Query 030994
Match_columns 168
No_of_seqs 173 out of 1069
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 07:39:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030994.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030994hhsearch_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 4.7E-21 1E-25 129.9 7.5 60 7-66 1-60 (61)
2 smart00380 AP2 DNA-binding dom 99.8 9.6E-21 2.1E-25 130.0 8.4 63 8-70 1-63 (64)
3 PHA00280 putative NHN endonucl 99.6 8.1E-15 1.8E-19 113.5 6.9 57 2-61 62-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 2.5E-11 5.5E-16 80.2 5.2 52 7-58 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 84.7 3.9 8.4E-05 26.0 5.3 38 19-56 1-42 (46)
6 PHA02601 int integrase; Provis 68.2 7.7 0.00017 32.7 4.0 44 11-55 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 61.2 20 0.00042 29.8 5.1 39 17-55 9-49 (357)
8 PF08846 DUF1816: Domain of un 52.8 29 0.00062 24.7 4.1 37 19-55 9-45 (68)
9 PRK09692 integrase; Provisiona 52.8 46 0.001 29.3 6.3 44 12-55 33-82 (413)
10 PF05036 SPOR: Sporulation rel 51.9 11 0.00024 24.7 1.7 22 31-52 44-65 (76)
11 PF13356 DUF4102: Domain of un 49.9 44 0.00096 23.5 4.8 43 13-55 28-74 (89)
12 PF08471 Ribonuc_red_2_N: Clas 47.5 21 0.00046 26.8 2.9 21 35-55 70-90 (93)
13 PF14112 DUF4284: Domain of un 39.7 19 0.00042 27.5 1.7 18 31-48 2-19 (122)
14 PF10729 CedA: Cell division a 31.4 95 0.0021 22.5 4.0 39 6-47 30-68 (80)
15 PF09954 DUF2188: Uncharacteri 28.1 1.8E+02 0.0039 19.1 4.8 39 12-54 3-41 (62)
16 PF00352 TBP: Transcription fa 26.8 1.9E+02 0.004 20.4 4.9 46 7-55 36-82 (86)
17 cd04516 TBP_eukaryotes eukaryo 24.9 3.6E+02 0.0078 21.9 6.9 48 6-56 33-81 (174)
18 PLN00062 TATA-box-binding prot 23.8 3.8E+02 0.0082 21.9 6.8 48 6-56 33-81 (179)
19 PF12286 DUF3622: Protein of u 23.1 2.3E+02 0.005 20.4 4.7 45 1-47 1-49 (71)
20 cd04517 TLF TBP-like factors ( 22.8 3.2E+02 0.0069 22.2 6.1 45 8-55 35-80 (174)
21 TIGR01164 rplP_bact ribosomal 22.6 1.7E+02 0.0037 22.6 4.4 34 19-55 91-124 (126)
22 COG0197 RplP Ribosomal protein 21.9 1.5E+02 0.0032 24.0 3.9 36 20-58 96-131 (146)
23 cd04518 TBP_archaea archaeal T 21.4 3.9E+02 0.0084 21.7 6.4 49 5-56 32-81 (174)
24 PRK09203 rplP 50S ribosomal pr 21.3 1.7E+02 0.0036 23.0 4.1 36 19-57 92-127 (138)
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=4.7e-21 Score=129.91 Aligned_cols=60 Identities=65% Similarity=1.115 Sum_probs=56.8
Q ss_pred CCeeEeEECCCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCC
Q 030994 7 GHYRGVRKRPWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSLRGAKAKTNFPA 66 (168)
Q Consensus 7 S~yRGVr~r~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~~G~~A~~NFp~ 66 (168)
|+|+||+++++|||+|+|+++..++++|||+|+|+|||+.|||.++++++|.++.+|||.
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 789999988889999999995559999999999999999999999999999999999996
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=9.6e-21 Score=129.99 Aligned_cols=63 Identities=63% Similarity=1.098 Sum_probs=60.0
Q ss_pred CeeEeEECCCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 030994 8 HYRGVRKRPWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSLRGAKAKTNFPAPVTN 70 (168)
Q Consensus 8 ~yRGVr~r~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~~G~~A~~NFp~~~~~ 70 (168)
+|+||+++++|||+|+|+++.+++.+|||+|+|+||||.|||.++++++|.++.+|||...|+
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 599999888999999999998999999999999999999999999999999999999998775
No 3
>PHA00280 putative NHN endonuclease
Probab=99.55 E-value=8.1e-15 Score=113.51 Aligned_cols=57 Identities=18% Similarity=0.208 Sum_probs=51.9
Q ss_pred CCCCCCCeeEeEEC-CCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 030994 2 ASSREGHYRGVRKR-PWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSLRGAKAK 61 (168)
Q Consensus 2 ~~~ntS~yRGVr~r-~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~~G~~A~ 61 (168)
.++|+|||+||++. ..|||+|+|.+ +||+++||.|+++|+|+.||+ ++.++||++|.
