Query 017932
Match_columns 363
No_of_seqs 324 out of 1027
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:41:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017932.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017932hhsearch_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 8.1E-32 1.8E-36 254.1 9.8 181 1-191 1-182 (240)
2 COG5531 SWIB-domain-containing 99.9 2.2E-25 4.8E-30 209.3 5.2 182 6-188 6-200 (237)
3 PF02201 SWIB: SWIB/MDM2 domai 99.9 1.8E-25 3.9E-30 177.0 0.8 76 253-328 1-76 (76)
4 PF02201 SWIB: SWIB/MDM2 domai 99.9 1.9E-25 4.2E-30 176.8 0.9 75 109-183 1-75 (76)
5 smart00151 SWIB SWI complex, B 99.9 3.4E-24 7.4E-29 170.1 7.5 76 254-329 2-77 (77)
6 smart00151 SWIB SWI complex, B 99.9 4.2E-24 9.1E-29 169.6 7.7 76 110-185 2-77 (77)
7 KOG1946 RNA polymerase I trans 99.9 7.3E-24 1.6E-28 200.2 7.9 87 249-335 96-182 (240)
8 COG5531 SWIB-domain-containing 99.8 2.7E-21 5.8E-26 181.8 5.1 82 250-331 118-199 (237)
9 PRK14724 DNA topoisomerase III 99.8 1.7E-19 3.7E-24 199.2 8.0 77 108-184 911-987 (987)
10 PRK14724 DNA topoisomerase III 99.8 3.3E-19 7.1E-24 197.0 7.9 77 252-328 911-987 (987)
11 KOG2570 SWI/SNF transcription 99.7 9.8E-19 2.1E-23 174.2 6.1 95 98-192 183-288 (420)
12 KOG2570 SWI/SNF transcription 99.7 1.5E-17 3.2E-22 165.9 5.6 85 252-336 204-288 (420)
13 PF08766 DEK_C: DEK C terminal 99.5 2.4E-14 5.2E-19 106.4 6.0 54 3-56 1-54 (54)
14 PRK06319 DNA topoisomerase I/S 99.3 7.1E-13 1.5E-17 145.5 5.6 73 112-184 787-859 (860)
15 PRK06319 DNA topoisomerase I/S 99.3 7.9E-13 1.7E-17 145.1 5.5 75 254-328 785-859 (860)
16 KOG2266 Chromatin-associated p 98.3 6.7E-07 1.5E-11 91.5 6.2 59 1-59 519-577 (594)
17 PF09312 SurA_N: SurA N-termin 78.0 3.2 7E-05 35.1 4.1 46 2-51 67-112 (118)
18 KOG2522 Filamentous baseplate 74.7 5 0.00011 42.1 5.1 60 271-330 381-449 (560)
19 PRK05350 acyl carrier protein; 74.1 2.9 6.2E-05 33.0 2.6 55 272-329 2-56 (82)
20 KOG2522 Filamentous baseplate 69.3 8.6 0.00019 40.4 5.3 71 119-189 370-452 (560)
21 PRK05828 acyl carrier protein; 60.5 11 0.00025 30.3 3.5 54 272-328 1-54 (84)
22 PRK05350 acyl carrier protein; 60.4 7.7 0.00017 30.6 2.5 54 128-185 2-56 (82)
23 CHL00124 acpP acyl carrier pro 55.3 10 0.00022 29.6 2.4 54 272-328 1-54 (82)
24 PRK12449 acyl carrier protein; 54.6 18 0.00039 28.1 3.7 54 272-328 1-54 (80)
25 PF03705 CheR_N: CheR methyltr 51.5 30 0.00065 24.9 4.3 34 25-58 5-39 (57)
26 PTZ00171 acyl carrier protein; 46.2 22 0.00048 31.8 3.3 60 268-330 62-121 (148)
27 PRK05828 acyl carrier protein; 45.4 29 0.00063 28.0 3.6 54 128-184 1-54 (84)
28 PF13565 HTH_32: Homeodomain-l 45.2 48 0.001 25.1 4.7 35 4-40 32-66 (77)
29 PF00538 Linker_histone: linke 43.2 86 0.0019 24.4 5.9 45 12-56 11-57 (77)
30 CHL00124 acpP acyl carrier pro 43.2 21 0.00046 27.8 2.4 54 128-184 1-54 (82)
31 PRK12449 acyl carrier protein; 42.7 36 0.00078 26.3 3.7 54 128-184 1-54 (80)
32 PTZ00171 acyl carrier protein; 40.4 32 0.00068 30.8 3.4 60 122-184 60-119 (148)
33 smart00526 H15 Domain in histo 33.9 1.7E+02 0.0036 22.0 6.1 46 11-56 12-57 (66)
34 PF00550 PP-binding: Phosphopa 31.7 69 0.0015 23.3 3.5 39 5-43 1-52 (67)
35 PF13699 DUF4157: Domain of un 30.0 38 0.00082 27.0 2.0 23 26-48 4-26 (79)
36 PF02881 SRP54_N: SRP54-type p 29.2 1.8E+02 0.0038 22.1 5.6 44 5-48 24-69 (75)
37 cd00923 Cyt_c_Oxidase_Va Cytoc 27.0 1.2E+02 0.0026 25.8 4.5 47 3-52 4-50 (103)
38 KOG2076 RNA polymerase III tra 25.8 92 0.002 35.5 4.6 77 249-332 125-207 (895)
39 PF03511 Fanconi_A: Fanconi an 23.6 39 0.00084 26.3 0.9 23 313-335 7-29 (64)
40 PF01047 MarR: MarR family; I 23.5 23 0.0005 25.5 -0.4 39 117-155 21-59 (59)
41 cd00073 H15 linker histone 1 a 23.2 2.8E+02 0.006 22.2 5.9 46 11-56 12-57 (88)
42 PRK07117 acyl carrier protein; 22.6 86 0.0019 24.9 2.7 52 272-327 1-53 (79)
43 PRK07117 acyl carrier protein; 22.6 84 0.0018 25.0 2.7 53 128-184 1-54 (79)
No 1
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.97 E-value=8.1e-32 Score=254.14 Aligned_cols=181 Identities=35% Similarity=0.461 Sum_probs=141.0
Q ss_pred CCChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHhhhhhhhhhccccCCchhhcccCc-
Q 017932 1 MVSDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQTLEKEREEIEDDGNGAVEANADD- 79 (363)
Q Consensus 1 mvsd~ei~~~I~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~kK~~I~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~- 79 (363)
|.+...+...++.||...+++++|...||++++..||++++..+..++.+|...+...... +.. ...... ....
