Query 028913
Match_columns 202
No_of_seqs 218 out of 1173
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:30:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028913.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028913hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00380 AP2 DNA-binding dom 99.9 1.8E-21 3.9E-26 137.3 8.2 63 6-68 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.9 1.9E-21 4.1E-26 135.5 7.4 61 5-65 1-61 (61)
3 PHA00280 putative NHN endonucl 99.4 7.3E-13 1.6E-17 105.3 6.6 53 4-59 66-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 9.2E-11 2E-15 79.7 5.9 52 5-56 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 82.6 5.3 0.00012 26.0 5.4 38 17-54 1-42 (46)
6 PF08846 DUF1816: Domain of un 64.5 12 0.00026 27.2 3.9 38 17-54 9-46 (68)
7 PHA02601 int integrase; Provis 63.7 11 0.00024 32.8 4.3 44 9-53 2-46 (333)
8 cd00801 INT_P4 Bacteriophage P 60.1 19 0.00041 31.0 5.1 40 15-54 9-50 (357)
9 PF05036 SPOR: Sporulation rel 45.4 15 0.00034 24.7 1.8 24 27-50 42-65 (76)
10 PF10729 CedA: Cell division a 39.7 67 0.0014 23.8 4.4 39 3-44 29-67 (80)
11 PF13356 DUF4102: Domain of un 39.1 88 0.0019 22.6 5.1 42 11-52 28-73 (89)
12 PRK09692 integrase; Provisiona 38.1 85 0.0018 28.6 5.9 38 11-48 34-77 (413)
13 PF12286 DUF3622: Protein of u 38.1 67 0.0015 23.7 4.2 42 1-43 1-47 (71)
14 COG0197 RplP Ribosomal protein 37.7 43 0.00094 27.8 3.5 36 18-56 96-131 (146)
15 PF08471 Ribonuc_red_2_N: Clas 35.1 39 0.00085 26.1 2.7 21 33-53 70-90 (93)
16 COG3906 Uncharacterized protei 27.5 62 0.0013 25.5 2.7 17 127-143 37-53 (105)
17 PF11239 DUF3040: Protein of u 27.4 61 0.0013 23.6 2.5 21 174-194 3-23 (82)
18 PF01525 Rota_NS26: Rotavirus 25.3 34 0.00073 29.8 0.9 10 179-188 203-212 (212)
19 PRK10113 cell division modulat 22.9 66 0.0014 23.8 1.9 39 4-45 30-68 (80)
20 PF14112 DUF4284: Domain of un 22.5 53 0.0011 25.8 1.5 18 29-46 2-19 (122)
21 PF00352 TBP: Transcription fa 22.3 2.4E+02 0.0053 20.4 4.9 46 5-53 36-82 (86)
22 cd04516 TBP_eukaryotes eukaryo 21.6 3.7E+02 0.008 22.5 6.5 47 5-54 34-81 (174)
23 PLN00062 TATA-box-binding prot 21.3 3.7E+02 0.008 22.7 6.4 47 5-54 34-81 (179)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.85 E-value=1.8e-21 Score=137.28 Aligned_cols=63 Identities=60% Similarity=1.056 Sum_probs=60.1
Q ss_pred CeeeeeECCCCeEEEEeeeCCCCeEEecCCcchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 028913 6 KFRGVRQRQWGSWVSEIRHPLLKRRVWLGTFETAEAAARAYDQAAVLMNGQNAKTNFPILKPN 68 (202)
Q Consensus 6 kyRGVr~r~~GkW~A~I~~~~~~k~i~LGtFdT~EeAA~AYD~AA~k~~G~~A~tNFP~~~~~ 68 (202)
+|+||+++++|||+|+|+++..++++|||+|+|+||||.|||.|+++++|.++.+|||.+.|+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 699998888999999999977799999999999999999999999999999999999999886
No 2
>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=1.9e-21 Score=135.53 Aligned_cols=61 Identities=62% Similarity=1.083 Sum_probs=58.1
Q ss_pred CCeeeeeECCCCeEEEEeeeCCCCeEEecCCcchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 028913 5 KKFRGVRQRQWGSWVSEIRHPLLKRRVWLGTFETAEAAARAYDQAAVLMNGQNAKTNFPIL 65 (202)
Q Consensus 5 SkyRGVr~r~~GkW~A~I~~~~~~k~i~LGtFdT~EeAA~AYD~AA~k~~G~~A~tNFP~~ 65 (202)
|+||||+++++|||+|+|+++..++++|||+|+|+||||.|||.|+++++|.++.+|||.+
