Query 010689
Match_columns 504
No_of_seqs 265 out of 1182
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 03:26:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010689.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010689hhsearch_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 3.5E-75 7.6E-80 608.0 25.2 458 2-496 1-472 (521)
2 PRK00423 tfb transcription ini 100.0 2.8E-53 6E-58 433.3 27.1 250 2-260 12-302 (310)
3 COG1405 SUA7 Transcription ini 100.0 2.2E-52 4.8E-57 418.3 25.5 252 1-261 1-278 (285)
4 KOG1597 Transcription initiati 100.0 5.7E-48 1.2E-52 377.2 24.4 264 2-273 1-298 (308)
5 PF00382 TFIIB: Transcription 99.7 1.5E-16 3.2E-21 128.2 9.7 71 78-150 1-71 (71)
6 PF00382 TFIIB: Transcription 99.6 2.3E-15 4.9E-20 121.2 8.9 71 179-251 1-71 (71)
7 PF07741 BRF1: Brf1-like TBP-b 99.5 1.3E-15 2.8E-20 130.1 0.8 75 423-497 1-83 (97)
8 TIGR00569 ccl1 cyclin ccl1. Un 99.4 2.9E-11 6.2E-16 123.4 20.7 163 68-237 52-226 (305)
9 KOG0835 Cyclin L [General func 99.3 3.8E-11 8.1E-16 120.2 17.5 187 68-261 20-231 (367)
10 PRK00423 tfb transcription ini 99.3 7.2E-12 1.6E-16 128.6 12.0 89 74-164 219-307 (310)
11 KOG0834 CDK9 kinase-activating 99.3 1.8E-11 3.9E-16 125.0 11.6 161 69-236 37-214 (323)
12 PF08271 TF_Zn_Ribbon: TFIIB z 99.2 1E-11 2.2E-16 90.4 2.0 42 2-43 1-42 (43)
13 COG5333 CCL1 Cdk activating ki 99.1 1.1E-09 2.4E-14 109.7 13.0 158 72-236 46-211 (297)
14 COG1405 SUA7 Transcription ini 99.0 1.9E-09 4.1E-14 108.9 10.3 91 73-165 193-283 (285)
15 KOG1597 Transcription initiati 98.9 9E-09 2E-13 102.2 10.3 87 74-162 203-289 (308)
16 cd00043 CYCLIN Cyclin box fold 98.9 2.3E-08 5E-13 81.2 10.9 83 73-157 4-87 (88)
17 cd00043 CYCLIN Cyclin box fold 98.8 2.4E-08 5.3E-13 81.1 9.4 84 173-258 3-87 (88)
18 smart00385 CYCLIN domain prese 98.8 3.7E-08 8.1E-13 79.2 9.3 81 177-259 1-82 (83)
19 smart00385 CYCLIN domain prese 98.8 4.4E-08 9.6E-13 78.7 8.8 79 77-158 2-82 (83)
20 KOG0794 CDK8 kinase-activating 98.7 1.8E-07 3.9E-12 90.1 13.1 155 74-236 44-213 (264)
21 KOG0656 G1/S-specific cyclin D 98.5 4.8E-06 1E-10 85.6 16.7 178 72-256 79-268 (335)
22 KOG1598 Transcription initiati 98.1 2E-06 4.3E-11 92.0 4.9 157 77-234 169-334 (521)
23 KOG4557 Origin recognition com 97.6 0.0021 4.5E-08 61.7 15.1 159 77-249 2-168 (262)
24 PF00134 Cyclin_N: Cyclin, N-t 97.6 0.0011 2.4E-08 58.2 11.6 94 69-164 29-125 (127)
25 KOG2496 Cdk activating kinase 97.4 0.0022 4.8E-08 64.7 12.0 147 78-228 63-219 (325)
26 PF01857 RB_B: Retinoblastoma- 97.3 0.0015 3.2E-08 59.4 9.7 84 70-155 10-95 (135)
27 KOG0653 Cyclin B and related k 97.3 0.0029 6.3E-08 67.3 12.8 153 74-235 161-317 (391)
28 PF02984 Cyclin_C: Cyclin, C-t 97.0 0.0015 3.3E-08 56.3 6.3 85 174-260 2-87 (118)
29 COG5024 Cyclin [Cell division 96.7 0.012 2.5E-07 63.2 10.7 148 75-232 217-368 (440)
30 PF11781 RRN7: RNA polymerase 96.3 0.0021 4.6E-08 44.9 1.8 27 3-31 10-36 (36)
31 COG2051 RPS27A Ribosomal prote 95.5 0.0061 1.3E-07 48.0 1.3 31 2-32 20-50 (67)
32 PRK00415 rps27e 30S ribosomal 95.5 0.0057 1.2E-07 47.3 1.0 31 2-32 12-42 (59)
33 PF01667 Ribosomal_S27e: Ribos 95.4 0.0062 1.3E-07 46.5 0.8 31 2-32 8-38 (55)
34 KOG0835 Cyclin L [General func 95.2 0.13 2.7E-06 52.8 9.6 104 75-186 142-246 (367)
35 PLN00209 ribosomal protein S27 94.7 0.015 3.2E-07 48.2 1.4 31 2-32 37-67 (86)
36 PF09862 DUF2089: Protein of u 94.7 0.5 1.1E-05 41.6 10.9 56 135-194 51-107 (113)
37 PF02984 Cyclin_C: Cyclin, C-t 94.7 0.16 3.5E-06 43.5 8.0 86 75-162 4-90 (118)
38 PTZ00083 40S ribosomal protein 94.6 0.017 3.6E-07 47.8 1.5 31 2-32 36-66 (85)
39 PF14803 Nudix_N_2: Nudix N-te 94.4 0.021 4.6E-07 39.4 1.3 28 3-30 2-32 (34)
40 PF02150 RNA_POL_M_15KD: RNA p 94.4 0.021 4.6E-07 39.6 1.4 31 1-31 1-31 (35)
41 PF13248 zf-ribbon_3: zinc-rib 94.3 0.023 4.9E-07 36.7 1.3 23 1-28 2-24 (26)
42 PHA00626 hypothetical protein 94.3 0.03 6.5E-07 42.6 2.0 31 2-32 1-35 (59)
43 TIGR01206 lysW lysine biosynth 94.3 0.029 6.3E-07 42.8 2.0 31 1-31 2-33 (54)
44 PF08792 A2L_zn_ribbon: A2L zi 94.0 0.037 7.9E-07 38.0 1.8 27 3-30 5-31 (33)
45 PF13240 zinc_ribbon_2: zinc-r 93.9 0.03 6.4E-07 35.2 1.1 22 3-29 1-22 (23)
46 KOG0655 G1/S-specific cyclin E 93.8 0.6 1.3E-05 48.1 10.9 171 74-259 148-332 (408)
47 TIGR00569 ccl1 cyclin ccl1. Un 93.8 0.25 5.5E-06 50.9 8.4 67 178-244 62-128 (305)
48 PRK00420 hypothetical protein; 93.7 0.045 9.7E-07 48.1 2.4 27 3-31 25-51 (112)
49 TIGR02098 MJ0042_CXXC MJ0042 f 93.5 0.04 8.6E-07 38.6 1.4 30 2-31 3-36 (38)
50 PF00134 Cyclin_N: Cyclin, N-t 93.3 0.29 6.4E-06 42.7 7.1 66 177-244 36-102 (127)
51 PF08274 PhnA_Zn_Ribbon: PhnA 92.8 0.077 1.7E-06 35.6 1.9 28 1-30 2-29 (30)
52 PF03966 Trm112p: Trm112p-like 92.2 0.11 2.3E-06 41.5 2.3 17 14-30 47-63 (68)
53 smart00778 Prim_Zn_Ribbon Zinc 92.0 0.13 2.8E-06 36.2 2.3 27 2-28 4-33 (37)
54 COG1997 RPL43A Ribosomal prote 91.7 0.11 2.4E-06 43.2 2.0 29 3-32 37-65 (89)
55 PRK00432 30S ribosomal protein 91.6 0.13 2.8E-06 38.7 2.1 26 3-30 22-47 (50)
56 smart00661 RPOL9 RNA polymeras 91.0 0.17 3.7E-06 37.7 2.3 30 3-32 2-32 (52)
57 PF14354 Lar_restr_allev: Rest 91.0 0.18 3.8E-06 39.0 2.4 27 2-28 4-37 (61)
58 PF13404 HTH_AsnC-type: AsnC-t 90.8 0.47 1E-05 34.2 4.3 31 229-259 12-42 (42)
59 COG1645 Uncharacterized Zn-fin 90.7 0.16 3.5E-06 45.7 2.1 22 3-27 30-51 (131)
60 KOG0834 CDK9 kinase-activating 90.1 0.45 9.8E-06 49.3 5.2 83 176-260 43-129 (323)
61 PF13719 zinc_ribbon_5: zinc-r 90.0 0.2 4.2E-06 35.2 1.7 29 2-30 3-35 (37)
62 PRK11827 hypothetical protein; 89.9 0.24 5.1E-06 38.7 2.2 28 2-30 9-36 (60)
63 PRK00398 rpoP DNA-directed RNA 89.7 0.23 5E-06 36.4 1.9 27 3-30 5-31 (46)
64 TIGR03655 anti_R_Lar restricti 89.5 0.22 4.7E-06 37.7 1.8 31 2-32 2-38 (53)
65 PRK00464 nrdR transcriptional 89.1 0.24 5.2E-06 46.0 2.0 29 2-30 1-38 (154)
66 KOG4164 Cyclin ik3-1/CABLES [C 89.0 1.4 2.9E-05 46.4 7.6 90 74-165 385-479 (497)
67 PF08613 Cyclin: Cyclin; Inte 88.9 6.6 0.00014 36.0 11.5 88 74-163 54-147 (149)
68 PRK05657 RNA polymerase sigma 88.5 24 0.00052 36.7 16.7 26 233-258 281-306 (325)
69 PF09538 FYDLN_acid: Protein o 88.2 0.29 6.2E-06 42.8 1.8 29 3-33 11-39 (108)
70 PF05460 ORC6: Origin recognit 87.9 0.16 3.4E-06 53.5 0.0 86 80-165 3-89 (353)
71 COG2835 Uncharacterized conser 87.6 0.34 7.4E-06 37.7 1.7 28 2-30 9-36 (60)
72 COG1998 RPS31 Ribosomal protei 87.1 0.42 9E-06 35.6 1.8 26 3-29 21-46 (51)
73 smart00342 HTH_ARAC helix_turn 87.0 2.5 5.5E-05 33.2 6.7 71 78-157 4-75 (84)
74 KOG1779 40s ribosomal protein 86.7 0.29 6.2E-06 39.9 0.9 30 2-31 35-64 (84)
75 PF01857 RB_B: Retinoblastoma- 86.5 2.6 5.5E-05 38.4 7.1 66 178-245 17-84 (135)
76 COG1594 RPB9 DNA-directed RNA 86.4 0.41 8.8E-06 42.2 1.7 33 1-33 2-35 (113)
77 COG4888 Uncharacterized Zn rib 86.3 0.34 7.3E-06 41.4 1.1 29 3-31 24-57 (104)
78 PF10571 UPF0547: Uncharacteri 86.2 0.42 9.1E-06 31.0 1.3 23 3-30 2-24 (26)
79 PRK09210 RNA polymerase sigma 86.1 49 0.0011 35.0 17.8 91 66-156 130-255 (367)
80 TIGR00686 phnA alkylphosphonat 86.0 0.89 1.9E-05 39.5 3.6 50 2-53 3-54 (109)
81 PF13412 HTH_24: Winged helix- 85.8 1.5 3.1E-05 32.0 4.2 29 232-260 15-43 (48)
82 COG4640 Predicted membrane pro 85.8 0.4 8.6E-06 50.3 1.6 27 1-32 1-27 (465)
83 TIGR02393 RpoD_Cterm RNA polym 85.7 38 0.00082 33.2 18.5 26 233-258 195-220 (238)
84 PF12760 Zn_Tnp_IS1595: Transp 85.4 0.65 1.4E-05 34.0 2.1 27 2-28 19-45 (46)
85 KOG2496 Cdk activating kinase 85.2 2.1 4.5E-05 43.8 6.2 70 176-245 60-129 (325)
86 PRK14892 putative transcriptio 84.9 0.57 1.2E-05 40.3 1.9 31 2-32 22-54 (99)
87 PF07282 OrfB_Zn_ribbon: Putat 84.9 0.66 1.4E-05 36.7 2.2 28 3-31 30-57 (69)
88 TIGR02300 FYDLN_acid conserved 84.8 0.57 1.2E-05 41.9 1.9 29 3-33 11-39 (129)
89 PF05191 ADK_lid: Adenylate ki 84.4 0.37 8E-06 33.7 0.4 28 3-30 3-31 (36)
90 smart00342 HTH_ARAC helix_turn 84.2 8.6 0.00019 30.1 8.5 27 234-260 50-77 (84)
91 KOG4557 Origin recognition com 84.2 3.1 6.7E-05 40.5 6.6 82 77-161 95-181 (262)
92 PF01780 Ribosomal_L37ae: Ribo 84.0 0.55 1.2E-05 39.6 1.4 32 3-35 37-68 (90)
93 PF08273 Prim_Zn_Ribbon: Zinc- 83.9 0.79 1.7E-05 32.8 2.0 27 3-29 5-35 (40)
94 PF09297 zf-NADH-PPase: NADH p 83.7 0.82 1.8E-05 30.8 1.9 28 2-30 4-31 (32)
95 PRK09678 DNA-binding transcrip 83.6 0.76 1.6E-05 37.2 2.0 31 1-31 1-40 (72)
96 PRK11169 leucine-responsive tr 82.9 1.6 3.5E-05 40.6 4.2 38 226-263 20-57 (164)
97 COG2888 Predicted Zn-ribbon RN 82.4 0.8 1.7E-05 35.5 1.6 9 20-28 50-58 (61)
98 PF05876 Terminase_GpA: Phage 81.7 0.69 1.5E-05 51.7 1.4 34 1-34 200-243 (557)
99 PF13936 HTH_38: Helix-turn-he 81.5 2.1 4.6E-05 31.0 3.5 30 227-256 13-42 (44)
100 PF13717 zinc_ribbon_4: zinc-r 81.2 0.95 2.1E-05 31.6 1.5 29 2-30 3-35 (36)
101 smart00440 ZnF_C2C2 C2C2 Zinc 80.9 0.91 2E-05 32.4 1.3 27 3-29 2-37 (40)
102 PF04967 HTH_10: HTH DNA bindi 80.9 3.3 7.1E-05 31.5 4.4 26 234-259 23-48 (53)
103 PRK09710 lar restriction allev 80.8 1.1 2.3E-05 35.4 1.8 28 3-30 8-37 (64)
104 PRK11179 DNA-binding transcrip 80.7 2.3 4.9E-05 39.1 4.3 38 226-263 15-52 (153)
105 PF13730 HTH_36: Helix-turn-he 80.6 3.3 7.1E-05 30.9 4.4 26 235-260 26-51 (55)
106 PF06677 Auto_anti-p27: Sjogre 80.5 1.2 2.7E-05 32.0 1.9 23 3-27 19-41 (41)
107 PRK06266 transcription initiat 80.4 0.57 1.2E-05 44.6 0.2 30 3-32 119-148 (178)
108 PRK10220 hypothetical protein; 80.4 2.1 4.6E-05 37.2 3.7 51 2-54 4-56 (111)
109 PRK07405 RNA polymerase sigma 80.2 77 0.0017 32.8 17.6 25 232-256 274-298 (317)
110 PRK05932 RNA polymerase factor 79.9 16 0.00034 39.9 11.1 178 77-271 140-381 (455)
111 PRK14559 putative protein seri 79.9 0.95 2.1E-05 51.3 1.8 25 1-30 1-25 (645)
112 PF08613 Cyclin: Cyclin; Inte 79.8 15 0.00032 33.7 9.3 84 173-258 52-141 (149)
113 TIGR00244 transcriptional regu 79.6 1.4 2.9E-05 40.6 2.4 29 2-30 1-38 (147)
114 PF13542 HTH_Tnp_ISL3: Helix-t 79.0 3.5 7.5E-05 30.4 4.1 26 233-258 26-51 (52)
115 PF13384 HTH_23: Homeodomain-l 79.0 2.7 5.9E-05 30.7 3.5 28 234-261 17-44 (50)
116 PF08279 HTH_11: HTH domain; 78.8 3.8 8.2E-05 30.5 4.3 31 231-261 12-42 (55)
117 PTZ00255 60S ribosomal protein 78.7 1.5 3.2E-05 37.1 2.1 32 3-35 38-69 (90)
118 PF12773 DZR: Double zinc ribb 78.6 1.2 2.5E-05 32.9 1.4 11 20-30 29-39 (50)
119 PRK00135 scpB segregation and 78.4 7.8 0.00017 37.2 7.3 115 115-251 5-121 (188)
120 KOG1010 Rb (Retinoblastoma tum 78.0 5.5 0.00012 45.9 6.9 82 73-156 679-762 (920)
121 PF01325 Fe_dep_repress: Iron 77.9 4.7 0.0001 31.3 4.6 37 223-260 12-48 (60)
122 PF15616 TerY-C: TerY-C metal 77.2 1.4 3E-05 39.9 1.7 20 3-30 79-98 (131)
123 PRK13130 H/ACA RNA-protein com 76.9 1 2.3E-05 34.6 0.7 35 1-45 5-39 (56)
124 PRK12495 hypothetical protein; 76.7 1.6 3.4E-05 42.6 2.0 27 3-32 44-70 (226)
125 PF13545 HTH_Crp_2: Crp-like h 76.7 4.3 9.3E-05 32.1 4.3 29 233-261 27-55 (76)
126 TIGR02010 IscR iron-sulfur clu 76.5 5.6 0.00012 35.8 5.5 47 114-160 6-52 (135)
127 PF00356 LacI: Bacterial regul 76.5 2.7 5.8E-05 31.0 2.7 22 236-257 1-22 (46)
128 PF00325 Crp: Bacterial regula 76.0 2.5 5.4E-05 28.8 2.3 27 234-260 2-28 (32)
129 PF04545 Sigma70_r4: Sigma-70, 75.9 4.9 0.00011 29.5 4.1 28 231-258 17-44 (50)
130 TIGR00280 L37a ribosomal prote 75.9 1.8 3.8E-05 36.7 1.8 32 3-35 37-68 (91)
131 TIGR03697 NtcA_cyano global ni 75.8 9.9 0.00022 35.3 7.2 29 233-261 142-170 (193)
132 smart00419 HTH_CRP helix_turn_ 75.4 3.4 7.4E-05 29.4 3.1 30 232-261 6-35 (48)
133 PF02796 HTH_7: Helix-turn-hel 75.4 1.7 3.7E-05 31.5 1.5 28 229-256 16-43 (45)
134 TIGR01384 TFS_arch transcripti 75.1 1.8 3.9E-05 37.1 1.8 27 3-32 2-28 (104)
135 cd06571 Bac_DnaA_C C-terminal 74.6 9.8 0.00021 31.8 6.1 41 121-163 34-75 (90)
136 cd00092 HTH_CRP helix_turn_hel 74.6 8 0.00017 29.6 5.2 29 232-260 23-51 (67)
137 PF00325 Crp: Bacterial regula 74.1 4.1 8.9E-05 27.7 2.9 27 133-159 2-28 (32)
138 COG3478 Predicted nucleic-acid 73.9 2.1 4.6E-05 33.7 1.7 27 2-28 5-48 (68)
139 PF02082 Rrf2: Transcriptional 73.8 5.5 0.00012 32.6 4.3 46 116-161 8-53 (83)
140 KOG2906 RNA polymerase III sub 73.7 1.9 4.1E-05 36.8 1.5 31 1-31 1-32 (105)
141 PF10668 Phage_terminase: Phag 73.7 7.6 0.00017 30.4 4.7 40 214-256 5-44 (60)
142 PF08220 HTH_DeoR: DeoR-like h 73.5 3.3 7.2E-05 31.6 2.7 30 232-261 12-41 (57)
143 PF11672 DUF3268: Protein of u 73.3 2.5 5.5E-05 36.6 2.2 32 2-33 3-44 (102)
144 KOG0794 CDK8 kinase-activating 73.2 5.9 0.00013 39.2 4.9 75 177-256 46-120 (264)
145 PRK14890 putative Zn-ribbon RN 73.0 2.3 5.1E-05 33.0 1.7 26 3-29 9-34 (59)
146 PRK12286 rpmF 50S ribosomal pr 73.0 2.1 4.5E-05 33.1 1.5 25 2-32 28-52 (57)
147 PRK05949 RNA polymerase sigma 72.9 1.2E+02 0.0027 31.5 18.2 91 66-156 92-217 (327)
148 COG1326 Uncharacterized archae 72.7 2 4.2E-05 41.2 1.5 30 3-32 8-42 (201)
149 TIGR02395 rpoN_sigma RNA polym 72.7 37 0.00081 36.8 11.5 179 78-271 116-356 (429)
150 COG2824 PhnA Uncharacterized Z 72.0 3.8 8.2E-05 35.5 2.9 32 1-34 3-34 (112)
151 PRK03976 rpl37ae 50S ribosomal 71.8 2.6 5.5E-05 35.6 1.8 32 3-35 38-69 (90)
152 PF09986 DUF2225: Uncharacteri 71.7 8.7 0.00019 37.6 5.9 56 76-132 76-133 (214)
153 smart00659 RPOLCX RNA polymera 71.5 2.6 5.5E-05 30.8 1.6 25 3-29 4-28 (44)
154 PF01096 TFIIS_C: Transcriptio 71.4 2 4.3E-05 30.5 0.9 27 3-29 2-37 (39)
155 COG1522 Lrp Transcriptional re 71.3 5.6 0.00012 36.0 4.2 32 230-261 18-49 (154)
156 PF01783 Ribosomal_L32p: Ribos 71.3 1.7 3.6E-05 33.4 0.6 24 2-31 27-50 (56)
157 PF01726 LexA_DNA_bind: LexA D 71.0 4.6 0.0001 31.9 3.1 31 230-260 21-52 (65)
158 PRK05901 RNA polymerase sigma 70.9 1.8E+02 0.0039 32.4 16.5 89 66-154 272-395 (509)
159 TIGR02997 Sig70-cyanoRpoD RNA 70.8 1.3E+02 0.0028 30.7 17.7 26 232-257 267-292 (298)
160 smart00344 HTH_ASNC helix_turn 70.8 6.3 0.00014 33.5 4.2 30 232-261 15-44 (108)
161 PRK10857 DNA-binding transcrip 70.4 9.3 0.0002 35.8 5.5 47 114-160 6-52 (164)
162 TIGR01031 rpmF_bact ribosomal 69.9 3.2 6.9E-05 31.8 1.9 24 2-31 27-50 (55)
163 COG3809 Uncharacterized protei 69.9 2.9 6.3E-05 34.2 1.7 30 1-30 1-31 (88)
164 PF13545 HTH_Crp_2: Crp-like h 69.4 10 0.00022 29.9 4.9 47 118-164 3-59 (76)
165 PF01022 HTH_5: Bacterial regu 69.3 8.9 0.00019 27.9 4.1 32 230-261 11-42 (47)
166 smart00345 HTH_GNTR helix_turn 69.3 6.4 0.00014 29.1 3.5 29 232-260 17-46 (60)
167 TIGR00122 birA_repr_reg BirA b 68.8 8.1 0.00018 30.3 4.1 31 230-260 9-39 (69)
168 PRK07408 RNA polymerase sigma 68.6 1.3E+02 0.0028 29.9 15.3 26 233-258 218-243 (256)
169 PF05129 Elf1: Transcription e 68.5 2.2 4.8E-05 35.3 0.8 31 3-33 24-59 (81)
170 TIGR03879 near_KaiC_dom probab 68.3 4.7 0.0001 32.8 2.6 28 233-260 31-58 (73)
171 COG1318 Predicted transcriptio 68.3 7.6 0.00017 36.6 4.3 66 190-267 27-92 (182)
172 COG5333 CCL1 Cdk activating ki 68.1 4 8.6E-05 41.8 2.6 55 177-233 50-104 (297)
173 COG0333 RpmF Ribosomal protein 67.9 3.4 7.3E-05 32.0 1.6 25 1-31 27-51 (57)
174 smart00834 CxxC_CXXC_SSSS Puta 67.7 2.7 5.9E-05 29.4 1.0 28 3-30 7-36 (41)
175 COG1327 Predicted transcriptio 67.5 3.1 6.8E-05 38.3 1.6 29 2-30 1-38 (156)
176 TIGR03697 NtcA_cyano global ni 67.3 18 0.0004 33.5 6.9 30 132-161 142-171 (193)
177 PF12773 DZR: Double zinc ribb 67.2 3.9 8.5E-05 30.1 1.8 21 2-27 30-50 (50)
178 PF03604 DNA_RNApol_7kD: DNA d 66.4 3.6 7.8E-05 28.0 1.3 24 3-28 2-25 (32)
179 PRK11920 rirA iron-responsive 65.8 14 0.0003 34.2 5.6 46 114-160 6-51 (153)
180 TIGR02885 spore_sigF RNA polym 65.3 1.4E+02 0.003 29.0 16.7 27 232-258 197-223 (231)
181 PF09855 DUF2082: Nucleic-acid 65.2 4.2 9.1E-05 32.2 1.7 27 3-29 2-45 (64)
182 PF00165 HTH_AraC: Bacterial r 65.0 13 0.00029 26.1 4.2 28 232-259 6-33 (42)
183 smart00421 HTH_LUXR helix_turn 64.9 7.8 0.00017 28.1 3.1 26 234-259 18-43 (58)
184 PRK05978 hypothetical protein; 64.7 4.8 0.0001 37.2 2.3 30 2-31 34-63 (148)
185 PF10122 Mu-like_Com: Mu-like 64.3 2.1 4.5E-05 32.3 -0.2 29 2-30 5-34 (51)
186 COG1656 Uncharacterized conser 64.2 2.6 5.6E-05 39.5 0.4 29 2-30 98-140 (165)
187 TIGR01610 phage_O_Nterm phage 64.1 33 0.00072 28.9 7.2 30 231-260 44-73 (95)
188 PF14122 YokU: YokU-like prote 63.8 3.4 7.4E-05 34.4 1.0 21 19-39 34-54 (87)
189 PF12802 MarR_2: MarR family; 63.7 15 0.00032 27.7 4.6 27 234-260 21-47 (62)
190 COG0777 AccD Acetyl-CoA carbox 63.6 2.3 5E-05 42.9 -0.0 30 1-30 28-57 (294)
191 PRK07598 RNA polymerase sigma 63.2 2.3E+02 0.0049 30.8 18.7 98 66-163 176-308 (415)
192 PRK05654 acetyl-CoA carboxylas 63.2 2.3 5E-05 43.6 -0.1 29 2-30 28-56 (292)
193 TIGR00515 accD acetyl-CoA carb 63.1 2.3 5.1E-05 43.4 -0.1 29 2-30 27-55 (285)
194 PF11023 DUF2614: Protein of u 63.0 2.8 6.2E-05 36.7 0.4 40 1-43 69-108 (114)
195 PF06044 DRP: Dam-replacing fa 62.5 3.7 8.1E-05 40.7 1.2 29 2-30 32-63 (254)
196 PF14446 Prok-RING_1: Prokaryo 62.4 5.1 0.00011 30.7 1.6 26 2-30 6-31 (54)
197 PF01325 Fe_dep_repress: Iron 62.3 22 0.00048 27.5 5.3 38 122-160 12-49 (60)
198 PF05225 HTH_psq: helix-turn-h 62.3 13 0.00028 27.1 3.8 28 231-259 14-41 (45)
199 PRK07500 rpoH2 RNA polymerase 62.0 1.9E+02 0.0041 29.4 16.2 27 232-258 243-269 (289)
200 PF07754 DUF1610: Domain of un 61.7 6.5 0.00014 25.0 1.8 24 4-28 1-24 (24)
201 PF13613 HTH_Tnp_4: Helix-turn 61.7 9.9 0.00022 28.5 3.2 37 225-261 10-46 (53)
202 CHL00174 accD acetyl-CoA carbo 61.5 2.6 5.6E-05 43.3 -0.1 29 2-30 39-67 (296)
203 cd00350 rubredoxin_like Rubred 61.5 5.4 0.00012 27.1 1.5 23 3-28 3-25 (33)
204 PF13613 HTH_Tnp_4: Helix-turn 61.1 15 0.00033 27.5 4.1 35 130-164 16-50 (53)
205 PHA02591 hypothetical protein; 61.1 10 0.00022 31.1 3.3 31 226-256 51-81 (83)
206 PF14353 CpXC: CpXC protein 59.9 4.9 0.00011 35.7 1.4 29 2-30 2-48 (128)
207 PRK11161 fumarate/nitrate redu 59.5 31 0.00067 33.3 7.1 29 233-261 183-211 (235)
208 PRK13918 CRP/FNR family transc 59.3 31 0.00068 32.3 6.9 30 232-261 147-176 (202)
209 TIGR02479 FliA_WhiG RNA polyme 59.0 1.7E+02 0.0038 28.1 17.4 25 233-257 190-214 (224)
210 PF02954 HTH_8: Bacterial regu 59.0 13 0.00028 26.5 3.2 24 235-258 19-42 (42)
211 PRK05911 RNA polymerase sigma 58.8 2E+02 0.0043 28.7 18.3 27 232-258 219-245 (257)
212 PF08281 Sigma70_r4_2: Sigma-7 58.8 14 0.00029 27.4 3.5 26 232-257 24-49 (54)
213 cd00092 HTH_CRP helix_turn_hel 58.3 36 0.00078 25.8 6.0 31 130-160 22-52 (67)
214 COG5349 Uncharacterized protei 57.9 6 0.00013 35.2 1.5 28 3-31 23-51 (126)
215 PF08279 HTH_11: HTH domain; 57.7 25 0.00054 26.0 4.8 35 127-161 9-43 (55)
216 smart00420 HTH_DEOR helix_turn 57.4 21 0.00045 25.5 4.3 28 233-260 13-40 (53)
217 PF14255 Cys_rich_CPXG: Cystei 57.4 5.7 0.00012 30.2 1.2 29 2-30 1-34 (52)
218 TIGR02147 Fsuc_second hypothet 57.3 2.1E+02 0.0045 29.1 12.8 123 123-261 16-166 (271)
219 PF00165 HTH_AraC: Bacterial r 57.2 16 0.00034 25.7 3.4 27 131-157 6-32 (42)
220 PRK10434 srlR DNA-bindng trans 57.1 8.7 0.00019 38.5 2.8 29 232-260 17-45 (256)
221 TIGR00738 rrf2_super rrf2 fami 57.0 24 0.00052 31.1 5.4 45 116-160 8-52 (132)
222 KOG0402 60S ribosomal protein 56.3 4.8 0.0001 33.4 0.6 30 3-33 38-67 (92)
223 cd06170 LuxR_C_like C-terminal 56.3 14 0.00031 26.8 3.3 27 234-260 15-41 (57)
224 PRK06288 RNA polymerase sigma 56.3 2.2E+02 0.0047 28.4 16.6 25 233-257 227-251 (268)
225 PRK00241 nudC NADH pyrophospha 55.9 8.2 0.00018 38.8 2.4 31 2-33 100-130 (256)
226 COG3677 Transposase and inacti 55.5 7.1 0.00015 35.2 1.7 31 1-31 30-64 (129)
227 TIGR02605 CxxC_CxxC_SSSS putat 55.4 6 0.00013 29.4 1.0 26 3-28 7-34 (52)
228 PF01978 TrmB: Sugar-specific 55.3 13 0.00028 29.0 3.0 37 223-260 12-48 (68)
229 TIGR02394 rpoS_proteo RNA poly 55.2 2.4E+02 0.0051 28.5 18.0 25 233-257 241-265 (285)
230 COG3877 Uncharacterized protei 54.9 8.2 0.00018 33.5 1.9 61 123-193 52-114 (122)
231 PRK08402 replication factor A; 54.7 6.7 0.00015 41.4 1.6 26 3-29 214-239 (355)
232 PF02082 Rrf2: Transcriptional 54.5 14 0.0003 30.2 3.1 37 224-260 15-51 (83)
233 COG1996 RPC10 DNA-directed RNA 54.5 6.2 0.00013 29.6 0.9 25 3-28 8-32 (49)
234 PF14502 HTH_41: Helix-turn-he 54.3 14 0.00029 27.7 2.7 31 235-265 7-37 (48)
235 smart00418 HTH_ARSR helix_turn 54.3 23 0.00051 26.0 4.2 29 232-260 8-36 (66)
236 PF13518 HTH_28: Helix-turn-he 54.0 26 0.00056 25.3 4.3 25 236-260 14-38 (52)
237 PRK08215 sporulation sigma fac 53.7 2.3E+02 0.0051 28.0 17.5 25 233-257 224-248 (258)
238 TIGR02944 suf_reg_Xantho FeS a 53.7 32 0.00069 30.4 5.6 46 114-160 7-52 (130)
239 PRK09391 fixK transcriptional 53.5 49 0.0011 32.1 7.4 30 232-261 177-206 (230)
240 KOG1088 Uncharacterized conser 53.4 6.5 0.00014 34.7 1.0 18 14-31 92-109 (124)
241 PRK11161 fumarate/nitrate redu 53.4 49 0.0011 31.9 7.4 33 132-164 183-215 (235)
242 TIGR01321 TrpR trp operon repr 53.0 17 0.00036 31.1 3.4 30 230-259 51-80 (94)
243 KOG2593 Transcription initiati 52.9 6.6 0.00014 42.0 1.2 30 3-32 130-165 (436)
244 PF14206 Cys_rich_CPCC: Cystei 52.8 10 0.00022 31.2 2.1 28 2-29 2-29 (78)
245 PF01371 Trp_repressor: Trp re 52.8 21 0.00045 30.0 3.9 31 230-260 45-75 (87)
246 TIGR02844 spore_III_D sporulat 52.6 13 0.00028 30.8 2.6 24 233-256 18-41 (80)
247 smart00550 Zalpha Z-DNA-bindin 52.5 29 0.00062 27.4 4.6 32 229-260 16-48 (68)
248 PRK12380 hydrogenase nickel in 52.5 6.7 0.00015 34.5 1.0 35 2-41 71-105 (113)
249 PF04161 Arv1: Arv1-like famil 52.4 7.5 0.00016 37.8 1.4 31 2-32 1-36 (208)
250 PF12116 SpoIIID: Stage III sp 52.4 9.7 0.00021 31.5 1.8 35 224-258 9-43 (82)
251 PF12840 HTH_20: Helix-turn-he 52.3 23 0.0005 27.1 3.9 31 231-261 21-51 (61)
252 PF00392 GntR: Bacterial regul 52.3 16 0.00034 28.3 3.0 29 232-260 21-50 (64)
253 cd04762 HTH_MerR-trunc Helix-T 51.9 15 0.00033 25.7 2.7 22 236-257 2-23 (49)
254 cd07377 WHTH_GntR Winged helix 51.9 17 0.00036 27.4 3.1 25 236-260 27-51 (66)
255 cd00090 HTH_ARSR Arsenical Res 51.6 27 0.00059 26.4 4.3 26 235-260 21-46 (78)
256 TIGR01764 excise DNA binding d 51.4 15 0.00034 25.8 2.7 23 235-257 2-24 (49)
257 PF08299 Bac_DnaA_C: Bacterial 51.3 42 0.0009 26.7 5.4 35 121-157 35-70 (70)
258 PF00440 TetR_N: Bacterial reg 51.2 32 0.0007 24.8 4.3 34 222-256 4-38 (47)
259 COG1959 Predicted transcriptio 51.0 34 0.00074 31.5 5.5 45 116-160 8-52 (150)
260 smart00647 IBR In Between Ring 50.9 12 0.00027 28.4 2.2 29 2-30 19-50 (64)
261 PRK02935 hypothetical protein; 50.9 10 0.00022 32.9 1.8 39 2-43 71-109 (110)
262 PF07638 Sigma70_ECF: ECF sigm 50.8 24 0.00052 33.3 4.6 25 235-259 152-176 (185)
263 PF08280 HTH_Mga: M protein tr 50.8 22 0.00048 27.2 3.6 30 232-261 17-46 (59)
264 PF03119 DNA_ligase_ZBD: NAD-d 50.8 9 0.00019 25.2 1.1 22 3-25 1-22 (28)
265 smart00401 ZnF_GATA zinc finge 50.7 11 0.00024 28.4 1.8 28 3-30 5-35 (52)
266 PRK11511 DNA-binding transcrip 50.6 79 0.0017 27.9 7.7 54 215-274 7-60 (127)
267 cd00202 ZnF_GATA Zinc finger D 50.6 5.9 0.00013 30.2 0.3 29 3-31 1-32 (54)
268 PF00356 LacI: Bacterial regul 50.6 19 0.0004 26.5 2.9 20 135-154 1-20 (46)
269 TIGR02944 suf_reg_Xantho FeS a 50.6 31 0.00067 30.5 5.0 38 223-261 15-52 (130)
270 PRK10870 transcriptional repre 50.3 59 0.0013 30.6 7.1 29 232-260 69-97 (176)
271 COG1779 C4-type Zn-finger prot 50.2 8.4 0.00018 37.2 1.3 34 2-35 15-58 (201)
272 PRK04217 hypothetical protein; 50.2 20 0.00044 31.4 3.6 27 233-259 57-83 (110)
273 PF10080 DUF2318: Predicted me 49.9 9.6 0.00021 33.0 1.5 28 3-32 37-64 (102)
274 PF13744 HTH_37: Helix-turn-he 49.9 49 0.0011 26.8 5.7 47 226-276 23-69 (80)
275 PRK13509 transcriptional repre 49.8 15 0.00033 36.6 3.2 29 232-260 17-45 (251)
276 PRK14088 dnaA chromosomal repl 49.6 1.3E+02 0.0029 32.5 10.7 51 208-260 360-413 (440)
277 TIGR00100 hypA hydrogenase nic 49.6 8.2 0.00018 34.0 1.1 25 2-29 71-95 (115)
278 cd06171 Sigma70_r4 Sigma70, re 49.4 30 0.00065 24.3 4.0 27 233-259 25-51 (55)
279 PF13824 zf-Mss51: Zinc-finger 49.4 11 0.00025 28.9 1.7 24 3-30 1-24 (55)
280 PF09526 DUF2387: Probable met 49.1 12 0.00025 30.3 1.8 30 2-31 9-41 (71)
281 PF00196 GerE: Bacterial regul 49.0 18 0.0004 27.2 2.9 28 233-260 17-44 (58)
282 COG1510 Predicted transcriptio 49.0 36 0.00077 32.3 5.2 60 196-262 10-69 (177)
283 PF00301 Rubredoxin: Rubredoxi 49.0 7.5 0.00016 28.9 0.6 14 21-34 2-15 (47)
284 PF12802 MarR_2: MarR family; 48.9 41 0.0009 25.2 4.9 42 120-161 8-49 (62)
285 PRK08329 threonine synthase; V 48.9 11 0.00024 39.4 2.2 26 1-31 1-26 (347)
286 PF13022 HTH_Tnp_1_2: Helix-tu 48.9 21 0.00047 32.6 3.7 41 216-256 13-56 (142)
287 TIGR00281 segregation and cond 48.9 64 0.0014 31.0 7.1 119 116-257 3-124 (186)
288 cd00569 HTH_Hin_like Helix-tur 48.8 18 0.00038 22.9 2.5 21 234-254 21-41 (42)
289 PF01485 IBR: IBR domain; Int 48.3 13 0.00029 28.1 2.0 28 2-30 19-50 (64)
290 PRK11014 transcriptional repre 48.3 22 0.00049 32.0 3.8 39 223-261 14-52 (141)
291 PF04606 Ogr_Delta: Ogr/Delta- 48.1 8.6 0.00019 28.3 0.8 28 3-30 1-37 (47)
292 TIGR03831 YgiT_finger YgiT-typ 47.8 13 0.00028 26.4 1.8 10 21-30 33-42 (46)
293 PF09339 HTH_IclR: IclR helix- 47.8 25 0.00054 26.0 3.3 31 231-261 15-45 (52)
294 PF09862 DUF2089: Protein of u 47.8 18 0.00039 31.9 2.9 27 234-260 49-75 (113)
295 smart00419 HTH_CRP helix_turn_ 47.6 29 0.00063 24.4 3.6 30 131-160 6-35 (48)
296 PF02042 RWP-RK: RWP-RK domain 47.4 23 0.0005 26.9 3.1 28 232-259 13-40 (52)
297 COG1725 Predicted transcriptio 47.3 20 0.00042 32.3 3.1 29 232-260 32-61 (125)
298 TIGR03830 CxxCG_CxxCG_HTH puta 47.3 13 0.00028 32.5 2.0 27 4-30 1-41 (127)
299 PRK10402 DNA-binding transcrip 47.1 42 0.00091 32.4 5.8 29 233-261 168-196 (226)
300 PF13551 HTH_29: Winged helix- 46.9 39 0.00085 28.3 5.0 27 236-262 14-40 (112)
301 TIGR02443 conserved hypothetic 46.6 14 0.0003 28.8 1.8 28 2-29 10-40 (59)
302 cd04761 HTH_MerR-SF Helix-Turn 46.5 18 0.0004 25.8 2.4 23 236-258 2-24 (49)
303 PRK00118 putative DNA-binding 46.5 24 0.00052 30.6 3.5 27 233-259 32-58 (104)
304 PRK11511 DNA-binding transcrip 46.3 61 0.0013 28.6 6.2 42 115-157 8-49 (127)
305 cd00730 rubredoxin Rubredoxin; 46.2 14 0.00029 27.8 1.6 13 21-33 2-14 (50)
306 PRK06030 hypothetical protein; 46.2 59 0.0013 29.2 6.0 39 121-161 59-97 (124)
307 smart00346 HTH_ICLR helix_turn 46.1 49 0.0011 26.8 5.3 28 233-260 19-46 (91)
308 PF01381 HTH_3: Helix-turn-hel 46.1 31 0.00067 25.3 3.7 40 232-276 7-46 (55)
309 PRK11753 DNA-binding transcrip 46.1 84 0.0018 29.5 7.6 30 132-161 167-196 (211)
310 PRK10219 DNA-binding transcrip 45.9 74 0.0016 26.9 6.5 39 118-157 7-45 (107)
311 PRK03824 hypA hydrogenase nick 45.7 9.9 0.00022 34.5 1.0 11 19-29 106-116 (135)
312 PF01396 zf-C4_Topoisom: Topoi 45.5 20 0.00044 25.3 2.4 30 2-31 2-35 (39)
313 KOG1010 Rb (Retinoblastoma tum 44.8 1.1E+02 0.0024 35.9 9.1 57 76-135 36-92 (920)
314 PF04079 DUF387: Putative tran 44.6 2.7E+02 0.0058 26.0 10.5 40 118-162 2-41 (159)
315 PF04216 FdhE: Protein involve 44.6 9.5 0.00021 38.9 0.8 29 2-30 173-207 (290)
316 PRK11753 DNA-binding transcrip 44.3 81 0.0018 29.6 7.2 29 233-261 167-195 (211)
317 PRK10402 DNA-binding transcrip 44.3 61 0.0013 31.3 6.5 50 115-164 151-200 (226)
318 COG3620 Predicted transcriptio 44.2 24 0.00052 33.2 3.3 43 231-273 15-72 (187)
319 PF01155 HypA: Hydrogenase exp 44.2 5 0.00011 35.2 -1.1 25 2-29 71-95 (113)
320 PF13542 HTH_Tnp_ISL3: Helix-t 44.2 85 0.0018 22.8 5.8 24 134-157 28-51 (52)
321 PF08646 Rep_fac-A_C: Replicat 44.1 15 0.00032 33.3 2.0 28 3-32 20-49 (146)
322 PF12728 HTH_17: Helix-turn-he 44.0 25 0.00054 25.6 2.8 22 235-256 2-23 (51)
323 PRK13413 mpi multiple promoter 44.0 55 0.0012 31.2 6.0 25 234-258 172-196 (200)
324 PRK12336 translation initiatio 43.9 9.7 0.00021 36.9 0.7 29 2-30 99-129 (201)
325 PF09723 Zn-ribbon_8: Zinc rib 43.8 10 0.00022 27.2 0.6 26 3-28 7-34 (42)
326 PRK07921 RNA polymerase sigma 43.6 4E+02 0.0086 27.7 17.1 90 66-155 87-211 (324)
327 TIGR02405 trehalos_R_Ecol treh 43.6 17 0.00037 36.6 2.5 43 234-278 1-43 (311)
328 COG1508 RpoN DNA-directed RNA 43.4 3.5E+02 0.0076 29.6 12.3 41 234-274 330-371 (444)
329 PF05460 ORC6: Origin recognit 43.3 7.9 0.00017 40.8 0.0 79 183-261 5-84 (353)
330 smart00550 Zalpha Z-DNA-bindin 43.1 62 0.0013 25.5 5.1 39 123-161 11-50 (68)
331 PF00376 MerR: MerR family reg 43.0 18 0.00039 25.4 1.8 20 236-255 1-20 (38)
332 PF13412 HTH_24: Winged helix- 43.0 71 0.0015 22.9 5.1 29 131-159 15-43 (48)
333 PF05344 DUF746: Domain of Unk 43.0 38 0.00083 26.9 3.8 32 229-260 8-39 (65)
334 PRK15418 transcriptional regul 43.0 31 0.00067 35.8 4.3 44 225-268 20-63 (318)
335 cd01104 HTH_MlrA-CarA Helix-Tu 42.5 25 0.00054 27.1 2.8 23 236-258 2-24 (68)
336 TIGR02985 Sig70_bacteroi1 RNA 42.5 24 0.00051 31.4 3.0 26 233-258 128-153 (161)
337 TIGR02392 rpoH_proteo alternat 42.4 3.6E+02 0.0078 26.9 16.6 26 232-257 234-259 (270)
338 PF13453 zf-TFIIB: Transcripti 42.3 14 0.00031 26.1 1.2 28 3-30 1-29 (41)
339 PRK10219 DNA-binding transcrip 42.1 74 0.0016 26.9 5.9 50 220-275 8-57 (107)
340 PF06397 Desulfoferrod_N: Desu 41.9 8.8 0.00019 26.9 0.1 21 3-23 8-28 (36)
341 COG4068 Uncharacterized protei 41.8 5.1 0.00011 31.0 -1.2 24 3-31 10-34 (64)
342 COG3877 Uncharacterized protei 41.8 1.5E+02 0.0032 25.9 7.4 25 3-32 8-32 (122)
343 PF04545 Sigma70_r4: Sigma-70, 41.2 52 0.0011 23.9 4.2 31 131-161 18-48 (50)
344 TIGR02980 SigBFG RNA polymeras 40.8 3.4E+02 0.0073 26.1 16.9 26 233-258 193-218 (227)
345 smart00354 HTH_LACI helix_turn 40.8 24 0.00051 27.9 2.4 22 235-256 1-22 (70)
346 PRK09526 lacI lac repressor; R 40.8 21 0.00045 36.2 2.7 43 234-278 5-47 (342)
347 PF13790 DUF4182: Domain of un 40.7 14 0.00031 26.2 0.9 13 19-31 2-14 (38)
348 PHA00542 putative Cro-like pro 40.7 24 0.00052 29.0 2.5 42 230-275 27-68 (82)
349 PF04703 FaeA: FaeA-like prote 40.4 57 0.0012 25.6 4.4 36 129-164 11-46 (62)
