Query 021438
Match_columns 312
No_of_seqs 197 out of 1138
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 02:58:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021438.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021438hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1597 Transcription initiati 100.0 4.6E-76 9.9E-81 507.7 28.2 301 4-311 1-306 (308)
2 PRK00423 tfb transcription ini 100.0 2.6E-72 5.7E-77 511.6 32.3 287 3-298 11-309 (310)
3 COG1405 SUA7 Transcription ini 100.0 4.3E-67 9.3E-72 465.5 26.9 279 3-298 1-284 (285)
4 KOG1598 Transcription initiati 100.0 2.1E-43 4.5E-48 328.1 16.3 253 4-297 1-258 (521)
5 KOG0835 Cyclin L [General func 99.8 1.7E-18 3.7E-23 152.3 16.5 188 107-300 24-236 (367)
6 PF00382 TFIIB: Transcription 99.8 2.9E-18 6.3E-23 122.6 9.9 71 113-184 1-71 (71)
7 KOG0834 CDK9 kinase-activating 99.7 2.2E-17 4.7E-22 149.0 12.6 187 107-293 40-245 (323)
8 PF00382 TFIIB: Transcription 99.7 1.8E-16 4E-21 113.3 9.2 69 214-282 1-71 (71)
9 TIGR00569 ccl1 cyclin ccl1. Un 99.7 2.6E-15 5.7E-20 135.8 18.9 160 103-268 52-226 (305)
10 PF08271 TF_Zn_Ribbon: TFIIB z 99.6 2.3E-16 4.9E-21 101.0 3.3 43 4-47 1-43 (43)
11 COG5333 CCL1 Cdk activating ki 99.5 8.3E-14 1.8E-18 123.0 13.0 155 107-267 46-211 (297)
12 PRK00423 tfb transcription ini 99.5 8.6E-14 1.9E-18 127.3 12.4 88 109-197 219-306 (310)
13 KOG0794 CDK8 kinase-activating 99.4 4.2E-12 9.1E-17 107.2 11.6 178 108-292 43-237 (264)
14 COG1405 SUA7 Transcription ini 99.3 1.1E-11 2.4E-16 110.9 9.6 89 108-197 193-281 (285)
15 KOG1597 Transcription initiati 99.3 2E-11 4.4E-16 106.8 10.2 89 108-197 202-290 (308)
16 cd00043 CYCLIN Cyclin box fold 99.2 3E-10 6.5E-15 83.4 11.2 83 108-191 4-87 (88)
17 smart00385 CYCLIN domain prese 99.1 7.8E-10 1.7E-14 80.3 9.1 80 112-192 2-82 (83)
18 cd00043 CYCLIN Cyclin box fold 99.1 1.6E-09 3.4E-14 79.5 10.6 83 208-290 3-88 (88)
19 smart00385 CYCLIN domain prese 99.1 1.1E-09 2.5E-14 79.4 9.5 80 212-291 1-83 (83)
20 KOG0656 G1/S-specific cyclin D 99.0 3.9E-08 8.4E-13 89.3 17.2 175 107-287 79-268 (335)
21 COG5024 Cyclin [Cell division 98.5 2.8E-06 6.1E-11 80.2 12.9 179 109-294 216-400 (440)
22 KOG2496 Cdk activating kinase 98.4 7.5E-06 1.6E-10 72.5 12.5 146 113-260 63-220 (325)
23 KOG0653 Cyclin B and related k 98.4 1E-05 2.2E-10 76.5 14.5 165 107-277 159-329 (391)
