Query 006219
Match_columns 656
No_of_seqs 238 out of 411
Neff 6.5
Searched_HMMs 46136
Date Thu Mar 28 20:06:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006219.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006219hhsearch_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 3.5E-45 7.5E-50 424.0 34.6 428 67-548 69-606 (846)
2 PF10551 MULE: MULE transposas 99.7 8E-18 1.7E-22 147.0 8.7 89 299-393 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.3 5.7E-13 1.2E-17 145.8 1.2 244 180-487 98-351 (381)
4 COG3328 Transposase and inacti 98.1 0.00014 3.1E-09 79.4 18.1 239 180-486 84-329 (379)
5 smart00575 ZnF_PMZ plant mutat 97.5 5.8E-05 1.3E-09 51.6 2.0 25 523-547 2-27 (28)
6 PF03101 FAR1: FAR1 DNA-bindin 97.4 0.00026 5.7E-09 61.5 6.0 72 74-156 16-87 (91)
7 PF04434 SWIM: SWIM zinc finge 97.3 0.00024 5.2E-09 52.4 3.3 28 518-545 11-39 (40)
8 PF15299 ALS2CR8: Amyotrophic 96.5 0.033 7.1E-07 57.0 12.7 138 87-236 33-221 (225)
9 PF01610 DDE_Tnp_ISL3: Transpo 95.0 0.043 9.3E-07 56.4 5.9 94 295-396 1-96 (249)
10 PF06782 UPF0236: Uncharacteri 91.0 27 0.00058 39.9 20.8 255 178-489 115-381 (470)
11 PF03050 DDE_Tnp_IS66: Transpo 89.1 0.42 9.1E-06 49.9 4.1 81 294-396 69-154 (271)
12 COG4279 Uncharacterized conser 88.1 0.25 5.4E-06 50.7 1.6 33 522-557 125-158 (266)
13 PF13610 DDE_Tnp_IS240: DDE do 87.6 0.16 3.6E-06 47.8 -0.0 79 294-380 3-81 (140)
14 PF00665 rve: Integrase core d 83.8 6.9 0.00015 34.7 8.7 75 293-372 7-82 (120)
15 PF08731 AFT: Transcription fa 81.1 5.4 0.00012 36.3 6.6 33 123-156 75-109 (111)
16 PF03106 WRKY: WRKY DNA -bindi 80.3 6.2 0.00013 32.0 6.1 30 127-157 30-59 (60)
17 PF04937 DUF659: Protein of un 76.1 27 0.00059 33.6 10.4 107 283-397 26-137 (153)
18 PRK14702 insertion element IS2 64.8 32 0.00069 36.0 8.8 76 293-370 88-165 (262)
19 COG4715 Uncharacterized conser 58.9 8.4 0.00018 44.1 3.3 39 510-549 61-99 (587)
20 PRK09409 IS2 transposase TnpB; 57.0 51 0.0011 35.2 8.8 76 293-370 127-204 (301)
21 COG3316 Transposase and inacti 51.5 57 0.0012 33.3 7.5 92 294-395 72-173 (215)
22 PF13936 HTH_38: Helix-turn-he 48.8 11 0.00024 28.3 1.6 27 179-205 3-29 (44)
23 PF02796 HTH_7: Helix-turn-hel 45.3 35 0.00077 25.6 3.9 39 179-232 4-42 (45)
24 PHA02517 putative transposase 38.9 70 0.0015 33.2 6.3 72 294-371 112-183 (277)
25 COG5431 Uncharacterized metal- 33.9 14 0.00031 33.2 0.1 22 521-542 49-76 (117)
26 PF13384 HTH_23: Homeodomain-l 30.3 70 0.0015 24.0 3.5 42 182-238 3-44 (50)
27 KOG0053 Cystathionine beta-lya 29.1 5E+02 0.011 29.2 11.0 104 224-332 129-239 (409)
28 KOG3941 Intermediate in Toll s 29.0 5.1E+02 0.011 28.0 10.4 111 187-303 144-271 (406)
29 PF08259 Periviscerokin: Periv 28.6 21 0.00046 19.2 0.2 8 40-47 4-11 (11)
30 PF00292 PAX: 'Paired box' dom 27.2 1.5E+02 0.0033 27.7 5.7 41 181-236 18-58 (125)
31 TIGR03147 cyt_nit_nrfF cytochr 26.7 71 0.0015 29.9 3.4 32 181-215 58-89 (126)
32 PF13683 rve_3: Integrase core 25.6 23 0.00049 28.8 -0.0 25 468-492 11-35 (67)
33 KOG3223 Uncharacterized conser 23.1 78 0.0017 31.6 3.1 42 536-577 166-212 (221)
34 PRK10144 formate-dependent nit 22.7 94 0.002 29.1 3.4 27 181-207 58-84 (126)
35 PF03918 CcmH: Cytochrome C bi 21.6 74 0.0016 30.6 2.6 27 181-207 58-84 (148)
36 smart00774 WRKY DNA binding do 21.3 1.2E+02 0.0025 24.7 3.3 30 126-156 30-59 (59)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=3.5e-45 Score=424.05 Aligned_cols=428 Identities=15% Similarity=0.204 Sum_probs=305.0
Q ss_pred cccccCCCCCCccccccceeEEEEEEeecCCC----cc-----------------CCCCcc-------ccccc--ccccc
Q 006219 67 ERGRKRSRGSLKEYKDDEYLEYRLYWCSFGPE----NY-----------------GEGGGV-------LPSRK--YRLNT 116 (656)
Q Consensus 67 ~~~~~~~~g~~~~~~~d~~~~y~~Y~Cs~Gp~----~~-----------------~~~~~~-------~p~~~--~~~~~ 116 (656)
...-.|-+||.|++.+++|-||+.|+...|=. .. ++|.+. +|... ...++
T Consensus 69 ~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~ 148 (846)
T PLN03097 69 DTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPE 148 (846)
T ss_pred CCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCcc
Confidence 34457999999999999999999988887711 11 111110 00000 00001
Q ss_pred CcCCCCCCcccCceeEEEEEEeecCCcEEEEEEecccccCCCCCccCCCCCcCcCCCCCCcCCCCCHHHHHHHHHHHHcC
Q 006219 117 RNRAARPQSMRGCTCHFVVKRLYARPSLALLIYNDRRHVNKSGFICHGPLDRDAIGPGAKKIPYICNEIQQQTMSMIYLG 196 (656)
Q Consensus 117 ~~r~~r~~tk~GC~c~~~Vkr~~~~~~v~v~i~~~~~H~~~~~~~~H~p~~~~~~~~~~~~~~rIs~e~r~~I~~ll~~G 196 (656)
..+++|..+++||+|+++|++. .++.|.|.-+. .+|+|.-. |. ..++...+
T Consensus 149 ~~~~rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv-~eHNH~L~-----p~------------~~~~~~~r---------- 199 (846)
T PLN03097 149 NGTGRRSCAKTDCKASMHVKRR-PDGKWVIHSFV-KEHNHELL-----PA------------QAVSEQTR---------- 199 (846)
T ss_pred cccccccccCCCCceEEEEEEc-CCCeEEEEEEe-cCCCCCCC-----Cc------------cccchhhh----------
Confidence 1112355688999999999984 45677777666 34765221 10 01222222
Q ss_pred CChHHHHHHHHHhhhhccCCCCccCCCcHHHHHHHHHHHhhccccCCcchHHHHHHHHHhcC--CeeEEecCCCCCCC-e
Q 006219 197 IPEESVLEKHIEGIQRYCGSDAKVNSLASQYVQKLGMIIRRSTHELDLDDQASIRLWVDRNK--KSIFFYQDSSETDP-F 273 (656)
Q Consensus 197 i~p~~Il~~ire~~~~~~g~~~r~~llT~kDV~Ni~~~~~~~~~~l~~~D~~Sv~~wv~~~~--~~vf~y~d~~d~~~-F 273 (656)
.|+..+...+ + ..... ..+.+|.+|.....+. ..+..+|+..+..++++++ +|-|||.-..|+++ .
