Query 015627
Match_columns 403
No_of_seqs 214 out of 459
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:04:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015627.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015627hhsearch_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 1.6E-65 3.5E-70 507.4 26.7 274 71-365 61-335 (354)
2 PF02319 E2F_TDP: E2F/DP famil 99.9 5.4E-23 1.2E-27 163.0 5.2 66 78-143 1-71 (71)
3 KOG2578 Transcription factor E 99.8 7.4E-20 1.6E-24 179.9 5.4 87 71-162 14-100 (388)
4 KOG2578 Transcription factor E 99.0 8.9E-11 1.9E-15 116.4 3.0 76 72-147 150-241 (388)
5 KOG2829 E2F-like protein [Tran 98.6 7.2E-07 1.6E-11 88.4 14.5 121 97-233 58-208 (326)
6 PF01978 TrmB: Sugar-specific 94.5 0.038 8.3E-07 42.6 3.1 45 98-142 19-63 (68)
7 PF08279 HTH_11: HTH domain; 93.7 0.097 2.1E-06 38.6 3.8 41 88-129 3-43 (55)
8 cd00092 HTH_CRP helix_turn_hel 92.2 0.27 5.8E-06 36.8 4.4 54 86-139 5-63 (67)
9 smart00420 HTH_DEOR helix_turn 92.0 0.19 4.2E-06 35.4 3.3 45 89-135 4-48 (53)
10 smart00550 Zalpha Z-DNA-bindin 90.6 0.35 7.6E-06 38.1 3.8 56 87-142 8-63 (68)
11 smart00346 HTH_ICLR helix_turn 89.9 0.5 1.1E-05 37.5 4.2 47 88-135 8-54 (91)
12 PF09339 HTH_IclR: IclR helix- 89.9 0.24 5.3E-06 36.6 2.2 45 89-134 7-51 (52)
13 COG1378 Predicted transcriptio 89.3 1.1 2.3E-05 43.9 6.7 51 90-143 22-72 (247)
14 PF13412 HTH_24: Winged helix- 87.1 0.76 1.7E-05 33.1 3.2 43 88-132 6-48 (48)
15 PF12802 MarR_2: MarR family; 87.0 0.71 1.5E-05 34.2 3.1 46 89-134 9-54 (62)
16 smart00418 HTH_ARSR helix_turn 86.6 0.73 1.6E-05 32.9 2.9 38 99-136 8-45 (66)
17 PF13730 HTH_36: Helix-turn-he 83.9 1.2 2.5E-05 32.8 2.9 30 102-131 26-55 (55)
18 COG3355 Predicted transcriptio 81.7 5.6 0.00012 35.9 6.8 85 90-189 33-120 (126)
19 PF02082 Rrf2: Transcriptional 81.6 1.9 4.1E-05 34.7 3.6 49 86-134 9-58 (83)
20 cd00090 HTH_ARSR Arsenical Res 81.3 2.9 6.2E-05 30.5 4.2 47 88-137 10-56 (78)
21 TIGR02944 suf_reg_Xantho FeS a 80.9 1.8 4E-05 37.2 3.5 46 89-134 13-58 (130)
22 PF01047 MarR: MarR family; I 80.7 1.4 3E-05 32.5 2.4 44 90-135 8-51 (59)
23 PF14394 DUF4423: Domain of un 80.6 19 0.0004 33.4 10.2 45 97-141 35-81 (171)
24 PF13463 HTH_27: Winged helix 80.2 2 4.3E-05 32.3 3.1 38 97-134 14-51 (68)
25 PF09079 Cdc6_C: CDC6, C termi 80.1 0.68 1.5E-05 37.2 0.5 29 106-134 27-58 (85)
26 smart00345 HTH_GNTR helix_turn 78.2 2.9 6.3E-05 30.0 3.4 40 98-137 16-56 (60)
27 cd08768 Cdc6_C Winged-helix do 78.0 1.1 2.4E-05 35.6 1.1 22 113-134 44-65 (87)
28 smart00419 HTH_CRP helix_turn_ 76.0 2.4 5.1E-05 29.6 2.3 38 101-139 8-45 (48)
29 cd00890 Prefoldin Prefoldin is 75.7 12 0.00026 31.6 6.9 54 135-188 68-121 (129)
30 PF08220 HTH_DeoR: DeoR-like h 73.6 3.8 8.2E-05 31.2 3.0 45 88-134 3-47 (57)
31 PF04182 B-block_TFIIIC: B-blo 73.0 3.9 8.4E-05 32.7 3.1 49 88-136 5-53 (75)
32 TIGR00122 birA_repr_reg BirA b 71.4 4.4 9.5E-05 31.3 3.0 40 89-131 4-43 (69)
33 PF00392 GntR: Bacterial regul 71.2 4.1 8.9E-05 31.1 2.7 50 88-137 7-60 (64)
34 PF01022 HTH_5: Bacterial regu 70.7 3.6 7.9E-05 29.8 2.2 41 90-133 7-47 (47)
35 PRK10163 DNA-binding transcrip 69.0 13 0.00028 36.1 6.2 54 89-143 29-82 (271)
36 PRK09834 DNA-binding transcrip 68.3 6.3 0.00014 38.0 3.9 50 90-140 16-66 (263)
37 PHA02943 hypothetical protein; 66.6 27 0.00059 32.9 7.5 48 88-138 14-61 (165)
38 PF01726 LexA_DNA_bind: LexA D 66.4 5.1 0.00011 31.7 2.4 46 90-135 14-60 (65)
39 TIGR02147 Fsuc_second hypothet 66.4 54 0.0012 32.7 10.1 42 98-139 134-177 (271)
40 cd04766 HTH_HspR Helix-Turn-He 66.3 15 0.00032 30.1 5.2 27 102-132 2-28 (91)
41 PF12840 HTH_20: Helix-turn-he 65.6 4.3 9.4E-05 30.7 1.8 46 88-135 13-58 (61)
42 cd04770 HTH_HMRTR Helix-Turn-H 65.5 15 0.00032 31.4 5.3 38 102-143 1-40 (123)
43 PF08784 RPA_C: Replication pr 65.5 7.1 0.00015 32.4 3.2 50 82-131 44-95 (102)
44 cd07377 WHTH_GntR Winged helix 65.1 8.2 0.00018 28.2 3.2 35 101-135 25-59 (66)
45 cd00584 Prefoldin_alpha Prefol 64.8 23 0.0005 30.5 6.4 54 136-189 69-122 (129)
46 PF09012 FeoC: FeoC like trans 64.8 2.8 6.1E-05 32.7 0.7 41 98-138 11-51 (69)
47 TIGR02702 SufR_cyano iron-sulf 64.6 42 0.00091 31.2 8.5 45 88-134 4-48 (203)
48 TIGR00738 rrf2_super rrf2 fami 64.6 8.6 0.00019 32.7 3.7 37 98-134 22-58 (132)
49 cd04775 HTH_Cfa-like Helix-Tur 63.9 20 0.00044 30.0 5.7 37 102-142 2-39 (102)
50 TIGR01610 phage_O_Nterm phage 63.9 9.7 0.00021 31.7 3.8 45 98-144 44-88 (95)
51 COG1414 IclR Transcriptional r 63.3 8.7 0.00019 37.1 3.9 51 89-140 8-59 (246)
52 TIGR02231 conserved hypothetic 62.7 48 0.001 35.3 9.5 96 155-267 139-240 (525)
53 PF08280 HTH_Mga: M protein tr 61.7 6.9 0.00015 29.9 2.3 36 89-126 9-44 (59)
54 PRK11414 colanic acid/biofilm 61.3 29 0.00062 32.2 6.7 50 88-137 18-70 (221)
55 cd04783 HTH_MerR1 Helix-Turn-H 61.0 24 0.00051 30.6 5.8 37 103-143 2-40 (126)
56 smart00347 HTH_MARR helix_turn 60.6 14 0.0003 28.9 3.9 45 88-134 13-57 (101)
57 cd04789 HTH_Cfa Helix-Turn-Hel 60.1 23 0.00051 29.7 5.4 38 102-143 2-40 (102)
58 cd01109 HTH_YyaN Helix-Turn-He 59.6 23 0.00049 30.1 5.3 36 103-142 2-39 (113)
59 PF12329 TMF_DNA_bd: TATA elem 59.3 25 0.00054 28.6 5.3 37 153-189 11-47 (74)
60 PRK10411 DNA-binding transcrip 59.1 38 0.00083 32.6 7.4 53 88-142 7-59 (240)
61 TIGR02337 HpaR homoprotocatech 59.1 6.9 0.00015 32.9 2.1 37 99-135 40-76 (118)
62 PF13518 HTH_28: Helix-turn-he 59.0 8.4 0.00018 27.5 2.3 37 90-130 5-41 (52)
63 COG2739 Uncharacterized protei 58.9 7.6 0.00016 34.2 2.3 40 84-123 16-55 (105)
64 PRK03573 transcriptional regul 58.9 70 0.0015 27.6 8.4 35 101-135 46-80 (144)
65 PRK03947 prefoldin subunit alp 58.7 35 0.00076 29.9 6.5 51 137-187 77-127 (140)
66 COG1474 CDC6 Cdc6-related prot 58.7 6.2 0.00013 40.6 2.1 29 104-132 304-332 (366)
67 PRK09954 putative kinase; Prov 58.6 9.6 0.00021 37.9 3.4 47 86-134 4-50 (362)
68 cd04784 HTH_CadR-PbrR Helix-Tu 58.3 25 0.00054 30.4 5.5 79 102-189 1-100 (127)
69 smart00344 HTH_ASNC helix_turn 57.7 12 0.00025 30.8 3.2 47 86-134 4-50 (108)
70 PF01325 Fe_dep_repress: Iron 57.6 17 0.00037 28.2 3.9 42 93-135 15-56 (60)
71 TIGR01764 excise DNA binding d 57.5 6.2 0.00013 27.3 1.3 22 102-123 2-23 (49)
72 PRK06474 hypothetical protein; 57.5 97 0.0021 28.8 9.5 47 88-135 14-61 (178)
73 TIGR02716 C20_methyl_CrtF C-20 57.0 6.6 0.00014 38.2 1.9 40 99-139 21-60 (306)
74 PRK10870 transcriptional repre 56.7 48 0.001 30.4 7.3 40 95-134 65-104 (176)
75 TIGR01889 Staph_reg_Sar staphy 56.4 13 0.00027 31.3 3.2 46 90-135 30-77 (109)
76 PF04977 DivIC: Septum formati 56.1 30 0.00064 26.9 5.1 36 155-190 18-53 (80)
77 PRK11511 DNA-binding transcrip 56.0 18 0.00038 31.3 4.1 42 83-124 7-48 (127)
78 PF07106 TBPIP: Tat binding pr 55.6 1.2E+02 0.0025 27.6 9.5 96 90-187 6-105 (169)
79 TIGR02047 CadR-PbrR Cd(II)/Pb( 55.6 26 0.00057 30.6 5.2 37 103-143 2-40 (127)
80 PRK00215 LexA repressor; Valid 55.2 13 0.00028 34.3 3.4 42 96-137 18-60 (205)
81 PF13545 HTH_Crp_2: Crp-like h 55.0 9.6 0.00021 29.2 2.1 51 86-136 3-63 (76)
82 PRK09413 IS2 repressor TnpA; R 54.6 1E+02 0.0022 26.6 8.6 31 100-130 28-58 (121)
83 cd00632 Prefoldin_beta Prefold 54.2 21 0.00045 30.2 4.2 76 108-187 22-103 (105)
84 PRK14165 winged helix-turn-hel 53.7 24 0.00052 34.2 5.0 55 87-141 6-61 (217)
85 TIGR02431 pcaR_pcaU beta-ketoa 53.5 16 0.00036 34.6 3.9 44 90-134 14-57 (248)
86 PRK05014 hscB co-chaperone Hsc 53.1 1.2E+02 0.0026 28.1 9.4 54 78-133 12-82 (171)
87 smart00529 HTH_DTXR Helix-turn 52.7 9.9 0.00021 30.5 2.0 33 104-136 2-34 (96)
88 PRK11569 transcriptional repre 52.4 48 0.001 32.2 6.9 45 90-135 33-77 (274)
89 PRK00888 ftsB cell division pr 52.1 38 0.00083 29.2 5.5 60 156-221 29-90 (105)
90 TIGR00293 prefoldin, archaeal 51.6 56 0.0012 28.0 6.5 54 136-189 68-121 (126)
91 PRK10219 DNA-binding transcrip 50.8 21 0.00047 29.3 3.7 40 85-124 5-44 (107)
92 PRK13509 transcriptional repre 49.5 14 0.0003 35.7 2.7 44 89-134 9-52 (251)
93 KOG1318 Helix loop helix trans 48.8 15 0.00033 39.0 3.0 76 112-189 239-318 (411)
94 COG1777 Predicted transcriptio 48.0 1.1E+02 0.0023 30.2 8.4 43 88-133 18-60 (217)
95 COG1846 MarR Transcriptional r 47.4 20 0.00044 28.7 3.0 44 90-135 27-70 (126)
96 TIGR00498 lexA SOS regulatory 47.2 22 0.00049 32.5 3.6 48 88-135 9-60 (199)
97 TIGR01884 cas_HTH CRISPR locus 47.2 24 0.00052 32.8 3.8 45 90-136 148-192 (203)
98 PF05565 Sipho_Gp157: Siphovir 47.0 1.8E+02 0.0039 26.6 9.4 32 82-113 2-33 (162)
99 PRK11050 manganese transport r 46.8 33 0.00072 30.8 4.5 38 99-136 49-86 (152)
100 TIGR02297 HpaA 4-hydroxyphenyl 46.8 21 0.00046 33.7 3.5 43 85-127 186-228 (287)
101 TIGR02010 IscR iron-sulfur clu 46.4 24 0.00051 30.9 3.5 38 96-133 20-57 (135)
102 TIGR02366 DHAK_reg probable di 46.1 22 0.00048 31.2 3.3 36 84-119 6-41 (176)
103 COG1382 GimC Prefoldin, chaper 45.3 51 0.0011 29.6 5.4 99 85-191 10-114 (119)
104 TIGR02338 gimC_beta prefoldin, 45.0 51 0.0011 28.1 5.2 83 105-188 20-108 (110)
105 PF05491 RuvB_C: Holliday junc 44.6 31 0.00068 28.7 3.7 59 81-139 4-64 (76)
106 COG1510 Predicted transcriptio 44.5 85 0.0019 30.0 7.0 38 98-135 38-75 (177)
107 KOG2255 Peptidyl-tRNA hydrolas 44.3 22 0.00047 34.9 3.1 64 49-134 29-92 (224)
108 cd07153 Fur_like Ferric uptake 44.1 27 0.00059 29.0 3.4 45 90-135 6-55 (116)
109 TIGR03338 phnR_burk phosphonat 43.3 45 0.00097 30.5 4.9 41 97-137 30-70 (212)
110 COG2894 MinD Septum formation 42.9 9.8 0.00021 38.1 0.6 28 102-129 41-68 (272)
111 PRK15090 DNA-binding transcrip 42.8 29 0.00063 33.2 3.8 47 89-137 18-64 (257)
112 PRK09514 zntR zinc-responsive 42.7 68 0.0015 28.6 5.8 38 102-143 2-41 (140)
113 PRK09802 DNA-binding transcrip 42.3 1.2E+02 0.0026 29.7 8.0 50 87-138 19-68 (269)
114 PRK10857 DNA-binding transcrip 42.1 29 0.00064 31.9 3.5 39 96-134 20-58 (164)
115 PF05732 RepL: Firmicute plasm 42.0 22 0.00047 32.9 2.6 39 101-139 75-113 (165)
116 cd04762 HTH_MerR-trunc Helix-T 41.9 21 0.00046 24.3 2.0 23 102-124 1-23 (49)
117 KOG3863 bZIP transcription fac 41.3 52 0.0011 36.7 5.7 65 123-190 484-554 (604)
118 PRK13626 transcriptional regul 41.3 57 0.0012 34.8 6.0 48 85-132 5-54 (552)
119 PRK09391 fixK transcriptional 41.2 41 0.00088 31.4 4.4 39 102-140 180-218 (230)
120 TIGR02051 MerR Hg(II)-responsi 41.0 75 0.0016 27.6 5.7 36 104-143 2-39 (124)
121 COG4189 Predicted transcriptio 41.0 24 0.00051 35.6 2.9 52 81-134 18-70 (308)
122 PRK09343 prefoldin subunit bet 40.8 62 0.0013 28.4 5.2 73 116-189 35-113 (121)
123 PLN03239 histone acetyltransfe 40.3 47 0.001 34.7 5.0 54 77-133 252-313 (351)
124 PRK13752 putative transcriptio 40.2 68 0.0015 28.9 5.5 79 102-189 8-105 (144)
125 PF02954 HTH_8: Bacterial regu 40.2 32 0.00069 24.6 2.7 37 83-121 2-38 (42)
126 TIGR02044 CueR Cu(I)-responsiv 40.2 78 0.0017 27.5 5.7 37 103-143 2-40 (127)
127 COG1802 GntR Transcriptional r 40.0 53 0.0011 30.7 4.9 40 97-136 35-74 (230)
128 TIGR02043 ZntR Zn(II)-responsi 40.0 91 0.002 27.4 6.1 81 102-189 2-102 (131)
129 cd01108 HTH_CueR Helix-Turn-He 38.7 91 0.002 27.1 5.9 37 103-143 2-40 (127)
130 PF10779 XhlA: Haemolysin XhlA 38.5 95 0.0021 24.7 5.5 35 155-189 14-48 (71)
131 PRK00080 ruvB Holliday junctio 38.2 40 0.00087 33.3 4.0 57 81-137 255-313 (328)
132 PF10018 Med4: Vitamin-D-recep 38.0 1.2E+02 0.0025 28.4 6.9 28 157-184 25-52 (188)
133 PF09940 DUF2172: Domain of un 37.8 23 0.0005 37.3 2.4 47 82-132 340-386 (386)
134 PRK10130 transcriptional regul 37.8 34 0.00073 35.0 3.5 40 84-123 239-278 (350)
135 PF14257 DUF4349: Domain of un 37.8 1.3E+02 0.0028 29.1 7.3 87 81-178 59-156 (262)
136 cd04785 HTH_CadR-PbrR-like Hel 37.7 80 0.0017 27.4 5.4 81 102-189 1-100 (126)
137 PF02796 HTH_7: Helix-turn-hel 37.7 16 0.00034 26.5 0.8 32 88-123 12-43 (45)
138 PF03374 ANT: Phage antirepres 37.7 30 0.00066 28.9 2.7 41 90-134 14-54 (111)
139 PF13384 HTH_23: Homeodomain-l 37.6 26 0.00057 25.0 2.0 35 90-128 10-44 (50)
140 PRK11014 transcriptional repre 37.5 35 0.00076 30.0 3.2 41 96-136 20-60 (141)
141 COG1522 Lrp Transcriptional re 37.2 40 0.00086 29.1 3.4 50 83-134 6-55 (154)
142 cd04787 HTH_HMRTR_unk Helix-Tu 37.0 95 0.002 27.2 5.8 36 103-142 2-39 (133)
143 PRK10869 recombination and rep 37.0 47 0.001 36.1 4.6 103 77-189 257-362 (553)
144 PF04111 APG6: Autophagy prote 36.4 72 0.0016 32.3 5.6 36 156-191 59-94 (314)
145 PF05930 Phage_AlpA: Prophage 35.8 21 0.00045 26.5 1.2 24 100-123 2-25 (51)
146 PRK11512 DNA-binding transcrip 35.7 25 0.00055 30.6 2.0 37 99-135 52-88 (144)
147 COG1373 Predicted ATPase (AAA+ 35.6 39 0.00085 35.0 3.6 50 85-134 220-270 (398)
148 PRK11534 DNA-binding transcrip 35.3 1.3E+02 0.0027 27.9 6.6 46 97-142 26-71 (224)
149 PLN03238 probable histone acet 35.1 67 0.0014 32.9 5.0 39 90-132 213-251 (290)
150 PRK10225 DNA-binding transcrip 35.0 1.8E+02 0.0038 27.6 7.7 52 85-136 13-68 (257)
151 KOG3026 Splicing factor SPF30 34.9 1.3E+02 0.0029 30.2 6.9 82 164-250 26-116 (262)
152 cd04790 HTH_Cfa-like_unk Helix 34.8 60 0.0013 29.9 4.4 37 102-144 2-42 (172)
153 PF04297 UPF0122: Putative hel 34.4 26 0.00056 30.5 1.8 41 84-124 16-56 (101)
154 PF04703 FaeA: FaeA-like prote 34.3 43 0.00093 26.6 2.9 44 90-134 5-48 (62)
155 PHA01750 hypothetical protein 34.3 90 0.002 25.8 4.7 30 155-184 43-72 (75)
156 PF14817 HAUS5: HAUS augmin-li 34.2 72 0.0016 35.7 5.5 52 132-184 53-109 (632)
157 PF13551 HTH_29: Winged helix- 33.9 32 0.0007 27.7 2.2 28 103-130 14-41 (112)
158 PF12793 SgrR_N: Sugar transpo 33.9 1.5E+02 0.0032 25.9 6.4 47 86-132 2-50 (115)
159 TIGR02928 orc1/cdc6 family rep 33.8 37 0.0008 33.4 3.0 31 106-136 319-352 (365)
160 cd04788 HTH_NolA-AlbR Helix-Tu 33.7 1.4E+02 0.0029 24.8 5.9 37 103-143 2-40 (96)
161 PF09756 DDRGK: DDRGK domain; 33.7 44 0.00095 31.9 3.3 47 86-134 100-146 (188)
162 PHA00738 putative HTH transcri 33.4 1.4E+02 0.003 26.5 6.1 72 88-166 15-86 (108)
163 PRK09863 putative frv operon r 33.3 1.4E+02 0.003 32.2 7.4 52 89-145 8-65 (584)
164 PF14947 HTH_45: Winged helix- 33.2 39 0.00084 27.0 2.5 42 99-141 17-58 (77)
165 PRK15121 right oriC-binding tr 33.2 48 0.001 32.1 3.6 44 85-128 5-48 (289)
166 PF01920 Prefoldin_2: Prefoldi 33.1 89 0.0019 25.4 4.7 31 156-186 71-101 (106)
167 PRK03902 manganese transport t 32.7 79 0.0017 27.7 4.6 46 88-135 11-56 (142)
168 PF03444 HrcA_DNA-bdg: Winged 32.4 78 0.0017 26.5 4.2 46 88-134 11-56 (78)
169 PF04218 CENP-B_N: CENP-B N-te 32.4 36 0.00078 25.7 2.1 42 79-123 3-44 (53)
170 PF12728 HTH_17: Helix-turn-he 32.0 27 0.00058 25.2 1.3 22 102-123 2-23 (51)
171 PF01475 FUR: Ferric uptake re 31.8 40 0.00087 28.4 2.5 49 88-137 11-64 (120)
172 PRK10402 DNA-binding transcrip 31.6 37 0.00081 31.5 2.5 53 87-140 152-207 (226)
173 PF01920 Prefoldin_2: Prefoldi 31.5 1.3E+02 0.0028 24.5 5.4 81 106-189 16-97 (106)
174 PF05377 FlaC_arch: Flagella a 31.1 1.4E+02 0.003 23.6 5.1 39 151-189 4-42 (55)
175 PF08781 DP: Transcription fac 31.0 1.2E+02 0.0026 28.0 5.5 19 215-233 59-77 (142)
176 PRK11886 bifunctional biotin-- 30.9 61 0.0013 32.1 4.0 52 88-141 7-59 (319)
177 PF01638 HxlR: HxlR-like helix 30.6 39 0.00084 27.6 2.1 42 94-135 11-53 (90)
178 COG3093 VapI Plasmid maintenan 30.3 25 0.00055 30.9 1.1 34 85-124 13-46 (104)
179 PF15513 DUF4651: Domain of un 30.2 32 0.0007 27.7 1.5 23 248-270 16-38 (62)
180 PRK09464 pdhR transcriptional 30.1 1.9E+02 0.004 27.4 6.9 54 82-135 10-68 (254)
181 PRK13503 transcriptional activ 29.7 65 0.0014 30.3 3.8 40 84-123 170-209 (278)
