Query 040097
Match_columns 516
No_of_seqs 188 out of 1592
Neff 9.1
Searched_HMMs 46136
Date Fri Mar 29 05:05:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040097.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040097hhsearch_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 1.2E-73 2.5E-78 610.7 39.5 466 1-495 76-624 (846)
2 PF10551 MULE: MULE transposas 99.9 3E-22 6.5E-27 162.0 9.1 90 200-293 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.9 1.4E-22 3E-27 205.2 5.3 189 193-384 162-366 (381)
4 COG3328 Transposase and inacti 99.6 6.1E-15 1.3E-19 146.3 16.2 219 96-371 98-328 (379)
5 PF03108 DBD_Tnp_Mut: MuDR fam 99.6 1.9E-15 4.1E-20 113.5 8.3 62 1-62 6-67 (67)
6 PF08731 AFT: Transcription fa 99.1 8.8E-10 1.9E-14 87.8 8.5 69 5-73 1-111 (111)
7 smart00575 ZnF_PMZ plant mutat 99.0 1E-10 2.2E-15 70.6 1.5 27 452-478 1-27 (28)
8 PF03101 FAR1: FAR1 DNA-bindin 98.9 2.7E-09 5.9E-14 85.5 6.3 62 13-75 1-91 (91)
9 PF04434 SWIM: SWIM zinc finge 98.2 9.4E-07 2E-11 58.6 2.7 31 447-477 10-40 (40)
10 PF01610 DDE_Tnp_ISL3: Transpo 95.9 0.017 3.6E-07 55.4 6.3 93 196-296 1-96 (249)
11 PF03106 WRKY: WRKY DNA -bindi 95.4 0.02 4.3E-07 41.4 3.5 40 33-72 20-59 (60)
12 PF06782 UPF0236: Uncharacteri 95.3 0.21 4.6E-06 52.4 12.1 133 233-371 235-377 (470)
13 PF13610 DDE_Tnp_IS240: DDE do 95.0 0.014 3.1E-07 50.5 2.1 81 193-279 1-81 (140)
14 PF04684 BAF1_ABF1: BAF1 / ABF 94.2 0.093 2E-06 52.8 5.9 54 2-55 25-79 (496)
15 PF00665 rve: Integrase core d 94.0 0.23 5E-06 41.2 7.3 74 193-269 6-80 (120)
16 PHA02517 putative transposase 92.8 0.79 1.7E-05 44.6 10.0 72 193-268 110-181 (277)
17 smart00774 WRKY DNA binding do 92.8 0.13 2.7E-06 36.9 3.1 38 34-71 21-59 (59)
18 PF04500 FLYWCH: FLYWCH zinc f 92.3 0.2 4.4E-06 36.1 3.9 46 22-71 14-62 (62)
19 PF03050 DDE_Tnp_IS66: Transpo 91.5 0.15 3.3E-06 49.4 3.1 85 193-298 67-156 (271)
20 PRK14702 insertion element IS2 91.3 5.4 0.00012 38.5 13.5 73 194-267 88-163 (262)
21 PRK09409 IS2 transposase TnpB; 90.2 8.7 0.00019 37.9 14.1 75 193-268 126-203 (301)
22 COG3316 Transposase and inacti 85.6 1.9 4E-05 39.7 5.6 84 193-283 70-153 (215)
23 PF04937 DUF659: Protein of un 80.1 21 0.00046 31.2 9.9 62 234-297 73-137 (153)
24 COG5431 Uncharacterized metal- 72.7 1.9 4.2E-05 34.2 1.2 39 435-475 35-78 (117)
25 PRK13907 rnhA ribonuclease H; 63.9 50 0.0011 27.6 8.3 78 195-276 3-81 (128)
26 PF13565 HTH_32: Homeodomain-l 58.9 21 0.00045 26.8 4.6 33 84-116 34-66 (77)
27 PF12762 DDE_Tnp_IS1595: ISXO2 57.5 34 0.00073 29.6 6.3 69 194-269 4-87 (151)
28 COG4279 Uncharacterized conser 48.2 8 0.00017 36.2 0.8 23 451-476 124-146 (266)
29 PF09713 A_thal_3526: Plant pr 44.7 20 0.00044 25.2 2.2 20 98-117 12-31 (54)
30 PRK00766 hypothetical protein; 43.5 2.1E+02 0.0046 26.1 9.2 89 194-282 10-128 (194)
31 PF08766 DEK_C: DEK C terminal 43.2 54 0.0012 22.9 4.3 35 83-117 3-39 (54)
32 KOG4027 Uncharacterized conser 42.5 36 0.00079 29.5 3.8 35 198-232 70-107 (187)
33 PF14420 Clr5: Clr5 domain 40.8 54 0.0012 22.9 4.0 22 96-117 18-39 (54)
34 PF08069 Ribosomal_S13_N: Ribo 40.3 30 0.00066 24.9 2.6 29 86-114 30-60 (60)
35 COG4715 Uncharacterized conser 39.0 65 0.0014 34.1 5.7 50 426-477 40-96 (587)
36 PF14201 DUF4318: Domain of un 38.5 56 0.0012 24.7 3.9 29 4-32 13-41 (74)
37 TIGR01589 A_thal_3526 uncharac 36.0 29 0.00063 24.6 1.9 20 98-117 15-34 (57)
38 PF13082 DUF3931: Protein of u 34.9 1E+02 0.0022 21.2 4.3 28 207-234 35-62 (66)
39 smart00816 Amb_V_allergen Amb 33.9 24 0.00052 22.8 1.1 22 33-54 13-36 (45)
40 COG3915 Uncharacterized protei 30.7 1.9E+02 0.0041 24.6 6.1 38 185-223 97-136 (155)
41 PF11447 DUF3201: Protein of u 28.1 3.7E+02 0.0081 22.8 7.4 69 142-238 9-82 (150)
42 PF13358 DDE_3: DDE superfamil 24.9 1E+02 0.0022 25.7 4.0 55 209-267 37-91 (146)
43 PF13877 RPAP3_C: Potential Mo 23.7 62 0.0014 25.4 2.2 36 312-347 5-40 (94)
44 KOG2909 Vacuolar H+-ATPase V1 23.0 1.1E+02 0.0023 30.4 3.9 98 137-296 141-238 (381)
45 COG0626 MetC Cystathionine bet 21.6 8.9E+02 0.019 24.9 12.0 67 185-252 171-244 (396)
46 PF11645 PDDEXK_5: PD-(D/E)XK 21.6 3.1E+02 0.0067 23.6 5.9 45 8-52 6-50 (149)
47 PF04800 ETC_C1_NDUFA4: ETC co 20.7 1.2E+02 0.0027 24.4 3.3 28 1-32 51-78 (101)
48 KOG3499 60S ribosomal protein 20.4 3E+02 0.0065 19.8 4.6 35 8-42 5-40 (69)
49 KOG3608 Zn finger proteins [Ge 20.0 73 0.0016 31.6 2.1 43 2-46 143-186 (467)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=1.2e-73 Score=610.65 Aligned_cols=466 Identities=14% Similarity=0.182 Sum_probs=372.3
Q ss_pred CCceeCCHHHHHHHHHHHHHHcCceEEEEeeCC-------cEEEEEeec-------------------------------
Q 040097 1 MGQRFKNDVEFKTALEVNAIRDGFKLCIIHNTT-------TCVSCECSN------------------------------- 42 (516)
Q Consensus 1 vG~~F~s~~e~~~ai~~ya~~~gf~~~~~rs~~-------~~~~~~C~~------------------------------- 42 (516)
|||+|+|.+||++||+.||...||++++.++.+ ...+++|++
T Consensus 76 vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~~~rR~ 155 (846)
T PLN03097 76 SGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENGTGRRS 155 (846)
T ss_pred CCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccccccccc
Confidence 799999999999999999999999999875432 123566654
Q ss_pred ---CCCccEEEEEEccCcceEEEEecCCCceecccCccc--cchhHHHHHHHHHHhhcCCccCHHHHHHHHHHHhCCcch
Q 040097 43 ---LHCDWKITAVKEHRSNVFVICDITPMHTCNQHSVKL--QGRTKWIAAKFLHIWKQSEHREVDKLRNEIATTYGIKCP 117 (516)
Q Consensus 43 ---~gCp~rv~~~~~~~~~~~~V~~~~~~Hnc~~~~~~~--~~s~~~l~~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~s 117 (516)
+|||+++++++. ..+.|.|+.+..+|||++.+... ..+++.+.. +...+....++.. ++... .+
T Consensus 156 ~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~-~~~~~~~~~~v~~------~~~d~---~~ 224 (846)
T PLN03097 156 CAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAA-MARQFAEYKNVVG------LKNDS---KS 224 (846)
T ss_pred ccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccchhhhhhHHH-HHhhhhccccccc------cchhh---cc
Confidence 479999999875 55789999999999999965322 111111111 0000000000000 00000 00
Q ss_pred hhhhHhhhHHHHHHhhcCChhHHHHHHHHHHHHHhhCCCcEEEEEecccccccccceeeEeeeccchHHHHhhcCceEEE
Q 040097 118 IWKLEAVDRMVRFWLRTDHPDGYAQLLQYKQEMEIVNSRNIVIIETKSQQQFTADIFHRMFVFLYDTAFVFKTRCRMLLT 197 (516)
Q Consensus 118 ~~r~k~~~~~~~~~~~g~~~~~~~~l~~~~~~l~~~npg~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~vi~ 197 (516)
.++.++. + .-...+.+.|++|+++++++||+|+|.+++|+ +++++++||+++.++..|.. |+|||.
