Query 005927
Match_columns 669
No_of_seqs 286 out of 1269
Neff 8.5
Searched_HMMs 46136
Date Thu Mar 28 15:49:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005927.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005927hhsearch_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 6E-134 1E-138 1135.8 55.5 612 13-653 67-694 (846)
2 PF10551 MULE: MULE transposas 99.8 7.8E-22 1.7E-26 168.8 5.3 90 242-333 1-93 (93)
3 PF03101 FAR1: FAR1 DNA-bindin 99.8 4.8E-20 1E-24 156.9 7.8 88 34-121 1-91 (91)
4 PF00872 Transposase_mut: Tran 99.5 1.5E-15 3.4E-20 162.9 0.1 184 236-422 163-352 (381)
5 PF08731 AFT: Transcription fa 99.1 3.2E-10 6.9E-15 95.8 9.5 88 26-119 1-111 (111)
6 smart00575 ZnF_PMZ plant mutat 98.9 5.7E-10 1.2E-14 71.6 1.5 26 528-553 2-27 (28)
7 COG3328 Transposase and inacti 98.8 2.4E-08 5.1E-13 105.5 10.8 197 236-436 146-347 (379)
8 PF03108 DBD_Tnp_Mut: MuDR fam 98.5 5.4E-07 1.2E-11 71.6 7.9 63 19-108 3-67 (67)
9 PF04434 SWIM: SWIM zinc finge 98.3 4.6E-07 9.9E-12 63.9 2.7 28 524-551 12-39 (40)
10 PF01610 DDE_Tnp_ISL3: Transpo 96.7 0.00062 1.3E-08 69.2 1.5 68 271-339 31-99 (249)
11 PF03106 WRKY: WRKY DNA -bindi 95.1 0.13 2.9E-06 39.5 7.3 54 44-118 4-59 (60)
12 PF13610 DDE_Tnp_IS240: DDE do 91.6 0.087 1.9E-06 48.4 1.4 81 235-319 1-81 (140)
13 smart00774 WRKY DNA binding do 90.8 0.51 1.1E-05 36.0 4.6 26 92-117 32-59 (59)
14 PF06782 UPF0236: Uncharacteri 89.4 6.4 0.00014 43.8 13.9 137 275-423 235-381 (470)
15 PF04684 BAF1_ABF1: BAF1 / ABF 87.1 1.2 2.5E-05 47.8 5.8 54 23-102 25-78 (496)
16 PF04500 FLYWCH: FLYWCH zinc f 85.0 1.5 3.1E-05 33.5 4.1 25 91-117 38-62 (62)
17 PF00665 rve: Integrase core d 84.2 2.3 5E-05 37.2 5.6 75 235-310 6-81 (120)
18 PF04937 DUF659: Protein of un 82.7 5.4 0.00012 37.1 7.6 110 228-339 26-139 (153)
19 COG5431 Uncharacterized metal- 49.8 11 0.00025 31.9 1.9 31 511-547 40-75 (117)
20 COG3316 Transposase and inacti 42.9 27 0.00058 34.2 3.5 82 235-322 70-152 (215)
21 PF12022 DUF3510: Domain of un 38.5 68 0.0015 28.6 5.3 38 623-660 77-114 (125)
22 COG4279 Uncharacterized conser 32.7 17 0.00037 36.1 0.5 24 526-552 124-147 (266)
23 PRK14702 insertion element IS2 25.9 1.7E+02 0.0036 29.8 6.3 72 235-307 87-163 (262)
24 PF15299 ALS2CR8: Amyotrophic 25.5 68 0.0015 31.9 3.3 19 83-101 70-88 (225)
25 PHA02517 putative transposase 25.1 1.6E+02 0.0035 29.9 6.2 71 235-307 110-180 (277)
26 PF03462 PCRF: PCRF domain; I 25.0 1.8E+02 0.004 25.4 5.6 36 30-65 66-101 (115)
27 PF04800 ETC_C1_NDUFA4: ETC co 24.5 55 0.0012 28.1 2.1 39 11-53 37-78 (101)
28 PF13773 DUF4170: Domain of un 23.8 81 0.0017 24.8 2.6 24 18-42 25-48 (69)
29 PF11433 DUF3198: Protein of u 23.0 1.2E+02 0.0026 21.9 3.1 44 348-392 6-49 (51)
30 PRK09409 IS2 transposase TnpB; 22.2 2E+02 0.0044 29.9 6.3 72 235-307 126-202 (301)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=5.5e-134 Score=1135.85 Aligned_cols=612 Identities=31% Similarity=0.521 Sum_probs=539.9
Q ss_pred CCCCCCCCCCCCccCCHHHHHHHHHHHHHhcCceEEeccee-ecCCCCeEEEEEEeeccCCCCCcchh------------
Q 005927 13 GIGNDGELKVGTEVKSDAEAYNLCNNYAFRKGFSLRKGHVR-RDASGNIRQRDFVCSKEGFPVDEDLC------------ 79 (669)
Q Consensus 13 ~~~~~~~p~~G~~F~S~eea~~fy~~YA~~~GF~vr~~~s~-~~~~g~~~~~~f~Csr~G~~~~~~~~------------ 79 (669)
+.++..+|.+||+|+|.|||++||+.||.+.||+||+.+++ ++.+|.+++++|+|+|+|+++.+..+
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 44677899999999999999999999999999999999998 66788999999999999987643210
Q ss_pred -hhhccCCccccccccceEEEEEE-cCeEEEEEeeccCCCCCCCcccccccccccccccccCccccccCCcccceeeccc
Q 005927 80 -AVKRCNRLETRTGCKVLMRFTVS-NGVWVISHINFEHNHELAKPEERQFLRSCRKIFEASGGVDVGRRRTKPLSYLGND 157 (669)
Q Consensus 80 -~~~~r~~~~~rtgCpa~i~v~~~-~~~w~V~~~~~~HNH~l~~~~~~~~l~s~r~l~~~~~~i~~~~~~~~~~~~~~~~ 157 (669)
...+++|+.+||||||+|+|++. +|+|+|+.++.+|||+|.++..... + .|++ +..+...
