Query 043551
Match_columns 408
No_of_seqs 343 out of 1900
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 06:09:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043551.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043551hhsearch_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 2.3E-18 4.9E-23 132.5 6.6 61 71-137 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.7 2.9E-18 6.2E-23 133.5 6.9 63 72-140 1-63 (64)
3 smart00380 AP2 DNA-binding dom 99.6 7E-16 1.5E-20 120.1 5.4 62 166-228 2-63 (64)
4 cd00018 AP2 DNA-binding domain 99.6 1.6E-15 3.6E-20 116.6 5.8 61 164-225 1-61 (61)
5 PHA00280 putative NHN endonucl 99.3 2.5E-12 5.5E-17 112.5 6.4 62 62-131 58-119 (121)
6 PHA00280 putative NHN endonucl 99.3 2.3E-12 5.1E-17 112.8 5.8 101 116-219 13-119 (121)
7 PF00847 AP2: AP2 domain; Int 99.0 5E-10 1.1E-14 84.2 4.4 56 71-128 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 98.8 9.7E-09 2.1E-13 77.2 4.4 53 164-216 1-56 (56)
9 PF14657 Integrase_AP2: AP2-li 41.6 57 0.0012 23.5 4.3 39 84-125 1-41 (46)
10 cd00652 TBP_TLF TATA box bindi 38.0 1.4E+02 0.003 27.8 7.4 133 70-213 33-172 (174)
11 cd04518 TBP_archaea archaeal T 36.8 1.6E+02 0.0034 27.6 7.5 134 69-214 32-172 (174)
12 PRK10545 nucleotide excision r 30.2 84 0.0018 31.8 4.9 120 103-236 141-278 (286)
13 PF08471 Ribonuc_red_2_N: Clas 29.9 50 0.0011 28.2 2.7 21 105-125 70-90 (93)
14 cd04517 TLF TBP-like factors ( 29.3 2.3E+02 0.005 26.4 7.3 130 72-212 35-171 (174)
15 PF08471 Ribonuc_red_2_N: Clas 26.9 57 0.0012 27.9 2.5 21 193-213 70-90 (93)
16 PF08846 DUF1816: Domain of un 21.9 90 0.002 25.1 2.7 38 177-214 9-46 (68)
17 PRK00394 transcription factor; 21.7 3.2E+02 0.007 25.6 6.8 135 69-214 31-173 (179)
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=99.75 E-value=2.3e-18 Score=132.53 Aligned_cols=61 Identities=48% Similarity=0.752 Sum_probs=57.3
Q ss_pred CCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhcCCCcccCCCcc
Q 043551 71 SKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYWGTSTFTNFPVS 137 (408)
Q Consensus 71 S~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~G~~a~~NFP~~ 137 (408)
|+|+||+++++ |||+|+|+.+. ++++++||+|+|+||||+|||.++++++|..+.+|||.+
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 68999999998 99999999974 489999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.74 E-value=2.9e-18 Score=133.50 Aligned_cols=63 Identities=46% Similarity=0.773 Sum_probs=59.1
Q ss_pred CeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhcCCCcccCCCcchhh
Q 043551 72 KYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYWGTSTFTNFPVSEYE 140 (408)
Q Consensus 72 ~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~G~~a~~NFP~~dy~ 140 (408)
+|+||+++++ |||+|+|+++. .+++++||+|+|+||||+|||.++++++|..+.+|||.++|+
T Consensus 1 ~~kGV~~~~~-gkw~A~I~~~~-----~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPW-GKWVAEIRDPS-----KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCC-CeEEEEEEecC-----CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 5999999888 99999999964 488999999999999999999999999999999999999986
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.61 E-value=7e-16 Score=120.06 Aligned_cols=62 Identities=44% Similarity=0.566 Sum_probs=57.6
Q ss_pred ccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHhcCCcccCCCCccccc
Q 043551 166 SRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEHRGINAVTNFDISTYI 228 (408)
Q Consensus 166 yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l~G~~A~tNFp~~~Y~ 228 (408)
|+||+++ ++|||+|+|+...+++.++||+|+|+||||.|||.++++++|.++.+|||+++|.
