Query 043648
Match_columns 841
No_of_seqs 333 out of 1120
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 07:00:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043648.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043648hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 4E-145 8E-150 1289.7 54.8 652 43-771 68-796 (846)
2 PF10551 MULE: MULE transposas 99.8 7.3E-20 1.6E-24 165.0 7.6 85 311-397 1-88 (93)
3 PF03101 FAR1: FAR1 DNA-bindin 99.7 3.1E-18 6.7E-23 154.0 7.4 77 63-139 1-91 (91)
4 cd04757 Commd9 COMM_Domain con 99.5 1.2E-15 2.7E-20 138.2 2.2 78 755-832 23-108 (108)
5 PF00872 Transposase_mut: Tran 98.9 4.1E-10 8.9E-15 127.3 1.1 164 305-470 163-352 (381)
6 smart00575 ZnF_PMZ plant mutat 98.6 4.2E-09 9.1E-14 73.2 -0.9 26 577-602 2-27 (28)
7 PF08731 AFT: Transcription fa 98.5 3.5E-07 7.7E-12 83.4 8.8 76 55-137 1-111 (111)
8 PF03108 DBD_Tnp_Mut: MuDR fam 98.4 1.8E-06 3.8E-11 73.2 8.3 64 48-126 3-67 (67)
9 cd04749 Commd1_MURR1 COMM_Doma 98.2 1.9E-06 4.1E-11 85.6 4.7 65 762-829 104-173 (174)
10 PF04434 SWIM: SWIM zinc finge 97.9 3.6E-06 7.9E-11 63.7 0.8 29 572-600 11-39 (40)
11 cd04748 Commd COMM_Domain, a f 97.3 0.00017 3.7E-09 64.3 3.4 65 761-827 18-87 (87)
12 cd04756 Commd8 COMM_Domain con 97.3 0.0002 4.4E-09 72.3 3.7 63 759-825 104-171 (176)
13 COG3328 Transposase and inacti 97.3 0.00056 1.2E-08 76.9 7.5 91 305-397 146-238 (379)
14 PF07258 HCaRG: HCaRG protein; 95.4 0.0041 8.9E-08 62.5 0.0 67 760-829 106-177 (178)
15 PLN03097 FHY3 Protein FAR-RED 95.3 0.0092 2E-07 73.5 2.6 51 714-767 761-815 (846)
16 PF13610 DDE_Tnp_IS240: DDE do 91.6 0.056 1.2E-06 52.6 0.1 81 304-388 1-81 (140)
17 cd04758 Commd10 COMM_Domain co 91.5 0.2 4.2E-06 51.3 4.1 66 761-829 115-185 (186)
18 PF03106 WRKY: WRKY DNA -bindi 90.9 0.75 1.6E-05 38.1 6.1 55 73-136 4-59 (60)
19 PF01610 DDE_Tnp_ISL3: Transpo 89.9 0.44 9.5E-06 50.7 5.1 84 308-397 2-88 (249)
20 cd04750 Commd2 COMM_Domain con 88.9 0.46 1E-05 47.7 4.1 64 756-822 89-157 (166)
21 PF00665 rve: Integrase core d 87.5 1.7 3.8E-05 40.0 6.8 75 304-379 6-81 (120)
22 cd04753 Commd5_HCaRG COMM_Doma 84.9 1.2 2.6E-05 41.6 4.2 62 756-824 28-101 (110)
23 cd04752 Commd4 COMM_Domain con 84.8 1.2 2.5E-05 45.2 4.4 67 760-828 101-172 (174)
24 PF04684 BAF1_ABF1: BAF1 / ABF 76.3 4.2 9E-05 46.5 5.4 56 51-120 24-79 (496)
25 PF04500 FLYWCH: FLYWCH zinc f 76.0 4.2 9E-05 33.0 4.2 48 73-135 15-62 (62)
26 smart00774 WRKY DNA binding do 75.8 4.8 0.0001 33.3 4.3 38 91-135 21-59 (59)
27 cd04751 Commd3 COMM_Domain con 64.0 11 0.00023 34.4 4.4 63 761-827 23-90 (95)
28 cd04754 Commd6 COMM_Domain con 60.1 10 0.00022 33.6 3.4 61 762-825 18-83 (86)
29 cd04755 Commd7 COMM_Domain con 51.1 18 0.00039 36.8 3.9 65 760-827 110-178 (180)
30 COG3316 Transposase and inacti 43.1 36 0.00079 35.6 4.8 84 304-392 70-153 (215)
31 PF04937 DUF659: Protein of un 36.5 1.1E+02 0.0024 30.4 6.8 95 301-397 30-128 (153)
32 PF04800 ETC_C1_NDUFA4: ETC co 26.9 63 0.0014 29.8 3.1 27 50-80 50-76 (101)
33 COG5431 Uncharacterized metal- 25.6 50 0.0011 30.4 2.1 29 562-596 42-75 (117)
34 PHA02517 putative transposase 25.2 1.6E+02 0.0034 31.7 6.4 69 304-377 110-181 (277)
35 PRK14702 insertion element IS2 20.2 3.1E+02 0.0066 29.6 7.3 72 304-376 87-163 (262)
36 COG5470 Uncharacterized conser 20.2 45 0.00097 30.3 0.7 29 49-77 54-82 (96)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=3.9e-145 Score=1289.66 Aligned_cols=652 Identities=35% Similarity=0.664 Sum_probs=584.4
Q ss_pred CCCCCCCCCCCeeCCHHHHHHHHHHHHHhcCcEEEEeeeccCCCCCCeEEEEeeccccccccc-----------------
Q 043648 43 DDGIMDPYVGMEFHTEDAAKTFYDEYARRVGFSSKVCHFSRPRPDEPIVFREFVCGREGLKRR----------------- 105 (841)
Q Consensus 43 ~~~~~~P~~Gm~F~S~eeA~~fy~~YA~~~GF~vr~~~s~rsk~~g~i~~~~fvCsreG~~Rk----------------- 105 (841)
.+...+|.+||+|+|+||||+||+.||+++||+||+.+++|++.+|.++.++|+|+|||++|+
T Consensus 68 ~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~ 147 (846)
T PLN03097 68 EDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDP 147 (846)
T ss_pred CCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCc
Confidence 466789999999999999999999999999999999999999999999999999999997521
Q ss_pred ---------cccCCccceEEEEeCcceEEEEEEecCCCCCCCCCccccccCCCCCCChhhhhhhhcccCCCchhhHHHhh
Q 043648 106 ---------HGESCDAMLRIELKGQNKWVVTKFVKEHSHPMVSPSKVHYLRPRRHFAGTTKAEVYQGVGIVPSGIMYVSM 176 (841)
Q Consensus 106 ---------~r~gC~a~i~v~~~~~~~W~V~~~~~eHNH~l~~~~~~~~l~~~r~~s~~~ki~~l~~~g~~p~~i~~~~~ 176 (841)
.||||||+|+|++.++|+|+|++|+++|||||.++..+. .. +++++..+.
