Query 016170
Match_columns 394
No_of_seqs 213 out of 467
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 04:26:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016170.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016170hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2577 Transcription factor E 100.0 7.8E-66 1.7E-70 508.5 26.8 272 63-355 61-334 (354)
2 PF02319 E2F_TDP: E2F/DP famil 99.9 5.6E-23 1.2E-27 162.6 5.6 66 70-135 1-71 (71)
3 KOG2578 Transcription factor E 99.8 1.6E-19 3.4E-24 177.2 5.6 87 63-154 14-100 (388)
4 KOG2578 Transcription factor E 99.1 1.3E-10 2.7E-15 115.1 7.9 76 64-139 150-241 (388)
5 KOG2829 E2F-like protein [Tran 98.9 1.4E-08 3.1E-13 100.0 13.0 127 83-225 51-208 (326)
6 PF01978 TrmB: Sugar-specific 94.5 0.035 7.6E-07 42.7 3.0 45 90-134 19-63 (68)
7 PF08279 HTH_11: HTH domain; 93.6 0.1 2.2E-06 38.3 3.9 41 80-121 3-43 (55)
8 smart00420 HTH_DEOR helix_turn 92.3 0.17 3.8E-06 35.5 3.3 45 81-127 4-48 (53)
9 cd00092 HTH_CRP helix_turn_hel 92.1 0.27 5.8E-06 36.7 4.3 54 78-131 5-63 (67)
10 COG1378 Predicted transcriptio 91.0 0.6 1.3E-05 45.4 6.5 52 82-136 22-73 (247)
11 smart00550 Zalpha Z-DNA-bindin 90.7 0.33 7E-06 38.2 3.7 55 80-134 9-63 (68)
12 PF09339 HTH_IclR: IclR helix- 90.3 0.18 4E-06 37.1 1.9 44 82-126 8-51 (52)
13 smart00346 HTH_ICLR helix_turn 89.9 0.49 1.1E-05 37.4 4.1 46 81-127 9-54 (91)
14 PF12802 MarR_2: MarR family; 87.6 0.65 1.4E-05 34.3 3.2 46 81-126 9-54 (62)
15 PF13412 HTH_24: Winged helix- 87.4 0.7 1.5E-05 33.2 3.2 43 80-124 6-48 (48)
16 smart00418 HTH_ARSR helix_turn 86.3 0.73 1.6E-05 32.8 2.8 38 91-128 8-45 (66)
17 PF13730 HTH_36: Helix-turn-he 84.9 1.1 2.3E-05 32.9 3.1 29 95-123 27-55 (55)
18 COG3355 Predicted transcriptio 83.3 6.4 0.00014 35.4 7.8 87 82-181 33-120 (126)
19 PF02082 Rrf2: Transcriptional 83.2 1.5 3.2E-05 35.2 3.5 49 78-126 9-58 (83)
20 TIGR02944 suf_reg_Xantho FeS a 82.8 1.2 2.6E-05 38.2 3.0 46 81-126 13-58 (130)
21 PF01047 MarR: MarR family; I 81.5 1.3 2.8E-05 32.6 2.4 42 83-126 9-50 (59)
22 cd00090 HTH_ARSR Arsenical Res 81.2 2.1 4.6E-05 31.1 3.5 47 80-129 10-56 (78)
23 PF13463 HTH_27: Winged helix 81.0 1.8 4E-05 32.4 3.1 38 89-126 14-51 (68)
24 PF09079 Cdc6_C: CDC6, C termi 80.5 0.61 1.3E-05 37.4 0.4 30 97-126 26-58 (85)
25 smart00345 HTH_GNTR helix_turn 79.2 2.4 5.3E-05 30.4 3.2 41 89-129 15-56 (60)
26 PF14394 DUF4423: Domain of un 79.1 21 0.00046 33.0 10.0 45 88-132 34-80 (171)
27 cd08768 Cdc6_C Winged-helix do 78.6 1 2.2E-05 35.7 1.1 22 105-126 44-65 (87)
28 PF08220 HTH_DeoR: DeoR-like h 77.6 2.7 5.9E-05 31.9 3.1 45 80-126 3-47 (57)
29 smart00419 HTH_CRP helix_turn_ 77.0 2.1 4.5E-05 29.8 2.2 38 93-131 8-45 (48)
30 cd00890 Prefoldin Prefoldin is 76.5 11 0.00023 31.9 6.8 55 127-181 68-122 (129)
31 PF00392 GntR: Bacterial regul 75.3 3 6.5E-05 31.7 2.8 50 80-129 7-60 (64)
32 PRK10163 DNA-binding transcrip 75.1 8 0.00017 37.4 6.4 53 82-135 30-82 (271)
33 PF08784 RPA_C: Replication pr 74.4 3.7 8E-05 34.0 3.4 50 74-123 44-95 (102)
34 TIGR00122 birA_repr_reg BirA b 72.7 3.7 8.1E-05 31.6 2.8 40 81-123 4-43 (69)
35 PF09012 FeoC: FeoC like trans 72.4 3.8 8.3E-05 31.9 2.9 46 83-130 6-51 (69)
36 PF01022 HTH_5: Bacterial regu 72.4 3.2 6.9E-05 30.0 2.3 42 81-125 6-47 (47)
37 PF04182 B-block_TFIIIC: B-blo 70.8 4.8 0.0001 32.1 3.1 49 80-128 5-53 (75)
38 PRK09834 DNA-binding transcrip 68.6 6 0.00013 38.0 3.9 49 83-132 17-66 (263)
39 cd04766 HTH_HspR Helix-Turn-He 68.0 13 0.00027 30.4 5.1 27 94-124 2-28 (91)
40 PHA02943 hypothetical protein; 67.3 24 0.00051 33.2 7.2 48 80-130 14-61 (165)
41 cd00584 Prefoldin_alpha Prefol 67.1 20 0.00043 30.8 6.4 54 128-181 69-122 (129)
42 TIGR01610 phage_O_Nterm phage 66.5 7.8 0.00017 32.2 3.6 46 90-137 44-89 (95)
43 TIGR00738 rrf2_super rrf2 fami 66.4 8.3 0.00018 32.8 3.9 37 90-126 22-58 (132)
44 PF12840 HTH_20: Helix-turn-he 64.8 3.8 8.2E-05 31.0 1.4 45 81-127 14-58 (61)
45 cd04775 HTH_Cfa-like Helix-Tur 64.5 21 0.00047 29.8 6.0 36 94-133 2-38 (102)
46 COG1414 IclR Transcriptional r 63.7 8.3 0.00018 37.1 3.8 50 81-131 8-58 (246)
47 cd04789 HTH_Cfa Helix-Turn-Hel 63.5 21 0.00044 30.0 5.7 37 94-134 2-39 (102)
48 PF01325 Fe_dep_repress: Iron 63.4 12 0.00025 29.0 3.8 42 85-127 15-56 (60)
49 TIGR02147 Fsuc_second hypothet 63.3 64 0.0014 32.1 9.9 40 90-129 134-175 (271)
50 smart00344 HTH_ASNC helix_turn 63.1 7.5 0.00016 31.9 3.0 47 78-126 4-50 (108)
51 TIGR02337 HpaR homoprotocatech 62.9 4.9 0.00011 33.7 1.9 37 91-127 40-76 (118)
52 PRK11414 colanic acid/biofilm 62.7 15 0.00032 34.0 5.1 56 74-129 11-70 (221)
53 cd07377 WHTH_GntR Winged helix 62.2 12 0.00026 27.3 3.6 34 94-127 26-59 (66)
54 TIGR02702 SufR_cyano iron-sulf 61.7 49 0.0011 30.7 8.4 45 80-126 4-48 (203)
55 smart00347 HTH_MARR helix_turn 61.5 12 0.00027 29.1 3.8 44 81-126 14-57 (101)
56 PRK09413 IS2 repressor TnpA; R 61.3 60 0.0013 27.9 8.3 31 92-122 28-58 (121)
57 PRK03947 prefoldin subunit alp 61.3 30 0.00066 30.2 6.6 50 130-179 78-127 (140)
58 cd04770 HTH_HMRTR Helix-Turn-H 60.7 16 0.00034 31.2 4.6 38 94-135 1-40 (123)
59 PRK11569 transcriptional repre 60.1 31 0.00067 33.4 7.0 45 83-128 34-78 (274)
60 PRK10411 DNA-binding transcrip 59.8 34 0.00075 32.9 7.2 52 81-134 8-59 (240)
61 TIGR02231 conserved hypothetic 59.5 61 0.0013 34.4 9.6 96 147-259 139-240 (525)
62 PRK10870 transcriptional repre 59.5 39 0.00084 30.9 7.2 40 87-126 65-104 (176)
63 PF12329 TMF_DNA_bd: TATA elem 59.3 25 0.00054 28.5 5.2 37 145-181 11-47 (74)
64 PRK09954 putative kinase; Prov 59.1 9.1 0.0002 38.0 3.2 46 79-126 5-50 (362)
65 PF13518 HTH_28: Helix-turn-he 59.1 7.6 0.00017 27.6 2.0 38 81-122 4-41 (52)
66 PF08280 HTH_Mga: M protein tr 58.9 7.9 0.00017 29.5 2.2 36 81-118 9-44 (59)
67 TIGR01764 excise DNA binding d 58.7 5.6 0.00012 27.5 1.2 22 94-115 2-23 (49)
68 PRK05014 hscB co-chaperone Hsc 58.2 96 0.0021 28.7 9.6 54 70-125 12-82 (171)
69 TIGR02716 C20_methyl_CrtF C-20 57.7 6 0.00013 38.5 1.7 40 91-131 21-60 (306)
70 PRK03573 transcriptional regul 57.1 40 0.00088 29.1 6.6 35 93-127 46-80 (144)
71 COG1474 CDC6 Cdc6-related prot 56.8 5.3 0.00012 41.0 1.2 29 96-124 304-332 (366)
72 PF04977 DivIC: Septum formati 56.8 27 0.0006 27.0 5.0 36 147-182 18-53 (80)
73 PF14257 DUF4349: Domain of un 56.5 44 0.00096 32.1 7.4 88 72-170 58-156 (262)
74 PF13545 HTH_Crp_2: Crp-like h 56.5 9.4 0.0002 29.2 2.3 51 78-128 3-63 (76)
75 TIGR01889 Staph_reg_Sar staphy 56.5 12 0.00026 31.4 3.1 45 83-127 31-77 (109)
76 PRK06474 hypothetical protein; 56.4 96 0.0021 28.7 9.3 46 81-127 15-61 (178)
77 TIGR02431 pcaR_pcaU beta-ketoa 56.3 13 0.00029 35.1 3.8 44 82-126 14-57 (248)
78 COG2739 Uncharacterized protei 56.2 8.3 0.00018 33.8 2.1 40 76-115 16-55 (105)
79 TIGR00293 prefoldin, archaeal 56.1 43 0.00094 28.6 6.5 54 128-181 68-121 (126)
80 PRK00215 LexA repressor; Valid 55.0 13 0.00027 34.3 3.2 42 88-129 18-60 (205)
81 PRK11511 DNA-binding transcrip 54.7 18 0.00039 31.2 4.0 42 75-116 7-48 (127)
82 COG1777 Predicted transcriptio 54.6 72 0.0016 31.3 8.3 43 80-125 18-60 (217)
83 COG1510 Predicted transcriptio 53.9 32 0.00069 32.8 5.7 39 90-128 38-76 (177)
84 PRK14165 winged helix-turn-hel 53.6 27 0.00058 33.8 5.3 49 81-129 8-57 (217)
85 cd04784 HTH_CadR-PbrR Helix-Tu 53.2 33 0.00072 29.6 5.4 79 94-181 1-100 (127)
86 PF01726 LexA_DNA_bind: LexA D 52.7 11 0.00023 29.8 2.0 46 82-127 14-60 (65)
87 PRK13509 transcriptional repre 52.7 13 0.00027 36.0 3.0 44 81-126 9-52 (251)
88 PF07106 TBPIP: Tat binding pr 52.2 1.3E+02 0.0029 27.1 9.4 55 82-137 6-64 (169)
89 smart00529 HTH_DTXR Helix-turn 52.1 10 0.00022 30.4 1.9 32 96-127 2-33 (96)
90 TIGR02338 gimC_beta prefoldin, 51.0 36 0.00077 29.0 5.1 84 96-180 19-108 (110)
91 cd04783 HTH_MerR1 Helix-Turn-H 51.0 88 0.0019 27.0 7.6 37 95-135 2-40 (126)
92 cd00632 Prefoldin_beta Prefold 50.9 20 0.00044 30.1 3.6 76 100-179 22-103 (105)
93 TIGR02366 DHAK_reg probable di 50.8 17 0.00036 31.9 3.2 36 76-111 6-41 (176)
94 PF05565 Sipho_Gp157: Siphovir 50.6 1.4E+02 0.003 27.3 9.2 32 74-105 2-33 (162)
95 PF01920 Prefoldin_2: Prefoldi 50.5 32 0.0007 28.0 4.7 80 97-179 15-95 (106)
96 PRK10219 DNA-binding transcrip 50.2 21 0.00045 29.3 3.5 40 77-116 5-44 (107)
97 COG1382 GimC Prefoldin, chaper 50.1 39 0.00084 30.3 5.3 71 112-183 38-114 (119)
98 cd01109 HTH_YyaN Helix-Turn-He 49.7 37 0.0008 28.7 5.1 35 95-133 2-38 (113)
99 PF09940 DUF2172: Domain of un 49.1 13 0.00029 39.0 2.7 47 74-124 340-386 (386)
100 TIGR02047 CadR-PbrR Cd(II)/Pb( 48.2 39 0.00085 29.4 5.1 37 95-135 2-40 (127)
101 PRK15090 DNA-binding transcrip 48.0 93 0.002 29.7 8.0 52 82-135 19-70 (257)
102 TIGR03338 phnR_burk phosphonat 47.9 36 0.00079 31.0 5.1 41 89-129 30-70 (212)
103 COG1846 MarR Transcriptional r 47.6 19 0.0004 28.8 2.8 44 82-127 27-70 (126)
104 TIGR00498 lexA SOS regulatory 47.6 21 0.00046 32.6 3.5 48 80-127 9-60 (199)
105 TIGR02010 IscR iron-sulfur clu 47.5 21 0.00047 31.0 3.4 38 88-125 20-57 (135)
106 PRK00888 ftsB cell division pr 47.4 17 0.00038 31.2 2.7 34 148-181 29-62 (105)
107 TIGR02297 HpaA 4-hydroxyphenyl 47.2 20 0.00043 33.9 3.3 44 77-120 186-229 (287)
108 COG4189 Predicted transcriptio 46.3 20 0.00044 36.0 3.3 52 73-126 18-70 (308)
109 PRK09343 prefoldin subunit bet 46.2 48 0.001 29.0 5.3 71 108-181 35-113 (121)
110 KOG1318 Helix loop helix trans 45.4 18 0.0004 38.3 3.0 76 104-181 239-318 (411)
111 COG1522 Lrp Transcriptional re 45.1 24 0.00051 30.5 3.2 50 75-126 6-55 (154)
112 PF05377 FlaC_arch: Flagella a 44.6 63 0.0014 25.4 5.1 39 143-181 4-42 (55)
113 PRK09802 DNA-binding transcrip 44.6 1.1E+02 0.0024 29.9 8.1 49 80-130 20-68 (269)
114 COG1802 GntR Transcriptional r 44.4 39 0.00085 31.5 4.8 41 88-128 34-74 (230)
115 PF05732 RepL: Firmicute plasm 44.3 27 0.00059 32.2 3.7 39 93-131 75-113 (165)
116 PRK11050 manganese transport r 44.0 37 0.00081 30.4 4.4 54 75-128 31-86 (152)
117 PRK09391 fixK transcriptional 44.0 38 0.00082 31.6 4.6 39 94-132 180-218 (230)
118 COG2894 MinD Septum formation 43.8 9.1 0.0002 38.2 0.5 30 92-121 39-68 (272)
119 PRK13626 transcriptional regul 43.4 50 0.0011 35.2 5.9 49 76-124 4-54 (552)
120 cd04762 HTH_MerR-trunc Helix-T 43.3 19 0.00041 24.5 1.9 23 94-116 1-23 (49)
121 cd07153 Fur_like Ferric uptake 43.2 27 0.00059 28.9 3.2 45 82-127 6-55 (116)
122 PRK11534 DNA-binding transcrip 43.0 69 0.0015 29.6 6.2 46 89-134 26-71 (224)
123 TIGR01884 cas_HTH CRISPR locus 42.9 26 0.00057 32.5 3.4 45 81-127 147-191 (203)
124 PF08781 DP: Transcription fac 42.6 65 0.0014 29.6 5.7 33 207-246 59-91 (142)
125 PRK10857 DNA-binding transcrip 42.1 22 0.00048 32.6 2.7 39 88-126 20-58 (164)
126 PF05491 RuvB_C: Holliday junc 41.7 38 0.00083 28.1 3.7 58 74-131 5-64 (76)
127 PF13384 HTH_23: Homeodomain-l 41.1 21 0.00046 25.4 2.0 36 82-121 10-45 (50)
128 PF02796 HTH_7: Helix-turn-hel 41.0 12 0.00027 26.9 0.7 32 80-115 12-43 (45)
129 KOG3863 bZIP transcription fac 40.9 54 0.0012 36.5 5.8 65 115-182 484-554 (604)
130 PF10779 XhlA: Haemolysin XhlA 40.9 83 0.0018 25.0 5.5 34 148-181 15-48 (71)
131 PF04111 APG6: Autophagy prote 40.7 56 0.0012 33.0 5.5 35 149-183 60-94 (314)
132 PF09756 DDRGK: DDRGK domain; 40.5 32 0.0007 32.7 3.6 47 78-126 100-146 (188)
133 PRK10225 DNA-binding transcrip 39.8 1.3E+02 0.0028 28.5 7.6 51 78-128 14-68 (257)
134 PRK11014 transcriptional repre 39.5 30 0.00065 30.3 3.0 41 88-128 20-60 (141)
135 PF03374 ANT: Phage antirepres 38.7 28 0.00061 29.0 2.6 42 81-126 13-54 (111)
136 PRK10130 transcriptional regul 38.5 31 0.00067 35.2 3.4 40 76-115 239-278 (350)
137 PRK11512 DNA-binding transcrip 38.5 20 0.00044 31.1 1.8 37 91-127 52-88 (144)
138 PF05930 Phage_AlpA: Prophage 37.8 20 0.00044 26.4 1.5 24 92-115 2-25 (51)
139 PRK09514 zntR zinc-responsive 37.4 89 0.0019 27.7 5.7 81 94-181 2-102 (140)
140 PRK09464 pdhR transcriptional 36.7 1.2E+02 0.0026 28.5 6.9 55 74-128 10-69 (254)
141 PF12793 SgrR_N: Sugar transpo 36.2 1.3E+02 0.0029 26.2 6.5 47 78-124 2-50 (115)
142 PHA01750 hypothetical protein 36.2 80 0.0017 26.0 4.7 31 146-176 42-72 (75)
143 PF13551 HTH_29: Winged helix- 36.2 26 0.00056 28.2 2.0 28 95-122 14-41 (112)
144 PRK00080 ruvB Holliday junctio 36.2 41 0.00089 33.2 3.7 57 73-129 255-313 (328)
145 TIGR02928 orc1/cdc6 family rep 35.9 31 0.00067 33.8 2.9 31 98-128 319-352 (365)
146 COG1373 Predicted ATPase (AAA+ 35.9 38 0.00082 35.1 3.6 50 77-126 220-270 (398)
147 PRK03902 manganese transport t 35.8 63 0.0014 28.2 4.5 47 79-127 10-56 (142)
148 TIGR02043 ZntR Zn(II)-responsi 35.7 1.1E+02 0.0024 26.7 6.0 81 94-181 2-102 (131)
149 PF02954 HTH_8: Bacterial regu 35.6 37 0.00081 24.1 2.5 37 75-113 2-38 (42)
150 PRK11169 leucine-responsive tr 35.1 49 0.0011 29.7 3.8 52 72-125 9-60 (164)
151 PF03444 HrcA_DNA-bdg: Winged 35.1 64 0.0014 27.0 4.1 47 79-126 10-56 (78)
152 PF01638 HxlR: HxlR-like helix 35.0 30 0.00065 28.1 2.2 42 86-127 11-53 (90)
153 PF10018 Med4: Vitamin-D-recep 34.8 1.2E+02 0.0026 28.2 6.4 29 149-177 25-53 (188)
154 KOG3026 Splicing factor SPF30 34.6 1.2E+02 0.0027 30.4 6.6 89 156-249 26-124 (262)
155 TIGR02051 MerR Hg(II)-responsi 34.4 1.1E+02 0.0024 26.5 5.7 79 96-181 2-97 (124)
156 PF14947 HTH_45: Winged helix- 34.1 35 0.00077 27.2 2.4 41 91-132 17-57 (77)
157 cd04790 HTH_Cfa-like_unk Helix 33.7 66 0.0014 29.6 4.4 37 94-136 2-42 (172)
158 PRK15121 right oriC-binding tr 33.6 45 0.00097 32.3 3.5 44 77-120 5-48 (289)
159 TIGR02044 CueR Cu(I)-responsiv 33.3 2E+02 0.0042 24.9 7.1 37 95-135 2-40 (127)
160 PF04297 UPF0122: Putative hel 33.1 27 0.00059 30.3 1.7 40 77-116 17-56 (101)
161 PRK09863 putative frv operon r 33.0 1.4E+02 0.003 32.1 7.3 52 81-137 8-65 (584)
162 PF12728 HTH_17: Helix-turn-he 32.7 25 0.00054 25.3 1.2 22 94-115 2-23 (51)
163 PF01475 FUR: Ferric uptake re 32.7 38 0.00082 28.5 2.5 48 81-129 12-64 (120)
164 PF04218 CENP-B_N: CENP-B N-te 32.5 30 0.00066 26.0 1.7 32 83-115 13-44 (53)
165 PRK10869 recombination and rep 32.5 56 0.0012 35.4 4.3 104 69-182 257-363 (553)
166 PRK10402 DNA-binding transcrip 32.5 34 0.00074 31.6 2.4 38 94-132 170-207 (226)
167 cd04785 HTH_CadR-PbrR-like Hel 32.5 1.1E+02 0.0023 26.6 5.3 81 94-181 1-100 (126)
168 cd04782 HTH_BltR Helix-Turn-He 32.5 69 0.0015 26.6 4.0 36 95-134 2-39 (97)
169 PRK11753 DNA-binding transcrip 32.1 56 0.0012 29.2 3.6 39 93-132 168-206 (211)
170 cd01106 HTH_TipAL-Mta Helix-Tu 32.1 1.3E+02 0.0029 24.9 5.6 17 95-111 2-18 (103)
171 COG3093 VapI Plasmid maintenan 31.9 23 0.00049 31.1 1.0 33 77-115 13-45 (104)
172 PF10779 XhlA: Haemolysin XhlA 31.7 1.3E+02 0.0029 23.8 5.3 39 144-182 4-42 (71)
173 PF15513 DUF4651: Domain of un 31.6 30 0.00064 27.8 1.5 23 240-262 16-38 (62)
174 PHA00738 putative HTH transcri 31.5 1.5E+02 0.0033 26.2 6.0 71 81-158 16-86 (108)
175 PRK13922 rod shape-determining 30.6 1E+02 0.0022 29.9 5.3 40 144-184 74-113 (276)
176 PRK03837 transcriptional regul 30.5 33 0.00072 31.8 1.9 51 78-128 18-72 (241)
177 COG2512 Predicted membrane-ass 30.4 65 0.0014 32.0 4.0 61 73-134 191-251 (258)
178 PRK10906 DNA-binding transcrip 30.4 47 0.001 32.2 3.0 44 81-126 9-52 (252)
179 PRK11886 bifunctional biotin-- 30.3 65 0.0014 31.9 4.1 52 80-133 7-59 (319)
180 PF04703 FaeA: FaeA-like prote 30.2 56 0.0012 25.9 2.9 44 82-126 5-48 (62)
181 PRK09990 DNA-binding transcrip 30.1 84 0.0018 29.5 4.6 40 89-128 26-66 (251)
182 PRK13503 transcriptional activ 29.8 61 0.0013 30.4 3.6 39 77-115 171-209 (278)
183 PF02295 z-alpha: Adenosine de 29.7 81 0.0018 25.0 3.7 57 78-134 5-61 (66)
184 PRK00888 ftsB cell division pr 29.6 1.2E+02 0.0027 26.0 5.1 60 143-213 31-90 (105)
185 PRK13729 conjugal transfer pil 29.1 84 0.0018 34.1 4.8 22 160-181 97-118 (475)
186 cd01108 HTH_CueR Helix-Turn-He 29.0 2.6E+02 0.0057 24.2 7.2 89 94-186 1-119 (127)
187 PRK09393 ftrA transcriptional 29.0 61 0.0013 31.7 3.6 42 77-118 218-259 (322)
188 KOG0804 Cytoplasmic Zn-finger 28.8 53 0.0011 35.5 3.3 59 109-181 390-449 (493)
189 smart00338 BRLZ basic region l 28.7 1.9E+02 0.0042 22.1 5.6 34 148-181 28-61 (65)
190 PF03836 RasGAP_C: RasGAP C-te 28.7 19 0.00041 32.1 0.0 26 106-133 5-30 (142)
191 PF01853 MOZ_SAS: MOZ/SAS fami 28.7 61 0.0013 31.0 3.4 59 70-131 120-185 (188)
192 COG4519 Uncharacterized protei 28.4 71 0.0015 27.3 3.3 35 90-124 19-53 (95)
193 PF10141 ssDNA-exonuc_C: Singl 28.2 2.8E+02 0.0062 25.8 7.7 46 81-126 102-149 (195)
194 COG2378 Predicted transcriptio 28.2 45 0.00097 33.5 2.5 44 78-123 6-52 (311)
195 PRK13752 putative transcriptio 28.0 1.5E+02 0.0033 26.6 5.7 81 94-181 8-105 (144)
196 PF09904 HTH_43: Winged helix- 27.9 58 0.0013 28.0 2.8 30 95-124 23-52 (90)
197 PRK01194 V-type ATP synthase s 27.8 3.1E+02 0.0067 25.6 7.8 33 150-182 67-99 (185)
198 PRK06266 transcription initiat 27.7 2.4E+02 0.0053 26.3 7.1 42 81-124 26-67 (178)
199 cd04772 HTH_TioE_rpt1 First He 27.7 1.2E+02 0.0027 25.2 4.7 37 95-135 2-40 (99)
200 PRK09333 30S ribosomal protein 27.6 55 0.0012 30.3 2.8 37 91-127 65-115 (150)
201 cd04787 HTH_HMRTR_unk Helix-Tu 27.2 3.8E+02 0.0083 23.3 7.9 82 94-179 1-112 (133)
202 PRK09975 DNA-binding transcrip 27.1 64 0.0014 29.0 3.1 38 76-113 14-51 (213)
203 cd04788 HTH_NolA-AlbR Helix-Tu 27.1 2E+02 0.0043 23.8 5.8 37 95-135 2-40 (96)
204 PHA02047 phage lambda Rz1-like 27.0 37 0.00081 29.6 1.5 33 131-170 26-58 (101)
205 PF09340 NuA4: Histone acetylt 26.8 1E+02 0.0022 25.4 4.0 27 153-179 2-28 (80)
206 PRK10434 srlR DNA-bindng trans 26.7 60 0.0013 31.4 3.0 44 81-126 9-52 (256)
