Query 037988
Match_columns 468
No_of_seqs 247 out of 757
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 06:24:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037988.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037988hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 7.3E-34 1.6E-38 312.4 34.4 308 119-454 156-546 (846)
2 PF00872 Transposase_mut: Tran 99.6 6.1E-16 1.3E-20 159.9 4.4 211 176-418 113-373 (381)
3 PF10551 MULE: MULE transposas 99.4 4.6E-13 9.9E-18 110.5 5.8 59 262-321 1-93 (93)
4 PF03108 DBD_Tnp_Mut: MuDR fam 99.4 7.5E-13 1.6E-17 102.9 5.8 53 89-141 1-67 (67)
5 COG3328 Transposase and inacti 99.1 6E-10 1.3E-14 114.0 14.2 202 176-414 99-345 (379)
6 PF08731 AFT: Transcription fa 97.1 0.0019 4.1E-08 54.5 7.0 30 123-152 82-111 (111)
7 PF03101 FAR1: FAR1 DNA-bindin 96.4 0.0091 2E-07 48.7 6.5 31 122-153 60-90 (91)
8 PF03106 WRKY: WRKY DNA -bindi 93.3 0.15 3.3E-06 38.5 4.4 41 111-151 19-59 (60)
9 PF13565 HTH_32: Homeodomain-l 91.7 0.44 9.5E-06 37.3 5.4 43 161-203 32-76 (77)
10 smart00774 WRKY DNA binding do 87.1 0.85 1.8E-05 34.4 3.5 40 111-150 19-59 (59)
11 PHA02517 putative transposase 81.6 7.2 0.00016 38.3 8.6 123 161-300 28-153 (277)
12 PF03050 DDE_Tnp_IS66: Transpo 68.1 22 0.00047 34.8 7.9 128 159-325 4-155 (271)
13 PF04500 FLYWCH: FLYWCH zinc f 66.4 11 0.00023 27.6 4.1 45 102-150 14-62 (62)
14 PF13592 HTH_33: Winged helix- 66.2 9.4 0.0002 28.5 3.8 29 175-203 2-30 (60)
15 PRK09409 IS2 transposase TnpB; 65.7 1.5E+02 0.0033 29.7 14.2 110 163-295 51-165 (301)
16 PF01498 HTH_Tnp_Tc3_2: Transp 63.1 5.9 0.00013 30.5 2.3 37 168-205 4-40 (72)
17 PF06524 NOA36: NOA36 protein; 56.1 12 0.00025 36.6 3.2 7 13-19 244-250 (314)
18 PF08766 DEK_C: DEK C terminal 55.9 28 0.0006 25.4 4.6 39 161-199 2-42 (54)
19 PF12762 DDE_Tnp_IS1595: ISXO2 54.0 32 0.0007 30.3 5.7 17 382-398 109-125 (151)
20 PF13551 HTH_29: Winged helix- 45.2 46 0.001 27.3 5.0 45 159-204 58-108 (112)
21 PF13276 HTH_21: HTH-like doma 41.7 66 0.0014 23.6 4.9 42 164-205 6-48 (60)
22 cd00131 PAX Paired Box domain 37.4 92 0.002 27.1 5.8 37 166-203 82-123 (128)
23 PF13877 RPAP3_C: Potential Mo 29.2 35 0.00075 27.7 1.7 33 341-376 6-38 (94)
24 smart00351 PAX Paired Box doma 29.1 1.2E+02 0.0026 26.1 5.2 38 165-203 81-123 (125)
25 PF10045 DUF2280: Uncharacteri 28.3 1.8E+02 0.004 24.4 5.7 24 179-202 21-44 (104)
26 PF14420 Clr5: Clr5 domain 24.8 1.7E+02 0.0037 21.3 4.5 25 175-199 18-42 (54)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=7.3e-34 Score=312.36 Aligned_cols=308 Identities=13% Similarity=0.175 Sum_probs=240.4
Q ss_pred EecCCCCcEEEEEEecCCCeEEEEeccCCCCCCCccccccccHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhCC--cCC
Q 037988 119 CLNKGCPWFIYAAQVEYGTKSIIQKLNKVHECNGVLETKEASYKWIASQFERTLENNPKMHVKAMKDELVSNLGI--KAN 196 (468)
Q Consensus 119 C~~~~CpWri~as~~~~~~~~~I~~~~~~HtC~~~~~~~~~ts~~ia~~~~~~i~~~p~~~~~~I~~~v~~~~g~--~vS 196 (468)
|...||+.+|...+. ..+.|.|+.++.+|||+...... ++. ..+.+...+...++. .+.
