Query 003898
Match_columns 788
No_of_seqs 70 out of 72
Neff 3.1
Searched_HMMs 46136
Date Thu Mar 28 13:59:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003898hhsearch_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 2.1E-90 4.5E-95 753.3 22.1 654 42-771 74-777 (782)
2 PF00249 Myb_DNA-binding: Myb- 98.3 1.1E-06 2.3E-11 69.1 5.5 44 52-95 2-47 (48)
3 smart00717 SANT SANT SWI3, AD 98.1 3.6E-06 7.7E-11 62.8 4.4 46 52-97 2-48 (49)
4 cd00167 SANT 'SWI3, ADA2, N-Co 98.0 1.2E-05 2.6E-10 59.3 5.1 43 53-95 1-44 (45)
5 KOG4167 Predicted DNA-binding 97.3 0.00023 5E-09 82.8 5.2 50 52-102 620-669 (907)
6 PF13921 Myb_DNA-bind_6: Myb-l 97.0 0.0027 5.8E-08 51.5 6.6 57 54-117 1-57 (60)
7 TIGR01557 myb_SHAQKYF myb-like 95.9 0.017 3.6E-07 48.6 5.1 43 52-94 4-52 (57)
8 KOG1194 Predicted DNA-binding 95.7 0.016 3.6E-07 65.3 5.9 57 46-103 182-238 (534)
9 KOG3554 Histone deacetylase co 94.4 0.033 7.2E-07 63.1 3.6 51 47-98 281-332 (693)
10 PLN03212 Transcription repress 93.5 0.12 2.5E-06 54.9 5.4 51 51-101 78-128 (249)
11 KOG4329 DNA-binding protein [G 93.3 0.085 1.8E-06 58.6 4.3 54 43-97 269-323 (445)
12 PLN03091 hypothetical protein; 93.3 0.15 3.3E-06 57.7 6.2 64 52-119 68-131 (459)
13 COG5118 BDP1 Transcription ini 91.9 0.29 6.3E-06 54.8 6.0 58 52-109 366-427 (507)
14 KOG0457 Histone acetyltransfer 90.4 0.41 8.9E-06 54.1 5.4 49 48-96 69-118 (438)
15 PLN03212 Transcription repress 88.5 3.4 7.3E-05 44.3 10.1 78 51-139 25-104 (249)
16 PLN03091 hypothetical protein; 86.9 4.5 9.8E-05 46.4 10.5 79 51-140 14-94 (459)
17 PLN03142 Probable chromatin-re 76.8 3.8 8.2E-05 51.1 5.7 51 51-101 824-875 (1033)
18 COG5114 Histone acetyltransfer 76.2 7.3 0.00016 43.5 7.0 48 50-97 62-110 (432)
19 COG5259 RSC8 RSC chromatin rem 72.4 3.6 7.7E-05 47.5 3.6 41 52-92 280-320 (531)
20 KOG1194 Predicted DNA-binding 68.6 2.3 5E-05 48.8 1.2 49 50-99 469-517 (534)
21 KOG2009 Transcription initiati 62.6 12 0.00025 44.4 5.3 76 37-114 397-478 (584)
22 KOG0049 Transcription factor, 61.2 17 0.00036 43.9 6.2 75 52-137 361-437 (939)
23 PF08897 DUF1841: Domain of un 46.3 14 0.0003 36.7 2.1 18 84-101 2-19 (137)
24 PHA02054 hypothetical protein 39.3 10 0.00022 35.2 0.0 17 357-373 51-67 (94)
25 KOG0048 Transcription factor, 37.3 65 0.0014 33.6 5.5 45 51-95 62-106 (238)
26 TIGR02937 sigma70-ECF RNA poly 36.8 79 0.0017 27.8 5.3 49 53-103 110-158 (158)
27 PF12776 Myb_DNA-bind_3: Myb/S 34.2 1.5E+02 0.0032 25.8 6.5 59 53-111 1-81 (96)
28 PTZ00249 variable surface prot 33.3 2.4E+02 0.0053 33.5 9.6 139 85-231 133-294 (516)
29 KOG1279 Chromatin remodeling f 32.6 42 0.0009 39.4 3.5 40 49-88 251-290 (506)
30 PF13873 Myb_DNA-bind_5: Myb/S 32.4 1.5E+02 0.0033 25.2 6.1 70 52-128 3-72 (78)
31 PF04192 Utp21: Utp21 specific 30.5 1.1E+02 0.0025 32.3 6.1 25 57-81 157-184 (237)
32 KOG0775 Transcription factor S 27.0 24 0.00051 38.8 0.4 21 625-645 171-191 (304)
33 PF08281 Sigma70_r4_2: Sigma-7 26.9 1.6E+02 0.0034 23.3 4.9 42 57-99 13-54 (54)
34 PF13837 Myb_DNA-bind_4: Myb/S 26.4 1.7E+02 0.0038 25.0 5.5 51 52-102 2-70 (90)
35 PF05757 PsbQ: Oxygen evolving 26.3 1.4E+02 0.0029 31.5 5.6 48 57-104 152-199 (202)
36 PF04545 Sigma70_r4: Sigma-70, 24.8 2.5E+02 0.0055 22.1 5.7 43 57-101 8-50 (50)
37 PF10979 DUF2786: Protein of u 23.9 1.1E+02 0.0025 24.8 3.6 40 94-134 2-41 (43)
38 PF14538 Raptor_N: Raptor N-te 22.7 1.2E+02 0.0027 30.2 4.4 77 318-416 63-140 (154)
39 PRK12539 RNA polymerase sigma 22.6 1.7E+02 0.0038 28.3 5.3 43 62-105 139-181 (184)
40 KOG3821 Heparin sulfate cell s 21.7 2.2E+02 0.0048 34.2 6.8 67 86-156 161-231 (563)
41 PF01285 TEA: TEA/ATTS domain 21.2 1E+02 0.0022 35.6 3.8 42 49-90 47-107 (431)
42 COG1655 Uncharacterized protei 21.1 2.1E+02 0.0045 31.3 5.9 51 60-124 67-117 (267)
No 1
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=100.00 E-value=2.1e-90 Score=753.29 Aligned_cols=654 Identities=45% Similarity=0.674 Sum_probs=525.6
Q ss_pred cccCCCccc---cc--ccCHHHHHHHHHHHHHhcccHHHHHHHhh----------hcchhhHHHHHHHHHHHHHhhc-CC
Q 003898 42 QSAKRPTRQ---WA--AWTREEEESFFTALRQVGKNFEKITHRVR----------SKNKDQVRHYYYRLVRRMNKLL-GP 105 (788)
Q Consensus 42 ~~~kk~~R~---w~--~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~----------~KnKdQVRhFYYrt~~rI~k~L-~~ 105 (788)
+++|++.++ |. +||++|+++||+||++||||||+|-+++. .|+|+||||||||+.|||+||+ ++
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-HHHHhcccchhhccc---c-hhhHHHHHHHHHHHhhhhccccccCCCC--CCCCCCC
Q 003898 106 GLCLDAKNSK-DTNAAMLRWWS-LLEKYSCKASKLHLK---P-RRFKIFVEALEHQLLKDRKRSVRKRPSQ--RDNYSPT 177 (788)
Q Consensus 106 ~~~iD~Kn~k-ev~~Am~~w~s-l~~K~gc~~sKL~~k---p-~r~k~f~~~L~~~llK~RkK~~~kr~~~--~~n~l~a 177 (788)
++..|+++.+ ..++|+++||. |+|||.|...+|++| | |||+.||+..+++.++.||+..+||.++ +.+....