350 PF00196 GerE: Bacterial regul 40.1 43 0.00092 25.2 3.7 33 132-164 17-49 (58)
351 PRK09492 treR trehalose repres 39.9 20 0.00042 36.0 2.3 43 234-278 4-46 (315)
352 PRK10572 DNA-binding transcrip 39.7 3.9E+02 0.0085 26.5 17.7 39 118-157 185-223 (290)
353 PF13556 HTH_30: PucR C-termin 39.3 35 0.00076 26.0 3.1 31 233-263 11-41 (59)
354 PF03444 HrcA_DNA-bdg: Winged 39.3 39 0.00083 27.9 3.4 30 231-260 20-49 (78)
355 cd04476 RPA1_DBD_C RPA1_DBD_C: 39.3 19 0.0004 33.4 1.8 27 3-31 36-62 (166)
356 PRK12529 RNA polymerase sigma 39.3 28 0.0006 32.4 3.0 24 233-256 142-165 (178)
357 TIGR02850 spore_sigG RNA polym 39.2 3.9E+02 0.0084 26.3 17.4 26 233-258 221-246 (254)
358 TIGR02702 SufR_cyano iron-sulf 39.2 48 0.001 31.8 4.7 28 233-260 14-41 (203)
359 PRK13918 CRP/FNR family transc 39.0 1.1E+02 0.0024 28.5 7.2 33 132-164 148-180 (202)
360 PRK09649 RNA polymerase sigma 38.8 20 0.00042 33.7 1.9 27 233-259 145-171 (185)
361 TIGR00155 pqiA_fam integral me 38.8 19 0.00042 38.6 2.1 29 3-31 15-44 (403)
362 KOG3507 DNA-directed RNA polym 38.7 17 0.00037 28.2 1.2 23 4-28 23-45 (62)
363 TIGR00310 ZPR1_znf ZPR1 zinc f 38.7 16 0.00036 35.2 1.4 29 3-31 2-41 (192)
364 PF13443 HTH_26: Cro/C1-type H 38.7 48 0.0011 25.0 3.8 40 233-276 9-48 (63)
365 PRK00564 hypA hydrogenase nick 38.6 14 0.00031 32.6 0.9 36 2-41 72-107 (117)
366 TIGR02999 Sig-70_X6 RNA polyme 38.5 29 0.00063 32.1 3.0 25 233-257 149-173 (183)
367 PRK10014 DNA-binding transcrip 38.5 23 0.00049 36.0 2.5 44 233-278 5-48 (342)
368 PF12833 HTH_18: Helix-turn-he 38.4 1.1E+02 0.0024 24.2 6.1 67 81-157 1-70 (81)
369 PRK07122 RNA polymerase sigma 38.3 4.2E+02 0.0091 26.5 17.1 27 232-258 229-255 (264)
370 PRK10411 DNA-binding transcrip 38.3 30 0.00065 34.3 3.3 28 233-260 17-44 (240)
371 PF14768 RPA_interact_C: Repli 38.3 26 0.00057 28.9 2.4 27 3-32 1-27 (82)
372 PF05344 DUF746: Domain of Unk 38.2 71 0.0015 25.4 4.6 36 127-162 7-42 (65)
373 PRK09391 fixK transcriptional 38.2 1.3E+02 0.0028 29.1 7.7 32 132-163 178-209 (230)
374 PRK03681 hypA hydrogenase nick 38.0 15 0.00031 32.4 0.8 36 2-41 71-106 (114)
375 PF14493 HTH_40: Helix-turn-he 38.0 58 0.0013 27.0 4.5 47 228-275 7-53 (91)
376 PF04703 FaeA: FaeA-like prote 38.0 50 0.0011 25.9 3.8 30 232-261 13-42 (62)
377 COG1386 scpB Chromosome segreg 37.9 1.8E+02 0.0038 27.9 8.2 120 116-260 10-132 (184)
378 PRK14559 putative protein seri 37.7 18 0.00038 41.3 1.7 25 3-32 29-53 (645)
379 PRK14086 dnaA chromosomal repl 37.6 69 0.0015 36.4 6.2 70 92-163 528-599 (617)
380 PRK07406 RNA polymerase sigma 37.5 5.3E+02 0.012 27.4 18.0 26 233-258 330-355 (373)
381 PF06892 Phage_CP76: Phage reg 37.3 37 0.0008 31.8 3.5 38 236-276 22-59 (162)
382 PRK01110 rpmF 50S ribosomal pr 37.3 17 0.00037 28.4 1.0 27 2-35 28-54 (60)
383 PF14471 DUF4428: Domain of un 37.2 12 0.00026 28.2 0.1 27 3-30 1-30 (51)
384 PF01047 MarR: MarR family; I 37.1 62 0.0014 24.0 4.2 27 234-260 17-43 (59)
385 PRK07670 RNA polymerase sigma 36.9 4.2E+02 0.0091 26.0 18.0 27 232-258 215-241 (251)
386 PF03811 Zn_Tnp_IS1: InsA N-te 36.8 28 0.00061 24.3 2.0 25 2-26 6-35 (36)
387 PRK01381 Trp operon repressor; 36.8 28 0.0006 30.0 2.3 37 226-262 47-83 (99)
388 TIGR00498 lexA SOS regulatory 36.6 36 0.00078 32.4 3.4 32 230-261 21-53 (199)
389 PF10668 Phage_terminase: Phag 36.6 90 0.002 24.4 4.9 38 113-153 5-42 (60)
390 TIGR00595 priA primosomal prot 36.5 22 0.00048 39.3 2.2 29 2-31 223-251 (505)
391 PRK09642 RNA polymerase sigma 36.5 17 0.00038 32.8 1.1 27 233-259 121-147 (160)
392 PRK11014 transcriptional repre 36.5 70 0.0015 28.8 5.1 46 116-161 8-53 (141)
393 PRK10572 DNA-binding transcrip 36.4 1.3E+02 0.0029 29.9 7.7 14 17-30 72-85 (290)
394 PF13463 HTH_27: Winged helix 36.4 70 0.0015 24.3 4.5 38 123-161 9-46 (68)
395 PRK00430 fis global DNA-bindin 36.3 1.5E+02 0.0033 25.1 6.8 26 234-259 68-93 (95)
396 PF10083 DUF2321: Uncharacteri 36.2 16 0.00034 34.0 0.7 27 3-37 30-56 (158)
397 TIGR03070 couple_hipB transcri 36.0 42 0.00091 24.4 3.0 40 232-276 13-52 (58)
398 smart00347 HTH_MARR helix_turn 36.0 78 0.0017 25.6 5.0 28 234-261 24-51 (101)
399 PRK09645 RNA polymerase sigma 35.9 33 0.00072 31.4 3.0 25 233-257 133-157 (173)
400 cd04764 HTH_MlrA-like_sg1 Heli 35.9 37 0.0008 26.2 2.8 23 236-258 2-24 (67)
401 COG0664 Crp cAMP-binding prote 35.8 1.3E+02 0.0028 27.7 7.0 29 233-261 170-198 (214)
402 COG2816 NPY1 NTP pyrophosphohy 35.8 25 0.00055 35.8 2.2 30 2-32 112-141 (279)
403 PRK09047 RNA polymerase factor 35.6 35 0.00075 30.7 3.0 26 233-258 121-146 (161)
404 PF04810 zf-Sec23_Sec24: Sec23 35.5 28 0.00061 24.7 1.8 28 2-29 3-33 (40)
405 PF13411 MerR_1: MerR HTH fami 35.5 30 0.00065 26.7 2.2 24 236-259 2-25 (69)
406 TIGR02531 yecD_yerC TrpR-relat 35.4 48 0.001 27.9 3.5 21 233-253 49-69 (88)
407 PRK09392 ftrB transcriptional 35.4 93 0.002 30.0 6.2 30 233-262 172-201 (236)
408 TIGR01562 FdhE formate dehydro 35.3 21 0.00045 36.9 1.6 27 3-29 186-219 (305)
409 PRK09954 putative kinase; Prov 35.3 48 0.0011 34.5 4.4 29 232-260 15-43 (362)
410 PRK14987 gluconate operon tran 35.3 23 0.00051 35.8 2.0 24 234-257 5-28 (331)
411 PF13463 HTH_27: Winged helix 35.2 53 0.0012 25.0 3.6 30 231-260 15-44 (68)
412 PRK15103 paraquat-inducible me 35.1 25 0.00054 38.0 2.2 30 3-32 12-42 (419)
413 cd00131 PAX Paired Box domain 35.0 50 0.0011 29.5 3.9 30 233-262 32-61 (128)
414 PRK12543 RNA polymerase sigma 35.0 52 0.0011 30.5 4.1 27 233-259 132-158 (179)
415 PRK06759 RNA polymerase factor 34.9 37 0.0008 30.3 3.0 25 233-257 121-145 (154)
416 smart00421 HTH_LUXR helix_turn 34.8 71 0.0015 22.8 4.1 31 134-164 19-49 (58)
417 COG1321 TroR Mn-dependent tran 34.8 57 0.0012 30.3 4.3 37 223-260 14-50 (154)
418 PF07900 DUF1670: Protein of u 34.8 36 0.00078 33.5 3.0 29 232-260 103-131 (220)
419 PF04218 CENP-B_N: CENP-B N-te 34.8 26 0.00057 26.4 1.7 24 234-257 22-45 (53)
420 PF13913 zf-C2HC_2: zinc-finge 34.7 20 0.00043 22.8 0.8 10 1-10 2-11 (25)
421 PF13011 LZ_Tnp_IS481: leucine 34.7 78 0.0017 26.5 4.6 36 225-260 16-51 (85)
422 PF01418 HTH_6: Helix-turn-hel 34.5 37 0.0008 27.4 2.7 27 233-259 33-59 (77)
423 PRK12525 RNA polymerase sigma 34.5 36 0.00077 31.2 2.9 25 233-257 133-157 (168)
424 smart00422 HTH_MERR helix_turn 34.4 35 0.00075 26.3 2.4 22 236-257 2-23 (70)
425 smart00351 PAX Paired Box doma 34.3 53 0.0012 29.1 3.9 29 234-262 33-61 (125)
426 PF06676 DUF1178: Protein of u 34.2 19 0.00041 33.3 1.0 24 91-114 99-122 (148)
427 COG3413 Predicted DNA binding 34.2 56 0.0012 31.6 4.4 26 234-259 178-203 (215)
428 PRK10130 transcriptional regul 34.1 2.9E+02 0.0063 29.0 10.0 54 115-182 239-292 (350)
429 PRK12523 RNA polymerase sigma 33.9 37 0.00079 31.2 2.9 25 233-257 134-158 (172)
430 cd00729 rubredoxin_SM Rubredox 33.9 27 0.00059 23.9 1.5 23 3-28 4-26 (34)
431 PF05732 RepL: Firmicute plasm 33.9 74 0.0016 29.8 4.9 28 234-261 75-102 (165)
432 PRK07218 replication factor A; 33.8 21 0.00045 38.7 1.3 31 3-42 299-329 (423)
433 COG2093 DNA-directed RNA polym 33.8 24 0.00052 27.8 1.3 22 3-29 6-27 (64)
434 PF00126 HTH_1: Bacterial regu 33.8 76 0.0016 24.1 4.2 27 236-262 15-41 (60)
435 TIGR02947 SigH_actino RNA poly 33.8 37 0.0008 31.8 3.0 27 233-259 146-172 (193)
436 PRK03564 formate dehydrogenase 33.7 24 0.00053 36.5 1.8 27 3-29 189-221 (309)
437 PF01726 LexA_DNA_bind: LexA D 33.6 69 0.0015 25.2 4.0 36 128-163 20-56 (65)
438 PRK09480 slmA division inhibit 33.4 49 0.0011 30.6 3.7 43 215-257 11-53 (194)
439 PRK10906 DNA-binding transcrip 33.4 35 0.00076 34.1 2.8 29 232-260 17-45 (252)
440 PRK08351 DNA-directed RNA poly 33.3 27 0.00059 27.4 1.6 20 3-29 5-24 (61)
441 PF10058 DUF2296: Predicted in 33.3 22 0.00048 27.1 1.1 27 2-28 23-52 (54)
442 PRK12366 replication factor A; 33.3 19 0.00042 41.0 1.1 24 3-29 534-557 (637)
443 COG3355 Predicted transcriptio 33.2 73 0.0016 28.7 4.5 39 224-262 32-70 (126)
444 TIGR02937 sigma70-ECF RNA poly 33.2 53 0.0012 28.3 3.7 27 233-259 125-151 (158)
445 PRK10703 DNA-binding transcrip 33.2 31 0.00066 35.1 2.5 42 235-278 2-43 (341)
446 PHA00689 hypothetical protein 33.2 22 0.00049 26.6 1.0 10 19-28 16-25 (62)
447 TIGR01481 ccpA catabolite cont 33.1 29 0.00064 34.9 2.3 42 235-278 2-43 (329)
448 PRK12531 RNA polymerase sigma 33.1 39 0.00084 31.8 3.0 26 233-258 156-181 (194)
449 PRK14088 dnaA chromosomal repl 33.1 58 0.0013 35.3 4.7 68 91-161 345-415 (440)
450 PRK12528 RNA polymerase sigma 33.1 41 0.00088 30.4 3.0 26 233-258 128-153 (161)
451 cd04763 HTH_MlrA-like Helix-Tu 33.0 43 0.00093 26.0 2.7 23 236-258 2-24 (68)
452 TIGR01562 FdhE formate dehydro 33.0 25 0.00055 36.3 1.8 9 22-30 254-262 (305)
453 PRK05572 sporulation sigma fac 32.9 4.8E+02 0.01 25.6 16.3 26 233-258 217-242 (252)
454 COG1510 Predicted transcriptio 32.9 79 0.0017 30.0 4.8 37 123-159 31-67 (177)
455 PF09339 HTH_IclR: IclR helix- 32.8 77 0.0017 23.3 4.0 35 125-159 10-44 (52)
456 smart00345 HTH_GNTR helix_turn 32.7 77 0.0017 23.1 4.0 26 135-160 22-47 (60)
457 COG1309 AcrR Transcriptional r 32.6 47 0.001 29.1 3.3 40 219-259 17-57 (201)
458 PRK14873 primosome assembly pr 32.6 25 0.00055 40.3 1.8 27 2-29 393-419 (665)
459 TIGR02297 HpaA 4-hydroxyphenyl 32.4 2.3E+02 0.005 28.0 8.6 38 119-157 189-226 (287)
460 PRK12423 LexA repressor; Provi 32.4 78 0.0017 30.4 5.0 31 230-260 21-52 (202)
461 TIGR02010 IscR iron-sulfur clu 32.3 66 0.0014 28.8 4.2 40 222-261 13-52 (135)
462 cd06170 LuxR_C_like C-terminal 32.3 86 0.0019 22.5 4.2 32 133-164 15-46 (57)
463 PRK05580 primosome assembly pr 32.2 28 0.0006 40.0 2.1 29 2-31 391-419 (679)
464 PF04967 HTH_10: HTH DNA bindi 32.2 1.5E+02 0.0033 22.5 5.5 26 134-159 24-49 (53)
465 TIGR01610 phage_O_Nterm phage 32.2 3E+02 0.0066 23.0 8.2 31 130-160 44-74 (95)
466 PF05043 Mga: Mga helix-turn-h 32.2 53 0.0011 26.8 3.3 31 230-260 26-56 (87)
467 PRK12520 RNA polymerase sigma 32.1 58 0.0013 30.5 4.0 27 233-259 146-172 (191)
468 PRK03564 formate dehydrogenase 32.1 29 0.00063 36.0 2.0 10 21-30 253-262 (309)
469 PRK00149 dnaA chromosomal repl 32.0 89 0.0019 33.8 5.9 71 91-163 360-433 (450)
470 COG4098 comFA Superfamily II D 31.9 53 0.0011 34.7 3.8 39 3-41 41-84 (441)
471 PF14319 Zn_Tnp_IS91: Transpos 31.8 23 0.00049 31.1 1.0 32 3-35 44-75 (111)
472 PRK11303 DNA-binding transcrip 31.7 34 0.00074 34.5 2.5 43 236-278 2-45 (328)
473 PF14369 zf-RING_3: zinc-finge 31.7 28 0.0006 24.1 1.3 26 3-28 4-29 (35)
474 PF04552 Sigma54_DBD: Sigma-54 31.6 28 0.00061 32.6 1.7 129 112-254 19-160 (160)
475 PRK10141 DNA-binding transcrip 31.6 80 0.0017 28.0 4.5 30 232-261 28-57 (117)
476 PF01807 zf-CHC2: CHC2 zinc fi 31.4 21 0.00046 30.3 0.8 27 2-28 34-62 (97)
477 TIGR02952 Sig70_famx2 RNA poly 31.4 45 0.00097 30.2 3.0 26 233-258 137-162 (170)
478 TIGR00319 desulf_FeS4 desulfof 31.4 22 0.00049 24.1 0.7 11 20-30 7-17 (34)
479 PRK12527 RNA polymerase sigma 31.3 45 0.00099 30.0 3.0 25 233-257 120-144 (159)
480 PRK15121 right oriC-binding tr 31.0 1E+02 0.0022 31.1 5.8 41 116-157 5-45 (289)
481 PHA03074 late transcription fa 31.0 22 0.00047 34.5 0.8 27 3-31 6-32 (225)
482 COG1102 Cmk Cytidylate kinase 30.9 1.5E+02 0.0033 28.1 6.4 122 136-271 17-150 (179)
483 PF05930 Phage_AlpA: Prophage 30.9 50 0.0011 24.4 2.7 23 235-257 4-26 (51)
484 COG1476 Predicted transcriptio 30.9 38 0.00082 27.2 2.1 26 232-257 12-37 (68)
485 PRK10401 DNA-binding transcrip 30.9 36 0.00078 34.7 2.5 42 235-278 2-43 (346)
486 PRK11512 DNA-binding transcrip 30.9 82 0.0018 28.2 4.6 29 232-260 52-80 (144)
487 PF01047 MarR: MarR family; I 30.8 1.3E+02 0.0028 22.2 5.1 38 122-161 8-45 (59)
488 PRK12542 RNA polymerase sigma 30.8 43 0.00093 31.2 2.9 26 233-258 137-162 (185)
489 PRK10339 DNA-binding transcrip 30.7 31 0.00068 34.9 2.0 23 235-257 2-24 (327)
490 PF01978 TrmB: Sugar-specific 30.6 63 0.0014 25.0 3.3 37 123-160 13-49 (68)
491 TIGR02954 Sig70_famx3 RNA poly 30.5 66 0.0014 29.3 4.0 25 234-258 135-159 (169)
492 TIGR02417 fruct_sucro_rep D-fr 30.5 35 0.00075 34.4 2.3 22 236-257 1-22 (327)
493 TIGR02950 SigM_subfam RNA poly 30.5 45 0.00096 29.7 2.8 26 233-258 120-145 (154)
494 PRK03902 manganese transport t 30.3 79 0.0017 28.4 4.4 29 233-261 21-49 (142)
495 PRK08301 sporulation sigma fac 30.3 45 0.00098 32.4 3.0 25 233-257 197-221 (234)
496 cd00974 DSRD Desulforedoxin (D 30.3 24 0.00053 23.9 0.8 21 3-23 6-26 (34)
497 COG1571 Predicted DNA-binding 30.3 31 0.00067 37.2 1.9 32 3-36 352-383 (421)
498 PRK14165 winged helix-turn-hel 30.2 54 0.0012 32.3 3.5 30 232-261 19-48 (217)
499 COG1349 GlpR Transcriptional r 30.2 39 0.00086 33.7 2.6 28 233-260 18-45 (253)
500 PF13560 HTH_31: Helix-turn-he 30.1 61 0.0013 24.8 3.2 31 223-253 3-33 (64)
No 1
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=3.5e-75 Score=608.03 Aligned_cols=458 Identities=29% Similarity=0.409 Sum_probs=372.3
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcccccccccccCCCCccccCcccccccccc---cChHHHHHHHHHHHH
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAAGQSQLSGNFVRTIQSEY---GASRERLMEKAFDDM 78 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f~~~~~G~s~v~G~~v~~~~~~~---~~srer~L~~a~~~I 78 (504)
++|++||++++..|.++|.++|+.||+|+++++|+++++|.+. ++|+||+..|.+. .++|++++++++..|
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 5899999999999999999999999999999999999999876 7899998776653 478999999999999
Q ss_pred HHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHH
Q 010689 79 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 158 (504)
Q Consensus 79 ~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~ 158 (504)
..++.+|+|+ + +++.|++||+++.++||++||+...|+|+|+|++||+++++++|+||+++++|++|+||++|++|+
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 HHhcccccccccccCCccchHHHHHHhh-CCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCH
Q 010689 159 QVLYIADESNVLKQVDPSIFLHKFTDRL-LPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSK 237 (504)
Q Consensus 159 ~~L~i~~~~~~~~~~dP~~~I~r~~~~L-~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~ 237 (504)
+.|.+... +.+++||+.||+||++.| +++.+++|+.+|.+|+++|++|||++||+|+||||||||+|||+||+++|.
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 99999742 556899999999999999 456778999999999999999999999999999999999999999999999
Q ss_pred hhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHhhhhcccCCCCCCCCCC------CCCcchhhhhccccCCCCc
Q 010689 238 SDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKELHEGVAANLPNNGPK------VSGMNEVLCKHKDTGKPFA 311 (504)
Q Consensus 238 keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~ 311 (504)
.||+.+++||+.||++||+||.+|+++.||+++|++++. +.+++||+++.++. ....+.+.+.|... .++.
T Consensus 230 ~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~ef~~~d~--e~~~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~-e~~~ 306 (521)
T KOG1598|consen 230 GDIAKVVHVCESTLSKRLKEFSDTLSGDLTIDELAEIDL--EYESDPPSFTASPSKEAKYVEDKKKMLSRTMQLV-ELAN 306 (521)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccccccccHHHHHhhhh--hhccCcchhhcccchhhhhhhhhhhhhhhhhhhh-hccc
Confidence 999999999999999999999999999999999999988 66889999887553 12345566666554 4888
Q ss_pred ccchhhhhhhhhhcccCCCCCCCChhhhHHHHHHHHHHHHhhhhhhhhccCCcccccccccCCCCCCCCCCCCCCccccc
Q 010689 312 CGLCRSCYEEFMTISEGLEGGADPPAFQVAERERMVKASAEENSSFERESDSPFMSRVDKVQSPEPESIGVPKNCTTQTA 391 (504)
Q Consensus 312 ~g~~~~~~~~~~~~~~~~~~~~~ppaf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 391 (504)
.++|..||..+..+++++.+...||+|+..+.+.- +....+ ..++++.. ..+...........+..+
T Consensus 307 ~~~~~~~~~~~~~~~~~l~~~~q~~~~~~~~~e~~-----~~~~~e-~~~ssE~~------dk~~~g~~~~~~~~~sd~- 373 (521)
T KOG1598|consen 307 ETWLVTLRHSLPVITGGLFLAWQDLQPRDRLVESY-----DDLASE-CPLSSEDE------DKPASGRLAELLAVLSDM- 373 (521)
T ss_pred chhhhccccCCcccchhhhcccccchhhhhhhhhh-----hhhhhc-Cccccccc------CCcCccccchhhhccccc-
Confidence 99999999999999999999999999998887751 111000 01111000 000000000000000000
Q ss_pred ccCCCCCCCCCCCCCCCccCCCCCCCCCCCChHHHhhcCCChhhHHHHHHhhhccCHHHHHHHHHHHHHHHHHHHHH---
Q 010689 392 SNEGEGDHTKTPGVDATTEASDGSDNFSDIDDFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAAL--- 468 (504)
Q Consensus 392 ~~~~~~~~~~~~~~~~~~~~~d~~~~lsdiDD~Eid~yil~eeE~~~K~~lW~~~N~eyL~EQ~~Ke~~~a~~~~~~--- 468 (504)
..+-.+.+ ......|....++++||.+++.++|++++.+.|+.+ | +|+|||.||..|.+++|+..+--
T Consensus 374 ~~~~~~~~-------~~~~~~d~~~~~~~~~~~~l~r~~l~~~a~~~a~~~-~-~n~e~l~E~~~~~~~~ak~~~~g~~~ 444 (521)
T KOG1598|consen 374 AEQLASVW-------LRVLTLDKRSGVKHIDDLLLERQLLEESAGRDATEP-M-ENAETLVEERPGKAKAAKEREEGINS 444 (521)
T ss_pred chhhhhcc-------hhhhhccccccccccCHHHHHHHHhhhHHhhhcchh-h-hhHHHHHhhchhhhhhhHhhhhcccc
Confidence 00000000 023456778899999999999999999999999999 7 99999999999999999887732
Q ss_pred -HHhhccCCcchhHHHhHHHHHHHHHHhc
Q 010689 469 -EASYKNCPEGLQAAQELAAAAAAAVAKS 496 (504)
Q Consensus 469 -~~~~~~~p~~~~~a~~~~~~~~~~~~~~ 496 (504)
..+....+.. +++.++.|+.+.+++..
T Consensus 445 ~~~k~~~r~~s-~~~~t~~eavk~~~~i~ 472 (521)
T KOG1598|consen 445 LSKKVGERRNS-PELLTAPEAVKSMKEIK 472 (521)
T ss_pred cccccccccCC-CcccccHHHHHHHHhcc
Confidence 1122222222 23466667777666543
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=2.8e-53 Score=433.35 Aligned_cols=250 Identities=23% Similarity=0.391 Sum_probs=225.9
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcccccccccccCC---C-CccccCc---------ccc-----------
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAA---G-QSQLSGN---------FVR----------- 57 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f~~~~~---G-~s~v~G~---------~v~----------- 57 (504)
..||+||+..+++|+.+|++||++||+||+|++||++|+|+.+++ + ++|+++. +.+
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 479999998899999999999999999999999999888875431 1 2333211 100
Q ss_pred ---------------ccccc--ccChHHHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHH
Q 010689 58 ---------------TIQSE--YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA 120 (504)
Q Consensus 58 ---------------~~~~~--~~~srer~L~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA 120 (504)
.||.+ ..++.||.|..|++.|+++|+.|+|| +.++++|..||+++++.++++||+.+.++|
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 12221 12667899999999999999999999 999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHH
Q 010689 121 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARD 200 (504)
Q Consensus 121 ACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~ 200 (504)
||||+|||++++|+||+||+.++++++++|+++|+.|.+.|+++.++ ++|.+||+|||+.|+ ++..|.+.|.+
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-----TDPIDYVPRFASELG--LSGEVQKKAIE 242 (310)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC-----CCHHHHHHHHHHHcC--CCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998765 899999999999998 89999999999
Q ss_pred HHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 201 ILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 201 I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
|++.+.+.|++.||+|.+|||||||+||+++|.++|+++|+.++||++.||++||++|..
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 999999999999999999999999999999999999999999999999999999999985
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=2.2e-52 Score=418.28 Aligned_cols=252 Identities=26% Similarity=0.472 Sum_probs=229.1
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceeeccCccccccccccc---CC---CCc---cccCccc---------------
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKN---AA---GQS---QLSGNFV--------------- 56 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f~~~---~~---G~s---~v~G~~v--------------- 56 (504)
|..||+||++.++.|+..|++||.+||.|++++.||.+|+|+.+ +. |.+ ..++..+
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 56899999999999999999999999999999999999999842 22 111 0111111
Q ss_pred cccccc--ccChHHHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCC
Q 010689 57 RTIQSE--YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF 134 (504)
Q Consensus 57 ~~~~~~--~~~srer~L~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~ 134 (504)
+.||.+ .++++++.+..++.+|..++..|+|| .++.++|..||++++++++++||+.+.++|||+|+|||+++.|+
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 223322 34678999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCC
Q 010689 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR 214 (504)
Q Consensus 135 tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR 214 (504)
||.||+.+++|+++.|+++|+.+.+.|++..+| .||.+||+|||+.|+ ++++|...|.+|++.+.+.+++.||
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-----VDPSDYIPRFASKLG--LSDEVRRKAIEIVKKAKRAGLTAGK 231 (285)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCC-----CCHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHHhCcccCC
Confidence 999999999999999999999999999998887 999999999999999 8999999999999999999999999
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 215 ~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+|.||||||||+|+.++|+++||++|+.++||+++|||+||+|+.+.
T Consensus 232 ~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel~~~ 278 (285)
T COG1405 232 SPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELADA 278 (285)
T ss_pred CchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999998764
No 4
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=5.7e-48 Score=377.16 Aligned_cols=264 Identities=21% Similarity=0.360 Sum_probs=230.2
Q ss_pred CCCCCCCCC--CcccccCCCceecCcCceeeccCccc---ccccccccCCC--CccccC--------cccc---------
Q 010689 2 VWCSSCARH--VTGHRPYDSQLCCDRCGKVLEDHNFS---TEATFVKNAAG--QSQLSG--------NFVR--------- 57 (504)
Q Consensus 2 ~~Cp~Cgs~--~iv~D~~~G~~VC~~CG~Vlee~~id---~~~~f~~~~~G--~s~v~G--------~~v~--------- 57 (504)
.+|++|+.. .+++|+.+|+.||..||.|+++++|| +|++|++++++ +++|++ ..++
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 37899999999999999999999998 56677665532 345432 1111
Q ss_pred ---------ccccc-ccChHHHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHH
Q 010689 58 ---------TIQSE-YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC 127 (504)
Q Consensus 58 ---------~~~~~-~~~srer~L~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC 127 (504)
.+|.+ .+++.++.+..++..|..|++.|+|| ..|.++|.++|+++.+.+.+|||+.++++|||||+||
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 13322 23566899999999999999999999 9999999999999999999999999999999999999
Q ss_pred HhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcc
Q 010689 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR 207 (504)
Q Consensus 128 R~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~ 207 (504)
|+++.|||++||+.+.+|+.++||++++.|.+.|+...+.+ .+...+||+|||+.|. ++..+++.|.++++.+..
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---SISTGDFMPRFCSNLG--LPKSAQEAATEIAEKAEE 233 (308)
T ss_pred HhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhh---hhhHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999876542 3567899999999998 999999999999999999
Q ss_pred cccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHH
Q 010689 208 DWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMA 273 (504)
Q Consensus 208 ~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~ 273 (504)
..+..||+|.+||||+|||++++.+.+++++||..++||+|+|||+-|++++.. ...|.+..|-.
T Consensus 234 ~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~-~~~liP~~~a~ 298 (308)
T KOG1597|consen 234 MDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPH-ADKLIPSWYAN 298 (308)
T ss_pred hccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHhhc-hhhhChhhhcc
Confidence 999999999999999999999999999999999999999999999999999974 33555665543
No 5
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.69 E-value=1.5e-16 Score=128.19 Aligned_cols=71 Identities=27% Similarity=0.516 Sum_probs=66.1
Q ss_pred HHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHH
Q 010689 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 150 (504)
Q Consensus 78 I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~L 150 (504)
|+++|+.|+|| .++.+.|..+|+.+.+.++++||++..++|||||+|||+++.|+|++||+++++|+.++|
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 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=99.61 E-value=2.3e-15 Score=121.25 Aligned_cols=71 Identities=18% Similarity=0.365 Sum_probs=66.6
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHH
Q 010689 179 LHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATL 251 (504)
Q Consensus 179 I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TI 251 (504)
|+|||+.|+ +++.|.+.|.+|++.+.+.|+..||+|.+|||||||+||+.+|.++|++||+++++|++.||
T Consensus 1 I~r~~~~L~--L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLG--LPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcC--CCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 689999999 99999999999999999999999999999999999999999999999999999999999997
No 7
>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=99.53 E-value=1.3e-15 Score=130.15 Aligned_cols=75 Identities=36% Similarity=0.496 Sum_probs=34.6
Q ss_pred hHHHhhcCCChhhHHHHHHhhhccCHHHHHHHHHHHHHHHHHHH----HHHHhh-ccCC--c-chhHHHhHHHHHHHHHH
Q 010689 423 DFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKA----ALEASY-KNCP--E-GLQAAQELAAAAAAAVA 494 (504)
Q Consensus 423 D~Eid~yil~eeE~~~K~~lW~~~N~eyL~EQ~~Ke~~~a~~~~----~~~~~~-~~~p--~-~~~~a~~~~~~~~~~~~ 494 (504)
|+|||.|||||+|+++|++||+++|+|||++|++|+++.++..+ ..+++. ++.. . ...+|.+++||++++|.
T Consensus 1 DdEid~~il~eeE~~~K~~iW~~~NkdyL~~~~~K~~~~~~~~~~~~~~~k~k~~rk~~~~~~~~~~a~ta~EA~~~ml~ 80 (97)
T PF07741_consen 1 DDEIDNYILSEEEVKIKERIWMEMNKDYLEEQEEKELKAKAEEEAGAKSRKKKKKRKRRKKKNQAPPAETAAEAARKMLK 80 (97)
T ss_dssp -HHHHTTC--HHHHHHHHHHHHHHTHHHHHHHHHCCCCT-----------------------------------------
T ss_pred ChHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCccccccccccccCCCCCCCCHHHHHHHHHH
Confidence 55999999999999999999999999999999999977665542 111111 1111 1 26789999999999998
Q ss_pred hcc
Q 010689 495 KSR 497 (504)
Q Consensus 495 ~~~ 497 (504)
+++
T Consensus 81 ~k~ 83 (97)
T PF07741_consen 81 KKK 83 (97)
T ss_dssp ---
T ss_pred hcC
Confidence 876
No 8
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.39 E-value=2.9e-11 Score=123.39 Aligned_cols=163 Identities=17% Similarity=0.118 Sum_probs=135.5
Q ss_pred HHHHH-HHHHHHHHHHHHcC--CCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhC
Q 010689 68 ERLME-KAFDDMRQMKNALN--IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN 144 (504)
Q Consensus 68 er~L~-~a~~~I~~i~~~L~--Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~ 144 (504)
|+.+. ..-..|.++|..|+ || +.++-+|..||++.+-.+.+.-..+..++++|||+||+.+..|+++.+|+..+.
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lp--q~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~ 129 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMP--TSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLK 129 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhcc
Confidence 45554 45588999999999 99 999999999999999988888788999999999999999999999999998765
Q ss_pred cC----hHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCC-----CCCHHHHHHHHHHHHHhcccccccCCC
Q 010689 145 IN----VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLP-----GGNKKVCDTARDILASMKRDWITTGRK 215 (504)
Q Consensus 145 vs----~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~-----~l~~~V~~~A~~I~~~~~~~~l~~GR~ 215 (504)
-. ...|...-..|++.|+++... ..|..++..|...|.. .....+...|+.+++.+....+.-=..
T Consensus 130 ~~~~~~~~~Il~~E~~lL~~L~F~L~V-----~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~ 204 (305)
T TIGR00569 130 ETPLKALEQVLEYELLLIQQLNFHLIV-----HNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYT 204 (305)
T ss_pred CCchhhHHHHHHHHHHHHHHCCCcEEe-----eCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCC
Confidence 43 377888888999999987654 6799888888765521 123567889999998776665555699
Q ss_pred hhHHHHHHHHHHHHhcCCCCCH
Q 010689 216 PSGLCGAALYVSALTHGLKFSK 237 (504)
Q Consensus 216 P~~IAAAalylAa~~~g~~~t~ 237 (504)
|+-||.||||+|++.+|++..-
T Consensus 205 Ps~IAlAAI~lA~~~~~~~l~~ 226 (305)
T TIGR00569 205 PSQIALAAILHTASRAGLNMES 226 (305)
T ss_pred HHHHHHHHHHHHHHHhCCCCcc
Confidence 9999999999999999987654
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.35 E-value=3.8e-11 Score=120.19 Aligned_cols=187 Identities=14% Similarity=0.151 Sum_probs=155.8
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCc--
Q 010689 68 ERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-- 145 (504)
Q Consensus 68 er~L~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~v-- 145 (504)
+-...=|...|++-|-.|+|| +...-++..+|++..-..-+.+-..++++.|||.+|.+.+..|++++||..++.-
T Consensus 20 ~el~~LG~e~Iqea~ILL~L~--q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~ 97 (367)
T KOG0835|consen 20 EELRILGCELIQEAGILLNLP--QVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLE 97 (367)
T ss_pred HHHHHHhHHHHHhhhHhhcCc--HHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHH
Confidence 334445789999999999999 9999999999999988888888999999999999999999999999999988641
Q ss_pred --------C-----------hHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhc
Q 010689 146 --------N-----------VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMK 206 (504)
Q Consensus 146 --------s-----------~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~ 206 (504)
. .-.+-++..++.+.||+..+. .+|..+|-.|.+.|+...+.++.+.+|.+.+...
