Query 046898
Match_columns 332
No_of_seqs 307 out of 1540
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 05:37:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046898hhsearch_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 1.5E-19 3.3E-24 134.4 7.3 59 47-105 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 4.5E-19 9.7E-24 133.4 8.2 61 48-108 1-63 (64)
3 PF02362 B3: B3 DNA binding do 99.7 1.1E-17 2.5E-22 134.2 10.7 99 172-288 1-99 (100)
4 PHA00280 putative NHN endonucl 99.6 4.8E-16 1E-20 130.9 6.0 76 23-99 43-119 (121)
5 PF00847 AP2: AP2 domain; Int 99.0 3.3E-10 7.1E-15 82.4 5.6 50 47-96 1-56 (56)
6 PF03754 DUF313: Domain of unk 98.8 7.8E-09 1.7E-13 86.5 5.3 86 168-254 20-114 (114)
7 PF09217 EcoRII-N: Restriction 98.1 7.2E-06 1.6E-10 71.5 6.2 92 170-268 8-112 (156)
8 PF14657 Integrase_AP2: AP2-li 66.5 23 0.00049 24.5 5.5 36 59-94 1-42 (46)
9 PF10844 DUF2577: Protein of u 57.6 14 0.00029 30.1 3.5 26 253-284 73-98 (100)
10 PF08846 DUF1816: Domain of un 52.4 26 0.00056 26.9 4.0 36 59-94 9-46 (68)
11 PF00352 TBP: Transcription fa 48.1 53 0.0011 25.6 5.4 47 46-93 35-82 (86)
12 smart00536 AXH domain in Ataxi 44.5 12 0.00025 31.7 1.2 27 240-266 77-113 (116)
13 PLN00062 TATA-box-binding prot 44.3 1E+02 0.0022 27.8 7.3 49 45-94 32-81 (179)
14 cd04516 TBP_eukaryotes eukaryo 43.3 1.1E+02 0.0023 27.5 7.3 49 45-94 32-81 (174)
15 PF05036 SPOR: Sporulation rel 41.8 23 0.0005 25.8 2.3 22 69-90 44-65 (76)
16 PF04014 Antitoxin-MazE: Antid 39.5 41 0.0009 23.1 3.2 23 249-271 13-35 (47)
17 PF13356 DUF4102: Domain of un 38.8 1.8E+02 0.004 22.4 7.3 39 55-93 30-74 (89)
18 cd04517 TLF TBP-like factors ( 38.3 1.3E+02 0.0028 27.0 7.0 46 48-94 35-81 (174)
19 PHA02601 int integrase; Provis 38.0 41 0.00088 32.0 4.0 41 51-92 2-45 (333)
20 PF08471 Ribonuc_red_2_N: Clas 35.1 39 0.00085 27.5 2.8 21 73-93 70-90 (93)
21 PRK03760 hypothetical protein; 34.5 1.1E+02 0.0024 25.6 5.6 25 240-267 90-116 (117)
22 cd04518 TBP_archaea archaeal T 34.1 1.5E+02 0.0032 26.6 6.7 49 45-94 32-81 (174)
23 PF03120 DNA_ligase_OB: NAD-de 33.4 35 0.00076 27.0 2.3 21 249-269 42-62 (82)
24 PF08517 AXH: Ataxin-1 and HBP 33.4 43 0.00092 28.3 2.9 27 239-265 75-111 (115)
25 PF10729 CedA: Cell division a 32.4 98 0.0021 23.9 4.4 39 46-85 30-68 (80)
26 cd00652 TBP_TLF TATA box bindi 30.2 1.8E+02 0.004 25.9 6.6 49 45-94 32-81 (174)
27 PF05382 Amidase_5: Bacterioph 29.9 28 0.00062 30.4 1.3 29 255-284 74-102 (145)
28 COG4043 Preprotein translocase 29.2 44 0.00096 27.7 2.2 16 252-267 29-44 (111)
29 PF12195 End_beta_barrel: Beta 27.7 35 0.00075 26.8 1.3 15 253-267 24-38 (83)
30 COG0197 RplP Ribosomal protein 27.4 96 0.0021 27.3 4.1 37 59-96 95-131 (146)
31 PF14250 AbrB-like: AbrB-like 25.5 2E+02 0.0044 22.3 5.1 40 223-266 23-62 (71)
32 PRK00394 transcription factor; 24.3 2.5E+02 0.0053 25.3 6.4 49 45-94 31-80 (179)
33 cd00801 INT_P4 Bacteriophage P 24.0 1.4E+02 0.003 28.1 5.0 36 58-93 10-49 (357)
34 PRK09203 rplP 50S ribosomal pr 23.3 1.3E+02 0.0029 25.9 4.3 35 59-94 92-126 (138)
35 TIGR01164 rplP_bact ribosomal 23.2 1.5E+02 0.0033 25.2 4.5 34 59-93 91-124 (126)
36 TIGR02609 doc_partner putative 22.0 1.9E+02 0.0041 22.0 4.5 32 234-268 4-35 (74)
37 cd04518 TBP_archaea archaeal T 22.0 3E+02 0.0064 24.6 6.4 49 45-94 123-172 (174)
38 COG2101 SPT15 TATA-box binding 20.6 3.3E+02 0.0072 24.8 6.3 50 45-95 38-88 (185)
