Query 036307
Match_columns 405
No_of_seqs 218 out of 1443
Neff 9.0
Searched_HMMs 46136
Date Fri Mar 29 11:21:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036307.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036307hhsearch_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 6.4E-59 1.4E-63 479.0 25.2 352 17-394 156-623 (846)
2 PF10551 MULE: MULE transposas 99.9 3.1E-24 6.8E-29 167.3 8.5 90 177-270 1-93 (93)
3 PF00872 Transposase_mut: Tran 99.9 9.5E-23 2.1E-27 198.4 3.1 224 74-349 113-350 (381)
4 COG3328 Transposase and inacti 99.6 7.4E-15 1.6E-19 140.5 15.7 221 74-349 99-329 (379)
5 smart00575 ZnF_PMZ plant mutat 98.7 3.6E-09 7.8E-14 62.0 1.5 27 353-379 2-28 (28)
6 PF03108 DBD_Tnp_Mut: MuDR fam 98.6 8.3E-08 1.8E-12 69.4 5.5 38 2-39 30-67 (67)
7 PF08731 AFT: Transcription fa 97.9 5.2E-05 1.1E-09 58.9 6.7 31 20-50 81-111 (111)
8 PF03101 FAR1: FAR1 DNA-bindin 97.3 0.00062 1.4E-08 52.2 6.1 30 20-50 60-89 (91)
9 PF04434 SWIM: SWIM zinc finge 97.2 0.00015 3.3E-09 46.3 1.6 27 350-376 13-39 (40)
10 PF13610 DDE_Tnp_IS240: DDE do 96.3 0.0021 4.6E-08 53.6 1.7 80 171-256 2-81 (140)
11 PF06782 UPF0236: Uncharacteri 96.2 0.11 2.4E-06 52.3 14.0 93 210-303 235-328 (470)
12 PF03106 WRKY: WRKY DNA -bindi 96.2 0.014 2.9E-07 40.9 5.1 42 8-49 18-59 (60)
13 PF01610 DDE_Tnp_ISL3: Transpo 96.1 0.01 2.2E-07 54.6 5.8 94 173-274 1-97 (249)
14 PF03050 DDE_Tnp_IS66: Transpo 94.3 0.2 4.4E-06 46.7 8.2 148 57-275 4-156 (271)
15 smart00774 WRKY DNA binding do 94.3 0.075 1.6E-06 36.8 3.9 41 8-48 18-59 (59)
16 PF04500 FLYWCH: FLYWCH zinc f 92.8 0.2 4.4E-06 34.8 4.3 42 3-48 18-62 (62)
17 PF13565 HTH_32: Homeodomain-l 90.7 0.78 1.7E-05 33.5 5.6 42 60-101 33-76 (77)
18 PHA02517 putative transposase 90.2 4.4 9.6E-05 37.7 11.6 151 61-246 30-182 (277)
19 COG3316 Transposase and inacti 89.7 0.63 1.4E-05 41.3 5.0 82 170-259 70-152 (215)
20 PF00665 rve: Integrase core d 88.0 2 4.3E-05 34.0 6.6 76 169-247 5-81 (120)
21 PF04937 DUF659: Protein of un 82.8 7.1 0.00015 33.0 7.7 99 172-274 35-137 (153)
22 PRK14702 insertion element IS2 79.1 48 0.001 30.6 12.6 149 59-246 10-165 (262)
23 PRK09409 IS2 transposase TnpB; 75.8 62 0.0013 30.6 12.6 147 61-246 51-204 (301)
24 PF12762 DDE_Tnp_IS1595: ISXO2 68.6 18 0.00039 30.1 6.4 69 171-246 4-87 (151)
25 PF01498 HTH_Tnp_Tc3_2: Transp 66.2 6.4 0.00014 28.3 2.8 39 65-104 3-41 (72)
26 PF08766 DEK_C: DEK C terminal 62.7 26 0.00056 23.7 5.1 39 60-98 3-43 (54)
27 PF13592 HTH_33: Winged helix- 62.1 13 0.00028 25.7 3.6 31 74-104 3-33 (60)
28 PRK13907 rnhA ribonuclease H; 60.0 76 0.0016 25.4 8.5 78 172-253 3-81 (128)
29 PRK00766 hypothetical protein; 56.5 1.3E+02 0.0029 26.4 9.7 97 170-269 9-135 (194)
30 PF13276 HTH_21: HTH-like doma 52.3 42 0.00091 23.0 4.9 43 62-104 6-49 (60)
31 KOG4027 Uncharacterized conser 45.7 32 0.00069 28.9 3.8 36 175-210 70-108 (187)
32 PF13082 DUF3931: Protein of u 43.0 63 0.0014 21.5 4.1 25 187-211 38-62 (66)
33 PF13551 HTH_29: Winged helix- 40.9 69 0.0015 24.6 5.2 40 64-103 64-109 (112)
34 PF10045 DUF2280: Uncharacteri 40.4 1.4E+02 0.003 23.3 6.3 24 76-99 20-43 (104)
35 PF14420 Clr5: Clr5 domain 40.1 91 0.002 21.0 4.9 26 73-98 18-43 (54)
36 cd00131 PAX Paired Box domain 37.8 89 0.0019 25.4 5.4 39 64-103 82-125 (128)
37 PRK06704 RNA polymerase factor 33.7 37 0.00081 30.7 2.8 24 181-204 203-226 (228)
38 COG4279 Uncharacterized conser 31.6 34 0.00074 31.1 2.1 42 332-376 98-146 (266)
39 COG3915 Uncharacterized protei 30.3 70 0.0015 26.2 3.4 37 162-199 97-135 (155)
40 PF01316 Arg_repressor: Argini 29.0 1.6E+02 0.0034 21.2 4.8 39 64-103 8-46 (70)
41 smart00816 Amb_V_allergen Amb 26.0 41 0.00088 21.2 1.1 17 15-31 18-36 (45)
42 TIGR01529 argR_whole arginine 25.5 1.5E+02 0.0033 24.6 4.9 35 65-100 6-40 (146)
43 smart00351 PAX Paired Box doma 25.2 1.7E+02 0.0037 23.5 5.1 38 63-101 81-123 (125)
44 PF08459 UvrC_HhH_N: UvrC Heli 25.0 2.1E+02 0.0045 24.2 5.6 46 211-256 53-102 (155)
45 PF03705 CheR_N: CheR methyltr 24.6 2.2E+02 0.0047 18.9 5.0 46 79-127 6-51 (57)
46 TIGR03147 cyt_nit_nrfF cytochr 23.8 79 0.0017 25.7 2.7 37 60-96 56-94 (126)
47 PF09713 A_thal_3526: Plant pr 23.0 78 0.0017 21.5 2.1 25 75-99 12-37 (54)
48 PF12385 Peptidase_C70: Papain 22.8 2E+02 0.0042 24.5 4.9 63 158-226 98-160 (166)
49 PF03913 Amb_V_allergen: Amb V 22.3 74 0.0016 19.9 1.7 14 16-29 18-33 (44)
50 PF11447 DUF3201: Protein of u 21.8 4.6E+02 0.0099 21.6 7.1 59 120-204 10-73 (150)
51 PRK10144 formate-dependent nit 21.5 92 0.002 25.3 2.7 37 60-96 56-94 (126)
52 PF13358 DDE_3: DDE superfamil 20.8 1.8E+02 0.0039 23.1 4.6 53 187-243 38-90 (146)
53 PF08069 Ribosomal_S13_N: Ribo 20.0 1.3E+02 0.0029 20.9 2.9 28 64-91 31-60 (60)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=6.4e-59 Score=479.00 Aligned_cols=352 Identities=14% Similarity=0.209 Sum_probs=282.4
Q ss_pred eecCCCceEEEEEEeCCCCEEEEEeeCCCceeccccccc-cchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhCCCCCH
Q 036307 17 CSNLHCDWKITAVKENRSNVFVICDITPMHTCNQRSVKL-QGETKWIAAKFLHIWKQSEHREVDKLRNEIATTYGIKCPI 95 (405)
Q Consensus 17 C~~~~Cpwrv~~~~~~~~~~~~I~~~~~~H~c~~~~~~~-~~ss~~ia~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~s~ 95 (405)
|+.+|||+++++.+..+ ++|.|+.++.+|||++..... ....+.+-..+...+....++.. ++.+. .