T Consensus 148 ~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~~---------~~------------~r~~~~~~~ 206 (846)
T PLN03097 148 ENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVS---------EQ------------TRKMYAAMA 206 (846)
T ss_pred ccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccccc---------hh------------hhhhHHHHH
Confidence 279999999999988999999999999999998764321 11 122222222
Q ss_pred ccccccccccCCCccccCCccccCCCCCCCCCCCCCCCCCCCCCccCCCCCCccCccccccCccccccchhhhhc-cchh
Q 043648 177 DGNRATVETNNHGARTATPVETRTAPPIESRTAPPVESRTAPPIESRTAPPVESNRAVKNTGALNYVVRPANRRR-TLGR 255 (841)
Q Consensus 177 ~~~~~~~~~~~~G~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~N~~~~~~~r~~-~~~~ 255 (841)
... +|. . ++.+...|..|. ....|+. ...+
T Consensus 207 ~~~--------~~~--------------------------------~-------~v~~~~~d~~~~--~~~~r~~~~~~g 237 (846)
T PLN03097 207 RQF--------AEY--------------------------------K-------NVVGLKNDSKSS--FDKGRNLGLEAG 237 (846)
T ss_pred hhh--------hcc--------------------------------c-------cccccchhhcch--hhHHHhhhcccc
Confidence 211 121 1 122444555666 2333433 3469
Q ss_pred hHHHHHHHHHHHHhcCCCCeEEEEeCCCCceeEEEecccccHHHHHhcCCeeeecccccccccCcceeeEEEEecCCcEE
Q 043648 256 DAQNLLDYFKKMQAENPGFFYAIQLDDDNRMANVFWADARSRTAYSHFGDAVTLDTRYRVYQYNVPFAPFTGINHHGQMI 335 (841)
Q Consensus 256 d~~~ll~~l~~~~~~np~f~y~i~~D~~~~l~~ifw~~~~s~~~y~~f~dVv~~D~Ty~tnky~~pL~~~~gvn~~~q~~ 335 (841)
|+++||+||+++|.+||+|||++++|++|+|+||||+|++|+.+|.+|||||+|||||+||+|+|||++|+|||||+|++
T Consensus 238 D~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtv 317 (846)
T PLN03097 238 DTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFM 317 (846)
T ss_pred hHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeeccCCChhhHHHHHHHHHhhhcCCCCeEecccccHHHHHHHHHhCCcccccccccch------------------
Q 043648 336 LFGCALLLDDSEASFVWLFKTFLTAMNDCQPVSITTDQDKAIQIAVAKVFPEVRHCISKWHV------------------ 397 (841)
Q Consensus 336 ~~g~alv~~Et~es~~Wl~~~f~~~m~~~~P~~IiTD~d~al~~AI~~vFP~a~h~lC~wHI------------------ 397 (841)
+||||||.+|+.|||.|||++|+++|+|++|++||||+|.+|++||++|||+|.||+|+|||
T Consensus 318 lfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f 397 (846)
T PLN03097 318 LLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQHENF 397 (846)
T ss_pred EEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhhhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred --hhhcccccCCCHHHHHHHHHHHHHHhccccchHHHHHhhcccccccccccCcccccccCCCCCc--cccccccccccC
Q 043648 398 --ELYNCINLTETIEEFELSWNSILDKYDLRGHDWLQSLYNARSQWVPVYFRDSFFAAISPNQGFD--GSFFDGYVNQQT 473 (841)
Q Consensus 398 --~~~~~i~~s~t~~eFe~~w~~~~~~~~l~~n~wL~~ly~~R~~Wa~ay~~~~f~~gm~tt~rsE--n~~~k~~v~~~~ 473 (841)
+|.+||+.+++++|||..|..|+++|+|++|+||+.||+.|++|||+|+++.|++||++|+|+| |++|++|+++++
T Consensus 398 ~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~t 477 (846)
T PLN03097 398 MAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKT 477 (846)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCC
Confidence 6789999999999999999999999999999999999999999999999999999999999999 999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCcccCCChHHHHhhhccCHHHHHHHHHHHHhhcceEEEEeecCCceEEE
Q 043648 474 TIPMFFRQYERALENSFEREIEADFDTICTTPRLRTPSPMERQAANSFTRKVFTKFQEELVETFVYTANGIESDGAISTF 553 (841)
Q Consensus 474 sL~~f~~~~~~~l~~~~~kE~~~d~~s~~~~p~lkt~~p~Ekqaa~~yT~~~F~kfq~el~~s~~~~v~~~~~dg~~~~y 553 (841)
+|.+|+++|+++++.++++|+++|+++.++.|.+++++|||+||+++||++||++||+|+..+..|.+..+.++|...+|
T Consensus 478 sL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y 557 (846)
T PLN03097 478 TVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITF 557 (846)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999888888889999
Q ss_pred EEEEeeCCCceEEEEEeCCCCceeeeecCcccCCccceeeeeeehhcccccCCccchHHhhccccccCCCccCccccccC
Q 043648 554 RVAKFEDDSRAYIVTFNHPEMRANCSCQMFEYSGILCRHVLTVFTVTNVLTLPSHYILKRWTRNAKTGIGVDERTAELHG 633 (841)
Q Consensus 554 ~V~~~~~~~k~y~V~~~~~~~~~sCsC~~fe~~GipCrHiLaVl~~~~v~~IP~~YIlkRWtk~ak~~~~~~~~~~~~~~ 633 (841)
.|.+.+. .+.|.|.+|..++.++|+|++||+.||||||||+||.++|+.+||++|||+||||+||.....+.... .
T Consensus 558 ~V~~~~~-~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdAK~~~~~~~~~~---~ 633 (846)
T PLN03097 558 RVQDFEK-NQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDAKSRHLLGEESE---Q 633 (846)
T ss_pred EEEEecC-CCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhchhhhhhcccCccccc---c
Confidence 9987654 46899999999999999999999999999999999999999999999999999999998766554322 2
Q ss_pred cccHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCC---CCC----------------
Q 043648 634 QESLTMRYNNLCREAIKYSEDGAVAQETYNVAMSSIREGWKKVAVVKKNVAKVPPPGS---HVS---------------- 694 (841)
Q Consensus 634 ~~s~~~Ry~~L~~~a~~~~~~gs~s~E~y~~a~~~L~e~~~~i~~~~~~~~~~~~~~~---~~~---------------- 694 (841)
..+.+.||+.||+++++++++|+.|+|.|+.|+++|+|+.++|+.++++...++.+.+ |+.
