Query psy14236
Match_columns 290
No_of_seqs 135 out of 200
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 22:53:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14236.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14236hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3095|consensus 100.0 1.4E-70 3E-75 503.5 19.6 276 1-290 1-284 (284)
2 COG5174 TFA2 Transcription ini 100.0 1E-57 2.2E-62 408.4 21.7 267 7-290 6-285 (285)
3 cd07977 TFIIE_beta_winged_heli 99.8 3.1E-21 6.7E-26 147.8 7.0 75 66-145 1-75 (75)
4 PF02186 TFIIE_beta: TFIIE bet 99.8 5.7E-20 1.2E-24 137.2 6.4 64 70-144 1-65 (65)
5 PHA02943 hypothetical protein; 93.3 0.12 2.6E-06 45.0 4.3 72 146-225 12-87 (165)
6 PF08784 RPA_C: Replication pr 90.3 0.49 1.1E-05 37.5 4.5 44 147-191 49-96 (102)
7 PF07106 TBPIP: Tat binding pr 88.5 4 8.7E-05 35.3 9.2 94 77-187 4-101 (169)
8 PF09756 DDRGK: DDRGK domain; 85.8 0.62 1.3E-05 41.8 2.6 85 74-176 99-185 (188)
9 KOG3054|consensus 82.8 2.5 5.4E-05 39.7 5.2 90 69-176 195-286 (299)
10 PF05158 RNA_pol_Rpc34: RNA po 79.4 17 0.00037 35.2 10.0 144 73-225 8-177 (327)
11 PF07106 TBPIP: Tat binding pr 79.4 7.6 0.00017 33.5 6.9 59 147-211 3-67 (169)
12 PF04703 FaeA: FaeA-like prote 76.0 7.2 0.00016 28.9 4.9 53 147-204 2-58 (62)
13 KOG4603|consensus 73.1 6 0.00013 35.3 4.5 66 146-218 8-81 (201)
14 PF08220 HTH_DeoR: DeoR-like h 71.7 11 0.00024 26.9 4.9 42 148-194 3-48 (57)
15 TIGR02702 SufR_cyano iron-sulf 69.4 17 0.00037 32.2 6.7 57 146-207 2-64 (203)
16 PF04703 FaeA: FaeA-like prote 68.9 5.7 0.00012 29.4 3.0 46 78-132 4-49 (62)
17 COG3355 Predicted transcriptio 67.7 14 0.0003 31.3 5.4 76 92-186 40-120 (126)
18 PF13412 HTH_24: Winged helix- 64.2 13 0.00027 25.1 3.8 39 147-190 5-47 (48)
19 PF04157 EAP30: EAP30/Vps36 fa 60.3 29 0.00063 31.4 6.5 118 66-192 86-222 (223)
20 PF01726 LexA_DNA_bind: LexA D 60.3 21 0.00046 26.4 4.7 51 74-132 10-60 (65)
21 COG2345 Predicted transcriptio 59.5 25 0.00053 32.4 5.9 57 145-206 11-73 (218)
22 COG0064 GatB Asp-tRNAAsn/Glu-t 58.1 53 0.0012 33.7 8.5 147 74-248 165-320 (483)
23 COG4190 Predicted transcriptio 57.4 22 0.00047 30.6 4.8 86 122-217 44-135 (144)
24 PF09339 HTH_IclR: IclR helix- 56.8 12 0.00026 25.9 2.7 48 75-131 4-51 (52)
25 PF12324 HTH_15: Helix-turn-he 55.4 43 0.00094 26.0 5.7 49 75-136 25-73 (77)
26 TIGR02337 HpaR homoprotocatech 55.1 36 0.00079 27.1 5.7 55 150-209 33-92 (118)
27 COG3682 Predicted transcriptio 54.4 51 0.0011 27.8 6.5 99 78-185 10-113 (123)
28 PF01047 MarR: MarR family; I 53.0 39 0.00085 23.3 4.9 46 149-199 7-56 (59)
29 TIGR00988 hip integration host 52.5 81 0.0018 24.3 7.1 42 146-191 2-44 (94)
30 smart00346 HTH_ICLR helix_turn 51.7 41 0.00088 25.2 5.2 57 74-139 5-62 (91)
31 PF09724 DUF2036: Uncharacteri 48.3 1.8E+02 0.0039 27.6 10.2 156 68-239 162-324 (325)
32 PRK10753 transcriptional regul 47.8 97 0.0021 24.1 6.9 41 146-191 2-43 (90)
33 PF12802 MarR_2: MarR family; 47.6 68 0.0015 22.1 5.5 47 149-198 9-59 (62)
34 PF11252 DUF3051: Protein of u 47.3 13 0.00029 32.1 2.0 22 4-25 106-127 (189)
35 PF13034 DUF3895: Protein of u 47.0 46 0.00099 25.9 4.7 30 173-202 46-75 (78)
36 COG3395 Uncharacterized protei 46.7 1.3E+02 0.0027 30.5 8.9 124 61-193 48-195 (413)
37 smart00550 Zalpha Z-DNA-bindin 46.5 37 0.0008 25.0 4.1 44 146-192 7-54 (68)
38 PRK11512 DNA-binding transcrip 46.4 45 0.00097 27.6 5.1 57 150-211 45-106 (144)
39 cd00090 HTH_ARSR Arsenical Res 45.7 89 0.0019 21.4 5.9 66 146-222 8-77 (78)
40 PRK10664 transcriptional regul 43.8 96 0.0021 24.2 6.3 42 146-192 2-44 (90)
41 smart00420 HTH_DEOR helix_turn 43.0 88 0.0019 20.4 5.3 41 148-193 3-47 (53)
42 smart00550 Zalpha Z-DNA-bindin 42.7 65 0.0014 23.7 4.9 48 76-132 8-56 (68)
43 PF06757 Ins_allergen_rp: Inse 42.6 21 0.00045 31.2 2.6 32 215-248 43-75 (179)
44 PF01316 Arg_repressor: Argini 42.0 96 0.0021 23.4 5.7 52 142-208 17-68 (70)
45 PF08279 HTH_11: HTH domain; 41.8 33 0.00073 23.5 3.1 26 76-106 2-27 (55)
46 TIGR03820 lys_2_3_AblA lysine- 41.7 1.1E+02 0.0025 30.7 7.8 102 73-193 140-250 (417)
47 smart00347 HTH_MARR helix_turn 41.5 90 0.0019 23.1 5.7 45 149-198 14-62 (101)
48 PRK10434 srlR DNA-bindng trans 39.7 57 0.0012 30.1 5.1 43 147-194 7-53 (256)
49 PF08220 HTH_DeoR: DeoR-like h 38.9 33 0.00073 24.3 2.7 45 76-131 2-47 (57)
50 PRK11569 transcriptional repre 38.8 87 0.0019 29.0 6.2 57 73-138 27-84 (274)
51 PF08679 DsrD: Dissimilatory s 38.8 62 0.0014 24.5 4.2 47 147-194 3-54 (67)
52 smart00345 HTH_GNTR helix_turn 38.6 1.1E+02 0.0025 20.4 5.4 46 148-193 3-53 (60)
53 PF13601 HTH_34: Winged helix 38.4 1E+02 0.0022 23.5 5.5 51 149-204 4-59 (80)
54 PF09066 B2-adapt-app_C: Beta2 38.4 25 0.00055 28.0 2.3 33 216-248 10-54 (114)
55 PF07904 Eaf7: Chromatin modif 38.0 44 0.00096 26.4 3.5 39 68-106 16-55 (91)
56 cd08029 LA_like_fungal La-moti 37.8 38 0.00083 26.0 3.0 41 92-135 32-72 (76)
57 PF05158 RNA_pol_Rpc34: RNA po 37.6 76 0.0017 30.8 5.8 46 147-194 11-61 (327)
58 PF11181 YflT: Heat induced st 37.4 34 0.00073 27.2 2.8 69 176-248 11-86 (103)
59 TIGR02533 type_II_gspE general 36.6 1.2E+02 0.0026 30.9 7.3 38 212-253 433-470 (486)
60 PHA00738 putative HTH transcri 36.4 76 0.0016 26.2 4.7 58 147-211 14-75 (108)
61 smart00715 LA Domain in the RN 34.0 40 0.00087 26.0 2.6 43 92-136 34-76 (80)
62 PF12840 HTH_20: Helix-turn-he 33.9 1.3E+02 0.0029 21.1 5.2 43 147-194 12-58 (61)
63 PHA02943 hypothetical protein; 33.7 1.4E+02 0.0031 26.3 6.2 62 66-138 3-64 (165)
64 cd08028 LARP_3 La RNA-binding 33.6 42 0.00091 26.2 2.7 51 82-135 26-78 (82)
65 PRK09834 DNA-binding transcrip 33.5 88 0.0019 28.7 5.3 58 73-139 10-68 (263)
66 COG1803 MgsA Methylglyoxal syn 32.6 47 0.001 28.4 3.0 56 163-227 49-104 (142)
67 PF09012 FeoC: FeoC like trans 32.4 62 0.0014 23.6 3.4 46 76-131 2-47 (69)
68 COG1349 GlpR Transcriptional r 32.3 78 0.0017 29.2 4.7 42 148-194 8-53 (253)
69 PRK13509 transcriptional repre 32.0 87 0.0019 28.8 5.0 42 148-194 8-53 (251)
70 TIGR02431 pcaR_pcaU beta-ketoa 31.6 1.2E+02 0.0025 27.5 5.7 55 73-137 8-62 (248)
71 PRK11511 DNA-binding transcrip 30.7 71 0.0015 26.1 3.8 30 73-106 8-37 (127)
72 PRK04280 arginine repressor; P 30.4 1.1E+02 0.0024 26.3 5.0 52 141-208 15-67 (148)
73 PRK10163 DNA-binding transcrip 30.3 1.3E+02 0.0029 27.8 6.0 57 73-138 24-81 (271)
74 PRK10906 DNA-binding transcrip 30.0 90 0.0019 28.8 4.8 42 147-193 7-52 (252)
75 TIGR02538 type_IV_pilB type IV 30.0 2.6E+02 0.0055 29.0 8.5 164 62-253 321-546 (564)
76 COG3888 Predicted transcriptio 29.3 1.2E+02 0.0026 29.2 5.4 56 146-206 5-65 (321)
77 PRK09802 DNA-binding transcrip 28.7 1E+02 0.0023 28.7 5.0 43 147-194 19-65 (269)
78 COG1414 IclR Transcriptional r 28.5 1E+02 0.0022 28.3 4.8 58 75-141 5-63 (246)
79 PRK00285 ihfA integration host 28.5 1.3E+02 0.0029 23.4 4.9 43 146-193 4-46 (99)
80 PRK05066 arginine repressor; P 27.8 1.5E+02 0.0032 25.8 5.4 51 142-208 21-73 (156)
81 PLN02289 ribulose-bisphosphate 27.8 1.1E+02 0.0024 27.3 4.6 18 140-157 128-145 (176)
82 PRK13777 transcriptional regul 27.7 1.6E+02 0.0035 26.1 5.8 56 149-209 49-109 (185)
83 TIGR01889 Staph_reg_Sar staphy 27.2 2E+02 0.0044 22.7 5.8 59 150-209 30-93 (109)
84 cd00092 HTH_CRP helix_turn_hel 27.1 2.2E+02 0.0047 19.7 5.6 46 91-140 22-67 (67)
85 PRK10141 DNA-binding transcrip 27.0 1.5E+02 0.0033 24.4 5.1 81 148-242 19-103 (117)
86 PRK10219 DNA-binding transcrip 26.6 89 0.0019 24.3 3.6 28 75-106 6-33 (107)
87 COG3355 Predicted transcriptio 26.5 1.9E+02 0.0041 24.5 5.6 58 146-208 29-93 (126)
88 TIGR01686 FkbH FkbH-like domai 26.4 34 0.00074 32.4 1.3 81 161-248 23-105 (320)
89 cd08033 LARP_6 La RNA-binding 26.4 70 0.0015 24.6 2.8 42 92-135 32-73 (77)
90 PF01978 TrmB: Sugar-specific 26.4 96 0.0021 22.2 3.5 57 75-141 9-65 (68)
91 PF04239 DUF421: Protein of un 26.3 48 0.001 26.4 2.0 91 121-245 3-95 (99)
92 PF02082 Rrf2: Transcriptional 26.0 2.8E+02 0.0061 20.7 6.4 55 77-138 11-67 (83)
93 smart00411 BHL bacterial (prok 25.8 1.8E+02 0.0039 21.8 5.1 43 146-193 2-44 (90)
94 PF06224 HTH_42: Winged helix 25.8 5.5E+02 0.012 23.9 11.2 118 70-196 81-217 (327)
95 cd08032 LARP_7 La RNA-binding 25.8 73 0.0016 24.9 2.8 42 92-135 37-78 (82)
96 cd00591 HU_IHF Integration hos 25.7 1.8E+02 0.004 21.6 5.1 44 146-194 1-44 (87)
97 PF01706 FliG_C: FliG C-termin 24.0 94 0.002 24.8 3.3 41 146-191 68-108 (110)
98 cd03409 Chelatase_Class_II Cla 23.9 53 0.0011 25.0 1.8 46 173-225 43-90 (101)
99 COG2425 Uncharacterized protei 23.7 3.2E+02 0.0069 27.8 7.6 90 117-225 300-391 (437)
100 PRK15090 DNA-binding transcrip 23.6 2.2E+02 0.0049 25.8 6.1 59 73-141 13-72 (257)
101 cd07323 LAM LA motif RNA-bindi 23.4 92 0.002 23.6 2.9 43 92-136 30-72 (75)
102 cd01396 MeCP2_MBD MeCP2, MBD1, 23.3 89 0.0019 23.9 2.9 33 134-169 27-60 (77)
103 TIGR02844 spore_III_D sporulat 22.9 1.3E+02 0.0028 23.4 3.7 29 71-106 3-31 (80)
104 PF05066 HARE-HTH: HB1, ASXL, 22.8 76 0.0017 23.3 2.4 28 74-106 2-29 (72)
105 TIGR00987 himA integration hos 22.6 2E+02 0.0044 22.3 4.9 43 146-193 3-45 (96)
106 PF08672 APC2: Anaphase promot 22.1 1.5E+02 0.0032 21.7 3.7 20 115-137 40-59 (60)
107 PRK13239 alkylmercury lyase; P 21.5 2.9E+02 0.0063 25.2 6.2 49 74-135 22-70 (206)
108 PRK03573 transcriptional regul 21.4 2.2E+02 0.0049 23.2 5.2 57 150-210 36-97 (144)
109 PF04558 tRNA_synt_1c_R1: Glut 21.4 1.2E+02 0.0027 26.5 3.7 36 73-113 84-119 (164)
110 TIGR01884 cas_HTH CRISPR locus 20.8 3.1E+02 0.0067 24.1 6.3 58 142-207 139-201 (203)
111 PLN02950 4-alpha-glucanotransf 20.5 2.1E+02 0.0046 31.7 6.1 75 133-219 630-708 (909)
112 cd08036 LARP_5 La RNA-binding 20.2 1.2E+02 0.0026 23.5 2.9 42 92-135 30-71 (75)
No 1
>KOG3095|consensus
Probab=100.00 E-value=1.4e-70 Score=503.46 Aligned_cols=276 Identities=41% Similarity=0.660 Sum_probs=231.6
Q ss_pred CChHHHHhHHHHHHhhccCCcccccCCCCCC-CCch-hhhhccCCCCCCCCCCCC--CCCCCCCccccCCCCcchhHHHH
Q psy14236 1 MDPALLRERDLFKKKALSTPTVEKRKAETSK-DEPW-KAKKAKTSSSSSSSLSSS--LGSSNNMAYKSMSGSSQYKFGVL 76 (290)
Q Consensus 1 md~~ll~~~~~fk~ra~~~p~ve~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~tg~~~~~~t~l 76 (290)
|||+||+||+||+|+|++||+|+++.+++.. ++++ ....+ .++++++++. ..+.++.++.+++|..++-|+.+
T Consensus 1 ~~~~Ll~ql~aFkK~~~~~p~v~~~~~ps~~~t~ss~~~~~~---~~~~~~p~~~~lk~~~~s~~~~~ls~~~~~~fgt~ 77 (284)
T KOG3095|consen 1 MDPALLRQLEAFKKKAASTPVVAKKSAPSRFPTPSSRANSNK---ASKASKPNLPRLKKDANSSNLKSLSNSSQSHFGTH 77 (284)
T ss_pred CCHHHHHHHHHHHHHHhcCcccccCCCCCCCCCCcchhcchh---hhccCCCCCcccccccchhhHHhhcCcccccchhH
Confidence 9999999999999999999999999877552 2222 11111 1223333322 12344789999999999999999
Q ss_pred HHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeEEeccCCCCCCHHHHHHHHHh
Q psy14236 77 AKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPVFKIKDRKGLLKLLKQ 156 (290)
Q Consensus 77 ~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f~yKP~y~Ik~k~~LL~lL~~ 156 (290)
++||.||+.+|+.+.++| ||++|++++|+..+ .|+..|+|++||||+|+ .+||+|||+|+|+|+++||++|++
T Consensus 78 ~kiv~~~~~~h~~~~~~P----E~i~E~~~~d~~~~--n~~l~esLkkNpri~~d-~~~FsfKp~y~Ird~~~Ll~llr~ 150 (284)
T KOG3095|consen 78 AKIVIYLLTEHLRGLTHP----EIIDELQHYDLKHK--NWLLLESLKKNPRIEYD-PRTFSFKPTYNIRDKKQLLKLLRK 150 (284)
T ss_pred HHHHHHHHHHHHhcCCcH----HHHHHHHHHHhhhc--cHHHHHHHhhCCceEec-CceeeccCccccCCHHHHHHHHHh
Confidence 999999999999998888 88899998898333 35555999999999999 559999999999999999999999
Q ss_pred cccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEEecCC-CCceEEEecCCCCCCCCCHHHHHHhhhcccCCCChhhH
Q psy14236 157 HDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYVTRPA-DKRKVMFYNDKSAQLDLDEDFQKLWRSISVDGMDNDKI 235 (290)
Q Consensus 157 ~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~~~~-~~~rivf~ND~~~~~~VD~EFk~lW~~v~VP~~de~di 235 (290)
|+ ++|||+|+||+||||+|+++|++|++.|+||||+++. ++++||||||.+|.+.||+||++|||+|.||++ +.||
T Consensus 151 ~~--~~~GI~v~DL~d~~pNv~~~lk~L~~s~eIl~l~t~~d~k~kivf~ND~~~~~~VDdEFk~LWr~V~Ip~~-~~dl 227 (284)
T KOG3095|consen 151 HD--TLGGILVSDLKDAWPNVDEDLKELEKSGEILVLRTPKDDKPKIVFYNDKSCSFSVDDEFKKLWRSVTIPSM-ELDL 227 (284)
T ss_pred cC--ccCceehHHhhhcccchHHHHHHHhcCCcEEEEeccCCCCCceEEecCCCCCcccCHHHHHHHHhCCCChH-HHHH
Confidence 86 4899999999999999999999999999999998886 899999999999999999999999999999975 8999
Q ss_pred HHHHHHcCCCCcccCCCCCCCCCCCc---CccccccCCCCCCChhhHHHHHhhhccCC
Q psy14236 236 KEYLEKQGIRPIQDHGFKKPVLPGRK---KNMNRKKQFKKPRDNEHLADVLENYEAVS 290 (290)
Q Consensus 236 ~~~L~~~Glkp~~~~~~kk~~~~~~~---Kkkkkkr~r~~K~TNtHm~~llkDYs~~~ 290 (290)
++||+++||+||++.++++.++++++ +|++++++|++|+|||||. +++||++++
T Consensus 228 e~eL~k~GLkp~~~v~p~~~~~~~~~k~~~Kkk~~~~r~~kitnthl~-~l~d~~~~~ 284 (284)
T KOG3095|consen 228 EEELQKQGLKPMKDVDPKKAAPQQRKKDKKKKKFKKTRRNKITNTHLK-ILEDYSSDK 284 (284)
T ss_pred HHHHHHhCCCcccccchHHhhhhhhhhhhhhhhhcccccchhhhhHHH-HHHhhcccC
Confidence 99999999999998777765453222 2334456688999999999 899998763
No 2
>COG5174 TFA2 Transcription initiation factor IIE, beta subunit [Transcription]
Probab=100.00 E-value=1e-57 Score=408.36 Aligned_cols=267 Identities=19% Similarity=0.321 Sum_probs=214.2
Q ss_pred HhHHHHHHhhccCCcccccCCCCCCCC--------chh--hhhccCCCCCCCCC-CCCCCCCCCCccccCCCCcchhHHH
Q psy14236 7 RERDLFKKKALSTPTVEKRKAETSKDE--------PWK--AKKAKTSSSSSSSL-SSSLGSSNNMAYKSMSGSSQYKFGV 75 (290)
Q Consensus 7 ~~~~~fk~ra~~~p~ve~~~~~~~~~~--------~~~--~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~tg~~~~~~t~ 75 (290)
-+.+|||++..++||+.+.......++ +.+ ....-..+||..++ ..+ .-.-...+++++|.+.|-.++
T Consensus 6 dnlnafkskvksapv~a~~q~kr~asp~~~e~~LnsndghsS~a~s~gs~~~kk~R~~-~~~~~~~q~~d~gv~~H~~s~ 84 (285)
T COG5174 6 DNLNAFKSKVKSAPVIAPAQKKRMASPCHFEVGLNSNDGHSSTAWSKGSSPTKKARIP-RMDRDRIQSIDRGVQRHTNSY 84 (285)
T ss_pred HHHHHHHHHhccCCcccCccccccCCccchhcccccCCCCcccccccCCCcccccccc-chhHhhhccccccccccchHH
Confidence 478999999999999986432100000 000 00000000110010 100 111223688999999999999
Q ss_pred HHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee-CCeEEeccCCCCCCHHHHHHHH
Q psy14236 76 LAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE-GNKYIFKPVFKIKDRKGLLKLL 154 (290)
Q Consensus 76 l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p-~~~f~yKP~y~Ik~k~~LL~lL 154 (290)
|++|++|||++ +.|++++||.++|++ ++.++. + ++|+.+.+|.|++ .+||.|+|.|+|++.++||++|
T Consensus 85 lh~aieylk~~-----~~P~~~eEi~dyls~-~l~~~~---v--~Llkk~~ri~~d~~~~Tf~fkply~irS~~~llk~l 153 (285)
T COG5174 85 LHAAIEYLKQH-----DRPLSFEEIKDYLSI-DLHNNY---V--LLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVL 153 (285)
T ss_pred HHHHHHHHHHc-----CCcccHHHHHHHhcC-ccchhH---H--HHHhhccCceeccCCceEEeeccccccCHHHHHHHH
Confidence 99999999998 899999999999998 988874 3 4799999999999 6899999999999999999999
Q ss_pred HhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEEecCC-CCceEEEecCCCCCCCCCHHHHHHhhhcccCCCChh
Q psy14236 155 KQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYVTRPA-DKRKVMFYNDKSAQLDLDEDFQKLWRSISVDGMDND 233 (290)
Q Consensus 155 ~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~~~~-~~~rivf~ND~~~~~~VD~EFk~lW~~v~VP~~de~ 233 (290)
+. |.++.||++++|+||||+|...|++||+.++||++++.+ +.|+|||+|+.+|.++||+||+.||++|.||. -.
