Query 018463
Match_columns 355
No_of_seqs 296 out of 943
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:14:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018463.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018463hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1946 RNA polymerase I trans 100.0 3.6E-29 7.9E-34 235.4 13.3 182 1-255 1-182 (240)
2 PF02201 SWIB: SWIB/MDM2 domai 99.9 1.5E-25 3.2E-30 176.9 2.3 76 274-351 1-76 (76)
3 smart00151 SWIB SWI complex, B 99.9 6.9E-24 1.5E-28 167.8 7.9 77 173-249 1-77 (77)
4 PF02201 SWIB: SWIB/MDM2 domai 99.9 5E-25 1.1E-29 173.9 1.0 76 173-248 1-76 (76)
5 smart00151 SWIB SWI complex, B 99.9 1.1E-23 2.3E-28 166.7 7.8 76 275-352 2-77 (77)
6 KOG1946 RNA polymerase I trans 99.9 3.3E-23 7.2E-28 195.2 6.8 81 272-354 98-178 (240)
7 COG5531 SWIB-domain-containing 99.8 1.4E-21 3E-26 183.2 7.4 82 170-251 118-199 (237)
8 COG5531 SWIB-domain-containing 99.8 2.5E-20 5.4E-25 174.7 6.6 80 271-352 118-197 (237)
9 PRK14724 DNA topoisomerase III 99.8 9.1E-19 2E-23 192.9 8.4 76 173-248 912-987 (987)
10 PRK14724 DNA topoisomerase III 99.7 1.1E-18 2.4E-23 192.2 7.7 75 274-350 912-986 (987)
11 KOG2570 SWI/SNF transcription 99.7 7.9E-17 1.7E-21 160.2 5.3 81 177-257 209-289 (420)
12 KOG2570 SWI/SNF transcription 99.5 4E-15 8.6E-20 148.2 5.3 77 274-352 205-281 (420)
13 PF08766 DEK_C: DEK C terminal 99.5 6.7E-14 1.5E-18 103.7 5.5 54 3-57 1-54 (54)
14 PRK06319 DNA topoisomerase I/S 99.4 6.6E-13 1.4E-17 145.3 6.2 76 275-352 785-860 (860)
15 PRK06319 DNA topoisomerase I/S 99.3 1.2E-12 2.7E-17 143.2 6.4 75 174-248 785-859 (860)
16 KOG2266 Chromatin-associated p 98.6 3.8E-08 8.3E-13 100.1 5.6 60 2-62 520-579 (594)
17 PRK05350 acyl carrier protein; 79.5 2.1 4.6E-05 33.7 3.2 53 295-350 2-54 (82)
18 PRK05828 acyl carrier protein; 76.3 4.4 9.5E-05 32.6 4.2 53 295-350 1-53 (84)
19 KOG2522 Filamentous baseplate 70.9 5.5 0.00012 41.7 4.3 41 293-333 380-420 (560)
20 PRK12449 acyl carrier protein; 67.3 9.9 0.00021 29.4 4.3 53 295-350 1-53 (80)
21 CHL00124 acpP acyl carrier pro 67.1 6 0.00013 30.8 3.0 53 295-350 1-53 (82)
22 PF09312 SurA_N: SurA N-termin 66.4 6.4 0.00014 33.2 3.2 47 2-53 67-113 (118)
23 PRK05350 acyl carrier protein; 64.2 8.3 0.00018 30.3 3.3 53 192-247 2-54 (82)
24 KOG2522 Filamentous baseplate 63.8 13 0.00028 39.0 5.4 61 190-250 380-449 (560)
25 PRK05828 acyl carrier protein; 51.4 27 0.00059 28.0 4.3 53 192-247 1-53 (84)
26 PRK07117 acyl carrier protein; 47.9 22 0.00048 28.2 3.3 52 295-350 1-53 (79)
27 PTZ00171 acyl carrier protein; 46.4 24 0.00052 31.5 3.6 55 293-350 64-118 (148)
28 CHL00124 acpP acyl carrier pro 44.7 25 0.00055 27.2 3.1 53 192-247 1-53 (82)
29 PF04155 Ground-like: Ground-l 42.5 27 0.0006 27.2 3.0 38 1-40 5-42 (76)
30 PRK12449 acyl carrier protein; 42.1 49 0.0011 25.5 4.3 53 192-247 1-53 (80)
31 PF13699 DUF4157: Domain of un 41.5 20 0.00044 28.4 2.1 23 27-49 4-26 (79)
32 PF07587 PSD1: Protein of unkn 40.1 38 0.00083 32.7 4.2 60 282-353 4-65 (266)
33 PTZ00171 acyl carrier protein; 37.4 49 0.0011 29.5 4.1 57 188-247 62-118 (148)
34 PF13565 HTH_32: Homeodomain-l 33.7 83 0.0018 23.7 4.4 35 4-41 32-66 (77)
35 PRK07639 acyl carrier protein; 31.1 69 0.0015 25.6 3.7 54 295-350 1-54 (86)
36 PF03705 CheR_N: CheR methyltr 28.0 96 0.0021 22.1 3.7 31 27-57 6-37 (57)
37 PF02881 SRP54_N: SRP54-type p 24.7 2.3E+02 0.0049 21.4 5.4 33 5-38 24-57 (75)
38 PF00538 Linker_histone: linke 24.1 2.8E+02 0.006 21.4 5.9 36 22-57 20-57 (77)
39 PRK07117 acyl carrier protein; 23.3 1.1E+02 0.0024 24.2 3.5 52 192-247 1-53 (79)
40 PF08134 cIII: cIII protein fa 23.1 70 0.0015 22.7 2.0 17 2-18 17-33 (44)
41 PF00550 PP-binding: Phosphopa 23.1 1.4E+02 0.0031 21.5 3.9 40 5-44 1-52 (67)
42 PRK05883 acyl carrier protein; 23.0 1.2E+02 0.0026 24.6 3.7 54 294-350 9-62 (91)
43 KOG0747 Putative NAD+-dependen 22.2 1.6E+02 0.0034 29.7 5.0 56 289-346 249-319 (331)
44 PF12872 OST-HTH: OST-HTH/LOTU 22.0 2E+02 0.0043 21.4 4.6 42 3-45 2-44 (74)
45 PF02037 SAP: SAP domain; Int 21.8 2E+02 0.0044 19.1 4.0 27 9-35 7-33 (35)
46 PF07830 PP2C_C: Protein serin 21.5 2.4E+02 0.0052 22.8 5.1 48 4-51 25-78 (81)
47 TIGR00517 acyl_carrier acyl ca 21.3 1E+02 0.0022 23.5 2.8 49 299-350 3-51 (77)
48 PF05696 DUF826: Protein of un 20.4 3.7E+02 0.008 21.7 5.8 42 10-59 12-53 (78)
49 PF13276 HTH_21: HTH-like doma 20.3 1.4E+02 0.003 21.7 3.3 40 4-45 3-42 (60)
50 cd04762 HTH_MerR-trunc Helix-T 20.2 2.2E+02 0.0048 18.6 4.1 24 282-314 4-27 (49)
51 COG1846 MarR Transcriptional r 20.0 92 0.002 24.6 2.5 50 179-230 37-91 (126)
No 1
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.96 E-value=3.6e-29 Score=235.44 Aligned_cols=182 Identities=26% Similarity=0.397 Sum_probs=138.3
Q ss_pred CCCHHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHHhCCCCccchhHHHHHHHHHhcCCCCCccccCCCCCCCCCCCCCC
Q 018463 1 MVSDQEIAKGVETLLRQSDRNASTSLNGVVKQLEAKLGLDLSHKAGFIRDQISLLLRSHPTPQQVATNTQPQPQPQPQQL 80 (355)
Q Consensus 1 m~Sd~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~~fgvDLs~kK~~I~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 80 (355)
|.+.......+..||...|+++ +|.+.||+.++..||++++..+..++..|...+.......
