Query 004183
Match_columns 770
No_of_seqs 185 out of 679
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 18:59:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004183.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004183hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1121 Tam3-transposase (Ac f 100.0 1.3E-31 2.8E-36 317.9 39.0 482 217-730 97-627 (641)
2 PF04937 DUF659: Protein of un 100.0 5E-32 1.1E-36 262.9 13.5 148 256-414 1-153 (153)
3 PF05699 Dimer_Tnp_hAT: hAT fa 99.6 9.9E-16 2.1E-20 134.6 3.7 68 661-728 19-86 (86)
4 PF14372 DUF4413: Domain of un 97.1 0.00032 6.9E-09 63.9 2.7 62 524-586 2-67 (101)
5 PF14291 DUF4371: Domain of un 96.1 0.029 6.3E-07 58.9 9.8 129 223-363 70-225 (235)
6 PF10683 DBD_Tnp_Hermes: Herme 95.5 0.023 5E-07 46.8 4.6 38 212-251 9-46 (68)
7 PF02892 zf-BED: BED zinc fing 90.0 0.097 2.1E-06 40.0 0.1 40 59-106 2-42 (45)
8 smart00614 ZnF_BED BED zinc fi 88.3 0.28 6.1E-06 38.6 1.7 46 60-111 2-49 (50)
9 PF12017 Tnp_P_element: Transp 82.4 10 0.00022 40.0 10.3 129 234-373 81-231 (236)
10 PF13909 zf-H2C2_5: C2H2-type 60.5 2.2 4.7E-05 27.9 -0.6 20 83-106 2-21 (24)
11 PF13717 zinc_ribbon_4: zinc-r 52.1 4.7 0.0001 29.6 -0.0 15 77-91 21-35 (36)
12 COG3364 Zn-ribbon containing p 48.9 8 0.00017 35.0 0.9 26 82-114 3-28 (112)
13 PF09845 DUF2072: Zn-ribbon co 42.6 11 0.00025 35.7 0.9 26 83-115 3-28 (131)
14 COG4049 Uncharacterized protei 38.2 9.9 0.00022 30.6 -0.1 17 77-93 13-29 (65)
15 PF10551 MULE: MULE transposas 36.2 2E+02 0.0042 24.8 7.9 54 331-391 36-91 (93)
16 PF01318 Bromo_coat: Bromoviru 34.8 11 0.00025 36.6 -0.4 40 62-101 24-63 (188)
17 PF13719 zinc_ribbon_5: zinc-r 31.6 15 0.00033 27.0 -0.1 16 77-92 21-36 (37)
18 TIGR02098 MJ0042_CXXC MJ0042 f 29.4 18 0.00038 26.5 -0.1 16 78-93 22-37 (38)
19 PRK06850 hypothetical protein; 28.4 1E+02 0.0022 36.2 5.8 78 178-258 39-133 (507)
20 PF13912 zf-C2H2_6: C2H2-type 26.5 21 0.00046 23.7 -0.0 23 82-107 2-24 (27)
21 PF10428 SOG2: RAM signalling 25.3 6.3E+02 0.014 29.3 11.5 89 453-548 346-434 (445)
22 PF12874 zf-met: Zinc-finger o 23.1 27 0.00059 22.7 -0.0 21 82-105 1-21 (25)
23 PF13894 zf-C2H2_4: C2H2-type 20.6 35 0.00075 21.3 0.1 11 83-93 2-12 (24)
24 PF00096 zf-C2H2: Zinc finger, 20.5 35 0.00076 21.6 0.1 11 83-93 2-12 (23)
No 1
>KOG1121 consensus Tam3-transposase (Ac family) [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-31 Score=317.87 Aligned_cols=482 Identities=16% Similarity=0.180 Sum_probs=333.9
Q ss_pred HHHHHHHHHHHHhcCCCccccccCCHHHHHHHHHcC--CCCCChhhHHHHHHHHHHHHHHHHHHHHHhh-ccceEEEecc
Q 004183 217 DSAVELLTDWFYDSCGSVSFSSFDHPKFRAFLSQVG--LPVVSRKEVLDARLDRKFVEAKTESEIRIRE-AMFFQVASDG 293 (770)
Q Consensus 217 ~~a~~~ia~~i~~~~~~iPfs~VE~p~Fr~~l~~l~--~~~PSr~~l~~~~L~~~y~evk~~v~~~lk~-a~~~sIttDg 293 (770)
+...+.+++||+-+ ++||+.||+++||.|+..++ |.+|+|.++....+.. |...|.+++..+.. ...+++|+|+
T Consensus 97 ~~~~~~~~~~ii~~--~lp~~~ve~~~~~~~~~~~~P~~~~~~~~t~~~~~~~~-~~~~k~~~~~~~~~~~~~v~lT~d~ 173 (641)
T KOG1121|consen 97 KVIREAIARMIILH--GLPLSTVEEPGFRELLKHLNPNYKLPSRSTLEADVLKI-YEAEKPKLKEILEKIIGRVSLTTDL 173 (641)
T ss_pred HHHHHHHHHHHHhc--CCChhhccchhHHHHHHhcCCCcccCChhHHHHHHHHH-HHHHHHHHHHHHHccCCceEEEEee
Confidence 45668899999999 99999999999999999998 8999999997765554 66667777776665 4579999999
Q ss_pred cccCCCCCCCCCCceeEEEeecCCCceeeeeeEe---cCCCCCHHHHHHHHHHHHHhhhcCC-cceEEEEEechhh---H
Q 004183 294 WKIRTCCGDGDDDNLVKFTVNLPNGTSVYQKALI---TGGSVSSKLAEDVFWETVMGICGNG-VQRCVGIVADKYK---A 366 (770)
Q Consensus 294 WTs~~~~~g~~~~s~i~~tvh~~~g~~~f~ksv~---~s~~~ta~~i~e~L~~vIee~~~~g-~~kVv~IVTDN~~---~ 366 (770)
|++.+ ....|+.+++||++..|-.++.+. +...|+++.++..+.+++.+| + ..+|..++.||.+ .