T Consensus 154 rs--q~t~~Gls~k~L~Dgwpnv~~~veeLek~~eIliLrt~kDg~p~~vW~n~~n~~c~vD~ef~~~W~~V~ip~--~~ 229 (285)
T COG5174 154 RS--QGTEEGLSMKKLMDGWPNVVPFVEELEKSNEILILRTDKDGSPVVVWNNTQNLECPVDPEFKSLWNQVRIPT--YH 229 (285)
T ss_pred Hh--hcccccccHHHhhcCCCcccHHHHHHhhcCcEEEEeecCCCCceEEEeCCCCcCCCCCHHHHHHHHhCCCch--HH
Confidence 99 689999999999999999999999999999999999666 77999999999999999999999999999994 47
Q ss_pred hHHHHHHHcCCCCcccCCCCCCCCCCCcCccccccCCCCCCChhhHHHHHhhhccCC
Q psy14236 234 KIKEYLEKQGIRPIQDHGFKKPVLPGRKKNMNRKKQFKKPRDNEHLADVLENYEAVS 290 (290)
Q Consensus 234 di~~~L~~~Glkp~~~~~~kk~~~~~~~Kkkkkkr~r~~K~TNtHm~~llkDYs~~~ 290 (290)
||.++|..+||+|+++++-.+..+.++-|+ +++++|++|||||||.|||.|||++.
T Consensus 230 dL~reL~~~GLKptsvdp~t~KR~t~~ik~-kk~~~RkgkITNTH~~gil~dys~~~ 285 (285)
T COG5174 230 DLIRELNTAGLKPTSVDPNTKKRPTIKIKK-KKRSRRKGKITNTHVKGILLDYSQDE 285 (285)
T ss_pred HHHHHHHhcCCCccccCcchhccccccccc-cccccccccccchhhhhhhccccccC
Confidence 899999999999999887432223333333 44678999999999999999999873
No 3
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=99.84 E-value=3.1e-21 Score=147.80 Aligned_cols=75 Identities=55% Similarity=0.858 Sum_probs=69.6
Q ss_pred CCCcchhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeEEeccCCCCC
Q psy14236 66 SGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPVFKIK 145 (290)
Q Consensus 66 tg~~~~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f~yKP~y~Ik 145 (290)
||+|.|+||||++||+|||+||| +|+|++||++||+++|++....+||+++++.+||++... +|||+|||+|+||
T Consensus 1 tg~g~~~~t~l~~aV~ymK~r~~----~Plt~~EIl~~ls~~d~~~~~~~~L~~~~~~~n~~~~~~-~~tf~fkP~y~Ir 75 (75)
T cd07977 1 TGSGTHVFTQLAKIVDYMKKRHQ----HPLTLDEILDYLSLLDIGPKLKEWLKSEALVNNPKIDPK-DGTFSFKPKYNIR 75 (75)
T ss_pred CCCCcchhhhHHHHHHHHHhcCC----CCccHHHHHHHHhccCccHHHHHHHHhhhhccCceeccC-CCEEEeccCCCCC
Confidence 69999999999999999999953 999999999999966999999899988899999998887 8999999999996
No 4
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=99.80 E-value=5.7e-20 Score=137.21 Aligned_cols=64 Identities=53% Similarity=0.791 Sum_probs=49.0
Q ss_pred chhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCC-eEEeccCCCC
Q psy14236 70 QYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGN-KYIFKPVFKI 144 (290)
Q Consensus 70 ~~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~-~f~yKP~y~I 144 (290)
+|.||||++||+|||++ ++|+|++||+++|+ +|++....+ .|++||||+|+|+| +|+|+|+|||
T Consensus 1 ~~~~tql~~~VeymK~r-----~~Plt~~eI~d~l~-~d~~~~~~~-----~Lk~npKI~~d~~~~~f~fkp~ynI 65 (65)
T PF02186_consen 1 SHKFTQLAKAVEYMKKR-----DHPLTLEEILDYLS-LDIGKKLKQ-----WLKNNPKIEYDPDGNTFSFKPKYNI 65 (65)
T ss_dssp -TTHHHHHHHHHHHHHH------S-B-HHHHHHHHT-SSS-HHHHH-----HHHH-TTEEEE-TT-CEEE--TTT-
T ss_pred CchhhHHHHHHHHHHhc-----CCCcCHHHHHHHHc-CCCCHHHHH-----HHHcCCCEEEecCCCEEEeccCCCC
Confidence 47899999999999999 89999999999999 599876544 57799999999976 9999999997
No 5
>PHA02943 hypothetical protein; Provisional
Probab=93.27 E-value=0.12 Score=45.03 Aligned_cols=72 Identities=18% Similarity=0.220 Sum_probs=56.2
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHh----hhhhHHHHHHHhhhCCcEEEEecCCCCceEEEecCCCCCCCCCHHHHHH
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRE----SLPHCEKALKHLSLQNEIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKL 221 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD----~~p~~~~~I~~Le~e~~Ilvv~~~~~~~rivf~ND~~~~~~VD~EFk~l 221 (290)
.++++|++| +. |+.+.++|.+ ||-.+.-.|.-||.||.|.-|+. ++..+.+.||..+..-|++=|+++
T Consensus 12 R~~eILE~L-k~-----G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~--G~~tyw~l~~day~~~v~~~~Rel 83 (165)
T PHA02943 12 RMIKTLRLL-AD-----GCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEI--GRAAIWCLDEDAYTNLVFEIKREL 83 (165)
T ss_pred HHHHHHHHH-hc-----CCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEee--cceEEEEEChHHHHHHHHHHHHHH
Confidence 367899999 42 6677777665 78899999999999999987753 455666667766666699999999
Q ss_pred hhhc
Q psy14236 222 WRSI 225 (290)
Q Consensus 222 W~~v 225 (290)
|+=|
T Consensus 84 wrlv 87 (165)
T PHA02943 84 WRLV 87 (165)
T ss_pred HHHH
Confidence 9865
No 6
>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=90.34 E-value=0.49 Score=37.48 Aligned_cols=44 Identities=27% Similarity=0.449 Sum_probs=35.3
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEE
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEII 191 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Il 191 (290)
.+.+|++|+.. .....||.|++|.... ..+.++|+.|..+|.|+
T Consensus 49 ~~~Vl~~i~~~-~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 49 QDKVLNFIKQQ-PNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp HHHHHHHHHC-----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHhc-CCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 46788999984 3567899999999887 45889999999999998
No 7
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=88.50 E-value=4 Score=35.28 Aligned_cols=94 Identities=22% Similarity=0.358 Sum_probs=64.8
Q ss_pred HHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCC-e--EEeccC-CCCCCHHHHHH
Q psy14236 77 AKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGN-K--YIFKPV-FKIKDRKGLLK 152 (290)
Q Consensus 77 ~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~-~--f~yKP~-y~Ik~k~~LL~ 152 (290)
..|++||+.. +.|++..||.+.|.- .++...-+-.. +.|...-+|..-.-| . |.+.-. +.+-+.++|-.
T Consensus 4 ~~Il~y~~~q-----NRPys~~di~~nL~~-~~~K~~v~k~L-d~L~~~g~i~~K~~GKqkiY~~~Q~~~~~~s~eel~~ 76 (169)
T PF07106_consen 4 DAILEYMKEQ-----NRPYSAQDIFDNLHN-KVGKTAVQKAL-DSLVEEGKIVEKEYGKQKIYFANQDELEVPSPEELAE 76 (169)
T ss_pred HHHHHHHHHc-----CCCCcHHHHHHHHHh-hccHHHHHHHH-HHHHhCCCeeeeeecceEEEeeCccccCCCCchhHHH
Confidence 5689999997 899999999999965 55554433333 789999999988655 3 333322 45556666444
Q ss_pred HHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhC
Q psy14236 153 LLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQ 187 (290)
Q Consensus 153 lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e 187 (290)
+=.. +.+|++-.......+..|+++
T Consensus 77 ld~e----------i~~L~~el~~l~~~~k~l~~e 101 (169)
T PF07106_consen 77 LDAE----------IKELREELAELKKEVKSLEAE 101 (169)
T ss_pred HHHH----------HHHHHHHHHHHHHHHHHHHHH
Confidence 3333 677777777777777777643
No 8
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=85.76 E-value=0.62 Score=41.83 Aligned_cols=85 Identities=12% Similarity=0.334 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceE--EeeCCeEEeccCCCCCCHHHHH
Q psy14236 74 GVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIE--VIEGNKYIFKPVFKIKDRKGLL 151 (290)
Q Consensus 74 t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~--~~p~~~f~yKP~y~Ik~k~~LL 151 (290)
..|...|+|+|.+ .-+.++||..++|+ ...... .-+ ..|.....|. +|..|+|.|...--+ ..+-
T Consensus 99 ~lL~~Fi~yIK~~------Kvv~ledla~~f~l-~t~~~i-~ri--~~L~~~g~ltGv~DdrGkfIyIs~eE~---~~va 165 (188)
T PF09756_consen 99 QLLQEFINYIKEH------KVVNLEDLAAEFGL-RTQDVI-NRI--QELEAEGRLTGVIDDRGKFIYISEEEM---EAVA 165 (188)
T ss_dssp -HHHHHHHHHHH-------SEE-HHHHHHHH-S--HHHHH-HHH--HHHHHHSSS-EEE-TT--EEE-------------
T ss_pred HHHHHHHHHHHHc------ceeeHHHHHHHcCC-CHHHHH-HHH--HHHHHCCCceeeEcCCCCeEEecHHHH---HHHH
Confidence 3799999999996 78999999999987 333222 234 3455555544 343599999987544 3455
Q ss_pred HHHHhcccCCCCccchhhhHhhhhh
Q psy14236 152 KLLKQHDLKGIGGILLDDVRESLPH 176 (290)
Q Consensus 152 ~lL~~~~q~~~~GI~v~dLkD~~p~ 176 (290)
.+|+++ |-|++.+|......
T Consensus 166 ~fi~~r-----GRvsi~el~~~~N~ 185 (188)
T PF09756_consen 166 KFIKQR-----GRVSISELAQESNR 185 (188)
T ss_dssp -------------------------
T ss_pred HHHHHc-----CCccHHHHHHHHHh
Confidence 677774 78999999876543
No 9
>KOG3054|consensus
Probab=82.76 E-value=2.5 Score=39.70 Aligned_cols=90 Identities=18% Similarity=0.328 Sum_probs=59.1
Q ss_pred cchhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccC--CCCchhHHHHhHHhhhcCCceEEeeCCeEEeccCCCCCC
Q psy14236 69 SQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQL--DVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPVFKIKD 146 (290)
Q Consensus 69 ~~~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~--di~~~~~~~L~~e~L~~npKI~~~p~~~f~yKP~y~Ik~ 146 (290)
|..--..|...|+|+|+ +..+.++||..+.++- |.....+.+|. +-| -.-| .|..|+|.|.+.-.
T Consensus 195 ~eeqdnll~eFv~YIk~------nKvV~ledLas~f~Lrtqd~inriq~~l~-eg~--ltGV-mDDRGKfIYIS~eE--- 261 (299)
T KOG3054|consen 195 GEEQDNLLSEFVEYIKK------NKVVPLEDLASEFGLRTQDSINRIQELLA-EGL--LTGV-MDDRGKFIYISMEE--- 261 (299)
T ss_pred cchHHHHHHHHHHHHHh------cCeeeHHHHHHHhCccHHHHHHHHHHHHH-hhh--heee-ecCCCceEEecHHH---
Confidence 33344789999999999 4799999999999872 44444444444 333 1122 23259999975411
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhhhh
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESLPH 176 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~ 176 (290)
-..+-+|++++ |-||+.+|.+.-.+
T Consensus 262 l~AVAkfIkqr-----GRVSIaelAe~SN~ 286 (299)
T KOG3054|consen 262 LAAVAKFIKQR-----GRVSIAELAEKSNQ 286 (299)
T ss_pred HHHHHHHHHHc-----CceeHHHHHHhhcc
Confidence 12334567774 78999999887554
No 10
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=79.40 E-value=17 Score=35.20 Aligned_cols=144 Identities=19% Similarity=0.339 Sum_probs=72.2
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee-CCeEEeccC-------C-C
Q psy14236 73 FGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE-GNKYIFKPV-------F-K 143 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p-~~~f~yKP~-------y-~ 143 (290)
...-..|.+.++++ . ....+|.+||.......++..-. ..+ ..|-+.-+|.... +|...|+.. + +
T Consensus 8 ~~~~~~l~~~~~~~--~-~~~~~~~~~L~~~~~~~~~~~~~-~~i--n~Ll~~~~~~~~~~~~~l~~~~~~~~~a~k~~~ 81 (327)
T PF05158_consen 8 SELEKKLLELCREN--P-SPKGFSQEDLQQLIPGLDLQELV-KAI--NELLSSGLLKLLKKGGGLSYKAVSEEEAKKLKG 81 (327)
T ss_dssp HHHHHHHHHHHHH------SS-EEHHHHHHH-TTS-HHHHH-HHH--HHHHHHTSEEEEE-SSSEEEEE--SSS-----S
T ss_pred HHHHHHHHHHHHHh--c-CCCCcCHHHHHhhcCCCCHHHHH-HHH--HHHHhCCCEEEEEcCCEEEEEEeCHHHHhhhcC
Confidence 34455677777775 1 14689999998884322333222 334 3566667777654 456666644 3 3
Q ss_pred CCCHH-HHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCCC-CceEE-Eec-CCCCC----
Q psy14236 144 IKDRK-GLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPAD-KRKVM-FYN-DKSAQ---- 211 (290)
Q Consensus 144 Ik~k~-~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~~-~~riv-f~N-D~~~~---- 211 (290)
+.+-+ -++.+++. .|..||-.+||+..- ..+.+.|+.||..+-|=-|..-.. +.+|. -|| .|+-.
T Consensus 82 l~~~e~lvy~~I~~---ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~~l~Ps~eiTGG 158 (327)
T PF05158_consen 82 LSDEERLVYQLIEE---AGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLYDLEPSEEITGG 158 (327)
T ss_dssp SSCCHHHHHHHHHH---HTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEESSS---------
T ss_pred CCHHHHHHHHHHHH---hCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEccCCcCcccCCC
Confidence 44444 44566666 688999999999865 357799999999998888775542 22222 122 33322
Q ss_pred -----CCCCHHHHHHhhhc
Q psy14236 212 -----LDLDEDFQKLWRSI 225 (290)
Q Consensus 212 -----~~VD~EFk~lW~~v 225 (290)
..+|.||.+-++.+
T Consensus 159 ~wy~d~e~D~efi~~l~~~ 177 (327)
T PF05158_consen 159 PWYTDGEFDTEFIDVLREQ 177 (327)
T ss_dssp -------------------
T ss_pred CcccCCcccHHHHHHHHHH
Confidence 45899999887765
No 11
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=79.38 E-value=7.6 Score=33.52 Aligned_cols=59 Identities=22% Similarity=0.362 Sum_probs=43.3
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhh------hhHHHHHHHhhhCCcEEEEecCCCCceEEEecCCCCC
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESL------PHCEKALKHLSLQNEIIYVTRPADKRKVMFYNDKSAQ 211 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~------p~~~~~I~~Le~e~~Ilvv~~~~~~~rivf~ND~~~~ 211 (290)
.+.+|.||+++. ---++-||-+.. ..+.++|+.|.++|+|++= . -|+-+|+|+|...+.