T Consensus 634 ~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~L~e~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 713 (846)
T PLN03097 634 VQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRALEEAFGNCISMNNSNKSLVEAGTSPTHGLLCIEDDNQSRSMTKTN 713 (846)
T ss_pred ccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhccCCCccccccccccCCccccccccccccCcCC
Confidence 3466789999999999999999999999999999999999999999999888876655 221
Q ss_pred --CCcccCCCCCCCCCCcCCC---Ccccccc-cccccccCCCCCCCCCCCcC-CCCCCCCcccccCC--CCCCccccccc
Q 043648 695 --GTGYDDRKISASPSDSTPL---LWPRQDE-MTRRFNLNDSGPAIQPVSDL-NLPRMAPVSLHRDD--GPSDNMVVLPC 765 (841)
Q Consensus 695 --~~~~~~~~~~~~~~~~~~~---~~~~~d~-~~~~~~~~~~~~~~~~v~~~-~~~~~~p~~~~~~~--~~~~~~~~~~~ 765 (841)
-++++|||+.++++.++.. +.+||+. +++.++++++|+|||++|+| .|++|+|. +|+ ++|++++++++
T Consensus 714 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~y~~q~~~q~~~~l~s~~~~---~~~~y~~q~~~~g~gq 790 (846)
T PLN03097 714 KKKNPTKKRKVNSEQEVTTVAAQDSLQQMDKLSSRAVALESYYGTQQSVQGMVQLNLMAPT---RDNYYGNQQTIQGLGQ 790 (846)
T ss_pred ccccccccccccCchhhhhhhhhhhhhhHHhhhcccCCcccccccHHhhhHHHHhhccCCC---CCCcccCccCcccccc
Confidence 0278889999999998755 7888887 78888999999999999998 48888888 887 88888888888
Q ss_pred cccchh
Q 043648 766 LKSMTW 771 (841)
Q Consensus 766 l~~~~~ 771 (841)
|+||.=
T Consensus 791 l~s~~~ 796 (846)
T PLN03097 791 LNSIAP 796 (846)
T ss_pred ccccCc
Confidence 888865
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=99.80 E-value=7.3e-20 Score=164.97 Aligned_cols=85 Identities=32% Similarity=0.571 Sum_probs=82.7
Q ss_pred ccccccccCcceee---EEEEecCCcEEEEEEeeccCCChhhHHHHHHHHHhhhcCCCCeEecccccHHHHHHHHHhCCc
Q 043648 311 TRYRVYQYNVPFAP---FTGINHHGQMILFGCALLLDDSEASFVWLFKTFLTAMNDCQPVSITTDQDKAIQIAVAKVFPE 387 (841)
Q Consensus 311 ~Ty~tnky~~pL~~---~~gvn~~~q~~~~g~alv~~Et~es~~Wl~~~f~~~m~~~~P~~IiTD~d~al~~AI~~vFP~ 387 (841)
+||+||+| +|++. ++|+|++|+.+|+||+++.+|+.++|.|+|+.|++.++.. |.+||||++.++.+||+++||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 69999999 88886 9999999999999999999999999999999999999987 9999999999999999999999
Q ss_pred ccccccccch
Q 043648 388 VRHCISKWHV 397 (841)
Q Consensus 388 a~h~lC~wHI 397 (841)
+.|++|.||+
T Consensus 79 ~~~~~C~~H~ 88 (93)
T PF10551_consen 79 ARHQLCLFHI 88 (93)
T ss_pred ceEehhHHHH
Confidence 9999999998
No 3
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=99.74 E-value=3.1e-18 Score=153.97 Aligned_cols=77 Identities=35% Similarity=0.690 Sum_probs=70.4
Q ss_pred HHHHHHHHhcCcEEEEeeeccCCCCCCeEEEEeeccccccccc--------------cccCCccceEEEEeCcceEEEEE
Q 043648 63 TFYDEYARRVGFSSKVCHFSRPRPDEPIVFREFVCGREGLKRR--------------HGESCDAMLRIELKGQNKWVVTK 128 (841)
Q Consensus 63 ~fy~~YA~~~GF~vr~~~s~rsk~~g~i~~~~fvCsreG~~Rk--------------~r~gC~a~i~v~~~~~~~W~V~~ 128 (841)
+||+.||+.+||+||+.++++++.+|.++++.|+|+++|.+++ .+|||||+|.|++..+|+|.|+.
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~~~~w~v~~ 80 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRKDGKWRVTS 80 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEccCCEEEEEE
Confidence 5999999999999999999988889999999999999997621 19999999999998899999999
Q ss_pred EecCCCCCCCC
Q 043648 129 FVKEHSHPMVS 139 (841)
Q Consensus 129 ~~~eHNH~l~~ 139 (841)
++.+|||+|.+
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999964
No 4
>cd04757 Commd9 COMM_Domain containing protein 9. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=99.55 E-value=1.2e-15 Score=138.19 Aligned_cols=78 Identities=26% Similarity=0.387 Sum_probs=67.4
Q ss_pred CCCCccccccccccchhhcc-----ccCCCCCccceEEEeecccCCCC---CCCceEEEEEeehhcHHHHHhhhhhhhcc
Q 043648 755 GPSDNMVVLPCLKSMTWVME-----NKNSAPGNRVAVINLKLHDYSKT---PSAELEVKFQLSKVTLEPMLRSMAYISDQ 826 (841)
Q Consensus 755 ~~~~~~~~~~~l~~~~~~~~-----~~~~~~~~~~~~~~~k~~~~~~~---~~~~~~~~~~l~~~tl~~ml~~~~~i~~q 826 (841)
.++++++++|+|.+++|..+ +..++++.|+++++||++|.++. .+..++|+|||||||||+||+||++||||
T Consensus 23 ~~~~~~~slp~l~dldWRldv~isS~sl~r~~~P~vll~lkv~~~~~~~~~~~~~~~v~~ELsKe~l~tml~~L~~i~~Q 102 (108)
T cd04757 23 EASENQISLPKLVDHDWRVDIKTSSDSLGRMAVPTCLLQMKIQEAPSLCGLLPPLSTLTMELSKETLDTMLDGLGRIRDQ 102 (108)
T ss_pred HHHhcCCCchhhhCccceehhHHHHHHHHhhhcCeEEEEEEeecCccccccCCCcceEEEEcCHHHHHHHHHHHHHHHHH
Confidence 45667899999999999544 44478999999999999998762 23367999999999999999999999999
Q ss_pred cccccc
Q 043648 827 LSTPAN 832 (841)
Q Consensus 827 ~~~~~~ 832 (841)
|+++|+
T Consensus 103 L~~va~ 108 (108)
T cd04757 103 LSAVAQ 108 (108)
T ss_pred HHHHhC
Confidence 999985
No 5
>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=98.88 E-value=4.1e-10 Score=127.30 Aligned_cols=164 Identities=15% Similarity=0.148 Sum_probs=121.9
Q ss_pred Ceeeeccccccccc-----CcceeeEEEEecCCcEEEEEEeeccCCChhhHHHHHHHHHhhhcCCCCeEecccccHHHHH
Q 043648 305 DAVTLDTRYRVYQY-----NVPFAPFTGINHHGQMILFGCALLLDDSEASFVWLFKTFLTAMNDCQPVSITTDQDKAIQI 379 (841)
Q Consensus 305 dVv~~D~Ty~tnky-----~~pL~~~~gvn~~~q~~~~g~alv~~Et~es~~Wl~~~f~~~m~~~~P~~IiTD~d~al~~ 379 (841)
++|.+|++|.+-+. +.++++++|+|..|+-.++|+.+...|+.++|.-+|+.+++- |-..|..||+|..++|..
T Consensus 163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ 241 (381)
T PF00872_consen 163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKE 241 (381)
T ss_pred cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccc
Confidence 57889999987552 567899999999999999999999999999999998888654 113599999999999999
Q ss_pred HHHHhCCcccccccccch------------------hhhcccccCCCHHHHHHHHHHHHHHhccccchHHHHHhhcc-cc
Q 043648 380 AVAKVFPEVRHCISKWHV------------------ELYNCINLTETIEEFELSWNSILDKYDLRGHDWLQSLYNAR-SQ 440 (841)
Q Consensus 380 AI~~vFP~a~h~lC~wHI------------------~~~~~i~~s~t~~eFe~~w~~~~~~~~l~~n~wL~~ly~~R-~~ 440 (841)
||+++||++.+..|.+|. ++ +-|+...+.++....|.++++++..+-......|-+.. +.
T Consensus 242 ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~L-k~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~ 320 (381)
T PF00872_consen 242 AIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADL-KAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDEL 320 (381)
T ss_pred cccccccchhhhhheechhhhhccccccccchhhhhhc-cccccccccchhhhhhhhcccccccccchhhhhhhhccccc
Confidence 999999999999999999 12 23455677888888888887766553333233221111 11
Q ss_pred cccccccCcccccccCCCCCc--ccccccccc
Q 043648 441 WVPVYFRDSFFAAISPNQGFD--GSFFDGYVN 470 (841)
Q Consensus 441 Wa~ay~~~~f~~gm~tt~rsE--n~~~k~~v~ 470 (841)
|.-.-+.....--+.|||..| |+.++....