39 cd04459 Rho_CSD Rho_CSD: Rho p 20.0 78 0.0017 24.1 1.9 21 249-269 33-53 (68)
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=99.79 E-value=1.5e-19 Score=134.42 Aligned_cols=59 Identities=47% Similarity=0.808 Sum_probs=56.6
Q ss_pred CceeeEEECCCCeEEEEEeeC--CeEEEEccCCCHHHHHHHHHHHHHHhhCCCCCCCCCCC
Q 046898 47 VKFKGVVPQQNGHWGAQIYAN--HQRIWLGTFKSEREAAMAYDSAAIKIRGGDSHRNFPWT 105 (332)
Q Consensus 47 S~yrGV~~~~~gkw~A~I~~~--~k~~~LG~f~t~eeAA~Ayd~aa~~~~g~~a~~NFp~~ 105 (332)
|+|+||+++++|+|+|+|+.+ ++++|||+|+|+||||.|||.|+++++|..+.+|||++
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 789999998789999999999 99999999999999999999999999999999999964
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.78 E-value=4.5e-19 Score=133.36 Aligned_cols=61 Identities=44% Similarity=0.767 Sum_probs=58.6
Q ss_pred ceeeEEECCCCeEEEEEee--CCeEEEEccCCCHHHHHHHHHHHHHHhhCCCCCCCCCCCCCC
Q 046898 48 KFKGVVPQQNGHWGAQIYA--NHQRIWLGTFKSEREAAMAYDSAAIKIRGGDSHRNFPWTDTN 108 (332)
Q Consensus 48 ~yrGV~~~~~gkw~A~I~~--~~k~~~LG~f~t~eeAA~Ayd~aa~~~~g~~a~~NFp~~~~~ 108 (332)
+|+||+++++|+|+|+|+. .++++|||+|+|+||||.|||.|+++++|..+.+|||.++|+
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 5999999888999999999 899999999999999999999999999999999999999886
No 3
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.74 E-value=1.1e-17 Score=134.24 Aligned_cols=99 Identities=32% Similarity=0.492 Sum_probs=72.2
Q ss_pred hccccccCCCCCCceEEeeccchhhcCCCCCccccccccCCCccceEEEEEeCCCCcEEEEEEEecCCCeeEEccChHHH
Q 046898 172 FQKELTPSDVGKLNRLVIPKKYAVKYFPFISENAGENAINGGVDDMELVFFDKLMRPWKFRYCFWRSSQSYVFTRGWNRF 251 (332)
Q Consensus 172 F~K~LT~SDV~~~~rLvIPk~~ae~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~gk~W~fr~~~~~~~~~yvLt~GW~~F 251 (332)
|.|+|++||+...++|.||++++++|... . ..++.+.+.|..|+.|.+++.+++++.+|+|++||..|
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~--~----------~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~F 68 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN--K----------RKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKF 68 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS----S----------S--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHH
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCC--c----------CCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHH
Confidence 78999999998888999999999998211 1 13467888999999999999999988889999999999
Q ss_pred hhhcCCCCCCEEEEEeeccCCCcccCcceEEEEEEec
Q 046898 252 VKEKKLKEKDIITFYACECANGAKEGQNFFLVDVIHC 288 (332)
Q Consensus 252 Vk~k~Lk~GD~i~F~r~~~g~~~~~~~~~~~i~~~~~ 288 (332)
|++|+|++||+|+|+...+.. ..+.+.+.++
T Consensus 69 v~~n~L~~GD~~~F~~~~~~~------~~~~v~i~~~ 99 (100)
T PF02362_consen 69 VRDNGLKEGDVCVFELIGNSN------FTLKVHIFRK 99 (100)
T ss_dssp HHHCT--TT-EEEEEE-SSSC------E-EEEEEE--
T ss_pred HHHcCCCCCCEEEEEEecCCC------ceEEEEEEEC
Confidence 999999999999999886422 2346665543
No 4
>PHA00280 putative NHN endonuclease
Probab=99.62 E-value=4.8e-16 Score=130.89 Aligned_cols=76 Identities=12% Similarity=0.100 Sum_probs=70.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhhCCCCC
Q 046898 23 DSNNSTSGLQPAPKRMRHDKNVSLVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIRGGDSH 99 (332)
Q Consensus 23 ~~~n~~~~~~~~~~r~~~~~~~~~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~g~~a~ 99 (332)
.-+||+.++..+|.+++...+.|+|||+||+|. ..|||+|+|..+||+++||.|+++|+|+.||+ ++.++||.+|.
