Query 016331
Match_columns 391
No_of_seqs 153 out of 276
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:53:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016331.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016331hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5259 RSC8 RSC chromatin rem 100.0 3.9E-45 8.4E-50 369.6 6.2 222 155-386 26-275 (531)
2 KOG1279 Chromatin remodeling f 100.0 1.3E-42 2.9E-47 357.5 11.9 207 155-379 23-245 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 1E-28 2.2E-33 199.4 5.6 86 181-270 1-86 (86)
4 PLN03000 amine oxidase 99.0 5.5E-10 1.2E-14 123.1 6.7 86 187-277 88-175 (881)
5 PLN02328 lysine-specific histo 99.0 6.8E-10 1.5E-14 121.6 6.8 88 186-277 138-226 (808)
6 cd02336 ZZ_RSC8 Zinc finger, Z 98.9 3.1E-10 6.8E-15 83.7 1.8 35 346-380 1-45 (45)
7 PLN02529 lysine-specific histo 98.5 1.8E-07 4E-12 101.9 6.4 86 187-277 64-151 (738)
8 PLN02976 amine oxidase 97.0 0.00058 1.3E-08 79.8 4.3 81 192-275 457-542 (1713)
9 smart00291 ZnF_ZZ Zinc-binding 90.9 0.13 2.7E-06 37.4 1.4 34 344-377 3-36 (44)
10 KOG1279 Chromatin remodeling f 82.1 1.7 3.6E-05 46.8 4.3 97 182-278 185-288 (506)
11 PF00569 ZZ: Zinc finger, ZZ t 80.2 0.53 1.2E-05 34.5 -0.1 34 344-377 3-37 (46)
12 cd02249 ZZ Zinc finger, ZZ typ 79.9 0.89 1.9E-05 33.2 1.0 33 346-378 1-33 (46)
13 cd02335 ZZ_ADA2 Zinc finger, Z 76.2 1.5 3.2E-05 32.6 1.3 32 346-377 1-33 (49)
14 COG1725 Predicted transcriptio 72.1 7.1 0.00015 34.9 4.8 56 216-271 10-68 (125)
15 cd02341 ZZ_ZZZ3 Zinc finger, Z 71.3 2.1 4.6E-05 32.2 1.1 32 346-377 1-35 (48)
16 KOG0847 Transcription factor, 70.2 2.7 5.9E-05 41.3 1.9 17 11-27 218-235 (288)
17 PF01475 FUR: Ferric uptake re 65.6 9.1 0.0002 32.2 4.0 52 220-272 7-62 (120)
18 smart00345 HTH_GNTR helix_turn 64.0 9.2 0.0002 27.3 3.2 50 219-270 2-52 (60)
19 cd02345 ZZ_dah Zinc finger, ZZ 63.8 3.4 7.3E-05 30.9 0.9 32 347-378 2-34 (49)
20 cd02337 ZZ_CBP Zinc finger, ZZ 62.5 3 6.4E-05 30.3 0.4 31 346-377 1-31 (41)
21 cd02343 ZZ_EF Zinc finger, ZZ 61.1 3.5 7.5E-05 31.3 0.6 32 347-378 2-33 (48)
22 PF00392 GntR: Bacterial regul 59.7 14 0.00029 28.1 3.6 53 216-270 3-56 (64)
23 PRK09462 fur ferric uptake reg 56.8 21 0.00046 31.5 4.9 50 222-271 18-71 (148)
24 PRK06474 hypothetical protein; 56.6 20 0.00043 33.1 4.8 52 221-273 11-62 (178)
25 cd07153 Fur_like Ferric uptake 54.7 21 0.00045 29.6 4.2 48 223-271 3-54 (116)
26 PF12802 MarR_2: MarR family; 53.4 28 0.00061 25.5 4.3 43 231-274 15-57 (62)
27 cd00090 HTH_ARSR Arsenical Res 51.1 33 0.00072 24.7 4.4 45 225-273 11-55 (78)
28 PF10446 DUF2457: Protein of u 51.1 9.3 0.0002 40.8 1.9 30 155-186 191-228 (458)
29 smart00550 Zalpha Z-DNA-bindin 49.9 39 0.00085 26.4 4.8 51 221-272 6-56 (68)
30 cd02338 ZZ_PCMF_like Zinc fing 49.1 9.3 0.0002 28.5 1.1 32 347-378 2-34 (49)
31 PF09339 HTH_IclR: IclR helix- 48.8 27 0.00058 25.6 3.6 44 225-270 7-50 (52)
32 cd02340 ZZ_NBR1_like Zinc fing 47.7 11 0.00023 27.6 1.3 31 347-377 2-32 (43)
33 COG5114 Histone acetyltransfer 43.5 24 0.00053 36.6 3.5 53 214-268 376-428 (432)
34 KOG4479 Transcription factor e 42.2 28 0.0006 29.7 3.0 46 216-265 35-89 (92)
35 PF10820 DUF2543: Protein of u 41.8 21 0.00045 29.7 2.2 55 194-266 23-79 (81)
36 PHA03082 DNA-dependent RNA pol 41.8 5.9 0.00013 31.6 -0.9 17 346-362 5-21 (63)
37 COG0735 Fur Fe2+/Zn2+ uptake r 41.8 50 0.0011 29.5 4.8 53 222-275 22-78 (145)
38 PF01022 HTH_5: Bacterial regu 41.7 58 0.0012 23.4 4.3 45 222-270 3-47 (47)
39 PF09862 DUF2089: Protein of u 41.5 16 0.00034 32.3 1.5 38 348-385 1-47 (113)
40 smart00346 HTH_ICLR helix_turn 39.9 48 0.001 26.0 4.0 43 226-270 10-52 (91)
41 PF13412 HTH_24: Winged helix- 39.0 77 0.0017 22.5 4.6 44 222-268 4-47 (48)
42 PRK11639 zinc uptake transcrip 38.1 40 0.00087 30.8 3.7 48 223-271 28-79 (169)
43 PF05864 Chordopox_RPO7: Chord 36.3 9.6 0.00021 30.4 -0.5 16 346-361 5-20 (63)
44 cd02334 ZZ_dystrophin Zinc fin 35.5 18 0.0004 27.3 0.9 32 347-378 2-34 (49)
45 PF03444 HrcA_DNA-bdg: Winged 33.6 1.6E+02 0.0034 24.7 6.1 53 217-271 4-56 (78)
46 PF09286 Pro-kuma_activ: Pro-k 33.4 33 0.00071 29.9 2.3 36 235-271 45-80 (143)
47 PF03979 Sigma70_r1_1: Sigma-7 31.6 85 0.0019 25.4 4.3 41 225-267 11-53 (82)
48 PRK11414 colanic acid/biofilm 30.4 69 0.0015 29.5 4.0 66 204-271 2-67 (221)
49 PF08784 RPA_C: Replication pr 28.4 1.2E+02 0.0025 25.0 4.7 47 221-268 47-95 (102)
50 PF08279 HTH_11: HTH domain; 28.3 1.7E+02 0.0037 21.1 5.1 41 224-266 3-43 (55)
51 KOG4752 Ribosomal protein L41 27.7 28 0.0006 23.3 0.7 6 12-17 2-8 (26)
52 PF13463 HTH_27: Winged helix 25.9 1.8E+02 0.004 21.4 5.0 53 224-277 5-57 (68)
53 KOG0486 Transcription factor P 25.3 25 0.00054 36.4 0.1 13 10-22 162-175 (351)
54 TIGR02702 SufR_cyano iron-sulf 25.1 1.1E+02 0.0023 28.4 4.3 48 222-272 2-49 (203)
55 cd02339 ZZ_Mind_bomb Zinc fing 24.9 39 0.00084 25.1 1.1 30 347-376 2-32 (45)
56 PRK03837 transcriptional regul 24.2 99 0.0021 28.6 3.9 58 213-272 13-71 (241)
57 PF08114 PMP1_2: ATPase proteo 24.0 32 0.0007 25.8 0.5 11 12-22 31-41 (43)
58 TIGR03338 phnR_burk phosphonat 23.7 1E+02 0.0022 28.0 3.8 57 214-272 12-68 (212)
59 KOG0457 Histone acetyltransfer 23.4 31 0.00068 36.8 0.5 36 341-376 10-46 (438)
60 TIGR02812 fadR_gamma fatty aci 22.1 99 0.0021 28.7 3.5 58 213-272 6-64 (235)
61 cd07377 WHTH_GntR Winged helix 21.7 1.4E+02 0.003 21.5 3.5 52 217-270 5-57 (66)
62 cd02344 ZZ_HERC2 Zinc finger, 21.2 55 0.0012 24.5 1.2 31 347-377 2-33 (45)
63 smart00420 HTH_DEOR helix_turn 21.0 2.2E+02 0.0049 19.4 4.4 34 236-270 13-46 (53)
64 PF08100 Dimerisation: Dimeris 20.9 1.3E+02 0.0027 22.9 3.2 28 235-262 20-50 (51)
65 PRK10225 DNA-binding transcrip 20.2 1.4E+02 0.003 28.2 4.1 58 213-272 9-67 (257)
66 PF11740 KfrA_N: Plasmid repli 20.1 1.4E+02 0.0029 25.1 3.6 30 235-267 17-46 (120)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=3.9e-45 Score=369.63 Aligned_cols=222 Identities=22% Similarity=0.383 Sum_probs=171.4
Q ss_pred CCCcceecCCCccCCCccceecCCceeeCCCCCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCC
Q 016331 155 SDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNP 234 (391)
Q Consensus 155 ~~~~~v~t~p~~~eg~~~~k~~~~~~~vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP 234 (391)
+.+.+..+.+.+.+.+..---.|+++++||+++.||++.+||+||++..||||+|+++.|||++|+.||||||+.||+||
T Consensus 26 ~ks~~e~~~~~l~~e~~~Fl~~Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p 105 (531)
T COG5259 26 SKSANEKKTTILRVEAETFLMEQTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNP 105 (531)
T ss_pred hcccCccccchhhhhhhhhhhccCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCC
Confidence 34555555555554443332348999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccccCCCCCCC---CC---CCCccccCCCCccccCCCcccccc---
Q 016331 235 EKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEP---WN---RGSYLREDSNGEVSVPSDALKSID--- 305 (391)
Q Consensus 235 ~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~~~~~~p~---~~---~~~~~~~~p~G~~~~~~~~l~~~~--- 305 (391)
.+|||+|+|||||+| ||++|.|||+|||+|||||||+++.++|. |+ +.+.+.++|.|.+.+.+..+....
