Query 004471
Match_columns 751
No_of_seqs 328 out of 1688
Neff 8.3
Searched_HMMs 46136
Date Thu Mar 28 23:57:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004471.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004471hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 1E-75 2.3E-80 676.4 46.5 472 173-669 70-623 (846)
2 PF10551 MULE: MULE transposas 99.8 2.8E-21 6E-26 169.0 6.8 90 376-471 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.7 1.1E-18 2.4E-23 191.1 5.3 223 277-549 113-350 (381)
4 PF03108 DBD_Tnp_Mut: MuDR fam 99.6 6E-16 1.3E-20 126.0 8.8 67 174-240 1-67 (67)
5 COG3328 Transposase and inacti 99.2 7.9E-11 1.7E-15 126.8 14.0 220 277-548 99-328 (379)
6 PF08731 AFT: Transcription fa 98.8 2.6E-08 5.7E-13 86.3 8.9 69 183-251 1-111 (111)
7 smart00575 ZnF_PMZ plant mutat 98.8 2.6E-09 5.7E-14 70.2 1.8 27 627-653 1-27 (28)
8 PF03101 FAR1: FAR1 DNA-bindin 98.7 4.5E-08 9.8E-13 84.9 6.4 61 191-252 1-90 (91)
9 PF04434 SWIM: SWIM zinc finge 98.0 5.3E-06 1.2E-10 59.8 2.9 30 622-651 10-39 (40)
10 PF00098 zf-CCHC: Zinc knuckle 96.0 0.0044 9.6E-08 36.1 1.7 18 732-749 1-18 (18)
11 PF15288 zf-CCHC_6: Zinc knuck 95.3 0.0082 1.8E-07 42.4 1.2 19 731-749 1-21 (40)
12 PF01610 DDE_Tnp_ISL3: Transpo 94.6 0.082 1.8E-06 54.8 7.1 94 372-475 1-97 (249)
13 PF06782 UPF0236: Uncharacteri 93.9 0.5 1.1E-05 53.7 11.9 132 409-547 235-376 (470)
14 PF13696 zf-CCHC_2: Zinc knuck 93.2 0.05 1.1E-06 36.5 1.4 23 728-750 5-27 (32)
15 PF03106 WRKY: WRKY DNA -bindi 92.7 0.25 5.3E-06 38.9 5.0 40 211-250 20-59 (60)
16 PF13610 DDE_Tnp_IS240: DDE do 92.5 0.059 1.3E-06 50.6 1.5 81 369-457 1-81 (140)
17 PF04684 BAF1_ABF1: BAF1 / ABF 92.3 0.29 6.2E-06 53.4 6.4 58 176-233 21-79 (496)
18 PRK14702 insertion element IS2 90.4 16 0.00036 38.1 17.3 148 263-446 11-164 (262)
19 smart00774 WRKY DNA binding do 87.0 0.97 2.1E-05 35.4 3.9 38 212-249 21-59 (59)
20 PF00665 rve: Integrase core d 85.5 3.5 7.6E-05 36.8 7.6 76 369-449 6-82 (120)
21 PF04500 FLYWCH: FLYWCH zinc f 84.9 1.9 4.1E-05 33.7 4.9 46 200-249 14-62 (62)
22 smart00343 ZnF_C2HC zinc finge 84.0 0.58 1.3E-05 30.0 1.2 17 733-749 1-17 (26)
23 PRK09409 IS2 transposase TnpB; 82.4 29 0.00064 37.0 14.2 146 265-446 52-203 (301)
24 PF03050 DDE_Tnp_IS66: Transpo 80.9 3.7 8E-05 43.0 6.6 85 369-476 67-156 (271)
25 PHA02517 putative transposase 80.4 17 0.00037 38.1 11.5 151 264-446 30-181 (277)
26 PF14392 zf-CCHC_4: Zinc knuck 79.3 0.74 1.6E-05 34.6 0.5 20 730-749 30-49 (49)
27 COG5179 TAF1 Transcription ini 77.8 1.3 2.8E-05 49.9 1.9 25 725-749 931-957 (968)
28 PF13565 HTH_32: Homeodomain-l 77.7 4.5 9.7E-05 33.3 4.8 41 264-304 34-76 (77)
29 COG3316 Transposase and inacti 76.2 22 0.00048 35.6 9.8 83 369-460 70-152 (215)
30 KOG1832 HIV-1 Vpr-binding prot 74.8 2.4 5.3E-05 49.8 3.1 31 72-102 1405-1435(1516)
31 PF04937 DUF659: Protein of un 68.7 37 0.0008 32.3 9.3 89 384-476 46-138 (153)
32 COG5431 Uncharacterized metal- 68.2 8.8 0.00019 33.3 4.3 30 616-647 41-75 (117)
33 PF02178 AT_hook: AT hook moti 61.8 3.6 7.8E-05 21.9 0.5 9 710-718 2-10 (13)
34 PF13917 zf-CCHC_3: Zinc knuck 55.4 6.9 0.00015 28.4 1.2 19 730-748 3-21 (42)
35 smart00384 AT_hook DNA binding 49.0 10 0.00022 24.2 1.1 12 710-721 2-13 (26)
36 KOG1832 HIV-1 Vpr-binding prot 48.8 16 0.00035 43.4 3.5 17 92-108 1416-1432(1516)
37 PRK09335 30S ribosomal protein 48.1 14 0.0003 31.8 2.1 27 706-739 2-28 (95)
38 COG5082 AIR1 Arginine methyltr 47.9 9.2 0.0002 37.3 1.2 17 732-748 98-114 (190)
39 PF13592 HTH_33: Winged helix- 43.1 38 0.00083 26.5 3.9 29 277-305 3-31 (60)
40 PLN00186 ribosomal protein S26 42.8 18 0.0004 31.7 2.1 27 706-739 2-28 (109)
41 PF12762 DDE_Tnp_IS1595: ISXO2 42.4 59 0.0013 30.5 5.9 71 370-449 4-89 (151)
42 PTZ00172 40S ribosomal protein 41.9 19 0.00041 31.6 2.1 27 706-739 2-28 (108)
43 PHA00689 hypothetical protein 39.8 16 0.00035 26.9 1.2 15 727-741 13-27 (62)
44 COG4715 Uncharacterized conser 36.3 79 0.0017 36.1 6.3 35 619-655 61-99 (587)
45 PRK13907 rnhA ribonuclease H; 35.6 1.3E+02 0.0028 27.2 6.9 77 371-453 3-80 (128)
46 PF14201 DUF4318: Domain of un 33.5 65 0.0014 26.6 3.9 31 181-211 12-42 (74)
47 PRK12286 rpmF 50S ribosomal pr 32.9 38 0.00083 26.4 2.3 32 706-739 4-35 (57)
48 PF13877 RPAP3_C: Potential Mo 29.7 41 0.00089 28.9 2.3 34 490-523 5-38 (94)
49 COG3915 Uncharacterized protei 27.7 1.9E+02 0.0042 26.7 6.1 43 354-398 91-135 (155)
50 PF01283 Ribosomal_S26e: Ribos 25.9 43 0.00093 29.9 1.7 27 706-739 2-28 (113)
51 COG4830 RPS26B Ribosomal prote 25.2 44 0.00096 28.7 1.6 27 706-739 2-28 (108)
52 PRK14892 putative transcriptio 24.1 59 0.0013 28.5 2.2 10 729-738 19-28 (99)
53 COG5082 AIR1 Arginine methyltr 23.8 37 0.00081 33.2 1.1 20 730-749 59-78 (190)
54 PF01498 HTH_Tnp_Tc3_2: Transp 23.8 60 0.0013 26.1 2.2 35 269-304 4-38 (72)
55 TIGR01031 rpmF_bact ribosomal 23.4 78 0.0017 24.5 2.5 42 706-748 2-43 (55)
56 PTZ00368 universal minicircle 22.5 51 0.0011 31.0 1.7 18 732-749 78-95 (148)
57 PF13719 zinc_ribbon_5: zinc-r 22.4 45 0.00098 23.3 1.0 14 726-739 20-33 (37)
58 PF12353 eIF3g: Eukaryotic tra 22.0 59 0.0013 29.9 2.0 22 727-749 102-123 (128)
59 PTZ00368 universal minicircle 22.0 51 0.0011 31.0 1.6 20 731-750 52-71 (148)
60 COG5222 Uncharacterized conser 21.9 58 0.0013 33.8 2.0 26 725-750 170-195 (427)
61 COG0333 RpmF Ribosomal protein 21.5 50 0.0011 25.7 1.1 41 706-748 4-44 (57)
62 COG4279 Uncharacterized conser 21.0 54 0.0012 33.5 1.6 23 627-652 125-147 (266)
63 PF14787 zf-CCHC_5: GAG-polypr 20.7 63 0.0014 22.6 1.3 18 732-749 3-20 (36)
64 COG4888 Uncharacterized Zn rib 20.3 74 0.0016 27.7 2.0 9 730-738 21-29 (104)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=1e-75 Score=676.38 Aligned_cols=472 Identities=15% Similarity=0.269 Sum_probs=381.7
Q ss_pred CCCccccCCeeCCHHHHHHHHHHHHHhcCeeEEEEeecCcE-------EEEEec--------------------------
Q 004471 173 SAFELAVGQEFPDVKSCRRALRDTAIALHFEMQTIKSDKTR-------FTAKCA-------------------------- 219 (751)
Q Consensus 173 ~~~~~~vG~~F~s~ee~~~a~~~yAi~~gf~i~~~ks~~~r-------~~~~C~-------------------------- 219 (751)
...+|.+||+|+|.++|+.||+.||...||++|+.++.+++ .+++|+
T Consensus 70 ~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~ 149 (846)
T PLN03097 70 TNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPEN 149 (846)
T ss_pred CCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccc
Confidence 55689999999999999999999999999999986554322 345664
Q ss_pred --------CCCCceEEEEEEcCCCCcEEEEeecCCccccCccccCcccchhhHHhhhhhhhhccCCCCChHHHHHHHHHH
Q 004471 220 --------AEGCPWRIHAAKLPGVPTFTIRTIHESHTCGGISHLGHQQASVQWVANSVEQRLRENPNYKPKEILEEIHRV 291 (751)
Q Consensus 220 --------~~gC~w~i~a~~~~~~~~w~I~~~~~~Hnc~~~~~~~~r~~ss~~ia~~~~~~i~~~~~~~~~~I~~~l~~~ 291 (751)
++||||+|++++. ..|.|+|+.+..+|||+..+......-+.+ +-..+...+....++.. ++..
