Query 045767
Match_columns 737
No_of_seqs 291 out of 1393
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 05:20:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045767.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045767hhsearch_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 8.4E-71 1.8E-75 636.8 46.9 467 167-667 70-624 (846)
2 PF10551 MULE: MULE transposas 99.8 3E-21 6.5E-26 169.1 8.9 90 372-465 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.8 1.9E-20 4.2E-25 205.2 5.5 237 268-556 112-366 (381)
4 PF03108 DBD_Tnp_Mut: MuDR fam 99.6 1.5E-15 3.3E-20 124.1 9.1 67 168-234 1-67 (67)
5 COG3328 Transposase and inacti 99.4 3.1E-12 6.6E-17 137.9 17.8 222 268-543 98-328 (379)
6 smart00575 ZnF_PMZ plant mutat 98.9 1.2E-09 2.5E-14 72.4 2.1 27 624-650 1-27 (28)
7 PF08731 AFT: Transcription fa 98.8 3.3E-08 7.2E-13 86.2 8.9 69 177-245 1-111 (111)
8 PF03101 FAR1: FAR1 DNA-bindin 98.4 4.3E-07 9.3E-12 78.9 6.5 61 185-246 1-90 (91)
9 PF04434 SWIM: SWIM zinc finge 97.9 6.2E-06 1.4E-10 59.8 2.3 30 619-648 10-39 (40)
10 PF06782 UPF0236: Uncharacteri 95.6 0.19 4.1E-06 57.1 14.0 131 405-543 235-377 (470)
11 PF01610 DDE_Tnp_ISL3: Transpo 94.4 0.068 1.5E-06 55.4 6.0 93 368-468 1-96 (249)
12 PF13610 DDE_Tnp_IS240: DDE do 94.1 0.024 5.1E-07 53.4 1.6 81 365-451 1-81 (140)
13 PF03106 WRKY: WRKY DNA -bindi 92.2 0.29 6.2E-06 38.8 4.7 40 205-244 20-59 (60)
14 PF04684 BAF1_ABF1: BAF1 / ABF 90.6 0.51 1.1E-05 51.6 6.2 56 172-227 23-79 (496)
15 COG3316 Transposase and inacti 85.4 9.2 0.0002 38.4 10.8 84 365-455 70-153 (215)
16 PF03050 DDE_Tnp_IS66: Transpo 85.2 1.6 3.4E-05 45.9 5.9 134 268-470 18-156 (271)
17 PHA02517 putative transposase 83.7 7.9 0.00017 40.6 10.5 151 256-440 30-181 (277)
18 smart00774 WRKY DNA binding do 82.3 1.6 3.4E-05 34.4 3.2 40 204-243 19-59 (59)
19 PF04500 FLYWCH: FLYWCH zinc f 81.6 2.5 5.5E-05 33.0 4.4 46 194-243 14-62 (62)
20 PF00665 rve: Integrase core d 81.5 6.2 0.00014 35.2 7.5 77 364-443 5-82 (120)
21 PRK14702 insertion element IS2 79.4 28 0.00061 36.4 12.5 146 255-439 11-163 (262)
22 PF13565 HTH_32: Homeodomain-l 77.0 3.2 7E-05 34.2 3.8 42 255-296 33-76 (77)
23 PRK09409 IS2 transposase TnpB; 76.1 44 0.00096 35.7 13.1 76 364-440 125-203 (301)
24 PF04937 DUF659: Protein of un 69.8 54 0.0012 31.3 10.7 62 407-470 74-138 (153)
25 COG5431 Uncharacterized metal- 63.5 9.9 0.00021 33.2 3.7 55 592-648 18-79 (117)
26 PF13696 zf-CCHC_2: Zinc knuck 59.6 3.7 8E-05 28.0 0.4 15 720-734 7-21 (32)
27 PF15288 zf-CCHC_6: Zinc knuck 59.4 4.2 9.1E-05 29.2 0.7 13 722-734 2-14 (40)
28 PF02178 AT_hook: AT hook moti 55.7 5.4 0.00012 21.5 0.6 9 697-705 2-10 (13)
29 PF00098 zf-CCHC: Zinc knuckle 55.0 6.9 0.00015 23.0 1.0 13 723-735 2-14 (18)
30 PRK13907 rnhA ribonuclease H; 48.7 1.3E+02 0.0029 27.2 9.2 78 367-448 3-81 (128)
31 PF13592 HTH_33: Winged helix- 44.1 32 0.00069 27.0 3.6 30 269-298 3-32 (60)
32 smart00384 AT_hook DNA binding 41.4 16 0.00034 23.6 1.1 15 696-710 1-15 (26)
33 PF12762 DDE_Tnp_IS1595: ISXO2 39.8 76 0.0016 29.8 6.2 69 366-441 4-87 (151)
34 COG4279 Uncharacterized conser 35.6 20 0.00043 36.6 1.5 24 623-649 124-147 (266)
35 PF01498 HTH_Tnp_Tc3_2: Transp 32.9 35 0.00076 27.6 2.3 38 261-299 4-41 (72)
36 COG4715 Uncharacterized conser 29.4 1.5E+02 0.0032 34.2 7.0 60 588-649 32-96 (587)
37 PF04800 ETC_C1_NDUFA4: ETC co 28.1 83 0.0018 27.8 3.9 33 169-205 46-79 (101)
38 COG3915 Uncharacterized protei 25.7 2.2E+02 0.0048 26.4 6.2 56 325-394 78-135 (155)
39 PF08766 DEK_C: DEK C terminal 23.8 77 0.0017 24.3 2.6 37 257-293 5-43 (54)
40 PRK00766 hypothetical protein; 22.9 5.8E+02 0.013 25.4 9.2 55 366-420 10-65 (194)
41 TIGR00334 5S_RNA_mat_M5 ribonu 22.8 1.2E+02 0.0026 29.5 4.3 43 414-459 37-82 (174)
42 PF13877 RPAP3_C: Potential Mo 22.1 60 0.0013 27.9 2.0 34 484-517 5-38 (94)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=8.4e-71 Score=636.78 Aligned_cols=467 Identities=14% Similarity=0.210 Sum_probs=378.3
Q ss_pred CCccccCCcEeCCHHHHHHHHHHHHHHcCceEEEEeecCe-------EEEEEEee-------------------------
Q 045767 167 HKMVLYQGQRFRDVGEFRKAVQVFAVREGFKLCVMENRSH-------VVCYECSD------------------------- 214 (737)
Q Consensus 167 ~~~~~~vG~~F~s~~e~~~av~~yAi~~gf~~~~~kS~~~-------r~~~~C~~------------------------- 214 (737)
.+..+.+||+|+|.+|++.||+.||.+.||.+++.++.++ ..+++|++
T Consensus 70 ~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~ 149 (846)
T PLN03097 70 TNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPEN 149 (846)
T ss_pred CCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccc
Confidence 4567899999999999999999999999999998765432 23566753
Q ss_pred ---------CCCceEEEEEEcCCCceEEEeeeCCCcccCCCCCCCCccchhhhhhhhheeccCCCCCHHHHHHHHHHHhC
Q 045767 215 ---------LRCDWVIQAGRVSDGTTFIVTDFMPQHTCIRPPLKFQPQSKWISAIYLHRWKLQPKVSTVEIRDEIEATYG 285 (737)
Q Consensus 215 ---------~gCpwri~a~~~~~~~~~~I~~~~~~HnC~~~~~~h~~ss~~ia~~~~~~l~~~~~~~~~~I~~~l~~~~g 285 (737)
+||+++|++++. ..+.|.|+.+..+|||++...... + ...+.+...+....+
T Consensus 150 ~~~rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~-~-----------------~~~r~~~~~~~~~~~ 210 (846)
T PLN03097 150 GTGRRSCAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAV-S-----------------EQTRKMYAAMARQFA 210 (846)
T ss_pred ccccccccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCcccc-c-----------------hhhhhhHHHHHhhhh
Confidence 479999999875 457899999999999999754210 0 011111111111111
Q ss_pred ----CCCChh----HHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhcCCccEEEEEecCCCCCCCCceeEEEEeehhhH
Q 045767 286 ----VVCPEG----KLLSAANRAKHILGMDHYDGYAKLNQLKKEMERIDSHNIVLLETDGDENGEGKRLNKMFVCWERTS 357 (737)
Q Consensus 286 ----~~~s~~----~~~rar~~~~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~~~~~~~~~~~~f~~lF~~~~~~~ 357 (737)
+..... ..-..|.+ +...| ..+.|..||+.++.+||+|+|.|++| ++++++++||+++.++
T Consensus 211 ~~~~v~~~~~d~~~~~~~~r~~--~~~~g----D~~~ll~yf~~~q~~nP~Ffy~~qlD-----e~~~l~niFWaD~~sr 279 (846)
T PLN03097 211 EYKNVVGLKNDSKSSFDKGRNL--GLEAG----DTKILLDFFTQMQNMNSNFFYAVDLG-----EDQRLKNLFWVDAKSR 279 (846)
T ss_pred ccccccccchhhcchhhHHHhh--hcccc----hHHHHHHHHHHHHhhCCCceEEEEEc-----cCCCeeeEEeccHHHH
Confidence 100000 11111221 11223 34789999999999999999999995 8999999999999999
Q ss_pred HHHHhcCccEEEecCeeecCCcCceeEEEEeecCCCceEEEEEEEeeccchhhHHHHHHHHHHHcccCCCCCEEEEccCc
Q 045767 358 YAFKYHCRGILAVDGWKMNNPYKSVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINNALRLENGKGICILGDGD 437 (737)
