Query 005549
Match_columns 691
No_of_seqs 351 out of 1579
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 01:13:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005549.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005549hhsearch_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 2E-125 5E-130 1067.9 61.5 583 48-668 67-676 (846)
2 PF10551 MULE: MULE transposas 99.9 9.9E-22 2.1E-26 168.5 8.6 90 297-388 1-93 (93)
3 PF03101 FAR1: FAR1 DNA-bindin 99.8 3.8E-20 8.2E-25 157.9 8.6 90 69-161 1-91 (91)
4 PF00872 Transposase_mut: Tran 99.8 4.7E-20 1E-24 198.2 4.5 255 167-478 92-352 (381)
5 COG3328 Transposase and inacti 99.3 3.7E-11 7.9E-16 126.8 18.6 263 170-493 81-348 (379)
6 PF08731 AFT: Transcription fa 99.3 2E-11 4.4E-16 103.0 9.9 91 61-159 1-111 (111)
7 smart00575 ZnF_PMZ plant mutat 98.8 9E-10 2E-14 70.6 1.0 27 574-600 1-27 (28)
8 PF03108 DBD_Tnp_Mut: MuDR fam 98.5 2.7E-07 5.9E-12 73.3 7.5 66 53-148 2-67 (67)
9 PF04434 SWIM: SWIM zinc finge 98.2 9.8E-07 2.1E-11 62.2 3.0 30 570-599 11-40 (40)
10 PF01610 DDE_Tnp_ISL3: Transpo 97.2 0.0004 8.7E-09 70.8 4.7 93 294-392 2-97 (249)
11 PF06782 UPF0236: Uncharacteri 95.8 1.1 2.4E-05 50.0 21.1 248 168-478 112-380 (470)
12 PF03106 WRKY: WRKY DNA -bindi 95.3 0.09 1.9E-06 40.4 7.0 57 78-158 3-59 (60)
13 PF13610 DDE_Tnp_IS240: DDE do 95.2 0.011 2.4E-07 54.4 2.1 81 290-374 1-81 (140)
14 PF00665 rve: Integrase core d 90.6 1.4 3E-05 38.8 8.2 75 290-365 6-81 (120)
15 smart00774 WRKY DNA binding do 88.3 0.96 2.1E-05 34.5 4.4 56 79-157 4-59 (59)
16 PF04937 DUF659: Protein of un 82.8 16 0.00034 34.1 10.7 106 285-393 28-138 (153)
17 PRK08561 rps15p 30S ribosomal 82.1 5.7 0.00012 36.3 7.1 90 175-264 30-143 (151)
18 PF04684 BAF1_ABF1: BAF1 / ABF 78.9 3.4 7.3E-05 44.5 5.3 55 57-138 24-78 (496)
19 PF03050 DDE_Tnp_IS66: Transpo 78.3 12 0.00025 38.5 9.2 146 175-392 5-155 (271)
20 PF04500 FLYWCH: FLYWCH zinc f 77.3 3.5 7.7E-05 31.4 3.9 25 127-157 38-62 (62)
21 PF13936 HTH_38: Helix-turn-he 76.5 2.8 6E-05 29.9 2.8 30 171-200 2-31 (44)
22 COG3316 Transposase and inacti 72.8 8.1 0.00017 37.8 5.7 83 290-377 70-152 (215)
23 PHA02517 putative transposase 65.4 48 0.001 34.0 10.2 73 290-364 110-182 (277)
24 KOG0400 40S ribosomal protein 59.4 34 0.00073 30.4 6.3 37 169-205 23-60 (151)
25 PF08069 Ribosomal_S13_N: Ribo 57.1 11 0.00025 28.8 2.7 30 176-205 31-60 (60)
26 COG5431 Uncharacterized metal- 56.0 21 0.00046 30.3 4.4 29 560-594 42-75 (117)
27 PRK14702 insertion element IS2 49.4 78 0.0017 32.3 8.4 72 290-362 87-163 (262)
28 PTZ00072 40S ribosomal protein 46.3 72 0.0016 29.1 6.5 49 175-223 27-91 (148)
29 PRK09409 IS2 transposase TnpB; 44.8 1E+02 0.0022 32.2 8.6 72 290-362 126-202 (301)
30 KOG3517 Transcription factor P 43.0 46 0.00099 32.9 5.1 80 170-261 17-98 (334)
31 PF02796 HTH_7: Helix-turn-hel 41.5 19 0.00041 25.7 1.8 27 173-199 5-31 (45)
32 PF11433 DUF3198: Protein of u 36.1 31 0.00067 24.7 2.0 44 405-448 6-49 (51)
33 PF03462 PCRF: PCRF domain; I 32.2 1.3E+02 0.0027 26.5 5.8 37 65-101 66-102 (115)
34 COG4715 Uncharacterized conser 31.9 1.6E+02 0.0036 33.0 7.7 35 563-599 62-96 (587)
35 KOG2925 Predicted translation 28.5 26 0.00056 31.9 0.8 13 3-15 53-65 (167)
36 COG4279 Uncharacterized conser 28.3 25 0.00055 35.0 0.8 24 573-599 124-147 (266)
37 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 26.3 87 0.0019 23.1 3.1 28 173-200 4-31 (50)
38 PF09451 ATG27: Autophagy-rela 25.9 1.3E+02 0.0029 30.8 5.6 83 11-108 64-147 (268)
39 PF02171 Piwi: Piwi domain; I 24.4 2.1E+02 0.0045 29.7 7.0 65 292-356 79-152 (302)
40 PF04800 ETC_C1_NDUFA4: ETC co 24.4 46 0.001 28.5 1.6 31 51-85 44-75 (101)
41 PF15299 ALS2CR8: Amyotrophic 24.3 66 0.0014 32.0 3.0 21 118-138 69-89 (225)
42 PF09713 A_thal_3526: Plant pr 23.0 97 0.0021 23.3 2.8 25 181-205 4-28 (54)
43 PRK00766 hypothetical protein; 21.7 4.7E+02 0.01 25.4 8.1 27 351-377 99-128 (194)
44 PF06361 RTBV_P12: Rice tungro 21.4 1E+02 0.0022 24.9 2.9 28 655-682 53-80 (110)
45 COG3464 Transposase and inacti 20.6 1.4E+02 0.0031 32.6 4.8 70 309-385 169-238 (402)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=2.3e-125 Score=1067.92 Aligned_cols=583 Identities=25% Similarity=0.453 Sum_probs=509.1
Q ss_pred CCcCCCCCCCCCccCCHHHHHHHHHHHhhhcCceEEEeeeeecCCC-ceEEEEEeeccCCcCcCCCCC----C-------
Q 005549 48 LNESMVAPYVGMVFKSDDDAFEYYGNFARKSGFSVRKERSRLSPQL-GVYKRDFVCYRSGFAPMRKKP----G------- 115 (691)
Q Consensus 48 ~~~~~~~P~~Gm~F~S~eea~~~y~~yA~~~GF~vr~~~s~~~~~~-~~~~~~~~C~r~G~~~~~~~~----~------- 115 (691)
+.+...+|.+||+|+|+|||++||+.||..+||+||++++++++.. .+++++|+|+|+|+++.+.+. .
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 4567789999999999999999999999999999999999887654 789999999999987543210 0
Q ss_pred -CCCcccCCcccccccceeEEEEeeecCcceEEEEEEeccccCCCCCccccccccccccCCHHHHHHHHHhhhcCCChhH
Q 005549 116 -GEHHRDRKSVRCGCDAKMYLSKEVVEGVSQWFVVQFSNVHNHELLESDQVRFLPAYRKIQEADQERILLLSKAGFPIHR 194 (691)
Q Consensus 116 -~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH~l~~~~~~~~l~shR~ls~~~k~~i~~l~~~g~~~~~ 194 (691)
...+++|+.+||||||+|.|++. .+|+|+|+.|+.+|||||.++... +. .++.
