Query 031402
Match_columns 160
No_of_seqs 201 out of 1164
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 13:36:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031402.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031402hhsearch_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 1.8E-21 3.9E-26 130.2 7.2 61 22-83 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 8.3E-21 1.8E-25 128.5 8.1 63 23-86 1-63 (64)
3 PHA00280 putative NHN endonucl 99.7 1.3E-16 2.9E-21 121.2 6.8 66 8-77 53-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.4 2.2E-12 4.8E-17 84.2 6.3 53 22-74 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 83.3 4.5 9.9E-05 25.1 5.1 39 34-72 1-42 (46)
6 PHA02601 int integrase; Provis 78.0 3.8 8.3E-05 34.3 4.5 45 26-71 2-46 (333)
7 PF08846 DUF1816: Domain of un 60.4 19 0.00041 24.9 4.1 36 34-70 9-44 (68)
8 PF05036 SPOR: Sporulation rel 53.2 9 0.00019 24.8 1.5 24 45-68 42-65 (76)
9 PF08471 Ribonuc_red_2_N: Clas 49.7 19 0.00041 26.5 2.8 20 52-71 71-90 (93)
10 PRK09692 integrase; Provisiona 49.3 56 0.0012 28.4 6.3 39 27-66 33-77 (413)
11 COG0197 RplP Ribosomal protein 48.4 31 0.00066 27.3 4.0 36 35-74 96-131 (146)
12 cd00801 INT_P4 Bacteriophage P 43.5 65 0.0014 26.4 5.5 39 33-72 10-50 (357)
13 PF14112 DUF4284: Domain of un 42.0 18 0.00038 27.2 1.8 16 47-62 2-17 (122)
14 PF13356 DUF4102: Domain of un 42.0 90 0.0019 21.5 5.3 44 27-71 27-74 (89)
15 PF09954 DUF2188: Uncharacteri 32.4 1.3E+02 0.0027 19.5 4.5 39 27-70 3-41 (62)
16 TIGR01164 rplP_bact ribosomal 32.2 84 0.0018 23.9 4.1 33 35-71 92-124 (126)
17 CHL00044 rpl16 ribosomal prote 30.8 88 0.0019 24.1 4.0 35 35-73 93-127 (135)
18 PRK09203 rplP 50S ribosomal pr 30.6 82 0.0018 24.3 3.9 36 35-74 93-128 (138)
19 cd04516 TBP_eukaryotes eukaryo 30.2 2.5E+02 0.0055 22.3 6.8 49 20-72 32-81 (174)
20 PF00352 TBP: Transcription fa 29.1 1.7E+02 0.0037 20.2 5.0 46 22-71 36-82 (86)
21 cd00652 TBP_TLF TATA box bindi 26.4 2.8E+02 0.006 22.0 6.4 48 20-71 32-80 (174)
22 COG2185 Sbm Methylmalonyl-CoA 23.1 63 0.0014 25.4 2.0 18 47-64 42-59 (143)
23 TIGR00279 L10e ribosomal prote 23.0 1E+02 0.0022 25.0 3.2 35 35-73 122-158 (172)
24 PF03799 FtsQ: Cell division p 21.2 2.7E+02 0.0058 19.1 4.9 44 23-71 60-103 (117)
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=1.8e-21 Score=130.24 Aligned_cols=61 Identities=69% Similarity=1.275 Sum_probs=56.7
Q ss_pred CceeeeEECCCCeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q 031402 22 VRYRGIRRRAWGKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAFRGHSAILNFPNE 83 (160)
Q Consensus 22 S~yrGV~~r~~Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~~G~~a~~NFp~~ 83 (160)
|+|+||+++++|||+|+|+++. .|+++|||+|+|+|||+.|||.+++.++|.++.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~-~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPS-GGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCC-CCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 6899999999999999999743 389999999999999999999999999999999999964
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=8.3e-21 Score=128.50 Aligned_cols=63 Identities=71% Similarity=1.227 Sum_probs=58.5
Q ss_pred ceeeeEECCCCeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhhcCCCCCCCCCCCccC
Q 031402 23 RYRGIRRRAWGKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAFRGHSAILNFPNEGQY 86 (160)
Q Consensus 23 ~yrGV~~r~~Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~~G~~a~~NFp~~~~~ 86 (160)
+|+||+++++|||+|+|+++. +|+.+|||+|+|+||||.|||.++.+++|.++.+|||.+.+.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~-~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPS-KGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecC-CCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 599999999999999999864 589999999999999999999999999999999999987663
No 3
>PHA00280 putative NHN endonuclease
Probab=99.67 E-value=1.3e-16 Score=121.24 Aligned_cols=66 Identities=12% Similarity=0.126 Sum_probs=60.0
Q ss_pred CCCccCCCCCCCCCCceeeeEECCC-CeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhhcCCCCC
Q 031402 8 GKNNEKQRSVSVSEVRYRGIRRRAW-GKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAFRGHSAI 77 (160)
Q Consensus 8 ~~n~~n~~~~~~~~S~yrGV~~r~~-Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~~G~~a~ 77 (160)
.+|.+|++.+++|+|+|+||++.+. |||+|+|.. +||+++||.|+++|+|+.||+ ++.++||+||.