T Consensus 156 ~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~-~~~-----------------~~r~~~~~~~~~~~~~~~v~ 216 (846)
T PLN03097 156 CAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQA-VSE-----------------QTRKMYAAMARQFAEYKNVV 216 (846)
T ss_pred ccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccc-cch-----------------hhhhhHHHHHhhhhcccccc
Confidence 555789999999774 56789999999999999973322 110 001111111111110 010
Q ss_pred ------HHHHHHHHHHHHHHhhCCchhhHHHHHHHHHHHHhcCCCcEEEEEechh------------hHHHHHhcCceEE
Q 037988 197 ------MKKMYRAKKRAMDKLNGNYTDSYQRLRDYTQILRHRNLDVLVKMKFVSA------------LKNAFINGCRWFM 258 (468)
Q Consensus 197 ------y~k~~raK~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPGs~v~v~~d~~------------~~~~F~~~cr~vi 258 (468)
....-+.+.+.+ ..+..+.|..|+..++..||++++.+++|++ ++..|. ++++||
T Consensus 217 ~~~~d~~~~~~~~r~~~~------~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~-~FGDvV 289 (846)
T PLN03097 217 GLKNDSKSSFDKGRNLGL------EAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYG-NFSDVV 289 (846)
T ss_pred ccchhhcchhhHHHhhhc------ccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHH-hcCCEE
Confidence 011112222211 2345678999999999999999999999873 344554 689999
Q ss_pred EeccccccCCCCCceEEEEeecCCCceEEeeEeeeccccchhHHHHHH-------------Hhch---------------
Q 037988 259 GLDDCHLNGPFGGVLLLAMALDAKNENFPIAVCICESECAGRWKWFFV-------------ILSE--------------- 310 (468)
Q Consensus 259 ~lD~t~l~~~y~g~Ll~avg~D~n~~~~piA~aiv~~E~~esw~WFl~-------------iisD--------------- 310 (468)
.+|+||++++|++||..++|+|+|+|++++|+|++..|+.++|.|+|+ ||||
T Consensus 290 ~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~ 369 (846)
T PLN03097 290 SFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPN 369 (846)
T ss_pred EEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCC
Confidence 999999999999999999999999999999999999999999999999 7788
Q ss_pred ----hhHHHHHHHHhhhCC-----ChhhHHHHHHHhh-cccHHHHHHHHHHHHHHhcCChHHHhHHhhc--cccchhc--
Q 037988 311 ----HCARHMFANLRSNHP-----DIIDRNLFWVDVR-ATSEDEWEDNMKKIKIAKKDTQAAYDYLIKI--DKKEWAR-- 376 (468)
Q Consensus 311 ----~C~~Hi~~N~~~~~~-----~~~~~~~~~~~~~-a~~~~~f~~~~~~l~~~~~~~~~~~~~L~~~--~~~~W~~-- 376 (468)
+|.|||++|+.+++. .+.+...|+.|.+ +.++++|+..|..|.+.+ +.+..+||..+ .+++|+.
T Consensus 370 t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky--~L~~n~WL~~LY~~RekWapaY 447 (846)
T PLN03097 370 AHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRF--ELKEDEWMQSLYEDRKQWVPTY 447 (846)
T ss_pred ceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhh--cccccHHHHHHHHhHhhhhHHH
Confidence 999999999999875 3578889999776 578999999999988776 88899999998 8899999
Q ss_pred -cCCce-eeecCcchhhhhHHhhhc--ccCCHHHHHHHHHHHHHHHHHHHHH-h----------------HhhccCCCCh
Q 037988 377 -YDIKV-DHVTNNLTESWNNWLNEY--RDKPVLTLTEFIKKNVMKSLYKRYS-D----------------VRKWIRKLPP 435 (468)
Q Consensus 377 -~~~~~-~~~t~N~~Es~N~~i~~~--R~~pi~~~le~ir~~~~~~~~~r~~-~----------------~~~~~~~~tp 435 (468)
.+..| |+.||+.+||+|+.|+++ +..+|..|++.+...+..+..+..+ . ..+.+..|||
T Consensus 448 ~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~ 527 (846)
T PLN03097 448 MRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTH 527 (846)
T ss_pred hcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHH
Confidence 66665 899999999999999985 9999999999998887766554321 1 1233579999
Q ss_pred HHHHHHHHHHhcccceeEE
Q 037988 436 IVRRKLNVSRQEGRFVRKE 454 (468)
Q Consensus 436 ~i~k~l~~~~~~s~~~~~~ 454 (468)
.|+++||+++..+..|.+.
T Consensus 528 ~iF~kFQ~El~~~~~~~~~ 546 (846)
T PLN03097 528 AVFKKFQVEVLGAVACHPK 546 (846)
T ss_pred HHHHHHHHHHHHhhheEEe
Confidence 9999999999999888774
No 2
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.59 E-value=6.1e-16 Score=159.93 Aligned_cols=211 Identities=13% Similarity=0.140 Sum_probs=158.3
Q ss_pred CCCCHHHHHHHHHHhhC-CcCCHHHHHHHHHHHHHHhhCCchhhHHHHHHHHHHHHhcCCCcEEEEEechhhHHHHHhcC
Q 037988 176 PKMHVKAMKDELVSNLG-IKANMKKMYRAKKRAMDKLNGNYTDSYQRLRDYTQILRHRNLDVLVKMKFVSALKNAFINGC 254 (468)
Q Consensus 176 p~~~~~~I~~~v~~~~g-~~vSy~k~~raK~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPGs~v~v~~d~~~~~~F~~~c 254 (468)
.+++.++|.+.+..-+| ..+|.+++.|..+.+.+.+ ..|...- +...