T Consensus 147 ~~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~~~-~-~r~~----------------~~~~~~~ 208 (846)
T PLN03097 147 PENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVSE-Q-TRKM----------------YAAMARQ 208 (846)
T ss_pred cccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccccch-h-hhhh----------------HHHHHhh
Confidence 01123567799999999999998 9999999999999999987643210 0 0110 0112223
Q ss_pred cCCCccccccccccCCcchhhhcCCCCCCChhhHHHHHHhhccCCCCceEEEEeccCCceeeEEecccchHHHHhHcCCE
Q 005927 158 FGGDRNVQFAKKDMGNYLPREMGNMMEPGDVQGLLNYFRRKKCEDPSFFYAVQVNQLNQATNFFWRDGRSKLDYDCFGDV 237 (669)
Q Consensus 158 ~g~~~~v~~~~~di~N~~~~~r~~~~~~~d~~~l~~~l~~~~~~np~f~~~~~~d~~~~l~~ifw~~~~~~~~~~~f~dv 237 (669)
.++..+++.++.|..|...+.|+..+..+|+++|++||+++|.+||+|||++++|++|+|++|||+|++++.+|.+||||
T Consensus 209 ~~~~~~v~~~~~d~~~~~~~~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~FGDv 288 (846)
T PLN03097 209 FAEYKNVVGLKNDSKSSFDKGRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGNFSDV 288 (846)
T ss_pred hhccccccccchhhcchhhHHHhhhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHhcCCE
Confidence 34556777788888898888888888999999999999999999999999999999999999999999999999999999
Q ss_pred EEecceeccccCCceeeeEEEeccCCChhhhhhhhhcCCChhHHHHHHHHHHHHhCCCCCcEEeCcccHHHHHHHHHHcc
Q 005927 238 VSFDATFRLNKYNLICAPFVGVNHHWKNMLFGCAFLLDESTHSYVWLFESFLESMGNTQPKTIFTNENEAMSKAIETVFM 317 (669)
Q Consensus 238 v~~D~Ty~~n~y~~pl~~~~gv~~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~a~~~Ai~~vfP 317 (669)
|+||+||+||+|+|||++|+|+|||+|+++|||||+.+|+.|+|.|||++|+++|+|+.|.+||||++.+|.+||++|||
T Consensus 289 V~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP 368 (846)
T PLN03097 289 VSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFP 368 (846)
T ss_pred EEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccccccchHHHHHHHHhhhhhc-cHHHHHHHHHHHhccCCHHHHHHHHHHHHhhcCCCchHHHHHHHHhhcccccccc
Q 005927 318 KTRHRLSTGHIVKDARRNLANQFA-NLEFMKYLNKCFYECHDETEFQVSWDDMINKFSLGDHLWLKKLYSLRDKWCLVFN 396 (669)
Q Consensus 318 ~a~h~~C~~Hi~~n~~~~l~~~~~-~~~~~~~~~~~v~~~~~~~eFe~~w~~l~~~~~~~~~~~l~~~~~~r~~W~~~y~ 396 (669)
+|.|++|.|||++|+.++|+.++. .+.|..+|.+||+++.+++|||..|..|+++|++++|+||+.+|+.|++|||+|+
T Consensus 369 ~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~ 448 (846)
T PLN03097 369 NAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYM 448 (846)
T ss_pred CceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHh
Confidence 999999999999999999998854 4689999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccccCCCCCchhhhhhcccCCCCCHHHHHHHHHHHHHHhhhhhhhhcccccCcccccchhhhHHHHHHHhccHH
Q 005927 397 SDTFSANIDSVQRSDSIDTVFHQVSTKRMDVISFVQHFEEKTKEMHLDELEDDHFCKHVVPRLQVWNGILNHAVYVYTSK 476 (669)
Q Consensus 397 ~~~f~~~~~tt~~~Es~n~~lk~~~~~~~~l~~f~~~~~~~~~~~~~~e~~~d~~s~~~~p~~~~~~~~e~q~~~~yT~~ 476 (669)
++.|++||+||+|+||+|++||+|++++++|..|+++|+++++.++++|+++|+.+.++.|.+++++|||+||+++||++
T Consensus 449 k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~ 528 (846)
T PLN03097 449 RDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHA 528 (846)
T ss_pred cccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccceEEEeeCCcEEEEEEEEecceeEEEEEEecCCCeEEeEeccccccCcchhhHHHHhhccccccC
Q 005927 477 IFNFFEMELLGCMGVRMKEVCKDGEVCIYEAIEEGQQKVCKINYNLSTQDISCSCKLFERMGILCRHALKAFDFNNLTQI 556 (669)
Q Consensus 477 ~f~~fq~el~~~~~~~~~~~~~~~~~~~V~~~~~~~~~~~~V~~~~~~~~~~CsC~~fe~~GipC~HiL~Vl~~~~v~~i 556 (669)
||++||+|+..+..+.+.....++..+++.+...+..+.|.|.+|.....++|+|++||+.||||||||+||.++||.+|
T Consensus 529 iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~I 608 (846)
T PLN03097 529 VFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAI 608 (846)
T ss_pred HHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccC
Confidence 99999999999887665555444554444433333456799999999999999999999999999999999999999999
Q ss_pred CccccccccccccccCcccccCCcccCCCCCccccchHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHHH
Q 005927 557 PVQYILKRWTKEAKKGIVVRVSNERHGLSSNTVKSVQSLRLSELMHMGSNVYSIASLSDSGTKIVKEKLAEAMELLEKDE 636 (669)
Q Consensus 557 P~~yil~RWtk~a~~~~~~~~~~~~~~~~~~~~~~~~~~Ry~~l~~~~~~~~~~a~~s~e~~~~~~~~l~~~~~~~~~~~ 636 (669)
|++|||+||||+||...+.+... + ..++.+.||+.||++++++|.+|+.|+|.|.+|+++|+++...+.
