Query 046901
Match_columns 172
No_of_seqs 241 out of 1265
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:39:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046901hhsearch_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 99.9 6.2E-22 1.3E-26 134.5 7.6 61 11-72 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1.8E-20 3.8E-25 128.9 8.4 61 12-73 1-61 (64)
3 PHA00280 putative NHN endonucl 99.6 5.8E-15 1.3E-19 114.3 7.6 62 1-66 57-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 6.5E-11 1.4E-15 78.4 6.0 52 11-62 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 77.8 11 0.00023 23.9 5.5 37 23-59 1-41 (46)
6 PHA02601 int integrase; Provis 68.7 9.2 0.0002 32.4 4.6 44 15-59 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 68.3 13 0.00028 31.1 5.4 39 21-59 9-49 (357)
8 PF10729 CedA: Cell division a 63.3 14 0.00031 26.6 3.9 40 10-52 30-69 (80)
9 PRK09692 integrase; Provisiona 56.1 34 0.00073 30.3 6.0 39 16-54 33-77 (413)
10 PF08846 DUF1816: Domain of un 52.5 30 0.00065 24.5 4.1 38 23-60 9-46 (68)
11 PF13356 DUF4102: Domain of un 50.3 58 0.0013 22.9 5.4 43 17-59 28-74 (89)
12 PRK10113 cell division modulat 44.9 18 0.00039 26.0 2.0 38 11-51 31-68 (80)
13 PF05036 SPOR: Sporulation rel 43.7 26 0.00057 22.8 2.7 29 28-56 37-65 (76)
14 PF14112 DUF4284: Domain of un 38.9 21 0.00047 27.3 1.8 18 35-52 2-19 (122)
15 PF08471 Ribonuc_red_2_N: Clas 30.3 56 0.0012 24.6 2.7 21 39-59 70-90 (93)
16 cd01433 Ribosomal_L16_L10e Rib 29.6 1.1E+02 0.0024 22.8 4.4 36 23-60 71-106 (112)
17 PF07494 Reg_prop: Two compone 25.2 80 0.0017 17.2 2.2 11 33-43 14-24 (24)
18 COG2185 Sbm Methylmalonyl-CoA 24.0 58 0.0013 26.1 2.0 18 35-52 42-59 (143)
19 COG0197 RplP Ribosomal protein 23.7 1.5E+02 0.0033 23.9 4.3 36 24-62 96-131 (146)
20 TIGR01164 rplP_bact ribosomal 23.4 1.6E+02 0.0036 22.7 4.4 33 24-59 92-124 (126)
21 PRK09203 rplP 50S ribosomal pr 22.5 1.8E+02 0.0039 22.8 4.5 36 24-62 93-128 (138)
22 PF09003 Phage_integ_N: Bacter 21.6 1.7E+02 0.0036 21.1 3.8 33 28-62 31-63 (75)
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=99.86 E-value=6.2e-22 Score=134.55 Aligned_cols=61 Identities=61% Similarity=1.100 Sum_probs=57.5
Q ss_pred CceeEEEECCCCcEEEEEeeCCCCeEEeccCCCCHHHHHHHHHHHHHHhCCCCCCCCCCCCC
Q 046901 11 SAFRGVRMRKWGKWVSEIRQPGTKTRIWLGSYETPEMAAAAYDVAALHFRGRSGAHLNFPEL 72 (172)
Q Consensus 11 S~yrGVr~r~~gKW~AeIr~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l~G~~~a~lNFp~s 72 (172)
|+|+||+++++|||+|+|+.+..++++|||+|+|+|||+.|||.++++++|. .+.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~-~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGS-SAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCC-ccccCCCCC
Confidence 7899999888899999999966699999999999999999999999999998 899999975
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=1.8e-20 Score=128.93 Aligned_cols=61 Identities=59% Similarity=1.132 Sum_probs=57.8
Q ss_pred ceeEEEECCCCcEEEEEeeCCCCeEEeccCCCCHHHHHHHHHHHHHHhCCCCCCCCCCCCCC
Q 046901 12 AFRGVRMRKWGKWVSEIRQPGTKTRIWLGSYETPEMAAAAYDVAALHFRGRSGAHLNFPELA 73 (172)
Q Consensus 12 ~yrGVr~r~~gKW~AeIr~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l~G~~~a~lNFp~s~ 73 (172)
+|+||+++++|||+|+|+.|.+++++|||+|+|+||||.|||.++++++|. .+.+|||.+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~-~a~~Nf~~~~ 61 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGR-SARLNFPNSL 61 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCC-ccccCCCCcc
Confidence 599998888899999999999999999999999999999999999999998 8999999754
No 3
>PHA00280 putative NHN endonuclease
Probab=99.57 E-value=5.8e-15 Score=114.35 Aligned_cols=62 Identities=15% Similarity=0.222 Sum_probs=55.3