T Consensus 113 ~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~-----------~~w~~R~---------------------L~~~ 160 (381)
T PF00872_consen 113 KGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEV-----------EAWRNRP---------------------LESE 160 (381)
T ss_pred cccccccccchhhhhhcccccCchhhhhhhhhhhhhH-----------HHHhhhc---------------------cccc
Confidence 46788899999999999 8899999998877665532 1121111 1245
Q ss_pred -ceEEEeccccccCCCC-----CceEEEEeecCCCceEEeeEeeeccccchhHHHHHH------------Hhch------
Q 037988 255 -RWFMGLDDCHLNGPFG-----GVLLLAMALDAKNENFPIAVCICESECAGRWKWFFV------------ILSE------ 310 (468)
Q Consensus 255 -r~vi~lD~t~l~~~y~-----g~Ll~avg~D~n~~~~piA~aiv~~E~~esw~WFl~------------iisD------ 310 (468)
.|+|.|||+|++.+.+ ..+++|+|+|.+|+..+||+.+.+.|+.++|.=||+ |++|
T Consensus 161 ~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~RGl~~~~lvv~Dg~~gl~ 240 (381)
T PF00872_consen 161 PYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKERGLKDILLVVSDGHKGLK 240 (381)
T ss_pred cccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhccccccceeecccccccc
Confidence 6899999999997754 468999999999999999999999999999999999 7788
Q ss_pred -------------hhHHHHHHHHhhhCCCh---hhHHHHHHHhhcccHHHHHHHHHHHHHHh-cCChHHHhHHhhccccc
Q 037988 311 -------------HCARHMFANLRSNHPDI---IDRNLFWVDVRATSEDEWEDNMKKIKIAK-KDTQAAYDYLIKIDKKE 373 (468)
Q Consensus 311 -------------~C~~Hi~~N~~~~~~~~---~~~~~~~~~~~a~~~~~f~~~~~~l~~~~-~~~~~~~~~L~~~~~~~ 373 (468)
.|.+|+++|+.++++.+ .+...++.+..+++.+++...++.+.+.. ...|.+.++|.+.-.+.
T Consensus 241 ~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~ 320 (381)
T PF00872_consen 241 EAIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDEL 320 (381)
T ss_pred ccccccccchhhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccccc
Confidence 99999999999999754 56677777878888777777777665432 23899999988754444
Q ss_pred hhc---cC-CceeeecCcchhhhhHHhhhc----ccCCHHHHHHHHHHHHHHH
Q 037988 374 WAR---YD-IKVDHVTNNLTESWNNWLNEY----RDKPVLTLTEFIKKNVMKS 418 (468)
Q Consensus 374 W~~---~~-~~~~~~t~N~~Es~N~~i~~~----R~~pi~~~le~ir~~~~~~ 418 (468)
|+. +. .+--+.|||++||+|+.|+.. +.+|=.+.+..+...++..
T Consensus 321 ~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~~~~Fp~~~s~lr~~~~~~~e 373 (381)
T PF00872_consen 321 LTFLDFPPEHRRSIRTTNAIESLNKEIRRRTKVVGIFPNEESALRLVYAVLME 373 (381)
T ss_pred cceeeecchhccccchhhhccccccchhhhccccccCCCHHHHHHHHHHHHHH
Confidence 444 11 222488999999999999873 4566554444444444433
No 3
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.39 E-value=4.6e-13 Score=110.51 Aligned_cols=59 Identities=29% Similarity=0.674 Sum_probs=55.6
Q ss_pred cccccCCCCCceEE---EEeecCCCceEEeeEeeeccccchhHHHHHH------------Hhch----------------
Q 037988 262 DCHLNGPFGGVLLL---AMALDAKNENFPIAVCICESECAGRWKWFFV------------ILSE---------------- 310 (468)
Q Consensus 262 ~t~l~~~y~g~Ll~---avg~D~n~~~~piA~aiv~~E~~esw~WFl~------------iisD---------------- 310 (468)
|||++|+| |+|+. ++|.|++++.+|+||++++.|+.++|.|||+ ||+|
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~p~~ii~D~~~~~~~Ai~~vfP~~ 79 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQKPKVIISDFDKALINAIKEVFPDA 79 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccCceeeeccccHHHHHHHHHHCCCc
Confidence 79999999 99986 9999999999999999999999999999999 5677
Q ss_pred ---hhHHHHHHHHh
Q 037988 311 ---HCARHMFANLR 321 (468)
Q Consensus 311 ---~C~~Hi~~N~~ 321 (468)
+|.+|+.+|++
T Consensus 80 ~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 80 RHQLCLFHILRNIK 93 (93)
T ss_pred eEehhHHHHHHhhC
Confidence 99999999984
No 4
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=99.37 E-value=7.5e-13 Score=102.88 Aligned_cols=53 Identities=40% Similarity=0.740 Sum_probs=50.9
Q ss_pred CCccccccEee-------------ecceE-EEEEecCCceEEEEEecCCCCcEEEEEEecCCCeEEE
Q 037988 89 VAGVAVGQEFE-------------IVQHF-IRVIKNDNKRFKAKCLNKGCPWFIYAAQVEYGTKSII 141 (468)
Q Consensus 89 ~~~~~vG~~F~-------------i~~~~-~~~~ksd~~r~~~~C~~~~CpWri~as~~~~~~~~~I 141 (468)
||.|.+||+|+ |+++| |++.+|+++|++++|..++|||+|+|++.++++.|+|
T Consensus 1 n~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 1 NPELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred CCccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 68999999999 88999 9999999999999999999999999999999999987
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.14 E-value=6e-10 Score=114.03 Aligned_cols=202 Identities=14% Similarity=0.112 Sum_probs=142.1
Q ss_pred CCCCHHHHHHHHHHhhCCcCCHHHHHHHHHHHHHHhhCCchhhHHHHHHHHHHHHhcCCCcEEEEEechhhHHHHHhcCc
Q 037988 176 PKMHVKAMKDELVSNLGIKANMKKMYRAKKRAMDKLNGNYTDSYQRLRDYTQILRHRNLDVLVKMKFVSALKNAFINGCR 255 (468)
Q Consensus 176 p~~~~~~I~~~v~~~~g~~vSy~k~~raK~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPGs~v~v~~d~~~~~~F~~~cr 255 (468)
.+++++++.+.+++.++..+|.+...+.....++.+ .+++..- + +..
