Query 016177
Match_columns 394
No_of_seqs 338 out of 1019
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 04:30:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016177.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016177hhsearch_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 1.7E-31 3.6E-36 254.9 10.0 181 1-191 1-182 (240)
2 COG5531 SWIB-domain-containing 99.9 9.4E-26 2E-30 214.3 5.0 182 6-188 6-200 (237)
3 PF02201 SWIB: SWIB/MDM2 domai 99.9 3.1E-25 6.7E-30 177.7 0.8 75 109-183 1-75 (76)
4 PF02201 SWIB: SWIB/MDM2 domai 99.9 3.9E-25 8.5E-30 177.1 0.8 76 253-328 1-76 (76)
5 smart00151 SWIB SWI complex, B 99.9 7.7E-24 1.7E-28 170.0 7.7 76 110-185 2-77 (77)
6 smart00151 SWIB SWI complex, B 99.9 7.3E-24 1.6E-28 170.2 7.4 77 253-329 1-77 (77)
7 KOG1946 RNA polymerase I trans 99.9 8.4E-24 1.8E-28 202.2 7.9 86 249-334 96-181 (240)
8 COG5531 SWIB-domain-containing 99.8 3.7E-21 8.1E-26 183.0 5.2 83 250-332 118-200 (237)
9 PRK14724 DNA topoisomerase III 99.8 2.1E-19 4.5E-24 200.7 8.0 77 108-184 911-987 (987)
10 PRK14724 DNA topoisomerase III 99.8 6.8E-19 1.5E-23 196.6 7.8 77 252-328 911-987 (987)
11 KOG2570 SWI/SNF transcription 99.7 1.5E-17 3.2E-22 167.8 5.5 90 253-342 205-294 (420)
12 KOG2570 SWI/SNF transcription 99.7 2.4E-17 5.2E-22 166.3 5.8 82 111-192 207-288 (420)
13 PF08766 DEK_C: DEK C terminal 99.5 3.6E-14 7.9E-19 106.7 6.1 54 3-56 1-54 (54)
14 PRK06319 DNA topoisomerase I/S 99.3 7.3E-13 1.6E-17 147.0 5.5 74 111-184 786-859 (860)
15 PRK06319 DNA topoisomerase I/S 99.3 1.3E-12 2.8E-17 145.1 5.4 75 254-328 785-859 (860)
16 KOG2266 Chromatin-associated p 98.3 1.3E-06 2.8E-11 90.5 6.3 59 1-59 519-577 (594)
17 PF09312 SurA_N: SurA N-termin 76.2 3.8 8.3E-05 35.1 4.1 46 2-51 67-112 (118)
18 PRK05350 acyl carrier protein; 72.8 3.2 7E-05 33.2 2.6 55 272-329 2-56 (82)
19 KOG2522 Filamentous baseplate 70.5 6.9 0.00015 41.6 5.0 60 270-329 380-448 (560)
20 KOG2522 Filamentous baseplate 61.4 14 0.0003 39.4 5.2 64 123-186 374-449 (560)
21 PRK05828 acyl carrier protein; 57.5 14 0.0003 30.3 3.6 55 272-329 1-55 (84)
22 PRK05350 acyl carrier protein; 53.8 11 0.00024 30.1 2.4 53 128-184 2-55 (82)
23 PRK12449 acyl carrier protein; 52.5 20 0.00044 28.1 3.7 54 272-328 1-54 (80)
24 CHL00124 acpP acyl carrier pro 52.1 12 0.00027 29.5 2.4 54 272-328 1-54 (82)
25 PF03705 CheR_N: CheR methyltr 50.1 33 0.00071 25.1 4.3 34 25-58 5-39 (57)
26 PTZ00171 acyl carrier protein; 45.8 23 0.0005 32.1 3.4 59 268-329 62-120 (148)
27 PF13565 HTH_32: Homeodomain-l 43.3 52 0.0011 25.3 4.7 35 4-40 32-66 (77)
28 PRK05828 acyl carrier protein; 40.4 38 0.00083 27.7 3.6 54 128-184 1-54 (84)
29 PF00538 Linker_histone: linke 40.2 1E+02 0.0022 24.3 6.0 45 12-56 11-57 (77)
30 PRK12449 acyl carrier protein; 37.1 49 0.0011 25.9 3.7 54 128-184 1-54 (80)
31 PTZ00171 acyl carrier protein; 36.5 38 0.00083 30.7 3.3 59 123-184 61-119 (148)
32 CHL00124 acpP acyl carrier pro 35.4 31 0.00068 27.2 2.3 54 128-184 1-54 (82)
33 smart00526 H15 Domain in histo 30.4 2.1E+02 0.0044 21.8 6.1 46 11-56 12-57 (66)
34 PF00550 PP-binding: Phosphopa 29.7 78 0.0017 23.3 3.6 39 5-43 1-52 (67)
35 PF02881 SRP54_N: SRP54-type p 29.0 1.8E+02 0.0038 22.4 5.6 43 5-47 24-68 (75)
36 cd00923 Cyt_c_Oxidase_Va Cytoc 28.5 1.1E+02 0.0023 26.5 4.5 49 3-54 4-52 (103)
37 PF13699 DUF4157: Domain of un 27.5 44 0.00095 27.0 2.0 23 26-48 4-26 (79)
38 KOG2076 RNA polymerase III tra 21.9 1.2E+02 0.0026 35.1 4.6 77 250-333 126-208 (895)
39 PF01047 MarR: MarR family; I 21.4 23 0.0005 25.9 -0.7 38 118-155 22-59 (59)
40 PF02084 Bindin: Bindin; Inte 21.2 46 0.001 32.5 1.1 15 159-173 107-121 (238)
41 PRK07117 acyl carrier protein; 20.8 97 0.0021 25.0 2.8 52 272-327 1-53 (79)
42 PF13545 HTH_Crp_2: Crp-like h 20.6 69 0.0015 24.4 1.8 51 253-307 23-75 (76)
43 PF02037 SAP: SAP domain; Int 20.2 2.1E+02 0.0045 19.4 3.9 34 21-55 2-35 (35)
No 1
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.97 E-value=1.7e-31 Score=254.94 Aligned_cols=181 Identities=35% Similarity=0.463 Sum_probs=140.6
Q ss_pred CCChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHhhhhhhcccccccCCcccccccCcc
Q 016177 1 MVSDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQTLEKEREEIEDDGNGAVEANADDK 80 (394)
Q Consensus 1 mvSd~ei~~~I~~IL~~sDL~tvT~k~IR~~LE~~fGvDLs~kK~~I~~~I~~~l~~~~~~~p~~~~~~~~~~~~~~~~~ 80 (394)
|.+...+...++.||...+++++|...||++++..||++++.++..++.+|...+...... +.. ...... .....
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 6788999999999999999999999999999999999999999999999998877532100 000 000000 00000
Q ss_pred hh-hHHHhHhhhhhcccccccccccCCCCCCccccCCHHHHhhhCCCCCcHHHHHHHHHHHHHhcCCCCCCCCCccccCh
Q 016177 81 EE-EEEESESKREKSIKVGRQVKRRGGGGFNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDE 159 (394)
Q Consensus 81 ~~-~~~~~~~k~~~~~k~~~~~k~k~~~g~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe 159 (394)
.. .....+.....+ ..+++.++|+++.|.|||.|+.|+|.+++||++|+++||+|||+||||||.|||.|+||+
T Consensus 76 ~~~~~~~~~~~~~~~-----~~~~~~~~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDe 150 (240)
T KOG1946|consen 76 RSRKPKSLESSGEKN-----KKKKKASWGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDE 150 (240)
T ss_pred ccccCcccccccccc-----hhccccCcCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHH
Confidence 00 000000000000 112235689999999999999999999999999999999999999999999999999999
Q ss_pred hHHhhhccCccChhhHHHHHhccCCCCCCCCc
Q 016177 160 SLQALFGVNSIDMFKMNRALSKHIWPLGAEDE 191 (394)
Q Consensus 160 ~Lk~lFg~d~i~~f~m~k~L~~Hl~p~~p~~~ 191 (394)
+|+.|||.++|+||+|+++|.+||++...+..
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 99999999999999999999999999887654
No 2
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.92 E-value=9.4e-26 Score=214.30 Aligned_cols=182 Identities=30% Similarity=0.408 Sum_probs=130.7
Q ss_pred HHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHhhhhhhcccc----cccCCccccc-ccCcc
Q 016177 6 DLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQTLEKEREEI----EDDGNGAVEA-NADDK 80 (394)
Q Consensus 6 ei~~~I~~IL~~sDL~tvT~k~IR~~LE~~fGvDLs~kK~~I~~~I~~~l~~~~~~~p~~----~~~~~~~~~~-~~~~~ 80 (394)
.+..++..+|+..+..+++.+.|++.++..++++|..+.++++..+...+.+... .+.. +.......+. +....
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 3556788899999999999999999999999999999999999999877665421 1110 0000000000 00000
Q ss_pred hhhHHHhHhh----hhhcccccccccc----cCCCCCCccccCCHHHHhhhCCCCCcHHHHHHHHHHHHHhcCCCCCCCC
Q 016177 81 EEEEEESESK----REKSIKVGRQVKR----RGGGGFNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNK 152 (394)
Q Consensus 81 ~~~~~~~~~k----~~~~~k~~~~~k~----k~~~g~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIK~nnLqDp~nk 152 (394)
+.+....+++ .....+.+.++|+ ..++.+...|.|||.||.|||..++||++||+.||+|||.||||||+||
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 0000000000 0000111111111 1245678899999999999999999999999999999999999999999
Q ss_pred CccccChhHHhhhccCccChhhHHHHHhccCCCCCC
Q 016177 153 RKILCDESLQALFGVNSIDMFKMNRALSKHIWPLGA 188 (394)
Q Consensus 153 r~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~p~~p 188 (394)
|+|+||++|+.|||.+.|.||+|++.|.+|+.+++-
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 999999999999999999999999999999999653
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=3.1e-25 Score=177.71 Aligned_cols=75 Identities=51% Similarity=0.927 Sum_probs=70.8
Q ss_pred CCccccCCHHHHhhhCCCCCcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccC
Q 016177 109 FNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHI 183 (394)
Q Consensus 109 ~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl 183 (394)
|+++|.|||+|++++|..++||++|+++||+||++||||||+|++.|+||+.|+.|||+++|+||+|+++|++||
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 578899999999999999999999999999999999999999999999999999999999999999999999997
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=3.9e-25 Score=177.08 Aligned_cols=76 Identities=54% Similarity=0.953 Sum_probs=71.4
Q ss_pred CCccccCCHHHHhhhCCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCC
Q 016177 253 FTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (394)
Q Consensus 253 f~~~~~LS~~La~flG~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~ 328 (394)
|+++|.||++|++|+|..++||++|+++||+||++||||||+|++.|+||++|+.|||+++|+|++|+++|++||.