T Consensus 53 ~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 53 KENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred HHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 4688999999999999999997655 999999995 899999999999999999997 77899999985
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=99.35 E-value=2.2e-12 Score=84.17 Aligned_cols=53 Identities=34% Similarity=0.500 Sum_probs=46.3
Q ss_pred CceeeeEECCC-CeEEEEEecCCCCC--eEeeccCCCCHHHHHHHHHHHHHhhcCC
Q 031402 22 VRYRGIRRRAW-GKFAAEIRDPTRNG--TRLWLGTFSTAEEAARAYDRAAFAFRGH 74 (160)
Q Consensus 22 S~yrGV~~r~~-Gkw~A~I~~~~~~g--kri~LGtF~t~eeAA~AYd~aa~~~~G~ 74 (160)
|+|+||++.+. ++|+|+|+++..+| ++++||.|++++||++||+.++..++|+
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 68999997764 99999999854443 9999999999999999999999999875
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=83.30 E-value=4.5 Score=25.12 Aligned_cols=39 Identities=15% Similarity=0.173 Sum_probs=28.3
Q ss_pred eEEEEEe-cCCCCC--eEeeccCCCCHHHHHHHHHHHHHhhc
Q 031402 34 KFAAEIR-DPTRNG--TRLWLGTFSTAEEAARAYDRAAFAFR 72 (160)
Q Consensus 34 kw~A~I~-~~~~~g--kri~LGtF~t~eeAA~AYd~aa~~~~ 72 (160)
+|..+|. .-...| ++++-+-|.|..||..+..++...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5778883 222344 56777899999999999988776654
No 6
>PHA02601 int integrase; Provisional
Probab=77.97 E-value=3.8 Score=34.26 Aligned_cols=45 Identities=27% Similarity=0.319 Sum_probs=31.3
Q ss_pred eeEECCCCeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhh
Q 031402 26 GIRRRAWGKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAF 71 (160)
Q Consensus 26 GV~~r~~Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~ 71 (160)
+|+..+.|+|.++|......|+++.. +|.|..||....+.....+
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 46667779999999853334777654 6999999876665554444
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=60.37 E-value=19 Score=24.91 Aligned_cols=36 Identities=22% Similarity=0.284 Sum_probs=25.4
Q ss_pred eEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHh
Q 031402 34 KFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFA 70 (160)
Q Consensus 34 kw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~ 70 (160)
.|-++|.--. -.-.+|.|-|.|.+||..+--.....
T Consensus 9 aWWveI~T~~-P~ctYyFGPF~s~~eA~~~~~gyieD 44 (68)
T PF08846_consen 9 AWWVEIETQN-PNCTYYFGPFDSREEAEAALPGYIED 44 (68)
T ss_pred cEEEEEEcCC-CCEEEEeCCcCCHHHHHHHhccHHHH
Confidence 4778887432 23778999999999998875443333
No 8
>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=53.20 E-value=9 Score=24.76 Aligned_cols=24 Identities=33% Similarity=0.403 Sum_probs=19.6
Q ss_pred CCeEeeccCCCCHHHHHHHHHHHH
Q 031402 45 NGTRLWLGTFSTAEEAARAYDRAA 68 (160)
Q Consensus 45 ~gkri~LGtF~t~eeAA~AYd~aa 68 (160)
.-.+|.+|.|++.+||..+-.+..
