Query 032263
Match_columns 144
No_of_seqs 148 out of 1202
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 11:47:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032263.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032263hhsearch_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 4.2E-22 9.1E-27 131.2 7.1 61 54-115 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 2.4E-20 5.2E-25 124.3 8.1 63 55-118 1-63 (64)
3 PHA00280 putative NHN endonucl 99.7 3.8E-17 8.3E-22 122.3 7.1 68 38-109 51-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.3 2.5E-12 5.4E-17 82.6 5.6 53 54-106 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 85.3 3.5 7.6E-05 25.2 5.1 39 66-104 1-42 (46)
6 PHA02601 int integrase; Provis 81.8 2.6 5.6E-05 34.6 4.6 45 58-103 2-46 (333)
7 PF08846 DUF1816: Domain of un 61.2 16 0.00035 24.9 3.8 42 66-108 9-50 (68)
8 cd00801 INT_P4 Bacteriophage P 57.0 27 0.00059 28.1 5.2 39 64-103 9-49 (357)
9 PF05036 SPOR: Sporulation rel 54.8 8.5 0.00018 24.4 1.5 22 79-100 44-65 (76)
10 PF13356 DUF4102: Domain of un 52.1 46 0.00099 22.6 5.0 43 60-103 28-74 (89)
11 PF10729 CedA: Cell division a 51.6 27 0.00059 24.3 3.7 38 54-95 31-68 (80)
12 PRK09692 integrase; Provisiona 49.1 57 0.0012 27.8 6.2 45 59-103 33-82 (413)
13 PF08471 Ribonuc_red_2_N: Clas 45.7 25 0.00054 25.5 2.9 21 83-103 70-90 (93)
14 COG0197 RplP Ribosomal protein 41.6 38 0.00083 26.3 3.6 37 66-106 95-131 (146)
15 PRK10113 cell division modulat 36.9 30 0.00065 24.0 2.1 38 54-95 31-68 (80)
16 cd04516 TBP_eukaryotes eukaryo 35.1 1.7E+02 0.0037 23.0 6.4 47 53-103 33-80 (174)
17 PLN00062 TATA-box-binding prot 34.5 1.7E+02 0.0037 23.1 6.4 47 53-103 33-80 (179)
18 cd04517 TLF TBP-like factors ( 30.2 2E+02 0.0043 22.5 6.0 45 55-103 35-80 (174)
19 PF00352 TBP: Transcription fa 28.4 1.3E+02 0.0028 20.5 4.2 46 54-103 36-82 (86)
20 PF09954 DUF2188: Uncharacteri 27.7 1.7E+02 0.0036 18.6 4.8 39 59-102 3-41 (62)
21 PF14112 DUF4284: Domain of un 26.5 34 0.00073 25.3 1.0 17 79-95 2-18 (122)
22 TIGR01164 rplP_bact ribosomal 25.4 1.1E+02 0.0024 22.8 3.7 33 66-103 91-124 (126)
23 PF12752 SUZ: SUZ domain; Int 25.2 93 0.002 20.0 2.8 23 85-107 36-58 (59)
24 COG2185 Sbm Methylmalonyl-CoA 24.0 58 0.0013 25.2 2.0 18 79-96 42-59 (143)
25 PRK09203 rplP 50S ribosomal pr 23.7 1.1E+02 0.0024 23.2 3.4 35 66-105 92-127 (138)
26 CHL00044 rpl16 ribosomal prote 23.5 1.2E+02 0.0026 22.9 3.6 34 66-104 92-126 (135)
27 cd04518 TBP_archaea archaeal T 22.9 3.2E+02 0.0069 21.4 6.0 49 52-104 32-81 (174)
28 PF13773 DUF4170: Domain of un 22.5 82 0.0018 21.6 2.2 25 79-103 25-49 (69)
29 cd00652 TBP_TLF TATA box bindi 22.0 3.3E+02 0.0072 21.2 5.9 47 53-103 33-80 (174)
30 cd07997 WGR_PARP WGR domain of 20.3 2.6E+02 0.0057 19.6 4.7 39 78-117 53-93 (102)
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=99.87 E-value=4.2e-22 Score=131.16 Aligned_cols=61 Identities=67% Similarity=1.169 Sum_probs=56.6
Q ss_pred CceeeeEECCCCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHhcCCCCCCCCccc
Q 032263 54 VNYRGVRKRPWGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKMRGSKAKLNFPSL 115 (144)
Q Consensus 54 SgyrGV~~~~~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l~G~~A~~NFP~~ 115 (144)
|+|+||+++++|||+|+|+++. .|+.+|||+|+|+|||+.|||.++++++|.++.+|||++
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 6899999888999999999943 189999999999999999999999999999999999974
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=2.4e-20 Score=124.25 Aligned_cols=63 Identities=65% Similarity=1.174 Sum_probs=58.1
Q ss_pred ceeeeEECCCCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHhcCCCCCCCCcccccC
Q 032263 55 NYRGVRKRPWGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKMRGSKAKLNFPSLIAS 118 (144)
Q Consensus 55 gyrGV~~~~~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l~G~~A~~NFP~~~~~ 118 (144)
+|+||+++++|||+|+|+++. +|+.+|||+|+|+||||.|||.++++++|.++.+|||...+.