T Consensus 150 ~~~rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~-~~~~~~~~~~~~~~v~~------~~~d 221 (846)
T PLN03097 150 GTGRRSCAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVSEQTRK-MYAAMARQFAEYKNVVG------LKND 221 (846)
T ss_pred ccccccccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccchhhhh-hHHHHHhhhhccccccc------cchh
Confidence 3579999999884 458999999999999987643211000001 10000000000000000 0000
Q ss_pred hCCccCHHHHHHHHHHHHHHHhcchHhhhccHHHHHHHHHhcCCCcEEEEEccCCcCceeEEEEEehhhHHHHHhhcCCc
Q 004471 292 HGITLSYKQAWRGKERIMAAMRGSFEEGYRLLPQYCEQVKRTNPGSIASVYGNPADNCFQRLFISFQASIYGFLNACRPL 371 (751)
Q Consensus 292 ~g~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~v~~~~~~~~f~~lf~~~~~~~~~~~~~~~~V 371 (751)
........|. ++...|| .+.|+.||.+++..||+|+|.|++| +++++++|||+++.|+.+| .+|+||
T Consensus 222 -----~~~~~~~~r~--~~~~~gD----~~~ll~yf~~~q~~nP~Ffy~~qlD-e~~~l~niFWaD~~sr~~Y-~~FGDv 288 (846)
T PLN03097 222 -----SKSSFDKGRN--LGLEAGD----TKILLDFFTQMQNMNSNFFYAVDLG-EDQRLKNLFWVDAKSRHDY-GNFSDV 288 (846)
T ss_pred -----hcchhhHHHh--hhcccch----HHHHHHHHHHHHhhCCCceEEEEEc-cCCCeeeEEeccHHHHHHH-HhcCCE
Confidence 0000111121 2222343 4789999999999999999999996 8999999999999999999 999999
Q ss_pred eeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCccccccccc
Q 004471 372 LGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVDGVE 451 (751)
Q Consensus 372 v~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~Ai~ 451 (751)
|.||+||+||+|++||+.|+|+|+|+++++|||||+.+|+.++|.|+|++|+++|+ +.+|.+||||++.+|.+||+
T Consensus 289 V~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~----gk~P~tIiTDqd~am~~AI~ 364 (846)
T PLN03097 289 VSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMG----GQAPKVIITDQDKAMKSVIS 364 (846)
T ss_pred EEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhC----CCCCceEEecCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999 57899999999999999999
Q ss_pred ccCCCCceecchhhHHHHHHHHcCc-----hhHHHHHHHHHH-hcCHHHHHHHHHHHHHh-cHHHHHHHhhc--CCCcee
Q 004471 452 ANFPTAFHGFCMRHLSESFRKEFNN-----TILVNLLWEAAH-ALTVIEFEAKILEIEEI-SQDAAYWIRRI--PPRLWA 522 (751)
Q Consensus 452 ~vfP~a~h~~C~~Hi~~n~~~~~~~-----~~~~~~~~~~~~-a~t~~eF~~~~~~l~~~-~~~~~~~L~~~--~~~~Wa 522 (751)
+|||+|.|++|+|||++|+.+++.. +.|...|+.|++ +.+++||+..|..|.+. +...++||..+ .|++||
T Consensus 365 ~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWa 444 (846)
T PLN03097 365 EVFPNAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWV 444 (846)
T ss_pred HHCCCceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhh
Confidence 9999999999999999999998863 589999999988 88999999999998865 77899999999 699999
Q ss_pred ecccCCCccccc-ccchhhHHHHHHhhc--cCCcHHHHHHHHHHHHHHHHHHhhhh-----------------hcccccc
Q 004471 523 TAYFEGTRFGHL-TANIVESLNSWILEA--SGLPIIQMMECIRRQLMTWFNERRET-----------------SMQWTSI 582 (751)
Q Consensus 523 ~ay~~~~~~g~~-Ttn~~ES~n~~lk~~--r~~pi~~lle~i~~~l~~~~~~r~~~-----------------s~~~~~~ 582 (751)
++|+++.+|+.| ||+++||+|++|++. +..+|..|++++.+.+..++.+..+. ..+.+.+
T Consensus 445 paY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~i 524 (846)
T PLN03097 445 PTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGV 524 (846)
T ss_pred HHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHH
Confidence 999999998766 788999999999985 57899999999988877665544332 1244679
Q ss_pred cchHHHHHHHHHHHHhcccEEEecc----CceEEEEe--cCcceEEeee----CccccCCcccccCCccccHHHHHHhcC
Q 004471 583 LVPSAERRVAEALERARTYQVLRAN----EAEFEVIS--HEGTNIVDIR----NRCCLCRGWQLYGLPCAHAVAALLSCR 652 (751)
Q Consensus 583 ~tp~~~~~~~~~~~~a~~~~V~~~~----~~~f~V~~--~~~~~~V~l~----~~~CsC~~~~~~GiPC~H~lavl~~~~ 652 (751)
|||.+|++|++++..+..|.+...+ ..+|.|.. ....|.|..+ ..+|+|++|+..||||+|||.||...+
T Consensus 525 YT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~ 604 (846)
T PLN03097 525 YTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQ 604 (846)
T ss_pred hHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcC
Confidence 9999999999999999888876543 25788876 3456777543 579999999999999999999999999
Q ss_pred C--Ccccccccccchhccc
Q 004471 653 Q--NVHRFTESCFTVATYR 669 (751)
Q Consensus 653 ~--~~~~yv~~~yt~~~~~ 669 (751)
+ .|+.||.+|||+++-.
T Consensus 605 v~~IP~~YILkRWTKdAK~ 623 (846)
T PLN03097 605 LSAIPSQYILKRWTKDAKS 623 (846)
T ss_pred cccCchhhhhhhchhhhhh
Confidence 8 5999999999988753
No 2
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.84 E-value=2.8e-21 Score=169.00 Aligned_cols=90 Identities=34% Similarity=0.732 Sum_probs=85.9
Q ss_pred eeeeccccCcceEE---EEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccccccc
Q 004471 376 RTFLKSKYLGTLLL---ATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVDGVEA 452 (751)
Q Consensus 376 ~T~~~~~y~~~ll~---~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~Ai~~ 452 (751)
|||+||+| ++++. ++|+|++|+.+|+||+++++|+.++|.|||+.+++.+.. . |.+||||++.|+.+||++
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~----~-p~~ii~D~~~~~~~Ai~~ 74 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQ----K-PKVIISDFDKALINAIKE 74 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcccc----C-ceeeeccccHHHHHHHHH
Confidence 79999999 98886 999999999999999999999999999999999999883 4 999999999999999999
Q ss_pred cCCCCceecchhhHHHHHH
Q 004471 453 NFPTAFHGFCMRHLSESFR 471 (751)
Q Consensus 453 vfP~a~h~~C~~Hi~~n~~ 471 (751)
+||++.|++|.||+.+|++
T Consensus 75 vfP~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 75 VFPDARHQLCLFHILRNIK 93 (93)
T ss_pred HCCCceEehhHHHHHHhhC
Confidence 9999999999999999984
No 3
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.74 E-value=1.1e-18 Score=191.10 Aligned_cols=223 Identities=23% Similarity=0.260 Sum_probs=180.6
Q ss_pred CCCChHHHHHHHHHHhC-CccCHHHHHHHHHHHHHHHhcchHhhhccHHHHHHHHHhcCCCcEEEEEccCCcCceeEEEE
Q 004471 277 PNYKPKEILEEIHRVHG-ITLSYKQAWRGKERIMAAMRGSFEEGYRLLPQYCEQVKRTNPGSIASVYGNPADNCFQRLFI 355 (751)
Q Consensus 277 ~~~~~~~I~~~l~~~~g-~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~v~~~~~~~~f~~lf~ 355 (751)
.|++.++|.+.++.-+| ..+|.+++.|..+.+.+.+. .|... .
T Consensus 113 ~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~-----------~w~~R----~--------------------- 156 (381)
T PF00872_consen 113 KGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVE-----------AWRNR----P--------------------- 156 (381)
T ss_pred cccccccccchhhhhhcccccCchhhhhhhhhhhhhHH-----------HHhhh----c---------------------
Confidence 47889999999999899 77888888877655543221 11110 0
Q ss_pred EehhhHHHHHhhc-CCceeeeeeeecccc-----CcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccc
Q 004471 356 SFQASIYGFLNAC-RPLLGLDRTFLKSKY-----LGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEIN 429 (751)
Q Consensus 356 ~~~~~~~~~~~~~-~~Vv~iD~T~~~~~y-----~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~ 429 (751)
+... =++|+|||+|.+-+. +..+++++|+|.+|+-.+||+.+...|+.++|.-||+.|++.
