Query 036655
Match_columns 243
No_of_seqs 181 out of 1192
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:12:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036655.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036655hhsearch_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 5.7E-20 1.2E-24 131.7 7.6 61 34-94 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 2.5E-19 5.5E-24 129.9 8.5 63 35-97 1-63 (64)
3 PHA00280 putative NHN endonucl 99.7 4.3E-18 9.3E-23 139.2 7.5 72 15-89 48-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 3.7E-11 8.1E-16 83.9 5.6 52 34-85 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 79.9 7.9 0.00017 26.1 5.7 38 46-83 1-42 (46)
6 PHA02601 int integrase; Provis 69.8 6.8 0.00015 35.2 4.3 44 38-82 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 63.3 15 0.00033 32.5 5.2 42 42-83 7-50 (357)
8 PRK09692 integrase; Provisiona 53.1 39 0.00085 31.7 6.3 36 45-80 41-80 (413)
9 PF05036 SPOR: Sporulation rel 49.9 12 0.00027 26.0 1.9 24 56-79 42-65 (76)
10 PF10729 CedA: Cell division a 42.9 40 0.00087 25.9 3.7 38 34-74 31-68 (80)
11 PF08846 DUF1816: Domain of un 40.7 56 0.0012 24.7 4.2 39 45-83 8-46 (68)
12 PF13356 DUF4102: Domain of un 32.0 1.6E+02 0.0035 22.0 5.7 38 45-82 35-74 (89)
13 cd04516 TBP_eukaryotes eukaryo 31.7 2.5E+02 0.0054 24.4 7.4 47 34-83 34-81 (174)
14 PLN00062 TATA-box-binding prot 31.5 2.5E+02 0.0053 24.6 7.4 48 34-84 34-82 (179)
15 COG0197 RplP Ribosomal protein 28.5 81 0.0018 27.1 3.8 37 46-85 95-131 (146)
16 PF00352 TBP: Transcription fa 28.1 1.8E+02 0.004 21.7 5.4 46 34-82 36-82 (86)
17 TIGR01164 rplP_bact ribosomal 27.2 1.1E+02 0.0024 25.2 4.3 35 45-82 90-124 (126)
18 PF09954 DUF2188: Uncharacteri 27.1 1.6E+02 0.0034 20.7 4.6 36 42-81 6-41 (62)
19 PRK09203 rplP 50S ribosomal pr 26.2 1.1E+02 0.0023 25.7 4.0 37 45-84 91-127 (138)
20 PRK10113 cell division modulat 25.8 54 0.0012 25.2 2.0 38 34-74 31-68 (80)
21 PF08471 Ribonuc_red_2_N: Clas 24.5 83 0.0018 25.2 2.9 21 62-82 70-90 (93)
22 KOG3422 Mitochondrial ribosoma 24.3 1.5E+02 0.0032 27.2 4.9 39 45-85 132-170 (221)
23 cd04517 TLF TBP-like factors ( 23.9 3.6E+02 0.0078 23.3 7.0 46 35-83 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=5.7e-20 Score=131.67 Aligned_cols=61 Identities=66% Similarity=1.152 Sum_probs=56.6
Q ss_pred CceeEEEECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 036655 34 CTYKGVRQRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLYGPDAKLNLPEL 94 (243)
Q Consensus 34 SgyRGVr~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~G~~A~~NFp~~ 94 (243)
|+||||+++++|||+|+|+++..||++|||+|+|+|||+.|||++++++||.++.+|||++
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 7899997777799999999944499999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.80 E-value=2.5e-19 Score=129.92 Aligned_cols=63 Identities=62% Similarity=1.098 Sum_probs=59.7
Q ss_pred ceeEEEECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHcCCCCCCCCCCCCCc
Q 036655 35 TYKGVRQRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLYGPDAKLNLPELPSA 97 (243)
Q Consensus 35 gyRGVr~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~G~~A~~NFp~~~~~ 97 (243)
+|+||+++++|||+|+|+++.+|+.++||+|+|+|||+.|||.+++++||.++.+|||...|.
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 589997778899999999998999999999999999999999999999999999999998875
No 3
>PHA00280 putative NHN endonuclease
Probab=99.74 E-value=4.3e-18 Score=139.23 Aligned_cols=72 Identities=18% Similarity=0.238 Sum_probs=66.9
Q ss_pred ccCCcccccCCCCCCCCCCCceeEE-EECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHcCCCCCC
Q 036655 15 QASSRKGCMRGKGGPENALCTYKGV-RQRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLYGPDAKL 89 (243)
Q Consensus 15 ~~str~~N~rN~~~~~~ntSgyRGV-r~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~G~~A~~ 89 (243)
+.+|+++|++|++.+++|+|||||| +++..|||+|+|++ +||+++||.|+++|+|+.||+ ++++|||+||..
