Query 037776
Match_columns 716
No_of_seqs 305 out of 1374
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 04:17:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037776.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037776hhsearch_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 7.7E-69 1.7E-73 619.6 47.4 465 160-648 71-624 (846)
2 PF10551 MULE: MULE transposas 99.8 6E-21 1.3E-25 166.9 9.1 89 353-446 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.8 2.6E-20 5.7E-25 203.7 5.2 223 261-525 113-350 (381)
4 PF03108 DBD_Tnp_Mut: MuDR fam 99.7 3.7E-16 8.1E-21 127.7 9.1 66 161-226 2-67 (67)
5 COG3328 Transposase and inacti 99.4 8.1E-13 1.8E-17 142.2 13.9 221 260-524 98-328 (379)
6 smart00575 ZnF_PMZ plant mutat 98.9 8.8E-10 1.9E-14 73.1 2.0 27 605-631 1-27 (28)
7 PF08731 AFT: Transcription fa 98.7 1E-07 2.2E-12 83.2 9.0 69 169-237 1-111 (111)
8 PF03101 FAR1: FAR1 DNA-bindin 98.4 5E-07 1.1E-11 78.4 6.5 61 177-238 1-90 (91)
9 PF04434 SWIM: SWIM zinc finge 98.1 2.7E-06 5.8E-11 61.8 3.3 31 600-630 10-40 (40)
10 PF13610 DDE_Tnp_IS240: DDE do 96.6 0.00094 2E-08 62.9 1.8 81 346-432 1-81 (140)
11 PF06782 UPF0236: Uncharacteri 94.9 1.5 3.2E-05 49.8 18.5 132 386-524 235-377 (470)
12 PHA02517 putative transposase 93.2 3.4 7.3E-05 43.3 16.1 148 248-421 30-181 (277)
13 PRK14702 insertion element IS2 92.2 7.5 0.00016 40.6 16.9 145 247-420 11-163 (262)
14 PF01610 DDE_Tnp_ISL3: Transpo 91.8 0.28 6E-06 50.7 5.7 92 349-449 1-96 (249)
15 PF03106 WRKY: WRKY DNA -bindi 91.3 0.75 1.6E-05 36.5 6.2 39 198-236 21-59 (60)
16 PRK09409 IS2 transposase TnpB; 91.2 13 0.00028 39.7 17.7 145 248-420 51-202 (301)
17 PF04684 BAF1_ABF1: BAF1 / ABF 91.1 0.4 8.6E-06 52.5 6.0 58 163-220 22-80 (496)
18 COG3316 Transposase and inacti 89.2 6.1 0.00013 39.6 12.0 119 271-434 33-151 (215)
19 PF13565 HTH_32: Homeodomain-l 84.5 2 4.3E-05 35.5 5.0 40 249-288 35-76 (77)
20 PF15288 zf-CCHC_6: Zinc knuck 84.0 0.45 9.8E-06 34.1 0.7 15 696-710 2-16 (40)
21 PF04500 FLYWCH: FLYWCH zinc f 80.6 2.8 6.1E-05 32.7 4.3 46 186-235 14-62 (62)
22 PF00665 rve: Integrase core d 79.8 7.5 0.00016 34.5 7.4 76 345-423 5-81 (120)
23 PF03050 DDE_Tnp_IS66: Transpo 78.2 3.2 6.9E-05 43.5 5.1 133 260-451 18-156 (271)
24 smart00774 WRKY DNA binding do 78.2 2.8 6.2E-05 33.0 3.4 38 198-235 21-59 (59)
25 PF00098 zf-CCHC: Zinc knuckle 76.3 1.5 3.3E-05 25.8 1.1 14 696-709 1-14 (18)
26 PF04937 DUF659: Protein of un 68.6 76 0.0016 30.2 11.4 120 302-450 13-137 (153)
27 KOG1832 HIV-1 Vpr-binding prot 60.0 7.4 0.00016 46.1 3.2 21 101-121 1402-1422(1516)
28 COG5431 Uncharacterized metal- 55.2 7.1 0.00015 34.1 1.5 48 588-638 35-88 (117)
29 PF13592 HTH_33: Winged helix- 47.6 28 0.00062 27.3 3.8 31 260-290 2-32 (60)
30 PF13696 zf-CCHC_2: Zinc knuck 46.7 11 0.00023 25.9 1.0 15 694-708 7-21 (32)
31 PF09026 CENP-B_dimeris: Centr 44.6 6.5 0.00014 33.9 -0.3 6 178-183 49-54 (101)
32 COG4715 Uncharacterized conser 41.7 81 0.0017 36.1 7.4 44 587-632 51-98 (587)
33 PF12762 DDE_Tnp_IS1595: ISXO2 41.5 72 0.0016 29.9 6.3 69 347-422 4-87 (151)
34 PRK13907 rnhA ribonuclease H; 38.9 2.6E+02 0.0057 25.2 9.5 78 348-429 3-81 (128)
35 PF01498 HTH_Tnp_Tc3_2: Transp 37.9 27 0.00059 28.3 2.4 38 253-291 4-41 (72)
36 PF02178 AT_hook: AT hook moti 36.1 16 0.00035 19.8 0.5 7 679-685 4-10 (13)
37 COG4279 Uncharacterized conser 34.8 23 0.0005 36.2 1.7 23 605-630 125-147 (266)
38 KOG3130 Uncharacterized conser 34.4 22 0.00047 38.6 1.6 11 95-105 264-274 (514)
39 PHA00689 hypothetical protein 33.8 22 0.00047 26.6 1.0 15 692-706 14-28 (62)
40 COG4888 Uncharacterized Zn rib 33.6 30 0.00065 30.2 2.0 25 680-704 2-31 (104)
41 PF13276 HTH_21: HTH-like doma 31.5 84 0.0018 24.4 4.2 43 249-291 6-49 (60)
42 PRK14892 putative transcriptio 28.1 50 0.0011 29.0 2.5 22 680-702 2-28 (99)
43 PRK09335 30S ribosomal protein 27.7 50 0.0011 28.6 2.3 27 674-704 2-29 (95)
44 PRK00766 hypothetical protein; 27.5 5.3E+02 0.012 25.6 9.9 88 347-434 10-127 (194)
45 PLN00186 ribosomal protein S26 25.6 54 0.0012 29.1 2.2 27 674-704 2-29 (109)
46 PTZ00172 40S ribosomal protein 25.1 55 0.0012 29.0 2.2 27 674-704 2-29 (108)
47 PF03400 DDE_Tnp_IS1: IS1 tran 24.7 2.6E+02 0.0057 25.9 6.8 68 354-434 12-79 (131)
48 smart00384 AT_hook DNA binding 24.3 43 0.00092 21.7 1.0 8 679-686 4-11 (26)
49 KOG1824 TATA-binding protein-i 24.0 48 0.001 40.2 2.1 33 98-131 311-343 (1233)
50 smart00343 ZnF_C2HC zinc finge 23.7 38 0.00082 21.6 0.8 13 697-709 1-13 (26)
51 PF13551 HTH_29: Winged helix- 23.6 1.4E+02 0.0031 25.8 4.8 39 252-290 65-109 (112)
52 COG3915 Uncharacterized protei 23.6 2.2E+02 0.0048 26.4 5.8 54 317-375 78-135 (155)
53 KOG0943 Predicted ubiquitin-pr 23.3 66 0.0014 39.9 3.1 18 213-230 1965-1982(3015)
54 PF13917 zf-CCHC_3: Zinc knuck 23.2 45 0.00097 24.4 1.1 13 695-707 4-16 (42)
55 PF04931 DNA_pol_phi: DNA poly 23.1 51 0.0011 40.2 2.3 17 58-74 603-619 (784)
56 COG5179 TAF1 Transcription ini 23.0 41 0.00088 38.6 1.3 15 694-708 936-950 (968)
57 PF14201 DUF4318: Domain of un 23.0 1.2E+02 0.0027 25.1 3.8 29 168-196 13-41 (74)
58 PF13877 RPAP3_C: Potential Mo 22.2 70 0.0015 27.5 2.4 34 465-498 5-38 (94)
59 PF14392 zf-CCHC_4: Zinc knuck 22.1 40 0.00087 25.3 0.7 15 695-709 31-45 (49)
60 KOG0262 RNA polymerase I, larg 21.5 2.3E+02 0.0049 35.8 7.0 17 27-43 1261-1277(1640)
61 PF10587 EF-1_beta_acid: Eukar 20.8 87 0.0019 20.8 1.9 16 47-62 3-18 (28)
62 KOG2141 Protein involved in hi 20.8 2.3E+02 0.0049 33.7 6.5 14 301-314 377-390 (822)
63 PF14420 Clr5: Clr5 domain 20.5 2.1E+02 0.0046 21.9 4.5 25 260-284 18-42 (54)
64 COG5406 Nucleosome binding fac 20.4 61 0.0013 37.4 1.9 8 100-107 939-946 (1001)
65 PF10446 DUF2457: Protein of u 20.2 1.8E+02 0.004 32.4 5.4 41 52-108 201-241 (458)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=7.7e-69 Score=619.55 Aligned_cols=465 Identities=13% Similarity=0.155 Sum_probs=371.7
Q ss_pred CCCcCCCcEECCHHHHHHHHHHHHHHcCceEEEEeecCe-------EEEEEecc--------------------------
Q 037776 160 KMILYHGQRFRDVSHFRKAIEVFAIRDGFKLCVMENRAH-------AVSYECSD-------------------------- 206 (716)
Q Consensus 160 ~~~l~vG~~F~s~ee~k~ai~~yAi~~gf~~~~~kS~~~-------r~~~~C~~-------------------------- 206 (716)
...+.+||+|+|.++++.+|+.||.+.||++++.++.+. ..+++|++
T Consensus 71 ~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~ 150 (846)
T PLN03097 71 NLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENG 150 (846)
T ss_pred CccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCcccc
Confidence 446799999999999999999999999999998755431 23577754
Q ss_pred --------CCCceEEEEEEecCcceEEEEEecCccccccccccccc-h-hhHHHHHHhhhhhcCCCCCHHHHHHHHHHHh
Q 037776 207 --------LRCDWKIKAERVVNGRTFIVTEFVAQHKCTRRHQQFQH-R-SKWISAIYLHRWKLQPNLRTVDIKDEIKATY 276 (716)
Q Consensus 207 --------~gCpwri~as~~~~~~~w~V~~~~~~HtC~~~~~~~~~-~-s~~ia~~~~~~i~~~~~~~~~~I~~~l~~~~ 276 (716)
.||+++|++.+ ...+.|.|+.+..+|||++....... + ++.+.. +...+....++.. ++...
