Query 030591
Match_columns 175
No_of_seqs 244 out of 1164
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 16:03:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030591.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030591hhsearch_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 1.4E-21 3E-26 132.4 7.1 60 13-72 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 3.3E-20 7.1E-25 127.1 8.1 61 14-74 1-62 (64)
3 PHA00280 putative NHN endonucl 99.5 1.3E-13 2.7E-18 106.2 7.5 58 6-66 60-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 5.6E-11 1.2E-15 78.5 6.0 51 13-63 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 80.4 5.8 0.00013 24.9 4.9 37 24-60 1-41 (46)
6 cd00801 INT_P4 Bacteriophage P 79.8 3.7 8.1E-05 34.5 5.0 43 18-60 4-49 (357)
7 PF13356 DUF4102: Domain of un 69.8 8.2 0.00018 27.3 3.9 37 24-60 36-74 (89)
8 PHA02601 int integrase; Provis 61.2 13 0.00028 31.6 4.1 43 17-60 2-46 (333)
9 PRK09692 integrase; Provisiona 60.2 27 0.00059 30.9 6.2 38 18-55 33-77 (413)
10 PF05036 SPOR: Sporulation rel 51.4 18 0.0004 23.6 2.9 25 33-57 41-65 (76)
11 PF12167 DUF3596: Domain of un 48.4 79 0.0017 21.3 5.6 57 16-72 2-63 (64)
12 PF14112 DUF4284: Domain of un 46.7 13 0.00029 28.2 1.8 18 36-53 2-19 (122)
13 PF08846 DUF1816: Domain of un 36.2 76 0.0017 22.2 4.1 41 24-64 9-49 (68)
14 PF10729 CedA: Cell division a 34.4 89 0.0019 22.2 4.1 42 9-52 27-68 (80)
15 cd01433 Ribosomal_L16_L10e Rib 31.1 80 0.0017 23.4 3.8 42 17-60 59-105 (112)
16 PF08471 Ribonuc_red_2_N: Clas 29.1 62 0.0013 24.0 2.8 21 40-60 70-90 (93)
17 TIGR01164 rplP_bact ribosomal 27.1 1.2E+02 0.0026 23.3 4.3 34 24-60 91-124 (126)
18 PRK09203 rplP 50S ribosomal pr 26.7 1.1E+02 0.0023 24.0 3.9 36 24-62 92-127 (138)
19 PF07494 Reg_prop: Two compone 26.6 27 0.00058 19.0 0.4 11 34-44 14-24 (24)
20 PF12286 DUF3622: Protein of u 22.5 1.5E+02 0.0033 20.9 3.6 33 18-50 11-47 (71)
21 PRK10113 cell division modulat 21.3 83 0.0018 22.3 2.1 39 11-51 29-67 (80)
22 PRK10905 cell division protein 20.7 1.1E+02 0.0024 27.5 3.3 19 37-55 287-305 (328)
23 COG2185 Sbm Methylmalonyl-CoA 20.6 75 0.0016 25.3 2.0 17 36-52 42-58 (143)
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=99.85 E-value=1.4e-21 Score=132.44 Aligned_cols=60 Identities=62% Similarity=1.035 Sum_probs=57.0
Q ss_pred CceeEeEeeC-CeeEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 030591 13 PSYRGIRCRN-SKWVSEIREPRKSTRIWLGTYPTPEMAAAAYDVAALALKGSDAVLNFPNF 72 (175)
Q Consensus 13 s~yrGVr~r~-GkW~a~I~~~~k~~ri~LGtf~t~eeAA~Ayd~aa~~~~G~~a~lNFp~s 72 (175)
|+|+||++++ |||+|+|+++..++++|||+|+|+|||++|||.+++.++|..+.+|||++
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 6899999988 99999999976688999999999999999999999999999999999985
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.82 E-value=3.3e-20 Score=127.14 Aligned_cols=61 Identities=56% Similarity=0.980 Sum_probs=57.8
Q ss_pred ceeEeEeeC-CeeEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q 030591 14 SYRGIRCRN-SKWVSEIREPRKSTRIWLGTYPTPEMAAAAYDVAALALKGSDAVLNFPNFVS 74 (175)
Q Consensus 14 ~yrGVr~r~-GkW~a~I~~~~k~~ri~LGtf~t~eeAA~Ayd~aa~~~~G~~a~lNFp~s~~ 74 (175)
+|+||++++ |||+|+|+++.+++++|||+|+|+|||++|||.+++.++|..+++|||.+.+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y 62 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLY 62 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccC
