Query 044693
Match_columns 897
No_of_seqs 457 out of 1810
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 05:51:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044693.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044693hhsearch_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 1.6E-35 3.4E-40 286.3 13.8 153 351-503 1-153 (153)
2 KOG1121 Tam3-transposase (Ac f 100.0 3.1E-30 6.8E-35 312.6 39.3 464 306-794 94-627 (641)
3 PF05699 Dimer_Tnp_hAT: hAT fa 99.5 2E-15 4.3E-20 133.2 2.5 69 724-792 18-86 (86)
4 PF14291 DUF4371: Domain of un 99.3 1.2E-11 2.5E-16 130.3 9.6 139 314-458 69-232 (235)
5 PF02892 zf-BED: BED zinc fing 98.4 1.6E-07 3.4E-12 71.6 1.9 38 135-172 1-41 (45)
6 PF02892 zf-BED: BED zinc fing 97.9 6.3E-06 1.4E-10 62.8 2.2 37 11-47 1-40 (45)
7 smart00614 ZnF_BED BED zinc fi 97.2 0.00025 5.3E-09 55.3 2.8 37 137-173 2-45 (50)
8 PF14372 DUF4413: Domain of un 96.6 0.0024 5.2E-08 57.8 4.4 64 604-669 1-67 (101)
9 PF10683 DBD_Tnp_Hermes: Herme 95.5 0.012 2.6E-07 47.2 2.8 38 305-342 10-47 (68)
10 smart00614 ZnF_BED BED zinc fi 90.3 0.25 5.4E-06 38.4 2.7 37 13-49 2-45 (50)
11 PF12017 Tnp_P_element: Transp 75.6 16 0.00034 38.5 9.1 121 326-463 83-231 (236)
12 PF13894 zf-C2H2_4: C2H2-type 68.0 3.6 7.8E-05 25.7 1.6 21 27-48 1-21 (24)
13 PF00872 Transposase_mut: Tran 59.5 4.1 8.9E-05 46.3 1.1 156 313-487 104-268 (381)
14 PF05605 zf-Di19: Drought indu 55.1 18 0.0004 28.4 3.8 45 150-196 2-49 (54)
15 smart00451 ZnF_U1 U1-like zinc 52.8 11 0.00023 26.4 1.9 24 150-174 3-26 (35)
16 PF10551 MULE: MULE transposas 51.6 81 0.0018 27.4 7.9 55 423-481 37-91 (93)
17 PLN03097 FHY3 Protein FAR-RED 50.7 1.9E+02 0.004 36.5 13.2 62 423-487 327-388 (846)
18 PF10276 zf-CHCC: Zinc-finger 49.7 12 0.00027 27.5 1.8 16 21-36 24-39 (40)
19 PF06220 zf-U1: U1 zinc finger 49.5 7.9 0.00017 28.2 0.8 26 150-175 3-29 (38)
20 PF12874 zf-met: Zinc-finger o 47.7 14 0.00031 23.6 1.8 23 27-50 1-23 (25)
21 PF00096 zf-C2H2: Zinc finger, 47.2 14 0.00031 23.0 1.7 21 27-48 1-21 (23)
22 PF13913 zf-C2HC_2: zinc-finge 45.4 11 0.00024 24.6 0.9 20 27-48 3-22 (25)
23 COG5188 PRP9 Splicing factor 3 43.5 26 0.00057 38.0 3.8 27 25-52 237-263 (470)
24 PF13465 zf-H2C2_2: Zinc-finge 40.4 20 0.00042 23.6 1.5 15 23-37 11-25 (26)
25 PF02748 PyrI_C: Aspartate car 38.1 21 0.00046 28.0 1.6 18 20-37 29-46 (52)
26 PF05605 zf-Di19: Drought indu 34.6 40 0.00087 26.4 2.8 45 26-72 2-49 (54)
27 PF04810 zf-Sec23_Sec24: Sec23 34.4 25 0.00055 25.8 1.5 17 20-36 18-34 (40)
28 PF12171 zf-C2H2_jaz: Zinc-fin 34.2 19 0.00042 23.7 0.8 23 27-50 2-24 (27)
29 PF01780 Ribosomal_L37ae: Ribo 33.4 22 0.00048 31.2 1.2 19 26-44 53-71 (90)
30 TIGR00280 L37a ribosomal prote 32.3 24 0.00052 31.0 1.3 18 26-43 53-70 (91)
31 KOG1832 HIV-1 Vpr-binding prot 28.9 41 0.00088 41.2 2.7 28 23-50 218-245 (1516)
32 PF01610 DDE_Tnp_ISL3: Transpo 28.4 1.1E+02 0.0025 32.1 6.0 92 386-485 1-95 (249)
33 COG1997 RPL43A Ribosomal prote 28.3 30 0.00066 30.0 1.1 17 25-41 52-68 (89)
34 KOG0562 Predicted hydrolase (H 27.3 35 0.00075 33.3 1.5 23 149-172 152-174 (184)
35 PTZ00255 60S ribosomal protein 27.2 33 0.00072 30.1 1.3 18 26-43 54-71 (90)
36 PRK03976 rpl37ae 50S ribosomal 27.2 34 0.00073 30.1 1.3 17 26-42 54-70 (90)
37 PF08209 Sgf11: Sgf11 (transcr 24.8 38 0.00082 23.9 0.9 22 149-172 3-24 (33)
38 COG4391 Uncharacterized protei 24.1 45 0.00097 26.9 1.3 16 22-37 44-59 (62)
39 KOG1074 Transcriptional repres 23.4 30 0.00065 42.0 0.4 27 26-53 353-379 (958)
40 PF12756 zf-C2H2_2: C2H2 type 22.5 51 0.0011 28.9 1.6 25 26-51 50-74 (100)
41 PF13909 zf-H2C2_5: C2H2-type 20.9 82 0.0018 19.9 1.9 21 151-173 1-21 (24)
42 PF13912 zf-C2H2_6: C2H2-type 20.2 68 0.0015 20.8 1.5 21 27-48 2-22 (27)
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=1.6e-35 Score=286.33 Aligned_cols=153 Identities=50% Similarity=0.929 Sum_probs=150.7
Q ss_pred CchhhhhhhHHHHHHHHHHHHHHHHHhhccccceEEEeeccccCCCCeEEEEEEEcCCceEEeeeeccCCCcccHHHHHH
Q 044693 351 PSSRLISGRFLQDEIATIKENLAEVKASWSITGCSVMADCWNDVQGRTLINFLVSCPRGLYFISSMDATDSIEDAANIFK 430 (897)
Q Consensus 351 PS~~~l~~~lL~~~~~~ik~~l~~~~~~~~~~~~SI~~D~Wtd~~~~~~l~~~v~~~~~~~fl~~vd~s~~~~tae~L~~ 430 (897)
