Query 043364
Match_columns 335
No_of_seqs 186 out of 1327
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 04:19:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043364.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043364hhsearch_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 1.8E-51 3.8E-56 410.4 19.9 276 1-280 308-623 (846)
2 PF10551 MULE: MULE transposas 99.8 8.2E-21 1.8E-25 143.4 7.0 76 1-79 18-93 (93)
3 PF00872 Transposase_mut: Tran 99.8 1.5E-19 3.3E-24 170.1 3.5 154 1-157 189-349 (381)
4 COG3328 Transposase and inacti 99.3 8.4E-12 1.8E-16 115.9 9.3 153 1-157 169-328 (379)
5 smart00575 ZnF_PMZ plant mutat 99.2 9E-12 1.9E-16 71.3 2.2 27 238-264 1-27 (28)
6 PF04434 SWIM: SWIM zinc finge 98.5 6.1E-08 1.3E-12 60.7 3.1 31 233-263 10-40 (40)
7 PF06782 UPF0236: Uncharacteri 94.9 0.11 2.3E-06 50.8 8.1 94 18-112 234-328 (470)
8 PF01610 DDE_Tnp_ISL3: Transpo 94.1 0.046 1E-06 48.5 3.4 66 14-82 30-96 (249)
9 PF13610 DDE_Tnp_IS240: DDE do 91.9 0.038 8.1E-07 44.6 -0.6 59 2-65 23-81 (140)
10 COG5431 Uncharacterized metal- 83.6 0.56 1.2E-05 35.1 1.1 47 225-273 39-90 (117)
11 COG3316 Transposase and inacti 81.0 3.3 7.1E-05 35.7 5.0 61 2-68 92-152 (215)
12 COG4715 Uncharacterized conser 75.1 7.1 0.00015 38.3 5.9 44 218-263 45-96 (587)
13 COG4279 Uncharacterized conser 68.4 3.2 7E-05 36.4 1.8 23 238-263 125-147 (266)
14 PF00665 rve: Integrase core d 47.0 18 0.00039 27.4 2.6 45 10-56 37-81 (120)
15 PF04937 DUF659: Protein of un 32.1 50 0.0011 26.9 3.1 48 37-84 88-138 (153)
16 PF03050 DDE_Tnp_IS66: Transpo 30.5 14 0.00029 33.1 -0.6 35 44-83 121-155 (271)
17 KOG2703 C4-type Zn-finger prot 21.4 53 0.0012 31.0 1.5 43 8-53 370-412 (460)
18 PF13877 RPAP3_C: Potential Mo 20.4 69 0.0015 23.4 1.7 33 98-130 5-37 (94)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=1.8e-51 Score=410.41 Aligned_cols=276 Identities=14% Similarity=0.240 Sum_probs=237.0
Q ss_pred CcccCCCCeEEEEEEEeeccccccHHHHHHHhhhcccccCCCceEEEcCCchhHHHHHHhhCCccchhhhHHHHHHhhhh
Q 043364 1 MCRDGNDVVLPIAFCEVQEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNGVDEAVEEFLPYGVYRQCCFSLYGRMVV 80 (335)
Q Consensus 1 vg~D~~~~~~~lafa~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~ 80 (335)
||+|+|+|.+++||||+.+|+.++|.|+|++| +.+|+++.|.+||||++.+|.+||++|||++.||+|+|||++|+.+
T Consensus 308 vGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tf--l~aM~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e 385 (846)
T PLN03097 308 VGVNQHYQFMLLGCALISDESAATYSWLMQTW--LRAMGGQAPKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSE 385 (846)
T ss_pred EEecCCCCeEEEEEEEcccCchhhHHHHHHHH--HHHhCCCCCceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHH
Confidence 69999999999999999999999999999999 7899999999999999999999999999999999999999999999
Q ss_pred hCC-----CchHHHHHHHHhh-cccHHHHHHHHHH-HHHhchhhhhhhhhc--CCcccccccCCCCCccceeecChHHHH
Q 043364 81 KFP-----DVQLHSAFWGACR-STDRKSFIHHMSI-IETVNIECHNWLKDT--DSKTWALFSMPQWVKSTEVTKSSSEQL 151 (335)
Q Consensus 81 ~~~-----~~~~~~~~~~~~~-~~~~~~F~~~~~~-l~~~~~~~~~~L~~~--~~~~Wa~~~~~~~~~~~~~TtN~~Es~ 151 (335)
+++ .+.|.+.|.+|++ +.+++||+..|.. |.+++.+.++||..+ .|++||++|+...+..|+.||+++||+
T Consensus 386 ~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~agm~sTqRSES~ 465 (846)