T Consensus 98 ~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv-----~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDsl 172 (367)
T KOG0835|consen 98 QRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHV-----EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSL 172 (367)
T ss_pred HHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeee-----eccHHHHHHHHHHhcCCCchhHHHHHHHhhhhcc
Confidence 1 123445677899999998875 8999999999999974445568999999999999
Q ss_pred ccccccCCChhHHHHHHHHHHHHhcCCCCC-HhhHHhhhccCHHHHH---HHHHHhhcc
Q 010689 207 RDWITTGRKPSGLCGAALYVSALTHGLKFS-KSDIVKIVHICEATLM---KRLIEFENT 261 (504)
Q Consensus 207 ~~~l~~GR~P~~IAAAalylAa~~~g~~~t-~keIa~v~~Vse~TIr---kr~kE~~~t 261 (504)
+..++.--.|.+||+|||||||+..++++. +..+-.+++++...|. -++-.|+..
T Consensus 173 RT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 173 RTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred ccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999987643 4478888888877555 445555544
No 10
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.33 E-value=7.2e-12 Score=128.59 Aligned_cols=89 Identities=16% Similarity=0.227 Sum_probs=85.6
Q ss_pred HHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHH
Q 010689 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 153 (504)
Q Consensus 74 a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~ 153 (504)
...+|.++|+.|+|| ..+.+.|..+++.+.+.+++.||++..++|||||+|||.+|.|+|++||+++++|+..+|++.
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 468899999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccc
Q 010689 154 YLQLCQVLYIA 164 (504)
Q Consensus 154 ~~~L~~~L~i~ 164 (504)
|+.|.+.|++.
T Consensus 297 ykel~~~l~~~ 307 (310)
T PRK00423 297 YKELAEKLDIK 307 (310)
T ss_pred HHHHHHHhCcc
Confidence 99999999764
No 11
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.28 E-value=1.8e-11 Score=124.96 Aligned_cols=161 Identities=21% Similarity=0.258 Sum_probs=131.9
Q ss_pred HHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhC--cC
Q 010689 69 RLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN--IN 146 (504)
Q Consensus 69 r~L~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~--vs 146 (504)
+....+...|.+++.+|++| ...+.+|..||.+++-...++.-.+..+|++|||+|++.++.|+.++||..+.. .+
T Consensus 37 ~~r~~~~~fI~elg~~L~~~--~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~ 114 (323)
T KOG0834|consen 37 RLRQEGAKFIQELGVRLKMP--QKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLN 114 (323)
T ss_pred HHHHHHHHHHHHHHHHcCCC--ccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcC
Confidence 34467899999999999999 888999999999999988888888889999999999999999999999988753 33
Q ss_pred h--HHHHHHH-----------HHHHHHhcccccccccccCCccchHHHHHHhhCCCCC--HHHHHHHHHHHHHhcccccc
Q 010689 147 V--YELGAVY-----------LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGN--KKVCDTARDILASMKRDWIT 211 (504)
Q Consensus 147 ~--~~Lg~~~-----------~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~--~~V~~~A~~I~~~~~~~~l~ 211 (504)
+ ..+...| +.+++.|+++... -.|..|+-+|+..|....+ ..++..|+.+++......++
T Consensus 115 ~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v-----~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~c 189 (323)
T KOG0834|consen 115 PKDLELEEVYWELKERIVQLELLLLETLGFDLNV-----EHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLC 189 (323)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHccCceec-----cCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeee
Confidence 3 2344444 3455666665543 6799999999999964433 25899999999988876677
Q ss_pred cCCChhHHHHHHHHHHHHhcCCCCC
Q 010689 212 TGRKPSGLCGAALYVSALTHGLKFS 236 (504)
Q Consensus 212 ~GR~P~~IAAAalylAa~~~g~~~t 236 (504)
---.|..||.||||+|+.++|+...
T Consensus 190 L~y~p~~IAva~i~lA~~~~~~~~~ 214 (323)
T KOG0834|consen 190 LQYSPHSIAVACIHLAAKLLGVELP 214 (323)
T ss_pred EeecCcEEEeehhhHHHHHcCCCCC
Confidence 7789999999999999999987544
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=99.17 E-value=1e-11 Score=90.36 Aligned_cols=42 Identities=24% Similarity=0.561 Sum_probs=37.6
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcccccccccc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f~~ 43 (504)
+.||+||++.+++|+.+|++||+.||.||++++++++++|++
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~ 42 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEENIIDEGPEWRE 42 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCH
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeecccccCCccccc
Confidence 479999999989999999999999999999999999999975
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=99.09 E-value=1.1e-09 Score=109.72 Aligned_cols=158 Identities=18% Similarity=0.163 Sum_probs=133.1
Q ss_pred HHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHh--------
Q 010689 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYL-------- 143 (504)
Q Consensus 72 ~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~-------- 143 (504)
...+..|..+|.+|++| ..+..+|..+|++.+-++..++.....++++|||+|||.+..|+-+.-.+-..
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 45679999999999999 99999999999999999999999999999999999999999765443333222
Q ss_pred CcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHH
Q 010689 144 NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAA 223 (504)
Q Consensus 144 ~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAa 223 (504)
--+...|-..-..+.+.|+.+... ..|..++..|...+....+.++.+.|+.++...-+..++-=-.|..||.||
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 246677777788899999987664 779999999998884222347899999999999888888889999999999
Q ss_pred HHHHHHhcCCCCC
Q 010689 224 LYVSALTHGLKFS 236 (504)
Q Consensus 224 lylAa~~~g~~~t 236 (504)
|++|+...|.+.-
T Consensus 199 l~ia~~~~~~~~~ 211 (297)
T COG5333 199 LLIACEVLGMPII 211 (297)
T ss_pred HHHHHHhcCCccc
Confidence 9999999887644
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.99 E-value=1.9e-09 Score=108.92 Aligned_cols=91 Identities=18% Similarity=0.212 Sum_probs=86.9
Q ss_pred HHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHH
Q 010689 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 152 (504)
Q Consensus 73 ~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~ 152 (504)
+...+|.++|+.|+|| +.+...|.++.+++...+.+-||++..++|||||+|++.++.++|.++|+.+++|...+|..
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 3568899999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcccc
Q 010689 153 VYLQLCQVLYIAD 165 (504)
Q Consensus 153 ~~~~L~~~L~i~~ 165 (504)
.|+.|.+.+++..
T Consensus 271 rykel~~~~~i~~ 283 (285)
T COG1405 271 RYKELADALDIEV 283 (285)
T ss_pred HHHHHHHhhcccc
Confidence 9999999998753
No 15
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.88 E-value=9e-09 Score=102.23 Aligned_cols=87 Identities=13% Similarity=0.128 Sum_probs=83.4
Q ss_pred HHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHH
Q 010689 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 153 (504)
Q Consensus 74 a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~ 153 (504)
.-+.|.++|+.|+|| ..+++.|.++.+++.+..+..||++..|+||.+|++|+....+++++||..++||..-+|..+
T Consensus 203 t~~~m~RFCs~L~L~--~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~s 280 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLP--KSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNS 280 (308)
T ss_pred HHHHHHHHHHhcCCC--HHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHH
Confidence 567899999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhc
Q 010689 154 YLQLCQVLY 162 (504)
Q Consensus 154 ~~~L~~~L~ 162 (504)
|+.|...+.
T Consensus 281 YK~Lyp~~~ 289 (308)
T KOG1597|consen 281 YKDLYPHAD 289 (308)
T ss_pred HHHHhhchh
Confidence 999987775
No 16
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.87 E-value=2.3e-08 Score=81.19 Aligned_cols=83 Identities=23% Similarity=0.257 Sum_probs=77.7
Q ss_pred HHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCc-ChHHHH
Q 010689 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELG 151 (504)
Q Consensus 73 ~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~v-s~~~Lg 151 (504)
.+.+.|.+++..++++ ..+...|..+++++...+.+.++++..+++||||+||+.++.|.++.+|...++. +..+|.
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 9999999999999999888899999999999999999999999999999999999 999998
Q ss_pred HHHHHH
Q 010689 152 AVYLQL 157 (504)
Q Consensus 152 ~~~~~L 157 (504)
+.++.+
T Consensus 82 ~~e~~i 87 (88)
T cd00043 82 RMEKLL 87 (88)
T ss_pred HHHHHh
Confidence 887765
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=98.82 E-value=2.4e-08 Score=81.05 Aligned_cols=84 Identities=23% Similarity=0.276 Sum_probs=78.8
Q ss_pred CCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhcc-CHHHH
Q 010689 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATL 251 (504)
Q Consensus 173 ~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~V-se~TI 251 (504)
..|..||.+++..++ +++.+...|..+++++...+...|++|..||+||||+|+++.+...+.++++..++. +..+|
T Consensus 3 ~~~~~~l~~~~~~~~--~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i 80 (88)
T cd00043 3 PTPLDFLRRVAKALG--LSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEI 80 (88)
T ss_pred chHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHH
Confidence 457889999999998 899999999999999988888889999999999999999999999999999999999 99999
Q ss_pred HHHHHHh
Q 010689 252 MKRLIEF 258 (504)
Q Consensus 252 rkr~kE~ 258 (504)
.+.++++
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 9998876
No 18
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.79 E-value=3.7e-08 Score=79.18 Aligned_cols=81 Identities=20% Similarity=0.214 Sum_probs=73.9
Q ss_pred chHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhcc-CHHHHHHHH
Q 010689 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI-CEATLMKRL 255 (504)
Q Consensus 177 ~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~V-se~TIrkr~ 255 (504)
.||.+++..++ +++++...|..+++++....-..+++|+.||+||||+|+++.+.+++.++++..+++ ++.+|.+.+
T Consensus 1 ~~l~~~~~~~~--~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 1 DFLRRVCKALN--LDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred CHHHHHHHHcC--CCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHH
Confidence 48899999998 889999999999999987544556999999999999999999999999999999999 999999999
Q ss_pred HHhh
Q 010689 256 IEFE 259 (504)
Q Consensus 256 kE~~ 259 (504)
+++.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 9875
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=4.4e-08 Score=78.73 Aligned_cols=79 Identities=22% Similarity=0.270 Sum_probs=71.7
Q ss_pred HHHHHHHHcCCCCchHHHHHHHHHHHHHHh-CcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCc-ChHHHHHHH
Q 010689 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVA-RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVY 154 (504)
Q Consensus 77 ~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~-~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~v-s~~~Lg~~~ 154 (504)
.|.+++..+++| ..+...|..+++++.. .++.+ +++..++|||+|+|||.++.+.+..++...+++ +..+|.+.+
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 999999888
Q ss_pred HHHH
Q 010689 155 LQLC 158 (504)
Q Consensus 155 ~~L~ 158 (504)
+.|.
T Consensus 79 ~~il 82 (83)
T smart00385 79 KLLL 82 (83)
T ss_pred HHHh
Confidence 7764
No 20
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.72 E-value=1.8e-07 Score=90.09 Aligned_cols=155 Identities=16% Similarity=0.200 Sum_probs=117.3
Q ss_pred HHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcH-HHHH---HHh------
Q 010689 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLL-IDFS---NYL------ 143 (504)
Q Consensus 74 a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL-~dIs---~~~------ 143 (504)
....|+.++..|+|. +.++.+|..+|++.+-++.+++-.+..+|+.|||+||+.+..|+.- +-++ ..+
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 357899999999999 9999999999999999888999999999999999999999998321 1111 111
Q ss_pred -----CcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhH
Q 010689 144 -----NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSG 218 (504)
Q Consensus 144 -----~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~ 218 (504)
..+...|-..-..|.+.|+-=. -...|..-+..+.+.++. .+.+....++.|++.--+..++-=..|.-
T Consensus 122 ~~e~~~~~~~~I~e~Ef~llE~Ld~~L-----IVhHPYrsL~q~~qd~gi-~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~ 195 (264)
T KOG0794|consen 122 WPEKFPYERKDILEMEFYLLEALDCYL-----IVHHPYRSLLQFVQDMGI-NDQKLLQLAWSIVNDSYRMDLCLLYPPHQ 195 (264)
T ss_pred chhhcCCCcCcchhhhhhHHhhhceeE-----EEecCCccHHHHHHHhcc-cchhhhhhhHhhhcchhhcceeeecCHHH
Confidence 1122233333334455554211 125677778888888862 35668899999999988888888899999
Q ss_pred HHHHHHHHHHHhcCCCCC
Q 010689 219 LCGAALYVSALTHGLKFS 236 (504)
Q Consensus 219 IAAAalylAa~~~g~~~t 236 (504)
||-||||+|+-..|...+
T Consensus 196 IalAcl~Ia~~~~~k~~~ 213 (264)
T KOG0794|consen 196 IALACLYIACVIDEKDIP 213 (264)
T ss_pred HHHHHHHHHHhhcCCChH
Confidence 999999999988876654
No 21
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.49 E-value=4.8e-06 Score=85.57 Aligned_cols=178 Identities=16% Similarity=0.213 Sum_probs=140.0
Q ss_pred HHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhC-cccCCC--chhHHHHHHHHHHHHhcCC--CCcHHHHHHHh--C
Q 010689 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVAR-NFTKGR--RTEQVQASCLYLACRQKSK--PFLLIDFSNYL--N 144 (504)
Q Consensus 72 ~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~-~~~rGR--~~~~vaAACLYiACR~~~~--p~tL~dIs~~~--~ 144 (504)
..|.+.|-++|...+.. ..+.=-|.+|+.+.+.- ++.+++ -.+.+++|||.+|.+.+.+ |.++.-....+ -
T Consensus 79 ~~A~~WIl~V~~~~~~~--~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~ 156 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFE--PLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNV 156 (335)
T ss_pred HHHHHHHHHHHHHhCCc--hHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccc
Confidence 46899999999999999 89999999999999764 444433 3788999999999999776 66555455553 3
Q ss_pred cChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCC--CCHHHHHHHHHHHHHhcccccccCCChhHHHHH
Q 010689 145 INVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPG--GNKKVCDTARDILASMKRDWITTGRKPSGLCGA 222 (504)
Q Consensus 145 vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~--l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAA 222 (504)
+..++|.+.-+.+...|+=...+ +.|..||..|+.+++.. ..+.+...+..++-....+.-..+-.|+.||||
T Consensus 157 feaktI~rmELLVLstL~Wrl~a-----VTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa 231 (335)
T KOG0656|consen 157 FEAKTIQRMELLVLSTLKWRLRA-----VTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAA 231 (335)
T ss_pred ccHHHHHHHHHHHHhhccccccC-----CCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHH
Confidence 68899999999999999987776 88999999999999632 345677777777777767777789999999999
Q ss_pred HHHHHHHh-cCCC--CCHhhHHhhhccCHHHHHHHHH
Q 010689 223 ALYVSALT-HGLK--FSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 223 alylAa~~-~g~~--~t~keIa~v~~Vse~TIrkr~k 256 (504)
++..++.. .+.. .....+.....|+.-.+++.|.
T Consensus 232 ~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 232 AILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 88766653 3333 3345666778888888887776
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.14 E-value=2e-06 Score=92.03 Aligned_cols=157 Identities=14% Similarity=0.194 Sum_probs=102.4
Q ss_pred HHHHHHHHcCCCC-chHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHH
Q 010689 77 DMRQMKNALNIGE-SDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYL 155 (504)
Q Consensus 77 ~I~~i~~~L~Lp~-~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~ 155 (504)
+|.+++..|-..+ ...|+.+|.++..+...-=+..||++..+++||||+|||.+|+++|..||+.+..|+..+|.+.|.
T Consensus 169 ~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~ 248 (521)
T KOG1598|consen 169 YIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLK 248 (521)
T ss_pred eeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHH
Confidence 4556666664442 123555555555544333346899999999999999999999999999999999999999999999
Q ss_pred HHHHHhccccccc------ccccCCccchHHHH--HHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHH
Q 010689 156 QLCQVLYIADESN------VLKQVDPSIFLHKF--TDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVS 227 (504)
Q Consensus 156 ~L~~~L~i~~~~~------~~~~~dP~~~I~r~--~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylA 227 (504)
.+.+.+..+.+.. ...-.||..|-..= ..+-. ....+....-...+.-+...|..+++.|...+-+.++.+
T Consensus 249 Ef~~T~s~~Lti~ef~~~d~e~~~~ppsft~~~~~~~k~~-~~~k~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~l~~~ 327 (521)
T KOG1598|consen 249 EFSDTLSGDLTIDELAEIDLEYESDPPSFTASPSKEAKYV-EDKKKMLSRTMQLVELANETWLVTLRHSLPVITGGLFLA 327 (521)
T ss_pred HHhccccccccHHHHHhhhhhhccCcchhhcccchhhhhh-hhhhhhhhhhhhhhhcccchhhhccccCCcccchhhhcc
Confidence 9988876544320 01123343332110 00000 011223333334445556678999999999999999888
Q ss_pred HHhcCCC
Q 010689 228 ALTHGLK 234 (504)
Q Consensus 228 a~~~g~~ 234 (504)
++-....
T Consensus 328 ~q~~~~~ 334 (521)
T KOG1598|consen 328 WQDLQPR 334 (521)
T ss_pred cccchhh
Confidence 8744433
No 23
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=97.63 E-value=0.0021 Score=61.74 Aligned_cols=159 Identities=14% Similarity=0.160 Sum_probs=122.5
Q ss_pred HHHHHHHHcCCCCchHHHHHHHHHHHHHHhC--cccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHH
Q 010689 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVY 154 (504)
Q Consensus 77 ~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~--~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~ 154 (504)
.|.+++.+|||..+..+++.|.+|.+...-+ +..-|-.-..-+.-|+=+|.-.-++|+--.......|.+.+...+.|
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 4788999999965579999999999887543 33344444556778999998888999887777788899999999999
Q ss_pred HHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhccc-----ccccC-CChhHHHHHHHHHHH
Q 010689 155 LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRD-----WITTG-RKPSGLCGAALYVSA 228 (504)
Q Consensus 155 ~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~-----~l~~G-R~P~~IAAAalylAa 228 (504)
+.+...|+++... -|..+|-+|+ . .+|++.|..|+...+.. .+-.. -+| -.++||+|.||
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--C-VEVIKSAQNVLSSYKERLPATRRANADFSRP-VFTAAAFYLAC 147 (262)
T ss_pred HHHHHHhcchhhc----------CHHHHHHHHh--H-HHHHHHHHHHHHHHHhcCchhhhcCCcccch-HHHHHHHHHHH
Confidence 9999999987542 2456777775 2 47888888888877642 11112 234 47888999999
Q ss_pred HhcCCCCCHhhHHhhhccCHH
Q 010689 229 LTHGLKFSKSDIVKIVHICEA 249 (504)
Q Consensus 229 ~~~g~~~t~keIa~v~~Vse~ 249 (504)
+....+++...+..+.|++++
T Consensus 148 k~lKlKVdK~kli~~sg~~~s 168 (262)
T KOG4557|consen 148 KKLKLKVDKLKLIEVSGTSES 168 (262)
T ss_pred HHHHHhhhHhhcccccCCCHH
Confidence 999999998888888888887
No 24
>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=97.55 E-value=0.0011 Score=58.21 Aligned_cols=94 Identities=13% Similarity=0.249 Sum_probs=76.6
Q ss_pred HHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCC-CCcHHHHHHHhC--c
Q 010689 69 RLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--I 145 (504)
Q Consensus 69 r~L~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~-p~tL~dIs~~~~--v 145 (504)
.......++|..++..++++ ..+.-.|..+|.+.......+......++++|+|+||+.+.. +.++.++....+ .
T Consensus 29 ~~r~~~~~~i~~~~~~~~l~--~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~ 106 (127)
T PF00134_consen 29 EMRQIIIDWIIELCQRLKLS--PETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTF 106 (127)
T ss_dssp HHHHHHHHHHHHHHHHTT-B--HHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSS
T ss_pred HHHHHHHHHHHHHHHhcccc--hhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCC
Confidence 34456789999999999999 999999999999999888778888889999999999999777 788889888773 6
Q ss_pred ChHHHHHHHHHHHHHhccc
Q 010689 146 NVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 146 s~~~Lg~~~~~L~~~L~i~ 164 (504)
+..+|...-+.+...|+.+
T Consensus 107 ~~~~i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 107 TKKDILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHHHHHTTT-
T ss_pred CHHHHHHHHHHHHHHCCCC
Confidence 7888888888888877654
No 25
>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=97.36 E-value=0.0022 Score=64.67 Aligned_cols=147 Identities=18% Similarity=0.179 Sum_probs=94.2
Q ss_pred HHHHHHHc--CCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhC----cChHHHH
Q 010689 78 MRQMKNAL--NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN----INVYELG 151 (504)
Q Consensus 78 I~~i~~~L--~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~----vs~~~Lg 151 (504)
+-+++..+ +|| .+|+-+|..+|++++=.+.+.--.+..|+++|+|+||+.+..-+++.+|+.-.. -....+-
T Consensus 63 l~~f~~k~~p~lp--~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vL 140 (325)
T KOG2496|consen 63 LVNFYSKFKPNLP--TSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVL 140 (325)
T ss_pred HHHHHHHhcCCCc--hHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHH
Confidence 33444444 788 999999999999999888888889999999999999999999999999998776 3444555
Q ss_pred HHHHHHHHHhcccccccccccCCc-cchHHHHHHhhCCCCCHHHH-HHH--HHHHHHhcccccccCCChhHHHHHHHHHH
Q 010689 152 AVYLQLCQVLYIADESNVLKQVDP-SIFLHKFTDRLLPGGNKKVC-DTA--RDILASMKRDWITTGRKPSGLCGAALYVS 227 (504)
Q Consensus 152 ~~~~~L~~~L~i~~~~~~~~~~dP-~~~I~r~~~~L~~~l~~~V~-~~A--~~I~~~~~~~~l~~GR~P~~IAAAalylA 227 (504)
+--..+++.|...... ..+-.| .-|+--+-..|.+-.++... ... .+.++++.-....-=..|+-||-|||+.|
T Consensus 141 k~E~~llqsL~f~L~v--h~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a 218 (325)
T KOG2496|consen 141 KYEFLLLQSLKFSLTV--HNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHA 218 (325)
T ss_pred hchHHHHHhhhhhhee--cCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHH
Confidence 5555667777655331 111233 23444443443211222221 111 13333332222333478999999999544
Q ss_pred H
Q 010689 228 A 228 (504)
Q Consensus 228 a 228 (504)
+
T Consensus 219 ~ 219 (325)
T KOG2496|consen 219 A 219 (325)
T ss_pred h
Confidence 3
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=97.34 E-value=0.0015 Score=59.36 Aligned_cols=84 Identities=12% Similarity=0.216 Sum_probs=65.4
Q ss_pred HHHHHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHh--CcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcCh
Q 010689 70 LMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINV 147 (504)
Q Consensus 70 ~L~~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~--~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~ 147 (504)
.+.-|..+|+.+|..|+|+ +.+.+....+|..+.. -.++++|..++++.+|+|..||..+.+.+++||-....--+
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 4455788999999999999 8899999999998875 35789999999999999999999999999999998776544
Q ss_pred HHHHHHHH
Q 010689 148 YELGAVYL 155 (504)
Q Consensus 148 ~~Lg~~~~ 155 (504)
..-..+|+
T Consensus 88 q~~~~Vyr 95 (135)
T PF01857_consen 88 QASSHVYR 95 (135)
T ss_dssp T--THHHH
T ss_pred cccccceE
Confidence 44444444
No 27
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.29 E-value=0.0029 Score=67.33 Aligned_cols=153 Identities=14% Similarity=0.095 Sum_probs=120.1
Q ss_pred HHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHH-HHHHhcC-CCCcHHHHHHHhC--cChHH
Q 010689 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLY-LACRQKS-KPFLLIDFSNYLN--INVYE 149 (504)
Q Consensus 74 a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLY-iACR~~~-~p~tL~dIs~~~~--vs~~~ 149 (504)
-.+.+-++-.+++|. ....-.|..|+.+.+....+..++...|..+||+ |||+.+. .+-++.|+.-+.+ .+..+
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 457888899999999 8999999999999988766777888878778855 9999643 3344667666654 78889
Q ss_pred HHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHH
Q 010689 150 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSAL 229 (504)
Q Consensus 150 Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~ 229 (504)
|.+.-+.+...|+.... ...|-.|+.||..... ........+..++....-+.-+....|+.++||+.+++.+
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 ILRMEKYILNVLEFDLS-----VPTPLSFLRRFLKAAD--YDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALR 311 (391)
T ss_pred HHHHHHHHHhccCeeec-----CCchHHHHHHHHHhhh--cchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHH
Confidence 99988888888887654 3678999999988886 4555666677777766656656778999999999999999
Q ss_pred hcCCCC
Q 010689 230 THGLKF 235 (504)
Q Consensus 230 ~~g~~~ 235 (504)
+.+...
T Consensus 312 ~~~~~~ 317 (391)
T KOG0653|consen 312 MLSKGD 317 (391)
T ss_pred HhccCC
Confidence 886553
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=97.03 E-value=0.0015 Score=56.34 Aligned_cols=85 Identities=19% Similarity=0.169 Sum_probs=65.8
Q ss_pred CccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCC-CCCHhhHHhhhccCHHHHH
Q 010689 174 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIVHICEATLM 252 (504)
Q Consensus 174 dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~-~~t~keIa~v~~Vse~TIr 252 (504)
.|..|+.+|....+ .+..+...|..|++.+.-+.-..+-+|+.|||||||+|....+. ..-...+...+|+....|+
T Consensus 2 Tp~~Fl~~~~~~~~--~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~ 79 (118)
T PF02984_consen 2 TPYDFLRRFLKISN--ADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLK 79 (118)
T ss_dssp -HHHHHHHHHTSSS--HHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHHHHcC--CcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHH
Confidence 47789999944323 45678899999999877777788999999999999999998875 3444567888899999988
Q ss_pred HHHHHhhc
Q 010689 253 KRLIEFEN 260 (504)
Q Consensus 253 kr~kE~~~ 260 (504)
..++.+.+
T Consensus 80 ~c~~~i~~ 87 (118)
T PF02984_consen 80 ECIELIQE 87 (118)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 88877764
No 29
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=96.67 E-value=0.012 Score=63.19 Aligned_cols=148 Identities=14% Similarity=0.057 Sum_probs=110.0
Q ss_pred HHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCC-CCcHHHHHHHhC--cChHHHH
Q 010689 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYELG 151 (504)
Q Consensus 75 ~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~-p~tL~dIs~~~~--vs~~~Lg 151 (504)
.+.|.++=..+++- ......|..|..+.+..+.+.=.+...|.++|+||||+-+.+ +.+++++.-++. .+..+|.
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 35566677788887 688889999999999988887778889999999999998665 456888888764 7899999
Q ss_pred HHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhccc-ccccCCChhHHHHHHHHHHHHh
Q 010689 152 AVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRD-WITTGRKPSGLCGAALYVSALT 230 (504)
Q Consensus 152 ~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~-~l~~GR~P~~IAAAalylAa~~ 230 (504)
++.+-+...|+.+.-- ..|..|+.|+..... ........+..+.....=+ .+...+ |+.++|||-|++-.+
T Consensus 295 ~aE~~ml~~l~f~is~-----P~P~sFLRriSka~d--yd~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~ 366 (440)
T COG5024 295 RAERYMLEVLDFNISW-----PSPMSFLRRISKASD--YDIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKI 366 (440)
T ss_pred HHHHHHhhhcccccCC-----CChHHHHHHHHhhcc--cchhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhh
Confidence 9999999999886543 678889877766554 2333333344433332211 233455 999999999999887
Q ss_pred cC
Q 010689 231 HG 232 (504)
Q Consensus 231 ~g 232 (504)
.+
T Consensus 367 ~~ 368 (440)
T COG5024 367 LS 368 (440)
T ss_pred hc
Confidence 65
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=96.34 E-value=0.0021 Score=44.90 Aligned_cols=27 Identities=33% Similarity=0.637 Sum_probs=23.2
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeec
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
.|+.||+. .+...+|..+|..||.|++
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 49999998 5666789999999999974
No 31
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=95.52 E-value=0.0061 Score=47.97 Aligned_cols=31 Identities=23% Similarity=0.521 Sum_probs=28.8
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
+.||.||...+++++.+-.+.|-.||.+|-+
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEEe
Confidence 5799999999999999999999999999864
No 32
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=95.48 E-value=0.0057 Score=47.26 Aligned_cols=31 Identities=26% Similarity=0.541 Sum_probs=28.8
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
++||.|+...+++++++-.+.|..||.+|..
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 5899999999999999999999999999864
No 33
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=95.37 E-value=0.0062 Score=46.54 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=23.9
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
++||.|+...+++++++-.+.|..||.+|-.
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 5899999999999999999999999999964
No 34
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=95.15 E-value=0.13 Score=52.81 Aligned_cols=104 Identities=16% Similarity=0.283 Sum_probs=76.0
Q ss_pred HHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHH-HHHHHhCcChHHHHHH
Q 010689 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLI-DFSNYLNINVYELGAV 153 (504)
Q Consensus 75 ~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~-dIs~~~~vs~~~Lg~~ 153 (504)
.+.|-.+..-|++|++..+...+.+|.....--.++.--+++.||+||+|+|.|..++|.+.. ..-.+++++..+|-..
T Consensus 142 hklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~i 221 (367)
T KOG0835|consen 142 HKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEI 221 (367)
T ss_pred HHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHH
Confidence 456777888999997666788888888888777777778899999999999999999887654 4446677888887766
Q ss_pred HHHHHHHhcccccccccccCCccchHHHHHHhh
Q 010689 154 YLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL 186 (504)
Q Consensus 154 ~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L 186 (504)
..++........+ -..+|.-|+..+
T Consensus 222 c~~l~~lY~~~~p--------~~~li~~~vd~~ 246 (367)
T KOG0835|consen 222 CYRLIPLYKRAKP--------DETLIEAFVDRL 246 (367)
T ss_pred HHHHHHHHHhccc--------CHHHHHHHHHHh
Confidence 6665554433211 124666666665
No 35
>PLN00209 ribosomal protein S27; Provisional
Probab=94.74 E-value=0.015 Score=48.23 Aligned_cols=31 Identities=26% Similarity=0.487 Sum_probs=28.9
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
+.||.|+...+++.+++-.+.|..||.+|-+
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 5799999999999999999999999999964
No 36
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=94.67 E-value=0.5 Score=41.58 Aligned_cols=56 Identities=11% Similarity=0.025 Sum_probs=42.7
Q ss_pred cHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhh-CCCCCHHH
Q 010689 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-LPGGNKKV 194 (504)
Q Consensus 135 tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L-~~~l~~~V 194 (504)
+|++++..+|||--++...+..|.+.|+....+ ..........+.++| .+.++.+.
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~----~~~~~~~~~~IL~~L~~GeIs~ee 107 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGYEEDE----EEEEEDERKEILDKLEKGEISVEE 107 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCc----ccccchhHHHHHHHHHcCCCCHHH
Confidence 589999999999999999999999999983322 134456778888888 44465443
No 37
>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=94.66 E-value=0.16 Score=43.52 Aligned_cols=86 Identities=14% Similarity=0.150 Sum_probs=63.8
Q ss_pred HHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCC-CCcHHHHHHHhCcChHHHHHH
Q 010689 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLNINVYELGAV 153 (504)
Q Consensus 75 ~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~-p~tL~dIs~~~~vs~~~Lg~~ 153 (504)
+..|+.+....+.. ..+...|..+.....-...+-+-++..+||||+|+|.+..+. +.--..+...++++...|..+
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 45666664433444 678888888888876554456688889999999999999765 444556778889999999999
Q ss_pred HHHHHHHhc
Q 010689 154 YLQLCQVLY 162 (504)
Q Consensus 154 ~~~L~~~L~ 162 (504)
+..|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999988875
No 38
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=94.64 E-value=0.017 Score=47.81 Aligned_cols=31 Identities=23% Similarity=0.473 Sum_probs=28.9
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
+.||.|+...+++.+++-.+.|..||.+|-.
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 5899999999999999999999999999964
No 39
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=94.38 E-value=0.021 Score=39.37 Aligned_cols=28 Identities=21% Similarity=0.634 Sum_probs=16.2
Q ss_pred CCCCCCCCCc---ccccCCCceecCcCceee
Q 010689 3 WCSSCARHVT---GHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~i---v~D~~~G~~VC~~CG~Vl 30 (504)
.||.||+... ...+..--.||+.||.|-
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 6999999732 222345679999999984
No 40
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=94.38 E-value=0.021 Score=39.62 Aligned_cols=31 Identities=19% Similarity=0.574 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
|..||.||.--+......+...|..||.+.+
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 7889999986444443445558999999864
No 41
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=94.30 E-value=0.023 Score=36.74 Aligned_cols=23 Identities=22% Similarity=0.723 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCce
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
++.||+||.. + ..+..+|..||.
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 4689999984 2 357899999996
No 42
>PHA00626 hypothetical protein
Probab=94.28 E-value=0.03 Score=42.65 Aligned_cols=31 Identities=16% Similarity=0.456 Sum_probs=23.2
Q ss_pred CCCCCCCCCCcccc----cCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D----~~~G~~VC~~CG~Vlee 32 (504)
+.||.||+..++-. ..+..++|.+||.-..-
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 47999999766532 23689999999986543
No 43
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=94.26 E-value=0.029 Score=42.83 Aligned_cols=31 Identities=29% Similarity=0.632 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCcccccCCC-ceecCcCceeec
Q 010689 1 MVWCSSCARHVTGHRPYDS-QLCCDRCGKVLE 31 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G-~~VC~~CG~Vle 31 (504)
|..||.||...-+-+...| .+.|..||.-++
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 4589999997444444445 678999999886
No 44
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=93.97 E-value=0.037 Score=37.96 Aligned_cols=27 Identities=26% Similarity=0.465 Sum_probs=22.5
Q ss_pred CCCCCCCCCcccccCCCceecCcCceee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
.|+.||+..++. ..++..+|..||.+-
T Consensus 5 ~C~~C~~~~i~~-~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 5 KCSKCGGNGIVN-KEDDYEVCIFCGSSF 31 (33)
T ss_pred EcCCCCCCeEEE-ecCCeEEcccCCcEe
Confidence 699999987653 467999999999974
No 45
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=93.87 E-value=0.03 Score=35.21 Aligned_cols=22 Identities=27% Similarity=0.889 Sum_probs=17.5
Q ss_pred CCCCCCCCCcccccCCCceecCcCcee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
+||+||... ..+..+|..||.-
T Consensus 1 ~Cp~CG~~~-----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEI-----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCC-----CCcCcchhhhCCc
Confidence 599999873 2477889999974
No 46
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=93.82 E-value=0.6 Score=48.05 Aligned_cols=171 Identities=12% Similarity=0.068 Sum_probs=107.8
Q ss_pred HHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcc-cCCCchhHHHHHHHHHHHHhcCC-CCcHHHHHHHhC--cChHH
Q 010689 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNF-TKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYE 149 (504)
Q Consensus 74 a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~-~rGR~~~~vaAACLYiACR~~~~-p~tL~dIs~~~~--vs~~~ 149 (504)
.++.+-.+|.-.+|. ....--|..||.+.+.-.. ..--....+--+|||||.+.+.+ |--+.|||-++. ++..+
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 468899999999999 8888899999998865221 12223345556999999998664 888999999975 78899
Q ss_pred HHHHHHHHHHHhcccccccccccCCccchHHHHHHhhC-CC--------CCHH-HHHHHHHHHHHhcccccccCCChhHH
Q 010689 150 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PG--------GNKK-VCDTARDILASMKRDWITTGRKPSGL 219 (504)
Q Consensus 150 Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~-~~--------l~~~-V~~~A~~I~~~~~~~~l~~GR~P~~I 219 (504)
|...-+.|.+.|+-..-| +....++.-|..-+. ++ .+.. .+..| .|+....-+.=.---....+
T Consensus 226 IltmE~iilkal~W~l~P-----iTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqia-qlLDlc~ldids~~fsYril 299 (408)
T KOG0655|consen 226 ILTMELIILKALKWELSP-----ITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIA-QLLDLCILDIDSLEFSYRIL 299 (408)
T ss_pred HHHHHHHHHHHhcccccc-----eehHHHHHHHHHHHhcCCCCceeccccchHHHHHHH-HHHHHHHhccccccchHHHH
Confidence 999999999999877655 333344455544332 11 1111 12222 23333221111123556677
Q ss_pred HHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 220 CGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 220 AAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
||||||.-. . ..-+-++.|.--..|.+..+=+.
T Consensus 300 aAAal~h~~-----s--~e~v~kaSG~~w~~ie~cv~wm~ 332 (408)
T KOG0655|consen 300 AAAALCHFT-----S--IEVVKKASGLEWDSIEECVDWMV 332 (408)
T ss_pred HHHHHHHHh-----H--HHHHHHcccccHHHHHHHHHHHH
Confidence 888876432 1 12234556777777777665443
No 47
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=93.77 E-value=0.25 Score=50.91 Aligned_cols=67 Identities=13% Similarity=0.099 Sum_probs=54.4
Q ss_pred hHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhh
Q 010689 178 FLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIV 244 (504)
Q Consensus 178 ~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~ 244 (504)
+|..++..|.+.++..|+.+|.-+.++.--.+-..-..|.-|+++||||||..-...++..+++..+
T Consensus 62 ~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~ 128 (305)
T TIGR00569 62 RLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNL 128 (305)
T ss_pred HHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhc
Confidence 5667777776558899999999999887554444568999999999999999999999988877644
No 48
>PRK00420 hypothetical protein; Validated
Probab=93.73 E-value=0.045 Score=48.06 Aligned_cols=27 Identities=26% Similarity=0.533 Sum_probs=21.7
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeec
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
.||.||..- +...+|..+|..||.++.
T Consensus 25 ~CP~Cg~pL--f~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPL--FELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCcc--eecCCCceECCCCCCeee
Confidence 699999753 333679999999999864
No 49
>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=93.45 E-value=0.04 Score=38.60 Aligned_cols=30 Identities=20% Similarity=0.575 Sum_probs=21.4
Q ss_pred CCCCCCCCCCcccc----cCCCceecCcCceeec
Q 010689 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D----~~~G~~VC~~CG~Vle 31 (504)
+.||+||...-+-+ ...+.+.|..||.++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 57999998633222 2345799999999874
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=93.35 E-value=0.29 Score=42.69 Aligned_cols=66 Identities=15% Similarity=0.105 Sum_probs=50.6
Q ss_pred chHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCC-CCCHhhHHhhh
Q 010689 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIVKIV 244 (504)
Q Consensus 177 ~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~-~~t~keIa~v~ 244 (504)
.||...+..+. +++.+.-.|..+++++..........+.-|++||+++|+++.+. ..+..+++...
T Consensus 36 ~~i~~~~~~~~--l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~ 102 (127)
T PF00134_consen 36 DWIIELCQRLK--LSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRIS 102 (127)
T ss_dssp HHHHHHHHHTT---BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHT
T ss_pred HHHHHHHHhcc--cchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHH
Confidence 47777888887 89999999999999987666677899999999999999998876 34445554443
No 51
>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=92.84 E-value=0.077 Score=35.57 Aligned_cols=28 Identities=25% Similarity=0.531 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceee
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
+..||.|++...-. +...+||..||.-.
T Consensus 2 ~p~Cp~C~se~~y~--D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 2 LPKCPLCGSEYTYE--DGELLVCPECGHEW 29 (30)
T ss_dssp S---TTT-----EE---SSSEEETTTTEEE
T ss_pred CCCCCCCCCcceec--cCCEEeCCcccccC
Confidence 35899999985544 46799999999753
No 52
>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=92.15 E-value=0.11 Score=41.46 Aligned_cols=17 Identities=24% Similarity=0.638 Sum_probs=14.5
Q ss_pred cccCCCceecCcCceee
Q 010689 14 HRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 14 ~D~~~G~~VC~~CG~Vl 30 (504)
++..+|.++|.+||.+.
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 45678999999999985
No 53
>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=91.98 E-value=0.13 Score=36.18 Aligned_cols=27 Identities=19% Similarity=0.377 Sum_probs=20.7
Q ss_pred CCCCCCCCCC-ccccc--CCCceecCcCce
Q 010689 2 VWCSSCARHV-TGHRP--YDSQLCCDRCGK 28 (504)
Q Consensus 2 ~~Cp~Cgs~~-iv~D~--~~G~~VC~~CG~ 28 (504)
..||.||+.. +-+|. ..|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 4699999973 44554 459999999985
No 54
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=91.72 E-value=0.11 Score=43.21 Aligned_cols=29 Identities=28% Similarity=0.571 Sum_probs=25.0
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
.||.||+. .+.....|-..|..||.+..-
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 69999998 566678999999999998754
No 55
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=91.61 E-value=0.13 Score=38.65 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=20.9
Q ss_pred CCCCCCCCCcccccCCCceecCcCceee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
.||.||+. +..+ ..+...|..||...
T Consensus 22 fCP~Cg~~-~m~~-~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMAE-HLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hhec-cCCcEECCCcCCEE
Confidence 69999997 5554 44899999999864
No 56
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.03 E-value=0.17 Score=37.66 Aligned_cols=30 Identities=17% Similarity=0.561 Sum_probs=20.8
Q ss_pred CCCCCCCCCcccccCC-CceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYD-SQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~-G~~VC~~CG~Vlee 32 (504)
.||.||.-....+... ..++|..||.+...