T Consensus 99 ~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e~v---------------~~~~~r~-----------------l-~~~ 145 (379)
T COG3328 99 KGVTTREIEALLEELYGHKVSPSVISVVTDRLDEKV---------------KAWQNRP-----------------L-GDY 145 (379)
T ss_pred cCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHHHH---------------HHHHhcc-----------------c-cCc
Confidence 467899999999999998888887777666555432 2222221 1 578
Q ss_pred eEEEeccccccCC--CCCceEEEEeecCCCceEEeeEeeeccccchhHHHHHH------------Hhch-----------
Q 037988 256 WFMGLDDCHLNGP--FGGVLLLAMALDAKNENFPIAVCICESECAGRWKWFFV------------ILSE----------- 310 (468)
Q Consensus 256 ~vi~lD~t~l~~~--y~g~Ll~avg~D~n~~~~piA~aiv~~E~~esw~WFl~------------iisD----------- 310 (468)
|++.+||+|++.+ -+.++++|+|++.+|+-.++++.+-+.|+ ..|.=||. +++|
T Consensus 146 ~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl~~v~l~v~Dg~~gl~~aI~~ 224 (379)
T COG3328 146 PYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGLSDVLLVVVDGLKGLPEAISA 224 (379)
T ss_pred eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccccceeEEecchhhhhHHHHHH
Confidence 9999999999998 36789999999999999999999999999 99994444 4556
Q ss_pred --------hhHHHHHHHHhhhCCChh---hHHHHHHHhhcccHHHHHHHH----HHHHHHhcCChHHHhHHhhccccchh
Q 037988 311 --------HCARHMFANLRSNHPDII---DRNLFWVDVRATSEDEWEDNM----KKIKIAKKDTQAAYDYLIKIDKKEWA 375 (468)
Q Consensus 311 --------~C~~Hi~~N~~~~~~~~~---~~~~~~~~~~a~~~~~f~~~~----~~l~~~~~~~~~~~~~L~~~~~~~W~ 375 (468)
.|..|+.+|+..+.+.+. ....+..+..+++..+-...+ +.+... .|....++.+.--+.|+
T Consensus 225 v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~---yP~i~~~~~~~~~~~~~ 301 (379)
T COG3328 225 VFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKR---YPAILKSWRNALEELLP 301 (379)
T ss_pred hccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhh---cchHHHHHHHHHHHhcc
Confidence 999999999999988653 334444555555544444444 434445 77887777764333333
Q ss_pred c----cCCceeeecCcchhhhhHHhhhc-ccCCHHHHHHHHHHH
Q 037988 376 R----YDIKVDHVTNNLTESWNNWLNEY-RDKPVLTLTEFIKKN 414 (468)
Q Consensus 376 ~----~~~~~~~~t~N~~Es~N~~i~~~-R~~pi~~~le~ir~~ 414 (468)
- ...|--+.|||..|++|+.|+.. +..++.+--++++..
T Consensus 302 F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~ 345 (379)
T COG3328 302 FFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNEESVEKL 345 (379)
T ss_pred cccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCHHHHHHH
Confidence 3 11112478999999999988753 554454444444443
No 6
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=97.09 E-value=0.0019 Score=54.47 Aligned_cols=30 Identities=23% Similarity=0.260 Sum_probs=28.4
Q ss_pred CCCcEEEEEEecCCCeEEEEeccCCCCCCC
Q 037988 123 GCPWFIYAAQVEYGTKSIIQKLNKVHECNG 152 (468)
Q Consensus 123 ~CpWri~as~~~~~~~~~I~~~~~~HtC~~ 152 (468)
.|||+|+|........|.|..++..|+|+.