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 5
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.90 E-value=7.7e-24 Score=170.03 Aligned_cols=76 Identities=54% Similarity=0.993 Sum_probs=74.0
Q ss_pred CccccCCHHHHhhhCCCCCcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccCCC
Q 016177 110 NKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIWP 185 (394)
Q Consensus 110 ~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~p 185 (394)
+++|.|||+|++|+|..++||++|+++||+|||.||||||+|++.|+||+.|+.+||+++|.|++|+++|++||.|
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 6
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.90 E-value=7.3e-24 Score=170.16 Aligned_cols=77 Identities=48% Similarity=0.928 Sum_probs=74.7
Q ss_pred CCccccCCHHHHhhhCCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCCC
Q 016177 253 FTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWP 329 (394)
Q Consensus 253 f~~~~~LS~~La~flG~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~p 329 (394)
++++|.||++|+.|+|..++||++|+++||+|||.||||||.|++.|+||+.|++|||+++|.|++|+++|++||.|
T Consensus 1 ~~~~~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence 36889999999999999999999999999999999999999999999999999999999999999999999999975
No 7
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.89 E-value=8.4e-24 Score=202.17 Aligned_cols=86 Identities=53% Similarity=0.865 Sum_probs=82.8
Q ss_pred CCCCCCccccCCHHHHhhhCCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCC
Q 016177 249 RRGGFTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (394)
Q Consensus 249 ~~~gf~~~~~LS~~La~flG~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~ 328 (394)
.++|+++.|.||+.|+.|+|.+++||++|++.||+|||+||||||.||+.|+||++|+.|||...|+||+|+++|.+||+
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 CCCccc
Q 016177 329 PLDEAD 334 (394)
Q Consensus 329 p~dp~~ 334 (394)
+...+.
T Consensus 176 ~~~d~~ 181 (240)
T KOG1946|consen 176 KNQDMV 181 (240)
T ss_pred Cccccc
Confidence 988764
No 8
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.83 E-value=3.7e-21 Score=182.99 Aligned_cols=83 Identities=37% Similarity=0.682 Sum_probs=79.2
Q ss_pred CCCCCccccCCHHHHhhhCCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCCC
Q 016177 250 RGGFTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWP 329 (394)
Q Consensus 250 ~~gf~~~~~LS~~La~flG~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~p 329 (394)
++.+..+|.+|+.||.|||..++||++||+.||+|||.||||||.|||.|+||++|+.|||.+.+.||+|++.|.+|+.+
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 CCc
Q 016177 330 LDE 332 (394)
Q Consensus 330 ~dp 332 (394)
.+.
T Consensus 198 ~~~ 200 (237)
T COG5531 198 YTI 200 (237)
T ss_pred Ccc
Confidence 543
No 9
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.78 E-value=2.1e-19 Score=200.72 Aligned_cols=77 Identities=42% Similarity=0.652 Sum_probs=74.6
Q ss_pred CCCccccCCHHHHhhhCCCCCcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccCC
Q 016177 108 GFNKLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (394)
Q Consensus 108 g~~k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~ 184 (394)
.+...+.|||+|++|||..++||++||++||+|||.||||||.|||.|+||++|+.|||+++|+||+|+++|++||.
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 37778999999999999999999999999999999999999999999999999999999999999999999999984
No 10
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.76 E-value=6.8e-19 Score=196.63 Aligned_cols=77 Identities=34% Similarity=0.596 Sum_probs=74.9
Q ss_pred CCCccccCCHHHHhhhCCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCC
Q 016177 252 GFTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (394)
Q Consensus 252 gf~~~~~LS~~La~flG~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~ 328 (394)
.|..++.|||+|++|||..++||++||++||+|||.||||||.|+|.|+||++|+.|||+++|.||+|+++|++||.
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=99.69 E-value=1.5e-17 Score=167.79 Aligned_cols=90 Identities=28% Similarity=0.505 Sum_probs=84.0
Q ss_pred CCccccCCHHHHhhhCCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCCCCCc
Q 016177 253 FTKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWPLDE 332 (394)
Q Consensus 253 f~~~~~LS~~La~flG~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~p~dp 332 (394)
-+..|+|||.||.+||+.+.||++||.+||+|||.|+||||.++.+|+||..|+++||++++.|..|+.+|++||.|++|
T Consensus 205 ~P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~dP 284 (420)
T KOG2570|consen 205 QPEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPDP 284 (420)
T ss_pred CCcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCCC
Confidence 34568999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccchhhhh
Q 016177 333 ADAKSKEKEK 342 (394)
Q Consensus 333 ~~~~~~~~~~ 342 (394)
|.+....+..
