Query 013236
Match_columns 447
No_of_seqs 153 out of 224
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 01:47:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013236.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013236hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4183 RNA polymerase I 49 kD 100.0 1.1E-75 2.4E-80 570.6 28.3 373 52-446 7-410 (413)
2 PF06870 RNA_pol_I_A49: A49-li 100.0 6.5E-73 1.4E-77 584.0 15.3 351 88-447 3-384 (385)
3 PF04801 Sin_N: Sin-like prote 66.2 7.1 0.00015 41.2 4.2 51 383-436 341-391 (421)
4 PF02042 RWP-RK: RWP-RK domain 65.0 8.4 0.00018 28.7 3.2 29 391-419 13-41 (52)
5 cd00092 HTH_CRP helix_turn_hel 57.6 30 0.00066 25.7 5.4 42 376-417 3-49 (67)
6 cd02420 Peptidase_C39D A sub-f 57.0 14 0.0003 31.3 3.7 45 379-423 13-62 (125)
7 smart00342 HTH_ARAC helix_turn 54.0 86 0.0019 23.6 7.6 35 386-421 44-80 (84)
8 cd02421 Peptidase_C39_likeD A 52.1 21 0.00045 30.1 4.0 43 381-423 10-57 (124)
9 PF01418 HTH_6: Helix-turn-hel 52.0 18 0.00038 28.7 3.3 47 370-420 14-61 (77)
10 PF00165 HTH_AraC: Bacterial r 50.3 21 0.00045 24.6 3.1 29 394-422 9-38 (42)
11 PF04967 HTH_10: HTH DNA bindi 47.3 43 0.00092 25.0 4.4 36 382-417 8-47 (53)
12 PF04703 FaeA: FaeA-like prote 46.5 32 0.0007 26.5 3.8 39 374-417 1-39 (62)
13 PF01325 Fe_dep_repress: Iron 46.0 71 0.0015 24.1 5.7 28 390-417 19-46 (60)
14 PF04760 IF2_N: Translation in 45.3 25 0.00054 25.7 3.0 29 395-423 5-34 (54)
15 PF13412 HTH_24: Winged helix- 44.9 32 0.00069 24.3 3.4 34 384-417 8-41 (48)
16 PRK15340 transcriptional regul 44.7 29 0.00064 33.4 4.1 47 376-422 107-155 (216)
17 cd02423 Peptidase_C39G A sub-f 44.5 25 0.00054 29.7 3.3 43 381-423 15-63 (129)
18 PRK11337 DNA-binding transcrip 44.1 47 0.001 32.8 5.7 64 349-420 10-73 (292)
19 PF08279 HTH_11: HTH domain; 38.8 71 0.0015 23.0 4.6 41 382-423 5-48 (55)
20 cd02417 Peptidase_C39_likeA A 38.1 55 0.0012 27.3 4.5 43 381-423 10-57 (121)
21 TIGR00122 birA_repr_reg BirA b 37.7 1.2E+02 0.0025 23.1 5.9 50 388-440 9-61 (69)
22 smart00874 B5 tRNA synthetase 37.5 70 0.0015 24.5 4.6 43 393-435 5-49 (71)
23 cd02419 Peptidase_C39C A sub-f 36.9 44 0.00095 28.2 3.7 43 381-423 15-62 (127)
24 PRK10219 DNA-binding transcrip 36.1 39 0.00085 28.0 3.2 29 394-422 22-51 (107)
25 PF01022 HTH_5: Bacterial regu 34.9 66 0.0014 22.7 3.8 26 392-417 14-39 (47)
26 PF14056 DUF4250: Domain of un 33.4 1.1E+02 0.0023 23.1 4.7 37 386-423 13-50 (55)
27 PF13730 HTH_36: Helix-turn-he 32.3 1.1E+02 0.0023 22.1 4.6 23 395-417 27-49 (55)
28 PF02082 Rrf2: Transcriptional 32.1 1.1E+02 0.0023 24.4 5.0 39 379-417 11-49 (83)
29 cd00240 TFIIFa Transcription i 30.6 1.6E+02 0.0035 27.1 6.4 45 118-168 96-140 (162)
30 PRK11511 DNA-binding transcrip 28.4 91 0.002 27.0 4.3 29 394-422 26-55 (127)
31 cd02418 Peptidase_C39B A sub-f 27.7 1E+02 0.0022 26.0 4.5 42 382-423 16-62 (136)
32 cd02424 Peptidase_C39E A sub-f 26.8 1.3E+02 0.0029 25.5 5.1 44 380-423 14-63 (129)
33 cd07377 WHTH_GntR Winged helix 26.6 99 0.0022 22.5 3.7 24 394-417 26-49 (66)
34 PRK10141 DNA-binding transcrip 25.6 95 0.0021 26.9 3.8 30 389-418 26-55 (117)
35 COG3413 Predicted DNA binding 25.6 1.1E+02 0.0023 29.1 4.5 35 382-416 163-201 (215)
36 PF03484 B5: tRNA synthetase B 25.4 1.5E+02 0.0032 22.9 4.6 32 393-424 5-38 (70)
37 PF09012 FeoC: FeoC like trans 24.8 71 0.0015 24.5 2.7 32 386-417 7-38 (69)
38 COG1321 TroR Mn-dependent tran 23.0 1.9E+02 0.0041 26.2 5.5 48 370-421 4-55 (154)
39 COG2207 AraC AraC-type DNA-bin 22.8 1.8E+02 0.004 23.7 5.1 29 394-422 37-66 (127)
40 PF12840 HTH_20: Helix-turn-he 22.7 1.3E+02 0.0027 22.4 3.6 29 389-417 20-48 (61)
41 smart00345 HTH_GNTR helix_turn 22.3 1.3E+02 0.0028 21.3 3.6 23 395-417 22-44 (60)
42 PRK15186 AraC family transcrip 21.8 2E+02 0.0043 28.9 5.9 29 394-422 198-226 (291)
43 PF09816 EAF: RNA polymerase I 21.7 4.9E+02 0.011 21.9 10.1 38 119-164 65-102 (109)
44 cd02425 Peptidase_C39F A sub-f 21.4 1.2E+02 0.0027 25.2 3.7 40 383-422 17-61 (126)
45 COG1737 RpiR Transcriptional r 21.0 78 0.0017 31.4 2.8 60 353-420 4-63 (281)
46 smart00419 HTH_CRP helix_turn_ 20.7 1.2E+02 0.0025 20.7 2.9 26 392-417 7-32 (48)
47 smart00550 Zalpha Z-DNA-bindin 20.1 1.7E+02 0.0036 22.6 3.9 24 394-417 23-46 (68)
No 1
>KOG4183 consensus RNA polymerase I 49 kDa subunit [Transcription]
Probab=100.00 E-value=1.1e-75 Score=570.60 Aligned_cols=373 Identities=27% Similarity=0.447 Sum_probs=299.0
Q ss_pred eeEEEEEEecCCCCCCCCEEEEc--CCCCCCCCCCCCCCCCCcEEEEeccccccCCCCcccEEEecCCCCeeEEeccCC-
