Query 047253
Match_columns 679
No_of_seqs 295 out of 1348
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 09:13:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047253.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047253hhsearch_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-129 8E-134 1095.2 60.4 606 33-668 59-685 (846)
2 PF10551 MULE: MULE transposas 99.9 3.8E-22 8.3E-27 170.5 7.8 90 282-373 1-93 (93)
3 PF03101 FAR1: FAR1 DNA-bindin 99.8 9.1E-20 2E-24 154.9 8.8 91 62-156 1-91 (91)
4 PF00872 Transposase_mut: Tran 99.8 1.7E-19 3.6E-24 193.3 3.1 255 161-462 91-351 (381)
5 PF08731 AFT: Transcription fa 99.3 4.3E-11 9.3E-16 100.6 10.0 91 54-154 1-111 (111)
6 COG3328 Transposase and inacti 99.2 2.2E-10 4.8E-15 120.4 17.1 262 164-476 80-346 (379)
7 smart00575 ZnF_PMZ plant mutat 98.9 7.2E-10 1.6E-14 70.8 1.6 26 565-590 2-27 (28)
8 PF03108 DBD_Tnp_Mut: MuDR fam 98.6 2.4E-07 5.1E-12 73.4 7.9 66 46-143 2-67 (67)
9 PF04434 SWIM: SWIM zinc finge 98.2 9.3E-07 2E-11 62.1 3.1 30 560-589 11-40 (40)
10 PF01610 DDE_Tnp_ISL3: Transpo 96.8 0.00089 1.9E-08 68.0 3.7 80 294-377 15-97 (249)
11 PF06782 UPF0236: Uncharacteri 95.6 0.94 2E-05 50.4 19.3 249 163-464 112-381 (470)
12 PF03106 WRKY: WRKY DNA -bindi 94.5 0.15 3.2E-06 39.1 6.2 57 71-153 3-59 (60)
13 PF13610 DDE_Tnp_IS240: DDE do 92.3 0.037 7.9E-07 50.8 -0.3 81 275-359 1-81 (140)
14 PF00665 rve: Integrase core d 89.0 1.4 3E-05 38.5 6.9 75 275-350 6-81 (120)
15 smart00774 WRKY DNA binding do 85.4 1.5 3.3E-05 33.3 4.2 29 122-152 31-59 (59)
16 PRK08561 rps15p 30S ribosomal 81.5 2.9 6.2E-05 38.1 5.0 79 171-249 31-143 (151)
17 PF04500 FLYWCH: FLYWCH zinc f 80.8 3.4 7.3E-05 31.3 4.7 25 122-152 38-62 (62)
18 PF04937 DUF659: Protein of un 80.5 15 0.00032 34.1 9.6 108 268-377 26-137 (153)
19 PF13936 HTH_38: Helix-turn-he 76.4 2.8 6E-05 29.8 2.7 29 166-194 2-30 (44)
20 PF04684 BAF1_ABF1: BAF1 / ABF 76.1 5.7 0.00012 42.7 6.0 55 50-133 24-78 (496)
21 PF03050 DDE_Tnp_IS66: Transpo 68.1 13 0.00029 37.9 6.7 146 170-377 5-155 (271)
22 COG3316 Transposase and inacti 59.2 12 0.00027 36.4 4.1 81 276-362 71-152 (215)
23 COG5431 Uncharacterized metal- 55.9 25 0.00053 29.8 4.7 29 550-584 42-75 (117)
24 PF08069 Ribosomal_S13_N: Ribo 55.1 12 0.00026 28.5 2.6 30 171-200 31-60 (60)
25 KOG3517 Transcription factor P 53.7 23 0.0005 34.8 4.9 70 166-246 18-98 (334)
26 PHA02517 putative transposase 52.4 76 0.0017 32.4 9.1 73 275-349 110-182 (277)
27 PF11433 DUF3198: Protein of u 52.1 14 0.00031 26.2 2.3 44 390-433 6-49 (51)
28 PF00292 PAX: 'Paired box' dom 46.9 33 0.00073 30.5 4.5 70 166-246 15-95 (125)
29 COG3464 Transposase and inacti 45.3 42 0.00091 36.6 5.9 70 294-370 169-238 (402)
30 KOG0400 40S ribosomal protein 42.8 34 0.00074 30.2 3.8 38 163-200 22-60 (151)
31 COG4279 Uncharacterized conser 42.1 13 0.00027 36.9 1.2 24 563-589 124-147 (266)
32 PF02796 HTH_7: Helix-turn-hel 37.9 40 0.00086 23.9 3.0 27 168-194 5-31 (45)
33 PF04800 ETC_C1_NDUFA4: ETC co 31.7 31 0.00067 29.5 1.8 34 42-79 42-76 (101)
34 PF15299 ALS2CR8: Amyotrophic 30.7 44 0.00096 33.2 3.0 20 114-133 70-89 (225)
35 PRK14702 insertion element IS2 29.8 1.4E+02 0.003 30.5 6.5 72 275-347 87-163 (262)
36 COG5470 Uncharacterized conser 28.1 33 0.0007 28.8 1.3 43 35-77 41-83 (96)
37 PRK09409 IS2 transposase TnpB; 26.7 1.8E+02 0.004 30.2 6.9 72 275-347 126-202 (301)
38 PTZ00072 40S ribosomal protein 26.5 99 0.0021 28.1 4.1 31 170-200 27-57 (148)
39 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 22.9 1.1E+02 0.0024 22.5 3.0 28 168-195 4-31 (50)
40 PF09713 A_thal_3526: Plant pr 22.4 90 0.002 23.3 2.6 26 175-200 3-28 (54)
41 PF02171 Piwi: Piwi domain; I 22.2 2.2E+02 0.0047 29.4 6.6 97 277-373 79-199 (302)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=3.7e-129 Score=1095.22 Aligned_cols=606 Identities=26% Similarity=0.462 Sum_probs=535.3
Q ss_pred CCcccCCcCCCCCCCCCCCCccCCHHHHHHHHHHHHHhcCceEEEcceecccCCCcceEEEEEeeccCCCCCccCCC---
Q 047253 33 PDETRLSLESTNDVVPYIGQRFPTHDAAYEYYSEFAKSCGFSIRRHRTEGKDGVGKGLTRRYFVCHRAGNTPIKASN--- 109 (679)
Q Consensus 33 ~~~~~~~~~~~~~~~P~vGm~F~S~eea~~fy~~yA~~~GF~ir~~~s~~~~~~~k~~~~~~f~C~r~G~~~~k~~~--- 109 (679)
+++..+..+.+...+|.+||+|+|.|||++||+.||+..||+||+.++++++.. +++++++|+|+|+|+++.+.+.
T Consensus 59 ~~~~~~~~~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~-~~ii~r~fvCsreG~~~~~~~~~~~ 137 (846)
T PLN03097 59 PTGELVEFKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTS-REFIDAKFACSRYGTKREYDKSFNR 137 (846)
T ss_pred cccccccccCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCC-CcEEEEEEEEcCCCCCccccccccc
Confidence 344455667778899999999999999999999999999999999999887654 3789999999999987643210
Q ss_pred C---------CCCCCCCCccccCccceEEEEEeecCCCCcEEEEecCCCCCCCCCCCCccCCCccccCCChhhHHHHHHH
Q 047253 110 E---------NKPQRNRKSSRCGCQAYMRISKVTELGAPEWRVTGFANNHNHELLEPNQVRFLPAYRTISETDKSRILMF 180 (679)
Q Consensus 110 ~---------~~~~r~~~s~r~gCpa~i~v~~~~~~~~~~w~V~~~~~~HNH~l~~~~~~~~l~s~R~i~~~~k~~i~~l 180 (679)
. ...+++|+.+|+||||+|+|++. ..|+|+|+.|+.+|||||.++..+ +
T Consensus 138 ~~~~~~k~~~~~~~~rR~~tRtGC~A~m~Vk~~---~~gkW~V~~fv~eHNH~L~p~~~~---------~---------- 195 (846)
T PLN03097 138 PRARQTKQDPENGTGRRSCAKTDCKASMHVKRR---PDGKWVIHSFVKEHNHELLPAQAV---------S---------- 195 (846)
T ss_pred ccccccccCcccccccccccCCCCceEEEEEEc---CCCeEEEEEEecCCCCCCCCcccc---------c----------
Confidence 0 01123456789999999999886 368999999999999999876432 1
Q ss_pred hhcCCCHHHHHHHHHHhhcCCCCCCCcchhhhhhHHHhhhcc-CCcchHHHHHHHHHhhccCCCCcEEEEeeCCCCccce
Q 047253 181 AKTGISVQQMMRLMELEKCVEPGYLPFTEKDVRNLLQSIRKL-DPEDESVDLLRMCRNIKEKDPNFRYEYTLDSNNRLEN 259 (679)
Q Consensus 181 ~~~gi~~~~i~~~l~~~~g~~~~~~~~~~~dv~N~~~~~r~~-~~~~d~~~ll~~~~~~~~~np~~~~~~~~d~~~~~~~ 259 (679)
+.++.++..+....+ ...++..+..|..|...+.|+. ...+|++.|++||+++|.+||+|||++++|++|++++
T Consensus 196 ----~~~r~~~~~~~~~~~-~~~~v~~~~~d~~~~~~~~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~n 270 (846)
T PLN03097 196 ----EQTRKMYAAMARQFA-EYKNVVGLKNDSKSSFDKGRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKN 270 (846)
T ss_pred ----hhhhhhHHHHHhhhh-ccccccccchhhcchhhHHHhhhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeee
Confidence 123334444433333 2456667778888877766643 4579999999999999999999999999999999999
Q ss_pred eEecchhhHHHHHHcCcEEEEcccccCCCCCCcceEEEEEecCCcceeeeeccccccchhhHHHHHHHHHHHhcCCCCce
Q 047253 260 IAWSYASSIQAYEIFGDAVVFDTTHRLTALDMPLGIWVGVNNYGVPCFFGCTLLREENLRSFSWALKAFLAFMDGKAPQT 339 (679)
Q Consensus 260 ifw~~~~~~~~~~~f~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~E~~es~~w~l~~f~~~~~~~~p~~ 339 (679)