T Consensus 285 Ivi~h~I~v~ 294 (420)
T KOG2570|consen 285 IVIDHTISVD 294 (420)
T ss_pred eeecceeccC
Confidence 9987555443
No 12
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.68 E-value=2.4e-17 Score=166.27 Aligned_cols=82 Identities=32% Similarity=0.562 Sum_probs=79.5
Q ss_pred ccccCCHHHHhhhCCCCCcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccCCCCCCCC
Q 016177 111 KLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIWPLGAED 190 (394)
Q Consensus 111 k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~p~~p~~ 190 (394)
..|+|||.||.+||..+.||+.||.+||+|||.|+||||+++.+|+||..|+.+||++++.|..|+.+|++||.|++||.
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 34789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cc
Q 016177 191 EN 192 (394)
Q Consensus 191 ~~ 192 (394)
++
T Consensus 287 i~ 288 (420)
T KOG2570|consen 287 ID 288 (420)
T ss_pred ec
Confidence 85
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=99.50 E-value=3.6e-14 Score=106.73 Aligned_cols=54 Identities=52% Similarity=0.781 Sum_probs=45.7
Q ss_pred ChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHh
Q 016177 3 SDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQ 56 (394)
Q Consensus 3 Sd~ei~~~I~~IL~~sDL~tvT~k~IR~~LE~~fGvDLs~kK~~I~~~I~~~l~ 56 (394)
||++|...|++||+++||+++|.|+||++||+.||+||+++|+||+++|+.+|.
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 799999999999999999999999999999999999999999999999999873
No 14
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.34 E-value=7.3e-13 Score=147.03 Aligned_cols=74 Identities=42% Similarity=0.719 Sum_probs=71.1
Q ss_pred ccccCCHHHHhhhCCCCCcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccCC
Q 016177 111 KLCSLSTQLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (394)
Q Consensus 111 k~~~LSp~La~~lG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~ 184 (394)
.+|.+|+.|+.++|..+++|+++++.||+||+.|+||||.|||.|+||++|+.+||++.+.||.|+++|++||.
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 34669999999999999999999999999999999999999999999999999999999999999999999985
No 15
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.31 E-value=1.3e-12 Score=145.10 Aligned_cols=75 Identities=39% Similarity=0.690 Sum_probs=72.1
Q ss_pred CccccCCHHHHhhhCCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCC
Q 016177 254 TKLCSLSPDLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (394)
Q Consensus 254 ~~~~~LS~~La~flG~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~ 328 (394)
..+|.+|+.|+.++|..+++|+++++.||+||+.|+||||.|++.|+||++|+.+||++.+.||.|+++|++||.
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=98.26 E-value=1.3e-06 Score=90.47 Aligned_cols=59 Identities=27% Similarity=0.510 Sum_probs=56.1
Q ss_pred CCChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHhhhh
Q 016177 1 MVSDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQTLE 59 (394)
Q Consensus 1 mvSd~ei~~~I~~IL~~sDL~tvT~k~IR~~LE~~fGvDLs~kK~~I~~~I~~~l~~~~ 59 (394)
.|||.+|...|..||..+||+|+|.+.|-++|-+.|++||+++|.||..+|...|..+.
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 39999999999999999999999999999999999999999999999999999887653
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=76.22 E-value=3.8 Score=35.09 Aligned_cols=46 Identities=22% Similarity=0.419 Sum_probs=36.7
Q ss_pred CChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHH
Q 016177 2 VSDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQI 51 (394)
Q Consensus 2 vSd~ei~~~I~~IL~~sDL~tvT~k~IR~~LE~~fGvDLs~kK~~I~~~I 51 (394)
|||+++-..|..|.+...+ |..+++++|+. -|+++...+..|+..|
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 5999999999999886
No 18
>PRK05350 acyl carrier protein; Provisional
Probab=72.80 E-value=3.2 Score=33.20 Aligned_cols=55 Identities=18% Similarity=0.255 Sum_probs=46.9
Q ss_pred ccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCCC
Q 016177 272 LARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWP 329 (394)
Q Consensus 272 ~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~p 329 (394)
|+|.+|...|+++|.+. +.- +...|.+|..|..-+|-||+.+.+|.-.|..+|.=
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~--~~~~i~~d~~l~~dlg~DSld~veli~~lE~~fgI 56 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEI--DPEDITPEANLYEDLDLDSIDAVDLVVHLQKLTGK 56 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCC--CHHHCCCCccchhhcCCCHHHHHHHHHHHHHHHCC
Confidence 78999999999999987 432 22579999999888899999999999999988754
No 19
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=70.49 E-value=6.9 Score=41.60 Aligned_cols=60 Identities=22% Similarity=0.248 Sum_probs=46.2
Q ss_pred CcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhcc---------CccChhhHHHHHhccCCC
Q 016177 270 SELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRV---------NSINMFQMNKALTRHIWP 329 (394)
Q Consensus 270 ~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~---------d~i~~~~m~klL~~Hl~p 329 (394)
.-.|-++|...+-+||..|||-|+.||..|+.|+-|-..... ..+..-.+...+..-|.|
T Consensus 380 ~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~k~~K~~~a~~~~~pw~~l~~~~~~rmtp 448 (560)
T KOG2522|consen 380 TLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVNKKKKVLNASRIIAPWEILHPLLTNRMTP 448 (560)
T ss_pred ceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHHhhhhccccccccccHHHHHHHHHhcCCc
Confidence 378889999999999999999999999998888887766543 233444566666655555
No 20
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=61.43 E-value=14 Score=39.40 Aligned_cols=64 Identities=23% Similarity=0.284 Sum_probs=47.8
Q ss_pred hCC---CCCcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhcc---------CccChhhHHHHHhccCCCC
Q 016177 123 VGA---PELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGV---------NSIDMFKMNRALSKHIWPL 186 (394)
Q Consensus 123 lG~---~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~---------d~i~~f~m~k~L~~Hl~p~ 186 (394)
+|. .-.+-.+|...+-+||+.|||-|+.||..|+.|+-|-..... ..+.--.+...+..-+.|.
