Query 019609
Match_columns 338
No_of_seqs 310 out of 1776
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 03:07:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019609.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019609hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00018 AP2 DNA-binding domain 99.7 4.3E-18 9.3E-23 127.6 6.7 59 158-217 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.7 1.5E-17 3.2E-22 126.1 7.8 61 159-220 1-63 (64)
3 smart00380 AP2 DNA-binding dom 99.7 9.9E-18 2.1E-22 127.0 6.4 63 251-313 1-63 (64)
4 cd00018 AP2 DNA-binding domain 99.7 1.9E-17 4.2E-22 124.0 6.7 61 250-310 1-61 (61)
5 PHA00280 putative NHN endonucl 99.5 4.3E-14 9.4E-19 120.3 8.1 65 146-211 55-119 (121)
6 PHA00280 putative NHN endonucl 99.4 1.8E-12 4E-17 110.4 8.4 103 195-304 12-119 (121)
7 PF00847 AP2: AP2 domain; Int 99.1 1.2E-10 2.5E-15 85.3 5.6 51 158-208 1-56 (56)
8 PF00847 AP2: AP2 domain; Int 98.9 5.2E-09 1.1E-13 76.5 6.3 52 250-301 1-56 (56)
9 cd04518 TBP_archaea archaeal T 81.2 42 0.00091 30.4 12.7 134 158-299 34-172 (174)
10 cd00652 TBP_TLF TATA box bindi 72.3 72 0.0016 28.8 11.5 134 158-298 34-172 (174)
11 cd04517 TLF TBP-like factors ( 69.7 87 0.0019 28.3 12.0 131 159-296 35-170 (174)
12 PRK00394 transcription factor; 66.2 1E+02 0.0023 28.0 11.9 132 158-298 33-172 (179)
13 PF08846 DUF1816: Domain of un 64.4 9.4 0.0002 29.8 3.5 37 262-298 9-45 (68)
14 PF14657 Integrase_AP2: AP2-li 54.5 43 0.00093 23.4 5.3 35 171-205 1-41 (46)
15 cd04516 TBP_eukaryotes eukaryo 49.7 2E+02 0.0044 26.0 11.9 131 158-295 34-168 (174)
16 PLN00062 TATA-box-binding prot 44.7 2.5E+02 0.0054 25.6 12.0 134 158-298 34-171 (179)
17 PRK10927 essential cell divisi 39.5 1E+02 0.0022 30.9 6.9 22 275-296 285-306 (319)
18 PF14657 Integrase_AP2: AP2-li 38.0 90 0.002 21.7 4.8 38 262-299 1-42 (46)
19 PF07384 DUF1497: Protein of u 35.1 75 0.0016 23.5 4.0 32 278-309 1-32 (59)
20 COG3087 FtsN Cell division pro 33.1 96 0.0021 30.2 5.6 26 183-210 193-218 (264)
21 PF08846 DUF1816: Domain of un 31.0 85 0.0019 24.5 4.0 29 170-198 8-38 (68)
22 PHA02601 int integrase; Provis 27.7 82 0.0018 30.0 4.2 41 163-205 3-46 (333)
23 PRK10545 nucleotide excision r 24.1 1.5E+02 0.0033 29.1 5.3 25 182-206 140-164 (286)
24 PF08471 Ribonuc_red_2_N: Clas 23.4 83 0.0018 26.0 2.8 21 278-298 70-90 (93)
25 cd00801 INT_P4 Bacteriophage P 23.0 2.8E+02 0.006 26.0 6.8 38 261-298 10-49 (357)
26 PF00352 TBP: Transcription fa 22.1 1.9E+02 0.0041 22.7 4.7 46 159-205 37-82 (86)
27 COG2101 SPT15 TATA-box binding 21.9 6.4E+02 0.014 23.4 11.4 134 156-298 38-179 (185)
28 PF08471 Ribonuc_red_2_N: Clas 21.9 94 0.002 25.7 2.8 21 185-205 70-90 (93)
29 PF05036 SPOR: Sporulation rel 21.7 59 0.0013 23.7 1.6 21 182-202 45-65 (76)
30 cd00801 INT_P4 Bacteriophage P 20.0 2.2E+02 0.0047 26.8 5.4 37 169-205 9-49 (357)
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=4.3e-18 Score=127.57 Aligned_cols=59 Identities=53% Similarity=0.885 Sum_probs=55.4
Q ss_pred CCeEEEEEecCCCeEEEEEEeC--CEEEecCCCCCHHHHHHHHHHHHHHhcCccCCcccccc
Q 019609 158 SQYRGVTFYRRTGRWESHIWDS--GKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSIE 217 (338)
Q Consensus 158 S~yrGV~~~r~~gkW~A~I~~~--gK~i~LGtF~T~eeAArAYD~Aa~~~~G~~a~~NFp~s 217 (338)
|+|+||++++ +|||+|+|+++ +|++|||+|+|+||||+|||.|+++++|..+.+|||.+
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 6899999765 59999999999 99999999999999999999999999999999999864
