Query 043400
Match_columns 264
No_of_seqs 262 out of 1195
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:40:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043400.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043400hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA00280 putative NHN endonucl 99.9 5E-22 1.1E-26 162.9 5.1 106 27-164 13-119 (121)
2 cd00018 AP2 DNA-binding domain 99.8 6.8E-21 1.5E-25 137.7 7.5 61 110-170 1-61 (61)
3 smart00380 AP2 DNA-binding dom 99.8 9.6E-21 2.1E-25 138.5 8.3 63 111-173 1-63 (64)
4 PF00847 AP2: AP2 domain; Int 99.1 1E-10 2.2E-15 82.6 5.8 52 110-161 1-56 (56)
5 PF13392 HNH_3: HNH endonuclea 93.1 0.022 4.7E-07 38.8 -0.5 25 50-74 19-43 (46)
6 PF14657 Integrase_AP2: AP2-li 85.3 3.2 7E-05 28.0 5.5 38 122-159 1-42 (46)
7 PHA02601 int integrase; Provis 65.6 9.4 0.0002 35.0 4.4 44 114-158 2-46 (333)
8 PRK09692 integrase; Provisiona 51.7 40 0.00087 32.2 6.3 42 115-156 33-80 (413)
9 cd00801 INT_P4 Bacteriophage P 48.6 42 0.00091 30.3 5.6 39 121-159 10-50 (357)
10 PF05036 SPOR: Sporulation rel 46.9 17 0.00036 25.6 2.2 24 132-155 42-65 (76)
11 PF09003 Phage_integ_N: Bacter 39.7 56 0.0012 24.9 4.2 33 127-161 31-63 (75)
12 PF08471 Ribonuc_red_2_N: Clas 32.7 47 0.001 26.4 2.8 21 138-158 70-90 (93)
13 PF08846 DUF1816: Domain of un 32.5 88 0.0019 23.4 4.1 37 122-158 9-45 (68)
14 PF13356 DUF4102: Domain of un 27.5 1.8E+02 0.0038 21.9 5.2 36 121-158 35-74 (89)
15 TIGR01164 rplP_bact ribosomal 25.1 1.3E+02 0.0029 24.8 4.4 35 121-158 90-124 (126)
16 PRK09203 rplP 50S ribosomal pr 24.4 1.2E+02 0.0027 25.4 4.2 37 121-160 91-127 (138)
17 COG0197 RplP Ribosomal protein 24.1 1.1E+02 0.0024 26.2 3.9 37 122-161 95-131 (146)
18 PF10729 CedA: Cell division a 23.8 1.3E+02 0.0029 22.8 3.8 39 108-149 29-67 (80)
19 PF00352 TBP: Transcription fa 22.7 2.4E+02 0.0051 21.2 5.1 46 110-158 36-82 (86)
20 PF14112 DUF4284: Domain of un 20.8 64 0.0014 26.3 1.7 17 134-150 2-18 (122)
No 1
>PHA00280 putative NHN endonuclease
Probab=99.85 E-value=5e-22 Score=162.91 Aligned_cols=106 Identities=14% Similarity=0.102 Sum_probs=88.1
Q ss_pred CCCcEEEEEEeCCCCCCCCCchhhhhcccCcccccccccccCcccccccccccccccccccccccccccccCCCCCCCCC
Q 043400 27 GPQKLVRIILTDADATDSSSDDEQVINHVRRVKRHVKQINLNNHHRRQHQQQQRGQQSNKLQHNKKIKRHAHQPPPQSDV 106 (264)
Q Consensus 27 ~~~r~vri~~~DpdATDSssd~e~~idh~~~~K~~nreiNLr~~~~~~~~~~n~~~~~nn~s~~k~~k~~~~~~~~~~~~ 106 (264)
..-|+||..++++.+.. .+|||+++++.||++.|||.++..+ |++|+... .