T Consensus 321 ~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~ 352 (381)
T PF00872_consen 321 LTFLDFPPEHRRSIRTTNAIESLNKEIRRRTK 352 (381)
T ss_pred cceeeecchhccccchhhhccccccchhhhcc
Confidence 221113344445678999999 888886443
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.62 E-value=4.2e-09 Score=73.25 Aligned_cols=26 Identities=42% Similarity=0.880 Sum_probs=24.6
Q ss_pred eeeecCcccCCccceeeeeeehhccc
Q 043648 577 NCSCQMFEYSGILCRHVLTVFTVTNV 602 (841)
Q Consensus 577 sCsC~~fe~~GipCrHiLaVl~~~~v 602 (841)
+|+|++||..||||+|+|+|+.+.++
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 79999999999999999999998876
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=98.53 E-value=3.5e-07 Score=83.35 Aligned_cols=76 Identities=20% Similarity=0.391 Sum_probs=64.3
Q ss_pred eCCHHHHHHHHHHHHHhcCcEEEEeeeccCCCCCCeEEEEeecccccccc------------------------------
Q 043648 55 FHTEDAAKTFYDEYARRVGFSSKVCHFSRPRPDEPIVFREFVCGREGLKR------------------------------ 104 (841)
Q Consensus 55 F~S~eeA~~fy~~YA~~~GF~vr~~~s~rsk~~g~i~~~~fvCsreG~~R------------------------------ 104 (841)
|.+.+|.+.|+...+...||.|.|.+|..+ ...|.|--.|.+|
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~-------ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~ 73 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKK-------KIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKK 73 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCc-------eEEEEEecCCCcccccccccccccccccccccccccccccccC
Confidence 889999999999999999999999998653 4578886554321
Q ss_pred c----cccCCccceEEEEeC-cceEEEEEEecCCCCCC
Q 043648 105 R----HGESCDAMLRIELKG-QNKWVVTKFVKEHSHPM 137 (841)
Q Consensus 105 k----~r~gC~a~i~v~~~~-~~~W~V~~~~~eHNH~l 137 (841)
+ +++.||++|++.... ..+|.|..++..|||||
T Consensus 74 k~t~srk~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 74 KRTKSRKNTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred CcccccccCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 0 288999999999875 89999999999999996
No 8
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=98.36 E-value=1.8e-06 Score=73.16 Aligned_cols=64 Identities=22% Similarity=0.330 Sum_probs=56.2
Q ss_pred CCCCCCeeCCHHHHHHHHHHHHHhcCcEEEEeeeccCCCCCCeEEEEeeccccccccccccCCccceEEEEeC-cceEEE
Q 043648 48 DPYVGMEFHTEDAAKTFYDEYARRVGFSSKVCHFSRPRPDEPIVFREFVCGREGLKRRHGESCDAMLRIELKG-QNKWVV 126 (841)
Q Consensus 48 ~P~~Gm~F~S~eeA~~fy~~YA~~~GF~vr~~~s~rsk~~g~i~~~~fvCsreG~~Rk~r~gC~a~i~v~~~~-~~~W~V 126 (841)
...+||.|+|.+|++.++..||-..||.+++.++.+ .+...+|. ..||||+|++.+.+ ++.|.|
T Consensus 3 ~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~-------~r~~~~C~--------~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 3 ELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDK-------KRYRAKCK--------DKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred ccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCC-------EEEEEEEc--------CCCCCEEEEEEEcCCCCEEEC
Confidence 467999999999999999999999999999997653 46789998 67899999999986 677875
No 9
>cd04749 Commd1_MURR1 COMM_Domain containing protein 1, also called Murr1. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=98.16 E-value=1.9e-06 Score=85.59 Aligned_cols=65 Identities=17% Similarity=0.329 Sum_probs=55.5
Q ss_pred cccccccchhhc-----cccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhccccc
Q 043648 762 VLPCLKSMTWVM-----ENKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISDQLST 829 (841)
Q Consensus 762 ~~~~l~~~~~~~-----~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~q~~~ 829 (841)
=+|+|++|.|.. ++..+.+++|+|+++||+++.+.. ...|.|+++++||+.||++|..|++++++
T Consensus 104 ~~~~L~~l~WRVD~~tsS~~~~evn~P~~~l~L~v~~~~~~---~~~v~~emd~ek~~~lL~eLk~iq~~m~~ 173 (174)
T cd04749 104 WENSLRGLSWRVDLKTQSRHIAQINSPVAIVELELGKTGQE---SEFVCLEFDEAKVNRVLKQLAEIQESLDA 173 (174)
T ss_pred hcccccCCCCeeeeecccchhhhccCCeEEEEEeeccCCCC---CceEEEEecHHHHHHHHHHHHHHHHHHhc
Confidence 579999999954 444567899999999999886553 33999999999999999999999999875
No 10
>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=97.89 E-value=3.6e-06 Score=63.71 Aligned_cols=29 Identities=31% Similarity=0.773 Sum_probs=25.3
Q ss_pred CCCceeeeecCcccCCccceeeeeeehhc
Q 043648 572 PEMRANCSCQMFEYSGILCRHVLTVFTVT 600 (841)
Q Consensus 572 ~~~~~sCsC~~fe~~GipCrHiLaVl~~~ 600 (841)
.....+|+|..|+..|.||+|+++|+..+
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHhh
Confidence 35578999999999999999999998654
No 11
>cd04748 Commd COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals.
Probab=97.32 E-value=0.00017 Score=64.35 Aligned_cols=65 Identities=22% Similarity=0.355 Sum_probs=54.2
Q ss_pred ccccccccchhh-----ccccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhccc
Q 043648 761 VVLPCLKSMTWV-----MENKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISDQL 827 (841)
Q Consensus 761 ~~~~~l~~~~~~-----~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~q~ 827 (841)
.++|+|.++.|. +++.......|+|+++||+.++... ....|.||++.+.|..++..|..|..||
T Consensus 18 ~~~~~L~d~~Wrld~~~sS~~~~~~~~P~~~~~L~l~~~~~~--~~~~v~~E~~~~~l~~l~~~L~~a~~~l 87 (87)
T cd04748 18 LSLPQLVDFDWRLDVQISSSSLAKVKQPTILVQLKLQVGDNN--SSEKICFEMTKEELQNFLNKLKKIKAQL 87 (87)
T ss_pred cCCCeeeeeeeEEEEEEchhHHHHhhCCeEEEEEEEecCCCC--ccceEEEEeCHHHHHHHHHHHHHHHhcC
Confidence 378999999993 3344446788999999999986543 3568999999999999999999999986
No 12
>cd04756 Commd8 COMM_Domain containing protein 8. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=97.27 E-value=0.0002 Score=72.34 Aligned_cols=63 Identities=16% Similarity=0.296 Sum_probs=53.1
Q ss_pred ccccccccccchh-----hccccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhc
Q 043648 759 NMVVLPCLKSMTW-----VMENKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISD 825 (841)
Q Consensus 759 ~~~~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~ 825 (841)
++.++|+|.+|+| .++++.+.+..|.|+++||++++ ...+.|.||+||++|+.|+++|.-.+.
T Consensus 104 ~~is~~~L~d~dWrv~l~lSSd~~~~l~~P~~~L~L~v~~~----~~~~~v~~Ems~eel~~li~~Le~a~~ 171 (176)
T cd04756 104 NSISSAQLQDFDWQLKLALSSDKLSSLQEPLLNLDLDVKEN----GILKPVSIEMNKEELQNLISSLEAANK 171 (176)
T ss_pred hccCchhhccccCeeeeeechhhHHHhcCCeEEEEEEecCC----CCeeEEEEEEcHHHHHHHHHHHHHHHH
Confidence 4679999999999 55667778999999999999843 224799999999999999999986553
No 13
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=97.26 E-value=0.00056 Score=76.87 Aligned_cols=91 Identities=18% Similarity=0.201 Sum_probs=75.5
Q ss_pred Ceeeecccccccc--cCcceeeEEEEecCCcEEEEEEeeccCCChhhHHHHHHHHHhhhcCCCCeEecccccHHHHHHHH
Q 043648 305 DAVTLDTRYRVYQ--YNVPFAPFTGINHHGQMILFGCALLLDDSEASFVWLFKTFLTAMNDCQPVSITTDQDKAIQIAVA 382 (841)
Q Consensus 305 dVv~~D~Ty~tnk--y~~pL~~~~gvn~~~q~~~~g~alv~~Et~es~~Wl~~~f~~~m~~~~P~~IiTD~d~al~~AI~ 382 (841)
.+|.+|++|.+-+ -+..+++++||+.+|+-.++|+.+-..|+ ..|.-++..|+.--- ..-..+++|..+++.+||.