||+++|++.+|++.+++++..++.++++|+.+||||++|+|||..++++|||+|+|+.|.+|++++++++..+|+++|++
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 HHHHHHHHhCCccEEEEEecCCccHHHHHHHHHHhcCCeeeeCchhHHHHHHHHHHhchhhHHHHHHHHHHHH
Q 044693 431 LLDKVVEEIGEENVVQVITKNTASFKAAGKMLEEKRRNLFWTPCAVDCIDRMLDDILNIKWVGECLDKAKKLT 503 (897)
Q Consensus 431 ~l~~vl~e~g~~nvv~ivtDnAsnm~~a~~lL~~~~p~i~~~~C~aH~LnLil~d~~k~~~v~~~l~k~~~I~ 503 (897)
+|+++++++|.+||++|||||++||.+|+++|++++|++||.||+||||||+++|+++++++++++.+|+.|+
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=3.1e-30 Score=312.62 Aligned_cols=464 Identities=16% Similarity=0.235 Sum_probs=344.3
Q ss_pred HHHHHHHHHHHHHHHhcCCCccccCCHHHHHHHHHHHhcCCCCCCCchhhhhhhHHHHHHHHHHHHHHHHHhhccccceE
Q 044693 306 KIRKEVISAICKFFYHAGIPSNAANSPYFHNMLELVGQYGQGLQGPSSRLISGRFLQDEIATIKENLAEVKASWSITGCS 385 (897)
Q Consensus 306 ~~~~~~~~~ia~~i~~~~iPfs~ve~~~F~~ll~~l~~~~~~~~~PS~~~l~~~lL~~~~~~ik~~l~~~~~~~~~~~~S 385 (897)
..+..+.+++++||+.+++||+.|+++.|+.++..+ .|.|.+|++.++...++...+.+.......+... .+.++
T Consensus 94 ~~~~~~~~~~~~~ii~~~lp~~~ve~~~~~~~~~~~---~P~~~~~~~~t~~~~~~~~~~~~k~~~~~~~~~~--~~~v~ 168 (641)
T KOG1121|consen 94 LDQKVIREAIARMIILHGLPLSTVEEPGFRELLKHL---NPNYKLPSRSTLEADVLKIYEAEKPKLKEILEKI--IGRVS 168 (641)
T ss_pred chHHHHHHHHHHHHHhcCCChhhccchhHHHHHHhc---CCCcccCChhHHHHHHHHHHHHHHHHHHHHHHcc--CCceE
Confidence 466788999999999999999999999999999998 4999999999999988888777766666555553 78899
Q ss_pred EEeeccccC-CCCeEEEEEEEcCCceE-----EeeeeccCCCcccHHHHHHHHHHHHHHhCC-ccEEEEEecCCccHHH-
Q 044693 386 VMADCWNDV-QGRTLINFLVSCPRGLY-----FISSMDATDSIEDAANIFKLLDKVVEEIGE-ENVVQVITKNTASFKA- 457 (897)
Q Consensus 386 I~~D~Wtd~-~~~~~l~~~v~~~~~~~-----fl~~vd~s~~~~tae~L~~~l~~vl~e~g~-~nvv~ivtDnAsnm~~- 457 (897)
+++|.|++. ....|+.+++|+.+..+ ++... -...|+++.|+..+..++.+|++ ++|..++.|| .+...
T Consensus 169 lT~d~w~~~~~~~~y~~~t~h~id~~~~l~~~il~~~--~~~~~~~~~i~~~~~~~~~~~~i~~kv~~~~~~n-~~~~~~ 245 (641)
T KOG1121|consen 169 LTTDLWSDSGTDEGYMVLTAHYIDRDWELHNKILSFC--IPPPHLGKALASVLNECLLEWGIEKKVFSITVDN-VNVSNI 245 (641)
T ss_pred EEEeeecCCCCCcceEEEEEEEeccchHhhhheeeee--cCCcchHHHHHHHHHHHHHhhChhheEEEEeecc-cchhHH
Confidence 999999987 67899999999977543 33333 33468999999999999999996 6888899999 33222
Q ss_pred --HHHHHHHhcC-----CeeeeCchhHHHHHHHHHHhchhhHHHHHHHHHHHHHHHhhcHHHHHHHHHHhcc-----Ccc
Q 044693 458 --AGKMLEEKRR-----NLFWTPCAVDCIDRMLDDILNIKWVGECLDKAKKLTRFIYNSTWLLNVMKKEFTK-----GQE 525 (897)
Q Consensus 458 --a~~lL~~~~p-----~i~~~~C~aH~LnLil~d~~k~~~v~~~l~k~~~I~~fi~~s~~~~~~~~k~~~~-----~~~ 525 (897)
....+....+ .+++++|++|.+++++++.++ ..+...+..+++.+.+++.+......|...... ...
T Consensus 246 ~~~~~~l~~~~~~~~~~~~~~~~C~~~~~~~~v~~~l~-~~~~~~l~~ir~~v~~vk~s~~~~~~f~~~~~~~~~~~~~~ 324 (641)
T KOG1121|consen 246 ETLRDHLKSSNALLLLGKFFHVRCFAHILNLIVQEGLK-EEFSSLLEKLRESVKYVKSSESRESSFEECQEQLGIPSDVL 324 (641)
T ss_pred HHhhHHHhhcccceecceeeeeehhhhhhhHHHHHHHH-HHHhHHHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccccc
Confidence 2222333222 356889999999999999998 788999999999999999999998888732221 112
Q ss_pred ccccccccccccHHhHHHHHHHHHHHHHHhhchhhhccccCCCchhhhHHHhhcCHHHHHHHHHHHHHHhhHHHHHHHhh
Q 044693 526 LLRPATTKFATSFNTLQSLLDQRIGLKRLFQSNKWLSSRFSKSDEGKEMEKIVLNLTFWKKMQYVKKSLGPIVQVLQKID 605 (897)
Q Consensus 526 L~~~~~TRW~S~~~~L~~ll~~~~~L~~~~~s~e~~~s~~~~~~~~~~~~~~i~~~~fW~~l~~l~~il~Pl~~~l~~l~ 605 (897)
++ +.++||++++.||.++++.+.+|..+...+. ......+...|..++.++.+|+||.++...++
T Consensus 325 ~~-d~~~~w~st~~ml~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~s 389 (641)
T KOG1121|consen 325 LL-DVSTRWNSTYLMLSRALKLKDAFSKLEEEDK--------------SYKSYPSDEEWNRLEELCDFLQPFSEVTKLLS 389 (641)
T ss_pred cc-cCCccchhHHHHHHHHHHHHHHHHHHHHhcc--------------ccccCcCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33 7999999999999999999999999876531 11223455569999999999999999999999
Q ss_pred CCCCcchhhhHHHHHHHHHHHHHHhCCCccc----cccHHHHHHHHHhhhccchhHHHHhhcCCCcccCC-------CCC
Q 044693 606 STESRSISFLYNDMYRAKLAIKAIHGDDARK----YGPFWSVIDSQWNSLFHHPLHVAAYFLNPSYRYRP-------DFI 674 (897)
Q Consensus 606 ~~~~~tis~v~~~m~~lk~~i~~~~~~~~~~----~~~~~~~i~~r~~~~~~~pl~~aa~~LdPr~ky~~-------~f~ 674 (897)
+..+|+...+++.+..+...+.......... ...+...++++|... ...+.++|.+|||||++.. .+.