T Consensus 200 ----~~~~~~~~~~---~-~~~~v-~~~~~d~~~~~~~~r~--~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l 268 (846)
T PLN03097 200 ----KMYAAMARQF---A-EYKNV-VGLKNDSKSSFDKGRN--LGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRL 268 (846)
T ss_pred ----hhHHHHHhhh---h-ccccc-cccchhhcchhhHHHh--hhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCe
Confidence 1221111111 1 11111 2355677776655543 2456789999999999885 89999985554444 4
Q ss_pred EeecCcHHH-HHHHHHhCCCeEEEEeccccccccCCceEEEEEEcCCCCeEEEEEEEecCCChhhHHHHHHHHHHHHhcc
Q 006219 274 ILGIQTEWQ-LQQMIRFGHRSLIAADSTFGIKRLKYPLCTLLVFDSRQHALPVAWVVTRSSAKPDVTKWMKSLLDRARSI 352 (656)
Q Consensus 274 ~l~iqt~~Q-~~~l~~fg~~~vv~iDsT~~tnky~~pL~tl~v~d~~g~~~PvA~~i~~~et~e~~~~~L~~l~~~~~~~ 352 (656)
.-+++.+.. +..+..||+ ||++|+||.||+|++||..++|+|+|++.+++|++|+.+|+.++|.|+|++|+++|+.+
T Consensus 269 ~niFWaD~~sr~~Y~~FGD--vV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk 346 (846)
T PLN03097 269 KNLFWVDAKSRHDYGNFSD--VVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQ 346 (846)
T ss_pred eeEEeccHHHHHHHHhcCC--EEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCC
Confidence 444666664 556788998 99999999999999999999999999999999999999999999999999999999764
Q ss_pred CCCcceEEEEEcCchhhhhHHHHhcCCC-cccchHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHhhhcCCCChHHHHH
Q 006219 353 EPGWKISGFLIDDAAAEIDPIREIFCCP-LLFSLWRVRRSWLRNIVKKCTNIKIQREIFKRLGNILYSIWDGADPFVNLE 431 (656)
Q Consensus 353 ~p~~~P~~fmtD~d~A~~~AI~~VFp~~-~LLC~wHV~qaw~k~l~~k~~~~e~~~~i~k~L~~ll~~~~~~~~f~~~le 431 (656)
.|++|+||+|.|+.+||.+|||.+ |.+|.|||.++..++|...+. ....+...+..+|+....+++|+..|.
T Consensus 347 ----~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~---~~~~f~~~f~~cv~~s~t~eEFE~~W~ 419 (846)
T PLN03097 347 ----APKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIK---QHENFMAKFEKCIYRSWTEEEFGKRWW 419 (846)
T ss_pred ----CCceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhh---hhhHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 689999999999999999999997 999999999998888855332 234567778888888877778888888
Q ss_pred HHHHHhhc-hhHHHHHHHhhccchHHHHHHhh-hcCCCCCCCcChHHHHhHHhhhhhhcccCcc--chhhhHhhh-----
Q 006219 432 VLIQDFVD-QTAFIEYFKASWMPKLAMWLSTM-RALPLASQEASGAIEAYHVKLKTKLFDDSHL--GALQRVDWV----- 502 (656)
Q Consensus 432 ~~~~~~~d-~~~F~~Yf~~~Wl~~~e~Wa~~~-R~lp~~~~~TNn~iES~h~~LK~~ll~~~~~--~~~~RvD~L----- 502 (656)
+++.+|.- .. +|++..| ..+++||.+| +....+++.||++.||+|+.||.+ ++.... .++.++|.+
T Consensus 420 ~mi~ky~L~~n---~WL~~LY-~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~y-v~~~tsL~~Fv~qye~~l~~~~ 494 (846)
T PLN03097 420 KILDRFELKED---EWMQSLY-EDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKY-VHKKTTVQEFVKQYETILQDRY 494 (846)
T ss_pred HHHHhhccccc---HHHHHHH-HhHhhhhHHHhcccccCCcccccccccHHHHHHHH-hCcCCCHHHHHHHHHHHHHHHH
Confidence 88888742 22 4566666 4568999998 555678999999999999999984 444432 255555544
Q ss_pred --------------------------------------------------hh---cc------------CCCceEEEecC
Q 006219 503 --------------------------------------------------SS---QK------------DSSLTHLVWNP 517 (656)
Q Consensus 503 --------------------------------------------------~~---q~------------d~~~~~vv~n~ 517 (656)
.. +. ....+.|++|+
T Consensus 495 ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~ 574 (846)
T PLN03097 495 EEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQ 574 (846)
T ss_pred HHHHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEec
Confidence 00 00 11245677899
Q ss_pred CCceeeeecc-CCCCCccchhHHHHHHHhccC
Q 006219 518 GSEFAFCDCA-WSMQGNICKHVVKVNMICANN 548 (656)
Q Consensus 518 ~~~~~~CsC~-~~~~G~~CkH~~kV~~~~~~~ 548 (656)
..+...|+|. |+..|+||.|+++|+.+.+..
T Consensus 575 ~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~ 606 (846)
T PLN03097 575 TKLEVSCICRLFEYKGYLCRHALVVLQMCQLS 606 (846)
T ss_pred CCCeEEeeccCeecCccchhhHHHHHhhcCcc
Confidence 8999999996 999999999999999888653
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=99.73 E-value=8e-18 Score=146.97 Aligned_cols=89 Identities=19% Similarity=0.267 Sum_probs=81.6
Q ss_pred ccccccccCCceEE---EEEEcCCCCeEEEEEEEecCCChhhHHHHHHHHHHHHhccCCCcceEEEEEcCchhhhhHHHH
Q 006219 299 STFGIKRLKYPLCT---LLVFDSRQHALPVAWVVTRSSAKPDVTKWMKSLLDRARSIEPGWKISGFLIDDAAAEIDPIRE 375 (656)
Q Consensus 299 sT~~tnky~~pL~t---l~v~d~~g~~~PvA~~i~~~et~e~~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A~~~AI~~ 375 (656)
+||+||+| ++|++ +++.|+.|+++|+||+++++|+.+++.|+|+.+++.+.. . |.+||+|.+.++++||++
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~----~-p~~ii~D~~~~~~~Ai~~ 74 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQ----K-PKVIISDFDKALINAIKE 74 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcccc----C-ceeeeccccHHHHHHHHH
Confidence 69999999 87775 999999999999999999999999999999988777643 4 999999999999999999
Q ss_pred hcCCC-cccchHHHHHHHH
Q 006219 376 IFCCP-LLFSLWRVRRSWL 393 (656)
Q Consensus 376 VFp~~-~LLC~wHV~qaw~ 393 (656)
+||.. +++|.||+.|+|+
T Consensus 75 vfP~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 75 VFPDARHQLCLFHILRNIK 93 (93)
T ss_pred HCCCceEehhHHHHHHhhC
Confidence 99997 9999999999873
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=99.29 E-value=5.7e-13 Score=145.76 Aligned_cols=244 Identities=16% Similarity=0.211 Sum_probs=174.1
Q ss_pred CCCHHHHHHHHHHHHcCCChHHHHHHHHHhhhhccCCCCccCCCcHHHHHHHHHHHhhccccCCcchHHHHHHHHHhcCC
Q 006219 180 YICNEIQQQTMSMIYLGIPEESVLEKHIEGIQRYCGSDAKVNSLASQYVQKLGMIIRRSTHELDLDDQASIRLWVDRNKK 259 (656)
Q Consensus 180 rIs~e~r~~I~~ll~~Gi~p~~Il~~ire~~~~~~g~~~r~~llT~kDV~Ni~~~~~~~~~~l~~~D~~Sv~~wv~~~~~ 259 (656)
+.++++-+.|.+|-..|++..+|-+.+.+ .+|+. -++..-|.++...+. ..+..|-.+-
T Consensus 98 r~~~~l~~~i~~ly~~G~Str~i~~~l~~----l~g~~----~~S~s~vSri~~~~~-----------~~~~~w~~R~-- 156 (381)
T PF00872_consen 98 RREDSLEELIISLYLKGVSTRDIEEALEE----LYGEV----AVSKSTVSRITKQLD-----------EEVEAWRNRP-- 156 (381)
T ss_pred hhhhhhhhhhhhhhccccccccccchhhh----hhccc----ccCchhhhhhhhhhh-----------hhHHHHhhhc--
Confidence 35677888999999999999988654422 24421 256666666654443 2345554332
Q ss_pred eeEEecCCCCCCCeEeecCcHHHHHHHHHhCCCeEEEEeccccccc-----cCCceEEEEEEcCCCCeEEEEEEEecCCC
Q 006219 260 SIFFYQDSSETDPFILGIQTEWQLQQMIRFGHRSLIAADSTFGIKR-----LKYPLCTLLVFDSRQHALPVAWVVTRSSA 334 (656)
Q Consensus 260 ~vf~y~d~~d~~~F~l~iqt~~Q~~~l~~fg~~~vv~iDsT~~tnk-----y~~pL~tl~v~d~~g~~~PvA~~i~~~et 334 (656)
|.... -.+|++|+||-.-+ -+-.+++++|+|..|.-.++|+.+..+|+
T Consensus 157 --------------------------L~~~~-y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es 209 (381)
T PF00872_consen 157 --------------------------LESEP-YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRES 209 (381)
T ss_pred --------------------------ccccc-ccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCc
Confidence 11110 01689999986543 34678999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHhccCCCcceEEEEEcCchhhhhHHHHhcCCC-cccchHHHHHHHHHHHHhhcCChHHHHHHHHHH
Q 006219 335 KPDVTKWMKSLLDRARSIEPGWKISGFLIDDAAAEIDPIREIFCCP-LLFSLWRVRRSWLRNIVKKCTNIKIQREIFKRL 413 (656)
Q Consensus 335 ~e~~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A~~~AI~~VFp~~-~LLC~wHV~qaw~k~l~~k~~~~e~~~~i~k~L 413 (656)
...+..+|..|.++= --.|..|++|...+..+||+++||.+ +..|.+|..++..+++.+ ..+.++...|
T Consensus 210 ~~~W~~~l~~L~~RG-----l~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~-----k~~~~v~~~L 279 (381)
T PF00872_consen 210 AASWREFLQDLKERG-----LKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK-----KDRKEVKADL 279 (381)
T ss_pred cCEeeecchhhhhcc-----ccccceeeccccccccccccccccchhhhhheechhhhhcccccc-----ccchhhhhhc
Confidence 998877777775541 12488999999999999999999986 999999999876655532 3456677777
Q ss_pred HHHHhhhcCCCChHHHHHHHHHHhhc-hhHHHHHHHhhccchHHHHHHhhhcCCC---CCCCcChHHHHhHHhhhhhh
Q 006219 414 GNILYSIWDGADPFVNLEVLIQDFVD-QTAFIEYFKASWMPKLAMWLSTMRALPL---ASQEASGAIEAYHVKLKTKL 487 (656)
Q Consensus 414 ~~ll~~~~~~~~f~~~le~~~~~~~d-~~~F~~Yf~~~Wl~~~e~Wa~~~R~lp~---~~~~TNn~iES~h~~LK~~l 487 (656)
..+.+.. +.+++...+++|...|.+ .+.+.++++..|... |+ |-.+|- ....|||.+|++|+.||+..