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.72 E-value=1.5e-17 Score=126.11 Aligned_cols=61 Identities=57% Similarity=0.945 Sum_probs=57.8
Q ss_pred CeEEEEEecCCCeEEEEEEe--CCEEEecCCCCCHHHHHHHHHHHHHHhcCccCCcccccccch
Q 019609 159 QYRGVTFYRRTGRWESHIWD--SGKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSIEDYE 220 (338)
Q Consensus 159 ~yrGV~~~r~~gkW~A~I~~--~gK~i~LGtF~T~eeAArAYD~Aa~~~~G~~a~~NFp~s~y~ 220 (338)
+|+||++ +++|||+|+|++ .++++|||+|+|+||||+|||.|+++++|..+.+|||.++|+
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 5899996 667999999999 899999999999999999999999999999999999999886
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.72 E-value=9.9e-18 Score=127.04 Aligned_cols=63 Identities=52% Similarity=0.769 Sum_probs=58.9
Q ss_pred cccCeeeeecccEEEEeccccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCcCCCCCCcch
Q 019609 251 KYRGVTLHKCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPSLYQ 313 (338)
Q Consensus 251 ~yrGV~~~k~gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aaikl~G~~a~tNFp~s~Y~ 313 (338)
+|+||++++.|+|+|+|+...+++.++||+|+|+||||+|||.|+++++|..+.+|||+++|.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 589999988899999996555899999999999999999999999999999999999999996
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=99.71 E-value=1.9e-17 Score=124.02 Aligned_cols=61 Identities=52% Similarity=0.797 Sum_probs=55.7
Q ss_pred CcccCeeeeecccEEEEeccccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCcCCCCCC
Q 019609 250 SKYRGVTLHKCGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAVTNFDPS 310 (338)
Q Consensus 250 S~yrGV~~~k~gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aaikl~G~~a~tNFp~s 310 (338)
|+|+||++++.|+|+|+|+....++.++||+|+|+||||+|||.|+++++|..+.+|||.+
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 6899999988899999995433389999999999999999999999999999999999875
No 5
>PHA00280 putative NHN endonuclease
Probab=99.51 E-value=4.3e-14 Score=120.30 Aligned_cols=65 Identities=20% Similarity=0.322 Sum_probs=59.0
Q ss_pred cccCCCCCCCCCCCeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHhcCccCC
Q 019609 146 LKKSRRGPRSRSSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEAD 211 (338)
Q Consensus 146 ~~k~~~~~~~~tS~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~~G~~a~ 211 (338)
..++++.+++++|||+||+|++..+||+|+|+++||+++||+|+++|+|+.||+ ++.+++|.+|+
T Consensus 55 N~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 55 NSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred HhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 455666778899999999999999999999999999999999999999999997 77889998774
No 6
>PHA00280 putative NHN endonuclease
Probab=99.37 E-value=1.8e-12 Score=110.36 Aligned_cols=103 Identities=16% Similarity=0.104 Sum_probs=79.0
Q ss_pred HHHHHHHHHHhcCccCC---ccccc-ccchhhhhhhcccchhhhhhhhccccCCCCCCCCcccCeeeee-cccEEEEecc
Q 019609 195 ARAYDRAAIKFRGAEAD---INFSI-EDYEDDLKQMSNLTKEEFVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQ 269 (338)
Q Consensus 195 ArAYD~Aa~~~~G~~a~---~NFp~-s~y~~eL~qLr~lSkEE~V~aLRRqs~g~~~~sS~yrGV~~~k-~gkW~A~I~~ 269 (338)
-+++..+...++|.-.. +.+.. ......+..|+.++..+...+.+.. ..++|+|+||+|++ .|||+|+|
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 44666777788885331 22211 2234567888888888887775544 46789999999986 79999999
Q ss_pred ccCceeeeccCCCCHHHHHHHHHHHHHHhcCCCCc
Q 019609 270 FLGKKYVYLGLFDTEVEAARAYDRAAVKCNGKDAV 304 (338)
Q Consensus 270 ~~~~k~~~LG~FdTeeEAArAYD~Aaikl~G~~a~ 304 (338)
..++|.++||+|+++|+|+.||+ ++.+++|..|.
