Query 037093
Match_columns 282
No_of_seqs 192 out of 1187
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 08:35:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037093.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037093hhsearch_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 6.9E-21 1.5E-25 140.8 8.4 63 28-90 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.8 1.4E-20 3E-25 137.4 7.5 61 27-87 1-61 (61)
3 PHA00280 putative NHN endonucl 99.6 2.1E-15 4.5E-20 126.1 7.1 77 2-81 42-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 1.2E-10 2.7E-15 82.9 5.1 52 27-78 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 78.8 7 0.00015 27.1 5.3 38 39-76 1-42 (46)
6 PHA02601 int integrase; Provis 66.1 8.9 0.00019 35.2 4.3 44 31-75 2-46 (333)
7 PF08846 DUF1816: Domain of un 57.5 23 0.0005 27.4 4.5 41 39-79 9-49 (68)
8 cd00801 INT_P4 Bacteriophage P 55.4 28 0.00061 31.4 5.5 39 37-75 9-49 (357)
9 PF05036 SPOR: Sporulation rel 43.5 17 0.00038 25.8 1.8 24 49-72 42-65 (76)
10 PRK09692 integrase; Provisiona 41.0 77 0.0017 30.4 6.3 39 32-70 33-77 (413)
11 PF13356 DUF4102: Domain of un 34.9 1.1E+02 0.0024 23.5 5.2 36 39-74 36-73 (89)
12 COG0197 RplP Ribosomal protein 30.1 82 0.0018 27.8 4.2 36 40-78 96-131 (146)
13 PF08471 Ribonuc_red_2_N: Clas 25.5 74 0.0016 26.2 2.9 21 55-75 70-90 (93)
14 PF00352 TBP: Transcription fa 24.9 2.1E+02 0.0045 22.1 5.2 46 28-76 37-83 (86)
15 PRK09203 rplP 50S ribosomal pr 24.7 1.2E+02 0.0025 26.1 4.2 36 39-77 92-127 (138)
16 TIGR01164 rplP_bact ribosomal 24.6 1.3E+02 0.0029 25.4 4.4 34 39-75 91-124 (126)
17 PF09954 DUF2188: Uncharacteri 24.5 2E+02 0.0043 20.8 4.8 39 32-74 3-41 (62)
18 cd01433 Ribosomal_L16_L10e Rib 21.9 1.6E+02 0.0034 24.0 4.2 36 39-76 71-106 (112)
19 PF10729 CedA: Cell division a 20.8 1.8E+02 0.0039 23.1 4.1 37 27-66 31-67 (80)
20 cd04516 TBP_eukaryotes eukaryo 20.2 4.8E+02 0.01 23.2 7.2 47 27-76 34-81 (174)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=6.9e-21 Score=140.82 Aligned_cols=63 Identities=63% Similarity=1.012 Sum_probs=60.7
Q ss_pred ceeEEEeCCCCcEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 037093 28 RFLGVRRRPWGRYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMRGPRARTNFVYSDMP 90 (282)
Q Consensus 28 ~YRGV~~r~~GKW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~A~lNFp~sdy~ 90 (282)
+||||+++++|||+|+|+++.++++++||+|+|+||||+|||+|+++++|..+++|||.++|+
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 599999988999999999988999999999999999999999999999999999999999986
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=99.83 E-value=1.4e-20 Score=137.44 Aligned_cols=61 Identities=64% Similarity=1.039 Sum_probs=57.3
Q ss_pred CceeEEEeCCCCcEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 037093 27 NRFLGVRRRPWGRYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMRGPRARTNFVYS 87 (282)
Q Consensus 27 S~YRGV~~r~~GKW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~A~lNFp~s 87 (282)
|+||||+++++|||+|+|++...++++|||+|+|+||||+|||+|+++++|.++++|||++
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 6899999988999999999955599999999999999999999999999999999999864
No 3
>PHA00280 putative NHN endonuclease
Probab=99.59 E-value=2.1e-15 Score=126.11 Aligned_cols=77 Identities=17% Similarity=0.204 Sum_probs=68.2
Q ss_pred CCCChhHhhhhhhhcCCCCCCCCCCCceeEEEeCC-CCcEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhcCCCC
Q 037093 2 NSSSSTKIKKKQTQQGQDTTGGSNGNRFLGVRRRP-WGRYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMRGPRA 80 (282)
Q Consensus 2 ~s~Ss~~~~~~q~rq~~~~~~~~ntS~YRGV~~r~-~GKW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~A 80 (282)
+.+++++.+...++..++..++.++|+||||++.+ .|||+|+|++ ++|+++||.|+++|+|+.||+ ++++++|++|
T Consensus 42 nri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa 118 (121)
T PHA00280 42 DALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFA 118 (121)
T ss_pred CcHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhccc
Confidence 45677888888888887778889999999999764 7999999998 999999999999999999997 7889999998
Q ss_pred C
Q 037093 81 R 81 (282)
Q Consensus 81 ~ 81 (282)
+
T Consensus 119 ~ 119 (121)
T PHA00280 119 R 119 (121)
T ss_pred c
Confidence 5
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=99.10 E-value=1.2e-10 Score=82.88 Aligned_cols=52 Identities=33% Similarity=0.429 Sum_probs=45.0
Q ss_pred CceeEEEeCC-CCcEEEEEeCCCC---CceEeecCCCCHHHHHHHHHHHHHHhcCC
Q 037093 27 NRFLGVRRRP-WGRYAAEIRDPST---KERHWLGTFDTAEEAALAYDRAARSMRGP 78 (282)
Q Consensus 27 S~YRGV~~r~-~GKW~A~I~~~~~---gKri~LGtFdTeEEAArAYD~AAikl~G~ 78 (282)
|+|+||++.+ .++|+|+|++... +|+++||.|+++|||++|+++++++++|+
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 6899999664 7999999998321 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=78.85 E-value=7 Score=27.05 Aligned_cols=38 Identities=18% Similarity=0.245 Sum_probs=29.1
Q ss_pred cEEEEEe--CCCC--CceEeecCCCCHHHHHHHHHHHHHHhc
Q 037093 39 RYAAEIR--DPST--KERHWLGTFDTAEEAALAYDRAARSMR 76 (282)
Q Consensus 39 KW~A~I~--~~~~--gKri~LGtFdTeEEAArAYD~AAikl~ 76 (282)
+|..+|. .+.. .++++-+-|.|..||..+...+..++.