207 COG1321 TroR Mn-dependent tran 26.7 76 0.0016 29.0 3.5 40 90-129 21-60 (154)
208 TIGR00373 conserved hypothetic 26.6 2.2E+02 0.0047 26.0 6.4 35 90-124 25-59 (158)
209 PF13851 GAS: Growth-arrest sp 26.6 1.3E+02 0.0028 28.6 5.2 36 146-181 27-62 (201)
210 KOG2747 Histone acetyltransfer 26.5 1.2E+02 0.0027 32.2 5.4 58 73-135 303-366 (396)
211 TIGR00635 ruvB Holliday juncti 26.5 77 0.0017 30.4 3.7 51 79-129 240-292 (305)
212 PF10018 Med4: Vitamin-D-recep 26.2 1.6E+02 0.0035 27.3 5.7 54 145-198 28-88 (188)
213 PRK04984 fatty acid metabolism 26.0 46 0.00099 31.0 2.1 39 89-127 26-65 (239)
214 PRK03578 hscB co-chaperone Hsc 26.0 5.2E+02 0.011 24.1 8.9 51 70-122 17-84 (176)
215 PRK10572 DNA-binding transcrip 25.8 77 0.0017 30.2 3.6 38 78-115 184-221 (290)
216 cd00592 HTH_MerR-like Helix-Tu 25.6 99 0.0022 25.1 3.7 21 95-115 2-22 (100)
217 COG2919 Septum formation initi 25.5 61 0.0013 28.2 2.6 31 145-175 56-86 (117)
218 PF05103 DivIVA: DivIVA protei 25.5 27 0.00059 29.6 0.4 48 131-181 13-60 (131)
219 PRK10803 tol-pal system protei 25.3 1.3E+02 0.0028 29.5 5.1 31 151-181 59-89 (263)
220 cd04777 HTH_MerR-like_sg1 Heli 25.3 2.1E+02 0.0046 23.9 5.7 25 95-125 2-28 (107)
221 PF09107 SelB-wing_3: Elongati 25.1 76 0.0016 24.1 2.7 41 90-130 7-47 (50)
222 PF01710 HTH_Tnp_IS630: Transp 25.0 81 0.0017 27.1 3.2 43 80-127 60-102 (119)
223 COG1349 GlpR Transcriptional r 24.8 67 0.0014 31.2 3.0 45 80-126 8-52 (253)
224 PRK11179 DNA-binding transcrip 24.8 78 0.0017 28.1 3.2 50 75-126 7-56 (153)
225 PF14712 Snapin_Pallidin: Snap 24.7 2.1E+02 0.0045 23.2 5.4 36 146-181 14-49 (92)
226 PF00170 bZIP_1: bZIP transcri 24.5 2.8E+02 0.006 21.2 5.8 33 148-180 28-60 (64)
227 cd04768 HTH_BmrR-like Helix-Tu 24.4 1.4E+02 0.0031 24.6 4.5 39 94-136 1-41 (96)
228 PF04977 DivIC: Septum formati 24.4 1.4E+02 0.003 23.0 4.2 29 144-172 22-50 (80)
229 TIGR02338 gimC_beta prefoldin, 24.3 1.4E+02 0.0031 25.4 4.6 33 149-181 70-102 (110)
230 PRK10371 DNA-binding transcrip 23.9 80 0.0017 31.0 3.4 39 78-116 192-230 (302)
231 COG2207 AraC AraC-type DNA-bin 23.8 91 0.002 24.9 3.2 43 81-123 24-66 (127)
232 PRK10265 chaperone-modulator p 23.7 1.5E+02 0.0033 25.0 4.6 80 93-180 7-98 (101)
233 PRK09685 DNA-binding transcrip 23.4 74 0.0016 30.3 3.0 37 79-115 199-236 (302)
234 PF13600 DUF4140: N-terminal d 23.3 2.1E+02 0.0045 23.6 5.3 35 145-179 69-103 (104)
235 PF10805 DUF2730: Protein of u 23.3 4.7E+02 0.01 22.3 8.3 80 82-183 23-102 (106)
236 PF05225 HTH_psq: helix-turn-h 23.3 58 0.0013 23.9 1.7 26 91-116 14-39 (45)
237 PF14817 HAUS5: HAUS augmin-li 23.2 1.4E+02 0.003 33.4 5.4 52 124-176 53-109 (632)
238 KOG3501 Molecular chaperone Pr 23.0 1.8E+02 0.004 25.9 5.0 40 143-182 71-110 (114)
239 KOG2255 Peptidyl-tRNA hydrolas 22.9 40 0.00086 33.0 1.0 29 96-126 64-92 (224)
240 PF02996 Prefoldin: Prefoldin 22.9 1.6E+02 0.0034 24.7 4.5 69 110-179 42-110 (120)
241 PRK01203 prefoldin subunit alp 22.8 2E+02 0.0043 26.1 5.4 37 143-179 4-40 (130)
242 KOG3990 Uncharacterized conser 22.8 95 0.0021 31.5 3.6 40 147-186 226-265 (305)
243 PF11853 DUF3373: Protein of u 22.6 57 0.0012 35.4 2.2 33 143-175 28-60 (489)
244 PF11932 DUF3450: Protein of u 22.1 1.8E+02 0.0039 28.0 5.3 32 148-179 58-89 (251)
245 PRK11642 exoribonuclease R; Pr 21.6 97 0.0021 35.5 3.9 51 81-132 23-77 (813)
246 TIGR02063 RNase_R ribonuclease 21.4 1E+02 0.0022 34.4 3.9 55 80-134 5-63 (709)
247 cd00890 Prefoldin Prefoldin is 21.4 2.4E+02 0.0051 23.7 5.3 34 145-178 93-126 (129)
248 PF06005 DUF904: Protein of un 21.3 3.3E+02 0.0071 22.2 5.8 38 146-183 18-55 (72)
249 PF03428 RP-C: Replication pro 21.2 2.8E+02 0.006 26.2 6.2 31 97-127 74-105 (177)
250 PF08317 Spc7: Spc7 kinetochor 20.9 2.5E+02 0.0055 28.2 6.3 66 153-223 237-309 (325)
251 PRK04214 rbn ribonuclease BN/u 20.5 1.1E+02 0.0024 31.6 3.8 43 90-132 307-349 (412)
252 PF03961 DUF342: Protein of un 20.5 7.8E+02 0.017 25.8 10.0 27 212-249 420-446 (451)
253 smart00342 HTH_ARAC helix_turn 20.5 63 0.0014 23.9 1.5 27 94-120 2-28 (84)
254 PRK05638 threonine synthase; V 20.4 1.3E+02 0.0027 31.5 4.1 61 63-126 357-419 (442)
255 PRK15185 transcriptional regul 20.4 1E+02 0.0022 31.5 3.4 39 77-115 206-244 (309)
256 PF13542 HTH_Tnp_ISL3: Helix-t 20.2 89 0.0019 22.3 2.2 38 78-115 12-49 (52)
257 PF05158 RNA_pol_Rpc34: RNA po 20.1 1.6E+02 0.0035 30.1 4.7 63 74-136 6-71 (327)
258 cd04773 HTH_TioE_rpt2 Second H 20.1 3.1E+02 0.0068 23.1 5.8 27 95-125 2-28 (108)
259 cd01279 HTH_HspR-like Helix-Tu 20.1 3.1E+02 0.0068 22.8 5.7 28 94-125 2-29 (98)
No 1
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=100.00 E-value=7.8e-66 Score=508.52 Aligned_cols=272 Identities=43% Similarity=0.603 Sum_probs=212.8
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCC
Q 016170 63 LTPAGSCRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPG 142 (394)
Q Consensus 63 ~tp~~~~R~d~SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~ 142 (394)
..|.+++|+++|||+||+|||.|++++|+|++|||+||+.|+|||||||||||||||||||+|++||+|+|+|.+....+
T Consensus 61 ~s~~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~VqKRRIYDITNVLEGI~LIeKksKN~IqW~G~~~~~~~ 140 (354)
T KOG2577|consen 61 SSPSESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLNVQKRRIYDITNVLEGIGLIEKKSKNNIQWIGGDFNSTG 140 (354)
T ss_pred cCCCCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhccccceeeehhhhhhcccceeeccccceeeecCCCcccc
Confidence 56778999999999999999999999999999999999999999999999999999999999999999999999988766
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCHHHHhhccCCCCceEEEEeCCCCCeEEecC
Q 016170 143 EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLHCFQNQTLIAIKAPQGTTLEVPD 222 (394)
Q Consensus 143 ~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT~LEVPd 222 (394)
+..++.+.|++|++.|.++|+.||++|++|+++|+.|++|..|++|+|||++||++|+.|++|||||||||++|+||||+
T Consensus 141 ~~~e~~~~l~~e~~~L~~~E~~LD~~i~~~q~~L~~lted~~n~~laYVT~eDI~~i~~f~~q~vi~vkap~et~levp~ 220 (354)
T KOG2577|consen 141 GVPERLNGLEAEVEDLSQEEDDLDQLIRDCQQNLRLLTEDVENRRLAYVTYEDIRSIPGFDEQTVIAVKAPPETRLEVPD 220 (354)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhcccceeeeHHHHhhccccCCceEEEEecCCcceEeccc
Confidence 77888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccCCCCCCceEEEEecCCCceEEEEecCccccccccCCCCCCCCCCCCCCCCCccchhhhhhhccccCcchhhhhhhh
Q 016170 223 PDEAVDYPQRRYRIILRSTMGPIDVYLVSRFEEKFEETNSVEPPASVPPVSSSDSNENQVKEIINVDRAGNETEAQAQQA 302 (394)
Q Consensus 223 P~e~~~~~~r~YqI~LkS~~GPIdVyLv~~~~~~~e~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 302 (394)
|++ .+|+|+|+|++||||||||+.++.. .......|...+.....+....+. ++.. . .....+.+
T Consensus 221 ~~~------~~~~i~L~s~~GpI~v~l~~~e~~~--~~~~~~~~~~~~~~~~~~~~~sp~--~~~~-~--~~~~~~p~-- 285 (354)
T KOG2577|consen 221 PDE------DRYQIRLKSNQGPIDVYLCSEEEGE--ESEPTAKPVGSSSSSEDTISPSPY--LPEQ-P--ASLALNPQ-- 285 (354)
T ss_pred CCC------CceEEEeccCCCceeEEeccccccC--ccCCCCCCCCCccccccCCCCCCC--cCCc-h--hhhhcCcc--
Confidence 984 4799999999999999999988762 222222222111100001111110 0000 0 00000011
Q ss_pred hccCCCCcccccccCCeeeeccCCC-CCCCCeeeecCCCCcchhccccCC-CCcc
Q 016170 303 HQIYSDLNSSQEVVGGMMKIVPSDV-DNDADYWLLSDADVSITDMWKTDC-AEWD 355 (394)
Q Consensus 303 ~~~~~~~~~~~~~~~g~~ki~psd~-~~d~Dywl~sd~~vsitd~w~~~~-~~w~ 355 (394)
+++.... .+-...-.|++. ..+.|||++...+++...+|-+.+ .+||
T Consensus 286 ---~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~i~l~~~~~~~d 334 (354)
T KOG2577|consen 286 ---QSEELLD---SSNLLSFFPSTSASGSSDIRESFSDDLSEPLISLSPPPRQED 334 (354)
T ss_pred ---cccchhh---cccccccCccccccCCcceeccccccccCCcccCCCCccccc
Confidence 0110000 011111111111 356899999999999999999998 8888
No 2
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=99.87 E-value=5.6e-23 Score=162.56 Aligned_cols=66 Identities=52% Similarity=0.859 Sum_probs=63.0
Q ss_pred CCCCcHHHHHHHHHHHHhhCCCCeecHHHHHHHh---cc--ceeehhhhHHHhhhccchhhccCCeEEEec
Q 016170 70 RYDSSLGLLTKKFINLIKHAEDGILDLNKAAETL---EV--QKRRIYDITNVLEGIGLIEKKLKNRIRWKG 135 (394)
Q Consensus 70 R~d~SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L---~V--qKRRIYDItNVLEgIGLIeK~sKN~i~W~G 135 (394)
|+++||+.||++||++|...+++.++|+++|+.| ++ +|||||||+||||++|||+|..|+.|+|+|
T Consensus 1 r~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K~~k~~~~W~G 71 (71)
T PF02319_consen 1 RKEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEKQSKNSYKWIG 71 (71)
T ss_dssp TTTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEEEETTEEEE--
T ss_pred CCcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHcccccccccchhhHHHHHHHHhCceeecCCCceEecC
Confidence 7899999999999999999999999999999999 99 999999999999999999999999999998
No 3
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.78 E-value=1.6e-19 Score=177.18 Aligned_cols=87 Identities=37% Similarity=0.592 Sum_probs=77.3
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCC
Q 016170 63 LTPAGSCRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPG 142 (394)
Q Consensus 63 ~tp~~~~R~d~SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~ 142 (394)
..+.-++|+++|||+||.+|+.++....-..+-|..||.+|||.|||||||+||||+||++.|.+||.|+|+|+...
T Consensus 14 l~lqvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~ai--- 90 (388)
T KOG2578|consen 14 LDLQVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFGAI--- 90 (388)
T ss_pred ccchhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccchhhh---
Confidence 55667899999999999999999988777889999999999999999999999999999999999999999998754
Q ss_pred CchHHHHHHHHH
Q 016170 143 EVDADASILQAD 154 (394)
Q Consensus 143 ~~~~~~~~Lq~E 154 (394)
..-+..||+|
T Consensus 91 --Pral~eLqeE 100 (388)
T KOG2578|consen 91 --PRALFELQEE 100 (388)
T ss_pred --hHHHHHHHHH
Confidence 3445566654
No 4
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.12 E-value=1.3e-10 Score=115.09 Aligned_cols=76 Identities=37% Similarity=0.598 Sum_probs=65.4
Q ss_pred CCCCCCCCCCcHHHHHHHHHHHHhhCCCC-eecHHHHHHHhc----------cceeehhhhHHHhhhccchhhc-----c
Q 016170 64 TPAGSCRYDSSLGLLTKKFINLIKHAEDG-ILDLNKAAETLE----------VQKRRIYDITNVLEGIGLIEKK-----L 127 (394)
Q Consensus 64 tp~~~~R~d~SLglLTkKFi~Ll~~ap~g-~ldLn~aA~~L~----------VqKRRIYDItNVLEgIGLIeK~-----s 127 (394)
.+.-..|+++||++||++||.++-.+++. .|.|+.||..|= -.-||+|||.|||-++|||+|+ .
T Consensus 150 ~~k~DnrkekSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~tr 229 (388)
T KOG2578|consen 150 SSKRDNRKEKSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTR 229 (388)
T ss_pred CCcccchhhhHHHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccc
Confidence 34445789999999999999999888887 899999999882 3569999999999999999998 4
Q ss_pred CCeEEEeccCCC
Q 016170 128 KNRIRWKGLDNS 139 (394)
Q Consensus 128 KN~i~W~G~~~s 139 (394)
|..|+|.|....
T Consensus 230 kPafrwlG~~~~ 241 (388)
T KOG2578|consen 230 KPAFRWLGSKPI 241 (388)
T ss_pred cchhheeCCCcc
Confidence 788999996654
No 5
>KOG2829 consensus E2F-like protein [Transcription]
Probab=98.92 E-value=1.4e-08 Score=100.00 Aligned_cols=127 Identities=25% Similarity=0.442 Sum_probs=82.6
Q ss_pred HHHH-hhCCCCeecHHHHHHHh----------------------ccceeehhhhHHHhhhccchhhccCCeEEEeccCCC
Q 016170 83 INLI-KHAEDGILDLNKAAETL----------------------EVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNS 139 (394)
Q Consensus 83 i~Ll-~~ap~g~ldLn~aA~~L----------------------~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s 139 (394)
+..| +....|....|++|+.| .-.|||+||.+|||.++.+|.|. |..|+|+|+...
T Consensus 51 ~kVCeKve~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KKEIrW~GLP~~ 129 (326)
T KOG2829|consen 51 MKVCEKVERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KKEIRWIGLPAT 129 (326)
T ss_pred HHHHHHHHhcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cceeeeeccCcc
Confidence 3445 34567888899998888 24699999999999999999999 667999999865
Q ss_pred CCCCchHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHhhhcccccccccC----HHHHhhccCCCCceEEEEe
Q 016170 140 IPGEVDADASILQADIDNL----SMEELRVDEQTRELRERLRELIENENNRKWLFVT----EEDIKNLHCFQNQTLIAIK 211 (394)
Q Consensus 140 ~~~~~~~~~~~Lq~El~~L----~~~E~~LDe~I~~~~~~L~~Lted~~n~~~aYVT----~eDI~~l~~f~~qTvIAIK 211 (394)
. .+++.+|+.|...+ .++-..|.++|.. .-.+++|.+- | +.++.+ .++|. | ..|.|.
T Consensus 130 s----s~dv~~le~Er~k~~erI~kK~a~lqEl~~q-~~~fknLV~R--N-~~~e~~~~~P~~~i~-L------PFiiin 194 (326)
T KOG2829|consen 130 S----SQDVSELEEERKKRMERIKKKAAQLQELIEQ-VSAFKNLVQR--N-RHAESQGQPPSENIH-L------PFIIIN 194 (326)
T ss_pred c----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHh--h-hhhhhccCCCCcccc-c------ceEEEe
Confidence 3 23455555554333 3344445555443 2445555441 2 122332 12221 2 368899
Q ss_pred CCCCCeEEecCCCc
Q 016170 212 APQGTTLEVPDPDE 225 (394)
Q Consensus 212 AP~gT~LEVPdP~e 225 (394)
.-+.|.+++-..++
T Consensus 195 T~k~a~IeceiseD 208 (326)
T KOG2829|consen 195 TSKKAVIECEISED 208 (326)
T ss_pred cCCCceEEEEeccc
Confidence 99999999987654
No 6
>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=94.50 E-value=0.035 Score=42.70 Aligned_cols=45 Identities=22% Similarity=0.397 Sum_probs=40.8
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 134 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 134 (394)
..|..+..++|+.+++.|..+|++++-|+.-|||++...+.+.|.
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~ 63 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYR 63 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEE
Confidence 467799999999999999999999999999999999977766665
No 7
>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=93.63 E-value=0.1 Score=38.31 Aligned_cols=41 Identities=24% Similarity=0.366 Sum_probs=35.2
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhcc
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIG 121 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIG 121 (394)
.+.+.+|..+.+. +...++|+.|+|++|-||--++.|+..|
T Consensus 3 ~~il~~L~~~~~~-it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEP-ITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTS-BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 4677777666666 9999999999999999999999999998
No 8
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=92.25 E-value=0.17 Score=35.54 Aligned_cols=45 Identities=27% Similarity=0.372 Sum_probs=38.6
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
.++.++... +.+.+.++|+.|++.++.+|.++.-|+..|+|.+..
T Consensus 4 ~il~~l~~~--~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQ--GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 466666653 459999999999999999999999999999998764
No 9
>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=92.07 E-value=0.27 Score=36.67 Aligned_cols=54 Identities=20% Similarity=0.233 Sum_probs=42.9
Q ss_pred HHHHHHHHHhhC-----CCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 016170 78 LTKKFINLIKHA-----EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 131 (394)
Q Consensus 78 LTkKFi~Ll~~a-----p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 131 (394)
+..-|+.++... ..+.+...++|+.+++.+..++.+++.|+.-|+|++.....|
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~~~~~ 63 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKY 63 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeE
Confidence 444555555443 456789999999999999999999999999999998764444
No 10
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=90.98 E-value=0.6 Score=45.43 Aligned_cols=52 Identities=21% Similarity=0.387 Sum_probs=41.2
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEecc
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGL 136 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~ 136 (394)
++.|+. -|...-.++|+..||.+=|+|||++.||+=|+|+....+--+++-.
T Consensus 22 Y~aLl~---~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av 73 (247)
T COG1378 22 YLALLC---LGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAV 73 (247)
T ss_pred HHHHHH---hCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeC
Confidence 445553 3556778999999999999999999999999999986555555543
No 11
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=90.74 E-value=0.33 Score=38.16 Aligned_cols=55 Identities=20% Similarity=0.306 Sum_probs=46.2
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 134 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 134 (394)
.+.+.+|+.+++..+.+.++|+.||+.|+-+.-++.-|+.-|+|++...+.=.|.
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~ 63 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWK 63 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence 5778888877553599999999999999999999999999999999865433564
No 12
>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=90.33 E-value=0.18 Score=37.13 Aligned_cols=44 Identities=18% Similarity=0.329 Sum_probs=36.1
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
.++++..++.+ +.+.++|+.+|+.|=-+|-+++.|+..|+++|.
T Consensus 8 iL~~l~~~~~~-~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 8 ILEALAESGGP-LTLSEIARALGLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHCHHCTBSC-EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHcCCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence 44555555444 799999999999999999999999999999874
No 13
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=89.92 E-value=0.49 Score=37.45 Aligned_cols=46 Identities=24% Similarity=0.350 Sum_probs=39.0
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
+.++++...+ +.+.+.++|+.+++.+..+|-+++.|+..|+|++..
