Query 039513
Match_columns 690
No_of_seqs 299 out of 577
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 10:26:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039513hhsearch_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 4.4E-60 9.5E-65 548.1 37.7 501 69-630 70-623 (846)
2 PF10551 MULE: MULE transposas 99.7 3.4E-18 7.3E-23 149.7 8.7 89 303-397 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.4 1.2E-13 2.5E-18 151.6 1.1 245 185-490 99-350 (381)
4 PF03101 FAR1: FAR1 DNA-bindin 98.5 2.2E-07 4.8E-12 80.9 6.5 71 77-160 18-89 (91)
5 COG3328 Transposase and inacti 98.3 3.6E-05 7.9E-10 83.8 17.8 180 294-490 143-329 (379)
6 smart00575 ZnF_PMZ plant mutat 97.7 2.7E-05 5.8E-10 52.4 2.0 25 587-611 2-27 (28)
7 PF04434 SWIM: SWIM zinc finge 97.0 0.0007 1.5E-08 49.5 3.6 26 583-608 12-38 (40)
8 PF15299 ALS2CR8: Amyotrophic 95.8 0.13 2.7E-06 52.7 12.6 59 182-240 155-221 (225)
9 PF08731 AFT: Transcription fa 95.4 0.07 1.5E-06 47.7 7.6 30 130-159 80-110 (111)
10 PF01610 DDE_Tnp_ISL3: Transpo 94.8 0.049 1.1E-06 56.2 5.8 94 300-401 2-97 (249)
11 PF13610 DDE_Tnp_IS240: DDE do 88.4 0.15 3.3E-06 48.0 0.3 77 298-382 3-79 (140)
12 PF06782 UPF0236: Uncharacteri 88.2 53 0.0011 37.5 23.1 132 347-494 242-382 (470)
13 PF00665 rve: Integrase core d 85.1 7.5 0.00016 34.6 9.6 75 297-376 7-82 (120)
14 COG4279 Uncharacterized conser 80.5 0.84 1.8E-05 46.5 1.4 45 586-632 125-172 (266)
15 PF03050 DDE_Tnp_IS66: Transpo 79.3 2.1 4.6E-05 44.7 4.1 81 298-400 69-154 (271)
16 PF03106 WRKY: WRKY DNA -bindi 75.9 3.4 7.5E-05 33.1 3.4 28 131-158 30-58 (60)
17 PF04937 DUF659: Protein of un 75.7 33 0.00073 32.8 10.8 108 287-402 26-138 (153)
18 COG4715 Uncharacterized conser 68.9 7.5 0.00016 44.2 5.2 47 562-611 50-97 (587)
19 smart00774 WRKY DNA binding do 68.9 5.5 0.00012 31.8 3.0 29 130-158 30-59 (59)
20 PRK14702 insertion element IS2 62.6 40 0.00086 35.2 9.0 75 297-372 88-163 (262)
21 PRK09409 IS2 transposase TnpB; 56.5 59 0.0013 34.7 9.2 75 296-371 126-201 (301)
22 COG3316 Transposase and inacti 56.2 21 0.00046 36.1 5.3 76 297-382 71-147 (215)
23 PF13936 HTH_38: Helix-turn-he 53.5 8.6 0.00019 28.6 1.6 28 183-210 3-30 (44)
24 COG5431 Uncharacterized metal- 48.9 5 0.00011 35.4 -0.4 19 587-605 51-75 (117)
25 PF08259 Periviscerokin: Periv 48.7 6.1 0.00013 20.5 0.1 8 41-48 4-11 (11)
26 PF04500 FLYWCH: FLYWCH zinc f 43.0 20 0.00043 27.9 2.3 25 131-158 38-62 (62)
27 PHA02517 putative transposase 36.3 1E+02 0.0022 32.1 7.1 71 297-373 111-181 (277)
28 PF02796 HTH_7: Helix-turn-hel 25.9 51 0.0011 24.4 1.9 27 183-209 4-30 (45)
29 COG3464 Transposase and inacti 23.8 2.5E+02 0.0054 31.4 7.7 54 333-394 184-238 (402)
30 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 23.5 1.1E+02 0.0023 23.7 3.2 27 184-210 4-30 (50)
31 KOG0053 Cystathionine beta-lya 21.2 8E+02 0.017 27.5 10.7 103 228-335 129-238 (409)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.4e-60 Score=548.11 Aligned_cols=501 Identities=13% Similarity=0.155 Sum_probs=371.9
Q ss_pred ccccCCCCCcccccccceeeEEEEeeecCCCccccCCCCCCCCCCcc-----cCC-CC---------------------C
Q 039513 69 SRRKRSEGSISKPRVDGYLEYTLYWCSYGPEDYRDSESGNGDGSNVK-----PAT-GK---------------------G 121 (690)
Q Consensus 69 ~~~~~~~g~~~~~~~d~~~~~~~y~Cs~g~~~~~~~~~~~~~~g~~~-----p~~-~~---------------------~ 121 (690)
..-.|.+||+|.+.++++.||+.|+...||...+++++..+..|.+. +++ |. .
T Consensus 70 ~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~ 149 (846)
T PLN03097 70 TNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPEN 149 (846)
T ss_pred CCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccc
Confidence 34579999999999999999999999999987654432111112110 111 10 0
Q ss_pred CCCCCCccccCcceEEEEEEeeeCCcEEEEEE-eccCCCCCCCCCCCCCCcccccccccccCCCCCHHHHHHHHHHHHcC
Q 039513 122 SRPGRRHMMRGCLCHFTVKRLYTRPLLALIIY-NQRKHVDKTGAPCHGILDRDAVGTRAMYAPRISEDLRQKVMSMLYVG 200 (690)
Q Consensus 122 ~r~~r~~tk~gC~a~~~vk~~~~~~~~~v~~~-~eHnH~~~~~~~~h~~~~~~~~g~~~~~~~~is~~~r~~i~~ll~~G 200 (690)
.+++|..+|+||+|+|.|++ ..+++|.|..+ .+|||++..+ + .++...+
T Consensus 150 ~~~rR~~tRtGC~A~m~Vk~-~~~gkW~V~~fv~eHNH~L~p~-------~------------~~~~~~r---------- 199 (846)
T PLN03097 150 GTGRRSCAKTDCKASMHVKR-RPDGKWVIHSFVKEHNHELLPA-------Q------------AVSEQTR---------- 199 (846)
T ss_pred ccccccccCCCCceEEEEEE-cCCCeEEEEEEecCCCCCCCCc-------c------------ccchhhh----------
Confidence 01235678999999999997 46778988887 8999965521 1 1121111
Q ss_pred CCHHHHHHHHHHhhhcCCCCCCCCCcCcHHHHHHHHHHHhhccccccCChHHHHHHHHHhhc--CceeEEEeccCCCC-e
Q 039513 201 ISLDNIIQHHIEAVQGHGGPHNRDDFLTRNDVRNMERVIRNSSHELHVDDECSVKMWVQRHH--KHVFFFQDYSVSEP-F 277 (690)
Q Consensus 201 i~~~~Il~~~~~~~~~~~g~~~r~~~~t~~Di~Ni~~~~~~~~~~l~~~D~~Sv~~~v~~~~--~~vf~y~~~~d~~~-f 277 (690)
.|+..+...+ ++. +....+..|.+|..++.++ ..+..+|+..+..+++++| +|.|||.-+.|+++ .
