Query 047665
Match_columns 530
No_of_seqs 189 out of 1126
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 13:25:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047665.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047665hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1598 Transcription initiati 100.0 2.3E-65 5.1E-70 541.6 17.7 492 1-528 1-505 (521)
2 PRK00423 tfb transcription ini 100.0 1E-49 2.2E-54 410.5 29.0 251 1-261 12-306 (310)
3 COG1405 SUA7 Transcription ini 100.0 2.6E-48 5.7E-53 393.6 26.6 250 1-260 2-280 (285)
4 KOG1597 Transcription initiati 100.0 1.8E-47 3.8E-52 379.9 26.1 266 1-278 1-306 (308)
5 PF00382 TFIIB: Transcription 99.6 2E-15 4.3E-20 123.2 9.5 71 74-144 1-71 (71)
6 PF00382 TFIIB: Transcription 99.4 5.2E-13 1.1E-17 108.9 9.1 71 168-248 1-71 (71)
7 PRK00423 tfb transcription ini 99.3 1.7E-11 3.7E-16 127.0 11.9 91 70-160 219-309 (310)
8 KOG0835 Cyclin L [General func 99.2 1.9E-09 4.1E-14 110.1 18.8 184 60-251 16-221 (367)
9 TIGR00569 ccl1 cyclin ccl1. Un 99.2 1.9E-09 4.2E-14 111.4 18.9 174 64-243 52-234 (305)
10 KOG0834 CDK9 kinase-activating 98.9 2E-08 4.4E-13 104.2 14.6 189 65-259 37-245 (323)
11 COG1405 SUA7 Transcription ini 98.9 5.7E-09 1.2E-13 106.9 9.8 91 70-160 194-284 (285)
12 PF08271 TF_Zn_Ribbon: TFIIB z 98.8 3E-09 6.6E-14 78.8 3.1 36 1-36 1-36 (43)
13 cd00043 CYCLIN Cyclin box fold 98.8 9.2E-08 2E-12 78.0 10.7 83 69-151 4-87 (88)
14 COG5333 CCL1 Cdk activating ki 98.7 1.6E-07 3.5E-12 95.8 12.8 158 68-233 46-211 (297)
15 KOG1597 Transcription initiati 98.7 9.5E-08 2.1E-12 96.7 9.8 88 70-157 203-290 (308)
16 smart00385 CYCLIN domain prese 98.6 1.7E-07 3.7E-12 75.7 8.7 79 73-152 2-82 (83)
17 cd00043 CYCLIN Cyclin box fold 98.5 1.4E-06 3.1E-11 70.9 10.2 84 162-255 3-87 (88)
18 smart00385 CYCLIN domain prese 98.4 1.9E-06 4.1E-11 69.5 8.9 81 166-256 1-82 (83)
19 KOG1598 Transcription initiati 98.4 4.6E-07 1E-11 98.2 5.8 139 87-229 186-332 (521)
20 KOG0794 CDK8 kinase-activating 98.3 1.1E-05 2.4E-10 79.5 13.4 178 70-257 44-236 (264)
21 KOG0656 G1/S-specific cyclin D 98.1 0.00013 2.8E-09 76.3 17.2 179 68-253 79-268 (335)
22 PF00134 Cyclin_N: Cyclin, N-t 97.4 0.0022 4.7E-08 56.8 11.4 92 67-158 31-125 (127)
23 PF01857 RB_B: Retinoblastoma- 97.3 0.0012 2.7E-08 60.9 8.8 81 69-149 13-95 (135)
24 KOG2496 Cdk activating kinase 97.3 0.0053 1.1E-07 63.1 13.9 139 82-225 73-219 (325)
25 KOG4557 Origin recognition com 97.2 0.023 5.1E-07 55.8 17.1 205 73-295 2-220 (262)
26 KOG0653 Cyclin B and related k 96.8 0.015 3.3E-07 62.6 12.4 151 71-231 162-316 (391)
27 PF02984 Cyclin_C: Cyclin, C-t 96.5 0.02 4.4E-07 49.6 9.6 91 163-263 2-93 (118)
28 COG5024 Cyclin [Cell division 96.4 0.022 4.8E-07 62.0 10.9 147 72-229 218-368 (440)
29 PF11781 RRN7: RNA polymerase 96.4 0.0025 5.4E-08 45.7 2.4 28 1-30 9-36 (36)
30 PHA00626 hypothetical protein 95.9 0.0062 1.3E-07 47.6 2.7 35 1-35 1-39 (59)
31 PF09862 DUF2089: Protein of u 95.1 0.34 7.3E-06 43.6 11.0 49 129-177 51-100 (113)
32 COG2051 RPS27A Ribosomal prote 94.6 0.022 4.7E-07 46.1 2.1 31 2-32 21-51 (67)
33 PF01667 Ribosomal_S27e: Ribos 94.2 0.022 4.8E-07 44.7 1.2 30 2-31 9-38 (55)
34 KOG0835 Cyclin L [General func 94.1 0.3 6.4E-06 51.1 9.6 101 72-175 143-246 (367)
35 PRK00415 rps27e 30S ribosomal 94.1 0.032 6.9E-07 44.3 2.0 30 2-31 13-42 (59)
36 KOG0655 G1/S-specific cyclin E 94.0 5.3 0.00011 42.2 18.3 187 70-268 148-344 (408)
37 TIGR01206 lysW lysine biosynth 93.7 0.044 9.6E-07 42.8 2.1 29 2-30 4-33 (54)
38 PRK00420 hypothetical protein; 93.5 0.056 1.2E-06 48.4 2.7 28 2-31 25-52 (112)
39 PF13248 zf-ribbon_3: zinc-rib 93.1 0.045 9.7E-07 36.3 1.1 22 1-27 3-24 (26)
40 PRK00464 nrdR transcriptional 93.0 0.069 1.5E-06 50.5 2.7 29 1-29 1-38 (154)
41 PF02984 Cyclin_C: Cyclin, C-t 93.0 0.56 1.2E-05 40.5 8.3 86 70-156 3-90 (118)
42 PLN00209 ribosomal protein S27 92.7 0.082 1.8E-06 44.9 2.4 30 2-31 38-67 (86)
43 COG1645 Uncharacterized Zn-fin 92.6 0.083 1.8E-06 48.4 2.5 22 2-26 30-51 (131)
44 PTZ00083 40S ribosomal protein 92.6 0.091 2E-06 44.6 2.5 30 2-31 37-66 (85)
45 PF08792 A2L_zn_ribbon: A2L zi 92.5 0.12 2.6E-06 36.4 2.7 28 2-30 5-32 (33)
46 TIGR02393 RpoD_Cterm RNA polym 91.9 14 0.00031 36.7 17.7 34 230-263 195-228 (238)
47 PF14803 Nudix_N_2: Nudix N-te 91.2 0.084 1.8E-06 37.4 0.7 27 2-29 2-32 (34)
48 PF08274 PhnA_Zn_Ribbon: PhnA 91.2 0.2 4.3E-06 34.6 2.4 26 2-29 4-29 (30)
49 PF13240 zinc_ribbon_2: zinc-r 91.0 0.12 2.5E-06 33.5 1.1 22 2-28 1-22 (23)
50 smart00778 Prim_Zn_Ribbon Zinc 90.9 0.19 4.1E-06 36.3 2.3 27 1-27 4-33 (37)
51 PF02150 RNA_POL_M_15KD: RNA p 90.9 0.21 4.6E-06 35.5 2.5 31 2-32 3-33 (35)
52 PRK00432 30S ribosomal protein 90.2 0.22 4.7E-06 38.4 2.2 26 2-29 22-47 (50)
53 COG1997 RPL43A Ribosomal prote 90.1 0.31 6.7E-06 41.7 3.2 34 2-36 37-70 (89)
54 TIGR02098 MJ0042_CXXC MJ0042 f 89.9 0.16 3.6E-06 36.2 1.3 29 2-30 4-36 (38)
55 PRK11827 hypothetical protein; 89.5 0.29 6.3E-06 39.1 2.5 28 2-30 10-37 (60)
56 TIGR00244 transcriptional regu 89.3 0.33 7.2E-06 45.4 3.1 28 1-28 1-37 (147)
57 PF13404 HTH_AsnC-type: AsnC-t 89.3 0.86 1.9E-05 33.6 4.7 29 228-256 14-42 (42)
58 smart00661 RPOL9 RNA polymeras 88.8 0.32 7E-06 36.8 2.3 30 2-31 2-32 (52)
59 PF03966 Trm112p: Trm112p-like 88.7 0.43 9.2E-06 38.7 3.1 18 13-30 47-64 (68)
60 PF14354 Lar_restr_allev: Rest 88.6 0.41 9E-06 37.6 2.8 26 2-27 5-37 (61)
61 smart00342 HTH_ARAC helix_turn 88.5 1.4 3.1E-05 35.1 6.0 71 74-151 4-75 (84)
62 PRK07408 RNA polymerase sigma 88.2 23 0.00049 35.8 15.9 35 230-264 218-252 (256)
63 TIGR00569 ccl1 cyclin ccl1. Un 87.8 3.3 7.2E-05 43.4 9.7 69 166-244 61-131 (305)
64 PRK00398 rpoP DNA-directed RNA 87.5 0.44 9.5E-06 35.6 2.2 28 2-30 5-32 (46)
65 PF00134 Cyclin_N: Cyclin, N-t 87.4 4.4 9.5E-05 35.5 9.0 68 165-242 35-103 (127)
66 PF01780 Ribosomal_L37ae: Ribo 87.3 1.4 3E-05 38.1 5.4 35 2-37 37-71 (90)
67 PF06677 Auto_anti-p27: Sjogre 87.3 0.54 1.2E-05 34.8 2.5 23 2-26 19-41 (41)
68 PF09538 FYDLN_acid: Protein o 86.1 0.39 8.4E-06 42.8 1.5 29 2-32 11-39 (108)
69 COG4888 Uncharacterized Zn rib 86.1 0.5 1.1E-05 41.4 2.1 29 2-30 24-57 (104)
70 PRK05657 RNA polymerase sigma 86.0 49 0.0011 34.8 18.2 36 230-265 281-316 (325)
71 TIGR02394 rpoS_proteo RNA poly 85.7 41 0.00088 34.4 16.3 39 230-268 241-279 (285)
72 COG2835 Uncharacterized conser 84.7 0.82 1.8E-05 36.5 2.5 28 2-30 10-37 (60)
73 PF09297 zf-NADH-PPase: NADH p 83.9 1.1 2.4E-05 30.9 2.7 27 2-29 5-31 (32)
74 PF08613 Cyclin: Cyclin; Inte 83.9 15 0.00033 34.1 11.1 89 70-158 54-148 (149)
75 KOG1010 Rb (Retinoblastoma tum 83.9 2.3 4.9E-05 49.6 6.6 87 65-151 674-763 (920)
76 PF13412 HTH_24: Winged helix- 83.6 2.7 5.8E-05 31.2 4.9 29 229-257 15-43 (48)
77 PTZ00255 60S ribosomal protein 83.3 1.2 2.7E-05 38.4 3.3 35 2-37 38-72 (90)
78 PF10571 UPF0547: Uncharacteri 83.2 0.63 1.4E-05 31.0 1.1 23 2-29 2-24 (26)
79 TIGR03655 anti_R_Lar restricti 83.1 1.1 2.3E-05 34.7 2.6 31 1-31 2-38 (53)
80 PF07282 OrfB_Zn_ribbon: Putat 82.8 0.93 2E-05 36.4 2.2 28 2-30 30-57 (69)
81 COG2888 Predicted Zn-ribbon RN 82.6 0.73 1.6E-05 36.7 1.5 25 2-27 11-35 (61)
82 PF13730 HTH_36: Helix-turn-he 82.3 3.3 7.2E-05 31.4 5.1 26 232-257 26-51 (55)
83 TIGR00686 phnA alkylphosphonat 81.9 1.1 2.3E-05 39.9 2.4 29 2-32 4-32 (109)
84 PF04545 Sigma70_r4: Sigma-70, 81.9 4 8.6E-05 30.6 5.3 31 229-259 18-48 (50)
85 PF01325 Fe_dep_repress: Iron 81.7 3.7 8E-05 32.6 5.2 37 220-257 12-48 (60)
86 PF08273 Prim_Zn_Ribbon: Zinc- 81.7 1.2 2.6E-05 32.8 2.2 27 2-28 5-35 (40)
87 PF04967 HTH_10: HTH DNA bindi 81.5 4.9 0.00011 31.3 5.7 30 231-260 23-52 (53)
88 PRK11169 leucine-responsive tr 81.5 2.4 5.2E-05 40.0 4.8 31 228-258 25-55 (164)
89 TIGR02300 FYDLN_acid conserved 81.3 0.85 1.8E-05 41.7 1.6 29 2-32 11-39 (129)
90 KOG1779 40s ribosomal protein 81.1 0.93 2E-05 38.0 1.6 29 2-30 36-64 (84)
91 KOG0834 CDK9 kinase-activating 80.7 4.2 9.2E-05 42.9 6.8 87 165-261 43-133 (323)
92 PF08613 Cyclin: Cyclin; Inte 80.7 18 0.0004 33.5 10.4 81 158-248 48-134 (149)
93 TIGR00280 L37a ribosomal prote 80.6 1.7 3.6E-05 37.6 3.1 35 2-37 37-71 (91)
94 KOG4557 Origin recognition com 80.5 4.6 0.0001 40.2 6.5 83 73-156 95-182 (262)
95 COG1998 RPS31 Ribosomal protei 80.5 0.99 2.1E-05 34.7 1.5 26 2-28 21-46 (51)
96 PRK00135 scpB segregation and 80.4 32 0.0007 33.6 12.3 44 109-156 5-49 (188)
97 PF12760 Zn_Tnp_IS1595: Transp 80.2 1.9 4.1E-05 32.2 3.0 26 2-27 20-45 (46)
98 smart00440 ZnF_C2C2 C2C2 Zinc 79.9 1.4 3.1E-05 32.2 2.1 27 2-28 2-37 (40)
99 PRK07598 RNA polymerase sigma 79.8 1E+02 0.0022 33.9 20.0 172 71-259 185-398 (415)
100 PRK11179 DNA-binding transcrip 79.7 3.2 7E-05 38.6 5.0 31 228-258 20-50 (153)
101 PF04161 Arv1: Arv1-like famil 79.4 0.85 1.8E-05 45.0 1.1 30 1-30 1-35 (208)
102 PRK10220 hypothetical protein; 79.2 1.4 3.1E-05 39.2 2.3 28 2-31 5-32 (111)
103 PRK03976 rpl37ae 50S ribosomal 78.9 2 4.3E-05 37.1 3.0 35 2-37 38-72 (90)
104 PRK05911 RNA polymerase sigma 78.8 77 0.0017 32.0 20.2 35 230-264 220-254 (257)
105 PRK14892 putative transcriptio 78.6 1.4 3.1E-05 38.7 2.1 29 2-30 23-53 (99)
106 PF08279 HTH_11: HTH domain; 78.4 5 0.00011 30.4 4.9 31 229-259 13-43 (55)
107 TIGR01384 TFS_arch transcripti 78.0 1.4 3E-05 38.4 1.9 28 1-31 1-28 (104)
108 PRK12495 hypothetical protein; 78.0 2 4.3E-05 42.8 3.1 28 2-32 44-71 (226)
109 smart00421 HTH_LUXR helix_turn 77.7 4.1 8.8E-05 30.1 4.2 29 231-259 18-46 (58)
110 PF00325 Crp: Bacterial regula 77.5 2.9 6.3E-05 29.3 3.0 28 126-153 1-28 (32)
111 PF09862 DUF2089: Protein of u 77.1 3 6.5E-05 37.5 3.7 31 231-261 49-79 (113)
112 PF13719 zinc_ribbon_5: zinc-r 76.9 1.4 3.1E-05 31.6 1.4 29 2-30 4-36 (37)
113 PRK07405 RNA polymerase sigma 76.9 1E+02 0.0022 32.3 18.3 32 230-261 275-306 (317)
114 PF09986 DUF2225: Uncharacteri 76.8 6.7 0.00015 38.9 6.6 48 73-120 77-125 (214)
115 COG1327 Predicted transcriptio 76.1 1.9 4.1E-05 40.6 2.2 28 1-28 1-37 (156)
116 TIGR02010 IscR iron-sulfur clu 75.9 5.6 0.00012 36.2 5.4 47 108-154 6-52 (135)
117 COG1326 Uncharacterized archae 75.8 0.82 1.8E-05 44.6 -0.2 29 1-30 7-41 (201)
118 PRK05901 RNA polymerase sigma 75.6 1.5E+02 0.0032 33.5 18.0 32 230-261 466-497 (509)
119 PF05460 ORC6: Origin recognit 75.0 0.95 2.1E-05 48.3 0.0 84 76-159 3-89 (353)
120 PF02082 Rrf2: Transcriptional 74.7 5.2 0.00011 33.3 4.4 46 109-154 7-52 (83)
121 COG1522 Lrp Transcriptional re 74.6 5 0.00011 36.7 4.7 30 229-258 20-49 (154)
122 PRK12286 rpmF 50S ribosomal pr 73.8 2.1 4.5E-05 33.9 1.7 20 2-27 29-48 (57)
123 PF13613 HTH_Tnp_4: Helix-turn 73.7 7.4 0.00016 29.8 4.7 36 229-264 17-52 (53)
124 PRK14890 putative Zn-ribbon RN 73.7 2.4 5.2E-05 33.8 2.0 25 2-28 9-34 (59)
125 PRK09678 DNA-binding transcrip 73.3 3.2 7E-05 34.4 2.7 30 1-30 2-40 (72)
126 PRK09210 RNA polymerase sigma 73.1 1.4E+02 0.003 32.0 18.4 32 230-261 324-355 (367)
127 PRK05949 RNA polymerase sigma 72.6 1.3E+02 0.0029 31.7 19.4 32 230-261 285-316 (327)
128 PF00356 LacI: Bacterial regul 72.6 4.2 9.2E-05 30.6 3.0 21 233-253 1-21 (46)
129 PF13936 HTH_38: Helix-turn-he 72.4 6 0.00013 29.2 3.8 28 226-253 15-42 (44)
130 PRK06288 RNA polymerase sigma 72.3 1.1E+02 0.0025 30.8 17.5 33 230-262 227-259 (268)
131 PF13384 HTH_23: Homeodomain-l 71.9 6 0.00013 29.3 3.8 27 231-257 17-43 (50)
132 PF13545 HTH_Crp_2: Crp-like h 71.7 9 0.0002 30.7 5.1 28 230-257 27-54 (76)
133 PF08220 HTH_DeoR: DeoR-like h 71.4 5 0.00011 31.3 3.3 28 230-257 13-40 (57)
134 cd06170 LuxR_C_like C-terminal 71.3 7.2 0.00016 28.9 4.1 29 231-259 15-43 (57)
135 PF10668 Phage_terminase: Phag 71.2 9.1 0.0002 30.7 4.7 38 211-251 5-42 (60)
136 smart00419 HTH_CRP helix_turn_ 70.9 6.6 0.00014 28.4 3.7 28 230-257 7-34 (48)
137 PRK08215 sporulation sigma fac 70.7 1.2E+02 0.0026 30.4 18.3 33 230-262 224-256 (258)
138 TIGR01610 phage_O_Nterm phage 70.7 26 0.00057 30.1 8.0 29 229-257 45-73 (95)
139 PF00440 TetR_N: Bacterial reg 70.6 10 0.00023 28.0 4.8 42 218-259 3-44 (47)
140 PF08281 Sigma70_r4_2: Sigma-7 70.5 7.1 0.00015 29.5 3.9 29 230-258 25-53 (54)
141 smart00659 RPOLCX RNA polymera 70.2 3.6 7.8E-05 30.8 2.1 27 2-30 4-30 (44)
142 PRK05978 hypothetical protein; 70.2 2.4 5.2E-05 39.9 1.5 30 1-30 34-63 (148)
143 cd00092 HTH_CRP helix_turn_hel 70.1 15 0.00032 28.5 5.8 29 230-258 24-52 (67)
144 PRK04217 hypothetical protein; 69.9 8.9 0.00019 34.3 5.0 36 230-265 57-92 (110)
145 PF13542 HTH_Tnp_ISL3: Helix-t 69.8 9.3 0.0002 28.6 4.4 23 232-254 28-50 (52)
146 PRK09710 lar restriction allev 69.8 4.4 9.6E-05 32.8 2.7 31 2-32 8-40 (64)
147 TIGR01031 rpmF_bact ribosomal 69.7 3 6.5E-05 32.7 1.7 20 2-27 28-47 (55)
148 PF12802 MarR_2: MarR family; 69.1 12 0.00025 28.7 5.0 28 230-257 20-47 (62)
149 PF02796 HTH_7: Helix-turn-hel 68.9 3.4 7.4E-05 30.6 1.8 28 225-252 15-42 (45)
150 PF09855 DUF2082: Nucleic-acid 68.7 3.5 7.7E-05 33.4 2.0 27 2-28 2-45 (64)
151 PF05129 Elf1: Transcription e 68.6 3.6 7.7E-05 34.8 2.1 31 2-32 24-59 (81)
152 PF03604 DNA_RNApol_7kD: DNA d 68.5 2.7 5.8E-05 29.5 1.0 25 2-28 2-26 (32)
153 PF13545 HTH_Crp_2: Crp-like h 68.4 12 0.00027 29.9 5.2 29 126-154 27-55 (76)
154 smart00344 HTH_ASNC helix_turn 68.4 9.6 0.00021 32.8 4.8 29 230-258 16-44 (108)
155 PF14353 CpXC: CpXC protein 68.4 3.5 7.6E-05 37.2 2.1 12 19-30 38-49 (128)
156 PF00196 GerE: Bacterial regul 68.4 6.9 0.00015 30.2 3.5 30 231-260 18-47 (58)
157 PRK10857 DNA-binding transcrip 68.2 10 0.00023 36.0 5.4 47 108-154 6-52 (164)
158 smart00345 HTH_GNTR helix_turn 67.8 9.4 0.0002 28.6 4.2 27 231-257 19-46 (60)
159 PRK07670 RNA polymerase sigma 67.7 1.4E+02 0.003 29.9 19.8 34 230-263 216-249 (251)
160 PF00325 Crp: Bacterial regula 67.5 7.1 0.00015 27.4 3.0 27 231-257 2-28 (32)
161 PRK00118 putative DNA-binding 67.2 7.9 0.00017 34.3 4.1 37 230-266 32-68 (104)
162 TIGR03697 NtcA_cyano global ni 67.0 25 0.00055 32.9 7.8 29 230-258 142-170 (193)
163 TIGR02997 Sig70-cyanoRpoD RNA 66.9 1.6E+02 0.0035 30.4 18.3 28 230-257 268-295 (298)
164 smart00342 HTH_ARAC helix_turn 66.9 36 0.00077 26.7 7.7 26 231-256 50-76 (84)
165 COG4640 Predicted membrane pro 66.7 2.9 6.2E-05 45.0 1.4 26 2-32 3-28 (465)
166 PF05876 Terminase_GpA: Phage 66.6 3.2 7E-05 46.9 1.9 32 1-32 201-242 (557)
167 PRK07500 rpoH2 RNA polymerase 66.6 1.6E+02 0.0035 30.3 17.9 35 230-264 244-278 (289)
168 COG1594 RPB9 DNA-directed RNA 66.4 4.3 9.3E-05 36.4 2.3 32 2-33 4-36 (113)
169 PF00392 GntR: Bacterial regul 66.4 16 0.00035 28.7 5.4 30 228-257 20-50 (64)
170 TIGR00122 birA_repr_reg BirA b 66.4 13 0.00028 29.7 4.8 30 229-258 11-40 (69)
171 cd06571 Bac_DnaA_C C-terminal 66.1 28 0.00062 29.5 7.2 42 115-158 34-76 (90)
172 PF01325 Fe_dep_repress: Iron 66.1 16 0.00034 29.0 5.2 36 117-153 13-48 (60)
173 TIGR03879 near_KaiC_dom probab 65.6 4.4 9.6E-05 33.7 2.0 28 230-257 31-58 (73)
174 PF03119 DNA_ligase_ZBD: NAD-d 64.4 5.3 0.00012 27.0 1.9 22 2-24 1-22 (28)
175 TIGR02395 rpoN_sigma RNA polym 64.4 1.6E+02 0.0035 32.3 14.4 78 73-156 115-210 (429)
176 PRK05932 RNA polymerase factor 64.1 1.3E+02 0.0028 33.4 13.6 77 73-156 140-236 (455)
177 PF08279 HTH_11: HTH domain; 64.1 13 0.00029 28.1 4.3 35 121-155 9-43 (55)
178 smart00834 CxxC_CXXC_SSSS Puta 63.8 4.4 9.5E-05 28.9 1.5 26 2-27 7-34 (41)
179 PF05191 ADK_lid: Adenylate ki 63.7 1.1 2.4E-05 32.1 -1.6 28 2-29 3-31 (36)
180 PF13613 HTH_Tnp_4: Helix-turn 63.3 15 0.00033 28.1 4.5 42 119-160 11-52 (53)
181 PF01857 RB_B: Retinoblastoma- 62.8 32 0.00069 31.8 7.3 67 168-242 18-84 (135)
182 PF08280 HTH_Mga: M protein tr 62.7 7.3 0.00016 30.5 2.7 32 230-261 18-49 (59)
183 TIGR02392 rpoH_proteo alternat 62.7 1.8E+02 0.0039 29.5 18.8 34 229-262 234-267 (270)
184 TIGR02479 FliA_WhiG RNA polyme 62.3 1.6E+02 0.0035 28.7 19.0 32 230-261 190-221 (224)
185 PF15616 TerY-C: TerY-C metal 62.0 4.9 0.00011 37.1 1.8 21 2-30 79-99 (131)
186 PF07754 DUF1610: Domain of un 61.9 5.8 0.00013 26.1 1.6 23 3-27 1-24 (24)
187 PRK11920 rirA iron-responsive 61.8 17 0.00037 34.1 5.5 45 109-154 7-51 (153)
188 PRK09642 RNA polymerase sigma 61.8 13 0.00028 34.0 4.7 36 230-265 121-156 (160)
189 cd00350 rubredoxin_like Rubred 61.4 5.6 0.00012 27.7 1.6 23 2-27 3-25 (33)
190 COG5349 Uncharacterized protei 61.4 3 6.5E-05 37.9 0.3 31 2-32 23-53 (126)
191 cd06171 Sigma70_r4 Sigma70, re 61.3 19 0.00042 25.7 4.7 29 230-258 25-53 (55)
192 TIGR02443 conserved hypothetic 61.3 7.3 0.00016 31.1 2.4 29 2-30 11-42 (59)
193 TIGR00738 rrf2_super rrf2 fami 60.9 18 0.00039 32.3 5.3 45 109-153 7-51 (132)
194 PF01096 TFIIS_C: Transcriptio 60.8 6 0.00013 28.7 1.8 27 2-28 2-37 (39)
195 KOG4164 Cyclin ik3-1/CABLES [C 60.7 35 0.00075 37.1 8.0 56 70-125 385-440 (497)
196 PF11672 DUF3268: Protein of u 60.5 6.8 0.00015 34.7 2.3 29 2-30 4-42 (102)
197 cd00092 HTH_CRP helix_turn_hel 60.1 29 0.00062 26.8 5.7 31 124-154 22-52 (67)
198 PF02082 Rrf2: Transcriptional 60.1 11 0.00024 31.3 3.6 37 221-257 15-51 (83)
199 COG2824 PhnA Uncharacterized Z 60.0 6.3 0.00014 35.0 2.0 29 2-32 5-33 (112)
200 PF01022 HTH_5: Bacterial regu 59.7 19 0.00041 26.7 4.4 30 228-257 12-41 (47)
201 PF13717 zinc_ribbon_4: zinc-r 59.6 4.9 0.00011 28.7 1.1 28 2-29 4-35 (36)
202 PRK06266 transcription initiat 59.5 2.3 5.1E-05 41.1 -0.8 30 2-31 119-148 (178)
203 PRK12532 RNA polymerase sigma 58.8 15 0.00031 35.1 4.6 42 230-272 151-192 (195)
204 COG3478 Predicted nucleic-acid 58.6 5.3 0.00012 32.4 1.2 13 2-14 6-18 (68)
205 PF01978 TrmB: Sugar-specific 58.5 17 0.00038 28.8 4.3 38 219-257 11-48 (68)
206 PF06044 DRP: Dam-replacing fa 58.4 3.9 8.5E-05 41.4 0.6 30 1-30 32-64 (254)
207 PF12773 DZR: Double zinc ribb 58.3 4.7 0.0001 30.3 0.9 23 3-30 1-23 (50)
208 PRK08301 sporulation sigma fac 58.1 14 0.0003 36.4 4.4 36 230-265 197-232 (234)
209 PRK14088 dnaA chromosomal repl 58.1 1.3E+02 0.0027 33.1 12.2 51 207-259 362-415 (440)
210 TIGR02937 sigma70-ECF RNA poly 58.1 16 0.00035 31.9 4.5 31 231-261 126-156 (158)
211 COG0333 RpmF Ribosomal protein 57.9 5.5 0.00012 31.6 1.2 20 2-27 29-48 (57)
212 TIGR02605 CxxC_CxxC_SSSS putat 57.6 5.6 0.00012 30.1 1.2 26 2-27 7-34 (52)
213 TIGR02985 Sig70_bacteroi1 RNA 57.6 16 0.00035 32.8 4.5 32 230-261 128-159 (161)
214 PF12802 MarR_2: MarR family; 57.4 22 0.00047 27.2 4.6 38 116-153 10-47 (62)
215 TIGR02405 trehalos_R_Ecol treh 57.1 11 0.00024 38.2 3.6 38 231-268 1-45 (311)
216 PRK07122 RNA polymerase sigma 57.0 2.3E+02 0.0049 28.8 19.0 32 230-261 230-261 (264)
217 PF01783 Ribosomal_L32p: Ribos 56.8 2.7 5.8E-05 33.0 -0.7 21 2-28 28-48 (56)
218 PRK05658 RNA polymerase sigma 56.7 3.6E+02 0.0078 31.0 17.4 79 71-149 390-505 (619)
219 PF13453 zf-TFIIB: Transcripti 56.5 9.8 0.00021 27.7 2.3 27 2-29 1-29 (41)
220 smart00420 HTH_DEOR helix_turn 56.5 29 0.00063 25.1 5.0 28 231-258 14-41 (53)
221 PF05043 Mga: Mga helix-turn-h 56.4 17 0.00037 30.2 4.1 35 228-262 27-61 (87)
222 TIGR03697 NtcA_cyano global ni 56.2 39 0.00084 31.6 7.0 29 126-154 142-170 (193)
223 PF07900 DUF1670: Protein of u 56.2 76 0.0016 31.9 9.1 66 73-161 74-139 (220)
224 PF14446 Prok-RING_1: Prokaryo 55.9 7.8 0.00017 30.4 1.7 26 2-30 7-32 (54)
225 PRK14559 putative protein seri 55.6 6.4 0.00014 45.4 1.7 16 245-260 312-327 (645)
226 TIGR02366 DHAK_reg probable di 55.5 18 0.00039 33.6 4.5 50 215-264 7-56 (176)
227 PF09526 DUF2387: Probable met 55.5 10 0.00022 31.3 2.5 30 2-31 10-42 (71)
228 TIGR02999 Sig-70_X6 RNA polyme 55.4 18 0.00039 33.8 4.5 33 230-262 149-181 (183)
229 PRK12531 RNA polymerase sigma 55.2 17 0.00037 34.6 4.4 35 230-264 156-190 (194)
230 smart00418 HTH_ARSR helix_turn 55.1 27 0.00058 26.0 4.7 29 229-257 8-36 (66)
231 COG1779 C4-type Zn-finger prot 55.1 7.5 0.00016 38.2 1.9 30 1-30 15-54 (201)
232 PRK09652 RNA polymerase sigma 55.0 16 0.00035 33.6 4.1 35 230-264 143-177 (182)
233 PRK09643 RNA polymerase sigma 55.0 21 0.00046 34.1 5.0 38 230-267 149-186 (192)
234 PF01371 Trp_repressor: Trp re 54.9 29 0.00063 29.8 5.2 30 227-256 45-74 (87)
235 TIGR02944 suf_reg_Xantho FeS a 54.8 28 0.00061 31.2 5.5 44 109-153 8-51 (130)
236 cd00569 HTH_Hin_like Helix-tur 54.7 17 0.00037 23.2 3.2 21 231-251 21-41 (42)
237 TIGR02980 SigBFG RNA polymeras 54.7 2.1E+02 0.0046 27.8 17.7 32 230-261 193-224 (227)
238 KOG2496 Cdk activating kinase 54.4 52 0.0011 34.6 7.9 54 189-242 76-129 (325)
239 PRK08402 replication factor A; 54.4 8.8 0.00019 41.1 2.5 26 2-28 214-239 (355)
240 cd04762 HTH_MerR-trunc Helix-T 54.4 15 0.00032 26.2 3.0 23 232-254 1-23 (49)
241 PRK13413 mpi multiple promoter 54.0 49 0.0011 31.9 7.4 62 190-254 126-195 (200)
242 smart00419 HTH_CRP helix_turn_ 54.0 19 0.00042 25.8 3.6 29 125-153 6-34 (48)
243 PF00165 HTH_AraC: Bacterial r 53.7 16 0.00036 26.2 3.1 27 125-151 6-32 (42)
244 PF07638 Sigma70_ECF: ECF sigm 53.5 20 0.00044 34.2 4.6 31 231-261 151-181 (185)
245 PRK09047 RNA polymerase factor 53.5 20 0.00043 32.6 4.4 35 230-264 121-155 (161)
246 TIGR02983 SigE-fam_strep RNA p 53.4 21 0.00046 32.6 4.6 34 231-264 126-159 (162)
247 KOG1010 Rb (Retinoblastoma tum 53.2 67 0.0014 38.1 9.2 62 71-133 35-96 (920)
248 PRK12543 RNA polymerase sigma 53.2 14 0.00031 34.7 3.4 36 230-265 132-167 (179)
249 PF13022 HTH_Tnp_1_2: Helix-tu 52.9 39 0.00085 31.6 6.1 70 213-292 13-88 (142)
250 PRK11161 fumarate/nitrate redu 52.8 55 0.0012 31.9 7.6 28 230-257 183-210 (235)
251 TIGR02948 SigW_bacill RNA poly 52.6 22 0.00048 33.2 4.6 35 230-264 151-185 (187)
252 TIGR02835 spore_sigmaE RNA pol 52.6 21 0.00046 35.3 4.8 36 230-265 197-232 (234)
253 PRK11014 transcriptional repre 52.5 20 0.00044 32.8 4.2 39 219-257 13-51 (141)
254 PF09339 HTH_IclR: IclR helix- 52.5 23 0.00051 26.7 3.9 37 117-153 8-44 (52)
255 PF05225 HTH_psq: helix-turn-h 52.4 37 0.0008 25.3 4.8 27 228-255 14-40 (45)
256 PF04810 zf-Sec23_Sec24: Sec23 52.3 15 0.00033 26.7 2.7 30 1-30 3-35 (40)
257 TIGR01610 phage_O_Nterm phage 52.3 70 0.0015 27.4 7.3 30 124-153 44-73 (95)
258 TIGR02950 SigM_subfam RNA poly 52.1 23 0.00049 32.0 4.5 33 230-262 120-152 (154)
259 TIGR02947 SigH_actino RNA poly 52.0 20 0.00044 34.0 4.3 35 230-264 146-180 (193)
260 PHA02591 hypothetical protein; 52.0 23 0.00049 30.0 3.9 30 224-253 52-81 (83)
261 PRK09645 RNA polymerase sigma 51.9 24 0.00052 32.7 4.7 36 230-265 133-168 (173)
262 PRK12518 RNA polymerase sigma 51.8 22 0.00048 32.9 4.5 36 230-265 135-170 (175)
263 PF09723 Zn-ribbon_8: Zinc rib 51.7 8 0.00017 28.4 1.1 26 2-27 7-34 (42)
264 PRK00241 nudC NADH pyrophospha 51.7 9.8 0.00021 38.8 2.2 29 2-31 101-129 (256)
265 PF05732 RepL: Firmicute plasm 51.6 43 0.00094 32.0 6.4 28 231-258 75-102 (165)
266 COG1309 AcrR Transcriptional r 51.5 20 0.00043 31.7 4.0 47 216-263 17-64 (201)
267 PRK12522 RNA polymerase sigma 51.4 20 0.00043 33.4 4.1 35 230-264 134-168 (173)
268 COG3809 Uncharacterized protei 51.3 12 0.00027 31.5 2.3 31 1-32 2-34 (88)
269 PRK09415 RNA polymerase factor 51.3 23 0.00049 33.3 4.5 35 230-264 142-176 (179)
270 PF13412 HTH_24: Winged helix- 51.3 41 0.00089 24.7 5.0 29 125-153 15-43 (48)
271 cd04761 HTH_MerR-SF Helix-Turn 51.1 16 0.00036 26.5 2.8 21 232-252 1-21 (49)
272 PRK13918 CRP/FNR family transc 51.0 63 0.0014 30.5 7.6 28 230-257 148-175 (202)
273 PF00356 LacI: Bacterial regul 51.0 17 0.00036 27.4 2.8 20 129-148 1-20 (46)
274 PF04703 FaeA: FaeA-like prote 51.0 28 0.0006 28.0 4.2 36 122-157 10-45 (62)
275 PRK09644 RNA polymerase sigma 50.9 23 0.0005 32.7 4.4 36 230-265 123-158 (165)
276 PF13542 HTH_Tnp_ISL3: Helix-t 50.8 48 0.001 24.6 5.4 43 106-151 9-51 (52)
277 PF01726 LexA_DNA_bind: LexA D 50.8 34 0.00075 27.5 4.8 31 227-257 21-52 (65)
278 TIGR02944 suf_reg_Xantho FeS a 50.8 35 0.00075 30.6 5.4 37 220-257 15-51 (130)
279 TIGR02952 Sig70_famx2 RNA poly 50.7 24 0.00052 32.3 4.5 32 230-261 137-168 (170)
280 smart00550 Zalpha Z-DNA-bindin 50.7 37 0.0008 27.4 5.0 38 117-154 11-49 (68)
281 TIGR02954 Sig70_famx3 RNA poly 50.4 24 0.00053 32.6 4.5 33 231-263 135-167 (169)
282 PF02609 Exonuc_VII_S: Exonucl 50.3 13 0.00028 28.6 2.2 43 416-458 11-53 (53)
283 PRK09492 treR trehalose repres 50.3 15 0.00033 37.0 3.4 38 231-268 4-48 (315)
284 TIGR03830 CxxCG_CxxCG_HTH puta 50.3 13 0.00028 32.9 2.5 27 3-29 1-41 (127)
285 PRK09639 RNA polymerase sigma 50.2 23 0.00051 32.4 4.3 35 230-264 126-160 (166)
286 PF10122 Mu-like_Com: Mu-like 50.1 4.4 9.6E-05 31.4 -0.4 31 2-32 6-37 (51)
287 PRK12527 RNA polymerase sigma 50.0 25 0.00053 32.2 4.4 36 230-265 120-155 (159)
288 PRK13919 putative RNA polymera 50.0 25 0.00053 33.0 4.5 35 230-264 150-184 (186)
289 PRK12520 RNA polymerase sigma 49.9 22 0.00048 33.6 4.3 35 231-265 147-181 (191)
290 COG1508 RpoN DNA-directed RNA 49.9 4E+02 0.0086 29.7 14.1 91 60-155 105-223 (444)
291 cd07377 WHTH_GntR Winged helix 49.9 24 0.00053 26.9 3.8 25 233-257 27-51 (66)
292 TIGR02939 RpoE_Sigma70 RNA pol 49.6 25 0.00054 32.9 4.5 35 230-264 153-187 (190)
293 PF05269 Phage_CII: Bacterioph 49.6 12 0.00026 32.4 2.1 39 231-269 23-61 (91)
294 PRK12529 RNA polymerase sigma 49.5 26 0.00055 33.0 4.6 32 230-261 142-173 (178)
295 smart00346 HTH_ICLR helix_turn 49.5 47 0.001 27.3 5.7 28 230-257 19-46 (91)
296 PRK12525 RNA polymerase sigma 49.3 27 0.00058 32.4 4.6 33 230-262 133-165 (168)
297 PRK12542 RNA polymerase sigma 49.2 26 0.00056 33.0 4.5 35 230-264 137-171 (185)
298 PRK11923 algU RNA polymerase s 49.2 22 0.00048 33.6 4.1 35 230-264 153-187 (193)
299 PF05344 DUF746: Domain of Unk 49.1 41 0.00089 27.5 4.9 43 226-268 8-50 (65)
300 TIGR02943 Sig70_famx1 RNA poly 49.1 23 0.00051 33.7 4.2 36 230-265 146-181 (188)
301 PRK05602 RNA polymerase sigma 49.0 26 0.00057 33.0 4.6 36 230-265 143-178 (186)
302 PRK06759 RNA polymerase factor 48.9 24 0.00053 31.8 4.2 31 230-260 121-151 (154)
303 PRK09480 slmA division inhibit 48.9 27 0.00058 32.7 4.6 44 214-257 13-56 (194)
304 TIGR02885 spore_sigF RNA polym 48.8 2.7E+02 0.0058 27.2 18.7 31 230-260 198-228 (231)
305 PRK12513 RNA polymerase sigma 48.7 24 0.00052 33.5 4.3 35 230-264 154-188 (194)
306 COG1959 Predicted transcriptio 48.6 38 0.00082 31.7 5.4 46 109-154 7-52 (150)
307 PRK10434 srlR DNA-bindng trans 48.5 17 0.00037 36.8 3.4 29 230-258 18-46 (256)
308 TIGR01764 excise DNA binding d 48.4 21 0.00045 25.6 3.0 22 232-253 2-23 (49)
309 PF01047 MarR: MarR family; I 48.3 44 0.00096 25.3 5.0 27 231-257 17-43 (59)
310 PF14122 YokU: YokU-like prote 48.0 18 0.00039 31.0 2.8 31 2-32 1-48 (87)
311 COG5333 CCL1 Cdk activating ki 47.9 30 0.00064 36.2 5.0 89 166-264 50-142 (297)
312 PRK12547 RNA polymerase sigma 47.8 28 0.00061 32.1 4.5 34 230-263 127-160 (164)
313 TIGR02859 spore_sigH RNA polym 47.8 28 0.0006 32.9 4.5 34 230-263 164-197 (198)
314 TIGR00721 tfx DNA-binding prot 47.8 28 0.00062 32.3 4.4 32 230-261 20-51 (137)
315 COG3877 Uncharacterized protei 47.5 16 0.00036 32.5 2.6 24 2-30 8-31 (122)
316 COG1725 Predicted transcriptio 47.5 23 0.0005 32.5 3.7 31 228-258 31-62 (125)
317 PF10058 DUF2296: Predicted in 47.3 9.9 0.00021 29.7 1.1 28 1-28 23-53 (54)
318 PF04606 Ogr_Delta: Ogr/Delta- 47.3 15 0.00033 27.6 2.1 28 2-29 1-37 (47)
319 PF00126 HTH_1: Bacterial regu 47.2 31 0.00067 26.8 4.0 30 232-261 14-43 (60)
320 CHL00174 accD acetyl-CoA carbo 47.0 3.8 8.1E-05 42.8 -1.7 29 2-30 40-68 (296)
321 smart00550 Zalpha Z-DNA-bindin 46.8 67 0.0015 25.8 6.0 30 228-257 18-48 (68)
322 TIGR00515 accD acetyl-CoA carb 46.7 4 8.6E-05 42.4 -1.5 29 2-30 28-56 (285)
323 COG1318 Predicted transcriptio 46.7 30 0.00066 33.4 4.4 27 228-254 58-84 (182)
324 PRK08295 RNA polymerase factor 46.5 28 0.00061 33.2 4.4 35 230-264 169-203 (208)
325 PRK12517 RNA polymerase sigma 46.4 27 0.00059 33.3 4.2 35 230-264 143-177 (188)