T Consensus 225 ~~~~~r~----~----~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe-----~~~l~niFWaD~~sr~~Y~~-FGDvV~ 290 (846)
T PLN03097 225 SFDKGRN----L----GLEAGDTKILLDFFTQMQNMNSNFFYAVDLGE-----DQRLKNLFWVDAKSRHDYGN-FSDVVS 290 (846)
T ss_pred hhhHHHh----h----hcccchHHHHHHHHHHHHhhCCCceEEEEEcc-----CCCeeeEEeccHHHHHHHHh-cCCEEE
Confidence 1111111 1 11234568899999999999999999999999 99999999999999999997 999999
Q ss_pred EeCeeecCCCCceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHHHHHhhhCC
Q 040097 198 VDGWEIDSPYKSVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVEEFLP 277 (516)
Q Consensus 198 ~D~t~~~~~y~~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~~Ai~~vfP 277 (516)
+|+||++|+|++||..++|+|+|+++++|||||+.+|+.|+|.|+|++|+++|++.. |.+||||++.+|.+||.+|||
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 FDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQA--PKVIITDQDKAMKSVISEVFP 368 (846)
T ss_pred EeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCC--CceEEecCCHHHHHHHHHHCC
Confidence 999999999999999999999999999999999999999999999999999999988 999999999999999999999
Q ss_pred CCcccccHHHHHHHHhhhCCC-----CCChhhHhHhhh-ccchHHHHHHHHHH-HhhCHHHHHHhhcC--CCcccccccC
Q 040097 278 SAVYRQCCFSLYTKMVDEFPR-----VTVHSPFWGACR-STDGNTFTNQMAVI-QTISVECYNWLKDT--DWHKWALFSM 348 (516)
Q Consensus 278 ~a~~~~C~~Hi~~n~~~~~~~-----~~~~~~~~~~~~-~~~~~~f~~~~~~l-~~~~~~~~~~l~~~--~~~~W~~~~~ 348 (516)
++.|++|.|||++|+.+++.. ..+...|..+++ +.++++|+..|..| .+++.+.++||..+ .+++|+++|+
T Consensus 369 ~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~ 448 (846)
T PLN03097 369 NAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYM 448 (846)
T ss_pred CceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHh
Confidence 999999999999999998763 478889999886 56999999999998 56789999999997 8999999999
Q ss_pred CCCccccccCCChHHHHHHHHHh--cccChHHHHHHHHHHHHHHHHHHHHhh-h---------------hcccCCccCHH
Q 040097 349 PEWVKSTEITISATEQLRIWLLK--QLDFNIAQRYTTITRKVAEIFQRRYLL-G---------------WEWVYDKITPA 410 (516)
Q Consensus 349 ~~~~~~~~~t~n~~Es~n~~lk~--~r~~pi~~~~~~~~~~~~~~~~~r~~~-~---------------~~~~~~~~tp~ 410 (516)
++.+..|+.||+++||+|+.|++ ....++..|++.+...+..+...-.+. . ++..+..|||.
T Consensus 449 k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~ 528 (846)
T PLN03097 449 RDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHA 528 (846)
T ss_pred cccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHH
Confidence 99899999999999999999998 567788888888777665544322111 0 11113789999
Q ss_pred HHHHHHHhhhhccCCeEEeec--CCc---eEEEee--CCeeEEEE----ecccccccCccccCCCCCcchhHHHhhcCC-
Q 040097 411 VRQQIIQNTFEGEGWTVDVTS--RNA---IAVVTR--DGLAYEIN----RELMTCTCRLWQLSGIPCPHACRCIDTWGD- 478 (516)
Q Consensus 411 ~~~kl~~~~~~~a~~~~~v~~--~~~---~~v~~~--~~~~~~V~----~~~~~CsC~~~~~~giPC~H~la~~~~~~~- 478 (516)
+|+++ |+++..+. .|.+.. .++ .|.|.. ....|.|. ....+|+|++|+..||||+|||+|+...++
T Consensus 529 iF~kF-Q~El~~~~-~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~ 606 (846)
T PLN03097 529 VFKKF-QVEVLGAV-ACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLS 606 (846)
T ss_pred HHHHH-HHHHHHhh-heEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcc
Confidence 99999 99999887 666553 222 344432 24567775 457899999999999999999999999997
Q ss_pred -ChhhhhhhcccHHHHHh
Q 040097 479 -KLDTYVHRLMTVDEYRS 495 (516)
Q Consensus 479 -~~~~~v~~~y~~~~~~~ 495 (516)
.|..||.++||+++-..
T Consensus 607 ~IP~~YILkRWTKdAK~~ 624 (846)
T PLN03097 607 AIPSQYILKRWTKDAKSR 624 (846)
T ss_pred cCchhhhhhhchhhhhhc
Confidence 69999999999998643
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=99.87 E-value=3e-22 Score=161.99 Aligned_cols=90 Identities=29% Similarity=0.465 Sum_probs=85.9
Q ss_pred CeeecCCCCceeEE---EEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHHHHHhhhC
Q 040097 200 GWEIDSPYKSVMLV---AVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVEEFL 276 (516)
Q Consensus 200 ~t~~~~~y~~~l~~---~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~~Ai~~vf 276 (516)
|||++|+| ++++. ++|+|++|+.+|+||+++++|++++|.|||+.+++.++.. |.+||+|++.|+.+||+++|
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~---p~~ii~D~~~~~~~Ai~~vf 76 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK---PKVIISDFDKALINAIKEVF 76 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC---ceeeeccccHHHHHHHHHHC
Confidence 79999999 98885 9999999999999999999999999999999999998873 79999999999999999999
Q ss_pred CCCcccccHHHHHHHHh
Q 040097 277 PSAVYRQCCFSLYTKMV 293 (516)
Q Consensus 277 P~a~~~~C~~Hi~~n~~ 293 (516)
|++.|++|.||+.+|++
T Consensus 77 P~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 77 PDARHQLCLFHILRNIK 93 (93)
T ss_pred CCceEehhHHHHHHhhC
Confidence 99999999999999974
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=99.86 E-value=1.4e-22 Score=205.21 Aligned_cols=189 Identities=18% Similarity=0.227 Sum_probs=158.7
Q ss_pred ceEEEEeCeeecCCCC-----ceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcch
Q 040097 193 RMLLTVDGWEIDSPYK-----SVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNG 267 (516)
Q Consensus 193 ~~vi~~D~t~~~~~y~-----~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~ 267 (516)
-++|++||+|.+.+.+ ..+++++|+|.+|+..+||+.+.+.|+.++|.-||+.|++.+... |..|++|+++|
T Consensus 162 y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~RGl~~---~~lvv~Dg~~g 238 (381)
T PF00872_consen 162 YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKERGLKD---ILLVVSDGHKG 238 (381)
T ss_pred ccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhccccc---cceeecccccc
Confidence 3789999999987754 457999999999999999999999999999999999999987765 58999999999
Q ss_pred HHHHHhhhCCCCcccccHHHHHHHHhhhCCCC---CChhhHhHhhhccchHHHHHHHHHHH----hhCHHHHHHhhcCCC
Q 040097 268 IDEAVEEFLPSAVYRQCCFSLYTKMVDEFPRV---TVHSPFWGACRSTDGNTFTNQMAVIQ----TISVECYNWLKDTDW 340 (516)
Q Consensus 268 l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~~~~---~~~~~~~~~~~~~~~~~f~~~~~~l~----~~~~~~~~~l~~~~~ 340 (516)
|.+||.++||++.++.|.+|+++|+.++++.+ .+.+.++.+..+.+.++....++++. ..+|.+.+++.+...