T Consensus 200 ----~~~~~~~~~~---~~~--~~v~~~~~d~~~~~~~~r~--~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l 268 (846)
T PLN03097 200 ----KMYAAMARQF---AEY--KNVVGLKNDSKSSFDKGRN--LGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRL 268 (846)
T ss_pred ----hhHHHHHhhh---hcc--ccccccchhhcchhhHHHh--hhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCe
Confidence 2222222211 121 2234456677776655543 4566899999999999986 89999998776665 4
Q ss_pred EEEecCHHH-HHHHHhhCCCcEEEEeecccccccCCceEEEEEEcCCCCeeEEEEEEeeccchHHHHHHHHHHHHHHhcc
Q 039513 278 ILVIQTDWQ-LQQMLHYGNNGLMSFHSTFGSKKLKYPLSTLLVFDSSHNAIPVAWIITSSFVGQFVHKWIGLLAERIRTK 356 (690)
Q Consensus 278 ~l~i~t~~q-~~~l~~fg~~~vv~~DsT~~tn~~~~pL~~~~v~d~~g~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~ 356 (690)
.-+||++.. +..+..||+ ||+||+||.||+|++||.+|+|+|+||+++++||+|+.+|+.++|.|+|++|+.+|++
T Consensus 269 ~niFWaD~~sr~~Y~~FGD--vV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~g- 345 (846)
T PLN03097 269 KNLFWVDAKSRHDYGNFSD--VVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGG- 345 (846)
T ss_pred eeEEeccHHHHHHHHhcCC--EEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCC-
Confidence 457777765 556899999 9999999999999999999999999999999999999999999999999999999964
Q ss_pred CCCcceeEEEecCChhHHHHHHHhCc-cceeechhhHHHHHHHHHHhhcCChHHHHHHHHHHHHHHhccCCCCchHHHHH
Q 039513 357 DPRWRLSAFLVDNPSFDISTIRENFQ-CRILLCVWHVRRAWIKNLLKKCYNVEVQQEMFKQLSWILYSSRSSPNSVDTIE 435 (690)
Q Consensus 357 ~p~~~P~~~mtD~d~a~~~AI~~vFp-~~~llC~wHV~qaw~k~l~~~~~~~e~~~~i~~~l~~lv~~~~~~~~~~~~~e 435 (690)
..|++||||+|.|+.+||++||| +.|++|.|||+++..++|...+. ....+...|..||+.+.++++|+..|.
T Consensus 346 ---k~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~---~~~~f~~~f~~cv~~s~t~eEFE~~W~ 419 (846)
T PLN03097 346 ---QAPKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIK---QHENFMAKFEKCIYRSWTEEEFGKRWW 419 (846)
T ss_pred ---CCCceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhh---hhhHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 47999999999999999999999 79999999999999999976442 235688899999999988888999999
Q ss_pred HHHHHhhchhHHHHHHHhhhhhhHHHHhhhc-cccCCCCCCCCchHHHHHHHhhhhhccccCC-CccccHHHHHHHHhh-
Q 039513 436 EFMQVFVDQCAFMDYFKSQWLPHIELWVTGI-RSLPVTTPEPLAAIETYHLRLKSKLFHEQNV-NFWPRVDWLIHTLTT- 512 (690)
Q Consensus 436 ~~~~~~~~~~~f~~Yf~~~Wl~~~~~Wa~~y-r~~~~~g~~Tnn~~Es~h~~LK~~~l~~~~~-~~~~rvD~lv~~L~~- 512 (690)
.++++|.... .+|+...| ..+++||++| +..+++|+.||+++||+|+.||.++-....+ .|..++|.++.....
T Consensus 420 ~mi~ky~L~~--n~WL~~LY-~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ek 496 (846)
T PLN03097 420 KILDRFELKE--DEWMQSLY-EDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEE 496 (846)
T ss_pred HHHHhhcccc--cHHHHHHH-HhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHH
Confidence 9999986432 36788887 4579999999 7788999999999999999999854333333 467778877775432
Q ss_pred h----hhhh---------hhHHhhhc---cccchHhhhhhhcccchhHhHhccCCceEEeccCcceeEEEeeccCCceeE
Q 039513 513 E----FHSL---------YWLDQYSM---ETGYFENLRDDSFSTNAWSQALHIPDVNVMLDEQNLQLAKIISQADRTLAY 576 (690)
Q Consensus 513 ~----v~s~---------y~l~~~s~---~~~~f~~~q~e~~~~~s~~~a~~i~~~~V~~~~~~~~~~~V~S~~~~~~~~ 576 (690)
+ +.+. +-++..+. +..+|+.||+|+..... +.+ ..+ .++.....+.|........+.
T Consensus 497 E~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~----~~~--~~~-~~dg~~~~y~V~~~~~~~~~~ 569 (846)
T PLN03097 497 EAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVA----CHP--KME-SQDETSITFRVQDFEKNQDFT 569 (846)
T ss_pred HHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhhh----eEE--eee-ccCCceEEEEEEEecCCCcEE
Confidence 1 2111 11222221 35678999999875221 111 111 112223456787765555566
Q ss_pred EEeCCCCCeeeeecCCCC-CCccchhHHHHHHhhhccccCCChhhHHHHHHHHHh
Q 039513 577 TIWNPGSEFSLCDCPWSR-LGNVCEHVIKLAMVCKSRQVARPLLAAQVYRQALLS 630 (690)
Q Consensus 577 vV~n~~~~~~~CsC~~f~-~G~lCkHil~Vl~~~~~~~~~~p~~~~~~~~~~~~~ 630 (690)
|+||......+|+|+.|+ .|+||+|||+||.+.+.... ||.+.+.+|++....