Confidence 599999888 9999999999889999999999999999999999999999999999998654
No 3
>PHA00280 putative NHN endonuclease
Probab=99.47 E-value=1.3e-13 Score=106.20 Aligned_cols=58 Identities=14% Similarity=0.225 Sum_probs=52.3
Q ss_pred CCCCCCCCceeEeEeeC--CeeEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHhcCCCCC
Q 030591 6 SSSTKKHPSYRGIRCRN--SKWVSEIREPRKSTRIWLGTYPTPEMAAAAYDVAALALKGSDAV 66 (175)
Q Consensus 6 ~~~~~~~s~yrGVr~r~--GkW~a~I~~~~k~~ri~LGtf~t~eeAA~Ayd~aa~~~~G~~a~ 66 (175)
..+++++|+|+||++++ |||+|+|++ +||+++||.|+++|+|+.||+ ++..++|.+++
T Consensus 60 ~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 60 KTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 45678999999999877 999999999 888999999999999999997 67789999875
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=99.18 E-value=5.6e-11 Score=78.52 Aligned_cols=51 Identities=25% Similarity=0.406 Sum_probs=45.1
Q ss_pred CceeEeEeeC--CeeEEEEecCCC---CeEEeccCCCCHHHHHHHHHHHHHHhcCC
Q 030591 13 PSYRGIRCRN--SKWVSEIREPRK---STRIWLGTYPTPEMAAAAYDVAALALKGS 63 (175)
Q Consensus 13 s~yrGVr~r~--GkW~a~I~~~~k---~~ri~LGtf~t~eeAA~Ayd~aa~~~~G~ 63 (175)
|+|+||++++ ++|+|+|++... +++++||.|.++++|+++++.+.+.++|+
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 6899999887 999999999421 48999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=80.36 E-value=5.8 Score=24.93 Aligned_cols=37 Identities=16% Similarity=0.171 Sum_probs=29.5
Q ss_pred eeEEEEe--cC--CCCeEEeccCCCCHHHHHHHHHHHHHHh
Q 030591 24 KWVSEIR--EP--RKSTRIWLGTYPTPEMAAAAYDVAALAL 60 (175)
Q Consensus 24 kW~a~I~--~~--~k~~ri~LGtf~t~eeAA~Ayd~aa~~~ 60 (175)
+|..+|. .+ ++.++++-+-|.|..||-.+.......+
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 33 5568999999999999999988876665
No 6
>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=79.81 E-value=3.7 Score=34.48 Aligned_cols=43 Identities=28% Similarity=0.371 Sum_probs=31.5
Q ss_pred eEeeC-CeeEEEEecCCCCeEEeccCCC--CHHHHHHHHHHHHHHh
Q 030591 18 IRCRN-SKWVSEIREPRKSTRIWLGTYP--TPEMAAAAYDVAALAL 60 (175)
Q Consensus 18 Vr~r~-GkW~a~I~~~~k~~ri~LGtf~--t~eeAA~Ayd~aa~~~ 60 (175)
|+..+ +.|+.+++..++..++.||+|+ +.++|..........+
T Consensus 4 ~~~~g~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 4 VSPSGSKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EcCCCCEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 34444 6799999998888899999995 6677776665544444
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=69.78 E-value=8.2 Score=27.26 Aligned_cols=37 Identities=24% Similarity=0.214 Sum_probs=27.4
Q ss_pred eeEEEEecCCCCeEEeccCCCC--HHHHHHHHHHHHHHh
Q 030591 24 KWVSEIREPRKSTRIWLGTYPT--PEMAAAAYDVAALAL 60 (175)
Q Consensus 24 kW~a~I~~~~k~~ri~LGtf~t--~eeAA~Ayd~aa~~~ 60 (175)
.|+-+.+..++.+++-||.|++ ..+|..........+
T Consensus 36 t~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 36 TFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 6999999888889999999976 566655555444444
No 8
>PHA02601 int integrase; Provisional
Probab=61.23 E-value=13 Score=31.61 Aligned_cols=43 Identities=26% Similarity=0.338 Sum_probs=28.8
Q ss_pred EeEeeC-CeeEEEEecC-CCCeEEeccCCCCHHHHHHHHHHHHHHh
Q 030591 17 GIRCRN-SKWVSEIREP-RKSTRIWLGTYPTPEMAAAAYDVAALAL 60 (175)
