Query 048027
Match_columns 735
No_of_seqs 292 out of 1517
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 05:35:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048027.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048027hhsearch_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 4.1E-69 9E-74 625.7 46.6 468 187-689 71-624 (846)
2 PF10551 MULE: MULE transposas 99.8 5.9E-21 1.3E-25 168.0 9.2 90 391-487 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.8 1.2E-19 2.5E-24 199.9 6.1 175 385-565 163-349 (381)
4 PF03108 DBD_Tnp_Mut: MuDR fam 99.6 6E-16 1.3E-20 127.4 9.1 67 187-253 1-67 (67)
5 COG3328 Transposase and inacti 99.4 1.3E-12 2.8E-17 141.6 11.4 184 383-573 144-337 (379)
6 smart00575 ZnF_PMZ plant mutat 98.8 2.2E-09 4.8E-14 71.9 1.4 27 646-672 1-27 (28)
7 PF08731 AFT: Transcription fa 98.5 5.1E-07 1.1E-11 79.6 9.3 69 196-264 1-111 (111)
8 PF03101 FAR1: FAR1 DNA-bindin 98.2 2.5E-06 5.4E-11 74.5 6.3 61 204-265 1-90 (91)
9 PF04434 SWIM: SWIM zinc finge 98.0 3.9E-06 8.4E-11 61.5 2.8 31 641-671 10-40 (40)
10 cd06410 PB1_UP2 Uncharacterize 96.7 0.00041 9E-09 61.1 0.1 55 39-93 18-78 (97)
11 PF13610 DDE_Tnp_IS240: DDE do 96.6 0.0011 2.4E-08 62.9 1.9 81 384-473 1-81 (140)
12 PF06782 UPF0236: Uncharacteri 94.9 0.43 9.3E-06 54.5 14.3 133 424-565 235-377 (470)
13 PF01610 DDE_Tnp_ISL3: Transpo 94.4 0.088 1.9E-06 54.7 6.8 93 387-490 1-96 (249)
14 PF03106 WRKY: WRKY DNA -bindi 89.6 0.76 1.7E-05 36.8 5.0 39 225-263 21-59 (60)
15 PF04684 BAF1_ABF1: BAF1 / ABF 88.5 0.9 2E-05 50.2 6.2 59 188-246 20-79 (496)
16 PRK14702 insertion element IS2 87.5 12 0.00026 39.4 13.9 75 383-461 86-163 (262)
17 PHA02517 putative transposase 86.9 6.6 0.00014 41.4 11.7 73 383-462 109-181 (277)
18 PRK09409 IS2 transposase TnpB; 86.1 17 0.00037 39.0 14.4 77 383-462 125-203 (301)
19 PF03050 DDE_Tnp_IS66: Transpo 85.0 1.1 2.3E-05 47.3 4.5 86 383-492 66-156 (271)
20 PF00665 rve: Integrase core d 79.4 13 0.00028 33.2 8.9 76 383-464 5-81 (120)
21 PF04500 FLYWCH: FLYWCH zinc f 78.5 3.6 7.9E-05 32.3 4.4 46 213-262 14-62 (62)
22 smart00774 WRKY DNA binding do 77.5 3.2 6.9E-05 33.1 3.6 38 225-262 21-59 (59)
23 PF04937 DUF659: Protein of un 75.5 33 0.00071 33.0 10.7 89 399-492 46-138 (153)
24 COG3316 Transposase and inacti 72.5 8.3 0.00018 39.0 5.9 83 384-477 70-153 (215)
25 PF02178 AT_hook: AT hook moti 68.5 2.3 5E-05 23.3 0.6 11 718-728 1-11 (13)
26 smart00384 AT_hook DNA binding 65.1 4.3 9.3E-05 26.5 1.4 15 718-732 1-15 (26)
27 COG5431 Uncharacterized metal- 43.5 16 0.00034 32.4 1.8 45 636-682 42-91 (117)
28 PRK13907 rnhA ribonuclease H; 37.9 2.2E+02 0.0049 25.8 8.9 78 386-470 3-81 (128)
29 smart00666 PB1 PB1 domain. Pho 36.3 11 0.00023 31.7 -0.3 35 42-76 9-46 (81)
30 COG4279 Uncharacterized conser 34.1 19 0.00041 37.0 1.1 23 646-671 125-147 (266)
31 PF12762 DDE_Tnp_IS1595: ISXO2 31.8 1.3E+02 0.0028 28.3 6.4 69 385-463 4-87 (151)
32 PF13565 HTH_32: Homeodomain-l 30.4 69 0.0015 26.3 3.8 32 275-306 34-65 (77)
33 COG4715 Uncharacterized conser 26.1 95 0.0021 35.8 4.9 34 639-674 62-99 (587)
34 PF14201 DUF4318: Domain of un 24.2 1.1E+02 0.0025 25.5 3.8 30 194-223 12-41 (74)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.1e-69 Score=625.69 Aligned_cols=468 Identities=14% Similarity=0.164 Sum_probs=371.8
Q ss_pred CCCCCCCCeeCCHHHHHHHHHHHHHHcCcEEEEeeecCc-------eEEEEeec--------------------------
Q 048027 187 GITMELGQRFKDEFHFRRAVEIQAMRDGIKLCVMENTST-------LISCECSN-------------------------- 233 (735)
Q Consensus 187 ~~~l~vG~~F~s~ee~k~ai~~yAi~~~f~~~~~ks~~~-------r~~~~C~~-------------------------- 233 (735)
...+.+||+|.|.+|++++|..||...||++|+.++.++ ..+++|++
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 468999999999999999999999999999998755432 23466654
Q ss_pred --------CCCceEEEEEEecCCceEEEeeecCCCccCCCCCcc-ccchhhHHHHHhhhhhhCCCCChhhHHHHHHHhcC
Q 048027 234 --------LMCDWKVSAAKVRKGNVFVLKEIIPNHTCKRHNNNF-ALGTMWNAAKFLHLWVENPNIDLDRLGDEIERCSG 304 (735)
Q Consensus 234 --------~gCpwrv~as~~~~~~~~~V~~~~~~HnC~~~~~~~-~~s~~~ia~~~~~~l~~~~~~~~~~I~~~l~~~~g 304 (735)
+||+++|.+.+. ..+.|+|+.+..+|||++..... ....+.+-..+...+....++. +
T Consensus 151 ~~rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~~~~~~~~~v~------------~ 217 (846)
T PLN03097 151 TGRRSCAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMARQFAEYKNVV------------G 217 (846)
T ss_pred cccccccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccchhhhhhHHHHHhhhhcccccc------------c
Confidence 379999999874 55789999999999999953222 1111111000000000000000 0
Q ss_pred Cc--c-chhh-hHHHHHHhhhhhccCchhhHHHHHHHHHHHHhhCCCcEEEEEeeccccCCccceeeEEEechHhHHHHH
Q 048027 305 IK--Y-PTWK-VEAIDKVAKFWLRTDHSYGYEHLLHYKNEMLKVNKDNIIKIQTKTYDDLVAPIFDRMFVLFADCSHAFK 380 (735)
Q Consensus 305 ~~--y-~~~r-ak~~a~~~~~~~~g~~~~~y~~L~~y~~~l~~~NPg~~~~i~~~~~~~~~~~~f~~~F~~~~~s~~~f~ 380 (735)
+. . ...+ .|++.+ ...+...|..|+++++..||+++|+|++ |++++++++||+++.|+.+|.