T Consensus 3 e~~Il~y~~~qN----RPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K-~-~GKqkiY~~~Q~~~~ 67 (169)
T PF07106_consen 3 EDAILEYMKEQN----RPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEK-E-YGKQKIYFANQDELE 67 (169)
T ss_pred HHHHHHHHHHcC----CCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeee-e-ecceEEEeeCccccC
Confidence 357899999964 244566666665 3478999999999998832 2 278899999976655
No 12
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=75.99 E-value=7.2 Score=28.88 Aligned_cols=53 Identities=13% Similarity=0.298 Sum_probs=39.0
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhhh----hHHHHHHHhhhCCcEEEEecCCCCceEEE
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESLP----HCEKALKHLSLQNEIIYVTRPADKRKVMF 204 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~p----~~~~~I~~Le~e~~Ilvv~~~~~~~rivf 204 (290)
|+++|++|+.+. ++++-.||.|+.- .+...|..|+.+|.|-.+....+.+ .+|
T Consensus 2 ke~Il~~i~~~~----~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~-~~W 58 (62)
T PF04703_consen 2 KEKILEYIKEQN----GPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKS-TYW 58 (62)
T ss_dssp HHCHHHHHHHHT----S-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS--EE
T ss_pred cHHHHHHHHHcC----CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcc-eee
Confidence 578999999952 7899999999764 5778899999999998654333443 455
No 13
>KOG4603|consensus
Probab=73.15 E-value=6 Score=35.32 Aligned_cols=66 Identities=23% Similarity=0.320 Sum_probs=40.8
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhh-------hhHHHHHHHhhhCCcEEEEecCC-CCceEEEecCCCCCCCCCHH
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESL-------PHCEKALKHLSLQNEIIYVTRPA-DKRKVMFYNDKSAQLDLDED 217 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~-------p~~~~~I~~Le~e~~Ilvv~~~~-~~~rivf~ND~~~~~~VD~E 217 (290)
+..-||++|+++.. -.+-.|+-+.+ .-+.++|+.|++.|+|. .+. ++.+|.|.|.--+.+.-|+|
T Consensus 8 ~e~ivl~~~~eqNr----P~ssq~v~~~lq~e~lgktavqk~Ld~La~~Gki~---~K~YGKqKIY~a~QDqF~~~~~ee 80 (201)
T KOG4603|consen 8 AEGIVLRYLQEQNR----PYSSQDVFGNLQREHLGKTAVQKTLDQLAQQGKIK---EKMYGKQKIYFADQDQFDMVSDEE 80 (201)
T ss_pred cHHHHHHHHHHhcC----CCchHHHHHHHHHHhccchHHHHHHHHHHHcCchh---HHhccceeeEeecHHhhcCCChHH
Confidence 34557777777532 22223322222 34778999999999987 444 88999999865555443333
Q ss_pred H
Q psy14236 218 F 218 (290)
Q Consensus 218 F 218 (290)
+
T Consensus 81 l 81 (201)
T KOG4603|consen 81 L 81 (201)
T ss_pred H
Confidence 3
No 14
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=71.71 E-value=11 Score=26.88 Aligned_cols=42 Identities=24% Similarity=0.375 Sum_probs=34.0
Q ss_pred HHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEe
Q psy14236 148 KGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 148 ~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~ 194 (290)
+.+|++|+.+ +-++++||.+-+ ..+-.||+.|+++|.|..+.
T Consensus 3 ~~Il~~l~~~-----~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEK-----GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHc-----CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 5789999986 689999988865 45788999999999876553
No 15
>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=69.40 E-value=17 Score=32.22 Aligned_cols=57 Identities=18% Similarity=0.257 Sum_probs=42.6
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEec--CCCCceEEEecC
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTR--PADKRKVMFYND 207 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~--~~~~~rivf~ND 207 (290)
++..+|.+|..+ +++++.+|.+.. +.+-..|+.|+++|-|..... ..+.+.++|.--
T Consensus 2 tr~~IL~~L~~~-----~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT 64 (203)
T TIGR02702 2 TKEDILSYLLKQ-----GQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLS 64 (203)
T ss_pred HHHHHHHHHHHc-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEEC
Confidence 567899999885 679999988754 668899999999998865432 236777776543
No 16
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=68.90 E-value=5.7 Score=29.40 Aligned_cols=46 Identities=28% Similarity=0.414 Sum_probs=35.6
Q ss_pred HHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee
Q psy14236 78 KIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE 132 (290)
Q Consensus 78 ~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p 132 (290)
.|++||+.. +.|++-.||.+.+++ .+..-- .+| +.|..--+|+-.|
T Consensus 4 ~Il~~i~~~-----~~p~~T~eiA~~~gl-s~~~aR-~yL--~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 4 KILEYIKEQ-----NGPLKTREIADALGL-SIYQAR-YYL--EKLEKEGKVERSP 49 (62)
T ss_dssp CHHHHHHHH-----TS-EEHHHHHHHHTS--HHHHH-HHH--HHHHHCTSEEEES
T ss_pred HHHHHHHHc-----CCCCCHHHHHHHhCC-CHHHHH-HHH--HHHHHCCCEEEec
Confidence 489999997 589999999999987 444432 566 5899999999877
No 17
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=67.71 E-value=14 Score=31.30 Aligned_cols=76 Identities=22% Similarity=0.421 Sum_probs=47.3
Q ss_pred CCCcCHHHHHHhhccCCCCchhHHHHh---HHhhhcCCceEEeeCC--eEEeccCCCCCCHHHHHHHHHhcccCCCCccc
Q psy14236 92 DHPLTIDEILDETNQLDVGNKVKIWLS---TEALQNNPKIEVIEGN--KYIFKPVFKIKDRKGLLKLLKQHDLKGIGGIL 166 (290)
Q Consensus 92 ~~pltl~eIl~~l~~~di~~~~~~~L~---~e~L~~npKI~~~p~~--~f~yKP~y~Ik~k~~LL~lL~~~~q~~~~GI~ 166 (290)
+.|+|.+||...++. +.+.-++ -|+ .--|..-.++.++ .| .|.|+|. +.+++-+.+.
T Consensus 40 ~~~~tvdelae~lnr-~rStv~r-sl~~L~~~GlV~Rek~~~~-~Ggy~yiY~~i----~~ee~k~~i~----------- 101 (126)
T COG3355 40 NGPLTVDELAEILNR-SRSTVYR-SLQNLLEAGLVEREKVNLK-GGGYYYLYKPI----DPEEIKKKIL----------- 101 (126)
T ss_pred cCCcCHHHHHHHHCc-cHHHHHH-HHHHHHHcCCeeeeeeccC-CCceeEEEecC----CHHHHHHHHH-----------
Confidence 479999999999876 5444332 222 1122233445553 45 4555554 5566554444
Q ss_pred hhhhHhhhhhHHHHHHHhhh
Q psy14236 167 LDDVRESLPHCEKALKHLSL 186 (290)
Q Consensus 167 v~dLkD~~p~~~~~I~~Le~ 186 (290)
++|.+.|-.+...|++.+.
T Consensus 102 -~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 102 -KDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred -HHHHHHHHHHHHHHHHHhc
Confidence 4788888899999998874
No 18
>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=64.16 E-value=13 Score=25.08 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=30.6
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHh----hhhhHHHHHHHhhhCCcE
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRE----SLPHCEKALKHLSLQNEI 190 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD----~~p~~~~~I~~Le~e~~I 190 (290)
...+|.+|..+ +|++..||.+ +++.+-..|+.|+++|-|
T Consensus 5 ~~~Il~~l~~~-----~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 5 QRKILNYLREN-----PRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHC-----TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHc-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 45789999996 6899999888 467788999999988755
No 19
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=60.33 E-value=29 Score=31.37 Aligned_cols=118 Identities=14% Similarity=0.233 Sum_probs=74.8
Q ss_pred CCCcchhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccC-----CCCchhHHHHhHHhhh-----cCCceEEee--C
Q psy14236 66 SGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQL-----DVGNKVKIWLSTEALQ-----NNPKIEVIE--G 133 (290)
Q Consensus 66 tg~~~~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~-----di~~~~~~~L~~e~L~-----~npKI~~~p--~ 133 (290)
+|.+.+....-..|++++-... ...+.-+++.|++..++-. -|+++. ++ .|++ +.| +.+.. .
T Consensus 86 ~~~~~f~~ELa~qi~e~c~~~~-~~~GGii~L~dl~~~~nr~R~g~~lISp~D--i~--~A~~~l~~lg~g-~~l~~~~s 159 (223)
T PF04157_consen 86 KGSGDFYYELAVQIAEVCLATR-SKNGGIISLSDLYCRYNRARGGSELISPED--IL--RACKLLEVLGLG-FRLRKFGS 159 (223)
T ss_dssp SCHHHHHHHHHHHHHHHHHHHC-CTTTSEEEHHHHHHHHHHCTTTSST--HHH--HH--HHHHHHCCCTSS-EEEEEETT
T ss_pred ccchhHHHHHHHHHHHHHHHHH-hcCCCEEEHHHHHHHHHHhcccCCCcCHHH--HH--HHHHHHHHcCCC-eEEEEeCC
Confidence 4677777777778888887542 3334679999999887652 334443 22 2332 222 55443 3
Q ss_pred C-eEEeccC-CCC-CCHHHHHHHHHhcccCCCCccchhhhHh--hhhh--HHHHHHHhhhCCcEEE
Q psy14236 134 N-KYIFKPV-FKI-KDRKGLLKLLKQHDLKGIGGILLDDVRE--SLPH--CEKALKHLSLQNEIIY 192 (290)
Q Consensus 134 ~-~f~yKP~-y~I-k~k~~LL~lL~~~~q~~~~GI~v~dLkD--~~p~--~~~~I~~Le~e~~Ilv 192 (290)
| +|.--++ ... .+...+|+++.. ...+|+++.+|.+ +|+- |...|+.|+++|-+|+
T Consensus 160 g~~vv~s~~~~e~~~~~~~il~~~~~---~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~~ 222 (223)
T PF04157_consen 160 GVKVVQSVPYSELSKDQSRILELAEE---ENGGGVTASELAEKLGWSVERAKEALEELEREGLLWR 222 (223)
T ss_dssp TEEEEECST-CHH-HHHHHHHHHH-----TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEEE
T ss_pred CcEEEEeCCchhhhHHHHHHHHHHHh---hcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEee
Confidence 5 3444444 344 677889999932 1248999999986 5665 7789999999998874
No 20
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=60.30 E-value=21 Score=26.38 Aligned_cols=51 Identities=22% Similarity=0.177 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee
Q psy14236 74 GVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE 132 (290)
Q Consensus 74 t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p 132 (290)
-+|.+|.+|+..+ ..|-|+.||.+.+|+-..+.-+ .-| ++|..-=-|..++
T Consensus 10 ~vL~~I~~~~~~~-----G~~Pt~rEIa~~~g~~S~~tv~-~~L--~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 10 EVLEFIREYIEEN-----GYPPTVREIAEALGLKSTSTVQ-RHL--KALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHHHHH-----SS---HHHHHHHHTSSSHHHHH-HHH--HHHHHTTSEEEGC
T ss_pred HHHHHHHHHHHHc-----CCCCCHHHHHHHhCCCChHHHH-HHH--HHHHHCcCccCCC
Confidence 4678888999887 6889999999999983233222 344 5787766666653
No 21
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=59.55 E-value=25 Score=32.39 Aligned_cols=57 Identities=19% Similarity=0.322 Sum_probs=45.8
Q ss_pred CCHHHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCC--CCceEEEec
Q psy14236 145 KDRKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPA--DKRKVMFYN 206 (290)
Q Consensus 145 k~k~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~--~~~rivf~N 206 (290)
++++.||.+|.++ +++++.||.+-. ..+...++.|+++|-|-+-..+. +.|..+|.=
T Consensus 11 ~tr~~il~lL~~~-----g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~L 73 (218)
T COG2345 11 STRERILELLKKS-----GPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRL 73 (218)
T ss_pred cHHHHHHHHHhcc-----CCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeee
Confidence 4788999999987 799999988754 67889999999999776664443 778888874
No 22
>COG0064 GatB Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis]
Probab=58.06 E-value=53 Score=33.69 Aligned_cols=147 Identities=10% Similarity=0.228 Sum_probs=85.3
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeEEeccCCCCCCHHHHHHH
Q psy14236 74 GVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPVFKIKDRKGLLKL 153 (290)
Q Consensus 74 t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f~yKP~y~Ik~k~~LL~l 153 (290)
.--..++.||++ |..|+.++++.|..+.. -.|+----|.+.|-|.=.|-+.-.|+|-.++-..
T Consensus 165 rs~~eA~ayl~~-----------Lr~ilrylgisd~~mee------GsmR~DaNvSvr~~g~~~~GtrvEiKNiNS~~~v 227 (483)
T COG0064 165 RSPEEARAYLKK-----------LRSILRYLGISDGNMEE------GSMRCDANVSVRPKGQEEFGTRVEIKNLNSFRNV 227 (483)
T ss_pred CCHHHHHHHHHH-----------HHHHHHHcCCCCCCccc------CceEeeeeeeeccccccccCceeeeecCccHHHH
Confidence 334566777766 46788888776655432 1344444455554444444455444443332222
Q ss_pred -------HHhcccCCCCccchhhhHhhhhhHHHHHHHhhh-CCcEEEEecCCCCceEEEecCCCCC-CCCCHHHHHHhhh
Q psy14236 154 -------LKQHDLKGIGGILLDDVRESLPHCEKALKHLSL-QNEIIYVTRPADKRKVMFYNDKSAQ-LDLDEDFQKLWRS 224 (290)
Q Consensus 154 -------L~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~-e~~Ilvv~~~~~~~rivf~ND~~~~-~~VD~EFk~lW~~ 224 (290)
.+++ +..|.+| -.+.+.-...-. .|.=...|.+.+....-|+.||.+. +.+++++.+-|+
T Consensus 228 ~kAi~yE~~RQ---------~~~l~~g-~~i~qeTR~~d~~~g~T~~mR~KE~a~DYRYfpePDl~p~~is~~~i~~~~- 296 (483)
T COG0064 228 EKAIEYEIQRQ---------IELLESG-GEIEQETRRFDEATGKTVSMRSKEEAEDYRYFPEPDLPPLEISDEWIEEVR- 296 (483)
T ss_pred HHHHHHHHHHH---------HHHHHcC-CCeeehccccccCCCeEeeccccccccccccCCCCCcCCccCCHHHHHHHH-
Confidence 2221 2223333 111111111211 2333334444477788899999885 789999999999
Q ss_pred cccCCCChhhHHHHHHHcCCCCcc
Q psy14236 225 ISVDGMDNDKIKEYLEKQGIRPIQ 248 (290)
Q Consensus 225 v~VP~~de~di~~~L~~~Glkp~~ 248 (290)
-.+|...+++.+++....|++...
T Consensus 297 ~~lPelP~~~~~r~~~~~gls~~d 320 (483)
T COG0064 297 ATLPELPDEKRERYIKEYGLSEYD 320 (483)
T ss_pred HhCCCCCHHHHHHHHHHcCCCHHH
Confidence 568888889999999999998763
No 23
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=57.35 E-value=22 Score=30.57 Aligned_cols=86 Identities=16% Similarity=0.340 Sum_probs=56.9
Q ss_pred hhcCCceEEeeCCeEEeccCCCCC--CHHHHHHHHHhcccCCCCccchhhhHh----hhhhHHHHHHHhhhCCcEEEEec
Q psy14236 122 LQNNPKIEVIEGNKYIFKPVFKIK--DRKGLLKLLKQHDLKGIGGILLDDVRE----SLPHCEKALKHLSLQNEIIYVTR 195 (290)
Q Consensus 122 L~~npKI~~~p~~~f~yKP~y~Ik--~k~~LL~lL~~~~q~~~~GI~v~dLkD----~~p~~~~~I~~Le~e~~Ilvv~~ 195 (290)
--.+|.|.|. +|-..+.|= +--+||++|..+ +--++.||.+ .++++-.++..|+.-|-|.+=..
T Consensus 44 ~~~~Ptl~F~-----Sye~la~vLsp~nleLl~~Ia~~-----~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~~ 113 (144)
T COG4190 44 MDATPTLWFT-----SYEDLARVLSPRNLELLELIAQE-----EPASINELAELVGRDVKNVHRTLSTLADLGLIFFEED 113 (144)
T ss_pred ccCCceeccc-----cHHHHHHHhChhHHHHHHHHHhc-----CcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEecC
Confidence 3445555555 333333322 234788888886 5677888877 58999999999998777765554
Q ss_pred CCCCceEEEecCCCCCCCCCHH
Q psy14236 196 PADKRKVMFYNDKSAQLDLDED 217 (290)
Q Consensus 196 ~~~~~rivf~ND~~~~~~VD~E 217 (290)
...+.-.|||.+--+.++.|.+
T Consensus 114 gq~k~P~~~y~~l~I~lpf~~~ 135 (144)
T COG4190 114 GQRKQPVVWYDELVIDLPFDPE 135 (144)
T ss_pred CcccCceeeccccEEeeecCcc
Confidence 3356677888876666666644
No 24
>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=56.76 E-value=12 Score=25.90 Aligned_cols=48 Identities=19% Similarity=0.194 Sum_probs=33.2
Q ss_pred HHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEe
Q psy14236 75 VLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVI 131 (290)
Q Consensus 75 ~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~ 131 (290)
....|+++|... ..++|+.||...+++ ..+.-+ ..| ..|...-=|+.+
T Consensus 4 ral~iL~~l~~~-----~~~~t~~eia~~~gl-~~stv~-r~L--~tL~~~g~v~~d 51 (52)
T PF09339_consen 4 RALRILEALAES-----GGPLTLSEIARALGL-PKSTVH-RLL--QTLVEEGYVERD 51 (52)
T ss_dssp HHHHHHHCHHCT-----BSCEEHHHHHHHHTS--HHHHH-HHH--HHHHHTTSEEEC
T ss_pred HHHHHHHHHHcC-----CCCCCHHHHHHHHCc-CHHHHH-HHH--HHHHHCcCeecC
Confidence 456788999887 678999999999987 544443 344 466666555544
No 25
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=55.43 E-value=43 Score=25.99 Aligned_cols=49 Identities=16% Similarity=0.311 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeE
Q psy14236 75 VLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKY 136 (290)
Q Consensus 75 ~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f 136 (290)
.+--++..|-. ..|+|.++|...++. .+. -+. .+|..-|-|+||.+|..