T Consensus 9 ~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 9 AVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence 4555665543 479999999999999999999999999999999863
No 14
>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=87.64 E-value=0.65 Score=34.32 Aligned_cols=46 Identities=24% Similarity=0.351 Sum_probs=40.3
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
..+.++...++..+.+.++|+.|++.|=.+--+++-||.-|||+|.
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 4555667777778999999999999999999999999999999987
No 15
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=87.41 E-value=0.7 Score=33.18 Aligned_cols=43 Identities=26% Similarity=0.415 Sum_probs=35.8
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
++.+.++.+. +.+...++|+.+++.+..++.+++-|+.-|+|+
T Consensus 6 ~~Il~~l~~~--~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLREN--PRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHC--TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHc--CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 5677778774 449999999999999999999999999999985
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=86.32 E-value=0.73 Score=32.83 Aligned_cols=38 Identities=24% Similarity=0.336 Sum_probs=34.4
Q ss_pred CCeecHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 91 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 91 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
.+.+.++++++.|++.+..++.+++.|+.-|+|++..+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 56689999999999999999999999999999997653
No 17
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.90 E-value=1.1 Score=32.91 Aligned_cols=29 Identities=31% Similarity=0.394 Sum_probs=27.9
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccch
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLI 123 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLI 123 (394)
....+|+.+|+.+|.|+-.++.||-.|+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 78999999999999999999999999986
No 18
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=83.29 E-value=6.4 Score=35.37 Aligned_cols=87 Identities=23% Similarity=0.337 Sum_probs=57.6
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCC-CCCCchHHHHHHHHHHHHHHH
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNS-IPGEVDADASILQADIDNLSM 160 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s-~~~~~~~~~~~Lq~El~~L~~ 160 (394)
|..|++ +++.++.+++|+.|+..|=.+|-.+|=|.-.|||.|.--+. +|..-- -.. .-...+++..+
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~---~~Ggy~yiY~--~i~~ee~k~~i----- 100 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL---KGGGYYYLYK--PIDPEEIKKKI----- 100 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc---CCCceeEEEe--cCCHHHHHHHH-----
Confidence 455554 68889999999999999999999999999999999984442 332210 000 01122333222
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 016170 161 EELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 161 ~E~~LDe~I~~~~~~L~~Lte 181 (394)
++.|+++-..+.+-|.++..
T Consensus 101 -~~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 101 -LKDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred -HHHHHHHHHHHHHHHHHHhc
Confidence 34577777777777766644
No 19
>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=83.18 E-value=1.5 Score=35.15 Aligned_cols=49 Identities=22% Similarity=0.331 Sum_probs=39.3
Q ss_pred HHHHHHHHHhhCCCC-eecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 78 LTKKFINLIKHAEDG-ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 78 LTkKFi~Ll~~ap~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
.+-+++.+|...+++ .+.+.++|+.+++..+.+..|++-|+.-|||+..
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 344566666655554 5999999999999999999999999999999865
No 20
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=82.83 E-value=1.2 Score=38.22 Aligned_cols=46 Identities=13% Similarity=0.187 Sum_probs=40.1
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
+.+.++..++++.+++.++|+.|++.+..++.+++.|+.-|+|+..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 4455666666788999999999999999999999999999999864
No 21
>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=81.50 E-value=1.3 Score=32.64 Aligned_cols=42 Identities=24% Similarity=0.419 Sum_probs=35.1
Q ss_pred HHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 83 INLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 83 i~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
+.++.+.++ +.+.++|+.+++.+-.+-.+++-|+.-|+|+|.
T Consensus 9 L~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 9 LRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence 344444444 999999999999999999999999999999987
No 22
>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=81.22 E-value=2.1 Score=31.12 Aligned_cols=47 Identities=21% Similarity=0.360 Sum_probs=38.7
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
.+++.++...+ +...++++.|++.+..++-+++.|+.-|+|.+....
T Consensus 10 ~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 10 LRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 34555555543 899999999999999999999999999999976443
No 23
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=81.00 E-value=1.8 Score=32.40 Aligned_cols=38 Identities=34% Similarity=0.478 Sum_probs=31.9
Q ss_pred CCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 89 AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 89 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
..++.+.+.++|+.|++.+--+..+++-|+..|||+|.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 37889999999999999999999999999999999887
No 24
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=80.50 E-value=0.61 Score=37.40 Aligned_cols=30 Identities=40% Similarity=0.532 Sum_probs=23.7
Q ss_pred HHHHHHhcc---ceeehhhhHHHhhhccchhhc
Q 016170 97 NKAAETLEV---QKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 97 n~aA~~L~V---qKRRIYDItNVLEgIGLIeK~ 126 (394)
..+|+.+++ ..|||||+++-|+-+|||+..
T Consensus 26 ~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 26 EELCESLGVDPLSYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp HHHHHHTTS----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEE
Confidence 345555654 789999999999999999866
No 25
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=79.19 E-value=2.4 Score=30.37 Aligned_cols=41 Identities=20% Similarity=0.286 Sum_probs=35.6
Q ss_pred CCCCee-cHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 016170 89 AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 89 ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
.++..+ ...++|+.+++.+=-+...++.|+.-|+|++....
T Consensus 15 ~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 15 RPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 345567 89999999999999999999999999999876543
No 26
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=79.07 E-value=21 Score=32.96 Aligned_cols=45 Identities=22% Similarity=0.203 Sum_probs=38.9
Q ss_pred hCCCCeecHHHHHHHh--ccceeehhhhHHHhhhccchhhccCCeEE
Q 016170 88 HAEDGILDLNKAAETL--EVQKRRIYDITNVLEGIGLIEKKLKNRIR 132 (394)
Q Consensus 88 ~ap~g~ldLn~aA~~L--~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 132 (394)
.-.++.-|...+|.+| +|.--.+=+.++.|+-+|||+|...+.|.
T Consensus 34 ~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~ 80 (171)
T PF14394_consen 34 PLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYV 80 (171)
T ss_pred hcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEE
Confidence 3456666999999999 99999999999999999999999774443
No 27
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=78.63 E-value=1 Score=35.74 Aligned_cols=22 Identities=41% Similarity=0.685 Sum_probs=19.9
Q ss_pred cceeehhhhHHHhhhccchhhc
Q 016170 105 VQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 105 VqKRRIYDItNVLEgIGLIeK~ 126 (394)
...|||+|++|-||..|||+-.
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEE
Confidence 4789999999999999999865
No 28
>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=77.56 E-value=2.7 Score=31.85 Aligned_cols=45 Identities=29% Similarity=0.446 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
++.++++++ .+.+.+.++|+.|+|+..-|.-=+|.|+.-|+|.|.
T Consensus 3 ~~Il~~l~~--~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 3 QQILELLKE--KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHH--cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 356677766 588999999999999999999999999999999887
No 29
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=76.96 E-value=2.1 Score=29.79 Aligned_cols=38 Identities=29% Similarity=0.334 Sum_probs=33.2
Q ss_pred eecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 016170 93 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 131 (394)
Q Consensus 93 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 131 (394)
.+...++|+.+++.+..++.+++.|+.-|+|++.. +.|
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~-~~~ 45 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG-GRI 45 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC-CEE
Confidence 36778999999999999999999999999998764 444
No 30
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=76.54 E-value=11 Score=31.90 Aligned_cols=55 Identities=15% Similarity=0.239 Sum_probs=33.1
Q ss_pred cCCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 127 LKNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 127 sKN~i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
...-+.|.|.+..-....++-...|+..++.|..+-..|++.|..+++++..+..
T Consensus 68 ~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~ 122 (129)
T cd00890 68 DDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQE 122 (129)
T ss_pred CCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788886654322334445566666666666666666666666666666543
No 31
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=75.27 E-value=3 Score=31.72 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.2
Q ss_pred HHHHHHHhh---CCCCee-cHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 016170 80 KKFINLIKH---AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 80 kKFi~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
..+.+.+.. .++..+ +..++|++++|++.-+...++.|+.-|+|++..+.
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~ 60 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPGR 60 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCc
Confidence 344444433 356688 99999999999999999999999999999987554
No 32
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=75.09 E-value=8 Score=37.44 Aligned_cols=53 Identities=9% Similarity=0.223 Sum_probs=41.2
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEec
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKG 135 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G 135 (394)
.++++.... ..+.+.++|+.|++.|=.+|.+++-|+..|++++.....--..|
T Consensus 30 IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG 82 (271)
T PRK10163 30 ILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIG 82 (271)
T ss_pred HHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEec
Confidence 445554443 45899999999999999999999999999999886443333345
No 33
>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=74.45 E-value=3.7 Score=34.01 Aligned_cols=50 Identities=22% Similarity=0.363 Sum_probs=40.4
Q ss_pred cHHHHHHHHHHHHhhCC--CCeecHHHHHHHhccceeehhhhHHHhhhccch
Q 016170 74 SLGLLTKKFINLIKHAE--DGILDLNKAAETLEVQKRRIYDITNVLEGIGLI 123 (394)
Q Consensus 74 SLglLTkKFi~Ll~~ap--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 123 (394)
+|..+.++.+++|++.+ +.-+.+++++++|++....|..++.-|..-|+|
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 78899999999998721 224899999999999999999999999998887
No 34
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=72.69 E-value=3.7 Score=31.60 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=33.0
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccch
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLI 123 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 123 (394)
+.+.++.+. .+..+++|+.|+|+++-|+--++.|+.-|++
T Consensus 4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 556666543 4669999999999999999999999888883
No 35
>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=72.45 E-value=3.8 Score=31.89 Aligned_cols=46 Identities=15% Similarity=0.210 Sum_probs=36.4
Q ss_pred HHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCe
Q 016170 83 INLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNR 130 (394)
Q Consensus 83 i~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~ 130 (394)
.++++. .+.+++.++|..|++...-+=.++.+|+..|.|+|...+.
T Consensus 6 ~~~l~~--~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 6 RDYLRE--RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHH--S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 344444 7889999999999999999999999999999999986543
No 36
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=72.40 E-value=3.2 Score=30.02 Aligned_cols=42 Identities=26% Similarity=0.461 Sum_probs=35.0
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhh
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 125 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 125 (394)
+.+.++.. +.....++|+.|++.+--++-=++.|+..|+|+|
T Consensus 6 ~Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 6 RILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 34445533 7799999999999999999999999999999975
No 37
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=70.83 E-value=4.8 Score=32.09 Aligned_cols=49 Identities=20% Similarity=0.210 Sum_probs=40.6
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
.++++.+-.+...-+.-.+++..++...|-++=++++|+..|||.|..-
T Consensus 5 ~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 5 YCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 4567777666555556678889999999999999999999999999865
No 38
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=68.63 E-value=6 Score=38.00 Aligned_cols=49 Identities=14% Similarity=0.293 Sum_probs=39.1
Q ss_pred HHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc-CCeEE
Q 016170 83 INLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL-KNRIR 132 (394)
Q Consensus 83 i~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s-KN~i~ 132 (394)
++++... ++.+.+.++|+.|++.|=.+|-+++-|+..|++++.. .+.|.
T Consensus 17 L~~l~~~-~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 17 LRALNRL-DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 4445444 3349999999999999999999999999999999863 34443
No 39
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=68.02 E-value=13 Score=30.40 Aligned_cols=27 Identities=22% Similarity=0.274 Sum_probs=21.9
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
+.+.++|+.+||+.+-|.-. |..|+|.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~y----e~~Gli~ 28 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLY----ERLGLLS 28 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHH----HHCCCcC
Confidence 56889999999999987766 4568886
No 40
>PHA02943 hypothetical protein; Provisional
Probab=67.27 E-value=24 Score=33.19 Aligned_cols=48 Identities=23% Similarity=0.234 Sum_probs=41.8
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCe
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNR 130 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~ 130 (394)
..+++++ ..|.....++|+.||++--....++=|||--|.|++.....
T Consensus 14 ~eILE~L---k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~ 61 (165)
T PHA02943 14 IKTLRLL---ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGR 61 (165)
T ss_pred HHHHHHH---hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecc
Confidence 3577777 67888999999999999999999999999999999975543
No 41
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=67.09 E-value=20 Score=30.83 Aligned_cols=54 Identities=11% Similarity=0.245 Sum_probs=33.1
Q ss_pred CCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 128 KNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 128 KN~i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
+.-+-|.|.+..-...+.+-..-++..++.|...-..|.+.|..+++++..+.+
T Consensus 69 ~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~ 122 (129)
T cd00584 69 DKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEA 122 (129)
T ss_pred CEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334778887654322344445566666777766666677777777666666543
No 42
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=66.46 E-value=7.8 Score=32.19 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=37.6
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccC
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLD 137 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~ 137 (394)
....+.-.++|+.+|+.|.-+..+++.||--|+|++..+ ..|.|..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~--~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM--MGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC--CceeecC
Confidence 455788899999999999999999999999999997643 3344543
No 43
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=66.39 E-value=8.3 Score=32.76 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=33.8
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
..+.+...++|+.+++.++.+++|+..|...|+|...
T Consensus 22 ~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 22 DEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 3458999999999999999999999999999999864
No 44
>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=64.77 E-value=3.8 Score=30.95 Aligned_cols=45 Identities=27% Similarity=0.423 Sum_probs=37.6
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
+.+.++ ..++.+...++|+.|++.+-.+|-=+++|+..|||+...
T Consensus 14 ~Il~~L--~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 14 RILRLL--ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHH--HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHH--hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 455555 357789999999999999999999999999999998763
No 45
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=64.47 E-value=21 Score=29.82 Aligned_cols=36 Identities=19% Similarity=0.355 Sum_probs=24.7
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchh-hccCCeEEE
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE-KKLKNRIRW 133 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe-K~sKN~i~W 133 (394)
+.+.++|+.+||+.+-| -..|-.||+. +...|.++.
T Consensus 2 ~~i~eva~~~gvs~~tL----R~ye~~Gll~~~r~~~g~R~ 38 (102)
T cd04775 2 YTIGQMSRKFGVSRSTL----LYYESIGLIPSARSEANYRL 38 (102)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCCCCCCCee
Confidence 56889999999998877 3456678883 333454544
No 46
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=63.72 E-value=8.3 Score=37.13 Aligned_cols=50 Identities=24% Similarity=0.454 Sum_probs=42.7
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCC-eE
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN-RI 131 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN-~i 131 (394)
..++++...+.+ +.+.++|+++|+.|=.+|-+++.|+-.|++++...+ +|
T Consensus 8 ~iL~~l~~~~~~-l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y 58 (246)
T COG1414 8 AILDLLAEGPGG-LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRY 58 (246)
T ss_pred HHHHHHHhCCCC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcE
Confidence 456777764444 899999999999999999999999999999999865 44
No 47
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=63.45 E-value=21 Score=30.00 Aligned_cols=37 Identities=22% Similarity=0.346 Sum_probs=24.2
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchh-hccCCeEEEe
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE-KKLKNRIRWK 134 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe-K~sKN~i~W~ 134 (394)
+.+.++|+.+||..+-|- -.|-.|||. ....|.+++-
T Consensus 2 ~~i~eva~~~gvs~~tlR----~ye~~Gll~~~r~~~g~R~Y 39 (102)
T cd04789 2 YTISELAEKAGISRSTLL----YYEKLGLITGTRNANGYRLY 39 (102)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCcCCCCCeeC
Confidence 568899999999887543 345567775 2334555554
No 48
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=63.38 E-value=12 Score=28.99 Aligned_cols=42 Identities=24% Similarity=0.310 Sum_probs=36.8
Q ss_pred HHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 85 LIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 85 Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
.+.. .++.+...++|+.|+|.+=-+.+.++-|+.-|||++..
T Consensus 15 ~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 15 ELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 3444 88999999999999999999999999999999998764
No 49
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=63.27 E-value=64 Score=32.15 Aligned_cols=40 Identities=20% Similarity=0.213 Sum_probs=35.7
Q ss_pred CCCeecHHHHHHHhc--cceeehhhhHHHhhhccchhhccCC
Q 016170 90 EDGILDLNKAAETLE--VQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 90 p~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
.++.-|...+|++|+ |.--.+=+.+..|+-+|||+|...+
T Consensus 134 ~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g 175 (271)
T TIGR02147 134 MPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDG 175 (271)
T ss_pred CCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCC
Confidence 567778999999998 8888999999999999999998655
No 50
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=63.14 E-value=7.5 Score=31.86 Aligned_cols=47 Identities=15% Similarity=0.285 Sum_probs=41.0
Q ss_pred HHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 78 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 78 LTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
+-++.+.+|+.. +.+...++|+.||+.+.-++..++-|+.-|+|.+.
T Consensus 4 ~D~~il~~L~~~--~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKD--ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHh--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeece
Confidence 346788888764 56899999999999999999999999999999853
No 51
>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=62.91 E-value=4.9 Score=33.71 Aligned_cols=37 Identities=19% Similarity=0.294 Sum_probs=34.2
Q ss_pred CCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 91 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 91 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
.+.+.+.++|+.+++.|-.++-+++-||.-|||++..
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 4568999999999999999999999999999999973
No 52
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=62.67 E-value=15 Score=33.97 Aligned_cols=56 Identities=14% Similarity=0.105 Sum_probs=43.2
Q ss_pred cHHH-HHHHHHHHHhh---CCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 016170 74 SLGL-LTKKFINLIKH---AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 74 SLgl-LTkKFi~Ll~~---ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
++.. +..++.+.+.. .|+..+.-.++|+.|||+|=-+=+.+..|+..|||+.....
T Consensus 11 ~~~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~ 70 (221)
T PRK11414 11 SLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQ 70 (221)
T ss_pred CHHHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCC
Confidence 4443 33444444432 47888999999999999999999999999999999976543
No 53
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=62.18 E-value=12 Score=27.28 Aligned_cols=34 Identities=26% Similarity=0.362 Sum_probs=31.2
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
....++|+.+++.+=.+...++-|+.-|+|++..
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4599999999999999999999999999998764
No 54
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=61.71 E-value=49 Score=30.65 Aligned_cols=45 Identities=22% Similarity=0.287 Sum_probs=38.5
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
.+.+.++... +.+...++|+.|++.+=-+.-.++.||.-|||++.
T Consensus 4 ~~IL~~L~~~--~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQ--GQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 3566667654 44999999999999999999999999999999876
No 55
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=61.55 E-value=12 Score=29.09 Aligned_cols=44 Identities=23% Similarity=0.367 Sum_probs=37.1
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
+.+.++... +.+...++|+.+++.+..|+-+++-|+.-|+|++.
T Consensus 14 ~il~~l~~~--~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 14 LVLRILYEE--GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 444555543 35889999999999999999999999999999976
No 56
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=61.33 E-value=60 Score=27.90 Aligned_cols=31 Identities=10% Similarity=0.041 Sum_probs=26.4
Q ss_pred CeecHHHHHHHhccceeehhhhHHHhhhccc
Q 016170 92 GILDLNKAAETLEVQKRRIYDITNVLEGIGL 122 (394)
Q Consensus 92 g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 122 (394)
+-..+.++|..|||+.--||-+.+-+..-|+
T Consensus 28 ~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~ 58 (121)
T PRK09413 28 PGMTVSLVARQHGVAASQLFLWRKQYQEGSL 58 (121)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHhhccc
Confidence 3458999999999999999999999875444
No 57
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=61.27 E-value=30 Score=30.24 Aligned_cols=50 Identities=22% Similarity=0.281 Sum_probs=26.2
Q ss_pred eEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 130 RIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 130 ~i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
-+-|.|.+..-...+.+-+..|+..++.|...-..|.+.|.++++++..+
T Consensus 78 V~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~ 127 (140)
T PRK03947 78 VIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQL 127 (140)
T ss_pred EEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46677765442223344455555555555555555555555555555444
No 58
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=60.66 E-value=16 Score=31.20 Aligned_cols=38 Identities=26% Similarity=0.402 Sum_probs=27.6
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 135 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 135 (394)
+.+.++|+.+||..|-|- -.|-.|||. +...|.|+|-.
T Consensus 1 ~~I~eva~~~gvs~~tLR----yYe~~GLl~p~~r~~~gyR~Y~ 40 (123)
T cd04770 1 MKIGELAKAAGVSPDTIR----YYERIGLLPPPQRSENGYRLYG 40 (123)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCCCCCCCccCC
Confidence 357899999999888653 367888886 44567777753
No 59
>PRK11569 transcriptional repressor IclR; Provisional
Probab=60.09 E-value=31 Score=33.44 Aligned_cols=45 Identities=11% Similarity=0.250 Sum_probs=37.6
Q ss_pred HHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 83 INLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 83 i~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
++++.. ....+.|.++|+.||+.|=.+|-+++-|+..|++++...
T Consensus 34 L~~l~~-~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~ 78 (274)
T PRK11569 34 LEWIAE-SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGE 78 (274)
T ss_pred HHHHHh-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 444444 355689999999999999999999999999999997643
No 60
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=59.85 E-value=34 Score=32.87 Aligned_cols=52 Identities=23% Similarity=0.203 Sum_probs=42.5
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 134 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 134 (394)
+.++++++ .+.+...++|+.|+|+.+.|..-++.|+.-|+|.+....-+.+.
T Consensus 8 ~Il~~l~~--~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~ 59 (240)
T PRK10411 8 AIVDLLLN--HTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKYIH 59 (240)
T ss_pred HHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCeEEEec
Confidence 45666664 56899999999999999999999999999999988755544444
No 61
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=59.53 E-value=61 Score=34.42 Aligned_cols=96 Identities=14% Similarity=0.209 Sum_probs=53.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCHHHHhhccCCCCceEEEEeCCCCC--eEEecCCC
Q 016170 147 DASILQADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLHCFQNQTLIAIKAPQGT--TLEVPDPD 224 (394)
Q Consensus 147 ~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT--~LEVPdP~ 224 (394)
++..+..++..|..+.++|++.|..++++|..+...... ......+.|.+|.+. .|+|-.--
T Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~~~~----------------~~~~v~v~l~~~~~g~~~l~lsY~v 202 (525)
T TIGR02231 139 EIERLLTEDREAERRIRELEKQLSELQNELNALLTGKSQ----------------RSHTVLVRLEAPEDAEAELNLTYQV 202 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCcc----------------ceEEEEEEEeccCCceEEEEEEEEe
Confidence 345555666666666677777777777777666542111 112345666666544 34443221
Q ss_pred ccCCCCCCceEEEEecCCCceEEEE----ecCccccccc
Q 016170 225 EAVDYPQRRYRIILRSTMGPIDVYL----VSRFEEKFEE 259 (394)
Q Consensus 225 e~~~~~~r~YqI~LkS~~GPIdVyL----v~~~~~~~e~ 259 (394)
.+.. =+-.|.|.|.+..+++++-. .....+.+.+
T Consensus 203 ~~a~-W~P~Ydlrl~~~~~~~~l~~~A~V~Q~TGeDW~~ 240 (525)
T TIGR02231 203 GNAS-WTPSYDARLDTGAPTVELTYLAEIRQSTGEDWSD 240 (525)
T ss_pred CCCc-EeeeeEEEecCCCceEEEEEEEEEEeCCCCCCCC
Confidence 1111 13479999999999887643 3444555444
No 62
>PRK10870 transcriptional repressor MprA; Provisional
Probab=59.52 E-value=39 Score=30.95 Aligned_cols=40 Identities=20% Similarity=0.289 Sum_probs=36.1
Q ss_pred hhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 87 KHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 87 ~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
...+++.+...++|+.|++.+=.+--+++-||.-|||+|.
T Consensus 65 ~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~ 104 (176)
T PRK10870 65 ESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERR 104 (176)
T ss_pred hcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 3445778999999999999999999999999999999997
No 63
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=59.27 E-value=25 Score=28.51 Aligned_cols=37 Identities=27% Similarity=0.507 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 145 DADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 145 ~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
+..+..|..|.+.|...|..+...|+.++.++.++-.
T Consensus 11 De~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~ 47 (74)
T PF12329_consen 11 DEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEK 47 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 4668899999999999999999999999888877643
No 64
>PRK09954 putative kinase; Provisional
Probab=59.07 E-value=9.1 Score=38.00 Aligned_cols=46 Identities=20% Similarity=0.349 Sum_probs=40.5
Q ss_pred HHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 79 TKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 79 TkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
-++.+++|++. +.+...++|+.|+|.|..++..++=|+.-|+|++.