Q Consensus 17 GVr~r~-GkW~a~I~~~-~k~~ri~LGtf~t~eeAA~Ayd~aa~~~ 60 (175)
+|++.+ |+|.++|+.. ..|+++.. +|.|..||-...+.....+
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 466666 8999999863 23556543 6999998876655544433
No 9
>PRK09692 integrase; Provisional
Probab=60.16 E-value=27 Score=30.91 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=24.8
Q ss_pred eEeeC-C--eeEEEEecC--CCCeEEeccCCC--CHHHHHHHHHH
Q 030591 18 IRCRN-S--KWVSEIREP--RKSTRIWLGTYP--TPEMAAAAYDV 55 (175)
Q Consensus 18 Vr~r~-G--kW~a~I~~~--~k~~ri~LGtf~--t~eeAA~Ayd~ 55 (175)
|+-++ | .|+.+.+.+ ++.+++-||+|+ |..+|......
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 34444 4 599888754 444568899999 67666554444
No 10
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=51.39 E-value=18 Score=23.56 Aligned_cols=25 Identities=24% Similarity=0.258 Sum_probs=19.3
Q ss_pred CCCeEEeccCCCCHHHHHHHHHHHH
Q 030591 33 RKSTRIWLGTYPTPEMAAAAYDVAA 57 (175)
Q Consensus 33 ~k~~ri~LGtf~t~eeAA~Ayd~aa 57 (175)
+...++.+|.|.|.++|..+-....
T Consensus 41 ~~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 41 GPWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TTCEEEEECCECTCCHHHHHHHHHH
T ss_pred CceEEEEECCCCCHHHHHHHHHHHh
Confidence 3456889999999999888766554
No 11
>PF12167 DUF3596: Domain of unknown function (DUF3596); InterPro: IPR022000 This N-terminal domain is found in Bacteriophage P27p02, it is functionally uncharacterised, though it is considered to be an integrase. Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome. This domain is found in related proteins in other bacteriophage, and prophage regions of bacterial genomes. The domain is approximately 90 amino acids in length and is found is associated with the C-terminal domain characterised by PF00589 from PFAM.
Probab=48.36 E-value=79 Score=21.33 Aligned_cols=57 Identities=28% Similarity=0.260 Sum_probs=36.7
Q ss_pred eEeEeeCCeeEEEEecCCCCeEEeccCCCCHHHHHHHHHHHH----HHhcCCCC-CCCCCCC
Q 030591 16 RGIRCRNSKWVSEIREPRKSTRIWLGTYPTPEMAAAAYDVAA----LALKGSDA-VLNFPNF 72 (175)
Q Consensus 16 rGVr~r~GkW~a~I~~~~k~~ri~LGtf~t~eeAA~Ayd~aa----~~~~G~~a-~lNFp~s 72 (175)
.||+-|+|+-+-..++.++..+..||.-+|+.-=..|-.... ....|.+- .--||+|
T Consensus 2 ~gV~~r~~~L~i~F~y~G~R~re~l~l~dT~~N~k~a~~~~~~I~~~I~~G~Fdy~~~FP~S 63 (64)
T PF12167_consen 2 AGVRVRNGKLRIDFTYQGKRCRESLGLPDTPANRKKAERLRAEIEAEIALGTFDYAKYFPDS 63 (64)
T ss_pred CCEEEECCEEEEEEEECCEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhCCCcHHHhCcCC
Confidence 489888988888888866667888999999765433322211 11246554 3457765
No 12
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=46.72 E-value=13 Score=28.23 Aligned_cols=18 Identities=17% Similarity=0.663 Sum_probs=13.8
Q ss_pred eEEeccCCCCHHHHHHHH
Q 030591 36 TRIWLGTYPTPEMAAAAY 53 (175)
Q Consensus 36 ~ri~LGtf~t~eeAA~Ay 53 (175)
..||||+|+|.++--.=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 479999999987765543
No 13
>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=36.23 E-value=76 Score=22.16 Aligned_cols=41 Identities=22% Similarity=0.323 Sum_probs=29.8
Q ss_pred eeEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHhcCCC
Q 030591 24 KWVSEIREPRKSTRIWLGTYPTPEMAAAAYDVAALALKGSD 64 (175)
Q Consensus 24 kW~a~I~~~~k~~ri~LGtf~t~eeAA~Ayd~aa~~~~G~~ 64 (175)
.|=++|.-..-.-..|.|-|.|.+||..+.---..-|....