182 PF02295 z-alpha: Adenosine de 29.6 85 0.0018 25.0 3.9 57 86-142 5-61 (66)
183 PF10141 ssDNA-exonuc_C: Singl 29.3 2.8E+02 0.006 26.0 7.9 47 88-134 101-149 (195)
184 PRK11169 leucine-responsive tr 29.2 76 0.0016 28.6 4.0 52 80-133 9-60 (164)
185 cd01106 HTH_TipAL-Mta Helix-Tu 29.1 1.8E+02 0.0039 24.1 6.0 17 103-119 2-18 (103)
186 PRK09393 ftrA transcriptional 29.0 65 0.0014 31.6 3.8 42 85-126 218-259 (322)
187 cd04782 HTH_BltR Helix-Turn-He 29.0 84 0.0018 26.1 3.9 37 103-143 2-40 (97)
188 cd04768 HTH_BmrR-like Helix-Tu 29.0 1.1E+02 0.0024 25.4 4.6 38 103-144 2-41 (96)
189 PRK11753 DNA-binding transcrip 28.3 67 0.0014 28.8 3.5 39 101-140 168-206 (211)
190 PRK13922 rod shape-determining 28.3 1.1E+02 0.0024 29.6 5.3 40 152-192 74-113 (276)
191 PRK01194 V-type ATP synthase s 28.1 3E+02 0.0066 25.7 7.9 33 158-190 67-99 (185)
192 cd04777 HTH_MerR-like_sg1 Heli 28.0 1.8E+02 0.004 24.3 5.8 25 103-133 2-28 (107)
193 cd04769 HTH_MerR2 Helix-Turn-H 28.0 2E+02 0.0043 24.6 6.1 86 102-189 1-114 (116)
194 KOG2747 Histone acetyltransfer 27.6 1.2E+02 0.0026 32.3 5.6 58 81-143 303-366 (396)
195 PF10779 XhlA: Haemolysin XhlA 27.6 1.7E+02 0.0038 23.2 5.3 39 152-190 4-42 (71)
196 PF01853 MOZ_SAS: MOZ/SAS fami 27.2 63 0.0014 31.1 3.2 49 88-139 136-185 (188)
197 COG2512 Predicted membrane-ass 27.0 74 0.0016 31.6 3.8 61 81-142 191-251 (258)
198 PRK03837 transcriptional regul 27.0 45 0.00097 31.0 2.2 51 86-136 18-72 (241)
199 PF13851 GAS: Growth-arrest sp 26.9 1.3E+02 0.0027 28.7 5.2 35 155-189 28-62 (201)
200 PF09904 HTH_43: Winged helix- 26.9 66 0.0014 27.7 2.9 30 103-132 23-52 (90)
201 PRK00888 ftsB cell division pr 26.8 1.5E+02 0.0033 25.5 5.2 54 151-205 31-84 (105)
202 PRK09975 DNA-binding transcrip 26.4 71 0.0015 28.7 3.3 37 84-120 14-50 (213)
203 TIGR00635 ruvB Holliday juncti 26.3 79 0.0017 30.4 3.8 52 86-137 239-292 (305)
204 COG2378 Predicted transcriptio 26.1 52 0.0011 33.1 2.6 44 86-131 6-52 (311)
205 PRK10572 DNA-binding transcrip 26.0 81 0.0017 30.1 3.8 38 86-123 184-221 (290)
206 COG4519 Uncharacterized protei 25.8 86 0.0019 26.9 3.4 42 90-132 12-53 (95)
207 cd04779 HTH_MerR-like_sg4 Heli 25.7 56 0.0012 29.3 2.4 82 102-189 1-102 (134)
208 cd04772 HTH_TioE_rpt1 First He 25.5 1.3E+02 0.0028 25.2 4.4 37 103-143 2-40 (99)
209 cd04773 HTH_TioE_rpt2 Second H 25.5 2.2E+02 0.0048 24.1 5.9 27 103-133 2-28 (108)
210 PF10018 Med4: Vitamin-D-recep 25.4 1.7E+02 0.0038 27.2 5.7 54 153-206 28-88 (188)
211 cd04776 HTH_GnyR Helix-Turn-He 25.4 1.4E+02 0.0031 25.8 4.9 8 88-95 45-52 (118)
212 PRK13729 conjugal transfer pil 25.3 1.1E+02 0.0023 33.4 4.8 22 168-189 97-118 (475)
213 TIGR02338 gimC_beta prefoldin, 25.3 1.3E+02 0.0029 25.6 4.6 32 157-188 70-101 (110)
214 PRK09990 DNA-binding transcrip 25.2 95 0.0021 29.3 4.0 49 88-136 14-66 (251)
215 PF09340 NuA4: Histone acetylt 25.0 1.1E+02 0.0025 25.2 4.0 28 161-188 2-29 (80)
216 PLN00104 MYST -like histone ac 24.6 1.3E+02 0.0029 32.5 5.3 53 77-133 345-403 (450)
217 smart00338 BRLZ basic region l 24.5 2.6E+02 0.0057 21.5 5.7 33 156-188 28-60 (65)
218 PRK04984 fatty acid metabolism 24.4 53 0.0011 30.6 2.1 39 97-135 26-65 (239)
219 PRK10371 DNA-binding transcrip 23.9 84 0.0018 30.9 3.5 39 86-124 192-230 (302)
220 PRK09333 30S ribosomal protein 23.9 75 0.0016 29.6 2.9 37 99-135 65-115 (150)
221 cd01279 HTH_HspR-like Helix-Tu 23.8 2.5E+02 0.0054 23.4 5.9 28 102-133 2-29 (98)
222 KOG3990 Uncharacterized conser 23.8 91 0.002 31.7 3.7 40 155-194 226-265 (305)
223 PRK06266 transcription initiat 23.8 3.2E+02 0.0069 25.6 7.2 41 90-132 27-67 (178)
224 PF03836 RasGAP_C: RasGAP C-te 23.6 27 0.00057 31.2 0.0 26 114-141 5-30 (142)
225 cd00592 HTH_MerR-like Helix-Tu 23.6 1.2E+02 0.0025 24.8 3.8 21 103-123 2-22 (100)
226 COG2207 AraC AraC-type DNA-bin 23.5 1E+02 0.0022 24.7 3.4 43 89-131 24-66 (127)
227 PF05225 HTH_psq: helix-turn-h 23.4 66 0.0014 23.6 2.1 26 99-124 14-39 (45)
228 PF03428 RP-C: Replication pro 23.2 2.4E+02 0.0053 26.6 6.3 31 105-135 74-105 (177)
229 COG1321 TroR Mn-dependent tran 23.2 1.1E+02 0.0024 28.0 3.9 42 98-139 21-62 (154)
230 PRK05638 threonine synthase; V 23.2 1.2E+02 0.0026 31.7 4.7 61 71-134 357-419 (442)
231 PRK10906 DNA-binding transcrip 23.0 58 0.0013 31.6 2.2 45 88-134 8-52 (252)
232 PRK09685 DNA-binding transcrip 23.0 79 0.0017 30.2 3.1 38 86-123 198-236 (302)
233 TIGR00373 conserved hypothetic 23.0 2.7E+02 0.0058 25.5 6.4 34 99-132 26-59 (158)
234 PF01710 HTH_Tnp_IS630: Transp 23.0 95 0.002 26.8 3.3 43 88-135 60-102 (119)
235 PF09107 SelB-wing_3: Elongati 22.4 94 0.002 23.6 2.8 39 98-136 7-45 (50)
236 COG2919 Septum formation initi 22.4 74 0.0016 27.8 2.5 31 153-183 56-86 (117)
237 PRK11179 DNA-binding transcrip 22.3 98 0.0021 27.5 3.3 50 83-134 7-56 (153)
238 PF14712 Snapin_Pallidin: Snap 22.3 2.5E+02 0.0054 22.8 5.5 36 154-189 14-49 (92)
239 PRK11642 exoribonuclease R; Pr 21.6 1E+02 0.0022 35.4 4.0 51 89-140 23-77 (813)
240 COG1730 GIM5 Predicted prefold 21.5 6.5E+02 0.014 23.2 9.1 88 151-266 10-97 (145)
241 PF13600 DUF4140: N-terminal d 21.5 2.5E+02 0.0054 23.3 5.4 35 153-187 69-103 (104)
242 PRK04214 rbn ribonuclease BN/u 21.4 1.1E+02 0.0024 31.8 4.0 43 98-140 307-349 (412)
243 PRK03578 hscB co-chaperone Hsc 21.2 6.9E+02 0.015 23.4 8.9 51 78-130 17-84 (176)
244 PRK10434 srlR DNA-bindng trans 21.2 85 0.0018 30.5 2.9 44 89-134 9-52 (256)
245 TIGR02063 RNase_R ribonuclease 21.1 1.1E+02 0.0023 34.2 4.0 55 88-142 5-63 (709)
246 PF05103 DivIVA: DivIVA protei 21.0 38 0.00083 28.8 0.5 48 139-189 13-60 (131)
247 PRK04217 hypothetical protein; 21.0 84 0.0018 27.6 2.6 47 77-123 34-80 (110)
248 PRK15185 transcriptional regul 21.0 1E+02 0.0022 31.6 3.6 39 85-123 206-244 (309)
249 PTZ00064 histone acetyltransfe 20.9 1.5E+02 0.0032 32.8 4.9 30 102-134 472-501 (552)
250 PF11853 DUF3373: Protein of u 20.9 66 0.0014 35.0 2.3 33 151-183 28-60 (489)
251 KOG0804 Cytoplasmic Zn-finger 20.8 1.7E+02 0.0037 32.0 5.2 59 117-189 390-449 (493)
252 PRK10803 tol-pal system protei 20.8 1.8E+02 0.0039 28.6 5.1 31 159-189 59-89 (263)
253 PF11932 DUF3450: Protein of u 20.6 2E+02 0.0044 27.7 5.4 34 155-188 57-90 (251)
254 PF00170 bZIP_1: bZIP transcri 20.5 3.8E+02 0.0083 20.5 5.9 33 156-188 28-60 (64)
255 PF13542 HTH_Tnp_ISL3: Helix-t 20.4 95 0.0021 22.3 2.4 38 86-123 12-49 (52)
256 PF04977 DivIC: Septum formati 20.3 1.9E+02 0.0042 22.2 4.3 29 152-180 22-50 (80)
257 TIGR00634 recN DNA repair prot 20.3 1.5E+02 0.0031 32.1 4.7 83 79-171 264-346 (563)
258 smart00342 HTH_ARAC helix_turn 20.1 68 0.0015 23.8 1.6 27 102-128 2-28 (84)
259 TIGR01950 SoxR redox-sensitive 20.1 2.7E+02 0.0058 25.1 5.6 80 101-189 1-108 (142)
260 PF02996 Prefoldin: Prefoldin 20.0 1.9E+02 0.0042 24.1 4.5 51 137-187 60-110 (120)
261 PF08317 Spc7: Spc7 kinetochor 20.0 2.8E+02 0.0062 28.0 6.4 67 159-231 235-309 (325)
No 1
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=100.00 E-value=1.6e-65 Score=507.36 Aligned_cols=274 Identities=42% Similarity=0.596 Sum_probs=214.0
Q ss_pred CCCCCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCC
Q 015627 71 LTPAGSCRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPG 150 (403)
Q Consensus 71 ~~p~~~~R~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~ 150 (403)
..|...+|+++|||+||||||.|++++|+|++|||+||+.|+|||||||||||||||||||+|++||+|+|+|.+....+
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 45667899999999999999999999999999999999999999999999999999999999999999999999887666
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccccccCHHHHhhccCCCCceEEEEeCCCCCeEEecC
Q 015627 151 EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLHCFQNQTLIAIKAPQGTTLEVPD 230 (403)
Q Consensus 151 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT~LEVPd 230 (403)
+..++.+.|++|++.|.++|+.||++|++|+++|+.|++|..|++|+|||++||++|+.|++|||||||||++|+||||+
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 CCcccCCCCCcEEEEEecCCCceEEEEecCccccccccCCCCCCCCCCCCCCCCCcccchhhhhhccccCcchhhhhhhh
Q 015627 231 PDEAVDYPQRRYRIILRSTMGPIDVYLVSRFEEKFEETNSVEPPASVPPVSSSDSNENQVKEIINVDRAGNETEAQAQQA 310 (403)
Q Consensus 231 P~e~~~~~q~~YqI~LkSt~GPIdVyL~~~~~~~~e~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (403)
|++ .+|+|+|+|++||||||||+.++.. .......|...+.....+...-+. + ....... ...
T Consensus 221 ~~~------~~~~i~L~s~~GpI~v~l~~~e~~~--~~~~~~~~~~~~~~~~~~~~~sp~--~----~~~~~~~---~~~ 283 (354)
T KOG2577|consen 221 PDE------DRYQIRLKSNQGPIDVYLCSEEEGE--ESEPTAKPVGSSSSSEDTISPSPY--L----PEQPASL---ALN 283 (354)
T ss_pred CCC------CceEEEeccCCCceeEEeccccccC--ccCCCCCCCCCccccccCCCCCCC--c----CCchhhh---hcC
Confidence 984 4799999999999999999988762 222222222111100001111110 0 0000000 000
Q ss_pred hccCCCCcccccccCCeeeeccCCC-CCCCCeeeecCCCCcccccccCCCCCCccc
Q 015627 311 HQIYSDLNSSQEVVGGMMKIVPSDV-DNDADYWLLSDADVSITDMWKTDSGAEWDG 365 (403)
Q Consensus 311 ~~~~s~~~~~~~~~~g~~ki~psd~-~~d~dywl~sd~~vsitd~w~~~~~~~w~~ 365 (403)
+.. ++... + .+-...-.|++. ..+.|||++...+++...+|-+.+..+||-
T Consensus 284 p~~-~~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~i~l~~~~~~~dy 335 (354)
T KOG2577|consen 284 PQQ-SEELL--D-SSNLLSFFPSTSASGSSDIRESFSDDLSEPLISLSPPPRQEDY 335 (354)
T ss_pred ccc-ccchh--h-cccccccCccccccCCcceeccccccccCCcccCCCCcccccc
Confidence 010 11000 0 011111122222 356899999999999999999999889983
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=5.4e-23 Score=163.02 Aligned_cols=66 Identities=52% Similarity=0.859 Sum_probs=63.1
Q ss_pred CCcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHh---cc--ceeehhhhHHHhhhccchhhccCCeEEEec
Q 015627 78 RYDSSLGLLTKKFINLIKHAEDGILDLNKAAETL---EV--QKRRIYDITNVLEGIGLIEKKLKNRIRWKG 143 (403)
Q Consensus 78 R~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L---~V--qKRRIYDItNVLEgIGLIeK~sKN~i~W~G 143 (403)
|+++||+.||++||++|...+++.++|+++|+.| ++ +|||||||+||||++|||+|..|+.|+|+|
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=99.79 E-value=7.4e-20 Score=179.88 Aligned_cols=87 Identities=37% Similarity=0.592 Sum_probs=76.5
Q ss_pred CCCCCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCC
Q 015627 71 LTPAGSCRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPG 150 (403)
Q Consensus 71 ~~p~~~~R~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~ 150 (403)
..+.-++|++||||+||.+|+.++....-..+-|+.||.+|||.|||||||+||||+||++.|.+||.|+|+|+...
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 44566899999999999999999987777789999999999999999999999999999999999999999998643
Q ss_pred CchHHHHHHHHH
Q 015627 151 EVDADASILQAD 162 (403)
Q Consensus 151 ~~~~~~~~Lk~E 162 (403)
..-+..||+|
T Consensus 91 --Pral~eLqeE 100 (388)
T KOG2578|consen 91 --PRALFELQEE 100 (388)
T ss_pred --hHHHHHHHHH
Confidence 3445566644
No 4
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.04 E-value=8.9e-11 Score=116.44 Aligned_cols=76 Identities=37% Similarity=0.598 Sum_probs=65.7
Q ss_pred CCCCCCCCcCcHHHHHHHHHHHHhhCCCC-cccHHHHHHHhc----------cceeehhhhHHHhhhccchhhc-----c
Q 015627 72 TPAGSCRYDSSLGLLTKKFINLIKHAEDG-ILDLNKAAETLE----------VQKRRIYDITNVLEGIGLIEKK-----L 135 (403)
Q Consensus 72 ~p~~~~R~dkSLglLTkKFI~Ll~~ap~g-~ldLn~aA~~L~----------VqKRRIYDItNVLEgIGLIeK~-----s 135 (403)
.+....|+++||++||++||.++-.+++. .|.|+.||..|= -.-||+|||.|||-+++||+|. .
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 34456889999999999999999998888 899999999871 2559999999999999999997 5
Q ss_pred CCeEEEeccCCC
Q 015627 136 KNRIRWKGLDNS 147 (403)
Q Consensus 136 KN~i~W~G~~~s 147 (403)
|..|+|.|....
T Consensus 230 kPafrwlG~~~~ 241 (388)
T KOG2578|consen 230 KPAFRWLGSKPI 241 (388)
T ss_pred cchhheeCCCcc
Confidence 899999997543
No 5
>KOG2829 consensus E2F-like protein [Transcription]
Probab=98.63 E-value=7.2e-07 Score=88.43 Aligned_cols=121 Identities=26% Similarity=0.458 Sum_probs=78.2
Q ss_pred CCCCcccHHHHHHHh----------------------ccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchH
Q 015627 97 AEDGILDLNKAAETL----------------------EVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDA 154 (403)
Q Consensus 97 ap~g~ldLn~aA~~L----------------------~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~ 154 (403)
...|...-|++|+.| .--|||+||..|||.++.+|.|. |..|+|+|+.... .+
T Consensus 58 e~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KKEIrW~GLP~~s----s~ 132 (326)
T KOG2829|consen 58 ERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KKEIRWIGLPATS----SQ 132 (326)
T ss_pred HhcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cceeeeeccCccc----hH
Confidence 345666777777666 23689999999999999999999 5569999998653 23
Q ss_pred HHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhhhhcccccccccC----HHHHhhccCCCCceEEEEeCCCCCeE
Q 015627 155 DASILQADIDNLS----MEELRVDEQTRELRERLRELIENENNRKWLFVT----EEDIKNLHCFQNQTLIAIKAPQGTTL 226 (403)
Q Consensus 155 ~~~~Lk~El~~L~----~~E~~LD~lI~~~~q~L~~Lted~~n~~~aYVT----~eDI~~l~~f~~qTvIAIKAP~gT~L 226 (403)
.+.+|+.|...+. ++-..|.++|... -.+++|.+ .| +.++.+ .+.| .| .+|.|..-+.|.+
T Consensus 133 dv~~le~Er~k~~erI~kK~a~lqEl~~q~-~~fknLV~--RN-~~~e~~~~~P~~~i-~L------PFiiinT~k~a~I 201 (326)
T KOG2829|consen 133 DVSELEEERKKRMERIKKKAAQLQELIEQV-SAFKNLVQ--RN-RHAESQGQPPSENI-HL------PFIIINTSKKAVI 201 (326)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH--hh-hhhhhccCCCCccc-cc------ceEEEecCCCceE
Confidence 4566665554443 3444555554432 34566654 22 223333 1222 12 2688999999999
Q ss_pred EecCCCc
Q 015627 227 EVPDPDE 233 (403)
Q Consensus 227 EVPdP~e 233 (403)
++-..++
T Consensus 202 eceiseD 208 (326)
T KOG2829|consen 202 ECEISED 208 (326)
T ss_pred EEEeccc
Confidence 9987654
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=94.45 E-value=0.038 Score=42.61 Aligned_cols=45 Identities=22% Similarity=0.397 Sum_probs=40.8
Q ss_pred CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 015627 98 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 142 (403)
Q Consensus 98 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 142 (403)
..+.....++|+.+++.|..+|++++-|+.-|||++...+.+.|.
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 457799999999999999999999999999999999987776665
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=93.68 E-value=0.097 Score=38.55 Aligned_cols=41 Identities=24% Similarity=0.366 Sum_probs=35.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhcc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIG 129 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIG 129 (403)
.+.+.+|..+.+. +...++|+.|+|++|-||--++.|+..|
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 4677788666666 9999999999999999999999999988
No 8
>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=92.18 E-value=0.27 Score=36.76 Aligned_cols=54 Identities=20% Similarity=0.233 Sum_probs=42.8
Q ss_pred HHHHHHHHHhhC-----CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 015627 86 LTKKFINLIKHA-----EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 139 (403)
Q Consensus 86 LTkKFI~Ll~~a-----p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 139 (403)
+++-|+.+.... ..+.+...++|+.+++.+..++.+++.|+.-|+|++.....|
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 446789999999999999999999999999999998764444
No 9
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=92.04 E-value=0.19 Score=35.39 Aligned_cols=45 Identities=27% Similarity=0.372 Sum_probs=38.5
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.++.++... +.+.+.++|+.|++.++.+|.++.-|+.-|+|.+..