T Consensus 157 ---------L~~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R---- 223 (381)
T PF00872_consen 157 ---------LESEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER---- 223 (381)
T ss_pred ---------cccccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc----
Confidence 0222 268999999998764 356899999999999999999999999999999999999876
Q ss_pred cCCCCceEEeecCcccccccccccCCCCceecchhhHHHHHHHHcCch---hHHHHHHHHHHhcCHHHHHHHHHHHHH--
Q 004471 430 TENMPRLTILSDRQKGIVDGVEANFPTAFHGFCMRHLSESFRKEFNNT---ILVNLLWEAAHALTVIEFEAKILEIEE-- 504 (751)
Q Consensus 430 ~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~---~~~~~~~~~~~a~t~~eF~~~~~~l~~-- 504 (751)
|...|..||+|..+||.+||+++||.+.++.|.+|+++|+.++++.+ .+...++.+..+.+.+++...++.+.+
T Consensus 224 -Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~ 302 (381)
T PF00872_consen 224 -GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKW 302 (381)
T ss_pred -cccccceeeccccccccccccccccchhhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhccccc
Confidence 23568999999999999999999999999999999999999998753 667778888778888888888888765
Q ss_pred --hcHHHHHHHhhcCCCceeecccCCCcc-cccccchhhHHHHHHhhc
Q 004471 505 --ISQDAAYWIRRIPPRLWATAYFEGTRF-GHLTANIVESLNSWILEA 549 (751)
Q Consensus 505 --~~~~~~~~L~~~~~~~Wa~ay~~~~~~-g~~Ttn~~ES~n~~lk~~ 549 (751)
.+|.+.++|.+...+.|+..-|+...+ -..|||.+||+|+.||..
T Consensus 303 ~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr 350 (381)
T PF00872_consen 303 EKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRR 350 (381)
T ss_pred ccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhh
Confidence 488999999988777777665665544 456999999999999873
No 4
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=99.64 E-value=6e-16 Score=125.97 Aligned_cols=67 Identities=46% Similarity=0.794 Sum_probs=65.1
Q ss_pred CCccccCCeeCCHHHHHHHHHHHHHhcCeeEEEEeecCcEEEEEecCCCCceEEEEEEcCCCCcEEE
Q 004471 174 AFELAVGQEFPDVKSCRRALRDTAIALHFEMQTIKSDKTRFTAKCAAEGCPWRIHAAKLPGVPTFTI 240 (751)
Q Consensus 174 ~~~~~vG~~F~s~ee~~~a~~~yAi~~gf~i~~~ks~~~r~~~~C~~~gC~w~i~a~~~~~~~~w~I 240 (751)
+|.|.+||+|+|++||+.||..||++.+|.+++.+|++.|++++|...||||+|+|++.++++.|+|
T Consensus 1 n~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 1 NPELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred CCccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 5789999999999999999999999999999999999999999999999999999999999999986
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.24 E-value=7.9e-11 Score=126.76 Aligned_cols=220 Identities=21% Similarity=0.178 Sum_probs=162.6
Q ss_pred CCCChHHHHHHHHHHhCCccCHHHHHHHHHHHHHHHhcchHhhhccHHHHHHHHHhcCCCcEEEEEccCCcCceeEEEEE
Q 004471 277 PNYKPKEILEEIHRVHGITLSYKQAWRGKERIMAAMRGSFEEGYRLLPQYCEQVKRTNPGSIASVYGNPADNCFQRLFIS 356 (751)
Q Consensus 277 ~~~~~~~I~~~l~~~~g~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~v~~~~~~~~f~~lf~~ 356 (751)
.+++++++...+++.++..++-..+.+.-.+.++ .+..++.+-.
T Consensus 99 ~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e---------------~v~~~~~r~l--------------------- 142 (379)
T COG3328 99 KGVTTREIEALLEELYGHKVSPSVISVVTDRLDE---------------KVKAWQNRPL--------------------- 142 (379)
T ss_pred cCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHH---------------HHHHHHhccc---------------------
Confidence 4789999999999888876766665554444333 2222222111
Q ss_pred ehhhHHHHHhhcCCceeeeeeeeccc--cCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCC
Q 004471 357 FQASIYGFLNACRPLLGLDRTFLKSK--YLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMP 434 (751)
Q Consensus 357 ~~~~~~~~~~~~~~Vv~iD~T~~~~~--y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~ 434 (751)
..-+++++|++|++-+ -+..+++++|++.+|+-..+++.+-..|+ ..|.-||..|+...- ..
T Consensus 143 ----------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl-----~~ 206 (379)
T COG3328 143 ----------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGL-----SD 206 (379)
T ss_pred ----------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccc-----cc
Confidence 1236889999999988 46689999999999999999999999999 999988888876622 24
Q ss_pred ceEEeecCcccccccccccCCCCceecchhhHHHHHHHHcCchhH---HHHHHHHHHhcCHHHHHHHHHHHHH----hcH
Q 004471 435 RLTILSDRQKGIVDGVEANFPTAFHGFCMRHLSESFRKEFNNTIL---VNLLWEAAHALTVIEFEAKILEIEE----ISQ 507 (751)
Q Consensus 435 p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~~~---~~~~~~~~~a~t~~eF~~~~~~l~~----~~~ 507 (751)
...+++|..+++.+||..+||.+.++.|..|+.+|+..+...+.. ...+..+..+.+.++....|..+.+ .+|
T Consensus 207 v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP 286 (379)
T COG3328 207 VLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYP 286 (379)
T ss_pred eeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcc
Confidence 566788999999999999999999999999999999998876533 3344444557777777777766544 477
Q ss_pred HHHHHHhhcCCCceeecccC-CCcccccccchhhHHHHHHhh
Q 004471 508 DAAYWIRRIPPRLWATAYFE-GTRFGHLTANIVESLNSWILE 548 (751)
Q Consensus 508 ~~~~~L~~~~~~~Wa~ay~~-~~~~g~~Ttn~~ES~n~~lk~ 548 (751)
....|+.+..-+.|...-|. ..+--..|||..|++|+.++.
T Consensus 287 ~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 287 AILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred hHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 77777777644444433333 223346799999999998764
No 6
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=98.79 E-value=2.6e-08 Score=86.27 Aligned_cols=69 Identities=22% Similarity=0.339 Sum_probs=65.0
Q ss_pred eCCHHHHHHHHHHHHHhcCeeEEEEeecCcEEEEEecC------------------------------------------
Q 004471 183 FPDVKSCRRALRDTAIALHFEMQTIKSDKTRFTAKCAA------------------------------------------ 220 (751)
Q Consensus 183 F~s~ee~~~a~~~yAi~~gf~i~~~ks~~~r~~~~C~~------------------------------------------ 220 (751)
|.+++|++-+|+.++...||+|.+-+|+.+.+.++|..
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k~t~srk 80 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKKIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKKRTKSRK 80 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCceEEEEEecCCCcccccccccccccccccccccccccccccccCCcccccc
Confidence 88999999999999999999999999999999999962
Q ss_pred CCCceEEEEEEcCCCCcEEEEeecCCccccC
Q 004471 221 EGCPWRIHAAKLPGVPTFTIRTIHESHTCGG 251 (751)
Q Consensus 221 ~gC~w~i~a~~~~~~~~w~I~~~~~~Hnc~~ 251 (751)
.+|||+|+|......+.|.|..++..|+|+.
T Consensus 81 ~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 81 NTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 4799999999999999999999999999973
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.78 E-value=2.6e-09 Score=70.18 Aligned_cols=27 Identities=44% Similarity=0.934 Sum_probs=25.1
Q ss_pred ccccCCcccccCCccccHHHHHHhcCC
Q 004471 627 RCCLCRGWQLYGLPCAHAVAALLSCRQ 653 (751)
Q Consensus 627 ~~CsC~~~~~~GiPC~H~lavl~~~~~ 653 (751)
++|||++|+..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998875
No 8
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=98.66 E-value=4.5e-08 Score=84.91 Aligned_cols=61 Identities=20% Similarity=0.243 Sum_probs=53.8
Q ss_pred HHHHHHHHhcCeeEEEEeecCc-------EEEEEecC----------------------CCCceEEEEEEcCCCCcEEEE
Q 004471 191 RALRDTAIALHFEMQTIKSDKT-------RFTAKCAA----------------------EGCPWRIHAAKLPGVPTFTIR 241 (751)
Q Consensus 191 ~a~~~yAi~~gf~i~~~ks~~~-------r~~~~C~~----------------------~gC~w~i~a~~~~~~~~w~I~ 241 (751)
++|+.||...||.+++.++.+. ++.++|.+ +||||+|.++..+ ++.|.|+
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~ 79 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK-DGKWRVT 79 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc-CCEEEEE
Confidence 4799999999999999887654 68899974 6999999999987 8999999
Q ss_pred eecCCccccCc
Q 004471 242 TIHESHTCGGI 252 (751)
Q Consensus 242 ~~~~~Hnc~~~ 252 (751)
.+..+|||+..
T Consensus 80 ~~~~~HNH~L~ 90 (91)
T PF03101_consen 80 SFVLEHNHPLC 90 (91)
T ss_pred ECcCCcCCCCC
Confidence 99999999853
No 9
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.98 E-value=5.3e-06 Score=59.85 Aligned_cols=30 Identities=43% Similarity=0.784 Sum_probs=27.0
Q ss_pred EeeeCccccCCcccccCCccccHHHHHHhc
Q 004471 622 VDIRNRCCLCRGWQLYGLPCAHAVAALLSC 651 (751)
Q Consensus 622 V~l~~~~CsC~~~~~~GiPC~H~lavl~~~ 651 (751)
+++...+|+|..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 566788999999999999999999999764
No 10
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=96.01 E-value=0.0044 Score=36.10 Aligned_cols=18 Identities=28% Similarity=0.842 Sum_probs=16.5
Q ss_pred eeCcccCcCCCCCCCCCC
Q 004471 732 VHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 732 ~~Cs~C~~~GHn~rtC~~ 749 (751)
++|-+|++.||.++.||+
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 479999999999999995
No 11
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=95.30 E-value=0.0082 Score=42.38 Aligned_cols=19 Identities=37% Similarity=0.940 Sum_probs=16.6
Q ss_pred eeeCcccCcCCCCC--CCCCC
Q 004471 731 VVHCSRCNQTGHFR--TTCAA 749 (751)
Q Consensus 731 ~~~Cs~C~~~GHn~--rtC~~ 749 (751)
+++|+.||+.||.+ ++||.
