Query 008555
Match_columns 561
No_of_seqs 215 out of 624
Neff 5.1
Searched_HMMs 46136
Date Thu Mar 28 13:38:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008555.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008555hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2570 SWI/SNF transcription 100.0 4E-111 8E-116 874.4 34.4 393 135-553 20-415 (420)
2 COG5531 SWIB-domain-containing 99.9 9.8E-26 2.1E-30 223.6 8.0 202 227-453 3-224 (237)
3 smart00151 SWIB SWI complex, B 99.9 1E-21 2.3E-26 164.9 7.8 76 344-419 2-77 (77)
4 PF02201 SWIB: SWIB/MDM2 domai 99.8 2.4E-22 5.1E-27 168.4 1.1 74 344-417 2-75 (76)
5 KOG1946 RNA polymerase I trans 99.7 4.8E-18 1E-22 170.1 6.4 82 343-424 100-181 (240)
6 PRK14724 DNA topoisomerase III 99.6 3.2E-16 7E-21 183.5 7.4 73 346-418 915-987 (987)
7 PRK06319 DNA topoisomerase I/S 99.0 1.2E-10 2.7E-15 135.6 5.0 74 345-418 786-859 (860)
8 PF03366 YEATS: YEATS family; 83.5 3.3 7.2E-05 35.8 6.0 55 286-349 16-72 (84)
9 KOG2522 Filamentous baseplate 70.1 6.2 0.00013 43.8 4.8 65 355-419 372-448 (560)
10 KOG0487 Transcription factor A 59.8 8.8 0.00019 40.8 3.5 37 196-235 246-285 (308)
11 PRK05350 acyl carrier protein; 46.5 19 0.00042 30.2 2.9 54 362-418 2-55 (82)
12 KOG0993 Rab5 GTPase effector R 45.3 46 0.00099 36.9 6.0 59 463-529 158-226 (542)
13 KOG1151 Tousled-like protein k 40.0 30 0.00065 39.1 3.7 15 501-515 718-732 (775)
14 PF09804 DUF2347: Uncharacteri 35.5 39 0.00085 35.5 3.7 37 294-333 3-41 (280)
15 PRK05849 hypothetical protein; 30.6 5E+02 0.011 31.4 12.0 44 354-402 266-315 (783)
16 PF03678 Adeno_hexon_C: Hexon, 29.6 70 0.0015 32.6 4.1 39 284-329 77-115 (237)
17 KOG1151 Tousled-like protein k 28.8 35 0.00076 38.5 2.1 44 196-239 269-318 (775)
18 PRK05828 acyl carrier protein; 26.5 96 0.0021 26.7 4.0 53 362-417 1-53 (84)
19 PF01047 MarR: MarR family; I 20.3 30 0.00066 26.6 -0.3 38 352-389 22-59 (59)
20 PF07898 DUF1676: Protein of u 20.1 87 0.0019 27.3 2.5 53 318-381 17-69 (106)
No 1
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=3.6e-111 Score=874.44 Aligned_cols=393 Identities=45% Similarity=0.805 Sum_probs=370.6
Q ss_pred ccccCCCCCCC-CCCCCCCCCCCccccccCCChHHHhhcCCCCCCC-CchHHHhhccchHHHHHHHHHHHHHHHHHHHhh
Q 008555 135 AKRATQKPPSR-PPGSSSNTNSGSLFKTTELTPAARRKKRKLPEKQ-IPDKVAAILPECALYTQLLEFEARVDSALARKK 212 (561)
Q Consensus 135 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~aa~rkkrk~tDk~-iP~~v~~lvPes~~Y~~L~e~ErrLD~~I~RKr 212 (561)
++|..++||.. |++++ .. ..||+|+.||. ||+++.+++||++.|..|+++|+|||++|+|||
T Consensus 20 ~~~~~~~~~~~~p~~~~---------------~~-~~kk~kl~dk~~i~~~~~~~ipes~~y~~Ll~~e~Kld~~i~Rk~ 83 (420)
T KOG2570|consen 20 MSRQTPMPPLQDPPQAP---------------EP-ELKKKKLADKLNIPQRILELIPESQAYMDLLAFERKLDSTIIRKR 83 (420)
T ss_pred cccCCCCCCCCCCCCCC---------------cc-hhhhhhcchhcccCHHHHhhCccHHHHHHHHHHHHHhhhHHHHhh