T Consensus 82 ~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 82 TCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred CCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 699999999999999999999999999974
No 7
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=96.45 E-value=0.0091 Score=48.68 Aligned_cols=31 Identities=16% Similarity=0.105 Sum_probs=28.6
Q ss_pred CCCCcEEEEEEecCCCeEEEEeccCCCCCCCc
Q 037988 122 KGCPWFIYAAQVEYGTKSIIQKLNKVHECNGV 153 (468)
Q Consensus 122 ~~CpWri~as~~~~~~~~~I~~~~~~HtC~~~ 153 (468)
.|||++|.+.+.+ .+.|.|..+..+|||+..
T Consensus 60 tgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~ 90 (91)
T PF03101_consen 60 TGCKARINVKRRK-DGKWRVTSFVLEHNHPLC 90 (91)
T ss_pred cCCCEEEEEEEcc-CCEEEEEECcCCcCCCCC
Confidence 7999999999887 999999999999999863
No 8
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=93.33 E-value=0.15 Score=38.52 Aligned_cols=41 Identities=17% Similarity=0.233 Sum_probs=33.4
Q ss_pred CCceEEEEEecCCCCcEEEEEEecCCCeEEEEeccCCCCCC
Q 037988 111 DNKRFKAKCLNKGCPWFIYAAQVEYGTKSIIQKLNKVHECN 151 (468)
Q Consensus 111 d~~r~~~~C~~~~CpWri~as~~~~~~~~~I~~~~~~HtC~ 151 (468)
.-.|.-.+|+..+||.+-...+..+.....+++|.++|||+
T Consensus 19 ~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 19 PYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp TCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred ceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 34577799999999999999998878888899999999996
No 9
>PF13565 HTH_32: Homeodomain-like domain
Probab=91.67 E-value=0.44 Score=37.28 Aligned_cols=43 Identities=16% Similarity=0.289 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhCCcC--CHHHHHHH
Q 037988 161 YKWIASQFERTLENNPKMHVKAMKDELVSNLGIKA--NMKKMYRA 203 (468)
Q Consensus 161 s~~ia~~~~~~i~~~p~~~~~~I~~~v~~~~g~~v--Sy~k~~ra 203 (468)
...+...+...+..+|.|++.+|.+.|.+++|+.+ |.+.+||.
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 34454677788889999999999999999999876 99999985
No 10
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=87.13 E-value=0.85 Score=34.35 Aligned_cols=40 Identities=15% Similarity=0.188 Sum_probs=32.2
Q ss_pred CCceEEEEEec-CCCCcEEEEEEecCCCeEEEEeccCCCCC
Q 037988 111 DNKRFKAKCLN-KGCPWFIYAAQVEYGTKSIIQKLNKVHEC 150 (468)
Q Consensus 111 d~~r~~~~C~~-~~CpWri~as~~~~~~~~~I~~~~~~HtC 150 (468)
...|--.+|.. .+|+.+=...+..+.+...+++|.++|||
T Consensus 19 ~~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 19 PFPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cCcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 33456689998 89999888877766666778899999998
No 11
>PHA02517 putative transposase OrfB; Reviewed
Probab=81.62 E-value=7.2 Score=38.32 Aligned_cols=123 Identities=13% Similarity=0.075 Sum_probs=66.9
Q ss_pred HHHHHHHHHHHhhc-CCCCCHHHHHHHHHHhhCCcCCHHHHHHHHHHHHHHhhCCchhhHHHHHHHHHHHHhcCCCcEEE
Q 037988 161 YKWIASQFERTLEN-NPKMHVKAMKDELVSNLGIKANMKKMYRAKKRAMDKLNGNYTDSYQRLRDYTQILRHRNLDVLVK 239 (468)
Q Consensus 161 s~~ia~~~~~~i~~-~p~~~~~~I~~~v~~~~g~~vSy~k~~raK~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPGs~v~ 239 (468)
...+...+...+.. .|.+..+.|...|++. |+.+|.++++|.-..+ |-.... .. .-.....+....
T Consensus 28 ~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~-----gl~~~~-~~------k~~~~~~~~~~~ 94 (277)
T PHA02517 28 DDWLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKEL-----GLAGVL-RG------KKVRTTISRKAV 94 (277)
T ss_pred hHHHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHc-----CCceEe-cC------CCcCCCCCCCCC
Confidence 34566666666654 6789999999998765 9999999999864321 110000 00 000000000000
Q ss_pred EEechh-hHHHHHh-cCceEEEeccccccCCCCCceEEEEeecCCCceEEeeEeeeccccchh
Q 037988 240 MKFVSA-LKNAFIN-GCRWFMGLDDCHLNGPFGGVLLLAMALDAKNENFPIAVCICESECAGR 300 (468)
Q Consensus 240 v~~d~~-~~~~F~~-~cr~vi~lD~t~l~~~y~g~Ll~avg~D~n~~~~piA~aiv~~E~~es 300 (468)
..+. ..+.|.. .-..+++.|-|++...- |....++-+|.... +++||.+...++.+.
