Query 008401
Match_columns 567
No_of_seqs 267 out of 1158
Neff 6.5
Searched_HMMs 46136
Date Thu Mar 28 23:21:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008401hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1598 Transcription initiati 100.0 7.5E-84 1.6E-88 684.0 27.6 480 2-548 1-492 (521)
2 PRK00423 tfb transcription ini 100.0 6.2E-54 1.4E-58 445.6 26.7 250 2-260 12-302 (310)
3 COG1405 SUA7 Transcription ini 100.0 2E-53 4.3E-58 433.0 24.2 251 1-260 1-277 (285)
4 KOG1597 Transcription initiati 100.0 7.8E-49 1.7E-53 389.4 24.2 266 2-275 1-300 (308)
5 PF07741 BRF1: Brf1-like TBP-b 100.0 1.7E-29 3.6E-34 219.3 1.7 96 423-543 1-97 (97)
6 PF00382 TFIIB: Transcription 99.7 1.3E-16 2.7E-21 130.8 9.5 71 78-150 1-71 (71)
7 PF00382 TFIIB: Transcription 99.6 3.6E-15 7.8E-20 122.2 9.0 71 179-251 1-71 (71)
8 TIGR00569 ccl1 cyclin ccl1. Un 99.4 1.8E-11 3.9E-16 127.0 20.4 164 67-237 51-226 (305)
9 KOG0835 Cyclin L [General func 99.4 2.2E-11 4.8E-16 123.8 18.3 182 66-254 18-221 (367)
10 PRK00423 tfb transcription ini 99.3 5.9E-12 1.3E-16 131.5 11.8 89 74-164 219-307 (310)
11 KOG0834 CDK9 kinase-activating 99.3 2.5E-11 5.4E-16 126.1 11.1 158 72-236 40-214 (323)
12 PF08271 TF_Zn_Ribbon: TFIIB z 99.2 4.7E-12 1E-16 93.8 2.5 43 2-44 1-43 (43)
13 COG5333 CCL1 Cdk activating ki 99.1 1.2E-09 2.7E-14 111.2 12.9 158 72-236 46-211 (297)
14 COG1405 SUA7 Transcription ini 99.0 1.1E-09 2.3E-14 112.7 10.1 91 73-165 193-283 (285)
15 cd00043 CYCLIN Cyclin box fold 98.9 2.6E-08 5.7E-13 82.3 10.8 83 73-157 4-87 (88)
16 KOG1597 Transcription initiati 98.8 1.3E-08 2.8E-13 102.9 10.2 88 73-162 202-289 (308)
17 cd00043 CYCLIN Cyclin box fold 98.8 4.4E-08 9.6E-13 80.9 9.8 84 173-258 3-87 (88)
18 KOG0794 CDK8 kinase-activating 98.8 1.1E-07 2.3E-12 93.2 13.4 176 74-258 44-234 (264)
19 smart00385 CYCLIN domain prese 98.7 4.6E-08 1E-12 80.0 8.9 79 77-158 2-82 (83)
20 smart00385 CYCLIN domain prese 98.7 6.6E-08 1.4E-12 79.1 9.4 81 177-259 1-82 (83)
21 KOG0656 G1/S-specific cyclin D 98.5 3.5E-06 7.5E-11 88.1 16.9 177 73-256 80-268 (335)
22 KOG1598 Transcription initiati 98.2 1E-06 2.2E-11 95.8 5.5 159 76-234 168-334 (521)
23 KOG4557 Origin recognition com 97.7 0.0015 3.2E-08 63.9 14.8 159 77-249 2-168 (262)
24 KOG2496 Cdk activating kinase 97.6 0.00056 1.2E-08 70.0 11.9 161 77-258 62-233 (325)
25 PF00134 Cyclin_N: Cyclin, N-t 97.6 0.0007 1.5E-08 60.6 10.9 91 72-164 32-125 (127)
26 PF01857 RB_B: Retinoblastoma- 97.3 0.0015 3.2E-08 60.4 9.8 84 70-155 10-95 (135)
27 KOG0653 Cyclin B and related k 97.3 0.003 6.5E-08 68.4 13.5 153 74-235 161-317 (391)
28 PF02984 Cyclin_C: Cyclin, C-t 97.0 0.0025 5.3E-08 56.0 7.1 84 174-259 2-86 (118)
29 COG5024 Cyclin [Cell division 96.6 0.013 2.7E-07 64.0 10.6 149 75-233 217-369 (440)
30 PF11781 RRN7: RNA polymerase 96.2 0.0031 6.8E-08 44.9 1.9 27 3-31 10-36 (36)
31 KOG0835 Cyclin L [General func 95.9 0.047 1E-06 56.8 10.0 105 74-186 141-246 (367)
32 PF09862 DUF2089: Protein of u 95.3 0.21 4.5E-06 44.8 10.5 55 135-193 51-106 (113)
33 PRK00415 rps27e 30S ribosomal 95.1 0.011 2.5E-07 46.5 1.5 31 2-32 12-42 (59)
34 COG2051 RPS27A Ribosomal prote 95.0 0.013 2.8E-07 47.0 1.6 31 2-32 20-50 (67)
35 PF01667 Ribosomal_S27e: Ribos 94.9 0.011 2.4E-07 46.0 1.2 31 2-32 8-38 (55)
36 PF02984 Cyclin_C: Cyclin, C-t 94.4 0.22 4.8E-06 43.5 8.3 86 75-162 4-90 (118)
37 PF13248 zf-ribbon_3: zinc-rib 94.3 0.022 4.8E-07 37.5 1.3 23 1-28 2-24 (26)
38 PLN00209 ribosomal protein S27 94.3 0.025 5.5E-07 47.7 1.8 31 2-32 37-67 (86)
39 PTZ00083 40S ribosomal protein 94.2 0.028 6.2E-07 47.3 1.9 31 2-32 36-66 (85)
40 PF13240 zinc_ribbon_2: zinc-r 94.0 0.028 6.1E-07 36.0 1.2 22 3-29 1-22 (23)
41 TIGR01206 lysW lysine biosynth 93.8 0.037 8.1E-07 43.0 1.8 31 1-31 2-33 (54)
42 PHA00626 hypothetical protein 93.6 0.052 1.1E-06 42.1 2.3 30 2-31 1-34 (59)
43 KOG0655 G1/S-specific cyclin E 93.5 1.5 3.3E-05 46.0 13.3 171 74-258 148-331 (408)
44 PRK00420 hypothetical protein; 93.5 0.052 1.1E-06 48.5 2.4 27 3-31 25-51 (112)
45 PF02150 RNA_POL_M_15KD: RNA p 93.3 0.051 1.1E-06 38.5 1.6 31 1-31 1-31 (35)
46 PF08792 A2L_zn_ribbon: A2L zi 93.3 0.064 1.4E-06 37.5 2.1 27 3-30 5-31 (33)
47 PF14803 Nudix_N_2: Nudix N-te 93.0 0.041 8.9E-07 38.7 0.9 28 3-30 2-32 (34)
48 TIGR02098 MJ0042_CXXC MJ0042 f 92.9 0.054 1.2E-06 38.6 1.3 30 2-31 3-36 (38)
49 TIGR00569 ccl1 cyclin ccl1. Un 92.6 0.45 9.8E-06 50.0 8.3 68 177-244 61-128 (305)
50 PF00134 Cyclin_N: Cyclin, N-t 92.3 0.47 1E-05 42.2 7.1 67 176-244 35-102 (127)
51 COG1645 Uncharacterized Zn-fin 92.0 0.092 2E-06 48.1 2.0 23 3-28 30-52 (131)
52 PF08274 PhnA_Zn_Ribbon: PhnA 92.0 0.12 2.7E-06 35.3 2.1 28 1-30 2-29 (30)
53 PF03966 Trm112p: Trm112p-like 91.3 0.16 3.5E-06 41.2 2.6 17 14-30 47-63 (68)
54 PF13404 HTH_AsnC-type: AsnC-t 90.9 0.44 9.6E-06 35.0 4.3 32 227-258 10-41 (42)
55 smart00342 HTH_ARAC helix_turn 90.6 2.2 4.8E-05 34.2 8.9 75 133-259 1-76 (84)
56 COG1997 RPL43A Ribosomal prote 90.5 0.2 4.3E-06 42.5 2.4 29 3-32 37-65 (89)
57 PRK00432 30S ribosomal protein 90.4 0.19 4.1E-06 38.5 2.0 26 3-30 22-47 (50)
58 PF08613 Cyclin: Cyclin; Inte 89.4 5 0.00011 37.5 11.2 89 74-164 54-148 (149)
59 PRK05657 RNA polymerase sigma 89.3 22 0.00048 37.6 17.3 26 233-258 281-306 (325)
60 smart00778 Prim_Zn_Ribbon Zinc 89.1 0.29 6.3E-06 35.1 2.0 27 2-28 4-33 (37)
61 smart00661 RPOL9 RNA polymeras 89.0 0.28 6.2E-06 37.2 2.1 30 3-32 2-32 (52)
62 TIGR02393 RpoD_Cterm RNA polym 88.9 27 0.00059 34.9 18.3 26 233-258 195-220 (238)
63 PF14354 Lar_restr_allev: Rest 88.9 0.37 7.9E-06 38.0 2.7 27 2-28 4-37 (61)
64 PRK00398 rpoP DNA-directed RNA 88.8 0.32 6.9E-06 36.3 2.2 27 3-30 5-31 (46)
65 KOG4164 Cyclin ik3-1/CABLES [C 88.6 1.3 2.9E-05 47.3 7.4 91 74-166 385-480 (497)
66 PRK00464 nrdR transcriptional 88.5 0.31 6.7E-06 46.1 2.4 29 2-30 1-38 (154)
67 PF13719 zinc_ribbon_5: zinc-r 88.2 0.26 5.7E-06 35.2 1.3 28 3-30 4-35 (37)
68 KOG0834 CDK9 kinase-activating 88.0 0.78 1.7E-05 48.5 5.2 82 176-259 43-128 (323)
69 PF05460 ORC6: Origin recognit 87.6 0.17 3.6E-06 54.3 0.0 86 80-165 3-89 (353)
70 PRK11827 hypothetical protein; 87.2 0.48 1E-05 37.7 2.3 27 3-30 10-36 (60)
71 PRK09210 RNA polymerase sigma 86.7 49 0.0011 35.6 18.2 92 65-156 129-255 (367)
72 PF13412 HTH_24: Winged helix- 86.4 1.3 2.8E-05 32.9 4.3 29 232-260 15-43 (48)
73 PF09538 FYDLN_acid: Protein o 86.0 0.41 8.9E-06 42.6 1.6 29 3-33 11-39 (108)
74 smart00342 HTH_ARAC helix_turn 85.9 2.7 5.9E-05 33.7 6.4 71 78-157 4-75 (84)
75 KOG1779 40s ribosomal protein 85.8 0.37 8.1E-06 40.0 1.1 30 2-31 35-64 (84)
76 TIGR03655 anti_R_Lar restricti 85.7 0.61 1.3E-05 36.0 2.2 31 2-32 2-38 (53)
77 COG2835 Uncharacterized conser 85.6 0.56 1.2E-05 37.2 2.0 28 2-30 9-36 (60)
78 PF10571 UPF0547: Uncharacteri 85.6 0.48 1E-05 31.3 1.3 24 3-31 2-25 (26)
79 COG1998 RPS31 Ribosomal protei 85.4 0.5 1.1E-05 35.9 1.5 26 3-29 21-46 (51)
80 KOG2496 Cdk activating kinase 84.7 2.3 4.9E-05 44.3 6.4 70 176-245 60-129 (325)
81 COG4888 Uncharacterized Zn rib 84.2 0.56 1.2E-05 40.9 1.5 29 3-31 24-57 (104)
82 PF06677 Auto_anti-p27: Sjogre 83.8 0.89 1.9E-05 33.4 2.2 23 3-27 19-41 (41)
83 PRK11169 leucine-responsive tr 83.7 1.6 3.5E-05 41.4 4.6 38 226-263 20-57 (164)
84 PF07282 OrfB_Zn_ribbon: Putat 83.3 0.82 1.8E-05 36.8 2.1 29 3-32 30-58 (69)
85 PRK09678 DNA-binding transcrip 82.9 0.98 2.1E-05 37.3 2.4 30 1-30 1-39 (72)
86 PRK14892 putative transcriptio 82.6 0.84 1.8E-05 40.0 2.0 30 3-32 23-54 (99)
87 PF13730 HTH_36: Helix-turn-he 82.3 2.8 6E-05 31.9 4.7 25 236-260 27-51 (55)
88 TIGR02300 FYDLN_acid conserved 82.1 0.8 1.7E-05 41.7 1.8 29 3-33 11-39 (129)
89 COG4640 Predicted membrane pro 82.0 0.72 1.6E-05 49.3 1.6 26 1-31 1-26 (465)
90 PF09297 zf-NADH-PPase: NADH p 82.0 1.2 2.5E-05 30.7 2.2 27 3-30 5-31 (32)
91 PF04967 HTH_10: HTH DNA bindi 81.4 3.1 6.6E-05 32.3 4.5 34 225-258 9-47 (53)
92 smart00440 ZnF_C2C2 C2C2 Zinc 81.1 1 2.2E-05 32.8 1.7 27 3-29 2-37 (40)
93 PRK12495 hypothetical protein; 81.1 0.98 2.1E-05 44.8 2.1 27 3-32 44-70 (226)
94 COG1594 RPB9 DNA-directed RNA 81.0 1 2.2E-05 40.5 2.0 33 1-33 2-35 (113)
95 PF13936 HTH_38: Helix-turn-he 81.0 2.1 4.6E-05 31.6 3.4 30 227-256 13-42 (44)
96 PF05191 ADK_lid: Adenylate ki 80.9 0.43 9.3E-06 34.0 -0.3 28 3-30 3-31 (36)
97 PRK10219 DNA-binding transcrip 80.4 37 0.00081 29.3 12.0 39 118-157 7-45 (107)
98 PRK11179 DNA-binding transcrip 80.4 2.3 5.1E-05 39.8 4.4 38 226-263 15-52 (153)
99 PF12760 Zn_Tnp_IS1595: Transp 80.3 1.5 3.3E-05 32.7 2.5 26 3-28 20-45 (46)
100 PF08273 Prim_Zn_Ribbon: Zinc- 80.0 1.4 3.1E-05 32.1 2.1 27 3-29 5-35 (40)
101 PF08279 HTH_11: HTH domain; 79.4 3.4 7.4E-05 31.4 4.3 30 231-260 12-41 (55)
102 PF01857 RB_B: Retinoblastoma- 79.4 7.3 0.00016 36.1 7.2 64 178-243 17-82 (135)
103 PF13717 zinc_ribbon_4: zinc-r 79.4 1.1 2.3E-05 31.9 1.3 28 3-30 4-35 (36)
104 PRK00135 scpB segregation and 79.4 11 0.00024 36.9 8.8 115 115-251 5-121 (188)
105 PF13542 HTH_Tnp_ISL3: Helix-t 79.2 6.9 0.00015 29.3 5.9 26 233-258 26-51 (52)
106 COG2888 Predicted Zn-ribbon RN 79.1 1.1 2.3E-05 35.5 1.3 8 20-27 27-34 (61)
107 TIGR00244 transcriptional regu 79.1 1.6 3.4E-05 40.9 2.7 28 2-29 1-37 (147)
108 PF01780 Ribosomal_L37ae: Ribo 78.8 1.1 2.3E-05 38.6 1.3 32 3-35 37-68 (90)
109 PRK14559 putative protein seri 78.6 1.1 2.4E-05 51.7 1.8 25 1-30 1-25 (645)
110 PRK09710 lar restriction allev 78.5 1.6 3.5E-05 35.1 2.2 28 3-30 8-37 (64)
111 PRK06266 transcription initiat 78.1 0.64 1.4E-05 45.1 -0.2 30 3-32 119-148 (178)
112 KOG1010 Rb (Retinoblastoma tum 78.0 5.4 0.00012 46.8 7.0 84 71-156 677-762 (920)
113 PF13384 HTH_23: Homeodomain-l 77.4 3.2 7E-05 30.9 3.5 29 234-262 17-45 (50)
114 PF13545 HTH_Crp_2: Crp-like h 76.1 4.6 9.9E-05 32.6 4.4 29 233-261 27-55 (76)
115 PF10668 Phage_terminase: Phag 75.9 6.3 0.00014 31.4 4.9 38 214-254 5-42 (60)
116 PRK10220 hypothetical protein; 75.7 2 4.4E-05 38.1 2.2 27 3-31 5-31 (111)
117 cd06571 Bac_DnaA_C C-terminal 75.5 10 0.00022 32.3 6.6 41 121-163 34-75 (90)
118 PRK05932 RNA polymerase factor 75.4 22 0.00047 39.6 10.7 187 77-274 140-384 (455)
119 PF02796 HTH_7: Helix-turn-hel 75.4 1.6 3.6E-05 32.3 1.4 28 229-256 16-43 (45)
120 PF12773 DZR: Double zinc ribb 74.8 1.7 3.7E-05 32.7 1.4 13 19-31 11-23 (50)
121 cd00092 HTH_CRP helix_turn_hel 74.7 8.2 0.00018 30.1 5.4 29 232-260 23-51 (67)
122 PF01325 Fe_dep_repress: Iron 74.6 6.6 0.00014 31.0 4.8 37 223-260 12-48 (60)
123 TIGR00686 phnA alkylphosphonat 74.6 4.3 9.2E-05 36.0 3.9 30 2-33 3-32 (109)
124 PF00165 HTH_AraC: Bacterial r 74.5 6.7 0.00014 28.2 4.4 36 232-272 6-41 (42)
125 PRK07598 RNA polymerase sigma 74.3 1.4E+02 0.0031 32.8 18.1 99 65-163 175-308 (415)
126 PF05876 Terminase_GpA: Phage 74.2 1.6 3.4E-05 49.8 1.5 34 1-34 200-243 (557)
127 PF04545 Sigma70_r4: Sigma-70, 73.9 5.7 0.00012 29.7 4.1 27 232-258 18-44 (50)
128 PRK05949 RNA polymerase sigma 73.9 1.3E+02 0.0027 32.0 18.5 90 66-155 92-216 (327)
129 PTZ00255 60S ribosomal protein 73.7 2.3 4.9E-05 36.7 2.0 32 3-35 38-69 (90)
130 PF15616 TerY-C: TerY-C metal 73.6 1.9 4.2E-05 39.7 1.6 19 3-29 79-97 (131)
131 TIGR02297 HpaA 4-hydroxyphenyl 73.3 55 0.0012 33.2 12.5 97 119-273 189-286 (287)
132 PRK07405 RNA polymerase sigma 73.3 1.3E+02 0.0028 31.8 18.6 25 232-256 274-298 (317)
133 PRK13130 H/ACA RNA-protein com 73.2 1.5 3.4E-05 34.4 0.8 24 1-31 5-28 (56)
134 TIGR02395 rpoN_sigma RNA polym 73.0 16 0.00035 40.3 8.9 183 77-274 115-359 (429)
135 TIGR03697 NtcA_cyano global ni 72.9 14 0.0003 35.0 7.5 30 233-262 142-171 (193)
136 PF00356 LacI: Bacterial regul 72.7 3.8 8.2E-05 30.8 2.8 21 236-256 1-21 (46)
137 PF09986 DUF2225: Uncharacteri 72.4 12 0.00026 37.3 7.2 43 83-126 83-125 (214)
138 PRK05901 RNA polymerase sigma 72.3 1.8E+02 0.0038 33.1 16.9 91 65-155 271-396 (509)
139 PF00325 Crp: Bacterial regula 71.5 4.7 0.0001 28.0 2.8 27 133-159 2-28 (32)
140 TIGR03879 near_KaiC_dom probab 71.5 8.6 0.00019 31.9 4.8 26 233-258 31-56 (73)
141 PF08613 Cyclin: Cyclin; Inte 71.3 26 0.00056 32.7 8.7 79 173-253 52-136 (149)
142 COG1522 Lrp Transcriptional re 71.2 5.6 0.00012 36.6 4.3 33 230-262 18-50 (154)
143 PF01096 TFIIS_C: Transcriptio 71.0 2 4.4E-05 31.0 0.9 27 3-29 2-37 (39)
144 PF08220 HTH_DeoR: DeoR-like h 70.7 4.3 9.2E-05 31.6 2.8 29 232-260 12-40 (57)
145 KOG4557 Origin recognition com 70.6 26 0.00057 34.9 8.7 94 178-271 2-99 (262)
146 smart00419 HTH_CRP helix_turn_ 70.3 5.6 0.00012 28.8 3.3 29 232-260 6-34 (48)
147 COG1318 Predicted transcriptio 70.3 6.4 0.00014 37.8 4.3 72 191-274 28-99 (182)
148 PF00325 Crp: Bacterial regula 70.3 4.4 9.5E-05 28.2 2.4 27 234-260 2-28 (32)
149 TIGR00280 L37a ribosomal prote 70.2 2.9 6.3E-05 36.0 1.9 32 3-35 37-68 (91)
150 COG2207 AraC AraC-type DNA-bin 69.8 70 0.0015 27.5 10.8 38 119-157 23-60 (127)
151 PRK07406 RNA polymerase sigma 69.8 67 0.0015 34.8 12.6 88 67-155 163-261 (373)
152 smart00344 HTH_ASNC helix_turn 69.8 6.8 0.00015 34.0 4.2 30 232-261 15-44 (108)
153 KOG2906 RNA polymerase III sub 69.7 2.9 6.3E-05 36.4 1.8 31 1-31 1-32 (105)
154 COG1326 Uncharacterized archae 69.6 2.2 4.7E-05 41.7 1.1 29 3-32 8-42 (201)
155 TIGR01384 TFS_arch transcripti 69.2 2.8 6.1E-05 36.6 1.7 27 3-32 2-28 (104)
156 PRK14890 putative Zn-ribbon RN 68.9 3.2 7E-05 32.9 1.7 26 3-29 9-34 (59)
157 COG1327 Predicted transcriptio 68.8 3.1 6.6E-05 39.1 1.8 28 2-29 1-37 (156)
158 TIGR02010 IscR iron-sulfur clu 68.6 9.1 0.0002 35.0 5.0 47 114-160 6-52 (135)
159 TIGR02885 spore_sigF RNA polym 68.2 1.3E+02 0.0028 29.7 17.1 27 232-258 197-223 (231)
160 TIGR01031 rpmF_bact ribosomal 68.1 3.4 7.3E-05 32.3 1.7 25 2-32 27-51 (55)
161 COG3809 Uncharacterized protei 68.1 3.7 7.9E-05 34.3 1.9 30 1-30 1-31 (88)
162 smart00834 CxxC_CXXC_SSSS Puta 67.8 3.1 6.6E-05 29.8 1.3 28 3-30 7-36 (41)
163 COG3478 Predicted nucleic-acid 67.8 3.2 7E-05 33.3 1.5 14 2-15 5-18 (68)
164 TIGR00122 birA_repr_reg BirA b 67.2 9.3 0.0002 30.6 4.2 31 230-260 9-39 (69)
165 COG5333 CCL1 Cdk activating ki 67.1 4.4 9.6E-05 42.2 2.8 55 176-232 49-103 (297)
166 smart00345 HTH_GNTR helix_turn 66.7 8.1 0.00018 29.1 3.6 30 232-261 17-47 (60)
167 PRK15121 right oriC-binding tr 66.6 66 0.0014 33.1 11.5 41 116-157 5-45 (289)
168 PRK07500 rpoH2 RNA polymerase 66.6 1.7E+02 0.0036 30.4 16.2 27 232-258 243-269 (289)
169 PF02082 Rrf2: Transcriptional 66.6 7.9 0.00017 32.3 3.8 45 116-160 8-52 (83)
170 COG2824 PhnA Uncharacterized Z 66.5 3.9 8.5E-05 36.1 1.9 31 2-34 4-34 (112)
171 COG1656 Uncharacterized conser 66.4 2.6 5.6E-05 40.2 0.9 30 1-30 97-140 (165)
172 PF11672 DUF3268: Protein of u 66.3 4.5 9.7E-05 35.7 2.3 31 2-32 3-43 (102)
173 PRK03976 rpl37ae 50S ribosomal 65.8 3.8 8.3E-05 35.3 1.7 32 3-35 38-69 (90)
174 PF12773 DZR: Double zinc ribb 65.6 4.3 9.4E-05 30.5 1.8 30 2-33 13-42 (50)
175 KOG0794 CDK8 kinase-activating 65.5 11 0.00023 38.1 4.9 57 176-234 45-101 (264)
176 PF01371 Trp_repressor: Trp re 65.3 6.5 0.00014 33.7 3.0 32 230-261 45-76 (87)
177 PRK10572 DNA-binding transcrip 65.2 1.6E+02 0.0036 29.9 17.8 99 118-274 185-284 (290)
178 PF05225 HTH_psq: helix-turn-h 65.1 11 0.00024 28.1 3.9 27 231-258 14-40 (45)
179 smart00421 HTH_LUXR helix_turn 64.8 8.6 0.00019 28.4 3.4 26 234-259 18-43 (58)
180 PRK07408 RNA polymerase sigma 64.8 1.6E+02 0.0036 29.7 17.2 90 65-154 25-150 (256)
181 PRK12286 rpmF 50S ribosomal pr 64.7 4.1 8.9E-05 32.1 1.6 26 2-33 28-53 (57)
182 PF13545 HTH_Crp_2: Crp-like h 64.6 14 0.00031 29.6 4.9 46 118-163 3-58 (76)
183 PF01022 HTH_5: Bacterial regu 64.5 12 0.00027 27.7 4.1 32 230-261 11-42 (47)
184 TIGR03697 NtcA_cyano global ni 64.1 31 0.00067 32.6 7.9 29 132-160 142-170 (193)
185 TIGR02479 FliA_WhiG RNA polyme 63.9 1.5E+02 0.0033 29.1 16.8 25 233-257 190-214 (224)
186 PF01783 Ribosomal_L32p: Ribos 63.8 2.8 6.1E-05 32.8 0.5 25 2-32 27-51 (56)
187 PRK13500 transcriptional activ 63.3 1.9E+02 0.0042 30.0 14.5 99 118-274 208-307 (312)
188 PF05129 Elf1: Transcription e 62.9 4.4 9.5E-05 34.2 1.5 31 3-33 24-59 (81)
189 smart00659 RPOLCX RNA polymera 62.8 4.6 9.9E-05 30.1 1.5 25 3-29 4-28 (44)
190 PRK11511 DNA-binding transcrip 62.7 32 0.00068 31.1 7.3 55 215-275 7-61 (127)
191 TIGR02394 rpoS_proteo RNA poly 62.2 1.9E+02 0.0042 29.7 18.5 25 233-257 241-265 (285)
192 PF13613 HTH_Tnp_4: Helix-turn 62.2 15 0.00034 28.0 4.4 36 130-165 16-51 (53)
193 COG0333 RpmF Ribosomal protein 62.0 4.6 9.9E-05 31.9 1.4 26 1-32 27-52 (57)
194 PRK13502 transcriptional activ 61.8 90 0.0019 31.6 11.3 101 116-274 176-277 (282)
195 PRK08215 sporulation sigma fac 61.0 1.9E+02 0.0041 29.2 17.7 26 233-258 224-249 (258)
196 PRK10857 DNA-binding transcrip 60.6 15 0.00034 35.0 5.0 47 114-160 6-52 (164)
197 PRK09393 ftrA transcriptional 60.5 1E+02 0.0022 32.1 11.7 99 118-274 220-319 (322)
198 PF01726 LexA_DNA_bind: LexA D 60.4 9.8 0.00021 30.7 3.1 32 229-260 20-52 (65)
199 PF10122 Mu-like_Com: Mu-like 60.3 2.7 5.9E-05 32.3 -0.1 29 2-30 5-34 (51)
200 TIGR02980 SigBFG RNA polymeras 60.0 1.8E+02 0.0039 28.6 17.4 26 233-258 193-218 (227)
201 PF07754 DUF1610: Domain of un 59.9 6.7 0.00015 25.5 1.6 24 4-28 1-24 (24)
202 PRK14962 DNA polymerase III su 59.9 2.2E+02 0.0048 31.9 14.7 135 133-277 229-381 (472)
203 cd00350 rubredoxin_like Rubred 59.6 6.9 0.00015 27.1 1.8 24 2-28 2-25 (33)
204 PF03604 DNA_RNApol_7kD: DNA d 59.5 6 0.00013 27.5 1.5 24 3-28 2-25 (32)
205 TIGR02997 Sig70-cyanoRpoD RNA 59.5 2.2E+02 0.0048 29.5 18.6 25 233-257 268-292 (298)
206 smart00420 HTH_DEOR helix_turn 59.5 23 0.00049 25.8 4.8 27 234-260 14-40 (53)
207 PRK12469 RNA polymerase factor 59.2 51 0.0011 37.0 9.5 190 77-274 162-410 (481)
208 PF13613 HTH_Tnp_4: Helix-turn 59.2 12 0.00025 28.7 3.2 35 226-260 11-45 (53)
209 PF11023 DUF2614: Protein of u 59.0 3.7 8E-05 36.7 0.5 39 2-43 70-108 (114)
210 PF12802 MarR_2: MarR family; 58.8 20 0.00044 27.5 4.7 27 234-260 21-47 (62)
211 PF14122 YokU: YokU-like prote 58.8 5.3 0.00011 34.0 1.3 22 19-40 34-55 (87)
212 TIGR00515 accD acetyl-CoA carb 58.6 2.7 5.9E-05 43.8 -0.5 29 2-30 27-55 (285)
213 PF09855 DUF2082: Nucleic-acid 58.2 6.8 0.00015 31.6 1.8 27 3-29 2-45 (64)
214 COG0777 AccD Acetyl-CoA carbox 58.1 2.9 6.4E-05 43.0 -0.4 30 1-30 28-57 (294)
215 PF04079 DUF387: Putative tran 58.1 85 0.0018 29.9 9.6 109 118-258 2-120 (159)
216 PF08281 Sigma70_r4_2: Sigma-7 57.8 13 0.00029 27.9 3.4 27 232-258 24-50 (54)
217 PRK05654 acetyl-CoA carboxylas 57.7 2.9 6.2E-05 43.7 -0.5 29 2-30 28-56 (292)
218 PF14353 CpXC: CpXC protein 57.7 6.4 0.00014 35.7 1.8 29 2-30 2-48 (128)
219 PF01325 Fe_dep_repress: Iron 57.4 27 0.0006 27.5 5.2 38 122-160 12-49 (60)
220 PRK13501 transcriptional activ 57.2 2.3E+02 0.0049 28.9 14.0 88 130-274 189-277 (290)
221 PF14446 Prok-RING_1: Prokaryo 57.2 6.9 0.00015 30.5 1.6 26 3-31 7-32 (54)
222 cd06170 LuxR_C_like C-terminal 57.1 14 0.00031 27.3 3.4 26 234-259 15-40 (57)
223 CHL00174 accD acetyl-CoA carbo 56.9 2.9 6.3E-05 43.7 -0.6 29 2-30 39-67 (296)
224 PRK11920 rirA iron-responsive 56.8 21 0.00046 33.6 5.2 46 114-160 6-51 (153)
225 PF02082 Rrf2: Transcriptional 56.8 13 0.00028 31.0 3.4 38 223-260 14-51 (83)
226 PRK13918 CRP/FNR family transc 56.6 39 0.00085 32.2 7.2 30 233-262 148-177 (202)
227 PHA02591 hypothetical protein; 56.3 14 0.00029 31.1 3.3 32 225-256 50-81 (83)
228 PRK10219 DNA-binding transcrip 56.3 56 0.0012 28.2 7.5 51 219-275 7-57 (107)
229 PF02954 HTH_8: Bacterial regu 56.2 14 0.0003 26.9 3.0 26 233-258 17-42 (42)
230 PF14255 Cys_rich_CPXG: Cystei 56.0 7.1 0.00015 30.2 1.5 28 3-30 2-34 (52)
231 PRK06288 RNA polymerase sigma 55.1 2.4E+02 0.0053 28.6 17.0 25 233-257 227-251 (268)
232 PF02042 RWP-RK: RWP-RK domain 54.8 15 0.00032 28.5 3.1 28 232-259 13-40 (52)
233 TIGR01610 phage_O_Nterm phage 54.7 34 0.00074 29.4 5.8 30 231-260 44-73 (95)
234 PRK11161 fumarate/nitrate redu 54.6 44 0.00095 32.8 7.4 31 233-263 183-213 (235)
235 PF00440 TetR_N: Bacterial reg 54.3 26 0.00056 25.8 4.3 35 221-256 3-38 (47)
236 TIGR02605 CxxC_CxxC_SSSS putat 54.1 6.9 0.00015 29.6 1.2 26 3-28 7-34 (52)
237 PF06044 DRP: Dam-replacing fa 54.0 7 0.00015 39.6 1.5 29 2-30 32-63 (254)
238 KOG1088 Uncharacterized conser 53.9 5.8 0.00013 35.7 0.8 18 14-31 92-109 (124)
239 PF08280 HTH_Mga: M protein tr 53.8 16 0.00035 28.5 3.3 28 232-259 17-44 (59)
240 PRK05911 RNA polymerase sigma 53.6 2.6E+02 0.0056 28.4 18.7 27 232-258 219-245 (257)
241 cd00092 HTH_CRP helix_turn_hel 53.4 42 0.00091 25.9 5.7 30 131-160 23-52 (67)
242 PRK10434 srlR DNA-bindng trans 53.4 15 0.00032 37.5 3.8 28 232-259 17-44 (256)
243 COG3877 Uncharacterized protei 53.4 10 0.00022 33.5 2.2 60 135-202 59-120 (122)
244 KOG2593 Transcription initiati 53.2 6.2 0.00013 43.0 1.1 30 3-32 130-165 (436)
245 PF07638 Sigma70_ECF: ECF sigm 53.2 21 0.00046 34.3 4.8 25 235-259 152-176 (185)
246 PF08279 HTH_11: HTH domain; 53.0 33 0.00071 25.9 4.9 34 128-161 10-43 (55)
247 PRK08402 replication factor A; 53.0 8.3 0.00018 41.5 2.0 26 3-29 214-239 (355)
248 smart00418 HTH_ARSR helix_turn 52.9 26 0.00056 26.3 4.3 29 232-260 8-36 (66)
249 PRK05978 hypothetical protein; 52.4 10 0.00022 35.7 2.3 30 2-31 34-63 (148)
250 PF01978 TrmB: Sugar-specific 52.4 14 0.00031 29.3 2.9 37 223-260 12-48 (68)
251 PF00165 HTH_AraC: Bacterial r 52.0 19 0.00041 25.8 3.2 27 131-157 6-32 (42)
252 PRK02935 hypothetical protein; 52.0 9.4 0.0002 33.7 1.8 39 2-43 71-109 (110)
253 TIGR01321 TrpR trp operon repr 51.9 16 0.00036 31.7 3.3 29 231-259 52-80 (94)
254 PRK04217 hypothetical protein; 51.6 19 0.00042 32.2 3.8 27 233-259 57-83 (110)
255 cd00090 HTH_ARSR Arsenical Res 51.3 31 0.00067 26.6 4.7 26 235-260 21-46 (78)
256 TIGR02844 spore_III_D sporulat 51.1 22 0.00047 30.0 3.8 23 233-255 18-40 (80)
257 PF00301 Rubredoxin: Rubredoxi 51.0 8.4 0.00018 29.2 1.2 13 21-33 2-14 (47)
258 TIGR02944 suf_reg_Xantho FeS a 50.5 34 0.00074 30.8 5.4 38 223-261 15-52 (130)
259 PRK00241 nudC NADH pyrophospha 50.1 12 0.00025 38.4 2.5 30 2-32 100-129 (256)
260 COG3877 Uncharacterized protei 50.1 65 0.0014 28.6 6.6 25 3-32 8-32 (122)
261 COG1191 FliA DNA-directed RNA 50.1 3E+02 0.0065 28.2 16.8 72 69-140 27-109 (247)
262 cd06171 Sigma70_r4 Sigma70, re 49.6 30 0.00065 24.8 4.1 27 233-259 25-51 (55)
263 PRK09391 fixK transcriptional 49.5 66 0.0014 31.8 7.8 30 233-262 178-207 (230)
264 TIGR00281 segregation and cond 49.4 90 0.0019 30.5 8.4 120 116-258 3-125 (186)
265 COG4068 Uncharacterized protei 49.3 4.1 8.9E-05 32.1 -0.7 24 3-31 10-34 (64)
266 PRK12380 hydrogenase nickel in 49.2 9.7 0.00021 34.1 1.5 35 2-41 71-105 (113)
267 PRK07122 RNA polymerase sigma 48.9 3.1E+02 0.0067 28.0 17.3 27 232-258 229-255 (264)
268 PRK11511 DNA-binding transcrip 48.8 49 0.0011 29.8 6.1 42 115-157 8-49 (127)
269 PF14502 HTH_41: Helix-turn-he 48.6 19 0.00041 27.5 2.7 34 232-265 3-37 (48)
270 PRK11014 transcriptional repre 48.6 24 0.00053 32.4 4.2 38 222-259 13-50 (141)
271 cd07377 WHTH_GntR Winged helix 48.4 21 0.00046 27.3 3.2 25 236-260 27-51 (66)
272 TIGR00738 rrf2_super rrf2 fami 48.2 32 0.0007 30.8 4.9 45 115-159 7-51 (132)
273 PF00392 GntR: Bacterial regul 48.1 21 0.00045 28.1 3.1 29 232-260 21-50 (64)
274 COG3677 Transposase and inacti 47.8 12 0.00026 34.4 1.9 30 1-31 30-64 (129)
275 smart00550 Zalpha Z-DNA-bindin 47.8 39 0.00085 27.2 4.7 36 225-260 12-48 (68)
276 PF03119 DNA_ligase_ZBD: NAD-d 47.6 12 0.00027 25.1 1.4 22 3-25 1-22 (28)
277 PRK11161 fumarate/nitrate redu 47.6 77 0.0017 31.1 7.9 32 132-163 183-214 (235)
278 PF12116 SpoIIID: Stage III sp 47.5 12 0.00027 31.4 1.8 34 224-257 9-42 (82)
279 PRK15418 transcriptional regul 47.2 16 0.00034 38.7 3.0 46 225-270 20-65 (318)
280 PF12833 HTH_18: Helix-turn-he 47.2 61 0.0013 26.2 6.0 67 81-157 1-70 (81)
281 KOG0402 60S ribosomal protein 47.2 7.3 0.00016 32.9 0.4 30 3-33 38-67 (92)
282 COG5349 Uncharacterized protei 47.2 11 0.00023 34.3 1.4 28 3-31 23-51 (126)
283 TIGR02392 rpoH_proteo alternat 47.0 3.3E+02 0.0071 27.7 16.2 27 232-258 234-260 (270)
284 PRK14088 dnaA chromosomal repl 47.0 1.6E+02 0.0034 32.6 10.9 51 208-260 360-413 (440)
285 cd00569 HTH_Hin_like Helix-tur 47.0 19 0.00042 23.2 2.5 21 234-254 21-41 (42)
286 PF00196 GerE: Bacterial regul 46.8 20 0.00043 27.6 2.8 27 233-259 17-43 (58)
287 TIGR01764 excise DNA binding d 46.3 21 0.00046 25.6 2.8 23 235-257 2-24 (49)
288 TIGR02944 suf_reg_Xantho FeS a 46.2 41 0.0009 30.2 5.2 46 114-160 7-52 (130)
289 PF09862 DUF2089: Protein of u 46.1 20 0.00043 32.3 3.0 25 235-259 50-74 (113)
290 TIGR02850 spore_sigG RNA polym 45.9 3.3E+02 0.0071 27.4 17.9 26 233-258 221-246 (254)
291 PRK10572 DNA-binding transcrip 45.8 74 0.0016 32.4 7.7 14 17-30 72-85 (290)
292 PRK13413 mpi multiple promoter 45.7 60 0.0013 31.6 6.6 26 233-258 171-196 (200)
293 PRK00118 putative DNA-binding 45.6 29 0.00063 30.7 3.9 27 233-259 32-58 (104)
294 PRK12336 translation initiatio 45.4 10 0.00022 37.5 1.2 29 2-30 99-129 (201)
295 PF12840 HTH_20: Helix-turn-he 45.3 36 0.00078 26.5 4.1 32 230-261 20-51 (61)
296 PRK13509 transcriptional repre 45.3 28 0.00061 35.4 4.4 28 232-259 17-44 (251)
297 COG1996 RPC10 DNA-directed RNA 45.2 10 0.00022 29.0 0.9 25 3-28 8-32 (49)
298 COG1725 Predicted transcriptio 45.0 22 0.00048 32.5 3.2 28 232-259 32-60 (125)
299 PRK10402 DNA-binding transcrip 44.9 54 0.0012 32.3 6.3 30 233-262 168-197 (226)
300 cd04762 HTH_MerR-trunc Helix-T 44.7 24 0.00051 25.2 2.8 22 236-257 2-23 (49)
301 cd00730 rubredoxin Rubredoxin; 44.7 16 0.00035 28.0 1.9 13 21-33 2-14 (50)
302 cd00202 ZnF_GATA Zinc finger D 44.6 8.7 0.00019 29.9 0.4 29 3-31 1-32 (54)
303 TIGR03830 CxxCG_CxxCG_HTH puta 44.2 17 0.00036 32.4 2.3 27 4-30 1-41 (127)
304 PRK01381 Trp operon repressor; 44.0 18 0.00038 31.8 2.2 37 226-262 47-83 (99)
305 PF04606 Ogr_Delta: Ogr/Delta- 43.7 14 0.0003 27.7 1.4 27 3-29 1-36 (47)
306 smart00647 IBR In Between Ring 43.7 18 0.00038 28.0 2.1 29 2-30 19-50 (64)
307 COG1779 C4-type Zn-finger prot 43.6 10 0.00023 37.2 0.9 34 2-35 15-58 (201)
308 PF13518 HTH_28: Helix-turn-he 43.6 35 0.00075 25.2 3.6 25 236-260 14-38 (52)
309 PF13551 HTH_29: Winged helix- 43.5 34 0.00074 29.3 4.1 27 236-262 14-40 (112)
310 PF10080 DUF2318: Predicted me 43.4 17 0.00038 32.0 2.2 31 3-35 37-67 (102)
311 PF12802 MarR_2: MarR family; 43.2 53 0.0011 25.1 4.7 41 120-160 8-48 (62)
312 PF00356 LacI: Bacterial regul 42.9 26 0.00057 26.2 2.8 20 135-154 1-20 (46)
313 PRK06030 hypothetical protein; 42.8 76 0.0016 29.0 6.3 39 121-161 59-97 (124)
314 PF00376 MerR: MerR family reg 42.5 18 0.00039 25.9 1.8 18 236-253 1-18 (38)
315 PF13022 HTH_Tnp_1_2: Helix-tu 42.5 40 0.00086 31.5 4.4 40 216-255 13-55 (142)
316 PF09526 DUF2387: Probable met 42.3 18 0.00039 29.9 1.9 29 3-31 10-41 (71)
317 PF08646 Rep_fac-A_C: Replicat 42.1 18 0.0004 33.4 2.3 28 3-32 20-49 (146)
318 PF01396 zf-C4_Topoisom: Topoi 42.0 28 0.0006 25.1 2.7 30 2-31 2-35 (39)
319 KOG0654 G2/Mitotic-specific cy 41.9 2.5E+02 0.0054 30.4 10.9 133 121-259 185-320 (359)
320 TIGR02985 Sig70_bacteroi1 RNA 41.7 25 0.00054 31.9 3.1 26 233-258 128-153 (161)
321 smart00419 HTH_CRP helix_turn_ 41.7 37 0.0008 24.4 3.5 30 131-160 6-35 (48)
322 KOG1010 Rb (Retinoblastoma tum 41.5 1.5E+02 0.0032 35.4 9.7 57 75-134 35-91 (920)
323 PF05460 ORC6: Origin recognit 41.4 8.8 0.00019 41.2 0.0 79 182-260 4-83 (353)
324 TIGR02443 conserved hypothetic 41.4 20 0.00044 28.5 2.0 27 3-29 11-40 (59)
325 PF04545 Sigma70_r4: Sigma-70, 41.2 47 0.001 24.6 4.0 31 131-161 18-48 (50)
326 PF09723 Zn-ribbon_8: Zinc rib 41.2 14 0.00031 27.0 1.1 26 3-28 7-34 (42)
327 TIGR00100 hypA hydrogenase nic 41.2 14 0.0003 33.2 1.3 34 3-41 72-105 (115)
328 PF05344 DUF746: Domain of Unk 41.0 44 0.00095 27.1 3.9 31 229-259 8-38 (65)
329 PF13453 zf-TFIIB: Transcripti 41.0 19 0.00041 26.1 1.7 27 3-29 1-28 (41)
330 COG4977 Transcriptional regula 40.7 2.2E+02 0.0048 30.4 10.3 84 133-273 236-320 (328)
331 PRK01110 rpmF 50S ribosomal pr 40.4 13 0.00028 29.6 0.8 27 2-35 28-54 (60)
332 PRK08329 threonine synthase; V 40.3 18 0.00038 38.6 2.1 26 1-31 1-26 (347)
333 TIGR03831 YgiT_finger YgiT-typ 40.2 20 0.00044 25.9 1.8 10 21-30 33-42 (46)
334 smart00346 HTH_ICLR helix_turn 40.1 73 0.0016 26.3 5.5 28 233-260 19-46 (91)
335 PF04216 FdhE: Protein involve 40.0 14 0.0003 38.4 1.2 30 2-31 173-208 (290)
336 PRK11753 DNA-binding transcrip 40.0 1.1E+02 0.0024 29.3 7.5 30 233-262 167-196 (211)
337 PF04703 FaeA: FaeA-like prote 39.9 44 0.00096 26.8 3.8 28 232-259 13-40 (62)
338 COG2260 Predicted Zn-ribbon RN 39.6 14 0.0003 29.2 0.9 32 1-42 5-36 (59)
339 PRK03824 hypA hydrogenase nick 39.5 17 0.00036 33.7 1.5 11 19-29 106-116 (135)
340 COG1959 Predicted transcriptio 39.4 55 0.0012 30.7 5.0 46 115-160 7-52 (150)
341 PRK12529 RNA polymerase sigma 39.3 28 0.00061 33.0 3.1 25 233-257 142-166 (178)
342 PF09339 HTH_IclR: IclR helix- 39.1 43 0.00092 25.2 3.5 30 231-260 15-44 (52)
343 PF06397 Desulfoferrod_N: Desu 38.9 13 0.00029 26.5 0.6 21 3-23 8-28 (36)
344 PRK09642 RNA polymerase sigma 38.9 15 0.00032 33.9 1.1 27 233-259 121-147 (160)
345 smart00401 ZnF_GATA zinc finge 38.8 21 0.00045 27.5 1.7 28 3-30 5-35 (52)
346 PRK03681 hypA hydrogenase nick 38.5 19 0.00041 32.3 1.7 35 3-41 72-106 (114)
347 PF13542 HTH_Tnp_ISL3: Helix-t 38.4 89 0.0019 23.1 5.2 24 134-157 28-51 (52)
348 PRK09526 lacI lac repressor; R 38.4 25 0.00054 36.4 2.8 44 234-279 5-48 (342)
349 PF13824 zf-Mss51: Zinc-finger 38.2 21 0.00046 28.0 1.7 24 3-30 1-24 (55)
350 PRK14559 putative protein seri 38.1 17 0.00037 42.2 1.6 25 3-32 29-53 (645)
351 PRK00430 fis global DNA-bindin 38.0 1.6E+02 0.0034 25.5 7.3 25 234-258 68-92 (95)
352 TIGR02405 trehalos_R_Ecol treh 38.0 24 0.00051 36.2 2.6 24 234-257 1-24 (311)
353 PF13412 HTH_24: Winged helix- 37.9 84 0.0018 23.0 4.9 29 131-159 15-43 (48)
354 COG1510 Predicted transcriptio 37.9 69 0.0015 31.0 5.4 55 198-259 12-66 (177)
355 PF13556 HTH_30: PucR C-termin 37.9 40 0.00087 26.2 3.3 31 233-263 11-41 (59)
356 PRK14088 dnaA chromosomal repl 37.8 75 0.0016 35.1 6.6 68 91-161 345-415 (440)
357 PF10083 DUF2321: Uncharacteri 37.7 14 0.0003 35.0 0.7 28 3-38 30-57 (158)
358 TIGR02999 Sig-70_X6 RNA polyme 37.7 31 0.00066 32.5 3.1 26 233-258 149-174 (183)
359 TIGR02702 SufR_cyano iron-sulf 37.6 54 0.0012 32.1 4.9 27 234-260 15-41 (203)
360 PRK10402 DNA-binding transcrip 37.6 85 0.0018 30.9 6.4 46 115-160 151-196 (226)
361 PF04703 FaeA: FaeA-like prote 37.4 74 0.0016 25.5 4.7 35 130-164 12-46 (62)
362 PF13744 HTH_37: Helix-turn-he 37.4 55 0.0012 27.1 4.2 46 226-275 23-68 (80)
363 cd04761 HTH_MerR-SF Helix-Turn 37.4 32 0.00069 25.0 2.5 23 236-258 2-24 (49)
364 PF00196 GerE: Bacterial regul 37.2 52 0.0011 25.2 3.8 33 132-164 17-49 (58)
365 TIGR00155 pqiA_fam integral me 37.2 20 0.00044 39.2 2.0 29 3-31 15-44 (403)
366 PRK10014 DNA-binding transcrip 37.2 26 0.00057 36.2 2.8 24 233-256 5-28 (342)
367 PRK11753 DNA-binding transcrip 36.9 1.4E+02 0.0031 28.4 7.8 29 132-160 167-195 (211)
368 PF01485 IBR: IBR domain; Int 36.8 21 0.00046 27.5 1.6 28 2-30 19-50 (64)
369 COG1309 AcrR Transcriptional r 36.7 36 0.00079 30.4 3.3 39 219-258 17-56 (201)
370 PF05732 RepL: Firmicute plasm 36.6 49 0.0011 31.6 4.3 26 235-260 76-101 (165)
371 PRK09954 putative kinase; Prov 36.6 45 0.00098 35.4 4.5 30 231-260 14-43 (362)
372 PF13443 HTH_26: Cro/C1-type H 36.5 57 0.0012 25.2 4.0 40 233-276 9-48 (63)
373 COG2093 DNA-directed RNA polym 36.5 20 0.00043 28.8 1.3 22 3-29 6-27 (64)
374 PF04161 Arv1: Arv1-like famil 36.4 17 0.00037 36.0 1.2 31 2-32 1-36 (208)
375 PHA00542 putative Cro-like pro 36.4 29 0.00062 29.1 2.4 42 230-275 27-68 (82)
376 PRK14086 dnaA chromosomal repl 36.2 87 0.0019 36.3 6.8 71 91-163 527-599 (617)
377 PF01155 HypA: Hydrogenase exp 36.2 8.8 0.00019 34.3 -0.8 34 3-41 72-105 (113)
378 COG3413 Predicted DNA binding 36.1 50 0.0011 32.6 4.4 25 234-258 178-202 (215)
379 smart00354 HTH_LACI helix_turn 36.1 32 0.00069 27.7 2.5 35 235-274 1-35 (70)
380 smart00550 Zalpha Z-DNA-bindin 36.1 84 0.0018 25.2 5.0 38 123-160 11-49 (68)
381 COG1102 Cmk Cytidylate kinase 36.1 1E+02 0.0022 29.8 6.2 120 137-270 18-149 (179)
382 PRK10411 DNA-binding transcrip 36.1 36 0.00077 34.4 3.4 28 233-260 17-44 (240)
383 TIGR00595 priA primosomal prot 35.9 25 0.00054 39.6 2.5 28 3-31 224-251 (505)
384 PRK10870 transcriptional repre 35.9 2.1E+02 0.0045 27.4 8.6 28 232-259 69-96 (176)
385 PRK09645 RNA polymerase sigma 35.8 34 0.00073 32.0 3.0 26 233-258 133-158 (173)
386 PF01381 HTH_3: Helix-turn-hel 35.6 35 0.00076 25.5 2.6 39 232-275 7-45 (55)
387 PF04552 Sigma54_DBD: Sigma-54 35.5 28 0.0006 33.2 2.4 24 132-155 48-71 (160)
388 PRK13918 CRP/FNR family transc 35.5 1.5E+02 0.0033 28.1 7.6 30 132-161 148-177 (202)
389 PRK12543 RNA polymerase sigma 35.5 50 0.0011 31.2 4.2 27 233-259 132-158 (179)