326 PRK12533 RNA polymerase sigma 46.2 29 0.00064 34.2 4.6 35 230-264 149-183 (216)
327 PRK12516 RNA polymerase sigma 45.9 29 0.00064 33.1 4.4 36 230-265 131-166 (187)
328 TIGR03831 YgiT_finger YgiT-typ 45.8 15 0.00034 26.5 1.9 10 20-29 33-42 (46)
329 PF04967 HTH_10: HTH DNA bindi 45.7 65 0.0014 25.1 5.4 30 124-153 18-49 (53)
330 KOG3134 Predicted membrane pro 45.6 6 0.00013 39.4 -0.4 30 1-30 1-35 (225)
331 PRK12336 translation initiatio 45.6 13 0.00028 36.6 1.9 29 2-30 100-130 (201)
332 PRK13509 transcriptional repre 45.5 24 0.00052 35.7 3.9 28 230-257 18-45 (251)
333 TIGR02989 Sig-70_gvs1 RNA poly 45.4 31 0.00067 31.3 4.3 32 230-261 126-157 (159)
334 PF00165 HTH_AraC: Bacterial r 45.4 29 0.00062 24.9 3.3 26 230-255 7-32 (42)
335 PRK12528 RNA polymerase sigma 45.3 30 0.00065 31.7 4.2 30 230-259 128-157 (161)
336 PRK07037 extracytoplasmic-func 45.3 33 0.00072 31.4 4.5 34 230-263 124-157 (163)
337 TIGR02959 SigZ RNA polymerase 45.1 32 0.00069 32.1 4.4 36 230-265 115-150 (170)
338 PF00301 Rubredoxin: Rubredoxi 45.1 10 0.00022 28.9 0.8 14 20-33 2-15 (47)
339 COG0777 AccD Acetyl-CoA carbox 44.7 6 0.00013 40.8 -0.6 29 2-30 30-58 (294)
340 PRK12536 RNA polymerase sigma 44.7 33 0.00072 32.2 4.5 34 230-263 144-177 (181)
341 PF13518 HTH_28: Helix-turn-he 44.7 33 0.00072 25.2 3.6 25 233-257 14-38 (52)
342 PF12840 HTH_20: Helix-turn-he 44.7 43 0.00093 26.0 4.4 30 228-257 21-50 (61)
343 PRK12511 RNA polymerase sigma 44.6 32 0.00068 32.8 4.4 36 230-265 126-161 (182)
344 COG2888 Predicted Zn-ribbon RN 44.3 14 0.0003 29.6 1.5 27 2-28 29-59 (61)
345 PRK11924 RNA polymerase sigma 44.2 32 0.00069 31.5 4.3 35 230-264 140-174 (179)
346 PRK12519 RNA polymerase sigma 44.1 32 0.0007 32.5 4.4 33 231-263 157-189 (194)
347 PRK10840 transcriptional regul 44.1 33 0.00071 32.8 4.4 31 230-260 164-194 (216)
348 PF04079 DUF387: Putative tran 44.1 83 0.0018 29.9 7.0 40 112-156 2-41 (159)
349 PRK12534 RNA polymerase sigma 44.0 32 0.00069 32.4 4.3 34 230-263 152-185 (187)
350 KOG1088 Uncharacterized conser 44.0 9.9 0.00022 34.4 0.7 18 13-30 92-109 (124)
351 PRK09641 RNA polymerase sigma 43.9 36 0.00079 31.7 4.6 35 230-264 151-185 (187)
352 TIGR02844 spore_III_D sporulat 43.8 24 0.00053 29.8 3.0 24 230-253 18-41 (80)
353 KOG2906 RNA polymerase III sub 43.8 16 0.00035 32.1 2.0 29 2-30 3-32 (105)
354 PF01726 LexA_DNA_bind: LexA D 43.8 37 0.00081 27.4 4.0 32 122-153 20-52 (65)
355 cd00090 HTH_ARSR Arsenical Res 43.8 56 0.0012 24.9 5.0 26 232-257 21-46 (78)
356 PRK05654 acetyl-CoA carboxylas 43.7 4.7 0.0001 42.0 -1.6 29 2-30 29-57 (292)
357 COG1996 RPC10 DNA-directed RNA 43.7 12 0.00025 28.9 1.0 27 2-29 8-34 (49)
358 PRK12545 RNA polymerase sigma 43.6 31 0.00067 33.2 4.2 35 230-264 154-188 (201)
359 smart00354 HTH_LACI helix_turn 43.4 36 0.00078 27.4 3.9 22 232-253 1-22 (70)
360 TIGR02147 Fsuc_second hypothet 43.3 3.9E+02 0.0085 27.6 12.3 129 117-257 16-165 (271)
361 TIGR02984 Sig-70_plancto1 RNA 43.2 37 0.00079 31.7 4.5 34 230-263 155-188 (189)
362 PRK12514 RNA polymerase sigma 43.1 35 0.00077 31.8 4.4 33 230-262 144-176 (179)
363 PF13463 HTH_27: Winged helix 43.0 43 0.00093 26.0 4.2 32 123-154 14-45 (68)
364 PRK12537 RNA polymerase sigma 42.9 35 0.00076 32.1 4.4 33 230-262 148-180 (182)
365 PF00376 MerR: MerR family reg 42.8 19 0.00041 26.0 1.9 18 233-250 1-18 (38)
366 PRK12526 RNA polymerase sigma 42.8 35 0.00077 32.9 4.5 35 230-264 168-202 (206)
367 PRK09637 RNA polymerase sigma 42.7 35 0.00077 32.3 4.4 36 230-265 121-156 (181)
368 PRK12530 RNA polymerase sigma 42.7 34 0.00074 32.5 4.3 34 231-264 150-183 (189)
369 COG1595 RpoE DNA-directed RNA 42.7 37 0.00079 32.0 4.5 35 230-264 142-176 (182)
370 PRK06930 positive control sigm 42.6 35 0.00075 32.7 4.3 36 230-265 129-164 (170)
371 PRK12512 RNA polymerase sigma 42.1 42 0.00091 31.4 4.8 34 231-264 147-180 (184)
372 cd00729 rubredoxin_SM Rubredox 42.0 19 0.00041 25.4 1.8 23 2-27 4-26 (34)
373 PF08646 Rep_fac-A_C: Replicat 42.0 20 0.00043 33.0 2.4 27 2-30 20-48 (146)
374 PRK09649 RNA polymerase sigma 41.9 39 0.00085 32.0 4.6 32 230-261 145-176 (185)
375 PF13463 HTH_27: Winged helix 41.9 47 0.001 25.7 4.3 31 228-258 15-45 (68)
376 KOG2593 Transcription initiati 41.8 11 0.00025 41.0 0.9 30 2-31 130-165 (436)
377 PF04545 Sigma70_r4: Sigma-70, 41.7 49 0.0011 24.5 4.2 31 125-155 18-48 (50)
378 PRK09638 RNA polymerase sigma 41.6 39 0.00085 31.3 4.5 33 230-262 141-173 (176)
379 PRK12524 RNA polymerase sigma 41.6 38 0.00082 32.3 4.4 35 230-264 151-185 (196)
380 smart00401 ZnF_GATA zinc finge 41.5 18 0.00038 27.9 1.7 30 1-30 4-36 (52)
381 PRK11014 transcriptional repre 41.5 49 0.0011 30.2 5.0 46 109-154 7-52 (141)
382 PF01418 HTH_6: Helix-turn-hel 41.3 26 0.00057 28.8 2.9 25 230-254 33-57 (77)
383 cd00730 rubredoxin Rubredoxin; 41.2 19 0.00042 27.7 1.8 13 20-32 2-14 (50)
384 PF13404 HTH_AsnC-type: AsnC-t 41.0 59 0.0013 23.9 4.3 29 123-151 13-41 (42)
385 cd01104 HTH_MlrA-CarA Helix-Tu 41.0 31 0.00067 27.0 3.1 22 233-254 2-23 (68)
386 PRK06986 fliA flagellar biosyn 40.9 39 0.00084 33.4 4.5 35 230-264 199-233 (236)
387 PRK15411 rcsA colanic acid cap 40.9 34 0.00074 33.3 4.1 30 231-260 152-181 (207)
388 PRK11161 fumarate/nitrate redu 40.8 91 0.002 30.3 7.1 29 126-154 183-211 (235)
389 PRK09647 RNA polymerase sigma 40.7 39 0.00084 32.8 4.4 35 230-264 153-187 (203)
390 PRK13130 H/ACA RNA-protein com 40.6 12 0.00026 29.6 0.6 22 2-30 7-28 (56)
391 TIGR01321 TrpR trp operon repr 40.5 31 0.00066 30.2 3.2 30 227-256 51-80 (94)
392 PRK10401 DNA-binding transcrip 40.5 28 0.00061 35.8 3.6 37 232-268 2-45 (346)
393 PRK03975 tfx putative transcri 40.5 45 0.00098 31.2 4.5 32 230-261 20-51 (141)
394 TIGR00310 ZPR1_znf ZPR1 zinc f 40.5 20 0.00043 35.2 2.3 29 2-30 2-41 (192)
395 PRK10870 transcriptional repre 40.4 2.7E+02 0.0058 26.5 10.0 29 229-257 69-97 (176)
396 PF01978 TrmB: Sugar-specific 40.3 39 0.00084 26.7 3.6 36 117-153 13-48 (68)
397 PRK09646 RNA polymerase sigma 40.2 41 0.0009 32.0 4.5 35 230-264 157-191 (194)
398 COG1321 TroR Mn-dependent tran 40.2 49 0.0011 31.2 4.8 48 220-270 14-61 (154)
399 PRK12523 RNA polymerase sigma 40.2 49 0.0011 30.7 4.8 32 230-261 134-165 (172)
400 PF10080 DUF2318: Predicted me 40.1 26 0.00056 31.0 2.7 32 2-35 37-68 (102)
401 TIGR00595 priA primosomal prot 40.1 22 0.00048 39.8 2.9 29 2-31 224-252 (505)
402 PRK07921 RNA polymerase sigma 39.9 4.8E+02 0.01 27.6 19.0 30 230-259 281-310 (324)
403 PRK09651 RNA polymerase sigma 39.9 44 0.00096 31.1 4.5 33 230-262 134-166 (172)
404 PRK10703 DNA-binding transcrip 39.9 29 0.00062 35.5 3.5 37 232-268 2-45 (341)
405 PF01807 zf-CHC2: CHC2 zinc fi 39.8 23 0.00051 30.6 2.4 26 2-27 35-62 (97)
406 smart00347 HTH_MARR helix_turn 39.7 83 0.0018 25.7 5.8 28 231-258 24-51 (101)
407 KOG0794 CDK8 kinase-activating 39.5 89 0.0019 31.8 6.6 83 74-157 157-240 (264)
408 smart00421 HTH_LUXR helix_turn 39.5 52 0.0011 23.9 4.0 31 128-158 19-49 (58)
409 PF12728 HTH_17: Helix-turn-he 39.4 33 0.00071 25.5 2.9 21 232-252 2-22 (51)
410 PF03444 HrcA_DNA-bdg: Winged 39.4 48 0.001 28.0 4.0 30 228-257 20-49 (78)
411 PRK12515 RNA polymerase sigma 39.4 43 0.00093 31.6 4.4 35 230-264 146-180 (189)
412 PRK14559 putative protein seri 39.3 16 0.00034 42.2 1.6 8 404-411 501-508 (645)
413 PRK05572 sporulation sigma fac 39.3 4E+02 0.0087 26.5 16.9 34 230-263 217-250 (252)
414 COG1191 FliA DNA-directed RNA 39.3 4.4E+02 0.0095 27.0 15.6 35 229-263 210-244 (247)
415 PRK09391 fixK transcriptional 39.3 1.3E+02 0.0028 29.5 7.9 29 230-258 178-206 (230)
416 PRK12540 RNA polymerase sigma 39.2 44 0.00095 31.7 4.4 36 230-265 126-161 (182)
417 PRK06704 RNA polymerase factor 39.1 41 0.0009 33.7 4.4 35 231-265 132-166 (228)
418 PF02042 RWP-RK: RWP-RK domain 39.1 39 0.00084 26.4 3.2 26 230-255 14-39 (52)
419 PRK12380 hydrogenase nickel in 39.0 17 0.00037 32.5 1.5 7 2-8 72-78 (113)
420 PRK13719 conjugal transfer tra 39.0 48 0.001 33.2 4.7 31 230-260 157-187 (217)
421 PRK11753 DNA-binding transcrip 38.9 1.4E+02 0.0029 28.3 7.8 28 230-257 167-194 (211)
422 PRK09648 RNA polymerase sigma 38.7 47 0.001 31.3 4.6 32 231-262 155-186 (189)
423 COG3355 Predicted transcriptio 38.6 59 0.0013 29.9 4.9 37 117-153 32-68 (126)
424 PRK14087 dnaA chromosomal repl 38.5 5.7E+02 0.012 28.2 13.5 40 219-260 391-431 (450)
425 PRK12535 RNA polymerase sigma 38.5 47 0.001 32.0 4.5 36 230-265 148-183 (196)
426 cd04764 HTH_MlrA-like_sg1 Heli 38.5 38 0.00082 26.7 3.3 22 233-254 2-23 (67)
427 TIGR00340 zpr1_rel ZPR1-relate 38.4 24 0.00051 33.8 2.4 28 3-30 1-39 (163)
428 PF07900 DUF1670: Protein of u 38.2 38 0.00083 33.9 3.9 35 231-265 105-139 (220)
429 PF09339 HTH_IclR: IclR helix- 38.2 48 0.001 24.9 3.7 28 230-257 17-44 (52)
430 PF14255 Cys_rich_CPXG: Cystei 38.1 23 0.0005 27.6 1.9 29 2-30 2-35 (52)
431 PRK12539 RNA polymerase sigma 38.0 47 0.001 31.3 4.4 34 230-263 146-179 (184)
432 TIGR03001 Sig-70_gmx1 RNA poly 37.8 42 0.00091 33.8 4.2 35 230-264 176-210 (244)
433 TIGR03020 EpsA transcriptional 37.7 41 0.00089 34.2 4.2 31 230-260 204-234 (247)
434 COG1510 Predicted transcriptio 37.7 88 0.0019 30.4 6.1 85 196-292 13-98 (177)
435 PF14206 Cys_rich_CPCC: Cystei 37.5 21 0.00045 30.2 1.6 34 2-35 3-36 (78)
436 PRK12541 RNA polymerase sigma 37.5 50 0.0011 30.2 4.4 32 230-261 127-158 (161)
437 PF01381 HTH_3: Helix-turn-hel 37.5 32 0.00069 25.7 2.6 24 230-253 8-31 (55)
438 PRK11922 RNA polymerase sigma 37.4 44 0.00096 32.9 4.3 36 230-265 164-199 (231)
439 cd04476 RPA1_DBD_C RPA1_DBD_C: 37.3 23 0.00049 33.3 2.1 27 2-30 36-62 (166)
440 PRK10402 DNA-binding transcrip 37.2 83 0.0018 30.7 6.2 28 231-258 169-196 (226)
441 smart00422 HTH_MERR helix_turn 37.0 34 0.00074 26.8 2.8 19 233-251 2-20 (70)
442 PF01396 zf-C4_Topoisom: Topoi 36.9 43 0.00094 24.2 3.0 29 2-30 3-35 (39)
443 PF00196 GerE: Bacterial regul 36.8 54 0.0012 25.1 3.8 33 126-158 17-49 (58)
444 PRK10219 DNA-binding transcrip 36.7 1E+02 0.0022 26.3 6.0 36 219-255 10-45 (107)
445 cd06170 LuxR_C_like C-terminal 36.6 64 0.0014 23.6 4.1 32 127-158 15-46 (57)
446 COG3413 Predicted DNA binding 36.5 80 0.0017 30.9 5.9 31 231-261 178-208 (215)
447 TIGR00100 hypA hydrogenase nic 36.5 20 0.00044 32.1 1.6 20 10-29 61-80 (115)
448 PF05864 Chordopox_RPO7: Chord 36.5 11 0.00023 30.0 -0.2 45 19-87 4-48 (63)
449 PRK11753 DNA-binding transcrip 36.3 91 0.002 29.6 6.2 29 126-154 167-195 (211)
450 PRK09640 RNA polymerase sigma 36.2 47 0.001 31.4 4.1 34 230-263 149-182 (188)
451 PRK05580 primosome assembly pr 36.0 27 0.00059 40.5 2.9 28 2-30 392-419 (679)
452 PRK12546 RNA polymerase sigma 35.9 57 0.0012 31.2 4.7 35 230-264 128-162 (188)
453 PF13551 HTH_29: Winged helix- 35.7 80 0.0017 26.7 5.1 27 233-259 14-40 (112)
454 PRK15418 transcriptional regul 35.7 60 0.0013 34.1 5.1 35 222-256 20-54 (318)
455 cd04763 HTH_MlrA-like Helix-Tu 35.6 43 0.00094 26.4 3.2 22 233-254 2-23 (68)
456 TIGR02960 SigX5 RNA polymerase 35.4 52 0.0011 33.9 4.6 36 230-265 157-192 (324)
457 PRK10219 DNA-binding transcrip 35.3 1.2E+02 0.0026 26.0 6.2 50 112-170 7-56 (107)
458 PRK07406 RNA polymerase sigma 35.2 6.1E+02 0.013 27.4 19.5 32 230-261 330-361 (373)
459 PRK03824 hypA hydrogenase nick 35.1 22 0.00047 32.8 1.6 25 7-31 58-82 (135)
460 TIGR02010 IscR iron-sulfur clu 35.1 57 0.0012 29.6 4.3 39 219-257 13-51 (135)
461 PF13556 HTH_30: PucR C-termin 35.1 69 0.0015 24.9 4.2 31 230-260 11-41 (59)
462 TIGR03829 YokU_near_AblA uncha 35.1 30 0.00064 30.0 2.2 30 2-31 1-47 (89)
463 PF13730 HTH_36: Helix-turn-he 35.1 86 0.0019 23.5 4.7 25 129-153 27-51 (55)
464 PRK10411 DNA-binding transcrip 35.1 44 0.00095 33.6 3.9 28 230-257 17-44 (240)
465 PF02954 HTH_8: Bacterial regu 34.9 65 0.0014 23.4 3.8 24 231-254 18-41 (42)
466 PRK14873 primosome assembly pr 34.9 27 0.00058 40.6 2.6 26 2-28 394-419 (665)
467 PHA03082 DNA-dependent RNA pol 34.9 12 0.00026 29.8 -0.2 45 19-87 4-48 (63)
468 PRK10014 DNA-binding transcrip 34.9 31 0.00066 35.3 2.8 39 230-268 5-50 (342)
469 PRK12366 replication factor A; 34.8 20 0.00044 41.3 1.6 24 2-28 534-557 (637)
470 cd00202 ZnF_GATA Zinc finger D 34.8 13 0.00028 29.0 0.0 29 2-30 1-32 (54)
471 PRK10188 DNA-binding transcrip 34.6 49 0.0011 33.2 4.1 31 230-260 193-223 (240)
472 PRK01110 rpmF 50S ribosomal pr 34.5 20 0.00043 28.7 1.0 21 2-29 29-49 (60)
473 PRK11511 DNA-binding transcrip 34.5 1.2E+02 0.0025 27.2 6.2 42 213-255 8-49 (127)
474 PRK09526 lacI lac repressor; R 34.5 34 0.00074 34.9 3.0 38 231-268 5-49 (342)
475 TIGR03613 RutR pyrimidine util 34.4 68 0.0015 30.3 4.9 36 228-263 24-60 (202)
476 PF04703 FaeA: FaeA-like prote 34.4 71 0.0015 25.7 4.2 29 229-257 13-41 (62)
477 PF13744 HTH_37: Helix-turn-he 34.2 77 0.0017 26.2 4.6 30 223-252 23-52 (80)
478 PRK12469 RNA polymerase factor 34.1 7.2E+02 0.016 27.9 14.6 82 73-156 162-263 (481)
479 PRK03902 manganese transport t 34.0 77 0.0017 28.9 5.0 28 231-258 22-49 (142)
480 COG2816 NPY1 NTP pyrophosphohy 33.9 23 0.0005 36.7 1.7 30 2-32 113-142 (279)
481 PRK12538 RNA polymerase sigma 33.8 55 0.0012 32.6 4.3 35 230-264 186-220 (233)
482 smart00345 HTH_GNTR helix_turn 33.8 69 0.0015 23.7 4.0 26 129-154 22-47 (60)
483 TIGR00281 segregation and cond 33.7 4.6E+02 0.01 25.6 12.0 42 110-155 3-46 (186)
484 PF01047 MarR: MarR family; I 33.7 95 0.0021 23.4 4.8 28 126-153 16-43 (59)
485 PF09082 DUF1922: Domain of un 33.6 33 0.00072 28.2 2.2 26 2-30 5-30 (68)
486 PF13411 MerR_1: MerR HTH fami 33.2 36 0.00079 26.7 2.4 19 233-251 2-20 (69)
487 PF08299 Bac_DnaA_C: Bacterial 32.9 86 0.0019 25.4 4.6 64 72-151 4-70 (70)
488 PRK09975 DNA-binding transcrip 32.9 71 0.0015 30.4 4.8 36 228-263 27-63 (213)
489 PRK08583 RNA polymerase sigma 32.9 61 0.0013 32.4 4.5 33 230-262 220-252 (257)
490 TIGR03070 couple_hipB transcri 32.7 46 0.001 24.6 2.8 22 230-251 14-35 (58)
491 PF13936 HTH_38: Helix-turn-he 32.6 73 0.0016 23.4 3.7 27 124-150 17-43 (44)
492 KOG0654 G2/Mitotic-specific cy 32.5 4.7E+02 0.01 28.3 11.2 133 115-256 185-320 (359)
493 PRK06030 hypothetical protein; 32.5 1E+02 0.0022 28.2 5.4 39 115-155 59-97 (124)
494 PRK10727 DNA-binding transcrip 32.4 40 0.00086 34.6 3.2 38 232-269 2-46 (343)
495 PRK15320 transcriptional activ 32.4 60 0.0013 32.4 4.1 31 230-260 178-208 (251)
496 PRK12544 RNA polymerase sigma 32.3 64 0.0014 31.4 4.4 35 230-264 163-197 (206)
497 PRK15201 fimbriae regulatory p 32.2 74 0.0016 31.2 4.6 31 230-260 147-177 (198)
498 COG1510 Predicted transcriptio 32.2 52 0.0011 31.9 3.6 37 117-153 31-67 (177)
499 PRK06811 RNA polymerase factor 31.9 67 0.0014 30.4 4.4 30 231-260 147-176 (189)
500 TIGR02702 SufR_cyano iron-sulf 31.9 91 0.002 30.3 5.4 28 231-258 15-42 (203)
No 1
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=2.3e-65 Score=541.60 Aligned_cols=492 Identities=24% Similarity=0.277 Sum_probs=415.7
Q ss_pred CCCCCCCCCCeEEecCCCcEEcCCCceeecccCcccCCCCCCCCCCcEEeecccCCCCCcchHhHHHHHHHHHHHHHHhh
Q 047665 1 MPCTSCGSKTLTREDISGSLICVSCGVVQAFDNYDAQLYGRDGPTGIYVHVGTAGTGSALNYKEKKIYESNKLIDELTFK 80 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~~~~~~~g~p~gt~i~~g~~g~gs~~s~rer~L~~a~~~I~~i~~~ 80 (530)
|.|++||++++..|..+|..+|+.||+|+++++|..+....-+++|+|++.+++|.+.+..++++.++++.+.|+.++.+
T Consensus 1 ~~C~~C~~s~fe~d~a~g~~~C~~CG~v~E~~~ivsev~F~e~~~G~~v~~~~~g~~~s~e~r~~t~~n~r~~i~~~~~~ 80 (521)
T KOG1598|consen 1 MVCKNCGGSNFERDEATGNLYCTACGTVLEYNNIVAEVTFVEGAQGQFVRVGQSGAGSSLESREKTIYNARRLIEELTER 80 (521)
T ss_pred CcCCCCCCCCcccccccCCceeccccceeeccceeEEeeeecccceeEEeccccCCccchHHHHHHHHHHHhHHHHHHHh
Confidence 89999999999999999999999999999999998775444449999999999998877899999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhhhc--
Q 047665 81 LDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNLK-- 158 (530)
Q Consensus 81 LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~-- 158 (530)
|+|++ +++.|..+|+.+.+++|++||+...++|||+|++||+++.++.+.|++++++++++.||++|+++++.|.+.
T Consensus 81 l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~~l~l~~~L~i~en 159 (521)
T KOG1598|consen 81 LNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSNFLEVTDSLSIGEN 159 (521)
T ss_pred cCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHHHHHHHHHhccccc
Confidence 99999 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -CCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHH
Q 047665 159 -LPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENV 237 (530)
Q Consensus 159 -~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eI 237 (530)
.|.+||+.||+||+..|.. .+ ..++|+.+|.+|+++|+++|+.+||+|.+||+||||+|++++|+++|..||
T Consensus 160 ~~plvDpsL~i~Rfa~~L~~--g~-----~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dI 232 (521)
T KOG1598|consen 160 VSPLVDPSLYIVRFSCRLLF--GD-----KTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDI 232 (521)
T ss_pred cccccCcceeeechhHhhhc--CC-----chHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHH
Confidence 9999999999999998876 22 237899999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCHHHHHHHHHHHHHHHHhhccc--CCCCccCcc----cccccChhHHHHHhHHHHHhhhhhhccCCcCCCCchh
Q 047665 238 AKEVHCTVVTCRKRYKELLEALVKVAQA--LPWGKDVTV----KNVLKNAPFVMNYMEMKSMEKRKEERDGLNCGGIDLG 311 (530)
Q Consensus 238 A~~~~VS~~TIrkRyKEL~e~L~~l~~~--lpW~~~v~~----knl~~~~pdIi~~~e~~~~~~~~~~~~~~~~~~~~~~ 311 (530)
+++++|++.||++||+||.+++..-++. + |-.++.. ........--=++++ .+++ +-.+...++..++-.
T Consensus 233 v~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~ef-~~~d~e~~~~ppsft~~~~~~~k~~~--~~k~-~l~~~~~~~e~~~~~ 308 (521)
T KOG1598|consen 233 AKVVHVCESTLSKRLKEFSDTLSGDLTIDEL-AEIDLEYESDPPSFTASPSKEAKYVE--DKKK-MLSRTMQLVELANET 308 (521)
T ss_pred HHHHHHhHHHHHHHHHHHhccccccccHHHH-HhhhhhhccCcchhhcccchhhhhhh--hhhh-hhhhhhhhhhcccch
Confidence 9999999999999999999988655442 3 3212222 111111110001111 1111 111233455667777
Q ss_pred hhHHHhhhcCc--ceeccCCcccCCCcchhhhhccccccccccCccccccCHHHHHHHHHHHhhc--ccccchhhhhhcc
Q 047665 312 DVVSECLKKDV--EYRIEGGGVESDPRYLEVEERSGLALTGVDCVHKTQLSHECLAMIYTRFANE--IDDGKLLEESEVI 387 (530)
Q Consensus 312 ~~v~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~~~~~~~~~~~~ 387 (530)
..|..|..... +|..+..+.. +.++++++. . ++ .+++--||. ++.+. .+.+.+.-++-+.
T Consensus 309 ~~~~~~~~~~~~~~~l~~~~q~~-~~~~~~~e~---~-----~~----~~~e~~~ss---E~~dk~~~g~~~~~~~~~sd 372 (521)
T KOG1598|consen 309 WLVTLRHSLPVITGGLFLAWQDL-QPRDRLVES---Y-----DD----LASECPLSS---EDEDKPASGRLAELLAVLSD 372 (521)
T ss_pred hhhccccCCcccchhhhcccccc-hhhhhhhhh---h-----hh----hhhcCcccc---cccCCcCccccchhhhcccc
Confidence 77777777776 5556666666 777776665 1 11 244443444 55555 5667778888888
Q ss_pred cccccccccccccccccccccchhhHHHHHHHHHhhhcCCCCCCchhhhhhHHHHHHHHHHHHHHHhHHhhcCCCCCCCC
Q 047665 388 HGVKGRGGYELHAYRDWWCGKSELSKKVLLKKILEKDVGLDVMPPSFVNGCMVNERRRAKINAAKIRIDKIMNPSRASTG 467 (530)
Q Consensus 388 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pp~~~~~~~~~~~~~~~i~~ak~r~~~~~~~~~~~~~ 467 (530)
.+++.+....+....+||.++++.++..+.+++|++|.|.++.||+ +|++.+.|+|+.|+.+||.|+..|.||+....+
T Consensus 373 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~l~r~~l~~~a~~~a~~~~-~n~e~l~E~~~~~~~~ak~~~~g~~~~~~k~~~ 451 (521)
T KOG1598|consen 373 MAEQLASVWLRVLTLDKRSGVKHIDDLLLERQLLEESAGRDATEPM-ENAETLVEERPGKAKAAKEREEGINSLSKKVGE 451 (521)
T ss_pred cchhhhhcchhhhhccccccccccCHHHHHHHHhhhHHhhhcchhh-hhHHHHHhhchhhhhhhHhhhhccccccccccc
Confidence 8888887677777788999999999999999999999999999996 999999999999999999999999999999988
Q ss_pred CCcccchhhhhhhhhhccCCCCCCChhHHHHHHHHhccCCHHHHhhcccccchhhhcccCC
Q 047665 468 DVDNVYFLESVHTRKRKRKPVAEIDWEDLIIETLLLHQVKEEEIEAGHYNTLLDLHVFNSG 528 (530)
Q Consensus 468 ~~~~~~~~~~~~~~~~~~~~~~~~d~~d~~i~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~ 528 (530)
...+. .+.|..++.+++.. |+|++-+|.+..||++.++|||+ .|..+.|||+++
T Consensus 452 r~~s~---~~~t~~eavk~~~~-i~~~s~~in~~~L~~i~d~~~e~---~~~~p~~v~~~~ 505 (521)
T KOG1598|consen 452 RRNSP---ELLTAPEAVKSMKE-IKPVSSVINYSVLENISDAEIEQ---YTRTPQHVRDFQ 505 (521)
T ss_pred ccCCC---cccccHHHHHHHHh-ccccccchHHHHHHHHhhhhccc---ccCCchhhhhHH
Confidence 88888 88888888888843 99999999999999999999999 799999999976
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=1e-49 Score=410.50 Aligned_cols=251 Identities=25% Similarity=0.339 Sum_probs=225.5
Q ss_pred CCCCCCCCCCeEEecCCCcEEcCCCceeec---------ccCcccCC----CCCCCCCCcEEeecc---------cC-CC
Q 047665 1 MPCTSCGSKTLTREDISGSLICVSCGVVQA---------FDNYDAQL----YGRDGPTGIYVHVGT---------AG-TG 57 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle---------~~~f~~~~----~~~g~p~gt~i~~g~---------~g-~g 57 (530)
+.||+||++.+++|+.+|++||++||+|++ |++|+++. .+.|+|.+++++..+ .+ .|
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~~g 91 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRNKDSYG 91 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCcccccccccCCCccCCCccccCCccccCCCCCccccCCCCceEeecCCccccc
Confidence 479999998999999999999999999998 44565432 344777766655311 10 11
Q ss_pred C---------------------CcchHhHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHH
Q 047665 58 S---------------------ALNYKEKKIYESNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGAC 116 (530)
Q Consensus 58 s---------------------~~s~rer~L~~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAc 116 (530)
. ..++.||+|..|++.|+++|+.|+||..++++|..+|+++.+.++.+|++.+.++|||
T Consensus 92 ~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAc 171 (310)
T PRK00423 92 KSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAA 171 (310)
T ss_pred ccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHH
Confidence 1 1256689999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHH
Q 047665 117 SYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGV 196 (530)
Q Consensus 117 lYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~ 196 (530)
||+|||++++|+|++||+.++++++++|+++|+.|.+.|++++|+.+|+.||+|||+.|++ + ..+.+.|.
T Consensus 172 lYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L---~-------~~v~~~A~ 241 (310)
T PRK00423 172 LYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGL---S-------GEVQKKAI 241 (310)
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCC---C-------HHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999997 4 47889999
Q ss_pred HHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 197 LLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 197 ~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
.|++.+.+.|++.||+|.+|||||||+|++++|.++|+++||++++|++.||++|||||.+.+..
T Consensus 242 ~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~~ 306 (310)
T PRK00423 242 EILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDI 306 (310)
T ss_pred HHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCc
Confidence 99999999999999999999999999999999999999999999999999999999999998754
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=2.6e-48 Score=393.59 Aligned_cols=250 Identities=26% Similarity=0.377 Sum_probs=227.5
Q ss_pred CCCCCCCCCCeEEecCCCcEEcCCCceeeccc---------CcccC-CCCCCCCCCcEEeecc----cCC----------
Q 047665 1 MPCTSCGSKTLTREDISGSLICVSCGVVQAFD---------NYDAQ-LYGRDGPTGIYVHVGT----AGT---------- 56 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~---------~f~~~-~~~~g~p~gt~i~~g~----~g~---------- 56 (530)
|.||+||+..++.|+..|+.||.+||+|+++. .|++. ..+.|+|.+..+++.+ .|.
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~e~~~~r~g~P~t~~~~d~~l~t~i~~~~~~~~~rlr 81 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDERHERRVGAPLTPSIHDKGLSTIIGWGDKDKMYRLR 81 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEeccccccCCCCcccccccccccccCCCccccCccchhhhcccchhHHHHHHH
Confidence 68999999999999999999999999999854 44222 2344778777776421 111
Q ss_pred -----CCCcchHhHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChH
Q 047665 57 -----GSALNYKEKKIYESNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPIS 131 (530)
Q Consensus 57 -----gs~~s~rer~L~~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~ 131 (530)
.+..+..|+++..+++.|+.++..|+||.++.++|..+|+.+.+.++.+||+.+.++|||+|+|||+++.|+|+.
T Consensus 82 ~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~ 161 (285)
T COG1405 82 KWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLD 161 (285)
T ss_pred HHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHH
Confidence 223457899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCHHHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhccccccc
Q 047665 132 EVASVLNCDVYELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGR 211 (530)
Q Consensus 132 DIA~~~~vd~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR 211 (530)
||+.+++++.++|+++|+.+.+.|++.+|+.||.+||+|||+.|++ + +.+.+.|.+|++.+.+.+++.||
T Consensus 162 eIa~a~~V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l---~-------~~v~~~a~ei~~~~~~~g~~~Gk 231 (285)
T COG1405 162 EIAKALGVSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGL---S-------DEVRRKAIEIVKKAKRAGLTAGK 231 (285)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCC---C-------HHHHHHHHHHHHHHHHhCcccCC
Confidence 9999999999999999999999999999999999999999999998 4 47889999999999999999999
Q ss_pred CchhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 212 RPMPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 212 ~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
+|.++||||||+|+.++|+++||++||.+++||++|||+||+||.+.+.
T Consensus 232 ~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel~~~~~ 280 (285)
T COG1405 232 SPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELADALD 280 (285)
T ss_pred CchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHHHHhhc
Confidence 9999999999999999999999999999999999999999999998874
No 4
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=1.8e-47 Score=379.87 Aligned_cols=266 Identities=20% Similarity=0.350 Sum_probs=234.2
Q ss_pred CCCCCCCC-CC-eEEecCCCcEEcCCCceeeccc---------CcccC-----CCCCCCCCCcEEeecc------cCCC-
Q 047665 1 MPCTSCGS-KT-LTREDISGSLICVSCGVVQAFD---------NYDAQ-----LYGRDGPTGIYVHVGT------AGTG- 57 (530)
Q Consensus 1 M~Cp~CG~-~~-iv~D~~~G~~VCt~CG~Vle~~---------~f~~~-----~~~~g~p~gt~i~~g~------~g~g- 57 (530)
|.||+|+. +. +|+|+..|..||..||+|++++ .|.++ +.++|++.++++..|. .|.|
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~g~ 80 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGTGT 80 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCCCC
Confidence 78999997 44 9999999999999999999844 44433 2234777776665432 1111
Q ss_pred --------------CCcchHhHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHh
Q 047665 58 --------------SALNYKEKKIYESNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRL 123 (530)
Q Consensus 58 --------------s~~s~rer~L~~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~ 123 (530)
.+++..|+.+..||..|..||+.++||..+.++|.++|+++.+.+..+||+.++++|||||+||||
T Consensus 81 ~s~~~s~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq 160 (308)
T KOG1597|consen 81 SSSFASSLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQ 160 (308)
T ss_pred CHHHHHHHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHh
Confidence 134677899999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhhhcCCcc--chhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHH
Q 047665 124 DDKSLPISEVASVLNCDVYELGRMITRVVEFLNLKLPEV--DIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNC 201 (530)
Q Consensus 124 ~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~~p~v--dp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~ 201 (530)
++.|||++||+.+++++.++|||+++.|.+.|+..++.. ...+||+|||+.|++ + ..+++.|.++++.
