Query 031071
Match_columns 166
No_of_seqs 211 out of 1198
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:48:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031071.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031071hhsearch_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 5.8E-22 1.3E-26 133.6 7.2 61 57-118 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.9 2.8E-21 6E-26 131.8 8.3 63 58-121 1-63 (64)
3 PHA00280 putative NHN endonucl 99.6 2.3E-15 4.9E-20 115.5 7.0 68 41-112 51-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.3 5.4E-12 1.2E-16 82.9 6.1 53 57-109 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 85.6 3.6 7.7E-05 25.8 5.4 39 69-107 1-42 (46)
6 PHA02601 int integrase; Provis 79.2 3.5 7.7E-05 34.7 4.6 45 61-106 2-46 (333)
7 PF08846 DUF1816: Domain of un 76.3 5.5 0.00012 27.9 4.1 39 68-107 8-46 (68)
8 PF07913 DUF1678: Protein of u 62.0 28 0.0006 28.8 5.9 64 5-91 2-72 (201)
9 PF05036 SPOR: Sporulation rel 59.2 6.6 0.00014 25.6 1.6 24 80-103 42-65 (76)
10 PF08471 Ribonuc_red_2_N: Clas 55.0 14 0.0003 27.4 2.8 20 87-106 71-90 (93)
11 cd00801 INT_P4 Bacteriophage P 48.8 47 0.001 27.5 5.5 39 67-106 9-49 (357)
12 PRK09692 integrase; Provisiona 47.3 64 0.0014 28.3 6.3 43 62-104 33-80 (413)
13 COG0197 RplP Ribosomal protein 43.5 34 0.00074 27.3 3.6 37 69-109 95-131 (146)
14 PF13356 DUF4102: Domain of un 33.2 1.6E+02 0.0035 20.4 5.5 43 63-106 28-74 (89)
15 PF14112 DUF4284: Domain of un 31.9 25 0.00054 26.6 1.2 18 82-99 2-19 (122)
16 PF09954 DUF2188: Uncharacteri 31.3 1.4E+02 0.0031 19.4 4.7 39 62-105 3-41 (62)
17 cd04516 TBP_eukaryotes eukaryo 29.9 2.7E+02 0.0059 22.4 6.9 46 57-106 34-80 (174)
18 PF10729 CedA: Cell division a 29.1 1.5E+02 0.0033 21.1 4.6 41 55-99 29-69 (80)
19 TIGR01164 rplP_bact ribosomal 28.5 90 0.0019 23.9 3.7 34 68-106 90-124 (126)
20 PRK09203 rplP 50S ribosomal pr 28.3 80 0.0017 24.6 3.5 36 68-108 91-127 (138)
21 COG2185 Sbm Methylmalonyl-CoA 26.6 51 0.0011 26.2 2.1 18 82-99 42-59 (143)
22 CHL00044 rpl16 ribosomal prote 26.6 97 0.0021 24.1 3.6 35 68-107 91-126 (135)
23 KOG3422 Mitochondrial ribosoma 26.3 1.2E+02 0.0026 25.8 4.4 38 68-109 132-170 (221)
24 cd00652 TBP_TLF TATA box bindi 23.7 3.1E+02 0.0067 21.9 6.2 46 57-106 34-80 (174)
25 PF00352 TBP: Transcription fa 20.5 3E+02 0.0066 19.0 5.0 45 58-106 37-82 (86)
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=5.8e-22 Score=133.60 Aligned_cols=61 Identities=69% Similarity=1.246 Sum_probs=56.5
Q ss_pred CceeEeEECCCCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCcc
Q 031071 57 KHYRGVRRRPWGKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRMRGAKALLNFPAE 118 (166)
Q Consensus 57 S~YrGV~~r~~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~~G~~A~lNFp~~ 118 (166)
|+|+||+++++|||+|+|++.. .|+++|||+|+|+||||.|||.+++++||.++.+|||++
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 6899999888999999999842 289999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.85 E-value=2.8e-21 Score=131.82 Aligned_cols=63 Identities=67% Similarity=1.204 Sum_probs=58.9
Q ss_pred ceeEeEECCCCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCccccc
Q 031071 58 HYRGVRRRPWGKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRMRGAKALLNFPAEVVA 121 (166)
Q Consensus 58 ~YrGV~~r~~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~~G~~A~lNFp~~~~~ 121 (166)
+|+||+++++|||+|+|+++. +|+.+|||+|+|+||||.|||.+++++||..+.+|||.+.|.
