Query 044338
Match_columns 704
No_of_seqs 289 out of 1100
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 13:40:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044338.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044338hhsearch_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 3.2E-70 7E-75 632.0 42.4 444 160-612 71-623 (846)
2 PF10551 MULE: MULE transposas 99.7 1.8E-17 3.9E-22 145.0 6.3 77 332-410 1-92 (93)
3 PF00872 Transposase_mut: Tran 99.7 1.5E-17 3.2E-22 182.3 6.1 208 260-489 112-349 (381)
4 PF03108 DBD_Tnp_Mut: MuDR fam 99.7 9.8E-17 2.1E-21 131.6 8.7 67 160-226 1-67 (67)
5 COG3328 Transposase and inacti 99.2 2.6E-11 5.7E-16 130.9 8.4 164 324-489 144-328 (379)
6 smart00575 ZnF_PMZ plant mutat 98.8 8.2E-10 1.8E-14 73.8 0.7 27 570-596 1-27 (28)
7 PF08731 AFT: Transcription fa 98.6 2.6E-07 5.7E-12 81.2 9.1 69 169-237 1-111 (111)
8 PF03101 FAR1: FAR1 DNA-bindin 98.5 3.1E-07 6.6E-12 79.9 6.3 61 177-238 1-90 (91)
9 PF04434 SWIM: SWIM zinc finge 98.0 3.5E-06 7.5E-11 61.5 2.3 31 565-595 10-40 (40)
10 PF15288 zf-CCHC_6: Zinc knuck 91.3 0.17 3.8E-06 36.5 2.3 21 660-680 1-23 (40)
11 PF03106 WRKY: WRKY DNA -bindi 90.8 0.39 8.4E-06 38.3 4.2 40 197-236 20-59 (60)
12 PF13610 DDE_Tnp_IS240: DDE do 90.8 0.27 5.9E-06 46.2 3.9 70 325-397 1-81 (140)
13 PF04684 BAF1_ABF1: BAF1 / ABF 87.7 0.82 1.8E-05 50.3 5.2 56 164-219 23-79 (496)
14 PF00098 zf-CCHC: Zinc knuckle 82.2 1.1 2.4E-05 26.7 1.8 17 661-677 1-17 (18)
15 PF04500 FLYWCH: FLYWCH zinc f 82.1 2.6 5.6E-05 33.0 4.6 46 186-235 14-62 (62)
16 smart00774 WRKY DNA binding do 80.9 2.2 4.9E-05 33.8 3.6 38 198-235 21-59 (59)
17 PF06782 UPF0236: Uncharacteri 75.7 8.3 0.00018 43.9 7.8 68 375-444 259-328 (470)
18 PF01610 DDE_Tnp_ISL3: Transpo 71.0 3.7 8.1E-05 42.2 3.3 40 374-414 56-96 (249)
19 COG5431 Uncharacterized metal- 44.9 18 0.00038 32.0 2.3 49 553-603 35-88 (117)
20 PF13696 zf-CCHC_2: Zinc knuck 42.2 15 0.00033 25.3 1.3 21 658-678 6-26 (32)
21 COG5179 TAF1 Transcription ini 38.8 20 0.00044 41.1 2.2 21 659-679 936-958 (968)
22 COG4715 Uncharacterized conser 37.5 63 0.0014 37.0 5.8 45 551-597 50-98 (587)
23 PF02178 AT_hook: AT hook moti 32.1 21 0.00045 19.5 0.5 7 644-650 4-10 (13)
24 COG4279 Uncharacterized conser 31.2 17 0.00037 37.2 0.2 23 570-595 125-147 (266)
25 PRK09409 IS2 transposase TnpB; 30.4 3.3E+02 0.0071 29.0 9.8 40 324-364 125-164 (301)
26 PHA02517 putative transposase 27.7 1.9E+02 0.004 30.1 7.4 42 324-367 109-150 (277)
27 PF12762 DDE_Tnp_IS1595: ISXO2 27.3 89 0.0019 29.2 4.4 17 473-489 109-125 (151)
28 PF14201 DUF4318: Domain of un 27.3 92 0.002 26.0 3.8 30 168-197 13-42 (74)
29 COG4888 Uncharacterized Zn rib 26.3 39 0.00085 29.7 1.5 25 645-669 2-31 (104)
30 PRK14702 insertion element IS2 26.2 3.5E+02 0.0075 28.2 8.9 40 324-364 86-125 (262)
31 KOG3802 Transcription factor O 23.8 58 0.0013 35.7 2.6 22 165-186 252-273 (398)
32 PF13917 zf-CCHC_3: Zinc knuck 21.8 49 0.0011 24.4 1.1 19 660-678 4-22 (42)
33 smart00384 AT_hook DNA binding 21.8 50 0.0011 21.6 1.0 7 644-650 4-10 (26)
34 PF09713 A_thal_3526: Plant pr 20.8 50 0.0011 25.8 1.0 31 262-292 12-50 (54)
35 PF10587 EF-1_beta_acid: Eukar 20.7 94 0.002 20.8 2.1 16 47-62 3-18 (28)
36 PRK00766 hypothetical protein; 20.7 2.5E+02 0.0054 28.1 6.1 24 374-397 99-125 (194)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=3.2e-70 Score=631.99 Aligned_cols=444 Identities=14% Similarity=0.204 Sum_probs=365.1
Q ss_pred CccccCCcEeCCHHHHHHHHHHHHHHcCceEEEEeecce-------EEEEEeec--------------------------
Q 044338 160 KMILYHGQRFRDVSHFRKAIEVFAICDGFKLCVMENRAH-------VVSYECFD-------------------------- 206 (704)
Q Consensus 160 n~~l~vG~~F~s~~e~k~ai~~yAi~~~f~~rv~kS~~~-------r~~~~C~~-------------------------- 206 (704)
+..+.+||+|.|.++++.+|+.||...||.+|+.++.++ ..+++|++
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 467899999999999999999999999999998765432 24567764
Q ss_pred --------cCCCceEEEEEEecCceEEEEEeccccccccccccccc-c-hhHHHHHHhhhcccCCCc-----------ch
Q 044338 207 --------LRCDWKIKAERVVNGRTFIVTEFVAQHKCTRRHQQFQH-R-SKWISAIYLHRWKLQPNL-----------RT 265 (704)
Q Consensus 207 --------~gCpwrv~as~~~~s~~w~I~~~~~~H~C~~~~~~~~~-~-~~~ia~~~~~~l~~~~~~-----------~~ 265 (704)
.||+++|++.+ ...+.|.|+.++.+|||++....... + ++.+..... .+....++ ..