T Consensus 239 l~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~ 318 (381)
T PF00872_consen 239 LKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWD 318 (381)
T ss_pred ccccccccccchhhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhcccccccccchhhhhhhhccc
Confidence 99999999999999999999999999998744 66777777877877777777777664 458999999999888
Q ss_pred cccccccCCCCccccccCCChHHHHHHHHHhc----ccChHHHHHHHH
Q 040097 341 HKWALFSMPEWVKSTEITISATEQLRIWLLKQ----LDFNIAQRYTTI 384 (516)
Q Consensus 341 ~~W~~~~~~~~~~~~~~t~n~~Es~n~~lk~~----r~~pi~~~~~~~ 384 (516)
+.|+..-||...+--+.|||.+|++|+.||+. +.+|-.+.+..+
T Consensus 319 ~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~~~~Fp~~~s~lr~ 366 (381)
T PF00872_consen 319 ELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTKVVGIFPNEESALRL 366 (381)
T ss_pred cccceeeecchhccccchhhhccccccchhhhccccccCCCHHHHHHH
Confidence 88887767775666778999999999999882 345544443333
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.63 E-value=6.1e-15 Score=146.29 Aligned_cols=219 Identities=16% Similarity=0.180 Sum_probs=166.4
Q ss_pred CCccCHHHHHHHHHHHhCCcch---hhhhHhhhHHHHHHhhcCChhHHHHHHHHHHHHHhhCCCcEEEEEeccccccccc
Q 040097 96 SEHREVDKLRNEIATTYGIKCP---IWKLEAVDRMVRFWLRTDHPDGYAQLLQYKQEMEIVNSRNIVIIETKSQQQFTAD 172 (516)
Q Consensus 96 ~~~~~~~~i~~~l~~~~g~~~s---~~r~k~~~~~~~~~~~g~~~~~~~~l~~~~~~l~~~npg~~~~~~~~~~~~~~~~ 172 (516)
..+++++++...+++.++..++ +.+-- ..+...+.+++..-+
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~------------------~~~~e~v~~~~~r~l----------------- 142 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVT------------------DRLDEKVKAWQNRPL----------------- 142 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHH------------------HHHHHHHHHHHhccc-----------------
Confidence 4689999999999999887666 11111 123344444444321
Q ss_pred ceeeEeeeccchHHHHhhcCceEEEEeCeeecCC--CCceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhcc
Q 040097 173 IFHRMFVFLYDTAFVFKTRCRMLLTVDGWEIDSP--YKSVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGL 250 (516)
Q Consensus 173 ~~~~~f~~~~~~~~~~~~~~~~vi~~D~t~~~~~--y~~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~ 250 (516)
+..+++++||+|++.+ -+..+++|+|++.+|+..++++.+...|+ ..|.-||..|+..+
T Consensus 143 ------------------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rg 203 (379)
T COG3328 143 ------------------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRG 203 (379)
T ss_pred ------------------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhcc
Confidence 1348999999999988 45679999999999999999999999999 99999999999986
Q ss_pred CCCCCCcEEEEcCCcchHHHHHhhhCCCCcccccHHHHHHHHhhhCCCC---CChhhHhHhhhccchHHHHHHHHH----
Q 040097 251 RLERGEGLCIMGDGDNGIDEAVEEFLPSAVYRQCCFSLYTKMVDEFPRV---TVHSPFWGACRSTDGNTFTNQMAV---- 323 (516)
Q Consensus 251 ~~~~~~~~~iitD~~~~l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~~~~---~~~~~~~~~~~~~~~~~f~~~~~~---- 323 (516)
-... ..+++|+.+|+.+||..+||.+.++.|..|+.+|+.++.+.+ .....+..+..+.+.++....+..
T Consensus 204 l~~v---~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~ 280 (379)
T COG3328 204 LSDV---LLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSEL 280 (379)
T ss_pred ccce---eEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHh
Confidence 6654 677779999999999999999999999999999999988755 333344444444554444444444
Q ss_pred HHhhCHHHHHHhhcCCCcccccccCCCCccccccCCChHHHHHHHHHh
Q 040097 324 IQTISVECYNWLKDTDWHKWALFSMPEWVKSTEITISATEQLRIWLLK 371 (516)
Q Consensus 324 l~~~~~~~~~~l~~~~~~~W~~~~~~~~~~~~~~t~n~~Es~n~~lk~ 371 (516)
+....|....++.+...+.|...-|+...+--+.|||..|++|+.++.
T Consensus 281 w~~~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 281 WGKRYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred hhhhcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 455678888888887777776666665344567899999999998775
No 5
>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=99.62 E-value=1.9e-15 Score=113.50 Aligned_cols=62 Identities=32% Similarity=0.661 Sum_probs=60.4
Q ss_pred CCceeCCHHHHHHHHHHHHHHcCceEEEEeeCCcEEEEEeecCCCccEEEEEEccCcceEEE
Q 040097 1 MGQRFKNDVEFKTALEVNAIRDGFKLCIIHNTTTCVSCECSNLHCDWKITAVKEHRSNVFVI 62 (516)
Q Consensus 1 vG~~F~s~~e~~~ai~~ya~~~gf~~~~~rs~~~~~~~~C~~~gCp~rv~~~~~~~~~~~~V 62 (516)
+||+|+|++|+++||..||+.++|++++.+|++++++++|...||||+|+|++.++++.|+|
T Consensus 6 ~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 6 VGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred cCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 69999999999999999999999999999999999999999999999999999999999986
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=99.05 E-value=8.8e-10 Score=87.80 Aligned_cols=69 Identities=17% Similarity=0.307 Sum_probs=65.5
Q ss_pred eCCHHHHHHHHHHHHHHcCceEEEEeeCCcEEEEEeec------------------------------------------
Q 040097 5 FKNDVEFKTALEVNAIRDGFKLCIIHNTTTCVSCECSN------------------------------------------ 42 (516)
Q Consensus 5 F~s~~e~~~ai~~ya~~~gf~~~~~rs~~~~~~~~C~~------------------------------------------ 42 (516)
|.|++|++.+|+.++...|+.+.+.|||...+.|.|..
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 89999999999999999999999999999999999973
Q ss_pred CCCccEEEEEEccCcceEEEEecCCCceecc
Q 040097 43 LHCDWKITAVKEHRSNVFVICDITPMHTCNQ 73 (516)
Q Consensus 43 ~gCp~rv~~~~~~~~~~~~V~~~~~~Hnc~~ 73 (516)
.+|||+|+|......+.|.|..+++.|||++
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 3799999999999999999999999999985
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=99.02 E-value=1e-10 Score=70.56 Aligned_cols=27 Identities=52% Similarity=0.891 Sum_probs=25.1
Q ss_pred cccccCccccCCCCCcchhHHHhhcCC
Q 040097 452 MTCTCRLWQLSGIPCPHACRCIDTWGD 478 (516)
Q Consensus 452 ~~CsC~~~~~~giPC~H~la~~~~~~~ 478 (516)
.+|||++|+..||||+|+|+|+...++
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=98.90 E-value=2.7e-09 Score=85.50 Aligned_cols=62 Identities=16% Similarity=0.232 Sum_probs=54.6
Q ss_pred HHHHHHHHHcCceEEEEeeCC-------cEEEEEeec----------------------CCCccEEEEEEccCcceEEEE
Q 040097 13 TALEVNAIRDGFKLCIIHNTT-------TCVSCECSN----------------------LHCDWKITAVKEHRSNVFVIC 63 (516)
Q Consensus 13 ~ai~~ya~~~gf~~~~~rs~~-------~~~~~~C~~----------------------~gCp~rv~~~~~~~~~~~~V~ 63 (516)
+||+.||..+||++++.+|.+ .++.++|++ +||||+|.+.+.. ++.|.|+
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 489999999999999987654 378899985 5999999999887 9999999
Q ss_pred ecCCCceecccC
Q 040097 64 DITPMHTCNQHS 75 (516)
Q Consensus 64 ~~~~~Hnc~~~~ 75 (516)
.+..+|||++.+
T Consensus 80 ~~~~~HNH~L~P 91 (91)
T PF03101_consen 80 SFVLEHNHPLCP 91 (91)
T ss_pred ECcCCcCCCCCC
Confidence 999999999753
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=98.21 E-value=9.4e-07 Score=58.63 Aligned_cols=31 Identities=26% Similarity=0.650 Sum_probs=27.7
Q ss_pred EEecccccccCccccCCCCCcchhHHHhhcC
