Query 004769
Match_columns 731
No_of_seqs 280 out of 1251
Neff 8.4
Searched_HMMs 46136
Date Thu Mar 28 12:36:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004769.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004769hhsearch_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 4E-121 9E-126 1045.5 60.7 578 31-638 63-683 (846)
2 PF03101 FAR1: FAR1 DNA-bindin 99.8 2.6E-19 5.7E-24 154.6 8.6 91 56-150 1-91 (91)
3 PF10551 MULE: MULE transposas 99.6 5.9E-16 1.3E-20 134.3 6.5 68 276-344 1-93 (93)
4 PF00872 Transposase_mut: Tran 99.5 3.5E-15 7.5E-20 162.5 1.9 233 156-434 92-352 (381)
5 PF08731 AFT: Transcription fa 99.3 2.4E-11 5.1E-16 104.0 10.1 91 48-148 1-111 (111)
6 smart00575 ZnF_PMZ plant mutat 98.9 3.4E-10 7.5E-15 73.6 1.7 27 536-562 1-27 (28)
7 COG3328 Transposase and inacti 98.9 3.6E-08 7.8E-13 105.6 15.3 238 159-449 81-348 (379)
8 PF03108 DBD_Tnp_Mut: MuDR fam 98.4 1.1E-06 2.4E-11 70.8 8.0 66 40-137 2-67 (67)
9 PF04434 SWIM: SWIM zinc finge 98.2 8.9E-07 1.9E-11 63.3 3.2 29 532-560 11-39 (40)
10 PF15288 zf-CCHC_6: Zinc knuck 94.9 0.018 3.9E-07 40.3 2.0 22 700-721 2-25 (40)
11 PF03106 WRKY: WRKY DNA -bindi 94.8 0.13 2.9E-06 40.1 6.9 57 65-147 3-59 (60)
12 PF00098 zf-CCHC: Zinc knuckle 94.7 0.025 5.5E-07 32.6 1.9 17 701-717 2-18 (18)
13 PF01610 DDE_Tnp_ISL3: Transpo 92.9 0.088 1.9E-06 54.2 3.5 73 272-349 1-98 (249)
14 PF13696 zf-CCHC_2: Zinc knuck 92.1 0.071 1.5E-06 35.5 1.0 24 698-721 7-30 (32)
15 COG5179 TAF1 Transcription ini 88.5 0.29 6.2E-06 54.4 2.5 30 695-724 933-964 (968)
16 PRK08561 rps15p 30S ribosomal 86.7 1.2 2.7E-05 41.1 5.1 79 165-243 31-143 (151)
17 PF06782 UPF0236: Uncharacteri 86.5 29 0.00063 39.3 17.0 52 157-213 112-163 (470)
18 smart00774 WRKY DNA binding do 86.5 1.4 3.1E-05 34.1 4.6 57 65-146 3-59 (59)
19 PF14392 zf-CCHC_4: Zinc knuck 79.6 0.73 1.6E-05 34.4 0.5 17 701-717 33-49 (49)
20 PF13936 HTH_38: Helix-turn-he 77.0 2.2 4.8E-05 30.9 2.4 30 160-189 2-31 (44)
21 smart00343 ZnF_C2HC zinc finge 75.0 1.6 3.4E-05 27.6 1.0 19 701-719 1-19 (26)
22 PF04500 FLYWCH: FLYWCH zinc f 72.6 5.1 0.00011 30.9 3.7 25 116-146 38-62 (62)
23 KOG4602 Nanos and related prot 69.8 16 0.00035 36.6 7.0 31 695-725 264-297 (318)
24 PF04684 BAF1_ABF1: BAF1 / ABF 68.7 9 0.0002 41.9 5.5 55 44-127 24-78 (496)
25 KOG3517 Transcription factor P 59.3 15 0.00033 36.6 4.7 70 160-240 18-98 (334)
26 KOG0400 40S ribosomal protein 59.3 9.7 0.00021 34.1 3.1 38 157-194 22-60 (151)
27 PF00292 PAX: 'Paired box' dom 55.9 16 0.00035 33.0 4.0 71 159-240 14-95 (125)
28 PTZ00072 40S ribosomal protein 55.9 19 0.00041 33.2 4.4 48 165-212 28-91 (148)
29 PF08069 Ribosomal_S13_N: Ribo 51.7 11 0.00024 29.3 1.9 32 162-193 27-59 (60)
30 PF05741 zf-nanos: Nanos RNA b 49.4 5.9 0.00013 30.2 0.2 21 698-718 32-55 (55)
31 PF02796 HTH_7: Helix-turn-hel 40.5 25 0.00053 25.5 2.3 28 161-188 4-31 (45)
32 COG5431 Uncharacterized metal- 40.0 67 0.0014 27.8 5.0 20 537-556 51-75 (117)
33 PRK14892 putative transcriptio 39.2 21 0.00045 30.9 2.0 10 697-706 19-28 (99)
34 PF11433 DUF3198: Protein of u 38.9 34 0.00073 24.9 2.6 45 360-404 5-49 (51)
35 KOG0341 DEAD-box protein abstr 38.6 13 0.00029 39.7 0.8 19 701-719 572-590 (610)
36 COG4888 Uncharacterized Zn rib 32.8 28 0.00062 29.9 1.7 11 697-707 20-30 (104)
37 COG5222 Uncharacterized conser 27.6 43 0.00094 34.4 2.3 27 699-725 176-202 (427)
38 PF09713 A_thal_3526: Plant pr 27.6 86 0.0019 23.9 3.3 26 169-194 3-28 (54)
39 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 27.3 60 0.0013 24.3 2.4 29 162-190 4-32 (50)
40 PF15299 ALS2CR8: Amyotrophic 26.8 50 0.0011 33.4 2.7 20 108-127 70-89 (225)
41 COG4279 Uncharacterized conser 26.4 34 0.00073 34.6 1.3 24 535-561 124-147 (266)
42 PF12353 eIF3g: Eukaryotic tra 25.6 42 0.0009 30.7 1.7 22 697-719 104-125 (128)
43 PF03050 DDE_Tnp_IS66: Transpo 24.9 1.2E+02 0.0026 31.3 5.3 43 166-214 7-50 (271)
44 smart00351 PAX Paired Box doma 24.8 2E+02 0.0043 26.0 6.0 68 161-239 16-94 (125)
45 COG4715 Uncharacterized conser 24.5 3.1E+02 0.0067 31.4 8.3 33 526-560 63-95 (587)
46 PF13384 HTH_23: Homeodomain-l 24.1 72 0.0016 23.3 2.5 39 166-215 5-43 (50)
47 PF00196 GerE: Bacterial regul 24.0 1.7E+02 0.0038 22.1 4.7 53 162-226 3-55 (58)
48 smart00421 HTH_LUXR helix_turn 23.5 2E+02 0.0044 20.8 5.1 44 162-217 3-46 (58)
49 PHA00689 hypothetical protein 23.5 32 0.00069 25.2 0.4 13 697-709 15-27 (62)
50 COG5082 AIR1 Arginine methyltr 23.1 43 0.00092 32.6 1.3 19 700-718 98-117 (190)
51 PRK12286 rpmF 50S ribosomal pr 23.0 64 0.0014 24.9 2.0 43 672-717 3-45 (57)
52 PF13917 zf-CCHC_3: Zinc knuck 21.8 46 0.001 23.9 0.9 17 701-717 6-22 (42)
53 cd06170 LuxR_C_like C-terminal 21.4 2.5E+02 0.0055 20.4 5.2 53 164-228 2-54 (57)
54 PF02178 AT_hook: AT hook moti 21.3 43 0.00093 17.7 0.5 9 677-685 2-10 (13)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.4e-121 Score=1045.52 Aligned_cols=578 Identities=26% Similarity=0.469 Sum_probs=511.1
Q ss_pred cCCccCCCCCCCCCCCccCCHHHHHHHHHHHHHhcCceEEEcceeccCCCCcceEEEEeeecCCCCCCCCCCC-------
Q 004769 31 ILSQQTSVNLVPFIGQRFVSQDAAYEFYCSFAKQCGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSD------- 103 (731)
Q Consensus 31 ~~~~~~~~~~~P~~g~~F~S~eea~~~y~~yA~~~GF~ir~~~s~~~~~~gk~~~~~~~~C~r~G~~~~k~~~------- 103 (731)
++..+.+..++|.+||+|+|+|||++||+.||+..||+||+.++++++..| .++.++|+|+|+|+++.+.+.
