Query 003906
Match_columns 787
No_of_seqs 69 out of 71
Neff 3.1
Searched_HMMs 46136
Date Thu Mar 28 14:07:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003906.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003906hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4468 Polycomb-group transcr 100.0 4.1E-90 8.9E-95 751.0 22.3 654 42-770 74-777 (782)
2 PF00249 Myb_DNA-binding: Myb- 98.3 1.1E-06 2.4E-11 69.0 5.5 44 52-95 2-47 (48)
3 smart00717 SANT SANT SWI3, AD 98.1 3.7E-06 8.1E-11 62.6 4.5 46 52-97 2-48 (49)
4 cd00167 SANT 'SWI3, ADA2, N-Co 98.0 1.2E-05 2.7E-10 59.2 5.2 43 53-95 1-44 (45)
5 KOG4167 Predicted DNA-binding 97.2 0.00032 6.9E-09 81.7 5.3 50 52-102 620-669 (907)
6 PF13921 Myb_DNA-bind_6: Myb-l 96.9 0.003 6.4E-08 51.2 6.6 56 54-116 1-56 (60)
7 KOG1194 Predicted DNA-binding 95.8 0.015 3.3E-07 65.5 6.0 56 46-102 182-237 (534)
8 TIGR01557 myb_SHAQKYF myb-like 95.7 0.022 4.7E-07 47.9 5.2 43 52-94 4-52 (57)
9 KOG3554 Histone deacetylase co 94.3 0.035 7.6E-07 63.0 3.6 55 47-102 281-336 (693)
10 PLN03091 hypothetical protein; 93.2 0.17 3.7E-06 57.4 6.4 62 52-117 68-129 (459)
11 PLN03212 Transcription repress 93.1 0.17 3.6E-06 53.8 5.8 51 51-101 78-128 (249)
12 KOG4329 DNA-binding protein [G 93.0 0.11 2.5E-06 57.7 4.6 55 43-98 269-324 (445)
13 COG5118 BDP1 Transcription ini 92.1 0.27 5.9E-06 55.0 6.1 58 52-109 366-427 (507)
14 KOG0457 Histone acetyltransfer 90.0 0.47 1E-05 53.7 5.5 49 48-96 69-118 (438)
15 PLN03212 Transcription repress 87.7 4.2 9E-05 43.6 10.2 78 51-139 25-104 (249)
16 PLN03091 hypothetical protein; 87.0 4.5 9.8E-05 46.4 10.5 79 51-140 14-94 (459)
17 PLN03142 Probable chromatin-re 76.4 4 8.6E-05 50.9 5.7 51 51-101 824-875 (1033)
18 COG5114 Histone acetyltransfer 73.6 9.3 0.0002 42.6 7.0 48 50-97 62-110 (432)
19 COG5259 RSC8 RSC chromatin rem 71.0 4 8.7E-05 47.1 3.7 38 52-89 280-317 (531)
20 KOG1194 Predicted DNA-binding 67.3 2.6 5.6E-05 48.5 1.2 50 50-100 469-518 (534)
21 KOG0049 Transcription factor, 62.2 16 0.00034 44.1 6.2 71 52-133 361-432 (939)
22 KOG2009 Transcription initiati 61.7 13 0.00027 44.2 5.3 75 37-113 397-477 (584)
23 PF08897 DUF1841: Domain of un 45.4 15 0.00032 36.5 2.2 18 84-101 2-19 (137)
24 PHA02054 hypothetical protein 39.4 10 0.00022 35.2 0.0 17 356-372 51-67 (94)
25 KOG0048 Transcription factor, 38.5 62 0.0013 33.7 5.6 46 51-96 62-107 (238)
26 TIGR02937 sigma70-ECF RNA poly 36.2 82 0.0018 27.7 5.3 49 53-103 110-158 (158)
27 PF13873 Myb_DNA-bind_5: Myb/S 32.4 1.6E+02 0.0034 25.1 6.2 70 52-128 3-72 (78)
28 KOG1279 Chromatin remodeling f 31.9 44 0.00095 39.3 3.6 40 49-88 251-290 (506)
29 PF04192 Utp21: Utp21 specific 31.4 1.1E+02 0.0024 32.5 6.1 25 57-81 157-184 (237)
30 PF12776 Myb_DNA-bind_3: Myb/S 31.1 1.9E+02 0.004 25.3 6.6 40 53-92 1-58 (96)
31 PF05757 PsbQ: Oxygen evolving 27.8 1.3E+02 0.0027 31.8 5.7 48 57-104 152-199 (202)
32 PF08281 Sigma70_r4_2: Sigma-7 27.3 1.5E+02 0.0033 23.4 5.0 42 57-99 13-54 (54)
33 KOG0775 Transcription factor S 27.1 24 0.00051 38.8 0.4 21 624-644 171-191 (304)
34 PF13837 Myb_DNA-bind_4: Myb/S 25.6 1.9E+02 0.0041 24.8 5.6 51 52-102 2-70 (90)
35 PF04545 Sigma70_r4: Sigma-70, 24.4 2.6E+02 0.0057 22.0 5.8 43 57-101 8-50 (50)
36 PRK12539 RNA polymerase sigma 22.9 1.7E+02 0.0037 28.3 5.4 43 62-105 139-181 (184)
37 PF14538 Raptor_N: Raptor N-te 22.7 1.2E+02 0.0027 30.2 4.4 77 317-415 63-140 (154)
38 PF01285 TEA: TEA/ATTS domain 21.0 1E+02 0.0022 35.6 3.9 21 49-69 47-67 (431)
39 PTZ00249 variable surface prot 20.9 4.8E+02 0.01 31.2 9.1 136 85-228 133-291 (516)
No 1
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=100.00 E-value=4.1e-90 Score=750.98 Aligned_cols=654 Identities=45% Similarity=0.673 Sum_probs=526.2
Q ss_pred cccCCCccc---cc--cCCHHHHHHHHHHHHHhcccHHHHHHHhh----------hcchhHHHHHHHHHHHHHHhhc-CC
Q 003906 42 QSAKRPTRQ---WA--AWTREEEESFFTALRQVGKNFEKITHRVR----------SKNKDQVRHYYYRLVRRMNKLL-GP 105 (787)
Q Consensus 42 ~~~kk~~R~---w~--~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~----------~KnKdQVRhFYYrt~~rI~k~L-~~ 105 (787)
+++|++.++ |. +||++|+++||+||++||||||+|-+++. .|+|+||||||||++|||+||+ ++
T Consensus 74 ~~~k~~qk~Lkt~~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~F~~ 153 (782)
T KOG4468|consen 74 FPAKKPQKQLKTWAKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLLFGP 153 (782)
T ss_pred cccccchhhcccccccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhhccc
Confidence 467888888 77 99999999999999999999999966653 8899999999999999999999 55
Q ss_pred CcccCCCChh-hHHHHHHHHHH-HHHHhccchhhhccC---c-hhhHHHHHHHHHHHhhhhhcccccCCCC--CCCCCCC
Q 003906 106 GLCLDAKNSK-DTNAAMLRWWS-LLEKYSCKASKLHLK---P-RRFKIFVEALEHQLLKDRKRSVRKRPSQ--RDNYSPT 177 (787)
Q Consensus 106 ~~~iD~kn~k-ev~~Am~~w~s-l~~K~gc~~sKL~~k---p-~r~k~f~~~L~~~llK~RkK~~~kr~~q--~~n~l~a 177 (787)
++..|+++.+ ..++|+++||. |+|||.|...+|+++ | ||++.|++..+++.++.||+..+||..+ +.++...