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 6999998643332222 38999999997643
No 57
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=90.96 E-value=0.18 Score=39.03 Aligned_cols=27 Identities=22% Similarity=0.429 Sum_probs=20.1
Q ss_pred CCCCCCCCCCcccccCCC-------ceecCcCce
Q 010689 2 VWCSSCARHVTGHRPYDS-------QLCCDRCGK 28 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G-------~~VC~~CG~ 28 (504)
..||.||+..+.++...+ .+.|.+||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 469999988776654433 366999999
No 58
>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=90.76 E-value=0.47 Score=34.22 Aligned_cols=31 Identities=19% Similarity=0.316 Sum_probs=24.3
Q ss_pred HhcCCCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 229 LTHGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 229 ~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...+-+.|..+||..+|+|+.|+.+|++.+.
T Consensus 12 Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 12 LQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 3456789999999999999999999998763
No 59
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=90.65 E-value=0.16 Score=45.68 Aligned_cols=22 Identities=32% Similarity=0.922 Sum_probs=18.7
Q ss_pred CCCCCCCCCcccccCCCceecCcCc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCG 27 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG 27 (504)
.||.||..- |. .+|.++|..||
T Consensus 30 hCp~Cg~PL--F~-KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL--FR-KDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc--ee-eCCeEECCCCC
Confidence 699999863 43 67999999999
No 60
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=90.11 E-value=0.45 Score=49.33 Aligned_cols=83 Identities=17% Similarity=0.140 Sum_probs=63.0
Q ss_pred cchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhcc----CHHHH
Q 010689 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI----CEATL 251 (504)
Q Consensus 176 ~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~V----se~TI 251 (504)
..||...+.+|+ ++..-..+|.-+..+.---.....-.|..||++|||||+...+..+..++|..+..- ...+.
T Consensus 43 ~~fI~elg~~L~--~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~ 120 (323)
T KOG0834|consen 43 AKFIQELGVRLK--MPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLEL 120 (323)
T ss_pred HHHHHHHHHHcC--CCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccH
Confidence 357888888887 555557778888888765556677888999999999999999999999999877542 22356
Q ss_pred HHHHHHhhc
Q 010689 252 MKRLIEFEN 260 (504)
Q Consensus 252 rkr~kE~~~ 260 (504)
..+|-++.+
T Consensus 121 ~~~~~~~~~ 129 (323)
T KOG0834|consen 121 EEVYWELKE 129 (323)
T ss_pred HHHHHHHHH
Confidence 666666653
No 61
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.95 E-value=0.2 Score=35.18 Aligned_cols=29 Identities=21% Similarity=0.623 Sum_probs=21.6
Q ss_pred CCCCCCCCCCcccc----cCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D----~~~G~~VC~~CG~Vl 30 (504)
..||+|+..--+-| ...+.+-|+.||.|.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 37999998733333 246799999999875
No 62
>PRK11827 hypothetical protein; Provisional
Probab=89.85 E-value=0.24 Score=38.69 Aligned_cols=28 Identities=14% Similarity=0.280 Sum_probs=22.9
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
..||.|++. +.+|.....++|..||.+.
T Consensus 9 LaCP~ckg~-L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 9 IACPVCNGK-LWYNQEKQELICKLDNLAF 36 (60)
T ss_pred eECCCCCCc-CeEcCCCCeEECCccCeec
Confidence 479999886 5577667899999999875
No 63
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.71 E-value=0.23 Score=36.39 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=21.1
Q ss_pred CCCCCCCCCcccccCCCceecCcCceee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
.|++||.. +.+++..+...|..||.-+
T Consensus 5 ~C~~CG~~-~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGRE-VELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCE-EEECCCCCceECCCCCCeE
Confidence 79999986 4556565689999999743
No 64
>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=89.53 E-value=0.22 Score=37.71 Aligned_cols=31 Identities=19% Similarity=0.332 Sum_probs=21.8
Q ss_pred CCCCCCCCCCc-c---ccc--CCCceecCcCceeecc
Q 010689 2 VWCSSCARHVT-G---HRP--YDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~i-v---~D~--~~G~~VC~~CG~Vlee 32 (504)
..||.||+... + ++. ..|...|..||.....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 47999999865 2 232 2455689999998653
No 65
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.05 E-value=0.24 Score=46.02 Aligned_cols=29 Identities=24% Similarity=0.450 Sum_probs=19.5
Q ss_pred CCCCCCCCCC-cccccC---CCc-----eecCcCceee
Q 010689 2 VWCSSCARHV-TGHRPY---DSQ-----LCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~-iv~D~~---~G~-----~VC~~CG~Vl 30 (504)
+.||+||+.. .+.+.. .|. .-|++||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5799999865 344432 453 4599999853
No 66
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=89.04 E-value=1.4 Score=46.45 Aligned_cols=90 Identities=18% Similarity=0.238 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCC-c---HHH-HHHHhCcChH
Q 010689 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF-L---LID-FSNYLNINVY 148 (504)
Q Consensus 74 a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~-t---L~d-Is~~~~vs~~ 148 (504)
..++|++++..-+|. ...+.+|..||.++.=+|++.-.++..+|+|||.+|.+.+..-. + |+| .-+.+..+..
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 457788888888888 78999999999999888888777778899999999999876542 2 332 2234566666
Q ss_pred HHHHHHHHHHHHhcccc
Q 010689 149 ELGAVYLQLCQVLYIAD 165 (504)
Q Consensus 149 ~Lg~~~~~L~~~L~i~~ 165 (504)
+|-..-.-++-.|.+..
T Consensus 463 dLia~Ef~VlvaLefaL 479 (497)
T KOG4164|consen 463 DLIAFEFPVLVALEFAL 479 (497)
T ss_pred hhhhhhhhHHHhhhhhc
Confidence 65554444444454433
No 67
>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=88.94 E-value=6.6 Score=35.99 Aligned_cols=88 Identities=11% Similarity=0.095 Sum_probs=66.4
Q ss_pred HHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHh---Ccc--cCCCchhHHHHHHHHHHHHh-cCCCCcHHHHHHHhCcCh
Q 010689 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA---RNF--TKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNINV 147 (504)
Q Consensus 74 a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~---~~~--~rGR~~~~vaAACLYiACR~-~~~p~tL~dIs~~~~vs~ 147 (504)
..++|.++....+++ ..+.-.|..|..+... ... +.......+..+|+-+|.+. .....+.+.+|.+.|++.
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 567899999999999 8888889888888877 222 34455677889999999996 788899999999999999
Q ss_pred HHHHHHHHHHHHHhcc
Q 010689 148 YELGAVYLQLCQVLYI 163 (504)
Q Consensus 148 ~~Lg~~~~~L~~~L~i 163 (504)
.+|++.-..+...|+.
T Consensus 132 ~eln~lE~~fL~~l~~ 147 (149)
T PF08613_consen 132 KELNELEREFLKLLDY 147 (149)
T ss_dssp HHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHCCC
Confidence 9999998888887764
No 68
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=88.50 E-value=24 Score=36.66 Aligned_cols=26 Identities=8% Similarity=0.107 Sum_probs=23.0
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|.++||..+||+..||++++..-
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rA 306 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEA 306 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56999999999999999999887654
No 69
>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=88.15 E-value=0.29 Score=42.82 Aligned_cols=29 Identities=21% Similarity=0.527 Sum_probs=23.5
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccC
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (504)
.||+||.. .||-...-+||..||.++.-.
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 79999998 456556779999999998754
No 70
>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=87.92 E-value=0.16 Score=53.52 Aligned_cols=86 Identities=13% Similarity=0.092 Sum_probs=0.0
Q ss_pred HHHHHcCCCCchHHHHHHHHHHHHHH-hCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHH
Q 010689 80 QMKNALNIGESDEIVHVAKRFYGIAV-ARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 158 (504)
Q Consensus 80 ~i~~~L~Lp~~~~i~e~A~~iyk~a~-~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~ 158 (504)
.|+-.++++.+..++..|..||+... ....+++..-..-+.+|+||||...+.++-+..+....+++++...+.|..|.
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 34445544423899999999999998 45566777777788999999999999999888888888999998888888888
Q ss_pred HHhcccc
Q 010689 159 QVLYIAD 165 (504)
Q Consensus 159 ~~L~i~~ 165 (504)
+.|....
T Consensus 83 ~~L~~~s 89 (353)
T PF05460_consen 83 NLLGNSS 89 (353)
T ss_dssp -------
T ss_pred HHHhCCC
Confidence 8887654
No 71
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=87.59 E-value=0.34 Score=37.65 Aligned_cols=28 Identities=21% Similarity=0.442 Sum_probs=24.9
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
+.||.|.+. +.+|...+.++|..||...
T Consensus 9 LaCP~~kg~-L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 9 LACPVCKGP-LVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeccCcCCc-ceEeccCCEEEecccCcee
Confidence 579999988 7788889999999999875
No 72
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=87.13 E-value=0.42 Score=35.63 Aligned_cols=26 Identities=27% Similarity=0.701 Sum_probs=21.5
Q ss_pred CCCCCCCCCcccccCCCceecCcCcee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.||.||...+.-++.+ -+.|..||..
T Consensus 21 ~CPrCG~gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGPGVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred cCCCCCCcchhhhcCc-eeEeccccce
Confidence 6999998777667654 8999999986
No 73
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=87.04 E-value=2.5 Score=33.24 Aligned_cols=71 Identities=7% Similarity=0.136 Sum_probs=44.5
Q ss_pred HHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCc-ChHHHHHHHHH
Q 010689 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 156 (504)
Q Consensus 78 I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~v-s~~~Lg~~~~~ 156 (504)
|..++..++++ ...... +|+.........-.....+.-|+-|+.- + +.++.+||..+|+ +...+.+.|++
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---T-DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHhCCC--HHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHc---C-CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 67889999998 544333 3443332222111122234445555532 2 8999999999999 99999888876
Q ss_pred H
Q 010689 157 L 157 (504)
Q Consensus 157 L 157 (504)
.
T Consensus 75 ~ 75 (84)
T smart00342 75 L 75 (84)
T ss_pred H
Confidence 5
No 74
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=86.66 E-value=0.29 Score=39.90 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=27.4
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
++||.|-....++.++...++|.+|+.|+=
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~il~ 64 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCSTILC 64 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCceEEE
Confidence 589999988889999999999999999974
No 75
>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=86.55 E-value=2.6 Score=38.37 Aligned_cols=66 Identities=15% Similarity=0.117 Sum_probs=51.0
Q ss_pred hHHHHHHhhCCCCCHHHHHHHHHHHHHhc--ccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhc
Q 010689 178 FLHKFTDRLLPGGNKKVCDTARDILASMK--RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH 245 (504)
Q Consensus 178 ~I~r~~~~L~~~l~~~V~~~A~~I~~~~~--~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~ 245 (504)
=|..+|++|+ +++++....+.+++.+. ..++.-+|+---|.-.|||+.|++++..+|.++|-..-.
T Consensus 17 Rl~~LC~~L~--l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr 84 (135)
T PF01857_consen 17 RLQDLCERLD--LSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYR 84 (135)
T ss_dssp HHHHHHHHHT--TSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHT
T ss_pred HHHHHHHHcC--CcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHH
Confidence 3566888887 77778788888887764 467899999999999999999999998899888876544
No 76
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=86.37 E-value=0.41 Score=42.20 Aligned_cols=33 Identities=24% Similarity=0.579 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCcc-cccCCCceecCcCceeeccC
Q 010689 1 MVWCSSCARHVTG-HRPYDSQLCCDRCGKVLEDH 33 (504)
Q Consensus 1 m~~Cp~Cgs~~iv-~D~~~G~~VC~~CG~Vlee~ 33 (504)
|..||.||+-.+. .|...+.++|..||...+-.
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 6789999987443 34456899999999987654
No 77
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=86.32 E-value=0.34 Score=41.45 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=23.0
Q ss_pred CCCCCCCCCcc---ccc--CCCceecCcCceeec
Q 010689 3 WCSSCARHVTG---HRP--YDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv---~D~--~~G~~VC~~CG~Vle 31 (504)
.||.||+..++ ++- .-|.++|..||.-.+
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 59999998766 553 358999999998654
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=86.15 E-value=0.42 Score=30.98 Aligned_cols=23 Identities=30% Similarity=0.710 Sum_probs=18.5
Q ss_pred CCCCCCCCCcccccCCCceecCcCceee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
.||.|+... ......|..||.+.
T Consensus 2 ~CP~C~~~V-----~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEV-----PESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCc-----hhhcCcCCCCCCCC
Confidence 699999873 34678999999875
No 79
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=86.14 E-value=49 Score=34.96 Aligned_cols=91 Identities=9% Similarity=0.030 Sum_probs=53.1
Q ss_pred hHHHHHHHHHHHHHHHHHHcC---CCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHH--------------
Q 010689 66 SRERLMEKAFDDMRQMKNALN---IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACR-------------- 128 (504)
Q Consensus 66 srer~L~~a~~~I~~i~~~L~---Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR-------------- 128 (504)
.+++.+..-...|..+|.++. +.-.+-+.+.-..+++.+..-...+|.+....|.-.|+-+-+
T Consensus 130 A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~ 209 (367)
T PRK09210 130 AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPV 209 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccH
Confidence 334444445556666766652 221134445555566666555555677776666666664431
Q ss_pred ------------------hcCCCCcHHHHHHHhCcChHHHHHHHHH
Q 010689 129 ------------------QKSKPFLLIDFSNYLNINVYELGAVYLQ 156 (504)
Q Consensus 129 ------------------~~~~p~tL~dIs~~~~vs~~~Lg~~~~~ 156 (504)
..|.+-|..+||..+|+++..+......
T Consensus 210 ~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~ 255 (367)
T PRK09210 210 HMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI 255 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 1233446778889999998888776543
No 80
>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=86.02 E-value=0.89 Score=39.47 Aligned_cols=50 Identities=24% Similarity=0.451 Sum_probs=31.0
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcc--cccccccccCCCCccccC
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF--STEATFVKNAAGQSQLSG 53 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i--d~~~~f~~~~~G~s~v~G 53 (504)
..||.|++.-.-.| ...+||..||.--..... ..+.....|+.|.....|
T Consensus 3 p~CP~C~seytY~d--g~~~iCpeC~~EW~~~~~~~~~~~~~~kDsnG~~L~dG 54 (109)
T TIGR00686 3 PPCPKCNSEYTYHD--GTQLICPSCLYEWNENEVNDDDDELIVKDCNGNLLANG 54 (109)
T ss_pred CcCCcCCCcceEec--CCeeECccccccccccccccccCCceEEcCCCCCccCC
Confidence 57999999854343 457999999987654322 122224456666544444
No 81
>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=85.84 E-value=1.5 Score=32.00 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=24.7
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+-..|+++||..+|+|..|++++++++.+
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 55699999999999999999999999875
No 82
>COG4640 Predicted membrane protein [Function unknown]
Probab=85.82 E-value=0.4 Score=50.32 Aligned_cols=27 Identities=22% Similarity=0.780 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
|..||.||+.. .+|+.-|+.||.-+.+
T Consensus 1 M~fC~kcG~qk-----~Ed~~qC~qCG~~~t~ 27 (465)
T COG4640 1 MKFCPKCGSQK-----AEDDVQCTQCGHKFTS 27 (465)
T ss_pred CCccccccccc-----ccccccccccCCcCCc
Confidence 89999999763 3566779999986653
No 83
>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=85.72 E-value=38 Score=33.24 Aligned_cols=26 Identities=4% Similarity=-0.019 Sum_probs=22.7
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|+++||..+|||..+|++++..-
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~a 220 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKA 220 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 57999999999999999999876543
No 84
>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=85.38 E-value=0.65 Score=34.04 Aligned_cols=27 Identities=19% Similarity=0.434 Sum_probs=20.0
Q ss_pred CCCCCCCCCCcccccCCCceecCcCce
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
..||+||+.....-...+..-|..|+.
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 369999998443333469999999984
No 85
>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=85.15 E-value=2.1 Score=43.76 Aligned_cols=70 Identities=14% Similarity=0.191 Sum_probs=61.8
Q ss_pred cchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhc
Q 010689 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVH 245 (504)
Q Consensus 176 ~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~ 245 (504)
...+..|++++.+.++..|+.+|.....++--.|-..--.|..|.++|+|+||..-.+.+|..++++-..
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 4467888999876789999999999999887778888899999999999999999999999999987766
No 86
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=84.93 E-value=0.57 Score=40.29 Aligned_cols=31 Identities=19% Similarity=0.413 Sum_probs=23.2
Q ss_pred CCCCCCCCCCc--ccccCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVT--GHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~i--v~D~~~G~~VC~~CG~Vlee 32 (504)
..||+||...+ ..|...+.++|..||+.-+-
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 36999996533 24556789999999998653
No 87
>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=84.92 E-value=0.66 Score=36.67 Aligned_cols=28 Identities=21% Similarity=0.590 Sum_probs=20.8
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeec
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
.||.||..... .......+|..||.+.+
T Consensus 30 ~C~~CG~~~~~-~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 30 TCPRCGHRNKK-RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccccccc-ccccceEEcCCCCCEEC
Confidence 69999987433 34557889999999865
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=84.83 E-value=0.57 Score=41.89 Aligned_cols=29 Identities=7% Similarity=0.033 Sum_probs=23.7
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccC
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (504)
.||+||.. .||-..--+||..||.+....
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 69999997 466566889999999997644
No 89
>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=84.40 E-value=0.37 Score=33.70 Aligned_cols=28 Identities=32% Similarity=0.695 Sum_probs=21.7
Q ss_pred CCCCCCCC-CcccccCCCceecCcCceee
Q 010689 3 WCSSCARH-VTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~-~iv~D~~~G~~VC~~CG~Vl 30 (504)
.|+.||.. ++.+++..-..+|..||.-|
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 77788777888999999854
No 90
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=84.18 E-value=8.6 Score=30.09 Aligned_cols=27 Identities=11% Similarity=0.164 Sum_probs=24.3
Q ss_pred CCCHhhHHhhhcc-CHHHHHHHHHHhhc
Q 010689 234 KFSKSDIVKIVHI-CEATLMKRLIEFEN 260 (504)
Q Consensus 234 ~~t~keIa~v~~V-se~TIrkr~kE~~~ 260 (504)
+.++.+||..+|. +...+.+.++....
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~g 77 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLFG 77 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHC
Confidence 7899999999999 99999999987753
No 91
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=84.15 E-value=3.1 Score=40.53 Aligned_cols=82 Identities=16% Similarity=0.183 Sum_probs=57.4
Q ss_pred HHHHHHHHcCCCCchHHHHHHHHHHHHHHhC-ccc----CCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHH
Q 010689 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVAR-NFT----KGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELG 151 (504)
Q Consensus 77 ~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~-~~~----rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg 151 (504)
-|+.+|=+||+. .++..|.++++..-++ .-+ ---+.....+|.+|.|||..+....-.-+..+.|++...+.
T Consensus 95 ~VrdlaVQfgc~---evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~sg~~~s~F~ 171 (262)
T KOG4557|consen 95 NVRDLAVQFGCV---EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVSGTSESEFS 171 (262)
T ss_pred CHHHHHHHHhHH---HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccccCCCHHHHH
Confidence 378888888888 7888888888876552 111 12334578899999999998887766666667778777666
Q ss_pred HHHHHHHHHh
Q 010689 152 AVYLQLCQVL 161 (504)
Q Consensus 152 ~~~~~L~~~L 161 (504)
...+++-+..
T Consensus 172 ~l~kqler~~ 181 (262)
T KOG4557|consen 172 CLSKQLERNY 181 (262)
T ss_pred HHHHHHHHHH
Confidence 5555555443
No 92
>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=83.97 E-value=0.55 Score=39.59 Aligned_cols=32 Identities=22% Similarity=0.540 Sum_probs=25.4
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccCcc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (504)
.||.||... +.....|-..|..||.++.....
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 45567899999999999875443
No 93
>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=83.92 E-value=0.79 Score=32.84 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=15.3
Q ss_pred CCCCCCCCC-c-cccc--CCCceecCcCcee
Q 010689 3 WCSSCARHV-T-GHRP--YDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~-i-v~D~--~~G~~VC~~CG~V 29 (504)
.||.||++. + +++. .+|..+|..||-+
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 699999984 3 2543 3699999999434
No 94
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=83.69 E-value=0.82 Score=30.85 Aligned_cols=28 Identities=21% Similarity=0.508 Sum_probs=15.8
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
..|+.||+..... ...-..+|..||...
T Consensus 4 rfC~~CG~~t~~~-~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 4 RFCGRCGAPTKPA-PGGWARRCPSCGHEH 31 (32)
T ss_dssp SB-TTT--BEEE--SSSS-EEESSSS-EE
T ss_pred cccCcCCccccCC-CCcCEeECCCCcCEe
Confidence 3799999874433 345689999999863
No 95
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=83.61 E-value=0.76 Score=37.23 Aligned_cols=31 Identities=16% Similarity=0.469 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCccccc-------CCCceecC--cCceeec
Q 010689 1 MVWCSSCARHVTGHRP-------YDSQLCCD--RCGKVLE 31 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~-------~~G~~VC~--~CG~Vle 31 (504)
|+.||.||+...+.+. .+-...|+ +||...-
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 8999999998765442 23456799 8998643
No 96
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=82.93 E-value=1.6 Score=40.64 Aligned_cols=38 Identities=16% Similarity=0.259 Sum_probs=31.8
Q ss_pred HHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCC
Q 010689 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (504)
Q Consensus 226 lAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~ 263 (504)
|.+...+-+.|.++||+.+|+|++|+++|++.+.+..-
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 33444678899999999999999999999999987543
No 97
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.42 E-value=0.8 Score=35.51 Aligned_cols=9 Identities=33% Similarity=0.958 Sum_probs=4.5
Q ss_pred ceecCcCce
Q 010689 20 QLCCDRCGK 28 (504)
Q Consensus 20 ~~VC~~CG~ 28 (504)
.++|.+||+
T Consensus 50 ~Y~Cp~CGF 58 (61)
T COG2888 50 PYRCPKCGF 58 (61)
T ss_pred ceECCCcCc
Confidence 445555554
No 98
>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=81.65 E-value=0.69 Score=51.67 Aligned_cols=34 Identities=26% Similarity=0.641 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCcc------cc----cCCCceecCcCceeeccCc
Q 010689 1 MVWCSSCARHVTG------HR----PYDSQLCCDRCGKVLEDHN 34 (504)
Q Consensus 1 m~~Cp~Cgs~~iv------~D----~~~G~~VC~~CG~Vlee~~ 34 (504)
++.||+||..... ++ +..-.++|..||..++++.
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 3689999997432 22 3457899999999999854
No 99
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=81.49 E-value=2.1 Score=30.99 Aligned_cols=30 Identities=17% Similarity=0.079 Sum_probs=20.6
Q ss_pred HHHhcCCCCCHhhHHhhhccCHHHHHHHHH
Q 010689 227 SALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 227 Aa~~~g~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
...++....|+++||+.+|++.+||.+-++
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 100
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=81.20 E-value=0.95 Score=31.56 Aligned_cols=29 Identities=24% Similarity=0.729 Sum_probs=20.6
Q ss_pred CCCCCCCCCCcccc----cCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D----~~~G~~VC~~CG~Vl 30 (504)
+.||+|+..--+-| .....+-|+.||.+.
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 47999998733333 234578999999874
No 101
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=80.89 E-value=0.91 Score=32.41 Aligned_cols=27 Identities=22% Similarity=0.580 Sum_probs=19.4
Q ss_pred CCCCCCCCCccc-----c-cC---CCceecCcCcee
Q 010689 3 WCSSCARHVTGH-----R-PY---DSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~-----D-~~---~G~~VC~~CG~V 29 (504)
.||.||+...++ . .+ +-.++|.+||..
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 699999986543 1 12 348999999964
No 102
>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=80.87 E-value=3.3 Score=31.54 Aligned_cols=26 Identities=15% Similarity=0.286 Sum_probs=23.0
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
++|..|||+.+|||.+|+..+++.-.
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 47899999999999999999998643
No 103
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=80.84 E-value=1.1 Score=35.37 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=21.7
Q ss_pred CCCCCCCCCcccccCCC--ceecCcCceee
Q 010689 3 WCSSCARHVTGHRPYDS--QLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G--~~VC~~CG~Vl 30 (504)
.||.||...+......| ..+|..||...
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcCc
Confidence 69999999766555554 57999999963
No 104
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=80.69 E-value=2.3 Score=39.15 Aligned_cols=38 Identities=13% Similarity=0.228 Sum_probs=31.8
Q ss_pred HHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCC
Q 010689 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (504)
Q Consensus 226 lAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~ 263 (504)
+.+...+-+.|..+||+.+|+|++|+++|++.+.+...
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 34445578899999999999999999999999986543
No 105
>PF13730 HTH_36: Helix-turn-helix domain
Probab=80.64 E-value=3.3 Score=30.91 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=24.2
Q ss_pred CCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 235 FSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.|++.||+.+|++..||++.++++.+
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 48999999999999999999999875
No 106
>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=80.48 E-value=1.2 Score=32.00 Aligned_cols=23 Identities=30% Similarity=0.781 Sum_probs=18.0
Q ss_pred CCCCCCCCCcccccCCCceecCcCc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCG 27 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG 27 (504)
.||.||.. .+...+|..+|..||
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 69999743 344578999999997
No 107
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=80.43 E-value=0.57 Score=44.59 Aligned_cols=30 Identities=27% Similarity=0.741 Sum_probs=23.4
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
.||.||..-...|.-+....|..||.+|.+
T Consensus 119 ~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 599999774444555678999999999875
No 108
>PRK10220 hypothetical protein; Provisional
Probab=80.40 E-value=2.1 Score=37.22 Aligned_cols=51 Identities=22% Similarity=0.455 Sum_probs=30.4
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCccc--ccccccccCCCCccccCc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFS--TEATFVKNAAGQSQLSGN 54 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id--~~~~f~~~~~G~s~v~G~ 54 (504)
..||.|++.-.-.| ...+||..||.--....-. .+.....|+.|+....|-
T Consensus 4 P~CP~C~seytY~d--~~~~vCpeC~hEW~~~~~~~~~~~~~vkDsnG~~L~dGD 56 (111)
T PRK10220 4 PHCPKCNSEYTYED--NGMYICPECAHEWNDAEPAQESDELIVKDANGNLLADGD 56 (111)
T ss_pred CcCCCCCCcceEcC--CCeEECCcccCcCCccccccccCCceEEcCCCCCccCCC
Confidence 47999999854343 4689999999865433211 111234566665444443
No 109
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=80.25 E-value=77 Score=32.79 Aligned_cols=25 Identities=12% Similarity=0.111 Sum_probs=22.1
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHH
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
+...|++||+..+|||..+||++..
T Consensus 274 ~~~~Tl~EIa~~lgiS~erVRqi~~ 298 (317)
T PRK07405 274 GQPLTLAKIGERLNISRERVRQIER 298 (317)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3679999999999999999997754
No 110
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=79.92 E-value=16 Score=39.92 Aligned_cols=178 Identities=15% Similarity=0.209 Sum_probs=97.3
Q ss_pred HHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcC-C------------------CCcHH
Q 010689 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKS-K------------------PFLLI 137 (504)
Q Consensus 77 ~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~-~------------------p~tL~ 137 (504)
-+..++..|+++ ...++.|..++..+.-.|+.- |+ ..=||.+=.+..+ . -.-+.
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 368889999999 888999988888765555432 11 1233333333311 1 12356
Q ss_pred HHHHHhCcChHHHHHHHHHHHHHhccccccc--c----cccCCccchHH----------------------HHHHhhCCC
Q 010689 138 DFSNYLNINVYELGAVYLQLCQVLYIADESN--V----LKQVDPSIFLH----------------------KFTDRLLPG 189 (504)
Q Consensus 138 dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~--~----~~~~dP~~~I~----------------------r~~~~L~~~ 189 (504)
.|+..++++..+|..+...|+ .|+- .|. + ...+-|..+|. .|.+.+...
T Consensus 213 ~ia~~l~is~~~v~~~~~~Ir-~L~P--~Pg~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~in~~Y~~~~~~~ 289 (455)
T PRK05932 213 TLAKKLGVKEEDLQEALDLIR-SLDP--KPGAGFGTEEPEYVVPDVFVRKINGGWLVELNPDSLPRLRINQEYAALVSRS 289 (455)
T ss_pred HHHHHHCcCHHHHHHHHHHHh-CCCC--CCccccCCCCCCccCCCEEEEEeCCEEEEEECCCCCceEEECHHHHHHHHhc
Confidence 788889999999988876554 4531 121 0 01122333322 222222100
Q ss_pred CCHHH-------HHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHh-----cC----CCCCHhhHHhhhccCHHHHHH
Q 010689 190 GNKKV-------CDTARDILASMKRDWITTGRKPSGLCGAALYVSALT-----HG----LKFSKSDIVKIVHICEATLMK 253 (504)
Q Consensus 190 l~~~V-------~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~-----~g----~~~t~keIa~v~~Vse~TIrk 253 (504)
.+.++ ...|..+++.+. +|-.+|---+-.|+-+- .| .+.|+++||..+|++++||.+
T Consensus 290 ~~~e~~~ylk~k~~~A~~li~~i~-------~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSR 362 (455)
T PRK05932 290 ARDEDKQFLREKLQEAKWLIKSLE-------QRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISR 362 (455)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhh
Confidence 01111 122333333322 34444444444444432 24 368999999999999999998
Q ss_pred HHHH-hhccCCCCCChHHH
Q 010689 254 RLIE-FENTDSGSLTIEDF 271 (504)
Q Consensus 254 r~kE-~~~t~~~~lt~~~~ 271 (504)
..+. +..|+-|-.-+..|
T Consensus 363 av~~Kyv~tp~Gi~~lk~F 381 (455)
T PRK05932 363 ATTNKYMATPRGIFELKYF 381 (455)
T ss_pred hhcCceeecCCceEEHHHh
Confidence 7653 33555555555555
No 111
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=79.91 E-value=0.95 Score=51.29 Aligned_cols=25 Identities=28% Similarity=0.798 Sum_probs=14.2
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceee
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
|..||.||..+. .|.-+|..||.-+
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 777888877632 3444455554444
No 112
>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=79.76 E-value=15 Score=33.69 Aligned_cols=84 Identities=15% Similarity=0.055 Sum_probs=58.0
Q ss_pred CCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcc---c--ccccCCChhHHHHHHHHHHHHhc-CCCCCHhhHHhhhcc
Q 010689 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR---D--WITTGRKPSGLCGAALYVSALTH-GLKFSKSDIVKIVHI 246 (504)
Q Consensus 173 ~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~---~--~l~~GR~P~~IAAAalylAa~~~-g~~~t~keIa~v~~V 246 (504)
++-..|+.|+..... .++.+.-.|+-++.++.. . ...+...+.-+-.+||.+|+.+. +...+.+..|++.|+
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 ISIRDFLSRILKYTQ--CSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGI 129 (149)
T ss_dssp S-HHHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS
T ss_pred CcHHHHHHHHHHHcC--CChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCC
Confidence 556678888887776 788999999999998876 1 12445677789999999999976 566888999999999
Q ss_pred CHHHHHHHHHHh
Q 010689 247 CEATLMKRLIEF 258 (504)
Q Consensus 247 se~TIrkr~kE~ 258 (504)
+..-+.+-=.+|
T Consensus 130 s~~eln~lE~~f 141 (149)
T PF08613_consen 130 SLKELNELEREF 141 (149)
T ss_dssp -HHHHHHHHHHH
T ss_pred CHHHHHHHHHHH
Confidence 877665544444
No 113
>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=79.62 E-value=1.4 Score=40.57 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=21.5
Q ss_pred CCCCCCCCCC-ccccc---CCCcee-----cCcCceee
Q 010689 2 VWCSSCARHV-TGHRP---YDSQLC-----CDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~-iv~D~---~~G~~V-----C~~CG~Vl 30 (504)
|.||+||+.. -+.|+ .+|..| |..||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 5899999974 45664 467766 99999743
No 114
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=78.99 E-value=3.5 Score=30.36 Aligned_cols=26 Identities=12% Similarity=0.105 Sum_probs=23.2
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|+++||+..||+..||++.++.+
T Consensus 26 ~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 26 ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 33899999999999999999998764
No 115
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=78.97 E-value=2.7 Score=30.67 Aligned_cols=28 Identities=14% Similarity=0.331 Sum_probs=19.1
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
..|.++||..+|||..||.+-++.|.+.
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~ 44 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREE 44 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-----
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcccc
Confidence 7889999999999999999998887653
No 116
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=78.83 E-value=3.8 Score=30.55 Aligned_cols=31 Identities=6% Similarity=0.164 Sum_probs=26.0
Q ss_pred cCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
++-++|..++|+.++||..||++-++++.+.
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 3445999999999999999999999998653
No 117
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=78.71 E-value=1.5 Score=37.08 Aligned_cols=32 Identities=22% Similarity=0.600 Sum_probs=25.5
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccCcc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (504)
.||.||...+ .....|-..|..||.++.-...
T Consensus 38 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PTZ00255 38 FCPFCGKHAV-KRQAVGIWRCKGCKKTVAGGAW 69 (90)
T ss_pred cCCCCCCCce-eeeeeEEEEcCCCCCEEeCCcc
Confidence 6999998754 4456799999999999875544
No 118
>PF12773 DZR: Double zinc ribbon
Probab=78.60 E-value=1.2 Score=32.94 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.4
Q ss_pred ceecCcCceee
Q 010689 20 QLCCDRCGKVL 30 (504)
Q Consensus 20 ~~VC~~CG~Vl 30 (504)
..+|..||..+
T Consensus 29 ~~~C~~Cg~~~ 39 (50)
T PF12773_consen 29 KKICPNCGAEN 39 (50)
T ss_pred CCCCcCCcCCC
Confidence 44555555543
No 119
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=78.40 E-value=7.8 Score=37.22 Aligned_cols=115 Identities=14% Similarity=0.146 Sum_probs=67.0
Q ss_pred hhHHHHHHHHHHHHhcCCC-CcHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHH
Q 010689 115 TEQVQASCLYLACRQKSKP-FLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 193 (504)
Q Consensus 115 ~~~vaAACLYiACR~~~~p-~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~ 193 (504)
...++=|+||+ .+-| +++.+|+.+++++...+..+...|.+...-...+.. |..+.+...+...++
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----SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLK---------LIEFNDVYKLVTKEE 71 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEE---------EEEECCEEEEEEcHH
Confidence 34567788887 5777 999999999999998898888888887753221210 011111110012233
Q ss_pred HHHHHHHHHHHhcccccccCCChhHHHHHHHH-HHHHhcCCCCCHhhHHhhhccCHHHH
Q 010689 194 VCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALTHGLKFSKSDIVKIVHICEATL 251 (504)
Q Consensus 194 V~~~A~~I~~~~~~~~l~~GR~P~~IAAAaly-lAa~~~g~~~t~keIa~v~~Vse~TI 251 (504)
......+++ ...+|.-+--|++= +|...+.-++|..+|+++.||+...+
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 333322221 11222233333332 33344578999999999999996433
No 120
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=77.99 E-value=5.5 Score=45.91 Aligned_cols=82 Identities=12% Similarity=0.211 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHhC--cccCCCchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHH
Q 010689 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 150 (504)
Q Consensus 73 ~a~~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~--~~~rGR~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~L 150 (504)
=|..+|+.+|.+|.+. +.+.+....+|.-.... .+.+-|...++.-+|+|+.||..+...++.+|....+-.+...
T Consensus 679 LAavRL~~Lc~rL~l~--~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa~ 756 (920)
T KOG1010|consen 679 LAAVRLNDLCERLSLS--DELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQAV 756 (920)
T ss_pred HHHHHHHHHHHHhhhh--hHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCchhh
Confidence 3678899999999999 88999888888877643 4678899999999999999999999999999988766555444
Q ss_pred HHHHHH
Q 010689 151 GAVYLQ 156 (504)
Q Consensus 151 g~~~~~ 156 (504)
..+|+.
T Consensus 757 ~~vyRs 762 (920)
T KOG1010|consen 757 SLVYRS 762 (920)
T ss_pred hhhhhh
Confidence 445543
No 121
>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=77.94 E-value=4.7 Score=31.28 Aligned_cols=37 Identities=19% Similarity=0.261 Sum_probs=30.1
Q ss_pred HHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 223 alylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+||.... .+..++.++||+.++|+.+|+..-++.|.+
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 4555555 678899999999999999999999988864
No 122
>PF15616 TerY-C: TerY-C metal binding domain
Probab=77.24 E-value=1.4 Score=39.85 Aligned_cols=20 Identities=30% Similarity=0.855 Sum_probs=12.8
Q ss_pred CCCCCCCCCcccccCCCceecCcCceee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
-||+||.. .+..+| .||.|.
T Consensus 79 gCP~CGn~-------~~fa~C-~CGkl~ 98 (131)
T PF15616_consen 79 GCPHCGNQ-------YAFAVC-GCGKLF 98 (131)
T ss_pred CCCCCcCh-------hcEEEe-cCCCEE
Confidence 59999985 355555 455553
No 123
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=76.94 E-value=1 Score=34.63 Aligned_cols=35 Identities=17% Similarity=0.379 Sum_probs=24.1
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceeeccCcccccccccccC
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNA 45 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f~~~~ 45 (504)
|..|+.||...+ ..+|..||.... ..+-+-|+-++
T Consensus 5 mr~C~~CgvYTL-------k~~CP~CG~~t~---~~~P~rfSp~D 39 (56)
T PRK13130 5 IRKCPKCGVYTL-------KEICPVCGGKTK---NPHPPRFSPED 39 (56)
T ss_pred ceECCCCCCEEc-------cccCcCCCCCCC---CCCCCCCCCCC
Confidence 568999998644 568999998753 23445676443
No 124
>PRK12495 hypothetical protein; Provisional
Probab=76.74 E-value=1.6 Score=42.62 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=22.6
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
.|+.||...+ ...|..+|..|+.++..
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 7999998744 24799999999999865
No 125
>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=76.72 E-value=4.3 Score=32.15 Aligned_cols=29 Identities=14% Similarity=0.383 Sum_probs=26.5
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
++.|+.+||..+|+|..|+.+-+++|.+-
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 57899999999999999999999999863
No 126
>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=76.53 E-value=5.6 Score=35.76 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=39.6
Q ss_pred chhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 114 ~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
+.+.-+.+++|+|-+..+.|.+..+||..++++...+.++..+|.+.
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 34556778899998766779999999999999999999988888774
No 127
>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=76.51 E-value=2.7 Score=30.97 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=20.0
Q ss_pred CHhhHHhhhccCHHHHHHHHHH
Q 010689 236 SKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE 257 (504)
|++|||+.+|||..|+.+-|..
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 6899999999999999998864
No 128
>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=76.05 E-value=2.5 Score=28.80 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=22.1
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+.|..|||+.+|++..|+.+-++.|..
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 578899999999999999999999875
No 129
>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=75.91 E-value=4.9 Score=29.47 Aligned_cols=28 Identities=14% Similarity=0.059 Sum_probs=23.8
Q ss_pred cCCCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 231 HGLKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
+....|+.|||...|+|..||+++++.-
T Consensus 17 y~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 17 YFEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp HTST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hcCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 3678999999999999999999988754
No 130
>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=75.89 E-value=1.8 Score=36.66 Aligned_cols=32 Identities=19% Similarity=0.553 Sum_probs=25.6
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccCcc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (504)
.||.||... +.....|-..|..||.++.-...
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 45557899999999999875543
No 131
>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=75.78 E-value=9.9 Score=35.32 Aligned_cols=29 Identities=17% Similarity=0.306 Sum_probs=26.9
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
++.|+.+||..+|++..|+.+-+++|.+-
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 67899999999999999999999999864
No 132
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=75.43 E-value=3.4 Score=29.41 Aligned_cols=30 Identities=17% Similarity=0.409 Sum_probs=27.0
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
.++.++++||+.++++..|+++.++.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 467899999999999999999999998763
No 133
>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=75.35 E-value=1.7 Score=31.53 Aligned_cols=28 Identities=18% Similarity=0.131 Sum_probs=20.4
Q ss_pred HhcCCCCCHhhHHhhhccCHHHHHHHHH
Q 010689 229 LTHGLKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 229 ~~~g~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
+|+....|..+||+.+|||..||.+.++
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 4444459999999999999999988764
No 134
>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=75.13 E-value=1.8 Score=37.12 Aligned_cols=27 Identities=26% Similarity=0.743 Sum_probs=21.2
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
.||.||.-- .+..|.++|..||.+...
T Consensus 2 fC~~Cg~~l---~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLM---TPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCccc---ccCCCeEECcCCCCcccc
Confidence 699999863 344689999999998653
No 135
>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=74.59 E-value=9.8 Score=31.77 Aligned_cols=41 Identities=12% Similarity=0.078 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhC-cChHHHHHHHHHHHHHhcc
Q 010689 121 SCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQLCQVLYI 163 (504)
Q Consensus 121 ACLYiACR~~~~p~tL~dIs~~~~-vs~~~Lg~~~~~L~~~L~i 163 (504)
.|.|++-+.. ..++.+|+..+| .+..++...++++.+.+..