T Consensus 1 ~~~~~~~~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~~~k~~~~~~~~~~~~~~~~~-~~k---~~~~k~-~~~~~ 75 (240)
T KOG1946|consen 1 MDSLSWEYLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGTAQKSLLAKAIDESSDEDSAL-PVK---GSKKKK-RGSKT 75 (240)
T ss_pred CcchhhhhhhhHHHhcccccccCCHHHHHHHhccccCCCCcchhhhhhhhhhccccccccc-ccc---cccccc-ccccc
Confidence 6788999999999999999999999999999999999999999999999998877542110 000 000000 0000
Q ss_pred chhhHHhhHHhhhhhccccccccccCCCCCCccccCcHHHHhhhCCCCccHHHHHHHHHHHHHHcCCCCCCCCCcccCCh
Q 017932 80 KEEEEEESESKREKSIKVGRQVKRRGGGGFNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDE 159 (363)
Q Consensus 80 ~~~~~~~~~~~~~~~~k~~~~~k~k~~~g~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe 159 (363)
........+.....+. .+++.++|+++.|.|||.|+.|+|.+++||++||+.||+|||+||||||.|||.|+||+
T Consensus 76 ~~~~~~~~~~~~~~~~-----~~~~~~~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDe 150 (240)
T KOG1946|consen 76 RSRKPKSLESSGEKNK-----KKKKASWGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDE 150 (240)
T ss_pred ccccCcccccccccch-----hccccCcCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHH
Confidence 0000000000000111 12335689999999999999999999999999999999999999999999999999999
Q ss_pred hHhhhhcCCccChhhHHHHHhccCCCCCCCCc
Q 017932 160 SLQALFGVNSIDMFKMNRALSKHIWPLGAEDE 191 (363)
Q Consensus 160 ~Lk~lF~~d~i~~~~m~k~L~~Hl~p~~p~~~ 191 (363)
+|+.|||..+|+||+|+++|.+||++...+..
T Consensus 151 kL~~iF~~k~v~~fem~KLL~~H~~~~~d~~~ 182 (240)
T KOG1946|consen 151 KLKSIFGKKRVGMFEMLKLLTKHFLKNQDMVG 182 (240)
T ss_pred HHHHHhccCccceeeHHHHHHHhccCcccccc
Confidence 99999999999999999999999999888654
No 2
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.91 E-value=2.2e-25 Score=209.30 Aligned_cols=182 Identities=31% Similarity=0.414 Sum_probs=129.2
Q ss_pred HHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHhhhhhhhhhcc--ccCCchhhc---ccCcc
Q 017932 6 DLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQTLEKEREEIE--DDGNGAVEA---NADDK 80 (363)
Q Consensus 6 ei~~~I~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~kK~~I~~~I~~~l~~~~~~~~~~~--~~~~~~~~~---~~~~~ 80 (363)
.+..++..+|+..+..+++.+.|++.+...++++|..+..+++..+...+.+... .+... ...++.... ++...
T Consensus 6 ~~~~~~~~~~~~~e~~~~~ek~v~~~~~~~~~~~l~~r~k~~~~~~~~~~~s~~~-~~~~~~~~k~~~~r~~~~~~~~~~ 84 (237)
T COG5531 6 RYGTMNDSWLQLDERDTNNEKDVGKLLFSEWTVRLEGRFKDNNDLIRDKFDSLAE-EPRVLRKEKYNITRKTTGKNDLPK 84 (237)
T ss_pred ccccccceeeecccccccChhhcccccchhhheehhhhhhhccchhhhhhhhhcc-cchhhhhhhhccCccccccccccc
Confidence 3456788899999999999999999999999999999999999999877665421 11000 000000000 00000
Q ss_pred hhhHHhhHHhh-hh---hccccccccc----cCCCCCCccccCcHHHHhhhCCCCccHHHHHHHHHHHHHHcCCCCCCCC
Q 017932 81 EEEEEESESKR-EK---SIKVGRQVKR----RGGGGFNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNK 152 (363)
Q Consensus 81 ~~~~~~~~~~~-~~---~~k~~~~~k~----k~~~g~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nk 152 (363)
+.+....+.++ +. ..+.+.++++ ..++.+...|.|||.||.|||..++||++||+.||+||+.||||||+|+
T Consensus 85 ~~~~~~~s~k~~~n~~te~k~~~~~k~~~~~~~~~~~~~~~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nk 164 (237)
T COG5531 85 EEDSSLPSSKETENGDTEGKETDKKKKSSTISKNSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNK 164 (237)
T ss_pred ccccccCcchhhhcCccccccccccccccccccccCCCCceecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCcccc
Confidence 00000000000 00 0000111111 1245577889999999999999999999999999999999999999999
Q ss_pred CcccCChhHhhhhcCCccChhhHHHHHhccCCCCCC
Q 017932 153 RKILCDESLQALFGVNSIDMFKMNRALSKHIWPLGA 188 (363)
Q Consensus 153 r~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~p~~p 188 (363)
|+|+||++|+.|||.+.+.||+|++.|++|+.+++-
T Consensus 165 r~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl~~~~~ 200 (237)
T COG5531 165 RLILCDSKLKKVLGSDPIDMFELTKPLSPHLIKYTI 200 (237)
T ss_pred ceecccHHHHHHhCCCchhhhhhhcccccceecCcc
Confidence 999999999999999999999999999999999644
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=1.8e-25 Score=176.97 Aligned_cols=76 Identities=54% Similarity=0.953 Sum_probs=71.4
Q ss_pred CcccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCC
Q 017932 253 FTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (363)
Q Consensus 253 ~~~~~~LS~~La~flG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~ 328 (363)
|+++|.||++|++|+|..++||++|+++||+||++||||||.|++.|+||+.|+.|||+++|+|++|+++|++||.