T Consensus 13 ~~Hrlvw~~~~G~~P~g------~~VdHidg~~~dnri~NLr~~T~~e-N~~N~~~~----------------------~ 63 (121)
T PHA00280 13 RRHIQVWEAANGPIPKG------YYIDHIDGNPLNDALDNLRLALPKE-NSWNMKTP----------------------K 63 (121)
T ss_pred hHhHhhhHHHHCCCCCC------CEEEcCCCCCCCCcHHHhhhcCHHH-HhcccCCC----------------------C
Confidence 34689999999877542 2699999999999999999999987 54443222 1
Q ss_pred CCCcceeeEEECC-CCeEEEEEecCCCCeEeeccCCCCHHHHHHHHHHHHHHhhCCCCC
Q 043400 107 THRKKFRGVRRRP-WGRWAAEIRDPNRRKRLWLGTFDTPEEAASVYDQAAVKLKGANAV 164 (264)
Q Consensus 107 ~~~s~yrGVr~r~-~gkW~A~I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l~G~~a~ 164 (264)
.++|+|+||++.+ .|||+|+|+ ++||+++||.|+++|+|+.||. ++.+|||+||.
T Consensus 64 ~N~SG~kGV~~~k~~~kw~A~I~--~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 64 SNTSGLKGLSWSKEREMWRGTVT--AEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred CCCCCCCeeEEecCCCeEEEEEE--ECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 3678889998554 499999999 9999999999999999999997 78899999985
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=99.84 E-value=6.8e-21 Score=137.74 Aligned_cols=61 Identities=66% Similarity=1.276 Sum_probs=57.7
Q ss_pred cceeeEEECCCCeEEEEEecCCCCeEeeccCCCCHHHHHHHHHHHHHHhhCCCCCCCCCCC
Q 043400 110 KKFRGVRRRPWGRWAAEIRDPNRRKRLWLGTFDTPEEAASVYDQAAVKLKGANAVTNFPNP 170 (264)
Q Consensus 110 s~yrGVr~r~~gkW~A~I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l~G~~a~~Nfp~~ 170 (264)
|+|+||+++++|||+|+|+++..|+++|||+|+|+|||+.|||.|+++++|.++.+|||++
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 6899999999999999999666699999999999999999999999999999999999975
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=9.6e-21 Score=138.54 Aligned_cols=63 Identities=63% Similarity=1.213 Sum_probs=60.4
Q ss_pred ceeeEEECCCCeEEEEEecCCCCeEeeccCCCCHHHHHHHHHHHHHHhhCCCCCCCCCCCCCC
Q 043400 111 KFRGVRRRPWGRWAAEIRDPNRRKRLWLGTFDTPEEAASVYDQAAVKLKGANAVTNFPNPVLT 173 (264)
Q Consensus 111 ~yrGVr~r~~gkW~A~I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l~G~~a~~Nfp~~~~~ 173 (264)
+|+||+++++|||+|+|++|.+|+.+|||+|+|+||||.|||.|+++++|.++.+|||.+.|.
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 599999999999999999888999999999999999999999999999999999999999885
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=1e-10 Score=82.61 Aligned_cols=52 Identities=37% Similarity=0.550 Sum_probs=45.0
Q ss_pred cceeeEEECC-CCeEEEEEecCCC---CeEeeccCCCCHHHHHHHHHHHHHHhhCC
Q 043400 110 KKFRGVRRRP-WGRWAAEIRDPNR---RKRLWLGTFDTPEEAASVYDQAAVKLKGA 161 (264)
Q Consensus 110 s~yrGVr~r~-~gkW~A~I~~~~~---~k~~~LGtf~t~EeAa~Ayd~aa~~l~G~ 161 (264)
|+|+||++.+ .++|+|+|+++.. +++++||.|++++||++||++++++++|+
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 6899998766 4999999996432 49999999999999999999999999874
No 5
>PF13392 HNH_3: HNH endonuclease; PDB: 1U3E_M.