Confidence 67777777755 33322 00 14677788887 999999999999999999999999999999999
Q ss_pred hhHHHHhcCCCCCceeEEEEEEEeecCCCCCCCCCCCCCCCceEEEEEEEEcCCCCCchhhcccCCCCCCCcccccccce
Q 008555 213 IDIQESLKNPPRVQKTLRMYVFNTFANQDETSPEKKTGEAPCWSLKLIGRILEDGQDPVLAGLMQKSDTLYPKFSSFFKK 292 (561)
Q Consensus 213 lDiqesl~rp~k~~rtLRIfIsNT~enQpwq~~~~~~~~~psWtLrIEGRLLdd~~~~~~~~~~~~~~~~~~KFSSFfk~ 292 (561)
+||||+|+++.+.+|+|||||||||+||+|+......+..|+|||||||||||+..+. . .++|||||||+
T Consensus 84 ~diqealK~p~~~kk~LRIyI~ntf~~~~~~~~~~~~a~~~sWtLriEGrLLd~~~~~---------~-~krkFSsFfks 153 (420)
T KOG2570|consen 84 LDIQEALKRPPKIKKKLRIYISNTFENQKPSTKDTPEADLPSWTLRIEGRLLDDPVDD---------W-GKRKFSSFFKS 153 (420)
T ss_pred hhHHHHhcCCccccceEEEEEEecccCCCCCCCCCCCCCCcceeeeeeeeecccCccc---------c-ccccchHHHhh
Confidence 9999999999999999999999999999998766556779999999999999987321 1 17999999999
Q ss_pred eeEeeCCCCC-CCCceEEecCCCCCCCCcceEEEecCCCcccEEEEEeecccCccccCCHHHHhhhCCCccCHHHHHHHH
Q 008555 293 ITIYLDQSLY-PDNHVILWESARSPALHEGFEVKRKGDKEFTAIIRIEMNYFPEKSKLSPSLMELLGIEVDTRPRIIAAI 371 (561)
Q Consensus 293 I~VelD~~ly-Pd~~~VEW~k~~s~~efDGfeIKR~Gden~~itI~L~~~~~Per~kLSpeLa~~LG~~e~TR~eiv~~L 371 (561)
|+|+||+++| |++|.||||+..++++||||+|||.||.++.|+|.|+++++|++|+|||.||.+||+.++||++||.+|
T Consensus 154 lvIelDk~~y~P~~~lvEW~r~~~~~etdGf~VKR~Gd~~v~ctIll~l~~~P~~fklsp~La~lLGi~t~Trp~iI~al 233 (420)
T KOG2570|consen 154 LVIELDKDLYGPDNHLVEWHRDPNTNETDGFQVKRPGDRNVRCTILLLLDYQPEEFKLSPRLANLLGIHTGTRPDIVTAL 233 (420)
T ss_pred hhhhhhhhhccCccceeeeeecCCCCCcCceeeeccCCCccceEEEEeeccCCcccccCHHHHHHhhhccCcchHHHHHH
Confidence 9999999887 999999999998999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccCCCCCCceeeeeeecCCCCCCCCceeeeEeeccCc
Q 008555 372 WHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHLIPPPPIHLEHKIKLSGNSPAGTSCYDMLVDVPFP 451 (561)
Q Consensus 372 W~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL~P~~PI~L~ytIrvd~~~~~~~t~yDV~Vdv~dp 451 (561)
|+|||.|+|||++|+.+|+||..|+++||+++++|.+|+.+|++||.|++||+|+|+|+||++.+++++||||+|+|++|
T Consensus 234 WqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~dPIvi~h~I~v~~~~~~~tacyDIdV~v~~p 313 (420)
T KOG2570|consen 234 WQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPDPIVIDHTISVDGNDTKVTACYDIDVEVEDP 313 (420)
T ss_pred HHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCCCeeecceeccCCCcccceeEEeeeeccCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhhchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHHHcCCCCCCcchhcc
Q 008555 452 LEKEMAAFLANMEKNKEIDACDELICASIKKIHEHRRRRAFFLGFSQSPGEFINALIASQSKDLKLVAGDASRNAEKERR 531 (561)
Q Consensus 452 l~~~~~~fl~~~~~~keI~~LDekIa~~i~~I~~~k~rr~F~~~fSeDPv~FI~~wI~SQsrDLkvl~gd~~~~~E~~RR 531 (561)
++.+|..|+.+++..+||+.||++|+.++++||+++.||+||++||+||++||++||+||++|||+|.||.++|+|++||
T Consensus 314 ~~~q~~nfl~~~~~~~eI~alD~kI~~li~~ine~~~rr~Ff~~Fs~dPvefin~wi~Sq~~Dlkv~~gd~~~N~e~eRr 393 (420)