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 6778776655 567899999999 9999999999999998854
No 136
>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=74.58 E-value=8 Score=29.56 Aligned_cols=29 Identities=21% Similarity=0.414 Sum_probs=26.3
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
....++.+||+.+|++..|+++.++.|.+
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999999998875
No 137
>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=74.09 E-value=4.1 Score=27.74 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=22.1
Q ss_pred CCcHHHHHHHhCcChHHHHHHHHHHHH
Q 010689 133 PFLLIDFSNYLNINVYELGAVYLQLCQ 159 (504)
Q Consensus 133 p~tL~dIs~~~~vs~~~Lg~~~~~L~~ 159 (504)
|.+-.|||+.+|++..++.|.+++|.+
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 677899999999999999999998875
No 138
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=73.93 E-value=2.1 Score=33.73 Aligned_cols=27 Identities=19% Similarity=0.564 Sum_probs=18.3
Q ss_pred CCCCCCCCCCccccc--CCC---------------ceecCcCce
Q 010689 2 VWCSSCARHVTGHRP--YDS---------------QLCCDRCGK 28 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~--~~G---------------~~VC~~CG~ 28 (504)
..||.||.++...+. .+| .+.|.+||.
T Consensus 5 ~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgY 48 (68)
T COG3478 5 FKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGY 48 (68)
T ss_pred ccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCc
Confidence 469999998765543 122 256899987
No 139
>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=73.78 E-value=5.5 Score=32.60 Aligned_cols=46 Identities=22% Similarity=0.207 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 116 ~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
..-+-+.+|++-...+.|.+..+||+.++++...+.+....|.+.=
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~G 53 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAG 53 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCC
Confidence 3455577888887777889999999999999999999999888743
No 140
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=73.75 E-value=1.9 Score=36.80 Aligned_cols=31 Identities=19% Similarity=0.569 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCcccccC-CCceecCcCceeec
Q 010689 1 MVWCSSCARHVTGHRPY-DSQLCCDRCGKVLE 31 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~-~G~~VC~~CG~Vle 31 (504)
|..||.||.--++.... -....|..|+.|..
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 78999999875544322 36789999999963
No 141
>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=73.73 E-value=7.6 Score=30.35 Aligned_cols=40 Identities=23% Similarity=0.238 Sum_probs=30.9
Q ss_pred CChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHH
Q 010689 214 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 214 R~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
|.|.-=-|=-||+. ++-.++.++||+.+||++.|||+.=.
T Consensus 5 Rsp~rdkA~e~y~~---~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 5 RSPNRDKAFEIYKE---SNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CCcCHHHHHHHHHH---hCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 55555555556654 57889999999999999999997543
No 142
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=73.54 E-value=3.3 Score=31.61 Aligned_cols=30 Identities=20% Similarity=0.247 Sum_probs=26.3
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
.-.++.+++|..++||+.|||+=+.++.+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 457899999999999999999999888753
No 143
>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=73.33 E-value=2.5 Score=36.56 Aligned_cols=32 Identities=19% Similarity=0.381 Sum_probs=22.3
Q ss_pred CCCCCCCCCCcccc--------cCC-Cc-eecCcCceeeccC
Q 010689 2 VWCSSCARHVTGHR--------PYD-SQ-LCCDRCGKVLEDH 33 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D--------~~~-G~-~VC~~CG~Vlee~ 33 (504)
+.||+||+.....+ +.. +. ++|+.|+.-|.=+
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~H 44 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVGCH 44 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceeeee
Confidence 47999999755443 112 33 8999999988743
No 144
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=73.17 E-value=5.9 Score=39.16 Aligned_cols=75 Identities=15% Similarity=0.124 Sum_probs=51.4
Q ss_pred chHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHH
Q 010689 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 177 ~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
.+|..++.+|. +...|+.+|.-..++.--..-..+-.|.-+|..|||+||..-..+++. ++.......++.+|+.
T Consensus 46 n~I~~lg~~lk--lRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~---~r~l~~~a~~L~~~f~ 120 (264)
T KOG0794|consen 46 NVIQKLGQHLK--LRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVH---IRLLVNEAKVLKTRFS 120 (264)
T ss_pred HHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHH---HHHHHHHHHHHhhhcc
Confidence 46677777776 778899999888887644334788999999999999999865554332 2223333345555543
No 145
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=73.01 E-value=2.3 Score=32.98 Aligned_cols=26 Identities=27% Similarity=0.733 Sum_probs=12.0
Q ss_pred CCCCCCCCCcccccCCCceecCcCcee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.|..||......+ ..-...|.+||.+
T Consensus 9 ~CtSCg~~i~~~~-~~~~F~CPnCG~~ 34 (59)
T PRK14890 9 KCTSCGIEIAPRE-KAVKFLCPNCGEV 34 (59)
T ss_pred cccCCCCcccCCC-ccCEeeCCCCCCe
Confidence 4666665421111 1234556666654
No 146
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=73.01 E-value=2.1 Score=33.09 Aligned_cols=25 Identities=24% Similarity=0.524 Sum_probs=18.7
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
+.||.||... .-..||..||+--+-
T Consensus 28 ~~C~~CG~~~------~~H~vC~~CG~Y~gr 52 (57)
T PRK12286 28 VECPNCGEPK------LPHRVCPSCGYYKGR 52 (57)
T ss_pred eECCCCCCcc------CCeEECCCCCcCCCE
Confidence 4799999863 356799999976543
No 147
>PRK05949 RNA polymerase sigma factor; Validated
Probab=72.94 E-value=1.2e+02 Score=31.47 Aligned_cols=91 Identities=8% Similarity=0.006 Sum_probs=51.3
Q ss_pred hHHHHHHHHHHHHHHHHHHcC---CCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHH---------------------
Q 010689 66 SRERLMEKAFDDMRQMKNALN---IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQAS--------------------- 121 (504)
Q Consensus 66 srer~L~~a~~~I~~i~~~L~---Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAA--------------------- 121 (504)
..++.+..-...|-.+|.++- ++-.+-+.+.-..+++.+..-...+|.+....+.-
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 344444455566777777752 22114455666667776655555566544333331
Q ss_pred ----HHHHHH-------HhcCCCCcHHHHHHHhCcChHHHHHHHHH
Q 010689 122 ----CLYLAC-------RQKSKPFLLIDFSNYLNINVYELGAVYLQ 156 (504)
Q Consensus 122 ----CLYiAC-------R~~~~p~tL~dIs~~~~vs~~~Lg~~~~~ 156 (504)
++...- ...|..-+..+||..+|+++..+......
T Consensus 172 ~~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~ 217 (327)
T PRK05949 172 HITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSM 217 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 111111 12345566889999999999888775443
No 148
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=72.73 E-value=2 Score=41.19 Aligned_cols=30 Identities=27% Similarity=0.614 Sum_probs=20.5
Q ss_pred CCCCCCCCCcccc--cCCC---ceecCcCceeecc
Q 010689 3 WCSSCARHVTGHR--PYDS---QLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D--~~~G---~~VC~~CG~Vlee 32 (504)
.||.||+..+.+. -..| .+-|.+||+|-.+
T Consensus 8 ~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 8 ECPSCGSEEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred ECCCCCcchhhHHHHHhcCCceEEEccCCCcEeec
Confidence 6999996544211 1223 5789999999855
No 149
>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=72.73 E-value=37 Score=36.79 Aligned_cols=179 Identities=14% Similarity=0.200 Sum_probs=95.5
Q ss_pred HHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCC------------------CCcHHHH
Q 010689 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK------------------PFLLIDF 139 (504)
Q Consensus 78 I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~------------------p~tL~dI 139 (504)
+..++..|+++ ...++.|..++..+.-.|+.- |+ ..=||.+=.+..+. ..-+..|
T Consensus 116 ~~eia~~l~~~--~~~ve~~l~~iq~leP~GIgA-r~----L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i 188 (429)
T TIGR02395 116 LEEIADELEVS--EEEVEKVLELIQRLDPAGVGA-RD----LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRL 188 (429)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHH
Confidence 78889999999 899999988888765555432 11 12234333333211 1235678
Q ss_pred HHHhCcChHHHHHHHHHHHHHhcccccccc-----cccCCccchHHH----------------------HHHhhCCCCCH
Q 010689 140 SNYLNINVYELGAVYLQLCQVLYIADESNV-----LKQVDPSIFLHK----------------------FTDRLLPGGNK 192 (504)
Q Consensus 140 s~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~-----~~~~dP~~~I~r----------------------~~~~L~~~l~~ 192 (504)
+..++++..++..+...|.. |+-..-..+ ...+-|..+|.+ |...+......
T Consensus 189 ~~~l~is~~~v~~~~~~I~~-L~P~Pg~~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~~ 267 (429)
T TIGR02395 189 AKKLGLSEEELKEALDLIKS-LSPKPGKEFADPEEVEYVIPDVIVTKKNGEWVVELNGRSLPELRINEEYFKLLKDAEKE 267 (429)
T ss_pred HHHHCcCHHHHHHHHHHHhC-CCCCCcccccCCCCCCccCCCEEEEEECCEEEEEEcCCCCceEEECHHHHHHHHhccch
Confidence 88899999999887665544 431100000 011223333322 22222100011
Q ss_pred HH-------HHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHh-----cC----CCCCHhhHHhhhccCHHHHHHHHH
Q 010689 193 KV-------CDTARDILASMKRDWITTGRKPSGLCGAALYVSALT-----HG----LKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 193 ~V-------~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~-----~g----~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
++ ...|..+++.+. +|-.+|--.+-.|+-+- .| .+.|+++||..+|++++||.+..+
T Consensus 268 ~~~~ylk~k~~~A~~li~~i~-------~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 268 AAAQYLKQKLKEARWLIKALE-------QREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 11 122333333332 33344443333433321 34 468999999999999999998765
Q ss_pred H-hhccCCCCCChHHH
Q 010689 257 E-FENTDSGSLTIEDF 271 (504)
Q Consensus 257 E-~~~t~~~~lt~~~~ 271 (504)
. +..|+-|-.-+..|
T Consensus 341 ~Kyi~tp~Gi~~lk~F 356 (429)
T TIGR02395 341 NKYLQTPRGVFELKYF 356 (429)
T ss_pred CceEecCCceEEHHHh
Confidence 3 23455555555554
No 150
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=72.05 E-value=3.8 Score=35.54 Aligned_cols=32 Identities=19% Similarity=0.476 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceeeccCc
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~ 34 (504)
|..||+|++.- +++ ..+.++|..|+.--.++.
T Consensus 3 lp~cp~c~sEy-tYe-d~~~~~cpec~~ew~~~~ 34 (112)
T COG2824 3 LPPCPKCNSEY-TYE-DGGQLICPECAHEWNENE 34 (112)
T ss_pred CCCCCccCCce-EEe-cCceEeCchhcccccccc
Confidence 35799999873 343 346999999998765433
No 151
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=71.78 E-value=2.6 Score=35.64 Aligned_cols=32 Identities=22% Similarity=0.541 Sum_probs=25.5
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccCcc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (504)
.||.||...+ -....|-..|..||.++.....
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 6999987754 4457899999999999876544
No 152
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=71.68 E-value=8.7 Score=37.55 Aligned_cols=56 Identities=16% Similarity=0.233 Sum_probs=32.4
Q ss_pred HHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHH--HHhcCC
Q 010689 76 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLA--CRQKSK 132 (504)
Q Consensus 76 ~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiA--CR~~~~ 132 (504)
..|...-....++. ....+.|..-|++|.-....++-+...++..||=+| +|..+-
T Consensus 76 ~~i~~~~~~~~~~~-~Rt~~~ai~~YkLAll~~~~~~~~~s~~A~l~LrlAWlyR~~~~ 133 (214)
T PF09986_consen 76 ENISSRWKPRDFSG-ERTLEEAIESYKLALLCAQIKKEKPSKKAGLCLRLAWLYRDLGD 133 (214)
T ss_pred HHHHhhcccCCCCC-CCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhccCC
Confidence 33333333335553 456677888888887655555655556666776666 444433
No 153
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=71.50 E-value=2.6 Score=30.84 Aligned_cols=25 Identities=24% Similarity=0.646 Sum_probs=18.9
Q ss_pred CCCCCCCCCcccccCCCceecCcCcee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.|..||.... .+ ..+.+-|..||.=
T Consensus 4 ~C~~Cg~~~~-~~-~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENE-IK-SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEee-cC-CCCceECCCCCce
Confidence 5999998733 33 4588999999973
No 154
>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=71.35 E-value=2 Score=30.47 Aligned_cols=27 Identities=22% Similarity=0.560 Sum_probs=16.3
Q ss_pred CCCCCCCCCccc--------c-cCCCceecCcCcee
Q 010689 3 WCSSCARHVTGH--------R-PYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~--------D-~~~G~~VC~~CG~V 29 (504)
.||.||+...++ | +.+-.++|.+||..
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 699999985432 1 12347899999964
No 155
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.30 E-value=5.6 Score=35.98 Aligned_cols=32 Identities=16% Similarity=0.407 Sum_probs=28.6
Q ss_pred hcCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
..+.+.++++||+.+|+|+.|+++|++.+.+.
T Consensus 18 ~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 18 QEDARISNAELAERVGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 34677999999999999999999999999864
No 156
>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=71.29 E-value=1.7 Score=33.42 Aligned_cols=24 Identities=25% Similarity=0.555 Sum_probs=17.5
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
+.||.||.- .....||.+||+.=.
T Consensus 27 ~~c~~cg~~------~~~H~vc~~cG~y~~ 50 (56)
T PF01783_consen 27 VKCPNCGEP------KLPHRVCPSCGYYKG 50 (56)
T ss_dssp EESSSSSSE------ESTTSBCTTTBBSSS
T ss_pred eeeccCCCE------ecccEeeCCCCeECC
Confidence 469999964 235689999996543
No 157
>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=71.00 E-value=4.6 Score=31.91 Aligned_cols=31 Identities=16% Similarity=0.280 Sum_probs=25.1
Q ss_pred hcCCCCCHhhHHhhhccC-HHHHHHHHHHhhc
Q 010689 230 THGLKFSKSDIVKIVHIC-EATLMKRLIEFEN 260 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vs-e~TIrkr~kE~~~ 260 (504)
-+|++.|++||++.+|++ .+|+...++.+.+
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 469999999999999996 9999999998864
No 158
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=70.90 E-value=1.8e+02 Score=32.41 Aligned_cols=89 Identities=9% Similarity=0.078 Sum_probs=52.1
Q ss_pred hHHHHHHHHHHHHHHHHHHc---CCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHH---------------
Q 010689 66 SRERLMEKAFDDMRQMKNAL---NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC--------------- 127 (504)
Q Consensus 66 srer~L~~a~~~I~~i~~~L---~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC--------------- 127 (504)
.+++.+..-+..+..++.++ |++-.+-|.+...-+.+-+..-...+|-+....|.-+|--+.
T Consensus 272 Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~ 351 (509)
T PRK05901 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 351 (509)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCH
Confidence 34445555566677777775 333214445555557776666566677665555554443222
Q ss_pred -----------------HhcCCCCcHHHHHHHhCcChHHHHHHH
Q 010689 128 -----------------RQKSKPFLLIDFSNYLNINVYELGAVY 154 (504)
Q Consensus 128 -----------------R~~~~p~tL~dIs~~~~vs~~~Lg~~~ 154 (504)
...|.+-+..+||..+++++..|....
T Consensus 352 ~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~ 395 (509)
T PRK05901 352 HMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ 395 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 112444556788888898888877653
No 159
>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=70.79 E-value=1.3e+02 Score=30.70 Aligned_cols=26 Identities=8% Similarity=0.160 Sum_probs=22.9
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
+...|++|||..+|||..|||++...
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~r 292 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEAK 292 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35799999999999999999988754
No 160
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=70.76 E-value=6.3 Score=33.55 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=27.2
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+-+.|.++|++.+|+++.|+++|++.+.+-
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 457999999999999999999999999863
No 161
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=70.42 E-value=9.3 Score=35.81 Aligned_cols=47 Identities=19% Similarity=0.230 Sum_probs=39.0
Q ss_pred chhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 114 ~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
+.+.-+.+++|+|-...+-|.++.+||+.++++...+.+++..|.+.
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 34566778899996556679999999999999999999988888774
No 162
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=69.93 E-value=3.2 Score=31.81 Aligned_cols=24 Identities=25% Similarity=0.587 Sum_probs=17.8
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
+.||+||... .-.-||..||+--+
T Consensus 27 ~~C~~cG~~~------~~H~vc~~cG~Y~g 50 (55)
T TIGR01031 27 VVCPNCGEFK------LPHRVCPSCGYYKG 50 (55)
T ss_pred eECCCCCCcc------cCeeECCccCeECC
Confidence 4699999853 35679999997644
No 163
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.85 E-value=2.9 Score=34.25 Aligned_cols=30 Identities=23% Similarity=0.411 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCcccc-cCCCceecCcCceee
Q 010689 1 MVWCSSCARHVTGHR-PYDSQLCCDRCGKVL 30 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D-~~~G~~VC~~CG~Vl 30 (504)
|+.||.|+..-+-.+ ..--.-.|..|+=|-
T Consensus 1 ~llCP~C~v~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 1 MLLCPICGVELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred CcccCcCCceeeeeeecCceeeeCCccccEe
Confidence 789999998733222 222356799998774
No 164
>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=69.35 E-value=10 Score=29.90 Aligned_cols=47 Identities=17% Similarity=0.128 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhcC----------CCCcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 118 VQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 118 vaAACLYiACR~~~----------~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
++...++++.+... .|.+..+||+.+|++...+.++++.|.+.=-+.
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 45555666655432 578999999999999999999999998864443
No 165
>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=69.31 E-value=8.9 Score=27.87 Aligned_cols=32 Identities=9% Similarity=0.189 Sum_probs=26.9
Q ss_pred hcCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+..-+.+..+|++.++++.+||++.++.+.+.
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 44577899999999999999999999988753
No 166
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=69.27 E-value=6.4 Score=29.14 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=25.4
Q ss_pred CCCC-CHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKF-SKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~-t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
|... |.+++++.++||..|+++.++.+.+
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3345 8999999999999999999999875
No 167
>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=68.85 E-value=8.1 Score=30.31 Aligned_cols=31 Identities=10% Similarity=0.165 Sum_probs=26.8
Q ss_pred hcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 230 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+.+-..+.++||..++||..||+++++.+..
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3445678999999999999999999999865
No 168
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=68.63 E-value=1.3e+02 Score=29.93 Aligned_cols=26 Identities=12% Similarity=0.189 Sum_probs=23.1
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|+++||..+|++..||++++..-
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~~~ra 243 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRRVKKG 243 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 57899999999999999999987654
No 169
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=68.51 E-value=2.2 Score=35.33 Aligned_cols=31 Identities=19% Similarity=0.425 Sum_probs=17.2
Q ss_pred CCCCCCCC-Cc--ccccC--CCceecCcCceeeccC
Q 010689 3 WCSSCARH-VT--GHRPY--DSQLCCDRCGKVLEDH 33 (504)
Q Consensus 3 ~Cp~Cgs~-~i--v~D~~--~G~~VC~~CG~Vlee~ 33 (504)
.||.||+. .+ .+|.. .|.+.|..||...+-.
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 59999965 33 34443 5899999999987643
No 170
>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=68.30 E-value=4.7 Score=32.77 Aligned_cols=28 Identities=18% Similarity=0.071 Sum_probs=24.2
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
...|++|||..+|+|+.||++++.....
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 4579999999999999999999986543
No 171
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=68.29 E-value=7.6 Score=36.63 Aligned_cols=66 Identities=21% Similarity=0.293 Sum_probs=44.1
Q ss_pred CCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCC
Q 010689 190 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLT 267 (504)
Q Consensus 190 l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt 267 (504)
..+.|.........+. .|+.+ ..+||+|+ +| .-.-.|..+||.-.|.|+.|||+.++. +|.+++|-
T Consensus 27 ~~~evlkli~~~~~~l--TWvdS----LavAAga~---ar-ekag~Ti~EIAeelG~TeqTir~hlkg--etkAG~lv 92 (182)
T COG1318 27 FRPEVLKLIKDPYERL--TWVDS----LAVAAGAL---AR-EKAGMTISEIAEELGRTEQTVRNHLKG--ETKAGQLV 92 (182)
T ss_pred ccHHHHHHHhCccccc--chhhH----HHHHHHHH---HH-HHccCcHHHHHHHhCCCHHHHHHHHhc--chhhhhHH
Confidence 3456666655544444 35532 33444333 44 567789999999999999999999984 56666663
No 172
>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=68.08 E-value=4 Score=41.80 Aligned_cols=55 Identities=11% Similarity=0.043 Sum_probs=47.1
Q ss_pred chHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCC
Q 010689 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL 233 (504)
Q Consensus 177 ~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~ 233 (504)
.+|.++|.+|. ++..+..+|.-+.++..-..-..+-.|..||.+|||+|++.-+-
T Consensus 50 k~i~~l~~~L~--lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~ 104 (297)
T COG5333 50 KLIMDLCTRLN--LPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDT 104 (297)
T ss_pred HHHHHHHHhcC--CCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccc
Confidence 46888999998 78889999999998876555678999999999999999987663
No 173
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=67.88 E-value=3.4 Score=31.98 Aligned_cols=25 Identities=20% Similarity=0.545 Sum_probs=18.1
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
|+.|++||...+ -.-||..||+--+
T Consensus 27 ~~~c~~cG~~~l------~Hrvc~~cg~Y~g 51 (57)
T COG0333 27 LSVCPNCGEYKL------PHRVCLKCGYYKG 51 (57)
T ss_pred ceeccCCCCccc------CceEcCCCCCccC
Confidence 457999998643 4468999997543
No 174
>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=67.70 E-value=2.7 Score=29.43 Aligned_cols=28 Identities=21% Similarity=0.548 Sum_probs=18.7
Q ss_pred CCCCCCCCC-ccccc-CCCceecCcCceee
Q 010689 3 WCSSCARHV-TGHRP-YDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~-iv~D~-~~G~~VC~~CG~Vl 30 (504)
.|+.||..- +.... ......|..||.-+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 699999852 22221 24678899999843
No 175
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=67.52 E-value=3.1 Score=38.32 Aligned_cols=29 Identities=21% Similarity=0.444 Sum_probs=20.4
Q ss_pred CCCCCCCCCCc-cccc---CCCce-----ecCcCceee
Q 010689 2 VWCSSCARHVT-GHRP---YDSQL-----CCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~i-v~D~---~~G~~-----VC~~CG~Vl 30 (504)
|.||.|++... +.|+ .+|.. .|.+||.=.
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 58999999843 5664 34654 499999743
No 176
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=67.33 E-value=18 Score=33.50 Aligned_cols=30 Identities=3% Similarity=-0.095 Sum_probs=27.5
Q ss_pred CCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 132 ~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
.|.|-.|||+.+|++..++.+++++|.+.=
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g 171 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKKK 171 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 688999999999999999999999998863
No 177
>PF12773 DZR: Double zinc ribbon
Probab=67.20 E-value=3.9 Score=30.08 Aligned_cols=21 Identities=24% Similarity=0.689 Sum_probs=14.7
Q ss_pred CCCCCCCCCCcccccCCCceecCcCc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCG 27 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG 27 (504)
+.||.||.. ...+..+|..||
T Consensus 30 ~~C~~Cg~~-----~~~~~~fC~~CG 50 (50)
T PF12773_consen 30 KICPNCGAE-----NPPNAKFCPNCG 50 (50)
T ss_pred CCCcCCcCC-----CcCCcCccCccc
Confidence 457777764 135778888888
No 178
>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=66.37 E-value=3.6 Score=28.03 Aligned_cols=24 Identities=25% Similarity=0.700 Sum_probs=16.3
Q ss_pred CCCCCCCCCcccccCCCceecCcCce
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
.|..||..+. ......+-|..||.
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 4889998743 23456788999996
No 179
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=65.81 E-value=14 Score=34.16 Aligned_cols=46 Identities=13% Similarity=0.105 Sum_probs=37.4
Q ss_pred chhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 114 ~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
+.+.-+-+++|+|-. .+.+.+..+||+..+++...|.+.+..|.+.
T Consensus 6 ~~~YAlr~L~~LA~~-~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 6 QTNYAIRMLMYCAAN-DGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHhHHHHHHHHHHhC-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344556688999944 5668899999999999999999998888774
No 180
>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=65.27 E-value=1.4e+02 Score=28.96 Aligned_cols=27 Identities=4% Similarity=0.091 Sum_probs=23.0
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
....|+++||...|||..||++..+..
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~~~~a 223 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRLEKKV 223 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356899999999999999999876654
No 181
>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=65.15 E-value=4.2 Score=32.21 Aligned_cols=27 Identities=19% Similarity=0.529 Sum_probs=17.8
Q ss_pred CCCCCCCCCccccc--CC-C--------------ceecCcCcee
Q 010689 3 WCSSCARHVTGHRP--YD-S--------------QLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~--~~-G--------------~~VC~~CG~V 29 (504)
.||.||+.....+. .+ | .++|++||..
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 59999997543331 11 1 3689999986
No 182
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=64.99 E-value=13 Score=26.11 Aligned_cols=28 Identities=11% Similarity=0.086 Sum_probs=21.8
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
..+.++.+||..+|+|+..+++.+++..
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4568999999999999999999999865
No 183
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=64.93 E-value=7.8 Score=28.11 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=23.2
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
..+.++||..+++|..||++++..+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36899999999999999999988764
No 184
>PRK05978 hypothetical protein; Provisional
Probab=64.70 E-value=4.8 Score=37.21 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=21.1
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
.+||+||...+-.-.-.=.--|..||.-++
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccc
Confidence 479999998653222234557999999765
No 185
>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=64.33 E-value=2.1 Score=32.27 Aligned_cols=29 Identities=17% Similarity=0.591 Sum_probs=21.7
Q ss_pred CCCCCCCCCCcc-cccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTG-HRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv-~D~~~G~~VC~~CG~Vl 30 (504)
++|++|+.--.. -+....++-|..||+|-
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 589999986332 23456899999999983
No 186
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=64.20 E-value=2.6 Score=39.48 Aligned_cols=29 Identities=28% Similarity=0.760 Sum_probs=19.4
Q ss_pred CCCCCCCCCCcc--------------cccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTG--------------HRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv--------------~D~~~G~~VC~~CG~Vl 30 (504)
..||.|++.-.- +-..+-..+|+.||.|-
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 579999985211 12234577899999974
No 187
>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=64.09 E-value=33 Score=28.89 Aligned_cols=30 Identities=3% Similarity=0.134 Sum_probs=27.2
Q ss_pred cCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
....+|+.+||+.+|++..|+.+.++++..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 457899999999999999999999999875
No 188
>PF14122 YokU: YokU-like protein
Probab=63.82 E-value=3.4 Score=34.44 Aligned_cols=21 Identities=29% Similarity=0.686 Sum_probs=15.8
Q ss_pred CceecCcCceeeccCcccccc
Q 010689 19 SQLCCDRCGKVLEDHNFSTEA 39 (504)
Q Consensus 19 G~~VC~~CG~Vlee~~id~~~ 39 (504)
-.++|++||.|--+..+..+.
T Consensus 34 P~i~C~~CgmvYq~d~vi~EI 54 (87)
T PF14122_consen 34 PAIICSNCGMVYQDDEVIKEI 54 (87)
T ss_pred ceeeecCCCcEEehhHHHHHH
Confidence 458999999998776665443
No 189
>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=63.75 E-value=15 Score=27.71 Aligned_cols=27 Identities=15% Similarity=0.363 Sum_probs=23.8
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.+|+.+|++.++++.+|+.+.++.+..
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 489999999999999999999998864
No 190
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=63.55 E-value=2.3 Score=42.93 Aligned_cols=30 Identities=20% Similarity=0.515 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceee
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
+.+||.||.-...-|-.....||..||.-.
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 357999998655455567899999999864
No 191
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=63.21 E-value=2.3e+02 Score=30.76 Aligned_cols=98 Identities=12% Similarity=0.118 Sum_probs=58.3
Q ss_pred hHHHHHHHHHHHHHHHHHHc---CCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHH------HHHHHH----------
Q 010689 66 SRERLMEKAFDDMRQMKNAL---NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA------SCLYLA---------- 126 (504)
Q Consensus 66 srer~L~~a~~~I~~i~~~L---~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA------ACLYiA---------- 126 (504)
++++.+..-...+-.+|.++ ++.-.+-+.+...-+++.+..-.-.+|.+....+- ..-+++
T Consensus 176 A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~ 255 (415)
T PRK07598 176 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPV 255 (415)
T ss_pred HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhH
Confidence 44555555556677777775 22211455666666777776655566766544442 222221
Q ss_pred ----------------HHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhcc
Q 010689 127 ----------------CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (504)
Q Consensus 127 ----------------CR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i 163 (504)
....|.+-+..+||..+++++..+..+.......+.+
T Consensus 256 ~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SL 308 (415)
T PRK07598 256 HITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSL 308 (415)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCccc
Confidence 0123566778899999999999998876655444333
No 192
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=63.17 E-value=2.3 Score=43.61 Aligned_cols=29 Identities=21% Similarity=0.530 Sum_probs=22.1
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
.+||.|+......|-.....||..||.-.
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 57999998755445445678999999865
No 193
>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=63.06 E-value=2.3 Score=43.45 Aligned_cols=29 Identities=14% Similarity=0.432 Sum_probs=22.4
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
.+||.|+......|-.....||..||.-.
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 47999998755445456779999999864
No 194
>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=62.99 E-value=2.8 Score=36.67 Aligned_cols=40 Identities=18% Similarity=0.273 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceeeccCcccccccccc
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f~~ 43 (504)
++.||+|+...-..- -..-|..||.-|.=..--++-+|.+
T Consensus 69 ~V~CP~C~K~TKmLG---r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 69 QVECPNCGKQTKMLG---RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred eeECCCCCChHhhhc---hhhccCcCCCcCccCchhhcchhhH
Confidence 358999999743221 1248999999875322224556654
No 195
>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=62.50 E-value=3.7 Score=40.71 Aligned_cols=29 Identities=14% Similarity=0.552 Sum_probs=11.7
Q ss_pred CCCCCCCCCCccc---ccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGH---RPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~---D~~~G~~VC~~CG~Vl 30 (504)
+.||+||+..+.. ...-.+..|.+|+--.
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 4799999986532 1234789999998643
No 196
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=62.40 E-value=5.1 Score=30.66 Aligned_cols=26 Identities=23% Similarity=0.647 Sum_probs=19.4
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
..|+.||.... +.+--+||..||.+.
T Consensus 6 ~~C~~Cg~~~~---~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCPVCGKKFK---DGDDIVVCPECGAPY 31 (54)
T ss_pred ccChhhCCccc---CCCCEEECCCCCCcc
Confidence 37999998622 234579999999975
No 197
>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=62.32 E-value=22 Score=27.47 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=31.2
Q ss_pred HHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 122 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 122 CLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
+||.... .+.+.+..+||..++|+.-++....++|.+.
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 3565555 8899999999999999999999998888764
No 198
>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=62.27 E-value=13 Score=27.08 Aligned_cols=28 Identities=25% Similarity=0.196 Sum_probs=21.3
Q ss_pred cCCCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 231 HGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
.|- .|+...|+..||..+||+.|++.-.
T Consensus 14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 14 NGK-MSIRKAAKKYGVPRSTLRRRLRGKP 41 (45)
T ss_dssp TTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred hCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 454 9999999999999999999988643
No 199
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=62.00 E-value=1.9e+02 Score=29.45 Aligned_cols=27 Identities=4% Similarity=-0.141 Sum_probs=23.6
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
....|+++||...|||..||+++...-
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~A 269 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARA 269 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467999999999999999999877654
No 200
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=61.68 E-value=6.5 Score=25.05 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=14.8
Q ss_pred CCCCCCCCcccccCCCceecCcCce
Q 010689 4 CSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 4 Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
|..||.... -....-...|.+||.
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 778887522 111234788999984
No 201
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=61.65 E-value=9.9 Score=28.48 Aligned_cols=37 Identities=14% Similarity=0.176 Sum_probs=29.5
Q ss_pred HHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 225 ylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
++.-...-...+..++|...||+++|+.+.+.++.++
T Consensus 10 ll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~ 46 (53)
T PF13613_consen 10 LLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPL 46 (53)
T ss_pred HHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHH
Confidence 3333444577899999999999999999999987654
No 202
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=61.54 E-value=2.6 Score=43.30 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=22.8
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
.+||.|+......+-.....||..||.-.
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 47999998755555557789999999854
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=61.54 E-value=5.4 Score=27.09 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=16.3
Q ss_pred CCCCCCCCCcccccCCCceecCcCce
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
.|+.||- ++|.......|..||.
T Consensus 3 ~C~~CGy---~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY---IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC---EECCCcCCCcCcCCCC
Confidence 5888885 4555556778888886
No 204
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=61.08 E-value=15 Score=27.47 Aligned_cols=35 Identities=11% Similarity=0.224 Sum_probs=30.2
Q ss_pred cCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 130 ~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
.+.-.+..++|..+||+..++.+.+..+...|...
T Consensus 16 LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 34457899999999999999999999999988654
No 205
>PHA02591 hypothetical protein; Provisional
Probab=61.07 E-value=10 Score=31.13 Aligned_cols=31 Identities=13% Similarity=0.142 Sum_probs=26.0
Q ss_pred HHHHhcCCCCCHhhHHhhhccCHHHHHHHHH
Q 010689 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 226 lAa~~~g~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
+|..+.....|+.+||..+||+..|+++-++
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4456666778999999999999999998765
No 206
>PF14353 CpXC: CpXC protein
Probab=59.86 E-value=4.9 Score=35.72 Aligned_cols=29 Identities=24% Similarity=0.741 Sum_probs=18.9
Q ss_pred CCCCCCCCCCc--cc---c----c------CCC---ceecCcCceee
Q 010689 2 VWCSSCARHVT--GH---R----P------YDS---QLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~i--v~---D----~------~~G---~~VC~~CG~Vl 30 (504)
+.||+||.... ++ | + -+| ..+|..||...
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 57999998621 11 1 1 122 68999999865
No 207
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=59.46 E-value=31 Score=33.30 Aligned_cols=29 Identities=21% Similarity=0.368 Sum_probs=26.6
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+++|+++||+.+|++..|+.+-+++|..-
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~ 211 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKS 211 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 57899999999999999999999998854
No 208
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=59.31 E-value=31 Score=32.30 Aligned_cols=30 Identities=13% Similarity=0.132 Sum_probs=27.5
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
.++.|+.+||..+|++..|+.+-+++|.+.
T Consensus 147 ~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 147 MIYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred EecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 367899999999999999999999999865
No 209
>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=58.99 E-value=1.7e+02 Score=28.10 Aligned_cols=25 Identities=8% Similarity=0.158 Sum_probs=22.1
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|.++||..+|++..||++++..
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~r 214 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQ 214 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5679999999999999999987754
No 210
>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=58.95 E-value=13 Score=26.47 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=18.9
Q ss_pred CCHhhHHhhhccCHHHHHHHHHHh
Q 010689 235 FSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
=++...|..+||+..|+.++++.+
T Consensus 19 gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 19 GNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp T-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhC
Confidence 345689999999999999999863
No 211
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=58.83 E-value=2e+02 Score=28.66 Aligned_cols=27 Identities=15% Similarity=0.086 Sum_probs=23.4
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
....|.+|||..+|+|..||++++..-
T Consensus 219 ~e~~t~~EIA~~lgis~~~V~~~~~ra 245 (257)
T PRK05911 219 YEELVLKEIGKILGVSESRVSQIHSKA 245 (257)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899999999999999999887653
No 212
>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=58.75 E-value=14 Score=27.37 Aligned_cols=26 Identities=31% Similarity=0.365 Sum_probs=19.6
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
-...|.+|||...|+|+.||++++..
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 45688999999999999999998864
No 213
>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=58.30 E-value=36 Score=25.81 Aligned_cols=31 Identities=13% Similarity=0.220 Sum_probs=27.0
Q ss_pred cCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 130 ~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
...+.+..+||+.++++...+.+.+..|.+.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3467899999999999999999988888774
No 214
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.86 E-value=6 Score=35.17 Aligned_cols=28 Identities=21% Similarity=0.485 Sum_probs=18.9
Q ss_pred CCCCCCCCCcccc-cCCCceecCcCceeec
Q 010689 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VC~~CG~Vle 31 (504)
.||+||...+ +| .-.-.-.|..||.-+.
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 6999998754 33 1123457999998654
No 215
>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=57.66 E-value=25 Score=26.03 Aligned_cols=35 Identities=9% Similarity=0.056 Sum_probs=28.8
Q ss_pred HHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 127 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 127 CR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
...++-|+|..+||+.++|+..+|.+....|...+
T Consensus 9 L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 9 LLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 33566679999999999999999999998887666
No 216
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=57.44 E-value=21 Score=25.53 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=25.2
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
-..+..+|+..++++..|+++.++.|..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3589999999999999999999998865
No 217
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=57.39 E-value=5.7 Score=30.16 Aligned_cols=29 Identities=17% Similarity=0.422 Sum_probs=20.2
Q ss_pred CCCCCCCCC-CcccccCCCc----eecCcCceee
Q 010689 2 VWCSSCARH-VTGHRPYDSQ----LCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~-~iv~D~~~G~----~VC~~CG~Vl 30 (504)
..||+||.. .+..|.+.|. -=|..|..=+
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence 369999998 5668877663 2377776544
No 218
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=57.26 E-value=2.1e+02 Score=29.10 Aligned_cols=123 Identities=12% Similarity=0.066 Sum_probs=69.4
Q ss_pred HHHHHHhcCC-CCcHHHHHHHhCcCh-HHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHH------
Q 010689 123 LYLACRQKSK-PFLLIDFSNYLNINV-YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKV------ 194 (504)
Q Consensus 123 LYiACR~~~~-p~tL~dIs~~~~vs~-~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V------ 194 (504)
=|+..|.... -+|+++||..+|++. .-| ..++.-+-+ . +...+.+++..|+ +++.-
T Consensus 16 d~ye~rk~~~p~fS~R~fa~~~G~ss~s~L-------~~v~~Gkr~------L-s~~~~~k~a~~l~--L~~~E~~yF~~ 79 (271)
T TIGR02147 16 DYYEERKKTDPAFSWRFFAEKAGFSSTSYL-------NDIIKGKKN------L-TKRMIPKFAEALG--LDEKEAAYFEA 79 (271)
T ss_pred HHHHHHhccCcCcCHHHHHHHhCCCCHHHH-------HHHHcCCCC------C-CHHHHHHHHHHcC--CCHHHHHHHHH
Confidence 3677777655 589999999999876 333 223332221 1 3557788888776 43322
Q ss_pred ------------HHHHHHHHHHhcc---cccccC---CChhHHHHHHHHHHHHhcCCCCCHhhHHhhhc--cCHHHHHHH
Q 010689 195 ------------CDTARDILASMKR---DWITTG---RKPSGLCGAALYVSALTHGLKFSKSDIVKIVH--ICEATLMKR 254 (504)
Q Consensus 195 ------------~~~A~~I~~~~~~---~~l~~G---R~P~~IAAAalylAa~~~g~~~t~keIa~v~~--Vse~TIrkr 254 (504)
.+.+..=+..+.. ..++.+ +=-..+.-.+|.-.+.+.+...+..+||+.++ ||..-++..
T Consensus 80 lV~f~~ak~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~s 159 (271)
T TIGR02147 80 MVNFGQAKTDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKES 159 (271)
T ss_pred HHHHhccCCHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHH
Confidence 2222111111111 011111 11113334455555555667767889999998 899999998
Q ss_pred HHHhhcc
Q 010689 255 LIEFENT 261 (504)
Q Consensus 255 ~kE~~~t 261 (504)
+.-+...
T Consensus 160 L~~L~~~ 166 (271)
T TIGR02147 160 LDLLERL 166 (271)
T ss_pred HHHHHHC
Confidence 8877654
No 219
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=57.19 E-value=16 Score=25.70 Aligned_cols=27 Identities=7% Similarity=0.114 Sum_probs=19.9
Q ss_pred CCCCcHHHHHHHhCcChHHHHHHHHHH
Q 010689 131 SKPFLLIDFSNYLNINVYELGAVYLQL 157 (504)
Q Consensus 131 ~~p~tL~dIs~~~~vs~~~Lg~~~~~L 157 (504)
..+.++.|||..+|++...+.+.|++.
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 457899999999999999998877754
No 220
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=57.06 E-value=8.7 Score=38.46 Aligned_cols=29 Identities=21% Similarity=0.227 Sum_probs=26.1
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.-+++.+|+|+.++||+.|||+.++++.+
T Consensus 17 ~~~v~v~eLa~~l~VS~~TIRRDL~~Le~ 45 (256)
T PRK10434 17 QGKTSVEELAQYFDTTGTTIRKDLVILEH 45 (256)
T ss_pred cCCEEHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35689999999999999999999999865
No 221
>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=57.01 E-value=24 Score=31.06 Aligned_cols=45 Identities=18% Similarity=0.140 Sum_probs=34.9
Q ss_pred hHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 116 ~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
...+.+.+|++-...+.|.+..+||+.++++...+.+....|.+.
T Consensus 8 ~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 8 EYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 445566777774333459999999999999999999888888763
No 222
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=56.29 E-value=4.8 Score=33.36 Aligned_cols=30 Identities=27% Similarity=0.514 Sum_probs=24.2
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccC
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (504)
.|+.||...+ -...-|...|..|..|+.-.
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 5999998754 44567999999999998754
No 223
>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=56.28 E-value=14 Score=26.79 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=23.7
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
..+.++||...+++..||+++++.+..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 469999999999999999999887653
No 224
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=56.26 E-value=2.2e+02 Score=28.39 Aligned_cols=25 Identities=12% Similarity=0.213 Sum_probs=22.0
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|.++||..+|++..||++++..