T Consensus 154 ~l~~dAkel~tliNa~e~rrk~fl~ek~~~Klk~Lv~~Gqi~VR~~~k~I~iktp~c~alrR~~~~k~~~~lP~~~~~~~ 233 (782)
T KOG4468|consen 154 DLSLDAKELKTLINAAELRRKSFLLEKYSCKLKKLVLKGQIPVRRFKKFIEIKTPQCLALRRKSIRKRTCQLPGENLSSA 233 (782)
T ss_pred ccCcchhhHHHHhhHHHHHHHHHHHHHHHHHHHHHhhcceeeeeeccceeEecCCccHHHHHHHhhhhhccCCccceeee
Confidence 7899999988 88899999999 679999999999999 7 8999999999999999999999888877 7778888
Q ss_pred CCCCCCCccccCCCCccce-EEEeecchhhhhcCCCCCCcccccccccccCCC-cCCcccccc-ccccCCCCcchHHHHH
Q 003906 178 VPTPIPNQSRTSGQDTCTV-KLVLVDSQNIQKLGPAKGSLKRNVNIGINRSNN-KADSATLKP-RQRRKPDSISSAAYKK 254 (787)
Q Consensus 178 ~~~~ls~~sR~~g~~~~~v-kl~~~~~qn~~k~g~~kgs~~~~~~~~v~~~~~-k~ds~a~~~-rqr~k~~~~~~~a~kk 254 (787)
+++.++.++|..|-+..+. +|++.+.+|+.|++.+.-+..+..+.++..+.. +.|++..++ |+|++.+ .|.+
T Consensus 234 ~p~n~~~h~r~r~l~qnPfgr~il~~~~~v~kl~~~~~~kw~~a~~S~p~~~~L~pd~a~~~~s~c~q~~A-----~~rp 308 (782)
T KOG4468|consen 234 SPGNISSHSRERGLDQNPFGRLILSDGQNVKKLGPGRASKWHGASLSVPLGDELKPDTAFGRGSRCRQKQA-----GYRP 308 (782)
T ss_pred cccccchhhhhhhhccCcceeEEecCchhHHHhccchhhhcccccccCccccccCcccccccccceecccc-----ccCc
Confidence 9999999999998888887 999999999999999988877777888888866 889999998 8888874 7999
Q ss_pred HHHH----HHhccchHH--HHHhhhhcccchhHHHHhhhhhcccccccCCCCCCCCCCC--ccccCCCCCCceEEEEEec
Q 003906 255 WEKA----AIAGVSLVA--DAAEHLERTSTDKEVERQQEHTALETADKVLPPLPTISPT--LFAEGNVQTPVKLKLQLYP 326 (787)
Q Consensus 255 ~~ka----a~~gvs~va--daae~ler~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~--~~~~~~~~~~~KikLQLFP 326 (787)
|+++ +|.||..|+ |+|||||++.+++.++.+....++. +.++..|+..+..- ..-.++.|-+.+|++||||
T Consensus 309 ~~s~Sisi~i~~vee~~fK~~ae~le~tgi~va~d~~~~tkP~~-~~t~p~p~sL~d~~~~~~~~~~~n~s~~l~~elf~ 387 (782)
T KOG4468|consen 309 WESASISIAIDGVEEVAFKDAAEHLERTGIDVAMDDQTDTKPTR-YLTGPSPLSLCDAGDVPLSDANMNFSAKLKLELFP 387 (782)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHhhhhhccceeecccccccCCcc-cccCCCCcccccccccccchhhhhhHHHHHhHhhh
Confidence 9999 999999999 9999999999999999887766655 33333343333321 1112555778999999999
Q ss_pred CcHHHHH-HHhhcCCCceeEEeecCccchhHHHHHHhhhhccCccCCcceEeeccccccccccCCcCccccCCccHHHHH
Q 003906 327 IDDGTRK-ALEMDNHNPHLELTLSTRKKISSVLEHLNRKWGNASVASGELMLFPYGAQRENLVGYQRWTQDSVFSAADVY 405 (787)
Q Consensus 327 ide~Tr~-~le~~g~nP~LELTLs~rKkiSsvl~HLn~KWg~S~~a~Gel~LfPy~~~~~nLa~~~~Wt~~~~~ta~DV~ 405 (787)
|+.-++- .|+++.||||++|+++-+|||+ |++|||+|||.++||.|++.||||.+..+.....
T Consensus 388 i~g~~~ptsl~~~~hn~h~p~q~s~p~ki~-~~n~lnr~~g~ssCaa~~~~l~~~~t~~~~vp~~--------------- 451 (782)
T KOG4468|consen 388 IDGCTRPTSLEMDKHNPHLPLQLSNPKKIS-VLNHLNRKWGSSSCAAGELLLFPYNTRKETVPCH--------------- 451 (782)
T ss_pred hccCCCcceeeeeccCCCCchhhcCcchhh-HHHHHhhccccccccccccccCcccccccccchh---------------
Confidence 9999998 9999999999999999999999 9999999999999999999999999865432221
Q ss_pred HHhCCCCEEEEeecccccCcccccCCCCCCCCCCCCCCCcccccccccccccCCCCCCCCCCCC---Ccccccccccccc
Q 003906 406 AMIGSPPMFRLRYGWFSDTELGYVAPHAPSASGCVPSFHNINVENKKEQIVDSVPGRVPSTSDQ---SENFVDPYKKLTS 482 (787)
Q Consensus 406 ~avGsP~vFRLRYgWf~~~e~~~~~~~~Pss~~~l~~~~n~n~e~~~~~~~d~~p~~~~~t~d~---~~~~~e~~k~~t~ 482 (787)
-||+||...+- +...|+|...+|+...- |+.. .+.+.+..+..+++ +-++-+.++|.