T Consensus 174 w~~~~-----~~~~y~~~t~h~id~~~~l~~~il~~~~~~~~~~~~i~~~~~~~~~~~---~i~~kv~~~~~~n~~~~~~ 245 (641)
T KOG1121|consen 174 WSDSG-----TDEGYMVLTAHYIDRDWELHNKILSFCIPPPHLGKALASVLNECLLEW---GIEKKVFSITVDNVNVSNI 245 (641)
T ss_pred ecCCC-----CCcceEEEEEEEeccchHhhhheeeeecCCcchHHHHHHHHHHHHHhh---ChhheEEEEeecccchhHH
Confidence 99864 244999999999987654444332 234799999999999999999 6 4577777788822 1
Q ss_pred HHHHH-HHhhcC-----cceecchhHHHHHHHHhHhhccCchhhhHHHHHHHHHHHHcCchHHHHHHHHHhhhccccccc
Q 004183 367 KALRN-LETQNQ-----WMVNVSCQLQGFLSLLKDFGKELPVFTSVRETCLKIGNFVNNKPQIRSSLRKHKMVGLEYVEL 440 (770)
Q Consensus 367 kA~~~-L~~k~~-----~i~~l~C~aH~LnLivkD~~k~l~~v~~vi~karkIv~ff~~s~~~~~~Lrk~q~q~~g~~~L 440 (770)
...+. +....+ ..++.+|.+|.+|+++++.++ ..+...+.+++..|.+++.+......|.+.+.+. +....
T Consensus 246 ~~~~~~l~~~~~~~~~~~~~~~~C~~~~~~~~v~~~l~--~~~~~~l~~ir~~v~~vk~s~~~~~~f~~~~~~~-~~~~~ 322 (641)
T KOG1121|consen 246 ETLRDHLKSSNALLLLGKFFHVRCFAHILNLIVQEGLK--EEFSSLLEKLRESVKYVKSSESRESSFEECQEQL-GIPSD 322 (641)
T ss_pred HHhhHHHhhcccceecceeeeeehhhhhhhHHHHHHHH--HHHhHHHHHHHHHHHHHhcChHHHHHHHHHHHhc-CCccc
Confidence 22221 111111 124889999999999999965 7899999999999999999999999999998653 22111
Q ss_pred cccCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHhhcc-cccccCCCCccccchheeecChhHHHHHHHHHHHHHHHHHH
Q 004183 441 IRVPSNKCDCRNNFVHLFGMLEDVWSSARVLQMAVLDD-SIKVSCMDDPVSREVVAIIQSEVFWNELEAVYSLVKLIKGM 519 (770)
Q Consensus 441 lr~~~t~~~~~tRW~S~y~mLerlle~k~aL~~l~~~e-~~~~~~~~~~~a~ev~~ivld~~FW~~Le~vv~lLkP~~~a 519 (770)
.... +..+||+++|.||.+.++.+.++..+...+ .+ ....+...|..++.++.+|+||.++
T Consensus 323 --~~~~--d~~~~w~st~~ml~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~l~~~l~~~~~~ 384 (641)
T KOG1121|consen 323 --VLLL--DVSTRWNSTYLMLSRALKLKDAFSKLEEEDKSY--------------KSYPSDEEWNRLEELCDFLQPFSEV 384 (641)
T ss_pred --cccc--cCCccchhHHHHHHHHHHHHHHHHHHHHhcccc--------------ccCcCHHHHHHHHHHHHHHHHHHHH
Confidence 1111 234699999999999999999999988754 22 1233445599999999999999999
Q ss_pred HHHHhccC-CcccchHHHHHHHHHHHHHHhhhcCC----ChhhHHHHHHHHHhccCChHHHHHHHhCcccccccCCCCCC
Q 004183 520 TQEIEAER-PLIGQCLPLWEELRSKVKNWCAKFSI----PGENVEKIVEKRFRKNYHPAWSAAFILDPLYLIKDNSGKYL 594 (770)
Q Consensus 520 t~~le~d~-ptls~V~Pl~~~L~~k~k~~~~~~~~----~~~~i~~~Id~Rw~~~~~pl~~aA~~LDPry~~kd~~~~yl 594 (770)
+..+++.. |+.+.++|.+..+..-+..+...+.. ....+.+.++++|........++|.+|||||++......|.
T Consensus 385 ~~~~s~~~~~ts~~~~~~i~~i~~~l~~~~~~~~~~~~~~a~~m~~k~dk~~~~~~~~~~~~atvlDPR~k~~~~~~~~~ 464 (641)
T KOG1121|consen 385 TKLLSGSSYPTSNQYFPEIWKIENLLKTYASGEDEVVRSMAEEMFEKFDKYWSYSICDLLAIATLLDPRFKLKLLESSFE 464 (641)
T ss_pred HHHhcCCCCchHHHHHHHHHHHHHHHHhcccCccHHHHHHHHHHHHHhhhhcccchhHHHHHHHhcChHhHHHHHHHHhh
Confidence 99999887 77779999888877766555433211 12257777888887222478999999999997644322111
Q ss_pred CCCCcchH---HHHHHHHHHHHHhcCcHHHH-HH-H-HHHhhhhhcCCCh--------HHHHHHHhhcc-----------
Q 004183 595 PPFKCLTE---EQEKDVDKLITRLVSREEAH-FA-L-MELMKWRSEGLDP--------LYAQAVQVKQR----------- 649 (770)
Q Consensus 595 p~~~~lt~---e~~~~v~~~i~rl~~~~e~~-~~-l-~El~~~r~e~~d~--------~~~~~~~~~~~----------- 649 (770)
.-+..... +....+.+.+..+...-... .. . .+...|......+ .+...+.....