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 6789999999999999999999999999999999999999999999999999999999999999999999999973
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=1.9e-25 Score=176.78 Aligned_cols=75 Identities=51% Similarity=0.927 Sum_probs=70.7
Q ss_pred CCccccCcHHHHhhhCCCCccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccC
Q 017932 109 FNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHI 183 (363)
Q Consensus 109 ~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl 183 (363)
|+++|.|||+|++++|..++||++|+++||+||++||||||+|++.|+||+.|+.|||+++|+||+|+++|++||
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 577899999999999999999999999999999999999999999999999999999999999999999999997
No 5
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.90 E-value=3.4e-24 Score=170.06 Aligned_cols=76 Identities=49% Similarity=0.936 Sum_probs=74.3
Q ss_pred cccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCCC
Q 017932 254 TKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWP 329 (363)
Q Consensus 254 ~~~~~LS~~La~flG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~p 329 (363)
+++|.||++|+.|+|..++||++|+++||+||+.||||||.|++.|+||+.|+.|||+++|.|++|+++|++||.|
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 6789999999999999999999999999999999999999999999999999999999999999999999999975
No 6
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.90 E-value=4.2e-24 Score=169.56 Aligned_cols=76 Identities=54% Similarity=0.993 Sum_probs=74.0
Q ss_pred CccccCcHHHHhhhCCCCccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCCC
Q 017932 110 NKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIWP 185 (363)
Q Consensus 110 ~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~p 185 (363)
+++|.|||+|++|+|..++||++|+++||+||+.||||||+|++.|+||+.|+.+||++++.|++|+++|++||.|
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
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.89 E-value=7.3e-24 Score=200.23 Aligned_cols=87 Identities=53% Similarity=0.857 Sum_probs=83.7
Q ss_pred CCCCCcccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCC
Q 017932 249 RRGGFTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (363)
Q Consensus 249 ~~~g~~~~~~LS~~La~flG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~ 328 (363)
.++|+++.+.||+.|+.|+|...+||.+|++.||+|||+||||||.|++.|+||++|+.|||...|+||+|++||.+||+
T Consensus 96 ~~~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H~~ 175 (240)
T KOG1946|consen 96 ASWGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKHFL 175 (240)
T ss_pred cCcCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHhcc
Confidence 34799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccch
Q 017932 329 PLDEADA 335 (363)
Q Consensus 329 p~~pi~~ 335 (363)
+......
T Consensus 176 ~~~d~~~ 182 (240)
T KOG1946|consen 176 KNQDMVG 182 (240)
T ss_pred Ccccccc
Confidence 9988764
No 8
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.83 E-value=2.7e-21 Score=181.80 Aligned_cols=82 Identities=38% Similarity=0.701 Sum_probs=78.8
Q ss_pred CCCCcccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCCC
Q 017932 250 RGGFTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWP 329 (363)
Q Consensus 250 ~~g~~~~~~LS~~La~flG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~p 329 (363)
++.+..+|.||+.||.|||..++||++||+.||+||+.||||||.|+|.|+||++|+.|||.+.+.||+|.++|.+|+.+
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 55678999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CC
Q 017932 330 LD 331 (363)
Q Consensus 330 ~~ 331 (363)
.+
T Consensus 198 ~~ 199 (237)
T COG5531 198 YT 199 (237)
T ss_pred Cc
Confidence 54
No 9
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.78 E-value=1.7e-19 Score=199.16 Aligned_cols=77 Identities=42% Similarity=0.652 Sum_probs=74.3
Q ss_pred CCCccccCcHHHHhhhCCCCccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCC
Q 017932 108 GFNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (363)
Q Consensus 108 g~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~ 184 (363)
.+...+.|||+|++|||..++||++||++||+|||.||||||.|+|.|+||++|+.|||+++|+||+|+++|++||.
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 36678999999999999999999999999999999999999999999999999999999999999999999999984
No 10
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.77 E-value=3.3e-19 Score=196.96 Aligned_cols=77 Identities=34% Similarity=0.596 Sum_probs=74.9
Q ss_pred CCcccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCC
Q 017932 252 GFTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (363)
Q Consensus 252 g~~~~~~LS~~La~flG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~ 328 (363)
.|..++.|||+|+.|||..++||++|+++||+|||.||||||.|+|.|+||++|+.|||+++|.||+|+++|++||.
