Query 043802
Match_columns 701
No_of_seqs 323 out of 1463
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 08:27:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043802.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043802hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 7.9E-71 1.7E-75 632.0 45.1 466 109-606 71-623 (846)
2 PF10551 MULE: MULE transposas 99.8 2E-21 4.3E-26 168.8 8.7 90 312-405 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.8 2.6E-20 5.6E-25 202.5 4.3 223 209-483 113-349 (381)
4 PF03108 DBD_Tnp_Mut: MuDR fam 99.7 4.4E-16 9.5E-21 126.2 8.9 67 109-175 1-67 (67)
5 COG3328 Transposase and inacti 99.5 6.9E-13 1.5E-17 141.7 15.8 222 208-483 98-328 (379)
6 smart00575 ZnF_PMZ plant mutat 98.9 1E-09 2.2E-14 72.0 2.2 27 564-590 1-27 (28)
7 PF08731 AFT: Transcription fa 98.8 3.6E-08 7.9E-13 85.2 9.2 69 118-186 1-111 (111)
8 PF03101 FAR1: FAR1 DNA-bindin 98.5 2.7E-07 5.8E-12 79.5 6.6 60 126-186 1-89 (91)
9 PF04434 SWIM: SWIM zinc finge 98.1 2.2E-06 4.8E-11 61.6 3.2 30 559-588 10-39 (40)
10 PF13610 DDE_Tnp_IS240: DDE do 96.3 0.0024 5.1E-08 59.7 2.3 80 305-390 1-80 (140)
11 PHA02517 putative transposase 96.1 0.39 8.4E-06 50.2 18.2 151 196-380 30-181 (277)
12 PRK14702 insertion element IS2 95.9 0.85 1.8E-05 47.4 19.4 151 191-380 7-164 (262)
13 PF06782 UPF0236: Uncharacteri 95.3 0.25 5.4E-06 55.8 13.8 130 345-482 235-376 (470)
14 PF03050 DDE_Tnp_IS66: Transpo 94.9 0.11 2.5E-06 54.1 9.2 148 192-410 4-156 (271)
15 PF01610 DDE_Tnp_ISL3: Transpo 94.3 0.093 2E-06 53.9 6.5 93 308-408 1-96 (249)
16 PF04684 BAF1_ABF1: BAF1 / ABF 92.9 0.21 4.5E-06 54.1 6.4 59 110-168 20-79 (496)
17 PRK09409 IS2 transposase TnpB; 92.9 2.3 5.1E-05 45.0 14.4 146 196-380 51-203 (301)
18 PF03106 WRKY: WRKY DNA -bindi 92.6 0.27 5.9E-06 38.5 5.1 39 147-185 21-59 (60)
19 COG3316 Transposase and inacti 90.0 3.9 8.5E-05 40.6 11.3 85 304-395 69-153 (215)
20 PF04500 FLYWCH: FLYWCH zinc f 86.3 1.4 3E-05 34.2 4.7 46 135-184 14-62 (62)
21 PF00665 rve: Integrase core d 85.4 4.5 9.8E-05 35.8 8.2 77 304-383 5-82 (120)
22 smart00774 WRKY DNA binding do 84.6 1.3 2.8E-05 34.6 3.6 38 147-184 21-59 (59)
23 PF13565 HTH_32: Homeodomain-l 81.0 3.6 7.9E-05 33.6 5.3 42 195-236 33-76 (77)
24 PF04937 DUF659: Protein of un 72.0 40 0.00087 31.9 10.2 63 346-410 73-138 (153)
25 COG5431 Uncharacterized metal- 68.7 8.9 0.00019 33.2 4.4 50 535-586 21-77 (117)
26 PF02178 AT_hook: AT hook moti 59.9 3.8 8.3E-05 21.8 0.4 9 649-657 3-11 (13)
27 COG4715 Uncharacterized conser 48.5 35 0.00076 38.6 5.9 42 547-590 52-97 (587)
28 PF12762 DDE_Tnp_IS1595: ISXO2 46.6 51 0.0011 30.7 6.1 69 307-382 5-88 (151)
29 COG4279 Uncharacterized conser 43.9 13 0.00028 37.6 1.6 23 564-589 125-147 (266)
30 smart00384 AT_hook DNA binding 42.4 15 0.00032 23.5 1.1 12 649-660 3-14 (26)
31 PRK13907 rnhA ribonuclease H; 40.5 1.6E+02 0.0034 26.4 8.2 78 307-388 3-81 (128)
32 PF13592 HTH_33: Winged helix- 39.8 42 0.0009 26.1 3.6 31 208-238 2-32 (60)
33 PF01498 HTH_Tnp_Tc3_2: Transp 31.3 38 0.00083 27.1 2.3 37 201-238 4-40 (72)
34 PF08766 DEK_C: DEK C terminal 31.2 1.1E+02 0.0024 23.1 4.7 39 195-233 3-43 (54)
35 PRK00766 hypothetical protein; 30.6 3.1E+02 0.0067 27.1 8.8 89 306-394 10-128 (194)
36 PF13276 HTH_21: HTH-like doma 24.1 1.6E+02 0.0035 22.6 4.6 42 197-238 6-48 (60)
37 PF14201 DUF4318: Domain of un 22.6 1.3E+02 0.0029 24.7 3.8 29 117-145 13-41 (74)
38 PF13551 HTH_29: Winged helix- 20.8 1.9E+02 0.004 24.9 4.9 40 199-238 64-109 (112)
39 KOG4027 Uncharacterized conser 20.6 1.3E+02 0.0029 28.4 3.8 35 310-344 70-107 (187)
40 PF04800 ETC_C1_NDUFA4: ETC co 20.3 1.2E+02 0.0026 26.5 3.4 33 113-149 50-82 (101)
41 PF13877 RPAP3_C: Potential Mo 20.1 75 0.0016 27.1 2.1 34 424-457 5-38 (94)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=7.9e-71 Score=632.04 Aligned_cols=466 Identities=15% Similarity=0.194 Sum_probs=379.3
Q ss_pred CccccCCceeCCHHHHHHHHHHHHHHcCeEEEEeeeCCc-------eEEEEEec--------------------------
Q 043802 109 KMIMRQGQLFRDEFQFRRAVEVFSLREGFKLCIIENGPD-------LIHLECSS-------------------------- 155 (701)
Q Consensus 109 ~~~~~vG~~F~s~~e~k~av~~yAi~~gf~~~~~ks~~~-------r~~~~C~~-------------------------- 155 (701)
...+.+||+|.|.++++++|..||...||.+++.++.+. ..+++|++
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 557999999999999999999999999999988654432 23466654
Q ss_pred --------CCCceEEEEEEecCCCeEEEEecCCCcccCCcCccccchHHHHHHHhhhhhcCCCCChHHHHHHHHHHhC--
Q 043802 156 --------LRCDWKIVGAKISTGNSFIVKDISLTHACHIKRAFKCTSKWIAANYLHLWKQNPETASVEVKQQIIQTFG-- 225 (701)
Q Consensus 156 --------~gCpwrv~as~~~~~~~w~V~~~~~~Hnc~~~~~~~~ss~~ia~~~~~~i~~~~~~~~~~i~~~l~~~~g-- 225 (701)
.||+++|++++. ..+.|.|+.+..+|||++.....++. ..+.+...+.+..+
T Consensus 151 ~~rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~~-----------------~~r~~~~~~~~~~~~~ 212 (846)
T PLN03097 151 TGRRSCAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVSE-----------------QTRKMYAAMARQFAEY 212 (846)
T ss_pred cccccccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccch-----------------hhhhhHHHHHhhhhcc
Confidence 479999999874 56889999999999999921111110 01111111111111
Q ss_pred --CcCChh----HHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhhCCCcEEEEEeccCCCCcccceEEEEEeeCcchhH
Q 043802 226 --VVCPEW----KIFKAEKRAQQLLGKDHVQGYTRLTQLKTEIERINSHNIVVLETKDEDSGCSKIFHRMFVCFHEPAFT 299 (701)
Q Consensus 226 --~~~s~~----~~~rak~~a~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~~~~~~~~~~~~f~~~F~~~~~~~~~ 299 (701)
+..... ..-+.|.+ +...| ....|.+||++++..||+|+|.+++| +++ +++++||+++.++.+
T Consensus 213 ~~v~~~~~d~~~~~~~~r~~--~~~~g----D~~~ll~yf~~~q~~nP~Ffy~~qlD-e~~----~l~niFWaD~~sr~~ 281 (846)
T PLN03097 213 KNVVGLKNDSKSSFDKGRNL--GLEAG----DTKILLDFFTQMQNMNSNFFYAVDLG-EDQ----RLKNLFWVDAKSRHD 281 (846)
T ss_pred ccccccchhhcchhhHHHhh--hcccc----hHHHHHHHHHHHHhhCCCceEEEEEc-cCC----CeeeEEeccHHHHHH
