Query 002062
Match_columns 973
No_of_seqs 325 out of 1289
Neff 6.4
Searched_HMMs 46136
Date Thu Mar 28 15:39:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002062.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002062hhsearch_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 4E-130 9E-135 1182.3 58.8 588 193-803 71-679 (846)
2 PF10551 MULE: MULE transposas 99.8 1.3E-20 2.8E-25 173.2 8.8 90 412-503 1-93 (93)
3 PF03101 FAR1: FAR1 DNA-bindin 99.8 1.4E-18 3.1E-23 159.4 8.8 88 210-297 1-91 (91)
4 PF00872 Transposase_mut: Tran 99.5 1.9E-14 4.2E-19 165.3 5.3 186 406-594 163-354 (381)
5 PF08731 AFT: Transcription fa 98.9 7.5E-09 1.6E-13 96.8 9.7 88 202-295 1-111 (111)
6 COG3328 Transposase and inacti 98.5 1.9E-07 4.2E-12 106.6 9.3 198 406-607 146-348 (379)
7 smart00575 ZnF_PMZ plant mutat 98.5 3.1E-08 6.7E-13 71.2 1.1 26 699-724 2-27 (28)
8 PF03108 DBD_Tnp_Mut: MuDR fam 98.1 8.3E-06 1.8E-10 70.8 8.1 64 194-284 2-67 (67)
9 PF04434 SWIM: SWIM zinc finge 97.8 1.2E-05 2.6E-10 62.7 2.6 29 694-722 11-39 (40)
10 PF01610 DDE_Tnp_ISL3: Transpo 96.3 0.0031 6.7E-08 68.5 3.8 94 409-508 2-98 (249)
11 PF03106 WRKY: WRKY DNA -bindi 91.5 0.82 1.8E-05 39.1 7.1 54 220-294 4-59 (60)
12 PF13610 DDE_Tnp_IS240: DDE do 91.5 0.081 1.8E-06 52.7 1.2 81 405-489 1-81 (140)
13 PF00665 rve: Integrase core d 87.6 2.5 5.3E-05 39.9 8.0 76 405-481 6-82 (120)
14 PF04500 FLYWCH: FLYWCH zinc f 78.4 4 8.8E-05 34.0 4.8 25 267-293 38-62 (62)
15 PF06782 UPF0236: Uncharacteri 75.4 30 0.00065 41.6 12.8 142 445-594 235-382 (470)
16 smart00774 WRKY DNA binding do 74.9 5.3 0.00012 34.1 4.5 27 267-293 31-59 (59)
17 PF04937 DUF659: Protein of un 57.0 55 0.0012 33.4 8.6 107 399-508 27-138 (153)
18 COG3316 Transposase and inacti 45.0 61 0.0013 34.9 6.9 83 405-492 70-152 (215)
19 PF04684 BAF1_ABF1: BAF1 / ABF 34.9 56 0.0012 38.7 5.1 54 199-278 25-78 (496)
20 COG5431 Uncharacterized metal- 25.8 52 0.0011 31.3 2.3 31 682-718 40-75 (117)
21 PF12179 IKKbetaNEMObind: I-ka 25.0 21 0.00046 27.8 -0.3 15 48-62 23-37 (38)
22 PHA02517 putative transposase 23.9 1.9E+02 0.0041 31.8 6.8 73 404-478 109-181 (277)
23 PRK14702 insertion element IS2 22.6 3.2E+02 0.0069 30.2 8.2 72 405-477 87-163 (262)
24 PRK09409 IS2 transposase TnpB; 21.2 3.6E+02 0.0079 30.4 8.5 73 404-477 125-202 (301)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.3e-130 Score=1182.35 Aligned_cols=588 Identities=29% Similarity=0.517 Sum_probs=522.4
Q ss_pred CCCCCCCCeeCCHHHHHHHHHHHhhhcCeEEEEeeeeecC-CCceEEEEEEeccCCcccccccc-------------ccc
Q 002062 193 SQNPELGMVFSSQEEAYMFYTTYAKRIGFSVRKAKVRRLS-NGAIRKRLFYCSRQGFRAKKQST-------------KAT 258 (973)
Q Consensus 193 ~~~P~vGm~F~S~eeA~~fyn~YA~~~GFsIRk~~s~r~~-~g~i~~~~fvCsreG~~~~~~~~-------------~~~ 258 (973)
..+|++||+|+|+|||++||+.||+++||+||+.+++|++ ++.++.++|+|+|+|+++++... ...
T Consensus 71 ~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~ 150 (846)
T PLN03097 71 NLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENG 150 (846)
T ss_pred CccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCcccc
Confidence 4689999999999999999999999999999999998877 78899999999999987643110 001
Q ss_pred cccccccccCCcceEEEEEe-cceEEEEEeecCCCCCCCCCCCCcccCCCCccccchhhhhhhccccccccccccccCcc
Q 002062 259 KYQRKETRTGCDAMVEFTVE-NGKWMISGFTPEHNHDLEGKSKPVVGSSTKVSEDHSISTTMNKAATVKEAQPLNSVGFQ 337 (973)
Q Consensus 259 kr~r~stRtgCpA~m~vk~~-~gkW~V~~f~~eHNH~L~~~~~~~~l~s~R~s~~q~ii~~l~~~~~~~~i~~~~~~g~~ 337 (973)
+++|+.+||||||+|+|++. +|+|+|+.|+++|||+|.++..... +.++ +...+.. .+ .+..