T Consensus 280 k~I~~a~-~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~---~t--f~~fP~~~~~~i~TTN~iEsln~~irrr~ 351 (381)
T PF00872_consen 280 KAIYQAP-DKEEAREALEEFAEKWEKKYPKAAKSLEENWDEL---LT--FLDFPPEHRRSIRTTNAIESLNKEIRRRT 351 (381)
T ss_pred ccccccc-ccchhhhhhhhcccccccccchhhhhhhhccccc---cc--eeeecchhccccchhhhccccccchhhhc
Confidence 7765544 335567778888777764 688999999888533 22 112332 24689999999999999853
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.10 E-value=0.00014 Score=79.42 Aligned_cols=239 Identities=13% Similarity=0.176 Sum_probs=147.8
Q ss_pred CCCHHHHHHHHHHHHcCCChHHHHHHHHHhhhhccCCCCccCCCcHHHHHHHHHHHhhccccCCcchHHHHHHHHHhcCC
Q 006219 180 YICNEIQQQTMSMIYLGIPEESVLEKHIEGIQRYCGSDAKVNSLASQYVQKLGMIIRRSTHELDLDDQASIRLWVDRNKK 259 (656)
Q Consensus 180 rIs~e~r~~I~~ll~~Gi~p~~Il~~ire~~~~~~g~~~r~~llT~kDV~Ni~~~~~~~~~~l~~~D~~Sv~~wv~~~~~ 259 (656)
+.....-+.|.+|-..||+..+|=+.+ +.+ ++. .+..--|..+...+. ..|.+|..+-
T Consensus 84 r~~~~~~~~v~~~y~~gv~Tr~i~~~~-~~~---~~~-----~~s~~~iS~~~~~~~-----------e~v~~~~~r~-- 141 (379)
T COG3328 84 RRERALDLPVLSMYAKGVTTREIEALL-EEL---YGH-----KVSPSVISVVTDRLD-----------EKVKAWQNRP-- 141 (379)
T ss_pred hhhhhHHHHHHHHHHcCCcHHHHHHHH-HHh---hCc-----ccCHHHhhhHHHHHH-----------HHHHHHHhcc--
Confidence 344556688999999999998874333 222 322 123323333333222 2344443321
Q ss_pred eeEEecCCCCCCCeEeecCcHHHHHHHHHhCCCeEEEEeccccccc--cCCceEEEEEEcCCCCeEEEEEEEecCCChhh
Q 006219 260 SIFFYQDSSETDPFILGIQTEWQLQQMIRFGHRSLIAADSTFGIKR--LKYPLCTLLVFDSRQHALPVAWVVTRSSAKPD 337 (656)
Q Consensus 260 ~vf~y~d~~d~~~F~l~iqt~~Q~~~l~~fg~~~vv~iDsT~~tnk--y~~pL~tl~v~d~~g~~~PvA~~i~~~et~e~ 337 (656)
+ |+..++++|++|.--+ -+-.++..+|++..|.--.+++.+...|+ .-
T Consensus 142 --------------------------l---~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~ 191 (379)
T COG3328 142 --------------------------L---GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KF 191 (379)
T ss_pred --------------------------c---cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hh
Confidence 2 3334799999997666 44688999999999999999999999999 66
Q ss_pred HHHHHHHHHHHHhccCCCcceEEEEEcCchhhhhHHHHhcCCC-cccchHHHHHHHHHHHHhhcCChHHHHHHHHHHHHH
Q 006219 338 VTKWMKSLLDRARSIEPGWKISGFLIDDAAAEIDPIREIFCCP-LLFSLWRVRRSWLRNIVKKCTNIKIQREIFKRLGNI 416 (656)
Q Consensus 338 ~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A~~~AI~~VFp~~-~LLC~wHV~qaw~k~l~~k~~~~e~~~~i~k~L~~l 416 (656)
+..||..|..+--. ....+++|.-...-+||.++||.. +..|..|+.++...... .+.+..+...+..+
T Consensus 192 w~~~l~~l~~rgl~-----~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~-----~k~~d~i~~~~~~I 261 (379)
T COG3328 192 WLSFLLDLKNRGLS-----DVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVP-----RKDQDAVLSDLRSI 261 (379)
T ss_pred HHHHHHHHHhcccc-----ceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhh-----hhhhHHHHhhhhhh
Confidence 66666666654211 244567799999999999999986 99999999976544442 23455555555444
Q ss_pred HhhhcCCCChHHHHHHHHHHhhc-hhHHHHHHHhhccchHHHHHHhhhcCCCC---CCCcChHHHHhHHhhhhh
Q 006219 417 LYSIWDGADPFVNLEVLIQDFVD-QTAFIEYFKASWMPKLAMWLSTMRALPLA---SQEASGAIEAYHVKLKTK 486 (656)
Q Consensus 417 l~~~~~~~~f~~~le~~~~~~~d-~~~F~~Yf~~~Wl~~~e~Wa~~~R~lp~~---~~~TNn~iES~h~~LK~~ 486 (656)
.-.. +..+....+.++...|.. .+....-..+.|.. .|. |-.+|-. ...|||.+|++|..++..
T Consensus 262 ~~a~-~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~---~~~--F~~fp~~~r~~i~ttN~IE~~n~~ir~~ 329 (379)
T COG3328 262 YIAP-DAEEALLALLAFSELWGKRYPAILKSWRNALEE---LLP--FFAFPSEIRKIIYTTNAIESLNKLIRRR 329 (379)
T ss_pred hccC-CcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHH---hcc--cccCcHHHHhHhhcchHHHHHHHHHHHH
Confidence 3222 222344455555554442 33333333333321 111 1123431 368999999999988754
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=97.50 E-value=5.8e-05 Score=51.57 Aligned_cols=25 Identities=20% Similarity=0.626 Sum_probs=22.1
Q ss_pred eeecc-CCCCCccchhHHHHHHHhcc
Q 006219 523 FCDCA-WSMQGNICKHVVKVNMICAN 547 (656)
Q Consensus 523 ~CsC~-~~~~G~~CkH~~kV~~~~~~ 547 (656)
.|+|. |+..|+||+|+++|+...+.
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 69995 99999999999999987653
No 6
>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=97.44 E-value=0.00026 Score=61.47 Aligned_cols=72 Identities=22% Similarity=0.366 Sum_probs=48.7
Q ss_pred CCCCccccccceeEEEEEEeecCCCccCCCCccccccccccccCcCCCCCCcccCceeEEEEEEeecCCcEEEEEEeccc
Q 006219 74 RGSLKEYKDDEYLEYRLYWCSFGPENYGEGGGVLPSRKYRLNTRNRAARPQSMRGCTCHFVVKRLYARPSLALLIYNDRR 153 (656)
Q Consensus 74 ~g~~~~~~~d~~~~y~~Y~Cs~Gp~~~~~~~~~~p~~~~~~~~~~r~~r~~tk~GC~c~~~Vkr~~~~~~v~v~i~~~~~ 153 (656)
.+...+.+.++.+.+..|.|+. +|..++..+. ..+++..+++.++||+|+|.|++.. ++.|.|..+. .+
T Consensus 16 ~~~s~~~~~~~~~~~~~~~C~r-------~G~~~~~~~~--~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~~~~-~~ 84 (91)
T PF03101_consen 16 KSSSRKSKKNGEIKRVTFVCSR-------GGKYKSKKKN--EEKRRRNRPSKKTGCKARINVKRRK-DGKWRVTSFV-LE 84 (91)
T ss_pred EeeeEeCCCCceEEEEEEEECC-------cccccccccc--cccccccccccccCCCEEEEEEEcc-CCEEEEEECc-CC
Confidence 3455566789999999999995 3322221111 1223446788899999999999875 7777776666 34
Q ss_pred ccC
Q 006219 154 HVN 156 (656)
Q Consensus 154 H~~ 156 (656)
|+|
T Consensus 85 HNH 87 (91)
T PF03101_consen 85 HNH 87 (91)
T ss_pred cCC
Confidence 765
No 7
>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=97.29 E-value=0.00024 Score=52.43 Aligned_cols=28 Identities=36% Similarity=0.738 Sum_probs=23.8
Q ss_pred CCceeeeecc-CCCCCccchhHHHHHHHh
Q 006219 518 GSEFAFCDCA-WSMQGNICKHVVKVNMIC 545 (656)
Q Consensus 518 ~~~~~~CsC~-~~~~G~~CkH~~kV~~~~ 545 (656)
+.....|+|+ |+..|.+|+|++||+...