T Consensus 2 ~kGV~~~-~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 2 YRGVRQR-PWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred EeeEEeC-CCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 7999975 6799999997655899999999999999999999999999999999999999985
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=99.59 E-value=1.6e-15 Score=116.61 Aligned_cols=61 Identities=44% Similarity=0.617 Sum_probs=54.3
Q ss_pred CcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHhcCCcccCCCCcc
Q 043551 164 GFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEHRGINAVTNFDIS 225 (408)
Q Consensus 164 g~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l~G~~A~tNFp~~ 225 (408)
+.|+||++++ +|||+|+|+....++.++||+|+|+||||.|||.++++++|.++.+|||++
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 3589999875 599999997544489999999999999999999999999999999999863
No 5
>PHA00280 putative NHN endonuclease
Probab=99.32 E-value=2.5e-12 Score=112.55 Aligned_cols=62 Identities=16% Similarity=0.116 Sum_probs=56.1
Q ss_pred hcccCCCCCCCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhcCCCcc
Q 043551 62 AAATTVKRSSKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYWGTSTF 131 (408)
Q Consensus 62 ~~~~~~~~sS~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~G~~a~ 131 (408)
+....++++|+|+||+|++..|||+|+|+.. ||+++||.|+++|+|+.||+ ++.+++|++|.
T Consensus 58 N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~-------gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 58 NMKTPKSNTSGLKGLSWSKEREMWRGTVTAE-------GKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred ccCCCCCCCCCCCeeEEecCCCeEEEEEEEC-------CEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 4556788999999999999999999999986 89999999999999999997 78899998775
No 6
>PHA00280 putative NHN endonuclease
Probab=99.31 E-value=2.3e-12 Score=112.76 Aligned_cols=101 Identities=13% Similarity=0.090 Sum_probs=79.2
Q ss_pred HHHHHHhHhhcCCCc---ccCCCc-chhhHHHHHhhhhhhhhhhhhh--hccCCCcccCceeccCCCcceeeeccccCCc
Q 043551 116 RAYDLAALKYWGTST---FTNFPV-SEYEKEIEIMKTVTREEYLATL--RRRSSGFSRGVSKHHHNRRWEARIGRVFGNK 189 (408)
Q Consensus 116 rAYD~AA~~~~G~~a---~~NFP~-~dy~~EI~eL~~vSkeE~va~l--Rrkssg~yRGVs~~~~~GkW~A~I~~~~~~k 189 (408)
+++-.+...++|+-- ...+.. ......+.+|+.++..|+.... ++.++++++||+|++..|||+|+|. +++|
T Consensus 13 ~~Hrlvw~~~~G~~P~g~~VdHidg~~~dnri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~--~~gK 90 (121)
T PHA00280 13 RRHIQVWEAANGPIPKGYYIDHIDGNPLNDALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVT--AEGK 90 (121)
T ss_pred hHhHhhhHHHHCCCCCCCEEEcCCCCCCCCcHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEE--ECCE
Confidence 455566667777632 122221 1234689999999999997754 4567788999999999999999994 7899
Q ss_pred ccccccCCCHHHHHhhhHHHHHHhcCCccc
Q 043551 190 YLYLGTYGTQEEAAHAYDIAAIEHRGINAV 219 (408)
Q Consensus 190 ~i~LGtF~TeEEAA~AYD~Aa~~l~G~~A~ 219 (408)
.++||.|+++|+|+.||+ ++.+++|++|.