T Consensus 151 ~~rR~~tRtGC~A~m~Vk~-~~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~~-~~~~~~~v~~~~~d~~~~~~~ 228 (846)
T PLN03097 151 TGRRSCAKTDCKASMHVKR-RPDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMAR-QFAEYKNVVGLKNDSKSSFDK 228 (846)
T ss_pred cccccccCCCCceEEEEEE-cCCCeEEEEEEecCCCCCCCCccccchhhhhhHHHHHh-hhhccccccccchhhcchhhH
Confidence 36999999977 56789999999999999997543311 1 121111111 01110000 00
Q ss_pred ---Hhh-HHHHHhhcchHHHHHHhcCCCeEEEEecccccccccceeEEEEeehhhHHHHHHhCccceeeeceeeccCCCc
Q 044338 266 ---VDI-RDEIKATYGFKDEMERINSRNIVLLETKRHEYGEVERFKRMFVCWERTSYAFKNQCRRLLAVDGWKINNPYNS 341 (704)
Q Consensus 266 ---~~i-~~~i~~~~g~~~~l~~~NPgs~~~i~~~~~~~d~~~~f~~~F~a~~~~~~~f~~~~r~vi~iD~t~l~~~y~g 341 (704)
..| ..+++....|..+++..||+|+|++++ |++++++++||+++.|+.+|.+ |+|||.||+||++|+|++
T Consensus 229 ~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~ql-----De~~~l~niFWaD~~sr~~Y~~-FGDvV~fDTTY~tN~y~~ 302 (846)
T PLN03097 229 GRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDL-----GEDQRLKNLFWVDAKSRHDYGN-FSDVVSFDTTYVRNKYKM 302 (846)
T ss_pred HHhhhcccchHHHHHHHHHHHHhhCCCceEEEEE-----ccCCCeeeEEeccHHHHHHHHh-cCCEEEEeceeeccccCc
Confidence 011 135666678889999999999999999 9999999999999999999998 999999999999999999
Q ss_pred eeeeeeeecCCCCeEEEEEEEeecCCccceee------------cCeEEEcCCCchHHHHHHhhcCCCcccccchhHHHH
Q 044338 342 VMLVAAALDGNNGILPIAFCEVHVEDLDSWHG------------EGLCIMGDGDNGIDYAVEEFLPKTVYRQCCLKIFTE 409 (704)
Q Consensus 342 ~ll~a~g~D~~~~~~pla~alv~~Et~esw~W------------~~~~iitD~~~~l~~Ai~~vfP~a~~h~~C~~Hi~~ 409 (704)
||++|+|+|||+|+++|||||+.+|+.++|.| .|.+||||++.+|.+||++|||+| .||+|+|||++
T Consensus 303 Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t-~Hr~C~wHI~~ 381 (846)
T PLN03097 303 PLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNA-HHCFFLWHILG 381 (846)
T ss_pred EEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCc-eehhhHHHHHH
Confidence 99999999999999999999999999999999 899999999999999999999999 99999999999
Q ss_pred -HHHhCC-----CchhHHHHhHhhcc-CCHHHHHHHHHHHHh-hChhHHHHHhcc--ccccceecccCCcccccccccch
Q 044338 410 -MVKRFP-----TTPVEHFFWSACRS-TSATSFNKYMDLIHN-ESEECHDWLLQT--DWSSWALFTIPKWVKCTCVTLSI 479 (704)
Q Consensus 410 -~~~~~~-----~~~~~~~~~~~~~a-~t~~eFe~~~~~l~~-~~~~~~~~L~~~--~~~~Wa~a~~~~~~~~~~~TtN~ 479 (704)
+.++++ .+.|...|++|++. .++++|+..|..|.. ++++.++||+.+ .|++|+++|+++.|+.|+.||++
T Consensus 382 ~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~agm~sTqR 461 (846)
T PLN03097 382 KVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQR 461 (846)
T ss_pred HHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhcccccCCcccccc
Confidence 998875 35899999999874 799999999999875 899999999997 89999999999999999999999
Q ss_pred hHHHHHHHhhh--cccChHhHHHHHHHHHHHHHHHhHH-H---------------HHhhhccCCCHHHHHHHHHHHHhCC
Q 044338 480 TDKLRNYLHQY--LEMSIASRFVAIARLTAKLFERRRI-E---------------VWNWYREKVTPTVREVIKDRTIDGQ 541 (704)
Q Consensus 480 ~ES~N~~lk~~--r~~pi~~lle~i~~~~~~~~~~r~~-~---------------a~~~~~~~~Tp~~~k~lq~~~~~a~ 541 (704)
+||+|++|++. +..+|..|++.+...+..+..+-.+ . ..++++.+|||.||++||+++..+.
