Query 044763
Match_columns 453
No_of_seqs 215 out of 1460
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 06:32:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044763.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044763hhsearch_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 6E-58 1.3E-62 483.3 30.0 392 12-420 156-624 (846)
2 PF00872 Transposase_mut: Tran 99.9 1E-24 2.2E-29 217.5 3.8 217 67-297 111-350 (381)
3 PF10551 MULE: MULE transposas 99.9 5.9E-22 1.3E-26 158.1 8.6 88 124-218 3-93 (93)
4 COG3328 Transposase and inacti 99.7 2.3E-17 5.1E-22 161.4 12.2 214 67-297 97-329 (379)
5 smart00575 ZnF_PMZ plant mutat 99.0 8.4E-11 1.8E-15 70.5 1.7 27 377-403 1-27 (28)
6 PF04434 SWIM: SWIM zinc finge 98.4 1.4E-07 3E-12 62.1 2.8 40 361-402 1-40 (40)
7 PF03108 DBD_Tnp_Mut: MuDR fam 98.3 6.7E-07 1.5E-11 66.2 4.7 34 1-34 34-67 (67)
8 PF03101 FAR1: FAR1 DNA-bindin 96.9 0.0012 2.6E-08 51.9 4.1 32 14-46 59-90 (91)
9 PF08731 AFT: Transcription fa 96.7 0.002 4.4E-08 51.4 4.1 31 15-45 81-111 (111)
10 PF06782 UPF0236: Uncharacteri 95.7 0.12 2.7E-06 53.4 11.8 133 155-296 235-377 (470)
11 PF03106 WRKY: WRKY DNA -bindi 94.8 0.089 1.9E-06 37.6 5.4 40 5-44 20-59 (60)
12 PF01610 DDE_Tnp_ISL3: Transpo 94.6 0.06 1.3E-06 50.7 5.5 79 134-221 15-96 (249)
13 PF13610 DDE_Tnp_IS240: DDE do 93.2 0.034 7.4E-07 47.5 0.9 65 132-204 17-81 (140)
14 smart00774 WRKY DNA binding do 91.4 0.31 6.7E-06 34.6 3.7 38 6-43 21-59 (59)
15 PF04937 DUF659: Protein of un 65.5 36 0.00079 29.4 7.8 63 156-223 73-138 (153)
16 COG5431 Uncharacterized metal- 64.4 4.8 0.0001 31.8 1.8 36 361-398 36-76 (117)
17 COG3316 Transposase and inacti 64.1 13 0.00029 33.8 4.9 63 137-208 91-153 (215)
18 PF00665 rve: Integrase core d 54.5 31 0.00066 27.6 5.3 62 129-196 21-82 (120)
19 PHA02517 putative transposase 52.6 1.7E+02 0.0038 27.6 10.9 57 130-192 124-180 (277)
20 PF04500 FLYWCH: FLYWCH zinc f 51.0 14 0.0003 25.9 2.3 35 5-43 25-62 (62)
21 COG4715 Uncharacterized conser 47.8 26 0.00057 36.4 4.5 34 368-403 60-97 (587)
22 COG4279 Uncharacterized conser 42.7 14 0.00029 34.3 1.4 23 377-402 125-147 (266)
23 PRK14702 insertion element IS2 40.7 3.2E+02 0.0069 25.8 13.1 59 131-192 103-163 (262)
24 PF13565 HTH_32: Homeodomain-l 40.2 20 0.00042 26.6 1.8 22 67-88 45-66 (77)
25 COG4451 RbcS Ribulose bisphosp 38.4 2.2E+02 0.0048 23.3 8.0 78 67-156 15-107 (127)
26 PF13592 HTH_33: Winged helix- 34.5 33 0.00071 24.3 2.1 22 68-89 2-23 (60)
27 PRK09409 IS2 transposase TnpB; 26.1 6E+02 0.013 24.5 13.6 59 131-192 142-202 (301)
28 PF03050 DDE_Tnp_IS66: Transpo 25.4 45 0.00098 31.6 2.0 59 147-223 98-156 (271)
29 PF14420 Clr5: Clr5 domain 21.7 1E+02 0.0022 21.3 2.6 23 67-89 17-39 (54)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=6e-58 Score=483.33 Aligned_cols=392 Identities=13% Similarity=0.170 Sum_probs=301.9
Q ss_pred eecCCCceEEEEEEeCCCceEEEEeeCCCceecCCccCCcc--cceeee--------eccccccccC---C-------CC
Q 044763 12 CSDLMCDWKVSAAKVRKGNVFVLKEITPNHTCKRHNNNFAL--GTMWNA--------VNFLHLWVEN---P-------NI 71 (453)
Q Consensus 12 C~~~~C~w~v~~~~~~~~~~~~i~~~~~~H~c~~~~~~~~~--~~~~l~--------~~~i~~~~~~---~-------~~ 71 (453)
|+.+||++++.+++. ..|.|.|+.++.+|||++.+..... +++... .+.+.....+ + .+
T Consensus 156 ~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~~~~~~~~~v~~~~~d~~~~~~~~r~~~~ 234 (846)
T PLN03097 156 CAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMARQFAEYKNVVGLKNDSKSSFDKGRNLGL 234 (846)
T ss_pred ccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccchhhhhhHHHHHhhhhccccccccchhhcchhhHHHhhhc
Confidence 667899999999874 5578999999999999997543211 111100 0000000000 0 00
Q ss_pred ---CHHHHHHHHHHHhCCcceeecccccceEEEEeccCCCCcceeEEEE--------ecc--eee-----eecccCCcee