T Consensus 63 ~~~~~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~-~ii~r~fvCsreG~~~~~~~~~~~~~~~ 141 (846)
T PLN03097 63 LVEFKEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSR-EFIDAKFACSRYGTKREYDKSFNRPRAR 141 (846)
T ss_pred cccccCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCC-cEEEEEEEEcCCCCCccccccccccccc
Confidence 344456677899999999999999999999999999999999998877654 688999999999987543210
Q ss_pred -----CccccccCCcccccccceEEEEEeecCCCCcEEEEEEeCCccCCCCCccccccCCcCCCCCcchhhHHHHhhhcC
Q 004769 104 -----DGKMQRNRKSSRCGCQAYMRIVKRVDFDVPEWHVTGFSNVHNHELLKLNEVRLLPAYCSITPDDKTRICMFAKAG 178 (731)
Q Consensus 104 -----~~~~~r~~~s~rtgCpa~i~~~~~~~~~~~~W~V~~~~~~HNH~l~~~~~~~~l~shR~ls~~~k~~i~~l~~~g 178 (731)
....+++|+.+||||||+|+|++. ..|+|+|+.|+.+|||||.++..+ +
T Consensus 142 ~~k~~~~~~~~rR~~tRtGC~A~m~Vk~~---~~gkW~V~~fv~eHNH~L~p~~~~---------~-------------- 195 (846)
T PLN03097 142 QTKQDPENGTGRRSCAKTDCKASMHVKRR---PDGKWVIHSFVKEHNHELLPAQAV---------S-------------- 195 (846)
T ss_pred ccccCcccccccccccCCCCceEEEEEEc---CCCeEEEEEEecCCCCCCCCcccc---------c--------------
Confidence 001123456799999999999875 468999999999999999865421 1
Q ss_pred CcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhc-cccccHHHHHHHHHHhhcCCCCcEEEEeecCCCCeeEEEec
Q 004769 179 MSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNV-NRDYDAIDLIAMCKKMKDKNPNFQYDFKMDGHNRLEHIAWS 257 (731)
Q Consensus 179 ~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~-~~~~d~~~l~~~~~~~~~~np~~~~~~~~d~~~~~~~if~~ 257 (731)
..++.++..+....+. +.++.++..|..|...+.|+. ...+|++.|++||++++.+||+|||++++|++|++++|||+
T Consensus 196 ~~~r~~~~~~~~~~~~-~~~v~~~~~d~~~~~~~~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWa 274 (846)
T PLN03097 196 EQTRKMYAAMARQFAE-YKNVVGLKNDSKSSFDKGRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWV 274 (846)
T ss_pred hhhhhhHHHHHhhhhc-cccccccchhhcchhhHHHhhhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEec
Confidence 1233444444444443 567777888888887776644 56799999999999999999999999999999999999999
Q ss_pred chhhHHHHHhcCCEEEecCcccccccCcceeeEEEecCCCCeeeeeehhccCCchhhHHHHHH-----------------
Q 004769 258 YASSVQLYEAFGDALVFDTTHRLDSYDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFSWSLK----------------- 320 (731)
Q Consensus 258 ~~~s~~~~~~f~~vl~~D~Ty~tn~y~~pl~~~~g~d~~~~~~~~a~al~~~E~~es~~W~l~----------------- 320 (731)
|+.|+.+|.+|||||+||+||+||+|+|||++|+|||||+|+++||||||.+|+.+||.|+|+
T Consensus 275 D~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTD 354 (846)
T PLN03097 275 DAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITD 354 (846)
T ss_pred cHHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEec
Confidence 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ------HHHHhhCCCCCccccHHHHHHHhhhccCcccCCChhhHHHHHHh-HccCCCHHHHHHHHHHhhhhcccccchHH
Q 004769 321 ------EAVAVEMPETKHAVYIWHILAKLSDSLPTFLGSSYDDWKAEFYR-LYNLELEEDFEEEWSKMVNKYGLREYKHI 393 (731)
Q Consensus 321 ------~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~f~~-~~~~~t~~eFe~~w~~l~~~~~~~~~~~l 393 (731)
+||++|||+|.||+|+|||++|+.++++..+ ..++.|+.+|+. |+++.+++|||..|..|+++|++++|+||
T Consensus 355 qd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~-~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL 433 (846)
T PLN03097 355 QDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVI-KQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWM 433 (846)
T ss_pred CCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHh-hhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHH
Confidence 9999999999999999999999999998765 346789999986 67789999999999999999999999999
Q ss_pred HHHHHhhccccccccccccccCcccCCccchHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccc
Q 004769 394 TSLYALRTFWALPFLRHYFFAGLLSPCQSEAINAFIQRILSAQSQLDRFVERVAEIVEFNDRAATKQKMQRKLQKICLKT 473 (731)
Q Consensus 394 ~~l~~~r~~Wa~ay~~~~~~~g~~tt~r~Es~n~~lk~~l~~~~~l~~f~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~t 473 (731)
+.||+.|++||++|+++.|++||.||+|+||+|++||+|+++.++|..|+++|+.+++.++++|+++++.+....|.+++
T Consensus 434 ~~LY~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t 513 (846)
T PLN03097 434 QSLYEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKS 513 (846)
T ss_pred HHHHHhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988888889999
Q ss_pred CChHHHHHHhhccHHHHHHHHHHHHhccCceEEEee-CC---eEEEEEeeeecCceEEEEccCCCceEeecCCcccCCcc
Q 004769 474 GSPIESHAATVLTPYAFGKLQEELLMAPQYASLLVD-EG---CFQVKHHTETDGGCKVIWIPCQEHISCSCHQFEFSGIL 549 (731)
Q Consensus 474 ~~~~e~~a~~iyT~~~f~~~q~e~~~s~~~~v~~~~-~~---~y~V~~~~~~~~~~~V~~~~~~~~~~CsC~~fe~~GiP 549 (731)
++|||+||+.+|||+||++||+|+..+..|.+.... +| .|.|....+ .+.+.|.+|.....++|+|++||+.|||
T Consensus 514 ~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~-~~~~~V~~d~~~~~v~CsC~kFE~~GIL 592 (846)
T PLN03097 514 PSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEK-NQDFTVTWNQTKLEVSCICRLFEYKGYL 592 (846)
T ss_pred ccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecC-CCcEEEEEecCCCeEEeeccCeecCccc
Confidence 999999999999999999999999999998886643 33 688876543 5679999999999999999999999999
Q ss_pred hhhHHHHhhcCCCccCCCCCcccccccccCCCCCCCCCC--CCChhHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Q 004769 550 CRHVLRVLSTDNCFQIPDQYLPIRWRNVTSASTNPLRTT--TRDRSEKIQLLESMASALVSESLETEERLDVACEQVAMV 627 (731)
Q Consensus 550 C~Hil~vl~~~~i~~ip~~yi~~RWtk~a~~~~~~~~~~--~~~~~~r~~~l~~~~~~~~~~~~~s~e~~~~~~~~l~~~ 627 (731)
|+|||+||.+++|.+||++||++||||+|+.....+... ..+...||+.|++.+.+++.+|+.|+|.|..|++.|+++
T Consensus 593 CrHaLkVL~~~~v~~IP~~YILkRWTKdAK~~~~~~~~~~~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~L~e~ 672 (846)
T PLN03097 593 CRHALVVLQMCQLSAIPSQYILKRWTKDAKSRHLLGEESEQVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRALEEA 672 (846)
T ss_pred hhhHHHHHhhcCcccCchhhhhhhchhhhhhcccCccccccccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999876654432 234567999999999999999999999999999999999
Q ss_pred HHHhhcCCCCC
Q 004769 628 LNHVKDLPRPI 638 (731)
Q Consensus 628 ~~~~~~~~~~~ 638 (731)
+.++..|..+.
T Consensus 673 ~~~~~~~~n~~ 683 (846)
T PLN03097 673 FGNCISMNNSN 683 (846)
T ss_pred HHHHHHhhccC
Confidence 99998766544
No 2
>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=99.79 E-value=2.6e-19 Score=154.59 Aligned_cols=91 Identities=37% Similarity=0.701 Sum_probs=78.9
Q ss_pred HHHHHHHHhcCceEEEcceeccCCCCcceEEEEeeecCCCCCCCCCCCCccccccCCcccccccceEEEEEeecCCCCcE
Q 004769 56 EFYCSFAKQCGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSDDGKMQRNRKSSRCGCQAYMRIVKRVDFDVPEW 135 (731)
Q Consensus 56 ~~y~~yA~~~GF~ir~~~s~~~~~~gk~~~~~~~~C~r~G~~~~k~~~~~~~~r~~~s~rtgCpa~i~~~~~~~~~~~~W 135 (731)
+||+.||+.+||+|++.++++++..| .++++.|+|+++|.++.+.......++++++++|||||+|.+++.. ++.|
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~-~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~---~~~w 76 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNG-EIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK---DGKW 76 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCc-eEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc---CCEE
Confidence 59999999999999999998764443 6889999999999998776554456788899999999999999863 6999
Q ss_pred EEEEEeCCccCCCCC
Q 004769 136 HVTGFSNVHNHELLK 150 (731)
Q Consensus 136 ~V~~~~~~HNH~l~~ 150 (731)
.|+.+..+|||||.|
T Consensus 77 ~v~~~~~~HNH~L~P 91 (91)
T PF03101_consen 77 RVTSFVLEHNHPLCP 91 (91)
T ss_pred EEEECcCCcCCCCCC
Confidence 999999999999964
No 3
>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=99.62 E-value=5.9e-16 Score=134.25 Aligned_cols=68 Identities=25% Similarity=0.493 Sum_probs=65.5
Q ss_pred CcccccccCcceee---EEEecCCCCeeeeeehhccCCchhhHHHHHH----------------------HHHHhhCCCC
Q 004769 276 TTHRLDSYDMLFGI---WVGLDNHGMACFFGCVLLRDENMQSFSWSLK----------------------EAVAVEMPET 330 (731)
Q Consensus 276 ~Ty~tn~y~~pl~~---~~g~d~~~~~~~~a~al~~~E~~es~~W~l~----------------------~Ai~~vfP~a 330 (731)
+||+||+| +||+. ++|+|++|+.+|+||+|+.+|+.++|.|+|+ +||+++||++
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~p~~ii~D~~~~~~~Ai~~vfP~~ 79 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQKPKVIISDFDKALINAIKEVFPDA 79 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccCceeeeccccHHHHHHHHHHCCCc
Confidence 69999999 98886 9999999999999999999999999999999 9999999999
Q ss_pred CccccHHHHHHHhh
Q 004769 331 KHAVYIWHILAKLS 344 (731)
Q Consensus 331 ~h~lC~~Hi~~n~~ 344 (731)
.|++|.||+.+|++
T Consensus 80 ~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 80 RHQLCLFHILRNIK 93 (93)
T ss_pred eEehhHHHHHHhhC
Confidence 99999999999974
No 4
>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=99.51 E-value=3.5e-15 Score=162.54 Aligned_cols=233 Identities=18% Similarity=0.177 Sum_probs=172.7
Q ss_pred cCCcCCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhccccccHHHHHHHHHHhhcC
Q 004769 156 LLPAYCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVNRDYDAIDLIAMCKKMKDK 235 (731)
Q Consensus 156 ~l~shR~ls~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~~~~d~~~l~~~~~~~~~~ 235 (731)
+++.+++.++...+.|..|--.|+++++|...+....|. ..+.+.-|+++...... .+-+| +.....