T Consensus 1 ~~~~~~~~~~~~~~l~~~~~~~-lt~~~vr~~~~~~~~v~~~~~k~~~~~~~~~~~~~~~~~~----------------- 62 (240)
T KOG1946|consen 1 MDSLSWEYLFKDYILSLKDQET-LTPDDVRRAMAPRSGVDGTAQKSLLAKAIDESSDEDSALP----------------- 62 (240)
T ss_pred CcchhhhhhhhHHHhccccccc-CCHHHHHHHhccccCCCCcchhhhhhhhhhcccccccccc-----------------
Confidence 5677888889999999999986 8999999999999999999999999999987664321110
Q ss_pred CCCCcccccCCCCCCCCCCCCCCCccCCCCCCCCCCCccccccCCCCCCCCCCCCCCCCCcccccccCCcchhhhhccCC
Q 018463 81 PPKDHFTLQHHPQFSLPPQQFPPHFALHHPHPHLPQFPQELNFSQPQPSQAAAPPPQPHSNVSKAEAFPQISAEVAKENP 160 (355)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (355)
.++. +.. .... . . . ...... .. .+.
T Consensus 63 -~k~~-----------------------~~k----~~~~-----~--------------~-~---~~~~~~--~~--~~~ 87 (240)
T KOG1946|consen 63 -VKGS-----------------------KKK----KRGS-----K--------------T-R---SRKPKS--LE--SSG 87 (240)
T ss_pred -cccc-----------------------ccc----cccc-----c--------------c-c---cccCcc--cc--ccc
Confidence 0000 000 0000 0 0 0 000000 00 001
Q ss_pred CCCCCccCCCCCCCccccCCHHHHHhhCCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHH
Q 018463 161 PVGAKRRGGPGGLNKVCGVSPELQAVVGQPAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMN 240 (355)
Q Consensus 161 ~~~~k~~~~~~g~~k~~~lSpeLa~~lG~~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~ 240 (355)
....+.+..++|+++.|.||+.|+.|+|.++++|++|++.||+|||+||||||.||+.|+||++|+.||+..+|+||+|+
T Consensus 88 ~~~~~~~~~~~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~ 167 (240)
T KOG1946|consen 88 EKNKKKKKASWGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEML 167 (240)
T ss_pred ccchhccccCcCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHH
Confidence 11111112458999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhccCCCCCCcc
Q 018463 241 KLLAKHIIPLEPTKE 255 (355)
Q Consensus 241 klL~~Hl~p~dp~~~ 255 (355)
+||.+||++......
T Consensus 168 KLL~~H~~~~~d~~~ 182 (240)
T KOG1946|consen 168 KLLTKHFLKNQDMVG 182 (240)
T ss_pred HHHHHhccCcccccc
Confidence 999999999887643
No 2
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.91 E-value=1.5e-25 Score=176.88 Aligned_cols=76 Identities=38% Similarity=0.730 Sum_probs=70.7
Q ss_pred CCccccccHHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhccC
Q 018463 274 GPSSVIISEALAKFLGTGGREMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNHF 351 (355)
Q Consensus 274 ~~~~~~lS~~La~flG~~~~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~~ 351 (355)
++++|+||++|++|+|.. ++||++|+++||+|||+||||||.|++.|+||++|+.|||+++|++++|+++|.+||+
T Consensus 1 ~~k~~~ls~~L~~~lg~~--~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl~ 76 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGED--ELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHLI 76 (76)
T ss_dssp -EEEEHHHHHHHHHTT-S--CEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHHE
T ss_pred CCCCccCCHHHHHHhCCC--CCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhcC
Confidence 467899999999999995 7999999999999999999999999999999999999999999999999999999985
No 3
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.90 E-value=6.9e-24 Score=167.79 Aligned_cols=77 Identities=55% Similarity=0.975 Sum_probs=74.6
Q ss_pred CCccccCCHHHHHhhCCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhccCC
Q 018463 173 LNKVCGVSPELQAVVGQPAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHIIP 249 (355)
Q Consensus 173 ~~k~~~lSpeLa~~lG~~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl~p 249 (355)
++++|.||++|++|+|..++||++|+++||+|||.||||||+|++.|+||+.|+.+||++++.|++|+++|++||.|
T Consensus 1 ~~~~~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999975
No 4
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.90 E-value=5e-25 Score=173.90 Aligned_cols=76 Identities=46% Similarity=0.888 Sum_probs=71.3
Q ss_pred CCccccCCHHHHHhhCCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhccC
Q 018463 173 LNKVCGVSPELQAVVGQPAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHII 248 (355)
Q Consensus 173 ~~k~~~lSpeLa~~lG~~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl~ 248 (355)
|+++|.||++|++++|..++||++|++.||+||++||||||+|++.|+||+.|+.||++++|.|++|+++|++||.