Q 044763 72 ---DLDRLGYEIERCSGIKYPTWKVEAIDKIAKFWLRTDHSYGYERLLH--------YKN--EML-----KIDSSYKSVM 133 (453)
Q Consensus 72 ---~~~~i~~~l~~~~g~~~s~~rak~~gs~~~~~~~~~~~~~f~~~f~--------f~~--pvi-----~l~~~y~~~l 133 (453)
-...+++.++++-..++ +=...+..|++ +++.++|| |.+ ||| |.+++|++||
T Consensus 235 ~~gD~~~ll~yf~~~q~~nP--------~Ffy~~qlDe~--~~l~niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pf 304 (846)
T PLN03097 235 EAGDTKILLDFFTQMQNMNS--------NFFYAVDLGED--QRLKNLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPL 304 (846)
T ss_pred ccchHHHHHHHHHHHHhhCC--------CceEEEEEccC--CCeeeEEeccHHHHHHHHhcCCEEEEeceeeccccCcEE
Confidence 01111111111111111 22344555666 99999999 555 777 5666779999
Q ss_pred EEEEEEcCCCCeEEEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHHHhhccCCCceeccHHHH
Q 044763 134 LVAVCRDGNNGVLPIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEAASEFLPYAQYRQCCFSI 213 (453)
Q Consensus 134 l~a~g~d~~~~~~~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi 213 (453)
..++|+|+|+|.+++||||+.+|+.++|.|+|++|+++|++ +.|.+||||++.+|.+||++|||++.|++|.|||
T Consensus 305 a~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~g-----k~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI 379 (846)
T PLN03097 305 ALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGG-----QAPKVIITDQDKAMKSVISEVFPNAHHCFFLWHI 379 (846)
T ss_pred EEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCC-----CCCceEEecCCHHHHHHHHHHCCCceehhhHHHH
Confidence 99999999999999999999999999999999999999998 9999999999999999999999999999999999
Q ss_pred HHHHHhhCC-----ChhHHHHHHHHhh-hhcHHHHHHHHHH-HHhcCHHHHHHHHhc--ccCcEEEeecCCCcccccccc
Q 044763 214 NNKLMEQFP-----HALVYSLFWSACR-STNKATFQQQMML-LQYHNKNCYKWLIDR--ECRTWALYCMPEWAKSTDITI 284 (453)
Q Consensus 214 ~~n~~~~~~-----~~~~~~~~~~~~~-~~~~~ef~~~~~~-l~~~~~~~~~~l~~~--~~~~W~~~~~~~~~~~~~~Tt 284 (453)
++|+.++++ .+.+...|+++++ +.+++||+..|.. |.+++....+||... .+++|+++|+++.++.|+.||
T Consensus 380 ~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~agm~sT 459 (846)
T PLN03097 380 LGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFLAGMSTV 459 (846)
T ss_pred HHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhcccccCCcccc
Confidence 999999985 3589999999886 7899999999988 467799999999996 799999999998888889999
Q ss_pred chHHHHHHHHHhcc--cCchHHHHHHHHHHHHHHHHHhhh-----------------hcccCCCCCCChhHHHHHHhhhc
Q 044763 285 SATEQLQIWLLKYL--DMNVANRFTAITKETAKIFQKRYL-----------------VGWDWVHDNITPTARQQITQNVI 345 (453)
Q Consensus 285 n~~Es~N~~lk~~r--~~pi~~~~e~i~~~l~~~~~~r~~-----------------~~~~~~~~~~t~~~~~~l~~~~~ 345 (453)
+++||+|+.|++.. ..++..|++.+.+.+..+..+... ..++.+. +|||.+|++||+++.
T Consensus 460 qRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~-iYT~~iF~kFQ~El~ 538 (846)
T PLN03097 460 QRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSG-VYTHAVFKKFQVEVL 538 (846)
T ss_pred cccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHH-HhHHHHHHHHHHHHH
Confidence 99999999999874 567888888877766544432211 0123345 999999999999999
Q ss_pred ccCCceeEEc-ccC--ceEEEEEe--CeEEEEEcc----CCceeeCCeecCCCCcchhhHHHHHhhC--Chhhhhhhhcc
Q 044763 346 EDDGWNTHSG-ADP--KILTITMN--GLSFVVNKE----LAICSCGLWQLSKIPCPHTCRCIIHWAA--LYADFVHDFMT 414 (453)
Q Consensus 346 ~s~~~~~~~~-~~~--~~f~V~~~--~~~~~V~l~----~~~CsC~~~~~~giPC~H~lavl~~~~~--~~~~~v~~~y~ 414 (453)
.+..+.+... .++ ..|.|... ...|.|..+ ..+|+|++|+..||||+|||+||...++ +|+.||.++||
T Consensus 539 ~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWT 618 (846)
T PLN03097 539 GAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWT 618 (846)
T ss_pred HhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhch
Confidence 7665544332 222 36888762 456777554 5799999999999999999999999997 99999999999
Q ss_pred HHHHHh
Q 044763 415 VEVYRS 420 (453)
Q Consensus 415 ~~~~~~ 420 (453)
+++-..