|||+|+.|+.+|.+|||||+||+||+||+|++||++|+|||||+|+++|||||+.+|+.+||.|||++|+++|+++.|++
T Consensus 271 iFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~t 350 (846)
T PLN03097 271 LFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKV 350 (846)
T ss_pred EEeccHHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccHHHHHHHHhhCCCCccccchhhhhhhhcccchhhhccchhHHHHHHhh-hccCCCHHHHHHHHHHhHhhcCCCc
Q 047253 340 ILTDQNMCLKEAIAMEMPVTKHALCIWMIVVKFPSWFNAVLGERYNEWKAEFYR-LYNLESIEDFEMGWRDMVNSFGLHT 418 (679)
Q Consensus 340 iitD~~~~~~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~-~~~~~t~~eF~~~w~~l~~~~~~~~ 418 (679)
||||+|.+|++||++|||+|.|++|.|||++|+.++++.... ..+.|..+|+. ++.+.+++||+..|..|+++|++++
T Consensus 351 IiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~-~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~ 429 (846)
T PLN03097 351 IITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIK-QHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKE 429 (846)
T ss_pred EEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhh-hhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccc
Confidence 999999999999999999999999999999999999987653 35789999987 5668999999999999999999999
Q ss_pred cHHHHHHHHhhcccccccccccccccccccCCcchhHHHHHhhcCccccHHHHHHHHHHHHHhHHHHHHHHHHHHhhccc
Q 047253 419 NRHIANLFALRMQWALPYLRSNFFAGMTTTGHSKAINAFIQRFLGAQTRLAHFVEQVAVAVDFKDQAAEQQTMQQNLQNI 498 (679)
Q Consensus 419 ~~~l~~~~~~re~W~~~y~~~~~~~g~~tt~~~Es~n~~lk~~~~~~~~l~~f~~~~~~~~~~~~~~e~~~~~~~~~~~~ 498 (679)
++||+.||+.|++||++|+++.|++||.||+|+||+|++||+|+++.++|..|+++|+.+++.++++|+++++.+..+.|
T Consensus 430 n~WL~~LY~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P 509 (846)
T PLN03097 430 DEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQP 509 (846)
T ss_pred cHHHHHHHHhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998888889
Q ss_pred ccccCChhHHHHHhhchHHHHHHHHHHHHHhcCceeeec-cCC----eEEEEeeeecCceEEEEccCCCeEEEeccCccc
Q 047253 499 CLKTGAPMESHAASVLTPFAFSKLQEQLVLAAHYASFPF-EDG----FLVRHHTKLEGGRKVYWAPQEGIISCSCHQFEF 573 (679)
Q Consensus 499 ~l~t~~~~e~qa~~~yT~~~f~~fq~el~~s~~~~v~~~-~~g----y~V~~~~~~~~~~~V~~~~~~~~~~CsC~~f~~ 573 (679)
.+++.+|||+||+++|||+||++||+|+..+..|.+... ++| |.|....+ ...|.|.+++....++|+|++|++
T Consensus 510 ~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~-~~~~~V~~d~~~~~v~CsC~kFE~ 588 (846)
T PLN03097 510 ALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEK-NQDFTVTWNQTKLEVSCICRLFEY 588 (846)
T ss_pred ccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecC-CCcEEEEEecCCCeEEeeccCeec
Confidence 999999999999999999999999999999999887654 333 88876544 567999999999999999999999
Q ss_pred cCccchhHHHHHhcCCcccCCCCCcccccccccCCcccccCCC--CCChhHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Q 047253 574 SGILCRHTLRVLSTGNCFQIPERYLPLRWRKISTHSVKLLQSS--PSDHAERIQFLQSMVSSLIAESVKSKERLDLATEQ 651 (679)
Q Consensus 574 ~GipC~Hil~Vl~~~~i~~iP~~yil~RWtk~a~~~~~~~~~~--~~~~~~r~~~l~~~~~~~~~~a~~s~e~~~~~~~~ 651 (679)
.||||+|||+||.++||.+||++||++||||+|+.....+... ..+...||+.|++.+.+++.+|+.|+|.|..|+++
T Consensus 589 ~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdAK~~~~~~~~~~~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~ 668 (846)
T PLN03097 589 KGYLCRHALVVLQMCQLSAIPSQYILKRWTKDAKSRHLLGEESEQVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRA 668 (846)
T ss_pred CccchhhHHHHHhhcCcccCchhhhhhhchhhhhhcccCccccccccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 9999999999999999999999999999999999876544332 33456799999999999999999999999999999
Q ss_pred HHHHHHhhccccccccC
Q 047253 652 VSYLLSRIRQQPVSTQG 668 (679)
Q Consensus 652 l~~~~~~~~~~~~~~~~ 668 (679)
|++++++++.|.-+...
T Consensus 669 L~e~~~~~~~~~n~~~~ 685 (846)
T PLN03097 669 LEEAFGNCISMNNSNKS 685 (846)
T ss_pred HHHHHHHHHHhhccCCC
Confidence 99999999876655433
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=99.86 E-value=3.8e-22 Score=170.48 Aligned_cols=90 Identities=27% Similarity=0.428 Sum_probs=86.8
Q ss_pred ccccCCCCCCcceE---EEEEecCCcceeeeeccccccchhhHHHHHHHHHHHhcCCCCceecccccHHHHHHHHhhCCC
Q 047253 282 TTHRLTALDMPLGI---WVGVNNYGVPCFFGCTLLREENLRSFSWALKAFLAFMDGKAPQTILTDQNMCLKEAIAMEMPV 358 (679)
Q Consensus 282 ~Ty~tn~y~~pl~~---~~gvd~~~~~~~~~~al~~~E~~es~~w~l~~f~~~~~~~~p~~iitD~~~~~~~Ai~~vfP~ 358 (679)
+||+||+| +|++. ++|+|++|+.+|+||+++.+|+.++|.|+|+.+++.++.. |.+||||++.++++||+++||+
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 9999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred Cccccchhhhhhhhc
Q 047253 359 TKHALCIWMIVVKFP 373 (679)
Q Consensus 359 a~h~lC~~Hi~~n~~ 373 (679)
+.|++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999985
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=99.80 E-value=9.1e-20 Score=154.94 Aligned_cols=91 Identities=35% Similarity=0.686 Sum_probs=78.6
Q ss_pred HHHHHHHHhcCceEEEcceecccCCCcceEEEEEeeccCCCCCccCCCCCCCCCCCCccccCccceEEEEEeecCCCCcE
Q 047253 62 EYYSEFAKSCGFSIRRHRTEGKDGVGKGLTRRYFVCHRAGNTPIKASNENKPQRNRKSSRCGCQAYMRISKVTELGAPEW 141 (679)
Q Consensus 62 ~fy~~yA~~~GF~ir~~~s~~~~~~~k~~~~~~f~C~r~G~~~~k~~~~~~~~r~~~s~r~gCpa~i~v~~~~~~~~~~w 141 (679)
+||+.||..+||+|++.++++.+.. ..+++++|+|+++|.++.+.......+++++++++||||+|.|++.. .+.|
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~-~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~---~~~w 76 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKN-GEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK---DGKW 76 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCC-ceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc---CCEE
Confidence 5999999999999999998776332 36889999999999998776654456788899999999999999873 6899
Q ss_pred EEEecCCCCCCCCCC
Q 047253 142 RVTGFANNHNHELLE 156 (679)
Q Consensus 142 ~V~~~~~~HNH~l~~ 156 (679)
.|+.+..+|||||.|
T Consensus 77 ~v~~~~~~HNH~L~P 91 (91)
T PF03101_consen 77 RVTSFVLEHNHPLCP 91 (91)
T ss_pred EEEECcCCcCCCCCC
Confidence 999999999999975
No 4
>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=99.76 E-value=1.7e-19 Score=193.28 Aligned_cols=255 Identities=15% Similarity=0.151 Sum_probs=191.6
Q ss_pred CCCccccCCChhhHHHHHHHhhcCCCHHHHHHHHHHhhcCCCCCCCcchhhhhhHHHhhhccCCcchHHHHHHHHHhhcc
Q 047253 161 RFLPAYRTISETDKSRILMFAKTGISVQQMMRLMELEKCVEPGYLPFTEKDVRNLLQSIRKLDPEDESVDLLRMCRNIKE 240 (679)
Q Consensus 161 ~~l~s~R~i~~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~~~~~~~~~~~dv~N~~~~~r~~~~~~d~~~ll~~~~~~~~ 240 (679)
.+++.+++.++.....|..|.-.|+++++|.+.+....|. ..+....|.++..... .-+.-++....
