Query 046610
Match_columns 411
No_of_seqs 172 out of 1074
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 02:36:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046610.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046610hhsearch_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 2.7E-37 5.8E-42 333.6 29.0 254 123-411 76-380 (846)
2 PF10551 MULE: MULE transposas 99.8 4.6E-21 1E-25 155.7 7.3 86 322-411 1-89 (93)
3 PF03108 DBD_Tnp_Mut: MuDR fam 99.5 1.3E-13 2.9E-18 105.4 7.9 62 123-184 6-67 (67)
4 PF00872 Transposase_mut: Tran 99.3 5E-13 1.1E-17 135.7 0.2 93 315-411 162-260 (381)
5 COG3328 Transposase and inacti 99.0 2.1E-09 4.5E-14 108.3 10.0 93 314-411 144-239 (379)
6 PF08731 AFT: Transcription fa 98.7 7.6E-08 1.7E-12 79.5 8.8 69 127-195 1-111 (111)
7 PF03101 FAR1: FAR1 DNA-bindin 98.4 7.8E-07 1.7E-11 71.7 6.4 59 136-195 2-89 (91)
8 PF03106 WRKY: WRKY DNA -bindi 94.6 0.11 2.3E-06 38.8 5.6 42 153-194 18-59 (60)
9 PF01610 DDE_Tnp_ISL3: Transpo 92.5 0.27 6E-06 46.6 6.1 86 318-411 1-89 (249)
10 PF13610 DDE_Tnp_IS240: DDE do 90.9 0.12 2.7E-06 44.9 1.6 79 316-400 2-80 (140)
11 smart00774 WRKY DNA binding do 89.6 0.56 1.2E-05 34.8 3.9 40 154-193 19-59 (59)
12 PF04500 FLYWCH: FLYWCH zinc f 84.5 1.9 4.1E-05 31.2 4.4 46 144-193 14-62 (62)
13 PF04684 BAF1_ABF1: BAF1 / ABF 83.4 2.2 4.7E-05 44.1 5.6 54 123-176 24-78 (496)
14 PF06782 UPF0236: Uncharacteri 80.9 5.8 0.00013 41.8 7.9 55 355-410 235-289 (470)
15 PF00665 rve: Integrase core d 80.5 11 0.00023 30.8 8.0 76 314-392 5-81 (120)
16 COG3316 Transposase and inacti 58.9 21 0.00045 33.6 5.4 81 316-404 71-152 (215)
17 PF13565 HTH_32: Homeodomain-l 58.0 13 0.00029 28.2 3.4 26 213-238 41-66 (77)
18 PF04937 DUF659: Protein of un 54.9 60 0.0013 28.7 7.5 53 356-410 73-128 (153)
19 PF03050 DDE_Tnp_IS66: Transpo 42.8 29 0.00063 33.2 3.9 76 314-410 66-146 (271)
20 PRK09409 IS2 transposase TnpB; 40.4 1.3E+02 0.0029 29.5 8.2 77 314-391 125-204 (301)
21 PRK14702 insertion element IS2 39.5 1.4E+02 0.0031 28.7 8.1 76 314-390 86-164 (262)
22 PHA02517 putative transposase 37.0 1.2E+02 0.0026 29.0 7.2 73 314-391 109-182 (277)
23 PF14201 DUF4318: Domain of un 34.0 59 0.0013 25.3 3.6 30 126-155 13-42 (74)
24 PF12762 DDE_Tnp_IS1595: ISXO2 31.3 1.2E+02 0.0026 26.0 5.7 67 317-391 5-87 (151)
25 COG3915 Uncharacterized protei 30.8 55 0.0012 28.5 3.1 37 307-344 97-135 (155)
26 PRK00766 hypothetical protein; 25.6 4.8E+02 0.01 24.1 8.6 90 316-405 10-129 (194)
27 PF13592 HTH_33: Winged helix- 24.8 61 0.0013 23.7 2.2 21 219-239 3-23 (60)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=2.7e-37 Score=333.60 Aligned_cols=254 Identities=11% Similarity=0.123 Sum_probs=202.7
Q ss_pred CChhhhcHHHHHHHHHHHHHHcCeeEEEeeCCCe-------EEEEEecC-------------------------------
Q 046610 123 EDDEELQRSWFRRALEVQAIRDGIKLCKMDNTST-------CISCECSD------------------------------- 164 (411)
Q Consensus 123 ~d~~~~s~ee~r~av~~yAi~~~f~~~v~rS~~~-------r~~~~C~~------------------------------- 164 (411)
.+-+|.+.++++++++.||...||.+++.++.+. ..+++|.+
T Consensus 76 vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~~~rR~ 155 (846)
T PLN03097 76 SGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENGTGRRS 155 (846)
T ss_pred CCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccccccccc
Confidence 3456889999999999999999999988654321 22456653
Q ss_pred ---CCCceEEEEEEccCcceEEEeeecCCCCCcccccccchhhhHHHHHHhhhhhcCCCCCHHHHHHHHHHHhcc--cCC
Q 046610 165 ---LSCDWKITTMKEHATKMFIISYITPVHKCTKRLSKLKWGTKWITAKFLHKWKQNPHQQLHVLGNEIAATYGI--KCP 239 (411)
Q Consensus 165 ---~~CpwrV~as~~~~~~~w~I~~~~~~HnC~~r~~t~~~ia~~i~~kf~~~l~~np~~~p~~I~~~v~k~~gi--~is 239 (411)
+|||++|.+.+. ..|.|.|+.+..+|||++..... +... .+.+...+.+..+. .+.
