Query 019644
Match_columns 338
No_of_seqs 326 out of 1003
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 03:24:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019644.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019644hhsearch_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 1.2E-30 2.5E-35 242.7 11.1 181 1-221 1-181 (240)
2 COG5531 SWIB-domain-containing 99.9 1.9E-25 4.1E-30 206.5 6.5 192 8-218 8-199 (237)
3 PF02201 SWIB: SWIB/MDM2 domai 99.9 2.8E-25 6E-30 173.3 1.8 76 259-336 1-76 (76)
4 PF02201 SWIB: SWIB/MDM2 domai 99.9 2E-25 4.4E-30 174.1 0.9 75 140-214 1-75 (76)
5 KOG1946 RNA polymerase I trans 99.9 3.5E-24 7.6E-29 199.4 8.9 82 255-338 96-177 (240)
6 smart00151 SWIB SWI complex, B 99.9 6E-24 1.3E-28 166.2 7.5 76 141-216 2-77 (77)
7 smart00151 SWIB SWI complex, B 99.9 1.4E-23 3E-28 164.1 7.5 76 260-337 2-77 (77)
8 COG5531 SWIB-domain-containing 99.8 2.5E-20 5.4E-25 172.5 5.9 80 256-337 118-197 (237)
9 PRK14724 DNA topoisomerase III 99.8 1.8E-19 3.8E-24 196.7 7.8 77 139-215 911-987 (987)
10 PRK14724 DNA topoisomerase III 99.7 1.6E-18 3.4E-23 189.4 7.4 77 258-336 911-987 (987)
11 KOG2570 SWI/SNF transcription 99.7 2.4E-17 5.2E-22 161.8 5.7 82 142-223 207-288 (420)
12 PF08766 DEK_C: DEK C terminal 99.6 6.1E-15 1.3E-19 107.8 6.2 54 3-56 1-54 (54)
13 KOG2570 SWI/SNF transcription 99.5 7.8E-15 1.7E-19 144.3 5.8 77 260-338 206-282 (420)
14 PRK06319 DNA topoisomerase I/S 99.3 1.1E-12 2.5E-17 142.3 5.1 77 259-337 784-860 (860)
15 PRK06319 DNA topoisomerase I/S 99.3 1.3E-12 2.9E-17 141.7 5.2 74 142-215 786-859 (860)
16 KOG2266 Chromatin-associated p 98.8 7.5E-09 1.6E-13 103.7 6.3 60 1-60 519-578 (594)
17 PRK05350 acyl carrier protein; 75.6 2.6 5.7E-05 32.7 2.7 53 280-335 2-54 (82)
18 PF09312 SurA_N: SurA N-termin 74.1 4.8 0.0001 33.5 4.1 46 2-51 67-112 (118)
19 PRK05828 acyl carrier protein; 70.8 6.1 0.00013 31.3 3.7 53 280-335 1-53 (84)
20 KOG2522 Filamentous baseplate 70.8 7.2 0.00016 40.2 5.1 61 157-217 380-449 (560)
21 KOG2522 Filamentous baseplate 67.9 6.3 0.00014 40.6 4.0 45 273-317 374-419 (560)
22 PRK05350 acyl carrier protein; 66.2 5.4 0.00012 31.0 2.5 54 159-215 2-55 (82)
23 CHL00124 acpP acyl carrier pro 65.0 5.9 0.00013 30.5 2.5 53 280-335 1-53 (82)
24 PRK12449 acyl carrier protein; 62.7 11 0.00024 28.7 3.7 53 280-335 1-53 (80)
25 PRK12449 acyl carrier protein; 55.1 18 0.00039 27.6 3.7 54 159-215 1-54 (80)
26 PRK05828 acyl carrier protein; 55.1 17 0.00038 28.7 3.7 54 159-215 1-54 (84)
27 PF13565 HTH_32: Homeodomain-l 54.2 29 0.00063 25.9 4.7 35 4-40 32-66 (77)
28 CHL00124 acpP acyl carrier pro 51.6 13 0.00029 28.5 2.5 54 159-215 1-54 (82)
29 PF02881 SRP54_N: SRP54-type p 50.1 68 0.0015 24.0 6.2 41 5-45 24-66 (75)
30 PTZ00171 acyl carrier protein; 45.6 27 0.00058 30.7 3.7 54 279-335 65-118 (148)
31 PF00538 Linker_histone: linke 42.3 82 0.0018 24.1 5.6 43 14-56 13-57 (77)
32 PTZ00171 acyl carrier protein; 38.2 37 0.0008 29.8 3.4 59 154-215 61-119 (148)
33 PF03705 CheR_N: CheR methyltr 35.8 79 0.0017 22.2 4.3 31 26-56 6-37 (57)
34 PF00550 PP-binding: Phosphopa 35.4 70 0.0015 22.8 4.1 39 5-43 1-52 (67)
35 PF13545 HTH_Crp_2: Crp-like h 33.5 55 0.0012 24.2 3.3 49 261-315 25-75 (76)
36 smart00526 H15 Domain in histo 31.6 1.7E+02 0.0036 21.5 5.6 44 12-55 13-56 (66)
37 PF07587 PSD1: Protein of unkn 31.3 60 0.0013 30.9 3.9 57 268-336 5-63 (266)
38 PF13699 DUF4157: Domain of un 31.3 36 0.00078 26.6 2.0 21 26-46 4-24 (79)
39 PF01047 MarR: MarR family; I 29.2 18 0.00039 25.6 0.0 38 149-186 22-59 (59)
40 PRK07117 acyl carrier protein; 27.0 68 0.0015 25.0 2.9 51 280-334 1-52 (79)
41 PRK07117 acyl carrier protein; 26.5 67 0.0015 25.0 2.8 53 159-215 1-54 (79)
42 TIGR03697 NtcA_cyano global ni 26.4 88 0.0019 27.0 3.9 48 263-316 142-191 (193)
43 PRK07639 acyl carrier protein; 26.2 79 0.0017 24.9 3.2 54 280-335 1-54 (86)
44 PF09357 RteC: RteC protein; 24.9 3E+02 0.0065 25.7 7.3 40 3-42 143-184 (218)
45 PF13551 HTH_29: Winged helix- 24.8 1.2E+02 0.0026 23.7 4.1 40 4-43 59-102 (112)
46 PRK13918 CRP/FNR family transc 24.5 1.1E+02 0.0024 26.8 4.2 49 264-318 149-199 (202)
47 PRK05883 acyl carrier protein; 23.8 96 0.0021 24.7 3.3 54 279-335 9-62 (91)
48 cd00923 Cyt_c_Oxidase_Va Cytoc 22.7 1.9E+02 0.0042 24.0 4.8 44 3-49 4-47 (103)
49 PRK07639 acyl carrier protein; 21.5 1.1E+02 0.0024 24.0 3.2 55 159-215 1-55 (86)
50 TIGR03697 NtcA_cyano global ni 20.9 1.3E+02 0.0029 25.9 3.9 49 143-195 141-191 (193)
51 PF13276 HTH_21: HTH-like doma 20.8 1.6E+02 0.0035 21.0 3.8 40 4-44 3-42 (60)
52 TIGR00517 acyl_carrier acyl ca 20.4 88 0.0019 23.5 2.3 49 284-335 3-51 (77)
53 cd04762 HTH_MerR-trunc Helix-T 20.3 1.3E+02 0.0028 19.5 3.0 24 148-178 4-27 (49)
54 PRK09392 ftrB transcriptional 20.2 1.3E+02 0.0027 27.3 3.7 49 263-318 172-222 (236)
55 PF03511 Fanconi_A: Fanconi an 20.1 69 0.0015 24.3 1.6 19 201-219 8-26 (64)
56 cd00073 H15 linker histone 1 a 20.1 3E+02 0.0065 21.6 5.5 44 12-55 13-56 (88)
No 1
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.97 E-value=1.2e-30 Score=242.71 Aligned_cols=181 Identities=35% Similarity=0.494 Sum_probs=136.5
Q ss_pred CCCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHhhhhhcccCCCCCCcccccccCchh
Q 019644 1 MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQQEEDDGEDD 80 (338)
Q Consensus 1 ~~sd~ei~~~i~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK~~I~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (338)
|.+...+...+..||...+++++|...||++++..||++++..|..++..|...+......... +...