T Consensus 92 ll~~y~r~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~----~~~S~s~vSri~~~~~~--------~~~~w-~~R~L~ 158 (381)
T PF00872_consen 92 LLPKYQRREDSLEELIISLYLKGVSTRDIEEALEELYGE----VAVSKSTVSRITKQLDE--------EVEAW-RNRPLE 158 (381)
T ss_pred ccchhhhhhhhhhhhhhhhhccccccccccchhhhhhcc----cccCchhhhhhhhhhhh--------hHHHH-hhhccc
Confidence 355666667777778888899999999999999887662 22455556555443311 11122 111111
Q ss_pred CCCcEEEEeecCCCCeeEEEecchhhHHHHHhcCCEEEecCccccccc-----CcceeeEEEecCCCCeeeeeehhccCC
Q 004769 236 NPNFQYDFKMDGHNRLEHIAWSYASSVQLYEAFGDALVFDTTHRLDSY-----DMLFGIWVGLDNHGMACFFGCVLLRDE 310 (731)
Q Consensus 236 np~~~~~~~~d~~~~~~~if~~~~~s~~~~~~f~~vl~~D~Ty~tn~y-----~~pl~~~~g~d~~~~~~~~a~al~~~E 310 (731)
+.. =++|.+|++|.+-+. +.++++++|+|..|+-.++|+.+...|
T Consensus 159 ~~~------------------------------y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~E 208 (381)
T PF00872_consen 159 SEP------------------------------YPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRE 208 (381)
T ss_pred ccc------------------------------ccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCC
Confidence 100 147889999987553 467899999999999999999999999
Q ss_pred chhhHHHHHH----------------------HHHHhhCCCCCccccHHHHHHHhhhccCcccCCChhhHHHHHHhHccC
Q 004769 311 NMQSFSWSLK----------------------EAVAVEMPETKHAVYIWHILAKLSDSLPTFLGSSYDDWKAEFYRLYNL 368 (731)
Q Consensus 311 ~~es~~W~l~----------------------~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~f~~~~~~ 368 (731)
+.++|.-+|+ .||.++||++.++.|.+|+++|+.+++.. +..+.+..+++.++.+
T Consensus 209 s~~~W~~~l~~L~~RGl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~---k~~~~v~~~Lk~I~~a 285 (381)
T PF00872_consen 209 SAASWREFLQDLKERGLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPK---KDRKEVKADLKAIYQA 285 (381)
T ss_pred ccCEeeecchhhhhccccccceeeccccccccccccccccchhhhhheechhhhhcccccc---ccchhhhhhccccccc
Confidence 9999999988 99999999999999999999999998865 3456788899999999
Q ss_pred CCHHHHHHHHHHhhhhcccccchHHHHHHH-hhccccccccccccccCcccCCccchHHHHHHHhhc
Q 004769 369 ELEEDFEEEWSKMVNKYGLREYKHITSLYA-LRTFWALPFLRHYFFAGLLSPCQSEAINAFIQRILS 434 (731)
Q Consensus 369 ~t~~eFe~~w~~l~~~~~~~~~~~l~~l~~-~r~~Wa~ay~~~~~~~g~~tt~r~Es~n~~lk~~l~ 434 (731)
.+.++....++++.+++...-......+-+ ..+.|+..-|+...+--+.|||.+|++|+.||+...
T Consensus 286 ~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~ 352 (381)
T PF00872_consen 286 PDKEEAREALEEFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTK 352 (381)
T ss_pred cccchhhhhhhhcccccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhcc
Confidence 999999999999988876644433333321 112334333556656678999999999999997543
No 5
>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=99.28 E-value=2.4e-11 Score=104.00 Aligned_cols=91 Identities=23% Similarity=0.322 Sum_probs=73.7
Q ss_pred cCCHHHHHHHHHHHHHhcCceEEEcceeccCCCCcceEEEEeeecCCCCCCCCCCCC-------------------c-cc
Q 004769 48 FVSQDAAYEFYCSFAKQCGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSDD-------------------G-KM 107 (731)
Q Consensus 48 F~S~eea~~~y~~yA~~~GF~ir~~~s~~~~~~gk~~~~~~~~C~r~G~~~~k~~~~-------------------~-~~ 107 (731)
|.+.+|+..|++.++...||.|++.+|..++ .+|.|--+|.++...... . ..
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~k--------i~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k 72 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKK--------IVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKK 72 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCce--------EEEEEecCCCccccccccccccccccccccccccccccccc
Confidence 8899999999999999999999999996543 579999888876544310 0 11
Q ss_pred cccCCcccccccceEEEEEeecCCCCcEEEEEEeCCccCCC
Q 004769 108 QRNRKSSRCGCQAYMRIVKRVDFDVPEWHVTGFSNVHNHEL 148 (731)
Q Consensus 108 ~r~~~s~rtgCpa~i~~~~~~~~~~~~W~V~~~~~~HNH~l 148 (731)
.....+.++.|||+|++..+. ..+.|.|..++..|||||
T Consensus 73 ~k~t~srk~~CPFriRA~yS~--k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 73 KKRTKSRKNTCPFRIRANYSK--KNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred CCcccccccCCCeEEEEEEEe--cCCeEEEEEecCCcCCCC
Confidence 122345679999999999887 789999999999999996
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.94 E-value=3.4e-10 Score=73.60 Aligned_cols=27 Identities=41% Similarity=0.808 Sum_probs=25.0
Q ss_pred eEeecCCcccCCcchhhHHHHhhcCCC
Q 004769 536 ISCSCHQFEFSGILCRHVLRVLSTDNC 562 (731)
Q Consensus 536 ~~CsC~~fe~~GiPC~Hil~vl~~~~i 562 (731)
.+|+|++||..||||+|+|+|+.+.++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 379999999999999999999998876
No 7
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.87 E-value=3.6e-08 Score=105.61 Aligned_cols=238 Identities=15% Similarity=0.123 Sum_probs=158.7
Q ss_pred cCCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhccccccHHHHHHHHHHhhcCCCC
Q 004769 159 AYCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVNRDYDAIDLIAMCKKMKDKNPN 238 (731)
Q Consensus 159 shR~ls~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~~~~d~~~l~~~~~~~~~~np~ 238 (731)
.+++.....-..|..|-..|+++++|-.+++.+.+. .+.+.-++.+-. .+.+.+...+..-.
T Consensus 81 ~~~r~~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~-----~~s~~~iS~~~~------------~~~e~v~~~~~r~l- 142 (379)
T COG3328 81 RYQRRERALDLPVLSMYAKGVTTREIEALLEELYGH-----KVSPSVISVVTD------------RLDEKVKAWQNRPL- 142 (379)
T ss_pred hhHhhhhhHHHHHHHHHHcCCcHHHHHHHHHHhhCc-----ccCHHHhhhHHH------------HHHHHHHHHHhccc-
Confidence 333434445556778889999999999999876542 222222322211 22233333222211
Q ss_pred cEEEEeecCCCCeeEEEecchhhHHHHHhcCCEEEecCcccccc--cCcceeeEEEecCCCCeeeeeehhccCCchhhHH
Q 004769 239 FQYDFKMDGHNRLEHIAWSYASSVQLYEAFGDALVFDTTHRLDS--YDMLFGIWVGLDNHGMACFFGCVLLRDENMQSFS 316 (731)
Q Consensus 239 ~~~~~~~d~~~~~~~if~~~~~s~~~~~~f~~vl~~D~Ty~tn~--y~~pl~~~~g~d~~~~~~~~a~al~~~E~~es~~ 316 (731)
+ --.+|.+|++|.+-+ -+..++.++|++.+|+-.++|+-+-..|+ ..|.