T KOG2570|consen 314 RKSQMSNFLASTESQKEIAALDRKITELIQQINESKERRDFFLEFSKDPVEFINEWIESQSSDLKVLAGDVSGNPEEERR 393 (420)
T ss_pred cchhhhhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCHHHHHHHHHHhcchhhHHhhccccCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCchhHHHHHHHHHhccCC
Q 008555 532 SDFFNQPWVEDAVIRYMNRKSA 553 (561)
Q Consensus 532 sefy~qpWV~eAV~rYL~~k~~ 553 (561)
++||++|||+|||+||+++++.
T Consensus 394 aefy~qpw~~eav~ry~~~~~~ 415 (420)
T KOG2570|consen 394 AEFYKQPWTDEAVSRYMFLKVQ 415 (420)
T ss_pred HHHHcCccHHHHHHHHHHHHHh
Confidence 9999999999999999999976
No 2
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.92 E-value=9.8e-26 Score=223.56 Aligned_cols=202 Identities=23% Similarity=0.309 Sum_probs=156.8
Q ss_pred eeEEEEEEEeecCCCCCCCCC-----CCCCCCceEEEEEEEEcCCCCCchhhcccCCCCCCCcccccccceeeEeeCC--
Q 008555 227 KTLRMYVFNTFANQDETSPEK-----KTGEAPCWSLKLIGRILEDGQDPVLAGLMQKSDTLYPKFSSFFKKITIYLDQ-- 299 (561)
Q Consensus 227 rtLRIfIsNT~enQpwq~~~~-----~~~~~psWtLrIEGRLLdd~~~~~~~~~~~~~~~~~~KFSSFfk~I~VelD~-- 299 (561)
...|+.+.|+...|.|..... .....+.|+++|+||+++-.. ..+.+|.++.....+....
T Consensus 3 ~~~~~~~~~~~~~~~~e~~~~~ek~v~~~~~~~~~~~l~~r~k~~~~------------~~~~~~~s~~~~~~~~~~~k~ 70 (237)
T COG5531 3 CYNRYGTMNDSWLQLDERDTNNEKDVGKLLFSEWTVRLEGRFKDNND------------LIRDKFDSLAEEPRVLRKEKY 70 (237)
T ss_pred cccccccccceeeecccccccChhhcccccchhhheehhhhhhhccc------------hhhhhhhhhcccchhhhhhhh
Confidence 457888888888888864321 234568999999999998321 1257788877776665432
Q ss_pred ------CCCCCCceEEecCCC-------CCCCCcceEEEecCCCcccEEEEEeecccCccccCCHHHHhhhCCCccCHHH
Q 008555 300 ------SLYPDNHVILWESAR-------SPALHEGFEVKRKGDKEFTAIIRIEMNYFPEKSKLSPSLMELLGIEVDTRPR 366 (561)
Q Consensus 300 ------~lyPd~~~VEW~k~~-------s~~efDGfeIKR~Gden~~itI~L~~~~~Per~kLSpeLa~~LG~~e~TR~e 366 (561)
.++.+..-.+|..-+ +..+++|...+|.+... ......+++|+||+.||.|||..++||++
T Consensus 71 ~~~r~~~~~~~~~~~~~~~~~s~k~~~n~~te~k~~~~~k~~~~~------~~~~~~~~~~~lS~~La~ilG~~~~tr~~ 144 (237)
T COG5531 71 NITRKTTGKNDLPKEEDSSLPSSKETENGDTEGKETDKKKKSSTI------SKNSPSGEKVKLSPKLAAILGLEPGTRPE 144 (237)
T ss_pred ccCcccccccccccccccccCcchhhhcCcccccccccccccccc------ccccCCCCceecCHHHHHHhCCCCCCccH
Confidence 234555555665432 22467777777777532 33456788999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccCCCCCCceeeeeeecCCCCCCCCceeeeEe
Q 008555 367 IIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHLIPPPPIHLEHKIKLSGNSPAGTSCYDMLV 446 (561)
Q Consensus 367 iv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL~P~~PI~L~ytIrvd~~~~~~~t~yDV~V 446 (561)
||+.||+|||.||||+|+||++|.||+.|+.|||.+.|.|++|.+ |+.|+.+.|++++++..+++.++.|++|
T Consensus 145 ~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k-------~l~~hl~~~~~~vs~~~~~~~~~~d~ei 217 (237)
T COG5531 145 AVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTK-------PLSPHLIKYTIDVSKAPTYGGTTLDIEI 217 (237)