T Consensus 5 ~~~il~~l~~~--~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 5 EKEILAILRRN--PLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred HHHHHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCc
Confidence 45788888865 47999999999999999999999999999999755
No 65
>PF13518 HTH_28: Helix-turn-helix domain
Probab=59.07 E-value=7.6 Score=27.60 Aligned_cols=38 Identities=13% Similarity=0.337 Sum_probs=30.9
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGL 122 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 122 (394)
+.|.++. +|. .+.++|..+||.++.||.+++-++.-|+
T Consensus 4 ~iv~~~~---~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 4 QIVELYL---EGE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHH---cCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 3455554 244 9999999999999999999999998664
No 66
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=58.88 E-value=7.9 Score=29.48 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=28.5
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhh
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLE 118 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLE 118 (394)
+.+++|-. .+.+.+.++|+.|+++.|-|.--++-|.
T Consensus 9 ~Ll~~L~~--~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLK--NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHH--HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHc--CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46666666 6778999999999999999987777766
No 67
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=58.67 E-value=5.6 Score=27.46 Aligned_cols=22 Identities=36% Similarity=0.575 Sum_probs=20.1
Q ss_pred ecHHHHHHHhccceeehhhhHH
Q 016170 94 LDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItN 115 (394)
+++.++|+.|||.++.||..++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999985
No 68
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=58.24 E-value=96 Score=28.66 Aligned_cols=54 Identities=31% Similarity=0.471 Sum_probs=38.8
Q ss_pred CCCCcHHHHHHHHHHHHh-hCCCCee---------------cHHHHHHHhcc-ceeehhhhHHHhhhccchhh
Q 016170 70 RYDSSLGLLTKKFINLIK-HAEDGIL---------------DLNKAAETLEV-QKRRIYDITNVLEGIGLIEK 125 (394)
Q Consensus 70 R~d~SLglLTkKFi~Ll~-~ap~g~l---------------dLn~aA~~L~V-qKRRIYDItNVLEgIGLIeK 125 (394)
.++.+...|.++|..+.+ -+||... -||+|-..|.= .+|+.|++ -|.|+.+...
T Consensus 12 ~~~~d~~~L~~~yr~l~~~~HPDk~~~~~~~~~~~a~~~s~~iN~AY~~L~dp~~Ra~Yll--~l~g~~~~~~ 82 (171)
T PRK05014 12 RYDIDTQLLASRYQELQRQFHPDKFANASERERLLAVQQAATINDAYQTLKHPLKRAEYLL--SLHGFDLAHE 82 (171)
T ss_pred CCCCCHHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHHHHHHHHHHHHCChhHHHHHHH--HhcCCccccc
Confidence 456788899999999864 4676532 37888888876 78999985 5567666543
No 69
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=57.67 E-value=6 Score=38.46 Aligned_cols=40 Identities=18% Similarity=0.172 Sum_probs=35.7
Q ss_pred CCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 016170 91 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 131 (394)
Q Consensus 91 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 131 (394)
++..++.++|+++++..|+++-+.+.|.++||+++.. +.|
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~-~~y 60 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED-GKW 60 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC-CcE
Confidence 4688999999999999999999999999999999863 443
No 70
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=57.09 E-value=40 Score=29.05 Aligned_cols=35 Identities=17% Similarity=0.250 Sum_probs=32.5
Q ss_pred eecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 93 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 93 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
.+...++|+.|++.+-.+--+++.||.-|+|+|..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 46789999999999999999999999999999983
No 71
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=56.81 E-value=5.3 Score=40.98 Aligned_cols=29 Identities=34% Similarity=0.634 Sum_probs=26.7
Q ss_pred HHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 96 LNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 96 Ln~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
+..+++.+++++||+|||+|-|+.+|+|.
T Consensus 304 y~~~~~~~~~~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 304 YESLCERLRTSQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHhhhCchHHHHHHHHHHHHhcCeEE
Confidence 46788888899999999999999999998
No 72
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=56.78 E-value=27 Score=26.96 Aligned_cols=36 Identities=22% Similarity=0.333 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 016170 147 DASILQADIDNLSMEELRVDEQTRELRERLRELIEN 182 (394)
Q Consensus 147 ~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted 182 (394)
....++.++..|+.+-+.|.+.+..+++++..|..|
T Consensus 18 ~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~ 53 (80)
T PF04977_consen 18 RYYQLNQEIAELQKEIEELKKENEELKEEIERLKND 53 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 356777888888888888888888888888888333
No 73
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=56.49 E-value=44 Score=32.13 Aligned_cols=88 Identities=20% Similarity=0.203 Sum_probs=57.3
Q ss_pred CCcHHHHHHHHHHHHhhCCCCeecHHHH-----------HHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCC
Q 016170 72 DSSLGLLTKKFINLIKHAEDGILDLNKA-----------AETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSI 140 (394)
Q Consensus 72 d~SLglLTkKFi~Ll~~ap~g~ldLn~a-----------A~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~ 140 (394)
.+.+....++..+++....+.+...+.- .-.+.|..-++-+.++-|.++|-+...+-+
T Consensus 58 v~d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g~v~~~~~~----------- 126 (262)
T PF14257_consen 58 VKDVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSELGKVTSRNIS----------- 126 (262)
T ss_pred ECCHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhccCceeeeecc-----------
Confidence 3456666777777887776555444432 345667888999999999999866544221
Q ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 141 PGEVDADASILQADIDNLSMEELRVDEQTR 170 (394)
Q Consensus 141 ~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~ 170 (394)
..++..+...+++.+++|+.++++|-++++
T Consensus 127 ~~DvT~~y~D~~arl~~l~~~~~rl~~ll~ 156 (262)
T PF14257_consen 127 SEDVTEQYVDLEARLKNLEAEEERLLELLE 156 (262)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 224445555666777777777777666654
No 74
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=56.48 E-value=9.4 Score=29.21 Aligned_cols=51 Identities=24% Similarity=0.276 Sum_probs=40.3
Q ss_pred HHHHHHHHHhhCC----------CCeecHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 78 LTKKFINLIKHAE----------DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 78 LTkKFi~Ll~~ap----------~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
|+.-|+.++...+ ...+...++|+.+|+.++.+--+++-|+.-|+|++..+
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 5566666665432 12467899999999999999999999999999997644
No 75
>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=56.46 E-value=12 Score=31.36 Aligned_cols=45 Identities=16% Similarity=0.324 Sum_probs=39.5
Q ss_pred HHHHh--hCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 83 INLIK--HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 83 i~Ll~--~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
+.++. .++.+.+.+.++|+.|++.+=.+-=+++-||.-|+|.|..
T Consensus 31 L~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 31 LYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred HHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 44444 5577899999999999999999999999999999999873
No 76
>PRK06474 hypothetical protein; Provisional
Probab=56.43 E-value=96 Score=28.70 Aligned_cols=46 Identities=13% Similarity=0.223 Sum_probs=38.5
Q ss_pred HHHHHHhhCCCCeecHHHHHHHh-ccceeehhhhHHHhhhccchhhcc
Q 016170 81 KFINLIKHAEDGILDLNKAAETL-EVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
+.+.+|...+. .+...++++.| ++.+=-+|-.+++|+-.|||++..
T Consensus 15 ~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 15 KICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence 56667766544 39999999999 789999999999999999999754
No 77
>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=56.33 E-value=13 Score=35.10 Aligned_cols=44 Identities=16% Similarity=0.181 Sum_probs=37.0
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
.++++..+ ...+.+.++|+.||+.|=.+|-+++-|+..|++++.
T Consensus 14 IL~~l~~~-~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~ 57 (248)
T TIGR02431 14 VIEAFGAE-RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSD 57 (248)
T ss_pred HHHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 34444443 456899999999999999999999999999999975
No 78
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.15 E-value=8.3 Score=33.78 Aligned_cols=40 Identities=35% Similarity=0.381 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 76 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 76 glLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
++||+|=..++.--=..-++|.++|+.++|+|-.|||=++
T Consensus 16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK 55 (105)
T COG2739 16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK 55 (105)
T ss_pred HHHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence 5788776666554444568999999999999999999765
No 79
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=56.11 E-value=43 Score=28.60 Aligned_cols=54 Identities=17% Similarity=0.228 Sum_probs=36.9
Q ss_pred CCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 128 KNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 128 KN~i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
+.-+.|.|.+..--..+++-+.-|+..++.|...-..|.+.|.++++++..+.+
T Consensus 68 ~~v~v~iG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i~~ 121 (126)
T TIGR00293 68 DKVLVSIGSGYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQ 121 (126)
T ss_pred CEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455778887654323445556677777777777777777777777777776644
No 80
>PRK00215 LexA repressor; Validated
Probab=54.97 E-value=13 Score=34.29 Aligned_cols=42 Identities=14% Similarity=0.150 Sum_probs=36.9
Q ss_pred hCCCCeecHHHHHHHhcc-ceeehhhhHHHhhhccchhhccCC
Q 016170 88 HAEDGILDLNKAAETLEV-QKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 88 ~ap~g~ldLn~aA~~L~V-qKRRIYDItNVLEgIGLIeK~sKN 129 (394)
...+....+.++|+.|++ .|=.++.+++-||.-|+|++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 445667899999999999 999999999999999999987544
No 81
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=54.72 E-value=18 Score=31.21 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHH
Q 016170 75 LGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 116 (394)
Q Consensus 75 LglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 116 (394)
-.....++++++.......++|.++|+.+|+.+|.|.-+..-
T Consensus 7 ~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 7 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred cHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 355667999999999999999999999999999998776643
No 82
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=54.55 E-value=72 Score=31.33 Aligned_cols=43 Identities=19% Similarity=0.417 Sum_probs=33.4
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhh
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 125 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 125 (394)
++.+.+|.+-| .=..+++..|||....|-+=.-.||--|||+-
T Consensus 18 R~Il~lLt~~p---~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 18 RRILQLLTRRP---CYVSEISRELGVSQKAVLKHLRILERAGLVES 60 (217)
T ss_pred HHHHHHHhcCc---hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchh
Confidence 45777777766 34467788899988888888888888888875
No 83
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=53.86 E-value=32 Score=32.76 Aligned_cols=39 Identities=23% Similarity=0.263 Sum_probs=35.8
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
....+.|.++++.||++|=++-=.+-+|++.||+.|+-+
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~ 76 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFE 76 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhc
Confidence 367899999999999999999999999999999999843
No 84
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=53.58 E-value=27 Score=33.79 Aligned_cols=49 Identities=16% Similarity=0.165 Sum_probs=39.4
Q ss_pred HHHHHH-hhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 016170 81 KFINLI-KHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 81 KFi~Ll-~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
|.|.++ .......+...++|+.|++.+..+.-+++-||--|+|+|....
T Consensus 8 k~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~ 57 (217)
T PRK14165 8 KKLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVP 57 (217)
T ss_pred HHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcC
Confidence 334433 3344557899999999999999999999999999999998543
No 85
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=53.23 E-value=33 Score=29.56 Aligned_cols=79 Identities=22% Similarity=0.241 Sum_probs=0.0
Q ss_pred ecHHHHHHHhcccee--ehhhhHHHhhhccchh--hccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHHH--
Q 016170 94 LDLNKAAETLEVQKR--RIYDITNVLEGIGLIE--KKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSME-- 161 (394)
Q Consensus 94 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIe--K~sKN~i~W~G~~~s~~~~~~~~~~~Lq------~El~~L~~~-- 161 (394)
+.+.++|+.+||++| |.| |.+|||. +...|.|++-..... ..-..+..|+ +|+..+-..
T Consensus 1 m~IgevA~~~gvs~~tLRyY------e~~GLl~p~~r~~~gyR~Y~~~~l---~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYY------EKEGLLPAPARSANNYRLYDEEHL---ERLLFIRRCRSLDMSLDEIRTLLQLQD 71 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHH------HHCCCCCCCCcCCCCCeecCHHHH---HHHHHHHHHHHcCCCHHHHHHHHHhhh
Q ss_pred ---------HHHHHHHHHHHHHHHHHHhh
Q 016170 162 ---------ELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 162 ---------E~~LDe~I~~~~~~L~~Lte 181 (394)
...|.+++..+.+++.+|..
T Consensus 72 ~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd04784 72 DPEASCAEVNALIDEHLAHVRARIAELQA 100 (127)
T ss_pred cCCCcHHHHHHHHHHHHHHHHHHHHHHHH
No 86
>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=52.74 E-value=11 Score=29.82 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=34.6
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccc-eeehhhhHHHhhhccchhhcc
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQ-KRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIGLIeK~s 127 (394)
||.-+....+-.-.+.++|+.||+. ..-++..+..||.-|+|++..
T Consensus 14 ~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 14 FIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 3333333445567999999999996 999999999999999999873
No 87
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=52.69 E-value=13 Score=35.96 Aligned_cols=44 Identities=20% Similarity=0.302 Sum_probs=38.2
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
+.+++++ ..+.+.+.++|+.|+|++.-|+--++.||..|+|.|.
T Consensus 9 ~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 9 ILLELLA--QLGFVTVEKVIERLGISPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 4555665 4788999999999999999999889999999999885
No 88
>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=52.19 E-value=1.3e+02 Score=27.09 Aligned_cols=55 Identities=20% Similarity=0.260 Sum_probs=31.0
Q ss_pred HHHHHhhCCCCeecHHHHHHHhc--cceeehhhhHHHhhhccchh-hc-cCCeEEEeccC
Q 016170 82 FINLIKHAEDGILDLNKAAETLE--VQKRRIYDITNVLEGIGLIE-KK-LKNRIRWKGLD 137 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIe-K~-sKN~i~W~G~~ 137 (394)
.++||+. .+.+++.+.+..-|+ |.|=-+==+..-|..=|.|. |. +|-.|-|.--+
T Consensus 6 Il~y~~~-qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 6 ILEYMKE-QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQD 64 (169)
T ss_pred HHHHHHH-cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecceEEEeeCcc
Confidence 3455544 467788888888885 55544333344444444443 43 56667665433
No 89
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=52.10 E-value=10 Score=30.39 Aligned_cols=32 Identities=28% Similarity=0.333 Sum_probs=30.1
Q ss_pred HHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 96 LNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 96 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
+.++|+.|++.+=.++.++.-|+.-|||.+..
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 56899999999999999999999999999985
No 90
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=50.98 E-value=36 Score=29.00 Aligned_cols=84 Identities=19% Similarity=0.235 Sum_probs=43.6
Q ss_pred HHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCC------CCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 96 LNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIP------GEVDADASILQADIDNLSMEELRVDEQT 169 (394)
Q Consensus 96 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~Lq~El~~L~~~E~~LDe~I 169 (394)
+..++..+..-.+.+=....|++.+.-+. -+...|+=.|.-.... .++..++..+...++.|..+...|...+
T Consensus 19 ~~~l~~q~~~le~~~~E~~~v~~eL~~l~-~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l 97 (110)
T TIGR02338 19 LQAVATQKQQVEAQLKEAEKALEELERLP-DDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQL 97 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344443333333444555555555554 2334444444322211 1233445556666777777777777777
Q ss_pred HHHHHHHHHHh
Q 016170 170 RELRERLRELI 180 (394)
Q Consensus 170 ~~~~~~L~~Lt 180 (394)
..++++|+.+.
T Consensus 98 ~e~q~~l~~~~ 108 (110)
T TIGR02338 98 KELQEKIQEAL 108 (110)
T ss_pred HHHHHHHHHHh
Confidence 77777777653
No 91
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=50.98 E-value=88 Score=26.97 Aligned_cols=37 Identities=16% Similarity=0.196 Sum_probs=26.7
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 135 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 135 (394)
.+.++|..+||..|-| =-.|-+|||. +...|.|++-+
T Consensus 2 ~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~ 40 (126)
T cd04783 2 TIGELAKAAGVNVETI----RYYQRRGLLPEPPRPEGGYRRYP 40 (126)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCeecC
Confidence 5788999999988855 3348899997 34566677653
No 92
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=50.89 E-value=20 Score=30.10 Aligned_cols=76 Identities=17% Similarity=0.195 Sum_probs=41.0
Q ss_pred HHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCC------CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 100 AETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIP------GEVDADASILQADIDNLSMEELRVDEQTRELR 173 (394)
Q Consensus 100 A~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~ 173 (394)
-..|..+++...++.+-|+.+. -..+.|+=.|.-.... ..+..++..+..+++.|..+...|...+..++
T Consensus 22 ~~~l~~~~~E~~~v~~EL~~l~----~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk 97 (105)
T cd00632 22 RQKVEAQLNENKKALEELEKLA----DDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQ 97 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC----CcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445567777888888777765 2223333344322211 01233344555566666666666666666666
Q ss_pred HHHHHH
Q 016170 174 ERLREL 179 (394)
Q Consensus 174 ~~L~~L 179 (394)
..|+++
T Consensus 98 ~~l~~~ 103 (105)
T cd00632 98 EKIQQA 103 (105)
T ss_pred HHHHHH
Confidence 666654
No 93
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=50.82 E-value=17 Score=31.89 Aligned_cols=36 Identities=14% Similarity=0.325 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehh
Q 016170 76 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIY 111 (394)
Q Consensus 76 glLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIY 111 (394)
..+..-|++|++..+=..+.++++|++-||.|.-+|
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 356778999999999999999999999999999987
No 94
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=50.58 E-value=1.4e+02 Score=27.25 Aligned_cols=32 Identities=38% Similarity=0.502 Sum_probs=24.0
Q ss_pred cHHHHHHHHHHHHhhCCCCeecHHHHHHHhcc
Q 016170 74 SLGLLTKKFINLIKHAEDGILDLNKAAETLEV 105 (394)
Q Consensus 74 SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L~V 105 (394)
+|..|+..|.+++....++.+|-..+++.|.-
T Consensus 2 ~LYel~~~~~~l~~~~e~~~~d~e~~~dtLe~ 33 (162)
T PF05565_consen 2 KLYELTDEYLELLELLEEGDLDEEAIADTLES 33 (162)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 68889999999997776666777766655543
No 95
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=50.47 E-value=32 Score=27.96 Aligned_cols=80 Identities=18% Similarity=0.354 Sum_probs=34.6
Q ss_pred HHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCC-CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 97 NKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIP-GEVDADASILQADIDNLSMEELRVDEQTRELRER 175 (394)
Q Consensus 97 n~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~-~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~ 175 (394)
..+...+.--++.+..+.-|++-|..+. .+...|++++..-. .....-...|+++++.+..+-..|...++.+..+
T Consensus 15 ~~~~~q~~~l~~~~~~~~~~~~eL~~l~---~~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~ 91 (106)
T PF01920_consen 15 QQLEQQIQQLERQLRELELTLEELEKLD---DDRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKK 91 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTSS---TT-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCC---CcchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444333333444444555554443 34566766544311 1122223444444444444444444444444444
Q ss_pred HHHH
Q 016170 176 LREL 179 (394)
Q Consensus 176 L~~L 179 (394)
|.++
T Consensus 92 l~~~ 95 (106)
T PF01920_consen 92 LKEL 95 (106)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 4443
No 96
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=50.17 E-value=21 Score=29.33 Aligned_cols=40 Identities=15% Similarity=0.168 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHH
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 116 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 116 (394)
.+..+++.++.......+++.++|+.+++++|.+.-+..=
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3567888999888888999999999999999998877653
No 97
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=50.14 E-value=39 Score=30.26 Aligned_cols=71 Identities=17% Similarity=0.261 Sum_probs=42.1
Q ss_pred hhHHHhhhccchhhccCCeEEEeccCCCCC------CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 016170 112 DITNVLEGIGLIEKKLKNRIRWKGLDNSIP------GEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIENE 183 (394)
Q Consensus 112 DItNVLEgIGLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~ 183 (394)
+|.-||+-+..+.--. .-|+=.|.-.... .++.++...|.-+++-|+.+|+.|++.+..++..|+.+..+.
T Consensus 38 E~~~al~Ele~l~eD~-~vYk~VG~llvk~~k~~~~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~l~~~ 114 (119)
T COG1382 38 EIEKALEELEKLDEDA-PVYKKVGNLLVKVSKEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSEIQKALGDA 114 (119)
T ss_pred HHHHHHHHHhcCCccc-HHHHHhhhHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4666677666655331 2222233221111 133445556666777788888888888888888888776553
No 98
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=49.75 E-value=37 Score=28.67 Aligned_cols=35 Identities=26% Similarity=0.284 Sum_probs=23.6
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEE
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRW 133 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W 133 (394)
.+.++|+.+||..|.|.-. |..|||. ....|.+++
T Consensus 2 ~i~e~a~~~gvs~~tlr~y----e~~gll~~~~r~~~gyR~ 38 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYY----EKEGLLPPVKRDENGIRD 38 (113)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCcc
Confidence 5788999999998866433 5678883 334455554
No 99
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=49.13 E-value=13 Score=38.95 Aligned_cols=47 Identities=21% Similarity=0.217 Sum_probs=35.0
Q ss_pred cHHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 74 SLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 74 SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
....+.-.|+.++ ||..+|-++|+++++.-++++|+.+.|...|||+
T Consensus 340 ~~~~~~l~~L~~~----DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 340 AQQMAMLWVLNYS----DGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp --HHHHHHHHHH-----EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHHhc----cCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 3444444555555 8999999999999999999999999999999985
No 100
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=48.22 E-value=39 Score=29.42 Aligned_cols=37 Identities=22% Similarity=0.249 Sum_probs=25.1
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 135 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 135 (394)
.+.++|+.+||..+-|. ..|.+||+. +...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tlR----~Ye~~GLl~~~~r~~~gyR~Y~ 40 (127)
T TIGR02047 2 KIGELAQKTGVSVETIR----FYEKQGLLPPPARTDNNYRVYT 40 (127)
T ss_pred cHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCCCcCC
Confidence 47788999999887553 235678884 45566676643
No 101
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=48.04 E-value=93 Score=29.68 Aligned_cols=52 Identities=6% Similarity=0.222 Sum_probs=40.6
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEec
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKG 135 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G 135 (394)
.++++.. .+.+.+.++|+.|++.|=.+|-+++.|+..|++++...+.--..|
T Consensus 19 IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG 70 (257)
T PRK15090 19 ILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLT 70 (257)
T ss_pred HHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEec
Confidence 4445543 346899999999999999999999999999999987543322344
No 102
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=47.93 E-value=36 Score=30.99 Aligned_cols=41 Identities=20% Similarity=0.283 Sum_probs=37.1
Q ss_pred CCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 016170 89 AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 89 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
.|+..+.-.++|+.|||+|=-+=+.+..|+.-|||+...+.
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~ 70 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNR 70 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCC
Confidence 57888999999999999999999999999999999976443
No 103
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=47.60 E-value=19 Score=28.83 Aligned_cols=44 Identities=23% Similarity=0.277 Sum_probs=35.6
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
++..+...++... .++|+.|++.+=.+.-+++-||.-|+|++..
T Consensus 27 ~L~~l~~~~~~~~--~~la~~l~i~~~~vt~~l~~Le~~glv~r~~ 70 (126)
T COG1846 27 VLLALYEAGGITV--KELAERLGLDRSTVTRLLKRLEDKGLIERLR 70 (126)
T ss_pred HHHHHHHhCCCcH--HHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence 3444445444444 9999999999999999999999999999883
No 104
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=47.59 E-value=21 Score=32.65 Aligned_cols=48 Identities=17% Similarity=0.263 Sum_probs=38.9
Q ss_pred HHHHHHHh---hCCCCeecHHHHHHHhccc-eeehhhhHHHhhhccchhhcc
Q 016170 80 KKFINLIK---HAEDGILDLNKAAETLEVQ-KRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 80 kKFi~Ll~---~ap~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIGLIeK~s 127 (394)
++.+.++. ...+....+.++|+.|++. +=-++..++.||..|+|++..
T Consensus 9 ~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 9 QEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 34555554 3334458899999999998 999999999999999999974
No 105
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=47.46 E-value=21 Score=31.04 Aligned_cols=38 Identities=21% Similarity=0.307 Sum_probs=34.0
Q ss_pred hCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhh
Q 016170 88 HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 125 (394)
Q Consensus 88 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 125 (394)
+..++.+.+.++|+.+++..+-+..|+..|.--|||.-
T Consensus 20 ~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 20 NAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 33455899999999999999999999999999999974
No 106
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=47.44 E-value=17 Score=31.19 Aligned_cols=34 Identities=6% Similarity=0.108 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 148 ASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 148 ~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
...++++++.++++-++|.+....++.++..|.+
T Consensus 29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 29 YWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3344455555555545555555555555555544
No 107
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=47.18 E-value=20 Score=33.91 Aligned_cols=44 Identities=25% Similarity=0.354 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhc
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGI 120 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgI 120 (394)
.+..+|+.++.+.....++|..+|+.+++++|.|..+..-..|+
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~ 229 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSAL 229 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCC
Confidence 45688999998888889999999999999999999887654433
No 108
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=46.34 E-value=20 Score=36.00 Aligned_cols=52 Identities=27% Similarity=0.440 Sum_probs=41.8
Q ss_pred CcHHHHHH-HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 73 SSLGLLTK-KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 73 ~SLglLTk-KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
++|+..++ +.++||. ..+.+++|++|+.||...--+--=+.|||-.|||+-.
