Query 005579
Match_columns 690
No_of_seqs 350 out of 1395
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 01:41:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005579.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005579hhsearch_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 5E-125 1E-129 1064.5 60.1 590 49-676 66-682 (846)
2 PF10551 MULE: MULE transposas 99.9 7.3E-22 1.6E-26 169.2 8.3 90 299-390 1-93 (93)
3 PF03101 FAR1: FAR1 DNA-bindin 99.8 8.5E-20 1.9E-24 155.5 8.7 90 71-163 1-91 (91)
4 PF00872 Transposase_mut: Tran 99.8 3.5E-19 7.6E-24 191.2 3.9 255 168-479 91-351 (381)
5 PF08731 AFT: Transcription fa 99.4 5.1E-12 1.1E-16 106.4 10.0 91 63-161 1-111 (111)
6 COG3328 Transposase and inacti 99.3 7.5E-11 1.6E-15 124.3 16.3 262 170-493 79-346 (379)
7 smart00575 ZnF_PMZ plant mutat 98.9 5.2E-10 1.1E-14 71.6 1.9 27 576-602 2-28 (28)
8 PF03108 DBD_Tnp_Mut: MuDR fam 98.4 6.1E-07 1.3E-11 71.3 7.2 66 55-150 2-67 (67)
9 PF04434 SWIM: SWIM zinc finge 98.3 6.7E-07 1.5E-11 63.0 3.2 30 571-600 11-40 (40)
10 PF01610 DDE_Tnp_ISL3: Transpo 96.8 0.0014 3E-08 66.8 4.5 80 311-394 15-97 (249)
11 PF06782 UPF0236: Uncharacteri 94.7 2.6 5.6E-05 47.0 19.6 141 332-481 235-381 (470)
12 PF03106 WRKY: WRKY DNA -bindi 94.3 0.21 4.5E-06 38.4 6.7 56 81-160 4-59 (60)
13 PF13610 DDE_Tnp_IS240: DDE do 93.4 0.035 7.6E-07 51.0 1.3 81 292-376 1-81 (140)
14 PF00665 rve: Integrase core d 88.8 1.9 4.1E-05 37.8 7.7 75 292-367 6-81 (120)
15 smart00774 WRKY DNA binding do 85.8 1.5 3.2E-05 33.4 4.3 29 129-159 31-59 (59)
16 PF04937 DUF659: Protein of un 82.2 10 0.00023 35.2 9.3 106 288-395 29-138 (153)
17 PF03050 DDE_Tnp_IS66: Transpo 78.8 12 0.00027 38.3 9.6 43 346-394 113-155 (271)
18 PF04500 FLYWCH: FLYWCH zinc f 77.1 4.6 9.9E-05 30.7 4.4 25 129-159 38-62 (62)
19 PF04684 BAF1_ABF1: BAF1 / ABF 74.0 5.4 0.00012 42.9 5.3 55 59-140 24-78 (496)
20 PRK08561 rps15p 30S ribosomal 72.5 10 0.00023 34.6 6.0 87 178-266 31-143 (151)
21 PF13936 HTH_38: Helix-turn-he 64.6 4.5 9.7E-05 28.8 1.6 30 173-202 2-31 (44)
22 KOG3517 Transcription factor P 61.5 13 0.00029 36.5 4.7 79 173-263 18-98 (334)
23 COG3316 Transposase and inacti 59.3 19 0.00041 35.3 5.3 82 293-379 71-152 (215)
24 COG5431 Uncharacterized metal- 56.6 25 0.00055 29.8 4.9 29 561-595 42-75 (117)
25 PHA02517 putative transposase 55.3 82 0.0018 32.2 9.9 70 292-366 110-182 (277)
26 PF08069 Ribosomal_S13_N: Ribo 53.5 15 0.00032 28.1 2.8 30 178-207 31-60 (60)
27 PF00292 PAX: 'Paired box' dom 46.6 24 0.00053 31.4 3.6 80 172-263 14-95 (125)
28 COG3464 Transposase and inacti 38.6 79 0.0017 34.5 6.8 69 312-387 170-238 (402)
29 PF09713 A_thal_3526: Plant pr 35.8 47 0.001 24.9 3.1 26 182-207 3-28 (54)
30 PRK14702 insertion element IS2 34.3 1.5E+02 0.0034 30.1 7.8 72 292-364 87-163 (262)
31 COG4715 Uncharacterized conser 33.3 1.8E+02 0.0039 32.7 8.3 53 545-599 43-95 (587)
32 PF11433 DUF3198: Protein of u 32.2 56 0.0012 23.4 2.8 44 407-450 6-49 (51)
33 COG4279 Uncharacterized conser 31.3 21 0.00046 35.4 0.9 25 573-600 123-147 (266)
34 PF03462 PCRF: PCRF domain; I 31.2 1.3E+02 0.0029 26.4 5.8 37 67-103 66-102 (115)
35 PRK09409 IS2 transposase TnpB; 29.2 2.1E+02 0.0047 29.8 8.0 72 292-364 126-202 (301)
36 KOG2925 Predicted translation 28.6 25 0.00053 32.0 0.7 13 3-15 53-65 (167)
37 KOG0400 40S ribosomal protein 27.6 46 0.001 29.5 2.1 31 177-207 30-60 (151)
38 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 25.7 96 0.0021 22.9 3.2 28 175-202 4-31 (50)
39 PF02171 Piwi: Piwi domain; I 25.7 2.6E+02 0.0057 28.9 8.0 96 294-390 79-199 (302)
40 PF15299 ALS2CR8: Amyotrophic 22.7 76 0.0016 31.6 3.0 19 121-139 70-88 (225)
41 COG5470 Uncharacterized conser 22.4 45 0.00098 28.0 1.1 29 49-77 46-74 (96)
42 COG5216 Uncharacterized conser 20.2 44 0.00095 25.2 0.5 7 15-21 24-30 (67)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.7e-125 Score=1064.45 Aligned_cols=590 Identities=26% Similarity=0.497 Sum_probs=514.8
Q ss_pred cCCCCCCCCCCCCccCCHHHHHHHHHHHHhhcCcEEEEeeeeecCCC-eeEEEEEeeccccccccCcCC-C---------
Q 005579 49 LSSEVVFTPYVGQIFKSDDEAFEYYSNFARKNGFSIRKARSTESQNL-GIYRRDFVCYRSGFNQPRKKA-N--------- 117 (690)
Q Consensus 49 ~~~~~~~~P~vG~~F~S~eea~~fy~~yA~~~GF~vr~~~s~~~~~~-~~~~~~~~C~r~G~~~~~~~~-~--------- 117 (690)
.+.+...+|.+||+|+|+|||++||+.||+.+||+||+.++++++.+ +++.++|+|+|+|+++.+.+. +
T Consensus 66 ~~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~ 145 (846)
T PLN03097 66 FKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQ 145 (846)
T ss_pred ccCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCccccccccccccccccc
Confidence 45677889999999999999999999999999999999999887754 788999999999987543210 0
Q ss_pred --CCCCCCCCcccccccceeEEEEeeecCcccEEEEEeecCcCCCCCCCcccccccccccCCHHHHHHHHHHhhcCCChh
Q 005579 118 --VEHPRDRKSVRCGCDAKLYLTKEIVDGVTQWYVSQFSNVHNHELLEDDQVRMLPAYRKIQEADQERILLLSKAGFPVN 195 (690)
Q Consensus 118 --~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH~l~~~~~~~~l~s~R~l~~~~~~~i~~l~~~gi~~~ 195 (690)
...+++|+.+||||||+|+|++. ..|+|+|+.|+.+|||||.++..+ + +.++
T Consensus 146 ~~~~~~~rR~~tRtGC~A~m~Vk~~---~~gkW~V~~fv~eHNH~L~p~~~~---------~--------------~~~r 199 (846)
T PLN03097 146 DPENGTGRRSCAKTDCKASMHVKRR---PDGKWVIHSFVKEHNHELLPAQAV---------S--------------EQTR 199 (846)
T ss_pred CcccccccccccCCCCceEEEEEEc---CCCeEEEEEEecCCCCCCCCcccc---------c--------------hhhh
Confidence 01123456789999999999875 458999999999999999876432 1 1233
Q ss_pred HHHHHHHHhcCCCCCCCCcccccchhhHHHhhhhhhhhhhhhhhcccchHHHHHHHHHhhhcCCCCeEEEEeecCcccee
Q 005579 196 RIVKVLELEKGVQPGQLPFIEKDVRNFVRTCKKTVQENDALLTEKRENDTLELLEACKNMAERDVDFVYDYTTDENEKVE 275 (690)
Q Consensus 196 ~I~~~l~~~~g~~~~~~~~t~~Di~N~~~~~rk~~~~~~~~~~~~~~~d~~~ll~~~~~~~~~np~~~~~~~~d~~~~~~ 275 (690)
+++..+....+ ...+++.+..|..|...+.|+. .+..+|++.|++||+++|.+||+|+|++++|++|+++