Q Consensus 358 ~~f~~~~~~vi~iD~T~~~~~y~~~ll~~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~~~~~~~~~p~~iitD~~ 437 (737)
.+|.+ |++||.+|+||++|+|++||++++|+|+|+|+++|||||+.+|+.++|.|||++|+++| ++..|.+||||++
T Consensus 280 ~~Y~~-FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM--~gk~P~tIiTDqd 356 (846)
T PLN03097 280 HDYGN-FSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAM--GGQAPKVIITDQD 356 (846)
T ss_pred HHHHh-cCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHh--CCCCCceEEecCC
Confidence 99998 99999999999999999999999999999999999999999999999999999999999 6899999999999
Q ss_pred chHHHHHHhhccccceecchhHHHHHHHHhCCC-----chhHHHHHHHHhc-CCHHHHHHHHHHHHh-cChhHHHHHhcC
Q 045767 438 NGIDYAVEEFLPEAAYRQCCHKVFTEMVKRFPA-----APVQHLFWSACRS-TSEASFHKYMDLIQQ-QSKECHEWLLQT 510 (737)
Q Consensus 438 ~~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~~-----~~~~~~~~~~~~~-~t~~eFe~~~~~l~~-~~~~~~~yL~~~ 510 (737)
.+|.+||++|||++.|++|+|||++|+.+++.. ..+...|+.+++. .++++|+..|..|.+ ++.+.++||..+
T Consensus 357 ~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~L 436 (846)
T PLN03097 357 KAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSL 436 (846)
T ss_pred HHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHH
Confidence 999999999999999999999999999999863 4899999998875 699999999998875 578899999997
Q ss_pred --CCccccccccCCccccccccCCcchHHhHHhhhh--hcccHHHHHHHHHHHHHHHHHHHHHHH---------------
Q 045767 511 --NWSSWALFSIPKWVKCTSVTLSITDKLHTRLRQY--LEMSIARRFTGIARLTADLFERRRMAV--------------- 571 (737)
Q Consensus 511 --~~~~Wa~a~~~~~~~~g~~TtN~~ES~N~~lk~~--r~~pi~~lle~i~~k~~~~~~~r~~~a--------------- 571 (737)
.+++|+++|+++.+..|+.||+++||+|+.|++. +..+|..|++.+...+..+..+..+.-
T Consensus 437 Y~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~p 516 (846)
T PLN03097 437 YEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSP 516 (846)
T ss_pred HHhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccH
Confidence 8999999999997888999999999999999984 668899999887766655443322210
Q ss_pred --hhhcCcccChHHHHHHHHHHhcccceEEEEeCC----cEEEEEe-CCeeEEEe--e--cCCcccccCCcccCCCCcch
Q 045767 572 --WNWYREKVTPTVREVIHDRTIDGQRFAMVEQNG----TTLKLTD-TISMFYDL--D--MEAMSCSCGLWQISGIPCAH 640 (737)
Q Consensus 572 --~~~~~~~~tp~~~k~l~~~~~~s~~~~V~~~~~----~~f~V~~-~~~~~y~V--~--l~~~tCsC~~~~~~GiPC~H 640 (737)
.+.+. .|||.||++||+++..+..|.+..... .+|.|.+ +....|.| | ..+.+|+|++|+..||||+|
T Consensus 517 iEkQAs~-iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrH 595 (846)
T PLN03097 517 LEKSVSG-VYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRH 595 (846)
T ss_pred HHHHHHH-HhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhh
Confidence 12234 999999999999999998888765432 3788877 32222334 3 35789999999999999999
Q ss_pred HHHHHHHhcC--CchhhhhhcccHHHHHh
Q 045767 641 ACRAIQLNMG--NVEEYVDNMMSVQNYCS 667 (737)
Q Consensus 641 alavl~~~~~--~~~~yv~~~yt~~~~~~ 667 (737)
||+||...++ .|..||.+|||+++-..
T Consensus 596 aLkVL~~~~v~~IP~~YILkRWTKdAK~~ 624 (846)
T PLN03097 596 ALVVLQMCQLSAIPSQYILKRWTKDAKSR 624 (846)
T ss_pred HHHHHhhcCcccCchhhhhhhchhhhhhc
Confidence 9999999997 49999999999998643
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=3e-21 Score=169.07 Aligned_cols=90 Identities=31% Similarity=0.523 Sum_probs=85.9
Q ss_pred CeeecCCcCceeEE---EEeecCCCceEEEEEEEeeccchhhHHHHHHHHHHHcccCCCCCEEEEccCcchHHHHHHhhc
Q 045767 372 GWKMNNPYKSVMLV---AAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINNALRLENGKGICILGDGDNGIDYAVEEFL 448 (737)
Q Consensus 372 ~T~~~~~y~~~ll~---~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~~~~~~~~~p~~iitD~~~~l~~Ai~~vf 448 (737)
|||++|+| ++++. ++|+|++|+.+|+||+++.+|+.++|.|||+.|++.+. .. |.+||||+++|+.+||+++|
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~--~~-p~~ii~D~~~~~~~Ai~~vf 76 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMP--QK-PKVIISDFDKALINAIKEVF 76 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccc--cC-ceeeeccccHHHHHHHHHHC
Confidence 79999999 98886 99999999999999999999999999999999999994 45 99999999999999999999
Q ss_pred cccceecchhHHHHHHH
Q 045767 449 PEAAYRQCCHKVFTEMV 465 (737)
Q Consensus 449 P~a~h~~C~~Hi~~N~~ 465 (737)
|++.|++|.||+.+|++
T Consensus 77 P~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 77 PDARHQLCLFHILRNIK 93 (93)
T ss_pred CCceEehhHHHHHHhhC
Confidence 99999999999999974
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=99.80 E-value=1.9e-20 Score=205.22 Aligned_cols=237 Identities=16% Similarity=0.239 Sum_probs=188.0
Q ss_pred CCCCCHHHHHHHHHHHhC-CCCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhcCCccEEEEEecCCCCCCCCce
Q 045767 268 QPKVSTVEIRDEIEATYG-VVCPEGKLLSAANRAKHILGMDHYDGYAKLNQLKKEMERIDSHNIVLLETDGDENGEGKRL 346 (737)
Q Consensus 268 ~~~~~~~~I~~~l~~~~g-~~~s~~~~~rar~~~~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~~~~~~~~~~~~f 346 (737)
-.+++.++|.+.++.-+| ..+|.+++.+....+.+.+ ..|. ..- +
T Consensus 112 ~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~-----------~~w~----~R~--------L----------- 157 (381)
T PF00872_consen 112 LKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEV-----------EAWR----NRP--------L----------- 157 (381)
T ss_pred ccccccccccchhhhhhcccccCchhhhhhhhhhhhhH-----------HHHh----hhc--------c-----------
Confidence 358899999999999999 7899999887665543222 1111 110 0
Q ss_pred eEEEEeehhhHHHHHhcC-ccEEEecCeeecCCcC-----ceeEEEEeecCCCceEEEEEEEeeccchhhHHHHHHHHHH
Q 045767 347 NKMFVCWERTSYAFKYHC-RGILAVDGWKMNNPYK-----SVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINN 420 (737)
Q Consensus 347 ~~lF~~~~~~~~~f~~~~-~~vi~iD~T~~~~~y~-----~~ll~~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~ 420 (737)
. .. -++|++||+|.+.+.+ ..+++++|+|.+|+..+||+.+...|+.++|.-||+.|++
T Consensus 158 --------------~-~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~ 222 (381)
T PF00872_consen 158 --------------E-SEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKE 222 (381)
T ss_pred --------------c-cccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhh
Confidence 0 13 4789999999987754 4689999999999999999999999999999999999999
Q ss_pred HcccCCCCCEEEEccCcchHHHHHHhhccccceecchhHHHHHHHHhCCCc---hhHHHHHHHHhcCCHHHHHHHHHHHH
Q 045767 421 ALRLENGKGICILGDGDNGIDYAVEEFLPEAAYRQCCHKVFTEMVKRFPAA---PVQHLFWSACRSTSEASFHKYMDLIQ 497 (737)
Q Consensus 421 ~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~~~---~~~~~~~~~~~~~t~~eFe~~~~~l~ 497 (737)
.+ ...|..||+|+.+||..||.++||++.++.|++|+++|+.++++.. .+...++.+..+.+.+++...++.+.
