Query psy6534
Match_columns 309
No_of_seqs 174 out of 1290
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 20:31:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6534.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6534hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1597|consensus 100.0 1.9E-75 4.1E-80 502.1 26.9 303 6-308 1-307 (308)
2 PRK00423 tfb transcription ini 100.0 1.9E-71 4E-76 504.4 33.4 289 4-293 10-308 (310)
3 COG1405 SUA7 Transcription ini 100.0 3E-65 6.4E-70 452.1 26.3 278 6-290 2-280 (285)
4 KOG1598|consensus 100.0 1.1E-43 2.3E-48 328.9 14.6 257 6-298 1-264 (521)
5 PF00382 TFIIB: Transcription 99.7 7.7E-18 1.7E-22 120.0 9.3 71 114-184 1-71 (71)
6 PF00382 TFIIB: Transcription 99.7 2.6E-17 5.6E-22 117.3 9.7 71 208-278 1-71 (71)
7 KOG0835|consensus 99.7 1.9E-15 4.2E-20 132.7 17.9 179 105-283 21-223 (367)
8 TIGR00569 ccl1 cyclin ccl1. Un 99.7 2.9E-15 6.3E-20 135.0 19.5 180 104-284 52-247 (305)
9 KOG0834|consensus 99.6 2E-15 4.3E-20 135.9 13.3 180 107-286 39-242 (323)
10 PF08271 TF_Zn_Ribbon: TFIIB z 99.6 2E-16 4.3E-21 100.9 3.1 43 6-48 1-43 (43)
11 COG5333 CCL1 Cdk activating ki 99.5 2E-13 4.3E-18 120.2 13.3 157 108-264 46-212 (297)
12 KOG0794|consensus 99.5 7.9E-13 1.7E-17 111.1 12.2 177 109-286 43-235 (264)
13 PRK00423 tfb transcription ini 99.4 8.4E-13 1.8E-17 120.3 12.0 90 110-199 219-308 (310)
14 COG1405 SUA7 Transcription ini 99.4 2E-12 4.3E-17 115.3 8.7 102 203-308 99-200 (285)
15 cd00043 CYCLIN Cyclin box fold 99.1 6.8E-10 1.5E-14 81.2 10.9 84 202-285 3-87 (88)
16 cd00043 CYCLIN Cyclin box fold 99.1 8.1E-10 1.8E-14 80.8 10.6 83 109-191 4-87 (88)
17 smart00385 CYCLIN domain prese 99.1 6.6E-10 1.4E-14 80.4 9.3 81 206-286 1-82 (83)
18 KOG0656|consensus 99.1 1.3E-08 2.8E-13 92.1 17.6 176 108-283 79-268 (335)
19 smart00385 CYCLIN domain prese 99.0 1.5E-09 3.3E-14 78.5 8.3 80 113-192 2-82 (83)
20 KOG1597|consensus 98.9 8.6E-09 1.9E-13 90.2 9.8 88 110-197 203-290 (308)
21 KOG4557|consensus 98.8 2.7E-07 5.9E-12 77.1 15.2 175 113-293 2-185 (262)
22 COG5024 Cyclin [Cell division 98.5 1.2E-06 2.6E-11 82.4 12.7 182 111-293 217-403 (440)
23 KOG0653|consensus 98.5 2.5E-06 5.4E-11 80.4 13.6 163 110-272 161-328 (391)
24 KOG2496|consensus 98.5 1.8E-06 3.8E-11 76.1 11.3 140 116-255 65-219 (325)
25 PF00134 Cyclin_N: Cyclin, N-t 98.4 4.8E-06 1E-10 65.6 12.3 94 106-199 30-126 (127)
26 KOG1598|consensus 98.3 5.7E-07 1.2E-11 85.0 4.2 88 112-199 168-258 (521)
27 PF02984 Cyclin_C: Cyclin, C-t 98.1 1.8E-05 3.9E-10 61.3 7.8 88 203-290 2-90 (118)
28 PF01857 RB_B: Retinoblastoma- 97.8 0.00011 2.4E-09 58.6 7.9 82 108-189 12-95 (135)
29 KOG0655|consensus 97.6 0.00058 1.3E-08 61.2 10.7 167 111-286 149-332 (408)
30 PF11781 RRN7: RNA polymerase 97.4 0.00015 3.2E-09 43.9 2.3 33 1-35 4-36 (36)
31 PRK00415 rps27e 30S ribosomal 96.8 0.00085 1.8E-08 44.9 2.3 31 6-36 12-42 (59)
32 PHA00626 hypothetical protein 96.8 0.001 2.2E-08 43.6 2.5 30 6-35 1-34 (59)
33 COG2051 RPS27A Ribosomal prote 96.6 0.0011 2.4E-08 45.1 1.7 31 6-36 20-50 (67)
34 KOG0835|consensus 96.6 0.014 3E-07 52.5 9.0 102 111-215 142-246 (367)
35 PF01667 Ribosomal_S27e: Ribos 96.6 0.0012 2.5E-08 43.8 1.5 31 6-36 8-38 (55)
36 PF01857 RB_B: Retinoblastoma- 96.5 0.013 2.9E-07 46.7 7.4 80 206-285 16-97 (135)
37 TIGR00569 ccl1 cyclin ccl1. Un 96.5 0.023 5E-07 51.7 9.8 69 206-274 61-131 (305)
38 PF00134 Cyclin_N: Cyclin, N-t 96.3 0.043 9.2E-07 42.8 9.5 81 205-285 35-118 (127)
39 PLN00209 ribosomal protein S27 96.3 0.003 6.5E-08 45.4 2.3 31 6-36 37-67 (86)
40 PTZ00083 40S ribosomal protein 96.2 0.0037 8.1E-08 44.8 2.3 31 6-36 36-66 (85)
41 PF02984 Cyclin_C: Cyclin, C-t 95.9 0.05 1.1E-06 41.7 7.9 86 111-196 4-90 (118)
42 KOG0834|consensus 95.9 0.031 6.7E-07 51.1 7.4 83 205-287 43-129 (323)
43 PRK00420 hypothetical protein; 95.6 0.0086 1.9E-07 45.9 2.4 27 6-34 24-50 (112)
44 PF08274 PhnA_Zn_Ribbon: PhnA 95.5 0.011 2.3E-07 34.1 2.0 25 7-33 4-28 (30)
45 PRK00432 30S ribosomal protein 95.4 0.011 2.3E-07 38.6 2.0 27 6-34 21-47 (50)
46 TIGR02098 MJ0042_CXXC MJ0042 f 95.3 0.0083 1.8E-07 36.7 1.2 29 6-34 3-35 (38)
47 PF13240 zinc_ribbon_2: zinc-r 95.1 0.012 2.6E-07 31.8 1.3 22 7-33 1-22 (23)
48 smart00778 Prim_Zn_Ribbon Zinc 95.1 0.022 4.8E-07 34.6 2.5 28 5-32 3-33 (37)
49 PF08792 A2L_zn_ribbon: A2L zi 95.1 0.024 5.3E-07 33.5 2.6 29 5-34 3-31 (33)
50 COG1645 Uncharacterized Zn-fin 95.0 0.015 3.2E-07 45.6 2.0 23 7-32 30-52 (131)
51 KOG4164|consensus 95.0 0.11 2.5E-06 47.8 7.8 88 110-197 385-477 (497)
52 PF13248 zf-ribbon_3: zinc-rib 95.0 0.013 2.8E-07 32.7 1.1 22 6-32 3-24 (26)
53 COG1997 RPL43A Ribosomal prote 94.9 0.023 5E-07 41.0 2.6 29 5-34 35-63 (89)
54 PRK11827 hypothetical protein; 94.8 0.021 4.6E-07 38.6 2.2 29 5-34 8-36 (60)
55 PF14803 Nudix_N_2: Nudix N-te 94.8 0.013 2.8E-07 34.9 0.8 28 7-34 2-32 (34)
56 PF03966 Trm112p: Trm112p-like 94.7 0.026 5.6E-07 39.4 2.5 17 18-34 47-63 (68)
57 COG5333 CCL1 Cdk activating ki 94.7 0.089 1.9E-06 47.1 6.4 83 206-288 50-140 (297)
58 COG1998 RPS31 Ribosomal protei 94.7 0.019 4E-07 36.8 1.5 26 7-33 21-46 (51)
59 PF08613 Cyclin: Cyclin; Inte 94.6 0.64 1.4E-05 37.7 10.8 88 111-198 55-148 (149)
60 PF14354 Lar_restr_allev: Rest 94.6 0.035 7.6E-07 37.7 2.8 27 6-32 4-37 (61)
61 TIGR01206 lysW lysine biosynth 94.4 0.023 5E-07 37.6 1.6 30 5-34 2-32 (54)
62 PF02150 RNA_POL_M_15KD: RNA p 94.4 0.028 6.1E-07 33.7 1.8 28 7-34 3-30 (35)
63 PRK10220 hypothetical protein; 94.1 0.12 2.6E-06 39.0 4.9 26 6-33 4-29 (111)
64 PF08273 Prim_Zn_Ribbon: Zinc- 93.9 0.04 8.7E-07 34.0 1.7 28 6-33 4-35 (40)
65 PF08613 Cyclin: Cyclin; Inte 93.8 1.4 3E-05 35.7 11.2 91 198-288 48-144 (149)
66 COG2835 Uncharacterized conser 93.8 0.052 1.1E-06 36.4 2.3 29 5-34 8-36 (60)
67 PF12760 Zn_Tnp_IS1595: Transp 93.8 0.074 1.6E-06 34.0 3.0 29 4-32 17-45 (46)
68 COG4888 Uncharacterized Zn rib 93.8 0.041 8.9E-07 40.8 1.9 29 6-34 23-56 (104)
69 smart00661 RPOL9 RNA polymeras 93.7 0.052 1.1E-06 35.5 2.2 29 7-35 2-31 (52)
70 KOG2496|consensus 93.5 0.27 5.8E-06 44.0 6.9 68 205-272 60-129 (325)
71 TIGR00686 phnA alkylphosphonat 93.3 0.16 3.4E-06 38.4 4.3 28 6-35 3-30 (109)
72 PRK00464 nrdR transcriptional 93.3 0.066 1.4E-06 43.6 2.6 29 6-34 1-38 (154)
73 PF13404 HTH_AsnC-type: AsnC-t 93.2 0.23 5E-06 31.0 4.4 28 259-286 15-42 (42)
74 PRK00398 rpoP DNA-directed RNA 93.2 0.081 1.8E-06 33.8 2.4 29 5-34 3-31 (46)
75 PF09538 FYDLN_acid: Protein o 93.1 0.065 1.4E-06 41.0 2.1 33 3-37 7-39 (108)
76 PF05460 ORC6: Origin recognit 93.0 0.028 6.1E-07 52.3 0.0 84 116-199 3-89 (353)
77 PF00325 Crp: Bacterial regula 92.9 0.18 3.9E-06 29.5 3.4 28 261-288 2-29 (32)
78 PF06677 Auto_anti-p27: Sjogre 92.9 0.1 2.3E-06 32.4 2.5 24 6-31 18-41 (41)
79 PF10571 UPF0547: Uncharacteri 92.9 0.066 1.4E-06 29.8 1.4 23 7-34 2-24 (26)
80 COG2824 PhnA Uncharacterized Z 92.7 0.15 3.2E-06 38.2 3.5 28 6-35 4-31 (112)
81 COG3478 Predicted nucleic-acid 92.6 0.085 1.8E-06 35.7 1.9 32 1-33 1-49 (68)
82 TIGR03655 anti_R_Lar restricti 92.6 0.1 2.2E-06 34.4 2.3 29 7-35 3-37 (53)
83 PF08279 HTH_11: HTH domain; 92.5 0.33 7.2E-06 31.9 4.8 32 258-289 12-43 (55)
84 PF01780 Ribosomal_L37ae: Ribo 92.5 0.065 1.4E-06 39.3 1.3 30 5-35 35-64 (90)
85 KOG4557|consensus 92.5 0.47 1E-05 40.3 6.5 81 113-194 95-180 (262)
86 KOG1010|consensus 92.4 0.27 5.8E-06 49.8 5.9 82 110-191 680-763 (920)
87 PTZ00255 60S ribosomal protein 92.2 0.11 2.3E-06 38.1 2.2 31 4-35 35-65 (90)
88 KOG1779|consensus 92.2 0.075 1.6E-06 37.4 1.3 29 6-34 35-63 (84)
89 TIGR02300 FYDLN_acid conserved 92.1 0.1 2.3E-06 40.5 2.2 33 3-37 7-39 (129)
90 PF01325 Fe_dep_repress: Iron 92.1 0.5 1.1E-05 32.0 5.3 38 250-288 12-49 (60)
91 PRK05901 RNA polymerase sigma 92.1 13 0.00027 36.6 16.8 30 259-288 465-494 (509)
92 PF13719 zinc_ribbon_5: zinc-r 92.1 0.086 1.9E-06 32.0 1.3 29 6-34 3-35 (37)
93 TIGR02393 RpoD_Cterm RNA polym 92.0 7.7 0.00017 33.8 18.5 121 163-290 99-225 (238)
94 KOG0654|consensus 92.0 1.5 3.2E-05 40.7 9.8 137 150-286 180-320 (359)
95 smart00342 HTH_ARAC helix_turn 91.9 3.1 6.7E-05 29.0 10.0 26 261-286 50-76 (84)
96 PF13412 HTH_24: Winged helix- 91.8 0.63 1.4E-05 29.6 5.4 30 259-288 15-44 (48)
97 PF13730 HTH_36: Helix-turn-he 91.8 0.73 1.6E-05 30.2 5.8 26 263-288 27-52 (55)
98 TIGR00280 L37a ribosomal prote 91.6 0.12 2.7E-06 37.9 1.9 31 4-35 34-64 (91)
99 PF07282 OrfB_Zn_ribbon: Putat 91.2 0.15 3.3E-06 35.4 2.0 29 5-34 28-56 (69)
100 PRK14892 putative transcriptio 91.1 0.15 3.3E-06 38.2 2.1 31 5-35 21-53 (99)
101 PF00356 LacI: Bacterial regul 91.0 0.26 5.7E-06 31.5 2.8 21 263-283 1-21 (46)
102 PF09297 zf-NADH-PPase: NADH p 91.0 0.22 4.9E-06 29.0 2.3 27 6-33 4-30 (32)
103 PF10668 Phage_terminase: Phag 90.9 0.77 1.7E-05 31.1 5.1 37 241-280 5-41 (60)
104 PRK09210 RNA polymerase sigma 90.8 14 0.00031 34.6 17.9 171 109-286 137-350 (367)
105 COG2888 Predicted Zn-ribbon RN 90.6 0.17 3.8E-06 33.7 1.7 26 7-32 29-58 (61)
106 TIGR01610 phage_O_Nterm phage 90.3 2.8 6.1E-05 31.1 8.3 31 258-288 44-74 (95)
107 PRK03976 rpl37ae 50S ribosomal 90.3 0.19 4.2E-06 36.8 1.9 31 4-35 35-65 (90)
108 PRK05911 RNA polymerase sigma 90.2 13 0.00028 33.0 18.3 30 260-289 220-249 (257)
109 PF08220 HTH_DeoR: DeoR-like h 90.0 0.42 9.2E-06 31.9 3.3 31 259-289 12-42 (57)
110 cd00092 HTH_CRP helix_turn_hel 89.9 1.4 3E-05 29.9 6.0 30 259-288 23-52 (67)
111 PF13545 HTH_Crp_2: Crp-like h 89.9 0.76 1.6E-05 32.2 4.8 30 260-289 27-56 (76)
112 PF13613 HTH_Tnp_4: Helix-turn 89.8 0.57 1.2E-05 30.8 3.7 36 258-293 16-51 (53)
113 KOG0794|consensus 89.4 0.65 1.4E-05 40.0 4.7 58 204-261 44-101 (264)
114 PF04545 Sigma70_r4: Sigma-70, 89.3 0.88 1.9E-05 29.3 4.3 30 259-288 18-47 (50)
115 PF13936 HTH_38: Helix-turn-he 89.3 0.61 1.3E-05 29.3 3.4 28 256-283 15-42 (44)
116 smart00342 HTH_ARAC helix_turn 89.3 1.8 3.9E-05 30.3 6.4 71 114-191 4-75 (84)
117 PF02796 HTH_7: Helix-turn-hel 88.9 0.25 5.3E-06 31.3 1.4 28 256-283 16-43 (45)
118 PF13717 zinc_ribbon_4: zinc-r 88.9 0.25 5.5E-06 29.7 1.4 29 6-34 3-35 (36)
119 PRK07405 RNA polymerase sigma 88.9 19 0.0004 33.1 16.4 115 164-285 181-300 (317)
120 smart00419 HTH_CRP helix_turn_ 88.6 0.81 1.8E-05 28.7 3.8 30 259-288 6-35 (48)
121 PF01371 Trp_repressor: Trp re 88.6 0.8 1.7E-05 33.5 4.1 34 254-287 41-75 (87)
122 cd06571 Bac_DnaA_C C-terminal 88.5 1.7 3.7E-05 31.9 5.9 39 249-289 34-73 (90)
123 smart00345 HTH_GNTR helix_turn 88.5 0.94 2E-05 29.8 4.2 29 260-288 18-47 (60)
124 smart00440 ZnF_C2C2 C2C2 Zinc 88.4 0.37 8.1E-06 29.7 1.9 27 7-33 2-37 (40)
125 PRK09710 lar restriction allev 88.2 0.47 1E-05 32.3 2.4 28 6-33 7-36 (64)
126 COG5349 Uncharacterized protei 88.2 0.18 3.9E-06 38.8 0.5 35 3-37 19-53 (126)
127 TIGR00244 transcriptional regu 88.1 0.49 1.1E-05 38.0 2.9 29 6-34 1-38 (147)
128 PRK07406 RNA polymerase sigma 88.0 16 0.00034 34.5 13.3 178 104-289 164-359 (373)
129 PF13542 HTH_Tnp_ISL3: Helix-t 87.7 1.3 2.8E-05 28.6 4.3 25 260-284 26-50 (52)
130 TIGR03697 NtcA_cyano global ni 87.6 2.9 6.4E-05 34.7 7.7 29 260-288 142-170 (193)
131 PRK11169 leucine-responsive tr 87.5 1.1 2.3E-05 37.0 4.8 32 258-289 25-56 (164)
132 PRK02935 hypothetical protein; 87.5 0.48 1E-05 35.5 2.4 41 2-48 67-107 (110)
133 COG1191 FliA DNA-directed RNA 87.5 4.3 9.3E-05 35.9 8.7 31 259-289 210-240 (247)
134 TIGR02443 conserved hypothetic 87.4 0.61 1.3E-05 31.2 2.6 32 3-34 7-41 (59)
135 PF05129 Elf1: Transcription e 87.3 0.36 7.7E-06 34.9 1.6 31 5-35 22-57 (81)
136 PRK00135 scpB segregation and 87.3 3.7 8.1E-05 34.7 7.9 119 149-287 5-127 (188)
137 COG1725 Predicted transcriptio 87.0 0.86 1.9E-05 35.7 3.7 31 259-289 32-63 (125)
138 PF03604 DNA_RNApol_7kD: DNA d 86.9 0.47 1E-05 27.8 1.6 24 7-32 2-25 (32)
139 PF04967 HTH_10: HTH DNA bindi 86.9 2.9 6.3E-05 27.5 5.6 27 261-287 23-49 (53)
140 COG1326 Uncharacterized archae 86.8 0.31 6.6E-06 40.8 1.1 33 5-37 6-43 (201)
141 PF14446 Prok-RING_1: Prokaryo 86.8 0.59 1.3E-05 30.8 2.2 31 1-34 1-31 (54)
142 PRK05949 RNA polymerase sigma 86.8 26 0.00056 32.3 16.5 170 108-284 98-309 (327)
143 PF00325 Crp: Bacterial regula 86.7 1.1 2.4E-05 26.2 3.1 27 167-193 2-28 (32)
144 PRK14088 dnaA chromosomal repl 86.5 9.6 0.00021 36.7 11.4 50 237-288 362-414 (440)
145 PRK13130 H/ACA RNA-protein com 86.5 0.39 8.4E-06 32.0 1.3 27 1-34 1-27 (56)
146 PF09526 DUF2387: Probable met 86.5 0.7 1.5E-05 32.4 2.6 32 3-34 6-40 (71)
147 PRK05978 hypothetical protein; 86.4 0.55 1.2E-05 38.0 2.4 31 5-35 33-63 (148)
148 PRK14890 putative Zn-ribbon RN 86.3 0.71 1.5E-05 30.9 2.4 9 24-32 48-56 (59)
149 PRK11179 DNA-binding transcrip 86.3 1.5 3.1E-05 35.7 4.9 31 259-289 21-51 (153)
150 PF00392 GntR: Bacterial regul 86.1 1.1 2.5E-05 30.4 3.6 30 259-288 21-51 (64)
151 PF03811 Zn_Tnp_IS1: InsA N-te 86.0 0.88 1.9E-05 27.4 2.5 30 1-30 1-35 (36)
152 PRK12495 hypothetical protein; 86.0 0.53 1.1E-05 40.2 2.2 27 7-36 44-70 (226)
153 TIGR01384 TFS_arch transcripti 85.9 0.49 1.1E-05 35.8 1.8 27 7-36 2-28 (104)
154 PF00165 HTH_AraC: Bacterial r 85.9 1.3 2.9E-05 27.2 3.5 28 259-286 6-33 (42)
155 PF13384 HTH_23: Homeodomain-l 85.4 1.6 3.5E-05 27.9 3.8 27 261-287 17-43 (50)
156 PF05191 ADK_lid: Adenylate ki 85.4 0.17 3.8E-06 30.5 -0.8 29 6-34 2-31 (36)
157 PF12802 MarR_2: MarR family; 85.4 2.2 4.7E-05 28.5 4.7 29 260-288 20-48 (62)
158 PF14502 HTH_41: Helix-turn-he 85.2 1.5 3.4E-05 28.1 3.5 28 262-289 7-34 (48)
159 smart00834 CxxC_CXXC_SSSS Puta 85.1 0.63 1.4E-05 28.5 1.7 33 1-33 1-35 (41)
160 PF02082 Rrf2: Transcriptional 85.0 1.6 3.4E-05 31.5 4.0 39 251-289 15-53 (83)
161 COG1510 Predicted transcriptio 85.0 1.4 3E-05 36.4 4.1 72 225-305 12-83 (177)
162 TIGR01321 TrpR trp operon repr 85.0 1.2 2.6E-05 33.1 3.3 30 257-286 51-80 (94)
163 PF08299 Bac_DnaA_C: Bacterial 84.7 1.5 3.3E-05 30.6 3.7 65 204-285 2-70 (70)
164 smart00659 RPOLCX RNA polymera 84.5 0.74 1.6E-05 29.1 1.8 27 6-34 3-29 (44)
165 PRK12286 rpmF 50S ribosomal pr 84.2 0.84 1.8E-05 30.6 2.1 29 4-38 26-54 (57)
166 PF05225 HTH_psq: helix-turn-h 83.8 4.9 0.00011 25.4 5.4 28 258-286 14-41 (45)
167 PF01022 HTH_5: Bacterial regu 83.7 3.3 7.1E-05 26.2 4.7 32 257-288 11-42 (47)
168 PRK14086 dnaA chromosomal repl 83.7 12 0.00026 37.5 10.7 39 249-289 559-597 (617)
169 PF13413 HTH_25: Helix-turn-he 83.3 2.1 4.5E-05 29.2 3.8 56 161-220 4-60 (62)
170 PF12773 DZR: Double zinc ribb 83.2 0.81 1.8E-05 29.5 1.7 11 24-34 29-39 (50)
171 COG1594 RPB9 DNA-directed RNA 83.1 0.9 2E-05 35.0 2.1 32 6-37 3-35 (113)
172 PF09855 DUF2082: Nucleic-acid 82.9 0.89 1.9E-05 31.2 1.8 27 7-33 2-45 (64)
173 TIGR03879 near_KaiC_dom probab 82.8 1.2 2.5E-05 31.5 2.4 27 260-286 31-57 (73)
174 TIGR00122 birA_repr_reg BirA b 82.8 3.2 7E-05 28.6 4.8 31 259-289 11-41 (69)
175 cd06571 Bac_DnaA_C C-terminal 82.6 6.1 0.00013 28.9 6.4 42 155-198 34-76 (90)
176 TIGR02395 rpoN_sigma RNA polym 82.6 39 0.00085 32.4 13.5 164 114-283 116-340 (429)
177 PF11023 DUF2614: Protein of u 82.6 0.48 1.1E-05 36.0 0.5 42 3-50 67-108 (114)
178 PF03119 DNA_ligase_ZBD: NAD-d 82.5 1.1 2.4E-05 25.3 1.8 22 7-29 1-22 (28)
179 PRK11161 fumarate/nitrate redu 82.5 6.4 0.00014 34.0 7.6 30 260-289 183-212 (235)
180 PF01783 Ribosomal_L32p: Ribos 82.4 0.69 1.5E-05 30.9 1.1 26 4-35 25-50 (56)
181 PF15616 TerY-C: TerY-C metal 82.2 1.8 3.9E-05 34.2 3.6 29 6-34 78-115 (131)
182 smart00421 HTH_LUXR helix_turn 82.2 2.9 6.3E-05 26.9 4.2 28 261-288 18-45 (58)
183 PRK06266 transcription initiat 82.1 0.41 9E-06 40.1 -0.1 31 5-35 117-147 (178)
184 PF02082 Rrf2: Transcriptional 82.0 3.1 6.8E-05 29.9 4.6 45 150-194 8-52 (83)
185 TIGR02010 IscR iron-sulfur clu 81.6 3.9 8.6E-05 32.4 5.4 45 149-193 7-51 (135)
186 smart00550 Zalpha Z-DNA-bindin 81.4 5.2 0.00011 27.7 5.3 37 252-288 12-49 (68)
187 PF01096 TFIIS_C: Transcriptio 81.3 1 2.2E-05 27.6 1.5 27 7-33 2-37 (39)
188 COG3877 Uncharacterized protei 81.3 1.1 2.4E-05 33.7 1.9 23 7-34 8-30 (122)
189 COG1654 BirA Biotin operon rep 80.8 4.5 9.8E-05 29.0 4.9 35 258-292 16-50 (79)
190 PRK07122 RNA polymerase sigma 80.4 42 0.0009 29.8 17.0 29 260-288 230-258 (264)
191 PF08279 HTH_11: HTH domain; 80.3 5 0.00011 26.1 4.8 34 162-195 10-43 (55)
192 PRK07408 RNA polymerase sigma 80.2 41 0.00089 29.7 18.0 32 260-291 218-249 (256)
193 PF00196 GerE: Bacterial regul 80.2 2.5 5.3E-05 28.1 3.3 30 260-289 17-46 (58)
194 PRK11014 transcriptional repre 80.2 3.4 7.3E-05 33.0 4.7 41 249-289 13-53 (141)
195 KOG3507|consensus 80.2 1 2.2E-05 30.0 1.3 26 7-34 22-47 (62)
196 PHA02591 hypothetical protein; 80.1 2.7 6E-05 29.8 3.5 31 253-283 51-81 (83)
197 PF14319 Zn_Tnp_IS91: Transpos 80.1 0.71 1.5E-05 35.5 0.6 39 1-40 38-76 (111)
198 PF09862 DUF2089: Protein of u 80.0 3.8 8.3E-05 31.5 4.5 61 169-229 51-112 (113)
199 PRK01381 Trp operon repressor; 79.9 1.6 3.4E-05 32.7 2.3 35 253-287 47-81 (99)
200 PF09862 DUF2089: Protein of u 79.7 1.9 4.2E-05 33.1 2.9 31 261-291 49-79 (113)
201 PRK04217 hypothetical protein; 79.6 2.2 4.8E-05 32.7 3.2 33 260-292 57-89 (110)
202 PRK00149 dnaA chromosomal repl 79.6 18 0.00038 34.9 10.2 39 249-289 392-431 (450)
203 PRK07598 RNA polymerase sigma 79.5 60 0.0013 31.1 19.1 174 104-284 178-393 (415)
204 TIGR02147 Fsuc_second hypothet 79.4 47 0.001 29.8 13.2 124 157-288 16-166 (271)
205 cd06170 LuxR_C_like C-terminal 79.4 4.4 9.5E-05 26.1 4.3 28 261-288 15-42 (57)
206 PRK11337 DNA-binding transcrip 79.4 5.5 0.00012 35.8 6.3 62 200-285 8-70 (292)
207 PF11672 DUF3268: Protein of u 79.3 1.7 3.6E-05 32.8 2.4 31 5-35 2-42 (102)
208 PHA02942 putative transposase; 79.3 1.4 3.1E-05 41.5 2.5 28 6-35 326-353 (383)
209 cd07377 WHTH_GntR Winged helix 79.3 3.3 7.2E-05 27.6 3.8 27 263-289 27-53 (66)
210 PRK14087 dnaA chromosomal repl 79.3 30 0.00066 33.4 11.6 38 250-289 392-430 (450)
211 PF00301 Rubredoxin: Rubredoxi 79.2 1.4 3E-05 28.3 1.6 14 25-38 2-15 (47)
212 TIGR02392 rpoH_proteo alternat 79.2 46 0.001 29.6 16.7 31 259-289 234-264 (270)
213 smart00344 HTH_ASNC helix_turn 79.1 4.3 9.2E-05 30.5 4.7 29 260-288 16-44 (108)
214 PRK05657 RNA polymerase sigma 79.1 53 0.0011 30.2 17.6 30 260-289 281-310 (325)
215 PF01978 TrmB: Sugar-specific 79.0 2.5 5.4E-05 29.0 3.1 37 251-288 13-49 (68)
216 PF08281 Sigma70_r4_2: Sigma-7 79.0 3.3 7.2E-05 26.8 3.6 28 260-287 25-52 (54)
217 PF02042 RWP-RK: RWP-RK domain 78.8 3.3 7.2E-05 27.1 3.4 26 260-285 14-39 (52)
218 PF01325 Fe_dep_repress: Iron 78.7 8.1 0.00018 26.0 5.4 36 157-193 13-48 (60)
219 cd00350 rubredoxin_like Rubred 78.7 1.8 4E-05 25.4 2.0 23 7-32 3-25 (33)
220 COG1522 Lrp Transcriptional re 78.6 3.8 8.3E-05 32.9 4.6 31 259-289 20-50 (154)
221 PRK05932 RNA polymerase factor 78.6 38 0.00083 32.8 12.0 75 114-193 141-234 (455)
222 PF05876 Terminase_GpA: Phage 78.6 1.2 2.6E-05 44.2 1.9 42 6-47 201-255 (557)
223 TIGR02844 spore_III_D sporulat 78.6 2.6 5.6E-05 30.4 3.1 24 260-283 18-41 (80)
224 PF01599 Ribosomal_S27: Riboso 78.3 2.7 5.8E-05 26.9 2.7 26 6-32 19-46 (47)
225 PF13545 HTH_Crp_2: Crp-like h 78.3 5.9 0.00013 27.5 4.9 43 152-194 3-55 (76)
226 COG1318 Predicted transcriptio 78.2 4.6 9.9E-05 33.3 4.7 39 244-284 46-84 (182)
227 PRK13918 CRP/FNR family transc 78.1 11 0.00024 31.5 7.4 29 260-288 148-176 (202)
228 TIGR00373 conserved hypothetic 78.0 0.59 1.3E-05 38.3 -0.4 29 8-36 112-140 (158)
229 PRK05508 methionine sulfoxide 77.9 2.2 4.7E-05 33.1 2.7 33 18-50 27-61 (119)
230 TIGR01031 rpmF_bact ribosomal 77.8 1.7 3.7E-05 28.9 1.8 26 4-35 25-50 (55)
231 COG1327 Predicted transcriptio 77.8 1.5 3.3E-05 35.3 1.8 28 6-33 1-37 (156)
232 COG0675 Transposase and inacti 77.5 1.3 2.9E-05 40.4 1.7 23 6-34 310-332 (364)
233 smart00418 HTH_ARSR helix_turn 77.3 7 0.00015 25.6 4.9 30 259-288 8-37 (66)
234 PRK08402 replication factor A; 77.2 1.7 3.8E-05 40.4 2.4 27 6-33 213-239 (355)
235 PRK10857 DNA-binding transcrip 77.0 6.5 0.00014 32.4 5.5 46 149-194 7-52 (164)
236 smart00420 HTH_DEOR helix_turn 77.0 9.9 0.00021 23.9 5.4 29 260-288 13-41 (53)
237 TIGR02944 suf_reg_Xantho FeS a 76.9 8 0.00017 30.2 5.9 39 250-289 15-53 (130)
238 PF14255 Cys_rich_CPXG: Cystei 76.7 1.8 3.9E-05 28.4 1.7 26 7-32 2-32 (52)
239 PF05732 RepL: Firmicute plasm 76.7 6.7 0.00015 32.4 5.5 27 262-288 76-102 (165)
240 PRK00222 methionine sulfoxide 76.5 2.4 5.1E-05 34.0 2.6 34 18-51 37-72 (142)
241 PF01726 LexA_DNA_bind: LexA D 76.3 9.7 0.00021 26.1 5.3 32 257-288 21-53 (65)
242 PRK08215 sporulation sigma fac 76.3 54 0.0012 28.9 16.2 29 260-288 224-252 (258)
243 PF01418 HTH_6: Helix-turn-hel 76.0 2.6 5.6E-05 29.9 2.5 26 260-285 33-58 (77)
244 PF13309 HTH_22: HTH domain 76.0 16 0.00035 24.9 6.4 56 205-280 4-61 (64)
245 TIGR01764 excise DNA binding d 75.8 3.8 8.2E-05 25.5 3.1 23 262-284 2-24 (49)
246 PF01047 MarR: MarR family; I 75.7 8.7 0.00019 25.2 5.0 28 261-288 17-44 (59)
247 PRK11753 DNA-binding transcrip 75.7 16 0.00035 30.7 7.9 30 260-289 167-196 (211)
248 COG2093 DNA-directed RNA polym 75.5 1.7 3.7E-05 29.4 1.3 21 7-32 6-26 (64)
249 PF05344 DUF746: Domain of Unk 75.5 8.1 0.00018 26.5 4.6 40 256-295 8-47 (65)
250 PF00440 TetR_N: Bacterial reg 75.4 7.7 0.00017 24.4 4.4 37 249-285 4-40 (47)
251 PRK10219 DNA-binding transcrip 75.3 14 0.00031 27.6 6.7 36 249-285 10-45 (107)
252 TIGR02980 SigBFG RNA polymeras 75.3 52 0.0011 28.2 15.2 30 260-289 193-222 (227)
253 PRK11511 DNA-binding transcrip 75.1 14 0.00031 28.8 6.8 43 243-286 8-50 (127)
254 COG3355 Predicted transcriptio 75.1 7.8 0.00017 30.4 5.1 38 251-288 32-69 (126)
255 PF00376 MerR: MerR family reg 74.9 2.7 5.8E-05 25.6 2.0 19 263-281 1-19 (38)
256 PRK06030 hypothetical protein; 74.9 13 0.00028 29.2 6.3 72 203-288 24-96 (124)
257 TIGR02997 Sig70-cyanoRpoD RNA 74.9 65 0.0014 29.1 18.5 115 165-286 175-294 (298)
258 PRK09391 fixK transcriptional 74.8 18 0.00039 31.3 8.0 30 260-289 178-207 (230)
259 PF04161 Arv1: Arv1-like famil 74.5 1.8 3.9E-05 37.2 1.6 30 6-35 1-35 (208)
260 KOG2593|consensus 74.4 1.6 3.5E-05 41.0 1.4 32 3-34 126-163 (436)
261 PF08280 HTH_Mga: M protein tr 74.4 4.2 9.1E-05 27.2 3.1 30 259-288 17-46 (59)
262 COG4068 Uncharacterized protei 74.4 0.7 1.5E-05 30.7 -0.7 26 4-34 7-33 (64)
263 smart00354 HTH_LACI helix_turn 74.4 3.6 7.7E-05 28.6 2.8 22 262-283 1-22 (70)
264 PF01726 LexA_DNA_bind: LexA D 74.3 6.6 0.00014 27.0 4.1 32 162-193 20-52 (65)
265 cd04762 HTH_MerR-trunc Helix-T 74.2 4.5 9.8E-05 25.0 3.1 22 263-284 2-23 (49)
266 cd00092 HTH_CRP helix_turn_hel 74.1 13 0.00029 24.8 5.8 29 165-193 23-51 (67)
267 PF04079 DUF387: Putative tran 73.9 48 0.001 27.2 9.9 95 152-277 2-112 (159)
268 PF06044 DRP: Dam-replacing fa 72.9 2.1 4.6E-05 37.2 1.6 30 5-34 31-63 (254)
269 PF14122 YokU: YokU-like prote 72.8 2 4.3E-05 31.1 1.2 23 22-44 33-55 (87)
270 KOG1010|consensus 72.7 8 0.00017 39.7 5.8 80 207-286 683-764 (920)
271 PRK10402 DNA-binding transcrip 72.7 13 0.00029 31.9 6.7 29 261-289 169-197 (226)
272 PF09339 HTH_IclR: IclR helix- 72.7 7.6 0.00017 25.1 4.0 30 259-288 16-45 (52)
273 PF13613 HTH_Tnp_4: Helix-turn 72.7 9.1 0.0002 24.9 4.3 38 161-198 13-50 (53)
274 PRK07921 RNA polymerase sigma 72.4 80 0.0017 29.1 17.6 28 259-286 280-307 (324)
275 PRK09863 putative frv operon r 72.3 39 0.00085 33.7 10.7 105 166-290 16-121 (584)
276 COG1996 RPC10 DNA-directed RNA 72.3 2.3 4.9E-05 27.5 1.3 27 6-33 7-33 (49)
277 cd06171 Sigma70_r4 Sigma70, re 72.0 8.8 0.00019 23.9 4.2 28 260-287 25-52 (55)
278 PF01978 TrmB: Sugar-specific 71.8 9.6 0.00021 26.0 4.5 36 157-193 13-48 (68)
279 CHL00174 accD acetyl-CoA carbo 71.7 0.97 2.1E-05 40.8 -0.7 30 6-35 39-68 (296)
280 PF12840 HTH_20: Helix-turn-he 71.7 7.1 0.00015 26.1 3.8 31 258-288 21-51 (61)
281 PF03444 HrcA_DNA-bdg: Winged 71.6 15 0.00032 26.3 5.4 33 257-289 19-51 (78)
282 PF00356 LacI: Bacterial regul 71.6 4.6 9.9E-05 25.7 2.6 21 169-189 1-21 (46)
283 PF00165 HTH_AraC: Bacterial r 71.5 6.5 0.00014 24.1 3.3 27 165-191 6-32 (42)
284 PF04703 FaeA: FaeA-like prote 71.4 13 0.00028 25.3 4.9 33 162-194 10-42 (62)
285 smart00401 ZnF_GATA zinc finge 71.4 3.4 7.3E-05 27.0 2.0 30 5-34 3-35 (52)
286 PF12728 HTH_17: Helix-turn-he 71.3 5.4 0.00012 25.5 3.0 22 262-283 2-23 (51)
287 cd04761 HTH_MerR-SF Helix-Turn 71.3 5 0.00011 25.2 2.8 21 263-283 2-22 (49)
288 PRK00118 putative DNA-binding 71.2 5.1 0.00011 30.4 3.2 28 260-287 32-59 (104)
289 cd00730 rubredoxin Rubredoxin; 71.2 3.3 7.3E-05 26.9 1.9 13 25-37 2-14 (50)
290 PF01807 zf-CHC2: CHC2 zinc fi 71.2 3.5 7.7E-05 30.7 2.3 26 6-31 34-61 (97)
291 smart00346 HTH_ICLR helix_turn 70.9 18 0.0004 25.9 6.2 29 260-288 19-47 (91)
292 TIGR00515 accD acetyl-CoA carb 70.9 1.1 2.3E-05 40.5 -0.6 29 6-34 27-55 (285)
293 PF13412 HTH_24: Winged helix- 70.9 16 0.00034 22.9 5.1 29 165-193 15-43 (48)
294 COG4640 Predicted membrane pro 70.8 2.3 5E-05 39.6 1.5 25 6-35 2-26 (465)
295 PRK11920 rirA iron-responsive 70.8 12 0.00026 30.4 5.6 45 149-194 7-51 (153)
296 PRK06393 rpoE DNA-directed RNA 70.8 2.3 5.1E-05 29.1 1.1 25 1-32 1-25 (64)
297 PRK12520 RNA polymerase sigma 70.6 3.7 7.9E-05 34.4 2.6 33 261-293 147-179 (191)
298 PF12802 MarR_2: MarR family; 70.5 15 0.00033 24.2 5.3 37 157-193 11-47 (62)
299 PRK08351 DNA-directed RNA poly 70.4 2.8 6E-05 28.5 1.4 29 7-48 5-33 (61)
300 PF13463 HTH_27: Winged helix 70.3 9.8 0.00021 25.7 4.3 32 257-288 14-45 (68)
301 smart00550 Zalpha Z-DNA-bindin 70.2 14 0.00031 25.4 5.1 38 157-194 11-49 (68)
302 PRK07500 rpoH2 RNA polymerase 70.1 84 0.0018 28.3 15.3 33 259-291 243-275 (289)
303 smart00419 HTH_CRP helix_turn_ 70.1 8.1 0.00017 23.9 3.6 29 165-193 6-34 (48)
304 TIGR00721 tfx DNA-binding prot 70.0 7.1 0.00015 31.2 3.9 30 260-289 20-49 (137)
305 PF04703 FaeA: FaeA-like prote 69.7 9 0.00019 26.1 3.8 31 259-289 13-43 (62)
306 TIGR02937 sigma70-ECF RNA poly 69.6 7.3 0.00016 30.4 4.1 30 261-290 126-155 (158)
307 TIGR00738 rrf2_super rrf2 fami 69.6 19 0.0004 28.1 6.4 45 244-288 7-52 (132)
308 KOG1088|consensus 69.5 2.3 4.9E-05 32.6 0.9 16 19-34 93-108 (124)
309 PF08646 Rep_fac-A_C: Replicat 69.3 3.6 7.7E-05 33.0 2.2 27 7-35 20-48 (146)
310 PF05043 Mga: Mga helix-turn-h 69.3 6.5 0.00014 28.3 3.4 34 258-291 27-60 (87)
311 PRK10434 srlR DNA-bindng trans 69.2 5.1 0.00011 35.5 3.3 29 260-288 18-46 (256)
312 PRK09678 DNA-binding transcrip 69.2 4.9 0.00011 28.3 2.5 29 6-34 2-39 (72)
313 PF14353 CpXC: CpXC protein 69.1 4.3 9.2E-05 31.8 2.5 11 24-34 38-48 (128)
314 PRK05654 acetyl-CoA carboxylas 69.0 1.2 2.7E-05 40.3 -0.6 43 6-49 28-77 (292)
315 TIGR00738 rrf2_super rrf2 fami 69.0 13 0.00029 28.9 5.4 44 150-193 8-51 (132)
316 PRK15418 transcriptional regul 68.9 7.9 0.00017 35.6 4.6 36 252-287 20-55 (318)
317 TIGR02010 IscR iron-sulfur clu 68.8 11 0.00025 29.7 5.0 41 249-289 13-53 (135)
318 PF09339 HTH_IclR: IclR helix- 68.8 13 0.00027 24.0 4.4 35 159-193 10-44 (52)
319 TIGR02394 rpoS_proteo RNA poly 68.7 88 0.0019 28.0 16.9 30 260-289 241-270 (285)
320 TIGR03697 NtcA_cyano global ni 68.7 20 0.00044 29.6 6.8 29 166-194 142-170 (193)
321 TIGR02531 yecD_yerC TrpR-relat 68.5 8.1 0.00018 28.3 3.7 21 260-280 49-69 (88)
322 TIGR02943 Sig70_famx1 RNA poly 68.4 4.3 9.4E-05 34.0 2.6 39 260-298 146-184 (188)
323 PRK11920 rirA iron-responsive 68.4 12 0.00027 30.3 5.2 40 249-289 13-52 (153)
324 PHA02540 61 DNA primase; Provi 68.3 4.4 9.5E-05 37.5 2.7 28 5-32 27-63 (337)
325 PF01412 ArfGap: Putative GTPa 68.3 1.5 3.3E-05 33.9 -0.2 32 2-34 11-43 (116)
326 PRK09642 RNA polymerase sigma 68.2 7 0.00015 31.5 3.7 38 260-297 121-159 (160)
327 TIGR00357 methionine-R-sulfoxi 68.1 4.4 9.5E-05 32.2 2.3 34 18-51 34-69 (134)
328 cd00090 HTH_ARSR Arsenical Res 68.1 16 0.00034 24.6 5.1 27 262-288 21-47 (78)
329 TIGR00310 ZPR1_znf ZPR1 zinc f 67.5 4.1 8.9E-05 34.5 2.2 31 7-37 2-43 (192)
330 KOG0402|consensus 67.5 1.9 4E-05 30.9 0.1 30 5-35 36-65 (92)
331 TIGR02985 Sig70_bacteroi1 RNA 67.3 8.6 0.00019 30.6 4.1 30 260-289 128-157 (161)
332 PF07900 DUF1670: Protein of u 67.2 8.7 0.00019 33.1 4.1 37 260-296 104-140 (220)
333 COG1321 TroR Mn-dependent tran 67.2 13 0.00027 30.4 5.0 38 250-288 14-51 (154)
334 PF01381 HTH_3: Helix-turn-hel 67.2 6.6 0.00014 25.3 2.8 25 260-284 8-32 (55)
335 PRK15481 transcriptional regul 67.2 16 0.00035 34.8 6.5 30 259-288 26-56 (431)
336 COG0777 AccD Acetyl-CoA carbox 66.8 1.7 3.8E-05 38.5 -0.1 29 6-34 29-57 (294)
337 TIGR02605 CxxC_CxxC_SSSS putat 66.6 4.3 9.3E-05 26.3 1.7 32 1-32 1-34 (52)
338 PRK12336 translation initiatio 66.6 4.1 8.9E-05 34.8 2.1 29 6-34 99-129 (201)
339 PRK13509 transcriptional repre 65.9 8.2 0.00018 34.1 3.9 30 259-288 17-46 (251)
340 COG1476 Predicted transcriptio 65.8 6.2 0.00013 27.4 2.4 25 260-284 13-37 (68)
341 PF10058 DUF2296: Predicted in 65.2 4.2 9E-05 26.9 1.4 28 5-32 22-52 (54)
342 COG1656 Uncharacterized conser 65.1 3.1 6.8E-05 34.1 1.0 31 4-34 96-140 (165)
343 PF04545 Sigma70_r4: Sigma-70, 65.1 15 0.00033 23.3 4.2 31 165-195 18-48 (50)
344 TIGR00595 priA primosomal prot 65.1 5.5 0.00012 39.1 2.9 31 3-34 220-250 (505)
345 PRK12531 RNA polymerase sigma 64.8 7.8 0.00017 32.5 3.5 34 260-293 156-189 (194)
346 PF09723 Zn-ribbon_8: Zinc rib 64.6 5.2 0.00011 24.8 1.7 32 1-32 1-34 (42)
347 TIGR02787 codY_Gpos GTP-sensin 64.5 17 0.00037 31.9 5.4 30 260-289 197-226 (251)
348 COG1959 Predicted transcriptio 64.2 16 0.00034 29.7 5.0 41 249-289 13-53 (150)
349 PRK09644 RNA polymerase sigma 64.2 8.1 0.00018 31.3 3.4 34 260-293 123-156 (165)
350 PF13730 HTH_36: Helix-turn-he 64.1 20 0.00044 23.1 4.7 26 168-193 26-51 (55)
351 PF07638 Sigma70_ECF: ECF sigm 64.1 10 0.00022 31.7 4.0 27 262-288 152-178 (185)
352 PF13518 HTH_28: Helix-turn-he 63.9 16 0.00035 23.0 4.2 27 263-289 14-40 (52)
353 COG3355 Predicted transcriptio 63.9 18 0.00039 28.4 5.0 37 157-193 32-68 (126)
354 PF07754 DUF1610: Domain of un 63.7 6.3 0.00014 21.4 1.7 23 8-32 1-24 (24)
355 PRK09047 RNA polymerase factor 63.6 8 0.00017 31.0 3.2 30 260-289 121-150 (161)
356 PRK03975 tfx putative transcri 63.6 10 0.00023 30.4 3.7 27 260-286 20-46 (141)
357 PRK00241 nudC NADH pyrophospha 63.5 5 0.00011 35.7 2.1 29 5-34 99-127 (256)
358 PRK12366 replication factor A; 63.5 4.8 0.0001 40.7 2.2 25 6-33 533-557 (637)
359 KOG2906|consensus 63.4 4.8 0.0001 29.9 1.6 28 7-34 3-31 (105)
360 COG0593 DnaA ATPase involved i 63.3 84 0.0018 30.0 10.3 38 250-289 356-393 (408)
361 PF04218 CENP-B_N: CENP-B N-te 63.3 5.1 0.00011 26.2 1.6 23 262-284 23-45 (53)
362 PF10080 DUF2318: Predicted me 63.2 6.3 0.00014 29.8 2.3 27 7-35 37-63 (102)
363 COG0333 RpmF Ribosomal protein 63.0 6 0.00013 26.5 1.9 24 6-35 28-51 (57)
364 COG2390 DeoR Transcriptional r 62.9 12 0.00026 34.4 4.5 32 257-288 22-53 (321)
365 PRK05658 RNA polymerase sigma 62.9 1.8E+02 0.0038 29.4 16.4 28 260-287 575-602 (619)
366 cd01104 HTH_MlrA-CarA Helix-Tu 62.7 11 0.00023 25.6 3.3 22 263-284 2-23 (68)
367 PRK07670 RNA polymerase sigma 62.7 1.1E+02 0.0023 26.8 18.6 30 260-289 216-245 (251)
368 PF13022 HTH_Tnp_1_2: Helix-tu 62.6 22 0.00047 28.4 5.3 37 242-278 12-51 (142)
369 PRK12529 RNA polymerase sigma 62.5 13 0.00028 30.7 4.3 29 260-288 142-170 (178)
370 TIGR02404 trehalos_R_Bsub treh 62.5 9.9 0.00021 32.9 3.8 30 259-288 21-51 (233)
371 PF13443 HTH_26: Cro/C1-type H 62.4 8 0.00017 25.8 2.6 25 260-284 9-33 (63)
372 cd04476 RPA1_DBD_C RPA1_DBD_C: 62.2 6.4 0.00014 32.3 2.4 26 7-34 36-61 (166)
373 PRK09978 DNA-binding transcrip 62.1 94 0.002 27.9 10.0 41 243-284 141-181 (274)
374 PRK09685 DNA-binding transcrip 62.0 63 0.0014 28.9 9.1 42 243-284 196-237 (302)