Confidence 000000 01111111 11123 35689999999999999999999999 777 999999999999999
Q ss_pred HhhcCcceEEEeceEEecccCceEEEEEEecCCCCeeEEEEEEeecCchhhHHHHHHHHHHHcccCCCCCeEEEecCCch
Q 043802 300 FKMNCRNFIAVDGWVINSVHKSVMLVAAALDGNNDILPIALAEVEIEDFTSWYFFLNNLNRALRRENGEGLCIITDGDNG 379 (701)
Q Consensus 300 f~~~~~~vi~iD~T~~~~~y~~~ll~a~g~d~~~~~~pla~alv~~E~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~ 379 (701)
|.+ |+|||.+|+||++|+|++||+.++|+|+|++++++||||+.+|+.|+|.|+|++|+++|++.. |.+||||++.+
T Consensus 282 Y~~-FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~--P~tIiTDqd~a 358 (846)
T PLN03097 282 YGN-FSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQA--PKVIITDQDKA 358 (846)
T ss_pred HHh-cCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCC--CceEEecCCHH
Confidence 998 999999999999999999999999999999999999999999999999999999999999988 99999999999
Q ss_pred HHHHHHhhCCCcceeechhhHHHHHHHhCCC-----CchhHHHHHHhh-cCCHHHHHHHHHHHHh-cCchhHHHHhhc--
Q 043802 380 VLEAIEDCIPLAHCRQCCCSIYNQMLVQFPD-----PPVKDLFWAACR-STSEVQFTRYIKMIQS-SSIECHQWLFQT-- 450 (701)
Q Consensus 380 l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~-----~~~~~~~~~~~~-a~~~~eFe~~~~~l~~-~~~~~~~~L~~~-- 450 (701)
|.+||++|||++.|++|+|||++|+.++++. +.|...|+.+++ +.+++||+..|..|.. ++...++||+.+
T Consensus 359 m~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~ 438 (846)
T PLN03097 359 MKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYE 438 (846)
T ss_pred HHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHH
Confidence 9999999999999999999999999999863 588999999877 5699999999999865 578999999998
Q ss_pred cCccccccccCccccccccccchhhhHhhHhhhc--cccCHHHHHHHHHHHHHHH-H-HHHhhh--------------cc
Q 043802 451 QWKKWALHCMPVWVKCTNVTIMLTVYLRNSFAKF--FSLSIADRFAAISSFIADT-Y-ERRRLS--------------GW 512 (701)
Q Consensus 451 ~~e~W~~a~~~~~~~~~~~T~N~~Es~N~~lk~~--r~~pi~~lle~ir~~~~~~-~-~rr~~~--------------~~ 512 (701)
.+++|+++|+++.+..|+.||+++||+|++|++. +..+|..|++.+-..+..+ . +..... .+
T Consensus 439 ~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piE 518 (846)
T PLN03097 439 DRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLE 518 (846)
T ss_pred hHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHH
Confidence 8999999999999999999999999999999984 6788888888876666554 1 111110 02
Q ss_pred cccCCCCCHHHHHHHHHHHHcCceEEEEEeCC----ceEEEEeCC-CcEEEEEec----CceeccccccccCCCchhHhH
Q 043802 513 NWLRNKITPSVQQQIRNRVIQGQQIRILYSTG----RQMKVEDTD-SMTYEVDIT----SMTCTCRLWQLSGIPCSHACR 583 (701)
Q Consensus 513 ~~~~~~~tp~~~~~l~~~~~~a~~~~V~~~~~----~~feV~~~~-~~~~~V~l~----~~tCsC~~~~~~GiPC~Hala 583 (701)
++++..|||.+|++||+++..+..|.+...+. .+|.|...+ ...|.|..+ +.+|+|++|+..||||+|||.
T Consensus 519 kQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLk 598 (846)
T PLN03097 519 KSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALV 598 (846)
T ss_pred HHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHH
Confidence 44458999999999999999999998876432 368887643 356777654 689999999999999999999
Q ss_pred HHHHcCC--CchhhhhhhccHHHHH
Q 043802 584 CLEELGE--NIEDNVHQLFSMDQYR 606 (701)
Q Consensus 584 v~~~~~~--~~~~yv~~~ys~~~~~ 606 (701)
|+...++ .|+.||.++|+..+-.
T Consensus 599 VL~~~~v~~IP~~YILkRWTKdAK~ 623 (846)
T PLN03097 599 VLQMCQLSAIPSQYILKRWTKDAKS 623 (846)
T ss_pred HHhhcCcccCchhhhhhhchhhhhh
Confidence 9999998 5999999999988754
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=99.85 E-value=2e-21 Score=168.84 Aligned_cols=90 Identities=29% Similarity=0.433 Sum_probs=86.2
Q ss_pred ceEEecccCceEEE---EEEecCCCCeeEEEEEEeecCchhhHHHHHHHHHHHcccCCCCCeEEEecCCchHHHHHHhhC
Q 043802 312 GWVINSVHKSVMLV---AAALDGNNDILPIALAEVEIEDFTSWYFFLNNLNRALRRENGEGLCIITDGDNGVLEAIEDCI 388 (701)
Q Consensus 312 ~T~~~~~y~~~ll~---a~g~d~~~~~~pla~alv~~E~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vf 388 (701)
|||++|+| ++++. ++|+|++|+.+|+||+++++|+.++|.|||+.|++.++.. |.+||||+++|+++||+++|
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~---p~~ii~D~~~~~~~Ai~~vf 76 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK---PKVIISDFDKALINAIKEVF 76 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC---ceeeeccccHHHHHHHHHHC
Confidence 79999999 98886 9999999999999999999999999999999999999873 89999999999999999999
Q ss_pred CCcceeechhhHHHHHH
Q 043802 389 PLAHCRQCCCSIYNQML 405 (701)
Q Consensus 389 P~a~h~~C~~Hi~~n~~ 405 (701)
|++.|++|.||+.+|++
T Consensus 77 P~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 77 PDARHQLCLFHILRNIK 93 (93)
T ss_pred CCceEehhHHHHHHhhC
Confidence 99999999999999975
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=99.79 E-value=2.6e-20 Score=202.55 Aligned_cols=223 Identities=15% Similarity=0.212 Sum_probs=185.3
Q ss_pred CCCChHHHHHHHHHHhC-CcCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhhCCCcEEEEEeccCCCCcccceE
Q 043802 209 PETASVEVKQQIIQTFG-VVCPEWKIFKAEKRAQQLLGKDHVQGYTRLTQLKTEIERINSHNIVVLETKDEDSGCSKIFH 287 (701)
Q Consensus 209 ~~~~~~~i~~~l~~~~g-~~~s~~~~~rak~~a~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~~~~~~~~~~~~f~ 287 (701)
.+++.++|.+.++.-+| ..+|.+++.|......+. +..|... +-+
T Consensus 113 ~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~-----------~~~w~~R---------------~L~-------- 158 (381)
T PF00872_consen 113 KGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEE-----------VEAWRNR---------------PLE-------- 158 (381)
T ss_pred cccccccccchhhhhhcccccCchhhhhhhhhhhhh-----------HHHHhhh---------------ccc--------
Confidence 58899999999999999 889999988766554321 1111111 001
Q ss_pred EEEEeeCcchhHHhhcC-cceEEEeceEEecccC-----ceEEEEEEecCCCCeeEEEEEEeecCchhhHHHHHHHHHHH
Q 043802 288 RMFVCFHEPAFTFKMNC-RNFIAVDGWVINSVHK-----SVMLVAAALDGNNDILPIALAEVEIEDFTSWYFFLNNLNRA 361 (701)
Q Consensus 288 ~~F~~~~~~~~~f~~~~-~~vi~iD~T~~~~~y~-----~~ll~a~g~d~~~~~~pla~alv~~E~~es~~wfl~~l~~~ 361 (701)
.. -++|++||+|.+.+.+ ..+++++|+|.+|+..+||+.+...|+.++|.-||+.|++.