24 PF00134 Cyclin_N: Cyclin, N-t 98.3 9.5E-06 2.1E-10 64.1 11.5 93 105-197 30-124 (127)
25 KOG1598 Transcription initiati 98.2 1.6E-06 3.5E-11 82.2 5.2 91 106-197 163-256 (521)
26 PF02984 Cyclin_C: Cyclin, C-t 98.1 2.1E-05 4.4E-10 61.1 8.6 86 209-294 2-90 (118)
27 KOG4557 Origin recognition com 98.1 0.00034 7.3E-09 59.0 15.8 167 112-291 2-179 (262)
28 PF01857 RB_B: Retinoblastoma- 97.8 0.00012 2.7E-09 58.5 7.8 83 107-190 12-96 (135)
29 KOG0655 G1/S-specific cyclin E 97.5 0.0051 1.1E-07 55.5 15.1 172 109-293 148-335 (408)
30 PF11781 RRN7: RNA polymerase 97.3 0.0002 4.3E-09 43.5 2.4 27 5-34 10-36 (36)
31 PHA00626 hypothetical protein 96.8 0.0013 2.7E-08 43.3 2.7 31 4-35 1-35 (59)
32 PF08792 A2L_zn_ribbon: A2L zi 96.7 0.0015 3.2E-08 38.8 2.7 31 1-33 1-31 (33)
33 KOG0835 Cyclin L [General func 96.7 0.011 2.4E-07 53.3 9.4 90 106-196 138-230 (367)
34 PRK00415 rps27e 30S ribosomal 96.7 0.0012 2.5E-08 44.4 2.3 31 4-35 12-42 (59)
35 COG2051 RPS27A Ribosomal prote 96.7 0.001 2.2E-08 45.4 1.8 31 4-35 20-50 (67)
36 PF14803 Nudix_N_2: Nudix N-te 96.6 0.0015 3.3E-08 39.0 2.2 27 5-33 2-32 (34)
37 PF02984 Cyclin_C: Cyclin, C-t 96.5 0.023 5.1E-07 43.7 8.7 87 109-196 3-90 (118)
38 PF01667 Ribosomal_S27e: Ribos 96.5 0.0016 3.4E-08 43.3 1.6 31 4-35 8-38 (55)
39 PF13248 zf-ribbon_3: zinc-rib 96.1 0.0031 6.7E-08 35.3 1.4 22 4-31 3-24 (26)
40 smart00778 Prim_Zn_Ribbon Zinc 96.1 0.0056 1.2E-07 37.3 2.4 29 3-31 3-33 (37)
41 PLN00209 ribosomal protein S27 96.0 0.0045 9.8E-08 44.7 2.2 31 4-35 37-67 (86)
42 PF01857 RB_B: Retinoblastoma- 96.0 0.034 7.3E-07 44.5 7.3 77 211-287 15-95 (135)
43 PRK00420 hypothetical protein; 96.0 0.0053 1.2E-07 47.2 2.5 30 2-34 22-51 (112)
44 PF02150 RNA_POL_M_15KD: RNA p 95.9 0.0061 1.3E-07 36.7 2.1 31 3-34 1-31 (35)
45 PTZ00083 40S ribosomal protein 95.9 0.0057 1.2E-07 44.1 2.3 31 4-35 36-66 (85)
46 PRK00398 rpoP DNA-directed RNA 95.9 0.007 1.5E-07 38.9 2.4 31 1-33 1-31 (46)
47 PF13240 zinc_ribbon_2: zinc-r 95.8 0.0051 1.1E-07 33.4 1.3 22 5-32 1-22 (23)
48 PF00134 Cyclin_N: Cyclin, N-t 95.8 0.11 2.4E-06 40.5 9.5 65 211-275 35-102 (127)
49 PF08274 PhnA_Zn_Ribbon: PhnA 95.7 0.0085 1.8E-07 34.7 2.0 27 3-32 2-28 (30)
50 PRK10220 hypothetical protein; 95.7 0.026 5.7E-07 42.6 5.1 29 1-32 1-29 (111)