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 7888888888 88899999999 679999999999999 7 9999999999999999999999888877 6677888
Q ss_pred CCCCCCCcccCCCCCccce-EEEeccchhhhhcCCCCCCCCcccccccccCCC-cCCCccccc-ccccCCCCccchhHHH
Q 003898 178 VPTPIPNQSRTSGQDTCTV-KLVLVDSQNIQKLGPAKGSLKRNVNIGINRSNN-KADSATLKP-RQRRKPADSISSAAYK 254 (788)
Q Consensus 178 ~~~~ls~~sr~~g~~~~~v-kl~~~~~~n~~k~g~~kgs~~~~~~~~v~~~~~-k~Ds~a~~~-~qr~k~~~~~~~~ayk 254 (788)
+++.++.++|..|-+..+. +|++.+.+|++|++.+.-+..+..+.++..+.. +.|++..++ ++|++.+ .|.
T Consensus 234 ~p~n~~~h~r~r~l~qnPfgr~il~~~~~v~kl~~~~~~kw~~a~~S~p~~~~L~pd~a~~~~s~c~q~~A------~~r 307 (782)
T KOG4468|consen 234 SPGNISSHSRERGLDQNPFGRLILSDGQNVKKLGPGRASKWHGASLSVPLGDELKPDTAFGRGSRCRQKQA------GYR 307 (782)
T ss_pred cccccchhhhhhhhccCcceeEEecCchhHHHhccchhhhcccccccCccccccCcccccccccceecccc------ccC
Confidence 8899999999998888887 999999999999999988877777888888866 889999999 8888875 699
Q ss_pred HHHHH----HHhccchHH--HHHhhhhcccchhHHHHhhhhhhccccccCCCCCCCCCCC--ccccCCCCCCceEEEEEe
Q 003898 255 KWEKA----AIAGVSLVA--DAAEHLERTSTDKEVERQQEHTALETADKVLPPLPTISPT--LFAEGNVQTPVKLKLQLY 326 (788)
Q Consensus 255 k~~ka----a~~gvs~va--daae~ler~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~--~~~~~~~~~~~KikLQLF 326 (788)
+|+++ +|.||..|+ |+|||||++.+++.++.+....+.. +.++..|+..+..- ..-.++.|-+.+|++|||
T Consensus 308 p~~s~Sisi~i~~vee~~fK~~ae~le~tgi~va~d~~~~tkP~~-~~t~p~p~sL~d~~~~~~~~~~~n~s~~l~~elf 386 (782)
T KOG4468|consen 308 PWESASISIAIDGVEEVAFKDAAEHLERTGIDVAMDDQTDTKPTR-YLTGPSPLSLCDAGDVPLSDANMNFSAKLKLELF 386 (782)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHhhhhhccceeecccccccCCcc-cccCCCCcccccccccccchhhhhhHHHHHhHhh
Confidence 99999 999999999 9999999999999998887765554 33333344333321 111255577899999999
Q ss_pred cCcHHHHH-HHhhcCCCceeEEeecCccchhHHHHHHhhhhccCccCCcceEeeccccccccccCCcCccccCCccHHHH
Q 003898 327 PIDDGTRK-ALEMDNHNPHLELTLSTRKKISSVLEHLNRKWGNASVASGELMLFPYGAQRENLVGYQRWTQDSVFSAADV 405 (788)
Q Consensus 327 Pide~Tr~-~le~~g~nP~LELTLs~rKkiSsvl~HLn~KWg~S~~a~Gel~LfPy~~~~~nLa~~~~Wt~~~~~ta~DV 405 (788)
||+.-++- .|+++.||||++|+++-+|||+ |++|||+|||.++||.|++.||||.+..+.....
T Consensus 387 ~i~g~~~ptsl~~~~hn~h~p~q~s~p~ki~-~~n~lnr~~g~ssCaa~~~~l~~~~t~~~~vp~~-------------- 451 (782)
T KOG4468|consen 387 PIDGCTRPTSLEMDKHNPHLPLQLSNPKKIS-VLNHLNRKWGSSSCAAGELLLFPYNTRKETVPCH-------------- 451 (782)
T ss_pred hhccCCCcceeeeeccCCCCchhhcCcchhh-HHHHHhhccccccccccccccCcccccccccchh--------------
Confidence 99999998 9999999999999999999999 9999999999999999999999999865432221
Q ss_pred HHHhCCCCEEEEeecccccCcccccCCCCCCCCCCCCCCCcccccccccccccCCCCCCCCCCCC---Cccccccccccc
Q 003898 406 YAMIGSPPMFRLRYGWFSDTELGYVAPHAPSASGCVPSFHNINVENKKEQIVDSVPGRVPSTSDQ---SENFVDPYKKLT 482 (788)
Q Consensus 406 ~~avGsP~vFRLRYgWf~~~e~~~~~~~~Pss~~~l~~~~n~n~e~~~~~~~d~~p~~~~~t~d~---~~~~~e~~k~~t 482 (788)
-||+||...+- +...|+|...+|+...- |+.. .+.+.+..+..+++ +-++-+.++|.