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 9999999899999988887776544332222 233455667777622 3678899999999999742 111
Q ss_pred CC----HHHHHHHHHHH----HHhcc---Cch-------h-hhhhhcCchh-------HHHhh-cc-CC-ChH-------
Q 044693 675 MH----PEIIRGLNECI----VRLEV---DNG-------K-RISASMQIPD-------FVSAR-AD-FG-TDL------- 718 (897)
Q Consensus 675 ~~----~ei~~~l~~~i----~~l~~---~~~-------~-~~~~~~el~~-------y~~~~-~~-f~-~~~------- 718 (897)
.+ .+....+.+.+ ..+.. ... . .......... +.... +. -+ .++
T Consensus 469 ~~~~~~~~~~~~~~d~~~~l~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~y~~e~ 548 (641)
T KOG1121|consen 469 KDPEDAKEKVESVRDKLKKLLEEYKQLSPSNVSNSAHSWDLLDESPLEKDAFEYLFEPEVSIDSGSKSGKSELDHYLSES 548 (641)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHhccCCCCCCccccccccccccccccchhhhhhhHHHHHHhcCCCCCchHHHHHhhh
Confidence 01 11111222222 22221 000 0 0000000000 00000 00 00 011
Q ss_pred ---hhhccCCCChhhHHhhcCCChHHHHHHHHHHhccccCCccccccccccchhccccccchhhhhhchhhhhhhhhhh
Q 044693 719 ---AISTRSELDPAAWWQQHGISCLELQRIAIRILSQTCSSVGCEHTWSTYDQVHSRRRNCLSRKRWNDLTYVHYNLRL 794 (897)
Q Consensus 719 ---a~~~~~~~~Pl~wW~~~~~~~P~L~~lA~~iLsiP~SSa~~ER~FS~~~~I~t~~RnrL~~e~L~~Lv~l~~Nl~L 794 (897)
........++++||+.++.+||.|+.+|+++|++|+++++.|+.||..+++.++.|++|.+..+..|++.+.|++-
T Consensus 549 ~~~~~~~~~~~~~l~~w~~~~~~y~~ls~~a~d~l~~p~~~~~~e~~f~~~~~~~~~~r~~l~~~~~~~l~c~~~~~~~ 627 (641)
T KOG1121|consen 549 PRLLMPSFLDADVLQWWKGNGTRYPELSSMARDILSIPITSVASESSFSIGGRVLNKYRSRLLPENVQALICTRNWLPG 627 (641)
T ss_pred hhhhccccccccHHHHhhccCcccchHHHHHHHHHcCcccCccchhhcccCceecCchhccCCchhhHHhhchHhhhhh
Confidence 1123457899999999999999999999999999999999999999999999999999999999999999999873
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=99.54 E-value=2e-15 Score=133.20 Aligned_cols=69 Identities=32% Similarity=0.573 Sum_probs=57.2
Q ss_pred CCCChhhHHhhcCCChHHHHHHHHHHhccccCCccccccccccchhccccccchhhhhhchhhhhhhhh
Q 044693 724 SELDPAAWWQQHGISCLELQRIAIRILSQTCSSVGCEHTWSTYDQVHSRRRNCLSRKRWNDLTYVHYNL 792 (897)
Q Consensus 724 ~~~~Pl~wW~~~~~~~P~L~~lA~~iLsiP~SSa~~ER~FS~~~~I~t~~RnrL~~e~L~~Lv~l~~Nl 792 (897)
...+|++||+.++..||+|+++|+++|++|+||+.+||+||+++.+++..|++|+++++++|+||+.|+
T Consensus 18 ~~~~~l~~W~~~~~~fP~L~~lA~~~Lsip~ss~~~ER~FS~~~~~~~~~r~~l~~~~~~~l~~l~~nl 86 (86)
T PF05699_consen 18 SDMDPLEWWKQNSSRFPNLAKLARKYLSIPASSASSERSFSAMGKILTRNRNRLSPENVEALLFLKSNL 86 (86)
T ss_dssp -T--HHHHHHHTTTTSHHHHHHHHHHHTS-S-TTTTHHHHHHTHHHHH-TTT---HHHHHHHHHHHH--
T ss_pred CCCCHHHHHHHCchhchHHHHHHHHHHHhhccccccccccchhhcccccCccCCCHHHHHhhhceeccC
Confidence 367999999999999999999999999999999999999999999999999999999999999999985
No 4
>PF14291 DUF4371: Domain of unknown function (DUF4371)
Probab=99.27 E-value=1.2e-11 Score=130.34 Aligned_cols=139 Identities=19% Similarity=0.338 Sum_probs=110.1
Q ss_pred HHHHHHHhcCCCccc-------cCCHHHHHHHHHHHhcCCCCCC------C-----chhhhhhhHHHHHHHHHHHHHHHH
Q 044693 314 AICKFFYHAGIPSNA-------ANSPYFHNMLELVGQYGQGLQG------P-----SSRLISGRFLQDEIATIKENLAEV 375 (897)
Q Consensus 314 ~ia~~i~~~~iPfs~-------ve~~~F~~ll~~l~~~~~~~~~------P-----S~~~l~~~lL~~~~~~ik~~l~~~ 375 (897)
.+++|+..+|+||+- .+..+|++|++.+++++|...- | +.+++++.+ ..+...++..+.+.
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 467999999999974 3457999999999988776531 1 444555555 55556665543333
Q ss_pred HhhccccceEEEeeccccCCCCeEEEEEEEcCC--ce---EEeeeeccCCCcccHHHHHHHHHHHHHHhCC--ccEEEEE
Q 044693 376 KASWSITGCSVMADCWNDVQGRTLINFLVSCPR--GL---YFISSMDATDSIEDAANIFKLLDKVVEEIGE--ENVVQVI 448 (897)
Q Consensus 376 ~~~~~~~~~SI~~D~Wtd~~~~~~l~~~v~~~~--~~---~fl~~vd~s~~~~tae~L~~~l~~vl~e~g~--~nvv~iv 448 (897)
.. ..+|||++|+++|.+...+|+++|++.+ +. -||+++++.+ .||+.|++.|.++|+++|+ .+++|++
T Consensus 148 v~---~~~FSii~DettDis~~eQl~i~vRyv~~~~~i~E~Fl~f~~~~~--~ta~~l~~~i~~~L~~~~l~~~~~~gq~ 222 (235)
T PF14291_consen 148 VK---SKYFSIIVDETTDISNKEQLSICVRYVDKDGKIKERFLGFVELED--TTAESLFNAIKDVLEKLGLDLSNCRGQC 222 (235)
T ss_pred cc---ccceeeeeeccccccccchhhheeeeeccCcceeeeeeeeeccCC--ccHHHHHHHHHHHHHHcCCCHHHcCccc
Confidence 23 4689999999999999999999998765 32 4999999876 7999999999999999996 6999999
Q ss_pred ecCCccHHHH
Q 044693 449 TKNTASFKAA 458 (897)
Q Consensus 449 tDnAsnm~~a 458 (897)
||||+||.|.