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHhh
Confidence 3567799997 888999999999998653
No 8
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=96.54 E-value=0.033 Score=57.02 Aligned_cols=138 Identities=12% Similarity=0.199 Sum_probs=81.5
Q ss_pred EEEEEEeecCCCccCCCCcccccc----c-cccccCcCCCCCCcccCceeEEEEEEeecCCcEEEE--------------
Q 006219 87 EYRLYWCSFGPENYGEGGGVLPSR----K-YRLNTRNRAARPQSMRGCTCHFVVKRLYARPSLALL-------------- 147 (656)
Q Consensus 87 ~y~~Y~Cs~Gp~~~~~~~~~~p~~----~-~~~~~~~r~~r~~tk~GC~c~~~Vkr~~~~~~v~v~-------------- 147 (656)
-...|.|++|++.+......+-++ . ....++++..+++.+.+|||.+.|+....=|.+.+.
T Consensus 33 g~~~~~Cq~G~dr~~~~~~k~~~~~~~~~~~~~~~~~~~~~~skK~~CPA~I~Ik~I~~FPdykv~~~~~~~~~~~r~~~ 112 (225)
T PF15299_consen 33 GTKVYECQHGKDRNKKRKKKRKSQKNRDEEDKSKKKRRRSKPSKKRDCPARIYIKEIIKFPDYKVPTNSQKDTRRERRKA 112 (225)
T ss_pred eceEEEeeCCCccchhhhhhhhhhccccccccccccccccccccCCCCCeEEEEEEEEEcCCcccccchhhhhHHHHHHH
Confidence 346788999999986443222111 1 112333344556778999999988874222332222
Q ss_pred -------------------EEec----ccccCCCCCccCCCCCcCcCCC-CCCcCCCCCHHHHHHHHHHHHcCCCh-HHH
Q 006219 148 -------------------IYND----RRHVNKSGFICHGPLDRDAIGP-GAKKIPYICNEIQQQTMSMIYLGIPE-ESV 202 (656)
Q Consensus 148 -------------------i~~~----~~H~~~~~~~~H~p~~~~~~~~-~~~~~~rIs~e~r~~I~~ll~~Gi~p-~~I 202 (656)
+|-. .+|.+ |.. |. .+.....|.+++.+.|.+|+..|++. .+|
T Consensus 113 ~~~lk~~l~~~~~~~~~~r~yv~lP~~~~H~~------H~~------~~~~~~~~q~~~~~v~~ki~eLv~~gv~~v~e~ 180 (225)
T PF15299_consen 113 SKKLKKALLSGKSIEGERRFYVQLPSPEEHSG------HPI------GQEAAGLKQPLDPRVVEKIHELVAQGVTSVPEM 180 (225)
T ss_pred HHHHHHHHhcCCCCCceEEEEEECCChHhcCC------Ccc------ccccccccccCCHHHHHHHHHHHHcccccHHHH
Confidence 1111 22322 211 21 11345678999999999999999888 444
Q ss_pred HHHHHHhhhh-------ccCCCCccCCCcHHHHHHHHHHHh
Q 006219 203 LEKHIEGIQR-------YCGSDAKVNSLASQYVQKLGMIIR 236 (656)
Q Consensus 203 l~~ire~~~~-------~~g~~~r~~llT~kDV~Ni~~~~~ 236 (656)
.+.++..+.. .....+|...+|.+||+|......
T Consensus 181 k~~l~~fV~~~lf~~~~~p~~~n~~y~Pt~~di~n~~~~~~ 221 (225)
T PF15299_consen 181 KRHLKKFVEEELFKDQEPPPPTNRRYFPTDKDIRNHMYSAK 221 (225)
T ss_pred HHHHHHHhhhhccCCCCCCCCCccccCCchHHHHHHHHHHH
Confidence 4444333311 123447778899999999887654
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=94.96 E-value=0.043 Score=56.38 Aligned_cols=94 Identities=16% Similarity=0.122 Sum_probs=64.8
Q ss_pred EEEeccccccccCCceEEEEEEcCCC-CeEEEEEEEecCCChhhHHHHHHHHHHHHhccCCCcceEEEEEcCchhhhhHH
Q 006219 295 IAADSTFGIKRLKYPLCTLLVFDSRQ-HALPVAWVVTRSSAKPDVTKWMKSLLDRARSIEPGWKISGFLIDDAAAEIDPI 373 (656)
Q Consensus 295 v~iDsT~~tnky~~pL~tl~v~d~~g-~~~PvA~~i~~~et~e~~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A~~~AI 373 (656)
|+||=+.....+.. |..+++|... .+-++ .++.+-+.+++..||..++ .... .-.+++|.+|...+...|+
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~il--~i~~~r~~~~l~~~~~~~~---~~~~-~~~v~~V~~Dm~~~y~~~~ 72 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGRIL--DILPGRDKETLKDFFRSLY---PEEE-RKNVKVVSMDMSPPYRSAI 72 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCceEE--EEcCCccHHHHHHHHHHhC---cccc-ccceEEEEcCCCccccccc
Confidence 35666655554443 4555666521 23333 3778888888888876552 1111 1268899999999999999
Q ss_pred HHhcCCC-cccchHHHHHHHHHHH
Q 006219 374 REIFCCP-LLFSLWRVRRSWLRNI 396 (656)
Q Consensus 374 ~~VFp~~-~LLC~wHV~qaw~k~l 396 (656)
++.||++ +.+-.|||.|...+.+
T Consensus 73 ~~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 73 REYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred cccccccccccccchhhhhhhhcc
Confidence 9999997 8999999999765544
No 10
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=90.97 E-value=27 Score=39.86 Aligned_cols=255 Identities=12% Similarity=0.082 Sum_probs=122.9
Q ss_pred CCCCCHHHHHHHHHHHHcCCChHHHHHHHHHhhhhccCCCCccCCCcHHHHHHHHHHHhhccccCCcchHHHHHHHHHhc
Q 006219 178 IPYICNEIQQQTMSMIYLGIPEESVLEKHIEGIQRYCGSDAKVNSLASQYVQKLGMIIRRSTHELDLDDQASIRLWVDRN 257 (656)
Q Consensus 178 ~~rIs~e~r~~I~~ll~~Gi~p~~Il~~ire~~~~~~g~~~r~~llT~kDV~Ni~~~~~~~~~~l~~~D~~Sv~~wv~~~ 257 (656)
..++|++.+..|.++... +|..+.-+.+ ....|. ..++.+-|.|+.+........... .+..
T Consensus 115 ~~R~S~~~~~~i~~~a~~-~sYr~aa~~l----~~~~~~----~~iS~~tV~~~v~~~g~~~~~~~~---------~~k~ 176 (470)
T PF06782_consen 115 YQRISPELKEKIVELATE-MSYRKAAEIL----EELLGN----VSISKQTVWNIVKEAGFEEIKEEE---------KEKK 176 (470)
T ss_pred ccchhHHHHHHHHHHHhh-cCHHHHHHHH----hhccCC----CccCHHHHHHHHHhccchhhhccc---------cccC
Confidence 467999999999998765 8877664433 111221 258999999998877621100000 1122
Q ss_pred CCeeEEecCCCCCCCeEeecCcHHHHHHHHHhCCCeEEEEeccccccccCCceEEEEEEcCCCCeEEEEE-EEec--CCC
Q 006219 258 KKSIFFYQDSSETDPFILGIQTEWQLQQMIRFGHRSLIAADSTFGIKRLKYPLCTLLVFDSRQHALPVAW-VVTR--SSA 334 (656)
Q Consensus 258 ~~~vf~y~d~~d~~~F~l~iqt~~Q~~~l~~fg~~~vv~iDsT~~tnky~~pL~tl~v~d~~g~~~PvA~-~i~~--~et 334 (656)
+.+++|-. .|.+.+..|-.-.... .-.++.+..-+.- .....++...+.- .+++ .+.
