Query 017798
Match_columns 365
No_of_seqs 301 out of 1275
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:31:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017798.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017798hhsearch_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 5.3E-20 1.2E-24 138.8 7.8 61 173-233 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 8.8E-20 1.9E-24 139.4 8.2 63 174-236 1-63 (64)
3 PHA00280 putative NHN endonucl 99.5 8.3E-15 1.8E-19 126.5 6.8 71 154-228 49-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 1.3E-10 2.7E-15 85.6 6.3 52 173-224 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 80.3 7.9 0.00017 27.8 6.1 38 185-222 1-42 (46)
6 PHA02601 int integrase; Provis 69.1 7.8 0.00017 36.9 4.7 44 177-221 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 56.5 25 0.00053 33.0 5.5 43 180-222 6-50 (357)
8 PF08846 DUF1816: Domain of un 47.9 33 0.00071 27.7 4.1 38 185-222 9-46 (68)
9 PF05036 SPOR: Sporulation rel 41.2 33 0.00072 25.3 3.1 29 195-224 42-70 (76)
10 PF13356 DUF4102: Domain of un 39.3 88 0.0019 25.0 5.5 38 184-221 35-74 (89)
11 PRK09692 integrase; Provisiona 37.6 86 0.0019 31.3 6.3 36 184-219 41-80 (413)
12 PF10729 CedA: Cell division a 35.6 61 0.0013 26.7 3.9 39 172-213 30-68 (80)
13 PF08471 Ribonuc_red_2_N: Clas 33.9 43 0.00094 28.6 3.0 42 172-221 49-90 (93)
14 COG0197 RplP Ribosomal protein 27.8 78 0.0017 29.0 3.7 36 186-224 96-131 (146)
15 cd04516 TBP_eukaryotes eukaryo 23.2 3.9E+02 0.0084 24.7 7.5 57 173-232 34-91 (174)
16 PLN00062 TATA-box-binding prot 22.5 3.9E+02 0.0086 24.8 7.4 56 173-231 34-90 (179)
17 PRK10113 cell division modulat 22.0 76 0.0016 26.1 2.3 38 173-213 31-68 (80)
18 PF00352 TBP: Transcription fa 22.0 2.5E+02 0.0054 22.5 5.4 46 174-222 37-83 (86)
19 PF09954 DUF2188: Uncharacteri 21.1 2.2E+02 0.0048 21.4 4.6 39 178-220 3-41 (62)
20 cd04517 TLF TBP-like factors ( 20.1 4.2E+02 0.0092 24.4 7.1 46 174-222 35-81 (174)
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=99.81 E-value=5.3e-20 Score=138.75 Aligned_cols=61 Identities=72% Similarity=1.165 Sum_probs=56.8
Q ss_pred CCceeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCCCCCCCCC
Q 017798 173 KLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGDFARLNFPNL 233 (365)
Q Consensus 173 SgYRGVr~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klrG~~A~lNFP~~ 233 (365)
|+||||+++++|||+|+|+++..|+++|||+|+|+||||+|||+|+++++|.++++|||.+
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 6899998878899999999955599999999999999999999999999999999999963
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.81 E-value=8.8e-20 Score=139.37 Aligned_cols=63 Identities=71% Similarity=1.170 Sum_probs=60.0
Q ss_pred CceeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCCCCCCCCCCCC
Q 017798 174 LYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGDFARLNFPNLRHN 236 (365)
Q Consensus 174 gYRGVr~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klrG~~A~lNFP~~~~~ 236 (365)
+|+||+++++|||+|+|+++.+|+++|||+|+|+||||+|||.|+++++|.++++|||...|+
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 589998788999999999999999999999999999999999999999999999999998775
No 3
>PHA00280 putative NHN endonuclease
Probab=99.54 E-value=8.3e-15 Score=126.55 Aligned_cols=71 Identities=18% Similarity=0.262 Sum_probs=62.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCceee-EECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCCCC
Q 017798 154 LSPKPVPMKTVGCPPPKPAKLYRGV-RQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGDFARL 228 (365)
Q Consensus 154 l~pk~~~mK~~g~~~~~ntSgYRGV-r~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klrG~~A~l 228 (365)
+.+..+.++|.+.. ++|+|||+|| +++..|||+|+|++ +||+++||.|+++|+|+.||+ ++.+|||+||+.