T Consensus 223 yDgas~M~G~ 232 (235)
T PF14291_consen 223 YDGASNMSGK 232 (235)
T ss_pred ccChHhheec
Confidence 9999999874
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=98.37 E-value=1.6e-07 Score=71.62 Aligned_cols=38 Identities=42% Similarity=0.927 Sum_probs=29.8
Q ss_pred CCCCcccccccccCCceeecccccccc---chHHHHHHHHh
Q 044693 135 DPGWEHCVAQDEKKKRVKCNYCEKIIS---GGINRFKQHLA 172 (897)
Q Consensus 135 d~~w~h~~~~~~~~~~~~C~~C~~~~~---ggi~r~k~Hl~ 172 (897)
+++|+|+..++++...++|+||++++. ||+++|+.||.
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 579999998887778999999999984 49999999995
No 6
>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=97.89 E-value=6.3e-06 Score=62.78 Aligned_cols=37 Identities=49% Similarity=0.952 Sum_probs=29.1
Q ss_pred CCcccccccccCCCCeEEecccCceec---ccchhhhhhh
Q 044693 11 DPGWEHGIAQDERKKKVKCNYCGKIVS---GGIFRLKQHL 47 (897)
Q Consensus 11 d~~w~~~~~~~~~~~~~~c~~c~~~~~---g~i~r~k~hl 47 (897)
++.|+|-..++++.+.++|+||++++. ||+++|+.||
T Consensus 1 S~vW~~F~~~~~~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 1 SPVWKHFTKIPGDKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp GGCCCCCEE--GCSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CCccccEEEccCCcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 479999999886677999999999995 4999999999
No 7
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=97.21 E-value=0.00025 Score=55.27 Aligned_cols=37 Identities=41% Similarity=0.903 Sum_probs=29.9
Q ss_pred CCcccccc---cccCCceeeccccccc----cchHHHHHHHHhc
Q 044693 137 GWEHCVAQ---DEKKKRVKCNYCEKII----SGGINRFKQHLAR 173 (897)
Q Consensus 137 ~w~h~~~~---~~~~~~~~C~~C~~~~----~ggi~r~k~Hl~~ 173 (897)
+|+|+..+ +.++..++|+||++.+ .+|++.|+.||..
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 79999863 2234689999999997 2799999999973
No 8
>PF14372 DUF4413: Domain of unknown function (DUF4413)
Probab=96.62 E-value=0.0024 Score=57.82 Aligned_cols=64 Identities=14% Similarity=0.348 Sum_probs=48.9
Q ss_pred hhCCCCcchhhhHHHHHHHHHHHHHHhCCCc---cccccHHHHHHHHHhhhccchhHHHHhhcCCCccc
Q 044693 604 IDSTESRSISFLYNDMYRAKLAIKAIHGDDA---RKYGPFWSVIDSQWNSLFHHPLHVAAYFLNPSYRY 669 (897)
Q Consensus 604 l~~~~~~tis~v~~~m~~lk~~i~~~~~~~~---~~~~~~~~~i~~r~~~~~~~pl~~aa~~LdPr~ky 669 (897)
+++...||.+.+++.|..++..+.....++. .....+...++++|+.. ..++++|++||||||.
T Consensus 1 ~S~~~~pTsn~~f~~i~~i~~~l~~~~~~d~~l~~ma~~M~~KfdKYw~~~--~~~l~ia~ILDPR~Kl 67 (101)
T PF14372_consen 1 FSGSSYPTSNLYFHEIWKIKDLLRDWNNDDPDLKNMAKKMKEKFDKYWKDC--NLLLAIATILDPRFKL 67 (101)
T ss_pred CCCCCcCcHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHh--HHHHHHHHHhchHHHH
Confidence 3566789999999999999999987443322 23345667788999853 6778999999999985
No 9
>PF10683 DBD_Tnp_Hermes: Hermes transposase DNA-binding domain ; InterPro: IPR018473 This domain confers specific DNA-binding on Hermes transposase [].; PDB: 2BW3_B.
Probab=95.48 E-value=0.012 Score=47.21 Aligned_cols=38 Identities=11% Similarity=0.152 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccccCCHHHHHHHHHHH
Q 044693 305 KKIRKEVISAICKFFYHAGIPSNAANSPYFHNMLELVG 342 (897)
Q Consensus 305 ~~~~~~~~~~ia~~i~~~~iPfs~ve~~~F~~ll~~l~ 342 (897)
...++++.++++.|++.+..||++|++.+|++|++.+-
T Consensus 10 ~~~K~~~~~k~~qw~v~dcRpfsiv~gsGfk~la~~li 47 (68)
T PF10683_consen 10 EPDKKEATDKCTQWCVKDCRPFSIVSGSGFKKLAQFLI 47 (68)
T ss_dssp HHHHHHHHHHHHHHHHHCT--GGGGG-HHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHHHhcCCcceeeccccHHHHHHHHH
Confidence 35678899999999999999999999999999998874
No 10
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=90.34 E-value=0.25 Score=38.38 Aligned_cols=37 Identities=43% Similarity=0.881 Sum_probs=28.5
Q ss_pred cccccccc--cC-CCCeEEecccCceec----ccchhhhhhhcc
Q 044693 13 GWEHGIAQ--DE-RKKKVKCNYCGKIVS----GGIFRLKQHLAR 49 (897)
Q Consensus 13 ~w~~~~~~--~~-~~~~~~c~~c~~~~~----g~i~r~k~hl~~ 49 (897)
.|+|=..+ ++ ++...+|+||+++++ +|-+-|+.||..
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 58876653 22 335899999999993 789999999974
No 11
>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=75.55 E-value=16 Score=38.47 Aligned_cols=121 Identities=17% Similarity=0.196 Sum_probs=64.8
Q ss_pred ccccCCHHHHHHHHHHHhcCCCCCCCchhhhhhhH---------HHHHHHHHHHHHHHHHhhccccceEEEeeccccCCC
Q 044693 326 SNAANSPYFHNMLELVGQYGQGLQGPSSRLISGRF---------LQDEIATIKENLAEVKASWSITGCSVMADCWNDVQG 396 (897)
Q Consensus 326 fs~ve~~~F~~ll~~l~~~~~~~~~PS~~~l~~~l---------L~~~~~~ik~~l~~~~~~~~~~~~SI~~D~Wtd~~~ 396 (897)
+..+-...++-|.+ .+|.+||..+|++++ ++.....++. +.+.. ....|.|++|+-.=...