T Consensus 161 ~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L---~-------~~~q~aA~e~a~k 230 (308)
T KOG1597|consen 161 EDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGL---P-------KSAQEAATEIAEK 230 (308)
T ss_pred cCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCC---C-------HHHHHHHHHHHHH
Confidence 999999999999999999999999999999999876644 478999999999998 5 5788999999999
Q ss_pred HhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccCCCCc-cCcccccc
Q 047665 202 AVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQALPWGK-DVTVKNVL 278 (530)
Q Consensus 202 a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~lpW~~-~v~~knl~ 278 (530)
+....+..||+|.+||||+|||++++.+.+++++||+.++||+++|||+.||+||+++.++++. |.. .++.+|++
T Consensus 231 a~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~liP~--~~a~~~~lk~Lp 306 (308)
T KOG1597|consen 231 AEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHADKLIPS--WYANAVPLKNLP 306 (308)
T ss_pred HHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHhhchhhhChh--hhccccchhhcC
Confidence 9999999999999999999999999999999999999999999999999999999999999977 875 35566665
No 5
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.62 E-value=2e-15 Score=123.17 Aligned_cols=71 Identities=20% Similarity=0.257 Sum_probs=65.9
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHH
Q 047665 74 IDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYEL 144 (530)
Q Consensus 74 I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~L 144 (530)
|+++|+.|+||+.+.++|..+|+.+.+.++.+||++..++|||||+|||+++.|+|++||+++++++.++|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 67899999999999999999999999999999999999999999999999999999999999999999875
No 6
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.43 E-value=5.2e-13 Score=108.89 Aligned_cols=71 Identities=21% Similarity=0.321 Sum_probs=65.4
Q ss_pred HHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHH
Q 047665 168 FERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVT 247 (530)
Q Consensus 168 I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~T 247 (530)
|+++|+.|++ + +.+.+.|.+|++.+.+.++..||+|.++||||||+|++.++.++|++|||++++|++.|
T Consensus 1 I~r~~~~L~L---~-------~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~t 70 (71)
T PF00382_consen 1 IPRICSKLGL---P-------EDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKT 70 (71)
T ss_dssp HHHHHHHTT------------HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHH
T ss_pred ChHHHhHcCC---C-------HHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCc
Confidence 6899999998 4 58999999999999999999999999999999999999999999999999999999999
Q ss_pred H
Q 047665 248 C 248 (530)
Q Consensus 248 I 248 (530)
|
T Consensus 71 I 71 (71)
T PF00382_consen 71 I 71 (71)
T ss_dssp H
T ss_pred C
Confidence 7
No 7
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.29 E-value=1.7e-11 Score=127.03 Aligned_cols=91 Identities=19% Similarity=0.224 Sum_probs=86.4
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHH
Q 047665 70 SNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMIT 149 (530)
Q Consensus 70 a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k 149 (530)
...+|.++|+.|+||..+.+.|..+++.+.+.++..||++..+||||||+|||.++.|+|++|||.+++++..+|++.|+
T Consensus 219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~yk 298 (310)
T PRK00423 219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYK 298 (310)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH
Confidence 45789999999999999999999999999988899999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCC
Q 047665 150 RVVEFLNLKLP 160 (530)
Q Consensus 150 ~L~k~L~i~~p 160 (530)
.|.+.|++.+|
T Consensus 299 el~~~l~~~~~ 309 (310)
T PRK00423 299 ELAEKLDIKIP 309 (310)
T ss_pred HHHHHhCcccC
Confidence 99999987653
No 8
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.16 E-value=1.9e-09 Score=110.05 Aligned_cols=184 Identities=13% Similarity=0.130 Sum_probs=152.6
Q ss_pred cchHhHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCC
Q 047665 60 LNYKEKKIYESNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNC 139 (530)
Q Consensus 60 ~s~rer~L~~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~v 139 (530)
.++.+-...-+...|++-|-.|+||....-++.-+|..+....-..+-.++.++.|||.+|.+.+..|++++||..++.-
T Consensus 16 ~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~ 95 (367)
T KOG0835|consen 16 LETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHY 95 (367)
T ss_pred cchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHH
Confidence 34555555668899999999999999999999999999877666677789999999999999999999999999988643
Q ss_pred ----------C-----------HHHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHH
Q 047665 140 ----------D-----------VYELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLL 198 (530)
Q Consensus 140 ----------d-----------~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~L 198 (530)
. ...+-++..+|.+.||+.+-..+|..+|--|..-|++ .++ .++.+.++.+
T Consensus 96 L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~--~~~------~~l~Q~~wNf 167 (367)
T KOG0835|consen 96 LEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQL--PPN------LKLLQAAWNF 167 (367)
T ss_pred HHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcC--CCc------hhHHHHHHHh
Confidence 1 1234477788999999998888999999899888887 232 3688999999
Q ss_pred HHHHhhcccccccCchhHHHHHHHHHHHHcCCCCC-HHHHHHHhCCCHHHHHHH
Q 047665 199 LNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVK-IENVAKEVHCTVVTCRKR 251 (530)
Q Consensus 199 l~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t-~~eIA~~~~VS~~TIrkR 251 (530)
++.+.++.+..--+|.+||+|+||||++..+++++ +..+-++.+++..-|-.+
T Consensus 168 mNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~i 221 (367)
T KOG0835|consen 168 MNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEI 221 (367)
T ss_pred hhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHH
Confidence 99999999999999999999999999999987643 447788888886554443
No 9
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.15 E-value=1.9e-09 Score=111.43 Aligned_cols=174 Identities=10% Similarity=0.110 Sum_probs=135.2
Q ss_pred hHHHHH-HHHHHHHHHhhcC--CCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCC
Q 047665 64 EKKIYE-SNKLIDELTFKLD--LTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCD 140 (530)
Q Consensus 64 er~L~~-a~~~I~~i~~~Lg--Lp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd 140 (530)
|+.+.. ....|.++|..|+ ||..++-+|..+|++.+-.+...--.+..+++||+|+||+.+..|+++.+++..+.-+
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 445443 4489999999999 9999999999999999766555555789999999999999999999999999876644
Q ss_pred ----HHHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhccc--CCCCccchHHHHHHHHHHHHHHHHHhhcccccccCch
Q 047665 141 ----VYELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRL--QGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPM 214 (530)
Q Consensus 141 ----~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l--~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~ 214 (530)
...|..+-..|.+.|+..+-...|..++..+...+.- ++.. ..+.+.+.|..+++.+..+.+.-=-.|.
T Consensus 132 ~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~-----~~~~l~q~a~~~lndsl~Td~~L~y~Ps 206 (305)
T TIGR00569 132 PLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLE-----NPEYLRKHADKFLNRTLLTDAYLLYTPS 206 (305)
T ss_pred chhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhcccc-----chHHHHHHHHHHHHHHHcCCceecCCHH
Confidence 3778888889999999887666787777777654421 0011 1246778888998887776666568999
Q ss_pred hHHHHHHHHHHHHcCCCCCHHHHHHHhCC
Q 047665 215 PVVVAVLVFVVELNGVSVKIENVAKEVHC 243 (530)
Q Consensus 215 sIAAAAIYlAa~~~g~k~t~~eIA~~~~V 243 (530)
-||+||||+|++..+++..-.+. ++..+
T Consensus 207 ~IAlAAI~lA~~~~~~~l~~~~~-e~~~~ 234 (305)
T TIGR00569 207 QIALAAILHTASRAGLNMESYLT-EQLSV 234 (305)
T ss_pred HHHHHHHHHHHHHhCCCCcccch-hhhcc
Confidence 99999999999999987654332 44555
No 10
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=98.91 E-value=2e-08 Score=104.19 Aligned_cols=189 Identities=13% Similarity=0.146 Sum_probs=139.9
Q ss_pred HHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhC--CCH-
Q 047665 65 KKIYESNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLN--CDV- 141 (530)
Q Consensus 65 r~L~~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~--vd~- 141 (530)
+....+.++|.+++.+|++|...+.+|..+|.+++-.-..+.-....+|+||+|+|++.++.|+.++||..+.. .++
T Consensus 37 ~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~ 116 (323)
T KOG0834|consen 37 RLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPK 116 (323)
T ss_pred HHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcc
Confidence 34457889999999999999999999999999997554445556688999999999999999999999988743 333
Q ss_pred -HHHHHHHHH-----------HHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhccccc
Q 047665 142 -YELGRMITR-----------VVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTT 209 (530)
Q Consensus 142 -~~Lgr~~k~-----------L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~t 209 (530)
.++...|.. +.+.|++++..-.|..|+.+++..+.. .. +....++..|..+++.+....+.-
T Consensus 117 ~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~---~~---~~~~~~a~~Aw~~~nD~~~t~~cL 190 (323)
T KOG0834|consen 117 DLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKA---DE---NLKQPLAQAAWNFVNDSLRTTLCL 190 (323)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhh---hh---hccccHHHHHHHHhchhheeeeeE
Confidence 234444443 444556666556789999999999875 21 001257888998888887766665
Q ss_pred ccCchhHHHHHHHHHHHHcCCCCCHH---HHHHHhC--CCHHHHHHHHHHHHHHH
Q 047665 210 GRRPMPVVVAVLVFVVELNGVSVKIE---NVAKEVH--CTVVTCRKRYKELLEAL 259 (530)
Q Consensus 210 GR~P~sIAAAAIYlAa~~~g~k~t~~---eIA~~~~--VS~~TIrkRyKEL~e~L 259 (530)
--.|..||+|+||+|++..|...+.. ...+..+ ++..-+..-..++.+..
T Consensus 191 ~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y 245 (323)
T KOG0834|consen 191 QYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLY 245 (323)
T ss_pred eecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHH
Confidence 67899999999999999998754332 3566676 77766655555554433
No 11
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.89 E-value=5.7e-09 Score=106.86 Aligned_cols=91 Identities=16% Similarity=0.185 Sum_probs=86.4
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHH
Q 047665 70 SNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMIT 149 (530)
Q Consensus 70 a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k 149 (530)
-.++|..+|+.||||+.+...|.++.+++.+.+.+.|+++..+||||+|+|++.++.++|.+|||.++++...+|...|+
T Consensus 194 p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnryk 273 (285)
T COG1405 194 PSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYK 273 (285)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHH
Confidence 34689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCC
Q 047665 150 RVVEFLNLKLP 160 (530)
Q Consensus 150 ~L~k~L~i~~p 160 (530)
+|.+.+++..+
T Consensus 274 el~~~~~i~~~ 284 (285)
T COG1405 274 ELADALDIEVT 284 (285)
T ss_pred HHHHhhccccC
Confidence 99999987653
No 12
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=98.81 E-value=3e-09 Score=78.85 Aligned_cols=36 Identities=36% Similarity=0.778 Sum_probs=31.3
Q ss_pred CCCCCCCCCCeEEecCCCcEEcCCCceeecccCccc
Q 047665 1 MPCTSCGSKTLTREDISGSLICVSCGVVQAFDNYDA 36 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~~ 36 (530)
|+||+||+..+++|+.+|++||++||.|+++...++
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~i~~ 36 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEENIIDE 36 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-TTBSC
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeecccccC
Confidence 899999998899999999999999999999886654
No 13
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.75 E-value=9.2e-08 Score=77.97 Aligned_cols=83 Identities=14% Similarity=0.159 Sum_probs=76.9
Q ss_pred HHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCC-CHHHHHHH
Q 047665 69 ESNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNC-DVYELGRM 147 (530)
Q Consensus 69 ~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~v-d~~~Lgr~ 147 (530)
.+.++|.+++..+++|..+...|..+++++...+...++++..+++||+|+||+.++.|.++.++...++. +..+|.+.
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~ 83 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRM 83 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHH
Confidence 46789999999999999999999999999987777789999999999999999999999999999999999 99999888
Q ss_pred HHHH
Q 047665 148 ITRV 151 (530)
Q Consensus 148 ~k~L 151 (530)
++.+
T Consensus 84 e~~i 87 (88)
T cd00043 84 EKLL 87 (88)
T ss_pred HHHh
Confidence 7765
No 14
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=98.70 E-value=1.6e-07 Score=95.81 Aligned_cols=158 Identities=15% Similarity=0.106 Sum_probs=130.8
Q ss_pred HHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHh--------CC
Q 047665 68 YESNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVL--------NC 139 (530)
Q Consensus 68 ~~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~--------~v 139 (530)
..++..|..+|.+|+||..+..+|..+|++..-.+...+.....++++|||+||+.+..|+-+.-.+... --
T Consensus 46 i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~ 125 (297)
T COG5333 46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKS 125 (297)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccc
Confidence 3467899999999999999999999999999877777888999999999999999999775555444433 34
Q ss_pred CHHHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHH
Q 047665 140 DVYELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVA 219 (530)
Q Consensus 140 d~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAA 219 (530)
+...|-..-..+.+.|+.+.-...|..++..|...+-. ... .++.+.|..++..+-+..+.-=-.|..||.|
T Consensus 126 sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~--~~~------~~~~~~aw~~inDa~~t~~~llypphiIA~a 197 (297)
T COG5333 126 SRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQE--KDK------YKLLQIAWKIINDALRTDLCLLYPPHIIALA 197 (297)
T ss_pred cHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHh--ccH------HHHHHHHHHHHHhhhhceeeeecChHHHHHH
Confidence 67888888888999999887667788888888777765 221 3678889999999998887777889999999
Q ss_pred HHHHHHHHcCCCCC
Q 047665 220 VLVFVVELNGVSVK 233 (530)
Q Consensus 220 AIYlAa~~~g~k~t 233 (530)
|+++|+...|.+..
T Consensus 198 ~l~ia~~~~~~~~~ 211 (297)
T COG5333 198 ALLIACEVLGMPII 211 (297)
T ss_pred HHHHHHHhcCCccc
Confidence 99999999886543
No 15
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.66 E-value=9.5e-08 Score=96.72 Aligned_cols=88 Identities=11% Similarity=0.156 Sum_probs=83.1
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHH
Q 047665 70 SNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMIT 149 (530)
Q Consensus 70 a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k 149 (530)
.-++|.++|..|+||.++++.|.++.+++.+.++..||++..++||+||++++....++|++||..++|+..-+|...|+
T Consensus 203 t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK 282 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYK 282 (308)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHH
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhh
Q 047665 150 RVVEFLNL 157 (530)
Q Consensus 150 ~L~k~L~i 157 (530)
.|..++.-
T Consensus 283 ~Lyp~~~~ 290 (308)
T KOG1597|consen 283 DLYPHADK 290 (308)
T ss_pred HHhhchhh
Confidence 99877653
No 16
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.63 E-value=1.7e-07 Score=75.68 Aligned_cols=79 Identities=14% Similarity=0.125 Sum_probs=71.4
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHhh-CCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCC-CHHHHHHHHHH
Q 047665 73 LIDELTFKLDLTGQRSIQIKNMIDKITD-GEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNC-DVYELGRMITR 150 (530)
Q Consensus 73 ~I~~i~~~LgLp~~i~e~A~~i~k~a~~-~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~v-d~~~Lgr~~k~ 150 (530)
+|.+++..+++|..+...|..+++++.. ..+.+ +.+..++|||+|+||+.++.+.+..+++..++. +..+|.+.++.
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~-~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 80 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLK-YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEKL 80 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhccc-CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHHH
Confidence 6788999999999999999999999976 45544 899999999999999999999999999999999 99999988887
Q ss_pred HH
Q 047665 151 VV 152 (530)
Q Consensus 151 L~ 152 (530)
|.
T Consensus 81 il 82 (83)
T smart00385 81 LL 82 (83)
T ss_pred Hh
Confidence 64
No 17
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.47 E-value=1.4e-06 Score=70.88 Aligned_cols=84 Identities=18% Similarity=0.171 Sum_probs=75.7
Q ss_pred cchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHh
Q 047665 162 VDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEV 241 (530)
Q Consensus 162 vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~ 241 (530)
..+..|+.++++.+++ + ..+...|..++++....+...+++|..+|+||+|+|+++.+...+.++++..+
T Consensus 3 ~~~~~~l~~~~~~~~~---~-------~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~ 72 (88)
T cd00043 3 PTPLDFLRRVAKALGL---S-------PETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVT 72 (88)
T ss_pred chHHHHHHHHHHHcCC---C-------HHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHh
Confidence 3567899999999987 4 46888999999998887788899999999999999999999999999999999
Q ss_pred CC-CHHHHHHHHHHH
Q 047665 242 HC-TVVTCRKRYKEL 255 (530)
Q Consensus 242 ~V-S~~TIrkRyKEL 255 (530)
+. +..+|.+.+++|
T Consensus 73 ~~~~~~~i~~~e~~i 87 (88)
T cd00043 73 GYATEEEILRMEKLL 87 (88)
T ss_pred CCCCHHHHHHHHHHh
Confidence 99 999999988876
No 18
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.39 E-value=1.9e-06 Score=69.50 Aligned_cols=81 Identities=16% Similarity=0.110 Sum_probs=70.4
Q ss_pred hHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhCC-C
Q 047665 166 SMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVHC-T 244 (530)
Q Consensus 166 ~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~V-S 244 (530)
.|+.++++.+++ + ..+...|..+++.+....-..+++|..+|+||+|+|++..+...+.++++..+++ +
T Consensus 1 ~~l~~~~~~~~~---~-------~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~ 70 (83)
T smart00385 1 DFLRRVCKALNL---D-------PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFT 70 (83)
T ss_pred CHHHHHHHHcCC---C-------HHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCC
Confidence 378899999987 4 4688899999999877433456999999999999999999988899999999999 9
Q ss_pred HHHHHHHHHHHH
Q 047665 245 VVTCRKRYKELL 256 (530)
Q Consensus 245 ~~TIrkRyKEL~ 256 (530)
..+|.+.+++|.
T Consensus 71 ~~~i~~~~~~il 82 (83)
T smart00385 71 EEEILRMEKLLL 82 (83)
T ss_pred HHHHHHHHHHHh
Confidence 999999998875
No 19
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.35 E-value=4.6e-07 Score=98.19 Aligned_cols=139 Identities=15% Similarity=0.120 Sum_probs=98.1
Q ss_pred HHHHHHHHHHHHhhCCCC-CCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhhhcCCccchh
Q 047665 87 RSIQIKNMIDKITDGEFG-LGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNLKLPEVDIV 165 (530)
Q Consensus 87 i~e~A~~i~k~a~~~~l~-rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~~p~vdp~ 165 (530)
++.+|..+...+. +.|. .||++..+++||||+|||.||+++|+.||+.+..++..+|.+.|.++.+.+..+++..
T Consensus 186 Vv~~a~~L~~rMk-rdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~--- 261 (521)
T KOG1598|consen 186 VAKTATRLAQRMK-RDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLKEFSDTLSGDLTID--- 261 (521)
T ss_pred HHHHHHHHHHHHH-HHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHHHHhccccccccHH---
Confidence 4444444443332 3454 8999999999999999999999999999999999999999999999999887665532
Q ss_pred hHHHHHHHhcccCCC----C---ccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcC
Q 047665 166 SMFERVIRNSRLQGF----T---NLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNG 229 (530)
Q Consensus 166 ~~I~R~~~~L~l~~v----~---~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g 229 (530)
.|-..-...-..|+. + .......++.+......++.+...|..++++|.+.+-++++.+++-..
T Consensus 262 ef~~~d~e~~~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~l~~~~q~~~ 332 (521)
T KOG1598|consen 262 ELAEIDLEYESDPPSFTASPSKEAKYVEDKKKMLSRTMQLVELANETWLVTLRHSLPVITGGLFLAWQDLQ 332 (521)
T ss_pred HHHhhhhhhccCcchhhcccchhhhhhhhhhhhhhhhhhhhhcccchhhhccccCCcccchhhhcccccch
Confidence 222221111111000 0 000112345555666677778888999999999999999999988654
No 20
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.30 E-value=1.1e-05 Score=79.52 Aligned_cols=178 Identities=11% Similarity=0.094 Sum_probs=124.8
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCC-ChHHHHHHh-----------
Q 047665 70 SNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSL-PISEVASVL----------- 137 (530)
Q Consensus 70 a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~-TL~DIA~~~----------- 137 (530)
..+.|..++..|+|...++.+|..+|++.+-++-.++-.+..+|+-|+|+||+.+..|+ -.+-++..+
T Consensus 44 ~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~ 123 (264)
T KOG0794|consen 44 MANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWP 123 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccch
Confidence 45899999999999999999999999999877767888999999999999999999982 222332221
Q ss_pred ---CCCHHHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCch
Q 047665 138 ---NCDVYELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPM 214 (530)
Q Consensus 138 ---~vd~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~ 214 (530)
..+...|...--.+.+.|+-=+-...|..-+..++..++. .+ .++...|..|++..-+..+.-=-.|.
T Consensus 124 e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi--~d-------~~~l~~~W~ivNDSyr~Dl~Ll~PPh 194 (264)
T KOG0794|consen 124 EKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGI--ND-------QKLLQLAWSIVNDSYRMDLCLLYPPH 194 (264)
T ss_pred hhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcc--cc-------hhhhhhhHhhhcchhhcceeeecCHH
Confidence 1122333333334445444222222444446677777776 22 35778899999998887777778999
Q ss_pred hHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 215 PVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 215 sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
-||.||+|+|+...+-..+ +..-....+.-.-+.....+|..
T Consensus 195 ~IalAcl~Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I~~ 236 (264)
T KOG0794|consen 195 QIALACLYIACVIDEKDIP-KAWFAELSVDMEKVKDIVQEILK 236 (264)
T ss_pred HHHHHHHHHHHhhcCCChH-HHHHHHHhccHHHHHHHHHHHHH
Confidence 9999999999998775443 44444566665555555555544
No 21
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.10 E-value=0.00013 Score=76.30 Aligned_cols=179 Identities=13% Similarity=0.124 Sum_probs=135.6
Q ss_pred HHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhh-CCCCCCC--chhHHHHHHHHHHHHhcCC--CCChHHHHHH--hCCC
Q 047665 68 YESNKLIDELTFKLDLTGQRSIQIKNMIDKITD-GEFGLGD--WFPILIGACSYVVMRLDDK--SLPISEVASV--LNCD 140 (530)
Q Consensus 68 ~~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~-~~l~rGR--~~~~vaAAclYiACR~~~~--P~TL~DIA~~--~~vd 140 (530)
..|+.+|-++|+..+....+.=-|.+++.+... ..+.+++ -.+.+++||+.+|.+.+.. |.++.=.+.. .-..
T Consensus 79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~fe 158 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFE 158 (335)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccccc
Confidence 368999999999999999999999999999864 4454554 2789999999999998765 7766655555 3367
Q ss_pred HHHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHH-HHHHHHHhhcccccccCchhHHHH
Q 047665 141 VYELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQG-VLLLNCAVKWFLTTGRRPMPVVVA 219 (530)
Q Consensus 141 ~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A-~~Ll~~a~~~~l~tGR~P~sIAAA 219 (530)
.++|.|+-.-|+..|+=++-.+.|..|+..|+++++. .. .....+.+.+ ..|+..+.+.. ..+-.|..||||
T Consensus 159 aktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~--~~----~~~~~~~~~~s~~ll~~~~d~~-Fl~y~pSviAaa 231 (335)
T KOG0656|consen 159 AKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQ--KD----HNKHLFLKHASLFLLSVITDIK-FLEYPPSVIAAA 231 (335)
T ss_pred HHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCc--cc----chHHHHHHHHHHHHHHHhhhhh-hhcCChHHHHHH
Confidence 9999999999999999888899999999999999987 21 1233445554 44555555544 457889999999
Q ss_pred HHHHHHHHc-CCC--CCHHHHHHHhCCCHHHHHHHHH
Q 047665 220 VLVFVVELN-GVS--VKIENVAKEVHCTVVTCRKRYK 253 (530)
Q Consensus 220 AIYlAa~~~-g~k--~t~~eIA~~~~VS~~TIrkRyK 253 (530)
++..++... +.. ..+..+.....++.-.+++.|.
T Consensus 232 ~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 232 AILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 997777653 332 2245566777888877777776
No 22
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=97.39 E-value=0.0022 Score=56.80 Aligned_cols=92 Identities=14% Similarity=0.170 Sum_probs=74.7
Q ss_pred HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCC-CCChHHHHHHhC--CCHHH
Q 047665 67 IYESNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDK-SLPISEVASVLN--CDVYE 143 (530)
Q Consensus 67 L~~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~-P~TL~DIA~~~~--vd~~~ 143 (530)
.....++|..++..++++..+.-.|..++.+..............+++||+++||+.+.. +.++.++....+ .+..+
T Consensus 31 r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~ 110 (127)
T PF00134_consen 31 RQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKD 110 (127)
T ss_dssp HHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHH
T ss_pred HHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHH
Confidence 345778999999999999999999999999998766666678899999999999999876 788999988874 57888
Q ss_pred HHHHHHHHHHHhhhc
Q 047665 144 LGRMITRVVEFLNLK 158 (530)
Q Consensus 144 Lgr~~k~L~k~L~i~ 158 (530)
|-.+-+.|...|+.+
T Consensus 111 i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 111 ILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHCCCC
Confidence 888888888887754
No 23
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=97.29 E-value=0.0012 Score=60.86 Aligned_cols=81 Identities=11% Similarity=0.141 Sum_probs=62.7
Q ss_pred HHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhh--CCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHH
Q 047665 69 ESNKLIDELTFKLDLTGQRSIQIKNMIDKITD--GEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGR 146 (530)
Q Consensus 69 ~a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~--~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr 146 (530)
-|..+|+.+|++|+|++.+.+.+..+|..+.. -.+.++|-...++.+|+|+.||.++.++|++||-..-.--+..-..
T Consensus 13 la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qpq~~~~ 92 (135)
T PF01857_consen 13 LAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQPQASSH 92 (135)
T ss_dssp HHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTSTT--TH
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhccccccc
Confidence 37789999999999999999999999998753 4567999999999999999999999999999998875544444334
Q ss_pred HHH
Q 047665 147 MIT 149 (530)
Q Consensus 147 ~~k 149 (530)
+|+
T Consensus 93 Vyr 95 (135)
T PF01857_consen 93 VYR 95 (135)
T ss_dssp HHH
T ss_pred ceE
Confidence 444
No 24
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=97.28 E-value=0.0053 Score=63.12 Aligned_cols=139 Identities=9% Similarity=0.079 Sum_probs=91.0
Q ss_pred CCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhC----CCHHHHHHHHHHHHHHhhh
Q 047665 82 DLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLN----CDVYELGRMITRVVEFLNL 157 (530)
Q Consensus 82 gLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~----vd~~~Lgr~~k~L~k~L~i 157 (530)
+||.+|+-+|..+|++++=.+...--.+..|.++|+|+||+.+..-+|+-+|+.-.. -+...+-+.-..+.+.|+.
T Consensus 73 ~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk~E~~llqsL~f 152 (325)
T KOG2496|consen 73 NLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLKYEFLLLQSLKF 152 (325)
T ss_pred CCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHhchHHHHHhhhh
Confidence 699999999999999997555555557889999999999999999999999999877 4455555555566777765
Q ss_pred cCC---ccc-hhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHH
Q 047665 158 KLP---EVD-IVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVV 225 (530)
Q Consensus 158 ~~p---~vd-p~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa 225 (530)
.+. +.. .+.|+.-+-..|.. +.+ .............++.+.-+...-=-.|.-||.|||..|+
T Consensus 153 ~L~vh~PyRPleGFl~D~kt~l~~--~~n---~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~ 219 (325)
T KOG2496|consen 153 SLTVHNPYRPLEGFLLDMKTRLPA--LEN---PDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAA 219 (325)
T ss_pred hheecCCCCchHHHHHHHHHHHHh--ccC---HHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHh
Confidence 532 222 35555544444322 110 1111111222345555544444444689999999994443
No 25
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=97.23 E-value=0.023 Score=55.84 Aligned_cols=205 Identities=12% Similarity=0.004 Sum_probs=133.4
Q ss_pred HHHHHHhhcCCC--HHHHHHHHHHHHHHhhC--CCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHH
Q 047665 73 LIDELTFKLDLT--GQRSIQIKNMIDKITDG--EFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMI 148 (530)
Q Consensus 73 ~I~~i~~~LgLp--~~i~e~A~~i~k~a~~~--~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~ 148 (530)
.|.+++.+|||. +.+.+.|.+|.+...-+ +..-|-.-..-+.-|+=+|.-.-++|.-=...-...|.+.+.-.+.+
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k~~Y~~~~ 81 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLSGLSKKAYSRSF 81 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhccccHHHHHHHH
Confidence 478899999994 35899999988876421 22223233344566777887778888887888888999999999999
Q ss_pred HHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhh-------cccccccCchhHHHHHH
Q 047665 149 TRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVK-------WFLTTGRRPMPVVVAVL 221 (530)
Q Consensus 149 k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~-------~~l~tGR~P~sIAAAAI 221 (530)
+.+...||++.- .-|..+|=.++. .++++-|..++..-+. ......| | -.++||+
T Consensus 82 ~sfe~llgln~~-----~~VrdlaVQfgc-----------~evi~~a~~vl~syk~~lpaT~~~~~D~Sr-P-~ft~aA~ 143 (262)
T KOG4557|consen 82 NSFENLLGLNIK-----LNVRDLAVQFGC-----------VEVIKSAQNVLSSYKERLPATRRANADFSR-P-VFTAAAF 143 (262)
T ss_pred HHHHHHhcchhh-----cCHHHHHHHHhH-----------HHHHHHHHHHHHHHHhcCchhhhcCCcccc-h-HHHHHHH
Confidence 999999997632 124445555554 3455666666555433 1222222 3 4678999
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccC---CCCccCcccccccChhHHHHHhHHHHHhh
Q 047665 222 VFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQAL---PWGKDVTVKNVLKNAPFVMNYMEMKSMEK 295 (530)
Q Consensus 222 YlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~l---pW~~~v~~knl~~~~pdIi~~~e~~~~~~ 295 (530)
|.||+....+++...+-...|++++-...--+.+.....++-++. |-..+-..+-.++...+++.+.+.+-+++
T Consensus 144 ~~ack~lKlKVdK~kli~~sg~~~s~F~~l~kqler~~~qv~~e~~~V~~s~~k~~k~~v~~n~~~~~~~~~k~hkp 220 (262)
T KOG4557|consen 144 YLACKKLKLKVDKLKLIEVSGTSESEFSCLSKQLERNYKQVSTEMDCVGISKEKKDKKDVKGNRDLLDVLPGKRHKP 220 (262)
T ss_pred HHHHHHHHHhhhHhhcccccCCCHHHHHHHHHHHHHHHHHhcCCccccCCChhhhhhhhccCcHHHhhhccccCCCC
Confidence 999999999999999999999998766554444444444444442 22222222333444566666665555544
No 26
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=96.75 E-value=0.015 Score=62.59 Aligned_cols=151 Identities=13% Similarity=0.133 Sum_probs=112.5
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHH-HHHHhcCCC-CChHHHHHHhC--CCHHHHHH
Q 047665 71 NKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSY-VVMRLDDKS-LPISEVASVLN--CDVYELGR 146 (530)
Q Consensus 71 ~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclY-iACR~~~~P-~TL~DIA~~~~--vd~~~Lgr 146 (530)
.+++-++..+++|.....--|..++++.........+....+..+|++ |||+.+... -++.|+..+++ ++..+|.+
T Consensus 162 vdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~ 241 (391)
T KOG0653|consen 162 VDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILR 241 (391)
T ss_pred HHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHH
Confidence 478888999999999999999999999876544666677777777755 999964443 34667766654 68899999
Q ss_pred HHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHH
Q 047665 147 MITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVE 226 (530)
Q Consensus 147 ~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~ 226 (530)
+-+.+...|+..+....|-.|+.|+.+.... . ..+...+..+++...-..-.....|..+|||+.+++.+
T Consensus 242 mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~---d-------~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~ 311 (391)
T KOG0653|consen 242 MEKYILNVLEFDLSVPTPLSFLRRFLKAADY---D-------IKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALR 311 (391)
T ss_pred HHHHHHhccCeeecCCchHHHHHHHHHhhhc---c-------hhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHH
Confidence 9999999998877777889999999776653 1 12233344455554333334567899999999999999
Q ss_pred HcCCC
Q 047665 227 LNGVS 231 (530)
Q Consensus 227 ~~g~k 231 (530)
+.+..
T Consensus 312 ~~~~~ 316 (391)
T KOG0653|consen 312 MLSKG 316 (391)
T ss_pred HhccC
Confidence 87654
No 27
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=96.53 E-value=0.02 Score=49.64 Aligned_cols=91 Identities=14% Similarity=0.121 Sum_probs=67.9
Q ss_pred chhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCC-CCCHHHHHHHh
Q 047665 163 DIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGV-SVKIENVAKEV 241 (530)
Q Consensus 163 dp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~-k~t~~eIA~~~ 241 (530)
.|..|+.++.+..+. ...+...|..|++.+.-..-..+-+|..|||||+|+|....+. ..-...+...+
T Consensus 2 Tp~~Fl~~~~~~~~~----------~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t 71 (118)
T PF02984_consen 2 TPYDFLRRFLKISNA----------DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLT 71 (118)
T ss_dssp -HHHHHHHHHTSSSH----------HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHH
T ss_pred cHHHHHHHHHHHcCC----------cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhc
Confidence 467899998443322 2467788889999876665667889999999999999999874 34455688889
Q ss_pred CCCHHHHHHHHHHHHHHHHhhc
Q 047665 242 HCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 242 ~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
|++...++..++.|.+.+.+..
T Consensus 72 ~~~~~~l~~c~~~i~~~~~~~~ 93 (118)
T PF02984_consen 72 GYDKEDLKECIELIQELLSKAS 93 (118)
T ss_dssp TS-HHHHHHHHHHHHHHHHHCC
T ss_pred CCCHHHHHHHHHHHHHHHHhcC
Confidence 9999999999888888776433
No 28
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=96.41 E-value=0.022 Score=61.96 Aligned_cols=147 Identities=11% Similarity=0.116 Sum_probs=111.0
Q ss_pred HHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCC-CCChHHHHHHhC--CCHHHHHHHH
Q 047665 72 KLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDK-SLPISEVASVLN--CDVYELGRMI 148 (530)
Q Consensus 72 ~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~-P~TL~DIA~~~~--vd~~~Lgr~~ 148 (530)
++|-++-.++++-+.....|..|..++.......=.+...+.+.|++|||+-+.+ +-++++++-++. ++.+.|.++.
T Consensus 218 ~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE 297 (440)
T COG5024 218 DWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAE 297 (440)
T ss_pred HHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHH
Confidence 6788888999988889999999999998776666567899999999999998765 355788887764 6899999999
Q ss_pred HHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHh-hcccccccCchhHHHHHHHHHHHH
Q 047665 149 TRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAV-KWFLTTGRRPMPVVVAVLVFVVEL 227 (530)
Q Consensus 149 k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~-~~~l~tGR~P~sIAAAAIYlAa~~ 227 (530)
+.+...|+.++.-..|..|+.|+-....- +. .....+..+++... ...+...+ |..++|||-|++-.+
T Consensus 298 ~~ml~~l~f~is~P~P~sFLRriSka~dy---d~-------~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~ 366 (440)
T COG5024 298 RYMLEVLDFNISWPSPMSFLRRISKASDY---DI-------FSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKI 366 (440)
T ss_pred HHHhhhcccccCCCChHHHHHHHHhhccc---ch-------hhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhh
Confidence 99999999887777888998887665543 11 11112333333321 12244566 999999999999988
Q ss_pred cC
Q 047665 228 NG 229 (530)
Q Consensus 228 ~g 229 (530)
.+
T Consensus 367 ~~ 368 (440)
T COG5024 367 LS 368 (440)
T ss_pred hc
Confidence 75
No 29
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=96.40 E-value=0.0025 Score=45.71 Aligned_cols=28 Identities=32% Similarity=0.635 Sum_probs=24.2
Q ss_pred CCCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 1 MPCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
|.|+.|++. .+....|..+|..||+|++
T Consensus 9 ~~C~~C~~~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 9 EPCPVCGSR--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred CcCCCCCCe--EeEccCCEEEhhhCceEcC
Confidence 469999997 5677799999999999975
No 30
>PHA00626 hypothetical protein
Probab=95.93 E-value=0.0062 Score=47.56 Aligned_cols=35 Identities=31% Similarity=0.825 Sum_probs=26.6
Q ss_pred CCCCCCCCCCeEEecC----CCcEEcCCCceeecccCcc
Q 047665 1 MPCTSCGSKTLTREDI----SGSLICVSCGVVQAFDNYD 35 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~----~G~~VCt~CG~Vle~~~f~ 35 (530)
|.||.||+.+++.... ...++|.+||.-..-..|.
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeechhhhh
Confidence 8999999987765322 5789999999877655443
No 31
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=95.07 E-value=0.34 Score=43.56 Aligned_cols=49 Identities=10% Similarity=0.116 Sum_probs=37.6
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHHHHHhhhc-CCccchhhHHHHHHHhccc
Q 047665 129 PISEVASVLNCDVYELGRMITRVVEFLNLK-LPEVDIVSMFERVIRNSRL 177 (530)
Q Consensus 129 TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~-~p~vdp~~~I~R~~~~L~l 177 (530)
+++|++..+|++--+++..+.+|.+.|+.. .+..........+.++|.-
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~ 100 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEK 100 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHc
Confidence 689999999999999999999999999983 2333344566667777753
No 32
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=94.64 E-value=0.022 Score=46.08 Aligned_cols=31 Identities=26% Similarity=0.615 Sum_probs=28.7
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.||.||...+++++.+-.+.|..||.++-+.
T Consensus 21 kCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 21 KCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred ECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 6999999999999999999999999999754
No 33
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=94.16 E-value=0.022 Score=44.66 Aligned_cols=30 Identities=27% Similarity=0.494 Sum_probs=23.3
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.|+..++|+++.+-.+.|..||.++-.
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 699999999999999999999999999974
No 34
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=94.12 E-value=0.3 Score=51.11 Aligned_cols=101 Identities=16% Similarity=0.171 Sum_probs=70.3
Q ss_pred HHHHHHHhhcCCCHHH--HHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChH-HHHHHhCCCHHHHHHHH
Q 047665 72 KLIDELTFKLDLTGQR--SIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPIS-EVASVLNCDVYELGRMI 148 (530)
Q Consensus 72 ~~I~~i~~~LgLp~~i--~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~-DIA~~~~vd~~~Lgr~~ 148 (530)
..|-.+...|++|+.. ...+.++......-.+..--.++.||+||+|+|.|..++|++.. .--.+++.+..+|-...
T Consensus 143 klii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic 222 (367)
T KOG0835|consen 143 KLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEIC 222 (367)
T ss_pred HHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHH
Confidence 4566777889999854 77777776666544444444789999999999999999987665 55566888888888777
Q ss_pred HHHHHHhhhcCCccchhhHHHHHHHhc
Q 047665 149 TRVVEFLNLKLPEVDIVSMFERVIRNS 175 (530)
Q Consensus 149 k~L~k~L~i~~p~vdp~~~I~R~~~~L 175 (530)
..+........|. ..+|.-+++.+
T Consensus 223 ~~l~~lY~~~~p~---~~li~~~vd~~ 246 (367)
T KOG0835|consen 223 YRLIPLYKRAKPD---ETLIEAFVDRL 246 (367)
T ss_pred HHHHHHHHhcccC---HHHHHHHHHHh
Confidence 7666665543332 23455554444
No 35
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=94.08 E-value=0.032 Score=44.30 Aligned_cols=30 Identities=27% Similarity=0.614 Sum_probs=28.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
+||.|+...+++++.+-.+.|..||.++..
T Consensus 13 kCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 13 KCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred ECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 699999999999999999999999999874
No 36
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=94.03 E-value=5.3 Score=42.19 Aligned_cols=187 Identities=13% Similarity=0.106 Sum_probs=120.6
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhC--CCCCCCchhHHHHHHHHHHHHhcCC-CCChHHHHHHhC--CCHHHH
Q 047665 70 SNKLIDELTFKLDLTGQRSIQIKNMIDKITDG--EFGLGDWFPILIGACSYVVMRLDDK-SLPISEVASVLN--CDVYEL 144 (530)
Q Consensus 70 a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~--~l~rGR~~~~vaAAclYiACR~~~~-P~TL~DIA~~~~--vd~~~L 144 (530)
.+.++-++|+.-.|.....=-|..+|.+.+.- +. .--....+--+|+|||++.+.+ |--+.|+|.++. ++...|
T Consensus 148 LlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v-~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddI 226 (408)
T KOG0655|consen 148 LLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEV-SKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDI 226 (408)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHh-hhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHH
Confidence 45899999999999888888889999887532 22 2235677888999999998765 788999999975 789999
Q ss_pred HHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCC-----CCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHH
Q 047665 145 GRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQG-----FTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVA 219 (530)
Q Consensus 145 gr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~-----v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAA 219 (530)
..+-.-|.+.|+-.+.++.....+.-|..-..+-. ++.+.+... + +..+|++++.-.-=.---+-..+|||
T Consensus 227 ltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~ef---i-qiaqlLDlc~ldids~~fsYrilaAA 302 (408)
T KOG0655|consen 227 LTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEF---I-QIAQLLDLCILDIDSLEFSYRILAAA 302 (408)
T ss_pred HHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccchHHH---H-HHHHHHHHHHhccccccchHHHHHHH
Confidence 99999999999988888887777777655332200 233333322 1 22345555432211112345566777
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccCCC
Q 047665 220 VLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQALPW 268 (530)
Q Consensus 220 AIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~lpW 268 (530)
|+|.-. +..-+-++.|.--..|.+..+=+.....-+.+.-|.