T Consensus 91 ~ll~~y~r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~----~~~S~s~vSri~~~~~---------~~~~~w~~R~L 157 (381)
T PF00872_consen 91 QLLPKYQRREDSLEELIISLYLKGVSTRDIEEALEELYGE----VAVSKSTVSRITKQLD---------EEVEAWRNRPL 157 (381)
T ss_pred cccchhhhhhhhhhhhhhhhhccccccccccchhhhhhcc----cccCchhhhhhhhhhh---------hhHHHHhhhcc
Confidence 3466677777777788888999999999999999876651 2245555555433221 11122222111
Q ss_pred CCCCcEEEEeeCCCCccceeEecchhhHHHHHHcCcEEEEcccccCCC-----CCCcceEEEEEecCCcceeeeeccccc
Q 047253 241 KDPNFRYEYTLDSNNRLENIAWSYASSIQAYEIFGDAVVFDTTHRLTA-----LDMPLGIWVGVNNYGVPCFFGCTLLRE 315 (679)
Q Consensus 241 ~np~~~~~~~~d~~~~~~~ifw~~~~~~~~~~~f~dvl~~D~Ty~tn~-----y~~pl~~~~gvd~~~~~~~~~~al~~~ 315 (679)
.+.. =.+|++|++|.+-+ -+.++++++|+|.+|+..++|+.+...
T Consensus 158 ~~~~------------------------------y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~ 207 (381)
T PF00872_consen 158 ESEP------------------------------YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDR 207 (381)
T ss_pred cccc------------------------------ccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccC
Confidence 1100 13788999998755 356789999999999999999999999
Q ss_pred cchhhHHHHHHHHHHHhcCCCCceecccccHHHHHHHHhhCCCCccccchhhhhhhhcccchhhhccchhHHHHHHhhhc
Q 047253 316 ENLRSFSWALKAFLAFMDGKAPQTILTDQNMCLKEAIAMEMPVTKHALCIWMIVVKFPSWFNAVLGERYNEWKAEFYRLY 395 (679)
Q Consensus 316 E~~es~~w~l~~f~~~~~~~~p~~iitD~~~~~~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~ 395 (679)
|+.++|.-+|+.+++- |-..|..||+|..+++.+||+++||++.++.|.+|+.+|+.+++.. ...+.+..+++.++
T Consensus 208 Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~---k~~~~v~~~Lk~I~ 283 (381)
T PF00872_consen 208 ESAASWREFLQDLKER-GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK---KDRKEVKADLKAIY 283 (381)
T ss_pred CccCEeeecchhhhhc-cccccceeeccccccccccccccccchhhhhheechhhhhcccccc---ccchhhhhhccccc
Confidence 9999999999998765 3346999999999999999999999999999999999999998865 34568888999999
Q ss_pred cCCCHHHHHHHHHHhHhhcCCCccHHHHHHHHhh-cccccccccccccccccccCCcchhHHHHHhhc
Q 047253 396 NLESIEDFEMGWRDMVNSFGLHTNRHIANLFALR-MQWALPYLRSNFFAGMTTTGHSKAINAFIQRFL 462 (679)
Q Consensus 396 ~~~t~~eF~~~w~~l~~~~~~~~~~~l~~~~~~r-e~W~~~y~~~~~~~g~~tt~~~Es~n~~lk~~~ 462 (679)
.+.+.++....++.+.+++........+.|-... +.|...-++...+--+.|||.+|++|+.+|+..
T Consensus 284 ~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~ 351 (381)
T PF00872_consen 284 QAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRT 351 (381)
T ss_pred cccccchhhhhhhhcccccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhc
Confidence 9999999999999999887765554444332211 122322245666668899999999999999754
No 5
>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=99.25 E-value=4.3e-11 Score=100.63 Aligned_cols=91 Identities=22% Similarity=0.380 Sum_probs=73.1
Q ss_pred cCCHHHHHHHHHHHHHhcCceEEEcceecccCCCcceEEEEEeeccCCCCCccCCCC--------------------CCC
Q 047253 54 FPTHDAAYEYYSEFAKSCGFSIRRHRTEGKDGVGKGLTRRYFVCHRAGNTPIKASNE--------------------NKP 113 (679)
Q Consensus 54 F~S~eea~~fy~~yA~~~GF~ir~~~s~~~~~~~k~~~~~~f~C~r~G~~~~k~~~~--------------------~~~ 113 (679)
|.+.+|.+.|++..+...||.|++.+|..+ ..+|.|--+|.++.+.... ...
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~--------ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k 72 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKK--------KIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKK 72 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCc--------eEEEEEecCCCccccccccccccccccccccccccccccccc
Confidence 889999999999999999999999998754 3589998888776543310 011
Q ss_pred CCCCCccccCccceEEEEEeecCCCCcEEEEecCCCCCCCC
Q 047253 114 QRNRKSSRCGCQAYMRISKVTELGAPEWRVTGFANNHNHEL 154 (679)
Q Consensus 114 ~r~~~s~r~gCpa~i~v~~~~~~~~~~w~V~~~~~~HNH~l 154 (679)
.....+.++.|||+|++.... ..++|.|..++..|||||
T Consensus 73 ~k~t~srk~~CPFriRA~yS~--k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 73 KKRTKSRKNTCPFRIRANYSK--KNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred CCcccccccCCCeEEEEEEEe--cCCeEEEEEecCCcCCCC
Confidence 123345679999999999886 578999999999999996
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.24 E-value=2.2e-10 Score=120.44 Aligned_cols=262 Identities=13% Similarity=0.061 Sum_probs=175.8
Q ss_pred ccccCCChhhHHHHHHHhhcCCCHHHHHHHHHHhhcCCCCCCCcchhhhhhHHHhhhccCCcchHHHHHHHHHhhccCCC
Q 047253 164 PAYRTISETDKSRILMFAKTGISVQQMMRLMELEKCVEPGYLPFTEKDVRNLLQSIRKLDPEDESVDLLRMCRNIKEKDP 243 (679)
Q Consensus 164 ~s~R~i~~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~~~~~~~~~~~dv~N~~~~~r~~~~~~d~~~ll~~~~~~~~~np 243 (679)
..+++.....-..|..|...|+++++|-.+++...+. .+...-++.+- ..+.+.+...+..-.
T Consensus 80 ~~~~r~~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~-----~~s~~~iS~~~------------~~~~e~v~~~~~r~l 142 (379)
T COG3328 80 ERYQRRERALDLPVLSMYAKGVTTREIEALLEELYGH-----KVSPSVISVVT------------DRLDEKVKAWQNRPL 142 (379)
T ss_pred hhhHhhhhhHHHHHHHHHHcCCcHHHHHHHHHHhhCc-----ccCHHHhhhHH------------HHHHHHHHHHHhccc
Confidence 3444444555666788889999999999999876542 22222222221 122233333222211
Q ss_pred CcEEEEeeCCCCccceeEecchhhHHHHHHcCcEEEEcccccCCC--CCCcceEEEEEecCCcceeeeeccccccchhhH
Q 047253 244 NFRYEYTLDSNNRLENIAWSYASSIQAYEIFGDAVVFDTTHRLTA--LDMPLGIWVGVNNYGVPCFFGCTLLREENLRSF 321 (679)
Q Consensus 244 ~~~~~~~~d~~~~~~~ifw~~~~~~~~~~~f~dvl~~D~Ty~tn~--y~~pl~~~~gvd~~~~~~~~~~al~~~E~~es~ 321 (679)
+ --.+|++|++|.+-+ -+..+++++||+.+|+..++|+.+-..|+ ..|
T Consensus 143 ---~--------------------------~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w 192 (379)
T COG3328 143 ---G--------------------------DYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFW 192 (379)
T ss_pred ---c--------------------------CceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhH
Confidence 0 013688999999876 67888999999999999999999999999 888
Q ss_pred HHHHHHHHHHhcCCCCceecccccHHHHHHHHhhCCCCccccchhhhhhhhcccchhhhccchhHHHHHHhhhccCCCHH
Q 047253 322 SWALKAFLAFMDGKAPQTILTDQNMCLKEAIAMEMPVTKHALCIWMIVVKFPSWFNAVLGERYNEWKAEFYRLYNLESIE 401 (679)
Q Consensus 322 ~w~l~~f~~~~~~~~p~~iitD~~~~~~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~ 401 (679)
.-+|..|+.. |-.....+++|...++.+||..+||.+.++.|..|+.+|+..+... ...+.....++.++.+.+.+
T Consensus 193 ~~~l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~---k~~d~i~~~~~~I~~a~~~e 268 (379)
T COG3328 193 LSFLLDLKNR-GLSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPR---KDQDAVLSDLRSIYIAPDAE 268 (379)
T ss_pred HHHHHHHHhc-cccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhh---hhhHHHHhhhhhhhccCCcH
Confidence 7566566544 2234556778999999999999999999999999999999887664 33456777788888899999
Q ss_pred HHHHHHHHhHhhcCCCccHHHHHHHHhh-cccccccccccccccccccCCcchhHHHHHhhcC--ccccHHHHHHHHH
Q 047253 402 DFEMGWRDMVNSFGLHTNRHIANLFALR-MQWALPYLRSNFFAGMTTTGHSKAINAFIQRFLG--AQTRLAHFVEQVA 476 (679)
Q Consensus 402 eF~~~w~~l~~~~~~~~~~~l~~~~~~r-e~W~~~y~~~~~~~g~~tt~~~Es~n~~lk~~~~--~~~~l~~f~~~~~ 476 (679)
+-...|..+.+.+......-++.|.... +.|.-.-++....--+.|||.+|++|+.++.... ...+-..++..+.