390 PF14471 DUF4428: Domain of un 35.4 14 0.0003 28.4 0.2 27 3-30 1-30 (51)
391 PRK09047 RNA polymerase factor 35.4 36 0.00077 31.2 3.1 26 233-258 121-146 (161)
392 PF12728 HTH_17: Helix-turn-he 35.3 38 0.00083 25.1 2.7 22 235-256 2-23 (51)
393 TIGR02010 IscR iron-sulfur clu 35.2 63 0.0014 29.5 4.6 40 222-261 13-52 (135)
394 PF07278 DUF1441: Protein of u 35.2 31 0.00066 32.7 2.5 25 235-259 2-26 (152)
395 PRK04023 DNA polymerase II lar 34.9 23 0.00051 42.6 2.1 8 3-10 628-635 (1121)
396 cd04476 RPA1_DBD_C RPA1_DBD_C: 34.9 25 0.00055 33.1 2.0 27 3-31 36-62 (166)
397 PRK06759 RNA polymerase factor 34.8 37 0.00081 30.9 3.1 26 233-258 121-146 (154)
398 PRK09492 treR trehalose repres 34.8 27 0.00058 35.7 2.3 23 234-256 4-26 (315)
399 PRK12525 RNA polymerase sigma 34.5 38 0.00081 31.7 3.1 26 233-258 133-158 (168)
400 PF05043 Mga: Mga helix-turn-h 34.1 44 0.00095 27.8 3.2 30 230-259 26-55 (87)
401 PRK12523 RNA polymerase sigma 33.9 39 0.00084 31.7 3.1 25 233-257 134-158 (172)
402 COG1386 scpB Chromosome segreg 33.9 2.3E+02 0.005 27.7 8.5 120 116-259 10-131 (184)
403 PRK15103 paraquat-inducible me 33.9 24 0.00052 38.9 1.9 30 3-32 12-42 (419)
404 PRK10703 DNA-binding transcrip 33.9 36 0.00078 35.2 3.2 22 235-256 2-23 (341)
405 PRK00564 hypA hydrogenase nick 33.8 19 0.00042 32.4 0.9 35 3-41 73-107 (117)
406 COG3355 Predicted transcriptio 33.6 72 0.0016 29.3 4.6 39 224-262 32-70 (126)
407 cd01104 HTH_MlrA-CarA Helix-Tu 33.5 41 0.00089 26.4 2.8 23 236-258 2-24 (68)
408 TIGR02947 SigH_actino RNA poly 33.5 38 0.00083 32.4 3.0 27 233-259 146-172 (193)
409 PRK10141 DNA-binding transcrip 33.4 72 0.0016 28.8 4.6 31 232-262 28-58 (117)
410 PRK05580 primosome assembly pr 33.4 28 0.00061 40.7 2.5 28 3-31 392-419 (679)
411 COG1476 Predicted transcriptio 33.3 33 0.00072 28.1 2.1 25 233-257 13-37 (68)
412 PF14768 RPA_interact_C: Repli 33.1 34 0.00073 28.8 2.3 27 3-32 1-27 (82)
413 TIGR01562 FdhE formate dehydro 33.0 28 0.0006 36.7 2.1 9 20-28 224-232 (305)
414 PF13411 MerR_1: MerR HTH fami 32.9 32 0.0007 27.0 2.1 24 236-259 2-25 (69)
415 PRK09685 DNA-binding transcrip 32.8 1.7E+02 0.0036 29.9 7.9 55 215-275 195-249 (302)
416 TIGR03070 couple_hipB transcri 32.8 49 0.0011 24.5 3.0 39 232-275 13-51 (58)
417 KOG3507 DNA-directed RNA polym 32.7 24 0.00053 27.9 1.2 24 3-28 22-45 (62)
418 PRK11552 putative DNA-binding 32.7 61 0.0013 32.1 4.5 37 219-256 18-54 (225)
419 TIGR02531 yecD_yerC TrpR-relat 32.6 55 0.0012 28.1 3.5 23 233-256 49-71 (88)
420 PRK09391 fixK transcriptional 32.6 2E+02 0.0043 28.4 8.1 29 132-160 178-206 (230)
421 TIGR02937 sigma70-ECF RNA poly 32.5 57 0.0012 28.7 3.9 27 233-259 125-151 (158)
422 PRK10130 transcriptional regul 32.5 90 0.002 33.4 6.0 54 115-182 239-292 (350)
423 PRK12528 RNA polymerase sigma 32.5 43 0.00093 30.9 3.1 26 233-258 128-153 (161)
424 PRK12531 RNA polymerase sigma 32.4 41 0.00088 32.3 3.1 26 233-258 156-181 (194)
425 PRK14873 primosome assembly pr 32.4 28 0.00061 40.6 2.2 27 2-29 393-419 (665)
426 PRK09392 ftrB transcriptional 32.3 1.2E+02 0.0027 29.7 6.6 30 233-262 172-201 (236)
427 TIGR00310 ZPR1_znf ZPR1 zinc f 32.3 28 0.00061 34.2 1.9 30 3-32 2-42 (192)
428 PRK03564 formate dehydrogenase 32.2 31 0.00067 36.5 2.3 9 2-10 188-196 (309)
429 smart00421 HTH_LUXR helix_turn 32.2 78 0.0017 23.0 4.0 31 134-164 19-49 (58)
430 PF10058 DUF2296: Predicted in 32.1 24 0.00052 27.5 1.1 27 3-29 24-53 (54)
431 PF01599 Ribosomal_S27: Riboso 32.1 40 0.00086 25.6 2.2 25 3-28 20-46 (47)
432 PRK09480 slmA division inhibit 32.0 54 0.0012 30.9 3.8 42 216-257 12-53 (194)
433 PRK12520 RNA polymerase sigma 32.0 58 0.0013 31.0 4.1 27 233-259 146-172 (191)
434 cd00131 PAX Paired Box domain 32.0 61 0.0013 29.6 3.9 30 233-262 32-61 (128)
435 smart00347 HTH_MARR helix_turn 31.9 93 0.002 25.6 4.9 27 234-260 24-50 (101)
436 TIGR00498 lexA SOS regulatory 31.7 50 0.0011 32.0 3.6 32 230-261 21-53 (199)
437 PF13011 LZ_Tnp_IS481: leucine 31.6 94 0.002 26.6 4.7 36 225-260 16-51 (85)
438 PF13463 HTH_27: Winged helix 31.5 90 0.002 24.2 4.4 32 129-160 14-45 (68)
439 PF04810 zf-Sec23_Sec24: Sec23 31.3 41 0.00088 24.3 2.1 28 2-29 3-33 (40)
440 PRK10130 transcriptional regul 31.3 1.3E+02 0.0028 32.3 6.9 53 217-275 240-292 (350)
441 PRK07218 replication factor A; 31.3 24 0.00051 38.9 1.3 20 3-29 299-318 (423)
442 PF03444 HrcA_DNA-bdg: Winged 31.3 65 0.0014 27.1 3.6 29 231-259 20-48 (78)
443 PRK09649 RNA polymerase sigma 31.3 45 0.00098 31.8 3.1 26 233-258 145-170 (185)
444 PRK07921 RNA polymerase sigma 31.3 6.6E+02 0.014 26.6 17.9 91 65-155 86-211 (324)
445 PRK09956 hypothetical protein; 31.3 1.5E+02 0.0032 31.3 7.2 80 173-253 223-305 (308)
446 PF14206 Cys_rich_CPCC: Cystei 31.2 35 0.00075 28.7 2.0 27 3-29 3-29 (78)
447 PRK12527 RNA polymerase sigma 31.2 46 0.001 30.6 3.1 26 233-258 120-145 (159)
448 PHA03074 late transcription fa 31.1 25 0.00054 34.7 1.3 27 3-31 6-32 (225)
449 TIGR00319 desulf_FeS4 desulfof 31.0 28 0.0006 24.1 1.2 20 4-23 10-29 (34)
450 PF08299 Bac_DnaA_C: Bacterial 30.9 1.4E+02 0.003 24.2 5.5 64 76-157 4-70 (70)
451 PF10668 Phage_terminase: Phag 30.8 1.1E+02 0.0024 24.4 4.7 23 130-152 19-41 (60)
452 PF01498 HTH_Tnp_Tc3_2: Transp 30.8 49 0.0011 26.5 2.8 27 233-259 12-43 (72)
453 smart00351 PAX Paired Box doma 30.8 66 0.0014 29.1 3.9 29 234-262 33-61 (125)
454 PRK12542 RNA polymerase sigma 30.7 44 0.00096 31.7 3.0 42 233-274 137-181 (185)
455 TIGR02366 DHAK_reg probable di 30.7 66 0.0014 30.0 4.1 41 218-258 7-47 (176)
456 PF09339 HTH_IclR: IclR helix- 30.6 81 0.0018 23.7 3.8 34 126-159 11-44 (52)
457 cd06170 LuxR_C_like C-terminal 30.6 86 0.0019 23.0 4.0 32 133-164 15-46 (57)
458 PF01807 zf-CHC2: CHC2 zinc fi 30.6 26 0.00057 30.3 1.3 27 2-28 34-62 (97)
459 PRK12366 replication factor A; 30.5 23 0.0005 41.1 1.1 24 3-29 534-557 (637)
460 TIGR02952 Sig70_famx2 RNA poly 30.5 53 0.0012 30.3 3.4 27 233-259 137-163 (170)
461 PF04967 HTH_10: HTH DNA bindi 30.3 1.9E+02 0.0041 22.4 5.8 26 134-159 24-49 (53)
462 TIGR02954 Sig70_famx3 RNA poly 30.3 66 0.0014 29.9 4.1 27 233-259 134-160 (169)
463 COG1321 TroR Mn-dependent tran 30.2 76 0.0017 30.0 4.4 36 223-259 14-49 (154)
464 COG3620 Predicted transcriptio 30.2 54 0.0012 31.5 3.3 44 231-274 15-73 (187)
465 PF07900 DUF1670: Protein of u 30.1 50 0.0011 33.1 3.2 26 234-259 105-130 (220)
466 PF01047 MarR: MarR family; I 30.0 94 0.002 23.5 4.2 26 234-259 17-42 (59)
467 PRK09639 RNA polymerase sigma 29.9 63 0.0014 29.8 3.8 27 233-259 126-152 (166)
468 PRK12545 RNA polymerase sigma 29.9 45 0.00098 32.3 2.9 26 233-258 154-179 (201)
469 PRK08301 sporulation sigma fac 29.9 47 0.001 32.9 3.1 25 233-257 197-221 (234)
470 PRK07670 RNA polymerase sigma 29.8 5.8E+02 0.013 25.5 19.7 27 232-258 215-241 (251)
471 PRK14987 gluconate operon tran 29.8 40 0.00087 34.7 2.7 24 234-257 5-28 (331)
472 TIGR02950 SigM_subfam RNA poly 29.7 47 0.001 30.1 2.9 26 233-258 120-145 (154)
473 cd00974 DSRD Desulforedoxin (D 29.7 30 0.00066 24.0 1.2 22 3-24 6-27 (34)
474 PRK03564 formate dehydrogenase 29.7 35 0.00075 36.1 2.2 21 3-28 214-234 (309)
475 TIGR01481 ccpA catabolite cont 29.5 37 0.00081 34.8 2.4 23 235-257 2-24 (329)
476 PF14369 zf-RING_3: zinc-finge 29.5 31 0.00068 24.4 1.2 26 3-28 4-29 (35)
477 PF14493 HTH_40: Helix-turn-he 29.5 95 0.0021 26.3 4.5 46 228-274 7-52 (91)
478 PF00320 GATA: GATA zinc finge 29.5 22 0.00047 25.2 0.4 25 4-28 1-28 (36)
479 COG0664 Crp cAMP-binding prote 29.5 2.1E+02 0.0045 26.8 7.4 29 233-261 170-198 (214)
480 PF01047 MarR: MarR family; I 29.4 1.4E+02 0.003 22.6 5.1 28 133-160 17-44 (59)
481 PF13790 DUF4182: Domain of un 29.3 27 0.00059 25.3 0.9 14 19-32 2-15 (38)
482 PF01710 HTH_Tnp_IS630: Transp 29.2 3.3E+02 0.0072 24.2 8.2 75 76-160 19-98 (119)
483 PRK05572 sporulation sigma fac 29.1 6E+02 0.013 25.4 16.7 26 233-258 217-242 (252)
484 smart00760 Bac_DnaA_C Bacteria 29.1 1.1E+02 0.0023 23.9 4.4 32 111-144 23-56 (60)
485 PRK12519 RNA polymerase sigma 29.1 51 0.0011 31.4 3.1 25 233-257 156-180 (194)
486 PRK11512 DNA-binding transcrip 28.9 78 0.0017 28.9 4.2 28 232-259 52-79 (144)
487 COG2973 TrpR Trp operon repres 28.8 58 0.0013 28.6 3.0 39 221-259 47-85 (103)
488 PF01726 LexA_DNA_bind: LexA D 28.7 95 0.0021 24.9 4.1 32 128-159 20-52 (65)
489 PF04218 CENP-B_N: CENP-B N-te 28.7 35 0.00077 26.2 1.5 22 235-256 23-44 (53)
490 PF13463 HTH_27: Winged helix 28.5 79 0.0017 24.5 3.6 29 231-259 15-43 (68)
491 PF13913 zf-C2HC_2: zinc-finge 28.5 29 0.00062 22.5 0.8 10 1-10 2-11 (25)
492 PRK14165 winged helix-turn-hel 28.5 65 0.0014 32.3 3.7 30 231-260 18-47 (217)
493 TIGR00721 tfx DNA-binding prot 28.4 67 0.0015 29.9 3.6 27 233-259 20-46 (137)
494 PRK07037 extracytoplasmic-func 28.4 57 0.0012 30.0 3.2 24 233-256 124-147 (163)
495 PRK09685 DNA-binding transcrip 28.4 2.6E+02 0.0055 28.5 8.4 42 115-156 196-237 (302)
496 COG1595 RpoE DNA-directed RNA 28.3 56 0.0012 31.0 3.2 26 233-258 142-167 (182)
497 PRK10430 DNA-binding transcrip 28.2 87 0.0019 30.8 4.7 34 229-262 173-206 (239)
498 PRK10072 putative transcriptio 28.2 56 0.0012 28.5 2.8 29 230-258 42-70 (96)
499 PF05344 DUF746: Domain of Unk 28.2 1.4E+02 0.0031 24.2 4.9 35 127-161 7-41 (65)
500 PRK11303 DNA-binding transcrip 28.2 43 0.00094 34.4 2.6 22 236-257 2-23 (328)
No 1
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=7.5e-84 Score=684.00 Aligned_cols=480 Identities=33% Similarity=0.461 Sum_probs=393.2
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecccccccccccccccCCCccccCccceeecccc---cchHHHHHHHHHHHH
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAAGQSQLSGNFVRTIQSEY---GASRERLMEKAFDDM 78 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef~e~s~G~s~v~G~~v~~~~~~~---~~srer~l~~a~~~I 78 (567)
++|++||++++..|+++|+++|+.||+|+|+++|+++++|.+. ++|+||+..|.+. .++|++++++|++.|
T Consensus 1 ~~C~~C~~s~fe~d~a~g~~~C~~CG~v~E~~~ivsev~F~e~------~~G~~v~~~~~g~~~s~e~r~~t~~n~r~~i 74 (521)
T KOG1598|consen 1 MVCKNCGGSNFERDEATGNLYCTACGTVLEYNNIVAEVTFVEG------AQGQFVRVGQSGAGSSLESREKTIYNARRLI 74 (521)
T ss_pred CcCCCCCCCCcccccccCCceeccccceeeccceeEEeeeecc------cceeEEeccccCCccchHHHHHHHHHHHhHH
Confidence 5799999999999999999999999999999999999999987 7899998877653 489999999999999
Q ss_pred HHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHH
Q 008401 79 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 158 (567)
Q Consensus 79 ~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~ 158 (567)
..++.+|+|+ + +++.|++||++|.++||++||+...|+|+|+|++||+++++++|+||+++++|+||.||++|++|+
T Consensus 75 ~~~~~~l~l~--~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~~l~l~ 151 (521)
T KOG1598|consen 75 EELTERLNLG--N-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSNFLEVT 151 (521)
T ss_pred HHHHHhcCcc--h-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHHHHHHH
Confidence 9999999999 7 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccccccccccCCchhhHHHHHhhhC-CCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCH
Q 008401 159 QVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSK 237 (567)
Q Consensus 159 ~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~-~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~ 237 (567)
+.|.|... +.+++||+.||+||+.+|. ++++++|+.+|.+|+++|++|||++||+|+||||||||+|||+||+++|+
T Consensus 152 ~~L~i~en--~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi 229 (521)
T KOG1598|consen 152 DSLSIGEN--VSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTI 229 (521)
T ss_pred HHhccccc--cccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccH
Confidence 99999743 4568999999999999995 88889999999999999999999999999999999999999999999999
Q ss_pred hhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhHHhhhhcccCCCCCCCCCCCCc--------hhhhhccccCCCC
Q 008401 238 SDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHEGVAANLPNNGPKVSGM--------NEVLCKHKDTGKP 309 (567)
Q Consensus 238 ~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~le~e~~~~pp~~~~~~~~~--------~~~~~~~~~~~~~ 309 (567)
.||+.+||||+.||++||+||.+|+++.||+++|+++ |+|.+ +|||+|+..+.+. +.+.+.|.... +
T Consensus 230 ~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~ef~~~--d~e~~--~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~e-~ 304 (521)
T KOG1598|consen 230 GDIAKVVHVCESTLSKRLKEFSDTLSGDLTIDELAEI--DLEYE--SDPPSFTASPSKEAKYVEDKKKMLSRTMQLVE-L 304 (521)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccccccccHHHHHhh--hhhhc--cCcchhhcccchhhhhhhhhhhhhhhhhhhhh-c
Confidence 9999999999999999999999999999999999999 99998 9999999765322 22233332222 6
Q ss_pred CCCCchhhhhhhhhhcccCCCCCCCCchhHHHHHHHHHHhhhhhcchhhhccCCcccccccccCCCCCCCCCCCCCCCcc
Q 008401 310 FACGLCRSCYEEFMTISEGLEGGADPPAFQVAERERMVKASAEENSSFERESDSPFMSRVDKVQSPEPESIGVPKNCTTQ 389 (567)
Q Consensus 310 ~~~g~~~~~~~~~~~~~~~~~~~~dppa~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 389 (567)
+..+.|..++..+..+++++.++.++|.+++...++-..+.. +. .+.+.... .+...........+..
T Consensus 305 ~~~~~~~~~~~~~~~~~~~l~~~~q~~~~~~~~~e~~~~~~~-e~-----~~ssE~~d------k~~~g~~~~~~~~~sd 372 (521)
T KOG1598|consen 305 ANETWLVTLRHSLPVITGGLFLAWQDLQPRDRLVESYDDLAS-EC-----PLSSEDED------KPASGRLAELLAVLSD 372 (521)
T ss_pred ccchhhhccccCCcccchhhhcccccchhhhhhhhhhhhhhh-cC-----cccccccC------CcCccccchhhhcccc
Confidence 788899999999999999999999999999887664111100 00 00000000 0000000000000000
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChHHHhhcCCCHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHHHHHH
Q 008401 390 TASNEGEGDHTKTPGVDATTEASDGSDNFSDIDDFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAALE 469 (567)
Q Consensus 390 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lsdiDD~Eid~~il~eeE~~~K~~iW~~~N~dyl~eq~~K~~~~~~~~~~~~ 469 (567)
+.. +.. .........+....++++||.+++.++|++++.+.++.+ | +|++||.|+..+.++++++++.
T Consensus 373 ~~~-----~~~---~~~~~~~~~d~~~~~~~~~~~~l~r~~l~~~a~~~a~~~-~-~n~e~l~E~~~~~~~~ak~~~~-- 440 (521)
T KOG1598|consen 373 MAE-----QLA---SVWLRVLTLDKRSGVKHIDDLLLERQLLEESAGRDATEP-M-ENAETLVEERPGKAKAAKEREE-- 440 (521)
T ss_pred cch-----hhh---hcchhhhhccccccccccCHHHHHHHHhhhHHhhhcchh-h-hhHHHHHhhchhhhhhhHhhhh--
Confidence 000 000 001122345677889999999999999999999999999 7 9999999999988876653221
Q ss_pred hhhcCCCcchhHHHHHHHHHHHHHhhhhhHHHhhhhhhhcCCCCCCCHHHHHHHHHHhcCCCccCCHHHHhhhhCCCCc
Q 008401 470 ASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQKRAAEAKNSGPAQTALEATRRMLTKKRLSSKINYDVLEKLFDDSVC 548 (567)
Q Consensus 470 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~k~~k~~~~~~~~~~a~ta~EA~~~ml~~k~~S~kINYd~l~~L~~~~~~ 548 (567)
++ .+ ++++..+.++++++.||.||+++|++.+.+|++|||++|++|||....
T Consensus 441 ----------------------g~-~~----~~~k~~~r~~s~~~~t~~eavk~~~~i~~~s~~in~~~L~~i~d~~~e 492 (521)
T KOG1598|consen 441 ----------------------GI-NS----LSKKVGERRNSPELLTAPEAVKSMKEIKPVSSVINYSVLENISDAEIE 492 (521)
T ss_pred ----------------------cc-cc----cccccccccCCCcccccHHHHHHHHhccccccchHHHHHHHHhhhhcc
Confidence 11 11 112333456899999999999999999999999999999999986544
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=6.2e-54 Score=445.60 Aligned_cols=250 Identities=23% Similarity=0.390 Sum_probs=227.4
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecccccccccccccccC----CCccccCc------------cce--------
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAA----GQSQLSGN------------FVR-------- 57 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef~e~s~----G~s~v~G~------------~v~-------- 57 (567)
..||+||++.+++|+.+|++||++||+||+|++||.+++|+.+++ .++++++. .++
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~~g 91 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRNKDSYG 91 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCcccccccccCCCccCCCccccCCccccCCCCCccccCCCCceEeecCCccccc
Confidence 369999998899999999999999999999999999999987652 12333221 010
Q ss_pred ---------------eeccc--ccchHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHH
Q 008401 58 ---------------TIQSE--YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA 120 (567)
Q Consensus 58 ---------------~~~~~--~~~srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA 120 (567)
.||.+ ..++.||+|..|+..|+++|+.|+|| +.|+++|..||++++++++++||+.+.++|
T Consensus 92 ~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp--~~v~e~A~~iyk~~~~~~~~rgrs~~~i~A 169 (310)
T PRK00423 92 KSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLP--RSVREEAAVIYRKAVEKGLIRGRSIEGVVA 169 (310)
T ss_pred ccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence 12222 23678999999999999999999999 999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHH
Q 008401 121 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARD 200 (567)
Q Consensus 121 ACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~ 200 (567)
||||+|||++++|+||+||+.++++++++|+++|+.|.+.|+++.++ ++|+.||+|||+.|++ +..|.+.|.+
T Consensus 170 AclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~-----~~p~~~i~r~~~~L~L--~~~v~~~A~~ 242 (310)
T PRK00423 170 AALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPP-----TDPIDYVPRFASELGL--SGEVQKKAIE 242 (310)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC-----CCHHHHHHHHHHHcCC--CHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998765 8999999999999996 7899999999
Q ss_pred HHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 201 ILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 201 iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
|++.+.+.|++.||+|.+||||||||||+++|.++|++||+.++||++.||++||+||..
T Consensus 243 i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~ 302 (310)
T PRK00423 243 ILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAE 302 (310)
T ss_pred HHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999974
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=2e-53 Score=432.97 Aligned_cols=251 Identities=26% Similarity=0.481 Sum_probs=228.8
Q ss_pred CCCCCCCCCCCceeecCCCceecCcccceecccccccccccccc---cC---C-Ccc--ccCc----c-----------c
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKN---AA---G-QSQ--LSGN----F-----------V 56 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef~e~---s~---G-~s~--v~G~----~-----------v 56 (567)
|..||+||+.+++.|+..|++||.+||.|++++.||.+|+|+-+ .. | +.+ ..+. + +
T Consensus 1 ~~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~e~~~~r~g~P~t~~~~d~~l~t~i~~~~~~~~~rl 80 (285)
T COG1405 1 VMSCPECGSTNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDERHERRVGAPLTPSIHDKGLSTIIGWGDKDKMYRL 80 (285)
T ss_pred CCCCCCCCCccceeeccCCeEEeccCCEEeccccccCCCCcccccccccccccCCCccccCccchhhhcccchhHHHHHH
Confidence 56899999999999999999999999999999999999999943 21 1 110 1111 1 1
Q ss_pred eeeccc--ccchHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCc
Q 008401 57 RTIQSE--YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF 134 (567)
Q Consensus 57 ~~~~~~--~~~srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~ 134 (567)
+.||.+ .++++|+++..++.+|..++.+|+|| .++.++|..||++++++++++||+.+.++|||+|+|||++++|+
T Consensus 81 r~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP--~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~pr 158 (285)
T COG1405 81 RKWQIRIRVSSAKERNLITALEELERIASALGLP--ESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPR 158 (285)
T ss_pred HHHHhccccccchhhHHHHHHHHHHHHHHHhCCC--chHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCc
Confidence 234433 35679999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred cHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCC
Q 008401 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR 214 (567)
Q Consensus 135 tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR 214 (567)
||.||++++++++++|+++|+.+.+.|++..+| ++|.+||+|||+.|++ +++|...|.+|++.+.+.+++.||
T Consensus 159 tl~eIa~a~~V~~kei~rtyr~~~~~L~l~~~~-----~~p~~yi~rf~s~L~l--~~~v~~~a~ei~~~~~~~g~~~Gk 231 (285)
T COG1405 159 TLDEIAKALGVSKKEIGRTYRLLVRELKLKIPP-----VDPSDYIPRFASKLGL--SDEVRRKAIEIVKKAKRAGLTAGK 231 (285)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCC-----CCHHHHHHHHHHHcCC--CHHHHHHHHHHHHHHHHhCcccCC
Confidence 999999999999999999999999999998876 9999999999999997 799999999999999999999999
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 215 ~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
+|.||||||||||++++|+++||++|+.++|||++|||+||+|+.+
T Consensus 232 ~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel~~ 277 (285)
T COG1405 232 SPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELAD 277 (285)
T ss_pred CchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999864
No 4
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=7.8e-49 Score=389.44 Aligned_cols=266 Identities=20% Similarity=0.362 Sum_probs=236.5
Q ss_pred CCCCCCCCC--CceeecCCCceecCcccceecccccccccccccccC-----CCccccC---------cc---ce-----
Q 008401 2 VWCSSCARH--VTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAA-----GQSQLSG---------NF---VR----- 57 (567)
Q Consensus 2 ~~Cp~Cgs~--~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef~e~s~-----G~s~v~G---------~~---v~----- 57 (567)
++|++|+.. ++++|+..|++||..||+|+++++||.+.+|+.+++ .+|+|++ ++ ++
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 379999886 489999999999999999999999998878776542 2555532 11 11
Q ss_pred ---------eeccc-ccchHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHH
Q 008401 58 ---------TIQSE-YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC 127 (567)
Q Consensus 58 ---------~~~~~-~~~srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC 127 (567)
.+|++ ..++.++.+..||..|..|+++|+|| ..|.++|.++|+++.+.+.+|||+.++++|||||+||
T Consensus 81 ~s~~~s~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp--~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiAC 158 (308)
T KOG1597|consen 81 SSSFASSLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLP--ATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC 158 (308)
T ss_pred CHHHHHHHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCc--hHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence 23432 23567889999999999999999999 9999999999999999999999999999999999999
Q ss_pred HHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhh
Q 008401 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR 207 (567)
Q Consensus 128 R~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~ 207 (567)
|+++.||||+||+.+.+|+.++||+.++.|.+.|++..+.. .+...+||+|||+.|++ +..+++.|.++++.+..
T Consensus 159 Rq~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~---s~~t~~~m~RFCs~L~L--~~~~q~aA~e~a~ka~~ 233 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLI---SISTGDFMPRFCSNLGL--PKSAQEAATEIAEKAEE 233 (308)
T ss_pred HhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhh---hhhHHHHHHHHHHhcCC--CHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999876541 45678999999999996 89999999999999999
Q ss_pred ccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 208 DWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 208 ~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
..+..||.|.+||||+|||++++.+.++|++||..++||+|+|||+.||+++ ++...|.+.||....
T Consensus 234 ~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Ly-p~~~~liP~~~a~~~ 300 (308)
T KOG1597|consen 234 MDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLY-PHADKLIPSWYANAV 300 (308)
T ss_pred hccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHh-hchhhhChhhhcccc
Confidence 9999999999999999999999999999999999999999999999999996 677789999997664
No 5
>PF07741 BRF1: Brf1-like TBP-binding domain; InterPro: IPR011665 The Vaccinia virus has an infection-induced host cell cycle control mechanism. p53 and Rb, which are associated with the is inactivated Rb, which are associated with the RNA polymerase III transcription factor B (TFIIIB) subunits, TBP and Brf1, are inactivated [, ]. TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound pre-initiation complex, whereas Brf1 and Brf2 are involved in the recruitment of Pol III. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1 []. It is suggested that the structure of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. Entry of Brf1 and Bdp1 into the complex imposes a strict sequence preference for the downstream half of the TATA box []. This region covers both the Brf homology II and III regions []. ; GO: 0008270 zinc ion binding, 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NGM_J.
Probab=99.95 E-value=1.7e-29 Score=219.27 Aligned_cols=96 Identities=54% Similarity=0.796 Sum_probs=34.4
Q ss_pred hHHHhhcCCCHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHHHHHHhhhcCCCcchhHHHHHHHHHHHHHhhhhhHHHh
Q 008401 423 DFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAALEASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQ 502 (567)
Q Consensus 423 D~Eid~~il~eeE~~~K~~iW~~~N~dyl~eq~~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~k~~ 502 (567)
|+|||.|||||+|+++|++||+++|+|||++|++|+++.+++.+ .++ +++|++++
T Consensus 1 DdEid~~il~eeE~~~K~~iW~~~NkdyL~~~~~K~~~~~~~~~----------------------~~~---~~~k~k~~ 55 (97)
T PF07741_consen 1 DDEIDNYILSEEEVKIKERIWMEMNKDYLEEQEEKELKAKAEEE----------------------AGA---KSRKKKKK 55 (97)
T ss_dssp -HHHHTTC--HHHHHHHHHHHHHHTHHHHHHHHHCCCCT-----------------------------------------
T ss_pred ChHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----------------------hcc---CCCccccc
Confidence 56999999999999999999999999999999999976544211 111 12222222
Q ss_pred hhhhhhcC-CCCCCCHHHHHHHHHHhcCCCccCCHHHHhhhh
Q 008401 503 KRAAEAKN-SGPAQTALEATRRMLTKKRLSSKINYDVLEKLF 543 (567)
Q Consensus 503 k~~~~~~~-~~~a~ta~EA~~~ml~~k~~S~kINYd~l~~L~ 543 (567)
+++...++ .+||.||+||+++||++|+||+|||||+|++||
T Consensus 56 rk~~~~~~~~~~a~ta~EA~~~ml~~k~~S~KINYd~L~~LF 97 (97)
T PF07741_consen 56 RKRRKKKNQAPPAETAAEAARKMLKKKKFSKKINYDALESLF 97 (97)
T ss_dssp ------------------------------------------
T ss_pred cccccccCCCCCCCCHHHHHHHHHHhcCcccccCHHHHHhhC
Confidence 22223334 899999999999999999999999999999998
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=99.69 E-value=1.3e-16 Score=130.82 Aligned_cols=71 Identities=27% Similarity=0.516 Sum_probs=66.2
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHH
Q 008401 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 150 (567)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~L 150 (567)
|+++|+.|+|| .++.+.|.++|+.+.+.++++||++..++|||||+|||+++.|+|++||+++++|+.++|
T Consensus 1 I~r~~~~L~L~--~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLP--EDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCC--HHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 68999999999 999999999999999999999999999999999999999999999999999999999876
No 7
>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=99.60 E-value=3.6e-15 Score=122.20 Aligned_cols=71 Identities=18% Similarity=0.375 Sum_probs=66.6
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHH
Q 008401 179 LHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATL 251 (567)
Q Consensus 179 I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TI 251 (567)
|+|||+.|++ ++.|.+.|.+|++.+.+.|+..||+|.+|||||||+||+.+|.++|++||+.+++|++.||
T Consensus 1 I~r~~~~L~L--~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGL--PEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCC--CHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 6899999996 8899999999999999999999999999999999999999999999999999999999997
No 8
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.40 E-value=1.8e-11 Score=127.01 Aligned_cols=164 Identities=16% Similarity=0.114 Sum_probs=137.1
Q ss_pred HHHHHH-HHHHHHHHHHHHhC--CCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhh
Q 008401 67 RERLME-KAFDDMRQMKNALN--IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYL 143 (567)
Q Consensus 67 rer~l~-~a~~~I~~ia~~L~--Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~ 143 (567)
.|+.+. ..-..|.++|..|+ || +.++-+|..||++.+-.+.+.--.+..|+++|||+||+.+..|+++.+|+..+
T Consensus 51 eE~~l~~~y~~~i~~~~~~lkp~Lp--q~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~ 128 (305)
T TIGR00569 51 EELDLVKYYEKRLLDFCSAFKPTMP--TSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNL 128 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhc
Confidence 355554 45699999999999 99 99999999999999988877777899999999999999999999999999876
Q ss_pred ccC----hHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhC-----CCCCHHHHHHHHHHHHHhhhccccCCC
Q 008401 144 NIN----VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-----PGGNKKVCDTARDILASMKRDWITTGR 214 (567)
Q Consensus 144 ~v~----v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~-----~~~~~~V~~~A~~iv~~~~~~~i~~GR 214 (567)
.-+ ...|...-..|++.|+++... ..|..++..|...|. ......+.+.|+.+++.+....+.-=-
T Consensus 129 ~~~~~~~~~~Il~~E~~lL~~L~F~L~V-----~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y 203 (305)
T TIGR00569 129 KETPLKALEQVLEYELLLIQQLNFHLIV-----HNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLY 203 (305)
T ss_pred cCCchhhHHHHHHHHHHHHHHCCCcEEe-----eCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecC
Confidence 543 378889999999999998765 789998888876542 223456888899998877665555569
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCH
Q 008401 215 KPSGLCGAALYVSALTHGLKFSK 237 (567)
Q Consensus 215 ~P~~IaaAalylAa~~~g~~~t~ 237 (567)
.|+-||.||||+|++.+|.+..-
T Consensus 204 ~Ps~IAlAAI~lA~~~~~~~l~~ 226 (305)
T TIGR00569 204 TPSQIALAAILHTASRAGLNMES 226 (305)
T ss_pred CHHHHHHHHHHHHHHHhCCCCcc
Confidence 99999999999999999987654
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.38 E-value=2.2e-11 Score=123.82 Aligned_cols=182 Identities=13% Similarity=0.138 Sum_probs=155.9
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhcc
Q 008401 66 SRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI 145 (567)
Q Consensus 66 srer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v 145 (567)
..+-...-|-..|++-|-.|+|| +..+-++..+|+...-..-+.+-..++++.|||.+|.+.+..|++++||..+++-
T Consensus 18 ~e~el~~LG~e~Iqea~ILL~L~--q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~ 95 (367)
T KOG0835|consen 18 TEEELRILGCELIQEAGILLNLP--QVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHY 95 (367)
T ss_pred hHHHHHHHhHHHHHhhhHhhcCc--HHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHH
Confidence 33444455889999999999999 9999999999999988877788899999999999999999999999999988741
Q ss_pred ----------C-----------hHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHH
Q 008401 146 ----------N-----------VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILAS 204 (567)
Q Consensus 146 ----------~-----------v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~ 204 (567)
. .-.+-++..++++.||+..+. .+|..+|-.|...|++..+.++.++++.+.+.
T Consensus 96 L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv-----~hPhklii~YLqtL~~~~~~~l~Q~~wNfmND 170 (367)
T KOG0835|consen 96 LEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHV-----EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMND 170 (367)
T ss_pred HHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeee-----eccHHHHHHHHHHhcCCCchhHHHHHHHhhhh
Confidence 1 123456778999999999886 89999999999999976667789999999999
Q ss_pred hhhccccCCCChhHHHHHHHHHHHHhcCCCCC-HhhHHHHhccCHHHHHHH
Q 008401 205 MKRDWITTGRKPSGLCGAALYVSALTHGLKFS-KSDIVKIVHICEATLMKR 254 (567)
Q Consensus 205 ~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t-~~eIa~vv~Vse~TIrkR 254 (567)
..+..+..--.|.+||+||||||||-.++..+ +...-.+++++..-|..+
T Consensus 171 slRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~i 221 (367)
T KOG0835|consen 171 SLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEI 221 (367)
T ss_pred ccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHH
Confidence 99999999999999999999999999997653 557888888888765544
No 10
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.34 E-value=5.9e-12 Score=131.49 Aligned_cols=89 Identities=16% Similarity=0.227 Sum_probs=85.8
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHH
Q 008401 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 153 (567)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~ 153 (567)
...+|.++|+.|+|| ..+.+.|..+++.+.+.+++.||++..+||||||+|||.+|.|+|++||+++++|+..+|++.
T Consensus 219 p~~~i~r~~~~L~L~--~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ 296 (310)
T PRK00423 219 PIDYVPRFASELGLS--GEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNR 296 (310)
T ss_pred HHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 568999999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcc
Q 008401 154 YLQLCQVLYIA 164 (567)
Q Consensus 154 ~~~L~~~L~i~ 164 (567)
|+.|.+.|++.