T Consensus 200 ~~~~~~~~~~~-~~~~v~~~~~d~~~~~~~~r~~---------~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~ 269 (846)
T PLN03097 200 KMYAAMARQFA-EYKNVVGLKNDSKSSFDKGRNL---------GLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLK 269 (846)
T ss_pred hhHHHHHhhhh-ccccccccchhhcchhhHHHhh---------hcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCee
Confidence 34444443333 2456777788888877665543 2367899999999999999999999999999999999
Q ss_pred eeeecccccHHHHhhcCCEEEEcccccccccCceeeeEEEEeccCceEEEEEeeccCCCcchHHHHHHHHHHHhcCCCCe
Q 005579 276 NIAWSFGDSIRAYTLFGDVVTFDTSYRSITYGLLLGVWFGMDNHGKAIFFGCVLLQDESTHSFAWALQTFVRFMRGRHPQ 355 (690)
Q Consensus 276 ~if~~~~~~~~~~~~f~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~ 355 (690)
+|||+|+.++.+|.+|||||+||+||+||+|++||++|+|||||+++++|||||+.+|+.+||.|+|++|+++|++++|+
T Consensus 270 niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~ 349 (846)
T PLN03097 270 NLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPK 349 (846)
T ss_pred eEEeccHHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecccchHHHHHHHhhCCCCceecccchhhhhhhhhhhcccccchhhHHHHHhhh-cCCCCHHHHHHHHHHHHhhcCCc
Q 005579 356 TILTDIDLGLRDSIARELPNTKHVVCIWHILSKLSSWFSSLLGSQYEEFKAEFDML-CRLESVEDFEHQWNHFVARFGLV 434 (690)
Q Consensus 356 ~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~l-~~~~t~~eFe~~w~~l~~~~~~~ 434 (690)
+||||+|.+|++||++|||+|.|++|.|||++|+.++++... ...+.|..+|+.| +.+.+++||+..|..|+++|+|+
T Consensus 350 tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~-~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~ 428 (846)
T PLN03097 350 VIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVI-KQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELK 428 (846)
T ss_pred eEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHh-hhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccc
Confidence 999999999999999999999999999999999999998754 3457899999885 56899999999999999999999
Q ss_pred ccHHHHHHHHhhhhhhhhhcccccccccccccCCcchHHHHhhhcCCCCCHHHHHHHHHH-h--hhchhhhcc----ccc
Q 005579 435 SDKHVALLFSYRAFWLFSYIRGYFLARMMTVEFSQSVDTFFKKILSEQTCLQVFFEQVCA-A--AFGNSTREG----VQY 507 (690)
Q Consensus 435 ~~~~l~~~~~~r~~W~~~y~~~~~~~g~~t~~~~Es~n~~lk~~~~~~~~l~~f~~~~~~-~--~~~~~~~~~----~~~ 507 (690)
+++||+.||+.|++||++|+++.|++||.||+++||+|++|+++++++++|..|+++|+. + .+.++.+.+ ...
T Consensus 429 ~n~WL~~LY~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~ 508 (846)
T PLN03097 429 EDEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQ 508 (846)
T ss_pred ccHHHHHHHHhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCC
Confidence 999999999999999999999999999999999999999999999999999999999998 2 233333332 345
Q ss_pred eeecccChHHHHHHhhchHHHHHHHHHHHHHhhcceEEEee-CC---eEEEEEEEeeCCcEEEEEecCCceEEeecCCcc
Q 005579 508 VHIKTCMPIEEHARSILTPYAFRVLQHEIVLSTQYATTEMT-NG---SYLVRHYKKMDGEYLVIWIPEDEQIHCSCKEFE 583 (690)
Q Consensus 508 ~~~~~~~pie~~~~~vyT~~~f~~~q~el~~s~~~~v~~~~-~~---~y~V~~~~~~~~~~~V~~~~~~~~~~CsC~~fe 583 (690)
+.+++++|||+||+.+|||.||++||+|+..+..|.+.... +| +|.|....+ ++.|.|.+++..+.++|+|++||
T Consensus 509 P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~-~~~~~V~~d~~~~~v~CsC~kFE 587 (846)
T PLN03097 509 PALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEK-NQDFTVTWNQTKLEVSCICRLFE 587 (846)
T ss_pred cccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecC-CCcEEEEEecCCCeEEeeccCee
Confidence 68899999999999999999999999999999999876543 33 688876554 56899999999999999999999
Q ss_pred ccCccchhHHHHHhhcCcccCCCcchhhhhccccCCcccCCCCC--CCCchHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Q 005579 584 HSGILCRHSLRVLVVKNYFQLPEKYLLLRWRLENSLVTMEGPNP--QSSSDECAQAFHSLAAALLTESMISKERFSYVHK 661 (690)
Q Consensus 584 ~~GipC~Hil~Vl~~~~i~~iP~~yil~RWtk~a~~~~~~~~~~--~~~~~~r~~~l~~~~~~~~~~a~~s~e~~~~~~~ 661 (690)
+.||||+|||+||.++||.+||++|||+||||+|+.....+... ..+...||+.|++.+.+++.+|+.|.|.|..|++
T Consensus 588 ~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdAK~~~~~~~~~~~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~ 667 (846)
T PLN03097 588 YKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDAKSRHLLGEESEQVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFR 667 (846)
T ss_pred cCccchhhHHHHHhhcCcccCchhhhhhhchhhhhhcccCccccccccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 99999999999999999999999999999999999876544322 2345679999999999999999999999999999
Q ss_pred HHHHHHHhhccCCcc
Q 005579 662 ELTGLLDHVRNMPET 676 (690)
Q Consensus 662 ~l~~l~~~i~~~~~~ 676 (690)
+|++++++++.|.-+
T Consensus 668 ~L~e~~~~~~~~~n~ 682 (846)
T PLN03097 668 ALEEAFGNCISMNNS 682 (846)
T ss_pred HHHHHHHHHHHhhcc
Confidence 999999999887443
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=7.3e-22 Score=169.19 Aligned_cols=90 Identities=28% Similarity=0.590 Sum_probs=86.7
Q ss_pred ccccccccCceeee---EEEEeccCceEEEEEeeccCCCcchHHHHHHHHHHHhcCCCCeEEecccchHHHHHHHhhCCC
Q 005579 299 TSYRSITYGLLLGV---WFGMDNHGKAIFFGCVLLQDESTHSFAWALQTFVRFMRGRHPQTILTDIDLGLRDSIARELPN 375 (690)
Q Consensus 299 ~Ty~tn~y~~pl~~---~~gvd~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~ 375 (690)
+||+||+| +|++. ++|+|++|+.+|+||+++.+|+.++|.|+|+.+++.++.. |.+||||++.|+.+||+++||+
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 Cceecccchhhhhhh
Q 005579 376 TKHVVCIWHILSKLS 390 (690)
Q Consensus 376 a~h~lC~~Hi~~n~~ 390 (690)
+.|++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999984
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=8.5e-20 Score=155.50 Aligned_cols=90 Identities=37% Similarity=0.682 Sum_probs=79.2
Q ss_pred HHHHHHHhhcCcEEEEeeeeec-CCCeeEEEEEeeccccccccCcCCCCCCCCCCCcccccccceeEEEEeeecCcccEE
Q 005579 71 EYYSNFARKNGFSIRKARSTES-QNLGIYRRDFVCYRSGFNQPRKKANVEHPRDRKSVRCGCDAKLYLTKEIVDGVTQWY 149 (690)
Q Consensus 71 ~fy~~yA~~~GF~vr~~~s~~~-~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~ 149 (690)
+||+.||+.+||+|++.+++++ .++.++++.|+|+++|.++.+...+...++++++.+|||||+|.+++.. .|.|.