T Consensus 609 P~~YILkRWTKdAK~~~~~~~~~-------~-~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~L~e~~~~~~--- 677 (846)
T PLN03097 609 PSQYILKRWTKDAKSRHLLGEES-------E-QVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRALEEAFGNCI--- 677 (846)
T ss_pred chhhhhhhchhhhhhcccCcccc-------c-cccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH---
Confidence 99999999999999876553221 1 123467899999999999999999999999999999999998885
Q ss_pred HHHHhhhccccCCCCCC
Q 005927 637 EIVNRLAHAKKVDSSPS 653 (669)
Q Consensus 637 ~~~~~~~~~~~~~~~~~ 653 (669)
-+.+...+....+..+.
T Consensus 678 ~~~n~~~~~~~~~~~~~ 694 (846)
T PLN03097 678 SMNNSNKSLVEAGTSPT 694 (846)
T ss_pred HhhccCCCccccccccc
Confidence 33444444444444444
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=99.85 E-value=7.8e-22 Score=168.79 Aligned_cols=90 Identities=31% Similarity=0.517 Sum_probs=86.9
Q ss_pred ceeccccCCceeee---EEEeccCCChhhhhhhhhcCCChhHHHHHHHHHHHHhCCCCCcEEeCcccHHHHHHHHHHccc
Q 005927 242 ATFRLNKYNLICAP---FVGVNHHWKNMLFGCAFLLDESTHSYVWLFESFLESMGNTQPKTIFTNENEAMSKAIETVFMK 318 (669)
Q Consensus 242 ~Ty~~n~y~~pl~~---~~gv~~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~a~~~Ai~~vfP~ 318 (669)
+||+||+| +|++. ++|+|++|+.+|+||+++.+|+.++|.|+|+.+++.++.. |.+||||++.++.+||+++||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 69999999 88886 9999999999999999999999999999999999999987 9999999999999999999999
Q ss_pred CccccccchHHHHHH
Q 005927 319 TRHRLSTGHIVKDAR 333 (669)
Q Consensus 319 a~h~~C~~Hi~~n~~ 333 (669)
+.|++|.||+.||++
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=4.8e-20 Score=156.94 Aligned_cols=88 Identities=35% Similarity=0.644 Sum_probs=79.9
Q ss_pred HHHHHHHHhcCceEEeccee-ecCCCCeEEEEEEeeccCCCCCcchh-hhhccCCccccccccceEEEEEE-cCeEEEEE
Q 005927 34 NLCNNYAFRKGFSLRKGHVR-RDASGNIRQRDFVCSKEGFPVDEDLC-AVKRCNRLETRTGCKVLMRFTVS-NGVWVISH 110 (669)
Q Consensus 34 ~fy~~YA~~~GF~vr~~~s~-~~~~g~~~~~~f~Csr~G~~~~~~~~-~~~~r~~~~~rtgCpa~i~v~~~-~~~w~V~~ 110 (669)
+||+.||..+||+|++.+++ .+.+|.++++.|+|+++|.++.+... ...++++++++|||||+|.+++. +|.|.|+.
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~~~~w~v~~ 80 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRKDGKWRVTS 80 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEccCCEEEEEE
Confidence 59999999999999999998 45788899999999999999887765 34578899999999999999999 99999999
Q ss_pred eeccCCCCCCC
Q 005927 111 INFEHNHELAK 121 (669)
Q Consensus 111 ~~~~HNH~l~~ 121 (669)
+..+|||+|.|
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999964
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=99.52 E-value=1.5e-15 Score=162.88 Aligned_cols=184 Identities=14% Similarity=0.174 Sum_probs=147.9
Q ss_pred CEEEecceeccccC-----CceeeeEEEeccCCChhhhhhhhhcCCChhHHHHHHHHHHHHhCCCCCcEEeCcccHHHHH
Q 005927 236 DVVSFDATFRLNKY-----NLICAPFVGVNHHWKNMLFGCAFLLDESTHSYVWLFESFLESMGNTQPKTIFTNENEAMSK 310 (669)
Q Consensus 236 dvv~~D~Ty~~n~y-----~~pl~~~~gv~~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~a~~~ 310 (669)
++|.+|++|.+-+. +.++++++|+|.+|+-.++|+.+...|+.++|.-+|..+++- |-..|..||+|..+++.+
T Consensus 163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ 241 (381)
T PF00872_consen 163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKE 241 (381)
T ss_pred cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccc
Confidence 57899999987552 467899999999999999999999999999999999998764 223699999999999999
Q ss_pred HHHHHcccCccccccchHHHHHHHHhhhhhccHHHHHHHHHHHhccCCHHHHHHHHHHHHhhcCCCchHHHHHHHHhh-c
Q 005927 311 AIETVFMKTRHRLSTGHIVKDARRNLANQFANLEFMKYLNKCFYECHDETEFQVSWDDMINKFSLGDHLWLKKLYSLR-D 389 (669)
Q Consensus 311 Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~~~~~~~~~~~~~~v~~~~~~~eFe~~w~~l~~~~~~~~~~~l~~~~~~r-~ 389 (669)
||.++||++.++.|.+|.++|+.+++... ..+.+..+|+. |+.+.+.++....++.+.+++..+.+...+.+-+.. +
T Consensus 242 ai~~~fp~a~~QrC~vH~~RNv~~~v~~k-~~~~v~~~Lk~-I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~ 319 (381)
T PF00872_consen 242 AIREVFPGAKWQRCVVHLMRNVLRKVPKK-DRKEVKADLKA-IYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDE 319 (381)
T ss_pred cccccccchhhhhheechhhhhccccccc-cchhhhhhccc-cccccccchhhhhhhhcccccccccchhhhhhhhcccc
Confidence 99999999999999999999999998653 23477788876 677999999999999999888776665444332211 2
Q ss_pred cccccccCCccccccccCCCCCchhhhhhcccC
Q 005927 390 KWCLVFNSDTFSANIDSVQRSDSIDTVFHQVST 422 (669)
Q Consensus 390 ~W~~~y~~~~f~~~~~tt~~~Es~n~~lk~~~~ 422 (669)
.|...-++...+.-+.|||.+|++|+.+|+...