T Consensus 303 al~h~~-------s~e~v~kaSG~~w~~ie~cv~wm~Pf~rvi~~~~~~ 344 (408)
T KOG0655|consen 303 ALCHFT-------SIEVVKKASGLEWDSIEECVDWMVPFVRVIKSTSPV 344 (408)
T ss_pred HHHHHh-------HHHHHHHcccccHHHHHHHHHHHHHHHHHHhhccch
Confidence 776432 223344556666666777666666654444444333
No 37
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=93.68 E-value=0.044 Score=42.85 Aligned_cols=29 Identities=28% Similarity=0.681 Sum_probs=22.5
Q ss_pred CCCCCCCCCeEEecCCCc-EEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGS-LICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~-~VCt~CG~Vle 30 (530)
.||.||..--+.|...|+ +.|..||.-++
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 799999964344555576 68999999887
No 38
>PRK00420 hypothetical protein; Validated
Probab=93.51 E-value=0.056 Score=48.39 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=23.0
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.||.+-+ ...+|..+|..||.++.-
T Consensus 25 ~CP~Cg~pLf--~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 25 HCPVCGLPLF--ELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCcce--ecCCCceECCCCCCeeee
Confidence 6999998743 337899999999998773
No 39
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=93.07 E-value=0.045 Score=36.28 Aligned_cols=22 Identities=32% Similarity=0.883 Sum_probs=17.6
Q ss_pred CCCCCCCCCCeEEecCCCcEEcCCCce
Q 047665 1 MPCTSCGSKTLTREDISGSLICVSCGV 27 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~~VCt~CG~ 27 (530)
|.||+||... ..+..+|.+||.
T Consensus 3 ~~Cp~Cg~~~-----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEI-----DPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcC-----CcccccChhhCC
Confidence 5899999942 356889999996
No 40
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=93.05 E-value=0.069 Score=50.45 Aligned_cols=29 Identities=28% Similarity=0.633 Sum_probs=21.1
Q ss_pred CCCCCCCCCC-eEEecC---CCc-----EEcCCCceee
Q 047665 1 MPCTSCGSKT-LTREDI---SGS-----LICVSCGVVQ 29 (530)
Q Consensus 1 M~Cp~CG~~~-iv~D~~---~G~-----~VCt~CG~Vl 29 (530)
|.||+||++. -+.|.. .|. .-|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 8999999965 566655 353 4599999743
No 41
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=93.02 E-value=0.56 Score=40.46 Aligned_cols=86 Identities=13% Similarity=0.093 Sum_probs=59.8
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHh-hCCCCCCCchhHHHHHHHHHHHHhcCC-CCChHHHHHHhCCCHHHHHHH
Q 047665 70 SNKLIDELTFKLDLTGQRSIQIKNMIDKIT-DGEFGLGDWFPILIGACSYVVMRLDDK-SLPISEVASVLNCDVYELGRM 147 (530)
Q Consensus 70 a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~-~~~l~rGR~~~~vaAAclYiACR~~~~-P~TL~DIA~~~~vd~~~Lgr~ 147 (530)
.+.+|+.+....+....+...|..+..... +..+ -+-++..+||||+|+|.+..+. +.--..+...++++...|..+
T Consensus 3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~f-l~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c 81 (118)
T PF02984_consen 3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEF-LQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHH-TTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccc-cCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence 345666665444444556667766666543 3333 3446889999999999999765 444456778889999999999
Q ss_pred HHHHHHHhh
Q 047665 148 ITRVVEFLN 156 (530)
Q Consensus 148 ~k~L~k~L~ 156 (530)
++.|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999988776
No 42
>PLN00209 ribosomal protein S27; Provisional
Probab=92.69 E-value=0.082 Score=44.93 Aligned_cols=30 Identities=23% Similarity=0.410 Sum_probs=28.3
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.|+...+|+.+.+..+.|..||.++..
T Consensus 38 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 38 KCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 699999999999999999999999999974
No 43
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=92.58 E-value=0.083 Score=48.44 Aligned_cols=22 Identities=32% Similarity=0.982 Sum_probs=19.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCG 26 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG 26 (530)
.||.||.+-+. .+|.++|..||
T Consensus 30 hCp~Cg~PLF~---KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPLFR---KDGEVFCPVCG 51 (131)
T ss_pred hCcccCCccee---eCCeEECCCCC
Confidence 59999998654 68999999999
No 44
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=92.57 E-value=0.091 Score=44.57 Aligned_cols=30 Identities=17% Similarity=0.403 Sum_probs=28.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.|+..++|+++.+..+.|..||.++-.
T Consensus 37 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 37 KCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 699999999999999999999999999974
No 45
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=92.55 E-value=0.12 Score=36.41 Aligned_cols=28 Identities=21% Similarity=0.676 Sum_probs=22.7
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.|+.||++.++ ....+..+|..||.+..
T Consensus 5 ~C~~C~~~~i~-~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 5 KCSKCGGNGIV-NKEDDYEVCIFCGSSFP 32 (33)
T ss_pred EcCCCCCCeEE-EecCCeEEcccCCcEee
Confidence 59999997655 35689999999998853
No 46
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=91.89 E-value=14 Score=36.66 Aligned_cols=34 Identities=24% Similarity=0.200 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...|+++||+..|+|..+|+++.+.....|-+..
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 5699999999999999999999888777775543
No 47
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=91.20 E-value=0.084 Score=37.45 Aligned_cols=27 Identities=30% Similarity=0.770 Sum_probs=15.0
Q ss_pred CCCCCCCCCeEEecC----CCcEEcCCCceee
Q 047665 2 PCTSCGSKTLTREDI----SGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~----~G~~VCt~CG~Vl 29 (530)
.||.||++. ....- .--.||++||.|.
T Consensus 2 fC~~CG~~l-~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPL-ERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B--EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccChh-hhhcCCCCCccceECCCCCCEE
Confidence 599999962 33322 2348999999986
No 48
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=91.16 E-value=0.2 Score=34.60 Aligned_cols=26 Identities=31% Similarity=0.698 Sum_probs=14.7
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vl 29 (530)
.||.|++.....| ...+||.+||.-+
T Consensus 4 ~Cp~C~se~~y~D--~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYED--GELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE---SSSEEETTTTEEE
T ss_pred CCCCCCCcceecc--CCEEeCCcccccC
Confidence 5999999755544 5679999999754
No 49
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.99 E-value=0.12 Score=33.48 Aligned_cols=22 Identities=27% Similarity=0.818 Sum_probs=17.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~V 28 (530)
.||+||... ..+..+|..||.-
T Consensus 1 ~Cp~CG~~~-----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEI-----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCC-----CCcCcchhhhCCc
Confidence 599999962 2467889999973
No 50
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=90.93 E-value=0.19 Score=36.33 Aligned_cols=27 Identities=33% Similarity=0.898 Sum_probs=20.2
Q ss_pred CCCCCCCC-CCeEEec--CCCcEEcCCCce
Q 047665 1 MPCTSCGS-KTLTRED--ISGSLICVSCGV 27 (530)
Q Consensus 1 M~Cp~CG~-~~iv~D~--~~G~~VCt~CG~ 27 (530)
+.||.||+ ..+-+|. ..|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 36999998 3454555 358999999984
No 51
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=90.92 E-value=0.21 Score=35.54 Aligned_cols=31 Identities=26% Similarity=0.668 Sum_probs=22.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.||.||.--+......+...|..||.+.+-+
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEPIS 33 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE-S
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccCCC
Confidence 5999999655555556666999999987643
No 52
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.24 E-value=0.22 Score=38.36 Aligned_cols=26 Identities=31% Similarity=0.653 Sum_probs=20.7
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vl 29 (530)
.||.||+. +..+ ..+...|..||...
T Consensus 22 fCP~Cg~~-~m~~-~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMAE-HLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hhec-cCCcEECCCcCCEE
Confidence 69999997 5444 45899999999864
No 53
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=90.12 E-value=0.31 Score=41.66 Aligned_cols=34 Identities=26% Similarity=0.533 Sum_probs=28.8
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecccCccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFDNYDA 36 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~~ 36 (530)
.||.||.. .+.-..+|-..|..||.+..-..|.+
T Consensus 37 ~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 37 VCPFCGRT-TVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred cCCCCCCc-ceeeeccCeEEcCCCCCeeccccccc
Confidence 59999998 56777899999999999988666664
No 54
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=89.94 E-value=0.16 Score=36.20 Aligned_cols=29 Identities=24% Similarity=0.549 Sum_probs=20.1
Q ss_pred CCCCCCCCCeEEec----CCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTRED----ISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~----~~G~~VCt~CG~Vle 30 (530)
.||+|+...-+.+. ..+.+.|.+||.++.
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 59999984322221 234799999999874
No 55
>PRK11827 hypothetical protein; Provisional
Probab=89.47 E-value=0.29 Score=39.12 Aligned_cols=28 Identities=25% Similarity=0.430 Sum_probs=23.5
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||.|+++ +..|....+++|..||.+..
T Consensus 10 aCP~ckg~-L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 10 ACPVCNGK-LWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred ECCCCCCc-CeEcCCCCeEECCccCeecc
Confidence 69999885 56777778899999998865
No 56
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=89.26 E-value=0.33 Score=45.39 Aligned_cols=28 Identities=29% Similarity=0.606 Sum_probs=21.3
Q ss_pred CCCCCCCC-CCeEEecC---CCcEE-----cCCCcee
Q 047665 1 MPCTSCGS-KTLTREDI---SGSLI-----CVSCGVV 28 (530)
Q Consensus 1 M~Cp~CG~-~~iv~D~~---~G~~V-----Ct~CG~V 28 (530)
|.||.||+ .+-|.|.. .|..| |.+||.=
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~R 37 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHER 37 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCc
Confidence 99999998 56677763 46554 9999953
No 57
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=89.26 E-value=0.86 Score=33.63 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=23.2
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKELL 256 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL~ 256 (530)
.+-+.|..+||+.+|+|+.|+..|++.|.
T Consensus 14 ~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 14 EDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp H-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 34578899999999999999999999874
No 58
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=88.82 E-value=0.32 Score=36.81 Aligned_cols=30 Identities=23% Similarity=0.702 Sum_probs=21.2
Q ss_pred CCCCCCCCCeEEecCC-CcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDIS-GSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~-G~~VCt~CG~Vle~ 31 (530)
.||.||.-....+... ...+|..||.+..-
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 5999998543333323 37999999988764
No 59
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=88.73 E-value=0.43 Score=38.70 Aligned_cols=18 Identities=39% Similarity=0.715 Sum_probs=15.6
Q ss_pred EecCCCcEEcCCCceeec
Q 047665 13 REDISGSLICVSCGVVQA 30 (530)
Q Consensus 13 ~D~~~G~~VCt~CG~Vle 30 (530)
.+..+|.++|.+||.+..
T Consensus 47 ~~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 47 VEIVEGELICPECGREYP 64 (68)
T ss_dssp EETTTTEEEETTTTEEEE
T ss_pred ccccCCEEEcCCCCCEEe
Confidence 678899999999998753
No 60
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=88.59 E-value=0.41 Score=37.58 Aligned_cols=26 Identities=35% Similarity=0.847 Sum_probs=20.3
Q ss_pred CCCCCCCCCeEEecCCC------c-EEcCCCce
Q 047665 2 PCTSCGSKTLTREDISG------S-LICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G------~-~VCt~CG~ 27 (530)
.||-||+..+..+...+ . +.|.+||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 59999987777766554 2 66999999
No 61
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=88.49 E-value=1.4 Score=35.05 Aligned_cols=71 Identities=15% Similarity=0.116 Sum_probs=45.2
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCC-CHHHHHHHHHHH
Q 047665 74 IDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNC-DVYELGRMITRV 151 (530)
Q Consensus 74 I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~v-d~~~Lgr~~k~L 151 (530)
|.+++..+|++.....+. |+.........-.....+..|+-|+. .+ ++++.|||..+|. +...+.+.|++.
T Consensus 4 ~~~la~~~~~s~~~l~~~---f~~~~~~s~~~~~~~~r~~~a~~~l~---~~-~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 4 LEDLAEALGMSPRHLQRL---FKKETGTTPKQYLRDRRLERARRLLR---DT-DLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHhCCCHHHHHHH---HHHHhCcCHHHHHHHHHHHHHHHHHH---cC-CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 678899999997655444 55443221111111223344444543 22 8999999999999 999998888655
No 62
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=88.22 E-value=23 Score=35.81 Aligned_cols=35 Identities=26% Similarity=0.297 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|+++||+..|+|..||+.+++.....|-+.+.
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 47899999999999999999999988887766554
No 63
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=87.75 E-value=3.3 Score=43.35 Aligned_cols=69 Identities=6% Similarity=0.092 Sum_probs=50.4
Q ss_pred hHHHHHHHhcc--cCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhCC
Q 047665 166 SMFERVIRNSR--LQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVHC 243 (530)
Q Consensus 166 ~~I~R~~~~L~--l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~V 243 (530)
.+|..++..|+ + + ..+...|.-+.++---.+-+.--+|.-|++||+|+|++.-+..+++.+++..+.-
T Consensus 61 ~~i~~~~~~lkp~L---p-------q~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~ 130 (305)
T TIGR00569 61 KRLLDFCSAFKPTM---P-------TSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKE 130 (305)
T ss_pred HHHHHHHHHhcCCC---C-------chHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccC
Confidence 45666777777 5 3 3566777777755333333345689999999999999999988999999887654
Q ss_pred C
Q 047665 244 T 244 (530)
Q Consensus 244 S 244 (530)
+
T Consensus 131 ~ 131 (305)
T TIGR00569 131 T 131 (305)
T ss_pred C
Confidence 4
No 64
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.51 E-value=0.44 Score=35.65 Aligned_cols=28 Identities=21% Similarity=0.636 Sum_probs=22.1
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||+||.. +..|+..+...|..||.-+.
T Consensus 5 ~C~~CG~~-~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 5 KCARCGRE-VELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred ECCCCCCE-EEECCCCCceECCCCCCeEE
Confidence 69999984 56666666899999997554
No 65
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=87.36 E-value=4.4 Score=35.51 Aligned_cols=68 Identities=7% Similarity=0.109 Sum_probs=50.3
Q ss_pred hhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCC-CCCHHHHHHHhC
Q 047665 165 VSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGV-SVKIENVAKEVH 242 (530)
Q Consensus 165 ~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~-k~t~~eIA~~~~ 242 (530)
..++-.++..+++ + ..+.-.|..++++...........+.-+++||+++|+++.+. ..+..+++..++
T Consensus 35 ~~~i~~~~~~~~l---~-------~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~ 103 (127)
T PF00134_consen 35 IDWIIELCQRLKL---S-------PETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISD 103 (127)
T ss_dssp HHHHHHHHHHTT----B-------HHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTT
T ss_pred HHHHHHHHHhccc---c-------hhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHc
Confidence 3566677777776 4 467788888888876555677788999999999999999876 466778887773
No 66
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=87.34 E-value=1.4 Score=38.12 Aligned_cols=35 Identities=26% Similarity=0.562 Sum_probs=28.5
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecccCcccC
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFDNYDAQ 37 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~~~ 37 (530)
.||.||... +.-...|-..|..||.++.-+.|..+
T Consensus 37 ~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~AGGAy~~~ 71 (90)
T PF01780_consen 37 TCPFCGKTS-VKRVATGIWKCKKCGKKFAGGAYTPS 71 (90)
T ss_dssp EESSSSSSE-EEEEETTEEEETTTTEEEE-BSSSSS
T ss_pred cCCCCCCce-eEEeeeEEeecCCCCCEEeCCCcccc
Confidence 599999976 55667899999999999997777653
No 67
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=87.30 E-value=0.54 Score=34.77 Aligned_cols=23 Identities=43% Similarity=1.079 Sum_probs=18.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCG 26 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG 26 (530)
.||.||.+- ....+|..+|..|+
T Consensus 19 ~Cp~C~~PL--~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPL--MRDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCee--EEecCCCEECCCCC
Confidence 599998763 33568999999997
No 68
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=86.13 E-value=0.39 Score=42.84 Aligned_cols=29 Identities=28% Similarity=0.659 Sum_probs=24.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.||+||.. .+|-...-+||..||.++...
T Consensus 11 ~Cp~CG~k--FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAK--FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcch--hccCCCCCccCCCCCCccCcc
Confidence 69999996 577777779999999998855
No 69
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=86.07 E-value=0.5 Score=41.42 Aligned_cols=29 Identities=24% Similarity=0.767 Sum_probs=23.0
Q ss_pred CCCCCCCCCeE---EecC--CCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLT---REDI--SGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv---~D~~--~G~~VCt~CG~Vle 30 (530)
.||.||+..++ .+-. -|.++|.+||+-.+
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 59999997666 5544 37899999999776
No 70
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=85.99 E-value=49 Score=34.82 Aligned_cols=36 Identities=28% Similarity=0.313 Sum_probs=31.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|+++||+..|+|..||+.++..-...|-+.+..
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~ 316 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEALRRLREILQT 316 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 469999999999999999999999888888776654
No 71
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=85.67 E-value=41 Score=34.45 Aligned_cols=39 Identities=26% Similarity=0.181 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccCCC
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQALPW 268 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~lpW 268 (530)
...|+++||+.+|+|+.||+.++..-.+.|-+.+....|
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 469999999999999999999998877777666655333
No 72
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=84.73 E-value=0.82 Score=36.50 Aligned_cols=28 Identities=25% Similarity=0.640 Sum_probs=25.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||.|+++ +..|...++++|..||....
T Consensus 10 aCP~~kg~-L~~~~~~~~L~c~~~~~aYp 37 (60)
T COG2835 10 ACPVCKGP-LVYDEEKQELICPRCKLAYP 37 (60)
T ss_pred eccCcCCc-ceEeccCCEEEecccCceee
Confidence 59999998 78999999999999998765
No 73
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=83.90 E-value=1.1 Score=30.93 Aligned_cols=27 Identities=30% Similarity=0.493 Sum_probs=15.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vl 29 (530)
.|+.||++.... ...-..+|.+||...
T Consensus 5 fC~~CG~~t~~~-~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 5 FCGRCGAPTKPA-PGGWARRCPSCGHEH 31 (32)
T ss_dssp B-TTT--BEEE--SSSS-EEESSSS-EE
T ss_pred ccCcCCccccCC-CCcCEeECCCCcCEe
Confidence 499999975433 344568999999864
No 74
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=83.87 E-value=15 Score=34.09 Aligned_cols=89 Identities=11% Similarity=0.100 Sum_probs=64.8
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhh---CC-C-CCCCchhHHHHHHHHHHHHh-cCCCCChHHHHHHhCCCHHH
Q 047665 70 SNKLIDELTFKLDLTGQRSIQIKNMIDKITD---GE-F-GLGDWFPILIGACSYVVMRL-DDKSLPISEVASVLNCDVYE 143 (530)
Q Consensus 70 a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~---~~-l-~rGR~~~~vaAAclYiACR~-~~~P~TL~DIA~~~~vd~~~ 143 (530)
..+++.++....+++..+.-.|.-++.++.. .. + .......-+..+|+-+|.+- .....+.+..|.+.|++..+
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~e 133 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKE 133 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHH
Confidence 4568888999999999999999988888876 22 1 23345667788888888886 67889999999999999999
Q ss_pred HHHHHHHHHHHhhhc
Q 047665 144 LGRMITRVVEFLNLK 158 (530)
Q Consensus 144 Lgr~~k~L~k~L~i~ 158 (530)
|.+.-+.+...|+.+
T Consensus 134 ln~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 134 LNELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHCCCc
Confidence 999999988887753
No 75
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=83.86 E-value=2.3 Score=49.62 Aligned_cols=87 Identities=15% Similarity=0.248 Sum_probs=71.6
Q ss_pred HHHHH-HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhC--CCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCH
Q 047665 65 KKIYE-SNKLIDELTFKLDLTGQRSIQIKNMIDKITDG--EFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDV 141 (530)
Q Consensus 65 r~L~~-a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~--~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~ 141 (530)
|+.+. |..+|+.+|++|.+++...+....+|...... .+.+.|-...++-+|+|+.||..+..+++.+|.....--+
T Consensus 674 rKvY~LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QP 753 (920)
T KOG1010|consen 674 RKVYHLAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQP 753 (920)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCc
Confidence 34443 67899999999999999999999998866433 4568888999999999999999999999999988876666
Q ss_pred HHHHHHHHHH
Q 047665 142 YELGRMITRV 151 (530)
Q Consensus 142 ~~Lgr~~k~L 151 (530)
.....+|+.+
T Consensus 754 qa~~~vyRsV 763 (920)
T KOG1010|consen 754 QAVSLVYRSV 763 (920)
T ss_pred hhhhhhhhhe
Confidence 6666666654
No 76
>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=83.57 E-value=2.7 Score=31.16 Aligned_cols=29 Identities=17% Similarity=0.221 Sum_probs=24.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+-.+|+.+||+.+|+|..|++.++++|.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34599999999999999999999999876
No 77
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=83.25 E-value=1.2 Score=38.35 Aligned_cols=35 Identities=20% Similarity=0.454 Sum_probs=28.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecccCcccC
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFDNYDAQ 37 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~~~ 37 (530)
.||.||...+ .-...|-..|..||.++.-+.+..+
T Consensus 38 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGAy~~~ 72 (90)
T PTZ00255 38 FCPFCGKHAV-KRQAVGIWRCKGCKKTVAGGAWTLS 72 (90)
T ss_pred cCCCCCCCce-eeeeeEEEEcCCCCCEEeCCccccc
Confidence 6999998764 4456799999999999997777643
No 78
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=83.16 E-value=0.63 Score=31.04 Aligned_cols=23 Identities=26% Similarity=0.744 Sum_probs=18.0
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vl 29 (530)
.||+|+..- ......|..||.+.
T Consensus 2 ~CP~C~~~V-----~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEV-----PESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCc-----hhhcCcCCCCCCCC
Confidence 699999852 34677999999875
No 79
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=83.10 E-value=1.1 Score=34.65 Aligned_cols=31 Identities=29% Similarity=0.752 Sum_probs=20.9
Q ss_pred CCCCCCCCCCe-EE---ecC--CCcEEcCCCceeecc
Q 047665 1 MPCTSCGSKTL-TR---EDI--SGSLICVSCGVVQAF 31 (530)
Q Consensus 1 M~Cp~CG~~~i-v~---D~~--~G~~VCt~CG~Vle~ 31 (530)
..||.||+... +. +.. .|...|..||.....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 36999999654 32 322 244579999998764
No 80
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=82.80 E-value=0.93 Score=36.42 Aligned_cols=28 Identities=21% Similarity=0.647 Sum_probs=20.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||.||..... .......+|..||...+
T Consensus 30 ~C~~CG~~~~~-~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 30 TCPRCGHRNKK-RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccccccc-ccccceEEcCCCCCEEC
Confidence 69999985322 34456789999999865
No 81
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.64 E-value=0.73 Score=36.69 Aligned_cols=25 Identities=32% Similarity=0.818 Sum_probs=11.7
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCce
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~ 27 (530)
.|.+||.. |-.+...-...|.+||-
T Consensus 11 ~CtSCg~~-i~p~e~~v~F~CPnCGe 35 (61)
T COG2888 11 VCTSCGRE-IAPGETAVKFPCPNCGE 35 (61)
T ss_pred eeccCCCE-eccCCceeEeeCCCCCc
Confidence 46666653 11222223456666663
No 82
>PF13730 HTH_36: Helix-turn-helix domain
Probab=82.27 E-value=3.3 Score=31.41 Aligned_cols=26 Identities=31% Similarity=0.328 Sum_probs=24.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 232 VKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.|++.||+.+|+|..||++.+++|.+
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 48999999999999999999999876
No 83
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=81.93 E-value=1.1 Score=39.94 Aligned_cols=29 Identities=31% Similarity=0.594 Sum_probs=22.5
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.||.|++.-...| ...+||.+||.-....
T Consensus 4 ~CP~C~seytY~d--g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHD--GTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEec--CCeeECcccccccccc
Confidence 5999999765554 4469999999987644
No 84
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=81.90 E-value=4 Score=30.56 Aligned_cols=31 Identities=23% Similarity=0.282 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
....|+.+||+..|+|..|++++.+...+.|
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 5679999999999999999999998877665
No 85
>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=81.70 E-value=3.7 Score=32.56 Aligned_cols=37 Identities=22% Similarity=0.299 Sum_probs=29.7
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 220 VLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 220 AIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+||.... .+..++..+||+.++||++|+..-++.|.+
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 4566555 567899999999999999999998888765
No 86
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=81.69 E-value=1.2 Score=32.75 Aligned_cols=27 Identities=41% Similarity=0.903 Sum_probs=14.9
Q ss_pred CCCCCCCC-CeE-Eec--CCCcEEcCCCcee
Q 047665 2 PCTSCGSK-TLT-RED--ISGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~-~iv-~D~--~~G~~VCt~CG~V 28 (530)
.||.||+. .+- ++. ..|..+|..|+-+
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~ 35 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQCGGD 35 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred CCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence 59999984 333 544 3589999999433
No 87
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=81.51 E-value=4.9 Score=31.32 Aligned_cols=30 Identities=17% Similarity=0.309 Sum_probs=26.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
.+|+.++|+..|||.+|+..+++.-...+.
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 488999999999999999999988776654
No 88
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=81.46 E-value=2.4 Score=40.01 Aligned_cols=31 Identities=16% Similarity=0.240 Sum_probs=27.8
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
.+-+.|..+||+.+|+|++|+++|++.|.+.
T Consensus 25 ~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 25 KDGRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3457889999999999999999999999884
No 89
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=81.28 E-value=0.85 Score=41.69 Aligned_cols=29 Identities=17% Similarity=0.118 Sum_probs=24.7
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.||+||.. .+|-..--+||..||.++...
T Consensus 11 ~Cp~cg~k--FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSK--FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCcc--ccccCCCCccCCCcCCccCcc
Confidence 59999986 578778889999999998754
No 90
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=81.13 E-value=0.93 Score=37.99 Aligned_cols=29 Identities=17% Similarity=0.465 Sum_probs=26.9
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
+||.|-..+.++.+.+..++|.+|++|+=
T Consensus 36 kC~gc~~iT~vfSHaqtvVvc~~c~~il~ 64 (84)
T KOG1779|consen 36 KCPGCFKITTVFSHAQTVVVCEGCSTILC 64 (84)
T ss_pred EcCCceEEEEEeecCceEEEcCCCceEEE
Confidence 69999998889999999999999999975
No 91
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=80.74 E-value=4.2 Score=42.94 Aligned_cols=87 Identities=13% Similarity=0.149 Sum_probs=59.0
Q ss_pred hhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhC--
Q 047665 165 VSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVH-- 242 (530)
Q Consensus 165 ~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~-- 242 (530)
..||..+..+|+.+.. ....|.-+..+.--......-.|..+|+||+|||++..+..+..++|..++.
T Consensus 43 ~~fI~elg~~L~~~~~----------ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~ 112 (323)
T KOG0834|consen 43 AKFIQELGVRLKMPQK----------TIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRY 112 (323)
T ss_pred HHHHHHHHHHcCCCcc----------chhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHH
Confidence 3567777777776221 1233444444433333446677899999999999999999999999987753
Q ss_pred --CCHHHHHHHHHHHHHHHHh
Q 047665 243 --CTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 243 --VS~~TIrkRyKEL~e~L~~ 261 (530)
....+...+|.++++.+..
T Consensus 113 ~~~~~~~~~~~~~~~~~~Iv~ 133 (323)
T KOG0834|consen 113 LNPKDLELEEVYWELKERIVQ 133 (323)
T ss_pred cCcccccHHHHHHHHHHHHHH
Confidence 2224677888888876643
No 92
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=80.69 E-value=18 Score=33.52 Aligned_cols=81 Identities=9% Similarity=0.128 Sum_probs=52.3
Q ss_pred cCCccchhhHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhh-----cccccccCchhHHHHHHHHHHHHcC-CC
Q 047665 158 KLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVK-----WFLTTGRRPMPVVVAVLVFVVELNG-VS 231 (530)
Q Consensus 158 ~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~-----~~l~tGR~P~sIAAAAIYlAa~~~g-~k 231 (530)
.+|.++...|+.|+.+.... + ..+.-.|.-.+++... .......++.-+..+|+.+|++..+ ..
T Consensus 48 ~~p~i~i~~fl~ri~~~~~~---s-------~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~ 117 (149)
T PF08613_consen 48 SVPSISIRDFLSRILKYTQC---S-------PECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNT 117 (149)
T ss_dssp S--SS-HHHHHHHHHHHTT------------HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS-
T ss_pred CCCCCcHHHHHHHHHHHcCC---C-------hHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhccccc
Confidence 35788889999999988775 3 3455556666666655 1224566777899999999999976 56
Q ss_pred CCHHHHHHHhCCCHHHH
Q 047665 232 VKIENVAKEVHCTVVTC 248 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TI 248 (530)
.+.+.+|++.|++..-+
T Consensus 118 ~~n~~~a~v~gis~~el 134 (149)
T PF08613_consen 118 YSNKSWAKVGGISLKEL 134 (149)
T ss_dssp --HHHHHHHHTS-HHHH
T ss_pred ccHHHHHhhcCCCHHHH
Confidence 88999999999975433
No 93
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=80.59 E-value=1.7 Score=37.64 Aligned_cols=35 Identities=31% Similarity=0.614 Sum_probs=28.7
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecccCcccC
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFDNYDAQ 37 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~~~ 37 (530)
.||.||... +.-...|-..|..||.++.-+.+..+
T Consensus 37 ~CpfCgk~~-vkR~a~GIW~C~~C~~~~AGGAy~p~ 71 (91)
T TIGR00280 37 VCPFCGKKT-VKRGSTGIWTCRKCGAKFAGGAYTPV 71 (91)
T ss_pred cCCCCCCCc-eEEEeeEEEEcCCCCCEEeCCccccc
Confidence 699999876 45557899999999999997777653
No 94
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=80.53 E-value=4.6 Score=40.18 Aligned_cols=83 Identities=8% Similarity=0.075 Sum_probs=60.9
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHhhC-----CCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHH
Q 047665 73 LIDELTFKLDLTGQRSIQIKNMIDKITDG-----EFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRM 147 (530)
Q Consensus 73 ~I~~i~~~LgLp~~i~e~A~~i~k~a~~~-----~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~ 147 (530)
-|+++|-++|.-. ++..|..+.+.+.+. ...---+.+...+|++|.|||..+.-+.-.-+....|+++.++...
T Consensus 95 ~VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~sg~~~s~F~~l 173 (262)
T KOG4557|consen 95 NVRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVSGTSESEFSCL 173 (262)
T ss_pred CHHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccccCCCHHHHHHH
Confidence 4778888888776 677788877776542 1111236678999999999999988877777778889998887776
Q ss_pred HHHHHHHhh
Q 047665 148 ITRVVEFLN 156 (530)
Q Consensus 148 ~k~L~k~L~ 156 (530)
.+.+.+...
T Consensus 174 ~kqler~~~ 182 (262)
T KOG4557|consen 174 SKQLERNYK 182 (262)
T ss_pred HHHHHHHHH
Confidence 666665543
No 95
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=80.50 E-value=0.99 Score=34.67 Aligned_cols=26 Identities=23% Similarity=0.653 Sum_probs=20.8
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~V 28 (530)
.||.||...+-.|+.. -+.|.-||..
T Consensus 21 ~CPrCG~gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGPGVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred cCCCCCCcchhhhcCc-eeEeccccce
Confidence 5999998776666544 8999999975
No 96
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=80.41 E-value=32 Score=33.58 Aligned_cols=44 Identities=18% Similarity=0.382 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHHHHhcCCC-CChHHHHHHhCCCHHHHHHHHHHHHHHhh
Q 047665 109 FPILIGACSYVVMRLDDKS-LPISEVASVLNCDVYELGRMITRVVEFLN 156 (530)
Q Consensus 109 ~~~vaAAclYiACR~~~~P-~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~ 156 (530)
...++=|++|+ .+-| +|+.+|+.+++++..++..+...|.+.+.
T Consensus 5 ~~~~iEA~LF~----sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~ 49 (188)
T PRK00135 5 YKSIIEALLFV----SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYE 49 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 45677888887 4667 99999999999999889888888888775
No 97
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=80.24 E-value=1.9 Score=32.25 Aligned_cols=26 Identities=31% Similarity=0.662 Sum_probs=20.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCce
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~ 27 (530)
.||.||+.....-...+..-|.+|+.
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 69999997655555568999999984
No 98
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=79.86 E-value=1.4 Score=32.16 Aligned_cols=27 Identities=30% Similarity=0.687 Sum_probs=18.7
Q ss_pred CCCCCCCCCeEEe------cCCC---cEEcCCCcee
Q 047665 2 PCTSCGSKTLTRE------DISG---SLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D------~~~G---~~VCt~CG~V 28 (530)
.||.||+...++= .++| .++|.+||..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 6999998655531 1223 6899999975
No 99
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=79.81 E-value=1e+02 Score=33.90 Aligned_cols=172 Identities=11% Similarity=0.082 Sum_probs=87.7
Q ss_pred HHHHHHHHhhcC-----CCHHHHHHHHHHHHHHhhCCCCCCCchhHHHH-----H-HHHHH-------------------
Q 047665 71 NKLIDELTFKLD-----LTGQRSIQIKNMIDKITDGEFGLGDWFPILIG-----A-CSYVV------------------- 120 (530)
Q Consensus 71 ~~~I~~i~~~Lg-----Lp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaA-----A-clYiA------------------- 120 (530)
...+-.+|.++. +.+-+.+....+++.+..-.-.+|-++...+- + .-+++
T Consensus 185 lrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~l 264 (415)
T PRK07598 185 LRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKI 264 (415)
T ss_pred HHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHH
Confidence 356666666542 33446666667777776544456665555443 1 12221
Q ss_pred ---H----HhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhhhcCCccc--hhhHHHHHHHhcccCCCCccchHHHHHH
Q 047665 121 ---M----RLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNLKLPEVD--IVSMFERVIRNSRLQGFTNLDESMLDRM 191 (530)
Q Consensus 121 ---C----R~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~~p~vd--p~~~I~R~~~~L~l~~v~~v~~e~~~~V 191 (530)
- ...|.+-|..|||..+++++..+..+.......+.++.|.-+ ...+... +.....++ + +.+
T Consensus 265 rk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~----l~~~~~~p---e--e~~ 335 (415)
T PRK07598 265 KKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDL----LETDDISP---E--EML 335 (415)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCccccHHHh----ccCCCCCH---H--HHH
Confidence 0 113456788999999999999998887765544444433211 1112211 11100010 1 111
Q ss_pred H--HHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 192 R--KQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELN-GVSVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 192 ~--~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~-g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
. .....|.+.+.. | +|.- --+|.+---+. +...|+++||+..|+|..|||++...-...|
T Consensus 336 ~~~~l~~~L~~~L~~--L----~~re--R~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KL 398 (415)
T PRK07598 336 MRESLQRDLQHLLAD--L----TSRE--RDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKL 398 (415)
T ss_pred HHHHHHHHHHHHHHh--C----CHHH--HHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 1 111122222221 1 1111 11121111112 2569999999999999999999876644444
No 100
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=79.66 E-value=3.2 Score=38.64 Aligned_cols=31 Identities=16% Similarity=0.175 Sum_probs=27.6
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
.+-+.|..+||+.+|+|++|++.|++.|.+.
T Consensus 20 ~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 20 ENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3457889999999999999999999999884
No 101
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=79.43 E-value=0.85 Score=45.00 Aligned_cols=30 Identities=37% Similarity=0.777 Sum_probs=25.1
Q ss_pred CCCCCCCCC--CeEEecCCCc---EEcCCCceeec
Q 047665 1 MPCTSCGSK--TLTREDISGS---LICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~~--~iv~D~~~G~---~VCt~CG~Vle 30 (530)
|+|-+||.+ ++..++..|. ..|.+||.|.|
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaD 35 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVAD 35 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCccc
Confidence 899999985 4667777774 59999999998
No 102
>PRK10220 hypothetical protein; Provisional
Probab=79.18 E-value=1.4 Score=39.19 Aligned_cols=28 Identities=25% Similarity=0.530 Sum_probs=21.5
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.|++.-...| ...+||..||.-...
T Consensus 5 ~CP~C~seytY~d--~~~~vCpeC~hEW~~ 32 (111)
T PRK10220 5 HCPKCNSEYTYED--NGMYICPECAHEWND 32 (111)
T ss_pred cCCCCCCcceEcC--CCeEECCcccCcCCc
Confidence 5999999755554 456999999987653
No 103
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=78.88 E-value=2 Score=37.12 Aligned_cols=35 Identities=26% Similarity=0.543 Sum_probs=28.5
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecccCcccC
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFDNYDAQ 37 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~~~ 37 (530)
.||.||...+ .-...|-.-|..||.++.-+.+..+
T Consensus 38 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGAy~~~ 72 (90)
T PRK03976 38 VCPVCGRPKV-KRVGTGIWECRKCGAKFAGGAYTPE 72 (90)
T ss_pred cCCCCCCCce-EEEEEEEEEcCCCCCEEeCCccccc
Confidence 6999998764 4457899999999999997777654
No 104
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=78.84 E-value=77 Score=32.00 Aligned_cols=35 Identities=9% Similarity=0.044 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|+++||+..|+|..||+.++......|-+.+.
T Consensus 220 e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 254 (257)
T PRK05911 220 EELVLKEIGKILGVSESRVSQIHSKALLKLRATLS 254 (257)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999887777766544
No 105
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=78.63 E-value=1.4 Score=38.66 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=22.0
Q ss_pred CCCCCCCCCe--EEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTL--TREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~i--v~D~~~G~~VCt~CG~Vle 30 (530)
.||+||+..+ -.|...+.++|..||+--+
T Consensus 23 ~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 23 ECPRCGKVSISVKIKKNIAIITCGNCGLYTE 53 (99)
T ss_pred ECCCCCCeEeeeecCCCcceEECCCCCCccC
Confidence 5999997433 3455567899999999866
No 106
>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=78.42 E-value=5 Score=30.41 Aligned_cols=31 Identities=26% Similarity=0.225 Sum_probs=26.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
+..+|..++|+.++||..||++-+++|.+..
T Consensus 13 ~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 13 KEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3459999999999999999999999998766
No 107
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=77.96 E-value=1.4 Score=38.38 Aligned_cols=28 Identities=32% Similarity=0.667 Sum_probs=21.9
Q ss_pred CCCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 1 MPCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
+.||.||..- .+..+.++|..||.+...
T Consensus 1 ~fC~~Cg~~l---~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 1 KFCPKCGSLM---TPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCCcccCccc---ccCCCeEECcCCCCcccc
Confidence 5799999853 234689999999998663
No 108
>PRK12495 hypothetical protein; Provisional
Probab=77.96 E-value=2 Score=42.78 Aligned_cols=28 Identities=25% Similarity=0.611 Sum_probs=23.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.|+.||.+-+ ...|..+|..|+.++..+
T Consensus 44 hC~~CG~PIp---a~pG~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 44 HCDECGDPIF---RHDGQEFCPTCQQPVTED 71 (226)
T ss_pred hcccccCccc---CCCCeeECCCCCCccccc
Confidence 5999999854 348999999999998853
No 109
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=77.67 E-value=4.1 Score=30.07 Aligned_cols=29 Identities=10% Similarity=0.259 Sum_probs=25.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
..+..+||+.+++|..|++.+++.+.+.+
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 36899999999999999999999887655
No 110
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=77.54 E-value=2.9 Score=29.31 Aligned_cols=28 Identities=11% Similarity=0.240 Sum_probs=22.6
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 126 KSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 126 ~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
+|.|-.|||+.+|+....++|+++++.+
T Consensus 1 l~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 1 LPMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp EE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 3678899999999999999999998875
No 111
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=77.07 E-value=3 Score=37.54 Aligned_cols=31 Identities=23% Similarity=0.327 Sum_probs=27.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
+=+++++++..|||-+|+|+|+.+|.+.+..