Q 040097 447 INRELMTCTCRLWQLSGIPCPHACRCIDTWG 477 (516)
Q Consensus 447 V~~~~~~CsC~~~~~~giPC~H~la~~~~~~ 477 (516)
+.+...+|||+.|+..|.||+|++|++...+
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~~ 40 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLALN 40 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhhC
Confidence 5677899999999999999999999987653
No 10
>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=95.91 E-value=0.017 Score=55.44 Aligned_cols=93 Identities=16% Similarity=0.164 Sum_probs=69.4
Q ss_pred EEEeCeeecCCCCceeEEEEEecC--CCCeEEEEEEEeeccccccHHHHHHHH-HhccCCCCCCcEEEEcCCcchHHHHH
Q 040097 196 LTVDGWEIDSPYKSVMLVAVCRDG--NDAVLPIAFCEVVEENLDSWAFFLKNL-NYGLRLERGEGLCIMGDGDNGIDEAV 272 (516)
Q Consensus 196 i~~D~t~~~~~y~~~l~~~~g~d~--~~~~~~la~a~~~~E~~~~~~w~l~~l-~~~~~~~~~~~~~iitD~~~~l~~Ai 272 (516)
|+||-+.....+.. ++.+.+|. +++.. +.++++-+.++..-||..+ -...... ..+|++|...+..+|+
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---LDILPGRDKETLKDFFRSLYPEEERKN---VKVVSMDMSPPYRSAI 72 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCceE---EEEcCCccHHHHHHHHHHhCccccccc---eEEEEcCCCccccccc
Confidence 46777766554443 44445555 44332 4588899999998888877 4443332 5899999999999999
Q ss_pred hhhCCCCcccccHHHHHHHHhhhC
Q 040097 273 EEFLPSAVYRQCCFSLYTKMVDEF 296 (516)
Q Consensus 273 ~~vfP~a~~~~C~~Hi~~n~~~~~ 296 (516)
++.||+|.+..-.||+++++.+.+
T Consensus 73 ~~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 73 REYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred cccccccccccccchhhhhhhhcc
Confidence 999999999999999999987643
No 11
>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=95.42 E-value=0.02 Score=41.37 Aligned_cols=40 Identities=15% Similarity=0.151 Sum_probs=33.1
Q ss_pred CcEEEEEeecCCCccEEEEEEccCcceEEEEecCCCceec
Q 040097 33 TTCVSCECSNLHCDWKITAVKEHRSNVFVICDITPMHTCN 72 (516)
Q Consensus 33 ~~~~~~~C~~~gCp~rv~~~~~~~~~~~~V~~~~~~Hnc~ 72 (516)
-.|..++|+..+||++-.+.+..+++...++++.++|||+
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 3577899999999999999998878888899999999996
No 12
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=95.26 E-value=0.21 Score=52.43 Aligned_cols=133 Identities=19% Similarity=0.192 Sum_probs=92.2
Q ss_pred ccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHHHHHhhhCCCCcccccHHHHHHHHhhhCC-CCCChhhHhHhhhc
Q 040097 233 EENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVEEFLPSAVYRQCCFSLYTKMVDEFP-RVTVHSPFWGACRS 311 (516)
Q Consensus 233 ~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~~-~~~~~~~~~~~~~~ 311 (516)
..+.+.|..+.+.+.+.....+.--+++.+|+...+.+++. .+|++.|.+..+|+.+.+.+.++ .+.+.+.++++.+.
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~al~~ 313 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKALKK 313 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHHHHh
Confidence 55678899999988887765542246788999999998876 99999999999999999999886 44667767777777
Q ss_pred cchHHHHHHHHHHHhh--CH-------HHHHHhhcCCCcccccccCCCCccccccCCChHHHHHHHHHh
Q 040097 312 TDGNTFTNQMAVIQTI--SV-------ECYNWLKDTDWHKWALFSMPEWVKSTEITISATEQLRIWLLK 371 (516)
Q Consensus 312 ~~~~~f~~~~~~l~~~--~~-------~~~~~l~~~~~~~W~~~~~~~~~~~~~~t~n~~Es~n~~lk~ 371 (516)
....++...++.+... ++ ++..||.++.... ..|-. +-|.......|+.++.+..
T Consensus 314 ~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i--~~y~~---~~~~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 314 GDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGI--KPYRE---REGLRGIGAEESVSHVLSY 377 (470)
T ss_pred cCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHh--hhhhh---ccCCCccchhhhhhhHHHH
Confidence 7788888888777543 21 3455666542211 12211 1233444557777777643
No 13
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=94.99 E-value=0.014 Score=50.50 Aligned_cols=81 Identities=20% Similarity=0.056 Sum_probs=68.3
Q ss_pred ceEEEEeCeeecCCCCceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHHHHH
Q 040097 193 RMLLTVDGWEIDSPYKSVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAV 272 (516)
Q Consensus 193 ~~vi~~D~t~~~~~y~~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~~Ai 272 (516)
++.+.+|-||.+-+-+ ..++..++|.+|+ +|++-+.+.-+..+=..||..+.+..+.. |..|+||+.++...|+
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--ILDFYLSKRRDTAAAKRFLKRALKRHRGE---PRVIVTDKLPAYPAAI 74 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeeccc---cceeecccCCccchhh
Confidence 3578999999986533 4566788999999 88999999999999899999888887633 7999999999999999
Q ss_pred hhhCCCC
Q 040097 273 EEFLPSA 279 (516)
Q Consensus 273 ~~vfP~a 279 (516)
++++|.-
T Consensus 75 ~~l~~~~ 81 (140)
T PF13610_consen 75 KELNPEG 81 (140)
T ss_pred hhccccc
Confidence 9999974
No 14
>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=94.20 E-value=0.093 Score=52.84 Aligned_cols=54 Identities=9% Similarity=0.190 Sum_probs=49.2
Q ss_pred CceeCCHHHHHHHHHHHHHHcCceEEEEeeCC-cEEEEEeecCCCccEEEEEEcc
Q 040097 2 GQRFKNDVEFKTALEVNAIRDGFKLCIIHNTT-TCVSCECSNLHCDWKITAVKEH 55 (516)
Q Consensus 2 G~~F~s~~e~~~ai~~ya~~~gf~~~~~rs~~-~~~~~~C~~~gCp~rv~~~~~~ 55 (516)
|..|++.++-+.+|+.|-++.++.|..+.|-+ ++++|-|....|||+|.++..+
T Consensus 25 ~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g 79 (496)
T PF04684_consen 25 ARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCG 79 (496)
T ss_pred ccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeecc
Confidence 56799999999999999999999999998864 7899999999999999998654
No 15
>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=94.00 E-value=0.23 Score=41.20 Aligned_cols=74 Identities=14% Similarity=-0.055 Sum_probs=54.7
Q ss_pred ceEEEEeCeeec-CCCCceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHH
Q 040097 193 RMLLTVDGWEID-SPYKSVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGID 269 (516)
Q Consensus 193 ~~vi~~D~t~~~-~~y~~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~ 269 (516)
...+.+|.+... ...++..++.+.+|..-.. .+++.+-..++.+....+|.......+... |.+|++|+..+..
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--p~~i~tD~g~~f~ 80 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRGGRP--PRVIRTDNGSEFT 80 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS-SE---SEEEEESCHHHH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeeccccccccccccccccccccccc--ceecccccccccc
Confidence 457899999666 3455688888999987665 557777777788888888887766666553 6999999998865
No 16
>PHA02517 putative transposase OrfB; Reviewed
Probab=92.84 E-value=0.79 Score=44.59 Aligned_cols=72 Identities=14% Similarity=-0.047 Sum_probs=47.2
Q ss_pred ceEEEEeCeeecCCCCceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchH
Q 040097 193 RMLLTVDGWEIDSPYKSVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGI 268 (516)
Q Consensus 193 ~~vi~~D~t~~~~~y~~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l 268 (516)
..++..|-||..... +..++.+.+|..... ++|+.+...++.+...-.|+......+... +..|.||+....