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 78999999999999999999997 77899997664
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=99.11 E-value=1.2e-10 Score=85.33 Aligned_cols=51 Identities=33% Similarity=0.546 Sum_probs=46.9
Q ss_pred CCeEEEEEecCCCeEEEEEEeC-----CEEEecCCCCCHHHHHHHHHHHHHHhcCc
Q 019609 158 SQYRGVTFYRRTGRWESHIWDS-----GKQVYLGGFDTAHAAARAYDRAAIKFRGA 208 (338)
Q Consensus 158 S~yrGV~~~r~~gkW~A~I~~~-----gK~i~LGtF~T~eeAArAYD~Aa~~~~G~ 208 (338)
|+|+||+|++..++|+|.|++. +|.++||.|+++++|++|++.++..++|.
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 6899999999999999999983 49999999999999999999999999873
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=98.87 E-value=5.2e-09 Score=76.54 Aligned_cols=52 Identities=37% Similarity=0.554 Sum_probs=44.9
Q ss_pred CcccCeeeee-cccEEEEecccc-C--ceeeeccCCCCHHHHHHHHHHHHHHhcCC
Q 019609 250 SKYRGVTLHK-CGRWEARMGQFL-G--KKYVYLGLFDTEVEAARAYDRAAVKCNGK 301 (338)
Q Consensus 250 S~yrGV~~~k-~gkW~A~I~~~~-~--~k~~~LG~FdTeeEAArAYD~Aaikl~G~ 301 (338)
|+|+||++++ .++|+|+|+... + ++.++||.|++++||++||+.+.++++|.
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 6899999987 799999996531 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=81.23 E-value=42 Score=30.41 Aligned_cols=134 Identities=16% Similarity=0.225 Sum_probs=80.4
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHhcCcc--C--Ccccccccchhhhhhhcccchhh
Q 019609 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAE--A--DINFSIEDYEDDLKQMSNLTKEE 233 (338)
Q Consensus 158 S~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~~G~~--a--~~NFp~s~y~~eL~qLr~lSkEE 233 (338)
.+|.||.++-+.-+=.+.|+..||-+--|. .+.++|..|-++.+..+.... . ..+|....--.....-..+..+.
T Consensus 34 ~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGa-ks~~~a~~a~~~~~~~L~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~ 112 (174)
T cd04518 34 DQFPGLVYRLEDPKIAALIFRSGKMVCTGA-KSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVASADLGREVNLDA 112 (174)
T ss_pred CcCcEEEEEccCCcEEEEEECCCeEEEEcc-CCHHHHHHHHHHHHHHHHhcCCCccCCCceEEEEEEEEEEcCCccCHHH
Confidence 578899987777788889999999876664 678888888887766654322 1 12222211100000000112222
Q ss_pred hhhhhccccCCCCCCCCcccCeeeee-cccEEEEeccccCceeeeccCCCCHHHHHHHHHHHHHHhc
Q 019609 234 FVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKCN 299 (338)
Q Consensus 234 ~V~aLRRqs~g~~~~sS~yrGV~~~k-~gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aaikl~ 299 (338)
+...++ .. .=...+|.|+.++- .-+=..-| +..||-+-.|. .+++|+.+|.++-...+.
T Consensus 113 la~~~~-~~---~YePe~fpglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 113 IAIGLP-NA---EYEPEQFPGLVYRLDEPKVVLLL--FSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred HHhhCC-CC---ccCcccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 222222 11 11235888988764 34556666 88888887776 578899999888766553
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=72.34 E-value=72 Score=28.77 Aligned_cols=134 Identities=16% Similarity=0.172 Sum_probs=78.6
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHhc--CccC--Ccccccccchhhhhhhcccchhh
Q 019609 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFR--GAEA--DINFSIEDYEDDLKQMSNLTKEE 233 (338)
Q Consensus 158 S~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~~--G~~a--~~NFp~s~y~~eL~qLr~lSkEE 233 (338)
.+|.||.++-..-+=.+.|+..||-+--|. .+.++|..|.++.+..+. |... ..||....--.....-..+..+.
