Query 043751
Match_columns 275
No_of_seqs 228 out of 1183
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:00:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043751.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043751hhsearch_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 99.8 7E-20 1.5E-24 133.6 7.3 61 35-95 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1.1E-18 2.4E-23 128.8 8.1 62 36-97 1-62 (64)
3 PHA00280 putative NHN endonucl 99.7 4.9E-18 1.1E-22 141.2 6.5 75 13-90 44-120 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 7.5E-11 1.6E-15 83.9 5.1 52 35-86 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 82.6 3.9 8.4E-05 28.1 5.0 37 47-83 1-41 (46)
6 cd00801 INT_P4 Bacteriophage P 77.2 4.8 0.0001 36.5 5.2 43 41-83 5-49 (357)
7 PF13356 DUF4102: Domain of un 67.9 18 0.00039 27.7 5.8 38 46-83 35-74 (89)
8 PHA02601 int integrase; Provis 67.6 8.7 0.00019 35.3 4.6 44 39-83 2-46 (333)
9 PF05036 SPOR: Sporulation rel 52.9 13 0.00029 26.4 2.5 25 56-80 41-65 (76)
10 PF08846 DUF1816: Domain of un 50.4 31 0.00067 26.4 4.2 35 47-81 9-43 (68)
11 PRK09692 integrase; Provisiona 41.9 63 0.0014 31.0 5.9 42 40-81 33-80 (413)
12 PLN00062 TATA-box-binding prot 33.4 1.6E+02 0.0035 26.1 6.7 49 33-84 32-81 (179)
13 PRK10927 essential cell divisi 32.6 61 0.0013 31.7 4.1 34 48-81 273-306 (319)
14 PF08471 Ribonuc_red_2_N: Clas 31.8 45 0.00098 27.1 2.7 21 63-83 70-90 (93)
15 PF10729 CedA: Cell division a 31.4 58 0.0013 25.4 3.1 40 33-75 29-68 (80)
16 PF09954 DUF2188: Uncharacteri 31.3 1.3E+02 0.0028 21.6 4.8 36 43-82 6-41 (62)
17 cd04517 TLF TBP-like factors ( 30.9 1.5E+02 0.0032 26.2 6.0 47 33-83 33-80 (174)
18 cd04516 TBP_eukaryotes eukaryo 26.3 2.6E+02 0.0056 24.7 6.7 49 33-84 32-81 (174)
19 PHA03308 transcriptional regul 25.3 61 0.0013 35.5 2.9 14 194-207 1335-1348(1463)
20 PRK12757 cell division protein 25.2 1E+02 0.0022 29.3 4.1 34 48-81 210-243 (256)
21 PF00626 Gelsolin: Gelsolin re 24.6 98 0.0021 22.1 3.2 35 49-83 19-53 (76)
22 PRK10113 cell division modulat 24.1 62 0.0013 25.2 2.1 40 33-75 29-68 (80)
23 PRK11633 cell division protein 23.9 1.4E+02 0.0031 27.6 4.8 34 48-81 175-212 (226)
24 PF00352 TBP: Transcription fa 22.8 1.5E+02 0.0032 22.7 4.0 47 34-83 35-82 (86)
25 PF14112 DUF4284: Domain of un 21.3 65 0.0014 26.7 1.9 17 59-75 2-18 (122)
26 cd04518 TBP_archaea archaeal T 21.0 3.1E+02 0.0067 24.2 6.1 49 33-84 32-81 (174)
27 PRK13105 ubiA prenyltransferas 20.8 55 0.0012 31.0 1.5 20 242-261 45-64 (282)
28 cd00652 TBP_TLF TATA box bindi 20.7 3.1E+02 0.0068 24.0 6.1 48 33-83 32-80 (174)
29 PF05861 PhnI: Bacterial phosp 20.2 31 0.00067 34.1 -0.3 29 232-260 97-131 (358)
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=99.81 E-value=7e-20 Score=133.55 Aligned_cols=61 Identities=64% Similarity=1.014 Sum_probs=56.3
Q ss_pred CceEEEEECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhccCCCCCCCCCCC
Q 043751 35 SKFVGVRQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLLRGSNTRTNFDTN 95 (275)
Q Consensus 35 SgyrGV~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l~G~~A~~NFp~~ 95 (275)
|+|+||+++++|||+|+|+++..++++|||+|+|+|||++|||.++++++|.++++|||++
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 7899998777899999999996566799999999999999999999999999999999874
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.77 E-value=1.1e-18 Score=128.76 Aligned_cols=62 Identities=63% Similarity=1.031 Sum_probs=57.1
Q ss_pred ceEEEEECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhccCCCCCCCCCCCCC
Q 043751 36 KFVGVRQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLLRGSNTRTNFDTNVS 97 (275)
Q Consensus 36 gyrGV~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l~G~~A~~NFp~~~~ 97 (275)