Q 013236 52 RVKAKVQFIPEQPNKAPPLVGYF--PSIYKPDVDHPDEEMRPKVRVYRNMNEKKNRTGRMELVVSPRDSSVDYVGTSYS- 128 (447)
Q Consensus 52 ~~~v~v~~~~~~~~~~~P~v~~F--~~G~~p~~~~~~~~~~~~F~ly~~~~~~~~~~~r~~~vv~~e~~~l~YvG~~~~- 128 (447)
++.-.|..+...++...|+|++| .+|+.++ +++.|+||++++.++ .|.++||+|++++|+|+|.|++
T Consensus 7 rv~r~v~~~ae~svqi~plva~s~~~~gfr~p-------entrftlyKkkdssk---~r~q~vl~geteRleyvg~n~s~ 76 (413)
T KOG4183|consen 7 RVARWVYCGAEDSVQIAPLVAFSDPNGGFRSP-------ENTRFTLYKKKDSSK---PRNQRVLAGETERLEYVGNNFST 76 (413)
T ss_pred chhheeeccCcccccccceeeeecCcCCccCC-------CCceEEEeecccccC---cccceeeeCCCceeEEEecccch
Confidence 34445667777888999999997 8888764 889999999975433 3568999999999999999998
Q ss_pred CCCCCccCCceEEEEEeCCCCcEEEEeccccceeeecccccCccccccccCCccccHHHHHHHHHHHHHhhchhHHHHHH
Q 013236 129 GEAMAPQFCHYAVGVLDRSTQTLKIVPIAANKIFRLEPRVRGSDVADKDAGKGEISAEVQANMKAMLDTRYGTKKSLRQS 208 (447)
Q Consensus 129 ~~~~~~~~~~Y~VgV~dk~T~~l~l~Pv~~~ki~~l~p~vk~~~~~~~~~~~~~~~~~~~~~~r~~L~eaFGTKKaKkai 208 (447)
++.. .++|+|||+||.+++|+|+|+....++.+.+.++...... -+..++...+++|+.||+||||+|+||||
T Consensus 77 ~A~~---~nty~Vgvfnke~k~~~iypa~~ln~~~l~~~vk~e~~~~----lesk~~tv~~elr~~lgeafgT~K~KKAi 149 (413)
T KOG4183|consen 77 GALK---CNTYCVGVFNKESKQMEIYPAELLNMQPLFSDVKVESELA----LESKTKTVREELRDSLGEAFGTTKQKKAI 149 (413)
T ss_pred hhhh---hcceEEEEeccCCceeEEeehhhhceeecchhhhhhcchh----hhhccccchHHHHhhHHHhhCchHHHHHH
Confidence 3333 4678899999999999999997666666555554332221 01122233479999999999999999999
Q ss_pred HHHHHhccCCChhhHHHHHHHhhhhhhhhhhhccccc-----ccCCCCCCCCCCCCCCCCCccCCCCCChhHHHHHHHHH
Q 013236 209 KKMHALNKENDPESQKDLALKMKSVKINKEALESTTS-----DTVLNVPPYDANATTPQQAYPLDKIILKGEWDFVQDIF 283 (447)
Q Consensus 209 ~~~e~~~~~~d~~~~~~L~~~v~~v~~~~~~l~~~e~-----~~~r~iPp~N~dAt~pedVY~le~IIp~~e~~~L~e~~ 283 (447)
...++|+++.+.+.+.+.+ .|.++..++.++++++. ..+|||||||.+||+|+|+||||+|||++||.+|+...
T Consensus 150 ~~~~~nRv~~e~l~daa~q-~v~~v~~a~~~lpt~ad~~~~~~qdrpiPp~n~dAt~~edaYplEdIIpk~E~sfl~~~s 228 (413)
T KOG4183|consen 150 NTRRMNRVGNESLNDAAAQ-AVETVIDAKGVLPTVADAIHNDLQDRPIPPCNDDATKPEDAYPLEDIIPKAEYSFLQSPS 228 (413)
T ss_pred HHHHHhhhcccccchHHHH-HHHHHHhhccccccHHhhhhhccccCCCCCcccccCCHHhcccHHhcCChhhhhhhcChH
Confidence 9998888766655555544 67777766677776442 35899999999999999999999999999999999555
Q ss_pred HHhhcCc-c-c----ccCCCChhHHHHHhHhhccCchHHHHHHHHHHHHHHHHHHhhhccCcCcc-c-ccccCCCCHHHH
Q 013236 284 NHVSAGS-E-V----ISDAYPSFVCNRIHKLREIQDDVEKQTLASIFSYITHLVKFKDQHSMDGG-A-SAKQHRIPKILH 355 (447)
Q Consensus 284 ~~l~~~~-e-~----~~~~~s~fV~~rL~~l~~~~~~~~k~~~~~iL~Yls~Ll~f~~~~~~~k~-~-~~~l~~~p~~v~ 355 (447)
.|.+.+ + + .-...|.||..||.+|...+ ...+.++|||||++|++|+..|.++.+ . ..+++++|++++
T Consensus 229 -~l~n~d~e~~lel~py~~~~~fvnerl~sL~d~e---sdmkkar~lyylslL~~f~~~Rrv~nk~~l~~kl~~pPeIl~ 304 (413)
T KOG4183|consen 229 -ALRNVDSEEILELIPYNSHCTFVNERLKSLPDVE---SDMKKARCLYYLSLLIKFRAHRRVKNKSALGPKLHGPPEILN 304 (413)
T ss_pred -HHhCccHHHHHhhccccccchHHHHHHhhcccch---hhhHHHHHHHHHHHHHHHHHHHhcccccccchhhcCCcHHHH
Confidence 666654 2 1 12345789999999997322 344457899999999999854333332 3 678999999999
Q ss_pred HHHHhhcccCC------CCccCHHHHHHHHHHHHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHhCCEEeecC----
Q 013236 356 QKFLTSFSDAE------SKRLSDDKIHLLISYVLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKLGCKLLREK---- 425 (447)
Q Consensus 356 ~~il~~Ft~~~------~~~~s~~~~dkLl~yilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc~v~k~~---- 425 (447)
++|+++||+.. +..||+.++|||+|||||||||+|||.+|+++||+||++++++|+++||+|||+|.+.+
T Consensus 305 dkllsrFt~~t~~~~~~s~~Is~~~~dkIicYvLvL~LhvdNf~tD~t~La~DLnlst~k~~elfr~lgcki~k~tvtqa 384 (413)
T KOG4183|consen 305 DKLLSRFTCLTYNNGRLSNLISDSMKDKIICYVLVLALHVDNFQTDLTVLARDLNLSTKKMMELFRALGCKISKRTVTQA 384 (413)
T ss_pred HHHHhheeecccCCcccceecChHHhhHHHHHHHHHHHhhcccccchHHHHhhcccCHHHHHHHHHHhcceeeccchHHh
Confidence 99999999852 25799999999999999999999999999999999999999999999999999998853
Q ss_pred -----CeEEEEEcCCCCCCccccccC
Q 013236 426 -----NMLYATLPVPLQFPKAIQRRR 446 (447)
Q Consensus 426 -----~~kia~LkvPl~fP~~~rr~~ 446 (447)
+|++|||++||+||++.||+|
T Consensus 385 ~a~g~~hK~atLk~Pl~fpe~~rRgr 410 (413)
T KOG4183|consen 385 AASGEDHKLATLKLPLPFPETSRRGR 410 (413)
T ss_pred hhcccccceeeeccCCCCcccchhcc
Confidence 699999999999999977665
No 2
>PF06870 RNA_pol_I_A49: A49-like RNA polymerase I associated factor ; InterPro: IPR009668 Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homologue indicates that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3NFG_A 3NFH_B.