T Consensus 570 V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~I-P~~YILkRWTKdAK~ 623 (846)
T PLN03097 570 VTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAI-PSQYILKRWTKDAKS 623 (846)
T ss_pred EEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccC-chhhhhhhchhhhhh
Confidence 669999999999999999 99999999999999888765 889999999877764
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=99.75 E-value=3.4e-18 Score=149.70 Aligned_cols=89 Identities=25% Similarity=0.332 Sum_probs=81.1
Q ss_pred ecccccccCCceEE---EEEEcCCCCeeEEEEEEeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCChhHHHHHHH
Q 039513 303 STFGSKKLKYPLST---LLVFDSSHNAIPVAWIITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSFDISTIRE 379 (690)
Q Consensus 303 sT~~tn~~~~pL~~---~~v~d~~g~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a~~~AI~~ 379 (690)
+||+||+| .|+++ ++++|++|+++|+||+++++|+.++|.++|+.+++.+. .. |.+||||.+.++++||++
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~----~~-p~~ii~D~~~~~~~Ai~~ 74 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMP----QK-PKVIISDFDKALINAIKE 74 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccc----cC-ceeeeccccHHHHHHHHH
Confidence 69999999 87775 99999999999999999999999999998887776664 34 999999999999999999
Q ss_pred hCc-cceeechhhHHHHHH
Q 039513 380 NFQ-CRILLCVWHVRRAWI 397 (690)
Q Consensus 380 vFp-~~~llC~wHV~qaw~ 397 (690)
+|| +.|++|.||+.|+|+
T Consensus 75 vfP~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 75 VFPDARHQLCLFHILRNIK 93 (93)
T ss_pred HCCCceEehhHHHHHHhhC
Confidence 999 799999999999873
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=99.36 E-value=1.2e-13 Score=151.61 Aligned_cols=245 Identities=15% Similarity=0.197 Sum_probs=172.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHHHhhhcCCCCCCCCCcCcHHHHHHHHHHHhhccccccCChHHHHHHHHHhhcCc
Q 039513 185 ISEDLRQKVMSMLYVGISLDNIIQHHIEAVQGHGGPHNRDDFLTRNDVRNMERVIRNSSHELHVDDECSVKMWVQRHHKH 264 (690)
Q Consensus 185 is~~~r~~i~~ll~~Gi~~~~Il~~~~~~~~~~~g~~~r~~~~t~~Di~Ni~~~~~~~~~~l~~~D~~Sv~~~v~~~~~~ 264 (690)
.+++.-+.|.+|-..|+|..+|-..+.+. +|+. .+...-|.++...+. ..+..|-.+
T Consensus 99 ~~~~l~~~i~~ly~~G~Str~i~~~l~~l----~g~~----~~S~s~vSri~~~~~-----------~~~~~w~~R---- 155 (381)
T PF00872_consen 99 REDSLEELIISLYLKGVSTRDIEEALEEL----YGEV----AVSKSTVSRITKQLD-----------EEVEAWRNR---- 155 (381)
T ss_pred hhhhhhhhhhhhhccccccccccchhhhh----hccc----ccCchhhhhhhhhhh-----------hhHHHHhhh----
Confidence 36677888999999999999998776553 3411 245556666544433 123333322
Q ss_pred eeEEEeccCCCCeEEEecCHHHHHHHHhhCCCcEEEEeecccccc-----cCCceEEEEEEcCCCCeeEEEEEEeeccch
Q 039513 265 VFFFQDYSVSEPFILVIQTDWQLQQMLHYGNNGLMSFHSTFGSKK-----LKYPLSTLLVFDSSHNAIPVAWIITSSFVG 339 (690)
Q Consensus 265 vf~y~~~~d~~~f~l~i~t~~q~~~l~~fg~~~vv~~DsT~~tn~-----~~~pL~~~~v~d~~g~~~pva~~i~~~et~ 339 (690)
-+.... -.+|++|+||-.-+ -+-.+++++|+|..|+-.++|+.+...|+.
T Consensus 156 ------------------------~L~~~~-y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~ 210 (381)
T PF00872_consen 156 ------------------------PLESEP-YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESA 210 (381)
T ss_pred ------------------------cccccc-ccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCcc
Confidence 221110 01799999996544 246789999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhccCCCcceeEEEecCChhHHHHHHHhCc-cceeechhhHHHHHHHHHHhhcCChHHHHHHHHHHH
Q 039513 340 QFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSFDISTIRENFQ-CRILLCVWHVRRAWIKNLLKKCYNVEVQQEMFKQLS 418 (690)
Q Consensus 340 ~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a~~~AI~~vFp-~~~llC~wHV~qaw~k~l~~~~~~~e~~~~i~~~l~ 418 (690)
..+..+|..+.++ +-..|..|++|...++.+||+++|| +.++.|.+|..+++.+++.+ ..+..+...|+
T Consensus 211 ~~W~~~l~~L~~R-----Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~-----k~~~~v~~~Lk 280 (381)
T PF00872_consen 211 ASWREFLQDLKER-----GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK-----KDRKEVKADLK 280 (381)
T ss_pred CEeeecchhhhhc-----cccccceeeccccccccccccccccchhhhhheechhhhhcccccc-----ccchhhhhhcc
Confidence 8876666555443 2225899999999999999999999 79999999999988777644 24567778888
Q ss_pred HHHhccCCCCchHHHHHHHHHHhhc-hhHHHHHHHhhhhhhHHHHhhhccccCCCCCCCCchHHHHHHHhhhh
Q 039513 419 WILYSSRSSPNSVDTIEEFMQVFVD-QCAFMDYFKSQWLPHIELWVTGIRSLPVTTPEPLAAIETYHLRLKSK 490 (690)
Q Consensus 419 ~lv~~~~~~~~~~~~~e~~~~~~~~-~~~f~~Yf~~~Wl~~~~~Wa~~yr~~~~~g~~Tnn~~Es~h~~LK~~ 490 (690)
.+.+..+. +.....+++|.+.|.+ .+.+.++++..|......|. |.......+.|||.+||+|+.||+.
