Query 047254
Match_columns 836
No_of_seqs 370 out of 1253
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 09:14:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047254.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047254hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04937 DUF659: Protein of un 100.0 1.9E-39 4.1E-44 314.3 12.7 153 281-433 1-153 (153)
2 KOG1121 Tam3-transposase (Ac f 100.0 5.9E-32 1.3E-36 325.0 33.4 457 237-723 95-626 (641)
3 PF05699 Dimer_Tnp_hAT: hAT fa 99.6 3E-16 6.4E-21 138.4 3.5 68 655-722 19-86 (86)
4 PF14291 DUF4371: Domain of un 99.0 9.9E-10 2.1E-14 115.5 10.0 138 244-388 69-232 (235)
5 PF02892 zf-BED: BED zinc fing 98.3 3.3E-07 7.1E-12 70.2 2.2 38 68-105 1-41 (45)
6 smart00614 ZnF_BED BED zinc fi 96.9 0.00084 1.8E-08 52.6 3.1 37 70-106 2-45 (50)
7 PF14372 DUF4413: Domain of un 96.3 0.0075 1.6E-07 54.8 5.6 64 534-599 1-67 (101)
8 PF10683 DBD_Tnp_Hermes: Herme 95.2 0.016 3.5E-07 47.0 2.7 40 236-275 11-50 (68)
9 PF12017 Tnp_P_element: Transp 83.9 7.5 0.00016 40.9 10.0 126 255-393 82-231 (236)
10 PF13894 zf-C2H2_4: C2H2-type 67.3 4.9 0.00011 25.2 2.1 21 84-105 1-21 (24)
11 PF06220 zf-U1: U1 zinc finger 62.8 3.9 8.4E-05 30.1 1.0 27 83-109 3-30 (38)
12 smart00451 ZnF_U1 U1-like zinc 55.4 10 0.00023 26.6 2.2 25 83-108 3-27 (35)
13 PF12874 zf-met: Zinc-finger o 53.2 12 0.00025 24.2 2.0 23 84-107 1-23 (25)
14 PF13913 zf-C2HC_2: zinc-finge 52.7 11 0.00023 25.0 1.7 21 83-105 2-22 (25)
15 PF00096 zf-C2H2: Zinc finger, 48.6 15 0.00033 23.1 2.0 21 84-105 1-21 (23)
16 PF12171 zf-C2H2_jaz: Zinc-fin 45.3 12 0.00026 24.9 1.1 22 84-106 2-23 (27)
17 PF10551 MULE: MULE transposas 44.7 94 0.002 26.9 7.2 55 353-411 37-91 (93)
18 PF05605 zf-Di19: Drought indu 41.3 44 0.00095 26.4 4.0 45 83-129 2-49 (54)
19 PF10276 zf-CHCC: Zinc-finger 40.0 17 0.00037 27.1 1.3 17 77-93 23-39 (40)
20 PLN03097 FHY3 Protein FAR-RED 39.5 3.7E+02 0.0081 33.8 13.4 54 361-417 335-388 (846)
21 PF02748 PyrI_C: Aspartate car 39.2 16 0.00035 28.9 1.1 19 76-94 28-46 (52)
22 PF00665 rve: Integrase core d 35.6 2.9E+02 0.0064 24.6 9.4 35 353-387 47-81 (120)
23 TIGR00280 L37a ribosomal prote 35.0 17 0.00037 32.1 0.8 21 81-101 51-71 (91)
24 PF00872 Transposase_mut: Tran 31.4 20 0.00043 40.7 0.7 153 247-417 108-268 (381)
25 PTZ00255 60S ribosomal protein 31.3 22 0.00047 31.5 0.8 21 81-101 52-72 (90)
26 PF01780 Ribosomal_L37ae: Ribo 31.2 19 0.0004 31.9 0.4 21 81-101 51-71 (90)
27 PF08209 Sgf11: Sgf11 (transcr 30.8 37 0.0008 24.2 1.7 24 82-107 3-26 (33)
28 PF01610 DDE_Tnp_ISL3: Transpo 30.6 1E+02 0.0022 32.3 6.1 93 316-416 1-96 (249)
29 PRK03976 rpl37ae 50S ribosomal 29.8 23 0.0005 31.3 0.7 21 81-101 52-72 (90)
30 KOG0562 Predicted hydrolase (H 29.3 29 0.00064 33.9 1.4 24 81-105 151-174 (184)
31 COG4822 CbiK Cobalamin biosynt 28.5 4.7E+02 0.01 27.2 9.7 112 254-395 80-191 (265)
32 COG1997 RPL43A Ribosomal prote 26.6 33 0.00072 30.0 1.1 19 80-98 50-68 (89)
33 PF12756 zf-C2H2_2: C2H2 type 25.0 56 0.0012 28.5 2.4 24 83-107 50-73 (100)
34 COG4391 Uncharacterized protei 23.5 44 0.00095 27.2 1.2 15 79-93 44-58 (62)
35 PF13912 zf-C2H2_6: C2H2-type 22.1 66 0.0014 21.0 1.7 21 84-105 2-22 (27)
36 PF13909 zf-H2C2_5: C2H2-type 20.7 83 0.0018 20.0 1.9 20 85-106 2-21 (24)
37 KOG1074 Transcriptional repres 20.5 66 0.0014 39.3 2.4 47 82-134 352-402 (958)
38 smart00355 ZnF_C2H2 zinc finge 20.2 71 0.0015 19.9 1.5 20 85-105 2-21 (26)
39 PF13465 zf-H2C2_2: Zinc-finge 20.1 57 0.0012 21.6 1.0 14 81-94 12-25 (26)
No 1
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=100.00 E-value=1.9e-39 Score=314.31 Aligned_cols=153 Identities=48% Similarity=0.838 Sum_probs=150.9
Q ss_pred CChhhhhhhHHHHHHHHHHHHHHHHHhhhhccceEEEecccccCCCCeEEEEEeecCCcceEEEeeeCCCCCcchHHHHH
Q 047254 281 PPSQLIFGDLLQEEIETIRNNLAEHRASWAVTGCSVMADSWTDSESRTLINLFVSSPHGLYFLSSVDATDIVEDASNLFK 360 (836)
Q Consensus 281 PS~~~l~~~iL~~~~~~v~~~l~~~~~~w~~~~~sI~~D~WTd~~~~~~l~~~v~~~~g~~fL~svd~s~~~htge~I~e 360 (836)
||+++|++++|++++++++..++.+++.|..+||||++|+|||..++++|||+|+|+.|++||+++|++...|||++|++
T Consensus 1 PS~~~Lr~~lL~~~~~~v~~~~~~~k~~w~~~Gcsi~~DgWtd~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ 80 (153)
T PF04937_consen 1 PSYHELRGPLLDKEYKEVKEQVKEHKKSWKRTGCSIMSDGWTDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFE 80 (153)
T ss_pred CCHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCEEEEEecCcCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCccEEEEEEeCCcchhhhhhHHHHhcCCccccCchHHHHHHHHhhhhcchhHHHHHHHHHHHH