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 499999988999999999853 589999999999999999999999999999999999999885
No 3
>PHA00280 putative NHN endonuclease
Probab=99.59 E-value=2.3e-15 Score=115.48 Aligned_cols=68 Identities=12% Similarity=0.091 Sum_probs=57.7
Q ss_pred cccccCcCCCCCCCCCCceeEeEECC-CCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 031071 41 EVHTSSMLEPKRTISKKHYRGVRRRP-WGKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRMRGAKAL 112 (166)
Q Consensus 41 ~~~~~~~~~~~~~~~~S~YrGV~~r~-~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~~G~~A~ 112 (166)
+..+......+++.|+|||+||++.+ .|||+|+|+. +||+++||.|+++|+|+.||+ ++.++||++|.
T Consensus 51 T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~---~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 51 LPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA---EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE---CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 33344556666778999999998655 6999999998 799999999999999999997 78899999985
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=99.31 E-value=5.4e-12 Score=82.93 Aligned_cols=53 Identities=32% Similarity=0.454 Sum_probs=45.8
Q ss_pred CceeEeEECC-CCcEEEEEeeCCCCC--eEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 031071 57 KHYRGVRRRP-WGKFAAEIRDSARHG--QRIWLGTFETAEEAALAYDRAAFRMRGA 109 (166)
Q Consensus 57 S~YrGV~~r~-~gkW~A~I~~~~~~g--k~i~LGtF~T~eEAA~AYD~aa~~~~G~ 109 (166)
|+|+||++.+ .++|+|+|++...+| ++++||.|++++||++||+.++.+++|+
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 6899998665 699999999843343 9999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=85.63 E-value=3.6 Score=25.84 Aligned_cols=39 Identities=13% Similarity=0.103 Sum_probs=29.3
Q ss_pred cEEEEEe-eC--CCCCeEEecCCCCCHHHHHHHHHHHHHHhc
Q 031071 69 KFAAEIR-DS--ARHGQRIWLGTFETAEEAALAYDRAAFRMR 107 (166)
Q Consensus 69 kW~A~I~-~~--~~~gk~i~LGtF~T~eEAA~AYD~aa~~~~ 107 (166)
+|..+|. .. .++.++++-+-|.|..||..+..++...+.
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 22 344477888999999999999988766653
No 6
>PHA02601 int integrase; Provisional
Probab=79.19 E-value=3.5 Score=34.72 Aligned_cols=45 Identities=31% Similarity=0.353 Sum_probs=31.1
Q ss_pred EeEECCCCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 031071 61 GVRRRPWGKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRM 106 (166)
Q Consensus 61 GV~~r~~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~ 106 (166)
+|++.++|+|++++......|+++.. +|.|..||....+.....+
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 46666789999999853234777653 6999999876665544444
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=76.31 E-value=5.5 Score=27.87 Aligned_cols=39 Identities=21% Similarity=0.240 Sum_probs=28.6
Q ss_pred CcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHhc
Q 031071 68 GKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRMR 107 (166)
Q Consensus 68 gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~~ 107 (166)
-.|.++|.-... .-.+|.|-|.|.+||..+.--....+.
T Consensus 8 laWWveI~T~~P-~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 8 LAWWVEIETQNP-NCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred CcEEEEEEcCCC-CEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 348899965432 377899999999999988765554443
No 8
>PF07913 DUF1678: Protein of unknown function (DUF1678); InterPro: IPR012465 This family is composed of uncharacterised proteins expressed by Methanopyrus kandleri, a hyperthermophilic archaeon.
Probab=62.02 E-value=28 Score=28.80 Aligned_cols=64 Identities=27% Similarity=0.380 Sum_probs=41.0
Q ss_pred CCCCCCCCCCChHHHHHHHHHHhhhhccCCcCCCCccccccCcCCCCCCCCCCceeEeEECC-CCc-----EEEEEeeC-
Q 031071 5 SQIELPFNENDSQDMVIYQVINESTAQNISFMPQRSEVHTSSMLEPKRTISKKHYRGVRRRP-WGK-----FAAEIRDS- 77 (166)
Q Consensus 5 ~~~~lp~~~~d~~~m~~~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~S~YrGV~~r~-~gk-----W~A~I~~~- 77 (166)
+..-+|...|-.|-.-.+.+|.+.-. +++.-+-||+++. +|+ |+|+.++.