T Consensus 281 ~I~~a~~~-e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~--fP~~~~~~i~TTN~iEsln~~irrr 350 (381)
T PF00872_consen 281 AIYQAPDK-EEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLD--FPPEHRRSIRTTNAIESLNKEIRRR 350 (381)
T ss_pred cccccccc-chhhhhhhhcccccccccchhhhhhhhccccccceee--ecchhccccchhhhccccccchhhh
Confidence 77555433 3467778888887764 57888888887743221111 1111123568999999999999984
No 4
>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=98.50 E-value=2.2e-07 Score=80.87 Aligned_cols=71 Identities=20% Similarity=0.277 Sum_probs=51.1
Q ss_pred CcccccccceeeEEEEeeecCCCccccCCCCCCCCCCcccCCCCCCCCCCCccccCcceEEEEEEeeeCCcEEEEEE-ec
Q 039513 77 SISKPRVDGYLEYTLYWCSYGPEDYRDSESGNGDGSNVKPATGKGSRPGRRHMMRGCLCHFTVKRLYTRPLLALIIY-NQ 155 (690)
Q Consensus 77 ~~~~~~~d~~~~~~~y~Cs~g~~~~~~~~~~~~~~g~~~p~~~~~~r~~r~~tk~gC~a~~~vk~~~~~~~~~v~~~-~e 155 (690)
.+.+++.++.+.+..|+|++++....+.+ ...+.++.++++++||+|+|.|++.. ++.|.|..+ .+
T Consensus 18 ~s~~~~~~~~~~~~~~~C~r~G~~~~~~~------------~~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~~~~~~ 84 (91)
T PF03101_consen 18 SSRKSKKNGEIKRVTFVCSRGGKYKSKKK------------NEEKRRRNRPSKKTGCKARINVKRRK-DGKWRVTSFVLE 84 (91)
T ss_pred eeEeCCCCceEEEEEEEECCccccccccc------------ccccccccccccccCCCEEEEEEEcc-CCEEEEEECcCC
Confidence 34445678889999999999753221110 01234456799999999999999865 788888877 89
Q ss_pred cCCCC
Q 039513 156 RKHVD 160 (690)
Q Consensus 156 HnH~~ 160 (690)
|||++
T Consensus 85 HNH~L 89 (91)
T PF03101_consen 85 HNHPL 89 (91)
T ss_pred cCCCC
Confidence 99954
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.26 E-value=3.6e-05 Score=83.79 Aligned_cols=180 Identities=12% Similarity=0.143 Sum_probs=122.9
Q ss_pred CCCcEEEEeecccccc--cCCceEEEEEEcCCCCeeEEEEEEeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCCh
Q 039513 294 GNNGLMSFHSTFGSKK--LKYPLSTLLVFDSSHNAIPVAWIITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPS 371 (690)
Q Consensus 294 g~~~vv~~DsT~~tn~--~~~pL~~~~v~d~~g~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~ 371 (690)
|+..++++|++|.--+ -+-.++..+|++..|+--.+|+.+...|+ .-+..||..+..+-. -....+++|.-+
T Consensus 143 ~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl-----~~v~l~v~Dg~~ 216 (379)
T COG3328 143 GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGL-----SDVLLVVVDGLK 216 (379)
T ss_pred cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccc-----cceeEEecchhh
Confidence 3444899999997666 34578889999999999999999999999 555556665554411 124556779999
Q ss_pred hHHHHHHHhCc-cceeechhhHHHHHHHHHHhhcCChHHHHHHHHHHHHHHhccCCCCchHHHHHHHHHHhhc-hhHHHH
Q 039513 372 FDISTIRENFQ-CRILLCVWHVRRAWIKNLLKKCYNVEVQQEMFKQLSWILYSSRSSPNSVDTIEEFMQVFVD-QCAFMD 449 (690)
Q Consensus 372 a~~~AI~~vFp-~~~llC~wHV~qaw~k~l~~~~~~~e~~~~i~~~l~~lv~~~~~~~~~~~~~e~~~~~~~~-~~~f~~ 449 (690)
..-+||.++|| +.+..|..|+.++....+.. +.+..+...+..+ +.....+.....|.++.+.|.. .+....
T Consensus 217 gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~-----k~~d~i~~~~~~I-~~a~~~e~~~~~~~~~~~~w~~~yP~i~~ 290 (379)
T COG3328 217 GLPEAISAVFPQAAVQRCIVHLVRNLLDKVPR-----KDQDAVLSDLRSI-YIAPDAEEALLALLAFSELWGKRYPAILK 290 (379)
T ss_pred hhHHHHHHhccHhhhhhhhhHHHhhhhhhhhh-----hhhHHHHhhhhhh-hccCCcHHHHHHHHHHHHhhhhhcchHHH
Confidence 99999999999 89999999999876665543 3455666666555 3333333355567777766653 344444
Q ss_pred HHHhhhhhhHHHHhhhccccCC---CCCCCCchHHHHHHHhhhh
Q 039513 450 YFKSQWLPHIELWVTGIRSLPV---TTPEPLAAIETYHLRLKSK 490 (690)
Q Consensus 450 Yf~~~Wl~~~~~Wa~~yr~~~~---~g~~Tnn~~Es~h~~LK~~ 490 (690)
...+.|.. .|. |-.+|- --+.|||.+|++|+.++..
T Consensus 291 ~~~~~~~~---~~~--F~~fp~~~r~~i~ttN~IE~~n~~ir~~ 329 (379)
T COG3328 291 SWRNALEE---LLP--FFAFPSEIRKIIYTTNAIESLNKLIRRR 329 (379)
T ss_pred HHHHHHHH---hcc--cccCcHHHHhHhhcchHHHHHHHHHHHH
Confidence 44545532 221 111222 1368999999999988764
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=97.65 E-value=2.7e-05 Score=52.39 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=22.3
Q ss_pred eeecCCCC-CCccchhHHHHHHhhhc
Q 039513 587 LCDCPWSR-LGNVCEHVIKLAMVCKS 611 (690)
Q Consensus 587 ~CsC~~f~-~G~lCkHil~Vl~~~~~ 611 (690)
+|+|+.|+ .|+||+|+++|+...+.
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 69999998 99999999999987653
No 7
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.03 E-value=0.0007 Score=49.47 Aligned_cols=26 Identities=27% Similarity=0.809 Sum_probs=22.8
Q ss_pred CCeeeeecCCCC-CCccchhHHHHHHh
Q 039513 583 SEFSLCDCPWSR-LGNVCEHVIKLAMV 608 (690)
Q Consensus 583 ~~~~~CsC~~f~-~G~lCkHil~Vl~~ 608 (690)
....+|+|+.|+ .|.+|+|+++|+..
T Consensus 12 ~~~~~CsC~~~~~~~~~CkHi~av~~~ 38 (40)
T PF04434_consen 12 IEQASCSCPYFQFRGGPCKHIVAVLLA 38 (40)
T ss_pred ccccEeeCCCccccCCcchhHHHHHHh
Confidence 456689999998 99999999999864
No 8
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=95.81 E-value=0.13 Score=52.70 Aligned_cols=59 Identities=20% Similarity=0.302 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHcCCCH-HHHHHHHHHhhhc-------CCCCCCCCCcCcHHHHHHHHHHHh
Q 039513 182 APRISEDLRQKVMSMLYVGISL-DNIIQHHIEAVQG-------HGGPHNRDDFLTRNDVRNMERVIR 240 (690)
Q Consensus 182 ~~~is~~~r~~i~~ll~~Gi~~-~~Il~~~~~~~~~-------~~g~~~r~~~~t~~Di~Ni~~~~~ 240 (690)
...+.+++.+.|.+|+..|++. .+|.+.++..+.. ..-..++...+|.+||+|......