Q 047254 361 LLDKVVEEMGEENVVQVITQNTPSYKSAGKMLEEKRKNLFWTPCATYCIDKMLDGFLNLKSVWKCMEMAQKIT 433 (836)
Q Consensus 361 ~l~~viee~g~~nVv~vvTDnasn~~~a~~lL~~k~p~i~~~~C~aH~LnLvl~di~k~~~v~~~i~k~~~Iv 433 (836)
+|+++|+++|.+||+||||||++||.+|+++|+++||++||+||+|||||||++||++++++++++.+|+.|+
T Consensus 81 ll~~vIeeVG~~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k~~~i~~vi~~ak~it 153 (153)
T PF04937_consen 81 LLDEVIEEVGEENVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGKLPWIKEVIEKAKAIT 153 (153)
T ss_pred HHHHHHHHhhhhhhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhcChHHHHHHHhcccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999874
No 2
>KOG1121 consensus Tam3-transposase (Ac family) [Replication, recombination and repair]
Probab=100.00 E-value=5.9e-32 Score=324.99 Aligned_cols=457 Identities=16% Similarity=0.244 Sum_probs=336.3
Q ss_pred hHHHHHHHHHHHHHHcCCccccccCHHHHHHHHHHHHcCCCCCCCChhhhhhhHHHHHHHHHHHHHHHHHhhhhccceEE
Q 047254 237 SQKEIISAICKFFYYAGVPLEAANSQYFHNMLELVAQYGQGLVGPPSQLIFGDLLQEEIETIRNNLAEHRASWAVTGCSV 316 (836)
Q Consensus 237 ~~~~~~~~Iar~i~~~~iPfs~ve~~~F~~ml~~l~~~~p~~~~PS~~~l~~~iL~~~~~~v~~~l~~~~~~w~~~~~sI 316 (836)
....+.+++++||+.+++||+.|++++|+.++..+ +|.|++|++.++...++...+.+.......+.. -.+.+++
T Consensus 95 ~~~~~~~~~~~~ii~~~lp~~~ve~~~~~~~~~~~---~P~~~~~~~~t~~~~~~~~~~~~k~~~~~~~~~--~~~~v~l 169 (641)
T KOG1121|consen 95 DQKVIREAIARMIILHGLPLSTVEEPGFRELLKHL---NPNYKLPSRSTLEADVLKIYEAEKPKLKEILEK--IIGRVSL 169 (641)
T ss_pred hHHHHHHHHHHHHHhcCCChhhccchhHHHHHHhc---CCCcccCChhHHHHHHHHHHHHHHHHHHHHHHc--cCCceEE
Confidence 45677889999999999999999999999999988 899999999999988877665444443333322 2578999
Q ss_pred EecccccC-CCCeEEEEEeecCCcce-----EEEeeeCCCCCcchHHHHHHHHHHHHHhcC-ccEEEEEEeCCcchhh--
Q 047254 317 MADSWTDS-ESRTLINLFVSSPHGLY-----FLSSVDATDIVEDASNLFKLLDKVVEEMGE-ENVVQVITQNTPSYKS-- 387 (836)
Q Consensus 317 ~~D~WTd~-~~~~~l~~~v~~~~g~~-----fL~svd~s~~~htge~I~e~l~~viee~g~-~nVv~vvTDnasn~~~-- 387 (836)
++|.|++. ....++.+++|+.+..+ ++... -...|+++.|+..+..++.+||+ .+|..++.|| .+...
T Consensus 170 T~d~w~~~~~~~~y~~~t~h~id~~~~l~~~il~~~--~~~~~~~~~i~~~~~~~~~~~~i~~kv~~~~~~n-~~~~~~~ 246 (641)
T KOG1121|consen 170 TTDLWSDSGTDEGYMVLTAHYIDRDWELHNKILSFC--IPPPHLGKALASVLNECLLEWGIEKKVFSITVDN-VNVSNIE 246 (641)
T ss_pred EEeeecCCCCCcceEEEEEEEeccchHhhhheeeee--cCCcchHHHHHHHHHHHHHhhChhheEEEEeecc-cchhHHH
Confidence 99999987 67899999999875422 22222 34479999999999999999997 6788889999 33221
Q ss_pred -hhhHHHHhc-----CCccccCchHHHHHHHHhhhhcchhHHHHHHHHHHHHHHHHhhHHHHHHHHHhhc------cCcc
Q 047254 388 -AGKMLEEKR-----KNLFWTPCATYCIDKMLDGFLNLKSVWKCMEMAQKITKFIYNHIRLLNLMKKEFT------QGQE 455 (836)
Q Consensus 388 -a~~lL~~k~-----p~i~~~~C~aH~LnLvl~di~k~~~v~~~i~k~~~Iv~fi~~s~~~l~~~r~k~~------~~~~ 455 (836)
....+.... ..+++.+|.+|.+|+++++..+ ..+...+.++++.+++++.+......|. ... ....
T Consensus 247 ~~~~~l~~~~~~~~~~~~~~~~C~~~~~~~~v~~~l~-~~~~~~l~~ir~~v~~vk~s~~~~~~f~-~~~~~~~~~~~~~ 324 (641)
T KOG1121|consen 247 TLRDHLKSSNALLLLGKFFHVRCFAHILNLIVQEGLK-EEFSSLLEKLRESVKYVKSSESRESSFE-ECQEQLGIPSDVL 324 (641)
T ss_pred HhhHHHhhcccceecceeeeeehhhhhhhHHHHHHHH-HHHhHHHHHHHHHHHHHhcChHHHHHHH-HHHHhcCCccccc
Confidence 222222222 2456899999999999999876 7899999999999999999998888777 332 1222
Q ss_pred ccccccccchhhHHHHHHHHHhHHHHHHHhhhccccccccccCccchhHHhhhCCHHHHHHHHHHHHhHHHHHHHHHHHh
Q 047254 456 LLMPSVTRFASSFTTLQNLLDHRIDLRRMFQSEIWTSSWFSKSDKGKEVENIVLNAKFWKKVLYVVRSVNPIMKVLQKVD 535 (836)
Q Consensus 456 Li~~~~TRW~S~~~~L~rll~~k~~L~~~~~s~e~~~s~~~k~~~g~~v~~~il~~~fW~~l~~i~~il~Pl~~~l~~l~ 535 (836)
++ ++.|||+|+|.||.++++++.+|..+...+ . ......++..|..++.++.+++||.++...++
T Consensus 325 ~~-d~~~~w~st~~ml~~~~~~~~~~~~~~~~~-~-------------~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~s 389 (641)
T KOG1121|consen 325 LL-DVSTRWNSTYLMLSRALKLKDAFSKLEEED-K-------------SYKSYPSDEEWNRLEELCDFLQPFSEVTKLLS 389 (641)
T ss_pred cc-cCCccchhHHHHHHHHHHHHHHHHHHHHhc-c-------------ccccCcCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33 799999999999999999999999998764 1 01223566669999999999999999999999
Q ss_pred cCCCCchhcHHHHHHHHHHHHHHHhCCCc----ccccchHHHHHHHhhhccCCcchhheeecCccCCCCC-------CCC
Q 047254 536 TGQSLSMPYVYNDMYRAKLAIQSFHGDDV----RKYGPFWNVIDNHWDLLGHHPLYVAAYFLNPSYRYRP-------HFV 604 (836)
Q Consensus 536 ~d~~ps~~~iy~~~~~~k~~I~~~~~~~~----~~~~~~~~~id~rw~~~l~~pl~~aA~~LnPr~~y~~-------~~~ 604 (836)
+..+|+...+++.+..+...+........ .....+...++++|... ...+.++|.+|||||++.. .+.