T Consensus 151 ~~rR~~tRtGC~A~m~Vk~-~~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~-~~~~~~~~~~v~~------~~~d~ 222 (846)
T PLN03097 151 TGRRSCAKTDCKASMHVKR-RPDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAA-MARQFAEYKNVVG------LKNDS 222 (846)
T ss_pred cccccccCCCCceEEEEEE-cCCCeEEEEEEecCCCCCCCCccccchhhhhhHHH-HHhhhhccccccc------cchhh
Confidence 37999999987 45678999999999999997653322 1 111111 0000100000000 00000
Q ss_pred CcccCHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhCCCcEEEEEeccC---cCchhh---hHHHHHhcCccEEE
Q 037776 277 GVVCHEAKLLCAAKRAKHILGMDHEDGYAILNQFKDEMERINSRNIVLLETKRH---EYGEER---TSYAFKNHCRRLLA 350 (716)
Q Consensus 277 g~~~s~~k~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~~---~~~F~~---si~~f~~~~r~vi~ 350 (716)
...+-+.++..+ . ......|..||++++..||+|+|.+++|++ .++||. |+..| .+|++||+
T Consensus 223 -----~~~~~~~r~~~~--~----~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y-~~FGDvV~ 290 (846)
T PLN03097 223 -----KSSFDKGRNLGL--E----AGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDY-GNFSDVVS 290 (846)
T ss_pred -----cchhhHHHhhhc--c----cchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHH-HhcCCEEE
Confidence 001111122111 1 234578999999999999999999999985 479998 89999 57999999
Q ss_pred EeCceeccccCceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHHHHHhhcc
Q 037776 351 VDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDYAIEEFLP 430 (716)
Q Consensus 351 iD~T~~~~~y~~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~Ai~~vfP 430 (716)
||+||++|+|++||++++|+|+|+|+++|||||+.+|+.++|.|+|++|+++| ++.+|.+||||++.+|.+||++|||
T Consensus 291 fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM--~gk~P~tIiTDqd~am~~AI~~VfP 368 (846)
T PLN03097 291 FDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAM--GGQAPKVIITDQDKAMKSVISEVFP 368 (846)
T ss_pred EeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHh--CCCCCceEEecCCHHHHHHHHHHCC
Confidence 99999999999999999999999999999999999999999999999999999 6899999999999999999999999
Q ss_pred ccccccchHHHHH-HHhhhCCC-----ChhhHHHHHHhh-cCCHHHHHHHHHHHHh-hChhhHHHHhhc--CCCCccccc
Q 037776 431 KAVYRQCCLKIFT-EMVKRFPT-----APVEHFFWSACR-STSATSFNKYMDLIHN-ESEECHDWLLQT--DWSSWALFT 500 (716)
Q Consensus 431 ~a~h~~~C~~Hi~-N~~~~~~~-----~~~~~~~~~~~~-a~t~~eFe~~~~~l~~-~~~~~~~yL~~~--~~~~W~~a~ 500 (716)
++.| ++|+|||+ |+.+++.. ..+...|+.|++ +.++++|+..|..|.. ++.+.++||..+ .+++|+++|
T Consensus 369 ~t~H-r~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY 447 (846)
T PLN03097 369 NAHH-CFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTY 447 (846)
T ss_pred Ccee-hhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHH
Confidence 9999 99999999 99998853 588899999887 6899999999998864 889999999998 899999999
Q ss_pred cCCcccccccccchhhHHhHHHhh--hhcCcHHHHHHHHHHHHHHHHHHHHHh-----------------HhhhccCcCC
Q 037776 501 IPKWVKCICVTLSITDKLRNYLHQ--YLEMSIASRYVAIARLTAELFERRRME-----------------VWNWYREKVT 561 (716)
Q Consensus 501 ~~~~~~~~~~TtN~~Es~N~~lk~--~r~lpi~~lle~i~~~~~~~~~~r~~~-----------------~~~~~~~~~t 561 (716)
+++.|..|+.||+++||+|+.|++ .+..+|..|++.+...+..+..+..+. ..+.+. +||
T Consensus 448 ~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~-iYT 526 (846)
T PLN03097 448 MRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSG-VYT 526 (846)
T ss_pred hcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHH-HhH
Confidence 999999999999999999999998 467888888887766555444332211 112234 999
Q ss_pred HHHHHHHHHHhhccceEEEEEecC----eEEEEEecC-ceEEEEec----cCceeeecccccCCCCchhHHHHHHHhhc-
Q 037776 562 PTVREVIKDRTIDGQRFVLVEENG----NRLKLIDTT-SIIFYLNM----EAQSCSCGLRQKSGIPCAHACKGIQLIMG- 631 (716)
Q Consensus 562 p~~~k~l~~~~~~a~~~~V~~~~~----~~f~V~~~~-~~~~~V~l----~~~tCsC~~~~~~GiPC~H~lav~~~~~~- 631 (716)
|.+|++||+++..+..|.+...+. .+|.|...+ ...|.|.. ...+|+|++|+..||||+|||+|+...++
T Consensus 527 ~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~ 606 (846)
T PLN03097 527 HAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLS 606 (846)
T ss_pred HHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcc
Confidence 999999999999999988876432 378887632 22377743 36899999999999999999999999998
Q ss_pred -cchhhhcccchHHHHhh
Q 037776 632 -NVEEYVDNMMSVQNFCS 648 (716)
Q Consensus 632 -~~~~yi~~~ys~~~~~~ 648 (716)
.|..||.++||+++-..
T Consensus 607 ~IP~~YILkRWTKdAK~~ 624 (846)
T PLN03097 607 AIPSQYILKRWTKDAKSR 624 (846)
T ss_pred cCchhhhhhhchhhhhhc
Confidence 59999999999988653
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=6e-21 Score=166.88 Aligned_cols=89 Identities=30% Similarity=0.464 Sum_probs=84.8
Q ss_pred CceeccccCceeEE---EEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHHHHHhhc
Q 037776 353 GWKINNPYNSVMLV---AAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDYAIEEFL 429 (716)
Q Consensus 353 ~T~~~~~y~~~ll~---avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~Ai~~vf 429 (716)
|||++|+| ++++. ++|+|++|+.+|+||+++.+|+.++|.|||+.|++.+. .. |.+||||++.|+.+||+++|
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~--~~-p~~ii~D~~~~~~~Ai~~vf 76 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMP--QK-PKVIISDFDKALINAIKEVF 76 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccc--cC-ceeeeccccHHHHHHHHHHC
Confidence 79999999 98886 99999999999999999999999999999999999994 45 99999999999999999999
Q ss_pred cccccccchHHHHH-HHh
Q 037776 430 PKAVYRQCCLKIFT-EMV 446 (716)
Q Consensus 430 P~a~h~~~C~~Hi~-N~~ 446 (716)
|++.| ++|.||+. |++
T Consensus 77 P~~~~-~~C~~H~~~n~k 93 (93)
T PF10551_consen 77 PDARH-QLCLFHILRNIK 93 (93)
T ss_pred CCceE-ehhHHHHHHhhC
Confidence 99999 99999999 874
No 3
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.80 E-value=2.6e-20 Score=203.72 Aligned_cols=223 Identities=16% Similarity=0.242 Sum_probs=182.4
Q ss_pred CCCCHHHHHHHHHHHhC-cccCHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhCCCcEEEEEeccCcCchhhhHH
Q 037776 261 PNLRTVDIKDEIKATYG-VVCHEAKLLCAAKRAKHILGMDHEDGYAILNQFKDEMERINSRNIVLLETKRHEYGEERTSY 339 (716)
Q Consensus 261 ~~~~~~~I~~~l~~~~g-~~~s~~k~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~~~~~F~~si~ 339 (716)
.+++.++|.+.|+..+| ..+|.+++.|..+.+.+.+ ..|...-
T Consensus 113 ~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~-----------~~w~~R~------------------------- 156 (381)
T PF00872_consen 113 KGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEV-----------EAWRNRP------------------------- 156 (381)
T ss_pred cccccccccchhhhhhcccccCchhhhhhhhhhhhhH-----------HHHhhhc-------------------------
Confidence 58899999999999999 8899999988776654321 1111110
Q ss_pred HHHhcC-ccEEEEeCceeccccCc-----eeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEE
Q 037776 340 AFKNHC-RRLLAVDGWKINNPYNS-----VMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCI 413 (716)
Q Consensus 340 ~f~~~~-r~vi~iD~T~~~~~y~~-----~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~i 413 (716)
. ... -++|+|||+|.+.+.++ .+++++|+|.+|+..+||+.+...|+.++|.-||+.|++.+ ...|..|
T Consensus 157 -L-~~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~RG---l~~~~lv 231 (381)
T PF00872_consen 157 -L-ESEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKERG---LKDILLV 231 (381)
T ss_pred -c-ccccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhcc---cccccee
Confidence 0 123 48999999999877544 57999999999999999999999999999999999999987 4568999
Q ss_pred EcCCcchHHHHHHhhccccccccchHHHHH-HHhhhCCCC---hhhHHHHHHhhcCCHHHHHHHHHHHHh----hChhhH
Q 037776 414 MGDGDNGIDYAIEEFLPKAVYRQCCLKIFT-EMVKRFPTA---PVEHFFWSACRSTSATSFNKYMDLIHN----ESEECH 485 (716)
Q Consensus 414 itD~~~al~~Ai~~vfP~a~h~~~C~~Hi~-N~~~~~~~~---~~~~~~~~~~~a~t~~eFe~~~~~l~~----~~~~~~ 485 (716)
|+|+++||..||.++||++.+ +.|++|++ |+.++++.+ .+...++.+..+.+.+++...++.+.+ ..|.+.
T Consensus 232 v~Dg~~gl~~ai~~~fp~a~~-QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~ 310 (381)
T PF00872_consen 232 VSDGHKGLKEAIREVFPGAKW-QRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAA 310 (381)
T ss_pred eccccccccccccccccchhh-hhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhcccccccccchhh
Confidence 999999999999999999999 99999999 999998654 667778888788888888777777654 478888
Q ss_pred HHHhhcCCCCccccccCCcccccccccchhhHHhHHHhhh
Q 037776 486 DWLLQTDWSSWALFTIPKWVKCICVTLSITDKLRNYLHQY 525 (716)
Q Consensus 486 ~yL~~~~~~~W~~a~~~~~~~~~~~TtN~~Es~N~~lk~~ 525 (716)
++|.+.....|+..-|+...+--+.|||.+|++|+.||..
