Query 004138
Match_columns 771
No_of_seqs 435 out of 1472
Neff 8.0
Searched_HMMs 46136
Date Thu Mar 28 18:13:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004138.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004138hhsearch_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-134 1E-138 1170.5 56.5 578 188-769 66-678 (846)
2 PLN03097 FHY3 Protein FAR-RED 99.9 1.7E-27 3.8E-32 278.8 14.4 103 38-140 67-195 (846)
3 PF10551 MULE: MULE transposas 99.8 2E-21 4.2E-26 171.5 8.1 90 389-480 1-93 (93)
4 PF03101 FAR1: FAR1 DNA-bindin 99.8 6.2E-21 1.4E-25 167.6 8.7 77 59-135 1-91 (91)
5 PF03101 FAR1: FAR1 DNA-bindin 99.7 2E-18 4.3E-23 151.6 7.5 77 210-286 1-91 (91)
6 PF00872 Transposase_mut: Tran 99.6 5.7E-16 1.2E-20 171.2 0.9 178 383-565 163-353 (381)
7 COG3328 Transposase and inacti 99.0 2E-09 4.4E-14 117.0 12.6 195 383-580 146-349 (379)
8 PF08731 AFT: Transcription fa 98.8 1.5E-08 3.2E-13 88.9 8.0 76 202-284 1-111 (111)
9 smart00575 ZnF_PMZ plant mutat 98.8 3.7E-09 8E-14 70.5 2.0 26 669-694 2-27 (28)
10 PF03108 DBD_Tnp_Mut: MuDR fam 98.6 1.4E-07 3.1E-12 77.5 7.5 65 194-273 2-67 (67)
11 PF04434 SWIM: SWIM zinc finge 98.0 5.8E-06 1.3E-10 60.4 3.2 28 666-693 13-40 (40)
12 PF08731 AFT: Transcription fa 97.6 0.0003 6.6E-09 62.2 9.1 76 51-133 1-111 (111)
13 PF03108 DBD_Tnp_Mut: MuDR fam 97.1 0.0023 4.9E-08 52.5 7.4 63 45-122 4-67 (67)
14 PF13610 DDE_Tnp_IS240: DDE do 93.4 0.021 4.6E-07 54.2 -0.1 81 382-466 1-81 (140)
15 PF01610 DDE_Tnp_ISL3: Transpo 93.0 0.11 2.3E-06 54.3 4.4 82 401-486 15-99 (249)
16 PF03106 WRKY: WRKY DNA -bindi 92.9 0.42 9.2E-06 38.1 6.5 56 219-283 3-59 (60)
17 PF03106 WRKY: WRKY DNA -bindi 91.8 0.86 1.9E-05 36.4 7.1 56 68-132 3-59 (60)
18 PF00665 rve: Integrase core d 87.7 1.8 3.9E-05 39.1 7.0 76 382-458 6-82 (120)
19 PF04500 FLYWCH: FLYWCH zinc f 85.6 0.94 2E-05 35.8 3.4 49 219-282 14-62 (62)
20 PF06782 UPF0236: Uncharacteri 85.2 20 0.00043 41.2 15.2 142 422-566 235-382 (470)
21 PF04500 FLYWCH: FLYWCH zinc f 80.0 3.6 7.9E-05 32.4 4.8 35 89-131 28-62 (62)
22 smart00774 WRKY DNA binding do 79.8 3.2 7E-05 32.9 4.2 39 237-282 20-59 (59)
23 smart00774 WRKY DNA binding do 69.1 9.7 0.00021 30.3 4.4 56 68-131 3-59 (59)
24 PF04937 DUF659: Protein of un 68.6 36 0.00079 32.7 9.3 106 378-485 29-138 (153)
25 PF04684 BAF1_ABF1: BAF1 / ABF 68.1 8.6 0.00019 42.8 5.3 55 199-267 25-79 (496)
26 COG3316 Transposase and inacti 52.4 22 0.00047 36.0 4.7 82 383-469 71-152 (215)
27 smart00461 WH1 WASP homology r 37.5 18 0.0004 32.4 1.4 20 45-64 83-102 (106)
28 cd01205 WASP WASP-type EVH1 do 37.4 19 0.00042 32.2 1.5 21 44-64 81-101 (105)
29 cd00837 EVH1 EVH1 (Enabled, Va 34.8 22 0.00048 31.7 1.5 19 46-64 82-100 (104)
30 COG5431 Uncharacterized metal- 33.8 32 0.0007 30.4 2.2 31 654-688 40-75 (117)
31 PRK14702 insertion element IS2 32.5 1.3E+02 0.0027 31.7 7.0 71 382-453 87-162 (262)
32 COG4279 Uncharacterized conser 32.1 23 0.00049 36.5 1.2 22 669-693 126-147 (266)
33 COG5470 Uncharacterized conser 29.8 25 0.00053 30.7 0.9 27 189-215 47-73 (96)
34 PRK09409 IS2 transposase TnpB; 29.0 1.6E+02 0.0034 31.7 7.2 71 382-453 126-201 (301)
35 PF00568 WH1: WH1 domain; Int 29.0 31 0.00066 31.2 1.4 19 46-64 89-107 (111)
36 PHA02517 putative transposase 26.5 1.5E+02 0.0032 31.2 6.4 71 382-454 110-180 (277)
37 PF07576 BRAP2: BRCA1-associat 24.9 51 0.0011 29.8 2.1 21 46-66 56-76 (110)
38 COG5470 Uncharacterized conser 22.1 49 0.0011 28.9 1.3 25 44-68 53-77 (96)
39 PF03050 DDE_Tnp_IS66: Transpo 20.3 53 0.0011 34.5 1.5 40 439-484 116-155 (271)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.4e-134 Score=1170.55 Aligned_cols=578 Identities=33% Similarity=0.630 Sum_probs=531.8
Q ss_pred CCCCCCCCCCCCCcccCHHHHHHHHHHHHHhcCcEEEEeeeeeccCCCceEEEEEeecCCCccc----------------
Q 004138 188 GEGECIPEPYAGLEFNSANEAYQFYQAYAEKTGFRVRIGQLFRSKNDGSVTSRRFVCSKEGFQH---------------- 251 (771)
Q Consensus 188 ~~~~~~~~p~~Gm~F~S~eea~~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~~~C~r~G~~~---------------- 251 (771)
.+++..++|.+||+|+|+|||++||+.||+++||+||+++++|++.+|.+++++|+|+|+|+++
T Consensus 66 ~~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~ 145 (846)
T PLN03097 66 FKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQ 145 (846)
T ss_pred ccCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCccccccccccccccccc
Confidence 4567889999999999999999999999999999999999999999999999999999999742
Q ss_pred ----------CcccCccceeeeeecCcceEEEEEEeccccccccccccccccccccccceeecccCCCcccccccccccc
Q 004138 252 ----------PSRVGCGAFMRIKRKEFGSWIVDRLQKDHNHDLECQMGANKKTFATSKKFIEDVSGGLDSVDLAEINNGS 321 (771)
Q Consensus 252 ----------~~rtGC~a~i~v~~~~~~kW~V~~~~~~HNH~l~~~~~~hr~~~~~~k~~i~~~~g~~~~~~~~~~di~n 321 (771)
.+||||||+|+|++.++|+|+|+.|+.+|||||.|+...+.+..... ..+....++..++..++.|..|
T Consensus 146 ~~~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~-~~~~~~~~~~~~v~~~~~d~~~ 224 (846)
T PLN03097 146 DPENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVSEQTRKMY-AAMARQFAEYKNVVGLKNDSKS 224 (846)
T ss_pred CcccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccccchhhhhhH-HHHHhhhhccccccccchhhcc
Confidence 27899999999999889999999999999999998765431100000 0111133456677778888888
Q ss_pred hhHHhhhhccCCchHHHHHHHHHhhcccCCCceEEEEecCC-eeEEEEEeeCcchhhhhhcCcEEEEcccccccCCCCcc
Q 004138 322 IIKISQENNIGSAWYRVLFEYFQTRQSEDTGFFHSVEVDNG-RCMSVFWADGRSRFSCSQFGDAIIFDTSYRKTNYLIPF 400 (771)
Q Consensus 322 ~~~~~r~~~~~~d~~~~ll~~~~~~~~~np~f~y~v~~de~-~~~~lFwa~~~s~~~y~~f~dVv~~D~Ty~tn~y~~pl 400 (771)
+....|+..+..+|+++|++||++||.+||+|||++++|++ ++.+|||+|++|+.+|.+|||||+|||||+||+|+|||
T Consensus 225 ~~~~~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pf 304 (846)
T PLN03097 225 SFDKGRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPL 304 (846)
T ss_pred hhhHHHhhhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHhcCCEEEEeceeeccccCcEE
Confidence 88888877786666999999999999999999999999955 55569999999999999999999999999999999999
Q ss_pred cEEEEEccCCcceeeeeeecccccchhHhHHHHHHHHHhcCCCCeEEecchhHHHHHHHHHhCCCcccccchhhHHHHHH
Q 004138 401 ATFVGINHHRHPVLLGCALVANESKESFTWLFNTWIRAMFGCHPKTIIADQDMAIQQAIARIFPRTHHRFSMWQIRAKER 480 (771)
Q Consensus 401 ~~~~Gvn~~~~~~~~g~al~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~ai~~Ai~~vfP~a~h~~C~~Hi~~n~~ 480 (771)
++|+|||||+|+++||||||.+|+.+||.|||++|+++|+|++|++||||+|.+|++||++|||+|.|++|+|||++|+.