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 ccccCCcccccCCCCCcccccccccccccccCCCCCCCCcCCCccccCcccccccccccCcccccccccCCccccc-ccc
Q 003898 483 SVKENDTFATSSSSMPKETSSYISASKRDIADTSDPAANVSWPRKETGNEIITGQVEDMGDERLSSGTALSAGEWA-DSL 561 (788)
Q Consensus 483 ~~~~n~~~~~~S~~~~~~~s~~v~~~~~~~~~~~~pt~~~sw~~~~~~~~~~~~~l~~~~~~~~S~~~~lS~~eWa-DsL 561 (788)
-+.+-|.+ ++..++++.+. + +.|... +|+.| + -++.+++++.|||. +++
T Consensus 512 ----l~~l~c~~-~~~tapA~s~~-----t---~~P~st-----------sVtpq-~-----~~~~~na~~pGessSas~ 561 (782)
T KOG4468|consen 512 ----LQGLVCAS-GVHTAPARSRD-----T---YEPAST-----------SVTPQ-E-----HLSGGNAQSPGESSSASL 561 (782)
T ss_pred ----hcceeeec-ccccccccccC-----C---cCcccc-----------ccchh-h-----ccCCcCCCCCCccccccc
Confidence 11111222 24444444322 2 223221 23343 2 36778999999999 999
Q ss_pred cccchhhhccCCCCCCC----CCCcc--ccccccccccCccccHHHHHHHHHhccCCCCCCCCCcccCCCCCCCcccccc
Q 003898 562 TNISVGDLLAEVPHDLD----AAPVA--ESSQCLQQIPFSCDSFDAAIAAHISRHQNKMGALSTLASHASSIWDAEETCD 635 (788)
Q Consensus 562 TNISiG~LLSEAs~~~d----~~~~~--qsn~~lQqip~ssDSFDAaIAa~isr~Q~~~~~~~p~~s~~sSIwDAEETCh 635 (788)
+||++|+||+|++.+.| .++.. +...-|...+|++|+|||++||||-+||.+.+...|.++...|+|+.|+|-|
T Consensus 562 ~~~~~~~~l~~~P~d~ds~~r~ts~~sk~khlLL~~~h~~~~k~d~~t~A~~l~~~t~t~g~~~~~sg~fs~~p~~r~~D 641 (782)
T KOG4468|consen 562 TNISIGDLLSEVPDDIDSDGRDTSATSKGKHLLLRDVHFTSDKFDAATAAHILRHQTKTSGQLPLTSGSFSLWPDERTRD 641 (782)
T ss_pred cchhhhhhcccCCccccccCcccccccccceeEEecccccchhHHHHHHhhhccccccCCCcCCccceeecccccccccc
Confidence 99999999999998877 33322 2334457899999999999999999999999999999999999999999999
Q ss_pred ccccCCCcccccccccCCCCCCCCcchhhhhc-ccc---cccCCCCCCCCCCCCCCCcccCCCCCcCCCCcCCCCCCCCc
Q 003898 636 AFSFQKNPVLCNEVSRLPDIAPPAADCEQIAR-TNS---ELLDAEGPTDYPAHEDPMDDCLRNPHTLDNSVNDFNGLTDI 711 (788)
Q Consensus 636 AF~fqk~~~~~~~~~~~s~~~sp~s~~~~~~~-~~~---~~~~~~~~~d~~~~~~~~ee~~~~~~~~~n~~~~~~gL~dI 711 (788)
+|.||++..+...++. .+.+|+-.++ +.+ ..+ .++++++...++..+.+|++...+++.....++...||+|+
T Consensus 642 p~~~~l~R~~ns~~L~--s~r~p~pt~~-~d~s~~Ql~~g~~gD~~S~s~~~pgs~m~~~~As~~~~pg~~~t~~~l~D~ 718 (782)
T KOG4468|consen 642 PFSFQLNRFANSTELA--SVRSPKPTGR-VDGSPSQLVEGSSGDEGSYSPHDPGSPMEEGPASPHTMPGPGKTPCGLADV 718 (782)
T ss_pred hhHHHHHHhhhhhhhh--hccCCCCCCC-CCcCHHHHhccCCCcccccCCCCCCCcccCCCCCcccCCCCCCCcchhhhh
Confidence 9999998876654444 4444554444 432 111 35777788899899999999888887777666888999999
Q ss_pred cCCCCCCCCCCCCCCccccccccccccccchhhHHHhhhhhhccccceecccCCCCCCcc
Q 003898 712 YWPDSLGPLDLDIPSSKYRGEDIILSDSLGGLNRLIASSLDAFQNCSFFGLDKKEPTPTV 771 (788)
Q Consensus 712 ~WpDSlGPlDLgi~sSry~~edli~~DSL~gl~rlia~SLDAFqn~Sff~~dk~~~~~~~ 771 (788)
||++++||+||++.+.+| .+|+|+..|++|+.+||++|+|+||+||+|+||+|+.++.+
T Consensus 719 ~~q~~tn~~Dl~~~sn~a-~~d~~~~es~~~~h~li~Ss~D~~~d~sL~hfd~kk~t~~~ 777 (782)
T KOG4468|consen 719 YWQDSTNPLDLDIRSNKA-TDDLILSESLGGLHRLIASSLDAFQDCSLFHFDNKKDTSNM 777 (782)
T ss_pred hhhccCCCcccccccchh-hhhhhhhhhhhhHHHHHhhhhhhhhccceeccccccccccC
Confidence 999999999999999998 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=69.11 Aligned_cols=44 Identities=34% Similarity=0.703 Sum_probs=40.7
Q ss_pred cccCHHHHHHHHHHHHHhccc-HHHHHHHhh-hcchhhHHHHHHHH
Q 003898 52 AAWTREEEESFFTALRQVGKN-FEKITHRVR-SKNKDQVRHYYYRL 95 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~GKd-FEaI~~~i~-~KnKdQVRhFYYrt 95 (788)
..||.+|...|.+++++||++ |.+|+.+|. .|+..|+|++||+.