T Consensus 462 SES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~ 541 (846)
T PLN03097 462 SESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAV 541 (846)
T ss_pred cccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhh
Confidence 99999999984 6688999998886655443322111 0 1122249999999999999999998
Q ss_pred ceEEEee----CCeEEEEEecCc-eEEEeec----cceeeeecccccccccccchhhhhhhccc--cccccccccccHHH
Q 044338 542 RFVLVEE----NGTRLKLTDTTS-IIFDLNM----EAQSCNCGLWQISGIPCAHACKGIQLIMG--NVEEYVDNMMSIQN 610 (704)
Q Consensus 542 ~~~V~~~----~~~~yeV~~~~~-~~~~V~L----~~~tCSC~~fe~~GiPC~Halav~~~~~~--~p~~yv~~~yt~~~ 610 (704)
.|.+... ....|.|...++ ..|.|.. ...+|+|++|+..||||+|||.||.+.++ .|..||.++||+++
T Consensus 542 ~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdA 621 (846)
T PLN03097 542 ACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDA 621 (846)
T ss_pred heEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhchhhh
Confidence 8877643 235788887543 3344533 46899999999999999999999999998 69999999999887
Q ss_pred Hh
Q 044338 611 FC 612 (704)
Q Consensus 611 ~~ 612 (704)
-.
T Consensus 622 K~ 623 (846)
T PLN03097 622 KS 623 (846)
T ss_pred hh
Confidence 53
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=99.70 E-value=1.8e-17 Score=145.01 Aligned_cols=77 Identities=30% Similarity=0.436 Sum_probs=73.8
Q ss_pred ceeeccCCCceeee---eeeecCCCCeEEEEEEEeecCCccceee-----------cCeEEEcCCCchHHHHHHhhcCCC
Q 044338 332 GWKINNPYNSVMLV---AAALDGNNGILPIAFCEVHVEDLDSWHG-----------EGLCIMGDGDNGIDYAVEEFLPKT 397 (704)
Q Consensus 332 ~t~l~~~y~g~ll~---a~g~D~~~~~~pla~alv~~Et~esw~W-----------~~~~iitD~~~~l~~Ai~~vfP~a 397 (704)
|||++|+| |+++. ++|+|++++.+|+||+|+.+|+.++|.| .|.+||||+++|+.+||+++||++
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~p~~ii~D~~~~~~~Ai~~vfP~~ 79 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQKPKVIISDFDKALINAIKEVFPDA 79 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccCceeeeccccHHHHHHHHHHCCCc
Confidence 79999999 98885 9999999999999999999999999999 478999999999999999999999
Q ss_pred cccccchhHHHH-H
Q 044338 398 VYRQCCLKIFTE-M 410 (704)
Q Consensus 398 ~~h~~C~~Hi~~-~ 410 (704)
.|++|.||+.+ +
T Consensus 80 -~~~~C~~H~~~n~ 92 (93)
T PF10551_consen 80 -RHQLCLFHILRNI 92 (93)
T ss_pred -eEehhHHHHHHhh
Confidence 99999999998 5
No 3
>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=99.69 E-value=1.5e-17 Score=182.28 Aligned_cols=208 Identities=16% Similarity=0.242 Sum_probs=166.9
Q ss_pred CCCcchHhhHHHHHhhcc-hHHHHHHhcCCCeEEEEecccccccccceeEEEEeehhhHHHHHH----hC-ccceeeece
Q 044338 260 QPNLRTVDIRDEIKATYG-FKDEMERINSRNIVLLETKRHEYGEVERFKRMFVCWERTSYAFKN----QC-RRLLAVDGW 333 (704)
Q Consensus 260 ~~~~~~~~i~~~i~~~~g-~~~~l~~~NPgs~~~i~~~~~~~d~~~~f~~~F~a~~~~~~~f~~----~~-r~vi~iD~t 333 (704)
-.+++.++|.+.++..|| .. ..| ..+.++.=.+...+..|+. .. -++|.+||+
T Consensus 112 ~~G~Str~i~~~l~~l~g~~~-----~S~----------------s~vSri~~~~~~~~~~w~~R~L~~~~y~~l~iD~~ 170 (381)
T PF00872_consen 112 LKGVSTRDIEEALEELYGEVA-----VSK----------------STVSRITKQLDEEVEAWRNRPLESEPYPYLWIDGT 170 (381)
T ss_pred ccccccccccchhhhhhcccc-----cCc----------------hhhhhhhhhhhhhHHHHhhhccccccccceeeeee
Confidence 357888999999998888 32 111 2222322233344455542 24 478999999
Q ss_pred eeccCCC-----ceeeeeeeecCCCCeEEEEEEEeecCCccceee-----------cCeEEEcCCCchHHHHHHhhcCCC
Q 044338 334 KINNPYN-----SVMLVAAALDGNNGILPIAFCEVHVEDLDSWHG-----------EGLCIMGDGDNGIDYAVEEFLPKT 397 (704)
Q Consensus 334 ~l~~~y~-----g~ll~a~g~D~~~~~~pla~alv~~Et~esw~W-----------~~~~iitD~~~~l~~Ai~~vfP~a 397 (704)
|++.+.+ ..+++++|+|.+|+..+||+.+.+.|+.++|.= .+..||+|+++||..||.++||.|
T Consensus 171 ~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~RGl~~~~lvv~Dg~~gl~~ai~~~fp~a 250 (381)
T PF00872_consen 171 YFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKERGLKDILLVVSDGHKGLKEAIREVFPGA 250 (381)
T ss_pred ecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhccccccceeeccccccccccccccccch
Confidence 9997744 468999999999999999999999999999986 678999999999999999999999
Q ss_pred cccccchhHHHH-HHHhCCCc---hhHHHHhHhhccCCHHHHHHHHHHHHh----hChhHHHHHhccccccceecccCCc
Q 044338 398 VYRQCCLKIFTE-MVKRFPTT---PVEHFFWSACRSTSATSFNKYMDLIHN----ESEECHDWLLQTDWSSWALFTIPKW 469 (704)
Q Consensus 398 ~~h~~C~~Hi~~-~~~~~~~~---~~~~~~~~~~~a~t~~eFe~~~~~l~~----~~~~~~~~L~~~~~~~Wa~a~~~~~ 469 (704)
.++.|.+|+++ +.++++.+ .+...++.+..+.+.+++...++.+.. ..|.+.++|.+...+.|+..-|+..