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 466666553 459999999999999999999999999999998764
No 10
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=90.58 E-value=0.35 Score=38.07 Aligned_cols=56 Identities=20% Similarity=0.300 Sum_probs=46.7
Q ss_pred HHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 015627 87 TKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 142 (403)
Q Consensus 87 TkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 142 (403)
-.+.+.+|+.+++..+.+.++|+.||+.|+-+.-++.-|+.-|+|++...+.=.|.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~ 63 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWK 63 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence 36788888887554599999999999999999999999999999999765433564
No 11
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=89.95 E-value=0.5 Score=37.45 Aligned_cols=47 Identities=23% Similarity=0.328 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.+.++++...+ +.+.+.++|+.+++.+..+|-+++.|+..|+|++..
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence 34566665543 479999999999999999999999999999999864
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=89.89 E-value=0.24 Score=36.59 Aligned_cols=45 Identities=18% Similarity=0.342 Sum_probs=37.0
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
+.++++..++.+ +.+.++|+.+|+.|=-+|-+.+.|+..|+|+|.
T Consensus 7 ~iL~~l~~~~~~-~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 7 RILEALAESGGP-LTLSEIARALGLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHCHHCTBSC-EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHcCCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence 345556565555 699999999999999999999999999999874
No 13
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=89.25 E-value=1.1 Score=43.85 Aligned_cols=51 Identities=22% Similarity=0.397 Sum_probs=40.5
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEec
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKG 143 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G 143 (403)
++.|+.. |...-.++|+..||.+=|+|||++.||+=|+|+....+--+++-
T Consensus 22 Y~aLl~~---g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~a 72 (247)
T COG1378 22 YLALLCL---GEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRA 72 (247)
T ss_pred HHHHHHh---CCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEe
Confidence 4455533 56778899999999999999999999999999998555444543
No 14
>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=87.06 E-value=0.76 Score=33.08 Aligned_cols=43 Identities=26% Similarity=0.424 Sum_probs=35.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
++.+.++.+.+ .+...++|+.+++.+..++.+++-|+.-|+|+
T Consensus 6 ~~Il~~l~~~~--~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENP--RITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCT--TS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcC--CCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 56777887744 49999999999999999999999999999985
No 15
>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=87.02 E-value=0.71 Score=34.21 Aligned_cols=46 Identities=24% Similarity=0.351 Sum_probs=40.5
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
..+.++...++..+.+.++|+.|++.|=.+--+++-||.-|||+|.
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 4566677788888999999999999999999999999999999987
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=86.56 E-value=0.73 Score=32.90 Aligned_cols=38 Identities=24% Similarity=0.336 Sum_probs=34.4
Q ss_pred CCcccHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 99 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
.+.+.++++++.|++.+..++.+++.|+.-|+|++..+
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=83.87 E-value=1.2 Score=32.78 Aligned_cols=30 Identities=30% Similarity=0.356 Sum_probs=28.3
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccch
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLI 131 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 131 (403)
.+...+|+.+|+.+|.|+-.++.||-.|+|
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 378999999999999999999999999986
No 18
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=81.68 E-value=5.6 Score=35.85 Aligned_cols=85 Identities=22% Similarity=0.326 Sum_probs=56.9
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCC---CCCCchHHHHHHHHHHHHH
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNS---IPGEVDADASILQADIDNL 166 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s---~~~~~~~~~~~Lk~El~~L 166 (403)
|..|++ +++.++.+++|+.|+..|=.+|-.+|=|.-.|||.|..-+. +|..-- .+-+ ...++..
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~---~~Ggy~yiY~~i~----~ee~k~~---- 99 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL---KGGGYYYLYKPID----PEEIKKK---- 99 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc---CCCceeEEEecCC----HHHHHHH----
Confidence 555564 67889999999999999999999999999999999985442 222110 0101 1233322
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Q 015627 167 SMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 167 ~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
.++.|+++-..+.+-|.++..
T Consensus 100 --i~~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 100 --ILKDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred --HHHHHHHHHHHHHHHHHHHhc
Confidence 334667776777776666544
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=81.63 E-value=1.9 Score=34.69 Aligned_cols=49 Identities=22% Similarity=0.331 Sum_probs=39.6
Q ss_pred HHHHHHHHHhhCCCC-cccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 86 LTKKFINLIKHAEDG-ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
.+-+++.++...+++ .+.+.++|+.+++..+.+..|++-|+--|||+..
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 445566666655554 4999999999999999999999999999999854
No 20
>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=81.28 E-value=2.9 Score=30.47 Aligned_cols=47 Identities=21% Similarity=0.360 Sum_probs=38.8
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 137 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 137 (403)
.+++..+...+ +...++++.|++.+..++-+++.|+.-|+|.+....
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 44555555543 999999999999999999999999999999976443
No 21
>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=80.87 E-value=1.8 Score=37.18 Aligned_cols=46 Identities=13% Similarity=0.187 Sum_probs=40.1
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
+.+.++..+.++.+++.++|+.|++.+..++.+++.|+.-|+|+..
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 4555666667788999999999999999999999999999999864
No 22
>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=80.75 E-value=1.4 Score=32.54 Aligned_cols=44 Identities=23% Similarity=0.391 Sum_probs=36.0
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
++.++.+.++ +.+.++|+.+++.+-.+-.+++-||.-|+|+|..
T Consensus 8 iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 8 ILRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 3444445444 8999999999999999999999999999999873
No 23
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=80.63 E-value=19 Score=33.41 Aligned_cols=45 Identities=22% Similarity=0.192 Sum_probs=38.9
Q ss_pred CCCCcccHHHHHHHh--ccceeehhhhHHHhhhccchhhccCCeEEE
Q 015627 97 AEDGILDLNKAAETL--EVQKRRIYDITNVLEGIGLIEKKLKNRIRW 141 (403)
Q Consensus 97 ap~g~ldLn~aA~~L--~VqKRRIYDItNVLEgIGLIeK~sKN~i~W 141 (403)
-.++.-|...+|.+| +|.--.+=+.++.|+-+|||+|...+.|.=
T Consensus 35 l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~ 81 (171)
T PF14394_consen 35 LMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQ 81 (171)
T ss_pred cCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEE
Confidence 456666999999999 999999999999999999999997755443
No 24
>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=80.23 E-value=2 Score=32.31 Aligned_cols=38 Identities=34% Similarity=0.478 Sum_probs=31.8
Q ss_pred CCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 97 AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 97 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
..++.+.+.++|+.|++.+--+..+++-|+..|||+|.
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 47888999999999999999999999999999999887
No 25
>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=80.05 E-value=0.68 Score=37.24 Aligned_cols=29 Identities=41% Similarity=0.540 Sum_probs=23.5
Q ss_pred HHHHHhcc---ceeehhhhHHHhhhccchhhc
Q 015627 106 KAAETLEV---QKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 106 ~aA~~L~V---qKRRIYDItNVLEgIGLIeK~ 134 (403)
.+|+.+++ ..|||||+++-|+-+|||+..
T Consensus 27 ~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 27 ELCESLGVDPLSYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp HHHHHTTS----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEE
Confidence 45555665 789999999999999999876
No 26
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=78.21 E-value=2.9 Score=30.03 Aligned_cols=40 Identities=20% Similarity=0.298 Sum_probs=35.1
Q ss_pred CCCcc-cHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 015627 98 EDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 137 (403)
Q Consensus 98 p~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 137 (403)
++..+ +..++|+.++|++=-+...++.|+.-|+|++....
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 45566 89999999999999999999999999999876543
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=78.04 E-value=1.1 Score=35.61 Aligned_cols=22 Identities=41% Similarity=0.685 Sum_probs=19.9
Q ss_pred cceeehhhhHHHhhhccchhhc
Q 015627 113 VQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 113 VqKRRIYDItNVLEgIGLIeK~ 134 (403)
...|||+||+|-||..|||+-.
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEE
Confidence 4789999999999999999865
No 28
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=76.02 E-value=2.4 Score=29.58 Aligned_cols=38 Identities=29% Similarity=0.334 Sum_probs=33.3
Q ss_pred cccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 015627 101 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 139 (403)
Q Consensus 101 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 139 (403)
.+...++|+.+++.+..++.+++.|+.-|+|++.. +.|
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 29
>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=75.68 E-value=12 Score=31.60 Aligned_cols=54 Identities=13% Similarity=0.222 Sum_probs=31.6
Q ss_pred cCCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 015627 135 LKNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELI 188 (403)
Q Consensus 135 sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lt 188 (403)
...-+.|.|.+..-.....+-...|+..++.|..+-..|++.|..+++++..+.
T Consensus 68 ~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~ 121 (129)
T cd00890 68 DDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQ 121 (129)
T ss_pred CCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455688898654422233333455666666666666666666666666665554
No 30
>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=73.61 E-value=3.8 Score=31.18 Aligned_cols=45 Identities=29% Similarity=0.446 Sum_probs=39.3
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
++.++++++ .+.+.+.++|+.|+|+..-|.-=+|.|+.-|+|.|.
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 578999999999999999999899999999999887
No 31
>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=72.95 E-value=3.9 Score=32.73 Aligned_cols=49 Identities=20% Similarity=0.210 Sum_probs=41.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
.++++.+-.+...-+.-.+++..++...|-++=++++|+..|||.|..-
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 4577777766666666778889999999999999999999999999865
No 32
>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=71.42 E-value=4.4 Score=31.29 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=33.1
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccch
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLI 131 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 131 (403)
+.+.++.+. .+...++|+.|+|+++-|+--++.|+.-|++
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 33
>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=71.17 E-value=4.1 Score=31.06 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.0
Q ss_pred HHHHHHHhh---CCCCcc-cHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 015627 88 KKFINLIKH---AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 137 (403)
Q Consensus 88 kKFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 137 (403)
..+...+.. .++..+ +..++|++++|++.-+....+.|+.-|+|++..+.
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 344444443 355678 99999999999999999999999999999987554
No 34
>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=70.72 E-value=3.6 Score=29.82 Aligned_cols=41 Identities=27% Similarity=0.451 Sum_probs=34.6
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhh
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 133 (403)
.+.++.+ +.....++|+.|++.+--++-=.+.|+..|+|+|
T Consensus 7 Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 4445544 7799999999999999999999999999999975
No 35
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=69.01 E-value=13 Score=36.14 Aligned_cols=54 Identities=9% Similarity=0.216 Sum_probs=41.6
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEec
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKG 143 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G 143 (403)
..++++.... ..+.+.++|+.|++.|=.+|.+++-|+..|++++.....--..|
T Consensus 29 ~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG 82 (271)
T PRK10163 29 AILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIG 82 (271)
T ss_pred HHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEec
Confidence 3455564443 45899999999999999999999999999999986443333344
No 36
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=68.33 E-value=6.3 Score=37.95 Aligned_cols=50 Identities=12% Similarity=0.274 Sum_probs=39.7
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc-CCeEE
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL-KNRIR 140 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s-KN~i~ 140 (403)
.++++...+ ..+.+.++|+.|++.|=.+|-+++-|+..|+|++.. ...|.
T Consensus 16 iL~~l~~~~-~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 16 VLRALNRLD-GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 344554443 349999999999999999999999999999999863 34443
No 37
>PHA02943 hypothetical protein; Provisional
Probab=66.61 E-value=27 Score=32.92 Aligned_cols=48 Identities=23% Similarity=0.234 Sum_probs=42.0
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCe
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNR 138 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~ 138 (403)
..+++++ ..|.....++|+.||++--....++=|||--|.|++.....
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 4478888 67888999999999999999999999999999999976543
No 38
>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=66.41 E-value=5.1 Score=31.68 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=35.3
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccc-eeehhhhHHHhhhccchhhcc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQ-KRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIGLIeK~s 135 (403)
||.-+....+..-.+.++|+.||+. ..-++..+..||.-|+|++..
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 4443334456678999999999996 999999999999999999874
No 39
>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=66.41 E-value=54 Score=32.72 Aligned_cols=42 Identities=19% Similarity=0.172 Sum_probs=36.2
Q ss_pred CCCcccHHHHHHHhc--cceeehhhhHHHhhhccchhhccCCeE
Q 015627 98 EDGILDLNKAAETLE--VQKRRIYDITNVLEGIGLIEKKLKNRI 139 (403)
Q Consensus 98 p~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~sKN~i 139 (403)
.++.-|...+|+.|+ |.=-.+=+.+..|+-+|||+|...+.|
T Consensus 134 ~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y 177 (271)
T TIGR02147 134 MPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFY 177 (271)
T ss_pred CCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcE
Confidence 567778999999998 788889999999999999999875533
No 40
>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=66.31 E-value=15 Score=30.07 Aligned_cols=27 Identities=22% Similarity=0.274 Sum_probs=21.8
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
+.+.++|+.+||+.+-|.-. |..|+|.
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 46789999999999887766 5568886
No 41
>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=65.64 E-value=4.3 Score=30.73 Aligned_cols=46 Identities=26% Similarity=0.398 Sum_probs=38.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.+.+.++ ..++.....++|+.|++.+-.+|-=+++|+..|||+...
T Consensus 13 ~~Il~~L--~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 13 LRILRLL--ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHH--HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHH--hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 3455555 356789999999999999999999999999999998763
No 42
>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=65.53 E-value=15 Score=31.43 Aligned_cols=38 Identities=26% Similarity=0.402 Sum_probs=27.9
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 143 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 143 (403)
+.+.++|+.+||..|-|- -.|-.|||. +...|.|+|-.
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 367889886 44567787754
No 43
>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=65.47 E-value=7.1 Score=32.39 Aligned_cols=50 Identities=22% Similarity=0.363 Sum_probs=40.5
Q ss_pred cHHHHHHHHHHHHhhCC--CCcccHHHHHHHhccceeehhhhHHHhhhccch
Q 015627 82 SLGLLTKKFINLIKHAE--DGILDLNKAAETLEVQKRRIYDITNVLEGIGLI 131 (403)
Q Consensus 82 SLglLTkKFI~Ll~~ap--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 131 (403)
+|..+.++.+++|++.+ +.-+.+++++++|++....|..++.-|..-|+|
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 78999999999998822 234999999999999999999999999998887
No 44
>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=65.08 E-value=8.2 Score=28.21 Aligned_cols=35 Identities=26% Similarity=0.378 Sum_probs=31.6
Q ss_pred cccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 101 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 101 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.....++|+.+++.+=.+...++-|+.-|+|++..
T Consensus 25 ~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 25 LPSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 34599999999999999999999999999998764
No 45
>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=64.82 E-value=23 Score=30.50 Aligned_cols=54 Identities=11% Similarity=0.245 Sum_probs=32.3
Q ss_pred CCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 136 KNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 136 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
+.-+.|.|.+..-...+.+-..-++..++.|...-..|.+.|..+++++..+..
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 345778887654222334445566666666666666666666666666665543
No 46
>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=64.77 E-value=2.8 Score=32.71 Aligned_cols=41 Identities=20% Similarity=0.218 Sum_probs=34.2
Q ss_pred CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCe
Q 015627 98 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNR 138 (403)
Q Consensus 98 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~ 138 (403)
..+.+++.++|..|+++..-+=.++.+|+.-|.|+|...+.
T Consensus 11 ~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 11 ERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 36889999999999999999999999999999999986543
No 47
>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=64.56 E-value=42 Score=31.19 Aligned_cols=45 Identities=22% Similarity=0.287 Sum_probs=38.4
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
.+.+.++... +.+...++|+.|++.+=-+.-.++.||.-|||++.
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 4566667654 34999999999999999999999999999999876
No 48
>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=64.55 E-value=8.6 Score=32.72 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=33.8
Q ss_pred CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 98 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 98 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
..+.++..++|+.+++.++.+++|+..|..-|+|...
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 49
>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=63.90 E-value=20 Score=30.03 Aligned_cols=37 Identities=19% Similarity=0.327 Sum_probs=25.2
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchh-hccCCeEEEe
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE-KKLKNRIRWK 142 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe-K~sKN~i~W~ 142 (403)
+.+.++|+.+||+.+-| -..|-.|||. +...|.|+.-
T Consensus 2 ~~i~eva~~~gvs~~tL----R~ye~~Gll~~~r~~~g~R~Y 39 (102)
T cd04775 2 YTIGQMSRKFGVSRSTL----LYYESIGLIPSARSEANYRLY 39 (102)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCCCCCCCeee
Confidence 46789999999998877 3456678883 3344555543
No 50
>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=63.88 E-value=9.7 Score=31.71 Aligned_cols=45 Identities=13% Similarity=0.133 Sum_probs=37.2
Q ss_pred CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEecc
Q 015627 98 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGL 144 (403)
Q Consensus 98 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~ 144 (403)
....+.-.++|+.+|+.|.-+..+++.||--|+|++..+ ..|.|.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~--~~~~~~ 88 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM--MGIVGV 88 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC--Cceeec
Confidence 455688899999999999999999999999999997643 334454
No 51
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=63.30 E-value=8.7 Score=37.07 Aligned_cols=51 Identities=25% Similarity=0.476 Sum_probs=43.2
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCC-eEE
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN-RIR 140 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN-~i~ 140 (403)
+.++++...+.+ +.+.++|+++|+.|=..|-+.+.|+-.|++++...+ +|+
T Consensus 8 ~iL~~l~~~~~~-l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~ 59 (246)
T COG1414 8 AILDLLAEGPGG-LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYR 59 (246)
T ss_pred HHHHHHHhCCCC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEe
Confidence 466777774444 899999999999999999999999999999999865 443
No 52
>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=62.73 E-value=48 Score=35.28 Aligned_cols=96 Identities=14% Similarity=0.209 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccccccCHHHHhhccCCCCceEEEEeCCCCC--eEEecCCC
Q 015627 155 DASILQADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLHCFQNQTLIAIKAPQGT--TLEVPDPD 232 (403)
Q Consensus 155 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT--~LEVPdP~ 232 (403)
++..+..++..|..+.++|++.|..++++|..+...... ......+.|.+|.+. .|+|-.--
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 445556666667777777777777777777666542111 112345666666544 34443221
Q ss_pred cccCCCCCcEEEEEecCCCceEEEE----ecCccccccc
Q 015627 233 EAVDYPQRRYRIILRSTMGPIDVYL----VSRFEEKFEE 267 (403)
Q Consensus 233 e~~~~~q~~YqI~LkSt~GPIdVyL----~~~~~~~~e~ 267 (403)
.+.. =+-.|.|.|.+..+++++.. .....+.+.+
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 4445555544
No 53
>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=61.66 E-value=6.9 Score=29.90 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=28.8
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhh
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLE 126 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLE 126 (403)
+.+++|-. .+.+.+.++|+.|+++.|-|.--++-|.
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 46677766 6788999999999999999987777766
No 54
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=61.28 E-value=29 Score=32.18 Aligned_cols=50 Identities=10% Similarity=0.046 Sum_probs=40.6
Q ss_pred HHHHHHHhh---CCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 015627 88 KKFINLIKH---AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 137 (403)
Q Consensus 88 kKFI~Ll~~---ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 137 (403)
.++.+.+.. .|+..+.-.++|+.|||+|=-+=+-+..|+..|||+.....
T Consensus 18 ~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~ 70 (221)
T PRK11414 18 NDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQ 70 (221)
T ss_pred HHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCC
Confidence 444444433 47788899999999999999999999999999999976543
No 55
>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=61.04 E-value=24 Score=30.56 Aligned_cols=37 Identities=16% Similarity=0.196 Sum_probs=27.1
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 143 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 143 (403)
.+.++|..+||+.|-| =-.|-+|||. +...|.|++-+
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 44567777754
No 56
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=60.63 E-value=14 Score=28.92 Aligned_cols=45 Identities=20% Similarity=0.280 Sum_probs=37.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
.+.+.++...+ .+...++|+.+++.+..|+-+++-|+.-|+|++.
T Consensus 13 ~~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 13 FLVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 34455555433 5889999999999999999999999999999976
No 57
>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=60.08 E-value=23 Score=29.75 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=24.8
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchh-hccCCeEEEec
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE-KKLKNRIRWKG 143 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe-K~sKN~i~W~G 143 (403)
+.+.++|+.+||..+-|- -.|-.|||. ....|.+++-.
T Consensus 2 ~~i~eva~~~gvs~~tlR----~ye~~Gll~~~r~~~g~R~Y~ 40 (102)
T cd04789 2 YTISELAEKAGISRSTLL----YYEKLGLITGTRNANGYRLYP 40 (102)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCcCCCCCeeCC
Confidence 567899999999887543 345567775 23345566643
No 58
>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=59.60 E-value=23 Score=30.07 Aligned_cols=36 Identities=25% Similarity=0.245 Sum_probs=24.2
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEe
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWK 142 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~ 142 (403)
.+.++|+.+||..|.|.-. |..|||. +...|.+++-
T Consensus 2 ~i~e~a~~~gvs~~tlr~y----e~~gll~~~~r~~~gyR~Y 39 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYY----EKEGLLPPVKRDENGIRDF 39 (113)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCccC
Confidence 5788999999998866433 5678883 3344555543
No 59
>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=59.26 E-value=25 Score=28.58 Aligned_cols=37 Identities=27% Similarity=0.507 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 153 DADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 153 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
++.+..|..|.+.|...|..+...|+.++..+.++-.
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 5678899999999999999999999999988877643
No 60
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=59.13 E-value=38 Score=32.63 Aligned_cols=53 Identities=23% Similarity=0.209 Sum_probs=42.7
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 142 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 142 (403)
++.++++++ .+.+...++|+.|+|+.+.|..-++.|+.-|+|.+....-+.+.
T Consensus 7 ~~Il~~l~~--~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~ 59 (240)
T PRK10411 7 QAIVDLLLN--HTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKYIH 59 (240)
T ss_pred HHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCeEEEec
Confidence 345666764 56899999999999999999999999999999988654444444
No 61
>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=59.07 E-value=6.9 Score=32.93 Aligned_cols=37 Identities=19% Similarity=0.294 Sum_probs=34.1
Q ss_pred CCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 99 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.+.+.+.++|+.+++.|-.++-+++-||.-|||+|..