T ss_pred HHHHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhc-------ccccceecCccccccCCCcCcceecccC
Confidence 999999999999999999999999999999999988999999984 4555567899999999999999999998
Q ss_pred eccCchH
Q 008555 447 DVPFPLE 453 (561)
Q Consensus 447 dv~dpl~ 453 (561)
..+.+..
T Consensus 218 ~~~~~~~ 224 (237)
T COG5531 218 PLENDSL 224 (237)
T ss_pred Ccccccc
Confidence 7776543
No 3
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.85 E-value=1e-21 Score=164.94 Aligned_cols=76 Identities=33% Similarity=0.702 Sum_probs=74.0
Q ss_pred CccccCCHHHHhhhCCCccCHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccCCC
Q 008555 344 PEKSKLSPSLMELLGIEVDTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHLIP 419 (561)
Q Consensus 344 Per~kLSpeLa~~LG~~e~TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL~P 419 (561)
+++|+||++|++|+|..++||++|+++||+|||.|||+||+|++.|+||+.|+++||++++.|++|+++|++||.|
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 4789999999999999999999999999999999999999999999999999999999999999999999999975
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=99.84 E-value=2.4e-22 Score=168.45 Aligned_cols=74 Identities=36% Similarity=0.766 Sum_probs=70.7
Q ss_pred CccccCCHHHHhhhCCCccCHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccC
Q 008555 344 PEKSKLSPSLMELLGIEVDTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHL 417 (561)
Q Consensus 344 Per~kLSpeLa~~LG~~e~TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL 417 (561)
|++|+|||+|++++|..++||++|++.||+||++|+|+||+|++.|+||+.|++|||+++|.|++|+++|++||
T Consensus 2 ~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl 75 (76)
T PF02201_consen 2 PKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHL 75 (76)
T ss_dssp EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHH
T ss_pred CCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhc
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999997
No 5
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.72 E-value=4.8e-18 Score=170.06 Aligned_cols=82 Identities=24% Similarity=0.551 Sum_probs=77.8
Q ss_pred cCccccCCHHHHhhhCCCccCHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccCCCCCC
Q 008555 343 FPEKSKLSPSLMELLGIEVDTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHLIPPPP 422 (561)
Q Consensus 343 ~Per~kLSpeLa~~LG~~e~TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL~P~~P 422 (561)
.-+.+.||+.|+.++|.++++|.+|++.||+|||+||||||.|++.|.||+.|+.|||..+|.|++|+++|.+||.....
T Consensus 100 ~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H~~~~~d 179 (240)
T KOG1946|consen 100 STKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKHFLKNQD 179 (240)
T ss_pred cccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHhccCccc
Confidence 34668999999999999999999999999999999999999999999999999999999999999999999999998877
Q ss_pred ce
Q 008555 423 IH 424 (561)
Q Consensus 423 I~ 424 (561)
+.