T Consensus 156 ~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~--~~~~----------------~r~~~~~~~~~~~~~~~v~ 216 (846)
T PLN03097 156 CAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQA--VSEQ----------------TRKMYAAMARQFAEYKNVV 216 (846)
T ss_pred ccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccc--cchh----------------hhhhHHHHHhhhhcccccc
Confidence 479999999874 45789999999999999932111 1100 01111111111110 000
Q ss_pred --------cchhhhhhHHHHHhcccCcchhHHHHHHHHHHHHhhCCccEEEEEeCCCCCCCccceeeeeEeehhhHHHHH
Q 046610 240 --------IWKLKAIDTTARMWLGLDHGEGYAQLLQYREEMEMINSHNIIIIETSTKQQSSDEIFDCMFVFLYDTAYAFK 311 (411)
Q Consensus 240 --------~~raK~~a~~~l~~i~gd~~esy~~L~~yl~~l~~~NPgs~v~i~t~~~~~~~~~~F~~lf~~~~~si~~f~ 311 (411)
..+.++. ++. ..++...|..|+++++..||+++|.++.| ++++++++||+++.|+.+|.
T Consensus 217 ~~~~d~~~~~~~~r~----~~~----~~gD~~~ll~yf~~~q~~nP~Ffy~~qlD-----e~~~l~niFWaD~~sr~~Y~ 283 (846)
T PLN03097 217 GLKNDSKSSFDKGRN----LGL----EAGDTKILLDFFTQMQNMNSNFFYAVDLG-----EDQRLKNLFWVDAKSRHDYG 283 (846)
T ss_pred ccchhhcchhhHHHh----hhc----ccchHHHHHHHHHHHHhhCCCceEEEEEc-----cCCCeeeEEeccHHHHHHHH
Confidence 1111110 111 13467789999999999999999999999 89999999999999999999
Q ss_pred hcCceeeeeeceeeccCCCCceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhhcCCCCCCcEEEEccCchHHH
Q 046610 312 TRCRMLLTVDGWEIDGPYKSVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDGLRLERGKGLCILGDGDNGID 391 (411)
Q Consensus 312 ~~cr~vl~iD~t~~~~~y~g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~l~~~~~~~~~iisDr~~gL~ 391 (411)
+ |++||.+|+||++|+|++||..++|+|++++++++|+||+..|+.++|.|+|+.++++|++. +|.+||||++.+|.
T Consensus 284 ~-FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk--~P~tIiTDqd~am~ 360 (846)
T PLN03097 284 N-FSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQ--APKVIITDQDKAMK 360 (846)
T ss_pred h-cCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCC--CCceEEecCCHHHH
Confidence 8 99999999999999999999999999999999999999999999999999999999999987 46999999999999
Q ss_pred HHHHHhCCcccccccccccC
Q 046610 392 EAVEEFLPYAVYRQCCFSLY 411 (411)
Q Consensus 392 ~Ai~~vfP~a~h~~C~~Hi~ 411 (411)
+||.+|||++.|++|.|||+
T Consensus 361 ~AI~~VfP~t~Hr~C~wHI~ 380 (846)
T PLN03097 361 SVISEVFPNAHHCFFLWHIL 380 (846)
T ss_pred HHHHHHCCCceehhhHHHHH
Confidence 99999999999999999985
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=99.84 E-value=4.6e-21 Score=155.71 Aligned_cols=86 Identities=29% Similarity=0.453 Sum_probs=81.5
Q ss_pred ceeeccCCCCceEE---EEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhhcCCCCCCcEEEEccCchHHHHHHHHhC
Q 046610 322 GWEIDGPYKSVMLI---AVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDGLRLERGKGLCILGDGDNGIDEAVEEFL 398 (411)
Q Consensus 322 ~t~~~~~y~g~ll~---avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~l~~~~~~~~~iisDr~~gL~~Ai~~vf 398 (411)
|||++|+| |+++. ++|+|++++.+|+||+++++|+.++|.|||+.+++.++.. |.+||+|++.|+.+||+++|
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~---p~~ii~D~~~~~~~Ai~~vf 76 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK---PKVIISDFDKALINAIKEVF 76 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC---ceeeeccccHHHHHHHHHHC
Confidence 79999999 98886 9999999999999999999999999999999999988763 58999999999999999999
Q ss_pred CcccccccccccC
Q 046610 399 PYAVYRQCCFSLY 411 (411)
Q Consensus 399 P~a~h~~C~~Hi~ 411 (411)
|++.|++|.||++
T Consensus 77 P~~~~~~C~~H~~ 89 (93)
T PF10551_consen 77 PDARHQLCLFHIL 89 (93)
T ss_pred CCceEehhHHHHH
Confidence 9999999999974
No 3
>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=99.48 E-value=1.3e-13 Score=105.41 Aligned_cols=62 Identities=19% Similarity=0.418 Sum_probs=59.1