+|+||+++++|||+|+|+++..++++|||+|+|+||||+|||.++++++|.++++|||.+.+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y 62 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLY 62 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccC
Confidence 58999878889999999997667779999999999999999999999999999999998754
No 3
>PHA00280 putative NHN endonuclease
Probab=99.73 E-value=4.9e-18 Score=141.18 Aligned_cols=75 Identities=13% Similarity=0.110 Sum_probs=67.7
Q ss_pred HHhhhhccccccCCCCCCC-CCCCceEEE-EECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhccCCCCCC
Q 043751 13 KACINQVNRAGKFKGRNRT-KSNSKFVGV-RQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLLRGSNTRT 90 (275)
Q Consensus 13 ~~NLR~~t~~~n~~Nr~r~-~ntSgyrGV-~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l~G~~A~~ 90 (275)
.+|||++++.+|++|++.+ +|+|||+|| |++..|||+|+|++.||. ++||.|+++|+|+.||+ ++.+|||++|+.
T Consensus 44 i~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~--~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 44 LDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQ--HNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred HHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEE--EEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 5899999999999999766 688999999 678889999999997776 88999999999999997 778999998864
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=99.13 E-value=7.5e-11 Score=83.91 Aligned_cols=52 Identities=40% Similarity=0.522 Sum_probs=45.0
Q ss_pred CceEEE-EECCCCcEEEEEecC---CCCcEEEecCCCCHHHHHHHHHHHHHhccCC
Q 043751 35 SKFVGV-RQRPSGRWVAEIKDT---TKKIRVWLGTFETAEEAARAYDEAACLLRGS 86 (275)
Q Consensus 35 SgyrGV-~~r~~GKW~A~I~~~---gk~kri~LGtFdT~EEAA~AYD~AA~~l~G~ 86 (275)
|+|+|| +.+..++|+|+|++. |++++++||.|++++||++||++++++++|+
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 789999 567789999999983 2247899999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=82.61 E-value=3.9 Score=28.13 Aligned_cols=37 Identities=27% Similarity=0.348 Sum_probs=30.0
Q ss_pred cEEEEEe--c--CCCCcEEEecCCCCHHHHHHHHHHHHHhc
Q 043751 47 RWVAEIK--D--TTKKIRVWLGTFETAEEAARAYDEAACLL 83 (275)
Q Consensus 47 KW~A~I~--~--~gk~kri~LGtFdT~EEAA~AYD~AA~~l 83 (275)
+|..+|. . .|+.++++-+-|.|..||..+...+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5888883 2 56778899999999999999988876655
No 6
>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=77.23 E-value=4.8 Score=36.51 Aligned_cols=43 Identities=30% Similarity=0.405 Sum_probs=32.7
Q ss_pred EECCCCcEEEEEecCCCCcEEEecCCC--CHHHHHHHHHHHHHhc
Q 043751 41 RQRPSGRWVAEIKDTTKKIRVWLGTFE--TAEEAARAYDEAACLL 83 (275)
Q Consensus 41 ~~r~~GKW~A~I~~~gk~kri~LGtFd--T~EEAA~AYD~AA~~l 83 (275)
..++.+.|+.+++.+|+.+++.||+|+ +.++|.....+....+
T Consensus 5 ~~~g~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 5 SPSGSKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred cCCCCEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 334446799999999999999999995 7777777766655444
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=67.95 E-value=18 Score=27.71 Aligned_cols=38 Identities=21% Similarity=0.260 Sum_probs=28.3
Q ss_pred CcEEEEEecCCCCcEEEecCCCC--HHHHHHHHHHHHHhc
Q 043751 46 GRWVAEIKDTTKKIRVWLGTFET--AEEAARAYDEAACLL 83 (275)
Q Consensus 46 GKW~A~I~~~gk~kri~LGtFdT--~EEAA~AYD~AA~~l 83 (275)
..|.-+.+.+|+.+++.||.|.. ..+|.....+....+
T Consensus 35 kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 35 KTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred eEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 45999999999999999999965 666665554444433
No 8
>PHA02601 int integrase; Provisional
Probab=67.61 E-value=8.7 Score=35.31 Aligned_cols=44 Identities=25% Similarity=0.353 Sum_probs=29.2
Q ss_pred EEEECCCCcEEEEEecCC-CCcEEEecCCCCHHHHHHHHHHHHHhc
Q 043751 39 GVRQRPSGRWVAEIKDTT-KKIRVWLGTFETAEEAARAYDEAACLL 83 (275)
Q Consensus 39 GV~~r~~GKW~A~I~~~g-k~kri~LGtFdT~EEAA~AYD~AA~~l 83 (275)
+|+++++|+|+++|...+ .++++. .+|.|..||....+......