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 45567766444568899999999999998776666554433
No 14
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=34.38 E-value=89 Score=22.21 Aligned_cols=42 Identities=17% Similarity=0.131 Sum_probs=26.3
Q ss_pred CCCCCceeEeEeeCCeeEEEEecCCCCeEEeccCCCCHHHHHHH
Q 030591 9 TKKHPSYRGIRCRNSKWVSEIREPRKSTRIWLGTYPTPEMAAAA 52 (175)
Q Consensus 9 ~~~~s~yrGVr~r~GkW~a~I~~~~k~~ri~LGtf~t~eeAA~A 52 (175)
.-+--+||-|-.-.|||||.|.. +-.-.---.|..+|.|-|=
T Consensus 27 a~k~dgfrdvw~lrgkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 27 ALKMDGFRDVWQLRGKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp -B-TTTECCECCCCCEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred hhhcccccceeeeccceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 34556788887666999999987 4334444567888777653
No 15
>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=31.12 E-value=80 Score=23.41 Aligned_cols=42 Identities=24% Similarity=0.304 Sum_probs=29.2
Q ss_pred EeEeeC--C---eeEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHh
Q 030591 17 GIRCRN--S---KWVSEIREPRKSTRIWLGTYPTPEMAAAAYDVAALAL 60 (175)
Q Consensus 17 GVr~r~--G---kW~a~I~~~~k~~ri~LGtf~t~eeAA~Ayd~aa~~~ 60 (175)
++|.++ | .|+|.|+. +..-+-++.....+.|..+...+..++
T Consensus 59 ~~rMGkGKG~~~~~~a~v~~--G~iifEi~~~~~~~~~~~alk~a~~Kl 105 (112)
T cd01433 59 ETRMGKGKGKPEGWVARVKP--GQILFEVRGVPEEEVAKEALRRAAKKL 105 (112)
T ss_pred ccccCCCCCCccEEEEEECC--CCEEEEEeCcCcHHHHHHHHHHhhccC
Confidence 566555 3 59999987 545556666655888888887777665
No 16
>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=29.11 E-value=62 Score=24.03 Aligned_cols=21 Identities=38% Similarity=0.384 Sum_probs=17.9
Q ss_pred ccCCCCHHHHHHHHHHHHHHh
Q 030591 40 LGTYPTPEMAAAAYDVAALAL 60 (175)
Q Consensus 40 LGtf~t~eeAA~Ayd~aa~~~ 60 (175)
-|+|.|+|+|..-||.-...|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 599999999999999866554
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=27.13 E-value=1.2e+02 Score=23.28 Aligned_cols=34 Identities=24% Similarity=0.347 Sum_probs=26.0
Q ss_pred eeEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHh
Q 030591 24 KWVSEIREPRKSTRIWLGTYPTPEMAAAAYDVAALAL 60 (175)
Q Consensus 24 kW~a~I~~~~k~~ri~LGtf~t~eeAA~Ayd~aa~~~ 60 (175)
.|+|.|.. +..-+-++. .+.+.|..|...|+.+|
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 59999986 444555555 89999999988887665
No 18
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=26.72 E-value=1.1e+02 Score=23.99 Aligned_cols=36 Identities=22% Similarity=0.263 Sum_probs=27.4
Q ss_pred eeEEEEecCCCCeEEeccCCCCHHHHHHHHHHHHHHhcC
Q 030591 24 KWVSEIREPRKSTRIWLGTYPTPEMAAAAYDVAALALKG 62 (175)