T Consensus 106 ~eYLtvTa~RRNvag-DV~aivrvHrFLekWGLINYqvdp~trPs~IgPplt~h~q~l~dtP~gl~p~l~~~~~~~~~~~ 184 (531)
T COG5259 106 NEYLTVTACRRNVAG-DVAAIVRVHRFLEKWGLINYQVDPGTRPSTIGPPLTSHFQDLHDTPRGLSPFLPWGPINQRVLG 184 (531)
T ss_pred cceEEeeeehhccch-hHHHHHHHHHHHHHhcceeeccCCCCCccccCCCcchhhHHHhhCccccccccCCCCccccccc
Confidence 999999999999999 99999999999999999999999999995 33 334567788888666554443332
Q ss_pred -ccccccCCCcccccccccCCC---CC---CCCCCCccHHHHhc--ccCcccCcCCCCCCCceeeeeec----------c
Q 016331 306 -SLIKFDKPKCSLKVADVYSSS---CG---GADFFDLDNTIRER--LSENHCNYCSQPIPAVYYQSQKE----------V 366 (391)
Q Consensus 306 -~Li~fd~~~~~~~~~~v~~pt---~~---~~~~~dl~~~i~e~--l~ey~C~~Cg~DCs~~rYhsqK~----------~ 366 (391)
+.+.| ....++.++|+ +. ...+-+ +.++ ..-++|..||..|...|||+++. .
T Consensus 185 a~~~e~-----~~~k~~~~sps~~~~~k~s~~k~~e----l~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~ 255 (531)
T COG5259 185 AKEIEY-----ETHKEENYSPSLKSPKKESQGKVDE----LKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYD 255 (531)
T ss_pred cchhhh-----hhhccCCCCchhhhhhhhcCCCccc----cccccccCCceeeccCccccchhhhhhhhhhcccchHHHh
Confidence 22222 12233444442 10 011111 1222 23499999999999999999972 8
Q ss_pred CcccCCCcchhhhHHhhhcc
Q 016331 367 DGRFSPLTFVYLFICLFLSS 386 (391)
Q Consensus 367 dg~f~p~~~s~dFi~~~~~~ 386 (391)
.|+|+..+-+.||+|++..-
T Consensus 256 qg~f~s~~~ssDf~~v~~~~ 275 (531)
T COG5259 256 QGRFPSEFTSSDFKPVTISL 275 (531)
T ss_pred cCcCCCccccccchhhhhhc
Confidence 99999999999999998653
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=1.3e-42 Score=357.47 Aligned_cols=207 Identities=25% Similarity=0.417 Sum_probs=163.6
Q ss_pred CCCcceecCCCccCCCccceecCCceeeCCCCCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCC
Q 016331 155 SDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNP 234 (391)
Q Consensus 155 ~~~~~v~t~p~~~eg~~~~k~~~~~~~vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP 234 (391)
+...+++ |..+.......+.|++.|+||+|++||+|++||.||++.+||||+|++++|||++||+||||||++||+||
T Consensus 23 ~~~~~~~--~~~~~~~~~~~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrlnp 100 (506)
T KOG1279|consen 23 SQETLGG--PAAHDAAKTVVSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLNP 100 (506)
T ss_pred Ccccccc--cchhhhcccccccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccCc
Confidence 4444555 55667788888999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccccCCCCCCCC---C---CCCccccCCCCccccCCCccccccccc
Q 016331 235 EKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPW---N---RGSYLREDSNGEVSVPSDALKSIDSLI 308 (391)
Q Consensus 235 ~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~~~~~~p~~---~---~~~~~~~~p~G~~~~~~~~l~~~~~Li 308 (391)
.+|||+|+||++|+| ||++|.|||+|||+||||||+++++.+|.. + +...+.++|.|.+...+... ..
T Consensus 101 ~~ylt~ta~rrnl~g-Dv~ai~Rvh~FlE~WGLINy~~d~e~rp~~~~p~~t~h~~~~~~tp~~~~~~~~~~~-----~~ 174 (506)
T KOG1279|consen 101 QEYLTFTACRRNLAG-DVCAIARVHAFLEQWGLINYQVDAESRPHPIEPPETSHFQVLADTPRGLAPLTPEDP-----QS 174 (506)
T ss_pred ccchhHHHHHhcccc-hHHHHHHHHhhHHhhcccccccChhhCCcccCCCcccccccccCCCcccccCCCCCc-----cc
Confidence 999999999999999 999999999999999999999999999853 2 22344555666554333222 22
Q ss_pred cccCCCcccccccccCCCCCCCCCCCccHHHHhcccCcccCcCCCCCCCceeeeeec----------cCcccCCCcchhh
Q 016331 309 KFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKE----------VDGRFSPLTFVYL 378 (391)
Q Consensus 309 ~fd~~~~~~~~~~v~~pt~~~~~~~dl~~~i~e~l~ey~C~~Cg~DCs~~rYhsqK~----------~dg~f~p~~~s~d 378 (391)
.++.+++... ....-...+.+...+.+.+...||+.|+.. +||.++. ..|+|+..+-..|
T Consensus 175 ~~~~~~~~~~------~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~D 244 (506)
T KOG1279|consen 175 QPDLGNPRME------TLSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSD 244 (506)
T ss_pred cccccccccc------cccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCcccccc
Confidence 2333333221 112222334445566778889999999887 7777775 7899999999999
Q ss_pred h
Q 016331 379 F 379 (391)
Q Consensus 379 F 379 (391)
|
T Consensus 245 f 245 (506)
T KOG1279|consen 245 F 245 (506)
T ss_pred c
Confidence 9
No 3
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=99.95 E-value=1e-28 Score=199.42 Aligned_cols=86 Identities=43% Similarity=0.962 Sum_probs=78.7
Q ss_pred eeCCCCCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHH
Q 016331 181 HVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFR 260 (391)
Q Consensus 181 ~vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~ 260 (391)
+++|.+++||+++.+|++|++.+||||.| ++|+.||.|||.||+.|+.||.+|||+++|++++.|.|++.+.|||+
T Consensus 1 ~~~~~~~~~~~~~~l~~~E~~~~~e~~~~----~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~ 76 (86)
T PF04433_consen 1 VVIPAHSSWFDPDKLSEIEKQLCPEFFIG----KTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYD 76 (86)
T ss_dssp -HCHCCHTTTTTTSS-HHHHHHCHHCTTS----CHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHH
T ss_pred CCCccccCCCCcccCCHHHHHHhHHHhcc----CChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHH
Confidence 36899999999999999999999999988 89999999999999999999999999999999998779999999999
Q ss_pred hhhhhceecc
Q 016331 261 FLNHWGIINY 270 (391)
Q Consensus 261 FLE~WGLINy 270 (391)
||++||+|||
T Consensus 77 FL~~~G~INf 86 (86)
T PF04433_consen 77 FLERWGLINF 86 (86)
T ss_dssp HHHHTTSSSS
T ss_pred HHHHcCccCC
Confidence 9999999998
No 4
>PLN03000 amine oxidase
Probab=98.98 E-value=5.5e-10 Score=123.07 Aligned_cols=86 Identities=22% Similarity=0.322 Sum_probs=72.9
Q ss_pred CCCCCCCCCCHHHHhh--CCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhh
Q 016331 187 SDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNH 264 (391)
Q Consensus 187 s~WFd~d~Ih~iEk~~--lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~ 264 (391)
+.=|+.+.+++.|..+ || ... ...+..||.|||.||.+|+.||..+||+++|...+..--...+.++|+||.+
T Consensus 88 ~~~~p~d~l~~~e~~~~~~~-~~~----~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~r 162 (881)
T PLN03000 88 TAGFPADSLTEEEIEFGVVP-IVG----GIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLVT 162 (881)
T ss_pred HcCCCcccCCHHHHhccccC-ccc----ccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHHH
Confidence 4557999999999777 78 333 3678999999999999999999999999999988754234789999999999
Q ss_pred hceeccccCCCCC
Q 016331 265 WGIINYCAAVQSP 277 (391)
Q Consensus 265 WGLINy~~~~~~~ 277 (391)
.|+|||++.....