T PLN03097 386 NLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQRSESI 465 (846)
T ss_pred HhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhcccccCCcccccccccH
Confidence 875 3578999999987 7899999999987 568999999999987 899999999999999999999999999
Q ss_pred HHHHhhc--ccCcHHHHHHHHHHHHHHHHHHHHh-h---------------hhccccCCCCHHHHHHHHhhccccCccee
Q 043364 152 RIWLSKF--LDLNVAQRYTTITRTIAEMFQRRYL-A---------------GWEWVYDKITPAARQQIIHNVFESDGWNV 213 (335)
Q Consensus 152 N~~lk~~--r~~pi~~~~e~i~~~~~~~~~~r~~-~---------------~~~~~~~~~tp~~~~kl~~~~~~~~~~~~ 213 (335)
|+.|++. +..++..|++.+...+..+..+..+ . .++..+.+|||.+|++||+|+.. +..|
T Consensus 466 Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~--~~~~ 543 (846)
T PLN03097 466 NAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLG--AVAC 543 (846)
T ss_pred HHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHH--hhhe
Confidence 9999984 5678899988877666544332211 0 01111389999999999999995 7777
Q ss_pred EEeecC-C---cce-EEe--CCeEEEEEcc----cceecccCcccCCCcchhHHHHHHHhCC--CccccchhhhcHHHHH
Q 043364 214 DMPSNN-A---VSF-VSR--HGFVFEVNRE----LMTCSCRLWQLSGIPCEHACRCIHSWGD--KLDKYVHRLWSVDEYR 280 (335)
Q Consensus 214 ~v~~~~-~---~~f-V~~--~~~~~~V~l~----~~~CsC~~~~~~giPC~H~lav~~~~~~--~~~~~v~~~yt~~~~~ 280 (335)
.+...+ + .+| |.+ ....|.|..+ ..+|+|++|+..||||+|||+||...++ .|+.||.++||.++-.
T Consensus 544 ~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdAK~ 623 (846)
T PLN03097 544 HPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDAKS 623 (846)
T ss_pred EEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhchhhhhh
Confidence 776542 2 357 876 3467888665 3699999999999999999999999996 6999999999998753
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=99.83 E-value=8.2e-21 Score=143.43 Aligned_cols=76 Identities=26% Similarity=0.443 Sum_probs=72.0
Q ss_pred CcccCCCCeEEEEEEEeeccccccHHHHHHHhhhcccccCCCceEEEcCCchhHHHHHHhhCCccchhhhHHHHHHhhh
Q 043364 1 MCRDGNDVVLPIAFCEVQEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNGVDEAVEEFLPYGVYRQCCFSLYGRMV 79 (335)
Q Consensus 1 vg~D~~~~~~~lafa~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~ 79 (335)
+|+|++|+.+|+||+++++|+.++|.|||+.+ +..++.. |.+||||+++|+.+||+++||++.|++|.||+.+|++
T Consensus 18 ~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~--~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 18 VGIDGNGRGFPVAFALVSSESEESYEWFLEKL--KEAMPQK-PKVIISDFDKALINAIKEVFPDARHQLCLFHILRNIK 93 (93)
T ss_pred EEEcCCCCEEEEEEEEEcCCChhhhHHHHHHh--hhccccC-ceeeeccccHHHHHHHHHHCCCceEehhHHHHHHhhC
Confidence 48999999999999999999999999999999 6677766 9999999999999999999999999999999999974
No 3
>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=99.77 E-value=1.5e-19 Score=170.14 Aligned_cols=154 Identities=18% Similarity=0.298 Sum_probs=133.2
Q ss_pred CcccCCCCeEEEEEEEeeccccccHHHHHHHhhhcccccCCCceEEEcCCchhHHHHHHhhCCccchhhhHHHHHHhhhh
Q 043364 1 MCRDGNDVVLPIAFCEVQEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNGVDEAVEEFLPYGVYRQCCFSLYGRMVV 80 (335)
Q Consensus 1 vg~D~~~~~~~lafa~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~ 80 (335)
||+|.+|+..+||+.+.+.|+.++|.-||+.|++ +++. .+..||+|+++||.+||.++||++.++.|.+|+++|+.+