T Consensus 147 ~~~~~~rR~~tRtGC~A~m~Vk~~---~~gkW~V~~fv~eHNH~L~p~~~~---------~~--------------~~r~ 200 (846)
T PLN03097 147 PENGTGRRSCAKTDCKASMHVKRR---PDGKWVIHSFVKEHNHELLPAQAV---------SE--------------QTRK 200 (846)
T ss_pred cccccccccccCCCCceEEEEEEc---CCCeEEEEEEecCCCCCCCCcccc---------ch--------------hhhh
Confidence 01123456789999999999875 458999999999999999976432 11 1233
Q ss_pred HHHHHHHhhCcCCCCCCCchhhhhhHHHHHHHhhhhhhhhhhhcccCcHHHHHHHHHHhccCCCccEEEEEecCCCceee
Q 005549 195 IVKVLELEKGIQGGQLPFLERDVRNFVQNRRRAVQENDALLTEKRETDTMELLDICKATNETDEYFVYDFTVDENNKVEN 274 (691)
Q Consensus 195 i~~~l~~~~g~~~~~~~~~~~di~N~~~~~r~~~~~~~~~~~~~~~~d~~~ll~~~~~~~~~np~~~~~~~~d~~~~~~~ 274 (691)
++..+....+ ...++..+..|..|...+.|+. ....+|++.||+||++++.+||+|+|++++|++|++++
T Consensus 201 ~~~~~~~~~~-~~~~v~~~~~d~~~~~~~~r~~---------~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~n 270 (846)
T PLN03097 201 MYAAMARQFA-EYKNVVGLKNDSKSSFDKGRNL---------GLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKN 270 (846)
T ss_pred hHHHHHhhhh-ccccccccchhhcchhhHHHhh---------hcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeee
Confidence 3333333333 2456777778888887765544 23678999999999999999999999999999999999
Q ss_pred EEecccccHHHHhhcCCEEEEecccccccCCceeeEEEeeeccCceEEEeeeeccCCchhHHHHHHHHHHHHhcCCCCee
Q 005549 275 IAWSFPGSIHAYAMLGDVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKT 354 (691)
Q Consensus 275 if~~~~~~~~~~~~f~dvv~~D~Ty~~n~y~~~l~~~~gvd~~g~~~~~~~al~~~Et~es~~w~l~~~~~~~~~~~p~~ 354 (691)
|||+|+.++.+|.+|||||+||+||+||+|++||++|+|||||||+++||||||.+|+.+||.|+|++|+++|+++.|++
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 eecCCChHHHHHHHhhCCCCceecchhhhhhhHHhhhhhhhccchhHHHHHHhhh-ccCCCHHHHHHHHHHHHhhcCCCc
Q 005549 355 ILTDLDPGLGDAIRSALPNTRHVISVCNILPKLSGWFSLLLGSQFSEFKSEFDAL-CHVESTEDFELQWSQMVSMFGLGS 433 (691)
Q Consensus 355 iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~-~~~~t~~efe~~w~~l~~~~~~~~ 433 (691)
||||+|.+|.+||++|||+|.|++|.|||++|+.++++.++. ..+.|+.+|+.+ +.+.+++|||..|..|+++|++++
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 999999999999999999999999999999999999988653 457899999875 568999999999999999999999
Q ss_pred cHHHHHHHhhhccccccccccccccccccCccCchhhHHHhhhhcccCCHHHHHHHHHHHHhhhhh------hhhhcccc
Q 005549 434 DRHIALLYSIRTSWALSYIRGYFLARMATPAYLKSVDAFLKRIFAAQTCLRSFFEQVGIFSNLQNQ------PRQEMQYM 507 (691)
Q Consensus 434 ~~~l~~l~~~r~~W~~~y~~~~~~~g~~tt~~~Es~n~~lk~~~~~~~~l~~f~~~~~~~~~~~~~------~~~~~~~~ 507 (691)
|+||+.||+.|++||++|+++.|++||.||+|+||+|++||+|++++++|..|+++|+.+++.+.+ ..+..+.|
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 999999999999999999999999999999999999999999999999999999999999985543 22334567
Q ss_pred ccccCchHHHHHHhhhcHHHHHHHHHHHHHHhcCeEEEee-CC---eEEEEEEEeeCCceEEEEecCCCeeEeeecCccc
Q 005549 508 HMKTCIPIEEQARRTLTPFAFNAFQRELVLAMQYSASELA-NG---TYLVHHFKKMDGERRVIWIPDDEQLHCSCKEFES 583 (691)
Q Consensus 508 ~~kt~~p~e~q~~~~yT~~~f~~~q~el~~s~~~~v~~~~-~~---~y~V~~~~~~~~~~~V~~~~~~~~~~CsC~~fe~ 583 (691)
.+++.+|||+||+.+|||++|++||+|+..+..|.+.... +| +|.|....+ ++.|.|.++.....++|+|++|++
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 8899999999999999999999999999999999876543 33 688876544 567999999999999999999999
Q ss_pred CCccccchhHHhhhcCcccCCCCCccccccccccccccccccC---cchhHHHHHHHHHHHHHHHHHccCHHHHHHHHHH
Q 005549 584 SGIPCRHAFRVFITKNYFQLPEKYFPSRWLRESSLAFFYDHDA---QQNEEWIQEFHSLTERLFAESSITKERSDYIRKE 660 (691)
Q Consensus 584 ~GipC~Hil~Vl~~~~i~~iP~~yil~RWtk~a~~~~~~~~~~---~~~~~r~~~l~~~~~~l~~~~~~s~e~~~~~~~~ 660 (691)
.||||+|||+||.++||.+||++|||+||||+|+.....+... .+...||+.|++.+.+++.+|+.|+|.|+.|+++
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 9999999999999999999999999999999999876554332 2236799999999999999999999999999999
Q ss_pred HHHHHHHH
Q 005549 661 LTKELTRL 668 (691)
Q Consensus 661 l~~~~~~~ 668 (691)
|.+.+..+
T Consensus 669 L~e~~~~~ 676 (846)
T PLN03097 669 LEEAFGNC 676 (846)
T ss_pred HHHHHHHH
Confidence 95444443
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=9.9e-22 Score=168.52 Aligned_cols=90 Identities=32% Similarity=0.569 Sum_probs=86.7
Q ss_pred cccccccCCceeeE---EEeeeccCceEEEeeeeccCCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHHHHHHhhCCC
Q 005549 297 TTYRSITYGLIFGA---WLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGDAIRSALPN 373 (691)
Q Consensus 297 ~Ty~~n~y~~~l~~---~~gvd~~g~~~~~~~al~~~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~ 373 (691)
+||+||+| +|++. ++|+|++|+.+|+||+++.+|+.++|.|+|+.+++.++.. |.+||||++.|+.+||+++||+
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 88885 9999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred CceecchhhhhhhHH
Q 005549 374 TRHVISVCNILPKLS 388 (691)
Q Consensus 374 a~h~lC~~Hi~~n~~ 388 (691)
+.|++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999974
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=99.81 E-value=3.8e-20 Score=157.85 Aligned_cols=90 Identities=36% Similarity=0.627 Sum_probs=79.6
Q ss_pred HHHHHHhhhcCceEEEeeeeec-CCCceEEEEEeeccCCcCcCCCCCCCCCcccCCcccccccceeEEEEeeecCcceEE
Q 005549 69 EYYGNFARKSGFSVRKERSRLS-PQLGVYKRDFVCYRSGFAPMRKKPGGEHHRDRKSVRCGCDAKMYLSKEVVEGVSQWF 147 (691)
Q Consensus 69 ~~y~~yA~~~GF~vr~~~s~~~-~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~ 147 (691)
+||+.||..+||+|++.+++++ .++.++++.|+|+++|.++.+......+++++++++|||||+|.+++.. .|+|.
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~---~~~w~ 77 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK---DGKWR 77 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc---CCEEE
Confidence 5999999999999999999887 4457899999999999998877654467888999999999999999863 68999
Q ss_pred EEEEeccccCCCCC
Q 005549 148 VVQFSNVHNHELLE 161 (691)
Q Consensus 148 V~~~~~~HNH~l~~ 161 (691)
|+.+..+|||||.|
T Consensus 78 v~~~~~~HNH~L~P 91 (91)
T PF03101_consen 78 VTSFVLEHNHPLCP 91 (91)
T ss_pred EEECcCCcCCCCCC
Confidence 99999999999975
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=99.79 E-value=4.7e-20 Score=198.17 Aligned_cols=255 Identities=16% Similarity=0.183 Sum_probs=196.6
Q ss_pred cccccccCCHHHHHHHHHhhhcCCChhHHHHHHHHhhCcCCCCCCCchhhhhhHHHHHHHhhhhhhhhhhhcccCcHHHH
Q 005549 167 FLPAYRKIQEADQERILLLSKAGFPIHRIVKVLELEKGIQGGQLPFLERDVRNFVQNRRRAVQENDALLTEKRETDTMEL 246 (691)
Q Consensus 167 ~l~shR~ls~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~di~N~~~~~r~~~~~~~~~~~~~~~~d~~~l 246 (691)
+++.+++.+++..+.|..|.-.|+++++|.++++...|. .+++...|.++...+...
T Consensus 92 ll~~y~r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~----~~~S~s~vSri~~~~~~~------------------- 148 (381)
T PF00872_consen 92 LLPKYQRREDSLEELIISLYLKGVSTRDIEEALEELYGE----VAVSKSTVSRITKQLDEE------------------- 148 (381)
T ss_pred ccchhhhhhhhhhhhhhhhhccccccccccchhhhhhcc----cccCchhhhhhhhhhhhh-------------------
Confidence 455666667788888889999999999999999877661 235666666654443322
Q ss_pred HHHHHHhccCCCccEEEEEecCCCceeeEEecccccHHHHhhcCCEEEEecccccccC-----CceeeEEEeeeccCceE
Q 005549 247 LDICKATNETDEYFVYDFTVDENNKVENIAWSFPGSIHAYAMLGDVVYFDTTYRSITY-----GLIFGAWLGIDSNGRTI 321 (691)
Q Consensus 247 l~~~~~~~~~np~~~~~~~~d~~~~~~~if~~~~~~~~~~~~f~dvv~~D~Ty~~n~y-----~~~l~~~~gvd~~g~~~ 321 (691)
+.-++.....+.. =++|++|++|.+-+. +.++++++|+|.+|+..