T Consensus 180 ~~ 181 (240)
T KOG1946|consen 180 MV 181 (240)
T ss_pred cc
Confidence 64
No 6
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.62 E-value=3.2e-16 Score=183.48 Aligned_cols=73 Identities=29% Similarity=0.595 Sum_probs=71.7
Q ss_pred cccCCHHHHhhhCCCccCHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccCC
Q 008555 346 KSKLSPSLMELLGIEVDTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHLI 418 (561)
Q Consensus 346 r~kLSpeLa~~LG~~e~TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL~ 418 (561)
.|+|||+|++|||..++||++||++||+|||.||||||+|++.|+||++|+.|||+++|.|++|+++|++||.
T Consensus 915 ~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 915 GLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS 987 (987)
T ss_pred ccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999984
No 7
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.04 E-value=1.2e-10 Score=135.61 Aligned_cols=74 Identities=34% Similarity=0.539 Sum_probs=71.5
Q ss_pred ccccCCHHHHhhhCCCccCHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccCC
Q 008555 345 EKSKLSPSLMELLGIEVDTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHLI 418 (561)
Q Consensus 345 er~kLSpeLa~~LG~~e~TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL~ 418 (561)
..|.+|++|+.++|..+++|.++++.||+|||.|+||||+|++.|+||++|+++||++++.|++|+++|+.||.
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 44889999999999999999999999999999999999999999999999999999999999999999999985
No 8
>PF03366 YEATS: YEATS family; InterPro: IPR005033 Named the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit', this family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3QRL_A 2L7E_A 3FK3_C 3RLS_A.
Probab=83.48 E-value=3.3 Score=35.80 Aligned_cols=55 Identities=27% Similarity=0.303 Sum_probs=35.8
Q ss_pred cccccceeeEeeCCCCCCCCceEEecCCCCCCCCcceEEEecCCCcccEEEEEeecc--cCccccC
Q 008555 286 FSSFFKKITIYLDQSLYPDNHVILWESARSPALHEGFEVKRKGDKEFTAIIRIEMNY--FPEKSKL 349 (561)
Q Consensus 286 FSSFfk~I~VelD~~lyPd~~~VEW~k~~s~~efDGfeIKR~Gden~~itI~L~~~~--~Per~kL 349 (561)
.+.|+++++..|.++.-+.. ..=+++ =|+|.+.|=-++++.|.|+... ....+.+
T Consensus 16 ~~~~i~kV~f~LHpsF~~p~--r~v~~p-------PFevte~GWGeF~i~I~i~f~~~~~~~~~~~ 72 (84)
T PF03366_consen 16 LSYFIKKVTFKLHPSFPNPV--RVVTKP-------PFEVTETGWGEFEIPIKIHFKDPSNEKPVTI 72 (84)
T ss_dssp -TTTEEEEEEES-TTSSS-E--EECSST-------TEEEEEEESS--EEEEEEECCCGGCTCEEEE
T ss_pred ccceEEEEEEECCCCCCCCc--eEecCC-------CCEEEEeEeccEEEEEEEEEeCCCCCCcEEE
Confidence 68999999999997643332 222222 3999999999999999998766 3444443
No 9
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=70.14 E-value=6.2 Score=43.84 Aligned_cols=65 Identities=15% Similarity=0.296 Sum_probs=48.7
Q ss_pred hhhCCC---ccCHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCc---------CccchhhHHHHHHccCCC
Q 008555 355 ELLGIE---VDTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGE---------EKIKFATISQKISQHLIP 419 (561)
Q Consensus 355 ~~LG~~---e~TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~---------d~i~f~eL~~lL~~HL~P 419 (561)
.=+|.. -.|-.+|-..+-+||+.|||-|+.||..|+.|+.|-..... ..+....|..++...+.|
T Consensus 372 ~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~k~~K~~~a~~~~~pw~~l~~~~~~rmtp 448 (560)