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 7899999888999999999987799999999999999999999999999999999999974
No 3
>PHA00280 putative NHN endonuclease
Probab=99.38 E-value=7.3e-13 Score=105.33 Aligned_cols=53 Identities=15% Similarity=0.298 Sum_probs=48.5
Q ss_pred CCCeeeee-ECCCCeEEEEeeeCCCCeEEecCCcchHHHHHHHHHHHHHHhcCCCCC
Q 028913 4 SKKFRGVR-QRQWGSWVSEIRHPLLKRRVWLGTFETAEAAARAYDQAAVLMNGQNAK 59 (202)
Q Consensus 4 sSkyRGVr-~r~~GkW~A~I~~~~~~k~i~LGtFdT~EeAA~AYD~AA~k~~G~~A~ 59 (202)
+|+|+||+ +...|||+|+|... ||+++||.|+++|+|+.||+ ++.++||.||.
T Consensus 66 ~SG~kGV~~~k~~~kw~A~I~~~--gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 66 TSGLKGLSWSKEREMWRGTVTAE--GKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCeeEEecCCCeEEEEEEEC--CEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 69999995 66789999999997 99999999999999999997 78899999884
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=99.15 E-value=9.2e-11 Score=79.68 Aligned_cols=52 Identities=29% Similarity=0.484 Sum_probs=44.7
Q ss_pred CCeeeee-ECCCCeEEEEeeeCCC---CeEEecCCcchHHHHHHHHHHHHHHhcCC
Q 028913 5 KKFRGVR-QRQWGSWVSEIRHPLL---KRRVWLGTFETAEAAARAYDQAAVLMNGQ 56 (202)
Q Consensus 5 SkyRGVr-~r~~GkW~A~I~~~~~---~k~i~LGtFdT~EeAA~AYD~AA~k~~G~ 56 (202)
|+|+||+ .+..++|+|+|++... +++++||.|+++++|++||+.++..++|+
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 7899995 5558999999998321 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=82.59 E-value=5.3 Score=26.04 Aligned_cols=38 Identities=13% Similarity=0.213 Sum_probs=29.1
Q ss_pred eEEEEee--eCCCC--eEEecCCcchHHHHHHHHHHHHHHhc
Q 028913 17 SWVSEIR--HPLLK--RRVWLGTFETAEAAARAYDQAAVLMN 54 (202)
Q Consensus 17 kW~A~I~--~~~~~--k~i~LGtFdT~EeAA~AYD~AA~k~~ 54 (202)
+|..+|. ++..| ++++-+.|.|..||-.+...+...+.
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 43234 67888999999999999988776653
No 6
>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=64.54 E-value=12 Score=27.21 Aligned_cols=38 Identities=21% Similarity=0.313 Sum_probs=29.2
Q ss_pred eEEEEeeeCCCCeEEecCCcchHHHHHHHHHHHHHHhc
Q 028913 17 SWVSEIRHPLLKRRVWLGTFETAEAAARAYDQAAVLMN 54 (202)
Q Consensus 17 kW~A~I~~~~~~k~i~LGtFdT~EeAA~AYD~AA~k~~ 54 (202)
.|-++|.-..-....|.|-|+|.+||..+.--....+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 47788888655788999999999999988654444443
No 7
>PHA02601 int integrase; Provisional
Probab=63.71 E-value=11 Score=32.85 Aligned_cols=44 Identities=23% Similarity=0.262 Sum_probs=29.5
Q ss_pred eeeECCCCeEEEEeeeC-CCCeEEecCCcchHHHHHHHHHHHHHHh
Q 028913 9 GVRQRQWGSWVSEIRHP-LLKRRVWLGTFETAEAAARAYDQAAVLM 53 (202)
Q Consensus 9 GVr~r~~GkW~A~I~~~-~~~k~i~LGtFdT~EeAA~AYD~AA~k~ 53 (202)
+|++.+.|+|++++... ..|+++. .+|.|..||....+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHhc
Confidence 56677789999999863 2355554 36999988866655544433
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=60.10 E-value=19 Score=30.96 Aligned_cols=40 Identities=25% Similarity=0.362 Sum_probs=29.0
Q ss_pred CCeEEEEeeeCCCCeEEecCCcc--hHHHHHHHHHHHHHHhc
Q 028913 15 WGSWVSEIRHPLLKRRVWLGTFE--TAEAAARAYDQAAVLMN 54 (202)
Q Consensus 15 ~GkW~A~I~~~~~~k~i~LGtFd--T~EeAA~AYD~AA~k~~ 54 (202)
.+.|..+++.+...+++.||+|+ +.++|..........+.