T Consensus 218 ~~~d~~~~~~~~r~~~~---------~~gD~~~ll~yf~~~q~~nP~Ffy~~ql-----De~~~l~niFWaD~~sr~~Y~ 283 (846)
T PLN03097 218 LKNDSKSSFDKGRNLGL---------EAGDTKILLDFFTQMQNMNSNFFYAVDL-----GEDQRLKNLFWVDAKSRHDYG 283 (846)
T ss_pred cchhhcchhhHHHhhhc---------ccchHHHHHHHHHHHHhhCCCceEEEEE-----ccCCCeeeEEeccHHHHHHHH
Confidence 00 0 0111 122111 1235678999999999999999999988 789999999999999999999
Q ss_pred hhCCcEEEEcCeEeecCCCCceEEEEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCch
Q 048027 381 TTSRRLVIVDGWEIDSPYKSVMLVAVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDN 460 (735)
Q Consensus 381 ~~~~~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~ 460 (735)
+ |++||++|+||++|+|++||+.++|+|+|+|++++||||+.+|+.++|.|||++|+++|++ ..|.+||||++.
T Consensus 284 ~-FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~g-----k~P~tIiTDqd~ 357 (846)
T PLN03097 284 N-FSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGG-----QAPKVIITDQDK 357 (846)
T ss_pred h-cCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCC-----CCCceEEecCCH
Confidence 7 9999999999999999999999999999999999999999999999999999999999998 789999999999
Q ss_pred hHHHHHHhhCCCCeeecccchHHHHHHhhCCc-----HHHHHHHHHHHc-cchHHHHHHHHHHHH-hhCchhhhHHHhc-
Q 048027 461 GVDEAVSEFLPYAQYRQCCFSIYNKLMKQFPH-----ALVYSLFWSACR-STNKAAFQHQMMLLQ-CHNRDCYQWLIDR- 532 (735)
Q Consensus 461 ~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~~-----~~~~~~f~~~~~-~~t~~eFe~~~~~l~-~~~~~~~~~L~~~- 532 (735)
+|.+||++|||++.||+|.|||++|+.+++.. +.+...|..+++ +.+++||+..|..|. +++.+.++||..+
T Consensus 358 am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY 437 (846)
T PLN03097 358 AMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLY 437 (846)
T ss_pred HHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHH
Confidence 99999999999999999999999999998863 589999999887 679999999999974 6789999999998
Q ss_pred -CcccceecccCCCcccccCCCCchHHHhHHHhh--hccCchhhHHHHHHHHHHHHHHHhhhh----------------c
Q 048027 533 -GCHTWALYCMPEWAKSTDITISATEQLRIWLLK--YLDMNVANRFTAITKETAKIFQKRYLA----------------G 593 (735)
Q Consensus 533 -~~~~Wa~a~~~~~~~~g~~TtN~~Es~N~~lk~--~r~~pi~~~le~i~~~l~~~~~~r~~~----------------~ 593 (735)
.|++||++|+++.+..|+.||+++||+|++|++ .+..+|..|++.+...+..+..+..+. .
T Consensus 438 ~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~pi 517 (846)
T PLN03097 438 EDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPL 517 (846)
T ss_pred HhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHH
Confidence 899999999999999999999999999999998 567888888888777666554432211 0
Q ss_pred cccccCCCChHHHHHHHHHhhhcccceeee---CCCC--eEEEEEe--CCeEEEEEe----cCceEeecCccccccCcch
Q 048027 594 WDWVHDSITPTTRQQITQNVIEGDGWNIHS---GADP--KILTVTM--NGLSFVVNK----ELAICSCGLWQLSGIPCPH 662 (735)
Q Consensus 594 ~~~~~~~~tp~i~~~l~~~~~~~s~~~~~~---~~~~--~V~~v~~--~~~~~~V~l----~~~tCsC~~~~~~GiPC~H 662 (735)
++..+.+|||.||++||++ +..+. .++. ..++ ..|.|.. ....|.|.. ...+|+|++|+..||||+|
T Consensus 518 EkQAs~iYT~~iF~kFQ~E-l~~~~-~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrH 595 (846)
T PLN03097 518 EKSVSGVYTHAVFKKFQVE-VLGAV-ACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRH 595 (846)
T ss_pred HHHHHHHhHHHHHHHHHHH-HHHhh-heEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhh
Confidence 0111388999999999999 55444 1221 1122 2355543 234677754 3679999999999999999
Q ss_pred hhHHHHHhcc--cccccccccccHHHHhh
Q 048027 663 ACRCIIHWAA--SYADFVHDFMTVEVYRS 689 (735)
Q Consensus 663 alav~~~~~~--~~~~yv~~~yt~~~~~~ 689 (735)
||+|+.+.++ .|..||.++||+.+-..