T Consensus 269 ~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~~ 346 (379)
T COG3328 269 EALLALLAFSELWGKRYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNEESVEKLV 346 (379)
T ss_pred HHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCHHHHHHHH
Confidence 9999999887755443333222222111 2222111122222346799999999998886543 3445555554443
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.87 E-value=7.2e-10 Score=70.76 Aligned_cols=26 Identities=42% Similarity=0.864 Sum_probs=24.7
Q ss_pred EEeccCccccCccchhHHHHHhcCCc
Q 047253 565 SCSCHQFEFSGILCRHTLRVLSTGNC 590 (679)
Q Consensus 565 ~CsC~~f~~~GipC~Hil~Vl~~~~i 590 (679)
+|+|++||..||||+|+|+|+...++
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 79999999999999999999999876
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=98.57 E-value=2.4e-07 Score=73.44 Aligned_cols=66 Identities=24% Similarity=0.420 Sum_probs=55.0
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHHhcCceEEEcceecccCCCcceEEEEEeeccCCCCCccCCCCCCCCCCCCccccCcc
Q 047253 46 VVPYIGQRFPTHDAAYEYYSEFAKSCGFSIRRHRTEGKDGVGKGLTRRYFVCHRAGNTPIKASNENKPQRNRKSSRCGCQ 125 (679)
Q Consensus 46 ~~P~vGm~F~S~eea~~fy~~yA~~~GF~ir~~~s~~~~~~~k~~~~~~f~C~r~G~~~~k~~~~~~~~r~~~s~r~gCp 125 (679)
+...+||.|+|.+|++.++..||..+||.++..+|.+ .+...+|. ..|||
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~--------~r~~~~C~----------------------~~~C~ 51 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDK--------KRYRAKCK----------------------DKGCP 51 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCC--------EEEEEEEc----------------------CCCCC
Confidence 3457999999999999999999999999999988753 25688994 34599
Q ss_pred ceEEEEEeecCCCCcEEE
Q 047253 126 AYMRISKVTELGAPEWRV 143 (679)
Q Consensus 126 a~i~v~~~~~~~~~~w~V 143 (679)
|+|++++.. +.+.|+|
T Consensus 52 Wrv~as~~~--~~~~~~I 67 (67)
T PF03108_consen 52 WRVRASKRK--RSDTFQI 67 (67)
T ss_pred EEEEEEEcC--CCCEEEC
Confidence 999999875 5677875
No 9
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=98.23 E-value=9.3e-07 Score=62.12 Aligned_cols=30 Identities=40% Similarity=0.667 Sum_probs=26.5
Q ss_pred CCCeEEEeccCccccCccchhHHHHHhcCC
Q 047253 560 QEGIISCSCHQFEFSGILCRHTLRVLSTGN 589 (679)
Q Consensus 560 ~~~~~~CsC~~f~~~GipC~Hil~Vl~~~~ 589 (679)
.....+|+|..|+..|.||+||++|+..++
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 356889999999999999999999998753
No 10
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=96.83 E-value=0.00089 Score=68.02 Aligned_cols=80 Identities=11% Similarity=0.009 Sum_probs=60.2
Q ss_pred eEEEEEec--CCcceeeeeccccccchhhHHHHHHHH-HHHhcCCCCceecccccHHHHHHHHhhCCCCccccchhhhhh
Q 047253 294 GIWVGVNN--YGVPCFFGCTLLREENLRSFSWALKAF-LAFMDGKAPQTILTDQNMCLKEAIAMEMPVTKHALCIWMIVV 370 (679)
Q Consensus 294 ~~~~gvd~--~~~~~~~~~al~~~E~~es~~w~l~~f-~~~~~~~~p~~iitD~~~~~~~Ai~~vfP~a~h~lC~~Hi~~ 370 (679)
+..+.+|. .+..+ +.++.+-+.+++.-+|..+ -.. ....+++|.+|-..+...|+++.||+|.+.+-.|||++
T Consensus 15 y~t~~~d~~~~~~~i---l~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk 90 (249)
T PF01610_consen 15 YVTVVVDLDTDTGRI---LDILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVK 90 (249)
T ss_pred eeEEEEECccCCceE---EEEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccccccccccccccchhhh
Confidence 44555665 44333 3477888888877666554 222 34578899999999999999999999999999999999
Q ss_pred hhcccch
Q 047253 371 KFPSWFN 377 (679)
Q Consensus 371 n~~~~~~ 377 (679)
++.+.+.
T Consensus 91 ~~~~al~ 97 (249)
T PF01610_consen 91 LANRALD 97 (249)
T ss_pred hhhhcch
Confidence 8876554
No 11
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=95.59 E-value=0.94 Score=50.36 Aligned_cols=249 Identities=15% Similarity=0.142 Sum_probs=132.2
Q ss_pred CccccCCChhhHHHHHHHhhcCCCHHHHHHHHHHhhcCCCCCCCcchhhhhhHHHhhhccCCcchHHHHHHHHHhhccCC
Q 047253 163 LPAYRTISETDKSRILMFAKTGISVQQMMRLMELEKCVEPGYLPFTEKDVRNLLQSIRKLDPEDESVDLLRMCRNIKEKD 242 (679)
Q Consensus 163 l~s~R~i~~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~~~~~~~~~~~dv~N~~~~~r~~~~~~d~~~ll~~~~~~~~~n 242 (679)
+..+.++++..+..|..+... ++-++..+.+....| .+.++...|.|.+...-.. ....... -+...
T Consensus 112 l~~~~R~S~~~~~~i~~~a~~-~sYr~aa~~l~~~~~----~~~iS~~tV~~~v~~~g~~-------~~~~~~~-~k~~~ 178 (470)
T PF06782_consen 112 LKKYQRISPELKEKIVELATE-MSYRKAAEILEELLG----NVSISKQTVWNIVKEAGFE-------EIKEEEK-EKKKV 178 (470)
T ss_pred CCcccchhHHHHHHHHHHHhh-cCHHHHHHHHhhccC----CCccCHHHHHHHHHhccch-------hhhcccc-ccCCC
Confidence 567788999999988887544 888888888854332 3567788888877644200 0000000 00111
Q ss_pred CCcEEEEeeCCCCccceeEecchhhHHHHHHcCcEEEEcccccCC----CC--CCc-ceEEEE---Eec-CCcceeeee-
Q 047253 243 PNFRYEYTLDSNNRLENIAWSYASSIQAYEIFGDAVVFDTTHRLT----AL--DMP-LGIWVG---VNN-YGVPCFFGC- 310 (679)
Q Consensus 243 p~~~~~~~~d~~~~~~~ifw~~~~~~~~~~~f~dvl~~D~Ty~tn----~y--~~p-l~~~~g---vd~-~~~~~~~~~- 310 (679)
|.. -++ .|++|... +. .+. +++-.| ... .+...+..-
T Consensus 179 ~~L--yIE-----------------------------aDg~~v~~qg~~~~~~e~k~~~vheG~~~~~~~~~R~~L~n~~ 227 (470)
T PF06782_consen 179 PVL--YIE-----------------------------ADGVHVKLQGKKKKKKEVKLFVVHEGWEKEKPGGKRNKLKNKR 227 (470)
T ss_pred CeE--EEe-----------------------------cCcceecccccccccceeeEEEEEeeeeeeeccCCcceeecch
Confidence 111 111 24444321 11 111 123334 111 122222222
Q ss_pred cccc---ccchhhHHHHHHHHHHHhcCCCC--ceecccccHHHHHHHHhhCCCCccccchhhhhhhhcccchhhhccchh
Q 047253 311 TLLR---EENLRSFSWALKAFLAFMDGKAP--QTILTDQNMCLKEAIAMEMPVTKHALCIWMIVVKFPSWFNAVLGERYN 385 (679)
Q Consensus 311 al~~---~E~~es~~w~l~~f~~~~~~~~p--~~iitD~~~~~~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~ 385 (679)
.++. ....+-|.-+...+-+....... .++..|....+.+++. .||++.|.|..||+.+.+.+.++.. +
T Consensus 228 ~f~~~~~~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~-----~ 301 (470)
T PF06782_consen 228 HFVSGVGESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD-----P 301 (470)
T ss_pred heecccccchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC-----h
Confidence 2232 44455666666666555443333 2455999999988776 9999999999999999998877542 2
Q ss_pred HHHHHHhhhccCCCHHHHHHHHHHhHhhcCCCcc-HHHHHHH-Hhhcccc--cccccccccccccccCCcchhHHHHHhh
Q 047253 386 EWKAEFYRLYNLESIEDFEMGWRDMVNSFGLHTN-RHIANLF-ALRMQWA--LPYLRSNFFAGMTTTGHSKAINAFIQRF 461 (679)
Q Consensus 386 ~~~~~~~~~~~~~t~~eF~~~w~~l~~~~~~~~~-~~l~~~~-~~re~W~--~~y~~~~~~~g~~tt~~~Es~n~~lk~~ 461 (679)
.+...+++.....+...++...+.+......... +-+..+. .....|- .+|... .|+......|+.+..+...