T Consensus 2 ~~~~vPiP~dPVEriR~lRVLrE~~r-----------------------Rg~~P~levtYRtvnG~tcGPYYvARWr~~r 58 (201)
T PF07913_consen 2 SRAHVPIPSDPVERIRALRVLREVYR-----------------------RGKKPSLEVTYRTVNGSTCGPYYVARWRDSR 58 (201)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHH-----------------------cccCCccceeEEecCCcccCcceeeeecCcc
Confidence 45567767777777777788887654 2333355554333 232 67777644
Q ss_pred CCCCeEEecCCCCC
Q 031071 78 ARHGQRIWLGTFET 91 (166)
Q Consensus 78 ~~~gk~i~LGtF~T 91 (166)
.++|..+|||--++
T Consensus 59 ~~~GRTlYLGk~eN 72 (201)
T PF07913_consen 59 FERGRTLYLGKPEN 72 (201)
T ss_pred ccCCceeeccCCcC
Confidence 35689999998776
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=59.23 E-value=6.6 Score=25.61 Aligned_cols=24 Identities=29% Similarity=0.385 Sum_probs=20.0
Q ss_pred CCeEEecCCCCCHHHHHHHHHHHH
Q 031071 80 HGQRIWLGTFETAEEAALAYDRAA 103 (166)
Q Consensus 80 ~gk~i~LGtF~T~eEAA~AYD~aa 103 (166)
..-+|.+|.|+|.+||..+..+..
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 346789999999999998887666
No 10
>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=54.95 E-value=14 Score=27.40 Aligned_cols=20 Identities=35% Similarity=0.632 Sum_probs=18.0
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 031071 87 GTFETAEEAALAYDRAAFRM 106 (166)
Q Consensus 87 GtF~T~eEAA~AYD~aa~~~ 106 (166)
|+|+|+|+|..-||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999987655
No 11
>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=48.83 E-value=47 Score=27.47 Aligned_cols=39 Identities=21% Similarity=0.209 Sum_probs=26.8
Q ss_pred CCcEEEEEeeCCCCCeEEecCCCC--CHHHHHHHHHHHHHHh
Q 031071 67 WGKFAAEIRDSARHGQRIWLGTFE--TAEEAALAYDRAAFRM 106 (166)
Q Consensus 67 ~gkW~A~I~~~~~~gk~i~LGtF~--T~eEAA~AYD~aa~~~ 106 (166)
.+.|..+++.. ++.+++.||+|+ +.++|.....+....+
T Consensus 9 ~~~~~~~~~~~-g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLA-GKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccC-CceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 45699998874 233567799995 6777777766655554
No 12
>PRK09692 integrase; Provisional
Probab=47.29 E-value=64 Score=28.32 Aligned_cols=43 Identities=9% Similarity=0.077 Sum_probs=25.9
Q ss_pred eEECCCC--cEEEEEeeC-CCCCeEEecCCCC--CHHHHHHHHHHHHH
Q 031071 62 VRRRPWG--KFAAEIRDS-ARHGQRIWLGTFE--TAEEAALAYDRAAF 104 (166)
Q Consensus 62 V~~r~~g--kW~A~I~~~-~~~gk~i~LGtF~--T~eEAA~AYD~aa~ 104 (166)
|+.++.| .|..+.+.+ .++.+++-||.|+ |..||..+..++..
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~ 80 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRS 80 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHH
Confidence 4445554 499887643 2233347899999 67777665544433
No 13
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=43.53 E-value=34 Score=27.28 Aligned_cols=37 Identities=24% Similarity=0.196 Sum_probs=31.0
Q ss_pred cEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHhcCC
Q 031071 69 KFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRMRGA 109 (166)
Q Consensus 69 kW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~~G~ 109 (166)
.|.|+|.. |+.++-=...+++.|..|...|+.+|=+.