Q ss_pred CChhhhcHHHHHHHHHHHHHHcCeeEEEeeCCCeEEEEEecCCCCceEEEEEEccCcceEEE
Q 046610 123 EDDEELQRSWFRRALEVQAIRDGIKLCKMDNTSTCISCECSDLSCDWKITTMKEHATKMFII 184 (411)
Q Consensus 123 ~d~~~~s~ee~r~av~~yAi~~~f~~~v~rS~~~r~~~~C~~~~CpwrV~as~~~~~~~w~I 184 (411)
.+..|.+++||+.||..|||++++++++.+|++.|++++|...+|||+|+|++.+.++.|+|
T Consensus 6 ~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 6 VGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred cCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 46679999999999999999999999999999999999999999999999999999999986
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=99.28 E-value=5e-13 Score=135.71 Aligned_cols=93 Identities=26% Similarity=0.433 Sum_probs=84.9
Q ss_pred ceeeeeeceeeccCCC-----CceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHh-hcCCCCCCcEEEEccCch
Q 046610 315 RMLLTVDGWEIDGPYK-----SVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVND-GLRLERGKGLCILGDGDN 388 (411)
Q Consensus 315 r~vl~iD~t~~~~~y~-----g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~-~l~~~~~~~~~iisDr~~ 388 (411)
.|+|.|||+|++.+.+ ..+++|+|+|.+|+..+||+.+.+.|+.++|.-||+.|++ ++.. |..||+|+++
T Consensus 162 y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~RGl~~----~~lvv~Dg~~ 237 (381)
T PF00872_consen 162 YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKERGLKD----ILLVVSDGHK 237 (381)
T ss_pred ccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhccccc----cceeeccccc
Confidence 4789999999987744 4689999999999999999999999999999999999998 5653 4789999999
Q ss_pred HHHHHHHHhCCcccccccccccC
Q 046610 389 GIDEAVEEFLPYAVYRQCCFSLY 411 (411)
Q Consensus 389 gL~~Ai~~vfP~a~h~~C~~Hi~ 411 (411)
||.+||.++||+|.+|.|.+|++
T Consensus 238 gl~~ai~~~fp~a~~QrC~vH~~ 260 (381)
T PF00872_consen 238 GLKEAIREVFPGAKWQRCVVHLM 260 (381)
T ss_pred cccccccccccchhhhhheechh
Confidence 99999999999999999999985
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.98 E-value=2.1e-09 Score=108.28 Aligned_cols=93 Identities=20% Similarity=0.268 Sum_probs=83.8
Q ss_pred CceeeeeeceeeccC--CCCceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHh-hcCCCCCCcEEEEccCchHH
Q 046610 314 CRMLLTVDGWEIDGP--YKSVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVND-GLRLERGKGLCILGDGDNGI 390 (411)
Q Consensus 314 cr~vl~iD~t~~~~~--y~g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~-~l~~~~~~~~~iisDr~~gL 390 (411)
..+++.+||+|++.+ -+..+++|+|++.+|+...+++.+...|+ ..|.-||..|+. ++.+ ...+++|.++||
T Consensus 144 ~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl~~----v~l~v~Dg~~gl 218 (379)
T COG3328 144 DYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGLSD----VLLVVVDGLKGL 218 (379)
T ss_pred CceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccccc----eeEEecchhhhh
Confidence 678999999999988 45679999999999999999999999999 999988888888 4664 367788999999
Q ss_pred HHHHHHhCCcccccccccccC
Q 046610 391 DEAVEEFLPYAVYRQCCFSLY 411 (411)
Q Consensus 391 ~~Ai~~vfP~a~h~~C~~Hi~ 411 (411)
.+||.++||.+.++.|+.|++
T Consensus 219 ~~aI~~v~p~a~~Q~C~vH~~ 239 (379)
T COG3328 219 PEAISAVFPQAAVQRCIVHLV 239 (379)
T ss_pred HHHHHHhccHhhhhhhhhHHH
Confidence 999999999999999999974
No 6
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=98.71 E-value=7.6e-08 Score=79.51 Aligned_cols=69 Identities=13% Similarity=0.195 Sum_probs=64.2
Q ss_pred hhcHHHHHHHHHHHHHHcCeeEEEeeCCCeEEEEEecC------------------------------------------
Q 046610 127 ELQRSWFRRALEVQAIRDGIKLCKMDNTSTCISCECSD------------------------------------------ 164 (411)
Q Consensus 127 ~~s~ee~r~av~~yAi~~~f~~~v~rS~~~r~~~~C~~------------------------------------------ 164 (411)
|-+++|++.+|+.++..+|+++.+.||+...+.++|..