T Consensus 159 ---------------~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R 223 (381)
T PF00872_consen 159 ---------------SEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER 223 (381)
T ss_pred ---------------cccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc
Confidence 13 4899999999987643 46899999999999999999999999999999999999988
Q ss_pred cccCCCCCeEEEecCCchHHHHHHhhCCCcceeechhhHHHHHHHhCCCC---chhHHHHHHhhcCCHHHHHHHHHHHHh
Q 043802 362 LRRENGEGLCIITDGDNGVLEAIEDCIPLAHCRQCCCSIYNQMLVQFPDP---PVKDLFWAACRSTSEVQFTRYIKMIQS 438 (701)
Q Consensus 362 ~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~---~~~~~~~~~~~a~~~~eFe~~~~~l~~ 438 (701)
.... |..||+|+++||.+||.++||.+.++.|++|+++|+.+++..+ .+...++.+..+.+.++....++.+.+
T Consensus 224 Gl~~---~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~ 300 (381)
T PF00872_consen 224 GLKD---ILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAE 300 (381)
T ss_pred cccc---cceeeccccccccccccccccchhhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhccc
Confidence 5443 7999999999999999999999999999999999999999754 677888888888888888888877654
Q ss_pred ----cCchhHHHHhhccCccccccccCccccccccccchhhhHhhHhhh
Q 043802 439 ----SSIECHQWLFQTQWKKWALHCMPVWVKCTNVTIMLTVYLRNSFAK 483 (701)
Q Consensus 439 ----~~~~~~~~L~~~~~e~W~~a~~~~~~~~~~~T~N~~Es~N~~lk~ 483 (701)
.+|.+.++|.+...+.|+..-|+...+--+.|||.+||+|+.||.
T Consensus 301 ~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irr 349 (381)
T PF00872_consen 301 KWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRR 349 (381)
T ss_pred ccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhh
Confidence 478899999998888888877877766678999999999999987
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=99.65 E-value=4.4e-16 Score=126.21 Aligned_cols=67 Identities=19% Similarity=0.524 Sum_probs=65.1
Q ss_pred CccccCCceeCCHHHHHHHHHHHHHHcCeEEEEeeeCCceEEEEEecCCCceEEEEEEecCCCeEEE
Q 043802 109 KMIMRQGQLFRDEFQFRRAVEVFSLREGFKLCIIENGPDLIHLECSSLRCDWKIVGAKISTGNSFIV 175 (701)
Q Consensus 109 ~~~~~vG~~F~s~~e~k~av~~yAi~~gf~~~~~ks~~~r~~~~C~~~gCpwrv~as~~~~~~~w~V 175 (701)
+|.|.+||+|+|++||+.||..||+.++|++++.+|+++|++++|...||||+|+|++.++++.|+|
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 5789999999999999999999999999999999999999999999999999999999999999986
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.47 E-value=6.9e-13 Score=141.69 Aligned_cols=222 Identities=12% Similarity=0.106 Sum_probs=172.7
Q ss_pred CCCCChHHHHHHHHHHhCCcCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhhCCCcEEEEEeccCCCCcccceE
Q 043802 208 NPETASVEVKQQIIQTFGVVCPEWKIFKAEKRAQQLLGKDHVQGYTRLTQLKTEIERINSHNIVVLETKDEDSGCSKIFH 287 (701)
Q Consensus 208 ~~~~~~~~i~~~l~~~~g~~~s~~~~~rak~~a~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~~~~~~~~~~~~f~ 287 (701)
..+++++++.+.+++.++..++...+.+.-.... ..+.+++..-.
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~---------------e~v~~~~~r~l-------------------- 142 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVTDRLD---------------EKVKAWQNRPL-------------------- 142 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHH---------------HHHHHHHhccc--------------------
Confidence 3689999999999999988777766655433332 23333322110
Q ss_pred EEEEeeCcchhHHhhcCcceEEEeceEEecc--cCceEEEEEEecCCCCeeEEEEEEeecCchhhHHHHHHHHHHHcccC
Q 043802 288 RMFVCFHEPAFTFKMNCRNFIAVDGWVINSV--HKSVMLVAAALDGNNDILPIALAEVEIEDFTSWYFFLNNLNRALRRE 365 (701)
Q Consensus 288 ~~F~~~~~~~~~f~~~~~~vi~iD~T~~~~~--y~~~ll~a~g~d~~~~~~pla~alv~~E~~es~~wfl~~l~~~~~~~ 365 (701)
+..+++++|++|++-+ -+..+++|+|++.+|+-..+|+.+-..|+ ..|.-||..|+...-..
T Consensus 143 ---------------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl~~ 206 (379)
T COG3328 143 ---------------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGLSD 206 (379)
T ss_pred ---------------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccccc
Confidence 2668999999999988 46789999999999999999999999999 99998888888875443
Q ss_pred CCCCeEEEecCCchHHHHHHhhCCCcceeechhhHHHHHHHhCCCC---chhHHHHHHhhcCCHHHHHHHHHHH----Hh
Q 043802 366 NGEGLCIITDGDNGVLEAIEDCIPLAHCRQCCCSIYNQMLVQFPDP---PVKDLFWAACRSTSEVQFTRYIKMI----QS 438 (701)
Q Consensus 366 ~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~---~~~~~~~~~~~a~~~~eFe~~~~~l----~~ 438 (701)
...+++|+.+|+.+||..+||.+.++.|..|+.+|+..+...+ .+...+..+..+.+.++-...|..+ ..
T Consensus 207 ---v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~ 283 (379)
T COG3328 207 ---VLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGK 283 (379)
T ss_pred ---eeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhh
Confidence 4677789999999999999999999999999999999998766 3344455555566666655555554 44
Q ss_pred cCchhHHHHhhccCccccccccCccccccccccchhhhHhhHhhh
Q 043802 439 SSIECHQWLFQTQWKKWALHCMPVWVKCTNVTIMLTVYLRNSFAK 483 (701)
Q Consensus 439 ~~~~~~~~L~~~~~e~W~~a~~~~~~~~~~~T~N~~Es~N~~lk~ 483 (701)
..|....|+.+..-+.|...-|+...+--+.|||..|++|+.++.
T Consensus 284 ~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 284 RYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred hcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 568888888887777777777777655568999999999998775
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.87 E-value=1e-09 Score=71.98 Aligned_cols=27 Identities=52% Similarity=0.988 Sum_probs=25.1
Q ss_pred ceeccccccccCCCchhHhHHHHHcCC
Q 043802 564 MTCTCRLWQLSGIPCSHACRCLEELGE 590 (701)
Q Consensus 564 ~tCsC~~~~~~GiPC~Halav~~~~~~ 590 (701)
.+|||++|+..||||+|+|+|+...++
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=98.77 E-value=3.6e-08 Score=85.19 Aligned_cols=69 Identities=13% Similarity=0.283 Sum_probs=65.5
Q ss_pred eCCHHHHHHHHHHHHHHcCeEEEEeeeCCceEEEEEec------------------------------------------
Q 043802 118 FRDEFQFRRAVEVFSLREGFKLCIIENGPDLIHLECSS------------------------------------------ 155 (701)
Q Consensus 118 F~s~~e~k~av~~yAi~~gf~~~~~ks~~~r~~~~C~~------------------------------------------ 155 (701)
|.+++|++.||+.++...|+++.+.+|+...+.++|..