T Consensus 390 ~~~~~ts~~~~~~i~~i~~~l~~~~~~~~~~~~~~a~~m~~k~dk~~~~~-~~~~~~~atvlDPR~k~~~~~~~~~~~~~ 468 (641)
T KOG1121|consen 390 GSSYPTSNQYFPEIWKIENLLKTYASGEDEVVRSMAEEMFEKFDKYWSYS-ICDLLAIATLLDPRFKLKLLESSFEKLYG 468 (641)
T ss_pred CCCCchHHHHHHHHHHHHHHHHhcccCccHHHHHHHHHHHHHhhhhcccc-hhHHHHHHHhcChHhHHHHHHHHhhhhhc
Confidence 99999999999999888776654322211 13345667778888822 4577889999999998641 111
Q ss_pred Cch----HH----HHHHHHHHHHhcC---ChH--H------HHH------------------------HHHhhhhhhhhh
Q 047254 605 AYP----EV----VRGLNECIVRLEP---DKV--R------RIY------------------------AMSQISDYTTAK 641 (836)
Q Consensus 605 ~~~----ei----~~~l~~~i~~l~~---~~~--~------~~~------------------------i~~el~~y~~~~ 641 (836)
.+. +. ...+...+..+.. ... . ... ...+|..|....
T Consensus 469 ~~~~~~~~~~~~~~d~~~~l~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~y~~e~ 548 (641)
T KOG1121|consen 469 KDPEDAKEKVESVRDKLKKLLEEYKQLSPSNVSNSAHSWDLLDESPLEKDAFEYLFEPEVSIDSGSKSGKSELDHYLSES 548 (641)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHhccCCCCCCccccccccccccccccchhhhhhhHHHHHHhcCCCCCchHHHHHhhh
Confidence 011 11 1112222222221 000 0 000 001111111110
Q ss_pred hccCcHHHHhhhccccccchhccccCCchhHHHHHHHHhcccccCcccCCCcchhhhhhhcccccchHHhhhhHHHHHHh
Q 047254 642 ADFGTELAISTRTELEPAAWWQQHGISSLQLQQIAVRILSQTCSSIGCEHKWSIYDQVHGQRHSRAAQKRINDLIYVHYN 721 (836)
Q Consensus 642 ~~f~~~~ai~~~~~~~Pl~WW~~~~~~~P~L~klA~~iLsip~SSa~~ER~FS~~~~I~tk~RnrL~~e~l~~Lvfv~~N 721 (836)
..........++|++||+.++..||.|+.||+++|++|++++++|+.||+.+++..+.|++|.+.++..|+|.+.+
T Consensus 549 ----~~~~~~~~~~~~~l~~w~~~~~~y~~ls~~a~d~l~~p~~~~~~e~~f~~~~~~~~~~r~~l~~~~~~~l~c~~~~ 624 (641)
T KOG1121|consen 549 ----PRLLMPSFLDADVLQWWKGNGTRYPELSSMARDILSIPITSVASESSFSIGGRVLNKYRSRLLPENVQALICTRNW 624 (641)
T ss_pred ----hhhhccccccccHHHHhhccCcccchHHHHHHHHHcCcccCccchhhcccCceecCchhccCCchhhHHhhchHhh
Confidence 0000112246799999999999999999999999999999999999999999999999999999999999999888
Q ss_pred HH
Q 047254 722 LR 723 (836)
Q Consensus 722 ~~ 723 (836)
++
T Consensus 625 ~~ 626 (641)
T KOG1121|consen 625 LP 626 (641)
T ss_pred hh
Confidence 76
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=99.61 E-value=3e-16 Score=138.39 Aligned_cols=68 Identities=24% Similarity=0.519 Sum_probs=57.1
Q ss_pred cccccchhccccCCchhHHHHHHHHhcccccCcccCCCcchhhhhhhcccccchHHhhhhHHHHHHhH
Q 047254 655 ELEPAAWWQQHGISSLQLQQIAVRILSQTCSSIGCEHKWSIYDQVHGQRHSRAAQKRINDLIYVHYNL 722 (836)
Q Consensus 655 ~~~Pl~WW~~~~~~~P~L~klA~~iLsip~SSa~~ER~FS~~~~I~tk~RnrL~~e~l~~Lvfv~~N~ 722 (836)
..+|+.||+.+...||+|+++|+++|++|+||+.|||.||+.+.++++.|++|+++++++|+|++.|+
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 57999999999999999999999999999999999999999999999999999999999999999985
No 4
>PF14291 DUF4371: Domain of unknown function (DUF4371)
Probab=99.02 E-value=9.9e-10 Score=115.52 Aligned_cols=138 Identities=22% Similarity=0.348 Sum_probs=106.8
Q ss_pred HHHHHHHHcCCcccc-------ccCHHHHHHHHHHHHcCCCCCC------C-----ChhhhhhhHHHHHHHHHHHHH-HH
Q 047254 244 AICKFFYYAGVPLEA-------ANSQYFHNMLELVAQYGQGLVG------P-----PSQLIFGDLLQEEIETIRNNL-AE 304 (836)
Q Consensus 244 ~Iar~i~~~~iPfs~-------ve~~~F~~ml~~l~~~~p~~~~------P-----S~~~l~~~iL~~~~~~v~~~l-~~ 304 (836)
.+++|+...|+||+. .+..+|++|++.+++++|...- | +++++.+.+ ......+++.+ ++
T Consensus 69 ~~i~fL~~QgLa~RGh~e~~~s~n~GNFl~ll~l~~~~d~~l~~~~~~~~~~~~~~~s~~iq~~i-~~~a~~v~~~I~~~ 147 (235)
T PF14291_consen 69 DVILFLARQGLAFRGHDESEDSLNNGNFLELLELLAKYDPELKKHLSKNAPKNAKYSSKTIQNEI-EILADHVRQSIVEE 147 (235)
T ss_pred HHHHHHHhcccccccCCccccccccccHHHHHHHHHhhcccchhhhhcccccceeccHHHHHHHH-HHHHHHHHHHHHhh
Confidence 467999999999987 3567999999999998886531 2 234444443 44444444433 33
Q ss_pred HHhhhhccceEEEecccccCCCCeEEEEEeecCC--c---ceEEEeeeCCCCCcchHHHHHHHHHHHHHhcC--ccEEEE
Q 047254 305 HRASWAVTGCSVMADSWTDSESRTLINLFVSSPH--G---LYFLSSVDATDIVEDASNLFKLLDKVVEEMGE--ENVVQV 377 (836)
Q Consensus 305 ~~~~w~~~~~sI~~D~WTd~~~~~~l~~~v~~~~--g---~~fL~svd~s~~~htge~I~e~l~~viee~g~--~nVv~v 377 (836)
+ ....+||++|++||..+..+|+++|.+.+ + ..||+.+++. ..||+.|++.|.++++++|+ ++++++
T Consensus 148 v----~~~~FSii~DettDis~~eQl~i~vRyv~~~~~i~E~Fl~f~~~~--~~ta~~l~~~i~~~L~~~~l~~~~~~gq 221 (235)
T PF14291_consen 148 V----KSKYFSIIVDETTDISNKEQLSICVRYVDKDGKIKERFLGFVELE--DTTAESLFNAIKDVLEKLGLDLSNCRGQ 221 (235)
T ss_pred c----cccceeeeeeccccccccchhhheeeeeccCcceeeeeeeeeccC--CccHHHHHHHHHHHHHHcCCCHHHcCcc
Confidence 3 23589999999999999999999987653 3 2588888886 47999999999999999997 799999
Q ss_pred EEeCCcchhhh
Q 047254 378 ITQNTPSYKSA 388 (836)
Q Consensus 378 vTDnasn~~~a 388 (836)
.||||+||.+.