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 35699999998555678899995 67777776666555443
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=45.45 E-value=15 Score=24.69 Aligned_cols=24 Identities=29% Similarity=0.320 Sum_probs=19.5
Q ss_pred CCeEEecCCcchHHHHHHHHHHHH
Q 028913 27 LKRRVWLGTFETAEAAARAYDQAA 50 (202)
Q Consensus 27 ~~k~i~LGtFdT~EeAA~AYD~AA 50 (202)
..-+|++|.|+|.++|..+-....
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 346899999999999988877655
No 10
>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=39.69 E-value=67 Score=23.82 Aligned_cols=39 Identities=26% Similarity=0.305 Sum_probs=25.1
Q ss_pred CCCCeeeeeECCCCeEEEEeeeCCCCeEEecCCcchHHHHHH
Q 028913 3 QSKKFRGVRQRQWGSWVSEIRHPLLKRRVWLGTFETAEAAAR 44 (202)
Q Consensus 3 rsSkyRGVr~r~~GkW~A~I~~~~~~k~i~LGtFdT~EeAA~ 44 (202)
+--+||-|+.-+ |||+|.+... ..-..--.|...|.|-+
T Consensus 29 k~dgfrdvw~lr-gkyvafvl~g--e~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 29 KMDGFRDVWQLR-GKYVAFVLMG--EHFRRSPAFSVPESAQR 67 (80)
T ss_dssp -TTTECCECCCC-CEEEEEEESS--S-EEE---BSSHHHHHH
T ss_pred hcccccceeeec-cceEEEEEec--chhccCCCcCCcHHHHH
Confidence 456799997665 9999999884 33334456777777655
No 11
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=39.11 E-value=88 Score=22.62 Aligned_cols=42 Identities=19% Similarity=0.185 Sum_probs=26.1
Q ss_pred eECCC--CeEEEEeeeCCCCeEEecCCcch--HHHHHHHHHHHHHH
Q 028913 11 RQRQW--GSWVSEIRHPLLKRRVWLGTFET--AEAAARAYDQAAVL 52 (202)
Q Consensus 11 r~r~~--GkW~A~I~~~~~~k~i~LGtFdT--~EeAA~AYD~AA~k 52 (202)
+-.+. ..|..+.+.+...+++.||.|.+ ..+|..........
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~ 73 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRAL 73 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHH
Confidence 33444 34998888874447899999975 55555554444333
No 12
>PRK09692 integrase; Provisional
Probab=38.10 E-value=85 Score=28.57 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=23.4
Q ss_pred eECCCC--eEEEEeeeCCCCe--EEecCCcc--hHHHHHHHHHH
Q 028913 11 RQRQWG--SWVSEIRHPLLKR--RVWLGTFE--TAEAAARAYDQ 48 (202)
Q Consensus 11 r~r~~G--kW~A~I~~~~~~k--~i~LGtFd--T~EeAA~AYD~ 48 (202)
+-++.| .|..+.+.+.+++ ++.||.|. |..+|..+...
T Consensus 34 ~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 34 LIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 444444 4998876543343 47899998 56666554444
No 13
>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=38.08 E-value=67 Score=23.66 Aligned_cols=42 Identities=26% Similarity=0.473 Sum_probs=26.6
Q ss_pred CCCCCCeee-eeECCCCeEEEEeeeCCCCeEE----ecCCcchHHHHH
Q 028913 1 MVQSKKFRG-VRQRQWGSWVSEIRHPLLKRRV----WLGTFETAEAAA 43 (202)
Q Consensus 1 m~rsSkyRG-Vr~r~~GkW~A~I~~~~~~k~i----~LGtFdT~EeAA 43 (202)
|-+++||.= |.+.. +.|-|+|......++. .--.|+|+++|.