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 46899999999865 57999999999 999999999999999999997 77899999885
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=99.21 E-value=2.5e-11 Score=80.15 Aligned_cols=52 Identities=35% Similarity=0.427 Sum_probs=45.0
Q ss_pred CCeeEeEECC-CCcEEEEEeCCCC---CceEecCCCCCHHHHHHHHHHHHHHhcCC
Q 030994 7 GHYRGVRKRP-WGRYAAEIRDPWK---KTRVWLGTFDTPEEAALAYDGAARSLRGA 58 (168)
Q Consensus 7 S~yRGVr~r~-~GKW~A~I~~~~~---gkri~LGtFdT~EEAA~AYD~Aa~~~~G~ 58 (168)
|+|+||++.+ .++|+|+|++... +++++||.|++++||++|++.++.+++|+
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 7899997664 7999999998322 48999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=84.70 E-value=3.9 Score=25.98 Aligned_cols=38 Identities=18% Similarity=0.097 Sum_probs=29.3
Q ss_pred cEEEEEe--CCCCC--ceEecCCCCCHHHHHHHHHHHHHHhc
Q 030994 19 RYAAEIR--DPWKK--TRVWLGTFDTPEEAALAYDGAARSLR 56 (168)
Q Consensus 19 KW~A~I~--~~~~g--kri~LGtFdT~EEAA~AYD~Aa~~~~ 56 (168)
+|..+|. ++..| ++++-+-|.|..||..+.......+.
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 44455 46888999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=68.24 E-value=7.7 Score=32.73 Aligned_cols=44 Identities=25% Similarity=0.219 Sum_probs=29.9
Q ss_pred EeEECCCCcEEEEEeC-CCCCceEecCCCCCHHHHHHHHHHHHHHh
Q 030994 11 GVRKRPWGRYAAEIRD-PWKKTRVWLGTFDTPEEAALAYDGAARSL 55 (168)
Q Consensus 11 GVr~r~~GKW~A~I~~-~~~gkri~LGtFdT~EEAA~AYD~Aa~~~ 55 (168)
+|++.++|+|+++++. ...|+++. .+|.|..||....+......
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 5667778999999985 12356554 36999999876655544433
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=61.21 E-value=20 Score=29.80 Aligned_cols=39 Identities=26% Similarity=0.215 Sum_probs=27.7
Q ss_pred CCcEEEEEeCCCCCceEecCCCC--CHHHHHHHHHHHHHHh
Q 030994 17 WGRYAAEIRDPWKKTRVWLGTFD--TPEEAALAYDGAARSL 55 (168)
Q Consensus 17 ~GKW~A~I~~~~~gkri~LGtFd--T~EEAA~AYD~Aa~~~ 55 (168)
.+.|..+++.....+++.||+|+ |.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699999984444567899995 6778877766655555
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=52.84 E-value=29 Score=24.66 Aligned_cols=37 Identities=30% Similarity=0.418 Sum_probs=27.6
Q ss_pred cEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHh
Q 030994 19 RYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSL 55 (168)
Q Consensus 19 KW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~ 55 (168)
.|=++|.--.-.-..|.|-|+|.+||..+-..-...+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHH
Confidence 3668888744456889999999999998865544444
No 9
>PRK09692 integrase; Provisional
Probab=52.77 E-value=46 Score=29.32 Aligned_cols=44 Identities=20% Similarity=0.208 Sum_probs=28.4
Q ss_pred eEECCCCc--EEEEEeCCCCCce--EecCCCC--CHHHHHHHHHHHHHHh
Q 030994 12 VRKRPWGR--YAAEIRDPWKKTR--VWLGTFD--TPEEAALAYDGAARSL 55 (168)
Q Consensus 12 Vr~r~~GK--W~A~I~~~~~gkr--i~LGtFd--T~EEAA~AYD~Aa~~~ 55 (168)
|+.++.|. |..+-+.+.+|++ +-||.|+ |..||..+-.++...+
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 44555554 9988765444544 6799999 6777766655544444
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=51.92 E-value=11 Score=24.67 Aligned_cols=22 Identities=36% Similarity=0.441 Sum_probs=18.4
Q ss_pred ceEecCCCCCHHHHHHHHHHHH
Q 030994 31 TRVWLGTFDTPEEAALAYDGAA 52 (168)
Q Consensus 31 kri~LGtFdT~EEAA~AYD~Aa 52 (168)
-+|.+|.|+|.+||..+-....