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 RLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred hhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 4589999999999999999999999 68889999999999 999999999999999999997 778999999863
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=99.19 E-value=3.7e-11 Score=83.93 Aligned_cols=52 Identities=35% Similarity=0.502 Sum_probs=45.9
Q ss_pred CceeEE-EECCCCcEEEEEeecC-C--CeEEeecCCCCHHHHHHHHHHHHHHHcCC
Q 036655 34 CTYKGV-RQRTWGKWVAEIREPN-R--GARLWLGTFDTSHEAAMAYDAAARKLYGP 85 (243)
Q Consensus 34 SgyRGV-r~~~~GKW~A~I~~~~-~--gK~i~LGtFdT~EEAA~AYD~Aa~kl~G~ 85 (243)
|+|+|| +++..++|+|+|++.. + +|+++||.|++++||++||++++++++|+
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 789999 6888899999999842 2 49999999999999999999999999875
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=79.91 E-value=7.9 Score=26.09 Aligned_cols=38 Identities=21% Similarity=0.230 Sum_probs=29.2
Q ss_pred cEEEEEe-e-cCCC--eEEeecCCCCHHHHHHHHHHHHHHHc
Q 036655 46 KWVAEIR-E-PNRG--ARLWLGTFDTSHEAAMAYDAAARKLY 83 (243)
Q Consensus 46 KW~A~I~-~-~~~g--K~i~LGtFdT~EEAA~AYD~Aa~kl~ 83 (243)
+|..+|. . +..| ++++-+-|.|..||..+...+..++.
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 3 2244 67888999999999999988777664
No 6
>PHA02601 int integrase; Provisional
Probab=69.78 E-value=6.8 Score=35.23 Aligned_cols=44 Identities=30% Similarity=0.400 Sum_probs=30.5
Q ss_pred EEEECCCCcEEEEEeec-CCCeEEeecCCCCHHHHHHHHHHHHHHH
Q 036655 38 GVRQRTWGKWVAEIREP-NRGARLWLGTFDTSHEAAMAYDAAARKL 82 (243)
Q Consensus 38 GVr~~~~GKW~A~I~~~-~~gK~i~LGtFdT~EEAA~AYD~Aa~kl 82 (243)
+|+++++|+|++++... ..|+++.. +|.|..||..........+
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 46677789999999862 23776654 6999999876655544443
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=63.29 E-value=15 Score=32.46 Aligned_cols=42 Identities=26% Similarity=0.276 Sum_probs=29.0
Q ss_pred CCCCcEEEEEeecCCCeEEeecCCC--CHHHHHHHHHHHHHHHc
Q 036655 42 RTWGKWVAEIREPNRGARLWLGTFD--TSHEAAMAYDAAARKLY 83 (243)
Q Consensus 42 ~~~GKW~A~I~~~~~gK~i~LGtFd--T~EEAA~AYD~Aa~kl~ 83 (243)
+..+.|+.+++.....+++.||+|+ +.++|..........+.
T Consensus 7 ~g~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 7 SGSKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CCCEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 3346699999884344557799995 77888877766555553
No 8
>PRK09692 integrase; Provisional
Probab=53.12 E-value=39 Score=31.72 Aligned_cols=36 Identities=17% Similarity=0.184 Sum_probs=24.1
Q ss_pred CcEEEEEeecCCCeE--EeecCCC--CHHHHHHHHHHHHH
Q 036655 45 GKWVAEIREPNRGAR--LWLGTFD--TSHEAAMAYDAAAR 80 (243)
Q Consensus 45 GKW~A~I~~~~~gK~--i~LGtFd--T~EEAA~AYD~Aa~ 80 (243)
..|+.+.+.+.+|++ +.||.|. |..||..+...+..
T Consensus 41 k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 41 KIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 349999875434554 6899999 77777665544333
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=49.89 E-value=12 Score=26.01 Aligned_cols=24 Identities=25% Similarity=0.292 Sum_probs=19.6
Q ss_pred CCeEEeecCCCCHHHHHHHHHHHH
Q 036655 56 RGARLWLGTFDTSHEAAMAYDAAA 79 (243)
Q Consensus 56 ~gK~i~LGtFdT~EEAA~AYD~Aa 79 (243)
.--++.+|.|++.+||..+.....