T Consensus 43 ri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 43 ALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred cHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 345999999999999999999999999999995 77999999999999999999999999999997 77899999875
No 5
>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=99.05 E-value=3.3e-10 Score=82.36 Aligned_cols=50 Identities=34% Similarity=0.452 Sum_probs=44.8
Q ss_pred CceeeEEEC-CCCeEEEEEeeC-----CeEEEEccCCCHHHHHHHHHHHHHHhhCC
Q 046898 47 VKFKGVVPQ-QNGHWGAQIYAN-----HQRIWLGTFKSEREAAMAYDSAAIKIRGG 96 (332)
Q Consensus 47 S~yrGV~~~-~~gkw~A~I~~~-----~k~~~LG~f~t~eeAA~Ayd~aa~~~~g~ 96 (332)
|+|+||++. ..++|+|+|++. ++.++||.|++++||++||+.+++.++|.
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 789999995 679999999883 49999999999999999999999999874
No 6
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=98.78 E-value=7.8e-09 Score=86.50 Aligned_cols=86 Identities=26% Similarity=0.536 Sum_probs=68.6
Q ss_pred hhhhhccccccCCC-CCCceEEeeccchhhcCCCCCccccccc-----cCCCccceEEEEEeCCCCcEEEEEEEecC---
Q 046898 168 YRQLFQKELTPSDV-GKLNRLVIPKKYAVKYFPFISENAGENA-----INGGVDDMELVFFDKLMRPWKFRYCFWRS--- 238 (332)
Q Consensus 168 ~~~lF~K~LT~SDV-~~~~rLvIPk~~ae~~lP~l~~~~~~~~-----~~~~~~~~~l~~~D~~gk~W~fr~~~~~~--- 238 (332)
...+|.|+|+.||| .+++||.||-..... ..+|...+.... .+....++.+.+.|..++.|.++++.|..
T Consensus 20 ~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~ 98 (114)
T PF03754_consen 20 PKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNG 98 (114)
T ss_pred CeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCC
Confidence 56799999999999 467999999998866 466765432211 12234788999999999999999999998
Q ss_pred CCeeEEccChHHHhhh
Q 046898 239 SQSYVFTRGWNRFVKE 254 (332)
Q Consensus 239 ~~~yvLt~GW~~FVk~ 254 (332)
...|+|..||.++|++
T Consensus 99 ~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 99 TSNYVLNSGWNKVVED 114 (114)
T ss_pred ceEEEEEcChHhhccC
Confidence 4679999999999874
No 7
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=98.08 E-value=7.2e-06 Score=71.49 Aligned_cols=92 Identities=18% Similarity=0.245 Sum_probs=58.7
Q ss_pred hhhccccccCCCC----CCceEEeeccchhhcCCCCCccccccccCCCccceEEEEEeCCC--CcEEEEEEEecC-----
Q 046898 170 QLFQKELTPSDVG----KLNRLVIPKKYAVKYFPFISENAGENAINGGVDDMELVFFDKLM--RPWKFRYCFWRS----- 238 (332)
Q Consensus 170 ~lF~K~LT~SDV~----~~~rLvIPk~~ae~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~g--k~W~fr~~~~~~----- 238 (332)
.+|.|.|++.|++ ++.++.|||..++.+||.+..... .++++.|.+++..+ ..|.||++|.++
T Consensus 8 ~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~------~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~g 81 (156)
T PF09217_consen 8 AIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKE------ENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGG 81 (156)
T ss_dssp EEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSS------SS-EEEEEEEETTTT---EEEEEEEE-CCCTTS
T ss_pred EEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccc------cCCceeEEEEECCCCccceeEEEEEEcccccCC
Confidence 3799999999994 667899999999999999877443 25788998888776 668899999998
Q ss_pred -CCeeEEccChHHHhhhcC-CCCCCEEEEEee
Q 046898 239 -SQSYVFTRGWNRFVKEKK-LKEKDIITFYAC 268 (332)
Q Consensus 239 -~~~yvLt~GW~~FVk~k~-Lk~GD~i~F~r~ 268 (332)
.+-|.|| .|.....--+ =..||.++|.-.