T Consensus 311 ~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr 350 (381)
T PF00872_consen 311 KSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRR 350 (381)
T ss_pred hhhhhccccccceeeecchhccccchhhhccccccchhhh
Confidence 8888876666665545554355778999999999999983
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=99.66 E-value=3.7e-16 Score=127.66 Aligned_cols=66 Identities=27% Similarity=0.579 Sum_probs=64.0
Q ss_pred CCcCCCcEECCHHHHHHHHHHHHHHcCceEEEEeecCeEEEEEeccCCCceEEEEEEecCcceEEE
Q 037776 161 MILYHGQRFRDVSHFRKAIEVFAIRDGFKLCVMENRAHAVSYECSDLRCDWKIKAERVVNGRTFIV 226 (716)
Q Consensus 161 ~~l~vG~~F~s~ee~k~ai~~yAi~~gf~~~~~kS~~~r~~~~C~~~gCpwri~as~~~~~~~w~V 226 (716)
+.|.+||+|+|+++|+.||..||++++|++++.+|+++|++++|...+|||+|+|++.++++.|+|
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 469999999999999999999999999999999999999999999999999999999999999986
No 5
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.44 E-value=8.1e-13 Score=142.18 Aligned_cols=221 Identities=14% Similarity=0.152 Sum_probs=165.6
Q ss_pred CCCCCHHHHHHHHHHHhCcccCHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhCCCcEEEEEeccCcCchhhhHH
Q 037776 260 QPNLRTVDIKDEIKATYGVVCHEAKLLCAAKRAKHILGMDHEDGYAILNQFKDEMERINSRNIVLLETKRHEYGEERTSY 339 (716)
Q Consensus 260 ~~~~~~~~I~~~l~~~~g~~~s~~k~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~~~~~F~~si~ 339 (716)
..+++++++...+++.++..+|...+.+.-...++. +.+++..-
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e~---------------v~~~~~r~--------------------- 141 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVTDRLDEK---------------VKAWQNRP--------------------- 141 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHHH---------------HHHHHhcc---------------------
Confidence 358899999999999999888887777665544432 22222221
Q ss_pred HHHhcCccEEEEeCceeccc--cCceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEEEcCC
Q 037776 340 AFKNHCRRLLAVDGWKINNP--YNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCIMGDG 417 (716)
Q Consensus 340 ~f~~~~r~vi~iD~T~~~~~--y~~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~ 417 (716)
+ +..+++++||+|++-+ -+..+++|+|++.+|+..+||+.+...|+ ..|.-||..|+..+ ......+++|.
T Consensus 142 --l-~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rg---l~~v~l~v~Dg 214 (379)
T COG3328 142 --L-GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRG---LSDVLLVVVDG 214 (379)
T ss_pred --c-cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhcc---ccceeEEecch
Confidence 1 3568999999999988 44579999999999999999999999999 99998999998886 34556677899
Q ss_pred cchHHHHHHhhccccccccchHHHHH-HHhhhCCCC---hhhHHHHHHhhcCCHHHHHHHHHHH----HhhChhhHHHHh
Q 037776 418 DNGIDYAIEEFLPKAVYRQCCLKIFT-EMVKRFPTA---PVEHFFWSACRSTSATSFNKYMDLI----HNESEECHDWLL 489 (716)
Q Consensus 418 ~~al~~Ai~~vfP~a~h~~~C~~Hi~-N~~~~~~~~---~~~~~~~~~~~a~t~~eFe~~~~~l----~~~~~~~~~yL~ 489 (716)
.+|+.+||.++||.+.+ +.|..|+. |+..+...+ .+...+..+..+.+.++....|..+ ....|....++.
T Consensus 215 ~~gl~~aI~~v~p~a~~-Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~ 293 (379)
T COG3328 215 LKGLPEAISAVFPQAAV-QRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWR 293 (379)
T ss_pred hhhhHHHHHHhccHhhh-hhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHH
Confidence 99999999999999999 99999999 999988765 3334444455566666555555553 334677777777
Q ss_pred hcCCCCccccccCCcccccccccchhhHHhHHHhh
Q 037776 490 QTDWSSWALFTIPKWVKCICVTLSITDKLRNYLHQ 524 (716)
Q Consensus 490 ~~~~~~W~~a~~~~~~~~~~~TtN~~Es~N~~lk~ 524 (716)
+.--+.|.-.-|+...+--+.|||.+|++|+.++.
T Consensus 294 ~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 294 NALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred HHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 76444443222222213457899999999998875
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.87 E-value=8.8e-10 Score=73.09 Aligned_cols=27 Identities=44% Similarity=0.646 Sum_probs=25.1
Q ss_pred ceeeecccccCCCCchhHHHHHHHhhc
Q 037776 605 QSCSCGLRQKSGIPCAHACKGIQLIMG 631 (716)
Q Consensus 605 ~tCsC~~~~~~GiPC~H~lav~~~~~~ 631 (716)
.+|||++||..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998875
No 7
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=98.67 E-value=1e-07 Score=83.23 Aligned_cols=69 Identities=12% Similarity=0.355 Sum_probs=65.2
Q ss_pred ECCHHHHHHHHHHHHHHcCceEEEEeecCeEEEEEecc------------------------------------------
Q 037776 169 FRDVSHFRKAIEVFAIRDGFKLCVMENRAHAVSYECSD------------------------------------------ 206 (716)
Q Consensus 169 F~s~ee~k~ai~~yAi~~gf~~~~~kS~~~r~~~~C~~------------------------------------------ 206 (716)
|.+++|++-+|+.++...|++|.+.+||.+.+.|+|..
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 78999999999999999999999999999999999952
Q ss_pred CCCceEEEEEEecCcceEEEEEecCcccccc
Q 037776 207 LRCDWKIKAERVVNGRTFIVTEFVAQHKCTR 237 (716)
Q Consensus 207 ~gCpwri~as~~~~~~~w~V~~~~~~HtC~~ 237 (716)
..|||+|+|......+.|.|..++..|+|++
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 3899999999999999999999999999974
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=98.41 E-value=5e-07 Score=78.39 Aligned_cols=61 Identities=26% Similarity=0.429 Sum_probs=53.8
Q ss_pred HHHHHHHHHcCceEEEEeecCe-------EEEEEecc----------------------CCCceEEEEEEecCcceEEEE
Q 037776 177 KAIEVFAIRDGFKLCVMENRAH-------AVSYECSD----------------------LRCDWKIKAERVVNGRTFIVT 227 (716)
Q Consensus 177 ~ai~~yAi~~gf~~~~~kS~~~-------r~~~~C~~----------------------~gCpwri~as~~~~~~~w~V~ 227 (716)
++|+.||..+||.+++.+|.+. ++.++|.. .||||+|.+.+.. .+.|.|+
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 4789999999999999876553 78999974 5999999999877 8999999
Q ss_pred EecCccccccc
Q 037776 228 EFVAQHKCTRR 238 (716)
Q Consensus 228 ~~~~~HtC~~~ 238 (716)
.+..+|||++.
T Consensus 80 ~~~~~HNH~L~ 90 (91)
T PF03101_consen 80 SFVLEHNHPLC 90 (91)
T ss_pred ECcCCcCCCCC
Confidence 99999999875
No 9
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=98.10 E-value=2.7e-06 Score=61.79 Aligned_cols=31 Identities=32% Similarity=0.571 Sum_probs=27.5
Q ss_pred EeccCceeeecccccCCCCchhHHHHHHHhh
Q 037776 600 LNMEAQSCSCGLRQKSGIPCAHACKGIQLIM 630 (716)
Q Consensus 600 V~l~~~tCsC~~~~~~GiPC~H~lav~~~~~ 630 (716)
+++...+|||..|+..|.||+|++|++...+
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 5667899999999999999999999998753
No 10
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=96.61 E-value=0.00094 Score=62.87 Aligned_cols=81 Identities=21% Similarity=0.136 Sum_probs=67.8
Q ss_pred ccEEEEeCceeccccCceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHHHH
Q 037776 346 RRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDYAI 425 (716)
Q Consensus 346 r~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~Ai 425 (716)
++.+.+|-||.+.+=+ ..+...++|.+++ +|++-|-..-+..+=..||..+.+.. ...|..|+||+.++...|+
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~---~~~p~~ivtDk~~aY~~A~ 74 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRH---RGEPRVIVTDKLPAYPAAI 74 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceee---ccccceeecccCCccchhh
Confidence 3678999999875433 3455788899999 89999999999998899998888877 2689999999999999999
Q ss_pred Hhhcccc
Q 037776 426 EEFLPKA 432 (716)
Q Consensus 426 ~~vfP~a 432 (716)
++++|..
T Consensus 75 ~~l~~~~ 81 (140)
T PF13610_consen 75 KELNPEG 81 (140)
T ss_pred hhccccc
Confidence 9998874
No 11
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=94.87 E-value=1.5 Score=49.84 Aligned_cols=132 Identities=17% Similarity=0.165 Sum_probs=94.2
Q ss_pred cCCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHHHHHhhccccccccchHHHHH-HHhhhCCC-ChhhHHHHHHhh
Q 037776 386 VEDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDYAIEEFLPKAVYRQCCLKIFT-EMVKRFPT-APVEHFFWSACR 463 (716)
Q Consensus 386 ~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~Ai~~vfP~a~h~~~C~~Hi~-N~~~~~~~-~~~~~~~~~~~~ 463 (716)
..+.+-|.-+.+.+.+...+....-+++.+|+...|..++. .+|.+.| .+..+|+. .+.+.++. +.+...++.+.+
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~-~LD~FHl~k~i~~~~~~~~~~~~~~~~al~ 312 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEY-FLDRFHLNKKIKQALSHDPELKEKIRKALK 312 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceE-EecHHHHHHHHHHHhhhChHHHHHHHHHHH
Confidence 55678899999999998864444457788999999988776 9999999 99999999 99888863 467777888888
Q ss_pred cCCHHHHHHHHHHHHhh--Ch-------hhHHHHhhcCCCCccccccCCcccccccccchhhHHhHHHhh
Q 037776 464 STSATSFNKYMDLIHNE--SE-------ECHDWLLQTDWSSWALFTIPKWVKCICVTLSITDKLRNYLHQ 524 (716)
Q Consensus 464 a~t~~eFe~~~~~l~~~--~~-------~~~~yL~~~~~~~W~~a~~~~~~~~~~~TtN~~Es~N~~lk~ 524 (716)
.....+++..++.+... .+ +...||..+.... .+|-. +-|.......|+.+..+..
T Consensus 313 ~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i--~~y~~---~~~~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 313 KGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGI--KPYRE---REGLRGIGAEESVSHVLSY 377 (470)
T ss_pred hcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHh--hhhhh---ccCCCccchhhhhhhHHHH
Confidence 88888998888887653 22 3455665541111 12211 1233445567888777643
No 12
>PHA02517 putative transposase OrfB; Reviewed
Probab=93.16 E-value=3.4 Score=43.34 Aligned_cols=148 Identities=11% Similarity=0.039 Sum_probs=81.4
Q ss_pred HHHHHHhhhhhc-CCCCCHHHHHHHHHHHhCcccCHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhCCCcEEEEE
Q 037776 248 WISAIYLHRWKL-QPNLRTVDIKDEIKATYGVVCHEAKLLCAAKRAKHILGMDHEDGYAILNQFKDEMERINSRNIVLLE 326 (716)
Q Consensus 248 ~ia~~~~~~i~~-~~~~~~~~I~~~l~~~~g~~~s~~k~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~ 326 (716)
.+...+.+.+.. .+.++.+.|...|++. |+.+|.++++|..+.+ |-.... ...-.....+... .