375 PF00196 GerE: Bacterial regul 62.0 17 0.00037 23.9 4.1 33 166-198 17-49 (58)
376 PRK09649 RNA polymerase sigma 62.0 14 0.0003 30.7 4.5 30 260-289 145-174 (185)
377 PRK05580 primosome assembly pr 61.9 6.6 0.00014 40.0 2.9 30 4-34 389-418 (679)
378 PRK10857 DNA-binding transcrip 61.9 18 0.00039 29.8 5.0 44 246-289 9-53 (164)
379 TIGR03831 YgiT_finger YgiT-typ 61.9 6 0.00013 24.6 1.7 10 25-34 33-42 (46)
380 PRK14559 putative protein seri 61.9 4.7 0.0001 40.7 1.8 13 22-34 39-51 (645)
381 PRK15411 rcsA colanic acid cap 61.8 12 0.00027 31.8 4.2 30 260-289 151-180 (207)
382 PRK04984 fatty acid metabolism 61.7 12 0.00026 32.4 4.2 30 259-288 28-58 (239)
383 PF02954 HTH_8: Bacterial regu 61.7 15 0.00033 22.6 3.5 23 262-284 19-41 (42)
384 COG1779 C4-type Zn-finger prot 61.7 4.2 9E-05 34.4 1.2 36 5-40 14-59 (201)
385 PF13453 zf-TFIIB: Transcripti 61.6 7 0.00015 24.0 1.9 27 7-33 1-28 (41)
386 PF01641 SelR: SelR domain; I 61.5 5.8 0.00013 31.1 1.9 33 19-51 32-66 (124)
387 TIGR02944 suf_reg_Xantho FeS a 61.5 25 0.00053 27.4 5.6 44 149-193 8-51 (130)
388 TIGR02999 Sig-70_X6 RNA polyme 61.5 10 0.00023 31.2 3.6 29 260-288 149-177 (183)
389 PRK14999 histidine utilization 61.4 12 0.00027 32.5 4.2 30 259-288 33-63 (241)
390 PF05930 Phage_AlpA: Prophage 61.3 11 0.00025 24.2 3.0 23 262-284 4-26 (51)
391 PHA00542 putative Cro-like pro 61.2 11 0.00023 27.1 3.2 26 259-284 29-54 (82)
392 PRK10870 transcriptional repre 61.2 69 0.0015 26.5 8.5 42 258-301 68-109 (176)
393 PF13790 DUF4182: Domain of un 61.0 4.2 9.1E-05 24.7 0.8 13 23-35 2-14 (38)
394 TIGR02702 SufR_cyano iron-sulf 61.0 21 0.00045 30.3 5.5 29 260-288 14-42 (203)
395 smart00105 ArfGap Putative GTP 61.0 4.9 0.00011 30.8 1.4 31 3-34 2-33 (112)
396 COG2816 NPY1 NTP pyrophosphohy 61.0 5.4 0.00012 35.7 1.8 27 7-34 113-139 (279)
397 TIGR02983 SigE-fam_strep RNA p 60.9 12 0.00025 30.2 3.7 33 261-293 126-158 (162)
398 PRK10840 transcriptional regul 60.8 14 0.0003 31.3 4.4 30 260-289 164-193 (216)
399 PF09986 DUF2225: Uncharacteri 60.8 5.9 0.00013 34.2 2.0 9 5-13 5-13 (214)
400 PRK13719 conjugal transfer tra 60.7 15 0.00033 31.6 4.5 31 259-289 156-186 (217)
401 TIGR02885 spore_sigF RNA polym 60.6 1.1E+02 0.0024 26.3 18.6 29 260-288 198-226 (231)
402 TIGR03070 couple_hipB transcri 60.5 11 0.00024 24.2 2.9 23 260-282 14-36 (58)
403 TIGR02859 spore_sigH RNA polym 60.4 13 0.00029 31.0 4.1 33 260-292 164-196 (198)
404 PRK10411 DNA-binding transcrip 60.4 12 0.00026 32.8 4.0 29 260-288 17-45 (240)
405 TIGR03338 phnR_burk phosphonat 60.3 12 0.00025 31.9 3.8 30 259-288 32-61 (212)
406 TIGR02947 SigH_actino RNA poly 60.2 7.6 0.00017 32.5 2.6 32 260-291 146-177 (193)
407 COG1959 Predicted transcriptio 60.1 25 0.00054 28.4 5.5 45 150-194 8-52 (150)
408 PRK10079 phosphonate metabolis 60.1 11 0.00025 32.8 3.8 26 263-288 37-62 (241)
409 PF11740 KfrA_N: Plasmid repli 60.1 44 0.00095 25.5 6.7 36 258-293 16-52 (120)
410 cd04763 HTH_MlrA-like Helix-Tu 60.1 12 0.00027 25.4 3.2 22 263-284 2-23 (68)
411 COG3677 Transposase and inacti 60.0 5.7 0.00012 31.4 1.7 33 2-34 27-63 (129)
412 TIGR02366 DHAK_reg probable di 60.0 11 0.00024 30.8 3.5 48 244-291 6-53 (176)
413 PF14206 Cys_rich_CPCC: Cystei 60.0 6.4 0.00014 28.1 1.7 29 5-33 1-29 (78)
414 TIGR01889 Staph_reg_Sar staphy 59.7 26 0.00056 26.4 5.3 33 256-288 38-70 (109)
415 cd04764 HTH_MlrA-like_sg1 Heli 59.7 13 0.00028 25.2 3.3 22 263-284 2-23 (67)
416 PRK06759 RNA polymerase factor 59.7 16 0.00034 29.0 4.3 29 260-288 121-149 (154)
417 PF13463 HTH_27: Winged helix 59.4 23 0.00051 23.7 4.6 32 163-194 14-45 (68)
418 PRK15201 fimbriae regulatory p 59.4 18 0.00038 30.3 4.4 30 260-289 147-176 (198)
419 smart00400 ZnF_CHCC zinc finge 59.3 11 0.00023 24.8 2.7 25 7-31 4-30 (55)
420 PF04216 FdhE: Protein involve 59.3 4.8 0.0001 36.4 1.3 28 5-32 172-205 (290)
421 TIGR02950 SigM_subfam RNA poly 59.2 12 0.00026 29.7 3.6 30 260-289 120-149 (154)
422 COG1510 Predicted transcriptio 59.2 14 0.0003 30.6 3.8 37 157-193 31-67 (177)
423 COG0229 Conserved domain frequ 59.2 9 0.00019 30.4 2.5 34 18-51 36-71 (140)
424 TIGR01384 TFS_arch transcripti 59.1 7.8 0.00017 29.1 2.2 29 5-33 62-99 (104)
425 TIGR02018 his_ut_repres histid 59.1 14 0.00031 31.9 4.2 30 259-288 22-52 (230)
426 PF13404 HTH_AsnC-type: AsnC-t 59.1 30 0.00064 21.4 4.5 29 163-191 13-41 (42)
427 PF13744 HTH_37: Helix-turn-he 59.0 21 0.00044 25.4 4.3 31 253-283 23-53 (80)
428 TIGR02835 spore_sigmaE RNA pol 58.9 15 0.00032 31.9 4.3 27 260-286 197-223 (234)
429 TIGR02325 C_P_lyase_phnF phosp 58.9 12 0.00027 32.3 3.8 30 259-288 29-59 (238)
430 cd00569 HTH_Hin_like Helix-tur 58.8 15 0.00032 20.5 3.1 21 261-281 21-41 (42)
431 PF04552 Sigma54_DBD: Sigma-54 58.8 3.2 6.8E-05 34.1 0.0 27 260-286 48-74 (160)
432 PF03428 RP-C: Replication pro 58.7 57 0.0012 27.2 7.5 68 207-289 31-99 (177)
433 PF12116 SpoIIID: Stage III sp 58.7 10 0.00022 27.2 2.5 25 259-283 17-41 (82)
434 PRK15482 transcriptional regul 58.7 25 0.00054 31.5 5.8 25 261-285 34-58 (285)
435 KOG3134|consensus 58.6 3 6.6E-05 35.7 -0.1 30 6-35 1-35 (225)
436 PRK09392 ftrB transcriptional 58.6 39 0.00084 29.0 6.9 30 260-289 172-201 (236)
437 COG2197 CitB Response regulato 58.4 15 0.00033 31.4 4.2 33 257-289 159-191 (211)
438 PRK12547 RNA polymerase sigma 58.4 13 0.00028 30.1 3.6 32 260-291 127-158 (164)
439 COG2973 TrpR Trp operon repres 58.4 14 0.0003 27.5 3.2 38 249-286 48-85 (103)
440 PF05344 DUF746: Domain of Unk 58.3 28 0.0006 23.9 4.5 36 161-196 7-42 (65)
441 smart00421 HTH_LUXR helix_turn 58.3 23 0.0005 22.4 4.2 32 167-198 18-49 (58)
442 PF01710 HTH_Tnp_IS630: Transp 58.0 14 0.0003 28.5 3.5 28 259-286 69-96 (119)
443 PRK11302 DNA-binding transcrip 58.0 25 0.00055 31.3 5.7 25 261-285 34-58 (284)
444 PRK09643 RNA polymerase sigma 57.9 12 0.00025 31.4 3.3 34 260-293 149-182 (192)
445 PRK09764 DNA-binding transcrip 57.7 16 0.00034 31.9 4.2 30 259-288 26-56 (240)
446 PF08222 HTH_CodY: CodY helix- 57.7 18 0.00039 24.1 3.4 27 262-288 5-31 (61)
447 smart00347 HTH_MARR helix_turn 57.6 30 0.00065 24.9 5.2 28 261-288 24-51 (101)
448 PF13411 MerR_1: MerR HTH fami 57.6 9.3 0.0002 26.0 2.3 21 263-283 2-22 (69)
449 PF07191 zinc-ribbons_6: zinc- 57.6 8.8 0.00019 26.8 2.0 26 6-34 2-27 (70)
450 COG1349 GlpR Transcriptional r 57.5 11 0.00023 33.5 3.1 30 260-289 18-47 (253)
451 PRK09954 putative kinase; Prov 57.5 21 0.00046 33.1 5.4 29 260-288 16-44 (362)
452 TIGR02479 FliA_WhiG RNA polyme 57.5 1.2E+02 0.0026 25.8 18.1 28 260-287 190-217 (224)
453 PRK09645 RNA polymerase sigma 57.4 13 0.00028 30.3 3.5 29 260-288 133-161 (173)
454 PHA01976 helix-turn-helix prot 57.2 13 0.00029 25.1 3.0 23 260-282 14-36 (67)
455 PRK09415 RNA polymerase factor 57.2 13 0.00028 30.7 3.5 32 260-291 142-173 (179)
456 TIGR00281 segregation and cond 57.2 64 0.0014 27.2 7.6 110 150-277 3-117 (186)
457 PF08299 Bac_DnaA_C: Bacterial 57.2 23 0.0005 24.6 4.2 33 157-191 37-70 (70)
458 PRK14559 putative protein seri 57.1 5.8 0.00012 40.1 1.5 13 25-37 28-40 (645)
459 PRK11414 colanic acid/biofilm 57.0 14 0.00031 31.6 3.8 30 259-288 32-61 (221)
460 COG2188 PhnF Transcriptional r 56.9 14 0.0003 32.2 3.8 26 263-288 33-58 (236)
461 PRK12532 RNA polymerase sigma 56.8 9.7 0.00021 31.9 2.7 30 260-289 151-180 (195)
462 PF04606 Ogr_Delta: Ogr/Delta- 56.5 8.6 0.00019 24.5 1.8 28 7-34 1-37 (47)
463 PF08063 PADR1: PADR1 (NUC008) 56.5 4.8 0.0001 26.7 0.6 24 3-28 12-35 (55)
464 PRK03837 transcriptional regul 56.4 17 0.00038 31.4 4.3 30 259-288 34-64 (241)
465 TIGR01610 phage_O_Nterm phage 56.4 41 0.00088 24.8 5.7 30 164-193 44-73 (95)
466 TIGR02952 Sig70_famx2 RNA poly 56.3 17 0.00037 29.3 4.0 29 260-288 137-165 (170)
467 PRK09480 slmA division inhibit 56.3 18 0.00038 29.9 4.2 42 243-284 12-53 (194)
468 PF13560 HTH_31: Helix-turn-he 56.2 13 0.00029 24.9 2.8 23 260-282 13-35 (64)
469 PRK15320 transcriptional activ 56.1 18 0.00039 30.8 4.0 31 259-289 177-207 (251)
470 PRK12380 hydrogenase nickel in 56.1 7.7 0.00017 29.9 1.7 6 7-12 72-77 (113)
471 PRK11534 DNA-binding transcrip 56.0 17 0.00038 31.1 4.2 30 259-288 28-57 (224)
472 TIGR02989 Sig-70_gvs1 RNA poly 56.0 19 0.00042 28.7 4.3 29 260-288 126-154 (159)
473 PF06970 RepA_N: Replication i 55.9 11 0.00024 26.8 2.4 24 262-285 53-76 (76)
474 PF06397 Desulfoferrod_N: Desu 55.7 6.7 0.00015 23.6 1.0 23 5-27 6-28 (36)
475 COG2771 CsgD DNA-binding HTH d 55.6 32 0.0007 22.6 4.7 29 261-289 19-47 (65)
476 PRK10072 putative transcriptio 55.6 14 0.0003 27.6 3.0 24 259-282 44-67 (96)
477 cd06170 LuxR_C_like C-terminal 55.6 27 0.00059 22.1 4.2 32 167-198 15-46 (57)
478 PRK11922 RNA polymerase sigma 55.5 12 0.00025 32.5 3.0 34 260-293 164-197 (231)
479 PRK12543 RNA polymerase sigma 55.5 13 0.00028 30.6 3.2 31 260-290 132-162 (179)
480 PF10122 Mu-like_Com: Mu-like 55.5 3.6 7.9E-05 26.7 -0.1 30 5-34 4-34 (51)
481 PRK14873 primosome assembly pr 55.4 9.6 0.00021 38.7 2.8 29 4-33 391-419 (665)
482 PRK06288 RNA polymerase sigma 55.4 1.5E+02 0.0032 26.2 19.2 25 260-284 227-251 (268)
483 PRK05602 RNA polymerase sigma 55.3 14 0.00031 30.5 3.4 30 260-289 143-172 (186)
484 PF05460 ORC6: Origin recognit 55.3 3.9 8.5E-05 38.1 0.0 78 211-288 4-84 (353)
485 PRK09639 RNA polymerase sigma 55.2 14 0.0003 29.8 3.3 34 260-293 126-159 (166)
486 PRK11512 DNA-binding transcrip 55.1 28 0.0006 27.7 5.0 42 259-302 52-93 (144)
487 PF05269 Phage_CII: Bacterioph 55.0 4.6 9.9E-05 29.8 0.3 31 262-292 24-54 (91)
488 COG5024 Cyclin [Cell division 55.0 43 0.00093 32.2 6.9 85 206-290 218-305 (440)
489 PRK15044 transcriptional regul 54.9 36 0.00079 30.8 6.0 26 259-284 206-231 (295)
490 PRK11402 DNA-binding transcrip 54.8 16 0.00034 31.8 3.8 29 260-288 31-60 (241)
491 PF13556 HTH_30: PucR C-termin 54.8 25 0.00054 23.4 3.9 30 260-289 11-40 (59)
492 PRK08301 sporulation sigma fac 54.8 14 0.0003 32.0 3.4 26 260-285 197-222 (234)
493 PF09082 DUF1922: Domain of un 54.8 9 0.0002 26.5 1.7 26 6-34 4-29 (68)
494 TIGR02954 Sig70_famx3 RNA poly 54.7 17 0.00037 29.5 3.8 29 261-289 135-163 (169)
495 PRK03902 manganese transport t 54.6 31 0.00067 27.4 5.1 29 260-288 21-49 (142)
496 PRK10225 DNA-binding transcrip 54.6 19 0.00041 31.7 4.2 30 259-288 30-60 (257)
497 PF14952 zf-tcix: Putative tre 54.6 8.1 0.00018 24.2 1.3 25 6-35 12-38 (44)
498 PRK12542 RNA polymerase sigma 54.4 13 0.00028 30.8 3.0 29 260-288 137-165 (185)
499 cd00202 ZnF_GATA Zinc finger D 54.3 4.1 8.9E-05 26.9 -0.0 27 8-34 2-31 (54)
500 PRK10906 DNA-binding transcrip 54.2 14 0.00031 32.6 3.4 29 260-288 18-46 (252)
No 1
>KOG1597|consensus
Probab=100.00 E-value=1.9e-75 Score=502.10 Aligned_cols=303 Identities=61% Similarity=0.955 Sum_probs=285.4
Q ss_pred ccCCCCCCC--CeeeeCCCCceecCCCCccccCcccccCCCcccccCCCCCCCCCCCCCCCCCcccCCCCceeeccCCCC
Q psy6534 6 VCCYEHPDA--PLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGD 83 (309)
Q Consensus 6 ~~Cp~C~~~--~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~sr~g~~~~~~~~~~~l~t~i~~~~~~ 83 (309)
+.||+|+.. ++|+|+.+|+++|..||+|+++++||+++|||+|++++++.||||+|+++||++.+++|+|+|+++.|.
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 368888643 589999999999999999999999999999999999998999999999999999999999999998876
Q ss_pred CCCCCCCcccccccccCChhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHh
Q psy6534 84 ASFDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQ 163 (309)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~ 163 (309)
++....+..+||++..+++.|+.+..+|..|..|++.++||..+.++|.++|+++.+.+.++||+.++++|||||+|||+
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 54433334568888888899999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCC--CChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCC
Q psy6534 164 EGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDL--ITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGR 241 (309)
Q Consensus 164 ~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~--~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr 241 (309)
++.|||++||+.++++++++|++.++.|.+.|+..++. ++..+|++|||+.|+||+.++++|.++++++.+..+..||
T Consensus 161 ~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gR 240 (308)
T KOG1597|consen 161 EDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGR 240 (308)
T ss_pred cCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCC
Confidence 99999999999999999999999999999999987664 4588999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCcCCCCCCCCCCC
Q psy6534 242 SPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIHELPQ 308 (309)
Q Consensus 242 ~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~~~~~~~~~~~~~~ 308 (309)
+|.+||||+|||+++++..+++++||.+++||+++|||+.||+|++++.+|+|.||.+..|++.||.
T Consensus 241 sPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~liP~~~a~~~~lk~Lp~ 307 (308)
T KOG1597|consen 241 SPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHADKLIPSWYANAVPLKNLPG 307 (308)
T ss_pred CchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHhhchhhhChhhhccccchhhcCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999996
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=1.9e-71 Score=504.35 Aligned_cols=289 Identities=36% Similarity=0.637 Sum_probs=268.0
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCccccCcccccCCCcccccCCCCCCCCCCCCCCCCCcccCCCCceeeccCCCC
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGD 83 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~sr~g~~~~~~~~~~~l~t~i~~~~~~ 83 (309)
....||+||++++|+|+++|++||++||+|++|++||+|||||+|++|+. .|++|+|+|.|+++||.+++|.|+++.++
T Consensus 10 ~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~~-~~~~RvG~~~~~~~~~~gl~T~I~~~~~~ 88 (310)
T PRK00423 10 EKLVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQR-EKRSRVGAPMTYTIHDKGLSTDIDWRNKD 88 (310)
T ss_pred cCCcCcCCCCCCeeEECCCCeEeecccCCcccccccccCCCccCCCcccc-CCccccCCCCCccccCCCCceEeecCCcc
Confidence 45689999998999999999999999999999999999999999998764 58999999999999999999999876554
Q ss_pred CCCCCCC---------ccccccccc-CChhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHH
Q psy6534 84 ASFDGFG---------MSKYQNRRT-MNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIA 153 (309)
Q Consensus 84 ~~~~~~~---------~~~~~~~~~-~~~~~~~l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~va 153 (309)
+++..++ .++||++.+ .+++|++|..+++.|+++|+.|+||+.++++|..+|+++++.++++|++.+.++
T Consensus 89 ~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~ 168 (310)
T PRK00423 89 SYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV 168 (310)
T ss_pred cccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHH
Confidence 3333332 235766643 478899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCCCCHHHHHHHHHHHHHhh
Q psy6534 154 SACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAV 233 (309)
Q Consensus 154 aAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~ 233 (309)
|||||+|||++++|+|++||+.++++++++|+++|+.|.+.|++++++.+|++||.+||+.|+|++.+.+.|.+|++.+.
T Consensus 169 AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~ 248 (310)
T PRK00423 169 AAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAK 248 (310)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 234 ELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 234 ~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
+.++..||+|.+|||||||+||+++|.++|++|||+++||++.||+++||+|.+.....+
T Consensus 249 ~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~~~~ 308 (310)
T PRK00423 249 EKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDIKI 308 (310)
T ss_pred hcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCccc
Confidence 999999999999999999999999999999999999999999999999999999876543
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=3e-65 Score=452.14 Aligned_cols=278 Identities=38% Similarity=0.715 Sum_probs=258.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccccCcccccCCCcccccCCCCCCCCCCCCCCCCCcccCCCCceeeccCCCCCC
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGDAS 85 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~sr~g~~~~~~~~~~~l~t~i~~~~~~~~ 85 (309)
+.||+||+.++++|++.|+.||.+||+|++|..||.|||||.|+ +. ..+ |+|+|.++.+||.+++|.|+++.+.
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~-e~--~~~-r~g~P~t~~~~d~~l~t~i~~~~~~-- 75 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFD-ER--HER-RVGAPLTPSIHDKGLSTIIGWGDKD-- 75 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEeccccccCCCCccccc-cc--ccc-cccCCCccccCccchhhhcccchhH--
Confidence 58999999999999999999999999999999999999999993 32 234 9999999999999999999876432
Q ss_pred CCCCCccccccccc-CChhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhc
Q psy6534 86 FDGFGMSKYQNRRT-MNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQE 164 (309)
Q Consensus 86 ~~~~~~~~~~~~~~-~~~~~~~l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~ 164 (309)
......+||.+.+ .+++|+++..++..|..++..|+||.++.|+|..+|+++++.++++||+.+.++|||+|+|||++
T Consensus 76 -~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~ 154 (285)
T COG1405 76 -KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRIN 154 (285)
T ss_pred -HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHc
Confidence 1112346776654 45889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChH
Q psy6534 165 GVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPI 244 (309)
Q Consensus 165 ~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~ 244 (309)
+.|+|+.||+.++++++++|+++|+.+.+.|+..+++.+|.+||+|||+.|||++++...|.+|++++.+.++..||+|.
T Consensus 155 ~~prtl~eIa~a~~V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~ 234 (285)
T COG1405 155 GVPRTLDEIAKALGVSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPA 234 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q psy6534 245 SVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHAS 290 (309)
Q Consensus 245 ~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~ 290 (309)
++||||||+|+.++|+++||++||.++||+++||+++|++|.++..
T Consensus 235 glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel~~~~~ 280 (285)
T COG1405 235 GLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELADALD 280 (285)
T ss_pred hHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHHHHhhc
Confidence 9999999999999999999999999999999999999999988754
No 4
>KOG1598|consensus
Probab=100.00 E-value=1.1e-43 Score=328.87 Aligned_cols=257 Identities=24% Similarity=0.409 Sum_probs=228.1
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccccCcccccCCCcccccCCCCCCCCCCCCCCCCCcccCCCCceeeccCCCCCC
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLNGSDLSTMIGPGRGDAS 85 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~sr~g~~~~~~~~~~~l~t~i~~~~~~~~ 85 (309)
+.|++||++++-.|..+|..+|+.||+|+++..|...- +|... ++ |++|+-+..+..
T Consensus 1 ~~C~~C~~s~fe~d~a~g~~~C~~CG~v~E~~~ivsev---~F~e~-----------~~---------G~~v~~~~~g~~ 57 (521)
T KOG1598|consen 1 MVCKNCGGSNFERDEATGNLYCTACGTVLEYNNIVAEV---TFVEG-----------AQ---------GQFVRVGQSGAG 57 (521)
T ss_pred CcCCCCCCCCcccccccCCceeccccceeeccceeEEe---eeecc-----------cc---------eeEEeccccCCc
Confidence 47999999999999999999999999999999888432 56442 11 345543321110
Q ss_pred CCCCCcccccccccCChhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcC
Q psy6534 86 FDGFGMSKYQNRRTMNSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEG 165 (309)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~ 165 (309)
....++++++.++.+.|.+++..|+|+. +++.|..+|+.+.+.++.+||+...++|+|+|++||+++
T Consensus 58 ------------~s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~ 124 (521)
T KOG1598|consen 58 ------------SSLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEK 124 (521)
T ss_pred ------------cchHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhC
Confidence 0236889999999999999999999999 999999999999999999999999999999999999999
Q ss_pred CCccHHHHHHHhcccHHHHHHHHHHHHHHhccc---CCCCChHHHHHHHHhhCCCC---HHHHHHHHHHHHHhhhcCccC
Q psy6534 166 VPRTFKEICAVSKISKKEIGRCFKLILKALETS---VDLITTGDFMSRFCSNLSLP---NMVQKAATHIARKAVELDIVP 239 (309)
Q Consensus 166 ~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~---~~~~~p~~~i~~~~~~L~l~---~~~~~~a~~i~~~~~~~~l~~ 239 (309)
.++.+.|++.++++++++||+.|++|.+.|.+. .|.+||..|+.||+..|.+. +++...|..|++.|+++|+.+
T Consensus 125 t~hlliDfS~~Lqv~Vy~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~t 204 (521)
T KOG1598|consen 125 TDHLLIDFSSYLQVSVYDLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQT 204 (521)
T ss_pred CceEEEEeccceEEehhhhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999998 89999999999999998663 358899999999999999999
Q ss_pred CCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH-HhhcccCCCCcC
Q psy6534 240 GRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMY-PHASKLFPQDFV 298 (309)
Q Consensus 240 Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~-~~~~~l~~~~~~ 298 (309)
||+|.+|++||||+||+++|++++..||+.+++|++.||++||+||. ..+..|...+|.
T Consensus 205 GRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~ef~ 264 (521)
T KOG1598|consen 205 GRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLKEFSDTLSGDLTIDELA 264 (521)
T ss_pred CCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHHHHhccccccccHHHHH
Confidence 99999999999999999999999999999999999999999999996 566677665553
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=99.75 E-value=7.7e-18 Score=120.00 Aligned_cols=71 Identities=41% Similarity=0.797 Sum_probs=66.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHH
Q psy6534 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEI 184 (309)
Q Consensus 114 I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i 184 (309)
|.++|+.|+||+.+.++|.++|+.+.+.++.+||++..++|||||+|||+++.|+|++||+++++++.++|
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 67899999999999999999999999999999999999999999999999999999999999999998876
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=99.73 E-value=2.6e-17 Score=117.29 Aligned_cols=71 Identities=46% Similarity=0.685 Sum_probs=66.4
Q ss_pred HHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHH
Q psy6534 208 MSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTI 278 (309)
Q Consensus 208 i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti 278 (309)
|++||+.|+||+++.+.|.++++.+.+.++..||+|.++||||||+||+.++.+++++||++.+||++.||
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 67999999999999999999999999999999999999999999999999999999999999999999997
No 7
>KOG0835|consensus
Probab=99.69 E-value=1.9e-15 Score=132.71 Aligned_cols=179 Identities=20% Similarity=0.245 Sum_probs=155.1
Q ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhccc----
Q psy6534 105 RALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKIS---- 180 (309)
Q Consensus 105 ~~l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~---- 180 (309)
.-..=+-..|++-|-.|+||+...-++..+|++++..+.+.+.+.+.++.|||.+|.+.+..|++++||..+++.=
T Consensus 21 el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~ 100 (367)
T KOG0835|consen 21 ELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRR 100 (367)
T ss_pred HHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHH
Confidence 3345577899999999999999999999999999999999999999999999999999999999999999987530
Q ss_pred -----------------HHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCCCCHH--HHHHHHHHHHHhhhcCccCCC
Q psy6534 181 -----------------KKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNM--VQKAATHIARKAVELDIVPGR 241 (309)
Q Consensus 181 -----------------~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~~--~~~~a~~i~~~~~~~~l~~Gr 241 (309)
+-.+-++..+|.+.||+.+-+.+|+-++..|.+-|++++. +...+|.+++......+..--
T Consensus 101 ~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry 180 (367)
T KOG0835|consen 101 ESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRY 180 (367)
T ss_pred hccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeec
Confidence 2224456778999999999999999999999999999765 588999999999999999999
Q ss_pred ChHHHHHHHHHHHHHhCCCCCC-HHHHHHHhCCCHHHHHHHHH
Q psy6534 242 SPISVAAAAIYMASQASSDKRS-QKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 242 ~P~~iaaAaiyla~~~~~~~~~-~~~ia~~~~vs~~ti~~~~k 283 (309)
.|.+||+||||||++..+++++ +...-.+++++...|.....
T Consensus 181 ~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~ 223 (367)
T KOG0835|consen 181 SPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICY 223 (367)
T ss_pred CHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHH
Confidence 9999999999999999998764 34777888888887755433
No 8
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.69 E-value=2.9e-15 Score=135.01 Aligned_cols=180 Identities=14% Similarity=0.187 Sum_probs=147.1
Q ss_pred HHHH-HHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhccc
Q psy6534 104 DRAL-LNAIREINSMADRIN--LTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKIS 180 (309)
Q Consensus 104 ~~~l-~~~~~~I~~i~~~L~--Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~ 180 (309)
|..+ ...-..|.++|..|+ ||..++-+|..+|++++..+.+...++..++++|+|+||+.++.|+++.+++..+.-+
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 3444 456788999999999 9999999999999999998888888899999999999999999999999999876543
Q ss_pred ----HHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCC-----C--CHHHHHHHHHHHHHhhhcCccCCCChHHHHHH
Q psy6534 181 ----KKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLS-----L--PNMVQKAATHIARKAVELDIVPGRSPISVAAA 249 (309)
Q Consensus 181 ----~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~-----l--~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaA 249 (309)
..+|..+...|.+.|++++.+.+|+.++..|...|. + ++.+...|+.+++.+....+..-..|..||+|
T Consensus 132 ~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlA 211 (305)
T TIGR00569 132 PLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALA 211 (305)
T ss_pred chhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHH
Confidence 478999999999999999988899998888775432 2 34567889999998888777667899999999
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCC--CHHHHHHHHHH
Q psy6534 250 AIYMASQASSDKRSQKEIGDIAGV--AEVTIRQSYKL 284 (309)
Q Consensus 250 aiyla~~~~~~~~~~~~ia~~~~v--s~~ti~~~~ke 284 (309)
|||+|++..+++++-.+- +..++ .+.++......
T Consensus 212 AI~lA~~~~~~~l~~~~~-e~~~~~~~~~~~~~l~~~ 247 (305)
T TIGR00569 212 AILHTASRAGLNMESYLT-EQLSVPGNREELPQLIDI 247 (305)
T ss_pred HHHHHHHHhCCCCcccch-hhhcccccHHHHHHHHHH
Confidence 999999999987765432 55666 44444444333
No 9
>KOG0834|consensus
Probab=99.65 E-value=2e-15 Score=135.93 Aligned_cols=180 Identities=17% Similarity=0.235 Sum_probs=152.6
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhc--cc----
Q psy6534 107 LLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSK--IS---- 180 (309)
Q Consensus 107 l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~--~~---- 180 (309)
..++.+.|.+++.+|++|...+.+|..+|++++-...++.-.+..+|++|+|+|++.++.|+.++||..+.. ..
T Consensus 39 r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~ 118 (323)
T KOG0834|consen 39 RQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDL 118 (323)
T ss_pred HHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccc
Confidence 467899999999999999999999999999999998888888899999999999999999999999998752 12
Q ss_pred ---------HHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCCCCHH----HHHHHHHHHHHhhhcCccCCCChHHHH
Q psy6534 181 ---------KKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNM----VQKAATHIARKAVELDIVPGRSPISVA 247 (309)
Q Consensus 181 ---------~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~~----~~~~a~~i~~~~~~~~l~~Gr~P~~ia 247 (309)
+++|-...+.+.+.|++++...+|+.|+.+++..|+.... ....|+.+++......+..--.|..||
T Consensus 119 ~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IA 198 (323)
T KOG0834|consen 119 ELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIA 198 (323)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEE
Confidence 2334445667788899999999999999999999987664 788999999999887777778899999
Q ss_pred HHHHHHHHHhCCCCCCHH---HHHHHhC--CCHHHHHHHHHHHH
Q psy6534 248 AAAIYMASQASSDKRSQK---EIGDIAG--VAEVTIRQSYKLMY 286 (309)
Q Consensus 248 aAaiyla~~~~~~~~~~~---~ia~~~~--vs~~ti~~~~kei~ 286 (309)
+|+||+|++..++.++.. .....++ ++..-++....++.
T Consensus 199 va~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l 242 (323)
T KOG0834|consen 199 VACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFL 242 (323)
T ss_pred eehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHH
Confidence 999999999998755432 3466677 88888877776654
No 10
>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=99.62 E-value=2e-16 Score=100.86 Aligned_cols=43 Identities=35% Similarity=0.834 Sum_probs=39.3
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccccCcccccCCCcccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTF 48 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f 48 (309)
+.||+||+..+++|+.+|++||++||.|++|+.++.++|||+|
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEENIIDEGPEWREF 43 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCHC
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeecccccCCcccccC
Confidence 5899999988999999999999999999999999999999987
No 11
>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=99.52 E-value=2e-13 Score=120.17 Aligned_cols=157 Identities=20% Similarity=0.281 Sum_probs=137.0
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHH--------hcc
Q psy6534 108 LNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAV--------SKI 179 (309)
Q Consensus 108 ~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~--------~~~ 179 (309)
..++..|+.+|.+|+||..+..+|..+|++++-+...++.+.+.++++|||+|||.++.|+-+.-.+-. ..-
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 567889999999999999999999999999999999999999999999999999999976555433333 235
Q ss_pred cHHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCCCCH--HHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHh
Q psy6534 180 SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPN--MVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQA 257 (309)
Q Consensus 180 ~~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~--~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~ 257 (309)
+++.|......+.+.|+++.-+.+|+.++..|...+.+.. +..+.|+.+++.+.+..+.-=-+|..||+|++++|+..
T Consensus 126 sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~ 205 (297)
T COG5333 126 SRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEV 205 (297)
T ss_pred cHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHh
Confidence 7889999999999999999888999999999988876544 48899999999999988777789999999999999999
Q ss_pred CCCCCCH
Q psy6534 258 SSDKRSQ 264 (309)
Q Consensus 258 ~~~~~~~ 264 (309)
.|.++..
T Consensus 206 ~~~~~~~ 212 (297)
T COG5333 206 LGMPIIK 212 (297)
T ss_pred cCCccch
Confidence 9876543
No 12
>KOG0794|consensus
Probab=99.46 E-value=7.9e-13 Score=111.11 Aligned_cols=177 Identities=18% Similarity=0.245 Sum_probs=140.2
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCC-ccHHHHHHH-----------
Q psy6534 109 NAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVP-RTFKEICAV----------- 176 (309)
Q Consensus 109 ~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~-~tl~eia~~----------- 176 (309)
...+.|+.+++.|+|.+.++.+|..+|++++-++.+++-.+..+|..|+|+||+.+..| .-.+-++..