T Consensus 177 ~~~~LyIE----aDg~~v~~qg~~~~~~-----e~k~~~vheG~~~-----------~~~~~~R~~L~n~~~f~~~~~~~ 236 (470)
T PF06782_consen 177 KVPVLYIE----ADGVHVKLQGKKKKKK-----EVKLFVVHEGWEK-----------EKPGGKRNKLKNKRHFVSGVGES 236 (470)
T ss_pred CCCeEEEe----cCcceecccccccccc-----eeeEEEEEeeeee-----------eeccCCcceeecchheecccccc
Confidence 34566643 2334444331000000 0001111111000 0000111122211 2222 222
Q ss_pred hhhHHHHHHHHHHHHhccCCCcc--eEEEEEcCchhhhhHHHHhcCCC-cccchHHHHHHHHHHHHhhcCChHHHHHHHH
Q 006219 335 KPDVTKWMKSLLDRARSIEPGWK--ISGFLIDDAAAEIDPIREIFCCP-LLFSLWRVRRSWLRNIVKKCTNIKIQREIFK 411 (656)
Q Consensus 335 ~e~~~~~L~~l~~~~~~~~p~~~--P~~fmtD~d~A~~~AI~~VFp~~-~LLC~wHV~qaw~k~l~~k~~~~e~~~~i~k 411 (656)
.+ .+...+.+.+.....--. --++..|.+.=..++. +.||.. +.|..||+.|++.+.+.. ..+.+..+++
T Consensus 237 ~~---~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~-~~~~~~~~~LD~FHl~k~i~~~~~~---~~~~~~~~~~ 309 (470)
T PF06782_consen 237 AE---EFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGA-EFFPKAEYFLDRFHLNKKIKQALSH---DPELKEKIRK 309 (470)
T ss_pred hH---HHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHH-HhhcCceEEecHHHHHHHHHHHhhh---ChHHHHHHHH
Confidence 22 233455555544322111 2345567776555544 488876 899999999998877732 2344444554
Q ss_pred HHHHHHhhhcCCCChHHHHHHHHHHhhc------hhHHHHHHHhhccchHHHHHHhhhcCCCCCCCcChHHHHhHHhhhh
Q 006219 412 RLGNILYSIWDGADPFVNLEVLIQDFVD------QTAFIEYFKASWMPKLAMWLSTMRALPLASQEASGAIEAYHVKLKT 485 (656)
Q Consensus 412 ~L~~ll~~~~~~~~f~~~le~~~~~~~d------~~~F~~Yf~~~Wl~~~e~Wa~~~R~lp~~~~~TNn~iES~h~~LK~ 485 (656)
.|.. . +...++..++.+.....+ -..+..|+.++|-. + ..|+.- .+.......|+.|+.|.+
T Consensus 310 al~~----~-d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~-i----~~y~~~--~~~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 310 ALKK----G-DKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDG-I----KPYRER--EGLRGIGAEESVSHVLSY 377 (470)
T ss_pred HHHh----c-CHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHH-h----hhhhhc--cCCCccchhhhhhhHHHH
Confidence 4421 1 112233333333322221 24688999999953 2 234320 112233468999999877
Q ss_pred hhcc
Q 006219 486 KLFD 489 (656)
Q Consensus 486 ~ll~ 489 (656)
.+..
T Consensus 378 RmK~ 381 (470)
T PF06782_consen 378 RMKS 381 (470)
T ss_pred HhcC
Confidence 6443
No 11
>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=89.05 E-value=0.42 Score=49.86 Aligned_cols=81 Identities=14% Similarity=0.094 Sum_probs=49.6
Q ss_pred EEEEeccccc----cc-cCCceEEEEEEcCCCCeEEEEEEEecCCChhhHHHHHHHHHHHHhccCCCcceEEEEEcCchh
Q 006219 294 LIAADSTFGI----KR-LKYPLCTLLVFDSRQHALPVAWVVTRSSAKPDVTKWMKSLLDRARSIEPGWKISGFLIDDAAA 368 (656)
Q Consensus 294 vv~iDsT~~t----nk-y~~pL~tl~v~d~~g~~~PvA~~i~~~et~e~~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A 368 (656)
++++|-|.-. .+ -+.-+.++..-+ .+.|.+..+-..+.+..+|.. + ..++++|.-.+
T Consensus 69 ~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~-----------~-~GilvsD~y~~ 130 (271)
T PF03050_consen 69 VVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGD-----------F-SGILVSDGYSA 130 (271)
T ss_pred eeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcc-----------c-ceeeecccccc
Confidence 7778877654 22 222333333322 567777777777765555422 1 24788898876
Q ss_pred hhhHHHHhcCCCcccchHHHHHHHHHHH
Q 006219 369 EIDPIREIFCCPLLFSLWRVRRSWLRNI 396 (656)
Q Consensus 369 ~~~AI~~VFp~~~LLC~wHV~qaw~k~l 396 (656)
... +. +..+..|+-|+.+.+.+-.
T Consensus 131 Y~~-~~---~~~hq~C~AH~~R~~~~~~ 154 (271)
T PF03050_consen 131 YNK-LA---GITHQLCWAHLRRDFQDAA 154 (271)
T ss_pred ccc-cc---ccccccccccccccccccc
Confidence 655 22 5569999999998765444
No 12
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=88.07 E-value=0.25 Score=50.67 Aligned_cols=33 Identities=30% Similarity=0.649 Sum_probs=26.3
Q ss_pred eeeecc-CCCCCccchhHHHHHHHhccCCCCCCCcch
Q 006219 522 AFCDCA-WSMQGNICKHVVKVNMICANNEGYQPSMSF 557 (656)
Q Consensus 522 ~~CsC~-~~~~G~~CkH~~kV~~~~~~~~~~~~~~s~ 557 (656)
..|||+ ++ +||||+.+|+.+....-...|.+=+
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~lae~f~~dPflif 158 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLAEKFDEDPFLIF 158 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHHHHhccCCeeee
Confidence 479996 65 8999999999888887776676544
No 13
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=87.61 E-value=0.16 Score=47.84 Aligned_cols=79 Identities=14% Similarity=0.098 Sum_probs=60.5
Q ss_pred EEEEeccccccccCCceEEEEEEcCCCCeEEEEEEEecCCChhhHHHHHHHHHHHHhccCCCcceEEEEEcCchhhhhHH
Q 006219 294 LIAADSTFGIKRLKYPLCTLLVFDSRQHALPVAWVVTRSSAKPDVTKWMKSLLDRARSIEPGWKISGFLIDDAAAEIDPI 373 (656)
Q Consensus 294 vv~iDsT~~tnky~~pL~tl~v~d~~g~~~PvA~~i~~~et~e~~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A~~~AI 373 (656)
.+++|-||---+ |---|..-++|..|. .+.+.++...+......||+.+++... -.|..|+||+..+...|+
T Consensus 3 ~w~~DEt~iki~-G~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-----~~p~~ivtDk~~aY~~A~ 74 (140)
T PF13610_consen 3 SWHVDETYIKIK-GKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-----GEPRVIVTDKLPAYPAAI 74 (140)
T ss_pred EEEEeeEEEEEC-CEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-----cccceeecccCCccchhh
Confidence 689999994322 223445668898888 689999998888887777766655442 369999999999999999
Q ss_pred HHhcCCC
Q 006219 374 REIFCCP 380 (656)
Q Consensus 374 ~~VFp~~ 380 (656)
++.++..
T Consensus 75 ~~l~~~~ 81 (140)
T PF13610_consen 75 KELNPEG 81 (140)
T ss_pred hhccccc
Confidence 9999863
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=83.82 E-value=6.9 Score=34.69 Aligned_cols=75 Identities=11% Similarity=0.009 Sum_probs=51.8
Q ss_pred eEEEEeccccc-cccCCceEEEEEEcCCCCeEEEEEEEecCCChhhHHHHHHHHHHHHhccCCCcceEEEEEcCchhhhh
Q 006219 293 SLIAADSTFGI-KRLKYPLCTLLVFDSRQHALPVAWVVTRSSAKPDVTKWMKSLLDRARSIEPGWKISGFLIDDAAAEID 371 (656)
Q Consensus 293 ~vv~iDsT~~t-nky~~pL~tl~v~d~~g~~~PvA~~i~~~et~e~~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A~~~ 371 (656)
..+++|.++-- ...+-..+.++++|.+-+ +.+++.+...++.+.+...|...+...+. ..|+.+.+|...+..+
T Consensus 7 ~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 7 ERWQIDFTPMPIPDKGGRVYLLVFIDDYSR-FIYAFPVSSKETAEAALRALKRAIEKRGG----RPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TEEEEEEEEETGGCTT-CEEEEEEEETTTT-EEEEEEESSSSHHHHHHHHHHHHHHHHS-----SE-SEEEEESCHHHHS
T ss_pred CEEEEeeEEEecCCCCccEEEEEEEECCCC-cEEEEEeeccccccccccccccccccccc----ccceeccccccccccc
Confidence 37999999433 223337888999998644 55788888887888777777665555532 1289999999988775
Q ss_pred H
Q 006219 372 P 372 (656)
Q Consensus 372 A 372 (656)
.
