Query 044016
Match_columns 342
No_of_seqs 196 out of 1161
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:39:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044016hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00380 AP2 DNA-binding dom 99.8 1.8E-20 3.8E-25 141.6 8.4 63 53-115 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.8 2.6E-20 5.5E-25 138.9 7.3 61 52-112 1-61 (61)
3 PHA00280 putative NHN endonucl 99.6 5.1E-15 1.1E-19 126.7 5.9 81 17-106 38-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 6.9E-11 1.5E-15 86.0 4.9 52 52-103 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 81.5 4.7 0.0001 28.7 5.2 37 64-100 1-41 (46)
6 PHA02601 int integrase; Provis 67.4 7.3 0.00016 36.5 4.1 44 56-100 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 50.5 36 0.00079 31.4 5.5 39 62-100 9-49 (357)
8 PF08846 DUF1816: Domain of un 50.4 28 0.00061 27.8 4.1 38 64-101 9-46 (68)
9 PRK09692 integrase; Provisiona 43.5 64 0.0014 31.7 6.3 42 57-98 33-80 (413)
10 PF05036 SPOR: Sporulation rel 42.0 17 0.00037 26.5 1.6 23 75-97 43-65 (76)
11 PF13356 DUF4102: Domain of un 39.5 71 0.0015 25.2 4.9 44 57-100 27-74 (89)
12 PF00352 TBP: Transcription fa 38.5 51 0.0011 26.2 3.9 46 52-100 36-82 (86)
13 cd04517 TLF TBP-like factors ( 35.1 98 0.0021 28.2 5.7 47 50-100 33-80 (174)
14 PLN00062 TATA-box-binding prot 32.8 1.4E+02 0.003 27.5 6.3 49 50-101 32-81 (179)
15 cd04516 TBP_eukaryotes eukaryo 32.4 1.5E+02 0.0032 27.2 6.4 49 50-101 32-81 (174)
16 cd00652 TBP_TLF TATA box bindi 30.3 1.5E+02 0.0032 27.0 6.0 48 50-100 32-80 (174)
17 cd04518 TBP_archaea archaeal T 28.7 1.7E+02 0.0037 26.8 6.1 49 50-101 32-81 (174)
18 PF08471 Ribonuc_red_2_N: Clas 25.3 69 0.0015 27.2 2.8 21 80-100 70-90 (93)
19 cd01433 Ribosomal_L16_L10e Rib 24.9 1.3E+02 0.0027 25.3 4.3 36 64-101 71-106 (112)
20 COG0197 RplP Ribosomal protein 24.2 1.1E+02 0.0024 27.8 4.0 36 65-103 96-131 (146)
21 PF09954 DUF2188: Uncharacteri 23.8 1.9E+02 0.0042 21.5 4.7 39 57-99 3-41 (62)
22 PF10729 CedA: Cell division a 23.3 1.4E+02 0.003 24.5 4.0 38 52-92 31-68 (80)
23 TIGR01164 rplP_bact ribosomal 21.9 1.6E+02 0.0034 25.7 4.4 34 64-100 91-124 (126)
24 PRK09203 rplP 50S ribosomal pr 21.3 1.5E+02 0.0032 26.3 4.2 36 64-102 92-127 (138)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=1.8e-20 Score=141.64 Aligned_cols=63 Identities=57% Similarity=1.002 Sum_probs=60.7
Q ss_pred ceEEEEECCCCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhcCCccccCCCCCCCC
Q 044016 53 RFLGVRRRPWGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMKGAQARTNFIYTDNG 115 (342)
Q Consensus 53 rYRGV~~rk~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~G~~A~lNFp~s~y~ 115 (342)
+|+||+++++|||+|+|+++.+++++|||+|+|+||||+|||+|+++++|.++++|||.++|+
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 599999988999999999998999999999999999999999999999999999999999986
No 2
>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=99.82 E-value=2.6e-20 Score=138.91 Aligned_cols=61 Identities=59% Similarity=1.036 Sum_probs=57.2
Q ss_pred CceEEEEECCCCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhcCCccccCCCCC
Q 044016 52 GRFLGVRRRPWGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMKGAQARTNFIYT 112 (342)
Q Consensus 52 SrYRGV~~rk~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~G~~A~lNFp~s 112 (342)
|+||||+++++|||+|+|+++..+|++|||+|+|+||||+|||+|+++++|.++.+|||++
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 5799999988999999999955599999999999999999999999999999999999964
No 3
>PHA00280 putative NHN endonuclease
Probab=99.55 E-value=5.1e-15 Score=126.69 Aligned_cols=81 Identities=14% Similarity=0.159 Sum_probs=68.5
Q ss_pred ccccccccccchhccCCCCCCCCCCCCCCCCCCCCCceEEEEECC-CCeEEEEEecCCCCceEecCCCCCHHHHHHHHHH
Q 044016 17 DEQGQTQMGFALIQRNPNSTSPSSEKRGRRKQPEPGRFLGVRRRP-WGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDR 95 (342)
Q Consensus 17 d~~~~~~~~~~~~q~~~~s~s~~~~k~~rrr~~~tSrYRGV~~rk-~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~ 95 (342)
++.+++..+|+.+....+..+. +....++|+|+||++.+ .|||+|+|++ +||+++||.|+++|+|+.||+
T Consensus 38 ~~~dnri~NLr~~T~~eN~~N~------~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~- 108 (121)
T PHA00280 38 NPLNDALDNLRLALPKENSWNM------KTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR- 108 (121)
T ss_pred CCCCCcHHHhhhcCHHHHhccc------CCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-
Confidence 3667888888888887765442 23456789999999876 7999999999 999999999999999999997
Q ss_pred HHHhhcCCccc
Q 044016 96 AALSMKGAQAR 106 (342)
Q Consensus 96 AAikl~G~~A~ 106 (342)
+++++||++|+
T Consensus 109 ~~~~lhGeFa~ 119 (121)
T PHA00280 109 TRRELHGQFAR 119 (121)
T ss_pred HHHHHhhcccc
Confidence 78899999985
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=6.9e-11 Score=86.01 Aligned_cols=52 Identities=29% Similarity=0.379 Sum_probs=45.6
Q ss_pred CceEEEEECC-CCeEEEEEecCCC---CceEecCCCCCHHHHHHHHHHHHHhhcCC
Q 044016 52 GRFLGVRRRP-WGRYAAEIRDPTT---KERHWLGTFDTAHEAALAYDRAALSMKGA 103 (342)
Q Consensus 52 SrYRGV~~rk-~GKW~AqI~~~~~---gKri~LGTFdTaEEAArAYD~AAikl~G~ 103 (342)
|+|+||++.+ .++|+|+|++... +|+++||.|+++|||++|+++++++++|+
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 5799999877 7999999998321 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=81.48 E-value=4.7 Score=28.73 Aligned_cols=37 Identities=19% Similarity=0.200 Sum_probs=28.7
Q ss_pred eEEEEEe--cCCCC--ceEecCCCCCHHHHHHHHHHHHHhh
Q 044016 64 RYAAEIR--DPTTK--ERHWLGTFDTAHEAALAYDRAALSM 100 (342)
Q Consensus 64 KW~AqI~--~~~~g--Kri~LGTFdTaEEAArAYD~AAikl 100 (342)
+|..+|. .+..| ++++-+.|.|..||..+..++...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5888883 33244 6788899999999999998877665
No 6
>PHA02601 int integrase; Provisional
Probab=67.39 E-value=7.3 Score=36.52 Aligned_cols=44 Identities=23% Similarity=0.196 Sum_probs=30.1
Q ss_pred EEEECCCCeEEEEEecC-CCCceEecCCCCCHHHHHHHHHHHHHhh
Q 044016 56 GVRRRPWGRYAAEIRDP-TTKERHWLGTFDTAHEAALAYDRAALSM 100 (342)
Q Consensus 56 GV~~rk~GKW~AqI~~~-~~gKri~LGTFdTaEEAArAYD~AAikl 100 (342)
+|++.+.|+|+++++.. ..|+++.. +|.|..||.+..+.....+
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 46666678999999852 23666553 6999999877666554444
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=50.50 E-value=36 Score=31.37 Aligned_cols=39 Identities=21% Similarity=0.189 Sum_probs=27.6