T KOG2522|consen 372 KEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVNKKKKVLNASRIIAPWEILHPLLTNRMTP 448 (560)
T ss_pred HhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHHhhhhccccccccccHHHHHHHHHhcCCc
Confidence 334665 45679999999999999999999999999999998766543 233455666666655554
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=59.83 E-value=8.8 Score=40.83 Aligned_cols=37 Identities=19% Similarity=0.471 Sum_probs=25.0
Q ss_pred HHHHHHHH--HHHHHHH-hhhhHHHHhcCCCCCceeEEEEEEE
Q 008555 196 QLLEFEAR--VDSALAR-KKIDIQESLKNPPRVQKTLRMYVFN 235 (561)
Q Consensus 196 ~L~e~Err--LD~~I~R-KrlDiqesl~rp~k~~rtLRIfIsN 235 (561)
|++|+||+ .+.+|+| ||++|.-.|.-.. |-+-||.-|
T Consensus 246 QtlELEkEFlfN~YitkeKR~ElSr~lNLTe---RQVKIWFQN 285 (308)
T KOG0487|consen 246 QTLELEKEFLFNMYITKEKRLELSRTLNLTE---RQVKIWFQN 285 (308)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHhcccch---hheeeeehh
Confidence 66777776 6889988 6789888876433 334455544
No 11
>PRK05350 acyl carrier protein; Provisional
Probab=46.51 E-value=19 Score=30.24 Aligned_cols=54 Identities=13% Similarity=0.154 Sum_probs=45.2
Q ss_pred cCHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccCC
Q 008555 362 DTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHLI 418 (561)
Q Consensus 362 ~TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL~ 418 (561)
+||.++...|.++|... +- -+...|.+|..|..-+|-|++.+.+|.-.|..+|.
T Consensus 2 m~~~~i~~~v~~ii~~~-~~--~~~~~i~~d~~l~~dlg~DSld~veli~~lE~~fg 55 (82)
T PRK05350 2 MTREEILERLRAILVEL-FE--IDPEDITPEANLYEDLDLDSIDAVDLVVHLQKLTG 55 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hC--CCHHHCCCCccchhhcCCCHHHHHHHHHHHHHHHC
Confidence 68999999999999886 42 23357999999988889999999999998888763
No 12
>KOG0993 consensus Rab5 GTPase effector Rabaptin-5 [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.27 E-value=46 Score=36.93 Aligned_cols=59 Identities=19% Similarity=0.305 Sum_probs=45.4
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHH-HHHHH---------HHHhhhCHHHHHHHHHHHHHHHHHHHcCCCCCCcchh
Q 008555 463 MEKNKEIDACDELICASIKKIHEHR-RRRAF---------FLGFSQSPGEFINALIASQSKDLKLVAGDASRNAEKE 529 (561)
Q Consensus 463 ~~~~keI~~LDekIa~~i~~I~~~k-~rr~F---------~~~fSeDPv~FI~~wI~SQsrDLkvl~gd~~~~~E~~ 529 (561)
+.+.++|.+|.++++..-+.|.++. ++|.. ++.|++|| +-|-|-|+-+.||+|..+|..
T Consensus 158 ~pmekeI~elk~kl~~aE~~i~El~k~~~h~a~slh~~t~lL~L~RD~--------s~~l~~leel~gd~gps~d~F 226 (542)
T KOG0993|consen 158 TPMEKEINELKKKLAKAEQRIDELSKAKHHKAESLHVFTDLLNLARDK--------SEQLRQLEELDGDAGPSGDDF 226 (542)
T ss_pred hhHHHHHHHHHHHHHhHHHHHHHHHhhhcccchHHHHHHHHHHHhcCC--------chhhhHHHHhccCCCCCcchh
Confidence 4567899999999999999999974 66663 46678887 455677888889988766544
No 13
>KOG1151 consensus Tousled-like protein kinase [Signal transduction mechanisms]
Probab=39.97 E-value=30 Score=39.08 Aligned_cols=15 Identities=27% Similarity=0.372 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHH
Q 008555 501 GEFINALIASQSKDL 515 (561)
Q Consensus 501 v~FI~~wI~SQsrDL 515 (561)
..||.++|+=-++|-
T Consensus 718 kaFIRRCLaYRKeDR 732 (775)
T KOG1151|consen 718 KAFIRRCLAYRKEDR 732 (775)
T ss_pred HHHHHHHHHhhhhhh
Confidence 568888887766553
No 14
>PF09804 DUF2347: Uncharacterized conserved protein (DUF2347); InterPro: IPR018626 Members of this family of hypothetical proteins have no known function.