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 88999999999999999999999999999999999983
Q ss_pred CCCceEEEEEEecCCCeEEEEecCCCcccCC
Q 043802 156 LRCDWKIVGAKISTGNSFIVKDISLTHACHI 186 (701)
Q Consensus 156 ~gCpwrv~as~~~~~~~w~V~~~~~~Hnc~~ 186 (701)
..|||+|+|......+.|.|..++..|+|++
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 2799999999999999999999999999974
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=98.49 E-value=2.7e-07 Score=79.53 Aligned_cols=60 Identities=17% Similarity=0.290 Sum_probs=53.4
Q ss_pred HHHHHHHHHcCeEEEEeeeCCc-------eEEEEEec----------------------CCCceEEEEEEecCCCeEEEE
Q 043802 126 RAVEVFSLREGFKLCIIENGPD-------LIHLECSS----------------------LRCDWKIVGAKISTGNSFIVK 176 (701)
Q Consensus 126 ~av~~yAi~~gf~~~~~ks~~~-------r~~~~C~~----------------------~gCpwrv~as~~~~~~~w~V~ 176 (701)
++|..||...||.++..++.+. ++.++|.+ .||||+|.+.+.. ++.|.|+
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 4799999999999999876654 78899985 4899999999987 9999999
Q ss_pred ecCCCcccCC
Q 043802 177 DISLTHACHI 186 (701)
Q Consensus 177 ~~~~~Hnc~~ 186 (701)
.+..+|||++
T Consensus 80 ~~~~~HNH~L 89 (91)
T PF03101_consen 80 SFVLEHNHPL 89 (91)
T ss_pred ECcCCcCCCC
Confidence 9999999986
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=98.12 E-value=2.2e-06 Score=61.65 Aligned_cols=30 Identities=37% Similarity=0.795 Sum_probs=27.2
Q ss_pred EEecCceeccccccccCCCchhHhHHHHHc
Q 043802 559 VDITSMTCTCRLWQLSGIPCSHACRCLEEL 588 (701)
Q Consensus 559 V~l~~~tCsC~~~~~~GiPC~Halav~~~~ 588 (701)
+++...+|||..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 667789999999999999999999998764
No 10
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=96.27 E-value=0.0024 Score=59.73 Aligned_cols=80 Identities=21% Similarity=0.116 Sum_probs=66.5
Q ss_pred cceEEEeceEEecccCceEEEEEEecCCCCeeEEEEEEeecCchhhHHHHHHHHHHHcccCCCCCeEEEecCCchHHHHH
Q 043802 305 RNFIAVDGWVINSVHKSVMLVAAALDGNNDILPIALAEVEIEDFTSWYFFLNNLNRALRRENGEGLCIITDGDNGVLEAI 384 (701)
Q Consensus 305 ~~vi~iD~T~~~~~y~~~ll~a~g~d~~~~~~pla~alv~~E~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai 384 (701)
++.+.+|-||.+-+-+ ..+...++|.+++ .|.+-|...-+...=..||..+.+.... .|..|+||+.++...|+
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~~---~p~~ivtDk~~aY~~A~ 74 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHRG---EPRVIVTDKLPAYPAAI 74 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeecc---ccceeecccCCccchhh
Confidence 3678999999986543 3455778899999 8999999999988888999888777652 38999999999999999
Q ss_pred HhhCCC
Q 043802 385 EDCIPL 390 (701)
Q Consensus 385 ~~vfP~ 390 (701)
++++|.
T Consensus 75 ~~l~~~ 80 (140)
T PF13610_consen 75 KELNPE 80 (140)
T ss_pred hhcccc
Confidence 999876
No 11
>PHA02517 putative transposase OrfB; Reviewed
Probab=96.09 E-value=0.39 Score=50.21 Aligned_cols=151 Identities=15% Similarity=0.073 Sum_probs=83.7
Q ss_pred HHHHHHhhhhhc-CCCCChHHHHHHHHHHhCCcCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhhCCCcEEEEE
Q 043802 196 WIAANYLHLWKQ-NPETASVEVKQQIIQTFGVVCPEWKIFKAEKRAQQLLGKDHVQGYTRLTQLKTEIERINSHNIVVLE 274 (701)
Q Consensus 196 ~ia~~~~~~i~~-~~~~~~~~i~~~l~~~~g~~~s~~~~~rak~~a~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~ 274 (701)
.+.+.+.+++.. .+.+..+.|...|++. |+.++.++++|..+.+ |-.... . ..-.....+-...
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~-----gl~~~~-~------~k~~~~~~~~~~~-- 94 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKEL-----GLAGVL-R------GKKVRTTISRKAV-- 94 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHc-----CCceEe-c------CCCcCCCCCCCCC--
Confidence 455666666654 5788999999988755 9999999988754332 210000 0 0000000000000
Q ss_pred eccCCCCcccceEEEEEeeCcchhHHhhcCcceEEEeceEEecccCceEEEEEEecCCCCeeEEEEEEeecCchhhHHHH
Q 043802 275 TKDEDSGCSKIFHRMFVCFHEPAFTFKMNCRNFIAVDGWVINSVHKSVMLVAAALDGNNDILPIALAEVEIEDFTSWYFF 354 (701)
Q Consensus 275 ~~~~~~~~~~~f~~~F~~~~~~~~~f~~~~~~vi~iD~T~~~~~y~~~ll~a~g~d~~~~~~pla~alv~~E~~es~~wf 354 (701)
. ..+ .+.+-|-+ .....+++.|.|+..... +..+..+.+|...+ +++|+.+...++.+...-+
T Consensus 95 ~--~~n----~~~r~f~~---------~~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~ 157 (277)
T PHA02517 95 A--APD----RVNRQFVA---------TRPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDA 157 (277)
T ss_pred C--CCC----cccCCCCC---------CCCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHH
Confidence 0 000 11221211 124578999999986543 55677777887666 4678888887777755444
Q ss_pred HHHHHHHcccCCCCCeEEEecCCchH
Q 043802 355 LNNLNRALRRENGEGLCIITDGDNGV 380 (701)
Q Consensus 355 l~~l~~~~~~~~~~~~~iisD~~~~l 380 (701)
|+......+... +.+|.||+....
T Consensus 158 l~~a~~~~~~~~--~~i~~sD~G~~y 181 (277)
T PHA02517 158 LEQALWARGRPG--GLIHHSDKGSQY 181 (277)
T ss_pred HHHHHHhcCCCc--CcEeeccccccc
Confidence 444433333222 467789998754
No 12
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=95.90 E-value=0.85 Score=47.36 Aligned_cols=151 Identities=10% Similarity=-0.005 Sum_probs=90.2
Q ss_pred ccchHHHHHHHhhhhhcCCCCChHHHHHHHHHH---hCC-cCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhhC
Q 043802 191 KCTSKWIAANYLHLWKQNPETASVEVKQQIIQT---FGV-VCPEWKIFKAEKRAQQLLGKDHVQGYTRLTQLKTEIERIN 266 (701)
Q Consensus 191 ~~ss~~ia~~~~~~i~~~~~~~~~~i~~~l~~~---~g~-~~s~~~~~rak~~a~~~~~g~~~~~y~~L~~~~~~l~~~N 266 (701)
......+...+.+....++.+..+.|...|++. .|+ .++.+.++|..+.+ |-. ...+...
T Consensus 7 ~~~~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~-----gL~-----------~~~r~~~ 70 (262)
T PRK14702 7 HTDDTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQN-----ALL-----------LERKPAV 70 (262)
T ss_pred CcchHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHh-----CCc-----------cccCCCC
Confidence 334455666777776777889999999988875 377 48988888764432 100 0000000
Q ss_pred CCcEEEEEeccCCCCcccceEEEEEeeCcchhHHhhcCcceEEEeceEEecccCceEEEEEEecCCCCeeEEEEEEeec-
Q 043802 267 SHNIVVLETKDEDSGCSKIFHRMFVCFHEPAFTFKMNCRNFIAVDGWVINSVHKSVMLVAAALDGNNDILPIALAEVEI- 345 (701)
Q Consensus 267 Pg~~~~v~~~~~~~~~~~~f~~~F~~~~~~~~~f~~~~~~vi~iD~T~~~~~y~~~ll~a~g~d~~~~~~pla~alv~~- 345 (701)
+.+. .. ... .|. ...-..+++.|-||.....++.++.++-+|...+ .+|||++...
T Consensus 71 ~~~~--------~~----~~~-~~~---------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~ 127 (262)
T PRK14702 71 PPSK--------RA----HTG-RVA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGG 127 (262)
T ss_pred CCCC--------cC----CCC-ccc---------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCc
Confidence 0000 00 000 000 1114578999999987655557888888998877 6789999874
Q ss_pred CchhhHHHHHHHH-HHHccc-CCCCCeEEEecCCchH
Q 043802 346 EDFTSWYFFLNNL-NRALRR-ENGEGLCIITDGDNGV 380 (701)
Q Consensus 346 E~~es~~wfl~~l-~~~~~~-~~~~~~~iisD~~~~l 380 (701)
.+.+.-.-+|+.. ....+. .+..|.+|.||+...-
T Consensus 128 ~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy 164 (262)
T PRK14702 128 FNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 164 (262)
T ss_pred CCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCccc
Confidence 5666655555543 333221 1224789999998743
No 13
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=95.33 E-value=0.25 Score=55.75 Aligned_cols=130 Identities=13% Similarity=0.153 Sum_probs=93.2
Q ss_pred cCchhhHHHHHHHHHHHcccCCCCCeEEEecCCchHHHHHHhhCCCcceeechhhHHHHHHHhCC-CCchhHHHHHHhhc
Q 043802 345 IEDFTSWYFFLNNLNRALRRENGEGLCIITDGDNGVLEAIEDCIPLAHCRQCCCSIYNQMLVQFP-DPPVKDLFWAACRS 423 (701)
Q Consensus 345 ~E~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~-~~~~~~~~~~~~~a 423 (701)
..+.+-|.-+++.+-+.....+..-+++.+|+...|.+++. .+|.+.|.+..+|+.+.+.+.++ .+.+...++++.+.