T Consensus 465 ~~~~~~~~~~~~~~~~~~d~~~~l~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~y 544 (641)
T KOG1121|consen 465 KLYGKDPEDAKEKVESVRDKLKKLLEEYKQLSPSNVSNSAHSWDLLDESPLEKDAFEYLFEPEVSIDSGSKSGKSELDHY 544 (641)
T ss_pred hhhccchHHHHHHHHHHHHHHHHHHHHHhccCCCCCCccccccccccccccccchhhhhhhHHHHHHhcCCCCCchHHHH
Confidence 11100000 11111222222221100000 00 0 0000011000000 01000000000
Q ss_pred --CcccccccccCCCchhhHhhhhccccchHHHHHHHHhcccccCcccccccccchhhhccccCCCCHHHHhhhhhhhhc
Q 004183 650 --DPITGKMRIANPQSSRLVWETCLSEYKSLGKVAVRLIFLHATSFGFKCNWSFMKWYCVQRHSRASLERAQKMIFVAAH 727 (770)
Q Consensus 650 --~~~~~~~~~~~p~sp~~WW~~~~~~fP~L~kLA~riLsipaSS~~sER~FS~~g~I~t~kRnRL~~e~vekLvFl~~N 727 (770)
++..+.+....+.+++.||+.+..+||.|+++|+++|++|++++++|+.||..+.+..+.|++|.+++++.|+|.+.|
T Consensus 545 ~~e~~~~~~~~~~~~~~l~~w~~~~~~y~~ls~~a~d~l~~p~~~~~~e~~f~~~~~~~~~~r~~l~~~~~~~l~c~~~~ 624 (641)
T KOG1121|consen 545 LSESPRLLMPSFLDADVLQWWKGNGTRYPELSSMARDILSIPITSVASESSFSIGGRVLNKYRSRLLPENVQALICTRNW 624 (641)
T ss_pred HhhhhhhhccccccccHHHHhhccCcccchHHHHHHHHHcCcccCccchhhcccCceecCchhccCCchhhHHhhchHhh
Confidence 000000111223457899999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccc
Q 004183 728 AKL 730 (770)
Q Consensus 728 ~kL 730 (770)
.+-
T Consensus 625 ~~~ 627 (641)
T KOG1121|consen 625 LPG 627 (641)
T ss_pred hhh
Confidence 664
No 2
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=99.97 E-value=5e-32 Score=262.89 Aligned_cols=148 Identities=25% Similarity=0.350 Sum_probs=138.0
Q ss_pred CChhhHHHHHHHHHHHHHHHHHHHHHhh--ccceEEEecccccCCCCCCCCCCceeEEEeecCCCceeeeeeEecC-CCC
Q 004183 256 VSRKEVLDARLDRKFVEAKTESEIRIRE--AMFFQVASDGWKIRTCCGDGDDDNLVKFTVNLPNGTSVYQKALITG-GSV 332 (770)
Q Consensus 256 PSr~~l~~~~L~~~y~evk~~v~~~lk~--a~~~sIttDgWTs~~~~~g~~~~s~i~~tvh~~~g~~~f~ksv~~s-~~~ 332 (770)
||+++|++++|++.|++++.+++...+. ..||+|++||||+++ .+++|||+||++.|. +|+++++++ ..|
T Consensus 1 PS~~~Lr~~lL~~~~~~v~~~~~~~k~~w~~~Gcsi~~DgWtd~~------~~~lInf~v~~~~g~-~Flksvd~s~~~~ 73 (153)
T PF04937_consen 1 PSYHELRGPLLDKEYKEVKEQVKEHKKSWKRTGCSIMSDGWTDRK------GRSLINFMVYCPEGT-VFLKSVDASSIIK 73 (153)
T ss_pred CCHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCEEEEEecCcCCC------CCeEEEEEEEccccc-EEEEEEecccccc
Confidence 9999999999999999999999875554 679999999999984 459999999999999 889999998 589
Q ss_pred CHHHHHHHHHHHHHhhhcCCcceEEEEEech--hhHHHHHHHHhhcCcceecchhHHHHHHHHhHhhccCchhhhHHHHH
Q 004183 333 SSKLAEDVFWETVMGICGNGVQRCVGIVADK--YKAKALRNLETQNQWMVNVSCQLQGFLSLLKDFGKELPVFTSVRETC 410 (770)
Q Consensus 333 ta~~i~e~L~~vIee~~~~g~~kVv~IVTDN--~~~kA~~~L~~k~~~i~~l~C~aH~LnLivkD~~k~l~~v~~vi~ka 410 (770)
++++|++++.++|+++ |.++|||||||| ++.+|.+.|..++|+++|+||+|||||||++|++| +|+|++++.+|
T Consensus 74 ~a~~l~~ll~~vIeeV---G~~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k-~~~i~~vi~~a 149 (153)
T PF04937_consen 74 TAEYLFELLDEVIEEV---GEENVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK-LPWIKEVIEKA 149 (153)
T ss_pred cHHHHHHHHHHHHHHh---hhhhhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc-ChHHHHHHHhc
Confidence 9999999999999999 999999999999 67788899999999999999999999999999999 99999999999
Q ss_pred HHHH
Q 004183 411 LKIG 414 (770)
Q Consensus 411 rkIv 414 (770)
+.|+
T Consensus 150 k~it 153 (153)
T PF04937_consen 150 KAIT 153 (153)
T ss_pred ccCC
Confidence 9873
No 3
>PF05699 Dimer_Tnp_hAT: hAT family C-terminal dimerisation region; InterPro: IPR008906 This dimerisation domain is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation domain forms extremely stable dimers in vitro [].; GO: 0046983 protein dimerization activity; PDB: 2BW3_A.