T Consensus 49 rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 49 RGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 3478999999999999999999999988876
No 112
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=76.92 E-value=1.4 Score=31.56 Aligned_cols=29 Identities=24% Similarity=0.574 Sum_probs=20.8
Q ss_pred CCCCCCCCCeEEec----CCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTRED----ISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~----~~G~~VCt~CG~Vle 30 (530)
.||+|+..--+.|. ..+.+-|..||.+..
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 69999985333333 356789999999863
No 113
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=76.85 E-value=1e+02 Score=32.32 Aligned_cols=32 Identities=16% Similarity=0.253 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+++||+..|+|..+||.+.+.-...|-+
T Consensus 275 ~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 275 QPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999987765555544
No 114
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=76.78 E-value=6.7 Score=38.89 Aligned_cols=48 Identities=10% Similarity=-0.105 Sum_probs=24.4
Q ss_pred HHHHHHhhcCCCH-HHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHH
Q 047665 73 LIDELTFKLDLTG-QRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVV 120 (530)
Q Consensus 73 ~I~~i~~~LgLp~-~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiA 120 (530)
.|...-....++. -..++|...|+.|.--.-..+.+...+|..|+=+|
T Consensus 77 ~i~~~~~~~~~~~~Rt~~~ai~~YkLAll~~~~~~~~~s~~A~l~LrlA 125 (214)
T PF09986_consen 77 NISSRWKPRDFSGERTLEEAIESYKLALLCAQIKKEKPSKKAGLCLRLA 125 (214)
T ss_pred HHHhhcccCCCCCCCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3333333334444 25667777777775322223434445566565555
No 115
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=76.06 E-value=1.9 Score=40.61 Aligned_cols=28 Identities=32% Similarity=0.719 Sum_probs=20.3
Q ss_pred CCCCCCCC-CCeEEecCC---Cc-----EEcCCCcee
Q 047665 1 MPCTSCGS-KTLTREDIS---GS-----LICVSCGVV 28 (530)
Q Consensus 1 M~Cp~CG~-~~iv~D~~~---G~-----~VCt~CG~V 28 (530)
|.||.|++ .+-|.|+.. |. -.|.+||.=
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~R 37 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGER 37 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccc
Confidence 99999998 455667553 43 369999864
No 116
>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=75.89 E-value=5.6 Score=36.24 Aligned_cols=47 Identities=4% Similarity=0.071 Sum_probs=39.6
Q ss_pred chhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 108 WFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 108 ~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
+.++-+.+++|+|-+..+-|+|..+||+.++++...+.+.+..|.+.
T Consensus 6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 6 KGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34566788999997766678999999999999999999888888773
No 117
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=75.79 E-value=0.82 Score=44.58 Aligned_cols=29 Identities=34% Similarity=0.825 Sum_probs=19.3
Q ss_pred CCCCCCCCCCe----EEecCCC--cEEcCCCceeec
Q 047665 1 MPCTSCGSKTL----TREDISG--SLICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~~~i----v~D~~~G--~~VCt~CG~Vle 30 (530)
|.||.||...+ +.. ..+ .+-|.+||+|..
T Consensus 7 ~~Cp~Cg~eev~hEVik~-~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 7 IECPSCGSEEVSHEVIKE-RGREPLVRCEECGTVHP 41 (201)
T ss_pred EECCCCCcchhhHHHHHh-cCCceEEEccCCCcEee
Confidence 46999995333 221 122 478999999994
No 118
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=75.62 E-value=1.5e+02 Score=33.54 Aligned_cols=32 Identities=13% Similarity=0.100 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+.+||+..|||...||+.-+.....|-.
T Consensus 466 e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~ 497 (509)
T PRK05901 466 QPKTLDEIGQVYGVTRERIRQIESKTLRKLRH 497 (509)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46999999999999999999877766665544
No 119
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.
Probab=74.97 E-value=0.95 Score=48.31 Aligned_cols=84 Identities=8% Similarity=-0.050 Sum_probs=0.0
Q ss_pred HHHhhcC--CCHHHHHHHHHHHHHHh-hCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHH
Q 047665 76 ELTFKLD--LTGQRSIQIKNMIDKIT-DGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVV 152 (530)
Q Consensus 76 ~i~~~Lg--Lp~~i~e~A~~i~k~a~-~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~ 152 (530)
+|+-.++ +|..++..|..+|+... .....++..-.+-+.+|+|+||...+.++-+.......+++++...+.|..|.
T Consensus 3 ~l~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~ 82 (353)
T PF05460_consen 3 DLIPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFE 82 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhhhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHH
Confidence 3444444 45679999999999887 33444555556778899999999999999888888889999999999999888
Q ss_pred HHhhhcC
Q 047665 153 EFLNLKL 159 (530)
Q Consensus 153 k~L~i~~ 159 (530)
+.|+...
T Consensus 83 ~~L~~~s 89 (353)
T PF05460_consen 83 NLLGNSS 89 (353)
T ss_dssp -------
T ss_pred HHHhCCC
Confidence 8888654
No 120
>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=74.70 E-value=5.2 Score=33.32 Aligned_cols=46 Identities=15% Similarity=0.185 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 109 FPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 109 ~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
.+..+-+.+|+|-...+.|.|..|||+.++++...+.+.+..|.+.
T Consensus 7 ~~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 7 TDYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 3455667788887777778999999999999999999999988874
No 121
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=74.56 E-value=5 Score=36.67 Aligned_cols=30 Identities=23% Similarity=0.243 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
+-+.|+.+||+.+|+|++|+++|++.|.+.
T Consensus 20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 20 DARISNAELAERVGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 346899999999999999999999999883
No 122
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=73.79 E-value=2.1 Score=33.88 Aligned_cols=20 Identities=40% Similarity=1.057 Sum_probs=15.0
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCce
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~ 27 (530)
.||+||+..+- -.+|.+||+
T Consensus 29 ~C~~CG~~~~~------H~vC~~CG~ 48 (57)
T PRK12286 29 ECPNCGEPKLP------HRVCPSCGY 48 (57)
T ss_pred ECCCCCCccCC------eEECCCCCc
Confidence 59999986433 359999995
No 123
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=73.73 E-value=7.4 Score=29.80 Aligned_cols=36 Identities=14% Similarity=0.261 Sum_probs=31.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
-...+..++|...|||++|+.+.++++.+.+....+
T Consensus 17 R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 17 RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 356899999999999999999999999998876553
No 124
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=73.73 E-value=2.4 Score=33.81 Aligned_cols=25 Identities=36% Similarity=0.817 Sum_probs=15.0
Q ss_pred CCCCCCCCCeEEecC-CCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDI-SGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~-~G~~VCt~CG~V 28 (530)
.|.+||.. +...+ .-...|.+||.+
T Consensus 9 ~CtSCg~~--i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 9 KCTSCGIE--IAPREKAVKFLCPNCGEV 34 (59)
T ss_pred cccCCCCc--ccCCCccCEeeCCCCCCe
Confidence 47777764 22223 334678888877
No 125
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=73.28 E-value=3.2 Score=34.41 Aligned_cols=30 Identities=17% Similarity=0.365 Sum_probs=22.7
Q ss_pred CCCCCCCCCCeEEecCC---C----cEEcC--CCceeec
Q 047665 1 MPCTSCGSKTLTREDIS---G----SLICV--SCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~---G----~~VCt--~CG~Vle 30 (530)
|.||.||+...+.+... + -..|+ +||...-
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 79999999877777653 2 34788 9998755
No 126
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=73.08 E-value=1.4e+02 Score=32.04 Aligned_cols=32 Identities=22% Similarity=0.142 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+++||+..|||...||...+.-...|-.
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~ 355 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 355 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence 56999999999999999999887665555543
No 127
>PRK05949 RNA polymerase sigma factor; Validated
Probab=72.62 E-value=1.3e+02 Score=31.68 Aligned_cols=32 Identities=13% Similarity=0.197 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+++||+..|+|..+||.+...-...|-+
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~ 316 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56999999999999999999987765555544
No 128
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=72.57 E-value=4.2 Score=30.64 Aligned_cols=21 Identities=19% Similarity=0.328 Sum_probs=18.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKRYK 253 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkRyK 253 (530)
|++|||+.+|||..|+.+.+.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 689999999999999988765
No 129
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=72.40 E-value=6 Score=29.24 Aligned_cols=28 Identities=21% Similarity=0.246 Sum_probs=18.2
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 047665 226 ELNGVSVKIENVAKEVHCTVVTCRKRYK 253 (530)
Q Consensus 226 ~~~g~k~t~~eIA~~~~VS~~TIrkRyK 253 (530)
.+.....|+.+||+.+|++.+||.+-++
T Consensus 15 ~l~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 15 ALLEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 3455679999999999999999976543
No 130
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=72.33 E-value=1.1e+02 Score=30.81 Aligned_cols=33 Identities=9% Similarity=0.050 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|+++||..+|+|+.||++++......|-+.
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999998876655555443
No 131
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=71.87 E-value=6 Score=29.35 Aligned_cols=27 Identities=22% Similarity=0.215 Sum_probs=18.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
..|..+||+.+|||..|+.+-++.+.+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 688999999999999999988776543
No 132
>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=71.71 E-value=9 Score=30.70 Aligned_cols=28 Identities=18% Similarity=0.234 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.++|+.+||..+|+|..|+.+-+++|.+
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999888876
No 133
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=71.39 E-value=5 Score=31.28 Aligned_cols=28 Identities=21% Similarity=0.327 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
-.++.+++|+.++||+.|||+-+.+|.+
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~~L~~ 40 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLNKLEK 40 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4689999999999999999999888766
No 134
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=71.28 E-value=7.2 Score=28.86 Aligned_cols=29 Identities=10% Similarity=0.205 Sum_probs=25.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
..+.++||+..++|+.|++.+++.+.+.+
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 46999999999999999999999876644
No 135
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=71.17 E-value=9.1 Score=30.68 Aligned_cols=38 Identities=18% Similarity=0.195 Sum_probs=29.0
Q ss_pred cCchhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHH
Q 047665 211 RRPMPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKR 251 (530)
Q Consensus 211 R~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkR 251 (530)
|+|.-=-|=-+|+. ++-.+++++||+.+||++.|||+.
T Consensus 5 Rsp~rdkA~e~y~~---~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 5 RSPNRDKAFEIYKE---SNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCcCHHHHHHHHHH---hCCCccHHHHHHHHCCCHHHHHHH
Confidence 55555555556643 556899999999999999999973
No 136
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=70.92 E-value=6.6 Score=28.38 Aligned_cols=28 Identities=18% Similarity=0.198 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
++.++.++|+.++++.+|+++.++.|.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5689999999999999999998888876
No 137
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=70.68 E-value=1.2e+02 Score=30.40 Aligned_cols=33 Identities=18% Similarity=0.128 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|+++||+..|+|..||+.+.+...+.|-+.
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~ 256 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 256 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 458999999999999999999988777766543
No 138
>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=70.66 E-value=26 Score=30.08 Aligned_cols=29 Identities=14% Similarity=0.027 Sum_probs=25.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
...+|+.+||+.+|++..|+.+.+++|.+
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45799999999999999999998888776
No 139
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=70.56 E-value=10 Score=27.99 Aligned_cols=42 Identities=17% Similarity=0.159 Sum_probs=30.1
Q ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 218 VAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 218 AAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
-||+-+..+.--...|..+||+.+|++.+++-..+....+.+
T Consensus 3 ~aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~ 44 (47)
T PF00440_consen 3 EAALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPSKDDLL 44 (47)
T ss_dssp HHHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSHHHHH
T ss_pred HHHHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCCHHHHH
Confidence 345555544333579999999999999999988776554433
No 140
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=70.46 E-value=7.1 Score=29.45 Aligned_cols=29 Identities=10% Similarity=0.184 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
...|..|||+..|+|+.|+++++..-.+.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 46899999999999999999998766554
No 141
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=70.20 E-value=3.6 Score=30.83 Aligned_cols=27 Identities=22% Similarity=0.553 Sum_probs=19.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.|.+||... ..+ ..+.+-|.+||.=+-
T Consensus 4 ~C~~Cg~~~-~~~-~~~~irC~~CG~rIl 30 (44)
T smart00659 4 ICGECGREN-EIK-SKDVVRCRECGYRIL 30 (44)
T ss_pred ECCCCCCEe-ecC-CCCceECCCCCceEE
Confidence 599999852 222 467899999997543
No 142
>PRK05978 hypothetical protein; Provisional
Probab=70.20 E-value=2.4 Score=39.90 Aligned_cols=30 Identities=27% Similarity=0.509 Sum_probs=21.9
Q ss_pred CCCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 1 MPCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
++||+||...+-.-+-.=..-|..||.-.+
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccc
Confidence 479999997764433334568999998766
No 143
>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=70.13 E-value=15 Score=28.47 Aligned_cols=29 Identities=24% Similarity=0.249 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
..+|+.+||+.+|+|..|+.+.++.|.+.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56899999999999999999988888773
No 144
>PRK04217 hypothetical protein; Provisional
Probab=69.89 E-value=8.9 Score=34.33 Aligned_cols=36 Identities=8% Similarity=0.064 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|+++||+.+|+|..||+++++...+.|...+..
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~ 92 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVE 92 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 456999999999999999999999988888766654
No 145
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=69.80 E-value=9.3 Score=28.56 Aligned_cols=23 Identities=22% Similarity=0.384 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 047665 232 VKIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyKE 254 (530)
.|+++||+..|+|..|+++.++.
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 89999999999999999988765
No 146
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=69.75 E-value=4.4 Score=32.82 Aligned_cols=31 Identities=32% Similarity=0.764 Sum_probs=23.0
Q ss_pred CCCCCCCCCeEEecCCC--cEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISG--SLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G--~~VCt~CG~Vle~~ 32 (530)
.||.||...+......| ..+|..||......
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~~~ 40 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESRTGYG 40 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcCcccc
Confidence 59999997655555554 46999999976644
No 147
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=69.73 E-value=3 Score=32.74 Aligned_cols=20 Identities=40% Similarity=1.004 Sum_probs=14.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCce
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~ 27 (530)
.||+||+..+-. -||.+||+
T Consensus 28 ~C~~cG~~~~~H------~vc~~cG~ 47 (55)
T TIGR01031 28 VCPNCGEFKLPH------RVCPSCGY 47 (55)
T ss_pred ECCCCCCcccCe------eECCccCe
Confidence 488888854333 49999995
No 148
>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=69.13 E-value=12 Score=28.74 Aligned_cols=28 Identities=14% Similarity=0.131 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
..+++.+||+.++++.+|+...++.|.+
T Consensus 20 ~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 20 EELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp SGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3489999999999999999999888765
No 149
>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=68.93 E-value=3.4 Score=30.61 Aligned_cols=28 Identities=21% Similarity=0.232 Sum_probs=19.3
Q ss_pred HHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 047665 225 VELNGVSVKIENVAKEVHCTVVTCRKRY 252 (530)
Q Consensus 225 a~~~g~k~t~~eIA~~~~VS~~TIrkRy 252 (530)
.+++....|..+||+.+|||..||.+.+
T Consensus 15 ~~l~~~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 15 KELYAEGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3444445899999999999999997654
No 150
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=68.66 E-value=3.5 Score=33.41 Aligned_cols=27 Identities=22% Similarity=0.822 Sum_probs=17.3
Q ss_pred CCCCCCCCCeEEecC--------------CC---cEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDI--------------SG---SLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~--------------~G---~~VCt~CG~V 28 (530)
.||.||+.+...+.. .. .++|++||..
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 599999854333221 11 3689999987
No 151
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=68.62 E-value=3.6 Score=34.81 Aligned_cols=31 Identities=26% Similarity=0.533 Sum_probs=17.1
Q ss_pred CCCCCCC-CC--eEEecC--CCcEEcCCCceeeccc
Q 047665 2 PCTSCGS-KT--LTREDI--SGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~-~~--iv~D~~--~G~~VCt~CG~Vle~~ 32 (530)
.||.|++ .+ +..|.. .|.+.|..||...+..
T Consensus 24 ~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 24 DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp --TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 6999995 33 344444 3789999999987743
No 152
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=68.49 E-value=2.7 Score=29.48 Aligned_cols=25 Identities=24% Similarity=0.656 Sum_probs=17.1
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~V 28 (530)
.|.+||... .......+-|..||.=
T Consensus 2 ~C~~Cg~~~--~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEV--ELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE---BSTSSTSSBSSSS-S
T ss_pred CCCcCCCee--EcCCCCcEECCcCCCe
Confidence 588999862 3445567899999963
No 153
>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=68.38 E-value=12 Score=29.87 Aligned_cols=29 Identities=21% Similarity=0.322 Sum_probs=26.9
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 126 KSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 126 ~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
.|+|..+||+.+|++...+.++++.+.+.
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 57999999999999999999999999875
No 154
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=68.38 E-value=9.6 Score=32.81 Aligned_cols=29 Identities=28% Similarity=0.352 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
-+.|..+||+.+|+|+.|++++++.|.+.
T Consensus 16 ~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 16 ARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46899999999999999999999999883
No 155
>PF14353 CpXC: CpXC protein
Probab=68.37 E-value=3.5 Score=37.20 Aligned_cols=12 Identities=42% Similarity=0.742 Sum_probs=10.2
Q ss_pred cEEcCCCceeec
Q 047665 19 SLICVSCGVVQA 30 (530)
Q Consensus 19 ~~VCt~CG~Vle 30 (530)
..+|.+||....
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 579999999876
No 156
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=68.35 E-value=6.9 Score=30.18 Aligned_cols=30 Identities=13% Similarity=0.259 Sum_probs=26.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
..+.++||+..++|+.||+.+.+.|...+.
T Consensus 18 G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 18 GMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred cCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 578899999999999999999999988764
No 157
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=68.20 E-value=10 Score=36.03 Aligned_cols=47 Identities=11% Similarity=0.142 Sum_probs=38.6
Q ss_pred chhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 108 WFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 108 ~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
+.++-+.+++|+|....+-|+|..+||+..+++..-+.+.+..|.+.
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34667888899995556679999999999999999998888877663
No 158
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=67.80 E-value=9.4 Score=28.63 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=24.6
Q ss_pred CC-CHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 231 SV-KIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 231 k~-t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.+ |..++|+..++|..|+++.++.|.+
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45 8999999999999999999998887
No 159
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=67.72 E-value=1.4e+02 Score=29.88 Aligned_cols=34 Identities=9% Similarity=0.103 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...|.++||+..|+|+.||+.++......|-..+
T Consensus 216 ~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 249 (251)
T PRK07670 216 EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLL 249 (251)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5689999999999999999999988777775543
No 160
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=67.50 E-value=7.1 Score=27.37 Aligned_cols=27 Identities=19% Similarity=0.162 Sum_probs=21.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
++|..|||+.+|.|..|+.+-++.|.+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 568899999999999999999988875
No 161
>PRK00118 putative DNA-binding protein; Validated
Probab=67.22 E-value=7.9 Score=34.31 Aligned_cols=37 Identities=14% Similarity=0.131 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccC
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQAL 266 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~l 266 (530)
...|..+||+..|+|+.||++++......+-+....+
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~ 68 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKL 68 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999998888777776654
No 162
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=67.01 E-value=25 Score=32.85 Aligned_cols=29 Identities=17% Similarity=0.243 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
+++|+.+||..+|+|..|+.+-+++|.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 57899999999999999999999888773
No 163
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=66.94 E-value=1.6e+02 Score=30.36 Aligned_cols=28 Identities=7% Similarity=0.178 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
...|+++||+..|+|..|||.+...-..
T Consensus 268 ~~~Tl~EIa~~lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 268 EPLTLAEIGRRLNLSRERVRQIEAKALR 295 (298)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5799999999999999999998765443
No 164
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=66.91 E-value=36 Score=26.73 Aligned_cols=26 Identities=15% Similarity=0.322 Sum_probs=21.8
Q ss_pred CCCHHHHHHHhCC-CHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHC-TVVTCRKRYKELL 256 (530)
Q Consensus 231 k~t~~eIA~~~~V-S~~TIrkRyKEL~ 256 (530)
..++.+||..+|. +.....+.+++..
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 7889999999999 8888888777653
No 165
>COG4640 Predicted membrane protein [Function unknown]
Probab=66.66 E-value=2.9 Score=44.96 Aligned_cols=26 Identities=27% Similarity=0.650 Sum_probs=19.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.||.||+.. .+++.-|+.||.-+..+
T Consensus 3 fC~kcG~qk-----~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 3 FCPKCGSQK-----AEDDVQCTQCGHKFTSR 28 (465)
T ss_pred ccccccccc-----ccccccccccCCcCCch
Confidence 599999853 34566699999876643
No 166
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=66.65 E-value=3.2 Score=46.93 Aligned_cols=32 Identities=25% Similarity=0.704 Sum_probs=23.7
Q ss_pred CCCCCCCCC------CeEEe----cCCCcEEcCCCceeeccc
Q 047665 1 MPCTSCGSK------TLTRE----DISGSLICVSCGVVQAFD 32 (530)
Q Consensus 1 M~Cp~CG~~------~iv~D----~~~G~~VCt~CG~Vle~~ 32 (530)
..||+||.- .+.+| +.+.-++|..||..+++.
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHH
Confidence 369999972 34444 334678999999999965
No 167
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=66.56 E-value=1.6e+02 Score=30.31 Aligned_cols=35 Identities=17% Similarity=0.164 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|+++||+..|+|..||+++.+.-...|-..+.
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999988877766655443
No 168
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=66.45 E-value=4.3 Score=36.44 Aligned_cols=32 Identities=34% Similarity=0.780 Sum_probs=24.0
Q ss_pred CCCCCCCCCeE-EecCCCcEEcCCCceeecccC
Q 047665 2 PCTSCGSKTLT-REDISGSLICVSCGVVQAFDN 33 (530)
Q Consensus 2 ~Cp~CG~~~iv-~D~~~G~~VCt~CG~Vle~~~ 33 (530)
.||.||+--+. .|...+.++|..||...+.+.
T Consensus 4 FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGGKLVCRKCGYEEEASN 36 (113)
T ss_pred ccCCccCeeEEeEcCCCcEEECCCCCcchhccc
Confidence 69999994333 344567899999999988553
No 169
>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=66.42 E-value=16 Score=28.71 Aligned_cols=30 Identities=17% Similarity=0.202 Sum_probs=24.6
Q ss_pred cCCCC-CHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 228 NGVSV-KIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 228 ~g~k~-t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.|.++ +..++|+..+||..|++..++.|.+
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHH
Confidence 45678 8999999999999999999988765
No 170
>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=66.37 E-value=13 Score=29.71 Aligned_cols=30 Identities=13% Similarity=0.092 Sum_probs=26.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
+-..+..++|+.+++|..||+++++.|.+.
T Consensus 11 ~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~ 40 (69)
T TIGR00122 11 DNPFSGEKLGEALGMSRTAVNKHIQTLREW 40 (69)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 445779999999999999999999999763
No 171
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=66.14 E-value=28 Score=29.46 Aligned_cols=42 Identities=17% Similarity=0.311 Sum_probs=35.0
Q ss_pred HHHHHHHHhcCCCCChHHHHHHhC-CCHHHHHHHHHHHHHHhhhc
Q 047665 115 ACSYVVMRLDDKSLPISEVASVLN-CDVYELGRMITRVVEFLNLK 158 (530)
Q Consensus 115 AclYiACR~~~~P~TL~DIA~~~~-vd~~~Lgr~~k~L~k~L~i~ 158 (530)
.|+|++-+.. ..|+.+|+..+| .+..++..+++++.+.+..+
T Consensus 34 ia~yl~~~~~--~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~d 76 (90)
T cd06571 34 IAMYLARELT--GLSLPEIGRAFGGRDHSTVLHAVRKIEELLEED 76 (90)
T ss_pred HHHHHHHHHh--CCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHhC
Confidence 5677775555 567999999999 99999999999999988753
No 172
>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=66.09 E-value=16 Score=28.97 Aligned_cols=36 Identities=17% Similarity=0.300 Sum_probs=30.3
Q ss_pred HHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 117 SYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 117 lYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
||.... .+.+++..+||..+++++.++..++++|.+
T Consensus 13 Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 13 IYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 565554 888999999999999999999999988876
No 173
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=65.57 E-value=4.4 Score=33.70 Aligned_cols=28 Identities=21% Similarity=0.179 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
...|++|||+.+|+|+.||++++..+..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 4579999999999999999999886544
No 174
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=64.41 E-value=5.3 Score=27.01 Aligned_cols=22 Identities=41% Similarity=0.804 Sum_probs=11.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCC
Q 047665 2 PCTSCGSKTLTREDISGSLICVS 24 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~ 24 (530)
.||.||+. ++.+.++-.+.|++
T Consensus 1 ~CP~C~s~-l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSK-LVREEGEVDIRCPN 22 (28)
T ss_dssp B-TTT--B-EEE-CCTTCEEE--
T ss_pred CcCCCCCE-eEcCCCCEeEECCC
Confidence 59999996 45666666788875
No 175
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=64.38 E-value=1.6e+02 Score=32.35 Aligned_cols=78 Identities=14% Similarity=0.224 Sum_probs=51.0
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCC------------------CCChHHHH
Q 047665 73 LIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDK------------------SLPISEVA 134 (530)
Q Consensus 73 ~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~------------------P~TL~DIA 134 (530)
-+..++..++++...++.|..++..+.-.|..-- + ..=|+.+=.+..+. ..-+..|+
T Consensus 115 ~~~eia~~l~~~~~~ve~~l~~iq~leP~GIgAr-~----L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i~ 189 (429)
T TIGR02395 115 DLEEIADELEVSEEEVEKVLELIQRLDPAGVGAR-D----LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRLA 189 (429)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHhcCCCCccCcC-C----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHHH
Confidence 3788999999999999999888888765554311 1 12233333322111 12357788
Q ss_pred HHhCCCHHHHHHHHHHHHHHhh
Q 047665 135 SVLNCDVYELGRMITRVVEFLN 156 (530)
Q Consensus 135 ~~~~vd~~~Lgr~~k~L~k~L~ 156 (530)
..++++..++..++..|.. |+
T Consensus 190 ~~l~is~~~v~~~~~~I~~-L~ 210 (429)
T TIGR02395 190 KKLGLSEEELKEALDLIKS-LS 210 (429)
T ss_pred HHHCcCHHHHHHHHHHHhC-CC
Confidence 9999999999888766554 44
No 176
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=64.11 E-value=1.3e+02 Score=33.41 Aligned_cols=77 Identities=13% Similarity=0.157 Sum_probs=51.6
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCC-CCCchhHHHHHHHHHHHHhcC------------------C-CCChHH
Q 047665 73 LIDELTFKLDLTGQRSIQIKNMIDKITDGEFG-LGDWFPILIGACSYVVMRLDD------------------K-SLPISE 132 (530)
Q Consensus 73 ~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~-rGR~~~~vaAAclYiACR~~~------------------~-P~TL~D 132 (530)
-+..++..|+++...++.|..++..+.-.|.. +. ..=|+.+=.+..+ . -.-+..
T Consensus 140 ~~~eia~~l~~~~~~v~~~l~~lQ~leP~GigAr~------L~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~~ 213 (455)
T PRK05932 140 DLEEIAESLGVELDEVEAVLKRIQSFDPAGVGARD------LQECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFRT 213 (455)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHhcCCCCccCcCC------HHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHHH
Confidence 47889999999999999998888887655543 21 2223333333211 1 123677
Q ss_pred HHHHhCCCHHHHHHHHHHHHHHhh
Q 047665 133 VASVLNCDVYELGRMITRVVEFLN 156 (530)
Q Consensus 133 IA~~~~vd~~~Lgr~~k~L~k~L~ 156 (530)
||..++++..++..+...|. .|+
T Consensus 214 ia~~l~is~~~v~~~~~~Ir-~L~ 236 (455)
T PRK05932 214 LAKKLGVKEEDLQEALDLIR-SLD 236 (455)
T ss_pred HHHHHCcCHHHHHHHHHHHh-CCC
Confidence 89999999999999887654 454
No 177
>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=64.05 E-value=13 Score=28.05 Aligned_cols=35 Identities=17% Similarity=0.195 Sum_probs=28.9
Q ss_pred HHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHh
Q 047665 121 MRLDDKSLPISEVASVLNCDVYELGRMITRVVEFL 155 (530)
Q Consensus 121 CR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L 155 (530)
..+++-|+|..++|+.++++..++.+.+..|.+.+
T Consensus 9 L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 9 LLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 34566679999999999999999999999986655
No 178
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=63.78 E-value=4.4 Score=28.92 Aligned_cols=26 Identities=23% Similarity=0.593 Sum_probs=17.6
Q ss_pred CCCCCCCC-CeEEecC-CCcEEcCCCce
Q 047665 2 PCTSCGSK-TLTREDI-SGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~-~iv~D~~-~G~~VCt~CG~ 27 (530)
.|++||.. ++..... .....|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 59999983 3333322 34678999997
No 179
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=63.71 E-value=1.1 Score=32.10 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=18.1
Q ss_pred CCCCCCCC-CeEEecCCCcEEcCCCceee
Q 047665 2 PCTSCGSK-TLTREDISGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~-~iv~D~~~G~~VCt~CG~Vl 29 (530)
.||.||.. ++.+++-.-..+|..||.-+
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCee
Confidence 58888873 44555556677888888644
No 180
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=63.26 E-value=15 Score=28.08 Aligned_cols=42 Identities=12% Similarity=0.154 Sum_probs=33.9
Q ss_pred HHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhhhcCC
Q 047665 119 VVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNLKLP 160 (530)
Q Consensus 119 iACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~~p 160 (530)
++.-.-+...+..++|..+||+..++.+.+..+...|....|
T Consensus 11 l~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 11 LTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred HHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 333444556789999999999999999999999998876544
No 181
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=62.85 E-value=32 Score=31.85 Aligned_cols=67 Identities=7% Similarity=0.114 Sum_probs=43.6
Q ss_pred HHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhC
Q 047665 168 FERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVH 242 (530)
Q Consensus 168 I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~ 242 (530)
+..+|+.|++ ++ +..+.+...-..++. .+..|..+|+---+..+|+|..+++++..+|.++|-+.-.
T Consensus 18 l~~LC~~L~l---~~---~~~~~iwt~fe~~l~--~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr 84 (135)
T PF01857_consen 18 LQDLCERLDL---SS---DLREKIWTCFEHSLT--HHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYR 84 (135)
T ss_dssp HHHHHHHHTT---ST---THHHHHHHHHHHHHH--HSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHT
T ss_pred HHHHHHHcCC---cH---HHHHHHHHHHHHHHH--hhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHH
Confidence 4557888876 32 122344433333333 3578999999999999999999999988888888766544
No 182
>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=62.70 E-value=7.3 Score=30.54 Aligned_cols=32 Identities=19% Similarity=0.243 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
-.++.+++|+..++|+.||++.+.+|.+.+..
T Consensus 18 ~~~~~~ela~~l~~S~rti~~~i~~L~~~f~~ 49 (59)
T PF08280_consen 18 KWITLKELAKKLNISERTIKNDINELNEFFPE 49 (59)
T ss_dssp TSBBHHHHHHHCTS-HHHHHHHHHHHHTT--T
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHHhhh
Confidence 45889999999999999999999998876543
No 183
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=62.65 E-value=1.8e+02 Score=29.48 Aligned_cols=34 Identities=15% Similarity=0.174 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
+...|+++||+..|||..+|+++.+.....|-+.
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999999888777766543
No 184
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=62.31 E-value=1.6e+02 Score=28.73 Aligned_cols=32 Identities=9% Similarity=0.114 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|.++||+.+|+|..||+++++.-.+.|-+
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998876666644
No 185
>PF15616 TerY-C: TerY-C metal binding domain
Probab=62.05 E-value=4.9 Score=37.08 Aligned_cols=21 Identities=29% Similarity=0.888 Sum_probs=12.9
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
-||+||.. .+..+| +||.|.=
T Consensus 79 gCP~CGn~-------~~fa~C-~CGkl~C 99 (131)
T PF15616_consen 79 GCPHCGNQ-------YAFAVC-GCGKLFC 99 (131)
T ss_pred CCCCCcCh-------hcEEEe-cCCCEEE
Confidence 49999985 244455 4555554
No 186
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=61.89 E-value=5.8 Score=26.08 Aligned_cols=23 Identities=35% Similarity=0.800 Sum_probs=15.7
Q ss_pred CCCCCCCCeEEecC-CCcEEcCCCce
Q 047665 3 CTSCGSKTLTREDI-SGSLICVSCGV 27 (530)
Q Consensus 3 Cp~CG~~~iv~D~~-~G~~VCt~CG~ 27 (530)
|..||.. +.... .-...|.+||.
T Consensus 1 C~sC~~~--i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRP--IAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCc--ccCcccCceEeCCCCCC
Confidence 7888875 33444 34579999994
No 187
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=61.81 E-value=17 Score=34.08 Aligned_cols=45 Identities=22% Similarity=0.168 Sum_probs=37.6
Q ss_pred hhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 109 FPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 109 ~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
.++.+-|.+|+|- ..+.+++..+||+..+++..-|.+.+..|++.
T Consensus 7 ~~YAlr~L~~LA~-~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 7 TNYAIRMLMYCAA-NDGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HhHHHHHHHHHHh-CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4566778899994 45668999999999999999999998888774
No 188
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=61.76 E-value=13 Score=33.99 Aligned_cols=36 Identities=11% Similarity=0.001 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.|+++++.-....|-+.+..
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 468999999999999999999988877777665543
No 189
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=61.40 E-value=5.6 Score=27.70 Aligned_cols=23 Identities=26% Similarity=0.769 Sum_probs=16.0
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCce
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~ 27 (530)
.|+.||- +.|.......|..||.
T Consensus 3 ~C~~CGy---~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY---IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC---EECCCcCCCcCcCCCC
Confidence 5888876 4555556678888875
No 190
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.35 E-value=3 Score=37.87 Aligned_cols=31 Identities=29% Similarity=0.618 Sum_probs=21.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
+||+||+..+..-.-.-.-.|..||.=..+.
T Consensus 23 rCP~CGeGrLF~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 23 RCPRCGEGRLFRGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred CCCCCCCchhhhhhcccCchhhhccccccCC
Confidence 6999999765333333456899999876643
No 191
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=61.32 E-value=19 Score=25.68 Aligned_cols=29 Identities=21% Similarity=0.277 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
...++.+||+..|++..||+++.....+.
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45799999999999999999988776654
No 192
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=61.29 E-value=7.3 Score=31.13 Aligned_cols=29 Identities=28% Similarity=0.618 Sum_probs=18.9
Q ss_pred CCCCCCC-CCeEEecCCC--cEEcCCCceeec
Q 047665 2 PCTSCGS-KTLTREDISG--SLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~-~~iv~D~~~G--~~VCt~CG~Vle 30 (530)
.||.|+. ..+..=.+.| .+-|..||+--.
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 6999998 3333322233 378999998654
No 193
>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=60.89 E-value=18 Score=32.30 Aligned_cols=45 Identities=11% Similarity=0.135 Sum_probs=35.6
Q ss_pred hhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 109 FPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 109 ~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
.+..+.+.+|++-...+.|.+..+||+.++++...+.+....|.+
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 455567777777432345899999999999999999998888876
No 194
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=60.84 E-value=6 Score=28.70 Aligned_cols=27 Identities=22% Similarity=0.543 Sum_probs=15.3
Q ss_pred CCCCCCCCCeEEec------CCC---cEEcCCCcee
Q 047665 2 PCTSCGSKTLTRED------ISG---SLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~------~~G---~~VCt~CG~V 28 (530)
.||.||+...++=. +++ .++|.+||..
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 69999986433321 112 4799999975
No 195
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=60.74 E-value=35 Score=37.05 Aligned_cols=56 Identities=13% Similarity=0.096 Sum_probs=43.5
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcC
Q 047665 70 SNKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDD 125 (530)
Q Consensus 70 a~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~ 125 (530)
..+.+++++..-+|....+.+|-.+|.++.=+|+..-.+....|+||+.+|++.+.
T Consensus 385 lKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD 440 (497)
T KOG4164|consen 385 LKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMND 440 (497)
T ss_pred HHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhh
Confidence 44677777777788887888998889888656666555778999999999988654
No 196
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=60.51 E-value=6.8 Score=34.69 Aligned_cols=29 Identities=17% Similarity=0.478 Sum_probs=20.6
Q ss_pred CCCCCCCCCeEEec------C--C-Cc-EEcCCCceeec
Q 047665 2 PCTSCGSKTLTRED------I--S-GS-LICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~------~--~-G~-~VCt~CG~Vle 30 (530)
.||.||+.....+. . . .. ++|+.|+.=+.
T Consensus 4 ~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 4 ICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred ccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceee
Confidence 69999996555551 1 1 23 79999998776
No 197
>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=60.08 E-value=29 Score=26.80 Aligned_cols=31 Identities=19% Similarity=0.153 Sum_probs=27.1
Q ss_pred cCCCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 124 DDKSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 124 ~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
...+.|..|||+.++++...+.+.+..|.+.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3467999999999999999999999888774
No 198
>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=60.07 E-value=11 Score=31.26 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=27.1
Q ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 221 LVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 221 IYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+|+|..-.+..+|.++||+..++++..+++-++.|.+
T Consensus 15 ~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 15 LYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKK 51 (83)
T ss_dssp HHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 3444333333499999999999999999998888877
No 199
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=60.03 E-value=6.3 Score=35.05 Aligned_cols=29 Identities=31% Similarity=0.702 Sum_probs=21.3
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.||.|++.-...| .+.++|..|+.-..+.
T Consensus 5 ~cp~c~sEytYed--~~~~~cpec~~ew~~~ 33 (112)
T COG2824 5 PCPKCNSEYTYED--GGQLICPECAHEWNEN 33 (112)
T ss_pred CCCccCCceEEec--CceEeCchhccccccc
Confidence 5999988643333 4599999999876643
No 200
>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=59.71 E-value=19 Score=26.69 Aligned_cols=30 Identities=20% Similarity=0.263 Sum_probs=25.3
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
..-+.+..+|++.++++.+|+..-++.|.+
T Consensus 12 ~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 12 SEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp TTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 345688999999999999999999988876
No 201
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=59.63 E-value=4.9 Score=28.71 Aligned_cols=28 Identities=25% Similarity=0.614 Sum_probs=19.2
Q ss_pred CCCCCCCCCeEEec----CCCcEEcCCCceee
Q 047665 2 PCTSCGSKTLTRED----ISGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~----~~G~~VCt~CG~Vl 29 (530)
.||+|+..--+-|. ....+-|+.||.+.
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 69999984223332 23468999999875
No 202
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.50 E-value=2.3 Score=41.05 Aligned_cols=30 Identities=20% Similarity=0.422 Sum_probs=20.5
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.|+..-...|.-+....|..||.++.+
T Consensus 119 ~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 499998642223333567899999988875
No 203
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=58.75 E-value=15 Score=35.06 Aligned_cols=42 Identities=10% Similarity=0.128 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccCCCCccC
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQALPWGKDV 272 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~lpW~~~v 272 (530)
...|.++||+.+|+|+.|++.++......|-+.+..- |.+.-
T Consensus 151 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~-~~~~~ 192 (195)
T PRK12532 151 LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIK-WFNQE 192 (195)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh-hcccc
Confidence 4688999999999999999999988777776665431 54433
No 204
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=58.61 E-value=5.3 Score=32.40 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=9.3
Q ss_pred CCCCCCCCCeEEe
Q 047665 2 PCTSCGSKTLTRE 14 (530)
Q Consensus 2 ~Cp~CG~~~iv~D 14 (530)
.||.||..+...+
T Consensus 6 kCpKCgn~~~~ek 18 (68)
T COG3478 6 KCPKCGNTNYEEK 18 (68)
T ss_pred cCCCcCCcchhhc
Confidence 4999998655444
No 205
>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=58.48 E-value=17 Score=28.78 Aligned_cols=38 Identities=21% Similarity=0.211 Sum_probs=29.3
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 219 AVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 219 AAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+.+|.+-. ..-..|..+||+.++++..|+.+.++.|.+
T Consensus 11 ~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 11 AKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34555443 234789999999999999999998888766
No 206
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=58.42 E-value=3.9 Score=41.37 Aligned_cols=30 Identities=30% Similarity=0.687 Sum_probs=11.9
Q ss_pred CCCCCCCCCCeEE---ecCCCcEEcCCCceeec
Q 047665 1 MPCTSCGSKTLTR---EDISGSLICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~~~iv~---D~~~G~~VCt~CG~Vle 30 (530)
|.||+||+..+.. ...-.+..|.+|+.-.+
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EEE
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHHh
Confidence 6799999963322 22236789999997665
No 207
>PF12773 DZR: Double zinc ribbon
Probab=58.29 E-value=4.7 Score=30.25 Aligned_cols=23 Identities=26% Similarity=0.774 Sum_probs=11.6
Q ss_pred CCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 3 CTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 3 Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
||+||... ..+..+|..||..+.