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=98.12 E-value=3.6e-06 Score=62.75 Aligned_cols=46 Identities=28% Similarity=0.632 Sum_probs=43.4
Q ss_pred cccCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhhHHHHHHHHHH
Q 003898 52 AAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLVR 97 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~~ 97 (788)
..||.+|...|.+++++|| ++|+.|+.+|..|+..||+.+||+.++
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=59.29 Aligned_cols=43 Identities=33% Similarity=0.653 Sum_probs=41.1
Q ss_pred ccCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhhHHHHHHHH
Q 003898 53 AWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRL 95 (788)
Q Consensus 53 ~Ws~eEkn~FFeaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt 95 (788)
.||.+|.+.|..++.++| ++|+.|+.+|..|+..||+.+|++.
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=97.32 E-value=0.00023 Score=82.83 Aligned_cols=50 Identities=32% Similarity=0.499 Sum_probs=47.2
Q ss_pred cccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhh
Q 003898 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKL 102 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~ 102 (788)
..||.-|+..|=.||..|-|||..|+.+|..|+..|--.||| ||+||.++
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 579999999999999999999999999999999999999999 79998774
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=96.96 E-value=0.0027 Score=51.47 Aligned_cols=57 Identities=21% Similarity=0.501 Sum_probs=44.3
Q ss_pred cCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhcCCCcccCCCChhhH
Q 003898 54 WTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDT 117 (788)
Q Consensus 54 Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev 117 (788)
||.+|.....+++.+||.++..|+.+|..|+..|||..|++ +|.+..+-.+...+|.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~-------~l~~~~~~~~wt~eEd 57 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRN-------HLRPKISRGPWTKEED 57 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHH-------TTSTTSTSSSSSHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHH-------HCcccccCCCcCHHHH
Confidence 99999999999999999999999999987999999999998 2334444455555543
No 7
>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=95.85 E-value=0.017 Score=48.59 Aligned_cols=43 Identities=21% Similarity=0.506 Sum_probs=38.6
Q ss_pred cccCHHHHHHHHHHHHHhcc-cH---HHHHHHhh-hc-chhhHHHHHHH
Q 003898 52 AAWTREEEESFFTALRQVGK-NF---EKITHRVR-SK-NKDQVRHYYYR 94 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~GK-dF---EaI~~~i~-~K-nKdQVRhFYYr 94 (788)
..||.+|...|-+||..+|. |. .+|+++|. ++ +..||+-++-.
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 89999987644
No 8
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=95.71 E-value=0.016 Score=65.28 Aligned_cols=57 Identities=26% Similarity=0.445 Sum_probs=48.6
Q ss_pred CCcccccccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhc
Q 003898 46 RPTRQWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLL 103 (788)
Q Consensus 46 k~~R~w~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L 103 (788)
+.+-....||.||+-.|=.||-.|||+|-+|+..+.-|+---+++|||.. ++-.+|+
T Consensus 182 rr~~~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~-KK~~~~~ 238 (534)
T KOG1194|consen 182 RRTEFPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSW-KKTREYD 238 (534)
T ss_pred hcCCCcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHH-HHHhhHH
Confidence 34455689999999999999999999999999999999999999999964 4444443
No 9
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=94.38 E-value=0.033 Score=63.12 Aligned_cols=51 Identities=25% Similarity=0.484 Sum_probs=43.6
Q ss_pred CcccccccCHHHHHHHHHHHHHhcccHHHH-HHHhhhcchhhHHHHHHHHHHH
Q 003898 47 PTRQWAAWTREEEESFFTALRQVGKNFEKI-THRVRSKNKDQVRHYYYRLVRR 98 (788)
Q Consensus 47 ~~R~w~~Ws~eEkn~FFeaL~e~GKdFEaI-~~~i~~KnKdQVRhFYYrt~~r 98 (788)
=|-.-+.|+..|-|+|=|||-.|||||.-| ++|+.=|+-..+-.||| .|+.
T Consensus 281 CRDemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY-mwKt 332 (693)
T KOG3554|consen 281 CRDEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY-MWKT 332 (693)
T ss_pred ehhhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH-HHhh
Confidence 355679999999999999999999999998 47888999988889888 3443
No 10
>PLN03212 Transcription repressor MYB5; Provisional
Probab=93.51 E-value=0.12 Score=54.89 Aligned_cols=51 Identities=18% Similarity=0.397 Sum_probs=47.0
Q ss_pred ccccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHh
Q 003898 51 WAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNK 101 (788)
Q Consensus 51 w~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k 101 (788)
...||.+|.+.-++..+++|...-.|+.+|.-++-.||++.||..+++..+
T Consensus 78 kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~ 128 (249)
T PLN03212 78 RGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLL 128 (249)
T ss_pred cCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHH
Confidence 368999999999999999999999999999999999999999999887543
No 11
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=93.34 E-value=0.085 Score=58.61 Aligned_cols=54 Identities=28% Similarity=0.545 Sum_probs=45.3
Q ss_pred ccCCCcccccccCHHHHHHHHHHHHHhcccHHHHHH-HhhhcchhhHHHHHHHHHH
Q 003898 43 SAKRPTRQWAAWTREEEESFFTALRQVGKNFEKITH-RVRSKNKDQVRHYYYRLVR 97 (788)
Q Consensus 43 ~~kk~~R~w~~Ws~eEkn~FFeaL~e~GKdFEaI~~-~i~~KnKdQVRhFYYrt~~ 97 (788)
..|..|-.--.|+.+|=..|=++|+.|||||--|+. .|++|+.-+.-+|||. |+
T Consensus 269 nvk~~rd~l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl-WK 323 (445)
T KOG4329|consen 269 NVKTVRDDLSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL-WK 323 (445)
T ss_pred cceecccccccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH-hh
Confidence 445556667899999999999999999999999974 5779998888899983 55
No 12
>PLN03091 hypothetical protein; Provisional
Probab=93.27 E-value=0.15 Score=57.68 Aligned_cols=64 Identities=11% Similarity=0.358 Sum_probs=54.2
Q ss_pred cccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhcCCCcccCCCChhhHHH
Q 003898 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNA 119 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev~~ 119 (788)
..||.||....++..+++|...-+|+.+|.-|+-.|||+.||..++|..+..+ ||+...+.+..