T Consensus 302 ~~~~~~~~al~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i~~y~~~---~~~~g~g~ee~~~~~~s~R 378 (470)
T PF06782_consen 302 ELKEKIRKALKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGIKPYRER---EGLRGIGAEESVSHVLSYR 378 (470)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHhhhhhhc---cCCCccchhhhhhhHHHHH
Confidence 3444444544555667777777766654332211 1111111 1222332 233221 3334444578888888765
Q ss_pred cCc
Q 047253 462 LGA 464 (679)
Q Consensus 462 ~~~ 464 (679)
+++
T Consensus 379 mK~ 381 (470)
T PF06782_consen 379 MKS 381 (470)
T ss_pred hcC
Confidence 543
No 12
>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=94.48 E-value=0.15 Score=39.09 Aligned_cols=57 Identities=23% Similarity=0.533 Sum_probs=37.5
Q ss_pred cCceEEEcceecccCCCcceEEEEEeeccCCCCCccCCCCCCCCCCCCccccCccceEEEEEeecCCCCcEEEEecCCCC
Q 047253 71 CGFSIRRHRTEGKDGVGKGLTRRYFVCHRAGNTPIKASNENKPQRNRKSSRCGCQAYMRISKVTELGAPEWRVTGFANNH 150 (679)
Q Consensus 71 ~GF~ir~~~s~~~~~~~k~~~~~~f~C~r~G~~~~k~~~~~~~~r~~~s~r~gCpa~i~v~~~~~~~~~~w~V~~~~~~H 150 (679)
-||..|+--.+.-++. ..-+.+|.|+. .+|||+=.|.+.. .++.-.++....+|
T Consensus 3 Dgy~WRKYGqK~i~g~--~~pRsYYrCt~----------------------~~C~akK~Vqr~~--~d~~~~~vtY~G~H 56 (60)
T PF03106_consen 3 DGYRWRKYGQKNIKGS--PYPRSYYRCTH----------------------PGCPAKKQVQRSA--DDPNIVIVTYEGEH 56 (60)
T ss_dssp SSS-EEEEEEEEETTT--TCEEEEEEEEC----------------------TTEEEEEEEEEET--TCCCEEEEEEES--
T ss_pred CCCchhhccCcccCCC--ceeeEeeeccc----------------------cChhheeeEEEec--CCCCEEEEEEeeee
Confidence 4788887554433332 35577899952 2799999998875 35677888889999
Q ss_pred CCC
Q 047253 151 NHE 153 (679)
Q Consensus 151 NH~ 153 (679)
||+
T Consensus 57 ~h~ 59 (60)
T PF03106_consen 57 NHP 59 (60)
T ss_dssp SS-
T ss_pred CCC
Confidence 997
No 13
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=92.27 E-value=0.037 Score=50.77 Aligned_cols=81 Identities=21% Similarity=0.175 Sum_probs=66.4
Q ss_pred CcEEEEcccccCCCCCCcceEEEEEecCCcceeeeeccccccchhhHHHHHHHHHHHhcCCCCceecccccHHHHHHHHh
Q 047253 275 GDAVVFDTTHRLTALDMPLGIWVGVNNYGVPCFFGCTLLREENLRSFSWALKAFLAFMDGKAPQTILTDQNMCLKEAIAM 354 (679)
Q Consensus 275 ~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~E~~es~~w~l~~f~~~~~~~~p~~iitD~~~~~~~Ai~~ 354 (679)
|+.+.+|=||.+-+ |--.+....+|.+|+ ++++-+-..-+...=..||+..++..+ ..|..|+||+.++...|+++
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 57889999997633 234566888999999 777888888888888888877777654 78999999999999999999
Q ss_pred hCCCC
Q 047253 355 EMPVT 359 (679)
Q Consensus 355 vfP~a 359 (679)
.+|..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99875
No 14
>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=88.98 E-value=1.4 Score=38.54 Aligned_cols=75 Identities=19% Similarity=0.185 Sum_probs=54.0
Q ss_pred CcEEEEcccccC-CCCCCcceEEEEEecCCcceeeeeccccccchhhHHHHHHHHHHHhcCCCCceecccccHHHHH
Q 047253 275 GDAVVFDTTHRL-TALDMPLGIWVGVNNYGVPCFFGCTLLREENLRSFSWALKAFLAFMDGKAPQTILTDQNMCLKE 350 (679)
Q Consensus 275 ~dvl~~D~Ty~t-n~y~~pl~~~~gvd~~~~~~~~~~al~~~E~~es~~w~l~~f~~~~~~~~p~~iitD~~~~~~~ 350 (679)
+.++.+|.+... ...+...+.++.+|..-..+ +++.+-..++.+.+..+|.......++..|++|+||+..+...
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFI-YAFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTEE-EEEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHS
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCcE-EEEEeecccccccccccccccccccccccceeccccccccccc
Confidence 467888888544 34455788888888876654 4677777778888888888777766665699999999998863
No 15
>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=85.37 E-value=1.5 Score=33.29 Aligned_cols=29 Identities=21% Similarity=0.459 Sum_probs=22.6
Q ss_pred cCccceEEEEEeecCCCCcEEEEecCCCCCC
Q 047253 122 CGCQAYMRISKVTELGAPEWRVTGFANNHNH 152 (679)
Q Consensus 122 ~gCpa~i~v~~~~~~~~~~w~V~~~~~~HNH 152 (679)
.||||+=.|.+.. +++.-.++....+|||
T Consensus 31 ~~C~a~K~Vq~~~--~d~~~~~vtY~g~H~h 59 (59)
T smart00774 31 QGCPAKKQVQRSD--DDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCCCcccEEEEC--CCCCEEEEEEeeEeCC
Confidence 4699987787764 3567788888899998
No 16
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=81.51 E-value=2.9 Score=38.08 Aligned_cols=79 Identities=20% Similarity=0.265 Sum_probs=53.8
Q ss_pred hhhHHHHHHHhhcCCCHHHHHHHHHHhhcCCC----------------CCCCcchhhhhhHHHhhhcc------------
Q 047253 171 ETDKSRILMFAKTGISVQQMMRLMELEKCVEP----------------GYLPFTEKDVRNLLQSIRKL------------ 222 (679)
Q Consensus 171 ~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~~~----------------~~~~~~~~dv~N~~~~~r~~------------ 222 (679)
++..+.|..|.+.|.+|++|--+|+.++|+.. +-.+-...|++|+..++...
T Consensus 31 eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~~L~~ri~~L~~HL~~nkKD~~ 110 (151)
T PRK08561 31 EEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRKHLEENPKDLH 110 (151)
T ss_pred HHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHhCCCcch
Confidence 45667788899999999999999999987631 11123446888886664321
Q ss_pred ------CCcchHHHHHHHHHhhccCCCCcEEEE
Q 047253 223 ------DPEDESVDLLRMCRNIKEKDPNFRYEY 249 (679)
Q Consensus 223 ------~~~~d~~~ll~~~~~~~~~np~~~~~~ 249 (679)
...+-...|++|++....--|+|.|.-
T Consensus 111 skRgL~~~~skrrRLl~Yyk~~~~LP~~WkY~~ 143 (151)
T PRK08561 111 NKRGLQLIESKIRRLVKYYKRTGVLPADWRYSP 143 (151)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCCCCcCCH
Confidence 012344568888887777777877754
No 17
>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=80.80 E-value=3.4 Score=31.34 Aligned_cols=25 Identities=32% Similarity=0.502 Sum_probs=10.4
Q ss_pred cCccceEEEEEeecCCCCcEEEEecCCCCCC
Q 047253 122 CGCQAYMRISKVTELGAPEWRVTGFANNHNH 152 (679)
Q Consensus 122 ~gCpa~i~v~~~~~~~~~~w~V~~~~~~HNH 152 (679)
.+|+|++.+.. +.-.|.....+|||
T Consensus 38 ~~C~a~~~~~~------~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITDA------GDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE--------TTEEEE-S---SS
T ss_pred CCCeEEEEEEC------CCCEEEECCCccCC
Confidence 68999998762 12356666689999
No 18
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=80.50 E-value=15 Score=34.15 Aligned_cols=108 Identities=10% Similarity=-0.012 Sum_probs=75.1
Q ss_pred HHHHHHcCcEEEEcccccCCCCCCcceEEEEEecCCcceeeeeccc-cccchhhHHHHHHHHHHHhcCCCCceecccccH
Q 047253 268 IQAYEIFGDAVVFDTTHRLTALDMPLGIWVGVNNYGVPCFFGCTLL-REENLRSFSWALKAFLAFMDGKAPQTILTDQNM 346 (679)
Q Consensus 268 ~~~~~~f~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~-~~E~~es~~w~l~~f~~~~~~~~p~~iitD~~~ 346 (679)
+..+..+|=.|..|+= ++..+.+++.|+.....|..++-..-.- ...+.+.+.-+|+...+.+|....-.||||...
T Consensus 26 k~~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~ 103 (153)
T PF04937_consen 26 KKSWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNAS 103 (153)
T ss_pred HHHHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCch
Confidence 3455666767777876 5667778888887777666554332111 124566666777777777776777789999999
Q ss_pred HHHHHH---HhhCCCCccccchhhhhhhhcccch
Q 047253 347 CLKEAI---AMEMPVTKHALCIWMIVVKFPSWFN 377 (679)
Q Consensus 347 ~~~~Ai---~~vfP~a~h~lC~~Hi~~n~~~~~~ 377 (679)
.++.|- .+-+|.....-|.-|-..-+.+.+.
