Query 018103
Match_columns 360
No_of_seqs 292 out of 1270
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 06:10:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018103.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018103hhsearch_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 9.7E-20 2.1E-24 137.4 7.8 60 164-223 1-60 (61)
2 smart00380 AP2 DNA-binding dom 99.8 2.7E-19 5.9E-24 136.6 8.1 62 165-226 1-62 (64)
3 PHA00280 putative NHN endonucl 99.5 8.7E-15 1.9E-19 126.3 7.0 72 143-219 48-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 1.4E-10 3E-15 85.4 6.4 52 164-215 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 79.0 8.8 0.00019 27.5 6.0 38 176-213 1-42 (46)
6 PHA02601 int integrase; Provis 68.7 7.8 0.00017 36.9 4.6 44 168-212 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 57.0 24 0.00052 33.1 5.5 40 174-213 9-50 (357)
8 PF08846 DUF1816: Domain of un 47.5 42 0.00091 27.0 4.7 40 176-215 9-48 (68)
9 PF13356 DUF4102: Domain of un 46.2 56 0.0012 26.1 5.3 37 176-212 36-74 (89)
10 PRK09692 integrase; Provisiona 43.4 60 0.0013 32.3 6.2 44 169-212 33-82 (413)
11 PF10729 CedA: Cell division a 41.9 43 0.00094 27.4 4.0 41 161-204 28-68 (80)
12 PF05036 SPOR: Sporulation rel 40.1 36 0.00077 25.1 3.1 24 186-209 42-65 (76)
13 PF08471 Ribonuc_red_2_N: Clas 27.7 64 0.0014 27.5 3.0 42 163-212 49-90 (93)
14 cd04516 TBP_eukaryotes eukaryo 26.1 3.1E+02 0.0067 25.3 7.4 58 164-224 34-92 (174)
15 PLN00062 TATA-box-binding prot 25.7 3E+02 0.0066 25.5 7.3 57 164-223 34-91 (179)
16 PRK10113 cell division modulat 25.4 58 0.0013 26.6 2.2 40 162-204 29-68 (80)
17 COG0197 RplP Ribosomal protein 24.7 96 0.0021 28.3 3.7 36 177-215 96-131 (146)
18 PF00352 TBP: Transcription fa 23.6 2.4E+02 0.0051 22.6 5.5 47 164-213 36-83 (86)
19 cd04517 TLF TBP-like factors ( 22.3 3.5E+02 0.0076 24.8 7.0 46 165-213 35-81 (174)
20 KOG3422 Mitochondrial ribosoma 21.4 1.8E+02 0.0039 28.3 5.1 38 176-215 133-170 (221)
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=99.80 E-value=9.7e-20 Score=137.36 Aligned_cols=60 Identities=73% Similarity=1.177 Sum_probs=56.5
Q ss_pred CCceeeEECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCccCCCCC
Q 018103 164 KLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLRGEFARLNFPH 223 (360)
Q Consensus 164 S~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~G~~A~lNFP~ 223 (360)
|+||||+++++|||+|+|+++..|+++|||+|+|+||||+|||+|+++++|.++++|||.
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~ 60 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPD 60 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCC
Confidence 689999888889999999995559999999999999999999999999999999999996
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.79 E-value=2.7e-19 Score=136.64 Aligned_cols=62 Identities=71% Similarity=1.161 Sum_probs=58.6
Q ss_pred CceeeEECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCccCCCCCCCC
Q 018103 165 LYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLRGEFARLNFPHLKH 226 (360)
Q Consensus 165 ~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~G~~A~lNFP~~~~ 226 (360)
+|+||+++++|||+|+|+++.+|+++|||+|+|+||||+|||.|+++++|.++++|||...+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y 62 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLY 62 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccC
Confidence 59999888899999999999999999999999999999999999999999999999997654
No 3
>PHA00280 putative NHN endonuclease
Probab=99.55 E-value=8.7e-15 Score=126.28 Aligned_cols=72 Identities=18% Similarity=0.243 Sum_probs=64.0
Q ss_pred CCCCCCcCCcCCCCCCCCCCCCCceee-EECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCccC
Q 018103 143 LLSPKAVPMKHVSNAQVAKPTKLYRGV-RQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLRGEFARL 219 (360)
Q Consensus 143 ~l~~r~~pmK~~~~~~~~~~tS~YRGV-r~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~G~~A~l 219 (360)
-+.++.++++++... +.++|+|+|| +++..|||+|+|++ +||+++||.|+++|+|+.||+ ++.+|||+||+.