T Consensus 49 ~~T~~eN~~N~~~~-~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 49 LALPKENSWNMKTP-KSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred hcCHHHHhcccCCC-CCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 44555677887776 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=99.13 E-value=1.3e-10 Score=85.63 Aligned_cols=52 Identities=38% Similarity=0.597 Sum_probs=45.7
Q ss_pred CCceee-EECCCCcEEEEEeecC-C--CeEeecCCCCCHHHHHHHHHHHHHHHhCC
Q 017798 173 KLYRGV-RQRHWGKWVAEIRLPK-N--RTRLWLGTFDTAEEAALAYDKAAYKLRGD 224 (365)
Q Consensus 173 SgYRGV-r~r~~GKW~AeIr~p~-~--gKriyLGtFdTaEEAArAYD~AA~klrG~ 224 (365)
|+|+|| +++..++|+|+|+++. + +++++||.|++++||++|++.++++++|+
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 5788899999999842 2 49999999999999999999999999875
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=80.27 E-value=7.9 Score=27.85 Aligned_cols=38 Identities=21% Similarity=0.205 Sum_probs=29.9
Q ss_pred cEEEEEe--ecCCC--eEeecCCCCCHHHHHHHHHHHHHHHh
Q 017798 185 KWVAEIR--LPKNR--TRLWLGTFDTAEEAALAYDKAAYKLR 222 (365)
Q Consensus 185 KW~AeIr--~p~~g--KriyLGtFdTaEEAArAYD~AA~klr 222 (365)
+|...|. .+.+| ++++-+.|.|..||..+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 6888883 44355 66888999999999999988777664
No 6
>PHA02601 int integrase; Provisional
Probab=69.13 E-value=7.8 Score=36.87 Aligned_cols=44 Identities=27% Similarity=0.367 Sum_probs=31.1
Q ss_pred eeEECCCCcEEEEEeec-CCCeEeecCCCCCHHHHHHHHHHHHHHH
Q 017798 177 GVRQRHWGKWVAEIRLP-KNRTRLWLGTFDTAEEAALAYDKAAYKL 221 (365)
Q Consensus 177 GVr~r~~GKW~AeIr~p-~~gKriyLGtFdTaEEAArAYD~AA~kl 221 (365)
+|++.+.|+|+++|+.. ..|+++. .+|.|..||....+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHhc
Confidence 57777789999999862 3477765 36999998876665554443
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=56.49 E-value=25 Score=33.00 Aligned_cols=43 Identities=30% Similarity=0.356 Sum_probs=29.2
Q ss_pred ECCCCcEEEEEeecCCCeEeecCCCC--CHHHHHHHHHHHHHHHh
Q 017798 180 QRHWGKWVAEIRLPKNRTRLWLGTFD--TAEEAALAYDKAAYKLR 222 (365)
Q Consensus 180 ~r~~GKW~AeIr~p~~gKriyLGtFd--TaEEAArAYD~AA~klr 222 (365)
.+..+.|..++++....+++.||+|+ +.++|....++....+.
T Consensus 6 ~~g~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 6 PSGSKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CCCCEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 33345699999884444557799995 67777777666555553
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=47.90 E-value=33 Score=27.67 Aligned_cols=38 Identities=29% Similarity=0.448 Sum_probs=28.2
Q ss_pred cEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHh
Q 017798 185 KWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLR 222 (365)
Q Consensus 185 KW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klr 222 (365)
.|-++|.--.-.-.+|.|-|++.+||..+.-.-...|.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 48888886445577999999999999987554444443
No 9
>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=41.20 E-value=33 Score=25.28 Aligned_cols=29 Identities=34% Similarity=0.424 Sum_probs=21.2
Q ss_pred CCeEeecCCCCCHHHHHHHHHHHHHHHhCC
Q 017798 195 NRTRLWLGTFDTAEEAALAYDKAAYKLRGD 224 (365)
Q Consensus 195 ~gKriyLGtFdTaEEAArAYD~AA~klrG~ 224 (365)
..-+|.+|.|++.++|..+..+.. ...|.