Q ss_pred CCeEEEEEecCCCCceEecCCCC--CHHHHHHHHHHHHHhh
Q 044016 62 WGRYAAEIRDPTTKERHWLGTFD--TAHEAALAYDRAALSM 100 (342)
Q Consensus 62 ~GKW~AqI~~~~~gKri~LGTFd--TaEEAArAYD~AAikl 100 (342)
.+.|..+++.....+++.||+|+ +.++|..+..+....+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699998884444567899995 6777777766655554
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=50.39 E-value=28 Score=27.84 Aligned_cols=38 Identities=21% Similarity=0.298 Sum_probs=29.0
Q ss_pred eEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhc
Q 044016 64 RYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMK 101 (342)
Q Consensus 64 KW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~ 101 (342)
.|-++|.-..-.-..|-|-|.|.+||..+.-.-...+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 47789987444578899999999999998665554443
No 9
>PRK09692 integrase; Provisional
Probab=43.51 E-value=64 Score=31.72 Aligned_cols=42 Identities=19% Similarity=0.191 Sum_probs=25.9
Q ss_pred EEECCCC--eEEEEEecCCCCce--EecCCCC--CHHHHHHHHHHHHH
Q 044016 57 VRRRPWG--RYAAEIRDPTTKER--HWLGTFD--TAHEAALAYDRAAL 98 (342)
Q Consensus 57 V~~rk~G--KW~AqI~~~~~gKr--i~LGTFd--TaEEAArAYD~AAi 98 (342)
|+.++.| .|+.+-+.+.+||+ +-||.|+ |..||..+..++..
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 4444544 59988765434443 6899999 67676555444333
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=42.01 E-value=17 Score=26.53 Aligned_cols=23 Identities=26% Similarity=0.294 Sum_probs=18.8
Q ss_pred CceEecCCCCCHHHHHHHHHHHH
Q 044016 75 KERHWLGTFDTAHEAALAYDRAA 97 (342)
Q Consensus 75 gKri~LGTFdTaEEAArAYD~AA 97 (342)
.-++.+|.|++.+||..+-.+..
T Consensus 43 ~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 43 WYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp CEEEEECCECTCCHHHHHHHHHH
T ss_pred eEEEEECCCCCHHHHHHHHHHHh
Confidence 34688899999999998877665
No 11
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=39.50 E-value=71 Score=25.24 Aligned_cols=44 Identities=18% Similarity=0.138 Sum_probs=26.4
Q ss_pred EEECCC--CeEEEEEecCCCCceEecCCCCC--HHHHHHHHHHHHHhh
Q 044016 57 VRRRPW--GRYAAEIRDPTTKERHWLGTFDT--AHEAALAYDRAALSM 100 (342)
Q Consensus 57 V~~rk~--GKW~AqI~~~~~gKri~LGTFdT--aEEAArAYD~AAikl 100 (342)
|+..+. ..|..+.+...+.+++.||.|.. .+||.....++...+
T Consensus 27 l~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 27 LRVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 334454 35998888733346789999986 555555544443333
No 12
>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=38.55 E-value=51 Score=26.22 Aligned_cols=46 Identities=20% Similarity=0.152 Sum_probs=35.0
Q ss_pred CceEEEEECC-CCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhh
Q 044016 52 GRFLGVRRRP-WGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSM 100 (342)
Q Consensus 52 SrYRGV~~rk-~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl 100 (342)
.+|.||..|- .-+-.+.|.. .||-+..|. .++|||..|.++....+
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 3688986554 3467777776 898887775 78999999999877665
No 13
>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=35.07 E-value=98 Score=28.22 Aligned_cols=47 Identities=28% Similarity=0.247 Sum_probs=36.8