T Consensus 297 ykel~~~l~~~ 307 (310)
T PRK00423 297 YKELAEKLDIK 307 (310)
T ss_pred HHHHHHHhCcc
Confidence 99999999864
No 11
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.26 E-value=2.5e-11 Score=126.11 Aligned_cols=158 Identities=20% Similarity=0.226 Sum_probs=130.9
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhc--cCh--
Q 008401 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN--INV-- 147 (567)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~--v~v-- 147 (567)
..+...|.+++.+|++| ...+.+|..||.+++-...++.-....+|++|||+|++.++.|+.+.||..+.. .++
T Consensus 40 ~~~~~fI~elg~~L~~~--~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~ 117 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMP--QKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKD 117 (323)
T ss_pred HHHHHHHHHHHHHcCCC--ccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccc
Confidence 57899999999999999 899999999999999888888888889999999999999999999999988753 333
Q ss_pred HHHHHH-----------HHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCC--HHHHHHHHHHHHHhhhccccCCC
Q 008401 148 YELGAV-----------YLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGN--KKVCDTARDILASMKRDWITTGR 214 (567)
Q Consensus 148 ~~Lgr~-----------~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~--~~V~~~A~~iv~~~~~~~i~~GR 214 (567)
.++... -+.|++.|+++... -+|..|+-+|+..|..+.+ ..++.+|+.+++...+..+.---
T Consensus 118 ~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v-----~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y 192 (323)
T KOG0834|consen 118 LELEEVYWELKERIVQLELLLLETLGFDLNV-----EHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQY 192 (323)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHccCceec-----cCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEee
Confidence 233333 44566677776654 7899999999999974333 25889999999888776666678
Q ss_pred ChhHHHHHHHHHHHHhcCCCCC
Q 008401 215 KPSGLCGAALYVSALTHGLKFS 236 (567)
Q Consensus 215 ~P~~IaaAalylAa~~~g~~~t 236 (567)
.|..||.||||||+.++|+..+
T Consensus 193 ~p~~IAva~i~lA~~~~~~~~~ 214 (323)
T KOG0834|consen 193 SPHSIAVACIHLAAKLLGVELP 214 (323)
T ss_pred cCcEEEeehhhHHHHHcCCCCC
Confidence 9999999999999999998644
No 12
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=99.22 E-value=4.7e-12 Score=93.77 Aligned_cols=43 Identities=23% Similarity=0.524 Sum_probs=38.4
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecccccccccccccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKN 44 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef~e~ 44 (567)
++||+||+..+++|+.+|++||++||.||+++.|+++++|+++
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 4799999999999999999999999999999999999999864
No 13
>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=99.07 E-value=1.2e-09 Score=111.16 Aligned_cols=158 Identities=18% Similarity=0.163 Sum_probs=134.3
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhh--------
Q 008401 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYL-------- 143 (567)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~-------- 143 (567)
..++..|..+|.+|+|| ..+..+|..+|++.+-++...+-+...|+++|||+||+.+.+|+-+.-.+-..
T Consensus 46 i~~~k~i~~l~~~L~lp--~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~ 123 (297)
T COG5333 46 IYYLKLIMDLCTRLNLP--QTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEP 123 (297)
T ss_pred HHHHHHHHHHHHhcCCC--cchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccc
Confidence 45789999999999999 99999999999999999999999999999999999999999765443322222
Q ss_pred ccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHH
Q 008401 144 NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAA 223 (567)
Q Consensus 144 ~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAa 223 (567)
--+...|-..-..+++.|+.+... ..|..++..|...+......++.+.|+.++...-+..++-=-.|..||.||
T Consensus 124 ~~sr~~Il~~E~~lLEaL~fd~~V-----~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~ 198 (297)
T COG5333 124 KSSRERILEYEFELLEALDFDLHV-----HHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAA 198 (297)
T ss_pred cccHHHHHHHHHHHHHHcccceEe-----ccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHH
Confidence 246778888888999999988775 789999999999886322357999999999999888777788999999999
Q ss_pred HHHHHHhcCCCCC
Q 008401 224 LYVSALTHGLKFS 236 (567)
Q Consensus 224 lylAa~~~g~~~t 236 (567)
|++|+...|.+.-
T Consensus 199 l~ia~~~~~~~~~ 211 (297)
T COG5333 199 LLIACEVLGMPII 211 (297)
T ss_pred HHHHHHhcCCccc
Confidence 9999999987653
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.02 E-value=1.1e-09 Score=112.68 Aligned_cols=91 Identities=18% Similarity=0.212 Sum_probs=87.2
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHH
Q 008401 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 152 (567)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr 152 (567)
+...+|.++|+.|||+ +.+...|.++.+++...|.+-||++..+||||||+|++.+|.++|.++|+.+++|+.-+|..
T Consensus 193 ~p~~yi~rf~s~L~l~--~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrn 270 (285)
T COG1405 193 DPSDYIPRFASKLGLS--DEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRN 270 (285)
T ss_pred CHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHH
Confidence 4568999999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhccc
Q 008401 153 VYLQLCQVLYIAD 165 (567)
Q Consensus 153 ~~~~L~~~L~i~~ 165 (567)
.|+.|.+.+++..
T Consensus 271 rykel~~~~~i~~ 283 (285)
T COG1405 271 RYKELADALDIEV 283 (285)
T ss_pred HHHHHHHhhcccc
Confidence 9999999998753
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=98.85 E-value=2.6e-08 Score=82.25 Aligned_cols=83 Identities=23% Similarity=0.257 Sum_probs=78.0
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhcc-ChHHHH
Q 008401 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELG 151 (567)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v-~v~~Lg 151 (567)
.+...|.+++..++++ ..+...|..++.++...+.+.++++..+++||||+||+.++.|.++.+|..+++. +..+|.
T Consensus 4 ~~~~~l~~~~~~~~~~--~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~ 81 (88)
T cd00043 4 TPLDFLRRVAKALGLS--PETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEIL 81 (88)
T ss_pred hHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHH
Confidence 4678999999999999 9999999999999999988899999999999999999999999999999999999 999999
Q ss_pred HHHHHH
Q 008401 152 AVYLQL 157 (567)
Q Consensus 152 r~~~~L 157 (567)
+.++.|
T Consensus 82 ~~e~~i 87 (88)
T cd00043 82 RMEKLL 87 (88)
T ss_pred HHHHHh
Confidence 888765
No 16
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.85 E-value=1.3e-08 Score=102.87 Aligned_cols=88 Identities=13% Similarity=0.127 Sum_probs=84.1
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHH
Q 008401 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 152 (567)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr 152 (567)
..-.+|.++|+.|+|| .+++..|.++.+.+.+..+..||++..|+||.+|++|+....+++++||.+++||..-+|..
T Consensus 202 ~t~~~m~RFCs~L~L~--~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~ 279 (308)
T KOG1597|consen 202 STGDFMPRFCSNLGLP--KSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRN 279 (308)
T ss_pred hHHHHHHHHHHhcCCC--HHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHH
Confidence 3568999999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhh
Q 008401 153 VYLQLCQVLY 162 (567)
Q Consensus 153 ~~~~L~~~L~ 162 (567)
+|+.|..++.
T Consensus 280 sYK~Lyp~~~ 289 (308)
T KOG1597|consen 280 SYKDLYPHAD 289 (308)
T ss_pred HHHHHhhchh
Confidence 9999987764
No 17
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.78 E-value=4.4e-08 Score=80.89 Aligned_cols=84 Identities=23% Similarity=0.284 Sum_probs=78.6
Q ss_pred CCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhcc-CHHHH
Q 008401 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATL 251 (567)
Q Consensus 173 vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~V-se~TI 251 (567)
..|..||.+++..+++ +..+...|..+++++...+...|++|..||+||||+|+++.+...+.++++.+++. +..+|
T Consensus 3 ~~~~~~l~~~~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i 80 (88)
T cd00043 3 PTPLDFLRRVAKALGL--SPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEI 80 (88)
T ss_pred chHHHHHHHHHHHcCC--CHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHH
Confidence 4578899999999985 78999999999999988888889999999999999999999999999999999999 99999
Q ss_pred HHHHHHH
Q 008401 252 MKRLIEF 258 (567)
Q Consensus 252 rkR~kE~ 258 (567)
.+.++++
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 9999876
No 18
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.77 E-value=1.1e-07 Score=93.15 Aligned_cols=176 Identities=16% Similarity=0.201 Sum_probs=128.5
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCc----cHHHHHhhh------
Q 008401 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF----LLIDFSNYL------ 143 (567)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~----tL~Diad~~------ 143 (567)
-.+.|+.++..|+|. +.|+.+|..+||+.+-++.+++-.+..+|+.|||+||+.+..|+ +|.--+..+
T Consensus 44 ~~n~I~~lg~~lklR--Q~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~ 121 (264)
T KOG0794|consen 44 MANVIQKLGQHLKLR--QRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSY 121 (264)
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhccc
Confidence 458999999999999 99999999999999999889999999999999999999999882 221112222
Q ss_pred -----ccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhH
Q 008401 144 -----NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSG 218 (567)
Q Consensus 144 -----~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~ 218 (567)
......|-..--.|++.|+--+- .-+|..=+..|...++. .+.+....++.|++..-+..++-=-.|.-
T Consensus 122 ~~e~~~~~~~~I~e~Ef~llE~Ld~~LI-----VhHPYrsL~q~~qd~gi-~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~ 195 (264)
T KOG0794|consen 122 WPEKFPYERKDILEMEFYLLEALDCYLI-----VHHPYRSLLQFVQDMGI-NDQKLLQLAWSIVNDSYRMDLCLLYPPHQ 195 (264)
T ss_pred chhhcCCCcCcchhhhhhHHhhhceeEE-----EecCCccHHHHHHHhcc-cchhhhhhhHhhhcchhhcceeeecCHHH
Confidence 12233333344455566653221 24576668888888874 35668889999999988888888899999
Q ss_pred HHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 219 LCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 219 IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
||-||||+|+..++-..+ +..-..+.|--.-+.....++
T Consensus 196 IalAcl~Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I 234 (264)
T KOG0794|consen 196 IALACLYIACVIDEKDIP-KAWFAELSVDMEKVKDIVQEI 234 (264)
T ss_pred HHHHHHHHHHhhcCCChH-HHHHHHHhccHHHHHHHHHHH
Confidence 999999999988876654 333334444444444444444
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=98.75 E-value=4.6e-08 Score=80.00 Aligned_cols=79 Identities=22% Similarity=0.270 Sum_probs=72.1
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHh-ccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhcc-ChHHHHHHH
Q 008401 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVA-RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVY 154 (567)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~-~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v-~v~~Lgr~~ 154 (567)
.|.+++..++++ ..+...|..+++++.. .++.+ +++..++|||||+||+.++.+.+..++...++. +..+|.+.+
T Consensus 2 ~l~~~~~~~~~~--~~~~~~a~~~~~~~l~~~~~~~-~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 2 FLRRVCKALNLD--PETLNLAVNLLDRFLSDYKFLK-YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred HHHHHHHHcCCC--HHHHHHHHHHHHHHHHHhhccc-CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 578899999999 9999999999999988 45554 999999999999999999999999999999999 999999988
Q ss_pred HHHH
Q 008401 155 LQLC 158 (567)
Q Consensus 155 ~~L~ 158 (567)
+.|.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 8774
No 20
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.74 E-value=6.6e-08 Score=79.10 Aligned_cols=81 Identities=20% Similarity=0.223 Sum_probs=73.7
Q ss_pred hhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhcc-CHHHHHHHH
Q 008401 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRL 255 (567)
Q Consensus 177 ~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~V-se~TIrkR~ 255 (567)
.||.|++..+++ ++++...|..+++++..+.-..+++|..||+||||+|+++.+..++.++++..+++ +..+|.+.+
T Consensus 1 ~~l~~~~~~~~~--~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 1 DFLRRVCKALNL--DPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred CHHHHHHHHcCC--CHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 478999999986 78999999999999987544456999999999999999999999999999999999 999999999
Q ss_pred HHHH
Q 008401 256 IEFE 259 (567)
Q Consensus 256 kE~~ 259 (567)
+++.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 9885
No 21
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.52 E-value=3.5e-06 Score=88.11 Aligned_cols=177 Identities=16% Similarity=0.211 Sum_probs=139.4
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhc-cccCCC--chhHHHHHHHHHHHHHhCC--CccHHHHHhhh--cc
Q 008401 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVAR-NFTKGR--RTEQVQASCLYLACRQKSK--PFLLIDFSNYL--NI 145 (567)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~-~~~rGR--~~~~vaAACLYiACR~e~~--p~tL~Diad~~--~v 145 (567)
.|...|-++|...+.. ..+.=-|.+|+.+.+.- .+-+++ -.+.+++|||.+|.+.+.+ |.++.-....+ -+
T Consensus 80 ~A~~WIl~V~~~~~~~--~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~f 157 (335)
T KOG0656|consen 80 QALDWILKVCEEYNFE--PLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVF 157 (335)
T ss_pred HHHHHHHHHHHHhCCc--hHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccc
Confidence 5789999999999999 89999999999998764 444444 2688999999999998765 66555445443 36
Q ss_pred ChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCC--CCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHH
Q 008401 146 NVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLP--GGNKKVCDTARDILASMKRDWITTGRKPSGLCGAA 223 (567)
Q Consensus 146 ~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~--~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAa 223 (567)
..++|.+.-+.++..|+-...+ +.|..||..|+.++++ ...+.+...+..++-....+.-..+-.|+.||||+
T Consensus 158 eaktI~rmELLVLstL~Wrl~a-----VTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~ 232 (335)
T KOG0656|consen 158 EAKTIQRMELLVLSTLKWRLRA-----VTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAA 232 (335)
T ss_pred cHHHHHHHHHHHHhhccccccC-----CCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHH
Confidence 8899999999999999998876 9999999999999973 33456777777776666666666799999999998
Q ss_pred HHHHHHh-cCCC--CCHhhHHHHhccCHHHHHHHHH
Q 008401 224 LYVSALT-HGLK--FSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 224 lylAa~~-~g~~--~t~~eIa~vv~Vse~TIrkR~k 256 (567)
+..++.. .+.. .....+.....|+.-.+++.|.
T Consensus 233 ~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 233 ILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 8766543 3433 2345667778899988888887
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.25 E-value=1e-06 Score=95.75 Aligned_cols=159 Identities=14% Similarity=0.171 Sum_probs=105.4
Q ss_pred HHHHHHHHHhCCCCc-hHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHH
Q 008401 76 DDMRQMKNALNIGES-DEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVY 154 (567)
Q Consensus 76 ~~I~~ia~~L~Lp~~-~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~ 154 (567)
-+|.+++..|-..++ ..|+.+|.++......-.+..||++..+++||||||||.+|++++..||+.+++|+..+|.+.|
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 355666666644421 3456666666555544456689999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcccccc------ccccCCchhhHHHHH-hhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHH
Q 008401 155 LQLCQVLYIADESN------VLKQVDPSIFLHKFT-DRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVS 227 (567)
Q Consensus 155 ~~L~~~L~i~~~~~------~~~~vdP~~~I~Rf~-~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylA 227 (567)
+.+.+.+..+++.. ...-.||..|-..=- ..--.....+....-...+.-+...|..+++.+...+-+.++.+
T Consensus 248 ~Ef~~T~s~~Lti~ef~~~d~e~~~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~l~~~ 327 (521)
T KOG1598|consen 248 KEFSDTLSGDLTIDELAEIDLEYESDPPSFTASPSKEAKYVEDKKKMLSRTMQLVELANETWLVTLRHSLPVITGGLFLA 327 (521)
T ss_pred HHHhccccccccHHHHHhhhhhhccCcchhhcccchhhhhhhhhhhhhhhhhhhhhcccchhhhccccCCcccchhhhcc
Confidence 99999886554321 011233433322100 00000011222223333445566789999999999999999988
Q ss_pred HHhcCCC
Q 008401 228 ALTHGLK 234 (567)
Q Consensus 228 a~~~g~~ 234 (567)
++-....
T Consensus 328 ~q~~~~~ 334 (521)
T KOG1598|consen 328 WQDLQPR 334 (521)
T ss_pred cccchhh
Confidence 8755443
No 23
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=97.67 E-value=0.0015 Score=63.86 Aligned_cols=159 Identities=14% Similarity=0.162 Sum_probs=121.9
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhc--cccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHH
Q 008401 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVY 154 (567)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~--~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~ 154 (567)
.|.+++.+|||..+..+++.|.+|.|+..-+ +..-|-.-..-+.-|+=+|.-.-++|+--.-.-...|.+.....+.|
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 4889999999965689999999999886432 33344444556778999988888998887777788899999999999
Q ss_pred HHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhcc-----ccCC-CChhHHHHHHHHHHH
Q 008401 155 LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDW-----ITTG-RKPSGLCGAALYVSA 228 (567)
Q Consensus 155 ~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~-----i~~G-R~P~~IaaAalylAa 228 (567)
+-+-..|+++... -|..+|-.|+ -.+|++.|..|+...+..- +-+. -|| -.++||+|.||
T Consensus 82 ~sfe~llgln~~~----------~VrdlaVQfg---c~evi~~a~~vl~syk~~lpaT~~~~~D~SrP-~ft~aA~~~ac 147 (262)
T KOG4557|consen 82 NSFENLLGLNIKL----------NVRDLAVQFG---CVEVIKSAQNVLSSYKERLPATRRANADFSRP-VFTAAAFYLAC 147 (262)
T ss_pred HHHHHHhcchhhc----------CHHHHHHHHh---HHHHHHHHHHHHHHHHhcCchhhhcCCcccch-HHHHHHHHHHH
Confidence 9999999987543 2677888888 4788999999888765421 1111 234 36789999999
Q ss_pred HhcCCCCCHhhHHHHhccCHH
Q 008401 229 LTHGLKFSKSDIVKIVHICEA 249 (567)
Q Consensus 229 ~~~g~~~t~~eIa~vv~Vse~ 249 (567)
+....+++...+..+.|++++
T Consensus 148 k~lKlKVdK~kli~~sg~~~s 168 (262)
T KOG4557|consen 148 KKLKLKVDKLKLIEVSGTSES 168 (262)
T ss_pred HHHHHhhhHhhcccccCCCHH
Confidence 999888888777777776664
No 24
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=97.62 E-value=0.00056 Score=70.04 Aligned_cols=161 Identities=19% Similarity=0.172 Sum_probs=106.9
Q ss_pred HHHHHHHHh--CCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhc----cChHHH
Q 008401 77 DMRQMKNAL--NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN----INVYEL 150 (567)
Q Consensus 77 ~I~~ia~~L--~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~----v~v~~L 150 (567)
.+-.++..+ +|| .+|+-+|..+|++++=.+.+.--++..|+++|+|+||+.+..-++..+|+.-.. -+...+
T Consensus 62 ~l~~f~~k~~p~lp--~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~v 139 (325)
T KOG2496|consen 62 SLVNFYSKFKPNLP--TSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIV 139 (325)
T ss_pred HHHHHHHHhcCCCc--hHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHH
Confidence 334444444 788 999999999999999888888889999999999999999999999999998776 555666
Q ss_pred HHHHHHHHHHhhccccccccccCCc-hhhHHHHHhhhC-CCCCHHH-HHHHH--HHHHHhhhccccCCCChhHHHHHHHH
Q 008401 151 GAVYLQLCQVLYIADESNVLKQVDP-SIFLHKFTDRLL-PGGNKKV-CDTAR--DILASMKRDWITTGRKPSGLCGAALY 225 (567)
Q Consensus 151 gr~~~~L~~~L~i~~~~~~~~~vdP-~~~I~Rf~~~L~-~~~~~~V-~~~A~--~iv~~~~~~~i~~GR~P~~IaaAaly 225 (567)
-+--..|++.|...... ..+-.| .-|+..+-..|- ++ ++.. ..... +.++++.-....-=..|+-||-|||+
T Consensus 140 Lk~E~~llqsL~f~L~v--h~PyRPleGFl~D~kt~l~~~~-n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil 216 (325)
T KOG2496|consen 140 LKYEFLLLQSLKFSLTV--HNPYRPLEGFLLDMKTRLPALE-NPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAIL 216 (325)
T ss_pred HhchHHHHHhhhhhhee--cCCCCchHHHHHHHHHHHHhcc-CHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHH
Confidence 66666788888766432 112233 234444444442 21 2222 22222 34444333333334789999999984
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 226 lAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
.|+ +.+..|+..+|.+-
T Consensus 217 ~a~----------------~~~~~~l~s~~~e~ 233 (325)
T KOG2496|consen 217 HAA----------------GRTGETLESYLLES 233 (325)
T ss_pred HHh----------------ccccchHHHHHHHH
Confidence 443 44455666666663
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=97.59 E-value=0.0007 Score=60.63 Aligned_cols=91 Identities=13% Similarity=0.251 Sum_probs=76.1
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCC-CccHHHHHhhhc--cChH
Q 008401 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVY 148 (567)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-p~tL~Diad~~~--v~v~ 148 (567)
......|..++..++++ ..+.-.|..+|.+..............++++|+|+||+.+.. +.++.++....+ .+..
T Consensus 32 ~~~~~~i~~~~~~~~l~--~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~ 109 (127)
T PF00134_consen 32 QIIIDWIIELCQRLKLS--PETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKK 109 (127)
T ss_dssp HHHHHHHHHHHHHTT-B--HHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHH
T ss_pred HHHHHHHHHHHHhcccc--hhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHH
Confidence 45778999999999999 999999999999998888777788899999999999999876 788888888763 6788
Q ss_pred HHHHHHHHHHHHhhcc
Q 008401 149 ELGAVYLQLCQVLYIA 164 (567)
Q Consensus 149 ~Lgr~~~~L~~~L~i~ 164 (567)
+|-..-..+++.|+.+
T Consensus 110 ~i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 110 DILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHCCCC
Confidence 8988888898888764
No 26
>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=97.33 E-value=0.0015 Score=60.41 Aligned_cols=84 Identities=12% Similarity=0.216 Sum_probs=64.7
Q ss_pred HHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHh--ccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccCh
Q 008401 70 LMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINV 147 (567)
Q Consensus 70 ~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~--~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v 147 (567)
.+.-|..+|+.+|..|+|+ +.+.+....+|..+.. -.++++|...+++.+|+|+.||..+.+++++||-....--+
T Consensus 10 vy~la~~Rl~~LC~~L~l~--~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qp 87 (135)
T PF01857_consen 10 VYKLAAVRLQDLCERLDLS--SDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQP 87 (135)
T ss_dssp HHHHHHHHHHHHHHHHTTS--TTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTST
T ss_pred HHHHHHHHHHHHHHHcCCc--HHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcc
Confidence 3455889999999999999 8999999999998875 35789999999999999999999999999999988765443
Q ss_pred HHHHHHHH
Q 008401 148 YELGAVYL 155 (567)
Q Consensus 148 ~~Lgr~~~ 155 (567)
..-..+|+
T Consensus 88 q~~~~Vyr 95 (135)
T PF01857_consen 88 QASSHVYR 95 (135)
T ss_dssp T--THHHH
T ss_pred cccccceE
Confidence 33333443
No 27
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.31 E-value=0.003 Score=68.41 Aligned_cols=153 Identities=14% Similarity=0.093 Sum_probs=121.3
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHH-HHHHHhCC-CccHHHHHhhhc--cChHH
Q 008401 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLY-LACRQKSK-PFLLIDFSNYLN--INVYE 149 (567)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLY-iACR~e~~-p~tL~Diad~~~--v~v~~ 149 (567)
-.+.|-++-..++|. ....-.|..|+.+.+....+..++...|..+||+ |||+.+.+ +-++.|+.-+.+ .+..+
T Consensus 161 Lvdwlvevh~~F~L~--~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~ 238 (391)
T KOG0653|consen 161 LVDWLVEVHEKFGLS--PETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREE 238 (391)
T ss_pred HHHHHHHhhhhcCcC--HHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHH
Confidence 357888899999999 8999999999999988766888888888888855 99996433 334677766654 78899
Q ss_pred HHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHH
Q 008401 150 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSAL 229 (567)
Q Consensus 150 Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~ 229 (567)
|.+.-+.+...|+..... ..|..|+.||.....- .......+..++....-+.-.....|+.++||+.+++.+
T Consensus 239 il~mE~~il~~L~f~l~~-----p~~~~FLrr~~ka~~~--d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~ 311 (391)
T KOG0653|consen 239 ILRMEKYILNVLEFDLSV-----PTPLSFLRRFLKAADY--DIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALR 311 (391)
T ss_pred HHHHHHHHHhccCeeecC-----CchHHHHHHHHHhhhc--chhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHH
Confidence 999999999999876554 7899999999988863 344555566666666556555678999999999999999
Q ss_pred hcCCCC
Q 008401 230 THGLKF 235 (567)
Q Consensus 230 ~~g~~~ 235 (567)
+.+...
T Consensus 312 ~~~~~~ 317 (391)
T KOG0653|consen 312 MLSKGD 317 (391)
T ss_pred HhccCC
Confidence 987654
No 28
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=96.95 E-value=0.0025 Score=56.04 Aligned_cols=84 Identities=19% Similarity=0.167 Sum_probs=65.8
Q ss_pred CchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCC-CCCHhhHHHHhccCHHHHH
Q 008401 174 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIVHICEATLM 252 (567)
Q Consensus 174 dP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~-~~t~~eIa~vv~Vse~TIr 252 (567)
.|..|+.+|....+. ..++...|..|++.+..+.-..+-+|+.||+||||+|..+.+. ..-...+...+|+....|+
T Consensus 2 Tp~~Fl~~~~~~~~~--~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~ 79 (118)
T PF02984_consen 2 TPYDFLRRFLKISNA--DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLK 79 (118)
T ss_dssp -HHHHHHHHHTSSSH--HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHHHHcCC--cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHH
Confidence 478899999443332 5678889999999887777788999999999999999999875 3445567888899999999
Q ss_pred HHHHHHH
Q 008401 253 KRLIEFE 259 (567)
Q Consensus 253 kR~kE~~ 259 (567)
..++.+.
T Consensus 80 ~c~~~i~ 86 (118)
T PF02984_consen 80 ECIELIQ 86 (118)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9888875
No 29
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=96.61 E-value=0.013 Score=64.03 Aligned_cols=149 Identities=14% Similarity=0.056 Sum_probs=110.8
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCC-CccHHHHHhhhc--cChHHHH
Q 008401 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYELG 151 (567)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-p~tL~Diad~~~--v~v~~Lg 151 (567)
.+.|.++-..+++- ......|..|..+.+..+.+.=.+...|++.||+|||+-+.+ +-++.+++-++. .++..|.
T Consensus 217 v~wlvevH~~F~ll--peTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~ 294 (440)
T COG5024 217 VDWLVEVHGKFGLL--PETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDII 294 (440)
T ss_pred HHHHHHhccccccc--chHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHH
Confidence 35667777889998 788999999999999888877777899999999999998765 455788887764 7899999
Q ss_pred HHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhc-cccCCCChhHHHHHHHHHHHHh
Q 008401 152 AVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRD-WITTGRKPSGLCGAALYVSALT 230 (567)
Q Consensus 152 r~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~-~i~~GR~P~~IaaAalylAa~~ 230 (567)
++.+.+...|+.+... ..|..|+.|+...... ...-...+..+.....-+ .+...+ |+.+++||-|++-.+
T Consensus 295 ~aE~~ml~~l~f~is~-----P~P~sFLRriSka~dy--d~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~ 366 (440)
T COG5024 295 RAERYMLEVLDFNISW-----PSPMSFLRRISKASDY--DIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKI 366 (440)
T ss_pred HHHHHHhhhcccccCC-----CChHHHHHHHHhhccc--chhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhh
Confidence 9999999999987654 6788898887666652 222222333333322211 233445 999999999999887
Q ss_pred cCC
Q 008401 231 HGL 233 (567)
Q Consensus 231 ~g~ 233 (567)
.+-
T Consensus 367 ~~~ 369 (440)
T COG5024 367 LSQ 369 (440)
T ss_pred hcc
Confidence 764
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=96.17 E-value=0.0031 Score=44.91 Aligned_cols=27 Identities=33% Similarity=0.637 Sum_probs=23.4
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.|+.|++. .+...+|..+|..||+|++
T Consensus 10 ~C~~C~~~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 10 PCPVCGSR--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cCCCCCCe--EeEccCCEEEhhhCceEcC
Confidence 49999997 5667799999999999975
No 31
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=95.94 E-value=0.047 Score=56.79 Aligned_cols=105 Identities=16% Similarity=0.284 Sum_probs=78.1
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHH-HHHhhhccChHHHHH
Q 008401 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLI-DFSNYLNINVYELGA 152 (567)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~-Diad~~~v~v~~Lgr 152 (567)
..+.|-.+.+-|+++++..+...+.+|......-.+..--+++.||+||+|+|.|..++|++.. ..-.+++++..+|-.
T Consensus 141 Phklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ 220 (367)
T KOG0835|consen 141 PHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDE 220 (367)
T ss_pred cHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHH
Confidence 3467788889999997666788888888888776766667899999999999999999887665 455677888888877
Q ss_pred HHHHHHHHhhccccccccccCCchhhHHHHHhhh
Q 008401 153 VYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL 186 (567)
Q Consensus 153 ~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L 186 (567)
...++........ | -..+|.-|++.+
T Consensus 221 ic~~l~~lY~~~~-p-------~~~li~~~vd~~ 246 (367)
T KOG0835|consen 221 ICYRLIPLYKRAK-P-------DETLIEAFVDRL 246 (367)
T ss_pred HHHHHHHHHHhcc-c-------CHHHHHHHHHHh
Confidence 7766666544321 1 134666666666
No 32
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=95.33 E-value=0.21 Score=44.79 Aligned_cols=55 Identities=11% Similarity=0.033 Sum_probs=42.0
Q ss_pred cHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhC-CCCCHH
Q 008401 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGNKK 193 (567)
Q Consensus 135 tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~-~~~~~~ 193 (567)
.|++++..+||+--+++..+..|.+.|+....+ ..........+.++|. ++.+.+
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~----~~~~~~~~~~IL~~L~~GeIs~e 106 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGYEEDE----EEEEEDERKEILDKLEKGEISVE 106 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCc----ccccchhHHHHHHHHHcCCCCHH
Confidence 588999999999999999999999999983322 1344567788888884 555543
No 33
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=95.06 E-value=0.011 Score=46.49 Aligned_cols=31 Identities=26% Similarity=0.541 Sum_probs=28.7
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
++||.|+...+++++++-.+.|..||.+|-.
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 3799999999999999999999999999874
No 34
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=94.97 E-value=0.013 Score=47.04 Aligned_cols=31 Identities=23% Similarity=0.521 Sum_probs=28.7
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
++||.||...+++++.+-.+.|..||.+|-+
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEEe
Confidence 4799999999999999999999999999875
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=94.93 E-value=0.011 Score=45.99 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=23.8
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
++||.|+...+++++++-.+.|..||+||-+
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 4799999999999999999999999999964
No 36
>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=94.38 E-value=0.22 Score=43.50 Aligned_cols=86 Identities=14% Similarity=0.150 Sum_probs=63.3
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCC-CccHHHHHhhhccChHHHHHH
Q 008401 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLNINVYELGAV 153 (567)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-p~tL~Diad~~~v~v~~Lgr~ 153 (567)
+..|+.+....+.. ..+...|..+...+.-...+-+-++..+||||+|+|.+..+. +.--..+...++++...|..+
T Consensus 4 ~~Fl~~~~~~~~~~--~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c 81 (118)
T PF02984_consen 4 YDFLRRFLKISNAD--QEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHTSSSHH--HHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHcCCc--HHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence 45666664444444 678888888888865544345567889999999999999765 555566778889999999999
Q ss_pred HHHHHHHhh
Q 008401 154 YLQLCQVLY 162 (567)
Q Consensus 154 ~~~L~~~L~ 162 (567)
+..|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999988775
No 37
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=94.33 E-value=0.022 Score=37.49 Aligned_cols=23 Identities=22% Similarity=0.723 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCceeecCCCceecCcccc
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
++.||+||.. + ..+..+|..||.
T Consensus 2 ~~~Cp~Cg~~-~----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAE-I----DPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCc-C----CcccccChhhCC
Confidence 4589999984 2 357889999997
No 38
>PLN00209 ribosomal protein S27; Provisional
Probab=94.27 E-value=0.025 Score=47.73 Aligned_cols=31 Identities=26% Similarity=0.487 Sum_probs=28.8
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
++||.|+...+++.+++-.+.|..||++|-+
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 4799999999999999999999999999964
No 39
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=94.16 E-value=0.028 Score=47.32 Aligned_cols=31 Identities=23% Similarity=0.473 Sum_probs=28.8
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
+.||.|+...+++.+++-.+.|..||++|-+
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 4799999999999999999999999999964
No 40
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=93.99 E-value=0.028 Score=36.03 Aligned_cols=22 Identities=27% Similarity=0.889 Sum_probs=17.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
+||+||... ..+..+|..||+-
T Consensus 1 ~Cp~CG~~~-----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEI-----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCC-----CCcCcchhhhCCc
Confidence 599999873 2577899999974
No 41
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=93.80 E-value=0.037 Score=43.04 Aligned_cols=31 Identities=29% Similarity=0.632 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCceeecCCC-ceecCcccceec
Q 008401 1 MVWCSSCARHVTGHRPYDS-QLCCDRCGKVLE 31 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G-~~VC~~CG~Vle 31 (567)
|..||.||...-+.|...| .+.|..||.-++
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 3589999998444444445 567999999887
No 42
>PHA00626 hypothetical protein
Probab=93.63 E-value=0.052 Score=42.12 Aligned_cols=30 Identities=17% Similarity=0.465 Sum_probs=22.6
Q ss_pred CCCCCCCCCCceee----cCCCceecCcccceec
Q 008401 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVLE 31 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D----~~~G~~VC~~CG~Vle 31 (567)
+.||.||+.+++-. --...++|.+||.-..
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 46999999766542 2368999999998644
No 43
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=93.48 E-value=1.5 Score=45.98 Aligned_cols=171 Identities=13% Similarity=0.067 Sum_probs=109.7
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhcc-ccCCCchhHHHHHHHHHHHHHhCC-CccHHHHHhhhc--cChHH
Q 008401 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARN-FTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYE 149 (567)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~-~~rGR~~~~vaAACLYiACR~e~~-p~tL~Diad~~~--v~v~~ 149 (567)
.++.+-++|.-..|. ....--|..||.+.+.-. -+..-....+--+|||||.+.+.+ |--++|||-++. ++..+
T Consensus 148 LlDWlmEVCEvykLH--RETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~dd 225 (408)
T KOG0655|consen 148 LLDWLMEVCEVYKLH--RETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDD 225 (408)
T ss_pred HHHHHHHHHHHHHHh--hhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHH
Confidence 358888999999999 888889999998865422 112223455666999999998765 888999999875 78999
Q ss_pred HHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHH------HHHHHHHHHHhh---hccccCCCChhHHH
Q 008401 150 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKV------CDTARDILASMK---RDWITTGRKPSGLC 220 (567)
Q Consensus 150 Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V------~~~A~~iv~~~~---~~~i~~GR~P~~Ia 220 (567)
|...-+-|++.|+..+.| +....++.-|..-+.+...++| ...=+.|++.+. -+--.---.-..||
T Consensus 226 IltmE~iilkal~W~l~P-----iTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaqlLDlc~ldids~~fsYrila 300 (408)
T KOG0655|consen 226 ILTMELIILKALKWELSP-----ITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQLLDLCILDIDSLEFSYRILA 300 (408)
T ss_pred HHHHHHHHHHHhcccccc-----eehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHHHHHHHHhccccccchHHHHH
Confidence 999999999999988766 4444555555554432112111 112222222221 11111124556677
Q ss_pred HHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 221 GAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 221 aAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
|||||.- + +..-+-+++|.--..|.+..+=+
T Consensus 301 AAal~h~-----~--s~e~v~kaSG~~w~~ie~cv~wm 331 (408)
T KOG0655|consen 301 AAALCHF-----T--SIEVVKKASGLEWDSIEECVDWM 331 (408)
T ss_pred HHHHHHH-----h--HHHHHHHcccccHHHHHHHHHHH
Confidence 7777732 2 22223356688888888877654
No 44
>PRK00420 hypothetical protein; Validated
Probab=93.48 E-value=0.052 Score=48.54 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=22.0
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.||.||...+- ..+|..+|..||.++.
T Consensus 25 ~CP~Cg~pLf~--lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPLFE--LKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCccee--cCCCceECCCCCCeee
Confidence 69999976433 2689999999999865
No 45
>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=93.26 E-value=0.051 Score=38.47 Aligned_cols=31 Identities=19% Similarity=0.574 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCceeecCCCceecCcccceec
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
|..||.||.-.+......+..+|..||.+.+
T Consensus 1 m~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGNLLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp --BETTTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred CeeCCCCCccceEcCCCccCcCCCCCCCccC
Confidence 6789999986444444445558999999854
No 46
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=93.26 E-value=0.064 Score=37.49 Aligned_cols=27 Identities=26% Similarity=0.465 Sum_probs=22.5
Q ss_pred CCCCCCCCCceeecCCCceecCccccee
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.|+.||+..++. ..++..||..||.+-
T Consensus 5 ~C~~C~~~~i~~-~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 5 KCSKCGGNGIVN-KEDDYEVCIFCGSSF 31 (33)
T ss_pred EcCCCCCCeEEE-ecCCeEEcccCCcEe
Confidence 699999986543 568999999999874
No 47
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=93.01 E-value=0.041 Score=38.71 Aligned_cols=28 Identities=21% Similarity=0.582 Sum_probs=15.4
Q ss_pred CCCCCCCCCc--ee-ecCCCceecCccccee
Q 008401 3 WCSSCARHVT--GH-RPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~i--v~-D~~~G~~VC~~CG~Vl 30 (567)
.||.||+... +. ....--.||+.||.|-
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 6999999832 12 1234578999999984
No 48
>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=92.86 E-value=0.054 Score=38.65 Aligned_cols=30 Identities=20% Similarity=0.575 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceee----cCCCceecCcccceec
Q 008401 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVLE 31 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D----~~~G~~VC~~CG~Vle 31 (567)
..||+|+...-+.+ ...+.+.|..||.++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 47999998632222 1345799999999875
No 49
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=92.61 E-value=0.45 Score=49.97 Aligned_cols=68 Identities=13% Similarity=0.087 Sum_probs=54.6
Q ss_pred hhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHh
Q 008401 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV 244 (567)
Q Consensus 177 ~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv 244 (567)
.+|..+|..|....+..|+-+|.-+.+|.--.+-..--.|.-|+++||||||..-.+.+++.+++..+
T Consensus 61 ~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~ 128 (305)
T TIGR00569 61 KRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNL 128 (305)
T ss_pred HHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhc
Confidence 46677788887113889999999999887544444568999999999999999999999998888654
No 50
>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=92.32 E-value=0.47 Score=42.16 Aligned_cols=67 Identities=15% Similarity=0.105 Sum_probs=50.4
Q ss_pred hhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCC-CCCHhhHHHHh
Q 008401 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIV 244 (567)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~-~~t~~eIa~vv 244 (567)
..||...+..+++ ++.+...|..+++++..........+.-|++||+++|+.+.+. ..+..+++...
T Consensus 35 ~~~i~~~~~~~~l--~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~ 102 (127)
T PF00134_consen 35 IDWIIELCQRLKL--SPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRIS 102 (127)
T ss_dssp HHHHHHHHHHTT---BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHT
T ss_pred HHHHHHHHHhccc--chhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHH
Confidence 3467777787775 8999999999999987666677899999999999999998876 23444544433
No 51
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=92.00 E-value=0.092 Score=48.05 Aligned_cols=23 Identities=26% Similarity=0.739 Sum_probs=19.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
.||.||...+- .+|.++|..||+
T Consensus 30 hCp~Cg~PLF~---KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPLFR---KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCccee---eCCeEECCCCCc
Confidence 69999998654 689999999993
No 52
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=91.98 E-value=0.12 Score=35.31 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=15.0
Q ss_pred CCCCCCCCCCCceeecCCCceecCccccee
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
+..||.|++...-.| ...+||..||.-.
T Consensus 2 ~p~Cp~C~se~~y~D--~~~~vCp~C~~ew 29 (30)
T PF08274_consen 2 LPKCPLCGSEYTYED--GELLVCPECGHEW 29 (30)
T ss_dssp S---TTT-----EE---SSSEEETTTTEEE
T ss_pred CCCCCCCCCcceecc--CCEEeCCcccccC
Confidence 357999999855443 6799999999743
No 53
>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=91.34 E-value=0.16 Score=41.20 Aligned_cols=17 Identities=24% Similarity=0.638 Sum_probs=14.9
Q ss_pred eecCCCceecCccccee
Q 008401 14 HRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 14 ~D~~~G~~VC~~CG~Vl 30 (567)
++..+|.++|.+||++.
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 56789999999999974
No 54
>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=90.89 E-value=0.44 Score=35.04 Aligned_cols=32 Identities=16% Similarity=0.255 Sum_probs=24.7
Q ss_pred HHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 227 SALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 227 Aa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
.....+-+.|..+||+.+|+|+.|+.+|++.+
T Consensus 10 ~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 10 RLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 33445678899999999999999999999876
No 55
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=90.63 E-value=2.2 Score=34.23 Aligned_cols=75 Identities=16% Similarity=0.207 Sum_probs=50.5
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccC
Q 008401 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITT 212 (567)
Q Consensus 133 p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~ 212 (567)
|.++.+||..++++...|.+.|+.. .+ ..|..|+... +
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~---~~----------~s~~~~~~~~-----------------r------------ 38 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKE---TG----------TTPKQYLRDR-----------------R------------ 38 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH---hC----------cCHHHHHHHH-----------------H------------
Confidence 5688999999999988887776644 22 2233332210 0
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhcc-CHHHHHHHHHHHH
Q 008401 213 GRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRLIEFE 259 (567)
Q Consensus 213 GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~V-se~TIrkR~kE~~ 259 (567)
+.-|.-||.. .+.++.+||..+|+ +..++.+.++...
T Consensus 39 ------~~~a~~~l~~----~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 39 ------LERARRLLRD----TDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred ------HHHHHHHHHc----CCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 1223334322 28999999999999 9999999998775
No 56
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=90.46 E-value=0.2 Score=42.55 Aligned_cols=29 Identities=28% Similarity=0.571 Sum_probs=25.5
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
.||.||+. .+.....|-..|..||.+..-
T Consensus 37 ~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 37 VCPFCGRT-TVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCCCCCc-ceeeeccCeEEcCCCCCeecc
Confidence 59999998 677889999999999998653
No 57
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.42 E-value=0.19 Score=38.52 Aligned_cols=26 Identities=19% Similarity=0.539 Sum_probs=20.8
Q ss_pred CCCCCCCCCceeecCCCceecCccccee
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.||.||+. +..++ .+...|..||...
T Consensus 22 fCP~Cg~~-~m~~~-~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMAEH-LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hhecc-CCcEECCCcCCEE
Confidence 69999997 54544 5899999999863
No 58
>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=89.41 E-value=5 Score=37.50 Aligned_cols=89 Identities=11% Similarity=0.091 Sum_probs=66.9
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHh---cc--ccCCCchhHHHHHHHHHHHHH-hCCCccHHHHHhhhccCh
Q 008401 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA---RN--FTKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNINV 147 (567)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~---~~--~~rGR~~~~vaAACLYiACR~-e~~p~tL~Diad~~~v~v 147 (567)
...+|.++....+++ ..+.-.|..|..+... .. .+.......+..+||-+|.+- .....+.+.+|.+.|+++
T Consensus 54 i~~fl~ri~~~~~~s--~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~ 131 (149)
T PF08613_consen 54 IRDFLSRILKYTQCS--PECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISL 131 (149)
T ss_dssp HHHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-H
T ss_pred HHHHHHHHHHHcCCC--hHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCH
Confidence 457888899999999 8999999988888777 22 234456677999999999996 688899999999999999
Q ss_pred HHHHHHHHHHHHHhhcc
Q 008401 148 YELGAVYLQLCQVLYIA 164 (567)
Q Consensus 148 ~~Lgr~~~~L~~~L~i~ 164 (567)
.+|.+.-..++..|+.+
T Consensus 132 ~eln~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 132 KELNELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHCCCc
Confidence 99999999999888754
No 59
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=89.33 E-value=22 Score=37.64 Aligned_cols=26 Identities=8% Similarity=0.107 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.++||...||+..||++++..-
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rA 306 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEA 306 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999997654
No 60
>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=89.10 E-value=0.29 Score=35.15 Aligned_cols=27 Identities=19% Similarity=0.377 Sum_probs=20.2
Q ss_pred CCCCCCCCCC-ceeec--CCCceecCcccc
Q 008401 2 VWCSSCARHV-TGHRP--YDSQLCCDRCGK 28 (567)
Q Consensus 2 ~~Cp~Cgs~~-iv~D~--~~G~~VC~~CG~ 28 (567)
..||.||+.. +-+|. ..|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 3699999973 33443 459999999985
No 61
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.05 E-value=0.28 Score=37.18 Aligned_cols=30 Identities=17% Similarity=0.561 Sum_probs=20.7
Q ss_pred CCCCCCCCCceeecCC-CceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYD-SQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~-G~~VC~~CG~Vlee 32 (567)
.||.||.-....+... ..++|..||.+...