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 357889999999999988877655
No 9
>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=49.74 E-value=19 Score=26.47 Aligned_cols=20 Identities=35% Similarity=0.664 Sum_probs=17.7
Q ss_pred cCCCCHHHHHHHHHHHHHhh
Q 031402 52 GTFSTAEEAARAYDRAAFAF 71 (160)
Q Consensus 52 GtF~t~eeAA~AYd~aa~~~ 71 (160)
|.|+|+|+|..-||+.+..+
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999987654
No 10
>PRK09692 integrase; Provisional
Probab=49.27 E-value=56 Score=28.43 Aligned_cols=39 Identities=18% Similarity=0.241 Sum_probs=25.1
Q ss_pred eEECCCCe--EEEEEecCCCCCeE--eeccCCC--CHHHHHHHHHH
Q 031402 27 IRRRAWGK--FAAEIRDPTRNGTR--LWLGTFS--TAEEAARAYDR 66 (160)
Q Consensus 27 V~~r~~Gk--w~A~I~~~~~~gkr--i~LGtF~--t~eeAA~AYd~ 66 (160)
|+.++.|. |..+.+.+. +|++ +-||.|+ |..+|..+..+
T Consensus 33 l~v~~~G~k~~~~rY~~~~-~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPL-TKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEEECCCcEEEEEEEecCC-CCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 45566654 999887532 3444 6799999 67676554444
No 11
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=48.37 E-value=31 Score=27.30 Aligned_cols=36 Identities=28% Similarity=0.218 Sum_probs=31.3
Q ss_pred EEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhhcCC
Q 031402 35 FAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAFRGH 74 (160)
Q Consensus 35 w~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~~G~ 74 (160)
|+|+|.. |+.++-=..++++.|..|..+|+.+|=+.
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 9999993 88888888889999999999999887554
No 12
>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=43.51 E-value=65 Score=26.45 Aligned_cols=39 Identities=23% Similarity=0.261 Sum_probs=26.4
Q ss_pred CeEEEEEecCCCCCeEeeccCCC--CHHHHHHHHHHHHHhhc
Q 031402 33 GKFAAEIRDPTRNGTRLWLGTFS--TAEEAARAYDRAAFAFR 72 (160)
Q Consensus 33 Gkw~A~I~~~~~~gkri~LGtF~--t~eeAA~AYd~aa~~~~ 72 (160)
+.|+.+++... +..++.||+|+ +.++|.....+....+.
T Consensus 10 ~~~~~~~~~~g-~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 10 KSWRFRYRLAG-KRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred EEEEEEeccCC-ceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 46999988632 22457789995 77787777666555553
No 13
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=42.03 E-value=18 Score=27.21 Aligned_cols=16 Identities=25% Similarity=0.850 Sum_probs=12.8
Q ss_pred eEeeccCCCCHHHHHH
Q 031402 47 TRLWLGTFSTAEEAAR 62 (160)
Q Consensus 47 kri~LGtF~t~eeAA~ 62 (160)
..||||+|.|.+|-..
T Consensus 2 VsiWiG~f~s~~el~~ 17 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEE 17 (122)
T ss_pred eEEEEecCCCHHHHHH
Confidence 4699999999877643
No 14
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=41.98 E-value=90 Score=21.50 Aligned_cols=44 Identities=20% Similarity=0.203 Sum_probs=26.2
Q ss_pred eEECCCC--eEEEEEecCCCCCeEeeccCCCC--HHHHHHHHHHHHHhh
Q 031402 27 IRRRAWG--KFAAEIRDPTRNGTRLWLGTFST--AEEAARAYDRAAFAF 71 (160)
Q Consensus 27 V~~r~~G--kw~A~I~~~~~~gkri~LGtF~t--~eeAA~AYd~aa~~~ 71 (160)
|+..+.| .|..+.+.. .+.+++-||.|+. ..+|.....+....+
T Consensus 27 l~v~~~G~kt~~~r~~~~-gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 27 LRVTPSGSKTFYFRYRIN-GKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEE-TTS-EEEEEEEEET-TEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEEeCCCeEEEEEEEec-ceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 3455664 488888752 1224578899975 666665555544444
No 15
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=32.42 E-value=1.3e+02 Score=19.49 Aligned_cols=39 Identities=26% Similarity=0.180 Sum_probs=26.0
Q ss_pred eEECCCCeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHh
Q 031402 27 IRRRAWGKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFA 70 (160)
Q Consensus 27 V~~r~~Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~ 70 (160)
|..+..+.|..+... ..-=..+|+|.+||..+=...+..