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k~t~srk 80 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKKIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKKRTKSRK 80 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCceEEEEEecCCCcccccccccccccccccccccccccccccccCCcccccc
Confidence 45789999999999999999999999999999999982
Q ss_pred CCCceEEEEEEccCcceEEEeeecCCCCCcc
Q 046610 165 LSCDWKITTMKEHATKMFIISYITPVHKCTK 195 (411)
Q Consensus 165 ~~CpwrV~as~~~~~~~w~I~~~~~~HnC~~ 195 (411)
..|||+|+|+.....+.|.|..+++.|+|++
T Consensus 81 ~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 81 NTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 5899999999999999999999999999974
No 7
>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=98.38 E-value=7.8e-07 Score=71.73 Aligned_cols=59 Identities=15% Similarity=0.246 Sum_probs=52.0
Q ss_pred HHHHHHHHcCeeEEEeeCCC-------eEEEEEecC----------------------CCCceEEEEEEccCcceEEEee
Q 046610 136 ALEVQAIRDGIKLCKMDNTS-------TCISCECSD----------------------LSCDWKITTMKEHATKMFIISY 186 (411)
Q Consensus 136 av~~yAi~~~f~~~v~rS~~-------~r~~~~C~~----------------------~~CpwrV~as~~~~~~~w~I~~ 186 (411)
+++.||...||.++..+|.+ .++.++|.+ ++|||+|.+.+.+ .+.|.|+.
T Consensus 2 fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~~ 80 (91)
T PF03101_consen 2 FYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK-DGKWRVTS 80 (91)
T ss_pred HHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc-CCEEEEEE
Confidence 57899999999999987654 378889984 7999999999987 88999999
Q ss_pred ecCCCCCcc
Q 046610 187 ITPVHKCTK 195 (411)
Q Consensus 187 ~~~~HnC~~ 195 (411)
+..+|||++
T Consensus 81 ~~~~HNH~L 89 (91)
T PF03101_consen 81 FVLEHNHPL 89 (91)
T ss_pred CcCCcCCCC
Confidence 999999986
No 8
>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=94.61 E-value=0.11 Score=38.82 Aligned_cols=42 Identities=12% Similarity=0.141 Sum_probs=33.6
Q ss_pred CCCeEEEEEecCCCCceEEEEEEccCcceEEEeeecCCCCCc
Q 046610 153 NTSTCISCECSDLSCDWKITTMKEHATKMFIISYITPVHKCT 194 (411)
Q Consensus 153 S~~~r~~~~C~~~~CpwrV~as~~~~~~~w~I~~~~~~HnC~ 194 (411)
|.-.|.-++|+..+||.+-.+.+....+...++++.++|||+
T Consensus 18 ~~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 18 SPYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp TTCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 334677799999999999999998777788899999999996
No 9
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=92.52 E-value=0.27 Score=46.60 Aligned_cols=86 Identities=15% Similarity=0.184 Sum_probs=61.3
Q ss_pred eeeeceeeccCCCCceEEEEEecC--CCCEEEeeeeeecccchhhHHHHHHHH-HhhcCCCCCCcEEEEccCchHHHHHH
Q 046610 318 LTVDGWEIDGPYKSVMLIAVCRDR--NDVVLPVAFCEVQEENLDSWAFFLKNV-NDGLRLERGKGLCILGDGDNGIDEAV 394 (411)
Q Consensus 318 l~iD~t~~~~~y~g~ll~avg~d~--~~~~~~lAfalv~~E~~e~w~WfL~~l-~~~l~~~~~~~~~iisDr~~gL~~Ai 394 (411)
|+||=+.....+.. +..+-.|. ++... ++++++-+.+...=||..+ -..... .+.+|++|...+-.+||
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~i---l~i~~~r~~~~l~~~~~~~~~~~~~~---~v~~V~~Dm~~~y~~~~ 72 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGRI---LDILPGRDKETLKDFFRSLYPEEERK---NVKVVSMDMSPPYRSAI 72 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCceE---EEEcCCccHHHHHHHHHHhCcccccc---ceEEEEcCCCccccccc
Confidence 57787766543332 33444444 33322 3588899999988777776 333222 35789999999999999
Q ss_pred HHhCCcccccccccccC
Q 046610 395 EEFLPYAVYRQCCFSLY 411 (411)
Q Consensus 395 ~~vfP~a~h~~C~~Hi~ 411 (411)
.+.||+|.+..-.+|++
T Consensus 73 ~~~~P~A~iv~DrFHvv 89 (249)
T PF01610_consen 73 REYFPNAQIVADRFHVV 89 (249)
T ss_pred cccccccccccccchhh
Confidence 99999999999999985
No 10
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=90.89 E-value=0.12 Score=44.95 Aligned_cols=79 Identities=19% Similarity=0.044 Sum_probs=65.1
Q ss_pred eeeeeeceeeccCCCCceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhhcCCCCCCcEEEEccCchHHHHHHH
Q 046610 316 MLLTVDGWEIDGPYKSVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDGLRLERGKGLCILGDGDNGIDEAVE 395 (411)
Q Consensus 316 ~vl~iD~t~~~~~y~g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~l~~~~~~~~~iisDr~~gL~~Ai~ 395 (411)
..+.+|-||.+.+=. ..+..-.+|.+++ +|.|-|-+.-+...=..||..+.+.... .|..|++|+.++...|+.