T Consensus 95 --~~~n~~~r~f~~~~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~ 153 (277)
T PHA02517 95 --AAPDRVNRQFVATRPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDF 153 (277)
T ss_pred --CCCCcccCCCCCCCCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHH
Confidence 0000 0122322 23458999999986543 55555666666543 567788877666543
No 12
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=68.12 E-value=22 Score=34.84 Aligned_cols=128 Identities=14% Similarity=0.129 Sum_probs=78.0
Q ss_pred ccHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhCCcCCHHHHHHHHHHHHHHhhCCchhhHHHHHHHHHHHHhcCCCcEE
Q 037988 159 ASYKWIASQFERTLENNPKMHVKAMKDELVSNLGIKANMKKMYRAKKRAMDKLNGNYTDSYQRLRDYTQILRHRNLDVLV 238 (468)
Q Consensus 159 ~ts~~ia~~~~~~i~~~p~~~~~~I~~~v~~~~g~~vSy~k~~raK~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPGs~v 238 (468)
.++..+|-.+..... -.++...+.+.+.+. |+++|...+.+.-.++.+.+. .....|.+.
T Consensus 4 ~g~~~~a~i~~l~~~--~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l~-----------~~~~~l~~~------ 63 (271)
T PF03050_consen 4 YGPSLLALIAYLKYV--YHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEALK-----------PLYEALKEE------ 63 (271)
T ss_pred CCHHHHHHHHHHHhc--CCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhhh-----------hhhhhhhhh------
Confidence 455566655444332 233445566666555 999999988877665544321 111111111
Q ss_pred EEEechhhHHHHHhcCceEEEecccccc----CCCC-CceEEEEeecCCCceEEeeEeeeccccchhHHHHHH-----Hh
Q 037988 239 KMKFVSALKNAFINGCRWFMGLDDCHLN----GPFG-GVLLLAMALDAKNENFPIAVCICESECAGRWKWFFV-----IL 308 (468)
Q Consensus 239 ~v~~d~~~~~~F~~~cr~vi~lD~t~l~----~~y~-g~Ll~avg~D~n~~~~piA~aiv~~E~~esw~WFl~-----ii 308 (468)
. --.+|+++|-|..+ ++.+ +-+-++++-+ .+.|.+.++=..+.-.=+|. ++
T Consensus 64 -----------~--~~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~~~Gilv 124 (271)
T PF03050_consen 64 -----------L--RSSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGDFSGILV 124 (271)
T ss_pred -----------c--cccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcccceeee
Confidence 0 13579999999988 6553 4444444433 56666667666666666666 67
Q ss_pred ch--------------hhHHHHHHHHhhhCC
Q 037988 309 SE--------------HCARHMFANLRSNHP 325 (468)
Q Consensus 309 sD--------------~C~~Hi~~N~~~~~~ 325 (468)
|| .|..|+.|.+.+-..
T Consensus 125 sD~y~~Y~~~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 125 SDGYSAYNKLAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred ccccccccccccccccccccccccccccccc
Confidence 88 999999999987554
No 13
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=66.41 E-value=11 Score=27.65 Aligned_cols=45 Identities=13% Similarity=0.242 Sum_probs=21.6
Q ss_pred ceE-EEEEecCCceEEEEEecC---CCCcEEEEEEecCCCeEEEEeccCCCCC
Q 037988 102 QHF-IRVIKNDNKRFKAKCLNK---GCPWFIYAAQVEYGTKSIIQKLNKVHEC 150 (468)
Q Consensus 102 ~~~-~~~~ksd~~r~~~~C~~~---~CpWri~as~~~~~~~~~I~~~~~~HtC 150 (468)
+++ |...+.......-.|... +|+.+|... .+. ..|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~~--~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AGD--GRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE----T--TEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CCC--CEEEECCCccCC
Confidence 344 555555577888899974 899999887 222 335555578886
No 14
>PF13592 HTH_33: Winged helix-turn helix
Probab=66.16 E-value=9.4 Score=28.54 Aligned_cols=29 Identities=17% Similarity=0.339 Sum_probs=25.9
Q ss_pred CCCCCHHHHHHHHHHhhCCcCCHHHHHHH
Q 037988 175 NPKMHVKAMKDELVSNLGIKANMKKMYRA 203 (468)
Q Consensus 175 ~p~~~~~~I~~~v~~~~g~~vSy~k~~ra 203 (468)
++.|+.++|++.|.+.||+.+|.+.+++.