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 589999888999999999866 479999999999999999999999999999999999987654
No 3
>PHA00280 putative NHN endonuclease
Probab=99.70 E-value=3.8e-17 Score=122.35 Aligned_cols=68 Identities=13% Similarity=0.154 Sum_probs=61.3
Q ss_pred hhhhhhhhccccCCCCCceeeeEECC-CCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 032263 38 FRLQKAATMTREIHVRVNYRGVRKRP-WGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKMRGSKAK 109 (144)
Q Consensus 38 ~~~~~~~~~~~~~~~~SgyrGV~~~~-~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l~G~~A~ 109 (144)
-+.++..+++.+++|+|||+||++.+ .|||+|+|.+ +||+++||.|+++|+|+.||+ ++.+|||+||.
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 34578888888899999999999876 7999999999 999999999999999999997 77889999985
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=99.34 E-value=2.5e-12 Score=82.55 Aligned_cols=53 Identities=30% Similarity=0.439 Sum_probs=46.3
Q ss_pred CceeeeEECC-CCeEEEEEeccCCCC--eeeccCCCCCHHHHHHHHHHHHHHhcCC
Q 032263 54 VNYRGVRKRP-WGKFAAEIRDRKKNG--SRLWLGTYDTPEGAALAYDRAAFKMRGS 106 (144)
Q Consensus 54 SgyrGV~~~~-~gkW~A~I~~~~~~g--k~i~LGtF~t~EeAA~AYD~Aa~~l~G~ 106 (144)
|+|+||++.+ .++|+|+|++...+| ++++||.|++++||++|++.+++.++|+
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 6899999877 799999999843343 8999999999999999999999999875
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=85.26 E-value=3.5 Score=25.24 Aligned_cols=39 Identities=10% Similarity=0.112 Sum_probs=29.3
Q ss_pred eEEEEEe-ccCCCC--eeeccCCCCCHHHHHHHHHHHHHHhc
Q 032263 66 KFAAEIR-DRKKNG--SRLWLGTYDTPEGAALAYDRAAFKMR 104 (144)
Q Consensus 66 kW~A~I~-~~~~~g--k~i~LGtF~t~EeAA~AYD~Aa~~l~ 104 (144)
+|..+|. .....| ++++-+-|.|..||..+...+...+.