T Consensus 222 ~yDgas~M~G~ 232 (235)
T PF14291_consen 222 CYDGASNMSGK 232 (235)
T ss_pred cccChHhheec
Confidence 99999999873
No 5
>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=98.30 E-value=3.3e-07 Score=70.23 Aligned_cols=38 Identities=47% Similarity=0.944 Sum_probs=30.0
Q ss_pred CCccccceeccCCcCeeEcccCCCccc---CchHHHHHHhh
Q 047254 68 DPGWEHGVAQDQRKKKVKCNYCGKVVS---GGINRFKQHLA 105 (836)
Q Consensus 68 d~~W~h~~~~~~~~~~~~C~yC~~~~~---ggi~r~k~HL~ 105 (836)
|++|+|+...+++...++|+||++++. ||+++|+.||.
T Consensus 1 S~vW~~F~~~~~~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 1 SPVWKHFTKIPGDKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp GGCCCCCEE--GCSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CCccccEEEccCCcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 589999997777789999999999993 49999999994
No 6
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=96.88 E-value=0.00084 Score=52.58 Aligned_cols=37 Identities=41% Similarity=0.936 Sum_probs=30.1
Q ss_pred cccccee---ccCCcCeeEcccCCCcc----cCchHHHHHHhhc
Q 047254 70 GWEHGVA---QDQRKKKVKCNYCGKVV----SGGINRFKQHLAR 106 (836)
Q Consensus 70 ~W~h~~~---~~~~~~~~~C~yC~~~~----~ggi~r~k~HL~~ 106 (836)
+|+|+.. .+.++.+++|+||++.+ ++|++.|+.||..
T Consensus 2 vW~~F~~i~~~~~g~~~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 2 VWKHFTLILEKDNGKQRAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred cCccceEEEEcCCCCeEEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 7999984 22235789999999999 2799999999973
No 7
>PF14372 DUF4413: Domain of unknown function (DUF4413)
Probab=96.29 E-value=0.0075 Score=54.77 Aligned_cols=64 Identities=14% Similarity=0.305 Sum_probs=48.4
Q ss_pred HhcCCCCchhcHHHHHHHHHHHHHHHhCCCc---ccccchHHHHHHHhhhccCCcchhheeecCccCCC
Q 047254 534 VDTGQSLSMPYVYNDMYRAKLAIQSFHGDDV---RKYGPFWNVIDNHWDLLGHHPLYVAAYFLNPSYRY 599 (836)
Q Consensus 534 l~~d~~ps~~~iy~~~~~~k~~I~~~~~~~~---~~~~~~~~~id~rw~~~l~~pl~~aA~~LnPr~~y 599 (836)
++|..+||.+.+++.+..++..|.+...++. .....+.+.++++|.. ...++++|++|||||+.
T Consensus 1 ~S~~~~pTsn~~f~~i~~i~~~l~~~~~~d~~l~~ma~~M~~KfdKYw~~--~~~~l~ia~ILDPR~Kl 67 (101)
T PF14372_consen 1 FSGSSYPTSNLYFHEIWKIKDLLRDWNNDDPDLKNMAKKMKEKFDKYWKD--CNLLLAIATILDPRFKL 67 (101)
T ss_pred CCCCCcCcHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHH--hHHHHHHHHHhchHHHH
Confidence 3677799999999999999999987432211 2234667778899975 35668899999999984
No 8
>PF10683 DBD_Tnp_Hermes: Hermes transposase DNA-binding domain ; InterPro: IPR018473 This domain confers specific DNA-binding on Hermes transposase [].; PDB: 2BW3_B.
Probab=95.16 E-value=0.016 Score=47.01 Aligned_cols=40 Identities=13% Similarity=0.252 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHHHHHHcCCccccccCHHHHHHHHHHHHcC
Q 047254 236 KSQKEIISAICKFFYYAGVPLEAANSQYFHNMLELVAQYG 275 (836)
Q Consensus 236 ~~~~~~~~~Iar~i~~~~iPfs~ve~~~F~~ml~~l~~~~ 275 (836)
..++++.+.++.|.+++..||++|+..+|++|+..+-+.|
T Consensus 11 ~~K~~~~~k~~qw~v~dcRpfsiv~gsGfk~la~~li~IG 50 (68)
T PF10683_consen 11 PDKKEATDKCTQWCVKDCRPFSIVSGSGFKKLAQFLINIG 50 (68)
T ss_dssp HHHHHHHHHHHHHHHHCT--GGGGG-HHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHhcCCcceeeccccHHHHHHHHHHHh
Confidence 4568889999999999999999999999999998875444
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=83.91 E-value=7.5 Score=40.86 Aligned_cols=126 Identities=18% Similarity=0.193 Sum_probs=66.9
Q ss_pred ccccccCHHHHHHHHHHHHcCCCCCCCChhhhhhhHHHHH------HHHHHHHHHHHHhhhhccceEEEecccccCC---
Q 047254 255 PLEAANSQYFHNMLELVAQYGQGLVGPPSQLIFGDLLQEE------IETIRNNLAEHRASWAVTGCSVMADSWTDSE--- 325 (836)
Q Consensus 255 Pfs~ve~~~F~~ml~~l~~~~p~~~~PS~~~l~~~iL~~~------~~~v~~~l~~~~~~w~~~~~sI~~D~WTd~~--- 325 (836)
-+...-..+++-|.+ -+|.+||..+|++++ ... ...+-..++...-.-....|.|++|+-.=..
T Consensus 82 ~L~~~spr~Y~yL~k------k~~pLPs~rTL~r~l-~~v~~~pGi~~~il~~l~~~~~~~~dr~CvL~fDEm~l~~~~e 154 (236)
T PF12017_consen 82 SLYKCSPRAYNYLRK------KGYPLPSVRTLQRWL-SKVNIDPGILDFILDLLKNKSMSEEDRICVLSFDEMKLSPHLE 154 (236)
T ss_pred eeeecChHHHHHHHH------cCCCCCCHHHHHHHH-HhCCCCCCchHHHHHHHHHccCchhccEEEEEEeEEEccceee
Confidence 344455567776654 269999999999875 221 2222222322100012457999999764111
Q ss_pred ----CCe-------EEEEEeec----CCcceEEEeeeCCCCCcchHHHHHHHHHHHHHhcCccEEEEEEeCCcchhhhhh
Q 047254 326 ----SRT-------LINLFVSS----PHGLYFLSSVDATDIVEDASNLFKLLDKVVEEMGEENVVQVITQNTPSYKSAGK 390 (836)
Q Consensus 326 ----~~~-------~l~~~v~~----~~g~~fL~svd~s~~~htge~I~e~l~~viee~g~~nVv~vvTDnasn~~~a~~ 390 (836)
... +..++|-. -+..+|..+ +. .-+++.|.++|.+ +.+.|. +|++||+|.++++.++++
T Consensus 155 YD~~~d~v~~~~~~~~v~mvrGl~~~WKQpi~~~f-~t---~m~~~~l~~iI~~-l~~~g~-~VvAivsD~g~~N~~~w~ 228 (236)
T PF12017_consen 155 YDPSRDEVNEPANYVQVFMVRGLFKSWKQPIYFDF-DT---SMDADILKNIIEK-LHEIGY-NVVAIVSDMGSNNISLWR 228 (236)
T ss_pred eccccCcccChhhhhhHHHHHHHHhcCCccEEEEe-cC---cCCHHHHHHHHHH-HHHCCC-EEEEEECCCCcchHHHHH
Confidence 111 11111100 011233333 22 3456666554432 344554 699999999999999887
Q ss_pred HHH
Q 047254 391 MLE 393 (836)
Q Consensus 391 lL~ 393 (836)
.|.