T Consensus 1 ~~~~~~~~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~~~k~~~~~~~~~~~~~~~~~~~k-----~~~~------- 68 (240)
T KOG1946|consen 1 MDSLSWEYLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGTAQKSLLAKAIDESSDEDSALPVK-----GSKK------- 68 (240)
T ss_pred CcchhhhhhhhHHHhcccccccCCHHHHHHHhccccCCCCcchhhhhhhhhhcccccccccccc-----cccc-------
Confidence 5677889999999999999999999999999999999999999999888886655432110000 0000
Q ss_pred hhhhccCCCCCCCCcccccCCCCCCCCCCCChhhhhhcCCchhhhhhccccccccCCCCCcccccCCHHHHhhhCCCccc
Q 019644 81 QMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELA 160 (338)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~g~~~~~~lSp~La~~lG~~~~s 160 (338)
. + .+. .. .. ..+..... +.....+.++.++|+++.|.|||.|+.|+|.+++|
T Consensus 69 k--~-~~~----~~-------~~------------~~~~~~~~--~~~~~~~~~~~~~g~~kl~~ls~~L~~~~G~~~ls 120 (240)
T KOG1946|consen 69 K--K-RGS----KT-------RS------------RKPKSLES--SGEKNKKKKKASWGSTKLIPLSPSLARFVGTSELS 120 (240)
T ss_pred c--c-ccc----cc-------cc------------ccCccccc--ccccchhccccCcCcccccccCHHHHhhccccccc
Confidence 0 0 000 00 00 00000000 00000111125689999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCCCCCCCC
Q 019644 161 RTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDD 221 (338)
Q Consensus 161 R~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~p~~p~~ 221 (338)
|++|++.||+|||+||||||.|||.|+||++|+.|||..+|+||+|+++|.+||++...+.
T Consensus 121 R~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H~~~~~d~~ 181 (240)
T KOG1946|consen 121 RTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKHFLKNQDMV 181 (240)
T ss_pred HHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHhccCccccc
Confidence 9999999999999999999999999999999999999999999999999999998776654
No 2
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.92 E-value=1.9e-25 Score=206.49 Aligned_cols=192 Identities=23% Similarity=0.382 Sum_probs=128.8
Q ss_pred HHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHhhhhhcccCCCCCCcccccccCchhhhhhccC
Q 019644 8 IARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQQEEDDGEDDQMAKVKS 87 (338)
Q Consensus 8 ~~~i~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK~~I~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (338)
..++..+|...+..+++.+.|++.+...++++|..+.+++++.+...+.+.....-.. -..++ +...
T Consensus 8 ~~~~~~~~~~~e~~~~~ek~v~~~~~~~~~~~l~~r~k~~~~~~~~~~~s~~~~~~~~----~~~k~------~~~r--- 74 (237)
T COG5531 8 GTMNDSWLQLDERDTNNEKDVGKLLFSEWTVRLEGRFKDNNDLIRDKFDSLAEEPRVL----RKEKY------NITR--- 74 (237)
T ss_pred ccccceeeecccccccChhhcccccchhhheehhhhhhhccchhhhhhhhhcccchhh----hhhhh------ccCc---
Confidence 3456778899999999999999999999999999999999998877776543211000 00000 0000
Q ss_pred CCCCCCCcccccCCCCCCCCCCCChhhhhhcCCchhhhhhccccccccCCCCCcccccCCHHHHhhhCCCcccHHHHHHH
Q 019644 88 DETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVVKQ 167 (338)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~g~~~~~~lSp~La~~lG~~~~sR~~vvk~ 167 (338)
...+.....++ .+.+....-+.+.+....+...+++..+.-..++.+...|.|||.||.|||..++||++||+.