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~al~~ 313 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKALKK 313 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHHHHh
Confidence 45677899888888888765542346788999999988776 99999999999999999999886 45777778888888
Q ss_pred CCHHHHHHHHHHHHhcC--c-------hhHHHHhhccCccccc--cccCccccccccccchhhhHhhHhh
Q 043802 424 TSEVQFTRYIKMIQSSS--I-------ECHQWLFQTQWKKWAL--HCMPVWVKCTNVTIMLTVYLRNSFA 482 (701)
Q Consensus 424 ~~~~eFe~~~~~l~~~~--~-------~~~~~L~~~~~e~W~~--a~~~~~~~~~~~T~N~~Es~N~~lk 482 (701)
....+++..++.+.... + ++..||.. +|.. .|.. +-|.......|+.++.+.
T Consensus 314 ~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~----n~~~i~~y~~---~~~~~g~g~ee~~~~~~s 376 (470)
T PF06782_consen 314 GDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLN----NWDGIKPYRE---REGLRGIGAEESVSHVLS 376 (470)
T ss_pred cCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHH----CHHHhhhhhh---ccCCCccchhhhhhhHHH
Confidence 88899888888876542 2 23445554 3332 1111 123344455777777664
No 14
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=94.93 E-value=0.11 Score=54.05 Aligned_cols=148 Identities=11% Similarity=0.042 Sum_probs=90.1
Q ss_pred cchHHHHHHHhhhhhcCCCCChHHHHHHHHHHhCCcCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhhCCCcEE
Q 043802 192 CTSKWIAANYLHLWKQNPETASVEVKQQIIQTFGVVCPEWKIFKAEKRAQQLLGKDHVQGYTRLTQLKTEIERINSHNIV 271 (701)
Q Consensus 192 ~ss~~ia~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~s~~~~~rak~~a~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~ 271 (701)
++.+.+|-.+..... -.++...|.+.+.+. |+.+|...+.+.-.++.+.+ ....+.|.+.
T Consensus 4 ~g~~~~a~i~~l~~~--~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l-----------~~~~~~l~~~------ 63 (271)
T PF03050_consen 4 YGPSLLALIAYLKYV--YHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEAL-----------KPLYEALKEE------ 63 (271)
T ss_pred CCHHHHHHHHHHHhc--CCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhh-----------hhhhhhhhhh------
Confidence 344555544433332 455667777777777 99999999887765554321 1111111111
Q ss_pred EEEeccCCCCcccceEEEEEeeCcchhHHhhcCcceEEEeceEEe----ccc-CceEEEEEEecCCCCeeEEEEEEeecC
Q 043802 272 VLETKDEDSGCSKIFHRMFVCFHEPAFTFKMNCRNFIAVDGWVIN----SVH-KSVMLVAAALDGNNDILPIALAEVEIE 346 (701)
Q Consensus 272 ~v~~~~~~~~~~~~f~~~F~~~~~~~~~f~~~~~~vi~iD~T~~~----~~y-~~~ll~a~g~d~~~~~~pla~alv~~E 346 (701)
. . -.+|+.+|-|... ++. ++-+-++++-+ .+.|.+.++-
T Consensus 64 ----------------------------~-~-~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR 107 (271)
T PF03050_consen 64 ----------------------------L-R-SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSR 107 (271)
T ss_pred ----------------------------c-c-ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccc
Confidence 0 1 3578889988877 433 33444444433 5556666655
Q ss_pred chhhHHHHHHHHHHHcccCCCCCeEEEecCCchHHHHHHhhCCCcceeechhhHHHHHHHhCCC
Q 043802 347 DFTSWYFFLNNLNRALRRENGEGLCIITDGDNGVLEAIEDCIPLAHCRQCCCSIYNQMLVQFPD 410 (701)
Q Consensus 347 ~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~ 410 (701)
+.+...-+| ++. .-+++||+-.+-.. +..+.|+.|+.|+.+.+.+....
T Consensus 108 ~~~~~~~~L-------~~~---~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 108 SSKVIKEFL-------GDF---SGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred cccchhhhh-------ccc---ceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 555544443 332 45899999987655 23889999999999999886654
No 15
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.29 E-value=0.093 Score=53.92 Aligned_cols=93 Identities=16% Similarity=0.142 Sum_probs=68.2
Q ss_pred EEEeceEEecccCceEEEEEEecC--CCCeeEEEEEEeecCchhhHHHHHHHH-HHHcccCCCCCeEEEecCCchHHHHH
Q 043802 308 IAVDGWVINSVHKSVMLVAAALDG--NNDILPIALAEVEIEDFTSWYFFLNNL-NRALRRENGEGLCIITDGDNGVLEAI 384 (701)
Q Consensus 308 i~iD~T~~~~~y~~~ll~a~g~d~--~~~~~pla~alv~~E~~es~~wfl~~l-~~~~~~~~~~~~~iisD~~~~l~~Ai 384 (701)
|+||=+.....+.. ++.+.+|. +++. -++++++-+.++..-||..+ -..... ...+|++|...+...||
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~---il~i~~~r~~~~l~~~~~~~~~~~~~~---~v~~V~~Dm~~~y~~~~ 72 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGR---ILDILPGRDKETLKDFFRSLYPEEERK---NVKVVSMDMSPPYRSAI 72 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCce---EEEEcCCccHHHHHHHHHHhCcccccc---ceEEEEcCCCccccccc
Confidence 57887777654443 44444554 3332 23578888888888777766 333222 37899999999999999
Q ss_pred HhhCCCcceeechhhHHHHHHHhC
Q 043802 385 EDCIPLAHCRQCCCSIYNQMLVQF 408 (701)
Q Consensus 385 ~~vfP~a~h~~C~~Hi~~n~~~~~ 408 (701)
++.||+|.+..-.|||++++.+.+
T Consensus 73 ~~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 73 REYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred cccccccccccccchhhhhhhhcc
Confidence 999999999999999999887744
No 16
>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=92.92 E-value=0.21 Score=54.13 Aligned_cols=59 Identities=10% Similarity=0.190 Sum_probs=52.5
Q ss_pred ccccCCceeCCHHHHHHHHHHHHHHcCeEEEEeeeCC-ceEEEEEecCCCceEEEEEEec
Q 043802 110 MIMRQGQLFRDEFQFRRAVEVFSLREGFKLCIIENGP-DLIHLECSSLRCDWKIVGAKIS 168 (701)
Q Consensus 110 ~~~~vG~~F~s~~e~k~av~~yAi~~gf~~~~~ks~~-~r~~~~C~~~gCpwrv~as~~~ 168 (701)
+.-..+..|++.++-+.+|..|-+..+..|..+.|-+ +.|+|.|....|||+|.++..+
T Consensus 20 ~~~~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g 79 (496)
T PF04684_consen 20 PQSAQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCG 79 (496)
T ss_pred cccccccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeecc
Confidence 3445678899999999999999999999999988875 7899999999999999998764
No 17
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=92.87 E-value=2.3 Score=45.03 Aligned_cols=146 Identities=11% Similarity=0.028 Sum_probs=87.6
Q ss_pred HHHHHHhhhhhcCCCCChHHHHHHHHHHh---CC-cCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhhCCCcEE
Q 043802 196 WIAANYLHLWKQNPETASVEVKQQIIQTF---GV-VCPEWKIFKAEKRAQQLLGKDHVQGYTRLTQLKTEIERINSHNIV 271 (701)
Q Consensus 196 ~ia~~~~~~i~~~~~~~~~~i~~~l~~~~---g~-~~s~~~~~rak~~a~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~ 271 (701)
.+...+.++....+.+..+.|...|++.. |+ .++.++++|..+.+ |-.. ......+.+.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~-----Gl~~-----------~~~~~~~~~~- 113 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQN-----ALLL-----------ERKPAVPPSK- 113 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHc-----CCcc-----------cccCCCCCCC-
Confidence 45556666666678899999999887652 66 58888887754332 1000 0000000000
Q ss_pred EEEeccCCCCcccceEEEEEeeCcchhHHhhcCcceEEEeceEEecccCceEEEEEEecCCCCeeEEEEEEeec-Cchhh
Q 043802 272 VLETKDEDSGCSKIFHRMFVCFHEPAFTFKMNCRNFIAVDGWVINSVHKSVMLVAAALDGNNDILPIALAEVEI-EDFTS 350 (701)
Q Consensus 272 ~v~~~~~~~~~~~~f~~~F~~~~~~~~~f~~~~~~vi~iD~T~~~~~y~~~ll~a~g~d~~~~~~pla~alv~~-E~~es 350 (701)
.. .... |. ...-..+++.|-||....-++.++.++-+|...+ .+|||++... .+.+.