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 445788999999999998877665
No 10
>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=42.88 E-value=40 Score=25.92 Aligned_cols=38 Identities=21% Similarity=0.117 Sum_probs=26.4
Q ss_pred CceeEEEECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHH
Q 036655 34 CTYKGVRQRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMA 74 (243)
Q Consensus 34 SgyRGVr~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~A 74 (243)
-+||-||.-+ |||+|.+.. +..-.---.|..+|.|-+=
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 5899998655 999999988 5555556778888877653
No 11
>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=40.75 E-value=56 Score=24.66 Aligned_cols=39 Identities=28% Similarity=0.438 Sum_probs=28.7
Q ss_pred CcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHc
Q 036655 45 GKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLY 83 (243)
Q Consensus 45 GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~ 83 (243)
-.|=++|.--.-.-..|-|-|.+.+||..+..-...-|.
T Consensus 8 laWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 8 LAWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred CcEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 347788877444678999999999999988655444443
No 12
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=32.05 E-value=1.6e+02 Score=21.96 Aligned_cols=38 Identities=16% Similarity=0.149 Sum_probs=23.9
Q ss_pred CcEEEEEeecCCCeEEeecCCC--CHHHHHHHHHHHHHHH
Q 036655 45 GKWVAEIREPNRGARLWLGTFD--TSHEAAMAYDAAARKL 82 (243)
Q Consensus 45 GKW~A~I~~~~~gK~i~LGtFd--T~EEAA~AYD~Aa~kl 82 (243)
..|..+.+.....+++.||.|. |+.||..........+
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 4599998873334568999996 4556655554444444
No 13
>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=31.69 E-value=2.5e+02 Score=24.35 Aligned_cols=47 Identities=19% Similarity=0.147 Sum_probs=37.4
Q ss_pred CceeEE-EECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHc
Q 036655 34 CTYKGV-RQRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLY 83 (243)
Q Consensus 34 SgyRGV-r~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~ 83 (243)
.+|-|| .+-+.-+-.+.|.. .||-+--|. .++|+|..|.++.++.+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 578898 34455677788888 999998887 578899999988888774
No 14
>PLN00062 TATA-box-binding protein; Provisional
Probab=31.50 E-value=2.5e+02 Score=24.55 Aligned_cols=48 Identities=21% Similarity=0.174 Sum_probs=37.7
Q ss_pred CceeEE-EECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHcC
Q 036655 34 CTYKGV-RQRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLYG 84 (243)
Q Consensus 34 SgyRGV-r~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~G 84 (243)
.+|-|| .+-+.-|=.+.|.. .||-+--|. .++|+|..|.++.++.+..
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~~~~~L~~ 82 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFA--SGKMVCTGA-KSEHDSKLAARKYARIIQK 82 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHH
Confidence 578898 44455667788888 999888886 7889999999988887743
No 15
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=28.52 E-value=81 Score=27.11 Aligned_cols=37 Identities=27% Similarity=0.197 Sum_probs=29.8
Q ss_pred cEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHcCC
Q 036655 46 KWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLYGP 85 (243)
Q Consensus 46 KW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~G~ 85 (243)
-|.|+|.. |+.++-=...+++.|.+|...|+.||=+.
T Consensus 95 gwaArVkp---G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARVKP---GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEecC---CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 49999985 66676667788888999999999888544
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=28.10 E-value=1.8e+02 Score=21.74 Aligned_cols=46 Identities=20% Similarity=0.135 Sum_probs=34.9
Q ss_pred CceeEEE-ECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHH
Q 036655 34 CTYKGVR-QRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKL 82 (243)
Q Consensus 34 SgyRGVr-~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl 82 (243)
.+|.||. +-..-+-.+.|.. .||-+-.|. .+.|||..|.+.....+
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 4788883 4444567777777 999988886 78999999998877665
No 17
>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=27.15 E-value=1.1e+02 Score=25.23 Aligned_cols=35 Identities=26% Similarity=0.276 Sum_probs=29.3
Q ss_pred CcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHH
Q 036655 45 GKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKL 82 (243)
Q Consensus 45 GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl 82 (243)
..|+|+|.. +..-+-++. .+++.|..|...|+.+|
T Consensus 90 ~~~varV~~--G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 90 EYWVAVVKP--GKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred CEEEEEECC--CCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 349999998 777777777 89999999999988775
No 18
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=27.14 E-value=1.6e+02 Score=20.72 Aligned_cols=36 Identities=33% Similarity=0.352 Sum_probs=25.0
Q ss_pred CCCCcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHH
Q 036655 42 RTWGKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARK 81 (243)
Q Consensus 42 ~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~k 81 (243)
+..+.|..+.-. ...-..+|+|.+||..+=...++.