T Consensus 223 RG---l~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~ 299 (381)
T PF00872_consen 223 RG---LKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFA 299 (381)
T ss_pred cc---ccccceeeccccccccccccccccchhhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhcc
Confidence 97 5679999999999999999999999999999999999999999654 67778888888888888888887775
Q ss_pred h----cChhHHHHHhcCCCccccccccCCccccccccCCcchHHhHHhhhh----hcccHHHHHHHH
Q 045767 498 Q----QSKECHEWLLQTNWSSWALFSIPKWVKCTSVTLSITDKLHTRLRQY----LEMSIARRFTGI 556 (737)
Q Consensus 498 ~----~~~~~~~yL~~~~~~~Wa~a~~~~~~~~g~~TtN~~ES~N~~lk~~----r~~pi~~lle~i 556 (737)
+ .+|.+.++|.+...+.|+..-|+...+--+.|||.+|++|+.|+.. ...|-.+.+..+
T Consensus 300 ~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~~~~Fp~~~s~lr~ 366 (381)
T PF00872_consen 300 EKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTKVVGIFPNEESALRL 366 (381)
T ss_pred cccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhccccccCCCHHHHHHH
Confidence 5 4788989988876666665545552444678999999999999873 235544444433
No 4
>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=99.62 E-value=1.5e-15 Score=124.10 Aligned_cols=67 Identities=28% Similarity=0.553 Sum_probs=64.8
Q ss_pred CccccCCcEeCCHHHHHHHHHHHHHHcCceEEEEeecCeEEEEEEeeCCCceEEEEEEcCCCceEEE
Q 045767 168 KMVLYQGQRFRDVGEFRKAVQVFAVREGFKLCVMENRSHVVCYECSDLRCDWVIQAGRVSDGTTFIV 234 (737)
Q Consensus 168 ~~~~~vG~~F~s~~e~~~av~~yAi~~gf~~~~~kS~~~r~~~~C~~~gCpwri~a~~~~~~~~~~I 234 (737)
|+.|.+||+|+|++||+.||..||++++|++++.+|+++|++++|...+|||+|+|++.++++.|+|
T Consensus 1 n~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 1 NPELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred CCccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 5789999999999999999999999999999999999999999999999999999999999999986
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.44 E-value=3.1e-12 Score=137.90 Aligned_cols=222 Identities=15% Similarity=0.167 Sum_probs=165.9
Q ss_pred CCCCCHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhcCCccEEEEEecCCCCCCCCcee
Q 045767 268 QPKVSTVEIRDEIEATYGVVCPEGKLLSAANRAKHILGMDHYDGYAKLNQLKKEMERIDSHNIVLLETDGDENGEGKRLN 347 (737)
Q Consensus 268 ~~~~~~~~I~~~l~~~~g~~~s~~~~~rar~~~~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~~~~~~~~~~~~f~ 347 (737)
..+++++++.+.+++.++..+|...+.+.-...+ ..+.+++..-+
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~---------------e~v~~~~~r~l-------------------- 142 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVTDRLD---------------EKVKAWQNRPL-------------------- 142 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHH---------------HHHHHHHhccc--------------------
Confidence 4588999999999999988787776665443332 22333322210
Q ss_pred EEEEeehhhHHHHHhcCccEEEecCeeecCC--cCceeEEEEeecCCCceEEEEEEEeeccchhhHHHHHHHHHHHcccC
Q 045767 348 KMFVCWERTSYAFKYHCRGILAVDGWKMNNP--YKSVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINNALRLE 425 (737)
Q Consensus 348 ~lF~~~~~~~~~f~~~~~~vi~iD~T~~~~~--y~~~ll~~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~~~~~~ 425 (737)
+..+++++||+|++.+ -+..+++|+|++.+|+-..+++.+-..|+ ..|.-||..|+..+
T Consensus 143 ---------------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rg--- 203 (379)
T COG3328 143 ---------------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRG--- 203 (379)
T ss_pred ---------------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhcc---
Confidence 1558899999999988 44589999999999999999999999999 99999999999987
Q ss_pred CCCCEEEEccCcchHHHHHHhhccccceecchhHHHHHHHHhCCCc---hhHHHHHHHHhcCCHHHHHHHHHHHH----h
Q 045767 426 NGKGICILGDGDNGIDYAVEEFLPEAAYRQCCHKVFTEMVKRFPAA---PVQHLFWSACRSTSEASFHKYMDLIQ----Q 498 (737)
Q Consensus 426 ~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~~~---~~~~~~~~~~~~~t~~eFe~~~~~l~----~ 498 (737)
......+++|+.+|+.+||.++||.+.++.|..|+.+|+..+...+ .....+..+..+.+.++-...|..+. .
T Consensus 204 l~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~ 283 (379)
T COG3328 204 LSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGK 283 (379)
T ss_pred ccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhh
Confidence 4566777789999999999999999999999999999999988765 34444445555566665555555533 3
Q ss_pred cChhHHHHHhcCCCccccccccCCccccccccCCcchHHhHHhhh
Q 045767 499 QSKECHEWLLQTNWSSWALFSIPKWVKCTSVTLSITDKLHTRLRQ 543 (737)
Q Consensus 499 ~~~~~~~yL~~~~~~~Wa~a~~~~~~~~g~~TtN~~ES~N~~lk~ 543 (737)
.+|....++.+..-+.|.-.-|+...+--+.|||.+|++|+.++.
T Consensus 284 ~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 284 RYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred hcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 577777777775444443322222122347899999999997775
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.86 E-value=1.2e-09 Score=72.38 Aligned_cols=27 Identities=44% Similarity=0.691 Sum_probs=25.1
Q ss_pred cccccCCcccCCCCcchHHHHHHHhcC
Q 045767 624 MSCSCGLWQISGIPCAHACRAIQLNMG 650 (737)
Q Consensus 624 ~tCsC~~~~~~GiPC~Halavl~~~~~ 650 (737)
.+|||++||..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998875
No 7
>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=98.77 E-value=3.3e-08 Score=86.15 Aligned_cols=69 Identities=14% Similarity=0.305 Sum_probs=65.5
Q ss_pred eCCHHHHHHHHHHHHHHcCceEEEEeecCeEEEEEEe------------------------------------------e
Q 045767 177 FRDVGEFRKAVQVFAVREGFKLCVMENRSHVVCYECS------------------------------------------D 214 (737)
Q Consensus 177 F~s~~e~~~av~~yAi~~gf~~~~~kS~~~r~~~~C~------------------------------------------~ 214 (737)
|.+++|++.+|+.++...|+++.+.+|+.+.+.++|. .