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 4568899999999999999999999999999999973
No 62
>PF13518 HTH_28: Helix-turn-helix domain
Probab=59.04 E-value=8.4 Score=27.46 Aligned_cols=37 Identities=14% Similarity=0.312 Sum_probs=30.4
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGL 130 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 130 (403)
.|.++.+ |. .+.++|..++|.++.||.+++-++.-|+
T Consensus 5 iv~~~~~---g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 5 IVELYLE---GE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHc---CC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 4555542 44 9999999999999999999999988664
No 63
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.94 E-value=7.6 Score=34.16 Aligned_cols=40 Identities=35% Similarity=0.381 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 84 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 84 glLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
.+||+|=..++.-.=...++|.++|+.++|+|-.|||=++
T Consensus 16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK 55 (105)
T COG2739 16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK 55 (105)
T ss_pred HHHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence 5788886666655555679999999999999999999765
No 64
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=58.93 E-value=70 Score=27.64 Aligned_cols=35 Identities=17% Similarity=0.250 Sum_probs=32.4
Q ss_pred cccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 101 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 101 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.+...++|+.+++.+-.+--+++.||.-|+|+|..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 36789999999999999999999999999999983
No 65
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=58.70 E-value=35 Score=29.90 Aligned_cols=51 Identities=22% Similarity=0.281 Sum_probs=25.9
Q ss_pred CeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 015627 137 NRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLREL 187 (403)
Q Consensus 137 N~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~L 187 (403)
.-+.|.|.+..-...+.+-+..|+..++.|...-..|.+.|..+++++..+
T Consensus 77 kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~ 127 (140)
T PRK03947 77 KVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQL 127 (140)
T ss_pred eEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346677765432222334445555555555555555555555555554443
No 66
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=58.68 E-value=6.2 Score=40.62 Aligned_cols=29 Identities=34% Similarity=0.634 Sum_probs=26.5
Q ss_pred HHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 104 LNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 104 Ln~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
+..+++.+++++||+|||+|-|+++|+|.
T Consensus 304 y~~~~~~~~~~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 304 YESLCERLRTSQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHhhhCchHHHHHHHHHHHHhcCeEE
Confidence 46788888889999999999999999998
No 67
>PRK09954 putative kinase; Provisional
Probab=58.64 E-value=9.6 Score=37.88 Aligned_cols=47 Identities=19% Similarity=0.333 Sum_probs=41.0
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 86 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
.-++.+.+|++.+ .+...++|+.|+|.|..++..++=|+.-|+|++.
T Consensus 4 ~~~~il~~l~~~~--~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 4 REKEILAILRRNP--LIQQNEIADILQISRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred HHHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCc
Confidence 3467888888654 7999999999999999999999999999999755
No 68
>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=58.34 E-value=25 Score=30.40 Aligned_cols=79 Identities=22% Similarity=0.241 Sum_probs=0.0
Q ss_pred ccHHHHHHHhcccee--ehhhhHHHhhhccchh--hccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHHH--
Q 015627 102 LDLNKAAETLEVQKR--RIYDITNVLEGIGLIE--KKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSME-- 169 (403)
Q Consensus 102 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIe--K~sKN~i~W~G~~~s~~~~~~~~~~~Lk------~El~~L~~~-- 169 (403)
+.+.++|+.+||++| |.| |.+|||. +...|.|++-..+.. ..-..+..|+ +|+..+-..
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 015627 170 ---------ELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 170 ---------E~~LD~lI~~~~q~L~~Lte 189 (403)
...|.+++..+.+++.+|..
T Consensus 72 ~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd04784 72 DPEASCAEVNALIDEHLAHVRARIAELQA 100 (127)
T ss_pred cCCCcHHHHHHHHHHHHHHHHHHHHHHHH
No 69
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=57.65 E-value=12 Score=30.81 Aligned_cols=47 Identities=15% Similarity=0.285 Sum_probs=41.1
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 86 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
+=++++.+++.. +.+...++|+.|++.+.-++..++-|+.-|+|.+.
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 446788888774 56899999999999999999999999999999953
No 70
>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=57.57 E-value=17 Score=28.16 Aligned_cols=42 Identities=24% Similarity=0.310 Sum_probs=36.7
Q ss_pred HHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 93 LIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 93 Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.+.. .++.+...++|+.|+|.+=-..+.++-|+.-|||++..
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 88899999999999999999999999999999998764
No 71
>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=57.54 E-value=6.2 Score=27.29 Aligned_cols=22 Identities=36% Similarity=0.575 Sum_probs=20.1
Q ss_pred ccHHHHHHHhccceeehhhhHH
Q 015627 102 LDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItN 123 (403)
+++.++|+.|||.++.||..++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999985
No 72
>PRK06474 hypothetical protein; Provisional
Probab=57.45 E-value=97 Score=28.75 Aligned_cols=47 Identities=15% Similarity=0.287 Sum_probs=38.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHh-ccceeehhhhHHHhhhccchhhcc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETL-EVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.+.+.+|...+.. +...++++.| ++.+=-+|-.+++|+-.|||++..
T Consensus 14 ~~Il~~L~~~~~~-~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 14 MKICQVLMRNKEG-LTPLELVKILKDVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHHhCCCC-CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence 3466677665443 9999999999 789999999999999999999754
No 73
>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=56.97 E-value=6.6 Score=38.24 Aligned_cols=40 Identities=18% Similarity=0.172 Sum_probs=35.6
Q ss_pred CCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 015627 99 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 139 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 139 (403)
.+..++.++|+++++..|+++-+.+.|.++||+++.. +.|
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 3678999999999999999999999999999999863 444
No 74
>PRK10870 transcriptional repressor MprA; Provisional
Probab=56.67 E-value=48 Score=30.41 Aligned_cols=40 Identities=20% Similarity=0.289 Sum_probs=36.1
Q ss_pred hhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 95 KHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 95 ~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
...+++.+...++|+.|++.+=.+--+++-||.-|||+|.
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 3445678999999999999999999999999999999997
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=56.45 E-value=13 Score=31.33 Aligned_cols=46 Identities=15% Similarity=0.325 Sum_probs=40.0
Q ss_pred HHHHHh--hCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 90 FINLIK--HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 90 FI~Ll~--~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
++.++. .++++.+.+.++|+.|++.+=.+-=+++-||--|+|.|..
T Consensus 30 vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 30 ILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred HHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 344454 5677899999999999999999999999999999999874
No 76
>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=56.06 E-value=30 Score=26.86 Aligned_cols=36 Identities=22% Similarity=0.333 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 015627 155 DASILQADIDNLSMEELRVDEQTRELRERLRELIEN 190 (403)
Q Consensus 155 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted 190 (403)
....++.++..|+.+-+.|.+.+..+++++..|..|
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 77
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=55.99 E-value=18 Score=31.35 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHH
Q 015627 83 LGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 124 (403)
Q Consensus 83 LglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 124 (403)
-.....++++++.......++|.++|+.+|+.+|.+.-+..-
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 356678999999999999999999999999999988776543
No 78
>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=55.64 E-value=1.2e+02 Score=27.57 Aligned_cols=96 Identities=20% Similarity=0.253 Sum_probs=46.1
Q ss_pred HHHHHhhCCCCcccHHHHHHHhc--cceeehhhhHHHhhhccchh-hc-cCCeEEEeccCCCCCCCchHHHHHHHHHHHH
Q 015627 90 FINLIKHAEDGILDLNKAAETLE--VQKRRIYDITNVLEGIGLIE-KK-LKNRIRWKGLDNSIPGEVDADASILQADIDN 165 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIe-K~-sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~ 165 (403)
.++||+. .+.+++.+++..-|+ |.|=-+-=+..-|..=|.|. |. +|-.|-|.-.+.... ...+.+..+..++..
T Consensus 6 Il~y~~~-qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~~~~-~s~eel~~ld~ei~~ 83 (169)
T PF07106_consen 6 ILEYMKE-QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQDELEV-PSPEELAELDAEIKE 83 (169)
T ss_pred HHHHHHH-cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecceEEEeeCccccCC-CCchhHHHHHHHHHH
Confidence 3445543 566788888888884 55543333333333334443 33 566777754333210 112224444444444
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 015627 166 LSMEELRVDEQTRELRERLREL 187 (403)
Q Consensus 166 L~~~E~~LD~lI~~~~q~L~~L 187 (403)
|..+-..|...++.+..+|..|
T Consensus 84 L~~el~~l~~~~k~l~~eL~~L 105 (169)
T PF07106_consen 84 LREELAELKKEVKSLEAELASL 105 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444444444
No 79
>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=55.60 E-value=26 Score=30.58 Aligned_cols=37 Identities=22% Similarity=0.249 Sum_probs=25.5
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 143 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 143 (403)
.+.++|+.+||+.+-|. .-|.+||+. +...|.|++-.
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 46788999999887553 235678884 45567777654
No 80
>PRK00215 LexA repressor; Validated
Probab=55.23 E-value=13 Score=34.27 Aligned_cols=42 Identities=14% Similarity=0.150 Sum_probs=37.0
Q ss_pred hCCCCcccHHHHHHHhcc-ceeehhhhHHHhhhccchhhccCC
Q 015627 96 HAEDGILDLNKAAETLEV-QKRRIYDITNVLEGIGLIEKKLKN 137 (403)
Q Consensus 96 ~ap~g~ldLn~aA~~L~V-qKRRIYDItNVLEgIGLIeK~sKN 137 (403)
...+....+.++|+.|++ .|=.++.+++-||.-|+|++....
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
>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=54.97 E-value=9.6 Score=29.24 Aligned_cols=51 Identities=24% Similarity=0.276 Sum_probs=40.4
Q ss_pred HHHHHHHHHhhCC----------CCcccHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 86 LTKKFINLIKHAE----------DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 86 LTkKFI~Ll~~ap----------~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
|+.-|+.++...+ ...+...++|+.+|++++.+--+++-|+.-|+|++..+
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 12477899999999999999999999999999997644
No 82
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=54.55 E-value=1e+02 Score=26.58 Aligned_cols=31 Identities=10% Similarity=0.041 Sum_probs=26.3
Q ss_pred CcccHHHHHHHhccceeehhhhHHHhhhccc
Q 015627 100 GILDLNKAAETLEVQKRRIYDITNVLEGIGL 130 (403)
Q Consensus 100 g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 130 (403)
+-..+.++|..|||+.--||-+.+-+..-|+
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 4568999999999999999999999865444
No 83
>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=54.18 E-value=21 Score=30.17 Aligned_cols=76 Identities=17% Similarity=0.197 Sum_probs=42.9
Q ss_pred HHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCC------CchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 108 AETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPG------EVDADASILQADIDNLSMEELRVDEQTRELR 181 (403)
Q Consensus 108 A~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~------~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~ 181 (403)
-..|..+++...++.+-|+.+. ...+.|+=.|.-..... .+..++..+..+++.|..+...|...+..++
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 3445667788888888887775 23333444453222110 1233445555666666666666666666666
Q ss_pred HHHHHh
Q 015627 182 ERLREL 187 (403)
Q Consensus 182 q~L~~L 187 (403)
.+|+++
T Consensus 98 ~~l~~~ 103 (105)
T cd00632 98 EKIQQA 103 (105)
T ss_pred HHHHHH
Confidence 666654
No 84
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=53.66 E-value=24 Score=34.21 Aligned_cols=55 Identities=16% Similarity=0.147 Sum_probs=41.9
Q ss_pred HHHHHHHHhh-CCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEE
Q 015627 87 TKKFINLIKH-AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRW 141 (403)
Q Consensus 87 TkKFI~Ll~~-ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W 141 (403)
+-|.|.++.. ..+..+...++|+.|++.+..+.-+++-||--|+|+|.....-+|
T Consensus 6 ~Lk~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~ 61 (217)
T PRK14165 6 ALKKLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQL 61 (217)
T ss_pred HHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceE
Confidence 3444444433 344568999999999999999999999999999999985433333
No 85
>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=53.45 E-value=16 Score=34.59 Aligned_cols=44 Identities=16% Similarity=0.181 Sum_probs=37.2
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
.++++..+ ...+.+.++|+.||+.|=.+|-+++-|+..|++++.
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 44445443 456899999999999999999999999999999975
No 86
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=53.12 E-value=1.2e+02 Score=28.08 Aligned_cols=54 Identities=31% Similarity=0.471 Sum_probs=38.1
Q ss_pred CCcCcHHHHHHHHHHHHh-hCCCCcc---------------cHHHHHHHhcc-ceeehhhhHHHhhhccchhh
Q 015627 78 RYDSSLGLLTKKFINLIK-HAEDGIL---------------DLNKAAETLEV-QKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 78 R~dkSLglLTkKFI~Ll~-~ap~g~l---------------dLn~aA~~L~V-qKRRIYDItNVLEgIGLIeK 133 (403)
+++.+...|.++|..+.+ -+||... -||+|-..|.= .+|+.|++ -|.|+.+...
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 467788899999999864 4666432 36777777766 67999985 5567766543
No 87
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=52.72 E-value=9.9 Score=30.49 Aligned_cols=33 Identities=27% Similarity=0.302 Sum_probs=30.4
Q ss_pred HHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 104 LNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 104 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
+.++|+.|++.+=.++.++.-|+.-|||.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 568999999999999999999999999999853
No 88
>PRK11569 transcriptional repressor IclR; Provisional
Probab=52.36 E-value=48 Score=32.20 Aligned_cols=45 Identities=11% Similarity=0.256 Sum_probs=37.8
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.++++.. ....+.|.++|+.||+.|=.+|-+++-|+..|++++..
T Consensus 33 IL~~l~~-~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~ 77 (274)
T PRK11569 33 LLEWIAE-SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG 77 (274)
T ss_pred HHHHHHh-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 3445544 34568999999999999999999999999999999864
No 89
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=52.15 E-value=38 Score=29.19 Aligned_cols=60 Identities=12% Similarity=0.151 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccccccCHHHHhh-cc-CCCCceEEEEeCC
Q 015627 156 ASILQADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKN-LH-CFQNQTLIAIKAP 221 (403)
Q Consensus 156 ~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~~n~~~aYVT~eDI~~-l~-~f~~qTvIAIKAP 221 (403)
...++++++.++++-.+|.+....++.++..|.++. .|+.+. .+. +- .-.|+++|-|.-|
T Consensus 29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~-----dyiEe~-AR~~Lg~vk~gEivy~~~~~ 90 (105)
T PRK00888 29 YWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQ-----EAIEER-ARNELGMVKPGETFYRIVPD 90 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcH-----HHHHHH-HHHHcCCCCCCCEEEEeCCC
Confidence 344555555555555555555555555555554432 133211 111 10 2257777766655
No 90
>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=51.55 E-value=56 Score=28.00 Aligned_cols=54 Identities=17% Similarity=0.228 Sum_probs=36.2
Q ss_pred CCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 136 KNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 136 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
+.-+.|.|.+..--...++-+.-|+..++.|...-..|.+.|.++++++..+.+
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 455778887654222344556677777777777777777777777777776643
No 91
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=50.78 E-value=21 Score=29.34 Aligned_cols=40 Identities=15% Similarity=0.168 Sum_probs=34.5
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHH
Q 015627 85 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 124 (403)
Q Consensus 85 lLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 124 (403)
.+..+++.++.......+++.++|+.+++++|.+.-+..=
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4567889999988888999999999999999998877653
No 92
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=49.53 E-value=14 Score=35.73 Aligned_cols=44 Identities=20% Similarity=0.302 Sum_probs=38.0
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
+.+++++ ..+.+.+.++|+.|+|++.-|+--++.||..|+|.|.
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 4556665 4688999999999999999998889999999999885
No 93
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=48.80 E-value=15 Score=38.98 Aligned_cols=76 Identities=22% Similarity=0.316 Sum_probs=49.2
Q ss_pred ccceeehhhhHHHhhhcc-chhhccCCeEEEeccCCCCCCCchHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHh
Q 015627 112 EVQKRRIYDITNVLEGIG-LIEKKLKNRIRWKGLDNSIPGEVDADASILQADID---NLSMEELRVDEQTRELRERLREL 187 (403)
Q Consensus 112 ~VqKRRIYDItNVLEgIG-LIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~---~L~~~E~~LD~lI~~~~q~L~~L 187 (403)
.|.|||=|-|=+-.--+| ||-|.+-+..+|. ...+.. ...+.+..||++.+ ++....+.|+.-++.+.+++++|
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 578888776655444444 7888888888886 222211 22345677776655 45566677777788888887777
Q ss_pred hh
Q 015627 188 IE 189 (403)
Q Consensus 188 te 189 (403)
..
T Consensus 317 k~ 318 (411)
T KOG1318|consen 317 KS 318 (411)
T ss_pred HH
Confidence 44
No 94
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=47.98 E-value=1.1e+02 Score=30.23 Aligned_cols=43 Identities=19% Similarity=0.417 Sum_probs=31.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhh
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 133 (403)
++.|.+|.+-| .-..+++..|||....|-+=.-.||--|||+-
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 34456778899988888888888888887764
No 95
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=47.36 E-value=20 Score=28.67 Aligned_cols=44 Identities=23% Similarity=0.277 Sum_probs=36.1
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
++..+...++... .++|+.|++.+=.+--+++-||.-|+|+|..
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 4444555555444 9999999999999999999999999999884
No 96
>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=47.24 E-value=22 Score=32.54 Aligned_cols=48 Identities=17% Similarity=0.254 Sum_probs=39.2
Q ss_pred HHHHHHHhh---CCCCcccHHHHHHHhccc-eeehhhhHHHhhhccchhhcc
Q 015627 88 KKFINLIKH---AEDGILDLNKAAETLEVQ-KRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 88 kKFI~Ll~~---ap~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIGLIeK~s 135 (403)
++.+.++.+ ..+....+.++|+.|++. +=-++..++.||..|+|++..
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 445555553 344458899999999998 999999999999999999974
No 97
>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=47.18 E-value=24 Score=32.80 Aligned_cols=45 Identities=24% Similarity=0.298 Sum_probs=37.9
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
.+.++.+. +.+.+.++|+.|++.+-.++-.++-|+.-|+|++..+
T Consensus 148 IL~~l~~~--g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 148 VLEVLKAE--GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 44444432 5689999999999999999999999999999999863
No 98
>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=47.03 E-value=1.8e+02 Score=26.62 Aligned_cols=32 Identities=38% Similarity=0.502 Sum_probs=24.2
Q ss_pred cHHHHHHHHHHHHhhCCCCcccHHHHHHHhcc
Q 015627 82 SLGLLTKKFINLIKHAEDGILDLNKAAETLEV 113 (403)
Q Consensus 82 SLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~V 113 (403)
+|..|+..|.+++.-..++..|-..+++.|.-
T Consensus 2 ~LYel~~~~~~l~~~~e~~~~d~e~~~dtLe~ 33 (162)
T PF05565_consen 2 KLYELTDEYLELLELLEEGDLDEEAIADTLES 33 (162)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 58889999999997776666777766665543
No 99
>PRK11050 manganese transport regulator MntR; Provisional
Probab=46.84 E-value=33 Score=30.79 Aligned_cols=38 Identities=21% Similarity=0.174 Sum_probs=34.5
Q ss_pred CCcccHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 99 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
++.+.+.++|+.|+|.+-.+..+++-||.-|+|.+...
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~ 86 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPY 86 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 45689999999999999999999999999999998653
No 100
>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=46.80 E-value=21 Score=33.74 Aligned_cols=43 Identities=26% Similarity=0.341 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhh
Q 015627 85 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEG 127 (403)
Q Consensus 85 lLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEg 127 (403)
.+..+|+.++.+.....++|.++|+.+++++|.+..+..-..|
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G 228 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSA 228 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 4568899999988888999999999999999999988755443
No 101
>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=46.41 E-value=24 Score=30.86 Aligned_cols=38 Identities=21% Similarity=0.307 Sum_probs=34.0
Q ss_pred hCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhh
Q 015627 96 HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 96 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 133 (403)
+..++.+.+.++|+.+++..+-+..|+..|.--|||.-
T Consensus 20 ~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 20 NAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 33445899999999999999999999999999999974
No 102
>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=46.13 E-value=22 Score=31.19 Aligned_cols=36 Identities=14% Similarity=0.325 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehh
Q 015627 84 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIY 119 (403)
Q Consensus 84 glLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIY 119 (403)
..+..-|++|++..+=..+.+.++|++-||.|.-+|
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 356677999999999999999999999999998887
No 103
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=45.29 E-value=51 Score=29.60 Aligned_cols=99 Identities=16% Similarity=0.221 Sum_probs=55.9
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCC------CCchHHHHH
Q 015627 85 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIP------GEVDADASI 158 (403)
Q Consensus 85 lLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~ 158 (403)
.+..+|-.|-.+...-++....+...| -+|.-||+-+..|.--. .-|+=.|.=.... .++.++...
T Consensus 10 ~~l~q~QqLq~ql~~~~~qk~~le~qL-------~E~~~al~Ele~l~eD~-~vYk~VG~llvk~~k~~~~~eL~er~E~ 81 (119)
T COG1382 10 AQLAQLQQLQQQLQKVILQKQQLEAQL-------KEIEKALEELEKLDEDA-PVYKKVGNLLVKVSKEEAVDELEERKET 81 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHhcCCccc-HHHHHhhhHHhhhhHHHHHHHHHHHHHH
Confidence 344555555544433333443443333 34667777776665432 2233344322211 133445566
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 015627 159 LQADIDNLSMEELRVDEQTRELRERLRELIENE 191 (403)
Q Consensus 159 Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~ 191 (403)
|.-+++-|+.+|+.|.+.+..++..|+.+..+.
T Consensus 82 Le~ri~tLekQe~~l~e~l~eLq~~i~~~l~~~ 114 (119)
T COG1382 82 LELRIKTLEKQEEKLQERLEELQSEIQKALGDA 114 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 667777788888888888888888888776543
No 104
>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=44.95 E-value=51 Score=28.13 Aligned_cols=83 Identities=18% Similarity=0.226 Sum_probs=44.4
Q ss_pred HHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCC------CchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 105 NKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPG------EVDADASILQADIDNLSMEELRVDEQTR 178 (403)
Q Consensus 105 n~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~------~~~~~~~~Lk~El~~L~~~E~~LD~lI~ 178 (403)
..++..+..-.+.+=....|++.|.-+. ...+.|+=.|.=..... .+..++..+...++.|..+...|...+.