T Consensus 619 KdAK~~ 624 (846)
T PLN03097 619 KDAKSR 624 (846)
T ss_pred hhhhhc
Confidence 998754
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=99.90 E-value=1e-24 Score=217.49 Aligned_cols=217 Identities=18% Similarity=0.237 Sum_probs=174.4
Q ss_pred cCCCCCHHHHHHHHHHHhC-Ccce---eeccccc--ceEEEEeccCCCCcceeEEEEecceeeeecccC----------C
Q 044763 67 ENPNIDLDRLGYEIERCSG-IKYP---TWKVEAI--DKIAKFWLRTDHSYGYERLLHYKNEMLKIDSSY----------K 130 (453)
Q Consensus 67 ~~~~~~~~~i~~~l~~~~g-~~~s---~~rak~~--gs~~~~~~~~~~~~~f~~~f~f~~pvi~l~~~y----------~ 130 (453)
--.|++.++|.+.|+..+| ..+| +.|..+. ..+..+...+-.+..+ |+|++|+.| +
T Consensus 111 y~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~L~~~~y--------~~l~iD~~~~kvr~~~~~~~ 182 (381)
T PF00872_consen 111 YLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRPLESEPY--------PYLWIDGTYFKVREDGRVVK 182 (381)
T ss_pred hccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhccccccc--------cceeeeeeeccccccccccc
Confidence 4468999999999999999 6666 3332211 0111111111000112 667778766 3
Q ss_pred ceeEEEEEEcCCCCeEEEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHHHhhccCCCceeccH
Q 044763 131 SVMLVAVCRDGNNGVLPIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEAASEFLPYAQYRQCC 210 (453)
Q Consensus 131 ~~ll~a~g~d~~~~~~~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~ 210 (453)
..+++|+|+|.+|+..+||+.+.++|+.++|.-||+.|+++ |. ..|..||+|+++||.+||+++||++.+|.|.
T Consensus 183 ~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl-----~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~ 256 (381)
T PF00872_consen 183 KAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GL-----KDILLVVSDGHKGLKEAIREVFPGAKWQRCV 256 (381)
T ss_pred chhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-cc-----cccceeeccccccccccccccccchhhhhhe
Confidence 56899999999999999999999999999999999999999 54 7899999999999999999999999999999
Q ss_pred HHHHHHHHhhCCCh---hHHHHHHHHhhhhcHHHHHHHHHHHH----hcCHHHHHHHHhcccCcEEEeecCCCccccccc
Q 044763 211 FSINNKLMEQFPHA---LVYSLFWSACRSTNKATFQQQMMLLQ----YHNKNCYKWLIDRECRTWALYCMPEWAKSTDIT 283 (453)
Q Consensus 211 ~Hi~~n~~~~~~~~---~~~~~~~~~~~~~~~~ef~~~~~~l~----~~~~~~~~~l~~~~~~~W~~~~~~~~~~~~~~T 283 (453)
+|+++|+.++++.+ .+...++.+..+.+.+++...++.+. ...|++.+++.+...+.|+..-||...+-.+.|
T Consensus 257 vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~T 336 (381)
T PF00872_consen 257 VHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRT 336 (381)
T ss_pred echhhhhccccccccchhhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccccccceeeecchhccccch
Confidence 99999999999754 67788888888888887777777654 457899999999888889988888666777889
Q ss_pred cchHHHHHHHHHhc
Q 044763 284 ISATEQLQIWLLKY 297 (453)
Q Consensus 284 tn~~Es~N~~lk~~ 297 (453)
||.+||+|+.+|+.
T Consensus 337 TN~iEsln~~irrr 350 (381)
T PF00872_consen 337 TNAIESLNKEIRRR 350 (381)
T ss_pred hhhccccccchhhh
Confidence 99999999999975
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=99.86 E-value=5.9e-22 Score=158.12 Aligned_cols=88 Identities=30% Similarity=0.445 Sum_probs=83.2
Q ss_pred eecccCCceeEE---EEEEcCCCCeEEEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHHHhhc
Q 044763 124 KIDSSYKSVMLV---AVCRDGNNGVLPIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEAASEF 200 (453)
Q Consensus 124 ~l~~~y~~~ll~---a~g~d~~~~~~~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~v 200 (453)
|.+++| |+++. ++|+|++|+.+|+||+++++|+.++|.|||+.+++.++. . |.+||||++.|+.+||+++
T Consensus 3 ~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~-----~-p~~ii~D~~~~~~~Ai~~v 75 (93)
T PF10551_consen 3 YKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQ-----K-PKVIISDFDKALINAIKEV 75 (93)
T ss_pred cccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcccc-----C-ceeeeccccHHHHHHHHHH
Confidence 467899 88885 999999999999999999999999999999999999885 5 9999999999999999999
Q ss_pred cCCCceeccHHHHHHHHH
Q 044763 201 LPYAQYRQCCFSINNKLM 218 (453)
Q Consensus 201 fP~a~h~~C~~Hi~~n~~ 218 (453)
||++.|++|.||+.+|++
T Consensus 76 fP~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 76 FPDARHQLCLFHILRNIK 93 (93)
T ss_pred CCCceEehhHHHHHHhhC
Confidence 999999999999999974
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.73 E-value=2.3e-17 Score=161.35 Aligned_cols=214 Identities=16% Similarity=0.210 Sum_probs=165.2
Q ss_pred cCCCCCHHHHHHHHHHHhCCcce---eeccc-cc-ceEEEEeccCCCCcceeEEEEecceeeeecccC-------CceeE
Q 044763 67 ENPNIDLDRLGYEIERCSGIKYP---TWKVE-AI-DKIAKFWLRTDHSYGYERLLHYKNEMLKIDSSY-------KSVML 134 (453)
Q Consensus 67 ~~~~~~~~~i~~~l~~~~g~~~s---~~rak-~~-gs~~~~~~~~~~~~~f~~~f~f~~pvi~l~~~y-------~~~ll 134 (453)
...+++++++.+.+++.++..++ ..+.- .+ ..+..+...+- ..| |++++|++| +.+++
T Consensus 97 y~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e~v~~~~~r~l--~~~--------~~v~~D~~~~k~r~v~~~~~~ 166 (379)
T COG3328 97 YAKGVTTREIEALLEELYGHKVSPSVISVVTDRLDEKVKAWQNRPL--GDY--------PYVYLDAKYVKVRSVRNKAVY 166 (379)
T ss_pred HHcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHHHHHHHHhccc--cCc--------eEEEEecceeehhhhhhheee
Confidence 45689999999999999988776 11111 00 01111111111 122 778899988 46899
Q ss_pred EEEEEcCCCCeEEEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHHHhhccCCCceeccHHHHH
Q 044763 135 VAVCRDGNNGVLPIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEAASEFLPYAQYRQCCFSIN 214 (453)
Q Consensus 135 ~a~g~d~~~~~~~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~ 214 (453)
+|+|++.+|+..+||+.+.+.|+ ..|.-||..|+.+ |. .....+++|+++|+.+||.++||.+.++.|..|+.