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 47789999999999999999999999999999999999999999999999999999999999999999999999984
No 11
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.75 E-value=9.8e-19 Score=174.21 Aligned_cols=95 Identities=34% Similarity=0.553 Sum_probs=87.1
Q ss_pred cccccccCCCC-----------CCccccCcHHHHhhhCCCCccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhc
Q 017932 98 GRQVKRRGGGG-----------FNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFG 166 (363)
Q Consensus 98 ~~~~k~k~~~g-----------~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~ 166 (363)
|+++||.+.-. .+..|+|||.|+.+||..+.||+.||.+||.||+.|+||||+++.+|+||..|+++||
T Consensus 183 Gf~VKR~Gd~~v~ctIll~l~~~P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~ 262 (420)
T KOG2570|consen 183 GFQVKRPGDRNVRCTILLLLDYQPEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFG 262 (420)
T ss_pred ceeeeccCCCccceEEEEeeccCCcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhc
Confidence 78887765432 2234689999999999999999999999999999999999999999999999999999
Q ss_pred CCccChhhHHHHHhccCCCCCCCCcc
Q 017932 167 VNSIDMFKMNRALSKHIWPLGAEDEN 192 (363)
Q Consensus 167 ~d~i~~~~m~k~L~~Hl~p~~p~~~~ 192 (363)
++++.|..|+.+|++||.|++||.++
T Consensus 263 ~~rl~F~elp~~l~~lL~P~dPIvi~ 288 (420)
T KOG2570|consen 263 VDRLKFPELPQLLNPLLSPPDPIVID 288 (420)
T ss_pred ccccccccchhhhhhccCCCCCeeec
Confidence 99999999999999999999999995
No 12
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.69 E-value=1.5e-17 Score=165.88 Aligned_cols=85 Identities=29% Similarity=0.535 Sum_probs=81.7
Q ss_pred CCcccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCCCCC
Q 017932 252 GFTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWPLD 331 (363)
Q Consensus 252 g~~~~~~LS~~La~flG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~p~~ 331 (363)
+-+..|+|||.||.+||+..-||++||.+||.|||.|+||||.++.+|.||..|+++||++++.|..|+.+|++||.|++
T Consensus 204 ~~P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~d 283 (420)
T KOG2570|consen 204 YQPEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPD 283 (420)
T ss_pred cCCcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCC
Confidence 34556899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchh
Q 017932 332 EADAK 336 (363)
Q Consensus 332 pi~~~ 336 (363)
||.++
T Consensus 284 PIvi~ 288 (420)
T KOG2570|consen 284 PIVID 288 (420)
T ss_pred Ceeec
Confidence 99997
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=99.51 E-value=2.4e-14 Score=106.41 Aligned_cols=54 Identities=52% Similarity=0.781 Sum_probs=45.7
Q ss_pred ChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHh
Q 017932 3 SDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQ 56 (363)
Q Consensus 3 sd~ei~~~I~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~kK~~I~~~I~~~l~ 56 (363)
||++|...|++||+++||+++|.++||++|++.||+||+++|+||+++|+.||.
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 14
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.34 E-value=7.1e-13 Score=145.49 Aligned_cols=73 Identities=42% Similarity=0.732 Sum_probs=70.6
Q ss_pred cccCcHHHHhhhCCCCccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCC
Q 017932 112 LCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (363)
Q Consensus 112 ~~~LSp~La~~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~ 184 (363)
.|.+|+.|+.++|...++|+++++.||+||+.|+||||.|+|.|+||++|+.|||++.+.||.|+++|++||.
T Consensus 787 ~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~ 859 (860)
T PRK06319 787 LYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLI 859 (860)
T ss_pred ccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhc
Confidence 4669999999999999999999999999999999999999999999999999999999999999999999985
No 15
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.34 E-value=7.9e-13 Score=145.12 Aligned_cols=75 Identities=39% Similarity=0.690 Sum_probs=72.1
Q ss_pred cccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCC
Q 017932 254 TKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (363)
Q Consensus 254 ~~~~~LS~~La~flG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~ 328 (363)
..+|.+|+.|+.|+|..+++|+++++.||+||+.|+||||.|++.|+||++|+.+||++.+.||.|+++|++||.
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 345889999999999999999999999999999999999999999999999999999999999999999999985
No 16
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=98.34 E-value=6.7e-07 Score=91.46 Aligned_cols=59 Identities=27% Similarity=0.510 Sum_probs=56.3
Q ss_pred CCChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHhhhh
Q 017932 1 MVSDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQTLE 59 (363)
Q Consensus 1 mvsd~ei~~~I~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~kK~~I~~~I~~~l~~~~ 59 (363)
.|||++|...|..||..+||+++|.+.|-++|-+.|++||+++|.||..+|...|..+.
T Consensus 519 ePTdeelk~~V~kILk~vdfntaTm~dIlKkl~~~f~~dLt~rK~~IK~~Ike~I~~~~ 577 (594)
T KOG2266|consen 519 EPTDEELKEVVKKILKEVDFNTATMKDILKKLYAKFPIDLTHRKDFIKDTIKELINKMA 577 (594)
T ss_pred CCcHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHhc
Confidence 39999999999999999999999999999999999999999999999999999988663
No 17
>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=78.04 E-value=3.2 Score=35.09 Aligned_cols=46 Identities=22% Similarity=0.419 Sum_probs=36.6
Q ss_pred CChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHH
Q 017932 2 VSDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQI 51 (363)
Q Consensus 2 vsd~ei~~~I~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~kK~~I~~~I 51 (363)
|||+++-..|..|.+..++ |..+++++|+. .|+++...+..|+..|
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 7999999999999999887 68899999987 6999999999998876
No 18
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=74.72 E-value=5 Score=42.08 Aligned_cols=60 Identities=22% Similarity=0.251 Sum_probs=46.2
Q ss_pred CccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhcc---------CccChhhHHHHHHccCCCC
Q 017932 271 ELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRV---------NSINMFQMNKALTRHIWPL 330 (363)
Q Consensus 271 ~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~---------d~i~~~~i~klL~~Hl~p~ 330 (363)
..+-++|...+-.||..|||-|+.||..|+.|+-|-..... ..+..-.+..++...|.|.