T Consensus 320 ~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~ 352 (381)
T PF00872_consen 320 LLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTK 352 (381)
T ss_pred ccceeeecchhccccchhhhccccccchhhhcc
Confidence 223222445555678899999999999998543
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=99.13 E-value=3.2e-10 Score=95.79 Aligned_cols=88 Identities=18% Similarity=0.269 Sum_probs=70.5
Q ss_pred cCCHHHHHHHHHHHHHhcCceEEecceeecCCCCeEEEEEEeeccCCCCCcchh---------------------hhhcc
Q 005927 26 VKSDAEAYNLCNNYAFRKGFSLRKGHVRRDASGNIRQRDFVCSKEGFPVDEDLC---------------------AVKRC 84 (669)
Q Consensus 26 F~S~eea~~fy~~YA~~~GF~vr~~~s~~~~~g~~~~~~f~Csr~G~~~~~~~~---------------------~~~~r 84 (669)
|.+.+|...+++..+...||.|++.+|... .++|.|--+|.++..... ..+..
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 889999999999999999999999999732 479999777766543331 00112
Q ss_pred CCccccccccceEEEEEE--cCeEEEEEeeccCCCCC
Q 005927 85 NRLETRTGCKVLMRFTVS--NGVWVISHINFEHNHEL 119 (669)
Q Consensus 85 ~~~~~rtgCpa~i~v~~~--~~~w~V~~~~~~HNH~l 119 (669)
...+.+++|||+|++... .+.|.|..++..|||+|
T Consensus 75 ~t~srk~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 75 RTKSRKNTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cccccccCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 334556999999999988 88999999999999986
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.89 E-value=5.7e-10 Score=71.56 Aligned_cols=26 Identities=50% Similarity=0.855 Sum_probs=24.7
Q ss_pred EeEeccccccCcchhhHHHHhhcccc
Q 005927 528 SCSCKLFERMGILCRHALKAFDFNNL 553 (669)
Q Consensus 528 ~CsC~~fe~~GipC~HiL~Vl~~~~v 553 (669)
+|+|++||..||||+|+|+|+...++
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 79999999999999999999998876
No 7
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.80 E-value=2.4e-08 Score=105.48 Aligned_cols=197 Identities=13% Similarity=0.106 Sum_probs=138.4
Q ss_pred CEEEecceecccc--CCceeeeEEEeccCCChhhhhhhhhcCCChhHHHHHHHHHHHHhCCCCCcEEeCcccHHHHHHHH
Q 005927 236 DVVSFDATFRLNK--YNLICAPFVGVNHHWKNMLFGCAFLLDESTHSYVWLFESFLESMGNTQPKTIFTNENEAMSKAIE 313 (669)
Q Consensus 236 dvv~~D~Ty~~n~--y~~pl~~~~gv~~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~a~~~Ai~ 313 (669)
.+|.+|++|.+-+ -+..++.++|++.+|+-.++|+-+-..|+ ..|.-+|..|+.. +-.....+++|...++.+||.
T Consensus 146 ~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~ 223 (379)
T COG3328 146 PYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLVVVDGLKGLPEAIS 223 (379)
T ss_pred eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEEecchhhhhHHHHH
Confidence 5788999998877 56788999999999999999999999999 7887555555543 223456677799999999999
Q ss_pred HHcccCccccccchHHHHHHHHhhhhhccHHHHHHHHHHHhccCCHHHHHHHHHHHHhhcCCCchHHHHHHHHhhc-ccc
Q 005927 314 TVFMKTRHRLSTGHIVKDARRNLANQFANLEFMKYLNKCFYECHDETEFQVSWDDMINKFSLGDHLWLKKLYSLRD-KWC 392 (669)
Q Consensus 314 ~vfP~a~h~~C~~Hi~~n~~~~l~~~~~~~~~~~~~~~~v~~~~~~~eFe~~w~~l~~~~~~~~~~~l~~~~~~r~-~W~ 392 (669)
.+||.+.++.|..|+.+|+..+...... +....+++. ++.+.+.++-...|..+.+.+......-++.+....+ .|.
T Consensus 224 ~v~p~a~~Q~C~vH~~Rnll~~v~~k~~-d~i~~~~~~-I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~ 301 (379)
T COG3328 224 AVFPQAAVQRCIVHLVRNLLDKVPRKDQ-DAVLSDLRS-IYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLP 301 (379)
T ss_pred HhccHhhhhhhhhHHHhhhhhhhhhhhh-HHHHhhhhh-hhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcc
Confidence 9999999999999999999988876422 233444443 6778899999999998877655544433333322222 222
Q ss_pred ccccCCccccccccCCCCCchhhhhhcccCC--CCCHHHHHHHHHH
Q 005927 393 LVFNSDTFSANIDSVQRSDSIDTVFHQVSTK--RMDVISFVQHFEE 436 (669)
Q Consensus 393 ~~y~~~~f~~~~~tt~~~Es~n~~lk~~~~~--~~~l~~f~~~~~~ 436 (669)
-.=+......-+.|||.+|++|..++..... ..+-.+++..+..