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 5999998643332222 38999999987553
No 62
>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=88.87 E-value=27 Score=34.93 Aligned_cols=26 Identities=4% Similarity=-0.019 Sum_probs=22.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|+++||...|||..+|++++..-
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~a 220 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKA 220 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999886543
No 63
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=88.86 E-value=0.37 Score=37.96 Aligned_cols=27 Identities=22% Similarity=0.429 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeecCCC-------ceecCcccc
Q 008401 2 VWCSSCARHVTGHRPYDS-------QLCCDRCGK 28 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G-------~~VC~~CG~ 28 (567)
..||.||+..+.++...+ .+.|.+||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 469999888776655443 356999999
No 64
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.83 E-value=0.32 Score=36.34 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=21.2
Q ss_pred CCCCCCCCCceeecCCCceecCccccee
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.|++||.. +.+|+..+...|..||.-+
T Consensus 5 ~C~~CG~~-~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGRE-VELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCE-EEECCCCCceECCCCCCeE
Confidence 69999986 4566666689999999743
No 65
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=88.62 E-value=1.3 Score=47.27 Aligned_cols=91 Identities=18% Similarity=0.234 Sum_probs=65.5
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCC----ccHHH-HHhhhccChH
Q 008401 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKP----FLLID-FSNYLNINVY 148 (567)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p----~tL~D-iad~~~v~v~ 148 (567)
..++|++++..-+|. ...+.+|..||.+..=+|++...+...+|+|||.+|.+.+... .+|+| .-+.+..+..
T Consensus 385 lKREMr~l~~d~~id--~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrr 462 (497)
T KOG4164|consen 385 LKREMRELGEDCGID--VVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRR 462 (497)
T ss_pred HHHHHHHhhhccCcc--ceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHH
Confidence 457888888888888 7899999999999888888877778889999999999987543 22333 3345666666
Q ss_pred HHHHHHHHHHHHhhcccc
Q 008401 149 ELGAVYLQLCQVLYIADE 166 (567)
Q Consensus 149 ~Lgr~~~~L~~~L~i~~~ 166 (567)
+|-.--.-++-.|.+.++
T Consensus 463 dLia~Ef~VlvaLefaL~ 480 (497)
T KOG4164|consen 463 DLIAFEFPVLVALEFALH 480 (497)
T ss_pred hhhhhhhhHHHhhhhhcc
Confidence 665544445555554433
No 66
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=88.46 E-value=0.31 Score=46.14 Aligned_cols=29 Identities=24% Similarity=0.450 Sum_probs=20.0
Q ss_pred CCCCCCCCCC-ceeecC---CCc-----eecCccccee
Q 008401 2 VWCSSCARHV-TGHRPY---DSQ-----LCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~-iv~D~~---~G~-----~VC~~CG~Vl 30 (567)
++||+||+.. .+.|.. .|. .-|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5799999975 455532 454 4499999853
No 67
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.21 E-value=0.26 Score=35.20 Aligned_cols=28 Identities=21% Similarity=0.609 Sum_probs=20.8
Q ss_pred CCCCCCCCCceee----cCCCceecCccccee
Q 008401 3 WCSSCARHVTGHR----PYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D----~~~G~~VC~~CG~Vl 30 (567)
.||+|+..--+.| ...+.+-|+.||.|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 6999998732222 346789999999885
No 68
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=87.99 E-value=0.78 Score=48.47 Aligned_cols=82 Identities=17% Similarity=0.142 Sum_probs=60.4
Q ss_pred hhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhc----cCHHHH
Q 008401 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH----ICEATL 251 (567)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~----Vse~TI 251 (567)
..||...+.+|+. +..-+.+|.-+.++.--..-+..-.|..||++|||||+...+..+..++|..+.. ..+.+.
T Consensus 43 ~~fI~elg~~L~~--~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~ 120 (323)
T KOG0834|consen 43 AKFIQELGVRLKM--PQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLEL 120 (323)
T ss_pred HHHHHHHHHHcCC--CccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccH
Confidence 3577777788863 3444667777777765555567788899999999999999999999999998763 222356
Q ss_pred HHHHHHHH
Q 008401 252 MKRLIEFE 259 (567)
Q Consensus 252 rkR~kE~~ 259 (567)
..+|-+++
T Consensus 121 ~~~~~~~~ 128 (323)
T KOG0834|consen 121 EEVYWELK 128 (323)
T ss_pred HHHHHHHH
Confidence 66666665
No 69
>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=87.65 E-value=0.17 Score=54.29 Aligned_cols=86 Identities=13% Similarity=0.092 Sum_probs=0.0
Q ss_pred HHHHHhCCCCchHHHHHHHHHHHHHH-hccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHH
Q 008401 80 QMKNALNIGESDEIVHVAKRFYGIAV-ARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 158 (567)
Q Consensus 80 ~ia~~L~Lp~~~~i~e~A~~iyk~a~-~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~ 158 (567)
.|+-.++++.+..++..|..||++.. ....+++..-.+-+.+|+||||...+.++-+..+....+++.+...+.|..|.
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 34444544423899999999999988 45566777777788899999999999999888888888999888888888777
Q ss_pred HHhhccc
Q 008401 159 QVLYIAD 165 (567)
Q Consensus 159 ~~L~i~~ 165 (567)
+.|+...
T Consensus 83 ~~L~~~s 89 (353)
T PF05460_consen 83 NLLGNSS 89 (353)
T ss_dssp -------
T ss_pred HHHhCCC
Confidence 7776543
No 70
>PRK11827 hypothetical protein; Provisional
Probab=87.17 E-value=0.48 Score=37.71 Aligned_cols=27 Identities=15% Similarity=0.252 Sum_probs=22.5
Q ss_pred CCCCCCCCCceeecCCCceecCccccee
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.||.|++. +.+|.....+||..||.+.
T Consensus 10 aCP~ckg~-L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 10 ACPVCNGK-LWYNQEKQELICKLDNLAF 36 (60)
T ss_pred ECCCCCCc-CeEcCCCCeEECCccCeec
Confidence 69999886 5577667889999999874
No 71
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=86.65 E-value=49 Score=35.64 Aligned_cols=92 Identities=9% Similarity=0.029 Sum_probs=55.1
Q ss_pred chHHHHHHHHHHHHHHHHHHhC---CCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHH------------
Q 008401 65 ASRERLMEKAFDDMRQMKNALN---IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ------------ 129 (567)
Q Consensus 65 ~srer~l~~a~~~I~~ia~~L~---Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~------------ 129 (567)
..+++.+..-...+..+|.++. +.-.+-+.+.-..+++.+..-...+|-+..+.|.-.|+-+-+.
T Consensus 129 ~A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip 208 (367)
T PRK09210 129 EAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIP 208 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceecc
Confidence 3344444455566777777662 2211334444455666655545557878888777777755311
Q ss_pred --------------------hCCCccHHHHHhhhccChHHHHHHHHH
Q 008401 130 --------------------KSKPFLLIDFSNYLNINVYELGAVYLQ 156 (567)
Q Consensus 130 --------------------e~~p~tL~Diad~~~v~v~~Lgr~~~~ 156 (567)
.|.+-|..+||..+++++..+......
T Consensus 209 ~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~ 255 (367)
T PRK09210 209 VHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI 255 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 233446778888999998888776543
No 72
>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=86.45 E-value=1.3 Score=32.94 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=24.5
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
+-..|+++||+.+|+|..|++++++++.+
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 55699999999999999999999999864
No 73
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=86.04 E-value=0.41 Score=42.63 Aligned_cols=29 Identities=21% Similarity=0.527 Sum_probs=23.8
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (567)
.||+||.. .||-...-+||..||++....
T Consensus 11 ~Cp~CG~k--FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAK--FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcch--hccCCCCCccCCCCCCccCcc
Confidence 69999997 366666788999999998755
No 74
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=85.92 E-value=2.7 Score=33.68 Aligned_cols=71 Identities=7% Similarity=0.130 Sum_probs=45.2
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhcc-ChHHHHHHHHH
Q 008401 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 156 (567)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v-~v~~Lgr~~~~ 156 (567)
|..+|..+|++ ...... +|+......+..-.....+.-|+-|+.- .+.++.|||..+|+ +...+.+.|++
T Consensus 4 ~~~la~~~~~s--~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~~----~~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 4 LEDLAEALGMS--PRHLQR---LFKKETGTTPKQYLRDRRLERARRLLRD----TDLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHhCCC--HHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHc----CCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 67899999999 554433 3443332222111122234445555532 28999999999999 99999998876
Q ss_pred H
Q 008401 157 L 157 (567)
Q Consensus 157 L 157 (567)
.
T Consensus 75 ~ 75 (84)
T smart00342 75 L 75 (84)
T ss_pred H
Confidence 6
No 75
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=85.78 E-value=0.37 Score=39.98 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=27.0
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceec
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
++||.|-....++.++...+||.+|++|+=
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~il~ 64 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCSTILC 64 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCceEEE
Confidence 479999888889999999999999999974
No 76
>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=85.67 E-value=0.61 Score=35.96 Aligned_cols=31 Identities=19% Similarity=0.340 Sum_probs=21.3
Q ss_pred CCCCCCCCCCc-ee---ec--CCCceecCcccceecc
Q 008401 2 VWCSSCARHVT-GH---RP--YDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~i-v~---D~--~~G~~VC~~CG~Vlee 32 (567)
..||.||+... +. +. ..|...|..||.....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 46999999855 22 22 2355579999998653
No 77
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=85.59 E-value=0.56 Score=37.16 Aligned_cols=28 Identities=21% Similarity=0.442 Sum_probs=24.8
Q ss_pred CCCCCCCCCCceeecCCCceecCccccee
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
..||.|.+. +.+|.+.+.+||..||...
T Consensus 9 LaCP~~kg~-L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 9 LACPVCKGP-LVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeccCcCCc-ceEeccCCEEEecccCcee
Confidence 479999988 7888899999999999974
No 78
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=85.59 E-value=0.48 Score=31.34 Aligned_cols=24 Identities=33% Similarity=0.731 Sum_probs=18.6
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.||.|+... ......|..||.+..
T Consensus 2 ~CP~C~~~V-----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV-----PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc-----hhhcCcCCCCCCCCc
Confidence 699999873 246679999998753
No 79
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=85.45 E-value=0.5 Score=35.90 Aligned_cols=26 Identities=27% Similarity=0.701 Sum_probs=21.6
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
.||.||...+--|+.+ -+.|..||..
T Consensus 21 ~CPrCG~gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGPGVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred cCCCCCCcchhhhcCc-eeEeccccce
Confidence 5999998777777654 8999999986
No 80
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=84.72 E-value=2.3 Score=44.29 Aligned_cols=70 Identities=14% Similarity=0.191 Sum_probs=61.6
Q ss_pred hhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhc
Q 008401 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH 245 (567)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~ 245 (567)
...+-.|++++.-.++..|+.+|.....|+--.|-.+--.|..|.++|+|+|+....+.+|..++++-.+
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 4566678888865568999999999999988888889999999999999999999999999999987655
No 81
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=84.18 E-value=0.56 Score=40.86 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=22.9
Q ss_pred CCCCCCCCCce---eec--CCCceecCcccceec
Q 008401 3 WCSSCARHVTG---HRP--YDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv---~D~--~~G~~VC~~CG~Vle 31 (567)
.||.||+..++ ++- .-|.++|.+||.-.+
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 59999998665 553 468999999998654
No 82
>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=83.84 E-value=0.89 Score=33.41 Aligned_cols=23 Identities=30% Similarity=0.781 Sum_probs=18.1
Q ss_pred CCCCCCCCCceeecCCCceecCccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCG 27 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG 27 (567)
.||.||.. .....+|..+|..||
T Consensus 19 ~Cp~C~~P--L~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTP--LMRDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCe--eEEecCCCEECCCCC
Confidence 69999754 334568999999997
No 83
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=83.69 E-value=1.6 Score=41.44 Aligned_cols=38 Identities=16% Similarity=0.259 Sum_probs=32.1
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCC
Q 008401 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (567)
Q Consensus 226 lAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s 263 (567)
|.+...+-+.|..+||+.+|+|++|+++|++.+.+..-
T Consensus 20 L~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 20 LNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 44555678899999999999999999999999976554
No 84
>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=83.27 E-value=0.82 Score=36.83 Aligned_cols=29 Identities=21% Similarity=0.566 Sum_probs=21.1
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
.||.||..... .......+|..||.+.+-
T Consensus 30 ~C~~CG~~~~~-~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 30 TCPRCGHRNKK-RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccccccc-ccccceEEcCCCCCEECc
Confidence 59999887433 345678899999988653
No 85
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=82.89 E-value=0.98 Score=37.32 Aligned_cols=30 Identities=17% Similarity=0.517 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCceeecC-------CCceecC--ccccee
Q 008401 1 MVWCSSCARHVTGHRPY-------DSQLCCD--RCGKVL 30 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~-------~G~~VC~--~CG~Vl 30 (567)
|+.||.||....+.+.. +-...|+ +||...
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATF 39 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEE
Confidence 89999999997666532 3456799 899754
No 86
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=82.55 E-value=0.84 Score=40.03 Aligned_cols=30 Identities=20% Similarity=0.426 Sum_probs=22.7
Q ss_pred CCCCCCCCCc--eeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVT--GHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~i--v~D~~~G~~VC~~CG~Vlee 32 (567)
.||+||...+ ..|...+.++|..||+.-+-
T Consensus 23 ~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 23 ECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred ECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 6999996532 34556789999999998654
No 87
>PF13730 HTH_36: Helix-turn-helix domain
Probab=82.32 E-value=2.8 Score=31.92 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=23.6
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 236 SKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
|++.|++.+|++..||++.++++.+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999964
No 88
>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=82.14 E-value=0.8 Score=41.71 Aligned_cols=29 Identities=7% Similarity=0.033 Sum_probs=23.3
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (567)
.||+||.. .||-..--+||..||.+....
T Consensus 11 ~Cp~cg~k--FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSK--FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCcc--ccccCCCCccCCCcCCccCcc
Confidence 69999987 366667888999999987654
No 89
>COG4640 Predicted membrane protein [Function unknown]
Probab=82.03 E-value=0.72 Score=49.31 Aligned_cols=26 Identities=23% Similarity=0.804 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCceeecCCCceecCcccceec
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
|..||.||+.. .+|+.-|+.||.-+.
T Consensus 1 M~fC~kcG~qk-----~Ed~~qC~qCG~~~t 26 (465)
T COG4640 1 MKFCPKCGSQK-----AEDDVQCTQCGHKFT 26 (465)
T ss_pred CCccccccccc-----ccccccccccCCcCC
Confidence 88999999863 356667999998544
No 90
>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=82.03 E-value=1.2 Score=30.70 Aligned_cols=27 Identities=22% Similarity=0.560 Sum_probs=15.4
Q ss_pred CCCCCCCCCceeecCCCceecCccccee
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.|+.||+... .....-..+|..||...
T Consensus 5 fC~~CG~~t~-~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 5 FCGRCGAPTK-PAPGGWARRCPSCGHEH 31 (32)
T ss_dssp B-TTT--BEE-E-SSSS-EEESSSS-EE
T ss_pred ccCcCCcccc-CCCCcCEeECCCCcCEe
Confidence 6999999743 33445689999999863
No 91
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=81.38 E-value=3.1 Score=32.32 Aligned_cols=34 Identities=15% Similarity=0.247 Sum_probs=26.9
Q ss_pred HHHHHhcCC-----CCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 225 YVSALTHGL-----KFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 225 ylAa~~~g~-----~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
+.+|.-.|+ ++|..|||+.+|||.+|+..+++.-
T Consensus 9 L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 9 LKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred HHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 344445554 4789999999999999999999754
No 92
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=81.14 E-value=1 Score=32.82 Aligned_cols=27 Identities=22% Similarity=0.604 Sum_probs=19.7
Q ss_pred CCCCCCCCCceee---------cCCCceecCcccce
Q 008401 3 WCSSCARHVTGHR---------PYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D---------~~~G~~VC~~CG~V 29 (567)
.||.||....++= +.+-.++|.+||..
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 6999999865431 22458999999964
No 93
>PRK12495 hypothetical protein; Provisional
Probab=81.10 E-value=0.98 Score=44.83 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=22.9
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
.|+.||...+ ...|..+|..|+.++.+
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 6999999865 33799999999999865
No 94
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=81.04 E-value=1 Score=40.51 Aligned_cols=33 Identities=24% Similarity=0.579 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCce-eecCCCceecCcccceeccc
Q 008401 1 MVWCSSCARHVTG-HRPYDSQLCCDRCGKVLEDH 33 (567)
Q Consensus 1 M~~Cp~Cgs~~iv-~D~~~G~~VC~~CG~Vlee~ 33 (567)
|..||.||+-.+. .|...+.++|..||...+-+
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 6789999986432 34457799999999987655
No 95
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=80.96 E-value=2.1 Score=31.58 Aligned_cols=30 Identities=17% Similarity=0.079 Sum_probs=20.6
Q ss_pred HHHhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 008401 227 SALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 227 Aa~~~g~~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
...++....|+++||+.+|++.+||.+-++
T Consensus 13 I~~l~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 13 IEALLEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHHHCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 345567789999999999999999998765
No 96
>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=80.92 E-value=0.43 Score=34.02 Aligned_cols=28 Identities=32% Similarity=0.695 Sum_probs=20.6
Q ss_pred CCCCCCCC-CceeecCCCceecCccccee
Q 008401 3 WCSSCARH-VTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~-~iv~D~~~G~~VC~~CG~Vl 30 (567)
.|+.||.. ++.+++-.-..+|..||.-|
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCee
Confidence 59999987 67777666666999999754
No 97
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=80.42 E-value=37 Score=29.29 Aligned_cols=39 Identities=8% Similarity=0.135 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHH
Q 008401 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (567)
Q Consensus 118 vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L 157 (567)
+..++-|+... ...|.++.++|+.++++...|.+.|++.
T Consensus 7 ~~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34455555554 3457999999999999999999888865
No 98
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=80.40 E-value=2.3 Score=39.78 Aligned_cols=38 Identities=13% Similarity=0.228 Sum_probs=32.0
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCC
Q 008401 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (567)
Q Consensus 226 lAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s 263 (567)
|.+...+-+.|..+||+.+|+|+.|+++|++.+.+...
T Consensus 15 l~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 15 LEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 44455678899999999999999999999999976554
No 99
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=80.35 E-value=1.5 Score=32.69 Aligned_cols=26 Identities=19% Similarity=0.450 Sum_probs=19.4
Q ss_pred CCCCCCCCCceeecCCCceecCcccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
.||+||+.....-...+..-|..|+.
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 69999998443333468999999984
No 100
>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=79.98 E-value=1.4 Score=32.15 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=15.2
Q ss_pred CCCCCCCCC-c-eeec--CCCceecCcccce
Q 008401 3 WCSSCARHV-T-GHRP--YDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~-i-v~D~--~~G~~VC~~CG~V 29 (567)
.||.||++. + +++. .+|..+|..||.+
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~ 35 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQCGGD 35 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred CCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence 599999984 2 2442 3599999999434
No 101
>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=79.44 E-value=3.4 Score=31.40 Aligned_cols=30 Identities=7% Similarity=0.208 Sum_probs=25.5
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
++..+|..++|..++||..||++-++++.+
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344599999999999999999999999864
No 102
>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=79.39 E-value=7.3 Score=36.08 Aligned_cols=64 Identities=16% Similarity=0.134 Sum_probs=46.8
Q ss_pred hHHHHHhhhCCCCCHHHHHHHHHHHHHhh--hccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHH
Q 008401 178 FLHKFTDRLLPGGNKKVCDTARDILASMK--RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKI 243 (567)
Q Consensus 178 ~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~--~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~v 243 (567)
=|..+|++|++ +.++....+.+++.+. ...+..+|+---|.-.|||..|++++..+|.++|...
T Consensus 17 Rl~~LC~~L~l--~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~ 82 (135)
T PF01857_consen 17 RLQDLCERLDL--SSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKA 82 (135)
T ss_dssp HHHHHHHHHTT--STTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHH
T ss_pred HHHHHHHHcCC--cHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHH
Confidence 35567888874 4556666777777654 4678899999999999999999999988888887764
No 103
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=79.38 E-value=1.1 Score=31.92 Aligned_cols=28 Identities=25% Similarity=0.718 Sum_probs=19.8
Q ss_pred CCCCCCCCCceee----cCCCceecCccccee
Q 008401 3 WCSSCARHVTGHR----PYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D----~~~G~~VC~~CG~Vl 30 (567)
.||+|+..--+.| .....+-|+.||.+.
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 6999998732223 234578899999874
No 104
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=79.36 E-value=11 Score=36.88 Aligned_cols=115 Identities=14% Similarity=0.146 Sum_probs=66.5
Q ss_pred hhHHHHHHHHHHHHHhCCC-ccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHH
Q 008401 115 TEQVQASCLYLACRQKSKP-FLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 193 (567)
Q Consensus 115 ~~~vaAACLYiACR~e~~p-~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~ 193 (567)
...++=|+||+ .|-| +++.+|+.+++++...+..+...|.+...-...+. -|..+.+...+...++
T Consensus 5 ~~~~iEA~LF~----sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi---------~i~~~~~~y~l~tk~e 71 (188)
T PRK00135 5 YKSIIEALLFV----SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGL---------KLIEFNDVYKLVTKEE 71 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCE---------EEEEECCEEEEEEcHH
Confidence 45567788887 5777 99999999999999889888888888775322110 0111111111101222
Q ss_pred HHHHHHHHHHHhhhccccCCCChhHHHHHHH-HHHHHhcCCCCCHhhHHHHhccCHHHH
Q 008401 194 VCDTARDILASMKRDWITTGRKPSGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATL 251 (567)
Q Consensus 194 V~~~A~~iv~~~~~~~i~~GR~P~~IaaAal-ylAa~~~g~~~t~~eIa~vv~Vse~TI 251 (567)
......+++ ...+|.-+--|++ -||...++.++|..+|+++.||+..-+
T Consensus 72 ~~~~v~~~~---------~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~~~i 121 (188)
T PRK00135 72 NADYLQKLV---------KTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNSDGA 121 (188)
T ss_pred HHHHHHHHh---------cccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHH
Confidence 222221111 1122222333333 244445678999999999999996333
No 105
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=79.23 E-value=6.9 Score=29.33 Aligned_cols=26 Identities=12% Similarity=0.105 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|+++||+..|||..||++.++.+
T Consensus 26 ~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 26 ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 33899999999999999999998865
No 106
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=79.12 E-value=1.1 Score=35.47 Aligned_cols=8 Identities=38% Similarity=1.231 Sum_probs=3.8
Q ss_pred ceecCccc
Q 008401 20 QLCCDRCG 27 (567)
Q Consensus 20 ~~VC~~CG 27 (567)
...|.+||
T Consensus 27 ~F~CPnCG 34 (61)
T COG2888 27 KFPCPNCG 34 (61)
T ss_pred EeeCCCCC
Confidence 33455555
No 107
>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=79.09 E-value=1.6 Score=40.88 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=21.2
Q ss_pred CCCCCCCCCC-ceeec---CCCcee-----cCcccce
Q 008401 2 VWCSSCARHV-TGHRP---YDSQLC-----CDRCGKV 29 (567)
Q Consensus 2 ~~Cp~Cgs~~-iv~D~---~~G~~V-----C~~CG~V 29 (567)
|.||.||... -|+|. .+|..| |..||.=
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~R 37 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHER 37 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCc
Confidence 5799999973 46775 467666 9999974
No 108
>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=78.78 E-value=1.1 Score=38.65 Aligned_cols=32 Identities=22% Similarity=0.540 Sum_probs=25.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (567)
.||.||... +.....|-..|..||.++.....
T Consensus 37 ~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~AGGAy 68 (90)
T PF01780_consen 37 TCPFCGKTS-VKRVATGIWKCKKCGKKFAGGAY 68 (90)
T ss_dssp EESSSSSSE-EEEEETTEEEETTTTEEEE-BSS
T ss_pred cCCCCCCce-eEEeeeEEeecCCCCCEEeCCCc
Confidence 599999986 56678999999999998875443
No 109
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=78.59 E-value=1.1 Score=51.73 Aligned_cols=25 Identities=28% Similarity=0.798 Sum_probs=14.7
Q ss_pred CCCCCCCCCCCceeecCCCceecCccccee
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
|..||.||..+. .|.-+|..||.-+
T Consensus 1 M~~Cp~Cg~~n~-----~~akFC~~CG~~l 25 (645)
T PRK14559 1 MLICPQCQFENP-----NNNRFCQKCGTSL 25 (645)
T ss_pred CCcCCCCCCcCC-----CCCccccccCCCC
Confidence 777888877532 3444555555554
No 110
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=78.46 E-value=1.6 Score=35.07 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=21.5
Q ss_pred CCCCCCCCCceeecCCC--ceecCccccee
Q 008401 3 WCSSCARHVTGHRPYDS--QLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G--~~VC~~CG~Vl 30 (567)
.||.||...+.+-...| ..+|..||...
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcCc
Confidence 59999999665555455 47999999963
No 111
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.12 E-value=0.64 Score=45.05 Aligned_cols=30 Identities=27% Similarity=0.741 Sum_probs=23.8
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
.||.|+..-...|.-+....|..||.+|.+
T Consensus 119 ~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 599999874445555678999999999986
No 112
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=78.04 E-value=5.4 Score=46.77 Aligned_cols=84 Identities=12% Similarity=0.207 Sum_probs=67.7
Q ss_pred HHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhc--cccCCCchhHHHHHHHHHHHHHhCCCccHHHHHhhhccChH
Q 008401 71 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVY 148 (567)
Q Consensus 71 l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~--~~~rGR~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~ 148 (567)
..-|..+|+.+|.+|.|. +.+.+.-..+|.-.... .+++-|...++.-+|+|+.||..+...++.+|-...+--+.
T Consensus 677 Y~LAavRL~~Lc~rL~l~--~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPq 754 (920)
T KOG1010|consen 677 YHLAAVRLNDLCERLSLS--DELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQ 754 (920)
T ss_pred HHHHHHHHHHHHHHhhhh--hHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCch
Confidence 345778999999999999 88888888888765543 57789999999999999999999999999999877655444
Q ss_pred HHHHHHHH
Q 008401 149 ELGAVYLQ 156 (567)
Q Consensus 149 ~Lgr~~~~ 156 (567)
....+|+.
T Consensus 755 a~~~vyRs 762 (920)
T KOG1010|consen 755 AVSLVYRS 762 (920)
T ss_pred hhhhhhhh
Confidence 44445544
No 113
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=77.44 E-value=3.2 Score=30.89 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=19.2
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
..|.++||+.+|||..||.+-++.|.+..
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 78999999999999999999988886543
No 114
>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=76.08 E-value=4.6 Score=32.61 Aligned_cols=29 Identities=14% Similarity=0.383 Sum_probs=26.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
++.|+.+||..+|+|..|+.+-+++|.+-
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56899999999999999999999999753
No 115
>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=75.91 E-value=6.3 Score=31.41 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=30.7
Q ss_pred CChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHH
Q 008401 214 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKR 254 (567)
Q Consensus 214 R~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR 254 (567)
|.|.-=-|=-||+ -++-.++.++||..+||++.|||+-
T Consensus 5 Rsp~rdkA~e~y~---~~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 5 RSPNRDKAFEIYK---ESNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCcCHHHHHHHHH---HhCCCccHHHHHHHHCCCHHHHHHH
Confidence 5666556666775 4678999999999999999999964
No 116
>PRK10220 hypothetical protein; Provisional
Probab=75.67 E-value=2 Score=38.07 Aligned_cols=27 Identities=19% Similarity=0.528 Sum_probs=20.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.||.|++.-.-.| ...+||..||.--.
T Consensus 5 ~CP~C~seytY~d--~~~~vCpeC~hEW~ 31 (111)
T PRK10220 5 HCPKCNSEYTYED--NGMYICPECAHEWN 31 (111)
T ss_pred cCCCCCCcceEcC--CCeEECCcccCcCC
Confidence 6999999854443 46899999998554
No 117
>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=75.54 E-value=10 Score=32.26 Aligned_cols=41 Identities=12% Similarity=0.078 Sum_probs=34.9
Q ss_pred HHHHHHHHHhCCCccHHHHHhhhc-cChHHHHHHHHHHHHHhhc
Q 008401 121 SCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQLCQVLYI 163 (567)
Q Consensus 121 ACLYiACR~e~~p~tL~Diad~~~-v~v~~Lgr~~~~L~~~L~i 163 (567)
.|+|++-+.. ..++.+|+..|| .+..++...++++.+.+..
T Consensus 34 ia~yl~~~~~--~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 34 IAMYLARELT--GLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HHHHHHHHHh--CCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 6778776665 467899999999 9999999999999998864
No 118
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=75.41 E-value=22 Score=39.64 Aligned_cols=187 Identities=14% Similarity=0.208 Sum_probs=102.1
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhC-C------------------CccHH
Q 008401 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKS-K------------------PFLLI 137 (567)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~-~------------------p~tL~ 137 (567)
-+..++..|+++ ...++.|..+...+.-.|+.- |+ ..=||.+=.+..+ . ..-+.
T Consensus 140 ~~~eia~~l~~~--~~~v~~~l~~lQ~leP~GigA-r~----L~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~ 212 (455)
T PRK05932 140 DLEEIAESLGVE--LDEVEAVLKRIQSFDPAGVGA-RD----LQECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFR 212 (455)
T ss_pred CHHHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHH
Confidence 467789999999 889999998888765555431 11 1123333332211 0 12356
Q ss_pred HHHhhhccChHHHHHHHHHHHHHhhccccccc----cccCCchhhHHHH----------------------HhhhCCCCC
Q 008401 138 DFSNYLNINVYELGAVYLQLCQVLYIADESNV----LKQVDPSIFLHKF----------------------TDRLLPGGN 191 (567)
Q Consensus 138 Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~----~~~vdP~~~I~Rf----------------------~~~L~~~~~ 191 (567)
.|+..++++..+|..+...| +.|+-.+-..+ ...+-|..+|.+. ...+.....
T Consensus 213 ~ia~~l~is~~~v~~~~~~I-r~L~P~Pg~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~in~~Y~~~~~~~~~ 291 (455)
T PRK05932 213 TLAKKLGVKEEDLQEALDLI-RSLDPKPGAGFGTEEPEYVVPDVFVRKINGGWLVELNPDSLPRLRINQEYAALVSRSAR 291 (455)
T ss_pred HHHHHHCcCHHHHHHHHHHH-hCCCCCCccccCCCCCCccCCCEEEEEeCCEEEEEECCCCCceEEECHHHHHHHHhccc
Confidence 78888999999998877544 55642211011 1123344444322 111110000
Q ss_pred HHHHHHHHHHHHHhh-hccccC--CCChhHHHHHHHHHHHH-----hcCC----CCCHhhHHHHhccCHHHHHHHHH-HH
Q 008401 192 KKVCDTARDILASMK-RDWITT--GRKPSGLCGAALYVSAL-----THGL----KFSKSDIVKIVHICEATLMKRLI-EF 258 (567)
Q Consensus 192 ~~V~~~A~~iv~~~~-~~~i~~--GR~P~~IaaAalylAa~-----~~g~----~~t~~eIa~vv~Vse~TIrkR~k-E~ 258 (567)
.++.. .|-+++. -.|+.. .+|-.+|.-.+-.|+-+ ..|. +.|+++||..+|++++||.+..+ -+
T Consensus 292 ~e~~~---ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~~Ky 368 (455)
T PRK05932 292 DEDKQ---FLREKLQEAKWLIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATTNKY 368 (455)
T ss_pred hHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhcCce
Confidence 11101 1111111 123322 24444554444444442 2343 47999999999999999999883 45
Q ss_pred HccCCCCCCHHHHHHh
Q 008401 259 ENTDSGSLTIEDFMAR 274 (567)
Q Consensus 259 ~~t~s~~Lt~~ef~~~ 274 (567)
..||-|-+-+..|-+.
T Consensus 369 v~tp~Gi~~lk~FFs~ 384 (455)
T PRK05932 369 MATPRGIFELKYFFSS 384 (455)
T ss_pred eecCCceEEHHHhccc
Confidence 6788777777777655
No 119
>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=75.40 E-value=1.6 Score=32.27 Aligned_cols=28 Identities=18% Similarity=0.131 Sum_probs=20.5
Q ss_pred HhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 008401 229 LTHGLKFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 229 ~~~g~~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
+|+....|+.+||+.+|||..||.+.++
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 4454559999999999999999988764
No 120
>PF12773 DZR: Double zinc ribbon
Probab=74.77 E-value=1.7 Score=32.69 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=6.3
Q ss_pred CceecCcccceec
Q 008401 19 SQLCCDRCGKVLE 31 (567)
Q Consensus 19 G~~VC~~CG~Vle 31 (567)
+..+|..||..|.
T Consensus 11 ~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 11 DAKFCPHCGTPLP 23 (50)
T ss_pred cccCChhhcCChh
Confidence 3445555555444
No 121
>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=74.75 E-value=8.2 Score=30.09 Aligned_cols=29 Identities=21% Similarity=0.414 Sum_probs=26.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
....|+.+|++.+|++..|+++.++.|.+
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999999998864
No 122
>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=74.64 E-value=6.6 Score=31.05 Aligned_cols=37 Identities=19% Similarity=0.261 Sum_probs=30.5
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 223 alylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
+||.... .+..++..+||+..+|+.+|+..-++.|.+
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 4666555 678899999999999999999999998864
No 123
>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=74.60 E-value=4.3 Score=36.04 Aligned_cols=30 Identities=27% Similarity=0.498 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceeccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (567)
..||.|++.-.-.| ...+||..||.--...
T Consensus 3 p~CP~C~seytY~d--g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYHD--GTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceEec--CCeeECcccccccccc
Confidence 47999999855444 4579999999876543
No 124
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=74.48 E-value=6.7 Score=28.25 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=26.3
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFM 272 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~ 272 (567)
..+.++.+||..+|+|...+++.+++.. .+|+.+|.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~-----g~tp~~y~ 41 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET-----GMTPKQYR 41 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT-----SS-HHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHh
Confidence 3468999999999999999999998874 46777765
No 125
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=74.28 E-value=1.4e+02 Score=32.83 Aligned_cols=99 Identities=12% Similarity=0.117 Sum_probs=59.9
Q ss_pred chHHHHHHHHHHHHHHHHHHh---CCCCchHHHHHHHHHHHHHHhccccCCCchhHHHH------HHHHHH---------
Q 008401 65 ASRERLMEKAFDDMRQMKNAL---NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA------SCLYLA--------- 126 (567)
Q Consensus 65 ~srer~l~~a~~~I~~ia~~L---~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA------ACLYiA--------- 126 (567)
..+++-+..-...+..+|.++ ++.-.+-|.+....+++.+..-.-.+|-+..+.+- ..-+++
T Consensus 175 ~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP 254 (415)
T PRK07598 175 RAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLP 254 (415)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehh
Confidence 345555555566777777776 22221455556666777665555567766665553 222331
Q ss_pred ------------H-----HHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhc
Q 008401 127 ------------C-----RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (567)
Q Consensus 127 ------------C-----R~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i 163 (567)
. ...|.+-+..+||..+++++..|..........+.+
T Consensus 255 ~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SL 308 (415)
T PRK07598 255 VHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSL 308 (415)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCccc
Confidence 0 123556778999999999999998876655444433
No 126
>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=74.21 E-value=1.6 Score=49.78 Aligned_cols=34 Identities=26% Similarity=0.673 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCc------eee----cCCCceecCcccceecccc
Q 008401 1 MVWCSSCARHVT------GHR----PYDSQLCCDRCGKVLEDHN 34 (567)
Q Consensus 1 M~~Cp~Cgs~~i------v~D----~~~G~~VC~~CG~Vlee~~ 34 (567)
++.||+||.... .++ +..-.++|..||..+++..
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~ 243 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHD 243 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHH
Confidence 357999998733 222 3457899999999999854
No 127
>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=73.94 E-value=5.7 Score=29.71 Aligned_cols=27 Identities=15% Similarity=0.089 Sum_probs=23.6
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
....|+.|||...|+|..||+++++.-
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 678999999999999999999998764
No 128
>PRK05949 RNA polymerase sigma factor; Validated
Probab=73.93 E-value=1.3e+02 Score=32.01 Aligned_cols=90 Identities=7% Similarity=0.012 Sum_probs=51.9
Q ss_pred hHHHHHHHHHHHHHHHHHHhC---CCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHH-------------------
Q 008401 66 SRERLMEKAFDDMRQMKNALN---IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCL------------------- 123 (567)
Q Consensus 66 srer~l~~a~~~I~~ia~~L~---Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACL------------------- 123 (567)
..++.+..-...+-.+|..+- ++-.+-|.+.-..+++.+..-...+|-+..+.+.-+|
T Consensus 92 A~~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~ 171 (327)
T PRK05949 92 AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPI 171 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCH
Confidence 444444555677777777752 2211445555556777665545556655555544211
Q ss_pred ------HHHH-------HHhCCCccHHHHHhhhccChHHHHHHHH
Q 008401 124 ------YLAC-------RQKSKPFLLIDFSNYLNINVYELGAVYL 155 (567)
Q Consensus 124 ------YiAC-------R~e~~p~tL~Diad~~~v~v~~Lgr~~~ 155 (567)
...- ...|..-+..+||..+++++..+.....
T Consensus 172 ~~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~ 216 (327)
T PRK05949 172 HITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLS 216 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 1111 1124556788999999999988877544
No 129
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=73.70 E-value=2.3 Score=36.66 Aligned_cols=32 Identities=22% Similarity=0.565 Sum_probs=25.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (567)
.||.||... +.....|-..|..||.++.....
T Consensus 38 ~CpfCgk~~-vkR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PTZ00255 38 FCPFCGKHA-VKRQAVGIWRCKGCKKTVAGGAW 69 (90)
T ss_pred cCCCCCCCc-eeeeeeEEEEcCCCCCEEeCCcc
Confidence 699999875 45567899999999999876544
No 130
>PF15616 TerY-C: TerY-C metal binding domain
Probab=73.61 E-value=1.9 Score=39.68 Aligned_cols=19 Identities=32% Similarity=0.864 Sum_probs=12.3
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
-||+||.. .+..+| +||.|
T Consensus 79 gCP~CGn~-------~~fa~C-~CGkl 97 (131)
T PF15616_consen 79 GCPHCGNQ-------YAFAVC-GCGKL 97 (131)
T ss_pred CCCCCcCh-------hcEEEe-cCCCE
Confidence 59999985 344555 45555
No 131
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=73.28 E-value=55 Score=33.18 Aligned_cols=97 Identities=13% Similarity=0.122 Sum_probs=62.4
Q ss_pred HHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHH
Q 008401 119 QASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTA 198 (567)
Q Consensus 119 aAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A 198 (567)
..++-||...- ..++++.++|+.++++...|.+.|++.. | ..|..||.+. -...|
T Consensus 189 ~~~~~~I~~~~-~~~~sl~~lA~~~~~S~~~l~r~Fk~~~---G----------~t~~~yi~~~-----------Rl~~A 243 (287)
T TIGR02297 189 NRFNFLIEENY-KQHLRLPEYADRLGISESRLNDICRRFS---A----------LSPKRLIIER-----------VMQEA 243 (287)
T ss_pred HHHHHHHHHhh-ccCCCHHHHHHHHCCCHHHHHHHHHHHh---C----------CCHHHHHHHH-----------HHHHH
Confidence 34455665433 4589999999999999999998888653 2 3466666543 11122
Q ss_pred HHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccC-HHHHHHHHHHHHccCCCCCCHHHHHH
Q 008401 199 RDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMA 273 (567)
Q Consensus 199 ~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vs-e~TIrkR~kE~~~t~s~~Lt~~ef~~ 273 (567)
.++ +..-+.|+.+||..+|-+ .++..+.+|... .+||.+|++
T Consensus 244 ~~l----------------------------L~~t~~sI~eIA~~~GF~s~s~Fsr~FKk~~-----G~tP~~yR~ 286 (287)
T TIGR02297 244 RRL----------------------------LLFTQHSINQIAYDLGYKDPAYFARFFQKET-----GLSPSAFRD 286 (287)
T ss_pred HHH----------------------------HHcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHhc
Confidence 221 113456888888888875 457777777665 466777754
No 132
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=73.27 E-value=1.3e+02 Score=31.77 Aligned_cols=25 Identities=12% Similarity=0.111 Sum_probs=22.1
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
+...|.+||+..+|||..|||++..
T Consensus 274 ~~~~Tl~EIa~~lgiS~erVRqi~~ 298 (317)
T PRK07405 274 GQPLTLAKIGERLNISRERVRQIER 298 (317)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3579999999999999999998854
No 133
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=73.21 E-value=1.5 Score=34.37 Aligned_cols=24 Identities=21% Similarity=0.516 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCceeecCCCceecCcccceec
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
|.+|+.||...+ ..+|..||....
T Consensus 5 mr~C~~CgvYTL-------k~~CP~CG~~t~ 28 (56)
T PRK13130 5 IRKCPKCGVYTL-------KEICPVCGGKTK 28 (56)
T ss_pred ceECCCCCCEEc-------cccCcCCCCCCC
Confidence 568999998644 459999998744
No 134
>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=73.01 E-value=16 Score=40.33 Aligned_cols=183 Identities=15% Similarity=0.199 Sum_probs=100.4
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCC------------------CccHHH
Q 008401 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK------------------PFLLID 138 (567)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~------------------p~tL~D 138 (567)
-+..+|..|+++ ...++.|..+++.+.-.|+.- |+ ..=||.+=.+..+. ..-+..
T Consensus 115 ~~~eia~~l~~~--~~~ve~~l~~iq~leP~GIgA-r~----L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~ 187 (429)
T TIGR02395 115 DLEEIADELEVS--EEEVEKVLELIQRLDPAGVGA-RD----LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRR 187 (429)
T ss_pred CHHHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHH
Confidence 367789999999 899999988888765555431 11 11233333332211 123467
Q ss_pred HHhhhccChHHHHHHHHHHHHHhhccccccc-----cccCCchhhHHHHHhhhC----------CCCCH-----------
Q 008401 139 FSNYLNINVYELGAVYLQLCQVLYIADESNV-----LKQVDPSIFLHKFTDRLL----------PGGNK----------- 192 (567)
Q Consensus 139 iad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~-----~~~vdP~~~I~Rf~~~L~----------~~~~~----------- 192 (567)
|+..++++..++..+... .+.|+-.+-..+ ...+-|..+|.+.-..+. +..++
T Consensus 188 i~~~l~is~~~v~~~~~~-I~~L~P~Pg~~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~ 266 (429)
T TIGR02395 188 LAKKLGLSEEELKEALDL-IKSLSPKPGKEFADPEEVEYVIPDVIVTKKNGEWVVELNGRSLPELRINEEYFKLLKDAEK 266 (429)
T ss_pred HHHHHCcCHHHHHHHHHH-HhCCCCCCcccccCCCCCCccCCCEEEEEECCEEEEEEcCCCCceEEECHHHHHHHHhccc
Confidence 888899999999876654 444542111011 112334444433211110 00011
Q ss_pred -HH-------HHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHH-----hcC----CCCCHhhHHHHhccCHHHHHHHH
Q 008401 193 -KV-------CDTARDILASMKRDWITTGRKPSGLCGAALYVSAL-----THG----LKFSKSDIVKIVHICEATLMKRL 255 (567)
Q Consensus 193 -~V-------~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~-----~~g----~~~t~~eIa~vv~Vse~TIrkR~ 255 (567)
++ .+.|..|++.+. +|-.+|--.+-.|+-+ ..| .+.|+++||..+|++++||.+..
T Consensus 267 ~~~~~ylk~k~~~A~~li~~i~-------~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav 339 (429)
T TIGR02395 267 EAAAQYLKQKLKEARWLIKALE-------QREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAI 339 (429)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhh
Confidence 11 112333333222 3334444444443332 234 25799999999999999999988
Q ss_pred H-HHHccCCCCCCHHHHHHh
Q 008401 256 I-EFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 256 k-E~~~t~s~~Lt~~ef~~~ 274 (567)
+ -+..||-|-+-+..|-+.
T Consensus 340 ~~Kyi~tp~Gi~~lk~FFs~ 359 (429)
T TIGR02395 340 NNKYLQTPRGVFELKYFFSR 359 (429)
T ss_pred cCceEecCCceEEHHHhcCC
Confidence 3 345778777777777554
No 135
>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=72.85 E-value=14 Score=35.02 Aligned_cols=30 Identities=17% Similarity=0.301 Sum_probs=27.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
++.|+.+||..+|+|..|+.+-+++|.+-.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 171 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKKK 171 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 678999999999999999999999997554
No 136
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=72.70 E-value=3.8 Score=30.78 Aligned_cols=21 Identities=19% Similarity=0.276 Sum_probs=19.4
Q ss_pred CHhhHHHHhccCHHHHHHHHH
Q 008401 236 SKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~k 256 (567)
|++|||+.+|||..|+.+-|.