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 8899999999999999999999999999999999996 1
Q ss_pred CCCceEEEEEEcCCCceEEEeeeCCCcccCC
Q 045767 215 LRCDWVIQAGRVSDGTTFIVTDFMPQHTCIR 245 (737)
Q Consensus 215 ~gCpwri~a~~~~~~~~~~I~~~~~~HnC~~ 245 (737)
..|||+|+|......+.|.|+.++..|+|++
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 5999999999999999999999999999974
No 8
>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=98.43 E-value=4.3e-07 Score=78.92 Aligned_cols=61 Identities=25% Similarity=0.348 Sum_probs=54.1
Q ss_pred HHHHHHHHHcCceEEEEeecCe-------EEEEEEee----------------------CCCceEEEEEEcCCCceEEEe
Q 045767 185 KAVQVFAVREGFKLCVMENRSH-------VVCYECSD----------------------LRCDWVIQAGRVSDGTTFIVT 235 (737)
Q Consensus 185 ~av~~yAi~~gf~~~~~kS~~~-------r~~~~C~~----------------------~gCpwri~a~~~~~~~~~~I~ 235 (737)
+||+.||..+||.+++.+|.+. ++.++|.+ +||||+|.+.+.. ++.|.|+
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~ 79 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK-DGKWRVT 79 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc-CCEEEEE
Confidence 4799999999999999877653 78899972 7999999999887 8999999
Q ss_pred eeCCCcccCCC
Q 045767 236 DFMPQHTCIRP 246 (737)
Q Consensus 236 ~~~~~HnC~~~ 246 (737)
.+..+|||++.
T Consensus 80 ~~~~~HNH~L~ 90 (91)
T PF03101_consen 80 SFVLEHNHPLC 90 (91)
T ss_pred ECcCCcCCCCC
Confidence 99999999875
No 9
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.91 E-value=6.2e-06 Score=59.80 Aligned_cols=30 Identities=33% Similarity=0.699 Sum_probs=26.7
Q ss_pred eecCCcccccCCcccCCCCcchHHHHHHHh
Q 045767 619 LDMEAMSCSCGLWQISGIPCAHACRAIQLN 648 (737)
Q Consensus 619 V~l~~~tCsC~~~~~~GiPC~Halavl~~~ 648 (737)
+++...+|||..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 456688999999999999999999999875
No 10
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=95.55 E-value=0.19 Score=57.12 Aligned_cols=131 Identities=18% Similarity=0.249 Sum_probs=95.0
Q ss_pred ccchhhHHHHHHHHHHHcccCCCCCEEEEccCcchHHHHHHhhccccceecchhHHHHHHHHhCC-CchhHHHHHHHHhc
Q 045767 405 VEDLESWVYFLKNINNALRLENGKGICILGDGDNGIDYAVEEFLPEAAYRQCCHKVFTEMVKRFP-AAPVQHLFWSACRS 483 (737)
Q Consensus 405 ~E~~es~~wfl~~l~~~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~-~~~~~~~~~~~~~~ 483 (737)
..+.+.|.-+...+.+...+....-+++.+|+...|.+++. .+|.+.|.+..+|+.+.+.+.++ .+.+...++++.+.
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~al~~ 313 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKALKK 313 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHHHHh
Confidence 55678999999999998864444467889999999988776 99999999999999999999886 34677777888888
Q ss_pred CCHHHHHHHHHHHHhc--Ch-------hHHHHHhcCCCcccc--ccccCCccccccccCCcchHHhHHhhh
Q 045767 484 TSEASFHKYMDLIQQQ--SK-------ECHEWLLQTNWSSWA--LFSIPKWVKCTSVTLSITDKLHTRLRQ 543 (737)
Q Consensus 484 ~t~~eFe~~~~~l~~~--~~-------~~~~yL~~~~~~~Wa--~a~~~~~~~~g~~TtN~~ES~N~~lk~ 543 (737)
.....++..++.+... .+ ++..||.+ .|. ..|-. +-|.......|+.+..+..
T Consensus 314 ~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~----n~~~i~~y~~---~~~~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 314 GDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLN----NWDGIKPYRE---REGLRGIGAEESVSHVLSY 377 (470)
T ss_pred cCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHH----CHHHhhhhhh---ccCCCccchhhhhhhHHHH
Confidence 8888888888877653 22 34556655 342 12211 1234455567787776643
No 11
>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=94.43 E-value=0.068 Score=55.39 Aligned_cols=93 Identities=16% Similarity=0.183 Sum_probs=69.1
Q ss_pred EEecCeeecCCcCceeEEEEeecC--CCceEEEEEEEeeccchhhHHHHHHHH-HHHcccCCCCCEEEEccCcchHHHHH
Q 045767 368 LAVDGWKMNNPYKSVMLVAAGLDG--NNGILPVAFCEVDVEDLESWVYFLKNI-NNALRLENGKGICILGDGDNGIDYAV 444 (737)
Q Consensus 368 i~iD~T~~~~~y~~~ll~~~g~d~--~~~~~plafal~~~E~~es~~wfl~~l-~~~~~~~~~~p~~iitD~~~~l~~Ai 444 (737)
|+||-+.....+.. +..+-+|. +++.. +.++++-+.++..-||..+ -... .....+|++|...+...||
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---LDILPGRDKETLKDFFRSLYPEEE---RKNVKVVSMDMSPPYRSAI 72 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCceE---EEEcCCccHHHHHHHHHHhCcccc---ccceEEEEcCCCccccccc
Confidence 46777776554443 44444554 33332 4578888888888888766 3332 4568899999999999999
Q ss_pred HhhccccceecchhHHHHHHHHhC
Q 045767 445 EEFLPEAAYRQCCHKVFTEMVKRF 468 (737)
Q Consensus 445 ~~vfP~a~h~~C~~Hi~~N~~~~~ 468 (737)
++.||+|.+..-.||+++++.+.+
T Consensus 73 ~~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 73 REYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred cccccccccccccchhhhhhhhcc
Confidence 999999999999999999887654
No 12
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=94.14 E-value=0.024 Score=53.42 Aligned_cols=81 Identities=20% Similarity=0.137 Sum_probs=69.0
Q ss_pred ccEEEecCeeecCCcCceeEEEEeecCCCceEEEEEEEeeccchhhHHHHHHHHHHHcccCCCCCEEEEccCcchHHHHH
Q 045767 365 RGILAVDGWKMNNPYKSVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINNALRLENGKGICILGDGDNGIDYAV 444 (737)
Q Consensus 365 ~~vi~iD~T~~~~~y~~~ll~~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~~~~~~~~~p~~iitD~~~~l~~Ai 444 (737)
++.+.+|-||.+.+-. ..+...++|.+++ +|++-|...-+...=..||..+++.. ...|..|+||+.++...|+
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~---~~~p~~ivtDk~~aY~~A~ 74 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRH---RGEPRVIVTDKLPAYPAAI 74 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceee---ccccceeecccCCccchhh
Confidence 3578999999886522 4566888999999 88999999999999899998888877 3789999999999999999
Q ss_pred Hhhcccc
Q 045767 445 EEFLPEA 451 (737)
Q Consensus 445 ~~vfP~a 451 (737)
++++|.-
T Consensus 75 ~~l~~~~ 81 (140)
T PF13610_consen 75 KELNPEG 81 (140)
T ss_pred hhccccc
Confidence 9999874
No 13
>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=92.19 E-value=0.29 Score=38.78 Aligned_cols=40 Identities=18% Similarity=0.336 Sum_probs=33.4
Q ss_pred CeEEEEEEeeCCCceEEEEEEcCCCceEEEeeeCCCcccC
Q 045767 205 SHVVCYECSDLRCDWVIQAGRVSDGTTFIVTDFMPQHTCI 244 (737)
Q Consensus 205 ~~r~~~~C~~~gCpwri~a~~~~~~~~~~I~~~~~~HnC~ 244 (737)
-.|..++|+..+||++-.+.+..++....++++..+|||+
T Consensus 20 ~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 20 YPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp CEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred eeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 4577799999999999999998878889999999999996
No 14
>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=90.61 E-value=0.51 Score=51.64 Aligned_cols=56 Identities=9% Similarity=0.284 Sum_probs=50.5
Q ss_pred cCCcEeCCHHHHHHHHHHHHHHcCceEEEEeec-CeEEEEEEeeCCCceEEEEEEcC
Q 045767 172 YQGQRFRDVGEFRKAVQVFAVREGFKLCVMENR-SHVVCYECSDLRCDWVIQAGRVS 227 (737)
Q Consensus 172 ~vG~~F~s~~e~~~av~~yAi~~gf~~~~~kS~-~~r~~~~C~~~gCpwri~a~~~~ 227 (737)
..+..|++.++-+.+|+.|-+..+.+|..+.|- .+.|+|.|.-..|||+|..+..+
T Consensus 23 ~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g 79 (496)
T PF04684_consen 23 AQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCG 79 (496)
T ss_pred ccccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeecc
Confidence 457789999999999999999999999999886 47899999999999999998654
No 15
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=85.38 E-value=9.2 Score=38.37 Aligned_cols=84 Identities=15% Similarity=0.074 Sum_probs=61.2
Q ss_pred ccEEEecCeeecCCcCceeEEEEeecCCCceEEEEEEEeeccchhhHHHHHHHHHHHcccCCCCCEEEEccCcchHHHHH
Q 045767 365 RGILAVDGWKMNNPYKSVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINNALRLENGKGICILGDGDNGIDYAV 444 (737)
Q Consensus 365 ~~vi~iD~T~~~~~y~~~ll~~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~~~~~~~~~p~~iitD~~~~l~~Ai 444 (737)
.+++.+|-||.+.+-+. .+.--++|.+ ..+|.+-|...-+...=.-||..+++.. ..|.+|+||+.+....|+
T Consensus 70 ~~~w~vDEt~ikv~gkw-~ylyrAid~~--g~~Ld~~L~~rRn~~aAk~Fl~kllk~~----g~p~v~vtDka~s~~~A~ 142 (215)
T COG3316 70 GDSWRVDETYIKVNGKW-HYLYRAIDAD--GLTLDVWLSKRRNALAAKAFLKKLLKKH----GEPRVFVTDKAPSYTAAL 142 (215)
T ss_pred ccceeeeeeEEeeccEe-eehhhhhccC--CCeEEEEEEcccCcHHHHHHHHHHHHhc----CCCceEEecCccchHHHH
Confidence 45677888888754332 2233445555 3567778888777777777887777765 579999999999999999
Q ss_pred Hhhccccceec
Q 045767 445 EEFLPEAAYRQ 455 (737)
Q Consensus 445 ~~vfP~a~h~~ 455 (737)
.++-+.+.|+.