T Consensus 143 --~--------------------------~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~ 193 (379)
T COG3328 143 --G--------------------------DYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWL 193 (379)
T ss_pred --c--------------------------CceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHH
Confidence 0 114788999999877 56789999999999999999999999999 8888
Q ss_pred -HHHH---------------------HHHHhhCCCCCccccHHHHHHHhhhccCcccCCChhhHHHHHHhHccCCCHHHH
Q 004769 317 -WSLK---------------------EAVAVEMPETKHAVYIWHILAKLSDSLPTFLGSSYDDWKAEFYRLYNLELEEDF 374 (731)
Q Consensus 317 -W~l~---------------------~Ai~~vfP~a~h~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~f~~~~~~~t~~eF 374 (731)
|+.. +||..+||.+.++.|.-|+.+|+..+... +..+.....+..++.+.+.++-
T Consensus 194 ~~l~~l~~rgl~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~---k~~d~i~~~~~~I~~a~~~e~~ 270 (379)
T COG3328 194 SFLLDLKNRGLSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPR---KDQDAVLSDLRSIYIAPDAEEA 270 (379)
T ss_pred HHHHHHHhccccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhh---hhhHHHHhhhhhhhccCCcHHH
Confidence 5555 89999999999999999999999887654 3455677788888989999998
Q ss_pred HHHHHHhhhhcccccc----hHHHHHHHhhccccccccccccccCcccCCccchHHHHHHHhhcc--cchHHHHHHHHHH
Q 004769 375 EEEWSKMVNKYGLREY----KHITSLYALRTFWALPFLRHYFFAGLLSPCQSEAINAFIQRILSA--QSQLDRFVERVAE 448 (731)
Q Consensus 375 e~~w~~l~~~~~~~~~----~~l~~l~~~r~~Wa~ay~~~~~~~g~~tt~r~Es~n~~lk~~l~~--~~~l~~f~~~~~~ 448 (731)
...|..+.+.+...-. .|...+ -+.|...-|.....--+.|||.+|++|..++..... ..+-.+++..+..
T Consensus 271 ~~~~~~~~~~w~~~yP~i~~~~~~~~---~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~~y 347 (379)
T COG3328 271 LLALLAFSELWGKRYPAILKSWRNAL---EELLPFFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNEESVEKLVY 347 (379)
T ss_pred HHHHHHHHHhhhhhcchHHHHHHHHH---HHhcccccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCHHHHHHHHH
Confidence 8888887764442222 222222 122221111111113467999999999988866543 4455555554443
Q ss_pred H
Q 004769 449 I 449 (731)
Q Consensus 449 ~ 449 (731)
.
T Consensus 348 ~ 348 (379)
T COG3328 348 L 348 (379)
T ss_pred H
Confidence 3
No 8
>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=98.42 E-value=1.1e-06 Score=70.82 Aligned_cols=66 Identities=23% Similarity=0.353 Sum_probs=55.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHHHhcCceEEEcceeccCCCCcceEEEEeeecCCCCCCCCCCCCccccccCCccccccc
Q 004769 40 LVPFIGQRFVSQDAAYEFYCSFAKQCGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSDDGKMQRNRKSSRCGCQ 119 (731)
Q Consensus 40 ~~P~~g~~F~S~eea~~~y~~yA~~~GF~ir~~~s~~~~~~gk~~~~~~~~C~r~G~~~~k~~~~~~~~r~~~s~rtgCp 119 (731)
....+||+|+|.+|+..++..||..+||.++..+|.+ .++...|.. .|||
T Consensus 2 ~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~--------~r~~~~C~~----------------------~~C~ 51 (67)
T PF03108_consen 2 PELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDK--------KRYRAKCKD----------------------KGCP 51 (67)
T ss_pred CccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCC--------EEEEEEEcC----------------------CCCC
Confidence 4568999999999999999999999999999988743 356789962 2699
Q ss_pred ceEEEEEeecCCCCcEEE
Q 004769 120 AYMRIVKRVDFDVPEWHV 137 (731)
Q Consensus 120 a~i~~~~~~~~~~~~W~V 137 (731)
|+|++.+.. ..+.|.|
T Consensus 52 Wrv~as~~~--~~~~~~I 67 (67)
T PF03108_consen 52 WRVRASKRK--RSDTFQI 67 (67)
T ss_pred EEEEEEEcC--CCCEEEC
Confidence 999999876 5788875
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=98.24 E-value=8.9e-07 Score=63.34 Aligned_cols=29 Identities=41% Similarity=0.787 Sum_probs=26.0
Q ss_pred CCCceEeecCCcccCCcchhhHHHHhhcC
Q 004769 532 CQEHISCSCHQFEFSGILCRHVLRVLSTD 560 (731)
Q Consensus 532 ~~~~~~CsC~~fe~~GiPC~Hil~vl~~~ 560 (731)
.....+|+|..|+..|.||+|+++|+..+
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHhh
Confidence 35689999999999999999999998764
No 10
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=94.90 E-value=0.018 Score=40.25 Aligned_cols=22 Identities=27% Similarity=0.560 Sum_probs=18.4
Q ss_pred ccCCccCCCCCCC--CCCCCcCcC
Q 004769 700 CSEPCCRHFGHDA--SSCPIMGSD 721 (731)
Q Consensus 700 ~~Cs~C~~~gHn~--~tCp~~~~~ 721 (731)
++|..|++.||.+ ++||.+...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~ 25 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWS 25 (40)
T ss_pred ccccccccccccccCccCCCCCCC
Confidence 4699999999977 669998754
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=94.83 E-value=0.13 Score=40.06 Aligned_cols=57 Identities=23% Similarity=0.481 Sum_probs=40.7
Q ss_pred cCceEEEcceeccCCCCcceEEEEeeecCCCCCCCCCCCCccccccCCcccccccceEEEEEeecCCCCcEEEEEEeCCc
Q 004769 65 CGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSDDGKMQRNRKSSRCGCQAYMRIVKRVDFDVPEWHVTGFSNVH 144 (731)
Q Consensus 65 ~GF~ir~~~s~~~~~~gk~~~~~~~~C~r~G~~~~k~~~~~~~~r~~~s~rtgCpa~i~~~~~~~~~~~~W~V~~~~~~H 144 (731)
-||..|+--.+.-++. ..-+.+|.|+.. +|||+=.|.+.. .++.-.++....+|
T Consensus 3 Dgy~WRKYGqK~i~g~--~~pRsYYrCt~~----------------------~C~akK~Vqr~~--~d~~~~~vtY~G~H 56 (60)
T PF03106_consen 3 DGYRWRKYGQKNIKGS--PYPRSYYRCTHP----------------------GCPAKKQVQRSA--DDPNIVIVTYEGEH 56 (60)
T ss_dssp SSS-EEEEEEEEETTT--TCEEEEEEEECT----------------------TEEEEEEEEEET--TCCCEEEEEEES--
T ss_pred CCCchhhccCcccCCC--ceeeEeeecccc----------------------ChhheeeEEEec--CCCCEEEEEEeeee
Confidence 4888888777655544 456778999742 799999998875 46778888999999
Q ss_pred cCC
Q 004769 145 NHE 147 (731)
Q Consensus 145 NH~ 147 (731)
||+
T Consensus 57 ~h~ 59 (60)
T PF03106_consen 57 NHP 59 (60)
T ss_dssp SS-
T ss_pred CCC
Confidence 997
No 12
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=94.71 E-value=0.025 Score=32.58 Aligned_cols=17 Identities=35% Similarity=0.532 Sum_probs=15.7
Q ss_pred cCCccCCCCCCCCCCCC
Q 004769 701 SEPCCRHFGHDASSCPI 717 (731)
Q Consensus 701 ~Cs~C~~~gHn~~tCp~ 717 (731)
+|-+|++.||..+.||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 48899999999999995
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=92.88 E-value=0.088 Score=54.19 Aligned_cols=73 Identities=12% Similarity=0.084 Sum_probs=47.4
Q ss_pred EEecCcccccccCcceeeEEEecC--CCCeeeeeehhccCCchhhHHHHHH-----------------------HHHHhh
Q 004769 272 LVFDTTHRLDSYDMLFGIWVGLDN--HGMACFFGCVLLRDENMQSFSWSLK-----------------------EAVAVE 326 (731)
Q Consensus 272 l~~D~Ty~tn~y~~pl~~~~g~d~--~~~~~~~a~al~~~E~~es~~W~l~-----------------------~Ai~~v 326 (731)
|+||=+.......- +..+.+|. .+..++ .++.+-+.+++.-+|. .||++.
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~il---~i~~~r~~~~l~~~~~~~~~~~~~~~v~~V~~Dm~~~y~~~~~~~ 75 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGRIL---DILPGRDKETLKDFFRSLYPEEERKNVKVVSMDMSPPYRSAIREY 75 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCceEE---EEcCCccHHHHHHHHHHhCccccccceEEEEcCCCcccccccccc
Confidence 35555544433331 33334444 333333 3677777777666555 899999
Q ss_pred CCCCCccccHHHHHHHhhhccCc
Q 004769 327 MPETKHAVYIWHILAKLSDSLPT 349 (731)
Q Consensus 327 fP~a~h~lC~~Hi~~n~~~~~~~ 349 (731)
||+|.+.+-.|||++++.+.+..