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 689999999999999999876
No 137
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=72.44 E-value=12 Score=37.26 Aligned_cols=43 Identities=19% Similarity=0.256 Sum_probs=28.3
Q ss_pred HHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHH
Q 008401 83 NALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLA 126 (567)
Q Consensus 83 ~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiA 126 (567)
.....+. .-..+.|...|++|.--...++-+...+|-.||=+|
T Consensus 83 ~~~~~~~-~Rt~~~ai~~YkLAll~~~~~~~~~s~~A~l~LrlA 125 (214)
T PF09986_consen 83 KPRDFSG-ERTLEEAIESYKLALLCAQIKKEKPSKKAGLCLRLA 125 (214)
T ss_pred ccCCCCC-CCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3335553 456778888888887665556656666777777666
No 138
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=72.30 E-value=1.8e+02 Score=33.05 Aligned_cols=91 Identities=9% Similarity=0.066 Sum_probs=54.4
Q ss_pred chHHHHHHHHHHHHHHHHHHh---CCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHH--------------
Q 008401 65 ASRERLMEKAFDDMRQMKNAL---NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC-------------- 127 (567)
Q Consensus 65 ~srer~l~~a~~~I~~ia~~L---~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC-------------- 127 (567)
..+++.+..-+..+..+|.++ |++-.+-|.+.-.-+.+-+..-...+|-+..+.|.-+|--+.
T Consensus 271 ~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP 350 (509)
T PRK05901 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIP 350 (509)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecC
Confidence 344455555567777777775 333214444445556666655566778777777766663332
Q ss_pred ------------------HHhCCCccHHHHHhhhccChHHHHHHHH
Q 008401 128 ------------------RQKSKPFLLIDFSNYLNINVYELGAVYL 155 (567)
Q Consensus 128 ------------------R~e~~p~tL~Diad~~~v~v~~Lgr~~~ 155 (567)
...|.+-+..+||..+++++..|.....
T Consensus 351 ~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~ 396 (509)
T PRK05901 351 VHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK 396 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 1123444567888888888887776533
No 139
>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=71.51 E-value=4.7 Score=28.03 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=22.1
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHH
Q 008401 133 PFLLIDFSNYLNINVYELGAVYLQLCQ 159 (567)
Q Consensus 133 p~tL~Diad~~~v~v~~Lgr~~~~L~~ 159 (567)
|.+-.|||+.+|+++.++.|.+++|.+
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 667889999999999999999999876
No 140
>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=71.47 E-value=8.6 Score=31.90 Aligned_cols=26 Identities=19% Similarity=0.068 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|++|||..+|||+.||++++...
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 45799999999999999999999854
No 141
>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=71.28 E-value=26 Score=32.66 Aligned_cols=79 Identities=14% Similarity=0.036 Sum_probs=53.5
Q ss_pred CCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhh---c--cccCCCChhHHHHHHHHHHHHhcCC-CCCHhhHHHHhcc
Q 008401 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR---D--WITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIVHI 246 (567)
Q Consensus 173 vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~---~--~i~~GR~P~~IaaAalylAa~~~g~-~~t~~eIa~vv~V 246 (567)
++-..||.|+...... +..+.-.|+-++.++.. . .......+.-+-.+||.+|+.+++. ..+.+..+++.||
T Consensus 52 i~i~~fl~ri~~~~~~--s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gi 129 (149)
T PF08613_consen 52 ISIRDFLSRILKYTQC--SPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGI 129 (149)
T ss_dssp S-HHHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS
T ss_pred CcHHHHHHHHHHHcCC--ChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCC
Confidence 5667788888877764 78888889988888876 1 1234566777889999999988754 4688899999988
Q ss_pred CHHHHHH
Q 008401 247 CEATLMK 253 (567)
Q Consensus 247 se~TIrk 253 (567)
+..-|.+
T Consensus 130 s~~eln~ 136 (149)
T PF08613_consen 130 SLKELNE 136 (149)
T ss_dssp -HHHHHH
T ss_pred CHHHHHH
Confidence 7554443
No 142
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.24 E-value=5.6 Score=36.65 Aligned_cols=33 Identities=15% Similarity=0.396 Sum_probs=28.4
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
..+.++|+++||+.+|+|..|+++|++.+.+..
T Consensus 18 ~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 18 QEDARISNAELAERVGLSPSTVLRRIKRLEEEG 50 (154)
T ss_pred HHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 446679999999999999999999999986443
No 143
>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=70.98 E-value=2 Score=31.04 Aligned_cols=27 Identities=22% Similarity=0.524 Sum_probs=16.6
Q ss_pred CCCCCCCCCceee---------cCCCceecCcccce
Q 008401 3 WCSSCARHVTGHR---------PYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D---------~~~G~~VC~~CG~V 29 (567)
.||.||+...++- +.+-.++|.+||..
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 6999999854331 22457899999964
No 144
>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=70.66 E-value=4.3 Score=31.65 Aligned_cols=29 Identities=21% Similarity=0.256 Sum_probs=25.6
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.-.++..+++..++||+.|||+=+.++.+
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~ 40 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEK 40 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35689999999999999999999988854
No 145
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=70.64 E-value=26 Score=34.94 Aligned_cols=94 Identities=16% Similarity=0.146 Sum_probs=75.5
Q ss_pred hHHHHHhhhCCCCCHHHHHHHHHHHHHhh--hccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHH
Q 008401 178 FLHKFTDRLLPGGNKKVCDTARDILASMK--RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRL 255 (567)
Q Consensus 178 ~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~--~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~ 255 (567)
.|.++..+|+++..+.+.+.|.+|++-.. -++...|-.-.+=|.-|+-|||.+.++........+..|.+..|-.+.+
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 58889999998888899999999887543 3455556666777777888999999999999999999999999999999
Q ss_pred HHHHccCC--CCCCHHHH
Q 008401 256 IEFENTDS--GSLTIEDF 271 (567)
Q Consensus 256 kE~~~t~s--~~Lt~~ef 271 (567)
+-|...-. ..+.|.|.
T Consensus 82 ~sfe~llgln~~~~Vrdl 99 (262)
T KOG4557|consen 82 NSFENLLGLNIKLNVRDL 99 (262)
T ss_pred HHHHHHhcchhhcCHHHH
Confidence 98876543 45566654
No 146
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=70.34 E-value=5.6 Score=28.84 Aligned_cols=29 Identities=17% Similarity=0.424 Sum_probs=26.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.++.++.+|+..++++..|+++.++.|.+
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999999999865
No 147
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=70.33 E-value=6.4 Score=37.82 Aligned_cols=72 Identities=22% Similarity=0.259 Sum_probs=46.3
Q ss_pred CHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHH
Q 008401 191 NKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIED 270 (567)
Q Consensus 191 ~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~e 270 (567)
.+.|.........+. .|+. ++|-|| ++.+| .-...|..+||.-+|.|+.|||+.++. +|.+++|--+-
T Consensus 28 ~~evlkli~~~~~~l--TWvd------SLavAA-ga~ar-ekag~Ti~EIAeelG~TeqTir~hlkg--etkAG~lv~et 95 (182)
T COG1318 28 RPEVLKLIKDPYERL--TWVD------SLAVAA-GALAR-EKAGMTISEIAEELGRTEQTVRNHLKG--ETKAGQLVRET 95 (182)
T ss_pred cHHHHHHHhCccccc--chhh------HHHHHH-HHHHH-HHccCcHHHHHHHhCCCHHHHHHHHhc--chhhhhHHHHH
Confidence 345555444333333 4653 233333 33344 567799999999999999999999984 56777776555
Q ss_pred HHHh
Q 008401 271 FMAR 274 (567)
Q Consensus 271 f~~~ 274 (567)
|..+
T Consensus 96 Y~~l 99 (182)
T COG1318 96 YEKL 99 (182)
T ss_pred HHHH
Confidence 5444
No 148
>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=70.28 E-value=4.4 Score=28.19 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=22.0
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
+.|..|||..+|++..|+.+-++.|..
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 468899999999999999999999864
No 149
>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=70.21 E-value=2.9 Score=36.05 Aligned_cols=32 Identities=19% Similarity=0.553 Sum_probs=25.9
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (567)
.||.||... +.....|-..|..||.++....+
T Consensus 37 ~CpfCgk~~-vkR~a~GIW~C~~C~~~~AGGAy 68 (91)
T TIGR00280 37 VCPFCGKKT-VKRGSTGIWTCRKCGAKFAGGAY 68 (91)
T ss_pred cCCCCCCCc-eEEEeeEEEEcCCCCCEEeCCcc
Confidence 699999875 45667899999999999875544
No 150
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=69.84 E-value=70 Score=27.45 Aligned_cols=38 Identities=16% Similarity=0.268 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHH
Q 008401 119 QASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (567)
Q Consensus 119 aAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L 157 (567)
.-++-||.- ....+.++.++|..++++...|.+.|+..
T Consensus 23 ~~~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~ 60 (127)
T COG2207 23 ARALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKE 60 (127)
T ss_pred HHHHHHHHH-HhcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 345555555 66667999999999999999998877744
No 151
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=69.77 E-value=67 Score=34.83 Aligned_cols=88 Identities=8% Similarity=0.094 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccC-CC---chhHHH-------HHHHHHHHHHhCCCcc
Q 008401 67 RERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTK-GR---RTEQVQ-------ASCLYLACRQKSKPFL 135 (567)
Q Consensus 67 rer~l~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~r-GR---~~~~va-------AACLYiACR~e~~p~t 135 (567)
.+=.++.|+-.+-.-+.++.-.-+.....-|..+.+.+..+-+.. +| -+.++. -+.--+. ...|..-+
T Consensus 163 ~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~-~~lgr~Pt 241 (373)
T PRK07406 163 FQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLS-QEFGRKPT 241 (373)
T ss_pred HHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHHHHHHHHHHHHH-HHhCCCCC
Confidence 344556666666666666654322345666666666665443321 11 122221 1111111 12344447
Q ss_pred HHHHHhhhccChHHHHHHHH
Q 008401 136 LIDFSNYLNINVYELGAVYL 155 (567)
Q Consensus 136 L~Diad~~~v~v~~Lgr~~~ 155 (567)
..+||..+++++..|.....
T Consensus 242 ~~EIA~~lg~~~e~v~~~~~ 261 (373)
T PRK07406 242 EEEIAESMEMTIEKLRFIAK 261 (373)
T ss_pred HHHHHHHhCCCHHHHHHHHH
Confidence 99999999999999876533
No 152
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=69.75 E-value=6.8 Score=33.96 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=26.9
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
+-+.|..+|++.+|+++.|+++|++.+.+.
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 457899999999999999999999999753
No 153
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=69.65 E-value=2.9 Score=36.36 Aligned_cols=31 Identities=19% Similarity=0.609 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCceeecCC-CceecCcccceec
Q 008401 1 MVWCSSCARHVTGHRPYD-SQLCCDRCGKVLE 31 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~-G~~VC~~CG~Vle 31 (567)
|..||.||.-.++.-... ....|..|+.|..
T Consensus 1 m~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 1 MLFCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred CcccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 788999998755443222 5678999999954
No 154
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=69.61 E-value=2.2 Score=41.67 Aligned_cols=29 Identities=24% Similarity=0.532 Sum_probs=19.9
Q ss_pred CCCCCCCCCc---eeecCCC---ceecCcccceecc
Q 008401 3 WCSSCARHVT---GHRPYDS---QLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~i---v~D~~~G---~~VC~~CG~Vlee 32 (567)
.||.||+..+ ++- ..| .+-|.+||+|-.+
T Consensus 8 ~Cp~Cg~eev~hEVik-~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 8 ECPSCGSEEVSHEVIK-ERGREPLVRCEECGTVHPA 42 (201)
T ss_pred ECCCCCcchhhHHHHH-hcCCceEEEccCCCcEeec
Confidence 6999995543 222 223 5789999999854
No 155
>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=69.21 E-value=2.8 Score=36.59 Aligned_cols=27 Identities=26% Similarity=0.743 Sum_probs=21.2
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
.||.||.-. .+..|.++|..||.+.+.
T Consensus 2 fC~~Cg~~l---~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLM---TPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCccc---ccCCCeEECcCCCCcccc
Confidence 699999863 234689999999998653
No 156
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=68.90 E-value=3.2 Score=32.86 Aligned_cols=26 Identities=27% Similarity=0.733 Sum_probs=12.5
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
.|..||......+ ..-...|.+||.+
T Consensus 9 ~CtSCg~~i~~~~-~~~~F~CPnCG~~ 34 (59)
T PRK14890 9 KCTSCGIEIAPRE-KAVKFLCPNCGEV 34 (59)
T ss_pred cccCCCCcccCCC-ccCEeeCCCCCCe
Confidence 3666665422111 1234556666665
No 157
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=68.75 E-value=3.1 Score=39.12 Aligned_cols=28 Identities=21% Similarity=0.436 Sum_probs=20.2
Q ss_pred CCCCCCCCCCc-eeec---CCCce-----ecCcccce
Q 008401 2 VWCSSCARHVT-GHRP---YDSQL-----CCDRCGKV 29 (567)
Q Consensus 2 ~~Cp~Cgs~~i-v~D~---~~G~~-----VC~~CG~V 29 (567)
|+||.|++... +.|+ .+|.. .|.+||.=
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~R 37 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGER 37 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccc
Confidence 57999999843 6664 35654 59999964
No 158
>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=68.63 E-value=9.1 Score=35.04 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=39.5
Q ss_pred chhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
+...-+.+++|+|-+..+-|.+..+||..++++...+.+...+|.+.
T Consensus 6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 6 KGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 44566778999997766679999999999999999999988888774
No 159
>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=68.21 E-value=1.3e+02 Score=29.73 Aligned_cols=27 Identities=4% Similarity=0.091 Sum_probs=23.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
....|+++||...|||..||++..+..
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~~~~a 223 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRLEKKV 223 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356899999999999999999887654
No 160
>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=68.14 E-value=3.4 Score=32.31 Aligned_cols=25 Identities=24% Similarity=0.595 Sum_probs=17.9
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
+.||+||...+ ---||..||+--+-
T Consensus 27 ~~C~~cG~~~~------~H~vc~~cG~Y~gr 51 (55)
T TIGR01031 27 VVCPNCGEFKL------PHRVCPSCGYYKGR 51 (55)
T ss_pred eECCCCCCccc------CeeECCccCeECCE
Confidence 46999998532 44599999976543
No 161
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.07 E-value=3.7 Score=34.34 Aligned_cols=30 Identities=23% Similarity=0.411 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCceee-cCCCceecCccccee
Q 008401 1 MVWCSSCARHVTGHR-PYDSQLCCDRCGKVL 30 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D-~~~G~~VC~~CG~Vl 30 (567)
|+.||.|+....-.+ ..--.-.|..|+-|-
T Consensus 1 ~llCP~C~v~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 1 MLLCPICGVELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred CcccCcCCceeeeeeecCceeeeCCccccEe
Confidence 788999998733222 222345799998874
No 162
>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=67.84 E-value=3.1 Score=29.75 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=18.8
Q ss_pred CCCCCCCC-CceeecC-CCceecCccccee
Q 008401 3 WCSSCARH-VTGHRPY-DSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~-~iv~D~~-~G~~VC~~CG~Vl 30 (567)
.|+.||.. .+..... ....+|..||.-+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 69999986 2222222 4577899999843
No 163
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=67.77 E-value=3.2 Score=33.34 Aligned_cols=14 Identities=14% Similarity=0.449 Sum_probs=10.6
Q ss_pred CCCCCCCCCCceee
Q 008401 2 VWCSSCARHVTGHR 15 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D 15 (567)
..||.||.++...+
T Consensus 5 ~kCpKCgn~~~~ek 18 (68)
T COG3478 5 FKCPKCGNTNYEEK 18 (68)
T ss_pred ccCCCcCCcchhhc
Confidence 46999999866554
No 164
>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=67.22 E-value=9.3 Score=30.59 Aligned_cols=31 Identities=10% Similarity=0.165 Sum_probs=26.5
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 230 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
+.+-..+..+|+..++||..||+++++.+..
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3344578999999999999999999999864
No 165
>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=67.14 E-value=4.4 Score=42.22 Aligned_cols=55 Identities=11% Similarity=0.051 Sum_probs=47.3
Q ss_pred hhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcC
Q 008401 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHG 232 (567)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g 232 (567)
..+|.++|.+|.+ +..+..+|.-+.++..-..-..+-.|..||.+|||||++..+
T Consensus 49 ~k~i~~l~~~L~l--p~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed 103 (297)
T COG5333 49 LKLIMDLCTRLNL--PQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVED 103 (297)
T ss_pred HHHHHHHHHhcCC--CcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeeccc
Confidence 4578899999985 788999999999887666668899999999999999999776
No 166
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=66.73 E-value=8.1 Score=29.14 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=25.7
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 232 GLKF-SKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 232 g~~~-t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
|... |+++++...+||..||++.++.+.+.
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3345 89999999999999999999998643
No 167
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=66.63 E-value=66 Score=33.06 Aligned_cols=41 Identities=10% Similarity=0.233 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHH
Q 008401 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (567)
Q Consensus 116 ~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L 157 (567)
..+..++-||-... ..+.++.++|..++++...|.|.|+..
T Consensus 5 ~~i~~~~~~i~~~~-~~~~~l~~lA~~~~~S~~~l~r~F~~~ 45 (289)
T PRK15121 5 GIIRDLLIWLEGHL-DQPLSLDNVAAKAGYSKWHLQRMFKDV 45 (289)
T ss_pred HHHHHHHHHHHhcc-cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34566777777554 457999999999999999999988865
No 168
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=66.61 E-value=1.7e+02 Score=30.42 Aligned_cols=27 Identities=4% Similarity=-0.141 Sum_probs=23.9
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
....|++|||...|||..||+++...-
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~A 269 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARA 269 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 367899999999999999999888654
No 169
>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=66.57 E-value=7.9 Score=32.30 Aligned_cols=45 Identities=22% Similarity=0.244 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 116 ~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
..-+-+.+|+|-...+.|.+..+||+.++++...|.+....|.+.
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 445557788887777778999999999999999999999988874
No 170
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=66.52 E-value=3.9 Score=36.10 Aligned_cols=31 Identities=19% Similarity=0.453 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~ 34 (567)
..||+|++. .+++ ..+.++|..|+.--.++.
T Consensus 4 p~cp~c~sE-ytYe-d~~~~~cpec~~ew~~~~ 34 (112)
T COG2824 4 PPCPKCNSE-YTYE-DGGQLICPECAHEWNENE 34 (112)
T ss_pred CCCCccCCc-eEEe-cCceEeCchhcccccccc
Confidence 479999886 3443 356999999998665433
No 171
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=66.40 E-value=2.6 Score=40.23 Aligned_cols=30 Identities=27% Similarity=0.754 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCcee--------------ecCCCceecCccccee
Q 008401 1 MVWCSSCARHVTGH--------------RPYDSQLCCDRCGKVL 30 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~--------------D~~~G~~VC~~CG~Vl 30 (567)
++.||.|++...-+ -..+-.++|++||.|-
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 35799999863211 1234467799999874
No 172
>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=66.27 E-value=4.5 Score=35.73 Aligned_cols=31 Identities=16% Similarity=0.345 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceeec--------CC-Cc-eecCcccceecc
Q 008401 2 VWCSSCARHVTGHRP--------YD-SQ-LCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~--------~~-G~-~VC~~CG~Vlee 32 (567)
..||+||......+. .. .. ++|+.|+.-+.=
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceeee
Confidence 479999998554441 12 33 899999998763
No 173
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=65.78 E-value=3.8 Score=35.26 Aligned_cols=32 Identities=22% Similarity=0.541 Sum_probs=25.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (567)
.||.||...+ -....|-..|..||.++.....
T Consensus 38 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PRK03976 38 VCPVCGRPKV-KRVGTGIWECRKCGAKFAGGAY 69 (90)
T ss_pred cCCCCCCCce-EEEEEEEEEcCCCCCEEeCCcc
Confidence 5999987654 5567899999999999876544
No 174
>PF12773 DZR: Double zinc ribbon
Probab=65.57 E-value=4.3 Score=30.46 Aligned_cols=30 Identities=23% Similarity=0.616 Sum_probs=21.0
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceeccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (567)
..|++||.... .......+|..||..++.+
T Consensus 13 ~fC~~CG~~l~--~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLP--PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChh--hccCCCCCCcCCcCCCcCC
Confidence 46899988743 2234567899999976643
No 175
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=65.49 E-value=11 Score=38.10 Aligned_cols=57 Identities=16% Similarity=0.121 Sum_probs=42.9
Q ss_pred hhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCC
Q 008401 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLK 234 (567)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~ 234 (567)
..+|..++.+|.+ .+.|+.+|.-..+|.--..-..+-.|.-+|..|||+||..-...
T Consensus 45 ~n~I~~lg~~lkl--RQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~ 101 (264)
T KOG0794|consen 45 ANVIQKLGQHLKL--RQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP 101 (264)
T ss_pred HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence 3456667777764 68898888888877543333678999999999999999866544
No 176
>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=65.31 E-value=6.5 Score=33.71 Aligned_cols=32 Identities=13% Similarity=-0.049 Sum_probs=28.1
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
+.....|+++|++.+|||..||.+-=+.+..-
T Consensus 45 lL~~g~syreIa~~tgvS~aTItRvsr~Lk~~ 76 (87)
T PF01371_consen 45 LLDEGKSYREIAEETGVSIATITRVSRCLKYG 76 (87)
T ss_dssp HHHTTSSHHHHHHHHTSTHHHHHHHHHHHHHS
T ss_pred HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHcC
Confidence 66678999999999999999999988888643
No 177
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=65.21 E-value=1.6e+02 Score=29.86 Aligned_cols=99 Identities=14% Similarity=0.178 Sum_probs=63.1
Q ss_pred HHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHH
Q 008401 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDT 197 (567)
Q Consensus 118 vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~ 197 (567)
+..++-||.-. ..-++++.++|+.++++...|.+.|++. +| ..|..||.+. -...
T Consensus 185 i~~~~~~i~~~-~~~~isl~~lA~~~~lS~~~l~r~Fk~~---~G----------~tp~~~l~~~-----------Rl~~ 239 (290)
T PRK10572 185 VREACQYISDH-LASEFDIESVAQHVCLSPSRLAHLFRQQ---LG----------ISVLRWREDQ-----------RISR 239 (290)
T ss_pred HHHHHHHHHhc-ccCCCCHHHHHHHHCCCHHHHHHHHHHH---HC----------cCHHHHHHHH-----------HHHH
Confidence 45555565433 3468899999999999998888888765 33 3344555422 1112
Q ss_pred HHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccC-HHHHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 198 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 198 A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vs-e~TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
|..++. .-+.|+.+||..+|-+ .....+.+|... .+||.+|++.
T Consensus 240 A~~lL~----------------------------~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~-----G~SP~~yR~~ 284 (290)
T PRK10572 240 AKLLLQ----------------------------TTRMPIATIGRNVGYDDQLYFSRVFKKCT-----GASPSEFRAR 284 (290)
T ss_pred HHHHHH----------------------------cCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 222221 2357788888888876 557777777765 5778888765
No 178
>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=65.14 E-value=11 Score=28.08 Aligned_cols=27 Identities=26% Similarity=0.209 Sum_probs=20.9
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
+|. .|++..|+..||..+||+.|++.-
T Consensus 14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 14 NGK-MSIRKAAKKYGVPRSTLRRRLRGK 40 (45)
T ss_dssp TTS-S-HHHHHHHHT--HHHHHHHHHHT
T ss_pred hCC-CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 555 999999999999999999988754
No 179
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=64.83 E-value=8.6 Score=28.43 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=23.3
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
..+.++||..++||..||++++..+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36999999999999999999998764
No 180
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=64.83 E-value=1.6e+02 Score=29.75 Aligned_cols=90 Identities=14% Similarity=0.129 Sum_probs=54.2
Q ss_pred chHHHHHHHHHHHHHHHHHHh-C-CCC-chHHHH-HHHHHHHHHHhccccCCCchhHHHHHHHHHHHHH-----------
Q 008401 65 ASRERLMEKAFDDMRQMKNAL-N-IGE-SDEIVH-VAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ----------- 129 (567)
Q Consensus 65 ~srer~l~~a~~~I~~ia~~L-~-Lp~-~~~i~e-~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~----------- 129 (567)
..++..+..-...+..+|.++ + .+. -++++. .-.-+++.+..-...+|-+..+.+.-++.=+|..
T Consensus 25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr~ 104 (256)
T PRK07408 25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI 104 (256)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeeee
Confidence 445555566667777777775 2 221 133433 3344666665555566777777776666555432
Q ss_pred ---------------------hCCCccHHHHHhhhccChHHHHHHH
Q 008401 130 ---------------------KSKPFLLIDFSNYLNINVYELGAVY 154 (567)
Q Consensus 130 ---------------------e~~p~tL~Diad~~~v~v~~Lgr~~ 154 (567)
.|.+-+..+||..+++++..+....
T Consensus 105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 2334456789999999999887654
No 181
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=64.70 E-value=4.1 Score=32.12 Aligned_cols=26 Identities=23% Similarity=0.543 Sum_probs=19.0
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceeccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (567)
+.||+||.... --.||..||+--+..
T Consensus 28 ~~C~~CG~~~~------~H~vC~~CG~Y~gr~ 53 (57)
T PRK12286 28 VECPNCGEPKL------PHRVCPSCGYYKGRE 53 (57)
T ss_pred eECCCCCCccC------CeEECCCCCcCCCEE
Confidence 46999998643 456999999865543
No 182
>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=64.60 E-value=14 Score=29.63 Aligned_cols=46 Identities=17% Similarity=0.130 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHhC----------CCccHHHHHhhhccChHHHHHHHHHHHHHhhc
Q 008401 118 VQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (567)
Q Consensus 118 vaAACLYiACR~e~----------~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i 163 (567)
+|...++++.+... .|.+..+||+.+|++..++.++++.|.+.==+
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I 58 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGII 58 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 45555566655432 57899999999999999999999999875333
No 183
>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=64.47 E-value=12 Score=27.68 Aligned_cols=32 Identities=9% Similarity=0.189 Sum_probs=26.6
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
+..-+.++.||++.++++.+||+..++.+.+.
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 34467899999999999999999999988753
No 184
>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=64.08 E-value=31 Score=32.58 Aligned_cols=29 Identities=3% Similarity=-0.074 Sum_probs=27.0
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 132 ~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
.|.|..|||+.+|++..++.|++++|.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 68899999999999999999999999885
No 185
>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=63.90 E-value=1.5e+02 Score=29.06 Aligned_cols=25 Identities=8% Similarity=0.158 Sum_probs=22.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...|.++||...|++..||++++..
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~r 214 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQ 214 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5679999999999999999998754
No 186
>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=63.85 E-value=2.8 Score=32.79 Aligned_cols=25 Identities=24% Similarity=0.534 Sum_probs=17.6
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
+.||.||.-. -.-.||.+||+.=.-
T Consensus 27 ~~c~~cg~~~------~~H~vc~~cG~y~~r 51 (56)
T PF01783_consen 27 VKCPNCGEPK------LPHRVCPSCGYYKGR 51 (56)
T ss_dssp EESSSSSSEE------STTSBCTTTBBSSSS
T ss_pred eeeccCCCEe------cccEeeCCCCeECCE
Confidence 4699999632 355699999976443
No 187
>PRK13500 transcriptional activator RhaR; Provisional
Probab=63.27 E-value=1.9e+02 Score=30.01 Aligned_cols=99 Identities=15% Similarity=0.101 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHH
Q 008401 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDT 197 (567)
Q Consensus 118 vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~ 197 (567)
+...+-||-- ....++++.++|+.+++++..|.+.|++. .| ..|..||.++ -...
T Consensus 208 l~~i~~yI~~-~~~e~isl~~lA~~~~iS~~~L~r~FK~~---tG----------~T~~~yi~~~-----------RL~~ 262 (312)
T PRK13500 208 LDKLITRLAA-SLKSPFALDKFCDEASCSERVLRQQFRQQ---TG----------MTINQYLRQV-----------RVCH 262 (312)
T ss_pred HHHHHHHHHH-cccCCCCHHHHHHHHCcCHHHHHHHHHHH---HC----------cCHHHHHHHH-----------HHHH
Confidence 3334444433 23457899999999999999888887754 22 3455565533 1112
Q ss_pred HHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHH-HHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 198 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA-TLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 198 A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~-TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
|.+++ ..-..|+.|||..+|-... ...+-+|... .+||.+|++.
T Consensus 263 A~~LL----------------------------~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~-----G~TP~~yRk~ 307 (312)
T PRK13500 263 AQYLL----------------------------QHSRLLISDISTECGFEDSNYFSVVFTRET-----GMTPSQWRHL 307 (312)
T ss_pred HHHHH----------------------------HcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 22221 1236788999999998655 6666666665 5888898765
No 188
>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=62.93 E-value=4.4 Score=34.24 Aligned_cols=31 Identities=19% Similarity=0.404 Sum_probs=17.4
Q ss_pred CCCCCCCC-C--ceeec--CCCceecCcccceeccc
Q 008401 3 WCSSCARH-V--TGHRP--YDSQLCCDRCGKVLEDH 33 (567)
Q Consensus 3 ~Cp~Cgs~-~--iv~D~--~~G~~VC~~CG~Vlee~ 33 (567)
.||.||.. . +.+|. ..|.+.|..||...+-.
T Consensus 24 ~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 24 DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp --TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 59999954 3 34444 36899999999987643
No 189
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=62.83 E-value=4.6 Score=30.10 Aligned_cols=25 Identities=24% Similarity=0.636 Sum_probs=18.6
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
.|..||... ..+ ..+.+-|..||.=
T Consensus 4 ~C~~Cg~~~-~~~-~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGREN-EIK-SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEe-ecC-CCCceECCCCCce
Confidence 599999863 233 4678999999963
No 190
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=62.70 E-value=32 Score=31.09 Aligned_cols=55 Identities=4% Similarity=0.038 Sum_probs=42.9
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 215 ~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
....|..+.-||-.... .+.++.+||+.+|+|+.++.+.+++.. .+|+.+|....
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~~-----G~s~~~~l~~~ 61 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKET-----GHSLGQYIRSR 61 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHH-----CcCHHHHHHHH
Confidence 34445556667766654 469999999999999999999999885 57888887553
No 191
>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=62.22 E-value=1.9e+02 Score=29.67 Aligned_cols=25 Identities=8% Similarity=0.076 Sum_probs=22.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...|++|||..+|+|..||++|+..
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~r 265 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVE 265 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999998864
No 192
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=62.21 E-value=15 Score=27.98 Aligned_cols=36 Identities=11% Similarity=0.181 Sum_probs=30.8
Q ss_pred hCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccc
Q 008401 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIAD 165 (567)
Q Consensus 130 e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~ 165 (567)
-+...+..++|..+||+..++.+.+..+...|....
T Consensus 16 LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 345678999999999999999999999999886543
No 193
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=61.98 E-value=4.6 Score=31.88 Aligned_cols=26 Identities=19% Similarity=0.520 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
|+.|++||...+ ---||..||+--+.
T Consensus 27 ~~~c~~cG~~~l------~Hrvc~~cg~Y~g~ 52 (57)
T COG0333 27 LSVCPNCGEYKL------PHRVCLKCGYYKGR 52 (57)
T ss_pred ceeccCCCCccc------CceEcCCCCCccCe
Confidence 457999998643 33499999975443
No 194
>PRK13502 transcriptional activator RhaR; Provisional
Probab=61.77 E-value=90 Score=31.61 Aligned_cols=101 Identities=12% Similarity=0.008 Sum_probs=64.6
Q ss_pred hHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHH
Q 008401 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVC 195 (567)
Q Consensus 116 ~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~ 195 (567)
..+..++-||.-.. ..+.++.++|..+++++..|.+.|++. .| ..|..||.+. -.
T Consensus 176 ~~~~~~~~~I~~~~-~~~~~~~~lA~~~~iS~~~L~r~fk~~---~G----------~t~~~yi~~~-----------Rl 230 (282)
T PRK13502 176 TLLDKLITALANSL-ECPFALDAFCQQEQCSERVLRQQFRAQ---TG----------MTINQYLRQV-----------RI 230 (282)
T ss_pred HHHHHHHHHHHhcc-cCCCCHHHHHHHHCcCHHHHHHHHHHH---HC----------cCHHHHHHHH-----------HH
Confidence 34556666666433 346888888888888888888777753 22 3355555432 11
Q ss_pred HHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHH-HHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 196 DTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA-TLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 196 ~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~-TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
..|.+ + +..-+.|+.|||..+|.+.. ...+.+|... .+||.+|++.
T Consensus 231 ~~A~~------------------------l----L~~t~~sI~eIA~~~GF~d~s~F~r~FKk~~-----G~tP~~yRk~ 277 (282)
T PRK13502 231 CHAQY------------------------L----LQHSPLMISEISMQCGFEDSNYFSVVFTRET-----GMTPSQWRHL 277 (282)
T ss_pred HHHHH------------------------H----HHcCCCCHHHHHHHcCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 11111 1 11236789999999998654 7777777775 6889999876
No 195
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=61.02 E-value=1.9e+02 Score=29.19 Aligned_cols=26 Identities=8% Similarity=0.049 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|+++||...|||..||+++.+..
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~a 249 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAA 249 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887643
No 196
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=60.58 E-value=15 Score=34.99 Aligned_cols=47 Identities=19% Similarity=0.230 Sum_probs=38.7
Q ss_pred chhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
+.+.-+.+++|+|-...+-|.++.+||+.++++...|.+....|.+.
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 44566778899995555679999999999999999999888888774
No 197
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=60.53 E-value=1e+02 Score=32.11 Aligned_cols=99 Identities=12% Similarity=0.137 Sum_probs=61.1
Q ss_pred HHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHH
Q 008401 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDT 197 (567)
Q Consensus 118 vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~ 197 (567)
+..+.-||-- .-..++++.++|..++++...|.+.|++. ++ ..|..|+.++ . ...
T Consensus 220 ~~~~~~~i~~-~~~~~~sl~~lA~~~~~S~~~l~r~fk~~---~g----------~s~~~~~~~~----R-------l~~ 274 (322)
T PRK09393 220 LGPLIDWMRA-HLAEPHTVASLAARAAMSPRTFLRRFEAA---TG----------MTPAEWLLRE----R-------LAR 274 (322)
T ss_pred HHHHHHHHHh-ccCCCCCHHHHHHHHCcCHHHHHHHHHHH---HC----------cCHHHHHHHH----H-------HHH
Confidence 4444444443 23457899999999999999888877754 33 3455555533 1 111
Q ss_pred HHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccC-HHHHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 198 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHIC-EATLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 198 A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vs-e~TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
|..++ ..-..++.+||..+|-+ .....+.++.+. .+||.+|++.
T Consensus 275 A~~lL----------------------------~~~~~~i~~IA~~~Gf~~~s~F~r~Fk~~~-----G~tP~~yr~~ 319 (322)
T PRK09393 275 ARDLL----------------------------ESSALSIDQIAERAGFGSEESLRHHFRRRA-----ATSPAAYRKR 319 (322)
T ss_pred HHHHH----------------------------HcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 22211 11245778888888874 467888887775 5677787754
No 198
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=60.36 E-value=9.8 Score=30.66 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=25.3
Q ss_pred HhcCCCCCHhhHHHHhccC-HHHHHHHHHHHHc
Q 008401 229 LTHGLKFSKSDIVKIVHIC-EATLMKRLIEFEN 260 (567)
Q Consensus 229 ~~~g~~~t~~eIa~vv~Vs-e~TIrkR~kE~~~ 260 (567)
.-+|+..|++||++.+|++ .+|+...++-|.+
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 3568999999999999996 9999999998853
No 199
>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=60.25 E-value=2.7 Score=32.25 Aligned_cols=29 Identities=17% Similarity=0.591 Sum_probs=21.9
Q ss_pred CCCCCCCCCCce-eecCCCceecCccccee
Q 008401 2 VWCSSCARHVTG-HRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~iv-~D~~~G~~VC~~CG~Vl 30 (567)
.+|++|+.-... -+....++-|..||+|-
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 379999986433 24456899999999983
No 200
>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=60.02 E-value=1.8e+02 Score=28.56 Aligned_cols=26 Identities=15% Similarity=0.143 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|+++||...|++..||++++...
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra 218 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRA 218 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46799999999999999999998654
No 201
>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=59.92 E-value=6.7 Score=25.51 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=15.2
Q ss_pred CCCCCCCCceeecCCCceecCcccc
Q 008401 4 CSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 4 Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
|..||.... .....-...|.+||.
T Consensus 1 C~sC~~~i~-~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIA-PREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCccc-CcccCceEeCCCCCC
Confidence 778887632 222244788999984
No 202
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=59.88 E-value=2.2e+02 Score=31.90 Aligned_cols=135 Identities=15% Similarity=0.138 Sum_probs=69.0
Q ss_pred CccHHHHHhhhccChHHHH-------------HHHHHHHHHhhccccccccccCCchhhHHHHHhhh----CCCCCHHHH
Q 008401 133 PFLLIDFSNYLNINVYELG-------------AVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL----LPGGNKKVC 195 (567)
Q Consensus 133 p~tL~Diad~~~v~v~~Lg-------------r~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L----~~~~~~~V~ 195 (567)
.++..++..+++......- .++..|.+.+ ....||..++.|+...+ ++...+...
T Consensus 229 ~It~e~V~~~l~~~~~~~i~~li~si~~~d~~~Al~~l~~ll--------~~Gedp~~i~r~l~~~~~edi~~a~~~~~~ 300 (472)
T PRK14962 229 KITLETVHEALGLIPIEVVRDYINAIFNGDVKRVFTVLDDVY--------YSGKDYEVLIQQAIEDLVEDLERERANDII 300 (472)
T ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHcCCHHHHHHHHHHHH--------HcCCCHHHHHHHHHHHHHHHccCCCchHHH
Confidence 4888888888875543221 1111122221 12467888888877666 232226666
Q ss_pred HHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHh-ccCHHHHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 196 DTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV-HICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 196 ~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv-~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
..+..+++....-++-.||.|.+=.+- +-++..+.....-.+.|.... .....|=.+-.++-.+....+.+++ |...
T Consensus 301 ~~~~~~~~~~~~i~~~e~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 378 (472)
T PRK14962 301 QVSRQLLNILREIKFAEEKRLVCKLGS-ASIATRFSSPNVQENDVEEKNDNSNVQQKEKKKEESKAKEEKQEDIE-FEKR 378 (472)
T ss_pred HHHHHHHHHHHHhCCcchHHHHHHHHH-HHHHHhCCChhHHHHHHHhhccccccccccchhhhccchhhhhhhhh-HHHH
Confidence 666667777776777888887665544 333443333322222332211 1111122233344444445556666 6666
Q ss_pred HHh
Q 008401 275 KKE 277 (567)
Q Consensus 275 ~~~ 277 (567)
+++
T Consensus 379 ~~~ 381 (472)
T PRK14962 379 FKE 381 (472)
T ss_pred HHH
Confidence 443
No 203
>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=59.59 E-value=6.9 Score=27.11 Aligned_cols=24 Identities=21% Similarity=0.494 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeecCCCceecCcccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
-.|+.||- ++|......+|..||.
T Consensus 2 ~~C~~CGy---~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGY---IYDGEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCC---EECCCcCCCcCcCCCC
Confidence 35888885 4565556778888886
No 204
>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=59.54 E-value=6 Score=27.51 Aligned_cols=24 Identities=25% Similarity=0.700 Sum_probs=16.3
Q ss_pred CCCCCCCCCceeecCCCceecCcccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
.|..||.... ......+-|..||.
T Consensus 2 ~C~~Cg~~~~--~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVE--LKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE---BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeE--cCCCCcEECCcCCC
Confidence 4889988743 33456788999995
No 205
>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=59.47 E-value=2.2e+02 Score=29.49 Aligned_cols=25 Identities=4% Similarity=0.078 Sum_probs=22.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...|.+|||..+|||..|||++...
T Consensus 268 ~~~Tl~EIa~~lgiS~erVrq~~~r 292 (298)
T TIGR02997 268 EPLTLAEIGRRLNLSRERVRQIEAK 292 (298)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5799999999999999999998753
No 206
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=59.45 E-value=23 Score=25.84 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=24.8
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
..++.+|+..++++..|+++.++.|..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 489999999999999999999998864
No 207
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=59.25 E-value=51 Score=36.97 Aligned_cols=190 Identities=14% Similarity=0.227 Sum_probs=101.1
Q ss_pred HHHHHHHH----hCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHH-------------------hCC-
Q 008401 77 DMRQMKNA----LNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ-------------------KSK- 132 (567)
Q Consensus 77 ~I~~ia~~----L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~-------------------e~~- 132 (567)
-+..++.. |+++ ...++.|..++..+.-.|+.- |+ ..=||.+=.+. +..
T Consensus 162 ~~~eia~~~~~~l~~~--~~~ve~vL~~iQ~leP~GVgA-Rd----L~ECL~lQL~~~~~~~~~~~~a~~il~~~le~La 234 (481)
T PRK12469 162 DLSELAEAADPELGLS--EQELEVALRLVQSLDPPGVAA-RD----LSECLLLQLDALPADTPALEEAKEIARHHLERLA 234 (481)
T ss_pred CHHHHHhccccccCCC--HHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHHhccCCCchHHHHHHHHHHHHHHHH
Confidence 45678888 9999 889999998888765454321 11 11122222221 111
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHHHhhccccccc----cccCCchhhHHHHHhhhC--C--------CCCHHHHH--
Q 008401 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNV----LKQVDPSIFLHKFTDRLL--P--------GGNKKVCD-- 196 (567)
Q Consensus 133 p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~----~~~vdP~~~I~Rf~~~L~--~--------~~~~~V~~-- 196 (567)
-+-+..|+..++++..+|..+.. +.+.|+-.+-..+ ...+-|..+|.+.-..+. + ..+..-..
T Consensus 235 ~~~~~~i~~~l~~~~~~l~~a~~-~Ir~L~P~Pg~~f~~~~~~yi~PDv~V~~~~~~~~V~lN~~~~P~l~in~~Y~~~l 313 (481)
T PRK12469 235 RRETAEIQRRIGCDQETLREACA-LVRRLDPRPGNHFGSARADYVVPDVIVRQVRGKWVVTINPAVLPRARIHRRYAELF 313 (481)
T ss_pred ccCHHHHHHHhCcCHHHHHHHHH-HHhCCCCCCcccccCCCCCccCCCEEEEEeCCEEEEEECCCCCceEEECHHHHHHH
Confidence 24556678888999999988765 4445542111011 113445555433211110 0 00110000
Q ss_pred ------HHHHHHHHhh-hccccC--CCChhHHHHHHHHHHHH-----hcCC----CCCHhhHHHHhccCHHHHHHHH-HH
Q 008401 197 ------TARDILASMK-RDWITT--GRKPSGLCGAALYVSAL-----THGL----KFSKSDIVKIVHICEATLMKRL-IE 257 (567)
Q Consensus 197 ------~A~~iv~~~~-~~~i~~--GR~P~~IaaAalylAa~-----~~g~----~~t~~eIa~vv~Vse~TIrkR~-kE 257 (567)
....|-+.+. -.|+.. -+|-.+|--.+-.|+-+ .+|. +.++++||..+|++++||.+.. .-
T Consensus 314 ~~~~~~~~~yl~~kl~~A~wli~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~~K 393 (481)
T PRK12469 314 AQSSGERRSPLNQQLQEARWLIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATGNK 393 (481)
T ss_pred HhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhcCc
Confidence 0011111111 123322 13444454444444442 2443 4799999999999999999887 34
Q ss_pred HHccCCCCCCHHHHHHh
Q 008401 258 FENTDSGSLTIEDFMAR 274 (567)
Q Consensus 258 ~~~t~s~~Lt~~ef~~~ 274 (567)
+..||-|-+-...|-+.
T Consensus 394 Y~~tp~GifeLK~FFs~ 410 (481)
T PRK12469 394 YMATPRGTFEFKHFFPR 410 (481)
T ss_pred eeecCCceEeHHHhhcc
Confidence 56788888888887665
No 208
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=59.21 E-value=12 Score=28.69 Aligned_cols=35 Identities=14% Similarity=0.198 Sum_probs=28.4
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 226 lAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
+.-...-...+..++|...||+++|+.+.+.++.+
T Consensus 11 l~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 11 LTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred HHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 33334457789999999999999999999998753
No 209
>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=59.01 E-value=3.7 Score=36.65 Aligned_cols=39 Identities=18% Similarity=0.289 Sum_probs=24.3
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceeccccccccccccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef~e 43 (567)
+.||+|+...-..- -..-|..|+.-|.=..--++-+|.+
T Consensus 70 V~CP~C~K~TKmLG---r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 70 VECPNCGKQTKMLG---RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred eECCCCCChHhhhc---hhhccCcCCCcCccCchhhcchhhH
Confidence 57999999742221 1248999999775333234556654
No 210
>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=58.77 E-value=20 Score=27.47 Aligned_cols=27 Identities=15% Similarity=0.363 Sum_probs=23.7
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
..|+.+|++.++++.+|+.+.++.|..
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 389999999999999999999998853
No 211
>PF14122 YokU: YokU-like protein
Probab=58.75 E-value=5.3 Score=33.98 Aligned_cols=22 Identities=27% Similarity=0.653 Sum_probs=17.0
Q ss_pred CceecCcccceecccccccccc
Q 008401 19 SQLCCDRCGKVLEDHNFSTEAT 40 (567)
Q Consensus 19 G~~VC~~CG~Vlee~~id~~~e 40 (567)
-.++|++||.|--+..+..+.+
T Consensus 34 P~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 34 PAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred ceeeecCCCcEEehhHHHHHHh
Confidence 4589999999988777766554
No 212
>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=58.56 E-value=2.7 Score=43.76 Aligned_cols=29 Identities=14% Similarity=0.432 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceeecCCCceecCccccee
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.+||.|+......|-.....||..||.-.