T Consensus 381 lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~k~~K~~~a~~~~~pw~~l~~~~~~rmtp~ 449 (560)
T KOG2522|consen 381 LYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVNKKKKVLNASRIIAPWEILHPLLTNRMTPF 449 (560)
T ss_pred eeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHHhhhhccccccccccHHHHHHHHHhcCCcc
Confidence 78889999999999999999999999999999888776643 2333345555665555543
No 19
>PRK05350 acyl carrier protein; Provisional
Probab=74.14 E-value=2.9 Score=33.05 Aligned_cols=55 Identities=18% Similarity=0.265 Sum_probs=46.8
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCCC
Q 017932 272 LARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWP 329 (363)
Q Consensus 272 ~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~p 329 (363)
|+|.+|...|+++|... +. .+...|.+|..|..-+|-||+.+.+|.-.|..+|--
T Consensus 2 m~~~~i~~~v~~ii~~~-~~--~~~~~i~~d~~l~~dlg~DSld~veli~~lE~~fgI 56 (82)
T PRK05350 2 MTREEILERLRAILVEL-FE--IDPEDITPEANLYEDLDLDSIDAVDLVVHLQKLTGK 56 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hC--CCHHHCCCCccchhhcCCCHHHHHHHHHHHHHHHCC
Confidence 78999999999999987 42 223579999999888899999999999999998743
No 20
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=69.30 E-value=8.6 Score=40.39 Aligned_cols=71 Identities=24% Similarity=0.237 Sum_probs=52.2
Q ss_pred HHhhhCC---CCccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcC---------CccChhhHHHHHhccCCCC
Q 017932 119 LQKVVGA---PELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGV---------NSIDMFKMNRALSKHIWPL 186 (363)
Q Consensus 119 La~~lG~---~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~---------d~i~~~~m~k~L~~Hl~p~ 186 (363)
|-.=+|. .-.+-.+|...+-.||..|||-|+.||..|+.|+-|-..... ..+.--.+...+..-|.|.
T Consensus 370 Lf~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~k~~K~~~a~~~~~pw~~l~~~~~~rmtp~ 449 (560)
T KOG2522|consen 370 LFKEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVNKKKKVLNASRIIAPWEILHPLLTNRMTPF 449 (560)
T ss_pred HHHhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHHhhhhccccccccccHHHHHHHHHhcCCcc
Confidence 3333465 467889999999999999999999999999999888765543 2345556666666666654
Q ss_pred CCC
Q 017932 187 GAE 189 (363)
Q Consensus 187 ~p~ 189 (363)
--+
T Consensus 450 yqi 452 (560)
T KOG2522|consen 450 YQI 452 (560)
T ss_pred eEE
Confidence 433
No 21
>PRK05828 acyl carrier protein; Validated
Probab=60.54 E-value=11 Score=30.34 Aligned_cols=54 Identities=15% Similarity=0.282 Sum_probs=44.4
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCC
Q 017932 272 LARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (363)
Q Consensus 272 ~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~ 328 (363)
|+|.+|..+|-..|...++.= +...|.+|..|.. +|-||+.+.+|.-.|..+|-
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~--~~d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f~ 54 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAV--TLDESNINKPYRE-LKIDSLDMFSIIVSLESEFN 54 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCC--CcccccCCCCHHh-cCCCHHHHHHHHHHHHHHHC
Confidence 789999999999998765421 2345678888977 99999999999999998874
No 22
>PRK05350 acyl carrier protein; Provisional
Probab=60.42 E-value=7.7 Score=30.59 Aligned_cols=54 Identities=24% Similarity=0.355 Sum_probs=46.6
Q ss_pred ccHHHHHHHHHHHHHHcCCC-CCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCCC
Q 017932 128 LARTEVVKKLWVYIKENKLQ-DPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIWP 185 (363)
Q Consensus 128 ~sR~~vvk~lW~YIk~nnLq-Dp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~p 185 (363)
|+|.+|...|+.+|.+. +. +| ..|.+|..|..-+|-|++.+-+|.-.|..+|.-
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~~~---~~i~~d~~l~~dlg~DSld~veli~~lE~~fgI 56 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEIDP---EDITPEANLYEDLDLDSIDAVDLVVHLQKLTGK 56 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCCCH---HHCCCCccchhhcCCCHHHHHHHHHHHHHHHCC
Confidence 78999999999999987 42 33 369999999888999999999999999998843
No 23
>CHL00124 acpP acyl carrier protein; Validated
Probab=55.28 E-value=10 Score=29.59 Aligned_cols=54 Identities=9% Similarity=0.211 Sum_probs=45.3
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCC
Q 017932 272 LARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (363)
Q Consensus 272 ~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~ 328 (363)
|+|.+|...|-++|.+.-=.+| ..|.+|..|..-+|-||+.+.+|.-.|..+|-
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~---~~i~~d~~l~~dlg~DSl~~~eli~~le~~f~ 54 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEK---SEVTLDANFTRDLGADSLDVVELVMAIEEKFD 54 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhcCCcHHHHHHHHHHHHHHHC
Confidence 6889999999999988743344 35999999999999999999999999988765
No 24
>PRK12449 acyl carrier protein; Provisional
Probab=54.61 E-value=18 Score=28.07 Aligned_cols=54 Identities=17% Similarity=0.220 Sum_probs=43.7
Q ss_pred ccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCC
Q 017932 272 LARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (363)
Q Consensus 272 ~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~ 328 (363)
|+|.+|...|-+++.+.-=.++ ..|.+|..|..-+|.||+.+.+|.-.|...|-
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dlg~DSl~~~~li~~lE~~f~ 54 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLS---LAITEQTHLKDDLAVDSIELVEFIINVEDEFH 54 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCc---cccCCCCcHHHHcCCcHHHHHHHHHHHHHHhC
Confidence 5788899999898886442333 35999999999999999999999998877653
No 25
>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=51.55 E-value=30 Score=24.92 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhCCCChhhH-HHHHHHHHHHHhhh
Q 017932 25 AGSVRRLLEEDFKVDLSDRK-AFVSEQIDLFLQTL 58 (363)
Q Consensus 25 ~k~VR~~LE~~~gvDLs~kK-~~I~~~I~~~l~~~ 58 (363)
...|+..+.+.+|+||++.| ..|...|..++...