T Consensus 43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~ 122 (264)
T KOG0794|consen 43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYW 122 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccc
Confidence 45678999999999999999999999999999999999999999999999999999998 222222221
Q ss_pred ---hcccHHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCCC-CHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHH
Q psy6534 177 ---SKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSL-PNMVQKAATHIARKAVELDIVPGRSPISVAAAAIY 252 (309)
Q Consensus 177 ---~~~~~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l-~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiy 252 (309)
+..+...|....-.+.+.|+.-+-+-+|..-+..+.+.+|+ +.+....++.|++...+.++..=..|.-||.||||
T Consensus 123 ~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~ 202 (264)
T KOG0794|consen 123 PEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLY 202 (264)
T ss_pred hhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHH
Confidence 12345566677777888888766667888889999999998 44578899999999999988888999999999999
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 253 MASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 253 la~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
+||-..+.+.+ +..-..+.+.-.-+....++|.
T Consensus 203 Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I~ 235 (264)
T KOG0794|consen 203 IACVIDEKDIP-KAWFAELSVDMEKVKDIVQEIL 235 (264)
T ss_pred HHHhhcCCChH-HHHHHHHhccHHHHHHHHHHHH
Confidence 99998887665 2333335555555555555543
No 13
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.44 E-value=8.4e-13 Score=120.34 Aligned_cols=90 Identities=19% Similarity=0.364 Sum_probs=85.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHH
Q psy6534 110 AIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFK 189 (309)
Q Consensus 110 ~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~ 189 (309)
....|.++|+.|+||..+.+.|..+++++.+.++..||++..+||||||+||+.++.|+|++||+.+++++..+|.+.|+
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 35788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcccC
Q psy6534 190 LILKALETSV 199 (309)
Q Consensus 190 ~l~~~l~~~~ 199 (309)
.|.+.|++.+
T Consensus 299 el~~~l~~~~ 308 (310)
T PRK00423 299 ELAEKLDIKI 308 (310)
T ss_pred HHHHHhCccc
Confidence 9999988654
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.36 E-value=2e-12 Score=115.32 Aligned_cols=102 Identities=33% Similarity=0.443 Sum_probs=92.6
Q ss_pred ChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHH
Q psy6534 203 TTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSY 282 (309)
Q Consensus 203 ~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~ 282 (309)
.....+.+++..|+||..+.+.|..|++.+.+..+..||+..+++||+||+||+..+.++++.||+++++|++.-|.++|
T Consensus 99 ~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~kei~rty 178 (285)
T COG1405 99 TALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSKKEIGRTY 178 (285)
T ss_pred HHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCHHHHHHHH
Confidence 34568899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccCCCCcCCCCCCCCCCC
Q psy6534 283 KLMYPHASKLFPQDFVFHTPIHELPQ 308 (309)
Q Consensus 283 kei~~~~~~l~~~~~~~~~~~~~~~~ 308 (309)
+.+.+....- .++.+|.+|||+
T Consensus 179 r~~~~~L~l~----~~~~~p~~yi~r 200 (285)
T COG1405 179 RLLVRELKLK----IPPVDPSDYIPR 200 (285)
T ss_pred HHHHHhcCCC----CCCCCHHHHHHH
Confidence 9888774333 444889999886
No 15
>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=99.14 E-value=6.8e-10 Score=81.20 Aligned_cols=84 Identities=30% Similarity=0.320 Sum_probs=79.2
Q ss_pred CChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCC-CHHHHHH
Q psy6534 202 ITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGV-AEVTIRQ 280 (309)
Q Consensus 202 ~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~v-s~~ti~~ 280 (309)
..+..|+.++++.++++..+...|..++++........+++|..+|+||||+|+++.+.+.+.+++...++. ++.+|.+
T Consensus 3 ~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~ 82 (88)
T cd00043 3 PTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILR 82 (88)
T ss_pred chHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHH
Confidence 457889999999999999999999999999988887889999999999999999999999999999999999 9999999
Q ss_pred HHHHH
Q psy6534 281 SYKLM 285 (309)
Q Consensus 281 ~~kei 285 (309)
.+++|
T Consensus 83 ~e~~i 87 (88)
T cd00043 83 MEKLL 87 (88)
T ss_pred HHHHh
Confidence 99886
No 16
>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=99.12 E-value=8.1e-10 Score=80.79 Aligned_cols=83 Identities=27% Similarity=0.392 Sum_probs=77.6
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcc-cHHHHHHH
Q psy6534 109 NAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKI-SKKEIGRC 187 (309)
Q Consensus 109 ~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~-~~~~i~~~ 187 (309)
.+.++|.+++..++++..+...|..+++++.....+.++++..+++||+|+|||.++.|.+++++...++. +..+|.+.
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~ 83 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRM 83 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHH
Confidence 35688999999999999999999999999999888889999999999999999999999999999999999 99999988
Q ss_pred HHHH
Q psy6534 188 FKLI 191 (309)
Q Consensus 188 ~~~l 191 (309)
++.+
T Consensus 84 e~~i 87 (88)
T cd00043 84 EKLL 87 (88)
T ss_pred HHHh
Confidence 8765
No 17
>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=99.11 E-value=6.6e-10 Score=80.42 Aligned_cols=81 Identities=27% Similarity=0.330 Sum_probs=74.0
Q ss_pred HHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q psy6534 206 DFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGV-AEVTIRQSYKL 284 (309)
Q Consensus 206 ~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~v-s~~ti~~~~ke 284 (309)
+|+.++++.+++++++...|..+++++....-..+++|..+|+||+|+|++..+.+.+.+++...+++ ++.+|.+.+++
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 80 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEKL 80 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHHH
Confidence 37899999999999999999999999987443446999999999999999999998999999999999 99999999998
Q ss_pred HH
Q psy6534 285 MY 286 (309)
Q Consensus 285 i~ 286 (309)
|.
T Consensus 81 il 82 (83)
T smart00385 81 LL 82 (83)
T ss_pred Hh
Confidence 85
No 18
>KOG0656|consensus
Probab=99.06 E-value=1.3e-08 Score=92.12 Aligned_cols=176 Identities=19% Similarity=0.215 Sum_probs=136.3
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCc---hhHHHHHHHHHHHHhcCC--CccHHHHHHH--hccc
Q psy6534 108 LNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRS---NDAIASACLYIACRQEGV--PRTFKEICAV--SKIS 180 (309)
Q Consensus 108 ~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~---~~~vaaAcly~acR~~~~--~~tl~eia~~--~~~~ 180 (309)
..|+.+|-+.|...+..+.+.=-|..|+.++....-++.-+ .+.+++||+.+|.|.+.. |.++.=.+.. .-..
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 46889999999999999999999999999998765444334 789999999999999986 6555544444 2457
Q ss_pred HHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCCCCH----HHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHH
Q psy6534 181 KKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPN----MVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQ 256 (309)
Q Consensus 181 ~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~----~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~ 256 (309)
.+.|.++...|+..|+=++..+.|.+|+.-|+.+++... .+...+..++-......-+.+-.|+.||||++..+..
T Consensus 159 aktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~ 238 (335)
T KOG0656|consen 159 AKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSA 238 (335)
T ss_pred HHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHH
Confidence 899999999999999999999999999999999998843 3455555544333333344578999999998877766
Q ss_pred hC-CCC--CCHHHHHHHhCCCHHHHHHHHH
Q psy6534 257 AS-SDK--RSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 257 ~~-~~~--~~~~~ia~~~~vs~~ti~~~~k 283 (309)
.. +.. ....-+.....++...+++.|.
T Consensus 239 ~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 239 SVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred hhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 43 322 2345666778888888888877
No 19
>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=99.02 E-value=1.5e-09 Score=78.46 Aligned_cols=80 Identities=28% Similarity=0.356 Sum_probs=72.3
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcc-cHHHHHHHHHHH
Q psy6534 113 EINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKI-SKKEIGRCFKLI 191 (309)
Q Consensus 113 ~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~-~~~~i~~~~~~l 191 (309)
+|.+++..+++|+.+...|..+++++.....+.++++..+++||+|+|||.++.+.+..++...++. +.++|.+.++.|
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~i 81 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEKLL 81 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHHHH
Confidence 5788999999999999999999999988444445899999999999999999999999999999999 999999988876
Q ss_pred H
Q psy6534 192 L 192 (309)
Q Consensus 192 ~ 192 (309)
.
T Consensus 82 l 82 (83)
T smart00385 82 L 82 (83)
T ss_pred h
Confidence 4
No 20
>KOG1597|consensus
Probab=98.91 E-value=8.6e-09 Score=90.15 Aligned_cols=88 Identities=19% Similarity=0.266 Sum_probs=82.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHH
Q psy6534 110 AIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFK 189 (309)
Q Consensus 110 ~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~ 189 (309)
.-+.|.++|..|+||.++.+.|.++.+++.+.....||++..++||.+|++++....+++++||.+++|+..-.|...|+
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 45678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcc
Q psy6534 190 LILKALET 197 (309)
Q Consensus 190 ~l~~~l~~ 197 (309)
.|...+..
T Consensus 283 ~Lyp~~~~ 290 (308)
T KOG1597|consen 283 DLYPHADK 290 (308)
T ss_pred HHhhchhh
Confidence 88776653
No 21
>KOG4557|consensus
Probab=98.81 E-value=2.7e-07 Score=77.06 Aligned_cols=175 Identities=17% Similarity=0.178 Sum_probs=140.2
Q ss_pred HHHHHHHhcCCC--HHHHHHHHHHHHHHhc--CCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHH
Q psy6534 113 EINSMADRINLT--KTIVDRANNLFKQVHD--GKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCF 188 (309)
Q Consensus 113 ~I~~i~~~L~Lp--~~v~e~A~~~~~~~~~--~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~ 188 (309)
.|.+++.+|||. +.+++.|.+|.+...- .++.-|-.-...+.-|+-+|.-.-+++..-.......|.+++...+.+
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 378899999993 5799999999987743 344455566778889999999999999998899999999999999999
Q ss_pred HHHHHHhcccCCCCChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhc-----CccCCCChHHHHHHHHHHHHHhCCCCCC
Q psy6534 189 KLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVEL-----DIVPGRSPISVAAAAIYMASQASSDKRS 263 (309)
Q Consensus 189 ~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~-----~l~~Gr~P~~iaaAaiyla~~~~~~~~~ 263 (309)
+.+...||++.. .-|..+|-++|+.+ +++.|..++...+.. ..-.--+-.-.++||+|.||+..+.++.
T Consensus 82 ~sfe~llgln~~-----~~VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVd 155 (262)
T KOG4557|consen 82 NSFENLLGLNIK-----LNVRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVD 155 (262)
T ss_pred HHHHHHhcchhh-----cCHHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhh
Confidence 999999998642 34778888888866 677888888765441 1122223456788999999999999999
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 264 QKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 264 ~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
...+...+|++++.+...-+.+.+.-++..
T Consensus 156 K~kli~~sg~~~s~F~~l~kqler~~~qv~ 185 (262)
T KOG4557|consen 156 KLKLIEVSGTSESEFSCLSKQLERNYKQVS 185 (262)
T ss_pred HhhcccccCCCHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999888888776655554
No 22
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=98.54 E-value=1.2e-06 Score=82.37 Aligned_cols=182 Identities=13% Similarity=0.175 Sum_probs=141.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCC-CccHHHHHHHh--cccHHHHHHH
Q psy6534 111 IREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGV-PRTFKEICAVS--KISKKEIGRC 187 (309)
Q Consensus 111 ~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~-~~tl~eia~~~--~~~~~~i~~~ 187 (309)
.++|.++-.+|+|-+.....|..+..++...+...=.+...+++.|+||||+.+.+ +.++++++-++ .++.++|.++
T Consensus 217 v~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~a 296 (440)
T COG5024 217 VDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRA 296 (440)
T ss_pred HHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHH
Confidence 46777888999998889999999999999988777677899999999999999986 46678888776 5789999999
Q ss_pred HHHHHHHhcccCCCCChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhc-CccCCCChHHHHHHHHHHHHHhCCCCCCHHH
Q psy6534 188 FKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVEL-DIVPGRSPISVAAAAIYMASQASSDKRSQKE 266 (309)
Q Consensus 188 ~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~-~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ 266 (309)
.+.+...|++++....|..|+.++....+.+...+..+..++....-. .+...+ |+.+||||.|++-++.+..-.-..
T Consensus 297 E~~ml~~l~f~is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~~~~~~w~~~ 375 (440)
T COG5024 297 ERYMLEVLDFNISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKILSQNQWDRT 375 (440)
T ss_pred HHHHhhhcccccCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhhhccCCCCcc
Confidence 999999999999999999999998888777766666676666543322 344555 999999999999998875433333
Q ss_pred HHHHhC-CCHHHHHHHHHHHHHhhcccC
Q psy6534 267 IGDIAG-VAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 267 ia~~~~-vs~~ti~~~~kei~~~~~~l~ 293 (309)
..-..| -+...++.....+.+.....+
T Consensus 376 l~~ySg~y~~~~l~~~~~~~~~~l~~~~ 403 (440)
T COG5024 376 LIHYSGNYTNPDLKPLNESNKENLQNPS 403 (440)
T ss_pred ccccCCCCCchhHHHHHHHHHHHhcccc
Confidence 333444 566566666666666654433
No 23
>KOG0653|consensus
Probab=98.49 E-value=2.5e-06 Score=80.40 Aligned_cols=163 Identities=18% Similarity=0.211 Sum_probs=129.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHH-HHHHhcCC-CccHHHHHHHhc--ccHHHHH
Q psy6534 110 AIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLY-IACRQEGV-PRTFKEICAVSK--ISKKEIG 185 (309)
Q Consensus 110 ~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly-~acR~~~~-~~tl~eia~~~~--~~~~~i~ 185 (309)
-.+++-++..+++|..+..--|..+++++.....+..+....+..+|++ +|||.+.. +.++.|+.-+++ ++..+|.
T Consensus 161 Lvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il 240 (391)
T KOG0653|consen 161 LVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEIL 240 (391)
T ss_pred HHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHH
Confidence 3577888999999999999999999999998866777888888888866 99997554 344677766653 6899999
Q ss_pred HHHHHHHHHhcccCCCCChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCC-CCH
Q psy6534 186 RCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDK-RSQ 264 (309)
Q Consensus 186 ~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~-~~~ 264 (309)
++.+.+...|+++.....|..|+.++.+...........+..+++...-..-+....|..+|||+.+++.++...+ ...
T Consensus 241 ~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~~~w~ 320 (391)
T KOG0653|consen 241 RMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKGDVWS 320 (391)
T ss_pred HHHHHHHhccCeeecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccCCccC
Confidence 9999999999999999999999999999988766667777777776554443456788999999999999988765 344
Q ss_pred HHHHHHhC
Q psy6534 265 KEIGDIAG 272 (309)
Q Consensus 265 ~~ia~~~~ 272 (309)
..+...+|
T Consensus 321 ~~~~~~sg 328 (391)
T KOG0653|consen 321 PTLEHYSG 328 (391)
T ss_pred CCCeeccC
Confidence 43433344
No 24
>KOG2496|consensus
Probab=98.48 E-value=1.8e-06 Score=76.13 Aligned_cols=140 Identities=20% Similarity=0.299 Sum_probs=101.5
Q ss_pred HHHHhc--CCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhc----ccHHHHHHHHH
Q psy6534 116 SMADRI--NLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSK----ISKKEIGRCFK 189 (309)
Q Consensus 116 ~i~~~L--~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~----~~~~~i~~~~~ 189 (309)
++++++ .||.+|+-+|..+|++++-.+....-++..|.++|+|+||+.++..+|+.+|+.-+. -....+.+...
T Consensus 65 ~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk~E~ 144 (325)
T KOG2496|consen 65 NFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLKYEF 144 (325)
T ss_pred HHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHhchH
Confidence 445555 689999999999999999988888888999999999999999999999999999887 55666777777
Q ss_pred HHHHHhcccCCCCCh----HHHHHHHHhhC-CC-CHHH-HHH--HHHHHHHhhhcCccCCCChHHHHHHHHHHHH
Q psy6534 190 LILKALETSVDLITT----GDFMSRFCSNL-SL-PNMV-QKA--ATHIARKAVELDIVPGRSPISVAAAAIYMAS 255 (309)
Q Consensus 190 ~l~~~l~~~~~~~~p----~~~i~~~~~~L-~l-~~~~-~~~--a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~ 255 (309)
.+.+.|++++-+-.| +-|+..+-..| ++ +++. ... ....++.+...+...=..|+-||.|||..++
T Consensus 145 ~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~ 219 (325)
T KOG2496|consen 145 LLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAA 219 (325)
T ss_pred HHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHh
Confidence 888888876543333 33554444332 12 1111 111 1355556555555555789999999995443
No 25
>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=98.45 E-value=4.8e-06 Score=65.59 Aligned_cols=94 Identities=24% Similarity=0.332 Sum_probs=79.5
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCC-CccHHHHHHHh--cccHH
Q psy6534 106 ALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGV-PRTFKEICAVS--KISKK 182 (309)
Q Consensus 106 ~l~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~-~~tl~eia~~~--~~~~~ 182 (309)
......++|..++..++++..+...|..++.++.........+...++++|+++|||.++. +.++.++.... ..+.+
T Consensus 30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~ 109 (127)
T PF00134_consen 30 MRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKK 109 (127)
T ss_dssp HHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHH
T ss_pred HHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHH
Confidence 3456778999999999999999999999999999888778888999999999999999987 78899998887 46899
Q ss_pred HHHHHHHHHHHHhcccC
Q psy6534 183 EIGRCFKLILKALETSV 199 (309)
Q Consensus 183 ~i~~~~~~l~~~l~~~~ 199 (309)
+|..+.+.+.+.|++++
T Consensus 110 ~i~~~E~~iL~~L~f~l 126 (127)
T PF00134_consen 110 DILEMEREILSALNFDL 126 (127)
T ss_dssp HHHHHHHHHHHHTTT--
T ss_pred HHHHHHHHHHHHCCCCc
Confidence 99999999999998764
No 26
>KOG1598|consensus
Probab=98.30 E-value=5.7e-07 Score=85.00 Aligned_cols=88 Identities=22% Similarity=0.318 Sum_probs=70.7
Q ss_pred HHHHHHHHhcCC-CH--HHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHH
Q psy6534 112 REINSMADRINL-TK--TIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCF 188 (309)
Q Consensus 112 ~~I~~i~~~L~L-p~--~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~ 188 (309)
-+|.+++..|-. +. .++.+|..+..++.......||++..+++||||+|||.||+++|+.||+.+.+++...|.+.+
T Consensus 168 L~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl 247 (521)
T KOG1598|consen 168 LYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRL 247 (521)
T ss_pred eeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHH
Confidence 345555555544 32 366677777666655566789999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccC
Q psy6534 189 KLILKALETSV 199 (309)
Q Consensus 189 ~~l~~~l~~~~ 199 (309)
+.+.+.+.-++
T Consensus 248 ~Ef~~T~s~~L 258 (521)
T KOG1598|consen 248 KEFSDTLSGDL 258 (521)
T ss_pred HHHhccccccc
Confidence 99988765444
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=98.07 E-value=1.8e-05 Score=61.30 Aligned_cols=88 Identities=19% Similarity=0.193 Sum_probs=71.7
Q ss_pred ChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCC-CCCHHHHHHHhCCCHHHHHHH
Q psy6534 203 TTGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSD-KRSQKEIGDIAGVAEVTIRQS 281 (309)
Q Consensus 203 ~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~ia~~~~vs~~ti~~~ 281 (309)
.|..|+.+|....+.+..+...+..+++.+....-+.+-+|+.|||||+|+|....+. +.....+...+|++...+...
T Consensus 2 Tp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c 81 (118)
T PF02984_consen 2 TPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC 81 (118)
T ss_dssp -HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred cHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence 5889999996655666778899999999876655567899999999999999999875 577788999999999999999
Q ss_pred HHHHHHhhc
Q psy6534 282 YKLMYPHAS 290 (309)
Q Consensus 282 ~kei~~~~~ 290 (309)
++.|.+...
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999886543
No 28
>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=97.79 E-value=0.00011 Score=58.56 Aligned_cols=82 Identities=16% Similarity=0.307 Sum_probs=63.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhc--CCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHH
Q psy6534 108 LNAIREINSMADRINLTKTIVDRANNLFKQVHD--GKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIG 185 (309)
Q Consensus 108 ~~~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~--~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~ 185 (309)
.-|...|+.+|+.|+|++++.+....+|..+.. ..++++|....++.+|+|+.||.++.++|++||.....--+..-.
T Consensus 12 ~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qpq~~~ 91 (135)
T PF01857_consen 12 KLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQPQASS 91 (135)
T ss_dssp HHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTSTT--T
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcccccc
Confidence 447788999999999999999999999998864 468899999999999999999999999999999987654333333
Q ss_pred HHHH
Q psy6534 186 RCFK 189 (309)
Q Consensus 186 ~~~~ 189 (309)
..|+
T Consensus 92 ~Vyr 95 (135)
T PF01857_consen 92 HVYR 95 (135)
T ss_dssp HHHH
T ss_pred cceE
Confidence 3343
No 29
>KOG0655|consensus
Probab=97.64 E-value=0.00058 Score=61.17 Aligned_cols=167 Identities=19% Similarity=0.210 Sum_probs=117.7
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCC-CCCCCchhHHHHHHHHHHHHhcCC-CccHHHHHHHh--cccHHHHHH
Q psy6534 111 IREINSMADRINLTKTIVDRANNLFKQVHDGK-NLKGRSNDAIASACLYIACRQEGV-PRTFKEICAVS--KISKKEIGR 186 (309)
Q Consensus 111 ~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~-~~~gr~~~~vaaAcly~acR~~~~-~~tl~eia~~~--~~~~~~i~~ 186 (309)
++++.++|+-.+|-...---|..+|.+++... ....-....+..+|||+|++.+.+ |..+.|+|-++ -++..+|..
T Consensus 149 lDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIlt 228 (408)
T KOG0655|consen 149 LDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILT 228 (408)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHHH
Confidence 68889999999999888889999999997632 223345788999999999999996 78899999887 368999999
Q ss_pred HHHHHHHHhcccCCCCChHHHHHHHHhhCCCCH------------HHHHHHHHHHHHhh-hcCccCCCChHHHHHHHHHH
Q psy6534 187 CFKLILKALETSVDLITTGDFMSRFCSNLSLPN------------MVQKAATHIARKAV-ELDIVPGRSPISVAAAAIYM 253 (309)
Q Consensus 187 ~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~------------~~~~~a~~i~~~~~-~~~l~~Gr~P~~iaaAaiyl 253 (309)
+...|.+.|+-++.++..-.++.-|.+-+.+++ +.+..| +|+..+. +.+. ...+-..+||||||.
T Consensus 229 mE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqia-qlLDlc~ldids-~~fsYrilaAAal~h 306 (408)
T KOG0655|consen 229 MELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIA-QLLDLCILDIDS-LEFSYRILAAAALCH 306 (408)
T ss_pred HHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHH-HHHHHHHhcccc-ccchHHHHHHHHHHH
Confidence 999999999998888888888888887665432 122222 3333332 1111 234567788888874
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 254 ASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 254 a~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
-.. ..-+-+++|..-..|.+..+=+.
T Consensus 307 ~~s-------~e~v~kaSG~~w~~ie~cv~wm~ 332 (408)
T KOG0655|consen 307 FTS-------IEVVKKASGLEWDSIEECVDWMV 332 (408)
T ss_pred HhH-------HHHHHHcccccHHHHHHHHHHHH
Confidence 321 11222445666666665555444
No 30
>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=97.35 E-value=0.00015 Score=43.89 Aligned_cols=33 Identities=18% Similarity=0.128 Sum_probs=26.2
Q ss_pred CCCCcccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 1 MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
|.+..+.|+.|++. .+....|..+|..||.|++
T Consensus 4 ~~~~~~~C~~C~~~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 4 MRGPNEPCPVCGSR--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cccCCCcCCCCCCe--EeEccCCEEEhhhCceEcC
Confidence 34556679999986 5566789999999999863
No 31
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.83 E-value=0.00085 Score=44.88 Aligned_cols=31 Identities=16% Similarity=0.337 Sum_probs=28.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccccC
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVGD 36 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e 36 (309)
.+||.|+...+|+++.+-.+.|..||.++.+
T Consensus 12 VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 5799999999999999999999999999953
No 32
>PHA00626 hypothetical protein
Probab=96.82 E-value=0.001 Score=43.56 Aligned_cols=30 Identities=17% Similarity=0.509 Sum_probs=23.3
Q ss_pred ccCCCCCCCCeeeeC----CCCceecCCCCcccc
Q psy6534 6 VCCYEHPDAPLIEDY----RAGDQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~----~~G~~vC~~CG~V~~ 35 (309)
|.||.||+.+++..- -+..++|.+||+-..
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 579999998777521 267999999998753
No 33
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.64 E-value=0.0011 Score=45.12 Aligned_cols=31 Identities=16% Similarity=0.356 Sum_probs=28.3
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccccC
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVGD 36 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e 36 (309)
.+||+|+...+++++.+-.+.|..||.++.+
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEEe
Confidence 4799999999999999999999999999843
No 34
>KOG0835|consensus
Probab=96.62 E-value=0.014 Score=52.52 Aligned_cols=102 Identities=19% Similarity=0.301 Sum_probs=73.6
Q ss_pred HHHHHHHHHhcCCCHHH--HHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHH-HHHHHhcccHHHHHHH
Q psy6534 111 IREINSMADRINLTKTI--VDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFK-EICAVSKISKKEIGRC 187 (309)
Q Consensus 111 ~~~I~~i~~~L~Lp~~v--~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~-eia~~~~~~~~~i~~~ 187 (309)
.+.|-.+..-|++|++. ...+..+.....--.++.--+++.||+||+|+|.|..++|++.. .--.+++.++.+|...
T Consensus 142 hklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~i 221 (367)
T KOG0835|consen 142 HKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEI 221 (367)
T ss_pred HHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHH
Confidence 56677888999998754 77777777777666777777899999999999999999885544 5566778888888877
Q ss_pred HHHHHHHhcccCCCCChHHHHHHHHhhC
Q psy6534 188 FKLILKALETSVDLITTGDFMSRFCSNL 215 (309)
Q Consensus 188 ~~~l~~~l~~~~~~~~p~~~i~~~~~~L 215 (309)
...+........+ -..+|..+.+++
T Consensus 222 c~~l~~lY~~~~p---~~~li~~~vd~~ 246 (367)
T KOG0835|consen 222 CYRLIPLYKRAKP---DETLIEAFVDRL 246 (367)
T ss_pred HHHHHHHHHhccc---CHHHHHHHHHHh
Confidence 6666555443221 134555555544
No 35
>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=96.57 E-value=0.0012 Score=43.76 Aligned_cols=31 Identities=19% Similarity=0.268 Sum_probs=23.7
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccccC
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVGD 36 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e 36 (309)
.+||.|+...+|+++.+-.+.|..||.+|.+
T Consensus 8 VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 5799999999999999999999999999953
No 36
>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=96.49 E-value=0.013 Score=46.67 Aligned_cols=80 Identities=15% Similarity=0.191 Sum_probs=62.5
Q ss_pred HHHHHHHhhCCCCHHHHHHHHHHHHHhh--hcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy6534 206 DFMSRFCSNLSLPNMVQKAATHIARKAV--ELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 206 ~~i~~~~~~L~l~~~~~~~a~~i~~~~~--~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~k 283 (309)
.-+..+|+.|++++++.+.++.+++.+. +.+++.+|+-.-+...|||..|++++..++.++|-+.-.--+..-...|+
T Consensus 16 ~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qpq~~~~Vyr 95 (135)
T PF01857_consen 16 VRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQPQASSHVYR 95 (135)
T ss_dssp HHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTSTT--THHHH
T ss_pred HHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcccccccceE
Confidence 4577899999999988888898888765 45799999999999999999999999999999998877766666566666
Q ss_pred HH
Q psy6534 284 LM 285 (309)
Q Consensus 284 ei 285 (309)
+.
T Consensus 96 ~V 97 (135)
T PF01857_consen 96 SV 97 (135)
T ss_dssp SE
T ss_pred EE
Confidence 54
No 37
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=96.48 E-value=0.023 Score=51.71 Aligned_cols=69 Identities=14% Similarity=0.162 Sum_probs=59.5
Q ss_pred HHHHHHHhhCC--CCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCC
Q psy6534 206 DFMSRFCSNLS--LPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVA 274 (309)
Q Consensus 206 ~~i~~~~~~L~--l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs 274 (309)
.+|..+|..|+ +|..+.-+|..++++..-.+-+.-.+|.-|++||||+||+.-..++++.+++..+.-.
T Consensus 61 ~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 61 KRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 46888999999 9999999999999887765555567999999999999999999999999998876544
No 38
>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=96.32 E-value=0.043 Score=42.80 Aligned_cols=81 Identities=17% Similarity=0.207 Sum_probs=59.8
Q ss_pred HHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCC-CCCHHHHHHHhC--CCHHHHHHH
Q psy6534 205 GDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSD-KRSQKEIGDIAG--VAEVTIRQS 281 (309)
Q Consensus 205 ~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~ia~~~~--vs~~ti~~~ 281 (309)
..++..++..++++..+.-.|..++++...........+.-+++||+++|+++... ..+..++....+ .+...|.+.
T Consensus 35 ~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~ 114 (127)
T PF00134_consen 35 IDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEM 114 (127)
T ss_dssp HHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHH
T ss_pred HHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHH
Confidence 45788899999999999999999999887666667788999999999999999876 566788877763 343334333
Q ss_pred HHHH
Q psy6534 282 YKLM 285 (309)
Q Consensus 282 ~kei 285 (309)
=+.|
T Consensus 115 E~~i 118 (127)
T PF00134_consen 115 EREI 118 (127)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 3333
No 39
>PLN00209 ribosomal protein S27; Provisional
Probab=96.28 E-value=0.003 Score=45.39 Aligned_cols=31 Identities=16% Similarity=0.268 Sum_probs=28.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccccC
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVGD 36 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e 36 (309)
.+||.|+...+|+++.+-.+.|..||.++.+
T Consensus 37 VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 4799999999999999999999999999953
No 40
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=96.18 E-value=0.0037 Score=44.81 Aligned_cols=31 Identities=13% Similarity=0.220 Sum_probs=28.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccccC
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVGD 36 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e 36 (309)
.+||.|+...+|+++.+-.+.|..||.++.+
T Consensus 36 VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 4799999999999999999999999999943
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=95.90 E-value=0.05 Score=41.68 Aligned_cols=86 Identities=16% Similarity=0.198 Sum_probs=61.3
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCC-CccHHHHHHHhcccHHHHHHHHH
Q psy6534 111 IREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGV-PRTFKEICAVSKISKKEIGRCFK 189 (309)
Q Consensus 111 ~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~-~~tl~eia~~~~~~~~~i~~~~~ 189 (309)
+.+|+.+....+....+...|..+.....-...+-+-++-.+||||+|+|.+..+. +.--..+...++++..+|...++
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c~~ 83 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKECIE 83 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHHHH
Confidence 45666664444445567777777777765444455677899999999999999765 44445567777999999999999
Q ss_pred HHHHHhc
Q psy6534 190 LILKALE 196 (309)
Q Consensus 190 ~l~~~l~ 196 (309)
.|.+.+.
T Consensus 84 ~i~~~~~ 90 (118)
T PF02984_consen 84 LIQELLS 90 (118)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 8888765
No 42
>KOG0834|consensus
Probab=95.86 E-value=0.031 Score=51.05 Aligned_cols=83 Identities=16% Similarity=0.277 Sum_probs=65.8
Q ss_pred HHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHH----hCCCHHHHHH
Q psy6534 205 GDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDI----AGVAEVTIRQ 280 (309)
Q Consensus 205 ~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~----~~vs~~ti~~ 280 (309)
..||..++.+|+++......|.-++.+..-..-...-.|..+|++|||||++..+.++..++|..+ .+....+...
T Consensus 43 ~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~~~ 122 (323)
T KOG0834|consen 43 AKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLELEE 122 (323)
T ss_pred HHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccHHH
Confidence 468999999999999888888888877766556677788999999999999999999999999654 3433335566
Q ss_pred HHHHHHH
Q psy6534 281 SYKLMYP 287 (309)
Q Consensus 281 ~~kei~~ 287 (309)
.|-++.+
T Consensus 123 ~~~~~~~ 129 (323)
T KOG0834|consen 123 VYWELKE 129 (323)
T ss_pred HHHHHHH
Confidence 6666554
No 43
>PRK00420 hypothetical protein; Validated
Probab=95.63 E-value=0.0086 Score=45.90 Aligned_cols=27 Identities=26% Similarity=0.375 Sum_probs=21.7
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
..||.||.+ +..+ .+|..+|..||.++
T Consensus 24 ~~CP~Cg~p-Lf~l-k~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLP-LFEL-KDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCc-ceec-CCCceECCCCCCee
Confidence 479999964 4444 68999999999876
No 44
>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=95.52 E-value=0.011 Score=34.12 Aligned_cols=25 Identities=28% Similarity=0.409 Sum_probs=14.3
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
.||.|++.....| ...+||.+||.-
T Consensus 4 ~Cp~C~se~~y~D--~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTYED--GELLVCPECGHE 28 (30)
T ss_dssp --TTT-----EE---SSSEEETTTTEE
T ss_pred CCCCCCCcceecc--CCEEeCCccccc
Confidence 7999998876655 579999999964
No 45
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.42 E-value=0.011 Score=38.60 Aligned_cols=27 Identities=15% Similarity=0.401 Sum_probs=21.7
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
..||.||+. +..++ .+...|..||+..
T Consensus 21 ~fCP~Cg~~-~m~~~-~~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGSG-FMAEH-LDRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCcc-hhecc-CCcEECCCcCCEE
Confidence 479999987 66655 4899999999864
No 46
>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=95.35 E-value=0.0083 Score=36.67 Aligned_cols=29 Identities=24% Similarity=0.476 Sum_probs=21.3
Q ss_pred ccCCCCCCCCeeeeC----CCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDY----RAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~----~~G~~vC~~CG~V~ 34 (309)
..||+|+...-+.+. ..+.+.|..||.++
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 589999986444331 34579999999886
No 47
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.14 E-value=0.012 Score=31.78 Aligned_cols=22 Identities=23% Similarity=0.552 Sum_probs=16.9
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
.||+||... . .+..+|..||.-
T Consensus 1 ~Cp~CG~~~--~---~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEI--E---DDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCC--C---CcCcchhhhCCc
Confidence 499999763 2 468899999964
No 48
>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=95.11 E-value=0.022 Score=34.56 Aligned_cols=28 Identities=25% Similarity=0.367 Sum_probs=21.0
Q ss_pred cccCCCCCCCC-eeeeC--CCCceecCCCCc
Q psy6534 5 KVCCYEHPDAP-LIEDY--RAGDQICSECGL 32 (309)
Q Consensus 5 ~~~Cp~C~~~~-~v~D~--~~G~~vC~~CG~ 32 (309)
...||.||+++ +-+|. ..|..+|..||.
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 45899998764 43443 569999999984
No 49
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=95.09 E-value=0.024 Score=33.47 Aligned_cols=29 Identities=14% Similarity=0.330 Sum_probs=22.8
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
...|+.|+...++ ....+..+|.+||.+.
T Consensus 3 ~~~C~~C~~~~i~-~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIV-NKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEE-EecCCeEEcccCCcEe
Confidence 3479999886554 3567999999999875
No 50
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=94.99 E-value=0.015 Score=45.63 Aligned_cols=23 Identities=26% Similarity=0.730 Sum_probs=19.1
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGL 32 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~ 32 (309)
.||.||.+ ++. .+|+++|..||+
T Consensus 30 hCp~Cg~P-LF~--KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTP-LFR--KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCc-cee--eCCeEECCCCCc
Confidence 59999976 444 789999999993
No 51
>KOG4164|consensus
Probab=94.96 E-value=0.11 Score=47.85 Aligned_cols=88 Identities=18% Similarity=0.248 Sum_probs=62.7
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCC-ccHHHHH----HHhcccHHHH
Q psy6534 110 AIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVP-RTFKEIC----AVSKISKKEI 184 (309)
Q Consensus 110 ~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~-~tl~eia----~~~~~~~~~i 184 (309)
..+++.+++...+|..-.+.+|-.||.++.-++++...++..+|+|||.+|.+.+..- -+++... +.+..+..+|
T Consensus 385 lKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdL 464 (497)
T KOG4164|consen 385 LKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDL 464 (497)
T ss_pred HHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhh
Confidence 3567778888888888889999999999988888887889999999999999988653 2233322 2245555555
Q ss_pred HHHHHHHHHHhcc
Q psy6534 185 GRCFKLILKALET 197 (309)
Q Consensus 185 ~~~~~~l~~~l~~ 197 (309)
-...--++-.|++
T Consensus 465 ia~Ef~VlvaLef 477 (497)
T KOG4164|consen 465 IAFEFPVLVALEF 477 (497)
T ss_pred hhhhhhHHHhhhh
Confidence 4444444444444
No 52
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=94.96 E-value=0.013 Score=32.69 Aligned_cols=22 Identities=18% Similarity=0.632 Sum_probs=17.4
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGL 32 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~ 32 (309)
+.||+||.. + ..+..+|..||.
T Consensus 3 ~~Cp~Cg~~-~----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAE-I----DPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCc-C----CcccccChhhCC
Confidence 589999983 2 356899999996
No 53
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=94.90 E-value=0.023 Score=41.01 Aligned_cols=29 Identities=21% Similarity=0.356 Sum_probs=25.0
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
...||.|+.. .+.-..+|-..|..||.+.
T Consensus 35 ~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRT-TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCc-ceeeeccCeEEcCCCCCee
Confidence 4579999987 5677899999999999886
No 54
>PRK11827 hypothetical protein; Provisional
Probab=94.83 E-value=0.021 Score=38.55 Aligned_cols=29 Identities=17% Similarity=0.227 Sum_probs=24.1
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.+.||.|++ .+.+|.....++|..||.+.
T Consensus 8 ILaCP~ckg-~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 8 IIACPVCNG-KLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred heECCCCCC-cCeEcCCCCeEECCccCeec
Confidence 468999976 47777777899999999876
No 55
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=94.76 E-value=0.013 Score=34.90 Aligned_cols=28 Identities=18% Similarity=0.456 Sum_probs=15.6
Q ss_pred cCCCCCCCC---eeeeCCCCceecCCCCccc
Q psy6534 7 CCYEHPDAP---LIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~---~v~D~~~G~~vC~~CG~V~ 34 (309)
-||.||..- +..++..--.||..||.|.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 599999762 2222345579999999985
No 56
>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=94.75 E-value=0.026 Score=39.39 Aligned_cols=17 Identities=35% Similarity=0.749 Sum_probs=15.3
Q ss_pred eeCCCCceecCCCCccc
Q psy6534 18 EDYRAGDQICSECGLVV 34 (309)
Q Consensus 18 ~D~~~G~~vC~~CG~V~ 34 (309)
.+..+|.++|.+||.+.
T Consensus 47 ~~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEIVEGELICPECGREY 63 (68)
T ss_dssp EETTTTEEEETTTTEEE
T ss_pred ccccCCEEEcCCCCCEE
Confidence 57899999999999875
No 57
>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=94.71 E-value=0.089 Score=47.14 Aligned_cols=83 Identities=17% Similarity=0.178 Sum_probs=61.4
Q ss_pred HHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCC--CCCCHHHHHH------HhCCCHHH
Q psy6534 206 DFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASS--DKRSQKEIGD------IAGVAEVT 277 (309)
Q Consensus 206 ~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~--~~~~~~~ia~------~~~vs~~t 277 (309)
.+|.++|.+|++|..+..+|..++.+..-..-..+..|..||++|||+||+..+ ..+...-... ..--++..
T Consensus 50 k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr~~ 129 (297)
T COG5333 50 KLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRER 129 (297)
T ss_pred HHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccHHH
Confidence 578999999999999999999999988766667899999999999999999887 4443332222 33444545
Q ss_pred HHHHHHHHHHh
Q psy6534 278 IRQSYKLMYPH 288 (309)
Q Consensus 278 i~~~~kei~~~ 288 (309)
|-..=.++.+.
T Consensus 130 Il~~E~~lLEa 140 (297)
T COG5333 130 ILEYEFELLEA 140 (297)
T ss_pred HHHHHHHHHHH
Confidence 54444444444
No 58
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=94.70 E-value=0.019 Score=36.75 Aligned_cols=26 Identities=19% Similarity=0.512 Sum_probs=22.6
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
.||.||...+..|+.. .+.|..||+.
T Consensus 21 ~CPrCG~gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGPGVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred cCCCCCCcchhhhcCc-eeEeccccce
Confidence 6999998778888866 9999999986
No 59
>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=94.61 E-value=0.64 Score=37.68 Aligned_cols=88 Identities=16% Similarity=0.101 Sum_probs=66.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhc---CCC--CCCCchhHHHHHHHHHHHHhcC-CCccHHHHHHHhcccHHHH
Q psy6534 111 IREINSMADRINLTKTIVDRANNLFKQVHD---GKN--LKGRSNDAIASACLYIACRQEG-VPRTFKEICAVSKISKKEI 184 (309)
Q Consensus 111 ~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~---~~~--~~gr~~~~vaaAcly~acR~~~-~~~tl~eia~~~~~~~~~i 184 (309)
.+.+.++....+++..+.-.|..|+.++.. ... +......-+..+|+-+|.|... ...+-+..+.+.|++.+++
T Consensus 55 ~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~el 134 (149)
T PF08613_consen 55 RDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKEL 134 (149)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHHH
Confidence 467888889999999999999999999977 222 3345567778888999999764 6788999999999999999
Q ss_pred HHHHHHHHHHhccc
Q psy6534 185 GRCFKLILKALETS 198 (309)
Q Consensus 185 ~~~~~~l~~~l~~~ 198 (309)
.+..+.+...++++
T Consensus 135 n~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 135 NELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHCCCc
Confidence 99999999988864
No 60
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=94.56 E-value=0.035 Score=37.70 Aligned_cols=27 Identities=22% Similarity=0.381 Sum_probs=19.7
Q ss_pred ccCCCCCCCCeeeeCCCC-------ceecCCCCc
Q psy6534 6 VCCYEHPDAPLIEDYRAG-------DQICSECGL 32 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G-------~~vC~~CG~ 32 (309)
..||.||+..+..+...+ .+.|.+||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 369999887766654444 366999998
No 61
>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=94.43 E-value=0.023 Score=37.58 Aligned_cols=30 Identities=27% Similarity=0.482 Sum_probs=21.8
Q ss_pred cccCCCCCCCCeeeeCCCC-ceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAG-DQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G-~~vC~~CG~V~ 34 (309)
+..||.||..--+.|...| .+.|..||.-+
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 3489999986434454446 56799999987
No 62
>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=94.42 E-value=0.028 Score=33.72 Aligned_cols=28 Identities=18% Similarity=0.358 Sum_probs=19.0
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
=||.||.--+......+...|..||++.