T Consensus 6 ~~~~~W~v~~eg----~~ra~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 6 REDGGWAVKKEG----AKRASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred cCCCCceEEeCC----CcccccccCcHHHHHHHHHHHHHh
Confidence 455779877654 333379999999998775555544
No 19
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=26.16 E-value=1.1e+02 Score=25.73 Aligned_cols=37 Identities=24% Similarity=0.149 Sum_probs=30.4
Q ss_pred CcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHcC
Q 036655 45 GKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLYG 84 (243)
Q Consensus 45 GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~G 84 (243)
.-|+|+|.. +..-+-++. .+++.|..|...|+.+|=+
T Consensus 91 ~~~varVk~--G~iifEi~~-~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 91 EYWVAVVKP--GRILFEIAG-VSEELAREALRLAAAKLPI 127 (138)
T ss_pred cEEEEEECC--CCEEEEEeC-CCHHHHHHHHHHHhccCCC
Confidence 349999998 777777777 8999999999999887743
No 20
>PRK10113 cell division modulator; Provisional
Probab=25.75 E-value=54 Score=25.17 Aligned_cols=38 Identities=21% Similarity=0.178 Sum_probs=27.1
Q ss_pred CceeEEEECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHH
Q 036655 34 CTYKGVRQRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMA 74 (243)
Q Consensus 34 SgyRGVr~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~A 74 (243)
-+||-||.-+ |||+|.+.. +..-.---.|..+|.|-+=
T Consensus 31 d~frDVW~Lr-GKYVAFvl~--ge~FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 31 DSFRDVWMLR-GKYVAFVLM--GESFLRSPAFSVPESAQRW 68 (80)
T ss_pred cchhhhheec-cceEEEEEe--chhhccCCccCCcHHHHHH
Confidence 5788897655 999999987 4344444678888877653
No 21
>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=24.53 E-value=83 Score=25.21 Aligned_cols=21 Identities=33% Similarity=0.396 Sum_probs=17.7
Q ss_pred ecCCCCHHHHHHHHHHHHHHH
Q 036655 62 LGTFDTSHEAAMAYDAAARKL 82 (243)
Q Consensus 62 LGtFdT~EEAA~AYD~Aa~kl 82 (243)
-|.|+|+|+|..-||..+-.|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999876544
No 22
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=24.28 E-value=1.5e+02 Score=27.17 Aligned_cols=39 Identities=28% Similarity=0.235 Sum_probs=33.1
Q ss_pred CcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHcCC
Q 036655 45 GKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLYGP 85 (243)
Q Consensus 45 GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~G~ 85 (243)
..|+|+|.. +..-+-+|---+++||..|.+.||.++-+.
T Consensus 132 d~wva~V~~--GrIl~EmgG~~~~~~Ar~al~~aa~klp~~ 170 (221)
T KOG3422|consen 132 DHWVARVKA--GRILFEMGGDVEEEEARQALLQAAHKLPFK 170 (221)
T ss_pred ceeEEEecC--CcEEEEeCCcccHHHHHHHHHHHHhcCCcc
Confidence 359999998 778888888899999999999999887543
No 23
>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=23.86 E-value=3.6e+02 Score=23.28 Aligned_cols=46 Identities=26% Similarity=0.203 Sum_probs=36.5
Q ss_pred ceeEEE-ECCCCcEEEEEeecCCCeEEeecCCCCHHHHHHHHHHHHHHHc
Q 036655 35 TYKGVR-QRTWGKWVAEIREPNRGARLWLGTFDTSHEAAMAYDAAARKLY 83 (243)
Q Consensus 35 gyRGVr-~~~~GKW~A~I~~~~~gK~i~LGtFdT~EEAA~AYD~Aa~kl~ 83 (243)
+|.||. +-+.-+=.+.|.. +||-+-.|. .+.|+|++|.++.++.+.
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 889984 4444677888888 999887775 789999999988887773
Done!