T Consensus 305 a~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~ 384 (846)
T PLN03097 305 ALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVS 384 (846)
T ss_pred EEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccC---ChhhHHHHHhhhcccccHHHHHHHHHHHHHHhCCCccHHHHHHHHHhhcchhcccccccccCCccc---cc
Q 004138 481 ENLRSM---SNQFVFEYNKCIYQSQSIAQFSTMWTALIEKYGQRDNIWLKEMYEKRESWVPLYLRRSFFAGIPIG---KS 554 (771)
Q Consensus 481 ~~l~~~---~~~~~~~~~~~i~~~~t~~eFe~~w~~l~~~~~l~~~~~L~~ly~~r~~Wa~~y~~~~f~~~~~st---Es 554 (771)
++|+.+ .++|..+|.+||+.+.+++|||..|..|+++|+|++|+||+.||+.|++|||+|+++.|++||++| ||
T Consensus 385 e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~agm~sTqRSES 464 (846)
T PLN03097 385 ENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQRSES 464 (846)
T ss_pred HHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhcccccCCccccccccc
Confidence 999976 689999999999999999999999999999999999999999999999999999999999999999 99
Q ss_pred hhHHhhcccCCCCCHHHHHHHHHHHHHHHHHHHhHhhhhcccccccccCcchHHHHHHhhccHHHHHHHHHHHHhhccce
Q 004138 555 IESFFGATLTAQTPLREFISRYTQGLERRREEERKEDFNTWNLQAFLQTKEPIEEQCRRLYTRNMFKIFQNELLQSFDYL 634 (771)
Q Consensus 555 ~n~~lk~~~~~~~~l~~f~~~~~~~l~~~~~~e~~~d~~s~~~~p~l~t~~p~e~qa~~iyT~~if~~fq~el~~s~~~~ 634 (771)
+|++|++|++++++|.+|+++|+++++.++++|+++|+.+.++.|.+++++|||+||+++|||+||++||+|+..+..|.
T Consensus 465 ~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~ 544 (846)
T PLN03097 465 INAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACH 544 (846)
T ss_pred HHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeecCCcEEEEEEEEecCCCcceEEEecc--ceeeeecCCcccCCccchhHHHHHhhcCcccCCCccccccccccccc
Q 004138 635 VTKTNEEATIVRYLVRKCGNEDEKHVVTFSA--LNVSCSCQMFEFEGMLCGHILKVFNLLNVKEIPSQYILHRWTRNAEY 712 (771)
Q Consensus 635 ~~~~~~~g~~~~y~V~~~~~~~~~~~V~~~~--~~~~CsC~~fe~~GipC~HiL~Vl~~~~v~~iP~~yil~RWtk~ak~ 712 (771)
+..+.++|...+|.|..... .+.|+|.+|. ..++|+|++||+.||||+|||+||.++||.+||++|||+||||+||.
T Consensus 545 ~~~~~~dg~~~~y~V~~~~~-~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdAK~ 623 (846)
T PLN03097 545 PKMESQDETSITFRVQDFEK-NQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDAKS 623 (846)
T ss_pred EeeeccCCceEEEEEEEecC-CCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhchhhhhh
Confidence 98888889999999987543 5689999998 89999999999999999999999999999999999999999999998
Q ss_pred CccccCCCCCChHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhhhc
Q 004138 713 GVLRDTESGFSAQELKALMVWSLRETASKYVESGTGSLEKHKLAYEIMREGGNKLCW 769 (771)
Q Consensus 713 ~~~~~~~~~~~~~~~~~~r~~~L~~~~~~~~~~~~~s~e~~~~a~~~L~e~~~k~~~ 769 (771)
..+.+.... ...+.+.||+.||+++++++++|+.|.|.|+.|+++|+|+.++++.
T Consensus 624 ~~~~~~~~~--~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~L~e~~~~~~~ 678 (846)
T PLN03097 624 RHLLGEESE--QVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRALEEAFGNCIS 678 (846)
T ss_pred cccCccccc--cccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence 776654322 2345578999999999999999999999999999999999999863
No 2
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=99.95 E-value=1.7e-27 Score=278.76 Aligned_cols=103 Identities=35% Similarity=0.652 Sum_probs=95.3
Q ss_pred CCCCCCCCcCCCeeCCHHHHHHHHHHHhhccCeEEEEeeeeecCCCCcEEEEEEEecCccccc-----------------
Q 004138 38 EGWSRMEPSVGLEFDTADDAREFYTQYAERVGFKIRIGQLYRSRTDGSVSSRRFVCSKEGFQL----------------- 100 (771)
Q Consensus 38 ~~~~~~~p~~gm~F~s~~~a~~fy~~ya~~~GF~vr~~~~~~~~~~~~~~~~~~~C~~~g~~~----------------- 100 (771)
+.+...+|++||+|+|+||||+|||.||+++||+||+++++|++.+|+|++++|||||||+++
T Consensus 67 ~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~ 146 (846)
T PLN03097 67 KEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQD 146 (846)
T ss_pred cCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccC
Confidence 457788999999999999999999999999999999999999999999999999999999852
Q ss_pred ---------CCccCcccEEEEEEecCCcEEEEEEecCCCcCCCCCCCCC
Q 004138 101 ---------NSRTGCSAYIRVQKRDSGKWVLDQMKKDHNHEFDSAGENS 140 (771)
Q Consensus 101 ---------~~r~~C~a~~~v~~~~~~~w~v~~~~~~HnH~l~~~~~~~ 140 (771)
.+||||+|+|+|++.++|+|+|++|++||||||.|+....