T Consensus 114 -------~~----~~~~-~~---------~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~ 171 (301)
T PRK09409 114 -------RA----HTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSET 171 (301)
T ss_pred -------CC----CCCC-cC---------CCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHH
Confidence 00 0000 00 1125689999999986654557888888998887 6899999876 56666
Q ss_pred HHHHHHH-HHHHccc-CCCCCeEEEecCCchH
Q 043802 351 WYFFLNN-LNRALRR-ENGEGLCIITDGDNGV 380 (701)
Q Consensus 351 ~~wfl~~-l~~~~~~-~~~~~~~iisD~~~~l 380 (701)
-.-+|+. +....+. .+..|.+|.||+...-
T Consensus 172 v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 172 VQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred HHHHHHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 5556654 4444332 1224789999998743
No 18
>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=92.61 E-value=0.27 Score=38.55 Aligned_cols=39 Identities=10% Similarity=0.106 Sum_probs=32.5
Q ss_pred ceEEEEEecCCCceEEEEEEecCCCeEEEEecCCCcccC
Q 043802 147 DLIHLECSSLRCDWKIVGAKISTGNSFIVKDISLTHACH 185 (701)
Q Consensus 147 ~r~~~~C~~~gCpwrv~as~~~~~~~w~V~~~~~~Hnc~ 185 (701)
.|--++|+..+||++-.+.+..++....++++.++|||+
T Consensus 21 pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 21 PRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp EEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred eeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 466799999999999999998878888899999999996
No 19
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.96 E-value=3.9 Score=40.59 Aligned_cols=85 Identities=19% Similarity=0.120 Sum_probs=62.0
Q ss_pred CcceEEEeceEEecccCceEEEEEEecCCCCeeEEEEEEeecCchhhHHHHHHHHHHHcccCCCCCeEEEecCCchHHHH
Q 043802 304 CRNFIAVDGWVINSVHKSVMLVAAALDGNNDILPIALAEVEIEDFTSWYFFLNNLNRALRRENGEGLCIITDGDNGVLEA 383 (701)
Q Consensus 304 ~~~vi~iD~T~~~~~y~~~ll~a~g~d~~~~~~pla~alv~~E~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~A 383 (701)
-++++.||-||++.+-+..- .-.++|.+| .+|-+-|...-+...=.-||..+++.. +.|.+|+||+.+....|
T Consensus 69 ~~~~w~vDEt~ikv~gkw~y-lyrAid~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~----g~p~v~vtDka~s~~~A 141 (215)
T COG3316 69 AGDSWRVDETYIKVNGKWHY-LYRAIDADG--LTLDVWLSKRRNALAAKAFLKKLLKKH----GEPRVFVTDKAPSYTAA 141 (215)
T ss_pred cccceeeeeeEEeeccEeee-hhhhhccCC--CeEEEEEEcccCcHHHHHHHHHHHHhc----CCCceEEecCccchHHH
Confidence 34678899999876544332 223445554 467788888877777777888777765 23899999999999999
Q ss_pred HHhhCCCcceee
Q 043802 384 IEDCIPLAHCRQ 395 (701)
Q Consensus 384 i~~vfP~a~h~~ 395 (701)
+.++-+.+.|+-
T Consensus 142 ~~~l~~~~ehr~ 153 (215)
T COG3316 142 LRKLGSEVEHRT 153 (215)
T ss_pred HHhcCcchheec
Confidence 999998776664
No 20
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=86.29 E-value=1.4 Score=34.21 Aligned_cols=46 Identities=13% Similarity=0.220 Sum_probs=25.5
Q ss_pred cCeEEEEeeeCCceEEEEEecC---CCceEEEEEEecCCCeEEEEecCCCccc
Q 043802 135 EGFKLCIIENGPDLIHLECSSL---RCDWKIVGAKISTGNSFIVKDISLTHAC 184 (701)
Q Consensus 135 ~gf~~~~~ks~~~r~~~~C~~~---gCpwrv~as~~~~~~~w~V~~~~~~Hnc 184 (701)
.|+.|...+.........|... +|+++|... .+. -.|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~~--~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AGD--GRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE----T--TEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CCC--CEEEECCCccCC
Confidence 4778887777788889999874 899999987 122 345556688987
No 21
>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=85.38 E-value=4.5 Score=35.77 Aligned_cols=77 Identities=10% Similarity=-0.077 Sum_probs=56.5
Q ss_pred CcceEEEeceEEec-ccCceEEEEEEecCCCCeeEEEEEEeecCchhhHHHHHHHHHHHcccCCCCCeEEEecCCchHHH
Q 043802 304 CRNFIAVDGWVINS-VHKSVMLVAAALDGNNDILPIALAEVEIEDFTSWYFFLNNLNRALRRENGEGLCIITDGDNGVLE 382 (701)
Q Consensus 304 ~~~vi~iD~T~~~~-~y~~~ll~a~g~d~~~~~~pla~alv~~E~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~ 382 (701)
....+.+|.++... ..++..+..+.+|..-+. .+++.+-..++.+.+..+|.......+... |.+|+||+..+...
T Consensus 5 p~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 5 PGERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRGGRP--PRVIRTDNGSEFTS 81 (120)
T ss_dssp TTTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS-SE---SEEEEESCHHHHS
T ss_pred CCCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeeccccccccccccccccccccccc--ceeccccccccccc
Confidence 45789999996663 456688899999987664 557777777788888888876666655543 79999999998875
Q ss_pred H
Q 043802 383 A 383 (701)
Q Consensus 383 A 383 (701)
.
T Consensus 82 ~ 82 (120)
T PF00665_consen 82 H 82 (120)
T ss_dssp H
T ss_pred c
Confidence 3
No 22
>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=84.60 E-value=1.3 Score=34.55 Aligned_cols=38 Identities=13% Similarity=0.072 Sum_probs=32.0
Q ss_pred ceEEEEEec-CCCceEEEEEEecCCCeEEEEecCCCccc
Q 043802 147 DLIHLECSS-LRCDWKIVGAKISTGNSFIVKDISLTHAC 184 (701)
Q Consensus 147 ~r~~~~C~~-~gCpwrv~as~~~~~~~w~V~~~~~~Hnc 184 (701)
-|--++|+. .|||++=.+.+..+++...++++.++|||
T Consensus 21 pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 21 PRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 455689998 89999988888766777788899999998
No 23
>PF13565 HTH_32: Homeodomain-like domain
Probab=81.05 E-value=3.6 Score=33.61 Aligned_cols=42 Identities=12% Similarity=0.283 Sum_probs=35.7
Q ss_pred HHHHHHHhhhhhcCCCCChHHHHHHHHHHhCCcC--ChhHHHHH
Q 043802 195 KWIAANYLHLWKQNPETASVEVKQQIIQTFGVVC--PEWKIFKA 236 (701)
Q Consensus 195 ~~ia~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~--s~~~~~ra 236 (701)
..+.+.+.+.+..+|.+++.+|...|.+.+|+.+ |.+.+||.
T Consensus 33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 4445677788888999999999999999999876 99999874
No 24
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=71.96 E-value=40 Score=31.87 Aligned_cols=63 Identities=17% Similarity=0.276 Sum_probs=46.4
Q ss_pred CchhhHHHHHHHHHHHcccCCCCCeEEEecCCchHHHH---HHhhCCCcceeechhhHHHHHHHhCCC
Q 043802 346 EDFTSWYFFLNNLNRALRRENGEGLCIITDGDNGVLEA---IEDCIPLAHCRQCCCSIYNQMLVQFPD 410 (701)
Q Consensus 346 E~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~A---i~~vfP~a~h~~C~~Hi~~n~~~~~~~ 410 (701)
.+.+...-+|+...+.++..+ ..-||||-...+.+| +.+-+|......|..|-+.-+.+.+..