T Consensus 452 ----------~rsk~~~~~~s-s~asq~~~~kp~l~DD~--~~d~-----~~~~~~~~~~~~p~sd~~~~e~~ds~~~-- 511 (782)
T KOG4468|consen 452 ----------QRSKWFVHDAS-SIASQVPTSKPCLEDDM--NVDR-----LNEVNMLLTESGPLSDHSTAEQTDSVEP-- 511 (782)
T ss_pred ----------hhccceecchh-hhhhcCCCCCcccccch--hhhc-----ccchhhhhccCCcccceeeeecccchhh--
Confidence 28999998754 77789999999964333 3322 33333333333332 11111111111
Q ss_pred cccCCcccccCCCCCcccccccccccccccCCCCCCCCcCCCccccCcccccccccccCcccccccccCCccccc-cccc
Q 003906 483 VKENDTFATSSSSMPKETSSYISASKRDIADTSDPAANVSWPRKETGNEIITGQVEDMGDERLSSGTALSAGEWA-DSLT 561 (787)
Q Consensus 483 ~~~n~~~~~~S~~~~~~~s~~v~~~~~~~~~~~~pt~~~sw~~~~~~~~~~~~~l~~~~~~~~S~~~~lS~~eWa-DsLT 561 (787)
-+.+-|.+ ++..++++.+. + +.|... +|+.| + -++.+++++.|||. ++++
T Consensus 512 ---l~~l~c~~-~~~tapA~s~~-----t---~~P~st-----------sVtpq-~-----~~~~~na~~pGessSas~~ 562 (782)
T KOG4468|consen 512 ---LQGLVCAS-GVHTAPARSRD-----T---YEPAST-----------SVTPQ-E-----HLSGGNAQSPGESSSASLT 562 (782)
T ss_pred ---hcceeeec-ccccccccccC-----C---cCcccc-----------ccchh-h-----ccCCcCCCCCCcccccccc
Confidence 11111222 24444444322 2 223221 23343 2 36778999999999 9999
Q ss_pred ccchhhhccCCCCCCC----CCCcc--ccccccccccCccccHHHHHHHHHhccCCCCCCCCCcccCCCCCCCccccccc
Q 003906 562 NISVGDLLAEVPHDLD----AAPVA--ESSQCLQQIPFSCDSFDAAIAAHISRHQNKMGALSTLASHASSIWDAEETCDA 635 (787)
Q Consensus 562 NISiG~LLSEAs~~~d----~~~~~--qsn~~lQqip~ssDSFDAaIAa~isr~Q~~~~~~~p~~s~~sSIwDAEETChA 635 (787)
||++|+||+|++.+.| .++.. +...-|...+|++|+|||++||||-+||.+.+...|.++...|+|+.|+|-|+
T Consensus 563 ~~~~~~~l~~~P~d~ds~~r~ts~~sk~khlLL~~~h~~~~k~d~~t~A~~l~~~t~t~g~~~~~sg~fs~~p~~r~~Dp 642 (782)
T KOG4468|consen 563 NISIGDLLSEVPDDIDSDGRDTSATSKGKHLLLRDVHFTSDKFDAATAAHILRHQTKTSGQLPLTSGSFSLWPDERTRDP 642 (782)
T ss_pred chhhhhhcccCCccccccCcccccccccceeEEecccccchhHHHHHHhhhccccccCCCcCCccceeecccccccccch
Confidence 9999999999998877 33322 23344578999999999999999999999999999999999999999999999
Q ss_pred cccCCCcccccccccCCCCCCCCcchhhhhc-ccc---cccCCCCCCCCCCCCCCCcccCCCCCcCCCCcCCCCCCCCcc
Q 003906 636 FSFQKNPVLCNEVSRLPDIAPPAADCEQIAR-TNS---ELLDAEGPTDYPAHEDPMDDCLRNPHTLDNSVNDFNGLTDIY 711 (787)
Q Consensus 636 F~fqk~~~~~~~~~~~s~~~sp~s~~~~~~~-~~~---~~~~~~~~~d~~~~~~~~ee~~~~~~~~~n~~~~~~gL~dI~ 711 (787)
|.||++..+...++. .+.+|+-.++ +.+ ..+ .++++++...++..+.+|++...+++.....++...||+|+|
T Consensus 643 ~~~~l~R~~ns~~L~--s~r~p~pt~~-~d~s~~Ql~~g~~gD~~S~s~~~pgs~m~~~~As~~~~pg~~~t~~~l~D~~ 719 (782)
T KOG4468|consen 643 FSFQLNRFANSTELA--SVRSPKPTGR-VDGSPSQLVEGSSGDEGSYSPHDPGSPMEEGPASPHTMPGPGKTPCGLADVY 719 (782)
T ss_pred hHHHHHHhhhhhhhh--hccCCCCCCC-CCcCHHHHhccCCCcccccCCCCCCCcccCCCCCcccCCCCCCCcchhhhhh
Confidence 999998876654444 4444554444 432 111 357777888998999999998888887776668889999999
Q ss_pred CCCCCCCCCCCCCCccccccccccccccchhhHHHhhhhhhccccceecccCCCCCCcc
Q 003906 712 WPDSLGPLDLDIPSSKYRGEDIILSDSLGGLNRLIASSLDAFQNCSFFGLDKKEPTPTV 770 (787)
Q Consensus 712 WpDSlGplDLgi~sSry~~edli~~DSl~gl~rlia~SLDAFqn~Sff~~dk~~~~~~~ 770 (787)
|++++||+||++.+.+| .+|+|+..|++|+.+||++|+|+||+||+|+||+|+.++.+
T Consensus 720 ~q~~tn~~Dl~~~sn~a-~~d~~~~es~~~~h~li~Ss~D~~~d~sL~hfd~kk~t~~~ 777 (782)
T KOG4468|consen 720 WQDSTNPLDLDIRSNKA-TDDLILSESLGGLHRLIASSLDAFQDCSLFHFDNKKDTSNM 777 (782)
T ss_pred hhccCCCcccccccchh-hhhhhhhhhhhhHHHHHhhhhhhhhccceeccccccccccC
Confidence 99999999999999998 77899999999999999999999999999999999998764
No 2
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=98.31 E-value=1.1e-06 Score=68.99 Aligned_cols=44 Identities=34% Similarity=0.703 Sum_probs=40.7
Q ss_pred ccCCHHHHHHHHHHHHHhccc-HHHHHHHhh-hcchhHHHHHHHHH
Q 003906 52 AAWTREEEESFFTALRQVGKN-FEKITHRVR-SKNKDQVRHYYYRL 95 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~GKd-FEaI~~~i~-~KnKdQVRhFYYrt 95 (787)
..||.+|...|.+++++||++ |.+|+.+|. .|+..|+|++||+.