T Consensus 149 ~~~w~~R~L~~~~------------------------------y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~ 198 (381)
T PF00872_consen 149 VEAWRNRPLESEP------------------------------YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRRE 198 (381)
T ss_pred HHHHhhhcccccc------------------------------ccceeeeeeecccccccccccchhhhhhhhhcccccc
Confidence 1122222111110 147889999988663 57789999999999999
Q ss_pred EEeeeeccCCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHHHHHHhhCCCCceecchhhhhhhHHhhhhhhhccchhH
Q 005549 322 LFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGDAIRSALPNTRHVISVCNILPKLSGWFSLLLGSQFSE 401 (691)
Q Consensus 322 ~~~~al~~~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~ 401 (691)
++|+.+...|+.++|.-+|+.+++. |-..|..||+|..+|+.+||+++||++.++.|.+|+++|+.+++.. +..+.
T Consensus 199 vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~---k~~~~ 274 (381)
T PF00872_consen 199 VLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK---KDRKE 274 (381)
T ss_pred eeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccccccccccchhhhhheechhhhhcccccc---ccchh
Confidence 9999999999999999999998765 4456999999999999999999999999999999999999998865 55678
Q ss_pred HHHHHhhhccCCCHHHHHHHHHHHHhhcCCCccHHHHHHHhhh-ccccccccccccccccccCccCchhhHHHhhhhc
Q 005549 402 FKSEFDALCHVESTEDFELQWSQMVSMFGLGSDRHIALLYSIR-TSWALSYIRGYFLARMATPAYLKSVDAFLKRIFA 478 (691)
Q Consensus 402 ~~~~~~~~~~~~t~~efe~~w~~l~~~~~~~~~~~l~~l~~~r-~~W~~~y~~~~~~~g~~tt~~~Es~n~~lk~~~~ 478 (691)
+..+++.++.+.+.+++...++.+.+++....+.....|-... +.|.-.-++...+.-+.|||.+|++|+.+|+...
T Consensus 275 v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~ 352 (381)
T PF00872_consen 275 VKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTK 352 (381)
T ss_pred hhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhcc
Confidence 9999999999999999999999999988876665555443222 2223222455556678899999999999998644
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.35 E-value=3.7e-11 Score=126.76 Aligned_cols=263 Identities=14% Similarity=0.101 Sum_probs=182.9
Q ss_pred ccccCCHHHHHHHHHhhhcCCChhHHHHHHHHhhCcCCCCCCCchhhhhhHHHHHHHhhhhhhhhhhhcccCcHHHHHHH
Q 005549 170 AYRKIQEADQERILLLSKAGFPIHRIVKVLELEKGIQGGQLPFLERDVRNFVQNRRRAVQENDALLTEKRETDTMELLDI 249 (691)
Q Consensus 170 shR~ls~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~di~N~~~~~r~~~~~~~~~~~~~~~~d~~~ll~~ 249 (691)
.+++.....-..|..+...|++++++-.+++...+. .+.+.-++.+..+ +.+.
T Consensus 81 ~~~r~~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~-----~~s~~~iS~~~~~----------------------~~e~ 133 (379)
T COG3328 81 RYQRRERALDLPVLSMYAKGVTTREIEALLEELYGH-----KVSPSVISVVTDR----------------------LDEK 133 (379)
T ss_pred hhHhhhhhHHHHHHHHHHcCCcHHHHHHHHHHhhCc-----ccCHHHhhhHHHH----------------------HHHH
Confidence 344445566667788889999999999999876552 2333333222221 2222
Q ss_pred HHHhccCCCccEEEEEecCCCceeeEEecccccHHHHhhcCCEEEEeccccccc--CCceeeEEEeeeccCceEEEeeee
Q 005549 250 CKATNETDEYFVYDFTVDENNKVENIAWSFPGSIHAYAMLGDVVYFDTTYRSIT--YGLIFGAWLGIDSNGRTILFGVAL 327 (691)
Q Consensus 250 ~~~~~~~np~~~~~~~~d~~~~~~~if~~~~~~~~~~~~f~dvv~~D~Ty~~n~--y~~~l~~~~gvd~~g~~~~~~~al 327 (691)
+...+.+-. + --.+|++|++|.+-+ -+..+++++|++.+|+..++|+.+
T Consensus 134 v~~~~~r~l---~--------------------------~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~ 184 (379)
T COG3328 134 VKAWQNRPL---G--------------------------DYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWV 184 (379)
T ss_pred HHHHHhccc---c--------------------------CceEEEEecceeehhhhhhheeeeeeccCcccchhhhceee
Confidence 222222211 0 114688999999988 478999999999999999999999
Q ss_pred ccCCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHHHHHHhhCCCCceecchhhhhhhHHhhhhhhhccchhHHHHHHh
Q 005549 328 LQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGDAIRSALPNTRHVISVCNILPKLSGWFSLLLGSQFSEFKSEFD 407 (691)
Q Consensus 328 ~~~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~ 407 (691)
-..|+ ..|.-+|..|+.. |-.....+++|..+++.+||.++||.+.++.|..|+.+|+..+... +..+....+++
T Consensus 185 ~~~e~-~~w~~~l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~---k~~d~i~~~~~ 259 (379)
T COG3328 185 GVRES-KFWLSFLLDLKNR-GLSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPR---KDQDAVLSDLR 259 (379)
T ss_pred ecccc-hhHHHHHHHHHhc-cccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhh---hhhHHHHhhhh
Confidence 99999 7777566655544 3345667778999999999999999999999999999999988765 45577888899
Q ss_pred hhccCCCHHHHHHHHHHHHhhcCCCccHHHHHHHhhhc-cccccccccccccccccCccCchhhHHHhhhhcc--cCCHH
Q 005549 408 ALCHVESTEDFELQWSQMVSMFGLGSDRHIALLYSIRT-SWALSYIRGYFLARMATPAYLKSVDAFLKRIFAA--QTCLR 484 (691)
Q Consensus 408 ~~~~~~t~~efe~~w~~l~~~~~~~~~~~l~~l~~~r~-~W~~~y~~~~~~~g~~tt~~~Es~n~~lk~~~~~--~~~l~ 484 (691)
.++.+.+.++....|..+.+.+......-++.|....+ .|.-.-+......-+.|||.+|++|..++..... ..+-.
T Consensus 260 ~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~ 339 (379)
T COG3328 260 SIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNE 339 (379)
T ss_pred hhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCH
Confidence 99999999999999999888766555544444333222 2211111111113467999999999988865443 33445
Q ss_pred HHHHHHHHH
Q 005549 485 SFFEQVGIF 493 (691)
Q Consensus 485 ~f~~~~~~~ 493 (691)
+++..+...
T Consensus 340 ~sv~k~~y~ 348 (379)
T COG3328 340 ESVEKLVYL 348 (379)
T ss_pred HHHHHHHHH
Confidence 555544433
No 6
>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=99.29 E-value=2e-11 Score=102.97 Aligned_cols=91 Identities=23% Similarity=0.330 Sum_probs=74.4
Q ss_pred cCCHHHHHHHHHHHhhhcCceEEEeeeeecCCCceEEEEEeeccCCcCcCCCCCC--------------------CCCcc
Q 005549 61 FKSDDDAFEYYGNFARKSGFSVRKERSRLSPQLGVYKRDFVCYRSGFAPMRKKPG--------------------GEHHR 120 (691)
Q Consensus 61 F~S~eea~~~y~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~--------------------~~~~r 120 (691)
|.+.+|...|+++.+..+||.|++.+|... .+.|.|--+|.++...... .....