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 5999999999999999998887 4458899999999999998877654567788999999999999999752 58999
Q ss_pred EEEeecCcCCCCCC
Q 005579 150 VSQFSNVHNHELLE 163 (690)
Q Consensus 150 V~~~~~~HNH~l~~ 163 (690)
|+.+..+|||+|.|
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=99.75 E-value=3.5e-19 Score=191.24 Aligned_cols=255 Identities=18% Similarity=0.221 Sum_probs=192.4
Q ss_pred ccccccccCCHHHHHHHHHHhhcCCChhHHHHHHHHhcCCCCCCCCcccccchhhHHHhhhhhhhhhhhhhhcccchHHH
Q 005579 168 RMLPAYRKIQEADQERILLLSKAGFPVNRIVKVLELEKGVQPGQLPFIEKDVRNFVRTCKKTVQENDALLTEKRENDTLE 247 (690)
Q Consensus 168 ~~l~s~R~l~~~~~~~i~~l~~~gi~~~~I~~~l~~~~g~~~~~~~~t~~Di~N~~~~~rk~~~~~~~~~~~~~~~d~~~ 247 (690)
.+++.+++..+.....|..|.-.|+++++|.++|+.-.|. .++....|.++.......
T Consensus 91 ~ll~~y~r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~----~~~S~s~vSri~~~~~~~------------------ 148 (381)
T PF00872_consen 91 QLLPKYQRREDSLEELIISLYLKGVSTRDIEEALEELYGE----VAVSKSTVSRITKQLDEE------------------ 148 (381)
T ss_pred cccchhhhhhhhhhhhhhhhhccccccccccchhhhhhcc----cccCchhhhhhhhhhhhh------------------
Confidence 3456677777788888888999999999999999877661 235555555543332211
Q ss_pred HHHHHHhhhcCCCCeEEEEeecCccceeeeeecccccHHHHhhcCCEEEEccccccccc-----CceeeeEEEEeccCce
Q 005579 248 LLEACKNMAERDVDFVYDYTTDENEKVENIAWSFGDSIRAYTLFGDVVTFDTSYRSITY-----GLLLGVWFGMDNHGKA 322 (690)
Q Consensus 248 ll~~~~~~~~~np~~~~~~~~d~~~~~~~if~~~~~~~~~~~~f~dvl~~D~Ty~tn~y-----~~pl~~~~gvd~~~~~ 322 (690)
+.-++....++.. -++|++|++|.+-+. +.++++++|||.+|+.
T Consensus 149 -~~~w~~R~L~~~~------------------------------y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r 197 (381)
T PF00872_consen 149 -VEAWRNRPLESEP------------------------------YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRR 197 (381)
T ss_pred -HHHHhhhcccccc------------------------------ccceeeeeeecccccccccccchhhhhhhhhccccc
Confidence 1112211111100 146899999987552 4678999999999999
Q ss_pred EEEEEeeccCCCcchHHHHHHHHHHHhcCCCCeEEecccchHHHHHHHhhCCCCceecccchhhhhhhhhhhcccccchh
Q 005579 323 IFFGCVLLQDESTHSFAWALQTFVRFMRGRHPQTILTDIDLGLRDSIARELPNTKHVVCIWHILSKLSSWFSSLLGSQYE 402 (690)
Q Consensus 323 ~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~ 402 (690)
.++|+.+...|+.++|.-+|+.|++- |-..|..||+|..+|+..||.++||++.++.|.+|+++|+.+++.. +..+
T Consensus 198 ~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~---k~~~ 273 (381)
T PF00872_consen 198 EVLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK---KDRK 273 (381)
T ss_pred ceeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccccccccccchhhhhheechhhhhcccccc---ccch
Confidence 99999999999999999999998775 3356999999999999999999999999999999999999998765 4557
Q ss_pred hHHHHHhhhcCCCCHHHHHHHHHHHHhhcCCcccHHHHHHHHhh-hhhhhhhcccccccccccccCCcchHHHHhhhc
Q 005579 403 EFKAEFDMLCRLESVEDFEHQWNHFVARFGLVSDKHVALLFSYR-AFWLFSYIRGYFLARMMTVEFSQSVDTFFKKIL 479 (690)
Q Consensus 403 ~~~~~~~~l~~~~t~~eFe~~w~~l~~~~~~~~~~~l~~~~~~r-~~W~~~y~~~~~~~g~~t~~~~Es~n~~lk~~~ 479 (690)
.+..+|+.++.+.+.++....++.+.+++........+.+-... +.|...-++...+--+.|||.+|++|+.+|+..
T Consensus 274 ~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~ 351 (381)
T PF00872_consen 274 EVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRT 351 (381)
T ss_pred hhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhc
Confidence 88999999999999999999999999988765554444332211 122222245555567889999999999999754
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=99.35 E-value=5.1e-12 Score=106.38 Aligned_cols=91 Identities=22% Similarity=0.334 Sum_probs=74.9
Q ss_pred cCCHHHHHHHHHHHHhhcCcEEEEeeeeecCCCeeEEEEEeeccccccccCcCCC--------------------CCCCC
Q 005579 63 FKSDDEAFEYYSNFARKNGFSIRKARSTESQNLGIYRRDFVCYRSGFNQPRKKAN--------------------VEHPR 122 (690)
Q Consensus 63 F~S~eea~~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~--------------------~~~~r 122 (690)
|++.+|...|++..+...||.|++.+|..++ +.|.|--+|.++.+.... .....
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~k------i~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k 74 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKK------IVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKK 74 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCce------EEEEEecCCCcccccccccccccccccccccccccccccccCC
Confidence 8899999999999999999999999998765 789998888776554420 01122
Q ss_pred CCCcccccccceeEEEEeeecCcccEEEEEeecCcCCCC
Q 005579 123 DRKSVRCGCDAKLYLTKEIVDGVTQWYVSQFSNVHNHEL 161 (690)
Q Consensus 123 ~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH~l 161 (690)
...+.++.|||+|++.... ..+.|.|..+++.|||||
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 3456789999999999875 578999999999999996
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.28 E-value=7.5e-11 Score=124.28 Aligned_cols=262 Identities=15% Similarity=0.119 Sum_probs=178.8
Q ss_pred ccccccCCHHHHHHHHHHhhcCCChhHHHHHHHHhcCCCCCCCCcccccchhhHHHhhhhhhhhhhhhhhcccchHHHHH
Q 005579 170 LPAYRKIQEADQERILLLSKAGFPVNRIVKVLELEKGVQPGQLPFIEKDVRNFVRTCKKTVQENDALLTEKRENDTLELL 249 (690)
Q Consensus 170 l~s~R~l~~~~~~~i~~l~~~gi~~~~I~~~l~~~~g~~~~~~~~t~~Di~N~~~~~rk~~~~~~~~~~~~~~~d~~~ll 249 (690)
+..+++........|..+...|+++++|-..++...+. ++.+.-+..+. ..+.