Probab=100.00 E-value=6.5e-73 Score=584.00 Aligned_cols=351 Identities=32% Similarity=0.560 Sum_probs=181.9
Q ss_pred CCCCcEEEEeccccccCCCCcccEEEecCCCCeeEEeccCC-CCCCCccCCceEEEEEeCCCCcEEEEeccccceeee-c
Q 013236 88 EMRPKVRVYRNMNEKKNRTGRMELVVSPRDSSVDYVGTSYS-GEAMAPQFCHYAVGVLDRSTQTLKIVPIAANKIFRL-E 165 (447)
Q Consensus 88 ~~~~~F~ly~~~~~~~~~~~r~~~vv~~e~~~l~YvG~~~~-~~~~~~~~~~Y~VgV~dk~T~~l~l~Pv~~~ki~~l-~ 165 (447)
++++.|++|+|+ ..++++.+++|+|++++|+|+|++++ ++..++++|+||||||||+||+|+|+|+. .+.+ .
T Consensus 3 p~~~~F~~y~~~---~~~~~~~~~~l~~~~~~v~y~g~~~~~~~~~~~~~~~y~vgv~dk~T~~l~l~~a~---~~~~~~ 76 (385)
T PF06870_consen 3 PSSTKFTLYKHK---NKSRKKSELVLHGETDRVEYVGRNFGTGESAANQLCKYYVGVYDKETGTLELVPAP---LFTLRR 76 (385)
T ss_dssp -TT-EEEEEEE------------EEEEEE-SSEEEEEE--HHHHHHE----EEEEEEEETTTTEEEEEEE----EEEE-E
T ss_pred CCCCeeEEeccC---CCccccccEEEEcCCCceEEEEeecCcccccccccccEEEEEEeCCCCcEEEEEec---ceeecc
Confidence 388999999995 12334668999999999999999997 34445678999999999999999999985 4666 4
Q ss_pred ccccCccccccccCCccccHHHHHHHHHHHHHhhchhHHHHHHHHHHHhccCCChhhHHHHHHHhhhhhhhhhhhccc--
Q 013236 166 PRVRGSDVADKDAGKGEISAEVQANMKAMLDTRYGTKKSLRQSKKMHALNKENDPESQKDLALKMKSVKINKEALEST-- 243 (447)
Q Consensus 166 p~vk~~~~~~~~~~~~~~~~~~~~~~r~~L~eaFGTKKaKkai~~~e~~~~~~d~~~~~~L~~~v~~v~~~~~~l~~~-- 243 (447)
+.++...... .....+...+.+.++|++|+++|||||+||++.++++|+++.+.+ ...++..+++|..+..++++.
T Consensus 77 ~~~~~~~~~~-~~~~~~~~~~~~~~~r~~L~~aFGTkK~Kral~~~e~n~v~~~~l-~~~~~~~~~~i~~~~~~~~~~~e 154 (385)
T PF06870_consen 77 VIVKSKKELE-GPDDESLSDESYREQRNALGEAFGTKKAKRALQSRERNKVDSEAL-EDAASAIVSSIAEATADLPTKEE 154 (385)
T ss_dssp EEE-----------------------------------------------------------------------------
T ss_pred hhhhcccccc-ccccccccchhHHHHHHHHHHHhccHHHHHHHHHHHHhcccchhh-HHHHHHHHHhhhhhcccccchhH
Confidence 4444333221 111122356788999999999999999999999999998665533 233344456666555555542
Q ss_pred ---ccccCCCCCCCCCCCCCCCCCccCCCCCChhHHHHHHHHHHHhhcCc---cc--ccCCCChhHHHHHhHhhccCchH
Q 013236 244 ---TSDTVLNVPPYDANATTPQQAYPLDKIILKGEWDFVQDIFNHVSAGS---EV--ISDAYPSFVCNRIHKLREIQDDV 315 (447)
Q Consensus 244 ---e~~~~r~iPp~N~dAt~pedVY~le~IIp~~e~~~L~e~~~~l~~~~---e~--~~~~~s~fV~~rL~~l~~~~~~~ 315 (447)
+.+.+++|||||++|++|+|||||++|||.++|++|+ +...+.... ++ ....+|.||.+||..|...++..
T Consensus 155 ~~~~~~~~r~iPp~n~~At~p~dVY~l~~iI~~~e~~~l~-~~~~~~~~~~~~~~~~~~~~~s~~V~~rl~~l~~~~~~~ 233 (385)
T PF06870_consen 155 LAEASDANRPIPPYNLDATSPEDVYPLEDIIPPEELEALP-VEAWLEAVDPEEELQLLPYSYSEFVANRLKRLSESKDEK 233 (385)
T ss_dssp TTTTSSTTSSS----TT-SSGGGSS-HHHHS-HHHHTT----HHHHH--SHHHHHHTSS-S--HHHHHHHTT--SGGGH-
T ss_pred HHhhhhccCCCCCCCCCCCCHHHccCHHHcCCHHHHHhcc-chhhhhhccchhhhhcccccCCHHHHHHHHHhhccccch
Confidence 2345799999999999999999999999999999998 444444433 22 23378999999999998665544
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCcCccc--ccccCCCCHHHHHHHHhhcccC------CCCccCHHHHHHHHHHHHHHHH
Q 013236 316 EKQTLASIFSYITHLVKFKDQHSMDGGA--SAKQHRIPKILHQKFLTSFSDA------ESKRLSDDKIHLLISYVLVLTL 387 (447)
Q Consensus 316 ~k~~~~~iL~Yls~Ll~f~~~~~~~k~~--~~~l~~~p~~v~~~il~~Ft~~------~~~~~s~~~~dkLl~yilvLaL 387 (447)
.+.+.+|||+||++|+.|+..+.+.++. ...+..+|++|+++|+++|++. +++.||++++||||||||||||
T Consensus 234 ~~~~~~~~L~Yl~~Li~~~~~r~~~~k~~~~~~l~~~p~~v~~~ll~~Ft~~~~~~~~~~~~~s~~~~dkLl~~il~LaL 313 (385)
T PF06870_consen 234 DRKRKLRILRYLSHLIKFYRSRSVKKKDKLEEKLSPIPEIVIDKLLDRFTESSSSSGSRSYQISKTMKDKLLTYILALAL 313 (385)
T ss_dssp ---HHHHHHHHHHHHHHHHHTTT--CHHHHHHHS----HHHHHHHHHHHSEE-------BEE--HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHcCccccchhhhccccCCCHHHHHHHHHHccCcccCCCCcCcccCHHHHHHHHHHHHHHHH
Confidence 5677789999999999999887665443 4556779999999999999986 2367999999999999999999
Q ss_pred hcCCCccCcHhHHHHhCCCHHHHHHHHHHhCCEEee-----------cCCeEEEEEcCCCCCCccccccCC
Q 013236 388 HADDFRTNPTDIAKDLRMSEFKLRDHFEKLGCKLLR-----------EKNMLYATLPVPLQFPKAIQRRRR 447 (447)
Q Consensus 388 ~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc~v~k-----------~~~~kia~LkvPl~fP~~~rr~~r 447 (447)
|||||++|+++||+||+|++++|.+|||+|||+|++ .+++++|+|++||+||++++|++|
T Consensus 314 ~id~f~~d~~~L~~dLkl~~~~l~~~~r~LGC~v~~~~~~~~~~~~~~~~~~~a~L~~PL~fP~~~~~~~r 384 (385)
T PF06870_consen 314 HIDNFSVDITDLARDLKLSPKKLTQYFRELGCKVKKATEALGLSKSEAKTHKIATLKLPLKFPKPRRRRRR 384 (385)
T ss_dssp HHTTTEEEHHHHHHHHT--HHHHHHHHHHTT-EEEE--HHHT--GGGGGGSEEEE----------------
T ss_pred HhcCcccChHHHHHHhCCCHHHHHHHHHHhCCEecccccccccccccccceeEEEEeCCCCCCCcccccCC
Confidence 999999999999999999999999999999999988 236999999999999999999874
No 3
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=66.19 E-value=7.1 Score=41.20 Aligned_cols=51 Identities=8% Similarity=0.126 Sum_probs=38.5
Q ss_pred HHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHhCCEEeecCCeEEEEEcCCC
Q 013236 383 LVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKLGCKLLREKNMLYATLPVPL 436 (447)
Q Consensus 383 lvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc~v~k~~~~kia~LkvPl 436 (447)
+||+|+-.+=.|.-..|....++.+..+.+++..++..- ...+...|++|.