T Consensus 3 V~p~~~~~W~v~~eg-----~~ra~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG-----AKRASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeCC-----CcccccccCcHHHHHHHHHHHHHh
Confidence 444455789888763 333378999999997765555544
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=32.25 E-value=84 Score=23.85 Aligned_cols=33 Identities=24% Similarity=0.213 Sum_probs=26.2
Q ss_pred EEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhh
Q 031402 35 FAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAF 71 (160)
Q Consensus 35 w~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~ 71 (160)
|+|+|.. |+.++--.-.+++.|..|...|+.++
T Consensus 92 ~varV~~----G~ilfEi~~~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 92 WVAVVKP----GKILFEIAGVPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEECC----CCEEEEEeCCCHHHHHHHHHHHHhcC
Confidence 9999994 66665444489999999999988765
No 17
>CHL00044 rpl16 ribosomal protein L16
Probab=30.75 E-value=88 Score=24.09 Aligned_cols=35 Identities=20% Similarity=0.128 Sum_probs=26.6
Q ss_pred EEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhhcC
Q 031402 35 FAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAFRG 73 (160)
Q Consensus 35 w~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~~G 73 (160)
|+|+|.. |+.++=-.-.+++.|..|...|+.++-.
T Consensus 93 ~va~V~~----G~ilfEi~g~~~~~ak~al~~a~~KLP~ 127 (135)
T CHL00044 93 WVAVVKP----GRILYEMGGVSETIARAAIKIAAYKMPI 127 (135)
T ss_pred EEEEECC----CcEEEEEeCCCHHHHHHHHHHHhhcCCC
Confidence 9999994 6666544446778999999998887643
No 18
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=30.64 E-value=82 Score=24.29 Aligned_cols=36 Identities=22% Similarity=0.110 Sum_probs=27.7
Q ss_pred EEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhhcCC
Q 031402 35 FAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAFRGH 74 (160)
Q Consensus 35 w~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~~G~ 74 (160)
|+|+|.. |+.++--.-.+++.|..|...|+.++=+.
T Consensus 93 ~varVk~----G~iifEi~~~~~~~a~~al~~a~~KLP~~ 128 (138)
T PRK09203 93 WVAVVKP----GRILFEIAGVSEELAREALRLAAAKLPIK 128 (138)
T ss_pred EEEEECC----CCEEEEEeCCCHHHHHHHHHHHhccCCCc
Confidence 9999994 66665433389999999999998876543
No 19
>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=30.21 E-value=2.5e+02 Score=22.34 Aligned_cols=49 Identities=18% Similarity=0.178 Sum_probs=37.3
Q ss_pred CCCceeeeEECCC-CeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhhc
Q 031402 20 SEVRYRGIRRRAW-GKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAFR 72 (160)
Q Consensus 20 ~~S~yrGV~~r~~-Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~~ 72 (160)
+..+|.||..|-. -+-.+-|. ..||-+--|.. +.|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF---~SGKiviTGak-s~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIF---SSGKMVCTGAK-SEDDSKLAARKYARIIQ 81 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEE---CCCeEEEEecC-CHHHHHHHHHHHHHHHH
Confidence 3458899876544 56677777 47888888886 88999999998887773
No 20
>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=29.13 E-value=1.7e+02 Score=20.16 Aligned_cols=46 Identities=24% Similarity=0.260 Sum_probs=34.0
Q ss_pred CceeeeEECCC-CeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhh
Q 031402 22 VRYRGIRRRAW-GKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAF 71 (160)
Q Consensus 22 S~yrGV~~r~~-Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~ 71 (160)
.+|.||..|-. -+-.+.|. ..|+-+..|.- +.++|..|.++....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF---~sGki~itGak-s~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIF---SSGKIVITGAK-SEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEE---TTSEEEEEEES-SHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEE---cCCEEEEEecC-CHHHHHHHHHHHHHHH
Confidence 47889875543 45666777 47898888874 8999999988876554
No 21
>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=26.44 E-value=2.8e+02 Score=21.99 Aligned_cols=48 Identities=25% Similarity=0.225 Sum_probs=36.5
Q ss_pred CCCceeeeEECCC-CeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhh
Q 031402 20 SEVRYRGIRRRAW-GKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAF 71 (160)
Q Consensus 20 ~~S~yrGV~~r~~-Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~ 71 (160)
+..+|.||..|-. -+=.+-|. ..||-+--|.. +.|+|..|.++.+..+
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf---~sGKivitGak-s~~~~~~a~~~~~~~L 80 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIF---SSGKMVITGAK-SEEDAKLAARKYARIL 80 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEE---CCCEEEEEecC-CHHHHHHHHHHHHHHH
Confidence 3458999876654 55666676 47888888876 8899999998887776
No 22
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=23.12 E-value=63 Score=25.37 Aligned_cols=18 Identities=50% Similarity=0.575 Sum_probs=15.2
Q ss_pred eEeeccCCCCHHHHHHHH
Q 031402 47 TRLWLGTFSTAEEAARAY 64 (160)
Q Consensus 47 kri~LGtF~t~eeAA~AY 64 (160)
.-+++|.|.|++||+++-
T Consensus 42 eVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 42 EVINLGLFQTPEEAVRAA 59 (143)
T ss_pred eEEecCCcCCHHHHHHHH
Confidence 457999999999998763
No 23
>TIGR00279 L10e ribosomal protein L10.e. L10.e is distantly related to eubacterial ribosomal protein L16.
Probab=22.99 E-value=1e+02 Score=24.99 Aligned_cols=35 Identities=26% Similarity=0.265 Sum_probs=27.5
Q ss_pred EEEEEecCCCCCeEeeccCCC--CHHHHHHHHHHHHHhhcC
Q 031402 35 FAAEIRDPTRNGTRLWLGTFS--TAEEAARAYDRAAFAFRG 73 (160)
Q Consensus 35 w~A~I~~~~~~gkri~LGtF~--t~eeAA~AYd~aa~~~~G 73 (160)
|+|+|. .|+.++--.-. +++.|..|...|+.++-.
T Consensus 122 wvArVk----~Gqiifei~~~~~~~~~AkeAlr~A~~KLP~ 158 (172)
T TIGR00279 122 TAARVK----IGQKIFSVWTKPSNFDVAKEALRRAAMKFPV 158 (172)
T ss_pred EEEEEC----cCCEEEEEEeecCCHHHHHHHHHHHhccCCC
Confidence 999999 47777665444 889999999998887644
No 24
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=21.17 E-value=2.7e+02 Score=19.10 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=30.6
Q ss_pred ceeeeEECCCCeEEEEEecCCCCCeEeeccCCCCHHHHHHHHHHHHHhh
Q 031402 23 RYRGIRRRAWGKFAAEIRDPTRNGTRLWLGTFSTAEEAARAYDRAAFAF 71 (160)
Q Consensus 23 ~yrGV~~r~~Gkw~A~I~~~~~~gkri~LGtF~t~eeAA~AYd~aa~~~ 71 (160)
...-|...+.+.|...+. +|..|.||.-+ .++....|......+
T Consensus 60 ~i~~i~~~~~~~~~l~l~----dg~~V~lg~~~-~~~kl~~~~~i~~~~ 103 (117)
T PF03799_consen 60 QISEISYDPRGSWTLYLD----DGVEVKLGRSD-LAEKLQRLVKILPQL 103 (117)
T ss_dssp S-SEEEEETTSCEEEE-S----SS-EEEEESST-HHHHHHHHHHHHHCC
T ss_pred eeeEEEECCCCeEEEEEC----CCcEEEEcCcC-HHHHHHHHHHHHHHH
Confidence 345577777777988887 58999999997 777777776666554
Done!