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 47999998755555556778999999864
No 213
>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=58.23 E-value=6.8 Score=31.64 Aligned_cols=27 Identities=19% Similarity=0.534 Sum_probs=17.9
Q ss_pred CCCCCCCCCceeec---CCC--------------ceecCcccce
Q 008401 3 WCSSCARHVTGHRP---YDS--------------QLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~---~~G--------------~~VC~~CG~V 29 (567)
.||.||+.....+. ..| .++|++||..
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 59999988554332 111 3579999986
No 214
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=58.14 E-value=2.9 Score=42.97 Aligned_cols=30 Identities=20% Similarity=0.515 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCceeecCCCceecCccccee
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
+.+||.|+.-...-|-.....||..||.-.
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCccc
Confidence 357999998654445567889999999854
No 215
>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=58.12 E-value=85 Score=29.87 Aligned_cols=109 Identities=15% Similarity=0.242 Sum_probs=60.1
Q ss_pred HHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhcccccc--------ccccCCc--hhhHHHHHhhhC
Q 008401 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESN--------VLKQVDP--SIFLHKFTDRLL 187 (567)
Q Consensus 118 vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~--------~~~~vdP--~~~I~Rf~~~L~ 187 (567)
++=|.||.+ +-|+++.+++++++ +...+......|.+.+.-..... +.-.+.| ..||.+|...-
T Consensus 2 ~iEAlLF~s----~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~~- 75 (159)
T PF04079_consen 2 IIEALLFAS----GEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKKP- 75 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCTC-
T ss_pred hhHhhHHHc----CCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccC-
Confidence 345677764 67999999999999 99999999999999884322220 1001111 22333332221
Q ss_pred CCCCHHHHHHHHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 188 PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 188 ~~~~~~V~~~A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
......+.|++. ||.-.+..++|..||..+-||.-..+=+.|.+.
T Consensus 76 --~~~~LS~aalEt------------------------LAiIAY~QPiTr~eIe~IRGv~s~~~i~~L~e~ 120 (159)
T PF04079_consen 76 --KPPKLSQAALET------------------------LAIIAYKQPITRAEIEEIRGVNSDSVIKTLLER 120 (159)
T ss_dssp --CCHHHHHHHHHH------------------------HHHHHHH-SEEHHHHHHHHTS--HCHHHHHHHT
T ss_pred --ccCCCCHHHHHH------------------------HHHHHhcCCcCHHHHHHHcCCChHHHHHHHHHC
Confidence 123333333332 333445689999999999999755444444443
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=57.81 E-value=13 Score=27.94 Aligned_cols=27 Identities=30% Similarity=0.324 Sum_probs=20.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
-...|.+|||...|+|+.||++++..-
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 467899999999999999999998653
No 217
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=57.74 E-value=2.9 Score=43.74 Aligned_cols=29 Identities=21% Similarity=0.530 Sum_probs=22.2
Q ss_pred CCCCCCCCCCceeecCCCceecCccccee
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.+||.|+......|-.....||..||.-.
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 47999998755555555677999999865
No 218
>PF14353 CpXC: CpXC protein
Probab=57.67 E-value=6.4 Score=35.65 Aligned_cols=29 Identities=21% Similarity=0.602 Sum_probs=19.1
Q ss_pred CCCCCCCCCC-c-ee---ecC----------CC---ceecCccccee
Q 008401 2 VWCSSCARHV-T-GH---RPY----------DS---QLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~-i-v~---D~~----------~G---~~VC~~CG~Vl 30 (567)
..||+||... + ++ |.. +| ..+|..||...
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 4799999872 1 22 211 22 67999999865
No 219
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=57.42 E-value=27 Score=27.52 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=30.6
Q ss_pred HHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 122 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 122 CLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
+||.... .+.+.+..|||..++|+.-++....++|.+.
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 3455554 7889999999999999999999999988763
No 220
>PRK13501 transcriptional activator RhaR; Provisional
Probab=57.19 E-value=2.3e+02 Score=28.89 Aligned_cols=88 Identities=17% Similarity=0.147 Sum_probs=57.3
Q ss_pred hCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhcc
Q 008401 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDW 209 (567)
Q Consensus 130 e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~ 209 (567)
...++++.++|+.++++...|.+.|++. +| ..|..||.+. .+..|.++
T Consensus 189 ~~e~~sl~~lA~~~~lS~~~l~r~Fk~~---~G----------~T~~qyi~~~-----------Ri~~A~~L-------- 236 (290)
T PRK13501 189 LGAYFDMADFCHKNQLVERSLKQLFRQQ---TG----------MSISHYLRQI-----------RLCHAKCL-------- 236 (290)
T ss_pred hccCCCHHHHHHHHCcCHHHHHHHHHHH---HC----------cCHHHHHHHH-----------HHHHHHHH--------
Confidence 4557888888888888888888877743 33 3345555432 11122221
Q ss_pred ccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCH-HHHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 210 ITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICE-ATLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 210 i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse-~TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
+..-..|+.+||..+|-+. +...+.+|... .+||.+|++.
T Consensus 237 --------------------L~~t~~sI~eIA~~~GF~~~s~F~r~FKk~~-----G~TP~~yR~~ 277 (290)
T PRK13501 237 --------------------LRGSEHRISDIAARCGFEDSNYFSAVFTREA-----GMTPRDYRQR 277 (290)
T ss_pred --------------------HHcCCCCHHHHHHHhCCCCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 1234567889999999844 46777777665 5889999876
No 221
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=57.15 E-value=6.9 Score=30.52 Aligned_cols=26 Identities=23% Similarity=0.652 Sum_probs=19.5
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.|+.||.... +.+.-+||..||++.-
T Consensus 7 ~C~~Cg~~~~---~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 7 KCPVCGKKFK---DGDDIVVCPECGAPYH 32 (54)
T ss_pred cChhhCCccc---CCCCEEECCCCCCccc
Confidence 6999998632 2346789999999753
No 222
>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=57.13 E-value=14 Score=27.35 Aligned_cols=26 Identities=23% Similarity=0.285 Sum_probs=23.5
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
..|.++||+..+++..||+++++.+.
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46999999999999999999998764
No 223
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=56.91 E-value=2.9 Score=43.68 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=22.9
Q ss_pred CCCCCCCCCCceeecCCCceecCccccee
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.+||.|+......+-.....||..||.-.
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 47999998765555567788999999854
No 224
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=56.85 E-value=21 Score=33.57 Aligned_cols=46 Identities=13% Similarity=0.108 Sum_probs=37.6
Q ss_pred chhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
+.+.-+-+++|+|- ..+.+.+..+||+..+++..-|.+.+..|.+.
T Consensus 6 ~~~YAlr~L~~LA~-~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 6 QTNYAIRMLMYCAA-NDGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHhHHHHHHHHHHh-CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34556668899994 35668899999999999999999988888774
No 225
>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=56.76 E-value=13 Score=30.96 Aligned_cols=38 Identities=24% Similarity=0.327 Sum_probs=28.1
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 223 alylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.+|+|..-.+...|.++||+..++++.++++-+..|..
T Consensus 14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKK 51 (83)
T ss_dssp HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 34554443334489999999999999999999998863
No 226
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=56.61 E-value=39 Score=32.24 Aligned_cols=30 Identities=13% Similarity=0.172 Sum_probs=27.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
++.|+.+||..+|++..|+.+-+++|.+..
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 177 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREG 177 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCC
Confidence 578999999999999999999999997654
No 227
>PHA02591 hypothetical protein; Provisional
Probab=56.33 E-value=14 Score=31.06 Aligned_cols=32 Identities=13% Similarity=0.118 Sum_probs=26.4
Q ss_pred HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 008401 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 225 ylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
-+|..+.....|+.+||..+||+..|+++-++
T Consensus 50 ~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 50 SVTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 34555666778999999999999999998765
No 228
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=56.29 E-value=56 Score=28.15 Aligned_cols=51 Identities=8% Similarity=0.111 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 219 LCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 219 IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
|.-+.-|+...+ ...+++.+||+.+|+|..++.+++++.. .+|+.+|....
T Consensus 7 ~~~~~~~i~~~~-~~~~~~~~lA~~~~~S~~~l~r~f~~~~-----g~s~~~~i~~~ 57 (107)
T PRK10219 7 IQTLIAWIDEHI-DQPLNIDVVAKKSGYSKWYLQRMFRTVT-----HQTLGDYIRQR 57 (107)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHHHHH
Confidence 334445555553 4569999999999999999999999874 67888887654
No 229
>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=56.19 E-value=14 Score=26.87 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=19.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
..=++.+.|...||+..|+.++++.+
T Consensus 17 ~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 17 CGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 34456789999999999999999863
No 230
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=56.00 E-value=7.1 Score=30.23 Aligned_cols=28 Identities=18% Similarity=0.414 Sum_probs=20.3
Q ss_pred CCCCCCCC-CceeecCCCce----ecCccccee
Q 008401 3 WCSSCARH-VTGHRPYDSQL----CCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~-~iv~D~~~G~~----VC~~CG~Vl 30 (567)
.||+||.. .+.+|...|.. =|.-|..=+
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence 69999998 67889887742 277776544
No 231
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=55.12 E-value=2.4e+02 Score=28.61 Aligned_cols=25 Identities=12% Similarity=0.213 Sum_probs=22.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...|.++||...|+|..||++++..
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~r 251 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTK 251 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5689999999999999999988754
No 232
>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=54.83 E-value=15 Score=28.48 Aligned_cols=28 Identities=14% Similarity=0.169 Sum_probs=25.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
-|..++.+.|+.+|||..+++++.+++.
T Consensus 13 ~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 13 YFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 3778999999999999999999999874
No 233
>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=54.73 E-value=34 Score=29.40 Aligned_cols=30 Identities=3% Similarity=0.134 Sum_probs=26.7
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
....+|+.+||..+|++..|+++-+++|..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456799999999999999999999998853
No 234
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=54.60 E-value=44 Score=32.83 Aligned_cols=31 Identities=19% Similarity=0.330 Sum_probs=27.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccCC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s 263 (567)
+++|+++||..+|++..|+.+-+++|....-
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~ 213 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSGM 213 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCCC
Confidence 5789999999999999999999999975443
No 235
>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=54.34 E-value=26 Score=25.81 Aligned_cols=35 Identities=23% Similarity=0.259 Sum_probs=26.6
Q ss_pred HHHHHHHHHhcCC-CCCHhhHHHHhccCHHHHHHHHH
Q 008401 221 GAALYVSALTHGL-KFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 221 aAalylAa~~~g~-~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
-|++-+..+ .|+ ..|+++|++.+||+..+|-+.+.
T Consensus 3 ~aa~~l~~~-~G~~~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 3 EAALELFAE-KGYEAVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHHH-HHTTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred HHHHHHHHH-hCHHhCCHHHHHHHHccchhhHHHHcC
Confidence 345555554 455 58999999999999999987764
No 236
>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=54.09 E-value=6.9 Score=29.62 Aligned_cols=26 Identities=23% Similarity=0.653 Sum_probs=17.7
Q ss_pred CCCCCCCC-Cceee-cCCCceecCcccc
Q 008401 3 WCSSCARH-VTGHR-PYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~-~iv~D-~~~G~~VC~~CG~ 28 (567)
+|+.||.. .+..- .+.+...|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 69999985 32211 2246778999998
No 237
>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=54.01 E-value=7 Score=39.56 Aligned_cols=29 Identities=14% Similarity=0.552 Sum_probs=11.4
Q ss_pred CCCCCCCCCCcee---ecCCCceecCccccee
Q 008401 2 VWCSSCARHVTGH---RPYDSQLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~---D~~~G~~VC~~CG~Vl 30 (567)
+.||+||+..+.. ..--.+..|.+|+--.
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EE
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHH
Confidence 4799999985422 1224788999998643
No 238
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.95 E-value=5.8 Score=35.67 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=15.0
Q ss_pred eecCCCceecCcccceec
Q 008401 14 HRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 14 ~D~~~G~~VC~~CG~Vle 31 (567)
.|-.+|+++|.+||+|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 455689999999999954
No 239
>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=53.77 E-value=16 Score=28.53 Aligned_cols=28 Identities=18% Similarity=0.275 Sum_probs=24.5
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
+-..+..++|...++|+.||++-+.++.
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3457999999999999999999999997
No 240
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=53.57 E-value=2.6e+02 Score=28.39 Aligned_cols=27 Identities=15% Similarity=0.086 Sum_probs=23.7
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
....|.+|||...|||..||++++...
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~~~ra 245 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQIHSKA 245 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899999999999999999997654
No 241
>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=53.45 E-value=42 Score=25.95 Aligned_cols=30 Identities=13% Similarity=0.246 Sum_probs=26.5
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 131 ~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
..+.+..|||+.++++...+.+.+..|.+.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 457899999999999999999988888774
No 242
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=53.45 E-value=15 Score=37.54 Aligned_cols=28 Identities=21% Similarity=0.221 Sum_probs=25.2
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
.-.+++.|+++.++||+.|||+.+++|.
T Consensus 17 ~~~v~v~eLa~~l~VS~~TIRRDL~~Le 44 (256)
T PRK10434 17 QGKTSVEELAQYFDTTGTTIRKDLVILE 44 (256)
T ss_pred cCCEEHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3468999999999999999999999875
No 243
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.45 E-value=10 Score=33.54 Aligned_cols=60 Identities=15% Similarity=0.084 Sum_probs=40.2
Q ss_pred cHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhh-HHHHHhhhC-CCCCHHHHHHHHHHH
Q 008401 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIF-LHKFTDRLL-PGGNKKVCDTARDIL 202 (567)
Q Consensus 135 tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~-I~Rf~~~L~-~~~~~~V~~~A~~iv 202 (567)
.|++|-..+|++-.+++.-+-.+.+.++.+... .+|... =..+.+.|. ++.+++ .|.+++
T Consensus 59 nlKEvEr~lg~sYptvR~kld~vlramgy~p~~-----e~~~~i~~~~i~~qle~Gei~pe---eA~~~L 120 (122)
T COG3877 59 NLKEVERELGISYPTVRTKLDEVLRAMGYNPDS-----ENSVNIGKKKIIDQLEKGEISPE---EAIKML 120 (122)
T ss_pred CHHHHHHHHCCccHHHHHHHHHHHHHcCCCCCC-----CChhhhhHHHHHHHHHcCCCCHH---HHHHHh
Confidence 478888889999999999999999999886543 444432 134566664 545544 444444
No 244
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=53.22 E-value=6.2 Score=42.98 Aligned_cols=30 Identities=20% Similarity=0.565 Sum_probs=23.6
Q ss_pred CCCCCCCC--C----ceeecCCCceecCcccceecc
Q 008401 3 WCSSCARH--V----TGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~--~----iv~D~~~G~~VC~~CG~Vlee 32 (567)
.||.|++. . -.+|..+|...|..||.=|.+
T Consensus 130 ~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 130 VCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred cCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 59999997 1 245678999999999986554
No 245
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=53.19 E-value=21 Score=34.27 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=23.2
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 235 FSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
.|..|||..+|||+.||++++.-++
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5999999999999999999998775
No 246
>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=53.02 E-value=33 Score=25.88 Aligned_cols=34 Identities=9% Similarity=0.072 Sum_probs=28.1
Q ss_pred HHhCCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008401 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (567)
Q Consensus 128 R~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L 161 (567)
..++-|++..+||+.++|+..+|.+....|...+
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 3456679999999999999999999999886655
No 247
>PRK08402 replication factor A; Reviewed
Probab=52.96 E-value=8.3 Score=41.48 Aligned_cols=26 Identities=27% Similarity=0.609 Sum_probs=21.1
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
.||.|+.. ++.|..+|...|..||.|
T Consensus 214 aCp~CnKk-v~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 214 ACPECRRK-VDYDPATDTWICPEHGEV 239 (355)
T ss_pred cCCCCCeE-EEEecCCCCEeCCCCCCc
Confidence 69999885 344667899999999975
No 248
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=52.93 E-value=26 Score=26.27 Aligned_cols=29 Identities=10% Similarity=0.276 Sum_probs=26.0
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
+-..|..+|+..++++..|+++.++.|.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56689999999999999999999999863
No 249
>PRK05978 hypothetical protein; Provisional
Probab=52.44 E-value=10 Score=35.71 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=20.3
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceec
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.+||+||...+-.-.-.=.--|..||.-++
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccc
Confidence 479999998652212223347999999766
No 250
>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=52.36 E-value=14 Score=29.34 Aligned_cols=37 Identities=19% Similarity=0.326 Sum_probs=29.9
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 223 alylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.+|++-. ..-..|..+|+..++++..|+.+.++.+.+
T Consensus 12 ~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 12 KVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4455443 446789999999999999999999998864
No 251
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=52.02 E-value=19 Score=25.82 Aligned_cols=27 Identities=7% Similarity=0.114 Sum_probs=20.3
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHH
Q 008401 131 SKPFLLIDFSNYLNINVYELGAVYLQL 157 (567)
Q Consensus 131 ~~p~tL~Diad~~~v~v~~Lgr~~~~L 157 (567)
..+.++.|||..++++...+.+.|++.
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 457899999999999999999888764
No 252
>PRK02935 hypothetical protein; Provisional
Probab=51.96 E-value=9.4 Score=33.74 Aligned_cols=39 Identities=21% Similarity=0.332 Sum_probs=23.9
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceeccccccccccccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef~e 43 (567)
+.||+|++..-.. .-...|..|+.-|.=..--++.+|.+
T Consensus 71 V~CP~C~K~TKmL---GrvD~CM~C~~PLTLd~~legkefde 109 (110)
T PRK02935 71 VICPSCEKPTKML---GRVDACMHCNQPLTLDRSLEGKEFDE 109 (110)
T ss_pred eECCCCCchhhhc---cceeecCcCCCcCCcCccccccCcCc
Confidence 4799999863211 12348999999875333334555543
No 253
>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=51.91 E-value=16 Score=31.74 Aligned_cols=29 Identities=14% Similarity=0.159 Sum_probs=24.8
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
..-..||++|++..|||.+||.+-=+.+.
T Consensus 52 l~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 52 LNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 34679999999999999999998777664
No 254
>PRK04217 hypothetical protein; Provisional
Probab=51.55 E-value=19 Score=32.18 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=23.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|+++||+..|||..||.+++....
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445999999999999999999998653
No 255
>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=51.33 E-value=31 Score=26.59 Aligned_cols=26 Identities=15% Similarity=0.390 Sum_probs=24.2
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 235 FSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.+..+|++.++++..||++.++.+..
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 99999999999999999999998853
No 256
>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=51.11 E-value=22 Score=30.01 Aligned_cols=23 Identities=17% Similarity=0.286 Sum_probs=21.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRL 255 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~ 255 (567)
-..|+++||+.+|||..||++.+
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHh
Confidence 56799999999999999999966
No 257
>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=50.96 E-value=8.4 Score=29.18 Aligned_cols=13 Identities=31% Similarity=0.723 Sum_probs=7.7
Q ss_pred eecCcccceeccc
Q 008401 21 LCCDRCGKVLEDH 33 (567)
Q Consensus 21 ~VC~~CG~Vlee~ 33 (567)
++|+.||.|.++.
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 3566666666554
No 258
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=50.45 E-value=34 Score=30.81 Aligned_cols=38 Identities=13% Similarity=0.164 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 223 alylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
.+|||. ..+-..|..+|+..++++..+++++++.+...
T Consensus 15 l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 15 LTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 445553 34557899999999999999999999999643
No 259
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=50.13 E-value=12 Score=38.43 Aligned_cols=30 Identities=13% Similarity=0.427 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceecc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
..||.||+.... ....-..+|..||.+.-.
T Consensus 100 ~fC~~CG~~~~~-~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 100 RFCGYCGHPMHP-SKTEWAMLCPHCRERYYP 129 (256)
T ss_pred ccccccCCCCee-cCCceeEECCCCCCEECC
Confidence 479999997433 334457899999987654
No 260
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.11 E-value=65 Score=28.65 Aligned_cols=25 Identities=24% Similarity=0.700 Sum_probs=20.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
.||.||...|+. ++-|.+||+-+..
T Consensus 8 ~cPvcg~~~iVT-----eL~c~~~etTVrg 32 (122)
T COG3877 8 RCPVCGRKLIVT-----ELKCSNCETTVRG 32 (122)
T ss_pred CCCcccccceeE-----EEecCCCCceEec
Confidence 699999987764 5789999998764
No 261
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=50.10 E-value=3e+02 Score=28.17 Aligned_cols=72 Identities=13% Similarity=0.191 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHhC--CCCc-hHHHHH-HHHHHHHHHhccccCCCchhHHHHHHH----HHHHHHhC---CCccHH
Q 008401 69 RLMEKAFDDMRQMKNALN--IGES-DEIVHV-AKRFYGIAVARNFTKGRRTEQVQASCL----YLACRQKS---KPFLLI 137 (567)
Q Consensus 69 r~l~~a~~~I~~ia~~L~--Lp~~-~~i~e~-A~~iyk~a~~~~~~rGR~~~~vaAACL----YiACR~e~---~p~tL~ 137 (567)
+.+..-...+..++.++. +|+. ++.+.. ..-+.+.+..-...+|.+..+.|.=|+ +-=+|.++ +|+.+.
T Consensus 27 ~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~~v~vpR~~~ 106 (247)
T COG1191 27 RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKNDSVKVPRSLR 106 (247)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCCCccCcHHHH
Confidence 455666677777777773 4411 344443 444555554556778888888887666 33366655 577776
Q ss_pred HHH
Q 008401 138 DFS 140 (567)
Q Consensus 138 Dia 140 (567)
+..
T Consensus 107 ~~~ 109 (247)
T COG1191 107 ELG 109 (247)
T ss_pred HHH
Confidence 654
No 262
>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=49.62 E-value=30 Score=24.78 Aligned_cols=27 Identities=26% Similarity=0.277 Sum_probs=23.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...++.+||...|++..||.+++....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 557999999999999999999987664
No 263
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=49.52 E-value=66 Score=31.82 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=27.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
++.|+++||..+|++..|+.+-+++|.+..
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~G 207 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDRG 207 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 568999999999999999999999997554
No 264
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=49.44 E-value=90 Score=30.55 Aligned_cols=120 Identities=18% Similarity=0.203 Sum_probs=62.9
Q ss_pred hHHHHHHHHHHHHHhCCC-ccHHHHHhhhccCh-HHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHH
Q 008401 116 EQVQASCLYLACRQKSKP-FLLIDFSNYLNINV-YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 193 (567)
Q Consensus 116 ~~vaAACLYiACR~e~~p-~tL~Diad~~~v~v-~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~ 193 (567)
..++=|.||++ |-| +++.+|+.+++++. ..+......|.+...-...+ .-|..+.+...+...++
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~g---------l~l~~~~~~y~l~tk~e 69 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAG---------IEIIKFGQSYSLVTKPA 69 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCC---------EEEEEECCEEEEEEhHH
Confidence 45667888877 788 99999999999884 35544444454443221111 01111111111101222
Q ss_pred HHHHHHHHHHHhhhccccCCCChhHHHHHHH-HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 194 VCDTARDILASMKRDWITTGRKPSGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 194 V~~~A~~iv~~~~~~~i~~GR~P~~IaaAal-ylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
......+++. ..+++ +--|++ -||...+..++|..+|..+-||.-..+=+.|.+.
T Consensus 70 ~~~~i~~~~~--------~~~~~--LS~aaLEtLAIIAY~QPITr~eIe~IRGv~s~~~l~~L~er 125 (186)
T TIGR00281 70 FADYIHRFLP--------AKLKN--LNSASLEVLAIIAYKQPITRARINEIRGVKSYQIVDDLVEK 125 (186)
T ss_pred HHHHHHHHhc--------ccccc--CCHHHHHHHHHHHHcCCcCHHHHHHHcCCCHHHHHHHHHHC
Confidence 2222222211 01111 222333 2444566789999999999999755555555443
No 265
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=49.25 E-value=4.1 Score=32.12 Aligned_cols=24 Identities=25% Similarity=0.863 Sum_probs=17.3
Q ss_pred CCCCCCCCCceeecCCCceecCc-ccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDR-CGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~-CG~Vle 31 (567)
.|+.||... ..|+.+|++ ||-+++
T Consensus 10 HC~VCg~aI-----p~de~~CSe~C~eil~ 34 (64)
T COG4068 10 HCVVCGKAI-----PPDEQVCSEECGEILN 34 (64)
T ss_pred cccccCCcC-----CCccchHHHHHHHHHH
Confidence 699998762 246778886 887765
No 266
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=49.18 E-value=9.7 Score=34.11 Aligned_cols=35 Identities=17% Similarity=0.466 Sum_probs=21.0
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceeccccccccccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef 41 (567)
.+|+.||.. +....-...|..||.. +-.+..|.++
T Consensus 71 ~~C~~Cg~~---~~~~~~~~~CP~Cgs~--~~~i~~G~El 105 (113)
T PRK12380 71 AWCWDCSQV---VEIHQHDAQCPHCHGE--RLRVDTGDSL 105 (113)
T ss_pred EEcccCCCE---EecCCcCccCcCCCCC--CcEEccCCeE
Confidence 379999964 2222344569999964 3345555554
No 267
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=48.88 E-value=3.1e+02 Score=27.97 Aligned_cols=27 Identities=15% Similarity=0.149 Sum_probs=23.5
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
....|+++||...|||..||++++...
T Consensus 229 ~~~~t~~EIA~~lgis~~~V~~~~~ra 255 (264)
T PRK07122 229 FESMTQTQIAERVGISQMHVSRLLAKT 255 (264)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899999999999999999987654
No 268
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=48.83 E-value=49 Score=29.82 Aligned_cols=42 Identities=10% Similarity=0.140 Sum_probs=31.4
Q ss_pred hhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHH
Q 008401 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (567)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L 157 (567)
...+..+.-||.-... -+.++.++|+.+++++..|.+.|++.
T Consensus 8 ~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445555556655543 47999999999999999998887755
No 269
>PF14502 HTH_41: Helix-turn-helix domain
Probab=48.63 E-value=19 Score=27.46 Aligned_cols=34 Identities=15% Similarity=0.123 Sum_probs=27.9
Q ss_pred CCC-CCHhhHHHHhccCHHHHHHHHHHHHccCCCC
Q 008401 232 GLK-FSKSDIVKIVHICEATLMKRLIEFENTDSGS 265 (567)
Q Consensus 232 g~~-~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~ 265 (567)
|.+ .|+.|.++.++|+..||++.++.+.+...-+
T Consensus 3 GdRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 3 GDRIPTISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred CcccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 344 3799999999999999999999997665533
No 270
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.58 E-value=24 Score=32.40 Aligned_cols=38 Identities=18% Similarity=0.377 Sum_probs=31.0
Q ss_pred HHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 222 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 222 AalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
+.||++..-.|...+.++||+..+|+..+|++-+..+.
T Consensus 13 ~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~ 50 (141)
T PRK11014 13 ALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLS 50 (141)
T ss_pred HHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 44566554456678999999999999999999999885
No 271
>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=48.37 E-value=21 Score=27.34 Aligned_cols=25 Identities=20% Similarity=0.343 Sum_probs=23.2
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 236 SKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
|+.+|+..++|+..||++.++.|.+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999964
No 272
>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=48.21 E-value=32 Score=30.81 Aligned_cols=45 Identities=20% Similarity=0.158 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHH
Q 008401 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (567)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~ 159 (567)
....+.+.+|++-...+.|.+..+||+.++++...+.+....|.+
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344556677777322345999999999999999999998888876
No 273
>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=48.12 E-value=21 Score=28.12 Aligned_cols=29 Identities=17% Similarity=0.313 Sum_probs=24.3
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 232 GLKF-SKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 232 g~~~-t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
|.++ |..+|++..+||..|+|+.|..|..
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHH
Confidence 5678 9999999999999999999998853
No 274
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=47.83 E-value=12 Score=34.44 Aligned_cols=30 Identities=20% Similarity=0.476 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCceeec---C--CCceecCcccceec
Q 008401 1 MVWCSSCARHVTGHRP---Y--DSQLCCDRCGKVLE 31 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~---~--~G~~VC~~CG~Vle 31 (567)
|..||.|++.. +.-. . .--..|..||.-..
T Consensus 30 ~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 30 KVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred cCcCCCCCccc-eeeECCccccccccccCCcCccee
Confidence 56899999987 2221 1 23578999998543
No 275
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=47.79 E-value=39 Score=27.20 Aligned_cols=36 Identities=11% Similarity=0.055 Sum_probs=28.5
Q ss_pred HHHHHhcCC-CCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 225 YVSALTHGL-KFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 225 ylAa~~~g~-~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
+..-.-+|- ..|..+||+.+|++..|+++.|..|.+
T Consensus 12 L~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 12 LEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred HHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 333334455 499999999999999999999998853
No 276
>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=47.65 E-value=12 Score=25.07 Aligned_cols=22 Identities=14% Similarity=0.492 Sum_probs=9.9
Q ss_pred CCCCCCCCCceeecCCCceecCc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDR 25 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~ 25 (567)
.||.||+..+ ....+-.+.|++
T Consensus 1 ~CP~C~s~l~-~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSKLV-REEGEVDIRCPN 22 (28)
T ss_dssp B-TTT--BEE-E-CCTTCEEE--
T ss_pred CcCCCCCEeE-cCCCCEeEECCC
Confidence 5999998743 333444667764
No 277
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=47.58 E-value=77 Score=31.09 Aligned_cols=32 Identities=16% Similarity=0.183 Sum_probs=27.6
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHHhhc
Q 008401 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (567)
Q Consensus 132 ~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i 163 (567)
.|+|..+||+.+|++...|.|..++|.+.=-|
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I 214 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSGML 214 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCCCE
Confidence 57899999999999999999999888775433
No 278
>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=47.51 E-value=12 Score=31.44 Aligned_cols=34 Identities=15% Similarity=0.208 Sum_probs=22.4
Q ss_pred HHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 224 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 224 lylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
|-+|..+...+-|++..|+++|||.+||-+=+.|
T Consensus 9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvte 42 (82)
T PF12116_consen 9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVTE 42 (82)
T ss_dssp HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHH
Confidence 3444445566889999999999999999865544
No 279
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=47.25 E-value=16 Score=38.71 Aligned_cols=46 Identities=9% Similarity=0.026 Sum_probs=37.9
Q ss_pred HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHH
Q 008401 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIED 270 (567)
Q Consensus 225 ylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~e 270 (567)
-+|...+-...||.|||+..|||..||.+-|++=++..-=+.+|..
T Consensus 20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~ 65 (318)
T PRK15418 20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINS 65 (318)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeC
Confidence 3555556778999999999999999999999998877776666654
No 280
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=47.24 E-value=61 Score=26.22 Aligned_cols=67 Identities=7% Similarity=0.179 Sum_probs=36.1
Q ss_pred HHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHH--hCCCccHHHHHhhhcc-ChHHHHHHHHHH
Q 008401 81 MKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ--KSKPFLLIDFSNYLNI-NVYELGAVYLQL 157 (567)
Q Consensus 81 ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~--e~~p~tL~Diad~~~v-~v~~Lgr~~~~L 157 (567)
+|+.|+++ .. .-.++|+......+. ..+...=+-.|++. .+...++.|||..+|. +...+.+.|++.
T Consensus 1 lA~~~~~s--~~---~l~~~f~~~~g~s~~-----~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~ 70 (81)
T PF12833_consen 1 LADELGMS--ER---YLSRIFKKETGMSFK-----QYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRY 70 (81)
T ss_dssp HHHHCTS---HH---HHHHHHHHHHSS-HH-----HHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHH
T ss_pred ChHHhCcC--HH---HHHHHHHHHHCcCHH-----HHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHH
Confidence 57788888 43 333455554443332 22333444445543 2467899999999995 466676666654
No 281
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=47.23 E-value=7.3 Score=32.93 Aligned_cols=30 Identities=27% Similarity=0.514 Sum_probs=24.4
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (567)
.|+.||...+ -..+-|-..|..|..|+.-.
T Consensus 38 ~CsfCGK~~v-KR~AvGiW~C~~C~kv~agg 67 (92)
T KOG0402|consen 38 TCSFCGKKTV-KRKAVGIWKCGSCKKVVAGG 67 (92)
T ss_pred hhhhcchhhh-hhhceeEEecCCccceeccc
Confidence 5999998753 45578999999999998754
No 282
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.20 E-value=11 Score=34.30 Aligned_cols=28 Identities=21% Similarity=0.485 Sum_probs=18.5
Q ss_pred CCCCCCCCCceee-cCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VC~~CG~Vle 31 (567)
.||+||..-+ +| .-.-.-.|..||.=+.
T Consensus 23 rCP~CGeGrL-F~gFLK~~p~C~aCG~dyg 51 (126)
T COG5349 23 RCPRCGEGRL-FRGFLKVVPACEACGLDYG 51 (126)
T ss_pred CCCCCCCchh-hhhhcccCchhhhcccccc
Confidence 6999998744 22 1122347999998655
No 283
>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=47.01 E-value=3.3e+02 Score=27.75 Aligned_cols=27 Identities=4% Similarity=-0.025 Sum_probs=22.9
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
+...|+++||...|||..||+++.+.-
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 347899999999999999999776543
No 284
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=46.98 E-value=1.6e+02 Score=32.62 Aligned_cols=51 Identities=14% Similarity=0.139 Sum_probs=41.5
Q ss_pred ccccCCCChhHHHHH---HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 208 DWITTGRKPSGLCGA---ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 208 ~~i~~GR~P~~IaaA---alylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
..|..++|-..|+-| |.|++-.+.+ .|..+|+..+|.+.+||..-++.+..
T Consensus 360 ~~l~s~~R~~~i~~aR~iamyl~r~~~~--~s~~~Ig~~fgr~hstV~~a~~~i~~ 413 (440)
T PRK14088 360 EEILSNSRNVKALLARRIGMYVAKNYLG--SSLRTIAEKFNRSHPVVVDSVKKVKD 413 (440)
T ss_pred HHHhCCCCCccccHHHHHHHHHHHHHhC--CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 445666666778888 9999977555 49999999999999999999888864
No 285
>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=46.98 E-value=19 Score=23.16 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=18.5
Q ss_pred CCCHhhHHHHhccCHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKR 254 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR 254 (567)
..+..+|+..++++..||.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 459999999999999999875
No 286
>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=46.78 E-value=20 Score=27.59 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...+.++||...+|++.||+.+.+.+.
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHH
Confidence 457899999999999999999998874
No 287
>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=46.28 E-value=21 Score=25.63 Aligned_cols=23 Identities=9% Similarity=0.260 Sum_probs=20.4
Q ss_pred CCHhhHHHHhccCHHHHHHHHHH
Q 008401 235 FSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
.|.+|+|+.+||+..||.+-+++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 47899999999999999998764
No 288
>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=46.24 E-value=41 Score=30.25 Aligned_cols=46 Identities=17% Similarity=0.195 Sum_probs=36.5
Q ss_pred chhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 114 ~~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
..+....+++|++- ..+-+.+..+||+.++++...+.+....|.+.
T Consensus 7 ~~~yal~~l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 7 LTDYATLVLTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HHhHHHHHHHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34556777888874 34568999999999999999999888887763
No 289
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=46.05 E-value=20 Score=32.26 Aligned_cols=25 Identities=20% Similarity=0.101 Sum_probs=23.0
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 235 FSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
=+++++++..|||=.|+|+||.++.
T Consensus 50 GnlKe~e~~lgiSYPTvR~rLd~ii 74 (113)
T PF09862_consen 50 GNLKEMEKELGISYPTVRNRLDKII 74 (113)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHH
Confidence 4799999999999999999999985
No 290
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=45.93 E-value=3.3e+02 Score=27.41 Aligned_cols=26 Identities=8% Similarity=0.033 Sum_probs=22.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|+++||..+|||..||++..+.-
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~~~ra 246 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRLEKAA 246 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887654
No 291
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=45.84 E-value=74 Score=32.41 Aligned_cols=14 Identities=14% Similarity=0.009 Sum_probs=9.8
Q ss_pred CCCceecCccccee
Q 008401 17 YDSQLCCDRCGKVL 30 (567)
Q Consensus 17 ~~G~~VC~~CG~Vl 30 (567)
..|++++-..|.+.
T Consensus 72 ~~g~~i~i~p~~~h 85 (290)
T PRK10572 72 RPGDLLLFPPGEIH 85 (290)
T ss_pred CCCCEEEECCCCce
Confidence 45777777777764
No 292
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=45.67 E-value=60 Score=31.55 Aligned_cols=26 Identities=27% Similarity=0.234 Sum_probs=22.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
-..|..+||+.+|||.+|+.+.+++.
T Consensus 171 ~g~s~~~iak~lgis~~Tv~r~~k~~ 196 (200)
T PRK13413 171 KGTSKSEIARKLGVSRTTLARFLKTR 196 (200)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHhc
Confidence 34699999999999999999998854
No 293
>PRK00118 putative DNA-binding protein; Validated
Probab=45.65 E-value=29 Score=30.73 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=24.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|.++||...|||.+||.+++....
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RAr 58 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTE 58 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 578999999999999999999988654
No 294
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=45.37 E-value=10 Score=37.45 Aligned_cols=29 Identities=34% Similarity=0.503 Sum_probs=20.5
Q ss_pred CCCCCCCCCCcee--ecCCCceecCccccee
Q 008401 2 VWCSSCARHVTGH--RPYDSQLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~--D~~~G~~VC~~CG~Vl 30 (567)
+.|+.|++.++.+ +...=.+.|..||..-
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 4699999985533 3233367899999863
No 295
>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=45.34 E-value=36 Score=26.46 Aligned_cols=32 Identities=16% Similarity=0.235 Sum_probs=27.5
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
..+-..|..+|++.++++.+|+..+++.+.+.
T Consensus 20 ~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 35678999999999999999999999999753
No 296
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=45.28 E-value=28 Score=35.38 Aligned_cols=28 Identities=11% Similarity=0.095 Sum_probs=25.5
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
+-.++++++++.++||+.|||+.+++|.
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le 44 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLD 44 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4568999999999999999999999885
No 297
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=45.20 E-value=10 Score=28.98 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=19.1
Q ss_pred CCCCCCCCCceeecCCCceecCcccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
.|-.||... ..|.....+.|..||.
T Consensus 8 ~C~~Cg~~~-~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGREV-ELDQETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCCee-ehhhccCceeCCCCCc
Confidence 588998863 4455677889999996
No 298
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=45.03 E-value=22 Score=32.55 Aligned_cols=28 Identities=25% Similarity=0.319 Sum_probs=25.1
Q ss_pred CCCC-CHhhHHHHhccCHHHHHHHHHHHH
Q 008401 232 GLKF-SKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 232 g~~~-t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
|.++ |+++.|...+|...|+++.|++|.
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE 60 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELE 60 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5664 799999999999999999999874
No 299
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=44.94 E-value=54 Score=32.30 Aligned_cols=30 Identities=10% Similarity=0.139 Sum_probs=26.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
+..|+.+||..+|+|..|+.+-+++|.+-.
T Consensus 168 ~~~t~~~lA~~lG~sretvsR~L~~L~~~G 197 (226)
T PRK10402 168 YHEKHTQAAEYLGVSYRHLLYVLAQFIQDG 197 (226)
T ss_pred ccchHHHHHHHHCCcHHHHHHHHHHHHHCC
Confidence 345899999999999999999999997654
No 300
>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=44.73 E-value=24 Score=25.18 Aligned_cols=22 Identities=14% Similarity=0.321 Sum_probs=19.7
Q ss_pred CHhhHHHHhccCHHHHHHHHHH
Q 008401 236 SKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE 257 (567)
|..|+|+.+||+..||++-.+.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 6789999999999999987765
No 301
>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=44.69 E-value=16 Score=28.00 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=8.0
Q ss_pred eecCcccceeccc
Q 008401 21 LCCDRCGKVLEDH 33 (567)
Q Consensus 21 ~VC~~CG~Vlee~ 33 (567)
.+|+.||.|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 4566667666653
No 302
>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=44.65 E-value=8.7 Score=29.87 Aligned_cols=29 Identities=28% Similarity=0.623 Sum_probs=19.3
Q ss_pred CCCCCCCCC-ceee--cCCCceecCcccceec
Q 008401 3 WCSSCARHV-TGHR--PYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~-iv~D--~~~G~~VC~~CG~Vle 31 (567)
.|.+|+.+. ..+. +..+..+|..||.-.-
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 488888873 3343 3367788888887653
No 303
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=44.16 E-value=17 Score=32.45 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=0.0
Q ss_pred CCCCCCCCceeecCC--------------CceecCccccee
Q 008401 4 CSSCARHVTGHRPYD--------------SQLCCDRCGKVL 30 (567)
Q Consensus 4 Cp~Cgs~~iv~D~~~--------------G~~VC~~CG~Vl 30 (567)
||.||+..+..+... ...+|..||-++
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
No 304
>PRK01381 Trp operon repressor; Provisional
Probab=44.01 E-value=18 Score=31.85 Aligned_cols=37 Identities=11% Similarity=0.072 Sum_probs=29.7
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 226 lAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
++..+..-..||++|+...|||.+||.+-=+.++..+
T Consensus 47 I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~ 83 (99)
T PRK01381 47 IVEELLRGELSQREIKQELGVGIATITRGSNSLKTAP 83 (99)
T ss_pred HHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCC
Confidence 3444455679999999999999999999988886433
No 305
>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=43.75 E-value=14 Score=27.75 Aligned_cols=27 Identities=19% Similarity=0.521 Sum_probs=18.6
Q ss_pred CCCCCCCCCceee-------cCCCceecCc--ccce
Q 008401 3 WCSSCARHVTGHR-------PYDSQLCCDR--CGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D-------~~~G~~VC~~--CG~V 29 (567)
+||+||+...+.- ..+-...|++ ||.-
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~t 36 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHT 36 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCE
Confidence 5999999754432 1245678988 9975
No 306
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=43.71 E-value=18 Score=28.02 Aligned_cols=29 Identities=21% Similarity=0.698 Sum_probs=19.8
Q ss_pred CCCC--CCCCCCcee-ecCCCceecCccccee
Q 008401 2 VWCS--SCARHVTGH-RPYDSQLCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp--~Cgs~~iv~-D~~~G~~VC~~CG~Vl 30 (567)
.+|| .|+...... +.....+.|..||...
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeE
Confidence 4799 897764433 2356788898898753
No 307
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=43.62 E-value=10 Score=37.20 Aligned_cols=34 Identities=26% Similarity=0.524 Sum_probs=22.4
Q ss_pred CCCCCCCCCCc----eee-cCCC-----ceecCcccceeccccc
Q 008401 2 VWCSSCARHVT----GHR-PYDS-----QLCCDRCGKVLEDHNF 35 (567)
Q Consensus 2 ~~Cp~Cgs~~i----v~D-~~~G-----~~VC~~CG~Vlee~~i 35 (567)
+.||.||++.. .+| |.-| .++|..||.=..|-..
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~ 58 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKT 58 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceee
Confidence 47999999622 122 3344 4689999997766444
No 308
>PF13518 HTH_28: Helix-turn-helix domain
Probab=43.55 E-value=35 Score=25.15 Aligned_cols=25 Identities=16% Similarity=0.323 Sum_probs=22.9
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 236 SKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
|+.+||..+|||..||.+-++.|..
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 9999999999999999988888864
No 309
>PF13551 HTH_29: Winged helix-turn helix
Probab=43.48 E-value=34 Score=29.28 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=24.5
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 236 SKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
|+.+||+.+||+..||.+-++.|....
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999999987554
No 310
>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=43.38 E-value=17 Score=32.03 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=23.4
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (567)
.|--|+..-.. ...+.+||.+||++..-..|
T Consensus 37 aCeiC~~~GY~--q~g~~lvC~~C~~~~~~~~i 67 (102)
T PF10080_consen 37 ACEICGPKGYY--QEGDQLVCKNCGVRFNLPTI 67 (102)
T ss_pred eccccCCCceE--EECCEEEEecCCCEEehhhc
Confidence 58899776543 45789999999999865433
No 311
>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=43.19 E-value=53 Score=25.10 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 120 ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 120 AACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
..+|++.....+...++.||++.++++...+.+..+.|.+.
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34555555555545899999999999999999988888764
No 312
>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=42.87 E-value=26 Score=26.24 Aligned_cols=20 Identities=10% Similarity=0.140 Sum_probs=17.3
Q ss_pred cHHHHHhhhccChHHHHHHH
Q 008401 135 LLIDFSNYLNINVYELGAVY 154 (567)
Q Consensus 135 tL~Diad~~~v~v~~Lgr~~ 154 (567)
|++|||..+||+..++.+++
T Consensus 1 Ti~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 68999999999999887654
No 313
>PRK06030 hypothetical protein; Provisional
Probab=42.83 E-value=76 Score=29.04 Aligned_cols=39 Identities=8% Similarity=0.100 Sum_probs=32.3
Q ss_pred HHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008401 121 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (567)
Q Consensus 121 ACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L 161 (567)
.++|++-...+ .+|.+|+..||-+..++..+++++.+.+
T Consensus 59 IAMYL~r~~~~--~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVSLG--WPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHcC--CCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 67888766644 5899999999999999999999777754
No 314
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=42.52 E-value=18 Score=25.90 Aligned_cols=18 Identities=17% Similarity=0.314 Sum_probs=14.9
Q ss_pred CHhhHHHHhccCHHHHHH
Q 008401 236 SKSDIVKIVHICEATLMK 253 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrk 253 (567)
|..|+|+.+||+..|||.