T Consensus 20 ~~l~~q~~~le~~~~E~~~v~~eL~~l~-~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~ 98 (110)
T TIGR02338 20 QAVATQKQQVEAQLKEAEKALEELERLP-DDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLK 98 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCC-CcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333344555555555554 33455555554222110 2334455566667777777777777777
Q ss_pred HHHHHHHHhh
Q 015627 179 ELRERLRELI 188 (403)
Q Consensus 179 ~~~q~L~~Lt 188 (403)
.++++|+.+.
T Consensus 99 e~q~~l~~~~ 108 (110)
T TIGR02338 99 ELQEKIQEAL 108 (110)
T ss_pred HHHHHHHHHh
Confidence 7777777653
No 105
>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=44.58 E-value=31 Score=28.73 Aligned_cols=59 Identities=24% Similarity=0.433 Sum_probs=45.6
Q ss_pred CcHHHHHHHHHHHHhhC-CCCcccHHHHHHHhccceeehhhhHH-HhhhccchhhccCCeE
Q 015627 81 SSLGLLTKKFINLIKHA-EDGILDLNKAAETLEVQKRRIYDITN-VLEGIGLIEKKLKNRI 139 (403)
Q Consensus 81 kSLglLTkKFI~Ll~~a-p~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~sKN~i 139 (403)
..|..+=++++..+.+. .+|.+-|+.+|..|+..+.-|=|++- -|--.|+|+|+.+.++
T Consensus 4 ~GLd~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT~rGR~ 64 (76)
T PF05491_consen 4 LGLDELDRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRTPRGRV 64 (76)
T ss_dssp TS-BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEETTEEE
T ss_pred ccCCHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhCccHHH
Confidence 44667778999987664 88999999999999999999888764 5778999999988764
No 106
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=44.52 E-value=85 Score=30.05 Aligned_cols=38 Identities=24% Similarity=0.260 Sum_probs=35.3
Q ss_pred CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 98 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 98 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
....+.|.++++.||++|=++-=.+-+|++.||+.|+-
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhh
Confidence 36789999999999999999999999999999999983
No 107
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=44.28 E-value=22 Score=34.88 Aligned_cols=64 Identities=25% Similarity=0.322 Sum_probs=43.5
Q ss_pred CCCCccCCcccccccccCCCCCCCCCCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhc
Q 015627 49 TPQTPVSNAGEKISYHLGSPSALTPAGSCRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGI 128 (403)
Q Consensus 49 ~~~tp~~n~~~~~~~~~~sp~~~~p~~~~R~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgI 128 (403)
|--+|..-.+-.+.|-|+.|++.-+ +.|. ++|. .=|..+|++|+|+++.+-+ |.+++|
T Consensus 29 c~l~~~~~~k~wli~GLGNPg~~y~--gTRH--nvG~----------------~Ml~~larrlgv~~nt~s~--~a~~~l 86 (224)
T KOG2255|consen 29 CDLKPRVSIKPWLIVGLGNPGSKYV--GTRH--NVGF----------------EMLDMLARRLGVPMNTISS--KALEGL 86 (224)
T ss_pred eecccCCCCCceEEEecCCCccccc--ccch--hhHH----------------HHHHHHHHHhCCcccccCc--ccccce
Confidence 4444433344457777889987443 3453 2332 2256689999999999999 999999
Q ss_pred cchhhc
Q 015627 129 GLIEKK 134 (403)
Q Consensus 129 GLIeK~ 134 (403)
|+|+-.
T Consensus 87 ~~v~d~ 92 (224)
T KOG2255|consen 87 GLVGDV 92 (224)
T ss_pred eeecce
Confidence 999855
No 108
>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=44.13 E-value=27 Score=28.99 Aligned_cols=45 Identities=22% Similarity=0.412 Sum_probs=38.0
Q ss_pred HHHHHhhCCCCcccHHHHHHHh-----ccceeehhhhHHHhhhccchhhcc
Q 015627 90 FINLIKHAEDGILDLNKAAETL-----EVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L-----~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.++++..+ +..++..++.+.| .+.+=-+|-+++.|+..|+|.|..
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 45666665 5778999999998 588999999999999999999874
No 109
>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=43.32 E-value=45 Score=30.46 Aligned_cols=41 Identities=20% Similarity=0.283 Sum_probs=36.8
Q ss_pred CCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 015627 97 AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 137 (403)
Q Consensus 97 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 137 (403)
.|+..+.-.++|+.|||+|=-+=+.+..|+.-|||+...+.
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~ 70 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNR 70 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCC
Confidence 47788999999999999999999999999999999976443
No 110
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=42.92 E-value=9.8 Score=38.07 Aligned_cols=28 Identities=25% Similarity=0.554 Sum_probs=21.8
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhcc
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIG 129 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIG 129 (403)
+-|..+=-.||..+|=+||.+||+||=-
T Consensus 41 iGLRNLDlimGlE~RiVYd~vdVi~g~~ 68 (272)
T COG2894 41 IGLRNLDLIMGLENRIVYDLVDVIEGEA 68 (272)
T ss_pred cCchhhhhhhcccceeeeeehhhhcCcc
Confidence 3344444468999999999999999854
No 111
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=42.75 E-value=29 Score=33.16 Aligned_cols=47 Identities=6% Similarity=0.309 Sum_probs=38.9
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCC
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKN 137 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN 137 (403)
+.++++.. .+.+.+.++|+.|++.|=.+|-+++-|+..|++++...+
T Consensus 18 ~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~ 64 (257)
T PRK15090 18 GILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGES 64 (257)
T ss_pred HHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 34555543 346899999999999999999999999999999987543
No 112
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=42.70 E-value=68 Score=28.59 Aligned_cols=38 Identities=18% Similarity=0.199 Sum_probs=24.5
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 143 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 143 (403)
+.+.++|+.+||+.|-|--. |-.|||. +...|.|++-.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Y----e~~GLl~p~~r~~~gyR~Y~ 41 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFY----EKQGLMDPEVRTEGGYRLYT 41 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCCeeeC
Confidence 45778888888887754322 6667774 34456666643
No 113
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=42.25 E-value=1.2e+02 Score=29.72 Aligned_cols=50 Identities=16% Similarity=0.247 Sum_probs=40.1
Q ss_pred HHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCe
Q 015627 87 TKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNR 138 (403)
Q Consensus 87 TkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~ 138 (403)
-.+.++++++. +.+.+.++|+.|+|+.+-|.-=+..||.-|++.|.-...
T Consensus 19 ~~~Il~~L~~~--~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GGa 68 (269)
T PRK09802 19 REQIIQRLRQQ--GSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGA 68 (269)
T ss_pred HHHHHHHHHHc--CCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCCE
Confidence 34566777664 449999999999999988887788899999999875443
No 114
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=42.13 E-value=29 Score=31.89 Aligned_cols=39 Identities=18% Similarity=0.247 Sum_probs=34.8
Q ss_pred hCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 96 HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 96 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
...++.+.+.++|+.+++.++-+..|++-|.--|||.-.
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 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=42.00 E-value=22 Score=32.93 Aligned_cols=39 Identities=21% Similarity=0.228 Sum_probs=35.1
Q ss_pred cccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 015627 101 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 139 (403)
Q Consensus 101 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 139 (403)
+++..++|+.|+++++-++..+..|+--++|.|...+.|
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 577889999999999999999999999999999865544
No 116
>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=41.87 E-value=21 Score=24.29 Aligned_cols=23 Identities=26% Similarity=0.225 Sum_probs=19.9
Q ss_pred ccHHHHHHHhccceeehhhhHHH
Q 015627 102 LDLNKAAETLEVQKRRIYDITNV 124 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNV 124 (403)
+++.++|+.|+|.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999999988763
No 117
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=41.35 E-value=52 Score=36.70 Aligned_cols=65 Identities=22% Similarity=0.293 Sum_probs=46.5
Q ss_pred HHhhhccchhhccCCeEEEeccCCCCCC------CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 015627 123 NVLEGIGLIEKKLKNRIRWKGLDNSIPG------EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIEN 190 (403)
Q Consensus 123 NVLEgIGLIeK~sKN~i~W~G~~~s~~~------~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted 190 (403)
+-|..|.=|.|.+||++- ..+.+-. .++..+..|+.|-+.|..+...+|.-+..+.++|..|..+
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 678888889999999873 2333222 2344566677777777778888888888888888877554
No 118
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=41.29 E-value=57 Score=34.80 Aligned_cols=48 Identities=27% Similarity=0.414 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhhCC--CCcccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 85 LLTKKFINLIKHAE--DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 85 lLTkKFI~Ll~~ap--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
.|-+.|+.|++... ...+.|.++|+.|++++|-.==|+|-|+..|.|+
T Consensus 5 ~~~~~~~~L~~~~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~ 54 (552)
T PRK13626 5 RLQQQFIRLWQCCEGKSQETTLNELAELLNCSRRHMRTLLNTMQQRGWLT 54 (552)
T ss_pred HHHHHHHHHHHhcCCCcceeeHHHHHHHhcCChhHHHHHHHHHHHCCCee
Confidence 56778999987654 4579999999999999999999999999988865
No 119
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=41.23 E-value=41 Score=31.42 Aligned_cols=39 Identities=18% Similarity=0.192 Sum_probs=34.0
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 140 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 140 (403)
+.-.++|..||++|..+.-+++-|+--|+|++...++|.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 455899999999999999999999999999877655664
No 120
>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=40.99 E-value=75 Score=27.56 Aligned_cols=36 Identities=19% Similarity=0.196 Sum_probs=23.6
Q ss_pred HHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 015627 104 LNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 143 (403)
Q Consensus 104 Ln~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 143 (403)
+.++|+.+||+.+-|-- -|.+|||. +...|.|++-+
T Consensus 2 I~e~a~~~gvs~~tlR~----Ye~~GLl~~~~r~~~g~R~Y~ 39 (124)
T TIGR02051 2 IGELAKAAGVNVETIRY----YERKGLLPEPDRPEGGYRRYP 39 (124)
T ss_pred HHHHHHHHCcCHHHHHH----HHHCCCCCCCccCCCCCEeEC
Confidence 56788888887764422 17888885 34456666653
No 121
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=40.96 E-value=24 Score=35.62 Aligned_cols=52 Identities=27% Similarity=0.440 Sum_probs=41.9
Q ss_pred CcHHHHHH-HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 81 SSLGLLTK-KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 81 kSLglLTk-KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
++|+..++ +.+++|. ..+.+++|++|+.||...--+--=+.|||-.|||+-.
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 56666664 4566664 4577999999999999999999889999999999854
No 122
>PRK09343 prefoldin subunit beta; Provisional
Probab=40.76 E-value=62 Score=28.39 Aligned_cols=73 Identities=16% Similarity=0.253 Sum_probs=45.0
Q ss_pred eehhhhHHHhhhccchhhccCCeEEEeccCCCCC------CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 116 RRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIP------GEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 116 RRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
+.+=..-.|++.+..+.-- -.-|+=.|.=.... .++..++..+..+++.|+.++..|.+.+..++.+|+.+..
T Consensus 35 ~q~~e~~~~~~EL~~L~~d-~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l~~ll~ 113 (121)
T PRK09343 35 LELREINKALEELEKLPDD-TPIYKIVGNLLVKVDKTKVEKELKERKELLELRSRTLEKQEKKLREKLKELQAKINEMLS 113 (121)
T ss_pred HHHHHHHHHHHHHHcCCCc-chhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344556677766666522 22233334222111 1234456667788888888999999999999999988755
No 123
>PLN03239 histone acetyltransferase; Provisional
Probab=40.33 E-value=47 Score=34.75 Aligned_cols=54 Identities=19% Similarity=0.285 Sum_probs=38.9
Q ss_pred CCCcCcHHHHH------HHHHHHHhhCC--CCcccHHHHHHHhccceeehhhhHHHhhhccchhh
Q 015627 77 CRYDSSLGLLT------KKFINLIKHAE--DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 77 ~R~dkSLglLT------kKFI~Ll~~ap--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 133 (403)
.|==+-||++. ...+++|.... ...++|+++|...++. .-||+..|+.+|++..
T Consensus 252 EkPLSdlG~~sY~~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~---~~DIi~tL~~l~~l~~ 313 (351)
T PLN03239 252 EKPMSDLGQQAYIPYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIM---AEDIVFALNQLGILKF 313 (351)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEEE
Confidence 33344456555 33566665543 3579999999999995 6799999999999954
No 124
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=40.20 E-value=68 Score=28.91 Aligned_cols=79 Identities=22% Similarity=0.266 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccceeeh--hhhHHHhhhccch--hhccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHH---
Q 015627 102 LDLNKAAETLEVQKRRI--YDITNVLEGIGLI--EKKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSM--- 168 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRI--YDItNVLEgIGLI--eK~sKN~i~W~G~~~s~~~~~~~~~~~Lk------~El~~L~~--- 168 (403)
+.+.++|+.+||+.|-| || -+||| .+...|.|++-..... .--..+..|+ +|+..+-.
T Consensus 8 ~~IgevAk~~Gvs~~TLRyYE------~~GLl~p~~r~~~gyR~Y~~~~l---~rl~~I~~lr~~G~sL~eI~~ll~~~~ 78 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQ------RKGLLPEPDKPYGSIRRYGEADV---TRVRFVKSAQRLGFSLDEIAELLRLED 78 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHHH------HCCCCCCCccCCCCCeecCHHHH---HHHHHHHHHHHcCCCHHHHHHHHhccC
Q ss_pred ------HHHHHHHHHHHHHHHHHHhhh
Q 015627 169 ------EELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 169 ------~E~~LD~lI~~~~q~L~~Lte 189 (403)
....|.+++..+.+++.+|..
T Consensus 79 ~~~~~~~~~ll~~k~~~l~~~i~~L~~ 105 (144)
T PRK13752 79 GTHCEEASSLAEHKLKDVREKMADLAR 105 (144)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
No 125
>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=40.16 E-value=32 Score=24.58 Aligned_cols=37 Identities=27% Similarity=0.417 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhh
Q 015627 83 LGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDI 121 (403)
Q Consensus 83 LglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDI 121 (403)
|..+=+.+|.-.-...+| ++..||+.||+.|+-||.=
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 445556666654433343 3589999999999999853
No 126
>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=40.16 E-value=78 Score=27.48 Aligned_cols=37 Identities=19% Similarity=0.219 Sum_probs=26.6
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh--ccCCeEEEec
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK--KLKNRIRWKG 143 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~sKN~i~W~G 143 (403)
.+.++|+.+||+.+-|. ..|-.|||.. ...|.|++-.
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 4467888854 4567777754
No 127
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=40.04 E-value=53 Score=30.69 Aligned_cols=40 Identities=28% Similarity=0.303 Sum_probs=37.5
Q ss_pred CCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 97 AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 97 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
.|+..|+.+++|+.|||+|--|=+.+..|++-|||+....
T Consensus 35 ~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~ 74 (230)
T COG1802 35 APGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPN 74 (230)
T ss_pred CCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCC
Confidence 5888999999999999999999999999999999999843
No 128
>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=40.02 E-value=91 Score=27.37 Aligned_cols=81 Identities=17% Similarity=0.162 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHHHH---
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSMEE--- 170 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G~~~s~~~~~~~~~~~Lk------~El~~L~~~E--- 170 (403)
+.+.++|+.+||+.+ -+-.-|..|||. +...|.|++-+.+.. ..-..+..|+ +|+..+-...
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 015627 171 ---------LRVDEQTRELRERLRELIE 189 (403)
Q Consensus 171 ---------~~LD~lI~~~~q~L~~Lte 189 (403)
..|++++..+++++.+|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (131)
T TIGR02043 75 TEHSCAEVKAIVDAKLELVDEKINELTK 102 (131)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
No 129
>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=38.70 E-value=91 Score=27.10 Aligned_cols=37 Identities=27% Similarity=0.339 Sum_probs=24.5
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 143 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 143 (403)
.+.++|+.+||+.+-|- -.|-.||+. +...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tlR----yYe~~GLl~~~~r~~~g~R~Y~ 40 (127)
T cd01108 2 NIGEAAKLTGLSAKMIR----YYEEIGLIPPPSRSDNGYRVYN 40 (127)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCceecC
Confidence 56788888998876442 345678885 34556676653
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=38.54 E-value=95 Score=24.71 Aligned_cols=35 Identities=14% Similarity=0.280 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 155 DASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 155 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
++..+...+..|+.....++..|..+..+|..+.+
T Consensus 14 ~l~~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~ 48 (71)
T PF10779_consen 14 KLDNHEERIDKLEKRDAANEKDIKNLNKQLEKIKS 48 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566666777777777778888888877755
No 131
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=38.16 E-value=40 Score=33.34 Aligned_cols=57 Identities=21% Similarity=0.379 Sum_probs=47.1
Q ss_pred CcHHHHHHHHHH-HHhhCCCCcccHHHHHHHhccceeehhhhHH-HhhhccchhhccCC
Q 015627 81 SSLGLLTKKFIN-LIKHAEDGILDLNKAAETLEVQKRRIYDITN-VLEGIGLIEKKLKN 137 (403)
Q Consensus 81 kSLglLTkKFI~-Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~sKN 137 (403)
..|...-++|+. ++..-.++.+.+..+|..||.....+-|++- .|-..|||++..+.
T Consensus 255 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 313 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRG 313 (328)
T ss_pred CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCch
Confidence 455566778886 6677788899999999999999999988888 88899999877543
No 132
>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=38.02 E-value=1.2e+02 Score=28.35 Aligned_cols=28 Identities=36% Similarity=0.399 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 157 SILQADIDNLSMEELRVDEQTRELRERL 184 (403)
Q Consensus 157 ~~Lk~El~~L~~~E~~LD~lI~~~~q~L 184 (403)
+.++.+|..|.++-..||+.|+.+..+|
T Consensus 25 q~~~~~I~~L~~e~~~ld~~i~~~~~~L 52 (188)
T PF10018_consen 25 QENQARIQQLRAEIEELDEQIRDILKQL 52 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555555555544444
No 133
>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=37.84 E-value=23 Score=37.34 Aligned_cols=47 Identities=21% Similarity=0.231 Sum_probs=34.3
Q ss_pred cHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 82 SLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 82 SLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
....+---|+.+ .||..+|-++|+++++.-++++|+.+-|...|||+
T Consensus 340 ~~~~~~l~~L~~----~DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 340 AQQMAMLWVLNY----SDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp --HHHHHHHHHH-----EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHHh----ccCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 334444445554 48899999999999999999999999999999985
No 134
>PRK10130 transcriptional regulator EutR; Provisional
Probab=37.84 E-value=34 Score=34.99 Aligned_cols=40 Identities=10% Similarity=0.108 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 84 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 84 glLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
..+.+++++++.+..+..+++.++|+.++|++|.|+-...
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 5677888999988888899999999999999999987664
No 135
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=37.76 E-value=1.3e+02 Score=29.08 Aligned_cols=87 Identities=22% Similarity=0.221 Sum_probs=55.8
Q ss_pred CcHHHHHHHHHHHHhhCCCCcccHHH-----------HHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCC
Q 015627 81 SSLGLLTKKFINLIKHAEDGILDLNK-----------AAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIP 149 (403)
Q Consensus 81 kSLglLTkKFI~Ll~~ap~g~ldLn~-----------aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~ 149 (403)
+.+....++..+++....+.+..-+. +.-++.|..-++-+.++-|.++|-|....-+ .
T Consensus 59 ~d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g~v~~~~~~-----------~ 127 (262)
T PF14257_consen 59 KDVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSELGKVTSRNIS-----------S 127 (262)
T ss_pred CCHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhccCceeeeecc-----------c
Confidence 44566667777777776655544443 2335677888999999999999866544211 1
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 150 GEVDADASILQADIDNLSMEELRVDEQTR 178 (403)
Q Consensus 150 ~~~~~~~~~Lk~El~~L~~~E~~LD~lI~ 178 (403)
.++..+...+++.++.|+.++.+|-+++.
T Consensus 128 ~DvT~~y~D~~arl~~l~~~~~rl~~ll~ 156 (262)
T PF14257_consen 128 EDVTEQYVDLEARLKNLEAEEERLLELLE 156 (262)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 23444555666677777777776666654
No 136
>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=37.72 E-value=80 Score=27.43 Aligned_cols=81 Identities=20% Similarity=0.217 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEeccCCCCCCCchHHHHHHH------HHHHHHHHH----
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKGLDNSIPGEVDADASILQ------ADIDNLSME---- 169 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G~~~s~~~~~~~~~~~Lk------~El~~L~~~---- 169 (403)
+.+.++|+.+||+.+-|- --|..|||. +...|.|++-..+.. ..-..+..|+ +|+..+-..
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 015627 170 -------ELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 170 -------E~~LD~lI~~~~q~L~~Lte 189 (403)
...|.+++..+++++.+|..
T Consensus 74 ~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (126)
T cd04785 74 DRSCAEADAIARAHLADVRARIADLRR 100 (126)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
No 137
>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=37.71 E-value=16 Score=26.48 Aligned_cols=32 Identities=19% Similarity=0.432 Sum_probs=22.4
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
...++|+.+ | +.+.++|+.|+|+|.-||-|.+
T Consensus 12 ~~i~~l~~~---G-~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 12 EEIKELYAE---G-MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHT---T---HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHC---C-CCHHHHHHHHCcCHHHHHHHHh
Confidence 445555543 4 8999999999999999998764
No 138
>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=37.68 E-value=30 Score=28.86 Aligned_cols=41 Identities=20% Similarity=0.506 Sum_probs=33.0
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
|.+-+-++ ++.+.+.++|..|++.+++++++ |...|++-|.