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~-----gl~~~~-------~~k~~~~~~~~~~-~- 94 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKEL-----GLAGVL-------RGKKVRTTISRKA-V- 94 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHc-----CCceEe-------cCCCcCCCCCCCC-C-
Confidence 455555666554 5889999999998755 9999999998865432 110000 0000000000000 0
Q ss_pred eccC--cCchhhhHHHHHhcCccEEEEeCceeccccCceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcc
Q 037776 327 TKRH--EYGEERTSYAFKNHCRRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALR 404 (716)
Q Consensus 327 ~d~~--~~~F~~si~~f~~~~r~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~ 404 (716)
..++ ...|.. ..-..+++.|.|++...- +..++++-+|...+ +++|+.+...++.+. ++..|..++.
T Consensus 95 ~~~n~~~r~f~~------~~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~---~~~~l~~a~~ 163 (277)
T PHA02517 95 AAPDRVNRQFVA------TRPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDF---VLDALEQALW 163 (277)
T ss_pred CCCCcccCCCCC------CCCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHH---HHHHHHHHHH
Confidence 0000 111211 124568999999986543 55566666776555 467788887777775 4455554442
Q ss_pred c-CCCCCeEEEcCCcchH
Q 037776 405 L-DHGEGLCIMGDGDNGI 421 (716)
Q Consensus 405 ~-~~~~~~~iitD~~~al 421 (716)
. +...+..|.||+....
T Consensus 164 ~~~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 164 ARGRPGGLIHHSDKGSQY 181 (277)
T ss_pred hcCCCcCcEeeccccccc
Confidence 1 1222356779998754
No 13
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=92.19 E-value=7.5 Score=40.57 Aligned_cols=145 Identities=8% Similarity=-0.014 Sum_probs=85.2
Q ss_pred hHHHHHHhhhhhcCCCCCHHHHHHHHHHH---hCc-ccCHHHHHHHHHHH-HHHhcCChhhHHHHHHHHHHHHHHhCCCc
Q 037776 247 KWISAIYLHRWKLQPNLRTVDIKDEIKAT---YGV-VCHEAKLLCAAKRA-KHILGMDHEDGYAILNQFKDEMERINSRN 321 (716)
Q Consensus 247 ~~ia~~~~~~i~~~~~~~~~~I~~~l~~~---~g~-~~s~~k~~rak~~a-~~~~~g~~~~sy~~L~~y~~~l~~~NPg~ 321 (716)
..+...+.+.+..++.+..+.|...|+.. .|+ .++..+++|..+.+ +..... ...+.+
T Consensus 11 ~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~r-----------------~~~~~~ 73 (262)
T PRK14702 11 TDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLERK-----------------PAVPPS 73 (262)
T ss_pred HHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCccccC-----------------CCCCCC
Confidence 33455566666677889999999999875 377 49999999875442 110000 000000
Q ss_pred EEEEEeccCcCchhhhHHHHHhcCccEEEEeCceeccccCceeEEEEEEcCCCceEEEEEEEeec-CCchhHHHHHHH-H
Q 037776 322 IVLLETKRHEYGEERTSYAFKNHCRRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVHV-EDLDSWVFFIKN-I 399 (716)
Q Consensus 322 ~~~v~~d~~~~~F~~si~~f~~~~r~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~pla~alv~~-E~~es~~Wfl~~-l 399 (716)
.- .....|. ...-..+++.|-||....-++.++.++-+|...+ .++||++... .+.+.-.-+|+. +
T Consensus 74 ~~-----~~~~~~~------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~ 141 (262)
T PRK14702 74 KR-----AHTGRVA------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAV 141 (262)
T ss_pred Cc-----CCCCccc------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHH
Confidence 00 0000010 0123468999999987654446788888887776 6789999874 555554445543 3
Q ss_pred HHHccc-CCCCCeEEEcCCcch
Q 037776 400 NNALRL-DHGEGLCIMGDGDNG 420 (716)
Q Consensus 400 ~~~~~~-~~~~~~~iitD~~~a 420 (716)
....+. ....|..|.||+...
T Consensus 142 ~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 142 ERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred HHHhcccCCCCCeEEEcCCCcc
Confidence 333211 123578889999874
No 14
>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=91.84 E-value=0.28 Score=50.68 Aligned_cols=92 Identities=15% Similarity=0.144 Sum_probs=65.9
Q ss_pred EEEeCceeccccCceeEEEEEEcC--CCceEEEEEEEeecCCchhHHHHHHHH-HHHcccCCCCCeEEEcCCcchHHHHH
Q 037776 349 LAVDGWKINNPYNSVMLVAAALDG--NNGILPIAFCEVHVEDLDSWVFFIKNI-NNALRLDHGEGLCIMGDGDNGIDYAI 425 (716)
Q Consensus 349 i~iD~T~~~~~y~~~ll~avg~d~--~~~~~pla~alv~~E~~es~~Wfl~~l-~~~~~~~~~~~~~iitD~~~al~~Ai 425 (716)
|+||-+.....+.. +..+-+|. +++.+ ++++++-+.++..-||..+ -... .....+|++|...+...|+
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~i---l~i~~~r~~~~l~~~~~~~~~~~~---~~~v~~V~~Dm~~~y~~~~ 72 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGRI---LDILPGRDKETLKDFFRSLYPEEE---RKNVKVVSMDMSPPYRSAI 72 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCceE---EEEcCCccHHHHHHHHHHhCcccc---ccceEEEEcCCCccccccc
Confidence 46777666554442 33444554 33332 3578888888888777766 3332 3456889999999999999
Q ss_pred HhhccccccccchHHHHH-HHhhhC
Q 037776 426 EEFLPKAVYRQCCLKIFT-EMVKRF 449 (716)
Q Consensus 426 ~~vfP~a~h~~~C~~Hi~-N~~~~~ 449 (716)
++.||+|.+ ..-.|||+ ++.+.+
T Consensus 73 ~~~~P~A~i-v~DrFHvvk~~~~al 96 (249)
T PF01610_consen 73 REYFPNAQI-VADRFHVVKLANRAL 96 (249)
T ss_pred ccccccccc-ccccchhhhhhhhcc
Confidence 999999999 99999999 876533
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=91.27 E-value=0.75 Score=36.45 Aligned_cols=39 Identities=15% Similarity=0.421 Sum_probs=32.5
Q ss_pred eEEEEEeccCCCceEEEEEEecCcceEEEEEecCccccc
Q 037776 198 HAVSYECSDLRCDWKIKAERVVNGRTFIVTEFVAQHKCT 236 (716)
Q Consensus 198 ~r~~~~C~~~gCpwri~as~~~~~~~w~V~~~~~~HtC~ 236 (716)
.|--++|+..+||++-.+.+..+.....++++..+|||+
T Consensus 21 pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 21 PRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp EEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred eeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 566799999999999999998878888999999999996
No 16
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=91.19 E-value=13 Score=39.70 Aligned_cols=145 Identities=8% Similarity=0.021 Sum_probs=85.8
Q ss_pred HHHHHHhhhhhcCCCCCHHHHHHHHHHHh---Cc-ccCHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhCCCcEE
Q 037776 248 WISAIYLHRWKLQPNLRTVDIKDEIKATY---GV-VCHEAKLLCAAKRAKHILGMDHEDGYAILNQFKDEMERINSRNIV 323 (716)
Q Consensus 248 ~ia~~~~~~i~~~~~~~~~~I~~~l~~~~---g~-~~s~~k~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~ 323 (716)
.+...+.+.+..++.+..+.|...|+... |+ .++..+++|..+.+- +.+. .+...+.+.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~G--l~~~--------------~~~~~~~~~- 113 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNA--LLLE--------------RKPAVPPSK- 113 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHcC--Cccc--------------ccCCCCCCC-
Confidence 34555555556678999999999998752 66 589999988754420 0000 000000000
Q ss_pred EEEeccCcCchhhhHHHHHhcCccEEEEeCceeccccCceeEEEEEEcCCCceEEEEEEEeec-CCchhHHHHHH-HHHH
Q 037776 324 LLETKRHEYGEERTSYAFKNHCRRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVHV-EDLDSWVFFIK-NINN 401 (716)
Q Consensus 324 ~v~~d~~~~~F~~si~~f~~~~r~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~pla~alv~~-E~~es~~Wfl~-~l~~ 401 (716)
......|. ...-..+++.|-||....-++.++.++-+|...+ .+|||++... .+.+.-.-+|+ .+..
T Consensus 114 ----~~~~~~~~------~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~ 182 (301)
T PRK09409 114 ----RAHTGRVA------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVER 182 (301)
T ss_pred ----CCCCCCcC------CCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHH
Confidence 00000110 0123468999999986654556788888888777 6889999875 56555544554 4444
Q ss_pred Hccc-CCCCCeEEEcCCcch
Q 037776 402 ALRL-DHGEGLCIMGDGDNG 420 (716)
Q Consensus 402 ~~~~-~~~~~~~iitD~~~a 420 (716)
..+. ....|..|.||+...
T Consensus 183 ~~~~~~~~~~~iihSDrGsq 202 (301)
T PRK09409 183 RFGNDLPSSPVEWLTDNGSC 202 (301)
T ss_pred HhccCCCCCCcEEecCCCcc
Confidence 4321 123477889999874
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=91.13 E-value=0.4 Score=52.46 Aligned_cols=58 Identities=12% Similarity=0.303 Sum_probs=51.6
Q ss_pred cCCCcEECCHHHHHHHHHHHHHHcCceEEEEeecC-eEEEEEeccCCCceEEEEEEecC
Q 037776 163 LYHGQRFRDVSHFRKAIEVFAIRDGFKLCVMENRA-HAVSYECSDLRCDWKIKAERVVN 220 (716)
Q Consensus 163 l~vG~~F~s~ee~k~ai~~yAi~~gf~~~~~kS~~-~r~~~~C~~~gCpwri~as~~~~ 220 (716)
-..+..|++.++-+.+|+.|..+.+..|..+.|-+ +.|+|.|.-..|||+|..+..+.
T Consensus 22 ~~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g~ 80 (496)
T PF04684_consen 22 SAQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCGN 80 (496)
T ss_pred cccccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeeccc
Confidence 45578899999999999999999999999988865 78999999999999999987543
No 18
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.17 E-value=6.1 Score=39.58 Aligned_cols=119 Identities=13% Similarity=0.075 Sum_probs=80.0
Q ss_pred HHHHHhCcccCHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhCCCcEEEEEeccCcCchhhhHHHHHhcCccEEE
Q 037776 271 EIKATYGVVCHEAKLLCAAKRAKHILGMDHEDGYAILNQFKDEMERINSRNIVLLETKRHEYGEERTSYAFKNHCRRLLA 350 (716)
Q Consensus 271 ~l~~~~g~~~s~~k~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~~~~~F~~si~~f~~~~r~vi~ 350 (716)
.+....|+.+.+.++.|.=++. -+.|...+.+.++. -++++.