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 433334 66788899999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=81.85 E-value=2.6 Score=34.58 Aligned_cols=45 Identities=24% Similarity=0.275 Sum_probs=31.1
Q ss_pred eeEECCCCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHh
Q 032263 58 GVRKRPWGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 58 GV~~~~~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l 103 (144)
+|++.++|+|++++......|+++.. +|.|..||....+.....+
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 46666678999999864334777654 6999999876655544444
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=61.24 E-value=16 Score=24.89 Aligned_cols=42 Identities=19% Similarity=0.287 Sum_probs=31.1
Q ss_pred eEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHhcCCCC
Q 032263 66 KFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKMRGSKA 108 (144)
Q Consensus 66 kW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l~G~~A 108 (144)
.|-++|.-.. -.-..|.|-|.+.+||..+...-...+-.+.+
T Consensus 9 aWWveI~T~~-P~ctYyFGPF~s~~eA~~~~~gyieDL~~Ega 50 (68)
T PF08846_consen 9 AWWVEIETQN-PNCTYYFGPFDSREEAEAALPGYIEDLESEGA 50 (68)
T ss_pred cEEEEEEcCC-CCEEEEeCCcCCHHHHHHHhccHHHHHHhhCc
Confidence 4778887533 23789999999999999987766666654443
No 8
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=57.04 E-value=27 Score=28.13 Aligned_cols=39 Identities=26% Similarity=0.189 Sum_probs=26.7
Q ss_pred CCeEEEEEeccCCCCeeeccCCCC--CHHHHHHHHHHHHHHh
Q 032263 64 WGKFAAEIRDRKKNGSRLWLGTYD--TPEGAALAYDRAAFKM 103 (144)
Q Consensus 64 ~gkW~A~I~~~~~~gk~i~LGtF~--t~EeAA~AYD~Aa~~l 103 (144)
.+.|+.++....+ .+++.||.|+ +.++|..........+
T Consensus 9 ~~~~~~~~~~~g~-~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGK-RKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCc-eeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 3569999988432 2456799995 6777777766655554
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=54.76 E-value=8.5 Score=24.42 Aligned_cols=22 Identities=23% Similarity=0.379 Sum_probs=18.4
Q ss_pred eeeccCCCCCHHHHHHHHHHHH
Q 032263 79 SRLWLGTYDTPEGAALAYDRAA 100 (144)
Q Consensus 79 k~i~LGtF~t~EeAA~AYD~Aa 100 (144)
-++.+|.|++.++|..+.....
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 3688899999999998887665
No 10
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=52.06 E-value=46 Score=22.63 Aligned_cols=43 Identities=23% Similarity=0.162 Sum_probs=26.3
Q ss_pred EECCC--CeEEEEEeccCCCCeeeccCCCCC--HHHHHHHHHHHHHHh
Q 032263 60 RKRPW--GKFAAEIRDRKKNGSRLWLGTYDT--PEGAALAYDRAAFKM 103 (144)
Q Consensus 60 ~~~~~--gkW~A~I~~~~~~gk~i~LGtF~t--~EeAA~AYD~Aa~~l 103 (144)
+..++ ..|..+.....+ .+++-||.|+. ..+|..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~gk-~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGK-RRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEETTE-EEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecce-EEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 34454 359988877432 35688999976 666665555444443
No 11
>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=51.56 E-value=27 Score=24.26 Aligned_cols=38 Identities=21% Similarity=0.194 Sum_probs=24.1
Q ss_pred CceeeeEECCCCeEEEEEeccCCCCeeeccCCCCCHHHHHHH
Q 032263 54 VNYRGVRKRPWGKFAAEIRDRKKNGSRLWLGTYDTPEGAALA 95 (144)
Q Consensus 54 SgyrGV~~~~~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~A 95 (144)
-+|+.|..-+ |||+|.+.. .-.-.---.|..+|.|.+=
T Consensus 31 dgfrdvw~lr-gkyvafvl~---ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 31 DGFRDVWQLR-GKYVAFVLM---GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTECCECCCC-CEEEEEEES---SS-EEE---BSSHHHHHHH
T ss_pred ccccceeeec-cceEEEEEe---cchhccCCCcCCcHHHHHH
Confidence 4788886544 999999987 3223334568888777653
No 12
>PRK09692 integrase; Provisional
Probab=49.09 E-value=57 Score=27.84 Aligned_cols=45 Identities=13% Similarity=0.061 Sum_probs=26.9
Q ss_pred eEECCCC--eEEEEEeccC-CCCeeeccCCCC--CHHHHHHHHHHHHHHh
Q 032263 59 VRKRPWG--KFAAEIRDRK-KNGSRLWLGTYD--TPEGAALAYDRAAFKM 103 (144)
Q Consensus 59 V~~~~~g--kW~A~I~~~~-~~gk~i~LGtF~--t~EeAA~AYD~Aa~~l 103 (144)
|...++| .|+.+.+.+. .+.+++-||.|+ |..+|..+...+...+
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~~~~~~ 82 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAESRSLL 82 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHHHHHHH
Confidence 3444544 5999886432 122336899999 6777766555544433
No 13
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=45.70 E-value=25 Score=25.48 Aligned_cols=21 Identities=29% Similarity=0.453 Sum_probs=18.0
Q ss_pred cCCCCCHHHHHHHHHHHHHHh
Q 032263 83 LGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 83 LGtF~t~EeAA~AYD~Aa~~l 103 (144)
-|+|+|+|+|..=||.....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 399999999999999877654
No 14
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=41.61 E-value=38 Score=26.34 Aligned_cols=37 Identities=30% Similarity=0.184 Sum_probs=30.6
Q ss_pred eEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHhcCC
Q 032263 66 KFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKMRGS 106 (144)
Q Consensus 66 kW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l~G~ 106 (144)
-|.|+|.. |+.++-=...+++.|..|..+|+.+|=+.