Probab=99.57 E-value=9.9e-16 Score=134.62 Aligned_cols=68 Identities=19% Similarity=0.270 Sum_probs=56.7
Q ss_pred CCchhhHhhhhccccchHHHHHHHHhcccccCcccccccccchhhhccccCCCCHHHHhhhhhhhhcc
Q 004183 661 PQSSRLVWETCLSEYKSLGKVAVRLIFLHATSFGFKCNWSFMKWYCVQRHSRASLERAQKMIFVAAHA 728 (770)
Q Consensus 661 p~sp~~WW~~~~~~fP~L~kLA~riLsipaSS~~sER~FS~~g~I~t~kRnRL~~e~vekLvFl~~N~ 728 (770)
..+|+.||+.+...||.|+++|+++|++|+||+.+||.||..+.+++++|+||+++++++|+||+.|+
T Consensus 19 ~~~~l~~W~~~~~~fP~L~~lA~~~Lsip~ss~~~ER~FS~~~~~~~~~r~~l~~~~~~~l~~l~~nl 86 (86)
T PF05699_consen 19 DMDPLEWWKQNSSRFPNLAKLARKYLSIPASSASSERSFSAMGKILTRNRNRLSPENVEALLFLKSNL 86 (86)
T ss_dssp T--HHHHHHHTTTTSHHHHHHHHHHHTS-S-TTTTHHHHHHTHHHHH-TTT---HHHHHHHHHHHH--
T ss_pred CCCHHHHHHHCchhchHHHHHHHHHHHhhccccccccccchhhcccccCccCCCHHHHHhhhceeccC
Confidence 45788999999999999999999999999999999999999999999999999999999999999984
No 4
>PF14372 DUF4413: Domain of unknown function (DUF4413)
Probab=97.09 E-value=0.00032 Score=63.87 Aligned_cols=62 Identities=13% Similarity=0.249 Sum_probs=46.4
Q ss_pred hccC-CcccchHHHHHHHHHHHHHHhhhcCC---ChhhHHHHHHHHHhccCChHHHHHHHhCccccc
Q 004183 524 EAER-PLIGQCLPLWEELRSKVKNWCAKFSI---PGENVEKIVEKRFRKNYHPAWSAAFILDPLYLI 586 (770)
Q Consensus 524 e~d~-ptls~V~Pl~~~L~~k~k~~~~~~~~---~~~~i~~~Id~Rw~~~~~pl~~aA~~LDPry~~ 586 (770)
+|.. ||...+++.+..++..++++...... ....|.+.++++|++ .+.++++|++|||||+.
T Consensus 2 S~~~~pTsn~~f~~i~~i~~~l~~~~~~d~~l~~ma~~M~~KfdKYw~~-~~~~l~ia~ILDPR~Kl 67 (101)
T PF14372_consen 2 SGSSYPTSNLYFHEIWKIKDLLRDWNNDDPDLKNMAKKMKEKFDKYWKD-CNLLLAIATILDPRFKL 67 (101)
T ss_pred CCCCcCcHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHH-hHHHHHHHHHhchHHHH
Confidence 5665 89999999999999988885532111 112688888999974 45679999999999954
No 5
>PF14291 DUF4371: Domain of unknown function (DUF4371)
Probab=96.11 E-value=0.029 Score=58.85 Aligned_cols=129 Identities=9% Similarity=0.163 Sum_probs=91.2
Q ss_pred HHHHHHhcCCCcccccc-------CCHHHHHHHHHcC-C---------------CCCChhhHHHHHHHHHHHHHHHHHHH
Q 004183 223 LTDWFYDSCGSVSFSSF-------DHPKFRAFLSQVG-L---------------PVVSRKEVLDARLDRKFVEAKTESEI 279 (770)
Q Consensus 223 ia~~i~~~~~~iPfs~V-------E~p~Fr~~l~~l~-~---------------~~PSr~~l~~~~L~~~y~evk~~v~~ 279 (770)
+..|+..- ++||+== ++--|+++|+.+. + ..-+++++... |...-..++..+.+
T Consensus 70 ~i~fL~~Q--gLa~RGh~e~~~s~n~GNFl~ll~l~~~~d~~l~~~~~~~~~~~~~~~s~~iq~~-i~~~a~~v~~~I~~ 146 (235)
T PF14291_consen 70 VILFLARQ--GLAFRGHDESEDSLNNGNFLELLELLAKYDPELKKHLSKNAPKNAKYSSKTIQNE-IEILADHVRQSIVE 146 (235)
T ss_pred HHHHHHhc--ccccccCCccccccccccHHHHHHHHHhhcccchhhhhcccccceeccHHHHHHH-HHHHHHHHHHHHHh
Confidence 35777877 9998762 3347999998874 1 02233444333 36666666777767
Q ss_pred HHhhccceEEEecccccCCCCCCCCCCceeEEEeecCCCce-ee---eeeEecCCCCCHHHHHHHHHHHHHhhhcCCcce
Q 004183 280 RIREAMFFQVASDGWKIRTCCGDGDDDNLVKFTVNLPNGTS-VY---QKALITGGSVSSKLAEDVFWETVMGICGNGVQR 355 (770)
Q Consensus 280 ~lk~a~~~sIttDgWTs~~~~~g~~~~s~i~~tvh~~~g~~-~f---~ksv~~s~~~ta~~i~e~L~~vIee~~~~g~~k 355 (770)
.+++ .+++|.+|..+|.. +...++|.|.|.+... +. +..+++ ...||+.|++.|.++++++ ++..++
T Consensus 147 ~v~~-~~FSii~DettDis------~~eQl~i~vRyv~~~~~i~E~Fl~f~~~-~~~ta~~l~~~i~~~L~~~-~l~~~~ 217 (235)