T Consensus 596 aLkVL~~~~v~~IP~~YILkRWTKdAK~~ 624 (846)
T PLN03097 596 ALVVLQMCQLSAIPSQYILKRWTKDAKSR 624 (846)
T ss_pred HHHHHhhcCcccCchhhhhhhchhhhhhc
Confidence 9999999997 79999999999998643
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=99.84 E-value=5.9e-21 Score=167.99 Aligned_cols=90 Identities=31% Similarity=0.478 Sum_probs=86.3
Q ss_pred CeEeecCCCCceEE---EEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCchhHHHHHH
Q 048027 391 GWEIDSPYKSVMLV---AVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDNGVDEAVS 467 (735)
Q Consensus 391 ~T~~~~~y~~~ll~---avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~~l~~Ai~ 467 (735)
|||++|+| ++++. ++|+|++|+.+|+||+++++|+.++|.|||+.+++.++. . |.+||||+++|+.+||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~-----~-p~~ii~D~~~~~~~Ai~ 73 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQ-----K-PKVIISDFDKALINAIK 73 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcccc-----C-ceeeeccccHHHHHHHH
Confidence 79999999 98886 999999999999999999999999999999999999985 5 99999999999999999
Q ss_pred hhCCCCeeecccchHHHHHH
Q 048027 468 EFLPYAQYRQCCFSIYNKLM 487 (735)
Q Consensus 468 ~vfP~a~h~~C~~Hi~~N~~ 487 (735)
++||++.|++|.||+.+|++
T Consensus 74 ~vfP~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 74 EVFPDARHQLCLFHILRNIK 93 (93)
T ss_pred HHCCCceEehhHHHHHHhhC
Confidence 99999999999999999974
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=99.78 E-value=1.2e-19 Score=199.87 Aligned_cols=175 Identities=18% Similarity=0.242 Sum_probs=152.5
Q ss_pred cEEEEcCeEeecCCC-----CceEEEEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCc
Q 048027 385 RLVIVDGWEIDSPYK-----SVMLVAVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGD 459 (735)
Q Consensus 385 ~vi~iD~T~~~~~y~-----~~ll~avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~ 459 (735)
++|++||+|.+.+.+ ..+++++|+|.+|+..+||+.+...|+.++|.-||+.|++..- ..|..||+|++
T Consensus 163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~RGl------~~~~lvv~Dg~ 236 (381)
T PF00872_consen 163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKERGL------KDILLVVSDGH 236 (381)
T ss_pred cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhccc------cccceeecccc
Confidence 789999999987744 4689999999999999999999999999999999999998765 46899999999
Q ss_pred hhHHHHHHhhCCCCeeecccchHHHHHHhhCCcH---HHHHHHHHHHccchHHHHHHHHHHHHh----hCchhhhHHHhc
Q 048027 460 NGVDEAVSEFLPYAQYRQCCFSIYNKLMKQFPHA---LVYSLFWSACRSTNKAAFQHQMMLLQC----HNRDCYQWLIDR 532 (735)
Q Consensus 460 ~~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~~~---~~~~~f~~~~~~~t~~eFe~~~~~l~~----~~~~~~~~L~~~ 532 (735)
+||..||.++||++.++.|.+|+++|+.++++.+ .+...++.+..+.+.++....++.+.+ ..|.+.++|++.
T Consensus 237 ~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~ 316 (381)
T PF00872_consen 237 KGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEEN 316 (381)
T ss_pred ccccccccccccchhhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhc
Confidence 9999999999999999999999999999999754 677777888778888877777777643 478999999988
Q ss_pred CcccceecccCCCcccccCCCCchHHHhHHHhh
Q 048027 533 GCHTWALYCMPEWAKSTDITISATEQLRIWLLK 565 (735)
Q Consensus 533 ~~~~Wa~a~~~~~~~~g~~TtN~~Es~N~~lk~ 565 (735)
..+.|+..-|+...+--+.|||.+|++|+.||+
T Consensus 317 ~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irr 349 (381)
T PF00872_consen 317 WDELLTFLDFPPEHRRSIRTTNAIESLNKEIRR 349 (381)
T ss_pred cccccceeeecchhccccchhhhccccccchhh
Confidence 777887766665546677899999999999998
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=6e-16 Score=127.43 Aligned_cols=67 Identities=25% Similarity=0.559 Sum_probs=64.8
Q ss_pred CCCCCCCCeeCCHHHHHHHHHHHHHHcCcEEEEeeecCceEEEEeecCCCceEEEEEEecCCceEEE
Q 048027 187 GITMELGQRFKDEFHFRRAVEIQAMRDGIKLCVMENTSTLISCECSNLMCDWKVSAAKVRKGNVFVL 253 (735)
Q Consensus 187 ~~~l~vG~~F~s~ee~k~ai~~yAi~~~f~~~~~ks~~~r~~~~C~~~gCpwrv~as~~~~~~~~~V 253 (735)
||.|.+||+|+|++||+.||+.||++++|++++.+|+++|++++|...||||+|+|++.++++.|+|
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 4789999999999999999999999999999999999999999999999999999999999999986
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.39 E-value=1.3e-12 Score=141.59 Aligned_cols=184 Identities=15% Similarity=0.155 Sum_probs=140.9
Q ss_pred CCcEEEEcCeEeecC--CCCceEEEEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCch
Q 048027 383 SRRLVIVDGWEIDSP--YKSVMLVAVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDN 460 (735)
Q Consensus 383 ~~~vi~iD~T~~~~~--y~~~ll~avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~ 460 (735)
..+++++||+|++.+ -+.++++|+|++.+|+-..+++.+-..|+ ..|.-||..|+...- .....+++|+.+
T Consensus 144 ~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl------~~v~l~v~Dg~~ 216 (379)
T COG3328 144 DYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGL------SDVLLVVVDGLK 216 (379)
T ss_pred CceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccc------cceeEEecchhh
Confidence 567899999999988 46689999999999999999999999999 999988888888644 335777889999
Q ss_pred hHHHHHHhhCCCCeeecccchHHHHHHhhCCcHH---HHHHHHHHHccchHHHHHHHHHH----HHhhCchhhhHHHhcC
Q 048027 461 GVDEAVSEFLPYAQYRQCCFSIYNKLMKQFPHAL---VYSLFWSACRSTNKAAFQHQMML----LQCHNRDCYQWLIDRG 533 (735)
Q Consensus 461 ~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~~~~---~~~~f~~~~~~~t~~eFe~~~~~----l~~~~~~~~~~L~~~~ 533 (735)
|+.+||.++||.+.+++|..|+.+|+..+...++ ....+..+..+.+.++-...|.. +....|...+|+.+..