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 39999965 78888778888999999999999887543
No 15
>PRK10113 cell division modulator; Provisional
Probab=36.92 E-value=30 Score=24.01 Aligned_cols=38 Identities=26% Similarity=0.248 Sum_probs=25.5
Q ss_pred CceeeeEECCCCeEEEEEeccCCCCeeeccCCCCCHHHHHHH
Q 032263 54 VNYRGVRKRPWGKFAAEIRDRKKNGSRLWLGTYDTPEGAALA 95 (144)
Q Consensus 54 SgyrGV~~~~~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~A 95 (144)
-+|+.|..-+ |||+|.+.. .-.-.---.|..+|.|.+=
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 4788886555 999999987 2222234568888877653
No 16
>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=35.11 E-value=1.7e+02 Score=22.95 Aligned_cols=47 Identities=21% Similarity=0.162 Sum_probs=35.7
Q ss_pred CCceeeeEECC-CCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHh
Q 032263 53 RVNYRGVRKRP-WGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 53 ~SgyrGV~~~~-~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l 103 (144)
...|.||..+- .-+-.+-|+. .||-+.-|. .+.|+|..|.+..+..+
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~i~~~L 80 (174)
T cd04516 33 PKRFAAVIMRIREPKTTALIFS---SGKMVCTGA-KSEDDSKLAARKYARII 80 (174)
T ss_pred CccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 35788987554 4567788888 888888887 56788888888877666
No 17
>PLN00062 TATA-box-binding protein; Provisional
Probab=34.48 E-value=1.7e+02 Score=23.10 Aligned_cols=47 Identities=21% Similarity=0.140 Sum_probs=35.3
Q ss_pred CCceeeeEECC-CCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHh
Q 032263 53 RVNYRGVRKRP-WGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 53 ~SgyrGV~~~~-~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l 103 (144)
...|.||..+- .-+-.+-|.. .||-+.-|. .+.|+|..|.+..+..+
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~---SGKiviTGa-ks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 33 PKRFAAVIMRIREPKTTALIFA---SGKMVCTGA-KSEHDSKLAARKYARII 80 (179)
T ss_pred CccCcEEEEEeCCCcEEEEEEC---CCeEEEEec-CCHHHHHHHHHHHHHHH
Confidence 34789987554 4567888888 888877775 67888888888877666
No 18
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=30.18 E-value=2e+02 Score=22.49 Aligned_cols=45 Identities=27% Similarity=0.217 Sum_probs=35.1
Q ss_pred ceeeeEECC-CCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHh
Q 032263 55 NYRGVRKRP-WGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 55 gyrGV~~~~-~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l 103 (144)
+|.||..+- .-+-.+-|+. .||-+.-|. .+.|+|..|.+..+..+
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~---sGKiviTGa-ks~~~~~~a~~~~~~~l 80 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS---SGKITITGA-TSEEEAKQAARRAARLL 80 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC---CCeEEEEcc-CCHHHHHHHHHHHHHHH
Confidence 899987554 4577888888 888777664 78899999988877666
No 19
>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=28.35 E-value=1.3e+02 Score=20.46 Aligned_cols=46 Identities=20% Similarity=0.155 Sum_probs=33.9
Q ss_pred CceeeeEECC-CCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHh
Q 032263 54 VNYRGVRKRP-WGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 54 SgyrGV~~~~-~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l 103 (144)
..|.||..+- .-+-.+.|.. .||-+..|. .+.|+|..|.+.....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~---sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFS---SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEET---TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEc---CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 3688876444 4467788877 788888775 68889999988776554
No 20
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=27.72 E-value=1.7e+02 Score=18.59 Aligned_cols=39 Identities=26% Similarity=0.147 Sum_probs=26.0
Q ss_pred eEECCCCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHH
Q 032263 59 VRKRPWGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFK 102 (144)
Q Consensus 59 V~~~~~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~ 102 (144)
|..+..+.|....-. ...-..+|+|.+||..+=...+..