T Consensus 18 kalaS~vRv~Il~lL~--~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 18 KALASKVRVAILQLLH--RKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHH--HhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 45666664 4555664 4678999999999999999999999999999999854
No 109
>PRK09343 prefoldin subunit beta; Provisional
Probab=46.24 E-value=48 Score=29.02 Aligned_cols=71 Identities=18% Similarity=0.316 Sum_probs=44.9
Q ss_pred eehhhhHHHhhhccchhhccCCeEEEeccCCC--CC------CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 108 RRIYDITNVLEGIGLIEKKLKNRIRWKGLDNS--IP------GEVDADASILQADIDNLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 108 RRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s--~~------~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
+.+=..-.|++.+..+. .+.-.|++.... .. .++..++..+..+++.|+.++..|.+.+..++.+|+.+
T Consensus 35 ~q~~e~~~~~~EL~~L~---~d~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l~~l 111 (121)
T PRK09343 35 LELREINKALEELEKLP---DDTPIYKIVGNLLVKVDKTKVEKELKERKELLELRSRTLEKQEKKLREKLKELQAKINEM 111 (121)
T ss_pred HHHHHHHHHHHHHHcCC---CcchhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445566666666555 333334443322 11 12344566677788888889999999999999999887
Q ss_pred hh
Q 016170 180 IE 181 (394)
Q Consensus 180 te 181 (394)
..
T Consensus 112 l~ 113 (121)
T PRK09343 112 LS 113 (121)
T ss_pred HH
Confidence 65
No 110
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=45.40 E-value=18 Score=38.26 Aligned_cols=76 Identities=22% Similarity=0.316 Sum_probs=48.3
Q ss_pred ccceeehhhhHHHhhhcc-chhhccCCeEEEeccCCCCCCCchHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q 016170 104 EVQKRRIYDITNVLEGIG-LIEKKLKNRIRWKGLDNSIPGEVDADASILQADID---NLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 104 ~VqKRRIYDItNVLEgIG-LIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lq~El~---~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
.|.|||=|-|=+-.--+| ||-|.+-+..+|. ...+-. ...+-+..||++.+ ++....+.|+.-++.+.+++++|
T Consensus 239 eVERRRR~nIN~~IkeLg~liP~~~~~~~~~n-KgtILk-~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~~rieeL 316 (411)
T KOG1318|consen 239 EVERRRRENINDRIKELGQLIPKCNSEDMKSN-KGTILK-ASCDYIRELQQTLQRARELENRQKKLESTNQELALRIEEL 316 (411)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCcchhhcc-cchhhH-HHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHHHHHHHH
Confidence 478888776655444443 7788888888886 222211 22344666766554 55566677777788888777777
Q ss_pred hh
Q 016170 180 IE 181 (394)
Q Consensus 180 te 181 (394)
..
T Consensus 317 k~ 318 (411)
T KOG1318|consen 317 KS 318 (411)
T ss_pred HH
Confidence 44
No 111
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=45.07 E-value=24 Score=30.47 Aligned_cols=50 Identities=18% Similarity=0.300 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 75 LGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 75 LglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
|-.+=++-+++|+. ++...+.++|++||++...+...+.-||.-|+|.+.
T Consensus 6 lD~~D~~IL~~L~~--d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 6 LDDIDRRILRLLQE--DARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred ccHHHHHHHHHHHH--hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeE
Confidence 44455778888866 555999999999999999999999999999999977
No 112
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=44.62 E-value=63 Score=25.40 Aligned_cols=39 Identities=15% Similarity=0.454 Sum_probs=29.7
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 143 EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 143 ~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
+++.++.++...+..++.+-+.|-+.|..+.+.++.|..
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll~ 42 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEENVKDLLS 42 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677777777888888888888888888888877654
No 113
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=44.59 E-value=1.1e+02 Score=29.91 Aligned_cols=49 Identities=16% Similarity=0.261 Sum_probs=39.9
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCe
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNR 130 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~ 130 (394)
.+.+++|++ .+.+.+.++|+.|+|+.+-|.-=+..||.-|++.|.....
T Consensus 20 ~~Il~~L~~--~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GGa 68 (269)
T PRK09802 20 EQIIQRLRQ--QGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGA 68 (269)
T ss_pred HHHHHHHHH--cCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCCE
Confidence 345667766 4459999999999999999988888899999999886443
No 114
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=44.39 E-value=39 Score=31.46 Aligned_cols=41 Identities=27% Similarity=0.280 Sum_probs=38.0
Q ss_pred hCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 88 HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 88 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
-.|+..|+.+++|+.|||+|--|=+.+..|++-|||+....
T Consensus 34 l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~ 74 (230)
T COG1802 34 LAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPN 74 (230)
T ss_pred CCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCC
Confidence 35899999999999999999999999999999999999843
No 115
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=44.32 E-value=27 Score=32.17 Aligned_cols=39 Identities=21% Similarity=0.228 Sum_probs=35.3
Q ss_pred eecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 016170 93 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 131 (394)
Q Consensus 93 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 131 (394)
.++..++|+.|++.++-++..+..|+--++|.|...+.|
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y 113 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAY 113 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeE
Confidence 678899999999999999999999999999999865544
No 116
>PRK11050 manganese transport regulator MntR; Provisional
Probab=44.00 E-value=37 Score=30.37 Aligned_cols=54 Identities=24% Similarity=0.244 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHh--hCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 75 LGLLTKKFINLIK--HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 75 LglLTkKFi~Ll~--~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
...+...++..+. -..++.+.+.++|+.|++.+-.+..+++-||.-|+|.+...
T Consensus 31 ~~~~~e~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~ 86 (152)
T PRK11050 31 RRELIEDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPY 86 (152)
T ss_pred hHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3444445444332 12246689999999999999999999999999999998643
No 117
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=44.00 E-value=38 Score=31.57 Aligned_cols=39 Identities=18% Similarity=0.192 Sum_probs=33.9
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 132 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 132 (394)
+.-.++|..||++|..+.-+++-|+--|+|++...++|.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 445899999999999999999999999999877655664
No 118
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=43.79 E-value=9.1 Score=38.15 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=23.7
Q ss_pred CeecHHHHHHHhccceeehhhhHHHhhhcc
Q 016170 92 GILDLNKAAETLEVQKRRIYDITNVLEGIG 121 (394)
Q Consensus 92 g~ldLn~aA~~L~VqKRRIYDItNVLEgIG 121 (394)
.-+-|..+=--||..+|=+||.+||+||=-
T Consensus 39 ~DiGLRNLDlimGlE~RiVYd~vdVi~g~~ 68 (272)
T COG2894 39 FDIGLRNLDLIMGLENRIVYDLVDVIEGEA 68 (272)
T ss_pred cCcCchhhhhhhcccceeeeeehhhhcCcc
Confidence 344555555678999999999999999854
No 119
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=43.41 E-value=50 Score=35.16 Aligned_cols=49 Identities=27% Similarity=0.409 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHhhCC--CCeecHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 76 GLLTKKFINLIKHAE--DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 76 glLTkKFi~Ll~~ap--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
..|-+.|+.|++... ...+.|.++|+.|++++|-.==|+|-|+..|.|+
T Consensus 4 ~~~~~~~~~L~~~~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~ 54 (552)
T PRK13626 4 ARLQQQFIRLWQCCEGKSQETTLNELAELLNCSRRHMRTLLNTMQQRGWLT 54 (552)
T ss_pred hHHHHHHHHHHHhcCCCcceeeHHHHHHHhcCChhHHHHHHHHHHHCCCee
Confidence 367788999987643 5589999999999999999999999999988876
No 120
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=43.28 E-value=19 Score=24.48 Aligned_cols=23 Identities=26% Similarity=0.225 Sum_probs=19.9
Q ss_pred ecHHHHHHHhccceeehhhhHHH
Q 016170 94 LDLNKAAETLEVQKRRIYDITNV 116 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNV 116 (394)
+++.++|+.|+|.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999999988763
No 121
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=43.15 E-value=27 Score=28.91 Aligned_cols=45 Identities=22% Similarity=0.412 Sum_probs=38.0
Q ss_pred HHHHHhhCCCCeecHHHHHHHh-----ccceeehhhhHHHhhhccchhhcc
Q 016170 82 FINLIKHAEDGILDLNKAAETL-----EVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L-----~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
.++++..+ ++.++..++.+.| .+.+=-+|-+++.|+..|+|.|..
T Consensus 6 Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 6 ILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEE
Confidence 45666655 6778999999998 588999999999999999999874
No 122
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=43.03 E-value=69 Score=29.56 Aligned_cols=46 Identities=11% Similarity=0.044 Sum_probs=39.4
Q ss_pred CCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 016170 89 AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 134 (394)
Q Consensus 89 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 134 (394)
.|+..|...++|+.|||+|==|=+.+..|+.-|||+...+.-+.-.
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~ 71 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVA 71 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeC
Confidence 4788899999999999999999999999999999997755544433
No 123
>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=42.87 E-value=26 Score=32.47 Aligned_cols=45 Identities=27% Similarity=0.321 Sum_probs=38.0
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
+.+.++.+ .+.+.+.++|+.|++.+-.++-.++-|+..|+|++..
T Consensus 147 ~IL~~l~~--~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 147 KVLEVLKA--EGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred HHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 34444443 3568999999999999999999999999999999986
No 124
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=42.65 E-value=65 Score=29.62 Aligned_cols=33 Identities=9% Similarity=0.224 Sum_probs=18.1
Q ss_pred EEEEeCCCCCeEEecCCCccCCCCCCceEEEEecCCCceE
Q 016170 207 LIAIKAPQGTTLEVPDPDEAVDYPQRRYRIILRSTMGPID 246 (394)
Q Consensus 207 vIAIKAP~gT~LEVPdP~e~~~~~~r~YqI~LkS~~GPId 246 (394)
.|.|+.-+.|.+++-..++. ..++.+-..-|..
T Consensus 59 FIlV~T~~~a~I~ceiS~D~-------~~~~F~Fn~~pFe 91 (142)
T PF08781_consen 59 FILVNTSKKAVIECEISEDK-------SEYHFDFNSTPFE 91 (142)
T ss_dssp -EEEEEESS--EEEEE-TTS-------SEEEEEESS--EE
T ss_pred EEEEEecCCcEEEEEEcCCc-------cEEEEEcCCCcee
Confidence 68999999999999765542 3345555544443
No 125
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=42.12 E-value=22 Score=32.62 Aligned_cols=39 Identities=18% Similarity=0.247 Sum_probs=35.0
Q ss_pred hCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 88 HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 88 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
...++.+.+.++|+.+++.++-+..|++-|.--|||.-.
T Consensus 20 ~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 20 NSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 344568999999999999999999999999999999953
No 126
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=41.67 E-value=38 Score=28.13 Aligned_cols=58 Identities=24% Similarity=0.452 Sum_probs=45.0
Q ss_pred cHHHHHHHHHHHHhhC-CCCeecHHHHHHHhccceeehhhhHH-HhhhccchhhccCCeE
Q 016170 74 SLGLLTKKFINLIKHA-EDGILDLNKAAETLEVQKRRIYDITN-VLEGIGLIEKKLKNRI 131 (394)
Q Consensus 74 SLglLTkKFi~Ll~~a-p~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~sKN~i 131 (394)
-|..+=++++..+.+. .+|.+-|+.+|..|+..+.-|=|++- -|--.|+|+|+.+.++
T Consensus 5 GLd~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT~rGR~ 64 (76)
T PF05491_consen 5 GLDELDRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRTPRGRV 64 (76)
T ss_dssp S-BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEETTEEE
T ss_pred cCCHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhCccHHH
Confidence 4556778899977654 89999999999999999999888764 6778999999988764
No 127
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=41.10 E-value=21 Score=25.44 Aligned_cols=36 Identities=19% Similarity=0.344 Sum_probs=22.3
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhcc
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIG 121 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIG 121 (394)
.|.++.+ -....++|+.|||.++-+|.|++=.+.-|
T Consensus 10 ii~l~~~----G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 10 IIRLLRE----GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHHHHHH----T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HHHHHHC----CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 4555554 46889999999999999999988765433
No 128
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=41.02 E-value=12 Score=26.93 Aligned_cols=32 Identities=19% Similarity=0.456 Sum_probs=22.5
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
...+.|+. .| +.+.++|+.|||.|.-||-|.+
T Consensus 12 ~~i~~l~~---~G-~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 12 EEIKELYA---EG-MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHH---TT---HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHH---CC-CCHHHHHHHHCcCHHHHHHHHh
Confidence 34555653 34 8999999999999999998764
No 129
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=40.90 E-value=54 Score=36.45 Aligned_cols=65 Identities=22% Similarity=0.293 Sum_probs=46.5
Q ss_pred HHhhhccchhhccCCeEEEeccCCCCCC------CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 016170 115 NVLEGIGLIEKKLKNRIRWKGLDNSIPG------EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIEN 182 (394)
Q Consensus 115 NVLEgIGLIeK~sKN~i~W~G~~~s~~~------~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted 182 (394)
+-|..|.=|.+.+||++- ..+.+-. .++..+..|+.|-+.|..+...+|.-+..+.++|..|..+
T Consensus 484 ~QLslIrDIRRRgKNkvA---AQnCRKRKLd~I~nLE~ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls~L~~~ 554 (604)
T KOG3863|consen 484 EQLSLIRDIRRRGKNKVA---AQNCRKRKLDCILNLEDEVEKLQKEKEQLLRERDELDSTLGVMKQQLSELYQE 554 (604)
T ss_pred HHHHHhhccccccccchh---ccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578888889999999873 3333222 2344566677777777778888888899999998887654
No 130
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=40.86 E-value=83 Score=24.96 Aligned_cols=34 Identities=15% Similarity=0.283 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 148 ASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 148 ~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
+..+...+..|+.....++..|..+..+|..+.+
T Consensus 15 l~~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~ 48 (71)
T PF10779_consen 15 LDNHEERIDKLEKRDAANEKDIKNLNKQLEKIKS 48 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555666667777777777777777777755
No 131
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=40.69 E-value=56 Score=33.01 Aligned_cols=35 Identities=34% Similarity=0.482 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 016170 149 SILQADIDNLSMEELRVDEQTRELRERLRELIENE 183 (394)
Q Consensus 149 ~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~ 183 (394)
..|.+|++.|+.++.+|++.|..++.++..+.+.+
T Consensus 60 ~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE 94 (314)
T PF04111_consen 60 EELLQELEELEKEREELDQELEELEEELEELDEEE 94 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556777778888888888888887777765543
No 132
>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=40.47 E-value=32 Score=32.72 Aligned_cols=47 Identities=23% Similarity=0.403 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 78 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 78 LTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
|...||++++. ..++.|+++|..||+.-==+-+-++-|+.-|.|.=.
T Consensus 100 lL~~Fi~yIK~--~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv 146 (188)
T PF09756_consen 100 LLQEFINYIKE--HKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGV 146 (188)
T ss_dssp HHHHHHHHHHH---SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EE
T ss_pred HHHHHHHHHHH--cceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceee
Confidence 77899999988 568999999999999666666677777777776543
No 133
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=39.82 E-value=1.3e+02 Score=28.45 Aligned_cols=51 Identities=24% Similarity=0.220 Sum_probs=40.8
Q ss_pred HHHHHHHHHh---hCCCCee-cHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 78 LTKKFINLIK---HAEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 78 LTkKFi~Ll~---~ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
+...+.+.+. =.|+..+ .-.++|+.|||+|==+=+.+..|+.-|||+....
T Consensus 14 v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 68 (257)
T PRK10225 14 VGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRG 68 (257)
T ss_pred HHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4444444443 3578888 6999999999999999999999999999986643
No 134
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=39.50 E-value=30 Score=30.30 Aligned_cols=41 Identities=17% Similarity=0.267 Sum_probs=35.9
Q ss_pred hCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 88 HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 88 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
..++..+...++|+.++|.+.-+-.|+..|..-|||+....
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G 60 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecC
Confidence 34566899999999999999999999999999999986643
No 135
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=38.66 E-value=28 Score=28.99 Aligned_cols=42 Identities=19% Similarity=0.503 Sum_probs=33.5
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
.|.+-+-.+ ++.+.+.++|..|++.++++|++ |...|++-|.
T Consensus 13 ~~~d~~~~~-~~~~ti~~~AK~L~i~~~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 13 EFYDAFVDS-DGLYTIREAAKLLGIGRNKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHHcC-CCCccHHHHHHHhCCCHHHHHHH---HHhCCceEEC
Confidence 366655444 59999999999999999999876 6668888874
No 136
>PRK10130 transcriptional regulator EutR; Provisional
Probab=38.52 E-value=31 Score=35.19 Aligned_cols=40 Identities=10% Similarity=0.108 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 76 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 76 glLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
..+.+++++++....+..+++.++|+.++|++|.|+-...
T Consensus 239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk 278 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFH 278 (350)
T ss_pred HHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4577888899988888899999999999999999987664
No 137
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=38.50 E-value=20 Score=31.14 Aligned_cols=37 Identities=14% Similarity=0.127 Sum_probs=34.4
Q ss_pred CCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 91 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 91 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
.+.+...++|+.|++.|=.+--+++-||.-|+|+|..
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 4568999999999999999999999999999999973
No 138
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=37.81 E-value=20 Score=26.42 Aligned_cols=24 Identities=29% Similarity=0.538 Sum_probs=19.8
Q ss_pred CeecHHHHHHHhccceeehhhhHH
Q 016170 92 GILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 92 g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
..|+++++++.+|+.|..||..++
T Consensus 2 rll~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 2 RLLRIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp -EE-HHHHHHHHSS-HHHHHHHHH
T ss_pred ccccHHHHHHHHCCCHHHHHHHHh
Confidence 468999999999999999999987
No 139
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=37.40 E-value=89 Score=27.74 Aligned_cols=81 Identities=20% Similarity=0.156 Sum_probs=0.0
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccch--hhccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHH-----
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLI--EKKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSM----- 160 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLI--eK~sKN~i~W~G~~~s~~~~~~~~~~~Lq------~El~~L~~----- 160 (394)
+.+.++|+.+||+.|-|--. |-.||| .+...|.|++-..... ..-..+..|+ +|+..+-.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Y----e~~GLl~p~~r~~~gyR~Y~~~~l---~~l~~I~~lr~~G~sL~eI~~~l~~~~~~ 74 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFY----EKQGLMDPEVRTEGGYRLYTEQDL---QRLRFIRRAKQLGFTLEEIRELLSIRLDP 74 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCCeeeCHHHH---HHHHHHHHHHHcCCCHHHHHHHHHhcccC
Q ss_pred -------HHHHHHHHHHHHHHHHHHHhh
Q 016170 161 -------EELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 161 -------~E~~LDe~I~~~~~~L~~Lte 181 (394)
....|++++..+.+++.+|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (140)
T PRK09514 75 EHHTCQEVKGIVDEKLAEVEAKIAELQH 102 (140)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHH
No 140
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=36.74 E-value=1.2e+02 Score=28.51 Aligned_cols=55 Identities=18% Similarity=0.241 Sum_probs=43.0
Q ss_pred cHHH-HHHHHHHHHhh---CCCCee-cHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 74 SLGL-LTKKFINLIKH---AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 74 SLgl-LTkKFi~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
+|.. +...+.+.+.. .|+..| .-.++|+.|||+|=-+-+.+..|+..|||+...+
T Consensus 10 ~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 10 KLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4443 44555555543 467778 8999999999999999999999999999986643
No 141
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=36.23 E-value=1.3e+02 Score=26.15 Aligned_cols=47 Identities=21% Similarity=0.296 Sum_probs=39.7
Q ss_pred HHHHHHHHHhhCCCC--eecHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 78 LTKKFINLIKHAEDG--ILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 78 LTkKFi~Ll~~ap~g--~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
|...|..|++.-++. .+.|.++|+.|..++|-.==|++-|+..|.|+
T Consensus 2 l~~~y~~L~~~~~~~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~ 50 (115)
T PF12793_consen 2 LLEQYQRLWQHYGGQPVEVTLDELAELLFCSRRNARTLLKKMQEEGWIT 50 (115)
T ss_pred HHHHHHHHHHHcCCCCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 456788888776644 58999999999999999999999999888765
No 142
>PHA01750 hypothetical protein
Probab=36.22 E-value=80 Score=26.04 Aligned_cols=31 Identities=19% Similarity=0.481 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 146 ADASILQADIDNLSMEELRVDEQTRELRERL 176 (394)
Q Consensus 146 ~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L 176 (394)
+++.+|+.|++.+..+.++|.+++.++...+
T Consensus 42 ~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 42 SELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 3456666777777766666666666665544
No 143
>PF13551 HTH_29: Winged helix-turn helix
Probab=36.21 E-value=26 Score=28.24 Aligned_cols=28 Identities=18% Similarity=0.358 Sum_probs=26.2
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccc
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGL 122 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGL 122 (394)
.+.++|..||+.+|-||.+++-++.=|+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~ 41 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGI 41 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccH
Confidence 7999999999999999999999988883
No 144
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=36.21 E-value=41 Score=33.20 Aligned_cols=57 Identities=21% Similarity=0.379 Sum_probs=47.0
Q ss_pred CcHHHHHHHHHH-HHhhCCCCeecHHHHHHHhccceeehhhhHH-HhhhccchhhccCC
Q 016170 73 SSLGLLTKKFIN-LIKHAEDGILDLNKAAETLEVQKRRIYDITN-VLEGIGLIEKKLKN 129 (394)
Q Consensus 73 ~SLglLTkKFi~-Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~sKN 129 (394)
.-|...-++|+. +++.-.++.+.+..+|..||.....+-|++- .|-..|||++....
T Consensus 255 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 313 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRG 313 (328)
T ss_pred CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCch
Confidence 345556777886 6777788899999999999999999998888 88899999877544
No 145
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=35.93 E-value=31 Score=33.84 Aligned_cols=31 Identities=32% Similarity=0.584 Sum_probs=25.9
Q ss_pred HHHHHhc---cceeehhhhHHHhhhccchhhccC
Q 016170 98 KAAETLE---VQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 98 ~aA~~L~---VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
.+|+.++ +..|++|++++-||.+|||+-..+
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~ 352 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEER 352 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence 5677666 577999999999999999997643
No 146
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=35.91 E-value=38 Score=35.06 Aligned_cols=50 Identities=18% Similarity=0.167 Sum_probs=46.1
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHh-ccceeehhhhHHHhhhccchhhc
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETL-EVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
.+.++|+.++-...+..++++.+|+.+ ++.++-++.-++.||.+-|+-..
T Consensus 220 ~~~k~i~~~l~~~~g~~~s~~~la~~l~~is~~Ti~~Yl~~le~~fll~~~ 270 (398)
T COG1373 220 DLMKRILRFLASNIGSPISYSSLARELKGISKDTIRKYLSYLEDAFLLFLV 270 (398)
T ss_pred HHHHHHHHHHHhhcCCccCHHHHHHHHhccchHHHHHHHHHHHHhhheEEe
Confidence 577899999999999999999999999 89999999999999999999833
No 147
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=35.83 E-value=63 Score=28.21 Aligned_cols=47 Identities=19% Similarity=0.251 Sum_probs=37.7
Q ss_pred HHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 79 TKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 79 TkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
.+.|..++. ..+...+.++|+.|+|.+=.+--+++-|+.-|+|.+..
T Consensus 10 L~~I~~l~~--~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 10 IEQIYLLIE--EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHHHHh--cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence 334444443 35667899999999999999999999999999998653
No 148
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=35.69 E-value=1.1e+02 Score=26.72 Aligned_cols=81 Identities=17% Similarity=0.162 Sum_probs=0.0
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHHHH---
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSMEE--- 162 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G~~~s~~~~~~~~~~~Lq------~El~~L~~~E--- 162 (394)
+.+.++|+.+||+.+ -+-.-|..|||. +...|.|++-+.+.. ..-..+..|+ +|+..+-...