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~ys~~~v~~l 30 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKYSPSGVYRL 30 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEEcHHHHHHH
Confidence 45688999999999999999999998875
No 15
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=65.70 E-value=1.5e+02 Score=29.66 Aligned_cols=110 Identities=12% Similarity=0.107 Sum_probs=64.8
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHhh---CC-cCCHHHHHHHHHHH-HHHhhCCchhhHHHHHHHHHHHHhcCCCcE
Q 037988 163 WIASQFERTLENNPKMHVKAMKDELVSNL---GI-KANMKKMYRAKKRA-MDKLNGNYTDSYQRLRDYTQILRHRNLDVL 237 (468)
Q Consensus 163 ~ia~~~~~~i~~~p~~~~~~I~~~v~~~~---g~-~vSy~k~~raK~~a-~~~~~g~~~~sy~~L~~y~~~l~~~NPGs~ 237 (468)
.+...+.......|.+..+.|...|+++. |+ .++..+++|.-..+ +......... +. ....++.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~Gl~~~~~~~~~-----~~-----~~~~~~~- 119 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLERKPAVP-----PS-----KRAHTGR- 119 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHcCCcccccCCCC-----CC-----CCCCCCC-
Confidence 45555666656689999999999998763 66 58888888864331 1100000000 00 0000000
Q ss_pred EEEEechhhHHHHHhcCceEEEeccccccCCCCCceEEEEeecCCCceEEeeEeeecc
Q 037988 238 VKMKFVSALKNAFINGCRWFMGLDDCHLNGPFGGVLLLAMALDAKNENFPIAVCICES 295 (468)
Q Consensus 238 v~v~~d~~~~~~F~~~cr~vi~lD~t~l~~~y~g~Ll~avg~D~n~~~~piA~aiv~~ 295 (468)
+ ....-..+.+.|-||+...-++.+..++-+|.... .+|||++-..
T Consensus 120 --~---------~~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~ 165 (301)
T PRK09409 120 --V---------AVKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTG 165 (301)
T ss_pred --c---------CCCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccC
Confidence 0 01123458999999986554456777777888766 7889998754
No 16
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=63.11 E-value=5.9 Score=30.48 Aligned_cols=37 Identities=22% Similarity=0.450 Sum_probs=16.7
Q ss_pred HHHHhhcCCCCCHHHHHHHHHHhhCCcCCHHHHHHHHH
Q 037988 168 FERTLENNPKMHVKAMKDELVSNLGIKANMKKMYRAKK 205 (468)
Q Consensus 168 ~~~~i~~~p~~~~~~I~~~v~~~~g~~vSy~k~~raK~ 205 (468)
+...++.+|..+..+|...+.+. |+.+|...++|.-.
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L~ 40 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRLR 40 (72)
T ss_dssp ------------HHHHHHHT----T--S-HHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHHH
Confidence 45567789999999999999998 99999999998643
No 17
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=56.07 E-value=12 Score=36.60 Aligned_cols=7 Identities=43% Similarity=0.662 Sum_probs=3.2
Q ss_pred cCCCcCC
Q 037988 13 DDESELN 19 (468)
Q Consensus 13 ~~~~~~~ 19 (468)
||++.|+
T Consensus 244 Dd~~~y~ 250 (314)
T PF06524_consen 244 DDDSGYG 250 (314)
T ss_pred ccccccc
Confidence 4444444
No 18
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=55.90 E-value=28 Score=25.42 Aligned_cols=39 Identities=15% Similarity=0.295 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhhc-CC-CCCHHHHHHHHHHhhCCcCCHHH
Q 037988 161 YKWIASQFERTLEN-NP-KMHVKAMKDELVSNLGIKANMKK 199 (468)
Q Consensus 161 s~~ia~~~~~~i~~-~p-~~~~~~I~~~v~~~~g~~vSy~k 199 (468)
...|...+.+.++. +. +++.+.+...|.+.||++++..+
T Consensus 2 d~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~~K 42 (54)
T PF08766_consen 2 DEEIREAIREILREADLDTVTKKQVREQLEERFGVDLSSRK 42 (54)
T ss_dssp HHHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SHHH
T ss_pred HHHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHHHH
Confidence 34566677777774 43 68899999999999999998544
No 19
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=54.01 E-value=32 Score=30.34 Aligned_cols=17 Identities=29% Similarity=0.298 Sum_probs=14.2
Q ss_pred eeecCcchhhhhHHhhh
Q 037988 382 DHVTNNLTESWNNWLNE 398 (468)
Q Consensus 382 ~~~t~N~~Es~N~~i~~ 398 (468)
+...+|.+|++++.+|.
T Consensus 109 ~~~h~n~ie~~~s~~K~ 125 (151)
T PF12762_consen 109 GGVHTNWIESFWSRLKR 125 (151)
T ss_pred cccccchhhhHHHHHHH
Confidence 46789999999988875
No 20
>PF13551 HTH_29: Winged helix-turn helix
Probab=45.19 E-value=46 Score=27.28 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=34.8
Q ss_pred ccHHHHHHHHHHHhhcCC-----CCCHHHHHHHH-HHhhCCcCCHHHHHHHH
Q 037988 159 ASYKWIASQFERTLENNP-----KMHVKAMKDEL-VSNLGIKANMKKMYRAK 204 (468)
Q Consensus 159 ~ts~~ia~~~~~~i~~~p-----~~~~~~I~~~v-~~~~g~~vSy~k~~raK 204 (468)
++....+ .+.+.+..+| .+++..|.+.| .+.+|+.+|.+.++|.-
T Consensus 58 l~~~~~~-~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 58 LSEEQRA-QLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCHHHHH-HHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 5655555 4566777766 47899999976 89999999999999863
No 21
>PF13276 HTH_21: HTH-like domain
Probab=41.66 E-value=66 Score=23.64 Aligned_cols=42 Identities=17% Similarity=0.307 Sum_probs=33.6
Q ss_pred HHHHHHHHhhc-CCCCCHHHHHHHHHHhhCCcCCHHHHHHHHH
Q 037988 164 IASQFERTLEN-NPKMHVKAMKDELVSNLGIKANMKKMYRAKK 205 (468)
Q Consensus 164 ia~~~~~~i~~-~p~~~~~~I~~~v~~~~g~~vSy~k~~raK~ 205 (468)
+...+...... .+.+....|...|.+++|+.+|..+++|...