T Consensus 1 Cp~Cg~~~-----~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPN-----PDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcC-----CccccCChhhcCChh
Confidence 55665531 123455555555555
No 208
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=58.11 E-value=14 Score=36.43 Aligned_cols=36 Identities=14% Similarity=0.067 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.||++++......|-+.+.+
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~ 232 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999987776666555543
No 209
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=58.10 E-value=1.3e+02 Score=33.15 Aligned_cols=51 Identities=12% Similarity=0.212 Sum_probs=41.6
Q ss_pred cccccCchhHHHH---HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 207 LTTGRRPMPVVVA---VLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 207 l~tGR~P~sIAAA---AIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
|..+++-..++-| |.|++-++.+ .|+.+|++..|.+.+||...++.+.+.+
T Consensus 362 l~s~~R~~~i~~aR~iamyl~r~~~~--~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 362 ILSNSRNVKALLARRIGMYVAKNYLG--SSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HhCCCCCccccHHHHHHHHHHHHHhC--CCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4555566777778 9999977554 5999999999999999999999888855
No 210
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=58.06 E-value=16 Score=31.90 Aligned_cols=31 Identities=19% Similarity=0.275 Sum_probs=27.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
..+..+||+..|+|+.||+++++...+.+-+
T Consensus 126 g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 126 GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5789999999999999999999998877654
No 211
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=57.92 E-value=5.5 Score=31.60 Aligned_cols=20 Identities=35% Similarity=1.049 Sum_probs=14.3
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCce
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~ 27 (530)
.||+||...+-. -||.+||+
T Consensus 29 ~c~~cG~~~l~H------rvc~~cg~ 48 (57)
T COG0333 29 VCPNCGEYKLPH------RVCLKCGY 48 (57)
T ss_pred eccCCCCcccCc------eEcCCCCC
Confidence 488888854433 48999995
No 212
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=57.64 E-value=5.6 Score=30.14 Aligned_cols=26 Identities=27% Similarity=0.696 Sum_probs=16.7
Q ss_pred CCCCCCCC-CeEEe-cCCCcEEcCCCce
Q 047665 2 PCTSCGSK-TLTRE-DISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~-~iv~D-~~~G~~VCt~CG~ 27 (530)
+|++||.. ++..- .+.....|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 59999982 32221 2235678999997
No 213
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=57.64 E-value=16 Score=32.79 Aligned_cols=32 Identities=22% Similarity=0.234 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|..|||+.+|+|+.|+++++.-....|-+
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46799999999999999999999887776654
No 214
>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=57.41 E-value=22 Score=27.20 Aligned_cols=38 Identities=21% Similarity=0.277 Sum_probs=28.5
Q ss_pred HHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 116 CSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 116 clYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
++++.....+-+.|+.|||+.+++++..+.+.+++|.+
T Consensus 10 vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 10 VLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34444444444589999999999999999999888866
No 215
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=57.10 E-value=11 Score=38.25 Aligned_cols=38 Identities=18% Similarity=0.204 Sum_probs=30.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHhhcccCCC
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYK-------ELLEALVKVAQALPW 268 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyK-------EL~e~L~~l~~~lpW 268 (530)
+.|++|||+.+|||..|+++.+. +..+.+.+.++++=|
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY 45 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGF 45 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCC
Confidence 46899999999999999999884 666667777776544
No 216
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=56.99 E-value=2.3e+02 Score=28.80 Aligned_cols=32 Identities=16% Similarity=0.166 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+++||+.+|+|..||+++++.....|-+
T Consensus 230 ~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 230 ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999998877776654
No 217
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=56.80 E-value=2.7 Score=32.99 Aligned_cols=21 Identities=33% Similarity=0.865 Sum_probs=14.3
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~V 28 (530)
.||.||... ..-.+|.+||+.
T Consensus 28 ~c~~cg~~~------~~H~vc~~cG~y 48 (56)
T PF01783_consen 28 KCPNCGEPK------LPHRVCPSCGYY 48 (56)
T ss_dssp ESSSSSSEE------STTSBCTTTBBS
T ss_pred eeccCCCEe------cccEeeCCCCeE
Confidence 588888732 234699999843
No 218
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=56.72 E-value=3.6e+02 Score=31.02 Aligned_cols=79 Identities=11% Similarity=0.044 Sum_probs=48.4
Q ss_pred HHHHHHHHhhc---CCC--HHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHH----h------------------
Q 047665 71 NKLIDELTFKL---DLT--GQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMR----L------------------ 123 (530)
Q Consensus 71 ~~~I~~i~~~L---gLp--~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR----~------------------ 123 (530)
+..+..+|.+. |++ +-+.+--..+.+-+..-...+|-++...|.-+|--+.. .
T Consensus 390 lrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~ 469 (619)
T PRK05658 390 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 469 (619)
T ss_pred HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHH
Confidence 35666666653 444 44555556677777655666887777776666543321 1
Q ss_pred ----------cCCCCChHHHHHHhCCCHHHHHHHHH
Q 047665 124 ----------DDKSLPISEVASVLNCDVYELGRMIT 149 (530)
Q Consensus 124 ----------~~~P~TL~DIA~~~~vd~~~Lgr~~k 149 (530)
.|..-|..+||..++++..++.++.+
T Consensus 470 ~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~ 505 (619)
T PRK05658 470 NRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLK 505 (619)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 22333567788888888888777654
No 219
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=56.54 E-value=9.8 Score=27.67 Aligned_cols=27 Identities=26% Similarity=0.580 Sum_probs=16.9
Q ss_pred CCCCCCCCCeEEecCCC--cEEcCCCceee
Q 047665 2 PCTSCGSKTLTREDISG--SLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G--~~VCt~CG~Vl 29 (530)
.||.|+..-..... .+ ..+|.+||=+.
T Consensus 1 ~CP~C~~~l~~~~~-~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEE-CCEEEEECCCCCeEE
Confidence 59999984222222 22 24899998664
No 220
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=56.47 E-value=29 Score=25.13 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=25.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
..+..++|+.++++..|+++.++.|.+.
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4899999999999999999999888764
No 221
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=56.37 E-value=17 Score=30.19 Aligned_cols=35 Identities=31% Similarity=0.305 Sum_probs=28.8
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
.+...++.++|+...||.+|+.+.++++.+.+.+.
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~~ 61 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKKY 61 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHCC
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 45679999999999999999999999999988754
No 222
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=56.20 E-value=39 Score=31.57 Aligned_cols=29 Identities=10% Similarity=0.166 Sum_probs=27.2
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 126 KSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 126 ~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
+|+|-.|||+.+|++...+.|+++++.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 78999999999999999999999999885
No 223
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=56.19 E-value=76 Score=31.88 Aligned_cols=66 Identities=17% Similarity=0.161 Sum_probs=46.6
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHH
Q 047665 73 LIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVV 152 (530)
Q Consensus 73 ~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~ 152 (530)
.++...++.++..-......+++..|.+. |.-+|..|+|..+++++.+|++-.+.+.
T Consensus 74 D~e~~~~~~~~~elr~~rIvRl~~EAy~Q-----------------------gglLT~~Dla~LL~~S~~TI~~~i~~yq 130 (220)
T PF07900_consen 74 DIEMRNEKYGLSELRKHRIVRLTNEAYDQ-----------------------GGLLTQEDLAMLLGISPRTISKDIKEYQ 130 (220)
T ss_pred HHHHHHhhcCHHHHHHHHHHHHHHHHHHc-----------------------CCcccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34444444555554455555556555542 3346889999999999999999999999
Q ss_pred HHhhhcCCc
Q 047665 153 EFLNLKLPE 161 (530)
Q Consensus 153 k~L~i~~p~ 161 (530)
+..|.-+|.
T Consensus 131 ~e~g~vvPt 139 (220)
T PF07900_consen 131 KEHGVVVPT 139 (220)
T ss_pred HHcCceecc
Confidence 998877663
No 224
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=55.86 E-value=7.8 Score=30.43 Aligned_cols=26 Identities=27% Similarity=0.738 Sum_probs=19.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
+|+.||.. +.| ...-+||..||.+.-
T Consensus 7 ~C~~Cg~~--~~~-~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 7 KCPVCGKK--FKD-GDDIVVCPECGAPYH 32 (54)
T ss_pred cChhhCCc--ccC-CCCEEECCCCCCccc
Confidence 69999985 222 345689999999876
No 225
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=55.62 E-value=6.4 Score=45.38 Aligned_cols=16 Identities=31% Similarity=0.395 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 047665 245 VVTCRKRYKELLEALV 260 (530)
Q Consensus 245 ~~TIrkRyKEL~e~L~ 260 (530)
...++..+.++...+.
T Consensus 312 ~~~l~~~l~~~~~~~~ 327 (645)
T PRK14559 312 IAQLRLRLQELATELE 327 (645)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 4455555555554443
No 226
>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=55.54 E-value=18 Score=33.58 Aligned_cols=50 Identities=8% Similarity=0.080 Sum_probs=36.7
Q ss_pred hHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 215 PVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 215 sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
-|+.|++=|.....-.++|+++||+.+||+.+|.=..|+..++.+..+..
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK~dLl~~~~~ 56 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDKYELLTWIFE 56 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCHHHHHHHHHH
Confidence 34555554444333357999999999999999999999887777666543
No 227
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=55.48 E-value=10 Score=31.34 Aligned_cols=30 Identities=30% Similarity=0.631 Sum_probs=20.5
Q ss_pred CCCCCCCC-CeE--EecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSK-TLT--REDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~-~iv--~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.|++- .+. .+...-..-|..||+.-.-
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 69999983 333 2333334789999998763
No 228
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=55.40 E-value=18 Score=33.79 Aligned_cols=33 Identities=15% Similarity=0.215 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|.+|||+.+|+|+.|+++++.--...|.+.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999988777766543
No 229
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=55.17 E-value=17 Score=34.62 Aligned_cols=35 Identities=17% Similarity=0.175 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+.+|+|..|+++|+.-....|-+.+.
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 46899999999999999999999888877766554
No 230
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=55.08 E-value=27 Score=25.97 Aligned_cols=29 Identities=17% Similarity=0.117 Sum_probs=25.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+...+..+|++..++|.+|+++.++.|.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45689999999999999999999988776
No 231
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=55.08 E-value=7.5 Score=38.23 Aligned_cols=30 Identities=23% Similarity=0.598 Sum_probs=19.5
Q ss_pred CCCCCCCCCCeEE--e---cCCC-----cEEcCCCceeec
Q 047665 1 MPCTSCGSKTLTR--E---DISG-----SLICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~~~iv~--D---~~~G-----~~VCt~CG~Vle 30 (530)
|.||.||+.-..+ . +..| ..+|..||+=..
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 4799999942111 1 2235 468999998655
No 232
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=55.02 E-value=16 Score=33.64 Aligned_cols=35 Identities=29% Similarity=0.308 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+..|+|+.||++++......|.+.+.
T Consensus 143 ~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46799999999999999999998887777776654
No 233
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=54.99 E-value=21 Score=34.07 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccCC
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQALP 267 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~lp 267 (530)
...|.+|||+.+|+|..|+++|+.--...|-+.+..++
T Consensus 149 ~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~~ 186 (192)
T PRK09643 149 QGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYLR 186 (192)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35899999999999999999999877777777666544
No 234
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=54.91 E-value=29 Score=29.82 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=25.1
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 047665 227 LNGVSVKIENVAKEVHCTVVTCRKRYKELL 256 (530)
Q Consensus 227 ~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~ 256 (530)
++....|+.+|++.+|||..||.+-=+.|.
T Consensus 45 lL~~g~syreIa~~tgvS~aTItRvsr~Lk 74 (87)
T PF01371_consen 45 LLDEGKSYREIAEETGVSIATITRVSRCLK 74 (87)
T ss_dssp HHHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred HHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 666789999999999999999977655554
No 235
>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=54.81 E-value=28 Score=31.20 Aligned_cols=44 Identities=7% Similarity=0.066 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 109 FPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 109 ~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
.+..+.+.+|++- ..+-|.+..|||+.++++...+.+.+..|.+
T Consensus 8 ~~yal~~l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 8 TDYATLVLTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred HhHHHHHHHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4566777888874 3466899999999999999999999888877
No 236
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=54.72 E-value=17 Score=23.24 Aligned_cols=21 Identities=10% Similarity=0.164 Sum_probs=18.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKR 251 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkR 251 (530)
..+..+||+..+++..|+.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 358999999999999999764
No 237
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=54.66 E-value=2.1e+02 Score=27.79 Aligned_cols=32 Identities=9% Similarity=0.149 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+++||+..|+|..||+.+++.....|-+
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998887776644
No 238
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=54.43 E-value=52 Score=34.58 Aligned_cols=54 Identities=7% Similarity=0.124 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhC
Q 047665 189 DRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVH 242 (530)
Q Consensus 189 ~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~ 242 (530)
..|+..|.....++--.|.+.--+|..|.++++|+|++...+-+|..++++-..
T Consensus 76 ~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~ 129 (325)
T KOG2496|consen 76 TSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN 129 (325)
T ss_pred hHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence 478888888888877777888899999999999999999999999999999877
No 239
>PRK08402 replication factor A; Reviewed
Probab=54.42 E-value=8.8 Score=41.09 Aligned_cols=26 Identities=27% Similarity=0.640 Sum_probs=21.5
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~V 28 (530)
.||.|+.. ++.|...|...|..||.|
T Consensus 214 aCp~CnKk-v~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 214 ACPECRRK-VDYDPATDTWICPEHGEV 239 (355)
T ss_pred cCCCCCeE-EEEecCCCCEeCCCCCCc
Confidence 69999873 445888899999999975
No 240
>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=54.36 E-value=15 Score=26.18 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=19.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 047665 232 VKIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyKE 254 (530)
.|..|+|+.+||+..|+++..++
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 36789999999999999987654
No 241
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=54.04 E-value=49 Score=31.93 Aligned_cols=62 Identities=13% Similarity=0.027 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHhhcccccccCchhHHHH--------HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 047665 190 RMRKQGVLLLNCAVKWFLTTGRRPMPVVVA--------VLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 190 ~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAA--------AIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKE 254 (530)
.+..+...=++.+...+...|| |.+..-. ..+... .....|..+||+.+|||.+|+.+..++
T Consensus 126 ~i~~R~~~g~~~~~~~G~~~Gr-p~g~~~~~~~~~~~~~~i~~~--~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 126 LISQRTKEALARKKAEGVTLGR-PKGSTPKKYKLTGKEEKIKKL--LDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHHHHHHHHHHcCCccCC-CCCCcchhhhcchhHHHHHHH--HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3444444445566666666788 4332211 111222 223479999999999999999887664
No 242
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=54.00 E-value=19 Score=25.83 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=25.9
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 125 DKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 125 ~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
..|.+..|+|+.++++...+.+.++.+.+
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46899999999999999999999888876
No 243
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=53.71 E-value=16 Score=26.18 Aligned_cols=27 Identities=11% Similarity=0.258 Sum_probs=19.7
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHH
Q 047665 125 DKSLPISEVASVLNCDVYELGRMITRV 151 (530)
Q Consensus 125 ~~P~TL~DIA~~~~vd~~~Lgr~~k~L 151 (530)
..+.++.|||+.+|++...+.+.|++.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 457899999999999999998887653
No 244
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=53.49 E-value=20 Score=34.22 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=26.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
-.|.+|||+.+|+|+.|++++++-+...+..
T Consensus 151 Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 151 GLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3699999999999999999999988866543
No 245
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=53.46 E-value=20 Score=32.64 Aligned_cols=35 Identities=14% Similarity=0.266 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.+|||+..|+|+.|+++++..-...|-+.+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999999887777765544
No 246
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=53.37 E-value=21 Score=32.61 Aligned_cols=34 Identities=21% Similarity=0.262 Sum_probs=30.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
..|.++||+.+|+|+.|+++++.-....|-+.+.
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 6899999999999999999999988888877654
No 247
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=53.16 E-value=67 Score=38.12 Aligned_cols=62 Identities=15% Similarity=0.051 Sum_probs=47.5
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHH
Q 047665 71 NKLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEV 133 (530)
Q Consensus 71 ~~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DI 133 (530)
.+.....|..|+++.....+|...|..+...--..| +-..+.|+++|.+||...+|.-.+-+
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~~v~~~~ 96 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVPTVGGGI 96 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCCccCcce
Confidence 346677899999999999999888888865444456 46788999999999999766433333
No 248
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=53.15 E-value=14 Score=34.70 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.|++.++......|-+.+..
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 167 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQI 167 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 357999999999999999999988877777665543
No 249
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=52.85 E-value=39 Score=31.65 Aligned_cols=70 Identities=17% Similarity=0.038 Sum_probs=43.0
Q ss_pred chhHHHHHHHHHHHHcC---CCCCHHHHHHHhCCCHHHHHHHHH---HHHHHHHhhcccCCCCccCcccccccChhHHHH
Q 047665 213 PMPVVVAVLVFVVELNG---VSVKIENVAKEVHCTVVTCRKRYK---ELLEALVKVAQALPWGKDVTVKNVLKNAPFVMN 286 (530)
Q Consensus 213 P~sIAAAAIYlAa~~~g---~k~t~~eIA~~~~VS~~TIrkRyK---EL~e~L~~l~~~lpW~~~v~~knl~~~~pdIi~ 286 (530)
|.-.-||.+..+-.++. -+.|+.+||+.+||++.|+-+.-+ +|.+.+..++.. .+-.+++.|..
T Consensus 13 ~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~----------~~~~~~~eVy~ 82 (142)
T PF13022_consen 13 LQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADR----------FLSSHREEVYT 82 (142)
T ss_dssp HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHH----------HHHTTHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHH----------HHHHhHHHHHH
Confidence 44455666666666654 569999999999999999977553 477777776654 44455666644
Q ss_pred HhHHHH
Q 047665 287 YMEMKS 292 (530)
Q Consensus 287 ~~e~~~ 292 (530)
.+-.+.
T Consensus 83 ~L~~~i 88 (142)
T PF13022_consen 83 QLMKKI 88 (142)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 443333
No 250
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=52.81 E-value=55 Score=31.86 Aligned_cols=28 Identities=11% Similarity=0.135 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.++|+++||+.+|+|..|+.+-+++|.+
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~ 210 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQK 210 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 5789999999999999999998887766
No 251
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=52.61 E-value=22 Score=33.20 Aligned_cols=35 Identities=20% Similarity=0.218 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+.+|+|+.|+++++.-....|-..++
T Consensus 151 ~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T TIGR02948 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 46899999999999999999999888887766554
No 252
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=52.56 E-value=21 Score=35.30 Aligned_cols=36 Identities=17% Similarity=0.094 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.|+++++.-....|-+.+.+
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 469999999999999999999987777766665544
No 253
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=52.50 E-value=20 Score=32.79 Aligned_cols=39 Identities=15% Similarity=0.093 Sum_probs=30.6
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 219 AVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 219 AAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+.+|++..-.|...+..+||+..+||..++++.++.|..
T Consensus 13 ~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~ 51 (141)
T PRK11014 13 ALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSR 51 (141)
T ss_pred HHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 344555444456688999999999999999999888876
No 254
>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=52.49 E-value=23 Score=26.67 Aligned_cols=37 Identities=22% Similarity=0.286 Sum_probs=28.6
Q ss_pred HHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 117 SYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 117 lYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
|.-+...++-|.++.|||..++++..++.+....|.+
T Consensus 8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4444556777889999999999999998887776654
No 255
>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=52.38 E-value=37 Score=25.31 Aligned_cols=27 Identities=30% Similarity=0.372 Sum_probs=20.3
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKEL 255 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL 255 (530)
+|- +|+.+.|+..||+.+|++.|++..
T Consensus 14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 14 NGK-MSIRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp TTS-S-HHHHHHHHT--HHHHHHHHHHT
T ss_pred hCC-CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 444 999999999999999999887753
No 256
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=52.33 E-value=15 Score=26.71 Aligned_cols=30 Identities=23% Similarity=0.521 Sum_probs=19.5
Q ss_pred CCCCCCCC---CCeEEecCCCcEEcCCCceeec
Q 047665 1 MPCTSCGS---KTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~---~~iv~D~~~G~~VCt~CG~Vle 30 (530)
++|..|++ +-..+|......+|.-||..-+
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNP 35 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--EEE
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCcCC
Confidence 47999997 5677887778899999998654
No 257
>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=52.28 E-value=70 Score=27.42 Aligned_cols=30 Identities=7% Similarity=0.134 Sum_probs=27.0
Q ss_pred cCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 124 DDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 124 ~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
...++|..|||+.++++...+.+++..|.+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 567899999999999999999999888876
No 258
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=52.06 E-value=23 Score=31.97 Aligned_cols=33 Identities=9% Similarity=0.146 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|.++||+.+|+|+.|+++++.-....|.+.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999988777766554
No 259
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=52.05 E-value=20 Score=34.02 Aligned_cols=35 Identities=14% Similarity=0.052 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.+|||+.+|+|+.|+++++.--...|-+.+.
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999998877776665543
No 260
>PHA02591 hypothetical protein; Provisional
Probab=52.00 E-value=23 Score=29.97 Aligned_cols=30 Identities=20% Similarity=0.265 Sum_probs=23.6
Q ss_pred HHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 047665 224 VVELNGVSVKIENVAKEVHCTVVTCRKRYK 253 (530)
Q Consensus 224 Aa~~~g~k~t~~eIA~~~~VS~~TIrkRyK 253 (530)
|.++...-.|+.+||+.+|++..|+++-++
T Consensus 52 A~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 52 THELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 334444568999999999999999998654
No 261
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=51.93 E-value=24 Score=32.71 Aligned_cols=36 Identities=19% Similarity=0.123 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.|+++++.--...|-+.+..
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 168 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQE 168 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence 368999999999999999999988877777665543
No 262
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=51.76 E-value=22 Score=32.92 Aligned_cols=36 Identities=19% Similarity=0.127 Sum_probs=31.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.++||+.+|+|+.||++++.-....|.+.++.
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~ 170 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 457899999999999999999999888888776654
No 263
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=51.69 E-value=8 Score=28.43 Aligned_cols=26 Identities=23% Similarity=0.686 Sum_probs=16.1
Q ss_pred CCCCCCCC-CeEEecC-CCcEEcCCCce
Q 047665 2 PCTSCGSK-TLTREDI-SGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~-~iv~D~~-~G~~VCt~CG~ 27 (530)
+|+.||.. ++..-.. .....|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 58889862 2222222 35678999987
No 264
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=51.69 E-value=9.8 Score=38.78 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=21.1
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.||+..... ...-...|..||.+.-.
T Consensus 101 fC~~CG~~~~~~-~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 101 FCGYCGHPMHPS-KTEWAMLCPHCRERYYP 129 (256)
T ss_pred cccccCCCCeec-CCceeEECCCCCCEECC
Confidence 599999975443 33445799999987653
No 265
>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=51.60 E-value=43 Score=31.96 Aligned_cols=28 Identities=21% Similarity=0.234 Sum_probs=25.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
-.|+++||+.+++|.+|+.+.+++|.+.
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 3789999999999999999999999883
No 266
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=51.52 E-value=20 Score=31.67 Aligned_cols=47 Identities=17% Similarity=0.287 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHcCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 216 VVVAVLVFVVELNGV-SVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 216 IAAAAIYlAa~~~g~-k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
+..|++.+... .|+ .+|..+||+.+||+..|+...++.-.+.+..++
T Consensus 17 ii~aa~~l~~~-~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K~~l~~~~~ 64 (201)
T COG1309 17 ILDAALRLFAE-KGYAATTVDEIAKAAGVSKGTLYRHFPSKEDLLLALL 64 (201)
T ss_pred HHHHHHHHHHH-cCcCCCCHHHHHHHhCCCcchhHHHcCCHHHHHHHHH
Confidence 44445544444 674 599999999999999999988876554443333
No 267
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=51.44 E-value=20 Score=33.37 Aligned_cols=35 Identities=6% Similarity=0.058 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+.++||+.+|+|+.|++.++.-....|.+.++
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998877777766554
No 268
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.34 E-value=12 Score=31.52 Aligned_cols=31 Identities=26% Similarity=0.378 Sum_probs=21.3
Q ss_pred CCCCCCCCCCeEEecCCCc--EEcCCCceeeccc
Q 047665 1 MPCTSCGSKTLTREDISGS--LICVSCGVVQAFD 32 (530)
Q Consensus 1 M~Cp~CG~~~iv~D~~~G~--~VCt~CG~Vle~~ 32 (530)
|.||.|+..- +.-..+|. -.|..|+=|.-++
T Consensus 2 llCP~C~v~l-~~~~rs~vEiD~CPrCrGVWLDr 34 (88)
T COG3809 2 LLCPICGVEL-VMSVRSGVEIDYCPRCRGVWLDR 34 (88)
T ss_pred cccCcCCcee-eeeeecCceeeeCCccccEeecc
Confidence 5799999853 33333443 3899999997654
No 269
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=51.28 E-value=23 Score=33.32 Aligned_cols=35 Identities=23% Similarity=0.214 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+..|+|..|+++++.--++.|-+.+.
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~ 176 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999999988887766554
No 270
>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=51.26 E-value=41 Score=24.68 Aligned_cols=29 Identities=17% Similarity=0.282 Sum_probs=23.5
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 125 DKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 125 ~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
+-+.|..|||..++++...+.+.++++.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 44599999999999999999999888865
No 271
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, 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=51.11 E-value=16 Score=26.52 Aligned_cols=21 Identities=24% Similarity=0.067 Sum_probs=18.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHH
Q 047665 232 VKIENVAKEVHCTVVTCRKRY 252 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRy 252 (530)
.|..++|+.+||++.||+...
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHH
Confidence 367899999999999999753
No 272
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=51.04 E-value=63 Score=30.50 Aligned_cols=28 Identities=21% Similarity=0.150 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.++|+.+||..+|+|..|+.+-+++|.+
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSR 175 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 5789999999999999999999999886
No 273
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=51.04 E-value=17 Score=27.41 Aligned_cols=20 Identities=15% Similarity=0.295 Sum_probs=17.9
Q ss_pred ChHHHHHHhCCCHHHHHHHH
Q 047665 129 PISEVASVLNCDVYELGRMI 148 (530)
Q Consensus 129 TL~DIA~~~~vd~~~Lgr~~ 148 (530)
||+|||..+|++..++.+++
T Consensus 1 Ti~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 78999999999999988774
No 274
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=50.97 E-value=28 Score=28.04 Aligned_cols=36 Identities=14% Similarity=0.253 Sum_probs=27.6
Q ss_pred HhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhhh
Q 047665 122 RLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNL 157 (530)
Q Consensus 122 R~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i 157 (530)
++.+.|.+-+|||+.++++.+...+....|.+.=.+
T Consensus 10 ~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V 45 (62)
T PF04703_consen 10 KEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKV 45 (62)
T ss_dssp HHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSE
T ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 344889999999999999999998888877765433
No 275
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=50.94 E-value=23 Score=32.66 Aligned_cols=36 Identities=11% Similarity=0.053 Sum_probs=31.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...+.++||+.+|+|+.|++.++.-..+.|-+.+.+
T Consensus 123 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 123 HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999999988888777654
No 276
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=50.82 E-value=48 Score=24.61 Aligned_cols=43 Identities=14% Similarity=0.091 Sum_probs=29.4
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHH
Q 047665 106 GDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRV 151 (530)
Q Consensus 106 GR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L 151 (530)
+........+-|+-.|+.. .|+++||..+|++..++.+.+...
T Consensus 9 ~~r~T~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 9 YCRITKRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCcHHHHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3333343444444444433 799999999999999999988753
No 277
>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=50.81 E-value=34 Score=27.54 Aligned_cols=31 Identities=19% Similarity=0.285 Sum_probs=23.6
Q ss_pred HcCCCCCHHHHHHHhCCC-HHHHHHHHHHHHH
Q 047665 227 LNGVSVKIENVAKEVHCT-VVTCRKRYKELLE 257 (530)
Q Consensus 227 ~~g~k~t~~eIA~~~~VS-~~TIrkRyKEL~e 257 (530)
.+|..-|..|||+.+|++ ..|+...++.|.+
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 356777999999999997 9999998887764
No 278
>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=50.81 E-value=35 Score=30.61 Aligned_cols=37 Identities=14% Similarity=0.093 Sum_probs=30.1
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 220 VLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 220 AIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.+|+|. ..+-..+..+||+..+++.++++++++.|.+
T Consensus 15 l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 15 LTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred HHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 445543 2345689999999999999999999999887
No 279
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=50.74 E-value=24 Score=32.31 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|.++||+..|+|+.|+++++....+.|-+
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999999887776654
No 280
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=50.74 E-value=37 Score=27.35 Aligned_cols=38 Identities=11% Similarity=0.065 Sum_probs=30.7
Q ss_pred HHHHHHhcCC-CCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 117 SYVVMRLDDK-SLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 117 lYiACR~~~~-P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
|+...+.++- +++..|||..+|++...+.+....|.+.
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5555666666 4999999999999999999888777664
No 281
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=50.37 E-value=24 Score=32.57 Aligned_cols=33 Identities=18% Similarity=0.190 Sum_probs=28.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
..|.++||+.+|+|+.|+++++.-....|-+.+
T Consensus 135 g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 135 DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 589999999999999999999988887776554
No 282
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=50.33 E-value=13 Score=28.62 Aligned_cols=43 Identities=14% Similarity=0.349 Sum_probs=36.7
Q ss_pred HHHHHHhhhcCCCCCCchhhhhhHHHHHHHHHHHHHHHhHHhh
Q 047665 416 LLKKILEKDVGLDVMPPSFVNGCMVNERRRAKINAAKIRIDKI 458 (530)
Q Consensus 416 ~~~~~~~~~~~~~~~pp~~~~~~~~~~~~~~~i~~ak~r~~~~ 458 (530)
++++|=..|+.+|-...-|-.|+...+.=+++++.|+.+|..|
T Consensus 11 Iv~~Le~~~~sLdes~~lyeeg~~l~~~c~~~L~~~e~~i~~l 53 (53)
T PF02609_consen 11 IVEKLESGELSLDESLKLYEEGMELIKKCQERLEEAEQKIEEL 53 (53)
T ss_dssp HHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 5566667899999999999999999999999999999999765
No 283
>PRK09492 treR trehalose repressor; Provisional
Probab=50.33 E-value=15 Score=37.00 Aligned_cols=38 Identities=16% Similarity=0.162 Sum_probs=30.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHhhcccCCC
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYK-------ELLEALVKVAQALPW 268 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyK-------EL~e~L~~l~~~lpW 268 (530)
+.|++|||+.+|||..|+++.+. |-.+...+.+.++=|
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY 48 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGF 48 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCC
Confidence 57999999999999999999886 566666666666544
No 284
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=50.26 E-value=13 Score=32.92 Aligned_cols=27 Identities=33% Similarity=0.700 Sum_probs=0.0
Q ss_pred CCCCCCCCeEEecCC--------------CcEEcCCCceee
Q 047665 3 CTSCGSKTLTREDIS--------------GSLICVSCGVVQ 29 (530)
Q Consensus 3 Cp~CG~~~iv~D~~~--------------G~~VCt~CG~Vl 29 (530)
||.||+..++.+... ...+|..||-.+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
No 285
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=50.17 E-value=23 Score=32.39 Aligned_cols=35 Identities=6% Similarity=0.066 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+.++||+..|+|+.|+++++..-...|-+.+.
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999888877776654
No 286
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=50.10 E-value=4.4 Score=31.37 Aligned_cols=31 Identities=19% Similarity=0.430 Sum_probs=23.0
Q ss_pred CCCCCCCCCeE-EecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLT-REDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv-~D~~~G~~VCt~CG~Vle~~ 32 (530)
+|++|+.--.. .+....++-|.-||++-.-.
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKTINHVR 37 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence 79999974222 35556899999999997643
No 287
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=50.03 E-value=25 Score=32.20 Aligned_cols=36 Identities=6% Similarity=0.024 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.++||+.+|+|+.|++.++.--...|-+.+.+
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~ 155 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999998877777665543
No 288
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=49.98 E-value=25 Score=33.03 Aligned_cols=35 Identities=17% Similarity=0.142 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+.++||+..|+|+.|+++++.-..+.|-+.+.
T Consensus 150 ~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 150 QGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 36899999999999999999998887777765443
No 289
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=49.88 E-value=22 Score=33.64 Aligned_cols=35 Identities=11% Similarity=0.096 Sum_probs=30.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
..|.+|||+.+|+|+.||++++.-....|-+.+..
T Consensus 147 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 147 ELETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999999998888888766654
No 290
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=49.86 E-value=4e+02 Score=29.66 Aligned_cols=91 Identities=15% Similarity=0.188 Sum_probs=55.7
Q ss_pred cchHhHHHHHHH-----------HHHHHHHhhcC-CCHHHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhc--C
Q 047665 60 LNYKEKKIYESN-----------KLIDELTFKLD-LTGQRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLD--D 125 (530)
Q Consensus 60 ~s~rer~L~~a~-----------~~I~~i~~~Lg-Lp~~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~--~ 125 (530)
.+..|+.+...+ .-+..++..++ +....++.+...+..+.-.|...- + +.=|+.+-.++. .
T Consensus 105 ~s~~e~~Ia~~lI~~Ldd~GYl~~~le~~~~~l~~~~~~eve~vl~~iQ~ldP~GV~Ar-~----l~EcL~lQL~~~~~~ 179 (444)
T COG1508 105 LSDTERAIATYLIDALDDEGYLTESLEEIAELLGSVDEEEVEKVLARIQSLDPAGVGAR-D----LRECLLLQLERRPLD 179 (444)
T ss_pred CChHHHHHHHHHHhhcCcCCCcccCHHHHHHhcccccHHHHHHHHHHHhcCCCCccccC-c----HHHHHHHHHHhcCCC
Confidence 355666664432 13778888888 777788888777777655554310 0 222333333321 1
Q ss_pred CC--------------CChHHHHHHhCCCHHHHHHHHHHHHHHh
Q 047665 126 KS--------------LPISEVASVLNCDVYELGRMITRVVEFL 155 (530)
Q Consensus 126 ~P--------------~TL~DIA~~~~vd~~~Lgr~~k~L~k~L 155 (530)
.| +-+..|+..++++.+++..+...|....
T Consensus 180 ~~~~~~v~~~l~lla~~d~~~i~~~~~v~~~dl~~~l~~I~~l~ 223 (444)
T COG1508 180 DPALEIVIDHLELLARRDFTTIARELKVDEDELKEALLLIRSLD 223 (444)
T ss_pred ChhHHHHHHHHHHHHhhhHHHHHHHhCCCHHHHHHHHHHHHccC
Confidence 11 1256688899999999999888887654
No 291
>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=49.85 E-value=24 Score=26.85 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=23.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+..++|+.+++|.+|+++.++.|.+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5899999999999999999988877
No 292
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=49.64 E-value=25 Score=32.91 Aligned_cols=35 Identities=26% Similarity=0.333 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+..+||+.+|+|+.|+++++.-..+.|-+...
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 46899999999999999999999888887766554
No 293
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=49.57 E-value=12 Score=32.42 Aligned_cols=39 Identities=23% Similarity=0.295 Sum_probs=32.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccCCCC
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQALPWG 269 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~lpW~ 269 (530)
.++|..||+.+||+++||.+.-.++.+....++..+.|.
T Consensus 23 ~~gq~~vA~~~Gv~eStISR~k~~~~~~~a~lLa~L~~~ 61 (91)
T PF05269_consen 23 SVGQKKVAEAMGVDESTISRWKNDFIEKMAMLLAALELG 61 (91)
T ss_dssp HHHHHHHHHHHTSSTTTHHHHHHHHHHHHHHHHHHTTTT
T ss_pred HHhhHHHHHHhCCCHHHHHHHHhhHHHHHHHHHHHHHhc
Confidence 467899999999999999887778778888888777674
No 294
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=49.53 E-value=26 Score=33.01 Aligned_cols=32 Identities=13% Similarity=0.196 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|.+|||+.+|+|+.|++.++..-...+.+
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998865555543
No 295
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=49.45 E-value=47 Score=27.34 Aligned_cols=28 Identities=14% Similarity=0.204 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
-.++..+||+.++++.+|+++.++.|.+
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3699999999999999999998888865
No 296
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=49.30 E-value=27 Score=32.44 Aligned_cols=33 Identities=3% Similarity=0.057 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|.+|||+.+|+|+.|++++++.-...+...
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999988766666443
No 297
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=49.24 E-value=26 Score=33.04 Aligned_cols=35 Identities=9% Similarity=0.197 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+.+|+|+.|+++++.--...|-+.+.
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 45899999999999999999998887777766553
No 298
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=49.21 E-value=22 Score=33.62 Aligned_cols=35 Identities=31% Similarity=0.367 Sum_probs=29.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+..|+|+.||++++......|-+.++
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998877776655443
No 299
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=49.11 E-value=41 Score=27.45 Aligned_cols=43 Identities=14% Similarity=0.234 Sum_probs=37.4
Q ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccCCC
Q 047665 226 ELNGVSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQALPW 268 (530)
Q Consensus 226 ~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~lpW 268 (530)
.+++..+|..+.|+.+|+++.||++.++.+..-+.+|=+.--|
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPSG~~ 50 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPSGHW 50 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCCCh
Confidence 4567789999999999999999999999999999888665445
No 300
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=49.05 E-value=23 Score=33.70 Aligned_cols=36 Identities=8% Similarity=0.162 Sum_probs=31.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...+.++||+.+|+|..|+++|+.-....|-+.+..
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 368999999999999999999999888888777654
No 301
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=49.00 E-value=26 Score=32.95 Aligned_cols=36 Identities=11% Similarity=-0.078 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|..+||+..|+|..||++++.--...|-+.+..
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999988877777766654
No 302
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=48.93 E-value=24 Score=31.85 Aligned_cols=31 Identities=26% Similarity=0.318 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
...|.+|||+..|+|+.||++++......|-
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 4688999999999999999999887766653
No 303
>PRK09480 slmA division inhibitor protein; Provisional
Probab=48.90 E-value=27 Score=32.66 Aligned_cols=44 Identities=9% Similarity=0.134 Sum_probs=31.5
Q ss_pred hhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 214 MPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 214 ~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.-|..|++-+...-.|...|+.+||+.+|||..|+-..++.-.+
T Consensus 13 ~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 13 EQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 34444554444333356799999999999999999888876444
No 304
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=48.79 E-value=2.7e+02 Score=27.22 Aligned_cols=31 Identities=16% Similarity=0.143 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
...|+++||+..|+|+.+|++..+...+.|-
T Consensus 198 ~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 198 KDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4689999999999999999998887776664
No 305
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=48.74 E-value=24 Score=33.48 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.+|||+..|+|+.||++++..-...|-+.+.
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999988776666655544
No 306
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=48.57 E-value=38 Score=31.71 Aligned_cols=46 Identities=11% Similarity=0.112 Sum_probs=39.8
Q ss_pred hhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 109 FPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 109 ~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
.++.+-|.+|+|....+-|.|..+||...++++.-|.+.+..|++.
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 4566778899998777669999999999999999999999888874
No 307
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=48.46 E-value=17 Score=36.83 Aligned_cols=29 Identities=28% Similarity=0.178 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
-.++.+|+|+.++||+.|||+.+++|.+.
T Consensus 18 ~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 18 GKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred CCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 35899999999999999999999998765
No 308
>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=48.37 E-value=21 Score=25.60 Aligned_cols=22 Identities=14% Similarity=0.137 Sum_probs=18.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 047665 232 VKIENVAKEVHCTVVTCRKRYK 253 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyK 253 (530)
+|.+|+|+.+|||..||.+.++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999987653
No 309
>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=48.30 E-value=44 Score=25.34 Aligned_cols=27 Identities=15% Similarity=0.188 Sum_probs=23.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.+++.+||+.++++.+|+.+.++.|.+
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 489999999999999999998888765
No 310
>PF14122 YokU: YokU-like protein
Probab=48.04 E-value=18 Score=31.02 Aligned_cols=31 Identities=42% Similarity=0.806 Sum_probs=21.8
Q ss_pred CCCCCCCC-------CeEEecCCCc----------EEcCCCceeeccc
Q 047665 2 PCTSCGSK-------TLTREDISGS----------LICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~-------~iv~D~~~G~----------~VCt~CG~Vle~~ 32 (530)
.|--||+. ++.++-..|. ++|.+||.|.-+.