51 TIGR01206 lysW lysine biosynth 95.5 0.0095 2.1E-07 39.6 1.9 31 3-34 2-33 (54)
52 PRK00432 30S ribosomal protein 95.4 0.012 2.5E-07 38.6 2.0 28 3-33 20-47 (50)
53 KOG0834 CDK9 kinase-activating 95.2 0.053 1.1E-06 49.7 6.5 83 211-293 43-131 (323)
54 PRK11827 hypothetical protein; 95.2 0.013 2.9E-07 39.7 1.9 29 3-33 8-36 (60)
55 TIGR00569 ccl1 cyclin ccl1. Un 95.0 0.17 3.7E-06 46.3 9.2 68 211-278 60-131 (305)
56 PF10571 UPF0547: Uncharacteri 94.9 0.016 3.5E-07 32.4 1.4 24 5-34 2-25 (26)
57 PF09538 FYDLN_acid: Protein o 94.9 0.017 3.6E-07 44.3 1.9 31 3-36 9-39 (108)
58 PF08613 Cyclin: Cyclin; Inte 94.8 0.73 1.6E-05 37.5 11.7 88 109-197 54-147 (149)
59 COG2835 Uncharacterized conser 94.7 0.023 4.9E-07 38.3 2.0 31 1-33 6-36 (60)
60 KOG0654 G2/Mitotic-specific cy 94.7 0.35 7.5E-06 45.0 10.3 134 149-290 180-320 (359)
61 COG2824 PhnA Uncharacterized Z 94.6 0.069 1.5E-06 40.1 4.5 32 1-35 1-32 (112)
62 COG1997 RPL43A Ribosomal prote 94.5 0.035 7.5E-07 40.3 2.7 30 3-34 35-64 (89)
63 TIGR02098 MJ0042_CXXC MJ0042 f 94.4 0.02 4.3E-07 35.1 1.2 31 4-34 3-36 (38)
64 PF08273 Prim_Zn_Ribbon: Zinc- 94.4 0.034 7.5E-07 34.5 2.2 29 4-32 4-35 (40)
65 COG1998 RPS31 Ribosomal protei 94.3 0.026 5.7E-07 36.2 1.5 27 4-32 20-46 (51)
66 COG1645 Uncharacterized Zn-fin 94.3 0.021 4.6E-07 45.0 1.3 25 3-31 28-52 (131)
67 PF03966 Trm112p: Trm112p-like 94.2 0.046 1E-06 38.2 2.9 17 17-33 47-63 (68)
68 smart00661 RPOL9 RNA polymeras 94.1 0.042 9.1E-07 36.1 2.3 28 5-34 2-31 (52)
69 PF14354 Lar_restr_allev: Rest 94.1 0.061 1.3E-06 36.6 3.1 29 2-31 2-37 (61)
70 TIGR02300 FYDLN_acid conserved 94.0 0.035 7.7E-07 43.3 2.0 31 3-36 9-39 (129)
71 TIGR02393 RpoD_Cterm RNA polym 94.0 4 8.7E-05 35.7 19.0 33 264-296 195-227 (238)
72 PRK00464 nrdR transcriptional 93.9 0.049 1.1E-06 44.6 2.7 30 4-33 1-38 (154)
73 KOG4164 Cyclin ik3-1/CABLES [C 93.6 0.35 7.6E-06 44.9 7.9 60 107-166 383-442 (497)
74 PF13404 HTH_AsnC-type: AsnC-t 93.5 0.2 4.4E-06 31.4 4.5 28 263-290 15-42 (42)
75 TIGR03655 anti_R_Lar restricti 93.1 0.078 1.7E-06 35.1 2.2 31 4-34 2-37 (53)
76 PRK07408 RNA polymerase sigma 93.0 6.1 0.00013 35.1 15.8 34 264-297 218-251 (256)
77 TIGR00686 phnA alkylphosphonat 92.8 0.095 2.1E-06 39.6 2.6 30 3-35 2-31 (109)
78 PF09297 zf-NADH-PPase: NADH p 92.8 0.14 3.1E-06 30.0 2.9 28 3-32 3-30 (32)