T Consensus 341 ~iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~a~~~---~~~~~W~lk~~~ 391 (421)
T PF04801_consen 341 YILLLFTKSRYVKRKELMSATKLPPEDVKEILKEIAVLR---PSNRGWKLKLPP 391 (421)
T ss_pred HHHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHHhhcc---CCCCceEEccCc
Confidence 344555544448889999999999999999999999854 135667888774
No 4
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=65.04 E-value=8.4 Score=28.69 Aligned_cols=29 Identities=28% Similarity=0.368 Sum_probs=26.8
Q ss_pred CCccCcHhHHHHhCCCHHHHHHHHHHhCC
Q 013236 391 DFRTNPTDIAKDLRMSEFKLRDHFEKLGC 419 (447)
Q Consensus 391 nf~vd~~~La~dLkl~~~kl~~~fr~LGc 419 (447)
-|.+.+.+-|+.|+++...|...||.+|.
T Consensus 13 ~fhlp~~eAA~~Lgv~~T~LKr~CR~~GI 41 (52)
T PF02042_consen 13 YFHLPIKEAAKELGVSVTTLKRRCRRLGI 41 (52)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 47788999999999999999999999995
No 5
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=57.60 E-value=30 Score=25.70 Aligned_cols=42 Identities=21% Similarity=0.301 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHhc-----CCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 376 HLLISYVLVLTLHA-----DDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 376 dkLl~yilvLaL~l-----dnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
.++..|++-|+-.. .++.+...+||+.++++...+..+++.|
T Consensus 3 ~ria~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L 49 (67)
T cd00092 3 ERLASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKEL 49 (67)
T ss_pred hHHHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45666766666554 4566788999999999999998887655
No 6
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=57.01 E-value=14 Score=31.30 Aligned_cols=45 Identities=9% Similarity=-0.068 Sum_probs=36.4
Q ss_pred HHHHHHHHHhcCCCccCcHhHHHHhC-----CCHHHHHHHHHHhCCEEee
Q 013236 379 ISYVLVLTLHADDFRTNPTDIAKDLR-----MSEFKLRDHFEKLGCKLLR 423 (447)
Q Consensus 379 l~yilvLaL~ldnf~vd~~~La~dLk-----l~~~kl~~~fr~LGc~v~k 423 (447)
..++|++++..-+..++.+.|+..+. .+...|...++.+|.+...
T Consensus 13 gl~~l~~i~~~~g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl~~~~ 62 (125)
T cd02420 13 GAASLAIILAYYGRYVPLSELRIACGVSRDGSNASNLLKAAREYGLTAKG 62 (125)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHcCCCCCCCCHHHHHHHHHHcCcccce
Confidence 44566677778899999999999874 6788999999999976643
No 7
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=53.97 E-value=86 Score=23.65 Aligned_cols=35 Identities=23% Similarity=0.262 Sum_probs=27.9
Q ss_pred HHhcCCCccCcHhHHHHhCC-CHHHHHHHH-HHhCCEE
Q 013236 386 TLHADDFRTNPTDIAKDLRM-SEFKLRDHF-EKLGCKL 421 (447)
Q Consensus 386 aL~ldnf~vd~~~La~dLkl-~~~kl~~~f-r~LGc~v 421 (447)
.++.++ ...+.+||..+++ ++..+...| +..||.+
T Consensus 44 ~~l~~~-~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~sp 80 (84)
T smart00342 44 RLLRDT-DLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80 (84)
T ss_pred HHHHcC-CCCHHHHHHHhCCCChHHHHHHHHHHHCcCh
Confidence 333444 7889999999999 999999999 5567754
No 8
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=52.15 E-value=21 Score=30.12 Aligned_cols=43 Identities=14% Similarity=0.032 Sum_probs=34.7
Q ss_pred HHHHHHHhcCCCccCcHhHHHHhC-----CCHHHHHHHHHHhCCEEee
Q 013236 381 YVLVLTLHADDFRTNPTDIAKDLR-----MSEFKLRDHFEKLGCKLLR 423 (447)
Q Consensus 381 yilvLaL~ldnf~vd~~~La~dLk-----l~~~kl~~~fr~LGc~v~k 423 (447)
.+|++++..-+..++.+.|+..++ ++...+...++.+|.++..
T Consensus 10 ~~l~~i~~~~g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl~~~~ 57 (124)
T cd02421 10 DCLVLLARQFGKPASRDSLVAGLPLDDGRLSPALFPRAAARAGLSARV 57 (124)
T ss_pred HHHHHHHHHhCCCCCHHHHHhcCCCCCCCcCHHHHHHHHHHCCCccee
Confidence 456666777788899999998874 7888999999999976643
No 9
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=51.96 E-value=18 Score=28.69 Aligned_cols=47 Identities=21% Similarity=0.318 Sum_probs=31.2
Q ss_pred cCHHHHHHHHHHHHHHHHhcCCC-ccCcHhHHHHhCCCHHHHHHHHHHhCCE
Q 013236 370 LSDDKIHLLISYVLVLTLHADDF-RTNPTDIAKDLRMSEFKLRDHFEKLGCK 420 (447)
Q Consensus 370 ~s~~~~dkLl~yilvLaL~ldnf-~vd~~~La~dLkl~~~kl~~~fr~LGc~ 420 (447)
+++. ..++.-||+- +.+++ ...+.+||+.++++++.|..+++.||+.
T Consensus 14 ls~~-e~~Ia~yil~---~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 14 LSPT-EKKIADYILE---NPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp S-HH-HHHHHHHHHH----HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTT
T ss_pred CCHH-HHHHHHHHHh---CHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 4443 3456666654 33332 2577999999999999999999999984
No 10
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=50.26 E-value=21 Score=24.58 Aligned_cols=29 Identities=24% Similarity=0.184 Sum_probs=22.7
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
..+.+||..+++++.-+...|+.. ||.+.