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 579999999999999999999 999999999 99999999999975
No 3
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.11 E-value=3.7e-06 Score=62.65 Aligned_cols=46 Identities=28% Similarity=0.632 Sum_probs=43.4
Q ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhHHHHHHHHHHH
Q 003906 52 AAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLVR 97 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~~ 97 (787)
..||.+|...|.+++++|| ++|+.|+.+|..|+..||+.+||+.++
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 5799999999999999999 999999999999999999999998654
No 4
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=97.99 E-value=1.2e-05 Score=59.20 Aligned_cols=43 Identities=33% Similarity=0.653 Sum_probs=41.1
Q ss_pred cCCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhHHHHHHHHH
Q 003906 53 AWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRL 95 (787)
Q Consensus 53 ~Ws~eEkn~FFEaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt 95 (787)
.||.+|.+.|..++.++| ++|+.|+.+|..|+..||+.+|++.
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 499999999999999999 9999999999999999999999874
No 5
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=97.24 E-value=0.00032 Score=81.75 Aligned_cols=50 Identities=32% Similarity=0.499 Sum_probs=47.4
Q ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHhh
Q 003906 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKL 102 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~ 102 (787)
..||.-|+..|=.||..|-|||..|+.+|.+|+..|--.||| ||+||.++
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYY-tWKK~~~~ 669 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYY-TWKKIMRL 669 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHH-HHHHhccc
Confidence 679999999999999999999999999999999999999999 79998875
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=96.92 E-value=0.003 Score=51.23 Aligned_cols=56 Identities=21% Similarity=0.510 Sum_probs=43.7
Q ss_pred CCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHhhcCCCcccCCCChhh
Q 003906 54 WTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKD 116 (787)
Q Consensus 54 Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~kn~ke 116 (787)
||.+|.....+++.+||.++..|+.+|..|+..|||..|++ +|.+..+-.+...+|
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~-------~l~~~~~~~~wt~eE 56 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRN-------HLRPKISRGPWTKEE 56 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHH-------TTSTTSTSSSSSHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHH-------HCcccccCCCcCHHH
Confidence 99999999999999999999999999987999999999998 233444444555544
No 7
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=95.77 E-value=0.015 Score=65.53 Aligned_cols=56 Identities=27% Similarity=0.465 Sum_probs=48.5
Q ss_pred CCccccccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHhh
Q 003906 46 RPTRQWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKL 102 (787)
Q Consensus 46 k~~R~w~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~ 102 (787)
+.+-....||.||+-.|=.||-.|||+|-+|+..+.-|+---+++|||. |++-.+|
T Consensus 182 rr~~~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~-~KK~~~~ 237 (534)
T KOG1194|consen 182 RRTEFPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYS-WKKTREY 237 (534)
T ss_pred hcCCCcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHH-HHHHhhH
Confidence 3445568999999999999999999999999999999999999999996 4444444
No 8
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=95.68 E-value=0.022 Score=47.90 Aligned_cols=43 Identities=21% Similarity=0.506 Sum_probs=38.5
Q ss_pred ccCCHHHHHHHHHHHHHhcc-cH---HHHHHHhh-hc-chhHHHHHHHH
Q 003906 52 AAWTREEEESFFTALRQVGK-NF---EKITHRVR-SK-NKDQVRHYYYR 94 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~GK-dF---EaI~~~i~-~K-nKdQVRhFYYr 94 (787)
..||.+|...|-+||..+|. |. .+|++.|. ++ +..||+-++-.
T Consensus 4 ~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QK 52 (57)
T TIGR01557 4 VVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQK 52 (57)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHH
Confidence 67999999999999999998 99 99999998 56 89999987643
No 9
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=94.33 E-value=0.035 Score=62.99 Aligned_cols=55 Identities=24% Similarity=0.475 Sum_probs=45.3
Q ss_pred CccccccCCHHHHHHHHHHHHHhcccHHHH-HHHhhhcchhHHHHHHHHHHHHHHhh
Q 003906 47 PTRQWAAWTREEEESFFTALRQVGKNFEKI-THRVRSKNKDQVRHYYYRLVRRMNKL 102 (787)
Q Consensus 47 ~~R~w~~Ws~eEkn~FFEaL~e~GKdFEaI-~~~i~~KnKdQVRhFYYrt~~rI~k~ 102 (787)
=|-.-+.|+..|-|+|=|||-.|||||.-| ++|+.=|+-..+-.||| .|+.-..|
T Consensus 281 CRDemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY-mwKttdRY 336 (693)
T KOG3554|consen 281 CRDEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY-MWKTTDRY 336 (693)
T ss_pred ehhhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH-HHhhhhHH
Confidence 455679999999999999999999999998 47888999988889888 45543333
No 10
>PLN03091 hypothetical protein; Provisional
Probab=93.20 E-value=0.17 Score=57.38 Aligned_cols=62 Identities=11% Similarity=0.364 Sum_probs=53.1
Q ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHhhcCCCcccCCCChhhH
Q 003906 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDT 117 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~kn~kev 117 (787)
..||.||....++..+++|...-+|+.+|.-|+-.|||+.||..++|..+..+ ||+...+.+
T Consensus 68 gpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~----I~p~t~kpl 129 (459)
T PLN03091 68 GTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRG----IDPNTHKPL 129 (459)
T ss_pred CCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcC----CCCCCCCCc
Confidence 68999999999999999999999999999999999999999999988766543 555544443
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=93.11 E-value=0.17 Score=53.75 Aligned_cols=51 Identities=18% Similarity=0.397 Sum_probs=47.0
Q ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHh
Q 003906 51 WAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNK 101 (787)
Q Consensus 51 w~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k 101 (787)
...||.+|.+.-++..+++|...-.|+.+|.-++-.||++.||..+++..+
T Consensus 78 kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~ 128 (249)
T PLN03212 78 RGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLL 128 (249)
T ss_pred cCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHH
Confidence 368999999999999999999999999999999999999999998887543
No 12
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=93.00 E-value=0.11 Score=57.66 Aligned_cols=55 Identities=29% Similarity=0.588 Sum_probs=45.9
Q ss_pred ccCCCccccccCCHHHHHHHHHHHHHhcccHHHHHH-HhhhcchhHHHHHHHHHHHH