T Consensus 147 ~~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~~ 195 (846)
T PLN03097 147 PENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVS 195 (846)
T ss_pred cccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccccc
Confidence 2789999999999988899999999999999999887643
No 3
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.85 E-value=2e-21 Score=171.48 Aligned_cols=90 Identities=32% Similarity=0.564 Sum_probs=86.8
Q ss_pred ccccccCCCCcccE---EEEEccCCcceeeeeeecccccchhHhHHHHHHHHHhcCCCCeEEecchhHHHHHHHHHhCCC
Q 004138 389 TSYRKTNYLIPFAT---FVGINHHRHPVLLGCALVANESKESFTWLFNTWIRAMFGCHPKTIIADQDMAIQQAIARIFPR 465 (771)
Q Consensus 389 ~Ty~tn~y~~pl~~---~~Gvn~~~~~~~~g~al~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~ai~~Ai~~vfP~ 465 (771)
+||+||+| +|++. ++|+|++|+.+|+|++++.+|+.++|.|+|+.+++.++.+ |.+||||++.++.+||+++||+
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 cccccchhhHHHHHH
Q 004138 466 THHRFSMWQIRAKER 480 (771)
Q Consensus 466 a~h~~C~~Hi~~n~~ 480 (771)
+.|++|.||+++|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999974
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=99.84 E-value=6.2e-21 Score=167.55 Aligned_cols=77 Identities=36% Similarity=0.745 Sum_probs=72.2
Q ss_pred HHHHHHhhccCeEEEEeeeeecCCCCcEEEEEEEecCccccc--------------CCccCcccEEEEEEecCCcEEEEE
Q 004138 59 EFYTQYAERVGFKIRIGQLYRSRTDGSVSSRRFVCSKEGFQL--------------NSRTGCSAYIRVQKRDSGKWVLDQ 124 (771)
Q Consensus 59 ~fy~~ya~~~GF~vr~~~~~~~~~~~~~~~~~~~C~~~g~~~--------------~~r~~C~a~~~v~~~~~~~w~v~~ 124 (771)
+||+.||+.+||+||++++++++++|.+.+..|+|+++|+.. ++||||+|+|.|++..+|+|.|+.
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 599999999999999999999889999999999999999852 579999999999988789999999
Q ss_pred EecCCCcCCCC
Q 004138 125 MKKDHNHEFDS 135 (771)
Q Consensus 125 ~~~~HnH~l~~ 135 (771)
++.+|||||.|
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999987
No 5
>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=99.75 E-value=2e-18 Score=151.61 Aligned_cols=77 Identities=36% Similarity=0.695 Sum_probs=72.4
Q ss_pred HHHHHHHHhcCcEEEEeeeeeccCCCceEEEEEeecCCCccc--------------CcccCccceeeeeecCcceEEEEE
Q 004138 210 QFYQAYAEKTGFRVRIGQLFRSKNDGSVTSRRFVCSKEGFQH--------------PSRVGCGAFMRIKRKEFGSWIVDR 275 (771)
Q Consensus 210 ~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~~~C~r~G~~~--------------~~rtGC~a~i~v~~~~~~kW~V~~ 275 (771)
+||+.||..+||+|++.++++++.+|.++++.|+|+++|.+. ++++||||+|.+++..+|+|.|+.
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 599999999999999999999888999999999999999854 789999999999988899999999
Q ss_pred Eeccccccccc
Q 004138 276 LQKDHNHDLEC 286 (771)
Q Consensus 276 ~~~~HNH~l~~ 286 (771)
+..+|||+|.|
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999986
No 6
>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=99.56 E-value=5.7e-16 Score=171.22 Aligned_cols=178 Identities=14% Similarity=0.168 Sum_probs=144.1
Q ss_pred cEEEEcccccccCC-----CCcccEEEEEccCCcceeeeeeecccccchhHhHHHHHHHHHhcCCCCeEEecchhHHHHH
Q 004138 383 DAIIFDTSYRKTNY-----LIPFATFVGINHHRHPVLLGCALVANESKESFTWLFNTWIRAMFGCHPKTIIADQDMAIQQ 457 (771)
Q Consensus 383 dVv~~D~Ty~tn~y-----~~pl~~~~Gvn~~~~~~~~g~al~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~ai~~ 457 (771)
++|++|++|.+-+. +.++++++|||.+|+..++|+.+...|+.++|.-+|+.+++ -|-..|..||+|+.+||..
T Consensus 163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~-RGl~~~~lvv~Dg~~gl~~ 241 (381)
T PF00872_consen 163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKE-RGLKDILLVVSDGHKGLKE 241 (381)
T ss_pred cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhh-ccccccceeeccccccccc
Confidence 57999999998763 46789999999999999999999999999999999988643 3555699999999999999
Q ss_pred HHHHhCCCcccccchhhHHHHHHHhhccC-ChhhHHHHHhhhcccccHHHHHHHHHHHHHHhCCCccHHHHHHHHHhhcc
Q 004138 458 AIARIFPRTHHRFSMWQIRAKERENLRSM-SNQFVFEYNKCIYQSQSIAQFSTMWTALIEKYGQRDNIWLKEMYEKRESW 536 (771)
Q Consensus 458 Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~-~~~~~~~~~~~i~~~~t~~eFe~~w~~l~~~~~l~~~~~L~~ly~~r~~W 536 (771)
||+++||++.++.|.+|+++|+.+++... .+.+..+|+. |+.+.+.+++...++++.+++..........| ++.|
T Consensus 242 ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~-I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l---~~~~ 317 (381)
T PF00872_consen 242 AIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKA-IYQAPDKEEAREALEEFAEKWEKKYPKAAKSL---EENW 317 (381)
T ss_pred cccccccchhhhhheechhhhhccccccccchhhhhhccc-cccccccchhhhhhhhcccccccccchhhhhh---hhcc
Confidence 99999999999999999999999999876 7788888876 78889999999999999988776544333332 2333
Q ss_pred h--hcc--cccccccCCccc---cchhHHhhcccCC
Q 004138 537 V--PLY--LRRSFFAGIPIG---KSIESFFGATLTA 565 (771)
Q Consensus 537 a--~~y--~~~~f~~~~~st---Es~n~~lk~~~~~ 565 (771)
- .+| ++...+..+.|| ||+|+.+|+....
T Consensus 318 ~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~ 353 (381)
T PF00872_consen 318 DELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTKV 353 (381)
T ss_pred ccccceeeecchhccccchhhhccccccchhhhccc
Confidence 2 222 333444455455 9999999986553
No 7
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.02 E-value=2e-09 Score=117.03 Aligned_cols=195 Identities=13% Similarity=0.117 Sum_probs=137.2
Q ss_pred cEEEEcccccccC--CCCcccEEEEEccCCcceeeeeeecccccchhHhHHHHHHHHHhcCCCCeEEecchhHHHHHHHH
Q 004138 383 DAIIFDTSYRKTN--YLIPFATFVGINHHRHPVLLGCALVANESKESFTWLFNTWIRAMFGCHPKTIIADQDMAIQQAIA 460 (771)
Q Consensus 383 dVv~~D~Ty~tn~--y~~pl~~~~Gvn~~~~~~~~g~al~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~ai~~Ai~ 460 (771)
.+|++|++|.+-+ -+..+++++||+.+|+..++|+.+-..|+ ..|.-+|.. ++.-+-.....+++|..+++.+||.
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-KFWLSFLLD-LKNRGLSDVLLVVVDGLKGLPEAIS 223 (379)
T ss_pred eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHH-HHhccccceeEEecchhhhhHHHHH
Confidence 5789999999988 45789999999999999999999999999 777744443 3444445577888899999999999
Q ss_pred HhCCCcccccchhhHHHHHHHhhccC-ChhhHHHHHhhhcccccHHHHHHHHHHHHHHhCCCccHHHHHHHHHhh-cch-
Q 004138 461 RIFPRTHHRFSMWQIRAKERENLRSM-SNQFVFEYNKCIYQSQSIAQFSTMWTALIEKYGQRDNIWLKEMYEKRE-SWV- 537 (771)
Q Consensus 461 ~vfP~a~h~~C~~Hi~~n~~~~l~~~-~~~~~~~~~~~i~~~~t~~eFe~~w~~l~~~~~l~~~~~L~~ly~~r~-~Wa- 537 (771)
.+||.+.+++|..|+.+|+..++... .+....+++. |+.+.+.++-...|..+.+.+......-++.+....+ .|.