T Consensus 14 ~~d~~~~~-~~~~ti~~~AK~L~i~~~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 14 FYDAFVDS-DGLYTIREAAKLLGIGRNKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHcC-CCCccHHHHHHHhCCCHHHHHHH---HHhCCceEEC
Confidence 55555554 49999999999999999999876 6668888884
No 139
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=37.60 E-value=26 Score=25.01 Aligned_cols=35 Identities=17% Similarity=0.291 Sum_probs=22.0
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGI 128 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgI 128 (403)
.|.++.+ -....++|+.|||+++-+|.|++=.+--
T Consensus 10 ii~l~~~----G~s~~~ia~~lgvs~~Tv~~w~kr~~~~ 44 (50)
T PF13384_consen 10 IIRLLRE----GWSIREIAKRLGVSRSTVYRWIKRYREE 44 (50)
T ss_dssp HHHHHHH----T--HHHHHHHHTS-HHHHHHHHT-----
T ss_pred HHHHHHC----CCCHHHHHHHHCcCHHHHHHHHHHcccc
Confidence 4444444 5788999999999999999998865433
No 140
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=37.52 E-value=35 Score=29.95 Aligned_cols=41 Identities=17% Similarity=0.267 Sum_probs=35.6
Q ss_pred hCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 96 HAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 96 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
..++..+...++|+.++|.+.-+-.|+..|+.-|||+....
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 34556899999999999999999999999999999986643
No 141
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=37.25 E-value=40 Score=29.13 Aligned_cols=50 Identities=18% Similarity=0.300 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 83 LGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 83 LglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
|-.+=++-+++|+. ++...+.++|+.||++...+...+.-||.-|+|.+.
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 34455778888866 444999999999999999999999999999999976
No 142
>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=37.02 E-value=95 Score=27.21 Aligned_cols=36 Identities=19% Similarity=0.243 Sum_probs=23.1
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhhcc-C-CeEEEe
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL-K-NRIRWK 142 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s-K-N~i~W~ 142 (403)
.+.++|+.+||+.|.|- --|-+|||.-.. . |.|+.-
T Consensus 2 ~IgE~A~~~gvs~~TLR----yYE~~GLl~p~r~~~~gyR~Y 39 (133)
T cd04787 2 KVKELANAAGVTPDTVR----FYTRIGLLRPTRDPVNGYRLY 39 (133)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCcCCCCCeeeC
Confidence 56788999999887541 127788885332 2 556654
No 143
>PRK10869 recombination and repair protein; Provisional
Probab=37.00 E-value=47 Score=36.05 Aligned_cols=103 Identities=14% Similarity=0.175 Sum_probs=60.7
Q ss_pred CCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHH
Q 015627 77 CRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADA 156 (403)
Q Consensus 77 ~R~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~ 156 (403)
+++|.+|..+..++-..+-.-.+-.-+|....+.+.+.-.|+-.|-+=|.-|.=+.|+ | |.+ ..++-...
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 5666777666666666665555555666666666677666677776666666666666 2 422 22445556
Q ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHhhh
Q 015627 157 SILQADIDNLSMEELRVDEQ---TRELRERLRELIE 189 (403)
Q Consensus 157 ~~Lk~El~~L~~~E~~LD~l---I~~~~q~L~~Lte 189 (403)
..+++|++.|...+..+.++ +..+.+++..+.+
T Consensus 327 ~~l~~eL~~L~~~e~~l~~Le~e~~~l~~~l~~~A~ 362 (553)
T PRK10869 327 QQLLEEQQQLDDQEDDLETLALAVEKHHQQALETAQ 362 (553)
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777777766554443333 4444444444443
No 144
>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=36.40 E-value=72 Score=32.33 Aligned_cols=36 Identities=33% Similarity=0.469 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 015627 156 ASILQADIDNLSMEELRVDEQTRELRERLRELIENE 191 (403)
Q Consensus 156 ~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~ 191 (403)
...|.+|++.|+.++..|++.|..++.++..+.+.+
T Consensus 59 e~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE 94 (314)
T PF04111_consen 59 EEELLQELEELEKEREELDQELEELEEELEELDEEE 94 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345557777777888888888888877777765543
No 145
>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=35.79 E-value=21 Score=26.47 Aligned_cols=24 Identities=29% Similarity=0.538 Sum_probs=19.8
Q ss_pred CcccHHHHHHHhccceeehhhhHH
Q 015627 100 GILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 100 g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
..|+++++++.+|++|..||..++
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 468899999999999999999988
No 146
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=35.69 E-value=25 Score=30.59 Aligned_cols=37 Identities=14% Similarity=0.127 Sum_probs=34.4
Q ss_pred CCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 99 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.+.+...++|+.|++.|=.+--+++-||.-|+|+|..
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 4569999999999999999999999999999999983
No 147
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=35.63 E-value=39 Score=35.03 Aligned_cols=50 Identities=18% Similarity=0.167 Sum_probs=46.4
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHHHh-ccceeehhhhHHHhhhccchhhc
Q 015627 85 LLTKKFINLIKHAEDGILDLNKAAETL-EVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 85 lLTkKFI~Ll~~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
.+.++|+.++-...+..++.+.+|..+ ++.++-++.-++.||..-|+-..
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 89999999999999999999844
No 148
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=35.28 E-value=1.3e+02 Score=27.91 Aligned_cols=46 Identities=11% Similarity=0.044 Sum_probs=39.3
Q ss_pred CCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 015627 97 AEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 142 (403)
Q Consensus 97 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 142 (403)
.|+..+...++|+.|||+|==|=+.+..|+.-|||+...+.-+.-.
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 4777899999999999999999999999999999997755544444
No 149
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=35.08 E-value=67 Score=32.85 Aligned_cols=39 Identities=15% Similarity=0.334 Sum_probs=32.0
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
.++++.+ ....+++++++...++. .-||+..|+.+|++.
T Consensus 213 il~~L~~-~~~~isi~~is~~T~i~---~~Dii~tL~~l~~l~ 251 (290)
T PLN03238 213 LLEQLRD-VKGDVSIKDLSLATGIR---GEDIVSTLQSLNLIK 251 (290)
T ss_pred HHHHHHh-cCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEE
Confidence 5555643 45689999999999995 579999999999994
No 150
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=35.03 E-value=1.8e+02 Score=27.64 Aligned_cols=52 Identities=23% Similarity=0.216 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhh---CCCCcc-cHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 85 LLTKKFINLIKH---AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 85 lLTkKFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
.+...+.+.+.. .|+..+ .-.++|+.|||+|==+=+.+..|+.-|||+....
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 68 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRG 68 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 334444444433 477788 6999999999999999999999999999986643
No 151
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=34.91 E-value=1.3e+02 Score=30.24 Aligned_cols=82 Identities=15% Similarity=0.170 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcccccccccCHHHHhhcc---------CCCCceEEEEeCCCCCeEEecCCCcc
Q 015627 164 DNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLH---------CFQNQTLIAIKAPQGTTLEVPDPDEA 234 (403)
Q Consensus 164 ~~L~~~E~~LD~lI~~~~q~L~~Lted~~n~~~aYVT~eDI~~l~---------~f~~qTvIAIKAP~gT~LEVPdP~e~ 234 (403)
+.|...|..|+++|.--.+-|..-.++..+..++||+.+-+++-+ -|.+..+-|++=+.|+.+.++-++..
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 356677889999998655555555555567778999877666522 25677788899999999999988643
Q ss_pred cCCCCCcEEEEEecCC
Q 015627 235 VDYPQRRYRIILRSTM 250 (403)
Q Consensus 235 ~~~~q~~YqI~LkSt~ 250 (403)
+ -|...|.+-.
T Consensus 106 -~----~y~AtIe~it 116 (262)
T KOG3026|consen 106 -Q----IYDATIEHIT 116 (262)
T ss_pred -c----eEEeehhhcc
Confidence 2 3666666543
No 152
>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=34.79 E-value=60 Score=29.94 Aligned_cols=37 Identities=22% Similarity=0.436 Sum_probs=27.1
Q ss_pred ccHHHHHHHhcccee--ehhhhHHHhhhccchh--hccCCeEEEecc
Q 015627 102 LDLNKAAETLEVQKR--RIYDITNVLEGIGLIE--KKLKNRIRWKGL 144 (403)
Q Consensus 102 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIe--K~sKN~i~W~G~ 144 (403)
+.+.++|+.+||+++ |.|| .+|||. +...|.|++-+.
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 467899999999988 4554 578875 345677887654
No 153
>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=34.40 E-value=26 Score=30.48 Aligned_cols=41 Identities=27% Similarity=0.374 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHH
Q 015627 84 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 124 (403)
Q Consensus 84 glLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 124 (403)
.+||.|=-.++.-.=...++|.++|+.++|+|=-+||.+.-
T Consensus 16 ~LLT~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 16 ELLTEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp GGS-HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHCCHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35676644555544567799999999999999999998764
No 154
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=34.35 E-value=43 Score=26.59 Aligned_cols=44 Identities=23% Similarity=0.307 Sum_probs=34.7
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
.+++++.. ++.+.-.++|+.+++.+-..-=+.+.||.-|.|++.
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 155
>PHA01750 hypothetical protein
Probab=34.29 E-value=90 Score=25.84 Aligned_cols=30 Identities=20% Similarity=0.484 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 155 DASILQADIDNLSMEELRVDEQTRELRERL 184 (403)
Q Consensus 155 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L 184 (403)
++.+|+.|++++..+.++|.+++.++...+
T Consensus 43 ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 43 ELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 466777777777777777777776665544
No 156
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=34.24 E-value=72 Score=35.74 Aligned_cols=52 Identities=17% Similarity=0.300 Sum_probs=33.0
Q ss_pred hhccCCeEEEeccCCCCC--C--C-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 132 EKKLKNRIRWKGLDNSIP--G--E-VDADASILQADIDNLSMEELRVDEQTRELRERL 184 (403)
Q Consensus 132 eK~sKN~i~W~G~~~s~~--~--~-~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L 184 (403)
+|. +.++.|+|...... + + ...+...|++||+.|..+-..||..|+.+..++
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 344 44588998764321 0 1 112455777888888888888888877765554
No 157
>PF13551 HTH_29: Winged helix-turn helix
Probab=33.94 E-value=32 Score=27.74 Aligned_cols=28 Identities=18% Similarity=0.358 Sum_probs=26.1
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccc
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGL 130 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGL 130 (403)
...++|..||+.+|-+|.+++-++.=|+
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 158
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=33.88 E-value=1.5e+02 Score=25.94 Aligned_cols=47 Identities=21% Similarity=0.296 Sum_probs=39.5
Q ss_pred HHHHHHHHHhhCCCC--cccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 86 LTKKFINLIKHAEDG--ILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g--~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
|...|..|++..++. .+.|.++|+.|..++|-.==|++-|+..|.|+
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 456788888776654 58999999999999999999999999888765
No 159
>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=33.84 E-value=37 Score=33.38 Aligned_cols=31 Identities=32% Similarity=0.584 Sum_probs=25.7
Q ss_pred HHHHHhc---cceeehhhhHHHhhhccchhhccC
Q 015627 106 KAAETLE---VQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 106 ~aA~~L~---VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
.+|+.++ +..|++|++++-||.+|||+...+
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~ 352 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEER 352 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence 5666666 477999999999999999998643
No 160
>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=33.73 E-value=1.4e+02 Score=24.81 Aligned_cols=37 Identities=16% Similarity=0.273 Sum_probs=24.3
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh--ccCCeEEEec
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK--KLKNRIRWKG 143 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~sKN~i~W~G 143 (403)
.+.++|+.+||+.+.|-= -|..|||.. ...|.|+.-.
T Consensus 2 ~i~eva~~~gvs~~tlR~----ye~~Gll~p~~r~~~gyR~Y~ 40 (96)
T cd04788 2 KIGELARRTGLSVRTLHH----YDHIGLLSPSQRTEGGHRLYD 40 (96)
T ss_pred CHHHHHHHHCcCHHHHHH----HHHCCCCCCCccCCCCceeeC
Confidence 567899999998875432 356788854 3456666544
No 161
>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=33.72 E-value=44 Score=31.94 Aligned_cols=47 Identities=23% Similarity=0.394 Sum_probs=33.9
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 86 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
|-..||++++.+ .++.|+++|..|++.-==+-+-++-|+.-|.|.=.
T Consensus 100 lL~~Fi~yIK~~--Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv 146 (188)
T PF09756_consen 100 LLQEFINYIKEH--KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGV 146 (188)
T ss_dssp HHHHHHHHHHH---SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EE
T ss_pred HHHHHHHHHHHc--ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceee
Confidence 778999999884 68999999999999666666667777777776543
No 162
>PHA00738 putative HTH transcription regulator
Probab=33.43 E-value=1.4e+02 Score=26.51 Aligned_cols=72 Identities=19% Similarity=0.328 Sum_probs=50.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHHHHHHHHHHHH
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADASILQADIDNL 166 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L 166 (403)
++.|.+|... +.+...++++.|++.+=.|-==..||+..|||+.....+..+.-.... ....+.|..|++..
T Consensus 15 r~IL~lL~~~--e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~-----~~~~~l~~~~~~~~ 86 (108)
T PHA00738 15 RKILELIAEN--YILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIREN-----SKEIQILNSELEGF 86 (108)
T ss_pred HHHHHHHHHc--CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCC-----ccHHHHHhhHHHHH
Confidence 4566667553 347888999999999999999999999999999876665555433321 12355666666544
No 163
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=33.28 E-value=1.4e+02 Score=32.20 Aligned_cols=52 Identities=21% Similarity=0.254 Sum_probs=34.3
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH----Hhhhcc--chhhccCCeEEEeccC
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN----VLEGIG--LIEKKLKNRIRWKGLD 145 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN----VLEgIG--LIeK~sKN~i~W~G~~ 145 (403)
+.+.+|+ ++.+...++|+.|+|++|-|+-=++ +|++-| ++.+ ++-|+..+.+
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 3455553 3578999999999999998864444 345544 4455 2357776643
No 164
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=33.23 E-value=39 Score=27.05 Aligned_cols=42 Identities=19% Similarity=0.190 Sum_probs=32.5
Q ss_pred CCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEE
Q 015627 99 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRW 141 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W 141 (403)
.+.....+++...++.-+++..+++-|+.-|||++ .++.|.=
T Consensus 17 ~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y~l 58 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK-KDGKYRL 58 (77)
T ss_dssp TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE-ETTEEEE
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC-CCCEEEE
Confidence 67788899999999999999999999999999955 4555543
No 165
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=33.15 E-value=48 Score=32.12 Aligned_cols=44 Identities=14% Similarity=0.160 Sum_probs=36.7
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhc
Q 015627 85 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGI 128 (403)
Q Consensus 85 lLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgI 128 (403)
.+..+.+.++.......++|.++|+.+++++|.|.-+..-.-|+
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 35678899999999999999999999999999988777654443
No 166
>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=33.14 E-value=89 Score=25.40 Aligned_cols=31 Identities=23% Similarity=0.399 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 156 ASILQADIDNLSMEELRVDEQTRELRERLRE 186 (403)
Q Consensus 156 ~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~ 186 (403)
+..++.+++.|..+...+...+..++..|+.
T Consensus 71 ~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~ 101 (106)
T PF01920_consen 71 IEKLEKEIKKLEKQLKYLEKKLKELKKKLYE 101 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444444444444443
No 167
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=32.70 E-value=79 Score=27.65 Aligned_cols=46 Identities=20% Similarity=0.261 Sum_probs=37.2
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
+.|..++. .++.+.+.++|+.|+|.+=.+--.++-|+.-|+|.+..
T Consensus 11 ~~I~~l~~--~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 11 EQIYLLIE--EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHHHh--cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence 34444443 34667899999999999999999999999999999663
No 168
>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=32.39 E-value=78 Score=26.54 Aligned_cols=46 Identities=24% Similarity=0.291 Sum_probs=36.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
+-.|+++... +..|-=..+|+.|++.-=-|..+.-.||.+|||+++
T Consensus 11 ~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 11 KALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 3455555443 667788888999999988899999999999999975
No 169
>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=32.38 E-value=36 Score=25.73 Aligned_cols=42 Identities=26% Similarity=0.345 Sum_probs=25.1
Q ss_pred CcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 79 YDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 79 ~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
+-++|.+--+ +++++....|. ...++|..+||.+.-|++|..
T Consensus 3 kR~~LTl~eK--~~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 3 KRKSLTLEEK--LEIIKRLEEGE-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp SSSS--HHHH--HHHHHHHHCTT--HHHHHHHHT--CCHHHHHHH
T ss_pred CCccCCHHHH--HHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 3444444332 34444444555 899999999999999999985
No 170
>PF12728 HTH_17: Helix-turn-helix domain
Probab=32.02 E-value=27 Score=25.23 Aligned_cols=22 Identities=27% Similarity=0.489 Sum_probs=20.2
Q ss_pred ccHHHHHHHhccceeehhhhHH
Q 015627 102 LDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItN 123 (403)
+++.++|+.|+|.+..||.+++
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 171
>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=31.83 E-value=40 Score=28.43 Aligned_cols=49 Identities=22% Similarity=0.357 Sum_probs=39.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhc-----cceeehhhhHHHhhhccchhhccCC
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLE-----VQKRRIYDITNVLEGIGLIEKKLKN 137 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~-----VqKRRIYDItNVLEgIGLIeK~sKN 137 (403)
+..++++.+++. .++.+++.+.|. +.+=-||-.++.|+..|+|.|...+
T Consensus 11 ~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 11 LAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 347788888777 899999999885 4444699999999999999998544
No 172
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=31.63 E-value=37 Score=31.46 Aligned_cols=53 Identities=19% Similarity=0.137 Sum_probs=39.3
Q ss_pred HHHHHHHHhhC-CC--CcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 015627 87 TKKFINLIKHA-ED--GILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 140 (403)
Q Consensus 87 TkKFI~Ll~~a-p~--g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 140 (403)
-.|+..+|... .. ..+.-.++|+.||++|+.+.-+.+-|+--|+|++.. ++|.
T Consensus 152 ~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~-~~i~ 207 (226)
T PRK10402 152 ENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSK-RGYL 207 (226)
T ss_pred HHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeC-CEEE
Confidence 45555554332 11 235678999999999999999999999999999874 4454
No 173
>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=31.50 E-value=1.3e+02 Score=24.49 Aligned_cols=81 Identities=17% Similarity=0.348 Sum_probs=47.3
Q ss_pred HHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCC-CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 106 KAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSI-PGEVDADASILQADIDNLSMEELRVDEQTRELRERL 184 (403)
Q Consensus 106 ~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~-~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L 184 (403)
.+...+.--++.+..+.-|++-|..+. .+.-.|+..+..- ......-...|+++++.+..+-..|...+..+..+|
T Consensus 16 ~~~~q~~~l~~~~~~~~~~~~eL~~l~---~~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l 92 (106)
T PF01920_consen 16 QLEQQIQQLERQLRELELTLEELEKLD---DDRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKL 92 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTSS---TT-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCC---CcchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333344444555544443 3345565544321 112344567888888888888888888888888888
Q ss_pred HHhhh
Q 015627 185 RELIE 189 (403)
Q Consensus 185 ~~Lte 189 (403)
.++..
T Consensus 93 ~~~~~ 97 (106)
T PF01920_consen 93 KELKK 97 (106)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 88754
No 174
>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=31.10 E-value=1.4e+02 Score=23.62 Aligned_cols=39 Identities=15% Similarity=0.454 Sum_probs=25.6
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 151 EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 151 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
+++.++.++...+..++.+-+.|-+-|..+.+.++.|..
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 345556666666777776666777777777777766543
No 175
>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=30.96 E-value=1.2e+02 Score=28.05 Aligned_cols=19 Identities=11% Similarity=0.328 Sum_probs=12.8
Q ss_pred EEEEeCCCCCeEEecCCCc
Q 015627 215 LIAIKAPQGTTLEVPDPDE 233 (403)
Q Consensus 215 vIAIKAP~gT~LEVPdP~e 233 (403)
.|.|+.-+.|++++-..++
T Consensus 59 FIlV~T~~~a~I~ceiS~D 77 (142)
T PF08781_consen 59 FILVNTSKKAVIECEISED 77 (142)
T ss_dssp -EEEEEESS--EEEEE-TT
T ss_pred EEEEEecCCcEEEEEEcCC
Confidence 6899999999999976554
No 176
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=30.93 E-value=61 Score=32.11 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=40.2
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccc-hhhccCCeEEE
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGL-IEKKLKNRIRW 141 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL-IeK~sKN~i~W 141 (403)
.+.+.++.+ +..+...++|+.|+|+|..++-.+..|+.-|+ |.......|..
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 456777754 46788889999999999999999999999999 54433234544
No 177
>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=30.63 E-value=39 Score=27.56 Aligned_cols=42 Identities=17% Similarity=0.351 Sum_probs=35.7
Q ss_pred HhhCCCCcccHHHHHHHh-ccceeehhhhHHHhhhccchhhcc
Q 015627 94 IKHAEDGILDLNKAAETL-EVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 94 l~~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
+..-..|....+++.+.+ +++++-+.+=...|+..|||+|..
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 334444889999999999 999999999999999999999973
No 178
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=30.26 E-value=25 Score=30.87 Aligned_cols=34 Identities=26% Similarity=0.414 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHH
Q 015627 85 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 124 (403)
Q Consensus 85 lLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 124 (403)
.|..+|++.+ -++.+.+|+.|||++.+|-.|+|=
T Consensus 13 iL~eeflep~------glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 13 ILREEFLEPL------GLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHhccc------cCCHHHHHHHhCCCHHHHHHHHcC
Confidence 3456677644 478899999999999999999983
No 179
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=30.20 E-value=32 Score=27.74 Aligned_cols=23 Identities=26% Similarity=0.433 Sum_probs=18.8
Q ss_pred cCCCceEEEEecCccccccccCC
Q 015627 248 STMGPIDVYLVSRFEEKFEETNS 270 (403)
Q Consensus 248 St~GPIdVyL~~~~~~~~e~~~~ 270 (403)
|..|+|.|+.++.++.....+.|
T Consensus 16 s~lG~I~vLYvn~~eS~~~~~~G 38 (62)
T PF15513_consen 16 SQLGEIAVLYVNPYESDEDRLTG 38 (62)
T ss_pred HhcCcEEEEEEcccccCCCeEec
Confidence 68999999999988877655554
No 180
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=30.06 E-value=1.9e+02 Score=27.35 Aligned_cols=54 Identities=19% Similarity=0.252 Sum_probs=42.5
Q ss_pred cHHH-HHHHHHHHHhh---CCCCcc-cHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 82 SLGL-LTKKFINLIKH---AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 82 SLgl-LTkKFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
+|.. +...+.+.+.. .|+..+ .-.++|+.|||+|=-+-+.+..|+..|||+...