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 577778899999998642 122232 36999999876665554443
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=52.92 E-value=13 Score=26.36 Aligned_cols=25 Identities=32% Similarity=0.373 Sum_probs=19.1
Q ss_pred CCCcEEEecCCCCHHHHHHHHHHHH
Q 043751 56 TKKIRVWLGTFETAEEAARAYDEAA 80 (275)
Q Consensus 56 gk~kri~LGtFdT~EEAA~AYD~AA 80 (275)
+...+|.+|.|++.++|..+-....
T Consensus 41 ~~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 41 GPWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TTCEEEEECCECTCCHHHHHHHHHH
T ss_pred CceEEEEECCCCCHHHHHHHHHHHh
Confidence 3446788999999999888776655
No 10
>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=50.45 E-value=31 Score=26.43 Aligned_cols=35 Identities=26% Similarity=0.434 Sum_probs=27.4
Q ss_pred cEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHH
Q 043751 47 RWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAAC 81 (275)
Q Consensus 47 KW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~ 81 (275)
.|=++|.-..-....|-|-|+|.+||..+.-.-..
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyie 43 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIE 43 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHH
Confidence 57788887766667899999999999988644333
No 11
>PRK09692 integrase; Provisional
Probab=41.94 E-value=63 Score=31.01 Aligned_cols=42 Identities=19% Similarity=0.291 Sum_probs=27.2
Q ss_pred EEECCCC--cEEEEEec--CCCCcEEEecCCC--CHHHHHHHHHHHHH
Q 043751 40 VRQRPSG--RWVAEIKD--TTKKIRVWLGTFE--TAEEAARAYDEAAC 81 (275)
Q Consensus 40 V~~r~~G--KW~A~I~~--~gk~kri~LGtFd--T~EEAA~AYD~AA~ 81 (275)
|+-+++| .|+.+.+. .|+.+++.||.|. |..+|..+..++..
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 4434444 59998864 4566668899999 67777665544443
No 12
>PLN00062 TATA-box-binding protein; Provisional
Probab=33.36 E-value=1.6e+02 Score=26.12 Aligned_cols=49 Identities=14% Similarity=0.106 Sum_probs=37.8
Q ss_pred CCCceEEE-EECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhcc
Q 043751 33 SNSKFVGV-RQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLLR 84 (275)
Q Consensus 33 ntSgyrGV-~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l~ 84 (275)
+..+|-|| .|-..-|=.+.|...|| +.+=...+.|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~SGK---iviTGaks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFASGK---MVCTGAKSEHDSKLAARKYARIIQ 81 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEECCCe---EEEEecCCHHHHHHHHHHHHHHHH
Confidence 45689998 55556778899999887 445456889999999999887773
No 13
>PRK10927 essential cell division protein FtsN; Provisional
Probab=32.59 E-value=61 Score=31.68 Aligned_cols=34 Identities=18% Similarity=0.223 Sum_probs=27.0
Q ss_pred EEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHH
Q 043751 48 WVAEIKDTTKKIRVWLGTFETAEEAARAYDEAAC 81 (275)
Q Consensus 48 W~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~ 81 (275)
|.|+|..++.-.||.||-|.+.++|-++.++...