79 COG1594 RPB9 DNA-directed RNA 92.7 0.091 2E-06 40.7 2.5 34 3-36 2-35 (113)
80 PF06677 Auto_anti-p27: Sjogre 92.7 0.11 2.5E-06 32.3 2.5 25 3-30 17-41 (41)
81 TIGR00244 transcriptional regu 92.6 0.12 2.7E-06 41.5 3.1 30 4-33 1-38 (147)
82 PF12760 Zn_Tnp_IS1595: Transp 92.5 0.17 3.7E-06 32.4 3.2 28 3-31 18-45 (46)
83 PRK14892 putative transcriptio 92.4 0.066 1.4E-06 40.3 1.4 41 4-45 22-70 (99)
84 PF13719 zinc_ribbon_5: zinc-r 92.2 0.065 1.4E-06 32.7 0.9 30 4-33 3-35 (37)
85 PF13730 HTH_36: Helix-turn-he 92.2 0.4 8.6E-06 31.6 4.8 26 267-292 27-52 (55)
86 PF13613 HTH_Tnp_4: Helix-turn 92.0 0.29 6.3E-06 32.3 4.0 38 261-298 15-52 (53)
87 PF00325 Crp: Bacterial regula 91.9 0.24 5.3E-06 29.1 3.0 28 265-292 2-29 (32)
88 PF09862 DUF2089: Protein of u 91.9 0.12 2.6E-06 39.8 2.2 24 6-35 1-24 (113)
89 PF13412 HTH_24: Winged helix- 91.8 0.43 9.3E-06 30.5 4.6 30 263-292 15-44 (48)
90 PF08613 Cyclin: Cyclin; Inte 91.7 3.9 8.5E-05 33.1 11.2 89 205-293 49-145 (149)
91 PF04545 Sigma70_r4: Sigma-70, 91.6 0.5 1.1E-05 30.6 4.7 31 263-293 18-48 (50)
92 KOG1779 40s ribosomal protein 91.5 0.08 1.7E-06 37.4 0.8 30 4-34 35-64 (84)
93 COG4888 Uncharacterized Zn rib 91.3 0.13 2.9E-06 38.3 1.8 30 4-34 23-57 (104)
94 PF08279 HTH_11: HTH domain; 91.3 0.5 1.1E-05 31.1 4.6 31 263-293 13-43 (55)
95 KOG4557 Origin recognition com 91.1 1.1 2.4E-05 38.3 7.4 82 113-196 96-182 (262)
96 PF01325 Fe_dep_repress: Iron 91.1 0.62 1.3E-05 31.6 4.9 38 254-292 12-49 (60)
97 PF01780 Ribosomal_L37ae: Ribo 90.9 0.13 2.9E-06 37.8 1.5 31 3-35 35-65 (90)
98 PRK05657 RNA polymerase sigma 90.9 13 0.00029 34.3 17.2 34 264-297 281-314 (325)
99 smart00834 CxxC_CXXC_SSSS Puta 90.9 0.12 2.7E-06 31.9 1.2 31 2-32 4-35 (41)
100 PRK09210 RNA polymerase sigma 90.8 15 0.00032 34.6 18.1 31 264-294 324-354 (367)
101 PF07282 OrfB_Zn_ribbon: Putat 90.6 0.18 3.8E-06 35.2 1.9 29 4-34 29-57 (69)
102 PRK12495 hypothetical protein; 90.5 0.18 3.8E-06 43.2 2.2 32 1-36 40-71 (226)
103 PF13936 HTH_38: Helix-turn-he 90.5 0.45 9.7E-06 30.1 3.5 29 259-287 14-42 (44)
104 PF01096 TFIIS_C: Transcriptio 90.2 0.26 5.7E-06 30.4 2.2 28 5-32 2-37 (39)
105 TIGR01384 TFS_arch transcripti 90.1 0.2 4.4E-06 38.1 2.0 27 5-35 2-28 (104)
106 KOG1010 Rb (Retinoblastoma tum 90.1 0.61 1.3E-05 47.5 5.8 82 109-191 680-763 (920)