T Consensus 143 ~~l~~~~ehr~ 153 (215)
T COG3316 143 RKLGSEVEHRT 153 (215)
T ss_pred HhcCcchheec
Confidence 99988666653
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=85.21 E-value=1.6 Score=45.89 Aligned_cols=134 Identities=13% Similarity=0.165 Sum_probs=84.5
Q ss_pred CCCCCHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhcCCccEEEEEecCCCCCCCCcee
Q 045767 268 QPKVSTVEIRDEIEATYGVVCPEGKLLSAANRAKHILGMDHYDGYAKLNQLKKEMERIDSHNIVLLETDGDENGEGKRLN 347 (737)
Q Consensus 268 ~~~~~~~~I~~~l~~~~g~~~s~~~~~rar~~~~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~~~~~~~~~~~~f~ 347 (737)
...++...|.+.+... |+.+|.+++.+.-.++.+.. ....+.|.+.
T Consensus 18 ~~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l-----------~~~~~~l~~~---------------------- 63 (271)
T PF03050_consen 18 VYHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEAL-----------KPLYEALKEE---------------------- 63 (271)
T ss_pred cCCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhh-----------hhhhhhhhhh----------------------
Confidence 4466777777777777 99999998877655443321 1112222111
Q ss_pred EEEEeehhhHHHHHhcCccEEEecCeeec----CCcC-ceeEEEEeecCCCceEEEEEEEeeccchhhHHHHHHHHHHHc
Q 045767 348 KMFVCWERTSYAFKYHCRGILAVDGWKMN----NPYK-SVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINNAL 422 (737)
Q Consensus 348 ~lF~~~~~~~~~f~~~~~~vi~iD~T~~~----~~y~-~~ll~~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~~~ 422 (737)
.. -.+|+.+|-|... ++.. +-+.++++-+ .+.|.+.++-+.+...-+|..
T Consensus 64 ------------~~--~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~----- 118 (271)
T PF03050_consen 64 ------------LR--SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGD----- 118 (271)
T ss_pred ------------cc--ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcc-----
Confidence 11 3578888888887 4433 3344444333 556666666666665555422
Q ss_pred ccCCCCCEEEEccCcchHHHHHHhhccccceecchhHHHHHHHHhCCC
Q 045767 423 RLENGKGICILGDGDNGIDYAVEEFLPEAAYRQCCHKVFTEMVKRFPA 470 (737)
Q Consensus 423 ~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~N~~~~~~~ 470 (737)
-.-+++||+..+=.. +..+.|+.|+.|+.+.+.+-...
T Consensus 119 -----~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 119 -----FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred -----cceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 234899999987544 23889999999999998876653
No 17
>PHA02517 putative transposase OrfB; Reviewed
Probab=83.75 E-value=7.9 Score=40.65 Aligned_cols=151 Identities=11% Similarity=0.019 Sum_probs=80.4
Q ss_pred hhhhhhhheecc-CCCCCHHHHHHHHHHHhCCCCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhcCCccEEEEE
Q 045767 256 WISAIYLHRWKL-QPKVSTVEIRDEIEATYGVVCPEGKLLSAANRAKHILGMDHYDGYAKLNQLKKEMERIDSHNIVLLE 334 (737)
Q Consensus 256 ~ia~~~~~~l~~-~~~~~~~~I~~~l~~~~g~~~s~~~~~rar~~~~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~~~v~ 334 (737)
.+.+.+.+.+.. .+.+..+.|...|++. |+.+|.++++|....+ |-... ......... .
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~-----gl~~~-----------~~~k~~~~~---~ 89 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKEL-----GLAGV-----------LRGKKVRTT---I 89 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHc-----CCceE-----------ecCCCcCCC---C
Confidence 344555555544 5788999999988755 9999999988764332 11000 000000000 0
Q ss_pred ecCCCCCCCCceeEEEEeehhhHHHHHhcCccEEEecCeeecCCcCceeEEEEeecCCCceEEEEEEEeeccchhhHHHH
Q 045767 335 TDGDENGEGKRLNKMFVCWERTSYAFKYHCRGILAVDGWKMNNPYKSVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYF 414 (737)
Q Consensus 335 ~~~~~~~~~~~f~~lF~~~~~~~~~f~~~~~~vi~iD~T~~~~~y~~~ll~~~g~d~~~~~~plafal~~~E~~es~~wf 414 (737)
. .......+.+.+-|-+. .-..++..|.|+..... +..++++.+|...+ +++|+.+...++.+...-+
T Consensus 90 ~-~~~~~~~n~~~r~f~~~---------~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~ 157 (277)
T PHA02517 90 S-RKAVAAPDRVNRQFVAT---------RPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDA 157 (277)
T ss_pred C-CCCCCCCCcccCCCCCC---------CCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHH
Confidence 0 00000011111112111 13468999999986543 45667777776554 4667888777777754444
Q ss_pred HHHHHHHcccCCCCCEEEEccCcchH
Q 045767 415 LKNINNALRLENGKGICILGDGDNGI 440 (737)
Q Consensus 415 l~~l~~~~~~~~~~p~~iitD~~~~l 440 (737)
|+...... +...++.|.||+....