T Consensus 25 L~r~LLr~LA~------G~PVt~~~LA~a~g~-~~e-----~v~-~~L~~~p~tEyD~~GrI 73 (77)
T PF12324_consen 25 LLRPLLRLLAK------GQPVTVEQLAAALGW-PVE-----EVR-AALAAMPDTEYDDQGRI 73 (77)
T ss_dssp HHHHHHHHHTT------TS-B-HHHHHHHHT---HH-----HHH-HHHHH-TTSEEETTSEE
T ss_pred HHHHHHHHHHc------CCCcCHHHHHHHHCC-CHH-----HHH-HHHHhCCCceEcCCCCe
Confidence 34445555544 689999999999986 222 233 58888899999987754
No 26
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=55.06 E-value=36 Score=27.12 Aligned_cols=55 Identities=16% Similarity=0.307 Sum_probs=38.4
Q ss_pred HHHHHHhcccCCCCccchhhhHhh----hhhHHHHHHHhhhCCcEEEEecCCCC-ceEEEecCCC
Q psy14236 150 LLKLLKQHDLKGIGGILLDDVRES----LPHCEKALKHLSLQNEIIYVTRPADK-RKVMFYNDKS 209 (290)
Q Consensus 150 LL~lL~~~~q~~~~GI~v~dLkD~----~p~~~~~I~~Le~e~~Ilvv~~~~~~-~rivf~ND~~ 209 (290)
+|..|..+ +|+++.+|.+. -+.+-..|+.|++.|-|.....+.|+ ..+|...+.+
T Consensus 33 iL~~l~~~-----~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G 92 (118)
T TIGR02337 33 ILRILAEQ-----GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKG 92 (118)
T ss_pred HHHHHHHc-----CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhH
Confidence 66667664 68999999987 45688999999999888766555443 3444444433
No 27
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=54.37 E-value=51 Score=27.79 Aligned_cols=99 Identities=16% Similarity=0.226 Sum_probs=57.6
Q ss_pred HHHHHHhhhcCCCCCCCcCHHHHHHhhcc-CCCCchhHHHHhHHhhhcCCceEEeeCCeEEeccCCCCCCHHHHH--HHH
Q psy14236 78 KIVKHMKQRHQDGDDHPLTIDEILDETNQ-LDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPVFKIKDRKGLL--KLL 154 (290)
Q Consensus 78 ~iV~~LK~r~~~g~~~pltl~eIl~~l~~-~di~~~~~~~L~~e~L~~npKI~~~p~~~f~yKP~y~Ik~k~~LL--~lL 154 (290)
.|.++|=.+ .|.|..||..+++- .+++...-.-|.+.+.+.+==-.+-.++.|.|.|.++...-.++. .+|
T Consensus 10 eVM~ilW~~------~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdgr~~~y~pL~~~~~~~~~~~~~~l 83 (123)
T COG3682 10 EVMEILWSR------GPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDGRAFRYSPLLTRDQYVAGESQDLL 83 (123)
T ss_pred HHHHHHHHc------CCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcCCeeeeecccCHHHHHHHHHHHHH
Confidence 355566554 59999999999986 245555433333244444333333335799999999866554433 355
Q ss_pred HhcccCCCCcc--chhhhHhhhhhHHHHHHHhh
Q psy14236 155 KQHDLKGIGGI--LLDDVRESLPHCEKALKHLS 185 (290)
Q Consensus 155 ~~~~q~~~~GI--~v~dLkD~~p~~~~~I~~Le 185 (290)
++... +|+ .|....|.-+=-.++|++|+
T Consensus 84 ~k~~d---~~~~~lv~~F~~~~~l~~~eie~L~ 113 (123)
T COG3682 84 DKICD---GGLASLVAHFAEKEKLTADEIEALK 113 (123)
T ss_pred HHHHc---ccchHHHHHHHHhccCCHHHHHHHH
Confidence 55431 333 24666666444455555554
No 28
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=52.95 E-value=39 Score=23.34 Aligned_cols=46 Identities=26% Similarity=0.465 Sum_probs=36.3
Q ss_pred HHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCCCC
Q psy14236 149 GLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPADK 199 (290)
Q Consensus 149 ~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~~~ 199 (290)
.+|.+|..+ +|+++.+|.+.. +.+-..|+.|++.|-|--.+.+.|+
T Consensus 7 ~iL~~l~~~-----~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 7 RILRILYEN-----GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHHH-----SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTET
T ss_pred HHHHHHHHc-----CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCC
Confidence 467778775 689999998865 5688899999999988877666543
No 29
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=52.48 E-value=81 Score=24.32 Aligned_cols=42 Identities=12% Similarity=0.237 Sum_probs=32.1
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHH-hhhCCcEE
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKH-LSLQNEII 191 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~-Le~e~~Il 191 (290)
|+++|++.+..+. .|++-.+++..+-...+.|.+ |.+.+.|.
T Consensus 2 ~k~eli~~i~~~~----~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~ 44 (94)
T TIGR00988 2 TKSELIERIATQQ----SHLPAKDVEDAVKTMLEHMASALAQGDRIE 44 (94)
T ss_pred CHHHHHHHHHHHc----CCCCHHHHHHHHHHHHHHHHHHHHcCCeEE
Confidence 6889999998741 588999999999998888755 66544444
No 30
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=51.74 E-value=41 Score=25.17 Aligned_cols=57 Identities=14% Similarity=0.146 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee-CCeEEec
Q psy14236 74 GVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE-GNKYIFK 139 (290)
Q Consensus 74 t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p-~~~f~yK 139 (290)
.....|+++|... ..++++.||..++++ ..+.-. ..| ..|..+--|..++ +|.|+.-
T Consensus 5 ~r~~~Il~~l~~~-----~~~~t~~~ia~~l~i-~~~tv~-r~l--~~L~~~g~l~~~~~~~~y~l~ 62 (91)
T smart00346 5 ERGLAVLRALAEE-----PGGLTLAELAERLGL-SKSTAH-RLL--NTLQELGYVEQDGQNGRYRLG 62 (91)
T ss_pred HHHHHHHHHHHhC-----CCCcCHHHHHHHhCC-CHHHHH-HHH--HHHHHCCCeeecCCCCceeec
Confidence 4456788888764 368999999999976 333332 344 5788888887765 4566553
No 31
>PF09724 DUF2036: Uncharacterized conserved protein (DUF2036); InterPro: IPR019128 Sister chromatid cohesion protein DCC1 is a component of the RFC-like complex CTF18-RFC. This complex is required for the efficient establishment of chromosome cohesion during S-phase and may load or unload POL30/PCNA. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC. The complex presumably provides bipartite ATP sites in which one subunit supplies a catalytic site for hydrolysis of ATP bound to the neighbouring subunit. Dissociation of RFC from the clamp leaves the clamp encircling DNA [, ].
Probab=48.35 E-value=1.8e+02 Score=27.59 Aligned_cols=156 Identities=17% Similarity=0.257 Sum_probs=96.5
Q ss_pred CcchhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeEEeccCCCCCCH
Q psy14236 68 SSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPVFKIKDR 147 (290)
Q Consensus 68 ~~~~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f~yKP~y~Ik~k 147 (290)
+..+.+..|..|+.++-.+... -..++++++...+.-..++.. .+. ..|+..-...-+++..|.+...--++--
T Consensus 162 s~~~~~~~L~~il~~~~~~~~~--~~~~~~~~~~~~l~~~~~p~~---v~~-~vl~~~~~~~~~~~~~~~Ld~~ki~~~~ 235 (325)
T PF09724_consen 162 SPSYLFEILDLILTSAVEESWD--LDQFPVEEVVEALEEDEYPRE---VVE-HVLRKFGTREDDDDSWWKLDEDKICRWF 235 (325)
T ss_pred CHHHHHHHHHHHHHHHHHcCCC--cccCCHHHHHHHhcccCCCHH---HHH-HHHHHhCCCccCCCceEEcCHHHHHHHH
Confidence 4567788999999999886422 257999999888875234433 222 3454442221111234555332111111
Q ss_pred HHHHHHHHhcccCCCCccchhhhHhhhhhHH-------HHHHHhhhCCcEEEEecCCCCceEEEecCCCCCCCCCHHHHH
Q psy14236 148 KGLLKLLKQHDLKGIGGILLDDVRESLPHCE-------KALKHLSLQNEIIYVTRPADKRKVMFYNDKSAQLDLDEDFQK 220 (290)
Q Consensus 148 ~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~-------~~I~~Le~e~~Ilvv~~~~~~~rivf~ND~~~~~~VD~EFk~ 220 (290)
. ..+|+.+ ..+.+.++|..+.|.+.. -+++-|+ |..++-.++ ....|.|.+...+-..+-+=|+.
T Consensus 236 a--~~lL~~~---~~~~~~~~eFl~~Wk~~lP~~~~~~~~l~~L~--G~~~~~~~~-~~~~I~y~~~~~Lp~dp~~Rf~~ 307 (325)
T PF09724_consen 236 A--IQLLKAH---ASSSFPLDEFLEAWKSSLPEFFGMDPDLEMLR--GLALIDDRP-SPTTIQYFPESDLPTDPKERFKE 307 (325)
T ss_pred H--HHHHHhc---ccCCCCHHHHHHHHHHhCCCcCCCCCCHHHhC--CeeEeecCC-CCCEEEEecHHHCCCCHHHHHHH
Confidence 1 2345553 113788999988887644 4588887 766644233 66788888988887788888999
Q ss_pred HhhhcccCCCChhhHHHHH
Q psy14236 221 LWRSISVDGMDNDKIKEYL 239 (290)
Q Consensus 221 lW~~v~VP~~de~di~~~L 239 (290)
||+--+- =+.+||.-|+
T Consensus 308 LF~~~~k--W~~~ei~Pyi 324 (325)
T PF09724_consen 308 LFKLRPK--WTLDEIEPYI 324 (325)
T ss_pred HHhcCCC--CCHHHHHHhh
Confidence 9987653 3556676665
No 32
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=47.83 E-value=97 Score=24.07 Aligned_cols=41 Identities=10% Similarity=0.238 Sum_probs=31.9
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHH-hhhCCcEE
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKH-LSLQNEII 191 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~-Le~e~~Il 191 (290)
++.+|.+.|... .|++..|.+...-...+.|.+ |.+.+.|-
T Consensus 2 ~K~eli~~ia~~-----~~~s~~~~~~~v~~~~~~i~~~L~~g~~V~ 43 (90)
T PRK10753 2 NKTQLIDVIADK-----AELSKTQAKAALESTLAAITESLKEGDAVQ 43 (90)
T ss_pred CHHHHHHHHHHH-----hCCCHHHHHHHHHHHHHHHHHHHHcCCeEE
Confidence 688999999885 589999999999888888855 55544443
No 33
>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=47.62 E-value=68 Score=22.13 Aligned_cols=47 Identities=19% Similarity=0.258 Sum_probs=35.0
Q ss_pred HHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCCC
Q psy14236 149 GLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPAD 198 (290)
Q Consensus 149 ~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~~ 198 (290)
.+|.+|..++ ..++++.||.+.+ +.+-..|+.|++.|-|.....+.|
T Consensus 9 ~vL~~l~~~~---~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 9 RVLMALARHP---GEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp HHHHHHHHST---TSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred HHHHHHHHCC---CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 5778888863 1249999999876 568889999999998886655433
No 34
>PF11252 DUF3051: Protein of unknown function (DUF3051); InterPro: IPR021411 This entry is represented by Sugarcane yellow leaf virus (SCYLV), Orf0; it is a family of uncharacterised viral proteins.
Probab=47.28 E-value=13 Score=32.14 Aligned_cols=22 Identities=27% Similarity=0.490 Sum_probs=19.8
Q ss_pred HHHHhHHHHHHhhccCCccccc
Q psy14236 4 ALLRERDLFKKKALSTPTVEKR 25 (290)
Q Consensus 4 ~ll~~~~~fk~ra~~~p~ve~~ 25 (290)
-+|+|||.|-.|++-+|+++.-
T Consensus 106 v~l~e~erfv~rileqp~~~p~ 127 (189)
T PF11252_consen 106 VHLREHERFVSRILEQPPMDPC 127 (189)
T ss_pred HHHHHHHHHHHHHhcCCCCChh
Confidence 3799999999999999999864
No 35
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=46.98 E-value=46 Score=25.94 Aligned_cols=30 Identities=10% Similarity=0.266 Sum_probs=23.8
Q ss_pred hhhhHHHHHHHhhhCCcEEEEecCCCCceE
Q psy14236 173 SLPHCEKALKHLSLQNEIIYVTRPADKRKV 202 (290)
Q Consensus 173 ~~p~~~~~I~~Le~e~~Ilvv~~~~~~~ri 202 (290)
.||.|-..|+-|.++|.|.++.+..-..|+
T Consensus 46 iY~~Vc~yLe~L~~eg~l~~i~~~~~~dRi 75 (78)
T PF13034_consen 46 IYPYVCNYLEYLVKEGKLSFIENDGTRDRI 75 (78)
T ss_pred eHHHHHHHHHHHHHCCeEEEEecCcchhhh
Confidence 478899999999999999999776433343
No 36
>COG3395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.70 E-value=1.3e+02 Score=30.46 Aligned_cols=124 Identities=22% Similarity=0.199 Sum_probs=84.0
Q ss_pred ccccCCCCcchhHHHHHHHHHHHhhhc--------------CCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCC
Q psy14236 61 AYKSMSGSSQYKFGVLAKIVKHMKQRH--------------QDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNP 126 (290)
Q Consensus 61 ~~~~~tg~~~~~~t~l~~iV~~LK~r~--------------~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~np 126 (290)
+.++-+=....-..+...+..|||... +.| +-+.-.+=+++.++ .++. ++. .+|..|-
T Consensus 48 ~~~sRs~~~~eA~~~~~~A~~~Lk~~~~~~~~kvcstfDST~~G-NIG~~~dal~~alg-~~~a-----vv~-PA~P~~g 119 (413)
T COG3395 48 ALKSRSLPADEAISQVLAALSWLKEAGAQVHYKVCSTFDSTLRG-NIGPETDALLDALG-FSIA-----VVV-PALPLNG 119 (413)
T ss_pred ecccccCCHHHHHHHHHHHHHHHHhcCccceEEEEecccCCCCC-CccHHHHHHHHhcC-CCce-----EEe-cCccCCC
Confidence 333434466677899999999999974 222 23333455556655 2322 233 6888888
Q ss_pred ceEEee----CC------eEEeccCCCCCCHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEE
Q psy14236 127 KIEVIE----GN------KYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYV 193 (290)
Q Consensus 127 KI~~~p----~~------~f~yKP~y~Ik~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv 193 (290)
|+.|+. +| -+.+-|...+++ ..|.++|.++.+-.-|=+.+.|+.++-..+.+.|.+|++++--+++
T Consensus 120 Rtv~~gyl~v~Gvlv~es~~~~~PvtPm~~-s~l~r~v~~qt~~~~g~v~l~~~~~g~~~~~~~L~~l~~~g~~~~v 195 (413)
T COG3395 120 RTVFGGYLFVNGVLVDESGMARDPVTPMKD-SYLPRHVAKQTKGKIGLVDLADVRQGADAVRAALADLQAEGCRVAV 195 (413)
T ss_pred eeEEeeEEEEcCEEcccCccccCCCCccch-hhHHHHHHHHhcCCcccccHHHHhhhHHHHHHHHHHHHhcCCcEEe
Confidence 888873 23 233344444444 5799999998766666678889999999999999999999985544
No 37
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=46.53 E-value=37 Score=25.00 Aligned_cols=44 Identities=14% Similarity=0.179 Sum_probs=34.4
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEE
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIY 192 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilv 192 (290)
.++.+|.+|.++ |..|++..||.+.. ..+...|..|+++|.|..
T Consensus 7 ~~~~IL~~L~~~---g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 7 LEEKILEFLENS---GDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHHHC---CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 467899999995 22259999988765 368899999999998753
No 38
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=46.40 E-value=45 Score=27.63 Aligned_cols=57 Identities=14% Similarity=0.171 Sum_probs=41.9
Q ss_pred HHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCCC-CceEEEecCCCCC
Q psy14236 150 LLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPAD-KRKVMFYNDKSAQ 211 (290)
Q Consensus 150 LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~~-~~rivf~ND~~~~ 211 (290)
+|..|..+ +|++..+|.+.. +.+-..|+.|++.|-|.-...+.| ....|+.-+.+..
T Consensus 45 vL~~l~~~-----~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~ 106 (144)
T PRK11512 45 VLCSIRCA-----ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAA 106 (144)
T ss_pred HHHHHHHc-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHH
Confidence 45556442 689999988865 678899999999998887766654 4666777776653
No 39
>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=45.68 E-value=89 Score=21.39 Aligned_cols=66 Identities=20% Similarity=0.194 Sum_probs=40.1
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHh----hhhhHHHHHHHhhhCCcEEEEecCCCCceEEEecCCCCCCCCCHHHHHH
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRE----SLPHCEKALKHLSLQNEIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKL 221 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD----~~p~~~~~I~~Le~e~~Ilvv~~~~~~~rivf~ND~~~~~~VD~EFk~l 221 (290)
+...+|.+|..+ +++..||.+ +.+.+...|+.|++.|-|...... ....+.+++ ...+-+.+..+
T Consensus 8 ~~~~il~~l~~~------~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~--~~~~~~~~~---g~~~~~~~~~~ 76 (78)
T cd00090 8 TRLRILRLLLEG------PLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG--RRVYYSLTD---AERLLALLESL 76 (78)
T ss_pred HHHHHHHHHHHC------CcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec--cEEEEEeCC---chHHHHHHHHh
Confidence 445667776663 377877775 456678999999988877655433 344444444 22444555555
Q ss_pred h
Q psy14236 222 W 222 (290)
Q Consensus 222 W 222 (290)
|
T Consensus 77 ~ 77 (78)
T cd00090 77 L 77 (78)
T ss_pred h
Confidence 4
No 40
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=43.78 E-value=96 Score=24.17 Aligned_cols=42 Identities=10% Similarity=0.158 Sum_probs=33.0
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHH-hhhCCcEEE
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKH-LSLQNEIIY 192 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~-Le~e~~Ilv 192 (290)
++.+|++.|... .|++-.|....+-...+.|.+ |.+.+.|-+
T Consensus 2 tK~eli~~ia~~-----~~~s~~~~~~~v~~~~~~i~~~L~~~~~v~l 44 (90)
T PRK10664 2 NKSQLIDKIAAG-----ADISKAAAGRALDAIIASVTESLKEGDDVAL 44 (90)
T ss_pred CHHHHHHHHHHH-----hCCCHHHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 688999999985 589999999999888877765 666555543
No 41
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=42.97 E-value=88 Score=20.36 Aligned_cols=41 Identities=27% Similarity=0.410 Sum_probs=31.6
Q ss_pred HHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEE
Q psy14236 148 KGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYV 193 (290)
Q Consensus 148 ~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv 193 (290)
..+|.+|.++ +++++.+|.+.+ +.+...|+.|++.|-|...