T Consensus 167 ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl-----~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~ 239 (379)
T COG3328 167 IAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GL-----SDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLV 239 (379)
T ss_pred eeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cc-----cceeEEecchhhhhHHHHHHhccHhhhhhhhhHHH
Confidence 99999999999999999999999 9999999999998 44 67888889999999999999999999999999999
Q ss_pred HHHHhhCCCh---hHHHHHHHHhhhhcHHHHHHHHH----HHHhcCHHHHHHHHhcccCcEEEeecCCCccccccccchH
Q 044763 215 NKLMEQFPHA---LVYSLFWSACRSTNKATFQQQMM----LLQYHNKNCYKWLIDRECRTWALYCMPEWAKSTDITISAT 287 (453)
Q Consensus 215 ~n~~~~~~~~---~~~~~~~~~~~~~~~~ef~~~~~----~l~~~~~~~~~~l~~~~~~~W~~~~~~~~~~~~~~Ttn~~ 287 (453)
+|+..+.+.+ .....+..+..+.+.++....+. .+....|....++.+...+.|...-|+...+--+.|||..
T Consensus 240 Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~I 319 (379)
T COG3328 240 RNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAI 319 (379)
T ss_pred hhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHH
Confidence 9999998765 44445555555555555444444 4555678889999988888888888885666678899999
Q ss_pred HHHHHHHHhc
Q 044763 288 EQLQIWLLKY 297 (453)
Q Consensus 288 Es~N~~lk~~ 297 (453)
|++|+.++..
T Consensus 320 E~~n~~ir~~ 329 (379)
T COG3328 320 ESLNKLIRRR 329 (379)
T ss_pred HHHHHHHHHH
Confidence 9999987754
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=99.04 E-value=8.4e-11 Score=70.51 Aligned_cols=27 Identities=44% Similarity=0.819 Sum_probs=25.1
Q ss_pred CceeeCCeecCCCCcchhhHHHHHhhC
Q 044763 377 AICSCGLWQLSKIPCPHTCRCIIHWAA 403 (453)
Q Consensus 377 ~~CsC~~~~~~giPC~H~lavl~~~~~ 403 (453)
.+|||++||..||||+|+|+|+...|+
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998875
No 6
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 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. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=98.44 E-value=1.4e-07 Score=62.12 Aligned_cols=40 Identities=28% Similarity=0.546 Sum_probs=31.2
Q ss_pred EEEEEeCeEEEEEccCCceeeCCeecCCCCcchhhHHHHHhh
Q 044763 361 LTITMNGLSFVVNKELAICSCGLWQLSKIPCPHTCRCIIHWA 402 (453)
Q Consensus 361 f~V~~~~~~~~V~l~~~~CsC~~~~~~giPC~H~lavl~~~~ 402 (453)
|+|.-++.. +++...+|||..|+..|.||+|++|++...+
T Consensus 1 y~V~i~~~~--~~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 1 YQVTIDDER--VSIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred CEEEEcCCc--ccccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 344443333 6677899999999999999999999998653
No 7
>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=98.34 E-value=6.7e-07 Score=66.20 Aligned_cols=34 Identities=24% Similarity=0.581 Sum_probs=31.9
Q ss_pred CCccceEEEEEeecCCCceEEEEEEeCCCceEEE
Q 044763 1 MENTCTLISCECSDLMCDWKVSAAKVRKGNVFVL 34 (453)
Q Consensus 1 ~ks~~~r~~~~C~~~~C~w~v~~~~~~~~~~~~i 34 (453)
.+|+++|++++|.+.||||+|+|++.++++.|+|
T Consensus 34 ~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 34 KKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred eccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 3799999999999999999999999999999986
No 8
>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=96.90 E-value=0.0012 Score=51.88 Aligned_cols=32 Identities=6% Similarity=0.180 Sum_probs=29.1
Q ss_pred cCCCceEEEEEEeCCCceEEEEeeCCCceecCC
Q 044763 14 DLMCDWKVSAAKVRKGNVFVLKEITPNHTCKRH 46 (453)
Q Consensus 14 ~~~C~w~v~~~~~~~~~~~~i~~~~~~H~c~~~ 46 (453)
.+||||+|.+.+.+ .+.|.|..+..+|||++.