Probab=35.51 E-value=39 Score=35.47 Aligned_cols=37 Identities=24% Similarity=0.396 Sum_probs=27.3
Q ss_pred eEeeCCCCCCCCceEEecCCCCCCCCcceEEEe--cCCCccc
Q 008555 294 TIYLDQSLYPDNHVILWESARSPALHEGFEVKR--KGDKEFT 333 (561)
Q Consensus 294 ~VelD~~lyPd~~~VEW~k~~s~~efDGfeIKR--~Gden~~ 333 (561)
.|+||.. .+++|+|.++....++||+|+|- .|--++.
T Consensus 3 l~~FD~k---~Gn~i~W~~~~~~i~L~gVEfKsLPSGlH~v~ 41 (280)
T PF09804_consen 3 LVKFDVK---KGNTIVWSRPAPDIDLEGVEFKSLPSGLHEVD 41 (280)
T ss_pred EEEecCC---CCcEEEEeccCCCCccCCeeEecCCccccccc
Confidence 4667754 36899999987778999999997 3444443
No 15
>PRK05849 hypothetical protein; Provisional
Probab=30.65 E-value=5e+02 Score=31.42 Aligned_cols=44 Identities=20% Similarity=0.368 Sum_probs=29.2
Q ss_pred HhhhCCCcc------CHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcC
Q 008555 354 MELLGIEVD------TRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEE 402 (561)
Q Consensus 354 a~~LG~~e~------TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d 402 (561)
|+|||+..- =|.=|+..+|.|-+.|= -=|.++.++.|..+.|..
T Consensus 266 AEiIG~~P~~La~SLYr~litd~~Wa~~r~~~-----GYr~~r~~~Lm~~f~g~P 315 (783)
T PRK05849 266 AEIIGLRPKPLAFSLYRELITDNIWAYQRDNY-----GYRDLRSHPLMHSFAGIP 315 (783)
T ss_pred HHHhCCCCccchHHHHHHHHhhHHHHHHHHhC-----CCCcCCCchHHHHhCCCc
Confidence 678888643 35667889999988752 123455666777777764
No 16
>PF03678 Adeno_hexon_C: Hexon, adenovirus major coat protein, C-terminal domain; InterPro: IPR016108 Hexon is a major coat protein found in various species-specific Adenoviruses, which are type II dsDNA viruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices []. The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a beta-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions []. This entry represents the C-terminal domain of hexon coat proteins.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2BVI_M 1VSZ_K 3IYN_D 3TG7_A 1P30_A 2OBE_B 2INY_A 1P2Z_A.
Probab=29.61 E-value=70 Score=32.62 Aligned_cols=39 Identities=28% Similarity=0.483 Sum_probs=26.2
Q ss_pred cccccccceeeEeeCCCCCCCCceEEecCCCCCCCCcceEEEecCC
Q 008555 284 PKFSSFFKKITIYLDQSLYPDNHVILWESARSPALHEGFEVKRKGD 329 (561)
Q Consensus 284 ~KFSSFfk~I~VelD~~lyPd~~~VEW~k~~s~~efDGfeIKR~Gd 329 (561)
--+|+=|++++|.+|.+ |-|--..----=..|||||.-|
T Consensus 77 FYL~HTFr~vsI~fDss-------V~WPGnDRlLtPN~FEIKR~~D 115 (237)
T PF03678_consen 77 FYLSHTFRRVSIQFDSS-------VPWPGNDRLLTPNEFEIKRNVD 115 (237)
T ss_dssp -SSGGGEEEEEEEETTT-------EECSSTTCSSSTTSEESB-SSC
T ss_pred EEEeeeeeeeeEEeccc-------cCCCCCccccCCCceeeeeccc
Confidence 45799999999999964 8884432111224799999855
No 17
>KOG1151 consensus Tousled-like protein kinase [Signal transduction mechanisms]
Probab=28.84 E-value=35 Score=38.54 Aligned_cols=44 Identities=25% Similarity=0.389 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHH-HHhhhhHHHHhc-----CCCCCceeEEEEEEEeecC