T Consensus 156 ~tRtGC~A~m~Vk~~~~-gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~~~~~~~~~v~~------~~~d~-----~ 223 (846)
T PLN03097 156 CAKTDCKASMHVKRRPD-GKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMARQFAEYKNVVG------LKNDS-----K 223 (846)
T ss_pred ccCCCCceEEEEEEcCC-CeEEEEEEecCCCCCCCCccccchhhhhhHHHHHhhhhccccccc------cchhh-----c
Confidence 56679999999987544 689999999999999933221 11111110110000000000000 00000 0
Q ss_pred HHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhhCCCcEEEEEecccccccccccceEEEechhhHHHHHhcCceEEEE
Q 036307 96 WKLEAVDKMARFWLRTDHADGYAQLLQYKQEMENVNSRNIVIIETKSQQQFTADIFDRMFVFLYDTAYAFKTRCRMLVIV 175 (405)
Q Consensus 96 ~~~~~ak~~~~~~~~g~~~~~~~~l~~~~~~l~~~npg~~~~~~~~~~~~~~~~~f~~~f~~~~~~~~~~~~~~~~vi~~ 175 (405)
...-+.|.+. +. ....+.|.+|+++++..||+++|.+++|++ ++++++||+++.++.+|.+ |++||.+
T Consensus 224 ~~~~~~r~~~---~~---~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~-----~~l~niFWaD~~sr~~Y~~-FGDvV~f 291 (846)
T PLN03097 224 SSFDKGRNLG---LE---AGDTKILLDFFTQMQNMNSNFFYAVDLGED-----QRLKNLFWVDAKSRHDYGN-FSDVVSF 291 (846)
T ss_pred chhhHHHhhh---cc---cchHHHHHHHHHHHHhhCCCceEEEEEccC-----CCeeeEEeccHHHHHHHHh-cCCEEEE
Confidence 0011112211 11 123578999999999999999999999999 9999999999999999999 9999999
Q ss_pred eceEEcCCCCceeEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHHHHHhhccc
Q 036307 176 DGWEIDSPYKSVMLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVEEFLPS 255 (405)
Q Consensus 176 D~t~~~~~~~~~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~ 255 (405)
|+||++|+|++||..++|+|+|++++++|+||+.+|+.++|.|+|++|+++| ++..|.+||||++.+|.+||++|||+
T Consensus 292 DTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM--~gk~P~tIiTDqd~am~~AI~~VfP~ 369 (846)
T PLN03097 292 DTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAM--GGQAPKVIITDQDKAMKSVISEVFPN 369 (846)
T ss_pred eceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHh--CCCCCceEEecCCHHHHHHHHHHCCC
Confidence 9999999999999999999999999999999999999999999999999999 89999999999999999999999999
Q ss_pred chhhhcHHHHHHhhhhhCCC-----Cccccchhhhhc-ccchhhHHHHHHHHH-hhCHHHHHHHhcc--Cccccccccc-
Q 036307 256 AVYRQCCFSLYTKMVHEFPG-----VTVHSPFWGACR-STNGNSFKNQMAVIE-TISMECYNWLKDT--DCQKWALYSM- 325 (405)
Q Consensus 256 a~~~~C~~Hi~~n~~~~~~~-----~~~~~~~~~~~~-~~~~~~f~~~~~~l~-~~~~~~~~~l~~~--~~~~W~~~~~- 325 (405)
+.|++|.|||++|+.+++.. +.+...|..+.+ +.++++|+..|..|. .++....+||+.+ .+++|+++|+
T Consensus 370 t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k 449 (846)
T PLN03097 370 AHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMR 449 (846)
T ss_pred ceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhc
Confidence 99999999999999998763 478888888766 579999999999886 5788999999998 8999999998
Q ss_pred ----------------cccccc---------------------------------------------------ccccccH
Q 036307 326 ----------------PEWVKS---------------------------------------------------TEITISA 338 (405)
Q Consensus 326 ----------------n~~~~~---------------------------------------------------~~~tp~~ 338 (405)
|+++.. ..|||.+
T Consensus 450 ~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~i 529 (846)
T PLN03097 450 DAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAV 529 (846)
T ss_pred ccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHH
Confidence 111110 6799999
Q ss_pred HHHHHHHHHhccc------------------------------------cccccchhhhcCCCchhhhHHhhhcCC--Cc
Q 036307 339 TEQLRIWLLKQLD------------------------------------LNVEQRLWQVSGIPCPHACRCIDTWGD--KL 380 (405)
Q Consensus 339 ~~~l~~~~~~~~~------------------------------------~~vsC~~~~~~giPC~Hala~~~~~~~--~~ 380 (405)
+++||+|+..+.. +.|+|++|+..||||+|||.||...++ .|
T Consensus 530 F~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP 609 (846)
T PLN03097 530 FKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIP 609 (846)
T ss_pred HHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCc
Confidence 9999999986521 123999999999999999999999997 89
Q ss_pred cccccCCccHHHHH
Q 036307 381 DTYVHRPMTVDEYR 394 (405)
Q Consensus 381 ~~~v~~~yt~~~~~ 394 (405)
+.||.++||+++-.
T Consensus 610 ~~YILkRWTKdAK~ 623 (846)
T PLN03097 610 SQYILKRWTKDAKS 623 (846)
T ss_pred hhhhhhhchhhhhh
Confidence 99999999999854
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=99.91 E-value=3.1e-24 Score=167.33 Aligned_cols=90 Identities=29% Similarity=0.471 Sum_probs=86.0
Q ss_pred ceEEcCCCCceeEE---EEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHHHHHhhc
Q 036307 177 GWEIDSPYKSVMLV---AVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVEEFL 253 (405)
Q Consensus 177 ~t~~~~~~~~~ll~---~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vf 253 (405)
|||++|+| |+++. ++|+|++|+.+|+||+++++|+.++|+|||+.+++.+ +.. |.+||||++.|+.+||+++|
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~--~~~-p~~ii~D~~~~~~~Ai~~vf 76 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAM--PQK-PKVIISDFDKALINAIKEVF 76 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhcc--ccC-ceeeeccccHHHHHHHHHHC
Confidence 79999999 98885 9999999999999999999999999999999999998 555 99999999999999999999
Q ss_pred ccchhhhcHHHHHHhhh
Q 036307 254 PSAVYRQCCFSLYTKMV 270 (405)
Q Consensus 254 P~a~~~~C~~Hi~~n~~ 270 (405)
|++.|++|.||+.+|++
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=9.5e-23 Score=198.37 Aligned_cols=224 Identities=15% Similarity=0.228 Sum_probs=175.9
Q ss_pred CCCCHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhhCCCcEEEEEecccccccccccc
Q 036307 74 EHREVDKLRNEIATTYG-IKCPIWKLEAVDKMARFWLRTDHADGYAQLLQYKQEMENVNSRNIVIIETKSQQQFTADIFD 152 (405)
Q Consensus 74 ~~~~~~~i~~~l~~~~g-~~~s~~~~~~ak~~~~~~~~g~~~~~~~~l~~~~~~l~~~npg~~~~~~~~~~~~~~~~~f~ 152 (405)
.+++.++|.+.++.-+| ..+|.+++.|..+.+.+.+ ..|...
T Consensus 113 ~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~-----------~~w~~R-------------------------- 155 (381)
T PF00872_consen 113 KGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEV-----------EAWRNR-------------------------- 155 (381)
T ss_pred cccccccccchhhhhhcccccCchhhhhhhhhhhhhH-----------HHHhhh--------------------------
Confidence 58899999999999999 7899999988776654322 111111
Q ss_pred eEEEechhhHHHHHhcC-ceEEEEeceEEcCCCCc-----eeEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhc
Q 036307 153 RMFVFLYDTAYAFKTRC-RMLVIVDGWEIDSPYKS-----VMLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYG 226 (405)
Q Consensus 153 ~~f~~~~~~~~~~~~~~-~~vi~~D~t~~~~~~~~-----~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~ 226 (405)
... +. .++|++||+|.+.+.++ .+++++|+|.+|+..+||+.+.+.|+.++|.-||+.|+++
T Consensus 156 -----------~L~-~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R 223 (381)
T PF00872_consen 156 -----------PLE-SEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER 223 (381)
T ss_pred -----------ccc-cccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc
Confidence 001 14 68999999999887554 5899999999999999999999999999999999999999
Q ss_pred ccccCCCCeEEEcCCcccHHHHHHhhcccchhhhcHHHHHHhhhhhCCCC---ccccchhhhhcccchhhHHHHHHHHHh
Q 036307 227 LRLERGEGLCIMGDGDNGIDEAVEEFLPSAVYRQCCFSLYTKMVHEFPGV---TVHSPFWGACRSTNGNSFKNQMAVIET 303 (405)
Q Consensus 227 ~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~~~~---~~~~~~~~~~~~~~~~~f~~~~~~l~~ 303 (405)
+ ...+..||+|+++||.+||+++||++.+|+|.+|+++|+.++++.+ .+.+.++.+..+.+.+++...++++.+
T Consensus 224 G---l~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~ 300 (381)
T PF00872_consen 224 G---LKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALEEFAE 300 (381)
T ss_pred c---ccccceeeccccccccccccccccchhhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhhhccc
Confidence 4 6678999999999999999999999999999999999999999755 666777778788888887777777654
Q ss_pred ----hCHHHHHHHhccCcccccccccccccccccccccHHHHHHHHHHhc
Q 036307 304 ----ISMECYNWLKDTDCQKWALYSMPEWVKSTEITISATEQLRIWLLKQ 349 (405)
Q Consensus 304 ----~~~~~~~~l~~~~~~~W~~~~~n~~~~~~~~tp~~~~~l~~~~~~~ 349 (405)
..|.+.+++++...+.|+..-|..-+....+|.|..+.++.++++.
T Consensus 301 ~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr 350 (381)
T PF00872_consen 301 KWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRR 350 (381)
T ss_pred ccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhh
Confidence 5788888887644344433222111111457889999999999873
No 4
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.63 E-value=7.4e-15 Score=140.47 Aligned_cols=221 Identities=14% Similarity=0.165 Sum_probs=162.0
Q ss_pred CCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhhCCCcEEEEEecccccccccccce
Q 036307 74 EHREVDKLRNEIATTYGIKCPIWKLEAVDKMARFWLRTDHADGYAQLLQYKQEMENVNSRNIVIIETKSQQQFTADIFDR 153 (405)
Q Consensus 74 ~~~~~~~i~~~l~~~~g~~~s~~~~~~ak~~~~~~~~g~~~~~~~~l~~~~~~l~~~npg~~~~~~~~~~~~~~~~~f~~ 153 (405)
.+++++++...++..++..++...+.+.-...++.+ .+++..-
T Consensus 99 ~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e~v---------------~~~~~r~---------------------- 141 (379)
T COG3328 99 KGVTTREIEALLEELYGHKVSPSVISVVTDRLDEKV---------------KAWQNRP---------------------- 141 (379)
T ss_pred cCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHHHH---------------HHHHhcc----------------------
Confidence 578999999999999888888887776665554332 2222211
Q ss_pred EEEechhhHHHHHhcCceEEEEeceEEcCC--CCceeEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhcccccC
Q 036307 154 MFVFLYDTAYAFKTRCRMLVIVDGWEIDSP--YKSVMLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYGLRLER 231 (405)
Q Consensus 154 ~f~~~~~~~~~~~~~~~~vi~~D~t~~~~~--~~~~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~~~~ 231 (405)
. +..+++++||+|++.+ -+..+++|+|++.+|+..++|+.+.+.|+ ..|.-||..|+..+ .