T Consensus 1 ti~e~A~~~gvs~~tlR~ 18 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRY 18 (38)
T ss_dssp EHHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 467999999999999984
No 315
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=42.45 E-value=40 Score=31.52 Aligned_cols=40 Identities=20% Similarity=0.117 Sum_probs=26.0
Q ss_pred hhHHHHHHHHHHHHhcC---CCCCHhhHHHHhccCHHHHHHHH
Q 008401 216 PSGLCGAALYVSALTHG---LKFSKSDIVKIVHICEATLMKRL 255 (567)
Q Consensus 216 P~~IaaAalylAa~~~g---~~~t~~eIa~vv~Vse~TIrkR~ 255 (567)
|.-+=||.|+.+-.++. -++|+.+||+-+||+++|+=+=-
T Consensus 13 ~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr 55 (142)
T PF13022_consen 13 LQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWR 55 (142)
T ss_dssp HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHH
Confidence 44455666666666664 46999999999999999996533
No 316
>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=42.27 E-value=18 Score=29.85 Aligned_cols=29 Identities=21% Similarity=0.323 Sum_probs=20.0
Q ss_pred CCCCCCCCCc-e--eecCCCceecCcccceec
Q 008401 3 WCSSCARHVT-G--HRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~i-v--~D~~~G~~VC~~CG~Vle 31 (567)
.||.|+.-.. . .+...-..-|..||..-.
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 7999999742 2 233345677999999743
No 317
>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=42.09 E-value=18 Score=33.38 Aligned_cols=28 Identities=29% Similarity=0.769 Sum_probs=19.7
Q ss_pred CCC--CCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCS--SCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp--~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
.|| .|++.. ..+ .+|.+.|..||..++.
T Consensus 20 aC~~~~C~kKv-~~~-~~~~y~C~~C~~~~~~ 49 (146)
T PF08646_consen 20 ACPNEKCNKKV-TEN-GDGSYRCEKCNKTVEN 49 (146)
T ss_dssp E-TSTTTS-B--EEE-TTTEEEETTTTEEESS
T ss_pred CCCCccCCCEe-ecC-CCcEEECCCCCCcCCC
Confidence 499 999873 333 5699999999998753
No 318
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=41.99 E-value=28 Score=25.13 Aligned_cols=30 Identities=20% Similarity=0.369 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeecCCC-ceecCc---ccceec
Q 008401 2 VWCSSCARHVTGHRPYDS-QLCCDR---CGKVLE 31 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G-~~VC~~---CG~Vle 31 (567)
..||.||+..+.-....| ++.|++ |.....
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKFLGCSNYPECKYTEP 35 (39)
T ss_pred cCCCCCCceeEEEECCCCCEEECCCCCCcCCeEe
Confidence 479999966554444444 678887 877654
No 319
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=41.90 E-value=2.5e+02 Score=30.39 Aligned_cols=133 Identities=17% Similarity=0.152 Sum_probs=79.8
Q ss_pred HHHHHHHHH-hCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCC--chhhHHHHHhhhCCCCCHHHHHH
Q 008401 121 SCLYLACRQ-KSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVD--PSIFLHKFTDRLLPGGNKKVCDT 197 (567)
Q Consensus 121 ACLYiACR~-e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vd--P~~~I~Rf~~~L~~~~~~~V~~~ 197 (567)
+|-+|+.+- +..+..+.+|.-.+. +-+....++......|..-.-. ++. ...|+.||...-.. -.-++...
T Consensus 185 s~m~I~sk~ee~~~~~~~ef~~itd-~ty~~~qv~~~~~~il~~l~~~----~~~pt~~~~l~~~~~~~~~-~~~~~e~~ 258 (359)
T KOG0654|consen 185 SAMLIASKYEEIKEPRVEEFCYITD-NTYTYWQVLRMEIDILNALTFE----LVRPTSKTFLRRFLRVAQT-PELQVEPL 258 (359)
T ss_pred ccceeeccchhhcchHHHHHHhhhh-hhhHHHHHHHHHHHHHHHhHHH----HhCchHHHHHHHHHHhhcc-hhHHHHHH
Confidence 455666664 344556666666554 3344555555554444321111 133 34677787443321 12344555
Q ss_pred HHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 198 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 198 A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
+..|..-..-+....--.|+-|||||+++|-..++..-=-.-+..-++++-.+++-.+..+-
T Consensus 259 ~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~ 320 (359)
T KOG0654|consen 259 ANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH 320 (359)
T ss_pred HHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence 55555544444455668999999999999988777433344567778888888888888775
No 320
>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=41.70 E-value=25 Score=31.89 Aligned_cols=26 Identities=15% Similarity=0.018 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|..|||..+|+|+.||++++.-.
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra 153 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKA 153 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46799999999999999999998754
No 321
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=41.66 E-value=37 Score=24.35 Aligned_cols=30 Identities=10% Similarity=0.136 Sum_probs=26.0
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 131 ~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
..|.+..|+|+.++++...+.+.++.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357899999999999999999888888763
No 322
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=41.46 E-value=1.5e+02 Score=35.44 Aligned_cols=57 Identities=26% Similarity=0.328 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHHHhCCCc
Q 008401 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF 134 (567)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p~ 134 (567)
.......|..|+++ ......|...|..+..+--.-| +-.++.|..||.+||..++|.
T Consensus 35 ~q~~~~~c~~lnld--~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~~ 91 (920)
T KOG1010|consen 35 EQDSDELCRPLNLD--EQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVPT 91 (920)
T ss_pred hhhhhhhhhhhccc--chhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCCc
Confidence 35567788999999 8999999999988776544444 467899999999999987653
No 323
>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=41.43 E-value=8.8 Score=41.25 Aligned_cols=79 Identities=14% Similarity=0.049 Sum_probs=0.0
Q ss_pred HHhhhCCCCCHHHHHHHHHHHHHhh-hccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 182 FTDRLLPGGNKKVCDTARDILASMK-RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 182 f~~~L~~~~~~~V~~~A~~iv~~~~-~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
++..+++..+++|+..|..|++... ...+..+-.=.+=+.+|+||||..++............++.....++-|..|.+
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 3445554456778888888887776 455666666677788999999999999888888888899999999988888865
No 324
>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=41.42 E-value=20 Score=28.46 Aligned_cols=27 Identities=22% Similarity=0.450 Sum_probs=18.1
Q ss_pred CCCCCCCCCc--eee-cCCCceecCcccce
Q 008401 3 WCSSCARHVT--GHR-PYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~i--v~D-~~~G~~VC~~CG~V 29 (567)
.||.|+.-.. .+. ...-..-|..||.-
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 7999998732 222 22234779999985
No 325
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=41.24 E-value=47 Score=24.64 Aligned_cols=31 Identities=13% Similarity=0.129 Sum_probs=26.0
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008401 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (567)
Q Consensus 131 ~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L 161 (567)
..+.|+.|||..+|++...+.+...+..+.|
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 5678999999999999999998888777665
No 326
>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=41.20 E-value=14 Score=26.99 Aligned_cols=26 Identities=23% Similarity=0.626 Sum_probs=17.2
Q ss_pred CCCCCCCC-Cceee-cCCCceecCcccc
Q 008401 3 WCSSCARH-VTGHR-PYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~-~iv~D-~~~G~~VC~~CG~ 28 (567)
.|+.||.. .+..- .+.....|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 59999975 22221 1246889999998
No 327
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=41.17 E-value=14 Score=33.18 Aligned_cols=34 Identities=15% Similarity=0.389 Sum_probs=19.6
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccccccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef 41 (567)
+|+.||.. +....-...|..||.. ...|..|.++
T Consensus 72 ~C~~Cg~~---~~~~~~~~~CP~Cgs~--~~~i~~G~El 105 (115)
T TIGR00100 72 ECEDCSEE---VSPEIDLYRCPKCHGI--MLQVRAGKEL 105 (115)
T ss_pred EcccCCCE---EecCCcCccCcCCcCC--CcEEecCCeE
Confidence 68999854 2222235679999864 2234455443
No 328
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=41.03 E-value=44 Score=27.14 Aligned_cols=31 Identities=10% Similarity=0.012 Sum_probs=29.2
Q ss_pred HhcCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 229 LTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 229 ~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
++.+..+|..+.|..+|+.+.||++.++.|.
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR 38 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFR 38 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6789999999999999999999999999986
No 329
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=40.98 E-value=19 Score=26.07 Aligned_cols=27 Identities=22% Similarity=0.482 Sum_probs=16.6
Q ss_pred CCCCCCCCCceeecC-CCceecCcccce
Q 008401 3 WCSSCARHVTGHRPY-DSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~-~G~~VC~~CG~V 29 (567)
.||.|+......... ---.+|..||=+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeE
Confidence 599999863222221 124469999876
No 330
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=40.70 E-value=2.2e+02 Score=30.43 Aligned_cols=84 Identities=13% Similarity=0.241 Sum_probs=0.0
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccC
Q 008401 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITT 212 (567)
Q Consensus 133 p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~ 212 (567)
|+++.++|+.++++...|-|.|++-.. ..|..|..++ =...|.+|+..
T Consensus 236 plsl~~LA~~~~~S~R~leRlF~~~lG-------------~sP~~yy~~l-----------RL~~Ar~LL~~-------- 283 (328)
T COG4977 236 PLSLEELADRAGLSRRQLERLFRAELG-------------VSPARYYLRL-----------RLERARRLLEQ-------- 283 (328)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHhC-------------CCHHHHHHHH-----------HHHHHHHHHHh--------
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhc-cCHHHHHHHHHHHHccCCCCCCHHHHHH
Q 008401 213 GRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH-ICEATLMKRLIEFENTDSGSLTIEDFMA 273 (567)
Q Consensus 213 GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~-Vse~TIrkR~kE~~~t~s~~Lt~~ef~~ 273 (567)
-+.++.+||..+| ++....++.|++.. .+++.+++.
T Consensus 284 --------------------t~~si~~IA~~~GF~sa~~fsr~fr~~f-----g~~P~~~R~ 320 (328)
T COG4977 284 --------------------TRLSIAEIAVACGFSSASHFSRAFRRQF-----GLSPSEYRR 320 (328)
T ss_pred --------------------CCCcHHHHHHHhCCCCHHHHHHHHHHHh-----CCChHHHHH
No 331
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=40.38 E-value=13 Score=29.60 Aligned_cols=27 Identities=4% Similarity=-0.162 Sum_probs=17.8
Q ss_pred CCCCCCCCCCceeecCCCceecCcccceeccccc
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (567)
+.|++||...+ ---||. ||+.-+..++
T Consensus 28 ~~c~~cg~~~~------pH~vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 28 SVDKTTGEYHL------PHHVSP-KGYYKGRKVL 54 (60)
T ss_pred eEcCCCCceec------cceecC-CcccCCeEee
Confidence 46899987532 334799 9977665444
No 332
>PRK08329 threonine synthase; Validated
Probab=40.26 E-value=18 Score=38.62 Aligned_cols=26 Identities=35% Similarity=0.737 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCceeecCCCceecCcccceec
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
|..|..||..- +.... ..| .||-.|+
T Consensus 1 ~l~C~~Cg~~~---~~~~~-~~C-~c~~~l~ 26 (347)
T PRK08329 1 MLRCTKCGRTY---EEKFK-LRC-DCGGTLL 26 (347)
T ss_pred CcCcCCCCCCc---CCCCc-eec-CCCCcEE
Confidence 88999999873 22223 789 7997765
No 333
>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=40.19 E-value=20 Score=25.92 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=7.6
Q ss_pred eecCccccee
Q 008401 21 LCCDRCGKVL 30 (567)
Q Consensus 21 ~VC~~CG~Vl 30 (567)
.+|..||-.+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3699999765
No 334
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=40.11 E-value=73 Score=26.30 Aligned_cols=28 Identities=7% Similarity=0.159 Sum_probs=25.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
-..|..+|+..++++.+|+++.++.|..
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999998853
No 335
>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=40.02 E-value=14 Score=38.41 Aligned_cols=30 Identities=23% Similarity=0.480 Sum_probs=13.2
Q ss_pred CCCCCCCCCC-c-eeecCC--C--ceecCcccceec
Q 008401 2 VWCSSCARHV-T-GHRPYD--S--QLCCDRCGKVLE 31 (567)
Q Consensus 2 ~~Cp~Cgs~~-i-v~D~~~--G--~~VC~~CG~Vle 31 (567)
.+||.||+.- + ++.... | .++|+-||+.=.
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~ 208 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR 208 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee
Confidence 3799999982 2 333322 5 789999998643
No 336
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=39.98 E-value=1.1e+02 Score=29.27 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=26.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
+++|+++||..+|++..|+.+-+++|..-.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 579999999999999999999999997543
No 337
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=39.94 E-value=44 Score=26.76 Aligned_cols=28 Identities=11% Similarity=0.045 Sum_probs=23.6
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
+.+++-+|||+.+++|..|+|.-|..+.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le 40 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLE 40 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5668999999999999999999999875
No 338
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=39.64 E-value=14 Score=29.24 Aligned_cols=32 Identities=22% Similarity=0.460 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCceeecCCCceecCcccceecccccccccccc
Q 008401 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFV 42 (567)
Q Consensus 1 M~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef~ 42 (567)
|..|+.||.-.+. -.|..||-+.- +..-+-|+
T Consensus 5 ~rkC~~cg~YTLk-------e~Cp~CG~~t~---~~~PprFS 36 (59)
T COG2260 5 IRKCPKCGRYTLK-------EKCPVCGGDTK---VPHPPRFS 36 (59)
T ss_pred hhcCcCCCceeec-------ccCCCCCCccc---cCCCCCCC
Confidence 4479999986442 38999998743 33344454
No 339
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.54 E-value=17 Score=33.66 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=6.8
Q ss_pred CceecCcccce
Q 008401 19 SQLCCDRCGKV 29 (567)
Q Consensus 19 G~~VC~~CG~V 29 (567)
....|..||..
T Consensus 106 ~~~~CP~Cgs~ 116 (135)
T PRK03824 106 AFLKCPKCGSR 116 (135)
T ss_pred cCcCCcCCCCC
Confidence 44557777753
No 340
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=39.40 E-value=55 Score=30.71 Aligned_cols=46 Identities=20% Similarity=0.171 Sum_probs=39.0
Q ss_pred hhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
.+..+=|.+|+|....+-|.++.+||...+++..-|.+.+..|.+.
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 3455667889998877669999999999999999999999888774
No 341
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=39.34 E-value=28 Score=32.99 Aligned_cols=25 Identities=20% Similarity=0.248 Sum_probs=22.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...|.+|||...|+|++||+.|+..
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~r 166 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQ 166 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5689999999999999999999863
No 342
>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=39.12 E-value=43 Score=25.22 Aligned_cols=30 Identities=17% Similarity=0.253 Sum_probs=24.9
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
++-..|+.||++.+|++.+|+.+-+..|.+
T Consensus 15 ~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 15 SGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp TBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344579999999999999999999998864
No 343
>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=38.88 E-value=13 Score=26.54 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=9.1
Q ss_pred CCCCCCCCCceeecCCCceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCC 23 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC 23 (567)
+|..||.-.-+.+...|.++|
T Consensus 8 kC~~CGniVev~~~g~g~lvC 28 (36)
T PF06397_consen 8 KCEHCGNIVEVVHDGGGPLVC 28 (36)
T ss_dssp E-TTT--EEEEEE--SS-EEE
T ss_pred EccCCCCEEEEEECCCCCEEe
Confidence 477777654445555666776
No 344
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=38.87 E-value=15 Score=33.94 Aligned_cols=27 Identities=19% Similarity=0.015 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|.+|||...|+++.||+.|+.--.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar 147 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRAR 147 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 568999999999999999999886543
No 345
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=38.79 E-value=21 Score=27.47 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=17.4
Q ss_pred CCCCCCCC-Cceeec-CCCc-eecCccccee
Q 008401 3 WCSSCARH-VTGHRP-YDSQ-LCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~-~iv~D~-~~G~-~VC~~CG~Vl 30 (567)
.|.+|+.. ...+.. ..|. .+|..||.-.
T Consensus 5 ~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 5 SCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 58888876 334432 3454 7888888743
No 346
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.47 E-value=19 Score=32.29 Aligned_cols=35 Identities=20% Similarity=0.460 Sum_probs=20.0
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccccccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef 41 (567)
+|+.||...... ......|..||.. +-.+..|.+|
T Consensus 72 ~C~~Cg~~~~~~--~~~~~~CP~Cgs~--~~~i~~G~El 106 (114)
T PRK03681 72 WCETCQQYVTLL--TQRVRRCPQCHGD--MLRIVADDGL 106 (114)
T ss_pred EcccCCCeeecC--CccCCcCcCcCCC--CcEEccCCeE
Confidence 799999642211 1233569999964 2345555544
No 347
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=38.45 E-value=89 Score=23.12 Aligned_cols=24 Identities=8% Similarity=0.110 Sum_probs=21.8
Q ss_pred ccHHHHHhhhccChHHHHHHHHHH
Q 008401 134 FLLIDFSNYLNINVYELGAVYLQL 157 (567)
Q Consensus 134 ~tL~Diad~~~v~v~~Lgr~~~~L 157 (567)
.++.+||..+|++..++.+.|...
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 799999999999999999988753
No 348
>PRK09526 lacI lac repressor; Reviewed
Probab=38.44 E-value=25 Score=36.40 Aligned_cols=44 Identities=18% Similarity=0.165 Sum_probs=30.1
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhHHhhh
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELH 279 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~~le 279 (567)
+.|++|||+.+|||.+|+++-|..- ..-+.-|.+.-+..+++|-
T Consensus 5 ~~ti~dIA~~aGVS~~TVSrvLn~~--~~vs~~tr~rV~~~a~elg 48 (342)
T PRK09526 5 PVTLYDVARYAGVSYQTVSRVLNQA--SHVSAKTREKVEAAMAELN 48 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhcCC--CCCCHHHHHHHHHHHHHHC
Confidence 5699999999999999999999742 1223334444555544443
No 349
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=38.22 E-value=21 Score=27.95 Aligned_cols=24 Identities=25% Similarity=0.751 Sum_probs=18.5
Q ss_pred CCCCCCCCCceeecCCCceecCccccee
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (567)
.||.|++.. ...-...|..||...
T Consensus 1 ~Cpv~~~~~----~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL----PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc----ccccCCcCCCCCCcC
Confidence 499999863 345677999999874
No 350
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.09 E-value=17 Score=42.20 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=17.0
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
.||+||... ..|...|.+||+-+..
T Consensus 29 ~Cp~CG~~~-----~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 29 PCPQCGTEV-----PVDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCCC-----CcccccccccCCcccc
Confidence 466666542 3577789999987654
No 351
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=38.03 E-value=1.6e+02 Score=25.52 Aligned_cols=25 Identities=20% Similarity=0.311 Sum_probs=21.6
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
.-.+...|+..||+..|++++++.+
T Consensus 68 ~gn~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 68 RGNQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 3457788999999999999999986
No 352
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=37.97 E-value=24 Score=36.23 Aligned_cols=24 Identities=21% Similarity=0.374 Sum_probs=21.7
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
+.|++|||+.+|||.+|+++-|..
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~ 24 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNN 24 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCC
Confidence 468999999999999999999963
No 353
>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=37.94 E-value=84 Score=22.95 Aligned_cols=29 Identities=10% Similarity=0.093 Sum_probs=23.1
Q ss_pred CCCccHHHHHhhhccChHHHHHHHHHHHH
Q 008401 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (567)
Q Consensus 131 ~~p~tL~Diad~~~v~v~~Lgr~~~~L~~ 159 (567)
+-+.+..|+|..++++...+.+.+++|.+
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 33489999999999999999998888865
No 354
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=37.92 E-value=69 Score=31.00 Aligned_cols=55 Identities=15% Similarity=0.204 Sum_probs=40.1
Q ss_pred HHHHHHHhhhccccCCCChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 198 ARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 198 A~~iv~~~~~~~i~~GR~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...+.+.|.+.++. +-.|..-|+|| +++-+.|..||+.++|+|.+.+..-++++.
T Consensus 12 Ie~fae~m~r~G~n---rtVG~iYgily----ls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~ 66 (177)
T COG1510 12 IEHFAETMSRWGIN---RTVGQIYGILY----LSRKPLTLDEIAEALGMSKSNVSMGLKKLQ 66 (177)
T ss_pred HHHHHHHHHHhCCc---chHHHHhhhhe----ecCCCccHHHHHHHHCCCcchHHHHHHHHH
Confidence 34455666665542 22344444555 678899999999999999999999999995
No 355
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=37.90 E-value=40 Score=26.25 Aligned_cols=31 Identities=26% Similarity=0.187 Sum_probs=24.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccCC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s 263 (567)
...+....|+..+|+..|++.|++.+.+.-.
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g 41 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELLG 41 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 3567888999999999999999999865443
No 356
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=37.79 E-value=75 Score=35.14 Aligned_cols=68 Identities=13% Similarity=0.151 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHHHHhccccCCCchhHHHHH---HHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008401 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQAS---CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (567)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAA---CLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L 161 (567)
+.|++....+|..-.+.=..++|+ ..++-| +.|++-+ -+..++.+|+..+|.+..++.++++++.+.+
T Consensus 345 ~~I~~~V~~~~~i~~~~l~s~~R~-~~i~~aR~iamyl~r~--~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 345 DELIEIVAKVTGVSREEILSNSRN-VKALLARRIGMYVAKN--YLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HHHHHHHHHHcCCcHHHHhCCCCC-ccccHHHHHHHHHHHH--HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 455566666664332221122333 344444 8888844 5566999999999999999999999998865
No 357
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=37.70 E-value=14 Score=34.96 Aligned_cols=28 Identities=18% Similarity=0.586 Sum_probs=15.6
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecccccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTE 38 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~ 38 (567)
.|..||...| .-|.+|++=+.....+.+
T Consensus 30 fC~kCG~~tI--------~~Cp~C~~~IrG~y~v~g 57 (158)
T PF10083_consen 30 FCSKCGAKTI--------TSCPNCSTPIRGDYHVEG 57 (158)
T ss_pred HHHHhhHHHH--------HHCcCCCCCCCCceecCC
Confidence 3666665433 157777776665544444
No 358
>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=37.70 E-value=31 Score=32.52 Aligned_cols=26 Identities=8% Similarity=0.092 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||..+|+++.||+.|+.--
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Ra 174 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFA 174 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56899999999999999999998643
No 359
>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=37.63 E-value=54 Score=32.07 Aligned_cols=27 Identities=11% Similarity=0.292 Sum_probs=25.0
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
..|+.+|+..++|+..|+++.|+.|..
T Consensus 15 ~~t~~eLA~~lgis~~tV~~~L~~Le~ 41 (203)
T TIGR02702 15 QATAAALAEALAISPQAVRRHLKDLET 41 (203)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 499999999999999999999999964
No 360
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=37.55 E-value=85 Score=30.86 Aligned_cols=46 Identities=20% Similarity=0.078 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
...-+|..|+........|.+..|||+.+|++..+|.|++++|.+.
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 3333444444322223456788999999999999999999999885
No 361
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=37.44 E-value=74 Score=25.51 Aligned_cols=35 Identities=11% Similarity=0.202 Sum_probs=26.8
Q ss_pred hCCCccHHHHHhhhccChHHHHHHHHHHHHHhhcc
Q 008401 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (567)
Q Consensus 130 e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~ 164 (567)
.+.|.+-.|||+.++++.+.+.+....|.+.=.+.
T Consensus 12 ~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 12 QNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 37899999999999999999988777776654444
No 362
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=37.43 E-value=55 Score=27.11 Aligned_cols=46 Identities=7% Similarity=0.213 Sum_probs=29.8
Q ss_pred HHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 226 lAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
+...+-....||+++|+.+||+.++|.+-. +-.....|++.+....
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~----~g~~~~~sl~~L~~~l 68 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLE----NGKIDDFSLDTLLRYL 68 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHH----TT-GCC--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHH----cCcccCCCHHHHHHHH
Confidence 455566678999999999999999997644 3344567888877664
No 363
>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=37.38 E-value=32 Score=25.00 Aligned_cols=23 Identities=13% Similarity=0.026 Sum_probs=19.2
Q ss_pred CHhhHHHHhccCHHHHHHHHHHH
Q 008401 236 SKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
|..++|+.+||+..||+.-.++-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 67899999999999999665444
No 364
>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=37.25 E-value=52 Score=25.25 Aligned_cols=33 Identities=9% Similarity=0.045 Sum_probs=27.9
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHHhhcc
Q 008401 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (567)
Q Consensus 132 ~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~ 164 (567)
...+..+||..++++..+|......+.+.|++.
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 356789999999999999999999999999875
No 365
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=37.20 E-value=20 Score=39.17 Aligned_cols=29 Identities=34% Similarity=0.693 Sum_probs=18.6
Q ss_pred CCCCCCCCCceee-cCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VC~~CG~Vle 31 (567)
.||+|+.-.-..+ ...+...|..||.++.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 4888886532222 2344678888888885
No 366
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=37.17 E-value=26 Score=36.19 Aligned_cols=24 Identities=17% Similarity=0.119 Sum_probs=22.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
-+.|++|||+.+|||.+|+++-|.
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln 28 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHC
Confidence 468999999999999999999986
No 367
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=36.86 E-value=1.4e+02 Score=28.43 Aligned_cols=29 Identities=10% Similarity=0.007 Sum_probs=26.4
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 132 ~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
.|++..+||+.+|++..++.|.+++|.+.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 48889999999999999999999988775
No 368
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=36.83 E-value=21 Score=27.50 Aligned_cols=28 Identities=21% Similarity=0.705 Sum_probs=14.0
Q ss_pred CCCCC--CCCCCceeecCCCc--eecCccccee
Q 008401 2 VWCSS--CARHVTGHRPYDSQ--LCCDRCGKVL 30 (567)
Q Consensus 2 ~~Cp~--Cgs~~iv~D~~~G~--~VC~~CG~Vl 30 (567)
.+||. |+.... .+..... +.|..||+..
T Consensus 19 ~~Cp~~~C~~~~~-~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIE-KDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---EC-S-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEE-ecCCCCCCeeECCCCCCcC
Confidence 47988 987633 3333333 8899999753
No 369
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=36.66 E-value=36 Score=30.41 Aligned_cols=39 Identities=23% Similarity=0.263 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhcCCC-CCHhhHHHHhccCHHHHHHHHHHH
Q 008401 219 LCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 219 IaaAalylAa~~~g~~-~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
|..+++.+... +|+. +|.++|++.+||+..||-+.++.-
T Consensus 17 ii~aa~~l~~~-~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K 56 (201)
T COG1309 17 ILDAALRLFAE-KGYAATTVDEIAKAAGVSKGTLYRHFPSK 56 (201)
T ss_pred HHHHHHHHHHH-cCcCCCCHHHHHHHhCCCcchhHHHcCCH
Confidence 44444444444 7876 899999999999999999888643
No 370
>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=36.63 E-value=49 Score=31.64 Aligned_cols=26 Identities=19% Similarity=0.367 Sum_probs=24.1
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 235 FSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.|+++|+..+++|..||.+.+++|.+
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e 101 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEE 101 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 68999999999999999999999864
No 371
>PRK09954 putative kinase; Provisional
Probab=36.60 E-value=45 Score=35.37 Aligned_cols=30 Identities=10% Similarity=0.329 Sum_probs=27.1
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.+-++|+.+|++.++||.+||++|++.|.+
T Consensus 14 ~~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 14 RNPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 345899999999999999999999999975
No 372
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.49 E-value=57 Score=25.16 Aligned_cols=40 Identities=15% Similarity=0.215 Sum_probs=25.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 276 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~~ 276 (567)
..+|+.++|+.+||+..||.+-++ -....++++.+.++++
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~----~~~~~~~~~~l~~ia~ 48 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILN----GKPSNPSLDTLEKIAK 48 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHT----TT-----HHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHh----cccccccHHHHHHHHH
Confidence 456999999999999999998776 2235788888888865
No 373
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=36.47 E-value=20 Score=28.81 Aligned_cols=22 Identities=27% Similarity=0.693 Sum_probs=14.0
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
.|.+|+.- . ....-+|..||.-
T Consensus 6 AC~~Ck~l---~--~~d~e~CP~Cgs~ 27 (64)
T COG2093 6 ACKNCKRL---T--PEDTEICPVCGST 27 (64)
T ss_pred HHhhcccc---C--CCCCccCCCCCCc
Confidence 58888763 1 1344588988863
No 374
>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=36.45 E-value=17 Score=35.96 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=21.7
Q ss_pred CCCCCCCCCC--ceeecCCC---ceecCcccceecc
Q 008401 2 VWCSSCARHV--TGHRPYDS---QLCCDRCGKVLED 32 (567)
Q Consensus 2 ~~Cp~Cgs~~--iv~D~~~G---~~VC~~CG~Vlee 32 (567)
+.|-+||... +-.+...| -..|.+||.|.|.
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDk 36 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADK 36 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCcccc
Confidence 4699999983 22233333 3789999999975
No 375
>PHA00542 putative Cro-like protein
Probab=36.43 E-value=29 Score=29.09 Aligned_cols=42 Identities=7% Similarity=0.018 Sum_probs=29.1
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
+.....|+.++|+.+||+..||.+-...-. ...+++...++.
T Consensus 27 l~~~glTq~elA~~lgIs~~tIsr~e~g~~----~~p~~~~l~ki~ 68 (82)
T PHA00542 27 LIRAGWSQEQIADATDVSQPTICRIYSGRH----KDPRYSVVEKLR 68 (82)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHcCCC----CCCCHHHHHHHH
Confidence 334568999999999999999998765432 123445555554
No 376
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=36.23 E-value=87 Score=36.29 Aligned_cols=71 Identities=13% Similarity=0.163 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHHHHhccccCCCchhHHHH--HHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhc
Q 008401 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (567)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA--ACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i 163 (567)
+.|++....+|..-.+.=..++|+...+.| .|+|++-.. +..+|.+|...||-+..+|..++++|.+.+.-
T Consensus 527 d~I~~~Va~~f~v~~~dl~s~~R~~~i~~aRqiAMYL~r~l--t~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 527 AAIMAATADYFGLTVEDLCGTSRSRVLVTARQIAMYLCREL--TDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred HHHHHHHHHHhCCCHHHHhCCCCCcccchHHHHHHHHHHHH--cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 344444444444333221223344333444 677877554 45678999999999999999999999987754
No 377
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=36.18 E-value=8.8 Score=34.31 Aligned_cols=34 Identities=24% Similarity=0.666 Sum_probs=18.5
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccccccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef 41 (567)
+|+.||.. +........|..||.- +-.|.+|.++
T Consensus 72 ~C~~Cg~~---~~~~~~~~~CP~Cgs~--~~~i~~G~el 105 (113)
T PF01155_consen 72 RCRDCGHE---FEPDEFDFSCPRCGSP--DVEIISGREL 105 (113)
T ss_dssp EETTTS-E---EECHHCCHH-SSSSSS---EEEEESS-E
T ss_pred ECCCCCCE---EecCCCCCCCcCCcCC--CcEEccCCeE
Confidence 69999875 3333344779999985 2234455443
No 378
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=36.14 E-value=50 Score=32.61 Aligned_cols=25 Identities=28% Similarity=0.328 Sum_probs=22.5
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
+++.+|||+..|||.+|+..+|+.-
T Consensus 178 ~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 178 RVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4689999999999999999999854
No 379
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=36.09 E-value=32 Score=27.71 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=25.0
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 235 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
.|++|||+.+|||..||.+-+.. ...++.+-...+
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~-----~~~v~~~t~~~i 35 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG-----NGRVSEETREKV 35 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC-----CCCCCHHHHHHH
Confidence 37899999999999999986642 233455544444
No 380
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=36.08 E-value=84 Score=25.25 Aligned_cols=38 Identities=11% Similarity=0.102 Sum_probs=29.0
Q ss_pred HHHHHHHhCC-CccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 123 LYLACRQKSK-PFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 123 LYiACR~e~~-p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
|+...+..|- ++++.|||..+|++...+.+....|.+.
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 3444455565 4999999999999999988877777664
No 381
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=36.06 E-value=1e+02 Score=29.83 Aligned_cols=120 Identities=12% Similarity=0.180 Sum_probs=68.9
Q ss_pred HHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCCCh
Q 008401 137 IDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKP 216 (567)
Q Consensus 137 ~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR~P 216 (567)
+.+|+.+|.....-|..|+.+.+..+++... +.+++..=. +....+=+....+++ ..+-++.||--
T Consensus 18 ~~lAe~~gl~~vsaG~iFR~~A~e~gmsl~e-----------f~~~AE~~p-~iD~~iD~rq~e~a~--~~nvVlegrLA 83 (179)
T COG1102 18 RELAEHLGLKLVSAGTIFREMARERGMSLEE-----------FSRYAEEDP-EIDKEIDRRQKELAK--EGNVVLEGRLA 83 (179)
T ss_pred HHHHHHhCCceeeccHHHHHHHHHcCCCHHH-----------HHHHHhcCc-hhhHHHHHHHHHHHH--cCCeEEhhhhH
Confidence 6789999999999999999999999875432 222332221 112333334444444 34555566643
Q ss_pred hHHHH----HHHHHHH-------Hhc-CCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHH
Q 008401 217 SGLCG----AALYVSA-------LTH-GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIED 270 (567)
Q Consensus 217 ~~Iaa----AalylAa-------~~~-g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~e 270 (567)
.=|+. -.|||-| |.. -..+++.++...+-.-|..=++||++|+...-..||+=+
T Consensus 84 ~Wi~k~~adlkI~L~Apl~vRa~Ria~REgi~~~~a~~~~~~RE~se~kRY~~~YgIDidDlSiyD 149 (179)
T COG1102 84 GWIVREYADLKIWLKAPLEVRAERIAKREGIDVDEALAETVEREESEKKRYKKIYGIDIDDLSIYD 149 (179)
T ss_pred HHHhccccceEEEEeCcHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHhCCCCccceeeE
Confidence 33332 1122211 111 123555555555555566667999999988777776644
No 382
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=36.05 E-value=36 Score=34.44 Aligned_cols=28 Identities=11% Similarity=0.322 Sum_probs=25.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
-.+++.|+++.++||+.|||+-+++|..
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4789999999999999999999999864
No 383
>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=35.90 E-value=25 Score=39.61 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=21.4
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.||+|+... .+....+.+.|..||....
T Consensus 224 ~C~~C~~~l-~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 224 CCPNCDVSL-TYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCCce-EEecCCCeEEcCCCcCcCC
Confidence 689998764 4444678999999998754
No 384
>PRK10870 transcriptional repressor MprA; Provisional
Probab=35.87 E-value=2.1e+02 Score=27.37 Aligned_cols=28 Identities=11% Similarity=0.064 Sum_probs=25.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
+..+|+.+|+...+++.+|+.+.++.+.
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe 96 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELE 96 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5568999999999999999999999885
No 385
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=35.79 E-value=34 Score=31.96 Aligned_cols=26 Identities=27% Similarity=0.186 Sum_probs=22.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||...|+++.||+.|+.--
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra 158 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYA 158 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999887543
No 386
>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=35.59 E-value=35 Score=25.50 Aligned_cols=39 Identities=8% Similarity=0.108 Sum_probs=28.0
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
....|++++|..+||+..||.+-.+. ....+++....++
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g-----~~~~~~~~~~~ia 45 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG-----KRNPSLDTLKKIA 45 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT-----SSTSBHHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC-----CCCCCHHHHHHHH
Confidence 35689999999999999999987765 3356666665554
No 387
>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=35.49 E-value=28 Score=33.22 Aligned_cols=24 Identities=17% Similarity=0.300 Sum_probs=0.0
Q ss_pred CCccHHHHHhhhccChHHHHHHHH
Q 008401 132 KPFLLIDFSNYLNINVYELGAVYL 155 (567)
Q Consensus 132 ~p~tL~Diad~~~v~v~~Lgr~~~ 155 (567)
.|.++.|||+.+|+++.+|.|+..
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ------------------------
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHc
Confidence 489999999999999999988765
No 388
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=35.48 E-value=1.5e+02 Score=28.10 Aligned_cols=30 Identities=7% Similarity=-0.199 Sum_probs=27.2
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008401 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (567)
Q Consensus 132 ~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L 161 (567)
.|+|..+||+.+|++..++.|.+++|.+.=
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 177 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREG 177 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCC
Confidence 588999999999999999999999998753
No 389
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=35.47 E-value=50 Score=31.17 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=23.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|.+|||...|+++.||+.++..-.
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 456999999999999999999987654
No 390
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=35.45 E-value=14 Score=28.44 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=19.1
Q ss_pred CCCCCCCCCcee---ecCCCceecCccccee
Q 008401 3 WCSSCARHVTGH---RPYDSQLCCDRCGKVL 30 (567)
Q Consensus 3 ~Cp~Cgs~~iv~---D~~~G~~VC~~CG~Vl 30 (567)
.|+-||...-.+ .-.+| +||.+|--=+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 499999873222 35678 7999998544
No 391
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=35.43 E-value=36 Score=31.21 Aligned_cols=26 Identities=4% Similarity=0.014 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||...|++..||+.|+..-
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra 146 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRA 146 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56889999999999999999998654
No 392
>PF12728 HTH_17: Helix-turn-helix domain
Probab=35.25 E-value=38 Score=25.14 Aligned_cols=22 Identities=9% Similarity=0.297 Sum_probs=19.1
Q ss_pred CCHhhHHHHhccCHHHHHHHHH
Q 008401 235 FSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~k 256 (567)
.|++|+|..+|||..||.+-.+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999987654
No 393
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=35.19 E-value=63 Score=29.46 Aligned_cols=40 Identities=15% Similarity=0.075 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 222 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 222 AalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
+.+|||.+-.+..+|.++|+...+++...+++-+..+...
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5667776544456899999999999999999999988643
No 394
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=35.18 E-value=31 Score=32.71 Aligned_cols=25 Identities=16% Similarity=0.256 Sum_probs=23.2
Q ss_pred CCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 235 FSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
.++..||.++|+...||++|++++.
T Consensus 2 ~nI~qlA~~~g~~R~TV~~RL~~~~ 26 (152)
T PF07278_consen 2 WNINQLAEAFGLHRQTVAKRLKGAN 26 (152)
T ss_pred CCHHHHHHHHcccHHHHHHHHccCC
Confidence 5778899999999999999999997
No 395
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.90 E-value=23 Score=42.60 Aligned_cols=8 Identities=38% Similarity=1.070 Sum_probs=4.3
Q ss_pred CCCCCCCC
Q 008401 3 WCSSCARH 10 (567)
Q Consensus 3 ~Cp~Cgs~ 10 (567)
.||.||..
T Consensus 628 fCpsCG~~ 635 (1121)
T PRK04023 628 KCPSCGKE 635 (1121)
T ss_pred cCCCCCCc
Confidence 45555554
No 396
>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=34.88 E-value=25 Score=33.13 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.||.|++... +...|.+.|..|+..++
T Consensus 36 aC~~C~kkv~--~~~~~~~~C~~C~~~~~ 62 (166)
T cd04476 36 ACPGCNKKVV--EEGNGTYRCEKCNKSVP 62 (166)
T ss_pred cccccCcccE--eCCCCcEECCCCCCcCC
Confidence 5999999732 22348999999999874
No 397
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.82 E-value=37 Score=30.87 Aligned_cols=26 Identities=4% Similarity=-0.143 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||...|++..||++++..-
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra 146 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQA 146 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998643
No 398
>PRK09492 treR trehalose repressor; Provisional
Probab=34.81 E-value=27 Score=35.70 Aligned_cols=23 Identities=22% Similarity=0.361 Sum_probs=21.6
Q ss_pred CCCHhhHHHHhccCHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
+.|++|||+.+|||.+|+++-|.
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn 26 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhC
Confidence 57999999999999999999996
No 399
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=34.47 E-value=38 Score=31.68 Aligned_cols=26 Identities=8% Similarity=0.115 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||..+|+++.||+.++..-
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra 158 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEA 158 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998643
No 400
>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=34.13 E-value=44 Score=27.81 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=24.5
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 230 THGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
+.+..+++.++|....||.+||.+.++.+.
T Consensus 26 l~~~~~s~~~la~~~~iS~sti~~~i~~l~ 55 (87)
T PF05043_consen 26 LNNEYVSIEDLAEELFISRSTIYRDIKKLN 55 (87)
T ss_dssp HH-SEEEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred HcCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 357789999999999999999999999885
No 401
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=33.94 E-value=39 Score=31.68 Aligned_cols=25 Identities=8% Similarity=0.155 Sum_probs=22.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...|.+|||..+|+++.||+.++.-
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999999853
No 402
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=33.91 E-value=2.3e+02 Score=27.68 Aligned_cols=120 Identities=15% Similarity=0.191 Sum_probs=67.6
Q ss_pred hHHHHHHHHHHHHHhCCCccHHHHHhhhcc-ChHHHHHHHHHHHHHhhccccccccccCCchhhHHHHHhhhCCCCCHHH
Q 008401 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKV 194 (567)
Q Consensus 116 ~~vaAACLYiACR~e~~p~tL~Diad~~~v-~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf~~~L~~~~~~~V 194 (567)
..++.|.||. .+.|+++.+++.++++ +...+......|.....-. . +. |..+.....+ .+...
T Consensus 10 ~~~vEall~a----~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~r--g-----~~----L~~~~~~~r~-~t~~~ 73 (184)
T COG1386 10 KALIEALLFA----GGEPLSLKELAEILGIVSADAIIDALAELKEEYEDR--G-----LE----LVEVAEGWRL-QTKQE 73 (184)
T ss_pred HHHHHHHHHh----cCCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCC--C-----ee----EEEEcCceeE-EehHH
Confidence 4456666664 3789999999999998 6666666666665554211 0 00 1111111110 01111
Q ss_pred HHHHHHHHHHhhhccccCCCChhHHHHHHH-HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 195 CDTARDILASMKRDWITTGRKPSGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 195 ~~~A~~iv~~~~~~~i~~GR~P~~IaaAal-ylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
.-..+..+ +-..-+ ..+--|++ -||...+..++|..+|..+-||....+-+.|.+..
T Consensus 74 ---~~~~~~~l---~~~~~~--~~LSraalEtLAiIAY~QPiTR~eI~~iRGv~~~~~i~~L~e~g 131 (184)
T COG1386 74 ---YAEYLEKL---QEQRPK--RELSRAALETLAIIAYKQPVTRSEIEEIRGVAVSQVISTLLERG 131 (184)
T ss_pred ---HHHHHHHH---hccccc--ccccHHHHHHHHHHHHcCCccHHHHHHHhCccHHHHHHHHHHCC
Confidence 11111211 111111 22333333 46667778999999999999999988888887763
No 403
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=33.87 E-value=24 Score=38.86 Aligned_cols=30 Identities=30% Similarity=0.615 Sum_probs=19.9
Q ss_pred CCCCCCCCCceee-cCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VC~~CG~Vlee 32 (567)
.||+|+.-.-..+ ...+...|..||.+|..
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 4999987532222 22346789999999853
No 404
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=33.87 E-value=36 Score=35.21 Aligned_cols=22 Identities=14% Similarity=0.151 Sum_probs=20.7
Q ss_pred CCHhhHHHHhccCHHHHHHHHH
Q 008401 235 FSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~k 256 (567)
.|++|||+.+|||.+|+++-|+
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 5899999999999999999996
No 405
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.76 E-value=19 Score=32.40 Aligned_cols=35 Identities=11% Similarity=0.309 Sum_probs=19.6
Q ss_pred CCCCCCCCCceeecCCCceecCcccceeccccccccccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~ef 41 (567)
+|+.||.... .+ ..+...|..||.- +-.|..|.++
T Consensus 73 ~C~~Cg~~~~-~~-~~~~~~CP~Cgs~--~~~i~~G~El 107 (117)
T PRK00564 73 ECKDCSHVFK-PN-ALDYGVCEKCHSK--NVIITQGNEM 107 (117)
T ss_pred EhhhCCCccc-cC-CccCCcCcCCCCC--ceEEecCCEE
Confidence 6899985421 11 1244469999964 2334555444
No 406
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=33.63 E-value=72 Score=29.31 Aligned_cols=39 Identities=13% Similarity=0.285 Sum_probs=31.9
Q ss_pred HHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 224 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 224 lylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
+|++-.-.+-+.|+.+||+.++.+.+|+.+.++-+.+..
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~G 70 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAG 70 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcC
Confidence 455554356789999999999999999999999886444
No 407
>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=33.52 E-value=41 Score=26.36 Aligned_cols=23 Identities=9% Similarity=0.180 Sum_probs=20.0
Q ss_pred CHhhHHHHhccCHHHHHHHHHHH
Q 008401 236 SKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
|..|||+.+||+..||++-.+++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 67899999999999999876654
No 408
>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=33.45 E-value=38 Score=32.38 Aligned_cols=27 Identities=26% Similarity=0.240 Sum_probs=23.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|.+|||.++|+|+.||+.|+.--.