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 4999987544444445555899999985
No 63
>PRK10220 hypothetical protein; Provisional
Probab=94.10 E-value=0.12 Score=39.01 Aligned_cols=26 Identities=31% Similarity=0.479 Sum_probs=20.8
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
..||.|++...+.| ...+||.+||.-
T Consensus 4 P~CP~C~seytY~d--~~~~vCpeC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYTYED--NGMYICPECAHE 29 (111)
T ss_pred CcCCCCCCcceEcC--CCeEECCcccCc
Confidence 46999998877666 458999999953
No 64
>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=93.87 E-value=0.04 Score=34.05 Aligned_cols=28 Identities=25% Similarity=0.277 Sum_probs=15.0
Q ss_pred ccCCCCCCCC-ee-ee--CCCCceecCCCCcc
Q psy6534 6 VCCYEHPDAP-LI-ED--YRAGDQICSECGLV 33 (309)
Q Consensus 6 ~~Cp~C~~~~-~v-~D--~~~G~~vC~~CG~V 33 (309)
..||.||+++ +- ++ ..+|..+|..|+-+
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~ 35 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGGD 35 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence 4799999875 32 33 46799999999434
No 65
>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=93.83 E-value=1.4 Score=35.73 Aligned_cols=91 Identities=15% Similarity=0.097 Sum_probs=64.7
Q ss_pred cCCCCChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhh---c--CccCCCChHHHHHHHHHHHHHhCC-CCCCHHHHHHHh
Q psy6534 198 SVDLITTGDFMSRFCSNLSLPNMVQKAATHIARKAVE---L--DIVPGRSPISVAAAAIYMASQASS-DKRSQKEIGDIA 271 (309)
Q Consensus 198 ~~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~---~--~l~~Gr~P~~iaaAaiyla~~~~~-~~~~~~~ia~~~ 271 (309)
.+|.++..+|+.++.....++..+.-.|...++++.. . .........-+-.+|+.+|.+... ...+.+..|++.
T Consensus 48 ~~p~i~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~ 127 (149)
T PF08613_consen 48 SVPSISIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVG 127 (149)
T ss_dssp S--SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHH
T ss_pred CCCCCcHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhc
Confidence 4577889999999999999999988888887777766 2 234456788899999999999864 567889999999
Q ss_pred CCCHHHHHHHHHHHHHh
Q psy6534 272 GVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 272 ~vs~~ti~~~~kei~~~ 288 (309)
|++...+.+.=+++...
T Consensus 128 gis~~eln~lE~~fL~~ 144 (149)
T PF08613_consen 128 GISLKELNELEREFLKL 144 (149)
T ss_dssp TS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 99998887777766654
No 66
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=93.82 E-value=0.052 Score=36.42 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=25.5
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.+.||.|+.. +..|.+.++++|..||...
T Consensus 8 iLaCP~~kg~-L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 8 ILACPVCKGP-LVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeeccCcCCc-ceEeccCCEEEecccCcee
Confidence 4689999775 8899999999999999875
No 67
>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=93.81 E-value=0.074 Score=33.97 Aligned_cols=29 Identities=14% Similarity=0.240 Sum_probs=22.7
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGL 32 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~ 32 (309)
+...||.||+.....-...+..-|.+|+.
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 45689999988655555579999999984
No 68
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=93.75 E-value=0.041 Score=40.77 Aligned_cols=29 Identities=21% Similarity=0.527 Sum_probs=23.4
Q ss_pred ccCCCCCCCCee---ee--CCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLI---ED--YRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v---~D--~~~G~~vC~~CG~V~ 34 (309)
..||.||...++ .| ..-|..+|.+||+-.
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 579999988766 44 467899999999876
No 69
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=93.69 E-value=0.052 Score=35.48 Aligned_cols=29 Identities=14% Similarity=0.373 Sum_probs=19.5
Q ss_pred cCCCCCCCCeeeeCCC-CceecCCCCcccc
Q psy6534 7 CCYEHPDAPLIEDYRA-GDQICSECGLVVG 35 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~-G~~vC~~CG~V~~ 35 (309)
-||.||.--...+... ...+|..||++..
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 5999987433332222 3899999998753
No 70
>KOG2496|consensus
Probab=93.51 E-value=0.27 Score=44.02 Aligned_cols=68 Identities=18% Similarity=0.154 Sum_probs=59.1
Q ss_pred HHHHHHHHhhC--CCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Q psy6534 205 GDFMSRFCSNL--SLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAG 272 (309)
Q Consensus 205 ~~~i~~~~~~L--~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~ 272 (309)
+..+..|++++ ++|..|.-+|...++++.-.|-...-+|..|.++|+|+||+....-++..++++-..
T Consensus 60 E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~ 129 (325)
T KOG2496|consen 60 ELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN 129 (325)
T ss_pred HHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence 34556677666 689999999999999988778788899999999999999999999999999998776
No 71
>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=93.30 E-value=0.16 Score=38.37 Aligned_cols=28 Identities=18% Similarity=0.196 Sum_probs=22.0
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
..||.|++...+.|. ..+||.+||.--.
T Consensus 3 p~CP~C~seytY~dg--~~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDG--TQLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecC--CeeECcccccccc
Confidence 479999988777763 5799999996543
No 72
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=93.28 E-value=0.066 Score=43.63 Aligned_cols=29 Identities=21% Similarity=0.383 Sum_probs=19.1
Q ss_pred ccCCCCCCCC-eeeeC---CCCc-----eecCCCCccc
Q psy6534 6 VCCYEHPDAP-LIEDY---RAGD-----QICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~-~v~D~---~~G~-----~vC~~CG~V~ 34 (309)
|.||+||+.. -+.|. +.|. .-|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5899999765 44443 2442 4599999654
No 73
>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=93.21 E-value=0.23 Score=31.02 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
+-+.+..+||+.+|+|+.|+.+|++.|.
T Consensus 15 d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 15 DGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp -TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 4678999999999999999999999873
No 74
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.16 E-value=0.081 Score=33.77 Aligned_cols=29 Identities=17% Similarity=0.281 Sum_probs=21.8
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
...||.||.. +..|+..+...|..||.-+
T Consensus 3 ~y~C~~CG~~-~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGRE-VELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCE-EEECCCCCceECCCCCCeE
Confidence 3579999874 5556666699999999643
No 75
>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=93.07 E-value=0.065 Score=40.95 Aligned_cols=33 Identities=18% Similarity=0.319 Sum_probs=26.1
Q ss_pred CCcccCCCCCCCCeeeeCCCCceecCCCCccccCc
Q psy6534 3 INKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDR 37 (309)
Q Consensus 3 ~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~ 37 (309)
|-+..||.||.. .+|-...-+||..||.++...
T Consensus 7 GtKR~Cp~CG~k--FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAK--FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcch--hccCCCCCccCCCCCCccCcc
Confidence 567899999875 467666789999999998544
No 76
>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=92.99 E-value=0.028 Score=52.30 Aligned_cols=84 Identities=17% Similarity=0.237 Sum_probs=0.0
Q ss_pred HHHHhcC--CCHHHHHHHHHHHHHHh-cCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHH
Q psy6534 116 SMADRIN--LTKTIVDRANNLFKQVH-DGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLIL 192 (309)
Q Consensus 116 ~i~~~L~--Lp~~v~e~A~~~~~~~~-~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~ 192 (309)
.++..++ +|+.++..|.+||+... ....+++..-.+-+.+|+|+||...+.+..+.......+++++...+.+..|.
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 3444554 45789999999999998 44566777777889999999999999999999988889999999999999998
Q ss_pred HHhcccC
Q psy6534 193 KALETSV 199 (309)
Q Consensus 193 ~~l~~~~ 199 (309)
+.|+...
T Consensus 83 ~~L~~~s 89 (353)
T PF05460_consen 83 NLLGNSS 89 (353)
T ss_dssp -------
T ss_pred HHHhCCC
Confidence 8887643
No 77
>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=92.94 E-value=0.18 Score=29.51 Aligned_cols=28 Identities=18% Similarity=0.315 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+++.+|||+.+|.+..|+.+..+++.+.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 5688999999999999999999999765
No 78
>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=92.93 E-value=0.1 Score=32.41 Aligned_cols=24 Identities=33% Similarity=0.832 Sum_probs=18.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCC
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECG 31 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG 31 (309)
..||.|+. .+..| .+|..+|-.|+
T Consensus 18 ~~Cp~C~~-PL~~~-k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGT-PLMRD-KDGKIYCVSCG 41 (41)
T ss_pred CccCCCCC-eeEEe-cCCCEECCCCC
Confidence 36999964 35554 58999999996
No 79
>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=92.89 E-value=0.066 Score=29.78 Aligned_cols=23 Identities=22% Similarity=0.590 Sum_probs=18.1
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.||+|+.. | ......|..||++.
T Consensus 2 ~CP~C~~~--V---~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAE--V---PESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCC--c---hhhcCcCCCCCCCC
Confidence 69999874 2 34688999999986
No 80
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=92.72 E-value=0.15 Score=38.24 Aligned_cols=28 Identities=29% Similarity=0.455 Sum_probs=20.9
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
..||.|++.-.++| .+.++|.+|+.--.
T Consensus 4 p~cp~c~sEytYed--~~~~~cpec~~ew~ 31 (112)
T COG2824 4 PPCPKCNSEYTYED--GGQLICPECAHEWN 31 (112)
T ss_pred CCCCccCCceEEec--CceEeCchhccccc
Confidence 36999987655544 45999999996544
No 81
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=92.62 E-value=0.085 Score=35.72 Aligned_cols=32 Identities=22% Similarity=0.366 Sum_probs=20.8
Q ss_pred CCCCcccCCCCCCCCeeeeC--CCC---------------ceecCCCCcc
Q psy6534 1 MNINKVCCYEHPDAPLIEDY--RAG---------------DQICSECGLV 33 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~~~v~D~--~~G---------------~~vC~~CG~V 33 (309)
|+... +||.||..+..+++ .+| .+.|.+||+-
T Consensus 1 M~~~~-kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 1 MKNAF-KCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred CCccc-cCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 55444 69999987765543 222 2569999964
No 82
>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=92.58 E-value=0.1 Score=34.40 Aligned_cols=29 Identities=24% Similarity=0.245 Sum_probs=20.3
Q ss_pred cCCCCCCCCe-ee---e--CCCCceecCCCCcccc
Q psy6534 7 CCYEHPDAPL-IE---D--YRAGDQICSECGLVVG 35 (309)
Q Consensus 7 ~Cp~C~~~~~-v~---D--~~~G~~vC~~CG~V~~ 35 (309)
.||.||+... +. | ...|-..|..||....
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 6999998765 32 2 2344557999998763
No 83
>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=92.51 E-value=0.33 Score=31.88 Aligned_cols=32 Identities=28% Similarity=0.364 Sum_probs=27.3
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.+.+++.+++|+.++||+.||++..++|.+..
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 34559999999999999999999999997764
No 84
>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=92.49 E-value=0.065 Score=39.26 Aligned_cols=30 Identities=20% Similarity=0.371 Sum_probs=24.6
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
...||.||... +.-...|-..|..||.++.
T Consensus 35 ky~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTS-VKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSE-EEEEETTEEEETTTTEEEE
T ss_pred CCcCCCCCCce-eEEeeeEEeecCCCCCEEe
Confidence 45799999876 5667899999999998873
No 85
>KOG4557|consensus
Probab=92.47 E-value=0.47 Score=40.33 Aligned_cols=81 Identities=16% Similarity=0.270 Sum_probs=59.5
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhcC-----CCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHH
Q psy6534 113 EINSMADRINLTKTIVDRANNLFKQVHDG-----KNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRC 187 (309)
Q Consensus 113 ~I~~i~~~L~Lp~~v~e~A~~~~~~~~~~-----~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~ 187 (309)
-|+++|-+||+-+ ++..|.++++.+-+. ..--.-++....+|++|.|||..+.-.+-.-+....|+++..+...
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 4667888888864 888888888877542 1112335678899999999999998877777777888888777666
Q ss_pred HHHHHHH
Q psy6534 188 FKLILKA 194 (309)
Q Consensus 188 ~~~l~~~ 194 (309)
.+.+.+.
T Consensus 174 ~kqler~ 180 (262)
T KOG4557|consen 174 SKQLERN 180 (262)
T ss_pred HHHHHHH
Confidence 5555444
No 86
>KOG1010|consensus
Probab=92.41 E-value=0.27 Score=49.79 Aligned_cols=82 Identities=17% Similarity=0.315 Sum_probs=70.1
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhc--CCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHH
Q psy6534 110 AIREINSMADRINLTKTIVDRANNLFKQVHD--GKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRC 187 (309)
Q Consensus 110 ~~~~I~~i~~~L~Lp~~v~e~A~~~~~~~~~--~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~ 187 (309)
|..+|+.+|++|.+.+...+....+|....- -.+++.|....+.-+|+|+.||..+..+++.+|.....--+.-...+
T Consensus 680 AavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa~~~v 759 (920)
T KOG1010|consen 680 AAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQAVSLV 759 (920)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCchhhhhh
Confidence 6678999999999999999999999998754 35788999999999999999999999999999998876655555566
Q ss_pred HHHH
Q psy6534 188 FKLI 191 (309)
Q Consensus 188 ~~~l 191 (309)
|+.+
T Consensus 760 yRsV 763 (920)
T KOG1010|consen 760 YRSV 763 (920)
T ss_pred hhhe
Confidence 6654
No 87
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=92.21 E-value=0.11 Score=38.14 Aligned_cols=31 Identities=19% Similarity=0.258 Sum_probs=25.1
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
....||.||...+ .-...|-..|..||.++.
T Consensus 35 a~y~CpfCgk~~v-kR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 35 AKYFCPFCGKHAV-KRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred CCccCCCCCCCce-eeeeeEEEEcCCCCCEEe
Confidence 3568999998764 455789999999999873
No 88
>KOG1779|consensus
Probab=92.17 E-value=0.075 Score=37.41 Aligned_cols=29 Identities=14% Similarity=0.258 Sum_probs=26.4
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.+||.|-....++-+++..++|.+|++|+
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~il 63 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCSTIL 63 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCceEE
Confidence 47999988888899999999999999997
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=92.14 E-value=0.1 Score=40.54 Aligned_cols=33 Identities=12% Similarity=0.056 Sum_probs=26.6
Q ss_pred CCcccCCCCCCCCeeeeCCCCceecCCCCccccCc
Q psy6534 3 INKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDR 37 (309)
Q Consensus 3 ~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~ 37 (309)
|-+..||.||.. .+|-...-+||..||.+....
T Consensus 7 GtKr~Cp~cg~k--FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 7 GTKRICPNTGSK--FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred CccccCCCcCcc--ccccCCCCccCCCcCCccCcc
Confidence 567899999875 467667899999999998544
No 90
>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=92.11 E-value=0.5 Score=31.99 Aligned_cols=38 Identities=26% Similarity=0.339 Sum_probs=31.5
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 250 AIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 250 aiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+||.... .+..++..+||+.+||+++|+....+.|.+.
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 4665555 6778999999999999999999999999765
No 91
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=92.07 E-value=13 Score=36.55 Aligned_cols=30 Identities=27% Similarity=0.365 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+.+.|+++|+..+|||...||+..+.....
T Consensus 465 ~e~~TL~EIa~~lGVSrERVRQIe~kAL~K 494 (509)
T PRK05901 465 GQPKTLDEIGQVYGVTRERIRQIESKTLRK 494 (509)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 357999999999999999999888765433
No 92
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.06 E-value=0.086 Score=32.01 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=21.5
Q ss_pred ccCCCCCCCCeeee----CCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIED----YRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D----~~~G~~vC~~CG~V~ 34 (309)
..||+|+..--+.| ...+.+-|..||.+.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 58999987643333 346789999999875
No 93
>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=92.03 E-value=7.7 Score=33.82 Aligned_cols=121 Identities=11% Similarity=0.051 Sum_probs=62.6
Q ss_pred hcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCC--CChHHHHHHHHhhCCC-CHHHH--HHHHHHHHHhhhcCc
Q psy6534 163 QEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDL--ITTGDFMSRFCSNLSL-PNMVQ--KAATHIARKAVELDI 237 (309)
Q Consensus 163 ~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~--~~p~~~i~~~~~~L~l-~~~~~--~~a~~i~~~~~~~~l 237 (309)
..+.+.|..|||..++++.+++....+.....+.++.+. .+...+...+.+.-.. |.+.. ......+..+.. .+
T Consensus 99 ~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~~~~~~~~~~l~~~l~-~L 177 (238)
T TIGR02393 99 ELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLE-TL 177 (238)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHHHHHHHHHHHHHHHHH-hC
Confidence 356677899999999999999987655433222222221 1111233333332111 11111 111222222222 11
Q ss_pred cCCCChHHHHHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q psy6534 238 VPGRSPISVAAAAIYMASQAS-SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHAS 290 (309)
Q Consensus 238 ~~Gr~P~~iaaAaiyla~~~~-~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~ 290 (309)
+|.--- +|.+-.-+. ....|++|||+.+|+|..+|++..+...+...
T Consensus 178 ----~~~er~--vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr 225 (238)
T TIGR02393 178 ----TERERK--VLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLR 225 (238)
T ss_pred ----CHHHHH--HHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 111111 111111112 25789999999999999999998877654443
No 94
>KOG0654|consensus
Probab=91.98 E-value=1.5 Score=40.71 Aligned_cols=137 Identities=18% Similarity=0.173 Sum_probs=91.3
Q ss_pred hHHHHHHHHHHHHhcCC-CccHHHHHHHhcc--cHHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhC-CCCHHHHHHH
Q psy6534 150 DAIASACLYIACRQEGV-PRTFKEICAVSKI--SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNL-SLPNMVQKAA 225 (309)
Q Consensus 150 ~~vaaAcly~acR~~~~-~~tl~eia~~~~~--~~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L-~l~~~~~~~a 225 (309)
+.+--+|-+++.+-+.. +..+.|+...+.. ...++.+....++..|.+.+-......|+.++...- +..-.+...+
T Consensus 180 ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~~~~~~e~~~ 259 (359)
T KOG0654|consen 180 QLVGISAMLIASKYEEIKEPRVEEFCYITDNTYTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQTPELQVEPLA 259 (359)
T ss_pred HHhCcccceeeccchhhcchHHHHHHhhhhhhhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcchhHHHHHHH
Confidence 34555666677776654 5667788776643 355566666667777777665566778888874332 2223344555
Q ss_pred HHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 226 THIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 226 ~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
-.+.+...-.-...--.|+-|||||+++|--..+..-+-..+.+.+|++..+++.....|.
T Consensus 260 ~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~ 320 (359)
T KOG0654|consen 260 NYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH 320 (359)
T ss_pred HHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence 5555543222223456799999999999988887666677788889999988888888877
No 95
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=91.93 E-value=3.1 Score=29.00 Aligned_cols=26 Identities=19% Similarity=0.322 Sum_probs=23.9
Q ss_pred CCCHHHHHHHhCC-CHHHHHHHHHHHH
Q psy6534 261 KRSQKEIGDIAGV-AEVTIRQSYKLMY 286 (309)
Q Consensus 261 ~~~~~~ia~~~~v-s~~ti~~~~kei~ 286 (309)
+.++.+||..+|. +...+.+.||+..
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 7899999999999 9999999998865
No 96
>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=91.85 E-value=0.63 Score=29.63 Aligned_cols=30 Identities=20% Similarity=0.348 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+-..++++||+.+|+|..|+.+..++|.+.
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 445999999999999999999999999764
No 97
>PF13730 HTH_36: Helix-turn-helix domain
Probab=91.77 E-value=0.73 Score=30.22 Aligned_cols=26 Identities=23% Similarity=0.308 Sum_probs=24.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+++.||+.+|+++.||++..++|.+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 79999999999999999999999864
No 98
>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=91.64 E-value=0.12 Score=37.86 Aligned_cols=31 Identities=19% Similarity=0.329 Sum_probs=25.2
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
....||.||...+ .-...|-..|..||.++.
T Consensus 34 a~y~CpfCgk~~v-kR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTV-KRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCce-EEEeeEEEEcCCCCCEEe
Confidence 3568999998764 556799999999999873
No 99
>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=91.19 E-value=0.15 Score=35.40 Aligned_cols=29 Identities=14% Similarity=0.259 Sum_probs=20.9
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
...||.||...-. +......+|..||...
T Consensus 28 Sq~C~~CG~~~~~-~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc-ccccceEEcCCCCCEE
Confidence 3479999875432 3556688999999886
No 100
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=91.14 E-value=0.15 Score=38.22 Aligned_cols=31 Identities=16% Similarity=0.274 Sum_probs=23.3
Q ss_pred cccCCCCCCCCee--eeCCCCceecCCCCcccc
Q psy6534 5 KVCCYEHPDAPLI--EDYRAGDQICSECGLVVG 35 (309)
Q Consensus 5 ~~~Cp~C~~~~~v--~D~~~G~~vC~~CG~V~~ 35 (309)
...||+||...+. .|...+..+|..||+.-+
T Consensus 21 ~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 21 IFECPRCGKVSISVKIKKNIAIITCGNCGLYTE 53 (99)
T ss_pred EeECCCCCCeEeeeecCCCcceEECCCCCCccC
Confidence 4579999964332 356778999999998863
No 101
>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=91.01 E-value=0.26 Score=31.48 Aligned_cols=21 Identities=29% Similarity=0.436 Sum_probs=19.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~k 283 (309)
|++|||+.+|||..|+.+.++
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 689999999999999998875
No 102
>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=90.96 E-value=0.22 Score=29.04 Aligned_cols=27 Identities=15% Similarity=0.212 Sum_probs=15.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
.-||.||+... .....-..+|.+||..
T Consensus 4 rfC~~CG~~t~-~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTK-PAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEE-E-SSSS-EEESSSS-E
T ss_pred cccCcCCcccc-CCCCcCEeECCCCcCE
Confidence 47999998643 3444568999999975
No 103
>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=90.91 E-value=0.77 Score=31.06 Aligned_cols=37 Identities=43% Similarity=0.518 Sum_probs=28.9
Q ss_pred CChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHH
Q psy6534 241 RSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQ 280 (309)
Q Consensus 241 r~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~ 280 (309)
|+|.-=-|=-||+. ++-.+++++||+.+||++.||++
T Consensus 5 Rsp~rdkA~e~y~~---~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 5 RSPNRDKAFEIYKE---SNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred CCcCHHHHHHHHHH---hCCCccHHHHHHHHCCCHHHHHH
Confidence 55555555566744 56789999999999999999975
No 104
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=90.79 E-value=14 Score=34.57 Aligned_cols=171 Identities=15% Similarity=0.140 Sum_probs=83.1
Q ss_pred HHHHHHHHHHHhcC---CC--HHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHH---------------------
Q psy6534 109 NAIREINSMADRIN---LT--KTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACR--------------------- 162 (309)
Q Consensus 109 ~~~~~I~~i~~~L~---Lp--~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR--------------------- 162 (309)
.-+..+..+|.++. ++ +-+.+.-..+++-+.....-+|.++.+.|.-.+.-+.+
T Consensus 137 ~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~~~ 216 (367)
T PRK09210 137 ANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN 216 (367)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHHHH
Confidence 34455556666652 22 23344444566666665555676676666666654431
Q ss_pred -----------hcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCC-ChHHHHHHHH-hhCCCCH-HH--HHHHH
Q psy6534 163 -----------QEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLI-TTGDFMSRFC-SNLSLPN-MV--QKAAT 226 (309)
Q Consensus 163 -----------~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~-~p~~~i~~~~-~~L~l~~-~~--~~~a~ 226 (309)
..+...|..|||..++++..++....+.-...+.++.+.. +....+..+. +.-..++ +. .....
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~ 296 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLK 296 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHHHH
Confidence 1233446778888888888888776543322222222111 1111122221 1111111 11 11111
Q ss_pred HHHHHhhhcCccCCCChHHHHHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 227 HIARKAVELDIVPGRSPISVAAAAIYMASQAS-SDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 227 ~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~-~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
..++.+.. .=.|.---.-.+++ -+. +.+.|++|||+.+|||...|++..+.-.
T Consensus 297 ~~l~~~l~-----~L~~rEr~Vl~lry--gl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al 350 (367)
T PRK09210 297 EQLEDVLD-----TLTDREENVLRLRF--GLDDGRTRTLEEVGKVFGVTRERIRQIEAKAL 350 (367)
T ss_pred HHHHHHHH-----hCCHHHHHHHHHHh--ccCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 12222221 11122111111111 111 3679999999999999999999876643
No 105
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.59 E-value=0.17 Score=33.75 Aligned_cols=26 Identities=15% Similarity=0.383 Sum_probs=12.4
Q ss_pred cCCCCCCCCeeeeC----CCCceecCCCCc
Q psy6534 7 CCYEHPDAPLIEDY----RAGDQICSECGL 32 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~----~~G~~vC~~CG~ 32 (309)
.||+||...+.... -...++|.+||+
T Consensus 29 ~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 29 PCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 46666544433321 122556666664
No 106
>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=90.34 E-value=2.8 Score=31.12 Aligned_cols=31 Identities=13% Similarity=0.335 Sum_probs=28.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...++++.|||+.+|++..|+.+..++|.+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3567999999999999999999999999875
No 107
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=90.29 E-value=0.19 Score=36.78 Aligned_cols=31 Identities=19% Similarity=0.333 Sum_probs=25.0
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
....||.|+...+ .-...|-..|..||.++.
T Consensus 35 a~y~CpfCgk~~v-kR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPKV-KRVGTGIWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCce-EEEEEEEEEcCCCCCEEe
Confidence 3568999987664 456799999999999874
No 108
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=90.16 E-value=13 Score=32.96 Aligned_cols=30 Identities=30% Similarity=0.327 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+++|||+.+|+|..+|++.........
T Consensus 220 e~~t~~EIA~~lgis~~~V~~~~~ral~kL 249 (257)
T PRK05911 220 EELVLKEIGKILGVSESRVSQIHSKALLKL 249 (257)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 568999999999999999999887655443
No 109
>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=90.00 E-value=0.42 Score=31.92 Aligned_cols=31 Identities=32% Similarity=0.424 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.-.++.+++|+.+|||+.|||+-+.+|.+.-
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3568999999999999999999999987653
No 110
>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=89.91 E-value=1.4 Score=29.89 Aligned_cols=30 Identities=20% Similarity=0.280 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
..++++.+||+.+|++..|+.+.++.|.+.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 356899999999999999999999999875
No 111
>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=89.86 E-value=0.76 Score=32.22 Aligned_cols=30 Identities=27% Similarity=0.327 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.++++++||+.+|+|..|+.+..++|.+.-
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g 56 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEG 56 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTT
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 468999999999999999999999998753
No 112
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=89.79 E-value=0.57 Score=30.77 Aligned_cols=36 Identities=8% Similarity=0.158 Sum_probs=30.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
.....+..++|..+||+++|+.+.++++.+...+..
T Consensus 16 LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 346689999999999999999999999987654433
No 113
>KOG0794|consensus
Probab=89.44 E-value=0.65 Score=40.05 Aligned_cols=58 Identities=16% Similarity=0.188 Sum_probs=46.2
Q ss_pred hHHHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCC
Q psy6534 204 TGDFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDK 261 (309)
Q Consensus 204 p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~ 261 (309)
-..+|..++++|++...+..+|.-.+++..-..-..+-.|.-+|..|||+||+.-..+
T Consensus 44 ~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~ 101 (264)
T KOG0794|consen 44 MANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP 101 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence 3567888889999999888888877776654444678899999999999999865443
No 114
>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=89.31 E-value=0.88 Score=29.25 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
....|+.|||+.+|+|..|+++..+...+.
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 567899999999999999999998876543
No 115
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=89.29 E-value=0.61 Score=29.35 Aligned_cols=28 Identities=21% Similarity=0.219 Sum_probs=18.6
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy6534 256 QASSDKRSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 256 ~~~~~~~~~~~ia~~~~vs~~ti~~~~k 283 (309)
.+.....++.+||+.+|++.+||.+-.+
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 3445678999999999999999987654
No 116
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=89.27 E-value=1.8 Score=30.28 Aligned_cols=71 Identities=17% Similarity=0.260 Sum_probs=43.6
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCccHHHHHHHhcc-cHHHHHHHHHHH
Q psy6534 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSKI-SKKEIGRCFKLI 191 (309)
Q Consensus 114 I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~tl~eia~~~~~-~~~~i~~~~~~l 191 (309)
|.++|..+|++.....+ +|+.........-.....+.-|+-|+. ++ +.++.|+|..+|+ +...+.+.|++.
T Consensus 4 ~~~la~~~~~s~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~---~~-~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 4 LEDLAEALGMSPRHLQR---LFKKETGTTPKQYLRDRRLERARRLLR---DT-DLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHhCCCHHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHH---cC-CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 67888999998654433 344432221111111223333444443 22 8999999999999 999998888755
No 117
>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=88.94 E-value=0.25 Score=31.32 Aligned_cols=28 Identities=21% Similarity=0.223 Sum_probs=19.6
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy6534 256 QASSDKRSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 256 ~~~~~~~~~~~ia~~~~vs~~ti~~~~k 283 (309)
+++....+..+||+.+|||..||.+..+
T Consensus 16 ~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 16 ELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 4444558999999999999999977653
No 118
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.93 E-value=0.25 Score=29.73 Aligned_cols=29 Identities=28% Similarity=0.528 Sum_probs=20.9
Q ss_pred ccCCCCCCCCeeeeC----CCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDY----RAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~----~~G~~vC~~CG~V~ 34 (309)
..||.|+..--|.|. ....+-|+.||.+.
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 589999876444442 34478999999874
No 119
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=88.89 E-value=19 Score=33.08 Aligned_cols=115 Identities=12% Similarity=0.144 Sum_probs=58.7
Q ss_pred cCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCC-C-hHHHHHHHHhhCCCCHHHHH--HHHHHHHHhhhcCccC
Q psy6534 164 EGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLI-T-TGDFMSRFCSNLSLPNMVQK--AATHIARKAVELDIVP 239 (309)
Q Consensus 164 ~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~-~-p~~~i~~~~~~L~l~~~~~~--~a~~i~~~~~~~~l~~ 239 (309)
.|...|..|||..++++..++..+.+...+.+.++.+.. + ...+..-+.+.-.-|.+... .....+..+.+ .+
T Consensus 181 ~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~~~pe~~~~~~~~~~~l~~al~-~L-- 257 (317)
T PRK07405 181 LGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSLQLDLERLME-DL-- 257 (317)
T ss_pred hCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCCCCHHHHHHHHHHHHHHHHHHH-cC--
Confidence 345567889999999999998887665544333332211 1 11222222221111222211 11222333322 11
Q ss_pred CCChHHHHHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 240 GRSPISVAAAAIYMASQAS-SDKRSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 240 Gr~P~~iaaAaiyla~~~~-~~~~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
.|.-= .+|.+-.-+. +.+.|++|||+.+|+|+.+|++..+.-
T Consensus 258 --~~rer--~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rA 300 (317)
T PRK07405 258 --TPQQK--EVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREA 300 (317)
T ss_pred --CHHHH--HHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 12111 1111111122 367999999999999999998886553
No 120
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=88.61 E-value=0.81 Score=28.72 Aligned_cols=30 Identities=17% Similarity=0.298 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.++.++.++|+.+|++..|+.+..+.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357899999999999999999999999875
No 121
>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=88.56 E-value=0.8 Score=33.53 Aligned_cols=34 Identities=21% Similarity=0.279 Sum_probs=29.1
Q ss_pred HHH-hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 254 ASQ-ASSDKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 254 a~~-~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
+++ ++....|+++|++.+|+|..||.+.-+.|..
T Consensus 41 va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 41 VAKELLDEGKSYREIAEETGVSIATITRVSRCLKY 75 (87)
T ss_dssp HHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence 344 6777899999999999999999999888864
No 122
>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=88.50 E-value=1.7 Score=31.89 Aligned_cols=39 Identities=23% Similarity=0.271 Sum_probs=32.9
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHhh
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAG-VAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~-vs~~ti~~~~kei~~~~ 289 (309)
.++|++-+.. ..+..+|+..+| .+.+|+...++.+.+..
T Consensus 34 ia~yl~~~~~--~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~ 73 (90)
T cd06571 34 IAMYLARELT--GLSLPEIGRAFGGRDHSTVLHAVRKIEELL 73 (90)
T ss_pred HHHHHHHHHh--CCCHHHHHHHhCCCCHhHHHHHHHHHHHHH
Confidence 4578887765 568999999999 99999999999987654
No 123
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=88.46 E-value=0.94 Score=29.78 Aligned_cols=29 Identities=28% Similarity=0.450 Sum_probs=26.1
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
..+ +.+++|+.+|+|..|+++.++.|.+.
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 345 89999999999999999999999875
No 124
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.39 E-value=0.37 Score=29.74 Aligned_cols=27 Identities=19% Similarity=0.267 Sum_probs=18.9
Q ss_pred cCCCCCCCCeee--------e-CCCCceecCCCCcc
Q psy6534 7 CCYEHPDAPLIE--------D-YRAGDQICSECGLV 33 (309)
Q Consensus 7 ~Cp~C~~~~~v~--------D-~~~G~~vC~~CG~V 33 (309)
.||.||....++ | +.+--.+|.+||..
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 699999776443 1 23447899999964
No 125
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=88.21 E-value=0.47 Score=32.32 Aligned_cols=28 Identities=14% Similarity=0.154 Sum_probs=20.0
Q ss_pred ccCCCCCCCCeeeeCCCC--ceecCCCCcc
Q psy6534 6 VCCYEHPDAPLIEDYRAG--DQICSECGLV 33 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G--~~vC~~CG~V 33 (309)
-.||.||...+..-...| ..+|..||..
T Consensus 7 KPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 7 KPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred cCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 379999987654433344 5789999975
No 126
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.17 E-value=0.18 Score=38.80 Aligned_cols=35 Identities=20% Similarity=0.287 Sum_probs=25.1
Q ss_pred CCcccCCCCCCCCeeeeCCCCceecCCCCccccCc
Q psy6534 3 INKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDR 37 (309)
Q Consensus 3 ~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~ 37 (309)
|-.-.||+||...+..-.-.=.-.|..||.=+..+
T Consensus 19 Gl~grCP~CGeGrLF~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 19 GLRGRCPRCGEGRLFRGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred HhcCCCCCCCCchhhhhhcccCchhhhccccccCC
Confidence 34557999998877554555577899999766433
No 127
>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=88.05 E-value=0.49 Score=37.96 Aligned_cols=29 Identities=24% Similarity=0.382 Sum_probs=19.6
Q ss_pred ccCCCCCCCC-eeeeC---CCCcee-----cCCCCccc
Q psy6534 6 VCCYEHPDAP-LIEDY---RAGDQI-----CSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~-~v~D~---~~G~~v-----C~~CG~V~ 34 (309)
|.||+||..+ -|.|. +.|..| |.+||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 6899998753 34453 566555 99999543
No 128
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=88.03 E-value=16 Score=34.47 Aligned_cols=178 Identities=11% Similarity=0.061 Sum_probs=86.6
Q ss_pred HHHHHHHHHHHHHHHHhcCCC--HHHHHHHHHHHHHHhcCC------CCC-CCch----hHHHHHHHHHHHHhcCCCccH
Q psy6534 104 DRALLNAIREINSMADRINLT--KTIVDRANNLFKQVHDGK------NLK-GRSN----DAIASACLYIACRQEGVPRTF 170 (309)
Q Consensus 104 ~~~l~~~~~~I~~i~~~L~Lp--~~v~e~A~~~~~~~~~~~------~~~-gr~~----~~vaaAcly~acR~~~~~~tl 170 (309)
+--+++++-.+-.-+.++.-. ..+...|.-+.+.....- .++ +++. ..+--+.--+. ...|...|.
T Consensus 164 eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~-~~lgr~Pt~ 242 (373)
T PRK07406 164 QDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLS-QEFGRKPTE 242 (373)
T ss_pred HHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHH-HHhCCCCCH
Confidence 334577777777777877654 356677776666554321 111 1111 11111111122 234555689
Q ss_pred HHHHHHhcccHHHHHHHHHHHHHHhcccCCC--CChHHHHHHHHhhCCCCHHHH--HHHHHHHHHhhhcCccCCCChHHH
Q psy6534 171 KEICAVSKISKKEIGRCFKLILKALETSVDL--ITTGDFMSRFCSNLSLPNMVQ--KAATHIARKAVELDIVPGRSPISV 246 (309)
Q Consensus 171 ~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~--~~p~~~i~~~~~~L~l~~~~~--~~a~~i~~~~~~~~l~~Gr~P~~i 246 (309)
.+||..++++..++..........+.++.+. .+...+..-+.+.-.-+.+.. ..-...+..+.. .+ .|.--
T Consensus 243 ~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~~pee~~~~~~~~~~L~~aL~--~L---~~rEr 317 (373)
T PRK07406 243 EEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDDVAKNLLREDLEGVLA--TL---SPRER 317 (373)
T ss_pred HHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCCCHHHHHHHHHHHHHHHHHHH--cC---CHHHH
Confidence 9999999999999976644322222222221 111122222212211122111 111111222221 11 11111
Q ss_pred HHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 247 AAAAIYMASQAS-SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 247 aaAaiyla~~~~-~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
- +|.+-.-+. +.+.|+++||+.+|||..+|++..+.-.+..
T Consensus 318 ~--IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KL 359 (373)
T PRK07406 318 D--VLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKL 359 (373)
T ss_pred H--HHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 1 111111112 3478999999999999999999887755443
No 129
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=87.68 E-value=1.3 Score=28.62 Aligned_cols=25 Identities=28% Similarity=0.423 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
...++++||+.+|||..|+++.++.
T Consensus 26 ~~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 26 ESRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3489999999999999999998875
No 130
>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=87.64 E-value=2.9 Score=34.71 Aligned_cols=29 Identities=21% Similarity=0.216 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+++|+++||+.+|+++.|+.+..++|.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 67899999999999999999999999876
No 131
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=87.54 E-value=1.1 Score=36.96 Aligned_cols=32 Identities=9% Similarity=0.156 Sum_probs=28.4
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.+-+.+..+||+.+|+|+.|+++|++.|.+..
T Consensus 25 ~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 25 KDGRISNVELSKRVGLSPTPCLERVRRLERQG 56 (164)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 35678999999999999999999999998754
No 132
>PRK02935 hypothetical protein; Provisional
Probab=87.51 E-value=0.48 Score=35.53 Aligned_cols=41 Identities=17% Similarity=0.306 Sum_probs=25.7
Q ss_pred CCCcccCCCCCCCCeeeeCCCCceecCCCCccccCcccccCCCcccc
Q psy6534 2 NINKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTF 48 (309)
Q Consensus 2 ~~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f 48 (309)
+.-+..||+|++..=+. --...|..|+.-+ .+|.+.|=.+|
T Consensus 67 kavqV~CP~C~K~TKmL---GrvD~CM~C~~PL---TLd~~legkef 107 (110)
T PRK02935 67 KAVQVICPSCEKPTKML---GRVDACMHCNQPL---TLDRSLEGKEF 107 (110)
T ss_pred cceeeECCCCCchhhhc---cceeecCcCCCcC---CcCccccccCc
Confidence 34577899998764222 1255899999776 45555443334
No 133
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=87.49 E-value=4.3 Score=35.85 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=26.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+|++||++.+|||++.+.+..+......
T Consensus 210 ~eelt~kEI~~~LgISes~VSql~kkai~kL 240 (247)
T COG1191 210 KEELTQKEIAEVLGISESRVSRLHKKAIKKL 240 (247)
T ss_pred HhccCHHHHHHHhCccHHHHHHHHHHHHHHH
Confidence 3569999999999999999999888765443
No 134
>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=87.43 E-value=0.61 Score=31.24 Aligned_cols=32 Identities=22% Similarity=0.299 Sum_probs=21.2
Q ss_pred CCcccCCCCCCCC-ee-e-eCCCCceecCCCCccc
Q psy6534 3 INKVCCYEHPDAP-LI-E-DYRAGDQICSECGLVV 34 (309)
Q Consensus 3 ~~~~~Cp~C~~~~-~v-~-D~~~G~~vC~~CG~V~ 34 (309)
++..+||.|+..+ +. + +...-..-|..||+--
T Consensus 7 IAGA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 7 IAGAVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred eccccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 3566899998765 22 2 3333357899999763
No 135
>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=87.33 E-value=0.36 Score=34.90 Aligned_cols=31 Identities=19% Similarity=0.195 Sum_probs=16.2
Q ss_pred cccCCCCCCC-Cee--ee--CCCCceecCCCCcccc
Q psy6534 5 KVCCYEHPDA-PLI--ED--YRAGDQICSECGLVVG 35 (309)
Q Consensus 5 ~~~Cp~C~~~-~~v--~D--~~~G~~vC~~CG~V~~ 35 (309)
...||.|+.. .+. .| ...|.+.|..||...+
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQ 57 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEESSS--EEE
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEE
Confidence 3579999844 333 34 4578999999998763
No 136
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=87.25 E-value=3.7 Score=34.67 Aligned_cols=119 Identities=15% Similarity=0.224 Sum_probs=66.7
Q ss_pred hhHHHHHHHHHHHHhcCCC-ccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhh--CCCCHHHHHHH
Q psy6534 149 NDAIASACLYIACRQEGVP-RTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSN--LSLPNMVQKAA 225 (309)
Q Consensus 149 ~~~vaaAcly~acR~~~~~-~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~--L~l~~~~~~~a 225 (309)
...++=|+||++ +-| +++.+++..++++..++..+...|.+.....-..+. |..+... |...++.....
T Consensus 5 ~~~~iEA~LF~s----g~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~----i~~~~~~y~l~tk~e~~~~v 76 (188)
T PRK00135 5 YKSIIEALLFVS----GEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLK----LIEFNDVYKLVTKEENADYL 76 (188)
T ss_pred HHHHHHHHHHHc----CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEE----EEEECCEEEEEEcHHHHHHH
Confidence 456777888874 666 999999999999998888888888776542100000 0000111 11122222222
Q ss_pred HHHHHHhhhcCccCCCChHHHHHHHH-HHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 226 THIARKAVELDIVPGRSPISVAAAAI-YMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 226 ~~i~~~~~~~~l~~Gr~P~~iaaAai-yla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
..++. .+.|..+--|++ -||.-.++.++|..+|++..|++. ....++|.+
T Consensus 77 ~~~~~---------~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~---~~ii~~L~~ 127 (188)
T PRK00135 77 QKLVK---------TPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNS---DGALQTLLA 127 (188)
T ss_pred HHHhc---------ccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence 22211 111112222222 234444568999999999999997 344555443
No 137
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=86.98 E-value=0.86 Score=35.73 Aligned_cols=31 Identities=26% Similarity=0.380 Sum_probs=26.7
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
|.++ +.+++|..+||.+.|++++|++|.+..