T Consensus 82 ~ 82 (120)
T PF00665_consen 82 H 82 (120)
T ss_dssp H
T ss_pred c
Confidence 4
No 15
>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=81.08 E-value=5.4 Score=36.28 Aligned_cols=33 Identities=24% Similarity=0.446 Sum_probs=22.9
Q ss_pred CCcccCceeEEEEEEee--cCCcEEEEEEecccccC
Q 006219 123 PQSMRGCTCHFVVKRLY--ARPSLALLIYNDRRHVN 156 (656)
Q Consensus 123 ~~tk~GC~c~~~Vkr~~--~~~~v~v~i~~~~~H~~ 156 (656)
....+.|.|+|+|+..+ ....|.+++.+ +.|+|
T Consensus 75 ~t~srk~~CPFriRA~yS~k~k~W~lvvvn-n~HnH 109 (111)
T PF08731_consen 75 RTKSRKNTCPFRIRANYSKKNKKWTLVVVN-NEHNH 109 (111)
T ss_pred cccccccCCCeEEEEEEEecCCeEEEEEec-CCcCC
Confidence 44557788888887753 35778888887 45765
No 16
>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=80.27 E-value=6.2 Score=32.01 Aligned_cols=30 Identities=23% Similarity=0.514 Sum_probs=22.9
Q ss_pred cCceeEEEEEEeecCCcEEEEEEecccccCC
Q 006219 127 RGCTCHFVVKRLYARPSLALLIYNDRRHVNK 157 (656)
Q Consensus 127 ~GC~c~~~Vkr~~~~~~v~v~i~~~~~H~~~ 157 (656)
.||+|.=.|.+...++.+.+++|. ++|+|.
T Consensus 30 ~~C~akK~Vqr~~~d~~~~~vtY~-G~H~h~ 59 (60)
T PF03106_consen 30 PGCPAKKQVQRSADDPNIVIVTYE-GEHNHP 59 (60)
T ss_dssp TTEEEEEEEEEETTCCCEEEEEEE-S--SS-
T ss_pred cChhheeeEEEecCCCCEEEEEEe-eeeCCC
Confidence 399999999997778999888898 668763
No 17
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=76.07 E-value=27 Score=33.59 Aligned_cols=107 Identities=11% Similarity=0.070 Sum_probs=69.5
Q ss_pred HHHHHHhCCCeEEEEeccccccccCCceEEEEEEcCCCCeEEEEEEEecC-CChhhHHHHHHHHHHHHhccCCCcceEEE
Q 006219 283 LQQMIRFGHRSLIAADSTFGIKRLKYPLCTLLVFDSRQHALPVAWVVTRS-SAKPDVTKWMKSLLDRARSIEPGWKISGF 361 (656)
Q Consensus 283 ~~~l~~fg~~~vv~iDsT~~tnky~~pL~tl~v~d~~g~~~PvA~~i~~~-et~e~~~~~L~~l~~~~~~~~p~~~P~~f 361 (656)
++....+|. -|..|+= ++..+.+|+.+++.-..|..|.-..-.++. .+.+.+...|....+.++. ...-.|
T Consensus 26 k~~w~~~Gc--si~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~----~nVvqV 97 (153)
T PF04937_consen 26 KKSWKRTGC--SIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGE----ENVVQV 97 (153)
T ss_pred HHHHHhcCE--EEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhh----hhhhHH
Confidence 345567787 5888985 555677899999987776655443333222 3444455555555555543 245568
Q ss_pred EEcCchhhhhHHHHhcCC-C---cccchHHHHHHHHHHHH
Q 006219 362 LIDDAAAEIDPIREIFCC-P---LLFSLWRVRRSWLRNIV 397 (656)
Q Consensus 362 mtD~d~A~~~AI~~VFp~-~---~LLC~wHV~qaw~k~l~ 397 (656)
+||.+..+..|.+-.-.. + ...|.-|...-..+.+.
T Consensus 98 VTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~ 137 (153)
T PF04937_consen 98 VTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIG 137 (153)
T ss_pred hccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHh
Confidence 999999999997655443 2 46799999976666654
No 18
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=64.80 E-value=32 Score=36.01 Aligned_cols=76 Identities=16% Similarity=0.099 Sum_probs=51.5
Q ss_pred eEEEEeccccccccCCceEEEEEEcCCCCeEEEEEEEecC-CChhhHHHHHHHHHHHH-hccCCCcceEEEEEcCchhhh
Q 006219 293 SLIAADSTFGIKRLKYPLCTLLVFDSRQHALPVAWVVTRS-SAKPDVTKWMKSLLDRA-RSIEPGWKISGFLIDDAAAEI 370 (656)
Q Consensus 293 ~vv~iDsT~~tnky~~pL~tl~v~d~~g~~~PvA~~i~~~-et~e~~~~~L~~l~~~~-~~~~p~~~P~~fmtD~d~A~~ 370 (656)
.+++.|-||-....+.-+|..+|+|.+.+- .|||.+... .+.+.+...|...++.. +...| ..|..|-||.-....
T Consensus 88 ~~W~~DiT~~~~~~g~~~Yl~~viD~~sR~-ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~-~~~~iihSD~Gsqy~ 165 (262)
T PRK14702 88 QRWCSDGFEFCCDNGERLRVTFALDCCDRE-ALHWAVTTGGFNSETVQDVMLGAVERRFGNDLP-SSPVEWLTDNGSCYR 165 (262)
T ss_pred CEEEeeeEEEEecCCcEEEEEEEEecccce-eeeEEeccCcCCHHHHHHHHHHHHHHHhcccCC-CCCeEEEcCCCcccc
Confidence 389999998655555568999999998664 599999874 56666666665443332 21112 357788999876543
No 19
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=58.89 E-value=8.4 Score=44.11 Aligned_cols=39 Identities=23% Similarity=0.517 Sum_probs=30.0
Q ss_pred ceEEEecCCCceeeeeccCCCCCccchhHHHHHHHhccCC
Q 006219 510 LTHLVWNPGSEFAFCDCAWSMQGNICKHVVKVNMICANNE 549 (656)
Q Consensus 510 ~~~vv~n~~~~~~~CsC~~~~~G~~CkH~~kV~~~~~~~~ 549 (656)
.+.|..+.+...++|+|+.+ .+--|||++||..-+....
T Consensus 61 ~v~vtL~~~~~ss~CTCP~~-~~gaCKH~VAvvl~~~~~p 99 (587)
T COG4715 61 RVRVTLEGGALSSICTCPYG-GSGACKHVVAVVLEYLDDP 99 (587)
T ss_pred eEEEEeecCCcCceeeCCCC-CCcchHHHHHHHHHHhhcc
Confidence 45666677888899999984 4557999999997776543
No 20
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=57.00 E-value=51 Score=35.23 Aligned_cols=76 Identities=16% Similarity=0.087 Sum_probs=50.9
Q ss_pred eEEEEeccccccccCCceEEEEEEcCCCCeEEEEEEEecC-CChhhHHHHHHHHHHHH-hccCCCcceEEEEEcCchhhh
Q 006219 293 SLIAADSTFGIKRLKYPLCTLLVFDSRQHALPVAWVVTRS-SAKPDVTKWMKSLLDRA-RSIEPGWKISGFLIDDAAAEI 370 (656)
Q Consensus 293 ~vv~iDsT~~tnky~~pL~tl~v~d~~g~~~PvA~~i~~~-et~e~~~~~L~~l~~~~-~~~~p~~~P~~fmtD~d~A~~ 370 (656)
.+++.|-||-...-+.-+|..+|+|.+.+ ..|||.+... .+.+.+...|...+... +...| ..|..|-||.-....