T Consensus 163 ~G~in~g~~~~~~ 175 (881)
T PLN03000 163 HGYINFGIAQAIK 175 (881)
T ss_pred cCcccHHHHHHHH
Confidence 9999999985443
No 5
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.97 E-value=6.8e-10 Score=121.56 Aligned_cols=88 Identities=23% Similarity=0.288 Sum_probs=77.8
Q ss_pred CCCCCCCCCCCHHHHhh-CCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhh
Q 016331 186 HSDWFSPDTVHRLERQV-VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNH 264 (391)
Q Consensus 186 ~s~WFd~d~Ih~iEk~~-lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~ 264 (391)
.+.=|..+.+|+.|..+ |++...+ ..+..||.|||.||.+|+.||..+||+++|+..+-......+.++|.||.+
T Consensus 138 ~~~~~p~~~l~~~e~~~~~~~~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~ 213 (808)
T PLN02328 138 ISVGFPVDSLTEEEIEANVVSTIGG----TEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLE 213 (808)
T ss_pred HHcCCCCccCCHHHHhhcCcchhcc----cceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhc
Confidence 34568999999999888 8887766 779999999999999999999999999999988754456799999999999
Q ss_pred hceeccccCCCCC
Q 016331 265 WGIINYCAAVQSP 277 (391)
Q Consensus 265 WGLINy~~~~~~~ 277 (391)
.|.|||++.+..+
T Consensus 214 ~g~in~gv~~~~~ 226 (808)
T PLN02328 214 HGYINFGVAPVIK 226 (808)
T ss_pred cCceeeecccccc
Confidence 9999999998765
No 6
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=98.94 E-value=3.1e-10 Score=83.74 Aligned_cols=35 Identities=31% Similarity=0.488 Sum_probs=33.3
Q ss_pred cccCcCCCCCCCceeeeeec----------cCcccCCCcchhhhH
Q 016331 346 NHCNYCSQPIPAVYYQSQKE----------VDGRFSPLTFVYLFI 380 (391)
Q Consensus 346 y~C~~Cg~DCs~~rYhsqK~----------~dg~f~p~~~s~dFi 380 (391)
|||+.||+|||++|||++|. .+|+|++++.++|||
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G~f~~~~~s~Dfv 45 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEGRFPSNFQSSDFI 45 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHhCcCCCCCCcccccC
Confidence 79999999999999999998 689999999999996
No 7
>PLN02529 lysine-specific histone demethylase 1
Probab=98.47 E-value=1.8e-07 Score=101.92 Aligned_cols=86 Identities=22% Similarity=0.255 Sum_probs=71.4
Q ss_pred CCCCCCCCCCHHHHhh--CCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhh
Q 016331 187 SDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNH 264 (391)
Q Consensus 187 s~WFd~d~Ih~iEk~~--lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~ 264 (391)
+-=|..+.+++.|+++ +|.. .++.++.||.|||.||.+|+.||..+||+++++..+..--...|...|+||.+
T Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~yl~irn~il~~w~~np~~~~~~~~a~~~~~~~i~~ci~~c~~~l~~ 138 (738)
T PLN02529 64 SVGFPIDALLEEEIRAGVVREL-----GGKEQNDYIVVRNHILARWRSNVGIWLSKGQIKETVSSEYEHLISAAYDFLLY 138 (738)
T ss_pred HcCCCccccCHHHHhccccCcc-----ccccceeeehHHHHHHHHHHHCCceeecHHHHhhhchhhHHHHHHHHHHHHHh
Confidence 4558899999999855 3332 35889999999999999999999999999999987654223467789999999
Q ss_pred hceeccccCCCCC
Q 016331 265 WGIINYCAAVQSP 277 (391)
Q Consensus 265 WGLINy~~~~~~~ 277 (391)
.|.|||++.++..
T Consensus 139 ~~~inc~vnp~~~ 151 (738)
T PLN02529 139 NGYINFGVSPSFA 151 (738)
T ss_pred CCCcceeeccccc
Confidence 9999999998764
No 8
>PLN02976 amine oxidase
Probab=97.00 E-value=0.00058 Score=79.85 Aligned_cols=81 Identities=22% Similarity=0.391 Sum_probs=66.7
Q ss_pred CCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhc---ccCC--CCHHHHHHHHHhhhhhc
Q 016331 192 PDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQG---LVDG--VSPEDLTRIFRFLNHWG 266 (391)
Q Consensus 192 ~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr---~L~G--~Dv~~I~RVh~FLE~WG 266 (391)
-..+.++||-.|.|...-+ -.-..||++||.||-+|-+|=.+-|.+++|-= -+.. .-..+|..|+.||++-|
T Consensus 457 a~~~~~~e~~~~k~~lkr~---~~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~v~~~~~~~e~~~~~l~r~~~~fld~~g 533 (1713)
T PLN02976 457 ARAVGPIEKIKFKEVLKRK---GGLQEYLECRNMILGLWSKDVSRILPLADCGVTDTPSEDESPRASLIREVYLFLDQRG 533 (1713)
T ss_pred ccccChHHHHHHHHHHHhc---cchHHHHHHHHHHHHHhhhhhhhcccHhhccccCCcccccCchhhHHHHHHHHhhccC
Confidence 4568899999999998765 45678999999999999999999999999932 1111 24578999999999999
Q ss_pred eeccccCCC
Q 016331 267 IINYCAAVQ 275 (391)
Q Consensus 267 LINy~~~~~ 275 (391)
.||-++...
T Consensus 534 yin~g~~s~ 542 (1713)
T PLN02976 534 YINAGIASE 542 (1713)
T ss_pred ceecccccc
Confidence 999998753
No 9
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=90.90 E-value=0.13 Score=37.43 Aligned_cols=34 Identities=24% Similarity=0.405 Sum_probs=29.9
Q ss_pred cCcccCcCCCCCCCceeeeeeccCcccCCCcchh
Q 016331 344 SENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVY 377 (391)
Q Consensus 344 ~ey~C~~Cg~DCs~~rYhsqK~~dg~f~p~~~s~ 377 (391)
..+.|+.|+.+++..||||+.-.|+-..+.+|+.