T Consensus 79 ~~~~~r~~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~-----~~s~~~iS~~~----------------------~~~~ 131 (379)
T COG3328 79 IERYQRRERALDLPVLSMYAKGVTTREIEALLEELYGH-----KVSPSVISVVT----------------------DRLD 131 (379)
T ss_pred chhhHhhhhhHHHHHHHHHHcCCcHHHHHHHHHHhhCc-----ccCHHHhhhHH----------------------HHHH
Confidence 34445555666677888999999999999999876552 22222222221 1222
Q ss_pred HHHHhhhcCCCCeEEEEeecCccceeeeeecccccHHHHhhcCCEEEEcccccccc--cCceeeeEEEEeccCceEEEEE
Q 005579 250 EACKNMAERDVDFVYDYTTDENEKVENIAWSFGDSIRAYTLFGDVVTFDTSYRSIT--YGLLLGVWFGMDNHGKAIFFGC 327 (690)
Q Consensus 250 ~~~~~~~~~np~~~~~~~~d~~~~~~~if~~~~~~~~~~~~f~dvl~~D~Ty~tn~--y~~pl~~~~gvd~~~~~~~~~~ 327 (690)
+.+...+.+-. . . -.+|++|++|.+-+ -+..+++++||+.+|+..++|+
T Consensus 132 e~v~~~~~r~l-~--~--------------------------~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~ 182 (379)
T COG3328 132 EKVKAWQNRPL-G--D--------------------------YPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGI 182 (379)
T ss_pred HHHHHHHhccc-c--C--------------------------ceEEEEecceeehhhhhhheeeeeeccCcccchhhhce
Confidence 33333332211 0 0 14689999999877 5688899999999999999999
Q ss_pred eeccCCCcchHHHHHHHHHHHhcCCCCeEEecccchHHHHHHHhhCCCCceecccchhhhhhhhhhhcccccchhhHHHH
Q 005579 328 VLLQDESTHSFAWALQTFVRFMRGRHPQTILTDIDLGLRDSIARELPNTKHVVCIWHILSKLSSWFSSLLGSQYEEFKAE 407 (690)
Q Consensus 328 al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~ 407 (690)
.+-..|+ ..|.-+|..|+.. +-.....+++|..+++.+||..+||.+.++.|..|+.+|+.++... +..+....+
T Consensus 183 ~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~---k~~d~i~~~ 257 (379)
T COG3328 183 WVGVRES-KFWLSFLLDLKNR-GLSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPR---KDQDAVLSD 257 (379)
T ss_pred eeecccc-hhHHHHHHHHHhc-cccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhh---hhhHHHHhh
Confidence 9999999 7787566666554 2244567778999999999999999999999999999999987664 445677778
Q ss_pred HhhhcCCCCHHHHHHHHHHHHhhcCCcccHHHHHHHHhhh-hhhh-hhcccccccccccccCCcchHHHHhhhcCC--CC
Q 005579 408 FDMLCRLESVEDFEHQWNHFVARFGLVSDKHVALLFSYRA-FWLF-SYIRGYFLARMMTVEFSQSVDTFFKKILSE--QT 483 (690)
Q Consensus 408 ~~~l~~~~t~~eFe~~w~~l~~~~~~~~~~~l~~~~~~r~-~W~~-~y~~~~~~~g~~t~~~~Es~n~~lk~~~~~--~~ 483 (690)
+..++.+.+.++-...|..+.+.+......-+..+....+ .|.- .|.+.. .--+.|||..|++|+.+++.... ..
T Consensus 258 ~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F~~fp~~~-r~~i~ttN~IE~~n~~ir~~~~~~~~f 336 (379)
T COG3328 258 LRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLPFFAFPSEI-RKIIYTTNAIESLNKLIRRRTKVVGIF 336 (379)
T ss_pred hhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcccccCcHHH-HhHhhcchHHHHHHHHHHHHHhhhccC
Confidence 8889999999999999999887665444433333222111 1211 111111 12467999999999988865432 44
Q ss_pred CHHHHHHHHH
Q 005579 484 CLQVFFEQVC 493 (690)
Q Consensus 484 ~l~~f~~~~~ 493 (690)
+-.+++..+.
T Consensus 337 pn~~sv~k~~ 346 (379)
T COG3328 337 PNEESVEKLV 346 (379)
T ss_pred CCHHHHHHHH
Confidence 4455555443
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.91 E-value=5.2e-10 Score=71.56 Aligned_cols=27 Identities=41% Similarity=0.843 Sum_probs=25.2
Q ss_pred EeecCCccccCccchhHHHHHhhcCcc
Q 005579 576 HCSCKEFEHSGILCRHSLRVLVVKNYF 602 (690)
Q Consensus 576 ~CsC~~fe~~GipC~Hil~Vl~~~~i~ 602 (690)
+|+|++||..||||+|+|+|+.+.|+.
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~~ 28 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGLS 28 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCCC
Confidence 799999999999999999999988863
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=98.45 E-value=6.1e-07 Score=71.27 Aligned_cols=66 Identities=27% Similarity=0.374 Sum_probs=55.5
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHhhcCcEEEEeeeeecCCCeeEEEEEeeccccccccCcCCCCCCCCCCCcccccccce
Q 005579 55 FTPYVGQIFKSDDEAFEYYSNFARKNGFSIRKARSTESQNLGIYRRDFVCYRSGFNQPRKKANVEHPRDRKSVRCGCDAK 134 (690)
Q Consensus 55 ~~P~vG~~F~S~eea~~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~ 134 (690)
+...+||.|+|.+|+..++..||..+||.++..++.+. ++..+|.. .||||+
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~------r~~~~C~~----------------------~~C~Wr 53 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKK------RYRAKCKD----------------------KGCPWR 53 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCE------EEEEEEcC----------------------CCCCEE
Confidence 45689999999999999999999999999999888754 57899962 359999
Q ss_pred eEEEEeeecCcccEEE
Q 005579 135 LYLTKEIVDGVTQWYV 150 (690)
Q Consensus 135 i~i~~~~~~~~~~w~V 150 (690)
|++++.. +.+.|.|
T Consensus 54 v~as~~~--~~~~~~I 67 (67)
T PF03108_consen 54 VRASKRK--RSDTFQI 67 (67)
T ss_pred EEEEEcC--CCCEEEC
Confidence 9999864 5677775
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=98.27 E-value=6.7e-07 Score=62.99 Aligned_cols=30 Identities=40% Similarity=0.693 Sum_probs=26.5
Q ss_pred CCceEEeecCCccccCccchhHHHHHhhcC
Q 005579 571 EDEQIHCSCKEFEHSGILCRHSLRVLVVKN 600 (690)
Q Consensus 571 ~~~~~~CsC~~fe~~GipC~Hil~Vl~~~~ 600 (690)
.....+|+|..|+..|.||+|+++|+...|
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 356899999999999999999999997654
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=96.77 E-value=0.0014 Score=66.78 Aligned_cols=80 Identities=14% Similarity=0.164 Sum_probs=59.8
Q ss_pred eeEEEEec--cCceEEEEEeeccCCCcchHHHHHHHH-HHHhcCCCCeEEecccchHHHHHHHhhCCCCceecccchhhh
Q 005579 311 GVWFGMDN--HGKAIFFGCVLLQDESTHSFAWALQTF-VRFMRGRHPQTILTDIDLGLRDSIARELPNTKHVVCIWHILS 387 (690)
Q Consensus 311 ~~~~gvd~--~~~~~~~~~al~~~Et~es~~w~l~~f-~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~ 387 (690)
+..+.+|. ++..++ .++.+-+.+++.-+|..+ -.. ....+++|.+|...+...||++.||+|.+..-.|||++
T Consensus 15 y~t~~~d~~~~~~~il---~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk 90 (249)
T PF01610_consen 15 YVTVVVDLDTDTGRIL---DILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVK 90 (249)
T ss_pred eeEEEEECccCCceEE---EEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccccccccccccccchhhh
Confidence 44455555 444333 478888888876665554 222 34578999999999999999999999999999999999
Q ss_pred hhhhhhh
Q 005579 388 KLSSWFS 394 (690)
Q Consensus 388 n~~~~~~ 394 (690)
++.+.+.
T Consensus 91 ~~~~al~ 97 (249)
T PF01610_consen 91 LANRALD 97 (249)
T ss_pred hhhhcch
Confidence 8876543
No 11
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=94.74 E-value=2.6 Score=47.05 Aligned_cols=141 Identities=11% Similarity=0.047 Sum_probs=82.5
Q ss_pred CCCcchHHHHHHHHHHHhcCCCC--eEEecccchHHHHHHHhhCCCCceecccchhhhhhhhhhhcccccchhhHHHHHh
Q 005579 332 DESTHSFAWALQTFVRFMRGRHP--QTILTDIDLGLRDSIARELPNTKHVVCIWHILSKLSSWFSSLLGSQYEEFKAEFD 409 (690)
Q Consensus 332 ~Et~es~~w~l~~f~~~~~~~~p--~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~~ 409 (690)
....+-|.-+.+.+-........ .++..|+...+++++. .||++.|.|..||+.+.+.+.++.. ++....++
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~-----~~~~~~~~ 308 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD-----PELKEKIR 308 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC-----hHHHHHHH
Confidence 34445565555555544432222 4567899999988776 9999999999999999999877542 23444444
Q ss_pred hhcCCCCHHHHHHHHHHHHhhcCCcc-cHHHHH-HHHhhhhhhh--hhcccccccccccccCCcchHHHHhhhcCC
Q 005579 410 MLCRLESVEDFEHQWNHFVARFGLVS-DKHVAL-LFSYRAFWLF--SYIRGYFLARMMTVEFSQSVDTFFKKILSE 481 (690)
Q Consensus 410 ~l~~~~t~~eFe~~w~~l~~~~~~~~-~~~l~~-~~~~r~~W~~--~y~~~~~~~g~~t~~~~Es~n~~lk~~~~~ 481 (690)
..+...+...++...+.+........ .+-+.. .-.....|-. +|... .|+......|+.+..+...++.