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~eG 63 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELEREG 63 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 4444 689999999999999999999998753
No 138
>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=86.90 E-value=0.47 Score=27.78 Aligned_cols=24 Identities=29% Similarity=0.403 Sum_probs=16.4
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGL 32 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~ 32 (309)
.|.+||... .+.....+-|.+||.
T Consensus 2 ~C~~Cg~~~--~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEV--ELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE---BSTSSTSSBSSSS-
T ss_pred CCCcCCCee--EcCCCCcEECCcCCC
Confidence 588898753 344566788999985
No 139
>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=86.87 E-value=2.9 Score=27.53 Aligned_cols=27 Identities=11% Similarity=0.263 Sum_probs=23.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
.+++.|+|+.+|||.+|+..+.+.-..
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 478999999999999999888877554
No 140
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=86.83 E-value=0.31 Score=40.79 Aligned_cols=33 Identities=21% Similarity=0.329 Sum_probs=21.7
Q ss_pred cccCCCCCCCCeeee--CCCC---ceecCCCCccccCc
Q psy6534 5 KVCCYEHPDAPLIED--YRAG---DQICSECGLVVGDR 37 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D--~~~G---~~vC~~CG~V~~e~ 37 (309)
-+.||.||+..+... -..| .+-|.+||+|..+.
T Consensus 6 y~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~~~ 43 (201)
T COG1326 6 YIECPSCGSEEVSHEVIKERGREPLVRCEECGTVHPAI 43 (201)
T ss_pred EEECCCCCcchhhHHHHHhcCCceEEEccCCCcEeece
Confidence 368999995444211 1123 58899999998553
No 141
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.81 E-value=0.59 Score=30.80 Aligned_cols=31 Identities=26% Similarity=0.443 Sum_probs=23.6
Q ss_pred CCCCcccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 1 MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
|+-....|+.||.. +.| ...-+||..||.+.
T Consensus 1 ~~~~~~~C~~Cg~~--~~~-~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 1 MNYEGCKCPVCGKK--FKD-GDDIVVCPECGAPY 31 (54)
T ss_pred CCccCccChhhCCc--ccC-CCCEEECCCCCCcc
Confidence 67777899999874 322 24589999999986
No 142
>PRK05949 RNA polymerase sigma factor; Validated
Probab=86.76 E-value=26 Score=32.33 Aligned_cols=170 Identities=12% Similarity=0.115 Sum_probs=82.3
Q ss_pred HHHHHHHHHHHHhc---CCC--HHHHHHHHHHHHHHhcCCCCCCCchhHHHHH-------------------------HH
Q psy6534 108 LNAIREINSMADRI---NLT--KTIVDRANNLFKQVHDGKNLKGRSNDAIASA-------------------------CL 157 (309)
Q Consensus 108 ~~~~~~I~~i~~~L---~Lp--~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaA-------------------------cl 157 (309)
..-+..+..+|.++ +++ +-+.|.-..+++.+.....-+|.++.+.|.- ++
T Consensus 98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~~ 177 (327)
T PRK05949 98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKL 177 (327)
T ss_pred HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHHH
Confidence 34455666677665 233 3344445567777665555566544333331 11
Q ss_pred HHHH-------HhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCC--ChHHHHHHHHhhCCCCHHHH--HHHH
Q psy6534 158 YIAC-------RQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLI--TTGDFMSRFCSNLSLPNMVQ--KAAT 226 (309)
Q Consensus 158 y~ac-------R~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~--~p~~~i~~~~~~L~l~~~~~--~~a~ 226 (309)
...- ...+...+..|||..++++..++......-...+.++.+.- ....+..-+.+.-.-|++.. ....
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~~~pe~~~~~~~~~ 257 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQELLR 257 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCCCCHHHHHHHHHHH
Confidence 1111 12345667889999999999988776543333222222211 11112221111111112111 1112
Q ss_pred HHHHHhhhcCccCCCChHHHHHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 227 HIARKAVELDIVPGRSPISVAAAAIYMASQAS-SDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 227 ~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~-~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
..+..+.. .+ .|.-- .+|.+-.-+. +.+.|++|||+.+|+|..+|++....
T Consensus 258 ~~L~~~L~-~L----~~rer--~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~r 309 (327)
T PRK05949 258 QDLNNLLA-EL----TPQQR--EVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQ 309 (327)
T ss_pred HHHHHHHH-hC----CHHHH--HHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 22222222 11 11111 2222222122 35799999999999999999887654
No 143
>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=86.71 E-value=1.1 Score=26.22 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=21.9
Q ss_pred CccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 167 PRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 167 ~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
|.|-.|||+.+|+..+.+.+.++++.+
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 678899999999999999999998865
No 144
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=86.55 E-value=9.6 Score=36.70 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=40.1
Q ss_pred ccCCCChHHHHHH---HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 237 IVPGRSPISVAAA---AIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 237 l~~Gr~P~~iaaA---aiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+..+++...++.| |+|++-++.+. +..+|++.+|.+.+||...++.|.+.
T Consensus 362 l~s~~R~~~i~~aR~iamyl~r~~~~~--s~~~Ig~~fgr~hstV~~a~~~i~~~ 414 (440)
T PRK14088 362 ILSNSRNVKALLARRIGMYVAKNYLGS--SLRTIAEKFNRSHPVVVDSVKKVKDS 414 (440)
T ss_pred HhCCCCCccccHHHHHHHHHHHHHhCC--CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4444455667767 89999775554 99999999999999999999999874
No 145
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=86.55 E-value=0.39 Score=32.01 Aligned_cols=27 Identities=26% Similarity=0.385 Sum_probs=21.7
Q ss_pred CCCCcccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 1 MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
|.+...+|+.||...+ ..+|..||...
T Consensus 1 Mks~mr~C~~CgvYTL-------k~~CP~CG~~t 27 (56)
T PRK13130 1 MKSKIRKCPKCGVYTL-------KEICPVCGGKT 27 (56)
T ss_pred CCccceECCCCCCEEc-------cccCcCCCCCC
Confidence 7777889999997554 67899999664
No 146
>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=86.46 E-value=0.7 Score=32.44 Aligned_cols=32 Identities=19% Similarity=0.349 Sum_probs=23.0
Q ss_pred CCcccCCCCCCCC---eeeeCCCCceecCCCCccc
Q psy6534 3 INKVCCYEHPDAP---LIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 3 ~~~~~Cp~C~~~~---~v~D~~~G~~vC~~CG~V~ 34 (309)
+++.+||.|+..+ +..+...-..-|-.||+.-
T Consensus 6 IAGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 6 IAGAVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred ecCccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 4567899998775 2235445577899999874
No 147
>PRK05978 hypothetical protein; Provisional
Probab=86.44 E-value=0.55 Score=37.98 Aligned_cols=31 Identities=16% Similarity=0.336 Sum_probs=22.8
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
..+||.||...+..-.-.=..-|..||.-++
T Consensus 33 ~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred cCcCCCCCCCcccccccccCCCccccCCccc
Confidence 4689999988775444444667999997763
No 148
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.33 E-value=0.71 Score=30.93 Aligned_cols=9 Identities=33% Similarity=1.117 Sum_probs=4.3
Q ss_pred ceecCCCCc
Q psy6534 24 DQICSECGL 32 (309)
Q Consensus 24 ~~vC~~CG~ 32 (309)
.+.|.+||+
T Consensus 48 ~Y~CP~CGF 56 (59)
T PRK14890 48 PYTCPKCGF 56 (59)
T ss_pred ceECCCCCC
Confidence 444555543
No 149
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=86.25 E-value=1.5 Score=35.70 Aligned_cols=31 Identities=19% Similarity=0.185 Sum_probs=28.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+-+.+..+||+.+|+|+.|+++|++.|.+..
T Consensus 21 d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 21 NARTPYAELAKQFGVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4678999999999999999999999998754
No 150
>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=86.13 E-value=1.1 Score=30.40 Aligned_cols=30 Identities=23% Similarity=0.480 Sum_probs=25.0
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +..++|+.+|||..|++++++.|...
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 4567 89999999999999999999999765
No 151
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=86.03 E-value=0.88 Score=27.40 Aligned_cols=30 Identities=20% Similarity=0.434 Sum_probs=20.4
Q ss_pred CCCCcccCCCCCCCC-eeee--CCCC--ceecCCC
Q psy6534 1 MNINKVCCYEHPDAP-LIED--YRAG--DQICSEC 30 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~~-~v~D--~~~G--~~vC~~C 30 (309)
|....+.||.|+++. ++.. ...| .+.|.+|
T Consensus 1 Ma~i~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred CCcEeeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 666778999999987 5543 1233 5667776
No 152
>PRK12495 hypothetical protein; Provisional
Probab=86.02 E-value=0.53 Score=40.24 Aligned_cols=27 Identities=26% Similarity=0.557 Sum_probs=22.4
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccccC
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVVGD 36 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e 36 (309)
.|+.||.+-+ ...|.++|..|+.++.+
T Consensus 44 hC~~CG~PIp---a~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 44 HCDECGDPIF---RHDGQEFCPTCQQPVTE 70 (226)
T ss_pred hcccccCccc---CCCCeeECCCCCCcccc
Confidence 6999998744 44899999999999865
No 153
>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=85.94 E-value=0.49 Score=35.79 Aligned_cols=27 Identities=19% Similarity=0.479 Sum_probs=20.6
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccccC
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVVGD 36 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e 36 (309)
-||.||.- + .+..+.++|..||.+...
T Consensus 2 fC~~Cg~~-l--~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSL-M--TPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcc-c--ccCCCeEECcCCCCcccc
Confidence 59999874 2 344689999999998643
No 154
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=85.93 E-value=1.3 Score=27.22 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
..+.++.+||+.+|+|+..+.+.+++..
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3568999999999999999999998863
No 155
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=85.38 E-value=1.6 Score=27.86 Aligned_cols=27 Identities=26% Similarity=0.194 Sum_probs=18.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
..+.++||+.+|||..|+.+-.+...+
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 689999999999999999887766543
No 156
>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=85.35 E-value=0.17 Score=30.48 Aligned_cols=29 Identities=14% Similarity=0.271 Sum_probs=18.3
Q ss_pred ccCCCCCCC-CeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDA-PLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~-~~v~D~~~G~~vC~~CG~V~ 34 (309)
..||.||.. ++.+++-.-+-+|-.||.-+
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCee
Confidence 368888765 45566656677888887533
No 157
>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=85.35 E-value=2.2 Score=28.46 Aligned_cols=29 Identities=17% Similarity=0.324 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
..+++.+|++.++++..|+.+..+.|.+.
T Consensus 20 ~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 20 EELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp SGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34899999999999999999999999875
No 158
>PF14502 HTH_41: Helix-turn-helix domain
Probab=85.15 E-value=1.5 Score=28.08 Aligned_cols=28 Identities=21% Similarity=0.298 Sum_probs=25.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.+..|.++.++++..||+++++.|.+.-
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~g 34 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENG 34 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCC
Confidence 4789999999999999999999998654
No 159
>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=85.14 E-value=0.63 Score=28.51 Aligned_cols=33 Identities=21% Similarity=0.390 Sum_probs=21.9
Q ss_pred CCCCcccCCCCCCC-CeeeeCC-CCceecCCCCcc
Q psy6534 1 MNINKVCCYEHPDA-PLIEDYR-AGDQICSECGLV 33 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~-~~v~D~~-~G~~vC~~CG~V 33 (309)
|..=...|+.||.. .+..... .....|..||.-
T Consensus 1 Mp~Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 1 MPIYEYRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred CCCEEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 55556789999874 3333322 457789999973
No 160
>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=85.05 E-value=1.6 Score=31.49 Aligned_cols=39 Identities=21% Similarity=0.365 Sum_probs=29.8
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 251 IYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 251 iyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+|++..-.+.+++.++||+.+++++..+++..+.|.+.-
T Consensus 15 ~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~G 53 (83)
T PF02082_consen 15 LYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAG 53 (83)
T ss_dssp HHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCC
Confidence 455544334459999999999999999999999998753
No 161
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=85.04 E-value=1.4 Score=36.35 Aligned_cols=72 Identities=15% Similarity=0.172 Sum_probs=46.3
Q ss_pred HHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCcCCCCCCC
Q psy6534 225 ATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTPIH 304 (309)
Q Consensus 225 a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~~~~~~~~~~ 304 (309)
...+.+.+..+++. +--+..-|++| ++..|.|+.||++++|.|.+.+....|+|... .|...-|-+.+..+
T Consensus 12 Ie~fae~m~r~G~n---rtVG~iYgily----ls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~--~lV~~~~~~G~Rk~ 82 (177)
T COG1510 12 IEHFAETMSRWGIN---RTVGQIYGILY----LSRKPLTLDEIAEALGMSKSNVSMGLKKLQDW--NLVKKVFEKGDRKD 82 (177)
T ss_pred HHHHHHHHHHhCCc---chHHHHhhhhe----ecCCCccHHHHHHHHCCCcchHHHHHHHHHhc--chHHhhhccCcchh
Confidence 34445555554442 22333444444 55789999999999999999999999999764 23333354444444
Q ss_pred C
Q psy6534 305 E 305 (309)
Q Consensus 305 ~ 305 (309)
|
T Consensus 83 ~ 83 (177)
T COG1510 83 Y 83 (177)
T ss_pred h
Confidence 3
No 162
>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=84.97 E-value=1.2 Score=33.07 Aligned_cols=30 Identities=27% Similarity=0.257 Sum_probs=25.7
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 257 ASSDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 257 ~~~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
+..-..||+|||+.+|||..||.+.-+.+.
T Consensus 51 Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 51 LLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 445679999999999999999998877765
No 163
>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=84.66 E-value=1.5 Score=30.61 Aligned_cols=65 Identities=17% Similarity=0.252 Sum_probs=41.3
Q ss_pred hHHHHHHHHhhCCCCHHHHHH---HHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhC-CCHHHHH
Q psy6534 204 TGDFMSRFCSNLSLPNMVQKA---ATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAG-VAEVTIR 279 (309)
Q Consensus 204 p~~~i~~~~~~L~l~~~~~~~---a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~-vs~~ti~ 279 (309)
|+..+..+|..+|++.+.... ...+. .|.. .++||+-+..+ .++.+|+..+| -+.+|+.
T Consensus 2 ~~~Ii~~Va~~~~v~~~~i~s~~R~~~i~------------~aR~---va~yL~r~~~~--~sl~~Ig~~fg~rdHstV~ 64 (70)
T PF08299_consen 2 IEDIIEAVAEYFGVSVEDIRSKSRKRKIV------------EARQ---VAMYLARELTG--LSLSEIGRYFGGRDHSTVI 64 (70)
T ss_dssp HHHHHHHHHHHTT--HHHHHSS---HHHH------------HHHH---HHHHHHHHHS-----HHHHHHHCTSSTHHHHH
T ss_pred HHHHHHHHHHHHCCCHHHHhCCCCChhhc------------chHH---HHHHHHHHHhC--CCHHHHHHHhCCCCHHHHH
Confidence 667788888888887643211 11111 0222 45788887764 78999999999 9999999
Q ss_pred HHHHHH
Q psy6534 280 QSYKLM 285 (309)
Q Consensus 280 ~~~kei 285 (309)
..++.+
T Consensus 65 ~a~~ki 70 (70)
T PF08299_consen 65 HAIRKI 70 (70)
T ss_dssp HHHHHH
T ss_pred HHHHhC
Confidence 988764
No 164
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=84.54 E-value=0.74 Score=29.08 Aligned_cols=27 Identities=22% Similarity=0.330 Sum_probs=19.2
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
..|..||...- .+ ..+.+-|.+||.=+
T Consensus 3 Y~C~~Cg~~~~-~~-~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRENE-IK-SKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCEee-cC-CCCceECCCCCceE
Confidence 46999987532 23 46789999999543
No 165
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=84.24 E-value=0.84 Score=30.58 Aligned_cols=29 Identities=28% Similarity=0.603 Sum_probs=20.3
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCccccCcc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRV 38 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~ 38 (309)
+...||.||...+ --.+|.+||+--+..+
T Consensus 26 ~l~~C~~CG~~~~------~H~vC~~CG~Y~gr~v 54 (57)
T PRK12286 26 GLVECPNCGEPKL------PHRVCPSCGYYKGREV 54 (57)
T ss_pred cceECCCCCCccC------CeEECCCCCcCCCEEe
Confidence 3457999987532 4789999997654433
No 166
>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=83.82 E-value=4.9 Score=25.36 Aligned_cols=28 Identities=18% Similarity=0.180 Sum_probs=20.9
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
.|. .++.+.|+..||..+||+++++...
T Consensus 14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 14 NGK-MSIRKAAKKYGVPRSTLRRRLRGKP 41 (45)
T ss_dssp TTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred hCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 444 9999999999999999998887644
No 167
>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=83.72 E-value=3.3 Score=26.25 Aligned_cols=32 Identities=16% Similarity=0.228 Sum_probs=27.1
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 257 ASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 257 ~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+..-+.+..||++.+|++.+|+....+.|.+.
T Consensus 11 L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 11 LSEGPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 34567899999999999999999999999875
No 168
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=83.71 E-value=12 Score=37.51 Aligned_cols=39 Identities=18% Similarity=0.266 Sum_probs=32.7
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.|+||+-++. ..++.+|+..+|-+..||...++.|.+..
T Consensus 559 iAMYL~r~lt--~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~ 597 (617)
T PRK14086 559 IAMYLCRELT--DLSLPKIGQQFGRDHTTVMHADRKIRALM 597 (617)
T ss_pred HHHHHHHHHc--CCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence 4589987755 46889999999999999999999987643
No 169
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=83.25 E-value=2.1 Score=29.19 Aligned_cols=56 Identities=13% Similarity=0.167 Sum_probs=31.9
Q ss_pred HHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCC-CCChHHHHHHHHhhCCCCHH
Q psy6534 161 CRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVD-LITTGDFMSRFCSNLSLPNM 220 (309)
Q Consensus 161 cR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~-~~~p~~~i~~~~~~L~l~~~ 220 (309)
-.++....|+.|++..++++...|.....- .++ .+| .+-...|+..||+.||++.+
T Consensus 4 ~~R~~~glsl~~va~~t~I~~~~l~aiE~~---~~~-~lp~~~y~rg~lr~Ya~~Lgld~~ 60 (62)
T PF13413_consen 4 EAREAKGLSLEDVAEETKISVSYLEAIENG---DFD-SLPSPVYARGYLRKYARFLGLDPD 60 (62)
T ss_dssp HHHHCTT--HHHHHHHCS--HHHHHHHHCT----GC-CSSSHHHHHHHHHHHHHHTT--HH
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHCc---Chh-hCCcHHHHHHHHHHHHHHhCcCcc
Confidence 345667899999999999998776433220 011 122 12346689999999999874
No 170
>PF12773 DZR: Double zinc ribbon
Probab=83.25 E-value=0.81 Score=29.47 Aligned_cols=11 Identities=36% Similarity=0.957 Sum_probs=5.5
Q ss_pred ceecCCCCccc
Q psy6534 24 DQICSECGLVV 34 (309)
Q Consensus 24 ~~vC~~CG~V~ 34 (309)
..+|..||..+
T Consensus 29 ~~~C~~Cg~~~ 39 (50)
T PF12773_consen 29 KKICPNCGAEN 39 (50)
T ss_pred CCCCcCCcCCC
Confidence 44555555443
No 171
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=83.08 E-value=0.9 Score=35.04 Aligned_cols=32 Identities=19% Similarity=0.380 Sum_probs=23.6
Q ss_pred ccCCCCCCCCee-eeCCCCceecCCCCccccCc
Q psy6534 6 VCCYEHPDAPLI-EDYRAGDQICSECGLVVGDR 37 (309)
Q Consensus 6 ~~Cp~C~~~~~v-~D~~~G~~vC~~CG~V~~e~ 37 (309)
.-||.||+--+. .|...+.++|..||+..+-.
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 469999875333 25567799999999987544
No 172
>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=82.93 E-value=0.89 Score=31.21 Aligned_cols=27 Identities=15% Similarity=0.383 Sum_probs=16.9
Q ss_pred cCCCCCCCCeeee--------------CCCC---ceecCCCCcc
Q psy6534 7 CCYEHPDAPLIED--------------YRAG---DQICSECGLV 33 (309)
Q Consensus 7 ~Cp~C~~~~~v~D--------------~~~G---~~vC~~CG~V 33 (309)
.||.||..+.-.+ -... .++|++||+.
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 6999987543222 1111 3689999976
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=82.85 E-value=1.2 Score=31.53 Aligned_cols=27 Identities=26% Similarity=0.281 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
...+.+|||+.+|+|+.||++.++.+.
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 457999999999999999999987643
No 174
>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=82.83 E-value=3.2 Score=28.58 Aligned_cols=31 Identities=10% Similarity=0.295 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+.+.+..++|+.+|+|..||+++.+.|.+..
T Consensus 11 ~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g 41 (69)
T TIGR00122 11 DNPFSGEKLGEALGMSRTAVNKHIQTLREWG 41 (69)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4467899999999999999999999997653
No 175
>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=82.65 E-value=6.1 Score=28.93 Aligned_cols=42 Identities=17% Similarity=0.166 Sum_probs=34.3
Q ss_pred HHHHHHHHhcCCCccHHHHHHHhc-ccHHHHHHHHHHHHHHhccc
Q psy6534 155 ACLYIACRQEGVPRTFKEICAVSK-ISKKEIGRCFKLILKALETS 198 (309)
Q Consensus 155 Acly~acR~~~~~~tl~eia~~~~-~~~~~i~~~~~~l~~~l~~~ 198 (309)
.+.|++-+.. ..|+.+|+..+| .+...+..+++++.+.++.+
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 4467775444 578999999998 99999999999999988754
No 176
>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=82.60 E-value=39 Score=32.43 Aligned_cols=164 Identities=12% Similarity=0.179 Sum_probs=0.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHhcCCCc------------------cHHHHHH
Q psy6534 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPR------------------TFKEICA 175 (309)
Q Consensus 114 I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~~~~~~------------------tl~eia~ 175 (309)
+.++|..++++...++.|..+++.+.-.|..-.- ..=|+.+=.+..+..- .+..|+.
T Consensus 116 ~~eia~~l~~~~~~ve~~l~~iq~leP~GIgAr~-----L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i~~ 190 (429)
T TIGR02395 116 LEEIADELEVSEEEVEKVLELIQRLDPAGVGARD-----LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRLAK 190 (429)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhcCCCCccCcCC-----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHHHH
Q ss_pred HhcccHHHHHHHHHHHHHHh----------------------------------cccCCCCChHHHHHHHHhhCCCCHHH
Q psy6534 176 VSKISKKEIGRCFKLILKAL----------------------------------ETSVDLITTGDFMSRFCSNLSLPNMV 221 (309)
Q Consensus 176 ~~~~~~~~i~~~~~~l~~~l----------------------------------~~~~~~~~p~~~i~~~~~~L~l~~~~ 221 (309)
.++++..++..++..|...- +...|.+.....-....+.-.-+ +.
T Consensus 191 ~l~is~~~v~~~~~~I~~L~P~Pg~~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~~-~~ 269 (429)
T TIGR02395 191 KLGLSEEELKEALDLIKSLSPKPGKEFADPEEVEYVIPDVIVTKKNGEWVVELNGRSLPELRINEEYFKLLKDAEKE-AA 269 (429)
T ss_pred HHCcCHHHHHHHHHHHhCCCCCCcccccCCCCCCccCCCEEEEEECCEEEEEEcCCCCceEEECHHHHHHHHhccch-HH
Q ss_pred HHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHH-----hCC----CCCCHHHHHHHhCCCHHHHHHHHH
Q psy6534 222 QKAATHIARKAVELDIVPGRSPISVAAAAIYMASQ-----ASS----DKRSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 222 ~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~-----~~~----~~~~~~~ia~~~~vs~~ti~~~~k 283 (309)
.+...+=++.+.-.--.-.++-.++--.+-.++-+ ..| .+.++++||+.+|++++||.++.+
T Consensus 270 ~~ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 270 AQYLKQKLKEARWLIKALEQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
No 177
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=82.59 E-value=0.48 Score=36.01 Aligned_cols=42 Identities=17% Similarity=0.258 Sum_probs=26.5
Q ss_pred CCcccCCCCCCCCeeeeCCCCceecCCCCccccCcccccCCCcccccC
Q psy6534 3 INKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSN 50 (309)
Q Consensus 3 ~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~ 50 (309)
.-+..||+|+...-+.- -..-|..|+.-+ .+|.+.|=..|++
T Consensus 67 av~V~CP~C~K~TKmLG---r~D~CM~C~~pL---TLd~~legkef~~ 108 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLG---RVDACMHCKEPL---TLDPSLEGKEFDE 108 (114)
T ss_pred ceeeECCCCCChHhhhc---hhhccCcCCCcC---ccCchhhcchhhH
Confidence 34678999998753321 135899999766 4555554444543
No 178
>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=82.52 E-value=1.1 Score=25.28 Aligned_cols=22 Identities=18% Similarity=0.299 Sum_probs=11.3
Q ss_pred cCCCCCCCCeeeeCCCCceecCC
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSE 29 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~ 29 (309)
.||.||+. ++.++.+-.+.|.+
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 49999864 66665555777764
No 179
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=82.46 E-value=6.4 Score=33.96 Aligned_cols=30 Identities=17% Similarity=0.192 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.++|+++||+.+|+++.|+.+..++|.+.-
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g 212 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSG 212 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 678999999999999999999999998653
No 180
>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=82.41 E-value=0.69 Score=30.86 Aligned_cols=26 Identities=27% Similarity=0.607 Sum_probs=18.5
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
+...||.||... ..-.+|.+||+.=.
T Consensus 25 ~l~~c~~cg~~~------~~H~vc~~cG~y~~ 50 (56)
T PF01783_consen 25 NLVKCPNCGEPK------LPHRVCPSCGYYKG 50 (56)
T ss_dssp SEEESSSSSSEE------STTSBCTTTBBSSS
T ss_pred ceeeeccCCCEe------cccEeeCCCCeECC
Confidence 445799998632 35789999996643
No 181
>PF15616 TerY-C: TerY-C metal binding domain
Probab=82.20 E-value=1.8 Score=34.18 Aligned_cols=29 Identities=17% Similarity=0.286 Sum_probs=17.0
Q ss_pred ccCCCCCCC-Ceee-e-------CCCCceecCCCCccc
Q psy6534 6 VCCYEHPDA-PLIE-D-------YRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~-~~v~-D-------~~~G~~vC~~CG~V~ 34 (309)
.-||+||.. .++. + ...++.+|.-||...
T Consensus 78 PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g 115 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEG 115 (131)
T ss_pred CCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCee
Confidence 469999875 2221 0 235566666666654
No 182
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=82.19 E-value=2.9 Score=26.87 Aligned_cols=28 Identities=21% Similarity=0.349 Sum_probs=24.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
..+.++||+.+|+|+.|+++..+.+.+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3689999999999999999998887654
No 183
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.13 E-value=0.41 Score=40.08 Aligned_cols=31 Identities=13% Similarity=0.201 Sum_probs=22.5
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
-..||.|+..-...|-.+....|..||.++.
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCCCCCe
Confidence 3469999865333355567899999999984
No 184
>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=82.05 E-value=3.1 Score=29.88 Aligned_cols=45 Identities=29% Similarity=0.337 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 150 DAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 150 ~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
+.-+-+.+|+|-...+.|.+.+|||+.++++...+.+.+..|.+.
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 344556778887777778999999999999999999999988773
No 185
>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=81.56 E-value=3.9 Score=32.37 Aligned_cols=45 Identities=24% Similarity=0.222 Sum_probs=37.5
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 149 NDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 149 ~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
.+.-+-+++|+|-+..+-|.+..+||+..+++..-+.+.+..|.+
T Consensus 7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~ 51 (135)
T TIGR02010 7 GRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRK 51 (135)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345566888998766667899999999999999999988888876
No 186
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=81.40 E-value=5.2 Score=27.66 Aligned_cols=37 Identities=8% Similarity=0.100 Sum_probs=29.4
Q ss_pred HHHHHhCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 252 YMASQASSD-KRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 252 yla~~~~~~-~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+......+. .++..+||+.+|++..++++....|.+.
T Consensus 12 L~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 12 LEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 333344455 4999999999999999999999888765
No 187
>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=81.34 E-value=1 Score=27.62 Aligned_cols=27 Identities=19% Similarity=0.263 Sum_probs=15.2
Q ss_pred cCCCCCCCCeee--------e-CCCCceecCCCCcc
Q psy6534 7 CCYEHPDAPLIE--------D-YRAGDQICSECGLV 33 (309)
Q Consensus 7 ~Cp~C~~~~~v~--------D-~~~G~~vC~~CG~V 33 (309)
.||.||..+.++ | ..+--++|.+||..
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 699999875332 1 12335789999953
No 188
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.28 E-value=1.1 Score=33.66 Aligned_cols=23 Identities=22% Similarity=0.444 Sum_probs=0.0
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.||.||..-+|+ ++-|.+||+-+
T Consensus 8 ~cPvcg~~~iVT-----eL~c~~~etTV 30 (122)
T COG3877 8 RCPVCGRKLIVT-----ELKCSNCETTV 30 (122)
T ss_pred CCCcccccceeE-----EEecCCCCceE
No 189
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=80.80 E-value=4.5 Score=29.02 Aligned_cols=35 Identities=6% Similarity=0.211 Sum_probs=30.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKL 292 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l 292 (309)
.+..++-.+|++.+|+|+.+|++..+.|.+.--++
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCce
Confidence 45689999999999999999999999999765433
No 190
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=80.41 E-value=42 Score=29.84 Aligned_cols=29 Identities=10% Similarity=0.299 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+++|||+.+|+|..||++..+...+.
T Consensus 230 ~~~t~~EIA~~lgis~~~V~~~~~ral~k 258 (264)
T PRK07122 230 ESMTQTQIAERVGISQMHVSRLLAKTLAR 258 (264)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 57899999999999999999987765544
No 191
>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=80.31 E-value=5 Score=26.08 Aligned_cols=34 Identities=24% Similarity=0.173 Sum_probs=28.2
Q ss_pred HhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHh
Q psy6534 162 RQEGVPRTFKEICAVSKISKKEIGRCFKLILKAL 195 (309)
Q Consensus 162 R~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l 195 (309)
..++-|+|..++|+.++++...|.+.++.|.+.+
T Consensus 10 ~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 10 LESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3456679999999999999999999999887655
No 192
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=80.25 E-value=41 Score=29.67 Aligned_cols=32 Identities=25% Similarity=0.293 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASK 291 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~ 291 (309)
...++++||+.+|+|..||+++.+.......+
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998776554433
No 193
>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=80.24 E-value=2.5 Score=28.06 Aligned_cols=30 Identities=23% Similarity=0.356 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.++||+..|+++.||+...+.|.+..
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 457889999999999999999999988763
No 194
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=80.22 E-value=3.4 Score=33.02 Aligned_cols=41 Identities=24% Similarity=0.297 Sum_probs=32.5
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+.||++..-.|..++.++||+..||++..+++.++.|...-
T Consensus 13 ~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~G 53 (141)
T PRK11014 13 ALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAG 53 (141)
T ss_pred HHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCC
Confidence 34455544445678899999999999999999999998753
No 195
>KOG3507|consensus
Probab=80.16 E-value=1 Score=29.98 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=17.3
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.|.+||..+.+- ....+-|.+||+=+
T Consensus 22 iCgdC~~en~lk--~~D~irCReCG~RI 47 (62)
T KOG3507|consen 22 ICGDCGQENTLK--RGDVIRCRECGYRI 47 (62)
T ss_pred Eecccccccccc--CCCcEehhhcchHH
Confidence 588888876543 23356799998643
No 196
>PHA02591 hypothetical protein; Provisional
Probab=80.13 E-value=2.7 Score=29.77 Aligned_cols=31 Identities=13% Similarity=0.265 Sum_probs=24.8
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy6534 253 MASQASSDKRSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 253 la~~~~~~~~~~~~ia~~~~vs~~ti~~~~k 283 (309)
+|-++.....++++||+.+|++..++++..+
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 3445556678999999999999999998654
No 197
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=80.12 E-value=0.71 Score=35.50 Aligned_cols=39 Identities=10% Similarity=0.335 Sum_probs=30.1
Q ss_pred CCCCcccCCCCCCCCeeeeCCCCceecCCCCccccCcccc
Q psy6534 1 MNINKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVID 40 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~id 40 (309)
|.+....|+.||...++.....+- .|..||..-.+..++
T Consensus 38 ~G~~~~~C~~Cg~~~~~~~SCk~R-~CP~C~~~~~~~W~~ 76 (111)
T PF14319_consen 38 LGFHRYRCEDCGHEKIVYNSCKNR-HCPSCQAKATEQWIE 76 (111)
T ss_pred CCcceeecCCCCceEEecCcccCc-CCCCCCChHHHHHHH
Confidence 456778899999888777655544 999999998766654
No 198
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=79.98 E-value=3.8 Score=31.52 Aligned_cols=61 Identities=16% Similarity=0.095 Sum_probs=44.6
Q ss_pred cHHHHHHHhcccHHHHHHHHHHHHHHhccc-CCCCChHHHHHHHHhhCCCCHHHHHHHHHHH
Q psy6534 169 TFKEICAVSKISKKEIGRCFKLILKALETS-VDLITTGDFMSRFCSNLSLPNMVQKAATHIA 229 (309)
Q Consensus 169 tl~eia~~~~~~~~~i~~~~~~l~~~l~~~-~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i~ 229 (309)
+++|++..+|++.-.++..+..|.+.|+.. .+..........+.++|.-++-..+.|.+++
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeIs~eeA~~~L 112 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEISVEEALEIL 112 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCCCHHHHHHHh
Confidence 689999999999999999999999999982 2333445566667777754444455565554
No 199
>PRK01381 Trp operon repressor; Provisional
Probab=79.87 E-value=1.6 Score=32.72 Aligned_cols=35 Identities=23% Similarity=0.239 Sum_probs=28.5
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 253 MASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 253 la~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
++..+..-..|++||++.+|||..||.+.-+.|..
T Consensus 47 I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~ 81 (99)
T PRK01381 47 IVEELLRGELSQREIKQELGVGIATITRGSNSLKT 81 (99)
T ss_pred HHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhcc
Confidence 44445566799999999999999999988887763
No 200
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=79.75 E-value=1.9 Score=33.11 Aligned_cols=31 Identities=16% Similarity=0.223 Sum_probs=26.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPHASK 291 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~ 291 (309)
.=+++++++.+|||-.|+|++..+|.+....
T Consensus 49 rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 49 RGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 3568899999999999999999998887655
No 201
>PRK04217 hypothetical protein; Provisional
Probab=79.56 E-value=2.2 Score=32.68 Aligned_cols=33 Identities=18% Similarity=0.278 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKL 292 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l 292 (309)
...+.+|||+.+|+|..||.+.++...+...+.
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456999999999999999999987765554433
No 202
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=79.55 E-value=18 Score=34.89 Aligned_cols=39 Identities=23% Similarity=0.295 Sum_probs=32.7
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHh-CCCHHHHHHHHHHHHHhh
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIA-GVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~-~vs~~ti~~~~kei~~~~ 289 (309)
.|+|++-++.+ .++.+|+..+ |-+.+|+...++.+.+..
T Consensus 392 iamyl~~~~~~--~s~~~Ig~~fg~rdhstV~~a~~~i~~~~ 431 (450)
T PRK00149 392 IAMYLAKELTD--LSLPEIGRAFGGRDHTTVLHAVRKIEKLL 431 (450)
T ss_pred HHHHHHHHhcC--CCHHHHHHHcCCCCHhHHHHHHHHHHHHH
Confidence 45899887765 4899999999 599999999999987653
No 203
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=79.46 E-value=60 Score=31.06 Aligned_cols=174 Identities=13% Similarity=0.131 Sum_probs=87.3
Q ss_pred HHHHHHHHHHHHHHHHhc---CCC--HHHHHHHHHHHHHHhcCCCCCCCchhHHHH-----H-HHHHH------------
Q psy6534 104 DRALLNAIREINSMADRI---NLT--KTIVDRANNLFKQVHDGKNLKGRSNDAIAS-----A-CLYIA------------ 160 (309)
Q Consensus 104 ~~~l~~~~~~I~~i~~~L---~Lp--~~v~e~A~~~~~~~~~~~~~~gr~~~~vaa-----A-cly~a------------ 160 (309)
++-+..-+..+..+|.++ ++. +-+.+-...+++-+......+|.++.+.+- + .-+++
T Consensus 178 e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i 257 (415)
T PRK07598 178 EHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHI 257 (415)
T ss_pred HHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHH
Confidence 333444455666677665 222 334555556777776666666666544443 1 11121
Q ss_pred -------H-------HhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCC--CChHHHHHHHHhhCCCCHHHH--
Q psy6534 161 -------C-------RQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDL--ITTGDFMSRFCSNLSLPNMVQ-- 222 (309)
Q Consensus 161 -------c-------R~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~--~~p~~~i~~~~~~L~l~~~~~-- 222 (309)
- ...|.+.+..|||..++++..++..........+-++.+. .....+..-+...-.-+++..
T Consensus 258 ~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee~~~~ 337 (415)
T PRK07598 258 TEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMR 337 (415)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCccccHHHhccCCCCCHHHHHHH
Confidence 0 1234567788999999999999988776554433332221 111112211111111112111
Q ss_pred HHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 223 KAATHIARKAVELDIVPGRSPISVAAAAIYMASQAS-SDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 223 ~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~-~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
......+..+... + +|.-- -+|.+-.-+. +.+.|++|||+.+|+|..+|++....
T Consensus 338 ~~l~~~L~~~L~~-L----~~reR--~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~r 393 (415)
T PRK07598 338 ESLQRDLQHLLAD-L----TSRER--DVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESK 393 (415)
T ss_pred HHHHHHHHHHHHh-C----CHHHH--HHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 1111222222211 1 12211 1111111112 36799999999999999999888655
No 204
>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=79.44 E-value=47 Score=29.81 Aligned_cols=124 Identities=10% Similarity=0.088 Sum_probs=74.5
Q ss_pred HHHHHHhcCC-CccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCCChHHHHHHHHhhCCCCHHHHHHHHHH-------
Q psy6534 157 LYIACRQEGV-PRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAATHI------- 228 (309)
Q Consensus 157 ly~acR~~~~-~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~L~l~~~~~~~a~~i------- 228 (309)
=|+..|+... ..|++++|..+|++.... +...++-+-+. +...+.+++..|+|++.-.+.-..+
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~~ak 87 (271)
T TIGR02147 16 DYYEERKKTDPAFSWRFFAEKAGFSSTSY------LNDIIKGKKNL--TKRMIPKFAEALGLDEKEAAYFEAMVNFGQAK 87 (271)
T ss_pred HHHHHHhccCcCcCHHHHHHHhCCCCHHH------HHHHHcCCCCC--CHHHHHHHHHHcCCCHHHHHHHHHHHHHhccC
Confidence 3666677655 599999999999875321 12222222211 2578899999999986433221111
Q ss_pred --------HHHhhh------cCccCCC---ChHHHHHHHHHHHHHhCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHh
Q psy6534 229 --------ARKAVE------LDIVPGR---SPISVAAAAIYMASQASSDKRSQKEIGDIAG--VAEVTIRQSYKLMYPH 288 (309)
Q Consensus 229 --------~~~~~~------~~l~~Gr---~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~--vs~~ti~~~~kei~~~ 288 (309)
.+.+.+ ..++.+. .-.+..-.+|.-...+.+..-+..+||+.++ ||...+++....|.+.
T Consensus 88 ~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~ 166 (271)
T TIGR02147 88 TDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERL 166 (271)
T ss_pred CHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHC
Confidence 111111 1112111 1224444555555556666667889999999 9999999999988765
No 205
>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=79.44 E-value=4.4 Score=26.05 Aligned_cols=28 Identities=29% Similarity=0.538 Sum_probs=24.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
..+.++||+.+++++.|++++.+.+.+.
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~ 42 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRK 42 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4699999999999999999998887654
No 206
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=79.40 E-value=5.5 Score=35.84 Aligned_cols=62 Identities=13% Similarity=0.077 Sum_probs=46.5
Q ss_pred CCCChHHHHHHHHhhCC-CCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHH
Q psy6534 200 DLITTGDFMSRFCSNLS-LPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTI 278 (309)
Q Consensus 200 ~~~~p~~~i~~~~~~L~-l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti 278 (309)
....|..++.++-+.++ |++...+.|.+|++. |..++ ..+.+++|+.+|||+.||
T Consensus 8 ~~~~~~~i~~~i~~~~~~Lt~~e~~Ia~yil~~-----------~~~v~-------------~~si~~lA~~~~vS~aTi 63 (292)
T PRK11337 8 ALPNGIGLGPYIRMKQEGLTPLESRVVEWLLKP-----------GDLSE-------------ATALKDIAEALAVSEAMI 63 (292)
T ss_pred cccCchhHHHHHHHHHhhcCHHHHHHHHHHHhC-----------HHHHH-------------hcCHHHHHHHhCCChHHH
Confidence 34568888888888885 888778888887743 33222 357789999999999999
Q ss_pred HHHHHHH
Q psy6534 279 RQSYKLM 285 (309)
Q Consensus 279 ~~~~kei 285 (309)
-+..|.|
T Consensus 64 ~Rf~kkL 70 (292)
T PRK11337 64 VKVAKKL 70 (292)
T ss_pred HHHHHHc
Confidence 8876654
No 207
>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=79.34 E-value=1.7 Score=32.83 Aligned_cols=31 Identities=19% Similarity=0.364 Sum_probs=20.2
Q ss_pred cccCCCCCCCCeeee------C--CC-Cc-eecCCCCcccc
Q psy6534 5 KVCCYEHPDAPLIED------Y--RA-GD-QICSECGLVVG 35 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D------~--~~-G~-~vC~~CG~V~~ 35 (309)
+..||+||......+ . .. .. .+|+.|+.-+.
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceee
Confidence 358999997654443 1 12 22 79999987663
No 208
>PHA02942 putative transposase; Provisional
Probab=79.30 E-value=1.4 Score=41.54 Aligned_cols=28 Identities=18% Similarity=0.288 Sum_probs=20.4
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
..||.||... .+.+.....|.+||+..+
T Consensus 326 q~Cs~CG~~~--~~l~~r~f~C~~CG~~~d 353 (383)
T PHA02942 326 VSCPKCGHKM--VEIAHRYFHCPSCGYEND 353 (383)
T ss_pred ccCCCCCCcc--CcCCCCEEECCCCCCEeC
Confidence 4799999753 233455789999999873
No 209
>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=79.29 E-value=3.3 Score=27.64 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=24.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+.++||+.++++..|+++.++.|.+.-
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G 53 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEG 53 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 599999999999999999999998753
No 210
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=79.28 E-value=30 Score=33.40 Aligned_cols=38 Identities=16% Similarity=0.267 Sum_probs=32.1
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHhh
Q psy6534 250 AIYMASQASSDKRSQKEIGDIAG-VAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 250 aiyla~~~~~~~~~~~~ia~~~~-vs~~ti~~~~kei~~~~ 289 (309)
|+||+-++.+ .++.+|++.+| -+.+|+-.+.+.|.+..