T Consensus 34 e~fpgli~R~~~P~~t~lIf~sGKivitGa-ks~~~~~~a~~~~~~~L~~~g~~~~~~~~~~v~NIvas~~l~~~i~L~~ 112 (174)
T cd00652 34 KRFPGVIMRLREPKTTALIFSSGKMVITGA-KSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCDLGFPIRLEE 112 (174)
T ss_pred CccceEEEEcCCCcEEEEEECCCEEEEEec-CCHHHHHHHHHHHHHHHHHcCCCccccCceEEEEEEEEEECCCcccHHH
Confidence 478899987777788899999999877775 467788888777766553 3221 23332211110000001122222
Q ss_pred hhhhhccccCCCCCCCCcccCeeeee-cccEEEEeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 019609 234 FVHVLRRQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (338)
Q Consensus 234 ~V~aLRRqs~g~~~~sS~yrGV~~~k-~gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aaikl 298 (338)
+....+.... =...+|.|+.++- .-+=..-| +..||-+-.|. .+++|+.+|+++-.-.+
T Consensus 113 la~~~~~~~~---YePe~fpgli~r~~~pk~t~lI--F~sGkvvitGa-ks~~~~~~a~~~i~~~L 172 (174)
T cd00652 113 LALKHPENAS---YEPELFPGLIYRMDEPKVVLLI--FVSGKIVITGA-KSREDIYEAVEKIYPIL 172 (174)
T ss_pred HHhhhhcccE---ECCccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 3322221111 1234788988874 33555666 78888777776 56889999987765443
No 11
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=69.67 E-value=87 Score=28.33 Aligned_cols=131 Identities=20% Similarity=0.202 Sum_probs=76.5
Q ss_pred CeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHhc--CccC--Ccccccccchhhhhhhcccchhhh
Q 019609 159 QYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFR--GAEA--DINFSIEDYEDDLKQMSNLTKEEF 234 (338)
Q Consensus 159 ~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~~--G~~a--~~NFp~s~y~~eL~qLr~lSkEE~ 234 (338)
+|.||.++-+.-+=.+.|+..||-+--| ..++++|.+|.++.+..+. |... ..||....--.....-..+..+++
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~sGKiviTG-aks~~~~~~a~~~~~~~l~~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~l 113 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSSGKITITG-ATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCSMPFPIRLDEL 113 (174)
T ss_pred CCCEEEEEecCCcEEEEEECCCeEEEEc-cCCHHHHHHHHHHHHHHHHHcCCCcccCCceEEEEEEEEEeCCCcccHHHH
Confidence 7889998777778889999999876555 4788899999888776653 3221 233432211000000001112222
Q ss_pred hhhhccccCCCCCCCCcccCeeeeec-ccEEEEeccccCceeeeccCCCCHHHHHHHHHHHHH
Q 019609 235 VHVLRRQSTGFPRGSSKYRGVTLHKC-GRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAV 296 (338)
Q Consensus 235 V~aLRRqs~g~~~~sS~yrGV~~~k~-gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aai 296 (338)
.....+... =...+|.|+.++-. -+=.+.| +..||-+-.|. .+++|+.+|+++-.-
T Consensus 114 a~~~~~~~~---YePE~fPgliyr~~~p~~t~lI--F~sGkivitGa-ks~~~~~~a~~~i~p 170 (174)
T cd04517 114 AAKNRSSAS---YEPELHPGVVYRITGPRATLSI--FSTGSVTVTGA-RSMEDVREAVEKIYP 170 (174)
T ss_pred HHhchhhcE---eCCccCCEEEEEECCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHH
Confidence 221111111 12347889888743 3445555 78888777775 568888888876543
No 12
>PRK00394 transcription factor; Reviewed
Probab=66.22 E-value=1e+02 Score=27.96 Aligned_cols=132 Identities=18% Similarity=0.245 Sum_probs=79.4
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHhc--CccC--Ccccccccchh--hhhhhcccch
Q 019609 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFR--GAEA--DINFSIEDYED--DLKQMSNLTK 231 (338)
Q Consensus 158 S~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~~--G~~a--~~NFp~s~y~~--eL~qLr~lSk 231 (338)
.+|-|+.++-+.-+=.+.|+..||-+--|.. ++++|..|-++.+..+. |... ..+|.....-. ++. ..+..