T Consensus 2 ~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~~---~p~~ivtDk~~aY~~A~~ 75 (140)
T PF13610_consen 2 DSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHRG---EPRVIVTDKLPAYPAAIK 75 (140)
T ss_pred CEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeecc---ccceeecccCCccchhhh
Confidence 467899999875422 3455677899998 8899999999999989999988887652 468999999999999999
Q ss_pred HhCCc
Q 046610 396 EFLPY 400 (411)
Q Consensus 396 ~vfP~ 400 (411)
++.|.
T Consensus 76 ~l~~~ 80 (140)
T PF13610_consen 76 ELNPE 80 (140)
T ss_pred hcccc
Confidence 99986
No 11
>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=89.60 E-value=0.56 Score=34.80 Aligned_cols=40 Identities=10% Similarity=0.059 Sum_probs=32.0
Q ss_pred CCeEEEEEecC-CCCceEEEEEEccCcceEEEeeecCCCCC
Q 046610 154 TSTCISCECSD-LSCDWKITTMKEHATKMFIISYITPVHKC 193 (411)
Q Consensus 154 ~~~r~~~~C~~-~~CpwrV~as~~~~~~~w~I~~~~~~HnC 193 (411)
...|.-++|.. .+||.+=.+.+....+.-.++++.++|||
T Consensus 19 ~~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 19 PFPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cCcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 34566689998 89999888887765666778889999998
No 12
>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=84.54 E-value=1.9 Score=31.21 Aligned_cols=46 Identities=15% Similarity=0.125 Sum_probs=24.8
Q ss_pred cCeeEEEeeCCCeEEEEEecCC---CCceEEEEEEccCcceEEEeeecCCCCC
Q 046610 144 DGIKLCKMDNTSTCISCECSDL---SCDWKITTMKEHATKMFIISYITPVHKC 193 (411)
Q Consensus 144 ~~f~~~v~rS~~~r~~~~C~~~---~CpwrV~as~~~~~~~w~I~~~~~~HnC 193 (411)
.|+.|...+.........|... +|+.+|... .. .-.+.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~--~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AG--DGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CC--CCEEEECCCccCC
Confidence 5778877766677888999963 899999988 22 2335555688987
No 13
>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=83.42 E-value=2.2 Score=44.06 Aligned_cols=54 Identities=7% Similarity=0.083 Sum_probs=47.6
Q ss_pred CChhhhcHHHHHHHHHHHHHHcCeeEEEeeCC-CeEEEEEecCCCCceEEEEEEc
Q 046610 123 EDDEELQRSWFRRALEVQAIRDGIKLCKMDNT-STCISCECSDLSCDWKITTMKE 176 (411)
Q Consensus 123 ~d~~~~s~ee~r~av~~yAi~~~f~~~v~rS~-~~r~~~~C~~~~CpwrV~as~~ 176 (411)
+...|+..+.--.+|+.|-...+.++..+.|- .+.|++-|--..|||+|..+-.
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~ 78 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYC 78 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeec
Confidence 34568999999999999999999999999885 5789999999999999988753
No 14
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=80.89 E-value=5.8 Score=41.75 Aligned_cols=55 Identities=31% Similarity=0.465 Sum_probs=45.5
Q ss_pred ccchhhHHHHHHHHHhhcCCCCCCcEEEEccCchHHHHHHHHhCCccccccccccc
Q 046610 355 EENLDSWAFFLKNVNDGLRLERGKGLCILGDGDNGIDEAVEEFLPYAVYRQCCFSL 410 (411)
Q Consensus 355 ~E~~e~w~WfL~~l~~~l~~~~~~~~~iisDr~~gL~~Ai~~vfP~a~h~~C~~Hi 410 (411)
..+.+-|.-+++.+.+.........+++.+|+...|.+++. .||++.|.+..+|+
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl 289 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHL 289 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHH
Confidence 56678899999988886655433348899999999988876 89999999999997
No 15
>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=80.48 E-value=11 Score=30.84 Aligned_cols=76 Identities=13% Similarity=-0.023 Sum_probs=54.3
Q ss_pred Cceeeeeeceeec-cCCCCceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhhcCCCCCCcEEEEccCchHHHH
Q 046610 314 CRMLLTVDGWEID-GPYKSVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDGLRLERGKGLCILGDGDNGIDE 392 (411)
Q Consensus 314 cr~vl~iD~t~~~-~~y~g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~l~~~~~~~~~iisDr~~gL~~ 392 (411)
....+.+|.+++. ...++.....+.+|..-+.. +++.+-..++.+.+.-+|.......+.. +|.+|++|+.+....