T Consensus 75 -----~~~~~~~~~~~-~~~~~~s~k~~~n~~te~k~~~~~k~~~~~~~~~~~~~~~~lS~~La~ilG~~~~tr~~~v~~ 148 (237)
T COG5531 75 -----KTTGKNDLPKE-EDSSLPSSKETENGDTEGKETDKKKKSSTISKNSPSGEKVKLSPKLAAILGLEPGTRPEAVKK 148 (237)
T ss_pred -----ccccccccccc-cccccCcchhhhcCccccccccccccccccccccCCCCceecCHHHHHHhCCCCCCccHHHHH
Confidence 00000000000 000000000000110000011111111111335677889999999999999999999999999
Q ss_pred HHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCCCCC
Q 019644 168 LWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLD 218 (338)
Q Consensus 168 lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~p~~ 218 (338)
||+||+.||||||+|||.|+||++|+.|||.+.+.||+|.+.|.+|+.+++
T Consensus 149 lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl~~~~ 199 (237)
T COG5531 149 LWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPLSPHLIKYT 199 (237)
T ss_pred HHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhcccccceecCc
Confidence 999999999999999999999999999999889999999999999998854
No 3
>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=2.8e-25 Score=173.34 Aligned_cols=76 Identities=57% Similarity=0.944 Sum_probs=71.0
Q ss_pred CCCCccccHHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhcccC
Q 019644 259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHFL 336 (338)
Q Consensus 259 ~~~~~~lS~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~~ 336 (338)
|+++|.||++|++|+|.. ++||++|+++||+||++||||||+|++.|+||+.|+.|||+++|.+++|+++|++||+
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 568899999999999987 7999999999999999999999999999999999999999999999999999999984
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=2e-25 Score=174.08 Aligned_cols=75 Identities=53% Similarity=1.027 Sum_probs=70.8
Q ss_pred CcccccCCHHHHhhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccC
Q 019644 140 FSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHI 214 (338)
Q Consensus 140 ~~~~~~lSp~La~~lG~~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl 214 (338)
|+++|.|||+|++|+|..++||++|++.||+||++||||||+|++.|+||+.|+.|||.++|+|++|+++|++||
T Consensus 1 ~~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl 75 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHL 75 (76)
T ss_dssp -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHH
T ss_pred CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhc
Confidence 678899999999999999999999999999999999999999999999999999999999999999999999997
No 5
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.90 E-value=3.5e-24 Score=199.42 Aligned_cols=82 Identities=49% Similarity=0.842 Sum_probs=78.7
Q ss_pred CCCCCCCCccccHHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhcc
Q 019644 255 GKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVH 334 (338)
Q Consensus 255 ~~~g~~~~~~lS~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H 334 (338)
.++|+++++.||+.|+.|+|.. ++||.+|+++||+|||+||||||.||+.|+||++|+.|||..+|+||+|++||.+|
T Consensus 96 ~~~g~~kl~~ls~~L~~~~G~~--~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H 173 (240)
T KOG1946|consen 96 ASWGSTKLIPLSPSLARFVGTS--ELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKH 173 (240)
T ss_pred cCcCcccccccCHHHHhhcccc--cccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHh
Confidence 4589999999999999999976 99999999999999999999999999999999999999999999999999999999
Q ss_pred cCCC
Q 019644 335 FLKT 338 (338)
Q Consensus 335 ~~k~ 338 (338)
|+++
T Consensus 174 ~~~~ 177 (240)
T KOG1946|consen 174 FLKN 177 (240)
T ss_pred ccCc
Confidence 9874
No 6
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.90 E-value=6e-24 Score=166.22 Aligned_cols=76 Identities=47% Similarity=0.966 Sum_probs=73.9
Q ss_pred cccccCCHHHHhhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCCC
Q 019644 141 SKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWP 216 (338)
Q Consensus 141 ~~~~~lSp~La~~lG~~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~p 216 (338)
+++|.|||+|++|+|..++||++|+++||+|||.||||||+|++.|+||+.|+.+||++++.|++|+++|++||.|
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 TKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999999975
No 7
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.89 E-value=1.4e-23 Score=164.15 Aligned_cols=76 Identities=46% Similarity=0.872 Sum_probs=73.4
Q ss_pred CCCccccHHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhcccCC
Q 019644 260 LAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHFLK 337 (338)
Q Consensus 260 ~~~~~lS~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~~k 337 (338)
+++|.+|++|+.|+|.. ++||++|+++||+||+.||||||.|++.|+||+.|+.|||+++|.|++|+++|++||.+
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 TKKVTLSPELAKVLGAP--EMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCcccCCHHHHHHhCCC--cCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence 57899999999999976 99999999999999999999999999999999999999999999999999999999975
No 8
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.80 E-value=2.5e-20 Score=172.55 Aligned_cols=80 Identities=40% Similarity=0.678 Sum_probs=77.1
Q ss_pred CCCCCCCccccHHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 256 KSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 256 ~~g~~~~~~lS~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
++.+..+|.+|+.||.|||.. ++||++||+.||+||+.||||||.|||+|+||++|+.|||.+.+.||+|+++|.+|+
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 566788999999999999988 999999999999999999999999999999999999999999999999999999999
Q ss_pred CC
Q 019644 336 LK 337 (338)
Q Consensus 336 ~k 337 (338)
++
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=99.78 E-value=1.8e-19 Score=196.74 Aligned_cols=77 Identities=38% Similarity=0.673 Sum_probs=74.9
Q ss_pred CCcccccCCHHHHhhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 139 GFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 139 g~~~~~~lSp~La~~lG~~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
.|+..+.|||+||+|||..++||++||++||+|||.||||||.|+|.|+||++|+.|||+++|.||+|+++|++||.
T Consensus 911 ~~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 911 PPAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS 987 (987)
T ss_pred ccccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence 48889999999999999999999999999999999999999999999999999999999999999999999999984
No 10
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.74 E-value=1.6e-18 Score=189.38 Aligned_cols=77 Identities=40% Similarity=0.646 Sum_probs=74.1
Q ss_pred CCCCCccccHHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhcccC
Q 019644 258 GFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHFL 336 (338)
Q Consensus 258 g~~~~~~lS~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~~ 336 (338)
.|..++.||++|+.|||.+ ++||++|+++||+|||.|+||||.|+|.|+||++|+.|||+++|.||+|+++|++||.
T Consensus 911 ~~~~~~~ls~~La~~lg~~--~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 911 PPAAGLKPSAALAAVIGAE--PVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS 987 (987)
T ss_pred ccccccCCCHHHHHHhCCC--cCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence 3778999999999999987 8999999999999999999999999999999999999999999999999999999984
No 11
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.68 E-value=2.4e-17 Score=161.79 Aligned_cols=82 Identities=32% Similarity=0.614 Sum_probs=79.2
Q ss_pred ccccCCHHHHhhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCCCCCCCC
Q 019644 142 KLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDD 221 (338)
Q Consensus 142 ~~~~lSp~La~~lG~~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~p~~p~~ 221 (338)
..|+|||.||.+||+.+.||+.||.+||+||+.|+||||.++.+|+||..|+.+||++++.|.+|+.+|++||.|++||.
T Consensus 207 ~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~dPIv 286 (420)
T KOG2570|consen 207 EEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPDPIV 286 (420)
T ss_pred cccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCCCee
Confidence 44789999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cc
Q 019644 222 VI 223 (338)
Q Consensus 222 ~~ 223 (338)
..
T Consensus 287 i~ 288 (420)
T KOG2570|consen 287 ID 288 (420)
T ss_pred ec
Confidence 64
No 12
>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=99.56 E-value=6.1e-15 Score=107.80 Aligned_cols=54 Identities=46% Similarity=0.762 Sum_probs=45.7
Q ss_pred CHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHh
Q 019644 3 SDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQ 56 (338)
Q Consensus 3 sd~ei~~~i~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK~~I~~~I~~~l~ 56 (338)
||++|...|++||+++||+++|.|+||++||++||+||+++|+||+++|+.+|.