T Consensus 9 ~~l~~iA~~~g~S~~~f~r~Fk~~~g~tp~ 38 (42)
T PF00165_consen 9 LTLEDIAEQAGFSPSYFSRLFKKETGMTPK 38 (42)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHTSS-HH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcCHH
Confidence 567999999999999999999987 98753
No 11
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=47.30 E-value=43 Score=24.98 Aligned_cols=36 Identities=17% Similarity=0.350 Sum_probs=28.1
Q ss_pred HHHHHHhcCCCc----cCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 382 VLVLTLHADDFR----TNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 382 ilvLaL~ldnf~----vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
+|..|+...=|. +.+.+||..|+++++.+..+.|..
T Consensus 8 ~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 8 ILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 455566655444 688999999999999999998853
No 12
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=46.47 E-value=32 Score=26.48 Aligned_cols=39 Identities=23% Similarity=0.291 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 374 KIHLLISYVLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 374 ~~dkLl~yilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
|+++++.||=-+ +--+...++|+.++|+..++..|...|
T Consensus 1 ~ke~Il~~i~~~-----~~p~~T~eiA~~~gls~~~aR~yL~~L 39 (62)
T PF04703_consen 1 MKEKILEYIKEQ-----NGPLKTREIADALGLSIYQARYYLEKL 39 (62)
T ss_dssp -HHCHHHHHHHH-----TS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CcHHHHHHHHHc-----CCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 577888887766 444778999999999999999998876
No 13
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=46.03 E-value=71 Score=24.14 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=24.6
Q ss_pred CCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 390 DDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 390 dnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
++-.+-..+||+.|++++..+..+++.|
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L 46 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRL 46 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHH
Confidence 7788999999999999999999988876
No 14
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=45.33 E-value=25 Score=25.74 Aligned_cols=29 Identities=17% Similarity=0.351 Sum_probs=22.4
Q ss_pred CcHhHHHHhCCCHHHHHHHH-HHhCCEEee
Q 013236 395 NPTDIAKDLRMSEFKLRDHF-EKLGCKLLR 423 (447)
Q Consensus 395 d~~~La~dLkl~~~kl~~~f-r~LGc~v~k 423 (447)
-+.+||++|+++++.|...+ ..+|-.+.+
T Consensus 5 ~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~ 34 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKKLFKELGIMVKS 34 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHHH-HHHTS---S
T ss_pred EHHHHHHHHCcCHHHHHHHHHHhCCcCcCC
Confidence 46799999999999999999 559988544
No 15
>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=44.88 E-value=32 Score=24.26 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=25.9
Q ss_pred HHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 384 VLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 384 vLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
+|.+..+|-.+....||+.++++...+..+++.|
T Consensus 8 Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 8 ILNYLRENPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp HHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3344445667999999999999999999999876
No 16
>PRK15340 transcriptional regulator InvF; Provisional
Probab=44.74 E-value=29 Score=33.42 Aligned_cols=47 Identities=26% Similarity=0.171 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHhcCCCc-cCcHhHHHHhCCCHHHHHHHHHH-hCCEEe
Q 013236 376 HLLISYVLVLTLHADDFR-TNPTDIAKDLRMSEFKLRDHFEK-LGCKLL 422 (447)
Q Consensus 376 dkLl~yilvLaL~ldnf~-vd~~~La~dLkl~~~kl~~~fr~-LGc~v~ 422 (447)
++.=||-|+..|+-+... ..++.||+.+++++..+..+|+. +|+.+.
T Consensus 107 r~~e~y~l~~~Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk~~~G~tpk 155 (216)
T PRK15340 107 RKSESYWLVGYLLAQSTSGNTMRMLGEDYGVSYTHFRRLCSRALGGKAK 155 (216)
T ss_pred HHHHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH
Confidence 444567777777776555 78999999999999999999998 588764
No 17
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=44.50 E-value=25 Score=29.68 Aligned_cols=43 Identities=21% Similarity=0.172 Sum_probs=32.1
Q ss_pred HHHHHHHhcCC-CccCcHhHHHHh-----CCCHHHHHHHHHHhCCEEee
Q 013236 381 YVLVLTLHADD-FRTNPTDIAKDL-----RMSEFKLRDHFEKLGCKLLR 423 (447)
Q Consensus 381 yilvLaL~ldn-f~vd~~~La~dL-----kl~~~kl~~~fr~LGc~v~k 423 (447)
+++++.+..-+ ..++...|+..+ +.+...|...++.+|.+...
T Consensus 15 ~~l~~~~~~~g~~~~~~~~l~~~~~~~~~~~s~~~l~~~a~~~Gl~~~~ 63 (129)
T cd02423 15 AALATLLRYYGGINITEQEVLKLMLIRSEGFSMLDLKRYAEALGLKANG 63 (129)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCcccCCcCHHHHHHHHHHCCCcceE
Confidence 34444444445 889999999876 47889999999999977644
No 18
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=44.11 E-value=47 Score=32.82 Aligned_cols=64 Identities=20% Similarity=0.094 Sum_probs=47.3
Q ss_pred CCCHHHHHHHHhhcccCCCCccCHHHHHHHHHHHHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHhCCE
Q 013236 349 RIPKILHQKFLTSFSDAESKRLSDDKIHLLISYVLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKLGCK 420 (447)
Q Consensus 349 ~~p~~v~~~il~~Ft~~~~~~~s~~~~dkLl~yilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc~ 420 (447)
+-|..|++.|..++.. +|+. ..++..||+-=.=.+- ...+.+||+..+.++..+.-++|.|||.
T Consensus 10 ~~~~~i~~~i~~~~~~-----Lt~~-e~~Ia~yil~~~~~v~--~~si~~lA~~~~vS~aTi~Rf~kkLGf~ 73 (292)
T PRK11337 10 PNGIGLGPYIRMKQEG-----LTPL-ESRVVEWLLKPGDLSE--ATALKDIAEALAVSEAMIVKVAKKLGFS 73 (292)
T ss_pred cCchhHHHHHHHHHhh-----cCHH-HHHHHHHHHhCHHHHH--hcCHHHHHHHhCCChHHHHHHHHHcCCC
Confidence 3577888899998864 5554 5577777763211111 1367999999999999999999999996
No 19
>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=38.79 E-value=71 Score=23.01 Aligned_cols=41 Identities=22% Similarity=0.399 Sum_probs=28.1
Q ss_pred HHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHh---CCEEee
Q 013236 382 VLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKL---GCKLLR 423 (447)
Q Consensus 382 ilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~L---Gc~v~k 423 (447)
||-+.+--+++ +....||+.|+++...+..+...| |+.|.+
T Consensus 5 il~~L~~~~~~-it~~eLa~~l~vS~rTi~~~i~~L~~~~~~I~~ 48 (55)
T PF08279_consen 5 ILKLLLESKEP-ITAKELAEELGVSRRTIRRDIKELREWGIPIES 48 (55)
T ss_dssp HHHHHHHTTTS-BEHHHHHHHCTS-HHHHHHHHHHHHHTT-EEEE
T ss_pred HHHHHHHcCCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEe
Confidence 33333345566 999999999999999998887665 544443
No 20
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=38.06 E-value=55 Score=27.27 Aligned_cols=43 Identities=19% Similarity=0.251 Sum_probs=35.4
Q ss_pred HHHHHHHhcCCCccCcHhHHHHhC-----CCHHHHHHHHHHhCCEEee
Q 013236 381 YVLVLTLHADDFRTNPTDIAKDLR-----MSEFKLRDHFEKLGCKLLR 423 (447)
Q Consensus 381 yilvLaL~ldnf~vd~~~La~dLk-----l~~~kl~~~fr~LGc~v~k 423 (447)
.+|++.+..-+..++.+.|+..+. ++...|...++.+|.+...