T Consensus 33 e~l~~rgi~v~h~Ti~rwv~k~--------------~~~~~~~~~~r~~~------------------------~~~~w~ 74 (215)
T COG3316 33 EMLAERGIEVDHETIHRWVQKY--------------GPLLARRLKRRKRK------------------------AGDSWR 74 (215)
T ss_pred HHHHHcCcchhHHHHHHHHHHH--------------hHHHHHHhhhhccc------------------------ccccee
Confidence 3455678888888887764432 12333444444332 346778
Q ss_pred EeCceeccccCceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHHHHHhhcc
Q 037776 351 VDGWKINNPYNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDYAIEEFLP 430 (716)
Q Consensus 351 iD~T~~~~~y~~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~Ai~~vfP 430 (716)
+|-||.+.+-+.. +.--++|.+ ..+|-+-|...-+...=.-||..+++.. ..|.+|+||+.+....|+.++-+
T Consensus 75 vDEt~ikv~gkw~-ylyrAid~~--g~~Ld~~L~~rRn~~aAk~Fl~kllk~~----g~p~v~vtDka~s~~~A~~~l~~ 147 (215)
T COG3316 75 VDETYIKVNGKWH-YLYRAIDAD--GLTLDVWLSKRRNALAAKAFLKKLLKKH----GEPRVFVTDKAPSYTAALRKLGS 147 (215)
T ss_pred eeeeEEeeccEee-ehhhhhccC--CCeEEEEEEcccCcHHHHHHHHHHHHhc----CCCceEEecCccchHHHHHhcCc
Confidence 8888887543332 222344555 4467777877777777777777777665 47889999999999999999988
Q ss_pred cccc
Q 037776 431 KAVY 434 (716)
Q Consensus 431 ~a~h 434 (716)
.+.|
T Consensus 148 ~~eh 151 (215)
T COG3316 148 EVEH 151 (215)
T ss_pred chhe
Confidence 7777
No 19
>PF13565 HTH_32: Homeodomain-like domain
Probab=84.53 E-value=2 Score=35.47 Aligned_cols=40 Identities=8% Similarity=0.183 Sum_probs=34.1
Q ss_pred HHHHHhhhhhcCCCCCHHHHHHHHHHHhCccc--CHHHHHHH
Q 037776 249 ISAIYLHRWKLQPNLRTVDIKDEIKATYGVVC--HEAKLLCA 288 (716)
Q Consensus 249 ia~~~~~~i~~~~~~~~~~I~~~l~~~~g~~~--s~~k~~ra 288 (716)
+...+.+.+..+|.+++.+|...|.+.+|+.+ |.+++||.
T Consensus 35 ~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 35 QRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 44566677788999999999999999999876 99999874
No 20
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=83.98 E-value=0.45 Score=34.10 Aligned_cols=15 Identities=7% Similarity=0.091 Sum_probs=13.1
Q ss_pred eeCCcCCcCCCCCCC
Q 037776 696 RQCIENNSDAATNNP 710 (716)
Q Consensus 696 ~~Cs~C~~~GHn~~~ 710 (716)
++|+.|++.||.+.-
T Consensus 2 ~kC~~CG~~GH~~t~ 16 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTN 16 (40)
T ss_pred ccccccccccccccC
Confidence 699999999998753
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=80.62 E-value=2.8 Score=32.69 Aligned_cols=46 Identities=15% Similarity=0.305 Sum_probs=24.7
Q ss_pred cCceEEEEeecCeEEEEEeccC---CCceEEEEEEecCcceEEEEEecCcccc
Q 037776 186 DGFKLCVMENRAHAVSYECSDL---RCDWKIKAERVVNGRTFIVTEFVAQHKC 235 (716)
Q Consensus 186 ~gf~~~~~kS~~~r~~~~C~~~---gCpwri~as~~~~~~~w~V~~~~~~HtC 235 (716)
.|+.|...+.........|..- +|+++|... . +.-.|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~--~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--A--GDGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--C--CCCEEEECCCccCC
Confidence 4777877776688889999873 899999987 1 22345555578887
No 22
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=79.79 E-value=7.5 Score=34.53 Aligned_cols=76 Identities=11% Similarity=-0.030 Sum_probs=54.1
Q ss_pred CccEEEEeCceec-cccCceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHH
Q 037776 345 CRRLLAVDGWKIN-NPYNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDY 423 (716)
Q Consensus 345 ~r~vi~iD~T~~~-~~y~~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~ 423 (716)
-..++.+|.++.. ...++.....+.+|..-.. .+++.+-..++.+.+.-+|....... +...|.+|+||+..+...
T Consensus 5 p~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 5 PGERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKR--GGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHH--S-SE-SEEEEESCHHHHS
T ss_pred CCCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeeccccccccccccccccccc--ccccceeccccccccccc
Confidence 3458899999766 3455688888888876665 55777777778888888887666665 233399999999998763
No 23
>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=78.23 E-value=3.2 Score=43.45 Aligned_cols=133 Identities=11% Similarity=0.120 Sum_probs=81.6
Q ss_pred CCCCCHHHHHHHHHHHhCcccCHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhCCCcEEEEEeccCcCchhhhHH
Q 037776 260 QPNLRTVDIKDEIKATYGVVCHEAKLLCAAKRAKHILGMDHEDGYAILNQFKDEMERINSRNIVLLETKRHEYGEERTSY 339 (716)
Q Consensus 260 ~~~~~~~~I~~~l~~~~g~~~s~~k~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~~~~~F~~si~ 339 (716)
.-.++...|.+.+... |+.+|.+++.+.-.++.+.+ ......|.+.
T Consensus 18 ~~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l-----------~~~~~~l~~~---------------------- 63 (271)
T PF03050_consen 18 VYHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEAL-----------KPLYEALKEE---------------------- 63 (271)
T ss_pred cCCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhh-----------hhhhhhhhhh----------------------
Confidence 3456677777777776 99999999887655543321 1111112111
Q ss_pred HHHhcCccEEEEeCceec----cccC-ceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEEE
Q 037776 340 AFKNHCRRLLAVDGWKIN----NPYN-SVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCIM 414 (716)
Q Consensus 340 ~f~~~~r~vi~iD~T~~~----~~y~-~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~ii 414 (716)
. --.+||.+|-|..+ ++.. +-+.++++-+ .+.|.+.++-..+...-+|. + ..-+++
T Consensus 64 -~--~~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~---------~-~~Gilv 124 (271)
T PF03050_consen 64 -L--RSSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLG---------D-FSGILV 124 (271)
T ss_pred -c--cccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhc---------c-cceeee
Confidence 1 14689999988887 4433 3344444433 55555656555554444432 2 224889
Q ss_pred cCCcchHHHHHHhhccccccccchHHHHH-HHhhhCCC
Q 037776 415 GDGDNGIDYAIEEFLPKAVYRQCCLKIFT-EMVKRFPT 451 (716)
Q Consensus 415 tD~~~al~~Ai~~vfP~a~h~~~C~~Hi~-N~~~~~~~ 451 (716)
||+..+-.. +..+.| +.|+.|+. .|.+-...
T Consensus 125 sD~y~~Y~~-----~~~~~h-q~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 125 SDGYSAYNK-----LAGITH-QLCWAHLRRDFQDAAES 156 (271)
T ss_pred ccccccccc-----cccccc-ccccccccccccccccc
Confidence 999988654 227889 99999999 88765543
No 24
>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=78.23 E-value=2.8 Score=33.02 Aligned_cols=38 Identities=16% Similarity=0.334 Sum_probs=31.4
Q ss_pred eEEEEEecc-CCCceEEEEEEecCcceEEEEEecCcccc
Q 037776 198 HAVSYECSD-LRCDWKIKAERVVNGRTFIVTEFVAQHKC 235 (716)
Q Consensus 198 ~r~~~~C~~-~gCpwri~as~~~~~~~w~V~~~~~~HtC 235 (716)
.|--++|+. .+|+++=.+.+..++....++++..+|||
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 455689998 89999888887766667788899999998
No 25
>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=76.34 E-value=1.5 Score=25.82 Aligned_cols=14 Identities=14% Similarity=0.401 Sum_probs=11.9
Q ss_pred eeCCcCCcCCCCCC
Q 037776 696 RQCIENNSDAATNN 709 (716)
Q Consensus 696 ~~Cs~C~~~GHn~~ 709 (716)
++|-+|++.||..+
T Consensus 1 ~~C~~C~~~GH~~~ 14 (18)
T PF00098_consen 1 RKCFNCGEPGHIAR 14 (18)
T ss_dssp SBCTTTSCSSSCGC
T ss_pred CcCcCCCCcCcccc
Confidence 37999999999765
No 26
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=68.59 E-value=76 Score=30.24 Aligned_cols=120 Identities=9% Similarity=0.143 Sum_probs=69.0
Q ss_pred hHHHHHHHHHHHHHHhCCCcEEEEEeccCcCchhhhHHHHHhcCccEEEEeCceeccccCceeEEEEEEcCCCceEEEEE
Q 037776 302 DGYAILNQFKDEMERINSRNIVLLETKRHEYGEERTSYAFKNHCRRLLAVDGWKINNPYNSVMLVAAALDGNNGILPIAF 381 (716)
Q Consensus 302 ~sy~~L~~y~~~l~~~NPg~~~~v~~d~~~~~F~~si~~f~~~~r~vi~iD~T~~~~~y~~~ll~avg~d~~~~~~pla~ 381 (716)
+.|..+..++..+++.-...-+ -|..||- ++..+.+|+.++..-+.|-.|.=..
T Consensus 13 ~~~~~v~~~~~~~k~~w~~~Gc------------------------si~~DgW--td~~~~~lInf~v~~~~g~~Flksv 66 (153)
T PF04937_consen 13 KEYKEVKEQVKEHKKSWKRTGC------------------------SIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSV 66 (153)
T ss_pred HHHHHHHHHHHHHHHHHHhcCE------------------------EEEEecC--cCCCCCeEEEEEEEcccccEEEEEE
Confidence 4456666777776665322223 3344443 3344455666665555565554332
Q ss_pred EEeec-CCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHHHHHh---hccccccccchHHHHH-HHhhhCC
Q 037776 382 CEVHV-EDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDYAIEE---FLPKAVYRQCCLKIFT-EMVKRFP 450 (716)
Q Consensus 382 alv~~-E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~Ai~~---vfP~a~h~~~C~~Hi~-N~~~~~~ 450 (716)
-.-.. .+.+...-+|+...+.+ +.....-||||....+.+|-+. -+|.... .-|..|-. -+.+.+.