T PF14291_consen 147 EVKS-KYFSIIVDETTDIS------NKEQLSICVRYVDKDGKIKERFLGFVEL-EDTTAESLFNAIKDVLEKL-GLDLSN 217 (235)
T ss_pred hccc-cceeeeeecccccc------ccchhhheeeeeccCcceeeeeeeeecc-CCccHHHHHHHHHHHHHHc-CCCHHH
Confidence 7765 58999999999984 3478999999976421 12 222233 3578999999999999999 667789
Q ss_pred EEEEEech
Q 004183 356 CVGIVADK 363 (770)
Q Consensus 356 Vv~IVTDN 363 (770)
|+|..+|+
T Consensus 218 ~~gq~yDg 225 (235)
T PF14291_consen 218 CRGQCYDG 225 (235)
T ss_pred cCcccccC
Confidence 99999998
No 6
>PF10683 DBD_Tnp_Hermes: Hermes transposase DNA-binding domain ; InterPro: IPR018473 This domain confers specific DNA-binding on Hermes transposase [].; PDB: 2BW3_B.
Probab=95.49 E-value=0.023 Score=46.84 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCccccccCCHHHHHHHHHc
Q 004183 212 SKDQIDSAVELLTDWFYDSCGSVSFSSFDHPKFRAFLSQV 251 (770)
Q Consensus 212 ~k~q~~~a~~~ia~~i~~~~~~iPfs~VE~p~Fr~~l~~l 251 (770)
+.+..+.+.+.++.|.+++ +.||++|+..||++|.+.+
T Consensus 9 S~~~K~~~~~k~~qw~v~d--cRpfsiv~gsGfk~la~~l 46 (68)
T PF10683_consen 9 SEPDKKEATDKCTQWCVKD--CRPFSIVSGSGFKKLAQFL 46 (68)
T ss_dssp -HHHHHHHHHHHHHHHHHC--T--GGGGG-HHHHHHHHHH
T ss_pred ccccHHHHHHHHHHHHHhc--CCcceeeccccHHHHHHHH
Confidence 5566778889999999999 8999999999999998876
No 7
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=89.98 E-value=0.097 Score=40.04 Aligned_cols=40 Identities=30% Similarity=0.505 Sum_probs=25.0
Q ss_pred eecccccceeecCCCCCcccchhhhccccccccccC-CCCcchhHhhhc
Q 004183 59 WYWVHLEPILVRHPETNLPKAVKLKCSLCDAVFSAS-NPSRTASEHLKR 106 (770)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 106 (770)
+.|.||+++- ...-+.+|-+|+.+|+++ +.....-.||++
T Consensus 2 ~vW~~F~~~~--------~~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 2 PVWKHFTKIP--------GDKKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp GCCCCCEE----------GCSS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred CccccEEEcc--------CCcCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 6799999887 445567899999999998 444467788855
No 8
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=88.25 E-value=0.28 Score=38.58 Aligned_cols=46 Identities=28% Similarity=0.584 Sum_probs=32.7
Q ss_pred ecccccceeecCCCCCcccchhhhccccccccccC--CCCcchhHhhhcCCCCC
Q 004183 60 YWVHLEPILVRHPETNLPKAVKLKCSLCDAVFSAS--NPSRTASEHLKRGTCPN 111 (770)
Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 111 (770)
.|-||+.|-.. +.|. .+-+|-.|+.++++. |-..+--.||++ +||.
T Consensus 2 vW~~F~~i~~~--~~g~---~~a~C~~C~~~l~~~~~~gTs~L~rHl~~-~h~~ 49 (50)
T smart00614 2 VWKHFTLILEK--DNGK---QRAKCKYCGKKLSRSSKGGTSNLRRHLRR-KHPA 49 (50)
T ss_pred cCccceEEEEc--CCCC---eEEEecCCCCEeeeCCCCCcHHHHHHHHh-HCcC
Confidence 49999986532 3455 456799999999987 555556677776 5774
No 9
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=82.44 E-value=10 Score=40.00 Aligned_cols=129 Identities=17% Similarity=0.142 Sum_probs=65.0
Q ss_pred ccccccCCHHHHHHHHHcCCCCCChhhHHHH---------HHHHHHHHHHHHHHHHHhhc-cceEEEecccccCC-----
Q 004183 234 VSFSSFDHPKFRAFLSQVGLPVVSRKEVLDA---------RLDRKFVEAKTESEIRIREA-MFFQVASDGWKIRT----- 298 (770)
Q Consensus 234 iPfs~VE~p~Fr~~l~~l~~~~PSr~~l~~~---------~L~~~y~evk~~v~~~lk~a-~~~sIttDgWTs~~----- 298 (770)
+.+...--.+++-|.+. +||+||.++|... .++..++-++.+ .+.+. ..|.++.|-=.=..
