Query 027990
Match_columns 216
No_of_seqs 244 out of 1205
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:35:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027990.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027990hhsearch_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 1.6E-21 3.4E-26 139.0 8.3 63 28-90 1-63 (64)
2 cd00018 AP2 DNA-binding domain 99.9 1.3E-21 2.7E-26 137.9 7.6 61 27-87 1-61 (61)
3 PHA00280 putative NHN endonucl 99.5 2.2E-14 4.8E-19 115.3 7.0 59 20-81 60-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.2 2.9E-11 6.2E-16 83.1 5.3 52 27-78 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 81.1 5.9 0.00013 26.2 5.3 38 39-76 1-42 (46)
6 PHA02601 int integrase; Provis 66.7 9.1 0.0002 33.8 4.4 44 31-75 2-46 (333)
7 cd00801 INT_P4 Bacteriophage P 61.1 18 0.00039 31.5 5.1 39 37-75 9-49 (357)
8 PF08846 DUF1816: Domain of un 52.4 26 0.00057 25.8 4.0 37 39-75 9-45 (68)
9 PF13356 DUF4102: Domain of un 48.1 44 0.00096 24.5 4.7 43 33-75 28-74 (89)
10 PRK09692 integrase; Provisiona 47.0 58 0.0012 30.0 6.3 39 32-70 33-77 (413)
11 PF05036 SPOR: Sporulation rel 46.6 14 0.00029 25.3 1.6 23 50-72 43-65 (76)
12 PF10729 CedA: Cell division a 34.4 79 0.0017 23.8 4.1 41 25-68 29-69 (80)
13 PF08471 Ribonuc_red_2_N: Clas 34.3 45 0.00097 26.1 2.9 20 56-75 71-90 (93)
14 PF14112 DUF4284: Domain of un 31.2 30 0.00065 27.6 1.6 18 51-68 2-19 (122)
15 PF12286 DUF3622: Protein of u 26.6 88 0.0019 23.4 3.2 30 38-67 16-49 (71)
16 COG0197 RplP Ribosomal protein 26.5 99 0.0021 26.0 3.9 36 39-77 95-130 (146)
17 cd04516 TBP_eukaryotes eukaryo 23.6 3.2E+02 0.0068 23.2 6.5 49 25-76 32-81 (174)
18 PF09954 DUF2188: Uncharacteri 23.6 2.3E+02 0.005 19.4 4.8 39 32-74 3-41 (62)
19 cd04517 TLF TBP-like factors ( 22.0 2.6E+02 0.0056 23.6 5.7 48 25-76 33-81 (174)
20 PF02084 Bindin: Bindin; Inte 21.8 80 0.0017 28.5 2.6 11 186-196 118-128 (238)
21 cd00652 TBP_TLF TATA box bindi 20.7 3.2E+02 0.0069 23.0 6.0 49 25-76 32-81 (174)
22 PF00352 TBP: Transcription fa 20.2 2.1E+02 0.0045 21.0 4.3 47 26-75 35-82 (86)
23 PRK10113 cell division modulat 20.0 88 0.0019 23.5 2.1 40 26-68 30-69 (80)
No 1
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.86 E-value=1.6e-21 Score=139.03 Aligned_cols=63 Identities=65% Similarity=1.151 Sum_probs=60.6
Q ss_pred ceeeeeeCCCCcEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 027990 28 RYRGVRKRPWGRFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSLRGPKAKTNFPLNISD 90 (216)
Q Consensus 28 ~yRGV~~r~~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l~G~~A~tNFp~s~~~ 90 (216)
+|+||+++++|||+|+|+++.+++.+|||+|+|+||||+|||.++++++|.++.+|||.+.|+
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 599999988999999999999999999999999999999999999999999999999998885
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=99.86 E-value=1.3e-21 Score=137.87 Aligned_cols=61 Identities=64% Similarity=1.116 Sum_probs=57.7
Q ss_pred CceeeeeeCCCCcEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 027990 27 IRYRGVRKRPWGRFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSLRGPKAKTNFPLN 87 (216)
Q Consensus 27 S~yRGV~~r~~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l~G~~A~tNFp~s 87 (216)
|+|+||+++++|||+|+|+++..|+++|||+|+|+||||+|||.++++++|.++.+|||.+
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 6899999999999999999955599999999999999999999999999999999999964
No 3
>PHA00280 putative NHN endonuclease
Probab=99.52 E-value=2.2e-14 Score=115.28 Aligned_cols=59 Identities=17% Similarity=0.160 Sum_probs=53.6
Q ss_pred CCCCCCCCceeeeeeCC-CCcEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 027990 20 GPEASPDIRYRGVRKRP-WGRFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSLRGPKAK 81 (216)
Q Consensus 20 ~~~~~~~S~yRGV~~r~-~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l~G~~A~ 81 (216)
+..+.|+|+|+||+|.+ .|||+|+|.+ +||+++||.|+++|+|+.||+ ++++|||++|.