T Consensus 83 L~~~spr~Y~yL~k------k~~pLPs~rTL~r~l~~v~~~pGi~~~il~~l~~--~~~~~--~dr~CvL~fDEm~l~~~ 152 (236)
T PF12017_consen 83 LYKCSPRAYNYLRK------KGYPLPSVRTLQRWLSKVNIDPGILDFILDLLKN--KSMSE--EDRICVLSFDEMKLSPH 152 (236)
T ss_pred eeecChHHHHHHHH------cCCCCCCHHHHHHHHHhCCCCCCchHHHHHHHHH--ccCch--hccEEEEEEeEEEccce
Confidence 34455566666653 369999999998764 2222222221 11111 24568999998752221
Q ss_pred CeE--------------EEEEE-----EcCCceEEeeeeccCCCcccHHHHHHHHHHHHHHhCCccEEEEEecCCccHHH
Q 044693 397 RTL--------------INFLV-----SCPRGLYFISSMDATDSIEDAANIFKLLDKVVEEIGEENVVQVITKNTASFKA 457 (897)
Q Consensus 397 ~~~--------------l~~~v-----~~~~~~~fl~~vd~s~~~~tae~L~~~l~~vl~e~g~~nvv~ivtDnAsnm~~ 457 (897)
-.| ..++| .| ...+|..+ +. ..+++.|.++|. -|.+.|. +|+++|+|.++++.+
T Consensus 153 ~eYD~~~d~v~~~~~~~~v~mvrGl~~~W-KQpi~~~f-~t---~m~~~~l~~iI~-~l~~~g~-~VvAivsD~g~~N~~ 225 (236)
T PF12017_consen 153 LEYDPSRDEVNEPANYVQVFMVRGLFKSW-KQPIYFDF-DT---SMDADILKNIIE-KLHEIGY-NVVAIVSDMGSNNIS 225 (236)
T ss_pred eeeccccCcccChhhhhhHHHHHHHHhcC-CccEEEEe-cC---cCCHHHHHHHHH-HHHHCCC-EEEEEECCCCcchHH
Confidence 111 11111 11 12233333 21 345666655443 2333443 799999999999999
Q ss_pred HHHHHH
Q 044693 458 AGKMLE 463 (897)
Q Consensus 458 a~~lL~ 463 (897)
+++.|.
T Consensus 226 ~w~~Lg 231 (236)
T PF12017_consen 226 LWRELG 231 (236)
T ss_pred HHHHcC
Confidence 887653
No 12
>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=68.02 E-value=3.6 Score=25.73 Aligned_cols=21 Identities=33% Similarity=0.705 Sum_probs=15.6
Q ss_pred EEecccCceecccchhhhhhhc
Q 044693 27 VKCNYCGKIVSGGIFRLKQHLA 48 (897)
Q Consensus 27 ~~c~~c~~~~~g~i~r~k~hl~ 48 (897)
++|.+|++.+. ....++.|+.
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 5788888875
No 13
>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=59.47 E-value=4.1 Score=46.33 Aligned_cols=156 Identities=15% Similarity=0.129 Sum_probs=89.3
Q ss_pred HHHHHHHHhcCCCccccCCHHHHHHHHHHHhcCCCCCCCchhhhhhhHHHHHHHHHHHHHHHHHhhcccc-ceEEEeecc
Q 044693 313 SAICKFFYHAGIPSNAANSPYFHNMLELVGQYGQGLQGPSSRLISGRFLQDEIATIKENLAEVKASWSIT-GCSVMADCW 391 (897)
Q Consensus 313 ~~ia~~i~~~~iPfs~ve~~~F~~ll~~l~~~~~~~~~PS~~~l~~~lL~~~~~~ik~~l~~~~~~~~~~-~~SI~~D~W 391 (897)
+.++-.+|..|+.-+-+. ..+..+. | -...|..+++. +.+...+++......-+. .. +..|.+|+-
T Consensus 104 ~~~i~~ly~~G~Str~i~-----~~l~~l~--g--~~~~S~s~vSr-i~~~~~~~~~~w~~R~L~---~~~y~~l~iD~~ 170 (381)
T PF00872_consen 104 EELIISLYLKGVSTRDIE-----EALEELY--G--EVAVSKSTVSR-ITKQLDEEVEAWRNRPLE---SEPYPYLWIDGT 170 (381)
T ss_pred hhhhhhhhcccccccccc-----chhhhhh--c--ccccCchhhhh-hhhhhhhhHHHHhhhccc---cccccceeeeee
Confidence 444555688888776443 4555552 2 11267777754 445555555554433333 44 788999987
Q ss_pred ccCC-------CCeEEEEEEEcCCce-EEeeeeccCCCcccHHHHHHHHHHHHHHhCCccEEEEEecCCccHHHHHHHHH
Q 044693 392 NDVQ-------GRTLINFLVSCPRGL-YFISSMDATDSIEDAANIFKLLDKVVEEIGEENVVQVITKNTASFKAAGKMLE 463 (897)
Q Consensus 392 td~~-------~~~~l~~~v~~~~~~-~fl~~vd~s~~~~tae~L~~~l~~vl~e~g~~nvv~ivtDnAsnm~~a~~lL~ 463 (897)
.-.- +..++.++.-..+|. ..|+...... .+...-.+++. -|.+=|+..+.-+|+|+...+..| +.
T Consensus 171 ~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~--Es~~~W~~~l~-~L~~RGl~~~~lvv~Dg~~gl~~a---i~ 244 (381)
T PF00872_consen 171 YFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDR--ESAASWREFLQ-DLKERGLKDILLVVSDGHKGLKEA---IR 244 (381)
T ss_pred ecccccccccccchhhhhhhhhcccccceeeeecccC--CccCEeeecch-hhhhccccccceeecccccccccc---cc
Confidence 4321 122222222334554 3444332222 22222222332 345567888999999998887776 44
Q ss_pred HhcCCeeeeCchhHHHHHHHHHHh
Q 044693 464 EKRRNLFWTPCAVDCIDRMLDDIL 487 (897)
Q Consensus 464 ~~~p~i~~~~C~aH~LnLil~d~~ 487 (897)
+.+|..-|..|..|.+.-++..+-
T Consensus 245 ~~fp~a~~QrC~vH~~RNv~~~v~ 268 (381)
T PF00872_consen 245 EVFPGAKWQRCVVHLMRNVLRKVP 268 (381)
T ss_pred ccccchhhhhheechhhhhccccc
Confidence 578999999999998877766554
No 14
>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=55.07 E-value=18 Score=28.39 Aligned_cols=45 Identities=18% Similarity=0.307 Sum_probs=31.3
Q ss_pred ceeeccccccccchHHHHHHHHhcCCC---CcccCCCCCHHHHHHHHHHH
Q 044693 150 RVKCNYCEKIISGGINRFKQHLARIPG---EVAYCDKAPEDVYLKIKENM 196 (897)
Q Consensus 150 ~~~C~~C~~~~~ggi~r~k~Hl~~~~~---~v~~C~~vp~~v~~~~~~~~ 196 (897)
.+.|-||++.+. ...|..|+...+. ....||-+...+...|..-|
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 478999999544 7789999877653 34679988875554444333
No 15
>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=52.83 E-value=11 Score=26.42 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=19.8
Q ss_pred ceeeccccccccchHHHHHHHHhcC
Q 044693 150 RVKCNYCEKIISGGINRFKQHLARI 174 (897)
Q Consensus 150 ~~~C~~C~~~~~ggi~r~k~Hl~~~ 174 (897)
...|.+|++.+. +-..++.|+.|.