T Consensus 67 d~s~~~~~a~~l~~ll~~vIeeV--G~~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw-~~CaaH~inLmledi~ 137 (153)
T PF04937_consen 67 DASSIIKTAEYLFELLDEVIEEV--GEENVVQVVTDNASNMKKAGKLLMEKYPHIFW-TPCAAHCINLMLEDIG 137 (153)
T ss_pred ecccccccHHHHHHHHHHHHHHh--hhhhhhHHhccCchhHHHHHHHHHhcCCCEEE-echHHHHHHHHHHHHh
Confidence 22111 34444444444444444 4556677899999998888444 4788888 89999988 4444443
No 27
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=60.01 E-value=7.4 Score=46.15 Aligned_cols=21 Identities=38% Similarity=0.776 Sum_probs=9.4
Q ss_pred CCCCCCCCcchhhhccCCcch
Q 037776 101 PTGRCSDDDDESQEENNDEED 121 (716)
Q Consensus 101 p~~~~~~~~~~~~~e~~d~~d 121 (716)
|.++.+|+||++++|+.|+||
T Consensus 1402 ~~~dd~DeeeD~e~Ed~dEdd 1422 (1516)
T KOG1832|consen 1402 PTDDDSDEEEDDETEDEDEDD 1422 (1516)
T ss_pred CCccccCccccchhhcccccc
Confidence 444444444444444444443
No 28
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=55.19 E-value=7.1 Score=34.11 Aligned_cols=48 Identities=21% Similarity=0.238 Sum_probs=29.2
Q ss_pred EEEEec-CceEEEEeccCceeeeccccc-----CCCCchhHHHHHHHhhccchhhhc
Q 037776 588 LKLIDT-TSIIFYLNMEAQSCSCGLRQK-----SGIPCAHACKGIQLIMGNVEEYVD 638 (716)
Q Consensus 588 f~V~~~-~~~~~~V~l~~~tCsC~~~~~-----~GiPC~H~lav~~~~~~~~~~yi~ 638 (716)
|.|--+ ++. |+++.+ -|||..|-. -.-||.|++..-...--.-.++|+
T Consensus 35 ~fVyvG~~rd-YIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~ 88 (117)
T COG5431 35 FFVYVGKERD-YILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYID 88 (117)
T ss_pred EEEEEccccc-eEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEE
Confidence 344433 445 898887 899998862 245799998764443323333443
No 29
>PF13592 HTH_33: Winged helix-turn helix
Probab=47.61 E-value=28 Score=27.32 Aligned_cols=31 Identities=16% Similarity=0.161 Sum_probs=26.4
Q ss_pred CCCCCHHHHHHHHHHHhCcccCHHHHHHHHH
Q 037776 260 QPNLRTVDIKDEIKATYGVVCHEAKLLCAAK 290 (716)
Q Consensus 260 ~~~~~~~~I~~~l~~~~g~~~s~~k~~rak~ 290 (716)
+..++...|...|.+.||+.+|.+.+++.-.
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~ 32 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKYSPSGVYRLLK 32 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEEcHHHHHHHHH
Confidence 3567889999999999999999999887644
No 30
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=46.70 E-value=11 Score=25.86 Aligned_cols=15 Identities=7% Similarity=-0.026 Sum_probs=12.8
Q ss_pred CeeeCCcCCcCCCCC
Q 037776 694 RARQCIENNSDAATN 708 (716)
Q Consensus 694 ~~~~Cs~C~~~GHn~ 708 (716)
..+.|-+|++.||--
T Consensus 7 ~~Y~C~~C~~~GH~i 21 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWI 21 (32)
T ss_pred CCCEeecCCCCCccH
Confidence 458999999999964
No 31
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=44.59 E-value=6.5 Score=33.85 Aligned_cols=6 Identities=33% Similarity=0.634 Sum_probs=2.3
Q ss_pred HHHHHH
Q 037776 178 AIEVFA 183 (716)
Q Consensus 178 ai~~yA 183 (716)
++.-|+
T Consensus 49 a~~~~~ 54 (101)
T PF09026_consen 49 AMAYFT 54 (101)
T ss_dssp HHHHHH
T ss_pred HHhhcc
Confidence 333333
No 32
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=41.72 E-value=81 Score=36.12 Aligned_cols=44 Identities=18% Similarity=0.395 Sum_probs=30.1
Q ss_pred EEEEEecCceEEEEecc----CceeeecccccCCCCchhHHHHHHHhhcc
Q 037776 587 RLKLIDTTSIIFYLNME----AQSCSCGLRQKSGIPCAHACKGIQLIMGN 632 (716)
Q Consensus 587 ~f~V~~~~~~~~~V~l~----~~tCsC~~~~~~GiPC~H~lav~~~~~~~ 632 (716)
...|.......+.|++. +.+|||.. ...| =|.|++||+......
T Consensus 51 ~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~~ 98 (587)
T COG4715 51 RAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLDD 98 (587)
T ss_pred EEEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhhc
Confidence 34455444444666763 57899998 5555 499999999987654
No 33
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=41.46 E-value=72 Score=29.86 Aligned_cols=69 Identities=16% Similarity=0.187 Sum_probs=39.9
Q ss_pred cEEEEeCceecccc--------------CceeEEEEEEcCC-CceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCe
Q 037776 347 RLLAVDGWKINNPY--------------NSVMLVAAALDGN-NGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGL 411 (716)
Q Consensus 347 ~vi~iD~T~~~~~y--------------~~~ll~avg~d~~-~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~ 411 (716)
-+|-||.||+.++- .....++++++-+ +..--+...++++.+.++..=+++ ..+ .+..
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~---~~i----~~gs 76 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQ---EHI----EPGS 76 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHH---Hhh----hccc
Confidence 37788888876433 2223444555544 333333344556777777654443 333 3457
Q ss_pred EEEcCCcchHH
Q 037776 412 CIMGDGDNGID 422 (716)
Q Consensus 412 ~iitD~~~al~ 422 (716)
+|+||..++-.
T Consensus 77 ~i~TD~~~aY~ 87 (151)
T PF12762_consen 77 TIITDGWRAYN 87 (151)
T ss_pred eeeecchhhcC
Confidence 89999998864
No 34
>PRK13907 rnhA ribonuclease H; Provisional
Probab=38.89 E-value=2.6e+02 Score=25.16 Aligned_cols=78 Identities=12% Similarity=0.054 Sum_probs=44.5
Q ss_pred EEEEeCceeccccCceeEEEEEEcCCCceEEEEEEE-eecCCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHHHHH
Q 037776 348 LLAVDGWKINNPYNSVMLVAAALDGNNGILPIAFCE-VHVEDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDYAIE 426 (716)
Q Consensus 348 vi~iD~T~~~~~y~~~ll~avg~d~~~~~~pla~al-v~~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~Ai~ 426 (716)
.|.+||.+..+.-.+-.-.++ .+..+.. .+++.+ ..+-+..-|.-++..|+.+.. ....++.|-||. +.+.+++.
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~~~-~~~~~~~~~tn~~AE~~All~aL~~a~~-~g~~~v~i~sDS-~~vi~~~~ 78 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQPAV-QLSLPLGTMSNHEAEYHALLAALKYCTE-HNYNIVSFRTDS-QLVERAVE 78 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeE-EEEecccccCCcHHHHHHHHHHHHHHHh-CCCCEEEEEech-HHHHHHHh
Confidence 478999998765333222222 4544433 333321 234455567777888887775 233467777876 55566666
Q ss_pred hhc
Q 037776 427 EFL 429 (716)
Q Consensus 427 ~vf 429 (716)
..+
T Consensus 79 ~~~ 81 (128)
T PRK13907 79 KEY 81 (128)
T ss_pred HHH
Confidence 544
No 35
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=37.90 E-value=27 Score=28.30 Aligned_cols=38 Identities=11% Similarity=0.300 Sum_probs=17.0
Q ss_pred HhhhhhcCCCCCHHHHHHHHHHHhCcccCHHHHHHHHHH
Q 037776 253 YLHRWKLQPNLRTVDIKDEIKATYGVVCHEAKLLCAAKR 291 (716)
Q Consensus 253 ~~~~i~~~~~~~~~~I~~~l~~~~g~~~s~~k~~rak~~ 291 (716)
+...++.+|..+..+|...+... |+.+|..+++|.-..
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L~~ 41 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRLRE 41 (72)
T ss_dssp ------------HHHHHHHT----T--S-HHHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHHHH
Confidence 34456789999999999999988 999999999886443
No 36
>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=36.11 E-value=16 Score=19.76 Aligned_cols=7 Identities=0% Similarity=-0.230 Sum_probs=3.5
Q ss_pred CCCCCcC
Q 037776 679 VNTLSMK 685 (716)
Q Consensus 679 ~GRpkk~ 685 (716)
+|||+|.
T Consensus 4 RGRP~k~ 10 (13)
T PF02178_consen 4 RGRPRKN 10 (13)
T ss_dssp SS--TT-
T ss_pred CCCCccc
Confidence 8999986
No 37
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=34.78 E-value=23 Score=36.18 Aligned_cols=23 Identities=30% Similarity=0.586 Sum_probs=19.7
Q ss_pred ceeeecccccCCCCchhHHHHHHHhh
Q 037776 605 QSCSCGLRQKSGIPCAHACKGIQLIM 630 (716)
Q Consensus 605 ~tCsC~~~~~~GiPC~H~lav~~~~~ 630 (716)
..|||..| -.||.||-||.....
T Consensus 125 ~dCSCPD~---anPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDY---ANPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCc---ccchHHHHHHHHHHH
Confidence 46999986 579999999998875
No 38
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.42 E-value=22 Score=38.56 Aligned_cols=11 Identities=0% Similarity=-0.203 Sum_probs=5.9
Q ss_pred CcCCCCCCCCC
Q 037776 95 GCKTQMPTGRC 105 (716)
Q Consensus 95 ~~~~~~p~~~~ 105 (716)
.++.++||...
T Consensus 264 sv~~~ss~~ed 274 (514)
T KOG3130|consen 264 SVNGSSSYHED 274 (514)
T ss_pred cccCCCCcccc
Confidence 34556666544
No 39
>PHA00689 hypothetical protein
Probab=33.79 E-value=22 Score=26.60 Aligned_cols=15 Identities=20% Similarity=0.302 Sum_probs=12.1
Q ss_pred CCCeeeCCcCCcCCC
Q 037776 692 SSRARQCIENNSDAA 706 (716)
Q Consensus 692 ~k~~~~Cs~C~~~GH 706 (716)
..|.++|.+|+.+|-
T Consensus 14 epravtckrcgktgl 28 (62)
T PHA00689 14 EPRAVTCKRCGKTGL 28 (62)
T ss_pred CcceeehhhccccCc
Confidence 347789999999874
No 40
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=33.60 E-value=30 Score=30.19 Aligned_cols=25 Identities=8% Similarity=0.037 Sum_probs=14.2
Q ss_pred CCCCcCCCCCC--C---CCCeeeCCcCCcC
Q 037776 680 NTLSMKGSNES--A---SSRARQCIENNSD 704 (716)
Q Consensus 680 GRpkk~Rr~e~--~---~k~~~~Cs~C~~~ 704 (716)
||+|++||+.. + -.++-.|.+|+..