Probab=93.06 E-value=0.022 Score=38.75 Aligned_cols=25 Identities=24% Similarity=0.231 Sum_probs=17.4
Q ss_pred hhhcccCcccccccccccCcccccc
Q 043400 50 QVINHVRRVKRHVKQINLNNHHRRQ 74 (264)
Q Consensus 50 ~~idh~~~~K~~nreiNLr~~~~~~ 74 (264)
.+|+|++++|.+|+..||+.+++.+
T Consensus 19 ~~v~H~~~~~~~n~~~NL~~~t~~e 43 (46)
T PF13392_consen 19 YVVDHKDGNKTDNRPENLRWVTRSE 43 (46)
T ss_dssp -EEEETTS-TT---GGGEEEE-HHH
T ss_pred CEEEeCCCCCCCCCHHHceECCHHH
Confidence 3799999999999999999998765
No 6
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=85.33 E-value=3.2 Score=28.03 Aligned_cols=38 Identities=21% Similarity=0.296 Sum_probs=30.7
Q ss_pred eEEEEE--ecCCCC--eEeeccCCCCHHHHHHHHHHHHHHhh
Q 043400 122 RWAAEI--RDPNRR--KRLWLGTFDTPEEAASVYDQAAVKLK 159 (264)
Q Consensus 122 kW~A~I--~~~~~~--k~~~LGtf~t~EeAa~Ayd~aa~~l~ 159 (264)
+|...| .+|.+| ++++-+-|.|..||..+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 588888 477676 56788999999999999988777664
No 7
>PHA02601 int integrase; Provisional
Probab=65.62 E-value=9.4 Score=34.97 Aligned_cols=44 Identities=27% Similarity=0.388 Sum_probs=30.2
Q ss_pred eEEECCCCeEEEEEec-CCCCeEeeccCCCCHHHHHHHHHHHHHHh
Q 043400 114 GVRRRPWGRWAAEIRD-PNRRKRLWLGTFDTPEEAASVYDQAAVKL 158 (264)
Q Consensus 114 GVr~r~~gkW~A~I~~-~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l 158 (264)
+|++.++|+|++++.. ...|+++. .+|.|..||..........+
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 5677777999999973 23467665 36999998876655544443
No 8
>PRK09692 integrase; Provisional
Probab=51.71 E-value=40 Score=32.17 Aligned_cols=42 Identities=17% Similarity=0.269 Sum_probs=27.4
Q ss_pred EEECCCC--eEEEEEecCCCCeE--eeccCCC--CHHHHHHHHHHHHH
Q 043400 115 VRRRPWG--RWAAEIRDPNRRKR--LWLGTFD--TPEEAASVYDQAAV 156 (264)
Q Consensus 115 Vr~r~~g--kW~A~I~~~~~~k~--~~LGtf~--t~EeAa~Ayd~aa~ 156 (264)
|+-++.| .|+.+-+++.+|++ +-||.|. |..+|..+..++..
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 4444544 49999887666655 6799999 67676655444333
No 9
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=48.62 E-value=42 Score=30.30 Aligned_cols=39 Identities=33% Similarity=0.463 Sum_probs=27.1
Q ss_pred CeEEEEEecCCCCeEeeccCCC--CHHHHHHHHHHHHHHhh
Q 043400 121 GRWAAEIRDPNRRKRLWLGTFD--TPEEAASVYDQAAVKLK 159 (264)
Q Consensus 121 gkW~A~I~~~~~~k~~~LGtf~--t~EeAa~Ayd~aa~~l~ 159 (264)
+.|+.+++.....+++.||+|+ +.++|.....+....+.
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 5799999943334557799995 77788777766555553
No 10
>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=46.93 E-value=17 Score=25.63 Aligned_cols=24 Identities=25% Similarity=0.381 Sum_probs=19.7
Q ss_pred CCeEeeccCCCCHHHHHHHHHHHH
Q 043400 132 RRKRLWLGTFDTPEEAASVYDQAA 155 (264)
Q Consensus 132 ~~k~~~LGtf~t~EeAa~Ayd~aa 155 (264)
..-++.+|.|++.++|..+.....