T Consensus 309 ~al~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i~~y~~~---~~~~g~g~ee~~~~~~s~RmK~ 381 (470)
T PF06782_consen 309 KALKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGIKPYRER---EGLRGIGAEESVSHVLSYRMKS 381 (470)
T ss_pred HHHHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHhhhhhhc---cCCCccchhhhhhhHHHHHhcC
Confidence 55555667777777776655332211 111111 1122334432 23221 3333444478888888765553
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=94.28 E-value=0.21 Score=38.35 Aligned_cols=56 Identities=21% Similarity=0.376 Sum_probs=36.3
Q ss_pred CcEEEEeeeeecCCCeeEEEEEeeccccccccCcCCCCCCCCCCCcccccccceeEEEEeeecCcccEEEEEeecCcCCC
Q 005579 81 GFSIRKARSTESQNLGIYRRDFVCYRSGFNQPRKKANVEHPRDRKSVRCGCDAKLYLTKEIVDGVTQWYVSQFSNVHNHE 160 (690)
Q Consensus 81 GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH~ 160 (690)
||.-|+--.+.-++...-+.+|.|+.. +|||+=.|.+.. +++.-.++....+|||+
T Consensus 4 gy~WRKYGqK~i~g~~~pRsYYrCt~~----------------------~C~akK~Vqr~~--~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 4 GYRWRKYGQKNIKGSPYPRSYYRCTHP----------------------GCPAKKQVQRSA--DDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SS-EEEEEEEEETTTTCEEEEEEEECT----------------------TEEEEEEEEEET--TCCCEEEEEEES--SS-
T ss_pred CCchhhccCcccCCCceeeEeeecccc----------------------ChhheeeEEEec--CCCCEEEEEEeeeeCCC
Confidence 666665444333444455678889652 699998888764 35678889999999997
No 13
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=93.40 E-value=0.035 Score=51.01 Aligned_cols=81 Identities=23% Similarity=0.320 Sum_probs=66.4
Q ss_pred CCEEEEcccccccccCceeeeEEEEeccCceEEEEEeeccCCCcchHHHHHHHHHHHhcCCCCeEEecccchHHHHHHHh
Q 005579 292 GDVVTFDTSYRSITYGLLLGVWFGMDNHGKAIFFGCVLLQDESTHSFAWALQTFVRFMRGRHPQTILTDIDLGLRDSIAR 371 (690)
Q Consensus 292 ~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~~l~~Ai~~ 371 (690)
|+.+.+|=||..-+ +--.+.+..||.+|+ ++++-+...-+..+=..||...++..+ ..|..|+||+..+...|+++
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 67899999997744 334567889999999 777888888888877787777776654 78999999999999999999
Q ss_pred hCCCC
Q 005579 372 ELPNT 376 (690)
Q Consensus 372 vfP~a 376 (690)
.+|..
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=88.83 E-value=1.9 Score=37.82 Aligned_cols=75 Identities=19% Similarity=0.179 Sum_probs=53.6
Q ss_pred CCEEEEcccccc-cccCceeeeEEEEeccCceEEEEEeeccCCCcchHHHHHHHHHHHhcCCCCeEEecccchHHHH
Q 005579 292 GDVVTFDTSYRS-ITYGLLLGVWFGMDNHGKAIFFGCVLLQDESTHSFAWALQTFVRFMRGRHPQTILTDIDLGLRD 367 (690)
Q Consensus 292 ~dvl~~D~Ty~t-n~y~~pl~~~~gvd~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~~l~~ 367 (690)
+.++.+|.+... ...+...+.++.+|..-.... ++.+...++.+.+..+|.......++..|++|+||+..++..
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFIY-AFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTEEE-EEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHS
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCcEE-EEEeecccccccccccccccccccccccceeccccccccccc
Confidence 467888888544 445557888888888776554 566777668887777777666666665699999999998863
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=85.84 E-value=1.5 Score=33.44 Aligned_cols=29 Identities=21% Similarity=0.288 Sum_probs=22.5
Q ss_pred ccccceeEEEEeeecCcccEEEEEeecCcCC
Q 005579 129 CGCDAKLYLTKEIVDGVTQWYVSQFSNVHNH 159 (690)
Q Consensus 129 ~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH 159 (690)
.||||+=.|.+.. +++.-.++....+|||
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 4699987777653 3467788888999998
No 16
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=82.22 E-value=10 Score=35.23 Aligned_cols=106 Identities=10% Similarity=0.049 Sum_probs=71.9
Q ss_pred HhhcCCEEEEcccccccccCceeeeEEEEeccCceEEEEEeecc-CCCcchHHHHHHHHHHHhcCCCCeEEecccchHHH
Q 005579 288 YTLFGDVVTFDTSYRSITYGLLLGVWFGMDNHGKAIFFGCVLLQ-DESTHSFAWALQTFVRFMRGRHPQTILTDIDLGLR 366 (690)
Q Consensus 288 ~~~f~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~-~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~~l~ 366 (690)
+...|=-|..|+= ++..+.+|+.|+.....|..++-..-.-. ..+.+.+.-+|+...+.+|......||||....++
T Consensus 29 w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~~~~ 106 (153)
T PF04937_consen 29 WKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNASNMK 106 (153)
T ss_pred HHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCchhHH
Confidence 3344444566655 45566778887777776665543322211 14566666666666666776777889999999988
Q ss_pred HHH---HhhCCCCceecccchhhhhhhhhhhc
Q 005579 367 DSI---ARELPNTKHVVCIWHILSKLSSWFSS 395 (690)
Q Consensus 367 ~Ai---~~vfP~a~h~lC~~Hi~~n~~~~~~~ 395 (690)
.|- .+-+|.....-|.-|-+.-+.+.+..
T Consensus 107 ~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 107 KAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred HHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 884 46689888889999998887776654
No 17
>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=78.83 E-value=12 Score=38.27 Aligned_cols=43 Identities=14% Similarity=0.230 Sum_probs=31.5
Q ss_pred HHHhcCCCCeEEecccchHHHHHHHhhCCCCceecccchhhhhhhhhhh
Q 005579 346 VRFMRGRHPQTILTDIDLGLRDSIARELPNTKHVVCIWHILSKLSSWFS 394 (690)
Q Consensus 346 ~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~ 394 (690)
.+.+++ ..-+++||+-.+-.. +..+.|+.|.-|+.|.+.+-..
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 345999999887654 3388999999999999986554
No 18
>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=77.13 E-value=4.6 Score=30.68 Aligned_cols=25 Identities=32% Similarity=0.456 Sum_probs=10.3
Q ss_pred ccccceeEEEEeeecCcccEEEEEeecCcCC
Q 005579 129 CGCDAKLYLTKEIVDGVTQWYVSQFSNVHNH 159 (690)
Q Consensus 129 ~gCpa~i~i~~~~~~~~~~w~V~~~~~~HNH 159 (690)
.+|+|++.+.. +.-.|.....+|||
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 57999998761 22356666689999
No 19
>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=74.05 E-value=5.4 Score=42.94 Aligned_cols=55 Identities=15% Similarity=0.260 Sum_probs=46.2
Q ss_pred CCCccCCHHHHHHHHHHHHhhcCcEEEEeeeeecCCCeeEEEEEeeccccccccCcCCCCCCCCCCCcccccccceeEEE
Q 005579 59 VGQIFKSDDEAFEYYSNFARKNGFSIRKARSTESQNLGIYRRDFVCYRSGFNQPRKKANVEHPRDRKSVRCGCDAKLYLT 138 (690)
Q Consensus 59 vG~~F~S~eea~~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~r~s~r~gCpa~i~i~ 138 (690)
.+..|+++++-|..++.|.....--|..+.|-+++ ..+|.|... .|||+|.+.