T Consensus 3 ~~il~~l~~~-----~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 3 QQILELLAQQ-----GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHHHc-----CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4678888774 578998888764 5688899999988877643
No 42
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=42.68 E-value=65 Score=23.65 Aligned_cols=48 Identities=13% Similarity=0.063 Sum_probs=36.1
Q ss_pred HHHHHHHHhhhcCCCCCC-CcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee
Q psy14236 76 LAKIVKHMKQRHQDGDDH-PLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE 132 (290)
Q Consensus 76 l~~iV~~LK~r~~~g~~~-pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p 132 (290)
=..|+++|+.+ .. +++..||...+|+ +...- .+.| ..|...-.|..++
T Consensus 8 ~~~IL~~L~~~-----g~~~~ta~eLa~~lgl-~~~~v-~r~L--~~L~~~G~V~~~~ 56 (68)
T smart00550 8 EEKILEFLENS-----GDETSTALQLAKNLGL-PKKEV-NRVL--YSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHC-----CCCCcCHHHHHHHHCC-CHHHH-HHHH--HHHHHCCCEEecC
Confidence 35799999997 23 3999999999998 44432 3456 4789998898874
No 43
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=42.55 E-value=21 Score=31.22 Aligned_cols=32 Identities=22% Similarity=0.651 Sum_probs=27.3
Q ss_pred CHHHHHHhhhc-ccCCCChhhHHHHHHHcCCCCcc
Q psy14236 215 DEDFQKLWRSI-SVDGMDNDKIKEYLEKQGIRPIQ 248 (290)
Q Consensus 215 D~EFk~lW~~v-~VP~~de~di~~~L~~~Glkp~~ 248 (290)
.++|+.+|+.+ .+| .-.++..||+.+|+....
T Consensus 43 s~~f~~l~~~l~~~p--E~~~l~~yL~~~gldv~~ 75 (179)
T PF06757_consen 43 SSEFKQLWQQLEALP--EVKALLDYLESAGLDVYY 75 (179)
T ss_pred ChHHHHHHHHHHcCH--HHHHHHHHHHHCCCCHHH
Confidence 56799999996 788 457899999999999875
No 44
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=42.04 E-value=96 Score=23.42 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=31.2
Q ss_pred CCCCCHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEEecCCCCceEEEecCC
Q psy14236 142 FKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYVTRPADKRKVMFYNDK 208 (290)
Q Consensus 142 y~Ik~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~~~~~~~rivf~ND~ 208 (290)
+.|.+.++|+++|+.+ |+.+. =+.+-.||++|. |+=+++..+....+.+++.
T Consensus 17 ~~i~sQ~eL~~~L~~~------Gi~vT-----QaTiSRDLkeL~----~vKv~~~~g~~~Y~l~~~~ 68 (70)
T PF01316_consen 17 HEISSQEELVELLEEE------GIEVT-----QATISRDLKELG----AVKVPDGNGKYRYVLPEET 68 (70)
T ss_dssp S---SHHHHHHHHHHT------T-T-------HHHHHHHHHHHT-----EEEECTTSSEEEE-TTST
T ss_pred CCcCCHHHHHHHHHHc------CCCcc-----hhHHHHHHHHcC----cEEeeCCCCCEEEEecCcC
Confidence 5788999999999993 77764 366788999996 2224444455666655543
No 45
>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=41.83 E-value=33 Score=23.49 Aligned_cols=26 Identities=23% Similarity=0.404 Sum_probs=21.1
Q ss_pred HHHHHHHHhhhcCCCCCCCcCHHHHHHhhcc
Q psy14236 76 LAKIVKHMKQRHQDGDDHPLTIDEILDETNQ 106 (290)
Q Consensus 76 l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~ 106 (290)
...|+.+|.+. +.|+|.+||.+.+++
T Consensus 2 ~~~il~~L~~~-----~~~it~~eLa~~l~v 27 (55)
T PF08279_consen 2 QKQILKLLLES-----KEPITAKELAEELGV 27 (55)
T ss_dssp HHHHHHHHHHT-----TTSBEHHHHHHHCTS
T ss_pred HHHHHHHHHHc-----CCCcCHHHHHHHhCC
Confidence 45788899665 567999999999876
No 46
>TIGR03820 lys_2_3_AblA lysine-2,3-aminomutase. This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Probab=41.68 E-value=1.1e+02 Score=30.73 Aligned_cols=102 Identities=23% Similarity=0.275 Sum_probs=66.6
Q ss_pred HHHHHHHHHHHhhhc------CCCCCCCcCHHH-HHHhhccCCCCchhHHHHhHHhhhcCCceEEee--CCeEEeccCCC
Q psy14236 73 FGVLAKIVKHMKQRH------QDGDDHPLTIDE-ILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE--GNKYIFKPVFK 143 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~------~~g~~~pltl~e-Il~~l~~~di~~~~~~~L~~e~L~~npKI~~~p--~~~f~yKP~y~ 143 (290)
...+..+++|++.+. +.| +.||.+.+ ++.. +| +.|+..|.|+... ...-.+-|. -
T Consensus 140 ~eei~~~i~yI~~~p~I~~VlLSG-GDPLll~d~~L~~------------iL--~~L~~IphV~~IRI~TR~pvv~P~-R 203 (417)
T TIGR03820 140 KEQILEGIEYIRNTPQIRDVLLSG-GDPLLLSDDYLDW------------IL--TELRAIPHVEVIRIGTRVPVVLPQ-R 203 (417)
T ss_pred HHHHHHHHHHHHhcCCCCEEEEeC-CccccCChHHHHH------------HH--HHHhhcCCCceEEEeecccccccc-c
Confidence 568889999999841 445 57887765 3322 12 4566677666442 233333332 3
Q ss_pred CCCHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEE
Q psy14236 144 IKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYV 193 (290)
Q Consensus 144 Ik~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv 193 (290)
|. ++|++.|+++. .-.=++.+.--.|-.+.+.++|+.|.+.|-.+..
T Consensus 204 IT--~ell~~Lk~~~-~~~v~~h~nhp~Eit~~a~~Al~~L~~aGI~l~n 250 (417)
T TIGR03820 204 IT--DELVAILKKHH-PVWLNTHFNHPREITASSKKALAKLADAGIPLGN 250 (417)
T ss_pred cC--HHHHHHHHhcC-CeEEEEeCCChHhChHHHHHHHHHHHHcCCEEEe
Confidence 43 59999999973 2234566666778899999999999988855443
No 47
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=41.53 E-value=90 Score=23.11 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=32.0
Q ss_pred HHHHHHHhcccCCCCccchhhhHhh----hhhHHHHHHHhhhCCcEEEEecCCC
Q psy14236 149 GLLKLLKQHDLKGIGGILLDDVRES----LPHCEKALKHLSLQNEIIYVTRPAD 198 (290)
Q Consensus 149 ~LL~lL~~~~q~~~~GI~v~dLkD~----~p~~~~~I~~Le~e~~Ilvv~~~~~ 198 (290)
.+|.+|..+ +++...+|.+. .+.+-..|+.|++.|-|.......+
T Consensus 14 ~il~~l~~~-----~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~ 62 (101)
T smart00347 14 LVLRILYEE-----GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPED 62 (101)
T ss_pred HHHHHHHHc-----CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCC
Confidence 456666664 46888887664 5678899999999888776544433
No 48
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=39.66 E-value=57 Score=30.10 Aligned_cols=43 Identities=16% Similarity=0.302 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEe
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~ 194 (290)
...+|++|+++ +-+++.||.+-+ ..+-.||++|+++|.|.-+.
T Consensus 7 ~~~Il~~L~~~-----~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 7 QAAILEYLQKQ-----GKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHc-----CCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 36789999996 569999998854 56889999999999887554
No 49
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=38.95 E-value=33 Score=24.32 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=31.7
Q ss_pred HHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhH-HHHhHHhhhcCCceEEe
Q psy14236 76 LAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVK-IWLSTEALQNNPKIEVI 131 (290)
Q Consensus 76 l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~-~~L~~e~L~~npKI~~~ 131 (290)
...|++||+++ ..++++||.+.+++ +.... .-| ..|.+.-.|.-.
T Consensus 2 ~~~Il~~l~~~------~~~s~~ela~~~~V---S~~TiRRDl--~~L~~~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEK------GKVSVKELAEEFGV---SEMTIRRDL--NKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHHHc------CCEEHHHHHHHHCc---CHHHHHHHH--HHHHHCCCEEEE
Confidence 45799999985 68999999999865 43332 223 367777666655
No 50
>PRK11569 transcriptional repressor IclR; Provisional
Probab=38.85 E-value=87 Score=28.96 Aligned_cols=57 Identities=7% Similarity=0.139 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee-CCeEEe
Q psy14236 73 FGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE-GNKYIF 138 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p-~~~f~y 138 (290)
...-..|+++|-.. ..|+++.||...+++ ..+.-+ .+| ..|...-=|+.++ +|+|+-
T Consensus 27 l~ral~IL~~l~~~-----~~~~~lseia~~lgl-pksTv~-RlL--~tL~~~G~l~~~~~~~~Y~l 84 (274)
T PRK11569 27 LTRGLKLLEWIAES-----NGSVALTELAQQAGL-PNSTTH-RLL--TTMQQQGFVRQVGELGHWAI 84 (274)
T ss_pred HHHHHHHHHHHHhC-----CCCcCHHHHHHHHCc-CHHHHH-HHH--HHHHHCCCEEEcCCCCeEec
Confidence 56677888888764 578999999999987 555554 466 4788888898886 477765
No 51
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=38.83 E-value=62 Score=24.50 Aligned_cols=47 Identities=17% Similarity=0.366 Sum_probs=35.7
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhhhh-----HHHHHHHhhhCCcEEEEe
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESLPH-----CEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~-----~~~~I~~Le~e~~Ilvv~ 194 (290)
++.+|++|+.. ..+..-..++|+..+.|+ +.+++.+|.+||.+.+-.
T Consensus 3 K~~Ile~L~~k-~~~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~yWS 54 (67)
T PF08679_consen 3 KQKILEFLEAK-KKKKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKLEYWS 54 (67)
T ss_dssp HHHHHHHHSSC-CCHSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHhc-cCCCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeEEEEc
Confidence 57889999844 244567889999999998 668999999999887654
No 52
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=38.62 E-value=1.1e+02 Score=20.40 Aligned_cols=46 Identities=13% Similarity=0.113 Sum_probs=29.4
Q ss_pred HHHHHHHHhcccCCCCcc-chhhhHhhh----hhHHHHHHHhhhCCcEEEE
Q psy14236 148 KGLLKLLKQHDLKGIGGI-LLDDVRESL----PHCEKALKHLSLQNEIIYV 193 (290)
Q Consensus 148 ~~LL~lL~~~~q~~~~GI-~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv 193 (290)
+.|...+........+.+ +..+|.+.+ +.+..+|+.|+++|-|...
T Consensus 3 ~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 3 ERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 345555555322222346 677777766 5788999999998876544
No 53
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=38.43 E-value=1e+02 Score=23.47 Aligned_cols=51 Identities=18% Similarity=0.246 Sum_probs=35.9
Q ss_pred HHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCC-CCceEEE
Q psy14236 149 GLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPA-DKRKVMF 204 (290)
Q Consensus 149 ~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~-~~~rivf 204 (290)
.+|.+|... +++...+|++.. .++-..++.|+++|-|-+-.... ..|+++|
T Consensus 4 ~Il~~L~~~-----~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~ 59 (80)
T PF13601_consen 4 AILALLYAN-----EEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWY 59 (80)
T ss_dssp HHHHHHHHH-----SEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEE
T ss_pred HHHHHHhhc-----CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEE
Confidence 467777774 688888888854 56889999999999887655444 3466555
No 54
>PF09066 B2-adapt-app_C: Beta2-adaptin appendage, C-terminal sub-domain; InterPro: IPR015151 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents a subdomain of the appendage (ear) domain of beta-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1E42_B 2G30_A 2IV9_B 2IV8_A 3HS9_A 3H1Z_A.
Probab=38.36 E-value=25 Score=28.03 Aligned_cols=33 Identities=33% Similarity=0.565 Sum_probs=23.1
Q ss_pred HHHHHHhhhcccC------------CCChhhHHHHHHHcCCCCcc
Q psy14236 216 EDFQKLWRSISVD------------GMDNDKIKEYLEKQGIRPIQ 248 (290)
Q Consensus 216 ~EFk~lW~~v~VP------------~~de~di~~~L~~~Glkp~~ 248 (290)
++|..+|.+++.- ..+.+.|++.|+..||-.+.
T Consensus 10 ~~F~~~W~sl~~~~~~e~~~~~~~~~~~~~~i~~~L~~~nI~~iA 54 (114)
T PF09066_consen 10 EEFQEMWKSLPDSNQQELSIQLNASVPSPDAIEEKLQANNIFTIA 54 (114)
T ss_dssp HHHHHHHHHS-GGG--EEEEEETT----HHHHHHHHHCTT-EEEE
T ss_pred HHHHHHHHhCCcccceEEEEeccccCCcHHHHHHHHHHCCEEEEe
Confidence 6899999986322 24667899999999998774
No 55
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=37.97 E-value=44 Score=26.38 Aligned_cols=39 Identities=18% Similarity=0.158 Sum_probs=30.6
Q ss_pred CcchhHHHHHHHHHHHhhhc-CCCCCCCcCHHHHHHhhcc
Q psy14236 68 SSQYKFGVLAKIVKHMKQRH-QDGDDHPLTIDEILDETNQ 106 (290)
Q Consensus 68 ~~~~~~t~l~~iV~~LK~r~-~~g~~~pltl~eIl~~l~~ 106 (290)
.|.|+--.|..|+++|.... ....+..+|.++|.+.|+.
T Consensus 16 vGi~KHF~M~~I~~~l~~~~~~~~~~~~~t~~~IW~kL~~ 55 (91)
T PF07904_consen 16 VGIHKHFHMICIVERLNNPGFDPKLNKHFTIDDIWKKLRT 55 (91)
T ss_pred CccchHHHHHHHHHHHhccccCCccCCcCCHHHHHHHHHH
Confidence 47777788999999999871 1112578999999999985
No 56
>cd08029 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen. This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=37.83 E-value=38 Score=25.97 Aligned_cols=41 Identities=20% Similarity=0.108 Sum_probs=29.7
Q ss_pred CCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCe
Q psy14236 92 DHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNK 135 (290)
Q Consensus 92 ~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~ 135 (290)
+++++++-|+..--+-.+... ..+. +||+.-+.|++++||+
T Consensus 32 ~G~Vpl~~i~~F~rmk~l~~~--~~i~-~Al~~S~~lev~~d~~ 72 (76)
T cd08029 32 NGWVPIKTIASFKRMRRFQPL--EAVV-EALRESELLEVSEDGE 72 (76)
T ss_pred CCcEehHHHhCchHHHHcCCH--HHHH-HHHHhCCeEEEeCCCC
Confidence 568999999755444444443 3444 8999999999998775
No 57
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=37.62 E-value=76 Score=30.75 Aligned_cols=46 Identities=22% Similarity=0.331 Sum_probs=35.9
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhhhh-----HHHHHHHhhhCCcEEEEe
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESLPH-----CEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~-----~~~~I~~Le~e~~Ilvv~ 194 (290)
++.||++++.+ .+..|++.+||.+..|+ ...+|++|-.++.|-+++
T Consensus 11 ~~~l~~~~~~~--~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~ 61 (327)
T PF05158_consen 11 EKKLLELCREN--PSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK 61 (327)
T ss_dssp HHHHHHHHHH-----SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE
T ss_pred HHHHHHHHHHh--cCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE
Confidence 57899999997 34589999999999775 568899999999999887
No 58
>PF11181 YflT: Heat induced stress protein YflT
Probab=37.35 E-value=34 Score=27.16 Aligned_cols=69 Identities=20% Similarity=0.408 Sum_probs=39.2
Q ss_pred hHHHHHHHhhhC----CcEEEEecCCCCceEEEec-CCCCCCCCCHHHHHHhhhcc--cCCCChhhHHHHHHHcCCCCcc
Q psy14236 176 HCEKALKHLSLQ----NEIIYVTRPADKRKVMFYN-DKSAQLDLDEDFQKLWRSIS--VDGMDNDKIKEYLEKQGIRPIQ 248 (290)
Q Consensus 176 ~~~~~I~~Le~e----~~Ilvv~~~~~~~rivf~N-D~~~~~~VD~EFk~lW~~v~--VP~~de~di~~~L~~~Glkp~~ 248 (290)
.+..+|++|.++ ..|+||...++.-..|-.+ +-.. +...+ ..+|.++. ... .+.++...|.+.|+....
T Consensus 11 E~~~~I~~L~~~Gy~~ddI~Vva~d~~~~~~l~~~t~~~~-~~~~~--~~~~d~~~~~f~~-~~d~~~~~l~~lGl~~~e 86 (103)
T PF11181_consen 11 EALSAIEELKAQGYSEDDIYVVAKDKDRTERLADQTDTNT-VGASE--ESFWDKIKNFFTS-GGDELRSKLESLGLSEDE 86 (103)
T ss_pred HHHHHHHHHHHcCCCcccEEEEEcCchHHHHHHHhcCCce-ecccc--ccHHHHHHHhccC-CcHHHHHHHHHcCCCHHH
Confidence 467788888875 5899997544333222222 2211 12222 45555541 111 345799999999987653
No 59
>TIGR02533 type_II_gspE general secretory pathway protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.
Probab=36.58 E-value=1.2e+02 Score=30.89 Aligned_cols=38 Identities=34% Similarity=0.629 Sum_probs=30.0
Q ss_pred CCCCHHHHHHhhhcccCCCChhhHHHHHHHcCCCCcccCCCC
Q psy14236 212 LDLDEDFQKLWRSISVDGMDNDKIKEYLEKQGIRPIQDHGFK 253 (290)
Q Consensus 212 ~~VD~EFk~lW~~v~VP~~de~di~~~L~~~Glkp~~~~~~k 253 (290)
+.+|++++.+.+.-. +..+|.+.+.++|+.++.+++..
T Consensus 433 l~~~~~i~~~I~~~~----~~~~l~~~~~~~G~~tl~~~~~~ 470 (486)
T TIGR02533 433 LIVDDDLRSLIHSRA----DEGEIKEIARAAGMRTLRDDGLR 470 (486)
T ss_pred EeCCHHHHHHHHcCC----CHHHHHHHHHHcCCcCHHHHHHH
Confidence 558999999998753 33579999999999999776543
No 60
>PHA00738 putative HTH transcription regulator
Probab=36.43 E-value=76 Score=26.21 Aligned_cols=58 Identities=16% Similarity=0.128 Sum_probs=40.5
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhh----hhhHHHHHHHhhhCCcEEEEecCCCCceEEEecCCCCC
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRES----LPHCEKALKHLSLQNEIIYVTRPADKRKVMFYNDKSAQ 211 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~----~p~~~~~I~~Le~e~~Ilvv~~~~~~~rivf~ND~~~~ 211 (290)
.-.+|.+|... ++++|.||.+. .|.+-..|+-|++.|-|- .++.++..++..|+....
T Consensus 14 Rr~IL~lL~~~-----e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~--srK~Gr~vyY~Ln~~~~~ 75 (108)
T PHA00738 14 RRKILELIAEN-----YILSASLISHTLLLSYTTVLRHLKILNEQGYIE--LYKEGRTLYAKIRENSKE 75 (108)
T ss_pred HHHHHHHHHHc-----CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceE--EEEECCEEEEEECCCccH
Confidence 45788888773 36889888886 688999999999866544 344355555555665443
No 61
>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function.