T Consensus 1 ~~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl~ 76 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHLI 76 (76)
T ss_dssp -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHHE
T ss_pred CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhcC
Confidence 5788999999999999999999999999999999999999999999999999999999999999999999999984
No 5
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.89 E-value=1.1e-23 Score=166.70 Aligned_cols=76 Identities=38% Similarity=0.687 Sum_probs=72.9
Q ss_pred CccccccHHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhccCC
Q 018463 275 PSSVIISEALAKFLGTGGREMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNHFL 352 (355)
Q Consensus 275 ~~~~~lS~~La~flG~~~~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~~~ 352 (355)
+++|.||++|+.|+|. .++||++|+++||+|||.||||||.|++.|+||+.|++|||+++|.|++|+++|++||.+
T Consensus 2 ~~~~~ls~~L~~~lg~--~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 2 TKKVTLSPELAKVLGA--PEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCcccCCHHHHHHhCC--CcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence 4789999999999998 499999999999999999999999999999999999999999999999999999999864
No 6
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.88 E-value=3.3e-23 Score=195.16 Aligned_cols=81 Identities=31% Similarity=0.644 Sum_probs=77.3
Q ss_pred CCCCccccccHHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhccC
Q 018463 272 ESGPSSVIISEALAKFLGTGGREMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNHF 351 (355)
Q Consensus 272 ~~~~~~~~lS~~La~flG~~~~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~~ 351 (355)
.|..+.+.||+.|+.|+|.. ++||.+|+++||+|||+||||||.||+.|+||++|+.|||..+|+||+|++||.+||+
T Consensus 98 ~g~~kl~~ls~~L~~~~G~~--~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H~~ 175 (240)
T KOG1946|consen 98 WGSTKLIPLSPSLARFVGTS--ELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKHFL 175 (240)
T ss_pred cCcccccccCHHHHhhcccc--cccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHhcc
Confidence 46789999999999999984 9999999999999999999999999999999999999999999999999999999999
Q ss_pred CCC
Q 018463 352 LRQ 354 (355)
Q Consensus 352 ~~~ 354 (355)
..+
T Consensus 176 ~~~ 178 (240)
T KOG1946|consen 176 KNQ 178 (240)
T ss_pred Ccc
Confidence 864
No 7
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.85 E-value=1.4e-21 Score=183.19 Aligned_cols=82 Identities=43% Similarity=0.727 Sum_probs=78.1
Q ss_pred CCCCCccccCCHHHHHhhCCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhccCC
Q 018463 170 PGGLNKVCGVSPELQAVVGQPAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHIIP 249 (355)
Q Consensus 170 ~~g~~k~~~lSpeLa~~lG~~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl~p 249 (355)
++-....+.+|+.||.|||..++||++||+.||+|||.||||||+|||.|.||++|+.|||.+.+.||+|.++|.+|+++
T Consensus 118 ~~~~~~~~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl~~ 197 (237)
T COG5531 118 NSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPLSPHLIK 197 (237)
T ss_pred ccCCCCceecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhcccccceec
Confidence 44577889999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CC
Q 018463 250 LE 251 (355)
Q Consensus 250 ~d 251 (355)
.+
T Consensus 198 ~~ 199 (237)
T COG5531 198 YT 199 (237)
T ss_pred Cc
Confidence 54
No 8
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.81 E-value=2.5e-20 Score=174.75 Aligned_cols=80 Identities=34% Similarity=0.583 Sum_probs=76.3
Q ss_pred CCCCCccccccHHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 271 MESGPSSVIISEALAKFLGTGGREMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 271 ~~~~~~~~~lS~~La~flG~~~~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
.+....+|.+|+.||.|||.+ ++||++||+.||+|||.||||||.|||.|+||++|+.|||.+.|.||+|.++|.+|+
T Consensus 118 ~~~~~~~~~lS~~La~ilG~~--~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl 195 (237)
T COG5531 118 NSPSGEKVKLSPKLAAILGLE--PGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPLSPHL 195 (237)
T ss_pred ccCCCCceecCHHHHHHhCCC--CCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhcccccce
Confidence 345678999999999999995 999999999999999999999999999999999999999999999999999999999
Q ss_pred CC
Q 018463 351 FL 352 (355)
Q Consensus 351 ~~ 352 (355)
++
T Consensus 196 ~~ 197 (237)
T COG5531 196 IK 197 (237)
T ss_pred ec
Confidence 87
No 9
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.76 E-value=9.1e-19 Score=192.85 Aligned_cols=76 Identities=41% Similarity=0.680 Sum_probs=73.8
Q ss_pred CCccccCCHHHHHhhCCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhccC
Q 018463 173 LNKVCGVSPELQAVVGQPAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHII 248 (355)
Q Consensus 173 ~~k~~~lSpeLa~~lG~~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl~ 248 (355)
+...+.|||+|++|||..++||++||++||+|||.||||||.|||.|+||++|+.|||++++.||+|+++|++||.
T Consensus 912 ~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 912 PAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS 987 (987)
T ss_pred cccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence 6678999999999999999999999999999999999999999999999999999999999999999999999984
No 10
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.75 E-value=1.1e-18 Score=192.16 Aligned_cols=75 Identities=29% Similarity=0.571 Sum_probs=72.4
Q ss_pred CCccccccHHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 274 GPSSVIISEALAKFLGTGGREMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 274 ~~~~~~lS~~La~flG~~~~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
+..+|.||++|+.|||.+ ++||++||++||+|||.||||||.|+|.|+||++|+.|||+++|.||+|+++|++||
T Consensus 912 ~~~~~~ls~~La~~lg~~--~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl 986 (987)
T PRK14724 912 PAAGLKPSAALAAVIGAE--PVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHL 986 (987)
T ss_pred cccccCCCHHHHHHhCCC--cCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhc
Confidence 456999999999999995 899999999999999999999999999999999999999999999999999999997
No 11
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.65 E-value=7.9e-17 Score=160.22 Aligned_cols=81 Identities=33% Similarity=0.583 Sum_probs=78.3
Q ss_pred ccCCHHHHHhhCCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhccCCCCCCccc
Q 018463 177 CGVSPELQAVVGQPAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHIIPLEPTKES 256 (355)
Q Consensus 177 ~~lSpeLa~~lG~~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl~p~dp~~~~ 256 (355)
|++||.|+.+||....||++||.+||.|||.|+||||.++.+|+||..|+.+||++++.|.+|+.+|++||.|++|+-..
T Consensus 209 fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~dPIvi~ 288 (420)
T KOG2570|consen 209 FKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPDPIVID 288 (420)
T ss_pred cccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCCCeeec
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999765
Q ss_pred c
Q 018463 257 S 257 (355)
Q Consensus 257 ~ 257 (355)
.
T Consensus 289 h 289 (420)
T KOG2570|consen 289 H 289 (420)
T ss_pred c
Confidence 3
No 12
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.54 E-value=4e-15 Score=148.18 Aligned_cols=77 Identities=27% Similarity=0.488 Sum_probs=73.4
Q ss_pred CCccccccHHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhccCC
Q 018463 274 GPSSVIISEALAKFLGTGGREMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNHFL 352 (355)
Q Consensus 274 ~~~~~~lS~~La~flG~~~~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~~~ 352 (355)
.|..|+|||.||.+||+. +.||++||..||.|||.|+||||.++.+|+||.-|+++||++++.|.+|+.+|++|+..
T Consensus 205 ~P~~fklsp~La~lLGi~--t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P 281 (420)
T KOG2570|consen 205 QPEEFKLSPRLANLLGIH--TGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSP 281 (420)
T ss_pred CCcccccCHHHHHHhhhc--cCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCC
Confidence 467799999999999995 89999999999999999999999999999999999999999999999999999999854
No 13
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=99.47 E-value=6.7e-14 Score=103.68 Aligned_cols=54 Identities=33% Similarity=0.612 Sum_probs=45.2
Q ss_pred CHHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHHhCCCCccchhHHHHHHHHHhc
Q 018463 3 SDQEIAKGVETLLRQSDRNASTSLNGVVKQLEAKLGLDLSHKAGFIRDQISLLLR 57 (355)
Q Consensus 3 Sd~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~~fgvDLs~kK~~I~~~i~~~l~ 57 (355)
||++|...|++||+++||++ +|.+.||++||++||+||++||.||+++|+.+|.