T Consensus 5 p~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 5 PGERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFI-YAFPVSSKETAEAALRALKRAIEKRGGR--PPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTTEEEEEEEEETGGCTT-CEEEEEEEETTTTEE-EEEEESSSSHHHHHHHHHHHHHHHHS-S--E-SEEEEESCHHHHS
T ss_pred CCCEEEEeeEEEecCCCCccEEEEEEEECCCCcE-EEEEeecccccccccccccccccccccc--cceeccccccccccc
Confidence 3457899999776 34566788888888876654 4677777778888888888766655543 158999999998873
No 16
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.91 E-value=21 Score=33.58 Aligned_cols=81 Identities=17% Similarity=0.031 Sum_probs=56.9
Q ss_pred eeeeeeceeeccCCCC-ceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhhcCCCCCCcEEEEccCchHHHHHH
Q 046610 316 MLLTVDGWEIDGPYKS-VMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDGLRLERGKGLCILGDGDNGIDEAV 394 (411)
Q Consensus 316 ~vl~iD~t~~~~~y~g-~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~l~~~~~~~~~iisDr~~gL~~Ai 394 (411)
.++.||-||.+.+-+- -|..| +|.+| .+|-+-|.+.-|...=.=||..+++..+ .|.+|++|+.+....|+
T Consensus 71 ~~w~vDEt~ikv~gkw~ylyrA--id~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~g----~p~v~vtDka~s~~~A~ 142 (215)
T COG3316 71 DSWRVDETYIKVNGKWHYLYRA--IDADG--LTLDVWLSKRRNALAAKAFLKKLLKKHG----EPRVFVTDKAPSYTAAL 142 (215)
T ss_pred cceeeeeeEEeeccEeeehhhh--hccCC--CeEEEEEEcccCcHHHHHHHHHHHHhcC----CCceEEecCccchHHHH
Confidence 4577888888754322 23344 45554 4556677777777777777777777552 35789999999999999
Q ss_pred HHhCCccccc
Q 046610 395 EEFLPYAVYR 404 (411)
Q Consensus 395 ~~vfP~a~h~ 404 (411)
.++-+.+.|+
T Consensus 143 ~~l~~~~ehr 152 (215)
T COG3316 143 RKLGSEVEHR 152 (215)
T ss_pred HhcCcchhee
Confidence 9998866665
No 17
>PF13565 HTH_32: Homeodomain-like domain
Probab=58.02 E-value=13 Score=28.18 Aligned_cols=26 Identities=12% Similarity=0.275 Sum_probs=23.3
Q ss_pred hhhhcCCCCCHHHHHHHHHHHhcccC
Q 046610 213 HKWKQNPHQQLHVLGNEIAATYGIKC 238 (411)
Q Consensus 213 ~~l~~np~~~p~~I~~~v~k~~gi~i 238 (411)
..+..+|.+++.+|...|.+++|+.+
T Consensus 41 ~~~~~~p~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 41 ALIEEHPRWTPREIAEYLEEEFGISV 66 (77)
T ss_pred HHHHhCCCCCHHHHHHHHHHHhCCCC
Confidence 66678999999999999999999866
No 18
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=54.90 E-value=60 Score=28.75 Aligned_cols=53 Identities=13% Similarity=0.172 Sum_probs=39.2
Q ss_pred cchhhHHHHHHHHHhhcCCCCCCcEEEEccCchHHHHHHHH---hCCccccccccccc
Q 046610 356 ENLDSWAFFLKNVNDGLRLERGKGLCILGDGDNGIDEAVEE---FLPYAVYRQCCFSL 410 (411)
Q Consensus 356 E~~e~w~WfL~~l~~~l~~~~~~~~~iisDr~~gL~~Ai~~---vfP~a~h~~C~~Hi 410 (411)
.+.+...-+|+.+.+.++..+ .+-||||-.....+|-+. -+|...+..|..|-
T Consensus 73 ~~a~~l~~ll~~vIeeVG~~n--VvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~ 128 (153)
T PF04937_consen 73 KTAEYLFELLDEVIEEVGEEN--VVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHC 128 (153)
T ss_pred ccHHHHHHHHHHHHHHhhhhh--hhHHhccCchhHHHHHHHHHhcCCCEEEechHHHH
Confidence 566666666777666666553 477899999998888544 48888888998883
No 19
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=42.81 E-value=29 Score=33.25 Aligned_cols=76 Identities=17% Similarity=0.138 Sum_probs=47.4
Q ss_pred Cceeeeeeceeec----cCCC-CceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhhcCCCCCCcEEEEccCch
Q 046610 314 CRMLLTVDGWEID----GPYK-SVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDGLRLERGKGLCILGDGDN 388 (411)
Q Consensus 314 cr~vl~iD~t~~~----~~y~-g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~l~~~~~~~~~iisDr~~ 388 (411)
-.+++.+|-|... ++.. +-+-++++-+ .+.|.+.++-+.+.-.=+ |+... =+++||+..