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 3323 367888999999999999988877654
No 6
>PHA02601 int integrase; Provisional
Probab=66.14 E-value=8.9 Score=35.17 Aligned_cols=44 Identities=23% Similarity=0.205 Sum_probs=29.7
Q ss_pred EEEeCCCCcEEEEEeCC-CCCceEeecCCCCHHHHHHHHHHHHHHh
Q 037093 31 GVRRRPWGRYAAEIRDP-STKERHWLGTFDTAEEAALAYDRAARSM 75 (282)
Q Consensus 31 GV~~r~~GKW~A~I~~~-~~gKri~LGtFdTeEEAArAYD~AAikl 75 (282)
+|++.++|+|+++|+.. ..++++.. +|.|.+||.+..+.....+
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 46667789999999852 23555543 6999999876665554443
No 7
>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=57.45 E-value=23 Score=27.44 Aligned_cols=41 Identities=22% Similarity=0.316 Sum_probs=31.7
Q ss_pred cEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhcCCC
Q 037093 39 RYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMRGPR 79 (282)
Q Consensus 39 KW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~G~~ 79 (282)
.|-++|.-..-.-..|.|-|.+.+||..+.-.....+..+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~Eg 49 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLESEG 49 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHhhC
Confidence 48899987555678999999999999998766665555433
No 8
>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=55.38 E-value=28 Score=31.41 Aligned_cols=39 Identities=21% Similarity=0.214 Sum_probs=27.8
Q ss_pred CCcEEEEEeCCCCCceEeecCCC--CHHHHHHHHHHHHHHh
Q 037093 37 WGRYAAEIRDPSTKERHWLGTFD--TAEEAALAYDRAARSM 75 (282)
Q Consensus 37 ~GKW~A~I~~~~~gKri~LGtFd--TeEEAArAYD~AAikl 75 (282)
.+.|..+++.....+++.||+|+ +.++|..+..+....+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699999985555678899995 6777776666654444
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=43.50 E-value=17 Score=25.80 Aligned_cols=24 Identities=29% Similarity=0.328 Sum_probs=19.3
Q ss_pred CCceEeecCCCCHHHHHHHHHHHH
Q 037093 49 TKERHWLGTFDTAEEAALAYDRAA 72 (282)
Q Consensus 49 ~gKri~LGtFdTeEEAArAYD~AA 72 (282)
..-+|.+|.|++.+||..+-.+..
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 345788899999999988877655
No 10
>PRK09692 integrase; Provisional
Probab=41.00 E-value=77 Score=30.41 Aligned_cols=39 Identities=18% Similarity=0.203 Sum_probs=24.0
Q ss_pred EEeCCCC--cEEEEEeCCCCCc--eEeecCCC--CHHHHHHHHHH
Q 037093 32 VRRRPWG--RYAAEIRDPSTKE--RHWLGTFD--TAEEAALAYDR 70 (282)
Q Consensus 32 V~~r~~G--KW~A~I~~~~~gK--ri~LGtFd--TeEEAArAYD~ 70 (282)
|+-++.| .|+.+-+.+.+++ ++.||.|+ |..+|.++-.+
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 3334444 4999987543333 47899999 66666554433
No 11
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=34.87 E-value=1.1e+02 Score=23.46 Aligned_cols=36 Identities=17% Similarity=0.111 Sum_probs=23.4
Q ss_pred cEEEEEeCCCCCceEeecCCCC--HHHHHHHHHHHHHH
Q 037093 39 RYAAEIRDPSTKERHWLGTFDT--AEEAALAYDRAARS 74 (282)
Q Consensus 39 KW~A~I~~~~~gKri~LGtFdT--eEEAArAYD~AAik 74 (282)
.|..+.+...+.+++.||.|+. .++|.....+....