T Consensus 1 k~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 1 KVKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred CccccccccccccccCccCCC
Confidence 37899999999998 78885
No 12
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.62 E-value=0.082 Score=54.77 Aligned_cols=94 Identities=13% Similarity=0.111 Sum_probs=68.2
Q ss_pred eeeeeeeeccccCcceEEEEEecC--CCCeEEEEEEEeecCchhhHHHHHHHH-HHHhccccCCCCceEEeecCcccccc
Q 004471 372 LGLDRTFLKSKYLGTLLLATGFDG--DGALFPLAFGVVDEENDDNWMWFLSEL-HNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 372 v~iD~T~~~~~y~~~ll~~~g~d~--~~~~~~la~alv~~E~~es~~w~l~~l-~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
|+||=+.....+.. +..+.+|. .... .+.++++-+.++..-||..+ -... .....+|++|...+..+
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~---il~i~~~r~~~~l~~~~~~~~~~~~-----~~~v~~V~~Dm~~~y~~ 70 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGR---ILDILPGRDKETLKDFFRSLYPEEE-----RKNVKVVSMDMSPPYRS 70 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCce---EEEEcCCccHHHHHHHHHHhCcccc-----ccceEEEEcCCCccccc
Confidence 57787766554442 33344444 3222 24588888888888888866 3321 24578999999999999
Q ss_pred cccccCCCCceecchhhHHHHHHHHcC
Q 004471 449 GVEANFPTAFHGFCMRHLSESFRKEFN 475 (751)
Q Consensus 449 Ai~~vfP~a~h~~C~~Hi~~n~~~~~~ 475 (751)
||++.||+|.+..-.|||++++.+.+.
T Consensus 71 ~~~~~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 71 AIREYFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred cccccccccccccccchhhhhhhhcch
Confidence 999999999999999999999876543
No 13
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=93.86 E-value=0.5 Score=53.68 Aligned_cols=132 Identities=18% Similarity=0.199 Sum_probs=93.1
Q ss_pred cCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccccccccCCCCceecchhhHHHHHHHHcC-chhHHHHHHHHH
Q 004471 409 EENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVDGVEANFPTAFHGFCMRHLSESFRKEFN-NTILVNLLWEAA 487 (751)
Q Consensus 409 ~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~-~~~~~~~~~~~~ 487 (751)
..+.+-|.-+.+.+.+..... ...-+++.+|+...+.+++. .||.+.|.+..||+.+.+.+.+. .+.+...++++.
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~--~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~al 311 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLD--KTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKAL 311 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcc--cceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHHH
Confidence 455778998888888777631 22246778999999998876 99999999999999999999886 457777788888
Q ss_pred HhcCHHHHHHHHHHHHHh--cH-------HHHHHHhhcCCCceeecccCCCcccccccchhhHHHHHHh
Q 004471 488 HALTVIEFEAKILEIEEI--SQ-------DAAYWIRRIPPRLWATAYFEGTRFGHLTANIVESLNSWIL 547 (751)
Q Consensus 488 ~a~t~~eF~~~~~~l~~~--~~-------~~~~~L~~~~~~~Wa~ay~~~~~~g~~Ttn~~ES~n~~lk 547 (751)
+.....++...++.+... .+ ++..||.+..... ..|-. +-+.......|+.++.|.
T Consensus 312 ~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i--~~y~~--~~~~~g~g~ee~~~~~~s 376 (470)
T PF06782_consen 312 KKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGI--KPYRE--REGLRGIGAEESVSHVLS 376 (470)
T ss_pred HhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHh--hhhhh--ccCCCccchhhhhhhHHH
Confidence 888889988888887753 11 3566776652111 11211 022234445778777774
No 14
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=93.15 E-value=0.05 Score=36.54 Aligned_cols=23 Identities=30% Similarity=0.671 Sum_probs=19.8
Q ss_pred CcceeeCcccCcCCCCCCCCCCC
Q 004471 728 VKRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 728 ~k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
+...+.|.+|++.||..+.||+.
T Consensus 5 pP~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 5 PPPGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCCCEeecCCCCCccHhHCCCC
Confidence 34568999999999999999974
No 15
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=92.74 E-value=0.25 Score=38.94 Aligned_cols=40 Identities=23% Similarity=0.397 Sum_probs=32.8
Q ss_pred CcEEEEEecCCCCceEEEEEEcCCCCcEEEEeecCCcccc
Q 004471 211 KTRFTAKCAAEGCPWRIHAAKLPGVPTFTIRTIHESHTCG 250 (751)
Q Consensus 211 ~~r~~~~C~~~gC~w~i~a~~~~~~~~w~I~~~~~~Hnc~ 250 (751)
-.|-.++|+..+||++-.+.+..+++...++++..+|||+
T Consensus 20 ~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 20 YPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp CEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred eeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 3566799999999999999998877888899999999996
No 16
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=92.53 E-value=0.059 Score=50.60 Aligned_cols=81 Identities=17% Similarity=0.154 Sum_probs=66.5
Q ss_pred CCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 369 RPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 369 ~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
++.+.+|-||.+-+=. ..++...+|.+++ .|.+-|...-+...=..||..+.+... ..|..|+||+.++...
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-----~~p~~ivtDk~~aY~~ 72 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-----GEPRVIVTDKLPAYPA 72 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-----cccceeecccCCccch
Confidence 4678999999885422 4456788999998 888999888888888888888777653 3689999999999999
Q ss_pred cccccCCCC
Q 004471 449 GVEANFPTA 457 (751)
Q Consensus 449 Ai~~vfP~a 457 (751)
|+++++|..
T Consensus 73 A~~~l~~~~ 81 (140)
T PF13610_consen 73 AIKELNPEG 81 (140)
T ss_pred hhhhccccc
Confidence 999999874
No 17
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=92.30 E-value=0.29 Score=53.38 Aligned_cols=58 Identities=19% Similarity=0.406 Sum_probs=51.5
Q ss_pred ccccCCeeCCHHHHHHHHHHHHHhcCeeEEEEeecCcE-EEEEecCCCCceEEEEEEcC
Q 004471 176 ELAVGQEFPDVKSCRRALRDTAIALHFEMQTIKSDKTR-FTAKCAAEGCPWRIHAAKLP 233 (751)
Q Consensus 176 ~~~vG~~F~s~ee~~~a~~~yAi~~gf~i~~~ks~~~r-~~~~C~~~gC~w~i~a~~~~ 233 (751)
.-..+..|++.++-+.+|+.|....+..|..+.|-+.+ |+|.|....|||+|..+..+
T Consensus 21 ~~~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g 79 (496)
T PF04684_consen 21 QSAQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCG 79 (496)
T ss_pred ccccccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeecc
Confidence 34456789999999999999999999999999997755 99999999999999998764
No 18
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=90.41 E-value=16 Score=38.06 Aligned_cols=148 Identities=14% Similarity=0.059 Sum_probs=84.5
Q ss_pred hHHhhhhhhhhccCCCCChHHHHHHHHHH---hCC-ccCHHHHHHHHHHH-HHHHhcchHhhhccHHHHHHHHHhcCCCc
Q 004471 263 QWVANSVEQRLRENPNYKPKEILEEIHRV---HGI-TLSYKQAWRGKERI-MAAMRGSFEEGYRLLPQYCEQVKRTNPGS 337 (751)
Q Consensus 263 ~~ia~~~~~~i~~~~~~~~~~I~~~l~~~---~g~-~~s~~~~~rak~~~-~~~~~g~~~~~~~~L~~~~~~l~~~npg~ 337 (751)
..+...+.+....++.+..+.|...|+++ .|+ .++.+.++|..+.+ +.... +...+.+
T Consensus 11 ~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~-----------------r~~~~~~ 73 (262)
T PRK14702 11 TDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLER-----------------KPAVPPS 73 (262)
T ss_pred HHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCcccc-----------------CCCCCCC
Confidence 34445555555567889999999988875 377 48988888764331 11000 0000000
Q ss_pred EEEEEccCCcCceeEEEEEehhhHHHHHhhcCCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeec-CchhhHH
Q 004471 338 IASVYGNPADNCFQRLFISFQASIYGFLNACRPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDE-ENDDNWM 416 (751)
Q Consensus 338 ~~~v~~~~~~~~f~~lf~~~~~~~~~~~~~~~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~-E~~es~~ 416 (751)
. ...... | ....-..|+..|-||....-++.++.++.+|...+ .+|||++... .+.+.-.
T Consensus 74 ~-----~~~~~~----~---------~~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~ 134 (262)
T PRK14702 74 K-----RAHTGR----V---------AVKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQ 134 (262)
T ss_pred C-----cCCCCc----c---------ccCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHH
Confidence 0 000000 0 00223468899999987554456888888988876 6889999874 5655555
Q ss_pred HHHHHHHHHhccccCCCCceEEeecCcccc
Q 004471 417 WFLSELHNLLEINTENMPRLTILSDRQKGI 446 (751)
Q Consensus 417 w~l~~l~~~~~~~~~~~~p~~iitD~~~~l 446 (751)
-+|+...+...+......|.+|.||+....