T Consensus 151 ~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~~~-~~r~------~~~~~~~-----~~-----~~~~ 213 (846)
T PLN03097 151 TGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVSE-QTRK------MYAAMAR-----QF-----AEYK 213 (846)
T ss_pred cccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccccch-hhhh------hHHHHHh-----hh-----hccc
Confidence 23566799999999999998 9999999999999999997653221 1000 1111110 00 0111
Q ss_pred CccCCCCCcccc-----ccCCCcccHHHHHHHHHHHHhcCCCCeeEEeeccCCceeEEEEccCcchhhhhhcCcEEEEee
Q 002062 338 GINCPGIPCDEK-----TSCPKLLDGQSLIKYFRRLEMEAPSFSYTVQVNAENCLTGFFWTDGRSRIDYDYFGDVVILDT 412 (973)
Q Consensus 338 ~~~~~~~d~~N~-----~~~l~~gD~~~Ll~yl~~~q~~nP~F~y~vq~De~~~l~~iFwad~~s~~~y~~FgDVV~~Dt 412 (973)
.+..+..+..|. +..+..||+++||+||+++|.+||+|||++|+|++++|+||||+|++|+.+|.+|||||+|||
T Consensus 214 ~v~~~~~d~~~~~~~~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~FGDvV~fDT 293 (846)
T PLN03097 214 NVVGLKNDSKSSFDKGRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGNFSDVVSFDT 293 (846)
T ss_pred cccccchhhcchhhHHHhhhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHhcCCEEEEec
Confidence 222233333333 345788999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeccCCccccceeeeecCcceeEEEEEEecCCchhhHHHHHHHHHhhhCCCCCcEEecCCchHHHHHHHhhCCCCccc
Q 002062 413 TFRIEANNMIYAPFLGLNHHRQYVLFGGAFLLDDSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQAMADAIKMVLPKTQHL 492 (973)
Q Consensus 413 Ty~tNky~~pL~~fvGvn~~gq~~~fg~ALl~dEt~esf~Wlf~~fl~~m~~~~P~tIITD~d~am~~AI~~VFP~t~H~ 492 (973)
||+||+|+|||++|+|||||+|+++||||||.+|+.+||.|||++|+++|+|++|++||||+|.+|++||++|||+|.|+
T Consensus 294 TY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr 373 (846)
T PLN03097 294 TYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNAHHC 373 (846)
T ss_pred eeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCceeh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHhhccc-CCCCchHHHHHhhhhccccCHHHHHHHHHHHHHHhhhccchHHHHhhhccccccccccccccC
Q 002062 493 LGIWYILRNAKANLSK-CYGEPGFNSLFNKCIFDCESEAEFESMWESLLEQYELCANPWLKTQYMLRRKWAHCFCKSAFS 571 (973)
Q Consensus 493 lC~wHI~kn~~kkl~~-~~~~~~f~~~f~k~v~~s~t~eeFe~~W~~l~~ky~l~~n~wL~~ly~~rekWa~ay~k~~f~ 571 (973)
+|+|||++|+.++|+. +...+.|..+|.+||+++++++|||..|..|+++|+|++|+||+.||+.|++||++|+++.|+
T Consensus 374 ~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~ 453 (846)
T PLN03097 374 FFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFL 453 (846)
T ss_pred hhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhccccc
Confidence 9999999999999999 777899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccccccccccccccCCCCChHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCccccCcHHHHHHHHHhcHHHHHH
Q 002062 572 AGIRSTQHCYDISHVFHSLTSKATTPLQFVQQYFKVAEQQRREELYEDFRCNGSAPPTILRSNAIEKEAAKIYSCTMFKL 651 (973)
Q Consensus 572 ~g~~TT~rsES~N~~lK~~v~~~tsL~~F~~~~~~~l~~~r~kE~~ad~~s~~~~p~~~~t~~piEkqaa~vYT~~iFkk 651 (973)
+||.||+|+||+|++||+||+++++|.+|+++|+++++.++++|+++|+.+.++.|.+. +.+|||+||+++|||+||++
T Consensus 454 agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~-t~~piEkQAs~iYT~~iF~k 532 (846)
T PLN03097 454 AGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALK-SPSPLEKSVSGVYTHAVFKK 532 (846)
T ss_pred CCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccc-cccHHHHHHHHHhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999775 68999999999999999999
Q ss_pred HHHHHHHhhcceEEEEecCCceeEEEEEEeCCeeeEEEEEecCCCeeEeeecCccccCCccchhhhhhhccCCccCCcch
Q 002062 652 FRAELLECLSVAIEEIQGDGMTAKFRLNEEGQKKEKIVEFNCVETHLTCSCKKYESVGILCVHALKVLNAKNIFHIPPQY 731 (973)
Q Consensus 652 Fq~El~~~~~~~~~e~~~dg~i~~y~V~~~~~~k~~~V~~d~~~~~~sCSC~~Fe~~GIPCrHaL~VL~~~~v~~IP~~Y 731 (973)
||+|+..+..+.+.+...+|.+.+|.|...+..+.|.|.+|...+.++|+|++||+.||||+|||+||.++||.+||++|
T Consensus 533 FQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~Y 612 (846)
T PLN03097 533 FQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQY 612 (846)
T ss_pred HHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhh
Confidence 99999998888777766678889999988766788999999999999999999999999999999999999999999999
Q ss_pred hHHhhhhhhhcCCcccCCCCccccccccchhHHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHHHHHH
Q 002062 732 ILKRWTKSAKDGMVVNGHEGEVVDDSQRHLHLDESKLMHKALNVITKSLPFEGTRMIADDYLSIALKNIEDA 803 (973)