T Consensus 392 amyL~r~~t~--~sl~~IG~~FggrdHsTV~~a~~ki~~~~ 430 (450)
T PRK14087 392 AMYLTKEILN--HTLAQIGEEFGGRDHTTVINAERKIEKML 430 (450)
T ss_pred HHHHHHHHcC--CCHHHHHHHhCCCChHHHHHHHHHHHHHH
Confidence 5899988765 48999999997 99999999999887654
No 211
>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=79.25 E-value=1.4 Score=28.31 Aligned_cols=14 Identities=29% Similarity=0.593 Sum_probs=7.5
Q ss_pred eecCCCCccccCcc
Q psy6534 25 QICSECGLVVGDRV 38 (309)
Q Consensus 25 ~vC~~CG~V~~e~~ 38 (309)
..|..||+|.++..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 35666666654443
No 212
>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=79.19 E-value=46 Score=29.60 Aligned_cols=31 Identities=29% Similarity=0.252 Sum_probs=25.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+...|++|||+.+|||..+|++..+......
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kL 264 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNAMKKL 264 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4478999999999999999998877755443
No 213
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=79.11 E-value=4.3 Score=30.52 Aligned_cols=29 Identities=17% Similarity=0.234 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
-+.+..+||+.+|+++.|++++++.|.+.
T Consensus 16 ~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 16 ARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46899999999999999999999999875
No 214
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=79.07 E-value=53 Score=30.23 Aligned_cols=30 Identities=10% Similarity=0.145 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...|+++||+.+|+++.|++++...-....
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL 310 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEALRRL 310 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 568999999999999999999876654443
No 215
>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=79.05 E-value=2.5 Score=29.03 Aligned_cols=37 Identities=19% Similarity=0.358 Sum_probs=29.9
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 251 IYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 251 iyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+|.+.. ..-+.+..|||+.+|++..|+.+..+.|.+.
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 444433 3456899999999999999999999999875
No 216
>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=79.04 E-value=3.3 Score=26.84 Aligned_cols=28 Identities=25% Similarity=0.385 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
...+.+|||+.+|+|++|+++.+..-.+
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 4678999999999999999998876543
No 217
>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=78.81 E-value=3.3 Score=27.14 Aligned_cols=26 Identities=19% Similarity=0.217 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
...+++|.|..+||+..+++++.+++
T Consensus 14 fhlp~~eAA~~Lgv~~T~LKr~CR~~ 39 (52)
T PF02042_consen 14 FHLPIKEAAKELGVSVTTLKRRCRRL 39 (52)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 46899999999999999999998854
No 218
>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=78.69 E-value=8.1 Score=26.01 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=29.8
Q ss_pred HHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 157 LYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 157 ly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
+|-... .+.+.+..+||+.+++++..+..++++|.+
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 555554 788999999999999999999999998865
No 219
>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=78.67 E-value=1.8 Score=25.35 Aligned_cols=23 Identities=26% Similarity=0.440 Sum_probs=14.2
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGL 32 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~ 32 (309)
.|+.||- ++|.......|..||.
T Consensus 3 ~C~~CGy---~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY---IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC---EECCCcCCCcCcCCCC
Confidence 5777764 3455555667777764
No 220
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=78.63 E-value=3.8 Score=32.88 Aligned_cols=31 Identities=16% Similarity=0.258 Sum_probs=27.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+-+.++++||+.+|+|+.|++++.+.|.+.-
T Consensus 20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 20 DARISNAELAERVGLSPSTVLRRIKRLEEEG 50 (154)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4459999999999999999999999998764
No 221
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=78.60 E-value=38 Score=32.78 Aligned_cols=75 Identities=13% Similarity=0.274 Sum_probs=49.1
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHh------------------cCC-CccHHHHH
Q psy6534 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQ------------------EGV-PRTFKEIC 174 (309)
Q Consensus 114 I~~i~~~L~Lp~~v~e~A~~~~~~~~~~~~~~gr~~~~vaaAcly~acR~------------------~~~-~~tl~eia 174 (309)
+.+++..|+++...++.|..+++.+.-.|..- |+.. =|+.+=.+. +.+ -..+..|+
T Consensus 141 ~~eia~~l~~~~~~v~~~l~~lQ~leP~GigA-r~L~----ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~~ia 215 (455)
T PRK05932 141 LEEIAESLGVELDEVEAVLKRIQSFDPAGVGA-RDLQ----ECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFRTLA 215 (455)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhcCCCCccCc-CCHH----HHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHHHHH
Confidence 45799999999999999999998876555431 1110 111111111 111 13467889
Q ss_pred HHhcccHHHHHHHHHHHHH
Q psy6534 175 AVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 175 ~~~~~~~~~i~~~~~~l~~ 193 (309)
..++++..++..+...|+.
T Consensus 216 ~~l~is~~~v~~~~~~Ir~ 234 (455)
T PRK05932 216 KKLGVKEEDLQEALDLIRS 234 (455)
T ss_pred HHHCcCHHHHHHHHHHHhC
Confidence 9999999999998876654
No 222
>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=78.59 E-value=1.2 Score=44.21 Aligned_cols=42 Identities=19% Similarity=0.401 Sum_probs=28.5
Q ss_pred ccCCCCCCCC------eeee----CCCCceecCCCCccccCcc---cccCCCccc
Q psy6534 6 VCCYEHPDAP------LIED----YRAGDQICSECGLVVGDRV---IDVGSEWRT 47 (309)
Q Consensus 6 ~~Cp~C~~~~------~v~D----~~~G~~vC~~CG~V~~e~~---id~~~ewr~ 47 (309)
..||+||... +..| +.+--++|..||..++|+. ....-+|+.
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~ 255 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVA 255 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEe
Confidence 4699998653 3333 4466899999999998864 223456654
No 223
>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=78.55 E-value=2.6 Score=30.37 Aligned_cols=24 Identities=21% Similarity=0.398 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~k 283 (309)
-.+++++||+.+|||..|+++...
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 557999999999999999999664
No 224
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=78.31 E-value=2.7 Score=26.91 Aligned_cols=26 Identities=15% Similarity=0.498 Sum_probs=19.7
Q ss_pred ccCC--CCCCCCeeeeCCCCceecCCCCc
Q psy6534 6 VCCY--EHPDAPLIEDYRAGDQICSECGL 32 (309)
Q Consensus 6 ~~Cp--~C~~~~~v~D~~~G~~vC~~CG~ 32 (309)
..|| .||..-+..++. ....|..||+
T Consensus 19 k~CP~~~CG~GvFMA~H~-dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHK-DRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTSSSEEEE-S-SEEEETTTSS
T ss_pred hcCCCcccCCceEeeecC-CCccCCCccc
Confidence 4699 899877778874 5899999996
No 225
>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=78.27 E-value=5.9 Score=27.55 Aligned_cols=43 Identities=26% Similarity=0.311 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhcC----------CCccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 152 IASACLYIACRQEG----------VPRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 152 vaaAcly~acR~~~----------~~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
+|...++++.+... .|.+..+||+.+|++...+.+.++.+.+.
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 44445555555432 56899999999999999999999998874
No 226
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=78.20 E-value=4.6 Score=33.31 Aligned_cols=39 Identities=31% Similarity=0.228 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 244 ISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 244 ~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
.++|-||--+|- .....|..+||+.+|.|+.|||+..+.
T Consensus 46 dSLavAAga~ar--ekag~Ti~EIAeelG~TeqTir~hlkg 84 (182)
T COG1318 46 DSLAVAAGALAR--EKAGMTISEIAEELGRTEQTVRNHLKG 84 (182)
T ss_pred hHHHHHHHHHHH--HHccCcHHHHHHHhCCCHHHHHHHHhc
Confidence 344444433333 456789999999999999999987653
No 227
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=78.08 E-value=11 Score=31.55 Aligned_cols=29 Identities=10% Similarity=0.100 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.++|+++||+.+|+++.|+.+..++|.+.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 67899999999999999999999999865
No 228
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=78.01 E-value=0.59 Score=38.35 Aligned_cols=29 Identities=14% Similarity=0.249 Sum_probs=0.0
Q ss_pred CCCCCCCCeeeeCCCCceecCCCCccccC
Q psy6534 8 CYEHPDAPLIEDYRAGDQICSECGLVVGD 36 (309)
Q Consensus 8 Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e 36 (309)
||.|+..-...|--+....|..||.++.+
T Consensus 112 Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 112 CPNMCVRFTFNEAMELNFTCPRCGAMLDY 140 (158)
T ss_pred CCCCCcEeeHHHHHHcCCcCCCCCCEeee
No 229
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=77.95 E-value=2.2 Score=33.09 Aligned_cols=33 Identities=21% Similarity=0.742 Sum_probs=27.7
Q ss_pred eeCCCCceecCCCCccc--cCcccccCCCcccccC
Q psy6534 18 EDYRAGDQICSECGLVV--GDRVIDVGSEWRTFSN 50 (309)
Q Consensus 18 ~D~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~ 50 (309)
...+.|.++|..||.-| .+.-+|.|.-|.+|.+
T Consensus 27 ~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~ 61 (119)
T PRK05508 27 DFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDD 61 (119)
T ss_pred CcCCCeEEEecCCCCccccccccccCCCCCcccCc
Confidence 34679999999999887 5667899999999965
No 230
>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=77.82 E-value=1.7 Score=28.86 Aligned_cols=26 Identities=23% Similarity=0.567 Sum_probs=17.9
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
+...||.||... .---||..||+--+
T Consensus 25 ~l~~C~~cG~~~------~~H~vc~~cG~Y~g 50 (55)
T TIGR01031 25 TLVVCPNCGEFK------LPHRVCPSCGYYKG 50 (55)
T ss_pred cceECCCCCCcc------cCeeECCccCeECC
Confidence 345699998743 24678999997543
No 231
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=77.75 E-value=1.5 Score=35.26 Aligned_cols=28 Identities=25% Similarity=0.424 Sum_probs=17.5
Q ss_pred ccCCCCCCCC-eeeeC---CCCc-----eecCCCCcc
Q psy6534 6 VCCYEHPDAP-LIEDY---RAGD-----QICSECGLV 33 (309)
Q Consensus 6 ~~Cp~C~~~~-~v~D~---~~G~-----~vC~~CG~V 33 (309)
|.||.|++.. -|.|. +.|. -.|.+||.=
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~R 37 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGER 37 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccc
Confidence 6899998763 23342 3443 358888854
No 232
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=77.51 E-value=1.3 Score=40.42 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=19.2
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
..||.||. ...+...|..||.+.
T Consensus 310 ~~C~~cg~------~~~r~~~C~~cg~~~ 332 (364)
T COG0675 310 KTCPCCGH------LSGRLFKCPRCGFVH 332 (364)
T ss_pred ccccccCC------ccceeEECCCCCCee
Confidence 57999998 446789999999986
No 233
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=77.25 E-value=7 Score=25.55 Aligned_cols=30 Identities=17% Similarity=0.278 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+.+.+..+|++.+|++..|+++..+.|.+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 567899999999999999999999999864
No 234
>PRK08402 replication factor A; Reviewed
Probab=77.18 E-value=1.7 Score=40.44 Aligned_cols=27 Identities=30% Similarity=0.325 Sum_probs=21.9
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
..||.|+. .++.|...|...|..||.|
T Consensus 213 ~aCp~CnK-kv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRR-KVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCe-EEEEecCCCCEeCCCCCCc
Confidence 47999976 3555888899999999975
No 235
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=77.01 E-value=6.5 Score=32.43 Aligned_cols=46 Identities=22% Similarity=0.218 Sum_probs=37.5
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 149 NDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 149 ~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
.+.-+.+++|+|-...+-|.+..+||+..+++..-+.+.+..|.+.
T Consensus 7 ~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 7 GRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4455667888885555678999999999999999999888888763
No 236
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=76.98 E-value=9.9 Score=23.89 Aligned_cols=29 Identities=31% Similarity=0.500 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+..++++.++++..|+++..+.|.+.
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 35899999999999999999999998875
No 237
>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=76.94 E-value=8 Score=30.25 Aligned_cols=39 Identities=23% Similarity=0.237 Sum_probs=31.8
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 250 AIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 250 aiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.+|++ +..+.+.+..+||+.+|++..++++..+.|.+.-
T Consensus 15 l~~la-~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~G 53 (130)
T TIGR02944 15 LTTLA-QNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAG 53 (130)
T ss_pred HHHHH-hCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 34555 3345678999999999999999999999998753
No 238
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=76.73 E-value=1.8 Score=28.37 Aligned_cols=26 Identities=31% Similarity=0.447 Sum_probs=17.4
Q ss_pred cCCCCCCCC-eeeeCCCCce----ecCCCCc
Q psy6534 7 CCYEHPDAP-LIEDYRAGDQ----ICSECGL 32 (309)
Q Consensus 7 ~Cp~C~~~~-~v~D~~~G~~----vC~~CG~ 32 (309)
.||+||... +..|.+.|.. =|.-|..
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~ 32 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCR 32 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCC
Confidence 699999874 5668777742 2555553
No 239
>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=76.66 E-value=6.7 Score=32.38 Aligned_cols=27 Identities=26% Similarity=0.401 Sum_probs=25.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.++++||+.+|+|..|+.+.+++|.+.
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 589999999999999999999999875
No 240
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=76.53 E-value=2.4 Score=34.00 Aligned_cols=34 Identities=26% Similarity=0.662 Sum_probs=28.1
Q ss_pred eeCCCCceecCCCCccc--cCcccccCCCcccccCC
Q psy6534 18 EDYRAGDQICSECGLVV--GDRVIDVGSEWRTFSNE 51 (309)
Q Consensus 18 ~D~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 51 (309)
.....|.++|..||.-| .+.-++.|.-|.+|.+.
T Consensus 37 ~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 72 (142)
T PRK00222 37 DNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKP 72 (142)
T ss_pred CCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcc
Confidence 34679999999999887 55678999999999754
No 241
>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=76.34 E-value=9.7 Score=26.14 Aligned_cols=32 Identities=16% Similarity=0.268 Sum_probs=25.4
Q ss_pred hCCCCCCHHHHHHHhCCC-HHHHHHHHHHHHHh
Q psy6534 257 ASSDKRSQKEIGDIAGVA-EVTIRQSYKLMYPH 288 (309)
Q Consensus 257 ~~~~~~~~~~ia~~~~vs-~~ti~~~~kei~~~ 288 (309)
.+|.+.|.+||++.+|++ .+|+....+.|.+.
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k 53 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLKALERK 53 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 468899999999999997 99999999988754
No 242
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=76.27 E-value=54 Score=28.85 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+++|||+.+|+|..+|++..+...+.
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~al~k 252 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAALKH 252 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45799999999999999999887765543
No 243
>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=76.05 E-value=2.6 Score=29.92 Aligned_cols=26 Identities=31% Similarity=0.273 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
...+..|||+.+|||++||-+..+.|
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHh
Confidence 35788999999999999999887765
No 244
>PF13309 HTH_22: HTH domain
Probab=76.04 E-value=16 Score=24.87 Aligned_cols=56 Identities=14% Similarity=0.230 Sum_probs=38.5
Q ss_pred HHHHHHHHhhCCCCHHH--HHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHH
Q psy6534 205 GDFMSRFCSNLSLPNMV--QKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQ 280 (309)
Q Consensus 205 ~~~i~~~~~~L~l~~~~--~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~ 280 (309)
...|..+....+.+... .+.=.++++.+.+.+++. .+-....||+.+|||+.||=+
T Consensus 4 ~~~i~~~~~~~~~~~~~l~~~~k~~iV~~L~~~G~F~--------------------lKgav~~vA~~L~iS~~TVY~ 61 (64)
T PF13309_consen 4 ESIIEEVIAEVGKPPSRLSKEEKKEIVRQLYEKGIFL--------------------LKGAVEYVAEKLGISRATVYR 61 (64)
T ss_pred HHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHCCCcc--------------------cCcHHHHHHHHHCCCHHHHHH
Confidence 45677777777776643 344456777777766653 455667889999999999743
No 245
>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=75.83 E-value=3.8 Score=25.51 Aligned_cols=23 Identities=17% Similarity=0.187 Sum_probs=19.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
.+.+|+|+.+|+++.||.+..++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 47899999999999999887653
No 246
>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=75.75 E-value=8.7 Score=25.22 Aligned_cols=28 Identities=18% Similarity=0.273 Sum_probs=25.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
++++.+||+.++++.+|+.+..+.|.+.
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 4899999999999999999999999876
No 247
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=75.68 E-value=16 Score=30.72 Aligned_cols=30 Identities=23% Similarity=0.388 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.++++++||+.+|+++.|+.+..++|.+.-
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 579999999999999999999999998653
No 248
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=75.54 E-value=1.7 Score=29.40 Aligned_cols=21 Identities=29% Similarity=0.687 Sum_probs=13.9
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGL 32 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~ 32 (309)
.|.+|+. ++. ...-+|..||.
T Consensus 6 AC~~Ck~--l~~---~d~e~CP~Cgs 26 (64)
T COG2093 6 ACKNCKR--LTP---EDTEICPVCGS 26 (64)
T ss_pred HHhhccc--cCC---CCCccCCCCCC
Confidence 6888865 332 23568888884
No 249
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=75.51 E-value=8.1 Score=26.52 Aligned_cols=40 Identities=20% Similarity=0.193 Sum_probs=35.8
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCC
Q psy6534 256 QASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQ 295 (309)
Q Consensus 256 ~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~ 295 (309)
++++.+++..+.|+.+|+++.++++-.+.+.+-..+|-|.
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPS 47 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPS 47 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCC
Confidence 5678899999999999999999999999999888777764
No 250
>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=75.37 E-value=7.7 Score=24.43 Aligned_cols=37 Identities=19% Similarity=0.243 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
|++-+..+.-=...+.++|++.+|++..++-+.|...
T Consensus 4 aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 4 AALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp HHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSH
T ss_pred HHHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCCH
Confidence 4444444433357899999999999999998877543
No 251
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=75.28 E-value=14 Score=27.60 Aligned_cols=36 Identities=3% Similarity=0.171 Sum_probs=28.5
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
+.-|+... ...++++.++|+.+|+|+.++.+.+++.
T Consensus 10 ~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 10 LIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 33444444 4467999999999999999999999886
No 252
>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=75.27 E-value=52 Score=28.18 Aligned_cols=30 Identities=13% Similarity=0.358 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+++|||+.+|++..||++..+...+..
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~~L 222 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRALKKL 222 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 467999999999999999988877655443
No 253
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=75.13 E-value=14 Score=28.78 Aligned_cols=43 Identities=9% Similarity=0.214 Sum_probs=32.3
Q ss_pred hHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 243 PISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 243 P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
...+..+.-|+-... ..+.++.++|+.+|+|+.++.+.+++..
T Consensus 8 ~~~i~~~~~~I~~~~-~~~~sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 8 AITIHSILDWIEDNL-ESPLSLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred HHHHHHHHHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344444444555554 4579999999999999999999998763
No 254
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=75.12 E-value=7.8 Score=30.42 Aligned_cols=38 Identities=16% Similarity=0.229 Sum_probs=31.9
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 251 IYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 251 iyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+|++.-..+-+.+..+||+.++.+.+|+.+..+.|.+.
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 45554435678999999999999999999999999875
No 255
>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=74.94 E-value=2.7 Score=25.57 Aligned_cols=19 Identities=26% Similarity=0.401 Sum_probs=15.2
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q psy6534 263 SQKEIGDIAGVAEVTIRQS 281 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~ 281 (309)
++.|+|+.+||+..|||.-
T Consensus 1 ti~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 4679999999999999753
No 256
>PRK06030 hypothetical protein; Provisional
Probab=74.90 E-value=13 Score=29.20 Aligned_cols=72 Identities=10% Similarity=0.062 Sum_probs=48.9
Q ss_pred ChHHHHHHHHhhCCCCHHHHHHHHHHHHHhhh-cCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHH
Q psy6534 203 TTGDFMSRFCSNLSLPNMVQKAATHIARKAVE-LDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQS 281 (309)
Q Consensus 203 ~p~~~i~~~~~~L~l~~~~~~~a~~i~~~~~~-~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~ 281 (309)
++...+.-+|..++++.+.. .-.... ..+. .|.- .|+||+-.+.+ .++.+|++.+|-+.+|+...
T Consensus 24 t~d~Ii~~Va~~f~I~~~di------~sk~R~rk~i~---~aRq---IAMYL~r~~~~--~sl~~IG~~FGRDHSTV~ha 89 (124)
T PRK06030 24 LCEAVIDLLALAFGVSGAEI------ASPLRGRREVS---RIRQ---IAMYVAHVSLG--WPMNEVALAFGRDRTTVGHA 89 (124)
T ss_pred CHHHHHHHHHHHhCCCHHHH------hCCCCCCcccc---hHHH---HHHHHHHHHcC--CCHHHHHHHHCCChhHHHHH
Confidence 66777788888888876422 111110 1121 2333 45899988765 48999999999999999999
Q ss_pred HHHHHHh
Q psy6534 282 YKLMYPH 288 (309)
Q Consensus 282 ~kei~~~ 288 (309)
++.+.+.
T Consensus 90 ikkIe~~ 96 (124)
T PRK06030 90 CHTVEDL 96 (124)
T ss_pred HHHHHHH
Confidence 9977654
No 257
>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=74.86 E-value=65 Score=29.11 Aligned_cols=115 Identities=9% Similarity=0.094 Sum_probs=57.9
Q ss_pred CCCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCCC-h-HHHHHHHHhhCCCCHHHH--HHHHHHHHHhhhcCccCC
Q psy6534 165 GVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLIT-T-GDFMSRFCSNLSLPNMVQ--KAATHIARKAVELDIVPG 240 (309)
Q Consensus 165 ~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~~-p-~~~i~~~~~~L~l~~~~~--~~a~~i~~~~~~~~l~~G 240 (309)
|...+..||+..++++..++..........+.++.+..+ . ..+...+.+.-.-|.+.. ......+..+.. .+
T Consensus 175 ~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~pe~~~~~~~~~~~L~~~L~-~L--- 250 (298)
T TIGR02997 175 GRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEEQVERESLRQDLESLLA-EL--- 250 (298)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCCCCHHHHHHHHHHHHHHHHHHH-cC---
Confidence 455688999999999999998776544333333322111 1 112222222111112111 111222223222 11
Q ss_pred CChHHHHHHHHHHHHHhC-CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 241 RSPISVAAAAIYMASQAS-SDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 241 r~P~~iaaAaiyla~~~~-~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
+|.-- -+|.+-.-+. ..+.|++|||+.+|+|+.+|++....-.
T Consensus 251 -~~rer--~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl 294 (298)
T TIGR02997 251 -TPRER--QVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKAL 294 (298)
T ss_pred -CHHHH--HHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 11111 1111111112 3579999999999999999998876543
No 258
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=74.79 E-value=18 Score=31.25 Aligned_cols=30 Identities=17% Similarity=0.252 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.++++++||+.+|+++.|+.+..++|.+.-
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~G 207 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDRG 207 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 578999999999999999999999998763
No 259
>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=74.49 E-value=1.8 Score=37.19 Aligned_cols=30 Identities=30% Similarity=0.650 Sum_probs=22.9
Q ss_pred ccCCCCCCC--CeeeeCCCC---ceecCCCCcccc
Q psy6534 6 VCCYEHPDA--PLIEDYRAG---DQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~--~~v~D~~~G---~~vC~~CG~V~~ 35 (309)
|.|-+||.+ .+..+++.| -..|.+||.|.|
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 579999876 355677655 478999999984
No 260
>KOG2593|consensus
Probab=74.43 E-value=1.6 Score=41.04 Aligned_cols=32 Identities=19% Similarity=0.405 Sum_probs=23.3
Q ss_pred CCcccCCCCCCCC------eeeeCCCCceecCCCCccc
Q psy6534 3 INKVCCYEHPDAP------LIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 3 ~~~~~Cp~C~~~~------~v~D~~~G~~vC~~CG~V~ 34 (309)
.+...||.|.+.- -..|..+|...|..||.=|
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 4567899998751 2246789999999996543
No 261
>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=74.40 E-value=4.2 Score=27.22 Aligned_cols=30 Identities=17% Similarity=0.195 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+..++.+++|+.+|+|+.||++...+|.+.
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~~ 46 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNEF 46 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 345789999999999999999999999865
No 262
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=74.36 E-value=0.7 Score=30.72 Aligned_cols=26 Identities=31% Similarity=0.613 Sum_probs=19.2
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCC-CCccc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSE-CGLVV 34 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~-CG~V~ 34 (309)
.-..|+.||..- ..|+.+|++ ||.++
T Consensus 7 PH~HC~VCg~aI-----p~de~~CSe~C~eil 33 (64)
T COG4068 7 PHRHCVVCGKAI-----PPDEQVCSEECGEIL 33 (64)
T ss_pred CCccccccCCcC-----CCccchHHHHHHHHH
Confidence 345799998752 256899995 99887
No 263
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=74.35 E-value=3.6 Score=28.56 Aligned_cols=22 Identities=23% Similarity=0.493 Sum_probs=18.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~k 283 (309)
.+++|||+.+|||..|+.+.++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3688999999999999987654
No 264
>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=74.33 E-value=6.6 Score=26.96 Aligned_cols=32 Identities=22% Similarity=0.425 Sum_probs=23.6
Q ss_pred HhcCCCccHHHHHHHhccc-HHHHHHHHHHHHH
Q psy6534 162 RQEGVPRTFKEICAVSKIS-KKEIGRCFKLILK 193 (309)
Q Consensus 162 R~~~~~~tl~eia~~~~~~-~~~i~~~~~~l~~ 193 (309)
..+|.|.|++||++.+|++ ...+.+.++.|.+
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 5789999999999999996 7777777776654
No 265
>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=74.17 E-value=4.5 Score=25.01 Aligned_cols=22 Identities=32% Similarity=0.446 Sum_probs=19.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~ke 284 (309)
+..|+|+.+||++.||++-.++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 6789999999999999987664
No 266
>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=74.15 E-value=13 Score=24.79 Aligned_cols=29 Identities=21% Similarity=0.345 Sum_probs=25.7
Q ss_pred CCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 165 GVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 165 ~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
..+.+..|+++.++++...+.+.++.+.+
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45789999999999999999998888876
No 267
>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=73.92 E-value=48 Score=27.15 Aligned_cols=95 Identities=19% Similarity=0.327 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhccc-----CC----------CCChHHHHHHHHhhCC
Q psy6534 152 IASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETS-----VD----------LITTGDFMSRFCSNLS 216 (309)
Q Consensus 152 vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~-----~~----------~~~p~~~i~~~~~~L~ 216 (309)
++-|.||++ +-|+++.++++.++ +..++.+....|.+.++.. +. ..+-..++.++...
T Consensus 2 ~iEAlLF~s----~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~-- 74 (159)
T PF04079_consen 2 IIEALLFAS----GEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKK-- 74 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCT--
T ss_pred hhHhhHHHc----CCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhcc--
Confidence 455777775 66899999999999 9999999999998887321 00 01223344433332
Q ss_pred CCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHH-HHHHHhCCCCCCHHHHHHHhCCCHHH
Q psy6534 217 LPNMVQKAATHIARKAVELDIVPGRSPISVAAAAI-YMASQASSDKRSQKEIGDIAGVAEVT 277 (309)
Q Consensus 217 l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAai-yla~~~~~~~~~~~~ia~~~~vs~~t 277 (309)
+++..+--|++ -||.-.++.|+|..||-+.=||+...
T Consensus 75 ------------------------~~~~~LS~aalEtLAiIAY~QPiTr~eIe~IRGv~s~~ 112 (159)
T PF04079_consen 75 ------------------------PKPPKLSQAALETLAIIAYKQPITRAEIEEIRGVNSDS 112 (159)
T ss_dssp ------------------------CCCHHHHHHHHHHHHHHHHH-SEEHHHHHHHHTS--HC
T ss_pred ------------------------CccCCCCHHHHHHHHHHHhcCCcCHHHHHHHcCCChHH
Confidence 12222222222 23333446899999999999998543
No 268
>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=72.92 E-value=2.1 Score=37.24 Aligned_cols=30 Identities=20% Similarity=0.443 Sum_probs=11.8
Q ss_pred cccCCCCCCCCeee---eCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIE---DYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~---D~~~G~~vC~~CG~V~ 34 (309)
.+.||.||+..+-. +.--.+..|.+|+.-.
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp H---TTT--SS-EE--------EEE-TTT--EE
T ss_pred CCcCCCCCChhHhhccCCCccceeECCCCchHH
Confidence 46899999875432 2334689999998543
No 269
>PF14122 YokU: YokU-like protein
Probab=72.84 E-value=2 Score=31.07 Aligned_cols=23 Identities=35% Similarity=0.562 Sum_probs=17.5
Q ss_pred CCceecCCCCccccCcccccCCC
Q psy6534 22 AGDQICSECGLVVGDRVIDVGSE 44 (309)
Q Consensus 22 ~G~~vC~~CG~V~~e~~id~~~e 44 (309)
+=.++|++||.|..+..+...-|
T Consensus 33 tP~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 33 TPAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred CceeeecCCCcEEehhHHHHHHh
Confidence 34589999999998877665444
No 270
>KOG1010|consensus
Probab=72.71 E-value=8 Score=39.67 Aligned_cols=80 Identities=14% Similarity=0.223 Sum_probs=68.7
Q ss_pred HHHHHHhhCCCCHHHHHHHHHHHHHhhh--cCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 207 FMSRFCSNLSLPNMVQKAATHIARKAVE--LDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 207 ~i~~~~~~L~l~~~~~~~a~~i~~~~~~--~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
-+..+|.+|.++++..+..|.+++.... ..++.-|+-.-|...|+|..++......+.++|-..-.-.+......||+
T Consensus 683 RL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa~~~vyRs 762 (920)
T KOG1010|consen 683 RLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQAVSLVYRS 762 (920)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCchhhhhhhhh
Confidence 3566789999999888899998886543 45888899999999999999999999999999999988888888889988
Q ss_pred HH
Q psy6534 285 MY 286 (309)
Q Consensus 285 i~ 286 (309)
..
T Consensus 763 V~ 764 (920)
T KOG1010|consen 763 VL 764 (920)
T ss_pred ee
Confidence 54
No 271
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=72.70 E-value=13 Score=31.92 Aligned_cols=29 Identities=7% Similarity=0.096 Sum_probs=26.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+.++.+||+.+|+|+.|+.+..++|.+..
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L~~L~~~G 197 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVLAQFIQDG 197 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHHHHHHHCC
Confidence 45899999999999999999999998764
No 272
>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=72.70 E-value=7.6 Score=25.05 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+.+.++.|||+.+|++.+|+.+..+.|.+.
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 455799999999999999999998888764
No 273
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=72.66 E-value=9.1 Score=24.91 Aligned_cols=38 Identities=18% Similarity=0.160 Sum_probs=31.0
Q ss_pred HHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhccc
Q psy6534 161 CRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETS 198 (309)
Q Consensus 161 cR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~ 198 (309)
.-.-+...+..++|..+|++...+.+.++.+...|...
T Consensus 13 L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 13 LMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 33444567889999999999999999999998887643
No 274
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=72.37 E-value=80 Score=29.06 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
+.+.|++|||+.+|||...|++..+.-.
T Consensus 280 ~~~~Tl~eIa~~lgvS~eRVrQIe~~Al 307 (324)
T PRK07921 280 GQPRTLDQIGKLFGLSRERVRQIEREVM 307 (324)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3578999999999999999988776543
No 275
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=72.32 E-value=39 Score=33.73 Aligned_cols=105 Identities=10% Similarity=0.028 Sum_probs=63.1
Q ss_pred CCccHHHHHHHhcccHHHHHHHHHHHHHHhcccCCCCChHHHHHH-HHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChH
Q psy6534 166 VPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSR-FCSNLSLPNMVQKAATHIARKAVELDIVPGRSPI 244 (309)
Q Consensus 166 ~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~~~~~~p~~~i~~-~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~ 244 (309)
-|+|..++|+.+++|.+.|.+-+..|.+.|...-.. .+.. -.-.|...+. .....+.. ...+.
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-----~i~~~~Gy~l~~~~~--~~~~~~~~---------~~~~e 79 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-----SISGSAKYHLEILNR--RSLFQLLQ---------KSDNE 79 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-----heecCCceEEEeCCH--HHHHHHHh---------cCCHH
Confidence 489999999999999999999999888877542100 0111 0011211111 11111111 01222
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q psy6534 245 SVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHAS 290 (309)
Q Consensus 245 ~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~ 290 (309)
-.. +.+. .+...+++..++|+.+.||++||.+-.+++.+...
T Consensus 80 ~~~---il~~-Ll~~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 80 DRL---LLLR-LLLNTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred HHH---HHHH-HHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 221 1111 11245789999999999999999999999986443
No 276
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.26 E-value=2.3 Score=27.48 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=19.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
..|-.||.. +..|.....+.|..||.=
T Consensus 7 Y~C~~Cg~~-~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGRE-VELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCCe-eehhhccCceeCCCCCcE
Confidence 468889864 333667788999999853
No 277
>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=72.03 E-value=8.8 Score=23.93 Aligned_cols=28 Identities=29% Similarity=0.415 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
...+.++||+.+|++..||.+..+...+
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578999999999999999888776654
No 278
>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=71.76 E-value=9.6 Score=26.01 Aligned_cols=36 Identities=28% Similarity=0.356 Sum_probs=28.9
Q ss_pred HHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 157 LYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 157 ly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
+|.+.- .+-+.|..||++.++++...+.+.++.|.+
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 444444 444899999999999999999988888865
No 279
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=71.70 E-value=0.97 Score=40.85 Aligned_cols=30 Identities=20% Similarity=0.373 Sum_probs=22.9
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
.+||.|+..-...|-.....||..||.-..
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 479999875444466677899999998764
No 280
>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=71.70 E-value=7.1 Score=26.10 Aligned_cols=31 Identities=16% Similarity=0.234 Sum_probs=27.3
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.+.+.+..+||+.+|++.+|+....+.|.+.
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4678999999999999999999999999875
No 281
>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=71.64 E-value=15 Score=26.25 Aligned_cols=33 Identities=18% Similarity=0.204 Sum_probs=29.0
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 257 ASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 257 ~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
..+.++.-++||+.+++++.|||+-...|.+.-
T Consensus 19 ~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lG 51 (78)
T PF03444_consen 19 ETGEPVGSKTIAEELGRSPATIRNEMADLEELG 51 (78)
T ss_pred hcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCC
Confidence 347899999999999999999999999887753
No 282
>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=71.56 E-value=4.6 Score=25.71 Aligned_cols=21 Identities=29% Similarity=0.491 Sum_probs=18.1
Q ss_pred cHHHHHHHhcccHHHHHHHHH
Q psy6534 169 TFKEICAVSKISKKEIGRCFK 189 (309)
Q Consensus 169 tl~eia~~~~~~~~~i~~~~~ 189 (309)
|++|||+.+|++...+.+++.
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 689999999999998876654
No 283
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=71.52 E-value=6.5 Score=24.07 Aligned_cols=27 Identities=22% Similarity=0.201 Sum_probs=19.5
Q ss_pred CCCccHHHHHHHhcccHHHHHHHHHHH
Q psy6534 165 GVPRTFKEICAVSKISKKEIGRCFKLI 191 (309)
Q Consensus 165 ~~~~tl~eia~~~~~~~~~i~~~~~~l 191 (309)
..+.++.|||+.++++...+.+.|++.
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 346899999999999999988877743
No 284
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=71.43 E-value=13 Score=25.34 Aligned_cols=33 Identities=15% Similarity=0.170 Sum_probs=25.7
Q ss_pred HhcCCCccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 162 RQEGVPRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 162 R~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
+..+.|.+-.|||+.++++.....+....|.+.
T Consensus 10 ~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~e 42 (62)
T PF04703_consen 10 KEQNGPLKTREIADALGLSIYQARYYLEKLEKE 42 (62)
T ss_dssp HHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHC
T ss_pred HHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 344789999999999999999988887777654
No 285
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=71.41 E-value=3.4 Score=27.04 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=18.8
Q ss_pred cccCCCCCCCC-eee-eCCCCc-eecCCCCccc
Q psy6534 5 KVCCYEHPDAP-LIE-DYRAGD-QICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~-~v~-D~~~G~-~vC~~CG~V~ 34 (309)
...|.+|+.+. ..+ +-..|. .+|..||+-.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 45788887543 222 334554 8888888654
No 286
>PF12728 HTH_17: Helix-turn-helix domain
Probab=71.34 E-value=5.4 Score=25.50 Aligned_cols=22 Identities=18% Similarity=0.347 Sum_probs=18.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~k 283 (309)
.+.+|+|+.+|||..|+.+..+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999876653
No 287
>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=71.30 E-value=5 Score=25.16 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~k 283 (309)
+..|+|+.+||++.||+.-.+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999996643
No 288
>PRK00118 putative DNA-binding protein; Validated
Probab=71.22 E-value=5.1 Score=30.39 Aligned_cols=28 Identities=21% Similarity=0.152 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
...+.++||+.+|+|++|+.++.+....
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4689999999999999999888765543
No 289
>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=71.21 E-value=3.3 Score=26.88 Aligned_cols=13 Identities=23% Similarity=0.593 Sum_probs=8.7
Q ss_pred eecCCCCccccCc
Q psy6534 25 QICSECGLVVGDR 37 (309)
Q Consensus 25 ~vC~~CG~V~~e~ 37 (309)
.+|+.||+|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 4677777777654
No 290
>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=71.20 E-value=3.5 Score=30.73 Aligned_cols=26 Identities=23% Similarity=0.390 Sum_probs=17.4
Q ss_pred ccCCCCCCC--CeeeeCCCCceecCCCC
Q psy6534 6 VCCYEHPDA--PLIEDYRAGDQICSECG 31 (309)
Q Consensus 6 ~~Cp~C~~~--~~v~D~~~G~~vC~~CG 31 (309)
..||.|+.. ++..+...|...|-.||
T Consensus 34 ~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg 61 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDKNRFKCFGCG 61 (97)
T ss_dssp E--SSS--SS--EEEETTTTEEEETTT-
T ss_pred EECcCCCCCCCceEEECCCCeEEECCCC
Confidence 459999754 57888889999999998
No 291
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=70.94 E-value=18 Score=25.87 Aligned_cols=29 Identities=10% Similarity=0.139 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.+.+..+||+.+|++..|+.+..+.|.+.
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 47999999999999999999999999764
No 292
>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=70.89 E-value=1.1 Score=40.49 Aligned_cols=29 Identities=10% Similarity=0.338 Sum_probs=21.8
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.+||.|+..-...|-.....||..||.-.
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 47999987543345556679999999875
No 293
>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=70.88 E-value=16 Score=22.94 Aligned_cols=29 Identities=24% Similarity=0.247 Sum_probs=23.1
Q ss_pred CCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 165 GVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 165 ~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
+-+.|..|+|+.++++...+.+.++++.+
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 33599999999999999999998888765
No 294
>COG4640 Predicted membrane protein [Function unknown]
Probab=70.84 E-value=2.3 Score=39.55 Aligned_cols=25 Identities=20% Similarity=0.440 Sum_probs=18.9
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
..||.||+.. .+|+.-|+.||.-+.
T Consensus 2 ~fC~kcG~qk-----~Ed~~qC~qCG~~~t 26 (465)
T COG4640 2 KFCPKCGSQK-----AEDDVQCTQCGHKFT 26 (465)
T ss_pred Cccccccccc-----ccccccccccCCcCC
Confidence 3699999754 356677999997764
No 295
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=70.83 E-value=12 Score=30.43 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=36.0
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 149 NDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 149 ~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
.+.-+-+.+|+|-. .+.+.+.++||+..+++..-+.+.+..|++.
T Consensus 7 ~~YAlr~L~~LA~~-~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 7 TNYAIRMLMYCAAN-DGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HhHHHHHHHHHHhC-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34455578899844 4568899999999999999999998888773
No 296
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=70.79 E-value=2.3 Score=29.06 Aligned_cols=25 Identities=20% Similarity=0.418 Sum_probs=17.7
Q ss_pred CCCCcccCCCCCCCCeeeeCCCCceecCCCCc
Q psy6534 1 MNINKVCCYEHPDAPLIEDYRAGDQICSECGL 32 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~ 32 (309)
|...-..|.+|+. ++ + ..+|..||.
T Consensus 1 ~~~~~~AC~~C~~--i~-~----~~~Cp~Cgs 25 (64)
T PRK06393 1 MKVQYRACKKCKR--LT-P----EKTCPVHGD 25 (64)
T ss_pred CcchhhhHhhCCc--cc-C----CCcCCCCCC
Confidence 6666778999976 33 2 228999996
No 297
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=70.59 E-value=3.7 Score=34.36 Aligned_cols=33 Identities=6% Similarity=-0.079 Sum_probs=25.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
..+.+|||+.+|+|++||+++.....+...+.+
T Consensus 147 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 147 ELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 588999999999999999988766554443333
No 298
>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=70.52 E-value=15 Score=24.16 Aligned_cols=37 Identities=30% Similarity=0.292 Sum_probs=27.5
Q ss_pred HHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 157 LYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 157 ly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
+++.....+-..++.||++.+++++..+.+.+++|.+
T Consensus 11 L~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 11 LMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3344333343489999999999999999999888865
No 299
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=70.44 E-value=2.8 Score=28.47 Aligned_cols=29 Identities=21% Similarity=0.504 Sum_probs=17.9
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccccCcccccCCCcccc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTF 48 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~e~~id~~~ewr~f 48 (309)
.|.+|+. ++ +. ..|..||..- ...+|..+
T Consensus 5 AC~~C~~--i~-~~----~~CP~Cgs~~------~T~~W~G~ 33 (61)
T PRK08351 5 ACRHCHY--IT-TE----DRCPVCGSRD------LSDEWFDL 33 (61)
T ss_pred hhhhCCc--cc-CC----CcCCCCcCCc------cccccccE
Confidence 7889975 22 22 2699999632 34567554
No 300
>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=70.30 E-value=9.8 Score=25.67 Aligned_cols=32 Identities=16% Similarity=0.270 Sum_probs=25.1
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 257 ASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 257 ~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
..+.+.++.+|++.++++..++.+..++|.+.
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 34678899999999999999999999999876
No 301
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=70.20 E-value=14 Score=25.43 Aligned_cols=38 Identities=18% Similarity=0.182 Sum_probs=29.2
Q ss_pred HHHHHHhcCC-CccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 157 LYIACRQEGV-PRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 157 ly~acR~~~~-~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
++...+..+- +.++.|||+.+|++...+.+.+..|.+.