T Consensus 2 ~~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l---~~l~~I~~lr~~G~sl~eI~~~l~~~~~~ 74 (131)
T TIGR02043 2 FQIGELAKLCGVTSD----TLRFYEKNGLIKPAGRTDSGYRLYTDEDQ---KRLRFILKAKELGFTLDEIKELLSIKLDA 74 (131)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHHHH---HHHHHHHHHHHcCCCHHHHHHHHHhhccC
Q ss_pred ---------HHHHHHHHHHHHHHHHHhh
Q 016170 163 ---------LRVDEQTRELRERLRELIE 181 (394)
Q Consensus 163 ---------~~LDe~I~~~~~~L~~Lte 181 (394)
..|++++..+++++.+|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (131)
T TIGR02043 75 TEHSCAEVKAIVDAKLELVDEKINELTK 102 (131)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
No 149
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=35.64 E-value=37 Score=24.14 Aligned_cols=37 Identities=27% Similarity=0.417 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhh
Q 016170 75 LGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDI 113 (394)
Q Consensus 75 LglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDI 113 (394)
|..+=+.+|.-.-...+| ++..||+.||+.|+-||.=
T Consensus 2 l~~~E~~~i~~aL~~~~g--n~~~aA~~Lgisr~tL~~k 38 (42)
T PF02954_consen 2 LEEFEKQLIRQALERCGG--NVSKAARLLGISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHHHHHTTT---HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCC--CHHHHHHHHCCCHHHHHHH
Confidence 444556666643332333 4689999999999999853
No 150
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=35.12 E-value=49 Score=29.74 Aligned_cols=52 Identities=15% Similarity=0.286 Sum_probs=45.4
Q ss_pred CCcHHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhh
Q 016170 72 DSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 125 (394)
Q Consensus 72 d~SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 125 (394)
...|-.+=++.+.+|+. ++.+...++|+++|++.--++.=++=||.-|+|++
T Consensus 9 ~~~lD~~D~~IL~~Lq~--d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 9 GKDLDRIDRNILNELQK--DGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred hhhHHHHHHHHHHHhcc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 34577777899998865 88899999999999999999999999999999986
No 151
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=35.08 E-value=64 Score=26.95 Aligned_cols=47 Identities=23% Similarity=0.275 Sum_probs=38.0
Q ss_pred HHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 79 TKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 79 TkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
.+-.|+++... +..|-=..+|+.|++.-=-|..+.-.||.+|||+++
T Consensus 10 L~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 10 LKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 34456666543 667888888999999988999999999999999975
No 152
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=35.00 E-value=30 Score=28.13 Aligned_cols=42 Identities=17% Similarity=0.351 Sum_probs=35.8
Q ss_pred HhhCCCCeecHHHHHHHh-ccceeehhhhHHHhhhccchhhcc
Q 016170 86 IKHAEDGILDLNKAAETL-EVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 86 l~~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
+..-..|....+++.+.+ +++++-+.+=...|+..|||+|..
T Consensus 11 L~~l~~g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 11 LRALFQGPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHTTSSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHhCCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccc
Confidence 334345899999999999 899999999999999999999973
No 153
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=34.82 E-value=1.2e+02 Score=28.17 Aligned_cols=29 Identities=34% Similarity=0.416 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 149 SILQADIDNLSMEELRVDEQTRELRERLR 177 (394)
Q Consensus 149 ~~Lq~El~~L~~~E~~LDe~I~~~~~~L~ 177 (394)
+.++.+|..|.++-..||+.|+.+..+|.
T Consensus 25 q~~~~~I~~L~~e~~~ld~~i~~~~~~L~ 53 (188)
T PF10018_consen 25 QENQARIQQLRAEIEELDEQIRDILKQLK 53 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666666666666665555443
No 154
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=34.63 E-value=1.2e+02 Score=30.39 Aligned_cols=89 Identities=15% Similarity=0.155 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCHHHHhhcc---------CCCCceEEEEeCCCCCeEEecCCCcc
Q 016170 156 DNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLH---------CFQNQTLIAIKAPQGTTLEVPDPDEA 226 (394)
Q Consensus 156 ~~L~~~E~~LDe~I~~~~~~L~~Lted~~n~~~aYVT~eDI~~l~---------~f~~qTvIAIKAP~gT~LEVPdP~e~ 226 (394)
+.|...|..|++.|.--.+-|..-.++..+..++||+.+-+++-+ -|.+..+-|++=+-|+.+.++-++..
T Consensus 26 eEllkLe~DLkEvIsLTedLlqT~~ee~~sss~a~~ssq~~h~s~~~~~~~~~~l~~~~~i~a~~w~vg~K~~A~~~ddg 105 (262)
T KOG3026|consen 26 EELLKLEKDLKEVISLTEDLLQTQKEEDKSSSDAFVSSQPTHSSFTPRWVSGDYLFYPSRITAVGWKVGDKVQAVFSDDG 105 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccccCccccCCCchhhhhhhhccccccchhcccccCCEEEEeecCCC
Confidence 467778889999997555555554555556778899877666522 25677888899999999999988642
Q ss_pred CCCCCCceEEEEecCCC-ceEEEE
Q 016170 227 VDYPQRRYRIILRSTMG-PIDVYL 249 (394)
Q Consensus 227 ~~~~~r~YqI~LkS~~G-PIdVyL 249 (394)
+ -|...|..-.- ++.|-+
T Consensus 106 -~----~y~AtIe~ita~~~~~ai 124 (262)
T KOG3026|consen 106 -Q----IYDATIEHITAMEGTVAI 124 (262)
T ss_pred -c----eEEeehhhccCCCCceeE
Confidence 2 36666665433 344333
No 155
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=34.38 E-value=1.1e+02 Score=26.48 Aligned_cols=79 Identities=14% Similarity=0.113 Sum_probs=0.0
Q ss_pred HHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHH-------
Q 016170 96 LNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSM------- 160 (394)
Q Consensus 96 Ln~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G~~~s~~~~~~~~~~~Lq------~El~~L~~------- 160 (394)
+.++|+.+||..+-|--. |.+|||. +...|.|++-+.... +.-..+..|+ +|+..+-.
T Consensus 2 I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~Y~~~~l---~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~ 74 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRRYPEETV---KRLRFIKRAQELGFSLEEIGGLLGLVDGTHC 74 (124)
T ss_pred HHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEeECHHHH---HHHHHHHHHHHCCCCHHHHHHHHhcccCCCH
Q ss_pred --HHHHHHHHHHHHHHHHHHHhh
Q 016170 161 --EELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 161 --~E~~LDe~I~~~~~~L~~Lte 181 (394)
....|.+++..+++++.+|..
T Consensus 75 ~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 75 REMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
No 156
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=34.08 E-value=35 Score=27.21 Aligned_cols=41 Identities=20% Similarity=0.200 Sum_probs=32.2
Q ss_pred CCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 016170 91 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 132 (394)
Q Consensus 91 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 132 (394)
.+.....+++...++.-+++..+++-|+.-|||++ .++.|.
T Consensus 17 ~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y~ 57 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK-KDGKYR 57 (77)
T ss_dssp TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE-ETTEEE
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC-CCCEEE
Confidence 67788999999999999999999999999999955 455554
No 157
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=33.73 E-value=66 Score=29.60 Aligned_cols=37 Identities=22% Similarity=0.436 Sum_probs=26.9
Q ss_pred ecHHHHHHHhcccee--ehhhhHHHhhhccchh--hccCCeEEEecc
Q 016170 94 LDLNKAAETLEVQKR--RIYDITNVLEGIGLIE--KKLKNRIRWKGL 136 (394)
Q Consensus 94 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIe--K~sKN~i~W~G~ 136 (394)
+.+.++|+.+||.++ |.|| .+|||. +...|.|++-+.
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe------~~GLl~p~~r~~~gyR~Y~~ 42 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYE------RIGLLSPSARSESNYRLYGE 42 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHH------HCCCCCCCccCCCCCccCCH
Confidence 568899999999988 5564 577875 345677777643
No 158
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=33.62 E-value=45 Score=32.27 Aligned_cols=44 Identities=14% Similarity=0.160 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhc
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGI 120 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgI 120 (394)
.+..+.+.++..+....++|.++|+.+++++|.|.-+..-.-|+
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~ 48 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGH 48 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence 35678889999999999999999999999999988777654443
No 159
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=33.28 E-value=2e+02 Score=24.90 Aligned_cols=37 Identities=19% Similarity=0.219 Sum_probs=26.3
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh--ccCCeEEEec
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK--KLKNRIRWKG 135 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~sKN~i~W~G 135 (394)
.+.++|+.+||..+-|. ..|-.|||.. ...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tlR----yYe~~GLl~p~~r~~~gyR~Y~ 40 (127)
T TIGR02044 2 NIGQVAKLTGLSSKMIR----YYEEKGLIPPPLRSEGGYRTYT 40 (127)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCCeecC
Confidence 57889999999887654 4567888864 4467677643
No 160
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=33.13 E-value=27 Score=30.25 Aligned_cols=40 Identities=28% Similarity=0.390 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHH
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 116 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 116 (394)
+||.|=-.++.--=..-++|.++|+.+||+|=-+||.+.-
T Consensus 17 LLT~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp GS-HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4676544444444566799999999999999999998764
No 161
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=32.96 E-value=1.4e+02 Score=32.10 Aligned_cols=52 Identities=21% Similarity=0.254 Sum_probs=34.1
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH----Hhhhcc--chhhccCCeEEEeccC
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN----VLEGIG--LIEKKLKNRIRWKGLD 137 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN----VLEgIG--LIeK~sKN~i~W~G~~ 137 (394)
+.+.+|+ ++.+...++|+.|+|++|-|+-=++ +|++-| ++.+ ++-|+..+.+
T Consensus 8 ~iL~~L~---~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~--~~Gy~l~~~~ 65 (584)
T PRK09863 8 KIVDLLE---QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISG--SAKYHLEILN 65 (584)
T ss_pred HHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheec--CCceEEEeCC
Confidence 3445553 3578999999999999998864444 345544 4455 2357776643
No 162
>PF12728 HTH_17: Helix-turn-helix domain
Probab=32.69 E-value=25 Score=25.33 Aligned_cols=22 Identities=27% Similarity=0.489 Sum_probs=20.2
Q ss_pred ecHHHHHHHhccceeehhhhHH
Q 016170 94 LDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItN 115 (394)
+++.++|+.|+|.+..||.+++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999985
No 163
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=32.68 E-value=38 Score=28.51 Aligned_cols=48 Identities=23% Similarity=0.379 Sum_probs=38.5
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhc-----cceeehhhhHHHhhhccchhhccCC
Q 016170 81 KFINLIKHAEDGILDLNKAAETLE-----VQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~-----VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
..++++.+++. .++.+++.+.|. +.+=-||-.++.|+..|+|.|...+
T Consensus 12 ~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 12 AILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 46778888777 899999999985 4444699999999999999998544
No 164
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=32.52 E-value=30 Score=26.04 Aligned_cols=32 Identities=22% Similarity=0.378 Sum_probs=22.3
Q ss_pred HHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 83 INLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 83 i~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
+++++..+.|. ...++|..+||.+.-|++|..
T Consensus 13 ~~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 13 LEIIKRLEEGE-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHHHHHHHCTT--HHHHHHHHT--CCHHHHHHH
T ss_pred HHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 34444445555 899999999999999999985
No 165
>PRK10869 recombination and repair protein; Provisional
Probab=32.50 E-value=56 Score=35.39 Aligned_cols=104 Identities=13% Similarity=0.162 Sum_probs=58.9
Q ss_pred CCCCCcHHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHH
Q 016170 69 CRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADA 148 (394)
Q Consensus 69 ~R~d~SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~ 148 (394)
++++.+|..+...+-..+-.-.+-.-+|....+.+.+.-.|+-.|-+=|.-|.=+.|+ | |.+ ..++-...
T Consensus 257 ~~~d~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~~dp~~l~~ie~Rl~~l~~L~rK----y---g~~---~~~~~~~~ 326 (553)
T PRK10869 257 IGMDSKLSGVLDMLEEALIQIQEASDELRHYLDRLDLDPNRLAELEQRLSKQISLARK----H---HVS---PEELPQHH 326 (553)
T ss_pred hhhCHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHH----h---CCC---HHHHHHHH
Confidence 4566666666666666554444555556666666666666666666666666666665 2 422 22444556
Q ss_pred HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHhhh
Q 016170 149 SILQADIDNLSMEELR---VDEQTRELRERLRELIEN 182 (394)
Q Consensus 149 ~~Lq~El~~L~~~E~~---LDe~I~~~~~~L~~Lted 182 (394)
..+++|++.|...+.. |.+.+..+.+++..+.+.
T Consensus 327 ~~l~~eL~~L~~~e~~l~~Le~e~~~l~~~l~~~A~~ 363 (553)
T PRK10869 327 QQLLEEQQQLDDQEDDLETLALAVEKHHQQALETAQK 363 (553)
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6777777766654443 444444444555544443
No 166
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=32.49 E-value=34 Score=31.64 Aligned_cols=38 Identities=21% Similarity=0.151 Sum_probs=33.4
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 132 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 132 (394)
+.-.++|+.||++|+.+.-+++-|+--|+|++.. ++|.
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~-~~i~ 207 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSK-RGYL 207 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeC-CEEE
Confidence 5679999999999999999999999999999874 4453
No 167
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=32.48 E-value=1.1e+02 Score=26.59 Aligned_cols=81 Identities=20% Similarity=0.217 Sum_probs=0.0
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHHH----
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSME---- 161 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G~~~s~~~~~~~~~~~Lq------~El~~L~~~---- 161 (394)
+.+.++|+.+||+.+-|- -.|..|||. +...|.|++-..... ..-..+..|+ +|+..+-..
T Consensus 1 ~~I~e~a~~~gvs~~tlR----~Ye~~Gll~~~~r~~~g~R~Y~~~~l---~~l~~I~~lr~~G~sL~eI~~~l~~~~~~ 73 (126)
T cd04785 1 LSIGELARRTGVNVETIR----YYESIGLLPEPARTAGGYRLYGAAHV---ERLRFIRRARDLGFSLEEIRALLALSDRP 73 (126)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCccccCHHHH---HHHHHHHHHHHCCCCHHHHHHHHhhhhcC
Q ss_pred -------HHHHHHHHHHHHHHHHHHhh
Q 016170 162 -------ELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 162 -------E~~LDe~I~~~~~~L~~Lte 181 (394)
...|.+++..+++++++|..
T Consensus 74 ~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (126)
T cd04785 74 DRSCAEADAIARAHLADVRARIADLRR 100 (126)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
No 168
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=32.47 E-value=69 Score=26.55 Aligned_cols=36 Identities=19% Similarity=0.354 Sum_probs=23.2
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh--ccCCeEEEe
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK--KLKNRIRWK 134 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~sKN~i~W~ 134 (394)
.+.++|+.+||+.+.|-- .|..|||.- ...|.|++-
T Consensus 2 ~i~eva~~~gvs~~tlR~----ye~~Gll~p~~~~~~gyR~Y 39 (97)
T cd04782 2 TTGEFAKLCGISKQTLFH----YDKIGLFKPEIVKENGYRYY 39 (97)
T ss_pred CHHHHHHHHCcCHHHHHH----HHHCCCCCCCccCCCCCccC
Confidence 567889999998876532 366788743 334555543
No 169
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=32.10 E-value=56 Score=29.23 Aligned_cols=39 Identities=15% Similarity=0.211 Sum_probs=33.4
Q ss_pred eecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 016170 93 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 132 (394)
Q Consensus 93 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 132 (394)
.+.-.++|..||+.++.+.-+.+-|+.-|+|++.. ++|.
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~-~~i~ 206 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHG-KTIV 206 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecC-CEEE
Confidence 46669999999999999999999999999998764 4443
No 170
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=32.10 E-value=1.3e+02 Score=24.88 Aligned_cols=17 Identities=18% Similarity=0.212 Sum_probs=11.5
Q ss_pred cHHHHHHHhccceeehh
Q 016170 95 DLNKAAETLEVQKRRIY 111 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIY 111 (394)
.+.++|+.+||..+-|-
T Consensus 2 ti~eva~~~gvs~~tlR 18 (103)
T cd01106 2 TVGEVAKLTGVSVRTLH 18 (103)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 46677777777766554
No 171
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=31.89 E-value=23 Score=31.08 Aligned_cols=33 Identities=27% Similarity=0.460 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
.|..+|++.+ -++.+.+|+.|||++.+|-.|+|
T Consensus 13 iL~eeflep~------glt~~~lA~~lgV~r~~is~lin 45 (104)
T COG3093 13 ILREEFLEPL------GLTQTELAEALGVTRNTISELIN 45 (104)
T ss_pred HHHHHHhccc------cCCHHHHHHHhCCCHHHHHHHHc
Confidence 3556777654 37899999999999999999998
No 172
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=31.66 E-value=1.3e+02 Score=23.78 Aligned_cols=39 Identities=8% Similarity=0.219 Sum_probs=31.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 016170 144 VDADASILQADIDNLSMEELRVDEQTRELRERLRELIEN 182 (394)
Q Consensus 144 ~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted 182 (394)
+.+++.+++..++++....+.|+........++.++.++
T Consensus 4 i~e~l~~ie~~l~~~~~~i~~lE~~~~~~e~~i~~~~~~ 42 (71)
T PF10779_consen 4 IKEKLNRIETKLDNHEERIDKLEKRDAANEKDIKNLNKQ 42 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456778888888888888888888888888888887665
No 173
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=31.56 E-value=30 Score=27.83 Aligned_cols=23 Identities=26% Similarity=0.433 Sum_probs=18.8
Q ss_pred cCCCceEEEEecCccccccccCC
Q 016170 240 STMGPIDVYLVSRFEEKFEETNS 262 (394)
Q Consensus 240 S~~GPIdVyLv~~~~~~~e~~~~ 262 (394)
|.+|+|.|+.++.++.....+.|
T Consensus 16 s~lG~I~vLYvn~~eS~~~~~~G 38 (62)
T PF15513_consen 16 SQLGEIAVLYVNPYESDEDRLTG 38 (62)
T ss_pred HhcCcEEEEEEcccccCCCeEec
Confidence 78999999999988877655554
No 174
>PHA00738 putative HTH transcription regulator
Probab=31.54 E-value=1.5e+02 Score=26.18 Aligned_cols=71 Identities=20% Similarity=0.332 Sum_probs=50.1
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHHHHHHHHHHHH
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADASILQADIDNL 158 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lq~El~~L 158 (394)
+.+.+|.. ++.+...++++.|++.+=.|-==+.||+..|||+.....+..+.-...- ....+.|..|++..
T Consensus 16 ~IL~lL~~--~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~-----~~~~~l~~~~~~~~ 86 (108)
T PHA00738 16 KILELIAE--NYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIREN-----SKEIQILNSELEGF 86 (108)
T ss_pred HHHHHHHH--cCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCC-----ccHHHHHhhHHHHH
Confidence 56667755 3347788999999999999999999999999999776665555433321 22355666666544
No 175
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=30.59 E-value=1e+02 Score=29.90 Aligned_cols=40 Identities=18% Similarity=0.279 Sum_probs=25.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 016170 144 VDADASILQADIDNLSMEELRVDEQTRELRERLRELIENEN 184 (394)
Q Consensus 144 ~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~~ 184 (394)
+.++.+.|++|++.|+.+..+++++.+ -.++|+.|.+-..
T Consensus 74 l~~en~~L~~e~~~l~~~~~~~~~l~~-en~~L~~lL~~~~ 113 (276)
T PRK13922 74 LREENEELKKELLELESRLQELEQLEA-ENARLRELLNLKE 113 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhcCcc
Confidence 345566777777777777777765443 3567777655443
No 176
>PRK03837 transcriptional regulator NanR; Provisional
Probab=30.48 E-value=33 Score=31.83 Aligned_cols=51 Identities=12% Similarity=0.213 Sum_probs=41.2
Q ss_pred HHHHHHHHHhh---CCCCee-cHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 78 LTKKFINLIKH---AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 78 LTkKFi~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
+-+.+.+.+.. .|+..+ ...++|++|||+|--+=+.+..|+.-|||+...+
T Consensus 18 v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~ 72 (241)
T PRK03837 18 VEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHG 72 (241)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 44555555432 467788 8999999999999999999999999999997643
No 177
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=30.42 E-value=65 Score=31.96 Aligned_cols=61 Identities=28% Similarity=0.343 Sum_probs=50.0
Q ss_pred CcHHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 016170 73 SSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 134 (394)
Q Consensus 73 ~SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 134 (394)
..|-.-=+.-|+++.. .+|.+.-+++.+.||..|=-++-|+-=||-.|||+|..++.=.|.
T Consensus 191 ~~L~~~e~~il~~i~~-~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V 251 (258)
T COG2512 191 YDLNEDEKEILDLIRE-RGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIV 251 (258)
T ss_pred CCCCHHHHHHHHHHHH-hCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEE
Confidence 3444455667777766 589999999999999999999999999999999999877655443
No 178
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=30.41 E-value=47 Score=32.18 Aligned_cols=44 Identities=23% Similarity=0.285 Sum_probs=38.2
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
+.++++++ .+.+.+.++|+.|+|+..-|+--+..||--|+|.|.
T Consensus 9 ~Il~~l~~--~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 9 AIIELVKQ--QGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHH--cCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45667754 668999999999999999998889999999999887
No 179
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=30.27 E-value=65 Score=31.86 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=40.0
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccc-hhhccCCeEEE
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGL-IEKKLKNRIRW 133 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL-IeK~sKN~i~W 133 (394)
.+.+.++.+ +..+...++|+.|+|+|..++-.+..|+.-|+ |.......|..
T Consensus 7 ~~il~~L~~--~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~~Gy~L 59 (319)
T PRK11886 7 LQLLSLLAD--GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYRL 59 (319)
T ss_pred HHHHHHHHc--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecCCeEEe
Confidence 456677754 56788889999999999999999999999999 54433223544
No 180
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=30.17 E-value=56 Score=25.88 Aligned_cols=44 Identities=23% Similarity=0.307 Sum_probs=34.9
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
.+++++.. ++.+.-.++|+.+++.+-..-=+.+.||.-|.|++.
T Consensus 5 Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 5 ILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERS 48 (62)
T ss_dssp HHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45555553 556888999999999998888899999999999963
No 181
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=30.10 E-value=84 Score=29.54 Aligned_cols=40 Identities=23% Similarity=0.281 Sum_probs=36.6
Q ss_pred CCCCee-cHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 016170 89 AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 128 (394)
Q Consensus 89 ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 128 (394)
.|+..| .-.++|+.|||+|==+-+.+..|+..|||+....
T Consensus 26 ~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 26 KVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 578889 8999999999999999999999999999997744
No 182
>PRK13503 transcriptional activator RhaS; Provisional
Probab=29.76 E-value=61 Score=30.37 Aligned_cols=39 Identities=5% Similarity=0.083 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
...+++++++.+.....++|.++|+.+++.++.+..+..
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 346778888888888899999999999999998876653
No 183
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=29.66 E-value=81 Score=24.99 Aligned_cols=57 Identities=21% Similarity=0.286 Sum_probs=47.2
Q ss_pred HHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 016170 78 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 134 (394)
Q Consensus 78 LTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 134 (394)
+-.+.+++|....+...---..+..|.+.|+.|==+..=|+.=|.|.|.+-+--.|.