Q Consensus 732 ILkRWTk~ak~~~~~~~~~~~~~~~~~~~~~~~r~~l~~~a~~l~~kas~s~e~~~~a~~~l~~~~~~le~~ 803 (973)
||+||||+||...+. +... ........+++.||+.|++++.+|+.|+|+|++|+++|+++.++++.|
T Consensus 613 ILkRWTKdAK~~~~~-~~~~----~~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~L~e~~~~~~~~ 679 (846)
T PLN03097 613 ILKRWTKDAKSRHLL-GEES----EQVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRALEEAFGNCISM 679 (846)
T ss_pred hhhhchhhhhhcccC-cccc----ccccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999987775 3221 112334455568999999999999999999999999999999999853
No 2
>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=99.83 E-value=1.3e-20 Score=173.20 Aligned_cols=90 Identities=27% Similarity=0.441 Sum_probs=87.0
Q ss_pred eeeeeccCCccccc---eeeeecCcceeEEEEEEecCCchhhHHHHHHHHHhhhCCCCCcEEecCCchHHHHHHHhhCCC
Q 002062 412 TTFRIEANNMIYAP---FLGLNHHRQYVLFGGAFLLDDSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQAMADAIKMVLPK 488 (973)
Q Consensus 412 tTy~tNky~~pL~~---fvGvn~~gq~~~fg~ALl~dEt~esf~Wlf~~fl~~m~~~~P~tIITD~d~am~~AI~~VFP~ 488 (973)
+||+||+| +|++. ++|+|++|+.+|+||+|+.+|+.++|.|+|+.|++.++.. |.+||||++.++.+||+++||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 69999999 88886 9999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred CcccchHHHHHHHHH
Q 002062 489 TQHLLGIWYILRNAK 503 (973)
Q Consensus 489 t~H~lC~wHI~kn~~ 503 (973)
+.|++|.||+++|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999974
No 3
>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=99.76 E-value=1.4e-18 Score=159.42 Aligned_cols=88 Identities=40% Similarity=0.736 Sum_probs=79.0
Q ss_pred HHHHHHhhhcCeEEEEeeeeec-CCCceEEEEEEeccCCcccccccc-ccccccccccccCCcceEEEEEe-cceEEEEE
Q 002062 210 MFYTTYAKRIGFSVRKAKVRRL-SNGAIRKRLFYCSRQGFRAKKQST-KATKYQRKETRTGCDAMVEFTVE-NGKWMISG 286 (973)
Q Consensus 210 ~fyn~YA~~~GFsIRk~~s~r~-~~g~i~~~~fvCsreG~~~~~~~~-~~~kr~r~stRtgCpA~m~vk~~-~gkW~V~~ 286 (973)
+||+.||..+||+||+.+++++ .+|.+.++.|+|+++|.+..+... ...+++++++||||||+|.|++. +|.|.|+.
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~~~~w~v~~ 80 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRKDGKWRVTS 80 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEccCCEEEEEE
Confidence 5999999999999999999887 488899999999999998876554 33457889999999999999999 99999999
Q ss_pred eecCCCCCCCC
Q 002062 287 FTPEHNHDLEG 297 (973)
Q Consensus 287 f~~eHNH~L~~ 297 (973)
++++|||+|.|
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999975
No 4
>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=99.48 E-value=1.9e-14 Score=165.32 Aligned_cols=186 Identities=15% Similarity=0.142 Sum_probs=150.3
Q ss_pred cEEEEeeeeeeccC-----CccccceeeeecCcceeEEEEEEecCCchhhHHHHHHHHHhhhCCCCCcEEecCCchHHHH
Q 002062 406 DVVILDTTFRIEAN-----NMIYAPFLGLNHHRQYVLFGGAFLLDDSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQAMAD 480 (973)
Q Consensus 406 DVV~~DtTy~tNky-----~~pL~~fvGvn~~gq~~~fg~ALl~dEt~esf~Wlf~~fl~~m~~~~P~tIITD~d~am~~ 480 (973)
++|++|++|.+-+. +.++++++|||.+|+..++|+.+...|+..+|.-+|+.|++- |-..|..||+|..++|..
T Consensus 163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ 241 (381)
T PF00872_consen 163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKE 241 (381)
T ss_pred cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccc
Confidence 57899999987663 467899999999999999999999999999999999998765 334699999999999999
Q ss_pred HHHhhCCCCcccchHHHHHHHHHhhcccCCCCchHHHHHhhhhccccCHHHHHHHHHHHHHHhhhccchHHHHhhhcc-c
Q 002062 481 AIKMVLPKTQHLLGIWYILRNAKANLSKCYGEPGFNSLFNKCIFDCESEAEFESMWESLLEQYELCANPWLKTQYMLR-R 559 (973)
Q Consensus 481 AI~~VFP~t~H~lC~wHI~kn~~kkl~~~~~~~~f~~~f~k~v~~s~t~eeFe~~W~~l~~ky~l~~n~wL~~ly~~r-e 559 (973)
||.++||++.++.|.+|+++|+.+++.. +..+.+..+|+. |+.+.+.++....|+.+.+++........+.|-+.. +
T Consensus 242 ai~~~fp~a~~QrC~vH~~RNv~~~v~~-k~~~~v~~~Lk~-I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~ 319 (381)
T PF00872_consen 242 AIREVFPGAKWQRCVVHLMRNVLRKVPK-KDRKEVKADLKA-IYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDE 319 (381)
T ss_pred cccccccchhhhhheechhhhhcccccc-ccchhhhhhccc-cccccccchhhhhhhhcccccccccchhhhhhhhcccc
Confidence 9999999999999999999999999865 334677788866 677889999999999999888776665554442211 2
Q ss_pred cccccccccccCCCccccccccccccccccccCCC
Q 002062 560 KWAHCFCKSAFSAGIRSTQHCYDISHVFHSLTSKA 594 (973)
Q Consensus 560 kWa~ay~k~~f~~g~~TT~rsES~N~~lK~~v~~~ 594 (973)
.|...-++....--+.|||.+|++|+.+|+..+..