T Consensus 142 -----------l--~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rg---l 204 (379)
T COG3328 142 -----------L--GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRG---L 204 (379)
T ss_pred -----------c--cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhcc---c
Confidence 0 1578999999999988 34479999999999999999999999999 99999999999984 5
Q ss_pred CCCeEEEcCCcccHHHHHHhhcccchhhhcHHHHHHhhhhhCCCCc---cccchhhhhcccchhhHHHHHHHH----Hhh
Q 036307 232 GEGLCIMGDGDNGIDEAVEEFLPSAVYRQCCFSLYTKMVHEFPGVT---VHSPFWGACRSTNGNSFKNQMAVI----ETI 304 (405)
Q Consensus 232 ~~~~~iisD~~~~l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~~~~~---~~~~~~~~~~~~~~~~f~~~~~~l----~~~ 304 (405)
.....+++|+++||.+||.++||.+.+|+|..|+.+|+..+...++ ....+..+..+.+.++....+..+ ...
T Consensus 205 ~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~ 284 (379)
T COG3328 205 SDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKR 284 (379)
T ss_pred cceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhh
Confidence 5567788899999999999999999999999999999999988663 334444455555555555554443 334
Q ss_pred CHHHHHHHhccCccccccccc-ccccccccccccHHHHHHHHHHhc
Q 036307 305 SMECYNWLKDTDCQKWALYSM-PEWVKSTEITISATEQLRIWLLKQ 349 (405)
Q Consensus 305 ~~~~~~~l~~~~~~~W~~~~~-n~~~~~~~~tp~~~~~l~~~~~~~ 349 (405)
.|....++.+.--+.|....| ..| ....++.++.+.+++++.+.
T Consensus 285 yP~i~~~~~~~~~~~~~F~~fp~~~-r~~i~ttN~IE~~n~~ir~~ 329 (379)
T COG3328 285 YPAILKSWRNALEELLPFFAFPSEI-RKIIYTTNAIESLNKLIRRR 329 (379)
T ss_pred cchHHHHHHHHHHHhcccccCcHHH-HhHhhcchHHHHHHHHHHHH
Confidence 566666666543333322211 111 01357888999999987753
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.74 E-value=3.6e-09 Score=61.97 Aligned_cols=27 Identities=37% Similarity=0.529 Sum_probs=24.2
Q ss_pred ccccchhhhcCCCchhhhHHhhhcCCC
Q 036307 353 NVEQRLWQVSGIPCPHACRCIDTWGDK 379 (405)
Q Consensus 353 ~vsC~~~~~~giPC~Hala~~~~~~~~ 379 (405)
.+||++||..||||+|+|+|+...+++
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~~ 28 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGLS 28 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCCC
Confidence 468999999999999999999988763
No 6
>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=98.60 E-value=8.3e-08 Score=69.44 Aligned_cols=38 Identities=26% Similarity=0.612 Sum_probs=35.9
Q ss_pred eEEEEcCCCeEEEEEeecCCCceEEEEEEeCCCCEEEE
Q 036307 2 MFSLERPWSTCVSCECSNLHCDWKITAVKENRSNVFVI 39 (405)
Q Consensus 2 ~~~~~rs~~~r~~~~C~~~~Cpwrv~~~~~~~~~~~~I 39 (405)
.|++.+|+++|++++|...+|||+|+|++.++++.|+|
T Consensus 30 ~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 30 EFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred EEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 48899999999999999999999999999999999986
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=97.86 E-value=5.2e-05 Score=58.94 Aligned_cols=31 Identities=13% Similarity=0.284 Sum_probs=28.8
Q ss_pred CCCceEEEEEEeCCCCEEEEEeeCCCceecc
Q 036307 20 LHCDWKITAVKENRSNVFVICDITPMHTCNQ 50 (405)
Q Consensus 20 ~~Cpwrv~~~~~~~~~~~~I~~~~~~H~c~~ 50 (405)
..|||+|+|+.....+.|.|..+++.|+|++
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 4799999999999999999999999999974
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=97.31 E-value=0.00062 Score=52.21 Aligned_cols=30 Identities=10% Similarity=0.207 Sum_probs=27.9
Q ss_pred CCCceEEEEEEeCCCCEEEEEeeCCCceecc
Q 036307 20 LHCDWKITAVKENRSNVFVICDITPMHTCNQ 50 (405)
Q Consensus 20 ~~Cpwrv~~~~~~~~~~~~I~~~~~~H~c~~ 50 (405)
+||||+|.+.+.+ ++.|.|..+..+|||++
T Consensus 60 tgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L 89 (91)
T PF03101_consen 60 TGCKARINVKRRK-DGKWRVTSFVLEHNHPL 89 (91)
T ss_pred cCCCEEEEEEEcc-CCEEEEEECcCCcCCCC
Confidence 6999999999987 67999999999999986
No 9
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.24 E-value=0.00015 Score=46.35 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=23.5
Q ss_pred cccccccchhhhcCCCchhhhHHhhhc
Q 036307 350 LDLNVEQRLWQVSGIPCPHACRCIDTW 376 (405)
Q Consensus 350 ~~~~vsC~~~~~~giPC~Hala~~~~~ 376 (405)
....|+|..|+..|.||.|++|++...
T Consensus 13 ~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 13 EQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred cccEeeCCCccccCCcchhHHHHHHhh
Confidence 346679999999999999999998764
No 10
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=96.26 E-value=0.0021 Score=53.65 Aligned_cols=80 Identities=21% Similarity=0.096 Sum_probs=68.7
Q ss_pred eEEEEeceEEcCCCCceeEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHHHHH
Q 036307 171 MLVIVDGWEIDSPYKSVMLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVE 250 (405)
Q Consensus 171 ~vi~~D~t~~~~~~~~~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~ 250 (405)
+.+.+|-||.+.+-+ ..+..-.+|.+|+ +|++-|-..-+...=..||..+.+.. ...|..|+||+..+...|++
T Consensus 2 ~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~---~~~p~~ivtDk~~aY~~A~~ 75 (140)
T PF13610_consen 2 DSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRH---RGEPRVIVTDKLPAYPAAIK 75 (140)
T ss_pred CEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceee---ccccceeecccCCccchhhh
Confidence 578999999876543 4566788999999 89999999999999999998888875 36789999999999999999
Q ss_pred hhcccc
Q 036307 251 EFLPSA 256 (405)
Q Consensus 251 ~vfP~a 256 (405)
++.|..
T Consensus 76 ~l~~~~ 81 (140)
T PF13610_consen 76 ELNPEG 81 (140)
T ss_pred hccccc
Confidence 999874
No 11
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=96.20 E-value=0.11 Score=52.34 Aligned_cols=93 Identities=22% Similarity=0.332 Sum_probs=73.4
Q ss_pred ccccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHHHHHhhcccchhhhcHHHHHHhhhhhCCC-Cccccchhhhhcc
Q 036307 210 EENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVEEFLPSAVYRQCCFSLYTKMVHEFPG-VTVHSPFWGACRS 288 (405)
Q Consensus 210 ~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~~~-~~~~~~~~~~~~~ 288 (405)
..+.+-|.-+...+.+..++....-+++.+|+...+.+++. .+|++.|.+..+|+.+.+.+.+.. +++.+.++++...
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 55677899999988888754444467889999999988776 999999999999999999988863 4566666777776
Q ss_pred cchhhHHHHHHHHHh
Q 036307 289 TNGNSFKNQMAVIET 303 (405)
Q Consensus 289 ~~~~~f~~~~~~l~~ 303 (405)
....++...++.+.+
T Consensus 314 ~d~~~l~~~L~~~~~ 328 (470)
T PF06782_consen 314 GDKKKLETVLDTAES 328 (470)
T ss_pred cCHHHHHHHHHHHHH
Confidence 677777777777664
No 12
>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=96.18 E-value=0.014 Score=40.86 Aligned_cols=42 Identities=14% Similarity=0.112 Sum_probs=33.8
Q ss_pred CCCeEEEEEeecCCCceEEEEEEeCCCCEEEEEeeCCCceec
Q 036307 8 PWSTCVSCECSNLHCDWKITAVKENRSNVFVICDITPMHTCN 49 (405)
Q Consensus 8 s~~~r~~~~C~~~~Cpwrv~~~~~~~~~~~~I~~~~~~H~c~ 49 (405)
|.-.|-..+|+..+||++-.+.+..++....++++.++|||+
T Consensus 18 ~~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 18 SPYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp TTCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 445777899999999999999998866678888999999996
No 13
>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=96.15 E-value=0.01 Score=54.63 Aligned_cols=94 Identities=16% Similarity=0.169 Sum_probs=70.2
Q ss_pred EEEeceEEcCCCCceeEEEEEEcC--CCCeEEEEEEEeeccccccHHHHHHHH-hhcccccCCCCeEEEcCCcccHHHHH
Q 036307 173 VIVDGWEIDSPYKSVMLVAVCRDG--NDSVLPIAFCEVVEENLDSWAFFLKNL-NYGLRLERGEGLCIMGDGDNGIDEAV 249 (405)
Q Consensus 173 i~~D~t~~~~~~~~~ll~~~g~d~--~~~~~~~a~a~~~~E~~~~~~wfl~~l-~~~~~~~~~~~~~iisD~~~~l~~Ai 249 (405)
|+||-+.....++. ++-+.+|. +++.. ++++++-+.++..-||..+ ... ......+|++|...+..+||
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---LDILPGRDKETLKDFFRSLYPEE---ERKNVKVVSMDMSPPYRSAI 72 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCceE---EEEcCCccHHHHHHHHHHhCccc---cccceEEEEcCCCccccccc
Confidence 46777776543332 44455555 44332 3578888899988888877 333 24457899999999999999
Q ss_pred HhhcccchhhhcHHHHHHhhhhhCC
Q 036307 250 EEFLPSAVYRQCCFSLYTKMVHEFP 274 (405)
Q Consensus 250 ~~vfP~a~~~~C~~Hi~~n~~~~~~ 274 (405)
++.||+|.+..--+|+++++.+.+.