T Consensus 224 ~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~-I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F 302 (379)
T COG3328 224 AVFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRS-IYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLPF 302 (379)
T ss_pred HhccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhh-hhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhccc
Confidence 99999999999999999999999866 4555555644 7888899999999999887655433222222211111 111
Q ss_pred hcccccccccCCccc--cchhHHhhcccCC--CCCHHHHHHHHHHHH
Q 004138 538 PLYLRRSFFAGIPIG--KSIESFFGATLTA--QTPLREFISRYTQGL 580 (771)
Q Consensus 538 ~~y~~~~f~~~~~st--Es~n~~lk~~~~~--~~~l~~f~~~~~~~l 580 (771)
-+|-+.....-.++| |++|+.++..... ..+-..++..+...+
T Consensus 303 ~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~~y~~ 349 (379)
T COG3328 303 FAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNEESVEKLVYLV 349 (379)
T ss_pred ccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCHHHHHHHHHHH
Confidence 111111111223344 9999988765543 455555655544433
No 8
>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=98.81 E-value=1.5e-08 Score=88.95 Aligned_cols=76 Identities=20% Similarity=0.320 Sum_probs=65.7
Q ss_pred ccCHHHHHHHHHHHHHhcCcEEEEeeeeeccCCCceEEEEEeecCCCccc------------------------------
Q 004138 202 FNSANEAYQFYQAYAEKTGFRVRIGQLFRSKNDGSVTSRRFVCSKEGFQH------------------------------ 251 (771)
Q Consensus 202 F~S~eea~~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~~~C~r~G~~~------------------------------ 251 (771)
|.+.+|.+.|++..+...||+|.+.+|...+ ..|.|--.|.++
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~k-------i~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~ 73 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKK-------IVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKK 73 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCce-------EEEEEecCCCcccccccccccccccccccccccccccccccC
Confidence 8899999999999999999999999997643 478886555322
Q ss_pred ----CcccCccceeeeeecC-cceEEEEEEeccccccc
Q 004138 252 ----PSRVGCGAFMRIKRKE-FGSWIVDRLQKDHNHDL 284 (771)
Q Consensus 252 ----~~rtGC~a~i~v~~~~-~~kW~V~~~~~~HNH~l 284 (771)
+..++||++|++.... .++|.|..++..|||||
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 5669999999999877 89999999999999997
No 9
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.76 E-value=3.7e-09 Score=70.52 Aligned_cols=26 Identities=31% Similarity=0.793 Sum_probs=24.7
Q ss_pred eeecCCcccCCccchhHHHHHhhcCc
Q 004138 669 SCSCQMFEFEGMLCGHILKVFNLLNV 694 (771)
Q Consensus 669 ~CsC~~fe~~GipC~HiL~Vl~~~~v 694 (771)
+|+|++||..||||+|+|+|+...++
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 69999999999999999999998876
No 10
>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=98.60 E-value=1.4e-07 Score=77.51 Aligned_cols=65 Identities=25% Similarity=0.418 Sum_probs=56.0
Q ss_pred CCCCCCCcccCHHHHHHHHHHHHHhcCcEEEEeeeeeccCCCceEEEEEeecCCCcccCcccCccceeeeeecC-cceEE
Q 004138 194 PEPYAGLEFNSANEAYQFYQAYAEKTGFRVRIGQLFRSKNDGSVTSRRFVCSKEGFQHPSRVGCGAFMRIKRKE-FGSWI 272 (771)
Q Consensus 194 ~~p~~Gm~F~S~eea~~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~~~C~r~G~~~~~rtGC~a~i~v~~~~-~~kW~ 272 (771)
....+||+|+|.+|++.++..||...||.+++.++.+. +..++|.. .||||+|++.+.+ ++.|.
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~-------r~~~~C~~--------~~C~Wrv~as~~~~~~~~~ 66 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKK-------RYRAKCKD--------KGCPWRVRASKRKRSDTFQ 66 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCE-------EEEEEEcC--------CCCCEEEEEEEcCCCCEEE
Confidence 35679999999999999999999999999998887642 66899974 4699999999887 78887
Q ss_pred E
Q 004138 273 V 273 (771)
Q Consensus 273 V 273 (771)
|
T Consensus 67 I 67 (67)
T PF03108_consen 67 I 67 (67)
T ss_pred C
Confidence 5
No 11
>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=97.98 E-value=5.8e-06 Score=60.43 Aligned_cols=28 Identities=46% Similarity=0.865 Sum_probs=25.1
Q ss_pred ceeeeecCCcccCCccchhHHHHHhhcC
Q 004138 666 LNVSCSCQMFEFEGMLCGHILKVFNLLN 693 (771)
Q Consensus 666 ~~~~CsC~~fe~~GipC~HiL~Vl~~~~ 693 (771)
...+|+|..|+..|.||+||++|+...+
T Consensus 13 ~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 13 EQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred cccEeeCCCccccCCcchhHHHHHHhhC
Confidence 6789999999999999999999997653
No 12
>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=97.65 E-value=0.0003 Score=62.17 Aligned_cols=76 Identities=22% Similarity=0.400 Sum_probs=60.6
Q ss_pred eCCHHHHHHHHHHHhhccCeEEEEeeeeecCCCCcEEEEEEEecCcccc-------------------------------
Q 004138 51 FDTADDAREFYTQYAERVGFKIRIGQLYRSRTDGSVSSRRFVCSKEGFQ------------------------------- 99 (771)
Q Consensus 51 F~s~~~a~~fy~~ya~~~GF~vr~~~~~~~~~~~~~~~~~~~C~~~g~~------------------------------- 99 (771)
|++-+|...|....+...||+|.+-+|..+ ...|.|--.|..