T Consensus 1 td~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~~K~~I~~~I~~~l~ 54 (54)
T PF08766_consen 1 TDEEIREAIREILREADLDTVTKKQVREQLEERFGVDLSSRKKFIKELIDEFLS 54 (54)
T ss_dssp -HHHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhC
Confidence 799999999999999999999999999999999999999999999999999874
No 13
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.53 E-value=7.8e-15 Score=144.26 Aligned_cols=77 Identities=32% Similarity=0.556 Sum_probs=73.5
Q ss_pred CCCccccHHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhcccCCC
Q 019644 260 LAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHFLKT 338 (338)
Q Consensus 260 ~~~~~lS~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~~k~ 338 (338)
+..|++||.||.+||+. .-||++||..||.||+.|+||||.++.+|+||..|+.+||++++.|..|+.+|++||.+|
T Consensus 206 P~~fklsp~La~lLGi~--t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~ 282 (420)
T KOG2570|consen 206 PEEFKLSPRLANLLGIH--TGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPP 282 (420)
T ss_pred CcccccCHHHHHHhhhc--cCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCC
Confidence 34588999999999998 889999999999999999999999999999999999999999999999999999999875
No 14
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.31 E-value=1.1e-12 Score=142.27 Aligned_cols=77 Identities=35% Similarity=0.569 Sum_probs=72.8
Q ss_pred CCCCccccHHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhcccCC
Q 019644 259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHFLK 337 (338)
Q Consensus 259 ~~~~~~lS~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~~k 337 (338)
...+|.+|+.|+.|+|.. +++|.++++.||+||+.|+||||.|++.|+||++|+.+||++.+.||.|+++|++||.|
T Consensus 784 ~~~~~~~S~~La~~~g~~--~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~~ 860 (860)
T PRK06319 784 AGPLYTPSPALAAMIGAE--PVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLIK 860 (860)
T ss_pred cccccccccccccccCcC--ccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhcC
Confidence 345688999999999977 89999999999999999999999999999999999999999999999999999999975
No 15
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.31 E-value=1.3e-12 Score=141.71 Aligned_cols=74 Identities=41% Similarity=0.759 Sum_probs=70.9
Q ss_pred ccccCCHHHHhhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 142 KLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 142 ~~~~lSp~La~~lG~~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
..|.+|+.|+.++|...++|+++++.||+||+.|+||||+|+|.|+||++|+++||++++.||.|+++|+.||.
T Consensus 786 ~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~ 859 (860)
T PRK06319 786 PLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLI 859 (860)
T ss_pred cccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhc
Confidence 34669999999999999999999999999999999999999999999999999999999999999999999984
No 16
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=98.79 E-value=7.5e-09 Score=103.68 Aligned_cols=60 Identities=28% Similarity=0.447 Sum_probs=58.0
Q ss_pred CCCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHhhhhh
Q 019644 1 MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60 (338)
Q Consensus 1 ~~sd~ei~~~i~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK~~I~~~I~~~l~~~~~ 60 (338)
.|||++|...|..||..+||+++|.+.|.++|.++|++||++||.||.++|..+|..+.+
T Consensus 519 ePTdeelk~~V~kILk~vdfntaTm~dIlKkl~~~f~~dLt~rK~~IK~~Ike~I~~~~d 578 (594)
T KOG2266|consen 519 EPTDEELKEVVKKILKEVDFNTATMKDILKKLYAKFPIDLTHRKDFIKDTIKELINKMAD 578 (594)
T ss_pred CCcHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHhcc
Confidence 499999999999999999999999999999999999999999999999999999998865
No 17
>PRK05350 acyl carrier protein; Provisional
Probab=75.62 E-value=2.6 Score=32.73 Aligned_cols=53 Identities=19% Similarity=0.303 Sum_probs=44.7
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 280 LPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 280 ~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
|+|.++...|+++|.+. +.- +...|.+|..|..-+|.||+.+.+|--.|..+|
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 421 224799999998888999999999988888776
No 18
>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=74.13 E-value=4.8 Score=33.50 Aligned_cols=46 Identities=30% Similarity=0.476 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHH
Q 019644 2 VSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQV 51 (338)
Q Consensus 2 ~sd~ei~~~i~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK~~I~~~I 51 (338)
|||++|-..|..|.+..++ |...++++|+. .|+++...+..|+..|
T Consensus 67 vsd~evd~~i~~ia~~n~l---s~~ql~~~L~~-~G~s~~~~r~~ir~~i 112 (118)
T PF09312_consen 67 VSDEEVDEAIANIAKQNNL---SVEQLRQQLEQ-QGISYEEYREQIRKQI 112 (118)
T ss_dssp --HHHHHHHHHHHHHHTT-----HHHHHHHCHH-CT--HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHcCC---CHHHHHHHHHH-cCCCHHHHHHHHHHHH
Confidence 7999999999999998877 67889999986 6999999999998775
No 19
>PRK05828 acyl carrier protein; Validated
Probab=70.83 E-value=6.1 Score=31.32 Aligned_cols=53 Identities=15% Similarity=0.322 Sum_probs=42.6
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 280 LPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 280 ~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
|+|.+|..+|-+.|.+.++.= +-.-|.+|..|.. +|-||+.+.+|--.|..+|
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 789999999999998855432 2235678889977 9999999999988887766
No 20
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=70.81 E-value=7.2 Score=40.19 Aligned_cols=61 Identities=18% Similarity=0.243 Sum_probs=46.5
Q ss_pred CcccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCC---------CccChhhHHHHHhccCCCC
Q 019644 157 TELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGV---------DTINMFQMNKALSKHIWPL 217 (338)
Q Consensus 157 ~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~---------~~~~~~~m~k~L~~Hl~p~ 217 (338)
...+-.+|...+..||..|||-|+.||..|+.|+-|-..... ..+.--.+...+...++|-
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 568889999999999999999999999998888887755432 2344446666666666553
No 21
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=67.92 E-value=6.3 Score=40.61 Aligned_cols=45 Identities=22% Similarity=0.386 Sum_probs=36.4
Q ss_pred hCCC-CCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhh
Q 019644 273 LGTG-ESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELF 317 (338)
Q Consensus 273 lG~~-~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf 317 (338)
+|.. .+-.+-++|...+..||..|||-|+.||..|+.|.-|-...
T Consensus 374 vg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~ 419 (560)
T KOG2522|consen 374 VGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMV 419 (560)
T ss_pred cCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHH
Confidence 3654 25679999999999999999999999999877776655444
No 22
>PRK05350 acyl carrier protein; Provisional
Probab=66.17 E-value=5.4 Score=30.95 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=46.2
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 159 ~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
|+|.+|...|+++|.+. +.- +...|.+|..|..-+|-|++.+-+|.-.|..+|.
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~--~~~~i~~d~~l~~dlg~DSld~veli~~lE~~fg 55 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEI--DPEDITPEANLYEDLDLDSIDAVDLVVHLQKLTG 55 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCC--CHHHCCCCccchhhcCCCHHHHHHHHHHHHHHHC
Confidence 78999999999999987 421 2247999999988889999999999999999884
No 23
>CHL00124 acpP acyl carrier protein; Validated
Probab=65.02 E-value=5.9 Score=30.48 Aligned_cols=53 Identities=9% Similarity=0.246 Sum_probs=43.2
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 280 LPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 280 ~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
|+|.+|...|-++|.+.-=.+| ..|.+|..|..-+|-||+.+.+|...|...|
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 6889999999999988743343 3599999999999999999988888777655
No 24
>PRK12449 acyl carrier protein; Provisional
Probab=62.71 E-value=11 Score=28.73 Aligned_cols=53 Identities=17% Similarity=0.236 Sum_probs=42.1
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 280 LPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 280 ~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
|+|.+|..+|-+++.+.-=.++ ..|.+|..|..-+|.|++.+.+|...|...|
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 6788999999999887443333 2589999999999999999988887776554
No 25
>PRK12449 acyl carrier protein; Provisional
Probab=55.07 E-value=18 Score=27.56 Aligned_cols=54 Identities=17% Similarity=0.264 Sum_probs=44.9
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 159 ~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
|+|.+|..+|-+++.+.--.++. .|.+|..|..-+|.|++.+.+|.-.|...|.