T Consensus 5 f~~~~~~i~~~~Gi~l~~~K~~~l~rRl~~rm~~~ 39 (57)
T PF03705_consen 5 FERFRELIYRRTGIDLSEYKRSLLERRLARRMRAL 39 (57)
T ss_dssp HHHHHHHHHHHH-----GGGHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCchhhHHHHHHHHHHHHHHc
Confidence 45788999999999999876 68888887777643
No 26
>PTZ00171 acyl carrier protein; Provisional
Probab=46.21 E-value=22 Score=31.80 Aligned_cols=60 Identities=10% Similarity=0.137 Sum_probs=50.3
Q ss_pred CCCCccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHHccCCCC
Q 017932 268 GVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWPL 330 (363)
Q Consensus 268 G~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl~p~ 330 (363)
|...|++.+|...|+++|.+.--.+| ..|.+|..|..-+|-||+.+.+|.-.|..+|--.
T Consensus 62 ~~~~~~~~~v~~~l~eiiae~l~vd~---~~I~~ds~~~~dLg~DSLd~veLv~~LEdeFgI~ 121 (148)
T PTZ00171 62 KQYLLSKEDVLTRVKKVVKNFEKVDA---SKITPESNFVKDLGADSLDVVELLIAIEQEFNLT 121 (148)
T ss_pred cccccCHHHHHHHHHHHHHHHhCCCH---hhCCCCcchhhhcCCCHHHHHHHHHHHHHHHCCc
Confidence 45578999999999999998753343 4589999999999999999999999999887433
No 27
>PRK05828 acyl carrier protein; Validated
Probab=45.37 E-value=29 Score=27.99 Aligned_cols=54 Identities=15% Similarity=0.244 Sum_probs=43.9
Q ss_pred ccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCC
Q 017932 128 LARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (363)
Q Consensus 128 ~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~ 184 (363)
|+|.+|..+|-..|.+..+.=+ -..|.+|..|.. +|-|++.+.+|.-.|..+|.
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~~--~d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f~ 54 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAVT--LDESNINKPYRE-LKIDSLDMFSIIVSLESEFN 54 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCCC--cccccCCCCHHh-cCCCHHHHHHHHHHHHHHHC
Confidence 7899999999999987554311 234778888977 99999999999999998874
No 28
>PF13565 HTH_32: Homeodomain-like domain
Probab=45.17 E-value=48 Score=25.13 Aligned_cols=35 Identities=20% Similarity=0.394 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCC
Q 017932 4 DSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDL 40 (363)
Q Consensus 4 d~ei~~~I~~IL~~sDl~tvT~k~VR~~LE~~~gvDL 40 (363)
++++...|.+++..-. ..|...|...|++.||+.+
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 4566666666666443 7889999999999999987
No 29
>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=43.20 E-value=86 Score=24.42 Aligned_cols=45 Identities=13% Similarity=0.245 Sum_probs=35.2
Q ss_pred HHHHhcCCCCCcCHHHHHHHHHHHhCCCChh--hHHHHHHHHHHHHh
Q 017932 12 RDILRNSDLDTATAGSVRRLLEEDFKVDLSD--RKAFVSEQIDLFLQ 56 (363)
Q Consensus 12 ~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~--kK~~I~~~I~~~l~ 56 (363)
++|-.-.|..-.|...|.+-|++.|++++.+ .+.+++..+...+.
T Consensus 11 eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~ 57 (77)
T PF00538_consen 11 EAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVE 57 (77)
T ss_dssp HHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHH
T ss_pred HHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHH
Confidence 3444446777789999999999999999875 77778777776665
No 30
>CHL00124 acpP acyl carrier protein; Validated
Probab=43.15 E-value=21 Score=27.79 Aligned_cols=54 Identities=13% Similarity=0.284 Sum_probs=45.6
Q ss_pred ccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCC
Q 017932 128 LARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (363)
Q Consensus 128 ~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~ 184 (363)
|+|.+|...|-++|.+.-=.+|. .|.+|..|...+|-|++.+.+|...|...|.
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 4999999999999999999999999988764
No 31
>PRK12449 acyl carrier protein; Provisional
Probab=42.66 E-value=36 Score=26.31 Aligned_cols=54 Identities=17% Similarity=0.247 Sum_probs=44.4
Q ss_pred ccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCC
Q 017932 128 LARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (363)
Q Consensus 128 ~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~ 184 (363)
|+|.+|..+|-+++.+.-=.++. .|.+|..|..-+|-|++.+.+|...|...|.
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 57888999999998875433443 4999999999999999999999999987663
No 32
>PTZ00171 acyl carrier protein; Provisional
Probab=40.43 E-value=32 Score=30.83 Aligned_cols=60 Identities=17% Similarity=0.224 Sum_probs=51.4
Q ss_pred hhCCCCccHHHHHHHHHHHHHHcCCCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCC
Q 017932 122 VVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (363)
Q Consensus 122 ~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~ 184 (363)
.-|...|++.+|...|+++|.+.--.+|. .|.+|..+..-+|-|++.+-+|.-.|..++.