T Consensus 3 ~~~C~~C~~~~~-~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFT-DEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccC-CHHHHHHHHChH
Confidence 478999999998 666679999874
No 16
>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=51.62 E-value=81 Score=27.38 Aligned_cols=55 Identities=16% Similarity=0.146 Sum_probs=39.5
Q ss_pred ccHHHHHHHHHHHHHHhCCccEEEEEecCCccHHHHHHHHHHhcCCeeeeCchhHHHHH
Q 044693 423 EDAANIFKLLDKVVEEIGEENVVQVITKNTASFKAAGKMLEEKRRNLFWTPCAVDCIDR 481 (897)
Q Consensus 423 ~tae~L~~~l~~vl~e~g~~nvv~ivtDnAsnm~~a~~lL~~~~p~i~~~~C~aH~LnL 481 (897)
.+.+.+..++..+.+.++.. ...|++|....+..|.+ +.+|...+..|.-|.+.-
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 45555666666555544444 77899999988887754 467999999999998653
No 17
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=50.69 E-value=1.9e+02 Score=36.53 Aligned_cols=62 Identities=16% Similarity=0.141 Sum_probs=46.1
Q ss_pred ccHHHHHHHHHHHHHHhCCccEEEEEecCCccHHHHHHHHHHhcCCeeeeCchhHHHHHHHHHHh
Q 044693 423 EDAANIFKLLDKVVEEIGEENVVQVITKNTASFKAAGKMLEEKRRNLFWTPCAVDCIDRMLDDIL 487 (897)
Q Consensus 423 ~tae~L~~~l~~vl~e~g~~nvv~ivtDnAsnm~~a~~lL~~~~p~i~~~~C~aH~LnLil~d~~ 487 (897)
.+.+...=++...++..|-..=..|+||....|..|.. +.+|...+--|.-|.+.-+.+.+.
T Consensus 327 Et~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~---~VfP~t~Hr~C~wHI~~~~~e~L~ 388 (846)
T PLN03097 327 ESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVIS---EVFPNAHHCFFLWHILGKVSENLG 388 (846)
T ss_pred CchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHH---HHCCCceehhhHHHHHHHHHHHhh
Confidence 34555555555566666755567789999999988754 467999999999999988877665
No 18
>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=49.72 E-value=12 Score=27.54 Aligned_cols=16 Identities=38% Similarity=0.839 Sum_probs=12.1
Q ss_pred cCCCCeEEecccCcee
Q 044693 21 DERKKKVKCNYCGKIV 36 (897)
Q Consensus 21 ~~~~~~~~c~~c~~~~ 36 (897)
+...+.+.|.|||..|
T Consensus 24 ~~~~~~~~CpYCg~~y 39 (40)
T PF10276_consen 24 DDEPGPVVCPYCGTRY 39 (40)
T ss_dssp TTTTCEEEETTTTEEE
T ss_pred CCCCCeEECCCCCCEE
Confidence 4433479999999876
No 19
>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=49.48 E-value=7.9 Score=28.17 Aligned_cols=26 Identities=31% Similarity=0.511 Sum_probs=12.6
Q ss_pred ceeeccccccccchH-HHHHHHHhcCC
Q 044693 150 RVKCNYCEKIISGGI-NRFKQHLARIP 175 (897)
Q Consensus 150 ~~~C~~C~~~~~ggi-~r~k~Hl~~~~ 175 (897)
+.-|.||+.-+.... +--|.|+.|.+
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~k 29 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWK 29 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--TH
T ss_pred CeecccccceecCCChHHHHHhhccHH
Confidence 467999999985444 45599999864
No 20
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=47.74 E-value=14 Score=23.56 Aligned_cols=23 Identities=35% Similarity=0.554 Sum_probs=19.6
Q ss_pred EEecccCceecccchhhhhhhccc
Q 044693 27 VKCNYCGKIVSGGIFRLKQHLARM 50 (897)
Q Consensus 27 ~~c~~c~~~~~g~i~r~k~hl~~~ 50 (897)
+.|.-|++.|. +-.-++.|+.|.
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 57999999998 678899999874
No 21
>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=47.23 E-value=14 Score=23.01 Aligned_cols=21 Identities=43% Similarity=0.738 Sum_probs=15.8
Q ss_pred EEecccCceecccchhhhhhhc
Q 044693 27 VKCNYCGKIVSGGIFRLKQHLA 48 (897)
Q Consensus 27 ~~c~~c~~~~~g~i~r~k~hl~ 48 (897)
.+|.+|++.|. .-+-|+.|+.
T Consensus 1 y~C~~C~~~f~-~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFS-SKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEES-SHHHHHHHHH
T ss_pred CCCCCCCCccC-CHHHHHHHHh
Confidence 47999999997 4566777753
No 22
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=45.38 E-value=11 Score=24.61 Aligned_cols=20 Identities=35% Similarity=0.650 Sum_probs=17.0
Q ss_pred EEecccCceecccchhhhhhhc
Q 044693 27 VKCNYCGKIVSGGIFRLKQHLA 48 (897)
Q Consensus 27 ~~c~~c~~~~~g~i~r~k~hl~ 48 (897)
+.|.+||..| +..||..|+.
T Consensus 3 ~~C~~CgR~F--~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF--NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE--CHHHHHHHHH
Confidence 6899999999 5888888864
No 23
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=43.48 E-value=26 Score=38.00 Aligned_cols=27 Identities=30% Similarity=0.383 Sum_probs=22.5
Q ss_pred CeEEecccCceecccchhhhhhhccccC
Q 044693 25 KKVKCNYCGKIVSGGIFRLKQHLARMSG 52 (897)
Q Consensus 25 ~~~~c~~c~~~~~g~i~r~k~hl~~~~~ 52 (897)
..+=|-+|++-|+ .|+=+.+||-|...
T Consensus 237 ~~~YC~~C~r~f~-~~~VFe~Hl~gK~H 263 (470)
T COG5188 237 PKVYCVKCGREFS-RSKVFEYHLEGKRH 263 (470)
T ss_pred cceeeHhhhhHhh-hhHHHHHHHhhhhh
Confidence 4789999999987 68889999988653
No 24
>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=40.41 E-value=20 Score=23.56 Aligned_cols=15 Identities=53% Similarity=1.001 Sum_probs=12.4
Q ss_pred CCCeEEecccCceec
Q 044693 23 RKKKVKCNYCGKIVS 37 (897)
Q Consensus 23 ~~~~~~c~~c~~~~~ 37 (897)
+.+..+|.+|++.|.
T Consensus 11 ~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSEEESSSSEEES
T ss_pred CCCCCCCCCCcCeeC
Confidence 456799999999884
No 25
>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=38.09 E-value=21 Score=27.98 Aligned_cols=18 Identities=33% Similarity=0.960 Sum_probs=12.4
Q ss_pred ccCCCCeEEecccCceec
Q 044693 20 QDERKKKVKCNYCGKIVS 37 (897)
Q Consensus 20 ~~~~~~~~~c~~c~~~~~ 37 (897)
++.+...++|.||++.+.