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~~---~i~~~~~l~~dlg~DSl~~~~li~~lE~~f~ 54 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLSL---AITEQTHLKDDLAVDSIELVEFIINVEDEFH 54 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCcc---ccCCCCcHHHHcCCcHHHHHHHHHHHHHHhC
Confidence 57889999999999875533433 5999999999999999999999999988764
No 26
>PRK05828 acyl carrier protein; Validated
Probab=55.06 E-value=17 Score=28.72 Aligned_cols=54 Identities=13% Similarity=0.285 Sum_probs=43.9
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 159 ~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
|+|.+|..+|-..|.+.++. -+-..|.+|..|.. +|-|++.+.+|.-.|..+|.
T Consensus 1 m~~~eI~~~i~~ii~e~~~~--~~~d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f~ 54 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFA--VTLDESNINKPYRE-LKIDSLDMFSIIVSLESEFN 54 (84)
T ss_pred CCHHHHHHHHHHHHHHhccC--CCcccccCCCCHHh-cCCCHHHHHHHHHHHHHHHC
Confidence 68999999999999875542 12245678888876 99999999999999999884
No 27
>PF13565 HTH_32: Homeodomain-like domain
Probab=54.20 E-value=29 Score=25.92 Aligned_cols=35 Identities=23% Similarity=0.413 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCC
Q 019644 4 DSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDL 40 (338)
Q Consensus 4 d~ei~~~i~~IL~~aDl~~vT~k~VR~~Le~~~gvdL 40 (338)
++++...|.+++..-- ..|...|...|++.||+.+
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 4677677777776443 7899999999999999987
No 28
>CHL00124 acpP acyl carrier protein; Validated
Probab=51.58 E-value=13 Score=28.47 Aligned_cols=54 Identities=9% Similarity=0.281 Sum_probs=45.4
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 159 ~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
|+|.+|...|-++|.+.-=.+|. .|.+|..|...+|-|++.+.+|.-.|...|.
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~~---~i~~d~~l~~dlg~DSl~~~eli~~le~~f~ 54 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEKS---EVTLDANFTRDLGADSLDVVELVMAIEEKFD 54 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCHH---HCCCCcchhhhcCCcHHHHHHHHHHHHHHHC
Confidence 67899999999999887433443 5999999999999999999999999988774
No 29
>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=50.11 E-value=68 Score=23.96 Aligned_cols=41 Identities=15% Similarity=0.258 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhhCCCCCccHHHHHHHHHH-HhCC-CCchhhH
Q 019644 5 SELIARLQEFLKNSDLNTTTTGIVRRQLEK-DFGV-DLTDKKI 45 (338)
Q Consensus 5 ~ei~~~i~~IL~~aDl~~vT~k~VR~~Le~-~~gv-dLs~kK~ 45 (338)
+++...|++.|=.||...-++..|...|.+ ..+. .+..+..
T Consensus 24 ~~~l~ele~~Li~aDVg~~~a~~i~~~ik~~~~~~~~~~~~~~ 66 (75)
T PF02881_consen 24 EEFLEELEEALIEADVGVEVAEKIIENIKKKLIKKKGINPREE 66 (75)
T ss_dssp HHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHCTTSSHHHHH
T ss_pred HHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhcccCCCcHHH
Confidence 567889999999999999999999999999 7763 3444443
No 30
>PTZ00171 acyl carrier protein; Provisional
Probab=45.61 E-value=27 Score=30.72 Aligned_cols=54 Identities=17% Similarity=0.266 Sum_probs=45.5
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 279 ALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 279 ~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
.|++.+|...|+++|.+.--.++ ..|.+|..+..-+|-|++.+.+|--.|..+|
T Consensus 65 ~~~~~~v~~~l~eiiae~l~vd~---~~I~~ds~~~~dLg~DSLd~veLv~~LEdeF 118 (148)
T PTZ00171 65 LLSKEDVLTRVKKVVKNFEKVDA---SKITPESNFVKDLGADSLDVVELLIAIEQEF 118 (148)
T ss_pred ccCHHHHHHHHHHHHHHHhCCCH---hhCCCCcchhhhcCCCHHHHHHHHHHHHHHH
Confidence 78999999999999998753343 3588999999999999999998888887765
No 31
>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=42.29 E-value=82 Score=24.07 Aligned_cols=43 Identities=9% Similarity=0.169 Sum_probs=33.5
Q ss_pred HHhhCCCCCccHHHHHHHHHHHhCCCCch--hhHHHHHHHHHHHh
Q 019644 14 FLKNSDLNTTTTGIVRRQLEKDFGVDLTD--KKIFIREQVDLFLQ 56 (338)
Q Consensus 14 IL~~aDl~~vT~k~VR~~Le~~~gvdLs~--kK~~I~~~I~~~l~ 56 (338)
|-.-.|..-.|...|.+-|++.|++++.. .+.+++..+...+.
T Consensus 13 I~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~ 57 (77)
T PF00538_consen 13 IKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVE 57 (77)
T ss_dssp HHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHH
T ss_pred HHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHH
Confidence 33446778899999999999999998876 67777776666554
No 32
>PTZ00171 acyl carrier protein; Provisional
Probab=38.19 E-value=37 Score=29.83 Aligned_cols=59 Identities=12% Similarity=0.225 Sum_probs=50.2
Q ss_pred hCCCcccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 154 IGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 154 lG~~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
-|...+++.+|...|+++|.+.--.++. .|.+|..+..-+|-|++.+-+|.-.|..+|.
T Consensus 61 ~~~~~~~~~~v~~~l~eiiae~l~vd~~---~I~~ds~~~~dLg~DSLd~veLv~~LEdeFg 119 (148)
T PTZ00171 61 SKQYLLSKEDVLTRVKKVVKNFEKVDAS---KITPESNFVKDLGADSLDVVELLIAIEQEFN 119 (148)
T ss_pred ccccccCHHHHHHHHHHHHHHHhCCCHh---hCCCCcchhhhcCCCHHHHHHHHHHHHHHHC
Confidence 3556789999999999999988534443 6889999999999999999999999999884
No 33
>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=35.76 E-value=79 Score=22.23 Aligned_cols=31 Identities=16% Similarity=0.325 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhCCCCchhh-HHHHHHHHHHHh
Q 019644 26 GIVRRQLEKDFGVDLTDKK-IFIREQVDLFLQ 56 (338)
Q Consensus 26 k~VR~~Le~~~gvdLs~kK-~~I~~~I~~~l~ 56 (338)
..++..|.+.+|+||++.| ..|..-|...+.