Q 003906 43 SAKRPTRQWAAWTREEEESFFTALRQVGKNFEKITH-RVRSKNKDQVRHYYYRLVRR 98 (787)
Q Consensus 43 ~~kk~~R~w~~Ws~eEkn~FFEaL~e~GKdFEaI~~-~i~~KnKdQVRhFYYrt~~r 98 (787)
..|..|-.--.|+.+|=..|=++|+.|||||--|+. .|++|+.-+.-+||| .|++
T Consensus 269 nvk~~rd~l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYY-lWKk 324 (445)
T KOG4329|consen 269 NVKTVRDDLSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYY-LWKK 324 (445)
T ss_pred cceecccccccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHH-Hhhc
Confidence 455566667899999999999999999999999974 577999888889998 4653
No 13
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=92.12 E-value=0.27 Score=54.99 Aligned_cols=58 Identities=22% Similarity=0.470 Sum_probs=51.1
Q ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHH----HHHhhcCCCccc
Q 003906 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVR----RMNKLLGPGLCL 109 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~----rI~k~L~~~~~i 109 (787)
..|+..|...||.||-+.|-||.-|+.+...|++.||.-=|-+.-+ ||+..|..-..+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~ 427 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKVNPERINEALNEKKPF 427 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhhCHHHHHHHHhccCCC
Confidence 7899999999999999999999999999999999999998888776 677777654433
No 14
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=90.01 E-value=0.47 Score=53.68 Aligned_cols=49 Identities=22% Similarity=0.430 Sum_probs=45.3
Q ss_pred ccccccCCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhHHHHHHHHHH
Q 003906 48 TRQWAAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLV 96 (787)
Q Consensus 48 ~R~w~~Ws~eEkn~FFEaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~ 96 (787)
..--..||++|+=.+-||+-.+| .|.+-|+++|-+|++++++.+|++.+
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 34457999999999999999999 89999999999999999999999876
No 15
>PLN03212 Transcription repressor MYB5; Provisional
Probab=87.75 E-value=4.2 Score=43.60 Aligned_cols=78 Identities=18% Similarity=0.311 Sum_probs=59.6
Q ss_pred cccCCHHHHHHHHHHHHHhc-ccHHHHHHHhh-hcchhHHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHH
Q 003906 51 WAAWTREEEESFFTALRQVG-KNFEKITHRVR-SKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLL 128 (787)
Q Consensus 51 w~~Ws~eEkn~FFEaL~e~G-KdFEaI~~~i~-~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~kn~kev~~Am~~w~sl~ 128 (787)
...||.||-+.-.+++++|| .+...|+..|. .|+..|.|.=|++ ||.|++.-+++-.+|-.. ++ ++.
T Consensus 25 Rg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N-------~L~P~I~kgpWT~EED~l-Ll---el~ 93 (249)
T PLN03212 25 RGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMN-------YLRPSVKRGGITSDEEDL-IL---RLH 93 (249)
T ss_pred CCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHH-------hhchhcccCCCChHHHHH-HH---HHH
Confidence 36799999999999999999 68999999985 8999999986654 667777777776666444 33 345
Q ss_pred HHhccchhhhc
Q 003906 129 EKYSCKASKLH 139 (787)
Q Consensus 129 ~K~gc~~sKL~ 139 (787)
.+||-.+.++.
T Consensus 94 ~~~GnKWs~IA 104 (249)
T PLN03212 94 RLLGNRWSLIA 104 (249)
T ss_pred HhccccHHHHH
Confidence 66776666553
No 16
>PLN03091 hypothetical protein; Provisional
Probab=86.96 E-value=4.5 Score=46.42 Aligned_cols=79 Identities=15% Similarity=0.293 Sum_probs=60.9
Q ss_pred cccCCHHHHHHHHHHHHHhc-ccHHHHHHHhh-hcchhHHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHH
Q 003906 51 WAAWTREEEESFFTALRQVG-KNFEKITHRVR-SKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLL 128 (787)
Q Consensus 51 w~~Ws~eEkn~FFEaL~e~G-KdFEaI~~~i~-~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~kn~kev~~Am~~w~sl~ 128 (787)
...||.+|-+...+++++|| ++...|+..|. .|+-.|.|.=| ..||.|++.=.++-.+|-.. ++ ++.
T Consensus 14 Kg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW-------~NyLdP~IkKgpWT~EED~l-LL---eL~ 82 (459)
T PLN03091 14 KGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRW-------INYLRPDLKRGTFSQQEENL-II---ELH 82 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHH-------HhccCCcccCCCCCHHHHHH-HH---HHH
Confidence 36799999999999999999 58999999886 79999999765 45788887777777776655 22 445
Q ss_pred HHhccchhhhcc
Q 003906 129 EKYSCKASKLHL 140 (787)
Q Consensus 129 ~K~gc~~sKL~~ 140 (787)
++||-.+.++..
T Consensus 83 k~~GnKWskIAk 94 (459)
T PLN03091 83 AVLGNRWSQIAA 94 (459)
T ss_pred HHhCcchHHHHH
Confidence 667866665543
No 17
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=76.41 E-value=4 Score=50.95 Aligned_cols=51 Identities=20% Similarity=0.504 Sum_probs=47.1
Q ss_pred cccCCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhHHHHHHHHHHHHHHh
Q 003906 51 WAAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLVRRMNK 101 (787)
Q Consensus 51 w~~Ws~eEkn~FFEaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k 101 (787)
...|+..|=+.|-.|...|| .|+++|+..|..|+.++||.|+--.|.|...
T Consensus 824 f~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~~ 875 (1033)
T PLN03142 824 FSTWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYKE 875 (1033)
T ss_pred cCcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhhh
Confidence 45799999999999999998 6899999999999999999999999988665
No 18
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=73.55 E-value=9.3 Score=42.65 Aligned_cols=48 Identities=23% Similarity=0.497 Sum_probs=44.9
Q ss_pred ccccCCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhHHHHHHHHHHH
Q 003906 50 QWAAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLVR 97 (787)
Q Consensus 50 ~w~~Ws~eEkn~FFEaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~~ 97 (787)
--+.|...|+=.|-+++-..| .|.+-|++||-.+.|++||..||.++-
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 347899999999999999999 899999999999999999999999876
No 19
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=71.01 E-value=4 Score=47.11 Aligned_cols=38 Identities=24% Similarity=0.530 Sum_probs=36.1
Q ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHH
Q 003906 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVR 89 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVR 89 (787)
+.|+.||.-+.-||+..||-|.++|+..|.+|.++|-=
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCI 317 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCI 317 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHH
Confidence 58999999999999999999999999999999999953
No 20
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=67.33 E-value=2.6 Score=48.46 Aligned_cols=50 Identities=20% Similarity=0.357 Sum_probs=40.8
Q ss_pred ccccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHH
Q 003906 50 QWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMN 100 (787)
Q Consensus 50 ~w~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~ 100 (787)
..-.||.+|+. ---++.-||-+||.|...|++|..+||.+||..-=+-|.