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 4788999999999988877655
No 11
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=49.90 E-value=44 Score=23.52 Aligned_cols=43 Identities=23% Similarity=0.222 Sum_probs=26.3
Q ss_pred EECCCC--cEEEEEeCCCCCceEecCCCCC--HHHHHHHHHHHHHHh
Q 030994 13 RKRPWG--RYAAEIRDPWKKTRVWLGTFDT--PEEAALAYDGAARSL 55 (168)
Q Consensus 13 r~r~~G--KW~A~I~~~~~gkri~LGtFdT--~EEAA~AYD~Aa~~~ 55 (168)
+..+.| .|.-+.+...+.+++-||.|.+ ..||..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 455554 4998888732234788999976 666665555444443
No 12
>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=47.54 E-value=21 Score=26.85 Aligned_cols=21 Identities=38% Similarity=0.415 Sum_probs=18.1
Q ss_pred cCCCCCHHHHHHHHHHHHHHh
Q 030994 35 LGTFDTPEEAALAYDGAARSL 55 (168)
Q Consensus 35 LGtFdT~EEAA~AYD~Aa~~~ 55 (168)
-|+|+|+|+|..=||+....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 399999999999999877654
No 13
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=39.66 E-value=19 Score=27.51 Aligned_cols=18 Identities=22% Similarity=0.754 Sum_probs=13.6
Q ss_pred ceEecCCCCCHHHHHHHH
Q 030994 31 TRVWLGTFDTPEEAALAY 48 (168)
Q Consensus 31 kri~LGtFdT~EEAA~AY 48 (168)
..+|||+|+|.+|-..=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 469999999987765433
No 14
>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=31.41 E-value=95 Score=22.54 Aligned_cols=39 Identities=23% Similarity=0.221 Sum_probs=25.1
Q ss_pred CCCeeEeEECCCCcEEEEEeCCCCCceEecCCCCCHHHHHHH
Q 030994 6 EGHYRGVRKRPWGRYAAEIRDPWKKTRVWLGTFDTPEEAALA 47 (168)
Q Consensus 6 tS~yRGVr~r~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~A 47 (168)
--+||-|+.-+ |||.|.+.. +-.-.---.|..+|.|-+-
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 35788885444 999999987 4444444678888877765
No 15
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=28.07 E-value=1.8e+02 Score=19.13 Aligned_cols=39 Identities=33% Similarity=0.282 Sum_probs=24.9
Q ss_pred eEECCCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHH
Q 030994 12 VRKRPWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARS 54 (168)
Q Consensus 12 Vr~r~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~ 54 (168)
|..+..|.|..+... ..+. ..+|+|.+||..+=...+..
T Consensus 3 V~p~~~~~W~v~~eg--~~ra--~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG--AKRA--SKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeCC--Cccc--ccccCcHHHHHHHHHHHHHh
Confidence 333456779888754 3322 58999999987665444443
No 16
>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=26.77 E-value=1.9e+02 Score=20.37 Aligned_cols=46 Identities=22% Similarity=0.159 Sum_probs=33.6
Q ss_pred CCeeEeEEC-CCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHh
Q 030994 7 GHYRGVRKR-PWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSL 55 (168)
Q Consensus 7 S~yRGVr~r-~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~ 55 (168)
.+|.||..+ ..-+-.+.|.. .||-+..|. .+.|||..|.++....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 468898544 33456677776 888887775 78999999988876654
No 17
>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=24.92 E-value=3.6e+02 Score=21.89 Aligned_cols=48 Identities=21% Similarity=0.192 Sum_probs=35.7
Q ss_pred CCCeeEeEEC-CCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHhc
Q 030994 6 EGHYRGVRKR-PWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSLR 56 (168)
Q Consensus 6 tS~yRGVr~r-~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~~ 56 (168)
-.+|.|+..| ..-+-.+.|.. .||-+--|. .|.|||..|.++.+..+.
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 33 PKRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred CccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 3578898544 34566778877 888887776 578899999888877763
No 18
>PLN00062 TATA-box-binding protein; Provisional
Probab=23.83 E-value=3.8e+02 Score=21.94 Aligned_cols=48 Identities=21% Similarity=0.170 Sum_probs=35.3
Q ss_pred CCCeeEeEEC-CCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHhc
Q 030994 6 EGHYRGVRKR-PWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSLR 56 (168)
Q Consensus 6 tS~yRGVr~r-~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~~ 56 (168)
-.+|.||..| ..-+-.+.|.. .||-+--|. .|.|||..|.++.+..+.