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 889999999999999999999999876442 456778322211
Q ss_pred ---cCCccCcccEEEEEEe-cCCcEEEEEEecCCCcCC
Q 004138 100 ---LNSRTGCSAYIRVQKR-DSGKWVLDQMKKDHNHEF 133 (771)
Q Consensus 100 ---~~~r~~C~a~~~v~~~-~~~~w~v~~~~~~HnH~l 133 (771)
.+..++||.+|+-... .+++|.|.-+..+|||||
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 0246899999999854 678999999999999997
No 13
>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=97.07 E-value=0.0023 Score=52.51 Aligned_cols=63 Identities=25% Similarity=0.509 Sum_probs=52.0
Q ss_pred CcCCCeeCCHHHHHHHHHHHhhccCeEEEEeeeeecCCCCcEEEEEEEecCcccccCCccCcccEEEEEEec-CCcEEE
Q 004138 45 PSVGLEFDTADDAREFYTQYAERVGFKIRIGQLYRSRTDGSVSSRRFVCSKEGFQLNSRTGCSAYIRVQKRD-SGKWVL 122 (771)
Q Consensus 45 p~~gm~F~s~~~a~~fy~~ya~~~GF~vr~~~~~~~~~~~~~~~~~~~C~~~g~~~~~r~~C~a~~~v~~~~-~~~w~v 122 (771)
=.+||+|.|.+|.......||-..||.++...+.+ .+.+.+|. ..||+-+|...+.+ ++.|.|
T Consensus 4 l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~-------~r~~~~C~--------~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 4 LEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDK-------KRYRAKCK--------DKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred cccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCC-------EEEEEEEc--------CCCCCEEEEEEEcCCCCEEEC
Confidence 36899999999999999999999999999865432 37788995 34599999999765 477875
No 14
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=93.45 E-value=0.021 Score=54.17 Aligned_cols=81 Identities=19% Similarity=0.222 Sum_probs=68.2
Q ss_pred CcEEEEcccccccCCCCcccEEEEEccCCcceeeeeeecccccchhHhHHHHHHHHHhcCCCCeEEecchhHHHHHHHHH
Q 004138 382 GDAIIFDTSYRKTNYLIPFATFVGINHHRHPVLLGCALVANESKESFTWLFNTWIRAMFGCHPKTIIADQDMAIQQAIAR 461 (771)
Q Consensus 382 ~dVv~~D~Ty~tn~y~~pl~~~~Gvn~~~~~~~~g~al~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~ai~~Ai~~ 461 (771)
||.+.+|=||.+-+ +-..++...||.+|+ ++++-|-..-+..+=..||+..++..+ ..|..|+||+.++...|+++
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 GDSWHVDETYIKIK-GKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEEC-CEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 68899999998755 335667899999999 888888888888888888877766655 67999999999999999999
Q ss_pred hCCCc
Q 004138 462 IFPRT 466 (771)
Q Consensus 462 vfP~a 466 (771)
.+|..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99974
No 15
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=92.99 E-value=0.11 Score=54.29 Aligned_cols=82 Identities=15% Similarity=0.186 Sum_probs=61.0
Q ss_pred cEEEEEcc--CCcceeeeeeecccccchhHhHHHHHH-HHHhcCCCCeEEecchhHHHHHHHHHhCCCcccccchhhHHH
Q 004138 401 ATFVGINH--HRHPVLLGCALVANESKESFTWLFNTW-IRAMFGCHPKTIIADQDMAIQQAIARIFPRTHHRFSMWQIRA 477 (771)
Q Consensus 401 ~~~~Gvn~--~~~~~~~g~al~~~E~~es~~W~~~~f-~~~~~~~~p~~iitD~~~ai~~Ai~~vfP~a~h~~C~~Hi~~ 477 (771)
+..+-+|. +...++ +++.+-+.+++.-+|..+ -.. ....+++|.+|-..+...||++.||+|.+..-.|||++
T Consensus 15 y~t~~~d~~~~~~~il---~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk 90 (249)
T PF01610_consen 15 YVTVVVDLDTDTGRIL---DILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVK 90 (249)
T ss_pred eeEEEEECccCCceEE---EEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccccccccccccccchhhh
Confidence 34444555 443332 367777887776555543 222 34568999999999999999999999999999999999
Q ss_pred HHHHhhccC
Q 004138 478 KERENLRSM 486 (771)
Q Consensus 478 n~~~~l~~~ 486 (771)
++.+.+...
T Consensus 91 ~~~~al~~v 99 (249)
T PF01610_consen 91 LANRALDKV 99 (249)
T ss_pred hhhhcchhh
Confidence 999877654
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=92.86 E-value=0.42 Score=38.14 Aligned_cols=56 Identities=20% Similarity=0.354 Sum_probs=37.2
Q ss_pred cCcEEEEeeeeeccCCCceEEEEEeecCCCcccCcccCccceeeeeecC-cceEEEEEEecccccc
Q 004138 219 TGFRVRIGQLFRSKNDGSVTSRRFVCSKEGFQHPSRVGCGAFMRIKRKE-FGSWIVDRLQKDHNHD 283 (771)
Q Consensus 219 ~GF~vr~~~s~r~k~~g~~~~~~~~C~r~G~~~~~rtGC~a~i~v~~~~-~~kW~V~~~~~~HNH~ 283 (771)
=||..|+=-.+.. .....-+..|.|+.. ||||+=.|.+.. ++.-.++....+|||+
T Consensus 3 Dgy~WRKYGqK~i-~g~~~pRsYYrCt~~--------~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 3 DGYRWRKYGQKNI-KGSPYPRSYYRCTHP--------GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SSS-EEEEEEEEE-TTTTCEEEEEEEECT--------TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCchhhccCccc-CCCceeeEeeecccc--------ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 3677765433322 222345668999764 799999998877 7888899999999997
No 17
>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=91.79 E-value=0.86 Score=36.39 Aligned_cols=56 Identities=21% Similarity=0.367 Sum_probs=37.9
Q ss_pred cCeEEEEeeeeecCCCCcEEEEEEEecCcccccCCccCcccEEEEEEec-CCcEEEEEEecCCCcC
Q 004138 68 VGFKIRIGQLYRSRTDGSVSSRRFVCSKEGFQLNSRTGCSAYIRVQKRD-SGKWVLDQMKKDHNHE 132 (771)
Q Consensus 68 ~GF~vr~~~~~~~~~~~~~~~~~~~C~~~g~~~~~r~~C~a~~~v~~~~-~~~w~v~~~~~~HnH~ 132 (771)
-||..|+--.+. -++..--+..+-|+-. ||+|.-.|.+.. |+.-+++....+||||
T Consensus 3 Dgy~WRKYGqK~-i~g~~~pRsYYrCt~~--------~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 3 DGYRWRKYGQKN-IKGSPYPRSYYRCTHP--------GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SSS-EEEEEEEE-ETTTTCEEEEEEEECT--------TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCchhhccCcc-cCCCceeeEeeecccc--------ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 488888865544 2333344567888542 999999999865 7888888899999997
No 18
>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=87.70 E-value=1.8 Score=39.08 Aligned_cols=76 Identities=14% Similarity=0.081 Sum_probs=54.4
Q ss_pred CcEEEEcccccc-cCCCCcccEEEEEccCCcceeeeeeecccccchhHhHHHHHHHHHhcCCCCeEEecchhHHHHHH
Q 004138 382 GDAIIFDTSYRK-TNYLIPFATFVGINHHRHPVLLGCALVANESKESFTWLFNTWIRAMFGCHPKTIIADQDMAIQQA 458 (771)
Q Consensus 382 ~dVv~~D~Ty~t-n~y~~pl~~~~Gvn~~~~~~~~g~al~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~ai~~A 458 (771)
+.++.+|.+... ...+.....++.+|.+-..+ +++.+-..++.+.+.-+|.......++..|.+|+||+..+....
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~~ 82 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFI-YAFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTSH 82 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTEE-EEEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHSH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCcE-EEEEeecccccccccccccccccccccccceecccccccccccc
Confidence 467888888554 33455788888888876655 46666666688888888887777777666999999999987643
No 19
>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=85.62 E-value=0.94 Score=35.83 Aligned_cols=49 Identities=31% Similarity=0.496 Sum_probs=23.1
Q ss_pred cCcEEEEeeeeeccCCCceEEEEEeecCCCcccCcccCccceeeeeecCcceEEEEEEeccccc
Q 004138 219 TGFRVRIGQLFRSKNDGSVTSRRFVCSKEGFQHPSRVGCGAFMRIKRKEFGSWIVDRLQKDHNH 282 (771)
Q Consensus 219 ~GF~vr~~~s~r~k~~g~~~~~~~~C~r~G~~~~~rtGC~a~i~v~~~~~~kW~V~~~~~~HNH 282 (771)
.||.....+.. +| ...+.|++.. ..+|+|++.+. ..++ .|.....+|||
T Consensus 14 ~Gy~y~~~~~~----~~---~~~WrC~~~~-----~~~C~a~~~~~-~~~~--~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRN----DG---KTYWRCSRRR-----SHGCRARLITD-AGDG--RVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-----SS----EEEEEGGGT-----TS----EEEEE---TT--EEEE-S---SS
T ss_pred CCeEEECcCCC----CC---cEEEEeCCCC-----CCCCeEEEEEE-CCCC--EEEECCCccCC
Confidence 36666554443 22 3478998764 25899999997 1122 45555688999
No 20
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=85.24 E-value=20 Score=41.23 Aligned_cols=142 Identities=11% Similarity=0.149 Sum_probs=84.0
Q ss_pred cccchhHhHHHHHHHHHhcCCC--CeEEecchhHHHHHHHHHhCCCcccccchhhHHHHHHHhhccCChhhHHHHHhhhc
Q 004138 422 NESKESFTWLFNTWIRAMFGCH--PKTIIADQDMAIQQAIARIFPRTHHRFSMWQIRAKERENLRSMSNQFVFEYNKCIY 499 (771)
Q Consensus 422 ~E~~es~~W~~~~f~~~~~~~~--p~~iitD~~~ai~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~~~~~~~~~~~~i~ 499 (771)
....+-|.-+.+.+-....... -..+.+|+...++.++. .||++.|.+..||+.+.+.+.++. .++....+.+++.