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDD 48 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehh
Confidence 36677752 4566655564 8999999998754
No 311
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=47.94 E-value=30 Score=36.23 Aligned_cols=89 Identities=11% Similarity=0.122 Sum_probs=59.7
Q ss_pred hHHHHHHHhcccCCCCccchHHHHHHHHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCC--CCCHHHHHHH-hC
Q 047665 166 SMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGV--SVKIENVAKE-VH 242 (530)
Q Consensus 166 ~~I~R~~~~L~l~~v~~v~~e~~~~V~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~--k~t~~eIA~~-~~ 242 (530)
.+|..+|.+|++ + .++..+|..+.++-.-..-+.+-+|..||+++||+|++..+- .+...-.... .+
T Consensus 50 k~i~~l~~~L~l---p-------~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~ 119 (297)
T COG5333 50 KLIMDLCTRLNL---P-------QTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLW 119 (297)
T ss_pred HHHHHHHHhcCC---C-------cchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccc
Confidence 567888999997 4 256677777777755555578999999999999999998773 3332222211 11
Q ss_pred CC-HHHHHHHHHHHHHHHHhhcc
Q 047665 243 CT-VVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 243 VS-~~TIrkRyKEL~e~L~~l~~ 264 (530)
-- ..+-|+|+-++...+.+...
T Consensus 120 se~~~~sr~~Il~~E~~lLEaL~ 142 (297)
T COG5333 120 SEEPKSSRERILEYEFELLEALD 142 (297)
T ss_pred cccccccHHHHHHHHHHHHHHcc
Confidence 11 35667788777777666554
No 312
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=47.85 E-value=28 Score=32.13 Aligned_cols=34 Identities=21% Similarity=0.241 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...|.+|||+..|+|+.|+++++......|-...
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4688999999999999999999988877776544
No 313
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=47.81 E-value=28 Score=32.91 Aligned_cols=34 Identities=12% Similarity=0.103 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...|.++||+.+|+|..||+.++.-..+.|-+.+
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 4799999999999999999999998888776543
No 314
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=47.77 E-value=28 Score=32.34 Aligned_cols=32 Identities=22% Similarity=0.241 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+++||+.+|+|..||+++.+...+.|..
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 45799999999999999999988887777764
No 315
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.54 E-value=16 Score=32.50 Aligned_cols=24 Identities=33% Similarity=0.800 Sum_probs=0.0
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
+||.||..-+++. +-|.+||+-+.
T Consensus 8 ~cPvcg~~~iVTe-----L~c~~~etTVr 31 (122)
T COG3877 8 RCPVCGRKLIVTE-----LKCSNCETTVR 31 (122)
T ss_pred CCCcccccceeEE-----EecCCCCceEe
No 316
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=47.47 E-value=23 Score=32.49 Aligned_cols=31 Identities=23% Similarity=0.358 Sum_probs=26.8
Q ss_pred cCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 228 NGVS-VKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 228 ~g~k-~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
.|.+ -|..++|..++|.+.|+++.|+||.+.
T Consensus 31 pGdkLPSvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 31 PGDKLPSVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred CCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 3555 568999999999999999999999873
No 317
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=47.29 E-value=9.9 Score=29.74 Aligned_cols=28 Identities=25% Similarity=0.464 Sum_probs=20.1
Q ss_pred CCCCCCCCC---CeEEecCCCcEEcCCCcee
Q 047665 1 MPCTSCGSK---TLTREDISGSLICVSCGVV 28 (530)
Q Consensus 1 M~Cp~CG~~---~iv~D~~~G~~VCt~CG~V 28 (530)
+.|++|... ....+...-..+|..||..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 369999862 2246666678999999963
No 318
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=47.25 E-value=15 Score=27.58 Aligned_cols=28 Identities=32% Similarity=0.606 Sum_probs=18.5
Q ss_pred CCCCCCCCCeEEecCC-------CcEEcCC--Cceee
Q 047665 2 PCTSCGSKTLTREDIS-------GSLICVS--CGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~-------G~~VCt~--CG~Vl 29 (530)
.||.||+...+.-... --..|++ ||.-.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 5999999765554332 2357887 98753
No 319
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=47.20 E-value=31 Score=26.77 Aligned_cols=30 Identities=23% Similarity=0.212 Sum_probs=27.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 232 VKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
-++...|+..++|.+++.+++++|.+.+..
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg~ 43 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELGV 43 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence 378889999999999999999999999853
No 320
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=47.02 E-value=3.8 Score=42.80 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=22.3
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
+||+|+..-...|-.....||..||.-..
T Consensus 40 kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 40 QCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred ECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 69999986545555567789999998654
No 321
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=46.84 E-value=67 Score=25.82 Aligned_cols=30 Identities=13% Similarity=0.087 Sum_probs=25.7
Q ss_pred cCC-CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 228 NGV-SVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 228 ~g~-k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.|- .++..+||+.+|++..++++.+..|.+
T Consensus 18 ~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 18 SGDETSTALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 444 499999999999999999998887766
No 322
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=46.73 E-value=4 Score=42.40 Aligned_cols=29 Identities=24% Similarity=0.492 Sum_probs=21.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||+|+......|-.....||..||.-..
T Consensus 28 ~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 28 KCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred ECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 69999986444445556789999998654
No 323
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=46.68 E-value=30 Score=33.45 Aligned_cols=27 Identities=26% Similarity=0.319 Sum_probs=23.3
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKE 254 (530)
...-.|..+||...|.|+.|||+.++.
T Consensus 58 ekag~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 58 EKAGMTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred HHccCcHHHHHHHhCCCHHHHHHHHhc
Confidence 335689999999999999999998773
No 324
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=46.46 E-value=28 Score=33.18 Aligned_cols=35 Identities=14% Similarity=0.163 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+..|+|+.|+++++.-....|.+.+.
T Consensus 169 e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~ 203 (208)
T PRK08295 169 DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLE 203 (208)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999999988888877654
No 325
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=46.43 E-value=27 Score=33.29 Aligned_cols=35 Identities=14% Similarity=0.028 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+.+|||+.+|+|+.|++.++.-....|.+.+.
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 143 GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999888877766654
No 326
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=46.24 E-value=29 Score=34.16 Aligned_cols=35 Identities=14% Similarity=0.091 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.+|||+.+|+|+.|+++++.-....|-+.+.
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 46899999999999999999999888887766654
No 327
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=45.93 E-value=29 Score=33.08 Aligned_cols=36 Identities=22% Similarity=0.269 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.|+++++..-...|-+.+..
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999998888777766653
No 328
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=45.77 E-value=15 Score=26.51 Aligned_cols=10 Identities=40% Similarity=0.986 Sum_probs=7.5
Q ss_pred EEcCCCceee
Q 047665 20 LICVSCGVVQ 29 (530)
Q Consensus 20 ~VCt~CG~Vl 29 (530)
.+|..||-.+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3599999765
No 329
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=45.71 E-value=65 Score=25.11 Aligned_cols=30 Identities=17% Similarity=0.204 Sum_probs=23.7
Q ss_pred cCCC--CChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 124 DDKS--LPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 124 ~~~P--~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
.++| .|+.|+|+.+|++...+...+++..+
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3455 78999999999999888877666544
No 330
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=45.65 E-value=6 Score=39.41 Aligned_cols=30 Identities=33% Similarity=0.666 Sum_probs=26.1
Q ss_pred CCCCCCCC--CCeEEecCCCc---EEcCCCceeec
Q 047665 1 MPCTSCGS--KTLTREDISGS---LICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~--~~iv~D~~~G~---~VCt~CG~Vle 30 (530)
|+|-+||+ .++..++..|. ..|.+|+.|+|
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vD 35 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVD 35 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhhHHH
Confidence 78999998 47888888894 58999999998
No 331
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=45.60 E-value=13 Score=36.63 Aligned_cols=29 Identities=34% Similarity=0.702 Sum_probs=20.4
Q ss_pred CCCCCCCCC--eEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKT--LTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~--iv~D~~~G~~VCt~CG~Vle 30 (530)
.||.|++++ ++.+...=.+.|..||..-.
T Consensus 100 ~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 100 ICSECGLPDTRLVKEDRVLMLRCDACGAHRP 130 (201)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCCcc
Confidence 599999964 44442222469999998865
No 332
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=45.51 E-value=24 Score=35.66 Aligned_cols=28 Identities=25% Similarity=0.278 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
-.++++++|+.++||+.|||+.+++|.+
T Consensus 18 ~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 18 GFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4689999999999999999999999865
No 333
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=45.45 E-value=31 Score=31.27 Aligned_cols=32 Identities=22% Similarity=0.179 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...+.++||+.+|+|+.|++.++......|-.
T Consensus 126 ~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 126 RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999998877766643
No 334
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=45.44 E-value=29 Score=24.90 Aligned_cols=26 Identities=12% Similarity=0.238 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKEL 255 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL 255 (530)
.+.++.+||..+|+|+...++.+++.
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999999988864
No 335
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=45.30 E-value=30 Score=31.69 Aligned_cols=30 Identities=10% Similarity=0.125 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
...|.+|||+.+|+|..|++.++.--.+.|
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 468999999999999999999988776655
No 336
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=45.29 E-value=33 Score=31.35 Aligned_cols=34 Identities=12% Similarity=0.074 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...|.+|||+.+|+|..||+.++.--...|-+.+
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999998776666555443
No 337
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=45.14 E-value=32 Score=32.11 Aligned_cols=36 Identities=8% Similarity=0.173 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...+.++||+.+|+|+.|+++++.-....|.+.+..
T Consensus 115 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999998888877776654
No 338
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=45.10 E-value=10 Score=28.92 Aligned_cols=14 Identities=29% Similarity=0.593 Sum_probs=10.1
Q ss_pred EEcCCCceeecccC
Q 047665 20 LICVSCGVVQAFDN 33 (530)
Q Consensus 20 ~VCt~CG~Vle~~~ 33 (530)
..|..||.|.++..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 57888888887543
No 339
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=44.72 E-value=6 Score=40.83 Aligned_cols=29 Identities=31% Similarity=0.598 Sum_probs=22.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||+||.-....|-.....||..||.-..
T Consensus 30 KCp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 30 KCPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred ECCCccceeeHHHHHhhhhcccccCcccc
Confidence 59999986545555667889999998765
No 340
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=44.71 E-value=33 Score=32.21 Aligned_cols=34 Identities=12% Similarity=0.066 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...|.+|||+.+|+|+.|+++++..-...|-+.+
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4689999999999999999999988777765543
No 341
>PF13518 HTH_28: Helix-turn-helix domain
Probab=44.70 E-value=33 Score=25.19 Aligned_cols=25 Identities=20% Similarity=0.248 Sum_probs=22.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
|+.++|+..|||..||...++.+.+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 9999999999999999888777766
No 342
>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=44.66 E-value=43 Score=26.02 Aligned_cols=30 Identities=20% Similarity=0.242 Sum_probs=26.2
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.+...|..+||+.++++.+|+...++.|.+
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456899999999999999999999999877
No 343
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=44.57 E-value=32 Score=32.75 Aligned_cols=36 Identities=14% Similarity=0.070 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.++||+.+|+|+.|+++++.-....|-++...
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~ 161 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEG 161 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 368899999999999999999988777777666553
No 344
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=44.32 E-value=14 Score=29.61 Aligned_cols=27 Identities=30% Similarity=0.762 Sum_probs=15.6
Q ss_pred CCCCCCCCCeEEecC----CCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDI----SGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~----~G~~VCt~CG~V 28 (530)
.||+||...|..... ...++|.+||+.
T Consensus 29 ~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 29 PCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence 377777655444332 234677777764
No 345
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=44.22 E-value=32 Score=31.52 Aligned_cols=35 Identities=14% Similarity=0.188 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+..+||+..|+|+.||++++......|-+.+.
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998887777765543
No 346
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=44.10 E-value=32 Score=32.50 Aligned_cols=33 Identities=18% Similarity=0.208 Sum_probs=27.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
..|.+|||+..|+|+.||+.++.--.+.|-+.+
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 589999999999999999988877666665543
No 347
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=44.08 E-value=33 Score=32.84 Aligned_cols=31 Identities=16% Similarity=0.196 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
.-.|-++||+..++|+.|+++..+.|+..|.
T Consensus 164 ~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 164 EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 3578899999999999999999999888764
No 348
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=44.07 E-value=83 Score=29.90 Aligned_cols=40 Identities=23% Similarity=0.331 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhh
Q 047665 112 LIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFLN 156 (530)
Q Consensus 112 vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~ 156 (530)
++=|.+|++ +-|+++.+++..++ +..++......|.+.++
T Consensus 2 ~iEAlLF~s----~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~ 41 (159)
T PF04079_consen 2 IIEALLFAS----GEPVSIEELAEILG-SEDEVEEALEELQEEYN 41 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHH
T ss_pred hhHhhHHHc----CCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhc
Confidence 456777765 56999999999999 99999999999999884
No 349
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=44.01 E-value=32 Score=32.36 Aligned_cols=34 Identities=15% Similarity=0.154 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...+.++||+.+|+|+.||++++.-....|-..+
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999988888776544
No 350
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.97 E-value=9.9 Score=34.39 Aligned_cols=18 Identities=33% Similarity=0.567 Sum_probs=15.4
Q ss_pred EecCCCcEEcCCCceeec
Q 047665 13 REDISGSLICVSCGVVQA 30 (530)
Q Consensus 13 ~D~~~G~~VCt~CG~Vle 30 (530)
.|-.+|+++|.+||.|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 455689999999999976
No 351
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=43.86 E-value=36 Score=31.71 Aligned_cols=35 Identities=20% Similarity=0.218 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+.++||+..|+|..|+++++.-....|-+.+.
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 47899999999999999999998877776665543
No 352
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=43.85 E-value=24 Score=29.80 Aligned_cols=24 Identities=17% Similarity=0.153 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYK 253 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyK 253 (530)
-..|+.+||+.+|||..||+..+.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 367899999999999999998653
No 353
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=43.85 E-value=16 Score=32.09 Aligned_cols=29 Identities=24% Similarity=0.574 Sum_probs=22.3
Q ss_pred CCCCCCCCCeEEecCC-CcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDIS-GSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~-G~~VCt~CG~Vle 30 (530)
.||.||.--++..... ....|..|+.|..
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 6999999655554444 4679999999976
No 354
>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=43.83 E-value=37 Score=27.35 Aligned_cols=32 Identities=13% Similarity=0.174 Sum_probs=23.6
Q ss_pred HhcCCCCChHHHHHHhCCC-HHHHHHHHHHHHH
Q 047665 122 RLDDKSLPISEVASVLNCD-VYELGRMITRVVE 153 (530)
Q Consensus 122 R~~~~P~TL~DIA~~~~vd-~~~Lgr~~k~L~k 153 (530)
..+|.|-|++||++.+|+. ...+....+.|.+
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 4789999999999999997 8887777666654
No 355
>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=43.78 E-value=56 Score=24.87 Aligned_cols=26 Identities=19% Similarity=0.317 Sum_probs=23.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 232 VKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.+..+|++.++++..|+++.++.|.+
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 89999999999999999998888755
No 356
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=43.74 E-value=4.7 Score=42.02 Aligned_cols=29 Identities=28% Similarity=0.572 Sum_probs=21.8
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||+|+......|-.....||..||.-..
T Consensus 29 ~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 29 KCPSCGQVLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred ECCCccchhhHHHHHhcCCCCCCCCCCee
Confidence 69999986444455556679999998754
No 357
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=43.70 E-value=12 Score=28.90 Aligned_cols=27 Identities=22% Similarity=0.656 Sum_probs=19.3
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vl 29 (530)
.|-.||.. +..|.....+-|+.||.=+
T Consensus 8 ~C~~Cg~~-~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 8 KCARCGRE-VELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EhhhcCCe-eehhhccCceeCCCCCcEE
Confidence 48889885 2335567788999999643
No 358
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=43.63 E-value=31 Score=33.21 Aligned_cols=35 Identities=14% Similarity=0.217 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.+|||+.+|+|+.|++.|+.--...|-+.+.
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999998876666655543
No 359
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=43.44 E-value=36 Score=27.36 Aligned_cols=22 Identities=18% Similarity=0.240 Sum_probs=18.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 047665 232 VKIENVAKEVHCTVVTCRKRYK 253 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyK 253 (530)
.++.+||+.+|||..||...+.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3788999999999999977543
No 360
>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=43.34 E-value=3.9e+02 Score=27.61 Aligned_cols=129 Identities=11% Similarity=0.036 Sum_probs=65.8
Q ss_pred HHHHHHhcCC-CCChHHHHHHhCCCH-HHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHH------
Q 047665 117 SYVVMRLDDK-SLPISEVASVLNCDV-YELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESML------ 188 (530)
Q Consensus 117 lYiACR~~~~-P~TL~DIA~~~~vd~-~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~------ 188 (530)
=|+..|+... ..|++++|..+|++. .-|. ..++-+-+. +...+++++..|++ +....+-.
T Consensus 16 d~ye~rk~~~p~fS~R~fa~~~G~ss~s~L~-------~v~~Gkr~L--s~~~~~k~a~~l~L---~~~E~~yF~~lV~f 83 (271)
T TIGR02147 16 DYYEERKKTDPAFSWRFFAEKAGFSSTSYLN-------DIIKGKKNL--TKRMIPKFAEALGL---DEKEAAYFEAMVNF 83 (271)
T ss_pred HHHHHHhccCcCcCHHHHHHHhCCCCHHHHH-------HHHcCCCCC--CHHHHHHHHHHcCC---CHHHHHHHHHHHHH
Confidence 3666777655 599999999999876 4333 333333222 24578888888887 32111111
Q ss_pred -----HHHHHHHHH-HHHHHh--hcccccccCch---hHHHHHHHHHHHHcCCCCCHHHHHHHhC--CCHHHHHHHHHHH
Q 047665 189 -----DRMRKQGVL-LLNCAV--KWFLTTGRRPM---PVVVAVLVFVVELNGVSVKIENVAKEVH--CTVVTCRKRYKEL 255 (530)
Q Consensus 189 -----~~V~~~A~~-Ll~~a~--~~~l~tGR~P~---sIAAAAIYlAa~~~g~k~t~~eIA~~~~--VS~~TIrkRyKEL 255 (530)
....+.+.. +.+.+. ...++.+..-. .-.-.+|.-...+.+..-+..+||+.++ ||..-++..+.-|
T Consensus 84 ~~ak~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L 163 (271)
T TIGR02147 84 GQAKTDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLL 163 (271)
T ss_pred hccCCHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 111122211 111111 11111111100 1111122222233445567889999998 8988888876655
Q ss_pred HH
Q 047665 256 LE 257 (530)
Q Consensus 256 ~e 257 (530)
.+
T Consensus 164 ~~ 165 (271)
T TIGR02147 164 ER 165 (271)
T ss_pred HH
Confidence 44
No 361
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=43.17 E-value=37 Score=31.70 Aligned_cols=34 Identities=12% Similarity=0.098 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...+.++||...|+|+.||++++......|-+++
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4679999999999999999999887777765543
No 362
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=43.13 E-value=35 Score=31.79 Aligned_cols=33 Identities=15% Similarity=0.159 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|.++||+..|+|+.|+++++.--...|-+.
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 358899999999999999999988777766554
No 363
>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=43.01 E-value=43 Score=25.98 Aligned_cols=32 Identities=22% Similarity=0.287 Sum_probs=24.2
Q ss_pred hcCCCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 123 LDDKSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 123 ~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
..+-|.++.+|++.++++...+.+.++++.+.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56788999999999999999999998888763
No 364
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=42.86 E-value=35 Score=32.10 Aligned_cols=33 Identities=18% Similarity=0.184 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|.+|||+..|+|+.|+++++.-..+.|-+.
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 468999999999999999999988877766543
No 365
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=42.80 E-value=19 Score=25.97 Aligned_cols=18 Identities=33% Similarity=0.226 Sum_probs=15.0
Q ss_pred CHHHHHHHhCCCHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRK 250 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrk 250 (530)
|..|+|+.+|||..|||.
T Consensus 1 ti~e~A~~~gvs~~tlR~ 18 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRY 18 (38)
T ss_dssp EHHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 467999999999999986
No 366
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=42.77 E-value=35 Score=32.94 Aligned_cols=35 Identities=17% Similarity=0.209 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+.+|+|+.|++.++..-...|.+.+.
T Consensus 168 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999998877777766543
No 367
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=42.73 E-value=35 Score=32.28 Aligned_cols=36 Identities=8% Similarity=0.139 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...+..+||..+|+|+.|+++++.-....|.+.+..
T Consensus 121 ~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 121 EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999998887777766654
No 368
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=42.71 E-value=34 Score=32.52 Aligned_cols=34 Identities=9% Similarity=0.020 Sum_probs=28.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
..|.+|||+.+|+|+.|++.|+.--...|-+.+.
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 150 ELSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 6889999999999999999998877766655443
No 369
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=42.66 E-value=37 Score=32.01 Aligned_cols=35 Identities=17% Similarity=0.190 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|..|||+.+||+..|+++|+..=...|-+...
T Consensus 142 ~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 142 EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999999877777766554
No 370
>PRK06930 positive control sigma-like factor; Validated
Probab=42.57 E-value=35 Score=32.66 Aligned_cols=36 Identities=6% Similarity=0.079 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.++||+.+|+|+.|++.++......|.+.+..
T Consensus 129 eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~ 164 (170)
T PRK06930 129 YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINE 164 (170)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999999888888766543
No 371
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=42.09 E-value=42 Score=31.44 Aligned_cols=34 Identities=18% Similarity=0.140 Sum_probs=29.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
..|..+||+.+|+|..|+++++......|-..+.
T Consensus 147 g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 147 GASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 6899999999999999999999888887766554
No 372
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=42.04 E-value=19 Score=25.37 Aligned_cols=23 Identities=30% Similarity=0.700 Sum_probs=11.8
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCce
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~ 27 (530)
+|+.||. +.+...--.+|..||.
T Consensus 4 ~C~~CG~---i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 4 VCPVCGY---IHEGEEAPEKCPICGA 26 (34)
T ss_pred ECCCCCC---EeECCcCCCcCcCCCC
Confidence 4666765 2232223346766665
No 373
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=41.98 E-value=20 Score=32.98 Aligned_cols=27 Identities=30% Similarity=0.662 Sum_probs=19.6
Q ss_pred CCC--CCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCT--SCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp--~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.|| .|+.. +..+ .+|.+.|..||..++
T Consensus 20 aC~~~~C~kK-v~~~-~~~~y~C~~C~~~~~ 48 (146)
T PF08646_consen 20 ACPNEKCNKK-VTEN-GDGSYRCEKCNKTVE 48 (146)
T ss_dssp E-TSTTTS-B--EEE-TTTEEEETTTTEEES
T ss_pred CCCCccCCCE-eecC-CCcEEECCCCCCcCC
Confidence 599 99985 3444 679999999999875
No 374
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=41.88 E-value=39 Score=31.98 Aligned_cols=32 Identities=25% Similarity=0.345 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|.+|||+.+|+|+.|+++++.--...|-+
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46889999999999999999998877776665
No 375
>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=41.86 E-value=47 Score=25.73 Aligned_cols=31 Identities=16% Similarity=0.162 Sum_probs=23.6
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
.+...++.+||+.++++..|+.+.+++|.+.
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3567999999999999999999988887763
No 376
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=41.84 E-value=11 Score=40.96 Aligned_cols=30 Identities=23% Similarity=0.516 Sum_probs=23.0
Q ss_pred CCCCCCCC------CeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSK------TLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~------~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||.|++. .-..|..+|...|..||.=+.+
T Consensus 130 ~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 130 VCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred cCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 59999974 2345677899999999976653
No 377
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=41.75 E-value=49 Score=24.51 Aligned_cols=31 Identities=23% Similarity=0.332 Sum_probs=25.3
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHHHHHh
Q 047665 125 DKSLPISEVASVLNCDVYELGRMITRVVEFL 155 (530)
Q Consensus 125 ~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L 155 (530)
.-+.|+.|||..+|++...+.+...+..+.|
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 5678999999999999999988877766554
No 378
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=41.57 E-value=39 Score=31.26 Aligned_cols=33 Identities=21% Similarity=0.186 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...+.++||+..|+|+.|+++++.--.+.|-+.
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 368999999999999999999988777766554
No 379
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=41.55 E-value=38 Score=32.32 Aligned_cols=35 Identities=11% Similarity=0.017 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+.++||+..|+|..||++++.--...|-+.+.
T Consensus 151 ~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999999887777765544
No 380
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=41.54 E-value=18 Score=27.93 Aligned_cols=30 Identities=30% Similarity=0.739 Sum_probs=20.3
Q ss_pred CCCCCCCC-CCeEEec-CCCc-EEcCCCceeec
Q 047665 1 MPCTSCGS-KTLTRED-ISGS-LICVSCGVVQA 30 (530)
Q Consensus 1 M~Cp~CG~-~~iv~D~-~~G~-~VCt~CG~Vle 30 (530)
+.|.+|+. .+..+-. ..|. .+|..||+-..
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~ 36 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYYK 36 (52)
T ss_pred CCcCCCCCCCCCccccCCCCCCcEeecccHHHH
Confidence 36999997 3445533 3455 89999997554
No 381
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=41.50 E-value=49 Score=30.21 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=37.7
Q ss_pred hhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 109 FPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 109 ~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
.++-+-+.+|++--..+.+.+..+||+.++++..-+.+++..|.+.
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 3455667777775556678999999999999999999999988874
No 382
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=41.32 E-value=26 Score=28.75 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=18.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKE 254 (530)
...|..+||+.++||++||.+-.+.
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHH
Confidence 4689999999999999999876553
No 383
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=41.19 E-value=19 Score=27.71 Aligned_cols=13 Identities=23% Similarity=0.488 Sum_probs=9.4
Q ss_pred EEcCCCceeeccc
Q 047665 20 LICVSCGVVQAFD 32 (530)
Q Consensus 20 ~VCt~CG~Vle~~ 32 (530)
.+|..||.|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 4688888887754
No 384
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=41.04 E-value=59 Score=23.89 Aligned_cols=29 Identities=24% Similarity=0.264 Sum_probs=22.8
Q ss_pred hcCCCCChHHHHHHhCCCHHHHHHHHHHH
Q 047665 123 LDDKSLPISEVASVLNCDVYELGRMITRV 151 (530)
Q Consensus 123 ~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L 151 (530)
+.+..+|..+||..+|++..++.+.+++|
T Consensus 13 q~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 13 QEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 55677999999999999999999888776
No 385
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=41.03 E-value=31 Score=26.99 Aligned_cols=22 Identities=23% Similarity=0.126 Sum_probs=18.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkRyKE 254 (530)
|..|||+.+||+..|+++..++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999986543
No 386
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=40.90 E-value=39 Score=33.40 Aligned_cols=35 Identities=3% Similarity=0.041 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||+.+|+|..||+++++.-...|-+.+.
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 233 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45799999999999999999998877777765543
No 387
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=40.86 E-value=34 Score=33.30 Aligned_cols=30 Identities=3% Similarity=0.050 Sum_probs=26.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
-.|-++||+..++|+.|+++..+.|++.|.
T Consensus 152 G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 152 GQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred CCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 467789999999999999999999888774
No 388
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=40.77 E-value=91 Score=30.29 Aligned_cols=29 Identities=14% Similarity=0.277 Sum_probs=26.7
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 126 KSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 126 ~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
.|+|..+||+.+|++...+.|..+++.+.
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~ 211 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKS 211 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 68999999999999999999999988875
No 389
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=40.71 E-value=39 Score=32.81 Aligned_cols=35 Identities=17% Similarity=0.152 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+.++||+.+|+|+.||++++.-....|.+.+.
T Consensus 153 ~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 153 EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999888887776554
No 390
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=40.59 E-value=12 Score=29.64 Aligned_cols=22 Identities=41% Similarity=0.838 Sum_probs=17.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.|+.||.-++ ..+|..||....
T Consensus 7 ~C~~CgvYTL-------k~~CP~CG~~t~ 28 (56)
T PRK13130 7 KCPKCGVYTL-------KEICPVCGGKTK 28 (56)
T ss_pred ECCCCCCEEc-------cccCcCCCCCCC
Confidence 5999998655 449999998765
No 391
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=40.49 E-value=31 Score=30.18 Aligned_cols=30 Identities=13% Similarity=0.186 Sum_probs=23.5
Q ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 047665 227 LNGVSVKIENVAKEVHCTVVTCRKRYKELL 256 (530)
Q Consensus 227 ~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~ 256 (530)
+..-.+||++||+.+|||..||.+-=+.+.
T Consensus 51 Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 51 LLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 334579999999999999999987544443
No 392
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=40.49 E-value=28 Score=35.80 Aligned_cols=37 Identities=24% Similarity=0.417 Sum_probs=30.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHhhcccCCC
Q 047665 232 VKIENVAKEVHCTVVTCRKRYK-------ELLEALVKVAQALPW 268 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyK-------EL~e~L~~l~~~lpW 268 (530)
.|++|||+.+|||..|+++.+. |-++...+.++++=|
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY 45 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGY 45 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCC
Confidence 5899999999999999999885 677777777777644
No 393
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=40.49 E-value=45 Score=31.18 Aligned_cols=32 Identities=13% Similarity=0.072 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+++||+.+|+|..||++..+-..+.+.+
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999988777665554433
No 394
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=40.47 E-value=20 Score=35.23 Aligned_cols=29 Identities=38% Similarity=0.726 Sum_probs=18.2
Q ss_pred CCCCCCCCC----eEEe--cCCC-----cEEcCCCceeec
Q 047665 2 PCTSCGSKT----LTRE--DISG-----SLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~----iv~D--~~~G-----~~VCt~CG~Vle 30 (530)
.||+||..- ..++ +.-| ...|.+||+=-.
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccc
Confidence 699999631 2222 2234 457999998654
No 395
>PRK10870 transcriptional repressor MprA; Provisional
Probab=40.36 E-value=2.7e+02 Score=26.52 Aligned_cols=29 Identities=10% Similarity=0.108 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+..+++.+||+..+++.+|+...++.|.+
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45689999999999999999988777765
No 396
>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=40.33 E-value=39 Score=26.75 Aligned_cols=36 Identities=17% Similarity=0.231 Sum_probs=29.3
Q ss_pred HHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 117 SYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 117 lYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
+|.+.- .+-|.|..|||..++++...+.++.+.|.+
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 455544 555789999999999999999988888766
No 397
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=40.23 E-value=41 Score=32.00 Aligned_cols=35 Identities=17% Similarity=0.177 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.+|||+..|+|..||++++..-+..|-+.+.
T Consensus 157 ~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 35899999999999999999998877777765543
No 398
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=40.20 E-value=49 Score=31.24 Aligned_cols=48 Identities=13% Similarity=0.239 Sum_probs=35.0
Q ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcccCCCCc
Q 047665 220 VLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQALPWGK 270 (530)
Q Consensus 220 AIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~lpW~~ 270 (530)
+||.... .+-....++||+..+|+++|+..-++.|.+ .-++...|+.+
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~--~GlV~~~~y~g 61 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLER--LGLVEYEPYGG 61 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHH--CCCeEEecCCC
Confidence 5565544 445688999999999999999988877765 34455556654
No 399
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=40.16 E-value=49 Score=30.75 Aligned_cols=32 Identities=13% Similarity=0.093 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|.+|||+.+|+|+.||+.++.-=...+-.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35899999999999999999998765555533
No 400
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=40.10 E-value=26 Score=31.01 Aligned_cols=32 Identities=28% Similarity=0.658 Sum_probs=23.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecccCcc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFDNYD 35 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~ 35 (530)
.|--|+..-.. ...+++||.+||+++.-..+.
T Consensus 37 aCeiC~~~GY~--q~g~~lvC~~C~~~~~~~~ig 68 (102)
T PF10080_consen 37 ACEICGPKGYY--QEGDQLVCKNCGVRFNLPTIG 68 (102)
T ss_pred eccccCCCceE--EECCEEEEecCCCEEehhhcc
Confidence 48889775444 346789999999999855444
No 401
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.09 E-value=22 Score=39.75 Aligned_cols=29 Identities=28% Similarity=0.608 Sum_probs=22.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.||+|+.+- .+-..++.+.|..||.....
T Consensus 224 ~C~~C~~~l-~~h~~~~~l~Ch~Cg~~~~~ 252 (505)
T TIGR00595 224 CCPNCDVSL-TYHKKEGKLRCHYCGYQEPI 252 (505)
T ss_pred CCCCCCCce-EEecCCCeEEcCCCcCcCCC
Confidence 699998864 44446789999999988763
No 402
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=39.89 E-value=4.8e+02 Score=27.55 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
...|+++||+..|||...||.--+.-...|
T Consensus 281 ~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KL 310 (324)
T PRK07921 281 QPRTLDQIGKLFGLSRERVRQIEREVMSKL 310 (324)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 469999999999999999987665544444
No 403
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=39.89 E-value=44 Score=31.12 Aligned_cols=33 Identities=12% Similarity=0.157 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|.+|||+.+|+|..|+++++.--...+...
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999998777666443
No 404
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=39.89 E-value=29 Score=35.52 Aligned_cols=37 Identities=22% Similarity=0.256 Sum_probs=28.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHhhcccCCC
Q 047665 232 VKIENVAKEVHCTVVTCRKRYK-------ELLEALVKVAQALPW 268 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyK-------EL~e~L~~l~~~lpW 268 (530)
.|++|||+.+|||..|+++.++ +-++.+.+.++++=|
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY 45 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHY 45 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCC
Confidence 4899999999999999998887 455556666666533
No 405
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=39.83 E-value=23 Score=30.58 Aligned_cols=26 Identities=15% Similarity=0.422 Sum_probs=16.9
Q ss_pred CCCCCCC--CCeEEecCCCcEEcCCCce
Q 047665 2 PCTSCGS--KTLTREDISGSLICVSCGV 27 (530)
Q Consensus 2 ~Cp~CG~--~~iv~D~~~G~~VCt~CG~ 27 (530)
.||-|+. +++..+...|...|-.||.
T Consensus 35 ~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 35 LCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp --SSS--SS--EEEETTTTEEEETTT--
T ss_pred ECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 5999986 5788999999999999984
No 406
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=39.73 E-value=83 Score=25.75 Aligned_cols=28 Identities=14% Similarity=0.232 Sum_probs=25.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
..++.+|++.++++.+||.+.++.|.+.
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 5899999999999999999999988874
No 407
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=39.51 E-value=89 Score=31.81 Aligned_cols=83 Identities=13% Similarity=0.209 Sum_probs=52.5
Q ss_pred HHHHHhhcCCCH-HHHHHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHH
Q 047665 74 IDELTFKLDLTG-QRSIQIKNMIDKITDGEFGLGDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVV 152 (530)
Q Consensus 74 I~~i~~~LgLp~-~i~e~A~~i~k~a~~~~l~rGR~~~~vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~ 152 (530)
+.++..-+|+-+ ...+-+..+...-+...+.-=-.+..++-||+|+||-..+.+++-.=++ .+.+|...+..+.++|.
T Consensus 157 L~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~~~w~~-el~vD~ekV~~~v~~I~ 235 (264)
T KOG0794|consen 157 LLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIPKAWFA-ELSVDMEKVKDIVQEIL 235 (264)
T ss_pred HHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChHHHHHH-HHhccHHHHHHHHHHHH
Confidence 444444555533 3555565555544433333223578899999999999988887633333 35788888888877777
Q ss_pred HHhhh
Q 047665 153 EFLNL 157 (530)
Q Consensus 153 k~L~i 157 (530)
+....
T Consensus 236 ~lYe~ 240 (264)
T KOG0794|consen 236 KLYEL 240 (264)
T ss_pred HHHHH
Confidence 76543
No 408
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=39.49 E-value=52 Score=23.90 Aligned_cols=31 Identities=16% Similarity=0.248 Sum_probs=27.3
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHHHHHhhhc
Q 047665 128 LPISEVASVLNCDVYELGRMITRVVEFLNLK 158 (530)
Q Consensus 128 ~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~ 158 (530)
.+..+||..++++..++.+...++.+.|+.+
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 5899999999999999999988888888753
No 409
>PF12728 HTH_17: Helix-turn-helix domain
Probab=39.44 E-value=33 Score=25.51 Aligned_cols=21 Identities=10% Similarity=0.112 Sum_probs=18.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHH
Q 047665 232 VKIENVAKEVHCTVVTCRKRY 252 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRy 252 (530)
.|.+|+|+.+|||..|+.+-.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~ 22 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWI 22 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 478999999999999997644
No 410
>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=39.38 E-value=48 Score=28.03 Aligned_cols=30 Identities=27% Similarity=0.338 Sum_probs=26.0
Q ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 228 NGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 228 ~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
.+.++.-++||+.+++|+.|||+-...|.+
T Consensus 20 ~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~ 49 (78)
T PF03444_consen 20 TGEPVGSKTIAEELGRSPATIRNEMADLEE 49 (78)
T ss_pred cCCCcCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 356788899999999999999999888776
No 411
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=39.38 E-value=43 Score=31.63 Aligned_cols=35 Identities=17% Similarity=0.129 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+.++||+.+|+|+.|+++++.-....|-+.+.
T Consensus 146 ~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 146 HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999998887777766554
No 412
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=39.33 E-value=16 Score=42.25 Aligned_cols=8 Identities=38% Similarity=0.389 Sum_probs=4.8
Q ss_pred cccccchh
Q 047665 404 WWCGKSEL 411 (530)
Q Consensus 404 ~~~~~~~~ 411 (530)
.|.|-|+.
T Consensus 501 anVGDSRa 508 (645)
T PRK14559 501 AHVGDSRL 508 (645)
T ss_pred EEecCceE
Confidence 36677764
No 413
>PRK05572 sporulation sigma factor SigF; Validated
Probab=39.33 E-value=4e+02 Score=26.53 Aligned_cols=34 Identities=18% Similarity=0.176 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...|+++||+..|+|..||+.+.+...+.|-+.+
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4699999999999999999999888877776544
No 414
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=39.30 E-value=4.4e+02 Score=26.95 Aligned_cols=35 Identities=11% Similarity=0.086 Sum_probs=28.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...+|+++||+++|||++.+....+.....|-+.+
T Consensus 210 ~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 210 KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 35699999999999999999988887776665443
No 415
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=39.26 E-value=1.3e+02 Score=29.50 Aligned_cols=29 Identities=14% Similarity=0.240 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
.++|+++||..+|++..|+.+.+++|.+.
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56899999999999999999999988873
No 416
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=39.23 E-value=44 Score=31.74 Aligned_cols=36 Identities=19% Similarity=0.205 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.|++.++..-.+.|-+.+..
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 468899999999999999999998888877666654
No 417
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=39.11 E-value=41 Score=33.66 Aligned_cols=35 Identities=14% Similarity=0.123 Sum_probs=30.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
..|.+|||+.+|+|+.|+++++.--.+.|-+.+.+
T Consensus 132 g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 132 QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 58999999999999999999988888777776654
No 418
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=39.07 E-value=39 Score=26.36 Aligned_cols=26 Identities=31% Similarity=0.507 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKEL 255 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL 255 (530)
+..++.+.|+..||+..+++++.+++
T Consensus 14 fhlp~~eAA~~Lgv~~T~LKr~CR~~ 39 (52)
T PF02042_consen 14 FHLPIKEAAKELGVSVTTLKRRCRRL 39 (52)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 56899999999999999999987753
No 419
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=38.99 E-value=17 Score=32.48 Aligned_cols=7 Identities=29% Similarity=0.743 Sum_probs=3.6
Q ss_pred CCCCCCC
Q 047665 2 PCTSCGS 8 (530)
Q Consensus 2 ~Cp~CG~ 8 (530)
+|+.||.
T Consensus 72 ~C~~Cg~ 78 (113)
T PRK12380 72 WCWDCSQ 78 (113)
T ss_pred EcccCCC
Confidence 3555553
No 420
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=38.98 E-value=48 Score=33.24 Aligned_cols=31 Identities=19% Similarity=0.266 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
.-.|.++||+..++|+.|+++....|++.|.