T Consensus 189 iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~-RGl~--~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~ 265 (381)
T PF00872_consen 189 IGIDEDGRREVLGFWVGDRESAASWREFLQDLKE-RGLK--DILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLR 265 (381)
T ss_pred hhhhcccccceeeeecccCCccCEeeecchhhhh-cccc--ccceeeccccccccccccccccchhhhhheechhhhhcc
Confidence 6999999999999999999999999999999975 4664 589999999999999999999999999999999999999
Q ss_pred hCCCc---hHHHHHHHHhhcccHHHHHHHHHHH----HHhchhhhhhhhhcCCcccccccCCCCCccceeecChHHHHHH
Q 043364 81 KFPDV---QLHSAFWGACRSTDRKSFIHHMSII----ETVNIECHNWLKDTDSKTWALFSMPQWVKSTEVTKSSSEQLRI 153 (335)
Q Consensus 81 ~~~~~---~~~~~~~~~~~~~~~~~F~~~~~~l----~~~~~~~~~~L~~~~~~~Wa~~~~~~~~~~~~~TtN~~Es~N~ 153 (335)
+++.+ .+.+.+..+..+.+.++....++.+ ....|.+.++|.+...+.|+...|+...+--+.|||.+||+|+
T Consensus 266 ~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~ 345 (381)
T PF00872_consen 266 KVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNK 345 (381)
T ss_pred ccccccchhhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccccccceeeecchhccccchhhhcccccc
Confidence 88644 5667777777777777777776665 3457888889988888888877777777777889999999999
Q ss_pred HHhh
Q 043364 154 WLSK 157 (335)
Q Consensus 154 ~lk~ 157 (335)
.||.
T Consensus 346 ~irr 349 (381)
T PF00872_consen 346 EIRR 349 (381)
T ss_pred chhh
Confidence 9987
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.30 E-value=8.4e-12 Score=115.93 Aligned_cols=153 Identities=15% Similarity=0.228 Sum_probs=118.8
Q ss_pred CcccCCCCeEEEEEEEeeccccccHHHHHHHhhhcccccCCCceEEEcCCchhHHHHHHhhCCccchhhhHHHHHHhhhh
Q 043364 1 MCRDGNDVVLPIAFCEVQEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNGVDEAVEEFLPYGVYRQCCFSLYGRMVV 80 (335)
Q Consensus 1 vg~D~~~~~~~lafa~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~ 80 (335)
+|++.+|+..++|+.+.+.|+ ..|.-||..|+. .++. ....+++|+++|+.+||.++||.+.++.|..|+.+|+..
T Consensus 169 ~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~-rgl~--~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~ 244 (379)
T COG3328 169 IGVTEEGRREILGIWVGVRES-KFWLSFLLDLKN-RGLS--DVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLD 244 (379)
T ss_pred eccCcccchhhhceeeecccc-hhHHHHHHHHHh-cccc--ceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhh
Confidence 699999999999999999999 999988888854 4554 457788899999999999999999999999999999998
Q ss_pred hCCCch---HHHHHHHHhhcccHHHHHHHH----HHHHHhchhhhhhhhhcCCcccccccCCCCCccceeecChHHHHHH
Q 043364 81 KFPDVQ---LHSAFWGACRSTDRKSFIHHM----SIIETVNIECHNWLKDTDSKTWALFSMPQWVKSTEVTKSSSEQLRI 153 (335)
Q Consensus 81 ~~~~~~---~~~~~~~~~~~~~~~~F~~~~----~~l~~~~~~~~~~L~~~~~~~Wa~~~~~~~~~~~~~TtN~~Es~N~ 153 (335)
+.+.++ ....+..+..+.+.++-...+ +.+....|....|+.+..-+.|....|+...+--+.|||.+|++|+
T Consensus 245 ~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~ 324 (379)
T COG3328 245 KVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNK 324 (379)
T ss_pred hhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHH
Confidence 876553 333444444455544444444 3344566777888887766777655566555556789999999999
Q ss_pred HHhh
Q 043364 154 WLSK 157 (335)
Q Consensus 154 ~lk~ 157 (335)
.++.