T Consensus 302 F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~~y 347 (379)
T COG3328 302 FFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNEESVEKLVY 347 (379)
T ss_pred cccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCHHHHHHHHH
Confidence 1111111113467999999999988865433 4444555554433
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=98.49 E-value=5.4e-07 Score=71.56 Aligned_cols=63 Identities=24% Similarity=0.468 Sum_probs=54.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHHHhcCceEEecceeecCCCCeEEEEEEeeccCCCCCcchhhhhccCCccccccccceEE
Q 005927 19 ELKVGTEVKSDAEAYNLCNNYAFRKGFSLRKGHVRRDASGNIRQRDFVCSKEGFPVDEDLCAVKRCNRLETRTGCKVLMR 98 (669)
Q Consensus 19 ~p~~G~~F~S~eea~~fy~~YA~~~GF~vr~~~s~~~~~g~~~~~~f~Csr~G~~~~~~~~~~~~r~~~~~rtgCpa~i~ 98 (669)
...+||+|+|.+|+..++..||...||.++..++.+ .++..+|... ||||+|+
T Consensus 3 ~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~------~r~~~~C~~~---------------------~C~Wrv~ 55 (67)
T PF03108_consen 3 ELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDK------KRYRAKCKDK---------------------GCPWRVR 55 (67)
T ss_pred ccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCC------EEEEEEEcCC---------------------CCCEEEE
Confidence 457999999999999999999999999999988862 3678889622 8999999
Q ss_pred EEEE--cCeEEE
Q 005927 99 FTVS--NGVWVI 108 (669)
Q Consensus 99 v~~~--~~~w~V 108 (669)
+++. ++.|.|
T Consensus 56 as~~~~~~~~~I 67 (67)
T PF03108_consen 56 ASKRKRSDTFQI 67 (67)
T ss_pred EEEcCCCCEEEC
Confidence 9988 677875
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=98.29 E-value=4.6e-07 Score=63.91 Aligned_cols=28 Identities=29% Similarity=0.539 Sum_probs=25.4
Q ss_pred CCeEEeEeccccccCcchhhHHHHhhcc
Q 005927 524 TQDISCSCKLFERMGILCRHALKAFDFN 551 (669)
Q Consensus 524 ~~~~~CsC~~fe~~GipC~HiL~Vl~~~ 551 (669)
....+|+|..|+..|.||+|+++|+..+
T Consensus 12 ~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 12 IEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccEeeCCCccccCCcchhHHHHHHhh
Confidence 4678999999999999999999998754
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=96.72 E-value=0.00062 Score=69.16 Aligned_cols=68 Identities=21% Similarity=0.199 Sum_probs=56.0
Q ss_pred hhhcCCChhHHHHHHHHH-HHHhCCCCCcEEeCcccHHHHHHHHHHcccCccccccchHHHHHHHHhhhh
Q 005927 271 AFLLDESTHSYVWLFESF-LESMGNTQPKTIFTNENEAMSKAIETVFMKTRHRLSTGHIVKDARRNLANQ 339 (669)
Q Consensus 271 al~~~Et~es~~w~l~~f-~~~~~~~~p~~iitD~~~a~~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~ 339 (669)
.++.+-+.+++.-+|..+ -.. ....+++|.+|...+...|+++.||+|.+..-.|||++++.+.+...
T Consensus 31 ~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk~~~~al~~v 99 (249)
T PF01610_consen 31 DILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVKLANRALDKV 99 (249)
T ss_pred EEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccccccccccccccchhhhhhhhcchhh
Confidence 478888888877666655 222 34578999999999999999999999999999999999998866543
No 11
>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=95.07 E-value=0.13 Score=39.48 Aligned_cols=54 Identities=24% Similarity=0.348 Sum_probs=36.0
Q ss_pred CceEEecceeecCCCCeEEEEEEeeccCCCCCcchhhhhccCCccccccccceEEEEEE--cCeEEEEEeeccCCCC
Q 005927 44 GFSLRKGHVRRDASGNIRQRDFVCSKEGFPVDEDLCAVKRCNRLETRTGCKVLMRFTVS--NGVWVISHINFEHNHE 118 (669)
Q Consensus 44 GF~vr~~~s~~~~~g~~~~~~f~Csr~G~~~~~~~~~~~~r~~~~~rtgCpa~i~v~~~--~~~w~V~~~~~~HNH~ 118 (669)
||.-|+--.+.-++...-|.+|.|+.. ||||+=.|.+. ++.-.++....+|||+
T Consensus 4 gy~WRKYGqK~i~g~~~pRsYYrCt~~---------------------~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 4 GYRWRKYGQKNIKGSPYPRSYYRCTHP---------------------GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SS-EEEEEEEEETTTTCEEEEEEEECT---------------------TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCchhhccCcccCCCceeeEeeecccc---------------------ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 677776655521222234677888742 99999999988 6678889999999996
No 12
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=91.57 E-value=0.087 Score=48.35 Aligned_cols=81 Identities=16% Similarity=0.135 Sum_probs=67.3
Q ss_pred CCEEEecceeccccCCceeeeEEEeccCCChhhhhhhhhcCCChhHHHHHHHHHHHHhCCCCCcEEeCcccHHHHHHHHH
Q 005927 235 GDVVSFDATFRLNKYNLICAPFVGVNHHWKNMLFGCAFLLDESTHSYVWLFESFLESMGNTQPKTIFTNENEAMSKAIET 314 (669)
Q Consensus 235 ~dvv~~D~Ty~~n~y~~pl~~~~gv~~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~a~~~Ai~~ 314 (669)
|+.+.+|-||.+-+- --.+....+|.+|+ ++++-|-..-+...=..||+.+++..+ ..|..|+||+..+...|+++
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 GDSWHVDETYIKIKG-KWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEECC-EEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 678999999977443 24566888999999 778888888888888888888777665 68999999999999999999
Q ss_pred HcccC
Q 005927 315 VFMKT 319 (669)
Q Consensus 315 vfP~a 319 (669)
.+|..