T Consensus 374 vg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~k~~K~~~a~~~~~pw~~l~~~~~~rmtp~ 449 (560)
T KOG2522|consen 374 VGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVNKKKKVLNASRIIAPWEILHPLLTNRMTPF 449 (560)
T ss_pred cCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHHhhhhccccccccccHHHHHHHHHhcCCcc
Confidence 465 457889999999999999999999999999888887655432 2344555666665555554
No 21
>PRK05828 acyl carrier protein; Validated
Probab=57.54 E-value=14 Score=30.25 Aligned_cols=55 Identities=15% Similarity=0.261 Sum_probs=44.9
Q ss_pred ccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCCC
Q 016177 272 LARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWP 329 (394)
Q Consensus 272 ~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~p 329 (394)
|||.+|..+|-+.|.+.++.= +-..|.+|..|.. +|-||+.+.+|.-.|..+|.=
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~--~~d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f~I 55 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAV--TLDESNINKPYRE-LKIDSLDMFSIIVSLESEFNI 55 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCC--CcccccCCCCHHh-cCCCHHHHHHHHHHHHHHHCC
Confidence 789999999999998765532 2245678889977 999999999999999988743
No 22
>PRK05350 acyl carrier protein; Provisional
Probab=53.78 E-value=11 Score=30.10 Aligned_cols=53 Identities=25% Similarity=0.365 Sum_probs=46.3
Q ss_pred CcHHHHHHHHHHHHHhcCCC-CCCCCCccccChhHHhhhccCccChhhHHHHHhccCC
Q 016177 128 LARTEVVKKLWVYIKENKLQ-DPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (394)
Q Consensus 128 ~sR~~vvk~lW~YIK~nnLq-Dp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~ 184 (394)
|+|.+|...|+++|.+. +. +| ..|.+|..|..-+|-|++.+-+|--.|..+|.
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~~~---~~i~~d~~l~~dlg~DSld~veli~~lE~~fg 55 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEIDP---EDITPEANLYEDLDLDSIDAVDLVVHLQKLTG 55 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCCCH---HHCCCCccchhhcCCCHHHHHHHHHHHHHHHC
Confidence 78999999999999987 43 33 46999999988889999999999999999884
No 23
>PRK12449 acyl carrier protein; Provisional
Probab=52.48 E-value=20 Score=28.13 Aligned_cols=54 Identities=17% Similarity=0.220 Sum_probs=43.9
Q ss_pred ccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCC
Q 016177 272 LARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (394)
Q Consensus 272 ~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~ 328 (394)
|+|.+|...|-+++.+.-=.++ ..|.+|..|..-+|.||+.+.+|.-.|...|.
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 35999999999999999999999998877654
No 24
>CHL00124 acpP acyl carrier protein; Validated
Probab=52.10 E-value=12 Score=29.50 Aligned_cols=54 Identities=9% Similarity=0.211 Sum_probs=45.3
Q ss_pred ccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCC
Q 016177 272 LARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIW 328 (394)
Q Consensus 272 ~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~ 328 (394)
|+|.+|...|-++|.+.-=.+| ..|.+|..|...+|-||+.+.+|.-.|..+|.
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 6889999999999988742333 35999999999999999999999999987765
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=50.06 E-value=33 Score=25.08 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhCCCChhhH-HHHHHHHHHHHhhh
Q 016177 25 AGSVRRLLEEDFKVDLSDRK-AFVSEQIDLFLQTL 58 (394)
Q Consensus 25 ~k~IR~~LE~~fGvDLs~kK-~~I~~~I~~~l~~~ 58 (394)
...++..+.+.+|+||+++| ..|...|..++...