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~------ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k 74 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKK------KIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKK 74 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCc------eEEEEEecCCCcccccccccccccccccccccccccccccccCC
Confidence 889999999999999999999999999876 4789999888876554420 01122
Q ss_pred cCCcccccccceeEEEEeeecCcceEEEEEEeccccCCC
Q 005549 121 DRKSVRCGCDAKMYLSKEVVEGVSQWFVVQFSNVHNHEL 159 (691)
Q Consensus 121 ~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH~l 159 (691)
...+.+++|||+|++.... ..+.|.|..+++.|||||
T Consensus 75 ~t~srk~~CPFriRA~yS~--k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 75 RTKSRKNTCPFRIRANYSK--KNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cccccccCCCeEEEEEEEe--cCCeEEEEEecCCcCCCC
Confidence 3345678999999998876 679999999999999996
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.84 E-value=9e-10 Score=70.56 Aligned_cols=27 Identities=48% Similarity=0.981 Sum_probs=25.1
Q ss_pred eEeeecCcccCCccccchhHHhhhcCc
Q 005549 574 LHCSCKEFESSGIPCRHAFRVFITKNY 600 (691)
Q Consensus 574 ~~CsC~~fe~~GipC~Hil~Vl~~~~i 600 (691)
.+|+|++||..||||+|+|+|+...|+
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 379999999999999999999999876
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=98.55 E-value=2.7e-07 Score=73.34 Aligned_cols=66 Identities=23% Similarity=0.324 Sum_probs=55.9
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhhcCceEEEeeeeecCCCceEEEEEeeccCCcCcCCCCCCCCCcccCCcccccccce
Q 005549 53 VAPYVGMVFKSDDDAFEYYGNFARKSGFSVRKERSRLSPQLGVYKRDFVCYRSGFAPMRKKPGGEHHRDRKSVRCGCDAK 132 (691)
Q Consensus 53 ~~P~~Gm~F~S~eea~~~y~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~ 132 (691)
+...+||.|+|.+|+.+++..||..+||.++..+|.+. ++..+|. ..||||+
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~------r~~~~C~----------------------~~~C~Wr 53 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKK------RYRAKCK----------------------DKGCPWR 53 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCE------EEEEEEc----------------------CCCCCEE
Confidence 45789999999999999999999999999999888654 6778884 2269999
Q ss_pred eEEEEeeecCcceEEE
Q 005549 133 MYLSKEVVEGVSQWFV 148 (691)
Q Consensus 133 i~i~~~~~~~~~~w~V 148 (691)
|++++.. ..+.|.|
T Consensus 54 v~as~~~--~~~~~~I 67 (67)
T PF03108_consen 54 VRASKRK--RSDTFQI 67 (67)
T ss_pred EEEEEcC--CCCEEEC
Confidence 9999875 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=98.21 E-value=9.8e-07 Score=62.23 Aligned_cols=30 Identities=40% Similarity=0.759 Sum_probs=26.7
Q ss_pred CCCeeEeeecCcccCCccccchhHHhhhcC
Q 005549 570 DDEQLHCSCKEFESSGIPCRHAFRVFITKN 599 (691)
Q Consensus 570 ~~~~~~CsC~~fe~~GipC~Hil~Vl~~~~ 599 (691)
.....+|+|..|+..|.||+|+++|+...+
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 356899999999999999999999997754
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=97.17 E-value=0.0004 Score=70.79 Aligned_cols=93 Identities=14% Similarity=0.111 Sum_probs=65.6
Q ss_pred EEecccccccCCceeeEEEeeec--cCceEEEeeeeccCCchhHHHHHHHHH-HHHhcCCCCeeeecCCChHHHHHHHhh
Q 005549 294 YFDTTYRSITYGLIFGAWLGIDS--NGRTILFGVALLQDETLRSFAWALQTF-VHFMKGRCPKTILTDLDPGLGDAIRSA 370 (691)
Q Consensus 294 ~~D~Ty~~n~y~~~l~~~~gvd~--~g~~~~~~~al~~~Et~es~~w~l~~~-~~~~~~~~p~~iitD~~~~l~~Ai~~v 370 (691)
+||=+.......- +..+.+|. ++..+ +.++.+-+.+++.-+|..+ -.. ....+++|.+|...+...||++.
T Consensus 2 giDE~~~~~g~~~--y~t~~~d~~~~~~~i---l~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~ 75 (249)
T PF01610_consen 2 GIDEFAFRKGHRS--YVTVVVDLDTDTGRI---LDILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREY 75 (249)
T ss_pred eEeeeeeecCCcc--eeEEEEECccCCceE---EEEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCcccccccccc
Confidence 4555444333321 44455555 33333 2367788888887666655 222 34568999999999999999999
Q ss_pred CCCCceecchhhhhhhHHhhhh
Q 005549 371 LPNTRHVISVCNILPKLSGWFS 392 (691)
Q Consensus 371 fP~a~h~lC~~Hi~~n~~~~~~ 392 (691)
||+|.+.+-.|||++++.+.+.
T Consensus 76 ~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 76 FPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred ccccccccccchhhhhhhhcch
Confidence 9999999999999999887654
No 11
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=95.84 E-value=1.1 Score=49.97 Aligned_cols=248 Identities=15% Similarity=0.125 Sum_probs=133.0
Q ss_pred ccccccCCHHHHHHHHHhhhcCCChhHHHHHHHHhhCcCCCCCCCchhhhhhHHHHHHHhhhhhhhhhhhcccCcHHHHH
Q 005549 168 LPAYRKIQEADQERILLLSKAGFPIHRIVKVLELEKGIQGGQLPFLERDVRNFVQNRRRAVQENDALLTEKRETDTMELL 247 (691)
Q Consensus 168 l~shR~ls~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~di~N~~~~~r~~~~~~~~~~~~~~~~d~~~ll 247 (691)
+..+.++|+..+..|..+... +|-++..+.+....| .+.++...|.|.+...-.. ...
T Consensus 112 l~~~~R~S~~~~~~i~~~a~~-~sYr~aa~~l~~~~~----~~~iS~~tV~~~v~~~g~~-----------------~~~ 169 (470)
T PF06782_consen 112 LKKYQRISPELKEKIVELATE-MSYRKAAEILEELLG----NVSISKQTVWNIVKEAGFE-----------------EIK 169 (470)
T ss_pred CCcccchhHHHHHHHHHHHhh-cCHHHHHHHHhhccC----CCccCHHHHHHHHHhccch-----------------hhh
Confidence 567888999999999888644 888888888865443 4567777777765432210 000
Q ss_pred HHHHHhccCCCccEEEEEecCCCceeeEEecccccHHHHhhcCCEEEEeccccccc----C--Cce-eeEEEe---ee-c
Q 005549 248 DICKATNETDEYFVYDFTVDENNKVENIAWSFPGSIHAYAMLGDVVYFDTTYRSIT----Y--GLI-FGAWLG---ID-S 316 (691)
Q Consensus 248 ~~~~~~~~~np~~~~~~~~d~~~~~~~if~~~~~~~~~~~~f~dvv~~D~Ty~~n~----y--~~~-l~~~~g---vd-~ 316 (691)
.... -....|. --++ .|++|.... . .+. +++-.| .. +
T Consensus 170 ~~~~-~k~~~~~--LyIE-----------------------------aDg~~v~~qg~~~~~~e~k~~~vheG~~~~~~~ 217 (470)
T PF06782_consen 170 EEEK-EKKKVPV--LYIE-----------------------------ADGVHVKLQGKKKKKKEVKLFVVHEGWEKEKPG 217 (470)
T ss_pred cccc-ccCCCCe--EEEe-----------------------------cCcceecccccccccceeeEEEEEeeeeeeecc
Confidence 0000 0011111 1112 233333211 1 111 233344 11 1
Q ss_pred cCceEEEee-eecc---CCchhHHHHHHHHHHHHhcCCCC--eeeecCCChHHHHHHHhhCCCCceecchhhhhhhHHhh
Q 005549 317 NGRTILFGV-ALLQ---DETLRSFAWALQTFVHFMKGRCP--KTILTDLDPGLGDAIRSALPNTRHVISVCNILPKLSGW 390 (691)
Q Consensus 317 ~g~~~~~~~-al~~---~Et~es~~w~l~~~~~~~~~~~p--~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~ 390 (691)
.++..+..- .++. ..+.+-|.-+.+.+-........ .++.+|+...+.+++. .||++.|.|..||+.+.+.+.
T Consensus 218 ~~R~~L~n~~~f~~~~~~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~ 296 (470)
T PF06782_consen 218 GKRNKLKNKRHFVSGVGESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQA 296 (470)
T ss_pred CCcceeecchheecccccchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHH
Confidence 223333332 2232 44455666666655555443333 3556999999988776 999999999999999999988
Q ss_pred hhhhhccchhHHHHHHhhhccCCCHHHHHHHHHHHHhhcCCCcc-HHHHHHH-hhhccccc--cccccccccccccCccC
Q 005549 391 FSLLLGSQFSEFKSEFDALCHVESTEDFELQWSQMVSMFGLGSD-RHIALLY-SIRTSWAL--SYIRGYFLARMATPAYL 466 (691)
Q Consensus 391 ~~~~~~~~~~~~~~~~~~~~~~~t~~efe~~w~~l~~~~~~~~~-~~l~~l~-~~r~~W~~--~y~~~~~~~g~~tt~~~ 466 (691)
++.. .++...+...+...+..+++...+.+......... +-+..+. .....|-. +|... .|+......