T Consensus 110 n~~w~~D~t~~~~~~-g~~yl~~iiD~~sr~-i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~--~~i~~sD~G~~y 181 (277)
T PHA02517 110 NQLWVADFTYVSTWQ-GWVYVAFIIDVFARR-IVGWRVSSSMDTDFVLDALEQALWARGRPG--GLIHHSDKGSQY 181 (277)
T ss_pred CCeEEeceeEEEeCC-CCEEEEEecccCCCe-eeecccCCCCChHHHHHHHHHHHHhcCCCc--CcEeeccccccc
Confidence 368999999986543 556777777776554 677888877777765555555444433221 356778987653
No 17
>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=92.82 E-value=0.13 Score=36.90 Aligned_cols=38 Identities=16% Similarity=0.139 Sum_probs=32.2
Q ss_pred cEEEEEeec-CCCccEEEEEEccCcceEEEEecCCCcee
Q 040097 34 TCVSCECSN-LHCDWKITAVKEHRSNVFVICDITPMHTC 71 (516)
Q Consensus 34 ~~~~~~C~~-~gCp~rv~~~~~~~~~~~~V~~~~~~Hnc 71 (516)
.|..++|+. .|||++=.+.+..+++...++++.++|||
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 567799998 89999988888776677777899999997
No 18
>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=92.32 E-value=0.2 Score=36.12 Aligned_cols=46 Identities=13% Similarity=0.247 Sum_probs=25.1
Q ss_pred cCceEEEEeeCCcEEEEEeecC---CCccEEEEEEccCcceEEEEecCCCcee
Q 040097 22 DGFKLCIIHNTTTCVSCECSNL---HCDWKITAVKEHRSNVFVICDITPMHTC 71 (516)
Q Consensus 22 ~gf~~~~~rs~~~~~~~~C~~~---gCp~rv~~~~~~~~~~~~V~~~~~~Hnc 71 (516)
.|+.+...+.......+.|+.- +|++++... .+.+ .+.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~~~--~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AGDG--RVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE----TT--EEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CCCC--EEEECCCccCC
Confidence 4778887777788899999874 899999997 2222 35555578987
No 19
>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=91.45 E-value=0.15 Score=49.44 Aligned_cols=85 Identities=15% Similarity=0.136 Sum_probs=57.8
Q ss_pred ceEEEEeCeeec----CCC-CceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcch
Q 040097 193 RMLLTVDGWEID----SPY-KSVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNG 267 (516)
Q Consensus 193 ~~vi~~D~t~~~----~~y-~~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~ 267 (516)
.+++.+|-|..+ ++. ++-+.++++-+ .+.|.+.++-+.+...-+|.. . .-+++||+..+
T Consensus 67 ~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~-------~---~GilvsD~y~~ 130 (271)
T PF03050_consen 67 SPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGD-------F---SGILVSDGYSA 130 (271)
T ss_pred cceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcc-------c---ceeeecccccc
Confidence 478889988887 443 33344444333 555666666666666555443 2 36899999887
Q ss_pred HHHHHhhhCCCCcccccHHHHHHHHhhhCCC
Q 040097 268 IDEAVEEFLPSAVYRQCCFSLYTKMVDEFPR 298 (516)
Q Consensus 268 l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~~~ 298 (516)
=.. +..+.|+.|+.|+.+.+.+....
T Consensus 131 Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 131 YNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred ccc-----ccccccccccccccccccccccc
Confidence 544 23889999999999999876653
No 20
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=91.29 E-value=5.4 Score=38.47 Aligned_cols=73 Identities=11% Similarity=0.034 Sum_probs=48.9
Q ss_pred eEEEEeCeeecCCCCceeEEEEEecCCCCeEEEEEEEeec-cccccHHHHHHH-HHhccCC-CCCCcEEEEcCCcch
Q 040097 194 MLLTVDGWEIDSPYKSVMLVAVCRDGNDAVLPIAFCEVVE-ENLDSWAFFLKN-LNYGLRL-ERGEGLCIMGDGDNG 267 (516)
Q Consensus 194 ~vi~~D~t~~~~~y~~~l~~~~g~d~~~~~~~la~a~~~~-E~~~~~~w~l~~-l~~~~~~-~~~~~~~iitD~~~~ 267 (516)
.++..|-||.....++.+++++-+|.... .++|+++... .+.+.-.-+|+. +....+. .+..|..|-||+...
T Consensus 88 ~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 88 QRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred CEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCcc
Confidence 68999999987654557888888998776 5788998874 555555555554 3333221 112368889998765
No 21
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=90.19 E-value=8.7 Score=37.88 Aligned_cols=75 Identities=11% Similarity=0.031 Sum_probs=51.1
Q ss_pred ceEEEEeCeeecCCCCceeEEEEEecCCCCeEEEEEEEeec-cccccHHHHHHH-HHhccCC-CCCCcEEEEcCCcchH
Q 040097 193 RMLLTVDGWEIDSPYKSVMLVAVCRDGNDAVLPIAFCEVVE-ENLDSWAFFLKN-LNYGLRL-ERGEGLCIMGDGDNGI 268 (516)
Q Consensus 193 ~~vi~~D~t~~~~~y~~~l~~~~g~d~~~~~~~la~a~~~~-E~~~~~~w~l~~-l~~~~~~-~~~~~~~iitD~~~~l 268 (516)
..++..|-||....-++.+++++-+|...+ .++|+++... .+.+.-.-+|+. +....+. .+..|..|-||+...-
T Consensus 126 N~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 126 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred CCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 368999999986655557888888998777 5889999875 566655555553 4443332 1223678899987653
No 22
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=85.60 E-value=1.9 Score=39.71 Aligned_cols=84 Identities=18% Similarity=0.014 Sum_probs=62.8
Q ss_pred ceEEEEeCeeecCCCCceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHHHHH
Q 040097 193 RMLLTVDGWEIDSPYKSVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAV 272 (516)
Q Consensus 193 ~~vi~~D~t~~~~~y~~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~~Ai 272 (516)
++.+.+|-||.+.+-+.. +.--++|.+ ..++.+-|...-+...=.-||..+++..+ .|.+|+||+.+....|+
T Consensus 70 ~~~w~vDEt~ikv~gkw~-ylyrAid~~--g~~Ld~~L~~rRn~~aAk~Fl~kllk~~g----~p~v~vtDka~s~~~A~ 142 (215)
T COG3316 70 GDSWRVDETYIKVNGKWH-YLYRAIDAD--GLTLDVWLSKRRNALAAKAFLKKLLKKHG----EPRVFVTDKAPSYTAAL 142 (215)
T ss_pred ccceeeeeeEEeeccEee-ehhhhhccC--CCeEEEEEEcccCcHHHHHHHHHHHHhcC----CCceEEecCccchHHHH
Confidence 367889999987654333 223445665 45677888888888888888888877762 27999999999999999
Q ss_pred hhhCCCCcccc
Q 040097 273 EEFLPSAVYRQ 283 (516)
Q Consensus 273 ~~vfP~a~~~~ 283 (516)
.++-+.+.|+.
T Consensus 143 ~~l~~~~ehr~ 153 (215)
T COG3316 143 RKLGSEVEHRT 153 (215)
T ss_pred HhcCcchheec
Confidence 99998666653
No 23
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=80.07 E-value=21 Score=31.24 Aligned_cols=62 Identities=13% Similarity=0.200 Sum_probs=46.6
Q ss_pred cccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHHHHHh---hhCCCCcccccHHHHHHHHhhhCC
Q 040097 234 ENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVE---EFLPSAVYRQCCFSLYTKMVDEFP 297 (516)
Q Consensus 234 E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~~Ai~---~vfP~a~~~~C~~Hi~~n~~~~~~ 297 (516)
.+.+...-+|....+.+|..+ -.-||||-...+.+|-+ +-+|.....-|..|-+.-+.+.+.
T Consensus 73 ~~a~~l~~ll~~vIeeVG~~n--VvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~ 137 (153)
T PF04937_consen 73 KTAEYLFELLDEVIEEVGEEN--VVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIG 137 (153)
T ss_pred ccHHHHHHHHHHHHHHhhhhh--hhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHh
Confidence 455666666666666666666 67899999999888844 448999999999998877765544
No 24
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=72.65 E-value=1.9 Score=34.21 Aligned_cols=39 Identities=18% Similarity=0.286 Sum_probs=28.0
Q ss_pred eEEEeeCCeeEEEEecccccccCcccc-----CCCCCcchhHHHhh
Q 040097 435 IAVVTRDGLAYEINRELMTCTCRLWQL-----SGIPCPHACRCIDT 475 (516)
Q Consensus 435 ~~v~~~~~~~~~V~~~~~~CsC~~~~~-----~giPC~H~la~~~~ 475 (516)
+||.-..++.|.++.+ -|||..|-. -.-||.|++.+=..
T Consensus 35 ~fVyvG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A 78 (117)
T COG5431 35 FFVYVGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVA 78 (117)
T ss_pred EEEEEccccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeee
Confidence 5666666778888776 899988762 24579999876443
No 25
>PRK13907 rnhA ribonuclease H; Provisional
Probab=63.87 E-value=50 Score=27.60 Aligned_cols=78 Identities=18% Similarity=0.174 Sum_probs=45.6
Q ss_pred EEEEeCeeecCCCCceeEEEEEecCCCCeEEEEE-EEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHHHHHh
Q 040097 195 LLTVDGWEIDSPYKSVMLVAVCRDGNDAVLPIAF-CEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVE 273 (516)
Q Consensus 195 vi~~D~t~~~~~y~~~l~~~~g~d~~~~~~~la~-a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~~Ai~ 273 (516)
.|.+||.+..++-.+-...++ .|..+... +.+ .-..+.+..-+.-++..|+.+..... .+..|-||. +.+.+++.