T Consensus 1 Msk~kK~~~rv~q~~-~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq 47 (71)
T PF12286_consen 1 MSKNKKYDFRVTQKR-NGWTAEITRRVTSRKTVVSKRQDGFASEAEAQ 47 (71)
T ss_pred CCCCCcccEEEEecC-CceeeeeeeeecCceeEEEecccCcccHHHHH
Confidence 667788754 34444 6699999874333221 225699988864
No 14
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=37.72 E-value=43 Score=27.77 Aligned_cols=36 Identities=19% Similarity=0.232 Sum_probs=30.8
Q ss_pred EEEEeeeCCCCeEEecCCcchHHHHHHHHHHHHHHhcCC
Q 028913 18 WVSEIRHPLLKRRVWLGTFETAEAAARAYDQAAVLMNGQ 56 (202)
Q Consensus 18 W~A~I~~~~~~k~i~LGtFdT~EeAA~AYD~AA~k~~G~ 56 (202)
|.|+|.. |+.++-=..++++.|.+|..+|+.+|=+.
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 9999988 77777777888888999999999887554
No 15
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=35.12 E-value=39 Score=26.08 Aligned_cols=21 Identities=33% Similarity=0.488 Sum_probs=17.8
Q ss_pred cCCcchHHHHHHHHHHHHHHh
Q 028913 33 LGTFETAEAAARAYDQAAVLM 53 (202)
Q Consensus 33 LGtFdT~EeAA~AYD~AA~k~ 53 (202)
-|+|+|+++|..=||.....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 399999999999999876554
No 16
>COG3906 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.45 E-value=62 Score=25.52 Aligned_cols=17 Identities=24% Similarity=0.458 Sum_probs=13.8
Q ss_pred CCCCCCceEEEEccCcc
Q 028913 127 SRSGSSWVMRVELGKNK 143 (202)
Q Consensus 127 ~~~~s~w~m~~~~g~~~ 143 (202)
.-.+++||.++.-|...
T Consensus 37 ~ef~KeYVll~p~~~e~ 53 (105)
T COG3906 37 EEFGKEYVLLVPAGSEE 53 (105)
T ss_pred hhcceeEEEEecccccc
Confidence 56788999999998754
No 17
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=27.44 E-value=61 Score=23.56 Aligned_cols=21 Identities=19% Similarity=0.295 Sum_probs=18.3
Q ss_pred CChHHHHHHHHHHHHhcCCCC
Q 028913 174 REDEDRIAMQMIEELLNWNCP 194 (202)
Q Consensus 174 ~~~e~~~~~~mi~ell~~~~~ 194 (202)
++|+||-+|+-||.=|-...|
T Consensus 3 LSe~E~r~L~eiEr~L~~~DP 23 (82)
T PF11239_consen 3 LSEHEQRRLEEIERQLRADDP 23 (82)
T ss_pred CCHHHHHHHHHHHHHHHhcCc
Confidence 678898899999999987777
No 18
>PF01525 Rota_NS26: Rotavirus NS26; InterPro: IPR002512 Rotaviruses are dsRNA viruses that appear to infect a wide range of mammals. Gene 11 product is a non-structural phosphoprotein designated as NS26, now more commonly annotated as non-structural protein 5 (NSP5) [].; GO: 0000287 magnesium ion binding, 0016887 ATPase activity, 0006200 ATP catabolic process, 0019079 viral genome replication, 0030430 host cell cytoplasm
Probab=25.26 E-value=34 Score=29.80 Aligned_cols=10 Identities=50% Similarity=0.996 Sum_probs=8.7
Q ss_pred HHHHHHHHHH
Q 028913 179 RIAMQMIEEL 188 (202)
Q Consensus 179 ~~~~~mi~el 188 (202)
.+|+||||||
T Consensus 203 ~Va~qlIedm 212 (212)
T PF01525_consen 203 QVAMQLIEDM 212 (212)
T ss_pred HHHHHHHhcC
Confidence 4899999986
No 19
>PRK10113 cell division modulator; Provisional
Probab=22.92 E-value=66 Score=23.80 Aligned_cols=39 Identities=23% Similarity=0.266 Sum_probs=26.0
Q ss_pred CCCeeeeeECCCCeEEEEeeeCCCCeEEecCCcchHHHHHHH