T Consensus 5 ~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~~PP~W~ 61 (66)
T PF02295_consen 5 LEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGGTPPKWS 61 (66)
T ss_dssp HHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECSSSTEEE
T ss_pred HHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCCCCCceE
Confidence 456778888777766777778888999999999999999999999999888888885
No 184
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=29.59 E-value=1.2e+02 Score=26.00 Aligned_cols=60 Identities=17% Similarity=0.178 Sum_probs=41.3
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCHHHHhhccCCCCceEEEEeCC
Q 016170 143 EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLHCFQNQTLIAIKAP 213 (394)
Q Consensus 143 ~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP 213 (394)
++.+++..+++|++.|+++.+.|.+.|..++... +..|...-..|.||- .|+++|-|.-|
T Consensus 31 ~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~-dyiEe~AR~~Lg~vk----------~gEivy~~~~~ 90 (105)
T PRK00888 31 RVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQ-EAIEERARNELGMVK----------PGETFYRIVPD 90 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcH-HHHHHHHHHHcCCCC----------CCCEEEEeCCC
Confidence 5567788999999999999999999999998743 333333323355443 45566555444
No 185
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=29.09 E-value=84 Score=34.09 Aligned_cols=22 Identities=14% Similarity=0.071 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 016170 160 MEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 160 ~~E~~LDe~I~~~~~~L~~Lte 181 (394)
.+.+.+++.|+.+++.++.|.+
T Consensus 97 aq~~dle~KIkeLEaE~~~Lk~ 118 (475)
T PRK13729 97 KQRGDDQRRIEKLGQDNAALAE 118 (475)
T ss_pred hhhhhHHHHHHHHHHHHHHHHH
Confidence 4444555556666555555543
No 186
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=29.05 E-value=2.6e+02 Score=24.15 Aligned_cols=89 Identities=17% Similarity=0.180 Sum_probs=0.0
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccch--hhccCCeEEEe----------------------------ccCCCCCCC
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLI--EKKLKNRIRWK----------------------------GLDNSIPGE 143 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLI--eK~sKN~i~W~----------------------------G~~~s~~~~ 143 (394)
+.+.++|+.+||+.+-|- -.|-.||+ .+...|.|++- .........
T Consensus 1 m~I~e~a~~~gvs~~tlR----yYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~ 76 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIR----YYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRA 76 (127)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCC
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q 016170 144 VDADASILQADIDNLSMEELRVDEQTRELRERLRELIENENNR 186 (394)
Q Consensus 144 ~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~~n~ 186 (394)
.......|++.++.|..+-..|..+...+...+.....+....
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~~~~~~~~~~~~ 119 (127)
T cd01108 77 SADVKALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPD 119 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCC
No 187
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=29.02 E-value=61 Score=31.70 Aligned_cols=42 Identities=7% Similarity=-0.026 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhh
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLE 118 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLE 118 (394)
....++++++.......++|.++|+.+++++|.|+-..+-.-
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~ 259 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAAT 259 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345688999999989999999999999999999988776443
No 188
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=28.77 E-value=53 Score=35.50 Aligned_cols=59 Identities=25% Similarity=0.315 Sum_probs=39.0
Q ss_pred ehhhhHHHhhhccchhhc-cCCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 109 RIYDITNVLEGIGLIEKK-LKNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 109 RIYDItNVLEgIGLIeK~-sKN~i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
++-++.|-|+++-=+.|. -||.-.|+| .|++..+.+...-...|+.|.++++||++|+-
T Consensus 390 k~~k~~kel~~~~E~n~~l~knq~vw~~--------------kl~~~~e~~~~~~~s~d~~I~dLqEQlrDlmf 449 (493)
T KOG0804|consen 390 KLKKCQKELKEEREENKKLIKNQDVWRG--------------KLKELEEREKEALGSKDEKITDLQEQLRDLMF 449 (493)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhe
Confidence 455666777666544433 455555654 34444455566667899999999999999864
No 189
>smart00338 BRLZ basic region leucin zipper.
Probab=28.74 E-value=1.9e+02 Score=22.11 Aligned_cols=34 Identities=24% Similarity=0.406 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 148 ASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 148 ~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
+..|+.++..|..+-..|-..+..+..++..|.+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566667777777666676666666666665543
No 190
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=28.71 E-value=19 Score=32.10 Aligned_cols=26 Identities=23% Similarity=0.443 Sum_probs=0.0
Q ss_pred ceeehhhhHHHhhhccchhhccCCeEEE
Q 016170 106 QKRRIYDITNVLEGIGLIEKKLKNRIRW 133 (394)
Q Consensus 106 qKRRIYDItNVLEgIGLIeK~sKN~i~W 133 (394)
-|+++-+-+..||.+|+|.+. |.|+=
T Consensus 5 lk~~~l~~l~~LE~~G~v~~~--n~yQ~ 30 (142)
T PF03836_consen 5 LKKKILENLKELESLGIVSRS--NNYQD 30 (142)
T ss_dssp ----------------------------
T ss_pred HHHHHHHHHHHHHHCCCCCCc--ccHHH
Confidence 477888899999999999988 66653
No 191
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=28.69 E-value=61 Score=31.03 Aligned_cols=59 Identities=17% Similarity=0.303 Sum_probs=41.0
Q ss_pred CCCCcHHHHH------HHHHHHHhhCCCC-eecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 016170 70 RYDSSLGLLT------KKFINLIKHAEDG-ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 131 (394)
Q Consensus 70 R~d~SLglLT------kKFi~Ll~~ap~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 131 (394)
|--+-||.++ ...+++|....+. .++++++++..++.+ -||+..|+.+|++.....+.+
T Consensus 120 rPLSdlG~~sY~sYW~~~i~~~L~~~~~~~~isi~~is~~Tgi~~---~DIi~tL~~l~~l~~~~~~~~ 185 (188)
T PF01853_consen 120 RPLSDLGRLSYRSYWRRVILEYLLEFKGKKSISIKDISQETGIRP---EDIISTLQQLGMLKYYKGQHI 185 (188)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHHHTSSE--EEHHHHHHHH-BTH---HHHHHHHHHTT-EEEETTEEE
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHhcCCCCeEEHHHHHHHHCCCH---HHHHHHHHHCCCEEEECCcEE
Confidence 3345678776 3366666665554 899999999999965 699999999999987755544
No 192
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.39 E-value=71 Score=27.34 Aligned_cols=35 Identities=14% Similarity=0.299 Sum_probs=30.6
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
.....+.-++-..-|-.||.+-|++-.|+|||+.-
T Consensus 19 S~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~l 53 (95)
T COG4519 19 SGETANVPELMAATGWPRRTAQDVIKALPGLGIVL 53 (95)
T ss_pred ccccCChHHHHHHcCCchhHHHHHHHhCcCCCeEE
Confidence 45567888888899999999999999999999863
No 193
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=28.18 E-value=2.8e+02 Score=25.83 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=36.3
Q ss_pred HHHHHHhhCCCCee--cHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 81 KFINLIKHAEDGIL--DLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 81 KFi~Ll~~ap~g~l--dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
++..++.+.+.-.+ .+..+|..||+.++-|-=++.|+.-+|+|+-.
T Consensus 102 ~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~FVti~ 149 (195)
T PF10141_consen 102 KLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLKVFFELGFVTIE 149 (195)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCcEEEe
Confidence 44555556554422 46889999999999999999999999999866
No 194
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=28.16 E-value=45 Score=33.48 Aligned_cols=44 Identities=20% Similarity=0.400 Sum_probs=34.9
Q ss_pred HHHHHHHH---HhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccch
Q 016170 78 LTKKFINL---IKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLI 123 (394)
Q Consensus 78 LTkKFi~L---l~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 123 (394)
...+++.+ |+..+. +...++|+.|+|.+|-||-=+|-|...|+=
T Consensus 6 ka~RL~~ii~~L~~~~~--vta~~lA~~~~VS~RTi~RDi~~L~~~gvP 52 (311)
T COG2378 6 KAERLLQIIQILRAKET--VTAAELADEFEVSVRTIYRDIATLRAAGVP 52 (311)
T ss_pred HHHHHHHHHHHHHhCcc--chHHHHHHhcCCCHHHHHHHHHHHHHCCCC
Confidence 34454444 344333 999999999999999999999999999985
No 195
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=27.95 E-value=1.5e+02 Score=26.58 Aligned_cols=81 Identities=20% Similarity=0.224 Sum_probs=0.0
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccch--hhccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHH-----
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLI--EKKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSM----- 160 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLI--eK~sKN~i~W~G~~~s~~~~~~~~~~~Lq------~El~~L~~----- 160 (394)
+.+.++|..+||+.|-|- ..|-+||| .+...|.|++-..... .--..+..|+ +|+..+-.
T Consensus 8 ~~IgevAk~~Gvs~~TLR----yYE~~GLl~p~~r~~~gyR~Y~~~~l---~rl~~I~~lr~~G~sL~eI~~ll~~~~~~ 80 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIR----FYQRKGLLPEPDKPYGSIRRYGEADV---TRVRFVKSAQRLGFSLDEIAELLRLEDGT 80 (144)
T ss_pred ccHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCCeecCHHHH---HHHHHHHHHHHcCCCHHHHHHHHhccCCC
Q ss_pred ----HHHHHHHHHHHHHHHHHHHhh
Q 016170 161 ----EELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 161 ----~E~~LDe~I~~~~~~L~~Lte 181 (394)
...-|.+++..+.+++.+|..
T Consensus 81 ~~~~~~~ll~~k~~~l~~~i~~L~~ 105 (144)
T PRK13752 81 HCEEASSLAEHKLKDVREKMADLAR 105 (144)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
No 196
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=27.92 E-value=58 Score=27.96 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=22.9
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
++..+-+.-|..||-+.|.++.|.++|+.-
T Consensus 23 nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~ 52 (90)
T PF09904_consen 23 NVPALMEATGMPRRTIQDTIKALPELGIEC 52 (90)
T ss_dssp -HHHHHHHH---HHHHHHHHHGGGGGT-EE
T ss_pred cHHHHHHHhCCCHhHHHHHHHHhhcCCeEE
Confidence 888888999999999999999999999754
No 197
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=27.77 E-value=3.1e+02 Score=25.59 Aligned_cols=33 Identities=9% Similarity=-0.009 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 016170 150 ILQADIDNLSMEELRVDEQTRELRERLRELIEN 182 (394)
Q Consensus 150 ~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted 182 (394)
.|+....-|..++.-|++.+..+.++|.+|..+
T Consensus 67 ~Le~R~~~L~aree~I~~v~~~a~e~L~~l~~~ 99 (185)
T PRK01194 67 NIEARSIKREKRREILKDYLDIAYEHLMNITKS 99 (185)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCC
Confidence 455666778899999999999999999999753
No 198
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=27.74 E-value=2.4e+02 Score=26.33 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=35.2
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
+++.+|. ..|.+.-.++|..||+++.-+=-+.+-|+.-|||.
T Consensus 26 ~Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 26 EVLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 3444443 34678999999999999999999999999999999
No 199
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=27.67 E-value=1.2e+02 Score=25.23 Aligned_cols=37 Identities=19% Similarity=0.290 Sum_probs=24.0
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 135 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 135 (394)
.+.++|+.+||+.+-|-- .|-.||+. +...|.+++-.
T Consensus 2 ~i~e~A~~~gvs~~tlR~----Ye~~Gll~~~~r~~~g~R~Y~ 40 (99)
T cd04772 2 RTVDLARAIGLSPQTVRN----YESLGLIPPAERTANGYRIYT 40 (99)
T ss_pred CHHHHHHHHCcCHHHHHH----HHHcCCCCCCCcCCCCCeecC
Confidence 467889999987764331 26778875 34556666643
No 200
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=27.61 E-value=55 Score=30.33 Aligned_cols=37 Identities=32% Similarity=0.443 Sum_probs=30.9
Q ss_pred CCeecHHHHHHHhccceee--------------hhhhHHHhhhccchhhcc
Q 016170 91 DGILDLNKAAETLEVQKRR--------------IYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 91 ~g~ldLn~aA~~L~VqKRR--------------IYDItNVLEgIGLIeK~s 127 (394)
.+.+-+..++..+|..||| |=-++..||.+|||+|..
T Consensus 65 ~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 65 DGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred cCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 5567788889999996664 778999999999999864
No 201
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=27.20 E-value=3.8e+02 Score=23.33 Aligned_cols=82 Identities=9% Similarity=0.129 Sum_probs=0.0
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchhhccC--CeEEEe----------------------------ccCCCCCCC
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK--NRIRWK----------------------------GLDNSIPGE 143 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK--N~i~W~----------------------------G~~~s~~~~ 143 (394)
+.+.++|..+||..|.| =-.|-+|||.-... |.|+.- .........
T Consensus 1 m~IgE~A~~~gvs~~TL----RyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~ 76 (133)
T cd04787 1 MKVKELANAAGVTPDTV----RFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESP 76 (133)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhccCCCc
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 144 VDADASILQADIDNLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 144 ~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
.......|++.++.|+.+-.+|.+++..+...+...
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~ 112 (133)
T cd04787 77 CPMVRRLIEQRLAETERRIKELLKLRDRMQQAVSQW 112 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 202
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=27.14 E-value=64 Score=28.97 Aligned_cols=38 Identities=21% Similarity=0.118 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhh
Q 016170 76 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDI 113 (394)
Q Consensus 76 glLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDI 113 (394)
..|...+++++.+..-.-+.++++|++.||.|+.||.-
T Consensus 14 ~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~ 51 (213)
T PRK09975 14 QELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYWH 51 (213)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHHH
Confidence 45667788899887777899999999999999999953
No 203
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.11 E-value=2e+02 Score=23.76 Aligned_cols=37 Identities=16% Similarity=0.251 Sum_probs=23.9
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh--ccCCeEEEec
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK--KLKNRIRWKG 135 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~sKN~i~W~G 135 (394)
.+.++|+.+||+.+-|- -.|..|||.. ...|.++.-.
T Consensus 2 ~i~eva~~~gvs~~tlR----~ye~~Gll~p~~r~~~gyR~Y~ 40 (96)
T cd04788 2 KIGELARRTGLSVRTLH----HYDHIGLLSPSQRTEGGHRLYD 40 (96)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCceeeC
Confidence 57789999999887443 2346788854 3346555543
No 204
>PHA02047 phage lambda Rz1-like protein
Probab=27.02 E-value=37 Score=29.62 Aligned_cols=33 Identities=15% Similarity=0.254 Sum_probs=15.0
Q ss_pred EEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 131 IRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTR 170 (394)
Q Consensus 131 i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~ 170 (394)
|+|.|... +....|...++.++.+-..+.++..
T Consensus 26 ~r~~g~~h-------~~a~~la~qLE~a~~r~~~~Q~~V~ 58 (101)
T PHA02047 26 YRALGIAH-------EEAKRQTARLEALEVRYATLQRHVQ 58 (101)
T ss_pred HHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66777542 2234444444444444333333333
No 205
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=26.80 E-value=1e+02 Score=25.44 Aligned_cols=27 Identities=7% Similarity=0.295 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 153 ADIDNLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 153 ~El~~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
++|..|.++-++|++.+..++++|-++
T Consensus 2 ~~L~~l~~~k~~Le~~L~~lE~qIy~~ 28 (80)
T PF09340_consen 2 KELKELLQKKKKLEKDLAALEKQIYDK 28 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567777888888888888888888776
No 206
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=26.71 E-value=60 Score=31.45 Aligned_cols=44 Identities=14% Similarity=0.262 Sum_probs=34.8
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
+.++++++ .+.+.++++|+.|+|++--|.-=++.||.-|+|.|.
T Consensus 9 ~Il~~L~~--~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 9 AILEYLQK--QGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHH--cCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 34556655 677999999999999765555557889999999887
No 207
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=26.66 E-value=76 Score=28.99 Aligned_cols=40 Identities=28% Similarity=0.401 Sum_probs=36.9
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 129 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 129 (394)
.++.+-..++|..|+|..--+-..+|=|+..|||++....
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~ 60 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYG 60 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCC
Confidence 7899999999999999999999999999999999986444
No 208
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=26.58 E-value=2.2e+02 Score=26.04 Aligned_cols=35 Identities=14% Similarity=0.165 Sum_probs=32.5
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchh
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 124 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 124 (394)
..+.+.-.++|..||++++-+=-+.+.|...|||.
T Consensus 25 ~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 25 IKGEFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 36679999999999999999999999999999995
No 209
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=26.57 E-value=1.3e+02 Score=28.57 Aligned_cols=36 Identities=19% Similarity=0.257 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 146 ADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 146 ~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
.-+..|++|+..+...+...+..+.++.+..+.|++
T Consensus 27 ~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~e 62 (201)
T PF13851_consen 27 ELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSE 62 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 347788899999998888888888888777666655
No 210
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=26.55 E-value=1.2e+02 Score=32.17 Aligned_cols=58 Identities=19% Similarity=0.340 Sum_probs=45.5
Q ss_pred CcHHHHHHH------HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEec
Q 016170 73 SSLGLLTKK------FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKG 135 (394)
Q Consensus 73 ~SLglLTkK------Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G 135 (394)
+-||+|+-+ .+++|....+..|.|+++|..-++. .-||++.|+.+++|... |. +.|..
T Consensus 303 SDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~---~~DIisTL~~L~m~~y~-k~-~~~~~ 366 (396)
T KOG2747|consen 303 SDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIR---PDDIISTLQSLNMIKYY-KG-YIISI 366 (396)
T ss_pred chhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCC---HHHHHHHHHhhCCcccc-CC-eeEEE
Confidence 357888844 6777777666669999999999984 57999999999999866 33 66654
No 211
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=26.49 E-value=77 Score=30.41 Aligned_cols=51 Identities=24% Similarity=0.415 Sum_probs=39.8
Q ss_pred HHHHHH-HHhhCCCCeecHHHHHHHhccceeehhhhHH-HhhhccchhhccCC
Q 016170 79 TKKFIN-LIKHAEDGILDLNKAAETLEVQKRRIYDITN-VLEGIGLIEKKLKN 129 (394)
Q Consensus 79 TkKFi~-Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~sKN 129 (394)
-+.|+. +++...++.+.+.++|..||+..+.+..++- .|--.|||++....
T Consensus 240 ~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 292 (305)
T TIGR00635 240 DRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRG 292 (305)
T ss_pred HHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCch
Confidence 344555 5565566678899999999999999999777 78889999866544
No 212
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=26.20 E-value=1.6e+02 Score=27.35 Aligned_cols=54 Identities=24% Similarity=0.272 Sum_probs=38.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc-------ccccccccCHHHHhh
Q 016170 145 DADASILQADIDNLSMEELRVDEQTRELRERLRELIENE-------NNRKWLFVTEEDIKN 198 (394)
Q Consensus 145 ~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~-------~n~~~aYVT~eDI~~ 198 (394)
..++..|++|++.|..+-+.+-..+..|+..|..+.... ....-.=|++++|.+
T Consensus 28 ~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~~v~~~eLL~ 88 (188)
T PF10018_consen 28 QARIQQLRAEIEELDEQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKRPVDYEELLS 88 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccCCCCHHHHHH
Confidence 456888999999998888888888888888888876211 111122377888876
No 213
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=26.03 E-value=46 Score=31.00 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=35.4
Q ss_pred CCCCee-cHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 89 AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 89 ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
.|+..+ .-.++|++|||+|=-|-+.+..|+.-|||+...
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 467788 799999999999999999999999999999763
No 214
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=26.01 E-value=5.2e+02 Score=24.13 Aligned_cols=51 Identities=24% Similarity=0.287 Sum_probs=36.7
Q ss_pred CCCCcHHHHHHHHHHHHh-hCCCCe---------------ecHHHHHHHhcc-ceeehhhhHHHhhhccc
Q 016170 70 RYDSSLGLLTKKFINLIK-HAEDGI---------------LDLNKAAETLEV-QKRRIYDITNVLEGIGL 122 (394)
Q Consensus 70 R~d~SLglLTkKFi~Ll~-~ap~g~---------------ldLn~aA~~L~V-qKRRIYDItNVLEgIGL 122 (394)
+++-+...|.++|..|-+ -+||.. --||+|-..|.- .+|..|++ .|.|+.+
T Consensus 17 ~f~~d~~~L~~~yr~lq~~~HPD~~~~~~~~e~~~a~~~s~~iN~AY~tL~~p~~Ra~Yll--~l~G~~~ 84 (176)
T PRK03578 17 RFALDEAALDAAYRTVQAQVHPDRFAAAGDAEKRVAMQWATRANEAYQTLRDPLKRARYLL--HLRGVDV 84 (176)
T ss_pred CCCCCHHHHHHHHHHHHHHHCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHH--HhcCCCC
Confidence 466778899999999864 466642 356777777876 57889987 5557655
No 215
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=25.82 E-value=77 Score=30.18 Aligned_cols=38 Identities=11% Similarity=0.162 Sum_probs=31.7
Q ss_pred HHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 78 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 78 LTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
...+++.++..+..+.+.|.++|+.+++++++|.-+..
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk 221 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFR 221 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45678888888888999999999999999998876654
No 216
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.58 E-value=99 Score=25.12 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=15.2
Q ss_pred cHHHHHHHhccceeehhhhHH
Q 016170 95 DLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItN 115 (394)
.+.++|+.+||..+.|--..+
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567888888888777665544
No 217
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=25.54 E-value=61 Score=28.20 Aligned_cols=31 Identities=16% Similarity=0.405 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 145 DADASILQADIDNLSMEELRVDEQTRELRER 175 (394)
Q Consensus 145 ~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~ 175 (394)
..++..+++|++.|.+++..|...|+.+++.
T Consensus 56 ~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 56 QRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3456677788888888888888888877776
No 218
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=25.53 E-value=27 Score=29.64 Aligned_cols=48 Identities=31% Similarity=0.439 Sum_probs=32.8
Q ss_pred EEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 131 IRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 131 i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
..|+|.+. .+++..+..|..+++.|..+-..|...+..++.+|..+..
T Consensus 13 ~~~rGYd~---~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~ 60 (131)
T PF05103_consen 13 KSMRGYDP---DEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELRE 60 (131)
T ss_dssp EEEEEEEH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT------
T ss_pred CCCCCcCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence 56788764 3677788888889988888878888877777777766643
No 219
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=25.30 E-value=1.3e+02 Score=29.53 Aligned_cols=31 Identities=19% Similarity=0.262 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 151 LQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 151 Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
|+..|+.|+.+-.+|--+|+..+-+|+.+.+
T Consensus 59 l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~ 89 (263)
T PRK10803 59 LQQQLSDNQSDIDSLRGQIQENQYQLNQVVE 89 (263)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 3444444444444444555555555555443
No 220
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.29 E-value=2.1e+02 Score=23.86 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=16.1
Q ss_pred cHHHHHHHhccceee--hhhhHHHhhhccchhh
Q 016170 95 DLNKAAETLEVQKRR--IYDITNVLEGIGLIEK 125 (394)
Q Consensus 95 dLn~aA~~L~VqKRR--IYDItNVLEgIGLIeK 125 (394)
.+.++|+.+||+.|- .|| .+|||..
T Consensus 2 ~Ige~a~~~gvs~~tlRyYe------~~GLl~p 28 (107)
T cd04777 2 KIGKFAKKNNITIDTVRHYI------DLGLLIP 28 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHH------HCCCcCC
Confidence 467788888887773 454 5555543
No 221
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=25.14 E-value=76 Score=24.06 Aligned_cols=41 Identities=12% Similarity=0.278 Sum_probs=35.8
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCe
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNR 130 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~ 130 (394)
.++.+++.++=+.|+++|+-.-=+..-|...|+..|..--+
T Consensus 7 ~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd~R 47 (50)
T PF09107_consen 7 KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGDKR 47 (50)
T ss_dssp TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTEE
T ss_pred cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCCEE
Confidence 38899999999999999999999999999999998886433
No 222
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=24.99 E-value=81 Score=27.10 Aligned_cols=43 Identities=28% Similarity=0.448 Sum_probs=34.1
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
..|..++...|+ +.|.++|+.|+|....|+ ..|.-+|+.-|+.
T Consensus 60 ~~L~~~v~~~pd--~tl~Ela~~l~Vs~~ti~---~~Lkrlg~t~KK~ 102 (119)
T PF01710_consen 60 DELKALVEENPD--ATLRELAERLGVSPSTIW---RALKRLGITRKKK 102 (119)
T ss_pred HHHHHHHHHCCC--cCHHHHHHHcCCCHHHHH---HHHHHcCchhccC
Confidence 567788888777 456799999999777776 6778889988883
No 223
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=24.78 E-value=67 Score=31.16 Aligned_cols=45 Identities=29% Similarity=0.400 Sum_probs=39.1
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
++.++++++ .|.+.+.++|+.|+|+.=-|+-=+|-||.-|++.|.
T Consensus 8 ~~Il~~l~~--~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLKE--KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHH--cCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 356777766 789999999999999887777778999999999998
No 224
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=24.76 E-value=78 Score=28.07 Aligned_cols=50 Identities=12% Similarity=0.173 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 75 LGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 75 LglLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
|-.+=++.+.+|+. ++.....++|+.||++.-.+..=++=|+.-|+|.+.