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99974
No 13
>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=90.79 E-value=0.51 Score=36.00 Aligned_cols=26 Identities=27% Similarity=0.301 Sum_probs=22.5
Q ss_pred cccceEEEEEE--cCeEEEEEeeccCCC
Q 005927 92 GCKVLMRFTVS--NGVWVISHINFEHNH 117 (669)
Q Consensus 92 gCpa~i~v~~~--~~~w~V~~~~~~HNH 117 (669)
||||+=.|.+. ++.-.++.+..+|||
T Consensus 32 ~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 32 GCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 89998888877 677888888999998
No 14
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=89.39 E-value=6.4 Score=43.85 Aligned_cols=137 Identities=11% Similarity=0.130 Sum_probs=82.7
Q ss_pred CCChhHHHHHHHHHHHHhCCCC--CcEEeCcccHHHHHHHHHHcccCccccccchHHHHHHHHhhhhhccHHHHHHHHHH
Q 005927 275 DESTHSYVWLFESFLESMGNTQ--PKTIFTNENEAMSKAIETVFMKTRHRLSTGHIVKDARRNLANQFANLEFMKYLNKC 352 (669)
Q Consensus 275 ~Et~es~~w~l~~f~~~~~~~~--p~~iitD~~~a~~~Ai~~vfP~a~h~~C~~Hi~~n~~~~l~~~~~~~~~~~~~~~~ 352 (669)
....+-|.-+.+.+-..-.... -.++..|....+.+++. .||++.|.|..||+.+.+.+.++.. +.....+.++
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~---~~~~~~~~~a 310 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD---PELKEKIRKA 310 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC---hHHHHHHHHH
Confidence 3445556655555544433222 34556799999988776 9999999999999999999988763 2345555566
Q ss_pred HhccCCHHHHHHHHHHHHhhcCCCc-h-------HHHHHHHHhhccccccccCCccccccccCCCCCchhhhhhcccCC
Q 005927 353 FYECHDETEFQVSWDDMINKFSLGD-H-------LWLKKLYSLRDKWCLVFNSDTFSANIDSVQRSDSIDTVFHQVSTK 423 (669)
Q Consensus 353 v~~~~~~~eFe~~w~~l~~~~~~~~-~-------~~l~~~~~~r~~W~~~y~~~~f~~~~~tt~~~Es~n~~lk~~~~~ 423 (669)
+. ......++...+.+........ . .||...|+. ..+|... .|+......|+.+..+...+++
T Consensus 311 l~-~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~----i~~y~~~---~~~~g~g~ee~~~~~~s~RmK~ 381 (470)
T PF06782_consen 311 LK-KGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDG----IKPYRER---EGLRGIGAEESVSHVLSYRMKS 381 (470)
T ss_pred HH-hcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHH----hhhhhhc---cCCCccchhhhhhhHHHHHhcC
Confidence 65 4566777777776665332221 1 344333321 1233221 2333344478888888765554
No 15
>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=87.08 E-value=1.2 Score=47.82 Aligned_cols=54 Identities=17% Similarity=0.373 Sum_probs=47.3
Q ss_pred CCccCCHHHHHHHHHHHHHhcCceEEecceeecCCCCeEEEEEEeeccCCCCCcchhhhhccCCccccccccceEEEEEE
Q 005927 23 GTEVKSDAEAYNLCNNYAFRKGFSLRKGHVRRDASGNIRQRDFVCSKEGFPVDEDLCAVKRCNRLETRTGCKVLMRFTVS 102 (669)
Q Consensus 23 G~~F~S~eea~~fy~~YA~~~GF~vr~~~s~~~~~g~~~~~~f~Csr~G~~~~~~~~~~~~r~~~~~rtgCpa~i~v~~~ 102 (669)
+..|+|+++.|+.+|.|-....-.|..+.|.+++ .++|.|... +|||+|.+...
T Consensus 25 ~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk-----hftfachlk---------------------~c~fkillsy~ 78 (496)
T PF04684_consen 25 ARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK-----HFTFACHLK---------------------NCPFKILLSYC 78 (496)
T ss_pred ccCCCcHHHHHHHHhhhhhhhcCceeeccccccc-----ceEEEeecc---------------------CCCceeeeeec
Confidence 6689999999999999999999999998887544 579999863 89999999866
No 16
>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=84.95 E-value=1.5 Score=33.51 Aligned_cols=25 Identities=32% Similarity=0.456 Sum_probs=10.1
Q ss_pred ccccceEEEEEEcCeEEEEEeeccCCC
Q 005927 91 TGCKVLMRFTVSNGVWVISHINFEHNH 117 (669)
Q Consensus 91 tgCpa~i~v~~~~~~w~V~~~~~~HNH 117 (669)
.+|+|++.+. .+.-.|.....+|||
T Consensus 38 ~~C~a~~~~~--~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITD--AGDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE----TTEEEE-S---SS
T ss_pred CCCeEEEEEE--CCCCEEEECCCccCC
Confidence 5999999888 233344455588999
No 17
>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=84.18 E-value=2.3 Score=37.18 Aligned_cols=75 Identities=13% Similarity=0.136 Sum_probs=54.5
Q ss_pred CCEEEecceecc-ccCCceeeeEEEeccCCChhhhhhhhhcCCChhHHHHHHHHHHHHhCCCCCcEEeCcccHHHHH
Q 005927 235 GDVVSFDATFRL-NKYNLICAPFVGVNHHWKNMLFGCAFLLDESTHSYVWLFESFLESMGNTQPKTIFTNENEAMSK 310 (669)
Q Consensus 235 ~dvv~~D~Ty~~-n~y~~pl~~~~gv~~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~a~~~ 310 (669)
++++.+|.+... ...+...+.++.+|..-..+ +++.+-..++.+.+..+|.......++..|.+|+||+..+..+
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 578889988554 34455788888888776554 4566666668888888888777777766699999999988763
No 18
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=82.67 E-value=5.4 Score=37.08 Aligned_cols=110 Identities=12% Similarity=0.081 Sum_probs=79.5
Q ss_pred HHHHhHcCCEEEecceeccccCCceeeeEEEeccCCChhhhhhhhh-cCCChhHHHHHHHHHHHHhCCCCCcEEeCcccH
Q 005927 228 KLDYDCFGDVVSFDATFRLNKYNLICAPFVGVNHHWKNMLFGCAFL-LDESTHSYVWLFESFLESMGNTQPKTIFTNENE 306 (669)
Q Consensus 228 ~~~~~~f~dvv~~D~Ty~~n~y~~pl~~~~gv~~~~~~~~~~~al~-~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~ 306 (669)
+..+...|=-|..|+= ++..+.+++.|+.....|..+.-..-.- ...+.+.+.-+|+...+.+|......||||-..