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 39999975 78888778888999999999999887544
No 14
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=33.24 E-value=1.6e+02 Score=20.37 Aligned_cols=43 Identities=23% Similarity=0.189 Sum_probs=25.9
Q ss_pred EECCC--CcEEEEEeeCCCCCeEEecCCCCC--HHHHHHHHHHHHHHh
Q 031071 63 RRRPW--GKFAAEIRDSARHGQRIWLGTFET--AEEAALAYDRAAFRM 106 (166)
Q Consensus 63 ~~r~~--gkW~A~I~~~~~~gk~i~LGtF~T--~eEAA~AYD~aa~~~ 106 (166)
+..+. ..|.-+.+.. ++.+++-||.|+. ..||..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~-gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRIN-GKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEET-TEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEec-ceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 34454 3488888763 2345688999975 666665555444444
No 15
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=31.92 E-value=25 Score=26.62 Aligned_cols=18 Identities=28% Similarity=0.765 Sum_probs=13.6
Q ss_pred eEEecCCCCCHHHHHHHH
Q 031071 82 QRIWLGTFETAEEAALAY 99 (166)
Q Consensus 82 k~i~LGtF~T~eEAA~AY 99 (166)
..+|||+|.|.+|-..=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 469999999987765433
No 16
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=31.30 E-value=1.4e+02 Score=19.37 Aligned_cols=39 Identities=28% Similarity=0.166 Sum_probs=26.7
Q ss_pred eEECCCCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHH
Q 031071 62 VRRRPWGKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFR 105 (166)
Q Consensus 62 V~~r~~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~ 105 (166)
|..+..|.|..+... ..--..+|+|.+||..+=...|..
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 444455789988754 223378999999998776666654
No 17
>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=29.88 E-value=2.7e+02 Score=22.38 Aligned_cols=46 Identities=24% Similarity=0.212 Sum_probs=35.7
Q ss_pred CceeEeEECC-CCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 031071 57 KHYRGVRRRP-WGKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRM 106 (166)
Q Consensus 57 S~YrGV~~r~-~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~ 106 (166)
.+|-|+..|- .-+-.+.|.. .||-+--|.. ++|+|..|.++.+..+
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~---SGKiviTGak-s~e~a~~a~~~i~~~L 80 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFS---SGKMVCTGAK-SEDDSKLAARKYARII 80 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEEC---CCeEEEEecC-CHHHHHHHHHHHHHHH
Confidence 4688986443 4567788876 6998888875 8899999999888776
No 18
>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=29.08 E-value=1.5e+02 Score=21.06 Aligned_cols=41 Identities=20% Similarity=0.127 Sum_probs=25.6
Q ss_pred CCCceeEeEECCCCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHH
Q 031071 55 SKKHYRGVRRRPWGKFAAEIRDSARHGQRIWLGTFETAEEAALAY 99 (166)
Q Consensus 55 ~~S~YrGV~~r~~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AY 99 (166)
.--+||-|+.-+ |||+|.+-.. ..-.---.|..+|.|.+--
T Consensus 29 k~dgfrdvw~lr-gkyvafvl~g---e~f~rsp~fs~pesaqrwa 69 (80)
T PF10729_consen 29 KMDGFRDVWQLR-GKYVAFVLMG---EHFRRSPAFSVPESAQRWA 69 (80)
T ss_dssp -TTTECCECCCC-CEEEEEEESS---S-EEE---BSSHHHHHHHH
T ss_pred hcccccceeeec-cceEEEEEec---chhccCCCcCCcHHHHHHH
Confidence 356799996544 9999999863 1222346788888877643
No 19
>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=28.46 E-value=90 Score=23.92 Aligned_cols=34 Identities=21% Similarity=0.316 Sum_probs=27.1
Q ss_pred CcEEEEEeeCCCCCeEEe-cCCCCCHHHHHHHHHHHHHHh
Q 031071 68 GKFAAEIRDSARHGQRIW-LGTFETAEEAALAYDRAAFRM 106 (166)
Q Consensus 68 gkW~A~I~~~~~~gk~i~-LGtF~T~eEAA~AYD~aa~~~ 106 (166)