T Consensus 104 ~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~ 137 (153)
T PF04937_consen 104 NMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIG 137 (153)
T ss_pred hHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHh
Confidence 998884 4567888888999998877665544
No 19
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=76.42 E-value=2.8 Score=29.83 Aligned_cols=29 Identities=14% Similarity=0.540 Sum_probs=14.5
Q ss_pred ccCCChhhHHHHHHHhhcCCCHHHHHHHH
Q 047253 166 YRTISETDKSRILMFAKTGISVQQMMRLM 194 (679)
Q Consensus 166 ~R~i~~~~k~~i~~l~~~gi~~~~i~~~l 194 (679)
+++|+.+++..|..+.+.|.+.++|...|
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~l 30 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRL 30 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHT
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHH
Confidence 56789999999999999999999998765
No 20
>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=76.07 E-value=5.7 Score=42.67 Aligned_cols=55 Identities=20% Similarity=0.358 Sum_probs=45.5
Q ss_pred CCCccCCHHHHHHHHHHHHHhcCceEEEcceecccCCCcceEEEEEeeccCCCCCccCCCCCCCCCCCCccccCccceEE
Q 047253 50 IGQRFPTHDAAYEYYSEFAKSCGFSIRRHRTEGKDGVGKGLTRRYFVCHRAGNTPIKASNENKPQRNRKSSRCGCQAYMR 129 (679)
Q Consensus 50 vGm~F~S~eea~~fy~~yA~~~GF~ir~~~s~~~~~~~k~~~~~~f~C~r~G~~~~k~~~~~~~~r~~~s~r~gCpa~i~ 129 (679)
-+..|+|+++-|..+|.|.....--|....|.+.+ ..+|.|.+ -.|||+|-
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk-------hftfachl----------------------k~c~fkil 74 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK-------HFTFACHL----------------------KNCPFKIL 74 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeeccccccc-------ceEEEeec----------------------cCCCceee
Confidence 35689999999999999999998888888887643 36899953 34999999
Q ss_pred EEEe
Q 047253 130 ISKV 133 (679)
Q Consensus 130 v~~~ 133 (679)
+...
T Consensus 75 lsy~ 78 (496)
T PF04684_consen 75 LSYC 78 (496)
T ss_pred eeec
Confidence 8865
No 21
>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=68.08 E-value=13 Score=37.94 Aligned_cols=146 Identities=11% Similarity=0.076 Sum_probs=78.9
Q ss_pred ChhhHHHHHHH-hhcCCCHHHHHHHHHHhhcCCCCCCCcchhhhhhHHHhhhccCCcchHHHHHHHHHhhccCCCCcEEE
Q 047253 170 SETDKSRILMF-AKTGISVQQMMRLMELEKCVEPGYLPFTEKDVRNLLQSIRKLDPEDESVDLLRMCRNIKEKDPNFRYE 248 (679)
Q Consensus 170 ~~~~k~~i~~l-~~~gi~~~~i~~~l~~~~g~~~~~~~~~~~dv~N~~~~~r~~~~~~d~~~ll~~~~~~~~~np~~~~~ 248 (679)
++.....|..+ ...++|..++.+.++.. | +.++...+.|+....... ...+.+.+.+..
T Consensus 5 g~~~~a~i~~l~~~~~lp~~r~~~~~~~~-G-----~~is~~ti~~~~~~~~~~-----l~~~~~~l~~~~--------- 64 (271)
T PF03050_consen 5 GPSLLALIAYLKYVYHLPLYRIQQMLEDL-G-----ITISRGTIANWIKRVAEA-----LKPLYEALKEEL--------- 64 (271)
T ss_pred CHHHHHHHHHHHhcCCCCHHHHhhhhhcc-c-----eeeccchhHhHhhhhhhh-----hhhhhhhhhhhc---------
Confidence 34445555554 35678888888888754 4 456777777776554322 112222222211
Q ss_pred EeeCCCCccceeEecchhhHHHHHHcCcEEEEcccccC----CCCCCcceEEEEEecCCcceeeeeccccccchhhHHHH
Q 047253 249 YTLDSNNRLENIAWSYASSIQAYEIFGDAVVFDTTHRL----TALDMPLGIWVGVNNYGVPCFFGCTLLREENLRSFSWA 324 (679)
Q Consensus 249 ~~~d~~~~~~~ifw~~~~~~~~~~~f~dvl~~D~Ty~t----n~y~~pl~~~~gvd~~~~~~~~~~al~~~E~~es~~w~ 324 (679)
.-.+||.+|-|.-. .+.. .-+..+-++.. .+-|.+..+-..+..
T Consensus 65 ------------------------~~~~~~~~DET~~~vl~~~~g~-~~~~Wv~~~~~----~v~f~~~~sR~~~~~--- 112 (271)
T PF03050_consen 65 ------------------------RSSPVVHADETGWRVLDKGKGK-KGYLWVFVSPE----VVLFFYAPSRSSKVI--- 112 (271)
T ss_pred ------------------------cccceeccCCceEEEecccccc-ceEEEeeeccc----eeeeeecccccccch---
Confidence 12345666666544 2211 11122222222 222333333333333
Q ss_pred HHHHHHHhcCCCCceecccccHHHHHHHHhhCCCCccccchhhhhhhhcccch
Q 047253 325 LKAFLAFMDGKAPQTILTDQNMCLKEAIAMEMPVTKHALCIWMIVVKFPSWFN 377 (679)
Q Consensus 325 l~~f~~~~~~~~p~~iitD~~~~~~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~ 377 (679)
.+.+++ .+-+++||.-.+-.. +..+.|+.|.-|+.|.+.+-..
T Consensus 113 ----~~~L~~-~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 113 ----KEFLGD-FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred ----hhhhcc-cceeeeccccccccc-----cccccccccccccccccccccc
Confidence 333444 345999999888764 3388999999999999986554
No 22
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=59.18 E-value=12 Score=36.42 Aligned_cols=81 Identities=19% Similarity=0.083 Sum_probs=50.2
Q ss_pred cEEEEcccccCCC-CCCcceEEEEEecCCcceeeeeccccccchhhHHHHHHHHHHHhcCCCCceecccccHHHHHHHHh
Q 047253 276 DAVVFDTTHRLTA-LDMPLGIWVGVNNYGVPCFFGCTLLREENLRSFSWALKAFLAFMDGKAPQTILTDQNMCLKEAIAM 354 (679)
Q Consensus 276 dvl~~D~Ty~tn~-y~~pl~~~~gvd~~~~~~~~~~al~~~E~~es~~w~l~~f~~~~~~~~p~~iitD~~~~~~~Ai~~ 354 (679)
+++-+|=||.+-+ -..=|+ -.||..|++. .+-|...-+...=.-||..+++.. ..|.+|+||+.+....|+.+
T Consensus 71 ~~w~vDEt~ikv~gkw~yly--rAid~~g~~L--d~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~~ 144 (215)
T COG3316 71 DSWRVDETYIKVNGKWHYLY--RAIDADGLTL--DVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALRK 144 (215)
T ss_pred cceeeeeeEEeeccEeeehh--hhhccCCCeE--EEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHHh
Confidence 3455666665422 111122 2344445543 344444444555566677777665 78999999999999999999
Q ss_pred hCCCCccc
Q 047253 355 EMPVTKHA 362 (679)
Q Consensus 355 vfP~a~h~ 362 (679)
+-+.+.|+
T Consensus 145 l~~~~ehr 152 (215)
T COG3316 145 LGSEVEHR 152 (215)
T ss_pred cCcchhee
Confidence 98866554
No 23
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=55.87 E-value=25 Score=29.82 Aligned_cols=29 Identities=28% Similarity=0.317 Sum_probs=20.0
Q ss_pred cCceEEEEccCCCeEEEeccCcccc-----CccchhHHHH
Q 047253 550 EGGRKVYWAPQEGIISCSCHQFEFS-----GILCRHTLRV 584 (679)
Q Consensus 550 ~~~~~V~~~~~~~~~~CsC~~f~~~-----GipC~Hil~V 584 (679)
++.|++.. ..|||.+|-.+ .-||.|++.+
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 34566542 38999998732 4579999865
No 24
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=55.14 E-value=12 Score=28.54 Aligned_cols=30 Identities=20% Similarity=0.264 Sum_probs=25.7
Q ss_pred hhhHHHHHHHhhcCCCHHHHHHHHHHhhcC
Q 047253 171 ETDKSRILMFAKTGISVQQMMRLMELEKCV 200 (679)
Q Consensus 171 ~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~ 200 (679)
++..+.|..|.+.|++|++|--+|+.++|+
T Consensus 31 ~eVe~~I~klakkG~tpSqIG~iLRD~~GI 60 (60)
T PF08069_consen 31 EEVEELIVKLAKKGLTPSQIGVILRDQYGI 60 (60)
T ss_dssp HHHHHHHHHHCCTTHCHHHHHHHHHHSCTC
T ss_pred HHHHHHHHHHHHcCCCHHHhhhhhhhccCC
Confidence 556677889999999999999999988763
No 25
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=53.74 E-value=23 Score=34.75 Aligned_cols=70 Identities=19% Similarity=0.303 Sum_probs=49.3
Q ss_pred ccCCChhhHHHHHHHhhcCCCHHHHHHHHHHhhcCCCCCCCcchhhhhhHHHhhhcc--CCc---------chHHHHHHH
Q 047253 166 YRTISETDKSRILMFAKTGISVQQMMRLMELEKCVEPGYLPFTEKDVRNLLQSIRKL--DPE---------DESVDLLRM 234 (679)
Q Consensus 166 ~R~i~~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~~~~~~~~~~~dv~N~~~~~r~~--~~~---------~d~~~ll~~ 234 (679)
-|.|+.+.+-.|.+|...|++|..|-..|+..+| . |..++.++... .+. -...++.+|
T Consensus 18 GRPLPna~RlrIVELarlGiRPCDISRQLrvSHG----C-------VSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~ 86 (334)
T KOG3517|consen 18 GRPLPNAIRLRIVELARLGIRPCDISRQLRVSHG----C-------VSKILARYNETGSILPGAIGGSKPRVTTPKVVKY 86 (334)
T ss_pred CccCcchhhhhHHHHHHcCCCccchhhhhhhccc----h-------HHHHHHHhccCCcccccccCCCCCccCChhHHHH
Confidence 3567788889999999999999999888875443 1 23333433321 111 134689999
Q ss_pred HHhhccCCCCcE
Q 047253 235 CRNIKEKDPNFR 246 (679)
Q Consensus 235 ~~~~~~~np~~~ 246 (679)
.++++..|||.|
T Consensus 87 IR~~Kq~DPGIF 98 (334)
T KOG3517|consen 87 IRSLKQRDPGIF 98 (334)
T ss_pred HHHhhccCCcee
Confidence 999999999975
No 26
>PHA02517 putative transposase OrfB; Reviewed
Probab=52.44 E-value=76 Score=32.38 Aligned_cols=73 Identities=12% Similarity=-0.112 Sum_probs=44.0
Q ss_pred CcEEEEcccccCCCCCCcceEEEEEecCCcceeeeeccccccchhhHHHHHHHHHHHhcCCCCceecccccHHHH
Q 047253 275 GDAVVFDTTHRLTALDMPLGIWVGVNNYGVPCFFGCTLLREENLRSFSWALKAFLAFMDGKAPQTILTDQNMCLK 349 (679)
Q Consensus 275 ~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~E~~es~~w~l~~f~~~~~~~~p~~iitD~~~~~~ 349 (679)
.+++..|.||..... +-.+.++.+|..... ++|+.+...++.+...-+|+......+...+..|.||+.....