T Consensus 146 ~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl-~~v~l~v~Dg~~gl~~aI~ 223 (379)
T COG3328 146 PYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGL-SDVLLVVVDGLKGLPEAIS 223 (379)
T ss_pred eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccc-cceeEEecchhhhhHHHHH
Confidence 4688999998877 67788999999999999999999999999 788744444444311 2235566799999999999
Q ss_pred HhCCcccccccccch
Q 043648 383 KVFPEVRHCISKWHV 397 (841)
Q Consensus 383 ~vFP~a~h~lC~wHI 397 (841)
.+||.+.+..|..|+
T Consensus 224 ~v~p~a~~Q~C~vH~ 238 (379)
T COG3328 224 AVFPQAAVQRCIVHL 238 (379)
T ss_pred HhccHhhhhhhhhHH
Confidence 999999999999999
No 14
>PF07258 HCaRG: HCaRG protein; InterPro: IPR009886 This family consists of several mammalian HCaRG(hypertension-related, calcium-regulated gene) proteins. HCaRG is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. HCaRG is a nuclear protein potentially involved in the control of cell proliferation [].; PDB: 2H2M_A.
Probab=95.41 E-value=0.0041 Score=62.45 Aligned_cols=67 Identities=24% Similarity=0.391 Sum_probs=0.0
Q ss_pred cccccccccchhhcc-----ccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhccccc
Q 043648 760 MVVLPCLKSMTWVME-----NKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISDQLST 829 (841)
Q Consensus 760 ~~~~~~l~~~~~~~~-----~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~q~~~ 829 (841)
..++|+|.+++|..+ +.......|+++++||+++. ....+.+.|+++++.|..|+..|..|++|+..
T Consensus 106 ~~~~~~l~d~~Wrl~~~~~s~~~~~~~~p~~~l~L~~~~~---~~~~~~~~~e~~~~~l~~l~~~L~~a~~~l~~ 177 (178)
T PF07258_consen 106 SFSFPHLVDVDWRLDVQVSSSSLAKINEPVVILQLKTQNG---NGKEETVTFELSKEELQDLLNELKDAQKQLDQ 177 (178)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred cccccccCCCcEEEEeeecccHhhhccCcEEEEEEEecCC---CCcCceEEEEECHHHHHHHHHHHHHHHHHHhc
Confidence 455999999999332 22234567899999999986 45578999999999999999999999999864
No 15
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=95.33 E-value=0.0092 Score=73.51 Aligned_cols=51 Identities=16% Similarity=0.102 Sum_probs=45.4
Q ss_pred Ccccccc-cccccccCCCCCCCCCCCcC-CCCCCCCcccccCC--CCCCccccccccc
Q 043648 714 LWPRQDE-MTRRFNLNDSGPAIQPVSDL-NLPRMAPVSLHRDD--GPSDNMVVLPCLK 767 (841)
Q Consensus 714 ~~~~~d~-~~~~~~~~~~~~~~~~v~~~-~~~~~~p~~~~~~~--~~~~~~~~~~~l~ 767 (841)
+.|++++ +++..+++++|+|||+++|| .|++|||. ||+ +.|++++||+||-
T Consensus 761 ~~q~~~~l~s~~~~~~~~y~~q~~~~g~gql~s~~~~---~~~~~~~q~~~~g~gq~~ 815 (846)
T PLN03097 761 SVQGMVQLNLMAPTRDNYYGNQQTIQGLGQLNSIAPS---HDGYYGTQQSIHGLGQMD 815 (846)
T ss_pred hhhHHHHhhccCCCCCCcccCccCccccccccccCcc---ccCccccCCCcccccccc
Confidence 4556666 89999999999999999999 59999999 998 9999999998765
No 16
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=91.57 E-value=0.056 Score=52.61 Aligned_cols=81 Identities=22% Similarity=0.236 Sum_probs=67.7
Q ss_pred CCeeeecccccccccCcceeeEEEEecCCcEEEEEEeeccCCChhhHHHHHHHHHhhhcCCCCeEecccccHHHHHHHHH
Q 043648 304 GDAVTLDTRYRVYQYNVPFAPFTGINHHGQMILFGCALLLDDSEASFVWLFKTFLTAMNDCQPVSITTDQDKAIQIAVAK 383 (841)
Q Consensus 304 ~dVv~~D~Ty~tnky~~pL~~~~gvn~~~q~~~~g~alv~~Et~es~~Wl~~~f~~~m~~~~P~~IiTD~d~al~~AI~~ 383 (841)
|+.+.+|=||.+-+-+ --+.+..||.+|+ ++++-|-..-+..+=..||+..++..+ ..|.+|+||+..+...|+++
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~ 76 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 6789999999775533 4567899999999 778888888888888888887777765 57999999999999999999
Q ss_pred hCCcc
Q 043648 384 VFPEV 388 (841)
Q Consensus 384 vFP~a 388 (841)
.+|..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99874
No 17
>cd04758 Commd10 COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=91.54 E-value=0.2 Score=51.34 Aligned_cols=66 Identities=14% Similarity=0.281 Sum_probs=53.4
Q ss_pred ccccccccchh-----hccccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhccccc
Q 043648 761 VVLPCLKSMTW-----VMENKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISDQLST 829 (841)
Q Consensus 761 ~~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~q~~~ 829 (841)
.+.|+|.+|.| .+++..+....|.++++||+.+... ....|.||+|++-|-..+..|..|..||-+
T Consensus 115 l~~~~L~D~~Wrl~~~~sSs~~~~~~~P~~~L~L~~~~~~g---~~e~v~~E~t~~el~~l~~~le~~q~~ld~ 185 (186)
T cd04758 115 LAPNQLEDVSWRLNLQMSSSTQAKLKSPLAVLELGVTSEDG---NLEKINLEFNHEELLEFYNQLESIQEQLDS 185 (186)
T ss_pred CCCCccccccceEEEEEccchhhhhcCCcEEEEeecCCCCC---CccceEEEEcHHHHHHHHHHHHHHHHHhcc
Confidence 37899999999 3444444566799999999987432 356999999999999999999999999854
No 18
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=90.86 E-value=0.75 Score=38.15 Aligned_cols=55 Identities=18% Similarity=0.361 Sum_probs=37.5
Q ss_pred CcEEEEeeeccCCCCCCeEEEEeeccccccccccccCCccceEEEEeC-cceEEEEEEecCCCCC
Q 043648 73 GFSSKVCHFSRPRPDEPIVFREFVCGREGLKRRHGESCDAMLRIELKG-QNKWVVTKFVKEHSHP 136 (841)
Q Consensus 73 GF~vr~~~s~rsk~~g~i~~~~fvCsreG~~Rk~r~gC~a~i~v~~~~-~~~W~V~~~~~eHNH~ 136 (841)
||..|+--.... .+...-+..|.|+ -.+|||.=.|.+.. ++.-.++....+|||+
T Consensus 4 gy~WRKYGqK~i-~g~~~pRsYYrCt--------~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 4 GYRWRKYGQKNI-KGSPYPRSYYRCT--------HPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SS-EEEEEEEEE-TTTTCEEEEEEEE--------CTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCchhhccCccc-CCCceeeEeeecc--------ccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 777876433221 1223456789998 45999999999986 7888899999999997
No 19
>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=89.88 E-value=0.44 Score=50.67 Aligned_cols=84 Identities=13% Similarity=0.159 Sum_probs=60.7
Q ss_pred eecccccccccCcceeeEEEEec--CCcEEEEEEeeccCCChhhHHHHHHHH-HhhhcCCCCeEecccccHHHHHHHHHh
Q 043648 308 TLDTRYRVYQYNVPFAPFTGINH--HGQMILFGCALLLDDSEASFVWLFKTF-LTAMNDCQPVSITTDQDKAIQIAVAKV 384 (841)
Q Consensus 308 ~~D~Ty~tnky~~pL~~~~gvn~--~~q~~~~g~alv~~Et~es~~Wl~~~f-~~~m~~~~P~~IiTD~d~al~~AI~~v 384 (841)
.||=+......+- +..+.+|. .+..++ +++.+-+.+++.-+|..+ -.. .....++|.+|...+...||++.