T Consensus 82 TRNE~RIT-~~G~~~~~~~~~~tGaL~vlaf~ 112 (156)
T PF09217_consen 82 TRNEYRIT-RFGRGFPLQNPENTGALLVLAFD 112 (156)
T ss_dssp S--EEEEE----TTSGGG-GGGTT-EEEEEEE
T ss_pred CcCceEEe-eecCCCccCCccccccEEEEEEc
Confidence 4679998 7877433222 368998888754
No 8
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=66.53 E-value=23 Score=24.47 Aligned_cols=36 Identities=19% Similarity=0.329 Sum_probs=27.9
Q ss_pred eEEEEEe-e---CC--eEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 59 HWGAQIY-A---NH--QRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 59 kw~A~I~-~---~~--k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
+|..+|. . .| ++++-+.|.|..||..+...+...+.
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 3 23 57888999999999999888776653
No 9
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=57.60 E-value=14 Score=30.07 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=19.8
Q ss_pred hhcCCCCCCEEEEEeeccCCCcccCcceEEEE
Q 046898 253 KEKKLKEKDIITFYACECANGAKEGQNFFLVD 284 (332)
Q Consensus 253 k~k~Lk~GD~i~F~r~~~g~~~~~~~~~~~i~ 284 (332)
-..+|++||.|.+.+... ||.++.+|
T Consensus 73 ~~~~Lk~GD~V~ll~~~~------gQ~yiVlD 98 (100)
T PF10844_consen 73 FTDGLKVGDKVLLLRVQG------GQKYIVLD 98 (100)
T ss_pred EecCCcCCCEEEEEEecC------CCEEEEEE
Confidence 368999999999998553 45566665
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=52.36 E-value=26 Score=26.90 Aligned_cols=36 Identities=22% Similarity=0.352 Sum_probs=27.4
Q ss_pred eEEEEEe--eCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 59 HWGAQIY--ANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 59 kw~A~I~--~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
.|=++|. .+.-..|.|-|+|.+||+.+.-.-...+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 4668887 45788999999999999988655444443
No 11
>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=48.13 E-value=53 Score=25.60 Aligned_cols=47 Identities=23% Similarity=0.307 Sum_probs=36.9
Q ss_pred CCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHh
Q 046898 46 LVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKI 93 (332)
Q Consensus 46 ~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~ 93 (332)
..+|.||..+ ..-+-.+.|+..||-+..|. .++|+|..|.++....+
T Consensus 35 Pe~fpgl~~r~~~p~~t~~IF~sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 35 PERFPGLIYRLRNPKATVLIFSSGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTTESSEEEEETTTTEEEEEETTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred eccCCeEEEeecCCcEEEEEEcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 4578898876 44578888999999888875 68899999988876655
No 12
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=44.50 E-value=12 Score=31.70 Aligned_cols=27 Identities=19% Similarity=0.325 Sum_probs=21.0
Q ss_pred CeeEEccChHHH----------hhhcCCCCCCEEEEE
Q 046898 240 QSYVFTRGWNRF----------VKEKKLKEKDIITFY 266 (332)
Q Consensus 240 ~~yvLt~GW~~F----------Vk~k~Lk~GD~i~F~ 266 (332)
.-||...||+.| ...+.|++||+|+-.
T Consensus 77 PfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~l 113 (116)
T smart00536 77 PFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLSL 113 (116)
T ss_pred CeEEcCccccccChhhhhhhcCCcceecccCCEEecc
Confidence 567888888877 356789999999753
No 13
>PLN00062 TATA-box-binding protein; Provisional
Probab=44.35 E-value=1e+02 Score=27.83 Aligned_cols=49 Identities=24% Similarity=0.312 Sum_probs=39.1
Q ss_pred CCCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 45 SLVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 45 ~~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
+..+|.|+..+ ..-+=.+.|+..||-+-.|. .++|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGa-ks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFASGKMVCTGA-KSEHDSKLAARKYARIIQ 81 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEECCCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 45689999886 55567889999999887774 688999999998887774
No 14
>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=43.32 E-value=1.1e+02 Score=27.47 Aligned_cols=49 Identities=20% Similarity=0.253 Sum_probs=39.3
Q ss_pred CCCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 45 SLVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 45 ~~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
+..+|.|+..+ ..-+=.+.|+..||-+-.|.. |+|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGak-s~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFSSGKMVCTGAK-SEDDSKLAARKYARIIQ 81 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEECCCeEEEEecC-CHHHHHHHHHHHHHHHH
Confidence 45688999886 445778999999999988864 78889989988887774
No 15
>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=41.75 E-value=23 Score=25.79 Aligned_cols=22 Identities=32% Similarity=0.440 Sum_probs=17.9
Q ss_pred eEEEEccCCCHHHHHHHHHHHH
Q 046898 69 QRIWLGTFKSEREAAMAYDSAA 90 (332)
Q Consensus 69 k~~~LG~f~t~eeAA~Ayd~aa 90 (332)
-++.+|.|+|.++|..+.....