T Consensus 1 td~~i~~~i~~iL~~~dl~~-vT~k~vr~~Le~~~~~dL~~~K~~I~~~I~~~l~ 54 (54)
T PF08766_consen 1 TDEEIREAIREILREADLDT-VTKKQVREQLEERFGVDLSSRKKFIKELIDEFLS 54 (54)
T ss_dssp -HHHHHHHHHHHHTTS-GGG---HHHHHHHHHHH-SS--SHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCHhH-hhHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhC
Confidence 79999999999999999997 8899999999999999999999999999999874
No 14
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.35 E-value=6.6e-13 Score=145.28 Aligned_cols=76 Identities=32% Similarity=0.509 Sum_probs=72.3
Q ss_pred CccccccHHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhccCC
Q 018463 275 PSSVIISEALAKFLGTGGREMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNHFL 352 (355)
Q Consensus 275 ~~~~~lS~~La~flG~~~~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~~~ 352 (355)
..+|.+|++|+.++|+. +++|.++++.||+|||.|+||||.|||.|+||++|+.+||++.+.||.|+++|++|+.+
T Consensus 785 ~~~~~~S~~La~~~g~~--~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~~ 860 (860)
T PRK06319 785 GPLYTPSPALAAMIGAE--PVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLIK 860 (860)
T ss_pred ccccccccccccccCcC--ccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhcC
Confidence 45689999999999984 89999999999999999999999999999999999999999999999999999999864
No 15
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.33 E-value=1.2e-12 Score=143.17 Aligned_cols=75 Identities=39% Similarity=0.667 Sum_probs=71.7
Q ss_pred CccccCCHHHHHhhCCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhccC
Q 018463 174 NKVCGVSPELQAVVGQPAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHII 248 (355)
Q Consensus 174 ~k~~~lSpeLa~~lG~~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl~ 248 (355)
...|.+|++|+.++|...++|+++++.||+|||.|+||||.|||.|+||++|+.+|+++.+.||.|+++|+.|+.
T Consensus 785 ~~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~ 859 (860)
T PRK06319 785 GPLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLI 859 (860)
T ss_pred ccccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhc
Confidence 344779999999999999999999999999999999999999999999999999999999999999999999985
No 16
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=98.62 E-value=3.8e-08 Score=100.08 Aligned_cols=60 Identities=30% Similarity=0.558 Sum_probs=57.6
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHHhCCCCccchhHHHHHHHHHhcCCCCC
Q 018463 2 VSDQEIAKGVETLLRQSDRNASTSLNGVVKQLEAKLGLDLSHKAGFIRDQISLLLRSHPTP 62 (355)
Q Consensus 2 ~Sd~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~~fgvDLs~kK~~I~~~i~~~l~~~~~~ 62 (355)
|||.+|...|..||..|||++ +|.+.|.++|-++|++||++||.||..+|..+|+.+.+.
T Consensus 520 PTdeelk~~V~kILk~vdfnt-aTm~dIlKkl~~~f~~dLt~rK~~IK~~Ike~I~~~~de 579 (594)
T KOG2266|consen 520 PTDEELKEVVKKILKEVDFNT-ATMKDILKKLYAKFPIDLTHRKDFIKDTIKELINKMADE 579 (594)
T ss_pred CcHHHHHHHHHHHHHhcCcch-hhHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHhcch
Confidence 899999999999999999996 999999999999999999999999999999999988664
No 17
>PRK05350 acyl carrier protein; Provisional
Probab=79.54 E-value=2.1 Score=33.72 Aligned_cols=53 Identities=25% Similarity=0.203 Sum_probs=45.3
Q ss_pred cCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 295 MLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 295 ~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
|+|.+|...|+++|.+. +.- +...|.+|..|..-+|-+|+.+.+|.-.|..+|
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~--~~~~i~~d~~l~~dlg~DSld~veli~~lE~~f 54 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEI--DPEDITPEANLYEDLDLDSIDAVDLVVHLQKLT 54 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCC--CHHHCCCCccchhhcCCCHHHHHHHHHHHHHHH
Confidence 78999999999999987 432 234699999998888999999999999888877
No 18
>PRK05828 acyl carrier protein; Validated
Probab=76.34 E-value=4.4 Score=32.64 Aligned_cols=53 Identities=21% Similarity=0.178 Sum_probs=43.3
Q ss_pred cCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 295 MLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 295 ~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
|+|.+|..+|-+.|.+.++.-+. -.|.+|..|.. +|-||+.+.+|.-.|...|
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~~~--d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f 53 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAVTL--DESNINKPYRE-LKIDSLDMFSIIVSLESEF 53 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCCCc--ccccCCCCHHh-cCCCHHHHHHHHHHHHHHH
Confidence 79999999999999886553222 34688899987 9999999999988887766
No 19
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=70.86 E-value=5.5 Score=41.66 Aligned_cols=41 Identities=24% Similarity=0.258 Sum_probs=36.3
Q ss_pred CccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhc
Q 018463 293 REMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLG 333 (355)
Q Consensus 293 ~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg 333 (355)
.-.+-+||...+..||+.|||-|+.||..|+.|.-|-+...
T Consensus 380 ~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~ 420 (560)
T KOG2522|consen 380 TLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVN 420 (560)
T ss_pred ceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHH
Confidence 57899999999999999999999999999888887766553
No 20
>PRK12449 acyl carrier protein; Provisional
Probab=67.34 E-value=9.9 Score=29.43 Aligned_cols=53 Identities=17% Similarity=0.182 Sum_probs=42.8
Q ss_pred cCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 295 MLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 295 ~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
|+|.+|..+|-++|.+.-=.++ ..|.+|..|..-+|.+++.+.+|.-.|...|
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dlg~DSl~~~~li~~lE~~f 53 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLS---LAITEQTHLKDDLAVDSIELVEFIINVEDEF 53 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCc---cccCCCCcHHHHcCCcHHHHHHHHHHHHHHh
Confidence 6788999999999987442233 2599999999999999999999888776655
No 21
>CHL00124 acpP acyl carrier protein; Validated
Probab=67.13 E-value=6 Score=30.83 Aligned_cols=53 Identities=13% Similarity=0.182 Sum_probs=44.0
Q ss_pred cCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 295 MLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 295 ~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
|+|.+|...|-++|.+.-=.++ ..|.+|..|..-+|-+|+.+.+|.-.|...|
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~---~~i~~d~~l~~dlg~DSl~~~eli~~le~~f 53 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEK---SEVTLDANFTRDLGADSLDVVELVMAIEEKF 53 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhcCCcHHHHHHHHHHHHHHH
Confidence 6899999999999988742333 3599999999999999999999988887765
No 22
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=66.36 E-value=6.4 Score=33.16 Aligned_cols=47 Identities=30% Similarity=0.451 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHHhCCCCccchhHHHHHHH
Q 018463 2 VSDQEIAKGVETLLRQSDRNASTSLNGVVKQLEAKLGLDLSHKAGFIRDQIS 53 (355)
Q Consensus 2 ~Sd~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~~fgvDLs~kK~~I~~~i~ 53 (355)
|||++|-..|..|.+...+ |...+++.|+. .|+++..-+..|+..|-
T Consensus 67 vsd~evd~~i~~ia~~n~l----s~~ql~~~L~~-~G~s~~~~r~~ir~~i~ 113 (118)
T PF09312_consen 67 VSDEEVDEAIANIAKQNNL----SVEQLRQQLEQ-QGISYEEYREQIRKQIL 113 (118)
T ss_dssp --HHHHHHHHHHHHHHTT------HHHHHHHCHH-CT--HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHcCC----CHHHHHHHHHH-cCCCHHHHHHHHHHHHH
Confidence 7999999999999988775 46899999987 69999999999988763
No 23
>PRK05350 acyl carrier protein; Provisional
Probab=64.20 E-value=8.3 Score=30.29 Aligned_cols=53 Identities=23% Similarity=0.254 Sum_probs=45.1
Q ss_pred CCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhcc
Q 018463 192 MPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 247 (355)
Q Consensus 192 ~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl 247 (355)
|+|.+|...|+++|.+. +.- +...|.+|..|..-+|-|++.+.+|--.|..+|
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~--~~~~i~~d~~l~~dlg~DSld~veli~~lE~~f 54 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEI--DPEDITPEANLYEDLDLDSIDAVDLVVHLQKLT 54 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCC--CHHHCCCCccchhhcCCCHHHHHHHHHHHHHHH
Confidence 78999999999999876 422 224799999998888999999999999998877
No 24
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=63.82 E-value=13 Score=38.98 Aligned_cols=61 Identities=28% Similarity=0.329 Sum_probs=45.4
Q ss_pred CCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhc---------CccChHHHHHHHHhccCCC
Q 018463 190 PAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFET---------DCTDMFKMNKLLAKHIIPL 250 (355)
Q Consensus 190 ~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~---------d~i~~~~m~klL~~Hl~p~ 250 (355)
.-.|-.+|...+-.||..|||-|+.||..|+.|+-|-..... ..+.--.+..++..-+.|.