T Consensus 73 ~~~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 73 REYFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred cccccccccccccchhhhhhhhcch
Confidence 9999999999999999999887543
No 14
>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=94.30 E-value=0.2 Score=46.66 Aligned_cols=148 Identities=13% Similarity=0.061 Sum_probs=89.8
Q ss_pred chHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhhCCCcEE
Q 036307 57 GETKWIAAKFLHIWKQSEHREVDKLRNEIATTYGIKCPIWKLEAVDKMARFWLRTDHADGYAQLLQYKQEMENVNSRNIV 136 (405)
Q Consensus 57 ~ss~~ia~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~s~~~~~~ak~~~~~~~~g~~~~~~~~l~~~~~~l~~~npg~~~ 136 (405)
.+.++++-.+... -...++...+.+.+... |+++|.+++.+.-.++.+... ...+.+.+.
T Consensus 4 ~g~~~~a~i~~l~--~~~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l~-----------~~~~~l~~~------ 63 (271)
T PF03050_consen 4 YGPSLLALIAYLK--YVYHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEALK-----------PLYEALKEE------ 63 (271)
T ss_pred CCHHHHHHHHHHH--hcCCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhhh-----------hhhhhhhhh------
Confidence 3444544443322 23456667777777766 999999999887666543321 111111110
Q ss_pred EEEecccccccccccceEEEechhhHHHHHhcCceEEEEeceEEc----CCCCc-eeEEEEEEcCCCCeEEEEEEEeecc
Q 036307 137 IIETKSQQQFTADIFDRMFVFLYDTAYAFKTRCRMLVIVDGWEID----SPYKS-VMLVAVCRDGNDSVLPIAFCEVVEE 211 (405)
Q Consensus 137 ~~~~~~~~~~~~~~f~~~f~~~~~~~~~~~~~~~~vi~~D~t~~~----~~~~~-~ll~~~g~d~~~~~~~~a~a~~~~E 211 (405)
. . -.+|+.+|-|..+ ++.+. -+-++++-+ .+.|.+.++-
T Consensus 64 ----------------------------~-~-~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR 107 (271)
T PF03050_consen 64 ----------------------------L-R-SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSR 107 (271)
T ss_pred ----------------------------c-c-ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccc
Confidence 1 1 3578899998877 44332 234443333 5556666666
Q ss_pred ccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHHHHHhhcccchhhhcHHHHHHhhhhhCCC
Q 036307 212 NLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVEEFLPSAVYRQCCFSLYTKMVHEFPG 275 (405)
Q Consensus 212 ~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~~~~C~~Hi~~n~~~~~~~ 275 (405)
+.+.-.-+|. + ..-+++||+-.+-.. +....|+.|..|+.|.+.+....
T Consensus 108 ~~~~~~~~L~---------~-~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 108 SSKVIKEFLG---------D-FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred cccchhhhhc---------c-cceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 6655444432 2 234899999988654 22789999999999998876654
No 15
>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=94.27 E-value=0.075 Score=36.83 Aligned_cols=41 Identities=15% Similarity=0.084 Sum_probs=32.6
Q ss_pred CCCeEEEEEeec-CCCceEEEEEEeCCCCEEEEEeeCCCcee
Q 036307 8 PWSTCVSCECSN-LHCDWKITAVKENRSNVFVICDITPMHTC 48 (405)
Q Consensus 8 s~~~r~~~~C~~-~~Cpwrv~~~~~~~~~~~~I~~~~~~H~c 48 (405)
|...|-..+|+. .+||++=.+.+..+++...++.+.++|||
T Consensus 18 s~~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 18 SPFPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CcCcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 444566789998 89999988887765556677899999998
No 16
>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=92.84 E-value=0.2 Score=34.80 Aligned_cols=42 Identities=10% Similarity=0.168 Sum_probs=21.8
Q ss_pred EEEEcCCCeEEEEEeecC---CCceEEEEEEeCCCCEEEEEeeCCCcee
Q 036307 3 FSLERPWSTCVSCECSNL---HCDWKITAVKENRSNVFVICDITPMHTC 48 (405)
Q Consensus 3 ~~~~rs~~~r~~~~C~~~---~Cpwrv~~~~~~~~~~~~I~~~~~~H~c 48 (405)
|.+.+.......++|... +|+++|... .+++ .|.....+|||
T Consensus 18 y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~~~--~~~~~~~~HnH 62 (62)
T PF04500_consen 18 YYFNKRNDGKTYWRCSRRRSHGCRARLITD--AGDG--RVVRTNGEHNH 62 (62)
T ss_dssp EEEEEE-SS-EEEEEGGGTTS----EEEEE----TT--EEEE-S---SS
T ss_pred EECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CCCC--EEEECCCccCC
Confidence 555565688889999983 899999998 2333 45566688987
No 17
>PF13565 HTH_32: Homeodomain-like domain
Probab=90.72 E-value=0.78 Score=33.51 Aligned_cols=42 Identities=5% Similarity=0.119 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHHhCCCC--CHHHHHHH
Q 036307 60 KWIAAKFLHIWKQSEHREVDKLRNEIATTYGIKC--PIWKLEAV 101 (405)
Q Consensus 60 ~~ia~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~--s~~~~~~a 101 (405)
..+.+.+.+.+..+|.+++.+|.+.|.+++|+.+ |.+++||.
T Consensus 33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 3444677777788899999999999999999876 99999874
No 18
>PHA02517 putative transposase OrfB; Reviewed
Probab=90.22 E-value=4.4 Score=37.69 Aligned_cols=151 Identities=15% Similarity=0.109 Sum_probs=83.0
Q ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhh-hhCCCcEEEE
Q 036307 61 WIAAKFLHIWKQ-SEHREVDKLRNEIATTYGIKCPIWKLEAVDKMARFWLRTDHADGYAQLLQYKQEME-NVNSRNIVII 138 (405)
Q Consensus 61 ~ia~~~~~~i~~-~~~~~~~~i~~~l~~~~g~~~s~~~~~~ak~~~~~~~~g~~~~~~~~l~~~~~~l~-~~npg~~~~~ 138 (405)
.+.+.+.+.+.. .+....+.|...|++. |+.+|.++++|..+.. |-... ..... ....+...
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~-----gl~~~--------~~~k~~~~~~~~~~-- 93 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKEL-----GLAGV--------LRGKKVRTTISRKA-- 93 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHc-----CCceE--------ecCCCcCCCCCCCC--
Confidence 455666666655 4788999999999765 9999999998775532 11000 00000 00000000
Q ss_pred EecccccccccccceEEEechhhHHHHHhcCceEEEEeceEEcCCCCceeEEEEEEcCCCCeEEEEEEEeeccccccHHH
Q 036307 139 ETKSQQQFTADIFDRMFVFLYDTAYAFKTRCRMLVIVDGWEIDSPYKSVMLVAVCRDGNDSVLPIAFCEVVEENLDSWAF 218 (405)
Q Consensus 139 ~~~~~~~~~~~~f~~~f~~~~~~~~~~~~~~~~vi~~D~t~~~~~~~~~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~w 218 (405)
.. .++...+-|-+. .-..++..|.||..... |..++.+.+|...+ +++|+.+...++.+...-
T Consensus 94 ~~------~~n~~~r~f~~~---------~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~ 156 (277)
T PHA02517 94 VA------APDRVNRQFVAT---------RPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLD 156 (277)
T ss_pred CC------CCCcccCCCCCC---------CCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHH
Confidence 00 001111111111 14568999999986543 55666666776544 467788877777775444
Q ss_pred HHHHHhhcccccCCCCeEEEcCCcccHH
Q 036307 219 FLKNLNYGLRLERGEGLCIMGDGDNGID 246 (405)
Q Consensus 219 fl~~l~~~~~~~~~~~~~iisD~~~~l~ 246 (405)
+|+...... +...+.+|.||+.....