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk-----hftfachlk----------------------~c~fkills 76 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK-----HFTFACHLK----------------------NCPFKILLS 76 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeeccccccc-----ceEEEeecc----------------------CCCceeeee
Confidence 36689999999999999999998888888887765 478999763 399999988
Q ss_pred Ee
Q 005579 139 KE 140 (690)
Q Consensus 139 ~~ 140 (690)
..
T Consensus 77 y~ 78 (496)
T PF04684_consen 77 YC 78 (496)
T ss_pred ec
Confidence 64
No 20
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=72.49 E-value=10 Score=34.62 Aligned_cols=87 Identities=25% Similarity=0.355 Sum_probs=55.8
Q ss_pred HHHHHHHHHHhhcCCChhHHHHHHHHhcCCCC----------------CCCCcccccchhhHHHhhhh---hhhhh----
Q 005579 178 EADQERILLLSKAGFPVNRIVKVLELEKGVQP----------------GQLPFIEKDVRNFVRTCKKT---VQEND---- 234 (690)
Q Consensus 178 ~~~~~~i~~l~~~gi~~~~I~~~l~~~~g~~~----------------~~~~~t~~Di~N~~~~~rk~---~~~~~---- 234 (690)
++..+.|..|.+.|.+|++|=-+|+.++|+.. +-.|-.+.|++|+..+.... ++.+-
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 55677889999999999999999999997621 12244557888887654321 11110
Q ss_pred ---hhhhhcccchHHHHHHHHHhhhcCCCCeEEEE
Q 005579 235 ---ALLTEKRENDTLELLEACKNMAERDVDFVYDY 266 (690)
Q Consensus 235 ---~~~~~~~~~d~~~ll~~~~~~~~~np~~~~~~ 266 (690)
.++ ...+-...|+.|+++...--|+|.|.-
T Consensus 111 skRgL~--~~~skrrRLl~Yyk~~~~LP~~WkY~~ 143 (151)
T PRK08561 111 NKRGLQ--LIESKIRRLVKYYKRTGVLPADWRYSP 143 (151)
T ss_pred hHHHHH--HHHHHHHHHHHHHHhcCCCCCCCcCCH
Confidence 000 012345668888887777777887753
No 21
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=64.59 E-value=4.5 Score=28.82 Aligned_cols=30 Identities=23% Similarity=0.488 Sum_probs=15.0
Q ss_pred cccCCHHHHHHHHHHhhcCCChhHHHHHHH
Q 005579 173 YRKIQEADQERILLLSKAGFPVNRIVKVLE 202 (690)
Q Consensus 173 ~R~l~~~~~~~i~~l~~~gi~~~~I~~~l~ 202 (690)
+++|+.+++..|..+.+.|.+.++|.+.|.
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 467999999999999999999999987763
No 22
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=61.51 E-value=13 Score=36.45 Aligned_cols=79 Identities=20% Similarity=0.284 Sum_probs=53.2
Q ss_pred cccCCHHHHHHHHHHhhcCCChhHHHHHHHHhcCCCCCCCCcccccchhhHHHhhhh--hhhhhhhhhhcccchHHHHHH
Q 005579 173 YRKIQEADQERILLLSKAGFPVNRIVKVLELEKGVQPGQLPFIEKDVRNFVRTCKKT--VQENDALLTEKRENDTLELLE 250 (690)
Q Consensus 173 ~R~l~~~~~~~i~~l~~~gi~~~~I~~~l~~~~g~~~~~~~~t~~Di~N~~~~~rk~--~~~~~~~~~~~~~~d~~~ll~ 250 (690)
-|-|..+.+-.|.+|...|++|..|-..|+-.+|. +..++.++.+. +..+ +|-.-+.+-..-.+.+
T Consensus 18 GRPLPna~RlrIVELarlGiRPCDISRQLrvSHGC-----------VSKILaRy~EtGsIlPG-aIGGSkPRVTTP~VV~ 85 (334)
T KOG3517|consen 18 GRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGC-----------VSKILARYNETGSILPG-AIGGSKPRVTTPKVVK 85 (334)
T ss_pred CccCcchhhhhHHHHHHcCCCccchhhhhhhccch-----------HHHHHHHhccCCccccc-ccCCCCCccCChhHHH
Confidence 46688888999999999999999999999988774 23333333321 1111 1101111224567899
Q ss_pred HHHhhhcCCCCeE
Q 005579 251 ACKNMAERDVDFV 263 (690)
Q Consensus 251 ~~~~~~~~np~~~ 263 (690)
|.+.++..||+.|
T Consensus 86 ~IR~~Kq~DPGIF 98 (334)
T KOG3517|consen 86 YIRSLKQRDPGIF 98 (334)
T ss_pred HHHHhhccCCcee
Confidence 9999999999965
No 23
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=59.28 E-value=19 Score=35.26 Aligned_cols=82 Identities=13% Similarity=0.175 Sum_probs=53.9
Q ss_pred CEEEEcccccccccCceeeeEEEEeccCceEEEEEeeccCCCcchHHHHHHHHHHHhcCCCCeEEecccchHHHHHHHhh
Q 005579 293 DVVTFDTSYRSITYGLLLGVWFGMDNHGKAIFFGCVLLQDESTHSFAWALQTFVRFMRGRHPQTILTDIDLGLRDSIARE 372 (690)
Q Consensus 293 dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~~l~~Ai~~v 372 (690)
+++-+|=||.+-+-+. .+....||..|++. .+-|...-+...=.-||..+++.. ..|.+|+||+.+....|+++.
T Consensus 71 ~~w~vDEt~ikv~gkw-~ylyrAid~~g~~L--d~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~~l 145 (215)
T COG3316 71 DSWRVDETYIKVNGKW-HYLYRAIDADGLTL--DVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALRKL 145 (215)
T ss_pred cceeeeeeEEeeccEe-eehhhhhccCCCeE--EEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHHhc
Confidence 4566666766522111 12334556665544 444555555555566677666665 789999999999999999999
Q ss_pred CCCCcee
Q 005579 373 LPNTKHV 379 (690)
Q Consensus 373 fP~a~h~ 379 (690)
-+...|+
T Consensus 146 ~~~~ehr 152 (215)
T COG3316 146 GSEVEHR 152 (215)
T ss_pred Ccchhee
Confidence 9866655
No 24
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=56.60 E-value=25 Score=29.82 Aligned_cols=29 Identities=24% Similarity=0.604 Sum_probs=19.8
Q ss_pred CCcEEEEEecCCceEEeecCCccc-----cCccchhHHHH
Q 005579 561 DGEYLVIWIPEDEQIHCSCKEFEH-----SGILCRHSLRV 595 (690)
Q Consensus 561 ~~~~~V~~~~~~~~~~CsC~~fe~-----~GipC~Hil~V 595 (690)
+..|.+. .-.|||.+|-. -.-||.|++.+
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 4456664 23899998872 34579999864
No 25
>PHA02517 putative transposase OrfB; Reviewed
Probab=55.35 E-value=82 Score=32.23 Aligned_cols=70 Identities=17% Similarity=0.103 Sum_probs=43.9
Q ss_pred CCEEEEcccccccccCceeeeEEEEeccCceEEEEEeeccCCCcchHHHHHHHHHHHhcCC-CC--eEEecccchHHH
Q 005579 292 GDVVTFDTSYRSITYGLLLGVWFGMDNHGKAIFFGCVLLQDESTHSFAWALQTFVRFMRGR-HP--QTILTDIDLGLR 366 (690)
Q Consensus 292 ~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~-~p--~~iitD~~~~l~ 366 (690)
.+++..|.||....- +-.++++.+|...+ .++|+.+...++.+.. +..|..++... .| ..|.||+.....