T Consensus 3 ~~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 3 HSYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred CCcCCCCCCCCCcCCEEECCCCCCccchHHHHhC
Confidence 4588999999999999999998888888888764
No 10
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=82.07 E-value=1.7 Score=46.84 Aligned_cols=97 Identities=10% Similarity=-0.036 Sum_probs=76.6
Q ss_pred eCCCCCCCCCCCCCCHHHHhhCCcccCCCC-CCCChHHHHHHHHHHHHHHHhCCCceee-----HHHHhcccCC-CCHHH
Q 016331 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKS-PDHTPEKYMECRNHIVAKYMDNPEKRLI-----VSDCQGLVDG-VSPED 254 (391)
Q Consensus 182 vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks-~~kTPe~Yl~iRN~II~~yr~NP~~yLT-----~T~cRr~L~G-~Dv~~ 254 (391)
..+..++=++...=+.-.....++|+.+++ ....+..|+.||+.+++.++---..+.+ -+..+++... ..+-+
T Consensus 185 ~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLL 264 (506)
T KOG1279|consen 185 TLSLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIGESARPNWTEQETLLL 264 (506)
T ss_pred cccccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhccccCCCCccHHHHHHH
Confidence 455566777777778888899999998873 3678889999999999999765555554 4556666653 57889
Q ss_pred HHHHHHhhhhhceeccccCCCCCC
Q 016331 255 LTRIFRFLNHWGIINYCAAVQSPE 278 (391)
Q Consensus 255 I~RVh~FLE~WGLINy~~~~~~~p 278 (391)
|-+|+.|.+.|+-|+.++-.+++.
T Consensus 265 LE~ie~y~ddW~kVa~hVg~ks~e 288 (506)
T KOG1279|consen 265 LEAIEMYGDDWNKVADHVGTKSQE 288 (506)
T ss_pred HHHHHHhcccHHHHHhccCCCCHH
Confidence 999999999999999999976654
No 11
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=80.18 E-value=0.53 Score=34.52 Aligned_cols=34 Identities=24% Similarity=0.319 Sum_probs=26.6
Q ss_pred cCcccCcCCC-CCCCceeeeeeccCcccCCCcchh
Q 016331 344 SENHCNYCSQ-PIPAVYYQSQKEVDGRFSPLTFVY 377 (391)
Q Consensus 344 ~ey~C~~Cg~-DCs~~rYhsqK~~dg~f~p~~~s~ 377 (391)
..+.|+.|+. .-...||+|+.-.|+.+...+|..
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 4588999999 558999999999999988888875
No 12
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=79.88 E-value=0.89 Score=33.17 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=28.7
Q ss_pred cccCcCCCCCCCceeeeeeccCcccCCCcchhh
Q 016331 346 NHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYL 378 (391)
Q Consensus 346 y~C~~Cg~DCs~~rYhsqK~~dg~f~p~~~s~d 378 (391)
|.|+.|+.+....||+|+.=.|+.....+|+..
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~ 33 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKG 33 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCcC
Confidence 689999999999999999988888887777654
No 13
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=76.24 E-value=1.5 Score=32.61 Aligned_cols=32 Identities=25% Similarity=0.450 Sum_probs=28.2
Q ss_pred cccCcCCCCCCC-ceeeeeeccCcccCCCcchh
Q 016331 346 NHCNYCSQPIPA-VYYQSQKEVDGRFSPLTFVY 377 (391)
Q Consensus 346 y~C~~Cg~DCs~-~rYhsqK~~dg~f~p~~~s~ 377 (391)
|+|+.|+.+... .||+|+.=.|......+|+.
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~ 33 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAECPDFDLCLECFSA 33 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCCCCcchhHHhhhC
Confidence 689999999999 99999998888888877764
No 14
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=72.10 E-value=7.1 Score=34.91 Aligned_cols=56 Identities=21% Similarity=0.250 Sum_probs=43.1
Q ss_pred hHHHHHHHHHHHHHHH---hCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccc
Q 016331 216 PEKYMECRNHIVAKYM---DNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (391)
Q Consensus 216 Pe~Yl~iRN~II~~yr---~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~ 271 (391)
-.+|.+|.|.|...=. ..|...|-.+--.-...|++.+.+.|.+.-||+-|+|.-.
T Consensus 10 ~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 10 KPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4599999999988765 4677776544333223468999999999999999999643
No 15
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=71.29 E-value=2.1 Score=32.18 Aligned_cols=32 Identities=25% Similarity=0.416 Sum_probs=26.6
Q ss_pred cccCcCCC-CCCCceeeeeecc--CcccCCCcchh
Q 016331 346 NHCNYCSQ-PIPAVYYQSQKEV--DGRFSPLTFVY 377 (391)
Q Consensus 346 y~C~~Cg~-DCs~~rYhsqK~~--dg~f~p~~~s~ 377 (391)
|.|+.|+. +-...||||+.=. |+-+...+|..
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~ 35 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVK 35 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhC
Confidence 68999998 9999999999988 66666666654
No 16
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=70.17 E-value=2.7 Score=41.33 Aligned_cols=17 Identities=24% Similarity=0.597 Sum_probs=10.7
Q ss_pred hh-HHHHhhcCcccccCC
Q 016331 11 TR-KWKRRKREPRKQLNK 27 (391)
Q Consensus 11 ~r-kw~~~k~~~~~~~~~ 27 (391)
.| |||||--..-++-++
T Consensus 218 RRTKWRKkhAaEmasakk 235 (288)
T KOG0847|consen 218 RRTKWRKKHAAEMASAKK 235 (288)
T ss_pred chhhhhhhhccchhhccc
Confidence 45 999998744444333
No 17
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=65.62 E-value=9.1 Score=32.24 Aligned_cols=52 Identities=19% Similarity=0.256 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHhCCCceeeHHHHhccc----CCCCHHHHHHHHHhhhhhceecccc
Q 016331 220 MECRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINYCA 272 (391)
Q Consensus 220 l~iRN~II~~yr~NP~~yLT~T~cRr~L----~G~Dv~~I~RVh~FLE~WGLINy~~ 272 (391)
-.-|..|++....++. .+|..+.-..| ..++...|.|...+|+.-|||.--.
T Consensus 7 T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~ 62 (120)
T PF01475_consen 7 TPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIE 62 (120)
T ss_dssp HHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEE
Confidence 4568899999988877 99999986655 2378889999999999999997543
No 18
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=63.97 E-value=9.2 Score=27.31 Aligned_cols=50 Identities=20% Similarity=0.285 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHhCCCcee-eHHHHhcccCCCCHHHHHHHHHhhhhhceecc
Q 016331 219 YMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (391)
Q Consensus 219 Yl~iRN~II~~yr~NP~~yL-T~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy 270 (391)
|-.+|+.|+.... .|...| |..+....+ |+....+.|.+.-|+.-|+|-.
T Consensus 2 ~~~l~~~i~~~~~-~~~~~l~s~~~la~~~-~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 2 AERLREDIVSGEL-RPGDKLPSERELAAQL-GVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHHHHHHcCCC-CCCCcCcCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEE
Confidence 6677887777642 456678 788876665 4677899999999999999953
No 19
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=63.83 E-value=3.4 Score=30.92 Aligned_cols=32 Identities=16% Similarity=0.244 Sum_probs=28.5
Q ss_pred ccCcCCC-CCCCceeeeeeccCcccCCCcchhh
Q 016331 347 HCNYCSQ-PIPAVYYQSQKEVDGRFSPLTFVYL 378 (391)
Q Consensus 347 ~C~~Cg~-DCs~~rYhsqK~~dg~f~p~~~s~d 378 (391)
.|+.|.. +....||+|++-.|+...-.+|+..
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~ 34 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKG 34 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCC
Confidence 6999999 9999999999999988888888754
No 20
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=62.46 E-value=3 Score=30.35 Aligned_cols=31 Identities=13% Similarity=0.231 Sum_probs=24.6
Q ss_pred cccCcCCCCCCCceeeeeeccCcccCCCcchh
Q 016331 346 NHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVY 377 (391)
Q Consensus 346 y~C~~Cg~DCs~~rYhsqK~~dg~f~p~~~s~ 377 (391)
|.|+.|+.... .||+|+.=.|+-....+|+.
T Consensus 1 y~C~~C~~~~~-~r~~C~~C~dfDLC~~C~~~ 31 (41)
T cd02337 1 YTCNECKHHVE-TRWHCTVCEDYDLCITCYNT 31 (41)
T ss_pred CcCCCCCCcCC-CceECCCCcchhhHHHHhCC
Confidence 68999999876 99999988777666666543
No 21
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=61.11 E-value=3.5 Score=31.34 Aligned_cols=32 Identities=19% Similarity=0.286 Sum_probs=28.0
Q ss_pred ccCcCCCCCCCceeeeeeccCcccCCCcchhh
Q 016331 347 HCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYL 378 (391)
Q Consensus 347 ~C~~Cg~DCs~~rYhsqK~~dg~f~p~~~s~d 378 (391)
.|..|.......||.|++-.|+-....+|+..