T Consensus 320 ~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~~ 354 (381)
T PF00872_consen 320 LLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTKVV 354 (381)
T ss_pred ccceeeecchhccccchhhhccccccchhhhcccc
Confidence 22222244555567889999999999999865533
No 5
>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=98.89 E-value=7.5e-09 Score=96.79 Aligned_cols=88 Identities=22% Similarity=0.346 Sum_probs=70.8
Q ss_pred eCCHHHHHHHHHHHhhhcCeEEEEeeeeecCCCceEEEEEEeccCCcccccccc---------------------ccccc
Q 002062 202 FSSQEEAYMFYTTYAKRIGFSVRKAKVRRLSNGAIRKRLFYCSRQGFRAKKQST---------------------KATKY 260 (973)
Q Consensus 202 F~S~eeA~~fyn~YA~~~GFsIRk~~s~r~~~g~i~~~~fvCsreG~~~~~~~~---------------------~~~kr 260 (973)
|.+.+|...|+...+...||.|++.+|..+ ...|.|--.|.++..... ..+..
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~------ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k 74 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKK------KIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKK 74 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCc------eEEEEEecCCCcccccccccccccccccccccccccccccccCC
Confidence 889999999999999999999999999876 378999777766543221 00112
Q ss_pred cccccccCCcceEEEEEe--cceEEEEEeecCCCCCC
Q 002062 261 QRKETRTGCDAMVEFTVE--NGKWMISGFTPEHNHDL 295 (973)
Q Consensus 261 ~r~stRtgCpA~m~vk~~--~gkW~V~~f~~eHNH~L 295 (973)
...+.++.||++|++... .++|.|..++..|||||
T Consensus 75 ~t~srk~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 75 RTKSRKNTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cccccccCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 233557899999999988 88999999999999997
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.55 E-value=1.9e-07 Score=106.59 Aligned_cols=198 Identities=15% Similarity=0.112 Sum_probs=136.9
Q ss_pred cEEEEeeeeeecc--CCccccceeeeecCcceeEEEEEEecCCchhhHHHHHHHHHhhhCCCCCcEEecCCchHHHHHHH
Q 002062 406 DVVILDTTFRIEA--NNMIYAPFLGLNHHRQYVLFGGAFLLDDSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQAMADAIK 483 (973)
Q Consensus 406 DVV~~DtTy~tNk--y~~pL~~fvGvn~~gq~~~fg~ALl~dEt~esf~Wlf~~fl~~m~~~~P~tIITD~d~am~~AI~ 483 (973)
.+|++|++|.+-| -+..++.++||+.+|+..++|+.+-..|+ ..|.-+|..|+.- |-..-..+++|...++.+||.
T Consensus 146 ~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~ 223 (379)
T COG3328 146 PYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLVVVDGLKGLPEAIS 223 (379)
T ss_pred eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEEecchhhhhHHHHH
Confidence 4688999999988 45588999999999999999999999999 7777555555443 223345677799999999999
Q ss_pred hhCCCCcccchHHHHHHHHHhhcccCCCCchHHHHHhhhhccccCHHHHHHHHHHHHHHhhhccchHHHHhhhc-ccccc
Q 002062 484 MVLPKTQHLLGIWYILRNAKANLSKCYGEPGFNSLFNKCIFDCESEAEFESMWESLLEQYELCANPWLKTQYML-RRKWA 562 (973)
Q Consensus 484 ~VFP~t~H~lC~wHI~kn~~kkl~~~~~~~~f~~~f~k~v~~s~t~eeFe~~W~~l~~ky~l~~n~wL~~ly~~-rekWa 562 (973)
.+||.+.+++|..|+.+|+..+.... ..+....+++. ++.+.+.++-...|..+.+.+......-++.+... -+.|.
T Consensus 224 ~v~p~a~~Q~C~vH~~Rnll~~v~~k-~~d~i~~~~~~-I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~ 301 (379)
T COG3328 224 AVFPQAAVQRCIVHLVRNLLDKVPRK-DQDAVLSDLRS-IYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLP 301 (379)
T ss_pred HhccHhhhhhhhhHHHhhhhhhhhhh-hhHHHHhhhhh-hhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcc
Confidence 99999999999999999999887752 22333344433 67788888888999888776654444333332221 12221
Q ss_pred ccccccccCCCccccccccccccccccccCC--CCChHHHHHHHHHH
Q 002062 563 HCFCKSAFSAGIRSTQHCYDISHVFHSLTSK--ATTPLQFVQQYFKV 607 (973)
Q Consensus 563 ~ay~k~~f~~g~~TT~rsES~N~~lK~~v~~--~tsL~~F~~~~~~~ 607 (973)
-.-+.....--+.|||-+|++|+.++..... ..+-.+++..+...