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~-~~~~~~~~~~al~ 312 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSH-DPELKEKIRKALK 312 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhh-ChHHHHHHHHHHH
Confidence 3344556655554444433222 24556899999988776 999999999999999999999976 4556666667665
Q ss_pred ccccHHHHHHHHHHHHHHhCCCc-cHHHHHHH-HHhhcch--hcccccccccCCccccchhHHhhcccCCC
Q 004138 500 QSQSIAQFSTMWTALIEKYGQRD-NIWLKEMY-EKRESWV--PLYLRRSFFAGIPIGKSIESFFGATLTAQ 566 (771)
Q Consensus 500 ~~~t~~eFe~~w~~l~~~~~l~~-~~~L~~ly-~~r~~Wa--~~y~~~~f~~~~~stEs~n~~lk~~~~~~ 566 (771)
. ....+++...+.+...-.... .+-+..+. ..+..|- .+|-...-..|+.+-|+.++.+...++..
T Consensus 313 ~-~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i~~y~~~~~~~g~g~ee~~~~~~s~RmK~r 382 (470)
T PF06782_consen 313 K-GDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGIKPYREREGLRGIGAEESVSHVLSYRMKSR 382 (470)
T ss_pred h-cCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHhhhhhhccCCCccchhhhhhhHHHHHhcCC
Confidence 3 456666666665554322211 12222221 1334443 23322111133333389998887666543
No 21
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=80.03 E-value=3.6 Score=32.35 Aligned_cols=35 Identities=26% Similarity=0.507 Sum_probs=16.3
Q ss_pred EEEEecCcccccCCccCcccEEEEEEecCCcEEEEEEecCCCc
Q 004138 89 RRFVCSKEGFQLNSRTGCSAYIRVQKRDSGKWVLDQMKKDHNH 131 (771)
Q Consensus 89 ~~~~C~~~g~~~~~r~~C~a~~~v~~~~~~~w~v~~~~~~HnH 131 (771)
..+.|++-. ..+|+|.+.+. . +.-.|.....+|||
T Consensus 28 ~~WrC~~~~-----~~~C~a~~~~~-~--~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 28 TYWRCSRRR-----SHGCRARLITD-A--GDGRVVRTNGEHNH 62 (62)
T ss_dssp EEEEEGGGT-----TS----EEEEE-----TTEEEE-S---SS
T ss_pred EEEEeCCCC-----CCCCeEEEEEE-C--CCCEEEECCCccCC
Confidence 456786643 37999999997 2 33345555589999
No 22
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=79.78 E-value=3.2 Score=32.95 Aligned_cols=39 Identities=21% Similarity=0.393 Sum_probs=30.9
Q ss_pred eEEEEEeecCCCcccCcccCccceeeeeecC-cceEEEEEEeccccc
Q 004138 237 VTSRRFVCSKEGFQHPSRVGCGAFMRIKRKE-FGSWIVDRLQKDHNH 282 (771)
Q Consensus 237 ~~~~~~~C~r~G~~~~~rtGC~a~i~v~~~~-~~kW~V~~~~~~HNH 282 (771)
.-+..|.|+.. .||||+=.|.+.. ++.-.++....+|||
T Consensus 20 ~pRsYYrCt~~-------~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 20 FPRSYYRCTYS-------QGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CcceEEecccc-------CCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 34567889762 4799998888776 788888889999998
No 23
>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=69.13 E-value=9.7 Score=30.29 Aligned_cols=56 Identities=21% Similarity=0.313 Sum_probs=37.5
Q ss_pred cCeEEEEeeeeecCCCCcEEEEEEEecCcccccCCccCcccEEEEEEec-CCcEEEEEEecCCCc
Q 004138 68 VGFKIRIGQLYRSRTDGSVSSRRFVCSKEGFQLNSRTGCSAYIRVQKRD-SGKWVLDQMKKDHNH 131 (771)
Q Consensus 68 ~GF~vr~~~~~~~~~~~~~~~~~~~C~~~g~~~~~r~~C~a~~~v~~~~-~~~w~v~~~~~~HnH 131 (771)
-||..|+=-.+.. ++..--+..+-|+- ..||+|+=.|.+.. |+.-.++-...+|||
T Consensus 3 DGy~WRKYGQK~i-kgs~~pRsYYrCt~-------~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 3 DGYQWRKYGQKVI-KGSPFPRSYYRCTY-------SQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CcccccccCcEec-CCCcCcceEEeccc-------cCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 3677776444432 22222344566743 47899999998764 678888888999998
No 24
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=68.56 E-value=36 Score=32.71 Aligned_cols=106 Identities=11% Similarity=0.031 Sum_probs=70.5
Q ss_pred hhhcCcEEEEcccccccCCCCcccEEEEEccCCcceeeeeee-cccccchhHhHHHHHHHHHhcCCCCeEEecchhHHHH
Q 004138 378 CSQFGDAIIFDTSYRKTNYLIPFATFVGINHHRHPVLLGCAL-VANESKESFTWLFNTWIRAMFGCHPKTIIADQDMAIQ 456 (771)
Q Consensus 378 y~~f~dVv~~D~Ty~tn~y~~pl~~~~Gvn~~~~~~~~g~al-~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~ai~ 456 (771)
+...|=-|..|+= ++..+.+|+.|+.....|-.++-..-. -...+.+.+.-+|+...+.+|......||||....++
T Consensus 29 w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~~~~ 106 (153)
T PF04937_consen 29 WKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNASNMK 106 (153)
T ss_pred HHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCchhHH
Confidence 3444444555554 445566777776665555544332211 1224556666677777777777778889999999998
Q ss_pred HHH---HHhCCCcccccchhhHHHHHHHhhcc
Q 004138 457 QAI---ARIFPRTHHRFSMWQIRAKERENLRS 485 (771)
Q Consensus 457 ~Ai---~~vfP~a~h~~C~~Hi~~n~~~~l~~ 485 (771)
+|- .+-+|.....-|.-|-+.-+.+.+..