Q ss_pred CCCCcCCCCCCceeEEE-ECCCCcEEEEEeeCCCCeEEeccCCCCHHHHHHHHHHHHHHhCCCCCCC
Q 046901 1 METNQVVTKQSAFRGVR-MRKWGKWVSEIRQPGTKTRIWLGSYETPEMAAAAYDVAALHFRGRSGAH 66 (172)
Q Consensus 1 ~n~~~~~~ntS~yrGVr-~r~~gKW~AeIr~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l~G~~~a~ 66 (172)
+|++++++|+|||+||. ..+.|||+|+|+. +||+++||.|+++|+|+.||+ ++.+|||. +|+
T Consensus 57 ~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGe-Fa~ 119 (121)
T PHA00280 57 WNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQ-FAR 119 (121)
T ss_pred cccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhc-ccc
Confidence 47778889999999996 4557999999999 999999999999999999997 67789998 765
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=99.17 E-value=6.5e-11 Score=78.38 Aligned_cols=52 Identities=27% Similarity=0.464 Sum_probs=44.8
Q ss_pred CceeEEEE-CCCCcEEEEEeeCCC---CeEEeccCCCCHHHHHHHHHHHHHHhCCC
Q 046901 11 SAFRGVRM-RKWGKWVSEIRQPGT---KTRIWLGSYETPEMAAAAYDVAALHFRGR 62 (172)
Q Consensus 11 S~yrGVr~-r~~gKW~AeIr~p~~---~kri~LGtf~t~EeAA~AyD~Aa~~l~G~ 62 (172)
|+|+||++ ++.++|+|.|+.+.. +++++||.|++++||+++++.++..++|.
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 78999965 457999999998522 49999999999999999999999999873
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=77.76 E-value=11 Score=23.89 Aligned_cols=37 Identities=11% Similarity=0.171 Sum_probs=28.6
Q ss_pred cEEEEEe--eCC--CCeEEeccCCCCHHHHHHHHHHHHHHh
Q 046901 23 KWVSEIR--QPG--TKTRIWLGSYETPEMAAAAYDVAALHF 59 (172)
Q Consensus 23 KW~AeIr--~p~--~~kri~LGtf~t~EeAA~AyD~Aa~~l 59 (172)
+|...|. .|. ++++++-+.|.|..||..+.......+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5788883 443 347799999999999999988776665
No 6
>PHA02601 int integrase; Provisional
Probab=68.69 E-value=9.2 Score=32.40 Aligned_cols=44 Identities=30% Similarity=0.308 Sum_probs=30.1
Q ss_pred EEEECCCCcEEEEEeeC-CCCeEEeccCCCCHHHHHHHHHHHHHHh
Q 046901 15 GVRMRKWGKWVSEIRQP-GTKTRIWLGSYETPEMAAAAYDVAALHF 59 (172)
Q Consensus 15 GVr~r~~gKW~AeIr~p-~~~kri~LGtf~t~EeAA~AyD~Aa~~l 59 (172)
+|++.++|+|.++++.. ..|+++. .+|.|..||....+......
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 56677778999999862 2356554 36999999877665544333
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=68.33 E-value=13 Score=31.06 Aligned_cols=39 Identities=28% Similarity=0.358 Sum_probs=28.7
Q ss_pred CCcEEEEEeeCCCCeEEeccCCC--CHHHHHHHHHHHHHHh
Q 046901 21 WGKWVSEIRQPGTKTRIWLGSYE--TPEMAAAAYDVAALHF 59 (172)
Q Consensus 21 ~gKW~AeIr~p~~~kri~LGtf~--t~EeAA~AyD~Aa~~l 59 (172)
.+.|..+++..++.+++.||+|+ +.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699999997777789999995 6777776665544443
No 8
>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=63.28 E-value=14 Score=26.63 Aligned_cols=40 Identities=23% Similarity=0.238 Sum_probs=26.5
Q ss_pred CCceeEEEECCCCcEEEEEeeCCCCeEEeccCCCCHHHHHHHH
Q 046901 10 QSAFRGVRMRKWGKWVSEIRQPGTKTRIWLGSYETPEMAAAAY 52 (172)
Q Consensus 10 tS~yrGVr~r~~gKW~AeIr~p~~~kri~LGtf~t~EeAA~Ay 52 (172)
--+||-||.-+ |||+|.+-. +-.-.---.|..+|.|-+--
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrwa 69 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRWA 69 (80)
T ss_dssp TTTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHHH
T ss_pred cccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHHH
Confidence 45799998655 999999987 44334445788888776653
No 9
>PRK09692 integrase; Provisional
Probab=56.08 E-value=34 Score=30.31 Aligned_cols=39 Identities=23% Similarity=0.266 Sum_probs=25.1
Q ss_pred EEECCCC--cEEEEEeeCCCC--eEEeccCCC--CHHHHHHHHHH
Q 046901 16 VRMRKWG--KWVSEIRQPGTK--TRIWLGSYE--TPEMAAAAYDV 54 (172)
Q Consensus 16 Vr~r~~g--KW~AeIr~p~~~--kri~LGtf~--t~EeAA~AyD~ 54 (172)
|+-++.| .|+.+.+.|.++ +++-||.|+ |..+|..+...