T Consensus 302 F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~~y~ 348 (379)
T COG3328 302 FFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNEESVEKLVYL 348 (379)
T ss_pred cccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCHHHHHHHHHH
Confidence 1111111112467899999999988765443 34445555544333
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.51 E-value=3.1e-08 Score=71.19 Aligned_cols=26 Identities=42% Similarity=0.814 Sum_probs=24.6
Q ss_pred EeeecCccccCCccchhhhhhhccCC
Q 002062 699 TCSCKKYESVGILCVHALKVLNAKNI 724 (973)
Q Consensus 699 sCSC~~Fe~~GIPCrHaL~VL~~~~v 724 (973)
+|+|++||..||||+|+|+|+...++
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 79999999999999999999998876
No 8
>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=98.15 E-value=8.3e-06 Score=70.82 Aligned_cols=64 Identities=25% Similarity=0.365 Sum_probs=54.3
Q ss_pred CCCCCCCeeCCHHHHHHHHHHHhhhcCeEEEEeeeeecCCCceEEEEEEeccCCccccccccccccccccccccCCcceE
Q 002062 194 QNPELGMVFSSQEEAYMFYTTYAKRIGFSVRKAKVRRLSNGAIRKRLFYCSRQGFRAKKQSTKATKYQRKETRTGCDAMV 273 (973)
Q Consensus 194 ~~P~vGm~F~S~eeA~~fyn~YA~~~GFsIRk~~s~r~~~g~i~~~~fvCsreG~~~~~~~~~~~kr~r~stRtgCpA~m 273 (973)
+...+||.|.|.+|+..++..||...||.++..++.+. +...+|. ..||||+|
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~------r~~~~C~---------------------~~~C~Wrv 54 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKK------RYRAKCK---------------------DKGCPWRV 54 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCE------EEEEEEc---------------------CCCCCEEE
Confidence 36789999999999999999999999999998887643 5778884 23599999
Q ss_pred EEEEe--cceEEE
Q 002062 274 EFTVE--NGKWMI 284 (973)
Q Consensus 274 ~vk~~--~gkW~V 284 (973)
++++. .+.|.|
T Consensus 55 ~as~~~~~~~~~I 67 (67)
T PF03108_consen 55 RASKRKRSDTFQI 67 (67)
T ss_pred EEEEcCCCCEEEC
Confidence 99988 678876
No 9
>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=97.81 E-value=1.2e-05 Score=62.65 Aligned_cols=29 Identities=31% Similarity=0.496 Sum_probs=25.8
Q ss_pred CCCeeEeeecCccccCCccchhhhhhhcc
Q 002062 694 VETHLTCSCKKYESVGILCVHALKVLNAK 722 (973)
Q Consensus 694 ~~~~~sCSC~~Fe~~GIPCrHaL~VL~~~ 722 (973)
+....+|+|..|+..|.||+|+++|+...
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHhh
Confidence 45678999999999999999999999654
No 10
>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=96.30 E-value=0.0031 Score=68.46 Aligned_cols=94 Identities=15% Similarity=0.170 Sum_probs=67.2
Q ss_pred EEeeeeeeccCCccccceeeeec--CcceeEEEEEEecCCchhhHHHHHHHH-HhhhCCCCCcEEecCCchHHHHHHHhh
Q 002062 409 ILDTTFRIEANNMIYAPFLGLNH--HRQYVLFGGAFLLDDSKDSFIWLLRTF-LDSMGRRQPSTIFTDGYQAMADAIKMV 485 (973)
Q Consensus 409 ~~DtTy~tNky~~pL~~fvGvn~--~gq~~~fg~ALl~dEt~esf~Wlf~~f-l~~m~~~~P~tIITD~d~am~~AI~~V 485 (973)
.||=+.......- +..+.+|. +...++ +++.+-+.+++.-+|..+ -.. .....++|.+|...+...||++.
T Consensus 2 giDE~~~~~g~~~--y~t~~~d~~~~~~~il---~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~ 75 (249)
T PF01610_consen 2 GIDEFAFRKGHRS--YVTVVVDLDTDTGRIL---DILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREY 75 (249)
T ss_pred eEeeeeeecCCcc--eeEEEEECccCCceEE---EEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCcccccccccc
Confidence 4555444333331 34455555 444444 478888888877666655 222 34577999999999999999999
Q ss_pred CCCCcccchHHHHHHHHHhhccc
Q 002062 486 LPKTQHLLGIWYILRNAKANLSK 508 (973)
Q Consensus 486 FP~t~H~lC~wHI~kn~~kkl~~ 508 (973)
||+|.+.+-.|||++++.+.+..