T Consensus 33 e~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~-S~~~a~~a~~~~~~~l~~~g~~~~~~~~~~i~NiVas~~l~--~~i~L 109 (179)
T PRK00394 33 EQFPGLVYRLEDPKIAALIFRSGKVVCTGAK-SVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASADLG--VELNL 109 (179)
T ss_pred ccCceEEEEecCCceEEEEEcCCcEEEEccC-CHHHHHHHHHHHHHHHHHcCCCccCCCceEEEEEEEEEEcC--CeEcH
Confidence 4688999877777888999999998888875 56677777777665553 3221 12232211100 011 01122
Q ss_pred hhhhhhhc-cccCCCCCCCCcccCeeeee-cccEEEEeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 019609 232 EEFVHVLR-RQSTGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (338)
Q Consensus 232 EE~V~aLR-Rqs~g~~~~sS~yrGV~~~k-~gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aaikl 298 (338)
+.+...+. +.. .=...+|.|+.++- .-|=..-| +..||-+-.|. .+++|+.+|.++-...+
T Consensus 110 ~~la~~~~~~~~---~YePe~fPglvyR~~~pk~~~lI--F~SGKvvitGa-ks~~~~~~a~~~i~~~l 172 (179)
T PRK00394 110 NAIAIGLGLENI---EYEPEQFPGLVYRLDDPKVVVLL--FGSGKLVITGA-KSEEDAEKAVEKILEKL 172 (179)
T ss_pred HHHHHhcCcCCc---EECcccCceEEEEecCCcEEEEE--EcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 22222221 111 11235888988874 34566666 88888887776 57889999988876655
No 13
>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=64.37 E-value=9.4 Score=29.75 Aligned_cols=37 Identities=22% Similarity=0.230 Sum_probs=29.3
Q ss_pred cEEEEeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 019609 262 RWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (338)
Q Consensus 262 kW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aaikl 298 (338)
.|.++|.-.......|.|-|+|.+||..+..-.+.-+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHH
Confidence 6999996666778999999999999998855444433
No 14
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=54.53 E-value=43 Score=23.36 Aligned_cols=35 Identities=26% Similarity=0.477 Sum_probs=26.8
Q ss_pred eEEEEEE-e---CC--EEEecCCCCCHHHHHHHHHHHHHHh
Q 019609 171 RWESHIW-D---SG--KQVYLGGFDTAHAAARAYDRAAIKF 205 (338)
Q Consensus 171 kW~A~I~-~---~g--K~i~LGtF~T~eeAArAYD~Aa~~~ 205 (338)
+|...|. . .| ++++-+.|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5777773 2 24 5889999999999999988776654
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=49.66 E-value=2e+02 Score=26.03 Aligned_cols=131 Identities=18% Similarity=0.235 Sum_probs=74.5
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHhc--CccC-Ccccccccchhhhhhhcccchhhh
Q 019609 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFR--GAEA-DINFSIEDYEDDLKQMSNLTKEEF 234 (338)
Q Consensus 158 S~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~~--G~~a-~~NFp~s~y~~eL~qLr~lSkEE~ 234 (338)
.+|.||.++-..-+=.+.|+..||-+--|. .++|+|..|.++.+..+. |-.. ..||...........-..+..+.+
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~SGKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~~~v~Nivat~~l~~~i~L~~l 112 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFSSGKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGL 112 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEECCCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEEEEEECCCcccHHHH
Confidence 478899987777788899999999877776 467788888887766653 3221 123322111110000011122222
Q ss_pred hhhhccccCCCCCCCCcccCeeeeec-ccEEEEeccccCceeeeccCCCCHHHHHHHHHHHH
Q 019609 235 VHVLRRQSTGFPRGSSKYRGVTLHKC-GRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAA 295 (338)
Q Consensus 235 V~aLRRqs~g~~~~sS~yrGV~~~k~-gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aa 295 (338)
........ .=....|.|+.++-. -+=...| +..||-+-.|. .+++|+.+|++.-.