T Consensus 155 ~q~~~~~v~~ki~eLv~~gv~~v~e~k~~l~~fV~~~lf~~~~~p~~~n~~y~Pt~~di~n~~~~~~ 221 (225)
T PF15299_consen 155 KQPLDPRVVEKIHELVAQGVTSVPEMKRHLKKFVEEELFKDQEPPPPTNRRYFPTDKDIRNHMYSAK 221 (225)
T ss_pred cccCCHHHHHHHHHHHHcccccHHHHHHHHHHHhhhhccCCCCCCCCCccccCCchHHHHHHHHHHH
Confidence 3467899999999999999875 5666666443321 112346667899999999876654
No 9
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=95.38 E-value=0.07 Score=47.69 Aligned_cols=30 Identities=13% Similarity=0.227 Sum_probs=19.5
Q ss_pred ccCcceEEEEEEeeeCCcEEEEEE-eccCCC
Q 039513 130 MRGCLCHFTVKRLYTRPLLALIIY-NQRKHV 159 (690)
Q Consensus 130 k~gC~a~~~vk~~~~~~~~~v~~~-~eHnH~ 159 (690)
+.+||.+|+..-......|.+++. +.|||+
T Consensus 80 k~~CPFriRA~yS~k~k~W~lvvvnn~HnH~ 110 (111)
T PF08731_consen 80 KNTCPFRIRANYSKKNKKWTLVVVNNEHNHP 110 (111)
T ss_pred ccCCCeEEEEEEEecCCeEEEEEecCCcCCC
Confidence 455555544443345666888888 799995
No 10
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.76 E-value=0.049 Score=56.25 Aligned_cols=94 Identities=17% Similarity=0.079 Sum_probs=64.3
Q ss_pred EEeecccccccCCceEEEEEEcCCC-CeeEEEEEEeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCChhHHHHHH
Q 039513 300 SFHSTFGSKKLKYPLSTLLVFDSSH-NAIPVAWIITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSFDISTIR 378 (690)
Q Consensus 300 ~~DsT~~tn~~~~pL~~~~v~d~~g-~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a~~~AI~ 378 (690)
+||=+.....+.. |..+++|... .+-++ .++.+-+.+++..||..++ ... ....+++|.+|-..+...|++
T Consensus 2 giDE~~~~~g~~~--y~t~~~d~~~~~~~il--~i~~~r~~~~l~~~~~~~~---~~~-~~~~v~~V~~Dm~~~y~~~~~ 73 (249)
T PF01610_consen 2 GIDEFAFRKGHRS--YVTVVVDLDTDTGRIL--DILPGRDKETLKDFFRSLY---PEE-ERKNVKVVSMDMSPPYRSAIR 73 (249)
T ss_pred eEeeeeeecCCcc--eeEEEEECccCCceEE--EEcCCccHHHHHHHHHHhC---ccc-cccceEEEEcCCCcccccccc
Confidence 4555554443432 4555666522 23333 3777888888877776541 111 123689999999999999999
Q ss_pred HhCc-cceeechhhHHHHHHHHHH
Q 039513 379 ENFQ-CRILLCVWHVRRAWIKNLL 401 (690)
Q Consensus 379 ~vFp-~~~llC~wHV~qaw~k~l~ 401 (690)
+.|| +.+.+-.|||+|...+.+.
T Consensus 74 ~~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 74 EYFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred ccccccccccccchhhhhhhhcch
Confidence 9999 7999999999998766543
No 11
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=88.36 E-value=0.15 Score=47.98 Aligned_cols=77 Identities=9% Similarity=-0.035 Sum_probs=57.2
Q ss_pred EEEEeecccccccCCceEEEEEEcCCCCeeEEEEEEeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCChhHHHHH
Q 039513 298 LMSFHSTFGSKKLKYPLSTLLVFDSSHNAIPVAWIITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSFDISTI 377 (690)
Q Consensus 298 vv~~DsT~~tn~~~~pL~~~~v~d~~g~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a~~~AI 377 (690)
.+.+|-||-.- -|---|..-++|..|+ .+.+.+...-+...-..+|+.++... + -.|..|+||+..+...|+
T Consensus 3 ~w~~DEt~iki-~G~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~----~-~~p~~ivtDk~~aY~~A~ 74 (140)
T PF13610_consen 3 SWHVDETYIKI-KGKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRH----R-GEPRVIVTDKLPAYPAAI 74 (140)
T ss_pred EEEEeeEEEEE-CCEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceee----c-cccceeecccCCccchhh
Confidence 79999999432 2334566778899888 68888888777776556665444433 1 369999999999999999
Q ss_pred HHhCc
Q 039513 378 RENFQ 382 (690)
Q Consensus 378 ~~vFp 382 (690)
++.++
T Consensus 75 ~~l~~ 79 (140)
T PF13610_consen 75 KELNP 79 (140)
T ss_pred hhccc
Confidence 98777
No 12
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=88.23 E-value=53 Score=37.49 Aligned_cols=132 Identities=14% Similarity=0.103 Sum_probs=73.4
Q ss_pred HHHHHHHhccCCCcce--eEEEecCChhHHHHHHHhCc-cceeechhhHHHHHHHHHHhhcCChHHHHHHHHHHHHHHhc
Q 039513 347 GLLAERIRTKDPRWRL--SAFLVDNPSFDISTIRENFQ-CRILLCVWHVRRAWIKNLLKKCYNVEVQQEMFKQLSWILYS 423 (690)
Q Consensus 347 ~~l~~~~~~~~p~~~P--~~~mtD~d~a~~~AI~~vFp-~~~llC~wHV~qaw~k~l~~~~~~~e~~~~i~~~l~~lv~~ 423 (690)
..+.+.+...+..-.. -++..|...=..++. +.|| +.+.|..||+.|++.+.+.. .++.+..+++.|. .
T Consensus 242 ~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~-~~~~~~~~~LD~FHl~k~i~~~~~~---~~~~~~~~~~al~----~ 313 (470)
T PF06782_consen 242 EEVLDYIYNHYDLDKTTKIIINGDGASWIKEGA-EFFPKAEYFLDRFHLNKKIKQALSH---DPELKEKIRKALK----K 313 (470)
T ss_pred HHHHHHHHHhcCcccceEEEEeCCCcHHHHHHH-HhhcCceEEecHHHHHHHHHHHhhh---ChHHHHHHHHHHH----h
Confidence 3445555444321112 234567776555544 5888 79999999999999887753 2334444544443 2
Q ss_pred cCCCCchHHHHHHHHHHhhc------hhHHHHHHHhhhhhhHHHHhhhccccCCCCCCCCchHHHHHHHhhhhhccc
Q 039513 424 SRSSPNSVDTIEEFMQVFVD------QCAFMDYFKSQWLPHIELWVTGIRSLPVTTPEPLAAIETYHLRLKSKLFHE 494 (690)
Q Consensus 424 ~~~~~~~~~~~e~~~~~~~~------~~~f~~Yf~~~Wl~~~~~Wa~~yr~~~~~g~~Tnn~~Es~h~~LK~~~l~~ 494 (690)
... ..+...++.+.....+ -.++..|+.++|-.- ..|+.- .|.......|+.|+.|...+-.+
T Consensus 314 ~d~-~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i-----~~y~~~--~~~~g~g~ee~~~~~~s~RmK~r 382 (470)
T PF06782_consen 314 GDK-KKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGI-----KPYRER--EGLRGIGAEESVSHVLSYRMKSR 382 (470)
T ss_pred cCH-HHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHh-----hhhhhc--cCCCccchhhhhhhHHHHHhcCC
Confidence 211 1233334444322211 246789999999532 234320 23344456899999987765443
No 13
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=85.12 E-value=7.5 Score=34.56 Aligned_cols=75 Identities=13% Similarity=-0.054 Sum_probs=51.0
Q ss_pred cEEEEeecccc-cccCCceEEEEEEcCCCCeeEEEEEEeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCChhHHH
Q 039513 297 GLMSFHSTFGS-KKLKYPLSTLLVFDSSHNAIPVAWIITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSFDIS 375 (690)
Q Consensus 297 ~vv~~DsT~~t-n~~~~pL~~~~v~d~~g~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a~~~ 375 (690)
..+++|.++-. ...+-..+.++++|.+-+ ...++.+...++.+.+...|...+...+ +..|+.|.||...+..+
T Consensus 7 ~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 7 ERWQIDFTPMPIPDKGGRVYLLVFIDDYSR-FIYAFPVSSKETAEAALRALKRAIEKRG----GRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TEEEEEEEEETGGCTT-CEEEEEEEETTTT-EEEEEEESSSSHHHHHHHHHHHHHHHHS-----SE-SEEEEESCHHHHS
T ss_pred CEEEEeeEEEecCCCCccEEEEEEEECCCC-cEEEEEeecccccccccccccccccccc----cccceeccccccccccc
Confidence 38999999433 223347888999998644 4567778777788777666665555543 22399999999998774
Q ss_pred H
Q 039513 376 T 376 (690)
Q Consensus 376 A 376 (690)
.