T Consensus 251 -~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~ 329 (381)
T PF00872_consen 251 -KWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPE 329 (381)
T ss_pred -hhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccccccceeeecch
Confidence 99999999999 98888643 677788888778887777777777654 5789999999988888888778866
Q ss_pred ccccccccchhHHHHHHHhh
Q 044338 470 VKCTCVTLSITDKLRNYLHQ 489 (704)
Q Consensus 470 ~~~~~~TtN~~ES~N~~lk~ 489 (704)
.+--+.|||.+|++|+.||.
T Consensus 330 ~~~~i~TTN~iEsln~~irr 349 (381)
T PF00872_consen 330 HRRSIRTTNAIESLNKEIRR 349 (381)
T ss_pred hccccchhhhccccccchhh
Confidence 56677899999999999997
No 4
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=99.68 E-value=9.8e-17 Score=131.56 Aligned_cols=67 Identities=27% Similarity=0.524 Sum_probs=65.1
Q ss_pred CccccCCcEeCCHHHHHHHHHHHHHHcCceEEEEeecceEEEEEeeccCCCceEEEEEEecCceEEE
Q 044338 160 KMILYHGQRFRDVSHFRKAIEVFAICDGFKLCVMENRAHVVSYECFDLRCDWKIKAERVVNGRTFIV 226 (704)
Q Consensus 160 n~~l~vG~~F~s~~e~k~ai~~yAi~~~f~~rv~kS~~~r~~~~C~~~gCpwrv~as~~~~s~~w~I 226 (704)
||.|++||+|+|+++|+.||..||++.+|++++.+|+++|++++|...+|||+|+|++.++++.|+|
T Consensus 1 n~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 1 NPELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred CCccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 5789999999999999999999999999999999999999999999999999999999999999987
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.21 E-value=2.6e-11 Score=130.88 Aligned_cols=164 Identities=13% Similarity=0.153 Sum_probs=130.6
Q ss_pred CccceeeeceeeccC--CCceeeeeeeecCCCCeEEEEEEEeecCCcccee-e----------cCeEEEcCCCchHHHHH
Q 044338 324 CRRLLAVDGWKINNP--YNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWH-G----------EGLCIMGDGDNGIDYAV 390 (704)
Q Consensus 324 ~r~vi~iD~t~l~~~--y~g~ll~a~g~D~~~~~~pla~alv~~Et~esw~-W----------~~~~iitD~~~~l~~Ai 390 (704)
..++|.+||+|++-+ -+..+++|+|++.+|+-.+||+.+.+.|+ ..|. | ....+++|+++||.+||
T Consensus 144 ~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl~~v~l~v~Dg~~gl~~aI 222 (379)
T COG3328 144 DYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGLSDVLLVVVDGLKGLPEAI 222 (379)
T ss_pred CceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccccceeEEecchhhhhHHHH
Confidence 667899999999998 45789999999999999999999999999 8888 5 45677889999999999
Q ss_pred HhhcCCCcccccchhHHHH-HHHhCCCc---hhHHHHhHhhccCCHHH----HHHHHHHHHhhChhHHHHHhccccccce
Q 044338 391 EEFLPKTVYRQCCLKIFTE-MVKRFPTT---PVEHFFWSACRSTSATS----FNKYMDLIHNESEECHDWLLQTDWSSWA 462 (704)
Q Consensus 391 ~~vfP~a~~h~~C~~Hi~~-~~~~~~~~---~~~~~~~~~~~a~t~~e----Fe~~~~~l~~~~~~~~~~L~~~~~~~Wa 462 (704)
..+||.+ .++.|..|+.+ +..+...+ .....+..+..+.+.++ |+...+.+....|....|+.+..-+.|.
T Consensus 223 ~~v~p~a-~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~ 301 (379)
T COG3328 223 SAVFPQA-AVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLP 301 (379)
T ss_pred HHhccHh-hhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcc
Confidence 9999999 99999999999 88776544 33344444444444444 4444444445678888888887777777
Q ss_pred ecccCCcccccccccchhHHHHHHHhh
Q 044338 463 LFTIPKWVKCTCVTLSITDKLRNYLHQ 489 (704)
Q Consensus 463 ~a~~~~~~~~~~~TtN~~ES~N~~lk~ 489 (704)
..-|+...+--+.|||..|++|+.++.
T Consensus 302 F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 302 FFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred cccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 766665535567899999999998875
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.83 E-value=8.2e-10 Score=73.78 Aligned_cols=27 Identities=41% Similarity=0.774 Sum_probs=25.2
Q ss_pred eeeeecccccccccccchhhhhhhccc
Q 044338 570 QSCNCGLWQISGIPCAHACKGIQLIMG 596 (704)
Q Consensus 570 ~tCSC~~fe~~GiPC~Halav~~~~~~ 596 (704)
.+|||++||..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998875
No 7
>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=98.59 E-value=2.6e-07 Score=81.17 Aligned_cols=69 Identities=12% Similarity=0.322 Sum_probs=65.2
Q ss_pred eCCHHHHHHHHHHHHHHcCceEEEEeecceEEEEEeec------------------------------------------
Q 044338 169 FRDVSHFRKAIEVFAICDGFKLCVMENRAHVVSYECFD------------------------------------------ 206 (704)
Q Consensus 169 F~s~~e~k~ai~~yAi~~~f~~rv~kS~~~r~~~~C~~------------------------------------------ 206 (704)
|.+++|++.+|+.++...||+|.+.+||.+.+.++|..