T Consensus 60 ~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 60 KTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 45668999999999876 5999999999 999999999999999999997 77899999885
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=99.20 E-value=2.9e-11 Score=83.06 Aligned_cols=52 Identities=35% Similarity=0.452 Sum_probs=45.5
Q ss_pred CceeeeeeCC-CCcEEEEEecCCC---CceEecCCCCCHHHHHHHHHHHHHHhcCC
Q 027990 27 IRYRGVRKRP-WGRFAAEIRDPWK---KTRVWLGTFDSAEDAARAYDAAARSLRGP 78 (216)
Q Consensus 27 S~yRGV~~r~-~GrW~A~I~~p~~---gk~i~LGtFdT~EEAArAYD~Aa~~l~G~ 78 (216)
|+|+||++.+ .++|+|+|++... +++++||.|+++|||+++|+.++++++|+
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 6899999876 5999999998322 49999999999999999999999999885
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=81.05 E-value=5.9 Score=26.16 Aligned_cols=38 Identities=13% Similarity=0.126 Sum_probs=29.5
Q ss_pred cEEEEEe--cCCCC--ceEecCCCCCHHHHHHHHHHHHHHhc
Q 027990 39 RFAAEIR--DPWKK--TRVWLGTFDSAEDAARAYDAAARSLR 76 (216)
Q Consensus 39 rW~A~I~--~p~~g--k~i~LGtFdT~EEAArAYD~Aa~~l~ 76 (216)
+|..+|. .+..| ++++-+-|.|..||-.+.......+.
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 44344 67888999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=66.72 E-value=9.1 Score=33.78 Aligned_cols=44 Identities=20% Similarity=0.226 Sum_probs=30.1
Q ss_pred eeeeCCCCcEEEEEecC-CCCceEecCCCCCHHHHHHHHHHHHHHh
Q 027990 31 GVRKRPWGRFAAEIRDP-WKKTRVWLGTFDSAEDAARAYDAAARSL 75 (216)
Q Consensus 31 GV~~r~~GrW~A~I~~p-~~gk~i~LGtFdT~EEAArAYD~Aa~~l 75 (216)
+|++.++|+|++++... ..|+++. .+|.|..||..........+
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 56667789999999852 2366554 36999999876666554444
No 7
>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=61.06 E-value=18 Score=31.46 Aligned_cols=39 Identities=26% Similarity=0.253 Sum_probs=28.1
Q ss_pred CCcEEEEEecCCCCceEecCCCC--CHHHHHHHHHHHHHHh
Q 027990 37 WGRFAAEIRDPWKKTRVWLGTFD--SAEDAARAYDAAARSL 75 (216)
Q Consensus 37 ~GrW~A~I~~p~~gk~i~LGtFd--T~EEAArAYD~Aa~~l 75 (216)
.+.|..+++..++.+++.||+|+ +.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699999985556678899995 6777777666655444
No 8
>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=52.45 E-value=26 Score=25.81 Aligned_cols=37 Identities=27% Similarity=0.365 Sum_probs=28.1
Q ss_pred cEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHh
Q 027990 39 RFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSL 75 (216)
Q Consensus 39 rW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l 75 (216)
.|=++|.-..-.-.+|.|-|.|.+||..+.-.-...+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHH
Confidence 4668888744567899999999999998865444444
No 9
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=48.15 E-value=44 Score=24.52 Aligned_cols=43 Identities=23% Similarity=0.271 Sum_probs=27.3
Q ss_pred eeCCCC--cEEEEEecCCCCceEecCCCCC--HHHHHHHHHHHHHHh
Q 027990 33 RKRPWG--RFAAEIRDPWKKTRVWLGTFDS--AEDAARAYDAAARSL 75 (216)
Q Consensus 33 ~~r~~G--rW~A~I~~p~~gk~i~LGtFdT--~EEAArAYD~Aa~~l 75 (216)
+..+.| .|.-+.+..++.+++-||.|.. ..+|..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 455654 4998888744556799999976 555555554444443
No 10
>PRK09692 integrase; Provisional
Probab=47.01 E-value=58 Score=30.02 Aligned_cols=39 Identities=18% Similarity=0.228 Sum_probs=24.9
Q ss_pred eeeCCCC--cEEEEEecCCCCc--eEecCCCC--CHHHHHHHHHH
Q 027990 32 VRKRPWG--RFAAEIRDPWKKT--RVWLGTFD--SAEDAARAYDA 70 (216)
Q Consensus 32 V~~r~~G--rW~A~I~~p~~gk--~i~LGtFd--T~EEAArAYD~ 70 (216)
|+.++.| .|..+-+.+.+|+ ++-||.|. |..+|..+-.+
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 4555655 4998887543444 37899999 66666554443
No 11
>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=46.63 E-value=14 Score=25.28 Aligned_cols=23 Identities=35% Similarity=0.391 Sum_probs=18.9
Q ss_pred CceEecCCCCCHHHHHHHHHHHH
Q 027990 50 KTRVWLGTFDSAEDAARAYDAAA 72 (216)
Q Consensus 50 gk~i~LGtFdT~EEAArAYD~Aa 72 (216)
--+|++|.|+|.+||..+-....