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-RIVGWRVSSSMDTDFV---LDALEQALWARGRPGGLIHHSDKGSQYV 182 (277)
T ss_pred CCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHH---HHHHHHHHHhcCCCcCcEeecccccccc
Confidence 478899999865433 34566777777665 4557777776766644 44554444322 33 466799987654
No 26
>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=53.52 E-value=15 Score=28.13 Aligned_cols=30 Identities=30% Similarity=0.407 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhhcCCChhHHHHHHHHhcCC
Q 005579 178 EADQERILLLSKAGFPVNRIVKVLELEKGV 207 (690)
Q Consensus 178 ~~~~~~i~~l~~~gi~~~~I~~~l~~~~g~ 207 (690)
++..+.|..|.+.|++|.+|=-+|+.++|+
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 556678899999999999999999998874
No 27
>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=46.58 E-value=24 Score=31.43 Aligned_cols=80 Identities=19% Similarity=0.260 Sum_probs=42.7
Q ss_pred ccccCCHHHHHHHHHHhhcCCChhHHHHHHHHhcCCCCCCCCcccccchhhHHHhhhh--hhhhhhhhhhcccchHHHHH
Q 005579 172 AYRKIQEADQERILLLSKAGFPVNRIVKVLELEKGVQPGQLPFIEKDVRNFVRTCKKT--VQENDALLTEKRENDTLELL 249 (690)
Q Consensus 172 s~R~l~~~~~~~i~~l~~~gi~~~~I~~~l~~~~g~~~~~~~~t~~Di~N~~~~~rk~--~~~~~~~~~~~~~~d~~~ll 249 (690)
.-|-|+.+.+..|..|...|++|..|...|.-.+| -|..++.++++. +..+. +-.....-....+.
T Consensus 14 nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~g-----------cVsKIl~Ry~eTGsi~Pg~-iGGskprv~tp~v~ 81 (125)
T PF00292_consen 14 NGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHG-----------CVSKILSRYRETGSIRPGP-IGGSKPRVATPEVV 81 (125)
T ss_dssp TTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HH-----------HHHHHHHHHHHHS-SS-----S----SSS-HCHH
T ss_pred CCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchh-----------HHHHHHHHHHHhcccCccc-ccCCCCCCCChHHH
Confidence 34668899999999999999999999988865544 244445444432 11110 00000111233466
Q ss_pred HHHHhhhcCCCCeE
Q 005579 250 EACKNMAERDVDFV 263 (690)
Q Consensus 250 ~~~~~~~~~np~~~ 263 (690)
.++...+.+||..|
T Consensus 82 ~~I~~~k~enP~if 95 (125)
T PF00292_consen 82 EKIEQYKRENPTIF 95 (125)
T ss_dssp HHHHHHHHH-TTS-
T ss_pred HHHHHHHhcCCCcc
Confidence 67777788899864
No 28
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.64 E-value=79 Score=34.53 Aligned_cols=69 Identities=12% Similarity=0.161 Sum_probs=49.0
Q ss_pred eEEEEeccCceEEEEEeeccCCCcchHHHHHHHHHHHhcCCCCeEEecccchHHHHHHHhhCCCCceecccchhhh
Q 005579 312 VWFGMDNHGKAIFFGCVLLQDESTHSFAWALQTFVRFMRGRHPQTILTDIDLGLRDSIARELPNTKHVVCIWHILS 387 (690)
Q Consensus 312 ~~~gvd~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~lC~~Hi~~ 387 (690)
.++.+|.+.... ..++.+=+.+++.-.|. ..+....+.|..|......+++++.||++.+.+=.||+.+
T Consensus 170 ~~i~~D~~~~~~---i~i~~~r~~~ti~~~l~----~~g~~~v~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~ 238 (402)
T COG3464 170 QTIAVDLDTRKV---IDILEGRSVRTLRRYLR----RGGSEQVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQ 238 (402)
T ss_pred EEEEEcCCCCce---eeecCCccHHHHHHHHH----hCCCcceeEEEccccHHHHHHHHHhCCChheeeeeeeeee
Confidence 445555553222 23566666665543333 2232367899999999999999999999999999999987
No 29
>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=35.77 E-value=47 Score=24.87 Aligned_cols=26 Identities=12% Similarity=0.073 Sum_probs=19.6
Q ss_pred HHHHHHhhcCCChhHHHHHHHHhcCC
Q 005579 182 ERILLLSKAGFPVNRIVKVLELEKGV 207 (690)
Q Consensus 182 ~~i~~l~~~gi~~~~I~~~l~~~~g~ 207 (690)
..|.....-.++..+++..|..+.++
T Consensus 3 ~lIErCl~~yMsk~E~v~~L~~~a~I 28 (54)
T PF09713_consen 3 NLIERCLQLYMSKEECVRALQKQANI 28 (54)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHcCC
Confidence 45666667788888999988877665
No 30
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=34.33 E-value=1.5e+02 Score=30.13 Aligned_cols=72 Identities=15% Similarity=-0.007 Sum_probs=46.9
Q ss_pred CCEEEEcccccccccCceeeeEEEEeccCceEEEEEeeccC-CCcchHHHHHHHHHHHh-c---CCCCeEEecccchH
Q 005579 292 GDVVTFDTSYRSITYGLLLGVWFGMDNHGKAIFFGCVLLQD-ESTHSFAWALQTFVRFM-R---GRHPQTILTDIDLG 364 (690)
Q Consensus 292 ~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~-Et~es~~w~l~~f~~~~-~---~~~p~~iitD~~~~ 364 (690)
..+++.|-||....-+.-++..+.+|.+.. .++|+++-.. .+.+...-+|+..++.. + ...|..|.||+-..
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 367888988866544446788888888877 6678888764 55555555555433332 2 23467888988553
No 31
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=33.34 E-value=1.8e+02 Score=32.71 Aligned_cols=53 Identities=17% Similarity=0.193 Sum_probs=31.3
Q ss_pred EEeeCCeEEEEEEEeeCCcEEEEEecCCceEEeecCCccccCccchhHHHHHhhc
Q 005579 545 TEMTNGSYLVRHYKKMDGEYLVIWIPEDEQIHCSCKEFEHSGILCRHSLRVLVVK 599 (690)
Q Consensus 545 ~~~~~~~y~V~~~~~~~~~~~V~~~~~~~~~~CsC~~fe~~GipC~Hil~Vl~~~ 599 (690)
+...++++.-.......--+.|+.........|+|.. ...| -|.|+.+|+...
T Consensus 43 i~~~g~~v~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~ 95 (587)
T COG4715 43 ITIRGGTVRAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEY 95 (587)
T ss_pred EeecCCeEEEEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHH
Confidence 3344555443332221112345555556678999998 4444 599999998653
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=32.21 E-value=56 Score=23.42 Aligned_cols=44 Identities=14% Similarity=0.088 Sum_probs=29.2
Q ss_pred HHhhhcCCCCHHHHHHHHHHHHhhcCCcccHHHHHHHHhhhhhh
Q 005579 407 EFDMLCRLESVEDFEHQWNHFVARFGLVSDKHVALLFSYRAFWL 450 (690)
Q Consensus 407 ~~~~l~~~~t~~eFe~~w~~l~~~~~~~~~~~l~~~~~~r~~W~ 450 (690)
.|..++++++...|-....+|-..-.--+..|...+-..+++|-
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 57788999999999998888754221123467777777888884
No 33
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=31.30 E-value=21 Score=35.43 Aligned_cols=25 Identities=24% Similarity=0.578 Sum_probs=20.3
Q ss_pred ceEEeecCCccccCccchhHHHHHhhcC
Q 005579 573 EQIHCSCKEFEHSGILCRHSLRVLVVKN 600 (690)
Q Consensus 573 ~~~~CsC~~fe~~GipC~Hil~Vl~~~~ 600 (690)
-...|||..+ ..||.||-+|.-++.
T Consensus 123 l~~dCSCPD~---anPCKHi~AvyY~la 147 (266)
T COG4279 123 LSTDCSCPDY---ANPCKHIAAVYYLLA 147 (266)
T ss_pred cccccCCCCc---ccchHHHHHHHHHHH
Confidence 3578999986 579999999987654
No 34
>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=31.25 E-value=1.3e+02 Score=26.35 Aligned_cols=37 Identities=19% Similarity=0.430 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhhcCcEEEEeeeeecCCCeeEEEEEe
Q 005579 67 DEAFEYYSNFARKNGFSIRKARSTESQNLGIYRRDFV 103 (690)
Q Consensus 67 eea~~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~ 103 (690)
.++.+.|..||...||.+.+-.......++++...+.