T Consensus 42 ~~yrV~~G~f~~~~~A~~~~~~l~-~~~~~ 70 (76)
T PF05036_consen 42 PWYRVRVGPFSSREEAEAALRKLK-KAAGP 70 (76)
T ss_dssp TCEEEEECCECTCCHHHHHHHHHH-HHHTS
T ss_pred ceEEEEECCCCCHHHHHHHHHHHh-HhhCC
Confidence 335677899999999998887665 34443
No 10
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=39.31 E-value=88 Score=24.96 Aligned_cols=38 Identities=18% Similarity=0.211 Sum_probs=24.1
Q ss_pred CcEEEEEeecCCCeEeecCCCCC--HHHHHHHHHHHHHHH
Q 017798 184 GKWVAEIRLPKNRTRLWLGTFDT--AEEAALAYDKAAYKL 221 (365)
Q Consensus 184 GKW~AeIr~p~~gKriyLGtFdT--aEEAArAYD~AA~kl 221 (365)
..|..+.+...+.+++-||.|.. ..+|.....+....+
T Consensus 35 kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 35 KTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred eEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 34988887733335588999976 566655555444444
No 11
>PRK09692 integrase; Provisional
Probab=37.61 E-value=86 Score=31.25 Aligned_cols=36 Identities=19% Similarity=0.231 Sum_probs=22.9
Q ss_pred CcEEEEEeecCCCeE--eecCCCC--CHHHHHHHHHHHHH
Q 017798 184 GKWVAEIRLPKNRTR--LWLGTFD--TAEEAALAYDKAAY 219 (365)
Q Consensus 184 GKW~AeIr~p~~gKr--iyLGtFd--TaEEAArAYD~AA~ 219 (365)
..|+.+-+.+.+|++ +-||.|+ |..+|..+..++..
T Consensus 41 k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 41 KIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 349888765444555 6799999 66666554444333
No 12
>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=35.58 E-value=61 Score=26.68 Aligned_cols=39 Identities=26% Similarity=0.225 Sum_probs=26.1
Q ss_pred CCCceeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHH
Q 017798 172 AKLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALA 213 (365)
Q Consensus 172 tSgYRGVr~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArA 213 (365)
--+||-||.-+ |||+|.+.. +-.-.---.|...|.|-+-
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred cccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 35899998766 999999986 3333334678888887754
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=33.85 E-value=43 Score=28.60 Aligned_cols=42 Identities=33% Similarity=0.384 Sum_probs=29.6
Q ss_pred CCCceeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHH
Q 017798 172 AKLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKL 221 (365)
Q Consensus 172 tSgYRGVr~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~kl 221 (365)
....|-|.+|--|-|..-- ++ -|+|+|+|+|..-||+.+..|
T Consensus 49 E~S~rQv~~Rla~tw~~wG------~~--~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 49 ETSVRQVFDRLAGTWTYWG------WK--GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred cchHHHHHHHHHHHHHHHH------Hh--CCCcCCHHHHHHHHHHHHHHH
Confidence 4556777666556553221 11 399999999999999988776
No 14
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=27.82 E-value=78 Score=29.01 Aligned_cols=36 Identities=28% Similarity=0.209 Sum_probs=30.3
Q ss_pred EEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHhCC
Q 017798 186 WVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGD 224 (365)
Q Consensus 186 W~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klrG~ 224 (365)
|+|+|. -|+.++-=..+.++.|..|..+|+.+|=+.