T Consensus 10 ~~l~~i~~~~g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl~~~~ 57 (121)
T cd02417 10 LALVLLARYHGIAADPEQLRHEFGLAGEPFNSTELLLAAKSLGLKAKA 57 (121)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhcCCCCCCCHHHHHHHHHHcCCeeEE
Confidence 455666667788899999999874 7889999999999987754
No 21
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=37.66 E-value=1.2e+02 Score=23.10 Aligned_cols=50 Identities=24% Similarity=0.314 Sum_probs=35.5
Q ss_pred hcCCCccCcHhHHHHhCCCHHHHHHHHHHh---CCEEeecCCeEEEEEcCCCCCCc
Q 013236 388 HADDFRTNPTDIAKDLRMSEFKLRDHFEKL---GCKLLREKNMLYATLPVPLQFPK 440 (447)
Q Consensus 388 ~ldnf~vd~~~La~dLkl~~~kl~~~fr~L---Gc~v~k~~~~kia~LkvPl~fP~ 440 (447)
..+++.. ...||+.|+++...+..+.+.| |..+... .+-..|..|+.+|.
T Consensus 9 L~~~~~~-~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~--~~g~~l~~~~~ll~ 61 (69)
T TIGR00122 9 LADNPFS-GEKLGEALGMSRTAVNKHIQTLREWGVDVLTV--GKGYRLPPPIPLLN 61 (69)
T ss_pred HHcCCcC-HHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec--CCceEecCccccCC
Confidence 3366654 9999999999999999998877 5544443 23445666666654
No 22
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=37.47 E-value=70 Score=24.46 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=30.1
Q ss_pred ccCcHhHHHHhC--CCHHHHHHHHHHhCCEEeecCCeEEEEEcCC
Q 013236 393 RTNPTDIAKDLR--MSEFKLRDHFEKLGCKLLREKNMLYATLPVP 435 (447)
Q Consensus 393 ~vd~~~La~dLk--l~~~kl~~~fr~LGc~v~k~~~~kia~LkvP 435 (447)
.++.+.+.+-|| ++..++..+++.|||.+...+........+|
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~~~~~~~~~~v~~P 49 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVEVSGDDDTLEVTVP 49 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEEecCCCCeEEEECC
Confidence 456677777776 6788999999999999975322223444555
No 23
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=36.87 E-value=44 Score=28.16 Aligned_cols=43 Identities=12% Similarity=0.104 Sum_probs=33.9
Q ss_pred HHHHHHHhcCCCccCcHhHHHHh-----CCCHHHHHHHHHHhCCEEee
Q 013236 381 YVLVLTLHADDFRTNPTDIAKDL-----RMSEFKLRDHFEKLGCKLLR 423 (447)
Q Consensus 381 yilvLaL~ldnf~vd~~~La~dL-----kl~~~kl~~~fr~LGc~v~k 423 (447)
.+|++.++.-+..++...|...+ +.+...+..+++.+|.+...
T Consensus 15 ~~l~~~~~~~g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl~~~~ 62 (127)
T cd02419 15 ACLAMIASYHGHHVDLASLRQRFPVSLKGATLADLIDIAQQLGLSTRA 62 (127)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHcCCCCCCcCHHHHHHHHHHCCCceeE
Confidence 34555566678889999999886 47888999999999987644
No 24
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=36.08 E-value=39 Score=28.01 Aligned_cols=29 Identities=24% Similarity=0.196 Sum_probs=26.2
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
+++++||+.+++++..+..+|+.. |..+.
T Consensus 22 ~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~ 51 (107)
T PRK10219 22 LNIDVVAKKSGYSKWYLQRMFRTVTHQTLG 51 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcCHH
Confidence 889999999999999999999996 87653
No 25
>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=34.94 E-value=66 Score=22.70 Aligned_cols=26 Identities=23% Similarity=0.386 Sum_probs=22.2
Q ss_pred CccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 392 FRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 392 f~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
-...+.+|++.|++++..+..|.+.|
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L 39 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKL 39 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCchhhHHHhccccchHHHHHHHHH
Confidence 56788999999999999999998765
No 26
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=33.35 E-value=1.1e+02 Score=23.12 Aligned_cols=37 Identities=11% Similarity=0.359 Sum_probs=31.4
Q ss_pred HHhc-CCCccCcHhHHHHhCCCHHHHHHHHHHhCCEEee
Q 013236 386 TLHA-DDFRTNPTDIAKDLRMSEFKLRDHFEKLGCKLLR 423 (447)
Q Consensus 386 aL~l-dnf~vd~~~La~dLkl~~~kl~~~fr~LGc~v~k 423 (447)
...+ |+|. +++.|+.++.++...|..-...+|.....
T Consensus 13 N~kLRD~~~-sLd~Lc~~~~id~~~l~~kL~~~Gy~Y~~ 50 (55)
T PF14056_consen 13 NMKLRDEYS-SLDELCYDYDIDKEELEEKLASIGYEYDE 50 (55)
T ss_pred HHHHHhccC-CHHHHHHHhCCCHHHHHHHHHHcCCeEch
Confidence 3445 5555 99999999999999999999999998765
No 27
>PF13730 HTH_36: Helix-turn-helix domain
Probab=32.32 E-value=1.1e+02 Score=22.06 Aligned_cols=23 Identities=26% Similarity=0.398 Sum_probs=20.7
Q ss_pred CcHhHHHHhCCCHHHHHHHHHHh
Q 013236 395 NPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 395 d~~~La~dLkl~~~kl~~~fr~L 417 (447)
....||.+++++..++..+.++|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 56999999999999999988876
No 28
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=32.12 E-value=1.1e+02 Score=24.38 Aligned_cols=39 Identities=31% Similarity=0.407 Sum_probs=26.9
Q ss_pred HHHHHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 379 ISYVLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 379 l~yilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
+-.++.|+.+-++-.+....||+.+++++..+..+++.|
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L 49 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKL 49 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 333444444444444999999999999999988888766
No 29
>cd00240 TFIIFa Transcription initiation factor IIF, alpha subunit, N-terminal region of RAP74. Subunit of transcription initiation complex involved in initiation, elongation and promoter escape.Tetramer of 2 alpha and 2 beta TFIIF subunits interacts directly with RNA polymerase II. TFIIF inhibits non-specific transcription initiation by PolII and recruits the polymerase to the preinitiation complex on promoter DNA for site-specific transcription initiation. The PolII/TFIIF-complex attaches through direct interactions of TFIIF with promoter DNA, TFIIB and the TAF250 subunit of TFIID, and provides scaffolding for addition of TFIIE and TFIIH. Together with TFIIE, TFIIF participates in DNA strand separation (open complex formation). N-terminal domains of RAP30 and RAP74 co-fold to form a single core structure, a triple barrel heterodimer, and has pseudo-2-fold symmetry.