T Consensus 26 k~~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~ 103 (153)
T PF04937_consen 26 KKSWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNAS 103 (153)
T ss_pred HHHHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCch
Confidence 4455666766777776 6667778888877766665554322111 125667777777777777777788889999999
Q ss_pred HHHHHH---HHHcccCccccccchHHHHHHHHhhhh
Q 005927 307 AMSKAI---ETVFMKTRHRLSTGHIVKDARRNLANQ 339 (669)
Q Consensus 307 a~~~Ai---~~vfP~a~h~~C~~Hi~~n~~~~l~~~ 339 (669)
.+.+|- .+-+|...-.-|.-|-+.-+.+.+..+
T Consensus 104 ~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k~ 139 (153)
T PF04937_consen 104 NMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGKL 139 (153)
T ss_pred hHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhcC
Confidence 888884 456788888899999999988888764
No 19
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=49.78 E-value=11 Score=31.86 Aligned_cols=31 Identities=23% Similarity=0.388 Sum_probs=20.9
Q ss_pred cceeEEEEEEecCCCeEEeEeccccc-----cCcchhhHHHH
Q 005927 511 GQQKVCKINYNLSTQDISCSCKLFER-----MGILCRHALKA 547 (669)
Q Consensus 511 ~~~~~~~V~~~~~~~~~~CsC~~fe~-----~GipC~HiL~V 547 (669)
+..+.|++..+ -|||..|-. -.-||.|++.+
T Consensus 40 G~~rdYIl~~g------fCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 40 GKERDYILEGG------FCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred ccccceEEEcC------cccCHHHHhHhhhcCcccchhhhhe
Confidence 33445666432 899999872 34579999875
No 20
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.89 E-value=27 Score=34.24 Aligned_cols=82 Identities=12% Similarity=0.141 Sum_probs=50.1
Q ss_pred CCEEEecceeccccCCce-eeeEEEeccCCChhhhhhhhhcCCChhHHHHHHHHHHHHhCCCCCcEEeCcccHHHHHHHH
Q 005927 235 GDVVSFDATFRLNKYNLI-CAPFVGVNHHWKNMLFGCAFLLDESTHSYVWLFESFLESMGNTQPKTIFTNENEAMSKAIE 313 (669)
Q Consensus 235 ~dvv~~D~Ty~~n~y~~p-l~~~~gv~~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~a~~~Ai~ 313 (669)
++++-+|-||.+-+-+.. |+-+ +|..|++. .+=|...-+...=.-||..+++.- ..|.+|+||+......|+.
T Consensus 70 ~~~w~vDEt~ikv~gkw~ylyrA--id~~g~~L--d~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~ 143 (215)
T COG3316 70 GDSWRVDETYIKVNGKWHYLYRA--IDADGLTL--DVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALR 143 (215)
T ss_pred ccceeeeeeEEeeccEeeehhhh--hccCCCeE--EEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHH
Confidence 356667777765322221 2222 23333332 223333333444455666766665 6899999999999999999
Q ss_pred HHcccCccc
Q 005927 314 TVFMKTRHR 322 (669)
Q Consensus 314 ~vfP~a~h~ 322 (669)
+.-+.+.|+
T Consensus 144 ~l~~~~ehr 152 (215)
T COG3316 144 KLGSEVEHR 152 (215)
T ss_pred hcCcchhee
Confidence 999977665
No 21
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=38.50 E-value=68 Score=28.63 Aligned_cols=38 Identities=32% Similarity=0.360 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccccCCCCCCcCCcccc
Q 005927 623 EKLAEAMELLEKDEEIVNRLAHAKKVDSSPSLNAISDI 660 (669)
Q Consensus 623 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 660 (669)
+...+.+..++++||.+.|+-+...-++|.+..+++|.
T Consensus 77 ~~~~evL~sv~KtEeSL~rlkk~~~~~~~~~~~~~sD~ 114 (125)
T PF12022_consen 77 EIASEVLTSVRKTEESLKRLKKRRKRTSGSSSGGMSDD 114 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCCCcH
Confidence 44556677889999999999888777777766888875
No 22
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=32.73 E-value=17 Score=36.09 Aligned_cols=24 Identities=21% Similarity=0.555 Sum_probs=19.8
Q ss_pred eEEeEeccccccCcchhhHHHHhhccc
Q 005927 526 DISCSCKLFERMGILCRHALKAFDFNN 552 (669)
Q Consensus 526 ~~~CsC~~fe~~GipC~HiL~Vl~~~~ 552 (669)
...|||..+. .||.||-+|.-++.
T Consensus 124 ~~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 124 STDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred ccccCCCCcc---cchHHHHHHHHHHH
Confidence 4689999975 69999999987654
No 23
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=25.86 E-value=1.7e+02 Score=29.85 Aligned_cols=72 Identities=8% Similarity=-0.064 Sum_probs=48.7
Q ss_pred CCEEEecceeccccCCceeeeEEEeccCCChhhhhhhhhcC-CChhHHHHHHHHHHHHh-C---CCCCcEEeCcccHH
Q 005927 235 GDVVSFDATFRLNKYNLICAPFVGVNHHWKNMLFGCAFLLD-ESTHSYVWLFESFLESM-G---NTQPKTIFTNENEA 307 (669)
Q Consensus 235 ~dvv~~D~Ty~~n~y~~pl~~~~gv~~~~~~~~~~~al~~~-Et~es~~w~l~~f~~~~-~---~~~p~~iitD~~~a 307 (669)
..+.+.|-||.....+.-++..+.+|.+.+ .++|+++-.. .+.+...-+|+..++.. + ...|..|.||+...
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 478889988866544556788888888776 5678888764 56666666666544433 2 23578889998743
No 24
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=25.52 E-value=68 Score=31.88 Aligned_cols=19 Identities=11% Similarity=0.272 Sum_probs=15.4
Q ss_pred ccCCccccccccceEEEEE
Q 005927 83 RCNRLETRTGCKVLMRFTV 101 (669)
Q Consensus 83 ~r~~~~~rtgCpa~i~v~~ 101 (669)
++...+.+.+|||+|.++.
T Consensus 70 ~~~~~skK~~CPA~I~Ik~ 88 (225)
T PF15299_consen 70 RRSKPSKKRDCPARIYIKE 88 (225)
T ss_pred cccccccCCCCCeEEEEEE
Confidence 4456788999999999983
No 25
>PHA02517 putative transposase OrfB; Reviewed
Probab=25.15 E-value=1.6e+02 Score=29.94 Aligned_cols=71 Identities=10% Similarity=-0.028 Sum_probs=43.5
Q ss_pred CCEEEecceeccccCCceeeeEEEeccCCChhhhhhhhhcCCChhHHHHHHHHHHHHhCCCCCcEEeCcccHH
Q 005927 235 GDVVSFDATFRLNKYNLICAPFVGVNHHWKNMLFGCAFLLDESTHSYVWLFESFLESMGNTQPKTIFTNENEA 307 (669)
Q Consensus 235 ~dvv~~D~Ty~~n~y~~pl~~~~gv~~~~~~~~~~~al~~~Et~es~~w~l~~f~~~~~~~~p~~iitD~~~a 307 (669)
+++++.|.||.....+ -.+.++.+|...+. ++|+.+-..++.+...-.|+......+...+..|.||+...