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 577777777788888999999999888544
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=23.20 E-value=3.9e+02 Score=24.71 Aligned_cols=57 Identities=19% Similarity=0.090 Sum_probs=39.5
Q ss_pred CCceeeE-ECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCCCCCCCC
Q 017798 173 KLYRGVR-QRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGDFARLNFPN 232 (365)
Q Consensus 173 SgYRGVr-~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klrG~~A~lNFP~ 232 (365)
..|-||. |-+.-|-.+.|+. .||-+-.|. .++|+|..|.++.+..+..-.-..+|++
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~ 91 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTD 91 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCc
Confidence 4788984 4444566777776 999888887 5788999999998888843322234543
No 16
>PLN00062 TATA-box-binding protein; Provisional
Probab=22.49 E-value=3.9e+02 Score=24.84 Aligned_cols=56 Identities=20% Similarity=0.066 Sum_probs=38.8
Q ss_pred CCceeeE-ECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHhCCCCCCCCC
Q 017798 173 KLYRGVR-QRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLRGDFARLNFP 231 (365)
Q Consensus 173 SgYRGVr-~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klrG~~A~lNFP 231 (365)
..|-||. +-+.-|=.+.|+. .||-+-.|. .++|+|..|.++.+..+..-.-..+|+
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~~~~~L~~lg~~~~~~ 90 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFA--SGKMVCTGA-KSEHDSKLAARKYARIIQKLGFPAKFK 90 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCcCCC
Confidence 4788983 4445566777775 888887775 788999999999888885332234444
No 17
>PRK10113 cell division modulator; Provisional
Probab=22.02 E-value=76 Score=26.08 Aligned_cols=38 Identities=26% Similarity=0.288 Sum_probs=26.9
Q ss_pred CCceeeEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHH
Q 017798 173 KLYRGVRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALA 213 (365)
Q Consensus 173 SgYRGVr~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArA 213 (365)
-+||-||.-+ |||+|.+.....-+| --.|...|.|-+-
T Consensus 31 d~frDVW~Lr-GKYVAFvl~ge~FrR--SPaFs~PEsAQRW 68 (80)
T PRK10113 31 DSFRDVWMLR-GKYVAFVLMGESFLR--SPAFSVPESAQRW 68 (80)
T ss_pred cchhhhheec-cceEEEEEechhhcc--CCccCCcHHHHHH
Confidence 4799998766 999999986222222 3678888887754
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=22.00 E-value=2.5e+02 Score=22.47 Aligned_cols=46 Identities=22% Similarity=0.124 Sum_probs=33.0
Q ss_pred CceeeE-ECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHh
Q 017798 174 LYRGVR-QRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLR 222 (365)
Q Consensus 174 gYRGVr-~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klr 222 (365)
.|-||. +-..-+-.+.|.- .||-+..|. .+.|+|..|.++....+.
T Consensus 37 ~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L~ 83 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPILQ 83 (86)
T ss_dssp TESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 688884 3333455556664 999888886 688999999988776653
No 19
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=21.07 E-value=2.2e+02 Score=21.39 Aligned_cols=39 Identities=31% Similarity=0.288 Sum_probs=24.9
Q ss_pred eEECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHH
Q 017798 178 VRQRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYK 220 (365)
Q Consensus 178 Vr~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~k 220 (365)
|..+..|.|....- |...-.++|+|-+||..+=...+..
T Consensus 3 V~p~~~~~W~v~~e----g~~ra~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKE----GAKRASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeC----CCcccccccCcHHHHHHHHHHHHHh
Confidence 33355678966544 3333379999999998765555544
No 20
>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=20.11 E-value=4.2e+02 Score=24.37 Aligned_cols=46 Identities=24% Similarity=0.129 Sum_probs=35.3
Q ss_pred CceeeE-ECCCCcEEEEEeecCCCeEeecCCCCCHHHHHHHHHHHHHHHh
Q 017798 174 LYRGVR-QRHWGKWVAEIRLPKNRTRLWLGTFDTAEEAALAYDKAAYKLR 222 (365)
Q Consensus 174 gYRGVr-~r~~GKW~AeIr~p~~gKriyLGtFdTaEEAArAYD~AA~klr 222 (365)
+|.||. |-+.-|=.+.|+. +||-+-.| ..+.|+|++|.++.+..+.
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~--sGKiviTG-aks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS--SGKITITG-ATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC--CCeEEEEc-cCCHHHHHHHHHHHHHHHH
Confidence 899994 4444566777775 88887666 4789999999999888774
Done!