T Consensus 29 ~~~~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 29 IDKEPIKLRCHYCERIIT 46 (52)
T ss_dssp EETTTCEEEETTT--EEE
T ss_pred EeCCCCEEEeeCCCCEec
Confidence 345556899999999985
No 26
>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=34.58 E-value=40 Score=26.43 Aligned_cols=45 Identities=24% Similarity=0.403 Sum_probs=31.3
Q ss_pred eEEecccCceecccchhhhhhhcccc---CCcccCCCCCHHHHHHHHHHh
Q 044693 26 KVKCNYCGKIVSGGIFRLKQHLARMS---GEVTHCEKVPDDVCLNMRKNL 72 (897)
Q Consensus 26 ~~~c~~c~~~~~g~i~r~k~hl~~~~---~~~~~c~~vp~~v~~~~~~~~ 72 (897)
...|.||++.+ ....|..|+.-.- +....||-....+...+..+|
T Consensus 2 ~f~CP~C~~~~--~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGKGF--SESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHL 49 (54)
T ss_pred CcCCCCCCCcc--CHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHH
Confidence 47899999943 4678999986532 235678887776666665555
No 27
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=34.42 E-value=25 Score=25.80 Aligned_cols=17 Identities=35% Similarity=0.698 Sum_probs=11.0
Q ss_pred ccCCCCeEEecccCcee
Q 044693 20 QDERKKKVKCNYCGKIV 36 (897)
Q Consensus 20 ~~~~~~~~~c~~c~~~~ 36 (897)
++.+.++|+|.+|+..-
T Consensus 18 ~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 18 FDDGGKTWICNFCGTKN 34 (40)
T ss_dssp EETTTTEEEETTT--EE
T ss_pred EcCCCCEEECcCCCCcC
Confidence 34455799999999754
No 28
>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=34.18 E-value=19 Score=23.70 Aligned_cols=23 Identities=35% Similarity=0.561 Sum_probs=18.5
Q ss_pred EEecccCceecccchhhhhhhccc
Q 044693 27 VKCNYCGKIVSGGIFRLKQHLARM 50 (897)
Q Consensus 27 ~~c~~c~~~~~g~i~r~k~hl~~~ 50 (897)
..|..|++.|. +-.-++.|+.+.
T Consensus 2 ~~C~~C~k~f~-~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFS-SENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBS-SHHHHHCCTTSH
T ss_pred CCcccCCCCcC-CHHHHHHHHccC
Confidence 56999999997 577788888663
No 29
>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=33.37 E-value=22 Score=31.20 Aligned_cols=19 Identities=37% Similarity=0.775 Sum_probs=14.8
Q ss_pred eEEecccCceecccchhhh
Q 044693 26 KVKCNYCGKIVSGGIFRLK 44 (897)
Q Consensus 26 ~~~c~~c~~~~~g~i~r~k 44 (897)
-|+|..|++.|.||.+-+.
T Consensus 53 IW~C~~C~~~~AGGAy~~~ 71 (90)
T PF01780_consen 53 IWKCKKCGKKFAGGAYTPS 71 (90)
T ss_dssp EEEETTTTEEEE-BSSSSS
T ss_pred EeecCCCCCEEeCCCcccc
Confidence 4999999999998876543
No 30
>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=32.30 E-value=24 Score=31.00 Aligned_cols=18 Identities=28% Similarity=0.683 Sum_probs=14.2
Q ss_pred eEEecccCceecccchhh
Q 044693 26 KVKCNYCGKIVSGGIFRL 43 (897)
Q Consensus 26 ~~~c~~c~~~~~g~i~r~ 43 (897)
-|+|..|++.|.||-+-.
T Consensus 53 IW~C~~C~~~~AGGAy~p 70 (91)
T TIGR00280 53 IWTCRKCGAKFAGGAYTP 70 (91)
T ss_pred EEEcCCCCCEEeCCcccc
Confidence 488888888888887663
No 31
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=28.88 E-value=41 Score=41.20 Aligned_cols=28 Identities=11% Similarity=0.307 Sum_probs=16.7
Q ss_pred CCCeEEecccCceecccchhhhhhhccc
Q 044693 23 RKKKVKCNYCGKIVSGGIFRLKQHLARM 50 (897)
Q Consensus 23 ~~~~~~c~~c~~~~~g~i~r~k~hl~~~ 50 (897)
++.-+--.-|...++.||.-+..|+-.+
T Consensus 218 g~~a~dv~~~~~~~~sg~mei~~~~~~~ 245 (1516)
T KOG1832|consen 218 GRNAEDVTVCLGKMKSGIMEIERETKNI 245 (1516)
T ss_pred cccchhhhhccchhcccceEEeecccch
Confidence 3444444456666666777777776443
No 32
>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=28.43 E-value=1.1e+02 Score=32.06 Aligned_cols=92 Identities=14% Similarity=0.114 Sum_probs=55.8
Q ss_pred EEeeccccCCCCe-EEEEEEEc--CCceEEeeeeccCCCcccHHHHHHHHHHHHHHhCCccEEEEEecCCccHHHHHHHH
Q 044693 386 VMADCWNDVQGRT-LINFLVSC--PRGLYFISSMDATDSIEDAANIFKLLDKVVEEIGEENVVQVITKNTASFKAAGKML 462 (897)
Q Consensus 386 I~~D~Wtd~~~~~-~l~~~v~~--~~~~~fl~~vd~s~~~~tae~L~~~l~~vl~e~g~~nvv~ivtDnAsnm~~a~~lL 462 (897)
|.+|++.-..+.. |+.+++.. ..+.+ +++.. ..+.+.|..-+.+....-...+|..|+.|..+.+..+..
T Consensus 1 lgiDE~~~~~g~~~y~t~~~d~~~~~~~i----l~i~~-~r~~~~l~~~~~~~~~~~~~~~v~~V~~Dm~~~y~~~~~-- 73 (249)
T PF01610_consen 1 LGIDEFAFRKGHRSYVTVVVDLDTDTGRI----LDILP-GRDKETLKDFFRSLYPEEERKNVKVVSMDMSPPYRSAIR-- 73 (249)
T ss_pred CeEeeeeeecCCcceeEEEEECccCCceE----EEEcC-CccHHHHHHHHHHhCccccccceEEEEcCCCcccccccc--
Confidence 4578887777666 66666654 23322 22222 234444444444332222457999999999999987643
Q ss_pred HHhcCCeeeeCchhHHHHHHHHH
Q 044693 463 EEKRRNLFWTPCAVDCIDRMLDD 485 (897)
Q Consensus 463 ~~~~p~i~~~~C~aH~LnLil~d 485 (897)
+.+|++..+----|.+.++-..