T Consensus 73 ~~a~~l~~ll~~vIeeVG~~n--VvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 73 KTAEYLFELLDEVIEEVGEEN--VVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred ccHHHHHHHHHHHHHHhhhhh--hhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 455555566666666666554 677999999988888 444589999999999988877665554
No 25
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=68.71 E-value=8.9 Score=33.17 Aligned_cols=50 Identities=20% Similarity=0.315 Sum_probs=31.0
Q ss_pred ceEEEEEeCCce--EEEEeCCCcEEEEEecCceecccccc----cc-CCCchhHhHHHH
Q 043802 535 QQIRILYSTGRQ--MKVEDTDSMTYEVDITSMTCTCRLWQ----LS-GIPCSHACRCLE 586 (701)
Q Consensus 535 ~~~~V~~~~~~~--feV~~~~~~~~~V~l~~~tCsC~~~~----~~-GiPC~Halav~~ 586 (701)
+.+--...+++. |.|--++.+.|+++.+ -|||..|- .- --||.|++.+-.
T Consensus 21 Grfv~l~l~~~~~~~fVyvG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~ 77 (117)
T COG5431 21 GRFVFLYLKRSKVKFFVYVGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKV 77 (117)
T ss_pred CcEEEEeeCCceEEEEEEEccccceEEEcC--cccCHHHHhHhhhcCcccchhhhheee
Confidence 333333334433 4444454478998887 89998886 22 247999987543
No 26
>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=59.90 E-value=3.8 Score=21.82 Aligned_cols=9 Identities=22% Similarity=0.272 Sum_probs=3.5
Q ss_pred CCCCCCCCc
Q 043802 649 QTLVPTQND 657 (701)
Q Consensus 649 ~~GRPk~~R 657 (701)
+.|||++.-
T Consensus 3 ~RGRP~k~~ 11 (13)
T PF02178_consen 3 KRGRPRKNA 11 (13)
T ss_dssp -SS--TT--
T ss_pred cCCCCcccc
Confidence 789998863
No 27
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=48.52 E-value=35 Score=38.60 Aligned_cols=42 Identities=29% Similarity=0.455 Sum_probs=28.6
Q ss_pred EEEEeCCCcEEEEEec----CceeccccccccCCCchhHhHHHHHcCC
Q 043802 547 MKVEDTDSMTYEVDIT----SMTCTCRLWQLSGIPCSHACRCLEELGE 590 (701)
Q Consensus 547 feV~~~~~~~~~V~l~----~~tCsC~~~~~~GiPC~Halav~~~~~~ 590 (701)
.+|.....-.+.|.+. +.+|||.. ...| -|.|++||+...-.
T Consensus 52 A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~ 97 (587)
T COG4715 52 AVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLD 97 (587)
T ss_pred EEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhh
Confidence 4455543345566663 58899987 4444 59999999987644
No 28
>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=46.63 E-value=51 Score=30.67 Aligned_cols=69 Identities=17% Similarity=0.116 Sum_probs=39.3
Q ss_pred eEEEeceEEeccc--------------CceEEEEEEecCC-CCeeEEEEEEeecCchhhHHHHHHHHHHHcccCCCCCeE
Q 043802 307 FIAVDGWVINSVH--------------KSVMLVAAALDGN-NDILPIALAEVEIEDFTSWYFFLNNLNRALRRENGEGLC 371 (701)
Q Consensus 307 vi~iD~T~~~~~y--------------~~~ll~a~g~d~~-~~~~pla~alv~~E~~es~~wfl~~l~~~~~~~~~~~~~ 371 (701)
+|-||.||..++- .....++++++-+ +..--+...++.+.+.++..=+++.... +..+
T Consensus 5 ~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~i~-------~gs~ 77 (151)
T PF12762_consen 5 IVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEHIE-------PGST 77 (151)
T ss_pred EEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHhhh-------ccce
Confidence 6778888875322 2233444444443 3333344455577777776555443322 2578
Q ss_pred EEecCCchHHH
Q 043802 372 IITDGDNGVLE 382 (701)
Q Consensus 372 iisD~~~~l~~ 382 (701)
|+||..++-..
T Consensus 78 i~TD~~~aY~~ 88 (151)
T PF12762_consen 78 IITDGWRAYNG 88 (151)
T ss_pred eeecchhhcCc
Confidence 99999987643
No 29
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=43.88 E-value=13 Score=37.59 Aligned_cols=23 Identities=26% Similarity=0.629 Sum_probs=18.7
Q ss_pred ceeccccccccCCCchhHhHHHHHcC
Q 043802 564 MTCTCRLWQLSGIPCSHACRCLEELG 589 (701)
Q Consensus 564 ~tCsC~~~~~~GiPC~Halav~~~~~ 589 (701)
..|||..|. .||.|+-||..+.+
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 459999876 49999999987753
No 30
>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=42.42 E-value=15 Score=23.49 Aligned_cols=12 Identities=8% Similarity=0.111 Sum_probs=9.4
Q ss_pred CCCCCCCCcccc
Q 043802 649 QTLVPTQNDTKE 660 (701)
Q Consensus 649 ~~GRPk~~R~~~ 660 (701)
++|||+|.....
T Consensus 3 kRGRPrK~~~~~ 14 (26)
T smart00384 3 KRGRPRKAPKDX 14 (26)
T ss_pred CCCCCCCCCCcc
Confidence 789999877653
No 31
>PRK13907 rnhA ribonuclease H; Provisional
Probab=40.47 E-value=1.6e+02 Score=26.45 Aligned_cols=78 Identities=15% Similarity=0.048 Sum_probs=44.3
Q ss_pred eEEEeceEEecccCceEEEEEEecCCCCeeEEEEE-EeecCchhhHHHHHHHHHHHcccCCCCCeEEEecCCchHHHHHH
Q 043802 307 FIAVDGWVINSVHKSVMLVAAALDGNNDILPIALA-EVEIEDFTSWYFFLNNLNRALRRENGEGLCIITDGDNGVLEAIE 385 (701)
Q Consensus 307 vi~iD~T~~~~~y~~~ll~a~g~d~~~~~~pla~a-lv~~E~~es~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~ 385 (701)
.|.+||.+..+.-.+-.-.++ .|..+.. .+++. -..+.+..-+.-++..|+.+..... .++.|-||. +.+++++.
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~~~-~~~~~~~~~tn~~AE~~All~aL~~a~~~g~-~~v~i~sDS-~~vi~~~~ 78 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQPAV-QLSLPLGTMSNHEAEYHALLAALKYCTEHNY-NIVSFRTDS-QLVERAVE 78 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeE-EEEecccccCCcHHHHHHHHHHHHHHHhCCC-CEEEEEech-HHHHHHHh
Confidence 378898887764332222222 4554443 23321 1234455667777777777765443 357778876 66667776
Q ss_pred hhC
Q 043802 386 DCI 388 (701)
Q Consensus 386 ~vf 388 (701)
..+
T Consensus 79 ~~~ 81 (128)
T PRK13907 79 KEY 81 (128)
T ss_pred HHH
Confidence 654
No 32
>PF13592 HTH_33: Winged helix-turn helix
Probab=39.79 E-value=42 Score=26.11 Aligned_cols=31 Identities=19% Similarity=0.219 Sum_probs=26.1
Q ss_pred CCCCChHHHHHHHHHHhCCcCChhHHHHHHH
Q 043802 208 NPETASVEVKQQIIQTFGVVCPEWKIFKAEK 238 (701)
Q Consensus 208 ~~~~~~~~i~~~l~~~~g~~~s~~~~~rak~ 238 (701)
+..++.++|...|.+.||+.++...+|+...
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~ 32 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKYSPSGVYRLLK 32 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEEcHHHHHHHHH
Confidence 3567889999999999999999998887544
No 33
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=31.28 E-value=38 Score=27.14 Aligned_cols=37 Identities=16% Similarity=0.373 Sum_probs=16.2
Q ss_pred HhhhhhcCCCCChHHHHHHHHHHhCCcCChhHHHHHHH
Q 043802 201 YLHLWKQNPETASVEVKQQIIQTFGVVCPEWKIFKAEK 238 (701)
Q Consensus 201 ~~~~i~~~~~~~~~~i~~~l~~~~g~~~s~~~~~rak~ 238 (701)
+...+..+|..+..+|...+.+. |..+|..+++|.-.