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g 33 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGG 33 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCC
Confidence 69999999999999999998888888877654
No 22
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=59.74 E-value=14 Score=28.08 Aligned_cols=53 Identities=25% Similarity=0.285 Sum_probs=39.4
Q ss_pred hHHHHHHHHHHHHHHHhCCCcee-eHHHHhcccCCCCHHHHHHHHHhhhhhceecc
Q 016331 216 PEKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (391)
Q Consensus 216 Pe~Yl~iRN~II~~yr~NP~~yL-T~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy 270 (391)
..+|-.|++.|++.- .-|..+| +..+..+.+ |+-...+.+.+..|+.+|+|--
T Consensus 3 ~~i~~~l~~~I~~g~-~~~g~~lps~~~la~~~-~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 3 EQIYDQLRQAILSGR-LPPGDRLPSERELAERY-GVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHHHHTTS-S-TTSBE--HHHHHHHH-TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHcCC-CCCCCEeCCHHHHHHHh-ccCCcHHHHHHHHHHHCCcEEE
Confidence 357888888887754 3467889 888876655 3577899999999999999953
No 23
>PRK09462 fur ferric uptake regulator; Provisional
Probab=56.84 E-value=21 Score=31.46 Aligned_cols=50 Identities=12% Similarity=0.191 Sum_probs=39.7
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhccc----CCCCHHHHHHHHHhhhhhceeccc
Q 016331 222 CRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINYC 271 (391)
Q Consensus 222 iRN~II~~yr~NP~~yLT~T~cRr~L----~G~Dv~~I~RVh~FLE~WGLINy~ 271 (391)
-|..|++.........||..++-..| .+++...|.|...+|+.-|||.=-
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~ 71 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH 71 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence 36677877766667899999985555 246889999999999999999743
No 24
>PRK06474 hypothetical protein; Provisional
Probab=56.64 E-value=20 Score=33.14 Aligned_cols=52 Identities=21% Similarity=0.246 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccccC
Q 016331 221 ECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAA 273 (391)
Q Consensus 221 ~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~~ 273 (391)
..|-.||+.-..++. .+|.+++...+.++....|.|....|+..|||.--..
T Consensus 11 p~R~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~ 62 (178)
T PRK06474 11 PVRMKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKE 62 (178)
T ss_pred HHHHHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 368889988877754 4999999877755667889999999999999985444
No 25
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=54.73 E-value=21 Score=29.63 Aligned_cols=48 Identities=15% Similarity=0.267 Sum_probs=38.9
Q ss_pred HHHHHHHHHhCCCceeeHHHHhcccC----CCCHHHHHHHHHhhhhhceeccc
Q 016331 223 RNHIVAKYMDNPEKRLIVSDCQGLVD----GVSPEDLTRIFRFLNHWGIINYC 271 (391)
Q Consensus 223 RN~II~~yr~NP~~yLT~T~cRr~L~----G~Dv~~I~RVh~FLE~WGLINy~ 271 (391)
|-.|++..... ...+|..++-..|. +++...+.|...+|..-|||.--
T Consensus 3 R~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 3 RLAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREI 54 (116)
T ss_pred HHHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEE
Confidence 67788877665 68899999866552 46889999999999999999743
No 26
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=53.35 E-value=28 Score=25.47 Aligned_cols=43 Identities=19% Similarity=0.288 Sum_probs=33.9
Q ss_pred HhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccccCC
Q 016331 231 MDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAV 274 (391)
Q Consensus 231 r~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~~~ 274 (391)
..+|...+|+++..+.+. .+...+.|+..=|+..|||--...+
T Consensus 15 ~~~~~~~~t~~~la~~l~-~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 15 ARHPGEELTQSELAERLG-ISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHSTTSGEEHHHHHHHHT-S-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHCCCCCcCHHHHHHHHC-cCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 356666799999988764 6889999999999999999766554
No 27
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=51.12 E-value=33 Score=24.65 Aligned_cols=45 Identities=22% Similarity=0.403 Sum_probs=33.4
Q ss_pred HHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccccC
Q 016331 225 HIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAA 273 (391)
Q Consensus 225 ~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~~ 273 (391)
.|+......+ ++..+..+.+ |+....+.|+..-|...|+|+....
T Consensus 11 ~il~~l~~~~---~~~~ei~~~~-~i~~~~i~~~l~~L~~~g~i~~~~~ 55 (78)
T cd00090 11 RILRLLLEGP---LTVSELAERL-GLSQSTVSRHLKKLEEAGLVESRRE 55 (78)
T ss_pred HHHHHHHHCC---cCHHHHHHHH-CcCHhHHHHHHHHHHHCCCeEEEEe
Confidence 3444433444 8898887766 4588899999999999999986543
No 28
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=51.11 E-value=9.3 Score=40.76 Aligned_cols=30 Identities=17% Similarity=0.177 Sum_probs=16.0
Q ss_pred CCCcceecCCCccCCCcc--------ceecCCceeeCCCC
Q 016331 155 SDTSCVITPPQIMEGKGV--------VKRFGSRVHVLPMH 186 (391)
Q Consensus 155 ~~~~~v~t~p~~~eg~~~--------~k~~~~~~~vIPs~ 186 (391)
++|+|||-- +.|-+.. .-|+..++++||.-
T Consensus 191 DSTDFVCGT--LDEDRPLE~AY~Scle~Rr~~K~~~iPQD 228 (458)
T PF10446_consen 191 DSTDFVCGT--LDEDRPLEAAYISCLEARRREKHIPIPQD 228 (458)
T ss_pred CcccccCCC--cCCcchHHHHHHHHHHHHHHcCCCCCCCC
Confidence 567888731 2222222 22445677888763
No 29
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=49.89 E-value=39 Score=26.41 Aligned_cols=51 Identities=10% Similarity=0.145 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceecccc
Q 016331 221 ECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (391)
Q Consensus 221 ~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~ 272 (391)
..++.|+.....++..-+|..+.-+.| |++...+.|+..=|+.-|+|.+..
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~l-gl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNL-GLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEecC
Confidence 357889999998877679999988876 578889999999999999997643
No 30
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=49.08 E-value=9.3 Score=28.50 Aligned_cols=32 Identities=13% Similarity=0.151 Sum_probs=28.5
Q ss_pred ccCcCC-CCCCCceeeeeeccCcccCCCcchhh
Q 016331 347 HCNYCS-QPIPAVYYQSQKEVDGRFSPLTFVYL 378 (391)
Q Consensus 347 ~C~~Cg-~DCs~~rYhsqK~~dg~f~p~~~s~d 378 (391)
.|+.|+ .+-...||+|++=.|+.....+|+..
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~ 34 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSG 34 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCC
Confidence 599999 89999999999999999998888754
No 31
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=48.83 E-value=27 Score=25.57 Aligned_cols=44 Identities=16% Similarity=0.295 Sum_probs=33.7
Q ss_pred HHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceecc
Q 016331 225 HIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (391)
Q Consensus 225 ~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy 270 (391)
.||+.....+. .+|+++.-+.+ |.....+.|+..=|+.+|+|..
T Consensus 7 ~iL~~l~~~~~-~~t~~eia~~~-gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 7 RILEALAESGG-PLTLSEIARAL-GLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHCHHCTBS-CEEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCCC-CCCHHHHHHHH-CcCHHHHHHHHHHHHHCcCeec
Confidence 35666655544 48999998766 4688999999999999999864
No 32
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=47.75 E-value=11 Score=27.58 Aligned_cols=31 Identities=23% Similarity=0.269 Sum_probs=26.8
Q ss_pred ccCcCCCCCCCceeeeeeccCcccCCCcchh
Q 016331 347 HCNYCSQPIPAVYYQSQKEVDGRFSPLTFVY 377 (391)
Q Consensus 347 ~C~~Cg~DCs~~rYhsqK~~dg~f~p~~~s~ 377 (391)
.|+.|+.+-...||+|++=.|+-+...+|..