T Consensus 74 -~~~P~A~iv~DrFHvvk~~~~a 95 (249)
T PF01610_consen 74 -EYFPNAQIVADRFHVVKLANRA 95 (249)
T ss_pred -ccccccccccccchhhhhhhhc
Confidence 4578877666666777776543
No 33
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.26 E-value=30 Score=29.97 Aligned_cols=17 Identities=35% Similarity=0.811 Sum_probs=13.9
Q ss_pred CeEEecccCceecccch
Q 044693 25 KKVKCNYCGKIVSGGIF 41 (897)
Q Consensus 25 ~~~~c~~c~~~~~g~i~ 41 (897)
.-|+|.-||..|.||-+
T Consensus 52 GIW~C~kCg~~fAGgay 68 (89)
T COG1997 52 GIWKCRKCGAKFAGGAY 68 (89)
T ss_pred CeEEcCCCCCeeccccc
Confidence 46999999999987654
No 34
>KOG0562 consensus Predicted hydrolase (HIT family) [General function prediction only]
Probab=27.35 E-value=35 Score=33.29 Aligned_cols=23 Identities=22% Similarity=0.576 Sum_probs=20.5
Q ss_pred CceeeccccccccchHHHHHHHHh
Q 044693 149 KRVKCNYCEKIISGGINRFKQHLA 172 (897)
Q Consensus 149 ~~~~C~~C~~~~~ggi~r~k~Hl~ 172 (897)
...+|.+|+ .++-.|+.||.||-
T Consensus 152 ~dLrC~~Cq-~~~~~~~kLK~Hl~ 174 (184)
T KOG0562|consen 152 EDLRCWRCQ-TFGPHFPKLKAHLR 174 (184)
T ss_pred cceeehhhh-hcccccHHHHHHHH
Confidence 468999999 88889999999995
No 35
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=27.23 E-value=33 Score=30.10 Aligned_cols=18 Identities=39% Similarity=0.807 Sum_probs=14.8
Q ss_pred eEEecccCceecccchhh
Q 044693 26 KVKCNYCGKIVSGGIFRL 43 (897)
Q Consensus 26 ~~~c~~c~~~~~g~i~r~ 43 (897)
-|+|..|++.|.||-+..
T Consensus 54 IW~C~~C~~~~AGGAy~~ 71 (90)
T PTZ00255 54 IWRCKGCKKTVAGGAWTL 71 (90)
T ss_pred EEEcCCCCCEEeCCcccc
Confidence 489999999998887764
No 36
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=27.15 E-value=34 Score=30.10 Aligned_cols=17 Identities=29% Similarity=0.790 Sum_probs=13.2
Q ss_pred eEEecccCceecccchh
Q 044693 26 KVKCNYCGKIVSGGIFR 42 (897)
Q Consensus 26 ~~~c~~c~~~~~g~i~r 42 (897)
-|+|+.|++.+.||-+-
T Consensus 54 IW~C~~C~~~~AGGAy~ 70 (90)
T PRK03976 54 IWECRKCGAKFAGGAYT 70 (90)
T ss_pred EEEcCCCCCEEeCCccc
Confidence 48888888888877665
No 37
>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=24.81 E-value=38 Score=23.89 Aligned_cols=22 Identities=32% Similarity=0.721 Sum_probs=17.4
Q ss_pred CceeeccccccccchHHHHHHHHh
Q 044693 149 KRVKCNYCEKIISGGINRFKQHLA 172 (897)
Q Consensus 149 ~~~~C~~C~~~~~ggi~r~k~Hl~ 172 (897)
..+.|.-|+..+. .+||-.||.
T Consensus 3 ~~~~C~nC~R~v~--a~RfA~HLe 24 (33)
T PF08209_consen 3 PYVECPNCGRPVA--ASRFAPHLE 24 (33)
T ss_dssp -EEE-TTTSSEEE--GGGHHHHHH
T ss_pred CeEECCCCcCCcc--hhhhHHHHH
Confidence 4689999999887 689999994
No 38
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.12 E-value=45 Score=26.91 Aligned_cols=16 Identities=25% Similarity=0.596 Sum_probs=12.8
Q ss_pred CCCCeEEecccCceec
Q 044693 22 ERKKKVKCNYCGKIVS 37 (897)
Q Consensus 22 ~~~~~~~c~~c~~~~~ 37 (897)
+..+-+.|-||+..|.
T Consensus 44 g~~gev~CPYC~t~y~ 59 (62)
T COG4391 44 GDEGEVVCPYCSTRYR 59 (62)
T ss_pred CCCCcEecCccccEEE
Confidence 4456899999999874
No 39
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=23.42 E-value=30 Score=42.05 Aligned_cols=27 Identities=37% Similarity=0.698 Sum_probs=23.9
Q ss_pred eEEecccCceecccchhhhhhhccccCC
Q 044693 26 KVKCNYCGKIVSGGIFRLKQHLARMSGE 53 (897)
Q Consensus 26 ~~~c~~c~~~~~g~i~r~k~hl~~~~~~ 53 (897)
+-||+||+|+|+ .-++|+-||+--.|.
T Consensus 353 khkCr~Cakvfg-S~SaLqiHlRSHTGE 379 (958)
T KOG1074|consen 353 KHKCRFCAKVFG-SDSALQIHLRSHTGE 379 (958)
T ss_pred cchhhhhHhhcC-chhhhhhhhhccCCC
Confidence 678999999996 789999999988774
No 40
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=22.49 E-value=51 Score=28.88 Aligned_cols=25 Identities=24% Similarity=0.571 Sum_probs=20.9
Q ss_pred eEEecccCceecccchhhhhhhcccc
Q 044693 26 KVKCNYCGKIVSGGIFRLKQHLARMS 51 (897)
Q Consensus 26 ~~~c~~c~~~~~g~i~r~k~hl~~~~ 51 (897)
.++|.+|++.|. +...|+.|+....
T Consensus 50 ~~~C~~C~~~f~-s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFR-SREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EES-SHHHHHHHHHHTT
T ss_pred CCCCCccCCCCc-CHHHHHHHHcCcc
Confidence 599999999987 7999999998763
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=20.93 E-value=82 Score=19.85 Aligned_cols=21 Identities=38% Similarity=0.635 Sum_probs=14.4
Q ss_pred eeeccccccccchHHHHHHHHhc
Q 044693 151 VKCNYCEKIISGGINRFKQHLAR 173 (897)
Q Consensus 151 ~~C~~C~~~~~ggi~r~k~Hl~~ 173 (897)
.+|.+|.-... -..|+.|+..
T Consensus 1 y~C~~C~y~t~--~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS--KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES--HHHHHHHHHH
T ss_pred CCCCCCCCcCC--HHHHHHHHHh
Confidence 37999996554 6789999853
No 42
>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=20.23 E-value=68 Score=20.78 Aligned_cols=21 Identities=33% Similarity=0.743 Sum_probs=16.6
Q ss_pred EEecccCceecccchhhhhhhc
Q 044693 27 VKCNYCGKIVSGGIFRLKQHLA 48 (897)
Q Consensus 27 ~~c~~c~~~~~g~i~r~k~hl~ 48 (897)
.+|..|++.|. ...-|-.|+.
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 58999999997 5777777763
Done!