T Consensus 48 r~~T~~eN~~N~~~~--~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 48 RLALPKENSWNMKTP--KSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred hhcCHHHHhcccCCC--CCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 356777888888776 8899999999 68888999999998 999999999999999999997 778999999853
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=99.12 E-value=1.4e-10 Score=85.41 Aligned_cols=52 Identities=40% Similarity=0.606 Sum_probs=45.5
Q ss_pred CCceee-EECCCCcEEEEEeccC-C--CeEeecCCCCCHHHHHHHHHHHHHHHhCC
Q 018103 164 KLYRGV-RQRHWGKWVAEIRLPK-N--RTRLWLGTFDTAEEAALAYDQAAYKLRGE 215 (360)
Q Consensus 164 S~YRGV-r~r~~GKW~AeIr~p~-~--gkri~LGtFdTaEEAA~AYD~AA~kl~G~ 215 (360)
|+|+|| +++..++|+|.|+++. + +++++||.|++++||++||++++++++|+
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 689999 5777899999999842 2 49999999999999999999999999885
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=79.02 E-value=8.8 Score=27.52 Aligned_cols=38 Identities=18% Similarity=0.190 Sum_probs=29.8
Q ss_pred cEEEEEe--ccCCC--eEeecCCCCCHHHHHHHHHHHHHHHh
Q 018103 176 KWVAEIR--LPKNR--TRLWLGTFDTAEEAALAYDQAAYKLR 213 (360)
Q Consensus 176 KW~AeIr--~p~~g--kri~LGtFdTaEEAA~AYD~AA~kl~ 213 (360)
+|...|. .+..| ++++-+.|.|..||..+..++...+.
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 44345 67888999999999999988877764
No 6
>PHA02601 int integrase; Provisional
Probab=68.75 E-value=7.8 Score=36.94 Aligned_cols=44 Identities=27% Similarity=0.357 Sum_probs=31.1
Q ss_pred eeEECCCCcEEEEEec-cCCCeEeecCCCCCHHHHHHHHHHHHHHH
Q 018103 168 GVRQRHWGKWVAEIRL-PKNRTRLWLGTFDTAEEAALAYDQAAYKL 212 (360)
Q Consensus 168 GVr~r~~GKW~AeIr~-p~~gkri~LGtFdTaEEAA~AYD~AA~kl 212 (360)
+|+++++|+|+++|+. ...|+++.. +|.|..||....+.....+
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 5777778999999985 234676653 6999988876666554444
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=57.00 E-value=24 Score=33.13 Aligned_cols=40 Identities=33% Similarity=0.402 Sum_probs=28.6
Q ss_pred CCcEEEEEeccCCCeEeecCCCC--CHHHHHHHHHHHHHHHh
Q 018103 174 WGKWVAEIRLPKNRTRLWLGTFD--TAEEAALAYDQAAYKLR 213 (360)
Q Consensus 174 ~GKW~AeIr~p~~gkri~LGtFd--TaEEAA~AYD~AA~kl~ 213 (360)
.+.|..+++.....+++.||+|+ +.++|....++....+.