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCc
Confidence 6999999999999999998888877777664
No 33
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=43.50 E-value=24 Score=36.64 Aligned_cols=53 Identities=15% Similarity=0.402 Sum_probs=46.6
Q ss_pred CChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhcee
Q 016331 214 HTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGII 268 (391)
Q Consensus 214 kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLI 268 (391)
-.|..||.+.--||..+.. ....+|.++|++++. .|+.-.-+|+.|.-.-|+|
T Consensus 376 i~PkpyL~LK~~~is~~l~-t~g~f~K~d~~~Lf~-id~~ka~~~YdfF~~~~Wi 428 (432)
T COG5114 376 ISPKPYLELKKEVISCFLR-TRGEFTKEDFNRLFG-IDLGKADGLYDFFLERGWI 428 (432)
T ss_pred CCCccHHHHHHHHHHHHHH-hCCCccHHHHHHHhC-cCcchhhHHHHHHHhcccc
Confidence 4599999999999999966 467899999999875 7888999999999888887
No 34
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=42.15 E-value=28 Score=29.68 Aligned_cols=46 Identities=30% Similarity=0.299 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHHHHhCCCceeeHHHHh-------cccCC--CCHHHHHHHHHhhhhh
Q 016331 216 PEKYMECRNHIVAKYMDNPEKRLIVSDCQ-------GLVDG--VSPEDLTRIFRFLNHW 265 (391)
Q Consensus 216 Pe~Yl~iRN~II~~yr~NP~~yLT~T~cR-------r~L~G--~Dv~~I~RVh~FLE~W 265 (391)
-++-.++||-|+.+=..| +|+.+.. |.|+- +--..++||+.||+.+
T Consensus 35 d~ik~mcrniimEkG~~n----~tvdqL~AeitPkaRaLVPd~VKkEll~rirt~L~~~ 89 (92)
T KOG4479|consen 35 DDIKEMCRNIIMEKGVDN----ITVDQLAAEITPKARALVPDVVKKELLLRIRTALDKH 89 (92)
T ss_pred HHHHHHHHHHHHHhcccc----ccHHHHHHHhCchhhhhchHHHHHHHHHHHHHHHHHH
Confidence 467788999999887666 6665532 22332 4456899999999976
No 35
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=41.83 E-value=21 Score=29.66 Aligned_cols=55 Identities=25% Similarity=0.573 Sum_probs=34.4
Q ss_pred CCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcc--cCCCCHHHHHHHHHhhhhhc
Q 016331 194 TVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGL--VDGVSPEDLTRIFRFLNHWG 266 (391)
Q Consensus 194 ~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~--L~G~Dv~~I~RVh~FLE~WG 266 (391)
-|++-|+..|-.+|+- +|-.-. -++.++-.+-+.. -+|+|..-|--|-.||.+||
T Consensus 23 pVse~erd~LAhYFQl----------------LitRLm--nneeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 23 PVSEAERDALAHYFQL----------------LITRLM--NNEEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred CcchhhhhHHHHHHHH----------------HHHHHh--ccHhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 4667777777777732 222221 2344443332222 25789889999999999999
No 36
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=41.83 E-value=5.9 Score=31.57 Aligned_cols=17 Identities=18% Similarity=0.489 Sum_probs=15.3
Q ss_pred cccCcCCCCCCCceeee
Q 016331 346 NHCNYCSQPIPAVYYQS 362 (391)
Q Consensus 346 y~C~~Cg~DCs~~rYhs 362 (391)
..|+.||.|.+..||+=
T Consensus 5 lVCsTCGrDlSeeRy~L 21 (63)
T PHA03082 5 LVCSTCGRDLSEERYRL 21 (63)
T ss_pred eeecccCcchhHHHHHH
Confidence 57999999999999974
No 37
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=41.76 E-value=50 Score=29.54 Aligned_cols=53 Identities=13% Similarity=0.205 Sum_probs=40.9
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhccc----CCCCHHHHHHHHHhhhhhceeccccCCC
Q 016331 222 CRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINYCAAVQ 275 (391)
Q Consensus 222 iRN~II~~yr~NP~~yLT~T~cRr~L----~G~Dv~~I~RVh~FLE~WGLINy~~~~~ 275 (391)
-|-.||+...+.+.. +|..+.-+.| .++....+.|+..||+.-|||+-..+..
T Consensus 22 qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 22 QRLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred HHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 467788877666555 9999985444 3467889999999999999998776653
No 38
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=41.74 E-value=58 Score=23.40 Aligned_cols=45 Identities=18% Similarity=0.240 Sum_probs=36.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceecc
Q 016331 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (391)
Q Consensus 222 iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy 270 (391)
.|-.||..-.+ ..+++.+..+.+. ..-..+.+=..-|...|||++
T Consensus 3 ~R~~Il~~L~~---~~~~~~el~~~l~-~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 3 TRLRILKLLSE---GPLTVSELAEELG-LSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHHTT---SSEEHHHHHHHHT-S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHh---CCCchhhHHHhcc-ccchHHHHHHHHHHHCcCeeC
Confidence 57788887766 5589999988764 688899999999999999974
No 39
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=41.50 E-value=16 Score=32.33 Aligned_cols=38 Identities=26% Similarity=0.534 Sum_probs=31.3
Q ss_pred cCcCCCCCCCceeeeee---ccCcccCCCcchh------hhHHhhhc
Q 016331 348 CNYCSQPIPAVYYQSQK---EVDGRFSPLTFVY------LFICLFLS 385 (391)
Q Consensus 348 C~~Cg~DCs~~rYhsqK---~~dg~f~p~~~s~------dFi~~~~~ 385 (391)
|-.||.+..-.+++|.. ...|.|...-|.. .||++|+-
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i~G~F~l~~~~~L~~E~~~Fi~~Fi~ 47 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEIEGEFELPWFARLSPEQLEFIKLFIK 47 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEEEeeeccchhhcCCHHHHHHHHHHHH
Confidence 88899999888888765 5899999988875 68888864
No 40
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=39.90 E-value=48 Score=25.96 Aligned_cols=43 Identities=16% Similarity=0.368 Sum_probs=32.8
Q ss_pred HHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceecc
Q 016331 226 IVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (391)
Q Consensus 226 II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy 270 (391)
||+....++ ..+|+++.-+.+ |+....+.|+...|+.+|+|-.
T Consensus 10 Il~~l~~~~-~~~t~~~ia~~l-~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 10 VLRALAEEP-GGLTLAELAERL-GLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHhCC-CCcCHHHHHHHh-CCCHHHHHHHHHHHHHCCCeee
Confidence 344333432 479999988776 5688899999999999999954
No 41
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=38.96 E-value=77 Score=22.46 Aligned_cols=44 Identities=20% Similarity=0.402 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhcee
Q 016331 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGII 268 (391)
Q Consensus 222 iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLI 268 (391)
.+-.||+.-.+||. +|.++..+.+ |.....+.+...-|+.-|+|
T Consensus 4 ~~~~Il~~l~~~~~--~t~~ela~~~-~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 4 TQRKILNYLRENPR--ITQKELAEKL-GISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHHCTT--S-HHHHHHHH-TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHcCC--CCHHHHHHHh-CCCHHHHHHHHHHHHHCcCc
Confidence 34567777777776 9999998765 46788999999999999998
No 42
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=38.11 E-value=40 Score=30.79 Aligned_cols=48 Identities=17% Similarity=0.214 Sum_probs=37.5
Q ss_pred HHHHHHHHHhCCCceeeHHHHhccc----CCCCHHHHHHHHHhhhhhceeccc
Q 016331 223 RNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINYC 271 (391)
Q Consensus 223 RN~II~~yr~NP~~yLT~T~cRr~L----~G~Dv~~I~RVh~FLE~WGLINy~ 271 (391)
|-.|++..... .+.||..+.-..| .+++...|.|...+|+.-|||+=-
T Consensus 28 R~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~ 79 (169)
T PRK11639 28 RLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKV 79 (169)
T ss_pred HHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEE
Confidence 56677777665 5799999985544 237788999999999999999743
No 43
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=36.29 E-value=9.6 Score=30.41 Aligned_cols=16 Identities=19% Similarity=0.563 Sum_probs=14.6
Q ss_pred cccCcCCCCCCCceee
Q 016331 346 NHCNYCSQPIPAVYYQ 361 (391)
Q Consensus 346 y~C~~Cg~DCs~~rYh 361 (391)
..|+.||.|.+..||.