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 4668899999999999999876655544456655543
No 35
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=29.17 E-value=2.1e+02 Score=29.77 Aligned_cols=72 Identities=17% Similarity=0.037 Sum_probs=47.2
Q ss_pred CCEEEEcccccccccCceeeeEEEEeccCceEEEEEeeccC-CCcchHHHHHHHHH-HHhcC---CCCeEEecccchH
Q 005579 292 GDVVTFDTSYRSITYGLLLGVWFGMDNHGKAIFFGCVLLQD-ESTHSFAWALQTFV-RFMRG---RHPQTILTDIDLG 364 (690)
Q Consensus 292 ~dvl~~D~Ty~tn~y~~pl~~~~gvd~~~~~~~~~~al~~~-Et~es~~w~l~~f~-~~~~~---~~p~~iitD~~~~ 364 (690)
..+++.|-||....-+.-++..+.+|.+.. .++|+++... .+.+...-+|+.-+ ...+. ..|..|.||+-..
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 368889999865443445777888888877 6778999875 56666555655433 33232 2356788887543
No 36
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=28.63 E-value=25 Score=31.95 Aligned_cols=13 Identities=46% Similarity=0.759 Sum_probs=9.1
Q ss_pred CCCCCceeEeecc
Q 005579 3 MKPPTNIWIRRQQ 15 (690)
Q Consensus 3 ~~~~~~~~~~~~~ 15 (690)
.|=.|||||||-+
T Consensus 53 ~KfRksiWiRRg~ 65 (167)
T KOG2925|consen 53 AKFRKSIWIRRGS 65 (167)
T ss_pred HhhhhceEEeeCC
Confidence 3445789999865
No 37
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=27.59 E-value=46 Score=29.50 Aligned_cols=31 Identities=26% Similarity=0.410 Sum_probs=27.0
Q ss_pred CHHHHHHHHHHhhcCCChhHHHHHHHHhcCC
Q 005579 177 QEADQERILLLSKAGFPVNRIVKVLELEKGV 207 (690)
Q Consensus 177 ~~~~~~~i~~l~~~gi~~~~I~~~l~~~~g~ 207 (690)
+++.++.|..+.+-|++|.+|=-+|+..+|+
T Consensus 30 ~ddvkeqI~K~akKGltpsqIGviLRDshGi 60 (151)
T KOG0400|consen 30 ADDVKEQIYKLAKKGLTPSQIGVILRDSHGI 60 (151)
T ss_pred HHHHHHHHHHHHHcCCChhHceeeeecccCc
Confidence 4678889999999999999998888888886
No 38
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=25.73 E-value=96 Score=22.86 Aligned_cols=28 Identities=18% Similarity=0.434 Sum_probs=21.1
Q ss_pred cCCHHHHHHHHHHhhcCCChhHHHHHHH
Q 005579 175 KIQEADQERILLLSKAGFPVNRIVKVLE 202 (690)
Q Consensus 175 ~l~~~~~~~i~~l~~~gi~~~~I~~~l~ 202 (690)
.|++.++..|..+...|++..+|-..+.
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 4889999999999999999999988775
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=25.67 E-value=2.6e+02 Score=28.86 Aligned_cols=96 Identities=18% Similarity=0.173 Sum_probs=51.4
Q ss_pred EEEEccccccccc-Cce-eeeEEEE-eccCceEEEEEeeccC---CCcch----HHHHHHHHHHHhcCCCCeEEecccc-
Q 005579 294 VVTFDTSYRSITY-GLL-LGVWFGM-DNHGKAIFFGCVLLQD---ESTHS----FAWALQTFVRFMRGRHPQTILTDID- 362 (690)
Q Consensus 294 vl~~D~Ty~tn~y-~~p-l~~~~gv-d~~~~~~~~~~al~~~---Et~es----~~w~l~~f~~~~~~~~p~~iitD~~- 362 (690)
||-+|.++..... ..| ++.+++. |.++..+. +...... |..+. +.++|+.|.+..+...|..||.=+|
T Consensus 79 iIGidv~h~~~~~~~~~sv~g~~~s~~~~~~~~~-~~~~~~~~~~e~~~~l~~~~~~~L~~~~~~~~~~~P~~IiiyRdG 157 (302)
T PF02171_consen 79 IIGIDVSHPSPGSDKNPSVVGFVASFDSDGSKYF-SSVRFQDSGQEIIDNLEEIIKEALKEFKKNNGKWLPERIIIYRDG 157 (302)
T ss_dssp EEEEEEEEESSTCTCSCEEEEEEEEESTTTCEEE-EEEEEECTTCCCHHHHHHHHHHHHHHHHHTTTT-TTSEEEEEEES
T ss_pred EEEEEEEecCcccCCcceeeEEEEeccCcccccc-ceeEEeccchhhhcchhhHHHHHHHHHHHHcCCCCCceEEEEEcc
Confidence 6889999988776 333 4444444 33444444 4443433 33333 4555666666666547766654332
Q ss_pred --------------hHHHHHHHhhCCCCceecccchhhhhhh
Q 005579 363 --------------LGLRDSIARELPNTKHVVCIWHILSKLS 390 (690)
Q Consensus 363 --------------~~l~~Ai~~vfP~a~h~lC~~Hi~~n~~ 390 (690)
.++++|+.+.-++....++...+.++..
T Consensus 158 vse~~~~~v~~~Ei~~i~~a~~~~~~~~~p~~~~i~v~K~~~ 199 (302)
T PF02171_consen 158 VSEGQFKKVLEEEIEAIKEAIKELGEDYNPKITYIVVQKRHN 199 (302)
T ss_dssp --GGGHHHHHHHHHHHHHHHHHHHTHTTCTEEEEEEEESSSS
T ss_pred cCHHhhcccHHHHHHHHHHHHhhcccCCCCcEEEEEeecccc
Confidence 2455555555544445555555555443
No 40
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=22.66 E-value=76 Score=31.60 Aligned_cols=19 Identities=26% Similarity=0.669 Sum_probs=15.0
Q ss_pred CCCCCcccccccceeEEEE
Q 005579 121 PRDRKSVRCGCDAKLYLTK 139 (690)
Q Consensus 121 ~r~r~s~r~gCpa~i~i~~ 139 (690)
.+...+.+.+|||.|+++.
T Consensus 70 ~~~~~skK~~CPA~I~Ik~ 88 (225)
T PF15299_consen 70 RRSKPSKKRDCPARIYIKE 88 (225)
T ss_pred cccccccCCCCCeEEEEEE
Confidence 3445688999999999874
No 41
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=22.35 E-value=45 Score=28.00 Aligned_cols=29 Identities=28% Similarity=0.117 Sum_probs=22.8
Q ss_pred cCCCCCCCCCCCCccCCHHHHHHHHHHHH
Q 005579 49 LSSEVVFTPYVGQIFKSDDEAFEYYSNFA 77 (690)
Q Consensus 49 ~~~~~~~~P~vG~~F~S~eea~~fy~~yA 77 (690)
.+++-...+.+=++|+|++.|.++|+.=+
T Consensus 46 lEG~w~ptr~vviEFps~~~ar~~y~Spe 74 (96)
T COG5470 46 LEGEWRPTRNVVIEFPSLEAARDCYNSPE 74 (96)
T ss_pred ccCCCCcccEEEEEcCCHHHHHHHhcCHH
Confidence 45555567778899999999999998543
No 42
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=20.17 E-value=44 Score=25.17 Aligned_cols=7 Identities=71% Similarity=1.906 Sum_probs=5.0
Q ss_pred ccCCCCc
Q 005579 15 QCPCGDW 21 (690)
Q Consensus 15 ~~~~~~~ 21 (690)
-|||||-
T Consensus 24 PCPCGDR 30 (67)
T COG5216 24 PCPCGDR 30 (67)
T ss_pred cCCCCCE
Confidence 5888875
Done!