T Consensus 2 giDE~~~~~g~~~--y~t~~~d~~~~~~~il---~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~ 75 (249)
T PF01610_consen 2 GIDEFAFRKGHRS--YVTVVVDLDTDTGRIL---DILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREY 75 (249)
T ss_pred eEeeeeeecCCcc--eeEEEEECccCCceEE---EEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCcccccccccc
Confidence 4554444332221 44455555 445554 588888998888776655 222 33568999999999999999999
Q ss_pred CCcccccccccch
Q 043648 385 FPEVRHCISKWHV 397 (841)
Q Consensus 385 FP~a~h~lC~wHI 397 (841)
||+|.+.+-.|||
T Consensus 76 ~P~A~iv~DrFHv 88 (249)
T PF01610_consen 76 FPNAQIVADRFHV 88 (249)
T ss_pred ccccccccccchh
Confidence 9999999999999
No 20
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=88.86 E-value=0.46 Score=47.74 Aligned_cols=64 Identities=16% Similarity=0.177 Sum_probs=50.1
Q ss_pred CCCccccccccccchhh-----ccccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhh
Q 043648 756 PSDNMVVLPCLKSMTWV-----MENKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAY 822 (841)
Q Consensus 756 ~~~~~~~~~~l~~~~~~-----~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~ 822 (841)
..++...+|+|.+|.|. +++....+.+|++.++||+++... ..+.+.||.+-++|--|+..|..
T Consensus 89 l~~~~~~lp~l~dleWRvDv~isS~~l~~~~~P~i~mkL~l~~~~~---~~~~~~l~td~~~l~~l~~eLe~ 157 (166)
T cd04750 89 LKELSPDLPHYHNLEWRLDVQIASRSLRSQVKPVITMKLHLEDENK---KIETHLLQTDPANLVHLTQTLEQ 157 (166)
T ss_pred HHhcCCCCccccCCceeEEeEEcchhhHhhcCceEEEEEEecCCCC---cccceEEEeCHHHHHHHHHHHHH
Confidence 33456799999999994 444455788999999999987655 34589999999999988887654
No 21
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=87.49 E-value=1.7 Score=40.04 Aligned_cols=75 Identities=12% Similarity=0.082 Sum_probs=55.5
Q ss_pred CCeeeecccccc-cccCcceeeEEEEecCCcEEEEEEeeccCCChhhHHHHHHHHHhhhcCCCCeEecccccHHHHH
Q 043648 304 GDAVTLDTRYRV-YQYNVPFAPFTGINHHGQMILFGCALLLDDSEASFVWLFKTFLTAMNDCQPVSITTDQDKAIQI 379 (841)
Q Consensus 304 ~dVv~~D~Ty~t-nky~~pL~~~~gvn~~~q~~~~g~alv~~Et~es~~Wl~~~f~~~m~~~~P~~IiTD~d~al~~ 379 (841)
+..+.+|.+... ...++..+.++.+|.+-..+. ++.+-..++.+.+.-+|.......++..|.+|+||+..+..+
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFIY-AFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTEEE-EEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHS
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCcEE-EEEeecccccccccccccccccccccccceeccccccccccc
Confidence 467888888544 345558889999999887665 666767678888888888777777766699999999998863
No 22
>cd04753 Commd5_HCaRG COMM_Domain containing protein 5, also called HCaRG (hypertension-related, calcium-regulated gene). HCaRG is a nuclear protein that might be involved in cell proliferation; it is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=84.93 E-value=1.2 Score=41.64 Aligned_cols=62 Identities=19% Similarity=0.319 Sum_probs=44.9
Q ss_pred CCCccccccccccchhhcccc-----CCCCCccceEEEeecccCCCCCCCceEEEEEeehhc-------HHHHHhhhhhh
Q 043648 756 PSDNMVVLPCLKSMTWVMENK-----NSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVT-------LEPMLRSMAYI 823 (841)
Q Consensus 756 ~~~~~~~~~~l~~~~~~~~~~-----~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~t-------l~~ml~~~~~i 823 (841)
..+....+|+|.++.|..+-. .+...+|+.+++||++|+. ...|+++-++ +-.||+.|..+
T Consensus 28 l~~~~~rlp~l~~l~WRVDv~lSSs~l~~~~~PtI~LkLkl~dg~-------~~~fe~~~~kF~~Lry~~a~~l~em~~l 100 (110)
T cd04753 28 ALQKGVRLPHLEDFKWRVDVAISTSSLSRVLQPSILMEMKLSDGK-------SHRFEVPVAKFHELRYNVALILKEMNDL 100 (110)
T ss_pred HHHhccCCcccccCcceEEEEEchhhhhcccCCeEEEEEEecCCC-------eEEEEeeHHHHHHHHHHHHHHHHHHHHH
Confidence 344456999999999955433 3457889999999997632 7788888776 45677777655
Q ss_pred h
Q 043648 824 S 824 (841)
Q Consensus 824 ~ 824 (841)
-
T Consensus 101 e 101 (110)
T cd04753 101 E 101 (110)
T ss_pred H
Confidence 3
No 23
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=84.81 E-value=1.2 Score=45.22 Aligned_cols=67 Identities=15% Similarity=0.242 Sum_probs=51.0
Q ss_pred cccccccccchh-----hccccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhcccc
Q 043648 760 MVVLPCLKSMTW-----VMENKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISDQLS 828 (841)
Q Consensus 760 ~~~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~q~~ 828 (841)
-..+|+|.+|.| .+++......+|...++|++.+.. . ...+++.||++.+.|-.++..|...+..+-
T Consensus 101 ~l~~~~L~d~~WRld~~lsSs~l~~~~~P~~~l~L~v~~~~-~-~~~~~v~~e~s~~ql~~L~~eLe~A~~~m~ 172 (174)
T cd04752 101 SLRLSRLESVDWRVDYILSSSELQEVNEPLVQLRLKVRNAD-T-GEITPHPFSVSADKFRVLLAELKQAQTLME 172 (174)
T ss_pred CCCCCcccccceeeEEEEcchhhhhcCCCeEEEEEeeecCC-C-CCcceEEEEecHHHHHHHHHHHHHHHHHHh
Confidence 467899999999 333333456788888999998632 2 224699999999999999999988776543
No 24
>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=76.31 E-value=4.2 Score=46.47 Aligned_cols=56 Identities=16% Similarity=0.227 Sum_probs=48.7
Q ss_pred CCCeeCCHHHHHHHHHHHHHhcCcEEEEeeeccCCCCCCeEEEEeeccccccccccccCCccceEEEEeC
Q 043648 51 VGMEFHTEDAAKTFYDEYARRVGFSSKVCHFSRPRPDEPIVFREFVCGREGLKRRHGESCDAMLRIELKG 120 (841)
Q Consensus 51 ~Gm~F~S~eeA~~fy~~YA~~~GF~vr~~~s~rsk~~g~i~~~~fvCsreG~~Rk~r~gC~a~i~v~~~~ 120 (841)
.|..|+|.++=|..+|.|....-..|..+.|.|.| ..+|.|. .-.||++|.+...+
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk------hftfach--------lk~c~fkillsy~g 79 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK------HFTFACH--------LKNCPFKILLSYCG 79 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeeccccccc------ceEEEee--------ccCCCceeeeeecc
Confidence 36689999999999999999999999988887643 5799999 78999999998754
No 25
>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=76.04 E-value=4.2 Score=32.97 Aligned_cols=48 Identities=23% Similarity=0.346 Sum_probs=21.1
Q ss_pred CcEEEEeeeccCCCCCCeEEEEeeccccccccccccCCccceEEEEeCcceEEEEEEecCCCC