T Consensus 107 ~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 107 KAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred HHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 884 45678888889999998888887765
No 25
>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=68.13 E-value=8.6 Score=42.81 Aligned_cols=55 Identities=15% Similarity=0.263 Sum_probs=47.5
Q ss_pred CCcccCHHHHHHHHHHHHHhcCcEEEEeeeeeccCCCceEEEEEeecCCCcccCcccCccceeeeeecC
Q 004138 199 GLEFNSANEAYQFYQAYAEKTGFRVRIGQLFRSKNDGSVTSRRFVCSKEGFQHPSRVGCGAFMRIKRKE 267 (771)
Q Consensus 199 Gm~F~S~eea~~fy~~YA~~~GF~vr~~~s~r~k~~g~~~~~~~~C~r~G~~~~~rtGC~a~i~v~~~~ 267 (771)
+..|+++++=|..+|.|-....--|....|-|.|. .+|.|... +||++|-+...+
T Consensus 25 ~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkh------ftfachlk--------~c~fkillsy~g 79 (496)
T PF04684_consen 25 ARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKH------FTFACHLK--------NCPFKILLSYCG 79 (496)
T ss_pred ccCCCcHHHHHHHHhhhhhhhcCceeecccccccc------eEEEeecc--------CCCceeeeeecc
Confidence 56799999999999999999999999988887653 68999875 599999998654
No 26
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.44 E-value=22 Score=36.04 Aligned_cols=82 Identities=16% Similarity=0.216 Sum_probs=51.9
Q ss_pred cEEEEcccccccCCCCcccEEEEEccCCcceeeeeeecccccchhHhHHHHHHHHHhcCCCCeEEecchhHHHHHHHHHh
Q 004138 383 DAIIFDTSYRKTNYLIPFATFVGINHHRHPVLLGCALVANESKESFTWLFNTWIRAMFGCHPKTIIADQDMAIQQAIARI 462 (771)
Q Consensus 383 dVv~~D~Ty~tn~y~~pl~~~~Gvn~~~~~~~~g~al~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~ai~~Ai~~v 462 (771)
|++.+|=||.+-+-+. .+.-..||..|+ ++.+-|...-+...=.-||..+++.- ..|.+|+||+.+....|+.++
T Consensus 71 ~~w~vDEt~ikv~gkw-~ylyrAid~~g~--~Ld~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~~l 145 (215)
T COG3316 71 DSWRVDETYIKVNGKW-HYLYRAIDADGL--TLDVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALRKL 145 (215)
T ss_pred cceeeeeeEEeeccEe-eehhhhhccCCC--eEEEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHHhc
Confidence 4555666665544322 122234455543 44444555544555555666666665 679999999999999999999
Q ss_pred CCCcccc
Q 004138 463 FPRTHHR 469 (771)
Q Consensus 463 fP~a~h~ 469 (771)
-+.+.|+
T Consensus 146 ~~~~ehr 152 (215)
T COG3316 146 GSEVEHR 152 (215)
T ss_pred Ccchhee
Confidence 9977665
No 27
>smart00461 WH1 WASP homology region 1. Region of the Wiskott-Aldrich syndrome protein (WASp) that contains point mutations in the majority of patients with WAS. Unknown function. Ena-like WH1 domains bind polyproline-containing peptides, and that Homer contains a WH1 domain.
Probab=37.48 E-value=18 Score=32.39 Aligned_cols=20 Identities=25% Similarity=0.532 Sum_probs=17.7
Q ss_pred CcCCCeeCCHHHHHHHHHHH
Q 004138 45 PSVGLEFDTADDAREFYTQY 64 (771)
Q Consensus 45 p~~gm~F~s~~~a~~fy~~y 64 (771)
=.+|+.|.|++||.+|++.-
T Consensus 83 ~~~GLnF~se~EA~~F~~~v 102 (106)
T smart00461 83 CVYGLNFASEEEAKKFRKKV 102 (106)
T ss_pred eEEEeecCCHHHHHHHHHHH
Confidence 36899999999999999864
No 28
>cd01205 WASP WASP-type EVH1 domain. WASP-type EVH1 domain. Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disease, characterized by eczema, immunodeficiency, and thrombocytopenia. The majority of patients with WAS, or a milder version of the disorder, X-linked thrombocytopenia (XLT), have point mutations in the EVH1 domain of WASP (Wiskott-Aldrich syndrome protein). WASP is an actin regulatory protein consisting of an N-terminal EVH1 domain, a basic region, a GTP binding domain, a proline rich region and a WH2 acidic region. Yeast members lack the GTP binding domain. WASP binds a 25 residue proline rich motif from the WASP Interacting Protein (WIP) via its N-terminal EVH1 domain.
Probab=37.40 E-value=19 Score=32.19 Aligned_cols=21 Identities=33% Similarity=0.540 Sum_probs=18.2
Q ss_pred CCcCCCeeCCHHHHHHHHHHH
Q 004138 44 EPSVGLEFDTADDAREFYTQY 64 (771)
Q Consensus 44 ~p~~gm~F~s~~~a~~fy~~y 64 (771)
.=.+|..|.|++||..||+.=
T Consensus 81 ~c~~GL~Fade~EA~~F~k~v 101 (105)
T cd01205 81 DCVVGLNFADETEAAEFRKKV 101 (105)
T ss_pred CcEEEEEECCHHHHHHHHHHH
Confidence 356899999999999999864
No 29
>cd00837 EVH1 EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. The EVH1 domain binds to other proteins at proline rich sequences in either FPPPP or PPXXF motifs. It is found in the cytoskeletal reorganization proteins Enabled VASP, and WASP, and in the synaptic scaffolding protein Homer. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=34.77 E-value=22 Score=31.73 Aligned_cols=19 Identities=26% Similarity=0.565 Sum_probs=17.3
Q ss_pred cCCCeeCCHHHHHHHHHHH
Q 004138 46 SVGLEFDTADDAREFYTQY 64 (771)
Q Consensus 46 ~~gm~F~s~~~a~~fy~~y 64 (771)
.+|..|.|++||.+|++.-
T Consensus 82 ~~GL~F~se~eA~~F~~~v 100 (104)
T cd00837 82 VYGLNFASEEEAAQFRKKV 100 (104)
T ss_pred EEEEeeCCHHHHHHHHHHH
Confidence 7899999999999999863
No 30
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=33.77 E-value=32 Score=30.37 Aligned_cols=31 Identities=23% Similarity=0.403 Sum_probs=21.3
Q ss_pred CCCcceEEEeccceeeeecCCccc-----CCccchhHHHH
Q 004138 654 NEDEKHVVTFSALNVSCSCQMFEF-----EGMLCGHILKV 688 (771)
Q Consensus 654 ~~~~~~~V~~~~~~~~CsC~~fe~-----~GipC~HiL~V 688 (771)
..+++|++.- ..|||..|-. ---||.|++.+
T Consensus 40 G~~rdYIl~~----gfCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 40 GKERDYILEG----GFCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred ccccceEEEc----CcccCHHHHhHhhhcCcccchhhhhe
Confidence 3456677743 3799999862 23469999864
No 31
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=32.54 E-value=1.3e+02 Score=31.74 Aligned_cols=71 Identities=8% Similarity=-0.071 Sum_probs=47.7
Q ss_pred CcEEEEcccccccCCCCcccEEEEEccCCcceeeeeeeccc-ccchhHhHHHHHHHHHh-c---CCCCeEEecchhH
Q 004138 382 GDAIIFDTSYRKTNYLIPFATFVGINHHRHPVLLGCALVAN-ESKESFTWLFNTWIRAM-F---GCHPKTIIADQDM 453 (771)
Q Consensus 382 ~dVv~~D~Ty~tn~y~~pl~~~~Gvn~~~~~~~~g~al~~~-E~~es~~W~~~~f~~~~-~---~~~p~~iitD~~~ 453 (771)
..|.+.|-||.....+..+++.+-+|.+.+ .++|+++-.. .+.+...-+|+..+... + ...|..|.||+-.
T Consensus 87 n~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gs 162 (262)
T PRK14702 87 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGS 162 (262)
T ss_pred CCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCc
Confidence 478889999977655556888888888776 6778888763 45555444555433333 2 2347888999875
No 32
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=32.13 E-value=23 Score=36.47 Aligned_cols=22 Identities=41% Similarity=0.859 Sum_probs=18.4
Q ss_pred eeecCCcccCCccchhHHHHHhhcC
Q 004138 669 SCSCQMFEFEGMLCGHILKVFNLLN 693 (771)
Q Consensus 669 ~CsC~~fe~~GipC~HiL~Vl~~~~ 693 (771)
-|||.-+. .||.||-+|.-++.