T Consensus 7 lD~~D~~Il~~Lq~--d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 7 IDNLDRGILEALME--NARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred cCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 45567889999977 588999999999999999999999999999999864
No 225
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=24.70 E-value=2.1e+02 Score=23.18 Aligned_cols=36 Identities=28% Similarity=0.388 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 146 ADASILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 146 ~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
..+..+++.+..|......|-..|..+...|+.+.+
T Consensus 14 P~l~~~~~~l~el~~sQ~~L~~~i~~~~~~L~~~~~ 49 (92)
T PF14712_consen 14 PDLDRLDQQLQELRQSQEELLQQIDRLNEKLKELNE 49 (92)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457888999999999999999999999999999877
No 226
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=24.55 E-value=2.8e+02 Score=21.21 Aligned_cols=33 Identities=15% Similarity=0.357 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 016170 148 ASILQADIDNLSMEELRVDEQTRELRERLRELI 180 (394)
Q Consensus 148 ~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lt 180 (394)
+..|+.++..|..+-..|-..+..+.+.+..|.
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~ 60 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEIQSLK 60 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556777777777777777777777777766664
No 227
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.40 E-value=1.4e+02 Score=24.62 Aligned_cols=39 Identities=23% Similarity=0.322 Sum_probs=25.9
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchhh--ccCCeEEEecc
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEK--KLKNRIRWKGL 136 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~sKN~i~W~G~ 136 (394)
+.+.++|+.+||..+.|- -.|..|||.- ...|.|++-+.
T Consensus 1 ~ti~eva~~~gvs~~tLR----yye~~Gll~p~~~~~~gyR~Y~~ 41 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLR----HYDDIGLFKPAKIAENGYRYYSY 41 (96)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCeeeCCH
Confidence 357889999999887552 2356688864 34566776543
No 228
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=24.35 E-value=1.4e+02 Score=22.95 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=24.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 144 VDADASILQADIDNLSMEELRVDEQTREL 172 (394)
Q Consensus 144 ~~~~~~~Lq~El~~L~~~E~~LDe~I~~~ 172 (394)
...++..|+.+++.|+.+-+.|.+.|+.+
T Consensus 22 ~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 22 LNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45667888889999988888888888888
No 229
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=24.30 E-value=1.4e+02 Score=25.36 Aligned_cols=33 Identities=30% Similarity=0.447 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 016170 149 SILQADIDNLSMEELRVDEQTRELRERLRELIE 181 (394)
Q Consensus 149 ~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lte 181 (394)
..|+..++.++..-..|++.+..++.+|.++-.
T Consensus 70 ~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~ 102 (110)
T TIGR02338 70 QELKEKKETLELRVKTLQRQEERLREQLKELQE 102 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455566666666666777777777777766643
No 230
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=23.94 E-value=80 Score=31.00 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=32.7
Q ss_pred HHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHH
Q 016170 78 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 116 (394)
Q Consensus 78 LTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 116 (394)
..++.+.++.+.....++|.++|+.+++.+|.++-+..-
T Consensus 192 ~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 456777888887778899999999999999998877654
No 231
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=23.79 E-value=91 Score=24.89 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=35.8
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccch
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLI 123 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 123 (394)
+++.++.......+.|+++|..+|+.++.+.-...-..|+...
T Consensus 24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~ 66 (127)
T COG2207 24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPS 66 (127)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
Confidence 7777776666777999999999999999999888877766655
No 232
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=23.75 E-value=1.5e+02 Score=25.02 Aligned_cols=80 Identities=20% Similarity=0.338 Sum_probs=45.6
Q ss_pred eecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe--ccCCCCCCCchHHHHHHHHHHH----------HHHH
Q 016170 93 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK--GLDNSIPGEVDADASILQADID----------NLSM 160 (394)
Q Consensus 93 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~--G~~~s~~~~~~~~~~~Lq~El~----------~L~~ 160 (394)
.+++.++|..-|+..-.|.+ |...|+|+-..-..=.|. +.+. ...+.+..|+.+++ +|-.
T Consensus 7 ~lt~~Elc~~~gi~~~~l~e----Lve~GlIep~~~~~~~~~F~~~~l----~r~~~a~rL~~dl~in~~gialvl~LLd 78 (101)
T PRK10265 7 TFTITEFCLHTGVSEEELNE----IVGLGVIEPREIQETTWVFDDHAA----IVVQRAVRLRHELALDWPGIAVALTLLD 78 (101)
T ss_pred EeeHHHHHHHHCcCHHHHHH----HHHCCCeecCCCCcccceECHHHH----HHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 47888888888888765554 667899986544333343 2111 11234555665432 3444
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 016170 161 EELRVDEQTRELRERLRELI 180 (394)
Q Consensus 161 ~E~~LDe~I~~~~~~L~~Lt 180 (394)
+-..|.+.++.++.+|+...
T Consensus 79 ~i~~Lr~el~~L~~~l~~~~ 98 (101)
T PRK10265 79 EIAHLKQENRLLRQRLSRFV 98 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 55556666666666665443
No 233
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=23.35 E-value=74 Score=30.33 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=29.1
Q ss_pred HHHHHHHHhhCCCCe-ecHHHHHHHhccceeehhhhHH
Q 016170 79 TKKFINLIKHAEDGI-LDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 79 TkKFi~Ll~~ap~g~-ldLn~aA~~L~VqKRRIYDItN 115 (394)
..+++.++.+.-... +++.++|..+|+++|.||-+.-
T Consensus 199 l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk 236 (302)
T PRK09685 199 FQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFA 236 (302)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 346777776665454 9999999999999999998763
No 234
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=23.33 E-value=2.1e+02 Score=23.64 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 145 DADASILQADIDNLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 145 ~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
...+..|+++++.|+.+...+...+.-+..++.-|
T Consensus 69 ~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~L 103 (104)
T PF13600_consen 69 SPELKELEEELEALEDELAALQDEIQALEAQIAFL 103 (104)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45677888888888888888888887777776544
No 235
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=23.29 E-value=4.7e+02 Score=22.33 Aligned_cols=80 Identities=25% Similarity=0.352 Sum_probs=57.7
Q ss_pred HHHHHhhCCCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHH
Q 016170 82 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADASILQADIDNLSME 161 (394)
Q Consensus 82 Fi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~ 161 (394)
|.-++...--..-++..+.+++.-..||+-.|=+.|+.+ | ..+++..|+-++..+..+
T Consensus 23 ~~~~l~~~~a~~~~~~~l~~~~~~~~~Rl~~lE~~l~~L--------------------P--t~~dv~~L~l~l~el~G~ 80 (106)
T PF10805_consen 23 FWLWLRRTYAKREDIEKLEERLDEHDRRLQALETKLEHL--------------------P--TRDDVHDLQLELAELRGE 80 (106)
T ss_pred HHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHhC--------------------C--CHHHHHHHHHHHHHHHhH
Confidence 334444433335677888888888888887765555422 2 135688999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhc
Q 016170 162 ELRVDEQTRELRERLRELIENE 183 (394)
Q Consensus 162 E~~LDe~I~~~~~~L~~Lted~ 183 (394)
=+.|...|+-+..++.-|.|.+
T Consensus 81 ~~~l~~~l~~v~~~~~lLlE~~ 102 (106)
T PF10805_consen 81 LKELSARLQGVSHQLDLLLENE 102 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999998888864
No 236
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=23.26 E-value=58 Score=23.86 Aligned_cols=26 Identities=19% Similarity=0.272 Sum_probs=19.5
Q ss_pred CCeecHHHHHHHhccceeehhhhHHH
Q 016170 91 DGILDLNKAAETLEVQKRRIYDITNV 116 (394)
Q Consensus 91 ~g~ldLn~aA~~L~VqKRRIYDItNV 116 (394)
.|.+.+.+||..+||.+.-|||.++-
T Consensus 14 ~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 14 NGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp TTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 44499999999999999999987764
No 237
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=23.24 E-value=1.4e+02 Score=33.45 Aligned_cols=52 Identities=17% Similarity=0.300 Sum_probs=33.2
Q ss_pred hhccCCeEEEeccCCCCC--C--C-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 124 EKKLKNRIRWKGLDNSIP--G--E-VDADASILQADIDNLSMEELRVDEQTRELRERL 176 (394)
Q Consensus 124 eK~sKN~i~W~G~~~s~~--~--~-~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L 176 (394)
+|. +.++.|.|...... + + ...+...|++|++.|..+-..||..|+.+..++
T Consensus 53 ~~i-RgNl~~~~~~~~~~~~~~~e~~~~~r~~L~~everLraei~~l~~~I~~~e~e~ 109 (632)
T PF14817_consen 53 RKI-RGNLLWYGHQQSKERKKSRENEARRRRELEKEVERLRAEIQELDKEIESREREV 109 (632)
T ss_pred HHH-HcceeeccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444 45588999765431 0 1 112455777888888888888888887765544
No 238
>KOG3501 consensus Molecular chaperone Prefoldin, subunit 1 [Posttranslational modification, protein turnover, chaperones]
Probab=22.99 E-value=1.8e+02 Score=25.88 Aligned_cols=40 Identities=20% Similarity=0.385 Sum_probs=34.6
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 016170 143 EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIEN 182 (394)
Q Consensus 143 ~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted 182 (394)
.++.++..+++.++.|+.+...|.....+..+.||+|.+.
T Consensus 71 ~leak~k~see~IeaLqkkK~YlEk~v~eaE~nLrellqs 110 (114)
T KOG3501|consen 71 HLEAKMKSSEEKIEALQKKKTYLEKTVSEAEQNLRELLQS 110 (114)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566677888899999999999999999999999999764
No 239
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=22.93 E-value=40 Score=33.00 Aligned_cols=29 Identities=34% Similarity=0.501 Sum_probs=25.8
Q ss_pred HHHHHHHhccceeehhhhHHHhhhccchhhc
Q 016170 96 LNKAAETLEVQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 96 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 126 (394)
|..+|++|+|+++.+-+ |.+++||+|+-.
T Consensus 64 l~~larrlgv~~nt~s~--~a~~~l~~v~d~ 92 (224)
T KOG2255|consen 64 LDMLARRLGVPMNTISS--KALEGLGLVGDV 92 (224)
T ss_pred HHHHHHHhCCcccccCc--ccccceeeecce
Confidence 45679999999999999 999999999865
No 240
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=22.88 E-value=1.6e+02 Score=24.66 Aligned_cols=69 Identities=13% Similarity=0.185 Sum_probs=33.3
Q ss_pred hhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 110 IYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 110 IYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
+-+|...+-.=|-|... ..-+-|.|.+..-....++-+.-++..++.|+..-+.|.+.+..++.++..+
T Consensus 42 lvplg~~~~v~g~i~~~-~~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~ 110 (120)
T PF02996_consen 42 LVPLGSGVFVPGKIPDT-DKVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQL 110 (120)
T ss_dssp EEEECTTEEEEEE-SST-TEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred eecCCCCeEEEEEeCCC-CEEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444433333444333 3356677755432112233344555556666655556666666665555544
No 241
>PRK01203 prefoldin subunit alpha; Provisional
Probab=22.81 E-value=2e+02 Score=26.08 Aligned_cols=37 Identities=14% Similarity=0.259 Sum_probs=22.3
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 143 EVDADASILQADIDNLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 143 ~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
++..+++.++++++.|.++-..|...+.+..+++..|
T Consensus 4 ~~~~~~~~~~~q~e~l~~ql~~L~~a~se~~~~ie~L 40 (130)
T PRK01203 4 DVEAQLNYIESLISSVDSQIDSLNKTLSEVQQTISFL 40 (130)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566677777776666666666665555554444
No 242
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.77 E-value=95 Score=31.50 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q 016170 147 DASILQADIDNLSMEELRVDEQTRELRERLRELIENENNR 186 (394)
Q Consensus 147 ~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~~n~ 186 (394)
.++.|++||..|+..-..-|++|-+-..+|-+|.-|.+++
T Consensus 226 ~i~~lkeeia~Lkk~L~qkdq~ileKdkqisnLKad~e~~ 265 (305)
T KOG3990|consen 226 KIQKLKEEIARLKKLLHQKDQLILEKDKQISNLKADKEYQ 265 (305)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHhhhhhhhccCcchhHH
Confidence 4889999999999999999999999999999998885554
No 243
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=22.64 E-value=57 Score=35.40 Aligned_cols=33 Identities=6% Similarity=0.278 Sum_probs=0.0
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 143 EVDADASILQADIDNLSMEELRVDEQTRELRER 175 (394)
Q Consensus 143 ~~~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~ 175 (394)
++.++++.|++||++|+++-..|++.|.+.+++
T Consensus 28 ~~~qkie~L~kql~~Lk~q~~~l~~~v~k~e~~ 60 (489)
T PF11853_consen 28 DLLQKIEALKKQLEELKAQQDDLNDRVDKVEKH 60 (489)
T ss_pred HHHHHHHHHHHHHHHHHHhhcccccccchhhHh
No 244
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=22.15 E-value=1.8e+02 Score=27.97 Aligned_cols=32 Identities=22% Similarity=0.339 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 148 ASILQADIDNLSMEELRVDEQTRELRERLREL 179 (394)
Q Consensus 148 ~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~L 179 (394)
+..|++|++.|+...+.|..++...+++|..|
T Consensus 58 ~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L 89 (251)
T PF11932_consen 58 YRQLEREIENLEVYNEQLERQVASQEQELASL 89 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444555555544444444444444444444
No 245
>PRK11642 exoribonuclease R; Provisional
Probab=21.62 E-value=97 Score=35.46 Aligned_cols=51 Identities=8% Similarity=0.046 Sum_probs=41.5
Q ss_pred HHHHHHhhCCCCeecHHHHHHHhccc----eeehhhhHHHhhhccchhhccCCeEE
Q 016170 81 KFINLIKHAEDGILDLNKAAETLEVQ----KRRIYDITNVLEGIGLIEKKLKNRIR 132 (394)
Q Consensus 81 KFi~Ll~~ap~g~ldLn~aA~~L~Vq----KRRIYDItNVLEgIGLIeK~sKN~i~ 132 (394)
+.+++|... ...+.+++++..|++. ++.|..+++-|+..|.|.+..++.|.
T Consensus 23 ~Il~~l~~~-~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~~~~~~ 77 (813)
T PRK11642 23 FILEHLTKR-EKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYA 77 (813)
T ss_pred HHHHHHHhc-CCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEe
Confidence 356666654 4899999999999995 35599999999999999988777663
No 246
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=21.41 E-value=1e+02 Score=34.35 Aligned_cols=55 Identities=15% Similarity=0.274 Sum_probs=45.9
Q ss_pred HHHHHHHhhCCCCeecHHHHHHHhccce----eehhhhHHHhhhccchhhccCCeEEEe
Q 016170 80 KKFINLIKHAEDGILDLNKAAETLEVQK----RRIYDITNVLEGIGLIEKKLKNRIRWK 134 (394)
Q Consensus 80 kKFi~Ll~~ap~g~ldLn~aA~~L~VqK----RRIYDItNVLEgIGLIeK~sKN~i~W~ 134 (394)
.+.+++++..+...+..++++..|++.+ .-++.+++-|+.-|.|.|..++.|...
T Consensus 5 ~~il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~~~~~~~~~ 63 (709)
T TIGR02063 5 ELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALP 63 (709)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEecC
Confidence 4577888888888999999999999853 459999999999999998877777543
No 247
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=21.39 E-value=2.4e+02 Score=23.69 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=17.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016170 145 DADASILQADIDNLSMEELRVDEQTRELRERLRE 178 (394)
Q Consensus 145 ~~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~ 178 (394)
.+++..|+.+++.|...-..+.+.|..++..|+.
T Consensus 93 ~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~ 126 (129)
T cd00890 93 KKRLETLEKQIEKLEKQLEKLQDQITELQEELQQ 126 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555555555555555555555554443
No 248
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=21.33 E-value=3.3e+02 Score=22.19 Aligned_cols=38 Identities=21% Similarity=0.361 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 016170 146 ADASILQADIDNLSMEELRVDEQTRELRERLRELIENE 183 (394)
Q Consensus 146 ~~~~~Lq~El~~L~~~E~~LDe~I~~~~~~L~~Lted~ 183 (394)
+.+..||.|++.|+.+-..|.+....+.+....|.++.
T Consensus 18 eti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~ 55 (72)
T PF06005_consen 18 ETIALLQMENEELKEKNNELKEENEELKEENEQLKQER 55 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 34667888888888877777777777776666665543
No 249
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=21.18 E-value=2.8e+02 Score=26.15 Aligned_cols=31 Identities=26% Similarity=0.281 Sum_probs=28.6
Q ss_pred HHHHHHh-ccceeehhhhHHHhhhccchhhcc
Q 016170 97 NKAAETL-EVQKRRIYDITNVLEGIGLIEKKL 127 (394)
Q Consensus 97 n~aA~~L-~VqKRRIYDItNVLEgIGLIeK~s 127 (394)
..+|..+ |+.-|.|.-....|...|||.+..
T Consensus 74 ~~La~r~~G~s~~tlrR~l~~LveaGLI~rrD 105 (177)
T PF03428_consen 74 AQLAERLNGMSERTLRRHLARLVEAGLIVRRD 105 (177)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHCCCeeecc
Confidence 6789999 999999999999999999999863
No 250
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=20.87 E-value=2.5e+02 Score=28.21 Aligned_cols=66 Identities=21% Similarity=0.308 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCHHHHhhcc-------CCCCceEEEEeCCCCCeEEecCC
Q 016170 153 ADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLH-------CFQNQTLIAIKAPQGTTLEVPDP 223 (394)
Q Consensus 153 ~El~~L~~~E~~LDe~I~~~~~~L~~Lted~~n~~~aYVT~eDI~~l~-------~f~~qTvIAIKAP~gT~LEVPdP 223 (394)
.+++.|..+-..+.+.+..++.+|.++....+..+ . +|..+|..|. .+.+=.++.+. |+.|++--.
T Consensus 237 ~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r-~-~t~~Ev~~Lk~~~~~Le~~~gw~~~~~~---~~~l~~~~~ 309 (325)
T PF08317_consen 237 EELEELEEKIEELEEQKQELLAEIAEAEKIREECR-G-WTRSEVKRLKAKVDALEKLTGWKIVSIS---GSTLEFRYK 309 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-C-CCHHHHHHHHHHHHHHHHHHCcEEEEEe---CCeEEEEEc
Confidence 33334444444444445555555555433322111 1 3777776652 23333344444 666766543
No 251
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=20.53 E-value=1.1e+02 Score=31.65 Aligned_cols=43 Identities=14% Similarity=0.197 Sum_probs=37.6
Q ss_pred CCCeecHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 016170 90 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 132 (394)
Q Consensus 90 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 132 (394)
.+..++..++++++++.-+.+-+|..-|+..|||.+...+.|.
T Consensus 307 ~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~g~~~ 349 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGERGQWV 349 (412)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCCCceE
Confidence 4568899999999999999999999999999999987656443
No 252
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=20.51 E-value=7.8e+02 Score=25.78 Aligned_cols=27 Identities=15% Similarity=0.392 Sum_probs=18.0
Q ss_pred CCCCCeEEecCCCccCCCCCCceEEEEecCCCceEEEE
Q 016170 212 APQGTTLEVPDPDEAVDYPQRRYRIILRSTMGPIDVYL 249 (394)
Q Consensus 212 AP~gT~LEVPdP~e~~~~~~r~YqI~LkS~~GPIdVyL 249 (394)
+=+|+.+.+.. ....++-+.+++-+|+
T Consensus 420 vypgv~i~i~~-----------~~~~i~~~~~~~~f~~ 446 (451)
T PF03961_consen 420 VYPGVEIHIGN-----------KSYKIKEEYGNVKFYL 446 (451)
T ss_pred EECCEEEEECC-----------EEEEEeeecCCEEEEE
Confidence 46788888763 2344565677777777
No 253
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=20.45 E-value=63 Score=23.90 Aligned_cols=27 Identities=26% Similarity=0.348 Sum_probs=22.6
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhc
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGI 120 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgI 120 (394)
+.|.++|+.+|+..+.|+.+.+-.-|+
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~ 28 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGT 28 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCc
Confidence 678999999999999999988765443
No 254
>PRK05638 threonine synthase; Validated
Probab=20.40 E-value=1.3e+02 Score=31.51 Aligned_cols=61 Identities=16% Similarity=0.209 Sum_probs=46.7
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHhhCCCCeecHHHHHHHhc--cceeehhhhHHHhhhccchhhc
Q 016170 63 LTPAGSCRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLE--VQKRRIYDITNVLEGIGLIEKK 126 (394)
Q Consensus 63 ~tp~~~~R~d~SLglLTkKFi~Ll~~ap~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~ 126 (394)
..+....|-.-.++.+..+.+.+|++. .....++++.|+ +.+--||-.+++||.-|||+..
T Consensus 357 k~~~~~~~~~~~~~~~r~~IL~~L~~~---~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~ 419 (442)
T PRK05638 357 KGYGEGGREKFTIGGTKLEILKILSER---EMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEA 419 (442)
T ss_pred CCCCCCchhhhcccchHHHHHHHHhhC---CccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEe
Confidence 444555665555666666677777654 467889999998 8999999999999999999864
No 255
>PRK15185 transcriptional regulator HilD; Provisional
Probab=20.39 E-value=1e+02 Score=31.50 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 77 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 77 lLTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
.+..+...++...+...+++.++|+.+++++|.|+-...
T Consensus 206 ~~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK 244 (309)
T PRK15185 206 TLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLA 244 (309)
T ss_pred HHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 366788888989999999999999999999999876643
No 256
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=20.18 E-value=89 Score=22.35 Aligned_cols=38 Identities=18% Similarity=0.170 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhCCCCeecHHHHHHHhccceeehhhhHH
Q 016170 78 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 115 (394)
Q Consensus 78 LTkKFi~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 115 (394)
+|++|..++-..-.....+..+|..+||.--.+..|++
T Consensus 12 ~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 12 ITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 56666665433222227999999999997666666654
No 257
>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=20.15 E-value=1.6e+02 Score=30.09 Aligned_cols=63 Identities=16% Similarity=0.210 Sum_probs=46.5
Q ss_pred cHHHHHHHHHHHHhhC-CCCeecHHHHHHH-hccceeehhhhHHHhhhccchhhc-cCCeEEEecc
Q 016170 74 SLGLLTKKFINLIKHA-EDGILDLNKAAET-LEVQKRRIYDITNVLEGIGLIEKK-LKNRIRWKGL 136 (394)
Q Consensus 74 SLglLTkKFi~Ll~~a-p~g~ldLn~aA~~-L~VqKRRIYDItNVLEgIGLIeK~-sKN~i~W~G~ 136 (394)
.|..+-++++++|..+ ....+...++... .+....-+-.++|-|..-|+|+=. ..+.+.|+-.
T Consensus 6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~~~~~l~~~~~ 71 (327)
T PF05158_consen 6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLKKGGGLSYKAV 71 (327)
T ss_dssp -HHHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE-SSSEEEEE-
T ss_pred hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEEcCCEEEEEEe
Confidence 7888999999999888 6667888888887 577899999999999999988732 4566777654
No 258
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=20.13 E-value=3.1e+02 Score=23.11 Aligned_cols=27 Identities=22% Similarity=0.279 Sum_probs=19.8
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh
Q 016170 95 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK 125 (394)
Q Consensus 95 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 125 (394)
.+.++|+.+||+.+-|.-. |-.|||..
T Consensus 2 ~i~eva~~~gvs~~tlR~y----e~~Gll~p 28 (108)
T cd04773 2 TIGELAHLLGVPPSTLRHW----EKEGLLSP 28 (108)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCC
Confidence 5778999999988866544 55677754
No 259
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.05 E-value=3.1e+02 Score=22.76 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=20.8
Q ss_pred ecHHHHHHHhccceeehhhhHHHhhhccchhh
Q 016170 94 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 125 (394)
Q Consensus 94 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 125 (394)
+.+.++|+.+||+.+.|--. |..|+|..
T Consensus 2 ~~i~eva~~~gVs~~tLR~y----e~~Gli~p 29 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVY----DRLGLVSP 29 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHH----HHCCCCCC
Confidence 57899999999988766544 45667653
Done!