T Consensus 217 gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~ 296 (379)
T COG3328 217 GLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNAL 296 (379)
T ss_pred hhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHH
Confidence 9999999999999999999999999999887663 33333333444555544444444 4445788888888876
Q ss_pred cccceecccCCCcccccCCCCchHHHhHHHhh-hccCchhh
Q 048027 534 CHTWALYCMPEWAKSTDITISATEQLRIWLLK-YLDMNVAN 573 (735)
Q Consensus 534 ~~~Wa~a~~~~~~~~g~~TtN~~Es~N~~lk~-~r~~pi~~ 573 (735)
-+.|...-|+...+--+.|||.+|++|+.++. .+..+++.
T Consensus 297 ~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fp 337 (379)
T COG3328 297 EELLPFFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFP 337 (379)
T ss_pred HHhcccccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCC
Confidence 66665444433224567899999999998875 33334443
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.77 E-value=2.2e-09 Score=71.90 Aligned_cols=27 Identities=52% Similarity=0.936 Sum_probs=25.1
Q ss_pred ceEeecCccccccCcchhhHHHHHhcc
Q 048027 646 AICSCGLWQLSGIPCPHACRCIIHWAA 672 (735)
Q Consensus 646 ~tCsC~~~~~~GiPC~Halav~~~~~~ 672 (735)
.+|||++||..||||+|+|+|+...++
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=98.52 E-value=5.1e-07 Score=79.61 Aligned_cols=69 Identities=17% Similarity=0.314 Sum_probs=65.2
Q ss_pred eCCHHHHHHHHHHHHHHcCcEEEEeeecCceEEEEeec------------------------------------------
Q 048027 196 FKDEFHFRRAVEIQAMRDGIKLCVMENTSTLISCECSN------------------------------------------ 233 (735)
Q Consensus 196 F~s~ee~k~ai~~yAi~~~f~~~~~ks~~~r~~~~C~~------------------------------------------ 233 (735)
|.+++|++.+|+.++...|+++.+.+|+.+.+.++|..
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 78999999999999999999999999999999999983
Q ss_pred CCCceEEEEEEecCCceEEEeeecCCCccCC
Q 048027 234 LMCDWKVSAAKVRKGNVFVLKEIIPNHTCKR 264 (735)
Q Consensus 234 ~gCpwrv~as~~~~~~~~~V~~~~~~HnC~~ 264 (735)
.+|||+|+|........|.|..++..|+|++
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 1699999999999999999999999999974
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=98.22 E-value=2.5e-06 Score=74.52 Aligned_cols=61 Identities=11% Similarity=0.218 Sum_probs=53.8
Q ss_pred HHHHHHHHHcCcEEEEeeecCc-------eEEEEeec----------------------CCCceEEEEEEecCCceEEEe
Q 048027 204 RAVEIQAMRDGIKLCVMENTST-------LISCECSN----------------------LMCDWKVSAAKVRKGNVFVLK 254 (735)
Q Consensus 204 ~ai~~yAi~~~f~~~~~ks~~~-------r~~~~C~~----------------------~gCpwrv~as~~~~~~~~~V~ 254 (735)
++|..||...||.++..++.+. ++.++|.+ .||||+|.+.+.+ ++.|.|+
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 3789999999999999877654 78999985 3899999999877 8999999
Q ss_pred eecCCCccCCC
Q 048027 255 EIIPNHTCKRH 265 (735)
Q Consensus 255 ~~~~~HnC~~~ 265 (735)
.+..+|||++.
T Consensus 80 ~~~~~HNH~L~ 90 (91)
T PF03101_consen 80 SFVLEHNHPLC 90 (91)
T ss_pred ECcCCcCCCCC
Confidence 99999999873
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=98.01 E-value=3.9e-06 Score=61.48 Aligned_cols=31 Identities=35% Similarity=0.704 Sum_probs=27.6
Q ss_pred EEecCceEeecCccccccCcchhhHHHHHhc
Q 048027 641 VNKELAICSCGLWQLSGIPCPHACRCIIHWA 671 (735)
Q Consensus 641 V~l~~~tCsC~~~~~~GiPC~Halav~~~~~ 671 (735)
+++...+|||..|+..|.||+|++|++...+
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 5667899999999999999999999997653
No 10
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=96.71 E-value=0.00041 Score=61.05 Aligned_cols=55 Identities=9% Similarity=0.236 Sum_probs=48.9
Q ss_pred ccccccccceee--ccccchhHHHhhhccCCCCCccccc---c-CchhccccccccccCCc
Q 048027 39 HVYGGSSSGVQL--QMPYGQCTIAIDSKYTSDQPRGVHI---S-DTEVINDLKDVDESDNV 93 (735)
Q Consensus 39 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~~~~~~~~~~~~~ 93 (735)
-|+||....|.| +|++.++++|+++.++++...+++| + |...+..+.+|+|..||
T Consensus 18 ~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~~~lky~Lp~edld~Lisv~~DeDl~~M 78 (97)
T cd06410 18 RYVGGETRIVSVDRSISFKELVSKLSELFGAGVVVTLKYQLPDEDLDALISVSNDEDLKNM 78 (97)
T ss_pred EEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCceEEEEEcCCCCcceeEEecCcHHHHHH
Confidence 489999999999 8999999999999999985588999 3 44568999999999999
No 11
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=96.55 E-value=0.0011 Score=62.88 Aligned_cols=81 Identities=20% Similarity=0.113 Sum_probs=68.7
Q ss_pred CcEEEEcCeEeecCCCCceEEEEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCchhHH
Q 048027 384 RRLVIVDGWEIDSPYKSVMLVAVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDNGVD 463 (735)
Q Consensus 384 ~~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~~l~ 463 (735)
++.+.+|-||.+.+-+ ..++..++|.+++ +|.+-|.+.-+...=..||..+.+... ..|..|+||+..+..
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~------~~p~~ivtDk~~aY~ 71 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR------GEPRVIVTDKLPAYP 71 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec------cccceeecccCCccc
Confidence 4678999999876533 4555788999999 899999999999999999999888775 469999999999999
Q ss_pred HHHHhhCCCC
Q 048027 464 EAVSEFLPYA 473 (735)
Q Consensus 464 ~Ai~~vfP~a 473 (735)
.|++++.|..