T Consensus 76 ~P~A~iv~DrFHvvk~~~~al~~ 98 (249)
T PF01610_consen 76 FPNAQIVADRFHVVKLANRALDK 98 (249)
T ss_pred ccccccccccchhhhhhhhcchh
Confidence 99999999999999999885543
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=91.53 E-value=0.82 Score=39.14 Aligned_cols=54 Identities=22% Similarity=0.485 Sum_probs=35.0
Q ss_pred CeEEEEeeeeecCCCceEEEEEEeccCCccccccccccccccccccccCCcceEEEEEe--cceEEEEEeecCCCCC
Q 002062 220 GFSVRKAKVRRLSNGAIRKRLFYCSRQGFRAKKQSTKATKYQRKETRTGCDAMVEFTVE--NGKWMISGFTPEHNHD 294 (973)
Q Consensus 220 GFsIRk~~s~r~~~g~i~~~~fvCsreG~~~~~~~~~~~kr~r~stRtgCpA~m~vk~~--~gkW~V~~f~~eHNH~ 294 (973)
||..|+--.+..++...-+..|.|+.. +|||+=.|.+. ++.-.++.+..+|||+
T Consensus 4 gy~WRKYGqK~i~g~~~pRsYYrCt~~---------------------~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 4 GYRWRKYGQKNIKGSPYPRSYYRCTHP---------------------GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SS-EEEEEEEEETTTTCEEEEEEEECT---------------------TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCchhhccCcccCCCceeeEeeecccc---------------------ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 777776554433333334456777421 79999999987 7778899999999997
No 12
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=91.48 E-value=0.081 Score=52.73 Aligned_cols=81 Identities=19% Similarity=0.181 Sum_probs=66.0
Q ss_pred CcEEEEeeeeeeccCCccccceeeeecCcceeEEEEEEecCCchhhHHHHHHHHHhhhCCCCCcEEecCCchHHHHHHHh
Q 002062 405 GDVVILDTTFRIEANNMIYAPFLGLNHHRQYVLFGGAFLLDDSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQAMADAIKM 484 (973)
Q Consensus 405 gDVV~~DtTy~tNky~~pL~~fvGvn~~gq~~~fg~ALl~dEt~esf~Wlf~~fl~~m~~~~P~tIITD~d~am~~AI~~ 484 (973)
|+.+.+|=||.+-+-. ..+.+..||.+|+ ++++-|-..-+..+=..||+..++... ..|..|+||+.++...|+++
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~ 76 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 6889999999875533 4566888999999 777777777777777777777777654 68999999999999999999
Q ss_pred hCCCC
Q 002062 485 VLPKT 489 (973)
Q Consensus 485 VFP~t 489 (973)
++|..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99974
No 13
>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=87.57 E-value=2.5 Score=39.88 Aligned_cols=76 Identities=13% Similarity=0.143 Sum_probs=56.4
Q ss_pred CcEEEEeeeeee-ccCCccccceeeeecCcceeEEEEEEecCCchhhHHHHHHHHHhhhCCCCCcEEecCCchHHHHH
Q 002062 405 GDVVILDTTFRI-EANNMIYAPFLGLNHHRQYVLFGGAFLLDDSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQAMADA 481 (973)
Q Consensus 405 gDVV~~DtTy~t-Nky~~pL~~fvGvn~~gq~~~fg~ALl~dEt~esf~Wlf~~fl~~m~~~~P~tIITD~d~am~~A 481 (973)
+.++.+|.+... ...+...+.++.+|..-..+. ++.+-..++.+++.-+|.......++..|++|+||+..+....
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~~ 82 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFIY-AFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTSH 82 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTEEE-EEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHSH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCcEE-EEEeecccccccccccccccccccccccceecccccccccccc
Confidence 578899988544 345557888888888777665 5677666788888888887777777766999999999988743
No 14
>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=78.45 E-value=4 Score=33.95 Aligned_cols=25 Identities=32% Similarity=0.446 Sum_probs=10.2
Q ss_pred cCCcceEEEEEecceEEEEEeecCCCC
Q 002062 267 TGCDAMVEFTVENGKWMISGFTPEHNH 293 (973)
Q Consensus 267 tgCpA~m~vk~~~gkW~V~~f~~eHNH 293 (973)
.+|+|++.+. .+.-.|.....+|||
T Consensus 38 ~~C~a~~~~~--~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITD--AGDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE----TTEEEE-S---SS
T ss_pred CCCeEEEEEE--CCCCEEEECCCccCC
Confidence 5799999997 233344555589999
No 15
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=75.43 E-value=30 Score=41.64 Aligned_cols=142 Identities=14% Similarity=0.220 Sum_probs=82.3
Q ss_pred CCchhhHHHHHHHHHhhhCCCCC--cEEecCCchHHHHHHHhhCCCCcccchHHHHHHHHHhhcccCCCCchHHHHHhhh
Q 002062 445 DDSKDSFIWLLRTFLDSMGRRQP--STIFTDGYQAMADAIKMVLPKTQHLLGIWYILRNAKANLSKCYGEPGFNSLFNKC 522 (973)
Q Consensus 445 dEt~esf~Wlf~~fl~~m~~~~P--~tIITD~d~am~~AI~~VFP~t~H~lC~wHI~kn~~kkl~~~~~~~~f~~~f~k~ 522 (973)
....+-|.-+...+-..-..... .++..|...-++.++. .||++.|.|..||+.+.+.+.++. .+.....+.++
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~---~~~~~~~~~~a 310 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSH---DPELKEKIRKA 310 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhh---ChHHHHHHHHH
Confidence 44455565555555444332222 4556799999988776 999999999999999999998875 33455556666
Q ss_pred hccccCHHHHHHHHHHHHHHhhhcc-chHHHHhh-hcccccc--ccccccccCCCccccccccccccccccccCCC
Q 002062 523 IFDCESEAEFESMWESLLEQYELCA-NPWLKTQY-MLRRKWA--HCFCKSAFSAGIRSTQHCYDISHVFHSLTSKA 594 (973)
Q Consensus 523 v~~s~t~eeFe~~W~~l~~ky~l~~-n~wL~~ly-~~rekWa--~ay~k~~f~~g~~TT~rsES~N~~lK~~v~~~ 594 (973)
+. ......++...+.+...-.... .+-+..+. .....|- .+|... .|+....-.|+.+..+...++++
T Consensus 311 l~-~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i~~y~~~---~~~~g~g~ee~~~~~~s~RmK~r 382 (470)
T PF06782_consen 311 LK-KGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGIKPYRER---EGLRGIGAEESVSHVLSYRMKSR 382 (470)
T ss_pred HH-hcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHhhhhhhc---cCCCccchhhhhhhHHHHHhcCC
Confidence 65 3356666666665544322111 11111111 1233342 233221 33344445788888887766554
No 16
>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=74.92 E-value=5.3 Score=34.15 Aligned_cols=27 Identities=22% Similarity=0.385 Sum_probs=23.0
Q ss_pred cCCcceEEEEEe--cceEEEEEeecCCCC
Q 002062 267 TGCDAMVEFTVE--NGKWMISGFTPEHNH 293 (973)
Q Consensus 267 tgCpA~m~vk~~--~gkW~V~~f~~eHNH 293 (973)
.||||+=.|.+. ++.-.++.+..+|||
T Consensus 31 ~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 31 QGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 579998888777 678888889999998
No 17
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=56.97 E-value=55 Score=33.36 Aligned_cols=107 Identities=13% Similarity=0.076 Sum_probs=72.5
Q ss_pred hhhhhcCcEEEEeeeeeeccCCccccceeeeecCcceeEEEEEEecC--CchhhHHHHHHHHHhhhCCCCCcEEecCCch
Q 002062 399 IDYDYFGDVVILDTTFRIEANNMIYAPFLGLNHHRQYVLFGGAFLLD--DSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQ 476 (973)
Q Consensus 399 ~~y~~FgDVV~~DtTy~tNky~~pL~~fvGvn~~gq~~~fg~ALl~d--Et~esf~Wlf~~fl~~m~~~~P~tIITD~d~ 476 (973)
..+...|=-|..|+= +++.+.+|+.|+.....|..++-.. =.++ .+.+.+.-+|+...+-+|......||||-..