Probab=34.00 E-value=40 Score=26.04 Aligned_cols=43 Identities=28% Similarity=0.329 Sum_probs=31.2
Q ss_pred CCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeE
Q psy14236 92 DHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKY 136 (290)
Q Consensus 92 ~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f 136 (290)
++.++++-|+..=-+-.+..+.. .+. +||+..+-|++++||+.
T Consensus 34 ~g~Vpl~~i~~F~r~k~l~~d~~-~i~-~Al~~S~~lel~~d~~~ 76 (80)
T smart00715 34 DGYVPISTIASFKRVKSLTTDVN-LIV-EALRSSPKLEVSEDGLK 76 (80)
T ss_pred CCCEEhHHHhCchhHHHHcCCHH-HHH-HHHHhCCeEEEcCCCCe
Confidence 56899999975544445555553 444 89999999999988753
No 62
>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=33.85 E-value=1.3e+02 Score=21.14 Aligned_cols=43 Identities=26% Similarity=0.330 Sum_probs=33.5
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEe
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~ 194 (290)
.-.+|.+|... +++++.+|.+.. +.+-..|+.|++.|-|-+.+
T Consensus 12 R~~Il~~L~~~-----~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 12 RLRILRLLASN-----GPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHHHC-----STBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHhcC-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 34678888443 799999998865 67889999999988776654
No 63
>PHA02943 hypothetical protein; Provisional
Probab=33.71 E-value=1.4e+02 Score=26.29 Aligned_cols=62 Identities=13% Similarity=0.061 Sum_probs=45.1
Q ss_pred CCCcchhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeEEe
Q psy14236 66 SGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIF 138 (290)
Q Consensus 66 tg~~~~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f~y 138 (290)
.|-+..+...+..|++|| + +.+.|..||...||+ +-.+.+|.. -.|...-+|+=..-|...|
T Consensus 3 r~~sd~v~~R~~eILE~L-k------~G~~TtseIAkaLGl---S~~qa~~~L-yvLErEG~VkrV~~G~~ty 64 (165)
T PHA02943 3 RGMSDTVHTRMIKTLRLL-A------DGCKTTSRIANKLGV---SHSMARNAL-YQLAKEGMVLKVEIGRAAI 64 (165)
T ss_pred cchhHHHHHHHHHHHHHH-h------cCCccHHHHHHHHCC---CHHHHHHHH-HHHHHcCceEEEeecceEE
Confidence 366778899999999999 3 468999999999876 444445544 4677777777665565444
No 64
>cd08028 LARP_3 La RNA-binding domain of La-related protein 3. This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).
Probab=33.59 E-value=42 Score=26.17 Aligned_cols=51 Identities=18% Similarity=0.274 Sum_probs=33.9
Q ss_pred HHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCC--ceEEeeCCe
Q psy14236 82 HMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNP--KIEVIEGNK 135 (290)
Q Consensus 82 ~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~np--KI~~~p~~~ 135 (290)
||++.-... +++++++.|+..--+-.+..+.. .+. +||+..+ .|++++||+
T Consensus 26 fLr~~m~~~-~G~Vpl~~i~~F~rmk~l~~d~~-~i~-~Al~~S~~~~lev~~d~~ 78 (82)
T cd08028 26 FLKEQIKED-DGWVPMEVMLKFNRLKSLSSDPE-VIA-KALKKSKSGLIEVSEDKT 78 (82)
T ss_pred HHHHHHhcc-CCCEEhHHHhCChhHHHhcCCHH-HHH-HHHHhCCCCEEEEcCCCC
Confidence 455443222 57899999976555545555553 444 8999988 899988764
No 65
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=33.45 E-value=88 Score=28.71 Aligned_cols=58 Identities=12% Similarity=0.118 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee-CCeEEec
Q psy14236 73 FGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE-GNKYIFK 139 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p-~~~f~yK 139 (290)
...-..|+++|-.+ ..++++.||...+++ +.+.-+ .+| ..|..+-=|+.++ +++|+-=
T Consensus 10 l~ral~iL~~l~~~-----~~~ls~~eia~~lgl-~kstv~-RlL--~tL~~~g~v~~~~~~~~Y~Lg 68 (263)
T PRK09834 10 LSRGLMVLRALNRL-----DGGATVGLLAELTGL-HRTTVR-RLL--ETLQEEGYVRRSASDDSFRLT 68 (263)
T ss_pred HHHHHHHHHHHHhc-----CCCCCHHHHHHHHCc-CHHHHH-HHH--HHHHHCCCEEEecCCCcEEEc
Confidence 44566777777664 467999999999987 655554 466 5899999999987 4666553
No 66
>COG1803 MgsA Methylglyoxal synthase [Carbohydrate transport and metabolism]
Probab=32.60 E-value=47 Score=28.43 Aligned_cols=56 Identities=18% Similarity=0.261 Sum_probs=48.2
Q ss_pred CccchhhhHhhhhhHHHHHHHhhhCCcEEEEecCCCCceEEEecCCCCCCCCCHHHHHHhhhccc
Q psy14236 163 GGILLDDVRESLPHCEKALKHLSLQNEIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKLWRSISV 227 (290)
Q Consensus 163 ~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~~~~~~~rivf~ND~~~~~~VD~EFk~lW~~v~V 227 (290)
.|+.|.-++-|.-|-.+-|-+|.+||+|-++ +|+-||-.-.+=|++.+.|-|=..|
T Consensus 49 tgL~v~~~~SGPmGGDQQiGa~Iaeg~id~l---------IFf~DPLtaqPHdpDVkAL~Rl~~V 104 (142)
T COG1803 49 TGLNVHRLKSGPMGGDQQIGALIAEGKIDVL---------IFFWDPLTAQPHDPDVKALLRLATV 104 (142)
T ss_pred hCCceEEeecCCCCccHHHHHHHhcCcceEE---------EEEecCCCCCCCCcCHHHHHHHHHh
Confidence 5888999999999999999999999999876 7888887777889999998876433
No 67
>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=32.43 E-value=62 Score=23.61 Aligned_cols=46 Identities=20% Similarity=0.244 Sum_probs=30.9
Q ss_pred HHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEe
Q psy14236 76 LAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVI 131 (290)
Q Consensus 76 l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~ 131 (290)
|..|-+||+.+ ..+|+.||..++++ +...- ...| +.|...=+|+-.
T Consensus 2 L~~i~~~l~~~------~~~S~~eLa~~~~~-s~~~v-e~mL--~~l~~kG~I~~~ 47 (69)
T PF09012_consen 2 LQEIRDYLRER------GRVSLAELAREFGI-SPEAV-EAML--EQLIRKGYIRKV 47 (69)
T ss_dssp CHHHHHHHHHS-------SEEHHHHHHHTT---HHHH-HHHH--HHHHCCTSCEEE
T ss_pred HHHHHHHHHHc------CCcCHHHHHHHHCc-CHHHH-HHHH--HHHHHCCcEEEe
Confidence 56788999996 68999999999876 32221 1334 577777777654
No 68
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=32.25 E-value=78 Score=29.22 Aligned_cols=42 Identities=24% Similarity=0.429 Sum_probs=35.0
Q ss_pred HHHHHHHHhcccCCCCccchhhhHhhhh----hHHHHHHHhhhCCcEEEEe
Q psy14236 148 KGLLKLLKQHDLKGIGGILLDDVRESLP----HCEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 148 ~~LL~lL~~~~q~~~~GI~v~dLkD~~p----~~~~~I~~Le~e~~Ilvv~ 194 (290)
+.+|++|+++ |=|+|+||.+-+- .+-.||.+|+++|.+.-+.
T Consensus 8 ~~Il~~l~~~-----g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 8 QKILELLKEK-----GKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHHc-----CcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEe
Confidence 5789999996 7899999998765 4678899999999887654
No 69
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=31.99 E-value=87 Score=28.78 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=33.9
Q ss_pred HHHHHHHHhcccCCCCccchhhhHhh----hhhHHHHHHHhhhCCcEEEEe
Q psy14236 148 KGLLKLLKQHDLKGIGGILLDDVRES----LPHCEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 148 ~~LL~lL~~~~q~~~~GI~v~dLkD~----~p~~~~~I~~Le~e~~Ilvv~ 194 (290)
..+|++|+++ +-+.++||.+- -..+..+|++|+++|.|.-++
T Consensus 8 ~~Il~~l~~~-----~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 8 QILLELLAQL-----GFVTVEKVIERLGISPATARRDINKLDESGKLKKVR 53 (251)
T ss_pred HHHHHHHHHc-----CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence 5688999985 68999999984 456889999999988886543
No 70
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=31.63 E-value=1.2e+02 Score=27.53 Aligned_cols=55 Identities=11% Similarity=0.119 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeEE
Q psy14236 73 FGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYI 137 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f~ 137 (290)
...-..|++++-.. ..|+++.||...+++ ..+.-+ .+| ..|...-=|+.+ +++|.
T Consensus 8 l~ral~IL~~l~~~-----~~~~~l~eia~~lgl-pksT~~-RlL--~tL~~~G~l~~~-~~~Y~ 62 (248)
T TIGR02431 8 LARGLAVIEAFGAE-----RPRLTLTDVAEATGL-TRAAAR-RFL--LTLVELGYVTSD-GRLFW 62 (248)
T ss_pred HHHHHHHHHHHhcC-----CCCCCHHHHHHHHCc-CHHHHH-HHH--HHHHHCCCEEeC-CCEEE
Confidence 45566778888654 579999999999987 555444 466 478777777765 56544
No 71
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=30.67 E-value=71 Score=26.09 Aligned_cols=30 Identities=10% Similarity=0.339 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhcc
Q psy14236 73 FGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQ 106 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~ 106 (290)
...+..|++||.++. ..+++++||..++++
T Consensus 8 ~~~i~~~~~~I~~~~----~~~~sl~~lA~~~g~ 37 (127)
T PRK11511 8 AITIHSILDWIEDNL----ESPLSLEKVSERSGY 37 (127)
T ss_pred HHHHHHHHHHHHHhc----CCCCCHHHHHHHHCc
Confidence 466889999999984 578999999998876
No 72
>PRK04280 arginine repressor; Provisional
Probab=30.41 E-value=1.1e+02 Score=26.29 Aligned_cols=52 Identities=19% Similarity=0.328 Sum_probs=36.7
Q ss_pred CCCCCCHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEE-EecCCCCceEEEecCC
Q psy14236 141 VFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIY-VTRPADKRKVMFYNDK 208 (290)
Q Consensus 141 ~y~Ik~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilv-v~~~~~~~rivf~ND~ 208 (290)
.+.|.+.++|+++|++ .|+.+.. +.+-.||++|. ++ +++.+++-+...+++.
T Consensus 15 ~~~I~tQeeL~~~L~~------~Gi~vTQ-----ATiSRDikeL~-----lvKv~~~~G~~~Y~lp~~~ 67 (148)
T PRK04280 15 NNEIETQDELVDRLRE------EGFNVTQ-----ATVSRDIKELH-----LVKVPLPDGRYKYSLPADQ 67 (148)
T ss_pred hCCCCCHHHHHHHHHH------cCCCeeh-----HHHHHHHHHcC-----CEEeecCCCcEEEeecccc
Confidence 3579999999999999 3777643 56778999996 32 4445455556666654
No 73
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=30.35 E-value=1.3e+02 Score=27.76 Aligned_cols=57 Identities=9% Similarity=0.027 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee-CCeEEe
Q psy14236 73 FGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE-GNKYIF 138 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p-~~~f~y 138 (290)
......|++++-.. +.++++.||...|++ ..+.-+ .+| ..|...-=|..++ +++|.-
T Consensus 24 l~r~l~IL~~~~~~-----~~~~tl~eIa~~lgl-pkStv~-RlL--~tL~~~G~l~~~~~~~~Y~l 81 (271)
T PRK10163 24 LERGIAILQYLEKS-----GGSSSVSDISLNLDL-PLSTTF-RLL--KVLQAADFVYQDSQLGWWHI 81 (271)
T ss_pred HHHHHHHHHHHHhC-----CCCcCHHHHHHHHCc-CHHHHH-HHH--HHHHHCCCEEEcCCCCeEEe
Confidence 56677788888654 568999999999987 555554 466 4788888888875 466654
No 74
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=30.03 E-value=90 Score=28.79 Aligned_cols=42 Identities=24% Similarity=0.427 Sum_probs=33.2
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEE
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYV 193 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv 193 (290)
.+.+|++|+++ +-+.+.||.+.+ ..+-.+|.+|+++|.|.-+
T Consensus 7 ~~~Il~~l~~~-----~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQ-----GYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHc-----CCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 46789999885 569999999965 3466889999999987644
No 75
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
Probab=29.98 E-value=2.6e+02 Score=29.03 Aligned_cols=164 Identities=16% Similarity=0.255 Sum_probs=89.4
Q ss_pred cccCCCCcchhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhh----cc----CCCCchhHHHHhHHhhhcCCceEEee-
Q psy14236 62 YKSMSGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDET----NQ----LDVGNKVKIWLSTEALQNNPKIEVIE- 132 (290)
Q Consensus 62 ~~~~tg~~~~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l----~~----~di~~~~~~~L~~e~L~~npKI~~~p- 132 (290)
.-..||||. -|.|+.++.++-.. ..+-+|++|=..+. ++ .+.+.+....|+ .+|+.+|-|.+..
T Consensus 321 v~G~tGSGK--TTtl~a~l~~~~~~----~~~i~tiEdpvE~~~~~~~q~~v~~~~g~~~~~~l~-~~LR~dPDvI~vGE 393 (564)
T TIGR02538 321 VTGPTGSGK--TVSLYTALNILNTE----EVNISTAEDPVEINLPGINQVNVNPKIGLTFAAALR-SFLRQDPDIIMVGE 393 (564)
T ss_pred EECCCCCCH--HHHHHHHHHhhCCC----CceEEEecCCceecCCCceEEEeccccCCCHHHHHH-HHhccCCCEEEeCC
Confidence 445567776 77888899998432 12345555542211 11 133345556676 7999999998874
Q ss_pred --C-------------CeEEeccCCCCCCHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEEecCC
Q psy14236 133 --G-------------NKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYVTRPA 197 (290)
Q Consensus 133 --~-------------~~f~yKP~y~Ik~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~~~~ 197 (290)
| |...|--.|.-.-...+.++ .. -|+.-..|.++.-+ .- .+-+ |++-+
T Consensus 394 iRd~eta~~a~~aa~tGHlv~tTlHa~~a~~~i~Rl-~~------lg~~~~~la~~l~~-------vi--~QrL-vr~lC 456 (564)
T TIGR02538 394 IRDLETAEIAIKAAQTGHLVLSTLHTNDAPETLARL-VN------MGIAPFNIASSVNL-------IM--AQRL-ARRLC 456 (564)
T ss_pred CCCHHHHHHHHHHHHcCCcEEEEeccCCHHHHHHHH-HH------cCCCHHHHHHHHHH-------hh--eeee-hhhcc
Confidence 1 44445444432222333333 22 14444444433222 12 1111 11110
Q ss_pred ----------------------CCceEEEecCCCCC----------------CCCCHHHHHHhhhcccCCCChhhHHHHH
Q psy14236 198 ----------------------DKRKVMFYNDKSAQ----------------LDLDEDFQKLWRSISVDGMDNDKIKEYL 239 (290)
Q Consensus 198 ----------------------~~~rivf~ND~~~~----------------~~VD~EFk~lW~~v~VP~~de~di~~~L 239 (290)
+...+.||+-..|. +.+|+++++++.+-. +..+|.+.+
T Consensus 457 ~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gC~~C~~~Gy~GR~~i~E~l~~~~~~~~~i~~~~----~~~~i~~~~ 532 (564)
T TIGR02538 457 SHCKAPEEVPAEALLELGFTQEDLADLKLYGPVGCDECSNTGYKGRVGIYEVMPMSEEIAELILKGG----NALQIAELA 532 (564)
T ss_pred cccCCCCCCCHHHHHHcCCCcccccceeeecCCCCcccCCCCCCCceEEEEEEeCCHHHHHHHHcCC----CHHHHHHHH
Confidence 11235566544332 558999999998742 335799999
Q ss_pred HHcCCCCcccCCCC
Q psy14236 240 EKQGIRPIQDHGFK 253 (290)
Q Consensus 240 ~~~Glkp~~~~~~k 253 (290)
.+.|+.++.+++..
T Consensus 533 ~~~g~~tl~~~~~~ 546 (564)
T TIGR02538 533 QKEGMRTLRRSGLL 546 (564)
T ss_pred HHcCCccHHHHHHH
Confidence 99999999877643
No 76
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=29.33 E-value=1.2e+02 Score=29.19 Aligned_cols=56 Identities=30% Similarity=0.370 Sum_probs=42.4
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHh----hhhhHHHHHHHhhhCCcEEEEecCC-CCceEEEec
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRE----SLPHCEKALKHLSLQNEIIYVTRPA-DKRKVMFYN 206 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD----~~p~~~~~I~~Le~e~~Ilvv~~~~-~~~rivf~N 206 (290)
.++-|++.|++ .+..||.-.+|-+ +=..+-+++.+||++| +|.|++- ++.+-||.-
T Consensus 5 ~reklir~Lk~---a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~g--iv~RrkvsGKs~rVwLa 65 (321)
T COG3888 5 LREKLIRELKR---AGPEGIDQTEIEELMGLSKSTVSEALSELEKQG--IVKRRKVSGKSKRVWLA 65 (321)
T ss_pred HHHHHHHHHHh---cCCCCccHHHHHHHhCcchhHHHHHHHHHHhcC--eeeeeeecCcceEEeec
Confidence 46778999999 4668898888766 3345889999999766 4456665 888999975
No 77
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=28.65 E-value=1e+02 Score=28.65 Aligned_cols=43 Identities=19% Similarity=0.308 Sum_probs=33.9
Q ss_pred HHHHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEe
Q psy14236 147 RKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 147 k~~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~ 194 (290)
...++++|+++ +-+++.||.+-+ ..+..||..|+++|.+..+.
T Consensus 19 ~~~Il~~L~~~-----~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 19 REQIIQRLRQQ-----GSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHc-----CCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 35788899886 459999998854 45779999999999887554
No 78
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=28.55 E-value=1e+02 Score=28.32 Aligned_cols=58 Identities=14% Similarity=0.137 Sum_probs=44.0
Q ss_pred HHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee-CCeEEeccC
Q psy14236 75 VLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE-GNKYIFKPV 141 (290)
Q Consensus 75 ~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p-~~~f~yKP~ 141 (290)
.-..|+++|-.. ..++++.||...+++ ..+.-+ .+| ..|..+-=|.+++ +|+|.--|.