T Consensus 68 gpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~----I~p~t~kpl~e 131 (459)
T PLN03091 68 GTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRG----IDPNTHKPLSE 131 (459)
T ss_pred CCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcC----CCCCCCCCccc
Confidence 68999999999999999999999999999999999999999999888766544 55555444433
No 13
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.95 E-value=0.29 Score=54.80 Aligned_cols=58 Identities=22% Similarity=0.470 Sum_probs=51.1
Q ss_pred cccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHH----HHHhhcCCCccc
Q 003898 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVR----RMNKLLGPGLCL 109 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~----rI~k~L~~~~~i 109 (788)
..|+..|...||.||-+.|-||.-|+.+...|++.||.-=|-+.-+ ||+..|..-..+
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 7899999999999999999999999999999999999999888776 677777754433
No 14
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=90.41 E-value=0.41 Score=54.14 Aligned_cols=49 Identities=22% Similarity=0.430 Sum_probs=45.4
Q ss_pred cccccccCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhhHHHHHHHHH
Q 003898 48 TRQWAAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLV 96 (788)
Q Consensus 48 ~R~w~~Ws~eEkn~FFeaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~ 96 (788)
..--..||++|+=.+-||+-.+| .|.+-|+++|-+|++++++.+|+..+
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=88.52 E-value=3.4 Score=44.27 Aligned_cols=78 Identities=18% Similarity=0.311 Sum_probs=60.1
Q ss_pred ccccCHHHHHHHHHHHHHhc-ccHHHHHHHhh-hcchhhHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHH
Q 003898 51 WAAWTREEEESFFTALRQVG-KNFEKITHRVR-SKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLL 128 (788)
Q Consensus 51 w~~Ws~eEkn~FFeaL~e~G-KdFEaI~~~i~-~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev~~Am~~w~sl~ 128 (788)
...||.||-+.-.+++++|| .+...|+..|. .|+..|.|.=|++ ||.|++.-+++-.+|-.. ++ ++.
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 667777677776666444 33 345
Q ss_pred HHhcccchhhc
Q 003898 129 EKYSCKASKLH 139 (788)
Q Consensus 129 ~K~gc~~sKL~ 139 (788)
.+||-.+.++.
T Consensus 94 ~~~GnKWs~IA 104 (249)
T PLN03212 94 RLLGNRWSLIA 104 (249)
T ss_pred HhccccHHHHH
Confidence 66776666654
No 16
>PLN03091 hypothetical protein; Provisional
Probab=86.93 E-value=4.5 Score=46.40 Aligned_cols=79 Identities=15% Similarity=0.302 Sum_probs=61.4
Q ss_pred ccccCHHHHHHHHHHHHHhc-ccHHHHHHHhh-hcchhhHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHH
Q 003898 51 WAAWTREEEESFFTALRQVG-KNFEKITHRVR-SKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLL 128 (788)
Q Consensus 51 w~~Ws~eEkn~FFeaL~e~G-KdFEaI~~~i~-~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev~~Am~~w~sl~ 128 (788)
...||.+|-+...+++++|| ++...|+..|. .|+-.|.|.=|+ .||.|++.=.++-.+|-.. ++ ++.
T Consensus 14 Kg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~-------NyLdP~IkKgpWT~EED~l-LL---eL~ 82 (459)
T PLN03091 14 KGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWI-------NYLRPDLKRGTFSQQEENL-II---ELH 82 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHH-------hccCCcccCCCCCHHHHHH-HH---HHH
Confidence 36799999999999999999 58999999886 799999997664 5788877777777766655 33 445
Q ss_pred HHhcccchhhcc
Q 003898 129 EKYSCKASKLHL 140 (788)
Q Consensus 129 ~K~gc~~sKL~~ 140 (788)
++||-.+.++..
T Consensus 83 k~~GnKWskIAk 94 (459)
T PLN03091 83 AVLGNRWSQIAA 94 (459)
T ss_pred HHhCcchHHHHH
Confidence 678876666544
No 17
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=76.75 E-value=3.8 Score=51.10 Aligned_cols=51 Identities=20% Similarity=0.504 Sum_probs=46.6
Q ss_pred ccccCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhhHHHHHHHHHHHHHh
Q 003898 51 WAAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLVRRMNK 101 (788)
Q Consensus 51 w~~Ws~eEkn~FFeaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k 101 (788)
...|+..|=+.|-.|...|| .|+++|+..|..|+.++||.|+--.|.|...