T Consensus 380 ~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~k~~K~~~a~~~~~pw~~l~~~~~~rmtp~ 449 (560)
T KOG2522|consen 380 TLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVNKKKKVLNASRIIAPWEILHPLLTNRMTPF 449 (560)
T ss_pred ceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHHhhhhccccccccccHHHHHHHHHhcCCcc
Confidence 467789999999999999999999999999888887765543 2333445555554444443
No 25
>PRK05828 acyl carrier protein; Validated
Probab=51.43 E-value=27 Score=28.03 Aligned_cols=53 Identities=21% Similarity=0.271 Sum_probs=42.8
Q ss_pred CCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhcc
Q 018463 192 MPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 247 (355)
Q Consensus 192 ~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl 247 (355)
|+|.+|..++-..|++..+.- +-..|.+|..|.. +|.|++.+.+|--.|...|
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~--~~d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f 53 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAV--TLDESNINKPYRE-LKIDSLDMFSIIVSLESEF 53 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCC--CcccccCCCCHHh-cCCCHHHHHHHHHHHHHHH
Confidence 799999999999998755422 2235678888876 9999999999999997776
No 26
>PRK07117 acyl carrier protein; Validated
Probab=47.92 E-value=22 Score=28.18 Aligned_cols=52 Identities=19% Similarity=0.165 Sum_probs=40.2
Q ss_pred cCHHHHHHHHHHHHHHcCCCCC-CCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 295 MLQAEATKRVWEYIKVNHLEDP-LNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 295 ~sR~evvk~lW~YIK~n~LqDp-~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
|+|.+|..+|-+-|++.- | -+...|..|..|+. ||.+|+.+.+|--.|..-|
T Consensus 1 M~~~ei~~~v~~ii~e~~---p~i~~~~I~~~~~l~D-Lg~DSlD~veiv~~led~f 53 (79)
T PRK07117 1 MDKQRIFDILVRHIREVL---PDLDQHQFQPEDSLVD-LGANSMDRAEIVIMTLESL 53 (79)
T ss_pred CCHHHHHHHHHHHHHHHc---CCCCHHHCCCCCChhh-cCCChHHHHHHHHHHHHHH
Confidence 678888888888888753 2 34457899999998 9999999998877665433
No 27
>PTZ00171 acyl carrier protein; Provisional
Probab=46.42 E-value=24 Score=31.46 Aligned_cols=55 Identities=15% Similarity=0.176 Sum_probs=46.1
Q ss_pred CccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 293 REMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 293 ~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
..|++.+|...|+++|.+.-=-+ ...|..|..|..-+|-||+.+.+|.-.|..+|
T Consensus 64 ~~~~~~~v~~~l~eiiae~l~vd---~~~I~~ds~~~~dLg~DSLd~veLv~~LEdeF 118 (148)
T PTZ00171 64 YLLSKEDVLTRVKKVVKNFEKVD---ASKITPESNFVKDLGADSLDVVELLIAIEQEF 118 (148)
T ss_pred cccCHHHHHHHHHHHHHHHhCCC---HhhCCCCcchhhhcCCCHHHHHHHHHHHHHHH
Confidence 36899999999999999875223 33589999999999999999999988887766
No 28
>CHL00124 acpP acyl carrier protein; Validated
Probab=44.71 E-value=25 Score=27.23 Aligned_cols=53 Identities=9% Similarity=0.211 Sum_probs=43.8
Q ss_pred CCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhcc
Q 018463 192 MPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 247 (355)
Q Consensus 192 ~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl 247 (355)
|+|.+|...|-++|.+.-=.++ ..|..|..|...+|-|++.+.+|.-.|...|
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~---~~i~~d~~l~~dlg~DSl~~~eli~~le~~f 53 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEK---SEVTLDANFTRDLGADSLDVVELVMAIEEKF 53 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhcCCcHHHHHHHHHHHHHHH
Confidence 6899999999999987742333 3599999999999999999999999886666
No 29
>PF04155 Ground-like: Ground-like domain; InterPro: IPR007284 This group of proteins contain one or more copies of the ground-like domain, which are specific to Caenorhabditis elegans and Caenorhabditis briggsae. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides [].
Probab=42.49 E-value=27 Score=27.17 Aligned_cols=38 Identities=16% Similarity=0.231 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHHhCCC
Q 018463 1 MVSDQEIAKGVETLLRQSDRNASTSLNGVVKQLEAKLGLD 40 (355)
Q Consensus 1 m~Sd~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~~fgvD 40 (355)
++.+.+|..-|.+-+...|+. .+++.|.+.+|.+||.+
T Consensus 5 ~Cn~~~L~~ii~~~~~~~~~~--~s~~~Iq~~~e~~f~~~ 42 (76)
T PF04155_consen 5 KCNSEELRKIILKNMKECNLS--ISKRAIQKAAEKRFGGS 42 (76)
T ss_pred ccCCHHHHHHHHHHhccCCHH--HHHHHHHHHHHHHhCCC
Confidence 467889999999999987874 58899999999999875
No 30
>PRK12449 acyl carrier protein; Provisional
Probab=42.07 E-value=49 Score=25.47 Aligned_cols=53 Identities=19% Similarity=0.208 Sum_probs=42.7
Q ss_pred CCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhcc
Q 018463 192 MPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 247 (355)
Q Consensus 192 ~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl 247 (355)
|+|.+|...|-+++.+.-=-++ ..|..|..|..-+|.|++.+.+|.-.|...|
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dlg~DSl~~~~li~~lE~~f 53 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLS---LAITEQTHLKDDLAVDSIELVEFIINVEDEF 53 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCc---cccCCCCcHHHHcCCcHHHHHHHHHHHHHHh
Confidence 6788999999999976442222 3599999999999999999999988886655
No 31
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=41.45 E-value=20 Score=28.45 Aligned_cols=23 Identities=26% Similarity=0.320 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhCCCCccchhHHH
Q 018463 27 NGVVKQLEAKLGLDLSHKAGFIR 49 (355)
Q Consensus 27 k~Vr~qLE~~fgvDLs~kK~~I~ 49 (355)
..+|..||..||+||+.=+-..+
T Consensus 4 ~~~r~~~e~~~G~dl~~Vrvh~~ 26 (79)
T PF13699_consen 4 ESIRSRLERAFGADLSDVRVHTG 26 (79)
T ss_pred HHHHHHHHHHhCCCccceEEEeC
Confidence 36899999999999987665555
No 32
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=40.08 E-value=38 Score=32.65 Aligned_cols=60 Identities=22% Similarity=0.327 Sum_probs=48.4
Q ss_pred HHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhcc--CccchhhHHHHHHhccCCC
Q 018463 282 EALAKFLGTGGREMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGC--ESISALGIQEMLARNHFLR 353 (355)
Q Consensus 282 ~~La~flG~~~~~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~--~~i~~~~~~klL~~H~~~~ 353 (355)
.+||++|-..+...+---+|.+||.|.=..+|-+|.|- ||. ..-+..+|.++|+.+|+..