T Consensus 59 ktgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~ 90 (91)
T PF03101_consen 59 KTGCKARINVKRRK-DGKWRVTSFVLEHNHPLC 90 (91)
T ss_pred ccCCCEEEEEEEcc-CCEEEEEECcCCcCCCCC
Confidence 37999999999987 889999999999999874
No 9
>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=96.72 E-value=0.002 Score=51.39 Aligned_cols=31 Identities=16% Similarity=0.333 Sum_probs=29.1
Q ss_pred CCCceEEEEEEeCCCceEEEEeeCCCceecC
Q 044763 15 LMCDWKVSAAKVRKGNVFVLKEITPNHTCKR 45 (453)
Q Consensus 15 ~~C~w~v~~~~~~~~~~~~i~~~~~~H~c~~ 45 (453)
.+|||+|+|..+...+.|.|..+++.|+|++
T Consensus 81 ~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 81 NTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 5899999999999999999999999999974
No 10
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=95.65 E-value=0.12 Score=53.36 Aligned_cols=133 Identities=19% Similarity=0.224 Sum_probs=93.0
Q ss_pred ccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHHHhhccCCCceeccHHHHHHHHHhhCC-ChhHHHHHHHH
Q 044763 155 EENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEAASEFLPYAQYRQCCFSINNKLMEQFP-HALVYSLFWSA 233 (453)
Q Consensus 155 ~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~-~~~~~~~~~~~ 233 (453)
..+.+-|.-+.+.+-+.... ....-+++.+|+.+.+.++++ .+|++.|.+..+|+.+.+.+.++ .+.+.+.++++
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~---~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~a 310 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDL---DKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKA 310 (470)
T ss_pred cchHHHHHHHHHHHHHhcCc---ccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHH
Confidence 45567899888888887764 112357889999999998876 99999999999999999999885 45677778888
Q ss_pred hhhhcHHHHHHHHHHHHhc--CH-------HHHHHHHhcccCcEEEeecCCCccccccccchHHHHHHHHHh
Q 044763 234 CRSTNKATFQQQMMLLQYH--NK-------NCYKWLIDRECRTWALYCMPEWAKSTDITISATEQLQIWLLK 296 (453)
Q Consensus 234 ~~~~~~~ef~~~~~~l~~~--~~-------~~~~~l~~~~~~~W~~~~~~~~~~~~~~Ttn~~Es~N~~lk~ 296 (453)
.......+++..++.+... ++ +...||..++..- ..|- .+-+.......|+.+..+..
T Consensus 311 l~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i--~~y~---~~~~~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 311 LKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGI--KPYR---EREGLRGIGAEESVSHVLSY 377 (470)
T ss_pred HHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHh--hhhh---hccCCCccchhhhhhhHHHH
Confidence 7777888888888877653 22 2344555432211 1111 11344456668888777643
No 11
>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=94.81 E-value=0.089 Score=37.65 Aligned_cols=40 Identities=13% Similarity=0.145 Sum_probs=32.8
Q ss_pred ceEEEEEeecCCCceEEEEEEeCCCceEEEEeeCCCceec
Q 044763 5 CTLISCECSDLMCDWKVSAAKVRKGNVFVLKEITPNHTCK 44 (453)
Q Consensus 5 ~~r~~~~C~~~~C~w~v~~~~~~~~~~~~i~~~~~~H~c~ 44 (453)
-.|--.+|+..+||++=.+.+..+++...++++.++|||.
T Consensus 20 ~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 20 YPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp CEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred eeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 4566699999999999999998878888999999999995
No 12
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 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 [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. 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=94.61 E-value=0.06 Score=50.68 Aligned_cols=79 Identities=18% Similarity=0.167 Sum_probs=62.9
Q ss_pred EEEEEEcC--CCCeEEEEEEeeeccccccHHHHHHHH-HhhccccccCCCCCEEEEcCCCchHHHHHhhccCCCceeccH
Q 044763 134 LVAVCRDG--NNGVLPIAFCEVQEENLDLWSFFLKNL-YEGLHMDYMDYGKGICIMCDKDNGVDEAASEFLPYAQYRQCC 210 (453)
Q Consensus 134 l~a~g~d~--~~~~~~la~a~~~~E~~~~w~wfl~~l-~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~ 210 (453)
++.+-+|. +++.. ++++++-+.++..-||..+ -.... ....+|++|...+...|+++.||+|.+..-.
T Consensus 15 y~t~~~d~~~~~~~i---l~i~~~r~~~~l~~~~~~~~~~~~~------~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~Dr 85 (249)
T PF01610_consen 15 YVTVVVDLDTDTGRI---LDILPGRDKETLKDFFRSLYPEEER------KNVKVVSMDMSPPYRSAIREYFPNAQIVADR 85 (249)
T ss_pred eeEEEEECccCCceE---EEEcCCccHHHHHHHHHHhCccccc------cceEEEEcCCCcccccccccccccccccccc
Confidence 55555665 44332 3588888888888888876 43322 6789999999999999999999999999999
Q ss_pred HHHHHHHHhhC
Q 044763 211 FSINNKLMEQF 221 (453)
Q Consensus 211 ~Hi~~n~~~~~ 221 (453)
||+++++.+.+
T Consensus 86 FHvvk~~~~al 96 (249)
T PF01610_consen 86 FHVVKLANRAL 96 (249)
T ss_pred chhhhhhhhcc
Confidence 99999988755
No 13
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=93.25 E-value=0.034 Score=47.49 Aligned_cols=65 Identities=18% Similarity=0.143 Sum_probs=57.4
Q ss_pred eeEEEEEEcCCCCeEEEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHHHhhccCCC
Q 044763 132 VMLVAVCRDGNNGVLPIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEAASEFLPYA 204 (453)
Q Consensus 132 ~ll~a~g~d~~~~~~~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a 204 (453)
..+..-.+|.+|+ +|++-+-+.-+...=..||+.+.+..+ ..|..|+||+.++...|+++++|+.