T Consensus 66 ~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~-------L~~~~---GilvsD~y~ 129 (271)
T PF03050_consen 66 SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEF-------LGDFS---GILVSDGYS 129 (271)
T ss_pred ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhh-------hcccc---eeeeccccc
Confidence 3578888888877 4433 3343443333 556666666665554333 33322 378999998
Q ss_pred HHHHHHHHhCCccccccccccc
Q 046610 389 GIDEAVEEFLPYAVYRQCCFSL 410 (411)
Q Consensus 389 gL~~Ai~~vfP~a~h~~C~~Hi 410 (411)
+-.. +..+.|+.|..|+
T Consensus 130 ~Y~~-----~~~~~hq~C~AH~ 146 (271)
T PF03050_consen 130 AYNK-----LAGITHQLCWAHL 146 (271)
T ss_pred cccc-----ccccccccccccc
Confidence 8754 2378999999997
No 20
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=40.40 E-value=1.3e+02 Score=29.48 Aligned_cols=77 Identities=12% Similarity=0.026 Sum_probs=51.8
Q ss_pred CceeeeeeceeeccCCCCceEEEEEecCCCCEEEeeeeeecc-cchhhHHHHHHH-HHhhcCC-CCCCcEEEEccCchHH
Q 046610 314 CRMLLTVDGWEIDGPYKSVMLIAVCRDRNDVVLPVAFCEVQE-ENLDSWAFFLKN-VNDGLRL-ERGKGLCILGDGDNGI 390 (411)
Q Consensus 314 cr~vl~iD~t~~~~~y~g~ll~avg~d~~~~~~~lAfalv~~-E~~e~w~WfL~~-l~~~l~~-~~~~~~~iisDr~~gL 390 (411)
--.+++.|-||....-++.++.++-+|...+ .+|||++... .+.+.-.=+|+. +....+. ....|.++-||+...-
T Consensus 125 pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 125 SNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred CCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 4568999999986554556888888888877 6889999875 566655555554 3333321 1113588999998654
Q ss_pred H
Q 046610 391 D 391 (411)
Q Consensus 391 ~ 391 (411)
.
T Consensus 204 ~ 204 (301)
T PRK09409 204 R 204 (301)
T ss_pred c
Confidence 3
No 21
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=39.50 E-value=1.4e+02 Score=28.68 Aligned_cols=76 Identities=11% Similarity=-0.000 Sum_probs=49.7
Q ss_pred CceeeeeeceeeccCCCCceEEEEEecCCCCEEEeeeeeecc-cchhhHHHHHHHHH-hhcCC-CCCCcEEEEccCchHH
Q 046610 314 CRMLLTVDGWEIDGPYKSVMLIAVCRDRNDVVLPVAFCEVQE-ENLDSWAFFLKNVN-DGLRL-ERGKGLCILGDGDNGI 390 (411)
Q Consensus 314 cr~vl~iD~t~~~~~y~g~ll~avg~d~~~~~~~lAfalv~~-E~~e~w~WfL~~l~-~~l~~-~~~~~~~iisDr~~gL 390 (411)
-..+++.|-||.....++.++.++-+|...+ .++||++-.. .+.+.-.=+|+... ...+. ....|.+|-||+...-
T Consensus 86 pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy 164 (262)
T PRK14702 86 SNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 164 (262)
T ss_pred CCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCccc
Confidence 3468899999987554556788887887776 7789998864 56555555555433 33221 1113588999997654
No 22
>PHA02517 putative transposase OrfB; Reviewed
Probab=36.99 E-value=1.2e+02 Score=28.95 Aligned_cols=73 Identities=15% Similarity=-0.014 Sum_probs=45.8
Q ss_pred CceeeeeeceeeccCCCCceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhhcCCCCC-CcEEEEccCchHHH
Q 046610 314 CRMLLTVDGWEIDGPYKSVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDGLRLERG-KGLCILGDGDNGID 391 (411)
Q Consensus 314 cr~vl~iD~t~~~~~y~g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~l~~~~~-~~~~iisDr~~gL~ 391 (411)
-..++..|.||+.... |..++.+-+|...+ +++||.+...++.+.. ++.|..++..... .+.+|.||+...-.
T Consensus 109 pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~---~~~l~~a~~~~~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 109 PNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFV---LDALEQALWARGRPGGLIHHSDKGSQYV 182 (277)
T ss_pred CCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHH---HHHHHHHHHhcCCCcCcEeecccccccc
Confidence 3457899999986543 55566666666554 5667888887887754 4444444322211 23567799987643
No 23
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=34.01 E-value=59 Score=25.26 Aligned_cols=30 Identities=17% Similarity=0.159 Sum_probs=26.1
Q ss_pred hhhcHHHHHHHHHHHHHHcCeeEEEeeCCC
Q 046610 126 EELQRSWFRRALEVQAIRDGIKLCKMDNTS 155 (411)
Q Consensus 126 ~~~s~ee~r~av~~yAi~~~f~~~v~rS~~ 155 (411)
.+++.+++-.||..|+.+++..+.+.+-+.
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~~ 42 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRDK 42 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecCC
Confidence 578899999999999999999999866653
No 24
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=31.35 E-value=1.2e+02 Score=26.02 Aligned_cols=67 Identities=18% Similarity=0.226 Sum_probs=36.2
Q ss_pred eeeeeceeeccCC----------------CCceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhhcCCCCCCcE
Q 046610 317 LLTVDGWEIDGPY----------------KSVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDGLRLERGKGL 380 (411)
Q Consensus 317 vl~iD~t~~~~~y----------------~g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~l~~~~~~~~ 380 (411)
++-||-||+.++- +.+++.++-++ ++..--+-..+++..+.++-.=| ++..+. +..