T Consensus 76 ~P~A~iv~DrFHvvk~~~~al~~ 98 (249)
T PF01610_consen 76 FPNAQIVADRFHVVKLANRALDK 98 (249)
T ss_pred ccccccccccchhhhhhhhcchh
Confidence 99999999999999998765543
No 14
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=92.13 E-value=0.071 Score=35.46 Aligned_cols=24 Identities=21% Similarity=0.303 Sum_probs=20.2
Q ss_pred ccccCCccCCCCCCCCCCCCcCcC
Q 004769 698 RHCSEPCCRHFGHDASSCPIMGSD 721 (731)
Q Consensus 698 r~~~Cs~C~~~gHn~~tCp~~~~~ 721 (731)
-.+.|-.|++.||-++-||....+
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~~Pk 30 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTNKPK 30 (32)
T ss_pred CCCEeecCCCCCccHhHCCCCCCC
Confidence 456699999999999999996554
No 15
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=88.53 E-value=0.29 Score=54.40 Aligned_cols=30 Identities=27% Similarity=0.452 Sum_probs=23.6
Q ss_pred cCCccccCCccCCCCCCC--CCCCCcCcCCcc
Q 004769 695 RKRRHCSEPCCRHFGHDA--SSCPIMGSDTLN 724 (731)
Q Consensus 695 ~k~r~~~Cs~C~~~gHn~--~tCp~~~~~~~~ 724 (731)
+|..+.+|+.||+.||-+ +.||++++++-.
T Consensus 933 RK~Ttr~C~nCGQvGHmkTNK~CP~f~s~~~~ 964 (968)
T COG5179 933 RKNTTRTCGNCGQVGHMKTNKACPKFSSKDNP 964 (968)
T ss_pred CCCcceecccccccccccccccCccccCCCCC
Confidence 445577899999999954 569999998753
No 16
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=86.70 E-value=1.2 Score=41.08 Aligned_cols=79 Identities=19% Similarity=0.222 Sum_probs=55.4
Q ss_pred cchhhHHHHhhhcCCcHHHHHHHHHHhhCcc----------------CCCCCcchhhhhhhHHHhhhc------------
Q 004769 165 PDDKTRICMFAKAGMSVRQMLRLMELEKGVK----------------LGCLPFTEIDVRNLLQSFRNV------------ 216 (731)
Q Consensus 165 ~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~----------------~~~~~~~~~Di~N~~~~~r~~------------ 216 (731)
++..+.|..|.+.|++|+||=-+|+.++|+. .+-.|-.+.|++|+..+....
T Consensus 31 eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~~L~~ri~~L~~HL~~nkKD~~ 110 (151)
T PRK08561 31 EEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRKHLEENPKDLH 110 (151)
T ss_pred HHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHhCCCcch
Confidence 3456778899999999999999999998651 122344668999987765422
Q ss_pred ------cccccHHHHHHHHHHhhcCCCCcEEEE
Q 004769 217 ------NRDYDAIDLIAMCKKMKDKNPNFQYDF 243 (731)
Q Consensus 217 ------~~~~d~~~l~~~~~~~~~~np~~~~~~ 243 (731)
...+....|++|+++...--|+|.|.-
T Consensus 111 skRgL~~~~skrrRLl~Yyk~~~~LP~~WkY~~ 143 (151)
T PRK08561 111 NKRGLQLIESKIRRLVKYYKRTGVLPADWRYSP 143 (151)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCCCCcCCH
Confidence 123345578888877666677777753
No 17
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=86.48 E-value=29 Score=39.29 Aligned_cols=52 Identities=27% Similarity=0.401 Sum_probs=39.4
Q ss_pred CCcCCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHh
Q 004769 157 LPAYCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSF 213 (731)
Q Consensus 157 l~shR~ls~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~ 213 (731)
+..+.++|+..+..|..+... ++-+++.+.|....| .+.++..-|.|.+...
T Consensus 112 l~~~~R~S~~~~~~i~~~a~~-~sYr~aa~~l~~~~~----~~~iS~~tV~~~v~~~ 163 (470)
T PF06782_consen 112 LKKYQRISPELKEKIVELATE-MSYRKAAEILEELLG----NVSISKQTVWNIVKEA 163 (470)
T ss_pred CCcccchhHHHHHHHHHHHhh-cCHHHHHHHHhhccC----CCccCHHHHHHHHHhc
Confidence 467889999999998877644 888999888865443 3557778888877754
No 18
>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=86.47 E-value=1.4 Score=34.08 Aligned_cols=57 Identities=21% Similarity=0.381 Sum_probs=39.3
Q ss_pred cCceEEEcceeccCCCCcceEEEEeeecCCCCCCCCCCCCccccccCCcccccccceEEEEEeecCCCCcEEEEEEeCCc
Q 004769 65 CGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSDDGKMQRNRKSSRCGCQAYMRIVKRVDFDVPEWHVTGFSNVH 144 (731)
Q Consensus 65 ~GF~ir~~~s~~~~~~gk~~~~~~~~C~r~G~~~~k~~~~~~~~r~~~s~rtgCpa~i~~~~~~~~~~~~W~V~~~~~~H 144 (731)
-||..|+--.+..++. ..-|.+|.|+.. .||||+=.|.+.. +++.-.++....+|
T Consensus 3 DGy~WRKYGQK~ikgs--~~pRsYYrCt~~---------------------~~C~a~K~Vq~~~--~d~~~~~vtY~g~H 57 (59)
T smart00774 3 DGYQWRKYGQKVIKGS--PFPRSYYRCTYS---------------------QGCPAKKQVQRSD--DDPSVVEVTYEGEH 57 (59)
T ss_pred CcccccccCcEecCCC--cCcceEEecccc---------------------CCCCCcccEEEEC--CCCCEEEEEEeeEe
Confidence 3777777655544433 344667888751 3799988787764 45777888889999
Q ss_pred cC
Q 004769 145 NH 146 (731)
Q Consensus 145 NH 146 (731)
||
T Consensus 58 ~h 59 (59)
T smart00774 58 TH 59 (59)
T ss_pred CC
Confidence 98
No 19
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=79.56 E-value=0.73 Score=34.35 Aligned_cols=17 Identities=29% Similarity=0.614 Sum_probs=15.9
Q ss_pred cCCccCCCCCCCCCCCC
Q 004769 701 SEPCCRHFGHDASSCPI 717 (731)
Q Consensus 701 ~Cs~C~~~gHn~~tCp~ 717 (731)
.|..|+..||..+.||+
T Consensus 33 ~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 33 FCFHCGRIGHSDKECPK 49 (49)
T ss_pred hhcCCCCcCcCHhHcCC
Confidence 59999999999999995
No 20
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=77.02 E-value=2.2 Score=30.92 Aligned_cols=30 Identities=27% Similarity=0.626 Sum_probs=15.1
Q ss_pred CCCCCcchhhHHHHhhhcCCcHHHHHHHHH
Q 004769 160 YCSITPDDKTRICMFAKAGMSVRQMLRLME 189 (731)
Q Consensus 160 hR~ls~~~k~~i~~l~~~g~~~~~I~~~l~ 189 (731)
+++||.+++..|..|.+.|.+.++|.+.|.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg 31 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLG 31 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHC
Confidence 467999999999999999999999987764
No 21
>smart00343 ZnF_C2HC zinc finger.
Probab=75.00 E-value=1.6 Score=27.65 Aligned_cols=19 Identities=32% Similarity=0.436 Sum_probs=16.1
Q ss_pred cCCccCCCCCCCCCCCCcC
Q 004769 701 SEPCCRHFGHDASSCPIMG 719 (731)
Q Consensus 701 ~Cs~C~~~gHn~~tCp~~~ 719 (731)
.|.+|++.||..+.||...
T Consensus 1 ~C~~CG~~GH~~~~C~~~~ 19 (26)
T smart00343 1 KCYNCGKEGHIARDCPKXX 19 (26)
T ss_pred CCccCCCCCcchhhCCccc
Confidence 3889999999999999543
No 22
>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=72.64 E-value=5.1 Score=30.87 Aligned_cols=25 Identities=28% Similarity=0.381 Sum_probs=10.5
Q ss_pred ccccceEEEEEeecCCCCcEEEEEEeCCccC
Q 004769 116 CGCQAYMRIVKRVDFDVPEWHVTGFSNVHNH 146 (731)
Q Consensus 116 tgCpa~i~~~~~~~~~~~~W~V~~~~~~HNH 146 (731)
.+|+|++.+.. +.-.|.....+|||
T Consensus 38 ~~C~a~~~~~~------~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITDA------GDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE--------TTEEEE-S---SS
T ss_pred CCCeEEEEEEC------CCCEEEECCCccCC
Confidence 58999998761 22356666689999
No 23
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=69.76 E-value=16 Score=36.63 Aligned_cols=31 Identities=29% Similarity=0.484 Sum_probs=24.3
Q ss_pred cCCccccCCccCCCC---CCCCCCCCcCcCCcch
Q 004769 695 RKRRHCSEPCCRHFG---HDASSCPIMGSDTLNA 725 (731)
Q Consensus 695 ~k~r~~~Cs~C~~~g---Hn~~tCp~~~~~~~~~ 725 (731)
.+-|.+-|+.||..| |+++-||+....+++.