T Consensus 72 ~A~~~l~~~~ 81 (140)
T PF13610_consen 72 AAIKELNPEG 81 (140)
T ss_pred hhhhhccccc
Confidence 9999998874
No 12
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=94.89 E-value=0.43 Score=54.53 Aligned_cols=133 Identities=17% Similarity=0.204 Sum_probs=92.5
Q ss_pred cCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCchhHHHHHHhhCCCCeeecccchHHHHHHhhCC-cHHHHHHHHHH
Q 048027 424 EENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDNGVDEAVSEFLPYAQYRQCCFSIYNKLMKQFP-HALVYSLFWSA 502 (735)
Q Consensus 424 ~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~-~~~~~~~f~~~ 502 (735)
..+.+-|.-+.+.+.+...... ..-+++.+|+...|.+++. .+|.+.|.+..+|+.+.+.+.++ .+.+.+.++++
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~---~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~a 310 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDK---TTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKA 310 (470)
T ss_pred cchHHHHHHHHHHHHHhcCccc---ceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHH
Confidence 5567889999998888776542 3357888999999988776 99999999999999999999886 45677777777
Q ss_pred HccchHHHHHHHHHHHHhh--Cc-------hhhhHHHhcCcccceecccCCCcccccCCCCchHHHhHHHhh
Q 048027 503 CRSTNKAAFQHQMMLLQCH--NR-------DCYQWLIDRGCHTWALYCMPEWAKSTDITISATEQLRIWLLK 565 (735)
Q Consensus 503 ~~~~t~~eFe~~~~~l~~~--~~-------~~~~~L~~~~~~~Wa~a~~~~~~~~g~~TtN~~Es~N~~lk~ 565 (735)
.+.....++...++.+... .+ ++..||..+.... .+|-. +-|.......|+.++.+..
T Consensus 311 l~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i--~~y~~---~~~~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 311 LKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGI--KPYRE---REGLRGIGAEESVSHVLSY 377 (470)
T ss_pred HHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHh--hhhhh---ccCCCccchhhhhhhHHHH
Confidence 7777888888888877643 21 3455555541111 12211 1233444457777776643
No 13
>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=94.42 E-value=0.088 Score=54.70 Aligned_cols=93 Identities=17% Similarity=0.179 Sum_probs=69.5
Q ss_pred EEEcCeEeecCCCCceEEEEEEcC--CCCEEEEEEEecccCCHHHHHHHHHHH-HHhhccCcCCCCCcEEEEecCchhHH
Q 048027 387 VIVDGWEIDSPYKSVMLVAVCRDG--NNAVLPIAFCEVQEENLDSWSFFLKNL-YEGLRMDYMDYGKGICIMCDGDNGVD 463 (735)
Q Consensus 387 i~iD~T~~~~~y~~~ll~avg~d~--~~~~~plafalv~~Et~esw~WfL~~l-~~~~~~~~~~~~~p~~iisD~~~~l~ 463 (735)
|+||-+.....+.. +..+-+|. +++. + +.++++-+.++..-||..+ -.... ....+|++|...+..
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~-i--l~i~~~r~~~~l~~~~~~~~~~~~~------~~v~~V~~Dm~~~y~ 69 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGR-I--LDILPGRDKETLKDFFRSLYPEEER------KNVKVVSMDMSPPYR 69 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCce-E--EEEcCCccHHHHHHHHHHhCccccc------cceEEEEcCCCcccc
Confidence 46777776554443 44455555 3333 2 3478888888888888876 33333 567999999999999
Q ss_pred HHHHhhCCCCeeecccchHHHHHHhhC
Q 048027 464 EAVSEFLPYAQYRQCCFSIYNKLMKQF 490 (735)
Q Consensus 464 ~Ai~~vfP~a~h~~C~~Hi~~N~~~~~ 490 (735)
.|+++.||+|.+..-.||+++++.+.+
T Consensus 70 ~~~~~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 70 SAIREYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred ccccccccccccccccchhhhhhhhcc
Confidence 999999999999999999999887643
No 14
>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=89.60 E-value=0.76 Score=36.77 Aligned_cols=39 Identities=13% Similarity=0.137 Sum_probs=32.2
Q ss_pred ceEEEEeecCCCceEEEEEEecCCceEEEeeecCCCccC
Q 048027 225 TLISCECSNLMCDWKVSAAKVRKGNVFVLKEIIPNHTCK 263 (735)
Q Consensus 225 ~r~~~~C~~~gCpwrv~as~~~~~~~~~V~~~~~~HnC~ 263 (735)
.|.-++|+..+||++-.+.+..++....++++.++|||+
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 466799999999999999988878888999999999996
No 15
>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=88.50 E-value=0.9 Score=50.17 Aligned_cols=59 Identities=7% Similarity=0.134 Sum_probs=51.6
Q ss_pred CCCCCCCeeCCHHHHHHHHHHHHHHcCcEEEEeeec-CceEEEEeecCCCceEEEEEEec
Q 048027 188 ITMELGQRFKDEFHFRRAVEIQAMRDGIKLCVMENT-STLISCECSNLMCDWKVSAAKVR 246 (735)
Q Consensus 188 ~~l~vG~~F~s~ee~k~ai~~yAi~~~f~~~~~ks~-~~r~~~~C~~~gCpwrv~as~~~ 246 (735)
+.-..+..|++.++-..+|..|-...++.|..+.|- .++|+|-|....|||+|..+...
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 344567889999999999999999999999998886 47899999999999999998543
No 16
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=87.52 E-value=12 Score=39.39 Aligned_cols=75 Identities=11% Similarity=0.019 Sum_probs=50.9
Q ss_pred CCcEEEEcCeEeecCCCCceEEEEEEcCCCCEEEEEEEeccc-CCHHHHHHHHHHHH-Hhhcc-CcCCCCCcEEEEecCc
Q 048027 383 SRRLVIVDGWEIDSPYKSVMLVAVCRDGNNAVLPIAFCEVQE-ENLDSWSFFLKNLY-EGLRM-DYMDYGKGICIMCDGD 459 (735)
Q Consensus 383 ~~~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~plafalv~~-Et~esw~WfL~~l~-~~~~~-~~~~~~~p~~iisD~~ 459 (735)
-..+++.|-||.....++.++.++-+|...+ .++||++... .+.+.-.-+|+... ...+. .. ..|..|.||+.
T Consensus 86 pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~---~~~~iihSD~G 161 (262)
T PRK14702 86 SNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLP---SSPVEWLTDNG 161 (262)
T ss_pred CCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCC---CCCeEEEcCCC
Confidence 3478999999987654556888888888776 6889999874 56666555555433 32221 00 45789999987
Q ss_pred hh
Q 048027 460 NG 461 (735)
Q Consensus 460 ~~ 461 (735)
..