T Consensus 157 ~l~~a~~~~--~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 157 ALEQALWAR--GRPGGLIHHSDKGSQYV 182 (277)
T ss_pred HHHHHHHhc--CCCcCcEeecccccccc
Confidence 444333332 22223577799987654
No 19
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.69 E-value=0.63 Score=41.25 Aligned_cols=82 Identities=20% Similarity=0.055 Sum_probs=61.6
Q ss_pred ceEEEEeceEEcCCCCce-eEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHHH
Q 036307 170 RMLVIVDGWEIDSPYKSV-MLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEA 248 (405)
Q Consensus 170 ~~vi~~D~t~~~~~~~~~-ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~A 248 (405)
++++.+|-||.+.+-+.. |+- .+|.+| .++.+-|...-|...=.-||..+.+.- +.|.+|+||+.+....|
T Consensus 70 ~~~w~vDEt~ikv~gkw~ylyr--Aid~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~----g~p~v~vtDka~s~~~A 141 (215)
T COG3316 70 GDSWRVDETYIKVNGKWHYLYR--AIDADG--LTLDVWLSKRRNALAAKAFLKKLLKKH----GEPRVFVTDKAPSYTAA 141 (215)
T ss_pred ccceeeeeeEEeeccEeeehhh--hhccCC--CeEEEEEEcccCcHHHHHHHHHHHHhc----CCCceEEecCccchHHH
Confidence 467889999987655443 333 445553 467777777777777778888877763 57889999999999999
Q ss_pred HHhhcccchhh
Q 036307 249 VEEFLPSAVYR 259 (405)
Q Consensus 249 i~~vfP~a~~~ 259 (405)
+.++-+.++|+
T Consensus 142 ~~~l~~~~ehr 152 (215)
T COG3316 142 LRKLGSEVEHR 152 (215)
T ss_pred HHhcCcchhee
Confidence 99998866554
No 20
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=87.97 E-value=2 Score=34.00 Aligned_cols=76 Identities=13% Similarity=-0.070 Sum_probs=53.9
Q ss_pred CceEEEEeceEEc-CCCCceeEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHH
Q 036307 169 CRMLVIVDGWEID-SPYKSVMLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDE 247 (405)
Q Consensus 169 ~~~vi~~D~t~~~-~~~~~~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~ 247 (405)
....+.+|.++.. ...++..++.+.+|..-+. .+++.+-..++.+...-+|....... +...|.+|+||+.+....
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 3568999999776 3455688888899886554 45677777778888877777655554 344489999999998764
No 21
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=82.82 E-value=7.1 Score=32.98 Aligned_cols=99 Identities=11% Similarity=0.160 Sum_probs=58.1
Q ss_pred EEEEeceEEcCCCCceeEEEEEEcCCCCeEEEEEEEee-ccccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHHHH-
Q 036307 172 LVIVDGWEIDSPYKSVMLVAVCRDGNDSVLPIAFCEVV-EENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAV- 249 (405)
Q Consensus 172 vi~~D~t~~~~~~~~~ll~~~g~d~~~~~~~~a~a~~~-~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai- 249 (405)
-|..||- ++.-+.+++.++...+.|-.|.=..-.-. ..+.+...-+|....+-+ |..+...||||-...+.+|-
T Consensus 35 si~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeV--G~~nVvqVVTDn~~~~~~a~~ 110 (153)
T PF04937_consen 35 SIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEV--GEENVVQVVTDNASNMKKAGK 110 (153)
T ss_pred EEEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHh--hhhhhhHHhccCchhHHHHHH
Confidence 3444444 33344455555554455544433322111 123334444444444333 66677889999998888874
Q ss_pred --HhhcccchhhhcHHHHHHhhhhhCC
Q 036307 250 --EEFLPSAVYRQCCFSLYTKMVHEFP 274 (405)
Q Consensus 250 --~~vfP~a~~~~C~~Hi~~n~~~~~~ 274 (405)
.+.+|...+..|..|-+.-+.+.+.
T Consensus 111 ~L~~k~p~ifw~~CaaH~inLmledi~ 137 (153)
T PF04937_consen 111 LLMEKYPHIFWTPCAAHCINLMLEDIG 137 (153)
T ss_pred HHHhcCCCEEEechHHHHHHHHHHHHh
Confidence 4558999999999999877766554
No 22
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=79.06 E-value=48 Score=30.64 Aligned_cols=149 Identities=8% Similarity=-0.006 Sum_probs=87.9
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHH---hCC-CCCHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhhCCCc
Q 036307 59 TKWIAAKFLHIWKQSEHREVDKLRNEIATT---YGI-KCPIWKLEAVDKMARFWLRTDHADGYAQLLQYKQEMENVNSRN 134 (405)
Q Consensus 59 s~~ia~~~~~~i~~~~~~~~~~i~~~l~~~---~g~-~~s~~~~~~ak~~~~~~~~g~~~~~~~~l~~~~~~l~~~npg~ 134 (405)
-..+...+.+....++......|...|+.+ .|+ .++.+.++|..+.+ |- .. ......+-+
T Consensus 10 ~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~-----gL--------~~---~~r~~~~~~ 73 (262)
T PRK14702 10 DTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQN-----AL--------LL---ERKPAVPPS 73 (262)
T ss_pred hHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHh-----CC--------cc---ccCCCCCCC
Confidence 345566677766777889999999999875 377 48999888876542 10 00 000000000
Q ss_pred EEEEEecccccccccccceEEEechhhHHHHHhcCceEEEEeceEEcCCCCceeEEEEEEcCCCCeEEEEEEEeec-ccc
Q 036307 135 IVIIETKSQQQFTADIFDRMFVFLYDTAYAFKTRCRMLVIVDGWEIDSPYKSVMLVAVCRDGNDSVLPIAFCEVVE-ENL 213 (405)
Q Consensus 135 ~~~~~~~~~~~~~~~~f~~~f~~~~~~~~~~~~~~~~vi~~D~t~~~~~~~~~ll~~~g~d~~~~~~~~a~a~~~~-E~~ 213 (405)
. .. ....+ . ...-..++..|-||.....++.++.++-+|...+ .++|+++... .+.
T Consensus 74 ~------~~---~~~~~----~---------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~ 130 (262)
T PRK14702 74 K------RA---HTGRV----A---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNS 130 (262)
T ss_pred C------cC---CCCcc----c---------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCH
Confidence 0 00 00110 0 0114568999999987655557888888887666 6888988864 555
Q ss_pred ccHHHHHHHH-hhcccc-cCCCCeEEEcCCcccHH
Q 036307 214 DSWAFFLKNL-NYGLRL-ERGEGLCIMGDGDNGID 246 (405)
Q Consensus 214 ~~~~wfl~~l-~~~~~~-~~~~~~~iisD~~~~l~ 246 (405)
+.-.-+|+.. ....+. ....|..|-||+.....
T Consensus 131 ~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy~ 165 (262)
T PRK14702 131 ETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCYR 165 (262)
T ss_pred HHHHHHHHHHHHHHhcccCCCCCeEEEcCCCcccc
Confidence 5555555543 332210 12347899999987643
No 23
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=75.84 E-value=62 Score=30.60 Aligned_cols=147 Identities=8% Similarity=0.005 Sum_probs=86.7
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHHh---CC-CCCHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhhCCCcEE
Q 036307 61 WIAAKFLHIWKQSEHREVDKLRNEIATTY---GI-KCPIWKLEAVDKMARFWLRTDHADGYAQLLQYKQEMENVNSRNIV 136 (405)
Q Consensus 61 ~ia~~~~~~i~~~~~~~~~~i~~~l~~~~---g~-~~s~~~~~~ak~~~~~~~~g~~~~~~~~l~~~~~~l~~~npg~~~ 136 (405)
.+...+.+.....+....+.|...|+.+. |+ .++.++++|..+.+ |- .. ......+.+.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~-----Gl--------~~---~~~~~~~~~~- 113 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQN-----AL--------LL---ERKPAVPPSK- 113 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHc-----CC--------cc---cccCCCCCCC-
Confidence 34556666666678889999999988652 66 58888888775542 10 00 0000000000
Q ss_pred EEEecccccccccccceEEEechhhHHHHHhcCceEEEEeceEEcCCCCceeEEEEEEcCCCCeEEEEEEEeec-ccccc
Q 036307 137 IIETKSQQQFTADIFDRMFVFLYDTAYAFKTRCRMLVIVDGWEIDSPYKSVMLVAVCRDGNDSVLPIAFCEVVE-ENLDS 215 (405)
Q Consensus 137 ~~~~~~~~~~~~~~f~~~f~~~~~~~~~~~~~~~~vi~~D~t~~~~~~~~~ll~~~g~d~~~~~~~~a~a~~~~-E~~~~ 215 (405)
.. ....| . ...-..+++.|-||....-++-++.++-+|...+ .++|+++... .+.+.
T Consensus 114 -----~~---~~~~~----~---------~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~ 171 (301)
T PRK09409 114 -----RA---HTGRV----A---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSET 171 (301)
T ss_pred -----CC---CCCCc----C---------CCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHH
Confidence 00 00111 0 1114579999999986655557888888888776 6889999875 56666
Q ss_pred HHHHHHH-Hhhcccc-cCCCCeEEEcCCcccHH
Q 036307 216 WAFFLKN-LNYGLRL-ERGEGLCIMGDGDNGID 246 (405)
Q Consensus 216 ~~wfl~~-l~~~~~~-~~~~~~~iisD~~~~l~ 246 (405)
-.-+|+. +....+. ....|..|-||+.....
T Consensus 172 v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy~ 204 (301)
T PRK09409 172 VQDVMLGAVERRFGNDLPSSPVEWLTDNGSCYR 204 (301)
T ss_pred HHHHHHHHHHHHhccCCCCCCcEEecCCCcccc
Confidence 5555554 4443210 12246799999987643
No 24
>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=68.64 E-value=18 Score=30.12 Aligned_cols=69 Identities=14% Similarity=0.125 Sum_probs=39.3
Q ss_pred eEEEEeceEEcCCC--------------CceeEEEEEEcCC-CCeEEEEEEEeeccccccHHHHHHHHhhcccccCCCCe
Q 036307 171 MLVIVDGWEIDSPY--------------KSVMLVAVCRDGN-DSVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGL 235 (405)
Q Consensus 171 ~vi~~D~t~~~~~~--------------~~~ll~~~g~d~~-~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~~~~~~~~ 235 (405)
.+|-+|.||..++- .....++++++-+ +..--+-..++++.+.++-.-+++. .+ .+..