T Consensus 81 l~L~~~spr~Y~yL~kk-~~pLPs~rTL~r~l~~v~~~pGi~~~il~~l~~~---~~~~~dr~CvL~fDEm~l~~~~eYD 156 (236)
T PF12017_consen 81 LSLYKCSPRAYNYLRKK-GYPLPSVRTLQRWLSKVNIDPGILDFILDLLKNK---SMSEEDRICVLSFDEMKLSPHLEYD 156 (236)
T ss_pred heeeecChHHHHHHHHc-CCCCCCHHHHHHHHHhCCCCCCchHHHHHHHHHc---cCchhccEEEEEEeEEEccceeeec
Confidence 44556666788887765 8999999999664 233333433321 13332 36777877543110
Q ss_pred ----CCCCCCCCcee-EEEeecCCCceeeeeeEecCCCCCHHHHHHHHHHHHHhhhcCCcceEEEEEech--hhHHHHHH
Q 004183 299 ----CCGDGDDDNLV-KFTVNLPNGTSVYQKALITGGSVSSKLAEDVFWETVMGICGNGVQRCVGIVADK--YKAKALRN 371 (770)
Q Consensus 299 ----~~~g~~~~s~i-~~tvh~~~g~~~f~ksv~~s~~~ta~~i~e~L~~vIee~~~~g~~kVv~IVTDN--~~~kA~~~ 371 (770)
-..|. ..++ -++|--....|-..=..+.....+++.|. ++|++.+..|. .|++||+|. +|..+++.
T Consensus 157 ~~~d~v~~~--~~~~~v~mvrGl~~~WKQpi~~~f~t~m~~~~l~----~iI~~l~~~g~-~VvAivsD~g~~N~~~w~~ 229 (236)
T PF12017_consen 157 PSRDEVNEP--ANYVQVFMVRGLFKSWKQPIYFDFDTSMDADILK----NIIEKLHEIGY-NVVAIVSDMGSNNISLWRE 229 (236)
T ss_pred cccCcccCh--hhhhhHHHHHHHHhcCCccEEEEecCcCCHHHHH----HHHHHHHHCCC-EEEEEECCCCcchHHHHHH
Confidence 00111 0111 11111111111110011112244555554 44555544465 799999997 67778887
Q ss_pred HH
Q 004183 372 LE 373 (770)
Q Consensus 372 L~ 373 (770)
|.
T Consensus 230 Lg 231 (236)
T PF12017_consen 230 LG 231 (236)
T ss_pred cC
Confidence 64
No 10
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=60.45 E-value=2.2 Score=27.92 Aligned_cols=20 Identities=50% Similarity=0.909 Sum_probs=15.0
Q ss_pred hccccccccccCCCCcchhHhhhc
Q 004183 83 KCSLCDAVFSASNPSRTASEHLKR 106 (770)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~ 106 (770)
+|..|+ |+++ ++ .-.+|+++
T Consensus 2 ~C~~C~--y~t~-~~-~l~~H~~~ 21 (24)
T PF13909_consen 2 KCPHCS--YSTS-KS-NLKRHLKR 21 (24)
T ss_dssp E-SSSS---EES-HH-HHHHHHHH
T ss_pred CCCCCC--CcCC-HH-HHHHHHHh
Confidence 799999 8886 55 89999987
No 11
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=52.12 E-value=4.7 Score=29.59 Aligned_cols=15 Identities=53% Similarity=1.105 Sum_probs=13.8
Q ss_pred ccchhhhcccccccc
Q 004183 77 PKAVKLKCSLCDAVF 91 (770)
Q Consensus 77 ~~~~~~~~~~~~~~~ 91 (770)
|+.++++|+-|+.+|
T Consensus 21 ~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 21 PKGRKVRCSKCGHVF 35 (36)
T ss_pred CCCcEEECCCCCCEe
Confidence 778999999999988
No 12
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=48.94 E-value=8 Score=34.97 Aligned_cols=26 Identities=35% Similarity=0.852 Sum_probs=20.7
Q ss_pred hhccccccccccCCCCcchhHhhhcCCCCCccc
Q 004183 82 LKCSLCDAVFSASNPSRTASEHLKRGTCPNFAA 114 (770)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (770)
-+|+-||++|+. -++-+-+| ||+-..
T Consensus 3 H~CtrCG~vf~~------g~~~il~G-Cp~CG~ 28 (112)
T COG3364 3 HQCTRCGEVFDD------GSEEILSG-CPKCGC 28 (112)
T ss_pred ceeccccccccc------ccHHHHcc-Cccccc
Confidence 379999999974 47889999 987443
No 13
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=42.64 E-value=11 Score=35.75 Aligned_cols=26 Identities=31% Similarity=0.813 Sum_probs=21.1
Q ss_pred hccccccccccCCCCcchhHhhhcCCCCCcccC
Q 004183 83 KCSLCDAVFSASNPSRTASEHLKRGTCPNFAAV 115 (770)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (770)
+|+-|+.+|. ..+.++.+| ||+-.+-
T Consensus 3 ~Ct~Cg~~f~------dgs~eil~G-CP~CGg~ 28 (131)
T PF09845_consen 3 QCTKCGRVFE------DGSKEILSG-CPECGGN 28 (131)
T ss_pred ccCcCCCCcC------CCcHHHHcc-CcccCCc
Confidence 7999999996 456779999 9986553
No 14
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=38.20 E-value=9.9 Score=30.58 Aligned_cols=17 Identities=29% Similarity=0.587 Sum_probs=13.4
Q ss_pred ccchhhhcccccccccc
Q 004183 77 PKAVKLKCSLCDAVFSA 93 (770)
Q Consensus 77 ~~~~~~~~~~~~~~~~~ 93 (770)
.+..-|||..||++|--
T Consensus 13 DGE~~lrCPRC~~~FR~ 29 (65)
T COG4049 13 DGEEFLRCPRCGMVFRR 29 (65)
T ss_pred CCceeeeCCchhHHHHH
Confidence 34556899999999964
No 15
>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=36.22 E-value=2e+02 Score=24.83 Aligned_cols=54 Identities=13% Similarity=-0.016 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHHhhhcCCcceEEEEEech--hhHHHHHHHHhhcCcceecchhHHHHHH
Q 004183 331 SVSSKLAEDVFWETVMGICGNGVQRCVGIVADK--YKAKALRNLETQNQWMVNVSCQLQGFLS 391 (770)
Q Consensus 331 ~~ta~~i~e~L~~vIee~~~~g~~kVv~IVTDN--~~~kA~~~L~~k~~~i~~l~C~aH~LnL 391 (770)
..+.+....++....+.+ ... ...|++|. ...+|++.. +|...+..|.-|.+..