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 4788999999999988876554
No 16
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=39.45 E-value=41 Score=23.15 Aligned_cols=23 Identities=13% Similarity=0.030 Sum_probs=18.9
Q ss_pred HHHhhhcCCCCCCEEEEEeeccC
Q 046898 249 NRFVKEKKLKEKDIITFYACECA 271 (332)
Q Consensus 249 ~~FVk~k~Lk~GD~i~F~r~~~g 271 (332)
..|.+..+|++||.|.|.-+++|
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g 35 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDG 35 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTS
T ss_pred HHHHHHcCCCCCCEEEEEEeCCC
Confidence 35777889999999999977654
No 17
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=38.77 E-value=1.8e+02 Score=22.45 Aligned_cols=39 Identities=21% Similarity=0.193 Sum_probs=26.0
Q ss_pred CCCC--eEEEEEeeCCe--EEEEccCCC--HHHHHHHHHHHHHHh
Q 046898 55 QQNG--HWGAQIYANHQ--RIWLGTFKS--EREAAMAYDSAAIKI 93 (332)
Q Consensus 55 ~~~g--kw~A~I~~~~k--~~~LG~f~t--~eeAA~Ayd~aa~~~ 93 (332)
.++| .|..+.+.+|+ ++.||.|+. ..+|..........+
T Consensus 30 ~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 30 TPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp -TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 3554 59999888876 689999975 566655555444444
No 18
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=38.29 E-value=1.3e+02 Score=26.97 Aligned_cols=46 Identities=22% Similarity=0.223 Sum_probs=37.9
Q ss_pred ceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 48 KFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 48 ~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
+|.||..+ ..-+=.+.|+..||-+-.| ..++|+|+.|.++.+..+.
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~sGKiviTG-aks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 35 RYPKVTMRLREPRATASVWSSGKITITG-ATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred CCCEEEEEecCCcEEEEEECCCeEEEEc-cCCHHHHHHHHHHHHHHHH
Confidence 89999886 5557789999999888666 5789999999998877774
No 19
>PHA02601 int integrase; Provisional
Probab=37.97 E-value=41 Score=31.97 Aligned_cols=41 Identities=27% Similarity=0.427 Sum_probs=28.0
Q ss_pred eEEECCCCeEEEEEeeC---CeEEEEccCCCHHHHHHHHHHHHHH
Q 046898 51 GVVPQQNGHWGAQIYAN---HQRIWLGTFKSEREAAMAYDSAAIK 92 (332)
Q Consensus 51 GV~~~~~gkw~A~I~~~---~k~~~LG~f~t~eeAA~Ayd~aa~~ 92 (332)
+|+..++|+|+++++.. |+++. .+|.|..||....+.....
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~ 45 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAE 45 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHh
Confidence 45555678999999864 66664 3699998887655544333
No 20
>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=35.13 E-value=39 Score=27.46 Aligned_cols=21 Identities=29% Similarity=0.434 Sum_probs=18.0
Q ss_pred EccCCCHHHHHHHHHHHHHHh
Q 046898 73 LGTFKSEREAAMAYDSAAIKI 93 (332)
Q Consensus 73 LG~f~t~eeAA~Ayd~aa~~~ 93 (332)
-|+|+|+|+|..-||.....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 499999999999999876655
No 21
>PRK03760 hypothetical protein; Provisional
Probab=34.48 E-value=1.1e+02 Score=25.58 Aligned_cols=25 Identities=20% Similarity=0.351 Sum_probs=19.3
Q ss_pred CeeEE--ccChHHHhhhcCCCCCCEEEEEe
Q 046898 240 QSYVF--TRGWNRFVKEKKLKEKDIITFYA 267 (332)
Q Consensus 240 ~~yvL--t~GW~~FVk~k~Lk~GD~i~F~r 267 (332)
-.|+| ..|| +.+.++++||.|.|-+
T Consensus 90 a~~VLEl~aG~---~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 90 ARYIIEGPVGK---IRVLKVEVGDEIEWID 116 (117)
T ss_pred ceEEEEeCCCh---HHHcCCCCCCEEEEee
Confidence 45888 4455 5689999999998865
No 22
>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=34.12 E-value=1.5e+02 Score=26.63 Aligned_cols=49 Identities=20% Similarity=0.287 Sum_probs=39.6
Q ss_pred CCCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 45 SLVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 45 ~~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
+..+|.|+..+ ..-+=.+.|+..||-+-.|. .++++|..|-++.+..+.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGa-ks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFRSGKMVCTGA-KSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEECCCeEEEEcc-CCHHHHHHHHHHHHHHHH
Confidence 45789999886 45577888899999887775 688999999998888775
No 23
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=33.41 E-value=35 Score=27.03 Aligned_cols=21 Identities=14% Similarity=0.265 Sum_probs=16.7
Q ss_pred HHHhhhcCCCCCCEEEEEeec
Q 046898 249 NRFVKEKKLKEKDIITFYACE 269 (332)
Q Consensus 249 ~~FVk~k~Lk~GD~i~F~r~~ 269 (332)
.+|+++++|..||.|.++|..