T Consensus 229 ~Lg 231 (236)
T PF12017_consen 229 ELG 231 (236)
T ss_pred HcC
Confidence 663
No 10
>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=67.29 E-value=4.9 Score=25.24 Aligned_cols=21 Identities=29% Similarity=0.744 Sum_probs=15.8
Q ss_pred eEcccCCCcccCchHHHHHHhh
Q 047254 84 VKCNYCGKVVSGGINRFKQHLA 105 (836)
Q Consensus 84 ~~C~yC~~~~~ggi~r~k~HL~ 105 (836)
++|.+|++.+. ....++.|+.
T Consensus 1 ~~C~~C~~~~~-~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFR-SKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EES-SHHHHHHHHH
T ss_pred CCCcCCCCcCC-cHHHHHHHHH
Confidence 57999999997 4788898985
No 11
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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 C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=62.81 E-value=3.9 Score=30.06 Aligned_cols=27 Identities=26% Similarity=0.487 Sum_probs=13.0
Q ss_pred eeEcccCCCcccCchHHH-HHHhhccCC
Q 047254 83 KVKCNYCGKVVSGGINRF-KQHLARIQG 109 (836)
Q Consensus 83 ~~~C~yC~~~~~ggi~r~-k~HL~~~~~ 109 (836)
+-=|.||+.-+....... |+|+.|.++
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH 30 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKH 30 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THH
T ss_pred CeecccccceecCCChHHHHHhhccHHH
Confidence 456999999995445444 999998764
No 12
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=55.35 E-value=10 Score=26.62 Aligned_cols=25 Identities=16% Similarity=0.328 Sum_probs=20.7
Q ss_pred eeEcccCCCcccCchHHHHHHhhccC
Q 047254 83 KVKCNYCGKVVSGGINRFKQHLARIQ 108 (836)
Q Consensus 83 ~~~C~yC~~~~~ggi~r~k~HL~~~~ 108 (836)
...|.+|++.+. +-.-++.|+.|.+
T Consensus 3 ~~~C~~C~~~~~-~~~~~~~H~~gk~ 27 (35)
T smart00451 3 GFYCKLCNVTFT-DEISVEAHLKGKK 27 (35)
T ss_pred CeEccccCCccC-CHHHHHHHHChHH
Confidence 578999999998 5666799998754
No 13
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=53.22 E-value=12 Score=24.21 Aligned_cols=23 Identities=35% Similarity=0.626 Sum_probs=19.4
Q ss_pred eEcccCCCcccCchHHHHHHhhcc
Q 047254 84 VKCNYCGKVVSGGINRFKQHLARI 107 (836)
Q Consensus 84 ~~C~yC~~~~~ggi~r~k~HL~~~ 107 (836)
+.|.-|++.++ +-.-++.|+.|.
T Consensus 1 ~~C~~C~~~f~-s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFS-SENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEES-SHHHHHHHHTTH
T ss_pred CCCCCCCCCcC-CHHHHHHHHCcC
Confidence 57999999997 478899999864
No 14
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=52.70 E-value=11 Score=24.99 Aligned_cols=21 Identities=29% Similarity=0.667 Sum_probs=18.1
Q ss_pred eeEcccCCCcccCchHHHHHHhh
Q 047254 83 KVKCNYCGKVVSGGINRFKQHLA 105 (836)
Q Consensus 83 ~~~C~yC~~~~~ggi~r~k~HL~ 105 (836)
.+.|.+|+..| +..|+..|+.
T Consensus 2 l~~C~~CgR~F--~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKF--NPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEE--CHHHHHHHHH
Confidence 46899999999 5889999985
No 15
>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=48.65 E-value=15 Score=23.13 Aligned_cols=21 Identities=38% Similarity=0.778 Sum_probs=16.5
Q ss_pred eEcccCCCcccCchHHHHHHhh
Q 047254 84 VKCNYCGKVVSGGINRFKQHLA 105 (836)
Q Consensus 84 ~~C~yC~~~~~ggi~r~k~HL~ 105 (836)
.+|.+|++.|.. -+-|+.|+.
T Consensus 1 y~C~~C~~~f~~-~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSS-KSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESS-HHHHHHHHH
T ss_pred CCCCCCCCccCC-HHHHHHHHh
Confidence 479999999963 667888864
No 16
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=45.32 E-value=12 Score=24.93 Aligned_cols=22 Identities=36% Similarity=0.676 Sum_probs=18.5
Q ss_pred eEcccCCCcccCchHHHHHHhhc
Q 047254 84 VKCNYCGKVVSGGINRFKQHLAR 106 (836)
Q Consensus 84 ~~C~yC~~~~~ggi~r~k~HL~~ 106 (836)
..|..|++.|+ +-.-++.|+.+
T Consensus 2 ~~C~~C~k~f~-~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFS-SENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBS-SHHHHHCCTTS
T ss_pred CCcccCCCCcC-CHHHHHHHHcc
Confidence 57999999997 47888999875
No 17
>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=44.71 E-value=94 Score=26.93 Aligned_cols=55 Identities=18% Similarity=0.134 Sum_probs=38.7
Q ss_pred cchHHHHHHHHHHHHHhcCccEEEEEEeCCcchhhhhhHHHHhcCCccccCchHHHHHH
Q 047254 353 EDASNLFKLLDKVVEEMGEENVVQVITQNTPSYKSAGKMLEEKRKNLFWTPCATYCIDK 411 (836)
Q Consensus 353 htge~I~e~l~~viee~g~~nVv~vvTDnasn~~~a~~lL~~k~p~i~~~~C~aH~LnL 411 (836)
.+.+.+...+..+.+.++.. ...|++|....+..|.+ +-+|...+..|.-|.+.-
T Consensus 37 e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~---~vfP~~~~~~C~~H~~~n 91 (93)
T PF10551_consen 37 ESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIK---EVFPDARHQLCLFHILRN 91 (93)
T ss_pred CChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHH---HHCCCceEehhHHHHHHh
Confidence 35555665555444444434 77899999988877754 457998899999998753
No 18
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=41.35 E-value=44 Score=26.36 Aligned_cols=45 Identities=20% Similarity=0.377 Sum_probs=30.7
Q ss_pred eeEcccCCCcccCchHHHHHHhhccC---CCcccCCCCCHHHHHHHHHHH
Q 047254 83 KVKCNYCGKVVSGGINRFKQHLARIQ---GEVAPCKDAPEDVYLKMKENM 129 (836)
Q Consensus 83 ~~~C~yC~~~~~ggi~r~k~HL~~~~---~~v~~C~~vp~~v~~~~~~~l 129 (836)
...|-||++.++ ...|..|+...- +....||-....+...|...|
T Consensus 2 ~f~CP~C~~~~~--~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGKGFS--ESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHL 49 (54)
T ss_pred CcCCCCCCCccC--HHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHH
Confidence 468999999444 678999976532 234679888776665555544
No 19
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=40.04 E-value=17 Score=27.09 Aligned_cols=17 Identities=35% Similarity=0.731 Sum_probs=11.9
Q ss_pred ccCCcCeeEcccCCCcc
Q 047254 77 QDQRKKKVKCNYCGKVV 93 (836)
Q Consensus 77 ~~~~~~~~~C~yC~~~~ 93 (836)
++.+...+.|.||+..|
T Consensus 23 l~~~~~~~~CpYCg~~y 39 (40)
T PF10276_consen 23 LDDEPGPVVCPYCGTRY 39 (40)
T ss_dssp -TTTTCEEEETTTTEEE
T ss_pred cCCCCCeEECCCCCCEE
Confidence 34433579999999875
No 20
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=39.48 E-value=3.7e+02 Score=33.84 Aligned_cols=54 Identities=19% Similarity=0.123 Sum_probs=40.7
Q ss_pred HHHHHHHHhcCccEEEEEEeCCcchhhhhhHHHHhcCCccccCchHHHHHHHHhhhh
Q 047254 361 LLDKVVEEMGEENVVQVITQNTPSYKSAGKMLEEKRKNLFWTPCATYCIDKMLDGFL 417 (836)
Q Consensus 361 ~l~~viee~g~~nVv~vvTDnasn~~~a~~lL~~k~p~i~~~~C~aH~LnLvl~di~ 417 (836)
++...++-+|-..=..|+||....|..|.. +.+|...|--|.-|++.-+.+.+.