T Consensus 4 ~~LA~wlt~~~Np~faRv~VNRvW~~~fGrGlV~p~dD------------~g~~~~~PshPeLLd~La~~F~~~ 65 (266)
T PF07587_consen 4 LALADWLTSPDNPLFARVIVNRVWQHLFGRGLVEPVDD------------FGPQGNPPSHPELLDWLAAEFVEH 65 (266)
T ss_pred HHHHHHhcCCCCcchHHHHHHHHHHHHcCCcCcCCHhh------------ccCCCCCCCCHHHHHHHHHHHHHc
Confidence 37899997656688888899999999999999999876 443 4566778888888888653
No 33
>PTZ00171 acyl carrier protein; Provisional
Probab=37.38 E-value=49 Score=29.52 Aligned_cols=57 Identities=11% Similarity=0.187 Sum_probs=47.4
Q ss_pred CCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccccChhhhhhhhcCccChHHHHHHHHhcc
Q 018463 188 GQPAMPRTEIVKQLWAYIRKNNLQDPSNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 247 (355)
Q Consensus 188 G~~~~sR~evvk~LW~YIK~nnLQDp~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl 247 (355)
|...|++.+|...|+++|.+.-=-++ ..|..|..+...+|-|++.+.+|--.|..+|
T Consensus 62 ~~~~~~~~~v~~~l~eiiae~l~vd~---~~I~~ds~~~~dLg~DSLd~veLv~~LEdeF 118 (148)
T PTZ00171 62 KQYLLSKEDVLTRVKKVVKNFEKVDA---SKITPESNFVKDLGADSLDVVELLIAIEQEF 118 (148)
T ss_pred cccccCHHHHHHHHHHHHHHHhCCCH---hhCCCCcchhhhcCCCHHHHHHHHHHHHHHH
Confidence 45678999999999999987752233 4588999999999999999999999997776
No 34
>PF13565 HTH_32: Homeodomain-like domain
Probab=33.65 E-value=83 Score=23.68 Aligned_cols=35 Identities=17% Similarity=0.335 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHHhCCCC
Q 018463 4 DQEIAKGVETLLRQSDRNASTSLNGVVKQLEAKLGLDL 41 (355)
Q Consensus 4 d~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~~fgvDL 41 (355)
+.++...|.+++.+-- ..|...|...|+.+||+.+
T Consensus 32 ~~e~~~~i~~~~~~~p---~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 32 DPEQRERIIALIEEHP---RWTPREIAEYLEEEFGISV 66 (77)
T ss_pred cHHHHHHHHHHHHhCC---CCCHHHHHHHHHHHhCCCC
Confidence 4677677777766443 2567899999999999987
No 35
>PRK07639 acyl carrier protein; Provisional
Probab=31.12 E-value=69 Score=25.63 Aligned_cols=54 Identities=15% Similarity=0.063 Sum_probs=41.9
Q ss_pred cCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 295 MLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 295 ~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
|+|.+|..+|-..|.+.= ..+. --.|..|..|..=+|-+|+.+.++.-.|..+|
T Consensus 1 M~~~ei~~~i~~il~e~l-~~~~-~~~i~~d~~l~edL~lDSld~velv~~lE~~f 54 (86)
T PRK07639 1 MRREALKNAVLKIMEEKL-ELKN-VTHLEETMRLNEDLYIDSVMMLQLIVYIEMDV 54 (86)
T ss_pred CCHHHHHHHHHHHHHHHh-CCCc-cccCCCCCCcccccCCChHHHHHHHHHHHHHH
Confidence 688889889988888753 2221 12588999998888999999999988887766
No 36
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=28.00 E-value=96 Score=22.13 Aligned_cols=31 Identities=16% Similarity=0.329 Sum_probs=19.7
Q ss_pred HHHHHHHHHHhCCCCccch-hHHHHHHHHHhc
Q 018463 27 NGVVKQLEAKLGLDLSHKA-GFIRDQISLLLR 57 (355)
Q Consensus 27 k~Vr~qLE~~fgvDLs~kK-~~I~~~i~~~l~ 57 (355)
+.++.-+..++|+||++.| .+|..-|...+.
T Consensus 6 ~~~~~~i~~~~Gi~l~~~K~~~l~rRl~~rm~ 37 (57)
T PF03705_consen 6 ERFRELIYRRTGIDLSEYKRSLLERRLARRMR 37 (57)
T ss_dssp HHHHHHHHHHH-----GGGHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCchhhHHHHHHHHHHHHH
Confidence 4678889999999998777 777777766654
No 37
>PF02881 SRP54_N: SRP54-type protein, helical bundle domain; InterPro: IPR013822 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 1J8M_F 1J8Y_F 2J37_W 2OG2_A 3B9Q_A 2V3C_C 3NDB_B 1ZU5_B 1ZU4_A 1WGW_A ....
Probab=24.67 E-value=2.3e+02 Score=21.38 Aligned_cols=33 Identities=12% Similarity=0.264 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhhcCCCCCccHHHHHHHHHH-HhC
Q 018463 5 QEIAKGVETLLRQSDRNASTSLNGVVKQLEA-KLG 38 (355)
Q Consensus 5 ~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~-~fg 38 (355)
+++...|++.|=.||..- -+...|...|.. ..+
T Consensus 24 ~~~l~ele~~Li~aDVg~-~~a~~i~~~ik~~~~~ 57 (75)
T PF02881_consen 24 EEFLEELEEALIEADVGV-EVAEKIIENIKKKLIK 57 (75)
T ss_dssp HHHHHHHHHHHHHTTTSH-HHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHcCcCH-HHHHHHHHHHHHHHhc
Confidence 577899999999999985 556799999999 776
No 38
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=24.06 E-value=2.8e+02 Score=21.42 Aligned_cols=36 Identities=19% Similarity=0.257 Sum_probs=30.7
Q ss_pred CCccHHHHHHHHHHHhCCCCcc--chhHHHHHHHHHhc
Q 018463 22 ASTSLNGVVKQLEAKLGLDLSH--KAGFIRDQISLLLR 57 (355)
Q Consensus 22 t~~T~k~Vr~qLE~~fgvDLs~--kK~~I~~~i~~~l~ 57 (355)
.+.|...|.+-+++.|++++.. -+.+++..+...+.