T Consensus 10 ~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~ 68 (254)
T PRK09464 10 KLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQ 68 (254)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4543 44555565544 366677 899999999999999999999999999998663
No 181
>PRK13503 transcriptional activator RhaS; Provisional
Probab=29.67 E-value=65 Score=30.26 Aligned_cols=40 Identities=5% Similarity=0.082 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 84 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 84 glLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
....+++++++.+.....++|.++|+.++++++.+..+..
T Consensus 170 ~~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 170 DARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3457889999988888899999999999999998876653
No 182
>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=29.61 E-value=85 Score=24.98 Aligned_cols=57 Identities=21% Similarity=0.286 Sum_probs=47.1
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 015627 86 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 142 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 142 (403)
+-.+.+++|....+...---..+..|.+.|+.|==+..=|+.=|.|.|.+-+--.|.
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 456778888777766777778888899999999999999999999999888888885
No 183
>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=29.32 E-value=2.8e+02 Score=25.97 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=37.2
Q ss_pred HHHHHHHhhCCCCcc--cHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 88 KKFINLIKHAEDGIL--DLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 88 kKFI~Ll~~ap~g~l--dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
+++..++.+.+...+ .+..+|..|++.++-|-=++.|+.-+|+|+..
T Consensus 101 ~~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~FVti~ 149 (195)
T PF10141_consen 101 KKLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLKVFFELGFVTIE 149 (195)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCcEEEe
Confidence 345555666555432 46889999999999999999999999999865
No 184
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=29.24 E-value=76 Score=28.62 Aligned_cols=52 Identities=15% Similarity=0.286 Sum_probs=45.3
Q ss_pred cCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhh
Q 015627 80 DSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 80 dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 133 (403)
...|-.+=++.|.+|+. ++.+...++|+.+|++.--++.=++=||.-|+|++
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 44577778899998864 77888999999999999999999999999999986
No 185
>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=29.11 E-value=1.8e+02 Score=24.14 Aligned_cols=17 Identities=18% Similarity=0.212 Sum_probs=11.9
Q ss_pred cHHHHHHHhccceeehh
Q 015627 103 DLNKAAETLEVQKRRIY 119 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIY 119 (403)
.+.++|+.+||..+-|-
T Consensus 2 ti~eva~~~gvs~~tlR 18 (103)
T cd01106 2 TVGEVAKLTGVSVRTLH 18 (103)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 46677888888766554
No 186
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=29.00 E-value=65 Score=31.61 Aligned_cols=42 Identities=7% Similarity=-0.026 Sum_probs=36.0
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhh
Q 015627 85 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLE 126 (403)
Q Consensus 85 lLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLE 126 (403)
....++++++.......++|.++|+.+++++|.|+-..+-.-
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~ 259 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAAT 259 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 456789999999999999999999999999999987776443
No 187
>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=28.99 E-value=84 Score=26.10 Aligned_cols=37 Identities=19% Similarity=0.335 Sum_probs=24.1
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh--ccCCeEEEec
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK--KLKNRIRWKG 143 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~sKN~i~W~G 143 (403)
.+.++|+.+||+.+.|-- .|..|||.- ...|.|++-.
T Consensus 2 ~i~eva~~~gvs~~tlR~----ye~~Gll~p~~~~~~gyR~Y~ 40 (97)
T cd04782 2 TTGEFAKLCGISKQTLFH----YDKIGLFKPEIVKENGYRYYT 40 (97)
T ss_pred CHHHHHHHHCcCHHHHHH----HHHCCCCCCCccCCCCCccCC
Confidence 467889999998776533 366788743 3345565543
No 188
>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=28.97 E-value=1.1e+02 Score=25.38 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=25.9
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh--ccCCeEEEecc
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK--KLKNRIRWKGL 144 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~sKN~i~W~G~ 144 (403)
.+.++|+.+||..+.|- --|..|||.- ...|.|++-+.
T Consensus 2 ti~eva~~~gvs~~tLR----yye~~Gll~p~~~~~~gyR~Y~~ 41 (96)
T cd04768 2 TIGEFAKLAGVSIRTLR----HYDDIGLFKPAKIAENGYRYYSY 41 (96)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCeeeCCH
Confidence 57889999999887552 2356688863 34677777654
No 189
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=28.34 E-value=67 Score=28.79 Aligned_cols=39 Identities=15% Similarity=0.211 Sum_probs=33.4
Q ss_pred cccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 015627 101 ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 140 (403)
Q Consensus 101 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 140 (403)
.+.-.++|..||+.++.+.-+.+-|+.-|+|++.. ++|.
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 190
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=28.29 E-value=1.1e+02 Score=29.62 Aligned_cols=40 Identities=18% Similarity=0.279 Sum_probs=25.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q 015627 152 VDADASILQADIDNLSMEELRVDEQTRELRERLRELIENEN 192 (403)
Q Consensus 152 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~~ 192 (403)
+.++.+.|++|++.|+.+..+++++.. -.++|+.|.+-..
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 344566778888888777777765544 3567777655433
No 191
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=28.10 E-value=3e+02 Score=25.70 Aligned_cols=33 Identities=9% Similarity=-0.009 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 015627 158 ILQADIDNLSMEELRVDEQTRELRERLRELIEN 190 (403)
Q Consensus 158 ~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted 190 (403)
.|+.....|..++.-|++.+..+.++|.+|..+
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 556666778999999999999999999999753
No 192
>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=28.01 E-value=1.8e+02 Score=24.29 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=16.2
Q ss_pred cHHHHHHHhccceee--hhhhHHHhhhccchhh
Q 015627 103 DLNKAAETLEVQKRR--IYDITNVLEGIGLIEK 133 (403)
Q Consensus 103 dLn~aA~~L~VqKRR--IYDItNVLEgIGLIeK 133 (403)
.+.++|+.+||+.|- .|| .+|||.-
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 193
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=27.97 E-value=2e+02 Score=24.58 Aligned_cols=86 Identities=14% Similarity=0.098 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccce--------------------eehhhhHHH--------hhhccchhhccCCeEEEeccCCCCCCCch
Q 015627 102 LDLNKAAETLEVQK--------------------RRIYDITNV--------LEGIGLIEKKLKNRIRWKGLDNSIPGEVD 153 (403)
Q Consensus 102 ldLn~aA~~L~VqK--------------------RRIYDItNV--------LEgIGLIeK~sKN~i~W~G~~~s~~~~~~ 153 (403)
+.+.++|+.+||++ +|+|+..+| |-.+|+=-+.-+.-+....... +....
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~p~~~~~~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~--~~~~~ 78 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRA--VLPWP 78 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccCC--cCcHH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 154 ADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 154 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
.....|++.++.|..+-++|..+++.+...+..+.+
T Consensus 79 ~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~ 114 (116)
T cd04769 79 HLQQALEDKKQEIRAQITELQQLLARLDAFEASLKD 114 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
No 194
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=27.56 E-value=1.2e+02 Score=32.28 Aligned_cols=58 Identities=19% Similarity=0.340 Sum_probs=45.8
Q ss_pred CcHHHHHHH------HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEec
Q 015627 81 SSLGLLTKK------FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKG 143 (403)
Q Consensus 81 kSLglLTkK------FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G 143 (403)
+-||+|+-+ .+++|....+..|.|+++|..-++. .-||++.|+.+++|... |. +.|..
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 347777744 7788877766669999999999984 57999999999999876 33 66664
No 195
>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=27.55 E-value=1.7e+02 Score=23.21 Aligned_cols=39 Identities=8% Similarity=0.219 Sum_probs=31.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 015627 152 VDADASILQADIDNLSMEELRVDEQTRELRERLRELIEN 190 (403)
Q Consensus 152 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted 190 (403)
+.+++..++..++++....+.|+........++.++.++
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 456677888888888888888888888888888877665
No 196
>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=27.25 E-value=63 Score=31.05 Aligned_cols=49 Identities=10% Similarity=0.268 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCCC-cccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 015627 88 KKFINLIKHAEDG-ILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 139 (403)
Q Consensus 88 kKFI~Ll~~ap~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 139 (403)
...++.|....+. .++++++++..++.+ -||+..|+.+|+|.....+++
T Consensus 136 ~~i~~~L~~~~~~~~isi~~is~~Tgi~~---~DIi~tL~~l~~l~~~~~~~~ 185 (188)
T PF01853_consen 136 RVILEYLLEFKGKKSISIKDISQETGIRP---EDIISTLQQLGMLKYYKGQHI 185 (188)
T ss_dssp HHHHHHHHHTSSE--EEHHHHHHHH-BTH---HHHHHHHHHTT-EEEETTEEE
T ss_pred HHHHHHHHhcCCCCeEEHHHHHHHHCCCH---HHHHHHHHHCCCEEEECCcEE
Confidence 4567777666664 899999999999965 699999999999987755543
No 197
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=27.05 E-value=74 Score=31.64 Aligned_cols=61 Identities=28% Similarity=0.343 Sum_probs=50.1
Q ss_pred CcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEe
Q 015627 81 SSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWK 142 (403)
Q Consensus 81 kSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~ 142 (403)
..|-.-=+.-|+++.. .+|.+.-+++.+.||.+|=-++-|+-=||-.|||+|..++.=.|.
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 3445555667777765 678999999999999999999999999999999999977665553
No 198
>PRK03837 transcriptional regulator NanR; Provisional
Probab=26.96 E-value=45 Score=31.03 Aligned_cols=51 Identities=12% Similarity=0.213 Sum_probs=41.2
Q ss_pred HHHHHHHHHhh---CCCCcc-cHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 86 LTKKFINLIKH---AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 86 LTkKFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
+-+.+.+.+.. .|+..+ ...++|+.|||+|--+=+.+..|+.-|||+...+
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 44555555543 466678 8999999999999999999999999999997643
No 199
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=26.94 E-value=1.3e+02 Score=28.71 Aligned_cols=35 Identities=20% Similarity=0.265 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 155 DASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 155 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
-+..||+|+..+...+...+..+.++.++.+.|++
T Consensus 28 lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~e 62 (201)
T PF13851_consen 28 LIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSE 62 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 47789999999999999998888888887766655
No 200
>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=26.87 E-value=66 Score=27.72 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=22.3
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
++..+-+..|..||-+.|.++.|.++|+.-
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 777888889999999999999999999753
No 201
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=26.80 E-value=1.5e+02 Score=25.54 Aligned_cols=54 Identities=15% Similarity=0.139 Sum_probs=39.1
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccccccCHHHHh
Q 015627 151 EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIK 205 (403)
Q Consensus 151 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~~n~~~aYVT~eDI~ 205 (403)
++.+++..+++|++.|+++.+.|...|..++... ...+...-..|.||-..+|-
T Consensus 31 ~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~-dyiEe~AR~~Lg~vk~gEiv 84 (105)
T PRK00888 31 RVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQ-EAIEERARNELGMVKPGETF 84 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcH-HHHHHHHHHHcCCCCCCCEE
Confidence 4567788999999999999999999999987742 23333333456677665553
No 202
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=26.36 E-value=71 Score=28.72 Aligned_cols=37 Identities=22% Similarity=0.141 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhh
Q 015627 84 GLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYD 120 (403)
Q Consensus 84 glLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYD 120 (403)
..|-..+++++.+..-.-+.++++|+..||.|+.||.
T Consensus 14 ~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~ 50 (213)
T PRK09975 14 QELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHH
Confidence 4566778889988777789999999999999999995
No 203
>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=26.33 E-value=79 Score=30.41 Aligned_cols=52 Identities=23% Similarity=0.425 Sum_probs=39.8
Q ss_pred HHHHHHH-HHhhCCCCcccHHHHHHHhccceeehhhhHH-HhhhccchhhccCC
Q 015627 86 LTKKFIN-LIKHAEDGILDLNKAAETLEVQKRRIYDITN-VLEGIGLIEKKLKN 137 (403)
Q Consensus 86 LTkKFI~-Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~sKN 137 (403)
.-+.|+. +++...++.+.+.++|..||+..+.+..++- .|--.|||++....
T Consensus 239 ~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 292 (305)
T TIGR00635 239 IDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRG 292 (305)
T ss_pred HHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCch
Confidence 3344555 5565566678899999999999999999777 78888999766443
No 204
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=26.08 E-value=52 Score=33.13 Aligned_cols=44 Identities=20% Similarity=0.400 Sum_probs=34.7
Q ss_pred HHHHHHHH---HhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccch
Q 015627 86 LTKKFINL---IKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLI 131 (403)
Q Consensus 86 LTkKFI~L---l~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 131 (403)
...+++.+ |+..+. +...++|+.|+|++|-||-=+|-|...|+=
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 34444444 444433 999999999999999999999999999985
No 205
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=25.96 E-value=81 Score=30.12 Aligned_cols=38 Identities=11% Similarity=0.162 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 86 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
...+++.++.......+.|.++|+.++++++++.-+..
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk 221 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFR 221 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46778888888888999999999999999998876654
No 206
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.77 E-value=86 Score=26.94 Aligned_cols=42 Identities=12% Similarity=0.318 Sum_probs=32.3
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
++.++-+ .....+.-++-+.-|-.||.+-|++-.|+|||++-
T Consensus 12 Yla~Li~-S~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~l 53 (95)
T COG4519 12 YLAYLID-SGETANVPELMAATGWPRRTAQDVIKALPGLGIVL 53 (95)
T ss_pred HHHHHHh-ccccCChHHHHHHcCCchhHHHHHHHhCcCCCeEE
Confidence 3444433 34466777888888999999999999999999863
No 207
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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=25.66 E-value=56 Score=29.26 Aligned_cols=82 Identities=22% Similarity=0.217 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccce--------------------eehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHHHHHHH
Q 015627 102 LDLNKAAETLEVQK--------------------RRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADASILQA 161 (403)
Q Consensus 102 ldLn~aA~~L~VqK--------------------RRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~ 161 (403)
+.+.++|+.+||+. +|.|+. ..++-|.+|.....- |+....-.++-.....+..
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~GLl~p~r~~~g~R~Y~~-~~l~~l~~I~~lr~~-----G~sL~eI~~~l~~~~~~~~ 74 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDE-TALDRLQLIEHLKGQ-----RLSLAEIKDQLEEVQRSDK 74 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCccCCCCCeeECH-HHHHHHHHHHHHHHC-----CCCHHHHHHHHHhhccccc
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 162 DIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 162 El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
+.+.+..+.+.|..+|+.++++++.|.+
T Consensus 75 ~~~~~~~~~~~l~~~i~~Le~~l~~L~~ 102 (134)
T cd04779 75 EQREVAQEVQLVCDQIDGLEHRLKQLKP 102 (134)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 208
>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=25.51 E-value=1.3e+02 Score=25.23 Aligned_cols=37 Identities=19% Similarity=0.290 Sum_probs=24.5
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchh--hccCCeEEEec
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIE--KKLKNRIRWKG 143 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~sKN~i~W~G 143 (403)
.+.++|+.+||+.+-|-- .|-.||+. +...|.+++-.
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 467889999998764432 26788875 34566677654
No 209
>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=25.49 E-value=2.2e+02 Score=24.13 Aligned_cols=27 Identities=22% Similarity=0.279 Sum_probs=20.0
Q ss_pred cHHHHHHHhccceeehhhhHHHhhhccchhh
Q 015627 103 DLNKAAETLEVQKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 133 (403)
.+.++|+.+||+.+-|.-. |-.|||..
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 5778999999988866554 55677754
No 210
>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=25.45 E-value=1.7e+02 Score=27.24 Aligned_cols=54 Identities=24% Similarity=0.272 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc-------ccccccccCHHHHhh
Q 015627 153 DADASILQADIDNLSMEELRVDEQTRELRERLRELIENE-------NNRKWLFVTEEDIKN 206 (403)
Q Consensus 153 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~-------~n~~~aYVT~eDI~~ 206 (403)
..++..|++|++.|..+-+.+-..+..|+..|..+.... ....-.=|++++|.+
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 457889999999999888888888888999998886211 111122378888876
No 211
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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=25.45 E-value=1.4e+02 Score=25.76 Aligned_cols=8 Identities=38% Similarity=0.027 Sum_probs=3.2
Q ss_pred HHHHHHHh
Q 015627 88 KKFINLIK 95 (403)
Q Consensus 88 kKFI~Ll~ 95 (403)
-+||..++
T Consensus 45 l~~I~~lr 52 (118)
T cd04776 45 LKLILRGK 52 (118)
T ss_pred HHHHHHHH
Confidence 33444443
No 212
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=25.29 E-value=1.1e+02 Score=33.39 Aligned_cols=22 Identities=14% Similarity=0.071 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhh
Q 015627 168 MEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 168 ~~E~~LD~lI~~~~q~L~~Lte 189 (403)
.+...+++.|+.++..++.|.+
T Consensus 97 aq~~dle~KIkeLEaE~~~Lk~ 118 (475)
T PRK13729 97 KQRGDDQRRIEKLGQDNAALAE 118 (475)
T ss_pred hhhhhHHHHHHHHHHHHHHHHH
Confidence 3344455555555555555533
No 213
>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=25.26 E-value=1.3e+02 Score=25.58 Aligned_cols=32 Identities=28% Similarity=0.423 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 015627 157 SILQADIDNLSMEELRVDEQTRELRERLRELI 188 (403)
Q Consensus 157 ~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lt 188 (403)
..|+..++.++..-..|++.+..++.+|.++-
T Consensus 70 ~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q 101 (110)
T TIGR02338 70 QELKEKKETLELRVKTLQRQEERLREQLKELQ 101 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666666666666666666666666653
No 214
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=25.21 E-value=95 Score=29.25 Aligned_cols=49 Identities=22% Similarity=0.292 Sum_probs=40.1
Q ss_pred HHHHHHHhh---CCCCcc-cHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 88 KKFINLIKH---AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 88 kKFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
..+.+.+.. .|+..+ .-.++|+.|||+|==+-+-+..|+.-|||+....
T Consensus 14 ~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 14 ERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 444444433 477889 8999999999999999999999999999987744
No 215
>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=24.99 E-value=1.1e+02 Score=25.20 Aligned_cols=28 Identities=7% Similarity=0.253 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 015627 161 ADIDNLSMEELRVDEQTRELRERLRELI 188 (403)
Q Consensus 161 ~El~~L~~~E~~LD~lI~~~~q~L~~Lt 188 (403)
++|..|.++-+.|++.+..++++|-++-
T Consensus 2 ~~L~~l~~~k~~Le~~L~~lE~qIy~~E 29 (80)
T PF09340_consen 2 KELKELLQKKKKLEKDLAALEKQIYDKE 29 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677788888888888888888887763
No 216
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=24.61 E-value=1.3e+02 Score=32.52 Aligned_cols=53 Identities=23% Similarity=0.449 Sum_probs=38.8
Q ss_pred CCCcCcHHHHH------HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhh
Q 015627 77 CRYDSSLGLLT------KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 77 ~R~dkSLglLT------kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 133 (403)
.|==+-||+++ ...+++|... .+.++|++++...++. .-||+.-|+.+|||..
T Consensus 345 EkPLSdlG~~sY~~YW~~~i~~~L~~~-~~~~si~~is~~T~i~---~~Dii~tL~~l~~l~~ 403 (450)
T PLN00104 345 ERPLSDLGLVSYRGYWTRVLLEILKKH-KGNISIKELSDMTAIK---AEDIVSTLQSLNLIQY 403 (450)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhc-CCCccHHHHHHHhCCC---HHHHHHHHHHCCCEEe
Confidence 34344566665 2356666543 4579999999999995 5799999999999953
No 217
>smart00338 BRLZ basic region leucin zipper.
Probab=24.52 E-value=2.6e+02 Score=21.45 Aligned_cols=33 Identities=24% Similarity=0.416 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 015627 156 ASILQADIDNLSMEELRVDEQTRELRERLRELI 188 (403)
Q Consensus 156 ~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lt 188 (403)
+..|+.++..|..+-..|-..+..+..++..|.
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk 60 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLK 60 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666666666666666666666665554
No 218
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=24.37 E-value=53 Score=30.65 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=35.1
Q ss_pred CCCCcc-cHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 97 AEDGIL-DLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 97 ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
.|+..+ .-.++|++|||+|=-+-+-+..|+.-|||+...
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 466778 799999999999999999999999999999763
No 219
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=23.92 E-value=84 Score=30.90 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=33.3
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHH
Q 015627 86 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNV 124 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 124 (403)
..++.+.++.+.....++|.++|+.+++++|.++-+..-
T Consensus 192 ~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 467788888888778899999999999999988877654
No 220
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=23.86 E-value=75 Score=29.60 Aligned_cols=37 Identities=32% Similarity=0.443 Sum_probs=29.9
Q ss_pred CCcccHHHHHHHhccceee--------------hhhhHHHhhhccchhhcc
Q 015627 99 DGILDLNKAAETLEVQKRR--------------IYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRR--------------IYDItNVLEgIGLIeK~s 135 (403)
.+.+-+..++..+|..||| |=-|+..||.+|||+|..
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 4566777778889986664 778999999999999864
No 221
>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=23.81 E-value=2.5e+02 Score=23.42 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=20.7
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchhh
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEK 133 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 133 (403)
+.+.++|+.+||+.+.|--. |..|+|.-
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 57889999999988766544 45667653
No 222
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.80 E-value=91 Score=31.73 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccc
Q 015627 155 DASILQADIDNLSMEELRVDEQTRELRERLRELIENENNR 194 (403)
Q Consensus 155 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~~n~ 194 (403)
.++.|++||..|+..-..-|++|-+-..+|-+|..|++++
T Consensus 226 ~i~~lkeeia~Lkk~L~qkdq~ileKdkqisnLKad~e~~ 265 (305)
T KOG3990|consen 226 KIQKLKEEIARLKKLLHQKDQLILEKDKQISNLKADKEYQ 265 (305)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHhhhhhhhccCcchhHH
Confidence 5889999999999999999999999999999998885544
No 223
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.79 E-value=3.2e+02 Score=25.61 Aligned_cols=41 Identities=15% Similarity=0.175 Sum_probs=34.4
Q ss_pred HHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 90 FINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 90 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
++..+. ..|.+.-.++|..||+++.-+=-+.+-|+.-|||.