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 6899999999999999999999999987654
No 18
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=76.24 E-value=7.3 Score=43.46 Aligned_cols=48 Identities=23% Similarity=0.497 Sum_probs=44.9
Q ss_pred cccccCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhhHHHHHHHHHH
Q 003898 50 QWAAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLVR 97 (788)
Q Consensus 50 ~w~~Ws~eEkn~FFeaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~~ 97 (788)
--+.|+..|+=.|-+++-..| .|.+-|+.||-.+.|++||.+||.++-
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 899999999999999999999999886
No 19
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=72.36 E-value=3.6 Score=47.53 Aligned_cols=41 Identities=22% Similarity=0.499 Sum_probs=37.4
Q ss_pred cccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHH
Q 003898 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYY 92 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFY 92 (788)
+.|+.+|.-+.-||+..||-|.++|+..|.+|+++|-=-.|
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~F 320 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHF 320 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHH
Confidence 58999999999999999999999999999999999964333
No 20
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=68.57 E-value=2.3 Score=48.82 Aligned_cols=49 Identities=20% Similarity=0.385 Sum_probs=40.4
Q ss_pred cccccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHH
Q 003898 50 QWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRM 99 (788)
Q Consensus 50 ~w~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI 99 (788)
..-.||.+|+. ---++.-||-+||.|...|.+|..+||.+||..-=+-|
T Consensus 469 ~~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~n~k~i 517 (534)
T KOG1194|consen 469 INYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMDNEKLI 517 (534)
T ss_pred ecCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcCchhhh
Confidence 34679999987 55566788999999999999999999999997654444
No 21
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=62.55 E-value=12 Score=44.42 Aligned_cols=76 Identities=22% Similarity=0.375 Sum_probs=56.5
Q ss_pred hhhhccccCCCcccccccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHH----HHHhhcCC--CcccC
Q 003898 37 NVILQQSAKRPTRQWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVR----RMNKLLGP--GLCLD 110 (788)
Q Consensus 37 ~~~~~~~~kk~~R~w~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~----rI~k~L~~--~~~iD 110 (788)
.|+-+--.+++-+ ..|+..|-..||.+|.+.|-+|--|++....+++.|||.=|-..-+ +|..-|.. .+..|
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 3444333344444 8899999999999999999999999999999999999998876555 45555554 44444
Q ss_pred CCCh
Q 003898 111 AKNS 114 (788)
Q Consensus 111 ~Kn~ 114 (788)
+.|.
T Consensus 475 ~~d~ 478 (584)
T KOG2009|consen 475 AYDD 478 (584)
T ss_pred cccc
Confidence 4443
No 22
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=61.17 E-value=17 Score=43.90 Aligned_cols=75 Identities=20% Similarity=0.345 Sum_probs=59.4
Q ss_pred cccCHHHHHHHHHHHHHhc-ccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHHHH
Q 003898 52 AAWTREEEESFFTALRQVG-KNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLLEK 130 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~G-KdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev~~Am~~w~sl~~K 130 (788)
..|+.+|--+.|-|..+|| ||.-+|...+..++-.|.|.=|.|..++=.|.=. -..++..++++ +.++
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 8889999999999999999999999887766433 22345556655 4577
Q ss_pred hcc-cchh
Q 003898 131 YSC-KASK 137 (788)
Q Consensus 131 ~gc-~~sK 137 (788)
||- .|.|
T Consensus 430 YG~g~Wak 437 (939)
T KOG0049|consen 430 YGKGNWAK 437 (939)
T ss_pred HccchHHH
Confidence 874 4444
No 23
>PF08897 DUF1841: Domain of unknown function (DUF1841); InterPro: IPR014993 This group of proteins are functionally uncharacterised.
Probab=46.26 E-value=14 Score=36.71 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=15.7
Q ss_pred chhhHHHHHHHHHHHHHh
Q 003898 84 NKDQVRHYYYRLVRRMNK 101 (788)
Q Consensus 84 nKdQVRhFYYrt~~rI~k 101 (788)
+++|||+||+.+|+|-.+
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=39.34 E-value=10 Score=35.17 Aligned_cols=17 Identities=35% Similarity=0.759 Sum_probs=15.2
Q ss_pred HHHHHHhhhhccCccCC
Q 003898 357 SVLEHLNRKWGNASVAS 373 (788)
Q Consensus 357 svl~HLn~KWg~S~~a~ 373 (788)
..++||++|||++.|..
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=37.35 E-value=65 Score=33.57 Aligned_cols=45 Identities=16% Similarity=0.337 Sum_probs=39.8
Q ss_pred ccccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHH
Q 003898 51 WAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRL 95 (788)
Q Consensus 51 w~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt 95 (788)
...||.||+..-+++-..+|=.-..|+.++.-++=..|.+|.-..
T Consensus 62 rg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~ 106 (238)
T KOG0048|consen 62 RGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTH 106 (238)
T ss_pred CCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHH
Confidence 479999999999999999999999999999988888888886333
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=36.79 E-value=79 Score=27.79 Aligned_cols=49 Identities=16% Similarity=0.254 Sum_probs=38.7
Q ss_pred ccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhc
Q 003898 53 AWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLL 103 (788)
Q Consensus 53 ~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L 103 (788)
..+..+++.|+.. ...|...+.|+..+.. +...||+.+++..++|.+.|
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 89999999999999998765
No 27
>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=34.22 E-value=1.5e+02 Score=25.82 Aligned_cols=59 Identities=20% Similarity=0.347 Sum_probs=37.6
Q ss_pred ccCHHHHHHHHHHHHHh---c----------ccHHHHHHHhh-----hcchhhHHHHHHH---HHHHHHhhcCC-CcccC
Q 003898 53 AWTREEEESFFTALRQV---G----------KNFEKITHRVR-----SKNKDQVRHYYYR---LVRRMNKLLGP-GLCLD 110 (788)
Q Consensus 53 ~Ws~eEkn~FFeaL~e~---G----------KdFEaI~~~i~-----~KnKdQVRhFYYr---t~~rI~k~L~~-~~~iD 110 (788)
.||.+....|.+.|.+. | ..++.|+..++ ..+++||++-|-+ .|+.+..++.- |+.-|
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l~~~sg~gwd 80 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKELRNHSGFGWD 80 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHHHcCCCceEc
Confidence 49999999999999666 2 23666777776 4467888887632 22333444443 45444
Q ss_pred C
Q 003898 111 A 111 (788)
Q Consensus 111 ~ 111 (788)
+
T Consensus 81 ~ 81 (96)
T PF12776_consen 81 P 81 (96)
T ss_pred C
Confidence 4
No 28
>PTZ00249 variable surface protein Vir28; Provisional
Probab=33.26 E-value=2.4e+02 Score=33.54 Aligned_cols=139 Identities=17% Similarity=0.142 Sum_probs=74.0
Q ss_pred hhhHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHHHHhcccchhhcccchhhHHHHHHHHHHHhhh-----
Q 003898 85 KDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLLEKYSCKASKLHLKPRRFKIFVEALEHQLLKD----- 159 (788)
Q Consensus 85 KdQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev~~Am~~w~sl~~K~gc~~sKL~~kp~r~k~f~~~L~~~llK~----- 159 (788)
|+..=.-+|..+-+|...... ...-.....-+..|-++++++-..-.+|+.+...||.++...+.+.-+.