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 345788999999999998887666
No 11
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=39.72 E-value=56 Score=24.93 Aligned_cols=33 Identities=27% Similarity=0.286 Sum_probs=22.5
Q ss_pred EecCCCCeEeeccCCCCHHHHHHHHHHHHHHhhCC
Q 043400 127 IRDPNRRKRLWLGTFDTPEEAASVYDQAAVKLKGA 161 (264)
Q Consensus 127 I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l~G~ 161 (264)
-++|..||.+.||+ +.++|..+=-+|-..+...
T Consensus 31 Yr~P~tGk~~~LG~--d~~~Ai~~A~eaN~~i~~~ 63 (75)
T PF09003_consen 31 YRNPITGKEHGLGT--DRAEAIAQAIEANLRIAEQ 63 (75)
T ss_dssp EE-TTTS-EEEEES---HHHHHHHHHHHHHHHTSS
T ss_pred EecCCCCceeeCCC--CHHHHHHHHHHHHHHHHHh
Confidence 45889999999999 7788877666666666433
No 12
>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=32.66 E-value=47 Score=26.41 Aligned_cols=21 Identities=38% Similarity=0.540 Sum_probs=18.2
Q ss_pred ccCCCCHHHHHHHHHHHHHHh
Q 043400 138 LGTFDTPEEAASVYDQAAVKL 158 (264)
Q Consensus 138 LGtf~t~EeAa~Ayd~aa~~l 158 (264)
-|+|+|+|+|..=||..+..|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999877655
No 13
>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=32.47 E-value=88 Score=23.45 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=25.9
Q ss_pred eEEEEEecCCCCeEeeccCCCCHHHHHHHHHHHHHHh
Q 043400 122 RWAAEIRDPNRRKRLWLGTFDTPEEAASVYDQAAVKL 158 (264)
Q Consensus 122 kW~A~I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l 158 (264)
.|=++|.--.=.-..|.|-|.+.+||..+.-.-...|
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHH
Confidence 4778888222346789999999999998754433333
No 14
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=27.50 E-value=1.8e+02 Score=21.87 Aligned_cols=36 Identities=17% Similarity=0.177 Sum_probs=23.8
Q ss_pred CeEEEEEecCCCC--eEeeccCCCC--HHHHHHHHHHHHHHh
Q 043400 121 GRWAAEIRDPNRR--KRLWLGTFDT--PEEAASVYDQAAVKL 158 (264)
Q Consensus 121 gkW~A~I~~~~~~--k~~~LGtf~t--~EeAa~Ayd~aa~~l 158 (264)
..|..+.+ .+| +++.||.|.. ..+|..........+
T Consensus 35 kt~~~r~~--~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 35 KTFYFRYR--INGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEE--ETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred eEEEEEEE--ecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 35888887 555 5678999975 666665555444444
No 15
>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=25.10 E-value=1.3e+02 Score=24.81 Aligned_cols=35 Identities=23% Similarity=0.279 Sum_probs=28.5
Q ss_pred CeEEEEEecCCCCeEeeccCCCCHHHHHHHHHHHHHHh
Q 043400 121 GRWAAEIRDPNRRKRLWLGTFDTPEEAASVYDQAAVKL 158 (264)
Q Consensus 121 gkW~A~I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l 158 (264)
--|+|+|. .+..-+-++. .+++.|..|...|+.+|
T Consensus 90 ~~~varV~--~G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 90 EYWVAVVK--PGKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred CEEEEEEC--CCCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 45999999 6666666766 89999999999998776
No 16
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=24.44 E-value=1.2e+02 Score=25.39 Aligned_cols=37 Identities=24% Similarity=0.205 Sum_probs=29.7