T Consensus 127 ~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~-~~~~iihSDrGsqy~ 204 (301)
T PRK09409 127 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLP-SSPVEWLTDNGSCYR 204 (301)
T ss_pred CEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCC-CCCcEEecCCCcccc
Confidence 49999999965544556888899999866 4599999876 57776666665433332 21112 246688899876543
No 21
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.46 E-value=57 Score=33.31 Aligned_cols=92 Identities=13% Similarity=0.051 Sum_probs=63.6
Q ss_pred EEEEeccccccc-cCCceEEEEEEcCCCCeEEEEEEEecCCChhhHHHHHHHHHHHHhccCCCcceEEEEEcCchhhhhH
Q 006219 294 LIAADSTFGIKR-LKYPLCTLLVFDSRQHALPVAWVVTRSSAKPDVTKWMKSLLDRARSIEPGWKISGFLIDDAAAEIDP 372 (656)
Q Consensus 294 vv~iDsT~~tnk-y~~pL~tl~v~d~~g~~~PvA~~i~~~et~e~~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A~~~A 372 (656)
.+.+|=||-.-+ -..-|+-. +|.. +.++-+.+...-+......||..+++..+ .|.+|+||+......|
T Consensus 72 ~w~vDEt~ikv~gkw~ylyrA--id~~--g~~Ld~~L~~rRn~~aAk~Fl~kllk~~g------~p~v~vtDka~s~~~A 141 (215)
T COG3316 72 SWRVDETYIKVNGKWHYLYRA--IDAD--GLTLDVWLSKRRNALAAKAFLKKLLKKHG------EPRVFVTDKAPSYTAA 141 (215)
T ss_pred ceeeeeeEEeeccEeeehhhh--hccC--CCeEEEEEEcccCcHHHHHHHHHHHHhcC------CCceEEecCccchHHH
Confidence 799999995543 22334443 3443 66788888888888877778877766542 5889999999999999
Q ss_pred HHHhcCC----C-----cccchHHHHHHHHHH
Q 006219 373 IREIFCC----P-----LLFSLWRVRRSWLRN 395 (656)
Q Consensus 373 I~~VFp~----~-----~LLC~wHV~qaw~k~ 395 (656)
++++-+. + .+.-.||.--.++.+
T Consensus 142 ~~~l~~~~ehr~~~ylnN~iE~dh~~iKrr~~ 173 (215)
T COG3316 142 LRKLGSEVEHRTSKYLNNRIEQDHRPIKRRTR 173 (215)
T ss_pred HHhcCcchheecccccccchhhcchhHHHHhc
Confidence 9988772 1 244556665555444
No 22
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=48.81 E-value=11 Score=28.29 Aligned_cols=27 Identities=11% Similarity=0.217 Sum_probs=13.0
Q ss_pred CCCCHHHHHHHHHHHHcCCChHHHHHH
Q 006219 179 PYICNEIQQQTMSMIYLGIPEESVLEK 205 (656)
Q Consensus 179 ~rIs~e~r~~I~~ll~~Gi~p~~Il~~ 205 (656)
++||.++|..|..|...|.+..+|-..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~s~~~IA~~ 29 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGMSIREIAKR 29 (44)
T ss_dssp ---------HHHHHHCS---HHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCCCHHHHHHH
Confidence 358999999999999999999998543
No 23
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=45.32 E-value=35 Score=25.58 Aligned_cols=39 Identities=10% Similarity=0.187 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHHHHHHcCCChHHHHHHHHHhhhhccCCCCccCCCcHHHHHHHH
Q 006219 179 PYICNEIQQQTMSMIYLGIPEESVLEKHIEGIQRYCGSDAKVNSLASQYVQKLG 232 (656)
Q Consensus 179 ~rIs~e~r~~I~~ll~~Gi~p~~Il~~ire~~~~~~g~~~r~~llT~kDV~Ni~ 232 (656)
+.+++++.+.|.+|...|++..+|... + .+++.-||++.
T Consensus 4 ~~~~~~~~~~i~~l~~~G~si~~IA~~----~-----------gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGMSIAEIAKQ----F-----------GVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--HHHHHHH----T-----------TS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHH----H-----------CcCHHHHHHHH
Confidence 357888889999999999999988543 1 36777777764
No 24
>PHA02517 putative transposase OrfB; Reviewed
Probab=38.90 E-value=70 Score=33.25 Aligned_cols=72 Identities=18% Similarity=0.086 Sum_probs=47.2
Q ss_pred EEEEeccccccccCCceEEEEEEcCCCCeEEEEEEEecCCChhhHHHHHHHHHHHHhccCCCcceEEEEEcCchhhhh
Q 006219 294 LIAADSTFGIKRLKYPLCTLLVFDSRQHALPVAWVVTRSSAKPDVTKWMKSLLDRARSIEPGWKISGFLIDDAAAEID 371 (656)
Q Consensus 294 vv~iDsT~~tnky~~pL~tl~v~d~~g~~~PvA~~i~~~et~e~~~~~L~~l~~~~~~~~p~~~P~~fmtD~d~A~~~ 371 (656)
+++.|-||-....+ -.+...++|.+.+. .+||.+....+.+.+..+|..++...+ .| .+..|.||....+.+
T Consensus 112 ~w~~D~t~~~~~~g-~~yl~~iiD~~sr~-i~~~~~~~~~~~~~~~~~l~~a~~~~~--~~--~~~i~~sD~G~~y~s 183 (277)
T PHA02517 112 LWVADFTYVSTWQG-WVYVAFIIDVFARR-IVGWRVSSSMDTDFVLDALEQALWARG--RP--GGLIHHSDKGSQYVS 183 (277)
T ss_pred eEEeceeEEEeCCC-CEEEEEecccCCCe-eeecccCCCCChHHHHHHHHHHHHhcC--CC--cCcEeecccccccch
Confidence 89999998544434 35778888886554 588999888888876666655443322 11 123677898876543
No 25
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=33.90 E-value=14 Score=33.19 Aligned_cols=22 Identities=27% Similarity=0.933 Sum_probs=14.5
Q ss_pred eeeeecc-CC----CCC-ccchhHHHHH
Q 006219 521 FAFCDCA-WS----MQG-NICKHVVKVN 542 (656)
Q Consensus 521 ~~~CsC~-~~----~~G-~~CkH~~kV~ 542 (656)
..+|||+ +- ..| .+|+|++.+-
T Consensus 49 ~gfCSCp~~~~svvl~Gk~~C~Hi~glk 76 (117)
T COG5431 49 GGFCSCPDFLGSVVLKGKSPCAHIIGLK 76 (117)
T ss_pred cCcccCHHHHhHhhhcCcccchhhhhee
Confidence 3499997 22 344 4599998653
No 26
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=30.31 E-value=70 Score=23.99 Aligned_cols=42 Identities=12% Similarity=0.139 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHcCCChHHHHHHHHHhhhhccCCCCccCCCcHHHHHHHHHHHhhc
Q 006219 182 CNEIQQQTMSMIYLGIPEESVLEKHIEGIQRYCGSDAKVNSLASQYVQKLGMIIRRS 238 (656)
Q Consensus 182 s~e~r~~I~~ll~~Gi~p~~Il~~ire~~~~~~g~~~r~~llT~kDV~Ni~~~~~~~ 238 (656)
+.+.|..|..+...|.+..+|-+.+ .++..-|+++...++..
T Consensus 3 ~~~~R~~ii~l~~~G~s~~~ia~~l---------------gvs~~Tv~~w~kr~~~~ 44 (50)
T PF13384_consen 3 SEERRAQIIRLLREGWSIREIAKRL---------------GVSRSTVYRWIKRYREE 44 (50)
T ss_dssp -------HHHHHHHT--HHHHHHHH---------------TS-HHHHHHHHT-----
T ss_pred chhHHHHHHHHHHCCCCHHHHHHHH---------------CcCHHHHHHHHHHcccc
Confidence 3567888899999999999985432 36888999988877643
No 27
>KOG0053 consensus Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]
Probab=29.14 E-value=5e+02 Score=29.24 Aligned_cols=104 Identities=19% Similarity=0.265 Sum_probs=58.7
Q ss_pred cHHHHHHHHHHHhhccccCCcchHHHHHHHHHhcCCeeEEecCCCCCCCeEeecCcHHHHHHHHHhCCCeEEEEeccccc
Q 006219 224 ASQYVQKLGMIIRRSTHELDLDDQASIRLWVDRNKKSIFFYQDSSETDPFILGIQTEWQLQQMIRFGHRSLIAADSTFGI 303 (656)
Q Consensus 224 T~kDV~Ni~~~~~~~~~~l~~~D~~Sv~~wv~~~~~~vf~y~d~~d~~~F~l~iqt~~Q~~~l~~fg~~~vv~iDsT~~t 303 (656)
|++-++++...+..++--.+.+|...+..-+++ ...++|.+ +-.+|+.-+..-+.-.++..++|- +|++|.||++
T Consensus 129 T~~~l~~~~~~~gie~~~vd~~~~~~~~~~i~~-~t~~V~~E--SPsNPll~v~DI~~l~~la~~~g~--~vvVDnTf~~ 203 (409)
T KOG0053|consen 129 TLRILRKFLPKFGGEGDFVDVDDLKKILKAIKE-NTKAVFLE--SPSNPLLKVPDIEKLARLAHKYGF--LVVVDNTFGS 203 (409)
T ss_pred HHHHHHHHHHHhCceeeeechhhHHHHHHhhcc-CceEEEEE--CCCCCccccccHHHHHHHHhhCCC--EEEEeCCcCc
Confidence 555555555544444333444555555444444 34555654 344577777777777777778887 8999999988
Q ss_pred c--ccCCce-EEEEEEcC----CCCeEEEEEEEecC
Q 006219 304 K--RLKYPL-CTLLVFDS----RQHALPVAWVVTRS 332 (656)
Q Consensus 304 n--ky~~pL-~tl~v~d~----~g~~~PvA~~i~~~ 332 (656)
- ..-++| .-+++.-. .|++=.+|=.++.+
T Consensus 204 p~~~~pL~lGADIV~hSaTKyi~Ghsdvi~G~iv~n 239 (409)
T KOG0053|consen 204 PYNQDPLPLGADIVVHSATKYIGGHSDVIGGSVVLN 239 (409)
T ss_pred ccccChhhcCCCEEEEeeeeeecCCcceeeeEEecC
Confidence 4 444566 33333322 14444455444443
No 28
>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]
Probab=29.02 E-value=5.1e+02 Score=28.00 Aligned_cols=111 Identities=14% Similarity=0.129 Sum_probs=65.4
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhhhhccCCCCccCCCcHHHHHHHH--HHHh-hcccc---CCcchHHHHHHH-HHhc--
Q 006219 187 QQTMSMIYLGIPEESVLEKHIEGIQRYCGSDAKVNSLASQYVQKLG--MIIR-RSTHE---LDLDDQASIRLW-VDRN-- 257 (656)
Q Consensus 187 ~~I~~ll~~Gi~p~~Il~~ire~~~~~~g~~~r~~llT~kDV~Ni~--~~~~-~~~~~---l~~~D~~Sv~~w-v~~~-- 257 (656)
+.+..|-.-||.|+.-++.+.-.+ +| |-..++++..+=+. -++. .+.+- --++|..-+.+. ++.+
T Consensus 144 ~vLeqME~hGVmPdkE~e~~lvn~--FG----r~~~p~~K~~Rm~yWmPkfkn~np~p~pr~vp~dp~ElA~~aL~~M~~ 217 (406)
T KOG3941|consen 144 KVLEQMEWHGVMPDKEIEDILVNA--FG----RWNFPTKKVKRMLYWMPKFKNSNPYPDPRHVPGDPSELAGIALKMMSR 217 (406)
T ss_pred HHHHHHHHcCCCCchHHHHHHHHH--hc----cccccHHHHHHHHHhhhhhccCCCCCCCCCCCCCHHHHHHHHHHHhCh
Confidence 456677888999976666553222 22 23456776554221 1222 22221 124555544444 3333
Q ss_pred --CCeeEEec-----CCCC-CCCeEeecCcHHHHHHHHHhCCCeEEEEeccccc
Q 006219 258 --KKSIFFYQ-----DSSE-TDPFILGIQTEWQLQQMIRFGHRSLIAADSTFGI 303 (656)
Q Consensus 258 --~~~vf~y~-----d~~d-~~~F~l~iqt~~Q~~~l~~fg~~~vv~iDsT~~t 303 (656)
...|-.|+ |.++ ..++++++|+|.|..++.......-|++|+-|+.