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 444345779988754 333478999999998776555544
No 21
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=26.50 E-value=34 Score=25.27 Aligned_cols=17 Identities=12% Similarity=0.550 Sum_probs=12.9
Q ss_pred eeeccCCCCCHHHHHHH
Q 032263 79 SRLWLGTYDTPEGAALA 95 (144)
Q Consensus 79 k~i~LGtF~t~EeAA~A 95 (144)
..+|||+|.+.++-..=
T Consensus 2 VsiWiG~f~s~~el~~Y 18 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEY 18 (122)
T ss_pred eEEEEecCCCHHHHHHH
Confidence 46899999988765543
No 22
>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=25.38 E-value=1.1e+02 Score=22.80 Aligned_cols=33 Identities=27% Similarity=0.308 Sum_probs=26.2
Q ss_pred eEEEEEeccCCCCeeec-cCCCCCHHHHHHHHHHHHHHh
Q 032263 66 KFAAEIRDRKKNGSRLW-LGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 66 kW~A~I~~~~~~gk~i~-LGtF~t~EeAA~AYD~Aa~~l 103 (144)
-|.|+|.. |+-++ ++. .+++.|..|...|+.+|
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 49999976 56665 544 89999999999988775
No 23
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=25.20 E-value=93 Score=20.02 Aligned_cols=23 Identities=22% Similarity=0.251 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHHHHHHhcCCC
Q 032263 85 TYDTPEGAALAYDRAAFKMRGSK 107 (144)
Q Consensus 85 tF~t~EeAA~AYD~Aa~~l~G~~ 107 (144)
.-.|.||=.++|.+|..+++|..
T Consensus 36 ~~kSlEERE~eY~~AR~RIFg~~ 58 (59)
T PF12752_consen 36 PSKSLEEREAEYAEARARIFGSS 58 (59)
T ss_pred ccCCHHHHHHHHHHHHHHHhCCC
Confidence 34799999999999999999875
No 24
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=23.97 E-value=58 Score=25.17 Aligned_cols=18 Identities=39% Similarity=0.484 Sum_probs=15.4
Q ss_pred eeeccCCCCCHHHHHHHH
Q 032263 79 SRLWLGTYDTPEGAALAY 96 (144)
Q Consensus 79 k~i~LGtF~t~EeAA~AY 96 (144)
.-+++|.|.|++|++++-
T Consensus 42 eVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 42 EVINLGLFQTPEEAVRAA 59 (143)
T ss_pred eEEecCCcCCHHHHHHHH
Confidence 348999999999999875
No 25
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=23.67 E-value=1.1e+02 Score=23.17 Aligned_cols=35 Identities=26% Similarity=0.195 Sum_probs=27.3
Q ss_pred eEEEEEeccCCCCeeec-cCCCCCHHHHHHHHHHHHHHhcC
Q 032263 66 KFAAEIRDRKKNGSRLW-LGTYDTPEGAALAYDRAAFKMRG 105 (144)
Q Consensus 66 kW~A~I~~~~~~gk~i~-LGtF~t~EeAA~AYD~Aa~~l~G 105 (144)
-|.|+|.. |+-++ ++. .+++.|..|+..|+.+|=+
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 49999976 56655 555 8999999999999887643
No 26
>CHL00044 rpl16 ribosomal protein L16
Probab=23.50 E-value=1.2e+02 Score=22.93 Aligned_cols=34 Identities=29% Similarity=0.374 Sum_probs=25.7
Q ss_pred eEEEEEeccCCCCeeec-cCCCCCHHHHHHHHHHHHHHhc
Q 032263 66 KFAAEIRDRKKNGSRLW-LGTYDTPEGAALAYDRAAFKMR 104 (144)
Q Consensus 66 kW~A~I~~~~~~gk~i~-LGtF~t~EeAA~AYD~Aa~~l~ 104 (144)
-|.|+|.. |+-++ ++. .+++.|..|...|+.+|=
T Consensus 92 ~~va~V~~----G~ilfEi~g-~~~~~ak~al~~a~~KLP 126 (135)
T CHL00044 92 YWVAVVKP----GRILYEMGG-VSETIARAAIKIAAYKMP 126 (135)
T ss_pred EEEEEECC----CcEEEEEeC-CCHHHHHHHHHHHhhcCC
Confidence 39999976 56666 544 667899999988888763