T Consensus 325 ~ir~ 328 (379)
T COG3328 325 LIRR 328 (379)
T ss_pred HHHH
Confidence 8764
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=99.19 E-value=9e-12 Score=71.26 Aligned_cols=27 Identities=56% Similarity=0.936 Sum_probs=25.1
Q ss_pred ceecccCcccCCCcchhHHHHHHHhCC
Q 043364 238 MTCSCRLWQLSGIPCEHACRCIHSWGD 264 (335)
Q Consensus 238 ~~CsC~~~~~~giPC~H~lav~~~~~~ 264 (335)
.+|||++||.+||||+|+|+|+...|+
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999999875
No 6
>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=98.55 E-value=6.1e-08 Score=60.65 Aligned_cols=31 Identities=32% Similarity=0.708 Sum_probs=27.2
Q ss_pred EEcccceecccCcccCCCcchhHHHHHHHhC
Q 043364 233 VNRELMTCSCRLWQLSGIPCEHACRCIHSWG 263 (335)
Q Consensus 233 V~l~~~~CsC~~~~~~giPC~H~lav~~~~~ 263 (335)
+++...+|+|..|+..|.||+|++|++...+
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 5566789999999999999999999997653
No 7
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=94.90 E-value=0.11 Score=50.81 Aligned_cols=94 Identities=20% Similarity=0.307 Sum_probs=76.1
Q ss_pred eccccccHHHHHHHhhhcccccCCCceEEEcCCchhHHHHHHhhCCccchhhhHHHHHHhhhhhCC-CchHHHHHHHHhh
Q 043364 18 QEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNGVDEAVEEFLPYGVYRQCCFSLYGRMVVKFP-DVQLHSAFWGACR 96 (335)
Q Consensus 18 ~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~-~~~~~~~~~~~~~ 96 (335)
...+.+.|.-+.+.+.+...+.+..-+++.+|+-+.+.+++. .+|++.|.+..+|+.+.+.+.++ .+.+...++++.+
T Consensus 234 ~~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~al~ 312 (470)
T PF06782_consen 234 GESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKALK 312 (470)
T ss_pred ccchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHHHH
Confidence 355678899888888555555555568899999999998876 99999999999999999998875 4567777888888
Q ss_pred cccHHHHHHHHHHHHH
Q 043364 97 STDRKSFIHHMSIIET 112 (335)
Q Consensus 97 ~~~~~~F~~~~~~l~~ 112 (335)
.....+++..++.+..
T Consensus 313 ~~d~~~l~~~L~~~~~ 328 (470)
T PF06782_consen 313 KGDKKKLETVLDTAES 328 (470)
T ss_pred hcCHHHHHHHHHHHHH
Confidence 8888888888877653
No 8
>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=94.12 E-value=0.046 Score=48.48 Aligned_cols=66 Identities=14% Similarity=0.116 Sum_probs=55.1
Q ss_pred EEEeeccccccHHHHHHHh-hhcccccCCCceEEEcCCchhHHHHHHhhCCccchhhhHHHHHHhhhhhC
Q 043364 14 FCEVQEENLDSWAFFLKNL-TYGLRFERGEGLCILADGDNGVDEAVEEFLPYGVYRQCCFSLYGRMVVKF 82 (335)
Q Consensus 14 fa~~~~E~~~~w~wfl~~l-~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~ 82 (335)
++++++-+.++..=||..+ -. . ......+|++|...+...|+.+.||+|.+..--+||++++.+.+
T Consensus 30 l~i~~~r~~~~l~~~~~~~~~~-~--~~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 30 LDILPGRDKETLKDFFRSLYPE-E--ERKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred EEEcCCccHHHHHHHHHHhCcc-c--cccceEEEEcCCCccccccccccccccccccccchhhhhhhhcc
Confidence 4578899999998888876 21 1 22467899999999999999999999999999999999987643
No 9
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=91.88 E-value=0.038 Score=44.62 Aligned_cols=59 Identities=24% Similarity=0.252 Sum_probs=50.1
Q ss_pred cccCCCCeEEEEEEEeeccccccHHHHHHHhhhcccccCCCceEEEcCCchhHHHHHHhhCCcc
Q 043364 2 CRDGNDVVLPIAFCEVQEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNGVDEAVEEFLPYG 65 (335)
Q Consensus 2 g~D~~~~~~~lafa~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a 65 (335)
++|.+++ +|++-|.+.-+...=..||+.+ ..... ..|..|+||+.++...|++++.+..