T Consensus 162 sq 163 (262)
T PRK14702 162 SC 163 (262)
T ss_pred cc
Confidence 64
No 17
>PHA02517 putative transposase OrfB; Reviewed
Probab=86.93 E-value=6.6 Score=41.40 Aligned_cols=73 Identities=12% Similarity=-0.064 Sum_probs=46.8
Q ss_pred CCcEEEEcCeEeecCCCCceEEEEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCchhH
Q 048027 383 SRRLVIVDGWEIDSPYKSVMLVAVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDNGV 462 (735)
Q Consensus 383 ~~~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~~l 462 (735)
-..+++.|-||....- +..++++.+|...+ +++|+.+...++.+...-+|+......+. ..+..|.||+....
T Consensus 109 pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~~~~~~-----~~~~i~~sD~G~~y 181 (277)
T PHA02517 109 PNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQALWARGR-----PGGLIHHSDKGSQY 181 (277)
T ss_pred CCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHHHhcCC-----CcCcEeeccccccc
Confidence 3578999999986543 56677777776555 46778888888887654444443333331 22356778877643
No 18
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=86.13 E-value=17 Score=39.02 Aligned_cols=77 Identities=12% Similarity=0.060 Sum_probs=52.4
Q ss_pred CCcEEEEcCeEeecCCCCceEEEEEEcCCCCEEEEEEEeccc-CCHHHHHHHHHH-HHHhhccCcCCCCCcEEEEecCch
Q 048027 383 SRRLVIVDGWEIDSPYKSVMLVAVCRDGNNAVLPIAFCEVQE-ENLDSWSFFLKN-LYEGLRMDYMDYGKGICIMCDGDN 460 (735)
Q Consensus 383 ~~~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~plafalv~~-Et~esw~WfL~~-l~~~~~~~~~~~~~p~~iisD~~~ 460 (735)
-..+++.|-||....-++.++.++-+|...+ .++||++... .+.+.-.-+|+. +....+.... ..|..|.||+..
T Consensus 125 pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~--~~~~iihSDrGs 201 (301)
T PRK09409 125 SNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLP--SSPVEWLTDNGS 201 (301)
T ss_pred CCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCC--CCCcEEecCCCc
Confidence 4579999999986654556888888888777 6889999876 566665555554 4333221000 357889999876
Q ss_pred hH
Q 048027 461 GV 462 (735)
Q Consensus 461 ~l 462 (735)
..
T Consensus 202 qy 203 (301)
T PRK09409 202 CY 203 (301)
T ss_pred cc
Confidence 43
No 19
>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=85.03 E-value=1.1 Score=47.34 Aligned_cols=86 Identities=15% Similarity=0.102 Sum_probs=55.7
Q ss_pred CCcEEEEcCeEee----cCCC-CceEEEEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEec
Q 048027 383 SRRLVIVDGWEID----SPYK-SVMLVAVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCD 457 (735)
Q Consensus 383 ~~~vi~iD~T~~~----~~y~-~~ll~avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD 457 (735)
-.+++.+|-|... ++.+ +-+.++++-+ .+.|.+.++-+.+.-.-+ +++ ..-+++||
T Consensus 66 ~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~-------L~~------~~GilvsD 126 (271)
T PF03050_consen 66 SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEF-------LGD------FSGILVSD 126 (271)
T ss_pred ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhh-------hcc------cceeeecc
Confidence 3578999988887 4433 3344444333 555666665555444333 332 13588999
Q ss_pred CchhHHHHHHhhCCCCeeecccchHHHHHHhhCCc
Q 048027 458 GDNGVDEAVSEFLPYAQYRQCCFSIYNKLMKQFPH 492 (735)
Q Consensus 458 ~~~~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~~ 492 (735)
+-.+-.. +..+.|+.|+.|+.|.+.+-...
T Consensus 127 ~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 127 GYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred ccccccc-----ccccccccccccccccccccccc
Confidence 9887654 33789999999999998876553
No 20
>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=79.38 E-value=13 Score=33.20 Aligned_cols=76 Identities=14% Similarity=-0.020 Sum_probs=55.8
Q ss_pred CCcEEEEcCeEee-cCCCCceEEEEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCchh
Q 048027 383 SRRLVIVDGWEID-SPYKSVMLVAVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDNG 461 (735)
Q Consensus 383 ~~~vi~iD~T~~~-~~y~~~ll~avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~~ 461 (735)
-...+.+|.++.. ...++..+..+.+|..-.. .+++.+...++.+.+..+|.......+. ..|.+|+||+..+
T Consensus 5 p~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~-----~~p~~i~tD~g~~ 78 (120)
T PF00665_consen 5 PGERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRGG-----RPPRVIRTDNGSE 78 (120)
T ss_dssp TTTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS------SE-SEEEEESCHH
T ss_pred CCCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeeccccccccccccccccccccc-----ccceecccccccc
Confidence 3568899998665 3455688888889886655 5577777777888888888877776663 2389999999998
Q ss_pred HHH
Q 048027 462 VDE 464 (735)
Q Consensus 462 l~~ 464 (735)
...
T Consensus 79 f~~ 81 (120)
T PF00665_consen 79 FTS 81 (120)
T ss_dssp HHS
T ss_pred ccc
Confidence 763
No 21
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=78.50 E-value=3.6 Score=32.31 Aligned_cols=46 Identities=13% Similarity=0.115 Sum_probs=24.6
Q ss_pred cCcEEEEeeecCceEEEEeecC---CCceEEEEEEecCCceEEEeeecCCCcc
Q 048027 213 DGIKLCVMENTSTLISCECSNL---MCDWKVSAAKVRKGNVFVLKEIIPNHTC 262 (735)
Q Consensus 213 ~~f~~~~~ks~~~r~~~~C~~~---gCpwrv~as~~~~~~~~~V~~~~~~HnC 262 (735)
.|+.|...+.........|... +|+++|... .+ ...|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~--~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AG--DGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CC--CCEEEECCCccCC
Confidence 4777777777788889999874 899999987 22 2344455578887
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=77.50 E-value=3.2 Score=33.07 Aligned_cols=38 Identities=16% Similarity=0.103 Sum_probs=31.2
Q ss_pred ceEEEEeec-CCCceEEEEEEecCCceEEEeeecCCCcc
Q 048027 225 TLISCECSN-LMCDWKVSAAKVRKGNVFVLKEIIPNHTC 262 (735)
Q Consensus 225 ~r~~~~C~~-~gCpwrv~as~~~~~~~~~V~~~~~~HnC 262 (735)
-|--++|.. .||+++=.+.+..++....++++.++|||
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 355689998 89999888877766667788899999998
No 23
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=75.48 E-value=33 Score=33.00 Aligned_cols=89 Identities=10% Similarity=0.115 Sum_probs=57.4
Q ss_pred CCceEEEEEEcCCCCEEEEEEEec-ccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCchhHHHH---HHhhCCCCe
Q 048027 399 KSVMLVAVCRDGNNAVLPIAFCEV-QEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDNGVDEA---VSEFLPYAQ 474 (735)
Q Consensus 399 ~~~ll~avg~d~~~~~~plafalv-~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~~l~~A---i~~vfP~a~ 474 (735)
+.+|+.++..-+.|-.|.=..-.- ...+.+...-+|+...+.++. ....-||||-...+.+| +.+-+|...