T Consensus 297 ~~~~-----~~~~~~~~~al~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i~~y~~~---~~~~g~g~e 368 (470)
T PF06782_consen 297 LSHD-----PELKEKIRKALKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGIKPYRER---EGLRGIGAE 368 (470)
T ss_pred hhhC-----hHHHHHHHHHHHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHhhhhhhc---cCCCccchh
Confidence 7542 23444444445555667777777766554332221 1111111 12333432 22211 344444557
Q ss_pred chhhHHHhhhhc
Q 005549 467 KSVDAFLKRIFA 478 (691)
Q Consensus 467 Es~n~~lk~~~~ 478 (691)
|+.+..+..-++
T Consensus 369 e~~~~~~s~RmK 380 (470)
T PF06782_consen 369 ESVSHVLSYRMK 380 (470)
T ss_pred hhhhhHHHHHhc
Confidence 888888765444
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=95.30 E-value=0.09 Score=40.41 Aligned_cols=57 Identities=21% Similarity=0.347 Sum_probs=39.4
Q ss_pred cCceEEEeeeeecCCCceEEEEEeeccCCcCcCCCCCCCCCcccCCcccccccceeEEEEeeecCcceEEEEEEeccccC
Q 005549 78 SGFSVRKERSRLSPQLGVYKRDFVCYRSGFAPMRKKPGGEHHRDRKSVRCGCDAKMYLSKEVVEGVSQWFVVQFSNVHNH 157 (691)
Q Consensus 78 ~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH 157 (691)
=||.+|+--.+.-++....+..|.|+. .||||+=.|.+.. .++.-.++....+|||
T Consensus 3 Dgy~WRKYGqK~i~g~~~pRsYYrCt~----------------------~~C~akK~Vqr~~--~d~~~~~vtY~G~H~h 58 (60)
T PF03106_consen 3 DGYRWRKYGQKNIKGSPYPRSYYRCTH----------------------PGCPAKKQVQRSA--DDPNIVIVTYEGEHNH 58 (60)
T ss_dssp SSS-EEEEEEEEETTTTCEEEEEEEEC----------------------TTEEEEEEEEEET--TCCCEEEEEEES--SS
T ss_pred CCCchhhccCcccCCCceeeEeeeccc----------------------cChhheeeEEEec--CCCCEEEEEEeeeeCC
Confidence 388888765555555555677888852 1799999898864 4567888999999999
Q ss_pred C
Q 005549 158 E 158 (691)
Q Consensus 158 ~ 158 (691)
+
T Consensus 59 ~ 59 (60)
T PF03106_consen 59 P 59 (60)
T ss_dssp -
T ss_pred C
Confidence 7
No 13
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=95.18 E-value=0.011 Score=54.43 Aligned_cols=81 Identities=26% Similarity=0.348 Sum_probs=69.2
Q ss_pred CCEEEEecccccccCCceeeEEEeeeccCceEEEeeeeccCCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHHHHHHh
Q 005549 290 GDVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGDAIRS 369 (691)
Q Consensus 290 ~dvv~~D~Ty~~n~y~~~l~~~~gvd~~g~~~~~~~al~~~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~Ai~~ 369 (691)
|+.+.+|=||.+-+ |-..+.+..+|.+|+ ++++-+...-+..+-..||...++..+ ..|..|+||+.++...|+++
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 67899999998755 346677899999999 788888888888888888888777755 67999999999999999999
Q ss_pred hCCCC
Q 005549 370 ALPNT 374 (691)
Q Consensus 370 vfP~a 374 (691)
++|..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99974
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=90.61 E-value=1.4 Score=38.75 Aligned_cols=75 Identities=24% Similarity=0.185 Sum_probs=54.9
Q ss_pred CCEEEEeccccc-ccCCceeeEEEeeeccCceEEEeeeeccCCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHHH
Q 005549 290 GDVVYFDTTYRS-ITYGLIFGAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGD 365 (691)
Q Consensus 290 ~dvv~~D~Ty~~-n~y~~~l~~~~gvd~~g~~~~~~~al~~~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~ 365 (691)
+.++.+|.+... ...+...+.++.+|..-+.. +++.+...++.+.+.-+|.......++..|++|+||+..+...
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 467888988544 34455888889998876654 4666666678888888888777777666699999999998764
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=88.28 E-value=0.96 Score=34.53 Aligned_cols=56 Identities=20% Similarity=0.306 Sum_probs=36.2
Q ss_pred CceEEEeeeeecCCCceEEEEEeeccCCcCcCCCCCCCCCcccCCcccccccceeEEEEeeecCcceEEEEEEeccccC
Q 005549 79 GFSVRKERSRLSPQLGVYKRDFVCYRSGFAPMRKKPGGEHHRDRKSVRCGCDAKMYLSKEVVEGVSQWFVVQFSNVHNH 157 (691)
Q Consensus 79 GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH 157 (691)
||.+|+--.+..++...-+..|.|+. ..||||+=.|.+.. +++.-.++....+|||
T Consensus 4 Gy~WRKYGQK~ikgs~~pRsYYrCt~---------------------~~~C~a~K~Vq~~~--~d~~~~~vtY~g~H~h 59 (59)
T smart00774 4 GYQWRKYGQKVIKGSPFPRSYYRCTY---------------------SQGCPAKKQVQRSD--DDPSVVEVTYEGEHTH 59 (59)
T ss_pred cccccccCcEecCCCcCcceEEeccc---------------------cCCCCCcccEEEEC--CCCCEEEEEEeeEeCC
Confidence 66666543333333333355677753 13799988787754 3567788888999998
No 16
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=82.76 E-value=16 Score=34.07 Aligned_cols=106 Identities=11% Similarity=0.035 Sum_probs=72.9
Q ss_pred HHhhcCCEEEEecccccccCCceeeEEEeeeccCceEEEeeeeccC--CchhHHHHHHHHHHHHhcCCCCeeeecCCChH
Q 005549 285 AYAMLGDVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQD--ETLRSFAWALQTFVHFMKGRCPKTILTDLDPG 362 (691)
Q Consensus 285 ~~~~f~dvv~~D~Ty~~n~y~~~l~~~~gvd~~g~~~~~~~al~~~--Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~ 362 (691)
.+...|=-|..|+= ++..+.+++.|+.....|-.++-.. -..+ .+.+.+.-+|+...+.+|......||||....
T Consensus 28 ~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksv-d~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~~ 104 (153)
T PF04937_consen 28 SWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSV-DASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNASN 104 (153)
T ss_pred HHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEE-ecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCchh
Confidence 34455556666765 4556677777777666655443332 2222 46666777777777777777777889999999
Q ss_pred HHHHHH---hhCCCCceecchhhhhhhHHhhhhh
Q 005549 363 LGDAIR---SALPNTRHVISVCNILPKLSGWFSL 393 (691)
Q Consensus 363 l~~Ai~---~vfP~a~h~lC~~Hi~~n~~~~~~~ 393 (691)
++.|-+ +-+|......|.-|-+.-+.+.+.+
T Consensus 105 ~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 105 MKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred HHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 988844 5578888889999998888776654
No 17
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=82.10 E-value=5.7 Score=36.33 Aligned_cols=90 Identities=24% Similarity=0.318 Sum_probs=57.9
Q ss_pred CHHHHHHHHHhhhcCCChhHHHHHHHHhhCcC----------------CCCCCCchhhhhhHHHHHHHh---hhhhh-hh
Q 005549 175 QEADQERILLLSKAGFPIHRIVKVLELEKGIQ----------------GGQLPFLERDVRNFVQNRRRA---VQEND-AL 234 (691)
Q Consensus 175 s~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~----------------~~~~~~~~~di~N~~~~~r~~---~~~~~-~~ 234 (691)
.++..+.|..|.+.|++|.+|=-+|+.++|+. .+..|-.+.|++|+..+..+. ++++. ..
T Consensus 30 ~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~~L~~ri~~L~~HL~~nkKD~ 109 (151)
T PRK08561 30 PEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRKHLEENPKDL 109 (151)
T ss_pred HHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 35567778899999999999999999999762 123456678999987654332 22211 00
Q ss_pred hh----hcccCcHHHHHHHHHHhccCCCccEEEE
Q 005549 235 LT----EKRETDTMELLDICKATNETDEYFVYDF 264 (691)
Q Consensus 235 ~~----~~~~~d~~~ll~~~~~~~~~np~~~~~~ 264 (691)
.. ..-.+-...|+.|+++...--|+|.|.-
T Consensus 110 ~skRgL~~~~skrrRLl~Yyk~~~~LP~~WkY~~ 143 (151)
T PRK08561 110 HNKRGLQLIESKIRRLVKYYKRTGVLPADWRYSP 143 (151)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCCCCCCcCCH
Confidence 00 0012344667888887766677777753
No 18
>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=78.90 E-value=3.4 Score=44.50 Aligned_cols=55 Identities=16% Similarity=0.213 Sum_probs=46.8
Q ss_pred CCCccCCHHHHHHHHHHHhhhcCceEEEeeeeecCCCceEEEEEeeccCCcCcCCCCCCCCCcccCCcccccccceeEEE
Q 005549 57 VGMVFKSDDDAFEYYGNFARKSGFSVRKERSRLSPQLGVYKRDFVCYRSGFAPMRKKPGGEHHRDRKSVRCGCDAKMYLS 136 (691)
Q Consensus 57 ~Gm~F~S~eea~~~y~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~ 136 (691)
.+..|+|+++-|+.+|.|.....--|....|-+.+ ..+|.|.. -.|||+|.+.
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk-----hftfachl----------------------k~c~fkills 76 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK-----HFTFACHL----------------------KNCPFKILLS 76 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeeccccccc-----ceEEEeec----------------------cCCCceeeee
Confidence 36789999999999999999999999998887765 57899963 2599999887
Q ss_pred Ee
Q 005549 137 KE 138 (691)
Q Consensus 137 ~~ 138 (691)
..