T Consensus 23 aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~--l~~~~-~~p~~ivtDk~~aY~~A~~~l~~~~ 81 (140)
T PF13610_consen 23 AIDAEGN--ILDFYLSKRRDTAAAKRFLKRA--LKRHR-GEPRVIVTDKLPAYPAAIKELNPEG 81 (140)
T ss_pred eeccccc--chhhhhhhhcccccceeecccc--ceeec-cccceeecccCCccchhhhhccccc
Confidence 5788888 8888899999999989999988 33332 5799999999999999999999874
No 10
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=83.65 E-value=0.56 Score=35.08 Aligned_cols=47 Identities=15% Similarity=0.182 Sum_probs=29.8
Q ss_pred EeCCeEEEEEcccceecccCcc-----cCCCcchhHHHHHHHhCCCccccchhh
Q 043364 225 SRHGFVFEVNRELMTCSCRLWQ-----LSGIPCEHACRCIHSWGDKLDKYVHRL 273 (335)
Q Consensus 225 ~~~~~~~~V~l~~~~CsC~~~~-----~~giPC~H~lav~~~~~~~~~~~v~~~ 273 (335)
...++.|+++.+ -|||..|- .-.-||.|++++-....-.-.++|+-+
T Consensus 39 vG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y 90 (117)
T COG5431 39 VGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAY 90 (117)
T ss_pred EccccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEe
Confidence 334568888877 89998876 234679999986554432223344433
No 11
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.03 E-value=3.3 Score=35.71 Aligned_cols=61 Identities=18% Similarity=0.161 Sum_probs=49.1
Q ss_pred cccCCCCeEEEEEEEeeccccccHHHHHHHhhhcccccCCCceEEEcCCchhHHHHHHhhCCccchh
Q 043364 2 CRDGNDVVLPIAFCEVQEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNGVDEAVEEFLPYGVYR 68 (335)
Q Consensus 2 g~D~~~~~~~lafa~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~ 68 (335)
+||.+|+ +|.+-|...-+...=.-||..+.+ .. ..|.+|+||+-+....|+.++.+.+.|+
T Consensus 92 Aid~~g~--~Ld~~L~~rRn~~aAk~Fl~kllk--~~--g~p~v~vtDka~s~~~A~~~l~~~~ehr 152 (215)
T COG3316 92 AIDADGL--TLDVWLSKRRNALAAKAFLKKLLK--KH--GEPRVFVTDKAPSYTAALRKLGSEVEHR 152 (215)
T ss_pred hhccCCC--eEEEEEEcccCcHHHHHHHHHHHH--hc--CCCceEEecCccchHHHHHhcCcchhee
Confidence 5777765 788888888888887888887733 23 4799999999999999999999866665
No 12
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=75.11 E-value=7.1 Score=38.35 Aligned_cols=44 Identities=20% Similarity=0.351 Sum_probs=29.1
Q ss_pred cCCcce--EEeCCeEE--EEEcc----cceecccCcccCCCcchhHHHHHHHhC
Q 043364 218 NNAVSF--VSRHGFVF--EVNRE----LMTCSCRLWQLSGIPCEHACRCIHSWG 263 (335)
Q Consensus 218 ~~~~~f--V~~~~~~~--~V~l~----~~~CsC~~~~~~giPC~H~lav~~~~~ 263 (335)
..++.+ |..|.+.| .|++. +.+|||.. ...| -|+|+.||+-...