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~---~i----~~gs 76 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQE---HI----EPGS 76 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHH---hh----hccc
Confidence 36778888875332 1224444555544 3333334445577777776555433 22 2346
Q ss_pred EEEcCCcccHH
Q 036307 236 CIMGDGDNGID 246 (405)
Q Consensus 236 ~iisD~~~~l~ 246 (405)
+|+||..++-.
T Consensus 77 ~i~TD~~~aY~ 87 (151)
T PF12762_consen 77 TIITDGWRAYN 87 (151)
T ss_pred eeeecchhhcC
Confidence 89999998764
No 25
>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=66.15 E-value=6.4 Score=28.25 Aligned_cols=39 Identities=8% Similarity=0.196 Sum_probs=17.3
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 036307 65 KFLHIWKQSEHREVDKLRNEIATTYGIKCPIWKLEAVDKM 104 (405)
Q Consensus 65 ~~~~~i~~~~~~~~~~i~~~l~~~~g~~~s~~~~~~ak~~ 104 (405)
.+...+..+|..+..+|...+.+. |..+|..+++|.-..
T Consensus 3 ~I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L~~ 41 (72)
T PF01498_consen 3 RIVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRLRE 41 (72)
T ss_dssp -------------HHHHHHHT----T--S-HHHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHHHH
Confidence 344566788999999999999988 999999999877543
No 26
>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=62.66 E-value=26 Score=23.66 Aligned_cols=39 Identities=13% Similarity=0.275 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhcC--CCCCHHHHHHHHHHHhCCCCCHHHH
Q 036307 60 KWIAAKFLHIWKQS--EHREVDKLRNEIATTYGIKCPIWKL 98 (405)
Q Consensus 60 ~~ia~~~~~~i~~~--~~~~~~~i~~~l~~~~g~~~s~~~~ 98 (405)
..+...+.++++.. .+++.++|++.|.+.+|..++..+.
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~~K~ 43 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVTKKQVREQLEERFGVDLSSRKK 43 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SHHHH
T ss_pred HHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHHHHH
Confidence 34566677777753 6799999999999999999885543
No 27
>PF13592 HTH_33: Winged helix-turn helix
Probab=62.13 E-value=13 Score=25.70 Aligned_cols=31 Identities=13% Similarity=0.145 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 036307 74 EHREVDKLRNEIATTYGIKCPIWKLEAVDKM 104 (405)
Q Consensus 74 ~~~~~~~i~~~l~~~~g~~~s~~~~~~ak~~ 104 (405)
.-++..+|...|.+.+|+.+|.+.+++.-.+
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r 33 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRLLKR 33 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHHHHH
Confidence 4567889999999999999999998877554
No 28
>PRK13907 rnhA ribonuclease H; Provisional
Probab=60.00 E-value=76 Score=25.40 Aligned_cols=78 Identities=18% Similarity=0.164 Sum_probs=43.5
Q ss_pred EEEEeceEEcCCCCceeEEEEEEcCCCCeEEEEEE-EeeccccccHHHHHHHHhhcccccCCCCeEEEcCCcccHHHHHH
Q 036307 172 LVIVDGWEIDSPYKSVMLVAVCRDGNDSVLPIAFC-EVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDNGIDEAVE 250 (405)
Q Consensus 172 vi~~D~t~~~~~~~~~ll~~~g~d~~~~~~~~a~a-~~~~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~~l~~Ai~ 250 (405)
.|.+||.+..++-.+-.-.++ .|..+... +.+. -..+.+..-+.-++..|+.+...+ ..+..|.||. ..+.+++.
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-LSLPLGTMSNHEAEYHALLAALKYCTEHN-YNIVSFRTDS-QLVERAVE 78 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHhCC-CCEEEEEech-HHHHHHHh
Confidence 378899987664333222222 55555433 3321 123444555666777777765322 2467788887 55677777
Q ss_pred hhc
Q 036307 251 EFL 253 (405)
Q Consensus 251 ~vf 253 (405)
..+
T Consensus 79 ~~~ 81 (128)
T PRK13907 79 KEY 81 (128)
T ss_pred HHH
Confidence 655
No 29
>PRK00766 hypothetical protein; Provisional
Probab=56.47 E-value=1.3e+02 Score=26.39 Aligned_cols=97 Identities=19% Similarity=0.177 Sum_probs=55.7
Q ss_pred ceEEEEece-EEcCCCCceeEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhccc--------ccC---------
Q 036307 170 RMLVIVDGW-EIDSPYKSVMLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYGLR--------LER--------- 231 (405)
Q Consensus 170 ~~vi~~D~t-~~~~~~~~~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~--------~~~--------- 231 (405)
-.|+++|-. |..+.-+-..++-+-.-+++-+.-++|+.+.-.-.|.=.-+.+.++.... +.+
T Consensus 9 irvlGidds~f~~~~~~~~~lvGvv~r~~~~idGv~~~~itvdG~DaT~~i~~mv~~~~~r~~i~~V~L~Git~agFNvv 88 (194)
T PRK00766 9 IRVLGIDDGTFLFKSSEKVILVGVVMRGGDWVDGVLSRWITVDGLDATEAIIEMVNSSRHKGQLRVIMLDGITYGGFNVV 88 (194)
T ss_pred ceEEEEecCccccCCCCCEEEEEEEEECCeEEeeEEEEEEEECCccHHHHHHHHHHhcccccceEEEEECCEeeeeeEEe
Confidence 357888844 44333333555555556666666777777766666665555555443110 000
Q ss_pred ---------CCCeEEEcCCc---ccHHHHHHhhcccchhhhcHHHHHHhh
Q 036307 232 ---------GEGLCIMGDGD---NGIDEAVEEFLPSAVYRQCCFSLYTKM 269 (405)
Q Consensus 232 ---------~~~~~iisD~~---~~l~~Ai~~vfP~a~~~~C~~Hi~~n~ 269 (405)
+-|..+++.+- .+|.+|+++.||+...+ +.+.+++
T Consensus 89 D~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k~f~~~~~R---~~~~~~~ 135 (194)
T PRK00766 89 DIEELYRETGLPVIVVMRKKPDFEAIESALKKHFSDWEER---IKLIKKA 135 (194)
T ss_pred cHHHHHHHHCCCEEEEEecCCCHHHHHHHHHHHCCCHHHH---HHHHHhC
Confidence 13555553333 47999999999998776 3445443
No 30
>PF13276 HTH_21: HTH-like domain
Probab=52.29 E-value=42 Score=22.96 Aligned_cols=43 Identities=14% Similarity=0.203 Sum_probs=34.7
Q ss_pred HHHHHHHHHhcC-CCCCHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 036307 62 IAAKFLHIWKQS-EHREVDKLRNEIATTYGIKCPIWKLEAVDKM 104 (405)
Q Consensus 62 ia~~~~~~i~~~-~~~~~~~i~~~l~~~~g~~~s~~~~~~ak~~ 104 (405)
+.+.+.+.+..+ +......|...|+.+.|+.+|..++++..+.
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 455666666665 7889999999999998899999999887653
No 31
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=45.66 E-value=32 Score=28.91 Aligned_cols=36 Identities=14% Similarity=0.059 Sum_probs=30.5
Q ss_pred EeceEE-cCCCCce--eEEEEEEcCCCCeEEEEEEEeec
Q 036307 175 VDGWEI-DSPYKSV--MLVAVCRDGNDSVLPIAFCEVVE 210 (405)
Q Consensus 175 ~D~t~~-~~~~~~~--ll~~~g~d~~~~~~~~a~a~~~~ 210 (405)
||.||+ ++.|+.| ++..-|.|+-|+-.+.|+|-+.-
T Consensus 70 ievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~hi 108 (187)
T KOG4027|consen 70 IEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLHI 108 (187)
T ss_pred eEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEec
Confidence 788997 5899998 56678999999999999997643
No 32
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=43.00 E-value=63 Score=21.51 Aligned_cols=25 Identities=12% Similarity=0.081 Sum_probs=17.6
Q ss_pred eeEEEEEEcCCCCeEEEEEEEeecc
Q 036307 187 VMLVAVCRDGNDSVLPIAFCEVVEE 211 (405)
Q Consensus 187 ~ll~~~g~d~~~~~~~~a~a~~~~E 211 (405)
.-++++|-+++|+..++.-.+-.+|
T Consensus 38 ssfvlcgetpdgrrlvlthmistde 62 (66)
T PF13082_consen 38 SSFVLCGETPDGRRLVLTHMISTDE 62 (66)
T ss_pred EEEEEEccCCCCcEEEEEEEecchh
Confidence 3467788888888888776655444
No 33
>PF13551 HTH_29: Winged helix-turn helix
Probab=40.93 E-value=69 Score=24.63 Aligned_cols=40 Identities=13% Similarity=0.326 Sum_probs=30.5
Q ss_pred HHHHHHHhcCC-----CCCHHHHHHHH-HHHhCCCCCHHHHHHHHH
Q 036307 64 AKFLHIWKQSE-----HREVDKLRNEI-ATTYGIKCPIWKLEAVDK 103 (405)
Q Consensus 64 ~~~~~~i~~~~-----~~~~~~i~~~l-~~~~g~~~s~~~~~~ak~ 103 (405)
+.+.+.+..+| .+++..|.+.+ ++.+|+.+|.+++++.-.