T Consensus 469 ~~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~n~k~i~ 518 (534)
T KOG1194|consen 469 INYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMDNEKLIL 518 (534)
T ss_pred ecCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcCchhhhc
Confidence 34689999987 555667789999999999999999999999976544443
No 21
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=62.18 E-value=16 Score=44.12 Aligned_cols=71 Identities=20% Similarity=0.357 Sum_probs=58.0
Q ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhHHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHHHH
Q 003906 52 AAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLLEK 130 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~kn~kev~~Am~~w~sl~~K 130 (787)
..|+.+|--+.|-|..+|| ||.-+|...+..++-.|.|.=|.|..++=.|.=. -..++..++++ +.++
T Consensus 361 g~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~r----W~l~edeqL~~-------~V~~ 429 (939)
T KOG0049|consen 361 GRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVER----WTLVEDEQLLY-------AVKV 429 (939)
T ss_pred CCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCc----eeecchHHHHH-------HHHH
Confidence 6799999999999999996 8889999999999999999999999988777522 33455566665 4567
Q ss_pred hcc
Q 003906 131 YSC 133 (787)
Q Consensus 131 ~gc 133 (787)
||-
T Consensus 430 YG~ 432 (939)
T KOG0049|consen 430 YGK 432 (939)
T ss_pred Hcc
Confidence 774
No 22
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=61.67 E-value=13 Score=44.19 Aligned_cols=75 Identities=23% Similarity=0.378 Sum_probs=55.5
Q ss_pred hhhhccccCCCccccccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHH----HHHhhcCC--CcccC
Q 003906 37 NVILQQSAKRPTRQWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVR----RMNKLLGP--GLCLD 110 (787)
Q Consensus 37 ~~~~~~~~kk~~R~w~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~----rI~k~L~~--~~~iD 110 (787)
.|+-+--.+++-+ ..|+.+|-..||.+|.+.|-+|--|++....+++.|||.=|-..-+ +|..-|.. .+..|
T Consensus 397 ~vn~~t~sk~~~~--~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r~p~~l~~al~~kk~~~~d 474 (584)
T KOG2009|consen 397 PVNYATYSKKLET--DKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKRNPLKLNTALRSKKPLDGD 474 (584)
T ss_pred ccchhhccCcccc--CcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhccchhhhhHHhhcCccccc
Confidence 3443333344444 8899999999999999999999999999999999999988876555 45555544 33444
Q ss_pred CCC
Q 003906 111 AKN 113 (787)
Q Consensus 111 ~kn 113 (787)
+.|
T Consensus 475 ~~d 477 (584)
T KOG2009|consen 475 AYD 477 (584)
T ss_pred ccc
Confidence 444
No 23
>PF08897 DUF1841: Domain of unknown function (DUF1841); InterPro: IPR014993 This group of proteins are functionally uncharacterised.
Probab=45.43 E-value=15 Score=36.54 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=15.8
Q ss_pred chhHHHHHHHHHHHHHHh
Q 003906 84 NKDQVRHYYYRLVRRMNK 101 (787)
Q Consensus 84 nKdQVRhFYYrt~~rI~k 101 (787)
+++|||+||+.+|+|-.+
T Consensus 2 sr~~~R~ff~~~w~K~~~ 19 (137)
T PF08897_consen 2 SRDQVRRFFCDAWRKYRA 19 (137)
T ss_pred CHHHHHHHHHHHHHHHHC
Confidence 689999999999997655
No 24
>PHA02054 hypothetical protein
Probab=39.42 E-value=10 Score=35.18 Aligned_cols=17 Identities=35% Similarity=0.759 Sum_probs=15.2
Q ss_pred HHHHHHhhhhccCccCC
Q 003906 356 SVLEHLNRKWGNASVAS 372 (787)
Q Consensus 356 svl~HLn~KWg~S~~a~ 372 (787)
..++||++|||++.|..
T Consensus 51 ~Flehl~~kw~svkCsd 67 (94)
T PHA02054 51 QFLEYLDTKWGSVGCSD 67 (94)
T ss_pred HHHHHHHHHHhhcchhH
Confidence 57999999999999876
No 25
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=38.53 E-value=62 Score=33.74 Aligned_cols=46 Identities=15% Similarity=0.343 Sum_probs=40.6
Q ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHH
Q 003906 51 WAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLV 96 (787)
Q Consensus 51 w~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~ 96 (787)
...||.||+..-+++-..+|=.-..|+.++.-++=..|.+|.-..+
T Consensus 62 rg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~l 107 (238)
T KOG0048|consen 62 RGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHL 107 (238)
T ss_pred CCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHH
Confidence 4799999999999999999999999999999888888988864433
No 26
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=36.25 E-value=82 Score=27.70 Aligned_cols=49 Identities=16% Similarity=0.254 Sum_probs=38.7
Q ss_pred cCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHhhc
Q 003906 53 AWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLL 103 (787)
Q Consensus 53 ~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L 103 (787)
..+..+++.|+.. ...|...+.|+..+.. +...||..+++..++|.+.|
T Consensus 110 ~L~~~~~~ii~~~-~~~g~s~~eIA~~l~~-s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 110 KLPEREREVLVLR-YLEGLSYKEIAEILGI-SVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred hCCHHHHHHHhhH-HhcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHhhC
Confidence 4566666666433 3469999999999987 89999999999999998764
No 27
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=32.38 E-value=1.6e+02 Score=25.14 Aligned_cols=70 Identities=9% Similarity=-0.001 Sum_probs=39.3
Q ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHH
Q 003906 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLL 128 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~kn~kev~~Am~~w~sl~ 128 (787)
..||.+|.+.+-+-+.+| .+.|.... +.......-.+.|..|...|..-... .++.+++.-...++-...