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-KGVQPAVQ-LSLPLGTMSNHEAEYHALLAALKYCTEHNY-NIVSFRTDS-QLVERAVE 78 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHhCCC-CEEEEEech-HHHHHHHh
Confidence 378999998775433333333 45555432 222 11234455667778888877654432 257777876 66677777
Q ss_pred hhC
Q 040097 274 EFL 276 (516)
Q Consensus 274 ~vf 276 (516)
..+
T Consensus 79 ~~~ 81 (128)
T PRK13907 79 KEY 81 (128)
T ss_pred HHH
Confidence 655
No 26
>PF13565 HTH_32: Homeodomain-like domain
Probab=58.90 E-value=21 Score=26.77 Aligned_cols=33 Identities=6% Similarity=0.193 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhcCCccCHHHHHHHHHHHhCCcc
Q 040097 84 WIAAKFLHIWKQSEHREVDKLRNEIATTYGIKC 116 (516)
Q Consensus 84 ~l~~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~ 116 (516)
.+.+.+.+.+..+|.+++.+|.+.|.+++|+.+
T Consensus 34 e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 34 EQRERIIALIEEHPRWTPREIAEYLEEEFGISV 66 (77)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC
Confidence 444666777778899999999999999999866
No 27
>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=57.47 E-value=34 Score=29.60 Aligned_cols=69 Identities=13% Similarity=0.092 Sum_probs=41.4
Q ss_pred eEEEEeCeeecCCC--------------CceeEEEEEecCC-CCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcE
Q 040097 194 MLLTVDGWEIDSPY--------------KSVMLVAVCRDGN-DAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGL 258 (516)
Q Consensus 194 ~vi~~D~t~~~~~y--------------~~~l~~~~g~d~~-~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~ 258 (516)
.+|-+|.||..++- .....++++++-+ +..--+...++++.+.++..-+++...+ +..
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~i~-------~gs 76 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEHIE-------PGS 76 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHhhh-------ccc
Confidence 46788888875332 2234455555554 4333444555677888877666554332 247
Q ss_pred EEEcCCcchHH
Q 040097 259 CIMGDGDNGID 269 (516)
Q Consensus 259 ~iitD~~~~l~ 269 (516)
+|+||..++-.
T Consensus 77 ~i~TD~~~aY~ 87 (151)
T PF12762_consen 77 TIITDGWRAYN 87 (151)
T ss_pred eeeecchhhcC
Confidence 89999988753
No 28
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=48.18 E-value=8 Score=36.20 Aligned_cols=23 Identities=22% Similarity=0.534 Sum_probs=19.0
Q ss_pred ccccccCccccCCCCCcchhHHHhhc
Q 040097 451 LMTCTCRLWQLSGIPCPHACRCIDTW 476 (516)
Q Consensus 451 ~~~CsC~~~~~~giPC~H~la~~~~~ 476 (516)
...|||..+ -.||.|+-||....
T Consensus 124 ~~dCSCPD~---anPCKHi~AvyY~l 146 (266)
T COG4279 124 STDCSCPDY---ANPCKHIAAVYYLL 146 (266)
T ss_pred ccccCCCCc---ccchHHHHHHHHHH
Confidence 467999885 57999999998774
No 29
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=44.73 E-value=20 Score=25.16 Aligned_cols=20 Identities=5% Similarity=-0.056 Sum_probs=15.8
Q ss_pred ccCHHHHHHHHHHHhCCcch
Q 040097 98 HREVDKLRNEIATTYGIKCP 117 (516)
Q Consensus 98 ~~~~~~i~~~l~~~~g~~~s 117 (516)
.++..+++..|.++.++.+.
T Consensus 12 yMsk~E~v~~L~~~a~I~P~ 31 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPV 31 (54)
T ss_pred cCCHHHHHHHHHHHcCCChH
Confidence 46778888899888887755
No 30
>PRK00766 hypothetical protein; Provisional
Probab=43.53 E-value=2.1e+02 Score=26.12 Aligned_cols=89 Identities=20% Similarity=0.200 Sum_probs=48.3
Q ss_pred eEEEEe-CeeecCCCCceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccC--C------------------
Q 040097 194 MLLTVD-GWEIDSPYKSVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLR--L------------------ 252 (516)
Q Consensus 194 ~vi~~D-~t~~~~~y~~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~--~------------------ 252 (516)
.|+++| +.|..+.-+-..++-+-.-++.-+.-++|+-+.-...+.=.-+.+.+++... +
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 467777 4444433333455555555555556666666665555554544444433110 0
Q ss_pred ------CCCCcEEEEcCCcc---hHHHHHhhhCCCCccc
Q 040097 253 ------ERGEGLCIMGDGDN---GIDEAVEEFLPSAVYR 282 (516)
Q Consensus 253 ------~~~~~~~iitD~~~---~l~~Ai~~vfP~a~~~ 282 (516)
.-+-|..+++..-+ +|.+|+++.||+...+
T Consensus 90 ~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k~f~~~~~R 128 (194)
T PRK00766 90 IEELYRETGLPVIVVMRKKPDFEAIESALKKHFSDWEER 128 (194)
T ss_pred HHHHHHHHCCCEEEEEecCCCHHHHHHHHHHHCCCHHHH
Confidence 00125555544433 7889999999987654
No 31
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=43.19 E-value=54 Score=22.89 Aligned_cols=35 Identities=11% Similarity=0.323 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhhc-C-CccCHHHHHHHHHHHhCCcch
Q 040097 83 KWIAAKFLHIWKQ-S-EHREVDKLRNEIATTYGIKCP 117 (516)
Q Consensus 83 ~~l~~~~~~~i~~-~-~~~~~~~i~~~l~~~~g~~~s 117 (516)
..+...+.+.+++ + ..++.++|+..|++.+|+.++
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~ 39 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVTKKQVREQLEERFGVDLS 39 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--S
T ss_pred HHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcH
Confidence 3455667777765 3 579999999999999999888
No 32
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.48 E-value=36 Score=29.52 Aligned_cols=35 Identities=14% Similarity=0.081 Sum_probs=29.7
Q ss_pred EeCeee-cCCCCce--eEEEEEecCCCCeEEEEEEEee
Q 040097 198 VDGWEI-DSPYKSV--MLVAVCRDGNDAVLPIAFCEVV 232 (516)
Q Consensus 198 ~D~t~~-~~~y~~~--l~~~~g~d~~~~~~~la~a~~~ 232 (516)
||.||+ +++|+.| ++...|.|+-|+-.+.|++.+.
T Consensus 70 ievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~h 107 (187)
T KOG4027|consen 70 IEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLH 107 (187)
T ss_pred eEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEe
Confidence 788998 6789987 5667899999999999999774
No 33
>PF14420 Clr5: Clr5 domain
Probab=40.84 E-value=54 Score=22.94 Aligned_cols=22 Identities=14% Similarity=0.350 Sum_probs=20.0
Q ss_pred CCccCHHHHHHHHHHHhCCcch
Q 040097 96 SEHREVDKLRNEIATTYGIKCP 117 (516)
Q Consensus 96 ~~~~~~~~i~~~l~~~~g~~~s 117 (516)
+.+.+..+|++.++..+|+.++
T Consensus 18 ~e~~tl~~v~~~M~~~~~F~at 39 (54)
T PF14420_consen 18 DENKTLEEVMEIMKEEHGFKAT 39 (54)
T ss_pred hCCCcHHHHHHHHHHHhCCCcC
Confidence 5788999999999999999888
No 34
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=40.28 E-value=30 Score=24.86 Aligned_cols=29 Identities=10% Similarity=0.178 Sum_probs=23.4
Q ss_pred HHHHHHHhhc--CCccCHHHHHHHHHHHhCC
Q 040097 86 AAKFLHIWKQ--SEHREVDKLRNEIATTYGI 114 (516)
Q Consensus 86 ~~~~~~~i~~--~~~~~~~~i~~~l~~~~g~ 114 (516)
++++.+.|.. .-+++|.+|--.|+++||+
T Consensus 30 ~~eVe~~I~klakkG~tpSqIG~iLRD~~GI 60 (60)
T PF08069_consen 30 PEEVEELIVKLAKKGLTPSQIGVILRDQYGI 60 (60)
T ss_dssp HHHHHHHHHHHCCTTHCHHHHHHHHHHSCTC
T ss_pred HHHHHHHHHHHHHcCCCHHHhhhhhhhccCC
Confidence 4566666654 7899999999999999985
No 35
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=39.00 E-value=65 Score=34.12 Aligned_cols=50 Identities=24% Similarity=0.387 Sum_probs=31.8
Q ss_pred eEEeecCCc-e-EEEeeC-CeeEEEEe----cccccccCccccCCCCCcchhHHHhhcC
Q 040097 426 TVDVTSRNA-I-AVVTRD-GLAYEINR----ELMTCTCRLWQLSGIPCPHACRCIDTWG 477 (516)
Q Consensus 426 ~~~v~~~~~-~-~v~~~~-~~~~~V~~----~~~~CsC~~~~~~giPC~H~la~~~~~~ 477 (516)
...++..++ + .+|+.+ .-.++|++ -..+|||.. +..|- |.|++||+....