T Consensus 64 ~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 64 AQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred HHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 45556666655 47889999976 888999999999987644
No 34
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=40.37 E-value=1.4e+02 Score=23.28 Aligned_cols=24 Identities=13% Similarity=0.314 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHHHhCCCCCHHHHH
Q 036307 76 REVDKLRNEIATTYGIKCPIWKLE 99 (405)
Q Consensus 76 ~~~~~i~~~l~~~~g~~~s~~~~~ 99 (405)
-+|+++.+.|++++|+.+|..++-
T Consensus 20 dTPs~v~~aVk~eFgi~vsrQqve 43 (104)
T PF10045_consen 20 DTPSEVAEAVKEEFGIDVSRQQVE 43 (104)
T ss_pred CCHHHHHHHHHHHhCCccCHHHHH
Confidence 379999999999999999987653
No 35
>PF14420 Clr5: Clr5 domain
Probab=40.13 E-value=91 Score=21.01 Aligned_cols=26 Identities=12% Similarity=0.268 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHHHHHHhCCCCCHHHH
Q 036307 73 SEHREVDKLRNEIATTYGIKCPIWKL 98 (405)
Q Consensus 73 ~~~~~~~~i~~~l~~~~g~~~s~~~~ 98 (405)
+.+.+..+|++.++..+|...|.++.
T Consensus 18 ~e~~tl~~v~~~M~~~~~F~at~rqy 43 (54)
T PF14420_consen 18 DENKTLEEVMEIMKEEHGFKATKRQY 43 (54)
T ss_pred hCCCcHHHHHHHHHHHhCCCcCHHHH
Confidence 56889999999999999999986543
No 36
>cd00131 PAX Paired Box domain
Probab=37.78 E-value=89 Score=25.37 Aligned_cols=39 Identities=8% Similarity=0.057 Sum_probs=30.4
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHhCC-----CCCHHHHHHHHH
Q 036307 64 AKFLHIWKQSEHREVDKLRNEIATTYGI-----KCPIWKLEAVDK 103 (405)
Q Consensus 64 ~~~~~~i~~~~~~~~~~i~~~l~~~~g~-----~~s~~~~~~ak~ 103 (405)
..+...+..+|+.+..+|.+.|.. .|+ .+|.++++|+-+
T Consensus 82 ~~i~~~v~~~p~~Tl~El~~~L~~-~gv~~~~~~~s~stI~R~L~ 125 (128)
T cd00131 82 KKIEIYKQENPGMFAWEIRDRLLQ-EGVCDKSNVPSVSSINRILR 125 (128)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHH-cCCcccCCCCCHHHHHHHHH
Confidence 445556788999999999999874 466 579999998843
No 37
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=33.66 E-value=37 Score=30.68 Aligned_cols=24 Identities=13% Similarity=0.120 Sum_probs=18.6
Q ss_pred cCCCCceeEEEEEEcCCCCeEEEE
Q 036307 181 DSPYKSVMLVAVCRDGNDSVLPIA 204 (405)
Q Consensus 181 ~~~~~~~ll~~~g~d~~~~~~~~a 204 (405)
+.+-.|+.+.+-..|++|..+.+.
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~ 226 (228)
T PRK06704 203 KLPSKQPVLLFNVKQPSSYSCMLC 226 (228)
T ss_pred ecccccceEEEEeeCCCccchhhc
Confidence 456678888888999998887654
No 38
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=31.62 E-value=34 Score=31.09 Aligned_cols=42 Identities=17% Similarity=0.101 Sum_probs=29.7
Q ss_pred ccccccHHHHHHHHHHh-----c--cccccccchhhhcCCCchhhhHHhhhc
Q 036307 332 TEITISATEQLRIWLLK-----Q--LDLNVEQRLWQVSGIPCPHACRCIDTW 376 (405)
Q Consensus 332 ~~~tp~~~~~l~~~~~~-----~--~~~~vsC~~~~~~giPC~Hala~~~~~ 376 (405)
|.+++++++.|..+-.. + -.+.|||-.|. -||.|+-|+....
T Consensus 98 gemP~sIedvf~~~GL~LfP~t~~dl~~dCSCPD~a---nPCKHi~AvyY~l 146 (266)
T COG4279 98 GEMPESIEDVFVGNGLSLFPFTLRDLSTDCSCPDYA---NPCKHIAAVYYLL 146 (266)
T ss_pred CCCCchHHHHHHhcCcccCCCchhhcccccCCCCcc---cchHHHHHHHHHH
Confidence 66777787777665221 1 34678999875 5999999987764
No 39
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.30 E-value=70 Score=26.21 Aligned_cols=37 Identities=5% Similarity=-0.024 Sum_probs=29.6
Q ss_pred HHHHHhcCceEE--EEeceEEcCCCCceeEEEEEEcCCCC
Q 036307 162 AYAFKTRCRMLV--IVDGWEIDSPYKSVMLVAVCRDGNDS 199 (405)
Q Consensus 162 ~~~~~~~~~~vi--~~D~t~~~~~~~~~ll~~~g~d~~~~ 199 (405)
+..+.. +.|++ -.||-|++.|.+|||.++--.|.+..
T Consensus 97 ~sDi~k-ynpIlA~~~nGn~M~IRerGPl~~IYplds~pe 135 (155)
T COG3915 97 YSDIEK-YNPILAIQNNGNYMQIRERGPLWSIYPLDSSPE 135 (155)
T ss_pred HHHhhh-cccEEEEEeCCcEEEEeccCceEEEeecCCChh
Confidence 456666 78874 57999999999999999887776554
No 40
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=29.04 E-value=1.6e+02 Score=21.21 Aligned_cols=39 Identities=13% Similarity=0.101 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 036307 64 AKFLHIWKQSEHREVDKLRNEIATTYGIKCPIWKLEAVDK 103 (405)
Q Consensus 64 ~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~s~~~~~~ak~ 103 (405)
..+++.|..++-.+-.+|++.|++. |+.+|-.++.|--+
T Consensus 8 ~~I~~li~~~~i~sQ~eL~~~L~~~-Gi~vTQaTiSRDLk 46 (70)
T PF01316_consen 8 ELIKELISEHEISSQEELVELLEEE-GIEVTQATISRDLK 46 (70)
T ss_dssp HHHHHHHHHS---SHHHHHHHHHHT-T-T--HHHHHHHHH
T ss_pred HHHHHHHHHCCcCCHHHHHHHHHHc-CCCcchhHHHHHHH
Confidence 5677778887777888999999875 99999998876643
No 41
>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=26.02 E-value=41 Score=21.15 Aligned_cols=17 Identities=24% Similarity=0.751 Sum_probs=11.3
Q ss_pred EEeecC--CCceEEEEEEe
Q 036307 15 CECSNL--HCDWKITAVKE 31 (405)
Q Consensus 15 ~~C~~~--~Cpwrv~~~~~ 31 (405)
..|+++ -|||.|.....
T Consensus 18 YCcSdpGrYCpwqvVCYeS 36 (45)
T smart00816 18 YCCSDPGRYCPWQVVCYES 36 (45)
T ss_pred cccCCCcccCCceEEEeeh
Confidence 445554 49999987643
No 42
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=25.47 E-value=1.5e+02 Score=24.64 Aligned_cols=35 Identities=11% Similarity=0.164 Sum_probs=29.5
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHhCCCCCHHHHHH
Q 036307 65 KFLHIWKQSEHREVDKLRNEIATTYGIKCPIWKLEA 100 (405)
Q Consensus 65 ~~~~~i~~~~~~~~~~i~~~l~~~~g~~~s~~~~~~ 100 (405)
.++..+.+++-.+..+|.+.+++. |+.+|..++||
T Consensus 6 ~i~~Li~~~~i~tqeeL~~~L~~~-G~~vsqaTIsR 40 (146)
T TIGR01529 6 RIKEIITEEKISTQEELVALLKAE-GIEVTQATVSR 40 (146)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHh-CCCcCHHHHHH
Confidence 456667778888999999999654 99999999998
No 43
>smart00351 PAX Paired Box domain.
Probab=25.17 E-value=1.7e+02 Score=23.51 Aligned_cols=38 Identities=8% Similarity=0.104 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHHhCCCC-----CHHHHHHH
Q 036307 63 AAKFLHIWKQSEHREVDKLRNEIATTYGIKC-----PIWKLEAV 101 (405)
Q Consensus 63 a~~~~~~i~~~~~~~~~~i~~~l~~~~g~~~-----s~~~~~~a 101 (405)
...+...+..+|++++.+|.+.|. +.|+.+ +.+++.+.
T Consensus 81 ~~~I~~~~~~~p~~t~~el~~~L~-~~gv~~~~~~Ps~sti~~~ 123 (125)
T smart00351 81 VKKIADYKQENPGIFAWEIRDRLL-SEGVCDKDNVPSVSSINRI 123 (125)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHH-HcCCCcCCCCCChhhHHHh
Confidence 345666678899999999999998 456544 77776654
No 44
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=24.96 E-value=2.1e+02 Score=24.23 Aligned_cols=46 Identities=24% Similarity=0.213 Sum_probs=30.3
Q ss_pred cccccHHHHHHHHhhcccc--c--CCCCeEEEcCCcccHHHHHHhhcccc
Q 036307 211 ENLDSWAFFLKNLNYGLRL--E--RGEGLCIMGDGDNGIDEAVEEFLPSA 256 (405)
Q Consensus 211 E~~~~~~wfl~~l~~~~~~--~--~~~~~~iisD~~~~l~~Ai~~vfP~a 256 (405)
+..++|.-+-+.+..+..- . ...|-.|+.|+.+|-.+|+.+++-..