T Consensus 335 Lf~tfl~aM~gk~P~tIiTDqd~am~~AI~---~VfP~t~Hr~C~wHI~~~~~e~L~ 388 (846)
T PLN03097 335 LMQTWLRAMGGQAPKVIITDQDKAMKSVIS---EVFPNAHHCFFLWHILGKVSENLG 388 (846)
T ss_pred HHHHHHHHhCCCCCceEEecCCHHHHHHHH---HHCCCceehhhHHHHHHHHHHHhh
Confidence 334445555655557799999998888754 458999999999999998887764
No 21
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=39.22 E-value=16 Score=28.88 Aligned_cols=19 Identities=26% Similarity=0.901 Sum_probs=13.5
Q ss_pred eccCCcCeeEcccCCCccc
Q 047254 76 AQDQRKKKVKCNYCGKVVS 94 (836)
Q Consensus 76 ~~~~~~~~~~C~yC~~~~~ 94 (836)
..+.+....+|.||++++.
T Consensus 28 v~~~~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 28 VIDKEPIKLRCHYCERIIT 46 (52)
T ss_dssp EEETTTCEEEETTT--EEE
T ss_pred EEeCCCCEEEeeCCCCEec
Confidence 3556678999999999884
No 22
>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=35.59 E-value=2.9e+02 Score=24.64 Aligned_cols=35 Identities=23% Similarity=0.349 Sum_probs=28.6
Q ss_pred cchHHHHHHHHHHHHHhcCccEEEEEEeCCcchhh
Q 047254 353 EDASNLFKLLDKVVEEMGEENVVQVITQNTPSYKS 387 (836)
Q Consensus 353 htge~I~e~l~~viee~g~~nVv~vvTDnasn~~~ 387 (836)
.+++.+...|.++++..|......++|||++.+..
T Consensus 47 ~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 47 ETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp SHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHS
T ss_pred cccccccccccccccccccccceeccccccccccc
Confidence 48899999999999999875577889999998874
No 23
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=34.96 E-value=17 Score=32.13 Aligned_cols=21 Identities=24% Similarity=0.423 Sum_probs=17.5
Q ss_pred cCeeEcccCCCcccCchHHHH
Q 047254 81 KKKVKCNYCGKVVSGGINRFK 101 (836)
Q Consensus 81 ~~~~~C~yC~~~~~ggi~r~k 101 (836)
...|+|+.|++.+.||.+.+.
T Consensus 51 ~GIW~C~~C~~~~AGGAy~p~ 71 (91)
T TIGR00280 51 TGIWTCRKCGAKFAGGAYTPV 71 (91)
T ss_pred eEEEEcCCCCCEEeCCccccc
Confidence 467999999999998887643
No 24
>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=31.40 E-value=20 Score=40.72 Aligned_cols=153 Identities=15% Similarity=0.131 Sum_probs=82.0
Q ss_pred HHHHHcCCccccccCHHHHHHHHHHHHcCCCCCCCChhhhhhhHHHHHHHHHHHHHHHHHhhhhcc-ceEEEecccccC-
Q 047254 247 KFFYYAGVPLEAANSQYFHNMLELVAQYGQGLVGPPSQLIFGDLLQEEIETIRNNLAEHRASWAVT-GCSVMADSWTDS- 324 (836)
Q Consensus 247 r~i~~~~iPfs~ve~~~F~~ml~~l~~~~p~~~~PS~~~l~~~iL~~~~~~v~~~l~~~~~~w~~~-~~sI~~D~WTd~- 324 (836)
-.+|..|+.-+-+ ...++.+. |+ ..+|..++++ +.+...+++...-. ...... +..|..|+-.-.
T Consensus 108 ~~ly~~G~Str~i-----~~~l~~l~--g~--~~~S~s~vSr-i~~~~~~~~~~w~~---R~L~~~~y~~l~iD~~~~kv 174 (381)
T PF00872_consen 108 ISLYLKGVSTRDI-----EEALEELY--GE--VAVSKSTVSR-ITKQLDEEVEAWRN---RPLESEPYPYLWIDGTYFKV 174 (381)
T ss_pred hhhhccccccccc-----cchhhhhh--cc--cccCchhhhh-hhhhhhhhHHHHhh---hccccccccceeeeeeeccc
Confidence 3446677765444 34444441 21 2267777765 44444444443322 112234 678889975432
Q ss_pred C------CCeEEEEEeecCCcceEEEeeeCCCCCcchHHHHHHHHHHHHHhcCccEEEEEEeCCcchhhhhhHHHHhcCC
Q 047254 325 E------SRTLINLFVSSPHGLYFLSSVDATDIVEDASNLFKLLDKVVEEMGEENVVQVITQNTPSYKSAGKMLEEKRKN 398 (836)
Q Consensus 325 ~------~~~~l~~~v~~~~g~~fL~svd~s~~~htge~I~e~l~~viee~g~~nVv~vvTDnasn~~~a~~lL~~k~p~ 398 (836)
. +..++.++-...+|.-.+-.+...+ ..++..=.++|. -|.+-|+..+.-||+|+...+..|. .+.||.
T Consensus 175 r~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~-~Es~~~W~~~l~-~L~~RGl~~~~lvv~Dg~~gl~~ai---~~~fp~ 249 (381)
T PF00872_consen 175 REDGRVVKKAVYVAIGIDEDGRREVLGFWVGD-RESAASWREFLQ-DLKERGLKDILLVVSDGHKGLKEAI---REVFPG 249 (381)
T ss_pred ccccccccchhhhhhhhhcccccceeeeeccc-CCccCEeeecch-hhhhccccccceeeccccccccccc---cccccc
Confidence 1 1223222223345543222222221 112222222232 3455688889999999988877664 456899
Q ss_pred ccccCchHHHHHHHHhhhh
Q 047254 399 LFWTPCATYCIDKMLDGFL 417 (836)
Q Consensus 399 i~~~~C~aH~LnLvl~di~ 417 (836)
.-|..|..|.+--++..+.