T Consensus 60 ~~~~~~~~~~~v~~~l~eiiae~l~vd~~---~I~~ds~~~~dLg~DSLd~veLv~~LEdeFg 119 (148)
T PTZ00171 60 KSKQYLLSKEDVLTRVKKVVKNFEKVDAS---KITPESNFVKDLGADSLDVVELLIAIEQEFN 119 (148)
T ss_pred cccccccCHHHHHHHHHHHHHHHhCCCHh---hCCCCcchhhhcCCCHHHHHHHHHHHHHHHC
Confidence 34667889999999999999988644554 4889999999999999999999999999874
No 33
>smart00526 H15 Domain in histone families 1 and 5.
Probab=33.91 E-value=1.7e+02 Score=21.96 Aligned_cols=46 Identities=9% Similarity=0.223 Sum_probs=32.8
Q ss_pred HHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHh
Q 017932 11 LRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQ 56 (363)
Q Consensus 11 I~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~kK~~I~~~I~~~l~ 56 (363)
+++|..-.+..-.|...|++-+++.|+++-...+.+++..+...+.
T Consensus 12 ~eAI~~l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~ 57 (66)
T smart00526 12 TEAISALKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVA 57 (66)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Confidence 3455555677778999999999999998765555666666655443
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=31.68 E-value=69 Score=23.28 Aligned_cols=39 Identities=23% Similarity=0.318 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHhc-------------CCCCCcCHHHHHHHHHHHhCCCChhh
Q 017932 5 SDLVTRLRDILRN-------------SDLDTATAGSVRRLLEEDFKVDLSDR 43 (363)
Q Consensus 5 ~ei~~~I~~IL~~-------------sDl~tvT~k~VR~~LE~~~gvDLs~k 43 (363)
++|...+.++|.. ..++++..-.++..|++.||+.++..
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 4567777777751 22444556788999999999998854
No 35
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=30.04 E-value=38 Score=27.01 Aligned_cols=23 Identities=39% Similarity=0.540 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhCCCChhhHHHHH
Q 017932 26 GSVRRLLEEDFKVDLSDRKAFVS 48 (363)
Q Consensus 26 k~VR~~LE~~~gvDLs~kK~~I~ 48 (363)
..||..||..||+||+.-+--.+
T Consensus 4 ~~~r~~~e~~~G~dl~~Vrvh~~ 26 (79)
T PF13699_consen 4 ESIRSRLERAFGADLSDVRVHTG 26 (79)
T ss_pred HHHHHHHHHHhCCCccceEEEeC
Confidence 36899999999999997554444
No 36
>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=29.19 E-value=1.8e+02 Score=22.05 Aligned_cols=44 Identities=14% Similarity=0.263 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHhcCCCCCcCHHHHHHHHHH-HhC-CCChhhHHHHH
Q 017932 5 SDLVTRLRDILRNSDLDTATAGSVRRLLEE-DFK-VDLSDRKAFVS 48 (363)
Q Consensus 5 ~ei~~~I~~IL~~sDl~tvT~k~VR~~LE~-~~g-vDLs~kK~~I~ 48 (363)
+++...|...|=.||...-++..|...|.. ..+ -.+.....+..
T Consensus 24 ~~~l~ele~~Li~aDVg~~~a~~i~~~ik~~~~~~~~~~~~~~v~~ 69 (75)
T PF02881_consen 24 EEFLEELEEALIEADVGVEVAEKIIENIKKKLIKKKGINPREEVKK 69 (75)
T ss_dssp HHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHCTTSSHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhcccCCCcHHHHHH
Confidence 567888999999999999999999999999 776 33444444433
No 37
>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=27.02 E-value=1.2e+02 Score=25.77 Aligned_cols=47 Identities=21% Similarity=0.349 Sum_probs=38.0
Q ss_pred ChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHH
Q 017932 3 SDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQID 52 (363)
Q Consensus 3 sd~ei~~~I~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~kK~~I~~~I~ 52 (363)
|++++-.+-.......|++. -.||+.|...||+||-+-=+.|.+...