T Consensus 27 ~~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksv-d~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~ 103 (153)
T PF04937_consen 27 KSWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSV-DASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNAS 103 (153)
T ss_pred HHHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEE-ecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCch
Confidence 344555655666664 5556667777776666555444321 1222 4566666666666666777777889999999
Q ss_pred HHHHHHH---hhCCCCcccchHHHHHHHHHhhccc
Q 002062 477 AMADAIK---MVLPKTQHLLGIWYILRNAKANLSK 508 (973)
Q Consensus 477 am~~AI~---~VFP~t~H~lC~wHI~kn~~kkl~~ 508 (973)
.+++|-+ +-+|...-.-|.-|-+.-+.+.+..
T Consensus 104 ~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 104 NMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred hHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 9988844 4578888889999988888877765
No 18
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.00 E-value=61 Score=34.92 Aligned_cols=83 Identities=13% Similarity=0.109 Sum_probs=55.2
Q ss_pred CcEEEEeeeeeeccCCccccceeeeecCcceeEEEEEEecCCchhhHHHHHHHHHhhhCCCCCcEEecCCchHHHHHHHh
Q 002062 405 GDVVILDTTFRIEANNMIYAPFLGLNHHRQYVLFGGAFLLDDSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQAMADAIKM 484 (973)
Q Consensus 405 gDVV~~DtTy~tNky~~pL~~fvGvn~~gq~~~fg~ALl~dEt~esf~Wlf~~fl~~m~~~~P~tIITD~d~am~~AI~~ 484 (973)
++++-+|=||.+-+-+. .+....||..|++.- +-|...-+...=.-||..+++.. ..|.+|+||+.+....|+.+
T Consensus 70 ~~~w~vDEt~ikv~gkw-~ylyrAid~~g~~Ld--~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~~ 144 (215)
T COG3316 70 GDSWRVDETYIKVNGKW-HYLYRAIDADGLTLD--VWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALRK 144 (215)
T ss_pred ccceeeeeeEEeeccEe-eehhhhhccCCCeEE--EEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHHh
Confidence 46677788886554332 223344566655543 44545544555555666666665 68999999999999999999
Q ss_pred hCCCCccc
Q 002062 485 VLPKTQHL 492 (973)
Q Consensus 485 VFP~t~H~ 492 (973)
+-+...|+
T Consensus 145 l~~~~ehr 152 (215)
T COG3316 145 LGSEVEHR 152 (215)
T ss_pred cCcchhee
Confidence 99866554
No 19
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=34.87 E-value=56 Score=38.69 Aligned_cols=54 Identities=15% Similarity=0.198 Sum_probs=43.5
Q ss_pred CCeeCCHHHHHHHHHHHhhhcCeEEEEeeeeecCCCceEEEEEEeccCCccccccccccccccccccccCCcceEEEEEe
Q 002062 199 GMVFSSQEEAYMFYTTYAKRIGFSVRKAKVRRLSNGAIRKRLFYCSRQGFRAKKQSTKATKYQRKETRTGCDAMVEFTVE 278 (973)
Q Consensus 199 Gm~F~S~eeA~~fyn~YA~~~GFsIRk~~s~r~~~g~i~~~~fvCsreG~~~~~~~~~~~kr~r~stRtgCpA~m~vk~~ 278 (973)
+..|+++++=|..+|.|.....-.|....|-|.+ -.+|.|... .|||+|.+...