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~r 251 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTK 251 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5689999999999999999987743
No 225
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=55.92 E-value=8.2 Score=38.82 Aligned_cols=31 Identities=13% Similarity=0.419 Sum_probs=22.3
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccC
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~ 33 (504)
..||.||+..... ...-..+|..||.+.-.+
T Consensus 100 ~fC~~CG~~~~~~-~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 100 RFCGYCGHPMHPS-KTEWAMLCPHCRERYYPR 130 (256)
T ss_pred ccccccCCCCeec-CCceeEECCCCCCEECCC
Confidence 4799999974433 344578999999876543
No 226
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=55.49 E-value=7.1 Score=35.21 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCccc-c---cCCCceecCcCceeec
Q 010689 1 MVWCSSCARHVTGH-R---PYDSQLCCDRCGKVLE 31 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~-D---~~~G~~VC~~CG~Vle 31 (504)
|+.||.|++..+.. - ...--..|..||.-..
T Consensus 30 ~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 30 KVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred cCcCCCCCccceeeECCccccccccccCCcCccee
Confidence 57899999987221 1 1134688999998643
No 227
>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=55.40 E-value=6 Score=29.39 Aligned_cols=26 Identities=23% Similarity=0.653 Sum_probs=17.7
Q ss_pred CCCCCCCC-Ccccc-cCCCceecCcCce
Q 010689 3 WCSSCARH-VTGHR-PYDSQLCCDRCGK 28 (504)
Q Consensus 3 ~Cp~Cgs~-~iv~D-~~~G~~VC~~CG~ 28 (504)
.|+.||.. .+... .+.+...|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 69999985 22211 1246788999998
No 228
>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=55.31 E-value=13 Score=29.00 Aligned_cols=37 Identities=19% Similarity=0.326 Sum_probs=30.0
Q ss_pred HHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 223 alylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.+|.+-. ..-..|..+||+.++++..|+.+.++.+.+
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 3455433 456789999999999999999999998875
No 229
>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=55.20 E-value=2.4e+02 Score=28.47 Aligned_cols=25 Identities=8% Similarity=0.076 Sum_probs=22.4
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|++|||..+|+++.||++++..
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~r 265 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVE 265 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999999988764
No 230
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.88 E-value=8.2 Score=33.49 Aligned_cols=61 Identities=18% Similarity=0.200 Sum_probs=41.4
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccch-HHHHHHhh-CCCCCHH
Q 010689 123 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIF-LHKFTDRL-LPGGNKK 193 (504)
Q Consensus 123 LYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~-I~r~~~~L-~~~l~~~ 193 (504)
||+-||= .|++|-..+|++-..+..-+..+.+.++.+... .+|... =..+.++| .+.++++
T Consensus 52 lf~r~RG-----nlKEvEr~lg~sYptvR~kld~vlramgy~p~~-----e~~~~i~~~~i~~qle~Gei~pe 114 (122)
T COG3877 52 LFLRCRG-----NLKEVERELGISYPTVRTKLDEVLRAMGYNPDS-----ENSVNIGKKKIIDQLEKGEISPE 114 (122)
T ss_pred HHHHHcc-----CHHHHHHHHCCccHHHHHHHHHHHHHcCCCCCC-----CChhhhhHHHHHHHHHcCCCCHH
Confidence 6777773 488898999999999988888888888876443 344332 23456666 3345544
No 231
>PRK08402 replication factor A; Reviewed
Probab=54.72 E-value=6.7 Score=41.38 Aligned_cols=26 Identities=27% Similarity=0.609 Sum_probs=21.2
Q ss_pred CCCCCCCCCcccccCCCceecCcCcee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.||.|+.. ++.|...|...|..||.|
T Consensus 214 aCp~CnKk-v~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 214 ACPECRRK-VDYDPATDTWICPEHGEV 239 (355)
T ss_pred cCCCCCeE-EEEecCCCCEeCCCCCCc
Confidence 69999985 444667899999999975
No 232
>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=54.50 E-value=14 Score=30.24 Aligned_cols=37 Identities=24% Similarity=0.346 Sum_probs=27.5
Q ss_pred HHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 224 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 224 lylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+|+|..-.+.+.|.++||+..++++..+++-+..+..
T Consensus 15 ~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 15 LYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKK 51 (83)
T ss_dssp HHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 3444333334599999999999999999999998875
No 233
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=54.48 E-value=6.2 Score=29.57 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=19.3
Q ss_pred CCCCCCCCCcccccCCCceecCcCce
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
.|-.||... ..+.....+-|+.||.
T Consensus 8 ~C~~Cg~~~-~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGREV-ELDQETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCCee-ehhhccCceeCCCCCc
Confidence 588999873 4455678899999996
No 234
>PF14502 HTH_41: Helix-turn-helix domain
Probab=54.34 E-value=14 Score=27.66 Aligned_cols=31 Identities=13% Similarity=0.077 Sum_probs=26.7
Q ss_pred CCHhhHHhhhccCHHHHHHHHHHhhccCCCC
Q 010689 235 FSKSDIVKIVHICEATLMKRLIEFENTDSGS 265 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~ 265 (504)
.|+.|.++.++|+..||++.++.+.+...-.
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 5688999999999999999999998765533
No 235
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=54.25 E-value=23 Score=25.97 Aligned_cols=29 Identities=10% Similarity=0.276 Sum_probs=26.3
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+-+.+..+|+..++++..|+++.++.+.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56789999999999999999999999875
No 236
>PF13518 HTH_28: Helix-turn-helix domain
Probab=54.00 E-value=26 Score=25.32 Aligned_cols=25 Identities=16% Similarity=0.323 Sum_probs=23.2
Q ss_pred CHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 236 SKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
|+.+||..+|||..||.+.++.|..
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 9999999999999999998888875
No 237
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=53.71 E-value=2.3e+02 Score=27.97 Aligned_cols=25 Identities=8% Similarity=0.081 Sum_probs=22.0
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|+++||..+|+|..||+++.+.
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~ 248 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKA 248 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4679999999999999999987664
No 238
>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=53.66 E-value=32 Score=30.41 Aligned_cols=46 Identities=17% Similarity=0.195 Sum_probs=36.6
Q ss_pred chhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 114 ~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
..+..+.+++|++- ..+-|.+..+||+.++++...+.+....|.+.
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 34456677888874 34568999999999999999999888888774
No 239
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=53.49 E-value=49 Score=32.15 Aligned_cols=30 Identities=20% Similarity=0.372 Sum_probs=27.3
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
.++.|+++||..+|++..|+.+.+++|.+.
T Consensus 177 ~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 177 ALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred EecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 367899999999999999999999999865
No 240
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.37 E-value=6.5 Score=34.72 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=14.9
Q ss_pred cccCCCceecCcCceeec
Q 010689 14 HRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 14 ~D~~~G~~VC~~CG~Vle 31 (504)
.|-.+|.++|.+||+|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 455689999999999963
No 241
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=53.37 E-value=49 Score=31.89 Aligned_cols=33 Identities=18% Similarity=0.202 Sum_probs=28.5
Q ss_pred CCCcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 132 ~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
.|+|..+||+.+|++...+.|..++|.+.=-|.
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~ 215 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSGMLA 215 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEE
Confidence 688999999999999999999998888764444
No 242
>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=52.99 E-value=17 Score=31.10 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=25.3
Q ss_pred hcCCCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 230 THGLKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
+..-..||++|++.+|||.+||.+-=+.+.
T Consensus 51 Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 51 LLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 344789999999999999999998766655
No 243
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=52.85 E-value=6.6 Score=42.01 Aligned_cols=30 Identities=20% Similarity=0.564 Sum_probs=23.4
Q ss_pred CCCCCCCCC------cccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHV------TGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~------iv~D~~~G~~VC~~CG~Vlee 32 (504)
.||.|++.- -.+|..+|...|..||.=|.+
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 699999972 235677899999999976543
No 244
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=52.80 E-value=10 Score=31.21 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=20.5
Q ss_pred CCCCCCCCCCcccccCCCceecCcCcee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
..||-||...+..+......||.-|+.-
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCcc
Confidence 3699999875544433238899999995
No 245
>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=52.80 E-value=21 Score=30.04 Aligned_cols=31 Identities=13% Similarity=-0.039 Sum_probs=27.1
Q ss_pred hcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 230 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+..-..|+++|++.+|||-.||.+-=+.+..
T Consensus 45 lL~~g~syreIa~~tgvS~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 45 LLDEGKSYREIAEETGVSIATITRVSRCLKY 75 (87)
T ss_dssp HHHTTSSHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence 6677899999999999999999987777664
No 246
>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=52.56 E-value=13 Score=30.77 Aligned_cols=24 Identities=17% Similarity=0.265 Sum_probs=21.6
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
-..|.++||+.+|||..||++.+.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 567899999999999999999774
No 247
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.52 E-value=29 Score=27.42 Aligned_cols=32 Identities=13% Similarity=0.123 Sum_probs=27.3
Q ss_pred HhcCC-CCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 229 LTHGL-KFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 229 ~~~g~-~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.-+|- ..+..+||+.+|++..|+++.|..|..
T Consensus 16 ~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 16 ENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred HHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34455 499999999999999999999998875
No 248
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=52.49 E-value=6.7 Score=34.46 Aligned_cols=35 Identities=20% Similarity=0.517 Sum_probs=20.5
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcccccccc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f 41 (504)
.+|+.||... ........|..||.. +-.+..|.++
T Consensus 71 ~~C~~Cg~~~---~~~~~~~~CP~Cgs~--~~~i~~G~El 105 (113)
T PRK12380 71 AWCWDCSQVV---EIHQHDAQCPHCHGE--RLRVDTGDSL 105 (113)
T ss_pred EEcccCCCEE---ecCCcCccCcCCCCC--CcEEccCCeE
Confidence 3799999642 222345569999964 3344455444
No 249
>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=52.41 E-value=7.5 Score=37.79 Aligned_cols=31 Identities=26% Similarity=0.534 Sum_probs=21.6
Q ss_pred CCCCCCCCCCc--ccccCCC---ceecCcCceeecc
Q 010689 2 VWCSSCARHVT--GHRPYDS---QLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~i--v~D~~~G---~~VC~~CG~Vlee 32 (504)
+.|-+||.... -.+...| -..|.+||.|.|.
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 47999999842 1233333 3789999999874
No 250
>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=52.39 E-value=9.7 Score=31.46 Aligned_cols=35 Identities=14% Similarity=0.171 Sum_probs=23.4
Q ss_pred HHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 224 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 224 lylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
|-++..+...+.|++..|.++|||.+||.+=+.|-
T Consensus 9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteR 43 (82)
T PF12116_consen 9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVTER 43 (82)
T ss_dssp HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTH
T ss_pred HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHH
Confidence 34444555678899999999999999999766553
No 251
>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=52.30 E-value=23 Score=27.06 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=27.4
Q ss_pred cCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
.+-+.|..+|++.++++.+|+..+++.+.+.
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5788999999999999999999999999863
No 252
>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=52.25 E-value=16 Score=28.26 Aligned_cols=29 Identities=17% Similarity=0.313 Sum_probs=24.4
Q ss_pred CCCC-CHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKF-SKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~-t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
|.++ +..+|++..+||..|+|+.|..+..
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 5677 9999999999999999999998865
No 253
>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=51.95 E-value=15 Score=25.69 Aligned_cols=22 Identities=14% Similarity=0.321 Sum_probs=19.8
Q ss_pred CHhhHHhhhccCHHHHHHHHHH
Q 010689 236 SKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE 257 (504)
|..|+|+.+||+..||++..+.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 6789999999999999988775
No 254
>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=51.87 E-value=17 Score=27.41 Aligned_cols=25 Identities=20% Similarity=0.343 Sum_probs=23.3
Q ss_pred CHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 236 SKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+..+||+.++++..|+++.++.|.+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5999999999999999999999875
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=51.61 E-value=27 Score=26.38 Aligned_cols=26 Identities=15% Similarity=0.390 Sum_probs=24.3
Q ss_pred CCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 235 FSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
++..+|++.++++..||++.++.+..
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 99999999999999999999998865
No 256
>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=51.43 E-value=15 Score=25.85 Aligned_cols=23 Identities=9% Similarity=0.260 Sum_probs=20.5
Q ss_pred CCHhhHHhhhccCHHHHHHHHHH
Q 010689 235 FSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE 257 (504)
.|.+|+|+.+||+..||.+.+++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 47899999999999999998865
No 257
>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=51.31 E-value=42 Score=26.72 Aligned_cols=35 Identities=14% Similarity=0.212 Sum_probs=24.3
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhC-cChHHHHHHHHHH
Q 010689 121 SCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQL 157 (504)
Q Consensus 121 ACLYiACR~~~~p~tL~dIs~~~~-vs~~~Lg~~~~~L 157 (504)
.+.|++-... ..++.+|+..+| -+..++...++++
T Consensus 35 va~yL~r~~~--~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 35 VAMYLARELT--GLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHS-----HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred HHHHHHHHHh--CCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 4567665444 578999999999 8988888777654
No 258
>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=51.18 E-value=32 Score=24.78 Aligned_cols=34 Identities=24% Similarity=0.247 Sum_probs=25.5
Q ss_pred HHHHHHHHhcC-CCCCHhhHHhhhccCHHHHHHHHH
Q 010689 222 AALYVSALTHG-LKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 222 AalylAa~~~g-~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
|++-+..+ .| ...|.++|++.+||+..++-+++.
T Consensus 4 aa~~l~~~-~G~~~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 4 AALELFAE-KGYEAVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHH-HHTTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred HHHHHHHH-hCHHhCCHHHHHHHHccchhhHHHHcC
Confidence 44444443 34 469999999999999999987764
No 259
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=51.04 E-value=34 Score=31.48 Aligned_cols=45 Identities=20% Similarity=0.183 Sum_probs=38.7
Q ss_pred hHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 116 ~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
+..+=|.+|+|....+-|.++.+||...+|+...|.+.+..|.+.
T Consensus 8 ~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 8 EYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred hHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 345667899998877669999999999999999999999888774
No 260
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=50.95 E-value=12 Score=28.37 Aligned_cols=29 Identities=21% Similarity=0.698 Sum_probs=20.1
Q ss_pred CCCC--CCCCCCccc-ccCCCceecCcCceee
Q 010689 2 VWCS--SCARHVTGH-RPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp--~Cgs~~iv~-D~~~G~~VC~~CG~Vl 30 (504)
.+|| .|+...... +.....+.|..||...
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeE
Confidence 5799 897764433 2356788998898754
No 261
>PRK02935 hypothetical protein; Provisional
Probab=50.94 E-value=10 Score=32.91 Aligned_cols=39 Identities=21% Similarity=0.332 Sum_probs=23.7
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcccccccccc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f~~ 43 (504)
+.||+|+...-.. .-...|-.|+.-|.=..--++.+|.+
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 5899999863222 12348999999875322224455543
No 262
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=50.81 E-value=24 Score=33.28 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=22.8
Q ss_pred CCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 235 FSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
.|.+|||..+|||+.||++++.-..
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4999999999999999999998764
No 263
>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=50.80 E-value=22 Score=27.19 Aligned_cols=30 Identities=17% Similarity=0.243 Sum_probs=25.6
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+-..+.+++|...|+|+.||++-+.++.+.
T Consensus 17 ~~~~~~~ela~~l~~S~rti~~~i~~L~~~ 46 (59)
T PF08280_consen 17 NKWITLKELAKKLNISERTIKNDINELNEF 46 (59)
T ss_dssp HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT
T ss_pred CCCCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 456889999999999999999999998754
No 264
>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=50.75 E-value=9 Score=25.19 Aligned_cols=22 Identities=14% Similarity=0.492 Sum_probs=9.9
Q ss_pred CCCCCCCCCcccccCCCceecCc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDR 25 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~ 25 (504)
.||.||+..+ ....+-.+.|++
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 4999998743 333444677764
No 265
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=50.71 E-value=11 Score=28.38 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=18.8
Q ss_pred CCCCCCCCC-ccccc-CCCc-eecCcCceee
Q 010689 3 WCSSCARHV-TGHRP-YDSQ-LCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~-iv~D~-~~G~-~VC~~CG~Vl 30 (504)
.|.+|+.+. ..+.. ..|. .+|..||.-.
T Consensus 5 ~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 5 SCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 688898763 34532 3454 8899998754
No 266
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=50.64 E-value=79 Score=27.92 Aligned_cols=54 Identities=4% Similarity=0.022 Sum_probs=40.9
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHH
Q 010689 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMAR 274 (504)
Q Consensus 215 ~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~ 274 (504)
....|..+.-||-.... .+.++.+||+.+|+|+.++.+.+++.. .+|+.++...
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~~-----G~s~~~~l~~ 60 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKET-----GHSLGQYIRS 60 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHH-----CcCHHHHHHH
Confidence 34445555556666544 579999999999999999999999876 4677777654
No 267
>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=50.60 E-value=5.9 Score=30.20 Aligned_cols=29 Identities=28% Similarity=0.623 Sum_probs=20.0
Q ss_pred CCCCCCCCC-cccc--cCCCceecCcCceeec
Q 010689 3 WCSSCARHV-TGHR--PYDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~-iv~D--~~~G~~VC~~CG~Vle 31 (504)
.|.+||.+. ..+. +..+..+|..||.-.-
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 488888873 3444 3367888999987653
No 268
>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=50.60 E-value=19 Score=26.52 Aligned_cols=20 Identities=10% Similarity=0.140 Sum_probs=17.6
Q ss_pred cHHHHHHHhCcChHHHHHHH
Q 010689 135 LLIDFSNYLNINVYELGAVY 154 (504)
Q Consensus 135 tL~dIs~~~~vs~~~Lg~~~ 154 (504)
|++|||..+|++..++.+++
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 68999999999999987753
No 269
>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=50.58 E-value=31 Score=30.47 Aligned_cols=38 Identities=13% Similarity=0.152 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 223 alylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
.+|+| +..+-+.+..+|+..++++.++++++++.+...
T Consensus 15 l~~la-~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 15 LTTLA-QNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HHHHH-hCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34554 334567899999999999999999999999864
No 270
>PRK10870 transcriptional repressor MprA; Provisional
Probab=50.29 E-value=59 Score=30.57 Aligned_cols=29 Identities=10% Similarity=0.071 Sum_probs=25.9
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+-.+++++||+.++++.+|+.+.++.+..
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56789999999999999999999988764
No 271
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=50.23 E-value=8.4 Score=37.17 Aligned_cols=34 Identities=26% Similarity=0.572 Sum_probs=22.7
Q ss_pred CCCCCCCCCCcc----cc-cCCC-----ceecCcCceeeccCcc
Q 010689 2 VWCSSCARHVTG----HR-PYDS-----QLCCDRCGKVLEDHNF 35 (504)
Q Consensus 2 ~~Cp~Cgs~~iv----~D-~~~G-----~~VC~~CG~Vlee~~i 35 (504)
+.||.||++-.. +| |.-| .++|..||+=..|-..
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 579999996221 22 3445 4689999997766444
No 272
>PRK04217 hypothetical protein; Provisional
Probab=50.19 E-value=20 Score=31.41 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=23.4
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...|+++||+.+|||..||.+++....
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445999999999999999999998643
No 273
>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=49.91 E-value=9.6 Score=33.02 Aligned_cols=28 Identities=25% Similarity=0.463 Sum_probs=21.9
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
.|--|+..... ...+.+||..||++..-
T Consensus 37 aCeiC~~~GY~--q~g~~lvC~~C~~~~~~ 64 (102)
T PF10080_consen 37 ACEICGPKGYY--QEGDQLVCKNCGVRFNL 64 (102)
T ss_pred eccccCCCceE--EECCEEEEecCCCEEeh
Confidence 58899877543 45689999999999753
No 274
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=49.85 E-value=49 Score=26.84 Aligned_cols=47 Identities=4% Similarity=0.171 Sum_probs=30.3
Q ss_pred HHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHh
Q 010689 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 276 (504)
Q Consensus 226 lAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~ 276 (504)
+...+-....||+++|+.+|++.++|.+-.+ -.....|++.+.....
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~----g~~~~~sl~~L~~~l~ 69 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN----GKIDDFSLDTLLRYLE 69 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT----T-GCC--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc----CcccCCCHHHHHHHHH
Confidence 4555567889999999999999999976443 2344678888877643
No 275
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=49.76 E-value=15 Score=36.59 Aligned_cols=29 Identities=10% Similarity=0.102 Sum_probs=26.2
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+-.++++++++.++||+.|||+.++++.+
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46789999999999999999999999864
No 276
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=49.62 E-value=1.3e+02 Score=32.53 Aligned_cols=51 Identities=14% Similarity=0.143 Sum_probs=41.5
Q ss_pred cccccCCChhHHHHH---HHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 208 DWITTGRKPSGLCGA---ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 208 ~~l~~GR~P~~IAAA---alylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
..|..+++-..|+-| |.|++-++.+. |..+|+..+|.+.+||...++.+..
T Consensus 360 ~~l~s~~R~~~i~~aR~iamyl~r~~~~~--s~~~Ig~~fgr~hstV~~a~~~i~~ 413 (440)
T PRK14088 360 EEILSNSRNVKALLARRIGMYVAKNYLGS--SLRTIAEKFNRSHPVVVDSVKKVKD 413 (440)
T ss_pred HHHhCCCCCccccHHHHHHHHHHHHHhCC--CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 446666677778888 89999775554 8999999999999999988888776
No 277
>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=49.56 E-value=8.2 Score=34.00 Aligned_cols=25 Identities=24% Similarity=0.639 Sum_probs=16.0
Q ss_pred CCCCCCCCCCcccccCCCceecCcCcee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.+|+.||... ....-...|..||..
T Consensus 71 ~~C~~Cg~~~---~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 71 CECEDCSEEV---SPEIDLYRCPKCHGI 95 (115)
T ss_pred EEcccCCCEE---ecCCcCccCcCCcCC
Confidence 3799999642 222235679999964
No 278
>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=49.45 E-value=30 Score=24.29 Aligned_cols=27 Identities=26% Similarity=0.277 Sum_probs=23.5
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...+.++||...|++..||.+++....
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 557899999999999999999887654
No 279
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=49.42 E-value=11 Score=28.86 Aligned_cols=24 Identities=25% Similarity=0.751 Sum_probs=18.8
Q ss_pred CCCCCCCCCcccccCCCceecCcCceee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vl 30 (504)
.||.|++.. ...-.+.|..||...
T Consensus 1 ~Cpv~~~~~----~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL----PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc----ccccCCcCCCCCCcC
Confidence 499999864 345678999999874
No 280
>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=49.13 E-value=12 Score=30.34 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=21.2
Q ss_pred CCCCCCCCCCcc--c-ccCCCceecCcCceeec
Q 010689 2 VWCSSCARHVTG--H-RPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv--~-D~~~G~~VC~~CG~Vle 31 (504)
..||.|+..+.+ + +...-..-|..||..-.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 379999997533 2 33345778999999743
No 281
>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=49.03 E-value=18 Score=27.23 Aligned_cols=28 Identities=18% Similarity=0.171 Sum_probs=23.4
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
...+.++||...+|++.||+.+.+.+..
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 4578889999999999999999887753
No 282
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=49.02 E-value=36 Score=32.30 Aligned_cols=60 Identities=12% Similarity=0.154 Sum_probs=42.1
Q ss_pred HHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccC
Q 010689 196 DTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (504)
Q Consensus 196 ~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~ 262 (504)
.-...+.+.|.+.++ -+-.| .||-+--++.-+.|..||+.++|+|.+.+..-++++....
T Consensus 10 ~~Ie~fae~m~r~G~---nrtVG----~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~ 69 (177)
T COG1510 10 IFIEHFAETMSRWGI---NRTVG----QIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWN 69 (177)
T ss_pred HHHHHHHHHHHHhCC---cchHH----HHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcc
Confidence 334455666665544 12223 4454444567999999999999999999999999987643
No 283
>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=49.01 E-value=7.5 Score=28.86 Aligned_cols=14 Identities=29% Similarity=0.691 Sum_probs=9.2
Q ss_pred eecCcCceeeccCc
Q 010689 21 LCCDRCGKVLEDHN 34 (504)
Q Consensus 21 ~VC~~CG~Vlee~~ 34 (504)
+.|+.||.|.++..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 46777777776543
No 284
>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=48.95 E-value=41 Score=25.17 Aligned_cols=42 Identities=12% Similarity=0.105 Sum_probs=31.8
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 120 ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 120 AACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
..+|++..+..+.+.++.+|++.++++...+.+..+.|.+.=
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 345555555555568999999999999999999988887643
No 285
>PRK08329 threonine synthase; Validated
Probab=48.95 E-value=11 Score=39.38 Aligned_cols=26 Identities=35% Similarity=0.737 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
|..|+.||..- +.... +.| .||-.|+
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 286
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=48.91 E-value=21 Score=32.62 Aligned_cols=41 Identities=20% Similarity=0.099 Sum_probs=27.0
Q ss_pred hhHHHHHHHHHHHHhcC---CCCCHhhHHhhhccCHHHHHHHHH
Q 010689 216 PSGLCGAALYVSALTHG---LKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 216 P~~IAAAalylAa~~~g---~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
|.=+=||.|+++-.++. -++|+.+||+.+||+++|+=+.-.
T Consensus 13 ~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 13 LQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHh
Confidence 44455666666666653 579999999999999999976653
No 287
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=48.87 E-value=64 Score=30.98 Aligned_cols=119 Identities=17% Similarity=0.192 Sum_probs=63.1
Q ss_pred hHHHHHHHHHHHHhcCCC-CcHHHHHHHhCcCh-HHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHH
Q 010689 116 EQVQASCLYLACRQKSKP-FLLIDFSNYLNINV-YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKK 193 (504)
Q Consensus 116 ~~vaAACLYiACR~~~~p-~tL~dIs~~~~vs~-~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~ 193 (504)
..++=|.||++ +-| +++.+|+.+++++. ..+......|.....-...+. -|..+.+...+...++
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~gl---------~l~~~~~~y~l~tk~e 69 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAGI---------EIIKFGQSYSLVTKPA 69 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCCE---------EEEEECCEEEEEEhHH
Confidence 35667888877 788 99999999999884 455555555555443211110 0111111111012233
Q ss_pred HHHHHHHHHHHhcccccccCCChhHHHHHHHH-HHHHhcCCCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 194 VCDTARDILASMKRDWITTGRKPSGLCGAALY-VSALTHGLKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 194 V~~~A~~I~~~~~~~~l~~GR~P~~IAAAaly-lAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
......+++.. .+++ +--|++= +|...+.-++|..+|-.+-||.-..+=+.|.+
T Consensus 70 ~~~~i~~~~~~--------~~~~--LS~aaLEtLAIIAY~QPITr~eIe~IRGv~s~~~l~~L~e 124 (186)
T TIGR00281 70 FADYIHRFLPA--------KLKN--LNSASLEVLAIIAYKQPITRARINEIRGVKSYQIVDDLVE 124 (186)
T ss_pred HHHHHHHHhcc--------cccc--CCHHHHHHHHHHHHcCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 33332222211 1111 2223332 33345678999999999999985555444444
No 288
>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=48.85 E-value=18 Score=22.87 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=18.5
Q ss_pred CCCHhhHHhhhccCHHHHHHH
Q 010689 234 KFSKSDIVKIVHICEATLMKR 254 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr 254 (504)
..+..+|+..++++..||.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 458999999999999999875
No 289
>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=48.29 E-value=13 Score=28.09 Aligned_cols=28 Identities=21% Similarity=0.693 Sum_probs=14.2
Q ss_pred CCCCC--CCCCCcccccCCCc--eecCcCceee
Q 010689 2 VWCSS--CARHVTGHRPYDSQ--LCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~--Cgs~~iv~D~~~G~--~VC~~CG~Vl 30 (504)
.+||. |+...... ..... +.|..||...
T Consensus 19 ~~Cp~~~C~~~~~~~-~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKD-DGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---ECS--SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEEec-CCCCCCeeECCCCCCcC
Confidence 58988 99764333 33333 8899999764
No 290
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.29 E-value=22 Score=32.01 Aligned_cols=39 Identities=15% Similarity=0.355 Sum_probs=31.5
Q ss_pred HHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 223 alylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
.||++..-.|...+.++||+..+|+..+||+-+..+...
T Consensus 14 ~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 14 LIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 445554444667899999999999999999999998753
No 291
>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=48.08 E-value=8.6 Score=28.28 Aligned_cols=28 Identities=18% Similarity=0.526 Sum_probs=19.0
Q ss_pred CCCCCCCCCcccc-------cCCCceecCc--Cceee
Q 010689 3 WCSSCARHVTGHR-------PYDSQLCCDR--CGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D-------~~~G~~VC~~--CG~Vl 30 (504)
.||+||+...+.. ..+-...|++ ||.-.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 5999999754432 1235678988 99753
No 292
>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=47.82 E-value=13 Score=26.39 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=7.6
Q ss_pred eecCcCceee
Q 010689 21 LCCDRCGKVL 30 (504)
Q Consensus 21 ~VC~~CG~Vl 30 (504)
.+|..||-.+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3699999765
No 293
>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=47.78 E-value=25 Score=26.00 Aligned_cols=31 Identities=16% Similarity=0.244 Sum_probs=25.6
Q ss_pred cCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 231 HGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
++-..++.||++.+|++.+|+.+-+..|.+.
T Consensus 15 ~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 15 SGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp TBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3455799999999999999999999988753
No 294
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=47.78 E-value=18 Score=31.94 Aligned_cols=27 Identities=19% Similarity=0.138 Sum_probs=23.9
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+=+++++++..|||=+|+|+||.++-.
T Consensus 49 rGnlKe~e~~lgiSYPTvR~rLd~ii~ 75 (113)
T PF09862_consen 49 RGNLKEMEKELGISYPTVRNRLDKIIE 75 (113)
T ss_pred cCCHHHHHHHHCCCcHHHHHHHHHHHH
Confidence 447899999999999999999998864
No 295
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=47.64 E-value=29 Score=24.42 Aligned_cols=30 Identities=10% Similarity=0.136 Sum_probs=26.1
Q ss_pred CCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 131 ~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
..|.+..|+++.++++...+.+.+..|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357899999999999999999888888764
No 296
>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=47.43 E-value=23 Score=26.87 Aligned_cols=28 Identities=14% Similarity=0.169 Sum_probs=25.0
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
-|..++++.|..+|||..+++++.+++.
T Consensus 13 ~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 13 YFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 3678999999999999999999998764
No 297
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=47.30 E-value=20 Score=32.28 Aligned_cols=29 Identities=24% Similarity=0.245 Sum_probs=25.8
Q ss_pred CCC-CCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLK-FSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~-~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
|.+ .|+++.|..++|...|+++.|+++..
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELER 61 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 444 67999999999999999999999875
No 298
>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=47.27 E-value=13 Score=32.50 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=0.0
Q ss_pred CCCCCCCCcccccCC--------------CceecCcCceee
Q 010689 4 CSSCARHVTGHRPYD--------------SQLCCDRCGKVL 30 (504)
Q Consensus 4 Cp~Cgs~~iv~D~~~--------------G~~VC~~CG~Vl 30 (504)
||.||+..+..+... ...+|..||-++
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
No 299
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=47.06 E-value=42 Score=32.43 Aligned_cols=29 Identities=10% Similarity=0.142 Sum_probs=26.0
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
++.|+.+||..+|+|..|+.+-+++|.+-
T Consensus 168 ~~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 168 YHEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred ccchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 34689999999999999999999999865
No 300
>PF13551 HTH_29: Winged helix-turn helix
Probab=46.94 E-value=39 Score=28.32 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=24.6
Q ss_pred CHhhHHhhhccCHHHHHHHHHHhhccC
Q 010689 236 SKSDIVKIVHICEATLMKRLIEFENTD 262 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~~~t~ 262 (504)
++.+||..+|++..||.+.++.|....
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999999988644
No 301
>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=46.64 E-value=14 Score=28.80 Aligned_cols=28 Identities=21% Similarity=0.425 Sum_probs=19.1
Q ss_pred CCCCCCCCCCcc--cc-cCCCceecCcCcee
Q 010689 2 VWCSSCARHVTG--HR-PYDSQLCCDRCGKV 29 (504)
Q Consensus 2 ~~Cp~Cgs~~iv--~D-~~~G~~VC~~CG~V 29 (504)
..||.|+.-+.+ +. ...-.+-|..||.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 379999997432 32 22235789999985
No 302
>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=46.55 E-value=18 Score=25.77 Aligned_cols=23 Identities=13% Similarity=0.026 Sum_probs=19.6
Q ss_pred CHhhHHhhhccCHHHHHHHHHHh
Q 010689 236 SKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
+.+++|+.+||+..||+...++-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 67899999999999999775554
No 303
>PRK00118 putative DNA-binding protein; Validated
Probab=46.52 E-value=24 Score=30.65 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=23.6
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...|.++||..+|+|+.||.+++....
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RAr 58 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTE 58 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 478899999999999999999887543
No 304
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=46.34 E-value=61 Score=28.62 Aligned_cols=42 Identities=10% Similarity=0.132 Sum_probs=30.6
Q ss_pred hhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHH
Q 010689 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (504)
Q Consensus 115 ~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L 157 (504)
...+..+.-||--.. ..|.++.++|+.+++++..|.+.|++.
T Consensus 8 ~~~i~~~~~~I~~~~-~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNL-ESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 334555555665554 457999999999999999998776644
No 305
>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=46.19 E-value=14 Score=27.84 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=8.6
Q ss_pred eecCcCceeeccC
Q 010689 21 LCCDRCGKVLEDH 33 (504)
Q Consensus 21 ~VC~~CG~Vlee~ 33 (504)
++|+.||.|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 4677777777653
No 306
>PRK06030 hypothetical protein; Provisional
Probab=46.19 E-value=59 Score=29.17 Aligned_cols=39 Identities=8% Similarity=0.083 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 121 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 121 ACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
.|+|++-... ..+|.+|+..+|-+..++...++++.+.+
T Consensus 59 IAMYL~r~~~--~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVSL--GWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 5688876554 45899999999999999999999888765
No 307
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=46.12 E-value=49 Score=26.80 Aligned_cols=28 Identities=7% Similarity=0.159 Sum_probs=25.7
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
-+.+..+|++.++++.+|+++.++.+.+
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999999865
No 308
>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=46.06 E-value=31 Score=25.31 Aligned_cols=40 Identities=10% Similarity=0.132 Sum_probs=29.5
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 276 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~ 276 (504)
....|++++|+.+||+..||.+-.+. ....+++.+.++..
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g-----~~~~~~~~~~~ia~ 46 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG-----KRNPSLDTLKKIAK 46 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT-----SSTSBHHHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC-----CCCCCHHHHHHHHH
Confidence 35689999999999999999988765 44567777766654
No 309
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=46.05 E-value=84 Score=29.50 Aligned_cols=30 Identities=10% Similarity=-0.042 Sum_probs=26.9
Q ss_pred CCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 132 ~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
.|.+..+||+.+|++...+.|.+++|++.=
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 478899999999999999999999888753
No 310
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=45.94 E-value=74 Score=26.86 Aligned_cols=39 Identities=8% Similarity=0.135 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHH
Q 010689 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (504)
Q Consensus 118 vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L 157 (504)
+..+.-|+... ...|.++.++|..++++...|.+.|++.
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 4567999999999999999998877764
No 311
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.72 E-value=9.9 Score=34.47 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=6.8
Q ss_pred CceecCcCcee
Q 010689 19 SQLCCDRCGKV 29 (504)
Q Consensus 19 G~~VC~~CG~V 29 (504)
....|..||..
T Consensus 106 ~~~~CP~Cgs~ 116 (135)
T PRK03824 106 AFLKCPKCGSR 116 (135)
T ss_pred cCcCCcCCCCC
Confidence 44557777753
No 312
>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=45.48 E-value=20 Score=25.31 Aligned_cols=30 Identities=20% Similarity=0.369 Sum_probs=20.1
Q ss_pred CCCCCCCCCCcccccCCC-ceecCc---Cceeec
Q 010689 2 VWCSSCARHVTGHRPYDS-QLCCDR---CGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G-~~VC~~---CG~Vle 31 (504)
..||.||+..++-....| ++.|++ |.....
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 479999966444433444 778987 877654
No 313
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=44.78 E-value=1.1e+02 Score=35.86 Aligned_cols=57 Identities=26% Similarity=0.361 Sum_probs=45.7
Q ss_pred HHHHHHHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCc
Q 010689 76 DDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFL 135 (504)
Q Consensus 76 ~~I~~i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~~~p~t 135 (504)
......|..|+++ ......|..-|..+..+-..-|- -.++.|.+||.+||..++|.-
T Consensus 36 q~~~~~c~~lnld--~~~~~ea~d~yta~~q~~slegs-~~hW~~cAlY~~~r~S~~~~v 92 (920)
T KOG1010|consen 36 QDSDELCRPLNLD--EQTETEAWDTYTAVSQRLSLEGS-ESHWLACALYTACRRSSVPTV 92 (920)
T ss_pred hhhhhhhhhhccc--chhhhhhHHHHHHHHhHhCCCcc-HHHHHHHHHHHHHHhccCCcc
Confidence 4566788999999 89999999999988765444444 568999999999999976643
No 314
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=44.62 E-value=2.7e+02 Score=25.99 Aligned_cols=40 Identities=13% Similarity=0.229 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhc
Q 010689 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLY 162 (504)
Q Consensus 118 vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~ 162 (504)
++=|.||.+ +-|.++.+++++++ +...+......|.+.+.
T Consensus 2 ~iEAlLF~s----~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~ 41 (159)
T PF04079_consen 2 IIEALLFAS----GEPVSIEELAEILG-SEDEVEEALEELQEEYN 41 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHH
T ss_pred hhHhhHHHc----CCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhc
Confidence 445777764 66999999999999 99999999999999884
No 315
>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=44.58 E-value=9.5 Score=38.92 Aligned_cols=29 Identities=24% Similarity=0.494 Sum_probs=12.9
Q ss_pred CCCCCCCCCCcc--cccCC--C--ceecCcCceee
Q 010689 2 VWCSSCARHVTG--HRPYD--S--QLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv--~D~~~--G--~~VC~~CG~Vl 30 (504)
..||.||+.... ++... | .++|+-||+-=
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEW 207 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCee
Confidence 379999998432 22222 5 78999999854
No 316
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=44.33 E-value=81 Score=29.61 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=26.7
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
++.|+++||+.+|++..|+.+-+++|.+-
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 68999999999999999999999998753
No 317
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=44.30 E-value=61 Score=31.25 Aligned_cols=50 Identities=20% Similarity=0.111 Sum_probs=35.0
Q ss_pred hhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 115 ~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
...-+|..|+........|.+..|||+.+|++...+.|++++|.+.=-|.
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~ 200 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLK 200 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEE
Confidence 33444444443332334567889999999999999999999998864343
No 318
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=44.24 E-value=24 Score=33.17 Aligned_cols=43 Identities=16% Similarity=0.326 Sum_probs=30.1
Q ss_pred cCCCCCHhhHHhhhccCHH---------------HHHHHHHHhhccCCCCCChHHHHH
Q 010689 231 HGLKFSKSDIVKIVHICEA---------------TLMKRLIEFENTDSGSLTIEDFMA 273 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~---------------TIrkr~kE~~~t~~~~lt~~~~~~ 273 (504)
....+||+++|+.+|||.+ |+++-|+.|.+.+...+|.+.+|.
T Consensus 15 k~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~ 72 (187)
T COG3620 15 KELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMH 72 (187)
T ss_pred HHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcceEeHhhhcc
Confidence 3567899999999999985 455556666666556666555554
No 319
>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=44.24 E-value=5 Score=35.20 Aligned_cols=25 Identities=28% Similarity=0.845 Sum_probs=15.3
Q ss_pred CCCCCCCCCCcccccCCCceecCcCcee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.+|+.||..- ........|..||.-
T Consensus 71 ~~C~~Cg~~~---~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEF---EPDEFDFSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EE---ECHHCCHH-SSSSSS
T ss_pred EECCCCCCEE---ecCCCCCCCcCCcCC
Confidence 3799999862 222334779999985
No 320
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=44.20 E-value=85 Score=22.75 Aligned_cols=24 Identities=8% Similarity=0.110 Sum_probs=21.7
Q ss_pred CcHHHHHHHhCcChHHHHHHHHHH
Q 010689 134 FLLIDFSNYLNINVYELGAVYLQL 157 (504)
Q Consensus 134 ~tL~dIs~~~~vs~~~Lg~~~~~L 157 (504)
.++++||..+|++..++.+.|...
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 899999999999999999988753
No 321
>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=44.10 E-value=15 Score=33.33 Aligned_cols=28 Identities=25% Similarity=0.729 Sum_probs=19.7
Q ss_pred CCC--CCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCS--SCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp--~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
.|| .|+.. +..+ .+|.+.|..||..++.
T Consensus 20 aC~~~~C~kK-v~~~-~~~~y~C~~C~~~~~~ 49 (146)
T PF08646_consen 20 ACPNEKCNKK-VTEN-GDGSYRCEKCNKTVEN 49 (146)
T ss_dssp E-TSTTTS-B--EEE-TTTEEEETTTTEEESS
T ss_pred CCCCccCCCE-eecC-CCcEEECCCCCCcCCC
Confidence 599 99987 3333 5699999999998753
No 322
>PF12728 HTH_17: Helix-turn-helix domain
Probab=44.00 E-value=25 Score=25.63 Aligned_cols=22 Identities=9% Similarity=0.297 Sum_probs=19.4
Q ss_pred CCHhhHHhhhccCHHHHHHHHH
Q 010689 235 FSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~k 256 (504)
.|.+|+|..+|||..||.+-.+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999997665
No 323
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=43.95 E-value=55 Score=31.16 Aligned_cols=25 Identities=28% Similarity=0.271 Sum_probs=22.3
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
..|..+||+.+|||.+|+.+.+++.