T Consensus 91 ~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 91 QHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred EEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 999999999999999997 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=98.98 E-value=5e-10 Score=84.21 Aligned_cols=56 Identities=34% Similarity=0.384 Sum_probs=47.6
Q ss_pred CCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhcCC
Q 043551 71 SKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYWGT 128 (408)
Q Consensus 71 S~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~G~ 128 (408)
|+|+||++++..++|+|+|++... +. +++..+||.|+++++|++||+.++++++|+
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 689999999999999999998421 11 248899999999999999999999999874
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=98.75 E-value=9.7e-09 Score=77.18 Aligned_cols=53 Identities=32% Similarity=0.350 Sum_probs=45.9
Q ss_pred CcccCceeccCCCcceeeecccc-C--CcccccccCCCHHHHHhhhHHHHHHhcCC
Q 043551 164 GFSRGVSKHHHNRRWEARIGRVF-G--NKYLYLGTYGTQEEAAHAYDIAAIEHRGI 216 (408)
Q Consensus 164 g~yRGVs~~~~~GkW~A~I~~~~-~--~k~i~LGtF~TeEEAA~AYD~Aa~~l~G~ 216 (408)
++++||++++..++|+|+|+... + +++++||.|++++||++||+.++++++|+
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 35899999999999999997521 1 49999999999999999999999999874
No 9
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=41.65 E-value=57 Score=23.49 Aligned_cols=39 Identities=13% Similarity=0.289 Sum_probs=26.5
Q ss_pred ceEEEEe--cCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhh
Q 043551 84 RYEAHLW--DKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKY 125 (408)
Q Consensus 84 kW~A~I~--~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~ 125 (408)
+|...|. ++.+ ...++++-+.|.|..||-.+...+-..+
T Consensus 1 ~w~~~v~g~~~~~---Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDET---GKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCC---CCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 4666662 3311 1345677789999999999988766554
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=37.97 E-value=1.4e+02 Score=27.78 Aligned_cols=133 Identities=17% Similarity=0.132 Sum_probs=74.0
Q ss_pred CCCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhh--cCCCc--ccCCCcchhhHHHHH
Q 043551 70 SSKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKY--WGTST--FTNFPVSEYEKEIEI 145 (408)
Q Consensus 70 sS~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~--~G~~a--~~NFP~~dy~~EI~e 145 (408)
..+|.||..|...-+=.+.|+.. ||-+--|. .++|+|..|.++.+..+ .|-.. ..||-...-..-...
T Consensus 33 Pe~fpgli~R~~~P~~t~lIf~s-------GKivitGa-ks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v~NIvas~~l 104 (174)
T cd00652 33 PKRFPGVIMRLREPKTTALIFSS-------GKMVITGA-KSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCDL 104 (174)
T ss_pred CCccceEEEEcCCCcEEEEEECC-------CEEEEEec-CCHHHHHHHHHHHHHHHHHcCCCccccCceEEEEEEEEEEC
Confidence 36799999998767888888876 55544464 57888999998887666 34322 112211100000000
Q ss_pred hhhhhhhhhhhhhhc---cCCCcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHh
Q 043551 146 MKTVTREEYLATLRR---RSSGFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEH 213 (408)
Q Consensus 146 L~~vSkeE~va~lRr---kssg~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l 213 (408)
--.+..+.+....+. -....|.|+-++-...+=...| +..||-+-.|. .+++|+.+|+++....+
T Consensus 105 ~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~i~~~L 172 (174)
T cd00652 105 GFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEKIYPIL 172 (174)
T ss_pred CCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 001111122111221 1122467888765554555555 55666665665 78999999987665443
No 11
>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=36.84 E-value=1.6e+02 Score=27.59 Aligned_cols=134 Identities=13% Similarity=0.085 Sum_probs=75.9
Q ss_pred CCCCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhcCCC--cc--cCCCcchhhHHHH
Q 043551 69 RSSKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYWGTS--TF--TNFPVSEYEKEIE 144 (408)
Q Consensus 69 ~sS~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~G~~--a~--~NFP~~dy~~EI~ 144 (408)
+..+|.||..|-..-+=.+.|+.. ||-+-.| ..++++|..|-++.+..+..-. .. .+|-...-..- .
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~S-------GKiv~tG-aks~~~a~~a~~~~~~~L~~~g~~~~~~~~~~i~NIVas-~ 102 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFRS-------GKMVCTG-AKSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVAS-A 102 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEECC-------CeEEEEc-cCCHHHHHHHHHHHHHHHHhcCCCccCCCceEEEEEEEE-E
Confidence 346799999998767888888875 5544444 4789999999998876664322 11 11111110000 0
Q ss_pred Hh-hhhhhhhhhhhhhc--cCCCcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHhc
Q 043551 145 IM-KTVTREEYLATLRR--RSSGFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEHR 214 (408)
Q Consensus 145 eL-~~vSkeE~va~lRr--kssg~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l~ 214 (408)
.| -.+..+.+...++. -....|.|+.++-..-+=..-| +..||-+-.|. .++||+..|.++....+.