T Consensus 218 Dl~s~it~~~~s~~KDs~d~~q~wiv~~qSP~Qq~ll~eh~~~~~vfveGpf~v 271 (406)
T KOG3941|consen 218 DLASSITLLKLSLPKDSSDPQQKWIVTSQSPMQQILLSEHRKGDEVFVEGPFKV 271 (406)
T ss_pred hhhhceEEEeccCccccCCcccceeeccCCHhHHHHHHhhCcCCceEeecchhh
Confidence 24566665 3333 3469999999999888888766668999988765
No 29
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=28.64 E-value=21 Score=19.16 Aligned_cols=8 Identities=63% Similarity=1.232 Sum_probs=6.5
Q ss_pred eccccccc
Q 006219 40 ALIPYARV 47 (656)
Q Consensus 40 ~~~~~~~~ 47 (656)
.||||-||
T Consensus 4 GlI~fpR~ 11 (11)
T PF08259_consen 4 GLIPFPRV 11 (11)
T ss_pred cccccCCC
Confidence 48999886
No 30
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=27.20 E-value=1.5e+02 Score=27.67 Aligned_cols=41 Identities=17% Similarity=0.222 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHHcCCChHHHHHHHHHhhhhccCCCCccCCCcHHHHHHHHHHHh
Q 006219 181 ICNEIQQQTMSMIYLGIPEESVLEKHIEGIQRYCGSDAKVNSLASQYVQKLGMIIR 236 (656)
Q Consensus 181 Is~e~r~~I~~ll~~Gi~p~~Il~~ire~~~~~~g~~~r~~llT~kDV~Ni~~~~~ 236 (656)
|+.++|..|.+|...|++|.+|-.++ .++..-|..|...|+
T Consensus 18 Lp~~~R~rIvela~~G~rp~~Isr~l---------------~Vs~gcVsKIl~Ry~ 58 (125)
T PF00292_consen 18 LPNELRQRIVELAKEGVRPCDISRQL---------------RVSHGCVSKILSRYR 58 (125)
T ss_dssp S-HHHHHHHHHHHHTT--HHHHHHHH---------------T--HHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHhhhcCCHHHHHHHH---------------ccchhHHHHHHHHHH
Confidence 88999999999999999999995432 245556666666555
No 31
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=26.70 E-value=71 Score=29.92 Aligned_cols=32 Identities=16% Similarity=0.387 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHcCCChHHHHHHHHHhhhhccC
Q 006219 181 ICNEIQQQTMSMIYLGIPEESVLEKHIEGIQRYCG 215 (656)
Q Consensus 181 Is~e~r~~I~~ll~~Gi~p~~Il~~ire~~~~~~g 215 (656)
|..++|.+|.+++..|-+.++|++.+. ++||.
T Consensus 58 iA~dmR~~Vr~~i~~G~Sd~eI~~~~v---~RYG~ 89 (126)
T TIGR03147 58 IAYDLRHEVYSMVNEGKSNQQIIDFMT---ARFGD 89 (126)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHH---HhcCC
Confidence 788999999999999999999987753 44543
No 32
>PF13683 rve_3: Integrase core domain
Probab=25.64 E-value=23 Score=28.75 Aligned_cols=25 Identities=20% Similarity=0.392 Sum_probs=20.8
Q ss_pred CCCCcChHHHHhHHhhhhhhcccCc
Q 006219 468 ASQEASGAIEAYHVKLKTKLFDDSH 492 (656)
Q Consensus 468 ~~~~TNn~iES~h~~LK~~ll~~~~ 492 (656)
+...+|..+|+||+.||..++....
T Consensus 11 ~~p~~N~~~Er~~~tlK~e~~~~~~ 35 (67)
T PF13683_consen 11 GSPQDNGKVERFNRTLKREFLYRHP 35 (67)
T ss_pred CCcccccceeeehhhhccchhcccc
Confidence 4457889999999999998887664
No 33
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.10 E-value=78 Score=31.59 Aligned_cols=42 Identities=14% Similarity=0.280 Sum_probs=32.4
Q ss_pred hhHHHHHHHhccCCC-----CCCCcchHHHHHHHHHhcCCCCCCccc
Q 006219 536 KHVVKVNMICANNEG-----YQPSMSFQSLREVLMNLWTKPMDDSVE 577 (656)
Q Consensus 536 kH~~kV~~~~~~~~~-----~~~~~s~~~y~~~~~~~~~~~~~~~~~ 577 (656)
+-.-+.+.-|..... -.|.|.+.+|.|.|.-.|..-||+||.
T Consensus 166 kRmrAA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP~N 212 (221)
T KOG3223|consen 166 KRMRAAFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNPFN 212 (221)
T ss_pred HHHHHHHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCChhh
Confidence 344445554544332 679999999999999999999999986
No 34
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=22.69 E-value=94 Score=29.12 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHHHcCCChHHHHHHHH
Q 006219 181 ICNEIQQQTMSMIYLGIPEESVLEKHI 207 (656)
Q Consensus 181 Is~e~r~~I~~ll~~Gi~p~~Il~~ir 207 (656)
|..++|.+|.+++..|-+.++|++.+.
T Consensus 58 iA~dmR~~Vr~~i~~G~sd~eI~~~~v 84 (126)
T PRK10144 58 VAVSMRHQVYSMVAEGKSEVEIIGWMT 84 (126)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 778999999999999999999987753
No 35
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=21.60 E-value=74 Score=30.56 Aligned_cols=27 Identities=15% Similarity=0.441 Sum_probs=22.1
Q ss_pred CCHHHHHHHHHHHHcCCChHHHHHHHH
Q 006219 181 ICNEIQQQTMSMIYLGIPEESVLEKHI 207 (656)
Q Consensus 181 Is~e~r~~I~~ll~~Gi~p~~Il~~ir 207 (656)
+..++|.+|.+++..|-+.++|++...
T Consensus 58 ~A~dmR~~I~~~l~~G~s~~eI~~~~v 84 (148)
T PF03918_consen 58 IARDMRREIREMLAEGKSDEEIIDYFV 84 (148)
T ss_dssp HHHHHHHHHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 678999999999999999999987653
No 36
>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=21.31 E-value=1.2e+02 Score=24.67 Aligned_cols=30 Identities=27% Similarity=0.491 Sum_probs=23.1
Q ss_pred ccCceeEEEEEEeecCCcEEEEEEecccccC
Q 006219 126 MRGCTCHFVVKRLYARPSLALLIYNDRRHVN 156 (656)
Q Consensus 126 k~GC~c~~~Vkr~~~~~~v~v~i~~~~~H~~ 156 (656)
..||+++=.|.+...++.+.+++|. ++|+|
T Consensus 30 ~~~C~a~K~Vq~~~~d~~~~~vtY~-g~H~h 59 (59)
T smart00774 30 SQGCPAKKQVQRSDDDPSVVEVTYE-GEHTH 59 (59)
T ss_pred cCCCCCcccEEEECCCCCEEEEEEe-eEeCC
Confidence 3689998788876667888888887 55764
Done!