T Consensus 77 y~ 78 (496)
T PF04684_consen 77 YC 78 (496)
T ss_pred ec
Confidence 54
No 19
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=78.29 E-value=12 Score=38.50 Aligned_cols=146 Identities=14% Similarity=0.121 Sum_probs=80.5
Q ss_pred CHHHHHHHHHhh-hcCCChhHHHHHHHHhhCcCCCCCCCchhhhhhHHHHHHHhhhhhhhhhhhcccCcHHHHHHHHHHh
Q 005549 175 QEADQERILLLS-KAGFPIHRIVKVLELEKGIQGGQLPFLERDVRNFVQNRRRAVQENDALLTEKRETDTMELLDICKAT 253 (691)
Q Consensus 175 s~~~k~~i~~l~-~~g~~~~~i~~~l~~~~g~~~~~~~~~~~di~N~~~~~r~~~~~~~~~~~~~~~~d~~~ll~~~~~~ 253 (691)
++.....+..+. ..++|...+.+.+... | +.++...|.|+.......+ ..+.+.+.+.
T Consensus 5 g~~~~a~i~~l~~~~~lp~~r~~~~~~~~-G-----~~is~~ti~~~~~~~~~~l---------------~~~~~~l~~~ 63 (271)
T PF03050_consen 5 GPSLLALIAYLKYVYHLPLYRIQQMLEDL-G-----ITISRGTIANWIKRVAEAL---------------KPLYEALKEE 63 (271)
T ss_pred CHHHHHHHHHHHhcCCCCHHHHhhhhhcc-c-----eeeccchhHhHhhhhhhhh---------------hhhhhhhhhh
Confidence 445556666554 6678888888888765 5 4566777777765443221 1122222221
Q ss_pred ccCCCccEEEEEecCCCceeeEEecccccHHHHhhcCCEEEEeccccc----ccCCceeeEEEeeeccCceEEEeeeecc
Q 005549 254 NETDEYFVYDFTVDENNKVENIAWSFPGSIHAYAMLGDVVYFDTTYRS----ITYGLIFGAWLGIDSNGRTILFGVALLQ 329 (691)
Q Consensus 254 ~~~np~~~~~~~~d~~~~~~~if~~~~~~~~~~~~f~dvv~~D~Ty~~----n~y~~~l~~~~gvd~~g~~~~~~~al~~ 329 (691)
.. -.+||.+|-|.-. .+.. .-+..+-++.. .+.|.+..
T Consensus 64 ~~---------------------------------~~~~~~~DET~~~vl~~~~g~-~~~~Wv~~~~~----~v~f~~~~ 105 (271)
T PF03050_consen 64 LR---------------------------------SSPVVHADETGWRVLDKGKGK-KGYLWVFVSPE----VVLFFYAP 105 (271)
T ss_pred cc---------------------------------ccceeccCCceEEEecccccc-ceEEEeeeccc----eeeeeecc
Confidence 11 1346666666554 2221 22223333322 33333333
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHHHHHHhhCCCCceecchhhhhhhHHhhhh
Q 005549 330 DETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGDAIRSALPNTRHVISVCNILPKLSGWFS 392 (691)
Q Consensus 330 ~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~ 392 (691)
+-+.+.. .+.+++ -+-+++||+-.+-.. +..+.|+.|.-|+.|.+.+-..
T Consensus 106 sR~~~~~-------~~~L~~-~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 106 SRSSKVI-------KEFLGD-FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred cccccch-------hhhhcc-cceeeeccccccccc-----cccccccccccccccccccccc
Confidence 3333322 233344 345999999988665 2288999999999999876554
No 20
>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=77.31 E-value=3.5 Score=31.36 Aligned_cols=25 Identities=36% Similarity=0.588 Sum_probs=10.3
Q ss_pred ccccceeEEEEeeecCcceEEEEEEeccccC
Q 005549 127 CGCDAKMYLSKEVVEGVSQWFVVQFSNVHNH 157 (691)
Q Consensus 127 ~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH 157 (691)
.+|+|++.+.. + .-.|.....+|||
T Consensus 38 ~~C~a~~~~~~----~--~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITDA----G--DGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE--------TTEEEE-S---SS
T ss_pred CCCeEEEEEEC----C--CCEEEECCCccCC
Confidence 58999998862 1 2355666688999
No 21
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=76.53 E-value=2.8 Score=29.94 Aligned_cols=30 Identities=27% Similarity=0.501 Sum_probs=15.2
Q ss_pred cccCCHHHHHHHHHhhhcCCChhHHHHHHH
Q 005549 171 YRKIQEADQERILLLSKAGFPIHRIVKVLE 200 (691)
Q Consensus 171 hR~ls~~~k~~i~~l~~~g~~~~~i~~~l~ 200 (691)
+++|+.+++..|..+.+.|.+.++|.+.|.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg 31 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLG 31 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHC
Confidence 467999999999999999999999988764
No 22
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=72.84 E-value=8.1 Score=37.81 Aligned_cols=83 Identities=22% Similarity=0.237 Sum_probs=58.8
Q ss_pred CCEEEEecccccccCCceeeEEEeeeccCceEEEeeeeccCCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHHHHHHh
Q 005549 290 GDVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGDAIRS 369 (691)
Q Consensus 290 ~dvv~~D~Ty~~n~y~~~l~~~~gvd~~g~~~~~~~al~~~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~Ai~~ 369 (691)
++++-+|=||.+.+-+ -.+....+|..|+ ++.+-|...-+...-.-||..+++.. ..|.+|+||+.+....|+++
T Consensus 70 ~~~w~vDEt~ikv~gk-w~ylyrAid~~g~--~Ld~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~~ 144 (215)
T COG3316 70 GDSWRVDETYIKVNGK-WHYLYRAIDADGL--TLDVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALRK 144 (215)
T ss_pred ccceeeeeeEEeeccE-eeehhhhhccCCC--eEEEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHHh
Confidence 4567778888764432 1233345555544 45556666666777777888877776 67999999999999999999
Q ss_pred hCCCCcee
Q 005549 370 ALPNTRHV 377 (691)
Q Consensus 370 vfP~a~h~ 377 (691)
+-+.+.|+
T Consensus 145 l~~~~ehr 152 (215)
T COG3316 145 LGSEVEHR 152 (215)
T ss_pred cCcchhee
Confidence 99866554
No 23
>PHA02517 putative transposase OrfB; Reviewed
Probab=65.38 E-value=48 Score=34.02 Aligned_cols=73 Identities=15% Similarity=-0.092 Sum_probs=45.7
Q ss_pred CCEEEEecccccccCCceeeEEEeeeccCceEEEeeeeccCCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHH
Q 005549 290 GDVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLG 364 (691)
Q Consensus 290 ~dvv~~D~Ty~~n~y~~~l~~~~gvd~~g~~~~~~~al~~~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~ 364 (691)
..++..|.||..... +..++++.+|...+ .++|+.+...++.+...-+|+......+...+..|.||+.....
T Consensus 110 n~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 110 NQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQALWARGRPGGLIHHSDKGSQYV 182 (277)
T ss_pred CCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHHHhcCCCcCcEeecccccccc
Confidence 478889999976544 44577777777665 45677777667766544444443333332223466799987654
No 24
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=59.39 E-value=34 Score=30.36 Aligned_cols=37 Identities=30% Similarity=0.479 Sum_probs=29.1
Q ss_pred cccccC-CHHHHHHHHHhhhcCCChhHHHHHHHHhhCc
Q 005549 169 PAYRKI-QEADQERILLLSKAGFPIHRIVKVLELEKGI 205 (691)
Q Consensus 169 ~shR~l-s~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~ 205 (691)
|+.-++ +++.+++|..+.+.|++|.+|--+|+..+|+
T Consensus 23 PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi 60 (151)
T KOG0400|consen 23 PTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGI 60 (151)
T ss_pred cHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCc
Confidence 344344 4668899999999999999998888877775
No 25
>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=57.09 E-value=11 Score=28.77 Aligned_cols=30 Identities=33% Similarity=0.396 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhhcCCChhHHHHHHHHhhCc
Q 005549 176 EADQERILLLSKAGFPIHRIVKVLELEKGI 205 (691)
Q Consensus 176 ~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~ 205 (691)
++..+.|..|.+.|++|.+|=-+|+.++|+
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 556778889999999999999999988874
No 26
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=55.97 E-value=21 Score=30.28 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=19.7
Q ss_pred CCceEEEEecCCCeeEeeecCcc-----cCCccccchhHH
Q 005549 560 DGERRVIWIPDDEQLHCSCKEFE-----SSGIPCRHAFRV 594 (691)
Q Consensus 560 ~~~~~V~~~~~~~~~~CsC~~fe-----~~GipC~Hil~V 594 (691)
+++|.+. ...|||..|- .-.-||.|++.+
T Consensus 42 ~rdYIl~------~gfCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 42 ERDYILE------GGFCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred ccceEEE------cCcccCHHHHhHhhhcCcccchhhhhe
Confidence 4566663 3489999876 223469999864
No 27
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=49.35 E-value=78 Score=32.34 Aligned_cols=72 Identities=14% Similarity=-0.037 Sum_probs=49.1
Q ss_pred CCEEEEecccccccCCceeeEEEeeeccCceEEEeeeeccC-CchhHHHHHHHHHHHHh-c---CCCCeeeecCCChH
Q 005549 290 GDVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQD-ETLRSFAWALQTFVHFM-K---GRCPKTILTDLDPG 362 (691)
Q Consensus 290 ~dvv~~D~Ty~~n~y~~~l~~~~gvd~~g~~~~~~~al~~~-Et~es~~w~l~~~~~~~-~---~~~p~~iitD~~~~ 362 (691)
..+.+.|-||.....+..++..+.+|.+.+ .++|+++-.. .+.+...-+|+..++.. + ...|..|.||+-..