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 35699999884445667899996 67787777766655553
No 8
>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=47.54 E-value=42 Score=26.96 Aligned_cols=40 Identities=30% Similarity=0.459 Sum_probs=30.2
Q ss_pred cEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHhCC
Q 018103 176 KWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLRGE 215 (360)
Q Consensus 176 KW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~G~ 215 (360)
.|-++|.--.-.-.+|.|-|++.+||..+.-.-...+..+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~E 48 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLESE 48 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHhh
Confidence 4888998745557889999999999998865555555443
No 9
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=46.21 E-value=56 Score=26.07 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=24.6
Q ss_pred cEEEEEeccCCCeEeecCCCCC--HHHHHHHHHHHHHHH
Q 018103 176 KWVAEIRLPKNRTRLWLGTFDT--AEEAALAYDQAAYKL 212 (360)
Q Consensus 176 KW~AeIr~p~~gkri~LGtFdT--aEEAA~AYD~AA~kl 212 (360)
.|..+.+.....+++.||.|.. ..+|.....+....+
T Consensus 36 t~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 36 TFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 4998888733346688999986 666665555554444
No 10
>PRK09692 integrase; Provisional
Probab=43.43 E-value=60 Score=32.34 Aligned_cols=44 Identities=20% Similarity=0.242 Sum_probs=27.5
Q ss_pred eEECCCC--cEEEEEeccCCCeE--eecCCCC--CHHHHHHHHHHHHHHH
Q 018103 169 VRQRHWG--KWVAEIRLPKNRTR--LWLGTFD--TAEEAALAYDQAAYKL 212 (360)
Q Consensus 169 Vr~r~~G--KW~AeIr~p~~gkr--i~LGtFd--TaEEAA~AYD~AA~kl 212 (360)
|+-+..| .|+.+.+.+.+|++ +-||.|. |..+|..+..++...+
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~~~ 82 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRSLL 82 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHHHH
Confidence 3333444 49988875544544 6799999 6777766555544443
No 11
>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=41.89 E-value=43 Score=27.37 Aligned_cols=41 Identities=24% Similarity=0.193 Sum_probs=27.2
Q ss_pred CCCCCceeeEECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHH
Q 018103 161 KPTKLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALA 204 (360)
Q Consensus 161 ~~tS~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~A 204 (360)
-.--+||-||.-+ |||+|.+.. +..-.---.|..+|.|-+-
T Consensus 28 ~k~dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 28 LKMDGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp B-TTTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred hhcccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 3456799998777 999999986 3333344678888877765
No 12
>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=40.13 E-value=36 Score=25.12 Aligned_cols=24 Identities=29% Similarity=0.387 Sum_probs=19.7
Q ss_pred CCeEeecCCCCCHHHHHHHHHHHH
Q 018103 186 NRTRLWLGTFDTAEEAALAYDQAA 209 (360)
Q Consensus 186 ~gkri~LGtFdTaEEAA~AYD~AA 209 (360)
..-||.+|.|++.+||..+.++..
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 346778899999999998887766
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=27.68 E-value=64 Score=27.50 Aligned_cols=42 Identities=33% Similarity=0.420 Sum_probs=28.6
Q ss_pred CCCceeeEECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHH
Q 018103 163 TKLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKL 212 (360)
Q Consensus 163 tS~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl 212 (360)
....|-|.+|--|.|.. -|.+ -|.|+|+|+|..-||+.+..|
T Consensus 49 E~S~rQv~~Rla~tw~~------wG~~--~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 49 ETSVRQVFDRLAGTWTY------WGWK--GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred cchHHHHHHHHHHHHHH------HHHh--CCCcCCHHHHHHHHHHHHHHH
Confidence 34466666665555521 1111 399999999999999988776
No 14
>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=26.08 E-value=3.1e+02 Score=25.27 Aligned_cols=58 Identities=17% Similarity=0.087 Sum_probs=40.5
Q ss_pred CCceeeE-ECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCccCCCCCC
Q 018103 164 KLYRGVR-QRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLRGEFARLNFPHL 224 (360)
Q Consensus 164 S~YRGVr-~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~G~~A~lNFP~~ 224 (360)
.+|-||. |.+.-|-.+.|.. .||-+..|. .+.|+|..|.++.+..++.-.-..+|++.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~~ 92 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTDF 92 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCce
Confidence 5799984 4444566777775 999888887 57889999999988887433222355443
No 15
>PLN00062 TATA-box-binding protein; Provisional
Probab=25.69 E-value=3e+02 Score=25.53 Aligned_cols=57 Identities=18% Similarity=0.064 Sum_probs=39.8
Q ss_pred CCceeeE-ECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCccCCCCC
Q 018103 164 KLYRGVR-QRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLRGEFARLNFPH 223 (360)
Q Consensus 164 S~YRGVr-~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~G~~A~lNFP~ 223 (360)
.+|-||. |-+.-|=.+-|.. .||-+.-|. .+.|+|..|.++.+..+..-.-..+|+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~~~~~L~~lg~~~~~~~ 91 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFA--SGKMVCTGA-KSEHDSKLAARKYARIIQKLGFPAKFKD 91 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCcCCCc
Confidence 4799984 4445566777775 888877775 7889999999998888743322344443
No 16
>PRK10113 cell division modulator; Provisional
Probab=25.40 E-value=58 Score=26.57 Aligned_cols=40 Identities=25% Similarity=0.270 Sum_probs=27.9
Q ss_pred CCCCceeeEECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHH
Q 018103 162 PTKLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALA 204 (360)
Q Consensus 162 ~tS~YRGVr~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~A 204 (360)
.--+||-||.-+ |||+|.+.. +-.-.---.|..+|.|-+-
T Consensus 29 kmd~frDVW~Lr-GKYVAFvl~--ge~FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 29 KMDSFRDVWMLR-GKYVAFVLM--GESFLRSPAFSVPESAQRW 68 (80)
T ss_pred hhcchhhhheec-cceEEEEEe--chhhccCCccCCcHHHHHH
Confidence 346799998776 999999986 2222234568888877665
No 17
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=24.65 E-value=96 Score=28.33 Aligned_cols=36 Identities=28% Similarity=0.205 Sum_probs=29.3
Q ss_pred EEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHhCC
Q 018103 177 WVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLRGE 215 (360)
Q Consensus 177 W~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~G~ 215 (360)
|+|+|. -|+.++-=..+.++.|.+|..+|+.+|=+.
T Consensus 96 waArVk---pG~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 96 WAARVK---PGRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEec---CCcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 999998 577777666788888999999999887443
No 18
>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=23.57 E-value=2.4e+02 Score=22.56 Aligned_cols=47 Identities=19% Similarity=0.118 Sum_probs=33.9
Q ss_pred CCceeeE-ECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHh
Q 018103 164 KLYRGVR-QRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLR 213 (360)
Q Consensus 164 S~YRGVr-~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~ 213 (360)
.+|.||. +-..-+-.+.|.. .||-+..|. .+.|+|..|.++....+.
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L~ 83 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPILQ 83 (86)
T ss_dssp TTESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 3789984 3333455666664 999888885 689999999988776653
No 19
>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=22.34 E-value=3.5e+02 Score=24.84 Aligned_cols=46 Identities=24% Similarity=0.141 Sum_probs=35.5
Q ss_pred CceeeE-ECCCCcEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHh
Q 018103 165 LYRGVR-QRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLR 213 (360)
Q Consensus 165 ~YRGVr-~r~~GKW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~ 213 (360)
+|.||. |-+.-|-.+-|+. .||-+-.|. .+.|+|++|.++.+..+.
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~--sGKiviTGa-ks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS--SGKITITGA-TSEEEAKQAARRAARLLQ 81 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC--CCeEEEEcc-CCHHHHHHHHHHHHHHHH
Confidence 899994 4444666777775 888777774 789999999999888773
No 20
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=21.39 E-value=1.8e+02 Score=28.29 Aligned_cols=38 Identities=37% Similarity=0.351 Sum_probs=30.7
Q ss_pred cEEEEEeccCCCeEeecCCCCCHHHHHHHHHHHHHHHhCC
Q 018103 176 KWVAEIRLPKNRTRLWLGTFDTAEEAALAYDQAAYKLRGE 215 (360)
Q Consensus 176 KW~AeIr~p~~gkri~LGtFdTaEEAA~AYD~AA~kl~G~ 215 (360)
.|+|.|.. ++.-+-+|.-=++++|..|.+.||.++-+.
T Consensus 133 ~wva~V~~--GrIl~EmgG~~~~~~Ar~al~~aa~klp~~ 170 (221)
T KOG3422|consen 133 HWVARVKA--GRILFEMGGDVEEEEARQALLQAAHKLPFK 170 (221)
T ss_pred eeEEEecC--CcEEEEeCCcccHHHHHHHHHHHHhcCCcc
Confidence 49999985 666666888889999999999999877443
Done!