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raG 62 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAG 62 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEET
T ss_pred HHHHHHcCCCCCCEEEEEECC
Confidence 568999999999999999865
No 24
>PF08517 AXH: Ataxin-1 and HBP1 module (AXH); InterPro: IPR013723 AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1)[]. ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression []. ; GO: 0005488 binding; PDB: 1OA8_C 3QVE_C 1V06_A.
Probab=33.39 E-value=43 Score=28.27 Aligned_cols=27 Identities=19% Similarity=0.394 Sum_probs=16.3
Q ss_pred CCeeEEccChHHH----------hhhcCCCCCCEEEE
Q 046898 239 SQSYVFTRGWNRF----------VKEKKLKEKDIITF 265 (332)
Q Consensus 239 ~~~yvLt~GW~~F----------Vk~k~Lk~GD~i~F 265 (332)
-.-||...||+-| ...+.|++||+|+-
T Consensus 75 hPFFV~gkGWsS~~P~~T~~~ygL~C~~L~vGDvCl~ 111 (115)
T PF08517_consen 75 HPFFVKGKGWSSCNPSLTVQLYGLPCRQLQVGDVCLS 111 (115)
T ss_dssp -EEEETTTEEEESSHHHHHHHHTS--EE--TT-EEEE
T ss_pred CceEEeCCcccccCcchhceecCCcccccccCCEEec
Confidence 3557888899776 45678999999974
No 25
>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=32.43 E-value=98 Score=23.91 Aligned_cols=39 Identities=18% Similarity=0.117 Sum_probs=27.3
Q ss_pred CCceeeEEECCCCeEEEEEeeCCeEEEEccCCCHHHHHHH
Q 046898 46 LVKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEREAAMA 85 (332)
Q Consensus 46 ~S~yrGV~~~~~gkw~A~I~~~~k~~~LG~f~t~eeAA~A 85 (332)
--+|+-| |.-.|||+|.+..+..-.---.|..+|.|-+=
T Consensus 30 ~dgfrdv-w~lrgkyvafvl~ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 30 MDGFRDV-WQLRGKYVAFVLMGEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTTECCE-CCCCCEEEEEEESSS-EEE---BSSHHHHHHH
T ss_pred cccccce-eeeccceEEEEEecchhccCCCcCCcHHHHHH
Confidence 4688888 55558999999887666666778889888754
No 26
>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=30.23 E-value=1.8e+02 Score=25.88 Aligned_cols=49 Identities=24% Similarity=0.337 Sum_probs=38.7
Q ss_pred CCCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 45 SLVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 45 ~~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
+..+|.|+..+ ..-+=.+.|+..||-+-.|. .++|+|..|.++.+..+.
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf~sGKivitGa-ks~~~~~~a~~~~~~~L~ 81 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIFSSGKMVITGA-KSEEDAKLAARKYARILQ 81 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEECCCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 45789999886 44577888899999887776 478888889888877774
No 27
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=29.85 E-value=28 Score=30.42 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=19.5
Q ss_pred cCCCCCCEEEEEeeccCCCcccCcceEEEE
Q 046898 255 KKLKEKDIITFYACECANGAKEGQNFFLVD 284 (332)
Q Consensus 255 k~Lk~GD~i~F~r~~~g~~~~~~~~~~~i~ 284 (332)
..|+.||+|++-...... ...|..-+|+|
T Consensus 74 ~~~q~GDI~I~g~~g~S~-G~~GHtgif~~ 102 (145)
T PF05382_consen 74 WNLQRGDIFIWGRRGNSA-GAGGHTGIFMD 102 (145)
T ss_pred ccccCCCEEEEcCCCCCC-CCCCeEEEEeC
Confidence 579999999964442222 24577778876
No 28
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.21 E-value=44 Score=27.69 Aligned_cols=16 Identities=31% Similarity=0.470 Sum_probs=13.5
Q ss_pred hhhcCCCCCCEEEEEe
Q 046898 252 VKEKKLKEKDIITFYA 267 (332)
Q Consensus 252 Vk~k~Lk~GD~i~F~r 267 (332)
-+.++.+.||.|+|--
T Consensus 29 ~krr~ik~GD~IiF~~ 44 (111)
T COG4043 29 PKRRQIKPGDKIIFNG 44 (111)
T ss_pred HhhcCCCCCCEEEEcC
Confidence 4578999999999984
No 29
>PF12195 End_beta_barrel: Beta barrel domain of bacteriophage endosialidase; InterPro: IPR024427 This entry represents the beta barrel domain of endosialidases which is nested in a beta propeller domain. This beta barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme [].; PDB: 1V0E_B 1V0F_E 3JU4_A 3GVL_A 3GVK_B 3GVJ_A.