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k~t~srk 80 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKKIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKKRTKSRK 80 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCceEEEEEecCCCcccccccccccccccccccccccccccccccCCcccccc
Confidence 78999999999999999999999999999999999973
Q ss_pred cCCCceEEEEEEecCceEEEEEecccccccc
Q 044338 207 LRCDWKIKAERVVNGRTFIVTEFVAQHKCTR 237 (704)
Q Consensus 207 ~gCpwrv~as~~~~s~~w~I~~~~~~H~C~~ 237 (704)
..|||+|+|........|.|..+++.|+|++
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 2699999999999999999999999999975
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=98.46 E-value=3.1e-07 Score=79.92 Aligned_cols=61 Identities=23% Similarity=0.357 Sum_probs=54.0
Q ss_pred HHHHHHHHHcCceEEEEeecce-------EEEEEeec----------------------cCCCceEEEEEEecCceEEEE
Q 044338 177 KAIEVFAICDGFKLCVMENRAH-------VVSYECFD----------------------LRCDWKIKAERVVNGRTFIVT 227 (704)
Q Consensus 177 ~ai~~yAi~~~f~~rv~kS~~~-------r~~~~C~~----------------------~gCpwrv~as~~~~s~~w~I~ 227 (704)
++|+.||...||.++..+|.+. ++.++|.. .||||+|.+.+.. .+.|.|+
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~ 79 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK-DGKWRVT 79 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc-CCEEEEE
Confidence 3789999999999999887654 78899985 4899999999877 9999999
Q ss_pred Eeccccccccc
Q 044338 228 EFVAQHKCTRR 238 (704)
Q Consensus 228 ~~~~~H~C~~~ 238 (704)
.+..+|||++.
T Consensus 80 ~~~~~HNH~L~ 90 (91)
T PF03101_consen 80 SFVLEHNHPLC 90 (91)
T ss_pred ECcCCcCCCCC
Confidence 99999999974
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=98.00 E-value=3.5e-06 Score=61.51 Aligned_cols=31 Identities=29% Similarity=0.677 Sum_probs=27.0
Q ss_pred eeccceeeeecccccccccccchhhhhhhcc
Q 044338 565 LNMEAQSCNCGLWQISGIPCAHACKGIQLIM 595 (704)
Q Consensus 565 V~L~~~tCSC~~fe~~GiPC~Halav~~~~~ 595 (704)
+++...+|||..|+..|.||+|++||+...+
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 4556889999999999999999999997653
No 10
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=91.28 E-value=0.17 Score=36.48 Aligned_cols=21 Identities=10% Similarity=-0.042 Sum_probs=16.2
Q ss_pred cccCcccccCCCC--CCCCCCCC
Q 044338 660 ARQCIENNSDAAI--NNPQWTHP 680 (704)
Q Consensus 660 ~~~Cs~C~~~gHn--~~~~~~~~ 680 (704)
+++|++|++.||. +..||...
T Consensus 1 k~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 1 KVKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred CccccccccccccccCccCCCCC
Confidence 4699999999998 45566643
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=90.80 E-value=0.39 Score=38.30 Aligned_cols=40 Identities=15% Similarity=0.350 Sum_probs=32.8
Q ss_pred ceEEEEEeeccCCCceEEEEEEecCceEEEEEeccccccc
Q 044338 197 AHVVSYECFDLRCDWKIKAERVVNGRTFIVTEFVAQHKCT 236 (704)
Q Consensus 197 ~~r~~~~C~~~gCpwrv~as~~~~s~~w~I~~~~~~H~C~ 236 (704)
-.|.-+.|+..+||++-.+.+..++....|+++.++|||+
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 3567799999999999999988778889999999999996
No 12
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=90.76 E-value=0.27 Score=46.25 Aligned_cols=70 Identities=19% Similarity=0.095 Sum_probs=52.4
Q ss_pred ccceeeeceeeccCCCceeeeeeeecCCCCeEEEEEEEeecCCccceee-----------cCeEEEcCCCchHHHHHHhh
Q 044338 325 RRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWHG-----------EGLCIMGDGDNGIDYAVEEF 393 (704)
Q Consensus 325 r~vi~iD~t~l~~~y~g~ll~a~g~D~~~~~~pla~alv~~Et~esw~W-----------~~~~iitD~~~~l~~Ai~~v 393 (704)
++.+.+|-||.+.+-+ ..+...++|.+++ +|++-|-..-+...=.. .|..|+||+.++...|+.++
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~~~p~~ivtDk~~aY~~A~~~l 77 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHRGEPRVIVTDKLPAYPAAIKEL 77 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeeccccceeecccCCccchhhhhc
Confidence 3578899999876533 3444677888888 67777766665544333 78899999999999999999
Q ss_pred cCCC
Q 044338 394 LPKT 397 (704)
Q Consensus 394 fP~a 397 (704)
+|..