T Consensus 40 V~~i~~~g~~v~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~ga-CKH~VAvvl~~~ 96 (587)
T COG4715 40 VLKITIRGGTVRAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSGA-CKHVVAVVLEYL 96 (587)
T ss_pred ceEEeecCCeEEEEEeccceeeEEEEeecCCcCceeeCCC-CCCcc-hHHHHHHHHHHh
Confidence 445553222 2 344443 34556665 458999998 56664 999999998864
No 36
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=38.47 E-value=56 Score=24.66 Aligned_cols=29 Identities=24% Similarity=0.374 Sum_probs=25.3
Q ss_pred eeCCHHHHHHHHHHHHHHcCceEEEEeeC
Q 040097 4 RFKNDVEFKTALEVNAIRDGFKLCIIHNT 32 (516)
Q Consensus 4 ~F~s~~e~~~ai~~ya~~~gf~~~~~rs~ 32 (516)
.++|.+++..+|..|+.++|-++.+.+-+
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~ 41 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRD 41 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecC
Confidence 47899999999999999999999876543
No 37
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=35.96 E-value=29 Score=24.63 Aligned_cols=20 Identities=10% Similarity=-0.032 Sum_probs=16.4
Q ss_pred ccCHHHHHHHHHHHhCCcch
Q 040097 98 HREVDKLRNEIATTYGIKCP 117 (516)
Q Consensus 98 ~~~~~~i~~~l~~~~g~~~s 117 (516)
-++..++++.|.++.|+.+.
T Consensus 15 yMsk~E~v~~L~~~a~I~P~ 34 (57)
T TIGR01589 15 YMSKEETVSFLFENAGISPK 34 (57)
T ss_pred HCCHHHHHHHHHHHcCCCch
Confidence 46778899999999888766
No 38
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=34.87 E-value=1e+02 Score=21.17 Aligned_cols=28 Identities=14% Similarity=0.141 Sum_probs=21.1
Q ss_pred CCceeEEEEEecCCCCeEEEEEEEeecc
Q 040097 207 YKSVMLVAVCRDGNDAVLPIAFCEVVEE 234 (516)
Q Consensus 207 y~~~l~~~~g~d~~~~~~~la~a~~~~E 234 (516)
|...-++++|-.++|+..++.-.+..+|
T Consensus 35 yefssfvlcgetpdgrrlvlthmistde 62 (66)
T PF13082_consen 35 YEFSSFVLCGETPDGRRLVLTHMISTDE 62 (66)
T ss_pred EEEEEEEEEccCCCCcEEEEEEEecchh
Confidence 4445578899999999988877766554
No 39
>smart00816 Amb_V_allergen Amb V Allergen. Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphhydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens.
Probab=33.89 E-value=24 Score=22.81 Aligned_cols=22 Identities=18% Similarity=0.504 Sum_probs=15.0
Q ss_pred CcEEEEEeecCC--CccEEEEEEc
Q 040097 33 TTCVSCECSNLH--CDWKITAVKE 54 (516)
Q Consensus 33 ~~~~~~~C~~~g--Cp~rv~~~~~ 54 (516)
++...+.|+..| |||.|.....
T Consensus 13 Gekr~YCcSdpGrYCpwqvVCYeS 36 (45)
T smart00816 13 GEKRKYCCSDPGRYCPWQVVCYES 36 (45)
T ss_pred cccCccccCCCcccCCceEEEeeh
Confidence 345556777665 9999887643
No 40
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.66 E-value=1.9e+02 Score=24.58 Aligned_cols=38 Identities=5% Similarity=-0.015 Sum_probs=30.1
Q ss_pred HHHHhhcCceE--EEEeCeeecCCCCceeEEEEEecCCCCe
Q 040097 185 AFVFKTRCRML--LTVDGWEIDSPYKSVMLVAVCRDGNDAV 223 (516)
Q Consensus 185 ~~~~~~~~~~v--i~~D~t~~~~~y~~~l~~~~g~d~~~~~ 223 (516)
+..+.. +.|+ +-.||-|++-|.+||++.+--.|.+...
T Consensus 97 ~sDi~k-ynpIlA~~~nGn~M~IRerGPl~~IYplds~peL 136 (155)
T COG3915 97 YSDIEK-YNPILAIQNNGNYMQIRERGPLWSIYPLDSSPEL 136 (155)
T ss_pred HHHhhh-cccEEEEEeCCcEEEEeccCceEEEeecCCChhh
Confidence 456665 7776 5679999999999999999888876643
No 41
>PF11447 DUF3201: Protein of unknown function (DUF3201); InterPro: IPR024505 This archaeal family of proteins has no known function.; PDB: 1YB3_A.
Probab=28.12 E-value=3.7e+02 Score=22.81 Aligned_cols=69 Identities=12% Similarity=0.044 Sum_probs=39.7
Q ss_pred HHHHHHHHHHhhCCCcEEEEEecccccccccceeeEeeeccchHHHHhhcCceEEEEeCeeecCCCCceeEEE-----EE
Q 040097 142 QLLQYKQEMEIVNSRNIVIIETKSQQQFTADIFHRMFVFLYDTAFVFKTRCRMLLTVDGWEIDSPYKSVMLVA-----VC 216 (516)
Q Consensus 142 ~l~~~~~~l~~~npg~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~vi~~D~t~~~~~y~~~l~~~-----~g 216 (516)
.+-.+-++|++.-||+.++-...- |.-.|.+||-+..-.|--|.+.+ +|
T Consensus 9 eif~l~eELkeel~gf~vE~v~ev--------------------------Fnayi~lDgeW~em~YPhPaf~ikp~gEvG 62 (150)
T PF11447_consen 9 EIFRLNEELKEELKGFKVEEVEEV--------------------------FNAYIYLDGEWREMKYPHPAFEIKPQGEVG 62 (150)
T ss_dssp HHHHHHHHHHHHSTTSEE---EEE---------------------------S-EEEETTEEEE--S-EEEEEEETTEEEE
T ss_pred HHHHHHHHHHHHcCCCcceeHhhh--------------------------hheeEEecCeeeeecCCCCceeeccCcccc
Confidence 344556778888889877643321 44569999999999999888764 67
Q ss_pred ecCCCCeEEEEEEEeecccccc
Q 040097 217 RDGNDAVLPIAFCEVVEENLDS 238 (516)
Q Consensus 217 ~d~~~~~~~la~a~~~~E~~~~ 238 (516)
.+..+-.++ +|+-..+-++.
T Consensus 63 at~q~~YFv--fav~kE~is~~ 82 (150)
T PF11447_consen 63 ATPQGFYFV--FAVPKEKISEE 82 (150)
T ss_dssp EETTEEEEE--EEEEGGG--HH
T ss_pred cccceEEEE--EEeeHHHhhHH
Confidence 777555544 44444443333
No 42
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=24.92 E-value=1e+02 Score=25.74 Aligned_cols=55 Identities=15% Similarity=0.063 Sum_probs=39.6
Q ss_pred ceeEEEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcch
Q 040097 209 SVMLVAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNG 267 (516)
Q Consensus 209 ~~l~~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~ 267 (516)
+.+.++.+++.++...+ +.....-+.+.|.-||+.+........ +.+|+.|....