T Consensus 46 ~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~-----~nVvqVVTDn~~~~~~a~~~L~~k~p~if 120 (153)
T PF04937_consen 46 GRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGE-----ENVVQVVTDNASNMKKAGKLLMEKYPHIF 120 (153)
T ss_pred CCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhh-----hhhhHHhccCchhHHHHHHHHHhcCCCEE
Confidence 334444444444444443332221 224566666666666666664 45677899999988887 444589999
Q ss_pred eecccchHHHHHHhhCCc
Q 048027 475 YRQCCFSIYNKLMKQFPH 492 (735)
Q Consensus 475 h~~C~~Hi~~N~~~~~~~ 492 (735)
...|..|-+.-+.+.+..
T Consensus 121 w~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 121 WTPCAAHCINLMLEDIGK 138 (153)
T ss_pred EechHHHHHHHHHHHHhc
Confidence 999999998877776543
No 24
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=72.45 E-value=8.3 Score=38.98 Aligned_cols=83 Identities=17% Similarity=0.067 Sum_probs=61.9
Q ss_pred CcEEEEcCeEeecCCCCc-eEEEEEEcCCCCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCchhH
Q 048027 384 RRLVIVDGWEIDSPYKSV-MLVAVCRDGNNAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDNGV 462 (735)
Q Consensus 384 ~~vi~iD~T~~~~~y~~~-ll~avg~d~~~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~~l 462 (735)
++.+.+|-||++.+-+.. |+- ++|.+| .+|-+-|...-+...=.-||..+++..+ .|.+|+||+.+..
T Consensus 70 ~~~w~vDEt~ikv~gkw~ylyr--Aid~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~g-------~p~v~vtDka~s~ 138 (215)
T COG3316 70 GDSWRVDETYIKVNGKWHYLYR--AIDADG--LTLDVWLSKRRNALAAKAFLKKLLKKHG-------EPRVFVTDKAPSY 138 (215)
T ss_pred ccceeeeeeEEeeccEeeehhh--hhccCC--CeEEEEEEcccCcHHHHHHHHHHHHhcC-------CCceEEecCccch
Confidence 467889999987653332 333 345554 4677778888777777788888777664 4899999999999
Q ss_pred HHHHHhhCCCCeeec
Q 048027 463 DEAVSEFLPYAQYRQ 477 (735)
Q Consensus 463 ~~Ai~~vfP~a~h~~ 477 (735)
..|+.++-+.+.|+.
T Consensus 139 ~~A~~~l~~~~ehr~ 153 (215)
T COG3316 139 TAALRKLGSEVEHRT 153 (215)
T ss_pred HHHHHhcCcchheec
Confidence 999999999777664
No 25
>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=68.45 E-value=2.3 Score=23.26 Aligned_cols=11 Identities=0% Similarity=-0.130 Sum_probs=4.1
Q ss_pred CCCCCCCCCcc
Q 048027 718 RLIDPMNGDDE 728 (735)
Q Consensus 718 ~r~~GRpkk~r 728 (735)
.|++|||+|.-
T Consensus 1 ~r~RGRP~k~~ 11 (13)
T PF02178_consen 1 KRKRGRPRKNA 11 (13)
T ss_dssp S--SS--TT--
T ss_pred CCcCCCCcccc
Confidence 36799999864
No 26
>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=65.13 E-value=4.3 Score=26.46 Aligned_cols=15 Identities=0% Similarity=-0.141 Sum_probs=11.8
Q ss_pred CCCCCCCCCcccccc
Q 048027 718 RLIDPMNGDDETQVN 732 (735)
Q Consensus 718 ~r~~GRpkk~r~~~~ 732 (735)
.|++|||+|......