T Consensus 82 ~ 82 (120)
T PF00665_consen 82 H 82 (120)
T ss_dssp H
T ss_pred c
Confidence 3
No 14
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=80.47 E-value=0.84 Score=46.51 Aligned_cols=45 Identities=27% Similarity=0.603 Sum_probs=33.2
Q ss_pred eeeecCCCCCCccchhHHHHHHhhhccccCCChhhHHHH---HHHHHhhh
Q 039513 586 SLCDCPWSRLGNVCEHVIKLAMVCKSRQVARPLLAAQVY---RQALLSLL 632 (690)
Q Consensus 586 ~~CsC~~f~~G~lCkHil~Vl~~~~~~~~~~p~~~~~~~---~~~~~~~~ 632 (690)
.-|||+ ...+|||||.+|+=+-+.....-|.+.+.=. +..|...+
T Consensus 125 ~dCSCP--D~anPCKHi~AvyY~lae~f~~dPflif~lRG~~k~eL~a~l 172 (266)
T COG4279 125 TDCSCP--DYANPCKHIAAVYYLLAEKFDEDPFLIFKLRGRNKEELLALL 172 (266)
T ss_pred cccCCC--CcccchHHHHHHHHHHHHHhccCCeeeeeecCCCHHHHHHHH
Confidence 369998 5679999999999998888777777765433 44454444
No 15
>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=79.26 E-value=2.1 Score=44.74 Aligned_cols=81 Identities=17% Similarity=0.160 Sum_probs=48.9
Q ss_pred EEEEeecccc----ccc-CCceEEEEEEcCCCCeeEEEEEEeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCChh
Q 039513 298 LMSFHSTFGS----KKL-KYPLSTLLVFDSSHNAIPVAWIITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSF 372 (690)
Q Consensus 298 vv~~DsT~~t----n~~-~~pL~~~~v~d~~g~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a 372 (690)
++++|-|.-. .+. +.=+.++ .+.. .+.|.+..+-..+.+..+|. ++ ..++++|.-.+
T Consensus 69 ~~~~DET~~~vl~~~~g~~~~~Wv~--~~~~----~v~f~~~~sR~~~~~~~~L~-----------~~-~GilvsD~y~~ 130 (271)
T PF03050_consen 69 VVHADETGWRVLDKGKGKKGYLWVF--VSPE----VVLFFYAPSRSSKVIKEFLG-----------DF-SGILVSDGYSA 130 (271)
T ss_pred eeccCCceEEEeccccccceEEEee--eccc----eeeeeecccccccchhhhhc-----------cc-ceeeecccccc
Confidence 7888877654 222 2222222 2222 55666666666665544442 22 35889999877
Q ss_pred HHHHHHHhCccceeechhhHHHHHHHHH
Q 039513 373 DISTIRENFQCRILLCVWHVRRAWIKNL 400 (690)
Q Consensus 373 ~~~AI~~vFp~~~llC~wHV~qaw~k~l 400 (690)
... +. ++.|..|+-|+.+.+.+-.
T Consensus 131 Y~~-~~---~~~hq~C~AH~~R~~~~~~ 154 (271)
T PF03050_consen 131 YNK-LA---GITHQLCWAHLRRDFQDAA 154 (271)
T ss_pred ccc-cc---ccccccccccccccccccc
Confidence 554 21 6799999999998765544
No 16
>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=75.89 E-value=3.4 Score=33.07 Aligned_cols=28 Identities=25% Similarity=0.570 Sum_probs=21.2
Q ss_pred cCcceEEEEEEeeeCCcEEEEEE-eccCC
Q 039513 131 RGCLCHFTVKRLYTRPLLALIIY-NQRKH 158 (690)
Q Consensus 131 ~gC~a~~~vk~~~~~~~~~v~~~-~eHnH 158 (690)
.||+|+=.|.+...++.+.++.| .+|||
T Consensus 30 ~~C~akK~Vqr~~~d~~~~~vtY~G~H~h 58 (60)
T PF03106_consen 30 PGCPAKKQVQRSADDPNIVIVTYEGEHNH 58 (60)
T ss_dssp TTEEEEEEEEEETTCCCEEEEEEES--SS
T ss_pred cChhheeeEEEecCCCCEEEEEEeeeeCC
Confidence 39999999988666788777777 89999
No 17
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=75.69 E-value=33 Score=32.84 Aligned_cols=108 Identities=10% Similarity=0.062 Sum_probs=70.4
Q ss_pred HHHHHhhCCCcEEEEeecccccccCCceEEEEEEcCCCCeeEEEEEEee-ccchHHHHHHHHHHHHHHhccCCCcceeEE
Q 039513 287 LQQMLHYGNNGLMSFHSTFGSKKLKYPLSTLLVFDSSHNAIPVAWIITS-SFVGQFVHKWIGLLAERIRTKDPRWRLSAF 365 (690)
Q Consensus 287 ~~~l~~fg~~~vv~~DsT~~tn~~~~pL~~~~v~d~~g~~~pva~~i~~-~et~~~~~~~l~~l~~~~~~~~p~~~P~~~ 365 (690)
++....+|. .+..|+= ++..+.+++.|++....|..+.-..-..+ ..+.+.+...|....+.++. ...-.|
T Consensus 26 k~~w~~~Gc--si~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~----~nVvqV 97 (153)
T PF04937_consen 26 KKSWKRTGC--SIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGE----ENVVQV 97 (153)
T ss_pred HHHHHhcCE--EEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhh----hhhhHH
Confidence 444566787 6888885 55667789999987776655533322222 23455555556555555542 245568
Q ss_pred EecCChhHHHHHHHh---Cc-cceeechhhHHHHHHHHHHh
Q 039513 366 LVDNPSFDISTIREN---FQ-CRILLCVWHVRRAWIKNLLK 402 (690)
Q Consensus 366 mtD~d~a~~~AI~~v---Fp-~~~llC~wHV~qaw~k~l~~ 402 (690)
+||.+..+..|.+-. +| -....|.-|.+.-+.+.+.+
T Consensus 98 VTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 98 VTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred hccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 999999999986544 44 25667999999877766653
No 18
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=68.94 E-value=7.5 Score=44.25 Aligned_cols=47 Identities=19% Similarity=0.425 Sum_probs=30.6
Q ss_pred eeEEEeeccCCceeEEE-eCCCCCeeeeecCCCCCCccchhHHHHHHhhhc
Q 039513 562 QLAKIISQADRTLAYTI-WNPGSEFSLCDCPWSRLGNVCEHVIKLAMVCKS 611 (690)
Q Consensus 562 ~~~~V~S~~~~~~~~vV-~n~~~~~~~CsC~~f~~G~lCkHil~Vl~~~~~ 611 (690)
..+.|..+. ..++.| .+.+...++|+|+. ..+..|||+.+|+..+-.