T Consensus 53 ~~~dDy~~M~Evl~RR~~~~~~~~~~lPDLilIDGG~gQl~aa~~~l~~l 102 (155)
T PF08459_consen 53 DGGDDYAAMREVLTRRFKRLKEEKEPLPDLILIDGGKGQLNAAKEVLKEL 102 (155)
T ss_dssp STT-HHHHHHHHHHHHHCCCHHHT----SEEEESSSHHHHHHHHHHHHCT
T ss_pred CCCcHHHHHHHHHHHHHhcccccCCCCCCEEEEcCCHHHHHHHHHHHHHc
Confidence 4457777777777666521 1 12478999999999999999987543
No 45
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=24.60 E-value=2.2e+02 Score=18.89 Aligned_cols=46 Identities=15% Similarity=0.242 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh
Q 036307 79 DKLRNEIATTYGIKCPIWKLEAVDKMARFWLRTDHADGYAQLLQYKQEM 127 (405)
Q Consensus 79 ~~i~~~l~~~~g~~~s~~~~~~ak~~~~~~~~g~~~~~~~~l~~~~~~l 127 (405)
..+.+.|.+..|+.++..+-.-.++++........ +..+.+|+..|
T Consensus 6 ~~~~~~i~~~~Gi~l~~~K~~~l~rRl~~rm~~~~---~~~~~~y~~~L 51 (57)
T PF03705_consen 6 ERFRELIYRRTGIDLSEYKRSLLERRLARRMRALG---LPSFAEYYELL 51 (57)
T ss_dssp HHHHHHHHHHH-----GGGHHHHHHHHHHHHHHHT------HHHHHHHH
T ss_pred HHHHHHHHHHHCCCCchhhHHHHHHHHHHHHHHcC---CCCHHHHHHHH
Confidence 45778888999999877665555555444332222 23344555554
No 46
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=23.84 E-value=79 Score=25.69 Aligned_cols=37 Identities=14% Similarity=0.046 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhc--CCCCCHHHHHHHHHHHhCCCCCHH
Q 036307 60 KWIAAKFLHIWKQ--SEHREVDKLRNEIATTYGIKCPIW 96 (405)
Q Consensus 60 ~~ia~~~~~~i~~--~~~~~~~~i~~~l~~~~g~~~s~~ 96 (405)
.-+|..++..++. ..+.+..+|.+.+.++||-.|-|.
T Consensus 56 a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly~ 94 (126)
T TIGR03147 56 SPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDFVLYN 94 (126)
T ss_pred CHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEec
Confidence 3566777776665 368889999999999999765443
No 47
>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=22.99 E-value=78 Score=21.53 Aligned_cols=25 Identities=4% Similarity=-0.109 Sum_probs=17.5
Q ss_pred CCCHHHHHHHHHHHhCCCCCHH-HHH
Q 036307 75 HREVDKLRNEIATTYGIKCPIW-KLE 99 (405)
Q Consensus 75 ~~~~~~i~~~l~~~~g~~~s~~-~~~ 99 (405)
.++..++++.|.+..++.+... .+|
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW 37 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVW 37 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHH
Confidence 4677888888888877765443 344
No 48
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=22.85 E-value=2e+02 Score=24.45 Aligned_cols=63 Identities=13% Similarity=0.002 Sum_probs=38.5
Q ss_pred chhhHHHHHhcCceEEEEeceEEcCCCCceeEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhc
Q 036307 158 LYDTAYAFKTRCRMLVIVDGWEIDSPYKSVMLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYG 226 (405)
Q Consensus 158 ~~~~~~~~~~~~~~vi~~D~t~~~~~~~~~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~ 226 (405)
.......+.. ++|+++-..+- ...+-++..+++|+|++|.... +.+.|..-+-+=-|+.|..+
T Consensus 98 ~e~~~~LL~~-yGPLwv~~~~P-~~~~~~H~~ViTGI~~dg~~i~----~~DP~~gP~~~m~l~~fn~~ 160 (166)
T PF12385_consen 98 AEGLANLLRE-YGPLWVAWEAP-GDSWVAHASVITGIDGDGDSIH----VHDPEQGPNLRMSLDMFNQA 160 (166)
T ss_pred HHHHHHHHHH-cCCeEEEecCC-CCcceeeEEEEEeecCCCCeEE----ecCcccCCCceecHHHHhhh
Confidence 3344455555 89998875544 2334468999999999996543 45555555544444444443
No 49
>PF03913 Amb_V_allergen: Amb V Allergen; InterPro: IPR005611 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 sulphydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens [].; PDB: 2BBG_A 3BBG_A 1BBG_A.
Probab=22.26 E-value=74 Score=19.94 Aligned_cols=14 Identities=29% Similarity=0.890 Sum_probs=4.4
Q ss_pred EeecC--CCceEEEEE
Q 036307 16 ECSNL--HCDWKITAV 29 (405)
Q Consensus 16 ~C~~~--~Cpwrv~~~ 29 (405)
.|++. -|||.|...
T Consensus 18 CcSdpGrYCpwqvVCY 33 (44)
T PF03913_consen 18 CCSDPGRYCPWQVVCY 33 (44)
T ss_dssp EE-SSSSS-----EEE
T ss_pred ecCCCcccccceeeee
Confidence 44444 499998765
No 50
>PF11447 DUF3201: Protein of unknown function (DUF3201); InterPro: IPR024505 This archaeal family of proteins has no known function.; PDB: 1YB3_A.
Probab=21.79 E-value=4.6e+02 Score=21.57 Aligned_cols=59 Identities=12% Similarity=0.074 Sum_probs=35.6
Q ss_pred HHHHHHHhhhhCCCcEEEEEecccccccccccceEEEechhhHHHHHhcCceEEEEeceEEcCCCCceeEEE-----EEE
Q 036307 120 LLQYKQEMENVNSRNIVIIETKSQQQFTADIFDRMFVFLYDTAYAFKTRCRMLVIVDGWEIDSPYKSVMLVA-----VCR 194 (405)
Q Consensus 120 l~~~~~~l~~~npg~~~~~~~~~~~~~~~~~f~~~f~~~~~~~~~~~~~~~~vi~~D~t~~~~~~~~~ll~~-----~g~ 194 (405)
+..+-.+|++.-||+.|.--.. + +.-.|.+||-+..-+|--|.+.+ +|.
T Consensus 10 if~l~eELkeel~gf~vE~v~e------------v--------------Fnayi~lDgeW~em~YPhPaf~ikp~gEvGa 63 (150)
T PF11447_consen 10 IFRLNEELKEELKGFKVEEVEE------------V--------------FNAYIYLDGEWREMKYPHPAFEIKPQGEVGA 63 (150)
T ss_dssp HHHHHHHHHHHSTTSEE---EE------------E---------------S-EEEETTEEEE--S-EEEEEEETTEEEEE
T ss_pred HHHHHHHHHHHcCCCcceeHhh------------h--------------hheeEEecCeeeeecCCCCceeeccCccccc
Confidence 4455667777788988742221 1 45569999999999999987764 777
Q ss_pred cCCCCeEEEE
Q 036307 195 DGNDSVLPIA 204 (405)
Q Consensus 195 d~~~~~~~~a 204 (405)
|..+--+++|
T Consensus 64 t~q~~YFvfa 73 (150)
T PF11447_consen 64 TPQGFYFVFA 73 (150)
T ss_dssp ETTEEEEEEE
T ss_pred ccceEEEEEE
Confidence 7755554443
No 51
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=21.47 E-value=92 Score=25.29 Aligned_cols=37 Identities=14% Similarity=0.032 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhc--CCCCCHHHHHHHHHHHhCCCCCHH
Q 036307 60 KWIAAKFLHIWKQ--SEHREVDKLRNEIATTYGIKCPIW 96 (405)
Q Consensus 60 ~~ia~~~~~~i~~--~~~~~~~~i~~~l~~~~g~~~s~~ 96 (405)
.-+|..++..++. ..+.+..+|.+.+.++||-.|.|.
T Consensus 56 a~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~~ 94 (126)
T PRK10144 56 APVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFVRYN 94 (126)
T ss_pred CHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEec
Confidence 3566777776665 367889999999999999776544
No 52
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=20.81 E-value=1.8e+02 Score=23.07 Aligned_cols=53 Identities=17% Similarity=0.123 Sum_probs=36.0
Q ss_pred eeEEEEEEcCCCCeEEEEEEEeeccccccHHHHHHHHhhcccccCCCCeEEEcCCcc
Q 036307 187 VMLVAVCRDGNDSVLPIAFCEVVEENLDSWAFFLKNLNYGLRLERGEGLCIMGDGDN 243 (405)
Q Consensus 187 ~ll~~~g~d~~~~~~~~a~a~~~~E~~~~~~wfl~~l~~~~~~~~~~~~~iisD~~~ 243 (405)
.+.++.+++.++...+ +..-..-+.+.|.-||+.+.... ....+.+||-|...
T Consensus 38 ~~~~~~ai~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~li~DNa~ 90 (146)
T PF13358_consen 38 RVSVWGAISYNGGIVL--FVVEGTMNSEDFIEFLEQLLRPY--PRKGRIVLIMDNAS 90 (146)
T ss_pred EEEEEEEecccccccc--eeeeeeecccccccccccccccc--ccceEEEEeccccc
Confidence 5666677777775555 44455667777777888877765 33237899999765
No 53
>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=20.01 E-value=1.3e+02 Score=20.90 Aligned_cols=28 Identities=11% Similarity=0.160 Sum_probs=20.9
Q ss_pred HHHHHHHh--cCCCCCHHHHHHHHHHHhCC
Q 036307 64 AKFLHIWK--QSEHREVDKLRNEIATTYGI 91 (405)
Q Consensus 64 ~~~~~~i~--~~~~~~~~~i~~~l~~~~g~ 91 (405)
+.+++.|- +..+++|++|--.|++.||+
T Consensus 31 ~eVe~~I~klakkG~tpSqIG~iLRD~~GI 60 (60)
T PF08069_consen 31 EEVEELIVKLAKKGLTPSQIGVILRDQYGI 60 (60)
T ss_dssp HHHHHHHHHHCCTTHCHHHHHHHHHHSCTC
T ss_pred HHHHHHHHHHHHcCCCHHHhhhhhhhccCC
Confidence 44444444 35789999999999999885
Done!