T Consensus 110 n~~w~~D~t~~~~~~g-~~yl~~iiD~~sr~-i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~i~~sD~G~~ 180 (277)
T PHA02517 110 NQLWVADFTYVSTWQG-WVYVAFIIDVFARR-IVGWRVSSSMDTDFVLDALEQALWARGRPGGLIHHSDKGSQ 180 (277)
T ss_pred CCeEEeceeEEEeCCC-CEEEEEecccCCCe-eeecccCCCCChHHHHHHHHHHHHhcCCCcCcEeecccccc
Confidence 4788899998654433 34666666666554 55777777777776554444444433322334667898744
No 26
>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=25.01 E-value=1.8e+02 Score=25.42 Aligned_cols=36 Identities=19% Similarity=0.418 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHhcCceEEecceeecCCCCeEEEEE
Q 005927 30 AEAYNLCNNYAFRKGFSLRKGHVRRDASGNIRQRDF 65 (669)
Q Consensus 30 eea~~fy~~YA~~~GF~vr~~~s~~~~~g~~~~~~f 65 (669)
.+.++.|.+||.+.||.+.+-.......|.++...+
T Consensus 66 ~~L~~MY~~~a~~~gw~~~~l~~~~~~~~G~k~a~~ 101 (115)
T PF03462_consen 66 EELFRMYQRYAERRGWKVEVLDYSPGEEGGIKSATL 101 (115)
T ss_dssp HHHHHHHHHHHHHTT-EEEEEEEEE-SSSSEEEEEE
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCCCccceeEEEE
Confidence 567899999999999999988776433355655555
No 27
>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=24.52 E-value=55 Score=28.05 Aligned_cols=39 Identities=26% Similarity=0.391 Sum_probs=24.5
Q ss_pred ccCCCCCCCC---CCCCccCCHHHHHHHHHHHHHhcCceEEeccee
Q 005927 11 LEGIGNDGEL---KVGTEVKSDAEAYNLCNNYAFRKGFSLRKGHVR 53 (669)
Q Consensus 11 ~~~~~~~~~p---~~G~~F~S~eea~~fy~~YA~~~GF~vr~~~s~ 53 (669)
|.|+--...| .+.+.|+|.|+|.. ||.++|....+.--.
T Consensus 37 LMGWtss~D~~~q~v~l~F~skE~Ai~----yaer~G~~Y~V~~p~ 78 (101)
T PF04800_consen 37 LMGWTSSGDPLSQSVRLKFDSKEDAIA----YAERNGWDYEVEEPK 78 (101)
T ss_dssp TT-SSSS--SEEE-CEEEESSHHHHHH----HHHHCT-EEEEE-ST
T ss_pred ccCCCCCCChhhCeeEeeeCCHHHHHH----HHHHcCCeEEEeCCC
Confidence 4444443444 37899999999985 688999888765543
No 28
>PF13773 DUF4170: Domain of unknown function (DUF4170)
Probab=23.80 E-value=81 Score=24.79 Aligned_cols=24 Identities=29% Similarity=0.124 Sum_probs=19.3
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHHh
Q 005927 18 GELKVGTEVKSDAEAYNLCNNYAFR 42 (669)
Q Consensus 18 ~~p~~G~~F~S~eea~~fy~~YA~~ 42 (669)
.+-.|| .|+++++|+++++.-|.+
T Consensus 25 ~~diVG-~fp~y~~A~~aWrakAq~ 48 (69)
T PF13773_consen 25 ALDIVG-IFPDYASAYAAWRAKAQR 48 (69)
T ss_pred cceEEe-cCCChHHHHHHHHHHHhC
Confidence 334566 899999999999988864
No 29
>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=23.03 E-value=1.2e+02 Score=21.89 Aligned_cols=44 Identities=9% Similarity=0.148 Sum_probs=27.2
Q ss_pred HHHHHHhccCCHHHHHHHHHHHHhhcCCCchHHHHHHHHhhcccc
Q 005927 348 YLNKCFYECHDETEFQVSWDDMINKFSLGDHLWLKKLYSLRDKWC 392 (669)
Q Consensus 348 ~~~~~v~~~~~~~eFe~~w~~l~~~~~~~~~~~l~~~~~~r~~W~ 392 (669)
.|...|. |++...|.....++...-.--+..|...+-+.+++|-
T Consensus 6 ~Fe~~In-S~SK~~Fv~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 49 (51)
T PF11433_consen 6 KFESYIN-SESKSVFVRNLTELERISKRLGKSYQIRLEEAKEKWK 49 (51)
T ss_dssp HHHHHHH-S--HHHHHHHHHHHHHHHHHH-SHHHHHHHHHHHHH-
T ss_pred HHHHHhC-CccHHHHHHhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 4555555 8888899988887765222223467777777888884
No 30
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=22.18 E-value=2e+02 Score=29.90 Aligned_cols=72 Identities=10% Similarity=-0.027 Sum_probs=49.2
Q ss_pred CCEEEecceeccccCCceeeeEEEeccCCChhhhhhhhhcC-CChhHHHHHHHHHHHH-hCC---CCCcEEeCcccHH
Q 005927 235 GDVVSFDATFRLNKYNLICAPFVGVNHHWKNMLFGCAFLLD-ESTHSYVWLFESFLES-MGN---TQPKTIFTNENEA 307 (669)
Q Consensus 235 ~dvv~~D~Ty~~n~y~~pl~~~~gv~~~~~~~~~~~al~~~-Et~es~~w~l~~f~~~-~~~---~~p~~iitD~~~a 307 (669)
..+.+.|-||....-+.-++..+.+|.+.+ .++|+++-.. .+.+...-+|+..+.. .+. ..|..|.||+...
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 478999999865444445777777887776 5678988875 5777766666654433 332 2467889998743
Done!