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 4688999999999999977 666555555554
No 34
>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=35.40 E-value=70 Score=22.85 Aligned_cols=39 Identities=21% Similarity=0.328 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhh-------------CCCCCccHHHHHHHHHHHhCCCCchh
Q 019644 5 SELIARLQEFLKN-------------SDLNTTTTGIVRRQLEKDFGVDLTDK 43 (338)
Q Consensus 5 ~ei~~~i~~IL~~-------------aDl~~vT~k~VR~~Le~~~gvdLs~k 43 (338)
++|+..+.++|.. -.++++..-.++..|++.||+.++..
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 4567777777752 22556666789999999999988865
No 35
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=33.47 E-value=55 Score=24.20 Aligned_cols=49 Identities=31% Similarity=0.553 Sum_probs=33.1
Q ss_pred CCccccH-HHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccc-hHHHh
Q 019644 261 APLQLSD-ALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICD-EKLKE 315 (338)
Q Consensus 261 ~~~~lS~-~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD-~kLk~ 315 (338)
-++.+|. +||.++|+ ||..|. ++....+..++-+-..+.+++.| +.|+.
T Consensus 25 ~~~~lt~~~iA~~~g~-----sr~tv~-r~l~~l~~~g~I~~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 25 IPLPLTQEEIADMLGV-----SRETVS-RILKRLKDEGIIEVKRGKIIILDPERLEE 75 (76)
T ss_dssp EEEESSHHHHHHHHTS-----CHHHHH-HHHHHHHHTTSEEEETTEEEESSHHHHHH
T ss_pred EEecCCHHHHHHHHCC-----CHHHHH-HHHHHHHHCCCEEEcCCEEEECCHHHHhc
Confidence 3455554 89999994 566644 45555666777777788888888 45543
No 36
>smart00526 H15 Domain in histone families 1 and 5.
Probab=31.61 E-value=1.7e+02 Score=21.54 Aligned_cols=44 Identities=5% Similarity=0.171 Sum_probs=30.8
Q ss_pred HHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHH
Q 019644 12 QEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFL 55 (338)
Q Consensus 12 ~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK~~I~~~I~~~l 55 (338)
++|..-.|....|...|++-+++.|+++-...+.+++..+...+
T Consensus 13 eAI~~l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v 56 (66)
T smart00526 13 EAISALKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLV 56 (66)
T ss_pred HHHHHcCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 34444567788899999999999999875544556555554444
No 37
>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=31.35 E-value=60 Score=30.94 Aligned_cols=57 Identities=21% Similarity=0.416 Sum_probs=43.7
Q ss_pred HHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcC--CccchhcHHHHHhcccC
Q 019644 268 ALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDV--DTFNGFTVTKLLVVHFL 336 (338)
Q Consensus 268 ~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~--d~i~~~~l~klL~~H~~ 336 (338)
+||++|-..+.++.---+|.+||.|.-..+|-+|.|- ||. ..-+..+|-++|..+|+
T Consensus 5 ~LA~wlt~~~Np~faRv~VNRvW~~~fGrGlV~p~dD------------~g~~~~~PshPeLLd~La~~F~ 63 (266)
T PF07587_consen 5 ALADWLTSPDNPLFARVIVNRVWQHLFGRGLVEPVDD------------FGPQGNPPSHPELLDWLAAEFV 63 (266)
T ss_pred HHHHHhcCCCCcchHHHHHHHHHHHHcCCcCcCCHhh------------ccCCCCCCCCHHHHHHHHHHHH
Confidence 6889986666788888899999999999999998763 442 34556677777777664
No 38
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=31.28 E-value=36 Score=26.59 Aligned_cols=21 Identities=38% Similarity=0.779 Sum_probs=17.4
Q ss_pred HHHHHHHHHHhCCCCchhhHH
Q 019644 26 GIVRRQLEKDFGVDLTDKKIF 46 (338)
Q Consensus 26 k~VR~~Le~~~gvdLs~kK~~ 46 (338)
..+|..||..||+||+.=+--
T Consensus 4 ~~~r~~~e~~~G~dl~~Vrvh 24 (79)
T PF13699_consen 4 ESIRSRLERAFGADLSDVRVH 24 (79)
T ss_pred HHHHHHHHHHhCCCccceEEE
Confidence 368999999999999985543
No 39
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=29.24 E-value=18 Score=25.61 Aligned_cols=38 Identities=26% Similarity=0.420 Sum_probs=23.4
Q ss_pred HHHhhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCCcc
Q 019644 149 QLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNI 186 (338)
Q Consensus 149 ~La~~lG~~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I 186 (338)
+||.++|.+..+-+.+++.|-+.==-..-++|.|+|.|
T Consensus 22 ~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R~v 59 (59)
T PF01047_consen 22 ELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDRRQV 59 (59)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTETTSE
T ss_pred HHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCCcC
Confidence 89999998777777777766542111223567777654
No 40
>PRK07117 acyl carrier protein; Validated
Probab=26.96 E-value=68 Score=24.98 Aligned_cols=51 Identities=8% Similarity=0.184 Sum_probs=38.7
Q ss_pred CCHHHHHHHHHHHHhhcC-CCCCCCCCccccchHHHhhhcCCccchhcHHHHHhcc
Q 019644 280 LPRSDVIKRMWDYIKEKN-LQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVH 334 (338)
Q Consensus 280 ~sr~~v~k~lW~YIk~n~-Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H 334 (338)
|++.+|..+|-+-|.+.- =-+ ...|..|..|+. ||.+|+.+.++-..|...
T Consensus 1 M~~~ei~~~v~~ii~e~~p~i~---~~~I~~~~~l~D-Lg~DSlD~veiv~~led~ 52 (79)
T PRK07117 1 MDKQRIFDILVRHIREVLPDLD---QHQFQPEDSLVD-LGANSMDRAEIVIMTLES 52 (79)
T ss_pred CCHHHHHHHHHHHHHHHcCCCC---HHHCCCCCChhh-cCCChHHHHHHHHHHHHH
Confidence 678888888888887764 123 357889999998 999999998877665543
No 41
>PRK07117 acyl carrier protein; Validated
Probab=26.49 E-value=67 Score=25.00 Aligned_cols=53 Identities=13% Similarity=0.173 Sum_probs=42.7
Q ss_pred ccHHHHHHHHHHHHhhcCC-CCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 159 LARTEVVKQLWAYIREKDL-QDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 159 ~sR~~vvk~lW~YIk~~~L-qdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
|+|.+|..+|-+.|.+.-- -+| ..|..|..|+. +|.+++.+.++.-.|...|.
T Consensus 1 M~~~ei~~~v~~ii~e~~p~i~~---~~I~~~~~l~D-Lg~DSlD~veiv~~led~f~ 54 (79)
T PRK07117 1 MDKQRIFDILVRHIREVLPDLDQ---HQFQPEDSLVD-LGANSMDRAEIVIMTLESLS 54 (79)
T ss_pred CCHHHHHHHHHHHHHHHcCCCCH---HHCCCCCChhh-cCCChHHHHHHHHHHHHHHC
Confidence 5788888888888888752 344 47889999987 99999999999888877663
No 42
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=26.39 E-value=88 Score=27.05 Aligned_cols=48 Identities=27% Similarity=0.399 Sum_probs=33.4
Q ss_pred cccc-HHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccc-hHHHhh
Q 019644 263 LQLS-DALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICD-EKLKEL 316 (338)
Q Consensus 263 ~~lS-~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD-~kLk~l 316 (338)
++++ .+||.++|+. |. .|.++....+..++-.-..++++++| ++|+..