T Consensus 158 l~~a~~~~--~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 158 LEQALWAR--GRPGGLIHHSDKGSQY 181 (277)
T ss_pred HHHHHHhc--CCCcCcEeeccccccc
Confidence 44433333 2223456779987653
No 18
>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=82.27 E-value=1.6 Score=34.40 Aligned_cols=40 Identities=20% Similarity=0.293 Sum_probs=32.8
Q ss_pred cCeEEEEEEee-CCCceEEEEEEcCCCceEEEeeeCCCccc
Q 045767 204 RSHVVCYECSD-LRCDWVIQAGRVSDGTTFIVTDFMPQHTC 243 (737)
Q Consensus 204 ~~~r~~~~C~~-~gCpwri~a~~~~~~~~~~I~~~~~~HnC 243 (737)
...|..++|+. .+||++=.+.+..+++...++++..+|||
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 33466789998 89999888877766777888999999998
No 19
>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=81.55 E-value=2.5 Score=33.00 Aligned_cols=46 Identities=13% Similarity=0.230 Sum_probs=25.1
Q ss_pred cCceEEEEeecCeEEEEEEeeC---CCceEEEEEEcCCCceEEEeeeCCCccc
Q 045767 194 EGFKLCVMENRSHVVCYECSDL---RCDWVIQAGRVSDGTTFIVTDFMPQHTC 243 (737)
Q Consensus 194 ~gf~~~~~kS~~~r~~~~C~~~---gCpwri~a~~~~~~~~~~I~~~~~~HnC 243 (737)
.|+.|...+.........|... +|+++|... . +...|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~--~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--A--GDGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--C--CCCEEEECCCccCC
Confidence 4777887777788889999863 899999996 2 23355556688887
No 20
>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=81.52 E-value=6.2 Score=35.16 Aligned_cols=77 Identities=14% Similarity=-0.033 Sum_probs=55.6
Q ss_pred CccEEEecCeeec-CCcCceeEEEEeecCCCceEEEEEEEeeccchhhHHHHHHHHHHHcccCCCCCEEEEccCcchHHH
Q 045767 364 CRGILAVDGWKMN-NPYKSVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINNALRLENGKGICILGDGDNGIDY 442 (737)
Q Consensus 364 ~~~vi~iD~T~~~-~~y~~~ll~~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~~~~~~~~~p~~iitD~~~~l~~ 442 (737)
-..++.+|.++.. ...++..+..+.+|..... .+++.+...++.+.+..+|....... +...|.+|+||+..+...
T Consensus 5 p~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 5 PGERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKR--GGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHH--S-SE-SEEEEESCHHHHS
T ss_pred CCCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeeccccccccccccccccccc--ccccceeccccccccccc
Confidence 3467899999666 3455688888999976654 55777777778888888888766666 233499999999998764
Q ss_pred H
Q 045767 443 A 443 (737)
Q Consensus 443 A 443 (737)
.
T Consensus 82 ~ 82 (120)
T PF00665_consen 82 H 82 (120)
T ss_dssp H
T ss_pred c
Confidence 3
No 21
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=79.40 E-value=28 Score=36.35 Aligned_cols=146 Identities=9% Similarity=-0.013 Sum_probs=84.0
Q ss_pred hhhhhhhhheeccCCCCCHHHHHHHHHHH---hCC-CCChhHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhcCCccE
Q 045767 255 KWISAIYLHRWKLQPKVSTVEIRDEIEAT---YGV-VCPEGKLLSAANRAKHILGMDHYDGYAKLNQLKKEMERIDSHNI 330 (737)
Q Consensus 255 ~~ia~~~~~~l~~~~~~~~~~I~~~l~~~---~g~-~~s~~~~~rar~~~~~~~~g~~~~~y~~L~~~~~~l~~~NPg~~ 330 (737)
..+...+.+....++....+.|...|+.. .|+ .++..+++|....+ |-. ...+...+.+.
T Consensus 11 ~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~-----gL~-----------~~~r~~~~~~~ 74 (262)
T PRK14702 11 TDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQN-----ALL-----------LERKPAVPPSK 74 (262)
T ss_pred HHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHh-----CCc-----------cccCCCCCCCC
Confidence 34445555555567788889998888875 366 48888888764432 100 00000000000
Q ss_pred EEEEecCCCCCCCCceeEEEEeehhhHHHHHhcCccEEEecCeeecCCcCceeEEEEeecCCCceEEEEEEEeec-cchh
Q 045767 331 VLLETDGDENGEGKRLNKMFVCWERTSYAFKYHCRGILAVDGWKMNNPYKSVMLVAAGLDGNNGILPVAFCEVDV-EDLE 409 (737)
Q Consensus 331 ~~v~~~~~~~~~~~~f~~lF~~~~~~~~~f~~~~~~vi~iD~T~~~~~y~~~ll~~~g~d~~~~~~plafal~~~-E~~e 409 (737)
. ..... |. ...-..++..|-||.....++.++.++-+|.... .++||++... .+.+
T Consensus 75 ------~---~~~~~----~~---------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~ 131 (262)
T PRK14702 75 ------R---AHTGR----VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSE 131 (262)
T ss_pred ------c---CCCCc----cc---------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHH
Confidence 0 00000 10 0113468999999987655557888888887766 6789998874 5666
Q ss_pred hHHHHHHH-HHHHccc-CCCCCEEEEccCcch
Q 045767 410 SWVYFLKN-INNALRL-ENGKGICILGDGDNG 439 (737)
Q Consensus 410 s~~wfl~~-l~~~~~~-~~~~p~~iitD~~~~ 439 (737)
.-.-+|+. +....+. ....|..|.||+...
T Consensus 132 ~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 132 TVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred HHHHHHHHHHHHHhcccCCCCCeEEEcCCCcc
Confidence 55555554 3333210 123578899998765
No 22
>PF13565 HTH_32: Homeodomain-like domain
Probab=77.01 E-value=3.2 Score=34.23 Aligned_cols=42 Identities=12% Similarity=0.192 Sum_probs=34.9
Q ss_pred hhhhhhhhheeccCCCCCHHHHHHHHHHHhCCCC--ChhHHHHH
Q 045767 255 KWISAIYLHRWKLQPKVSTVEIRDEIEATYGVVC--PEGKLLSA 296 (737)
Q Consensus 255 ~~ia~~~~~~l~~~~~~~~~~I~~~l~~~~g~~~--s~~~~~ra 296 (737)
..+.+.+.+.+..+|.+++.+|.+.|.+.+|+.+ |.+++||.
T Consensus 33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 3344666777778899999999999999999876 99999874
No 23
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=76.07 E-value=44 Score=35.67 Aligned_cols=76 Identities=11% Similarity=0.039 Sum_probs=52.1
Q ss_pred CccEEEecCeeecCCcCceeEEEEeecCCCceEEEEEEEeec-cchhhHHHHHHH-HHHHccc-CCCCCEEEEccCcchH
Q 045767 364 CRGILAVDGWKMNNPYKSVMLVAAGLDGNNGILPVAFCEVDV-EDLESWVYFLKN-INNALRL-ENGKGICILGDGDNGI 440 (737)
Q Consensus 364 ~~~vi~iD~T~~~~~y~~~ll~~~g~d~~~~~~plafal~~~-E~~es~~wfl~~-l~~~~~~-~~~~p~~iitD~~~~l 440 (737)
-..+++.|-||....-++-++.++-+|...+ .+|||++... .+.+.-.-+|+. +....+. ....|..|-||+...-
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 4579999999986654556888888887776 6889999875 566665555553 4444321 1235788899987653
No 24
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=69.80 E-value=54 Score=31.28 Aligned_cols=62 Identities=13% Similarity=0.225 Sum_probs=44.6
Q ss_pred chhhHHHHHHHHHHHcccCCCCCEEEEccCcchHHHHHH---hhccccceecchhHHHHHHHHhCCC
Q 045767 407 DLESWVYFLKNINNALRLENGKGICILGDGDNGIDYAVE---EFLPEAAYRQCCHKVFTEMVKRFPA 470 (737)
Q Consensus 407 ~~es~~wfl~~l~~~~~~~~~~p~~iitD~~~~l~~Ai~---~vfP~a~h~~C~~Hi~~N~~~~~~~ 470 (737)
+.+..--+|....+.+ +..+...||||-...+.+|-+ +-+|......|..|-+.-+.+.+..
T Consensus 74 ~a~~l~~ll~~vIeeV--G~~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 74 TAEYLFELLDEVIEEV--GEENVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred cHHHHHHHHHHHHHHh--hhhhhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 4444445555555554 456677899999999888854 4589999999999998877766544
No 25
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=63.50 E-value=9.9 Score=33.20 Aligned_cols=55 Identities=20% Similarity=0.183 Sum_probs=31.8
Q ss_pred hcccceEEEEeCCcEE--EEEeCCeeEEEeecCCcccccCCccc----C-CCCcchHHHHHHHh
Q 045767 592 IDGQRFAMVEQNGTTL--KLTDTISMFYDLDMEAMSCSCGLWQI----S-GIPCAHACRAIQLN 648 (737)
Q Consensus 592 ~~s~~~~V~~~~~~~f--~V~~~~~~~y~V~l~~~tCsC~~~~~----~-GiPC~Halavl~~~ 648 (737)
.++...--...+++.+ .|.-++...|.++.+ -|||..|-. - .-||.|++++-...