T Consensus 17 ~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~------~~p~~ivtDk~~aY~~A~~~l~~~~ 81 (140)
T PF13610_consen 17 WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR------GEPRVIVTDKLPAYPAAIKELNPEG 81 (140)
T ss_pred EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec------cccceeecccCCccchhhhhccccc
Confidence 4567788999999 899999999999999999999888864 4799999999999999999999974
No 14
>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=91.37 E-value=0.31 Score=34.62 Aligned_cols=38 Identities=16% Similarity=0.114 Sum_probs=31.3
Q ss_pred eEEEEEeec-CCCceEEEEEEeCCCceEEEEeeCCCcee
Q 044763 6 TLISCECSD-LMCDWKVSAAKVRKGNVFVLKEITPNHTC 43 (453)
Q Consensus 6 ~r~~~~C~~-~~C~w~v~~~~~~~~~~~~i~~~~~~H~c 43 (453)
.|--.+|+. .|||++=.+.+..+++.-.+.++.++|||
T Consensus 21 pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 21 PRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 455689998 79999888888776667778889999997
No 15
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=65.49 E-value=36 Score=29.35 Aligned_cols=63 Identities=14% Similarity=0.214 Sum_probs=48.3
Q ss_pred cccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHH---HhhccCCCceeccHHHHHHHHHhhCCC
Q 044763 156 ENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEA---ASEFLPYAQYRQCCFSINNKLMEQFPH 223 (453)
Q Consensus 156 E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~A---i~~vfP~a~h~~C~~Hi~~n~~~~~~~ 223 (453)
.+.+...-+|+...+.+|. .....||||-...+..| +.+-+|...+.-|..|-+.-+.+.+..
T Consensus 73 ~~a~~l~~ll~~vIeeVG~-----~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 73 KTAEYLFELLDEVIEEVGE-----ENVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred ccHHHHHHHHHHHHHHhhh-----hhhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 4555666666666666665 67888999999988888 555589999999999998877766543
No 16
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=64.36 E-value=4.8 Score=31.80 Aligned_cols=36 Identities=17% Similarity=0.368 Sum_probs=24.8
Q ss_pred EEEEEeCeEEEEEccCCceeeCCeec----CC-CCcchhhHHH
Q 044763 361 LTITMNGLSFVVNKELAICSCGLWQL----SK-IPCPHTCRCI 398 (453)
Q Consensus 361 f~V~~~~~~~~V~l~~~~CsC~~~~~----~g-iPC~H~lavl 398 (453)
|.+...++.|+++.. -|||..|-. -| -||.|++.+=
T Consensus 36 fVyvG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk 76 (117)
T COG5431 36 FVYVGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLK 76 (117)
T ss_pred EEEEccccceEEEcC--cccCHHHHhHhhhcCcccchhhhhee
Confidence 333345668888876 899998872 22 4799998653
No 17
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=64.13 E-value=13 Score=33.84 Aligned_cols=63 Identities=19% Similarity=0.164 Sum_probs=48.3
Q ss_pred EEEcCCCCeEEEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHHHhhccCCCceec
Q 044763 137 VCRDGNNGVLPIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEAASEFLPYAQYRQ 208 (453)
Q Consensus 137 ~g~d~~~~~~~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~ 208 (453)
-.+|.+| .+|.+-|...-+...=.-||..+++.. ..|.+|+||+.+....|+.++-+.+.|+-
T Consensus 91 rAid~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~-------g~p~v~vtDka~s~~~A~~~l~~~~ehr~ 153 (215)
T COG3316 91 RAIDADG--LTLDVWLSKRRNALAAKAFLKKLLKKH-------GEPRVFVTDKAPSYTAALRKLGSEVEHRT 153 (215)
T ss_pred hhhccCC--CeEEEEEEcccCcHHHHHHHHHHHHhc-------CCCceEEecCccchHHHHHhcCcchheec
Confidence 3455554 467788888877777777888777764 37999999999999999999988665543
No 18
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=54.52 E-value=31 Score=27.63 Aligned_cols=62 Identities=16% Similarity=-0.008 Sum_probs=44.8
Q ss_pred CCceeEEEEEEcCCCCeEEEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHH
Q 044763 129 YKSVMLVAVCRDGNNGVLPIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEA 196 (453)
Q Consensus 129 y~~~ll~a~g~d~~~~~~~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~A 196 (453)
.++..++.+.+|..-.. .+++.+-..++.+...-+|.......+. ..|.+|+||+.++....
