Query 026607
Match_columns 236
No_of_seqs 262 out of 1215
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:14:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026607.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026607hhsearch_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 99.8 6.5E-21 1.4E-25 135.9 7.2 61 108-169 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 8.8E-20 1.9E-24 131.7 8.0 61 109-170 1-61 (64)
3 PHA00280 putative NHN endonucl 99.4 3.9E-13 8.4E-18 109.8 7.0 57 103-163 62-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 2.1E-11 4.5E-16 84.8 5.8 53 108-160 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 80.3 5.7 0.00012 26.7 5.1 39 120-158 1-42 (46)
6 PHA02601 int integrase; Provis 78.8 3.4 7.5E-05 36.9 4.7 45 112-157 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 48.5 45 0.00098 29.3 5.6 40 118-158 9-50 (357)
8 PF08471 Ribonuc_red_2_N: Clas 46.0 22 0.00047 28.4 2.8 20 138-157 71-90 (93)
9 PF08846 DUF1816: Domain of un 45.5 45 0.00098 25.1 4.3 41 120-161 9-49 (68)
10 PF05036 SPOR: Sporulation rel 43.7 14 0.00031 25.5 1.4 22 133-154 44-65 (76)
11 cd04516 TBP_eukaryotes eukaryo 43.2 97 0.0021 26.8 6.7 47 108-158 34-81 (174)
12 PRK09692 integrase; Provisiona 32.6 1.3E+02 0.0028 28.1 6.3 41 113-153 33-78 (413)
13 cd00652 TBP_TLF TATA box bindi 31.1 1.6E+02 0.0034 25.3 6.0 47 108-158 34-81 (174)
14 PLN00062 TATA-box-binding prot 30.1 2.1E+02 0.0044 25.0 6.6 47 108-158 34-81 (179)
15 PF13356 DUF4102: Domain of un 28.5 1.4E+02 0.0031 22.1 4.8 38 119-157 35-74 (89)
16 COG0197 RplP Ribosomal protein 27.9 85 0.0019 26.9 3.8 36 121-160 96-131 (146)
17 PF06112 Herpes_capsid: Gammah 27.6 2.2E+02 0.0047 24.6 6.2 19 145-163 53-71 (147)
18 PF14112 DUF4284: Domain of un 26.8 34 0.00073 27.8 1.2 18 133-150 2-19 (122)
19 PF00352 TBP: Transcription fa 25.9 1.5E+02 0.0032 22.2 4.4 45 109-157 37-82 (86)
20 PHA03308 transcriptional regul 24.1 78 0.0017 34.2 3.4 9 144-152 1202-1210(1463)
21 cd04517 TLF TBP-like factors ( 22.0 3.1E+02 0.0067 23.6 6.2 45 109-157 35-80 (174)
22 PF09954 DUF2188: Uncharacteri 21.5 2.7E+02 0.0058 19.5 4.8 39 113-156 3-41 (62)
23 PRK00394 transcription factor; 20.0 3.1E+02 0.0066 23.8 5.8 47 108-158 33-80 (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=99.84 E-value=6.5e-21 Score=135.92 Aligned_cols=61 Identities=69% Similarity=1.253 Sum_probs=56.5
Q ss_pred CceeEEEeCCCCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q 026607 108 ARYRGVRRRPWGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMRGSKAKLNFPHL 169 (236)
Q Consensus 108 S~YRGVr~r~~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~G~~A~lNFP~~ 169 (236)
|+||||+++++|||+|+|+++. .|+++|||+|+|+||||+|||.|+++++|.++.+|||+.
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~-~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPS-GGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCC-CCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 6899999999999999999943 279999999999999999999999999999999999973
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.81 E-value=8.8e-20 Score=131.74 Aligned_cols=61 Identities=67% Similarity=1.298 Sum_probs=56.9
Q ss_pred ceeEEEeCCCCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhcCCCCCCCCCCCC
Q 026607 109 RYRGVRRRPWGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMRGSKAKLNFPHLI 170 (236)
Q Consensus 109 ~YRGVr~r~~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~G~~A~lNFP~~~ 170 (236)
+|+||+++++|||+|+|+++. +|+.+|||+|+|+||||+|||.|+++++|.++.+|||...
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~-~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~ 61 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPS-KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSL 61 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecC-CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCcc
Confidence 599999988999999999865 5799999999999999999999999999999999999854
No 3
>PHA00280 putative NHN endonuclease
Probab=99.41 E-value=3.9e-13 Score=109.77 Aligned_cols=57 Identities=12% Similarity=0.148 Sum_probs=51.5
Q ss_pred CCCCCCceeEEEeCC-CCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhcCCCCC
Q 026607 103 DTLVGARYRGVRRRP-WGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMRGSKAK 163 (236)
Q Consensus 103 ~~~~~S~YRGVr~r~-~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~G~~A~ 163 (236)
.+.++|+|+||++.+ .|||+|+|++ +||+++||.|+++|+|+.||+ ++.++||++|.