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L~ 40 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRLR 40 (72)
T ss_dssp ------------HHHHHHHT----T--S-HHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHHH
Confidence 44566778999999999999888 99999999987643
No 34
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=31.23 E-value=1.1e+02 Score=23.14 Aligned_cols=39 Identities=18% Similarity=0.266 Sum_probs=25.4
Q ss_pred HHHHHHHhhhhhc-C-CCCChHHHHHHHHHHhCCcCChhHH
Q 043802 195 KWIAANYLHLWKQ-N-PETASVEVKQQIIQTFGVVCPEWKI 233 (701)
Q Consensus 195 ~~ia~~~~~~i~~-~-~~~~~~~i~~~l~~~~g~~~s~~~~ 233 (701)
..+...+.++++. + .+++.++|...+.+.+|++++..+.
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~~K~ 43 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVTKKQVREQLEERFGVDLSSRKK 43 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SHHHH
T ss_pred HHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHHHHH
Confidence 4566677777775 3 4789999999999999999985543
No 35
>PRK00766 hypothetical protein; Provisional
Probab=30.63 E-value=3.1e+02 Score=27.08 Aligned_cols=89 Identities=13% Similarity=0.213 Sum_probs=48.2
Q ss_pred ceEEEe-ceEEecccCceEEEEEEecCCCCeeEEEEEEeecCchhhHHHHHHHHHHHcc---------------------
Q 043802 306 NFIAVD-GWVINSVHKSVMLVAAALDGNNDILPIALAEVEIEDFTSWYFFLNNLNRALR--------------------- 363 (701)
Q Consensus 306 ~vi~iD-~T~~~~~y~~~ll~a~g~d~~~~~~pla~alv~~E~~es~~wfl~~l~~~~~--------------------- 363 (701)
.|++|| +.|..+.-+-..++-+-.-++.-+--++|+.+.-.-.|.=.-+.+.++....
T Consensus 10 rvlGidds~f~~~~~~~~~lvGvv~r~~~~idGv~~~~itvdG~DaT~~i~~mv~~~~~r~~i~~V~L~Git~agFNvvD 89 (194)
T PRK00766 10 RVLGIDDGTFLFKSSEKVILVGVVMRGGDWVDGVLSRWITVDGLDATEAIIEMVNSSRHKGQLRVIMLDGITYGGFNVVD 89 (194)
T ss_pred eEEEEecCccccCCCCCEEEEEEEEECCeEEeeEEEEEEEECCccHHHHHHHHHHhcccccceEEEEECCEeeeeeEEec
Confidence 577787 4454432233444444455555555666666655554444444444433110
Q ss_pred -----cCCCCCeEEEecCCc---hHHHHHHhhCCCccee
Q 043802 364 -----RENGEGLCIITDGDN---GVLEAIEDCIPLAHCR 394 (701)
Q Consensus 364 -----~~~~~~~~iisD~~~---~l~~Ai~~vfP~a~h~ 394 (701)
..-+-|+++++..-+ +|.+|+.+.||+...+
T Consensus 90 ~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k~f~~~~~R 128 (194)
T PRK00766 90 IEELYRETGLPVIVVMRKKPDFEAIESALKKHFSDWEER 128 (194)
T ss_pred HHHHHHHHCCCEEEEEecCCCHHHHHHHHHHHCCCHHHH
Confidence 011236666655544 7889999999986543
No 36
>PF13276 HTH_21: HTH-like domain
Probab=24.11 E-value=1.6e+02 Score=22.58 Aligned_cols=42 Identities=7% Similarity=0.153 Sum_probs=33.4
Q ss_pred HHHHHhhhhhc-CCCCChHHHHHHHHHHhCCcCChhHHHHHHH
Q 043802 197 IAANYLHLWKQ-NPETASVEVKQQIIQTFGVVCPEWKIFKAEK 238 (701)
Q Consensus 197 ia~~~~~~i~~-~~~~~~~~i~~~l~~~~g~~~s~~~~~rak~ 238 (701)
+...+.+.+.. .+.+....|...|++..|+.++..+++|..+
T Consensus 6 l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~~v~~krV~RlM~ 48 (60)
T PF13276_consen 6 LRELIKEIFKESKPTYGYRRIWAELRREGGIRVSRKRVRRLMR 48 (60)
T ss_pred HHHHHHHHHHHcCCCeehhHHHHHHhccCcccccHHHHHHHHH
Confidence 45556666665 4789999999999999899999999887643
No 37
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=22.60 E-value=1.3e+02 Score=24.68 Aligned_cols=29 Identities=17% Similarity=0.337 Sum_probs=25.9
Q ss_pred eeCCHHHHHHHHHHHHHHcCeEEEEeeeC
Q 043802 117 LFRDEFQFRRAVEVFSLREGFKLCIIENG 145 (701)
Q Consensus 117 ~F~s~~e~k~av~~yAi~~gf~~~~~ks~ 145 (701)
.++|.+++..+|..|+.+++-.+.+.+-+
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~ 41 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRD 41 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecC
Confidence 47899999999999999999999987654
No 38
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.82 E-value=1.9e+02 Score=24.90 Aligned_cols=40 Identities=23% Similarity=0.320 Sum_probs=30.5
Q ss_pred HHHhhhhhcCC-----CCChHHHHHHH-HHHhCCcCChhHHHHHHH
Q 043802 199 ANYLHLWKQNP-----ETASVEVKQQI-IQTFGVVCPEWKIFKAEK 238 (701)
Q Consensus 199 ~~~~~~i~~~~-----~~~~~~i~~~l-~~~~g~~~s~~~~~rak~ 238 (701)
+.+.+.+.++| .+++..|...+ .+.+|+.+|...+++.-.
T Consensus 64 ~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 64 AQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred HHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 35556666655 57889999866 889999999999987543
No 39
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.61 E-value=1.3e+02 Score=28.37 Aligned_cols=35 Identities=9% Similarity=-0.098 Sum_probs=29.3
Q ss_pred EeceEE-ecccCce--EEEEEEecCCCCeeEEEEEEee
Q 043802 310 VDGWVI-NSVHKSV--MLVAAALDGNNDILPIALAEVE 344 (701)
Q Consensus 310 iD~T~~-~~~y~~~--ll~a~g~d~~~~~~pla~alv~ 344 (701)
||.||+ ++.|+.| ++...|.|+-|+-...|||.+.
T Consensus 70 ievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~h 107 (187)
T KOG4027|consen 70 IEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLH 107 (187)
T ss_pred eEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEe
Confidence 678887 5689887 5667899999999999999865
No 40
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=20.30 E-value=1.2e+02 Score=26.52 Aligned_cols=33 Identities=12% Similarity=0.077 Sum_probs=22.8
Q ss_pred cCCceeCCHHHHHHHHHHHHHHcCeEEEEeeeCCceE
Q 043802 113 RQGQLFRDEFQFRRAVEVFSLREGFKLCIIENGPDLI 149 (701)
Q Consensus 113 ~vG~~F~s~~e~k~av~~yAi~~gf~~~~~ks~~~r~ 149 (701)
.+.+.|+|+|++ ..||.++|..|.+..-...+.
T Consensus 50 ~v~l~F~skE~A----i~yaer~G~~Y~V~~p~~r~~ 82 (101)
T PF04800_consen 50 SVRLKFDSKEDA----IAYAERNGWDYEVEEPKKRKR 82 (101)
T ss_dssp -CEEEESSHHHH----HHHHHHCT-EEEEE-STT---
T ss_pred eeEeeeCCHHHH----HHHHHHcCCeEEEeCCCCCcC
Confidence 378899999998 468999999999876554433
No 41
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=20.08 E-value=75 Score=27.06 Aligned_cols=34 Identities=12% Similarity=0.106 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHhcCchhHHHHhhccCccccc
Q 043802 424 TSEVQFTRYIKMIQSSSIECHQWLFQTQWKKWAL 457 (701)
Q Consensus 424 ~~~~eFe~~~~~l~~~~~~~~~~L~~~~~e~W~~ 457 (701)
.+..+|+..|..+.......++||..++++....
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~ 38 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPK 38 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHH
Confidence 4678999999999877778999999987766543
Done!