T Consensus 45 ~~g~~v~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~ 96 (587)
T COG4715 45 IRGGTVRAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYL 96 (587)
T ss_pred ecCCeEEEEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHh
Confidence 444444 55565554 45553 36999987 4444 4999999987764
No 13
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=68.40 E-value=3.2 Score=36.39 Aligned_cols=23 Identities=26% Similarity=0.595 Sum_probs=19.4
Q ss_pred ceecccCcccCCCcchhHHHHHHHhC
Q 043364 238 MTCSCRLWQLSGIPCEHACRCIHSWG 263 (335)
Q Consensus 238 ~~CsC~~~~~~giPC~H~lav~~~~~ 263 (335)
..|||..|. .||.|+-||....+
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 479999875 79999999987774
No 14
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=47.02 E-value=18 Score=27.37 Aligned_cols=45 Identities=16% Similarity=-0.003 Sum_probs=30.9
Q ss_pred EEEEEEEeeccccccHHHHHHHhhhcccccCCCceEEEcCCchhHHH
Q 043364 10 LPIAFCEVQEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNGVDE 56 (335)
Q Consensus 10 ~~lafa~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~ 56 (335)
+.+++.+-..++.+...-+|+.. ....++..|.+|+||+.++...
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 37 FIYAFPVSSKETAEAALRALKRA--IEKRGGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp EEEEEEESSSSHHHHHHHHHHHH--HHHHS-SE-SEEEEESCHHHHS
T ss_pred cEEEEEeeccccccccccccccc--ccccccccceeccccccccccc
Confidence 45667777777888888888865 3334433399999999988763
No 15
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=32.06 E-value=50 Score=26.93 Aligned_cols=48 Identities=10% Similarity=0.142 Sum_probs=37.7
Q ss_pred cccCCCceEEEcCCchhHHHHHHh---hCCccchhhhHHHHHHhhhhhCCC
Q 043364 37 RFERGEGLCILADGDNGVDEAVEE---FLPYGVYRQCCFSLYGRMVVKFPD 84 (335)
Q Consensus 37 ~~~~~~~~~iisD~~~~l~~Ai~~---vfP~a~h~~C~~Hi~~n~~~~~~~ 84 (335)
.+|....+.||||....+.+|-+- -+|....-.|.-|-+.-+.+.+..
T Consensus 88 eVG~~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 88 EVGEENVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred HhhhhhhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 356667888999999999888444 479999999999998887765543
No 16
>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=30.50 E-value=14 Score=33.13 Aligned_cols=35 Identities=14% Similarity=0.086 Sum_probs=28.3
Q ss_pred eEEEcCCchhHHHHHHhhCCccchhhhHHHHHHhhhhhCC
Q 043364 44 LCILADGDNGVDEAVEEFLPYGVYRQCCFSLYGRMVVKFP 83 (335)
Q Consensus 44 ~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~ 83 (335)
-+++||+.++=.. +..+.|+.|..|+.+.+.+-..
T Consensus 121 GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 121 GILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred eeeeccccccccc-----cccccccccccccccccccccc
Confidence 4899999987643 3388999999999999987654
No 17
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=21.43 E-value=53 Score=31.05 Aligned_cols=43 Identities=16% Similarity=0.196 Sum_probs=33.8
Q ss_pred CeEEEEEEEeeccccccHHHHHHHhhhcccccCCCceEEEcCCchh
Q 043364 8 VVLPIAFCEVQEENLDSWAFFLKNLTYGLRFERGEGLCILADGDNG 53 (335)
Q Consensus 8 ~~~~lafa~~~~E~~~~w~wfl~~l~~~~~~~~~~~~~iisD~~~~ 53 (335)
+.+.++ --++....+.|.-||..| ...+.+..|.++|-|.-.|
T Consensus 370 ~~f~~~-DS~~~~~~~~~~~F~~~l--~~~i~~~~~~tlIldDp~~ 412 (460)
T KOG2703|consen 370 RSFTFG-DSMDEGQKARWQEFLAKL--DDIIAGKLPATLILDDPLG 412 (460)
T ss_pred Cceecc-ccCCHHHHHHHHHHHHHH--HHHHhcccceEEEeecCCc
Confidence 334444 456778889999999999 6688888999999988765
No 18
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=20.38 E-value=69 Score=23.44 Aligned_cols=33 Identities=12% Similarity=0.124 Sum_probs=27.4
Q ss_pred ccHHHHHHHHHHHHHhchhhhhhhhhcCCcccc
Q 043364 98 TDRKSFIHHMSIIETVNIECHNWLKDTDSKTWA 130 (335)
Q Consensus 98 ~~~~~F~~~~~~l~~~~~~~~~~L~~~~~~~Wa 130 (335)
.+..+|+..|..+.......++||..++++...
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~ 37 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLP 37 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHH
Confidence 467899999999977667889999999877764
Done!