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 3444456665 4999999999999999988887777653
No 302
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=70.15 E-value=84 Score=28.33 Aligned_cols=33 Identities=15% Similarity=0.269 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASK 291 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~ 291 (309)
....|++|||+.+|+|..+|++..+.-.+....
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~ 275 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARALEKLRR 275 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999888765544433
No 303
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=70.11 E-value=8.1 Score=23.93 Aligned_cols=29 Identities=24% Similarity=0.411 Sum_probs=25.4
Q ss_pred CCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 165 GVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 165 ~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
..|.+..|+++.++++...+.+.++.+.+
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35789999999999999999888888766
No 304
>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=69.96 E-value=7.1 Score=31.17 Aligned_cols=30 Identities=20% Similarity=0.099 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+++|||+.+|+|++|+++..+...+..
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~kkL 49 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAMENI 49 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHHHHH
Confidence 567999999999999999997776655443
No 305
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=69.70 E-value=9 Score=26.10 Aligned_cols=31 Identities=16% Similarity=0.188 Sum_probs=25.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+.+++-.|||+.+|+|..++|.....|.+.-
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG 43 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEG 43 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 5678899999999999999999999887653
No 306
>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=69.58 E-value=7.3 Score=30.39 Aligned_cols=30 Identities=27% Similarity=0.294 Sum_probs=26.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPHAS 290 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~~~ 290 (309)
..+..+||+.+|+++.||+++.+...+...
T Consensus 126 g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 126 GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 578999999999999999999988776543
No 307
>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=69.58 E-value=19 Score=28.07 Aligned_cols=45 Identities=16% Similarity=0.163 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHhCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 244 ISVAAAAIYMASQASS-DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 244 ~~iaaAaiyla~~~~~-~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
..+|..++++.++..+ .+++.++||+.++++..++++..+.|.+.
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3455555544444333 37899999999999999999999999875
No 308
>KOG1088|consensus
Probab=69.49 E-value=2.3 Score=32.63 Aligned_cols=16 Identities=38% Similarity=0.727 Sum_probs=14.0
Q ss_pred eCCCCceecCCCCccc
Q psy6534 19 DYRAGDQICSECGLVV 34 (309)
Q Consensus 19 D~~~G~~vC~~CG~V~ 34 (309)
|-.+|+.+|.+||.|.
T Consensus 93 ~v~EG~l~CpetG~vf 108 (124)
T KOG1088|consen 93 DVIEGELVCPETGRVF 108 (124)
T ss_pred hhccceEecCCCCcEe
Confidence 4468999999999997
No 309
>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=69.35 E-value=3.6 Score=33.05 Aligned_cols=27 Identities=22% Similarity=0.519 Sum_probs=19.4
Q ss_pred cCC--CCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 7 CCY--EHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 7 ~Cp--~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
.|| .|++. +..+ .+|...|..||..++
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 699 99864 5555 679999999998863
No 310
>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=69.31 E-value=6.5 Score=28.33 Aligned_cols=34 Identities=15% Similarity=0.129 Sum_probs=27.6
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASK 291 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~ 291 (309)
.+..+++.++|+..+||++|+.+..+++.+..++
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677899999999999999999999999887654
No 311
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=69.22 E-value=5.1 Score=35.52 Aligned_cols=29 Identities=21% Similarity=0.257 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
-.++.+|+|+.++||+.|||+..++|.+.
T Consensus 18 ~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 18 GKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred CCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 45899999999999999999999998765
No 312
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=69.20 E-value=4.9 Score=28.27 Aligned_cols=29 Identities=14% Similarity=0.271 Sum_probs=20.3
Q ss_pred ccCCCCCCCCeeeeC-------CCCceecC--CCCccc
Q psy6534 6 VCCYEHPDAPLIEDY-------RAGDQICS--ECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~-------~~G~~vC~--~CG~V~ 34 (309)
+.||.||....|.+. .+--..|+ +||.-.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATF 39 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEE
Confidence 789999988766652 11234688 899765
No 313
>PF14353 CpXC: CpXC protein
Probab=69.07 E-value=4.3 Score=31.83 Aligned_cols=11 Identities=27% Similarity=0.727 Sum_probs=9.2
Q ss_pred ceecCCCCccc
Q psy6534 24 DQICSECGLVV 34 (309)
Q Consensus 24 ~~vC~~CG~V~ 34 (309)
..+|..||...
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 67999999765
No 314
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=69.05 E-value=1.2 Score=40.26 Aligned_cols=43 Identities=21% Similarity=0.441 Sum_probs=28.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcccc-------CcccccCCCccccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVG-------DRVIDVGSEWRTFS 49 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~-------e~~id~~~ewr~f~ 49 (309)
.+||.|+..-...|-.....||..||.-.. +.++|.|+ |..++
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D~gs-F~E~~ 77 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHMRISARERLDLLLDEGS-FVELD 77 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCeeCCHHHHHHHHccCCc-cEEec
Confidence 479999875444455566789999998763 12466654 44443
No 315
>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=69.04 E-value=13 Score=28.92 Aligned_cols=44 Identities=20% Similarity=0.267 Sum_probs=33.7
Q ss_pred hHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 150 DAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 150 ~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
+..+.+.+|++-...+.|.+..+|++.++++...+.+....|.+
T Consensus 8 ~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 8 EYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34455666776332345899999999999999999988888876
No 316
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=68.90 E-value=7.9 Score=35.57 Aligned_cols=36 Identities=19% Similarity=0.179 Sum_probs=29.1
Q ss_pred HHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 252 YMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 252 yla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
-+|+..+-...||+|||+.+|+|+.++.+..++=++
T Consensus 20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344445567899999999999999999988877554
No 317
>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=68.83 E-value=11 Score=29.71 Aligned_cols=41 Identities=15% Similarity=0.208 Sum_probs=33.5
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+.+|+|..-.+.+++.++||+..+++...+++....|.+.-
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~g 53 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAG 53 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 55677765444578999999999999999999999998753
No 318
>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=68.77 E-value=13 Score=23.99 Aligned_cols=35 Identities=23% Similarity=0.349 Sum_probs=26.3
Q ss_pred HHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 159 IACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 159 ~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
-+...++-+.++.||++.+++++..+.+....+.+
T Consensus 10 ~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 10 EALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33445666789999999999999998777776654
No 319
>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=68.73 E-value=88 Score=28.01 Aligned_cols=30 Identities=13% Similarity=0.166 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...|++|||+.+|++++||+++...-.+..
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL 270 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEALKKL 270 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 468999999999999999988876544333
No 320
>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=68.73 E-value=20 Score=29.56 Aligned_cols=29 Identities=14% Similarity=0.120 Sum_probs=26.8
Q ss_pred CCccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 166 VPRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 166 ~~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
+|.|..|||+.+|++...+.+.++++.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 68899999999999999999999999874
No 321
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=68.47 E-value=8.1 Score=28.34 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=18.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQ 280 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~ 280 (309)
...+.++||+.+|+|..||.+
T Consensus 49 ~G~S~~eIA~~LgISrsTIyR 69 (88)
T TIGR02531 49 QGKTYSDIEAETGASTATISR 69 (88)
T ss_pred CCCCHHHHHHHHCcCHHHHHH
Confidence 446999999999999999987
No 322
>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=68.40 E-value=4.3 Score=33.96 Aligned_cols=39 Identities=5% Similarity=-0.102 Sum_probs=29.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCcC
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFV 298 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~~~~ 298 (309)
...+.+|||+.+|++++|+++++....+...+.+...|.
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~ 184 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRARLSLRACLSINWF 184 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 468999999999999999999887766555544444443
No 323
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=68.39 E-value=12 Score=30.34 Aligned_cols=40 Identities=18% Similarity=0.223 Sum_probs=32.9
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+.+|+|.. .+..++.++||+..++++.-+++....|.+.-
T Consensus 13 ~L~~LA~~-~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aG 52 (153)
T PRK11920 13 MLMYCAAN-DGKLSRIPEIARAYGVSELFLFKILQPLVEAG 52 (153)
T ss_pred HHHHHHhC-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 55677743 45568999999999999999999999998753
No 324
>PHA02540 61 DNA primase; Provisional
Probab=68.35 E-value=4.4 Score=37.49 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=22.4
Q ss_pred cccCCCCCCC-------CeeeeCCCC--ceecCCCCc
Q psy6534 5 KVCCYEHPDA-------PLIEDYRAG--DQICSECGL 32 (309)
Q Consensus 5 ~~~Cp~C~~~-------~~v~D~~~G--~~vC~~CG~ 32 (309)
...||.|+.+ .+...++.| ...|-+||.
T Consensus 27 ~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa 63 (337)
T PHA02540 27 NFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred EecCCCCCCccccCcCCcEEEeccCCceEEEecCCCC
Confidence 3479999874 377777888 999999984
No 325
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=68.32 E-value=1.5 Score=33.86 Aligned_cols=32 Identities=22% Similarity=0.271 Sum_probs=21.3
Q ss_pred CCCcccCCCCCCCCeee-eCCCCceecCCCCccc
Q psy6534 2 NINKVCCYEHPDAPLIE-DYRAGDQICSECGLVV 34 (309)
Q Consensus 2 ~~~~~~Cp~C~~~~~v~-D~~~G~~vC~~CG~V~ 34 (309)
++|+ .|-+||+.+..+ +-.-|..+|..|.-|.
T Consensus 11 ~~N~-~CaDCg~~~p~w~s~~~GiflC~~Cag~H 43 (116)
T PF01412_consen 11 PGNK-VCADCGAPNPTWASLNYGIFLCLECAGIH 43 (116)
T ss_dssp TTCT-B-TTT-SBS--EEETTTTEEE-HHHHHHH
T ss_pred cCcC-cCCCCCCCCCCEEEeecChhhhHHHHHHH
Confidence 3555 899999876544 5567999999999886
No 326
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=68.21 E-value=7 Score=31.46 Aligned_cols=38 Identities=13% Similarity=0.107 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH-hhcccCCCCc
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYP-HASKLFPQDF 297 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~-~~~~l~~~~~ 297 (309)
...+.+|||+.+|++++|++++...... .++.|-.++|
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 159 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEEF 159 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4688999999999999999888655443 3333433333
No 327
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=68.09 E-value=4.4 Score=32.15 Aligned_cols=34 Identities=21% Similarity=0.486 Sum_probs=27.9
Q ss_pred eeCCCCceecCCCCccc--cCcccccCCCcccccCC
Q psy6534 18 EDYRAGDQICSECGLVV--GDRVIDVGSEWRTFSNE 51 (309)
Q Consensus 18 ~D~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 51 (309)
.....|.++|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 34 ~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 69 (134)
T TIGR00357 34 DNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKP 69 (134)
T ss_pred CCCCCeEEEccCCCCccccccchhcCCCCCcCcCcc
Confidence 34578999999999887 55678999999999653
No 328
>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=68.05 E-value=16 Score=24.60 Aligned_cols=27 Identities=15% Similarity=0.257 Sum_probs=24.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.+..+|++.+|++..|+++..+.|...
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~ 47 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEA 47 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHC
Confidence 899999999999999999999998654
No 329
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=67.52 E-value=4.1 Score=34.53 Aligned_cols=31 Identities=23% Similarity=0.330 Sum_probs=18.7
Q ss_pred cCCCCCCCCee----ee--CCCC-----ceecCCCCccccCc
Q psy6534 7 CCYEHPDAPLI----ED--YRAG-----DQICSECGLVVGDR 37 (309)
Q Consensus 7 ~Cp~C~~~~~v----~D--~~~G-----~~vC~~CG~V~~e~ 37 (309)
.||.||....+ ++ +--| ...|..||+=-.|-
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev 43 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDV 43 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCcccee
Confidence 69999864322 12 1122 56799999875443
No 330
>KOG0402|consensus
Probab=67.48 E-value=1.9 Score=30.93 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=24.2
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
...|+.||... +-....|-.-|..|..|+.
T Consensus 36 ky~CsfCGK~~-vKR~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 36 KYTCSFCGKKT-VKRKAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhhcchhh-hhhhceeEEecCCccceec
Confidence 45799999865 4556789999999999984
No 331
>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=67.34 E-value=8.6 Score=30.58 Aligned_cols=30 Identities=20% Similarity=0.239 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.+|||+.+|+|+.|++++.....+..
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKALKEL 157 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 467999999999999999999887765543
No 332
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=67.23 E-value=8.7 Score=33.09 Aligned_cols=37 Identities=16% Similarity=0.246 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCC
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQD 296 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~~ 296 (309)
--+|+.|+|..+++|..||++..+++.+.-+.++|-.
T Consensus 104 glLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtr 140 (220)
T PF07900_consen 104 GLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTR 140 (220)
T ss_pred CcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccC
Confidence 3489999999999999999999999998877777653
No 333
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=67.21 E-value=13 Score=30.39 Aligned_cols=38 Identities=16% Similarity=0.166 Sum_probs=31.6
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 250 AIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 250 aiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+||...+ .+.....++||+.++|+++|+.+..++|.+.
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~ 51 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLERL 51 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHHC
Confidence 4665555 5567889999999999999999999998765
No 334
>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=67.21 E-value=6.6 Score=25.34 Aligned_cols=25 Identities=28% Similarity=0.288 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
...+++|+|+.+|++..||.+..+.
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhcC
Confidence 4689999999999999999887654
No 335
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=67.20 E-value=16 Score=34.79 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=26.6
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +.+++|+.+|||..|++++|.+|...
T Consensus 26 g~~lps~r~la~~~~vsr~tv~~a~~~L~~~ 56 (431)
T PRK15481 26 GDSLPPVRELASELGVNRNTVAAAYKRLVTA 56 (431)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4566 68999999999999999999999865
No 336
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=66.82 E-value=1.7 Score=38.51 Aligned_cols=29 Identities=14% Similarity=0.409 Sum_probs=22.4
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.+||.|+.--...|-.+...||..||.-.
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eECCCccceeeHHHHHhhhhcccccCccc
Confidence 47999987533346677899999999865
No 337
>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=66.57 E-value=4.3 Score=26.25 Aligned_cols=32 Identities=22% Similarity=0.387 Sum_probs=19.9
Q ss_pred CCCCcccCCCCCCC-Ceeee-CCCCceecCCCCc
Q psy6534 1 MNINKVCCYEHPDA-PLIED-YRAGDQICSECGL 32 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~-~~v~D-~~~G~~vC~~CG~ 32 (309)
|..=...|+.||.. .+..- .+.+...|..||.
T Consensus 1 MP~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 1 MPIYEYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred CCCEEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 55556789999863 33221 2245677999986
No 338
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=66.57 E-value=4.1 Score=34.82 Aligned_cols=29 Identities=28% Similarity=0.400 Sum_probs=20.4
Q ss_pred ccCCCCCCCC--eeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAP--LIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~--~v~D~~~G~~vC~~CG~V~ 34 (309)
..||.|++++ ++.|...=.+.|..||..-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 4699999875 5445333367899999764
No 339
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=65.90 E-value=8.2 Score=34.11 Aligned_cols=30 Identities=10% Similarity=0.101 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+-.++.+|+++.+|||+.|||+..++|.+.
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~~ 46 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLDES 46 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 356899999999999999999999998653
No 340
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=65.80 E-value=6.2 Score=27.42 Aligned_cols=25 Identities=28% Similarity=0.223 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
...||.++|+.+|||+.||-..=++
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 4579999999999999999665443
No 341
>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=65.20 E-value=4.2 Score=26.91 Aligned_cols=28 Identities=21% Similarity=0.440 Sum_probs=20.5
Q ss_pred cccCCCCCCCC-e--eeeCCCCceecCCCCc
Q psy6534 5 KVCCYEHPDAP-L--IEDYRAGDQICSECGL 32 (309)
Q Consensus 5 ~~~Cp~C~~~~-~--v~D~~~G~~vC~~CG~ 32 (309)
.+.|+.|...+ + ..+.+.-..+|..||.
T Consensus 22 aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 22 ALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred eEECcccchhhcccccccCCceEEEcCCCCC
Confidence 45699997654 3 3566667999999996
No 342
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=65.07 E-value=3.1 Score=34.08 Aligned_cols=31 Identities=16% Similarity=0.242 Sum_probs=18.8
Q ss_pred CcccCCCCCCCC--e------------eeeCCCCceecCCCCccc
Q psy6534 4 NKVCCYEHPDAP--L------------IEDYRAGDQICSECGLVV 34 (309)
Q Consensus 4 ~~~~Cp~C~~~~--~------------v~D~~~G~~vC~~CG~V~ 34 (309)
+...||+|+..= + ++-...-...|..||.+.
T Consensus 96 e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 96 EFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 456899998641 1 111122356699999886
No 343
>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=65.06 E-value=15 Score=23.26 Aligned_cols=31 Identities=32% Similarity=0.274 Sum_probs=24.5
Q ss_pred CCCccHHHHHHHhcccHHHHHHHHHHHHHHh
Q psy6534 165 GVPRTFKEICAVSKISKKEIGRCFKLILKAL 195 (309)
Q Consensus 165 ~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l 195 (309)
.-+.|+.|||+.+|++...+.+..++..+.|
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 5578999999999999999888777665544
No 344
>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=65.06 E-value=5.5 Score=39.09 Aligned_cols=31 Identities=23% Similarity=0.419 Sum_probs=23.6
Q ss_pred CCcccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 3 INKVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 3 ~~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
|....||+|+.+ +++-..++.+.|..||...
T Consensus 220 g~~~~C~~C~~~-l~~h~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 220 GYILCCPNCDVS-LTYHKKEGKLRCHYCGYQE 250 (505)
T ss_pred cCccCCCCCCCc-eEEecCCCeEEcCCCcCcC
Confidence 345679999754 6665678899999999875
No 345
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=64.83 E-value=7.8 Score=32.50 Aligned_cols=34 Identities=6% Similarity=0.221 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
...+.+|||+.+|+|..|++++.....+...+.+
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 4689999999999999999988776655544433
No 346
>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=64.64 E-value=5.2 Score=24.84 Aligned_cols=32 Identities=25% Similarity=0.483 Sum_probs=19.9
Q ss_pred CCCCcccCCCCCCC-CeeeeC-CCCceecCCCCc
Q psy6534 1 MNINKVCCYEHPDA-PLIEDY-RAGDQICSECGL 32 (309)
Q Consensus 1 ~~~~~~~Cp~C~~~-~~v~D~-~~G~~vC~~CG~ 32 (309)
|..=...|+.||.. .+..-. +.....|..||.
T Consensus 1 MP~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 1 MPIYEYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred CCCEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 55555678888854 222222 246788888886
No 347
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=64.53 E-value=17 Score=31.91 Aligned_cols=30 Identities=13% Similarity=0.192 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
-.++..++|+.+|||+++++++++.|....
T Consensus 197 grlse~eLAerlGVSRs~ireAlrkLE~aG 226 (251)
T TIGR02787 197 GLLVASKIADRVGITRSVIVNALRKLESAG 226 (251)
T ss_pred ccccHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 468899999999999999999999998764
No 348
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=64.22 E-value=16 Score=29.66 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=34.0
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
|-+|||.+--+...+.++||+..|++++-+.+.+..|.+.-
T Consensus 13 ~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaG 53 (150)
T COG1959 13 ALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAG 53 (150)
T ss_pred HHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcC
Confidence 45677766555578999999999999999999999998753
No 349
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=64.17 E-value=8.1 Score=31.35 Aligned_cols=34 Identities=9% Similarity=0.010 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
...+.+|||+.+|+++.|++.+.....+...+.+
T Consensus 123 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 123 HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999998877776665555
No 350
>PF13730 HTH_36: Helix-turn-helix domain
Probab=64.13 E-value=20 Score=23.09 Aligned_cols=26 Identities=12% Similarity=0.212 Sum_probs=23.2
Q ss_pred ccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 168 RTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 168 ~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
.+..+|++.+|++...+.++++.|.+
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 48999999999999999999988865
No 351
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=64.10 E-value=10 Score=31.74 Aligned_cols=27 Identities=26% Similarity=0.352 Sum_probs=24.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.|.+|||+.+|+|+.|++++++.+..-
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR~~ 178 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRARAW 178 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 599999999999999999999887643
No 352
>PF13518 HTH_28: Helix-turn-helix domain
Probab=63.92 E-value=16 Score=23.04 Aligned_cols=27 Identities=22% Similarity=0.191 Sum_probs=23.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+..++|..+||+..||.+-.+...+.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 999999999999999987777776643
No 353
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=63.88 E-value=18 Score=28.42 Aligned_cols=37 Identities=24% Similarity=0.368 Sum_probs=30.0
Q ss_pred HHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 157 LYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 157 ly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
+|.+.-+.+-|.|..|||+.++.++..+.++.++|.+
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~ 68 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLE 68 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHH
Confidence 4555555677999999999999999999888888765
No 354
>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=63.69 E-value=6.3 Score=21.40 Aligned_cols=23 Identities=26% Similarity=0.507 Sum_probs=12.5
Q ss_pred CCCCCCCCeeeeCC-CCceecCCCCc
Q psy6534 8 CYEHPDAPLIEDYR-AGDQICSECGL 32 (309)
Q Consensus 8 Cp~C~~~~~v~D~~-~G~~vC~~CG~ 32 (309)
|..||.. +...+ .-...|.+||.
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 5566543 23333 33677888873
No 355
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=63.62 E-value=8 Score=31.03 Aligned_cols=30 Identities=10% Similarity=0.098 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.+|||+.+|+|+.|++.++..-.+..
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATHAL 150 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 467899999999999999988876654433
No 356
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=63.58 E-value=10 Score=30.39 Aligned_cols=27 Identities=26% Similarity=0.292 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
...|++|||+.+|+|..||++..+...
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999877665543
No 357
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=63.50 E-value=5 Score=35.68 Aligned_cols=29 Identities=10% Similarity=0.069 Sum_probs=20.9
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
..-||.||+..... ...-...|..||.+.
T Consensus 99 ~~fC~~CG~~~~~~-~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHPMHPS-KTEWAMLCPHCRERY 127 (256)
T ss_pred CccccccCCCCeec-CCceeEECCCCCCEE
Confidence 34799999875443 344578999999765
No 358
>PRK12366 replication factor A; Reviewed
Probab=63.46 E-value=4.8 Score=40.70 Aligned_cols=25 Identities=28% Similarity=0.561 Sum_probs=19.7
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
..||.|+.. ++ + ..|...|..||.+
T Consensus 533 ~aCp~CnkK-v~-~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRKR-VE-E-VDGEYICEFCGEV 557 (637)
T ss_pred ecccccCeE-eE-c-CCCcEECCCCCCC
Confidence 469999763 43 3 5799999999987
No 359
>KOG2906|consensus
Probab=63.42 E-value=4.8 Score=29.85 Aligned_cols=28 Identities=18% Similarity=0.374 Sum_probs=20.0
Q ss_pred cCCCCCCCCeee-eCCCCceecCCCCccc
Q psy6534 7 CCYEHPDAPLIE-DYRAGDQICSECGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~~v~-D~~~G~~vC~~CG~V~ 34 (309)
-||.||.-=+|+ +..-....|..|++|.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCcee
Confidence 599998754444 2223577899999997
No 360
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=63.32 E-value=84 Score=29.97 Aligned_cols=38 Identities=24% Similarity=0.323 Sum_probs=31.4
Q ss_pred HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 250 AIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 250 aiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
|+||+=++. +.++.+|++.+|-+..|+--+++.|.+..
T Consensus 356 amyL~r~lt--~~Slp~IG~~FgrdHtTV~~a~~kI~~~~ 393 (408)
T COG0593 356 AMYLARELT--NLSLPEIGKAFGRDHTTVLHAVRKIEQLI 393 (408)
T ss_pred HHHHHHHHc--cCcHHHHHHHhCCCccHHHHHHHHHHHHH
Confidence 488886654 56888999999988899999999987654
No 361
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=63.30 E-value=5.1 Score=26.25 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=17.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
.++.+||..+||+.+||.+-++.
T Consensus 23 ~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 23 ESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp T-HHHHHHHHT--CCHHHHHHHC
T ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Confidence 38999999999999999887764
No 362
>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=63.17 E-value=6.3 Score=29.78 Aligned_cols=27 Identities=15% Similarity=0.449 Sum_probs=20.9
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
.|--|+...... ..+++||.+||.++.
T Consensus 37 aCeiC~~~GY~q--~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 37 ACEICGPKGYYQ--EGDQLVCKNCGVRFN 63 (102)
T ss_pred eccccCCCceEE--ECCEEEEecCCCEEe
Confidence 588897766543 467999999999983
No 363
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=63.03 E-value=6 Score=26.45 Aligned_cols=24 Identities=25% Similarity=0.628 Sum_probs=17.1
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCcccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~~ 35 (309)
..||.||...+ ---||..||+--+
T Consensus 28 ~~c~~cG~~~l------~Hrvc~~cg~Y~g 51 (57)
T COG0333 28 SVCPNCGEYKL------PHRVCLKCGYYKG 51 (57)
T ss_pred eeccCCCCccc------CceEcCCCCCccC
Confidence 47888887543 3678999997643
No 364
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=62.91 E-value=12 Score=34.42 Aligned_cols=32 Identities=16% Similarity=0.177 Sum_probs=27.3
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 257 ASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 257 ~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.+....||.|||+.+|+|+.++++..++-.+.
T Consensus 22 YY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~ 53 (321)
T COG2390 22 YYVEGLTQSEIAERLGISRATVSRLLAKAREE 53 (321)
T ss_pred HHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 34578999999999999999999988876654
No 365
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=62.86 E-value=1.8e+02 Score=29.44 Aligned_cols=28 Identities=21% Similarity=0.204 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
.+.|+++|++.+|||...|++..+.-..
T Consensus 575 ~~~tl~ei~~~lgvs~eRVrQie~~al~ 602 (619)
T PRK05658 575 TDHTLEEVGKQFDVTRERIRQIEAKALR 602 (619)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5799999999999999999987766443
No 366
>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=62.75 E-value=11 Score=25.62 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=19.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~ke 284 (309)
+..|+|+.+||+..|+++-.++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999999986654
No 367
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=62.65 E-value=1.1e+02 Score=26.83 Aligned_cols=30 Identities=17% Similarity=0.181 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.+|||+.+|+|+.||+++.....+..
T Consensus 216 ~~~s~~EIA~~lgis~~tV~~~~~ra~~~L 245 (251)
T PRK07670 216 EELTLTEIGQVLNLSTSRISQIHSKALFKL 245 (251)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 568999999999999999999886655443
No 368
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=62.56 E-value=22 Score=28.45 Aligned_cols=37 Identities=22% Similarity=0.381 Sum_probs=24.0
Q ss_pred ChHHHHHHHHHHHHHhCC---CCCCHHHHHHHhCCCHHHH
Q psy6534 242 SPISVAAAAIYMASQASS---DKRSQKEIGDIAGVAEVTI 278 (309)
Q Consensus 242 ~P~~iaaAaiyla~~~~~---~~~~~~~ia~~~~vs~~ti 278 (309)
+|.-+=||.+...-.++. .+.|+.+||+.+||+++|+
T Consensus 12 ~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tL 51 (142)
T PF13022_consen 12 TLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTL 51 (142)
T ss_dssp -HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHH
T ss_pred CHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHH
Confidence 345555666665556554 5699999999999999999
No 369
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=62.54 E-value=13 Score=30.71 Aligned_cols=29 Identities=24% Similarity=0.303 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+.+|||+.+|+|++|++.++..-...
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~~ 170 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYVT 170 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46899999999999999998887654433
No 370
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR 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 Gram-positive lineages and does not include the TreR from E. coli.
Probab=62.46 E-value=9.9 Score=32.92 Aligned_cols=30 Identities=27% Similarity=0.361 Sum_probs=25.9
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +-.++|+.+|||..|+|+++.+|...
T Consensus 21 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~e 51 (233)
T TIGR02404 21 GDYLPSEHELMDQYGASRETVRKALNLLTEA 51 (233)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4445 57899999999999999999999864
No 371
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=62.43 E-value=8 Score=25.80 Aligned_cols=25 Identities=16% Similarity=0.258 Sum_probs=17.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
..+++.++|+.+|++..|+.+.++.
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 4569999999999999999887763
No 372
>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=62.17 E-value=6.4 Score=32.31 Aligned_cols=26 Identities=19% Similarity=0.478 Sum_probs=20.1
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
.||.|++. ++ +...|...|..|+..+
T Consensus 36 aC~~C~kk-v~-~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNKK-VV-EEGNGTYRCEKCNKSV 61 (166)
T ss_pred cccccCcc-cE-eCCCCcEECCCCCCcC
Confidence 69999875 43 3334899999999876
No 373
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=62.06 E-value=94 Score=27.92 Aligned_cols=41 Identities=5% Similarity=0.067 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 243 PISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 243 P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
|.-+.-+.-|+-... ..++++.++|+.+|+|+.++.+.+|+
T Consensus 141 ~~~~~~v~~yI~~~~-~~~lsl~~lA~~~g~S~~~L~R~Fk~ 181 (274)
T PRK09978 141 PNMRTRVCTVINNNI-AHEWTLARIASELLMSPSLLKKKLRE 181 (274)
T ss_pred HHHHHHHHHHHHhcc-cCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 444444445655554 45899999999999999999999976
No 374
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=62.03 E-value=63 Score=28.88 Aligned_cols=42 Identities=5% Similarity=0.040 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 243 PISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 243 P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
+..+..+.-|+...+....+++.+||+.+|+|+.++.+.+++
T Consensus 196 ~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~ 237 (302)
T PRK09685 196 ERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 334444555666665555699999999999999999998886
No 375
>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=61.98 E-value=17 Score=23.86 Aligned_cols=33 Identities=27% Similarity=0.214 Sum_probs=27.1
Q ss_pred CCccHHHHHHHhcccHHHHHHHHHHHHHHhccc
Q psy6534 166 VPRTFKEICAVSKISKKEIGRCFKLILKALETS 198 (309)
Q Consensus 166 ~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~ 198 (309)
...+.+|||+.++++.+.+....+.+.+.|+..
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 457889999999999999998888888888863
No 376
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=61.96 E-value=14 Score=30.72 Aligned_cols=30 Identities=17% Similarity=0.030 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.+|||+.+|+|+.|++.++..-....
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARARDAL 174 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 457899999999999999998886655443
No 377
>PRK05580 primosome assembly protein PriA; Validated
Probab=61.91 E-value=6.6 Score=40.04 Aligned_cols=30 Identities=17% Similarity=0.175 Sum_probs=23.5
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
....||+|+. .+++....+.+.|..||...
T Consensus 389 ~~~~C~~C~~-~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 389 WVAECPHCDA-SLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred CccCCCCCCC-ceeEECCCCeEECCCCcCCC
Confidence 3467999976 56776678899999999875
No 378
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=61.88 E-value=18 Score=29.78 Aligned_cols=44 Identities=11% Similarity=0.179 Sum_probs=33.5
Q ss_pred HHHH-HHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 246 VAAA-AIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 246 iaaA-aiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+|.. .+|+|....+.+++.++||+..+++..-+.+....|.+.-
T Consensus 9 yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aG 53 (164)
T PRK10857 9 YAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNG 53 (164)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3444 4456633334579999999999999999999999998763
No 379
>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=61.87 E-value=6 Score=24.57 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=7.1
Q ss_pred eecCCCCccc
Q psy6534 25 QICSECGLVV 34 (309)
Q Consensus 25 ~vC~~CG~V~ 34 (309)
.+|..||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3588888654
No 380
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=61.85 E-value=4.7 Score=40.66 Aligned_cols=13 Identities=23% Similarity=0.726 Sum_probs=6.6
Q ss_pred CCceecCCCCccc
Q psy6534 22 AGDQICSECGLVV 34 (309)
Q Consensus 22 ~G~~vC~~CG~V~ 34 (309)
.|..+|.+||.-+
T Consensus 39 ~~~~fC~~CG~~~ 51 (645)
T PRK14559 39 VDEAHCPNCGAET 51 (645)
T ss_pred cccccccccCCcc
Confidence 3445555555544
No 381
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=61.79 E-value=12 Score=31.80 Aligned_cols=30 Identities=10% Similarity=0.075 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
.-.+.+|||+.+++|+.|+++..+.|+...
T Consensus 151 ~G~snkeIA~~L~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 151 AGQGTIQISDQMNIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 457889999999999999999998887654
No 382
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=61.75 E-value=12 Score=32.43 Aligned_cols=30 Identities=17% Similarity=0.387 Sum_probs=26.8
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +-.++|+.+|||..|||.+++.|...
T Consensus 28 G~~LPsE~eLae~~gVSRt~VReAL~~L~~e 58 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLREVLQRLARD 58 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5678 58999999999999999999999854
No 383
>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=61.69 E-value=15 Score=22.57 Aligned_cols=23 Identities=13% Similarity=0.235 Sum_probs=17.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
-.+.+.|+.+|++..|+.+..++
T Consensus 19 gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 19 GNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp T-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 34678999999999999887764
No 384
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=61.68 E-value=4.2 Score=34.36 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=22.8
Q ss_pred cccCCCCCCCCee----ee-CCCC-----ceecCCCCccccCcccc
Q psy6534 5 KVCCYEHPDAPLI----ED-YRAG-----DQICSECGLVVGDRVID 40 (309)
Q Consensus 5 ~~~Cp~C~~~~~v----~D-~~~G-----~~vC~~CG~V~~e~~id 40 (309)
.+.||.||+.-.. +| +-.| ..+|..||+=..|-...
T Consensus 14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~ 59 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTL 59 (201)
T ss_pred eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeec
Confidence 4689999984211 11 2233 57899999987665443
No 385
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=61.57 E-value=7 Score=24.02 Aligned_cols=27 Identities=15% Similarity=0.265 Sum_probs=15.3
Q ss_pred cCCCCCCCCeeeeC-CCCceecCCCCcc
Q psy6534 7 CCYEHPDAPLIEDY-RAGDQICSECGLV 33 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~-~~G~~vC~~CG~V 33 (309)
.||.|+..-..... .--..+|.+||=+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeE
Confidence 49999874211121 1124569999754
No 386
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=61.51 E-value=5.8 Score=31.08 Aligned_cols=33 Identities=27% Similarity=0.636 Sum_probs=26.2
Q ss_pred eCCCCceecCCCCccc--cCcccccCCCcccccCC
Q psy6534 19 DYRAGDQICSECGLVV--GDRVIDVGSEWRTFSNE 51 (309)
Q Consensus 19 D~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 51 (309)
....|.++|..||.-| .+.-++.|.-|.+|.+.
T Consensus 32 ~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 66 (124)
T PF01641_consen 32 HKEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQP 66 (124)
T ss_dssp TTSSEEEEETTTS-EEEEGGGEETSSSSSSEESSC
T ss_pred CCCCEEEEcCCCCCccccCcccccCCcCCccccCc
Confidence 3578999999999887 55567889999999653
No 387
>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=61.48 E-value=25 Score=27.42 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 149 NDAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 149 ~~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
.+..+.+..|++- ..+-+.+..||++.++++...+.+.++.|.+
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 3445556777874 3456899999999999999999998888876
No 388
>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=61.47 E-value=10 Score=31.15 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+.+|||+.+|+++.|++.+...-.+.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 46899999999999999999887665443
No 389
>PRK14999 histidine utilization repressor; Provisional
Probab=61.36 E-value=12 Score=32.53 Aligned_cols=30 Identities=20% Similarity=0.298 Sum_probs=26.2
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +-.++|+.+|||..|+|+++.+|...
T Consensus 33 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~e 63 (241)
T PRK14999 33 HDRIPSEAELVAQYGFSRMTINRALRELTDE 63 (241)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4455 68899999999999999999999865
No 390
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=61.26 E-value=11 Score=24.23 Aligned_cols=23 Identities=30% Similarity=0.342 Sum_probs=18.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
++.+||++.+|+|..||.+..++
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~ 26 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKD 26 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhc
Confidence 56889999999999999877763
No 391
>PHA00542 putative Cro-like protein
Probab=61.20 E-value=11 Score=27.13 Aligned_cols=26 Identities=31% Similarity=0.330 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
...+++.++|+.+||+..||.+..+.
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 45689999999999999999887643
No 392
>PRK10870 transcriptional repressor MprA; Provisional
Probab=61.17 E-value=69 Score=26.51 Aligned_cols=42 Identities=5% Similarity=-0.028 Sum_probs=32.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCcCCCC
Q psy6534 258 SSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHT 301 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~~~~~~~ 301 (309)
.+..+++.+||+.++++.+|+.+..+.|.+.- |+...-.+.+
T Consensus 68 ~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kG--lV~R~~~~~D 109 (176)
T PRK10870 68 ENHSIQPSELSCALGSSRTNATRIADELEKRG--WIERRESDND 109 (176)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC--CEEecCCCCC
Confidence 35678999999999999999999999998763 5533333333
No 393
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=61.01 E-value=4.2 Score=24.69 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=11.4
Q ss_pred CceecCCCCcccc
Q psy6534 23 GDQICSECGLVVG 35 (309)
Q Consensus 23 G~~vC~~CG~V~~ 35 (309)
|.+||+.|+.+++
T Consensus 2 GtIvCq~C~~~Id 14 (38)
T PF13790_consen 2 GTIVCQHCNETID 14 (38)
T ss_pred CEEEeccccceee
Confidence 8899999998883
No 394
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=61.00 E-value=21 Score=30.33 Aligned_cols=29 Identities=7% Similarity=0.210 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
-+.+..+||+.+|++..|+++.++.|.+.
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34999999999999999999999999875
No 395
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=60.99 E-value=4.9 Score=30.80 Aligned_cols=31 Identities=23% Similarity=0.349 Sum_probs=23.7
Q ss_pred CCcccCCCCCCCCeee-eCCCCceecCCCCccc
Q psy6534 3 INKVCCYEHPDAPLIE-DYRAGDQICSECGLVV 34 (309)
Q Consensus 3 ~~~~~Cp~C~~~~~v~-D~~~G~~vC~~CG~V~ 34 (309)
+|. .|-+||..+..+ ...-|..+|..|.-|.
T Consensus 2 ~N~-~CaDC~~~~p~w~s~~~GifvC~~CsgiH 33 (112)
T smart00105 2 GNK-KCFDCGAPNPTWASVNLGVFLCIECSGIH 33 (112)
T ss_pred CCC-cccCCCCCCCCcEEeccceeEhHHhHHHH
Confidence 455 899999876433 4556999999998887
No 396
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=60.95 E-value=5.4 Score=35.69 Aligned_cols=27 Identities=15% Similarity=0.330 Sum_probs=19.7
Q ss_pred cCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 7 CCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
-|+.||+.+...+. .=-.+|.+||...
T Consensus 113 FCg~CG~~~~~~~~-g~~~~C~~cg~~~ 139 (279)
T COG2816 113 FCGRCGTKTYPREG-GWARVCPKCGHEH 139 (279)
T ss_pred CCCCCCCcCccccC-ceeeeCCCCCCcc
Confidence 59999987544332 3378999999876
No 397
>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=60.87 E-value=12 Score=30.19 Aligned_cols=33 Identities=12% Similarity=0.260 Sum_probs=27.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
..+.+|||+.+|+++.|++++.....+...+.+
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 688999999999999999998877766554444
No 398
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=60.82 E-value=14 Score=31.25 Aligned_cols=30 Identities=17% Similarity=-0.030 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.++||+.+++|+.|+++..+.|+...
T Consensus 164 ~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 164 EGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 558899999999999999999999888653
No 399
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=60.79 E-value=5.9 Score=34.18 Aligned_cols=9 Identities=22% Similarity=0.368 Sum_probs=7.2
Q ss_pred cccCCCCCC
Q psy6534 5 KVCCYEHPD 13 (309)
Q Consensus 5 ~~~Cp~C~~ 13 (309)
+.+||.|+.
T Consensus 5 ~~~CPvC~~ 13 (214)
T PF09986_consen 5 KITCPVCGK 13 (214)
T ss_pred ceECCCCCC
Confidence 468999975
No 400
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=60.67 E-value=15 Score=31.64 Aligned_cols=31 Identities=10% Similarity=0.008 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
....+.+|||+.+++|+.|+++....|.+..
T Consensus 156 a~G~SnkEIA~~L~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 156 SFGFSHEYIAQLLNITVGSSKNKISEILKFF 186 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 3568899999999999999999999988764
No 401
>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=60.64 E-value=1.1e+02 Score=26.27 Aligned_cols=29 Identities=17% Similarity=0.425 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...|+++||+.+|+|+.+|++..+...+.
T Consensus 198 ~~~t~~eIA~~lgis~~~V~~~~~~al~~ 226 (231)
T TIGR02885 198 KDKTQTEVANMLGISQVQVSRLEKKVLKK 226 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46799999999999999999888776544
No 402
>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=60.51 E-value=11 Score=24.25 Aligned_cols=23 Identities=30% Similarity=0.318 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSY 282 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~ 282 (309)
..+++.++|+.+|++..|+.+..
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 46899999999999999998754
No 403
>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=60.44 E-value=13 Score=30.96 Aligned_cols=33 Identities=18% Similarity=0.102 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKL 292 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l 292 (309)
...+.+|||+.+|+++.|++.++....+...+.
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 478999999999999999999988877665443
No 404
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=60.38 E-value=12 Score=32.80 Aligned_cols=29 Identities=14% Similarity=0.247 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
-.++.+|+++.+|||+.|||+-.++|.+.
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~~ 45 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQTQ 45 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46899999999999999999999999774
No 405
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=60.28 E-value=12 Score=31.87 Aligned_cols=30 Identities=17% Similarity=0.350 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.+++..++|+.+|||..+||.+++.|...
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~e 61 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEA 61 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHC
Confidence 567899999999999999999999999754
No 406
>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=60.17 E-value=7.6 Score=32.46 Aligned_cols=32 Identities=22% Similarity=0.162 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASK 291 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~ 291 (309)
...+.+|||+.+|+|+.|++.+.....+...+
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 177 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45889999999999999999887655544433
No 407
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=60.15 E-value=25 Score=28.44 Aligned_cols=45 Identities=27% Similarity=0.273 Sum_probs=38.1
Q ss_pred hHHHHHHHHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 150 DAIASACLYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 150 ~~vaaAcly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
+..+-+.+|+|....+-+.+..+||+..++++.-+.+.+..|++.
T Consensus 8 ~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 8 EYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred hHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 455567889998877779999999999999999999998888763
No 408
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=60.12 E-value=11 Score=32.76 Aligned_cols=26 Identities=12% Similarity=0.229 Sum_probs=24.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+-.++|+.+|||..|+|+++.+|...
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~~e 62 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLVEK 62 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 57899999999999999999999865
No 409
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=60.08 E-value=44 Score=25.49 Aligned_cols=36 Identities=14% Similarity=0.117 Sum_probs=30.4
Q ss_pred CCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHhhcccC
Q psy6534 258 SSDKRSQKEIGDIAG-VAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 258 ~~~~~~~~~ia~~~~-vs~~ti~~~~kei~~~~~~l~ 293 (309)
.|.+.|...|-..+| -|..||.+.++++........