T Consensus 3 ~~fs~~E~~~Lv~~v~~~---~~il~~k~---~~~~~~~~k~~~W~~I~~~lN~~~~~-~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKH---KDILENKF---SDSVSNKEKRKAWEEIAEELNALGPG-KRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCHHHHHHHHHHHHHh---HHHHhccc---ccHHHHHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHHHH
Confidence 569999999988887765 22222111 11223333456666666666552223 777777777555554433
No 28
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=31.94 E-value=44 Score=39.27 Aligned_cols=40 Identities=23% Similarity=0.496 Sum_probs=37.2
Q ss_pred cccccCCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhHH
Q 003906 49 RQWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQV 88 (787)
Q Consensus 49 R~w~~Ws~eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQV 88 (787)
-....||.+|.-+--||+..||-|.++|+.-+.+|+++|-
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqC 290 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQC 290 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHH
Confidence 4568999999999999999999999999999999999884
No 29
>PF04192 Utp21: Utp21 specific WD40 associated putative domain ; InterPro: IPR007319 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp21 is a component of the SSU processome, which is required for pre-18S rRNA processing. It interacts with Utp18 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=31.41 E-value=1.1e+02 Score=32.46 Aligned_cols=25 Identities=28% Similarity=0.345 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHh---cccHHHHHHHhh
Q 003906 57 EEEESFFTALRQV---GKNFEKITHRVR 81 (787)
Q Consensus 57 eEkn~FFEaL~e~---GKdFEaI~~~i~ 81 (787)
++-..|..+|... ++|||.||.||+
T Consensus 157 ~~l~~Fl~~l~~~L~~~~dfElvQa~l~ 184 (237)
T PF04192_consen 157 EELVSFLRFLTYRLKSRRDFELVQAYLS 184 (237)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4455555554332 666666666664
No 30
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=31.14 E-value=1.9e+02 Score=25.25 Aligned_cols=40 Identities=20% Similarity=0.445 Sum_probs=29.9
Q ss_pred cCCHHHHHHHHHHHHHh---c----------ccHHHHHHHhh-----hcchhHHHHHH
Q 003906 53 AWTREEEESFFTALRQV---G----------KNFEKITHRVR-----SKNKDQVRHYY 92 (787)
Q Consensus 53 ~Ws~eEkn~FFEaL~e~---G----------KdFEaI~~~i~-----~KnKdQVRhFY 92 (787)
.||.+....|.+.|.+. | ..++.|...++ ..+++||++-|
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~ 58 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKW 58 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHH
Confidence 49999999999999666 2 23666777776 44678888875
No 31
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=27.80 E-value=1.3e+02 Score=31.77 Aligned_cols=48 Identities=21% Similarity=0.406 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHhhcC
Q 003906 57 EEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLG 104 (787)
Q Consensus 57 eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~ 104 (787)
++++.+=+..++.-.+||.+-.++..||..++..||=.++.-+..+|.
T Consensus 152 ~~kk~l~~La~~lf~~ie~LD~Aar~K~~~~a~~~Y~~t~~~Ldevla 199 (202)
T PF05757_consen 152 DEKKALTDLANKLFDNIEELDYAARSKDVPEAEKYYADTVKALDEVLA 199 (202)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 556665556677778999999999999999999999999999988765
No 32
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=27.33 E-value=1.5e+02 Score=23.37 Aligned_cols=42 Identities=14% Similarity=0.262 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHH
Q 003906 57 EEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRM 99 (787)
Q Consensus 57 eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI 99 (787)
++...-|......|..++.|+..+. -+...|+..++|..++|
T Consensus 13 ~~~r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 13 ERQREIFLLRYFQGMSYAEIAEILG-ISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHHHHhhC
Confidence 4555667777788999999999996 56778999999988765
No 33
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=27.07 E-value=24 Score=38.84 Aligned_cols=21 Identities=38% Similarity=0.689 Sum_probs=15.9
Q ss_pred CCCCCccccccccccCCCccc
Q 003906 624 SSIWDAEETCDAFSFQKNPVL 644 (787)
Q Consensus 624 sSIwDAEETChAF~fqk~~~~ 644 (787)
-+|||+|||-|-|-=+.+..+
T Consensus 171 rTIWDGEet~yCFKekSR~~L 191 (304)
T KOG0775|consen 171 RTIWDGEETVYCFKEKSRSLL 191 (304)
T ss_pred CccccCceeeeehhHhhHHHH
Confidence 579999999999865554443
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=25.59 E-value=1.9e+02 Score=24.84 Aligned_cols=51 Identities=18% Similarity=0.404 Sum_probs=29.8
Q ss_pred ccCCHHHHHHHHHHHHHh--cc------------cHHHHHHHhh----hcchhHHHHHHHHHHHHHHhh
Q 003906 52 AAWTREEEESFFTALRQV--GK------------NFEKITHRVR----SKNKDQVRHYYYRLVRRMNKL 102 (787)
Q Consensus 52 ~~Ws~eEkn~FFEaL~e~--GK------------dFEaI~~~i~----~KnKdQVRhFYYrt~~rI~k~ 102 (787)
..|+.+|...|.+.+.+. -. -|+.|+..|+ .++..|+|.=+-++.++-.++
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~ 70 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKI 70 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCS
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 579999999999998882 11 3556666665 455566666555555444443
No 35
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=24.41 E-value=2.6e+02 Score=21.97 Aligned_cols=43 Identities=23% Similarity=0.355 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHh
Q 003906 57 EEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNK 101 (787)
Q Consensus 57 eEkn~FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k 101 (787)
.|+.. +......|+.++.|+..+.. +...||..+.+..++|.+
T Consensus 8 ~er~v-i~~~y~~~~t~~eIa~~lg~-s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 8 REREV-IRLRYFEGLTLEEIAERLGI-SRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHHHH-HHHHHTST-SHHHHHHHHTS-CHHHHHHHHHHHHHHHHH
T ss_pred HHHHH-HHHHhcCCCCHHHHHHHHCC-cHHHHHHHHHHHHHHhcC
Confidence 34444 44444779999999999986 788999999999998853
No 36
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=22.94 E-value=1.7e+02 Score=28.33 Aligned_cols=43 Identities=16% Similarity=0.232 Sum_probs=35.9
Q ss_pred HHHHHHHhcccHHHHHHHhhhcchhHHHHHHHHHHHHHHhhcCC
Q 003906 62 FFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGP 105 (787)
Q Consensus 62 FFEaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~ 105 (787)
-|....-.|.+++.|+..+.. +..-||...+|..++|.++|..