Probab=27.72 E-value=35 Score=26.85 Aligned_cols=15 Identities=20% Similarity=0.315 Sum_probs=8.5
Q ss_pred hhcCCCCCCEEEEEe
Q 046898 253 KEKKLKEKDIITFYA 267 (332)
Q Consensus 253 k~k~Lk~GD~i~F~r 267 (332)
-+++|.+||.|.|.-
T Consensus 24 ~~HGl~vGD~VnFsn 38 (83)
T PF12195_consen 24 TDHGLFVGDFVNFSN 38 (83)
T ss_dssp TT----TT-EEEEES
T ss_pred ccCceeecceEEEec
Confidence 399999999999983
No 30
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=27.36 E-value=96 Score=27.28 Aligned_cols=37 Identities=22% Similarity=0.159 Sum_probs=29.4
Q ss_pred eEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhhCC
Q 046898 59 HWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIRGG 96 (332)
Q Consensus 59 kw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~g~ 96 (332)
-|.|+|.. |+.++-=...+++.|..|..+|+.+|=+.
T Consensus 95 gwaArVkp-G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 95 GWAARVKP-GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEEecC-CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 49999876 66666667788888999999999988443
No 31
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=25.48 E-value=2e+02 Score=22.25 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=31.3
Q ss_pred eCCCCcEEEEEEEecCCCeeEEccChHHHhhhcCCCCCCEEEEE
Q 046898 223 DKLMRPWKFRYCFWRSSQSYVFTRGWNRFVKEKKLKEKDIITFY 266 (332)
Q Consensus 223 D~~gk~W~fr~~~~~~~~~yvLt~GW~~FVk~k~Lk~GD~i~F~ 266 (332)
+..|+.=.||-+...|++ -++. ..|-+..+|++||.+.+-
T Consensus 23 ~~~GR~~syr~~Vq~NGn-LLIG---~AYT~~m~L~PGdEFeI~ 62 (71)
T PF14250_consen 23 GRRGRKASYRVSVQGNGN-LLIG---SAYTKQMGLKPGDEFEIK 62 (71)
T ss_pred CCCCcCceEEEEEecCCC-EEEc---HHHHHHhCCCCCCEEEEE
Confidence 456888899888887764 4443 578899999999998775
No 32
>PRK00394 transcription factor; Reviewed
Probab=24.33 E-value=2.5e+02 Score=25.28 Aligned_cols=49 Identities=18% Similarity=0.232 Sum_probs=39.1
Q ss_pred CCCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 45 SLVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 45 ~~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
+..+|.|+..+ ..-+=.+.|+..||-+-.|.. |+|+|..|-++.+..+.