T Consensus 37 ~~~~~~~ai~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~li~DNa~~ 91 (146)
T PF13358_consen 37 GRVSVWGAISYNGGIVL--FVVEGTMNSEDFIEFLEQLLRPYPRKG--RIVLIMDNASI 91 (146)
T ss_pred CEEEEEEEecccccccc--eeeeeeeccccccccccccccccccce--EEEEecccccc
Confidence 35666667777775555 445566778888889999888777663 58899998763
No 43
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=23.68 E-value=62 Score=25.43 Aligned_cols=36 Identities=14% Similarity=0.156 Sum_probs=28.6
Q ss_pred cchHHHHHHHHHHHhhCHHHHHHhhcCCCccccccc
Q 040097 312 TDGNTFTNQMAVIQTISVECYNWLKDTDWHKWALFS 347 (516)
Q Consensus 312 ~~~~~f~~~~~~l~~~~~~~~~~l~~~~~~~W~~~~ 347 (516)
.+..+|+..|..+.......++||..++++.+..-+
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~if 40 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPKIF 40 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHHHH
Confidence 367799999999977777899999999877665333
No 44
>KOG2909 consensus Vacuolar H+-ATPase V1 sector, subunit C [Energy production and conversion]
Probab=22.99 E-value=1.1e+02 Score=30.38 Aligned_cols=98 Identities=11% Similarity=0.160 Sum_probs=59.1
Q ss_pred hhHHHHHHHHHHHHHhhCCCcEEEEEecccccccccceeeEeeeccchHHHHhhcCceEEEEeCeeecCCCCceeEEEEE
Q 040097 137 PDGYAQLLQYKQEMEIVNSRNIVIIETKSQQQFTADIFHRMFVFLYDTAFVFKTRCRMLLTVDGWEIDSPYKSVMLVAVC 216 (516)
Q Consensus 137 ~~~~~~l~~~~~~l~~~npg~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~vi~~D~t~~~~~y~~~l~~~~g 216 (516)
...|+.+..=++.|++++-|+.....+.++.. ++=+.+|+-|+++ |
T Consensus 141 ~a~yn~ak~nl~nlerK~~GsL~~rsL~~IVk------------------------~edfvl~SEyL~t-----l----- 186 (381)
T KOG2909|consen 141 AAAYNNAKGNLQNLERKKTGSLSTRSLADIVK------------------------KEDFVLDSEYLTT-----L----- 186 (381)
T ss_pred HHHHHhHHHHHHHHhhhccCChhhhhHHHhCC------------------------chhhccchhhhee-----E-----
Confidence 45788888899999999999888776544111 1112234333332 2
Q ss_pred ecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCCCCCCcEEEEcCCcchHHHHHhhhCCCCcccccHHHHHHHHhhhC
Q 040097 217 RDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVEEFLPSAVYRQCCFSLYTKMVDEF 296 (516)
Q Consensus 217 ~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~~~~~~~~iitD~~~~l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~ 296 (516)
+.+|+.-....|.---++|-..+ ...+.+.+.-++...+|..|+.+...+.|
T Consensus 187 -----------lVvVPK~~~~df~~~YEtlsd~V-----------------vPrSskki~eD~Ey~Lf~V~lFkk~~edF 238 (381)
T KOG2909|consen 187 -----------LVVVPKALVKDFLKSYETLSDMV-----------------VPRSSKKINEDAEYVLFTVTLFKKVAEDF 238 (381)
T ss_pred -----------EEEeeccchHHHHHHHHhhcccc-----------------chhhhhhcccccceEEEEEEEeehhHHHH
Confidence 33455555566665555543322 22456667777788888888777655443
No 45
>COG0626 MetC Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]
Probab=21.64 E-value=8.9e+02 Score=24.90 Aligned_cols=67 Identities=7% Similarity=-0.060 Sum_probs=41.8
Q ss_pred HHHHhhcCceEEEEeCeeecCCCCceeE-------EEEEecCCCCeEEEEEEEeeccccccHHHHHHHHHhccCC
Q 040097 185 AFVFKTRCRMLLTVDGWEIDSPYKSVML-------VAVCRDGNDAVLPIAFCEVVEENLDSWAFFLKNLNYGLRL 252 (516)
Q Consensus 185 ~~~~~~~~~~vi~~D~t~~~~~y~~~l~-------~~~g~d~~~~~~~la~a~~~~E~~~~~~w~l~~l~~~~~~ 252 (516)
+....+..+-++.+|.||.+.-+..||- ....+=-+||.-++|= ++-..+++-|..++......++.
T Consensus 171 i~~~A~~~g~~vvVDNTfatP~~q~PL~~GaDIVvhSaTKyl~GHsDvl~G-~v~~~~~~~~~~~~~~~~~~~G~ 244 (396)
T COG0626 171 IARLAKAYGALVVVDNTFATPVLQRPLELGADIVVHSATKYLGGHSDVLGG-VVLTPNEELYELLFFAQRANTGA 244 (396)
T ss_pred HHHHHHhcCCEEEEECCcccccccChhhcCCCEEEEeccccccCCcceeee-EEecChHHHHHHHHHHHHhhcCC
Confidence 3333333557899999999988877752 2333334677777766 55555666666665555544443
No 46
>PF11645 PDDEXK_5: PD-(D/E)XK endonuclease; InterPro: IPR021671 This family are putative endonuclease proteins which are restricted to Synechocystis. ; PDB: 2OST_D.
Probab=21.61 E-value=3.1e+02 Score=23.65 Aligned_cols=45 Identities=9% Similarity=0.096 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHcCceEEEEeeCCcEEEEEeecCCCccEEEEE
Q 040097 8 DVEFKTALEVNAIRDGFKLCIIHNTTTCVSCECSNLHCDWKITAV 52 (516)
Q Consensus 8 ~~e~~~ai~~ya~~~gf~~~~~rs~~~~~~~~C~~~gCp~rv~~~ 52 (516)
.++.-.++....++.|+.+.+.-.+...+-++=...||.|||..+
T Consensus 6 GDite~~ii~~ll~~GY~V~~P~gDn~~YDLV~d~eg~L~RIQvK 50 (149)
T PF11645_consen 6 GDITEAKIINRLLEKGYSVSIPFGDNLKYDLVFDKEGILWRIQVK 50 (149)
T ss_dssp HHHHHHHHHHHHHHTT-EEEEESSTTSS-SEEEEETTEEEEEEEE
T ss_pred chHHHHHHHHHHHHcCcEEEeecCCCCCcCEEEecCCcEEEEEEe
Confidence 355667788889999999999999987776665678999999886
No 47
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=20.74 E-value=1.2e+02 Score=24.38 Aligned_cols=28 Identities=14% Similarity=0.240 Sum_probs=20.7
Q ss_pred CCceeCCHHHHHHHHHHHHHHcCceEEEEeeC
Q 040097 1 MGQRFKNDVEFKTALEVNAIRDGFKLCIIHNT 32 (516)
Q Consensus 1 vG~~F~s~~e~~~ai~~ya~~~gf~~~~~rs~ 32 (516)
|.+.|+|+|+|- .||.++|..+.+..-.
T Consensus 51 v~l~F~skE~Ai----~yaer~G~~Y~V~~p~ 78 (101)
T PF04800_consen 51 VRLKFDSKEDAI----AYAERNGWDYEVEEPK 78 (101)
T ss_dssp CEEEESSHHHHH----HHHHHCT-EEEEE-ST
T ss_pred eEeeeCCHHHHH----HHHHHcCCeEEEeCCC
Confidence 346899999885 5899999999887543
No 48
>KOG3499 consensus 60S ribosomal protein L38 [Translation, ribosomal structure and biogenesis]
Probab=20.36 E-value=3e+02 Score=19.83 Aligned_cols=35 Identities=23% Similarity=0.211 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHcCceEEEEeeC-CcEEEEEeec
Q 040097 8 DVEFKTALEVNAIRDGFKLCIIHNT-TTCVSCECSN 42 (516)
Q Consensus 8 ~~e~~~ai~~ya~~~gf~~~~~rs~-~~~~~~~C~~ 42 (516)
..|.+.|+..--..--.++++++|. ...+.+.|++
T Consensus 5 i~eiK~FL~~arR~Da~s~kiKkn~~~~KFKvRcsr 40 (69)
T KOG3499|consen 5 ITEIKDFLLTARRKDAKSVKIKKNKNNVKFKVRCSR 40 (69)
T ss_pred HHHHHHHHHHHHhcccceeEEEecCCceeEEEEeee
Confidence 4567777776655566788888765 4678888874
No 49
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=20.02 E-value=73 Score=31.56 Aligned_cols=43 Identities=19% Similarity=0.217 Sum_probs=34.5
Q ss_pred CceeCCHHHHHHHHHHHHHHcCceEEEEeeCC-cEEEEEeecCCCc
Q 040097 2 GQRFKNDVEFKTALEVNAIRDGFKLCIIHNTT-TCVSCECSNLHCD 46 (516)
Q Consensus 2 G~~F~s~~e~~~ai~~ya~~~gf~~~~~rs~~-~~~~~~C~~~gCp 46 (516)
|+.|.|.+|+++-|..+|+-. +|...++.+ ++..+-|.+.+|.
T Consensus 143 e~~F~s~~ef~dHV~~H~l~c--eyd~~~~~~D~~pv~~C~W~~Ct 186 (467)
T KOG3608|consen 143 EREFVSIVEFQDHVVKHALFC--EYDIQKTPEDERPVTMCNWAMCT 186 (467)
T ss_pred CCcccCHHHHHHHHHHhhhhh--hhhhhhCCCCCCceeeccchhhh
Confidence 789999999999999999855 454555554 5688899888886
Done!