107 PF13384 HTH_23: Homeodomain-l 89.6 0.55 1.2E-05 30.2 3.6 27 265-291 17-43 (50)
108 smart00440 ZnF_C2C2 C2C2 Zinc 89.6 0.3 6.5E-06 30.3 2.1 27 5-32 2-37 (40)
109 PTZ00255 60S ribosomal protein 89.4 0.27 5.9E-06 36.1 2.1 31 3-35 36-66 (90)
110 COG3478 Predicted nucleic-acid 89.4 0.25 5.5E-06 33.6 1.7 28 4-32 5-49 (68)
111 TIGR02394 rpoS_proteo RNA poly 89.3 16 0.00035 32.9 16.7 34 264-297 241-274 (285)
112 PF10668 Phage_terminase: Phag 89.2 0.97 2.1E-05 30.7 4.5 38 245-285 5-42 (60)
113 PF05129 Elf1: Transcription e 89.0 0.13 2.9E-06 37.2 0.3 33 4-36 23-59 (81)
114 COG2888 Predicted Zn-ribbon RN 88.8 0.29 6.2E-06 32.8 1.7 26 5-32 11-36 (61)
115 PF00356 LacI: Bacterial regul 88.7 0.53 1.1E-05 30.2 2.8 20 267-286 1-20 (46)
116 smart00659 RPOLCX RNA polymera 88.6 0.38 8.2E-06 30.5 2.1 27 4-33 3-29 (44)
117 PRK00135 scpB segregation and 88.5 5.7 0.00012 33.7 9.8 122 148-292 5-128 (188)
118 COG5333 CCL1 Cdk activating ki 88.4 1.2 2.7E-05 40.1 6.0 53 211-263 49-103 (297)
119 PRK12286 rpmF 50S ribosomal pr 88.4 0.36 7.8E-06 32.5 2.0 28 4-38 28-55 (57)
120 PF05460 ORC6: Origin recognit 88.4 0.14 3.1E-06 47.8 0.0 77 121-198 11-88 (353)
121 PF00196 GerE: Bacterial regul 88.2 0.74 1.6E-05 30.8 3.5 32 264-295 17-48 (58)
122 PF03119 DNA_ligase_ZBD: NAD-d 88.1 0.46 9.9E-06 27.0 2.0 22 5-28 1-22 (28)
123 PF13545 HTH_Crp_2: Crp-like h 88.0 1.1 2.5E-05 31.4 4.6 29 264-292 27-55 (76)
124 PRK05901 RNA polymerase sigma 88.0 29 0.00063 34.2 18.0 31 264-294 466-496 (509)
125 cd00092 HTH_CRP helix_turn_hel 87.9 1.9 4.2E-05 29.2 5.7 29 264-292 24-52 (67)
126 smart00421 HTH_LUXR helix_turn 87.9 0.88 1.9E-05 29.6 3.8 30 265-294 18-47 (58)
127 TIGR00280 L37a ribosomal prote 87.9 0.36 7.8E-06 35.6 1.9 31 3-35 35-65 (91)
128 COG5349 Uncharacterized protei 87.9 0.25 5.4E-06 38.2 1.1 32 4-36 22-53 (126)
129 PF03604 DNA_RNApol_7kD: DNA d 87.9 0.31 6.8E-06 28.6 1.3 25 5-32 2-26 (32)
130 PF01371 Trp_repressor: Trp re 87.8 0.94 2E-05 33.3 4.1 31 261-291 45-75 (87)
131 smart00342 HTH_ARAC helix_turn 87.8 2.3 5E-05 29.8 6.2 71 113-191 4-75 (84)
132 PRK05978 hypothetical protein; 87.8 0.41 8.8E-06 38.8 2.3 31 4-35 34-64 (148)
133 PRK11169 leucine-responsive tr 87.7 0.95 2.1E-05 37.4 4.6 30 263-292 26-55 (164)