T Consensus 31 ePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~-S~~~a~~a~~~~~~~l~ 80 (179)
T PRK00394 31 NPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAK-SVEDLHEAVKIIIKKLK 80 (179)
T ss_pred CcccCceEEEEecCCceEEEEEcCCcEEEEccC-CHHHHHHHHHHHHHHHH
Confidence 45689999886 555788999999999988875 67788888888777664
No 33
>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=23.96 E-value=1.4e+02 Score=28.07 Aligned_cols=36 Identities=25% Similarity=0.316 Sum_probs=25.7
Q ss_pred CeEEEEEeeCCeE--EEEccCC--CHHHHHHHHHHHHHHh
Q 046898 58 GHWGAQIYANHQR--IWLGTFK--SEREAAMAYDSAAIKI 93 (332)
Q Consensus 58 gkw~A~I~~~~k~--~~LG~f~--t~eeAA~Ayd~aa~~~ 93 (332)
+.|..+++.+|++ +.||+|+ +.++|..+.......+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 4699999888765 6789995 6677776665554444
No 34
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=23.31 E-value=1.3e+02 Score=25.88 Aligned_cols=35 Identities=26% Similarity=0.167 Sum_probs=30.2
Q ss_pred eEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 59 HWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 59 kw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
.|.|+|..+.--+-++. .+++.|..|+..|+.+|=
T Consensus 92 ~~varVk~G~iifEi~~-~~~~~a~~al~~a~~KLP 126 (138)
T PRK09203 92 YWVAVVKPGRILFEIAG-VSEELAREALRLAAAKLP 126 (138)
T ss_pred EEEEEECCCCEEEEEeC-CCHHHHHHHHHHHhccCC
Confidence 59999998877777777 899999999999998773
No 35
>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=23.25 E-value=1.5e+02 Score=25.17 Aligned_cols=34 Identities=24% Similarity=0.212 Sum_probs=29.4
Q ss_pred eEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHh
Q 046898 59 HWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKI 93 (332)
Q Consensus 59 kw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~ 93 (332)
.|.|+|..+..-+-++. .+++.|..|...|+.+|
T Consensus 91 ~~varV~~G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 91 YWVAVVKPGKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEEECCCCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 59999998877777777 89999999999998765
No 36
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=22.05 E-value=1.9e+02 Score=22.00 Aligned_cols=32 Identities=16% Similarity=0.031 Sum_probs=22.5
Q ss_pred EEecCCCeeEEccChHHHhhhcCCCCCCEEEEEee
Q 046898 234 CFWRSSQSYVFTRGWNRFVKEKKLKEKDIITFYAC 268 (332)
Q Consensus 234 ~~~~~~~~yvLt~GW~~FVk~k~Lk~GD~i~F~r~ 268 (332)
.-|+|+..-.|- ..++..-+|..||.|.+...
T Consensus 4 ~k~GNS~~vtIP---k~i~~~lgl~~Gd~v~v~~~ 35 (74)
T TIGR02609 4 RKVGNSLVVTLP---KEVLESLGLKEGDTLYVDEE 35 (74)
T ss_pred EEECCeeEEEEC---HHHHHHcCcCCCCEEEEEEE
Confidence 456655444444 45788999999999987644
No 37
>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=21.95 E-value=3e+02 Score=24.65 Aligned_cols=49 Identities=18% Similarity=0.289 Sum_probs=38.9
Q ss_pred CCCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhh
Q 046898 45 SLVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIR 94 (332)
Q Consensus 45 ~~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~ 94 (332)
+..+|.|+.++ ..-+-.+.|+..||-+-.|. .++||+..|.+.-...+.
T Consensus 123 ePe~fpglvyR~~~pk~~~lIF~SGKvvitGa-ks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 123 EPEQFPGLVYRLDEPKVVLLLFSSGKMVITGA-KSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred CcccCceEEEEecCCcEEEEEeCCCEEEEEec-CCHHHHHHHHHHHHHHHh
Confidence 66889999886 44578888999999988886 678899999887665553
No 38
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=20.60 E-value=3.3e+02 Score=24.83 Aligned_cols=50 Identities=22% Similarity=0.293 Sum_probs=42.9
Q ss_pred CCCceeeEEEC-CCCeEEEEEeeCCeEEEEccCCCHHHHHHHHHHHHHHhhC
Q 046898 45 SLVKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEREAAMAYDSAAIKIRG 95 (332)
Q Consensus 45 ~~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAA~Ayd~aa~~~~g 95 (332)
+..+|.|+.+| ..-|=.+-|...||-+..|. .+.|++.+|-.+-+..++.
T Consensus 38 nP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGa-Ks~ed~~~av~~~~~~L~~ 88 (185)
T COG2101 38 NPEQFPGLVYRLEEPKTAALIFRSGKVVCTGA-KSVEDVHRAVKKLAKKLKD 88 (185)
T ss_pred CHhHCCeeEEEecCCcceEEEEecCcEEEecc-CcHHHHHHHHHHHHHHHHh
Confidence 67899999886 66678899999999999986 7889999998888888875
No 39
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=20.02 E-value=78 Score=24.13 Aligned_cols=21 Identities=10% Similarity=0.039 Sum_probs=16.6
Q ss_pred HHHhhhcCCCCCCEEEEEeec
Q 046898 249 NRFVKEKKLKEKDIITFYACE 269 (332)
Q Consensus 249 ~~FVk~k~Lk~GD~i~F~r~~ 269 (332)
...++..+|+.||.|.=.-..
T Consensus 33 ~~~Irr~~LR~GD~V~G~vr~ 53 (68)
T cd04459 33 PSQIRRFNLRTGDTVVGQIRP 53 (68)
T ss_pred HHHHHHhCCCCCCEEEEEEeC
Confidence 358999999999999765444
Done!