T Consensus 36 t~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~ 73 (89)
T PF13356_consen 36 TFYFRYRINGKRRRITLGRYPELSLAEAREKARELRAL 73 (89)
T ss_dssp EEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHH
T ss_pred EEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHH
Confidence 4999998744557899999975 44554444443333
No 12
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=30.05 E-value=82 Score=27.80 Aligned_cols=36 Identities=22% Similarity=0.073 Sum_probs=29.4
Q ss_pred EEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhcCC
Q 037093 40 YAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMRGP 78 (282)
Q Consensus 40 W~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~G~ 78 (282)
|.|+|.. ++.++-=....++.|.+|..+|+.||=..
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 9999974 66677667788888999999999987544
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=25.47 E-value=74 Score=26.20 Aligned_cols=21 Identities=33% Similarity=0.423 Sum_probs=18.1
Q ss_pred ecCCCCHHHHHHHHHHHHHHh
Q 037093 55 LGTFDTAEEAALAYDRAARSM 75 (282)
Q Consensus 55 LGtFdTeEEAArAYD~AAikl 75 (282)
-|+|+|+|+|..=||..+..|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999876654
No 14
>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=24.87 E-value=2.1e+02 Score=22.06 Aligned_cols=46 Identities=22% Similarity=0.212 Sum_probs=34.8
Q ss_pred ceeEEEeC-CCCcEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhc
Q 037093 28 RFLGVRRR-PWGRYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMR 76 (282)
Q Consensus 28 ~YRGV~~r-~~GKW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~ 76 (282)
+|.||..| ..-+-.+.|.. .||-+..|. .++|+|..|.++....+.
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 78898744 44567777776 888877775 789999999998776653
No 15
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=24.74 E-value=1.2e+02 Score=26.11 Aligned_cols=36 Identities=17% Similarity=0.026 Sum_probs=28.9
Q ss_pred cEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhcC
Q 037093 39 RYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMRG 77 (282)
Q Consensus 39 KW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~G 77 (282)
.|+|+|.. +..-+-+.. .+++.|..|..+|+.+|=+
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 555566666 8999999999999987644
No 16
>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=24.63 E-value=1.3e+02 Score=25.40 Aligned_cols=34 Identities=21% Similarity=0.134 Sum_probs=27.7
Q ss_pred cEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHh
Q 037093 39 RYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSM 75 (282)
Q Consensus 39 KW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl 75 (282)
.|+|+|.. +..-+.+.. .+++.|..|..+|+.+|
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 555566666 89999999999998875
No 17
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=24.53 E-value=2e+02 Score=20.76 Aligned_cols=39 Identities=33% Similarity=0.279 Sum_probs=25.2
Q ss_pred EEeCCCCcEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHH
Q 037093 32 VRRRPWGRYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARS 74 (282)
Q Consensus 32 V~~r~~GKW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAik 74 (282)
|..+..+.|..+.-. ..+ -..+|+|.+||..+=...|..
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 444456789888753 222 278999999997664444433
No 18
>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=21.93 E-value=1.6e+02 Score=23.98 Aligned_cols=36 Identities=19% Similarity=0.172 Sum_probs=27.9
Q ss_pred cEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhc
Q 037093 39 RYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMR 76 (282)
Q Consensus 39 KW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~ 76 (282)
.|.|+|.. +..-+-++....++.|..|..+|+.++-
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 5555666666669999999999887763
No 19
>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=20.84 E-value=1.8e+02 Score=23.11 Aligned_cols=37 Identities=22% Similarity=0.217 Sum_probs=23.8
Q ss_pred CceeEEEeCCCCcEEEEEeCCCCCceEeecCCCCHHHHHH
Q 037093 27 NRFLGVRRRPWGRYAAEIRDPSTKERHWLGTFDTAEEAAL 66 (282)
Q Consensus 27 S~YRGV~~r~~GKW~A~I~~~~~gKri~LGtFdTeEEAAr 66 (282)
-+||-|. .-.|||+|.+.. +..-..--.|..+|.|-|
T Consensus 31 dgfrdvw-~lrgkyvafvl~--ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 31 DGFRDVW-QLRGKYVAFVLM--GEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp TTECCEC-CCCCEEEEEEES--SS-EEE---BSSHHHHHH
T ss_pred cccccee-eeccceEEEEEe--cchhccCCCcCCcHHHHH
Confidence 4677774 445999999997 544445567888887765
No 20
>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=20.18 E-value=4.8e+02 Score=23.17 Aligned_cols=47 Identities=23% Similarity=0.256 Sum_probs=36.6
Q ss_pred CceeEEEeC-CCCcEEEEEeCCCCCceEeecCCCCHHHHHHHHHHHHHHhc
Q 037093 27 NRFLGVRRR-PWGRYAAEIRDPSTKERHWLGTFDTAEEAALAYDRAARSMR 76 (282)
Q Consensus 27 S~YRGV~~r-~~GKW~A~I~~~~~gKri~LGtFdTeEEAArAYD~AAikl~ 76 (282)
.+|.||..| ..-|-.+.|.. .||-+--|. .++|+|..|.++.+..+.
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 388898744 45677888887 888887786 578899999999887774
Done!