T Consensus 135 ~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy 164 (262)
T PRK14702 135 DVMLGAVERRFGNDLPSSPVEWLTDNGSCY 164 (262)
T ss_pred HHHHHHHHHHhcccCCCCCeEEEcCCCccc
Confidence 555543333211101235788999997643
No 19
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=87.04 E-value=0.97 Score=35.36 Aligned_cols=38 Identities=24% Similarity=0.408 Sum_probs=32.0
Q ss_pred cEEEEEecC-CCCceEEEEEEcCCCCcEEEEeecCCccc
Q 004471 212 TRFTAKCAA-EGCPWRIHAAKLPGVPTFTIRTIHESHTC 249 (751)
Q Consensus 212 ~r~~~~C~~-~gC~w~i~a~~~~~~~~w~I~~~~~~Hnc 249 (751)
.|..++|+. .||+++-.+.+..+++...++++..+|||
T Consensus 21 pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 21 PRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 456689998 89999988888766677788899999998
No 20
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=85.49 E-value=3.5 Score=36.81 Aligned_cols=76 Identities=17% Similarity=0.100 Sum_probs=55.3
Q ss_pred CCceeeeeeeec-cccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCccccc
Q 004471 369 RPLLGLDRTFLK-SKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIV 447 (751)
Q Consensus 369 ~~Vv~iD~T~~~-~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~ 447 (751)
..++.+|.+... ...++...+.+.+|..-+. .+++.+-..++.+.+..+|.......+ ...|.+|+||+.++..
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~p~~i~tD~g~~f~ 80 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRG----GRPPRVIRTDNGSEFT 80 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS-----SE-SEEEEESCHHHH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeecccccccccccccccccccc----cccceecccccccccc
Confidence 468899999666 3455688899999988764 557777777788888888886666655 2228999999999876
Q ss_pred cc
Q 004471 448 DG 449 (751)
Q Consensus 448 ~A 449 (751)
+.
T Consensus 81 ~~ 82 (120)
T PF00665_consen 81 SH 82 (120)
T ss_dssp SH
T ss_pred cc
Confidence 44
No 21
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=84.92 E-value=1.9 Score=33.66 Aligned_cols=46 Identities=13% Similarity=0.192 Sum_probs=25.1
Q ss_pred cCeeEEEEeecCcEEEEEecCC---CCceEEEEEEcCCCCcEEEEeecCCccc
Q 004471 200 LHFEMQTIKSDKTRFTAKCAAE---GCPWRIHAAKLPGVPTFTIRTIHESHTC 249 (751)
Q Consensus 200 ~gf~i~~~ks~~~r~~~~C~~~---gC~w~i~a~~~~~~~~w~I~~~~~~Hnc 249 (751)
.||.+...+.........|.+. +|+++|... .+.-.|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~----~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD----AGDGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE----CCCCEEEECCCccCC
Confidence 4777777776677788999863 899999987 233456666688987
No 22
>smart00343 ZnF_C2HC zinc finger.
Probab=83.96 E-value=0.58 Score=29.97 Aligned_cols=17 Identities=29% Similarity=0.940 Sum_probs=15.4
Q ss_pred eCcccCcCCCCCCCCCC
Q 004471 733 HCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 733 ~Cs~C~~~GHn~rtC~~ 749 (751)
+|.+|++.||..+.||+
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 58999999999999984
No 23
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=82.45 E-value=29 Score=37.00 Aligned_cols=146 Identities=13% Similarity=0.066 Sum_probs=84.0
Q ss_pred HhhhhhhhhccCCCCChHHHHHHHHHHh---CC-ccCHHHHHHHHHHHHHHHhcchHhhhccHHHHHHHHHhcCCCcEEE
Q 004471 265 VANSVEQRLRENPNYKPKEILEEIHRVH---GI-TLSYKQAWRGKERIMAAMRGSFEEGYRLLPQYCEQVKRTNPGSIAS 340 (751)
Q Consensus 265 ia~~~~~~i~~~~~~~~~~I~~~l~~~~---g~-~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~ 340 (751)
+...+.......+.+..+.|...|+++. |+ .++.++++|..+.+ |- .. ..+...+.+.
T Consensus 52 l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~-----Gl--------~~---~~~~~~~~~~-- 113 (301)
T PRK09409 52 VLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQN-----AL--------LL---ERKPAVPPSK-- 113 (301)
T ss_pred HHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHc-----CC--------cc---cccCCCCCCC--
Confidence 3344444445578889999998887652 66 58888888764331 10 00 0000001100
Q ss_pred EEccCCcCceeEEEEEehhhHHHHHhhcCCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeec-CchhhHHHHH
Q 004471 341 VYGNPADNCFQRLFISFQASIYGFLNACRPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDE-ENDDNWMWFL 419 (751)
Q Consensus 341 v~~~~~~~~f~~lf~~~~~~~~~~~~~~~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~-E~~es~~w~l 419 (751)
. .....| ....-..|++.|-||....-++-++.++.+|...+ .+|||++... .+.+.-.-+|
T Consensus 114 -~--~~~~~~-------------~~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l 176 (301)
T PRK09409 114 -R--AHTGRV-------------AVKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVM 176 (301)
T ss_pred -C--CCCCCc-------------CCCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHH
Confidence 0 000111 01233468999999976554556888888898877 6889999875 5666655555
Q ss_pred HH-HHHHhccccCCCCceEEeecCcccc
Q 004471 420 SE-LHNLLEINTENMPRLTILSDRQKGI 446 (751)
Q Consensus 420 ~~-l~~~~~~~~~~~~p~~iitD~~~~l 446 (751)
+. +....+. .....|.+|.||+....
T Consensus 177 ~~a~~~~~~~-~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 177 LGAVERRFGN-DLPSSPVEWLTDNGSCY 203 (301)
T ss_pred HHHHHHHhcc-CCCCCCcEEecCCCccc
Confidence 54 3333221 01234678999997654
No 24
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=80.85 E-value=3.7 Score=43.04 Aligned_cols=85 Identities=19% Similarity=0.218 Sum_probs=55.8
Q ss_pred CCceeeeeeeec----ccc-CcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCc
Q 004471 369 RPLLGLDRTFLK----SKY-LGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQ 443 (751)
Q Consensus 369 ~~Vv~iD~T~~~----~~y-~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~ 443 (751)
.+||.+|-|..+ ++. ++-+-++++-+ .+.|.+.++-+.+...-+|.. ..-+++||+.
T Consensus 67 ~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~------------~~GilvsD~y 128 (271)
T PF03050_consen 67 SPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGD------------FSGILVSDGY 128 (271)
T ss_pred cceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcc------------cceeeecccc
Confidence 478888877776 433 33334444333 555666666665555544432 1248999999
Q ss_pred ccccccccccCCCCceecchhhHHHHHHHHcCc
Q 004471 444 KGIVDGVEANFPTAFHGFCMRHLSESFRKEFNN 476 (751)
Q Consensus 444 ~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~ 476 (751)
.+-.. +..+.|+.|+.|+.+.|.+-...
T Consensus 129 ~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 129 SAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred ccccc-----ccccccccccccccccccccccc
Confidence 88765 23889999999999999876654
No 25
>PHA02517 putative transposase OrfB; Reviewed
Probab=80.44 E-value=17 Score=38.10 Aligned_cols=151 Identities=19% Similarity=0.180 Sum_probs=81.0
Q ss_pred HHhhhhhhhhcc-CCCCChHHHHHHHHHHhCCccCHHHHHHHHHHHHHHHhcchHhhhccHHHHHHHHHhcCCCcEEEEE
Q 004471 264 WVANSVEQRLRE-NPNYKPKEILEEIHRVHGITLSYKQAWRGKERIMAAMRGSFEEGYRLLPQYCEQVKRTNPGSIASVY 342 (751)
Q Consensus 264 ~ia~~~~~~i~~-~~~~~~~~I~~~l~~~~g~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~v~ 342 (751)
.+.+.+..+... .+.+..+.|...|++. |+.++.++++|..+. .|-... .. ........+-. ..
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~-----~gl~~~-~~------~k~~~~~~~~~-~~- 94 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKE-----LGLAGV-LR------GKKVRTTISRK-AV- 94 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHH-----cCCceE-ec------CCCcCCCCCCC-CC-
Confidence 444555555544 5788999999998755 999999998876433 111000 00 00000000000 00
Q ss_pred ccCCcCceeEEEEEehhhHHHHHhhcCCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHH
Q 004471 343 GNPADNCFQRLFISFQASIYGFLNACRPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSEL 422 (751)
Q Consensus 343 ~~~~~~~f~~lf~~~~~~~~~~~~~~~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l 422 (751)
...+.+.+-|-+ ..-..++..|.||....- +..++++.+|...+ +++|+.+...++.+.. +..|
T Consensus 95 --~~~n~~~r~f~~---------~~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~---~~~l 158 (277)
T PHA02517 95 --AAPDRVNRQFVA---------TRPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFV---LDAL 158 (277)
T ss_pred --CCCCcccCCCCC---------CCCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHH---HHHH
Confidence 001111111100 223468999999986543 55677777777765 5677888877777754 4455
Q ss_pred HHHhccccCCCCceEEeecCcccc
Q 004471 423 HNLLEINTENMPRLTILSDRQKGI 446 (751)
Q Consensus 423 ~~~~~~~~~~~~p~~iitD~~~~l 446 (751)
..++.... ...+.+|.||+....
T Consensus 159 ~~a~~~~~-~~~~~i~~sD~G~~y 181 (277)
T PHA02517 159 EQALWARG-RPGGLIHHSDKGSQY 181 (277)
T ss_pred HHHHHhcC-CCcCcEeeccccccc
Confidence 44444211 122356779997754
No 26
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=79.34 E-value=0.74 Score=34.64 Aligned_cols=20 Identities=25% Similarity=0.615 Sum_probs=17.8
Q ss_pred ceeeCcccCcCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~ 749 (751)
-...|+.|+..||..+.||.