T Consensus 264 PkLR~YVCPiCGATgDnAHTiKyCPl~~~~~~s~ 297 (318)
T KOG4602|consen 264 PKLRSYVCPICGATGDNAHTIKYCPLAFGDDTSV 297 (318)
T ss_pred hhHhhhcCccccccCCcccceecccccCCCCccc
Confidence 445778899999665 7788899999887763
No 24
>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=68.65 E-value=9 Score=41.88 Aligned_cols=55 Identities=16% Similarity=0.283 Sum_probs=45.8
Q ss_pred CCCccCCHHHHHHHHHHHHHhcCceEEEcceeccCCCCcceEEEEeeecCCCCCCCCCCCCccccccCCcccccccceEE
Q 004769 44 IGQRFVSQDAAYEFYCSFAKQCGFSIRRHRTRGKDGVGRGVTRRDFTCHRGGFPQMKPSDDGKMQRNRKSSRCGCQAYMR 123 (731)
Q Consensus 44 ~g~~F~S~eea~~~y~~yA~~~GF~ir~~~s~~~~~~gk~~~~~~~~C~r~G~~~~k~~~~~~~~r~~~s~rtgCpa~i~ 123 (731)
.+..|++.++-|..+|.|.....--|..+.|.+.+ ..+|.|... .|||+|.
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk-------hftfachlk----------------------~c~fkil 74 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK-------HFTFACHLK----------------------NCPFKIL 74 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeeccccccc-------ceEEEeecc----------------------CCCceee
Confidence 35679999999999999999999999988887654 358999752 6999998
Q ss_pred EEEe
Q 004769 124 IVKR 127 (731)
Q Consensus 124 ~~~~ 127 (731)
+...
T Consensus 75 lsy~ 78 (496)
T PF04684_consen 75 LSYC 78 (496)
T ss_pred eeec
Confidence 8754
No 25
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=59.28 E-value=15 Score=36.61 Aligned_cols=70 Identities=14% Similarity=0.291 Sum_probs=51.8
Q ss_pred CCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhc--cc---------cccHHHHHHH
Q 004769 160 YCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNV--NR---------DYDAIDLIAM 228 (731)
Q Consensus 160 hR~ls~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~--~~---------~~d~~~l~~~ 228 (731)
-|.|..+.+-.|.+|...|++|..|-+.|+-.+|. +..+++++... .+ .-..-.+.+|
T Consensus 18 GRPLPna~RlrIVELarlGiRPCDISRQLrvSHGC-----------VSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~ 86 (334)
T KOG3517|consen 18 GRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGC-----------VSKILARYNETGSILPGAIGGSKPRVTTPKVVKY 86 (334)
T ss_pred CccCcchhhhhHHHHHHcCCCccchhhhhhhccch-----------HHHHHHHhccCCcccccccCCCCCccCChhHHHH
Confidence 46677888889999999999999999999988774 23344443321 11 1244589999
Q ss_pred HHHhhcCCCCcE
Q 004769 229 CKKMKDKNPNFQ 240 (731)
Q Consensus 229 ~~~~~~~np~~~ 240 (731)
++.++..||+.|
T Consensus 87 IR~~Kq~DPGIF 98 (334)
T KOG3517|consen 87 IRSLKQRDPGIF 98 (334)
T ss_pred HHHhhccCCcee
Confidence 999999999964
No 26
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=59.26 E-value=9.7 Score=34.08 Aligned_cols=38 Identities=24% Similarity=0.451 Sum_probs=29.6
Q ss_pred CCcCCCC-CcchhhHHHHhhhcCCcHHHHHHHHHHhhCc
Q 004769 157 LPAYCSI-TPDDKTRICMFAKAGMSVRQMLRLMELEKGV 194 (731)
Q Consensus 157 l~shR~l-s~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~ 194 (731)
.|++-++ .++.+++|..|.+.|++|+||--+|+..+|.
T Consensus 22 ~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi 60 (151)
T KOG0400|consen 22 VPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGI 60 (151)
T ss_pred CcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCc
Confidence 3444444 4556889999999999999998888888875
No 27
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=55.92 E-value=16 Score=33.05 Aligned_cols=71 Identities=18% Similarity=0.323 Sum_probs=42.1
Q ss_pred cCCCCCcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhc-------c----ccccHHHHHH
Q 004769 159 AYCSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNV-------N----RDYDAIDLIA 227 (731)
Q Consensus 159 shR~ls~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~-------~----~~~d~~~l~~ 227 (731)
.-|.|+.+.+..|..|...|++|.+|...|.-.+|. |+.++.++++. . ..--...+..
T Consensus 14 nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gc-----------VsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~ 82 (125)
T PF00292_consen 14 NGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGC-----------VSKILSRYRETGSIRPGPIGGSKPRVATPEVVE 82 (125)
T ss_dssp TTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHH-----------HHHHHHHHHHHS-SS----S----SSS-HCHHH
T ss_pred CCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhH-----------HHHHHHHHHHhcccCcccccCCCCCCCChHHHH
Confidence 346778888999999999999999998887655542 44455544422 0 0112234666
Q ss_pred HHHHhhcCCCCcE
Q 004769 228 MCKKMKDKNPNFQ 240 (731)
Q Consensus 228 ~~~~~~~~np~~~ 240 (731)
++...+.+||..|
T Consensus 83 ~I~~~k~enP~if 95 (125)
T PF00292_consen 83 KIEQYKRENPTIF 95 (125)
T ss_dssp HHHHHHHH-TTS-
T ss_pred HHHHHHhcCCCcc
Confidence 7777888899864
No 28
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=55.91 E-value=19 Score=33.16 Aligned_cols=48 Identities=25% Similarity=0.393 Sum_probs=35.3
Q ss_pred cchhhHHHHhhhcCCcHHHHHHHHHHhhCc----------------cCCCCCcchhhhhhhHHH
Q 004769 165 PDDKTRICMFAKAGMSVRQMLRLMELEKGV----------------KLGCLPFTEIDVRNLLQS 212 (731)
Q Consensus 165 ~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~----------------~~~~~~~~~~Di~N~~~~ 212 (731)
++..+.|..|.+.|++|+||--+|+.++|. ..+..|-.+.|+|.++.+
T Consensus 28 eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~vtG~kI~rILk~~Glap~iPeDly~LikK 91 (148)
T PTZ00072 28 SEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNVTGSKILRILKKNGLAPEIPEDLYFLIKK 91 (148)
T ss_pred HHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeeccchHHHHHHHhcCCCCCCchHHHHHHHH
Confidence 345677889999999999999999988843 122345566777777655
No 29
>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=51.68 E-value=11 Score=29.29 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=25.4
Q ss_pred CCC-cchhhHHHHhhhcCCcHHHHHHHHHHhhC
Q 004769 162 SIT-PDDKTRICMFAKAGMSVRQMLRLMELEKG 193 (731)
Q Consensus 162 ~ls-~~~k~~i~~l~~~g~~~~~I~~~l~~~~g 193 (731)
+++ ++..+.|..|.+.|++|+||=-+|+.++|
T Consensus 27 ~~~~~eVe~~I~klakkG~tpSqIG~iLRD~~G 59 (60)
T PF08069_consen 27 KYSPEEVEELIVKLAKKGLTPSQIGVILRDQYG 59 (60)
T ss_dssp -S-HHHHHHHHHHHCCTTHCHHHHHHHHHHSCT
T ss_pred CCCHHHHHHHHHHHHHcCCCHHHhhhhhhhccC
Confidence 344 34567788999999999999999998876
No 30
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=49.39 E-value=5.9 Score=30.19 Aligned_cols=21 Identities=29% Similarity=0.531 Sum_probs=8.7
Q ss_pred ccccCCccCC---CCCCCCCCCCc
Q 004769 698 RHCSEPCCRH---FGHDASSCPIM 718 (731)
Q Consensus 698 r~~~Cs~C~~---~gHn~~tCp~~ 718 (731)
|.+.|+.|+. ..|+.+-||++
T Consensus 32 r~y~Cp~CgAtGd~AHT~~yCP~k 55 (55)
T PF05741_consen 32 RKYVCPICGATGDNAHTIKYCPKK 55 (55)
T ss_dssp GG---TTT---GGG---GGG-TT-
T ss_pred hcCcCCCCcCcCccccccccCcCC
Confidence 5678999996 55777779975
No 31
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=40.50 E-value=25 Score=25.48 Aligned_cols=28 Identities=14% Similarity=0.268 Sum_probs=20.8
Q ss_pred CCCCcchhhHHHHhhhcCCcHHHHHHHH
Q 004769 161 CSITPDDKTRICMFAKAGMSVRQMLRLM 188 (731)
Q Consensus 161 R~ls~~~k~~i~~l~~~g~~~~~I~~~l 188 (731)
+.+++++.+.|..|...|++..+|.+.+
T Consensus 4 ~~~~~~~~~~i~~l~~~G~si~~IA~~~ 31 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGMSIAEIAKQF 31 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--HHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 4567777888999999999999987654
No 32
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=39.96 E-value=67 Score=27.82 Aligned_cols=20 Identities=30% Similarity=0.667 Sum_probs=15.1
Q ss_pred EeecCCccc-----CCcchhhHHHH
Q 004769 537 SCSCHQFEF-----SGILCRHVLRV 556 (731)
Q Consensus 537 ~CsC~~fe~-----~GiPC~Hil~v 556 (731)
.|||..|-. ---||.|++.+
T Consensus 51 fCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 51 FCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred cccCHHHHhHhhhcCcccchhhhhe
Confidence 899999862 23469999864
No 33
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.19 E-value=21 Score=30.94 Aligned_cols=10 Identities=20% Similarity=0.398 Sum_probs=7.6
Q ss_pred CccccCCccC
Q 004769 697 RRHCSEPCCR 706 (731)
Q Consensus 697 ~r~~~Cs~C~ 706 (731)
.....|+.|+
T Consensus 19 pt~f~CP~Cg 28 (99)
T PRK14892 19 PKIFECPRCG 28 (99)
T ss_pred CcEeECCCCC
Confidence 4566699998
No 34
>PF11433 DUF3198: Protein of unknown function (DUF3198); InterPro: IPR024504 This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.; PDB: 1X9B_A.