T Consensus 36 ~e~~~~~~~~l~~~~~~~---~~~-p~~ii~D~~~~~~~Ai~~v---fP~~~~~~C~~H~~~n 91 (93)
T PF10551_consen 36 SESEESYEWFLEKLKEAM---PQK-PKVIISDFDKALINAIKEV---FPDARHQLCLFHILRN 91 (93)
T ss_pred CCChhhhHHHHHHhhhcc---ccC-ceeeeccccHHHHHHHHHH---CCCceEehhHHHHHHh
Confidence 455666666666444444 223 66789997 555666654 6777789999998764
No 16
>PF01318 Bromo_coat: Bromovirus coat protein; InterPro: IPR002009 This family consists of Bromovirus coat proteins. RNA-protein interactions stabilise many viruses and also the nucleoprotein cores of enveloped animal viruses (e.g. retroviruses). The nucleoprotein particles are frequently pleomorphic and generally unstable due to the lack of strong protein-protein interactions in their capsids. The structure is known for Cowpea chlorotic mottle virus (CCMV) []. It shows novel quaternary structure interactions based on interwoven carboxyterminal polypeptides that extend from canonical capsid beta-barrel subunits. Additional particle stability is provided by intercapsomere contacts between metal ion mediated carboxyl cages and by protein interactions with regions of ordered RNA. ; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1YC6_V 1JS9_A 1ZA7_B 1CWP_C.
Probab=34.80 E-value=11 Score=36.56 Aligned_cols=40 Identities=23% Similarity=0.422 Sum_probs=20.9
Q ss_pred ccccceeecCCCCCcccchhhhccccccccccCCCCcchh
Q 004183 62 VHLEPILVRHPETNLPKAVKLKCSLCDAVFSASNPSRTAS 101 (770)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 (770)
..+.|++|.++.+|+-++.|-+-..|=.-|++|||--+|-
T Consensus 24 ~~~qPVIvep~asG~g~~~ka~~Gy~itkw~~s~~a~~AK 63 (188)
T PF01318_consen 24 KRVQPVIVEPPASGQGRAIKARAGYSITKWSSSCPAVKAK 63 (188)
T ss_dssp S-----------TTCSS--B--TTEEEEEEEEEEE-B-TT
T ss_pred ceecceEeecCccCCceeeehhcceEEEEeecCChhhccc
Confidence 3579999999999999999999999999999999987763
No 17
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=31.60 E-value=15 Score=27.01 Aligned_cols=16 Identities=31% Similarity=0.754 Sum_probs=13.9
Q ss_pred ccchhhhccccccccc
Q 004183 77 PKAVKLKCSLCDAVFS 92 (770)
Q Consensus 77 ~~~~~~~~~~~~~~~~ 92 (770)
++..++||+-|+.+|-
T Consensus 21 ~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 21 AGGRKVRCPKCGHVFR 36 (37)
T ss_pred cCCcEEECCCCCcEee
Confidence 5677999999999995
No 18
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=29.45 E-value=18 Score=26.51 Aligned_cols=16 Identities=31% Similarity=0.704 Sum_probs=11.8
Q ss_pred cchhhhcccccccccc
Q 004183 78 KAVKLKCSLCDAVFSA 93 (770)
Q Consensus 78 ~~~~~~~~~~~~~~~~ 93 (770)
+..+.+|+-|+..|.|
T Consensus 22 ~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 22 NGGKVRCGKCGHVWYA 37 (38)
T ss_pred CCCEEECCCCCCEEEe
Confidence 3347888888888865
No 19
>PRK06850 hypothetical protein; Provisional
Probab=28.40 E-value=1e+02 Score=36.24 Aligned_cols=78 Identities=15% Similarity=0.290 Sum_probs=46.9
Q ss_pred ccccCCccchhhhhhhHHHHhhcc-----------CCCCCCCCCCCHHHHHHHHHHHHHHHHhcCCCccccc--c----C
Q 004183 178 LVLSGGREDLGALAMLEDSVKKLK-----------SPKTRPGPVLSKDQIDSAVELLTDWFYDSCGSVSFSS--F----D 240 (770)
Q Consensus 178 ~~~~~~~~~~~~~~~~e~~~k~~k-----------s~~~~~~~~~~k~q~~~a~~~ia~~i~~~~~~iPfs~--V----E 240 (770)
+-.|||||..-.|..+=..+.++. +.+|..-.+...+-++...+.|.++.-+. ++||.+ | +
T Consensus 39 V~fSGGKDStavL~Lv~~Al~~lp~e~r~k~v~Vi~~DTgvE~Pe~~~~v~~~l~~i~~~a~~~--glpi~~~~v~P~~~ 116 (507)
T PRK06850 39 IGYSGGKDSTAVLQLVWNALAGLPPEKRTKPVYVISSDTLVENPVVVDWVNKSLERINEAAKKQ--GLPITPHKLTPKIN 116 (507)
T ss_pred EeCCCCchHHHHHHHHHHHHHhcchhccCCcEEEEECCCCCccHHHHHHHHHHHHHHHHHHHHc--CCceEEEeeCCCcc
Confidence 478999999877643333333331 11332233335556677778888888888 999964 2 3
Q ss_pred CHHHHHHHHHcCCCCCCh