T Consensus 30 lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 30 LPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred cChhhcCCCCcCcCHhHcCC
Confidence 45789999999999999984
No 27
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=77.78 E-value=1.3 Score=49.88 Aligned_cols=25 Identities=36% Similarity=0.917 Sum_probs=20.0
Q ss_pred CCCCcceeeCcccCcCCCCCC--CCCC
Q 004471 725 RGRVKRVVHCSRCNQTGHFRT--TCAA 749 (751)
Q Consensus 725 ~~~~k~~~~Cs~C~~~GHn~r--tC~~ 749 (751)
.||..++++|+.|||.||-++ .||+
T Consensus 931 ~GRK~Ttr~C~nCGQvGHmkTNK~CP~ 957 (968)
T COG5179 931 KGRKNTTRTCGNCGQVGHMKTNKACPK 957 (968)
T ss_pred CCCCCcceecccccccccccccccCcc
Confidence 345567999999999999874 5875
No 28
>PF13565 HTH_32: Homeodomain-like domain
Probab=77.72 E-value=4.5 Score=33.27 Aligned_cols=41 Identities=24% Similarity=0.411 Sum_probs=34.3
Q ss_pred HHhhhhhhhhccCCCCChHHHHHHHHHHhCCcc--CHHHHHHH
Q 004471 264 WVANSVEQRLRENPNYKPKEILEEIHRVHGITL--SYKQAWRG 304 (751)
Q Consensus 264 ~ia~~~~~~i~~~~~~~~~~I~~~l~~~~g~~~--s~~~~~ra 304 (751)
.+.+.+.+.+..+|.+++.+|.+.|.+++|+.+ |.+++||.
T Consensus 34 e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 34 EQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 343566777788999999999999999999876 99998874
No 29
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=76.22 E-value=22 Score=35.59 Aligned_cols=83 Identities=17% Similarity=0.109 Sum_probs=57.5
Q ss_pred CCceeeeeeeeccccCcceEEEEEecCCCCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCcccccc
Q 004471 369 RPLLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVD 448 (751)
Q Consensus 369 ~~Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~ 448 (751)
.+++.+|-||.+-+-+. .+.-.++|..|+ ++-+-|...-+...=.-||..+++..+ .|.+|+||+.+....
T Consensus 70 ~~~w~vDEt~ikv~gkw-~ylyrAid~~g~--~Ld~~L~~rRn~~aAk~Fl~kllk~~g------~p~v~vtDka~s~~~ 140 (215)
T COG3316 70 GDSWRVDETYIKVNGKW-HYLYRAIDADGL--TLDVWLSKRRNALAAKAFLKKLLKKHG------EPRVFVTDKAPSYTA 140 (215)
T ss_pred ccceeeeeeEEeeccEe-eehhhhhccCCC--eEEEEEEcccCcHHHHHHHHHHHHhcC------CCceEEecCccchHH
Confidence 45778888888744222 122334555544 566666666666666667776666644 588999999999999
Q ss_pred cccccCCCCcee
Q 004471 449 GVEANFPTAFHG 460 (751)
Q Consensus 449 Ai~~vfP~a~h~ 460 (751)
|+.++-+.+.|+
T Consensus 141 A~~~l~~~~ehr 152 (215)
T COG3316 141 ALRKLGSEVEHR 152 (215)
T ss_pred HHHhcCcchhee
Confidence 999998877665
No 30
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=74.78 E-value=2.4 Score=49.84 Aligned_cols=31 Identities=13% Similarity=0.092 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCCCCcchhhhccCCCCCCCCC
Q 004471 72 NHDQEGGDGHGYGHANELAMERKPEHGDHEM 102 (751)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (751)
+.+.++.+.--.+||++++++.++|-||.+.
T Consensus 1405 dd~DeeeD~e~Ed~dEddd~edd~D~dd~~e 1435 (1516)
T KOG1832|consen 1405 DDSDEEEDDETEDEDEDDDEEDDLDRDDGLE 1435 (1516)
T ss_pred cccCccccchhhccccccccccccccccchh
Confidence 3445555666666676666655555554444
No 31
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=68.72 E-value=37 Score=32.31 Aligned_cols=89 Identities=11% Similarity=0.214 Sum_probs=54.3
Q ss_pred CcceEEEEEecCCCCeEEEEEEEee-cCchhhHHHHHHHHHHHhccccCCCCceEEeecCccccccc---ccccCCCCce
Q 004471 384 LGTLLLATGFDGDGALFPLAFGVVD-EENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVDG---VEANFPTAFH 459 (751)
Q Consensus 384 ~~~ll~~~g~d~~~~~~~la~alv~-~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~A---i~~vfP~a~h 459 (751)
+.+++.++..-+.|..|.=..-.-+ ..+.+...-+|+...+.++ ...-+.||||....+.+| +.+-+|....
T Consensus 46 ~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG----~~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw 121 (153)
T PF04937_consen 46 GRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVG----EENVVQVVTDNASNMKKAGKLLMEKYPHIFW 121 (153)
T ss_pred CCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhh----hhhhhHHhccCchhHHHHHHHHHhcCCCEEE
Confidence 3344444444444444432221111 1345555555555555555 344677899999998888 4455899999
Q ss_pred ecchhhHHHHHHHHcCc
Q 004471 460 GFCMRHLSESFRKEFNN 476 (751)
Q Consensus 460 ~~C~~Hi~~n~~~~~~~ 476 (751)
..|.-|-+.-+.+.+..
T Consensus 122 ~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 122 TPCAAHCINLMLEDIGK 138 (153)
T ss_pred echHHHHHHHHHHHHhc
Confidence 99999998877766543
No 32
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=68.25 E-value=8.8 Score=33.29 Aligned_cols=30 Identities=30% Similarity=0.599 Sum_probs=22.3
Q ss_pred cCcceEEeeeCccccCCccc----cc-CCccccHHHH
Q 004471 616 HEGTNIVDIRNRCCLCRGWQ----LY-GLPCAHAVAA 647 (751)
Q Consensus 616 ~~~~~~V~l~~~~CsC~~~~----~~-GiPC~H~lav 647 (751)
.++.|+++.+ .|||..|- .. .-||.|++..
T Consensus 41 ~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 41 KERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred cccceEEEcC--cccCHHHHhHhhhcCcccchhhhhe
Confidence 5668888776 89998876 22 3479999864
No 33
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=61.78 E-value=3.6 Score=21.91 Aligned_cols=9 Identities=67% Similarity=1.139 Sum_probs=3.4
Q ss_pred CCCCCCCcc
Q 004471 710 RPPGRPRKK 718 (751)
Q Consensus 710 r~~GRPkk~ 718 (751)
|++|||+|.
T Consensus 2 r~RGRP~k~ 10 (13)
T PF02178_consen 2 RKRGRPRKN 10 (13)
T ss_dssp --SS--TT-
T ss_pred CcCCCCccc
Confidence 567999886
No 34
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=55.44 E-value=6.9 Score=28.39 Aligned_cols=19 Identities=37% Similarity=0.987 Sum_probs=17.2
Q ss_pred ceeeCcccCcCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCA 748 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~ 748 (751)
....|.+|++.||-.--||
T Consensus 3 ~~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 3 ARVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCCcCcccCCCCcchhhCC
Confidence 4578999999999999999
No 35
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=49.00 E-value=10 Score=24.24 Aligned_cols=12 Identities=50% Similarity=0.742 Sum_probs=9.3
Q ss_pred CCCCCCCccccc
Q 004471 710 RPPGRPRKKRVR 721 (751)
Q Consensus 710 r~~GRPkk~R~~ 721 (751)
|++|||+|....