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 478999999887653
No 27
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=43.49 E-value=16 Score=32.37 Aligned_cols=45 Identities=16% Similarity=0.399 Sum_probs=28.5
Q ss_pred CeEEEEEecCceEeecCccc-----cccCcchhhHHHHHhcccccccccccc
Q 048027 636 GLSFVVNKELAICSCGLWQL-----SGIPCPHACRCIIHWAASYADFVHDFM 682 (735)
Q Consensus 636 ~~~~~V~l~~~tCsC~~~~~-----~GiPC~Halav~~~~~~~~~~yv~~~y 682 (735)
++.|+++.+ -|||..|-. -.-||.|++.+-...--.-.+||+-+|
T Consensus 42 ~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y~ 91 (117)
T COG5431 42 ERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAYY 91 (117)
T ss_pred ccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEec
Confidence 446777776 899988762 235799998765444333445554444
No 28
>PRK13907 rnhA ribonuclease H; Provisional
Probab=37.93 E-value=2.2e+02 Score=25.81 Aligned_cols=78 Identities=18% Similarity=0.106 Sum_probs=44.7
Q ss_pred EEEEcCeEeecCCCCceEEEEEEcCCCCEEEEEEE-ecccCCHHHHHHHHHHHHHhhccCcCCCCCcEEEEecCchhHHH
Q 048027 386 LVIVDGWEIDSPYKSVMLVAVCRDGNNAVLPIAFC-EVQEENLDSWSFFLKNLYEGLRMDYMDYGKGICIMCDGDNGVDE 464 (735)
Q Consensus 386 vi~iD~T~~~~~y~~~ll~avg~d~~~~~~plafa-lv~~Et~esw~WfL~~l~~~~~~~~~~~~~p~~iisD~~~~l~~ 464 (735)
.|.+||.+..+.-.+-...++ .+..+... +++. -..+.+..-+.-++..|+.+.... ..+..|-||. +.+.+
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~~~~-~~~~~~~~tn~~AE~~All~aL~~a~~~g----~~~v~i~sDS-~~vi~ 75 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQPAVQ-LSLPLGTMSNHEAEYHALLAALKYCTEHN----YNIVSFRTDS-QLVER 75 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHhCC----CCEEEEEech-HHHHH
Confidence 378899888765333222222 45555432 3322 223445666777777777765532 3467788875 66666
Q ss_pred HHHhhC
Q 048027 465 AVSEFL 470 (735)
Q Consensus 465 Ai~~vf 470 (735)
++...+
T Consensus 76 ~~~~~~ 81 (128)
T PRK13907 76 AVEKEY 81 (128)
T ss_pred HHhHHH
Confidence 666654
No 29
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=36.34 E-value=11 Score=31.69 Aligned_cols=35 Identities=11% Similarity=0.339 Sum_probs=29.5
Q ss_pred cccccceee--ccccchhHHHhhhccCCC-CCcccccc
Q 048027 42 GGSSSGVQL--QMPYGQCTIAIDSKYTSD-QPRGVHIS 76 (735)
Q Consensus 42 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~-~~~~~~~~ 76 (735)
||...-+.+ +++|.++.++|..+|+.. +..+++|-
T Consensus 9 ~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~ 46 (81)
T smart00666 9 GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQ 46 (81)
T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEE
Confidence 676666777 799999999999999986 77788885
No 30
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=34.15 E-value=19 Score=37.04 Aligned_cols=23 Identities=30% Similarity=0.573 Sum_probs=19.5
Q ss_pred ceEeecCccccccCcchhhHHHHHhc
Q 048027 646 AICSCGLWQLSGIPCPHACRCIIHWA 671 (735)
Q Consensus 646 ~tCsC~~~~~~GiPC~Halav~~~~~ 671 (735)
..|||..|. .||.|+-||..+..
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 469999865 79999999998875
No 31
>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=31.79 E-value=1.3e+02 Score=28.27 Aligned_cols=69 Identities=14% Similarity=0.149 Sum_probs=39.1
Q ss_pred cEEEEcCeEeecCC--------------CCceEEEEEEcCC-CCEEEEEEEecccCCHHHHHHHHHHHHHhhccCcCCCC
Q 048027 385 RLVIVDGWEIDSPY--------------KSVMLVAVCRDGN-NAVLPIAFCEVQEENLDSWSFFLKNLYEGLRMDYMDYG 449 (735)
Q Consensus 385 ~vi~iD~T~~~~~y--------------~~~ll~avg~d~~-~~~~plafalv~~Et~esw~WfL~~l~~~~~~~~~~~~ 449 (735)
.+|-+|.||..++- .....++++++-+ +..--+...++++.+.++..=+++.. + .
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~---i-------~ 73 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEH---I-------E 73 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHh---h-------h
Confidence 36788888875332 2234445555554 33333334445667776655444332 2 3
Q ss_pred CcEEEEecCchhHH
Q 048027 450 KGICIMCDGDNGVD 463 (735)
Q Consensus 450 ~p~~iisD~~~~l~ 463 (735)
+..+|+||...+-.
T Consensus 74 ~gs~i~TD~~~aY~ 87 (151)
T PF12762_consen 74 PGSTIITDGWRAYN 87 (151)
T ss_pred ccceeeecchhhcC
Confidence 45789999988764
No 32
>PF13565 HTH_32: Homeodomain-like domain
Probab=30.40 E-value=69 Score=26.29 Aligned_cols=32 Identities=19% Similarity=0.267 Sum_probs=26.6
Q ss_pred hHHHHHhhhhhhCCCCChhhHHHHHHHhcCCc
Q 048027 275 WNAAKFLHLWVENPNIDLDRLGDEIERCSGIK 306 (735)
Q Consensus 275 ~ia~~~~~~l~~~~~~~~~~I~~~l~~~~g~~ 306 (735)
.+...+.+.+..+|.+++.+|...|++++|+.
T Consensus 34 e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~ 65 (77)
T PF13565_consen 34 EQRERIIALIEEHPRWTPREIAEYLEEEFGIS 65 (77)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCC
Confidence 44466777778899999999999999999864
No 33
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=26.10 E-value=95 Score=35.85 Aligned_cols=34 Identities=26% Similarity=0.537 Sum_probs=24.4
Q ss_pred EEEEec----CceEeecCccccccCcchhhHHHHHhcccc
Q 048027 639 FVVNKE----LAICSCGLWQLSGIPCPHACRCIIHWAASY 674 (735)
Q Consensus 639 ~~V~l~----~~tCsC~~~~~~GiPC~Halav~~~~~~~~ 674 (735)
+.|.+. +-.|||.. +..|- |.|++||+....-.|
T Consensus 62 v~vtL~~~~~ss~CTCP~-~~~ga-CKH~VAvvl~~~~~p 99 (587)
T COG4715 62 VRVTLEGGALSSICTCPY-GGSGA-CKHVVAVVLEYLDDP 99 (587)
T ss_pred EEEEeecCCcCceeeCCC-CCCcc-hHHHHHHHHHHhhcc
Confidence 456663 46899997 44443 999999998875433
No 34
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=24.24 E-value=1.1e+02 Score=25.54 Aligned_cols=30 Identities=13% Similarity=0.287 Sum_probs=26.3
Q ss_pred CeeCCHHHHHHHHHHHHHHcCcEEEEeeec
Q 048027 194 QRFKDEFHFRRAVEIQAMRDGIKLCVMENT 223 (735)
Q Consensus 194 ~~F~s~ee~k~ai~~yAi~~~f~~~~~ks~ 223 (735)
-+++|.+++..||..|+.+++-.+++...+
T Consensus 12 ~~yPs~e~i~~aIE~YC~~~~~~l~Fisr~ 41 (74)
T PF14201_consen 12 PKYPSKEEICEAIEKYCIKNGESLEFISRD 41 (74)
T ss_pred CCCCCHHHHHHHHHHHHHHcCCceEEEecC
Confidence 458899999999999999999999887554
Done!