T Consensus 110 n~~w~~D~t~~~~~~-g~~yl~~iiD~~sr~-i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 110 NQLWVADFTYVSTWQ-GWVYVAFIIDVFARR-IVGWRVSSSMDTDFVLDALEQALWARGRPGGLIHHSDKGSQYV 182 (277)
T ss_pred CCeEEeceeEEEeCC-CCEEEEEecccCCCe-eeecccCCCCChHHHHHHHHHHHHhcCCCcCcEeecccccccc
Confidence 478889999965443 345667777776554 5678777777766544444333333222222356699987654
No 27
>PF11433 DUF3198: Protein of unknown function (DUF3198); InterPro: IPR024504 This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.; PDB: 1X9B_A.
Probab=52.13 E-value=14 Score=26.23 Aligned_cols=44 Identities=16% Similarity=0.109 Sum_probs=30.8
Q ss_pred HHhhhccCCCHHHHHHHHHHhHhhcCCCccHHHHHHHHhhcccc
Q 047253 390 EFYRLYNLESIEDFEMGWRDMVNSFGLHTNRHIANLFALRMQWA 433 (679)
Q Consensus 390 ~~~~~~~~~t~~eF~~~w~~l~~~~~~~~~~~l~~~~~~re~W~ 433 (679)
.|..++++++..+|.....+|...-.--+..|...+-+.+++|-
T Consensus 6 ~Fe~~InS~SK~~Fv~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 49 (51)
T PF11433_consen 6 KFESYINSESKSVFVRNLTELERISKRLGKSYQIRLEEAKEKWK 49 (51)
T ss_dssp HHHHHHHS--HHHHHHHHHHHHHHHHHH-SHHHHHHHHHHHHH-
T ss_pred HHHHHhCCccHHHHHHhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 57788899999999999888765322224568888888888884
No 28
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=46.91 E-value=33 Score=30.49 Aligned_cols=70 Identities=17% Similarity=0.283 Sum_probs=40.5
Q ss_pred ccCCChhhHHHHHHHhhcCCCHHHHHHHHHHhhcCCCCCCCcchhhhhhHHHhhhcc--CC----cc-----hHHHHHHH
Q 047253 166 YRTISETDKSRILMFAKTGISVQQMMRLMELEKCVEPGYLPFTEKDVRNLLQSIRKL--DP----ED-----ESVDLLRM 234 (679)
Q Consensus 166 ~R~i~~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~~~~~~~~~~~dv~N~~~~~r~~--~~----~~-----d~~~ll~~ 234 (679)
-|.|+.+.+..|..|...|++|..|...|.- +..-|..++.++++. .. .| -...+..+
T Consensus 15 GrPLp~~~R~rIvela~~G~rp~~Isr~l~V-----------s~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~ 83 (125)
T PF00292_consen 15 GRPLPNELRQRIVELAKEGVRPCDISRQLRV-----------SHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEK 83 (125)
T ss_dssp TSSS-HHHHHHHHHHHHTT--HHHHHHHHT-------------HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHH
T ss_pred CccCcHHHHHHHHHHhhhcCCHHHHHHHHcc-----------chhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHH
Confidence 4667888999999999999999999876653 223344454444421 00 11 22345667
Q ss_pred HHhhccCCCCcE
Q 047253 235 CRNIKEKDPNFR 246 (679)
Q Consensus 235 ~~~~~~~np~~~ 246 (679)
+.+.+.+||..|
T Consensus 84 I~~~k~enP~if 95 (125)
T PF00292_consen 84 IEQYKRENPTIF 95 (125)
T ss_dssp HHHHHHH-TTS-
T ss_pred HHHHHhcCCCcc
Confidence 777778899875
No 29
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.29 E-value=42 Score=36.57 Aligned_cols=70 Identities=11% Similarity=0.018 Sum_probs=49.7
Q ss_pred eEEEEEecCCcceeeeeccccccchhhHHHHHHHHHHHhcCCCCceecccccHHHHHHHHhhCCCCccccchhhhhh
Q 047253 294 GIWVGVNNYGVPCFFGCTLLREENLRSFSWALKAFLAFMDGKAPQTILTDQNMCLKEAIAMEMPVTKHALCIWMIVV 370 (679)
Q Consensus 294 ~~~~gvd~~~~~~~~~~al~~~E~~es~~w~l~~f~~~~~~~~p~~iitD~~~~~~~Ai~~vfP~a~h~lC~~Hi~~ 370 (679)
+.++.+|.+.... ..++.+=+.+++.-.|. ..+....+.+..|-.....+++++.||++.+.+=.||+.+
T Consensus 169 ~~~i~~D~~~~~~---i~i~~~r~~~ti~~~l~----~~g~~~v~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~ 238 (402)
T COG3464 169 YQTIAVDLDTRKV---IDILEGRSVRTLRRYLR----RGGSEQVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQ 238 (402)
T ss_pred EEEEEEcCCCCce---eeecCCccHHHHHHHHH----hCCCcceeEEEccccHHHHHHHHHhCCChheeeeeeeeee
Confidence 3455556654332 23566666666653333 3332267799999999999999999999999999999986
No 30
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=42.81 E-value=34 Score=30.20 Aligned_cols=38 Identities=18% Similarity=0.356 Sum_probs=29.6
Q ss_pred CccccC-CChhhHHHHHHHhhcCCCHHHHHHHHHHhhcC
Q 047253 163 LPAYRT-ISETDKSRILMFAKTGISVQQMMRLMELEKCV 200 (679)
Q Consensus 163 l~s~R~-i~~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~ 200 (679)
.|++-+ ..++.++.|..|.+.|++|++|--+|+..+|+
T Consensus 22 ~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi 60 (151)
T KOG0400|consen 22 VPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGI 60 (151)
T ss_pred CcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCc
Confidence 444433 34677888999999999999998888887775
No 31
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=42.05 E-value=13 Score=36.88 Aligned_cols=24 Identities=25% Similarity=0.513 Sum_probs=19.6
Q ss_pred eEEEeccCccccCccchhHHHHHhcCC
Q 047253 563 IISCSCHQFEFSGILCRHTLRVLSTGN 589 (679)
Q Consensus 563 ~~~CsC~~f~~~GipC~Hil~Vl~~~~ 589 (679)
...|||..+ ..||.||-+|.-++.
T Consensus 124 ~~dCSCPD~---anPCKHi~AvyY~la 147 (266)
T COG4279 124 STDCSCPDY---ANPCKHIAAVYYLLA 147 (266)
T ss_pred ccccCCCCc---ccchHHHHHHHHHHH
Confidence 467999986 579999999987753
No 32
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=37.85 E-value=40 Score=23.91 Aligned_cols=27 Identities=15% Similarity=0.313 Sum_probs=20.0
Q ss_pred CCChhhHHHHHHHhhcCCCHHHHHHHH
Q 047253 168 TISETDKSRILMFAKTGISVQQMMRLM 194 (679)
Q Consensus 168 ~i~~~~k~~i~~l~~~gi~~~~i~~~l 194 (679)
.+++++.+.|..|...|++..+|...+
T Consensus 5 ~~~~~~~~~i~~l~~~G~si~~IA~~~ 31 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEGMSIAEIAKQF 31 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--HHHHHHHT
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 467777888999999999988887654
No 33
>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=31.69 E-value=31 Score=29.47 Aligned_cols=34 Identities=21% Similarity=0.409 Sum_probs=22.6
Q ss_pred CCCCCCC-CCCCccCCHHHHHHHHHHHHHhcCceEEEcc
Q 047253 42 STNDVVP-YIGQRFPTHDAAYEYYSEFAKSCGFSIRRHR 79 (679)
Q Consensus 42 ~~~~~~P-~vGm~F~S~eea~~fy~~yA~~~GF~ir~~~ 79 (679)
+..+..- .+.+.|+|.|+|..| |.++|....+..
T Consensus 42 ss~D~~~q~v~l~F~skE~Ai~y----aer~G~~Y~V~~ 76 (101)
T PF04800_consen 42 SSGDPLSQSVRLKFDSKEDAIAY----AERNGWDYEVEE 76 (101)
T ss_dssp SS--SEEE-CEEEESSHHHHHHH----HHHCT-EEEEE-
T ss_pred CCCChhhCeeEeeeCCHHHHHHH----HHHcCCeEEEeC
Confidence 3344444 388899999999865 999998876643
No 34
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=30.66 E-value=44 Score=33.16 Aligned_cols=20 Identities=25% Similarity=0.552 Sum_probs=15.6
Q ss_pred CCCCCccccCccceEEEEEe
Q 047253 114 QRNRKSSRCGCQAYMRISKV 133 (679)
Q Consensus 114 ~r~~~s~r~gCpa~i~v~~~ 133 (679)
.+...+.+.+|||+|+|+..