T Consensus 2 RkRGRPrK~~~~ 13 (26)
T smart00384 2 RKRGRPRKAPKD 13 (26)
T ss_pred CCCCCCCCCCCc
Confidence 678999998543
No 36
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=48.78 E-value=16 Score=43.40 Aligned_cols=17 Identities=29% Similarity=0.368 Sum_probs=8.0
Q ss_pred ccCCCCCCCCCCCCCCc
Q 004471 92 ERKPEHGDHEMPLPAQN 108 (751)
Q Consensus 92 ~~~~~~~~~~~~~~~~~ 108 (751)
+.+||.||+|-+++.++
T Consensus 1416 Ed~dEddd~edd~D~dd 1432 (1516)
T KOG1832|consen 1416 EDEDEDDDEEDDLDRDD 1432 (1516)
T ss_pred hcccccccccccccccc
Confidence 44444444455555543
No 37
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=48.13 E-value=14 Score=31.75 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCc
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQ 739 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~ 739 (751)
|+.++..||-|+.|-. -...+|++|++
T Consensus 2 ~kKRrn~GR~K~~rGh-------v~~V~C~nCgr 28 (95)
T PRK09335 2 PKKRENRGRRKGDKGH-------VGYVQCDNCGR 28 (95)
T ss_pred CcccccCCCCCCCCCC-------CccEEeCCCCC
Confidence 5566777777765332 25789999986
No 38
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=47.90 E-value=9.2 Score=37.31 Aligned_cols=17 Identities=35% Similarity=0.985 Sum_probs=15.2
Q ss_pred eeCcccCcCCCCCCCCC
Q 004471 732 VHCSRCNQTGHFRTTCA 748 (751)
Q Consensus 732 ~~Cs~C~~~GHn~rtC~ 748 (751)
.+|.+||+.||.++-|+
T Consensus 98 ~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 98 KKCYNCGETGHLSRDCN 114 (190)
T ss_pred cccccccccCccccccC
Confidence 68999999999999993
No 39
>PF13592 HTH_33: Winged helix-turn helix
Probab=43.12 E-value=38 Score=26.47 Aligned_cols=29 Identities=24% Similarity=0.240 Sum_probs=25.3
Q ss_pred CCCChHHHHHHHHHHhCCccCHHHHHHHH
Q 004471 277 PNYKPKEILEEIHRVHGITLSYKQAWRGK 305 (751)
Q Consensus 277 ~~~~~~~I~~~l~~~~g~~~s~~~~~rak 305 (751)
..++.++|.+.|.++||+.++.+.+++.-
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~lL 31 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRLL 31 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHHH
Confidence 45788999999999999999999888763
No 40
>PLN00186 ribosomal protein S26; Provisional
Probab=42.82 E-value=18 Score=31.73 Aligned_cols=27 Identities=30% Similarity=0.594 Sum_probs=18.3
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCc
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQ 739 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~ 739 (751)
|+.++..||-|+.|-. -+..+|++|++
T Consensus 2 ~kKRrN~GR~K~~rGh-------v~~V~C~nCgr 28 (109)
T PLN00186 2 TKKRRNGGRNKHGRGH-------VKRIRCSNCGK 28 (109)
T ss_pred CcccccCCCCCCCCCC-------CcceeeCCCcc
Confidence 5566677777765332 25789999986
No 41
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=42.36 E-value=59 Score=30.46 Aligned_cols=71 Identities=15% Similarity=0.219 Sum_probs=43.0
Q ss_pred Cceeeeeeeecccc--------------CcceEEEEEecCC-CCeEEEEEEEeecCchhhHHHHHHHHHHHhccccCCCC
Q 004471 370 PLLGLDRTFLKSKY--------------LGTLLLATGFDGD-GALFPLAFGVVDEENDDNWMWFLSELHNLLEINTENMP 434 (751)
Q Consensus 370 ~Vv~iD~T~~~~~y--------------~~~ll~~~g~d~~-~~~~~la~alv~~E~~es~~w~l~~l~~~~~~~~~~~~ 434 (751)
.+|-||-||..++- .....++++++-+ +..--+...++++.+.++..-+++.. +. +
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~---i~------~ 74 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEH---IE------P 74 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHh---hh------c
Confidence 47788888876332 2234445555554 43444455556777877776655433 22 3
Q ss_pred ceEEeecCccccccc
Q 004471 435 RLTILSDRQKGIVDG 449 (751)
Q Consensus 435 p~~iitD~~~~l~~A 449 (751)
..+|+||..++-..-
T Consensus 75 gs~i~TD~~~aY~~l 89 (151)
T PF12762_consen 75 GSTIITDGWRAYNGL 89 (151)
T ss_pred cceeeecchhhcCcc
Confidence 468999999887533
No 42
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=41.88 E-value=19 Score=31.62 Aligned_cols=27 Identities=30% Similarity=0.587 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCc
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQ 739 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~ 739 (751)
|+.++..||-|+.|-. -+..+|++|++
T Consensus 2 ~kKRrN~GR~K~~rGh-------v~~V~C~nCgr 28 (108)
T PTZ00172 2 TSKRRNNGRSKHGRGH-------VKPVRCSNCGR 28 (108)
T ss_pred CcccccCCCCCCCCCC-------CccEEeCCccc
Confidence 5566777777765332 35789999986
No 43
>PHA00689 hypothetical protein
Probab=39.83 E-value=16 Score=26.92 Aligned_cols=15 Identities=47% Similarity=1.015 Sum_probs=11.7
Q ss_pred CCcceeeCcccCcCC
Q 004471 727 RVKRVVHCSRCNQTG 741 (751)
Q Consensus 727 ~~k~~~~Cs~C~~~G 741 (751)
+..|..+|.+||++|
T Consensus 13 qepravtckrcgktg 27 (62)
T PHA00689 13 QEPRAVTCKRCGKTG 27 (62)
T ss_pred cCcceeehhhccccC
Confidence 345778999999876
No 44
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=36.30 E-value=79 Score=36.13 Aligned_cols=35 Identities=26% Similarity=0.434 Sum_probs=25.1
Q ss_pred ceEEeee----CccccCCcccccCCccccHHHHHHhcCCCc
Q 004471 619 TNIVDIR----NRCCLCRGWQLYGLPCAHAVAALLSCRQNV 655 (751)
Q Consensus 619 ~~~V~l~----~~~CsC~~~~~~GiPC~H~lavl~~~~~~~ 655 (751)
.+.|.+. +.+|||.. ...| -|.|+.||+....-.|
T Consensus 61 ~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~~p 99 (587)
T COG4715 61 RVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLDDP 99 (587)
T ss_pred eEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhhcc
Confidence 3455663 46999987 5555 5999999998876433
No 45
>PRK13907 rnhA ribonuclease H; Provisional
Probab=35.57 E-value=1.3e+02 Score=27.20 Aligned_cols=77 Identities=13% Similarity=0.032 Sum_probs=41.4
Q ss_pred ceeeeeeeeccccCcceEEEEEecCCCCeEEEEEE-EeecCchhhHHHHHHHHHHHhccccCCCCceEEeecCccccccc
Q 004471 371 LLGLDRTFLKSKYLGTLLLATGFDGDGALFPLAFG-VVDEENDDNWMWFLSELHNLLEINTENMPRLTILSDRQKGIVDG 449 (751)
Q Consensus 371 Vv~iD~T~~~~~y~~~ll~~~g~d~~~~~~~la~a-lv~~E~~es~~w~l~~l~~~~~~~~~~~~p~~iitD~~~~l~~A 449 (751)
.|.+||.+..+.-.+-...++ .+..+.. .+++. -..+....-|.-++..|+.+... ...++.|-||. ..++++
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~~~-~~~~~~~~~tn~~AE~~All~aL~~a~~~---g~~~v~i~sDS-~~vi~~ 76 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQPAV-QLSLPLGTMSNHEAEYHALLAALKYCTEH---NYNIVSFRTDS-QLVERA 76 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeE-EEEecccccCCcHHHHHHHHHHHHHHHhC---CCCEEEEEech-HHHHHH
Confidence 378999998765322222222 4444433 23321 12333455577777777777663 34567777876 444455
Q ss_pred cccc
Q 004471 450 VEAN 453 (751)
Q Consensus 450 i~~v 453 (751)
+...
T Consensus 77 ~~~~ 80 (128)
T PRK13907 77 VEKE 80 (128)
T ss_pred HhHH
Confidence 5443
No 46
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=33.55 E-value=65 Score=26.56 Aligned_cols=31 Identities=19% Similarity=0.274 Sum_probs=27.1
Q ss_pred CeeCCHHHHHHHHHHHHHhcCeeEEEEeecC
Q 004471 181 QEFPDVKSCRRALRDTAIALHFEMQTIKSDK 211 (751)
Q Consensus 181 ~~F~s~ee~~~a~~~yAi~~gf~i~~~ks~~ 211 (751)
-.++|.+++..+|..|+.+++-.+++.+.++
T Consensus 12 ~~yPs~e~i~~aIE~YC~~~~~~l~Fisr~~ 42 (74)
T PF14201_consen 12 PKYPSKEEICEAIEKYCIKNGESLEFISRDK 42 (74)
T ss_pred CCCCCHHHHHHHHHHHHHHcCCceEEEecCC
Confidence 3488999999999999999999999876554
No 47
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=32.88 E-value=38 Score=26.38 Aligned_cols=32 Identities=28% Similarity=0.573 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCc
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQ 739 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~ 739 (751)
|+.+.++.|..++|.. ..........|+.||.
T Consensus 4 PKrk~S~srr~~RRsh--~~l~~~~l~~C~~CG~ 35 (57)
T PRK12286 4 PKRKTSKSRKRKRRAH--FKLKAPGLVECPNCGE 35 (57)
T ss_pred CcCcCChhhcchhccc--ccccCCcceECCCCCC
Confidence 6777777777777654 2334456778999986
No 48
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=29.72 E-value=41 Score=28.87 Aligned_cols=34 Identities=18% Similarity=0.333 Sum_probs=27.3
Q ss_pred cCHHHHHHHHHHHHHhcHHHHHHHhhcCCCceee
Q 004471 490 LTVIEFEAKILEIEEISQDAAYWIRRIPPRLWAT 523 (751)
Q Consensus 490 ~t~~eF~~~~~~l~~~~~~~~~~L~~~~~~~Wa~ 523 (751)
.|..+|++.|..+.......++||..+.++....
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~ 38 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPK 38 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHH
Confidence 4678999999999876668999999987654443
No 49
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.74 E-value=1.9e+02 Score=26.68 Aligned_cols=43 Identities=12% Similarity=0.206 Sum_probs=33.9
Q ss_pred EEEehhhHHHHHhhcCCcee--eeeeeeccccCcceEEEEEecCCCC
Q 004471 354 FISFQASIYGFLNACRPLLG--LDRTFLKSKYLGTLLLATGFDGDGA 398 (751)
Q Consensus 354 f~~~~~~~~~~~~~~~~Vv~--iD~T~~~~~y~~~ll~~~g~d~~~~ 398 (751)
||+-- .+..+ +.|.||+. .||-|++-+.+|||+.+--.|.+..
T Consensus 91 Y~a~I-p~sDi-~kynpIlA~~~nGn~M~IRerGPl~~IYplds~pe 135 (155)
T COG3915 91 YWAEI-PYSDI-EKYNPILAIQNNGNYMQIRERGPLWSIYPLDSSPE 135 (155)
T ss_pred eeccC-cHHHh-hhcccEEEEEeCCcEEEEeccCceEEEeecCCChh
Confidence 44433 36677 88999865 5899999999999999988887764
No 50
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=25.93 E-value=43 Score=29.91 Aligned_cols=27 Identities=33% Similarity=0.621 Sum_probs=11.9
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCc
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQ 739 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~ 739 (751)
|+.+|..||-|+.|-. -...+|.+|+.