T Consensus 5 ral~iL~~l~~~-----~~~l~l~ela~~~gl-pksT~~-RlL--~tL~~~G~v~~d~~~g~Y~Lg~~ 63 (246)
T COG1414 5 RALAILDLLAEG-----PGGLSLAELAERLGL-PKSTVH-RLL--QTLVELGYVEQDPEDGRYRLGPR 63 (246)
T ss_pred HHHHHHHHHHhC-----CCCCCHHHHHHHhCc-CHHHHH-HHH--HHHHHCCCEEEcCCCCcEeehHH
Confidence 345678888774 566899999999987 555554 466 5899999999998 578887654
No 79
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=28.46 E-value=1.3e+02 Score=23.44 Aligned_cols=43 Identities=12% Similarity=0.142 Sum_probs=34.5
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEE
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYV 193 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv 193 (290)
++.+|++.|..+ .|++..|++..+-...+.|.+.-++|..+-+
T Consensus 4 tk~el~~~ia~~-----~~~s~~~v~~vl~~~~~~i~~~L~~g~~V~l 46 (99)
T PRK00285 4 TKADLAEALFEK-----VGLSKREAKELVELFFEEIRDALENGEQVKL 46 (99)
T ss_pred CHHHHHHHHHHH-----hCcCHHHHHHHHHHHHHHHHHHHHcCCeEEE
Confidence 689999999885 6899999999999999988775445554444
No 80
>PRK05066 arginine repressor; Provisional
Probab=27.80 E-value=1.5e+02 Score=25.79 Aligned_cols=51 Identities=8% Similarity=0.140 Sum_probs=35.8
Q ss_pred CCCCCHHHHHHHHHhcccCCCCccc-hhhhHhhhhhHHHHHHHhhhCCcEEE-EecCCCCceEEEecCC
Q psy14236 142 FKIKDRKGLLKLLKQHDLKGIGGIL-LDDVRESLPHCEKALKHLSLQNEIIY-VTRPADKRKVMFYNDK 208 (290)
Q Consensus 142 y~Ik~k~~LL~lL~~~~q~~~~GI~-v~dLkD~~p~~~~~I~~Le~e~~Ilv-v~~~~~~~rivf~ND~ 208 (290)
+.|.+.++|+++|+++ |+. |.. +.+-.||++|. ++ +++.++.-+...+++.
T Consensus 21 ~~I~tQeeL~~~L~~~------Gi~~vTQ-----ATiSRDikeL~-----lvKv~~~~G~~~Y~l~~~~ 73 (156)
T PRK05066 21 EKFGSQGEIVTALQEQ------GFDNINQ-----SKVSRMLTKFG-----AVRTRNAKMEMVYCLPAEL 73 (156)
T ss_pred CCCCCHHHHHHHHHHC------CCCeecH-----HHHHHHHHHcC-----CEEeeCCCCCEEEEeCCCC
Confidence 5799999999999994 776 533 45678899986 32 4455455566666654
No 81
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=27.76 E-value=1.1e+02 Score=27.25 Aligned_cols=18 Identities=33% Similarity=0.547 Sum_probs=15.9
Q ss_pred cCCCCCCHHHHHHHHHhc
Q psy14236 140 PVFKIKDRKGLLKLLKQH 157 (290)
Q Consensus 140 P~y~Ik~k~~LL~lL~~~ 157 (290)
|-|+.+|..++|..|..+
T Consensus 128 PMFg~tD~~~Vl~Ei~eC 145 (176)
T PLN02289 128 PMFGCTDSAQVLKELEEA 145 (176)
T ss_pred ccCCCCCHHHHHHHHHHH
Confidence 779999999999988875
No 82
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=27.67 E-value=1.6e+02 Score=26.14 Aligned_cols=56 Identities=11% Similarity=0.143 Sum_probs=40.9
Q ss_pred HHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCCC-CceEEEecCCC
Q psy14236 149 GLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPAD-KRKVMFYNDKS 209 (290)
Q Consensus 149 ~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~~-~~rivf~ND~~ 209 (290)
.+|..|..+ +|++.+||.+.+ +.+-..|+.||+.|-|...+.+.| ....|+.=+.+
T Consensus 49 ~iL~~L~~~-----~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG 109 (185)
T PRK13777 49 HILWIAYHL-----KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKG 109 (185)
T ss_pred HHHHHHHhC-----CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHH
Confidence 456666664 589999999863 568889999999998887666653 46666665554
No 83
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=27.16 E-value=2e+02 Score=22.66 Aligned_cols=59 Identities=17% Similarity=0.233 Sum_probs=39.8
Q ss_pred HHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCCCC-ceEEEecCCC
Q psy14236 150 LLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPADK-RKVMFYNDKS 209 (290)
Q Consensus 150 LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~~~-~rivf~ND~~ 209 (290)
+|.+|... ....+|+++.+|.+.. +.+-..|+.|++.|-|.-.+.+.|+ ...|+..+.+
T Consensus 30 vL~~l~~~-~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G 93 (109)
T TIGR01889 30 ILYYLGKL-ENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQ 93 (109)
T ss_pred HHHHHHhh-hccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHH
Confidence 46666621 1223789999998865 6788999999999988877666554 4444444433
No 84
>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=27.13 E-value=2.2e+02 Score=19.68 Aligned_cols=46 Identities=26% Similarity=0.206 Sum_probs=32.2
Q ss_pred CCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeEEecc
Q psy14236 91 DDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKP 140 (290)
Q Consensus 91 ~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f~yKP 140 (290)
...++|..||.+.+++ ..+.-. ..| ..|...--|...+.|.|...|
T Consensus 22 ~~~~~s~~ela~~~g~-s~~tv~-r~l--~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 22 VQLPLTRQEIADYLGL-TRETVS-RTL--KELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred ccCCcCHHHHHHHHCC-CHHHHH-HHH--HHHHHCCCEEecCCCeEEeCC
Confidence 3578999999999987 333222 345 578888888888557776543
No 85
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=27.02 E-value=1.5e+02 Score=24.41 Aligned_cols=81 Identities=12% Similarity=0.217 Sum_probs=47.6
Q ss_pred HHHHHHHHhcccCCCCccchhhhHhh----hhhHHHHHHHhhhCCcEEEEecCCCCceEEEecCCCCCCCCCHHHHHHhh
Q psy14236 148 KGLLKLLKQHDLKGIGGILLDDVRES----LPHCEKALKHLSLQNEIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKLWR 223 (290)
Q Consensus 148 ~~LL~lL~~~~q~~~~GI~v~dLkD~----~p~~~~~I~~Le~e~~Ilvv~~~~~~~rivf~ND~~~~~~VD~EFk~lW~ 223 (290)
-++|.+|... +++.|.||.+. -|.+-..|+.|++.|-|..-+. + ..++|.=++...--+..=|...|.
T Consensus 19 l~IL~~L~~~-----~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~--G-r~~~Y~l~~~~~~~~~~~~~~~w~ 90 (117)
T PRK10141 19 LGIVLLLRES-----GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQ--G-KWVHYRLSPHIPAWAAKIIEQAWL 90 (117)
T ss_pred HHHHHHHHHc-----CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEE--c-CEEEEEECchHHHHHHHHHHHHHH
Confidence 4677777653 56888887665 5678899999998776664332 3 344444444321112222556776
Q ss_pred hcccCCCChhhHHHHHHHc
Q psy14236 224 SISVDGMDNDKIKEYLEKQ 242 (290)
Q Consensus 224 ~v~VP~~de~di~~~L~~~ 242 (290)
.- .+++..+|++-
T Consensus 91 ~~------~~~l~~~l~~l 103 (117)
T PRK10141 91 CE------QEDVQAIVRNL 103 (117)
T ss_pred HH------HHHHHHHHHHH
Confidence 54 23466666543
No 86
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=26.57 E-value=89 Score=24.29 Aligned_cols=28 Identities=18% Similarity=0.503 Sum_probs=23.7
Q ss_pred HHHHHHHHHhhhcCCCCCCCcCHHHHHHhhcc
Q psy14236 75 VLAKIVKHMKQRHQDGDDHPLTIDEILDETNQ 106 (290)
Q Consensus 75 ~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~ 106 (290)
.+..++.||..+. ..|++++||...+++
T Consensus 6 ~~~~~~~~i~~~~----~~~~~~~~lA~~~~~ 33 (107)
T PRK10219 6 IIQTLIAWIDEHI----DQPLNIDVVAKKSGY 33 (107)
T ss_pred HHHHHHHHHHHhc----CCCCCHHHHHHHHCC
Confidence 5778899999875 678999999999876
No 87
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=26.54 E-value=1.9e+02 Score=24.47 Aligned_cols=58 Identities=17% Similarity=0.177 Sum_probs=41.1
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhh----hHHHHHHHhhhCCcEEEEecC--CCCceEEE-ecCC
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLP----HCEKALKHLSLQNEIIYVTRP--ADKRKVMF-YNDK 208 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p----~~~~~I~~Le~e~~Ilvv~~~--~~~~rivf-~ND~ 208 (290)
+.+-++.||..+ +++.++||.+... .|..+|+.|.+.|-|.-...+ .++++.+| +-|+
T Consensus 29 Dv~v~~~LL~~~-----~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ 93 (126)
T COG3355 29 DVEVYKALLEEN-----GPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDP 93 (126)
T ss_pred HHHHHHHHHhhc-----CCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCH
Confidence 345567777653 7899999988775 488999999988877654433 27788888 4443
No 88
>TIGR01686 FkbH FkbH-like domain. The C-terminal portion of this domain is unique to this family (by BLAST).
Probab=26.42 E-value=34 Score=32.38 Aligned_cols=81 Identities=17% Similarity=0.194 Sum_probs=46.2
Q ss_pred CCCccchhhhHhhhhhHHHHHHHhhhCCcEEEEecCCCC--ceEEEecCCCCCCCCCHHHHHHhhhcccCCCChhhHHHH
Q psy14236 161 GIGGILLDDVRESLPHCEKALKHLSLQNEIIYVTRPADK--RKVMFYNDKSAQLDLDEDFQKLWRSISVDGMDNDKIKEY 238 (290)
Q Consensus 161 ~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~~~~~~--~rivf~ND~~~~~~VD~EFk~lW~~v~VP~~de~di~~~ 238 (290)
|..||.+.+ .||++.+.|+.|.+.|-.+.|.++++. ..-+|-.-+. .+.+.+.|....-+. =| ..+-|.+-
T Consensus 23 g~~~i~~~~---~~~~~~e~L~~L~~~Gi~lai~S~n~~~~a~~~l~~~~~-~~~~~~~f~~~~~~~-~p--k~~~i~~~ 95 (320)
T TIGR01686 23 GIDNLNLSP---LHKTLQEKIKTLKKQGFLLALASKNDEDDAKKVFERRKD-FILQAEDFDARSINW-GP--KSESLRKI 95 (320)
T ss_pred CccccccCc---cHHHHHHHHHHHHhCCCEEEEEcCCCHHHHHHHHHhCcc-ccCcHHHeeEEEEec-Cc--hHHHHHHH
Confidence 334555544 499999999999999977777666432 1222322111 122333333321111 15 55678888
Q ss_pred HHHcCCCCcc
Q psy14236 239 LEKQGIRPIQ 248 (290)
Q Consensus 239 L~~~Glkp~~ 248 (290)
+++.|+.+-+
T Consensus 96 ~~~l~i~~~~ 105 (320)
T TIGR01686 96 AKKLNLGTDS 105 (320)
T ss_pred HHHhCCCcCc
Confidence 8888887664
No 89
>cd08033 LARP_6 La RNA-binding domain of La-related protein 6. This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=26.41 E-value=70 Score=24.64 Aligned_cols=42 Identities=19% Similarity=0.141 Sum_probs=29.4
Q ss_pred CCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCe
Q psy14236 92 DHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNK 135 (290)
Q Consensus 92 ~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~ 135 (290)
+++++++-|+..=-+-.+..+. .++. +||+.-+-|++++||+
T Consensus 32 dG~Vpl~~i~~F~rmk~l~~d~-~~I~-~Al~~S~~lev~~d~~ 73 (77)
T cd08033 32 EGYVPIKLIASFKKVKALTRDW-RVVA-AALRRSSKLVVSEDGK 73 (77)
T ss_pred CCcEehHHHhcchHHHHHcCCH-HHHH-HHHHhCCeEEEcCCCC
Confidence 5789998886544443444444 3444 8999999999997764
No 90
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=26.40 E-value=96 Score=22.24 Aligned_cols=57 Identities=23% Similarity=0.274 Sum_probs=39.3
Q ss_pred HHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeEEeccC
Q psy14236 75 VLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPV 141 (290)
Q Consensus 75 ~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f~yKP~ 141 (290)
.-+.|..+|-.+ .+.|..||...+++ +-+.-. ..| ..|...-=|+..+.+.+.|.|.
T Consensus 9 ~E~~vy~~Ll~~------~~~t~~eIa~~l~i-~~~~v~-~~L--~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 9 NEAKVYLALLKN------GPATAEEIAEELGI-SRSTVY-RAL--KSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHH------CHEEHHHHHHHHTS-SHHHHH-HHH--HHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHHc------CCCCHHHHHHHHCc-CHHHHH-HHH--HHHHHCCCEEEEcCceEEEEEe
Confidence 345666677653 69999999999977 433333 345 5788888888887666666653
No 91
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=26.30 E-value=48 Score=26.35 Aligned_cols=91 Identities=23% Similarity=0.348 Sum_probs=37.8
Q ss_pred hhhcCCceEEeeCCeEEeccCC-CCCCHHHHHHHHHhcccCCCCcc-chhhhHhhhhhHHHHHHHhhhCCcEEEEecCCC
Q psy14236 121 ALQNNPKIEVIEGNKYIFKPVF-KIKDRKGLLKLLKQHDLKGIGGI-LLDDVRESLPHCEKALKHLSLQNEIIYVTRPAD 198 (290)
Q Consensus 121 ~L~~npKI~~~p~~~f~yKP~y-~Ik~k~~LL~lL~~~~q~~~~GI-~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~~~~~ 198 (290)
.|...|.+-+. ||.|.+.-.- .==+.++|+..|+.+ || +++|+.-++ ||..|.|.|++....
T Consensus 3 l~~g~p~~Li~-dG~i~~~~l~~~~it~~dl~~~LR~~------gi~~l~dV~~a~---------lE~~G~lsv~~k~~~ 66 (99)
T PF04239_consen 3 LLEGKPTVLIR-DGKIDEDNLRRARITEEDLLSALREQ------GIESLSDVKAAV---------LEPNGQLSVIKKEDA 66 (99)
T ss_dssp ------EEEEE-TTEE-HHHHHHTT--HHHHHHHHHHT------T--SGGGEEEEE---------E-TTS-EEEEE-GGG
T ss_pred cccCCcEEEEE-CCEECHHHHhHcCCCHHHHHHHHHhh------CCCCHHHcCEEE---------ECCCCCEEEEEcCCC
Confidence 45667777777 8999988773 333788999999984 55 778877664 688899998876632
Q ss_pred CceEEEecCCCCCCCCCHHHHHHhhhcccCCCChhhHHHHHHHcCCC
Q psy14236 199 KRKVMFYNDKSAQLDLDEDFQKLWRSISVDGMDNDKIKEYLEKQGIR 245 (290)
Q Consensus 199 ~~rivf~ND~~~~~~VD~EFk~lW~~v~VP~~de~di~~~L~~~Glk 245 (290)
.+-..-.+ |+ . +- .|++-|.++|+++|.+
T Consensus 67 ~~~~~~l~-------I~--------~--~~-~~~~wl~~~L~~~~~~ 95 (99)
T PF04239_consen 67 QPVTPELN-------ID--------Q--IG-KDEEWLKEELKKQGYK 95 (99)
T ss_dssp S---TTTT---------------------------------------
T ss_pred CCCCccEE-------Ee--------e--ec-cccccccccccccccc
Confidence 21110011 22 2 22 4566789999999987
No 92
>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=26.04 E-value=2.8e+02 Score=20.69 Aligned_cols=55 Identities=18% Similarity=0.250 Sum_probs=33.9
Q ss_pred HHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee--CCeEEe
Q psy14236 77 AKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE--GNKYIF 138 (290)
Q Consensus 77 ~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p--~~~f~y 138 (290)
..++-||-.+ +...|+|.+||...+++ +......+. ..|+.+-=|+-.. +|-|.-
T Consensus 11 l~~l~~la~~---~~~~~~s~~eiA~~~~i---~~~~l~kil-~~L~~~Gli~s~~G~~GGy~L 67 (83)
T PF02082_consen 11 LRILLYLARH---PDGKPVSSKEIAERLGI---SPSYLRKIL-QKLKKAGLIESSRGRGGGYRL 67 (83)
T ss_dssp HHHHHHHHCT---TTSC-BEHHHHHHHHTS----HHHHHHHH-HHHHHTTSEEEETSTTSEEEE
T ss_pred HHHHHHHHhC---CCCCCCCHHHHHHHHCc---CHHHHHHHH-HHHhhCCeeEecCCCCCceee
Confidence 3445555443 34567999999998865 444443444 5788888887764 355654
No 93
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.84 E-value=1.8e+02 Score=21.84 Aligned_cols=43 Identities=9% Similarity=0.220 Sum_probs=33.1
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEE
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYV 193 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv 193 (290)
++++|.+.|..+ .|++..|++..+-...+.|.+--.+|..+.+
T Consensus 2 tk~eli~~ia~~-----~~~~~~~v~~vl~~l~~~i~~~L~~g~~V~i 44 (90)
T smart00411 2 TKSELIDAIAEK-----AGLSKKDAKAAVDAFLEIITEALKKGEKVEL 44 (90)
T ss_pred CHHHHHHHHHHH-----hCCCHHHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 678999999986 6899999999999988887764444544444
No 94
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=25.81 E-value=5.5e+02 Score=23.92 Aligned_cols=118 Identities=19% Similarity=0.217 Sum_probs=77.8
Q ss_pred chhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccC---C---CCchhHHHHhHHhhhcCCceEEee-C-Ce-EEecc
Q psy14236 70 QYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQL---D---VGNKVKIWLSTEALQNNPKIEVIE-G-NK-YIFKP 140 (290)
Q Consensus 70 ~~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~---d---i~~~~~~~L~~e~L~~npKI~~~p-~-~~-f~yKP 140 (290)
.........|.++|+. ..|+|-.||...+... . .+.....+| +.|...=.|.+-+ . |. ..|-+
T Consensus 81 ~~~~~~~~~v~~~L~~------~gplt~~eL~~~l~~~~~~~~~~~~~~~~~~l--~~l~~~G~l~~~~~~~g~~~~y~l 152 (327)
T PF06224_consen 81 EELERLAEAVLDALRA------DGPLTRAELREALAEAGWWGWGGPSSPWKHLL--EYLWYRGLLCVGPRPRGRWRTYDL 152 (327)
T ss_pred chHHHHHHHHHHHHHh------cCCCCHHHHHHHhhhccccCCCCCCchHHHHH--HHHHhCCeEEEeccCCCceEEEec
Confidence 3445557788899966 4799999999887653 1 122333566 5777777777776 4 53 55554
Q ss_pred CCCC------CCHHHHHHHHHhcccCCCCccchhhhHhh--hh--hHHHHHHHhhhCCcEEEEecC
Q psy14236 141 VFKI------KDRKGLLKLLKQHDLKGIGGILLDDVRES--LP--HCEKALKHLSLQNEIIYVTRP 196 (290)
Q Consensus 141 ~y~I------k~k~~LL~lL~~~~q~~~~GI~v~dLkD~--~p--~~~~~I~~Le~e~~Ilvv~~~ 196 (290)
.-.+ ...+.+-.+++++ ..+.|-.++.|+..= ++ .+...++.|.++++++-+.-.