Q 028913 4 SKKFRGVRQRQWGSWVSEIRHPLLKRRVWLGTFETAEAAARA 45 (202)
Q Consensus 4 sSkyRGVr~r~~GkW~A~I~~~~~~k~i~LGtFdT~EeAA~A 45 (202)
--+||-|+.-+ |||+|.+... ..-..--.|...|.|-+=
T Consensus 30 md~frDVW~Lr-GKYVAFvl~g--e~FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVLMG--ESFLRSPAFSVPESAQRW 68 (80)
T ss_pred hcchhhhheec-cceEEEEEec--hhhccCCccCCcHHHHHH
Confidence 35688887655 9999998874 222233567777776653
No 20
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=22.45 E-value=53 Score=25.84 Aligned_cols=18 Identities=17% Similarity=0.732 Sum_probs=13.6
Q ss_pred eEEecCCcchHHHHHHHH
Q 028913 29 RRVWLGTFETAEAAARAY 46 (202)
Q Consensus 29 k~i~LGtFdT~EeAA~AY 46 (202)
..+|||+|+++++-..=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 468999999887755443
No 21
>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=22.30 E-value=2.4e+02 Score=20.36 Aligned_cols=46 Identities=20% Similarity=0.251 Sum_probs=31.9
Q ss_pred CCeeeeeEC-CCCeEEEEeeeCCCCeEEecCCcchHHHHHHHHHHHHHHh
Q 028913 5 KKFRGVRQR-QWGSWVSEIRHPLLKRRVWLGTFETAEAAARAYDQAAVLM 53 (202)
Q Consensus 5 SkyRGVr~r-~~GkW~A~I~~~~~~k~i~LGtFdT~EeAA~AYD~AA~k~ 53 (202)
.+|.||..| ..-+-.+.|..+ ||-+-.|+ .++++|..|.++....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~s--Gki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFSS--GKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEETT--SEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEcC--CEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 468887433 334566777776 88877775 67888888888766544
No 22
>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=21.63 E-value=3.7e+02 Score=22.47 Aligned_cols=47 Identities=19% Similarity=0.189 Sum_probs=34.1
Q ss_pred CCeeeeeEC-CCCeEEEEeeeCCCCeEEecCCcchHHHHHHHHHHHHHHhc
Q 028913 5 KKFRGVRQR-QWGSWVSEIRHPLLKRRVWLGTFETAEAAARAYDQAAVLMN 54 (202)
Q Consensus 5 SkyRGVr~r-~~GkW~A~I~~~~~~k~i~LGtFdT~EeAA~AYD~AA~k~~ 54 (202)
.+|-||..| ..-+=.+-|+.+ ||-+-.|. .++|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~S--GKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFSS--GKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEECC--CeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 468898433 345567778876 88888887 467888888888877664
No 23
>PLN00062 TATA-box-binding protein; Provisional
Probab=21.26 E-value=3.7e+02 Score=22.65 Aligned_cols=47 Identities=17% Similarity=0.136 Sum_probs=33.8
Q ss_pred CCeeeee-ECCCCeEEEEeeeCCCCeEEecCCcchHHHHHHHHHHHHHHhc
Q 028913 5 KKFRGVR-QRQWGSWVSEIRHPLLKRRVWLGTFETAEAAARAYDQAAVLMN 54 (202)
Q Consensus 5 SkyRGVr-~r~~GkW~A~I~~~~~~k~i~LGtFdT~EeAA~AYD~AA~k~~ 54 (202)
.+|-||. +-+.-+=.+-|+.+ ||-+-.|. .++++|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~S--GKiviTGa-ks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFAS--GKMVCTGA-KSEHDSKLAARKYARIIQ 81 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEECC--CeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 4688984 33345567777776 88877775 678888888888877764
Done!