T Consensus 18 g~~Grfv~l~l~~~~~~~fVyvG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~ 79 (117)
T COG5431 18 GKRGRFVFLYLKRSKVKFFVYVGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAK 79 (117)
T ss_pred cccCcEEEEeeCCceEEEEEEEccccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeee
Confidence 3444444445555544 333344433447766 899988752 2 36799998765443
No 26
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=59.60 E-value=3.7 Score=28.02 Aligned_cols=15 Identities=13% Similarity=-0.062 Sum_probs=13.1
Q ss_pred ccccccccCccCcce
Q 045767 720 NYSHSATNNQQVHIV 734 (737)
Q Consensus 720 ~~~~C~~C~~~gHn~ 734 (737)
..|.|-+|++.||.|
T Consensus 7 ~~Y~C~~C~~~GH~i 21 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWI 21 (32)
T ss_pred CCCEeecCCCCCccH
Confidence 457999999999986
No 27
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=59.37 E-value=4.2 Score=29.23 Aligned_cols=13 Identities=8% Similarity=-0.028 Sum_probs=11.5
Q ss_pred ccccccCccCcce
Q 045767 722 SHSATNNQQVHIV 734 (737)
Q Consensus 722 ~~C~~C~~~gHn~ 734 (737)
.+|+.|++.||..
T Consensus 2 ~kC~~CG~~GH~~ 14 (40)
T PF15288_consen 2 VKCKNCGAFGHMR 14 (40)
T ss_pred ccccccccccccc
Confidence 4899999999975
No 28
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=55.71 E-value=5.4 Score=21.47 Aligned_cols=9 Identities=11% Similarity=0.143 Sum_probs=3.4
Q ss_pred CCCCCCCCC
Q 045767 697 SPKAVSAKG 705 (737)
Q Consensus 697 ~~~GRpkk~ 705 (737)
+++|||+|.
T Consensus 2 r~RGRP~k~ 10 (13)
T PF02178_consen 2 RKRGRPRKN 10 (13)
T ss_dssp --SS--TT-
T ss_pred CcCCCCccc
Confidence 578999875
No 29
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=54.98 E-value=6.9 Score=22.97 Aligned_cols=13 Identities=15% Similarity=0.095 Sum_probs=11.2
Q ss_pred cccccCccCccee
Q 045767 723 HSATNNQQVHIVL 735 (737)
Q Consensus 723 ~C~~C~~~gHn~~ 735 (737)
.|-.|++.||..-
T Consensus 2 ~C~~C~~~GH~~~ 14 (18)
T PF00098_consen 2 KCFNCGEPGHIAR 14 (18)
T ss_dssp BCTTTSCSSSCGC
T ss_pred cCcCCCCcCcccc
Confidence 6899999999863
No 30
>PRK13907 rnhA ribonuclease H; Provisional
Probab=48.73 E-value=1.3e+02 Score=27.18 Aligned_cols=78 Identities=15% Similarity=0.079 Sum_probs=45.1
Q ss_pred EEEecCeeecCCcCceeEEEEeecCCCceEEEEE-EEeeccchhhHHHHHHHHHHHcccCCCCCEEEEccCcchHHHHHH
Q 045767 367 ILAVDGWKMNNPYKSVMLVAAGLDGNNGILPVAF-CEVDVEDLESWVYFLKNINNALRLENGKGICILGDGDNGIDYAVE 445 (737)
Q Consensus 367 vi~iD~T~~~~~y~~~ll~~~g~d~~~~~~plaf-al~~~E~~es~~wfl~~l~~~~~~~~~~p~~iitD~~~~l~~Ai~ 445 (737)
.|.+||.+..+.-.+-.-.++ .+..+... +.+ .-..+.+..-|.-++..|+.+.. .+..++.|-||. +.+.+++.
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~~~~-~~~~~~~~tn~~AE~~All~aL~~a~~-~g~~~v~i~sDS-~~vi~~~~ 78 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQPAVQ-LSLPLGTMSNHEAEYHALLAALKYCTE-HNYNIVSFRTDS-QLVERAVE 78 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHh-CCCCEEEEEech-HHHHHHHh
Confidence 378999998764322222222 45554432 332 12234556667778888887775 334577788877 55566666
Q ss_pred hhc
Q 045767 446 EFL 448 (737)
Q Consensus 446 ~vf 448 (737)
..+
T Consensus 79 ~~~ 81 (128)
T PRK13907 79 KEY 81 (128)
T ss_pred HHH
Confidence 544
No 31
>PF13592 HTH_33: Winged helix-turn helix
Probab=44.07 E-value=32 Score=27.04 Aligned_cols=30 Identities=20% Similarity=0.231 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHHHHhCCCCChhHHHHHHH
Q 045767 269 PKVSTVEIRDEIEATYGVVCPEGKLLSAAN 298 (737)
Q Consensus 269 ~~~~~~~I~~~l~~~~g~~~s~~~~~rar~ 298 (737)
..++.++|.+.|.+.||+.+|...+|+.-.
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~ 32 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRLLK 32 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHHHH
Confidence 457889999999999999999999887544
No 32
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=41.40 E-value=16 Score=23.58 Aligned_cols=15 Identities=7% Similarity=0.167 Sum_probs=10.7
Q ss_pred CCCCCCCCCCCCCCC
Q 045767 696 HSPKAVSAKGSNEIV 710 (737)
Q Consensus 696 ~~~~GRpkk~R~~~~ 710 (737)
.+++|||+|......
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 367999988765443
No 33
>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=39.81 E-value=76 Score=29.77 Aligned_cols=69 Identities=20% Similarity=0.242 Sum_probs=40.0
Q ss_pred cEEEecCeeecCCc--------------CceeEEEEeecCC-CceEEEEEEEeeccchhhHHHHHHHHHHHcccCCCCCE
Q 045767 366 GILAVDGWKMNNPY--------------KSVMLVAAGLDGN-NGILPVAFCEVDVEDLESWVYFLKNINNALRLENGKGI 430 (737)
Q Consensus 366 ~vi~iD~T~~~~~y--------------~~~ll~~~g~d~~-~~~~plafal~~~E~~es~~wfl~~l~~~~~~~~~~p~ 430 (737)
.+|-||.||+.++- .....++++++-+ +..--+...++.+.+.++..-+++. .+ .+..
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~---~i----~~gs 76 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQE---HI----EPGS 76 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHH---hh----hccc
Confidence 47888888886433 1123444444443 3333333445567777776555433 33 3567
Q ss_pred EEEccCcchHH
Q 045767 431 CILGDGDNGID 441 (737)
Q Consensus 431 ~iitD~~~~l~ 441 (737)
+|+||..++-.
T Consensus 77 ~i~TD~~~aY~ 87 (151)
T PF12762_consen 77 TIITDGWRAYN 87 (151)
T ss_pred eeeecchhhcC
Confidence 89999998853
No 34
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=35.57 E-value=20 Score=36.58 Aligned_cols=24 Identities=29% Similarity=0.614 Sum_probs=19.6
Q ss_pred CcccccCCcccCCCCcchHHHHHHHhc
Q 045767 623 AMSCSCGLWQISGIPCAHACRAIQLNM 649 (737)
Q Consensus 623 ~~tCsC~~~~~~GiPC~Halavl~~~~ 649 (737)
...|||..| -.||.|+-||..+..
T Consensus 124 ~~dCSCPD~---anPCKHi~AvyY~la 147 (266)
T COG4279 124 STDCSCPDY---ANPCKHIAAVYYLLA 147 (266)
T ss_pred ccccCCCCc---ccchHHHHHHHHHHH
Confidence 456999876 579999999988754
No 35
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=32.93 E-value=35 Score=27.63 Aligned_cols=38 Identities=16% Similarity=0.348 Sum_probs=17.2
Q ss_pred hhheeccCCCCCHHHHHHHHHHHhCCCCChhHHHHHHHH
Q 045767 261 YLHRWKLQPKVSTVEIRDEIEATYGVVCPEGKLLSAANR 299 (737)
Q Consensus 261 ~~~~l~~~~~~~~~~I~~~l~~~~g~~~s~~~~~rar~~ 299 (737)
+...+..+|..+..+|...+.+. |..+|..++++.-..