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 35789999999999999877 68888888777643
No 26
>PTZ00171 acyl carrier protein; Provisional
Probab=45.76 E-value=23 Score=32.14 Aligned_cols=59 Identities=10% Similarity=0.147 Sum_probs=50.2
Q ss_pred CCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccCccChhhHHHHHhccCCC
Q 016177 268 GVSELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVNSINMFQMNKALTRHIWP 329 (394)
Q Consensus 268 G~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl~p 329 (394)
|...|++.+|...|+++|.+.--.+| ..|.+|..|..-+|-||+.+.+|.-.|..+|-=
T Consensus 62 ~~~~~~~~~v~~~l~eiiae~l~vd~---~~I~~ds~~~~dLg~DSLd~veLv~~LEdeFgI 120 (148)
T PTZ00171 62 KQYLLSKEDVLTRVKKVVKNFEKVDA---SKITPESNFVKDLGADSLDVVELLIAIEQEFNL 120 (148)
T ss_pred cccccCHHHHHHHHHHHHHHHhCCCH---hhCCCCcchhhhcCCCHHHHHHHHHHHHHHHCC
Confidence 55688999999999999998753343 468999999999999999999999999988754
No 27
>PF13565 HTH_32: Homeodomain-like domain
Probab=43.34 E-value=52 Score=25.28 Aligned_cols=35 Identities=20% Similarity=0.394 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCC
Q 016177 4 DSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDL 40 (394)
Q Consensus 4 d~ei~~~I~~IL~~sDL~tvT~k~IR~~LE~~fGvDL 40 (394)
++++...|.+++..-. ..|...|...|++.||+.+
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 4566566666666443 7899999999999999987
No 28
>PRK05828 acyl carrier protein; Validated
Probab=40.37 E-value=38 Score=27.67 Aligned_cols=54 Identities=15% Similarity=0.244 Sum_probs=44.1
Q ss_pred CcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccCC
Q 016177 128 LARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (394)
Q Consensus 128 ~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~ 184 (394)
|+|.+|..++-..|.+.++.=+ ...|.+|..|.. +|-|++.+.+|--.|..+|.
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 7899999999999987555321 234778889977 99999999999999998874
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=40.16 E-value=1e+02 Score=24.34 Aligned_cols=45 Identities=13% Similarity=0.245 Sum_probs=35.6
Q ss_pred HHHHhcCCCCCcCHHHHHHHHHHHhCCCChh--hHHHHHHHHHHHHh
Q 016177 12 RDILRNSDLDTATAGSVRRLLEEDFKVDLSD--RKAFVSEQIDLFLQ 56 (394)
Q Consensus 12 ~~IL~~sDL~tvT~k~IR~~LE~~fGvDLs~--kK~~I~~~I~~~l~ 56 (394)
++|-.-.|-.-.|...|.+-+++.|++++.+ .+.+++..+...+.
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 3444446778889999999999999999876 67788887776665
No 30
>PRK12449 acyl carrier protein; Provisional
Probab=37.13 E-value=49 Score=25.92 Aligned_cols=54 Identities=17% Similarity=0.247 Sum_probs=44.5
Q ss_pred CcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccCC
Q 016177 128 LARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (394)
Q Consensus 128 ~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~ 184 (394)
|+|.+|..+|-+++.+.-=.++. .|.+|..|..-+|-|++.+.+|.-.|...|.
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 57889999999999865433443 4999999999999999999999999987663
No 31
>PTZ00171 acyl carrier protein; Provisional
Probab=36.48 E-value=38 Score=30.71 Aligned_cols=59 Identities=17% Similarity=0.237 Sum_probs=50.7
Q ss_pred hCCCCCcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccCC
Q 016177 123 VGAPELARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (394)
Q Consensus 123 lG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~ 184 (394)
-|...|++.+|...|+++|.+.-=.+|. .|.+|..+..-+|-|++.+-+|--.|..++.
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 3556789999999999999988644554 4889999999999999999999999999874
No 32
>CHL00124 acpP acyl carrier protein; Validated
Probab=35.41 E-value=31 Score=27.17 Aligned_cols=54 Identities=13% Similarity=0.284 Sum_probs=45.6
Q ss_pred CcHHHHHHHHHHHHHhcCCCCCCCCCccccChhHHhhhccCccChhhHHHHHhccCC
Q 016177 128 LARTEVVKKLWVYIKENKLQDPNNKRKILCDESLQALFGVNSIDMFKMNRALSKHIW 184 (394)
Q Consensus 128 ~sR~~vvk~lW~YIK~nnLqDp~nkr~I~cDe~Lk~lFg~d~i~~f~m~k~L~~Hl~ 184 (394)
|+|.+|...|-++|.+.==.+|. .|.+|..|...+|-|++.+.+|.-.|...|.
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 68899999999999887433443 4999999999999999999999999988764
No 33
>smart00526 H15 Domain in histone families 1 and 5.
Probab=30.42 E-value=2.1e+02 Score=21.78 Aligned_cols=46 Identities=9% Similarity=0.223 Sum_probs=33.0
Q ss_pred HHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHh
Q 016177 11 LRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFLQ 56 (394)
Q Consensus 11 I~~IL~~sDL~tvT~k~IR~~LE~~fGvDLs~kK~~I~~~I~~~l~ 56 (394)
+++|..-.+..-.|...|++-+++.|+++-...+.+++..+.....