Q 043648 73 GFSSKVCHFSRPRPDEPIVFREFVCGREGLKRRHGESCDAMLRIELKGQNKWVVTKFVKEHSH 135 (841)
Q Consensus 73 GF~vr~~~s~rsk~~g~i~~~~fvCsreG~~Rk~r~gC~a~i~v~~~~~~~W~V~~~~~eHNH 135 (841)
||.....+.. +| .....|++. +..+|+|++.+. .+.-.|.....+|||
T Consensus 15 Gy~y~~~~~~----~~---~~~WrC~~~-----~~~~C~a~~~~~---~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 15 GYRYYFNKRN----DG---KTYWRCSRR-----RSHGCRARLITD---AGDGRVVRTNGEHNH 62 (62)
T ss_dssp TEEEEEEEE-----SS----EEEEEGGG-----TTS----EEEEE-----TTEEEE-S---SS
T ss_pred CeEEECcCCC----CC---cEEEEeCCC-----CCCCCeEEEEEE---CCCCEEEECCCccCC
Confidence 5655555432 33 236778742 146999999997 223344445588999
No 26
>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=75.76 E-value=4.8 Score=33.33 Aligned_cols=38 Identities=18% Similarity=0.340 Sum_probs=31.3
Q ss_pred EEEEeeccccccccccccCCccceEEEEeC-cceEEEEEEecCCCC
Q 043648 91 VFREFVCGREGLKRRHGESCDAMLRIELKG-QNKWVVTKFVKEHSH 135 (841)
Q Consensus 91 ~~~~fvCsreG~~Rk~r~gC~a~i~v~~~~-~~~W~V~~~~~eHNH 135 (841)
-+..|.|+. ..||||+=.|.+.. ++.-.++....+|||
T Consensus 21 pRsYYrCt~-------~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 21 PRSYYRCTY-------SQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cceEEeccc-------cCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 356788983 37999999999875 788888899999998
No 27
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=64.05 E-value=11 Score=34.37 Aligned_cols=63 Identities=10% Similarity=0.321 Sum_probs=45.1
Q ss_pred ccccccccchhhccc-----cCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhccc
Q 043648 761 VVLPCLKSMTWVMEN-----KNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISDQL 827 (841)
Q Consensus 761 ~~~~~l~~~~~~~~~-----~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~q~ 827 (841)
..+|.+.+..|..+- ....+..|+-.|+|+.++... .+.+.|+-+-|.|--|+..|.-+..++
T Consensus 23 ~~~p~l~dv~WRld~~lsS~~l~~~~~p~~~i~L~~~~~~~----~~~i~f~c~~e~L~~Li~~Lk~A~~~~ 90 (95)
T cd04751 23 ISFPHITDVNWRLDYVVSSKHLGKVNQPIYLIQLSTENGEN----KPDINFTCTLEQLQDLVNKLKDAAKNI 90 (95)
T ss_pred CCCCceecCceEEEEEEcccccCcccceeEEEEEeccCCCC----cceEEEEeCHHHHHHHHHHHHHHHHHH
Confidence 378999999994322 223455566568888865322 669999999999999998887666544
No 28
>cd04754 Commd6 COMM_Domain containing protein 6. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=60.13 E-value=10 Score=33.63 Aligned_cols=61 Identities=15% Similarity=0.265 Sum_probs=44.7
Q ss_pred cccccccchh-----hccccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhc
Q 043648 762 VLPCLKSMTW-----VMENKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISD 825 (841)
Q Consensus 762 ~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~ 825 (841)
...+|.+|+| .++++.+....|.--+.||+.++. ...+++-|||+..=+-..++.|..++.
T Consensus 18 ~~~qLvDm~WKlgva~sSd~~~sl~~Pfl~l~L~V~~~~---G~~~~~~~EmTlpEFq~f~~~~~~~~a 83 (86)
T cd04754 18 NIGQLVDFKWKLGMAVSSDTCRSLNSPYVAVTLKVADPS---GQVVTKSFEMTIPEFQNFSRQFKEMAA 83 (86)
T ss_pred cccceEeeeeeEeEEEechhhhhcCCceEEEEEEEEccC---CCccceEEEEcHHHHHHHHHHHHHHHH
Confidence 4789999999 555655555555555667776632 224667999999999999999988864
No 29
>cd04755 Commd7 COMM_Domain containing protein 7. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=51.07 E-value=18 Score=36.85 Aligned_cols=65 Identities=17% Similarity=0.198 Sum_probs=45.4
Q ss_pred cccccccccchh----hccccCCCCCccceEEEeecccCCCCCCCceEEEEEeehhcHHHHHhhhhhhhccc
Q 043648 760 MVVLPCLKSMTW----VMENKNSAPGNRVAVINLKLHDYSKTPSAELEVKFQLSKVTLEPMLRSMAYISDQL 827 (841)
Q Consensus 760 ~~~~~~l~~~~~----~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~tl~~ml~~~~~i~~q~ 827 (841)
.-.+++|.+|.| +++.....- -..++|+|||... .......|-|++|.+.+--.+..|..|+.++
T Consensus 110 tL~~~qL~d~~Wr~~~~~sSS~~~~-~~~p~vqLkl~~~--~~~~~e~v~~E~t~~qF~~f~~elk~a~a~m 178 (180)
T cd04755 110 TLMVNQLVDMEWKFGVTAGSSELQK-VGSIFLQLKLVVR--KGNQTENVYMELTLPQFYSFLHEMERAKASL 178 (180)
T ss_pred ccCccccccccceeeeEecchhhhh-cCCcEEEEEEEec--CCCCceeEEEEEcHHHHHHHHHHHHHHHHHh
Confidence 456789999999 233211111 1337899999874 2222457889999999999999998888765
No 30
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.11 E-value=36 Score=35.58 Aligned_cols=84 Identities=20% Similarity=0.203 Sum_probs=54.2
Q ss_pred CCeeeecccccccccCcceeeEEEEecCCcEEEEEEeeccCCChhhHHHHHHHHHhhhcCCCCeEecccccHHHHHHHHH
Q 043648 304 GDAVTLDTRYRVYQYNVPFAPFTGINHHGQMILFGCALLLDDSEASFVWLFKTFLTAMNDCQPVSITTDQDKAIQIAVAK 383 (841)
Q Consensus 304 ~dVv~~D~Ty~tnky~~pL~~~~gvn~~~q~~~~g~alv~~Et~es~~Wl~~~f~~~m~~~~P~~IiTD~d~al~~AI~~ 383 (841)
++++.+|=||.+-+-+. -+..-.+|..|++.- +=|...-+...=.-||..+++.- ..|.+|+||+......|+.+
T Consensus 70 ~~~w~vDEt~ikv~gkw-~ylyrAid~~g~~Ld--~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~~ 144 (215)
T COG3316 70 GDSWRVDETYIKVNGKW-HYLYRAIDADGLTLD--VWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALRK 144 (215)
T ss_pred ccceeeeeeEEeeccEe-eehhhhhccCCCeEE--EEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHHh
Confidence 35677777776443322 223344555565543 33444444444455666666665 57999999999999999999
Q ss_pred hCCcccccc
Q 043648 384 VFPEVRHCI 392 (841)
Q Consensus 384 vFP~a~h~l 392 (841)
+-+.+.|+-
T Consensus 145 l~~~~ehr~ 153 (215)
T COG3316 145 LGSEVEHRT 153 (215)
T ss_pred cCcchheec
Confidence 998776653
No 31
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=36.53 E-value=1.1e+02 Score=30.36 Aligned_cols=95 Identities=13% Similarity=0.142 Sum_probs=59.7
Q ss_pred HhcCCeeeecccccccccCcceeeEEEEecCCcEEEEEEeec-cCCChhhHHHHHHHHHhhhcCCCCeEecccccHHHHH
Q 043648 301 SHFGDAVTLDTRYRVYQYNVPFAPFTGINHHGQMILFGCALL-LDDSEASFVWLFKTFLTAMNDCQPVSITTDQDKAIQI 379 (841)
Q Consensus 301 ~~f~dVv~~D~Ty~tnky~~pL~~~~gvn~~~q~~~~g~alv-~~Et~es~~Wl~~~f~~~m~~~~P~~IiTD~d~al~~ 379 (841)
..+|=.|..|+= ++..+.+|..|+.....|-.|+-..-.- ...+.+.+.-+|+...+.+|...-..||||-...++.