Q 008555 196 QLLEFEARVDSAL-ARKKIDIQESLK-----NPPRVQKTLRMYVFNTFAN 239 (561)
Q Consensus 196 ~L~e~ErrLD~~I-~RKrlDiqesl~-----rp~k~~rtLRIfIsNT~en 239 (561)
-|..+-.||..++ |-|||=|.-+-. |-..-.-.|||=-+.|+-+
T Consensus 269 ~LEkyKerlnkcv~msKkLLIeKs~qEk~a~RdKsmqDrlRlGhFtTvRh 318 (775)
T KOG1151|consen 269 MLEKYKERLNKCVTMSKKLLIEKSKQEKMACRDKSMQDRLRLGHFTTVRH 318 (775)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhHHHHHhhhhhhhhhcccccceeeeec
Confidence 3444455566533 345555543221 2233445677766666544
No 18
>PRK05828 acyl carrier protein; Validated
Probab=26.53 E-value=96 Score=26.71 Aligned_cols=53 Identities=11% Similarity=0.147 Sum_probs=41.8
Q ss_pred cCHHHHHHHHHHHHHhcCCCCCCCCCceecChhhhhhhCcCccchhhHHHHHHccC
Q 008555 362 DTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEKIKFATISQKISQHL 417 (561)
Q Consensus 362 ~TR~eiv~~LW~YIK~n~Lqdp~dkr~I~cDe~Lk~LFg~d~i~f~eL~~lL~~HL 417 (561)
|||.+|+..|=+-|...++--+ ...|.+|..|.. +|-|++.+.+|.-.|...+
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~~--~d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f 53 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAVT--LDESNINKPYRE-LKIDSLDMFSIIVSLESEF 53 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCCC--cccccCCCCHHh-cCCCHHHHHHHHHHHHHHH
Confidence 6899999999999987655322 235688889977 9999999999888877655
No 19
>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=20.34 E-value=30 Score=26.65 Aligned_cols=38 Identities=29% Similarity=0.371 Sum_probs=26.9
Q ss_pred HHHhhhCCCccCHHHHHHHHHHHHHhcCCCCCCCCCce
Q 008555 352 SLMELLGIEVDTRPRIIAAIWHYVKVKKLQSPNDPSSF 389 (561)
Q Consensus 352 eLa~~LG~~e~TR~eiv~~LW~YIK~n~Lqdp~dkr~I 389 (561)
+|++.+|++..+-..++..|-+.=....-.+|+|+|.|
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 89999999888888888877664434444577777754
No 20
>PF07898 DUF1676: Protein of unknown function (DUF1676); InterPro: IPR012464 This family contains sequences derived from proteins of unknown function expressed by Drosophila melanogaster and Anopheles gambiae.
Probab=20.09 E-value=87 Score=27.28 Aligned_cols=53 Identities=11% Similarity=0.177 Sum_probs=29.9
Q ss_pred CCcceEEEecCCCcccEEEEEeecccCccccCCHHHHhhhCCCccCHHHHHHHHHHHHHhcCCC
Q 008555 318 LHEGFEVKRKGDKEFTAIIRIEMNYFPEKSKLSPSLMELLGIEVDTRPRIIAAIWHYVKVKKLQ 381 (561)
Q Consensus 318 efDGfeIKR~Gden~~itI~L~~~~~Per~kLSpeLa~~LG~~e~TR~eiv~~LW~YIK~n~Lq 381 (561)
-+||+.|.|.++......-. ......+.-. ..+.--.-++.++|.|+..|.|+
T Consensus 17 l~dgv~lvr~~~~~~~~~~~-------~~~~~~~~~~----~~~~l~~~l~~k~~~fl~th~L~ 69 (106)
T PF07898_consen 17 LTDGVSLVRNPEAAERSSEA-------ESRSVDEEDS----REEELDNLLLDKVERFLQTHSLR 69 (106)
T ss_pred ecCCEEEEECCCCccccccc-------cccccccccc----hhhHHHHHHHHHHHHHHHhceEE
Confidence 47999999999754321110 0011111000 11222355788999999999987
Done!