T Consensus 6 l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~~v~~krV~RlM~ 48 (60)
T PF13276_consen 6 LRELIKEIFKESKPTYGYRRIWAELRREGGIRVSRKRVRRLMR 48 (60)
T ss_pred HHHHHHHHHHHcCCCeehhHHHHHHhccCcccccHHHHHHHHH
Confidence 45556666664 5889999999999999999999999988643
No 22
>cd00131 PAX Paired Box domain
Probab=37.43 E-value=92 Score=27.09 Aligned_cols=37 Identities=22% Similarity=0.389 Sum_probs=30.0
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHhhCC-----cCCHHHHHHH
Q 037988 166 SQFERTLENNPKMHVKAMKDELVSNLGI-----KANMKKMYRA 203 (468)
Q Consensus 166 ~~~~~~i~~~p~~~~~~I~~~v~~~~g~-----~vSy~k~~ra 203 (468)
..+...+..+|..+..+|.+.|.+ .|+ .+|.+.++|+
T Consensus 82 ~~i~~~v~~~p~~Tl~El~~~L~~-~gv~~~~~~~s~stI~R~ 123 (128)
T cd00131 82 KKIEIYKQENPGMFAWEIRDRLLQ-EGVCDKSNVPSVSSINRI 123 (128)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHH-cCCcccCCCCCHHHHHHH
Confidence 445556789999999999999874 476 5799999987
No 23
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=29.20 E-value=35 Score=27.73 Aligned_cols=33 Identities=21% Similarity=0.468 Sum_probs=27.2
Q ss_pred cHHHHHHHHHHHHHHhcCChHHHhHHhhccccchhc
Q 037988 341 SEDEWEDNMKKIKIAKKDTQAAYDYLIKIDKKEWAR 376 (468)
Q Consensus 341 ~~~~f~~~~~~l~~~~~~~~~~~~~L~~~~~~~W~~ 376 (468)
|-.+|...|..+... ....++||..++|++...
T Consensus 6 ~~~eF~~~w~~~~~~---~~~~~~yL~~i~p~~l~~ 38 (94)
T PF13877_consen 6 NSYEFERDWRRLKKD---PEERYEYLKSIPPDSLPK 38 (94)
T ss_pred CHHHHHHHHHHHcCC---HHHHHHHHHhCChHHHHH
Confidence 467899999998765 568899999999987766
No 24
>smart00351 PAX Paired Box domain.
Probab=29.12 E-value=1.2e+02 Score=26.14 Aligned_cols=38 Identities=16% Similarity=0.342 Sum_probs=28.8
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhhCCcC-----CHHHHHHH
Q 037988 165 ASQFERTLENNPKMHVKAMKDELVSNLGIKA-----NMKKMYRA 203 (468)
Q Consensus 165 a~~~~~~i~~~p~~~~~~I~~~v~~~~g~~v-----Sy~k~~ra 203 (468)
...+...+..+|.+++.+|++.|. +.|+.+ +.+++.+.
T Consensus 81 ~~~I~~~~~~~p~~t~~el~~~L~-~~gv~~~~~~Ps~sti~~~ 123 (125)
T smart00351 81 VKKIADYKQENPGIFAWEIRDRLL-SEGVCDKDNVPSVSSINRI 123 (125)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHH-HcCCCcCCCCCChhhHHHh
Confidence 345666778999999999999988 466655 77777654
No 25
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=28.33 E-value=1.8e+02 Score=24.42 Aligned_cols=24 Identities=8% Similarity=0.241 Sum_probs=20.5
Q ss_pred CHHHHHHHHHHhhCCcCCHHHHHH
Q 037988 179 HVKAMKDELVSNLGIKANMKKMYR 202 (468)
Q Consensus 179 ~~~~I~~~v~~~~g~~vSy~k~~r 202 (468)
+|.+..+.|+++||+.||..++-.
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~ 44 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVES 44 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHH
Confidence 688999999999999999766543
No 26
>PF14420 Clr5: Clr5 domain
Probab=24.77 E-value=1.7e+02 Score=21.28 Aligned_cols=25 Identities=12% Similarity=0.279 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHHHHhhCCcCCHHH
Q 037988 175 NPKMHVKAMKDELVSNLGIKANMKK 199 (468)
Q Consensus 175 ~p~~~~~~I~~~v~~~~g~~vSy~k 199 (468)
+.+.+..++++.+.+.||..+|..+
T Consensus 18 ~e~~tl~~v~~~M~~~~~F~at~rq 42 (54)
T PF14420_consen 18 DENKTLEEVMEIMKEEHGFKATKRQ 42 (54)
T ss_pred hCCCcHHHHHHHHHHHhCCCcCHHH
Confidence 4567889999999999999999654
Done!