T Consensus 172 g~s~~~iak~lgis~~Tv~r~~k~~ 196 (200)
T PRK13413 172 GTSKSEIARKLGVSRTTLARFLKTR 196 (200)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHhc
Confidence 4699999999999999999988753
No 324
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=43.93 E-value=9.7 Score=36.92 Aligned_cols=29 Identities=34% Similarity=0.503 Sum_probs=20.5
Q ss_pred CCCCCCCCCCccc--ccCCCceecCcCceee
Q 010689 2 VWCSSCARHVTGH--RPYDSQLCCDRCGKVL 30 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~--D~~~G~~VC~~CG~Vl 30 (504)
|.|+.|++....+ +...=.+.|..||..-
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 5799999985433 3223367999999863
No 325
>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=43.81 E-value=10 Score=27.25 Aligned_cols=26 Identities=23% Similarity=0.664 Sum_probs=17.3
Q ss_pred CCCCCCCCCcc-cc-cCCCceecCcCce
Q 010689 3 WCSSCARHVTG-HR-PYDSQLCCDRCGK 28 (504)
Q Consensus 3 ~Cp~Cgs~~iv-~D-~~~G~~VC~~CG~ 28 (504)
.|+.||..--+ .. .+.....|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 59999976221 11 1256889999998
No 326
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=43.65 E-value=4e+02 Score=27.72 Aligned_cols=90 Identities=12% Similarity=0.060 Sum_probs=51.8
Q ss_pred hHHHHHHHHHHHHHHHHHHcC---CCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHH---------------
Q 010689 66 SRERLMEKAFDDMRQMKNALN---IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC--------------- 127 (504)
Q Consensus 66 srer~L~~a~~~I~~i~~~L~---Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC--------------- 127 (504)
.+++.+..-...|..++.++. ++-.+-+.+....+++.+..-.-.+|-+....|.-.|.-+.
T Consensus 87 A~~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~ 166 (324)
T PRK07921 87 ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPV 166 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCH
Confidence 344555555566677777653 22113344555567776655555677666555544443321
Q ss_pred -----------------HhcCCCCcHHHHHHHhCcChHHHHHHHH
Q 010689 128 -----------------RQKSKPFLLIDFSNYLNINVYELGAVYL 155 (504)
Q Consensus 128 -----------------R~~~~p~tL~dIs~~~~vs~~~Lg~~~~ 155 (504)
...|.+-+..+||..+|+++..+.....
T Consensus 167 ~~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~ 211 (324)
T PRK07921 167 HLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE 211 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 1123444677899999999988876543
No 327
>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=43.62 E-value=17 Score=36.62 Aligned_cols=43 Identities=16% Similarity=0.131 Sum_probs=29.8
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHhhh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKEL 278 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~~~ 278 (504)
+.|.+|||+.+|||.+|+++.|..- -..+..|-+-.++...++
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~~--~~vs~~tr~rV~~~a~~l 43 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNE--PKVSIETRERVEQVIQQS 43 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCCC--CCCCHHHHHHHHHHHHHH
Confidence 4689999999999999999999642 123344555555544433
No 328
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=43.41 E-value=3.5e+02 Score=29.59 Aligned_cols=41 Identities=15% Similarity=0.339 Sum_probs=33.4
Q ss_pred CCCHhhHHhhhccCHHHHHHHHH-HhhccCCCCCChHHHHHH
Q 010689 234 KFSKSDIVKIVHICEATLMKRLI-EFENTDSGSLTIEDFMAR 274 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~k-E~~~t~~~~lt~~~~~~~ 274 (504)
+.++++||..+|++++||.+... .+..||.|-+-+..|-..
T Consensus 330 PL~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~ 371 (444)
T COG1508 330 PLVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSS 371 (444)
T ss_pred cccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHH
Confidence 57889999999999999998775 355778888888877554
No 329
>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=43.32 E-value=7.9 Score=40.84 Aligned_cols=79 Identities=14% Similarity=0.035 Sum_probs=0.0
Q ss_pred HHhhCCCCCHHHHHHHHHHHHHhc-ccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 183 TDRLLPGGNKKVCDTARDILASMK-RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 183 ~~~L~~~l~~~V~~~A~~I~~~~~-~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+..++.+.+++++..|..+++... ...+..+..=.+=+.+|+||||..++....+.......++....-.+-|..|...
T Consensus 5 ~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~~~ 84 (353)
T PF05460_consen 5 IPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFENL 84 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHHHH
Confidence 344443456778888888887776 4556666666777889999999999988888888889999999999888888873
No 330
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=43.09 E-value=62 Score=25.50 Aligned_cols=39 Identities=10% Similarity=0.062 Sum_probs=30.0
Q ss_pred HHHHHHhcCC-CCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 123 LYLACRQKSK-PFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 123 LYiACR~~~~-p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
|+...+..|- +.++.|||..+|++...+.+....|.+.=
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4445556666 49999999999999999988777776643
No 331
>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=43.03 E-value=18 Score=25.40 Aligned_cols=20 Identities=15% Similarity=0.207 Sum_probs=15.8
Q ss_pred CHhhHHhhhccCHHHHHHHH
Q 010689 236 SKSDIVKIVHICEATLMKRL 255 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~ 255 (504)
|..|+|+.+||+..|||.-=
T Consensus 1 ti~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 45789999999999998643
No 332
>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=43.02 E-value=71 Score=22.87 Aligned_cols=29 Identities=10% Similarity=0.093 Sum_probs=22.9
Q ss_pred CCCCcHHHHHHHhCcChHHHHHHHHHHHH
Q 010689 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (504)
Q Consensus 131 ~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~ 159 (504)
+-+.+..+||..++++...+.+.+++|.+
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 33499999999999999999988888765
No 333
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=42.98 E-value=38 Score=26.93 Aligned_cols=32 Identities=9% Similarity=0.019 Sum_probs=29.0
Q ss_pred HhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 229 LTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 229 ~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
++.+..++..+.|+.+|+.+.||++..+.|..
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~ 39 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFRQ 39 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 67899999999999999999999999988753
No 334
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=42.96 E-value=31 Score=35.79 Aligned_cols=44 Identities=9% Similarity=0.016 Sum_probs=34.2
Q ss_pred HHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCCh
Q 010689 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTI 268 (504)
Q Consensus 225 ylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~ 268 (504)
-+|...+-...||.|||+..|||..++.+-|++=.+..-=+.+|
T Consensus 20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I 63 (318)
T PRK15418 20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQI 63 (318)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEE
Confidence 34555567889999999999999999999999877654333333
No 335
>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=42.48 E-value=25 Score=27.09 Aligned_cols=23 Identities=9% Similarity=0.180 Sum_probs=20.2
Q ss_pred CHhhHHhhhccCHHHHHHHHHHh
Q 010689 236 SKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
+..|||+.+||+..|||+..+++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 67899999999999999877654
No 336
>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=42.46 E-value=24 Score=31.44 Aligned_cols=26 Identities=15% Similarity=0.018 Sum_probs=22.8
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|.+|||..+|+|+.||++++.-.
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra 153 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKA 153 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46799999999999999999988654
No 337
>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=42.43 E-value=3.6e+02 Score=26.91 Aligned_cols=26 Identities=4% Similarity=0.004 Sum_probs=22.3
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
+...|+++||..+|||..+|+++.+.
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~ 259 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKN 259 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34789999999999999999976654
No 338
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=42.27 E-value=14 Score=26.14 Aligned_cols=28 Identities=21% Similarity=0.457 Sum_probs=16.9
Q ss_pred CCCCCCCCCcccccC-CCceecCcCceee
Q 010689 3 WCSSCARHVTGHRPY-DSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~-~G~~VC~~CG~Vl 30 (504)
.||.|+..-...... --..+|..||=|-
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeEE
Confidence 599999852222211 1245699998763
No 339
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=42.13 E-value=74 Score=26.86 Aligned_cols=50 Identities=8% Similarity=0.084 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHH
Q 010689 220 CGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (504)
Q Consensus 220 AAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~ 275 (504)
.-+.-|+... ...++++.+||+.+|+|..++.+++++.. .+|+.++...-
T Consensus 8 ~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~~-----g~s~~~~i~~~ 57 (107)
T PRK10219 8 QTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTVT-----HQTLGDYIRQR 57 (107)
T ss_pred HHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHHH-----CcCHHHHHHHH
Confidence 3334455544 34579999999999999999999999874 56777776543
No 340
>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=41.95 E-value=8.8 Score=26.90 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=7.5
Q ss_pred CCCCCCCCCcccccCCCceec
Q 010689 3 WCSSCARHVTGHRPYDSQLCC 23 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC 23 (504)
+|..||.-.-+.+...|.++|
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 356666543334444555555
No 341
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=41.85 E-value=5.1 Score=31.00 Aligned_cols=24 Identities=25% Similarity=0.812 Sum_probs=16.2
Q ss_pred CCCCCCCCCcccccCCCceecCc-Cceeec
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDR-CGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~-CG~Vle 31 (504)
.|+.||.. + ..|+.+|++ ||-+++
T Consensus 10 HC~VCg~a-I----p~de~~CSe~C~eil~ 34 (64)
T COG4068 10 HCVVCGKA-I----PPDEQVCSEECGEILN 34 (64)
T ss_pred cccccCCc-C----CCccchHHHHHHHHHH
Confidence 58888875 2 236778875 887664
No 342
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.75 E-value=1.5e+02 Score=25.94 Aligned_cols=25 Identities=24% Similarity=0.700 Sum_probs=20.6
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
.||.||...++. .+-|.+||+-+..
T Consensus 8 ~cPvcg~~~iVT-----eL~c~~~etTVrg 32 (122)
T COG3877 8 RCPVCGRKLIVT-----ELKCSNCETTVRG 32 (122)
T ss_pred CCCcccccceeE-----EEecCCCCceEec
Confidence 799999987665 5789999998764
No 343
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=41.22 E-value=52 Score=23.90 Aligned_cols=31 Identities=13% Similarity=0.129 Sum_probs=25.2
Q ss_pred CCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 131 ~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
..+.|+.|||..+|++...+.+...+..+.|
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 6678999999999999999988877666554
No 344
>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=40.83 E-value=3.4e+02 Score=26.07 Aligned_cols=26 Identities=15% Similarity=0.143 Sum_probs=22.8
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|+++||...|++..||++++...
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra 218 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRA 218 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46799999999999999999887653
No 345
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=40.79 E-value=24 Score=27.90 Aligned_cols=22 Identities=18% Similarity=0.318 Sum_probs=19.6
Q ss_pred CCHhhHHhhhccCHHHHHHHHH
Q 010689 235 FSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~k 256 (504)
.++++||+.+|||..||.+-+.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3788999999999999998775
No 346
>PRK09526 lacI lac repressor; Reviewed
Probab=40.76 E-value=21 Score=36.25 Aligned_cols=43 Identities=19% Similarity=0.149 Sum_probs=30.9
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHhhh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKEL 278 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~~~ 278 (504)
+.|.+|||+.+|||.+|+++-|..-. .-+.-|-+-.++...++
T Consensus 5 ~~ti~dIA~~aGVS~~TVSrvLn~~~--~vs~~tr~rV~~~a~el 47 (342)
T PRK09526 5 PVTLYDVARYAGVSYQTVSRVLNQAS--HVSAKTREKVEAAMAEL 47 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhcCCC--CCCHHHHHHHHHHHHHH
Confidence 56999999999999999999997421 23344555555555544
No 347
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=40.72 E-value=14 Score=26.18 Aligned_cols=13 Identities=15% Similarity=0.892 Sum_probs=12.1
Q ss_pred CceecCcCceeec
Q 010689 19 SQLCCDRCGKVLE 31 (504)
Q Consensus 19 G~~VC~~CG~Vle 31 (504)
|.+||+.|+.+++
T Consensus 2 GtIvCq~C~~~Id 14 (38)
T PF13790_consen 2 GTIVCQHCNETID 14 (38)
T ss_pred CEEEeccccceee
Confidence 8899999999997
No 348
>PHA00542 putative Cro-like protein
Probab=40.66 E-value=24 Score=28.98 Aligned_cols=42 Identities=7% Similarity=0.033 Sum_probs=29.3
Q ss_pred hcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHH
Q 010689 230 THGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~ 275 (504)
+.....|+.++|+.+||+.+||.+-+..-.. ..+++.+.++.
T Consensus 27 l~~~glTq~elA~~lgIs~~tIsr~e~g~~~----~p~~~~l~ki~ 68 (82)
T PHA00542 27 LIRAGWSQEQIADATDVSQPTICRIYSGRHK----DPRYSVVEKLR 68 (82)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHcCCCC----CCCHHHHHHHH
Confidence 3345689999999999999999987764321 23445555543
No 349
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=40.44 E-value=57 Score=25.60 Aligned_cols=36 Identities=11% Similarity=0.212 Sum_probs=27.2
Q ss_pred hcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 129 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 129 ~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
..+.|.+-.|||+.++++.+...+....|.+.=.+.
T Consensus 11 ~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 11 EQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred HcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 348899999999999999999988777776654443
No 350
>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=40.13 E-value=43 Score=25.20 Aligned_cols=33 Identities=9% Similarity=0.045 Sum_probs=28.1
Q ss_pred CCCcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 132 ~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
...+..+||..+++++.+|......+.+.|++.
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 457889999999999999999999999999875
No 351
>PRK09492 treR trehalose repressor; Provisional
Probab=39.88 E-value=20 Score=36.00 Aligned_cols=43 Identities=19% Similarity=0.162 Sum_probs=29.4
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHhhh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKEL 278 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~~~ 278 (504)
+.|.+|||+.+|||.+|+++.|..- ..-+..|-+-+++...++
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~~--~~vs~~tr~rV~~~a~el 46 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNNE--SGVSEETRERVEAVINQH 46 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCCC--CCCCHHHHHHHHHHHHHH
Confidence 5799999999999999999999741 122333444454444433
No 352
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=39.67 E-value=3.9e+02 Score=26.51 Aligned_cols=39 Identities=15% Similarity=0.316 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHH
Q 010689 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (504)
Q Consensus 118 vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L 157 (504)
+.-++-|+.-. ...++++.++|+.+++++..|.+.|++.
T Consensus 185 i~~~~~~i~~~-~~~~isl~~lA~~~~lS~~~l~r~Fk~~ 223 (290)
T PRK10572 185 VREACQYISDH-LASEFDIESVAQHVCLSPSRLAHLFRQQ 223 (290)
T ss_pred HHHHHHHHHhc-ccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44455555433 3468889999999999888888777654
No 353
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=39.34 E-value=35 Score=26.04 Aligned_cols=31 Identities=26% Similarity=0.187 Sum_probs=24.7
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhccCC
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDS 263 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~ 263 (504)
...+.+..|+..+|...|++.|++.+.+.-.
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 4567788999999999999999999987644
No 354
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=39.33 E-value=39 Score=27.90 Aligned_cols=30 Identities=17% Similarity=0.248 Sum_probs=26.2
Q ss_pred cCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.|.++.-++|++.++++.+|||+-+..+.+
T Consensus 20 ~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~ 49 (78)
T PF03444_consen 20 TGEPVGSKTIAEELGRSPATIRNEMADLEE 49 (78)
T ss_pred cCCCcCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 477888899999999999999998887764
No 355
>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=39.29 E-value=19 Score=33.42 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.7
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeec
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
.||.|++... +...|.+.|..|+..++
T Consensus 36 aC~~C~kkv~--~~~~~~~~C~~C~~~~~ 62 (166)
T cd04476 36 ACPGCNKKVV--EEGNGTYRCEKCNKSVP 62 (166)
T ss_pred cccccCcccE--eCCCCcEECCCCCCcCC
Confidence 5999999732 22339999999999874
No 356
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=39.27 E-value=28 Score=32.38 Aligned_cols=24 Identities=21% Similarity=0.235 Sum_probs=21.8
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLI 256 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~k 256 (504)
...|.+|||..+|++++|++.|+.
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 568899999999999999999876
No 357
>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=39.22 E-value=3.9e+02 Score=26.34 Aligned_cols=26 Identities=8% Similarity=0.033 Sum_probs=22.5
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|+++||..+|+|..+|++..+.-
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~~~ra 246 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRLEKAA 246 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999876643
No 358
>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=39.18 E-value=48 Score=31.80 Aligned_cols=28 Identities=11% Similarity=0.229 Sum_probs=25.8
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
-..|+.+|++.++++..|+++.|+.|..
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~Le~ 41 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDLET 41 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3499999999999999999999999876
No 359
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=39.01 E-value=1.1e+02 Score=28.49 Aligned_cols=33 Identities=12% Similarity=-0.068 Sum_probs=28.6
Q ss_pred CCCcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 132 ~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
.|.|..+||+.+|++...+.+.+++|.+.=-|.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 678999999999999999999999998754343
No 360
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=38.84 E-value=20 Score=33.68 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=23.1
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...|.+|||..+|+|+.||+.++.--.
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar 171 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARAR 171 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 557899999999999999999886544
No 361
>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=38.78 E-value=19 Score=38.61 Aligned_cols=29 Identities=34% Similarity=0.693 Sum_probs=19.4
Q ss_pred CCCCCCCCCcccc-cCCCceecCcCceeec
Q 010689 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VC~~CG~Vle 31 (504)
.||+|+.-.-+.+ ...+...|..||.++.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 5999987532222 2345678999999885
No 362
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=38.71 E-value=17 Score=28.19 Aligned_cols=23 Identities=26% Similarity=0.700 Sum_probs=11.0
Q ss_pred CCCCCCCCcccccCCCceecCcCce
Q 010689 4 CSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 4 Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
|-.||..+.+- ....+-|.+||.
T Consensus 23 CgdC~~en~lk--~~D~irCReCG~ 45 (62)
T KOG3507|consen 23 CGDCGQENTLK--RGDVIRCRECGY 45 (62)
T ss_pred ecccccccccc--CCCcEehhhcch
Confidence 55666554322 122344666664
No 363
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=38.69 E-value=16 Score=35.15 Aligned_cols=29 Identities=28% Similarity=0.622 Sum_probs=18.0
Q ss_pred CCCCCCCCCc----ccc--cCCC-----ceecCcCceeec
Q 010689 3 WCSSCARHVT----GHR--PYDS-----QLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~i----v~D--~~~G-----~~VC~~CG~Vle 31 (504)
.||+||.... .++ |.-| ...|..||+=-.
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccc
Confidence 6999997522 122 2223 457999998543
No 364
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=38.66 E-value=48 Score=25.03 Aligned_cols=40 Identities=15% Similarity=0.218 Sum_probs=25.4
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 276 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~ 276 (504)
..+|+.++|+.+|++..||.+-++. ....++++.+.++..
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~----~~~~~~~~~l~~ia~ 48 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNG----KPSNPSLDTLEKIAK 48 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTT----T-----HHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc----ccccccHHHHHHHHH
Confidence 4569999999999999999988872 235788888888755
No 365
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.58 E-value=14 Score=32.60 Aligned_cols=36 Identities=11% Similarity=0.317 Sum_probs=19.8
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcccccccc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f 41 (504)
.+|+.||.... .+ ..+...|..||.- +-.+..|.+|
T Consensus 72 ~~C~~Cg~~~~-~~-~~~~~~CP~Cgs~--~~~i~~G~El 107 (117)
T PRK00564 72 LECKDCSHVFK-PN-ALDYGVCEKCHSK--NVIITQGNEM 107 (117)
T ss_pred EEhhhCCCccc-cC-CccCCcCcCCCCC--ceEEecCCEE
Confidence 37999995422 11 1244569999964 2234444443
No 366
>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=38.51 E-value=29 Score=32.07 Aligned_cols=25 Identities=8% Similarity=0.126 Sum_probs=22.4
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|.+|||..+|+++.||+.|+.-
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5688999999999999999998864
No 367
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=38.50 E-value=23 Score=36.01 Aligned_cols=44 Identities=18% Similarity=0.055 Sum_probs=29.7
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHhhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKEL 278 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~~~ 278 (504)
.+.|.+|||+.+|||.+|+++.|..= -.-+.-|-+..++...++
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~--~~vs~~tr~~V~~~a~el 48 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSGK--GRISTATGERVNQAIEEL 48 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCCC--CCCCHHHHHHHHHHHHHh
Confidence 46899999999999999999998631 112233444455544443
No 368
>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=38.37 E-value=1.1e+02 Score=24.17 Aligned_cols=67 Identities=7% Similarity=0.162 Sum_probs=34.4
Q ss_pred HHHHcCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhc--CCCCcHHHHHHHhCc-ChHHHHHHHHHH
Q 010689 81 MKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK--SKPFLLIDFSNYLNI-NVYELGAVYLQL 157 (504)
Q Consensus 81 i~~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~~--~~p~tL~dIs~~~~v-s~~~Lg~~~~~L 157 (504)
+|+.|+++ ... -..+|+......+.+ .+...=+-.|++.- +...++.|||..+|. +...+.+.|++.
T Consensus 1 lA~~~~~s--~~~---l~~~f~~~~g~s~~~-----~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~ 70 (81)
T PF12833_consen 1 LADELGMS--ERY---LSRIFKKETGMSFKQ-----YLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRY 70 (81)
T ss_dssp HHHHCTS---HHH---HHHHHHHHHSS-HHH-----HHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHH
T ss_pred ChHHhCcC--HHH---HHHHHHHHHCcCHHH-----HHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHH
Confidence 56778887 332 333555554433322 22233344444432 367899999999995 466666655544
No 369
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=38.34 E-value=4.2e+02 Score=26.47 Aligned_cols=27 Identities=15% Similarity=0.149 Sum_probs=23.2
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
....|+++||..+|+|..||++++...
T Consensus 229 ~~~~t~~EIA~~lgis~~~V~~~~~ra 255 (264)
T PRK07122 229 FESMTQTQIAERVGISQMHVSRLLAKT 255 (264)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899999999999999999976643
No 370
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=38.27 E-value=30 Score=34.29 Aligned_cols=28 Identities=11% Similarity=0.322 Sum_probs=25.7
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
-.++++++++.++||+.|||+-++++..
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4799999999999999999999999865
No 371
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=38.25 E-value=26 Score=28.90 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=20.7
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
+||.|....+.. ..+.+.| .||.-+.-
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 699999987766 5688888 67866653
No 372
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=38.20 E-value=71 Score=25.43 Aligned_cols=36 Identities=14% Similarity=0.009 Sum_probs=31.6
Q ss_pred HHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhc
Q 010689 127 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLY 162 (504)
Q Consensus 127 CR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~ 162 (504)
.|..+.|+++.+.++.+|+++..+.+....+.+-|-
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll 42 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLL 42 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 467889999999999999999999998888877663
No 373
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=38.19 E-value=1.3e+02 Score=29.13 Aligned_cols=32 Identities=22% Similarity=0.289 Sum_probs=27.7
Q ss_pred CCCcHHHHHHHhCcChHHHHHHHHHHHHHhcc
Q 010689 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (504)
Q Consensus 132 ~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i 163 (504)
.|.+..+||+.+|++..++.|+.++|.+.=-|
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~GlI 209 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDRGLI 209 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCcE
Confidence 57889999999999999999999998875433
No 374
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.01 E-value=15 Score=32.40 Aligned_cols=36 Identities=19% Similarity=0.447 Sum_probs=20.2
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcccccccc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f 41 (504)
.+|+.||...... ......|..||.. +-.+..|.+|
T Consensus 71 ~~C~~Cg~~~~~~--~~~~~~CP~Cgs~--~~~i~~G~El 106 (114)
T PRK03681 71 CWCETCQQYVTLL--TQRVRRCPQCHGD--MLRIVADDGL 106 (114)
T ss_pred EEcccCCCeeecC--CccCCcCcCcCCC--CcEEccCCeE
Confidence 3799999642211 1233669999964 2334455443
No 375
>PF14493 HTH_40: Helix-turn-helix domain
Probab=37.99 E-value=58 Score=27.03 Aligned_cols=47 Identities=23% Similarity=0.304 Sum_probs=37.1
Q ss_pred HHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHH
Q 010689 228 ALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARK 275 (504)
Q Consensus 228 a~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~ 275 (504)
.++.....|+.+||..-+++++||...+-++....- .+.+++|...+
T Consensus 7 ~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~-~~~~~~~l~~e 53 (91)
T PF14493_consen 7 YELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGE-PLDIEELLSEE 53 (91)
T ss_pred HHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCC-CCCHHHhCCHH
Confidence 345556799999999999999999999999986522 37778775543
No 376
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=37.96 E-value=50 Score=25.92 Aligned_cols=30 Identities=10% Similarity=0.050 Sum_probs=24.8
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+.+++-.|||+.+|+|..++|.-|..+...
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~e 42 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKE 42 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHC
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 567888999999999999999999888653
No 377
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=37.94 E-value=1.8e+02 Score=27.93 Aligned_cols=120 Identities=16% Similarity=0.229 Sum_probs=68.1
Q ss_pred hHHHHHHHHHHHHhcCCCCcHHHHHHHhCc-ChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHH
Q 010689 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKV 194 (504)
Q Consensus 116 ~~vaAACLYiACR~~~~p~tL~dIs~~~~v-s~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V 194 (504)
..++.|.+|. .+.|.++++++.++++ +...+......+.....-.. +. |..+.+...+ .+...
T Consensus 10 ~~~vEall~a----~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~rg-------~~----L~~~~~~~r~-~t~~~ 73 (184)
T COG1386 10 KALIEALLFA----GGEPLSLKELAEILGIVSADAIIDALAELKEEYEDRG-------LE----LVEVAEGWRL-QTKQE 73 (184)
T ss_pred HHHHHHHHHh----cCCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCCC-------ee----EEEEcCceeE-EehHH
Confidence 3456666664 4789999999999998 77777776666666542111 00 0011111100 01111
Q ss_pred HHHHHHHHHHhcccccccCCCh-hHHHHHHH-HHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 195 CDTARDILASMKRDWITTGRKP-SGLCGAAL-YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 195 ~~~A~~I~~~~~~~~l~~GR~P-~~IAAAal-ylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.-.++..+. +..| ..+--|++ -+|...+..++|..+|.++-||....+-+.|.++..
T Consensus 74 ---~~~~~~~l~------~~~~~~~LSraalEtLAiIAY~QPiTR~eI~~iRGv~~~~~i~~L~e~gl 132 (184)
T COG1386 74 ---YAEYLEKLQ------EQRPKRELSRAALETLAIIAYKQPVTRSEIEEIRGVAVSQVISTLLERGL 132 (184)
T ss_pred ---HHHHHHHHh------cccccccccHHHHHHHHHHHHcCCccHHHHHHHhCccHHHHHHHHHHCCC
Confidence 111121111 1111 23434444 455566789999999999999998887777777653
No 378
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=37.71 E-value=18 Score=41.32 Aligned_cols=25 Identities=20% Similarity=0.481 Sum_probs=16.1
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
.||+||.. ...|.-.|.+||.-+..
T Consensus 29 ~Cp~CG~~-----~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 29 PCPQCGTE-----VPVDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCC-----CCcccccccccCCcccc
Confidence 35555554 23577788888887654
No 379
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=37.57 E-value=69 Score=36.43 Aligned_cols=70 Identities=13% Similarity=0.165 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHhCcccCCCchhHHHH--HHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhcc
Q 010689 92 EIVHVAKRFYGIAVARNFTKGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (504)
Q Consensus 92 ~i~e~A~~iyk~a~~~~~~rGR~~~~vaA--ACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i 163 (504)
.|++....+|..-.+.=..++|+...+.| .|+|++-+ -+..+|.+|...+|-+..++..++++|.+.+..
T Consensus 528 ~I~~~Va~~f~v~~~dl~s~~R~~~i~~aRqiAMYL~r~--lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 528 AIMAATADYFGLTVEDLCGTSRSRVLVTARQIAMYLCRE--LTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred HHHHHHHHHhCCCHHHHhCCCCCcccchHHHHHHHHHHH--HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 44444444444332211223344333333 67887655 445788999999999999999999999997754
No 380
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=37.52 E-value=5.3e+02 Score=27.44 Aligned_cols=26 Identities=8% Similarity=0.018 Sum_probs=22.5
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|+++|+..+|||..+||+....-
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQie~rA 355 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQIEAKA 355 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999999876543
No 381
>PF06892 Phage_CP76: Phage regulatory protein CII (CP76); InterPro: IPR009679 This entry is represented by Bacteriophage 186, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny [].
Probab=37.32 E-value=37 Score=31.78 Aligned_cols=38 Identities=16% Similarity=0.277 Sum_probs=31.6
Q ss_pred CHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHh
Q 010689 236 SKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 276 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~ 276 (504)
..++||..+|++..|+|+++.- ....+||+.|+..+..
T Consensus 22 ~~~~lA~~lGm~~~~LrNKLNP---~q~H~Lt~~el~~i~~ 59 (162)
T PF06892_consen 22 NMAALAERLGMNPQTLRNKLNP---EQPHKLTVDELIAITD 59 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHcCC---CCCCCCCHHHHHHHHH
Confidence 3689999999999999999864 2357999999988744
No 382
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=37.27 E-value=17 Score=28.37 Aligned_cols=27 Identities=4% Similarity=-0.162 Sum_probs=17.3
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeeccCcc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (504)
+.|++||...+ -.-||. ||+--+..++
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 46888887533 345788 8876554443
No 383
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=37.20 E-value=12 Score=28.20 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=18.9
Q ss_pred CCCCCCCCCcccc---cCCCceecCcCceee
Q 010689 3 WCSSCARHVTGHR---PYDSQLCCDRCGKVL 30 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D---~~~G~~VC~~CG~Vl 30 (504)
.|+-||...-.+. -.+| +||.+|--=+
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 4999998743332 4678 7999998544
No 384
>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=37.13 E-value=62 Score=24.04 Aligned_cols=27 Identities=15% Similarity=0.338 Sum_probs=23.6
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.+++.+|++.++++.+|+.+.++.+..
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 499999999999999999999988764
No 385
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=36.88 E-value=4.2e+02 Score=26.03 Aligned_cols=27 Identities=4% Similarity=0.133 Sum_probs=23.5
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
-...|.++||...|+|+.||+.++...
T Consensus 215 ~~~~s~~EIA~~lgis~~tV~~~~~ra 241 (251)
T PRK07670 215 KEELTLTEIGQVLNLSTSRISQIHSKA 241 (251)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 367899999999999999999988654
No 386
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=36.84 E-value=28 Score=24.31 Aligned_cols=25 Identities=20% Similarity=0.554 Sum_probs=16.3
Q ss_pred CCCCCCCCCCccccc---CCC--ceecCcC
Q 010689 2 VWCSSCARHVTGHRP---YDS--QLCCDRC 26 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~---~~G--~~VC~~C 26 (504)
+.||.|+++..+..+ ..| -+-|.+|
T Consensus 6 v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 479999999734332 233 5677777
No 387
>PRK01381 Trp operon repressor; Provisional
Probab=36.78 E-value=28 Score=30.03 Aligned_cols=37 Identities=11% Similarity=0.072 Sum_probs=29.6
Q ss_pred HHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccC
Q 010689 226 VSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (504)
Q Consensus 226 lAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~ 262 (504)
++..+..-..||++|+...|||.+||.+-=+.+...+
T Consensus 47 I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~ 83 (99)
T PRK01381 47 IVEELLRGELSQREIKQELGVGIATITRGSNSLKTAP 83 (99)
T ss_pred HHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCC
Confidence 4444556679999999999999999998888776543
No 388
>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=36.62 E-value=36 Score=32.37 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=28.4
Q ss_pred hcCCCCCHhhHHhhhccC-HHHHHHHHHHhhcc
Q 010689 230 THGLKFSKSDIVKIVHIC-EATLMKRLIEFENT 261 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vs-e~TIrkr~kE~~~t 261 (504)
-.++..|++|||+.++++ .+|++++++.+..-
T Consensus 21 ~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 21 STGYPPSIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred hcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 357889999999999998 99999999998754
No 389
>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=36.60 E-value=90 Score=24.43 Aligned_cols=38 Identities=16% Similarity=0.175 Sum_probs=26.5
Q ss_pred CchhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHH
Q 010689 113 RRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 153 (504)
Q Consensus 113 R~~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~ 153 (504)
|++..=-|==+|+. ++--++++|||+.++|+..+|++-
T Consensus 5 Rsp~rdkA~e~y~~---~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 5 RSPNRDKAFEIYKE---SNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCcCHHHHHHHHHH---hCCCccHHHHHHHHCCCHHHHHHH
Confidence 44444444445533 555689999999999999998753
No 390
>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=36.54 E-value=22 Score=39.31 Aligned_cols=29 Identities=21% Similarity=0.502 Sum_probs=21.2
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
..||+|+.. +.+....+.+.|..||....
T Consensus 223 ~~C~~C~~~-l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 223 LCCPNCDVS-LTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred cCCCCCCCc-eEEecCCCeEEcCCCcCcCC
Confidence 368888876 33434678999999998754
No 391
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=36.45 E-value=17 Score=32.83 Aligned_cols=27 Identities=19% Similarity=0.015 Sum_probs=22.9
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...|.+|||..+|+++.||+.|+.--.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar 147 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRAR 147 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467889999999999999998876543
No 392
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=36.45 E-value=70 Score=28.77 Aligned_cols=46 Identities=9% Similarity=0.112 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 116 ~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
+.-+-+.+|++-...|.+.+..+||..++|+...|.+++..|.+.=
T Consensus 8 ~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~G 53 (141)
T PRK11014 8 DYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAG 53 (141)
T ss_pred hHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCC
Confidence 3445566777765567788999999999999999999999888753
No 393
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=36.44 E-value=1.3e+02 Score=29.94 Aligned_cols=14 Identities=14% Similarity=0.009 Sum_probs=9.6
Q ss_pred CCCceecCcCceee
Q 010689 17 YDSQLCCDRCGKVL 30 (504)
Q Consensus 17 ~~G~~VC~~CG~Vl 30 (504)
..|++++-..|.+.
T Consensus 72 ~~g~~i~i~p~~~h 85 (290)
T PRK10572 72 RPGDLLLFPPGEIH 85 (290)
T ss_pred CCCCEEEECCCCce
Confidence 45777777777764
No 394
>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=36.38 E-value=70 Score=24.33 Aligned_cols=38 Identities=16% Similarity=0.160 Sum_probs=26.8
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 123 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 123 LYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
|+..+ ..+-|.++.+|++.++++...+.+..++|.+.=
T Consensus 9 L~~l~-~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~g 46 (68)
T PF13463_consen 9 LRALA-HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKG 46 (68)
T ss_dssp HHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHHHHTT
T ss_pred HHHHH-ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 33333 667889999999999999999999888887753
No 395
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=36.31 E-value=1.5e+02 Score=25.12 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=21.9
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
.-.+...|+.+|++..|++++++.+.
T Consensus 68 ~gn~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 68 RGNQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 34477889999999999999999863
No 396
>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=36.21 E-value=16 Score=34.03 Aligned_cols=27 Identities=19% Similarity=0.618 Sum_probs=14.4
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccCcccc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFST 37 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~ 37 (504)
.|..||...+ ..|.+|+.=+.....++
T Consensus 30 fC~kCG~~tI--------~~Cp~C~~~IrG~y~v~ 56 (158)
T PF10083_consen 30 FCSKCGAKTI--------TSCPNCSTPIRGDYHVE 56 (158)
T ss_pred HHHHhhHHHH--------HHCcCCCCCCCCceecC
Confidence 4666665432 24777776655444333
No 397
>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=36.01 E-value=42 Score=24.43 Aligned_cols=40 Identities=5% Similarity=0.091 Sum_probs=29.7
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHh
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKK 276 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~ 276 (504)
....|+.++|..+||+..||++-.+-- ...+++.+..+..
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~g~-----~~~~~~~~~~i~~ 52 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVENGK-----PTVRLDKVLRVLD 52 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCCC-----CCCCHHHHHHHHH
Confidence 457899999999999999998875421 2456777766643
No 398
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.99 E-value=78 Score=25.61 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=25.7
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
..++++|+..++++..||.+.++.|.+.
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 6899999999999999999999998763
No 399
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=35.92 E-value=33 Score=31.40 Aligned_cols=25 Identities=28% Similarity=0.224 Sum_probs=21.8
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|.+|||..+|+++.|++.|+.-
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~r 157 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHY 157 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4678999999999999999988754
No 400
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=35.86 E-value=37 Score=26.23 Aligned_cols=23 Identities=22% Similarity=0.245 Sum_probs=19.7
Q ss_pred CHhhHHhhhccCHHHHHHHHHHh
Q 010689 236 SKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
+..|||+.+||+..|||..-+++
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~g 24 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 57899999999999999776653
No 401
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=35.84 E-value=1.3e+02 Score=27.66 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=26.4
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
++++..+|+..+|++..|+.+.+.+|..-
T Consensus 170 ~~~~~~~ia~~~g~~~~~vsr~l~~l~~~ 198 (214)
T COG0664 170 LPLTHKDLAEYLGLSRETVSRILKELRKD 198 (214)
T ss_pred ccCCHHHHHHHhCCchhhHHHHHHHHHhC
Confidence 67999999999999999999999998753
No 402
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=35.83 E-value=25 Score=35.81 Aligned_cols=30 Identities=17% Similarity=0.417 Sum_probs=21.4
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeecc
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee 32 (504)
..|+.||+.....+ ..=..+|++||...=.
T Consensus 112 RFCg~CG~~~~~~~-~g~~~~C~~cg~~~fP 141 (279)
T COG2816 112 RFCGRCGTKTYPRE-GGWARVCPKCGHEHFP 141 (279)
T ss_pred cCCCCCCCcCcccc-CceeeeCCCCCCccCC
Confidence 37999999854332 2337899999997644
No 403
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=35.63 E-value=35 Score=30.68 Aligned_cols=26 Identities=4% Similarity=0.014 Sum_probs=22.5
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|.+|||...|+++.||+.++..-
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra 146 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRA 146 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46789999999999999999887653
No 404
>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=35.51 E-value=28 Score=24.66 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=16.5
Q ss_pred CCCCCCCCC---CcccccCCCceecCcCcee
Q 010689 2 VWCSSCARH---VTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 2 ~~Cp~Cgs~---~iv~D~~~G~~VC~~CG~V 29 (504)
++|..|++- -..+|......+|.-||..
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 689999985 2346666678999999985
No 405
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=35.47 E-value=30 Score=26.70 Aligned_cols=24 Identities=17% Similarity=0.098 Sum_probs=21.3
Q ss_pred CHhhHHhhhccCHHHHHHHHHHhh
Q 010689 236 SKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
|.+|||+.+||+..|||.--+++.
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 578999999999999999887766
No 406
>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=35.42 E-value=48 Score=27.90 Aligned_cols=21 Identities=24% Similarity=0.099 Sum_probs=18.9
Q ss_pred CCCCHhhHHhhhccCHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMK 253 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrk 253 (504)
...|.++||+.+|||.+||.+
T Consensus 49 ~G~S~~eIA~~LgISrsTIyR 69 (88)
T TIGR02531 49 QGKTYSDIEAETGASTATISR 69 (88)
T ss_pred CCCCHHHHHHHHCcCHHHHHH
Confidence 346999999999999999988
No 407
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=35.42 E-value=93 Score=29.98 Aligned_cols=30 Identities=10% Similarity=0.247 Sum_probs=26.8
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhccC
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t~ 262 (504)
++.++++||..+|++..|+.+-+++|.+..
T Consensus 172 i~~t~~~iA~~lG~tretvsR~l~~L~~~g 201 (236)
T PRK09392 172 LPYEKRVLASYLGMTPENLSRAFAALASHG 201 (236)
T ss_pred eeCCHHHHHHHhCCChhHHHHHHHHHHhCC
Confidence 567789999999999999999999998754
No 408
>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=35.35 E-value=21 Score=36.93 Aligned_cols=27 Identities=19% Similarity=0.489 Sum_probs=18.1
Q ss_pred CCCCCCCCCc---ccc--cCCC--ceecCcCcee
Q 010689 3 WCSSCARHVT---GHR--PYDS--QLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~i---v~D--~~~G--~~VC~~CG~V 29 (504)
.||.||+..+ +.. ..+| .+.|.-||+-
T Consensus 186 ~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~te 219 (305)
T TIGR01562 186 LCPACGSPPVASMVRQGGKETGLRYLSCSLCATE 219 (305)
T ss_pred cCCCCCChhhhhhhcccCCCCCceEEEcCCCCCc
Confidence 7999999853 222 1344 7788888774
No 409
>PRK09954 putative kinase; Provisional
Probab=35.34 E-value=48 Score=34.48 Aligned_cols=29 Identities=10% Similarity=0.334 Sum_probs=26.9
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+-++|+.+|++.++||..||++|++.+.+
T Consensus 15 ~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 15 NPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45899999999999999999999999886
No 410
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=35.33 E-value=23 Score=35.83 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=22.0
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHH
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
+.|.+|||+.+|||.+|+++.|..
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhhCC
Confidence 579999999999999999999964
No 411
>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=35.17 E-value=53 Score=25.03 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=23.7
Q ss_pred cCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 231 HGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 231 ~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.+-+.++++|++.++++..|+.+.++.+.+
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 467899999999999999999999988764
No 412
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=35.05 E-value=25 Score=38.03 Aligned_cols=30 Identities=30% Similarity=0.615 Sum_probs=20.3
Q ss_pred CCCCCCCCCcccc-cCCCceecCcCceeecc
Q 010689 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLED 32 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VC~~CG~Vlee 32 (504)
.||+|+.-.-..+ ...+...|..||.++..
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 5999997532222 23346889999999854
No 413
>cd00131 PAX Paired Box domain
Probab=35.00 E-value=50 Score=29.50 Aligned_cols=30 Identities=17% Similarity=0.227 Sum_probs=26.3
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhccC
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t~ 262 (504)
...+..+||..++|+..||.+.++.|.++.