T Consensus 27 Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 27 VLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 444443 34679999999999999999999999999999999
No 224
>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=23.63 E-value=27 Score=31.24 Aligned_cols=26 Identities=23% Similarity=0.443 Sum_probs=0.0
Q ss_pred ceeehhhhHHHhhhccchhhccCCeEEE
Q 015627 114 QKRRIYDITNVLEGIGLIEKKLKNRIRW 141 (403)
Q Consensus 114 qKRRIYDItNVLEgIGLIeK~sKN~i~W 141 (403)
-|+++-+-+..||..|+|.+. |.|+=
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 477888899999999999998 76664
No 225
>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=23.57 E-value=1.2e+02 Score=24.76 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=15.4
Q ss_pred cHHHHHHHhccceeehhhhHH
Q 015627 103 DLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 103 dLn~aA~~L~VqKRRIYDItN 123 (403)
.+.++|+.+||..+.|--..+
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567888888888777665544
No 226
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=23.52 E-value=1e+02 Score=24.72 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=35.7
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccch
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLI 131 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 131 (403)
+++.++.......++|+++|..+|+.++.+.-...-..|+...
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 7777777766777999999999999999999888877766654
No 227
>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=23.36 E-value=66 Score=23.63 Aligned_cols=26 Identities=19% Similarity=0.272 Sum_probs=19.5
Q ss_pred CCcccHHHHHHHhccceeehhhhHHH
Q 015627 99 DGILDLNKAAETLEVQKRRIYDITNV 124 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRRIYDItNV 124 (403)
.|.+.+.+||..+||.+.-|+|.++-
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 228
>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=23.22 E-value=2.4e+02 Score=26.62 Aligned_cols=31 Identities=26% Similarity=0.281 Sum_probs=28.6
Q ss_pred HHHHHHh-ccceeehhhhHHHhhhccchhhcc
Q 015627 105 NKAAETL-EVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 105 n~aA~~L-~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
..+|..+ |+.-|.|.-....|...|||.+..
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 6788999 999999999999999999999864
No 229
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=23.22 E-value=1.1e+02 Score=28.02 Aligned_cols=42 Identities=26% Similarity=0.399 Sum_probs=37.6
Q ss_pred CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeE
Q 015627 98 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRI 139 (403)
Q Consensus 98 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i 139 (403)
.++.+-..++|..|+|..--.-..+|=|+..|||++.....|
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi 62 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGV 62 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCe
Confidence 788999999999999999999999999999999998644433
No 230
>PRK05638 threonine synthase; Validated
Probab=23.21 E-value=1.2e+02 Score=31.69 Aligned_cols=61 Identities=16% Similarity=0.209 Sum_probs=48.6
Q ss_pred CCCCCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhc--cceeehhhhHHHhhhccchhhc
Q 015627 71 LTPAGSCRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLE--VQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 71 ~~p~~~~R~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~ 134 (403)
+.+....|-.-.++.+-.+.+.+|.+. .....++++.|+ +.+--||-..++||.-|||+..
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 555666666666777767777778754 477889999998 8999999999999999999864
No 231
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=23.05 E-value=58 Score=31.62 Aligned_cols=45 Identities=22% Similarity=0.282 Sum_probs=38.3
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
++.+++++. .+.+.+.++|+.|+|+..-|+--+..||--|+|.|.
T Consensus 8 ~~Il~~l~~--~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 8 DAIIELVKQ--QGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHH--cCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 345677754 568999999999999998888889999999999886
No 232
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=23.03 E-value=79 Score=30.22 Aligned_cols=38 Identities=21% Similarity=0.253 Sum_probs=30.2
Q ss_pred HHHHHHHHHhhCCCCc-ccHHHHHHHhccceeehhhhHH
Q 015627 86 LTKKFINLIKHAEDGI-LDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g~-ldLn~aA~~L~VqKRRIYDItN 123 (403)
+..+++.++.+.-... +++.++|+.+|+++|.||-+.-
T Consensus 198 ~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk 236 (302)
T PRK09685 198 QFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFA 236 (302)
T ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3457777777665554 9999999999999999998763
No 233
>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=22.96 E-value=2.7e+02 Score=25.49 Aligned_cols=34 Identities=15% Similarity=0.196 Sum_probs=32.0
Q ss_pred CCcccHHHHHHHhccceeehhhhHHHhhhccchh
Q 015627 99 DGILDLNKAAETLEVQKRRIYDITNVLEGIGLIE 132 (403)
Q Consensus 99 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 132 (403)
.+.+.-.++|..||++++-+=-+.+-|...|||+
T Consensus 26 ~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 26 KGEFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 5679999999999999999999999999999995
No 234
>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=22.95 E-value=95 Score=26.76 Aligned_cols=43 Identities=28% Similarity=0.448 Sum_probs=34.0
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhcc
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKL 135 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~s 135 (403)
..|..++.+.|+ +.|.++|+.|+|....|+ ..|.-+|+.-|+.
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 567888888777 556799999999777766 6778889988873
No 235
>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=22.40 E-value=94 Score=23.64 Aligned_cols=39 Identities=10% Similarity=0.245 Sum_probs=35.0
Q ss_pred CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccC
Q 015627 98 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLK 136 (403)
Q Consensus 98 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sK 136 (403)
.++.+++.++=+.|+++|+-.-=|..-|...|+..|..-
T Consensus 7 ~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd 45 (50)
T PF09107_consen 7 KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGD 45 (50)
T ss_dssp TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCC
Confidence 388999999999999999999999999999999988864
No 236
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=22.36 E-value=74 Score=27.76 Aligned_cols=31 Identities=16% Similarity=0.405 Sum_probs=24.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 153 DADASILQADIDNLSMEELRVDEQTRELRER 183 (403)
Q Consensus 153 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~ 183 (403)
..++..+++|++.|.+.+..|...|+.+++.
T Consensus 56 ~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 56 QRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 4456677788888888888888888887776
No 237
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=22.30 E-value=98 Score=27.53 Aligned_cols=50 Identities=12% Similarity=0.156 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 83 LGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 83 LglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
|-.+=++.+++|+.. +.....++|+.||++.-.+..=++=|+.-|+|.+.
T Consensus 7 lD~~D~~Il~~Lq~d--~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 7 IDNLDRGILEALMEN--ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred cCHHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 556678899999774 88999999999999998888889999999999864
No 238
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=22.26 E-value=2.5e+02 Score=22.79 Aligned_cols=36 Identities=28% Similarity=0.388 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 154 ADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 154 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
..+..+++.+..|......|-..|..+...|+++.+
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 357888999999999999999999999999999877
No 239
>PRK11642 exoribonuclease R; Provisional
Probab=21.58 E-value=1e+02 Score=35.43 Aligned_cols=51 Identities=8% Similarity=0.046 Sum_probs=41.6
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccc----eeehhhhHHHhhhccchhhccCCeEE
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQ----KRRIYDITNVLEGIGLIEKKLKNRIR 140 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~Vq----KRRIYDItNVLEgIGLIeK~sKN~i~ 140 (403)
+.+++|... +..+.+.+++..|++. ++.|..+++-|+..|.|.+..++.|.
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 456666653 4899999999999995 35599999999999999988777664
No 240
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=21.50 E-value=6.5e+02 Score=23.25 Aligned_cols=88 Identities=24% Similarity=0.312 Sum_probs=0.0
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccccccccCHHHHhhccCCCCceEEEEeCCCCCeEEecC
Q 015627 151 EVDADASILQADIDNLSMEELRVDEQTRELRERLRELIENENNRKWLFVTEEDIKNLHCFQNQTLIAIKAPQGTTLEVPD 230 (403)
Q Consensus 151 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT~LEVPd 230 (403)
++...++.|+++++.|..+-..|...|.+++..+..| ++++.+.. ...++|-|=|-.=....|-+
T Consensus 10 ~l~a~lq~l~~qie~L~~~i~~l~~~~~e~~~~~~tl--------------~~lk~~~~-g~E~LVpvGag~fv~~kv~~ 74 (145)
T COG1730 10 ELAAQLQILQSQIESLQAQIAALNAAISELQTAIETL--------------ENLKGAGE-GKEVLVPVGAGLFVKAKVKD 74 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHhcCC-CceEEEEcCCCceEEEEecc
Q ss_pred CCcccCCCCCcEEEEEecCCCceEEEEecCcccccc
Q 015627 231 PDEAVDYPQRRYRIILRSTMGPIDVYLVSRFEEKFE 266 (403)
Q Consensus 231 P~e~~~~~q~~YqI~LkSt~GPIdVyL~~~~~~~~e 266 (403)
.++ .-|+|-|. ||.--.+++-+|
T Consensus 75 ~~k--------viV~iGsg-----~~ae~~~~eAie 97 (145)
T COG1730 75 MDK--------VIVSIGSG-----YYAEKSADEAIE 97 (145)
T ss_pred Cce--------EEEEcCCc-----eeeeecHHHHHH
No 241
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=21.49 E-value=2.5e+02 Score=23.26 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 015627 153 DADASILQADIDNLSMEELRVDEQTRELRERLREL 187 (403)
Q Consensus 153 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~L 187 (403)
...+..|+++++.|+.+...+...+.-++.++.-|
T Consensus 69 ~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~L 103 (104)
T PF13600_consen 69 SPELKELEEELEALEDELAALQDEIQALEAQIAFL 103 (104)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44678888888888888888888888777776543
No 242
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=21.41 E-value=1.1e+02 Score=31.79 Aligned_cols=43 Identities=14% Similarity=0.197 Sum_probs=37.7
Q ss_pred CCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEE
Q 015627 98 EDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIR 140 (403)
Q Consensus 98 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~ 140 (403)
.+..++..++++.+++.-+.+-+|..-|+..|+|.+...+.|.
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 4568899999999999999999999999999999987666543
No 243
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=21.19 E-value=6.9e+02 Score=23.39 Aligned_cols=51 Identities=24% Similarity=0.287 Sum_probs=36.1
Q ss_pred CCcCcHHHHHHHHHHHHh-hCCCCc---------------ccHHHHHHHhcc-ceeehhhhHHHhhhccc
Q 015627 78 RYDSSLGLLTKKFINLIK-HAEDGI---------------LDLNKAAETLEV-QKRRIYDITNVLEGIGL 130 (403)
Q Consensus 78 R~dkSLglLTkKFI~Ll~-~ap~g~---------------ldLn~aA~~L~V-qKRRIYDItNVLEgIGL 130 (403)
+++-+...|-++|..+-+ -+||.. --||+|=.+|.- .+|..|++ .|.|+.+
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 567788899999999864 456542 356777777766 57889987 5557655
No 244
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=21.15 E-value=85 Score=30.47 Aligned_cols=44 Identities=14% Similarity=0.262 Sum_probs=34.1
Q ss_pred HHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 89 KFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 89 KFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
+.+++++. .+.+.++++|+.|+|++--|.-=++.||.-|+|.|.
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 35556654 667999999999999765554447789999999887
No 245
>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=21.08 E-value=1.1e+02 Score=34.23 Aligned_cols=55 Identities=15% Similarity=0.274 Sum_probs=46.3
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHhccce----eehhhhHHHhhhccchhhccCCeEEEe
Q 015627 88 KKFINLIKHAEDGILDLNKAAETLEVQK----RRIYDITNVLEGIGLIEKKLKNRIRWK 142 (403)
Q Consensus 88 kKFI~Ll~~ap~g~ldLn~aA~~L~VqK----RRIYDItNVLEgIGLIeK~sKN~i~W~ 142 (403)
.+.+++++..+...+..++++..|++.+ .-++.+++-|+.-|.|.|..++.|...
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 4578888888889999999999999953 459999999999999998877777554
No 246
>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=21.04 E-value=38 Score=28.80 Aligned_cols=48 Identities=31% Similarity=0.439 Sum_probs=32.7
Q ss_pred EEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 139 IRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 139 i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
..|+|.+. .+++..+..|..+++.|..+-..|...+..++.+|..+..
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 56778764 3677788888888888888888888887777777766643
No 247
>PRK04217 hypothetical protein; Provisional
Probab=21.01 E-value=84 Score=27.61 Aligned_cols=47 Identities=9% Similarity=0.082 Sum_probs=28.3
Q ss_pred CCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 77 CRYDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 77 ~R~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
|-++..-..|+..=.+++...--.-++..++|+.|+|++.-||-+++
T Consensus 34 ~~~~~p~~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 34 VGPPKPPIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred ccCCCCcccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44444445555332333332222446999999999998776666655
No 248
>PRK15185 transcriptional regulator HilD; Provisional
Probab=20.99 E-value=1e+02 Score=31.60 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=34.1
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 85 LLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 85 lLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
.++.+...++.+.+...+++.++|+.+++++|.++-...
T Consensus 206 ~~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK 244 (309)
T PRK15185 206 TLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLA 244 (309)
T ss_pred HHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 467889999999999999999999999999999876643
No 249
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.89 E-value=1.5e+02 Score=32.80 Aligned_cols=30 Identities=13% Similarity=0.272 Sum_probs=26.7
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhccchhhc
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGIGLIEKK 134 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 134 (403)
++|+++++..++. ..||+..|+.+||+...
T Consensus 472 iSI~dIS~~TgI~---~eDII~TLq~L~llky~ 501 (552)
T PTZ00064 472 KFIDNVVRSTGIR---REDVIRILEENGIMRNI 501 (552)
T ss_pred ccHHHHHHHhCCC---HHHHHHHHHHCCcEEEe
Confidence 8999999999995 68999999999999743
No 250
>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=20.86 E-value=66 Score=35.03 Aligned_cols=33 Identities=6% Similarity=0.278 Sum_probs=0.0
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 151 EVDADASILQADIDNLSMEELRVDEQTRELRER 183 (403)
Q Consensus 151 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~ 183 (403)
++.++++.|++||++|+++-..|++.|...+++
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 251
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=20.84 E-value=1.7e+02 Score=31.96 Aligned_cols=59 Identities=25% Similarity=0.315 Sum_probs=39.0
Q ss_pred ehhhhHHHhhhccchhhc-cCCeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 117 RIYDITNVLEGIGLIEKK-LKNRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 117 RIYDItNVLEgIGLIeK~-sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
++-++.|-|+++-=+.|. .||.-.|+| +|++..+.+...-...|+.|.++++||++|+-
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 455666666666544433 455555554 34444455666667889999999999999864
No 252
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=20.82 E-value=1.8e+02 Score=28.63 Aligned_cols=31 Identities=19% Similarity=0.262 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 159 LQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 159 Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
|+..|+.|..+-.+|-.+|+..+-+|+.+.+
T Consensus 59 l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~ 89 (263)
T PRK10803 59 LQQQLSDNQSDIDSLRGQIQENQYQLNQVVE 89 (263)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 3444444444444444445544444444443
No 253
>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=20.61 E-value=2e+02 Score=27.68 Aligned_cols=34 Identities=21% Similarity=0.319 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 015627 155 DASILQADIDNLSMEELRVDEQTRELRERLRELI 188 (403)
Q Consensus 155 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lt 188 (403)
++..|++|++.|+..-+.|..++...+++|..|.
T Consensus 57 e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~ 90 (251)
T PF11932_consen 57 EYRQLEREIENLEVYNEQLERQVASQEQELASLE 90 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555555555544444444443
No 254
>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=20.51 E-value=3.8e+02 Score=20.52 Aligned_cols=33 Identities=15% Similarity=0.357 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 015627 156 ASILQADIDNLSMEELRVDEQTRELRERLRELI 188 (403)
Q Consensus 156 ~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lt 188 (403)
+..|+.++..|..+-..|-..+..+.+.+..|.
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 556667777777777777777777766666654
No 255
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=20.42 E-value=95 Score=22.28 Aligned_cols=38 Identities=18% Similarity=0.170 Sum_probs=25.7
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHH
Q 015627 86 LTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITN 123 (403)
Q Consensus 86 LTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 123 (403)
+|++|...+-..-.....+..+|..+||.--.+..|++
T Consensus 12 ~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 12 ITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 56677666543333338999999999997666665554
No 256
>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=20.34 E-value=1.9e+02 Score=22.25 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=24.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015627 152 VDADASILQADIDNLSMEELRVDEQTREL 180 (403)
Q Consensus 152 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~ 180 (403)
...++..|+.+++.|..+-+.|.+.|..+
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 45567888888888888888888888888
No 257
>TIGR00634 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
Probab=20.25 E-value=1.5e+02 Score=32.15 Aligned_cols=83 Identities=24% Similarity=0.320 Sum_probs=45.2
Q ss_pred CcCcHHHHHHHHHHHHhhCCCCcccHHHHHHHhccceeehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHHHH
Q 015627 79 YDSSLGLLTKKFINLIKHAEDGILDLNKAAETLEVQKRRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADASI 158 (403)
Q Consensus 79 ~dkSLglLTkKFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~~~ 158 (403)
++..|..+..++-..+-.-.+-.-+|...++.|...--|+.+|-+=|..+.=..|+ .|.+ ..++......
T Consensus 264 ~d~~~~~~~~~l~~~~~~l~d~~~~l~~~~~~l~~dp~~L~ele~RL~~l~~LkrK-------yg~s---~e~l~~~~~~ 333 (563)
T TIGR00634 264 IDGSLRELAEQVGNALTEVEEATRELQNYLDELEFDPERLNEIEERLAQIKRLKRK-------YGAS---VEEVLEYAEK 333 (563)
T ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH-------hCCC---HHHHHHHHHH
Confidence 34455555555544444444555556666666666666677766666655544444 1322 1234455666
Q ss_pred HHHHHHHHHHHHH
Q 015627 159 LQADIDNLSMEEL 171 (403)
Q Consensus 159 Lk~El~~L~~~E~ 171 (403)
+++|++.|...+.
T Consensus 334 l~~eL~~l~~~~~ 346 (563)
T TIGR00634 334 IKEELDQLDDSDE 346 (563)
T ss_pred HHHHHHHHhCCHH
Confidence 6767666554433
No 258
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=20.10 E-value=68 Score=23.78 Aligned_cols=27 Identities=26% Similarity=0.348 Sum_probs=22.5
Q ss_pred ccHHHHHHHhccceeehhhhHHHhhhc
Q 015627 102 LDLNKAAETLEVQKRRIYDITNVLEGI 128 (403)
Q Consensus 102 ldLn~aA~~L~VqKRRIYDItNVLEgI 128 (403)
+.|.++|+.+++..+.|+.+.+-.-|+
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~ 28 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGT 28 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCc
Confidence 678999999999999999988755433
No 259
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=20.09 E-value=2.7e+02 Score=25.09 Aligned_cols=80 Identities=18% Similarity=0.184 Sum_probs=0.0
Q ss_pred cccHHHHHHHhccce--------------------eehhhhHHHhhhccchhhccCCeEEEeccCCCCCCCchHHHHH--
Q 015627 101 ILDLNKAAETLEVQK--------------------RRIYDITNVLEGIGLIEKKLKNRIRWKGLDNSIPGEVDADASI-- 158 (403)
Q Consensus 101 ~ldLn~aA~~L~VqK--------------------RRIYDItNVLEgIGLIeK~sKN~i~W~G~~~s~~~~~~~~~~~-- 158 (403)
.+.+.++|+.+||.. +|.|+ -..++-|.+|.....- |+... ++..-+..
T Consensus 1 ~~~IgevA~~~Gvs~~tLRyYE~~GLl~~~r~~~g~R~Y~-~~di~~l~~I~~lr~~-----G~sL~---eI~~~l~~~~ 71 (142)
T TIGR01950 1 ELTVGELAKRSGVAVSALHFYESKGLITSIRNSGNQRRYK-RDVLRRVAVIKAAQRV-----GIPLA---TIGEALAVLP 71 (142)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHCCCCCCccCCCCCEEEC-HHHHHHHHHHHHHHHc-----CCCHH---HHHHHHHhcc
Q ss_pred ------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 015627 159 ------LQADIDNLSMEELRVDEQTRELRERLRELIE 189 (403)
Q Consensus 159 ------Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lte 189 (403)
...-.+-|..+...|++.|.+++.....|..
T Consensus 72 ~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~ 108 (142)
T TIGR01950 72 EGRTPTADDWARLSSQWREELDERIDQLNALRDQLDG 108 (142)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 260
>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=20.04 E-value=1.9e+02 Score=24.15 Aligned_cols=51 Identities=14% Similarity=0.240 Sum_probs=25.7
Q ss_pred CeEEEeccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 015627 137 NRIRWKGLDNSIPGEVDADASILQADIDNLSMEELRVDEQTRELRERLREL 187 (403)
Q Consensus 137 N~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L~~L 187 (403)
.-+.|.|.+..--....+-+.-++..++.|+.+-+.|.+.+..++.++..+
T Consensus 60 ~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~ 110 (120)
T PF02996_consen 60 KVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQL 110 (120)
T ss_dssp EEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred EEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356677755321111233344555555555555555555555555555544
No 261
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=20.00 E-value=2.8e+02 Score=27.96 Aligned_cols=67 Identities=25% Similarity=0.360 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc-cccccccCHHHHhhc-------cCCCCceEEEEeCCCCCeEEecC
Q 015627 159 LQADIDNLSMEELRVDEQTRELRERLRELIENEN-NRKWLFVTEEDIKNL-------HCFQNQTLIAIKAPQGTTLEVPD 230 (403)
Q Consensus 159 Lk~El~~L~~~E~~LD~lI~~~~q~L~~Lted~~-n~~~aYVT~eDI~~l-------~~f~~qTvIAIKAP~gT~LEVPd 230 (403)
|+.+++.|..+-..+...+..+..+|.++....+ ++. .|..+|..| ..+.+=.++.+. |+.|++--
T Consensus 235 l~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r~---~t~~Ev~~Lk~~~~~Le~~~gw~~~~~~---~~~l~~~~ 308 (325)
T PF08317_consen 235 LQEELEELEEKIEELEEQKQELLAEIAEAEKIREECRG---WTRSEVKRLKAKVDALEKLTGWKIVSIS---GSTLEFRY 308 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCHHHHHHHHHHHHHHHHHHCcEEEEEe---CCeEEEEE
Confidence 3344444444444555555555555555543322 222 377777664 223344444444 66676654
Q ss_pred C
Q 015627 231 P 231 (403)
Q Consensus 231 P 231 (403)
.
T Consensus 309 ~ 309 (325)
T PF08317_consen 309 K 309 (325)
T ss_pred c
Confidence 3
Done!