T Consensus 157 ~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 157 FGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4689999999999999999999999988774
No 421
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=38.91 E-value=1.4e+02 Score=28.34 Aligned_cols=28 Identities=14% Similarity=0.305 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+++|+++||+.+|+|..|+.+-+++|.+
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5799999999999999999998888876
No 422
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=38.73 E-value=47 Score=31.30 Aligned_cols=32 Identities=22% Similarity=0.141 Sum_probs=27.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
..|.+|||+..|+|+.||+.++.--...|-+.
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 155 GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58899999999999999999988776666543
No 423
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=38.61 E-value=59 Score=29.92 Aligned_cols=37 Identities=22% Similarity=0.357 Sum_probs=32.2
Q ss_pred HHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 117 SYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 117 lYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
+|.+.-+.+-|.|.-|||+.++.+..++.|+.++|..
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~ 68 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLE 68 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHH
Confidence 6777666788999999999999999999888888766
No 424
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=38.50 E-value=5.7e+02 Score=28.19 Aligned_cols=40 Identities=10% Similarity=0.118 Sum_probs=32.0
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHH
Q 047665 219 AVLVFVVELNGVSVKIENVAKEVH-CTVVTCRKRYKELLEALV 260 (530)
Q Consensus 219 AAIYlAa~~~g~k~t~~eIA~~~~-VS~~TIrkRyKEL~e~L~ 260 (530)
.|.||+-++.+ .|+.+|++..| -+.+|+...++.+.+.+.
T Consensus 391 iamyL~r~~t~--~sl~~IG~~FggrdHsTV~~a~~ki~~~~~ 431 (450)
T PRK14087 391 IAMYLTKEILN--HTLAQIGEEFGGRDHTTVINAERKIEKMLK 431 (450)
T ss_pred HHHHHHHHHcC--CCHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 36788877654 68999999997 889999988888877554
No 425
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=38.48 E-value=47 Score=31.99 Aligned_cols=36 Identities=22% Similarity=0.208 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.|+++++.--...|-+++++
T Consensus 148 ~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 148 LGYTYEEAAKIADVRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 357899999999999999999988777777766654
No 426
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=38.48 E-value=38 Score=26.67 Aligned_cols=22 Identities=27% Similarity=0.200 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkRyKE 254 (530)
+..|||+.+|||+.|+|..-++
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999975443
No 427
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=38.44 E-value=24 Score=33.78 Aligned_cols=28 Identities=39% Similarity=0.867 Sum_probs=17.8
Q ss_pred CCCCCCCCeEE-e-----cCCC-----cEEcCCCceeec
Q 047665 3 CTSCGSKTLTR-E-----DISG-----SLICVSCGVVQA 30 (530)
Q Consensus 3 Cp~CG~~~iv~-D-----~~~G-----~~VCt~CG~Vle 30 (530)
||.||+..+.. . +.-| ...|.+||+=-.
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchh
Confidence 99999753222 1 2234 457999998654
No 428
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=38.19 E-value=38 Score=33.94 Aligned_cols=35 Identities=20% Similarity=0.074 Sum_probs=30.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
-+|+.|+|..+++|+.||++.++++.+.-..+++-
T Consensus 105 lLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPt 139 (220)
T PF07900_consen 105 LLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPT 139 (220)
T ss_pred cccHHHHHHHHCCCHHHHHHHHHHHHHHcCceecc
Confidence 58999999999999999999999999876665543
No 429
>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=38.17 E-value=48 Score=24.93 Aligned_cols=28 Identities=14% Similarity=0.261 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
...++.|||+.+|++.+|+.+-++.|.+
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3478999999999999999887776654
No 430
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=38.13 E-value=23 Score=27.56 Aligned_cols=29 Identities=21% Similarity=0.453 Sum_probs=20.9
Q ss_pred CCCCCCC-CCeEEecCCCc----EEcCCCceeec
Q 047665 2 PCTSCGS-KTLTREDISGS----LICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~-~~iv~D~~~G~----~VCt~CG~Vle 30 (530)
.||+||. ..+..|...|. .=|..|..=+.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~ 35 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIE 35 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccE
Confidence 6999998 47888888874 24777765554
No 431
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=38.00 E-value=47 Score=31.26 Aligned_cols=34 Identities=12% Similarity=0.119 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...+.++||+.+|+|..|++.++.--...|-+.+
T Consensus 146 ~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999987777776654
No 432
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=37.78 E-value=42 Score=33.79 Aligned_cols=35 Identities=9% Similarity=0.128 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.+|||+.+|+|+.|+++++.--...|-+.+.
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999999887777765543
No 433
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=37.74 E-value=41 Score=34.19 Aligned_cols=31 Identities=13% Similarity=0.183 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
...|.++||+..++|+.|++.+++.+++.+.
T Consensus 204 ~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 204 DGKTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 3588999999999999999999999988764
No 434
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=37.72 E-value=88 Score=30.38 Aligned_cols=85 Identities=13% Similarity=0.165 Sum_probs=52.4
Q ss_pred HHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH-HHhhcccCCCCccCcc
Q 047665 196 VLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLEA-LVKVAQALPWGKDVTV 274 (530)
Q Consensus 196 ~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e~-L~~l~~~lpW~~~v~~ 274 (530)
..+.+.|.++++. +-.|..-|++| ++.-++|+.||++++|.|.+.+..-+|+|.+. +++.. +.|...
T Consensus 13 e~fae~m~r~G~n---rtVG~iYgily----ls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~-~~~G~R---- 80 (177)
T COG1510 13 EHFAETMSRWGIN---RTVGQIYGILY----LSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV-FEKGDR---- 80 (177)
T ss_pred HHHHHHHHHhCCc---chHHHHhhhhe----ecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh-hccCcc----
Confidence 3455566666542 24444555555 45678999999999999999999999999883 33332 223322
Q ss_pred cccccChhHHHHHhHHHH
Q 047665 275 KNVLKNAPFVMNYMEMKS 292 (530)
Q Consensus 275 knl~~~~pdIi~~~e~~~ 292 (530)
++.-.-.+|+.+.--+..
T Consensus 81 k~~F~a~~df~~~f~t~f 98 (177)
T COG1510 81 KDYFEAEKDFSQIFRTLF 98 (177)
T ss_pred hhhhcccchHHHHHHHHH
Confidence 333333555555544333
No 435
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=37.51 E-value=21 Score=30.16 Aligned_cols=34 Identities=26% Similarity=0.382 Sum_probs=23.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeecccCcc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFDNYD 35 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~~f~ 35 (530)
.||-||..++..+......||.-|+.--+..++.
T Consensus 3 ~CPCCg~~Tl~~~~~~~ydIC~VC~WEdD~~q~~ 36 (78)
T PF14206_consen 3 PCPCCGYYTLEERGEGTYDICPVCFWEDDGVQLR 36 (78)
T ss_pred cCCCCCcEEeccCCCcCceECCCCCcccCCcccc
Confidence 6999999765444332378999999866644433
No 436
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=37.45 E-value=50 Score=30.17 Aligned_cols=32 Identities=3% Similarity=0.001 Sum_probs=27.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|..+||+.+|+|+.|+++++.--...|.+
T Consensus 127 ~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 127 YGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999998877776654
No 437
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=37.45 E-value=32 Score=25.70 Aligned_cols=24 Identities=8% Similarity=0.069 Sum_probs=18.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYK 253 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyK 253 (530)
..+|+.++|+.+|+|..||.+..+
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~ 31 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIEN 31 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhc
Confidence 468999999999999999987544
No 438
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=37.35 E-value=44 Score=32.93 Aligned_cols=36 Identities=14% Similarity=0.131 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.++||+.+|+|..|+++++.-....|-+.+..
T Consensus 164 ~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 164 EELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999998888877766653
No 439
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=37.32 E-value=23 Score=33.27 Aligned_cols=27 Identities=26% Similarity=0.637 Sum_probs=21.1
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||.|++. +.+...|...|..|+..++
T Consensus 36 aC~~C~kk--v~~~~~~~~~C~~C~~~~~ 62 (166)
T cd04476 36 ACPGCNKK--VVEEGNGTYRCEKCNKSVP 62 (166)
T ss_pred cccccCcc--cEeCCCCcEECCCCCCcCC
Confidence 69999986 3344449999999999874
No 440
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=37.18 E-value=83 Score=30.68 Aligned_cols=28 Identities=7% Similarity=-0.013 Sum_probs=24.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
..|+.+||+.+|+|..|+.+-+++|.+.
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 4589999999999999999998888873
No 441
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=37.01 E-value=34 Score=26.77 Aligned_cols=19 Identities=37% Similarity=0.244 Sum_probs=17.3
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKR 251 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkR 251 (530)
|..++|+.+||++.||+..
T Consensus 2 s~~eva~~~gvs~~tlr~~ 20 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYY 20 (70)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 6789999999999999975
No 442
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=36.93 E-value=43 Score=24.24 Aligned_cols=29 Identities=28% Similarity=0.693 Sum_probs=20.4
Q ss_pred CCCCCCCCCeEEecCCCc-EEcCC---Cceeec
Q 047665 2 PCTSCGSKTLTREDISGS-LICVS---CGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~-~VCt~---CG~Vle 30 (530)
.||.||+.-++.....|. +.|++ |.....
T Consensus 3 ~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKGKFLGCSNYPECKYTEP 35 (39)
T ss_pred CCCCCCceeEEEECCCCCEEECCCCCCcCCeEe
Confidence 699999776666656664 68886 766543
No 443
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=36.82 E-value=54 Score=25.12 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=27.0
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHHHHHhhhc
Q 047665 126 KSLPISEVASVLNCDVYELGRMITRVVEFLNLK 158 (530)
Q Consensus 126 ~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~ 158 (530)
...+..+||..+++++.++....+.+.+.||+.
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 356889999999999999998888888888864
No 444
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=36.75 E-value=1e+02 Score=26.34 Aligned_cols=36 Identities=11% Similarity=0.105 Sum_probs=27.4
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 047665 219 AVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKEL 255 (530)
Q Consensus 219 AAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL 255 (530)
+.-|+... ....+++.++|+.+++|+.++.+.+++.
T Consensus 10 ~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 10 LIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 33344443 3456999999999999999999988875
No 445
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=36.60 E-value=64 Score=23.58 Aligned_cols=32 Identities=16% Similarity=0.225 Sum_probs=28.2
Q ss_pred CCChHHHHHHhCCCHHHHHHHHHHHHHHhhhc
Q 047665 127 SLPISEVASVLNCDVYELGRMITRVVEFLNLK 158 (530)
Q Consensus 127 P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~ 158 (530)
..+..+||..++++...+.+...++.+.++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 46999999999999999999999888888764
No 446
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=36.54 E-value=80 Score=30.94 Aligned_cols=31 Identities=19% Similarity=0.309 Sum_probs=26.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
+++.+++|+..|||.+|+..+++.-...+..
T Consensus 178 ~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 178 RVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4889999999999999999998877766644
No 447
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=36.51 E-value=20 Score=32.07 Aligned_cols=20 Identities=25% Similarity=0.295 Sum_probs=9.0
Q ss_pred CeEEecCCCcEEcCCCceee
Q 047665 10 TLTREDISGSLICVSCGVVQ 29 (530)
Q Consensus 10 ~iv~D~~~G~~VCt~CG~Vl 29 (530)
.+..+..-+...|.+||...
T Consensus 61 ~L~I~~~p~~~~C~~Cg~~~ 80 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSEEV 80 (115)
T ss_pred EEEEEeeCcEEEcccCCCEE
Confidence 33444444444555555333
No 448
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=36.50 E-value=11 Score=29.99 Aligned_cols=45 Identities=24% Similarity=0.421 Sum_probs=30.7
Q ss_pred cEEcCCCceeecccCcccCCCCCCCCCCcEEeecccCCCCCcchHhHHHHHHHHHHHHHHhhcCCCHHH
Q 047665 19 SLICVSCGVVQAFDNYDAQLYGRDGPTGIYVHVGTAGTGSALNYKEKKIYESNKLIDELTFKLDLTGQR 87 (530)
Q Consensus 19 ~~VCt~CG~Vle~~~f~~~~~~~g~p~gt~i~~g~~g~gs~~s~rer~L~~a~~~I~~i~~~LgLp~~i 87 (530)
++||+.||.=+.+.-|- +--++..+.+.+..++..|-+|.|+.++
T Consensus 4 ~lvCSTCGrDlSeeRy~------------------------Lli~~~~Lk~Vl~~v~n~CCRlKLsTQI 48 (63)
T PF05864_consen 4 QLVCSTCGRDLSEERYR------------------------LLIKEMSLKKVLRTVKNSCCRLKLSTQI 48 (63)
T ss_pred eeeecccCCcchHHHHH------------------------HHHHHhhHHHHHHHhhccceeeeecccc
Confidence 47899999876643221 1123456777888888888888888643
No 449
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=36.33 E-value=91 Score=29.57 Aligned_cols=29 Identities=14% Similarity=0.371 Sum_probs=26.6
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 126 KSLPISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 126 ~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
.|+|..+||+.+|++..++.|+++++.+.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 58999999999999999999999988774
No 450
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=36.24 E-value=47 Score=31.38 Aligned_cols=34 Identities=21% Similarity=0.378 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
...|.++||+..|+|..|+++++.--...|-+.+
T Consensus 149 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999999876655554443
No 451
>PRK05580 primosome assembly protein PriA; Validated
Probab=35.97 E-value=27 Score=40.49 Aligned_cols=28 Identities=29% Similarity=0.673 Sum_probs=22.2
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
.||+|+.+ +.+....+.+.|..||....
T Consensus 392 ~C~~C~~~-l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 392 ECPHCDAS-LTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred CCCCCCCc-eeEECCCCeEECCCCcCCCC
Confidence 69999885 45556688899999998765
No 452
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=35.94 E-value=57 Score=31.20 Aligned_cols=35 Identities=20% Similarity=0.173 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.++||..+|+|+.|+++++.-....|-+.+.
T Consensus 128 ~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 128 SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999999888887776654
No 453
>PF13551 HTH_29: Winged helix-turn helix
Probab=35.65 E-value=80 Score=26.72 Aligned_cols=27 Identities=19% Similarity=0.166 Sum_probs=23.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKRYKELLEAL 259 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkRyKEL~e~L 259 (530)
+..+||+.+|+|..|+.+.++.+.+.=
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999888877543
No 454
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=35.65 E-value=60 Score=34.14 Aligned_cols=35 Identities=3% Similarity=-0.083 Sum_probs=27.5
Q ss_pred HHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 047665 222 VFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELL 256 (530)
Q Consensus 222 YlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~ 256 (530)
-+|+..+...+||.|||+..|+|..++.+-+++=.
T Consensus 20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar 54 (318)
T PRK15418 20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGR 54 (318)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 44555566789999999999999999988655533
No 455
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=35.59 E-value=43 Score=26.45 Aligned_cols=22 Identities=23% Similarity=0.059 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkRyKE 254 (530)
+..++|+.+|||+.|+|...++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999964333
No 456
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=35.43 E-value=52 Score=33.88 Aligned_cols=36 Identities=8% Similarity=0.115 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhccc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQA 265 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~~ 265 (530)
...|.+|||+.+|+|+.|+++++.--...|-+.++.
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 467999999999999999999998888877766553
No 457
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=35.26 E-value=1.2e+02 Score=25.96 Aligned_cols=50 Identities=18% Similarity=0.180 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHhhhcCCccchhhHHHH
Q 047665 112 LIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNLKLPEVDIVSMFER 170 (530)
Q Consensus 112 vaAAclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R 170 (530)
+..+.-|+.. ....|+++.++|..++++...+.+.|++. +|. .|..|+.+
T Consensus 7 ~~~~~~~i~~-~~~~~~~~~~lA~~~~~S~~~l~r~f~~~---~g~-----s~~~~i~~ 56 (107)
T PRK10219 7 IQTLIAWIDE-HIDQPLNIDVVAKKSGYSKWYLQRMFRTV---THQ-----TLGDYIRQ 56 (107)
T ss_pred HHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHH---HCc-----CHHHHHHH
Confidence 3444455544 45568999999999999999998887764 443 35555544
No 458
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=35.20 E-value=6.1e+02 Score=27.43 Aligned_cols=32 Identities=16% Similarity=0.113 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVK 261 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~ 261 (530)
...|+++||+.+|||..+||...+.-...|-+
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~ 361 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 361 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 46899999999999999999988877666644
No 459
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.15 E-value=22 Score=32.81 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=16.2
Q ss_pred CCCCeEEecCCCcEEcCCCceeecc
Q 047665 7 GSKTLTREDISGSLICVSCGVVQAF 31 (530)
Q Consensus 7 G~~~iv~D~~~G~~VCt~CG~Vle~ 31 (530)
.+..+..+..-+...|.+||.+...
T Consensus 58 ega~L~i~~~p~~~~C~~CG~~~~~ 82 (135)
T PRK03824 58 EGAEIIFEEEEAVLKCRNCGNEWSL 82 (135)
T ss_pred cCCEEEEEecceEEECCCCCCEEec
Confidence 3345556666677888888866653
No 460
>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=35.14 E-value=57 Score=29.62 Aligned_cols=39 Identities=10% Similarity=0.202 Sum_probs=30.9
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 219 AVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 219 AAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+.+|+|..-.+..+|.++||+..+++...+++-+..|.+
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~ 51 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRK 51 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566777653345689999999999999999888777766
No 461
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=35.13 E-value=69 Score=24.92 Aligned_cols=31 Identities=29% Similarity=0.263 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
...+..+.|+..++...|++.|++.|.+.+.
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g 41 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELLG 41 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 3577889999999999999999999988763
No 462
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=35.13 E-value=30 Score=29.96 Aligned_cols=30 Identities=30% Similarity=0.536 Sum_probs=20.9
Q ss_pred CCCCCCC-------CCeEEecCCC----------cEEcCCCceeecc
Q 047665 2 PCTSCGS-------KTLTREDISG----------SLICVSCGVVQAF 31 (530)
Q Consensus 2 ~Cp~CG~-------~~iv~D~~~G----------~~VCt~CG~Vle~ 31 (530)
.|+-|++ .++.+|...| .++|.+||.+.-.
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~ 47 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQD 47 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeec
Confidence 4899954 3456666554 4689999988753
No 463
>PF13730 HTH_36: Helix-turn-helix domain
Probab=35.10 E-value=86 Score=23.49 Aligned_cols=25 Identities=20% Similarity=0.186 Sum_probs=23.2
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 129 PISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 129 TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
|..+||+.+|++..++.++.+.|.+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999988865
No 464
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=35.09 E-value=44 Score=33.60 Aligned_cols=28 Identities=25% Similarity=0.359 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
-.+++.++|+.++||+.|||+-+++|.+
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3689999999999999999999999988
No 465
>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=34.94 E-value=65 Score=23.36 Aligned_cols=24 Identities=13% Similarity=0.144 Sum_probs=18.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKE 254 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKE 254 (530)
.=++.+.|+.+|+|..|+..+++.
T Consensus 18 ~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 18 GGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp TT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345678999999999999998875
No 466
>PRK14873 primosome assembly protein PriA; Provisional
Probab=34.87 E-value=27 Score=40.55 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=19.7
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~V 28 (530)
.||+|+.+-. +-...+.+.|..||.-
T Consensus 394 ~C~~C~~~L~-~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 394 RCRHCTGPLG-LPSAGGTPRCRWCGRA 419 (665)
T ss_pred ECCCCCCcee-EecCCCeeECCCCcCC
Confidence 6999988643 3335678999999984
No 467
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=34.87 E-value=12 Score=29.76 Aligned_cols=45 Identities=24% Similarity=0.437 Sum_probs=30.6
Q ss_pred cEEcCCCceeecccCcccCCCCCCCCCCcEEeecccCCCCCcchHhHHHHHHHHHHHHHHhhcCCCHHH
Q 047665 19 SLICVSCGVVQAFDNYDAQLYGRDGPTGIYVHVGTAGTGSALNYKEKKIYESNKLIDELTFKLDLTGQR 87 (530)
Q Consensus 19 ~~VCt~CG~Vle~~~f~~~~~~~g~p~gt~i~~g~~g~gs~~s~rer~L~~a~~~I~~i~~~LgLp~~i 87 (530)
.+||+.||.=+.+.-|- +--++.++.+.+..+...|-+|.|+.++
T Consensus 4 ~lVCsTCGrDlSeeRy~------------------------Lli~~~~L~~Vl~~v~~~CCRlKLsTQI 48 (63)
T PHA03082 4 QLVCSTCGRDLSEERYR------------------------LLIKKKSLKKVLRTVKNSCCRLKLSTQI 48 (63)
T ss_pred eeeecccCcchhHHHHH------------------------HHHHHhhHHHHHHHhhccceeeeeeccc
Confidence 46899999866643221 1123456777888888888888888643
No 468
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=34.86 E-value=31 Score=35.28 Aligned_cols=39 Identities=18% Similarity=0.151 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH-------HHHHHHhhcccCCC
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKE-------LLEALVKVAQALPW 268 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKE-------L~e~L~~l~~~lpW 268 (530)
-+.|++|||+.+|||..|+++.+.. ..+...+.++++=+
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY 50 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGF 50 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCC
Confidence 3689999999999999999988863 44555555655544
No 469
>PRK12366 replication factor A; Reviewed
Probab=34.85 E-value=20 Score=41.27 Aligned_cols=24 Identities=38% Similarity=0.948 Sum_probs=19.6
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCcee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVV 28 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~V 28 (530)
.||.|+.. +.+ ..|.+.|..||.+
T Consensus 534 aCp~CnkK--v~~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 534 LCPNCRKR--VEE-VDGEYICEFCGEV 557 (637)
T ss_pred cccccCeE--eEc-CCCcEECCCCCCC
Confidence 69999874 333 5799999999998
No 470
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=34.76 E-value=13 Score=28.99 Aligned_cols=29 Identities=31% Similarity=0.731 Sum_probs=20.7
Q ss_pred CCCCCCC-CCeEEecC--CCcEEcCCCceeec
Q 047665 2 PCTSCGS-KTLTREDI--SGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~-~~iv~D~~--~G~~VCt~CG~Vle 30 (530)
.|.+|+. .+..+-.. .+..+|..||+-..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 5899997 34445443 57789999998665
No 471
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=34.62 E-value=49 Score=33.21 Aligned_cols=31 Identities=10% Similarity=-0.002 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
..+|..|||.+.++|+.|++..++.+.+.|.
T Consensus 193 ~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 193 EGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3578899999999999999999999988774
No 472
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=34.54 E-value=20 Score=28.69 Aligned_cols=21 Identities=14% Similarity=0.126 Sum_probs=12.4
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceee
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQ 29 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vl 29 (530)
.||+||...+-. -+|. ||+--
T Consensus 29 ~c~~cg~~~~pH------~vc~-cG~Y~ 49 (60)
T PRK01110 29 VDKTTGEYHLPH------HVSP-KGYYK 49 (60)
T ss_pred EcCCCCceeccc------eecC-CcccC
Confidence 477777743322 3788 88543
No 473
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=34.47 E-value=1.2e+02 Score=27.25 Aligned_cols=42 Identities=10% Similarity=0.127 Sum_probs=32.0
Q ss_pred chhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 047665 213 PMPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKEL 255 (530)
Q Consensus 213 P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL 255 (530)
...+..+.-|+-.... .+.++.++|+.+|+|+.++...+++.
T Consensus 8 ~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4445555556665543 47999999999999999999988875
No 474
>PRK09526 lacI lac repressor; Reviewed
Probab=34.46 E-value=34 Score=34.94 Aligned_cols=38 Identities=16% Similarity=0.179 Sum_probs=29.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHhhcccCCC
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYK-------ELLEALVKVAQALPW 268 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyK-------EL~e~L~~l~~~lpW 268 (530)
+.|++|||+.+|||..|+++.+. |..+...+.++++=|
T Consensus 5 ~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY 49 (342)
T PRK09526 5 PVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNY 49 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCC
Confidence 46999999999999999998876 344555566666544
No 475
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=34.41 E-value=68 Score=30.28 Aligned_cols=36 Identities=11% Similarity=0.052 Sum_probs=27.5
Q ss_pred cC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 228 NG-VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 228 ~g-~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
.| ...|+.+||+.+|||..|+-..++.-.+.+..++
T Consensus 24 ~G~~~~s~~~IA~~agvs~~~lY~hF~sKe~L~~av~ 60 (202)
T TIGR03613 24 FGFHGTSLEQIAELAGVSKTNLLYYFPSKDALYLAVL 60 (202)
T ss_pred hCcccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHH
Confidence 34 4699999999999999999988775444444443
No 476
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=34.39 E-value=71 Score=25.68 Aligned_cols=29 Identities=14% Similarity=0.205 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 229 GVSVKIENVAKEVHCTVVTCRKRYKELLE 257 (530)
Q Consensus 229 g~k~t~~eIA~~~~VS~~TIrkRyKEL~e 257 (530)
+..++-.|||+++++|..++|.-+..|.+
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~ 41 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEK 41 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45678889999999999999987665554
No 477
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=34.19 E-value=77 Score=26.18 Aligned_cols=30 Identities=3% Similarity=-0.084 Sum_probs=20.6
Q ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHH
Q 047665 223 FVVELNGVSVKIENVAKEVHCTVVTCRKRY 252 (530)
Q Consensus 223 lAa~~~g~k~t~~eIA~~~~VS~~TIrkRy 252 (530)
+...+.....||.++|+.+|++.++|.+-.
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~ 52 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLE 52 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHH
Confidence 344445567999999999999999997644
No 478
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=34.11 E-value=7.2e+02 Score=27.94 Aligned_cols=82 Identities=18% Similarity=0.189 Sum_probs=49.8
Q ss_pred HHHHHHhh----cCCCHHHHHHHHHHHHHHhhCCCC-CC---------Cc----hhHHHHHHHHHHHH-hcCC-CCChHH
Q 047665 73 LIDELTFK----LDLTGQRSIQIKNMIDKITDGEFG-LG---------DW----FPILIGACSYVVMR-LDDK-SLPISE 132 (530)
Q Consensus 73 ~I~~i~~~----LgLp~~i~e~A~~i~k~a~~~~l~-rG---------R~----~~~vaAAclYiACR-~~~~-P~TL~D 132 (530)
-+..++.. |+++...++.|..++..+.-.|.. +. +. ...+ .-+..+... .... -.-+..
T Consensus 162 ~~~eia~~~~~~l~~~~~~ve~vL~~iQ~leP~GVgARdL~ECL~lQL~~~~~~~~~~-~~a~~il~~~le~La~~~~~~ 240 (481)
T PRK12469 162 DLSELAEAADPELGLSEQELEVALRLVQSLDPPGVAARDLSECLLLQLDALPADTPAL-EEAKEIARHHLERLARRETAE 240 (481)
T ss_pred CHHHHHhccccccCCCHHHHHHHHHHHhcCCCCccCcCCHHHHHHHHHHhccCCCchH-HHHHHHHHHHHHHHHccCHHH
Confidence 47788888 999999999998888877655543 21 00 0111 001111111 1111 245677
Q ss_pred HHHHhCCCHHHHHHHHHHHHHHhh
Q 047665 133 VASVLNCDVYELGRMITRVVEFLN 156 (530)
Q Consensus 133 IA~~~~vd~~~Lgr~~k~L~k~L~ 156 (530)
|+..++++..++..++..|. .|+
T Consensus 241 i~~~l~~~~~~l~~a~~~Ir-~L~ 263 (481)
T PRK12469 241 IQRRIGCDQETLREACALVR-RLD 263 (481)
T ss_pred HHHHhCcCHHHHHHHHHHHh-CCC
Confidence 88999999999998887555 453
No 479
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=33.98 E-value=77 Score=28.88 Aligned_cols=28 Identities=11% Similarity=0.203 Sum_probs=24.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
..+.++||+.++||.+|++..++.|.+.
T Consensus 22 ~~~~~ela~~l~vs~~svs~~l~~L~~~ 49 (142)
T PRK03902 22 YARVSDIAEALSVHPSSVTKMVQKLDKD 49 (142)
T ss_pred CcCHHHHHHHhCCChhHHHHHHHHHHHC
Confidence 4588999999999999999999888775
No 480
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.93 E-value=23 Score=36.71 Aligned_cols=30 Identities=33% Similarity=0.587 Sum_probs=20.9
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeeccc
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQAFD 32 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle~~ 32 (530)
.|+.||+.+...+ ..=..+|.+||...-.+
T Consensus 113 FCg~CG~~~~~~~-~g~~~~C~~cg~~~fPR 142 (279)
T COG2816 113 FCGRCGTKTYPRE-GGWARVCPKCGHEHFPR 142 (279)
T ss_pred CCCCCCCcCcccc-CceeeeCCCCCCccCCC
Confidence 5999999753332 12247999999987654
No 481
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=33.78 E-value=55 Score=32.62 Aligned_cols=35 Identities=14% Similarity=0.119 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...|.+|||+.+|+|+.|++.++.--...|-+.+.
T Consensus 186 eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 186 ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998877776665554
No 482
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=33.76 E-value=69 Score=23.73 Aligned_cols=26 Identities=15% Similarity=0.147 Sum_probs=24.0
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 129 PISEVASVLNCDVYELGRMITRVVEF 154 (530)
Q Consensus 129 TL~DIA~~~~vd~~~Lgr~~k~L~k~ 154 (530)
|..++|+.++++...+.++++.|.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 89999999999999999999998863
No 483
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=33.70 E-value=4.6e+02 Score=25.58 Aligned_cols=42 Identities=17% Similarity=0.367 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHHhcCCC-CChHHHHHHhCCCH-HHHHHHHHHHHHHh
Q 047665 110 PILIGACSYVVMRLDDKS-LPISEVASVLNCDV-YELGRMITRVVEFL 155 (530)
Q Consensus 110 ~~vaAAclYiACR~~~~P-~TL~DIA~~~~vd~-~~Lgr~~k~L~k~L 155 (530)
..++=|++|++ +-| +|+.+||..++++. ..+..+...+.+..
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~ 46 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYL 46 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHH
Confidence 45677888877 778 99999999999984 45555555554444
No 484
>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=33.66 E-value=95 Score=23.44 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=24.0
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 126 KSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 126 ~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
-|.++.+||..++++...+.+..++|.+
T Consensus 16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 16 GGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 3489999999999999999999888876
No 485
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=33.65 E-value=33 Score=28.23 Aligned_cols=26 Identities=27% Similarity=0.641 Sum_probs=19.5
Q ss_pred CCCCCCCCCeEEecCCCcEEcCCCceeec
Q 047665 2 PCTSCGSKTLTREDISGSLICVSCGVVQA 30 (530)
Q Consensus 2 ~Cp~CG~~~iv~D~~~G~~VCt~CG~Vle 30 (530)
+| .||.. ++.+...-.--| .||..+.
T Consensus 5 rC-~Cgr~-lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 5 RC-DCGRY-LYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EE-TTS---EEEETT-SEEEE-TTTEEEE
T ss_pred Ee-cCCCE-EEecCCcceeEe-cCCCeee
Confidence 58 79884 678878888999 9999987
No 486
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=33.23 E-value=36 Score=26.67 Aligned_cols=19 Identities=32% Similarity=0.235 Sum_probs=17.2
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 047665 233 KIENVAKEVHCTVVTCRKR 251 (530)
Q Consensus 233 t~~eIA~~~~VS~~TIrkR 251 (530)
|..|+|+.+|||+.|||..
T Consensus 2 ti~eva~~~gvs~~tlr~y 20 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYY 20 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHH
Confidence 5789999999999999884
No 487
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=32.93 E-value=86 Score=25.43 Aligned_cols=64 Identities=14% Similarity=0.174 Sum_probs=35.3
Q ss_pred HHHHHHHhhcCCCHHHHHHHHHHHHHHhhCCCCCCCchhHHH--HHHHHHHHHhcCCCCChHHHHHHhC-CCHHHHHHHH
Q 047665 72 KLIDELTFKLDLTGQRSIQIKNMIDKITDGEFGLGDWFPILI--GACSYVVMRLDDKSLPISEVASVLN-CDVYELGRMI 148 (530)
Q Consensus 72 ~~I~~i~~~LgLp~~i~e~A~~i~k~a~~~~l~rGR~~~~va--AAclYiACR~~~~P~TL~DIA~~~~-vd~~~Lgr~~ 148 (530)
..++.+|+.+|+|..-+ ..++|....+- -.+.|++-... +.|+.+|+..+| -|...+..++
T Consensus 4 ~Ii~~Va~~~~v~~~~i--------------~s~~R~~~i~~aR~va~yL~r~~~--~~sl~~Ig~~fg~rdHstV~~a~ 67 (70)
T PF08299_consen 4 DIIEAVAEYFGVSVEDI--------------RSKSRKRKIVEARQVAMYLARELT--GLSLSEIGRYFGGRDHSTVIHAI 67 (70)
T ss_dssp HHHHHHHHHTT--HHHH--------------HSS---HHHHHHHHHHHHHHHHHS-----HHHHHHHCTSSTHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHH--------------hCCCCChhhcchHHHHHHHHHHHh--CCCHHHHHHHhCCCCHHHHHHHH
Confidence 45677788888876311 11233322221 13356654434 578999999999 9999988887
Q ss_pred HHH
Q 047665 149 TRV 151 (530)
Q Consensus 149 k~L 151 (530)
+++
T Consensus 68 ~ki 70 (70)
T PF08299_consen 68 RKI 70 (70)
T ss_dssp HHH
T ss_pred HhC
Confidence 764
No 488
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=32.91 E-value=71 Score=30.43 Aligned_cols=36 Identities=11% Similarity=0.185 Sum_probs=28.3
Q ss_pred cCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhc
Q 047665 228 NGV-SVKIENVAKEVHCTVVTCRKRYKELLEALVKVA 263 (530)
Q Consensus 228 ~g~-k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~ 263 (530)
.|+ ..|+.+||+.+|||..|+-..++.-.+.+..++
T Consensus 27 ~G~~~~ti~~Ia~~agvsk~t~Y~~F~sKe~Ll~~v~ 63 (213)
T PRK09975 27 RGVSNTTLNDIADAANVTRGAIYWHFENKTQLFNEMW 63 (213)
T ss_pred cCcccCCHHHHHHHcCCCHHHHHHHcCCHHHHHHHHH
Confidence 454 699999999999999999988876555554443
No 489
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=32.90 E-value=61 Score=32.42 Aligned_cols=33 Identities=3% Similarity=0.128 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhh
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKV 262 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l 262 (530)
...|+++||+..|+|+.||+++++.-...|-+.
T Consensus 220 ~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 220 ENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999999988766666543
No 490
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=32.72 E-value=46 Score=24.58 Aligned_cols=22 Identities=9% Similarity=0.057 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKR 251 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkR 251 (530)
..+|+.++|+.+|+|..|+++-
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~ 35 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDV 35 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHH
Confidence 4689999999999999999874
No 491
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=32.59 E-value=73 Score=23.41 Aligned_cols=27 Identities=22% Similarity=0.323 Sum_probs=17.9
Q ss_pred cCCCCChHHHHHHhCCCHHHHHHHHHH
Q 047665 124 DDKSLPISEVASVLNCDVYELGRMITR 150 (530)
Q Consensus 124 ~~~P~TL~DIA~~~~vd~~~Lgr~~k~ 150 (530)
.....|+++||..+|++..+|.+.+++
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 345589999999999999999877653
No 492
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=32.51 E-value=4.7e+02 Score=28.27 Aligned_cols=133 Identities=8% Similarity=0.072 Sum_probs=77.4
Q ss_pred HHHHHHHHh-cCCCCChHHHHHHhCCC--HHHHHHHHHHHHHHhhhcCCccchhhHHHHHHHhcccCCCCccchHHHHHH
Q 047665 115 ACSYVVMRL-DDKSLPISEVASVLNCD--VYELGRMITRVVEFLNLKLPEVDIVSMFERVIRNSRLQGFTNLDESMLDRM 191 (530)
Q Consensus 115 AclYiACR~-~~~P~TL~DIA~~~~vd--~~~Lgr~~k~L~k~L~i~~p~vdp~~~I~R~~~~L~l~~v~~v~~e~~~~V 191 (530)
+|-+++.+- +..|..+.|+...+.-. ..++-+....++..|.+.+-......|+.++...-.. + .-++
T Consensus 185 s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~---~------~~~~ 255 (359)
T KOG0654|consen 185 SAMLIASKYEEIKEPRVEEFCYITDNTYTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQT---P------ELQV 255 (359)
T ss_pred ccceeeccchhhcchHHHHHHhhhhhhhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcc---h------hHHH
Confidence 445555554 34456677777765532 3444455555555555554444456777777443221 1 1345
Q ss_pred HHHHHHHHHHHhhcccccccCchhHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 047665 192 RKQGVLLLNCAVKWFLTTGRRPMPVVVAVLVFVVELNGVSVKIENVAKEVHCTVVTCRKRYKELL 256 (530)
Q Consensus 192 ~~~A~~Ll~~a~~~~l~tGR~P~sIAAAAIYlAa~~~g~k~t~~eIA~~~~VS~~TIrkRyKEL~ 256 (530)
...+..|.+..--....---.|+-|||||+++|--..+..-=-..+..-++.+..++...+..|.
T Consensus 256 e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~ 320 (359)
T KOG0654|consen 256 EPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH 320 (359)
T ss_pred HHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence 55566666653322223334599999999999987776322223566668888777777777666
No 493
>PRK06030 hypothetical protein; Provisional
Probab=32.50 E-value=1e+02 Score=28.21 Aligned_cols=39 Identities=23% Similarity=0.257 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHHHh
Q 047665 115 ACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFL 155 (530)
Q Consensus 115 AclYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k~L 155 (530)
.|+|++-... ..|+.+|+..+|-|-.++..+++++.+.+
T Consensus 59 IAMYL~r~~~--~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVSL--GWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 4578775544 45899999999999999999999888765
No 494
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=32.42 E-value=40 Score=34.63 Aligned_cols=38 Identities=18% Similarity=0.218 Sum_probs=29.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHhhcccCCCC
Q 047665 232 VKIENVAKEVHCTVVTCRKRYK-------ELLEALVKVAQALPWG 269 (530)
Q Consensus 232 ~t~~eIA~~~~VS~~TIrkRyK-------EL~e~L~~l~~~lpW~ 269 (530)
.|++|||+.+|||..|+.+.+. |..+...+.++++=|.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~ 46 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYH 46 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCC
Confidence 4899999999999999988775 4556666666665443
No 495
>PRK15320 transcriptional activator SprB; Provisional
Probab=32.41 E-value=60 Score=32.40 Aligned_cols=31 Identities=16% Similarity=0.005 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
.-.|++|||+..++|..||.++...|.+.|.
T Consensus 178 kG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 178 SGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred cCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 4689999999999999999999988888764
No 496
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=32.29 E-value=64 Score=31.40 Aligned_cols=35 Identities=9% Similarity=0.083 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcc
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALVKVAQ 264 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~~l~~ 264 (530)
...+..+||+.+|+|+.|+++|+.-....|-+.+.
T Consensus 163 ~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 163 IELETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 36889999999999999999999888777766554
No 497
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=32.18 E-value=74 Score=31.22 Aligned_cols=31 Identities=6% Similarity=0.095 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 230 VSVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 230 ~k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
...|.++||+..++|+.||++..+.|.+.|.
T Consensus 147 qGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 147 SGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3578899999999999999999999888764
No 498
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=32.16 E-value=52 Score=31.87 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=30.8
Q ss_pred HHHHHHhcCCCCChHHHHHHhCCCHHHHHHHHHHHHH
Q 047665 117 SYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVE 153 (530)
Q Consensus 117 lYiACR~~~~P~TL~DIA~~~~vd~~~Lgr~~k~L~k 153 (530)
||-+.-..+-|.|+.||++++|++...+.-+.++|..
T Consensus 31 iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 4444445688999999999999999999988888765
No 499
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=31.91 E-value=67 Score=30.41 Aligned_cols=30 Identities=27% Similarity=0.228 Sum_probs=25.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEALV 260 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~L~ 260 (530)
..|.+|||+..|+|..|+++++.-....|.
T Consensus 147 g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 147 GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 589999999999999999999877666553
No 500
>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=31.90 E-value=91 Score=30.26 Aligned_cols=28 Identities=14% Similarity=0.221 Sum_probs=25.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 047665 231 SVKIENVAKEVHCTVVTCRKRYKELLEA 258 (530)
Q Consensus 231 k~t~~eIA~~~~VS~~TIrkRyKEL~e~ 258 (530)
.+|+.+||+.++++..|+++.+++|.+.
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4999999999999999999999999774
Done!