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 457999999999999999999998888764
No 414
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=34.99 E-value=52 Score=30.47 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=22.8
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...|.+|||..+|+++.|++.++..-.
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346899999999999999998877653
No 415
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.88 E-value=37 Score=30.33 Aligned_cols=25 Identities=4% Similarity=-0.118 Sum_probs=22.2
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|.+|||...|+++.||++++..
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4688999999999999999998764
No 416
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=34.84 E-value=71 Score=22.79 Aligned_cols=31 Identities=10% Similarity=0.075 Sum_probs=27.5
Q ss_pred CcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 134 FLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 134 ~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
.+..+||..++++...+.+....+.+.|+.+
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 5889999999999999999888888888764
No 417
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=34.80 E-value=57 Score=30.27 Aligned_cols=37 Identities=14% Similarity=0.145 Sum_probs=29.8
Q ss_pred HHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 223 alylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+||.... .+.....++||...+|+.+|+.+-++.+..
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~ 50 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLER 50 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHH
Confidence 4565544 566788999999999999999988888764
No 418
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=34.78 E-value=36 Score=33.48 Aligned_cols=29 Identities=21% Similarity=0.419 Sum_probs=25.9
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
|--.|+.|++..+++|..||++.++++..
T Consensus 103 gglLT~~Dla~LL~~S~~TI~~~i~~yq~ 131 (220)
T PF07900_consen 103 GGLLTQEDLAMLLGISPRTISKDIKEYQK 131 (220)
T ss_pred CCcccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44578999999999999999999999875
No 419
>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=34.77 E-value=26 Score=26.36 Aligned_cols=24 Identities=25% Similarity=0.221 Sum_probs=17.6
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHH
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
..++.+||..+||+.+||+.-++.
T Consensus 22 g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 22 GESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp TT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Confidence 338999999999999999987653
No 420
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=34.74 E-value=20 Score=22.81 Aligned_cols=10 Identities=40% Similarity=0.953 Sum_probs=8.1
Q ss_pred CCCCCCCCCC
Q 010689 1 MVWCSSCARH 10 (504)
Q Consensus 1 m~~Cp~Cgs~ 10 (504)
|+.||.||..
T Consensus 2 l~~C~~CgR~ 11 (25)
T PF13913_consen 2 LVPCPICGRK 11 (25)
T ss_pred CCcCCCCCCE
Confidence 5789999876
No 421
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=34.73 E-value=78 Score=26.54 Aligned_cols=36 Identities=8% Similarity=0.039 Sum_probs=29.6
Q ss_pred HHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 225 YVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 225 ylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.|+-++.+-..++.++|..+|||..|..|.+.-|..
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 455556667788999999999999999998888764
No 422
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=34.50 E-value=37 Score=27.36 Aligned_cols=27 Identities=11% Similarity=0.148 Sum_probs=21.0
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...|..+||+.++||++||.+-.+.+.
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkLG 59 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKLG 59 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHCT
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHhC
Confidence 457899999999999999999888764
No 423
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=34.49 E-value=36 Score=31.22 Aligned_cols=25 Identities=8% Similarity=0.150 Sum_probs=22.4
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|.+|||..+|+++.||+.+++.
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~r 157 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVE 157 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5688999999999999999998864
No 424
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=34.45 E-value=35 Score=26.31 Aligned_cols=22 Identities=14% Similarity=0.064 Sum_probs=19.1
Q ss_pred CHhhHHhhhccCHHHHHHHHHH
Q 010689 236 SKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE 257 (504)
|.+++|+.+||+..||+...++
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 6789999999999999977554
No 425
>smart00351 PAX Paired Box domain.
Probab=34.29 E-value=53 Score=29.14 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=25.4
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhccC
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFENTD 262 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~t~ 262 (504)
..+..+||+.+||+..||.+-++.|.++.
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~~G 61 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYETG 61 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcC
Confidence 45889999999999999999998887654
No 426
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=34.23 E-value=19 Score=33.31 Aligned_cols=24 Identities=13% Similarity=0.032 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHHHHHhCcccCCCc
Q 010689 91 DEIVHVAKRFYGIAVARNFTKGRR 114 (504)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~ 114 (504)
+...++|..|..--.+..-++|.-
T Consensus 99 ~~FAeEAR~iHyGea~~R~I~G~a 122 (148)
T PF06676_consen 99 DRFAEEARKIHYGEAEERGIYGEA 122 (148)
T ss_pred HHHHHHHHHHHcCCCccccCcCcC
Confidence 677777777655433444455654
No 427
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=34.22 E-value=56 Score=31.64 Aligned_cols=26 Identities=31% Similarity=0.362 Sum_probs=23.0
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
+++.+|||+.+|||.+|+..+|+.-.
T Consensus 178 ~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 178 RVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 47899999999999999999998643
No 428
>PRK10130 transcriptional regulator EutR; Provisional
Probab=34.11 E-value=2.9e+02 Score=29.01 Aligned_cols=54 Identities=19% Similarity=0.374 Sum_probs=38.8
Q ss_pred hhHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 010689 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 182 (504)
Q Consensus 115 ~~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~ 182 (504)
...+..++-|+--. ...|+++.|||..++++...|.+.|++. ++ ..|..||.++
T Consensus 239 ~~~v~~~~~~i~~~-~~~~ltv~~lA~~~gvS~r~L~r~Fk~~---~G----------~sp~~ylr~~ 292 (350)
T PRK10130 239 RRLLSRAREYVLEN-MSEPVTVLDLCNQLHVSRRTLQNAFHAI---LG----------IGPNAWLKRI 292 (350)
T ss_pred HHHHHHHHHHHHhh-hcCCCCHHHHHHHHCCCHHHHHHHHHHH---HC----------cCHHHHHHHH
Confidence 34455666676544 4568999999999999999998888754 43 4466777643
No 429
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=33.95 E-value=37 Score=31.23 Aligned_cols=25 Identities=8% Similarity=0.155 Sum_probs=21.9
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...+.+|||..+|+++.||+.++.-
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4588999999999999999998753
No 430
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=33.88 E-value=27 Score=23.93 Aligned_cols=23 Identities=26% Similarity=0.616 Sum_probs=11.9
Q ss_pred CCCCCCCCCcccccCCCceecCcCce
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
.|+.||-. ++...--.+|..||.
T Consensus 4 ~C~~CG~i---~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 4 VCPVCGYI---HEGEEAPEKCPICGA 26 (34)
T ss_pred ECCCCCCE---eECCcCCCcCcCCCC
Confidence 47777743 221122347777775
No 431
>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=33.86 E-value=74 Score=29.83 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=25.4
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
-.|+++||..+++|..|+.+.+++|.+.
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 3789999999999999999999999864
No 432
>PRK07218 replication factor A; Provisional
Probab=33.84 E-value=21 Score=38.69 Aligned_cols=31 Identities=19% Similarity=0.430 Sum_probs=20.5
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccCccccccccc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFV 42 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id~~~~f~ 42 (504)
.||.|+... ....|..||.| +...+.-..|.
T Consensus 299 rCP~C~r~v-------~~~~C~~hG~v--e~~~dlrik~v 329 (423)
T PRK07218 299 RCPECGRVI-------QKGQCRSHGAV--EGEDDLRIKAI 329 (423)
T ss_pred cCcCccccc-------cCCcCCCCCCc--CCeeeeEEEEE
Confidence 699999863 22699999998 33444333443
No 433
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=33.83 E-value=24 Score=27.78 Aligned_cols=22 Identities=27% Similarity=0.693 Sum_probs=14.2
Q ss_pred CCCCCCCCCcccccCCCceecCcCcee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.|.+|+.- . ....-+|..||.-
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 2345678888863
No 434
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=33.79 E-value=76 Score=24.07 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=23.8
Q ss_pred CHhhHHhhhccCHHHHHHHHHHhhccC
Q 010689 236 SKSDIVKIVHICEATLMKRLIEFENTD 262 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~~~t~ 262 (504)
+....|+..+++.+||.++++.+.+.-
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~l 41 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEEL 41 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHHh
Confidence 777889999999999999999987643
No 435
>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=33.76 E-value=37 Score=31.84 Aligned_cols=27 Identities=26% Similarity=0.240 Sum_probs=23.3
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...|.+|||..+|+|+.||+.|+.--.
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar 172 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGR 172 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 458899999999999999999876543
No 436
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.73 E-value=24 Score=36.53 Aligned_cols=27 Identities=19% Similarity=0.465 Sum_probs=17.2
Q ss_pred CCCCCCCCCc---c-cccCCC--ceecCcCcee
Q 010689 3 WCSSCARHVT---G-HRPYDS--QLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~i---v-~D~~~G--~~VC~~CG~V 29 (504)
.||.||+..+ + ....+| .+.|.-||+-
T Consensus 189 ~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~te 221 (309)
T PRK03564 189 FCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESE 221 (309)
T ss_pred CCCCCCCcchhheeeccCCCCceEEEcCCCCCc
Confidence 6999999853 1 112344 6777777763
No 437
>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=33.64 E-value=69 Score=25.22 Aligned_cols=36 Identities=14% Similarity=0.157 Sum_probs=25.0
Q ss_pred HhcCCCCcHHHHHHHhCcC-hHHHHHHHHHHHHHhcc
Q 010689 128 RQKSKPFLLIDFSNYLNIN-VYELGAVYLQLCQVLYI 163 (504)
Q Consensus 128 R~~~~p~tL~dIs~~~~vs-~~~Lg~~~~~L~~~L~i 163 (504)
..+|.|-|++||++.+|++ ...+....+.|.+.=.|
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I 56 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYI 56 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSE
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCc
Confidence 4689999999999999996 87777766666554333
No 438
>PRK09480 slmA division inhibitor protein; Provisional
Probab=33.45 E-value=49 Score=30.57 Aligned_cols=43 Identities=14% Similarity=0.198 Sum_probs=31.1
Q ss_pred ChhHHHHHHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 215 KPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 215 ~P~~IAAAalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
+..-|.-|++-+...-.|...|+++||+.+||+..||-..++.
T Consensus 11 ~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 11 RREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence 3344555555544443467899999999999999999877654
No 439
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=33.35 E-value=35 Score=34.11 Aligned_cols=29 Identities=14% Similarity=0.211 Sum_probs=25.8
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.-.++++|+++.++||+.|||+-+.++.+
T Consensus 17 ~~~~~~~ela~~l~vS~~TiRRdL~~Le~ 45 (252)
T PRK10906 17 QGYVSTEELVEHFSVSPQTIRRDLNDLAE 45 (252)
T ss_pred cCCEeHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34689999999999999999999998875
No 440
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=33.33 E-value=27 Score=27.39 Aligned_cols=20 Identities=25% Similarity=0.559 Sum_probs=13.2
Q ss_pred CCCCCCCCCcccccCCCceecCcCcee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.|.+|+.-. +.. .|..||..
T Consensus 5 AC~~C~~i~---~~~----~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYIT---TED----RCPVCGSR 24 (61)
T ss_pred hhhhCCccc---CCC----cCCCCcCC
Confidence 688888632 211 69999983
No 441
>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=33.30 E-value=22 Score=27.10 Aligned_cols=27 Identities=30% Similarity=0.576 Sum_probs=18.5
Q ss_pred CCCCCCCCCC-c--ccccCCCceecCcCce
Q 010689 2 VWCSSCARHV-T--GHRPYDSQLCCDRCGK 28 (504)
Q Consensus 2 ~~Cp~Cgs~~-i--v~D~~~G~~VC~~CG~ 28 (504)
+.|++|.+.+ . ..+...-.++|..||.
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCC
Confidence 3688887753 2 3445556888999986
No 442
>PRK12366 replication factor A; Reviewed
Probab=33.26 E-value=19 Score=40.96 Aligned_cols=24 Identities=33% Similarity=0.948 Sum_probs=19.7
Q ss_pred CCCCCCCCCcccccCCCceecCcCcee
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
.||.|+...+ + ..|.+.|..||.+
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 6999988632 2 4699999999998
No 443
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=33.20 E-value=73 Score=28.71 Aligned_cols=39 Identities=13% Similarity=0.285 Sum_probs=31.6
Q ss_pred HHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhccC
Q 010689 224 LYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENTD 262 (504)
Q Consensus 224 lylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~ 262 (504)
+|.+-.-.+-+.|..+||+.++.+.+|+.+.++-+.+..
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~G 70 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAG 70 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcC
Confidence 355543357789999999999999999999999887543
No 444
>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=33.19 E-value=53 Score=28.31 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=23.6
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...+..+||...|+++.||++++....
T Consensus 125 ~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 125 EGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 357899999999999999999988754
No 445
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=33.18 E-value=31 Score=35.08 Aligned_cols=42 Identities=19% Similarity=0.092 Sum_probs=29.5
Q ss_pred CCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHhhh
Q 010689 235 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKEL 278 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~~~ 278 (504)
.|.+|||+.+|||.+|+++.|+.- ..-+.-|.+-.++...++
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~--~~vs~~tr~~V~~~a~el 43 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKT--RFVAEETRNAVWAAIKEL 43 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC--CCCCHHHHHHHHHHHHHH
Confidence 589999999999999999999631 123344555555555443
No 446
>PHA00689 hypothetical protein
Probab=33.17 E-value=22 Score=26.58 Aligned_cols=10 Identities=50% Similarity=1.295 Sum_probs=6.0
Q ss_pred CceecCcCce
Q 010689 19 SQLCCDRCGK 28 (504)
Q Consensus 19 G~~VC~~CG~ 28 (504)
-.+.|..||.
T Consensus 16 ravtckrcgk 25 (62)
T PHA00689 16 RAVTCKRCGK 25 (62)
T ss_pred ceeehhhccc
Confidence 3456666665
No 447
>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=33.13 E-value=29 Score=34.94 Aligned_cols=42 Identities=14% Similarity=0.109 Sum_probs=29.0
Q ss_pred CCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHhhh
Q 010689 235 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKEL 278 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~~~ 278 (504)
.|.+|||+.+|||.+|+.+-|+.-. .-+.-|.+-.++...+|
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~--~vs~~tr~rV~~~a~~l 43 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNP--NVKPATRKKVLEVIKRL 43 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCC--CCCHHHHHHHHHHHHHH
Confidence 5889999999999999999996421 22333445555555444
No 448
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=33.09 E-value=39 Score=31.82 Aligned_cols=26 Identities=15% Similarity=0.165 Sum_probs=22.8
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...+.+|||..+|+|..|++.|+.-.
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra 181 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLA 181 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence 56899999999999999999987643
No 449
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=33.08 E-value=58 Score=35.34 Aligned_cols=68 Identities=13% Similarity=0.151 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHHHHHhCcccCCCchhHHHHH---HHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQAS---CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAA---CLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
+.|++....+|..-.+.=..++|+ ..++-| +.|++-+ -+..++.+|+..+|.+..++.+.++++.+.+
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 455555555554332211122333 334444 7888844 5566999999999999999999999998865
No 450
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=33.07 E-value=41 Score=30.44 Aligned_cols=26 Identities=19% Similarity=0.102 Sum_probs=22.6
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...+.+|||..+|++..||+.|+..-
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra 153 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKA 153 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45788899999999999999998653
No 451
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=32.99 E-value=43 Score=26.00 Aligned_cols=23 Identities=17% Similarity=0.156 Sum_probs=19.9
Q ss_pred CHhhHHhhhccCHHHHHHHHHHh
Q 010689 236 SKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
+..++|+.+||+..|||...+++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~~ 24 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREF 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc
Confidence 57899999999999999776664
No 452
>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=32.98 E-value=25 Score=36.34 Aligned_cols=9 Identities=44% Similarity=1.029 Sum_probs=4.9
Q ss_pred ecCcCceee
Q 010689 22 CCDRCGKVL 30 (504)
Q Consensus 22 VC~~CG~Vl 30 (504)
+|..||.-+
T Consensus 254 ~C~~C~~Yl 262 (305)
T TIGR01562 254 TCDSCQGYL 262 (305)
T ss_pred eccccccch
Confidence 555555544
No 453
>PRK05572 sporulation sigma factor SigF; Validated
Probab=32.93 E-value=4.8e+02 Score=25.59 Aligned_cols=26 Identities=12% Similarity=0.149 Sum_probs=22.7
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|+++||...|++..||+++.+.-
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ra 242 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKI 242 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 56999999999999999999876654
No 454
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=32.86 E-value=79 Score=30.02 Aligned_cols=37 Identities=16% Similarity=0.189 Sum_probs=30.0
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHH
Q 010689 123 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (504)
Q Consensus 123 LYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~ 159 (504)
||-..-..+.|.|+.||+.++|+|...+.-+.++|..
T Consensus 31 iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 4444445688999999999999999999888877754
No 455
>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=32.79 E-value=77 Score=23.29 Aligned_cols=35 Identities=14% Similarity=0.195 Sum_probs=26.2
Q ss_pred HHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHH
Q 010689 125 LACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (504)
Q Consensus 125 iACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~ 159 (504)
-+....+.|.++.||+..++++..++.+....|..
T Consensus 10 ~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 10 EALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34455677789999999999999988776666554
No 456
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=32.69 E-value=77 Score=23.08 Aligned_cols=26 Identities=8% Similarity=0.004 Sum_probs=24.0
Q ss_pred cHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 135 LLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 135 tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
+..++++.++++...+.+.+..|.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 89999999999999999999998874
No 457
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=32.64 E-value=47 Score=29.11 Aligned_cols=40 Identities=25% Similarity=0.287 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhcCCC-CCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 219 LCGAALYVSALTHGLK-FSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 219 IAAAalylAa~~~g~~-~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
|..+++.+... +|+. .|.++||+.+||+..||-+.+..-.
T Consensus 17 ii~aa~~l~~~-~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 17 ILDAALRLFAE-KGYAATTVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred HHHHHHHHHHH-cCcCCCCHHHHHHHhCCCcchhHHHcCCHH
Confidence 44444444443 7875 8999999999999999998887543
No 458
>PRK14873 primosome assembly protein PriA; Provisional
Probab=32.55 E-value=25 Score=40.27 Aligned_cols=27 Identities=19% Similarity=0.522 Sum_probs=19.8
Q ss_pred CCCCCCCCCCcccccCCCceecCcCcee
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~V 29 (504)
..||+|+..-. +....+.+.|..||..
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 46899987633 3335688999999984
No 459
>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=32.42 E-value=2.3e+02 Score=28.03 Aligned_cols=38 Identities=11% Similarity=0.181 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHH
Q 010689 119 QASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (504)
Q Consensus 119 aAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L 157 (504)
..++-||.-. ...++++.++|+.++++...|.+.|++.
T Consensus 189 ~~~~~~I~~~-~~~~~sl~~lA~~~~~S~~~l~r~Fk~~ 226 (287)
T TIGR02297 189 NRFNFLIEEN-YKQHLRLPEYADRLGISESRLNDICRRF 226 (287)
T ss_pred HHHHHHHHHh-hccCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3445566544 3458999999999999999999888764
No 460
>PRK12423 LexA repressor; Provisional
Probab=32.39 E-value=78 Score=30.41 Aligned_cols=31 Identities=13% Similarity=0.128 Sum_probs=27.3
Q ss_pred hcCCCCCHhhHHhhhc-cCHHHHHHHHHHhhc
Q 010689 230 THGLKFSKSDIVKIVH-ICEATLMKRLIEFEN 260 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~-Vse~TIrkr~kE~~~ 260 (504)
.+|+..|..|||+.+| +|.+|+++.++.+..
T Consensus 21 ~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~ 52 (202)
T PRK12423 21 QAGQPPSLAEIAQAFGFASRSVARKHVQALAE 52 (202)
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3577799999999999 599999999998876
No 461
>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=32.34 E-value=66 Score=28.75 Aligned_cols=40 Identities=15% Similarity=0.075 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 222 AALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 222 AalylAa~~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+.+|||..-.+..++.++||+..+++...+++-+..+...
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3566775434457899999999999999999999988754
No 462
>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=32.33 E-value=86 Score=22.47 Aligned_cols=32 Identities=9% Similarity=0.027 Sum_probs=28.1
Q ss_pred CCcHHHHHHHhCcChHHHHHHHHHHHHHhccc
Q 010689 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (504)
Q Consensus 133 p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~ 164 (504)
..+..+||..+++++..+.....++.+.++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 46999999999999999999988888888764
No 463
>PRK05580 primosome assembly protein PriA; Validated
Probab=32.25 E-value=28 Score=40.01 Aligned_cols=29 Identities=21% Similarity=0.531 Sum_probs=21.5
Q ss_pred CCCCCCCCCCcccccCCCceecCcCceeec
Q 010689 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
..||+|+.. +.+....+.+.|..||....
T Consensus 391 ~~C~~C~~~-l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 391 AECPHCDAS-LTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred cCCCCCCCc-eeEECCCCeEECCCCcCCCC
Confidence 368888875 44545678999999998743
No 464
>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=32.24 E-value=1.5e+02 Score=22.45 Aligned_cols=26 Identities=12% Similarity=0.097 Sum_probs=20.7
Q ss_pred CcHHHHHHHhCcChHHHHHHHHHHHH
Q 010689 134 FLLIDFSNYLNINVYELGAVYLQLCQ 159 (504)
Q Consensus 134 ~tL~dIs~~~~vs~~~Lg~~~~~L~~ 159 (504)
.++.|+|+.+||+...+....++-.+
T Consensus 24 ~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 57999999999999888776655443
No 465
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=32.20 E-value=3e+02 Score=23.00 Aligned_cols=31 Identities=6% Similarity=0.033 Sum_probs=27.2
Q ss_pred cCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 130 ~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
...+++..+||+.++++...+.++...|.+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5678999999999999999999988888664
No 466
>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=32.18 E-value=53 Score=26.77 Aligned_cols=31 Identities=13% Similarity=0.241 Sum_probs=24.8
Q ss_pred hcCCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 230 THGLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 230 ~~g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
+.+-.+++.++|....||.+||.+.++.+.+
T Consensus 26 l~~~~~s~~~la~~~~iS~sti~~~i~~l~~ 56 (87)
T PF05043_consen 26 LNNEYVSIEDLAEELFISRSTIYRDIKKLNK 56 (87)
T ss_dssp HH-SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3578899999999999999999999988764
No 467
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=32.10 E-value=58 Score=30.45 Aligned_cols=27 Identities=15% Similarity=0.206 Sum_probs=22.9
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFE 259 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~ 259 (504)
...|.+|||...|+++.||+.|+.--.
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar 172 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRAR 172 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 358899999999999999999876543
No 468
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=32.06 E-value=29 Score=35.99 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=5.7
Q ss_pred eecCcCceee
Q 010689 21 LCCDRCGKVL 30 (504)
Q Consensus 21 ~VC~~CG~Vl 30 (504)
.+|..||.-+
T Consensus 253 e~C~~C~~Yl 262 (309)
T PRK03564 253 ESCGDCGTYL 262 (309)
T ss_pred eecccccccc
Confidence 4566666554
No 469
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=32.01 E-value=89 Score=33.82 Aligned_cols=71 Identities=17% Similarity=0.217 Sum_probs=46.1
Q ss_pred hHHHHHHHHHHHHHHhCcccCCCchhHHHH--HHHHHHHHhcCCCCcHHHHHHHh-CcChHHHHHHHHHHHHHhcc
Q 010689 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYL-NINVYELGAVYLQLCQVLYI 163 (504)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA--ACLYiACR~~~~p~tL~dIs~~~-~vs~~~Lg~~~~~L~~~L~i 163 (504)
+.|++....+|..-.+.=..++|+...+.| .+.|++-+..+ .++.+|+..+ |-+..++..+++++.+.+..
T Consensus 360 ~~i~~~v~~~~~i~~~~l~~~~R~~~~~~aR~iamyl~~~~~~--~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 360 ENIQKVVAEYYNIKVSDLKSKSRTRNIARPRQIAMYLAKELTD--LSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred HHHHHHHHHHcCCCHHHHhCCCCCcccChHHHHHHHHHHHhcC--CCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence 445555555554333322233444333333 56787755544 5899999999 59999999999999998753
No 470
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=31.87 E-value=53 Score=34.73 Aligned_cols=39 Identities=21% Similarity=0.395 Sum_probs=30.5
Q ss_pred CCCCCCCCCcccc--cCCCceecCcC---ceeeccCcccccccc
Q 010689 3 WCSSCARHVTGHR--PYDSQLCCDRC---GKVLEDHNFSTEATF 41 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D--~~~G~~VC~~C---G~Vlee~~id~~~~f 41 (504)
.|..||.+++.+- ...|.+.|.+| |+|-.+..+..++..
T Consensus 41 ~C~RC~~~~~~~~~~lp~~~~YCr~Cl~mgRv~sd~~Ly~~~~~ 84 (441)
T COG4098 41 RCNRCGNTHIELFAKLPCGCLYCRNCLMMGRVRSDQKLYYWKPY 84 (441)
T ss_pred EehhcCCcchhhhcccccceEeehhhhhcccccccceeeecCCc
Confidence 6999997765432 34689999999 899999888888753
No 471
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=31.84 E-value=23 Score=31.05 Aligned_cols=32 Identities=13% Similarity=0.338 Sum_probs=22.7
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccCcc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~i 35 (504)
.|++||...++.-.= +.-.|..||..-.+..+
T Consensus 44 ~C~~Cg~~~~~~~SC-k~R~CP~C~~~~~~~W~ 75 (111)
T PF14319_consen 44 RCEDCGHEKIVYNSC-KNRHCPSCQAKATEQWI 75 (111)
T ss_pred ecCCCCceEEecCcc-cCcCCCCCCChHHHHHH
Confidence 699999887666533 44499999987655433
No 472
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=31.72 E-value=34 Score=34.46 Aligned_cols=43 Identities=16% Similarity=0.149 Sum_probs=29.0
Q ss_pred CHhhHHhhhccCHHHHHHHHHHhhc-cCCCCCChHHHHHHHhhh
Q 010689 236 SKSDIVKIVHICEATLMKRLIEFEN-TDSGSLTIEDFMARKKEL 278 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE~~~-t~~~~lt~~~~~~~~~~~ 278 (504)
|++|||+.+|||.+|+.+-|..-.. ...+.-|.+..++...++
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~~~~~~~Vs~~tr~rV~~~a~el 45 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREH 45 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHh
Confidence 7899999999999999999964321 012333555555554443
No 473
>PF14369 zf-RING_3: zinc-finger
Probab=31.66 E-value=28 Score=24.10 Aligned_cols=26 Identities=38% Similarity=0.902 Sum_probs=16.8
Q ss_pred CCCCCCCCCcccccCCCceecCcCce
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~ 28 (504)
||=.|....-+....+..+.|..|+-
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 78899987444333344556999973
No 474
>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=31.64 E-value=28 Score=32.56 Aligned_cols=129 Identities=15% Similarity=0.100 Sum_probs=0.0
Q ss_pred CCchhHHHHHHHHHHHHhcCC---------CCcHHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHH
Q 010689 112 GRRTEQVQASCLYLACRQKSK---------PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 182 (504)
Q Consensus 112 GR~~~~vaAACLYiACR~~~~---------p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~ 182 (504)
.++...+...+-+++-++... |.+++|||+.+|+++.+|.|+...-.=.......| -..|+.+-
T Consensus 19 ~~R~~TL~~v~~~iv~~Q~~ff~~g~~~l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~p-------lk~fF~~~ 91 (160)
T PF04552_consen 19 EQRNETLLRVAQAIVERQKDFFLGGPGALKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFP-------LKDFFSRS 91 (160)
T ss_dssp -------------------------------------------------------------------------S-----S
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeee-------HHHhcccc
Q ss_pred HHhh-CCCCCHHHHHHHHHHHHHhcccccccCCChhHHHHHHHHHHHHhcCCCCCHhhHHhh---hccCHHHHHHH
Q 010689 183 TDRL-LPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKI---VHICEATLMKR 254 (504)
Q Consensus 183 ~~~L-~~~l~~~V~~~A~~I~~~~~~~~l~~GR~P~~IAAAalylAa~~~g~~~t~keIa~v---~~Vse~TIrkr 254 (504)
...- +...+.+.++... +.+|...-.-.++-=..|--.-...|+.++.+-|++- +|+..+.-|+|
T Consensus 92 ~~~~~~~~~S~~~ik~~i-------~~lI~~Ed~~~PlSD~~i~~~L~~~gi~isRRTVaKYR~~L~Ip~s~~Rkr 160 (160)
T PF04552_consen 92 VSSGSGEEFSSEAIKARI-------KELIEEEDKKKPLSDQEIAELLKEEGIKISRRTVAKYREELGIPSSSQRKR 160 (160)
T ss_dssp S--SS-SS---TTH-HHH-------HHHHTTS-TTS---HHHHHHHHTTTTS---HHHHHHHHHHHT-S-SHHHH-
T ss_pred ccCCCCcccHHHHHHHHH-------HHHHHhcCCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHcCCCChhhcCC
No 475
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=31.61 E-value=80 Score=27.95 Aligned_cols=30 Identities=7% Similarity=0.190 Sum_probs=26.5
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
+-..++.+|++.++++.+||.+.++.+.+.
T Consensus 28 ~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 28 SGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 346889999999999999999999998864
No 476
>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=31.39 E-value=21 Score=30.30 Aligned_cols=27 Identities=22% Similarity=0.465 Sum_probs=16.6
Q ss_pred CCCCCCCCCC--cccccCCCceecCcCce
Q 010689 2 VWCSSCARHV--TGHRPYDSQLCCDRCGK 28 (504)
Q Consensus 2 ~~Cp~Cgs~~--iv~D~~~G~~VC~~CG~ 28 (504)
..||.|+... +.+++..|...|-.||.
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 3699998764 45677789999999995
No 477
>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=31.39 E-value=45 Score=30.20 Aligned_cols=26 Identities=8% Similarity=0.121 Sum_probs=22.7
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...+.++||+..|+++.||++++...
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra 162 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRA 162 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45889999999999999999988654
No 478
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=31.37 E-value=22 Score=24.08 Aligned_cols=11 Identities=27% Similarity=0.960 Sum_probs=6.3
Q ss_pred ceecCcCceee
Q 010689 20 QLCCDRCGKVL 30 (504)
Q Consensus 20 ~~VC~~CG~Vl 30 (504)
.+.|..||.|+
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 45555565555
No 479
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=31.29 E-value=45 Score=30.05 Aligned_cols=25 Identities=16% Similarity=0.271 Sum_probs=22.2
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|.+|||..+|++++||+.|+..
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~r 144 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVN 144 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5678999999999999999998764
No 480
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=31.03 E-value=1e+02 Score=31.13 Aligned_cols=41 Identities=10% Similarity=0.233 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHH
Q 010689 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (504)
Q Consensus 116 ~~vaAACLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L 157 (504)
..+..++-||-... ..|.++.++|..+++|...|.|.|+..
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 457999999999999999998877754
No 481
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=31.02 E-value=22 Score=34.48 Aligned_cols=27 Identities=22% Similarity=0.460 Sum_probs=23.4
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeec
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vle 31 (504)
.|.+|++..++.. .|...|-.|+.|..
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 482
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=30.95 E-value=1.5e+02 Score=28.11 Aligned_cols=122 Identities=13% Similarity=0.216 Sum_probs=66.9
Q ss_pred HHHHHHHhCcChHHHHHHHHHHHHHhcccccccccccCCccchHHHHHHhhCCCCCHHHHHHHHHHHHHhcccccccCCC
Q 010689 136 LIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRK 215 (504)
Q Consensus 136 L~dIs~~~~vs~~~Lg~~~~~L~~~L~i~~~~~~~~~~dP~~~I~r~~~~L~~~l~~~V~~~A~~I~~~~~~~~l~~GR~ 215 (504)
-+.+|+.+|.+...-|..|+.+.+..+++... +.+++..- ++....+=+....++. ..+-++.||-
T Consensus 17 a~~lAe~~gl~~vsaG~iFR~~A~e~gmsl~e-----------f~~~AE~~-p~iD~~iD~rq~e~a~--~~nvVlegrL 82 (179)
T COG1102 17 ARELAEHLGLKLVSAGTIFREMARERGMSLEE-----------FSRYAEED-PEIDKEIDRRQKELAK--EGNVVLEGRL 82 (179)
T ss_pred HHHHHHHhCCceeeccHHHHHHHHHcCCCHHH-----------HHHHHhcC-chhhHHHHHHHHHHHH--cCCeEEhhhh
Confidence 46789999999999999999999999875321 23333322 1133334344444443 3344555553
Q ss_pred hhHHHH--H--HHHHHH-------Hhc-CCCCCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHH
Q 010689 216 PSGLCG--A--ALYVSA-------LTH-GLKFSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDF 271 (504)
Q Consensus 216 P~~IAA--A--alylAa-------~~~-g~~~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~ 271 (504)
-.=++. | .|||-| |.. -..++..++-..+-.=+..=++||++|+...-..||+=|+
T Consensus 83 A~Wi~k~~adlkI~L~Apl~vRa~Ria~REgi~~~~a~~~~~~RE~se~kRY~~~YgIDidDlSiyDL 150 (179)
T COG1102 83 AGWIVREYADLKIWLKAPLEVRAERIAKREGIDVDEALAETVEREESEKKRYKKIYGIDIDDLSIYDL 150 (179)
T ss_pred HHHHhccccceEEEEeCcHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHhCCCCccceeeEE
Confidence 222222 1 112111 111 1234444444444445555668999999887766665443
No 483
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=30.94 E-value=50 Score=24.39 Aligned_cols=23 Identities=4% Similarity=0.346 Sum_probs=18.3
Q ss_pred CCHhhHHhhhccCHHHHHHHHHH
Q 010689 235 FSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE 257 (504)
++.++|+..+|+|..||.+..++
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~ 26 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKD 26 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhc
Confidence 46789999999999999888773
No 484
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=30.91 E-value=38 Score=27.20 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=21.5
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
....||.++|+.+|||..||-.-=++
T Consensus 12 ~~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 12 ELGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred HhCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 35689999999999999999865444
No 485
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=30.90 E-value=36 Score=34.74 Aligned_cols=42 Identities=21% Similarity=0.162 Sum_probs=29.4
Q ss_pred CCHhhHHhhhccCHHHHHHHHHHhhccCCCCCChHHHHHHHhhh
Q 010689 235 FSKSDIVKIVHICEATLMKRLIEFENTDSGSLTIEDFMARKKEL 278 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE~~~t~~~~lt~~~~~~~~~~~ 278 (504)
.|.+|||+.+|||.+|+++-|..= -.-+..|-+-..+...++
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~--~~Vs~~tr~kV~~~a~el 43 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNS--ALVSADTREAVMKAVSEL 43 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCC--CCCCHHHHHHHHHHHHHH
Confidence 589999999999999999999641 122344555555555444
No 486
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=30.86 E-value=82 Score=28.23 Aligned_cols=29 Identities=10% Similarity=0.124 Sum_probs=25.9
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
.-.+|+++||..++++.+|+.+-++.+..
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45699999999999999999999988764
No 487
>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=30.84 E-value=1.3e+02 Score=22.24 Aligned_cols=38 Identities=11% Similarity=0.047 Sum_probs=28.1
Q ss_pred HHHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHHh
Q 010689 122 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (504)
Q Consensus 122 CLYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~L 161 (504)
+|++..... |.++.+|++.++++...+.+..++|.+.=
T Consensus 8 iL~~l~~~~--~~~~~~la~~~~~~~~~~t~~i~~L~~~g 45 (59)
T PF01047_consen 8 ILRILYENG--GITQSELAEKLGISRSTVTRIIKRLEKKG 45 (59)
T ss_dssp HHHHHHHHS--SEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHcC--CCCHHHHHHHHCCChhHHHHHHHHHHHCC
Confidence 344443333 38999999999999999999988887753
No 488
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=30.80 E-value=43 Score=31.15 Aligned_cols=26 Identities=19% Similarity=0.305 Sum_probs=22.1
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|.+|||..+|+++.||+.++.--
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Ra 162 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERA 162 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45889999999999999999886543
No 489
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=30.68 E-value=31 Score=34.87 Aligned_cols=23 Identities=22% Similarity=0.150 Sum_probs=21.0
Q ss_pred CCHhhHHhhhccCHHHHHHHHHH
Q 010689 235 FSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 235 ~t~keIa~v~~Vse~TIrkr~kE 257 (504)
.|.+|||+.+|||.+|+++.|+.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcC
Confidence 58999999999999999999963
No 490
>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=30.62 E-value=63 Score=25.03 Aligned_cols=37 Identities=22% Similarity=0.183 Sum_probs=29.1
Q ss_pred HHHHHHhcCCCCcHHHHHHHhCcChHHHHHHHHHHHHH
Q 010689 123 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (504)
Q Consensus 123 LYiACR~~~~p~tL~dIs~~~~vs~~~Lg~~~~~L~~~ 160 (504)
+|.+.- ..-|.|..|||..++++...+.++.+.|.+.
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344433 5567899999999999999998888887764
No 491
>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=30.54 E-value=66 Score=29.32 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=22.0
Q ss_pred CCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 234 KFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 234 ~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
..|.++||..+|+|+.||+.++.--
T Consensus 135 g~s~~eiA~~lgis~~tv~~~l~Ra 159 (169)
T TIGR02954 135 DLTIKEIAEVMNKPEGTVKTYLHRA 159 (169)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5889999999999999999887654
No 492
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=30.53 E-value=35 Score=34.45 Aligned_cols=22 Identities=23% Similarity=0.231 Sum_probs=20.1
Q ss_pred CHhhHHhhhccCHHHHHHHHHH
Q 010689 236 SKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 236 t~keIa~v~~Vse~TIrkr~kE 257 (504)
|.+|||+.+|||.+|+.+-|..
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 6789999999999999999964
No 493
>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=30.51 E-value=45 Score=29.72 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=22.5
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHh
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEF 258 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~ 258 (504)
...|.++||..+|+++.||+.++.-.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra 145 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRA 145 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 46889999999999999999887643
No 494
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=30.35 E-value=79 Score=28.39 Aligned_cols=29 Identities=14% Similarity=0.180 Sum_probs=25.1
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
-..++++||..++|+.+|++..++.+..-
T Consensus 21 ~~~~~~ela~~l~vs~~svs~~l~~L~~~ 49 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVTKMVQKLDKD 49 (142)
T ss_pred CCcCHHHHHHHhCCChhHHHHHHHHHHHC
Confidence 44588999999999999999999988753
No 495
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=30.34 E-value=45 Score=32.43 Aligned_cols=25 Identities=4% Similarity=0.134 Sum_probs=22.1
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHH
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIE 257 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE 257 (504)
...|.+|||..+||++.||++++..
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~r 221 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKR 221 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999999988643
No 496
>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=30.32 E-value=24 Score=23.93 Aligned_cols=21 Identities=24% Similarity=0.400 Sum_probs=9.1
Q ss_pred CCCCCCCCCcccccCCCceec
Q 010689 3 WCSSCARHVTGHRPYDSQLCC 23 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC 23 (504)
+|..||.-..+.+...|.++|
T Consensus 6 kC~~CGniv~v~~~~~~~l~C 26 (34)
T cd00974 6 KCEICGNIVEVLNVGGGTLVC 26 (34)
T ss_pred EcCCCCcEEEEEECCCcceee
Confidence 355555443333333444444
No 497
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.26 E-value=31 Score=37.16 Aligned_cols=32 Identities=16% Similarity=0.512 Sum_probs=23.4
Q ss_pred CCCCCCCCCcccccCCCceecCcCceeeccCccc
Q 010689 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFS 36 (504)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC~~CG~Vlee~~id 36 (504)
.||.||.+.-. .-.|.+-|..||+-.....+.
T Consensus 352 ~Cp~Cg~~m~S--~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMKS--AGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchhh--cCCCCcccccccccCCccccc
Confidence 79999997321 123478999999988766554
No 498
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=30.21 E-value=54 Score=32.26 Aligned_cols=30 Identities=20% Similarity=0.245 Sum_probs=27.1
Q ss_pred CCCCCHhhHHhhhccCHHHHHHHHHHhhcc
Q 010689 232 GLKFSKSDIVKIVHICEATLMKRLIEFENT 261 (504)
Q Consensus 232 g~~~t~keIa~v~~Vse~TIrkr~kE~~~t 261 (504)
...+|++++|+.++++..|+.++++.+.+-
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~ 48 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDE 48 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 457999999999999999999999999754
No 499
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=30.16 E-value=39 Score=33.75 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=25.2
Q ss_pred CCCCHhhHHhhhccCHHHHHHHHHHhhc
Q 010689 233 LKFSKSDIVKIVHICEATLMKRLIEFEN 260 (504)
Q Consensus 233 ~~~t~keIa~v~~Vse~TIrkr~kE~~~ 260 (504)
-.++++|+++.++||+.|||+=|.++.+
T Consensus 18 g~v~v~eLa~~~~VS~~TIRRDL~~Le~ 45 (253)
T COG1349 18 GKVSVEELAELFGVSEMTIRRDLNELEE 45 (253)
T ss_pred CcEEHHHHHHHhCCCHHHHHHhHHHHHH
Confidence 4688999999999999999998888874
No 500
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=30.08 E-value=61 Score=24.77 Aligned_cols=31 Identities=10% Similarity=0.207 Sum_probs=0.0
Q ss_pred HHHHHHHhcCCCCCHhhHHhhhccCHHHHHH
Q 010689 223 ALYVSALTHGLKFSKSDIVKIVHICEATLMK 253 (504)
Q Consensus 223 alylAa~~~g~~~t~keIa~v~~Vse~TIrk 253 (504)
+..|......-..|+.++|..+|++.+||++
T Consensus 3 g~~lr~~R~~~gls~~~lA~~~g~s~s~v~~ 33 (64)
T PF13560_consen 3 GRRLRRLRERAGLSQAQLADRLGVSQSTVSR 33 (64)
T ss_dssp HHHHHHHHHCHTS-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Done!