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 33 PKRFAAVIMRIREPKTTALIFA--SGKMVCTGA-KSEHDSKLAARKYARIIQ 81 (179)
T ss_pred CccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 3578898544 34566777777 888777664 788999999988887763
No 19
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=23.08 E-value=2.3e+02 Score=20.40 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=24.3
Q ss_pred CCCCCCCCeeEeEECCCCcEEEEEeCCCCCc-e-Ee--cCCCCCHHHHHHH
Q 030994 1 MASSREGHYRGVRKRPWGRYAAEIRDPWKKT-R-VW--LGTFDTPEEAALA 47 (168)
Q Consensus 1 ~~~~ntS~yRGVr~r~~GKW~A~I~~~~~gk-r-i~--LGtFdT~EEAA~A 47 (168)
|...++-.||= ... .+.|.|+|.--...+ . |- ---|+|++||..-
T Consensus 1 Msk~kK~~~rv-~q~-~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq~W 49 (71)
T PF12286_consen 1 MSKNKKYDFRV-TQK-RNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQAW 49 (71)
T ss_pred CCCCCcccEEE-Eec-CCceeeeeeeeecCceeEEEecccCcccHHHHHHH
Confidence 44444444442 233 456999998422222 1 11 2459999987643
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=22.80 E-value=3.2e+02 Score=22.16 Aligned_cols=45 Identities=31% Similarity=0.229 Sum_probs=34.6
Q ss_pred CeeEeEEC-CCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHh
Q 030994 8 HYRGVRKR-PWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSL 55 (168)
Q Consensus 8 ~yRGVr~r-~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~ 55 (168)
+|.||..| ..-+-.+.|.. .||-+--| ..|.|+|..|.++.+..+
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~--sGKiviTG-aks~~~~~~a~~~~~~~l 80 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS--SGKITITG-ATSEEEAKQAARRAARLL 80 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC--CCeEEEEc-cCCHHHHHHHHHHHHHHH
Confidence 78998655 34567788887 88877666 478999999998887776
No 21
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=22.61 E-value=1.7e+02 Score=22.62 Aligned_cols=34 Identities=24% Similarity=0.141 Sum_probs=26.7
Q ss_pred cEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHh
Q 030994 19 RYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSL 55 (168)
Q Consensus 19 KW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~ 55 (168)
.|+|+|.. +..-+-++. .+++.|..|...|+.++
T Consensus 91 ~~varV~~--G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 91 YWVAVVKP--GKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEEECC--CCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 39999986 444444666 89999999999998775
No 22
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=21.94 E-value=1.5e+02 Score=24.04 Aligned_cols=36 Identities=22% Similarity=0.057 Sum_probs=28.9
Q ss_pred EEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHhcCC
Q 030994 20 YAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSLRGA 58 (168)
Q Consensus 20 W~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~~G~ 58 (168)
|.|+|.. |+.++-=..++++.|..|...|+.+|-+.
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 9999975 66666666788888999999999988543
No 23
>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=21.36 E-value=3.9e+02 Score=21.72 Aligned_cols=49 Identities=20% Similarity=0.195 Sum_probs=36.0
Q ss_pred CCCCeeEeEEC-CCCcEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHhc
Q 030994 5 REGHYRGVRKR-PWGRYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSLR 56 (168)
Q Consensus 5 ntS~yRGVr~r-~~GKW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~~ 56 (168)
+..+|.|+..| ..-+-.+.|.. .||-+--|. .|.|||..|-++.+..+.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~--SGKiv~tGa-ks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFR--SGKMVCTGA-KSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEEC--CCeEEEEcc-CCHHHHHHHHHHHHHHHH
Confidence 34678998655 34456667766 888877775 789999999888877764
No 24
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=21.35 E-value=1.7e+02 Score=23.04 Aligned_cols=36 Identities=19% Similarity=0.033 Sum_probs=28.0
Q ss_pred cEEEEEeCCCCCceEecCCCCCHHHHHHHHHHHHHHhcC
Q 030994 19 RYAAEIRDPWKKTRVWLGTFDTPEEAALAYDGAARSLRG 57 (168)
Q Consensus 19 KW~A~I~~~~~gkri~LGtFdT~EEAA~AYD~Aa~~~~G 57 (168)
-|+|+|.. +..-+-++. .+++.|..|...|+.++-+
T Consensus 92 ~~varVk~--G~iifEi~~-~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 92 YWVAVVKP--GRILFEIAG-VSEELAREALRLAAAKLPI 127 (138)
T ss_pred EEEEEECC--CCEEEEEeC-CCHHHHHHHHHHHhccCCC
Confidence 39999986 444445666 8999999999999988744
Done!