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 367888999977655557888888998877 6778888764 45555555555433332 2 22477888998764
No 28
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=46.33 E-value=72 Score=29.09 Aligned_cols=49 Identities=22% Similarity=0.344 Sum_probs=36.9
Q ss_pred CHHHHHHHHHhhhcCCChhHHHHHHHHhhCcC----------------CCCCCCchhhhhhHHHH
Q 005549 175 QEADQERILLLSKAGFPIHRIVKVLELEKGIQ----------------GGQLPFLERDVRNFVQN 223 (691)
Q Consensus 175 s~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~----------------~~~~~~~~~di~N~~~~ 223 (691)
.++..+.|..|.+.|++|.+|=-+|+.++|+. .+..|-.+.|+|.++.+
T Consensus 27 ~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~vtG~kI~rILk~~Glap~iPeDly~LikK 91 (148)
T PTZ00072 27 SSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNVTGSKILRILKKNGLAPEIPEDLYFLIKK 91 (148)
T ss_pred HHHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeeccchHHHHHHHhcCCCCCCchHHHHHHHH
Confidence 45567788899999999999999999888541 23455666788887754
No 29
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=44.77 E-value=1e+02 Score=32.24 Aligned_cols=72 Identities=14% Similarity=-0.011 Sum_probs=49.5
Q ss_pred CCEEEEecccccccCCceeeEEEeeeccCceEEEeeeeccC-CchhHHHHHHHHHH-HHhcC---CCCeeeecCCChH
Q 005549 290 GDVVYFDTTYRSITYGLIFGAWLGIDSNGRTILFGVALLQD-ETLRSFAWALQTFV-HFMKG---RCPKTILTDLDPG 362 (691)
Q Consensus 290 ~dvv~~D~Ty~~n~y~~~l~~~~gvd~~g~~~~~~~al~~~-Et~es~~w~l~~~~-~~~~~---~~p~~iitD~~~~ 362 (691)
..|.+.|-||.....+.-++..+.+|...+ .++|+++... .+.+...-+|+.-+ ...+. ..|..|.||+-..
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 468888999976555556888888998877 6789998765 56666555665433 33332 2366888998654
No 30
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=43.03 E-value=46 Score=32.91 Aligned_cols=80 Identities=16% Similarity=0.193 Sum_probs=52.6
Q ss_pred ccccCCHHHHHHHHHhhhcCCChhHHHHHHHHhhCcCCCCCCCchhhhhhHHHHHHHh--hhhhhhhhhhcccCcHHHHH
Q 005549 170 AYRKIQEADQERILLLSKAGFPIHRIVKVLELEKGIQGGQLPFLERDVRNFVQNRRRA--VQENDALLTEKRETDTMELL 247 (691)
Q Consensus 170 shR~ls~~~k~~i~~l~~~g~~~~~i~~~l~~~~g~~~~~~~~~~~di~N~~~~~r~~--~~~~~~~~~~~~~~d~~~ll 247 (691)
.-|.|..+.+-.|.+|...|++|..|-+.|+..+|- |..++.++... +.-++.-=. ...-..-.+.
T Consensus 17 NGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGC-----------VSKILaRy~EtGsIlPGaIGGS-kPRVTTP~VV 84 (334)
T KOG3517|consen 17 NGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGC-----------VSKILARYNETGSILPGAIGGS-KPRVTTPKVV 84 (334)
T ss_pred cCccCcchhhhhHHHHHHcCCCccchhhhhhhccch-----------HHHHHHHhccCCcccccccCCC-CCccCChhHH
Confidence 347788899999999999999999999999877763 12223322221 111110000 0112345688
Q ss_pred HHHHHhccCCCccE
Q 005549 248 DICKATNETDEYFV 261 (691)
Q Consensus 248 ~~~~~~~~~np~~~ 261 (691)
+|+++++..|||.|
T Consensus 85 ~~IR~~Kq~DPGIF 98 (334)
T KOG3517|consen 85 KYIRSLKQRDPGIF 98 (334)
T ss_pred HHHHHhhccCCcee
Confidence 99999999999976
No 31
>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=41.46 E-value=19 Score=25.67 Aligned_cols=27 Identities=30% Similarity=0.386 Sum_probs=20.5
Q ss_pred cCCHHHHHHHHHhhhcCCChhHHHHHH
Q 005549 173 KIQEADQERILLLSKAGFPIHRIVKVL 199 (691)
Q Consensus 173 ~ls~~~k~~i~~l~~~g~~~~~i~~~l 199 (691)
.+++++.+.+..|...|++..+|.+.+
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 467777889999999999999988654
No 32
>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=36.12 E-value=31 Score=24.73 Aligned_cols=44 Identities=14% Similarity=0.183 Sum_probs=29.6
Q ss_pred HHhhhccCCCHHHHHHHHHHHHhhcCCCccHHHHHHHhhhcccc
Q 005549 405 EFDALCHVESTEDFELQWSQMVSMFGLGSDRHIALLYSIRTSWA 448 (691)
Q Consensus 405 ~~~~~~~~~t~~efe~~w~~l~~~~~~~~~~~l~~l~~~r~~W~ 448 (691)
.|..++++++..+|.....+|...-.--+..|...|-+-+++|-
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 57788899999999999888755322223567778877888884
No 33
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=32.23 E-value=1.3e+02 Score=26.52 Aligned_cols=37 Identities=16% Similarity=0.345 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhhhcCceEEEeeeeecCCCceEEEEEe
Q 005549 65 DDAFEYYGNFARKSGFSVRKERSRLSPQLGVYKRDFV 101 (691)
Q Consensus 65 eea~~~y~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~ 101 (691)
.++.+.|..||...||.+.+-.......++++...+.
T Consensus 66 ~~L~~MY~~~a~~~gw~~~~l~~~~~~~~G~k~a~~~ 102 (115)
T PF03462_consen 66 EELFRMYQRYAERRGWKVEVLDYSPGEEGGIKSATLE 102 (115)
T ss_dssp HHHHHHHHHHHHHTT-EEEEEEEEE-SSSSEEEEEEE
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCCCccceeEEEEE
Confidence 5778999999999999999877666555556665543
No 34
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=31.93 E-value=1.6e+02 Score=33.04 Aligned_cols=35 Identities=26% Similarity=0.422 Sum_probs=25.4
Q ss_pred eEEEEecCCCeeEeeecCcccCCccccchhHHhhhcC
Q 005549 563 RRVIWIPDDEQLHCSCKEFESSGIPCRHAFRVFITKN 599 (691)
Q Consensus 563 ~~V~~~~~~~~~~CsC~~fe~~GipC~Hil~Vl~~~~ 599 (691)
+.|+.........|+|.. ...| -|.|+.+|+....
T Consensus 62 v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~ 96 (587)
T COG4715 62 VRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYL 96 (587)
T ss_pred EEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHh
Confidence 455665566789999997 4444 6999999877643
No 35
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=28.54 E-value=26 Score=31.88 Aligned_cols=13 Identities=38% Similarity=0.710 Sum_probs=9.4
Q ss_pred cccccceeEeecc
Q 005549 3 LLTSKNIWMRRQQ 15 (691)
Q Consensus 3 ~~~~~~~~~~~~~ 15 (691)
.|=.|+|||||.+
T Consensus 53 ~KfRksiWiRRg~ 65 (167)
T KOG2925|consen 53 AKFRKSIWIRRGS 65 (167)
T ss_pred HhhhhceEEeeCC
Confidence 3445799999965
No 36
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=28.34 E-value=25 Score=34.96 Aligned_cols=24 Identities=29% Similarity=0.800 Sum_probs=19.6
Q ss_pred eeEeeecCcccCCccccchhHHhhhcC
Q 005549 573 QLHCSCKEFESSGIPCRHAFRVFITKN 599 (691)
Q Consensus 573 ~~~CsC~~fe~~GipC~Hil~Vl~~~~ 599 (691)
...|||..+ -.||.||-+|.-++.
T Consensus 124 ~~dCSCPD~---anPCKHi~AvyY~la 147 (266)
T COG4279 124 STDCSCPDY---ANPCKHIAAVYYLLA 147 (266)
T ss_pred ccccCCCCc---ccchHHHHHHHHHHH
Confidence 578999985 579999999877654
No 37
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=26.34 E-value=87 Score=23.10 Aligned_cols=28 Identities=18% Similarity=0.450 Sum_probs=21.1
Q ss_pred cCCHHHHHHHHHhhhcCCChhHHHHHHH
Q 005549 173 KIQEADQERILLLSKAGFPIHRIVKVLE 200 (691)
Q Consensus 173 ~ls~~~k~~i~~l~~~g~~~~~i~~~l~ 200 (691)
.|++.++.+|..+...|++..+|...+.