T Consensus 5 lvCSTCGrDlSeeRy~ 20 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCCcchHHHHH
Confidence 5799999999999996
No 44
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=35.52 E-value=18 Score=27.26 Aligned_cols=32 Identities=25% Similarity=0.471 Sum_probs=27.5
Q ss_pred ccCcCCC-CCCCceeeeeeccCcccCCCcchhh
Q 016331 347 HCNYCSQ-PIPAVYYQSQKEVDGRFSPLTFVYL 378 (391)
Q Consensus 347 ~C~~Cg~-DCs~~rYhsqK~~dg~f~p~~~s~d 378 (391)
.|+.|++ +....||.|++=.|+-....+|...
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g 34 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSG 34 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCC
Confidence 5999996 6999999999998888888888654
No 45
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=33.62 E-value=1.6e+02 Score=24.65 Aligned_cols=53 Identities=17% Similarity=0.243 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccc
Q 016331 217 EKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (391)
Q Consensus 217 e~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~ 271 (391)
++-.+|=..||+.|.+. .+.+...+.-+.| +.+...|..++.-||..|||-=+
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l-~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEEL-GRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHH-CCChHHHHHHHHHHHHCCCccCC
Confidence 45677888999999876 7777777776655 45778999999999999999633
No 46
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=33.38 E-value=33 Score=29.90 Aligned_cols=36 Identities=25% Similarity=0.337 Sum_probs=25.2
Q ss_pred CceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccc
Q 016331 235 EKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (391)
Q Consensus 235 ~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~ 271 (391)
.+|||..+....... ....+..|.+||...||=...
T Consensus 45 gk~Lt~~e~~~~~~p-~~~~v~~V~~wL~~~G~~~~~ 80 (143)
T PF09286_consen 45 GKYLTPEEFAALFAP-SPEDVAAVKSWLKSHGLTVVE 80 (143)
T ss_dssp T----HHHHHHHHS---HHHHHHHHHHHHHCT-EEEE
T ss_pred ccCCCHHHHHHHHCC-CHHHHHHHHHHHHHcCCceeE
Confidence 689999999998876 777899999999999985544
No 47
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=31.55 E-value=85 Score=25.38 Aligned_cols=41 Identities=20% Similarity=0.353 Sum_probs=29.3
Q ss_pred HHHHHHHhCCCceeeHHHHhcccCC--CCHHHHHHHHHhhhhhce
Q 016331 225 HIVAKYMDNPEKRLIVSDCQGLVDG--VSPEDLTRIFRFLNHWGI 267 (391)
Q Consensus 225 ~II~~yr~NP~~yLT~T~cRr~L~G--~Dv~~I~RVh~FLE~WGL 267 (391)
.+|.+-++ ..|||+.++...|.. .+...|-.|+.+|+..|+
T Consensus 11 ~Li~~gK~--~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 11 KLIEKGKK--KGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHH--HSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHhh--cCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 37777765 567999999998874 788999999999999997
No 48
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=30.37 E-value=69 Score=29.53 Aligned_cols=66 Identities=14% Similarity=0.094 Sum_probs=49.7
Q ss_pred CcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccc
Q 016331 204 PHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (391)
Q Consensus 204 PEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~ 271 (391)
|.|=+-+..+.+..+|-.||..|+..= ..|...|+-.+....+ |+--..|..-..-|+.-|||-..
T Consensus 2 ~~~~~~~~~~~~e~v~~~l~~~I~~g~-l~pG~~L~e~~La~~l-gVSRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 2 PGTEKTQHISLTLQVENDLKHQLSIGA-LKPGARLITKNLAEQL-GMSITPVREALLRLVSVNALSVA 67 (221)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHhCC-CCCCCccCHHHHHHHH-CCCchhHHHHHHHHHHCCCEEec
Confidence 444444444677889999999999764 6799999877665555 45556788888889999999754
No 49
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=28.39 E-value=1.2e+02 Score=25.02 Aligned_cols=47 Identities=19% Similarity=0.388 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHhCC--CceeeHHHHhcccCCCCHHHHHHHHHhhhhhcee
Q 016331 221 ECRNHIVAKYMDNP--EKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGII 268 (391)
Q Consensus 221 ~iRN~II~~yr~NP--~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLI 268 (391)
.++..|++..+.++ .+=+.+.++.+.| +.+...|..+.+||..-|+|
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQL-GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHS-TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHh-CcCHHHHHHHHHHHHhCCeE
Confidence 45556666665522 3349999998888 77999999999999999998
No 50
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=28.28 E-value=1.7e+02 Score=21.06 Aligned_cols=41 Identities=22% Similarity=0.458 Sum_probs=32.3
Q ss_pred HHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhc
Q 016331 224 NHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWG 266 (391)
Q Consensus 224 N~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WG 266 (391)
..||....++... +|..+.-..| |+....|.|-...|+.||
T Consensus 3 ~~il~~L~~~~~~-it~~eLa~~l-~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEP-ITAKELAEEL-GVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTS-BEHHHHHHHC-TS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHh-CCCHHHHHHHHHHHHHCC
Confidence 4567766566554 9999998876 478899999999999999
No 51
>KOG4752 consensus Ribosomal protein L41 [Translation, ribosomal structure and biogenesis]
Probab=27.71 E-value=28 Score=23.28 Aligned_cols=6 Identities=50% Similarity=1.675 Sum_probs=4.4
Q ss_pred h-HHHHh
Q 016331 12 R-KWKRR 17 (391)
Q Consensus 12 r-kw~~~ 17 (391)
| ||||+
T Consensus 2 r~kwrkk 8 (26)
T KOG4752|consen 2 RAKWRKK 8 (26)
T ss_pred chHHHHH
Confidence 5 89864
No 52
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=25.93 E-value=1.8e+02 Score=21.40 Aligned_cols=53 Identities=15% Similarity=0.229 Sum_probs=36.6
Q ss_pred HHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccccCCCCC
Q 016331 224 NHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSP 277 (391)
Q Consensus 224 N~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~~~~~~ 277 (391)
.+.|-.+..+....+|.++..+.+. .+...+.|+..=|...|||.-..++..+
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~~-~~~~~vs~~i~~L~~~glv~~~~~~~d~ 57 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERLG-ISKSTVSRIIKKLEEKGLVEKERDPHDK 57 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEESSCT
T ss_pred HHHHHHHHHccCCCcCHHHHHHHHC-cCHHHHHHHHHHHHHCCCEEecCCCCcC
Confidence 3444344345788999999988764 6888999999999999999777665443
No 53
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=25.29 E-value=25 Score=36.36 Aligned_cols=13 Identities=38% Similarity=1.084 Sum_probs=10.6
Q ss_pred chh-HHHHhhcCcc
Q 016331 10 DTR-KWKRRKREPR 22 (391)
Q Consensus 10 d~r-kw~~~k~~~~ 22 (391)
+.| |||||-|+.+
T Consensus 162 nrrakwrkrErN~~ 175 (351)
T KOG0486|consen 162 NRRAKWRKRERNQQ 175 (351)
T ss_pred cchhhhhhhhhhHH
Confidence 556 9999998766
No 54
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=25.09 E-value=1.1e+02 Score=28.38 Aligned_cols=48 Identities=19% Similarity=0.352 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceecccc
Q 016331 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (391)
Q Consensus 222 iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~ 272 (391)
-|+.||..-..+.. +|+++....+ |++...+.|...-|+.-|||-...
T Consensus 2 tr~~IL~~L~~~~~--~t~~eLA~~l-gis~~tV~~~L~~Le~~GlV~r~~ 49 (203)
T TIGR02702 2 TKEDILSYLLKQGQ--ATAAALAEAL-AISPQAVRRHLKDLETEGLIEYEA 49 (203)
T ss_pred HHHHHHHHHHHcCC--CCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeEEee
Confidence 37788876655433 8999988776 578999999999999999997653
No 55
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=24.93 E-value=39 Score=25.07 Aligned_cols=30 Identities=13% Similarity=0.318 Sum_probs=24.7
Q ss_pred ccCcCC-CCCCCceeeeeeccCcccCCCcch
Q 016331 347 HCNYCS-QPIPAVYYQSQKEVDGRFSPLTFV 376 (391)
Q Consensus 347 ~C~~Cg-~DCs~~rYhsqK~~dg~f~p~~~s 376 (391)
.|+.|+ ..-...||+|+.=.|+-+...+|+
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~ 32 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYH 32 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhC
Confidence 599999 567799999999888777777765
No 56
>PRK03837 transcriptional regulator NanR; Provisional
Probab=24.21 E-value=99 Score=28.64 Aligned_cols=58 Identities=14% Similarity=0.158 Sum_probs=48.6
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcee-eHHHHhcccCCCCHHHHHHHHHhhhhhceecccc
Q 016331 213 DHTPEKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (391)
Q Consensus 213 ~kTPe~Yl~iRN~II~~yr~NP~~yL-T~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~ 272 (391)
.....+|-.||+.|+.-. .-|...| +-.+....+ |+.-..|.....-|+.-|||....