Q ss_pred CeEEEEEecCCCCeEeeccCCCCHHHHHHHHHHHHHHhhC
Q 043400 121 GRWAAEIRDPNRRKRLWLGTFDTPEEAASVYDQAAVKLKG 160 (264)
Q Consensus 121 gkW~A~I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l~G 160 (264)
--|+|+|. .+..-+-++. .+++.|..|...|+.+|=+
T Consensus 91 ~~~varVk--~G~iifEi~~-~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 91 EYWVAVVK--PGRILFEIAG-VSEELAREALRLAAAKLPI 127 (138)
T ss_pred cEEEEEEC--CCCEEEEEeC-CCHHHHHHHHHHHhccCCC
Confidence 45999998 6666666766 8999999999999988744
No 17
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=24.07 E-value=1.1e+02 Score=26.20 Aligned_cols=37 Identities=27% Similarity=0.248 Sum_probs=29.5
Q ss_pred eEEEEEecCCCCeEeeccCCCCHHHHHHHHHHHHHHhhCC
Q 043400 122 RWAAEIRDPNRRKRLWLGTFDTPEEAASVYDQAAVKLKGA 161 (264)
Q Consensus 122 kW~A~I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l~G~ 161 (264)
-|+|+|. -|+-++-=....++.|..|...|+.+|=+.
T Consensus 95 gwaArVk---pG~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARVK---PGRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEec---CCcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 4999998 366666666788888999999999988544
No 18
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=23.82 E-value=1.3e+02 Score=22.81 Aligned_cols=39 Identities=23% Similarity=0.274 Sum_probs=24.6
Q ss_pred CCcceeeEEECCCCeEEEEEecCCCCeEeeccCCCCHHHHHH
Q 043400 108 HRKKFRGVRRRPWGRWAAEIRDPNRRKRLWLGTFDTPEEAAS 149 (264)
Q Consensus 108 ~~s~yrGVr~r~~gkW~A~I~~~~~~k~~~LGtf~t~EeAa~ 149 (264)
.--+||-|..-+ |||+|.+. .+-.-..--.|..+|.|.+
T Consensus 29 k~dgfrdvw~lr-gkyvafvl--~ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 29 KMDGFRDVWQLR-GKYVAFVL--MGEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp -TTTECCECCCC-CEEEEEEE--SSS-EEE---BSSHHHHHH
T ss_pred hcccccceeeec-cceEEEEE--ecchhccCCCcCCcHHHHH
Confidence 346788886555 99999987 5544444567888877654
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=22.71 E-value=2.4e+02 Score=21.22 Aligned_cols=46 Identities=22% Similarity=0.213 Sum_probs=34.2
Q ss_pred cceeeEE-ECCCCeEEEEEecCCCCeEeeccCCCCHHHHHHHHHHHHHHh
Q 043400 110 KKFRGVR-RRPWGRWAAEIRDPNRRKRLWLGTFDTPEEAASVYDQAAVKL 158 (264)
Q Consensus 110 s~yrGVr-~r~~gkW~A~I~~~~~~k~~~LGtf~t~EeAa~Ayd~aa~~l 158 (264)
.+|-||. +-..-+-.+.|. ..||-+..|. .+.|+|..|.+.....|
T Consensus 36 e~fpgl~~r~~~p~~t~~IF--~sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIF--SSGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEE--TTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEE--cCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 4677875 333356778888 8999888886 67889999988876655
No 20
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=20.82 E-value=64 Score=26.31 Aligned_cols=17 Identities=24% Similarity=0.739 Sum_probs=13.0
Q ss_pred eEeeccCCCCHHHHHHH
Q 043400 134 KRLWLGTFDTPEEAASV 150 (264)
Q Consensus 134 k~~~LGtf~t~EeAa~A 150 (264)
..+|||+|.+.++-..=
T Consensus 2 VsiWiG~f~s~~el~~Y 18 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEY 18 (122)
T ss_pred eEEEEecCCCHHHHHHH
Confidence 46899999988775543
Done!