-.|+|+|.. |+-++ ++. .+++.|..|...++.++
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 459999986 56655 555 89999999999998775
No 20
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=28.28 E-value=80 Score=24.56 Aligned_cols=36 Identities=19% Similarity=0.211 Sum_probs=28.2
Q ss_pred CcEEEEEeeCCCCCeEEe-cCCCCCHHHHHHHHHHHHHHhcC
Q 031071 68 GKFAAEIRDSARHGQRIW-LGTFETAEEAALAYDRAAFRMRG 108 (166)
Q Consensus 68 gkW~A~I~~~~~~gk~i~-LGtF~T~eEAA~AYD~aa~~~~G 108 (166)
..|+|+|.. |+-++ ++. .+++.|..|...|+.++=+
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 459999986 66655 555 8999999999999987743
No 21
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=26.59 E-value=51 Score=26.16 Aligned_cols=18 Identities=50% Similarity=0.530 Sum_probs=15.5
Q ss_pred eEEecCCCCCHHHHHHHH
Q 031071 82 QRIWLGTFETAEEAALAY 99 (166)
Q Consensus 82 k~i~LGtF~T~eEAA~AY 99 (166)
.-+|+|.|.|++||+++-
T Consensus 42 eVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 42 EVINLGLFQTPEEAVRAA 59 (143)
T ss_pred eEEecCCcCCHHHHHHHH
Confidence 558999999999999774
No 22
>CHL00044 rpl16 ribosomal protein L16
Probab=26.58 E-value=97 Score=24.08 Aligned_cols=35 Identities=23% Similarity=0.387 Sum_probs=26.5
Q ss_pred CcEEEEEeeCCCCCeEEe-cCCCCCHHHHHHHHHHHHHHhc
Q 031071 68 GKFAAEIRDSARHGQRIW-LGTFETAEEAALAYDRAAFRMR 107 (166)
Q Consensus 68 gkW~A~I~~~~~~gk~i~-LGtF~T~eEAA~AYD~aa~~~~ 107 (166)
..|+|+|.. |+-++ ++. .+++.|..|...++.++=
T Consensus 91 ~~~va~V~~----G~ilfEi~g-~~~~~ak~al~~a~~KLP 126 (135)
T CHL00044 91 EYWVAVVKP----GRILYEMGG-VSETIARAAIKIAAYKMP 126 (135)
T ss_pred cEEEEEECC----CcEEEEEeC-CCHHHHHHHHHHHhhcCC
Confidence 449999986 66666 554 667899999988887764
No 23
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=26.34 E-value=1.2e+02 Score=25.76 Aligned_cols=38 Identities=24% Similarity=0.331 Sum_probs=30.3
Q ss_pred CcEEEEEeeCCCCCeEEe-cCCCCCHHHHHHHHHHHHHHhcCC
Q 031071 68 GKFAAEIRDSARHGQRIW-LGTFETAEEAALAYDRAAFRMRGA 109 (166)
Q Consensus 68 gkW~A~I~~~~~~gk~i~-LGtF~T~eEAA~AYD~aa~~~~G~ 109 (166)
..|+|+|.. |+-++ +|---++++|..|.+.||.++-+.
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 559999976 55554 777789999999999999887543
No 24
>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=23.67 E-value=3.1e+02 Score=21.92 Aligned_cols=46 Identities=30% Similarity=0.268 Sum_probs=35.1
Q ss_pred CceeEeEECC-CCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 031071 57 KHYRGVRRRP-WGKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRM 106 (166)
Q Consensus 57 S~YrGV~~r~-~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~ 106 (166)
.+|.||..|- .-+-.+.|.. +||-+--|.. +.++|..|.++.+..+
T Consensus 34 e~fpgli~R~~~P~~t~lIf~---sGKivitGak-s~~~~~~a~~~~~~~L 80 (174)
T cd00652 34 KRFPGVIMRLREPKTTALIFS---SGKMVITGAK-SEEDAKLAARKYARIL 80 (174)
T ss_pred CccceEEEEcCCCcEEEEEEC---CCEEEEEecC-CHHHHHHHHHHHHHHH
Confidence 4699987544 4566777776 6998888875 8899999998887766
No 25
>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=20.54 E-value=3e+02 Score=19.04 Aligned_cols=45 Identities=22% Similarity=0.228 Sum_probs=33.2
Q ss_pred ceeEeEECC-CCcEEEEEeeCCCCCeEEecCCCCCHHHHHHHHHHHHHHh
Q 031071 58 HYRGVRRRP-WGKFAAEIRDSARHGQRIWLGTFETAEEAALAYDRAAFRM 106 (166)
Q Consensus 58 ~YrGV~~r~-~gkW~A~I~~~~~~gk~i~LGtF~T~eEAA~AYD~aa~~~ 106 (166)
+|.||..+- .-+-.+.|.. .||-+..|. .+++||..|.++....+
T Consensus 37 ~fpgl~~r~~~p~~t~~IF~---sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIFS---SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TESSEEEEETTTTEEEEEET---TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEEc---CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 588886443 3466777765 699888886 58999999998876654
Done!