Q ss_pred CCCceEEEEECC-CCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhh
Q 044016 50 EPGRFLGVRRRP-WGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSM 100 (342)
Q Consensus 50 ~tSrYRGV~~rk-~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl 100 (342)
++ +|.||..|- .-|-.+.|+. .||-+-.| ..++|+|++|.++.+..+
T Consensus 33 eP-~fpgli~R~~~Pk~t~lIF~--sGKiviTG-aks~~~~~~a~~~~~~~l 80 (174)
T cd04517 33 NP-RYPKVTMRLREPRATASVWS--SGKITITG-ATSEEEAKQAARRAARLL 80 (174)
T ss_pred eC-CCCEEEEEecCCcEEEEEEC--CCeEEEEc-cCCHHHHHHHHHHHHHHH
Confidence 44 799987654 4577888887 88876666 489999999999888777
No 14
>PLN00062 TATA-box-binding protein; Provisional
Probab=32.85 E-value=1.4e+02 Score=27.51 Aligned_cols=49 Identities=24% Similarity=0.249 Sum_probs=37.4
Q ss_pred CCCceEEEEECC-CCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhc
Q 044016 50 EPGRFLGVRRRP-WGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMK 101 (342)
Q Consensus 50 ~tSrYRGV~~rk-~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~ 101 (342)
++.+|.||..|- .-|-.+.|.. .||-+-.|. .++|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFA--SGKMVCTGA-KSEHDSKLAARKYARIIQ 81 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 344699987554 4567788887 888776664 789999999999888774
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=32.43 E-value=1.5e+02 Score=27.18 Aligned_cols=49 Identities=22% Similarity=0.217 Sum_probs=37.7
Q ss_pred CCCceEEEEECC-CCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhc
Q 044016 50 EPGRFLGVRRRP-WGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMK 101 (342)
Q Consensus 50 ~tSrYRGV~~rk-~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~ 101 (342)
++.+|.||..|- .-|-.+.|+. .||-+-.|. .++|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 344699987554 4567788887 898887786 678999999999888773
No 16
>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=30.35 E-value=1.5e+02 Score=26.98 Aligned_cols=48 Identities=27% Similarity=0.253 Sum_probs=36.4
Q ss_pred CCCceEEEEECC-CCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhh
Q 044016 50 EPGRFLGVRRRP-WGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSM 100 (342)
Q Consensus 50 ~tSrYRGV~~rk-~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl 100 (342)
++.+|.||..|- .-+-.+.|.. .||-+-.|. .+.|+|.+|.++.+..+
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf~--sGKivitGa-ks~~~~~~a~~~~~~~L 80 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIFS--SGKMVITGA-KSEEDAKLAARKYARIL 80 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEEC--CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 345699987664 4566777776 888777776 67889999999888777
No 17
>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=28.72 E-value=1.7e+02 Score=26.78 Aligned_cols=49 Identities=20% Similarity=0.192 Sum_probs=37.1
Q ss_pred CCCceEEEEECC-CCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhc
Q 044016 50 EPGRFLGVRRRP-WGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMK 101 (342)
Q Consensus 50 ~tSrYRGV~~rk-~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~ 101 (342)
++.+|.||..|- .-+-.+.|+. .||-+-.|. .++|+|..|-++.+..+.