T Consensus 103 ~l~~~i~L~~la~~~~~~~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 103 DLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred EcCCccCHHHHHhhCCCCccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 00 01111122112221 1122467887765555555666 55677666665 789999999887766553
No 12
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=30.23 E-value=84 Score=31.76 Aligned_cols=120 Identities=18% Similarity=0.105 Sum_probs=60.6
Q ss_pred cccCCCCCHHHHHHHHHHHhHhhcCCCccc-------CCCcchhhHH---HHHhhhhhhhhhhhh-------hhccCCCc
Q 043551 103 GKQGAYDEEESAARAYDLAALKYWGTSTFT-------NFPVSEYEKE---IEIMKTVTREEYLAT-------LRRRSSGF 165 (408)
Q Consensus 103 ~~LGtF~teEeAArAYD~AA~~~~G~~a~~-------NFP~~dy~~E---I~eL~~vSkeE~va~-------lRrkssg~ 165 (408)
.+.|.|.+..+|-++-...+..++-=...+ +=|.-.|.-. -+-....+.++|... ++-. .-.
T Consensus 141 ~~~GpF~s~~~a~~~L~~l~~~frlC~~~~gl~~~~~~~pC~~~~igrC~G~C~g~es~e~y~~rv~~aL~~~~~~-~Wp 219 (286)
T PRK10545 141 NLFGLFANRRAALQALQSIADEQKLCYGLLGLEPLSRGRACFRSALKRCAGACCGKESHEAHALRLRASLERLRVV-CWP 219 (286)
T ss_pred cEEEEECCHHHHHHHHHHHHHHHccCccccccccccCCCCChhHHHhCCCcCcCCCCCHHHHHHHHHHHHHhcccc-cCC
Confidence 578999999999999999888873111101 1111111100 001122334444221 2221 111
Q ss_pred ccC-ceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHhcCCcccCCCCccccccccccCCC
Q 043551 166 SRG-VSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEHRGINAVTNFDISTYIRWLKPAAG 236 (408)
Q Consensus 166 yRG-Vs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l~G~~A~tNFp~~~Y~~~l~p~~~ 236 (408)
|.| |-.......+. ++. +-..++|||++.++++++.. ..+. ..||+..|--.+.+-..
T Consensus 220 ~~g~v~i~E~g~~~~-~~h--v~~~W~~lg~~~~~~~~~~l-------~~~~---~~fd~d~y~il~~~l~~ 278 (286)
T PRK10545 220 WQGAVALKEQGPEMT-QYH--IIQNWLWLGAVNSLEEAATL-------IRTP---AGFDHDGYKILCKPLLS 278 (286)
T ss_pred CCCCEEEEecCCCCc-eEE--EEeceEEecccCCHHHHHHH-------hcCC---CCcChHHHHHHHHHHhc
Confidence 222 22221222222 332 23569999999998886642 1222 46999888765555443
No 13
>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=29.91 E-value=50 Score=28.19 Aligned_cols=21 Identities=29% Similarity=0.366 Sum_probs=18.0
Q ss_pred cCCCCCHHHHHHHHHHHhHhh
Q 043551 105 QGAYDEEESAARAYDLAALKY 125 (408)
Q Consensus 105 LGtF~teEeAArAYD~AA~~~ 125 (408)
-|+|+|+|+|..-||+.+-.+
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999876544
No 14
>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=29.29 E-value=2.3e+02 Score=26.43 Aligned_cols=130 Identities=20% Similarity=0.152 Sum_probs=71.1
Q ss_pred CeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhh--cCCCc--ccCCCcchhhHHHHHhh
Q 043551 72 KYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKY--WGTST--FTNFPVSEYEKEIEIMK 147 (408)
Q Consensus 72 ~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~--~G~~a--~~NFP~~dy~~EI~eL~ 147 (408)
+|.||..|-..-+=.+-||.. || +..=...++|+|.+|.++.+..+ .|-.. ..||-...-..-...--
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~s-------GK-iviTGaks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~~~~ 106 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSS-------GK-ITITGATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCSMPF 106 (174)
T ss_pred CCCEEEEEecCCcEEEEEECC-------Ce-EEEEccCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEeCCC
Confidence 799999998777888888876 44 33334589999999999988766 33221 11222111000000000
Q ss_pred hhhhhhhhhh-hh--ccCCCcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHH
Q 043551 148 TVTREEYLAT-LR--RRSSGFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIE 212 (408)
Q Consensus 148 ~vSkeE~va~-lR--rkssg~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~ 212 (408)
.+..+++... ++ .-....+.|+.++-..-+=.+.| +..||-+-.|. .+++|+..|+++..-.