T Consensus 25 ~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk-----hftfachlk---------------------~c~fkillsy~ 78 (496)
T PF04684_consen 25 ARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK-----HFTFACHLK---------------------NCPFKILLSYC 78 (496)
T ss_pred ccCCCcHHHHHHHHhhhhhhhcCceeeccccccc-----ceEEEeecc---------------------CCCceeeeeec
Confidence 5679999999999999999888888776666553 578999632 49999988754
No 20
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=25.79 E-value=52 Score=31.32 Aligned_cols=31 Identities=26% Similarity=0.605 Sum_probs=21.9
Q ss_pred CCeeeEEEEEecCCCeeEeeecCccc----c-CCccchhhhh
Q 002062 682 GQKKEKIVEFNCVETHLTCSCKKYES----V-GILCVHALKV 718 (973)
Q Consensus 682 ~~~k~~~V~~d~~~~~~sCSC~~Fe~----~-GIPCrHaL~V 718 (973)
+++++|++..+ .|||..|-. - .-||.|++.+
T Consensus 40 G~~rdYIl~~g------fCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 40 GKERDYILEGG------FCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred ccccceEEEcC------cccCHHHHhHhhhcCcccchhhhhe
Confidence 45678888653 699998862 2 3469999765
No 21
>PF12179 IKKbetaNEMObind: I-kappa-kinase-beta NEMO binding domain; InterPro: IPR022007 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with PF00069 from PFAM. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus of inflammatory cells and upregulation of transcription of proinflammatory cytokines. They perform this function by phosphorylating I-kappa-B proteins which are targeted for degradation to release NF-kappa-B. This kinase (I-kappa-kinase-beta) is found in association with IKK-alpha and NEMO (NF-kappa-B essential modulator). This domain is the binding site of IKK-beta for NEMO. ; GO: 0008384 IkappaB kinase activity; PDB: 3BRT_C 3BRV_C.
Probab=25.01 E-value=21 Score=27.79 Aligned_cols=15 Identities=33% Similarity=1.015 Sum_probs=8.8
Q ss_pred ccccccccccccccC
Q 002062 48 QEGTSTSMLDLDWCW 62 (973)
Q Consensus 48 ~~~~~~~~~~~~~~~ 62 (973)
.+....||.+|||-|
T Consensus 23 ~~Eq~~S~m~lDWSW 37 (38)
T PF12179_consen 23 MKEQDSSFMSLDWSW 37 (38)
T ss_dssp HHHCCS-GGGS--GG
T ss_pred HHHhcchHHhccccc
Confidence 344567899999999
No 22
>PHA02517 putative transposase OrfB; Reviewed
Probab=23.87 E-value=1.9e+02 Score=31.81 Aligned_cols=73 Identities=12% Similarity=-0.025 Sum_probs=42.5
Q ss_pred cCcEEEEeeeeeeccCCccccceeeeecCcceeEEEEEEecCCchhhHHHHHHHHHhhhCCCCCcEEecCCchHH
Q 002062 404 FGDVVILDTTFRIEANNMIYAPFLGLNHHRQYVLFGGAFLLDDSKDSFIWLLRTFLDSMGRRQPSTIFTDGYQAM 478 (973)
Q Consensus 404 FgDVV~~DtTy~tNky~~pL~~fvGvn~~gq~~~fg~ALl~dEt~esf~Wlf~~fl~~m~~~~P~tIITD~d~am 478 (973)
=++++..|.||.....+ -.+.++.+|.+.+. ++|+.+-...+.+...-.|+......+...+..|.||+....
T Consensus 109 pn~~w~~D~t~~~~~~g-~~yl~~iiD~~sr~-i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 109 PNQLWVADFTYVSTWQG-WVYVAFIIDVFARR-IVGWRVSSSMDTDFVLDALEQALWARGRPGGLIHHSDKGSQY 181 (277)
T ss_pred CCCeEEeceeEEEeCCC-CEEEEEecccCCCe-eeecccCCCCChHHHHHHHHHHHHhcCCCcCcEeeccccccc
Confidence 35789999999765443 44566666666554 556777666666644333333333333222346669986543
No 23
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=22.64 E-value=3.2e+02 Score=30.23 Aligned_cols=72 Identities=11% Similarity=-0.037 Sum_probs=47.1
Q ss_pred CcEEEEeeeeeeccCCccccceeeeecCcceeEEEEEEecC-CchhhHHHHHHHHHhhh-C---CCCCcEEecCCchH
Q 002062 405 GDVVILDTTFRIEANNMIYAPFLGLNHHRQYVLFGGAFLLD-DSKDSFIWLLRTFLDSM-G---RRQPSTIFTDGYQA 477 (973)
Q Consensus 405 gDVV~~DtTy~tNky~~pL~~fvGvn~~gq~~~fg~ALl~d-Et~esf~Wlf~~fl~~m-~---~~~P~tIITD~d~a 477 (973)
..|.+.|-||....-+..++..+.+|.+.. .++|+++-.. -+.+...-+|+..+... + ...|..|.||+...
T Consensus 87 n~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 87 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred CCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCcc
Confidence 478899999876554546778888888777 5668888764 45555444554433332 2 23578889998544
No 24
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=21.24 E-value=3.6e+02 Score=30.42 Aligned_cols=73 Identities=11% Similarity=-0.052 Sum_probs=48.2
Q ss_pred cCcEEEEeeeeeeccCCccccceeeeecCcceeEEEEEEecC-CchhhHHHHHHH-HHhhhCC---CCCcEEecCCchH
Q 002062 404 FGDVVILDTTFRIEANNMIYAPFLGLNHHRQYVLFGGAFLLD-DSKDSFIWLLRT-FLDSMGR---RQPSTIFTDGYQA 477 (973)
Q Consensus 404 FgDVV~~DtTy~tNky~~pL~~fvGvn~~gq~~~fg~ALl~d-Et~esf~Wlf~~-fl~~m~~---~~P~tIITD~d~a 477 (973)
=..|.+.|-||....-+.-++..+.+|.+.. .++|+++-.. .+.+...-+|+. +....+. ..|..|.||+-..
T Consensus 125 pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsq 202 (301)
T PRK09409 125 SNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 202 (301)
T ss_pred CCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCcc
Confidence 3478999999976544445777777888777 6778999865 566655555553 3333332 2467888998544
Done!