T Consensus 139 v~~l~~~~g~s~~eIA~~lgi-s~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12539 139 AIQAVKLEGLSVAEAATRSGM-SESAVKVSVHRGLKALAALIGR 181 (184)
T ss_pred HHHHHHHcCCcHHHHHHHHCc-CHHHHHHHHHHHHHHHHHHHhh
Confidence 344444459999999999987 8999999999999999999864
No 37
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=22.74 E-value=1.2e+02 Score=30.22 Aligned_cols=77 Identities=27% Similarity=0.399 Sum_probs=52.0
Q ss_pred CceEEEEEecCcHHHHHHHhhcCCCceeEEeecCccchhHHHHHHhhhhccCc-cCCcceEeeccccccccccCCcCccc
Q 003906 317 PVKLKLQLYPIDDGTRKALEMDNHNPHLELTLSTRKKISSVLEHLNRKWGNAS-VASGELMLFPYGAQRENLVGYQRWTQ 395 (787)
Q Consensus 317 ~~KikLQLFPide~Tr~~le~~g~nP~LELTLs~rKkiSsvl~HLn~KWg~S~-~a~Gel~LfPy~~~~~nLa~~~~Wt~ 395 (787)
+.+.|..+-|-=+++++.|.+.-+|..-| -||=|-|-- |--. ++.||+.+|. ++ -|.
T Consensus 63 ~~~~~~~~dpt~e~~~~~~~~~R~~a~~~----------RvLFHYnGh-GvP~Pt~~GeIw~f~-----~~------~tq 120 (154)
T PF14538_consen 63 RARYKQSLDPTVEDLKRLCQSLRRNAKDE----------RVLFHYNGH-GVPRPTENGEIWVFN-----KN------YTQ 120 (154)
T ss_pred cCcEEEecCCCHHHHHHHHHHHHhhCCCc----------eEEEEECCC-CCCCCCCCCeEEEEc-----CC------CCc
Confidence 36778888888888888887654443323 344555532 3233 5688888887 22 234
Q ss_pred cCCccHHHHHHHhCCCCEEE
Q 003906 396 DSVFSAADVYAMIGSPPMFR 415 (787)
Q Consensus 396 ~~~~ta~DV~~avGsP~vFR 415 (787)
-.-++..|++..+|.|.||=
T Consensus 121 yip~si~dL~~~lg~Psi~V 140 (154)
T PF14538_consen 121 YIPLSIYDLQSWLGSPSIYV 140 (154)
T ss_pred ceEEEHHHHHHhcCCCEEEE
Confidence 47799999999999998874
No 38
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=21.00 E-value=1e+02 Score=35.59 Aligned_cols=21 Identities=24% Similarity=0.349 Sum_probs=15.7
Q ss_pred cccccCCHHHHHHHHHHHHHh
Q 003906 49 RQWAAWTREEEESFFTALRQV 69 (787)
Q Consensus 49 R~w~~Ws~eEkn~FFEaL~e~ 69 (787)
..-..|+.+=++.|.|||+.+
T Consensus 47 ~~~~vw~~~~e~af~~al~~~ 67 (431)
T PF01285_consen 47 DGEGVWPPDIEQAFQEALAIY 67 (431)
T ss_dssp GGS--S-HHHHHHHHHHHHHS
T ss_pred CCCCCCCHHHHHHHHHHHHhC
Confidence 445789999999999999887
No 39
>PTZ00249 variable surface protein Vir28; Provisional
Probab=20.94 E-value=4.8e+02 Score=31.25 Aligned_cols=136 Identities=16% Similarity=0.136 Sum_probs=68.6
Q ss_pred hhHHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHHHHhccchhhhccCchhhHHHHHHHHHHHhhh-----
Q 003906 85 KDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLLEKYSCKASKLHLKPRRFKIFVEALEHQLLKD----- 159 (787)
Q Consensus 85 KdQVRhFYYrt~~rI~k~L~~~~~iD~kn~kev~~Am~~w~sl~~K~gc~~sKL~~kp~r~k~f~~~L~~~llK~----- 159 (787)
|++.=.-+|..+.+|...... ...-.....-+..|-++++++-..-.+|+.+...||.++...+.+.-+-
T Consensus 133 KMK~LYDLYDkYnklks~~~~-----~~~C~tf~~~~~~YN~~I~~y~~~Dd~L~~kL~~fK~LIek~kl~~k~eC~k~~ 207 (516)
T PTZ00249 133 KMEKLYDLYDYFTELKESKDS-----STLCRNISDLAEKYESMMKEYNEKDNKLCDKLTNLKNVIEKDKLVAKNICTKNT 207 (516)
T ss_pred HHHHHHHHHHHHHhhcccCCC-----CCCcccHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHhhhhhccccCcCCC
Confidence 444444456655554322111 1113344444568888999987766788888888888777665432221
Q ss_pred -------------hhccc---ccCCCCCCCCCCCCCCCCC--CccccCCCCccceEEEeecchhhhhcCCCCCCcccccc
Q 003906 160 -------------RKRSV---RKRPSQRDNYSPTVPTPIP--NQSRTSGQDTCTVKLVLVDSQNIQKLGPAKGSLKRNVN 221 (787)
Q Consensus 160 -------------RkK~~---~kr~~q~~n~l~a~~~~ls--~~sR~~g~~~~~vkl~~~~~qn~~k~g~~kgs~~~~~~ 221 (787)
-+|.+ +-|..-+.-+.|--+..-| ++.|.+| +|++...|-|-+. +.|||.-|.+-.+..
T Consensus 208 yd~~~lk~~~p~ee~k~~~~~~~~~~~~~~~~~~~~s~ss~~~h~r~~~-~t~~~~~vs~~s~--~ah~r~~~~t~tp~~ 284 (516)
T PTZ00249 208 FDSFILKIDPPREEQKAVTAHAHRRISGEARPPKHISFSSPHAHGRPPV-ETRPPNPVSVSSP--QAHGRHPGETHTPPL 284 (516)
T ss_pred CcHHHhccCCCcccccccchhhhccccccCCCCccccccCchhccCCCc-ccCCCCceeccCh--hhcCCCCCcCCCCCc
Confidence 01111 0000111112221111111 1445554 4666666666666 788888887555455
Q ss_pred cccccCC
Q 003906 222 IGINRSN 228 (787)
Q Consensus 222 ~~v~~~~ 228 (787)
++|-+++
T Consensus 285 v~~~ss~ 291 (516)
T PTZ00249 285 VTVPSSK 291 (516)
T ss_pred eeccccc
Confidence 5554443
Done!