Probab=38.95 E-value=34 Score=24.94 Aligned_cols=45 Identities=13% Similarity=0.084 Sum_probs=31.2
Q ss_pred HHHHhHccCCCHHHHHHHHHHhhhhcccccchHHHHHHHhhcccc
Q 004769 360 AEFYRLYNLELEEDFEEEWSKMVNKYGLREYKHITSLYALRTFWA 404 (731)
Q Consensus 360 ~~f~~~~~~~t~~eFe~~w~~l~~~~~~~~~~~l~~l~~~r~~Wa 404 (731)
..|..+.++++..+|-....+|-..-.--+..|...|-+-+++|-
T Consensus 5 ~~Fe~~InS~SK~~Fv~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 49 (51)
T PF11433_consen 5 IKFESYINSESKSVFVRNLTELERISKRLGKSYQIRLEEAKEKWK 49 (51)
T ss_dssp HHHHHHHHS--HHHHHHHHHHHHHHHHHH-SHHHHHHHHHHHHH-
T ss_pred HHHHHHhCCccHHHHHHhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 468889999999999999888765332334568888878888884
No 35
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=38.64 E-value=13 Score=39.73 Aligned_cols=19 Identities=26% Similarity=0.716 Sum_probs=17.4
Q ss_pred cCCccCCCCCCCCCCCCcC
Q 004769 701 SEPCCRHFGHDASSCPIMG 719 (731)
Q Consensus 701 ~Cs~C~~~gHn~~tCp~~~ 719 (731)
.|.+|++.||.++-||+..
T Consensus 572 GCayCgGLGHRItdCPKle 590 (610)
T KOG0341|consen 572 GCAYCGGLGHRITDCPKLE 590 (610)
T ss_pred ccccccCCCcccccCchhh
Confidence 4999999999999999864
No 36
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=32.75 E-value=28 Score=29.85 Aligned_cols=11 Identities=27% Similarity=0.640 Sum_probs=7.8
Q ss_pred CccccCCccCC
Q 004769 697 RRHCSEPCCRH 707 (731)
Q Consensus 697 ~r~~~Cs~C~~ 707 (731)
+++..|+.|+.
T Consensus 20 ~k~FtCp~Cgh 30 (104)
T COG4888 20 PKTFTCPRCGH 30 (104)
T ss_pred CceEecCccCC
Confidence 45667888864
No 37
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=27.65 E-value=43 Score=34.38 Aligned_cols=27 Identities=19% Similarity=0.313 Sum_probs=23.4
Q ss_pred cccCCccCCCCCCCCCCCCcCcCCcch
Q 004769 699 HCSEPCCRHFGHDASSCPIMGSDTLNA 725 (731)
Q Consensus 699 ~~~Cs~C~~~gHn~~tCp~~~~~~~~~ 725 (731)
-+-|=+||+.||-+..||.+.++..++
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~Dpnfdg 202 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQDPNFDG 202 (427)
T ss_pred ceeEEecCCCCchhhcCCCCCCCCccc
Confidence 345999999999999999999887665
No 38
>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=27.55 E-value=86 Score=23.91 Aligned_cols=26 Identities=15% Similarity=0.135 Sum_probs=20.4
Q ss_pred hHHHHhhhcCCcHHHHHHHHHHhhCc
Q 004769 169 TRICMFAKAGMSVRQMLRLMELEKGV 194 (731)
Q Consensus 169 ~~i~~l~~~g~~~~~I~~~l~~~~g~ 194 (731)
..|+......++..++++.|..+.++
T Consensus 3 ~lIErCl~~yMsk~E~v~~L~~~a~I 28 (54)
T PF09713_consen 3 NLIERCLQLYMSKEECVRALQKQANI 28 (54)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHcCC
Confidence 45777777888999999999877655
No 39
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=27.26 E-value=60 Score=24.34 Aligned_cols=29 Identities=24% Similarity=0.453 Sum_probs=21.1
Q ss_pred CCCcchhhHHHHhhhcCCcHHHHHHHHHH
Q 004769 162 SITPDDKTRICMFAKAGMSVRQMLRLMEL 190 (731)
Q Consensus 162 ~ls~~~k~~i~~l~~~g~~~~~I~~~l~~ 190 (731)
.|++.++.+|..|.+.|++..+|-..+..
T Consensus 4 ~Lt~~Eqaqid~m~qlG~s~~~isr~i~R 32 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQLGMSLREISRRIGR 32 (50)
T ss_dssp ---HHHHHHHHHHHHTT--HHHHHHHHT-
T ss_pred cCCHHHHHHHHHHHHhchhHHHHHHHhCc
Confidence 47889999999999999999999887753
No 40
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=26.84 E-value=50 Score=33.36 Aligned_cols=20 Identities=25% Similarity=0.431 Sum_probs=15.5
Q ss_pred cccCCcccccccceEEEEEe
Q 004769 108 QRNRKSSRCGCQAYMRIVKR 127 (731)
Q Consensus 108 ~r~~~s~rtgCpa~i~~~~~ 127 (731)
.+...+.+.+|||+|+++..
T Consensus 70 ~~~~~skK~~CPA~I~Ik~I 89 (225)
T PF15299_consen 70 RRSKPSKKRDCPARIYIKEI 89 (225)
T ss_pred cccccccCCCCCeEEEEEEE
Confidence 44556789999999998743
No 41
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=26.42 E-value=34 Score=34.60 Aligned_cols=24 Identities=25% Similarity=0.592 Sum_probs=19.7
Q ss_pred ceEeecCCcccCCcchhhHHHHhhcCC
Q 004769 535 HISCSCHQFEFSGILCRHVLRVLSTDN 561 (731)
Q Consensus 535 ~~~CsC~~fe~~GiPC~Hil~vl~~~~ 561 (731)
...|||-.| ..||.||-+|.-++.
T Consensus 124 ~~dCSCPD~---anPCKHi~AvyY~la 147 (266)
T COG4279 124 STDCSCPDY---ANPCKHIAAVYYLLA 147 (266)
T ss_pred ccccCCCCc---ccchHHHHHHHHHHH
Confidence 567999998 479999999986654
No 42
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=25.61 E-value=42 Score=30.66 Aligned_cols=22 Identities=23% Similarity=0.427 Sum_probs=18.9
Q ss_pred CccccCCccCCCCCCCCCCCCcC
Q 004769 697 RRHCSEPCCRHFGHDASSCPIMG 719 (731)
Q Consensus 697 ~r~~~Cs~C~~~gHn~~tCp~~~ 719 (731)
...+.|..|+ -+|-...||.+.
T Consensus 104 ~~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 104 KSKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred CceEEeCCCC-CCcccccCCccc
Confidence 4567799997 899999999875
No 43
>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=24.90 E-value=1.2e+02 Score=31.33 Aligned_cols=43 Identities=9% Similarity=0.143 Sum_probs=28.3
Q ss_pred chhhHHHHh-hhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhh
Q 004769 166 DDKTRICMF-AKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFR 214 (731)
Q Consensus 166 ~~k~~i~~l-~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r 214 (731)
.....|..+ ...++|-..|.+++... | +.+....|.|+..+..
T Consensus 7 ~~~a~i~~l~~~~~lp~~r~~~~~~~~-G-----~~is~~ti~~~~~~~~ 50 (271)
T PF03050_consen 7 SLLALIAYLKYVYHLPLYRIQQMLEDL-G-----ITISRGTIANWIKRVA 50 (271)
T ss_pred HHHHHHHHHHhcCCCCHHHHhhhhhcc-c-----eeeccchhHhHhhhhh
Confidence 344444433 46678888888888765 4 4567777888776653
No 44
>smart00351 PAX Paired Box domain.