T Consensus 107 ~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~pi 171 (174)
T cd04517 107 PIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIYPI 171 (174)
T ss_pred cccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHH
Confidence 0111111111 01 01223467888764544444455 55666555555 7889999988765443
No 15
>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=26.94 E-value=57 Score=27.87 Aligned_cols=21 Identities=29% Similarity=0.324 Sum_probs=17.9
Q ss_pred cccCCCHHHHHhhhHHHHHHh
Q 043551 193 LGTYGTQEEAAHAYDIAAIEH 213 (408)
Q Consensus 193 LGtF~TeEEAA~AYD~Aa~~l 213 (408)
-|+|+|+|+|..-||...-.|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 599999999999999876544
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=21.91 E-value=90 Score=25.15 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=27.2
Q ss_pred cceeeeccccCCcccccccCCCHHHHHhhhHHHHHHhc
Q 043551 177 RWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEHR 214 (408)
Q Consensus 177 kW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l~ 214 (408)
.|-++|.-..-...+|.|-|.+.+||..+-......+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 57788853334477899999999999987654444443
No 17
>PRK00394 transcription factor; Reviewed
Probab=21.66 E-value=3.2e+02 Score=25.60 Aligned_cols=135 Identities=13% Similarity=0.103 Sum_probs=76.5
Q ss_pred CCCCeEEeeEcCCCCceEEEEecCCCCCCCCCcccccCCCCCHHHHHHHHHHHhHhhc--CCCcc--cCCCcchhhHHHH
Q 043551 69 RSSKYRGVSRHRWTGRYEAHLWDKGSWNPTQRKKGKQGAYDEEESAARAYDLAALKYW--GTSTF--TNFPVSEYEKEIE 144 (408)
Q Consensus 69 ~sS~yrGV~~~~~~gkW~A~I~~~~~~~~~~~k~~~LGtF~teEeAArAYD~AA~~~~--G~~a~--~NFP~~dy~~EI~ 144 (408)
+..+|-|+..|-..-+=.+.|+.. ||-+-.|. .++++|..|-++.+..+. |-... .+|-...-..-..
T Consensus 31 ePe~fpgli~Rl~~Pk~t~lIf~s-------GKiv~tGa-~S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVas~~ 102 (179)
T PRK00394 31 NPEQFPGLVYRLEDPKIAALIFRS-------GKVVCTGA-KSVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASAD 102 (179)
T ss_pred CcccCceEEEEecCCceEEEEEcC-------CcEEEEcc-CCHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEEEEE
Confidence 345799999998877888888876 56555566 467788888888776553 32211 1111111000000
Q ss_pred Hhhhhhhhhhhhhh--hc--cCCCcccCceeccCCCcceeeeccccCCcccccccCCCHHHHHhhhHHHHHHhc
Q 043551 145 IMKTVTREEYLATL--RR--RSSGFSRGVSKHHHNRRWEARIGRVFGNKYLYLGTYGTQEEAAHAYDIAAIEHR 214 (408)
Q Consensus 145 eL~~vSkeE~va~l--Rr--kssg~yRGVs~~~~~GkW~A~I~~~~~~k~i~LGtF~TeEEAA~AYD~Aa~~l~ 214 (408)
.--.+..+.+...+ +. -....|.|+.++-..-|=..-| +..||-+-.|. .++||+..|.++....+.
T Consensus 103 l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 173 (179)
T PRK00394 103 LGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKLE 173 (179)
T ss_pred cCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 00011112221112 11 1112467888766665666666 55677666665 789999999887766553
Done!