T Consensus 273 ~~A~I~~~g~~~RVrVGPf~sr~eAe~a~~rLk~ 306 (319)
T PRK10927 273 FDSKITTNNGWNRVVIGPVKGKENADSTLNRLKM 306 (319)
T ss_pred CeeEEccCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence 5667766666788999999999999988877654
No 14
>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=31.84 E-value=45 Score=27.10 Aligned_cols=21 Identities=43% Similarity=0.594 Sum_probs=18.6
Q ss_pred ecCCCCHHHHHHHHHHHHHhc
Q 043751 63 LGTFETAEEAARAYDEAACLL 83 (275)
Q Consensus 63 LGtFdT~EEAA~AYD~AA~~l 83 (275)
-|+|+|+|+|..-||.....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 599999999999999987655
No 15
>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=31.44 E-value=58 Score=25.40 Aligned_cols=40 Identities=28% Similarity=0.227 Sum_probs=26.5
Q ss_pred CCCceEEEEECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHH
Q 043751 33 SNSKFVGVRQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARA 75 (275)
Q Consensus 33 ntSgyrGV~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~A 75 (275)
.--|||.||.-+ |||+|.+.....-.| --.|..+|.|-+-
T Consensus 29 k~dgfrdvw~lr-gkyvafvl~ge~f~r--sp~fs~pesaqrw 68 (80)
T PF10729_consen 29 KMDGFRDVWQLR-GKYVAFVLMGEHFRR--SPAFSVPESAQRW 68 (80)
T ss_dssp -TTTECCECCCC-CEEEEEEESSS-EEE-----BSSHHHHHHH
T ss_pred hcccccceeeec-cceEEEEEecchhcc--CCCcCCcHHHHHH
Confidence 457899998665 999999988554322 5678888877664
No 16
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=31.27 E-value=1.3e+02 Score=21.60 Aligned_cols=36 Identities=31% Similarity=0.406 Sum_probs=25.8
Q ss_pred CCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHh
Q 043751 43 RPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACL 82 (275)
Q Consensus 43 r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~ 82 (275)
+..|.|..+.-...+. .++|+|.+||..+=...+..
T Consensus 6 ~~~~~W~v~~eg~~ra----~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 6 REDGGWAVKKEGAKRA----SKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred cCCCCceEEeCCCccc----ccccCcHHHHHHHHHHHHHh
Confidence 4567898776654443 78999999998776665554
No 17
>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=30.88 E-value=1.5e+02 Score=26.17 Aligned_cols=47 Identities=26% Similarity=0.228 Sum_probs=37.3
Q ss_pred CCCceEEE-EECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhc
Q 043751 33 SNSKFVGV-RQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLL 83 (275)
Q Consensus 33 ntSgyrGV-~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l 83 (275)
+. +|.|| .|-+.-|-.+.|+.+|| +.+=...+.|+|..|.++.+..+
T Consensus 33 eP-~fpgli~R~~~Pk~t~lIF~sGK---iviTGaks~~~~~~a~~~~~~~l 80 (174)
T cd04517 33 NP-RYPKVTMRLREPRATASVWSSGK---ITITGATSEEEAKQAARRAARLL 80 (174)
T ss_pred eC-CCCEEEEEecCCcEEEEEECCCe---EEEEccCCHHHHHHHHHHHHHHH
Confidence 44 99998 45555788999999887 45555789999999999888766
No 18
>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=26.31 E-value=2.6e+02 Score=24.71 Aligned_cols=49 Identities=14% Similarity=0.106 Sum_probs=36.3
Q ss_pred CCCceEEE-EECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhcc
Q 043751 33 SNSKFVGV-RQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLLR 84 (275)
Q Consensus 33 ntSgyrGV-~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l~ 84 (275)
+..+|.|| .|...-+-.+.|...||- .+=.-.+.|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~SGKi---viTGaks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFSSGKM---VCTGAKSEDDSKLAARKYARIIQ 81 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEECCCeE---EEEecCCHHHHHHHHHHHHHHHH
Confidence 45688998 455556888999998874 34334688999999998887773
No 19
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=25.26 E-value=61 Score=35.50 Aligned_cols=14 Identities=14% Similarity=0.577 Sum_probs=7.7
Q ss_pred ccCCCCCCCCcchh
Q 043751 194 SWGSGNGVDQFSYT 207 (275)
Q Consensus 194 ~~~~~~~~~~f~~~ 207 (275)
-|+-+++.-..|.+
T Consensus 1335 awgrdtvipalpla 1348 (1463)
T PHA03308 1335 AWGRDTVIPALPLA 1348 (1463)
T ss_pred Hhcccccccccccc
Confidence 57666665444433
No 20
>PRK12757 cell division protein FtsN; Provisional
Probab=25.19 E-value=1e+02 Score=29.26 Aligned_cols=34 Identities=18% Similarity=0.173 Sum_probs=25.4
Q ss_pred EEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHH
Q 043751 48 WVAEIKDTTKKIRVWLGTFETAEEAARAYDEAAC 81 (275)
Q Consensus 48 W~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~ 81 (275)
+.++|...+.-.||++|-|.+.++|..+-++...