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 3444554 499888755333 447899999 77777654443
No 10
>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=52.47 E-value=30 Score=24.49 Aligned_cols=38 Identities=21% Similarity=0.363 Sum_probs=29.0
Q ss_pred cEEEEEeeCCCCeEEeccCCCCHHHHHHHHHHHHHHhC
Q 046901 23 KWVSEIRQPGTKTRIWLGSYETPEMAAAAYDVAALHFR 60 (172)
Q Consensus 23 KW~AeIr~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l~ 60 (172)
.|=++|.--.-.-..|.|-|.|.+||..+.---..-+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 46689987556678999999999999998754444443
No 11
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=50.26 E-value=58 Score=22.93 Aligned_cols=43 Identities=21% Similarity=0.176 Sum_probs=26.9
Q ss_pred EECCC--CcEEEEEeeCCCCeEEeccCCCC--HHHHHHHHHHHHHHh
Q 046901 17 RMRKW--GKWVSEIRQPGTKTRIWLGSYET--PEMAAAAYDVAALHF 59 (172)
Q Consensus 17 r~r~~--gKW~AeIr~p~~~kri~LGtf~t--~EeAA~AyD~Aa~~l 59 (172)
+-.+. ..|+-+.+..++.+++-||.|++ ..+|..........+
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 44444 34998888855667899999974 555555544433333
No 12
>PRK10113 cell division modulator; Provisional
Probab=44.89 E-value=18 Score=26.02 Aligned_cols=38 Identities=26% Similarity=0.392 Sum_probs=23.9
Q ss_pred CceeEEEECCCCcEEEEEeeCCCCeEEeccCCCCHHHHHHH
Q 046901 11 SAFRGVRMRKWGKWVSEIRQPGTKTRIWLGSYETPEMAAAA 51 (172)
Q Consensus 11 S~yrGVr~r~~gKW~AeIr~p~~~kri~LGtf~t~EeAA~A 51 (172)
-+||-||.-+ |||+|.+.. .-.-----.|..+|.|-+-
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 4688887655 899999976 2221222356666666554
No 13
>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=43.72 E-value=26 Score=22.84 Aligned_cols=29 Identities=24% Similarity=0.349 Sum_probs=22.1
Q ss_pred EeeCCCCeEEeccCCCCHHHHHHHHHHHH
Q 046901 28 IRQPGTKTRIWLGSYETPEMAAAAYDVAA 56 (172)
Q Consensus 28 Ir~p~~~kri~LGtf~t~EeAA~AyD~Aa 56 (172)
+......-+|.+|.|.|.++|..+.....