T Consensus 113 a~~~~~~~---~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~a~~~i~ 168 (174)
T cd04516 113 AHAHKQFS---SYEPELFPGLIYRMVKPKIVLLI--FVSGKIVLTGA-KSREEIYQAFENIY 168 (174)
T ss_pred HHhChhcc---EeCCccCceEEEEecCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHH
Confidence 22111111 112357889887643 2334444 88888877775 56778888876543
No 16
>PLN00062 TATA-box-binding protein; Provisional
Probab=44.66 E-value=2.5e+02 Score=25.62 Aligned_cols=134 Identities=16% Similarity=0.155 Sum_probs=76.2
Q ss_pred CCeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHhcCccCC---cccccccchhhhhhhcccchhhh
Q 019609 158 SQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEAD---INFSIEDYEDDLKQMSNLTKEEF 234 (338)
Q Consensus 158 S~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~~G~~a~---~NFp~s~y~~eL~qLr~lSkEE~ 234 (338)
.+|-||.++-+.-+=.+.|+..||-+--|. .++++|..|.++.+..+....-. .||...........-..+..+.+
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~SGKiviTGa-ks~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~l 112 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFASGKMVCTGA-KSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGL 112 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEECCCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEEEECCCcccHHHH
Confidence 468899987778888899999999776664 67888888888877666332111 23322111110000001112222
Q ss_pred hhhhccccCCCCCCCCcccCeeeeec-ccEEEEeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 019609 235 VHVLRRQSTGFPRGSSKYRGVTLHKC-GRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (338)
Q Consensus 235 V~aLRRqs~g~~~~sS~yrGV~~~k~-gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aaikl 298 (338)
........ .=....|.|+.++-. -+=...| +..||-+-.|. .+++|+..|.+.-.-.+
T Consensus 113 a~~~~~~~---~YePE~fPgliyr~~~pk~~~li--F~sGkvvitGa-ks~~~~~~ai~~i~p~L 171 (179)
T PLN00062 113 AYAHGAFS---SYEPELFPGLIYRMKQPKIVLLI--FVSGKIVITGA-KVREEIYTAFENIYPVL 171 (179)
T ss_pred HHhchhhc---ccCcccCceEEEEeCCCcEEEEE--eCCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 21111111 112358889887643 2444455 88888887776 56778888876644333
No 17
>PRK10927 essential cell division protein FtsN; Provisional
Probab=39.46 E-value=1e+02 Score=30.87 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=17.9
Q ss_pred eeeccCCCCHHHHHHHHHHHHH
Q 019609 275 YVYLGLFDTEVEAARAYDRAAV 296 (338)
Q Consensus 275 ~~~LG~FdTeeEAArAYD~Aai 296 (338)
++.||-|.+.++|-++.++...
T Consensus 285 RVrVGPf~sr~eAe~a~~rLk~ 306 (319)
T PRK10927 285 RVVIGPVKGKENADSTLNRLKM 306 (319)
T ss_pred EEEeCCCCCHHHHHHHHHHHHH
Confidence 5679999999999999776543
No 18
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=37.99 E-value=90 Score=21.70 Aligned_cols=38 Identities=21% Similarity=0.121 Sum_probs=27.1
Q ss_pred cEEEEec-cc-cCc--eeeeccCCCCHHHHHHHHHHHHHHhc
Q 019609 262 RWEARMG-QF-LGK--KYVYLGLFDTEVEAARAYDRAAVKCN 299 (338)
Q Consensus 262 kW~A~I~-~~-~~~--k~~~LG~FdTeeEAArAYD~Aaikl~ 299 (338)
+|..+|. .. ..| ++++-+-|.|..||-.+..+....+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 4666661 11 123 57788899999999999988777653
No 19
>PF07384 DUF1497: Protein of unknown function (DUF1497); InterPro: IPR009972 This entry is represented by Bacteriophage r1t, Orf17. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.
Probab=35.06 E-value=75 Score=23.52 Aligned_cols=32 Identities=22% Similarity=0.357 Sum_probs=24.0
Q ss_pred ccCCCCHHHHHHHHHHHHHHhcCCCCcCCCCC
Q 019609 278 LGLFDTEVEAARAYDRAAVKCNGKDAVTNFDP 309 (338)
Q Consensus 278 LG~FdTeeEAArAYD~Aaikl~G~~a~tNFp~ 309 (338)
+|+||+..||.|.-..|...+-....+..|.+
T Consensus 1 mgyyd~~nearrisklas~~isseq~~kefe~ 32 (59)
T PF07384_consen 1 MGYYDKRNEARRISKLASQNISSEQNRKEFEI 32 (59)
T ss_pred CCcccchhHHHHHHHHHhcccchhhhhhhhhh
Confidence 58999999999998888876655545555543
No 20
>COG3087 FtsN Cell division protein [Cell division and chromosome partitioning]
Probab=33.13 E-value=96 Score=30.22 Aligned_cols=26 Identities=31% Similarity=0.468 Sum_probs=19.5
Q ss_pred EecCCCCCHHHHHHHHHHHHHHhcCccC
Q 019609 183 VYLGGFDTAHAAARAYDRAAIKFRGAEA 210 (338)
Q Consensus 183 i~LGtF~T~eeAArAYD~Aa~~~~G~~a 210 (338)
+..|.|.+.++|-.. +|-+.|.|.++
T Consensus 193 LQcGaFk~~~qAE~~--rA~LAmlG~ss 218 (264)
T COG3087 193 LQCGAFKTAEQAESV--RAQLAMLGISS 218 (264)
T ss_pred EeecccccHHHHHHH--HHHHHhccccc
Confidence 567999999999876 56666777443
No 21
>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=30.97 E-value=85 Score=24.46 Aligned_cols=29 Identities=28% Similarity=0.405 Sum_probs=23.0
Q ss_pred CeEEEEEE--eCCEEEecCCCCCHHHHHHHH
Q 019609 170 GRWESHIW--DSGKQVYLGGFDTAHAAARAY 198 (338)
Q Consensus 170 gkW~A~I~--~~gK~i~LGtF~T~eeAArAY 198 (338)
-.|=++|. .+....|.|=|.+.+||..+.
