (429)
Q Consensus 222 kW~A~Ir--~~~~~--k~i~LGtF~t~EeAArAYD~Aa~~l~ 259 (429)
+|..+|. .+..| ++++-+-|.|..||-.+.......+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 4666662 23234 57888999999999999988776653
No 15
>PRK00394 transcription factor; Reviewed
Probab=51.94 E-value=1.4e+02 Score=28.11 Aligned_cols=135 Identities=13% Similarity=0.157 Sum_probs=79.9
Q ss_pred cceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhcccccccc-CCCcchhhhHHH-
Q 014204 107 SQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGATTHIN-FPLSTYEKELEE- 184 (429)
Q Consensus 107 S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~~a~~N-Fp~~~yenEIee- 184 (429)
.+|.||..|-..-+=.+.|+. .||-+--|.. ++|+|..|-++.+..+....-... ++.-.-.+.+..
T Consensus 33 e~fpgli~Rl~~Pk~t~lIf~----------sGKiv~tGa~-S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVas~ 101 (179)
T PRK00394 33 EQFPGLVYRLEDPKIAALIFR----------SGKVVCTGAK-SVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASA 101 (179)
T ss_pred ccCceEEEEecCCceEEEEEc----------CCcEEEEccC-CHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEEEE
Confidence 368999999887788888865 7888877874 677888888877666632211111 111000110000
Q ss_pred -hh-hhhhhhhhhhh--hcccCCCCCCCcccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHhh
Q 014204 185 -MK-HMTRQEFVANL--RRKSSGFSRGASVYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFR 259 (429)
Q Consensus 185 -LR-~mTkeE~va~l--Rr~ssg~s~~~S~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l~ 259 (429)
+. .+..++....+ +.-. =.-..|-|+.++-..-|=..-| ...||-+..|. .++||+.+|.+.....|.
T Consensus 102 ~l~~~i~L~~la~~~~~~~~~----YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 173 (179)
T PRK00394 102 DLGVELNLNAIAIGLGLENIE----YEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKLE 173 (179)
T ss_pred EcCCeEcHHHHHHhcCcCCcE----ECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 00 01111111111 1100 1125688998765666777777 57788888886 789999999988766654
No 16
>PLN00062 TATA-box-binding protein; Provisional
Probab=51.72 E-value=2e+02 Score=27.23 Aligned_cols=135 Identities=13% Similarity=0.086 Sum_probs=75.7
Q ss_pred cceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHhccccccccCCCcchhhhHHH--
Q 014204 107 SQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKYWGATTHINFPLSTYEKELEE-- 184 (429)
Q Consensus 107 S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~~a~~NFp~~~yenEIee-- 184 (429)
.+|.||..|-..-+=.+-|+. .||-+--| ..++|+|..|.++.+..+..-.-..+|+.-...+.+..
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~----------SGKiviTG-aks~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas~~ 102 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFA----------SGKMVCTG-AKSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCD 102 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEEC----------CCeEEEEe-cCCHHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEEEE
Confidence 369999999887788888865 67766555 57889999999988777743221222221000110000
Q ss_pred hh-hhhhhhhhhhhhcccCCCCCCCcccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHh
Q 014204 185 MK-HMTRQEFVANLRRKSSGFSRGASVYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKF 258 (429)
Q Consensus 185 LR-~mTkeE~va~lRr~ssg~s~~~S~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l 258 (429)
|. .+..+.....-+.. ..=.-..|-|+.++-..-|=..-| ...||-+..|. .++||+..|.+.-.-.|
T Consensus 103 l~~~i~L~~la~~~~~~---~~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~ai~~i~p~L 171 (179)
T PLN00062 103 VKFPIRLEGLAYAHGAF---SSYEPELFPGLIYRMKQPKIVLLI--FVSGKIVITGA-KVREEIYTAFENIYPVL 171 (179)
T ss_pred CCCcccHHHHHHhchhh---cccCcccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 00 00001110000000 011224688887654444555566 57888888887 78889988887654443
No 17
>PF11879 DUF3399: Domain of unknown function (DUF3399); InterPro: IPR024587 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The Shal potassium channel was found in Drosophila melanogaster (Fruit fly). Several vertebrate potassium channels with similar amino acid sequences were subsequently found and, together with the D. melanogaster Shal channel, now constitute the Kv4 family. These channels are the primary subunits contributing to transient, voltage-dependent potassium currents in the nervous system (A currents) and the heart (transient outward current), and are inhibited by free fatty acids []. This family can be further divided into 3 subfamilies, designated Kv4.1(KCND1), Kv4.2(KCND2) and Kv4.3(KCND3). This uncharacterised C-terminal domain is associated with the Shal (Kv4) potassium channel.