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar 172 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGR 172 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999986553
No 409
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=33.44 E-value=72 Score=28.81 Aligned_cols=31 Identities=6% Similarity=0.185 Sum_probs=26.8
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
+-..++.+|+..++++.+||.+.++.+.+..
T Consensus 28 ~~~~~v~ela~~l~lsqstvS~HL~~L~~AG 58 (117)
T PRK10141 28 SGELCVCDLCTALDQSQPKISRHLALLRESG 58 (117)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3468999999999999999999999997443
No 410
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.39 E-value=28 Score=40.67 Aligned_cols=28 Identities=21% Similarity=0.548 Sum_probs=21.6
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.||+|+.. +.+....+.+.|..||....
T Consensus 392 ~C~~C~~~-l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 392 ECPHCDAS-LTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred CCCCCCCc-eeEECCCCeEECCCCcCCCC
Confidence 68888875 45555678999999998754
No 411
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=33.31 E-value=33 Score=28.09 Aligned_cols=25 Identities=16% Similarity=0.327 Sum_probs=20.7
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...||.+.|+.+|||..||-.-=++
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 5689999999999999999754433
No 412
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=33.11 E-value=34 Score=28.82 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=20.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccceecc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (567)
+||-|....+.. ..+.+.| .||.-++-
T Consensus 1 iCPVC~~~~L~~--~~~~i~C-~Cgl~l~~ 27 (82)
T PF14768_consen 1 ICPVCQKGNLRE--NSNVISC-SCGLRLNT 27 (82)
T ss_pred CCCccCCCcccc--cCCeEEC-CCccEEec
Confidence 599999997765 4688888 78866653
No 413
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=32.95 E-value=28 Score=36.73 Aligned_cols=9 Identities=22% Similarity=0.925 Sum_probs=6.1
Q ss_pred ceecCcccc
Q 008401 20 QLCCDRCGK 28 (567)
Q Consensus 20 ~~VC~~CG~ 28 (567)
-+-|+.||-
T Consensus 224 R~~C~~Cg~ 232 (305)
T TIGR01562 224 RVKCSHCEE 232 (305)
T ss_pred CccCCCCCC
Confidence 356788875
No 414
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=32.89 E-value=32 Score=27.05 Aligned_cols=24 Identities=17% Similarity=0.098 Sum_probs=20.6
Q ss_pred CHhhHHHHhccCHHHHHHHHHHHH
Q 008401 236 SKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
|..|||+.+||+..|||.--+++.
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred cHHHHHHHHCcCHHHHHHHHHhcC
Confidence 578999999999999998766664
No 415
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=32.81 E-value=1.7e+02 Score=29.90 Aligned_cols=55 Identities=9% Similarity=0.121 Sum_probs=43.2
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 215 ~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
.+.-+.-+.-||...+....+|+.+||..+|||..++.+-+++. .+|+-+|....
T Consensus 195 ~~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~------G~T~~~yi~~~ 249 (302)
T PRK09685 195 RERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ------GLVVAQYIRNR 249 (302)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHc------CCCHHHHHHHH
Confidence 34445566678888877777999999999999999999988753 47888887654
No 416
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=32.80 E-value=49 Score=24.54 Aligned_cols=39 Identities=5% Similarity=0.089 Sum_probs=28.8
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
....|+.++|..+||+..||++-.+-- ...+++.+..+.
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~g~-----~~~~~~~~~~i~ 51 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVENGK-----PTVRLDKVLRVL 51 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCCC-----CCCCHHHHHHHH
Confidence 357899999999999999998765321 245677766664
No 417
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=32.75 E-value=24 Score=27.93 Aligned_cols=24 Identities=25% Similarity=0.646 Sum_probs=12.2
Q ss_pred CCCCCCCCCceeecCCCceecCcccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
.|-.||..+.+- ....+-|.+||.
T Consensus 22 iCgdC~~en~lk--~~D~irCReCG~ 45 (62)
T KOG3507|consen 22 ICGDCGQENTLK--RGDVIRCRECGY 45 (62)
T ss_pred Eecccccccccc--CCCcEehhhcch
Confidence 366666654322 123344666664
No 418
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=32.73 E-value=61 Score=32.07 Aligned_cols=37 Identities=24% Similarity=0.084 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHH
Q 008401 219 LCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 219 IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
|..||+-+-+. +|+..|+++||+.+||+..||-.++.
T Consensus 18 Il~aA~~lF~~-~Gy~~s~~~IA~~AGvsk~tiy~~F~ 54 (225)
T PRK11552 18 LIAAALAQFGE-YGLHATTRDIAAQAGQNIAAITYYFG 54 (225)
T ss_pred HHHHHHHHHHH-hCccCCHHHHHHHhCCCHHHHHHHcC
Confidence 44455544443 57778999999999999999988773
No 419
>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=32.60 E-value=55 Score=28.08 Aligned_cols=23 Identities=22% Similarity=0.086 Sum_probs=19.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
...|.++||..+|||..||.+ +.
T Consensus 49 ~G~S~~eIA~~LgISrsTIyR-i~ 71 (88)
T TIGR02531 49 QGKTYSDIEAETGASTATISR-VK 71 (88)
T ss_pred CCCCHHHHHHHHCcCHHHHHH-HH
Confidence 346999999999999999988 44
No 420
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=32.57 E-value=2e+02 Score=28.39 Aligned_cols=29 Identities=21% Similarity=0.323 Sum_probs=26.4
Q ss_pred CCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 132 ~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
.|.+..+||+.+|++..+|.|+.++|.+.
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 57888999999999999999999998875
No 421
>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=32.52 E-value=57 Score=28.71 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=23.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|..+||...||++.||++++....
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 357999999999999999999998764
No 422
>PRK10130 transcriptional regulator EutR; Provisional
Probab=32.50 E-value=90 Score=33.45 Aligned_cols=54 Identities=19% Similarity=0.376 Sum_probs=39.5
Q ss_pred hhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHhhccccccccccCCchhhHHHH
Q 008401 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 182 (567)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~~~~~~~~~vdP~~~I~Rf 182 (567)
...|..++-||--.. .-|+++.|||..++++...|.+.|++. ++ ..|..||.++
T Consensus 239 ~~~v~~~~~~i~~~~-~~~ltv~~lA~~~gvS~r~L~r~Fk~~---~G----------~sp~~ylr~~ 292 (350)
T PRK10130 239 RRLLSRAREYVLENM-SEPVTVLDLCNQLHVSRRTLQNAFHAI---LG----------IGPNAWLKRI 292 (350)
T ss_pred HHHHHHHHHHHHhhh-cCCCCHHHHHHHHCCCHHHHHHHHHHH---HC----------cCHHHHHHHH
Confidence 344566666776443 458999999999999999999988865 33 4567777743
No 423
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=32.47 E-value=43 Score=30.89 Aligned_cols=26 Identities=19% Similarity=0.102 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||..+|++..||+.|+.--
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra 153 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKA 153 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998654
No 424
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=32.44 E-value=41 Score=32.29 Aligned_cols=26 Identities=15% Similarity=0.165 Sum_probs=23.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||...|+|..||++|+.-.
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra 181 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLA 181 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence 57899999999999999999998654
No 425
>PRK14873 primosome assembly protein PriA; Provisional
Probab=32.37 E-value=28 Score=40.63 Aligned_cols=27 Identities=19% Similarity=0.522 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeecCCCceecCcccce
Q 008401 2 VWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
..||+|+.... +....+.+.|.-||..
T Consensus 393 ~~C~~C~~~L~-~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTGPLG-LPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCCcee-EecCCCeeECCCCcCC
Confidence 36999988743 4345678999999984
No 426
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=32.30 E-value=1.2e+02 Score=29.66 Aligned_cols=30 Identities=10% Similarity=0.247 Sum_probs=26.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
+..|+++||..+|++..|+.+-+++|.+..
T Consensus 172 i~~t~~~iA~~lG~tretvsR~l~~L~~~g 201 (236)
T PRK09392 172 LPYEKRVLASYLGMTPENLSRAFAALASHG 201 (236)
T ss_pred eeCCHHHHHHHhCCChhHHHHHHHHHHhCC
Confidence 456789999999999999999999997655
No 427
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=32.27 E-value=28 Score=34.23 Aligned_cols=30 Identities=30% Similarity=0.654 Sum_probs=18.3
Q ss_pred CCCCCCCCCc----eee--cCCC-----ceecCcccceecc
Q 008401 3 WCSSCARHVT----GHR--PYDS-----QLCCDRCGKVLED 32 (567)
Q Consensus 3 ~Cp~Cgs~~i----v~D--~~~G-----~~VC~~CG~Vlee 32 (567)
.||+||.... .++ |.-| ...|..||.=-.|
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 42 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSND 42 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccce
Confidence 5999997622 222 2223 4579999985443
No 428
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=32.23 E-value=31 Score=36.46 Aligned_cols=9 Identities=22% Similarity=0.870 Sum_probs=7.0
Q ss_pred CCCCCCCCC
Q 008401 2 VWCSSCARH 10 (567)
Q Consensus 2 ~~Cp~Cgs~ 10 (567)
..||.||+.
T Consensus 188 ~~CPvCGs~ 196 (309)
T PRK03564 188 QFCPVCGSM 196 (309)
T ss_pred CCCCCCCCc
Confidence 368888887
No 429
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.21 E-value=78 Score=23.04 Aligned_cols=31 Identities=10% Similarity=0.075 Sum_probs=27.6
Q ss_pred ccHHHHHhhhccChHHHHHHHHHHHHHhhcc
Q 008401 134 FLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (567)
Q Consensus 134 ~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~ 164 (567)
.+..+||..++++..++.+....+.+.|+.+
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 5889999999999999999999888888764
No 430
>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=32.11 E-value=24 Score=27.49 Aligned_cols=27 Identities=30% Similarity=0.576 Sum_probs=19.0
Q ss_pred CCCCCCCCC-c--eeecCCCceecCcccce
Q 008401 3 WCSSCARHV-T--GHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~-i--v~D~~~G~~VC~~CG~V 29 (567)
.|++|...+ . ..+...-.++|..||..
T Consensus 24 IC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 24 ICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred ECcccchhhcccccccCCceEEEcCCCCCc
Confidence 589997762 2 35555668899999863
No 431
>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=32.06 E-value=40 Score=25.64 Aligned_cols=25 Identities=24% Similarity=0.553 Sum_probs=18.3
Q ss_pred CCC--CCCCCCceeecCCCceecCcccc
Q 008401 3 WCS--SCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp--~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
.|| .||...+--++. .-..|..||.
T Consensus 20 ~CP~~~CG~GvFMA~H~-dR~~CGKCg~ 46 (47)
T PF01599_consen 20 ECPSPRCGAGVFMAEHK-DRHYCGKCGY 46 (47)
T ss_dssp E-TSTTTTSSSEEEE-S-SEEEETTTSS
T ss_pred cCCCcccCCceEeeecC-CCccCCCccc
Confidence 599 899987666654 5789999996
No 432
>PRK09480 slmA division inhibitor protein; Provisional
Probab=31.99 E-value=54 Score=30.85 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=30.4
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 216 PSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 216 P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
..-|.-|++-+...-.|...|+++||+.+||+..||-..++.
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 334555555544433467899999999999999999877653
No 433
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=31.98 E-value=58 Score=31.03 Aligned_cols=27 Identities=15% Similarity=0.206 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|.+|||...|+|+.||+.|+.--+
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar 172 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRAR 172 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 458999999999999999999986553
No 434
>cd00131 PAX Paired Box domain
Probab=31.96 E-value=61 Score=29.57 Aligned_cols=30 Identities=17% Similarity=0.227 Sum_probs=26.4
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
...+.++||..++|+..||.+-++.|.++.
T Consensus 32 ~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G 61 (128)
T cd00131 32 SGIRPCDISRQLRVSHGCVSKILNRYYETG 61 (128)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHcC
Confidence 457999999999999999999999887665
No 435
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=31.85 E-value=93 Score=25.65 Aligned_cols=27 Identities=22% Similarity=0.324 Sum_probs=25.1
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
..++++|+..++++..||.+.++.|.+
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 689999999999999999999999964
No 436
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=31.66 E-value=50 Score=32.00 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=28.0
Q ss_pred hcCCCCCHhhHHHHhccC-HHHHHHHHHHHHcc
Q 008401 230 THGLKFSKSDIVKIVHIC-EATLMKRLIEFENT 261 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vs-e~TIrkR~kE~~~t 261 (567)
-+++..|++|||+.++++ .+|+.++++.|...
T Consensus 21 ~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 21 STGYPPSIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred hcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 357789999999999998 99999999988643
No 437
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=31.60 E-value=94 Score=26.60 Aligned_cols=36 Identities=8% Similarity=0.039 Sum_probs=30.1
Q ss_pred HHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 225 ylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.|+-++.....++.++|..+|||..|..|-+.-|..
T Consensus 16 ~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 16 RLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred HHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 455666677889999999999999999998887763
No 438
>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=31.47 E-value=90 Score=24.19 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=24.5
Q ss_pred HhCCCccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 129 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 129 ~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
..+-+.++.+|++.++++.-.+.+..++|.+.
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 56778899999999999999999999888774
No 439
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=31.32 E-value=41 Score=24.33 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=16.8
Q ss_pred CCCCCCCCC---CceeecCCCceecCcccce
Q 008401 2 VWCSSCARH---VTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 2 ~~Cp~Cgs~---~iv~D~~~G~~VC~~CG~V 29 (567)
++|..|++- -..+|......+|.-||..
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 579999885 2466766678999999985
No 440
>PRK10130 transcriptional regulator EutR; Provisional
Probab=31.32 E-value=1.3e+02 Score=32.31 Aligned_cols=53 Identities=17% Similarity=0.170 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHhH
Q 008401 217 SGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (567)
Q Consensus 217 ~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~~ 275 (567)
.-|.-+.-||-.... ..+|+.+||..+|||..|+.+.+++.. .+|+-+|...-
T Consensus 240 ~~v~~~~~~i~~~~~-~~ltv~~lA~~~gvS~r~L~r~Fk~~~-----G~sp~~ylr~~ 292 (350)
T PRK10130 240 RLLSRAREYVLENMS-EPVTVLDLCNQLHVSRRTLQNAFHAIL-----GIGPNAWLKRI 292 (350)
T ss_pred HHHHHHHHHHHhhhc-CCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHHHHH
Confidence 334555556666544 569999999999999999999999875 57888887653
No 441
>PRK07218 replication factor A; Provisional
Probab=31.29 E-value=24 Score=38.93 Aligned_cols=20 Identities=30% Similarity=0.714 Sum_probs=15.9
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
.||.|+... + . ..|..||.|
T Consensus 299 rCP~C~r~v---~--~--~~C~~hG~v 318 (423)
T PRK07218 299 RCPECGRVI---Q--K--GQCRSHGAV 318 (423)
T ss_pred cCcCccccc---c--C--CcCCCCCCc
Confidence 699999863 1 2 499999998
No 442
>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=31.29 E-value=65 Score=27.13 Aligned_cols=29 Identities=17% Similarity=0.247 Sum_probs=25.3
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
.+.++.-++|++.++++.+|||+-+..+.
T Consensus 20 ~~~PVgSk~ia~~l~~s~aTIRN~M~~Le 48 (78)
T PF03444_consen 20 TGEPVGSKTIAEELGRSPATIRNEMADLE 48 (78)
T ss_pred cCCCcCHHHHHHHHCCChHHHHHHHHHHH
Confidence 46778889999999999999999888774
No 443
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=31.27 E-value=45 Score=31.80 Aligned_cols=26 Identities=19% Similarity=0.172 Sum_probs=23.2
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||...|+|+.||++|+.--
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Ra 170 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARA 170 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56889999999999999999998654
No 444
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=31.27 E-value=6.6e+02 Score=26.62 Aligned_cols=91 Identities=13% Similarity=0.037 Sum_probs=54.5
Q ss_pred chHHHHHHHHHHHHHHHHHHhCC---CCchHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHH-------------
Q 008401 65 ASRERLMEKAFDDMRQMKNALNI---GESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACR------------- 128 (567)
Q Consensus 65 ~srer~l~~a~~~I~~ia~~L~L---p~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR------------- 128 (567)
..+++.+..-...+..+|.++.- +-.+-+.+....+++.+..-.-.+|-+..+.|.-.|.-+-.
T Consensus 86 ~A~~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP 165 (324)
T PRK07921 86 AARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLP 165 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCC
Confidence 34455555556667777777632 21133444555566666555556787777777666543321
Q ss_pred -------------------HhCCCccHHHHHhhhccChHHHHHHHH
Q 008401 129 -------------------QKSKPFLLIDFSNYLNINVYELGAVYL 155 (567)
Q Consensus 129 -------------------~e~~p~tL~Diad~~~v~v~~Lgr~~~ 155 (567)
..|.+-+..+||..+++++..+.....
T Consensus 166 ~~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 166 VHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 123344677889999999888876543
No 445
>PRK09956 hypothetical protein; Provisional
Probab=31.26 E-value=1.5e+02 Score=31.28 Aligned_cols=80 Identities=13% Similarity=0.189 Sum_probs=54.9
Q ss_pred CCchhhHHHHHhhhCCCCCHHHHHHHHHHHHHhhhccccCCC---ChhHHHHHHHHHHHHhcCCCCCHhhHHHHhccCHH
Q 008401 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR---KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA 249 (567)
Q Consensus 173 vdP~~~I~Rf~~~L~~~~~~~V~~~A~~iv~~~~~~~i~~GR---~P~~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~ 249 (567)
.++..++..+...+.. ....+...|..+-+.....++..|| .-.|..-+++-+|-++.....+...|++++|.|..
T Consensus 223 ~~~~~~i~~l~~~~~~-~~e~iMTiAe~l~qeG~e~G~q~G~~eG~qeG~~e~~~eiA~~mL~~G~~~~~i~~~tgLs~e 301 (308)
T PRK09956 223 SRFTRFIQEIAERSPL-QKERLMTIAERLRQEGHQIGWQEGKLEGLQEGMHEQAIKIALRMLEQGFDRDQVLAATQLSEA 301 (308)
T ss_pred chHHHHHHHHHHhCcc-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHH
Confidence 3466777777777631 1345666777776665444444554 11234445678888888888999999999999999
Q ss_pred HHHH
Q 008401 250 TLMK 253 (567)
Q Consensus 250 TIrk 253 (567)
.|.+
T Consensus 302 el~~ 305 (308)
T PRK09956 302 DLAA 305 (308)
T ss_pred HHHH
Confidence 9876
No 446
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=31.24 E-value=35 Score=28.71 Aligned_cols=27 Identities=19% Similarity=0.226 Sum_probs=19.8
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
.||-||...+..+.....-||.-|+--
T Consensus 3 ~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 3 PCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred cCCCCCcEEeccCCCcCceECCCCCcc
Confidence 699999875544433238899999984
No 447
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=31.20 E-value=46 Score=30.59 Aligned_cols=26 Identities=15% Similarity=0.231 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||...|++++||+.|+.--
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra 145 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNA 145 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56899999999999999999998643
No 448
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=31.08 E-value=25 Score=34.67 Aligned_cols=27 Identities=22% Similarity=0.460 Sum_probs=23.4
Q ss_pred CCCCCCCCCceeecCCCceecCcccceec
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (567)
.|..|++..++.. .|...|..|+.|..
T Consensus 6 ~C~~C~~ngiv~~--k~~efC~fC~~~f~ 32 (225)
T PHA03074 6 LCSGCRHNGIVSE--KDYEFCIFCESVFQ 32 (225)
T ss_pred hcCCCCCCCeeee--cCEEEeecHHHHHh
Confidence 6999999988764 69999999999865
No 449
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=30.95 E-value=28 Score=24.13 Aligned_cols=20 Identities=30% Similarity=0.576 Sum_probs=9.4
Q ss_pred CCCCCCCCceeecCCCceec
Q 008401 4 CSSCARHVTGHRPYDSQLCC 23 (567)
Q Consensus 4 Cp~Cgs~~iv~D~~~G~~VC 23 (567)
|..||.-..+.+...|.++|
T Consensus 10 C~~Cgniv~v~~~~~~~l~C 29 (34)
T TIGR00319 10 CEVCGNIVEVLHAGGGQLVC 29 (34)
T ss_pred cCCCCcEEEEEECCCcceec
Confidence 55555443334444444554
No 450
>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=30.88 E-value=1.4e+02 Score=24.21 Aligned_cols=64 Identities=17% Similarity=0.236 Sum_probs=35.3
Q ss_pred HHHHHHHHHhCCCCchHHHHHHHHHHHHHHhccccCCCchhHHHH--HHHHHHHHHhCCCccHHHHHhhhc-cChHHHHH
Q 008401 76 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYLN-INVYELGA 152 (567)
Q Consensus 76 ~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA--ACLYiACR~e~~p~tL~Diad~~~-v~v~~Lgr 152 (567)
..|+.+|..+|++ .. .=..++|....+-| .+.|++-... ..++.+|+..++ -+..++..
T Consensus 4 ~Ii~~Va~~~~v~--~~--------------~i~s~~R~~~i~~aR~va~yL~r~~~--~~sl~~Ig~~fg~rdHstV~~ 65 (70)
T PF08299_consen 4 DIIEAVAEYFGVS--VE--------------DIRSKSRKRKIVEARQVAMYLARELT--GLSLSEIGRYFGGRDHSTVIH 65 (70)
T ss_dssp HHHHHHHHHTT----HH--------------HHHSS---HHHHHHHHHHHHHHHHHS-----HHHHHHHCTSSTHHHHHH
T ss_pred HHHHHHHHHHCCC--HH--------------HHhCCCCChhhcchHHHHHHHHHHHh--CCCHHHHHHHhCCCCHHHHHH
Confidence 3456667777777 21 11124444433333 4556665544 578999999999 89888888
Q ss_pred HHHHH
Q 008401 153 VYLQL 157 (567)
Q Consensus 153 ~~~~L 157 (567)
+++++
T Consensus 66 a~~ki 70 (70)
T PF08299_consen 66 AIRKI 70 (70)
T ss_dssp HHHHH
T ss_pred HHHhC
Confidence 77764
No 451
>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=30.82 E-value=1.1e+02 Score=24.41 Aligned_cols=23 Identities=13% Similarity=0.170 Sum_probs=19.1
Q ss_pred hCCCccHHHHHhhhccChHHHHH
Q 008401 130 KSKPFLLIDFSNYLNINVYELGA 152 (567)
Q Consensus 130 e~~p~tL~Diad~~~v~v~~Lgr 152 (567)
++--++++|||+.++|+..+|++
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHHH
Confidence 34457899999999999998875
No 452
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=30.80 E-value=49 Score=26.46 Aligned_cols=27 Identities=22% Similarity=0.357 Sum_probs=18.6
Q ss_pred CCCCHhhHHHHh-----ccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIV-----HICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv-----~Vse~TIrkR~kE~~ 259 (567)
-..|..+|+..+ +||..||+++|++..
T Consensus 12 p~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~g 43 (72)
T PF01498_consen 12 PRISAREIAQELQEAGISVSKSTIRRRLREAG 43 (72)
T ss_dssp ----HHHHHHHT---T--S-HHHHHHHHHHT-
T ss_pred CCCCHHHHHHHHHHccCCcCHHHHHHHHHHcC
Confidence 447899999977 999999999999874
No 453
>smart00351 PAX Paired Box domain.
Probab=30.80 E-value=66 Score=29.11 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=25.4
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
..+.++||+.++||..||.+-++.|.++.
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G 61 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETG 61 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcC
Confidence 46899999999999999999998887654
No 454
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=30.71 E-value=44 Score=31.67 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=29.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHc---cCCCCCCHHHHHHh
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFEN---TDSGSLTIEDFMAR 274 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~---t~s~~Lt~~ef~~~ 274 (567)
...|.+|||..+|+|+.||++|+.--.. ..-...+.++|.+.
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~~~~ 181 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDEFKEL 181 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHHHHHH
Confidence 5589999999999999999998743321 22245556666443
No 455
>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=30.67 E-value=66 Score=30.02 Aligned_cols=41 Identities=20% Similarity=0.129 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 218 GLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 218 ~IaaAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
-|..|++=|....-=.++|+++|++.+||+.+|.=..|+.-
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK 47 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDK 47 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCH
Confidence 36666666655433346899999999999999998777644
No 456
>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=30.64 E-value=81 Score=23.65 Aligned_cols=34 Identities=15% Similarity=0.228 Sum_probs=25.3
Q ss_pred HHHHhCCCccHHHHHhhhccChHHHHHHHHHHHH
Q 008401 126 ACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (567)
Q Consensus 126 ACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~ 159 (567)
+...++.|.++.||+..++++..++.+....|.+
T Consensus 11 ~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 11 ALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp CHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3345666789999999999999888776666654
No 457
>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=30.60 E-value=86 Score=22.96 Aligned_cols=32 Identities=9% Similarity=0.027 Sum_probs=28.3
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHHHhhcc
Q 008401 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (567)
Q Consensus 133 p~tL~Diad~~~v~v~~Lgr~~~~L~~~L~i~ 164 (567)
..+..+||..+++++..+.+...++.+.++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 46899999999999999999999998888764
No 458
>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=30.57 E-value=26 Score=30.29 Aligned_cols=27 Identities=22% Similarity=0.453 Sum_probs=16.8
Q ss_pred CCCCCCCCC--CceeecCCCceecCcccc
Q 008401 2 VWCSSCARH--VTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 2 ~~Cp~Cgs~--~iv~D~~~G~~VC~~CG~ 28 (567)
..||.|+.. .+.+++..|...|-.||.
T Consensus 34 ~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp E--SSS--SS--EEEETTTTEEEETTT--
T ss_pred EECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 369999876 457777889999999995
No 459
>PRK12366 replication factor A; Reviewed
Probab=30.50 E-value=23 Score=41.14 Aligned_cols=24 Identities=33% Similarity=0.948 Sum_probs=19.7
Q ss_pred CCCCCCCCCceeecCCCceecCcccce
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (567)
.||.|++..+ + ..|.+.|..||.+
T Consensus 534 aCp~CnkKv~--~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 534 LCPNCRKRVE--E-VDGEYICEFCGEV 557 (637)
T ss_pred cccccCeEeE--c-CCCcEECCCCCCC
Confidence 5999988632 2 4799999999998
No 460
>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=30.47 E-value=53 Score=30.29 Aligned_cols=27 Identities=7% Similarity=0.084 Sum_probs=23.6
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|.++||...|+++.||++++....
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~ 163 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAI 163 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999986543
No 461
>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=30.28 E-value=1.9e+02 Score=22.41 Aligned_cols=26 Identities=12% Similarity=0.097 Sum_probs=20.5
Q ss_pred ccHHHHHhhhccChHHHHHHHHHHHH
Q 008401 134 FLLIDFSNYLNINVYELGAVYLQLCQ 159 (567)
Q Consensus 134 ~tL~Diad~~~v~v~~Lgr~~~~L~~ 159 (567)
.++.|+|+.+||+..++....++-.+
T Consensus 24 ~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 58899999999999887766655443
No 462
>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=30.27 E-value=66 Score=29.87 Aligned_cols=27 Identities=15% Similarity=0.140 Sum_probs=23.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|.+|||...|||+.||+.++.--.
T Consensus 134 ~g~s~~eiA~~lgis~~tv~~~l~Ra~ 160 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPEGTVKTYLHRAL 160 (169)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358999999999999999999986543
No 463
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=30.20 E-value=76 Score=29.99 Aligned_cols=36 Identities=14% Similarity=0.146 Sum_probs=29.7
Q ss_pred HHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 223 alylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
+||.... .+....+++||...+|+.+|+.+-++.+.
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~ 49 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLE 49 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHH
Confidence 5665554 56678899999999999999999888885
No 464
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=30.17 E-value=54 Score=31.50 Aligned_cols=44 Identities=16% Similarity=0.317 Sum_probs=32.0
Q ss_pred cCCCCCHhhHHHHhccCHH---------------HHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 231 HGLKFSKSDIVKIVHICEA---------------TLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~---------------TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
....+||+|+|+.+|||.+ |+++-|+-|.+..-.++|....|..
T Consensus 15 k~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~s 73 (187)
T COG3620 15 KELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHS 73 (187)
T ss_pred HHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcceEeHhhhccC
Confidence 3467899999999999975 5666666666666666666666654
No 465
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=30.06 E-value=50 Score=33.13 Aligned_cols=26 Identities=19% Similarity=0.429 Sum_probs=24.0
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
=.|+.|++..+++|..||++.++++.
T Consensus 105 lLT~~Dla~LL~~S~~TI~~~i~~yq 130 (220)
T PF07900_consen 105 LLTQEDLAMLLGISPRTISKDIKEYQ 130 (220)
T ss_pred cccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36899999999999999999999985
No 466
>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=29.96 E-value=94 Score=23.54 Aligned_cols=26 Identities=15% Similarity=0.341 Sum_probs=23.1
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
..++.+|+..++++.+|+.+-++.+.
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 38999999999999999999999885
No 467
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=29.93 E-value=63 Score=29.76 Aligned_cols=27 Identities=19% Similarity=0.222 Sum_probs=23.9
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...+.++||...|+++.||++++..-.
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~ 152 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAK 152 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 678999999999999999999986553
No 468
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=29.91 E-value=45 Score=32.31 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=22.8
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.+|||..+|+++.||+.|+.--
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RA 179 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRA 179 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56889999999999999999887643
No 469
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=29.85 E-value=47 Score=32.93 Aligned_cols=25 Identities=4% Similarity=0.134 Sum_probs=22.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...|.+|||...|||..||++++.-
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~r 221 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKR 221 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999999988643
No 470
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=29.82 E-value=5.8e+02 Score=25.52 Aligned_cols=27 Identities=4% Similarity=0.133 Sum_probs=23.8
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
-...|.++||...|||..||++++...
T Consensus 215 ~~~~s~~EIA~~lgis~~tV~~~~~ra 241 (251)
T PRK07670 215 KEELTLTEIGQVLNLSTSRISQIHSKA 241 (251)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 367899999999999999999998654
No 471
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=29.75 E-value=40 Score=34.75 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=21.8
Q ss_pred CCCHhhHHHHhccCHHHHHHHHHH
Q 008401 234 KFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 234 ~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
+.|++|||+.+|||.+|+++-|..
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhhCC
Confidence 579999999999999999999863
No 472
>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=29.73 E-value=47 Score=30.12 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|.++||..+|+++.||++++.-.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra 145 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRA 145 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 57899999999999999999998644
No 473
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=29.69 E-value=30 Score=23.95 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=12.5
Q ss_pred CCCCCCCCCceeecCCCceecC
Q 008401 3 WCSSCARHVTGHRPYDSQLCCD 24 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~ 24 (567)
+|..||.-..+.+...|.++|-
T Consensus 6 kC~~CGniv~v~~~~~~~l~Cc 27 (34)
T cd00974 6 KCEICGNIVEVLNVGGGTLVCC 27 (34)
T ss_pred EcCCCCcEEEEEECCCcceeec
Confidence 4666666544445455566664
No 474
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=29.69 E-value=35 Score=36.07 Aligned_cols=21 Identities=19% Similarity=0.686 Sum_probs=10.1
Q ss_pred CCCCCCCCCceeecCCCceecCcccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
.|+-|+.. +.. --+-|+.||.
T Consensus 214 ~CslC~te---W~~--~R~~C~~Cg~ 234 (309)
T PRK03564 214 HCNLCESE---WHV--VRVKCSNCEQ 234 (309)
T ss_pred EcCCCCCc---ccc--cCccCCCCCC
Confidence 46666554 211 2335666663
No 475
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=29.54 E-value=37 Score=34.85 Aligned_cols=23 Identities=13% Similarity=0.141 Sum_probs=20.9
Q ss_pred CCHhhHHHHhccCHHHHHHHHHH
Q 008401 235 FSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
.|++|||+.+|||.+|+.+-|+.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 58999999999999999998863
No 476
>PF14369 zf-RING_3: zinc-finger
Probab=29.52 E-value=31 Score=24.35 Aligned_cols=26 Identities=38% Similarity=0.902 Sum_probs=16.6
Q ss_pred CCCCCCCCCceeecCCCceecCcccc
Q 008401 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (567)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (567)
+|-.|....-+....+..+.|..|+-
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 78899887433323344445999973
No 477
>PF14493 HTH_40: Helix-turn-helix domain
Probab=29.49 E-value=95 Score=26.26 Aligned_cols=46 Identities=24% Similarity=0.302 Sum_probs=36.1
Q ss_pred HHhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccCCCCCCHHHHHHh
Q 008401 228 ALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (567)
Q Consensus 228 a~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~s~~Lt~~ef~~~ 274 (567)
..+.....|+.+||+.-+++++||...+-++....- .+-+++|...
T Consensus 7 ~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~-~~~~~~~l~~ 52 (91)
T PF14493_consen 7 YELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGE-PLDIEELLSE 52 (91)
T ss_pred HHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCC-CCCHHHhCCH
Confidence 345556799999999999999999999999975532 3677777544
No 478
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=29.49 E-value=22 Score=25.17 Aligned_cols=25 Identities=28% Similarity=0.683 Sum_probs=14.4
Q ss_pred CCCCCCCC-ceee-cCCCce-ecCcccc
Q 008401 4 CSSCARHV-TGHR-PYDSQL-CCDRCGK 28 (567)
Q Consensus 4 Cp~Cgs~~-iv~D-~~~G~~-VC~~CG~ 28 (567)
|.+|+.+. +... ...|.. +|..||.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 77888873 3333 235766 8999986
No 479
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=29.49 E-value=2.1e+02 Score=26.78 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=26.3
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHHcc
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~~t 261 (567)
+.+|..+|+..+|++..|+.+-+.+|...
T Consensus 170 ~~~~~~~ia~~~g~~~~~vsr~l~~l~~~ 198 (214)
T COG0664 170 LPLTHKDLAEYLGLSRETVSRILKELRKD 198 (214)
T ss_pred ccCCHHHHHHHhCCchhhHHHHHHHHHhC
Confidence 67899999999999999999999999643
No 480
>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=29.36 E-value=1.4e+02 Score=22.56 Aligned_cols=28 Identities=11% Similarity=0.089 Sum_probs=24.1
Q ss_pred CccHHHHHhhhccChHHHHHHHHHHHHH
Q 008401 133 PFLLIDFSNYLNINVYELGAVYLQLCQV 160 (567)
Q Consensus 133 p~tL~Diad~~~v~v~~Lgr~~~~L~~~ 160 (567)
+.++.+||+.++++...+.+..++|.+.
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 4899999999999999999999888774
No 481
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=29.28 E-value=27 Score=25.29 Aligned_cols=14 Identities=14% Similarity=0.838 Sum_probs=12.5
Q ss_pred CceecCcccceecc
Q 008401 19 SQLCCDRCGKVLED 32 (567)
Q Consensus 19 G~~VC~~CG~Vlee 32 (567)
|.+||+.|+.+++.
T Consensus 2 GtIvCq~C~~~Id~ 15 (38)
T PF13790_consen 2 GTIVCQHCNETIDH 15 (38)
T ss_pred CEEEeccccceeee
Confidence 78999999999983
No 482
>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=29.21 E-value=3.3e+02 Score=24.22 Aligned_cols=75 Identities=12% Similarity=0.155 Sum_probs=44.3
Q ss_pred HHHHHHHHHhCCCCchHHHHHHHHHHHHHHhcccc----CCCc-hhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHH
Q 008401 76 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFT----KGRR-TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 150 (567)
Q Consensus 76 ~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~----rGR~-~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~L 150 (567)
.-+.++|..++++ ...+ .++++.. +.+-+ +|++ .. .- ...+.=.++--.++.|+|..++|+...|
T Consensus 19 ~s~~eaa~~F~VS--~~Tv---~~W~k~~-~~G~~~~k~r~~~Kid-~~---~L~~~v~~~pd~tl~Ela~~l~Vs~~ti 88 (119)
T PF01710_consen 19 KSIREAAKRFGVS--RNTV---YRWLKRK-ETGDLEPKPRGRKKID-RD---ELKALVEENPDATLRELAERLGVSPSTI 88 (119)
T ss_pred chHHHHHHHhCcH--HHHH---HHHHHhc-cccccccccccccccc-HH---HHHHHHHHCCCcCHHHHHHHcCCCHHHH
Confidence 3688899999998 5444 4555522 22222 3332 11 11 1222223455688999999999999888
Q ss_pred HHHHHHHHHH
Q 008401 151 GAVYLQLCQV 160 (567)
Q Consensus 151 gr~~~~L~~~ 160 (567)
++..++|--.
T Consensus 89 ~~~Lkrlg~t 98 (119)
T PF01710_consen 89 WRALKRLGIT 98 (119)
T ss_pred HHHHHHcCch
Confidence 8766655333
No 483
>PRK05572 sporulation sigma factor SigF; Validated
Probab=29.13 E-value=6e+02 Score=25.45 Aligned_cols=26 Identities=12% Similarity=0.149 Sum_probs=23.0
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|+++||...|||..||+++.+..
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ra 242 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKI 242 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56999999999999999999877654
No 484
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=29.13 E-value=1.1e+02 Score=23.85 Aligned_cols=32 Identities=28% Similarity=0.349 Sum_probs=19.4
Q ss_pred CCCchhHHHH--HHHHHHHHHhCCCccHHHHHhhhc
Q 008401 111 KGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYLN 144 (567)
Q Consensus 111 rGR~~~~vaA--ACLYiACR~e~~p~tL~Diad~~~ 144 (567)
++|+...+.| .+.|++-+..+. ++.+|+..||
T Consensus 23 ~~R~~~~~~aR~iamyla~~~~~~--sl~~Ig~~fg 56 (60)
T smart00760 23 KSRKREIVLARQIAMYLARELTDL--SLPEIGKIFG 56 (60)
T ss_pred CCCCcchhHHHHHHHHHHHHHHCC--CHHHHHHHhC
Confidence 3443433333 566887666654 6788887776
No 485
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=29.12 E-value=51 Score=31.44 Aligned_cols=25 Identities=28% Similarity=0.214 Sum_probs=22.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE 257 (567)
...|.+|||...|+|+.||+.++.-
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~R 180 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQ 180 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4689999999999999999988753
No 486
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=28.87 E-value=78 Score=28.94 Aligned_cols=28 Identities=11% Similarity=0.150 Sum_probs=25.4
Q ss_pred CCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 232 g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
.-.+|+.+|+...+++.+|+.+-++.+.
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le 79 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLV 79 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4569999999999999999999999885
No 487
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=28.80 E-value=58 Score=28.57 Aligned_cols=39 Identities=13% Similarity=0.159 Sum_probs=31.7
Q ss_pred HHHHHHHHHhcCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 221 GAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 221 aAalylAa~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
|.=+-+...+.+-..||+||+.-.||+-+||.+--..++
T Consensus 47 ~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK 85 (103)
T COG2973 47 GTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLK 85 (103)
T ss_pred HHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhc
Confidence 344556677778899999999999999999988766664
No 488
>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=28.70 E-value=95 Score=24.93 Aligned_cols=32 Identities=9% Similarity=0.117 Sum_probs=22.6
Q ss_pred HHhCCCccHHHHHhhhccC-hHHHHHHHHHHHH
Q 008401 128 RQKSKPFLLIDFSNYLNIN-VYELGAVYLQLCQ 159 (567)
Q Consensus 128 R~e~~p~tL~Diad~~~v~-v~~Lgr~~~~L~~ 159 (567)
..+|.|-|+.||++.+|++ ...+....+.|.+
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 4689999999999999997 7777666665554
No 489
>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=28.65 E-value=35 Score=26.18 Aligned_cols=22 Identities=27% Similarity=0.244 Sum_probs=16.8
Q ss_pred CCHhhHHHHhccCHHHHHHHHH
Q 008401 235 FSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 235 ~t~~eIa~vv~Vse~TIrkR~k 256 (567)
.++.+||..+||+.+||++-++
T Consensus 23 ~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 23 ESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp T-HHHHHHHHT--CCHHHHHHH
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 3999999999999999997765
No 490
>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=28.55 E-value=79 Score=24.54 Aligned_cols=29 Identities=17% Similarity=0.296 Sum_probs=23.1
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
.+-..++.+|+..++++..|+.+.++.+.
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~ 43 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLE 43 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46678999999999999999999999885
No 491
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=28.49 E-value=29 Score=22.54 Aligned_cols=10 Identities=40% Similarity=0.953 Sum_probs=7.8
Q ss_pred CCCCCCCCCC
Q 008401 1 MVWCSSCARH 10 (567)
Q Consensus 1 M~~Cp~Cgs~ 10 (567)
|..||.||..
T Consensus 2 l~~C~~CgR~ 11 (25)
T PF13913_consen 2 LVPCPICGRK 11 (25)
T ss_pred CCcCCCCCCE
Confidence 5678888876
No 492
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=28.48 E-value=65 Score=32.32 Aligned_cols=30 Identities=20% Similarity=0.259 Sum_probs=26.6
Q ss_pred cCCCCCHhhHHHHhccCHHHHHHHHHHHHc
Q 008401 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (567)
Q Consensus 231 ~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~ 260 (567)
.+..+|+.++++.++++..|+.++++.|.+
T Consensus 18 ~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe 47 (217)
T PRK14165 18 NTVKISSSEFANHTGTSSKTAARILKQLED 47 (217)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345689999999999999999999999954
No 493
>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=28.43 E-value=67 Score=29.89 Aligned_cols=27 Identities=15% Similarity=0.043 Sum_probs=23.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~~ 259 (567)
...|+++||..+|+|..||+++.+...
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~ 46 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAM 46 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHH
Confidence 557999999999999999998887653
No 494
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.40 E-value=57 Score=30.02 Aligned_cols=24 Identities=8% Similarity=0.036 Sum_probs=21.5
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLI 256 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~k 256 (567)
...|.+|||+.+|++..||+.++.
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999999998864
No 495
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=28.38 E-value=2.6e+02 Score=28.53 Aligned_cols=42 Identities=14% Similarity=0.072 Sum_probs=32.3
Q ss_pred hhHHHHHHHHHHHHHhCCCccHHHHHhhhccChHHHHHHHHH
Q 008401 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 156 (567)
Q Consensus 115 ~~~vaAACLYiACR~e~~p~tL~Diad~~~v~v~~Lgr~~~~ 156 (567)
...+..++-||.-....-.+++.+||..+++++..|.+.|++
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 344556667776665555589999999999999999888863
No 496
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=28.34 E-value=56 Score=30.99 Aligned_cols=26 Identities=27% Similarity=0.272 Sum_probs=23.1
Q ss_pred CCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 233 ~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
...|..|||...||+..||+.|+..=
T Consensus 142 ~gls~~EIA~~l~i~~~tVks~l~ra 167 (182)
T COG1595 142 EGLSYEEIAEILGISVGTVKSRLHRA 167 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56899999999999999999998643
No 497
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=28.22 E-value=87 Score=30.85 Aligned_cols=34 Identities=24% Similarity=0.323 Sum_probs=28.5
Q ss_pred HhcCCCCCHhhHHHHhccCHHHHHHHHHHHHccC
Q 008401 229 LTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (567)
Q Consensus 229 ~~~g~~~t~~eIa~vv~Vse~TIrkR~kE~~~t~ 262 (567)
...+...|.++||..+++|+.||++.+.-+....
T Consensus 173 ~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~ 206 (239)
T PRK10430 173 AHQDYEFSTDELANAVNISRVSCRKYLIWLVNCH 206 (239)
T ss_pred hCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC
Confidence 3356778999999999999999999999885443
No 498
>PRK10072 putative transcriptional regulator; Provisional
Probab=28.20 E-value=56 Score=28.50 Aligned_cols=29 Identities=10% Similarity=0.149 Sum_probs=24.2
Q ss_pred hcCCCCCHhhHHHHhccCHHHHHHHHHHH
Q 008401 230 THGLKFSKSDIVKIVHICEATLMKRLIEF 258 (567)
Q Consensus 230 ~~g~~~t~~eIa~vv~Vse~TIrkR~kE~ 258 (567)
......||.++|+.+||+..||++-..--
T Consensus 42 R~~~glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 42 RKGTGLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 34568999999999999999999876544
No 499
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=28.20 E-value=1.4e+02 Score=24.25 Aligned_cols=35 Identities=14% Similarity=0.009 Sum_probs=30.4
Q ss_pred HHHhCCCccHHHHHhhhccChHHHHHHHHHHHHHh
Q 008401 127 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (567)
Q Consensus 127 CR~e~~p~tL~Diad~~~v~v~~Lgr~~~~L~~~L 161 (567)
.|.-+.|+++.+.|+.+|+++..+.+....+.+-|
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wl 41 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWL 41 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 35678999999999999999999998888777765
No 500
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=28.19 E-value=43 Score=34.35 Aligned_cols=22 Identities=9% Similarity=0.134 Sum_probs=20.4
Q ss_pred CHhhHHHHhccCHHHHHHHHHH
Q 008401 236 SKSDIVKIVHICEATLMKRLIE 257 (567)
Q Consensus 236 t~~eIa~vv~Vse~TIrkR~kE 257 (567)
|++|||+.+|||.+|+.+-|..
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 7899999999999999999963
Done!