T Consensus 43 ~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 43 WYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp CEEEEECCECTCCHHHHHHHHHH
T ss_pred eEEEEECCCCCHHHHHHHHHHHh
Confidence 44788999999999988877655
No 12
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=34.40 E-value=79 Score=23.78 Aligned_cols=41 Identities=20% Similarity=0.114 Sum_probs=26.2
Q ss_pred CCCceeeeeeCCCCcEEEEEecCCCCceEecCCCCCHHHHHHHH
Q 027990 25 PDIRYRGVRKRPWGRFAAEIRDPWKKTRVWLGTFDSAEDAARAY 68 (216)
Q Consensus 25 ~~S~yRGV~~r~~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAY 68 (216)
+--+||-|..- .|||.|.+.. +..-.---.|...|.|-|.-
T Consensus 29 k~dgfrdvw~l-rgkyvafvl~--ge~f~rsp~fs~pesaqrwa 69 (80)
T PF10729_consen 29 KMDGFRDVWQL-RGKYVAFVLM--GEHFRRSPAFSVPESAQRWA 69 (80)
T ss_dssp -TTTECCECCC-CCEEEEEEES--SS-EEE---BSSHHHHHHHH
T ss_pred hcccccceeee-ccceEEEEEe--cchhccCCCcCCcHHHHHHH
Confidence 34578888543 3999999997 55555556788888887653
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=34.28 E-value=45 Score=26.10 Aligned_cols=20 Identities=40% Similarity=0.557 Sum_probs=17.3
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 027990 56 GTFDSAEDAARAYDAAARSL 75 (216)
Q Consensus 56 GtFdT~EEAArAYD~Aa~~l 75 (216)
|+|+|+|+|..-||..+-.|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999876543
No 14
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=31.20 E-value=30 Score=27.56 Aligned_cols=18 Identities=22% Similarity=0.818 Sum_probs=13.6
Q ss_pred ceEecCCCCCHHHHHHHH
Q 027990 51 TRVWLGTFDSAEDAARAY 68 (216)
Q Consensus 51 k~i~LGtFdT~EEAArAY 68 (216)
..||||+|.|++|-..=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 368999999988765443
No 15
>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=26.56 E-value=88 Score=23.37 Aligned_cols=30 Identities=20% Similarity=0.188 Sum_probs=18.8
Q ss_pred CcEEEEEecCCCCceEe----cCCCCCHHHHHHH
Q 027990 38 GRFAAEIRDPWKKTRVW----LGTFDSAEDAARA 67 (216)
Q Consensus 38 GrW~A~I~~p~~gk~i~----LGtFdT~EEAArA 67 (216)
+.|.|+|......++.- --.|+|++||..-
T Consensus 16 ~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq~W 49 (71)
T PF12286_consen 16 NGWTAEITRRVTSRKTVVSKRQDGFASEAEAQAW 49 (71)
T ss_pred CceeeeeeeeecCceeEEEecccCcccHHHHHHH
Confidence 56999998633332211 2459999887543
No 16
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=26.46 E-value=99 Score=26.00 Aligned_cols=36 Identities=22% Similarity=0.076 Sum_probs=28.8
Q ss_pred cEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHhcC
Q 027990 39 RFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSLRG 77 (216)
Q Consensus 39 rW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l~G 77 (216)
.|.|+|.- |+.++-=....++.|..|..+|+.+|=+
T Consensus 95 gwaArVkp---G~vlfei~g~~e~~A~EAlr~Aa~KLP~ 130 (146)
T COG0197 95 GWAARVKP---GRVLFEIAGVPEELAREALRRAAAKLPV 130 (146)
T ss_pred EEEEEecC---CcEEEEEecCcHHHHHHHHHHHhhcCCC
Confidence 39999984 6677766778888899999999987743
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=23.62 E-value=3.2e+02 Score=23.18 Aligned_cols=49 Identities=24% Similarity=0.172 Sum_probs=38.0
Q ss_pred CCCceeeeeeCC-CCcEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHhc
Q 027990 25 PDIRYRGVRKRP-WGRFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSLR 76 (216)
Q Consensus 25 ~~S~yRGV~~r~-~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l~ 76 (216)
+..+|-||..|- .-+-.+.|+. .||-+.-|. .|+|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 456888986553 3567788888 899888886 488999999999888774
No 18
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=23.57 E-value=2.3e+02 Score=19.41 Aligned_cols=39 Identities=28% Similarity=0.272 Sum_probs=24.6
Q ss_pred eeeCCCCcEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHH
Q 027990 32 VRKRPWGRFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARS 74 (216)
Q Consensus 32 V~~r~~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~ 74 (216)
|..+..|.|..+... ..+ -..+|+|.+||-.+=...+..