T Consensus 250 a~~QrC~vH~~RNv~~~v~ 268 (381)
T PF00872_consen 250 AKWQRCVVHLMRNVLRKVP 268 (381)
T ss_pred hhhhhheechhhhhccccc
Confidence 9999999999877776653
No 25
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=31.33 E-value=22 Score=31.46 Aligned_cols=21 Identities=29% Similarity=0.514 Sum_probs=17.6
Q ss_pred cCeeEcccCCCcccCchHHHH
Q 047254 81 KKKVKCNYCGKVVSGGINRFK 101 (836)
Q Consensus 81 ~~~~~C~yC~~~~~ggi~r~k 101 (836)
...|+|+.|++.+.||.+.+.
T Consensus 52 ~GIW~C~~C~~~~AGGAy~~~ 72 (90)
T PTZ00255 52 VGIWRCKGCKKTVAGGAWTLS 72 (90)
T ss_pred eEEEEcCCCCCEEeCCccccc
Confidence 468999999999999887753
No 26
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=31.17 E-value=19 Score=31.87 Aligned_cols=21 Identities=33% Similarity=0.566 Sum_probs=16.2
Q ss_pred cCeeEcccCCCcccCchHHHH
Q 047254 81 KKKVKCNYCGKVVSGGINRFK 101 (836)
Q Consensus 81 ~~~~~C~yC~~~~~ggi~r~k 101 (836)
...|+|..|++.|.||.+-+-
T Consensus 51 ~GIW~C~~C~~~~AGGAy~~~ 71 (90)
T PF01780_consen 51 TGIWKCKKCGKKFAGGAYTPS 71 (90)
T ss_dssp TTEEEETTTTEEEE-BSSSSS
T ss_pred eEEeecCCCCCEEeCCCcccc
Confidence 468999999999988876544
No 27
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=30.76 E-value=37 Score=24.21 Aligned_cols=24 Identities=38% Similarity=0.797 Sum_probs=18.5
Q ss_pred CeeEcccCCCcccCchHHHHHHhhcc
Q 047254 82 KKVKCNYCGKVVSGGINRFKQHLARI 107 (836)
Q Consensus 82 ~~~~C~yC~~~~~ggi~r~k~HL~~~ 107 (836)
..+.|.-|++.+. .+||-.||..-
T Consensus 3 ~~~~C~nC~R~v~--a~RfA~HLekC 26 (33)
T PF08209_consen 3 PYVECPNCGRPVA--ASRFAPHLEKC 26 (33)
T ss_dssp -EEE-TTTSSEEE--GGGHHHHHHHH
T ss_pred CeEECCCCcCCcc--hhhhHHHHHHH
Confidence 5689999999996 47999999743
No 28
>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=30.56 E-value=1e+02 Score=32.27 Aligned_cols=93 Identities=17% Similarity=0.148 Sum_probs=54.9
Q ss_pred EEecccccCCCCe-EEEEEeec--CCcceEEEeeeCCCCCcchHHHHHHHHHHHHHhcCccEEEEEEeCCcchhhhhhHH
Q 047254 316 VMADSWTDSESRT-LINLFVSS--PHGLYFLSSVDATDIVEDASNLFKLLDKVVEEMGEENVVQVITQNTPSYKSAGKML 392 (836)
Q Consensus 316 I~~D~WTd~~~~~-~l~~~v~~--~~g~~fL~svd~s~~~htge~I~e~l~~viee~g~~nVv~vvTDnasn~~~a~~lL 392 (836)
|..|++.-..+.. |+++++.. ..+. .+++.+ ..+.+.|.+-+.+....-...+|-.|++|..+.|..+.+
T Consensus 1 lgiDE~~~~~g~~~y~t~~~d~~~~~~~----il~i~~-~r~~~~l~~~~~~~~~~~~~~~v~~V~~Dm~~~y~~~~~-- 73 (249)
T PF01610_consen 1 LGIDEFAFRKGHRSYVTVVVDLDTDTGR----ILDILP-GRDKETLKDFFRSLYPEEERKNVKVVSMDMSPPYRSAIR-- 73 (249)
T ss_pred CeEeeeeeecCCcceeEEEEECccCCce----EEEEcC-CccHHHHHHHHHHhCccccccceEEEEcCCCcccccccc--
Confidence 3467776665555 65555533 2221 222222 345555555555442222457999999999999987653
Q ss_pred HHhcCCccccCchHHHHHHHHhhh
Q 047254 393 EEKRKNLFWTPCATYCIDKMLDGF 416 (836)
Q Consensus 393 ~~k~p~i~~~~C~aH~LnLvl~di 416 (836)
+.+|++..+-.--|++.++-+.+
T Consensus 74 -~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 74 -EYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred -ccccccccccccchhhhhhhhcc
Confidence 45787766666677776665543
No 29
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=29.75 E-value=23 Score=31.26 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=17.1
Q ss_pred cCeeEcccCCCcccCchHHHH
Q 047254 81 KKKVKCNYCGKVVSGGINRFK 101 (836)
Q Consensus 81 ~~~~~C~yC~~~~~ggi~r~k 101 (836)
...|+|+.|++.+.||.+-+.
T Consensus 52 ~GIW~C~~C~~~~AGGAy~~~ 72 (90)
T PRK03976 52 TGIWECRKCGAKFAGGAYTPE 72 (90)
T ss_pred EEEEEcCCCCCEEeCCccccc
Confidence 457999999999988877643
No 30
>KOG0562 consensus Predicted hydrolase (HIT family) [General function prediction only]
Probab=29.30 E-value=29 Score=33.95 Aligned_cols=24 Identities=25% Similarity=0.566 Sum_probs=21.1
Q ss_pred cCeeEcccCCCcccCchHHHHHHhh
Q 047254 81 KKKVKCNYCGKVVSGGINRFKQHLA 105 (836)
Q Consensus 81 ~~~~~C~yC~~~~~ggi~r~k~HL~ 105 (836)
+.-.+|.||+ .++-.|+.+|.||-
T Consensus 151 k~dLrC~~Cq-~~~~~~~kLK~Hl~ 174 (184)
T KOG0562|consen 151 KEDLRCWRCQ-TFGPHFPKLKAHLR 174 (184)
T ss_pred ccceeehhhh-hcccccHHHHHHHH
Confidence 4568999999 88888999999996
No 31
>COG4822 CbiK Cobalamin biosynthesis protein CbiK, Co2+ chelatase [Coenzyme metabolism]
Probab=28.52 E-value=4.7e+02 Score=27.17 Aligned_cols=112 Identities=15% Similarity=0.187 Sum_probs=72.0
Q ss_pred CccccccCHHHHHHHHHHHHcCCCCCCCChhhhhhhHHHHHHHHHHHHHHHHHhhhhccceEEEecccccCCCCeEEEEE
Q 047254 254 VPLEAANSQYFHNMLELVAQYGQGLVGPPSQLIFGDLLQEEIETIRNNLAEHRASWAVTGCSVMADSWTDSESRTLINLF 333 (836)
Q Consensus 254 iPfs~ve~~~F~~ml~~l~~~~p~~~~PS~~~l~~~iL~~~~~~v~~~l~~~~~~w~~~~~sI~~D~WTd~~~~~~l~~~ 333 (836)
.|+.++....|..++..+.++.+.|+- -.|.+.+|-- .+..+..++.++.... ..+....+.|+
T Consensus 80 Q~lhiIpG~EyEklvr~V~~~~~dF~~---lkig~PlLy~-k~DYe~~v~aik~~~p------------pl~k~e~~vlm 143 (265)
T COG4822 80 QPLHIIPGIEYEKLVREVNKYSNDFKR---LKIGRPLLYY-KNDYEICVEAIKDQIP------------PLNKDEILVLM 143 (265)
T ss_pred eeeeecCchHHHHHHHHHHHHhhhhhe---eecCCceeec-hhhHHHHHHHHHHhcC------------CcCcCeEEEEE
Confidence 588889999999999998887776642 2233333311 1233333444432211 11233444444
Q ss_pred eecCCcceEEEeeeCCCCCcchHHHHHHHHHHHHHhcCccEEEEEEeCCcchhhhhhHHHHh
Q 047254 334 VSSPHGLYFLSSVDATDIVEDASNLFKLLDKVVEEMGEENVVQVITQNTPSYKSAGKMLEEK 395 (836)
Q Consensus 334 v~~~~g~~fL~svd~s~~~htge~I~e~l~~viee~g~~nVv~vvTDnasn~~~a~~lL~~k 395 (836)
.|- ..|.+..-+..|+-++.+.|.++|+-..+.+=+-+..+.+.|++.