T Consensus 2 ~~KRrN~Gr~KkgrGh-------v~~V~C~nCgr 28 (113)
T PF01283_consen 2 TKKRRNNGRSKKGRGH-------VQPVRCDNCGR 28 (113)
T ss_dssp ----TTTTSS-SSSS----------EEE-TTTB-
T ss_pred CcccccCCCCCCCCCC-------CcCEeeCcccc
Confidence 4455666666655332 25789999985
No 51
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=25.20 E-value=44 Score=28.74 Aligned_cols=27 Identities=37% Similarity=0.743 Sum_probs=19.0
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCc
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQ 739 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~ 739 (751)
|+.++..||.|+-|-.. .-.+|-+|+.
T Consensus 2 pkkR~N~GR~K~~rGhv-------~~v~CdnCg~ 28 (108)
T COG4830 2 PKKRRNRGRNKKGRGHV-------KYVRCDNCGK 28 (108)
T ss_pred cchhhhcCCCCCCCCCc-------cceeeccccc
Confidence 66777778877764332 3578999986
No 52
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.10 E-value=59 Score=28.46 Aligned_cols=10 Identities=30% Similarity=1.139 Sum_probs=6.9
Q ss_pred cceeeCcccC
Q 004471 729 KRVVHCSRCN 738 (751)
Q Consensus 729 k~~~~Cs~C~ 738 (751)
.+...|..|+
T Consensus 19 pt~f~CP~Cg 28 (99)
T PRK14892 19 PKIFECPRCG 28 (99)
T ss_pred CcEeECCCCC
Confidence 3567777777
No 53
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=23.81 E-value=37 Score=33.21 Aligned_cols=20 Identities=35% Similarity=0.810 Sum_probs=17.5
Q ss_pred ceeeCcccCcCCCCCCCCCC
Q 004471 730 RVVHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 730 ~~~~Cs~C~~~GHn~rtC~~ 749 (751)
....|-+||+.||-++-||.
T Consensus 59 ~~~~C~nCg~~GH~~~DCP~ 78 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCPH 78 (190)
T ss_pred cccccchhcccCcccccCCh
Confidence 46789999999999999993
No 54
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=23.76 E-value=60 Score=26.13 Aligned_cols=35 Identities=29% Similarity=0.511 Sum_probs=15.3
Q ss_pred hhhhhccCCCCChHHHHHHHHHHhCCccCHHHHHHH
Q 004471 269 VEQRLRENPNYKPKEILEEIHRVHGITLSYKQAWRG 304 (751)
Q Consensus 269 ~~~~i~~~~~~~~~~I~~~l~~~~g~~~s~~~~~ra 304 (751)
+...+..+|..+..+|...+.+. |..+|..++++.
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~ 38 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRR 38 (72)
T ss_dssp ------------HHHHHHHT----T--S-HHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHH
Confidence 34456678999999999998888 999999998876
No 55
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=23.39 E-value=78 Score=24.46 Aligned_cols=42 Identities=24% Similarity=0.452 Sum_probs=24.2
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCcCCCCCCCCC
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQTGHFRTTCA 748 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~~GHn~rtC~ 748 (751)
|+.+.++-|.+++|.... .........|+.||+.--.=+-||
T Consensus 2 PKrk~Sksr~~~RRah~~-kl~~p~l~~C~~cG~~~~~H~vc~ 43 (55)
T TIGR01031 2 PKRKTSKSRKRKRRSHDA-KLTAPTLVVCPNCGEFKLPHRVCP 43 (55)
T ss_pred CCCcCCcccccchhcCcc-cccCCcceECCCCCCcccCeeECC
Confidence 566666666666655421 123446778999997443333343
No 56
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=22.53 E-value=51 Score=30.98 Aligned_cols=18 Identities=39% Similarity=0.914 Sum_probs=10.7
Q ss_pred eeCcccCcCCCCCCCCCC
Q 004471 732 VHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 732 ~~Cs~C~~~GHn~rtC~~ 749 (751)
..|.+|++.||..+.||.
T Consensus 78 ~~C~~Cg~~GH~~~~C~~ 95 (148)
T PTZ00368 78 RSCYNCGQTGHISRECPN 95 (148)
T ss_pred cccCcCCCCCcccccCCC
Confidence 346666666666666654
No 57
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=22.37 E-value=45 Score=23.34 Aligned_cols=14 Identities=29% Similarity=0.669 Sum_probs=10.8
Q ss_pred CCCcceeeCcccCc
Q 004471 726 GRVKRVVHCSRCNQ 739 (751)
Q Consensus 726 ~~~k~~~~Cs~C~~ 739 (751)
...++..+|++|+.
T Consensus 20 ~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 20 PAGGRKVRCPKCGH 33 (37)
T ss_pred ccCCcEEECCCCCc
Confidence 34567899999985
No 58
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=22.04 E-value=59 Score=29.91 Aligned_cols=22 Identities=27% Similarity=0.690 Sum_probs=18.7
Q ss_pred CCcceeeCcccCcCCCCCCCCCC
Q 004471 727 RVKRVVHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 727 ~~k~~~~Cs~C~~~GHn~rtC~~ 749 (751)
..+..+.|..|+ -.|....||-
T Consensus 102 ~~~~~v~CR~Ck-GdH~T~~CPy 123 (128)
T PF12353_consen 102 KGKSKVKCRICK-GDHWTSKCPY 123 (128)
T ss_pred cCCceEEeCCCC-CCcccccCCc
Confidence 345689999997 9999999994
No 59
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=22.02 E-value=51 Score=31.01 Aligned_cols=20 Identities=30% Similarity=0.798 Sum_probs=18.0
Q ss_pred eeeCcccCcCCCCCCCCCCC
Q 004471 731 VVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 731 ~~~Cs~C~~~GHn~rtC~~~ 750 (751)
...|.+|++.||..+.||++
T Consensus 52 ~~~C~~Cg~~GH~~~~Cp~~ 71 (148)
T PTZ00368 52 ERSCYNCGKTGHLSRECPEA 71 (148)
T ss_pred CcccCCCCCcCcCcccCCCc
Confidence 46799999999999999875
No 60
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=21.92 E-value=58 Score=33.78 Aligned_cols=26 Identities=27% Similarity=0.557 Sum_probs=21.5
Q ss_pred CCCCcceeeCcccCcCCCCCCCCCCC
Q 004471 725 RGRVKRVVHCSRCNQTGHFRTTCAAP 750 (751)
Q Consensus 725 ~~~~k~~~~Cs~C~~~GHn~rtC~~~ 750 (751)
.+.+.-.+-|=+||+.||-...||.+
T Consensus 170 ~kppPpgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 170 NKPPPPGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CCCCCCceeEEecCCCCchhhcCCCC
Confidence 34455678999999999999999864
No 61
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.51 E-value=50 Score=25.69 Aligned_cols=41 Identities=22% Similarity=0.415 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCccccccccCCCCcceeeCcccCcCCCCCCCCC
Q 004471 706 PKSLRPPGRPRKKRVRAEDRGRVKRVVHCSRCNQTGHFRTTCA 748 (751)
Q Consensus 706 P~~~r~~GRPkk~R~~~~~~~~~k~~~~Cs~C~~~GHn~rtC~ 748 (751)
|+.+.++-|..++|.. ..........|+.||+..--=+.|+
T Consensus 4 PkrktSksrr~~RRsh--~~l~~~~~~~c~~cG~~~l~Hrvc~ 44 (57)
T COG0333 4 PKRKTSKSRRRMRRSH--DALKAPTLSVCPNCGEYKLPHRVCL 44 (57)
T ss_pred CcccCChhhhhhhhhh--HhhhCccceeccCCCCcccCceEcC
Confidence 4445555555555443 2333344788999997555445554
No 62
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=21.03 E-value=54 Score=33.46 Aligned_cols=23 Identities=26% Similarity=0.589 Sum_probs=18.9
Q ss_pred ccccCCcccccCCccccHHHHHHhcC
Q 004471 627 RCCLCRGWQLYGLPCAHAVAALLSCR 652 (751)
Q Consensus 627 ~~CsC~~~~~~GiPC~H~lavl~~~~ 652 (751)
..|||..+ -.||.|+-||.....
T Consensus 125 ~dCSCPD~---anPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDY---ANPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCc---ccchHHHHHHHHHHH
Confidence 46999865 579999999987765
No 63
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.69 E-value=63 Score=22.56 Aligned_cols=18 Identities=28% Similarity=0.757 Sum_probs=11.4
Q ss_pred eeCcccCcCCCCCCCCCC
Q 004471 732 VHCSRCNQTGHFRTTCAA 749 (751)
Q Consensus 732 ~~Cs~C~~~GHn~rtC~~ 749 (751)
-.|.+|++..|=.+.|..
T Consensus 3 ~~CprC~kg~Hwa~~C~s 20 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRS 20 (36)
T ss_dssp -C-TTTSSSCS-TTT---
T ss_pred ccCcccCCCcchhhhhhh
Confidence 469999999999999964
No 64
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=20.28 E-value=74 Score=27.67 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=4.4
Q ss_pred ceeeCcccC
Q 004471 730 RVVHCSRCN 738 (751)
Q Consensus 730 ~~~~Cs~C~ 738 (751)
++-.|.+|+
T Consensus 21 k~FtCp~Cg 29 (104)
T COG4888 21 KTFTCPRCG 29 (104)
T ss_pred ceEecCccC
Confidence 344555554
Done!