T Consensus 21 ~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~-----~~p~~i~tD~g~~f~~~ 82 (120)
T PF00665_consen 21 KGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRGG-----RPPRVIRTDNGSEFTSH 82 (120)
T ss_dssp TT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS------SE-SEEEEESCHHHHSH
T ss_pred CCccEEEEEEEECCCCc-EEEEEeeccccccccccccccccccccc-----ccceecccccccccccc
Confidence 34578888889887654 5577777777888888888876666553 33999999999987644
No 19
>PHA02517 putative transposase OrfB; Reviewed
Probab=52.57 E-value=1.7e+02 Score=27.56 Aligned_cols=57 Identities=14% Similarity=-0.010 Sum_probs=35.6
Q ss_pred CceeEEEEEEcCCCCeEEEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCch
Q 044763 130 KSVMLVAVCRDGNNGVLPIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNG 192 (453)
Q Consensus 130 ~~~ll~a~g~d~~~~~~~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~ 192 (453)
+|..++++-+|...+ +++|+.+...++.+...-.|+......+. ..+..|.||+...
T Consensus 124 ~g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~~~~~~-----~~~~i~~sD~G~~ 180 (277)
T PHA02517 124 QGWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQALWARGR-----PGGLIHHSDKGSQ 180 (277)
T ss_pred CCCEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHHHhcCC-----CcCcEeecccccc
Confidence 356677777777654 57788888777777555445444443332 2345677888764
No 20
>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=50.95 E-value=14 Score=25.86 Aligned_cols=35 Identities=11% Similarity=0.052 Sum_probs=15.1
Q ss_pred ceEEEEEeec---CCCceEEEEEEeCCCceEEEEeeCCCcee
Q 044763 5 CTLISCECSD---LMCDWKVSAAKVRKGNVFVLKEITPNHTC 43 (453)
Q Consensus 5 ~~r~~~~C~~---~~C~w~v~~~~~~~~~~~~i~~~~~~H~c 43 (453)
.....-+|.. .+|+++|... .+. -.+.....+|||
T Consensus 25 ~~~~~WrC~~~~~~~C~a~~~~~--~~~--~~~~~~~~~HnH 62 (62)
T PF04500_consen 25 DGKTYWRCSRRRSHGCRARLITD--AGD--GRVVRTNGEHNH 62 (62)
T ss_dssp SS-EEEEEGGGTTS----EEEEE----T--TEEEE-S---SS
T ss_pred CCcEEEEeCCCCCCCCeEEEEEE--CCC--CEEEECCCccCC
Confidence 3445577886 3899999887 222 344445578886
No 21
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=47.77 E-value=26 Score=36.41 Aligned_cols=34 Identities=24% Similarity=0.495 Sum_probs=24.9
Q ss_pred eEEEEEcc----CCceeeCCeecCCCCcchhhHHHHHhhC
Q 044763 368 LSFVVNKE----LAICSCGLWQLSKIPCPHTCRCIIHWAA 403 (453)
Q Consensus 368 ~~~~V~l~----~~~CsC~~~~~~giPC~H~lavl~~~~~ 403 (453)
..++|++. +..|||.. ...| -|.|++||+.....
T Consensus 60 y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~ 97 (587)
T COG4715 60 YRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLD 97 (587)
T ss_pred eeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhh
Confidence 34556663 47899998 5555 69999999987653
No 22
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=42.73 E-value=14 Score=34.35 Aligned_cols=23 Identities=30% Similarity=0.576 Sum_probs=19.7
Q ss_pred CceeeCCeecCCCCcchhhHHHHHhh
Q 044763 377 AICSCGLWQLSKIPCPHTCRCIIHWA 402 (453)
Q Consensus 377 ~~CsC~~~~~~giPC~H~lavl~~~~ 402 (453)
..|||..+. .||.|+-||.-+.+
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 469999886 69999999998865
No 23
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=40.73 E-value=3.2e+02 Score=25.78 Aligned_cols=59 Identities=8% Similarity=-0.052 Sum_probs=37.7
Q ss_pred ceeEEEEEEcCCCCeEEEEEEeeec-cccccHHHHHHHHHhh-ccccccCCCCCEEEEcCCCch
Q 044763 131 SVMLVAVCRDGNNGVLPIAFCEVQE-ENLDLWSFFLKNLYEG-LHMDYMDYGKGICIMCDKDNG 192 (453)
Q Consensus 131 ~~ll~a~g~d~~~~~~~la~a~~~~-E~~~~w~wfl~~l~~~-~~~~~~~~~~~~~iisD~~~~ 192 (453)
+.++.++-+|.... .++|+++-.. .+.+.-.-+|+...+. .+. .....|..|.||+...