Probab=30.63 E-value=1.6e+02 Score=27.12 Aligned_cols=45 Identities=13% Similarity=0.301 Sum_probs=33.0
Q ss_pred CCeeEEeccCCCCCCCccCCceEEEEEeCCCCcEEEEeccccceeeecccc
Q 013236 118 SSVDYVGTSYSGEAMAPQFCHYAVGVLDRSTQTLKIVPIAANKIFRLEPRV 168 (447)
Q Consensus 118 ~~l~YvG~~~~~~~~~~~~~~Y~VgV~dk~T~~l~l~Pv~~~ki~~l~p~v 168 (447)
++-.|+|.-.++. +....|+|-++++ +|.++.+|+. +-|+++|..
T Consensus 96 g~~~~~G~~Eg~~---~es~ty~~f~~~~-~~~f~a~P~~--~WY~F~~~~ 140 (162)
T cd00240 96 GQRQFKGIREGGV---NENATYYVFTMQP-DGEFEAYPVG--EWYNFNPVA 140 (162)
T ss_pred CCcEEEEEEeecc---ccccceEEEEEcC-CCCEEEEEhh--heeeccccc
Confidence 5678999875532 1235688889998 6899999986 588887743
No 30
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.39 E-value=91 Score=26.96 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=26.4
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHh-CCEEe
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKL-GCKLL 422 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~L-Gc~v~ 422 (447)
.++.+||..+++++..+..+|++. |+.+.
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~ 55 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKKETGHSLG 55 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcCHH
Confidence 788999999999999999999976 88764
No 31
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=27.66 E-value=1e+02 Score=26.05 Aligned_cols=42 Identities=17% Similarity=0.047 Sum_probs=31.5
Q ss_pred HHHHHHhcCCCccCcHhHHHHh-----CCCHHHHHHHHHHhCCEEee
Q 013236 382 VLVLTLHADDFRTNPTDIAKDL-----RMSEFKLRDHFEKLGCKLLR 423 (447)
Q Consensus 382 ilvLaL~ldnf~vd~~~La~dL-----kl~~~kl~~~fr~LGc~v~k 423 (447)
+|++.+..-+..++.+.|+..+ +++...|...++.+|-+...
T Consensus 16 ~l~~~~~~~g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~Gl~~~~ 62 (136)
T cd02418 16 CLAMIAKYYGKNYSLAKLRELAGTDREGTSLLGLVKAAEKLGFETRA 62 (136)
T ss_pred HHHHHHHHhCCCCCHHHHHHHcCCCCCCcCHHHHHHHHHHCCCeeEE
Confidence 4444454556778889998775 47889999999999977644
No 32
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=26.76 E-value=1.3e+02 Score=25.50 Aligned_cols=44 Identities=11% Similarity=0.150 Sum_probs=35.1
Q ss_pred HHHHHHHHhc-CCCccCcHhHHHHhC-----CCHHHHHHHHHHhCCEEee
Q 013236 380 SYVLVLTLHA-DDFRTNPTDIAKDLR-----MSEFKLRDHFEKLGCKLLR 423 (447)
Q Consensus 380 ~yilvLaL~l-dnf~vd~~~La~dLk-----l~~~kl~~~fr~LGc~v~k 423 (447)
.++|++.+.. -+..++++.|+..++ ++...|...++.+|.+...
T Consensus 14 la~l~~i~~~~~g~~~~~~~l~~~~~~~~~g~s~~~l~~~a~~~Gl~~k~ 63 (129)
T cd02424 14 IAVIQMLYNHYYKKKYDLNELKIKANLKKNGLSIYDLENLAKKFGLETES 63 (129)
T ss_pred HHHHHHHHHHhcCCCccHHHHHHHhCCCCCCccHHHHHHHHHHcCCceeE
Confidence 4456666665 777899999999865 7889999999999987755
No 33
>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=26.64 E-value=99 Score=22.49 Aligned_cols=24 Identities=21% Similarity=0.462 Sum_probs=20.6
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
....+||..++++...+..+...|
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L 49 (66)
T cd07377 26 PSERELAEELGVSRTTVREALREL 49 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 348899999999999998887776
No 34
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=25.64 E-value=95 Score=26.94 Aligned_cols=30 Identities=20% Similarity=0.195 Sum_probs=25.4
Q ss_pred cCCCccCcHhHHHHhCCCHHHHHHHHHHhC
Q 013236 389 ADDFRTNPTDIAKDLRMSEFKLRDHFEKLG 418 (447)
Q Consensus 389 ldnf~vd~~~La~dLkl~~~kl~~~fr~LG 418 (447)
.++-...+..|++.|++++..+..|++.|-
T Consensus 26 ~~~~~~~v~ela~~l~lsqstvS~HL~~L~ 55 (117)
T PRK10141 26 RESGELCVCDLCTALDQSQPKISRHLALLR 55 (117)
T ss_pred HHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344568889999999999999999988774
No 35
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=25.56 E-value=1.1e+02 Score=29.10 Aligned_cols=35 Identities=31% Similarity=0.498 Sum_probs=29.2
Q ss_pred HHHHHHhcCCCc----cCcHhHHHHhCCCHHHHHHHHHH
Q 013236 382 VLVLTLHADDFR----TNPTDIAKDLRMSEFKLRDHFEK 416 (447)
Q Consensus 382 ilvLaL~ldnf~----vd~~~La~dLkl~~~kl~~~fr~ 416 (447)
+|.+|++.-=|. +.+.+||+.|||+++.+.+|.|.
T Consensus 163 vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr 201 (215)
T COG3413 163 VLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR 201 (215)
T ss_pred HHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 566777775444 78999999999999999999885
No 36
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=25.35 E-value=1.5e+02 Score=22.90 Aligned_cols=32 Identities=22% Similarity=0.227 Sum_probs=23.9
Q ss_pred ccCcHhHHHHhC--CCHHHHHHHHHHhCCEEeec
Q 013236 393 RTNPTDIAKDLR--MSEFKLRDHFEKLGCKLLRE 424 (447)
Q Consensus 393 ~vd~~~La~dLk--l~~~kl~~~fr~LGc~v~k~ 424 (447)
.++++.+.+-|| ++...+.++++.|||.+...
T Consensus 5 ~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~ 38 (70)
T PF03484_consen 5 TLSLDKINKLLGIDISPEEIIKILKRLGFKVEKI 38 (70)
T ss_dssp EEEHHHHHHHHTS---HHHHHHHHHHTT-EEEE-
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHCCCEEEEC
Confidence 356677788787 78999999999999999874
No 37
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=24.83 E-value=71 Score=24.54 Aligned_cols=32 Identities=16% Similarity=0.257 Sum_probs=23.8
Q ss_pred HHhcCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 386 TLHADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 386 aL~ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
.+.-++-.+.+.+||..|++++..|..+...|
T Consensus 7 ~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 7 DYLRERGRVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp HHHHHS-SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34446777899999999999999999888765
No 38
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=23.01 E-value=1.9e+02 Score=26.23 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=33.1
Q ss_pred cCHHHHHHHHHHHHHHHHhc-CCCccCcHhHHHHhCCCHHHHHHHHHH---hCCEE
Q 013236 370 LSDDKIHLLISYVLVLTLHA-DDFRTNPTDIAKDLRMSEFKLRDHFEK---LGCKL 421 (447)
Q Consensus 370 ~s~~~~dkLl~yilvLaL~l-dnf~vd~~~La~dLkl~~~kl~~~fr~---LGc~v 421 (447)
+++...| |+-++.... +++.+-+.+||..|+++|..+.++.+. .|-..