T Consensus 144 gHG--------------t~h~s~~~YacLd~~~~~~~f~~v~v~~ve~yP~~d~vi~~l~~~ 191 (265)
T COG4822 144 GHG--------------TDHHSNAAYACLDHVLDEYGFDNVFVAAVEGYPLVDTVIEYLRKN 191 (265)
T ss_pred ecC--------------CCccHHHHHHHHHHHHHhcCCCceEEEEecCCCcHHHHHHHHHHc
Confidence 442 246777888899999999999999988888888888877777643
No 32
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.58 E-value=33 Score=29.98 Aligned_cols=19 Identities=32% Similarity=0.611 Sum_probs=15.8
Q ss_pred CcCeeEcccCCCcccCchH
Q 047254 80 RKKKVKCNYCGKVVSGGIN 98 (836)
Q Consensus 80 ~~~~~~C~yC~~~~~ggi~ 98 (836)
....|+|..|+..|.||.+
T Consensus 50 a~GIW~C~kCg~~fAGgay 68 (89)
T COG1997 50 ATGIWKCRKCGAKFAGGAY 68 (89)
T ss_pred ccCeEEcCCCCCeeccccc
Confidence 3579999999999977755
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=24.98 E-value=56 Score=28.52 Aligned_cols=24 Identities=21% Similarity=0.635 Sum_probs=20.1
Q ss_pred eeEcccCCCcccCchHHHHHHhhcc
Q 047254 83 KVKCNYCGKVVSGGINRFKQHLARI 107 (836)
Q Consensus 83 ~~~C~yC~~~~~ggi~r~k~HL~~~ 107 (836)
.++|.+|++.+. ....++.|+...
T Consensus 50 ~~~C~~C~~~f~-s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFR-SREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EES-SHHHHHHHHHHT
T ss_pred CCCCCccCCCCc-CHHHHHHHHcCc
Confidence 689999999986 589999999854
No 34
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.50 E-value=44 Score=27.23 Aligned_cols=15 Identities=27% Similarity=0.645 Sum_probs=13.0
Q ss_pred CCcCeeEcccCCCcc
Q 047254 79 QRKKKVKCNYCGKVV 93 (836)
Q Consensus 79 ~~~~~~~C~yC~~~~ 93 (836)
|+.+-+.|-||+.+|
T Consensus 44 g~~gev~CPYC~t~y 58 (62)
T COG4391 44 GDEGEVVCPYCSTRY 58 (62)
T ss_pred CCCCcEecCccccEE
Confidence 567889999999987
No 35
>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=22.06 E-value=66 Score=21.01 Aligned_cols=21 Identities=29% Similarity=0.779 Sum_probs=17.3
Q ss_pred eEcccCCCcccCchHHHHHHhh
Q 047254 84 VKCNYCGKVVSGGINRFKQHLA 105 (836)
Q Consensus 84 ~~C~yC~~~~~ggi~r~k~HL~ 105 (836)
.+|..|++.|+ ....|..|+.
T Consensus 2 ~~C~~C~~~F~-~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFS-SLSALREHKR 22 (27)
T ss_dssp EEETTTTEEES-SHHHHHHHHC
T ss_pred CCCCccCCccC-ChhHHHHHhH
Confidence 47999999996 4788888874
No 36
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=20.67 E-value=83 Score=20.01 Aligned_cols=20 Identities=40% Similarity=0.712 Sum_probs=14.1
Q ss_pred EcccCCCcccCchHHHHHHhhc
Q 047254 85 KCNYCGKVVSGGINRFKQHLAR 106 (836)
Q Consensus 85 ~C~yC~~~~~ggi~r~k~HL~~ 106 (836)
+|.+|.-... -..|+.|+..
T Consensus 2 ~C~~C~y~t~--~~~l~~H~~~ 21 (24)
T PF13909_consen 2 KCPHCSYSTS--KSNLKRHLKR 21 (24)
T ss_dssp E-SSSS-EES--HHHHHHHHHH
T ss_pred CCCCCCCcCC--HHHHHHHHHh
Confidence 7999995554 7789999853
No 37
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=20.47 E-value=66 Score=39.31 Aligned_cols=47 Identities=32% Similarity=0.537 Sum_probs=32.8
Q ss_pred CeeEcccCCCcccCchHHHHHHhhccCCC----cccCCCCCHHHHHHHHHHHHHhhh
Q 047254 82 KKVKCNYCGKVVSGGINRFKQHLARIQGE----VAPCKDAPEDVYLKMKENMKWHRS 134 (836)
Q Consensus 82 ~~~~C~yC~~~~~ggi~r~k~HL~~~~~~----v~~C~~vp~~v~~~~~~~l~~~~~ 134 (836)
-+-||+||.|+|+ .-++++-||+-..|. -..|.+ ++--+.+|+++..
T Consensus 352 ~khkCr~Cakvfg-S~SaLqiHlRSHTGERPfqCnvCG~-----~FSTkGNLKvH~~ 402 (958)
T KOG1074|consen 352 FKHKCRFCAKVFG-SDSALQIHLRSHTGERPFQCNVCGN-----RFSTKGNLKVHFQ 402 (958)
T ss_pred ccchhhhhHhhcC-chhhhhhhhhccCCCCCeeeccccc-----ccccccceeeeee
Confidence 4558999999995 689999999987763 223544 3445566666554
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.16 E-value=71 Score=19.86 Aligned_cols=20 Identities=35% Similarity=0.820 Sum_probs=15.7
Q ss_pred EcccCCCcccCchHHHHHHhh
Q 047254 85 KCNYCGKVVSGGINRFKQHLA 105 (836)
Q Consensus 85 ~C~yC~~~~~ggi~r~k~HL~ 105 (836)
+|..|++.+. +-..+..|+.
T Consensus 2 ~C~~C~~~f~-~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFK-SKSALKEHMR 21 (26)
T ss_pred CCCCCcchhC-CHHHHHHHHH
Confidence 6999999996 4677777875
No 39
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=20.10 E-value=57 Score=21.56 Aligned_cols=14 Identities=57% Similarity=1.115 Sum_probs=11.2
Q ss_pred cCeeEcccCCCccc
Q 047254 81 KKKVKCNYCGKVVS 94 (836)
Q Consensus 81 ~~~~~C~yC~~~~~ 94 (836)
.+..+|.+|++.|.
T Consensus 12 ~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 12 EKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSEEESSSSEEES
T ss_pred CCCCCCCCCcCeeC
Confidence 35689999999873
Done!