T Consensus 3 V~p~~~~~W~v~~eg--~~r--a~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG--AKR--ASKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeCC--Ccc--cccccCcHHHHHHHHHHHHHh
Confidence 444445779877654 332 268999999887665444433
No 19
>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=22.03 E-value=2.6e+02 Score=23.62 Aligned_cols=48 Identities=31% Similarity=0.258 Sum_probs=37.3
Q ss_pred CCCceeeeeeCC-CCcEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHhc
Q 027990 25 PDIRYRGVRKRP-WGRFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSLR 76 (216)
Q Consensus 25 ~~S~yRGV~~r~-~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l~ 76 (216)
+. +|-||..|- .-+-.+.|+. .||-+--| ..++|+|.+|.++.+..+.
T Consensus 33 eP-~fpgli~R~~~Pk~t~lIF~--sGKiviTG-aks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 33 NP-RYPKVTMRLREPRATASVWS--SGKITITG-ATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred eC-CCCEEEEEecCCcEEEEEEC--CCeEEEEc-cCCHHHHHHHHHHHHHHHH
Confidence 44 899987553 3577888887 88877766 5799999999999887773
No 20
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=21.76 E-value=80 Score=28.55 Aligned_cols=11 Identities=45% Similarity=0.561 Sum_probs=8.7
Q ss_pred CCCccccCCCC
Q 027990 186 KVLPFDLNLPP 196 (216)
Q Consensus 186 ~~l~~dlnlpp 196 (216)
-.||+|+|-|-
T Consensus 118 iDLPVDINDPY 128 (238)
T PF02084_consen 118 IDLPVDINDPY 128 (238)
T ss_pred cccccccCChh
Confidence 45999999874
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=20.73 E-value=3.2e+02 Score=23.00 Aligned_cols=49 Identities=33% Similarity=0.231 Sum_probs=37.1
Q ss_pred CCCceeeeeeCC-CCcEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHhc
Q 027990 25 PDIRYRGVRKRP-WGRFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSLR 76 (216)
Q Consensus 25 ~~S~yRGV~~r~-~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l~ 76 (216)
+..+|.||..|- .-+-.+.|.. .||-+--|. .+.|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf~--sGKivitGa-ks~~~~~~a~~~~~~~L~ 81 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIFS--SGKMVITGA-KSEEDAKLAARKYARILQ 81 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEEC--CCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 457899987654 3466677776 898888786 488999999998887773
No 22
>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=20.21 E-value=2.1e+02 Score=20.98 Aligned_cols=47 Identities=23% Similarity=0.196 Sum_probs=35.0
Q ss_pred CCceeeeeeCC-CCcEEEEEecCCCCceEecCCCCCHHHHHHHHHHHHHHh
Q 027990 26 DIRYRGVRKRP-WGRFAAEIRDPWKKTRVWLGTFDSAEDAARAYDAAARSL 75 (216)
Q Consensus 26 ~S~yRGV~~r~-~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAYD~Aa~~l 75 (216)
..+|-||..+- .-+....|.. .||-+..|. .+.|+|..|+++....+
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 34788886553 3466777777 899888885 68999999998877655
No 23
>PRK10113 cell division modulator; Provisional
Probab=20.01 E-value=88 Score=23.47 Aligned_cols=40 Identities=20% Similarity=0.157 Sum_probs=26.3
Q ss_pred CCceeeeeeCCCCcEEEEEecCCCCceEecCCCCCHHHHHHHH
Q 027990 26 DIRYRGVRKRPWGRFAAEIRDPWKKTRVWLGTFDSAEDAARAY 68 (216)
Q Consensus 26 ~S~yRGV~~r~~GrW~A~I~~p~~gk~i~LGtFdT~EEAArAY 68 (216)
--+||-|..-+ |||.|.+.. +..-.---.|...|.|-|.-
T Consensus 30 md~frDVW~Lr-GKYVAFvl~--ge~FrRSPaFs~PEsAQRWA 69 (80)
T PRK10113 30 MDSFRDVWMLR-GKYVAFVLM--GESFLRSPAFSVPESAQRWA 69 (80)
T ss_pred hcchhhhheec-cceEEEEEe--chhhccCCccCCcHHHHHHH
Confidence 34677775433 999999986 43333345688888877653
Done!