134 PF02796 HTH_7: Helix-turn-hel 87.6 0.36 7.7E-06 30.7 1.5 29 258-286 14-42 (45)
135 PRK07406 RNA polymerase sigma 87.5 26 0.00056 33.1 14.5 32 264-295 330-361 (373)
136 PF05191 ADK_lid: Adenylate ki 87.4 0.084 1.8E-06 32.0 -1.4 30 4-33 2-31 (36)
137 smart00419 HTH_CRP helix_turn_ 87.2 0.96 2.1E-05 28.5 3.5 30 263-292 6-35 (48)
138 PF04967 HTH_10: HTH DNA bindi 87.2 2.3 5E-05 28.1 5.2 27 266-292 24-50 (53)
139 COG4640 Predicted membrane pro 87.2 0.34 7.4E-06 45.0 1.7 28 3-36 1-28 (465)
140 PF01022 HTH_5: Bacterial regu 87.0 1.3 2.8E-05 28.3 4.0 32 261-292 11-42 (47)
141 PRK09678 DNA-binding transcrip 87.0 0.7 1.5E-05 32.7 2.8 31 3-34 1-40 (72)
142 PRK07405 RNA polymerase sigma 86.9 25 0.00055 32.3 17.9 31 263-293 274-304 (317)
143 smart00345 HTH_GNTR helix_turn 86.8 1.2 2.5E-05 29.4 3.9 30 263-292 17-47 (60)
144 PRK11179 DNA-binding transcrip 86.8 1.2 2.6E-05 36.3 4.6 30 263-292 21-50 (153)
145 TIGR03879 near_KaiC_dom probab 86.7 0.53 1.1E-05 33.4 2.1 28 264-291 31-58 (73)
146 COG1725 Predicted transcriptio 86.7 1 2.2E-05 35.5 3.9 30 263-292 32-62 (125)
147 PRK03976 rpl37ae 50S ribosomal 86.7 0.45 9.8E-06 35.0 1.8 32 3-36 36-67 (90)
148 COG4068 Uncharacterized protei 86.5 0.16 3.4E-06 33.9 -0.6 26 3-34 8-34 (64)
149 PF01783 Ribosomal_L32p: Ribos 86.4 0.45 9.8E-06 31.9 1.6 27 4-37 27-53 (56)
150 PHA02591 hypothetical protein; 86.3 1.1 2.4E-05 31.9 3.5 32 256-287 50-81 (83)
151 PRK05911 RNA polymerase sigma 86.3 23 0.0005 31.4 18.8 32 264-295 220-251 (257)
152 PRK08402 replication factor A; 86.2 0.6 1.3E-05 43.6 2.8 27 4-32 213-239 (355)
153 PF12773 DZR: Double zinc ribb 86.1 0.44 9.5E-06 30.9 1.4 28 4-34 13-40 (50)
154 cd06571 Bac_DnaA_C C-terminal 86.1 6.7 0.00014 28.8 7.9 71 211-295 2-75 (90)
155 PF08281 Sigma70_r4_2: Sigma-7 86.0 1.2 2.6E-05 29.1 3.5 28 264-291 25-52 (54)
156 PF09855 DUF2082: Nucleic-acid 86.0 0.52 1.1E-05 32.5 1.8 27 5-32 2-45 (64)
157 PF13542 HTH_Tnp_ISL3: Helix-t 86.0 1.6 3.4E-05 28.3 4.1 24 265-288 27-50 (52)
158 PF13717 zinc_ribbon_4: zinc-r 85.9 0.35 7.6E-06 29.2 0.8 29 4-33 3-35 (36)
159 KOG2496 Cdk activating kinase 85.6 3.2 7E-05 37.5 6.9 66 211-276 60-129 (325)
160 PF08220 HTH_DeoR: DeoR-like h 85.5 1 2.2E-05 30.1 3.0 29 264-292 13-41 (57)
161 cd06170 LuxR_C_like C-terminal 85.3 1.6 3.4E-05 28.3 3.9 31 265-295 15-45 (57)