Probab=34.78 E-value=43 Score=29.21 Aligned_cols=11 Identities=45% Similarity=0.893 Sum_probs=9.6
Q ss_pred chhhhHHhhhh
Q 014204 3 HHHFLHQHQHS 13 (429)
Q Consensus 3 ~~~~~~~~~k~ 13 (429)
|||.||=.-|+
T Consensus 35 HhHLLhCLEKT 45 (104)
T PF11879_consen 35 HHHLLHCLEKT 45 (104)
T ss_pred HHHHHHHHHHc
Confidence 99999987776
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=31.54 E-value=48 Score=28.41 Aligned_cols=21 Identities=33% Similarity=0.447 Sum_probs=18.2
Q ss_pred cCCCCcHHHHHHHHHHHHHHh
Q 014204 238 LGTFSTQEEAAEAYDIAAIKF 258 (429)
Q Consensus 238 LGtF~t~EeAArAYD~Aa~~l 258 (429)
-|+|+|+|||..-||.-+..|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 599999999999999876654
No 19
>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=27.56 E-value=60 Score=27.81 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=17.9
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 014204 145 GGYDKEDKAARAYDLAALKY 164 (429)
Q Consensus 145 G~f~teEeAArAYD~Aal~~ 164 (429)
|+|+|+|+|..=||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999887654
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=26.87 E-value=45 Score=25.30 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=18.3
Q ss_pred CCeEEecCCCCCHHHHHHHHHHHH
Q 014204 138 KGRQVYLGGYDKEDKAARAYDLAA 161 (429)
Q Consensus 138 ~gk~i~LG~f~teEeAArAYD~Aa 161 (429)
.--+|.+|.|++.++|..+-....
T Consensus 42 ~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 42 PWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TCEEEEECCECTCCHHHHHHHHHH
T ss_pred ceEEEEECCCCCHHHHHHHHHHHh
Confidence 334677899999999988877554
No 21
>PRK10927 essential cell division protein FtsN; Provisional
Probab=26.30 E-value=2.9e+02 Score=28.75 Aligned_cols=21 Identities=14% Similarity=0.257 Sum_probs=17.5
Q ss_pred eeecCCCCcHHHHHHHHHHHH
Q 014204 235 DLYLGTFSTQEEAAEAYDIAA 255 (429)
Q Consensus 235 ~i~LGtF~t~EeAArAYD~Aa 255 (429)
|+.||=|.+.++|.++.++..
T Consensus 285 RVrVGPf~sr~eAe~a~~rLk 305 (319)
T PRK10927 285 RVVIGPVKGKENADSTLNRLK 305 (319)
T ss_pred EEEeCCCCCHHHHHHHHHHHH
Confidence 578899999999998887654
No 22
>COG2823 OsmY Predicted periplasmic or secreted lipoprotein [General function prediction only]
Probab=25.92 E-value=2.6e+02 Score=26.96 Aligned_cols=105 Identities=21% Similarity=0.223 Sum_probs=62.2
Q ss_pred ccCCeEEecCCCCCHHHHHHHHHHHHHHhcccccccc-------CCCcchhhhHHHhhhhhhhhhhhhhhcccCCCCCCC
Q 014204 136 TRKGRQVYLGGYDKEDKAARAYDLAALKYWGATTHIN-------FPLSTYEKELEEMKHMTRQEFVANLRRKSSGFSRGA 208 (429)
Q Consensus 136 ~~~gk~i~LG~f~teEeAArAYD~Aal~~~G~~a~~N-------Fp~~~yenEIeeLR~mTkeE~va~lRr~ssg~s~~~ 208 (429)
..+|+.++.|..+.+.+..+|=+.|. .+.|-....| +|...|.++ ....++..++|...+.