T Consensus 8 laWWveI~T~~P~ctYyFGPF~s~~eA~~~~ 38 (68)
T PF08846_consen 8 LAWWVEIETQNPNCTYYFGPFDSREEAEAAL 38 (68)
T ss_pred CcEEEEEEcCCCCEEEEeCCcCCHHHHHHHh
Confidence 34557776 467899999999999998763
No 22
>PHA02601 int integrase; Provisional
Probab=27.66 E-value=82 Score=29.99 Aligned_cols=41 Identities=22% Similarity=0.362 Sum_probs=28.3
Q ss_pred EEEecCCCeEEEEEEeC---CEEEecCCCCCHHHHHHHHHHHHHHh
Q 019609 163 VTFYRRTGRWESHIWDS---GKQVYLGGFDTAHAAARAYDRAAIKF 205 (338)
Q Consensus 163 V~~~r~~gkW~A~I~~~---gK~i~LGtF~T~eeAArAYD~Aa~~~ 205 (338)
|+ .+++|+|++.++.. |+++.. +|.|..||-...+.....+
T Consensus 3 ~~-~~~~g~w~~~~~~~~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 3 VR-KLKDGKWLCEIYPNGRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred eE-EcCCCCEEEEEEECCCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 44 46778999999864 676654 6899988876655544433
No 23
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=24.07 E-value=1.5e+02 Score=29.07 Aligned_cols=25 Identities=24% Similarity=0.219 Sum_probs=21.4
Q ss_pred EEecCCCCCHHHHHHHHHHHHHHhc
Q 019609 182 QVYLGGFDTAHAAARAYDRAAIKFR 206 (338)
Q Consensus 182 ~i~LGtF~T~eeAArAYD~Aa~~~~ 206 (338)
..++|.|.+..+|-.+-...+..++
T Consensus 140 ~~~~GpF~s~~~a~~~L~~l~~~fr 164 (286)
T PRK10545 140 PNLFGLFANRRAALQALQSIADEQK 164 (286)
T ss_pred CcEEEEECCHHHHHHHHHHHHHHHc
Confidence 4689999999999999888887773
No 24
>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=23.45 E-value=83 Score=26.02 Aligned_cols=21 Identities=33% Similarity=0.376 Sum_probs=17.7
Q ss_pred ccCCCCHHHHHHHHHHHHHHh
Q 019609 278 LGLFDTEVEAARAYDRAAVKC 298 (338)
Q Consensus 278 LG~FdTeeEAArAYD~Aaikl 298 (338)
-|+|+|++||..=||.-+..|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 699999999999999866544
No 25
>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=23.00 E-value=2.8e+02 Score=26.01 Aligned_cols=38 Identities=24% Similarity=0.242 Sum_probs=24.5
Q ss_pred ccEEEEeccccCceeeeccCCC--CHHHHHHHHHHHHHHh
Q 019609 261 GRWEARMGQFLGKKYVYLGLFD--TEVEAARAYDRAAVKC 298 (338)
Q Consensus 261 gkW~A~I~~~~~~k~~~LG~Fd--TeeEAArAYD~Aaikl 298 (338)
+.|+.++......+++.||.|+ +.++|..........+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 4688888432223467899995 6677776666655544
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=22.12 E-value=1.9e+02 Score=22.67 Aligned_cols=46 Identities=22% Similarity=0.367 Sum_probs=35.9
Q ss_pred CeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHh
Q 019609 159 QYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKF 205 (338)
Q Consensus 159 ~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~ 205 (338)
+|.||.++-..-+-.+.|+..||-+..|. .+.++|..|.+.....+
T Consensus 37 ~fpgl~~r~~~p~~t~~IF~sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIFSSGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TESSEEEEETTTTEEEEEETTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEEcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 56788877777788899999999887775 67888888888766544
No 27