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 4899999999999999999999988775
No 38
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=25.87 E-value=1.3e+02 Score=30.79 Aligned_cols=83 Identities=13% Similarity=0.249 Sum_probs=40.9
Q ss_pred EeecccCCCCceeeeecCCCCcc-ccccccccccccccCCcCCCCCCCCCccCCHHHHHHHHHHHhhhcCceEEEeeeee
Q 005549 11 MRRQQCPCGDWKCYVSHEGDSEE-TSVASQLAKNDENSLNESMVAPYVGMVFKSDDDAFEYYGNFARKSGFSVRKERSRL 89 (691)
Q Consensus 11 ~~~~~~~~~~~~~~~~~e~~~~~-~~~~~~~~~~~~~~~~~~~~~P~~Gm~F~S~eea~~~y~~yA~~~GF~vr~~~s~~ 89 (691)
=.-+|||-|++-|+|.+-...++ .....++..-.. .......|...- .=+...|..+...-...
T Consensus 64 ~~~~~Cp~~t~vCgi~~~~~~~~~~~~v~~vi~~~~--~~~~~~~~~~~~-------------~d~~~~Gl~l~l~G~~~ 128 (268)
T PF09451_consen 64 PKEDQCPTGTRVCGITRVNLPDKEDDRVTQVIPFAS--SGQGSFEPIDTR-------------SDSEKEGLRLKLKGGKW 128 (268)
T ss_pred CccccCcCCCcEEEEEEEecCCCCCCceEEEEEccc--CCCccccccccc-------------ccCCCCCEEEEEeCCCC
Confidence 35689999999999986444333 222222222111 000111111110 23445677777554222
Q ss_pred cCCCceEEEEEeeccCCcC
Q 005549 90 SPQLGVYKRDFVCYRSGFA 108 (691)
Q Consensus 90 ~~~~~~~~~~~~C~r~G~~ 108 (691)
.....-..+.|.|+.++..
T Consensus 129 ~~~~~~a~i~f~Cd~~~~~ 147 (268)
T PF09451_consen 129 GSNNQSAVIEFQCDKNASG 147 (268)
T ss_pred CCceEEEEEEEEcCCCCCC
Confidence 2222334678999877654
No 39
>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=24.43 E-value=2.1e+02 Score=29.66 Aligned_cols=65 Identities=15% Similarity=0.126 Sum_probs=37.1
Q ss_pred EEEEecccccccC-Cce-eeEEEeeeccCceEEEeeeecc---CCchhH----HHHHHHHHHHHhcCCCCeeee
Q 005549 292 VVYFDTTYRSITY-GLI-FGAWLGIDSNGRTILFGVALLQ---DETLRS----FAWALQTFVHFMKGRCPKTIL 356 (691)
Q Consensus 292 vv~~D~Ty~~n~y-~~~-l~~~~gvd~~g~~~~~~~al~~---~Et~es----~~w~l~~~~~~~~~~~p~~ii 356 (691)
||.+|.++..... ..| ++.+++.-+.+.....+..... .|..+. +.++|+.|.+..+...|..||
T Consensus 79 iIGidv~h~~~~~~~~~sv~g~~~s~~~~~~~~~~~~~~~~~~~e~~~~l~~~~~~~L~~~~~~~~~~~P~~Ii 152 (302)
T PF02171_consen 79 IIGIDVSHPSPGSDKNPSVVGFVASFDSDGSKYFSSVRFQDSGQEIIDNLEEIIKEALKEFKKNNGKWLPERII 152 (302)
T ss_dssp EEEEEEEEESSTCTCSCEEEEEEEEESTTTCEEEEEEEEECTTCCCHHHHHHHHHHHHHHHHHTTTT-TTSEEE
T ss_pred EEEEEEEecCcccCCcceeeEEEEeccCccccccceeEEeccchhhhcchhhHHHHHHHHHHHHcCCCCCceEE
Confidence 7889999988776 333 4444444333344444444333 243333 566667777776665776655
No 40
>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=24.43 E-value=46 Score=28.55 Aligned_cols=31 Identities=26% Similarity=0.437 Sum_probs=21.9
Q ss_pred CCCCC-CCCCccCCHHHHHHHHHHHhhhcCceEEEe
Q 005549 51 SMVAP-YVGMVFKSDDDAFEYYGNFARKSGFSVRKE 85 (691)
Q Consensus 51 ~~~~P-~~Gm~F~S~eea~~~y~~yA~~~GF~vr~~ 85 (691)
.+..- .+.+.|+|.|+|. .||+++|....+.
T Consensus 44 ~D~~~q~v~l~F~skE~Ai----~yaer~G~~Y~V~ 75 (101)
T PF04800_consen 44 GDPLSQSVRLKFDSKEDAI----AYAERNGWDYEVE 75 (101)
T ss_dssp --SEEE-CEEEESSHHHHH----HHHHHCT-EEEEE
T ss_pred CChhhCeeEeeeCCHHHHH----HHHHHcCCeEEEe
Confidence 34444 4889999999996 5899999877764
No 41
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=24.31 E-value=66 Score=32.05 Aligned_cols=21 Identities=24% Similarity=0.591 Sum_probs=15.7
Q ss_pred CcccCCcccccccceeEEEEe
Q 005549 118 HHRDRKSVRCGCDAKMYLSKE 138 (691)
Q Consensus 118 ~~r~r~s~r~gCpa~i~i~~~ 138 (691)
..+...+.+.+|||+|+++..
T Consensus 69 ~~~~~~skK~~CPA~I~Ik~I 89 (225)
T PF15299_consen 69 RRRSKPSKKRDCPARIYIKEI 89 (225)
T ss_pred ccccccccCCCCCeEEEEEEE
Confidence 344556788999999998753
No 42
>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=23.02 E-value=97 Score=23.27 Aligned_cols=25 Identities=16% Similarity=0.064 Sum_probs=17.1
Q ss_pred HHHHhhhcCCChhHHHHHHHHhhCc
Q 005549 181 RILLLSKAGFPIHRIVKVLELEKGI 205 (691)
Q Consensus 181 ~i~~l~~~g~~~~~i~~~l~~~~g~ 205 (691)
.|..-....++..+++..|....++
T Consensus 4 lIErCl~~yMsk~E~v~~L~~~a~I 28 (54)
T PF09713_consen 4 LIERCLQLYMSKEECVRALQKQANI 28 (54)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHcCC
Confidence 3444445667888888888776665
No 43
>PRK00766 hypothetical protein; Provisional
Probab=21.68 E-value=4.7e+02 Score=25.41 Aligned_cols=27 Identities=7% Similarity=0.197 Sum_probs=17.7
Q ss_pred CCeeeecCCC---hHHHHHHHhhCCCCcee
Q 005549 351 CPKTILTDLD---PGLGDAIRSALPNTRHV 377 (691)
Q Consensus 351 ~p~~iitD~~---~~l~~Ai~~vfP~a~h~ 377 (691)
.|..+++..- .++..||++.||+...+
T Consensus 99 ~PVI~V~r~~p~~~~ie~AL~k~f~~~~~R 128 (194)
T PRK00766 99 LPVIVVMRKKPDFEAIESALKKHFSDWEER 128 (194)
T ss_pred CCEEEEEecCCCHHHHHHHHHHHCCCHHHH
Confidence 4555553333 37888998999987553
No 44
>PF06361 RTBV_P12: Rice tungro bacilliform virus P12 protein; InterPro: IPR009417 This family consists of several Rice tungro bacilliform virus P12 proteins. The function of this family is unknown [].
Probab=21.44 E-value=1e+02 Score=24.91 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCcCcc
Q 005549 655 DYIRKELTKELTRLLNEVRDMPESDGIA 682 (691)
Q Consensus 655 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 682 (691)
-+|+++++|.+.+|-.++..+|..++.+
T Consensus 53 lyalqeidkkinnl~aqv~k~pttsgs~ 80 (110)
T PF06361_consen 53 LYALQEIDKKINNLSAQVSKIPTTSGSS 80 (110)
T ss_pred HHHHHHHHhhhhhhHhhhhcCccCCCCC
Confidence 3678999999999999999999988765
No 45
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.58 E-value=1.4e+02 Score=32.62 Aligned_cols=70 Identities=14% Similarity=0.258 Sum_probs=49.6
Q ss_pred eEEEeeeccCceEEEeeeeccCCchhHHHHHHHHHHHHhcCCCCeeeecCCChHHHHHHHhhCCCCceecchhhhhh
Q 005549 309 GAWLGIDSNGRTILFGVALLQDETLRSFAWALQTFVHFMKGRCPKTILTDLDPGLGDAIRSALPNTRHVISVCNILP 385 (691)
Q Consensus 309 ~~~~gvd~~g~~~~~~~al~~~Et~es~~w~l~~~~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~ 385 (691)
+.++.+|.+.... ..++.+=+.+++.-.|.. .+....+.|..|...+..+++++.||++.+.+=.||+.+
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---IDILEGRSVRTLRRYLRR----GGSEQVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQ 238 (402)
T ss_pred EEEEEEcCCCCce---eeecCCccHHHHHHHHHh----CCCcceeEEEccccHHHHHHHHHhCCChheeeeeeeeee
Confidence 3445555553222 235566666666544442 222267899999999999999999999999999999987
Done!