T Consensus 78 ~~~~ 81 (140)
T PF13610_consen 78 NPEG 81 (140)
T ss_pred cccc
Confidence 8864
No 13
>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=87.66 E-value=0.82 Score=50.27 Aligned_cols=56 Identities=11% Similarity=0.275 Sum_probs=49.6
Q ss_pred cCCcEeCCHHHHHHHHHHHHHHcCceEEEEeec-ceEEEEEeeccCCCceEEEEEEe
Q 044338 164 YHGQRFRDVSHFRKAIEVFAICDGFKLCVMENR-AHVVSYECFDLRCDWKIKAERVV 219 (704)
Q Consensus 164 ~vG~~F~s~~e~k~ai~~yAi~~~f~~rv~kS~-~~r~~~~C~~~gCpwrv~as~~~ 219 (704)
.-+..|++.++-+.+|+.|-++.+..|..+.|- .+.|+|.|.-..|||+|.++..+
T Consensus 23 ~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g 79 (496)
T PF04684_consen 23 AQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCG 79 (496)
T ss_pred ccccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeecc
Confidence 357789999999999999999999999888875 46799999999999999998644
No 14
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=82.22 E-value=1.1 Score=26.67 Aligned_cols=17 Identities=18% Similarity=0.263 Sum_probs=14.3
Q ss_pred ccCcccccCCCCCCCCC
Q 044338 661 RQCIENNSDAAINNPQW 677 (704)
Q Consensus 661 ~~Cs~C~~~gHn~~~~~ 677 (704)
++|-+|++.||...-++
T Consensus 1 ~~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCP 17 (18)
T ss_dssp SBCTTTSCSSSCGCTSS
T ss_pred CcCcCCCCcCcccccCc
Confidence 47999999999977665
No 15
>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=82.07 E-value=2.6 Score=33.00 Aligned_cols=46 Identities=13% Similarity=0.262 Sum_probs=25.2
Q ss_pred cCceEEEEeecceEEEEEeecc---CCCceEEEEEEecCceEEEEEecccccc
Q 044338 186 DGFKLCVMENRAHVVSYECFDL---RCDWKIKAERVVNGRTFIVTEFVAQHKC 235 (704)
Q Consensus 186 ~~f~~rv~kS~~~r~~~~C~~~---gCpwrv~as~~~~s~~w~I~~~~~~H~C 235 (704)
.|+.|...+.........|... +|+++|... .+...|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~----~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD----AGDGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE----CCCCEEEECCCccCC
Confidence 3777888777788889999864 899999876 333455556688987
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=80.87 E-value=2.2 Score=33.81 Aligned_cols=38 Identities=16% Similarity=0.289 Sum_probs=31.6
Q ss_pred eEEEEEeec-cCCCceEEEEEEecCceEEEEEecccccc
Q 044338 198 HVVSYECFD-LRCDWKIKAERVVNGRTFIVTEFVAQHKC 235 (704)
Q Consensus 198 ~r~~~~C~~-~gCpwrv~as~~~~s~~w~I~~~~~~H~C 235 (704)
-|.-+.|+. .+||++=.+.+..+++...++++.++|||
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 456689998 89999888877666777888899999998
No 17
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=75.73 E-value=8.3 Score=43.92 Aligned_cols=68 Identities=16% Similarity=0.209 Sum_probs=57.1
Q ss_pred CeEEEcCCCchHHHHHHhhcCCCcccccchhHHHH-HHHhCC-CchhHHHHhHhhccCCHHHHHHHHHHHHh
Q 044338 375 GLCIMGDGDNGIDYAVEEFLPKTVYRQCCLKIFTE-MVKRFP-TTPVEHFFWSACRSTSATSFNKYMDLIHN 444 (704)
Q Consensus 375 ~~~iitD~~~~l~~Ai~~vfP~a~~h~~C~~Hi~~-~~~~~~-~~~~~~~~~~~~~a~t~~eFe~~~~~l~~ 444 (704)
-+++.+|+...|.+++. .||.+ .|.+..+|+.+ +.+.++ .+.+...++++.+......++..++.+..
T Consensus 259 ~iiingDGa~WIk~~~~-~~~~~-~~~LD~FHl~k~i~~~~~~~~~~~~~~~~al~~~d~~~l~~~L~~~~~ 328 (470)
T PF06782_consen 259 KIIINGDGASWIKEGAE-FFPKA-EYFLDRFHLNKKIKQALSHDPELKEKIRKALKKGDKKKLETVLDTAES 328 (470)
T ss_pred EEEEeCCCcHHHHHHHH-hhcCc-eEEecHHHHHHHHHHHhhhChHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 46778899999988776 99999 99999999999 988875 45777778888888788888888887765
No 18
>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=71.01 E-value=3.7 Score=42.21 Aligned_cols=40 Identities=10% Similarity=0.020 Sum_probs=35.8
Q ss_pred cCeEEEcCCCchHHHHHHhhcCCCcccccchhHHHH-HHHhC
Q 044338 374 EGLCIMGDGDNGIDYAVEEFLPKTVYRQCCLKIFTE-MVKRF 414 (704)
Q Consensus 374 ~~~~iitD~~~~l~~Ai~~vfP~a~~h~~C~~Hi~~-~~~~~ 414 (704)
...+|++|...+...||.+.||+| .+..-.+|+++ +.+.+
T Consensus 56 ~v~~V~~Dm~~~y~~~~~~~~P~A-~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 56 NVKVVSMDMSPPYRSAIREYFPNA-QIVADRFHVVKLANRAL 96 (249)
T ss_pred ceEEEEcCCCcccccccccccccc-ccccccchhhhhhhhcc
Confidence 446899999999999999999999 99999999999 77644
No 19
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=44.94 E-value=18 Score=31.95 Aligned_cols=49 Identities=20% Similarity=0.218 Sum_probs=28.1
Q ss_pred EEEEecCceEEEeeccceeeeecccccc-----cccccchhhhhhhcccccccccc
Q 044338 553 LKLTDTTSIIFDLNMEAQSCNCGLWQIS-----GIPCAHACKGIQLIMGNVEEYVD 603 (704)
Q Consensus 553 yeV~~~~~~~~~V~L~~~tCSC~~fe~~-----GiPC~Halav~~~~~~~p~~yv~ 603 (704)
|.|--+.++.|.++++ -|||..|-.. .-||.|+|+.=...--.-.++|+
T Consensus 35 ~fVyvG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~ 88 (117)
T COG5431 35 FFVYVGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYID 88 (117)
T ss_pred EEEEEccccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEE
Confidence 4444443333446665 8999988732 35799998764443323334444
No 20
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=42.18 E-value=15 Score=25.33 Aligned_cols=21 Identities=10% Similarity=-0.062 Sum_probs=17.0
Q ss_pred cccccCcccccCCCCCCCCCC
Q 044338 658 SRARQCIENNSDAAINNPQWT 678 (704)
Q Consensus 658 kr~~~Cs~C~~~gHn~~~~~~ 678 (704)
...+.|-+|++.||-..-|+.