T Consensus 16 ~G~~pT~~~Vr~~lG~GS~~ti~~~l~~w~~~~~~~~ 52 (120)
T PF11740_consen 16 AGKKPTVRAVRERLGGGSMSTISKHLKEWREEREAQV 52 (120)
T ss_pred cCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHhhhccc
Confidence 377889999999999 999999999999987765444
No 410
>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=60.05 E-value=12 Score=25.45 Aligned_cols=22 Identities=14% Similarity=0.200 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~ke 284 (309)
+..|+|+.+||++.||+.-.++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999965444
No 411
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=60.04 E-value=5.7 Score=31.37 Aligned_cols=33 Identities=21% Similarity=0.396 Sum_probs=21.7
Q ss_pred CCCcccCCCCCCCCeeee----CCCCceecCCCCccc
Q psy6534 2 NINKVCCYEHPDAPLIED----YRAGDQICSECGLVV 34 (309)
Q Consensus 2 ~~~~~~Cp~C~~~~~v~D----~~~G~~vC~~CG~V~ 34 (309)
......||.|++.++..- ...--..|.+||.-.
T Consensus 27 ~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf 63 (129)
T COG3677 27 QITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTF 63 (129)
T ss_pred hcccCcCCCCCccceeeECCccccccccccCCcCcce
Confidence 344568999998883332 112367899999654
No 412
>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=60.03 E-value=11 Score=30.80 Aligned_cols=48 Identities=17% Similarity=0.077 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q psy6534 244 ISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASK 291 (309)
Q Consensus 244 ~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~ 291 (309)
..|+.|++=|-.+..=.++|.+||++.+||+++|+=..|+...+....
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK~dLl~~ 53 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDKYELLTW 53 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCHHHHHHH
Confidence 345555555554433357999999999999999998888765554433
No 413
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=59.98 E-value=6.4 Score=28.15 Aligned_cols=29 Identities=24% Similarity=0.149 Sum_probs=19.4
Q ss_pred cccCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
+..||-||...+..+....--||.-|+.-
T Consensus 1 K~~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred CccCCCCCcEEeccCCCcCceECCCCCcc
Confidence 35799999754433222227899999965
No 414
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=59.74 E-value=26 Score=26.44 Aligned_cols=33 Identities=15% Similarity=0.085 Sum_probs=29.0
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 256 QASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 256 ~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+..+++.+|++.++++.+|+.+..+.|.+.
T Consensus 38 ~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k 70 (109)
T TIGR01889 38 ENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK 70 (109)
T ss_pred hccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 334567999999999999999999999999876
No 415
>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=59.70 E-value=13 Score=25.22 Aligned_cols=22 Identities=36% Similarity=0.410 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~ke 284 (309)
+..|+|+.+||+..||+.--++
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999965444
No 416
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=59.66 E-value=16 Score=29.05 Aligned_cols=29 Identities=14% Similarity=0.109 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+.+|||+.+|+++.|++++.......
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46889999999999999999887665543
No 417
>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=59.38 E-value=23 Score=23.72 Aligned_cols=32 Identities=22% Similarity=0.255 Sum_probs=23.9
Q ss_pred hcCCCccHHHHHHHhcccHHHHHHHHHHHHHH
Q psy6534 163 QEGVPRTFKEICAVSKISKKEIGRCFKLILKA 194 (309)
Q Consensus 163 ~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~ 194 (309)
..+-+.++.+|++.++++...+.+.++++.+.
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 56778999999999999999999988888763
No 418
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=59.35 E-value=18 Score=30.33 Aligned_cols=30 Identities=7% Similarity=0.063 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.+|||+.+++|+.|+++..+.|.+..
T Consensus 147 qGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 147 SGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 467889999999999999999998888654
No 419
>smart00400 ZnF_CHCC zinc finger.
Probab=59.29 E-value=11 Score=24.77 Aligned_cols=25 Identities=20% Similarity=0.279 Sum_probs=20.1
Q ss_pred cCCCCCCC--CeeeeCCCCceecCCCC
Q psy6534 7 CCYEHPDA--PLIEDYRAGDQICSECG 31 (309)
Q Consensus 7 ~Cp~C~~~--~~v~D~~~G~~vC~~CG 31 (309)
.||.|... .+..+...+...|-.||
T Consensus 4 ~cPfh~d~~pSf~v~~~kn~~~Cf~cg 30 (55)
T smart00400 4 LCPFHGEKTPSFSVSPDKQFFHCFGCG 30 (55)
T ss_pred cCcCCCCCCCCEEEECCCCEEEEeCCC
Confidence 59998644 47778888899999997
No 420
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=59.27 E-value=4.8 Score=36.39 Aligned_cols=28 Identities=25% Similarity=0.478 Sum_probs=11.9
Q ss_pred cccCCCCCCCCe---eeeCC-CC--ceecCCCCc
Q psy6534 5 KVCCYEHPDAPL---IEDYR-AG--DQICSECGL 32 (309)
Q Consensus 5 ~~~Cp~C~~~~~---v~D~~-~G--~~vC~~CG~ 32 (309)
...||.||+... +.... .| -+.|+-||+
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t 205 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGT 205 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCC
Confidence 458999998742 22211 14 689999994
No 421
>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=59.24 E-value=12 Score=29.69 Aligned_cols=30 Identities=13% Similarity=0.144 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.+|||+.+|+++.|++++........
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~L 149 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKEL 149 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 468999999999999999998876655443
No 422
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=59.23 E-value=14 Score=30.58 Aligned_cols=37 Identities=22% Similarity=0.243 Sum_probs=30.9
Q ss_pred HHHHHHhcCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 157 LYIACRQEGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 157 ly~acR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
||-+.-.++-|.|+.||++++|+|+..+.-..+++..
T Consensus 31 iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 4444455688999999999999999999988888765
No 423
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=59.16 E-value=9 Score=30.36 Aligned_cols=34 Identities=24% Similarity=0.642 Sum_probs=27.4
Q ss_pred eeCCCCceecCCCCccc--cCcccccCCCcccccCC
Q psy6534 18 EDYRAGDQICSECGLVV--GDRVIDVGSEWRTFSNE 51 (309)
Q Consensus 18 ~D~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 51 (309)
...+.|.++|..||.-| .+.-+|.|--|.+|.+.
T Consensus 36 ~~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~p 71 (140)
T COG0229 36 DNKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKP 71 (140)
T ss_pred cccCCceEEeecCCCccccccccccCCCCCcccccc
Confidence 34678999999999876 55578899999999653
No 424
>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=59.15 E-value=7.8 Score=29.10 Aligned_cols=29 Identities=21% Similarity=0.275 Sum_probs=19.6
Q ss_pred cccCCCCCCCCeeee---------CCCCceecCCCCcc
Q psy6534 5 KVCCYEHPDAPLIED---------YRAGDQICSECGLV 33 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D---------~~~G~~vC~~CG~V 33 (309)
...||.||....++= ..+=..+|.+||..
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCe
Confidence 358999998764331 23336789999963
No 425
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=59.06 E-value=14 Score=31.86 Aligned_cols=30 Identities=13% Similarity=0.244 Sum_probs=26.1
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +-.++|+..|||..|+|+++.+|...
T Consensus 22 g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~e 52 (230)
T TIGR02018 22 GHRIPSEHELVAQYGCSRMTVNRALRELTDA 52 (230)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3455 67899999999999999999999875
No 426
>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=59.05 E-value=30 Score=21.40 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=21.9
Q ss_pred hcCCCccHHHHHHHhcccHHHHHHHHHHH
Q psy6534 163 QEGVPRTFKEICAVSKISKKEIGRCFKLI 191 (309)
Q Consensus 163 ~~~~~~tl~eia~~~~~~~~~i~~~~~~l 191 (309)
+.+..++..+|++.+|++...+.+.+++|
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 45567899999999999999998877766
No 427
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=58.98 E-value=21 Score=25.42 Aligned_cols=31 Identities=10% Similarity=0.189 Sum_probs=21.4
Q ss_pred HHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy6534 253 MASQASSDKRSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 253 la~~~~~~~~~~~~ia~~~~vs~~ti~~~~k 283 (309)
+...+.....||+++|+.+|++.++|.+.-+
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 3344445779999999999999999987653
No 428
>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=58.94 E-value=15 Score=31.92 Aligned_cols=27 Identities=26% Similarity=0.471 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
...+.+|||+.+|+|++|++++.....
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~ 223 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRIL 223 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999988864433
No 429
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=58.90 E-value=12 Score=32.29 Aligned_cols=30 Identities=17% Similarity=0.287 Sum_probs=25.8
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +-.|+|+.+|||..|+|+++.+|...
T Consensus 29 G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~e 59 (238)
T TIGR02325 29 GDYLPAEMQLAERFGVNRHTVRRAIAALVER 59 (238)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3445 67899999999999999999999865
No 430
>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=58.85 E-value=15 Score=20.46 Aligned_cols=21 Identities=29% Similarity=0.278 Sum_probs=18.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHH
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQS 281 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~ 281 (309)
..+..+|++.+|++..|+.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 458999999999999998763
No 431
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=58.84 E-value=3.2 Score=34.14 Aligned_cols=27 Identities=30% Similarity=0.410 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
.|+++++||+.+|++++||.++.+.-+
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~~Ky 74 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVKNKY 74 (160)
T ss_dssp ---------------------------
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHcCce
Confidence 478999999999999999999887654
No 432
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=58.74 E-value=57 Score=27.24 Aligned_cols=68 Identities=19% Similarity=0.226 Sum_probs=48.9
Q ss_pred HHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHh-CCCHHHHHHHHHHH
Q psy6534 207 FMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIA-GVAEVTIRQSYKLM 285 (309)
Q Consensus 207 ~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~-~vs~~ti~~~~kei 285 (309)
.+......|+|++.....-..++......++..|..|. +-.+-.+++..+ |+++.|+++....|
T Consensus 31 ~l~~a~~~lgl~~~~l~vL~aLls~~~~~d~~~~~~pi---------------VfpSN~~La~r~~G~s~~tlrR~l~~L 95 (177)
T PF03428_consen 31 ALKEARPALGLSDRALAVLDALLSFTPPDDWEPGRRPI---------------VFPSNAQLAERLNGMSERTLRRHLARL 95 (177)
T ss_pred HHHHHHHhcCCChhHHHHHHHHHHhCCcccccCCCCce---------------eecCHHHHHHHHcCCCHHHHHHHHHHH
Confidence 44555567888876666666666665555566666653 223556899999 99999999999999
Q ss_pred HHhh
Q psy6534 286 YPHA 289 (309)
Q Consensus 286 ~~~~ 289 (309)
.+.-
T Consensus 96 veaG 99 (177)
T PF03428_consen 96 VEAG 99 (177)
T ss_pred HHCC
Confidence 9864
No 433
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent 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. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=58.66 E-value=10 Score=27.20 Aligned_cols=25 Identities=16% Similarity=0.357 Sum_probs=17.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~k 283 (309)
..+-|.++.|..+|||.+|+-+-..
T Consensus 17 ~~~aTVR~~Ak~FGvSKSTVHkDvt 41 (82)
T PF12116_consen 17 ETKATVRQAAKVFGVSKSTVHKDVT 41 (82)
T ss_dssp HH---HHHHHHHHTS-HHHHHHHHT
T ss_pred HcccHHHHHHHHHCCcHHHHHHHHH
Confidence 4578899999999999999865443
No 434
>PRK15482 transcriptional regulator MurR; Provisional
Probab=58.66 E-value=25 Score=31.51 Aligned_cols=25 Identities=12% Similarity=0.248 Sum_probs=21.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
..+..|+|+.+|||+.||-+..|.|
T Consensus 34 ~~si~elA~~~~vS~aTv~Rf~kkL 58 (285)
T PRK15482 34 SVSSRKMAKQLGISQSSIVKFAQKL 58 (285)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHh
Confidence 3678899999999999998876654
No 435
>KOG3134|consensus
Probab=58.62 E-value=3 Score=35.66 Aligned_cols=30 Identities=30% Similarity=0.541 Sum_probs=24.4
Q ss_pred ccCCCCCCC--CeeeeCCCC---ceecCCCCcccc
Q psy6534 6 VCCYEHPDA--PLIEDYRAG---DQICSECGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~--~~v~D~~~G---~~vC~~CG~V~~ 35 (309)
+.|-+||.. .+..+++.| -..|.+|+.|++
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 479999975 477788888 568999999984
No 436
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=58.58 E-value=39 Score=29.05 Aligned_cols=30 Identities=7% Similarity=0.236 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
++.++++||+.+|+++.|+.+..++|.+.-
T Consensus 172 i~~t~~~iA~~lG~tretvsR~l~~L~~~g 201 (236)
T PRK09392 172 LPYEKRVLASYLGMTPENLSRAFAALASHG 201 (236)
T ss_pred eeCCHHHHHHHhCCChhHHHHHHHHHHhCC
Confidence 567889999999999999999999998654
No 437
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=58.42 E-value=15 Score=31.39 Aligned_cols=33 Identities=18% Similarity=0.209 Sum_probs=27.5
Q ss_pred hCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 257 ASSDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 257 ~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
+...-.+-+|||+.+++|+.|++.....|+...
T Consensus 159 lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 159 LLAEGLSNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred HHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 334567889999999999999999998887653
No 438
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=58.42 E-value=13 Score=30.15 Aligned_cols=32 Identities=19% Similarity=0.124 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASK 291 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~ 291 (309)
...+.+|||+.+|+++.|++++.....+...+
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888776654433
No 439
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=58.40 E-value=14 Score=27.51 Aligned_cols=38 Identities=21% Similarity=0.255 Sum_probs=31.4
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 249 AAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 249 Aaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
+=+-++.++..-..+|+||+..+||+..||.+--..|.
T Consensus 48 ~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK 85 (103)
T COG2973 48 TRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLK 85 (103)
T ss_pred HHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhc
Confidence 44567777778889999999999999999987766664
No 440
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=58.33 E-value=28 Score=23.95 Aligned_cols=36 Identities=8% Similarity=0.003 Sum_probs=32.1
Q ss_pred HHhcCCCccHHHHHHHhcccHHHHHHHHHHHHHHhc
Q psy6534 161 CRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALE 196 (309)
Q Consensus 161 cR~~~~~~tl~eia~~~~~~~~~i~~~~~~l~~~l~ 196 (309)
.|..+.|+++.+.++.+|++...+.+..+.+++.+-
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll 42 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLL 42 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 367789999999999999999999999998888764
No 441
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=58.28 E-value=23 Score=22.37 Aligned_cols=32 Identities=28% Similarity=0.251 Sum_probs=27.4
Q ss_pred CccHHHHHHHhcccHHHHHHHHHHHHHHhccc
Q psy6534 167 PRTFKEICAVSKISKKEIGRCFKLILKALETS 198 (309)
Q Consensus 167 ~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~ 198 (309)
..+..|||+.++++...+.+...++.+.|+.+
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 35889999999999999999888888877753
No 442
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=58.01 E-value=14 Score=28.54 Aligned_cols=28 Identities=21% Similarity=0.306 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMY 286 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~ 286 (309)
+...++.|+|+.+||+..||..+.+.+-
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg 96 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRALKRLG 96 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHHHHcC
Confidence 4678999999999999999999999873
No 443
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=58.01 E-value=25 Score=31.25 Aligned_cols=25 Identities=20% Similarity=0.310 Sum_probs=21.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
..+.+++|+.+|||+.||-+..|.|
T Consensus 34 ~~si~~lA~~~~vS~aTv~Rf~kkl 58 (284)
T PRK11302 34 HSSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 3678899999999999998876654
No 444
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=57.95 E-value=12 Score=31.44 Aligned_cols=34 Identities=21% Similarity=0.220 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
...+.+|||+.+|++..|++++...-.+...+.+
T Consensus 149 ~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 149 QGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4589999999999999999998755444433333
No 445
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=57.71 E-value=16 Score=31.90 Aligned_cols=30 Identities=23% Similarity=0.391 Sum_probs=26.3
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +-.++|+.+|||..|+|++..+|...
T Consensus 26 G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~e 56 (240)
T PRK09764 26 GDALPTESALQTEFGVSRVTVRQALRQLVEQ 56 (240)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4566 57899999999999999999999865
No 446
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=57.68 E-value=18 Score=24.14 Aligned_cols=27 Identities=15% Similarity=0.231 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
++-.+||+..|++.+.|-+++++|..+
T Consensus 5 lvas~iAd~~GiTRSvIVNALRKleSa 31 (61)
T PF08222_consen 5 LVASKIADRVGITRSVIVNALRKLESA 31 (61)
T ss_dssp E-HHHHHHHHT--HHHHHHHHHHHHHT
T ss_pred ehHHHHHHHhCccHHHHHHHHHHHHhc
Confidence 345689999999999999999999765
No 447
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=57.62 E-value=30 Score=24.88 Aligned_cols=28 Identities=18% Similarity=0.189 Sum_probs=26.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
..++++|++.++++..||.+.++.|.+.
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 5899999999999999999999999876
No 448
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=57.57 E-value=9.3 Score=25.97 Aligned_cols=21 Identities=29% Similarity=0.447 Sum_probs=17.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHH
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYK 283 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~k 283 (309)
+..|+|+.+||++.||+.--+
T Consensus 2 ti~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 568999999999999987644
No 449
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=57.56 E-value=8.8 Score=26.78 Aligned_cols=26 Identities=19% Similarity=0.308 Sum_probs=15.7
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
..||.|... +..+ .|.+.|..|+.-.
T Consensus 2 ~~CP~C~~~-L~~~--~~~~~C~~C~~~~ 27 (70)
T PF07191_consen 2 NTCPKCQQE-LEWQ--GGHYHCEACQKDY 27 (70)
T ss_dssp -B-SSS-SB-EEEE--TTEEEETTT--EE
T ss_pred CcCCCCCCc-cEEe--CCEEECccccccc
Confidence 479999765 5444 4899999998644
No 450
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=57.55 E-value=11 Score=33.46 Aligned_cols=30 Identities=30% Similarity=0.469 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
-.++.+|+++.++||+.|||+-.++|.+..
T Consensus 18 g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g 47 (253)
T COG1349 18 GKVSVEELAELFGVSEMTIRRDLNELEEQG 47 (253)
T ss_pred CcEEHHHHHHHhCCCHHHHHHhHHHHHHCC
Confidence 458899999999999999999999998753
No 451
>PRK09954 putative kinase; Provisional
Probab=57.53 E-value=21 Score=33.07 Aligned_cols=29 Identities=17% Similarity=0.172 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
-++++.+||+.+|+|+.|++++.+.|.+.
T Consensus 16 ~~~s~~~la~~l~~s~~~v~~~i~~L~~~ 44 (362)
T PRK09954 16 PLIQQNEIADILQISRSRVAAHIMDLMRK 44 (362)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 47999999999999999999999999873
No 452
>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=57.50 E-value=1.2e+02 Score=25.85 Aligned_cols=28 Identities=25% Similarity=0.396 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
...+.+|||+.+|++..|++++++.-.+
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4679999999999999999987765443
No 453
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=57.44 E-value=13 Score=30.29 Aligned_cols=29 Identities=17% Similarity=0.192 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+.+|||+.+|+++.|+++++..-.+.
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46889999999999999998776554433
No 454
>PHA01976 helix-turn-helix protein
Probab=57.23 E-value=13 Score=25.05 Aligned_cols=23 Identities=26% Similarity=0.157 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSY 282 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~ 282 (309)
..+++.++|+.+|++..||.+-.
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e 36 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFE 36 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 45899999999999999998743
No 455
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=57.20 E-value=13 Score=30.66 Aligned_cols=32 Identities=31% Similarity=0.386 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcc
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASK 291 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~ 291 (309)
...+.+|||+.+|+|++|+++++..-.+...+
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999988776554433
No 456
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=57.20 E-value=64 Score=27.20 Aligned_cols=110 Identities=19% Similarity=0.261 Sum_probs=57.6
Q ss_pred hHHHHHHHHHHHHhcCCC-ccHHHHHHHhcccH-HHHHHHHHHHHHHhcccCCCCChHHHHHHHHhh--CCCCHHHHHHH
Q psy6534 150 DAIASACLYIACRQEGVP-RTFKEICAVSKISK-KEIGRCFKLILKALETSVDLITTGDFMSRFCSN--LSLPNMVQKAA 225 (309)
Q Consensus 150 ~~vaaAcly~acR~~~~~-~tl~eia~~~~~~~-~~i~~~~~~l~~~l~~~~~~~~p~~~i~~~~~~--L~l~~~~~~~a 225 (309)
..++=|.||++ +-| +++++|++.++.+. ..+......+.+....+-..+. |..+... |...++.....
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~gl~----l~~~~~~y~l~tk~e~~~~i 74 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAGIE----IIKFGQSYSLVTKPAFADYI 74 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCCEE----EEEECCEEEEEEhHHHHHHH
Confidence 45677888887 777 99999999999884 4555555555544332100000 0001111 11122222222
Q ss_pred HHHHHHhhhcCccCCCChHHHHHHHH-HHHHHhCCCCCCHHHHHHHhCCCHHH
Q psy6534 226 THIARKAVELDIVPGRSPISVAAAAI-YMASQASSDKRSQKEIGDIAGVAEVT 277 (309)
Q Consensus 226 ~~i~~~~~~~~l~~Gr~P~~iaaAai-yla~~~~~~~~~~~~ia~~~~vs~~t 277 (309)
..++.. ...+ +--|++ -||.-.++.|+|..+|-+.=||+...
T Consensus 75 ~~~~~~--------~~~~--LS~aaLEtLAIIAY~QPITr~eIe~IRGv~s~~ 117 (186)
T TIGR00281 75 HRFLPA--------KLKN--LNSASLEVLAIIAYKQPITRARINEIRGVKSYQ 117 (186)
T ss_pred HHHhcc--------cccc--CCHHHHHHHHHHHHcCCcCHHHHHHHcCCCHHH
Confidence 222211 0111 221222 34444567899999999999997543
No 457
>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=57.15 E-value=23 Score=24.56 Aligned_cols=33 Identities=15% Similarity=0.165 Sum_probs=23.0
Q ss_pred HHHHHHhcCCCccHHHHHHHhc-ccHHHHHHHHHHH
Q psy6534 157 LYIACRQEGVPRTFKEICAVSK-ISKKEIGRCFKLI 191 (309)
Q Consensus 157 ly~acR~~~~~~tl~eia~~~~-~~~~~i~~~~~~l 191 (309)
.|++-+.. ..++.+|+..+| -|-..+..+++++
T Consensus 37 ~yL~r~~~--~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 37 MYLARELT--GLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHS-----HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred HHHHHHHh--CCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 46654433 588999999998 8988888887764
No 458
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=57.09 E-value=5.8 Score=40.08 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=9.9
Q ss_pred eecCCCCccccCc
Q psy6534 25 QICSECGLVVGDR 37 (309)
Q Consensus 25 ~vC~~CG~V~~e~ 37 (309)
..|..||.-+...
T Consensus 28 ~~Cp~CG~~~~~~ 40 (645)
T PRK14559 28 KPCPQCGTEVPVD 40 (645)
T ss_pred CcCCCCCCCCCcc
Confidence 5799999887543
No 459
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=57.04 E-value=14 Score=31.63 Aligned_cols=30 Identities=10% Similarity=0.212 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.+++..++|+.+|||..++|.+++.|...
T Consensus 32 G~~L~e~~La~~lgVSRtpVREAL~~L~~e 61 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVREALLRLVSV 61 (221)
T ss_pred CCccCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 567888999999999999999999999754
No 460
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=56.93 E-value=14 Score=32.23 Aligned_cols=26 Identities=23% Similarity=0.479 Sum_probs=23.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 263 SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 263 ~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
+-.++|+.+|||+.|+|+++++|.+.
T Consensus 33 sE~eLa~~f~VSR~TvRkAL~~L~~e 58 (236)
T COG2188 33 SERELAEQFGVSRMTVRKALDELVEE 58 (236)
T ss_pred CHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 56799999999999999999999875
No 461
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=56.81 E-value=9.7 Score=31.86 Aligned_cols=30 Identities=13% Similarity=0.082 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.+|||+.+|+++.|++.+.....+..
T Consensus 151 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 180 (195)
T PRK12532 151 LGFSSDEIQQMCGISTSNYHTIMHRARESL 180 (195)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 457899999999999999988876544433
No 462
>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=56.53 E-value=8.6 Score=24.46 Aligned_cols=28 Identities=21% Similarity=0.332 Sum_probs=17.6
Q ss_pred cCCCCCCCCeeeeC-------CCCceecCC--CCccc
Q psy6534 7 CCYEHPDAPLIEDY-------RAGDQICSE--CGLVV 34 (309)
Q Consensus 7 ~Cp~C~~~~~v~D~-------~~G~~vC~~--CG~V~ 34 (309)
.||.||+...+... .+--..|++ ||.-.
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 59999987655431 222456777 98654
No 463
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=56.52 E-value=4.8 Score=26.70 Aligned_cols=24 Identities=17% Similarity=0.077 Sum_probs=15.1
Q ss_pred CCcccCCCCCCCCeeeeCCCCceecC
Q psy6534 3 INKVCCYEHPDAPLIEDYRAGDQICS 28 (309)
Q Consensus 3 ~~~~~Cp~C~~~~~v~D~~~G~~vC~ 28 (309)
|.-..||.|+...+++|.. .++|+
T Consensus 12 Gal~~Cp~C~~~~l~~~~~--~Y~C~ 35 (55)
T PF08063_consen 12 GALEPCPKCKGGQLYFDGS--GYKCT 35 (55)
T ss_dssp TEE---SSSSE-EEEEETT--EEEEE
T ss_pred cCCCCCCCCCCCeEEecCC--ccEeC
Confidence 4456899999888888753 78886
No 464
>PRK03837 transcriptional regulator NanR; Provisional
Probab=56.43 E-value=17 Score=31.41 Aligned_cols=30 Identities=20% Similarity=0.371 Sum_probs=26.9
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +..++|+.+|||..++|.+++.|...
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~e 64 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKRK 64 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 5678 78999999999999999999999854
No 465
>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=56.42 E-value=41 Score=24.79 Aligned_cols=30 Identities=13% Similarity=0.200 Sum_probs=26.6
Q ss_pred cCCCccHHHHHHHhcccHHHHHHHHHHHHH
Q psy6534 164 EGVPRTFKEICAVSKISKKEIGRCFKLILK 193 (309)
Q Consensus 164 ~~~~~tl~eia~~~~~~~~~i~~~~~~l~~ 193 (309)
...+++..|||+.++++...+.++++.|.+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 467899999999999999999998888765
No 466
>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=56.33 E-value=17 Score=29.34 Aligned_cols=29 Identities=14% Similarity=0.082 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+.+|||+.+|+++.|++++.....+.
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAIKK 165 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45899999999999999999888765544
No 467
>PRK09480 slmA division inhibitor protein; Provisional
Probab=56.28 E-value=18 Score=29.90 Aligned_cols=42 Identities=12% Similarity=0.222 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 243 PISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 243 P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
...|.-|++-+...-.|...|.++||+.+||+..||=..|+.
T Consensus 12 r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 12 REQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred HHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence 344555555544444357899999999999999999877744
No 468
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=56.19 E-value=13 Score=24.95 Aligned_cols=23 Identities=26% Similarity=0.309 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSY 282 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~ 282 (309)
-.+|+.++|+.+|+|.+|+.+.-
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHH
Confidence 35899999999999999987653
No 469
>PRK15320 transcriptional activator SprB; Provisional
Probab=56.14 E-value=18 Score=30.81 Aligned_cols=31 Identities=16% Similarity=0.099 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
....+++|||+.+++|.+||.++-..|.+..
T Consensus 177 AkG~SNKEIAekL~LS~KTVSTYKnRLLeKL 207 (251)
T PRK15320 177 SSGHPAIELAKKFGLGTKTVSIYRKKVMYRL 207 (251)
T ss_pred HcCCCHHHHHHHhccchhhHHHHHHHHHHHc
Confidence 3567899999999999999999999888763
No 470
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=56.06 E-value=7.7 Score=29.86 Aligned_cols=6 Identities=17% Similarity=0.910 Sum_probs=3.3
Q ss_pred cCCCCC
Q psy6534 7 CCYEHP 12 (309)
Q Consensus 7 ~Cp~C~ 12 (309)
.|+.||
T Consensus 72 ~C~~Cg 77 (113)
T PRK12380 72 WCWDCS 77 (113)
T ss_pred EcccCC
Confidence 455555
No 471
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=56.04 E-value=17 Score=31.11 Aligned_cols=30 Identities=7% Similarity=0.078 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.+++..++|+.+|||..+||.+.+.|...
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L~~e 57 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQLVAE 57 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 678899999999999999999999999754
No 472
>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=56.01 E-value=19 Score=28.65 Aligned_cols=29 Identities=7% Similarity=0.043 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+.+|||+.+|+|+.|++.+.......
T Consensus 126 ~g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 126 RGVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 46899999999999999999887665543
No 473
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=55.88 E-value=11 Score=26.78 Aligned_cols=24 Identities=17% Similarity=0.198 Sum_probs=22.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
-|.+++++.+|+++.|+.+..+||
T Consensus 53 ~s~eel~~~L~~s~~tv~~~~keL 76 (76)
T PF06970_consen 53 FSIEELMELLNCSKSTVIKAKKEL 76 (76)
T ss_pred eeHHHHHHHHCCCHHHHHHHHHcC
Confidence 488999999999999999999875
No 474
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=55.66 E-value=6.7 Score=23.59 Aligned_cols=23 Identities=13% Similarity=0.192 Sum_probs=10.6
Q ss_pred cccCCCCCCCCeeeeCCCCceec
Q psy6534 5 KVCCYEHPDAPLIEDYRAGDQIC 27 (309)
Q Consensus 5 ~~~Cp~C~~~~~v~D~~~G~~vC 27 (309)
..+|..||..--+.+...|.++|
T Consensus 6 ~YkC~~CGniVev~~~g~g~lvC 28 (36)
T PF06397_consen 6 FYKCEHCGNIVEVVHDGGGPLVC 28 (36)
T ss_dssp EEE-TTT--EEEEEE--SS-EEE
T ss_pred EEEccCCCCEEEEEECCCCCEEe
Confidence 35688887643335666777877
No 475
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=55.65 E-value=32 Score=22.58 Aligned_cols=29 Identities=31% Similarity=0.546 Sum_probs=25.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
..+.++||..+++|+.|++...+.++...
T Consensus 19 G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 19 GKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 38899999999999999999988887653
No 476
>PRK10072 putative transcriptional regulator; Provisional
Probab=55.59 E-value=14 Score=27.58 Aligned_cols=24 Identities=8% Similarity=0.166 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHH
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSY 282 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~ 282 (309)
...++|.++|+.+|++..||++--
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE 67 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWE 67 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 457899999999999999997654
No 477
>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=55.57 E-value=27 Score=22.11 Aligned_cols=32 Identities=28% Similarity=0.381 Sum_probs=27.8
Q ss_pred CccHHHHHHHhcccHHHHHHHHHHHHHHhccc
Q psy6534 167 PRTFKEICAVSKISKKEIGRCFKLILKALETS 198 (309)
Q Consensus 167 ~~tl~eia~~~~~~~~~i~~~~~~l~~~l~~~ 198 (309)
..+.++||+.++++...+.....++.+.++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 46999999999999999999988888877753
No 478
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=55.53 E-value=12 Score=32.49 Aligned_cols=34 Identities=15% Similarity=0.172 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
...+.+|||+.+|+|..|+++++........+.+
T Consensus 164 ~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 164 EELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999988876554444433
No 479
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=55.48 E-value=13 Score=30.63 Aligned_cols=31 Identities=16% Similarity=0.186 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhc
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHAS 290 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~ 290 (309)
...+.+|||+.+|+++.|++.++........
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3569999999999999999888766554443
No 480
>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=55.46 E-value=3.6 Score=26.68 Aligned_cols=30 Identities=10% Similarity=0.185 Sum_probs=21.3
Q ss_pred cccCCCCCCCCee-eeCCCCceecCCCCccc
Q psy6534 5 KVCCYEHPDAPLI-EDYRAGDQICSECGLVV 34 (309)
Q Consensus 5 ~~~Cp~C~~~~~v-~D~~~G~~vC~~CG~V~ 34 (309)
...|+.|+.-=.- .+....++-|.-||.+-
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 4589999753211 24456899999999985
No 481
>PRK14873 primosome assembly protein PriA; Provisional
Probab=55.43 E-value=9.6 Score=38.73 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=21.2
Q ss_pred CcccCCCCCCCCeeeeCCCCceecCCCCcc
Q psy6534 4 NKVCCYEHPDAPLIEDYRAGDQICSECGLV 33 (309)
Q Consensus 4 ~~~~Cp~C~~~~~v~D~~~G~~vC~~CG~V 33 (309)
....||+|+.+ +++-...+...|.-||.-
T Consensus 391 ~~~~C~~C~~~-L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 391 TPARCRHCTGP-LGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred CeeECCCCCCc-eeEecCCCeeECCCCcCC
Confidence 45679999754 555445778999999974
No 482
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=55.39 E-value=1.5e+02 Score=26.21 Aligned_cols=25 Identities=36% Similarity=0.453 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
...+.+|||+.+|+++.|++++++.
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~r 251 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTK 251 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4689999999999999999976644
No 483
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=55.34 E-value=14 Score=30.54 Aligned_cols=30 Identities=7% Similarity=-0.060 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.+|||+.+|++..||+++.....+..
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 468999999999999999988775544433
No 484
>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=55.30 E-value=3.9 Score=38.14 Aligned_cols=78 Identities=12% Similarity=0.060 Sum_probs=0.0
Q ss_pred HHhhCC--CCHHHHHHHHHHHHHhh-hcCccCCCChHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy6534 211 FCSNLS--LPNMVQKAATHIARKAV-ELDIVPGRSPISVAAAAIYMASQASSDKRSQKEIGDIAGVAEVTIRQSYKLMYP 287 (309)
Q Consensus 211 ~~~~L~--l~~~~~~~a~~i~~~~~-~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~ia~~~~vs~~ti~~~~kei~~ 287 (309)
++..++ +++.+...|..+++... ......+..-.+=+.+|+|+||..++.+..+.......++.+...++.|+.|..
T Consensus 4 l~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~~ 83 (353)
T PF05460_consen 4 LIPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFEN 83 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHHH
Confidence 334443 35678888888888777 334455555566678999999999999888888888899998766666666654
Q ss_pred h
Q psy6534 288 H 288 (309)
Q Consensus 288 ~ 288 (309)
.
T Consensus 84 ~ 84 (353)
T PF05460_consen 84 L 84 (353)
T ss_dssp -
T ss_pred H
Confidence 3
No 485
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=55.22 E-value=14 Score=29.85 Aligned_cols=34 Identities=21% Similarity=0.299 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccC
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLF 293 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~ 293 (309)
...+.++||+.+|+++.|+++++....+...+.+
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5679999999999999999998876665544443
No 486
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=55.10 E-value=28 Score=27.66 Aligned_cols=42 Identities=5% Similarity=-0.086 Sum_probs=32.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHhhcccCCCCcCCCCC
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKLMYPHASKLFPQDFVFHTP 302 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l~~~~~~~~~~ 302 (309)
...+++.+||+.++++.+|+.+..+.|.+.- |+.....++|.
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~G--lI~R~~~~~Dr 93 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKG--WVERLPNPNDK 93 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC--CEEeccCcccC
Confidence 4569999999999999999999999998763 55333333333
No 487
>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=55.03 E-value=4.6 Score=29.81 Aligned_cols=31 Identities=26% Similarity=0.279 Sum_probs=23.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHhhccc
Q psy6534 262 RSQKEIGDIAGVAEVTIRQSYKLMYPHASKL 292 (309)
Q Consensus 262 ~~~~~ia~~~~vs~~ti~~~~kei~~~~~~l 292 (309)
++++.||+..||+++||.+.-.++.+....|
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~a~l 54 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKMAML 54 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHHHHH
Confidence 5788999999999999988765655444333
No 488
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=55.00 E-value=43 Score=32.19 Aligned_cols=85 Identities=14% Similarity=0.105 Sum_probs=64.5
Q ss_pred HHHHHHHhhCCCCHHHHHHHHHHHHHhhhcCccCCCChHHHHHHHHHHHHHhCCCCCC-HHHHHH--HhCCCHHHHHHHH
Q psy6534 206 DFMSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPISVAAAAIYMASQASSDKRS-QKEIGD--IAGVAEVTIRQSY 282 (309)
Q Consensus 206 ~~i~~~~~~L~l~~~~~~~a~~i~~~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~-~~~ia~--~~~vs~~ti~~~~ 282 (309)
+++..+-.++++-+++...|..|+++......+.=.+-.-++++|+++||+...+..+ +++++- .-..++.-|.+..
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 3555566777888888889999999887766665566788999999999998876554 555543 3567888889999
Q ss_pred HHHHHhhc
Q psy6534 283 KLMYPHAS 290 (309)
Q Consensus 283 kei~~~~~ 290 (309)
+.+.+...
T Consensus 298 ~~ml~~l~ 305 (440)
T COG5024 298 RYMLEVLD 305 (440)
T ss_pred HHHhhhcc
Confidence 98887654
No 489
>PRK15044 transcriptional regulator SirC; Provisional
Probab=54.86 E-value=36 Score=30.85 Aligned_cols=26 Identities=15% Similarity=0.167 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy6534 259 SDKRSQKEIGDIAGVAEVTIRQSYKL 284 (309)
Q Consensus 259 ~~~~~~~~ia~~~~vs~~ti~~~~ke 284 (309)
..+.++.+||+.+|+|+.++++++++
T Consensus 206 ~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 206 TRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 46799999999999999999998764
No 490
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=54.83 E-value=16 Score=31.82 Aligned_cols=29 Identities=17% Similarity=0.281 Sum_probs=25.2
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
.++ +-.++|+.+|||..|+|++..+|.+.
T Consensus 31 ~kLPsE~eLa~~~~VSR~TvR~Al~~L~~e 60 (241)
T PRK11402 31 QQIPTENELCTQYNVSRITIRKAISDLVAD 60 (241)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 344 57899999999999999999999875
No 491
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=54.82 E-value=25 Score=23.37 Aligned_cols=30 Identities=10% Similarity=0.051 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
...+.++.|+.+++.++|++.|.+.|.+..
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~ 40 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELL 40 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 346788999999999999999999998874
No 492
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=54.76 E-value=14 Score=32.01 Aligned_cols=26 Identities=27% Similarity=0.524 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLM 285 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei 285 (309)
...+.+|||+.+|+|+.|++++....
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA 222 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRI 222 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46899999999999999998886443
No 493
>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=54.76 E-value=9 Score=26.52 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=19.5
Q ss_pred ccCCCCCCCCeeeeCCCCceecCCCCccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSECGLVV 34 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~CG~V~ 34 (309)
..| .||.. ++.|...-.--| .||..+
T Consensus 4 frC-~Cgr~-lya~e~~kTkkC-~CG~~l 29 (68)
T PF09082_consen 4 FRC-DCGRY-LYAKEGAKTKKC-VCGKTL 29 (68)
T ss_dssp EEE-TTS---EEEETT-SEEEE-TTTEEE
T ss_pred EEe-cCCCE-EEecCCcceeEe-cCCCee
Confidence 468 79864 678888889999 999987
No 494
>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=54.72 E-value=17 Score=29.49 Aligned_cols=29 Identities=17% Similarity=0.192 Sum_probs=24.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHhh
Q psy6534 261 KRSQKEIGDIAGVAEVTIRQSYKLMYPHA 289 (309)
Q Consensus 261 ~~~~~~ia~~~~vs~~ti~~~~kei~~~~ 289 (309)
..+.+|||+.+|+|+.|++++.....+..
T Consensus 135 g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 135 DLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 58999999999999999988876655443
No 495
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=54.58 E-value=31 Score=27.38 Aligned_cols=29 Identities=7% Similarity=0.092 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+.++||+.++|+.+|+.+..+.|.+.
T Consensus 21 ~~~~~~ela~~l~vs~~svs~~l~~L~~~ 49 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVTKMVQKLDKD 49 (142)
T ss_pred CCcCHHHHHHHhCCChhHHHHHHHHHHHC
Confidence 45688999999999999999999998876
No 496
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=54.57 E-value=19 Score=31.69 Aligned_cols=30 Identities=13% Similarity=0.384 Sum_probs=26.7
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 259 SDKR-SQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 259 ~~~~-~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
|.++ +..++|+.+|||..++|.+++.|...
T Consensus 30 G~~LpsE~eLa~~~gVSRtpVREAL~~L~~e 60 (257)
T PRK10225 30 GERLPPEREIAEMLDVTRTVVREALIMLEIK 60 (257)
T ss_pred CCcCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 5678 58999999999999999999999754
No 497
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=54.55 E-value=8.1 Score=24.18 Aligned_cols=25 Identities=16% Similarity=0.252 Sum_probs=17.1
Q ss_pred ccCCCCCCCCeeeeCCCCceecCC--CCcccc
Q psy6534 6 VCCYEHPDAPLIEDYRAGDQICSE--CGLVVG 35 (309)
Q Consensus 6 ~~Cp~C~~~~~v~D~~~G~~vC~~--CG~V~~ 35 (309)
-+||.||..+ .+--+.|.+ |+.|..
T Consensus 12 rkCp~CGt~N-----G~R~~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 12 RKCPKCGTYN-----GTRGLSCKNKSCPQVFN 38 (44)
T ss_pred ccCCcCcCcc-----CcccccccCCccchhhh
Confidence 3799998754 223477875 998873
No 498
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=54.45 E-value=13 Score=30.80 Aligned_cols=29 Identities=17% Similarity=0.387 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
...+.+|||+.+|+|+.|+++++..-...
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERARKR 165 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45899999999999999998887554433
No 499
>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=54.31 E-value=4.1 Score=26.90 Aligned_cols=27 Identities=22% Similarity=0.525 Sum_probs=14.3
Q ss_pred CCCCCCCC-eee--eCCCCceecCCCCccc
Q psy6534 8 CYEHPDAP-LIE--DYRAGDQICSECGLVV 34 (309)
Q Consensus 8 Cp~C~~~~-~v~--D~~~G~~vC~~CG~V~ 34 (309)
|-+|+.+. ..+ .+..+..+|..||+-.
T Consensus 2 C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~ 31 (54)
T cd00202 2 CSNCGTTTTPLWRRGPSGGSTLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCcccccCCCCcchHHHHHHHHH
Confidence 66666442 222 2335566777777554
No 500
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=54.20 E-value=14 Score=32.60 Aligned_cols=29 Identities=21% Similarity=0.173 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q psy6534 260 DKRSQKEIGDIAGVAEVTIRQSYKLMYPH 288 (309)
Q Consensus 260 ~~~~~~~ia~~~~vs~~ti~~~~kei~~~ 288 (309)
-.++.+|+++.++||+.|||+-.++|.+.
T Consensus 18 ~~~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 18 GYVSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred CCEeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 46899999999999999999999999875
Done!