T Consensus 13 ~~~~~v~~~l~~~I~~g~-l~pG~~Lp~E~~Lae~~-gVSRt~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 13 KLSEEVEERLEQMIRSGE-FGPGDQLPSERELMAFF-GVGRPAVREALQALKRKGLVQISH 71 (241)
T ss_pred cHHHHHHHHHHHHHHhCC-CCCCCCCCCHHHHHHHh-CCCHHHHHHHHHHHHHCCCEEEec
Confidence 456789999999999998 5689999 888877766 467788999999999999998753
No 57
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=23.97 E-value=32 Score=25.77 Aligned_cols=11 Identities=55% Similarity=1.054 Sum_probs=9.1
Q ss_pred hHHHHhhcCcc
Q 016331 12 RKWKRRKREPR 22 (391)
Q Consensus 12 rkw~~~k~~~~ 22 (391)
|||..|||..+
T Consensus 31 RKw~aRkr~l~ 41 (43)
T PF08114_consen 31 RKWQARKRALQ 41 (43)
T ss_pred HHHHHHHHHHh
Confidence 79999999643
No 58
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=23.69 E-value=1e+02 Score=28.01 Aligned_cols=57 Identities=25% Similarity=0.214 Sum_probs=45.9
Q ss_pred CChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceecccc
Q 016331 214 HTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (391)
Q Consensus 214 kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~ 272 (391)
....+|..||+.|+.-- .-|...|+-.+..+.+ |+--..|.....-|+.-|||-+..
T Consensus 12 ~~~~v~~~l~~~I~~g~-l~pG~~L~e~~La~~l-gVSRtpVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 12 LTTLVQDEIERAILSGE-LPPGAKLNESDIAARL-GVSRGPVREAFRALEEAGLVRNEK 68 (212)
T ss_pred HHHHHHHHHHHHHHcCC-CCCCCEecHHHHHHHh-CCChHHHHHHHHHHHHCCCEEEec
Confidence 44679999999999975 5799999877776655 456678999999999999996543
No 59
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=23.42 E-value=31 Score=36.77 Aligned_cols=36 Identities=19% Similarity=0.348 Sum_probs=0.0
Q ss_pred hcccCcccCcCCCCCCCce-eeeeeccCcccCCCcch
Q 016331 341 ERLSENHCNYCSQPIPAVY-YQSQKEVDGRFSPLTFV 376 (391)
Q Consensus 341 e~l~ey~C~~Cg~DCs~~r-YhsqK~~dg~f~p~~~s 376 (391)
+....|+|++|..||+... .+|.-=.|-..+--||+
T Consensus 10 ~~g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs 46 (438)
T KOG0457|consen 10 DPGGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFS 46 (438)
T ss_pred cCCCCCCCccHhHHhccceEEEeecCCCcchhHHHHh
No 60
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=22.13 E-value=99 Score=28.74 Aligned_cols=58 Identities=16% Similarity=0.081 Sum_probs=47.1
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcee-eHHHHhcccCCCCHHHHHHHHHhhhhhceecccc
Q 016331 213 DHTPEKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (391)
Q Consensus 213 ~kTPe~Yl~iRN~II~~yr~NP~~yL-T~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~ 272 (391)
+.+..+|-.||+.|+.-- ..|...| +-.+....+ |+--..|..-..-|+..|||-...
T Consensus 6 ~~~~~v~~~l~~~I~~g~-l~pG~~LpsE~~La~~l-gVSRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 6 SPAGFAEEYIVESIWNNR-FPPGSILPAERELSELI-GVTRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred hhHHHHHHHHHHHHHcCC-CCCCCcCcCHHHHHHHH-CcCHHHHHHHHHHHHHCCCEEEeC
Confidence 456789999999999776 6799999 677776655 456678999999999999997554
No 61
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=21.69 E-value=1.4e+02 Score=21.52 Aligned_cols=52 Identities=21% Similarity=0.240 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHhCCCcee-eHHHHhcccCCCCHHHHHHHHHhhhhhceecc
Q 016331 217 EKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (391)
Q Consensus 217 e~Yl~iRN~II~~yr~NP~~yL-T~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy 270 (391)
+.|-.|++.|+..- ..+...+ |..+..+.+ |+....+.++..=|+..|+|-.
T Consensus 5 ~~~~~i~~~i~~~~-~~~~~~~~~~~~la~~~-~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 5 QIADQLREAILSGE-LKPGDRLPSERELAEEL-GVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred HHHHHHHHHHHcCC-CCCCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEe
Confidence 45555555555542 1233344 477766655 4577899999999999999953
No 62
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.16 E-value=55 Score=24.48 Aligned_cols=31 Identities=23% Similarity=0.393 Sum_probs=25.7
Q ss_pred ccCcCCC-CCCCceeeeeeccCcccCCCcchh
Q 016331 347 HCNYCSQ-PIPAVYYQSQKEVDGRFSPLTFVY 377 (391)
Q Consensus 347 ~C~~Cg~-DCs~~rYhsqK~~dg~f~p~~~s~ 377 (391)
.|+.|+. +-...||+|+.=.|+-+...+|..
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 5999996 666799999998888888877765
No 63
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=21.01 E-value=2.2e+02 Score=19.41 Aligned_cols=34 Identities=24% Similarity=0.363 Sum_probs=28.7
Q ss_pred ceeeHHHHhcccCCCCHHHHHHHHHhhhhhceecc
Q 016331 236 KRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (391)
Q Consensus 236 ~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy 270 (391)
..+|..+..+.+ |+....+.|....|+.-|+|..
T Consensus 13 ~~~s~~~l~~~l-~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 13 GKVSVEELAELL-GVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CCcCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEE
Confidence 358999988776 4688899999999999999964
No 64
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=20.93 E-value=1.3e+02 Score=22.93 Aligned_cols=28 Identities=29% Similarity=0.380 Sum_probs=22.1
Q ss_pred CceeeHHHHhcccC---CCCHHHHHHHHHhh
Q 016331 235 EKRLIVSDCQGLVD---GVSPEDLTRIFRFL 262 (391)
Q Consensus 235 ~~yLT~T~cRr~L~---G~Dv~~I~RVh~FL 262 (391)
...+|..+....|. ..+...+.||.+||
T Consensus 20 ~~~ls~~eia~~l~~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 20 GGPLSLSEIAARLPTSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp TS-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence 58999999977665 14788999999998
No 65
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=20.20 E-value=1.4e+02 Score=28.24 Aligned_cols=58 Identities=17% Similarity=0.173 Sum_probs=46.3
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcee-eHHHHhcccCCCCHHHHHHHHHhhhhhceecccc
Q 016331 213 DHTPEKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (391)
Q Consensus 213 ~kTPe~Yl~iRN~II~~yr~NP~~yL-T~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~ 272 (391)
...-.+|-.||+.|+..- .-|...| |-.+....+ |+--..|.....-|+..|||-...
T Consensus 9 ~~~~~v~~~l~~~I~~g~-l~pG~~LpsE~eLa~~~-gVSRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 9 RPYQEVGAMIRDLIIKTP-YNPGERLPPEREIAEML-DVTRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred cHHHHHHHHHHHHHHhCC-CCCCCcCcCHHHHHHHh-CCCHHHHHHHHHHHHHCCCEEEec
Confidence 456789999999999865 6799999 577766655 466778999999999999996443
No 66
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=20.13 E-value=1.4e+02 Score=25.07 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=24.3
Q ss_pred CceeeHHHHhcccCCCCHHHHHHHHHhhhhhce
Q 016331 235 EKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGI 267 (391)
Q Consensus 235 ~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGL 267 (391)
.++.|+..+|..|.++ +...|+.||..|.-
T Consensus 17 G~~pT~~~Vr~~lG~G---S~~ti~~~l~~w~~ 46 (120)
T PF11740_consen 17 GKKPTVRAVRERLGGG---SMSTISKHLKEWRE 46 (120)
T ss_pred CCCCCHHHHHHHHCCC---CHHHHHHHHHHHHH
Confidence 5577999999998731 68899999999963
Done!