T Consensus 6 P~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 6 PPGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCCEeecCCCCCccHhHCCC
Confidence 346899999999998666665
No 21
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=38.76 E-value=20 Score=41.06 Aligned_cols=21 Identities=14% Similarity=0.139 Sum_probs=15.9
Q ss_pred ccccCcccccCCCC--CCCCCCC
Q 044338 659 RARQCIENNSDAAI--NNPQWTH 679 (704)
Q Consensus 659 r~~~Cs~C~~~gHn--~~~~~~~ 679 (704)
.+++|++|+|.||. +..||..
T Consensus 936 Ttr~C~nCGQvGHmkTNK~CP~f 958 (968)
T COG5179 936 TTRTCGNCGQVGHMKTNKACPKF 958 (968)
T ss_pred cceecccccccccccccccCccc
Confidence 47899999999997 3345543
No 22
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=37.49 E-value=63 Score=37.04 Aligned_cols=45 Identities=18% Similarity=0.384 Sum_probs=31.5
Q ss_pred eEEEEEecCceEEEeecc----ceeeeecccccccccccchhhhhhhcccc
Q 044338 551 TRLKLTDTTSIIFDLNME----AQSCNCGLWQISGIPCAHACKGIQLIMGN 597 (704)
Q Consensus 551 ~~yeV~~~~~~~~~V~L~----~~tCSC~~fe~~GiPC~Halav~~~~~~~ 597 (704)
-..+|..+..+.+.|.|. +.+|||.. ...| -|.|+.||+......
T Consensus 50 v~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~~ 98 (587)
T COG4715 50 VRAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLDD 98 (587)
T ss_pred EEEEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhhc
Confidence 344565554477778883 46899987 5544 699999998876543
No 23
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=32.10 E-value=21 Score=19.53 Aligned_cols=7 Identities=0% Similarity=-0.230 Sum_probs=3.4
Q ss_pred CCCCCcC
Q 044338 644 VNTLSMK 650 (704)
Q Consensus 644 ~GRpkk~ 650 (704)
+|||+|.
T Consensus 4 RGRP~k~ 10 (13)
T PF02178_consen 4 RGRPRKN 10 (13)
T ss_dssp SS--TT-
T ss_pred CCCCccc
Confidence 8999876
No 24
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=31.19 E-value=17 Score=37.19 Aligned_cols=23 Identities=26% Similarity=0.652 Sum_probs=19.2
Q ss_pred eeeeecccccccccccchhhhhhhcc
Q 044338 570 QSCNCGLWQISGIPCAHACKGIQLIM 595 (704)
Q Consensus 570 ~tCSC~~fe~~GiPC~Halav~~~~~ 595 (704)
..|||.-| -.||.|+-||..+..
T Consensus 125 ~dCSCPD~---anPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDY---ANPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCc---ccchHHHHHHHHHHH
Confidence 46999875 479999999998865
No 25
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=30.38 E-value=3.3e+02 Score=29.03 Aligned_cols=40 Identities=15% Similarity=0.175 Sum_probs=29.4
Q ss_pred CccceeeeceeeccCCCceeeeeeeecCCCCeEEEEEEEee
Q 044338 324 CRRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVH 364 (704)
Q Consensus 324 ~r~vi~iD~t~l~~~y~g~ll~a~g~D~~~~~~pla~alv~ 364 (704)
-..+.+.|-||+...-++-++.++-+|.... .+|||++-.
T Consensus 125 pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~ 164 (301)
T PRK09409 125 SNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTT 164 (301)
T ss_pred CCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEecc
Confidence 4578999999986654556777777887766 577887754
No 26
>PHA02517 putative transposase OrfB; Reviewed
Probab=27.75 E-value=1.9e+02 Score=30.12 Aligned_cols=42 Identities=14% Similarity=-0.040 Sum_probs=25.1
Q ss_pred CccceeeeceeeccCCCceeeeeeeecCCCCeEEEEEEEeecCC
Q 044338 324 CRRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVHVED 367 (704)
Q Consensus 324 ~r~vi~iD~t~l~~~y~g~ll~a~g~D~~~~~~pla~alv~~Et 367 (704)
-..+++.|.||+.... |..++++-+|.... +++||.+...++
T Consensus 109 pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~ 150 (277)
T PHA02517 109 PNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMD 150 (277)
T ss_pred CCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCC
Confidence 4568999999986543 44555555665443 345555554443
No 27
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=27.33 E-value=89 Score=29.25 Aligned_cols=17 Identities=12% Similarity=0.112 Sum_probs=13.4
Q ss_pred cccccchhHHHHHHHhh
Q 044338 473 TCVTLSITDKLRNYLHQ 489 (704)
Q Consensus 473 ~~~TtN~~ES~N~~lk~ 489 (704)
+...+|.+|++++.||.
T Consensus 109 ~~~h~n~ie~~~s~~K~ 125 (151)
T PF12762_consen 109 GGVHTNWIESFWSRLKR 125 (151)
T ss_pred cccccchhhhHHHHHHH
Confidence 34678889999888876
No 28
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=27.32 E-value=92 Score=26.00 Aligned_cols=30 Identities=20% Similarity=0.333 Sum_probs=26.5
Q ss_pred EeCCHHHHHHHHHHHHHHcCceEEEEeecc
Q 044338 168 RFRDVSHFRKAIEVFAICDGFKLCVMENRA 197 (704)
Q Consensus 168 ~F~s~~e~k~ai~~yAi~~~f~~rv~kS~~ 197 (704)
.|+|.+++-.+|..|+.+++-.+.+.+.+.