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 3455555777788999999999999998755555666666654443
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=29.70 E-value=78 Score=23.32 Aligned_cols=39 Identities=23% Similarity=0.318 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHhc-------------CCCCCcCHHHHHHHHHHHhCCCChhh
Q 016177 5 SDLVTRLRDILRN-------------SDLDTATAGSVRRLLEEDFKVDLSDR 43 (394)
Q Consensus 5 ~ei~~~I~~IL~~-------------sDL~tvT~k~IR~~LE~~fGvDLs~k 43 (394)
++|...+.++|.. ..++++..-.++..|++.||+.++..
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 22445566788999999999998855
No 35
>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=28.95 E-value=1.8e+02 Score=22.41 Aligned_cols=43 Identities=14% Similarity=0.268 Sum_probs=33.4
Q ss_pred hHHHHHHHHHHhcCCCCCcCHHHHHHHHHH-HhC-CCChhhHHHH
Q 016177 5 SDLVTRLRDILRNSDLDTATAGSVRRLLEE-DFK-VDLSDRKAFV 47 (394)
Q Consensus 5 ~ei~~~I~~IL~~sDL~tvT~k~IR~~LE~-~fG-vDLs~kK~~I 47 (394)
+++...|...|=.||...-++..|...|.. ..+ -.+.....+.
T Consensus 24 ~~~l~ele~~Li~aDVg~~~a~~i~~~ik~~~~~~~~~~~~~~v~ 68 (75)
T PF02881_consen 24 EEFLEELEEALIEADVGVEVAEKIIENIKKKLIKKKGINPREEVK 68 (75)
T ss_dssp HHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHCTTSSHHHHHHH
T ss_pred HHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhcccCCCcHHHHH
Confidence 567888999999999999999999999999 776 3344434333
No 36
>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=28.46 E-value=1.1e+02 Score=26.47 Aligned_cols=49 Identities=20% Similarity=0.321 Sum_probs=39.5
Q ss_pred ChhHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHH
Q 016177 3 SDSDLVTRLRDILRNSDLDTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLF 54 (394)
Q Consensus 3 Sd~ei~~~I~~IL~~sDL~tvT~k~IR~~LE~~fGvDLs~kK~~I~~~I~~~ 54 (394)
|++++-.+-.......|++. =.||+.|...||+||-+-=+.|.+.....
T Consensus 4 t~EeF~aRye~~F~~~~iD~---we~rr~mN~l~~~DlVP~P~ii~aaLrAc 52 (103)
T cd00923 4 TDEEFDARYETYFNRPDIDG---WELRRGLNNLFGYDLVPEPKVIEAALRAC 52 (103)
T ss_pred cHHHHHHHHHHHhCCcCccH---HHHHHHHHHHhccccCCCcHHHHHHHHHH
Confidence 78888888888888887664 45999999999999998877776665443
No 37
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=27.49 E-value=44 Score=27.01 Aligned_cols=23 Identities=39% Similarity=0.540 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhCCCChhhHHHHH
Q 016177 26 GSVRRLLEEDFKVDLSDRKAFVS 48 (394)
Q Consensus 26 k~IR~~LE~~fGvDLs~kK~~I~ 48 (394)
..||..||..||+||+.-+--.+
T Consensus 4 ~~~r~~~e~~~G~dl~~Vrvh~~ 26 (79)
T PF13699_consen 4 ESIRSRLERAFGADLSDVRVHTG 26 (79)
T ss_pred HHHHHHHHHHhCCCccceEEEeC
Confidence 36899999999999996554444
No 38
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=21.91 E-value=1.2e+02 Score=35.08 Aligned_cols=77 Identities=23% Similarity=0.257 Sum_probs=53.1
Q ss_pred CCCCCccccCCHHHHhhhCCC-----cccHHHHHHHHHHHHHHcCCCCCCCCCccccchhhhhhhccC-ccChhhHHHHH
Q 016177 250 RGGFTKLCSLSPDLQTFVGVS-----ELARTEVVKKLWAYIREKNLQDPKNRRNIICDEALQVLFRVN-SINMFQMNKAL 323 (394)
Q Consensus 250 ~~gf~~~~~LS~~La~flG~~-----~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD~kLk~LFg~d-~i~~~~m~klL 323 (394)
+++--..-+|+++|+..+|.- .--..++...+-+-||. || +.+++=..|..|+..- .+.-+-..-+|
T Consensus 126 ~~~~r~~~~l~~~l~~ll~eAN~lfarg~~eeA~~i~~EvIkq----dp---~~~~ay~tL~~IyEqrGd~eK~l~~~ll 198 (895)
T KOG2076|consen 126 GRRSRGKSKLAPELRQLLGEANNLFARGDLEEAEEILMEVIKQ----DP---RNPIAYYTLGEIYEQRGDIEKALNFWLL 198 (895)
T ss_pred CCCCCcccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh----Cc---cchhhHHHHHHHHHHcccHHHHHHHHHH
Confidence 333346678999999999963 45557788888888885 44 4566666777777521 33334445678
Q ss_pred hccCCCCCcc
Q 016177 324 TRHIWPLDEA 333 (394)
Q Consensus 324 ~~Hl~p~dp~ 333 (394)
..|+-|.++.