T Consensus 78 ~y~G~VlL~G~~~~~~~~~~A~~~a~-~v~Gv~~v~n~l~i~~~~~~~~~~~D-----t~iTt~Vka~Ll~~~~------ 145 (196)
T COG2823 78 VYQGKVLLSGQVPNEAQKEKASQIAR-SVEGVTEVYNELTVGGPGSLGGRSND-----TWITTKVKAALLGDDN------ 145 (196)
T ss_pred EEcCEEEEeeccCCHHHHHHHHHHHH-hhhcchhhhhheeecCCCCcccccch-----HHHHHHHHHHhccCCC------
Confidence 47899999999999999999888654 3445332222 222222111 1222333344443321
Q ss_pred cccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHhhCCCCCC
Q 014204 209 SVYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRGTSAVT 265 (429)
Q Consensus 209 S~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l~G~~a~~ 265 (429)
....+.... ..+|.-..+|.-++++|+++|-+.| ..+.|-..+.
T Consensus 146 ---------v~s~~IkV~---t~~g~V~L~G~V~s~~e~~~A~~~A-~~v~GVk~V~ 189 (196)
T COG2823 146 ---------VKSSNIKVE---TENGEVYLSGLVDSQEEAERAEEIA-SKVSGVKKVV 189 (196)
T ss_pred ---------CCcceEEEE---EECCEEEEEEEeCCHHHHHHHHHHH-hcCCCHHHHh
Confidence 112222222 3577788889999999999998854 6677766543
No 23
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=25.84 E-value=73 Score=25.99 Aligned_cols=31 Identities=23% Similarity=0.473 Sum_probs=20.9
Q ss_pred ccCceEEeeeccccCCceeec----CCCCcHHHHH
Q 014204 218 HQHGRWQARIGRVAGNKDLYL----GTFSTQEEAA 248 (429)
Q Consensus 218 ~~~gkW~A~Ir~~~~~k~i~L----GtF~t~EeAA 248 (429)
...+.|.|+|.+.+..++..+ --|++++||.
T Consensus 13 q~~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq 47 (71)
T PF12286_consen 13 QKRNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQ 47 (71)
T ss_pred ecCCceeeeeeeeecCceeEEEecccCcccHHHHH
Confidence 345789999976665544333 3489998865
No 24
>PHA02601 int integrase; Provisional
Probab=25.40 E-value=89 Score=30.92 Aligned_cols=45 Identities=13% Similarity=0.341 Sum_probs=28.1
Q ss_pred ceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 014204 111 GVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKY 164 (429)
Q Consensus 111 GV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~ 164 (429)
+|++.+ +|+|++.|+.. ...|+++.. +|.|..||-...+.....+
T Consensus 2 ~~~~~~-~g~w~~~~~~~-------~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLK-DGKWLCEIYPN-------GRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcC-CCCEEEEEEEC-------CCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 455444 48999999641 124666553 5999988876655544443
No 25
>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=23.90 E-value=2.4e+02 Score=22.99 Aligned_cols=46 Identities=15% Similarity=0.274 Sum_probs=36.1
Q ss_pred ceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 014204 108 QYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAARAYDLAALKY 164 (429)
Q Consensus 108 ~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAArAYD~Aal~~ 164 (429)
+|.||..+-..-+-.+.|+. .||-+..|. .++|+|..|.+.....+
T Consensus 37 ~fpgl~~r~~~p~~t~~IF~----------sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIFS----------SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TESSEEEEETTTTEEEEEET----------TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEEc----------CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 58899888876788888855 788877775 68889999988776554
No 26
>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=23.63 E-value=1.7e+02 Score=23.80 Aligned_cols=47 Identities=17% Similarity=0.216 Sum_probs=35.8
Q ss_pred ccccceeeccCceEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHhh
Q 014204 210 VYRGVTRHHQHGRWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFR 259 (429)
Q Consensus 210 ~yrGV~r~~~~gkW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l~ 259 (429)
.|.||..+...-+-...| ...||-+..|. .++|||..|.++....|.