162 TIGR01031 rpmF_bact ribosomal 85.1 0.64 1.4E-05 31.0 1.8 25 4-35 27-51 (55)
163 TIGR03697 NtcA_cyano global ni 84.9 7.6 0.00017 32.3 8.9 29 264-292 142-170 (193)
164 PF14255 Cys_rich_CPXG: Cystei 84.6 0.68 1.5E-05 30.5 1.7 29 5-33 2-34 (52)
165 PRK09710 lar restriction allev 84.5 1.2 2.6E-05 30.5 2.9 29 3-32 6-36 (64)
166 PRK06266 transcription initiat 84.5 0.28 6E-06 41.3 -0.2 31 4-35 118-148 (178)
167 TIGR02443 conserved hypothetic 84.5 0.99 2.1E-05 30.4 2.4 30 3-32 9-40 (59)
168 KOG2906 RNA polymerase III sub 84.4 0.81 1.8E-05 34.0 2.2 31 3-34 1-32 (105)
169 PF00325 Crp: Bacterial regula 84.0 1.6 3.6E-05 25.6 3.0 27 166-193 2-28 (32)
170 TIGR02605 CxxC_CxxC_SSSS putat 83.9 0.53 1.2E-05 30.8 1.0 30 2-31 4-34 (52)
171 PF04161 Arv1: Arv1-like famil 83.9 0.55 1.2E-05 40.5 1.4 34 4-37 1-38 (208)
172 PF08646 Rep_fac-A_C: Replicat 83.9 0.86 1.9E-05 36.8 2.5 28 5-35 20-49 (146)
173 smart00342 HTH_ARAC helix_turn 83.9 12 0.00026 25.9 10.2 26 265-290 50-76 (84)
174 PRK04217 hypothetical protein; 83.7 1.4 3.1E-05 33.9 3.4 32 264-295 57-88 (110)
175 TIGR01321 TrpR trp operon repr 83.5 1.4 3.1E-05 32.8 3.2 31 260-290 50-80 (94)
176 cd00350 rubredoxin_like Rubred 83.3 0.93 2E-05 26.7 1.8 23 5-31 3-25 (33)
177 PF00392 GntR: Bacterial regul 83.1 1.6 3.5E-05 29.8 3.2 30 263-292 21-51 (64)
178 TIGR01610 phage_O_Nterm phage 83.1 7.6 0.00016 28.9 7.1 31 262-292 44-74 (95)
179 PF09723 Zn-ribbon_8: Zinc rib 83.0 0.63 1.4E-05 29.1 1.0 30 3-32 5-35 (42)
180 COG1996 RPC10 DNA-directed RNA 82.9 0.49 1.1E-05 30.7 0.5 27 4-32 7-33 (49)
181 TIGR00122 birA_repr_reg BirA b 82.9 2.9 6.2E-05 28.9 4.5 32 261-292 9-40 (69)
182 PF08280 HTH_Mga: M protein tr 82.7 1.8 3.9E-05 29.1 3.3 31 264-294 18-48 (59)
183 PF10122 Mu-like_Com: Mu-like 82.7 0.39 8.5E-06 31.2 0.0 32 2-33 3-34 (51)
184 PRK02935 hypothetical protein; 82.7 0.93 2E-05 34.2 2.0 38 4-48 71-108 (110)
185 PF02082 Rrf2: Transcriptional 82.3 2 4.3E-05 31.0 3.6 39 254-292 14-52 (83)
186 COG1326 Uncharacterized archae 82.1 0.52 1.1E-05 39.6 0.5 29 4-35 7-42 (201)
187 PF14122 YokU: YokU-like prote 82.1 0.87 1.9E-05 33.0 1.6 39 5-43 1-55 (87)
188 COG1522 Lrp Transcriptional re 82.0 2.4 5.1E-05 34.2 4.4 30 263-292 20-49 (154)
189 PRK05949 RNA polymerase sigma 81.9 43 0.00093 31.0 17.7 30 264-293 285-314 (327)