T Consensus 50 v~A~V~Gs~--~y~v~vtL~~~~~ss~CTCP~-~~~gaCKH~VAvvl~~~~ 97 (587)
T COG4715 50 VRAVVEGSR--RYRVRVTLEGGALSSICTCPY-GGSGACKHVVAVVLEYLD 97 (587)
T ss_pred EEEEEeccc--eeeEEEEeecCCcCceeeCCC-CCCcchHHHHHHHHHHhh
Confidence 345555432 233433 33444567999998 667999999999887633
No 19
>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=68.87 E-value=5.5 Score=31.82 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=23.3
Q ss_pred ccCcceEEEEEEeeeCCcEEEEEE-eccCC
Q 039513 130 MRGCLCHFTVKRLYTRPLLALIIY-NQRKH 158 (690)
Q Consensus 130 k~gC~a~~~vk~~~~~~~~~v~~~-~eHnH 158 (690)
..||+|+=.|.+...++.+.+++| .+|||
T Consensus 30 ~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 30 SQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 479999988877656788777777 89998
No 20
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=62.61 E-value=40 Score=35.25 Aligned_cols=75 Identities=17% Similarity=0.079 Sum_probs=47.7
Q ss_pred cEEEEeecccccccCCceEEEEEEcCCCCeeEEEEEEeec-cchHHHHHHHHHHHHHHhccCCCcceeEEEecCChh
Q 039513 297 GLMSFHSTFGSKKLKYPLSTLLVFDSSHNAIPVAWIITSS-FVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSF 372 (690)
Q Consensus 297 ~vv~~DsT~~tn~~~~pL~~~~v~d~~g~~~pva~~i~~~-et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a 372 (690)
.+++.|-||-....+..+|..+++|.+.+ ..|||.+..+ .+.+.....|...++..........|..|-||.-..
T Consensus 88 ~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 88 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred CEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCcc
Confidence 49999999865555556889999998766 4689999874 566555555543333221111122466777887653
No 21
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=56.45 E-value=59 Score=34.73 Aligned_cols=75 Identities=19% Similarity=0.099 Sum_probs=46.7
Q ss_pred CcEEEEeecccccccCCceEEEEEEcCCCCeeEEEEEEeec-cchHHHHHHHHHHHHHHhccCCCcceeEEEecCCh
Q 039513 296 NGLMSFHSTFGSKKLKYPLSTLLVFDSSHNAIPVAWIITSS-FVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPS 371 (690)
Q Consensus 296 ~~vv~~DsT~~tn~~~~pL~~~~v~d~~g~~~pva~~i~~~-et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~ 371 (690)
+.+++.|-||-....+.-+|..+++|.+.+ ..|||.+... .+.+.....|...+....+......|..|-||.-.
T Consensus 126 N~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGs 201 (301)
T PRK09409 126 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 201 (301)
T ss_pred CCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCc
Confidence 349999999965545556888889998766 5699999875 56665555554322222111001235567777654
No 22
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.19 E-value=21 Score=36.07 Aligned_cols=76 Identities=9% Similarity=0.034 Sum_probs=52.6
Q ss_pred cEEEEeecccccc-cCCceEEEEEEcCCCCeeEEEEEEeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCChhHHH
Q 039513 297 GLMSFHSTFGSKK-LKYPLSTLLVFDSSHNAIPVAWIITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSFDIS 375 (690)
Q Consensus 297 ~vv~~DsT~~tn~-~~~pL~~~~v~d~~g~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a~~~ 375 (690)
+.+.+|=||-.-+ -.+=|+- .+|.. +.++.+.+...-+...-..||..+++.. -.|.+|+||+..+...
T Consensus 71 ~~w~vDEt~ikv~gkw~ylyr--Aid~~--g~~Ld~~L~~rRn~~aAk~Fl~kllk~~------g~p~v~vtDka~s~~~ 140 (215)
T COG3316 71 DSWRVDETYIKVNGKWHYLYR--AIDAD--GLTLDVWLSKRRNALAAKAFLKKLLKKH------GEPRVFVTDKAPSYTA 140 (215)
T ss_pred cceeeeeeEEeeccEeeehhh--hhccC--CCeEEEEEEcccCcHHHHHHHHHHHHhc------CCCceEEecCccchHH
Confidence 3899999995433 2333343 34444 5677777877666665556666555543 2699999999999999
Q ss_pred HHHHhCc
Q 039513 376 TIRENFQ 382 (690)
Q Consensus 376 AI~~vFp 382 (690)
|++++-+
T Consensus 141 A~~~l~~ 147 (215)
T COG3316 141 ALRKLGS 147 (215)
T ss_pred HHHhcCc
Confidence 9998776
No 23
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=53.47 E-value=8.6 Score=28.57 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=13.6
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHH
Q 039513 183 PRISEDLRQKVMSMLYVGISLDNIIQHH 210 (690)
Q Consensus 183 ~~is~~~r~~i~~ll~~Gi~~~~Il~~~ 210 (690)
++||.++|..|..+...|.+..+|-..+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~s~~~IA~~l 30 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGMSIREIAKRL 30 (44)
T ss_dssp ---------HHHHHHCS---HHHHHHHT
T ss_pred cchhhhHHHHHHHHHHcCCCHHHHHHHH
Confidence 4689999999999999999999986543
No 24
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=48.91 E-value=5 Score=35.45 Aligned_cols=19 Identities=42% Similarity=0.947 Sum_probs=14.5
Q ss_pred eeecCCCC-----CC-ccchhHHHH
Q 039513 587 LCDCPWSR-----LG-NVCEHVIKL 605 (690)
Q Consensus 587 ~CsC~~f~-----~G-~lCkHil~V 605 (690)
.|||+.|- .| .+|.|++.+
T Consensus 51 fCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 51 FCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred cccCHHHHhHhhhcCcccchhhhhe
Confidence 79999662 55 669999865
No 25
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=48.69 E-value=6.1 Score=20.53 Aligned_cols=8 Identities=75% Similarity=1.310 Sum_probs=6.6
Q ss_pred ceecchhh
Q 039513 41 ALIPFARV 48 (690)
Q Consensus 41 ~~~~~~~~ 48 (690)
.||||.|+
T Consensus 4 GlI~fpR~ 11 (11)
T PF08259_consen 4 GLIPFPRV 11 (11)
T ss_pred cccccCCC
Confidence 48999986
No 26
>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=43.05 E-value=20 Score=27.88 Aligned_cols=25 Identities=12% Similarity=0.252 Sum_probs=9.1
Q ss_pred cCcceEEEEEEeeeCCcEEEEEEeccCC
Q 039513 131 RGCLCHFTVKRLYTRPLLALIIYNQRKH 158 (690)
Q Consensus 131 ~gC~a~~~vk~~~~~~~~~v~~~~eHnH 158 (690)
.+|+|.+.+. ++....+..-.+|||
T Consensus 38 ~~C~a~~~~~---~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITD---AGDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE-----TTEEEE-S---SS
T ss_pred CCCeEEEEEE---CCCCEEEECCCccCC
Confidence 6899998887 223333333368998
No 27
>PHA02517 putative transposase OrfB; Reviewed
Probab=36.35 E-value=1e+02 Score=32.12 Aligned_cols=71 Identities=18% Similarity=-0.003 Sum_probs=44.7
Q ss_pred cEEEEeecccccccCCceEEEEEEcCCCCeeEEEEEEeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCChhH
Q 039513 297 GLMSFHSTFGSKKLKYPLSTLLVFDSSHNAIPVAWIITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSFD 373 (690)
Q Consensus 297 ~vv~~DsT~~tn~~~~pL~~~~v~d~~g~~~pva~~i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a~ 373 (690)
.+++.|.||-....+ -.|.++++|.+.+ ..+||.+....+.+....+|...+... +.-.+..|.||.....