Q 004183 241 HPKFRAFLSQVGLPVVSR 258 (770)
Q Consensus 241 ~p~Fr~~l~~l~~~~PSr 258 (770)
...|..++. -|||.|++
T Consensus 117 ~sFwv~liG-rG~P~Ps~ 133 (507)
T PRK06850 117 DTFWVNLIG-KGYPAPRR 133 (507)
T ss_pred hhHHHHHhc-CCCCCCCC
Confidence 344554432 24888876
No 20
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=26.48 E-value=21 Score=23.70 Aligned_cols=23 Identities=26% Similarity=0.572 Sum_probs=15.5
Q ss_pred hhccccccccccCCCCcchhHhhhcC
Q 004183 82 LKCSLCDAVFSASNPSRTASEHLKRG 107 (770)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 (770)
.+|..|++.|+.. ..-.+|.+.+
T Consensus 2 ~~C~~C~~~F~~~---~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSL---SALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSH---HHHHHHHCTT
T ss_pred CCCCccCCccCCh---hHHHHHhHHh
Confidence 4799999999643 3345666544
No 21
>PF10428 SOG2: RAM signalling pathway protein; InterPro: IPR019487 The RAM signalling pathway regulates Ace2p transcription factor activity and cellular morphogenesis in Saccharomyces cerevisiae (Baker's yeast), and is thought to be conserved amongst eukaryotes []. This entry is found in one of the components of this pathway, the leucine-rich repeat-containing protein SOG2.
Probab=25.32 E-value=6.3e+02 Score=29.27 Aligned_cols=89 Identities=13% Similarity=0.174 Sum_probs=62.9
Q ss_pred chhhHHHHHHHHHHHHHHHHHHhhcccccccCCCCccccchheeecChhHHHHHHHHHHHHHHHHHHHHHHhccCCcccc
Q 004183 453 NFVHLFGMLEDVWSSARVLQMAVLDDSIKVSCMDDPVSREVVAIIQSEVFWNELEAVYSLVKLIKGMTQEIEAERPLIGQ 532 (770)
Q Consensus 453 RW~S~y~mLerlle~k~aL~~l~~~e~~~~~~~~~~~a~ev~~ivld~~FW~~Le~vv~lLkP~~~at~~le~d~ptls~ 532 (770)
.|...-.+....+++-+.|+.-+..-. . ..+++.+ ..-....||+++..+++..--|...++.+.++.+....
T Consensus 346 k~k~L~~~C~~~~~~T~~L~~rLs~ik--~-~~~ep~~----~~~~~~~fwe~~~~Fiks~i~l~~~iK~~~~~~~l~~d 418 (445)
T PF10428_consen 346 KWKELISKCNSAIDQTERLKSRLSTIK--N-QLKEPGG----GIREQKEFWEDCNSFIKSWISLLAKIKEIMKDLPLPPD 418 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH--h-hccCCCC----CccccHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHH
Confidence 588888888888888887776544210 0 0011200 12236789999999999888888899999999988888
Q ss_pred hHHHHHHHHHHHHHHh
Q 004183 533 CLPLWEELRSKVKNWC 548 (770)
Q Consensus 533 V~Pl~~~L~~k~k~~~ 548 (770)
+.+.+..|....||..
T Consensus 419 vr~~L~~l~k~tKE~t 434 (445)
T PF10428_consen 419 VRARLRPLQKATKEVT 434 (445)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8888887777666643
No 22
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=23.08 E-value=27 Score=22.71 Aligned_cols=21 Identities=33% Similarity=0.885 Sum_probs=14.2
Q ss_pred hhccccccccccCCCCcchhHhhh
Q 004183 82 LKCSLCDAVFSASNPSRTASEHLK 105 (770)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~ 105 (770)
+.|.+|+..|+..+ +...|++
T Consensus 1 ~~C~~C~~~f~s~~---~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSEN---SLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHH---HHHHHHT
T ss_pred CCCCCCCCCcCCHH---HHHHHHC
Confidence 36999999997542 4455554
No 23
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=20.63 E-value=35 Score=21.34 Aligned_cols=11 Identities=27% Similarity=1.038 Sum_probs=6.8
Q ss_pred hcccccccccc
Q 004183 83 KCSLCDAVFSA 93 (770)
Q Consensus 83 ~~~~~~~~~~~ 93 (770)
+|.+|+..|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 58888888864
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=20.48 E-value=35 Score=21.64 Aligned_cols=11 Identities=45% Similarity=1.162 Sum_probs=8.9
Q ss_pred hcccccccccc
Q 004183 83 KCSLCDAVFSA 93 (770)
Q Consensus 83 ~~~~~~~~~~~ 93 (770)
+|..|+..|+.
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 58899999864
Done!