T Consensus 210 ~~a~I~~~gg~yRVrVGPf~sr~~A~~~~~rLk~ 243 (256)
T PRK12757 210 IESRITTGGGWNRVVLGPYNSKAAADKMLQRLKG 243 (256)
T ss_pred CceEEeecCCEEEEEeCCCCCHHHHHHHHHHHHH
Confidence 4566666666678889999998888888776663
No 21
>PF00626 Gelsolin: Gelsolin repeat; InterPro: IPR007123 Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) []. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing. Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].; PDB: 3FG6_F 1RGI_G 2FGH_A 1D0N_B 3EGD_B 2NUP_B 2NUT_B 3EGX_B 1JHW_A 1J72_A ....
Probab=24.59 E-value=98 Score=22.10 Aligned_cols=35 Identities=37% Similarity=0.345 Sum_probs=29.4
Q ss_pred EEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhc
Q 043751 49 VAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLL 83 (275)
Q Consensus 49 ~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l 83 (275)
.+.|-+.+....+|+|.-.+..|-+.|.+.|....
T Consensus 19 ~~yIld~~~~i~vW~G~~~~~~e~~~a~~~a~~~~ 53 (76)
T PF00626_consen 19 DCYILDCGYEIFVWVGKKSSPEEKAFAAQLAQELL 53 (76)
T ss_dssp SEEEEEESSEEEEEEHTTSHHHHHHHHHHHHHHHH
T ss_pred CEEEEEeCCCcEEEEeccCCHHHHHHHHHHHHHhh
Confidence 46778888888999999999999999988877655
No 22
>PRK10113 cell division modulator; Provisional
Probab=24.13 E-value=62 Score=25.18 Aligned_cols=40 Identities=25% Similarity=0.245 Sum_probs=28.5
Q ss_pred CCCceEEEEECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHH
Q 043751 33 SNSKFVGVRQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARA 75 (275)
Q Consensus 33 ntSgyrGV~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~A 75 (275)
.--+|+.||.-+ |||+|.+.....-+| --.|..+|.|-+-
T Consensus 29 kmd~frDVW~Lr-GKYVAFvl~ge~FrR--SPaFs~PEsAQRW 68 (80)
T PRK10113 29 KMDSFRDVWMLR-GKYVAFVLMGESFLR--SPAFSVPESAQRW 68 (80)
T ss_pred hhcchhhhheec-cceEEEEEechhhcc--CCccCCcHHHHHH
Confidence 346788897654 999999987554333 4678888877654
No 23
>PRK11633 cell division protein DedD; Provisional
Probab=23.92 E-value=1.4e+02 Score=27.62 Aligned_cols=34 Identities=12% Similarity=0.128 Sum_probs=23.8
Q ss_pred EEEEEe----cCCCCcEEEecCCCCHHHHHHHHHHHHH
Q 043751 48 WVAEIK----DTTKKIRVWLGTFETAEEAARAYDEAAC 81 (275)
Q Consensus 48 W~A~I~----~~gk~kri~LGtFdT~EEAA~AYD~AA~ 81 (275)
|.|++. ..|+..|+|+|-|.+.++|-++..+...