T Consensus 111 ~~w~~D~t~~~~~~g-~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~~~~----~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 111 QLWVADFTYVSTWQG-WVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQALWAR----GRPGGLIHHSDKGSQY 181 (277)
T ss_pred CeEEeceeEEEeCCC-CEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHHHhc----CCCcCcEeeccccccc
Confidence 489999999654444 3577788887654 457888888788776555554433322 1111235668887653
No 28
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=25.85 E-value=51 Score=24.42 Aligned_cols=27 Identities=19% Similarity=0.486 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 039513 183 PRISEDLRQKVMSMLYVGISLDNIIQH 209 (690)
Q Consensus 183 ~~is~~~r~~i~~ll~~Gi~~~~Il~~ 209 (690)
+.+++++.+.|..|+..|++..+|...
T Consensus 4 ~~~~~~~~~~i~~l~~~G~si~~IA~~ 30 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGMSIAEIAKQ 30 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--HHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHH
Confidence 356777789999999999999888653
No 29
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.81 E-value=2.5e+02 Score=31.38 Aligned_cols=54 Identities=17% Similarity=0.190 Sum_probs=42.2
Q ss_pred EeeccchHHHHHHHHHHHHHHhccCCCcceeEEEecCChhHHHHHHHhCc-cceeechhhHHH
Q 039513 333 ITSSFVGQFVHKWIGLLAERIRTKDPRWRLSAFLVDNPSFDISTIRENFQ-CRILLCVWHVRR 394 (690)
Q Consensus 333 i~~~et~~~~~~~l~~l~~~~~~~~p~~~P~~~mtD~d~a~~~AI~~vFp-~~~llC~wHV~q 394 (690)
+..+-+.+++..|| +..+. . +.+.+.+|-.....+++++.|| +.+.+=.||+.+
T Consensus 184 i~~~r~~~ti~~~l----~~~g~---~-~v~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~ 238 (402)
T COG3464 184 ILEGRSVRTLRRYL----RRGGS---E-QVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQ 238 (402)
T ss_pred ecCCccHHHHHHHH----HhCCC---c-ceeEEEccccHHHHHHHHHhCCChheeeeeeeeee
Confidence 45556667666665 33332 1 6788999999999999999999 689999999988
No 30
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=23.48 E-value=1.1e+02 Score=23.71 Aligned_cols=27 Identities=19% Similarity=0.324 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHH
Q 039513 184 RISEDLRQKVMSMLYVGISLDNIIQHH 210 (690)
Q Consensus 184 ~is~~~r~~i~~ll~~Gi~~~~Il~~~ 210 (690)
.||+.++.+|..|...|++..+|-..+
T Consensus 4 ~Lt~~Eqaqid~m~qlG~s~~~isr~i 30 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQLGMSLREISRRI 30 (50)
T ss_dssp ---HHHHHHHHHHHHTT--HHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhchhHHHHHHHh
Confidence 589999999999999999998876554
No 31
>KOG0053 consensus Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]
Probab=21.22 E-value=8e+02 Score=27.53 Aligned_cols=103 Identities=19% Similarity=0.257 Sum_probs=53.3
Q ss_pred cHHHHHHHHHHHhhccccccCChHHHHHHHHHhhcCceeEEEeccCCCCeEEEecCHHHHHHHHhhCCCcEEEEeecccc
Q 039513 228 TRNDVRNMERVIRNSSHELHVDDECSVKMWVQRHHKHVFFFQDYSVSEPFILVIQTDWQLQQMLHYGNNGLMSFHSTFGS 307 (690)
Q Consensus 228 t~~Di~Ni~~~~~~~~~~l~~~D~~Sv~~~v~~~~~~vf~y~~~~d~~~f~l~i~t~~q~~~l~~fg~~~vv~~DsT~~t 307 (690)
|++-++++..++.......+.+|...+..-+++ +...+|.. +-.+|+.-+.--+.-.++..++|- ++++|.||.+
T Consensus 129 T~~~l~~~~~~~gie~~~vd~~~~~~~~~~i~~-~t~~V~~E--SPsNPll~v~DI~~l~~la~~~g~--~vvVDnTf~~ 203 (409)
T KOG0053|consen 129 TLRILRKFLPKFGGEGDFVDVDDLKKILKAIKE-NTKAVFLE--SPSNPLLKVPDIEKLARLAHKYGF--LVVVDNTFGS 203 (409)
T ss_pred HHHHHHHHHHHhCceeeeechhhHHHHHHhhcc-CceEEEEE--CCCCCccccccHHHHHHHHhhCCC--EEEEeCCcCc
Confidence 444444444444333333344444444444444 23444444 234566555545555667788888 8999999987
Q ss_pred c--ccCCce-EEEEEEcC----CCCeeEEEEEEee
Q 039513 308 K--KLKYPL-STLLVFDS----SHNAIPVAWIITS 335 (690)
Q Consensus 308 n--~~~~pL-~~~~v~d~----~g~~~pva~~i~~ 335 (690)
- ..-+|| .-+++... .|++=.+|=.++.
T Consensus 204 p~~~~pL~lGADIV~hSaTKyi~Ghsdvi~G~iv~ 238 (409)
T KOG0053|consen 204 PYNQDPLPLGADIVVHSATKYIGGHSDVIGGSVVL 238 (409)
T ss_pred ccccChhhcCCCEEEEeeeeeecCCcceeeeEEec
Confidence 4 344555 33443322 3455444444443
Done!