No 27
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, 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=22.95 E-value=3.2e+02 Score=21.43 Aligned_cols=49 Identities=22% Similarity=0.164 Sum_probs=36.3
Q ss_pred CCCceeeeEECC-CCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHhc
Q 032263 52 VRVNYRGVRKRP-WGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKMR 104 (144)
Q Consensus 52 ~~SgyrGV~~~~-~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l~ 104 (144)
+..+|.||..+- .-+-.+-|+. .||-+..|. .+.++|..|-++.+..+.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~---SGKiv~tGa-ks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFR---SGKMVCTGA-KSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEEC---CCeEEEEcc-CCHHHHHHHHHHHHHHHH
Confidence 346799987554 4567778877 888887775 688888888888776663
No 28
>PF13773 DUF4170: Domain of unknown function (DUF4170)
Probab=22.48 E-value=82 Score=21.64 Aligned_cols=25 Identities=16% Similarity=0.118 Sum_probs=20.6
Q ss_pred eeeccCCCCCHHHHHHHHHHHHHHh
Q 032263 79 SRLWLGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 79 k~i~LGtF~t~EeAA~AYD~Aa~~l 103 (144)
+--.+|-|++-++|..|+..++..-
T Consensus 25 ~~diVG~fp~y~~A~~aWrakAq~T 49 (69)
T PF13773_consen 25 ALDIVGIFPDYASAYAAWRAKAQRT 49 (69)
T ss_pred cceEEecCCChHHHHHHHHHHHhCc
Confidence 3456899999999999999887664
No 29
>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=22.02 E-value=3.3e+02 Score=21.16 Aligned_cols=47 Identities=28% Similarity=0.217 Sum_probs=35.1
Q ss_pred CCceeeeEECC-CCeEEEEEeccCCCCeeeccCCCCCHHHHHHHHHHHHHHh
Q 032263 53 RVNYRGVRKRP-WGKFAAEIRDRKKNGSRLWLGTYDTPEGAALAYDRAAFKM 103 (144)
Q Consensus 53 ~SgyrGV~~~~-~gkW~A~I~~~~~~gk~i~LGtF~t~EeAA~AYD~Aa~~l 103 (144)
..+|.||..+. .-+-.+-|.. .||-+.-|. .+.|+|..|.++.+..+
T Consensus 33 Pe~fpgli~R~~~P~~t~lIf~---sGKivitGa-ks~~~~~~a~~~~~~~L 80 (174)
T cd00652 33 PKRFPGVIMRLREPKTTALIFS---SGKMVITGA-KSEEDAKLAARKYARIL 80 (174)
T ss_pred CCccceEEEEcCCCcEEEEEEC---CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 35889987555 4567788887 888888786 46788888888776666
No 30
>cd07997 WGR_PARP WGR domain of poly(ADP-ribose) polymerases. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins and histones. Higher eukaryotes contain several PARPs and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. Poly-ADP-ribosylation was thought to be a reversible post-translational covalent modification that serves as a regulator
Probab=20.29 E-value=2.6e+02 Score=19.57 Aligned_cols=39 Identities=13% Similarity=0.172 Sum_probs=25.6
Q ss_pred CeeeccCCCCCHHHHHHHHHHHHHHhcCCCC--CCCCccccc
Q 032263 78 GSRLWLGTYDTPEGAALAYDRAAFKMRGSKA--KLNFPSLIA 117 (144)
Q Consensus 78 gk~i~LGtF~t~EeAA~AYD~Aa~~l~G~~A--~~NFP~~~~ 117 (144)
|.... =.|.++++|..++.+.-..--|..- +.+|+....
T Consensus 53 Gq~~~-~~~~~~~~A~~~F~k~f~~Kt~~~w~~r~~f~k~~~ 93 (102)
T cd07997 53 GQSQL-TPFGSLESAIKEFEKKFKDKTGNEWENRPLFKKQPG 93 (102)
T ss_pred Cceee-cCCCCHHHHHHHHHHHHHHHHCCccccccccccCCC
Confidence 44433 3488899999999876665544442 477776554
Done!