T Consensus 175 ~~Ay~~~~~~~~G~~tRV~VGP~~sk~~ae~~~~~Lk~ 212 (226)
T PRK11633 175 YRVYTVPSTPVQGKITRIYVGPDASKDKLKGSLGELKQ 212 (226)
T ss_pred CeeEEEeeecCCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence 555552 3445578888999988888888776644
No 24
>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=22.80 E-value=1.5e+02 Score=22.72 Aligned_cols=47 Identities=19% Similarity=0.239 Sum_probs=34.1
Q ss_pred CCceEEE-EECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhc
Q 043751 34 NSKFVGV-RQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLL 83 (275)
Q Consensus 34 tSgyrGV-~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l 83 (275)
..+|.|| .+-..-+-.+.|...|| +.+---.+.++|..|.++....+
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF~sGk---i~itGaks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIFSSGK---IVITGAKSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEETTSE---EEEEEESSHHHHHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEEcCCE---EEEEecCCHHHHHHHHHHHHHHH
Confidence 3578887 44445678888888776 34444578999999998877654
No 25
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=21.27 E-value=65 Score=26.69 Aligned_cols=17 Identities=24% Similarity=0.845 Sum_probs=12.8
Q ss_pred cEEEecCCCCHHHHHHH
Q 043751 59 IRVWLGTFETAEEAARA 75 (275)
Q Consensus 59 kri~LGtFdT~EEAA~A 75 (275)
..||||+|.+.++--.=
T Consensus 2 VsiWiG~f~s~~el~~Y 18 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEY 18 (122)
T ss_pred eEEEEecCCCHHHHHHH
Confidence 35999999988775543
No 26
>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=20.96 E-value=3.1e+02 Score=24.21 Aligned_cols=49 Identities=20% Similarity=0.182 Sum_probs=37.4
Q ss_pred CCCceEEE-EECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhcc
Q 043751 33 SNSKFVGV-RQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLLR 84 (275)
Q Consensus 33 ntSgyrGV-~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l~ 84 (275)
+..+|.|+ .+-+.-+-.+.|...|| +.+=-..+.++|..|-++.+..+.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~SGK---iv~tGaks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFRSGK---MVCTGAKSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEECCCe---EEEEccCCHHHHHHHHHHHHHHHH
Confidence 45789998 45555678888888887 445456899999999998887764
No 27
>PRK13105 ubiA prenyltransferase; Reviewed
Probab=20.84 E-value=55 Score=30.99 Aligned_cols=20 Identities=20% Similarity=0.270 Sum_probs=17.3
Q ss_pred hhhHhhhchHHHHHhhcccc
Q 043751 242 ASLYAINGVQEYMDTVHDAA 261 (275)
Q Consensus 242 aslya~ng~~e~~~~~~d~~ 261 (275)
++=.||||+++|+|...|.-
T Consensus 45 ~~n~am~~~Ndy~D~~~d~d 64 (282)
T PRK13105 45 PYNLAMYGINDVFDYESDLR 64 (282)
T ss_pred HHHHHHHhhhhhhhhhcCCC
Confidence 45679999999999999984
No 28
>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=20.74 E-value=3.1e+02 Score=24.02 Aligned_cols=48 Identities=23% Similarity=0.203 Sum_probs=35.9
Q ss_pred CCCceEEE-EECCCCcEEEEEecCCCCcEEEecCCCCHHHHHHHHHHHHHhc
Q 043751 33 SNSKFVGV-RQRPSGRWVAEIKDTTKKIRVWLGTFETAEEAARAYDEAACLL 83 (275)
Q Consensus 33 ntSgyrGV-~~r~~GKW~A~I~~~gk~kri~LGtFdT~EEAA~AYD~AA~~l 83 (275)
+..+|.|| .|...-+-.+.|...|| +.+=--.+.|+|..|.++.+..+
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf~sGK---ivitGaks~~~~~~a~~~~~~~L 80 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIFSSGK---MVITGAKSEEDAKLAARKYARIL 80 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEECCCE---EEEEecCCHHHHHHHHHHHHHHH
Confidence 45789998 45555678888888887 44434568889999988887766
No 29
>PF05861 PhnI: Bacterial phosphonate metabolism protein (PhnI); InterPro: IPR008773 This family consists of several proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex [].; GO: 0015716 phosphonate transport
Probab=20.24 E-value=31 Score=34.11 Aligned_cols=29 Identities=41% Similarity=0.574 Sum_probs=24.0
Q ss_pred hhhhheeehhhhhHhhhchH------HHHHhhccc
Q 043751 232 ERMKVERQISASLYAINGVQ------EYMDTVHDA 260 (275)
Q Consensus 232 ~r~kver~~saslya~ng~~------e~~~~~~d~ 260 (275)
++|.|||+|||..=-|-|=| +|--.+.|-
T Consensus 97 ~~M~v~RRISAafKDiPGGQ~LGpT~DYthRLLdf 131 (358)
T PF05861_consen 97 GDMRVERRISAAFKDIPGGQILGPTFDYTHRLLDF 131 (358)
T ss_pred cceeEEEEeeccccCCCCCceecCccchhhhhccc
Confidence 78999999999999999987 476666664
Done!