T Consensus 62 ~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 62 PKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 456789999999765 7999999999 999999999999999999997 77889999985
No 4
>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=99.22 E-value=2.1e-11 Score=84.84 Aligned_cols=53 Identities=30% Similarity=0.441 Sum_probs=46.4
Q ss_pred CceeEEEeCC-CCcEEEEEeCCCCCC--eeeecCCCCCHHHHHHHHHHHHHhhcCC
Q 026607 108 ARYRGVRRRP-WGKFVAEIRDPKKNG--TRIWLGTYNTPEDAALAYDRAAFNMRGS 160 (236)
Q Consensus 108 S~YRGVr~r~-~GKW~A~I~~~~k~G--krv~LGtFdT~EEAA~AYD~AA~~l~G~ 160 (236)
|+|+||++.+ .++|+|+|++...+| ++++||.|++++||++||+.++..++|+
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 6899999665 799999999854444 8999999999999999999999999884
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=80.28 E-value=5.7 Score=26.70 Aligned_cols=39 Identities=10% Similarity=0.147 Sum_probs=29.5
Q ss_pred cEEEEEe-CCCCCC--eeeecCCCCCHHHHHHHHHHHHHhhc
Q 026607 120 KFVAEIR-DPKKNG--TRIWLGTYNTPEDAALAYDRAAFNMR 158 (236)
Q Consensus 120 KW~A~I~-~~~k~G--krv~LGtFdT~EEAA~AYD~AA~~l~ 158 (236)
+|...|. ....+| ++++-+-|.|..||-.+..++...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5888883 333344 67899999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=78.83 E-value=3.4 Score=36.88 Aligned_cols=45 Identities=24% Similarity=0.317 Sum_probs=31.5
Q ss_pred EEEeCCCCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhh
Q 026607 112 GVRRRPWGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNM 157 (236)
Q Consensus 112 GVr~r~~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l 157 (236)
+|++.+.|+|+++++.....|+++.. +|.|..||....+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 56677789999999864335777653 6999998876665544433
No 7
>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=48.54 E-value=45 Score=29.27 Aligned_cols=40 Identities=23% Similarity=0.185 Sum_probs=27.6
Q ss_pred CCcEEEEEeCCCCCCeeeecCCCC--CHHHHHHHHHHHHHhhc
Q 026607 118 WGKFVAEIRDPKKNGTRIWLGTYN--TPEDAALAYDRAAFNMR 158 (236)
Q Consensus 118 ~GKW~A~I~~~~k~Gkrv~LGtFd--T~EEAA~AYD~AA~~l~ 158 (236)
.+.|+.+++...+ .+++.||+|+ +.++|.....+....+.
T Consensus 9 ~~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 9 SKSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CEEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 4569999988332 2467899995 67777777766555553
No 8
>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=45.97 E-value=22 Score=28.42 Aligned_cols=20 Identities=35% Similarity=0.612 Sum_probs=18.1
Q ss_pred CCCCCHHHHHHHHHHHHHhh
Q 026607 138 GTYNTPEDAALAYDRAAFNM 157 (236)
Q Consensus 138 GtFdT~EEAA~AYD~AA~~l 157 (236)
|+|+|+|+|..-||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999987755
No 9
>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=45.50 E-value=45 Score=25.10 Aligned_cols=41 Identities=17% Similarity=0.310 Sum_probs=28.6
Q ss_pred cEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhcCCC
Q 026607 120 KFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMRGSK 161 (236)
Q Consensus 120 KW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~G~~ 161 (236)
.|-++|.-..=+ ..+|.|-|+|.+||..+.-.-...+..+.
T Consensus 9 aWWveI~T~~P~-ctYyFGPF~s~~eA~~~~~gyieDL~~Eg 49 (68)
T PF08846_consen 9 AWWVEIETQNPN-CTYYFGPFDSREEAEAALPGYIEDLESEG 49 (68)
T ss_pred cEEEEEEcCCCC-EEEEeCCcCCHHHHHHHhccHHHHHHhhC
Confidence 366888753222 67999999999999998765555554433
No 10
>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=43.69 E-value=14 Score=25.51 Aligned_cols=22 Identities=23% Similarity=0.457 Sum_probs=18.5
Q ss_pred eeeecCCCCCHHHHHHHHHHHH
Q 026607 133 TRIWLGTYNTPEDAALAYDRAA 154 (236)
Q Consensus 133 krv~LGtFdT~EEAA~AYD~AA 154 (236)
-+|.+|.|++.+||..+-.+..