T Consensus 199 AAHL~p~d~e 208 (895)
T KOG2076|consen 199 AAHLNPKDYE 208 (895)
T ss_pred HHhcCCCChH
Confidence 8999999984
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=21.39 E-value=23 Score=25.85 Aligned_cols=38 Identities=21% Similarity=0.374 Sum_probs=20.7
Q ss_pred HHHhhhCCCCCcHHHHHHHHHHHHHhcCCCCCCCCCcc
Q 016177 118 QLQKVVGAPELARTEVVKKLWVYIKENKLQDPNNKRKI 155 (394)
Q Consensus 118 ~La~~lG~~~~sR~~vvk~lW~YIK~nnLqDp~nkr~I 155 (394)
+|+.++|....+-+.+++.|-+.==-..-++|+|+|.|
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 78888887555545555544331111233567777754
No 40
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=21.22 E-value=46 Score=32.48 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=10.0
Q ss_pred hhHHhhhccCccChh
Q 016177 159 ESLQALFGVNSIDMF 173 (394)
Q Consensus 159 e~Lk~lFg~d~i~~f 173 (394)
+++|.|++-.+|+..
T Consensus 107 ~~ikavLgaTKiDLP 121 (238)
T PF02084_consen 107 EDIKAVLGATKIDLP 121 (238)
T ss_pred HHHHHHhcccccccc
Confidence 456788887666554
No 41
>PRK07117 acyl carrier protein; Validated
Probab=20.83 E-value=97 Score=24.96 Aligned_cols=52 Identities=15% Similarity=0.216 Sum_probs=0.0
Q ss_pred ccHHHHHHHHHHHHHHcCCCCC-CCCCccccchhhhhhhccCccChhhHHHHHhccC
Q 016177 272 LARTEVVKKLWAYIREKNLQDP-KNRRNIICDEALQVLFRVNSINMFQMNKALTRHI 327 (394)
Q Consensus 272 ~sR~eVvk~lW~YIK~n~LqDP-~nkr~I~CD~kLk~LFg~d~i~~~~m~klL~~Hl 327 (394)
|+|.+|...|-+-|++.- | -+...|..|..|+. +|.||+.+.++--.|...|
T Consensus 1 M~~~ei~~~v~~ii~e~~---p~i~~~~I~~~~~l~D-Lg~DSlD~veiv~~led~f 53 (79)
T PRK07117 1 MDKQRIFDILVRHIREVL---PDLDQHQFQPEDSLVD-LGANSMDRAEIVIMTLESL 53 (79)
T ss_pred CCHHHHHHHHHHHHHHHc---CCCCHHHCCCCCChhh-cCCChHHHHHHHHHHHHHH
No 42
>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=20.63 E-value=69 Score=24.37 Aligned_cols=51 Identities=22% Similarity=0.367 Sum_probs=33.1
Q ss_pred CCccccCCH-HHHhhhCCCcccHHHHHHHHHHHHHHcCCCCCCCCCccccc-hhhhh
Q 016177 253 FTKLCSLSP-DLQTFVGVSELARTEVVKKLWAYIREKNLQDPKNRRNIICD-EALQV 307 (394)
Q Consensus 253 f~~~~~LS~-~La~flG~~~~sR~eVvk~lW~YIK~n~LqDP~nkr~I~CD-~kLk~ 307 (394)
..-++.+|. +||+++|++.. .|. ++-...+..++-+-..+.+++.| ++|++
T Consensus 23 ~~~~~~lt~~~iA~~~g~sr~---tv~-r~l~~l~~~g~I~~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 23 IRIPLPLTQEEIADMLGVSRE---TVS-RILKRLKDEGIIEVKRGKIIILDPERLEE 75 (76)
T ss_dssp EEEEEESSHHHHHHHHTSCHH---HHH-HHHHHHHHTTSEEEETTEEEESSHHHHHH
T ss_pred ceEEecCCHHHHHHHHCCCHH---HHH-HHHHHHHHCCCEEEcCCEEEECCHHHHhc
Confidence 334455554 89999997544 333 33344567778888888888888 44443
No 43
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=20.19 E-value=2.1e+02 Score=19.42 Aligned_cols=34 Identities=21% Similarity=0.253 Sum_probs=21.9
Q ss_pred CCcCHHHHHHHHHHHhCCCChhhHHHHHHHHHHHH
Q 016177 21 DTATAGSVRRLLEEDFKVDLSDRKAFVSEQIDLFL 55 (394)
Q Consensus 21 ~tvT~k~IR~~LE~~fGvDLs~kK~~I~~~I~~~l 55 (394)
+.+|...+|..|. .+|+..+..|+.+-+.|..|+
T Consensus 2 ~~l~v~eLk~~l~-~~gL~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 2 SKLTVAELKEELK-ERGLSTSGKKAELIERLKEHL 35 (35)
T ss_dssp TTSHHHHHHHHHH-HTTS-STSSHHHHHHHHHHHH
T ss_pred CcCcHHHHHHHHH-HCCCCCCCCHHHHHHHHHHhC
Confidence 4566677776665 458888777777766666553
Done!