T Consensus 30 ~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~~~~~ 107 (153)
T PF04937_consen 30 KRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNASNMKK 107 (153)
T ss_pred HhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCchhHHH
Confidence 344444555543 4445667777777666666554332111 1245666666666666666766778899999999988
Q ss_pred HHH---HhCCcccccccccch
Q 043648 380 AVA---KVFPEVRHCISKWHV 397 (841)
Q Consensus 380 AI~---~vFP~a~h~lC~wHI 397 (841)
|-+ +-+|+..-..|.-|-
T Consensus 108 a~~~L~~k~p~ifw~~CaaH~ 128 (153)
T PF04937_consen 108 AGKLLMEKYPHIFWTPCAAHC 128 (153)
T ss_pred HHHHHHhcCCCEEEechHHHH
Confidence 844 446777777787774
No 32
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=26.92 E-value=63 Score=29.83 Aligned_cols=27 Identities=30% Similarity=0.509 Sum_probs=21.1
Q ss_pred CCCCeeCCHHHHHHHHHHHHHhcCcEEEEee
Q 043648 50 YVGMEFHTEDAAKTFYDEYARRVGFSSKVCH 80 (841)
Q Consensus 50 ~~Gm~F~S~eeA~~fy~~YA~~~GF~vr~~~ 80 (841)
.+.+.|+|.|+|- +||+++|....+..
T Consensus 50 ~v~l~F~skE~Ai----~yaer~G~~Y~V~~ 76 (101)
T PF04800_consen 50 SVRLKFDSKEDAI----AYAERNGWDYEVEE 76 (101)
T ss_dssp -CEEEESSHHHHH----HHHHHCT-EEEEE-
T ss_pred eeEeeeCCHHHHH----HHHHHcCCeEEEeC
Confidence 4778999999997 57999999988764
No 33
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=25.60 E-value=50 Score=30.42 Aligned_cols=29 Identities=31% Similarity=0.589 Sum_probs=20.4
Q ss_pred CceEEEEEeCCCCceeeeecCccc-----CCccceeeeee
Q 043648 562 SRAYIVTFNHPEMRANCSCQMFEY-----SGILCRHVLTV 596 (841)
Q Consensus 562 ~k~y~V~~~~~~~~~sCsC~~fe~-----~GipCrHiLaV 596 (841)
.+.|++.. ..|||..|-. -.-||.|++.+
T Consensus 42 ~rdYIl~~------gfCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 42 ERDYILEG------GFCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred ccceEEEc------CcccCHHHHhHhhhcCcccchhhhhe
Confidence 45677753 2799998872 23469999874
No 34
>PHA02517 putative transposase OrfB; Reviewed
Probab=25.17 E-value=1.6e+02 Score=31.73 Aligned_cols=69 Identities=12% Similarity=-0.004 Sum_probs=43.2
Q ss_pred CCeeeecccccccccCcceeeEEEEecCCcEEEEEEeeccCCChhhHHHHHHHHHhhhcCC-CC--eEecccccHHH
Q 043648 304 GDAVTLDTRYRVYQYNVPFAPFTGINHHGQMILFGCALLLDDSEASFVWLFKTFLTAMNDC-QP--VSITTDQDKAI 377 (841)
Q Consensus 304 ~dVv~~D~Ty~tnky~~pL~~~~gvn~~~q~~~~g~alv~~Et~es~~Wl~~~f~~~m~~~-~P--~~IiTD~d~al 377 (841)
++++..|.||..... +-.+.++.+|.+.+.+ +|+.+-..++.+. ++..|..++... .| ..|.||+....
T Consensus 110 n~~w~~D~t~~~~~~-g~~yl~~iiD~~sr~i-~~~~~~~~~~~~~---~~~~l~~a~~~~~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 110 NQLWVADFTYVSTWQ-GWVYVAFIIDVFARRI-VGWRVSSSMDTDF---VLDALEQALWARGRPGGLIHHSDKGSQY 181 (277)
T ss_pred CCeEEeceeEEEeCC-CCEEEEEecccCCCee-eecccCCCCChHH---HHHHHHHHHHhcCCCcCcEeeccccccc
Confidence 477888999865443 3456777788777655 5677776666664 445554444322 23 46668887653
No 35
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=20.21 E-value=3.1e+02 Score=29.59 Aligned_cols=72 Identities=8% Similarity=-0.047 Sum_probs=47.5
Q ss_pred CCeeeecccccccccCcceeeEEEEecCCcEEEEEEeeccC-CChhhHHHHHHHHHhhh-c---CCCCeEecccccHH
Q 043648 304 GDAVTLDTRYRVYQYNVPFAPFTGINHHGQMILFGCALLLD-DSEASFVWLFKTFLTAM-N---DCQPVSITTDQDKA 376 (841)
Q Consensus 304 ~dVv~~D~Ty~tnky~~pL~~~~gvn~~~q~~~~g~alv~~-Et~es~~Wl~~~f~~~m-~---~~~P~~IiTD~d~a 376 (841)
..+++.|-||.....+.-++..+.+|.+.+ .++|+++-.. .+.+...-+|+..+... + ...|..|.||+...
T Consensus 87 n~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 87 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred CCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCcc
Confidence 477888988876544556888888988887 4568888764 55555544554333332 2 23578888998654
No 36
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=20.17 E-value=45 Score=30.29 Aligned_cols=29 Identities=21% Similarity=0.289 Sum_probs=21.0
Q ss_pred CCCCCeeCCHHHHHHHHHHHHHhcCcEEE
Q 043648 49 PYVGMEFHTEDAAKTFYDEYARRVGFSSK 77 (841)
Q Consensus 49 P~~Gm~F~S~eeA~~fy~~YA~~~GF~vr 77 (841)
+.+=++|+|++.|++||++=+...--++|
T Consensus 54 r~vviEFps~~~ar~~y~SpeYq~a~~~R 82 (96)
T COG5470 54 RNVVIEFPSLEAARDCYNSPEYQAAAAIR 82 (96)
T ss_pred cEEEEEcCCHHHHHHHhcCHHHHHHHHHH
Confidence 45668999999999999875544333343
Done!