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 444444456666655422221 1112334444568889999998777788888888888888776433221
Q ss_pred -----------h--cccc---ccCCCCCCCCCCCCCCCCCC--cccCCCCCccceEEEeccchhhhhcCCCCCCCCcccc
Q 003898 160 -----------R--KRSV---RKRPSQRDNYSPTVPTPIPN--QSRTSGQDTCTVKLVLVDSQNIQKLGPAKGSLKRNVN 221 (788)
Q Consensus 160 -----------R--kK~~---~kr~~~~~n~l~a~~~~ls~--~sr~~g~~~~~vkl~~~~~~n~~k~g~~kgs~~~~~~ 221 (788)
| .|.+ +-|.--+.-+.|--+..-|+ +.|.+| +|++...|-|-+. +.||+.-|.+-.+..
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 0 1111 01111111122221111111 445554 4667777766666 888888887555555
Q ss_pred cccccCCCcC
Q 003898 222 IGINRSNNKA 231 (788)
Q Consensus 222 ~~v~~~~~k~ 231 (788)
++|-+++-+|
T Consensus 285 v~~~ss~a~~ 294 (516)
T PTZ00249 285 VTVPSSKAHD 294 (516)
T ss_pred eecccccccC
Confidence 6665554443
No 29
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=32.59 E-value=42 Score=39.45 Aligned_cols=40 Identities=23% Similarity=0.496 Sum_probs=37.2
Q ss_pred ccccccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhH
Q 003898 49 RQWAAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQV 88 (788)
Q Consensus 49 R~w~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQV 88 (788)
-....||.+|.-+--||+..||-|.++|+.-+.+|+++|-
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 30
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=32.39 E-value=1.5e+02 Score=25.20 Aligned_cols=70 Identities=9% Similarity=-0.001 Sum_probs=39.9
Q ss_pred cccCHHHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHH
Q 003898 52 AAWTREEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLL 128 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev~~Am~~w~sl~ 128 (788)
..||.+|.+.+-+-+.+| .+.|.... +.......-.+.|..|...|..-... .++.+++.-...++-...
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 778888777555554433
No 31
>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=30.52 E-value=1.1e+02 Score=32.30 Aligned_cols=25 Identities=28% Similarity=0.345 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHh---cccHHHHHHHhh
Q 003898 57 EEEESFFTALRQV---GKNFEKITHRVR 81 (788)
Q Consensus 57 eEkn~FFeaL~e~---GKdFEaI~~~i~ 81 (788)
++-..|..+|... ++|||.||.||+
T Consensus 157 ~~l~~Fl~~l~~~L~~~~dfElvQa~l~ 184 (237)
T PF04192_consen 157 EELVSFLRFLTYRLKSRRDFELVQAYLS 184 (237)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4445555554332 566666666654
No 32
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=27.00 E-value=24 Score=38.83 Aligned_cols=21 Identities=38% Similarity=0.689 Sum_probs=15.9
Q ss_pred CCCCCccccccccccCCCccc
Q 003898 625 SSIWDAEETCDAFSFQKNPVL 645 (788)
Q Consensus 625 sSIwDAEETChAF~fqk~~~~ 645 (788)
-+|||+|||-|-|-=+.+..+
T Consensus 171 rTIWDGEet~yCFKekSR~~L 191 (304)
T KOG0775|consen 171 RTIWDGEETVYCFKEKSRSLL 191 (304)
T ss_pred CccccCceeeeehhHhhHHHH
Confidence 579999999999865554443
No 33
>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=26.93 E-value=1.6e+02 Score=23.34 Aligned_cols=42 Identities=14% Similarity=0.262 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHH
Q 003898 57 EEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRM 99 (788)
Q Consensus 57 eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI 99 (788)
++...-|......|..++.|+..+. -+...|+..++|..++|
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 4455666777788999999999996 56778999999988765
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=26.41 E-value=1.7e+02 Score=25.05 Aligned_cols=51 Identities=18% Similarity=0.404 Sum_probs=29.6
Q ss_pred cccCHHHHHHHHHHHHHh--cc------------cHHHHHHHhh----hcchhhHHHHHHHHHHHHHhh
Q 003898 52 AAWTREEEESFFTALRQV--GK------------NFEKITHRVR----SKNKDQVRHYYYRLVRRMNKL 102 (788)
Q Consensus 52 ~~Ws~eEkn~FFeaL~e~--GK------------dFEaI~~~i~----~KnKdQVRhFYYrt~~rI~k~ 102 (788)
..|+.+|...|.+.+.+. -. -|+.|+..|+ .++..|+|.=+-++.++-.++
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 579999999999999882 11 3555666665 455566666555555444443
No 35
>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=26.34 E-value=1.4e+02 Score=31.53 Aligned_cols=48 Identities=21% Similarity=0.406 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhcC
Q 003898 57 EEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLG 104 (788)
Q Consensus 57 eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~ 104 (788)
++++.+=+..++.-.+||.+-.++..||..++..||=.+..-+..+|.