T Consensus 70 ~~~~~skK~~CPA~I~Ik~I 89 (225)
T PF15299_consen 70 RRSKPSKKRDCPARIYIKEI 89 (225)
T ss_pred cccccccCCCCCeEEEEEEE
Confidence 34566889999999998743
No 35
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=29.80 E-value=1.4e+02 Score=30.45 Aligned_cols=72 Identities=11% Similarity=0.019 Sum_probs=46.2
Q ss_pred CcEEEEcccccCCCCCCcceEEEEEecCCcceeeeeccccc-cchhhHHHHHHHHHHH-hc---CCCCceecccccHH
Q 047253 275 GDAVVFDTTHRLTALDMPLGIWVGVNNYGVPCFFGCTLLRE-ENLRSFSWALKAFLAF-MD---GKAPQTILTDQNMC 347 (679)
Q Consensus 275 ~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~-E~~es~~w~l~~f~~~-~~---~~~p~~iitD~~~~ 347 (679)
..+.+.|-||.....+.-++..+.+|.+.. .++|+++-.. .+.+...-+|+..++. .+ ...|..|.||+-..
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 367888999876554556888888888877 5668888764 4555555555433332 22 12466777887654
No 36
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=28.14 E-value=33 Score=28.75 Aligned_cols=43 Identities=21% Similarity=0.229 Sum_probs=29.2
Q ss_pred cccCCcCCCCCCCCCCCCccCCHHHHHHHHHHHHHhcCceEEE
Q 047253 35 ETRLSLESTNDVVPYIGQRFPTHDAAYEYYSEFAKSCGFSIRR 77 (679)
Q Consensus 35 ~~~~~~~~~~~~~P~vGm~F~S~eea~~fy~~yA~~~GF~ir~ 77 (679)
|...++|.+....+-+=++|+|++.|.++|+.=+...--++|.
T Consensus 41 G~v~~lEG~w~ptr~vviEFps~~~ar~~y~SpeYq~a~~~Rq 83 (96)
T COG5470 41 GEVETLEGEWRPTRNVVIEFPSLEAARDCYNSPEYQAAAAIRQ 83 (96)
T ss_pred CCeeeccCCCCcccEEEEEcCCHHHHHHHhcCHHHHHHHHHHh
Confidence 3344555555556667789999999999999765544444443
No 37
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=26.71 E-value=1.8e+02 Score=30.21 Aligned_cols=72 Identities=11% Similarity=0.015 Sum_probs=46.8
Q ss_pred CcEEEEcccccCCCCCCcceEEEEEecCCcceeeeeccccc-cchhhHHHHHHH-HHHHhcC---CCCceecccccHH
Q 047253 275 GDAVVFDTTHRLTALDMPLGIWVGVNNYGVPCFFGCTLLRE-ENLRSFSWALKA-FLAFMDG---KAPQTILTDQNMC 347 (679)
Q Consensus 275 ~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~-E~~es~~w~l~~-f~~~~~~---~~p~~iitD~~~~ 347 (679)
..+.+.|-||....-+.-++..+.+|.+.. .++|+++-.. .+.+...-+|+. +....+. ..|..|.||+-..
T Consensus 126 N~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsq 202 (301)
T PRK09409 126 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 202 (301)
T ss_pred CCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCcc
Confidence 368889999965544555788888888877 5678988865 566665555553 3333332 2355777887654
No 38
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=26.53 E-value=99 Score=28.13 Aligned_cols=31 Identities=19% Similarity=0.241 Sum_probs=26.1
Q ss_pred ChhhHHHHHHHhhcCCCHHHHHHHHHHhhcC
Q 047253 170 SETDKSRILMFAKTGISVQQMMRLMELEKCV 200 (679)
Q Consensus 170 ~~~~k~~i~~l~~~gi~~~~i~~~l~~~~g~ 200 (679)
+++..+.|..|.+.|.+|++|--+|+.++|+
T Consensus 27 ~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi 57 (148)
T PTZ00072 27 SSEVEDQICKLAKKGLTPSQIGVILRDSMGI 57 (148)
T ss_pred HHHHHHHHHHHHHCCCCHhHhhhhhhhccCc
Confidence 3456677889999999999999999988864
No 39
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=22.86 E-value=1.1e+02 Score=22.51 Aligned_cols=28 Identities=18% Similarity=0.490 Sum_probs=20.6
Q ss_pred CCChhhHHHHHHHhhcCCCHHHHHHHHH
Q 047253 168 TISETDKSRILMFAKTGISVQQMMRLME 195 (679)
Q Consensus 168 ~i~~~~k~~i~~l~~~gi~~~~i~~~l~ 195 (679)
.|++.++..|..|...|++..+|-..+.
T Consensus 4 ~Lt~~Eqaqid~m~qlG~s~~~isr~i~ 31 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQLGMSLREISRRIG 31 (50)
T ss_dssp ---HHHHHHHHHHHHTT--HHHHHHHHT
T ss_pred cCCHHHHHHHHHHHHhchhHHHHHHHhC
Confidence 4789999999999999999999887764
No 40
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=22.40 E-value=90 Score=23.35 Aligned_cols=26 Identities=12% Similarity=0.105 Sum_probs=18.4
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHhhcC
Q 047253 175 SRILMFAKTGISVQQMMRLMELEKCV 200 (679)
Q Consensus 175 ~~i~~l~~~gi~~~~i~~~l~~~~g~ 200 (679)
..|.......++..+++..|....++
T Consensus 3 ~lIErCl~~yMsk~E~v~~L~~~a~I 28 (54)
T PF09713_consen 3 NLIERCLQLYMSKEECVRALQKQANI 28 (54)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHcCC
Confidence 44666666778888888888766554
No 41
>PF02171 Piwi: Piwi domain; InterPro: IPR003165 This domain is found in the stem cell self-renewal protein Piwi and its relatives in Drosophila melanogaster []. It has been found in the C-terminal of a number of proteins which also contain the PAZ domain (IPR003100 from INTERPRO) in their central region, for example the Argonaute proteins. Several of these proteins have been implicated in the development and maintenance of stem cells through the RNA-mediated gene-quelling mechanisms associated with the protein DICER. ; GO: 0005515 protein binding; PDB: 4F1N_B 3LUH_B 4EI1_A 3QX8_A 3LUC_C 3LUJ_B 3LUD_B 3QX9_A 3LUG_B 3LUK_B ....
Probab=22.23 E-value=2.2e+02 Score=29.42 Aligned_cols=97 Identities=16% Similarity=0.146 Sum_probs=50.6
Q ss_pred EEEEcccccCCCC-CCc-ceEEEEEecCCcceeeeeccc---cccchhh----HHHHHHHHHHHhcCCCCceeccccc--
Q 047253 277 AVVFDTTHRLTAL-DMP-LGIWVGVNNYGVPCFFGCTLL---REENLRS----FSWALKAFLAFMDGKAPQTILTDQN-- 345 (679)
Q Consensus 277 vl~~D~Ty~tn~y-~~p-l~~~~gvd~~~~~~~~~~al~---~~E~~es----~~w~l~~f~~~~~~~~p~~iitD~~-- 345 (679)
||.+|.++..... ..| ++.+++.-+.+.....+.... ..|..+. +.++|+.|.+..+...|..||.=+|
T Consensus 79 iIGidv~h~~~~~~~~~sv~g~~~s~~~~~~~~~~~~~~~~~~~e~~~~l~~~~~~~L~~~~~~~~~~~P~~IiiyRdGv 158 (302)
T PF02171_consen 79 IIGIDVSHPSPGSDKNPSVVGFVASFDSDGSKYFSSVRFQDSGQEIIDNLEEIIKEALKEFKKNNGKWLPERIIIYRDGV 158 (302)
T ss_dssp EEEEEEEEESSTCTCSCEEEEEEEEESTTTCEEEEEEEEECTTCCCHHHHHHHHHHHHHHHHHTTTT-TTSEEEEEEES-
T ss_pred EEEEEEEecCcccCCcceeeEEEEeccCccccccceeEEeccchhhhcchhhHHHHHHHHHHHHcCCCCCceEEEEEccc
Confidence 7889999988766 444 333444332333333333333 2243333 5666677777766657876553322
Q ss_pred -------------HHHHHHHHhhCCCCccccchhhhhhhhc
Q 047253 346 -------------MCLKEAIAMEMPVTKHALCIWMIVVKFP 373 (679)
Q Consensus 346 -------------~~~~~Ai~~vfP~a~h~lC~~Hi~~n~~ 373 (679)
.++++|+.+.-++-...++...+.++..
T Consensus 159 se~~~~~v~~~Ei~~i~~a~~~~~~~~~p~~~~i~v~K~~~ 199 (302)
T PF02171_consen 159 SEGQFKKVLEEEIEAIKEAIKELGEDYNPKITYIVVQKRHN 199 (302)
T ss_dssp -GGGHHHHHHHHHHHHHHHHHHHTHTTCTEEEEEEEESSSS
T ss_pred CHHhhcccHHHHHHHHHHHHhhcccCCCCcEEEEEeecccc
Confidence 2334444444444445555555555443
Done!