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 4789999999999988877655
No 11
>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=43.20 E-value=97 Score=26.76 Aligned_cols=47 Identities=26% Similarity=0.232 Sum_probs=37.3
Q ss_pred CceeEEEeCC-CCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhc
Q 026607 108 ARYRGVRRRP-WGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMR 158 (236)
Q Consensus 108 S~YRGVr~r~-~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~ 158 (236)
.+|-||..|- .-+=.+.|.. .||-+.-|.. ++|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~---SGKiviTGak-s~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFS---SGKMVCTGAK-SEDDSKLAARKYARIIQ 81 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEEC---CCeEEEEecC-CHHHHHHHHHHHHHHHH
Confidence 4688986444 4566788887 8999988986 89999999999887774
No 12
>PRK09692 integrase; Provisional
Probab=32.56 E-value=1.3e+02 Score=28.07 Aligned_cols=41 Identities=20% Similarity=0.177 Sum_probs=24.0
Q ss_pred EEeCCCC--cEEEEEeCCC-CCCeeeecCCCC--CHHHHHHHHHHH
Q 026607 113 VRRRPWG--KFVAEIRDPK-KNGTRIWLGTYN--TPEDAALAYDRA 153 (236)
Q Consensus 113 Vr~r~~G--KW~A~I~~~~-k~Gkrv~LGtFd--T~EEAA~AYD~A 153 (236)
|+.++.| .|..+.+.+. ++.+++-||.|. |..||..+..++
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~ 78 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAES 78 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHH
Confidence 3444544 4998876432 222347899999 666665544443
No 13
>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=31.07 E-value=1.6e+02 Score=25.33 Aligned_cols=47 Identities=32% Similarity=0.287 Sum_probs=36.9
Q ss_pred CceeEEEeCC-CCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhc
Q 026607 108 ARYRGVRRRP-WGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMR 158 (236)
Q Consensus 108 S~YRGVr~r~-~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~ 158 (236)
.+|.||..|- .-+=.+.|.. +||-+.-|.. +.|+|..|.++.+..+.
T Consensus 34 e~fpgli~R~~~P~~t~lIf~---sGKivitGak-s~~~~~~a~~~~~~~L~ 81 (174)
T cd00652 34 KRFPGVIMRLREPKTTALIFS---SGKMVITGAK-SEEDAKLAARKYARILQ 81 (174)
T ss_pred CccceEEEEcCCCcEEEEEEC---CCEEEEEecC-CHHHHHHHHHHHHHHHH
Confidence 5688987554 4566777777 8999888986 89999999999887773
No 14
>PLN00062 TATA-box-binding protein; Provisional
Probab=30.07 E-value=2.1e+02 Score=24.96 Aligned_cols=47 Identities=26% Similarity=0.230 Sum_probs=36.3
Q ss_pred CceeEEEeCC-CCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhc
Q 026607 108 ARYRGVRRRP-WGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMR 158 (236)
Q Consensus 108 S~YRGVr~r~-~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~ 158 (236)
.+|-||..|- .-|=.+-|.. .||-+.-|. .++|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFA---SGKMVCTGA-KSEHDSKLAARKYARIIQ 81 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 4688986443 4566788887 888888786 589999999999887774
No 15
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=28.52 E-value=1.4e+02 Score=22.14 Aligned_cols=38 Identities=24% Similarity=0.151 Sum_probs=23.6
Q ss_pred CcEEEEEeCCCCCCeeeecCCCCC--HHHHHHHHHHHHHhh
Q 026607 119 GKFVAEIRDPKKNGTRIWLGTYNT--PEDAALAYDRAAFNM 157 (236)
Q Consensus 119 GKW~A~I~~~~k~Gkrv~LGtFdT--~EEAA~AYD~AA~~l 157 (236)
..|..+.+...+ .+++-||.|.. ..||..........+
T Consensus 35 kt~~~r~~~~gk-~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 35 KTFYFRYRINGK-RRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEEETTE-EEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred eEEEEEEEecce-EEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 348888877222 25789999976 556655555444444
No 16
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=27.92 E-value=85 Score=26.90 Aligned_cols=36 Identities=22% Similarity=0.155 Sum_probs=29.8
Q ss_pred EEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhcCC
Q 026607 121 FVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMRGS 160 (236)
Q Consensus 121 W~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~G~ 160 (236)
|+|+|.. |+.++-=..+.++.|..|..+|+.+|=+.