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 345699987654 4466677776 888777775 789999999999888774
No 18
>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=25.33 E-value=69 Score=27.20 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=17.8
Q ss_pred cCCCCCHHHHHHHHHHHHHhh
Q 044016 80 LGTFDTAHEAALAYDRAALSM 100 (342)
Q Consensus 80 LGTFdTaEEAArAYD~AAikl 100 (342)
-|+|+|+|+|..-||..+-.|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 399999999999999876544
No 19
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=24.92 E-value=1.3e+02 Score=25.28 Aligned_cols=36 Identities=17% Similarity=0.101 Sum_probs=28.2
Q ss_pred eEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhc
Q 044016 64 RYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMK 101 (342)
Q Consensus 64 KW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~ 101 (342)
.|.|+|.. +..-+-++.....+.|..|..+|+.++-
T Consensus 71 ~~~a~v~~--G~iifEi~~~~~~~~~~~alk~a~~Klp 106 (112)
T cd01433 71 GWVARVKP--GQILFEVRGVPEEEVAKEALRRAAKKLP 106 (112)
T ss_pred EEEEEECC--CCEEEEEeCcCcHHHHHHHHHHhhccCC
Confidence 49999986 5555666666559999999999988873
No 20
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=24.24 E-value=1.1e+02 Score=27.80 Aligned_cols=36 Identities=19% Similarity=0.042 Sum_probs=29.7
Q ss_pred EEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhcCC
Q 044016 65 YAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMKGA 103 (342)
Q Consensus 65 W~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~G~ 103 (342)
|.|+|.. |+.++-=....++.|..|..+|+.+|=+.
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 9999884 66676667788888999999999998654
No 21
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=23.81 E-value=1.9e+02 Score=21.48 Aligned_cols=39 Identities=33% Similarity=0.232 Sum_probs=24.5
Q ss_pred EEECCCCeEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHh
Q 044016 57 VRRRPWGRYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALS 99 (342)
Q Consensus 57 V~~rk~GKW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAik 99 (342)
|..+..|.|..+.-. ..+ -..+|+|.+||..+=...|..
T Consensus 3 V~p~~~~~W~v~~eg--~~r--a~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG--AKR--ASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeCC--Ccc--cccccCcHHHHHHHHHHHHHh
Confidence 444445779777553 222 279999999987664444443
No 22
>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=23.26 E-value=1.4e+02 Score=24.54 Aligned_cols=38 Identities=18% Similarity=0.141 Sum_probs=25.9
Q ss_pred CceEEEEECCCCeEEEEEecCCCCceEecCCCCCHHHHHHH
Q 044016 52 GRFLGVRRRPWGRYAAEIRDPTTKERHWLGTFDTAHEAALA 92 (342)
Q Consensus 52 SrYRGV~~rk~GKW~AqI~~~~~gKri~LGTFdTaEEAArA 92 (342)
-+||.|..-+ |||+|.+.. +..-.---.|..+|.|-|-
T Consensus 31 dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 31 DGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred ccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 3588886555 999999998 5555555778888888765
No 23
>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=21.87 E-value=1.6e+02 Score=25.71 Aligned_cols=34 Identities=18% Similarity=0.084 Sum_probs=28.2
Q ss_pred eEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhh
Q 044016 64 RYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSM 100 (342)
Q Consensus 64 KW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl 100 (342)
.|+|+|.. +..-+-++. .+++.|..|..+|+.+|
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 49999997 666666666 89999999999998876
No 24
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=21.27 E-value=1.5e+02 Score=26.26 Aligned_cols=36 Identities=14% Similarity=-0.007 Sum_probs=29.7
Q ss_pred eEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHhhcC
Q 044016 64 RYAAEIRDPTTKERHWLGTFDTAHEAALAYDRAALSMKG 102 (342)
Q Consensus 64 KW~AqI~~~~~gKri~LGTFdTaEEAArAYD~AAikl~G 102 (342)
-|+|+|.. +..-+-++. .+++.|..|..+|+.+|-+
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 39999997 666666766 8999999999999988854
Done!