T Consensus 37 ~~~~~~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 37 VSKGGPWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEETTCEEEEECCECTCCHHHHHHHHHH
T ss_pred EecCCceEEEEECCCCCHHHHHHHHHHHh
Confidence 33333456899999999999999887665
No 14
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=38.87 E-value=21 Score=27.27 Aligned_cols=18 Identities=17% Similarity=0.704 Sum_probs=14.1
Q ss_pred eEEeccCCCCHHHHHHHH
Q 046901 35 TRIWLGSYETPEMAAAAY 52 (172)
Q Consensus 35 kri~LGtf~t~EeAA~Ay 52 (172)
..||||+|.|.++--.=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 469999999988765544
No 15
>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=30.26 E-value=56 Score=24.56 Aligned_cols=21 Identities=33% Similarity=0.338 Sum_probs=17.7
Q ss_pred ccCCCCHHHHHHHHHHHHHHh
Q 046901 39 LGSYETPEMAAAAYDVAALHF 59 (172)
Q Consensus 39 LGtf~t~EeAA~AyD~Aa~~l 59 (172)
-|+|+|+|+|..=||.....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999876554
No 16
>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=29.59 E-value=1.1e+02 Score=22.75 Aligned_cols=36 Identities=19% Similarity=0.267 Sum_probs=27.2
Q ss_pred cEEEEEeeCCCCeEEeccCCCCHHHHHHHHHHHHHHhC
Q 046901 23 KWVSEIRQPGTKTRIWLGSYETPEMAAAAYDVAALHFR 60 (172)
Q Consensus 23 KW~AeIr~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l~ 60 (172)
.|+|.|.. ...-+-++.....+.|..|...|+.+|-
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 39999997 5555666666558889999888877764
No 17
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=25.20 E-value=80 Score=17.25 Aligned_cols=11 Identities=27% Similarity=1.144 Sum_probs=8.4
Q ss_pred CCeEEeccCCC
Q 046901 33 TKTRIWLGSYE 43 (172)
Q Consensus 33 ~~kri~LGtf~ 43 (172)
+..+||+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 55689999873
No 18
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=23.96 E-value=58 Score=26.12 Aligned_cols=18 Identities=44% Similarity=0.508 Sum_probs=16.0
Q ss_pred eEEeccCCCCHHHHHHHH
Q 046901 35 TRIWLGSYETPEMAAAAY 52 (172)
Q Consensus 35 kri~LGtf~t~EeAA~Ay 52 (172)
.-|++|.|.|++|++++-
T Consensus 42 eVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 42 EVINLGLFQTPEEAVRAA 59 (143)
T ss_pred eEEecCCcCCHHHHHHHH
Confidence 569999999999999874
No 19
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=23.65 E-value=1.5e+02 Score=23.90 Aligned_cols=36 Identities=17% Similarity=0.233 Sum_probs=29.8
Q ss_pred EEEEEeeCCCCeEEeccCCCCHHHHHHHHHHHHHHhCCC
Q 046901 24 WVSEIRQPGTKTRIWLGSYETPEMAAAAYDVAALHFRGR 62 (172)
Q Consensus 24 W~AeIr~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l~G~ 62 (172)
|+|.|.. ++.++-=...+++.|..|...|+.+|-++
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 9999985 67777777788888999999999888654
No 20
>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=23.42 E-value=1.6e+02 Score=22.71 Aligned_cols=33 Identities=24% Similarity=0.416 Sum_probs=26.5
Q ss_pred EEEEEeeCCCCeEEeccCCCCHHHHHHHHHHHHHHh
Q 046901 24 WVSEIRQPGTKTRIWLGSYETPEMAAAAYDVAALHF 59 (172)
Q Consensus 24 W~AeIr~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l 59 (172)
|+|.|.. ...-+-++. .+++.|..|...|+.+|
T Consensus 92 ~varV~~--G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 92 WVAVVKP--GKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEECC--CCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 9999997 555555555 89999999999888765
No 21
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=22.47 E-value=1.8e+02 Score=22.83 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=28.8
Q ss_pred EEEEEeeCCCCeEEeccCCCCHHHHHHHHHHHHHHhCCC
Q 046901 24 WVSEIRQPGTKTRIWLGSYETPEMAAAAYDVAALHFRGR 62 (172)
Q Consensus 24 W~AeIr~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l~G~ 62 (172)
|+|.|.. ...-+-++. .+++.|..|+..|+.+|-++
T Consensus 93 ~varVk~--G~iifEi~~-~~~~~a~~al~~a~~KLP~~ 128 (138)
T PRK09203 93 WVAVVKP--GRILFEIAG-VSEELAREALRLAAAKLPIK 128 (138)
T ss_pred EEEEECC--CCEEEEEeC-CCHHHHHHHHHHHhccCCCc
Confidence 9999997 555555666 89999999999998887654
No 22
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=21.62 E-value=1.7e+02 Score=21.10 Aligned_cols=33 Identities=27% Similarity=0.168 Sum_probs=23.0
Q ss_pred EeeCCCCeEEeccCCCCHHHHHHHHHHHHHHhCCC
Q 046901 28 IRQPGTKTRIWLGSYETPEMAAAAYDVAALHFRGR 62 (172)
Q Consensus 28 Ir~p~~~kri~LGtf~t~EeAA~AyD~Aa~~l~G~ 62 (172)
-+.|..|+.+-||+ +..+|...--.|-..+...
T Consensus 31 Yr~P~tGk~~~LG~--d~~~Ai~~A~eaN~~i~~~ 63 (75)
T PF09003_consen 31 YRNPITGKEHGLGT--DRAEAIAQAIEANLRIAEQ 63 (75)
T ss_dssp EE-TTTS-EEEEES---HHHHHHHHHHHHHHHTSS
T ss_pred EecCCCCceeeCCC--CHHHHHHHHHHHHHHHHHh
Confidence 45788999999999 8888877766666666543
Done!