T Consensus 5 ~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~-~~~~~~~~~~~v~~~~~~tl~~~---i~~~i~----~gs 76 (151)
T PF12762_consen 5 IVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERN-DGGTGRVFMFVVPDRSAETLKPI---IQEHIE----PGS 76 (151)
T ss_pred EEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeec-ccCCceEEEEeecccccchhHHH---HHHhhh----ccc
Confidence 5677888875322 22455555554 12222222344566777664333 333443 237
Q ss_pred EEEccCchHHH
Q 046610 381 CILGDGDNGID 391 (411)
Q Consensus 381 ~iisDr~~gL~ 391 (411)
+|+||..++-.
T Consensus 77 ~i~TD~~~aY~ 87 (151)
T PF12762_consen 77 TIITDGWRAYN 87 (151)
T ss_pred eeeecchhhcC
Confidence 89999998764
No 25
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.84 E-value=55 Score=28.53 Aligned_cols=37 Identities=8% Similarity=0.010 Sum_probs=30.3
Q ss_pred HHHHHhcCceeeee--eceeeccCCCCceEEEEEecCCCC
Q 046610 307 AYAFKTRCRMLLTV--DGWEIDGPYKSVMLIAVCRDRNDV 344 (411)
Q Consensus 307 i~~f~~~cr~vl~i--D~t~~~~~y~g~ll~avg~d~~~~ 344 (411)
+..+.. +.|++.+ ||.|++.+.+|||..+--.|.+.+
T Consensus 97 ~sDi~k-ynpIlA~~~nGn~M~IRerGPl~~IYplds~pe 135 (155)
T COG3915 97 YSDIEK-YNPILAIQNNGNYMQIRERGPLWSIYPLDSSPE 135 (155)
T ss_pred HHHhhh-cccEEEEEeCCcEEEEeccCceEEEeecCCChh
Confidence 566776 8888765 999999999999999887777653
No 26
>PRK00766 hypothetical protein; Provisional
Probab=25.60 E-value=4.8e+02 Score=24.13 Aligned_cols=90 Identities=19% Similarity=0.137 Sum_probs=46.5
Q ss_pred eeeeeece-eeccCCCCceEEEEEecCCCCEEEeeeeeecccchhhHHHHHHHHHhh-c-CC------------------
Q 046610 316 MLLTVDGW-EIDGPYKSVMLIAVCRDRNDVVLPVAFCEVQEENLDSWAFFLKNVNDG-L-RL------------------ 374 (411)
Q Consensus 316 ~vl~iD~t-~~~~~y~g~ll~avg~d~~~~~~~lAfalv~~E~~e~w~WfL~~l~~~-l-~~------------------ 374 (411)
.||+||-. +..+.-+-..++-+-.-++.-+.-++|+.+...-.|.=.-+.+.++.. + ++
T Consensus 10 rvlGidds~f~~~~~~~~~lvGvv~r~~~~idGv~~~~itvdG~DaT~~i~~mv~~~~~r~~i~~V~L~Git~agFNvvD 89 (194)
T PRK00766 10 RVLGIDDGTFLFKSSEKVILVGVVMRGGDWVDGVLSRWITVDGLDATEAIIEMVNSSRHKGQLRVIMLDGITYGGFNVVD 89 (194)
T ss_pred eEEEEecCccccCCCCCEEEEEEEEECCeEEeeEEEEEEEECCccHHHHHHHHHHhcccccceEEEEECCEeeeeeEEec
Confidence 57888744 433222334444444445555555666655554444444333333321 0 00
Q ss_pred ------CCCCcEEEEccCch---HHHHHHHHhCCcccccc
Q 046610 375 ------ERGKGLCILGDGDN---GIDEAVEEFLPYAVYRQ 405 (411)
Q Consensus 375 ------~~~~~~~iisDr~~---gL~~Ai~~vfP~a~h~~ 405 (411)
.-+-|+++++.+-+ +|.+|+..-||+...++
T Consensus 90 ~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k~f~~~~~R~ 129 (194)
T PRK00766 90 IEELYRETGLPVIVVMRKKPDFEAIESALKKHFSDWEERI 129 (194)
T ss_pred HHHHHHHHCCCEEEEEecCCCHHHHHHHHHHHCCCHHHHH
Confidence 00124555644444 89999999999876553
No 27
>PF13592 HTH_33: Winged helix-turn helix
Probab=24.84 E-value=61 Score=23.67 Aligned_cols=21 Identities=19% Similarity=0.336 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHHhcccCC
Q 046610 219 PHQQLHVLGNEIAATYGIKCP 239 (411)
Q Consensus 219 p~~~p~~I~~~v~k~~gi~is 239 (411)
..++...|++.|.++||+.++
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys 23 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYS 23 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEc
Confidence 456788899999999999888
Done!