T Consensus 142 ~~~t~~~iA~~lG~t-----re-tvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~ 191 (193)
T TIGR03697 142 LRLSHQAIAEAIGST-----RV-TITRLLGDLRKKKLISIHKKKITVHDPIALGQR 191 (193)
T ss_pred CCCCHHHHHHHhCCc-----HH-HHHHHHHHHHHCCCEEecCCEEEEeCHHHHHHh
Confidence 4454 4899999943 44 44455566778888777788899998 556554
No 43
>PRK07639 acyl carrier protein; Provisional
Probab=26.25 E-value=79 Score=24.88 Aligned_cols=54 Identities=11% Similarity=0.131 Sum_probs=40.9
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 280 LPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 280 ~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
|+|.+|..+|-+.|.+.= ..+. -..|..|..|..=+|-||+.+.++--.|..+|
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 688888888888887753 2211 13677899998888999999998888877665
No 44
>PF09357 RteC: RteC protein; InterPro: IPR018534 Human colonic Bacteroides species harbour a family of large conjugative transposons, called tetracycline resistance (Tcr) elements. Activities of these elements are enhanced by pregrowth of bacteria in medium containing tetracycline, indicating that at least some Tcr element genes are regulated by tetracycline. An insertional disruption in the rteC gene abolished self-transfer of the Tcr element to Bacteroides recipients, indicating that the gene was essential for self-transfer [].
Probab=24.91 E-value=3e+02 Score=25.66 Aligned_cols=40 Identities=25% Similarity=0.381 Sum_probs=31.2
Q ss_pred CHHHHHHHHHHHHhhCCC--CCccHHHHHHHHHHHhCCCCch
Q 019644 3 SDSELIARLQEFLKNSDL--NTTTTGIVRRQLEKDFGVDLTD 42 (338)
Q Consensus 3 sd~ei~~~i~~IL~~aDl--~~vT~k~VR~~Le~~~gvdLs~ 42 (338)
|..+|++-|=++-....+ .+++-+.|-..+|..|||+|.+
T Consensus 143 sk~~LiELiYaL~~~g~in~G~~~i~~i~~~fe~~F~i~l~~ 184 (218)
T PF09357_consen 143 SKTDLIELIYALYASGCINNGNADIKEIARFFEKLFNIDLGD 184 (218)
T ss_pred hHHHHHHHHHHHHHcCCcCCCccCHHHHHHHHHHHhCCCcch
Confidence 345666777776666555 6778899999999999999976
No 45
>PF13551 HTH_29: Winged helix-turn helix
Probab=24.80 E-value=1.2e+02 Score=23.73 Aligned_cols=40 Identities=28% Similarity=0.391 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhhCCC---CCccHHHHHHHH-HHHhCCCCchh
Q 019644 4 DSELIARLQEFLKNSDL---NTTTTGIVRRQL-EKDFGVDLTDK 43 (338)
Q Consensus 4 d~ei~~~i~~IL~~aDl---~~vT~k~VR~~L-e~~~gvdLs~k 43 (338)
+++....|.+++..-.. ...|...|+..| ++.+|+++|..
T Consensus 59 ~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ 102 (112)
T PF13551_consen 59 SEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPS 102 (112)
T ss_pred CHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHH
Confidence 35566677777776443 357899999988 99999999873
No 46
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=24.54 E-value=1.1e+02 Score=26.76 Aligned_cols=49 Identities=18% Similarity=0.252 Sum_probs=33.6
Q ss_pred ccc-HHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccc-hHHHhhhc
Q 019644 264 QLS-DALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICD-EKLKELFD 318 (338)
Q Consensus 264 ~lS-~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD-~kLk~lf~ 318 (338)
++| .+||+++|+ ||..|. ++..-.+..++-.-..++++++| ++|+.+.+
T Consensus 149 ~~t~~~iA~~lG~-----tretvs-R~l~~l~~~g~I~~~~~~i~I~d~~~L~~~~~ 199 (202)
T PRK13918 149 YATHDELAAAVGS-----VRETVT-KVIGELSREGYIRSGYGKIQLLDLKGLEELAE 199 (202)
T ss_pred cCCHHHHHHHhCc-----cHHHHH-HHHHHHHHCCCEEcCCCEEEEECHHHHHHHHh
Confidence 344 389999994 454444 44455567777777778898988 57777654
No 47
>PRK05883 acyl carrier protein; Validated
Probab=23.78 E-value=96 Score=24.69 Aligned_cols=54 Identities=13% Similarity=0.090 Sum_probs=43.6
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 279 ALPRSDVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 279 ~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
.++..+|...|-++|.+.==.+| ..|..|..|...+|-||+.+..+--.|..+|
T Consensus 9 ~~~~~~I~~~l~~iia~~l~v~~---~~I~~d~~l~~dlg~DSL~~v~lv~~lE~~f 62 (91)
T PRK05883 9 TSSPSTVSATLLSILRDDLNVDL---TRVTPDARLVDDVGLDSVAFAVGMVAIEERL 62 (91)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCh---hhCCCCCchhhccCCChHHHHHHHHHHHHHH
Confidence 57899999999999987632333 3688999999999999999887777777665
No 48
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=22.72 E-value=1.9e+02 Score=24.02 Aligned_cols=44 Identities=30% Similarity=0.500 Sum_probs=36.0
Q ss_pred CHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHH
Q 019644 3 SDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIRE 49 (338)
Q Consensus 3 sd~ei~~~i~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK~~I~~ 49 (338)
|++++-.+-.......|.+.-. +|+.|...||.||-+-=+.|..
T Consensus 4 t~EeF~aRye~~F~~~~iD~we---~rr~mN~l~~~DlVP~P~ii~a 47 (103)
T cd00923 4 TDEEFDARYETYFNRPDIDGWE---LRRGLNNLFGYDLVPEPKVIEA 47 (103)
T ss_pred cHHHHHHHHHHHhCCcCccHHH---HHHHHHHHhccccCCCcHHHHH
Confidence 7888888888888888877654 9999999999999887665443
No 49
>PRK07639 acyl carrier protein; Provisional
Probab=21.48 E-value=1.1e+02 Score=24.00 Aligned_cols=55 Identities=15% Similarity=0.143 Sum_probs=43.8
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhHhhhhCCCccChhhHHHHHhccCC
Q 019644 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (338)
Q Consensus 159 ~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cDe~Lk~lf~~~~~~~~~m~k~L~~Hl~ 215 (338)
|+|.+|..+|-..|.+.-=-++ -..|..|..|..=+|.+++.+.++.-.|..+|.