T Consensus 20 ~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~ 57 (77)
T PF00538_consen 20 KGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVE 57 (77)
T ss_dssp SSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHH
Confidence 3689999999999999988875 77888888887775
No 39
>PRK07117 acyl carrier protein; Validated
Probab=23.30 E-value=1.1e+02 Score=24.17 Aligned_cols=52 Identities=17% Similarity=0.228 Sum_probs=40.6
Q ss_pred CCHHHHHHHHHHHHHHcCCCCC-CCCCccccChhhhhhhhcCccChHHHHHHHHhcc
Q 018463 192 MPRTEIVKQLWAYIRKNNLQDP-SNKRKIICDDALRVVFETDCTDMFKMNKLLAKHI 247 (355)
Q Consensus 192 ~sR~evvk~LW~YIK~nnLQDp-~nkr~I~cDdkLk~lF~~d~i~~~~m~klL~~Hl 247 (355)
|+|.+|...+-+-|++.- | -+...|..|..|+. +|.|++.+.++--.|...|
T Consensus 1 M~~~ei~~~v~~ii~e~~---p~i~~~~I~~~~~l~D-Lg~DSlD~veiv~~led~f 53 (79)
T PRK07117 1 MDKQRIFDILVRHIREVL---PDLDQHQFQPEDSLVD-LGANSMDRAEIVIMTLESL 53 (79)
T ss_pred CCHHHHHHHHHHHHHHHc---CCCCHHHCCCCCChhh-cCCChHHHHHHHHHHHHHH
Confidence 578888888888887764 2 23357889999987 9999999999988775544
No 40
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=23.10 E-value=70 Score=22.74 Aligned_cols=17 Identities=24% Similarity=0.550 Sum_probs=14.8
Q ss_pred CCHHHHHHHHHHHhhhc
Q 018463 2 VSDQEIAKGVETLLRQS 18 (355)
Q Consensus 2 ~Sd~el~~~i~~iL~~a 18 (355)
|+.+||.++||.++|.|
T Consensus 17 P~ESELskr~rrLIRaa 33 (44)
T PF08134_consen 17 PTESELSKRIRRLIRAA 33 (44)
T ss_pred CcHHHHHHHHHHHHHHH
Confidence 78999999999998754
No 41
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=23.08 E-value=1.4e+02 Score=21.46 Aligned_cols=40 Identities=15% Similarity=0.320 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhhh----cCCCCC--------ccHHHHHHHHHHHhCCCCccc
Q 018463 5 QEIAKGVETLLRQ----SDRNAS--------TSLNGVVKQLEAKLGLDLSHK 44 (355)
Q Consensus 5 ~el~~~i~~iL~~----aDL~t~--------~T~k~Vr~qLE~~fgvDLs~k 44 (355)
++|...|.++|.- .++++. +..-.++..|+..||++++..
T Consensus 1 e~l~~~~~~~l~~~~~~i~~~~~~~~lG~DSl~~~~l~~~l~~~~g~~i~~~ 52 (67)
T PF00550_consen 1 EQLREIIAEVLGVDPEEIDPDTDFFDLGLDSLDAIELVSELEEEFGIKIPPS 52 (67)
T ss_dssp HHHHHHHHHHHTSSGGCTSTTSBTTTTTSSHHHHHHHHHHHHHHHTSSTTHH
T ss_pred CHHHHHHHHHHCcCHhhCCCCCCHHHhCCchHHHHHHHHHHHHHHcCCCCHH
Confidence 4677778888861 222211 445578999999999998765
No 42
>PRK05883 acyl carrier protein; Validated
Probab=23.03 E-value=1.2e+02 Score=24.56 Aligned_cols=54 Identities=11% Similarity=0.077 Sum_probs=43.9
Q ss_pred ccCHHHHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 294 EMLQAEATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 294 ~~sR~evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
.++..+|...|-++|.+. |.-+ ...|..|..|...+|-+|+.+.+|--.|..+|
T Consensus 9 ~~~~~~I~~~l~~iia~~-l~v~--~~~I~~d~~l~~dlg~DSL~~v~lv~~lE~~f 62 (91)
T PRK05883 9 TSSPSTVSATLLSILRDD-LNVD--LTRVTPDARLVDDVGLDSVAFAVGMVAIEERL 62 (91)
T ss_pred CCCHHHHHHHHHHHHHHH-hCCC--hhhCCCCCchhhccCCChHHHHHHHHHHHHHH
Confidence 588999999999999876 3322 23589999999999999999888877777766
No 43
>KOG0747 consensus Putative NAD+-dependent epimerases [Carbohydrate transport and metabolism]
Probab=22.24 E-value=1.6e+02 Score=29.70 Aligned_cols=56 Identities=21% Similarity=0.243 Sum_probs=40.3
Q ss_pred cCCCCccCHHHHHHHHHHHHHHcCCCCC-------------CCCCcccCchhHHhhhc-cCccchh-hHHHHH
Q 018463 289 GTGGREMLQAEATKRVWEYIKVNHLEDP-------------LNSMVILCDAKLRELLG-CESISAL-GIQEML 346 (355)
Q Consensus 289 G~~~~~~sR~evvk~lW~YIK~n~LqDp-------------~nkr~I~CDekLk~Lfg-~~~i~~~-~~~klL 346 (355)
|++ .+|++.++.+-+-++|.....--+ +|-|.-+|++|++ =+| +....+- +|.+.+
T Consensus 249 gtd-~e~~~~~l~k~i~eli~~~~~~~~~~p~~~~v~dRp~nd~Ry~~~~eKik-~LGw~~~~p~~eGLrkti 319 (331)
T KOG0747|consen 249 GTD-DEMRVIDLAKDICELFEKRLPNIDTEPFIFFVEDRPYNDLRYFLDDEKIK-KLGWRPTTPWEEGLRKTI 319 (331)
T ss_pred cCc-chhhHHHHHHHHHHHHHHhccCCCCCCcceecCCCCcccccccccHHHHH-hcCCcccCcHHHHHHHHH
Confidence 443 699999999999999998554211 5778899999999 667 4444433 455544
No 44
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=22.01 E-value=2e+02 Score=21.40 Aligned_cols=42 Identities=24% Similarity=0.282 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHh-hhcCCCCCccHHHHHHHHHHHhCCCCccch
Q 018463 3 SDQEIAKGVETLL-RQSDRNASTSLNGVVKQLEAKLGLDLSHKA 45 (355)
Q Consensus 3 Sd~el~~~i~~iL-~~aDL~t~~T~k~Vr~qLE~~fgvDLs~kK 45 (355)
+.+++...|+++| ...+-+-.++...|...+...+ -++..|.
T Consensus 2 ~~~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~-~~f~~~~ 44 (74)
T PF12872_consen 2 SLEELKKLLRELLESQKGEDGWVSLSQLGQEYKKKY-PDFDPRD 44 (74)
T ss_dssp --HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHH-TT--TCC
T ss_pred hHHHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHC-CCCCccc
Confidence 4678999999999 4444222388999999999999 6666553
No 45
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=21.83 E-value=2e+02 Score=19.11 Aligned_cols=27 Identities=11% Similarity=0.215 Sum_probs=13.4
Q ss_pred HHHHHHhhhcCCCCCccHHHHHHHHHH
Q 018463 9 KGVETLLRQSDRNASTSLNGVVKQLEA 35 (355)
Q Consensus 9 ~~i~~iL~~aDL~t~~T~k~Vr~qLE~ 35 (355)
.+++++|+.-.|.++=++..+...|..