T Consensus 103 ~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~--~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 103 ERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGN--DLPSSPVEWLTDNGSC 163 (262)
T ss_pred cEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcc--cCCCCCeEEEcCCCcc
Confidence 36888888888765 6889999874 5555555566543333 221 0013578889998764
No 24
>PF13565 HTH_32: Homeodomain-like domain
Probab=40.18 E-value=20 Score=26.56 Aligned_cols=22 Identities=23% Similarity=0.262 Sum_probs=20.4
Q ss_pred cCCCCCHHHHHHHHHHHhCCcc
Q 044763 67 ENPNIDLDRLGYEIERCSGIKY 88 (453)
Q Consensus 67 ~~~~~~~~~i~~~l~~~~g~~~ 88 (453)
.+|.+++.+|.+.|.+++|+.+
T Consensus 45 ~~p~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 45 EHPRWTPREIAEYLEEEFGISV 66 (77)
T ss_pred hCCCCCHHHHHHHHHHHhCCCC
Confidence 7889999999999999999866
No 25
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=38.43 E-value=2.2e+02 Score=23.33 Aligned_cols=78 Identities=6% Similarity=-0.032 Sum_probs=50.5
Q ss_pred cCCCCCHHHHHHHHHHHhCCcceeecccccceEEEEeccCCCCcceeEEEE--ecceeeeec-------------ccCCc
Q 044763 67 ENPNIDLDRLGYEIERCSGIKYPTWKVEAIDKIAKFWLRTDHSYGYERLLH--YKNEMLKID-------------SSYKS 131 (453)
Q Consensus 67 ~~~~~~~~~i~~~l~~~~g~~~s~~rak~~gs~~~~~~~~~~~~~f~~~f~--f~~pvi~l~-------------~~y~~ 131 (453)
..|.++..+|.+.|+--.+-. -..-++..++ .+|+.-+| +..|++..+ ..|-+
T Consensus 15 ~lp~Ltd~qi~~QVrylL~QG----------ykigvE~~d~--rrprtgsWt~wg~p~f~~~~~~evlaele~Cr~dhp~ 82 (127)
T COG4451 15 SLPPLTDEQIAEQVRYLLSQG----------YKIGVEYVDD--RRPRTGSWTMWGTPMFGAKTAGEVLAELEACRADHPG 82 (127)
T ss_pred cCCcCcHHHHHHHHHHHHhCC----------cccceeeccc--CCcccceeeecCCccccccchHHHHHHHHHHHHhCCC
Confidence 556666677777776554221 1222333355 78888888 444555322 34567
Q ss_pred eeEEEEEEcCCCCeEEEEEEeeecc
Q 044763 132 VMLVAVCRDGNNGVLPIAFCEVQEE 156 (453)
Q Consensus 132 ~ll~a~g~d~~~~~~~la~a~~~~E 156 (453)
-..-++|+|.-|+..++.|-+-..+
T Consensus 83 eYIRliGfDp~gkrrv~sfIVhRPn 107 (127)
T COG4451 83 EYIRLIGFDPKGKRRVVSFIVHRPN 107 (127)
T ss_pred CeEEEEEecCCCceEEEEEEEECCC
Confidence 7788999999999999998776554
No 26
>PF13592 HTH_33: Winged helix-turn helix
Probab=34.51 E-value=33 Score=24.28 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=19.2
Q ss_pred CCCCCHHHHHHHHHHHhCCcce
Q 044763 68 NPNIDLDRLGYEIERCSGIKYP 89 (453)
Q Consensus 68 ~~~~~~~~i~~~l~~~~g~~~s 89 (453)
+..++..+|.+.|.+.||+.+|
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~ys 23 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKYS 23 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEEc
Confidence 3457889999999999999988
No 27
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=26.05 E-value=6e+02 Score=24.48 Aligned_cols=59 Identities=7% Similarity=-0.062 Sum_probs=38.4
Q ss_pred ceeEEEEEEcCCCCeEEEEEEeeec-cccccHHHHHHH-HHhhccccccCCCCCEEEEcCCCch
Q 044763 131 SVMLVAVCRDGNNGVLPIAFCEVQE-ENLDLWSFFLKN-LYEGLHMDYMDYGKGICIMCDKDNG 192 (453)
Q Consensus 131 ~~ll~a~g~d~~~~~~~la~a~~~~-E~~~~w~wfl~~-l~~~~~~~~~~~~~~~~iisD~~~~ 192 (453)
+-++.++-+|.... .+||+++... .+.+.-.-+|+. +....+. .....|..|-||+...
T Consensus 142 ~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~--~~~~~~~iihSDrGsq 202 (301)
T PRK09409 142 ERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGN--DLPSSPVEWLTDNGSC 202 (301)
T ss_pred CEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhcc--CCCCCCcEEecCCCcc
Confidence 46888888888876 6899999875 566655556654 3333221 0013578889998764
No 28
>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=25.44 E-value=45 Score=31.55 Aligned_cols=59 Identities=10% Similarity=0.125 Sum_probs=41.0
Q ss_pred EEEEEeeeccccccHHHHHHHHHhhccccccCCCCCEEEEcCCCchHHHHHhhccCCCceeccHHHHHHHHHhhCCC
Q 044763 147 PIAFCEVQEENLDLWSFFLKNLYEGLHMDYMDYGKGICIMCDKDNGVDEAASEFLPYAQYRQCCFSINNKLMEQFPH 223 (453)
Q Consensus 147 ~la~a~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~ 223 (453)
.+.|.+.++-+.+.-.-+|.. -.-+++||+..+=.. +....|+.|..|+.|.|.+-...
T Consensus 98 ~v~f~~~~sR~~~~~~~~L~~-------------~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 98 VVLFFYAPSRSSKVIKEFLGD-------------FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred eeeeeecccccccchhhhhcc-------------cceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 555566666665555555432 123899999987654 22889999999999999886653
No 29
>PF14420 Clr5: Clr5 domain
Probab=21.74 E-value=1e+02 Score=21.32 Aligned_cols=23 Identities=17% Similarity=0.151 Sum_probs=20.6
Q ss_pred cCCCCCHHHHHHHHHHHhCCcce
Q 044763 67 ENPNIDLDRLGYEIERCSGIKYP 89 (453)
Q Consensus 67 ~~~~~~~~~i~~~l~~~~g~~~s 89 (453)
-+.+.+..+|++.+++.||+.+|
T Consensus 17 ~~e~~tl~~v~~~M~~~~~F~at 39 (54)
T PF14420_consen 17 IDENKTLEEVMEIMKEEHGFKAT 39 (54)
T ss_pred HhCCCcHHHHHHHHHHHhCCCcC
Confidence 45688999999999999999987
Done!