T Consensus 4 ~s~~~ed----YL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~ 55 (154)
T COG1321 4 LSETEED----YLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVE 55 (154)
T ss_pred cchHHHH----HHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeE
Confidence 3444444 444444333 788999999999999999999666654 45544
No 39
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=22.78 E-value=1.8e+02 Score=23.70 Aligned_cols=29 Identities=28% Similarity=0.316 Sum_probs=26.5
Q ss_pred cCcHhHHHHhCCCHHHHHHHHH-HhCCEEe
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFE-KLGCKLL 422 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr-~LGc~v~ 422 (447)
..+..||..++|++..+...|+ ..|+.+.
T Consensus 37 ~~l~~la~~~g~S~~~l~r~f~~~~g~s~~ 66 (127)
T COG2207 37 LTLEDLARRLGMSRRTLSRLFKKETGTSPS 66 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
Confidence 7889999999999999999999 8888763
No 40
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=22.65 E-value=1.3e+02 Score=22.38 Aligned_cols=29 Identities=24% Similarity=0.373 Sum_probs=24.0
Q ss_pred cCCCccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 389 ADDFRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 389 ldnf~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
..+-...+..|++.|++++..+..+.+.|
T Consensus 20 ~~~~~~t~~ela~~l~~~~~t~s~hL~~L 48 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGISQSTVSYHLKKL 48 (61)
T ss_dssp HHCSTBEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred hcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 35666788999999999999999998876
No 41
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=22.30 E-value=1.3e+02 Score=21.32 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=20.4
Q ss_pred CcHhHHHHhCCCHHHHHHHHHHh
Q 013236 395 NPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 395 d~~~La~dLkl~~~kl~~~fr~L 417 (447)
....||+.++++...+...++.|
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L 44 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRL 44 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999998887766
No 42
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=21.83 E-value=2e+02 Score=28.86 Aligned_cols=29 Identities=21% Similarity=0.193 Sum_probs=25.7
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHhCCEEe
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKLGCKLL 422 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~LGc~v~ 422 (447)
..+++||+.++|++..+..+|+..|....
T Consensus 198 ~sl~~lA~~~gmS~stl~R~Fk~~g~s~~ 226 (291)
T PRK15186 198 WALKDISDSLYMSCSTLKRKLKQENTSFS 226 (291)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcCCCHH
Confidence 57799999999999999999999887653
No 43
>PF09816 EAF: RNA polymerase II transcription elongation factor; InterPro: IPR019194 This entry represents the N-terminal domain of ELL-associated factor (Eaf) proteins, which act as transcriptional transactivators of ELL and ELL2 RNA Polymerase II (Pol II) transcriptional elongation factors [, , , ]. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis []. EAF1 also has the capacity to interact with ELL1 and ELL2. The N terminus of approx 120 of EAF1 has a region of high serine, aspartic acid, and glutamic acid residues [, ].
Probab=21.69 E-value=4.9e+02 Score=21.93 Aligned_cols=38 Identities=13% Similarity=0.182 Sum_probs=26.9
Q ss_pred CeeEEeccCCCCCCCccCCceEEEEEeCCCCcEEEEeccccceeee
Q 013236 119 SVDYVGTSYSGEAMAPQFCHYAVGVLDRSTQTLKIVPIAANKIFRL 164 (447)
Q Consensus 119 ~l~YvG~~~~~~~~~~~~~~Y~VgV~dk~T~~l~l~Pv~~~ki~~l 164 (447)
.+.|.|.... + ..+-||-|||+.+|.+.|-++.. .++|
T Consensus 65 ~~~f~G~~~~----~--~~~ecVLifD~~~~~f~LErl~s--~~~~ 102 (109)
T PF09816_consen 65 TYVFKGSQRP----S--KEKECVLIFDPETGEFVLERLSS--TINL 102 (109)
T ss_pred cEEEEeccCC----C--CCcEEEEEEECCCCEEEEEEcce--EEEE
Confidence 4889997432 1 12345999999999999998864 3455
No 44
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=21.38 E-value=1.2e+02 Score=25.19 Aligned_cols=40 Identities=15% Similarity=0.240 Sum_probs=29.8
Q ss_pred HHHHHhcCCCccCcHhHHHHh-----CCCHHHHHHHHHHhCCEEe
Q 013236 383 LVLTLHADDFRTNPTDIAKDL-----RMSEFKLRDHFEKLGCKLL 422 (447)
Q Consensus 383 lvLaL~ldnf~vd~~~La~dL-----kl~~~kl~~~fr~LGc~v~ 422 (447)
+++.+..-+..++...|...+ +++...+..+++.+|.+..
T Consensus 17 l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~gl~~~ 61 (126)
T cd02425 17 YAMILNYFGYKVSLNELREKYELGRDGLSLSYLKQLLEEYGFKCK 61 (126)
T ss_pred HHHHHHHhCCCCCHHHHHHhccCCCCCcCHHHHHHHHHHCCCcce
Confidence 333344456678888898876 4778999999999997764
No 45
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=21.04 E-value=78 Score=31.41 Aligned_cols=60 Identities=15% Similarity=0.201 Sum_probs=38.7
Q ss_pred HHHHHHHhhcccCCCCccCHHHHHHHHHHHHHHHHhcCCCccCcHhHHHHhCCCHHHHHHHHHHhCCE
Q 013236 353 ILHQKFLTSFSDAESKRLSDDKIHLLISYVLVLTLHADDFRTNPTDIAKDLRMSEFKLRDHFEKLGCK 420 (447)
Q Consensus 353 ~v~~~il~~Ft~~~~~~~s~~~~dkLl~yilvLaL~ldnf~vd~~~La~dLkl~~~kl~~~fr~LGc~ 420 (447)
.+...|..++.. +|+ ..-++.-|||.=-=.+- ..-+.+||+..+++++.+.-++|.|||.
T Consensus 4 ~l~~~I~~~~~~-----Lt~-~er~iA~yil~~~~~~~--~~si~elA~~a~VS~aTv~Rf~~kLGf~ 63 (281)
T COG1737 4 NLLERIRERYDS-----LTK-SERKIADYILANPDEVA--LLSIAELAERAGVSPATVVRFARKLGFE 63 (281)
T ss_pred hHHHHHHHHHhc-----CCH-HHHHHHHHHHhCHHHHH--HHHHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 355555665543 444 33455556543111000 1356899999999999999999999996
No 46
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=20.74 E-value=1.2e+02 Score=20.72 Aligned_cols=26 Identities=15% Similarity=0.264 Sum_probs=21.8
Q ss_pred CccCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 392 FRTNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 392 f~vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
|.....+||+.++++...+..+++.|
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L 32 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRL 32 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44567899999999999998887766
No 47
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=20.10 E-value=1.7e+02 Score=22.56 Aligned_cols=24 Identities=17% Similarity=0.293 Sum_probs=21.0
Q ss_pred cCcHhHHHHhCCCHHHHHHHHHHh
Q 013236 394 TNPTDIAKDLRMSEFKLRDHFEKL 417 (447)
Q Consensus 394 vd~~~La~dLkl~~~kl~~~fr~L 417 (447)
+-..+||+.|+++.+.+..+...|
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHH
Confidence 778999999999999999887654
Done!