T Consensus 7 ~eLk~~l~~~gL~~~G~K~~Li~Rl~~ 33 (35)
T PF02037_consen 7 AELKEELKERGLSTSGKKAELIERLKE 33 (35)
T ss_dssp HHHHHHHHHTTS-STSSHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHH
Confidence 455666666666554444444444443
No 46
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=21.49 E-value=2.4e+02 Score=22.83 Aligned_cols=48 Identities=23% Similarity=0.331 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHHh------CCCCccchhHHHHH
Q 018463 4 DQEIAKGVETLLRQSDRNASTSLNGVVKQLEAKL------GLDLSHKAGFIRDQ 51 (355)
Q Consensus 4 d~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~~f------gvDLs~kK~~I~~~ 51 (355)
|..|..+|++||.........+...|-+.|...- |--|.+|+.+|...
T Consensus 25 d~~l~~rv~ei~~~~~~~~~~~l~~V~~~L~~e~ip~LPPGGGl~sKr~~Ie~v 78 (81)
T PF07830_consen 25 DKYLEQRVEEIIEKSSEEENPDLVYVMRTLASEDIPGLPPGGGLASKRSVIEAV 78 (81)
T ss_dssp HHHHHHHHHHHT----------HHHHHHHHHHTT-SS--TTTTCGGGHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcccCCCCHHHHHHHHHhccCCCCcCCcCHHHHHHHHHHH
Confidence 5678889999998743333466778888888873 78899999888764
No 47
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=21.29 E-value=1e+02 Score=23.51 Aligned_cols=49 Identities=24% Similarity=0.225 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHcCCCCCCCCCcccCchhHHhhhccCccchhhHHHHHHhcc
Q 018463 299 EATKRVWEYIKVNHLEDPLNSMVILCDAKLRELLGCESISALGIQEMLARNH 350 (355)
Q Consensus 299 evvk~lW~YIK~n~LqDp~nkr~I~CDekLk~Lfg~~~i~~~~~~klL~~H~ 350 (355)
++...|.++|.+.--.++ ..|.+|..|..-+|-||+.+.+|.-.|..+|
T Consensus 3 ~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dlglDSl~~veli~~lE~~f 51 (77)
T TIGR00517 3 EIFEKVKAIIKEQLNVDE---DQVTPDASFVEDLGADSLDTVELVMALEEEF 51 (77)
T ss_pred HHHHHHHHHHHHHHCCCH---HHCCCCcchhhhcCCcHHHHHHHHHHHHHHH
Confidence 566778888887522233 3588999998889999999999988887766
No 48
>PF05696 DUF826: Protein of unknown function (DUF826); InterPro: IPR008544 This entry is represented by Bacteriophage 933W, Orf26. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.37 E-value=3.7e+02 Score=21.68 Aligned_cols=42 Identities=21% Similarity=0.286 Sum_probs=24.8
Q ss_pred HHHHHhhhcCCCCCccHHHHHHHHHHHhCCCCccchhHHHHHHHHHhcCC
Q 018463 10 GVETLLRQSDRNASTSLNGVVKQLEAKLGLDLSHKAGFIRDQISLLLRSH 59 (355)
Q Consensus 10 ~i~~iL~~aDL~t~~T~k~Vr~qLE~~fgvDLs~kK~~I~~~i~~~l~~~ 59 (355)
.|...|++-.... .-+-+||+-||+++. ..++.+++.+|..+
T Consensus 12 ~VK~aL~Se~V~~-alK~qvr~~le~qiD-------a~VD~~L~~llg~~ 53 (78)
T PF05696_consen 12 AVKQALRSEEVTS-ALKQQVRQNLEAQID-------AEVDAALDELLGAP 53 (78)
T ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHH-------HHHHHHHHHHhCCC
Confidence 3555565554433 345678888887763 34556666666644
No 49
>PF13276 HTH_21: HTH-like domain
Probab=20.29 E-value=1.4e+02 Score=21.72 Aligned_cols=40 Identities=15% Similarity=0.315 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhhhcCCCCCccHHHHHHHHHHHhCCCCccch
Q 018463 4 DQEIAKGVETLLRQSDRNASTSLNGVVKQLEAKLGLDLSHKA 45 (355)
Q Consensus 4 d~el~~~i~~iL~~aDL~t~~T~k~Vr~qLE~~fgvDLs~kK 45 (355)
|++|...|.+|....... .--..|...|...+|+.++.++
T Consensus 3 ~~~l~~~I~~i~~~~~~~--yG~rri~~~L~~~~~~~v~~kr 42 (60)
T PF13276_consen 3 DEALRELIKEIFKESKPT--YGYRRIWAELRREGGIRVSRKR 42 (60)
T ss_pred hHHHHHHHHHHHHHcCCC--eehhHHHHHHhccCcccccHHH
Confidence 788999999999999763 5667899999999888887665
No 50
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=20.18 E-value=2.2e+02 Score=18.62 Aligned_cols=24 Identities=21% Similarity=0.444 Sum_probs=17.9
Q ss_pred HHHHHHhcCCCCccCHHHHHHHHHHHHHHcCCC
Q 018463 282 EALAKFLGTGGREMLQAEATKRVWEYIKVNHLE 314 (355)
Q Consensus 282 ~~La~flG~~~~~~sR~evvk~lW~YIK~n~Lq 314 (355)
.++|++||+. ...||.|++...+.
T Consensus 4 ~e~a~~lgvs---------~~tl~~~~~~g~~~ 27 (49)
T cd04762 4 KEAAELLGVS---------PSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHCcC---------HHHHHHHHHcCCCC
Confidence 5788899984 23789999987663
No 51
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=20.04 E-value=92 Score=24.61 Aligned_cols=50 Identities=26% Similarity=0.409 Sum_probs=37.3
Q ss_pred CC-HHHHHhhCCCCCCHHHHHHHHHH--HHHHcCCCCCCCCC--ccccChhhhhhhh
Q 018463 179 VS-PELQAVVGQPAMPRTEIVKQLWA--YIRKNNLQDPSNKR--KIICDDALRVVFE 230 (355)
Q Consensus 179 lS-peLa~~lG~~~~sR~evvk~LW~--YIK~nnLQDp~nkr--~I~cDdkLk~lF~ 230 (355)
.+ .+|++.+|....+=+.+++.|+. || ....+|.|+| .|..-++=+.++.
T Consensus 37 ~~~~~la~~l~i~~~~vt~~l~~Le~~glv--~r~~~~~DrR~~~l~lT~~G~~~~~ 91 (126)
T COG1846 37 ITVKELAERLGLDRSTVTRLLKRLEDKGLI--ERLRDPEDRRAVLVRLTEKGRELLE 91 (126)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHHHHHCCCe--eecCCccccceeeEEECccHHHHHH
Confidence 35 89999999999999999999998 77 6667888876 3444444444444
Done!