T Consensus 4 t~EeF~aRye~~F~~~~iD~---we~rr~mN~l~~~DlVP~P~ii~aaLr 50 (103)
T cd00923 4 TDEEFDARYETYFNRPDIDG---WELRRGLNNLFGYDLVPEPKVIEAALR 50 (103)
T ss_pred cHHHHHHHHHHHhCCcCccH---HHHHHHHHHHhccccCCCcHHHHHHHH
Confidence 78888888888888887664 459999999999999987777765543
No 38
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=25.75 E-value=92 Score=35.46 Aligned_cols=77 Identities=23% Similarity=0.259 Sum_probs=53.7
Q ss_pred CCCCCcccccCCHHHHhhhCCC-----CccHHHHHHHHHHHHhhcCCCCCCCCCccccchhhhhhhccC-ccChhhHHHH
Q 017932 249 RRGGFTKLCSLSPDLQTFVGVS-----ELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVN-SINMFQMNKA 322 (363)
Q Consensus 249 ~~~g~~~~~~LS~~La~flG~~-----~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cD~kLk~LFg~d-~i~~~~i~kl 322 (363)
++++--..-.|+++|+..||.- .--..+++..+-+-||.. | +.+.+=..|..|+..- .+.-+-..-+
T Consensus 125 ~~~~~r~~~~l~~~l~~ll~eAN~lfarg~~eeA~~i~~EvIkqd----p---~~~~ay~tL~~IyEqrGd~eK~l~~~l 197 (895)
T KOG2076|consen 125 RGRRSRGKSKLAPELRQLLGEANNLFARGDLEEAEEILMEVIKQD----P---RNPIAYYTLGEIYEQRGDIEKALNFWL 197 (895)
T ss_pred cCCCCCcccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC----c---cchhhHHHHHHHHHHcccHHHHHHHHH
Confidence 3344446678999999999974 455678888888889854 3 5566667777777421 3333344457
Q ss_pred HHccCCCCCc
Q 017932 323 LTRHIWPLDE 332 (363)
Q Consensus 323 L~~Hl~p~~p 332 (363)
|..||-|.++
T Consensus 198 lAAHL~p~d~ 207 (895)
T KOG2076|consen 198 LAAHLNPKDY 207 (895)
T ss_pred HHHhcCCCCh
Confidence 8999999998
No 39
>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=23.57 E-value=39 Score=26.29 Aligned_cols=23 Identities=26% Similarity=0.391 Sum_probs=18.9
Q ss_pred ccChhhHHHHHHccCCCCCccch
Q 017932 313 SINMFQMNKALTRHIWPLDEADA 335 (363)
Q Consensus 313 ~i~~~~i~klL~~Hl~p~~pi~~ 335 (363)
++.||.++.+|+.|+.|.+-.+-
T Consensus 7 sLfFFSLM~LlSs~l~p~~~~d~ 29 (64)
T PF03511_consen 7 SLFFFSLMGLLSSYLAPKEGADS 29 (64)
T ss_pred HHHHHHHHHHHHHhcCccccccc
Confidence 35689999999999999885543
No 40
>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=23.51 E-value=23 Score=25.52 Aligned_cols=39 Identities=21% Similarity=0.377 Sum_probs=22.7
Q ss_pred HHHHhhhCCCCccHHHHHHHHHHHHHHcCCCCCCCCCcc
Q 017932 117 TQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKI 155 (363)
Q Consensus 117 p~La~~lG~~~~sR~~vvk~lW~YIk~nnLqDp~nkr~I 155 (363)
.+|+.++|.+..+-+.+++.|-..=--..-++|+|+|.|
T Consensus 21 ~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R~v 59 (59)
T PF01047_consen 21 SELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDRRQV 59 (59)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTETTSE
T ss_pred HHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCCcC
Confidence 379999998666666666665441111222477777754
No 41
>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=23.17 E-value=2.8e+02 Score=22.20 Aligned_cols=46 Identities=11% Similarity=0.179 Sum_probs=33.8
Q ss_pred HHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHh
Q 017932 11 LRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQ 56 (363)
Q Consensus 11 I~~IL~~sDl~tvT~k~VR~~LE~~~gvDLs~kK~~I~~~I~~~l~ 56 (363)
+++|..-.+..-.|...|++-+++.|.++....+.+++..+...+.
T Consensus 12 ~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~ 57 (88)
T cd00073 12 TEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVA 57 (88)
T ss_pred HHHHHHcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHH
Confidence 4555556677788999999999999998875556666665555544
No 42
>PRK07117 acyl carrier protein; Validated
Probab=22.61 E-value=86 Score=24.91 Aligned_cols=52 Identities=15% Similarity=0.161 Sum_probs=41.0
Q ss_pred ccHHHHHHHHHHHHhhcC-CCCCCCCCccccchhhhhhhccCccChhhHHHHHHccC
Q 017932 272 LARTEVVKKLWAYIREKN-LQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHI 327 (363)
Q Consensus 272 ~sR~~vvk~lW~YIK~nn-LqDp~nkr~I~cD~kLk~LFg~d~i~~~~i~klL~~Hl 327 (363)
|+|.+|...|-+-|.+.- =-+ ...|..|..|+. +|.+|+.+.+|--.|...|
T Consensus 1 M~~~ei~~~v~~ii~e~~p~i~---~~~I~~~~~l~D-Lg~DSlD~veiv~~led~f 53 (79)
T PRK07117 1 MDKQRIFDILVRHIREVLPDLD---QHQFQPEDSLVD-LGANSMDRAEIVIMTLESL 53 (79)
T ss_pred CCHHHHHHHHHHHHHHHcCCCC---HHHCCCCCChhh-cCCChHHHHHHHHHHHHHH
Confidence 578888888888888764 123 467899999998 9999999999888776654
No 43
>PRK07117 acyl carrier protein; Validated
Probab=22.58 E-value=84 Score=24.97 Aligned_cols=53 Identities=19% Similarity=0.200 Sum_probs=42.4
Q ss_pred ccHHHHHHHHHHHHHHcC-CCCCCCCCcccCChhHhhhhcCCccChhhHHHHHhccCC
Q 017932 128 LARTEVVKKLWVYIKENK-LQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (363)
Q Consensus 128 ~sR~~vvk~lW~YIk~nn-LqDp~nkr~I~cDe~Lk~lF~~d~i~~~~m~k~L~~Hl~ 184 (363)
|+|.+|..+|-.-|.+.- =-+|. .|..|..|+. +|.|++.+.+|--.|...|.
T Consensus 1 M~~~ei~~~v~~ii~e~~p~i~~~---~I~~~~~l~D-Lg~DSlD~veiv~~led~f~ 54 (79)
T PRK07117 1 MDKQRIFDILVRHIREVLPDLDQH---QFQPEDSLVD-LGANSMDRAEIVIMTLESLS 54 (79)
T ss_pred CCHHHHHHHHHHHHHHHcCCCCHH---HCCCCCChhh-cCCChHHHHHHHHHHHHHHC
Confidence 578888888888888765 24544 5899999988 99999999999998877653
Done!