T Consensus 96 waArVkp----G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 96 WAARVKP----GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEecC----CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 9999985 67777777788999999999999887544
No 17
>PF06112 Herpes_capsid: Gammaherpesvirus capsid protein; InterPro: IPR009299 This family consists of several Gammaherpesvirus capsid proteins. The exact function of this family is unknown.; GO: 0019028 viral capsid
Probab=27.63 E-value=2.2e+02 Score=24.59 Aligned_cols=19 Identities=26% Similarity=0.298 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHhhcCCCCC
Q 026607 145 DAALAYDRAAFNMRGSKAK 163 (236)
Q Consensus 145 EAA~AYD~AA~~l~G~~A~ 163 (236)
-|...||.-+.+.+|-.-+
T Consensus 53 ~Aq~~Yd~yv~~~~Gv~RK 71 (147)
T PF06112_consen 53 IAQHCYDQYVRRTHGVRRK 71 (147)
T ss_pred hHHHHHHHHHHHHcCcchh
Confidence 3567788888888886543
No 18
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=26.83 E-value=34 Score=27.76 Aligned_cols=18 Identities=17% Similarity=0.724 Sum_probs=13.6
Q ss_pred eeeecCCCCCHHHHHHHH
Q 026607 133 TRIWLGTYNTPEDAALAY 150 (236)
Q Consensus 133 krv~LGtFdT~EEAA~AY 150 (236)
..||||+|.+++|-..=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 369999999887765543
No 19
>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=25.86 E-value=1.5e+02 Score=22.23 Aligned_cols=45 Identities=22% Similarity=0.235 Sum_probs=34.3
Q ss_pred ceeEEEeCC-CCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhh
Q 026607 109 RYRGVRRRP-WGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNM 157 (236)
Q Consensus 109 ~YRGVr~r~-~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l 157 (236)
+|.||..|- .-+-.+.|.. .||-+..|. .+.|||..|.++....+
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 577876443 3466777777 899999887 49999999999877655
No 20
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=24.09 E-value=78 Score=34.21 Aligned_cols=9 Identities=44% Similarity=0.434 Sum_probs=4.1
Q ss_pred HHHHHHHHH
Q 026607 144 EDAALAYDR 152 (236)
Q Consensus 144 EEAA~AYD~ 152 (236)
.+.|+|.|.
T Consensus 1202 rdvaramda 1210 (1463)
T PHA03308 1202 RDVARAMDA 1210 (1463)
T ss_pred HHHHHHHhc
Confidence 344455443
No 21
>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=21.96 E-value=3.1e+02 Score=23.59 Aligned_cols=45 Identities=29% Similarity=0.271 Sum_probs=35.8
Q ss_pred ceeEEEeCC-CCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhh
Q 026607 109 RYRGVRRRP-WGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNM 157 (236)
Q Consensus 109 ~YRGVr~r~-~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l 157 (236)
+|.||..|- .-|=.+-|+. +||-+.-|. .++|+|+.|.++.+..+
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~---sGKiviTGa-ks~~~~~~a~~~~~~~l 80 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS---SGKITITGA-TSEEEAKQAARRAARLL 80 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC---CCeEEEEcc-CCHHHHHHHHHHHHHHH
Confidence 789987553 4567788887 888887776 69999999999887777
No 22
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=21.48 E-value=2.7e+02 Score=19.48 Aligned_cols=39 Identities=23% Similarity=0.153 Sum_probs=25.5
Q ss_pred EEeCCCCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHh
Q 026607 113 VRRRPWGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFN 156 (236)
Q Consensus 113 Vr~r~~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~ 156 (236)
|..+..|.|....-. ...-..+|+|.+||..+=...|..
T Consensus 3 V~p~~~~~W~v~~eg-----~~ra~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG-----AKRASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeCC-----CcccccccCcHHHHHHHHHHHHHh
Confidence 444445779888764 223378999999987665554443
No 23
>PRK00394 transcription factor; Reviewed
Probab=20.02 E-value=3.1e+02 Score=23.77 Aligned_cols=47 Identities=21% Similarity=0.185 Sum_probs=36.8
Q ss_pred CceeEEEeCC-CCcEEEEEeCCCCCCeeeecCCCCCHHHHHHHHHHHHHhhc
Q 026607 108 ARYRGVRRRP-WGKFVAEIRDPKKNGTRIWLGTYNTPEDAALAYDRAAFNMR 158 (236)
Q Consensus 108 S~YRGVr~r~-~GKW~A~I~~~~k~Gkrv~LGtFdT~EEAA~AYD~AA~~l~ 158 (236)
.+|-|+..|- .-+=.+.|.. .||-+.-|.. ++|+|..|-++.+..+.
T Consensus 33 e~fpgli~Rl~~Pk~t~lIf~---sGKiv~tGa~-S~~~a~~a~~~~~~~l~ 80 (179)
T PRK00394 33 EQFPGLVYRLEDPKIAALIFR---SGKVVCTGAK-SVEDLHEAVKIIIKKLK 80 (179)
T ss_pred ccCceEEEEecCCceEEEEEc---CCcEEEEccC-CHHHHHHHHHHHHHHHH
Confidence 4688886443 4567788887 8999999987 89999999998877663
Done!