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=21.95 E-value=6.4e+02 Score=23.36 Aligned_cols=134 Identities=22% Similarity=0.278 Sum_probs=80.8
Q ss_pred CCCCeEEEEEecCCCeEEEEEEeCCEEEecCCCCCHHHHHHHHHHHHHHhcCccCCccccccc------chhhhhhhccc
Q 019609 156 RSSQYRGVTFYRRTGRWESHIWDSGKQVYLGGFDTAHAAARAYDRAAIKFRGAEADINFSIED------YEDDLKQMSNL 229 (338)
Q Consensus 156 ~tS~yrGV~~~r~~gkW~A~I~~~gK~i~LGtF~T~eeAArAYD~Aa~~~~G~~a~~NFp~s~------y~~eL~qLr~l 229 (338)
+..+|.|+-++-..-|=.+-|...||-+-.|. .+.|++.+|-.+-+..++.......|.+.- ...+|...-++
T Consensus 38 nP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGa-Ks~ed~~~av~~~~~~L~~~g~~~~~~p~i~iQNIVaSadL~~~lnL 116 (185)
T COG2101 38 NPEQFPGLVYRLEEPKTAALIFRSGKVVCTGA-KSVEDVHRAVKKLAKKLKDGGIDIDFEPEIKVQNIVASADLGVELNL 116 (185)
T ss_pred CHhHCCeeEEEecCCcceEEEEecCcEEEecc-CcHHHHHHHHHHHHHHHHhcCcCcCCCCceEEEEEEEEeccCccccH
Confidence 45689999988888999999999999888876 677788888777777766532222221100 00011111111
Q ss_pred chhhhhhhhccc-cCCCCCCCCcccCeeeee-cccEEEEeccccCceeeeccCCCCHHHHHHHHHHHHHHh
Q 019609 230 TKEEFVHVLRRQ-STGFPRGSSKYRGVTLHK-CGRWEARMGQFLGKKYVYLGLFDTEVEAARAYDRAAVKC 298 (338)
Q Consensus 230 SkEE~V~aLRRq-s~g~~~~sS~yrGV~~~k-~gkW~A~I~~~~~~k~~~LG~FdTeeEAArAYD~Aaikl 298 (338)
+.+.-.+.-. .. =-.-+|.|.-++- .-|-+.-| +..||-+.-|. .+++||.+|+.+...++
T Consensus 117 --~~iA~~lg~e~~e---YEPEqFPGLVYRl~~P~VV~Li--F~SGK~ViTGa-K~~ed~~~Av~~i~~~L 179 (185)
T COG2101 117 --NAIAIGLGLENIE---YEPEQFPGLVYRLDEPRVVLLL--FGSGKLVITGA-KSEEDAEQAVEKIQSRL 179 (185)
T ss_pred --HHHHHhccccccc---cccccCCeeEEEcCCCCEEEEE--ecCCcEEEecC-CCHHHHHHHHHHHHHHH
Confidence 1111111000 00 0113778876663 45666667 77888777776 56889999999877666
No 28
>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=21.88 E-value=94 Score=25.73 Aligned_cols=21 Identities=29% Similarity=0.306 Sum_probs=17.9
Q ss_pred cCCCCCHHHHHHHHHHHHHHh
Q 019609 185 LGGFDTAHAAARAYDRAAIKF 205 (338)
Q Consensus 185 LGtF~T~eeAArAYD~Aa~~~ 205 (338)
-|+|+|+++|..=||.....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 599999999999999876554
No 29
>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=21.70 E-value=59 Score=23.68 Aligned_cols=21 Identities=24% Similarity=0.377 Sum_probs=17.2
Q ss_pred EEecCCCCCHHHHHHHHHHHH
Q 019609 182 QVYLGGFDTAHAAARAYDRAA 202 (338)
Q Consensus 182 ~i~LGtF~T~eeAArAYD~Aa 202 (338)
++.+|.|.+.++|..+-....
T Consensus 45 rV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 45 RVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEECCECTCCHHHHHHHHHH
T ss_pred EEEECCCCCHHHHHHHHHHHh
Confidence 788999999999988766544
No 30
>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=20.03 E-value=2.2e+02 Score=26.75 Aligned_cols=37 Identities=22% Similarity=0.354 Sum_probs=26.1
Q ss_pred CCeEEEEEEeCCE--EEecCCCC--CHHHHHHHHHHHHHHh
Q 019609 169 TGRWESHIWDSGK--QVYLGGFD--TAHAAARAYDRAAIKF 205 (338)
Q Consensus 169 ~gkW~A~I~~~gK--~i~LGtF~--T~eeAArAYD~Aa~~~ 205 (338)
.+.|...++.+|+ ++.||+|+ +.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 3569999888876 46789995 6677776665554444
Done!