T Consensus 1 M~~~ei~~~i~~il~e~l~~~~--~~~i~~d~~l~edL~lDSld~velv~~lE~~fg 55 (86)
T PRK07639 1 MRREALKNAVLKIMEEKLELKN--VTHLEETMRLNEDLYIDSVMMLQLIVYIEMDVK 55 (86)
T ss_pred CCHHHHHHHHHHHHHHHhCCCc--cccCCCCCCcccccCCChHHHHHHHHHHHHHHC
Confidence 5788888898888887642222 136789999988789999999999999998874
No 50
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=20.90 E-value=1.3e+02 Score=25.90 Aligned_cols=49 Identities=27% Similarity=0.295 Sum_probs=34.0
Q ss_pred cccCCH-HHHhhhCCCcccHHHHHHHHHHHHhhcCCCCCCCCCccccc-hhHhhh
Q 019644 143 LCALSP-QLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLRAL 195 (338)
Q Consensus 143 ~~~lSp-~La~~lG~~~~sR~~vvk~lW~YIk~~~Lqdp~~kr~I~cD-e~Lk~l 195 (338)
.+.++- +||.++|.... . |.++..-.+..++-.-..++.+++| +.|++.
T Consensus 141 ~~~~t~~~iA~~lG~tre---t-vsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~ 191 (193)
T TIGR03697 141 DLRLSHQAIAEAIGSTRV---T-ITRLLGDLRKKKLISIHKKKITVHDPIALGQR 191 (193)
T ss_pred cCCCCHHHHHHHhCCcHH---H-HHHHHHHHHHCCCEEecCCEEEEeCHHHHHHh
Confidence 345554 99999995543 3 3344566788888888888999998 555554
No 51
>PF13276 HTH_21: HTH-like domain
Probab=20.84 E-value=1.6e+02 Score=21.00 Aligned_cols=40 Identities=23% Similarity=0.330 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCCchhh
Q 019644 4 DSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKK 44 (338)
Q Consensus 4 d~ei~~~i~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK 44 (338)
|++|...|.+|...+.. +.-...|...|...+|+.++.++
T Consensus 3 ~~~l~~~I~~i~~~~~~-~yG~rri~~~L~~~~~~~v~~kr 42 (60)
T PF13276_consen 3 DEALRELIKEIFKESKP-TYGYRRIWAELRREGGIRVSRKR 42 (60)
T ss_pred hHHHHHHHHHHHHHcCC-CeehhHHHHHHhccCcccccHHH
Confidence 67899999999998866 56678899999999888887765
No 52
>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=20.41 E-value=88 Score=23.49 Aligned_cols=49 Identities=18% Similarity=0.276 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhhcCCCCCCCCCccccchHHHhhhcCCccchhcHHHHHhccc
Q 019644 284 DVIKRMWDYIKEKNLQDPSDKRRIICDEKLKELFDVDTFNGFTVTKLLVVHF 335 (338)
Q Consensus 284 ~v~k~lW~YIk~n~Lqdp~~kr~I~cD~kLk~lf~~d~i~~~~l~klL~~H~ 335 (338)
++...|.++|.+.--.+| ..|.+|..|..-+|-||+.+.+|.-.|..+|
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 566778888877532333 3588899998889999999988888777665
No 53
>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=20.32 E-value=1.3e+02 Score=19.51 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=17.8
Q ss_pred HHHHhhhCCCcccHHHHHHHHHHHHhhcCCC
Q 019644 148 PQLQEFIGVTELARTEVVKQLWAYIREKDLQ 178 (338)
Q Consensus 148 p~La~~lG~~~~sR~~vvk~lW~YIk~~~Lq 178 (338)
.++|+++|++.- .||.|++...+.
T Consensus 4 ~e~a~~lgvs~~-------tl~~~~~~g~~~ 27 (49)
T cd04762 4 KEAAELLGVSPS-------TLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCC
Confidence 477888887644 679999987663
No 54
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=20.17 E-value=1.3e+02 Score=27.26 Aligned_cols=49 Identities=14% Similarity=0.259 Sum_probs=32.8
Q ss_pred cccc-HHHHHHhCCCCCCCCHHHHHHHHHHHHhhcCCCCCCCCCccccc-hHHHhhhc
Q 019644 263 LQLS-DALIKFLGTGESALPRSDVIKRMWDYIKEKNLQDPSDKRRIICD-EKLKELFD 318 (338)
Q Consensus 263 ~~lS-~~La~flG~~~~~~sr~~v~k~lW~YIk~n~Lqdp~~kr~I~cD-~kLk~lf~ 318 (338)
+.++ .+||.+||+ +|..|.+.+ .-.+..++ .-..+.++++| +.|+.+.+
T Consensus 172 i~~t~~~iA~~lG~-----tretvsR~l-~~L~~~gl-~~~~~~i~I~d~~~L~~~~~ 222 (236)
T PRK09392 172 LPYEKRVLASYLGM-----TPENLSRAF-AALASHGV-HVDGSAVTITDPAGLARFAK 222 (236)
T ss_pred eeCCHHHHHHHhCC-----ChhHHHHHH-HHHHhCCe-EeeCCEEEEcCHHHHHHhhc
Confidence 4454 699999995 444444444 44566668 55567788888 78887766
No 55
>PF03511 Fanconi_A: Fanconi anaemia group A protein; InterPro: IPR003516 Fanconi anaemia (FA) [, , ] is a recessive inherited disease characterised by defective DNA repair. FA cells are sensitive to DNA cross-linking agents that cause chromosomal instability and cell death. The disease is manifested clinically by progressive pancytopenia, variable physical anomalies, and predisposition to malignancy []. Four complementation groups have been identified, designated A to D. The FA group A gene (FAA) has been cloned [], but its function remains to be elucidated.
Probab=20.15 E-value=69 Score=24.31 Aligned_cols=19 Identities=21% Similarity=0.329 Sum_probs=15.8
Q ss_pred cChhhHHHHHhccCCCCCC
Q 019644 201 INMFQMNKALSKHIWPLDS 219 (338)
Q Consensus 201 ~~~~~m~k~L~~Hl~p~~p 219 (338)
+-||.++.+|+.|+.|-+.
T Consensus 8 LfFFSLM~LlSs~l~p~~~ 26 (64)
T PF03511_consen 8 LFFFSLMGLLSSYLAPKEG 26 (64)
T ss_pred HHHHHHHHHHHHhcCcccc
Confidence 4589999999999987543
No 56
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=20.15 E-value=3e+02 Score=21.55 Aligned_cols=44 Identities=7% Similarity=0.135 Sum_probs=31.8
Q ss_pred HHHHhhCCCCCccHHHHHHHHHHHhCCCCchhhHHHHHHHHHHH
Q 019644 12 QEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFL 55 (338)
Q Consensus 12 ~~IL~~aDl~~vT~k~VR~~Le~~~gvdLs~kK~~I~~~I~~~l 55 (338)
++|..-.|..-.|...|++-+++.|.++....+.+++..+...+
T Consensus 13 eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v 56 (88)
T cd00073 13 EAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGV 56 (88)
T ss_pred HHHHHcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHH
Confidence 44445567888899999999999999887555565555554444
Done!