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L~~ 41 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRLRE 41 (72)
T ss_dssp ------------HHHHHHHT----T--S-HHHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHHHH
Confidence 44566778999999999999988 999999999886543
No 36
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=29.41 E-value=1.5e+02 Score=34.19 Aligned_cols=60 Identities=12% Similarity=0.189 Sum_probs=36.8
Q ss_pred HHHHhcccceEEEEeCCc-EEEEEeCCeeEEEeec----CCcccccCCcccCCCCcchHHHHHHHhc
Q 045767 588 HDRTIDGQRFAMVEQNGT-TLKLTDTISMFYDLDM----EAMSCSCGLWQISGIPCAHACRAIQLNM 649 (737)
Q Consensus 588 ~~~~~~s~~~~V~~~~~~-~f~V~~~~~~~y~V~l----~~~tCsC~~~~~~GiPC~Halavl~~~~ 649 (737)
+..........+...++. ..+|...+.+.|.|++ .+.+|||.. .. +==|.|+.||+....
T Consensus 32 ~~y~e~G~V~~i~~~g~~v~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~-~gaCKH~VAvvl~~~ 96 (587)
T COG4715 32 EAYLEAGAVLKITIRGGTVRAVVEGSRRYRVRVTLEGGALSSICTCPY-GG-SGACKHVVAVVLEYL 96 (587)
T ss_pred HHHHhcCCceEEeecCCeEEEEEeccceeeEEEEeecCCcCceeeCCC-CC-CcchHHHHHHHHHHh
Confidence 334444444445433332 3445445566677877 367799987 33 335999999998864
No 37
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=28.11 E-value=83 Score=27.80 Aligned_cols=33 Identities=18% Similarity=0.235 Sum_probs=24.4
Q ss_pred ccc-cCCcEeCCHHHHHHHHHHHHHHcCceEEEEeecC
Q 045767 169 MVL-YQGQRFRDVGEFRKAVQVFAVREGFKLCVMENRS 205 (737)
Q Consensus 169 ~~~-~vG~~F~s~~e~~~av~~yAi~~gf~~~~~kS~~ 205 (737)
+.- .+.+.|+|+|++ ..||.++|..|.|..-..
T Consensus 46 ~~~q~v~l~F~skE~A----i~yaer~G~~Y~V~~p~~ 79 (101)
T PF04800_consen 46 PLSQSVRLKFDSKEDA----IAYAERNGWDYEVEEPKK 79 (101)
T ss_dssp SEEE-CEEEESSHHHH----HHHHHHCT-EEEEE-STT
T ss_pred hhhCeeEeeeCCHHHH----HHHHHHcCCeEEEeCCCC
Confidence 444 388999999998 568999999999976554
No 38
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.66 E-value=2.2e+02 Score=26.42 Aligned_cols=56 Identities=9% Similarity=0.070 Sum_probs=39.7
Q ss_pred cCCccEEEEEecCCCCCCCCceeEEEEeehhhHHHHHhcCccE--EEecCeeecCCcCceeEEEEeecCCCc
Q 045767 325 IDSHNIVLLETDGDENGEGKRLNKMFVCWERTSYAFKYHCRGI--LAVDGWKMNNPYKSVMLVAAGLDGNNG 394 (737)
Q Consensus 325 ~NPg~~~~v~~~~~~~~~~~~f~~lF~~~~~~~~~f~~~~~~v--i~iD~T~~~~~y~~~ll~~~g~d~~~~ 394 (737)
..+.+...+-++| ||+-- ....+++ |.|+ +-.||-|++.+.+|||+.+--.|.+..
T Consensus 78 ak~tslt~iALNd------------Y~a~I-p~sDi~k-ynpIlA~~~nGn~M~IRerGPl~~IYplds~pe 135 (155)
T COG3915 78 AKQTSLTVIALND------------YWAEI-PYSDIEK-YNPILAIQNNGNYMQIRERGPLWSIYPLDSSPE 135 (155)
T ss_pred ccCcceEEEEecc------------eeccC-cHHHhhh-cccEEEEEeCCcEEEEeccCceEEEeecCCChh
Confidence 3455666666643 44433 3456666 8887 567999999999999999988887654
No 39
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=23.83 E-value=77 Score=24.31 Aligned_cols=37 Identities=19% Similarity=0.271 Sum_probs=23.5
Q ss_pred hhhhhhheecc--CCCCCHHHHHHHHHHHhCCCCChhHH
Q 045767 257 ISAIYLHRWKL--QPKVSTVEIRDEIEATYGVVCPEGKL 293 (737)
Q Consensus 257 ia~~~~~~l~~--~~~~~~~~I~~~l~~~~g~~~s~~~~ 293 (737)
+...+.+.++. -..++.++|...|.+.+|+.++..+.
T Consensus 5 i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~~K~ 43 (54)
T PF08766_consen 5 IREAIREILREADLDTVTKKQVREQLEERFGVDLSSRKK 43 (54)
T ss_dssp HHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SHHHH
T ss_pred HHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHHHHH
Confidence 44556666664 24789999999999999999986553
No 40
>PRK00766 hypothetical protein; Provisional
Probab=22.94 E-value=5.8e+02 Score=25.39 Aligned_cols=55 Identities=20% Similarity=0.264 Sum_probs=31.9
Q ss_pred cEEEec-CeeecCCcCceeEEEEeecCCCceEEEEEEEeeccchhhHHHHHHHHHH
Q 045767 366 GILAVD-GWKMNNPYKSVMLVAAGLDGNNGILPVAFCEVDVEDLESWVYFLKNINN 420 (737)
Q Consensus 366 ~vi~iD-~T~~~~~y~~~ll~~~g~d~~~~~~plafal~~~E~~es~~wfl~~l~~ 420 (737)
.|++|| ++|..+.-+-..++-+-.-++.-+.-++|+.++-.-.|.=.-+.+.++.
T Consensus 10 rvlGidds~f~~~~~~~~~lvGvv~r~~~~idGv~~~~itvdG~DaT~~i~~mv~~ 65 (194)
T PRK00766 10 RVLGIDDGTFLFKSSEKVILVGVVMRGGDWVDGVLSRWITVDGLDATEAIIEMVNS 65 (194)
T ss_pred eEEEEecCccccCCCCCEEEEEEEEECCeEEeeEEEEEEEECCccHHHHHHHHHHh
Confidence 578887 4454432233444444455566666777777776666665555555544
No 41
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=22.84 E-value=1.2e+02 Score=29.53 Aligned_cols=43 Identities=26% Similarity=0.261 Sum_probs=33.4
Q ss_pred HHHHHHHHcccCCCCCEEEEccCcch---HHHHHHhhccccceecchhH
Q 045767 414 FLKNINNALRLENGKGICILGDGDNG---IDYAVEEFLPEAAYRQCCHK 459 (737)
Q Consensus 414 fl~~l~~~~~~~~~~p~~iitD~~~~---l~~Ai~~vfP~a~h~~C~~H 459 (737)
.++.++.+. ...++.|+||.+.+ |.+-|.+.+|++.|.+=..+
T Consensus 37 ~i~~i~~~~---~~rgVIIfTDpD~~GekIRk~i~~~vp~~khafi~~~ 82 (174)
T TIGR00334 37 TINLIKKAQ---KKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKH 82 (174)
T ss_pred HHHHHHHHh---hcCCEEEEeCCCCchHHHHHHHHHHCCCCeEEeeeHH
Confidence 455566655 67899999999965 88999999999999874443
No 42
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=22.11 E-value=60 Score=27.90 Aligned_cols=34 Identities=15% Similarity=0.139 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhcChhHHHHHhcCCCccccc
Q 045767 484 TSEASFHKYMDLIQQQSKECHEWLLQTNWSSWAL 517 (737)
Q Consensus 484 ~t~~eFe~~~~~l~~~~~~~~~yL~~~~~~~Wa~ 517 (737)
.+..+|+..|..+.......++||..++++.+..
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~ 38 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPK 38 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHH
Confidence 3678999999999877778999999998766653
Done!