T Consensus 126 dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 126 DCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred ccCCCCcc---cchHHHHHHHHHHH
Confidence 49999875 89999999976654
No 33
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=29.78 E-value=25 Score=30.69 Aligned_cols=27 Identities=33% Similarity=0.421 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCCcccCHHHHHHHHHHH
Q 004138 189 EGECIPEPYAGLEFNSANEAYQFYQAY 215 (771)
Q Consensus 189 ~~~~~~~p~~Gm~F~S~eea~~fy~~Y 215 (771)
||.-+..+-+=++|+|++.|++||++=
T Consensus 47 EG~w~ptr~vviEFps~~~ar~~y~Sp 73 (96)
T COG5470 47 EGEWRPTRNVVIEFPSLEAARDCYNSP 73 (96)
T ss_pred cCCCCcccEEEEEcCCHHHHHHHhcCH
Confidence 555555666779999999999999973
No 34
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=28.99 E-value=1.6e+02 Score=31.70 Aligned_cols=71 Identities=8% Similarity=-0.062 Sum_probs=48.3
Q ss_pred CcEEEEcccccccCCCCcccEEEEEccCCcceeeeeeeccc-ccchhHhHHHHHHHHHh-cC---CCCeEEecchhH
Q 004138 382 GDAIIFDTSYRKTNYLIPFATFVGINHHRHPVLLGCALVAN-ESKESFTWLFNTWIRAM-FG---CHPKTIIADQDM 453 (771)
Q Consensus 382 ~dVv~~D~Ty~tn~y~~pl~~~~Gvn~~~~~~~~g~al~~~-E~~es~~W~~~~f~~~~-~~---~~p~~iitD~~~ 453 (771)
..|.+.|-||.....+.-+++.+-+|.+.+ .++|+++-.. .+.+...-+|+..+... ++ ..|..|.||+-.
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 478999999976655556778888888776 6788888765 56555555555433332 22 236788899874
No 35
>PF00568 WH1: WH1 domain; InterPro: IPR000697 The EVH1 (WH1, RanBP1-WASP) domain is found in multi-domain proteins implicated in a diverse range of signalling, nuclear transport and cytoskeletal events. This domain of around 115 amino acids is present in species ranging from yeast to mammals. Many EVH1-containing proteins associate with actin-based structures and play a role in cytoskeletal organisation. EVH1 domains recognise and bind the proline-rich motif FPPPP with low-affinity, further interactions then form between flanking residues [][]. WASP family proteins contain a EVH1 (WH1) in their N-terminals which bind proline-rich sequences in the WASP interacting protein. Proteins of the RanBP1 family contain a WH1 domain in their N-terminal region, which seems to bind a different sequence motif present in the C-terminal part of RanGTP protein [,]. Tertiary structure of the WH1 domain of the Mena protein revealed structure similarities with the pleckstrin homology (PH) domain. The overall fold consists of a compact parallel beta-sandwich, closed along one edge by a long alpha-helix. A highly conserved cluster of three surface-exposed aromatic side-chains forms the recognition site for the molecules target ligands. [].; GO: 0005515 protein binding; PDB: 1I2H_A 1DDV_A 1DDW_A 1EGX_A 3SYX_A 1TJ6_B 1XOD_B 1EVH_A 1I7A_B 2JP2_A ....
Probab=28.98 E-value=31 Score=31.17 Aligned_cols=19 Identities=32% Similarity=0.739 Sum_probs=17.5
Q ss_pred cCCCeeCCHHHHHHHHHHH
Q 004138 46 SVGLEFDTADDAREFYTQY 64 (771)
Q Consensus 46 ~~gm~F~s~~~a~~fy~~y 64 (771)
.+|+.|.|++||..|++.-
T Consensus 89 ~~GLnF~se~eA~~F~~~v 107 (111)
T PF00568_consen 89 VYGLNFASEEEADQFYKKV 107 (111)
T ss_dssp EEEEEESSHHHHHHHHHHH
T ss_pred EEEEecCCHHHHHHHHHHH
Confidence 7899999999999999864
No 36
>PHA02517 putative transposase OrfB; Reviewed
Probab=26.54 E-value=1.5e+02 Score=31.24 Aligned_cols=71 Identities=10% Similarity=-0.086 Sum_probs=42.2
Q ss_pred CcEEEEcccccccCCCCcccEEEEEccCCcceeeeeeecccccchhHhHHHHHHHHHhcCCCCeEEecchhHH
Q 004138 382 GDAIIFDTSYRKTNYLIPFATFVGINHHRHPVLLGCALVANESKESFTWLFNTWIRAMFGCHPKTIIADQDMA 454 (771)
Q Consensus 382 ~dVv~~D~Ty~tn~y~~pl~~~~Gvn~~~~~~~~g~al~~~E~~es~~W~~~~f~~~~~~~~p~~iitD~~~a 454 (771)
++++..|.||.....+ ..++++-+|.+.+ .++|+.+...++.+...-.|+..+...+...+..|.||+...
T Consensus 110 n~~w~~D~t~~~~~~g-~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~i~~sD~G~~ 180 (277)
T PHA02517 110 NQLWVADFTYVSTWQG-WVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQALWARGRPGGLIHHSDKGSQ 180 (277)
T ss_pred CCeEEeceeEEEeCCC-CEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHHHhcCCCcCcEeecccccc
Confidence 4789999999765543 4466666666654 456677766666664443333333333322234666998753
No 37
>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []. These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.
Probab=24.89 E-value=51 Score=29.84 Aligned_cols=21 Identities=29% Similarity=0.594 Sum_probs=18.0
Q ss_pred cCCCeeCCHHHHHHHHHHHhh
Q 004138 46 SVGLEFDTADDAREFYTQYAE 66 (771)
Q Consensus 46 ~~gm~F~s~~~a~~fy~~ya~ 66 (771)
.|=|.|++.+.|.+||..|-.
T Consensus 56 mVLikF~~~~~Ad~Fy~~fNG 76 (110)
T PF07576_consen 56 MVLIKFRDQESADEFYEEFNG 76 (110)
T ss_pred EEEEEECCHHHHHHHHHHhCC
Confidence 355699999999999999964
No 38
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=22.06 E-value=49 Score=28.91 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=20.0
Q ss_pred CCcCCCeeCCHHHHHHHHHHHhhcc
Q 004138 44 EPSVGLEFDTADDAREFYTQYAERV 68 (771)
Q Consensus 44 ~p~~gm~F~s~~~a~~fy~~ya~~~ 68 (771)
.+.|=++|+|++.|++|||+=+...
T Consensus 53 tr~vviEFps~~~ar~~y~SpeYq~ 77 (96)
T COG5470 53 TRNVVIEFPSLEAARDCYNSPEYQA 77 (96)
T ss_pred ccEEEEEcCCHHHHHHHhcCHHHHH
Confidence 5667789999999999999644433
No 39
>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=20.32 E-value=53 Score=34.55 Aligned_cols=40 Identities=10% Similarity=0.168 Sum_probs=30.2
Q ss_pred hcCCCCeEEecchhHHHHHHHHHhCCCcccccchhhHHHHHHHhhc
Q 004138 439 MFGCHPKTIIADQDMAIQQAIARIFPRTHHRFSMWQIRAKERENLR 484 (771)
Q Consensus 439 ~~~~~p~~iitD~~~ai~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~ 484 (771)
+++ -+.+++||+-.+-.. +..+.|+.|.-|+.+.+..-..
T Consensus 116 L~~-~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 116 LGD-FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred hcc-cceeeeccccccccc-----cccccccccccccccccccccc
Confidence 344 446999999987644 3388999999999998776554
Done!