Q Consensus 24 kW~a~I~~~~k~~ri~LGtf~t~eeAA~Ayd~aa~~~~G 62 (175)
.|+|.|.. +..-+-++. .+.+.|..|...|+.+|-+
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 59999986 444555555 8999999999988877643
No 19
>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=26.60 E-value=27 Score=18.97 Aligned_cols=11 Identities=36% Similarity=1.078 Sum_probs=8.2
Q ss_pred CCeEEeccCCC
Q 030591 34 KSTRIWLGTYP 44 (175)
Q Consensus 34 k~~ri~LGtf~ 44 (175)
+..+||+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 44599999973
No 20
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=22.51 E-value=1.5e+02 Score=20.93 Aligned_cols=33 Identities=15% Similarity=0.330 Sum_probs=20.1
Q ss_pred eEeeCCeeEEEEecCCCCeEEec----cCCCCHHHHH
Q 030591 18 IRCRNSKWVSEIREPRKSTRIWL----GTYPTPEMAA 50 (175)
Q Consensus 18 Vr~r~GkW~a~I~~~~k~~ri~L----Gtf~t~eeAA 50 (175)
|.+..+.|.++|..-...++.-+ --|.|+++|.
T Consensus 11 v~q~~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq 47 (71)
T PF12286_consen 11 VTQKRNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQ 47 (71)
T ss_pred EEecCCceeeeeeeeecCceeEEEecccCcccHHHHH
Confidence 45555899999986432222222 3488887754
No 21
>PRK10113 cell division modulator; Provisional
Probab=21.29 E-value=83 Score=22.29 Aligned_cols=39 Identities=21% Similarity=0.269 Sum_probs=24.7
Q ss_pred CCCceeEeEeeCCeeEEEEecCCCCeEEeccCCCCHHHHHH
Q 030591 11 KHPSYRGIRCRNSKWVSEIREPRKSTRIWLGTYPTPEMAAA 51 (175)
Q Consensus 11 ~~s~yrGVr~r~GkW~a~I~~~~k~~ri~LGtf~t~eeAA~ 51 (175)
+--+||-|-.-.|||||.+.... .-.---.|..+|.|-|
T Consensus 29 kmd~frDVW~LrGKYVAFvl~ge--~FrRSPaFs~PEsAQR 67 (80)
T PRK10113 29 KMDSFRDVWMLRGKYVAFVLMGE--SFLRSPAFSVPESAQR 67 (80)
T ss_pred hhcchhhhheeccceEEEEEech--hhccCCccCCcHHHHH
Confidence 44568888766799999987621 1222335666766655
No 22
>PRK10905 cell division protein DamX; Validated
Probab=20.72 E-value=1.1e+02 Score=27.53 Aligned_cols=19 Identities=26% Similarity=0.291 Sum_probs=16.6
Q ss_pred EEeccCCCCHHHHHHHHHH
Q 030591 37 RIWLGTYPTPEMAAAAYDV 55 (175)
Q Consensus 37 ri~LGtf~t~eeAA~Ayd~ 55 (175)
++..|.|.+.++|.+|-..
T Consensus 287 VV~yG~YaSraeAk~Aiak 305 (328)
T PRK10905 287 VLVSGVYASKEEAKRAVST 305 (328)
T ss_pred EEEecCCCCHHHHHHHHHH
Confidence 7778999999999998665
No 23
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=20.57 E-value=75 Score=25.28 Aligned_cols=17 Identities=47% Similarity=0.560 Sum_probs=15.5
Q ss_pred eEEeccCCCCHHHHHHH
Q 030591 36 TRIWLGTYPTPEMAAAA 52 (175)
Q Consensus 36 ~ri~LGtf~t~eeAA~A 52 (175)
.-|++|.|.|+||++++
T Consensus 42 eVi~~g~~~tp~e~v~a 58 (143)
T COG2185 42 EVINLGLFQTPEEAVRA 58 (143)
T ss_pred eEEecCCcCCHHHHHHH
Confidence 57899999999999987
Done!