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~~ 42 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRDK 42 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecCC
Confidence 478999999999999999999999977653
No 29
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=26.31 E-value=39 Score=29.69 Aligned_cols=25 Identities=8% Similarity=0.037 Sum_probs=11.9
Q ss_pred CCCCcCcCCCC--C---CcccccCcccccC
Q 044338 645 NTLSMKGSNES--A---SSRARQCIENNSD 669 (704)
Q Consensus 645 GRpkk~Rr~es--~---~kr~~~Cs~C~~~ 669 (704)
||+|++||+.. + -.++.+|.+|+..
T Consensus 2 G~rr~krr~~ik~~~~~L~k~FtCp~Cghe 31 (104)
T COG4888 2 GRRRRKRRKIIKRRPQVLPKTFTCPRCGHE 31 (104)
T ss_pred CcccccccccCcccCccCCceEecCccCCe
Confidence 55555543332 1 1244566666543
No 30
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=26.16 E-value=3.5e+02 Score=28.19 Aligned_cols=40 Identities=15% Similarity=0.175 Sum_probs=28.1
Q ss_pred CccceeeeceeeccCCCceeeeeeeecCCCCeEEEEEEEee
Q 044338 324 CRRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVH 364 (704)
Q Consensus 324 ~r~vi~iD~t~l~~~y~g~ll~a~g~D~~~~~~pla~alv~ 364 (704)
-..+.+.|-||.....++-++.++-+|.... .++||++-.
T Consensus 86 pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~ 125 (262)
T PRK14702 86 SNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTT 125 (262)
T ss_pred CCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEecc
Confidence 3568899999987654446777777886665 566777653
No 31
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=23.82 E-value=58 Score=35.75 Aligned_cols=22 Identities=9% Similarity=0.206 Sum_probs=16.8
Q ss_pred CCcEeCCHHHHHHHHHHHHHHc
Q 044338 165 HGQRFRDVSHFRKAIEVFAICD 186 (704)
Q Consensus 165 vG~~F~s~~e~k~ai~~yAi~~ 186 (704)
+-..|++|-.+|--+.+|--..
T Consensus 252 LqLSFKNMCKLKPLL~KWLeEA 273 (398)
T KOG3802|consen 252 LQLSFKNMCKLKPLLEKWLEEA 273 (398)
T ss_pred hccCHHHHhhhHHHHHHHHHHH
Confidence 4455899999999888886554
No 32
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=21.84 E-value=49 Score=24.42 Aligned_cols=19 Identities=5% Similarity=-0.022 Sum_probs=16.3
Q ss_pred cccCcccccCCCCCCCCCC
Q 044338 660 ARQCIENNSDAAINNPQWT 678 (704)
Q Consensus 660 ~~~Cs~C~~~gHn~~~~~~ 678 (704)
...|.+|++.||-.+.|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4689999999999888873
No 33
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=21.83 E-value=50 Score=21.62 Aligned_cols=7 Identities=0% Similarity=-0.287 Sum_probs=6.4
Q ss_pred CCCCCcC
Q 044338 644 VNTLSMK 650 (704)
Q Consensus 644 ~GRpkk~ 650 (704)
+|||+|.
T Consensus 4 RGRPrK~ 10 (26)
T smart00384 4 RGRPRKA 10 (26)
T ss_pred CCCCCCC
Confidence 8999988
No 34
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=20.78 E-value=50 Score=25.75 Aligned_cols=31 Identities=6% Similarity=0.122 Sum_probs=24.4
Q ss_pred CcchHhhHHHHHhhcchH--------HHHHHhcCCCeEE
Q 044338 262 NLRTVDIRDEIKATYGFK--------DEMERINSRNIVL 292 (704)
Q Consensus 262 ~~~~~~i~~~i~~~~g~~--------~~l~~~NPgs~~~ 292 (704)
.|+..+++..++++.++. .+|++.||+++-+
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF~a 50 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFFKA 50 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHHHH
Confidence 456778888888887765 8899999988643
No 35
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=20.68 E-value=94 Score=20.82 Aligned_cols=16 Identities=13% Similarity=0.432 Sum_probs=9.2
Q ss_pred CCCCCCCChhhHHHHH
Q 044338 47 GNSANDTDRPEQLLKT 62 (704)
Q Consensus 47 ~~~~~~~~~~~~~~~~ 62 (704)
|..+.++|+||+.||.
T Consensus 3 GSddEeed~ea~r~re 18 (28)
T PF10587_consen 3 GSDDEEEDEEAERIRE 18 (28)
T ss_pred CCccccccHHHHHHHH
Confidence 4333346777777664
No 36
>PRK00766 hypothetical protein; Provisional
Probab=20.66 E-value=2.5e+02 Score=28.05 Aligned_cols=24 Identities=8% Similarity=0.098 Sum_probs=17.8
Q ss_pred cCeEEEcCCCc---hHHHHHHhhcCCC
Q 044338 374 EGLCIMGDGDN---GIDYAVEEFLPKT 397 (704)
Q Consensus 374 ~~~~iitD~~~---~l~~Ai~~vfP~a 397 (704)
.|..+++..-+ +|..|+.+.||+.
T Consensus 99 ~PVI~V~r~~p~~~~ie~AL~k~f~~~ 125 (194)
T PRK00766 99 LPVIVVMRKKPDFEAIESALKKHFSDW 125 (194)
T ss_pred CCEEEEEecCCCHHHHHHHHHHHCCCH
Confidence 56666744443 7899999999987
Done!