Probab=24.82 E-value=2e+02 Score=26.00 Aligned_cols=68 Identities=15% Similarity=0.244 Sum_probs=45.4
Q ss_pred CCCCcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhcc------ccc-----cHHHHHHHH
Q 004769 161 CSITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVN------RDY-----DAIDLIAMC 229 (731)
Q Consensus 161 R~ls~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~------~~~-----d~~~l~~~~ 229 (731)
+.++.+.+..|..+...|.+.++|...+. ++..-|+.++++++... ..+ -......++
T Consensus 16 ~~~s~~~R~riv~~~~~G~s~~~iA~~~g-----------vs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I 84 (125)
T smart00351 16 RPLPDEERQRIVELAQNGVRPCDISRQLC-----------VSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKI 84 (125)
T ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHHC-----------cCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHH
Confidence 55788899999888889999999876552 46677888888776431 001 112344556
Q ss_pred HHhhcCCCCc
Q 004769 230 KKMKDKNPNF 239 (731)
Q Consensus 230 ~~~~~~np~~ 239 (731)
..+..+||.+
T Consensus 85 ~~~~~~~p~~ 94 (125)
T smart00351 85 ADYKQENPGI 94 (125)
T ss_pred HHHHHHCCCC
Confidence 6666778875
No 45
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=24.52 E-value=3.1e+02 Score=31.36 Aligned_cols=33 Identities=27% Similarity=0.405 Sum_probs=23.5
Q ss_pred EEEEccCCCceEeecCCcccCCcchhhHHHHhhcC
Q 004769 526 KVIWIPCQEHISCSCHQFEFSGILCRHVLRVLSTD 560 (731)
Q Consensus 526 ~V~~~~~~~~~~CsC~~fe~~GiPC~Hil~vl~~~ 560 (731)
.|++.....+..|+|.. ...| -|.|+.+|+...
T Consensus 63 ~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~ 95 (587)
T COG4715 63 RVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEY 95 (587)
T ss_pred EEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHH
Confidence 45554455678999998 4444 599999988653
No 46
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.12 E-value=72 Score=23.26 Aligned_cols=39 Identities=15% Similarity=0.422 Sum_probs=20.5
Q ss_pred chhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhh
Q 004769 166 DDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRN 215 (731)
Q Consensus 166 ~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~ 215 (731)
..+..|..+...|.+.++|.+.+. ++...|++++.+++.
T Consensus 5 ~~R~~ii~l~~~G~s~~~ia~~lg-----------vs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 5 ERRAQIIRLLREGWSIREIAKRLG-----------VSRSTVYRWIKRYRE 43 (50)
T ss_dssp -----HHHHHHHT--HHHHHHHHT-----------S-HHHHHHHHT----
T ss_pred hHHHHHHHHHHCCCCHHHHHHHHC-----------cCHHHHHHHHHHccc
Confidence 345566666666999999987663 466778888777654
No 47
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=24.01 E-value=1.7e+02 Score=22.08 Aligned_cols=53 Identities=17% Similarity=0.207 Sum_probs=32.8
Q ss_pred CCCcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhccccccHHHHH
Q 004769 162 SITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVNRDYDAIDLI 226 (731)
Q Consensus 162 ~ls~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~~~~d~~~l~ 226 (731)
.||+.+.+ |..+.-.|.++.+|...+. ++.+.|++++...++...-.+-..++
T Consensus 3 ~LT~~E~~-vl~~l~~G~~~~eIA~~l~-----------is~~tV~~~~~~i~~Kl~~~~~~~l~ 55 (58)
T PF00196_consen 3 SLTERELE-VLRLLAQGMSNKEIAEELG-----------ISEKTVKSHRRRIMKKLGVKNRAELI 55 (58)
T ss_dssp SS-HHHHH-HHHHHHTTS-HHHHHHHHT-----------SHHHHHHHHHHHHHHHHT-SSHHHHH
T ss_pred ccCHHHHH-HHHHHHhcCCcchhHHhcC-----------cchhhHHHHHHHHHHHhCCCCHHHHH
Confidence 35555554 5566778999999988773 46677888888776554333333443
No 48
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=23.51 E-value=2e+02 Score=20.79 Aligned_cols=44 Identities=16% Similarity=0.332 Sum_probs=28.9
Q ss_pred CCCcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhcc
Q 004769 162 SITPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVN 217 (731)
Q Consensus 162 ~ls~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~ 217 (731)
.+++.++. |..+...|.+..+|.+.+. ++..-|++++.+.++..
T Consensus 3 ~l~~~e~~-i~~~~~~g~s~~eia~~l~-----------is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPRERE-VLRLLAEGLTNKEIAERLG-----------ISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHH-HHHHHHcCCCHHHHHHHHC-----------CCHHHHHHHHHHHHHHH
Confidence 35666665 4455678999999886653 45566777776655443
No 49
>PHA00689 hypothetical protein
Probab=23.48 E-value=32 Score=25.17 Aligned_cols=13 Identities=23% Similarity=0.365 Sum_probs=10.8
Q ss_pred CccccCCccCCCC
Q 004769 697 RRHCSEPCCRHFG 709 (731)
Q Consensus 697 ~r~~~Cs~C~~~g 709 (731)
+|.++|.+|++.|
T Consensus 15 pravtckrcgktg 27 (62)
T PHA00689 15 PRAVTCKRCGKTG 27 (62)
T ss_pred cceeehhhccccC
Confidence 6788899999875
No 50
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=23.11 E-value=43 Score=32.55 Aligned_cols=19 Identities=26% Similarity=0.422 Sum_probs=0.0
Q ss_pred ccCCccCCCCCCCCCC-CCc
Q 004769 700 CSEPCCRHFGHDASSC-PIM 718 (731)
Q Consensus 700 ~~Cs~C~~~gHn~~tC-p~~ 718 (731)
..|.+|+..||-++-| |.+
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~ 117 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSK 117 (190)
T ss_pred cccccccccCccccccCccc
No 51
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=23.00 E-value=64 Score=24.90 Aligned_cols=43 Identities=14% Similarity=0.268 Sum_probs=23.9
Q ss_pred CCCccccCCCCccCCCCCCcccccCCccccCCccCCCCCCCCCCCC
Q 004769 672 NSHESFTLGKLKERRPRDGVDVSRKRRHCSEPCCRHFGHDASSCPI 717 (731)
Q Consensus 672 ~P~~~~~kGRpkk~r~k~~~~~~~k~r~~~Cs~C~~~gHn~~tCp~ 717 (731)
-|..+.++.|..+||.- ..+ ...-...|+.||..-=.-+-||.
T Consensus 3 vPKrk~S~srr~~RRsh--~~l-~~~~l~~C~~CG~~~~~H~vC~~ 45 (57)
T PRK12286 3 VPKRKTSKSRKRKRRAH--FKL-KAPGLVECPNCGEPKLPHRVCPS 45 (57)
T ss_pred cCcCcCChhhcchhccc--ccc-cCCcceECCCCCCccCCeEECCC
Confidence 36666677776665542 222 23456669999954333334443
No 52
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=21.77 E-value=46 Score=23.94 Aligned_cols=17 Identities=29% Similarity=0.487 Sum_probs=15.7
Q ss_pred cCCccCCCCCCCCCCCC
Q 004769 701 SEPCCRHFGHDASSCPI 717 (731)
Q Consensus 701 ~Cs~C~~~gHn~~tCp~ 717 (731)
.|-+|++.||-.--||.
T Consensus 6 ~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 6 RCQKCGQKGHWTYECPN 22 (42)
T ss_pred cCcccCCCCcchhhCCC
Confidence 49999999999999995
No 53
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=21.44 E-value=2.5e+02 Score=20.38 Aligned_cols=53 Identities=15% Similarity=0.276 Sum_probs=31.6
Q ss_pred CcchhhHHHHhhhcCCcHHHHHHHHHHhhCccCCCCCcchhhhhhhHHHhhhccccccHHHHHHH
Q 004769 164 TPDDKTRICMFAKAGMSVRQMLRLMELEKGVKLGCLPFTEIDVRNLLQSFRNVNRDYDAIDLIAM 228 (731)
Q Consensus 164 s~~~k~~i~~l~~~g~~~~~I~~~l~~~~g~~~~~~~~~~~Di~N~~~~~r~~~~~~d~~~l~~~ 228 (731)
++.++. +..+...|.+..+|.+.+. ++...|+.++.+.++....+.-..++.+
T Consensus 2 ~~~e~~-i~~~~~~~~s~~eia~~l~-----------~s~~tv~~~~~~~~~~l~~~~~~~l~~~ 54 (57)
T cd06170 2 TPRERE-VLRLLAEGKTNKEIADILG-----------ISEKTVKTHLRNIMRKLGVKSRTQLVAY 54 (57)
T ss_pred CHHHHH-HHHHHHcCCCHHHHHHHHC-----------CCHHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence 334444 4445568899988887653 4566777777776655444343444443
No 54
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=21.31 E-value=43 Score=17.68 Aligned_cols=9 Identities=11% Similarity=0.220 Sum_probs=3.0
Q ss_pred ccCCCCccC
Q 004769 677 FTLGKLKER 685 (731)
Q Consensus 677 ~~kGRpkk~ 685 (731)
+..|||++.
T Consensus 2 r~RGRP~k~ 10 (13)
T PF02178_consen 2 RKRGRPRKN 10 (13)
T ss_dssp --SS--TT-
T ss_pred CcCCCCccc
Confidence 456888864
Done!