T Consensus 153 ~~~~lP~~~~~~~ea~~~Lv~Ry-l~~~GPat~~d~a~w~gl~~~~~r~~l~~l~~~~~L~~v~~~ 217 (327)
T PF06224_consen 153 TERWLPAPDDDREEALAELVRRY-LRAYGPATLADFAWWSGLPKTQARRALAQLVEEGELVEVEVE 217 (327)
T ss_pred hHHhCCCCcCCHHHHHHHHHHHH-HHHcCCccHHHHHHHhccCHHHHHHHHHhhccCCcEEEEEEc
Confidence 4222 3455555555554 677888889987742 23 677889999888888877544
No 95
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=25.78 E-value=73 Score=24.86 Aligned_cols=42 Identities=17% Similarity=0.190 Sum_probs=29.2
Q ss_pred CCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCe
Q psy14236 92 DHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNK 135 (290)
Q Consensus 92 ~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~ 135 (290)
+++++++-|+..=-+-.+..+.. ++. +||+.-+.++++++|+
T Consensus 37 dG~Vpl~~i~~F~rmk~lt~d~~-~i~-~Al~~S~~lev~ed~~ 78 (82)
T cd08032 37 DGYIDISLLVSFNKMKKLTTDGK-LIA-RALKNSSVVELNLEGT 78 (82)
T ss_pred CCCEeHHHHhcchHHHHHcCCHH-HHH-HHHhcCCEEEEcCCCC
Confidence 67888888865433434444442 444 8999999999997764
No 96
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=25.74 E-value=1.8e+02 Score=21.62 Aligned_cols=44 Identities=9% Similarity=0.200 Sum_probs=34.2
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEEe
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~ 194 (290)
|+++|.+.|... .|++..|++.-.....+.|.+.-.+|..+.+.
T Consensus 1 ~K~~l~~~ia~~-----~~~~~~~v~~vl~~~~~~i~~~L~~g~~V~l~ 44 (87)
T cd00591 1 TKSELIEAIAEK-----TGLSKKDAEAAVDAFLDVITEALAKGEKVELP 44 (87)
T ss_pred CHHHHHHHHHHH-----hCcCHHHHHHHHHHHHHHHHHHHhCCCeEEEe
Confidence 688999999995 59999999999999888876655555554443
No 97
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=23.95 E-value=94 Score=24.83 Aligned_cols=41 Identities=20% Similarity=0.292 Sum_probs=31.5
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEE
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEII 191 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Il 191 (290)
..+.|..-+.. .|.|+.+|+.++=-.+...+.+|.++|+|.
T Consensus 68 ~a~~l~~e~~~-----~g~v~~~di~~Aq~~iv~~~r~l~~~G~I~ 108 (110)
T PF01706_consen 68 AAEMLREEMEA-----LGPVRLSDIEEAQREIVEIVRRLEEEGEIE 108 (110)
T ss_dssp HHHHHHHHHHH-----H-S--HHHHHHHHHHHHHHHHHHHHTTSS-
T ss_pred HHHHHHHHHHh-----cCCCCHHHHHHHHHHHHHHHHHHHHCcCEe
Confidence 34566666666 378999999999999999999999999986
No 98
>cd03409 Chelatase_Class_II Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III).
Probab=23.88 E-value=53 Score=24.99 Aligned_cols=46 Identities=15% Similarity=0.299 Sum_probs=31.0
Q ss_pred hhhhHHHHHHHhhhCC--cEEEEecCCCCceEEEecCCCCCCCCCHHHHHHhhhc
Q psy14236 173 SLPHCEKALKHLSLQN--EIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKLWRSI 225 (290)
Q Consensus 173 ~~p~~~~~I~~Le~e~--~Ilvv~~~~~~~rivf~ND~~~~~~VD~EFk~lW~~v 225 (290)
..|.++++|++|.++| .|+|+ |=.++ .-......|..++...|.++
T Consensus 43 ~~P~i~~~l~~l~~~g~~~vvvv------Pl~~~-~g~h~~~di~~~~~~~~~~~ 90 (101)
T cd03409 43 LGPDTEEAIRELAEEGYQRVVIV------PLAPV-SGDEVFYDIDSEIGLVRKQV 90 (101)
T ss_pred CCCCHHHHHHHHHHcCCCeEEEE------eCccc-cChhhHHHHHHHHHHHHHhc
Confidence 4789999999998764 67766 32333 22222336888999999873
No 99
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=23.65 E-value=3.2e+02 Score=27.81 Aligned_cols=90 Identities=23% Similarity=0.230 Sum_probs=63.8
Q ss_pred HhHHhhhcCCceEEee--CCeEEeccCCCCCCHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEEe
Q psy14236 117 LSTEALQNNPKIEVIE--GNKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYVT 194 (290)
Q Consensus 117 L~~e~L~~npKI~~~p--~~~f~yKP~y~Ik~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~ 194 (290)
|+.-||..|-++-+.- +..+.|+.-..+++-++++++|-... .|| -|+.-+.-.+.+++++-+-
T Consensus 300 l~~~alaenR~~~~~lF~s~~~~~el~~k~~~~~e~i~fL~~~f---~GG---TD~~~~l~~al~~~k~~~~-------- 365 (437)
T COG2425 300 LMRIALAENRDCYVILFDSEVIEYELYEKKIDIEELIEFLSYVF---GGG---TDITKALRSALEDLKSREL-------- 365 (437)
T ss_pred HHHHHHHhccceEEEEecccceeeeecCCccCHHHHHHHHhhhc---CCC---CChHHHHHHHHHHhhcccc--------
Confidence 3335888997766533 58999999999999999999999963 467 7888777777777765431
Q ss_pred cCCCCceEEEecCCCCCCCCCHHHHHHhhhc
Q psy14236 195 RPADKRKVMFYNDKSAQLDLDEDFQKLWRSI 225 (290)
Q Consensus 195 ~~~~~~rivf~ND~~~~~~VD~EFk~lW~~v 225 (290)
.+.++||.-|.-..+ +++|..-|...
T Consensus 366 ---~~adiv~ITDg~~~~--~~~~~~~v~e~ 391 (437)
T COG2425 366 ---FKADIVVITDGEDER--LDDFLRKVKEL 391 (437)
T ss_pred ---cCCCEEEEeccHhhh--hhHHHHHHHHH
Confidence 225556666665543 37787777654
No 100
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=23.63 E-value=2.2e+02 Score=25.82 Aligned_cols=59 Identities=10% Similarity=0.129 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEee-CCeEEeccC
Q psy14236 73 FGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIE-GNKYIFKPV 141 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p-~~~f~yKP~ 141 (290)
......|++++-. ..++++.||...|++ ..+.-+ .+| ..|...-=|+.++ +|.|.-=|.
T Consensus 13 l~r~l~IL~~l~~------~~~l~l~eia~~lgl-~kstv~-Rll--~tL~~~G~l~~~~~~~~Y~lG~~ 72 (257)
T PRK15090 13 VLKVFGILQALGE------EREIGITELSQRVMM-SKSTVY-RFL--QTMKTLGYVAQEGESEKYSLTLK 72 (257)
T ss_pred HHHHHHHHHHhhc------CCCCCHHHHHHHHCc-CHHHHH-HHH--HHHHHCCCEEEcCCCCcEEecHH
Confidence 4566677777754 248999999999987 555554 466 5788888898876 577776543
No 101
>cd07323 LAM LA motif RNA-binding domain. This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=23.36 E-value=92 Score=23.64 Aligned_cols=43 Identities=19% Similarity=0.208 Sum_probs=31.5
Q ss_pred CCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCeE
Q psy14236 92 DHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKY 136 (290)
Q Consensus 92 ~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~f 136 (290)
++.++++-|+.-=-+..+..+.. .+. +||+..+.|+++++|+.
T Consensus 30 ~g~Vpl~~i~~F~r~k~l~~~~~-~i~-~Al~~s~~lel~~~~~~ 72 (75)
T cd07323 30 DGWVPLSLLASFNRVKKLTTDVE-LIL-EALRDSSVVEVSEDGTK 72 (75)
T ss_pred CCCEEHHHHhCchHHHHHcCCHH-HHH-HHHHhCCeEEEeCCCCc
Confidence 57899999976555556666653 344 89999999999977543
No 102
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=23.35 E-value=89 Score=23.92 Aligned_cols=33 Identities=21% Similarity=0.393 Sum_probs=25.9
Q ss_pred CeEEeccC-CCCCCHHHHHHHHHhcccCCCCccchhh
Q psy14236 134 NKYIFKPV-FKIKDRKGLLKLLKQHDLKGIGGILLDD 169 (290)
Q Consensus 134 ~~f~yKP~-y~Ik~k~~LL~lL~~~~q~~~~GI~v~d 169 (290)
+.|-|-|. ..+||+.+|.+||..+. .+++.+++
T Consensus 27 DvyY~sP~Gkk~RS~~ev~~yL~~~~---~~~~~~~~ 60 (77)
T cd01396 27 DVYYISPTGKKFRSKVELARYLEKNG---PTSLDLSD 60 (77)
T ss_pred eEEEECCCCCEEECHHHHHHHHHhCC---CCCCcHhH
Confidence 47778787 58999999999999963 35666655
No 103
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=22.87 E-value=1.3e+02 Score=23.36 Aligned_cols=29 Identities=17% Similarity=0.063 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhcc
Q psy14236 71 YKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQ 106 (290)
Q Consensus 71 ~~~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~ 106 (290)
|+...+..|++||.+ + .+|+.||...+|+
T Consensus 3 ~~~~R~~~I~e~l~~-~------~~ti~dvA~~~gv 31 (80)
T TIGR02844 3 YIEERVLEIGKYIVE-T------KATVRETAKVFGV 31 (80)
T ss_pred cHHHHHHHHHHHHHH-C------CCCHHHHHHHhCC
Confidence 567789999999988 4 6899999999876
No 104
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 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. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=22.77 E-value=76 Score=23.25 Aligned_cols=28 Identities=18% Similarity=0.347 Sum_probs=20.6
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhcc
Q psy14236 74 GVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQ 106 (290)
Q Consensus 74 t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~ 106 (290)
|.+-.|.+-|++. +.|+++.||.++..-
T Consensus 2 t~~eaa~~vL~~~-----~~pm~~~eI~~~i~~ 29 (72)
T PF05066_consen 2 TFKEAAYEVLEEA-----GRPMTFKEIWEEIQE 29 (72)
T ss_dssp -HHHHHHHHHHHH------S-EEHHHHHHHHHH
T ss_pred CHHHHHHHHHHhc-----CCCcCHHHHHHHHHH
Confidence 4566788889987 689999999988764
No 105
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=22.60 E-value=2e+02 Score=22.34 Aligned_cols=43 Identities=9% Similarity=0.114 Sum_probs=33.3
Q ss_pred CHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEE
Q psy14236 146 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYV 193 (290)
Q Consensus 146 ~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv 193 (290)
++.+|.+.|..+ .|++..|++..+-.+.+.|.+.-.+|+-+.+
T Consensus 3 tk~eli~~ia~~-----~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~l 45 (96)
T TIGR00987 3 TKAEMSEYLFDE-----LGLSKREAKELVELFFEEIRRALENGEQVKL 45 (96)
T ss_pred CHHHHHHHHHHH-----hCcCHHHHHHHHHHHHHHHHHHHHcCCeEEe
Confidence 678999999885 6899999999999999888774344444433
No 106
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=22.14 E-value=1.5e+02 Score=21.68 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=14.4
Q ss_pred HHHhHHhhhcCCceEEeeCCeEE
Q psy14236 115 IWLSTEALQNNPKIEVIEGNKYI 137 (290)
Q Consensus 115 ~~L~~e~L~~npKI~~~p~~~f~ 137 (290)
.+| +.+....++++. +|.|.
T Consensus 40 ~fL--~~lv~e~~L~~~-~G~Yk 59 (60)
T PF08672_consen 40 EFL--DRLVEEGKLECS-GGSYK 59 (60)
T ss_dssp HHH--HHHHHTTSEE---TTEEE
T ss_pred HHH--HHHHHCCcEEec-CCEEe
Confidence 455 578899999999 89885
No 107
>PRK13239 alkylmercury lyase; Provisional
Probab=21.48 E-value=2.9e+02 Score=25.22 Aligned_cols=49 Identities=12% Similarity=0.215 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCe
Q psy14236 74 GVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNK 135 (290)
Q Consensus 74 t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~ 135 (290)
..+..|+..|-. +.|+|..+|...++. +.. +.. .+|..-+-|+||++|.
T Consensus 22 ~~~~~llr~la~------G~pvt~~~lA~~~~~---~~~--~v~--~~L~~l~~~~~d~~g~ 70 (206)
T PRK13239 22 TLLVPLLRLLAK------GRPVSVTTLAAALGW---PVE--EVE--AVLEAMPDTEYDEDGR 70 (206)
T ss_pred HHHHHHHHHHHc------CCCCCHHHHHHHhCC---CHH--HHH--HHHHhCCCeEECCCCC
Confidence 456666666653 689999999988765 322 222 5788888999999764
No 108
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=21.39 E-value=2.2e+02 Score=23.21 Aligned_cols=57 Identities=18% Similarity=0.166 Sum_probs=38.7
Q ss_pred HHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCCC-CceEEEecCCCC
Q psy14236 150 LLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPAD-KRKVMFYNDKSA 210 (290)
Q Consensus 150 LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~~-~~rivf~ND~~~ 210 (290)
+|..|...+ +|++..||.+.. +.+-..|+.|++.|-|...+.+.| ....|+.-+.+.
T Consensus 36 vL~~l~~~~----~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~ 97 (144)
T PRK03573 36 TLHNIHQLP----PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAE 97 (144)
T ss_pred HHHHHHHcC----CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHH
Confidence 455554421 467777777654 678899999999998887766654 456666666654
No 109
>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3TL4_X.
Probab=21.37 E-value=1.2e+02 Score=26.45 Aligned_cols=36 Identities=17% Similarity=0.121 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHhhhcCCCCCCCcCHHHHHHhhccCCCCchh
Q psy14236 73 FGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKV 113 (290)
Q Consensus 73 ~t~l~~iV~~LK~r~~~g~~~pltl~eIl~~l~~~di~~~~ 113 (290)
.-||..+++|++.+. ..|+..++...++|+ .|.-+.
T Consensus 84 ~~Ql~AA~~Yl~~~~----~~~~d~~~Fe~~cGV-GV~VT~ 119 (164)
T PF04558_consen 84 NLQLDAALKYLKSNP----SEPIDVAEFEKACGV-GVVVTP 119 (164)
T ss_dssp HHHHHHHHHHHHHHG----G-G--HHHHHHTTTT-T----H
T ss_pred HHHHHHHHHHHHHCC----CCCCCHHHHHHHcCC-CeEECH
Confidence 468999999999984 358999999999998 444443
No 110
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=20.84 E-value=3.1e+02 Score=24.11 Aligned_cols=58 Identities=16% Similarity=0.210 Sum_probs=40.6
Q ss_pred CCCCCHH-HHHHHHHhcccCCCCccchhhhHhhh----hhHHHHHHHhhhCCcEEEEecCCCCceEEEecC
Q psy14236 142 FKIKDRK-GLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKHLSLQNEIIYVTRPADKRKVMFYND 207 (290)
Q Consensus 142 y~Ik~k~-~LL~lL~~~~q~~~~GI~v~dLkD~~----p~~~~~I~~Le~e~~Ilvv~~~~~~~rivf~ND 207 (290)
+++...+ .+|.+|.++ +++++.||.+.. +.+-..|+.|++.|-|.... +..+.++..+
T Consensus 139 ~~ls~~~~~IL~~l~~~-----g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~---~r~~~~~lT~ 201 (203)
T TIGR01884 139 AGLSREELKVLEVLKAE-----GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG---RKGKRYSLTK 201 (203)
T ss_pred cCCCHHHHHHHHHHHHc-----CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc---CCccEEEeCC
Confidence 4554443 788888875 678999988755 66889999999988777553 2445555443
No 111
>PLN02950 4-alpha-glucanotransferase
Probab=20.54 E-value=2.1e+02 Score=31.69 Aligned_cols=75 Identities=23% Similarity=0.280 Sum_probs=43.0
Q ss_pred CCeEEeccCCCCCCHHHHHHHHHhcccCCCCccchhhhHhhhhhHHHHHHHhhhCCcEEEEecCCC----CceEEEecCC
Q psy14236 133 GNKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKHLSLQNEIIYVTRPAD----KRKVMFYNDK 208 (290)
Q Consensus 133 ~~~f~yKP~y~Ik~k~~LL~lL~~~~q~~~~GI~v~dLkD~~p~~~~~I~~Le~e~~Ilvv~~~~~----~~rivf~ND~ 208 (290)
+|.|.|||.|+ +...+++.+.+. +..+. ..+..+ .+.+-|-.|. +.|++|+.+++ .|++.+.++-
T Consensus 630 ~~~y~~k~~~~--te~~i~~~~~~~---~~~~~-~~~~~~---~~~~~l~~l~--~~v~~~~d~~~~~~f~pr~~~~~~~ 698 (909)
T PLN02950 630 KGCYEFKEDCN--TEKKIAAKLKRL---AEKSW-LLEEEE---KIRRGLFDLL--QNVVLIRDPEDPRKFYPRFNLEDTS 698 (909)
T ss_pred CCcEEeccccc--hHHHHHHhhccc---cccch-hhhhHH---HHHHHHHHHh--hceeEEecCCCCCCcccceeccccc
Confidence 68999999995 667777776553 11111 122222 3444555666 68888886653 3666665555
Q ss_pred CCCCCCCHHHH
Q psy14236 209 SAQLDLDEDFQ 219 (290)
Q Consensus 209 ~~~~~VD~EFk 219 (290)
++. ..++.-+
T Consensus 699 s~~-~L~~~~~ 708 (909)
T PLN02950 699 SFQ-DLDDHSK 708 (909)
T ss_pred chh-hcCHHHH
Confidence 553 3444443
No 112
>cd08036 LARP_5 La RNA-binding domain of La-related protein 5. This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=20.16 E-value=1.2e+02 Score=23.49 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=30.2
Q ss_pred CCCcCHHHHHHhhccCCCCchhHHHHhHHhhhcCCceEEeeCCe
Q psy14236 92 DHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNK 135 (290)
Q Consensus 92 ~~pltl~eIl~~l~~~di~~~~~~~L~~e~L~~npKI~~~p~~~ 135 (290)
+..+++.-|+.---+-.+..+. .++. +||++-+-|+++++|+
T Consensus 30 ~g~Vpi~~ia~F~rik~Lt~D~-~lI~-~aL~~S~~vevse~g~ 71 (75)
T cd08036 30 DQYVPIMTVANLDHIKKLSTDV-DLIV-DVLRSLPLVQVDEKGE 71 (75)
T ss_pred CCCEehHHHhccHHHHHhcCCH-HHHH-HHHhhCCeEEECCCCC
Confidence 4678888886554444556555 3444 8999999999997764
Done!