T Consensus 2 G~rr~krr~~ik~~~~~L~k~FtCp~Cghe 31 (104)
T COG4888 2 GRRRRKRRKIIKRRPQVLPKTFTCPRCGHE 31 (104)
T ss_pred CcccccccccCcccCccCCceEecCccCCe
Confidence 66665554433 1 2366778888643
No 41
>PF13276 HTH_21: HTH-like domain
Probab=31.50 E-value=84 Score=24.40 Aligned_cols=43 Identities=12% Similarity=0.176 Sum_probs=34.3
Q ss_pred HHHHHhhhhhc-CCCCCHHHHHHHHHHHhCcccCHHHHHHHHHH
Q 037776 249 ISAIYLHRWKL-QPNLRTVDIKDEIKATYGVVCHEAKLLCAAKR 291 (716)
Q Consensus 249 ia~~~~~~i~~-~~~~~~~~I~~~l~~~~g~~~s~~k~~rak~~ 291 (716)
+...+.+.+.. .+.+....|...|....|+.+|..+++|..+.
T Consensus 6 l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~~v~~krV~RlM~~ 49 (60)
T PF13276_consen 6 LRELIKEIFKESKPTYGYRRIWAELRREGGIRVSRKRVRRLMRE 49 (60)
T ss_pred HHHHHHHHHHHcCCCeehhHHHHHHhccCcccccHHHHHHHHHH
Confidence 44556666665 48999999999999999999999999887543
No 42
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.14 E-value=50 Score=29.05 Aligned_cols=22 Identities=9% Similarity=0.068 Sum_probs=13.2
Q ss_pred CCCCcCCCCCC-----CCCCeeeCCcCC
Q 037776 680 NTLSMKGSNES-----ASSRARQCIENN 702 (716)
Q Consensus 680 GRpkk~Rr~e~-----~~k~~~~Cs~C~ 702 (716)
||+|++|+ .+ +..+...|..|+
T Consensus 2 GkRk~~~k-~~~k~k~klpt~f~CP~Cg 28 (99)
T PRK14892 2 GRRRKKRK-KIIRPKPKLPKIFECPRCG 28 (99)
T ss_pred CCccccCC-CCcccccCCCcEeECCCCC
Confidence 66666643 22 223667888888
No 43
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=27.72 E-value=50 Score=28.63 Aligned_cols=27 Identities=11% Similarity=0.005 Sum_probs=17.6
Q ss_pred CCCCC-CCCCCcCCCCCCCCCCeeeCCcCCcC
Q 037776 674 PMIES-VNTLSMKGSNESASSRARQCIENNSD 704 (716)
Q Consensus 674 P~~~r-~GRpkk~Rr~e~~~k~~~~Cs~C~~~ 704 (716)
|..++ .||.|+.| ..-..++|+.|+..
T Consensus 2 ~kKRrn~GR~K~~r----Ghv~~V~C~nCgr~ 29 (95)
T PRK09335 2 PKKRENRGRRKGDK----GHVGYVQCDNCGRR 29 (95)
T ss_pred CcccccCCCCCCCC----CCCccEEeCCCCCc
Confidence 34455 77777775 12256899999864
No 44
>PRK00766 hypothetical protein; Provisional
Probab=27.54 E-value=5.3e+02 Score=25.64 Aligned_cols=88 Identities=20% Similarity=0.271 Sum_probs=49.9
Q ss_pred cEEEEe-CceeccccCceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcc--------cC-----------
Q 037776 347 RLLAVD-GWKINNPYNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALR--------LD----------- 406 (716)
Q Consensus 347 ~vi~iD-~T~~~~~y~~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~--------~~----------- 406 (716)
.||+|| +.|..+.-+-..++-+-+-++.-+.-++|+.+...-.|.=.-+.+.++.... |.
T Consensus 10 rvlGidds~f~~~~~~~~~lvGvv~r~~~~idGv~~~~itvdG~DaT~~i~~mv~~~~~r~~i~~V~L~Git~agFNvvD 89 (194)
T PRK00766 10 RVLGIDDGTFLFKSSEKVILVGVVMRGGDWVDGVLSRWITVDGLDATEAIIEMVNSSRHKGQLRVIMLDGITYGGFNVVD 89 (194)
T ss_pred eEEEEecCccccCCCCCEEEEEEEEECCeEEeeEEEEEEEECCccHHHHHHHHHHhcccccceEEEEECCEeeeeeEEec
Confidence 588888 5555432233555555556666656667776666655555555555443110 00
Q ss_pred -------CCCCeEEEcCCcc---hHHHHHHhhcccccc
Q 037776 407 -------HGEGLCIMGDGDN---GIDYAIEEFLPKAVY 434 (716)
Q Consensus 407 -------~~~~~~iitD~~~---al~~Ai~~vfP~a~h 434 (716)
...|+.+++...+ +|..|+.+.||+...
T Consensus 90 ~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k~f~~~~~ 127 (194)
T PRK00766 90 IEELYRETGLPVIVVMRKKPDFEAIESALKKHFSDWEE 127 (194)
T ss_pred HHHHHHHHCCCEEEEEecCCCHHHHHHHHHHHCCCHHH
Confidence 1245555544443 688888888888766
No 45
>PLN00186 ribosomal protein S26; Provisional
Probab=25.64 E-value=54 Score=29.10 Aligned_cols=27 Identities=4% Similarity=-0.071 Sum_probs=17.5
Q ss_pred CCCCC-CCCCCcCCCCCCCCCCeeeCCcCCcC
Q 037776 674 PMIES-VNTLSMKGSNESASSRARQCIENNSD 704 (716)
Q Consensus 674 P~~~r-~GRpkk~Rr~e~~~k~~~~Cs~C~~~ 704 (716)
|.-++ .||-|+.| ..-..++|+.|+..
T Consensus 2 ~kKRrN~GR~K~~r----Ghv~~V~C~nCgr~ 29 (109)
T PLN00186 2 TKKRRNGGRNKHGR----GHVKRIRCSNCGKC 29 (109)
T ss_pred CcccccCCCCCCCC----CCCcceeeCCCccc
Confidence 34455 77777775 12256899999864
No 46
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=25.08 E-value=55 Score=29.03 Aligned_cols=27 Identities=4% Similarity=-0.034 Sum_probs=17.7
Q ss_pred CCCCC-CCCCCcCCCCCCCCCCeeeCCcCCcC
Q 037776 674 PMIES-VNTLSMKGSNESASSRARQCIENNSD 704 (716)
Q Consensus 674 P~~~r-~GRpkk~Rr~e~~~k~~~~Cs~C~~~ 704 (716)
|.-++ .||-|+.| ..-+.++|+.|+..
T Consensus 2 ~kKRrN~GR~K~~r----Ghv~~V~C~nCgr~ 29 (108)
T PTZ00172 2 TSKRRNNGRSKHGR----GHVKPVRCSNCGRC 29 (108)
T ss_pred CcccccCCCCCCCC----CCCccEEeCCcccc
Confidence 34455 77777775 12256899999864
No 47
>PF03400 DDE_Tnp_IS1: IS1 transposase; InterPro: IPR005063 Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 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=24.68 E-value=2.6e+02 Score=25.86 Aligned_cols=68 Identities=16% Similarity=0.032 Sum_probs=39.7
Q ss_pred ceeccccCceeEEEEEEcCCCceEEEEEEEeecCCchhHHHHHHHHHHHcccCCCCCeEEEcCCcchHHHHHHhhccccc
Q 037776 354 WKINNPYNSVMLVAAALDGNNGILPIAFCEVHVEDLDSWVFFIKNINNALRLDHGEGLCIMGDGDNGIDYAIEEFLPKAV 433 (716)
Q Consensus 354 T~~~~~y~~~ll~avg~d~~~~~~pla~alv~~E~~es~~Wfl~~l~~~~~~~~~~~~~iitD~~~al~~Ai~~vfP~a~ 433 (716)
||..+|-+ ...+..++|..... ++||.+ .+-+.+++.-+++.|. ......+.||.-.+- ..++|...
T Consensus 12 tfVg~K~n-~~Wiw~A~dr~t~~-Iva~v~-G~Rs~~T~~~L~~~L~------~~~i~~~~TD~w~~Y----~~~ip~~~ 78 (131)
T PF03400_consen 12 TFVGNKKN-KRWIWYAIDRKTGG-IVAFVF-GDRSDKTFRKLWALLK------PFNIGFIYTDDWESY----ERVIPEEK 78 (131)
T ss_pred hhhccCCC-ceEEEEEEeccCCc-ceeEEE-ecchhhHHHHHhhhhc------cccceEEecCCCccc----cccCccch
Confidence 33334433 44455556655543 446655 6667777777776552 223456899998754 34567766
Q ss_pred c
Q 037776 434 Y 434 (716)
Q Consensus 434 h 434 (716)
|
T Consensus 79 H 79 (131)
T PF03400_consen 79 H 79 (131)
T ss_pred h
Confidence 6
No 48
>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=24.26 E-value=43 Score=21.75 Aligned_cols=8 Identities=0% Similarity=-0.317 Sum_probs=7.0
Q ss_pred CCCCCcCC
Q 037776 679 VNTLSMKG 686 (716)
Q Consensus 679 ~GRpkk~R 686 (716)
+|||+|..
T Consensus 4 RGRPrK~~ 11 (26)
T smart00384 4 RGRPRKAP 11 (26)
T ss_pred CCCCCCCC
Confidence 89999985
No 49
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=24.01 E-value=48 Score=40.16 Aligned_cols=33 Identities=21% Similarity=0.403 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCcchhhhccCCcchhccCCCCCCC
Q 037776 98 TQMPTGRCSDDDDESQEENNDEEDQIEGYSSEND 131 (716)
Q Consensus 98 ~~~p~~~~~~~~~~~~~e~~d~~d~~~g~s~~~d 131 (716)
++--|+.. ||||.+..|+++++++.|++|+|+|
T Consensus 311 PNy~yd~~-eDed~~~~ed~eDde~~deYsDDeD 343 (1233)
T KOG1824|consen 311 PNYNYDTE-EDEDAMFLEDEEDDEQDDEYSDDED 343 (1233)
T ss_pred CCCCCCCc-cchhhhhhhccccchhccccccccc
Confidence 44334433 4555555555555555566666554
No 50
>smart00343 ZnF_C2HC zinc finger.