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 556665555677777999999999999999999999999999988775
No 36
>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=24.76 E-value=2.5e+02 Score=22.05 Aligned_cols=43 Identities=23% Similarity=0.355 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHh
Q 003898 57 EEEESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNK 101 (788)
Q Consensus 57 eEkn~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k 101 (788)
.|+..+ ......|+.++.|+..+.. +...||+.+.+..++|.+
T Consensus 8 ~er~vi-~~~y~~~~t~~eIa~~lg~-s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 8 REREVI-RLRYFEGLTLEEIAERLGI-SRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHHHHH-HHHHTST-SHHHHHHHHTS-CHHHHHHHHHHHHHHHHH
T ss_pred HHHHHH-HHHhcCCCCHHHHHHHHCC-cHHHHHHHHHHHHHHhcC
Confidence 344444 4444779999999999986 788999999999998853
No 37
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=23.87 E-value=1.1e+02 Score=24.80 Aligned_cols=40 Identities=23% Similarity=0.407 Sum_probs=31.0
Q ss_pred HHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHHHHhccc
Q 003898 94 RLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLLEKYSCK 134 (788)
Q Consensus 94 rt~~rI~k~L~~~~~iD~Kn~kev~~Am~~w~sl~~K~gc~ 134 (788)
+...||.|+|.-..+- ..+..|--.|+..-.+|+.||+.+
T Consensus 2 kil~kI~kLLalA~~~-~~~~~EA~~A~~kAq~Lm~ky~i~ 41 (43)
T PF10979_consen 2 KILEKIRKLLALAEST-GSNEHEAEAALAKAQRLMAKYGID 41 (43)
T ss_pred hHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHHHHhCCc
Confidence 3568999999864432 345668889999999999999974
No 38
>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=52.3
Q ss_pred CceEEEEEecCcHHHHHHHhhcCCCceeEEeecCccchhHHHHHHhhhhccCc-cCCcceEeeccccccccccCCcCccc
Q 003898 318 PVKLKLQLYPIDDGTRKALEMDNHNPHLELTLSTRKKISSVLEHLNRKWGNAS-VASGELMLFPYGAQRENLVGYQRWTQ 396 (788)
Q Consensus 318 ~~KikLQLFPide~Tr~~le~~g~nP~LELTLs~rKkiSsvl~HLn~KWg~S~-~a~Gel~LfPy~~~~~nLa~~~~Wt~ 396 (788)
+.+.|..+-|-=+++++.|.+.-+|..-| -||=|-|-- |--. ++.||+.+|. ++ -|.
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 003898 397 DSVFSAADVYAMIGSPPMFR 416 (788)
Q Consensus 397 ~~~~ta~DV~~avGsP~vFR 416 (788)
-.-++..|++..+|.|.||=
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 39
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=22.60 E-value=1.7e+02 Score=28.29 Aligned_cols=43 Identities=16% Similarity=0.232 Sum_probs=35.8
Q ss_pred HHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhcCC
Q 003898 62 FFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGP 105 (788)
Q Consensus 62 FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~ 105 (788)
-|....-.|.+++.|+..+.. +..-||...+|..++|.++|..
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 344434459999999999987 8899999999999999999874
No 40
>KOG3821 consensus Heparin sulfate cell surface proteoglycan [Signal transduction mechanisms]
Probab=21.71 E-value=2.2e+02 Score=34.16 Aligned_cols=67 Identities=21% Similarity=0.312 Sum_probs=53.7
Q ss_pred hhHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHHHHHHHHhcccchhhcccchh----hHHHHHHHHHHH
Q 003898 86 DQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRWWSLLEKYSCKASKLHLKPRR----FKIFVEALEHQL 156 (788)
Q Consensus 86 dQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev~~Am~~w~sl~~K~gc~~sKL~~kp~r----~k~f~~~L~~~l 156 (788)
|-|++||.+++-+|=..|.+--++ +.|-+.||..+..=++-||-.+++|.+..-| -+.|.++|+.-+
T Consensus 161 e~l~eff~~Lf~~~f~~l~~~~~~----~~Dy~eCl~~~~~~l~pFGdiPq~l~~Q~trsl~~ar~Flq~L~~g~ 231 (563)
T KOG3821|consen 161 ETLNEFFARLFEVMFSQLNPQYDF----TLDYLECLSKARRELKPFGDIPQKLMLQVTRSLVAARTFLQGLEVGI 231 (563)
T ss_pred HHHHHHHHHHHHHHHHHhcCCcCC----cHHHHHHHHHHHHhcCCcccchHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 679999999999999999963333 5678899999988889999999998876544 356888887543
No 41
>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=21.17 E-value=1e+02 Score=35.64 Aligned_cols=42 Identities=26% Similarity=0.474 Sum_probs=23.9
Q ss_pred ccccccCHHHHHHHHHHHHHh-----------cccH---HHHHHHhh-----hcchhhHHH
Q 003898 49 RQWAAWTREEEESFFTALRQV-----------GKNF---EKITHRVR-----SKNKDQVRH 90 (788)
Q Consensus 49 R~w~~Ws~eEkn~FFeaL~e~-----------GKdF---EaI~~~i~-----~KnKdQVRh 90 (788)
..-..|+.+=++.|.|||+.| ||.| |-|++||. .++++||--
T Consensus 47 ~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvss 107 (431)
T PF01285_consen 47 DGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSS 107 (431)
T ss_dssp GGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHH
Confidence 445789999999999999887 3333 55666665 345555543
No 42
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.10 E-value=2.1e+02 Score=31.33 Aligned_cols=51 Identities=18% Similarity=0.305 Sum_probs=35.4
Q ss_pred HHHHHHHHHhcccHHHHHHHhhhcchhhHHHHHHHHHHHHHhhcCCCcccCCCChhhHHHHHHHH
Q 003898 60 ESFFTALRQVGKNFEKITHRVRSKNKDQVRHYYYRLVRRMNKLLGPGLCLDAKNSKDTNAAMLRW 124 (788)
Q Consensus 60 n~FFeaL~e~GKdFEaI~~~i~~KnKdQVRhFYYrt~~rI~k~L~~~~~iD~Kn~kev~~Am~~w 124 (788)
+|.|-|+.+ |||.|..+. .+...|++.---+.||. ++-.|...+.+|.-+|
T Consensus 67 ~C~yAaf~s---DFe~I~~~~-~~t~~~rkk~ie~~~~~----------v~fs~irtl~eaiary 117 (267)
T COG1655 67 ICYYAAFKS---DFEKIKSYQ-EKTEELRKKNIELKWHS----------VKFSDIRTLNEAIARY 117 (267)
T ss_pred hhhHHHhhH---HHHhhhhcc-hhhHHHHHHHHHHHhhh----------cccccHhHHHHHHHHH
Confidence 688888876 999999998 55667777766666653 4456666666554433
Done!