T Consensus 37 ~fpgl~~r~~~p~~t~~I--F~sGki~itGa-ks~~~~~~a~~~i~~~L~ 83 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLI--FSSGKIVITGA-KSEEEAKKAIEKILPILQ 83 (86)
T ss_dssp TESSEEEEETTTTEEEEE--ETTSEEEEEEE-SSHHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 688888665555677777 56788777776 799999999998876653
No 27
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=23.38 E-value=1.4e+02 Score=24.34 Aligned_cols=39 Identities=21% Similarity=0.288 Sum_probs=23.9
Q ss_pred CCcceeceeEecCCCeEEEEEecCCccccCcccCCeEEecCCCCCHHHHHH
Q 014204 105 RTSQYRGVTRHRWTGRYEAHLWDNSCRKEGQTRKGRQVYLGGYDKEDKAAR 155 (429)
Q Consensus 105 ~~S~yrGV~~~~~~grW~A~I~~~~~~~~~~~~~gk~i~LG~f~teEeAAr 155 (429)
+--+||-|..-+ |||+|.|.. ...-.---.|..+|.|-|
T Consensus 29 k~dgfrdvw~lr--gkyvafvl~----------ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 29 KMDGFRDVWQLR--GKYVAFVLM----------GEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp -TTTECCECCCC--CEEEEEEES----------SS-EEE---BSSHHHHHH
T ss_pred hcccccceeeec--cceEEEEEe----------cchhccCCCcCCcHHHHH
Confidence 445699998765 999999965 112222356888877765
No 28
>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=22.76 E-value=1.2e+02 Score=24.63 Aligned_cols=39 Identities=26% Similarity=0.372 Sum_probs=28.0
Q ss_pred eEEeeeccccCCceeecCCCCcHHHHHHHHHHHHHHhhC
Q 014204 222 RWQARIGRVAGNKDLYLGTFSTQEEAAEAYDIAAIKFRG 260 (429)
Q Consensus 222 kW~A~Ir~~~~~k~i~LGtF~t~EeAArAYD~Aa~~l~G 260 (429)
.|=++|.-..-.-..|.|=|.+.+||..+.-.-..-|..
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~ 47 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLES 47 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHh
Confidence 366888533344689999999999999887655554443
No 29
>COG3087 FtsN Cell division protein [Cell division and chromosome partitioning]
Probab=20.72 E-value=2.3e+02 Score=28.60 Aligned_cols=20 Identities=20% Similarity=0.386 Sum_probs=15.6
Q ss_pred eeecCCCCcHHHHHHHHHHH
Q 014204 235 DLYLGTFSTQEEAAEAYDIA 254 (429)
Q Consensus 235 ~i~LGtF~t~EeAArAYD~A 254 (429)
|+-||-|.+.++|..|-++.
T Consensus 230 RV~vGP~n~~~~a~~aq~rL 249 (264)
T COG3087 230 RVRVGPFNSKADAVKAQKRL 249 (264)
T ss_pred EEEecCCCcHHHHHHHHHHH
Confidence 45678899999999877653
No 30
>PRK09692 integrase; Provisional
Probab=20.63 E-value=1.9e+02 Score=29.80 Aligned_cols=32 Identities=22% Similarity=0.240 Sum_probs=20.8
Q ss_pred eEEeeeccccCCce--eecCCCC--cHHHHHHHHHH
Q 014204 222 RWQARIGRVAGNKD--LYLGTFS--TQEEAAEAYDI 253 (429)
Q Consensus 222 kW~A~Ir~~~~~k~--i~LGtF~--t~EeAArAYD~ 253 (429)
.|+.+.+.+.+|++ +.||.|+ |..||..+..+
T Consensus 42 ~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 42 IWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 49988764444554 7899999 56565544433
No 31
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=20.38 E-value=1.7e+02 Score=28.62 Aligned_cols=38 Identities=29% Similarity=0.392 Sum_probs=25.2
Q ss_pred ceEEeeeccccCCceeecCCCC--cHHHHHHHHHHHHHHh
Q 014204 221 GRWQARIGRVAGNKDLYLGTFS--TQEEAAEAYDIAAIKF 258 (429)
Q Consensus 221 gkW~A~Ir~~~~~k~i~LGtF~--t~EeAArAYD~Aa~~l 258 (429)
+.|+.+++.....+++.||+|+ +.++|....+.....+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 4699988643334468899995 6677776666654444
Done!