Probab=23.72 E-value=38 Score=21.62 Aligned_cols=13 Identities=8% Similarity=0.353 Sum_probs=10.7
Q ss_pred eCCcCCcCCCCCC
Q 037776 697 QCIENNSDAATNN 709 (716)
Q Consensus 697 ~Cs~C~~~GHn~~ 709 (716)
.|.+|++.||..+
T Consensus 1 ~C~~CG~~GH~~~ 13 (26)
T smart00343 1 KCYNCGKEGHIAR 13 (26)
T ss_pred CCccCCCCCcchh
Confidence 4899999999654
No 51
>PF13551 HTH_29: Winged helix-turn helix
Probab=23.63 E-value=1.4e+02 Score=25.82 Aligned_cols=39 Identities=8% Similarity=0.192 Sum_probs=29.8
Q ss_pred HHhhhhhcCC-----CCCHHHHHHHH-HHHhCcccCHHHHHHHHH
Q 037776 252 IYLHRWKLQP-----NLRTVDIKDEI-KATYGVVCHEAKLLCAAK 290 (716)
Q Consensus 252 ~~~~~i~~~~-----~~~~~~I~~~l-~~~~g~~~s~~k~~rak~ 290 (716)
.+.+.+..+| .+++..|...| ++.+|+.+|.+++++.-.
T Consensus 65 ~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 65 QLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred HHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 4445555555 57899999976 899999999999987643
No 52
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.58 E-value=2.2e+02 Score=26.44 Aligned_cols=54 Identities=9% Similarity=0.065 Sum_probs=37.6
Q ss_pred hCCCcEEEEEeccCcCchhh--hHHHHHhcCccEEE--EeCceeccccCceeEEEEEEcCCCc
Q 037776 317 INSRNIVLLETKRHEYGEER--TSYAFKNHCRRLLA--VDGWKINNPYNSVMLVAAALDGNNG 375 (716)
Q Consensus 317 ~NPg~~~~v~~d~~~~~F~~--si~~f~~~~r~vi~--iD~T~~~~~y~~~ll~avg~d~~~~ 375 (716)
.-+.+...+-+++ ++. .+..|. .+.|+++ .||-|++-+.+|||..+--.|.+..
T Consensus 78 ak~tslt~iALNd----Y~a~Ip~sDi~-kynpIlA~~~nGn~M~IRerGPl~~IYplds~pe 135 (155)
T COG3915 78 AKQTSLTVIALND----YWAEIPYSDIE-KYNPILAIQNNGNYMQIRERGPLWSIYPLDSSPE 135 (155)
T ss_pred ccCcceEEEEecc----eeccCcHHHhh-hcccEEEEEeCCcEEEEeccCceEEEeecCCChh
Confidence 3445555565543 222 456663 5888764 6999999999999999887776654
No 53
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=23.28 E-value=66 Score=39.87 Aligned_cols=18 Identities=6% Similarity=0.134 Sum_probs=8.6
Q ss_pred EEEEEecCcceEEEEEec
Q 037776 213 IKAERVVNGRTFIVTEFV 230 (716)
Q Consensus 213 i~as~~~~~~~w~V~~~~ 230 (716)
.-|+...+.+..+|+.+.
T Consensus 1965 apASa~Agann~qiRqip 1982 (3015)
T KOG0943|consen 1965 APASALAGANNIQIRQIP 1982 (3015)
T ss_pred CchhhhcccCceeeeecC
Confidence 334433444556665443
No 54
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=23.16 E-value=45 Score=24.45 Aligned_cols=13 Identities=8% Similarity=0.136 Sum_probs=11.2
Q ss_pred eeeCCcCCcCCCC
Q 037776 695 ARQCIENNSDAAT 707 (716)
Q Consensus 695 ~~~Cs~C~~~GHn 707 (716)
...|-+|++.||-
T Consensus 4 ~~~CqkC~~~GH~ 16 (42)
T PF13917_consen 4 RVRCQKCGQKGHW 16 (42)
T ss_pred CCcCcccCCCCcc
Confidence 4689999999994
No 55
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=23.13 E-value=51 Score=40.17 Aligned_cols=17 Identities=12% Similarity=0.204 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHh
Q 037776 58 QLLKTKCRRMRRKIARE 74 (716)
Q Consensus 58 ~~~~~~~~~~~~~~~~~ 74 (716)
..+|+-+..+=.-+-+.
T Consensus 603 ~llR~~~~~vf~~~~~~ 619 (784)
T PF04931_consen 603 ALLRKVSEQVFEAFCPH 619 (784)
T ss_pred hHHHHHHHHHHHHHHhh
Confidence 35677666666555543
No 56
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=23.03 E-value=41 Score=38.60 Aligned_cols=15 Identities=13% Similarity=0.197 Sum_probs=13.4
Q ss_pred CeeeCCcCCcCCCCC
Q 037776 694 RARQCIENNSDAATN 708 (716)
Q Consensus 694 ~~~~Cs~C~~~GHn~ 708 (716)
++++|+.|||-||-+
T Consensus 936 Ttr~C~nCGQvGHmk 950 (968)
T COG5179 936 TTRTCGNCGQVGHMK 950 (968)
T ss_pred cceeccccccccccc
Confidence 589999999999965
No 57
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=22.97 E-value=1.2e+02 Score=25.11 Aligned_cols=29 Identities=21% Similarity=0.411 Sum_probs=25.5
Q ss_pred EECCHHHHHHHHHHHHHHcCceEEEEeec
Q 037776 168 RFRDVSHFRKAIEVFAIRDGFKLCVMENR 196 (716)
Q Consensus 168 ~F~s~ee~k~ai~~yAi~~gf~~~~~kS~ 196 (716)
+|+|.+++-.+|..|+.+++-.+.+.+-+
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~ 41 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRD 41 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecC
Confidence 47899999999999999999999886544
No 58
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=22.23 E-value=70 Score=27.45 Aligned_cols=34 Identities=15% Similarity=0.175 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhhChhhHHHHhhcCCCCccc
Q 037776 465 TSATSFNKYMDLIHNESEECHDWLLQTDWSSWAL 498 (716)
Q Consensus 465 ~t~~eFe~~~~~l~~~~~~~~~yL~~~~~~~W~~ 498 (716)
.|..+|+..|..+.......++||..++++....
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~ 38 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPK 38 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHH
Confidence 4778999999999876668999999998776654
No 59
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=22.14 E-value=40 Score=25.34 Aligned_cols=15 Identities=13% Similarity=0.315 Sum_probs=12.3
Q ss_pred eeeCCcCCcCCCCCC
Q 037776 695 ARQCIENNSDAATNN 709 (716)
Q Consensus 695 ~~~Cs~C~~~GHn~~ 709 (716)
...|+.|+..||+.+
T Consensus 31 p~~C~~C~~~gH~~~ 45 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDK 45 (49)
T ss_pred ChhhcCCCCcCcCHh
Confidence 357999999999853
No 60
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=21.46 E-value=2.3e+02 Score=35.76 Aligned_cols=17 Identities=6% Similarity=-0.144 Sum_probs=8.6
Q ss_pred cccccCccceeeccccc
Q 037776 27 TINKTSPEYIRTHSCGS 43 (716)
Q Consensus 27 ~~~~~~~~~~~~~~~~~ 43 (716)
-.+-..+|++-.+.|-.
T Consensus 1261 r~~~~~~~~y~~e~~v~ 1277 (1640)
T KOG0262|consen 1261 RFDLLPREEYQEEYDVR 1277 (1640)
T ss_pred EEeecCHHHhhhhcCCC
Confidence 34445555555555544
No 61
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=20.84 E-value=87 Score=20.79 Aligned_cols=16 Identities=13% Similarity=0.432 Sum_probs=10.6
Q ss_pred CCCCCCCCcHHHHHHH
Q 037776 47 GNSANDTDRPEQLLKT 62 (716)
Q Consensus 47 ~~~~~~~~~~~~~~~~ 62 (716)
|.+..++|+|+..||.
T Consensus 3 GSddEeed~ea~r~re 18 (28)
T PF10587_consen 3 GSDDEEEDEEAERIRE 18 (28)
T ss_pred CCccccccHHHHHHHH
Confidence 5444457888887765
No 62
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=20.83 E-value=2.3e+02 Score=33.67 Aligned_cols=14 Identities=29% Similarity=0.313 Sum_probs=7.9
Q ss_pred hhHHHHHHHHHHHH
Q 037776 301 EDGYAILNQFKDEM 314 (716)
Q Consensus 301 ~~sy~~L~~y~~~l 314 (716)
.-.|..|+.+++.+
T Consensus 377 ~~~y~AL~~~l~~~ 390 (822)
T KOG2141|consen 377 LTTYAALAAMLHTM 390 (822)
T ss_pred HHHHHHHHHHHHHH
Confidence 34455666666555
No 63
>PF14420 Clr5: Clr5 domain
Probab=20.45 E-value=2.1e+02 Score=21.93 Aligned_cols=25 Identities=12% Similarity=0.186 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHHHHHHhCcccCHHH
Q 037776 260 QPNLRTVDIKDEIKATYGVVCHEAK 284 (716)
Q Consensus 260 ~~~~~~~~I~~~l~~~~g~~~s~~k 284 (716)
+.+.+..+|++.++..||+..|..+
T Consensus 18 ~e~~tl~~v~~~M~~~~~F~at~rq 42 (54)
T PF14420_consen 18 DENKTLEEVMEIMKEEHGFKATKRQ 42 (54)
T ss_pred hCCCcHHHHHHHHHHHhCCCcCHHH
Confidence 5678899999999999999998654
No 64
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=20.45 E-value=61 Score=37.40 Aligned_cols=8 Identities=25% Similarity=0.077 Sum_probs=3.4
Q ss_pred CCCCCCCC
Q 037776 100 MPTGRCSD 107 (716)
Q Consensus 100 ~p~~~~~~ 107 (716)
|-|+.||+
T Consensus 939 SEyeaS~d 946 (1001)
T COG5406 939 SEYEASSD 946 (1001)
T ss_pred hhhhccCC
Confidence 44444443
No 65
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=20.23 E-value=1.8e+02 Score=32.38 Aligned_cols=41 Identities=24% Similarity=0.351 Sum_probs=30.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHhhCCCCCccccccccccccCCCcCCCCCCCCCCCC
Q 037776 52 DTDRPEQLLKTKCRRMRRKIARELFPSNSHSNEQCNKHSRTGMGCKTQMPTGRCSDD 108 (716)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~ 108 (716)
|+|+++++.+.-|-+=+|.-|-.+ ..| +-|+.-|+.+-+++
T Consensus 201 DEDRPLE~AY~Scle~Rr~~K~~~-----------iPQ-----DIDPSFPtSDpeDe 241 (458)
T PF10446_consen 201 DEDRPLEAAYISCLEARRREKHIP-----------IPQ-----DIDPSFPTSDPEDE 241 (458)
T ss_pred CCcchHHHHHHHHHHHHHHcCCCC-----------CCC-----CCCCCCCCCCcccc
Confidence 899999999999999998766521 111 33688888886544
Done!