190 COG1327 Predicted transcriptio 81.5 1.2 2.6E-05 36.0 2.3 29 4-32 1-37 (156)
191 PF02042 RWP-RK: RWP-RK domain 81.3 2.1 4.5E-05 28.2 3.0 26 264-289 14-39 (52)
192 PF01726 LexA_DNA_bind: LexA D 81.2 2.4 5.2E-05 29.3 3.5 31 261-291 21-52 (65)
193 PHA02942 putative transposase; 81.1 1 2.2E-05 42.6 2.2 29 4-35 326-354 (383)
194 PF05876 Terminase_GpA: Phage 81.1 0.88 1.9E-05 45.3 1.8 43 4-46 201-255 (557)
195 TIGR02479 FliA_WhiG RNA polyme 81.0 35 0.00076 29.3 19.3 31 264-294 190-220 (224)
196 COG1191 FliA DNA-directed RNA 80.9 40 0.00086 29.9 16.0 170 105-295 28-242 (247)
197 PF12773 DZR: Double zinc ribb 80.9 1.2 2.6E-05 28.7 1.9 22 3-30 29-50 (50)
198 PRK11337 DNA-binding transcrip 80.9 6.6 0.00014 35.5 7.4 63 204-288 6-69 (292)
199 TIGR02395 rpoN_sigma RNA polym 80.6 12 0.00026 36.1 9.2 163 113-287 116-340 (429)
200 smart00344 HTH_ASNC helix_turn 80.4 3.4 7.3E-05 31.2 4.5 29 264-292 16-44 (108)
201 PF10058 DUF2296: Predicted in 80.1 0.95 2E-05 30.1 1.1 30 3-32 22-53 (54)
202 PRK13130 H/ACA RNA-protein com 80.1 0.91 2E-05 30.4 1.0 25 2-34 4-28 (56)
203 PF05225 HTH_psq: helix-turn-h 80.0 6.8 0.00015 24.8 5.1 29 262-291 14-42 (45)
204 PF12802 MarR_2: MarR family; 79.8 5.1 0.00011 26.7 4.8 28 265-292 21-48 (62)
205 PRK07598 RNA polymerase sigma 79.8 59 0.0013 31.2 18.5 179 106-292 181-397 (415)
206 PRK12336 translation initiatio 79.7 1.2 2.7E-05 38.1 2.1 30 4-33 99-129 (201)
207 PF07754 DUF1610: Domain of un 79.6 1.6 3.4E-05 23.9 1.7 24 6-31 1-24 (24)
208 PF11672 DUF3268: Protein of u 79.5 1.7 3.8E-05 32.9 2.5 31 4-35 3-43 (102)
209 PF07900 DUF1670: Protein of u 79.5 2.4 5.2E-05 36.5 3.7 37 264-300 104-140 (220)
210 PRK05932 RNA polymerase factor 79.5 26 0.00057 34.0 11.2 167 113-287 141-365 (455)
211 PF00301 Rubredoxin: Rubredoxi 79.4 1.1 2.5E-05 28.8 1.3 14 24-37 2-15 (47)
212 PRK14088 dnaA chromosomal repl 79.2 23 0.00049 34.2 10.8 51 241-293 362-415 (440)
213 COG3877 Uncharacterized protei 79.1 1.6 3.5E-05 32.9 2.2 26 4-35 7-32 (122)
214 PRK00118 putative DNA-binding 79.0 2.4 5.1E-05 32.3 3.1 32 264-295 32-63 (104)
215 cd04762 HTH_MerR-trunc Helix-T 79.0 2.4 5.1E-05 26.5 2.8 22 267-288 2-23 (49)
216 COG0333 RpmF Ribosomal protein 78.9 1.6 3.4E-05 29.3 1.9 27 3-36 27-53 (57)
217 PF15616 TerY-C: TerY-C metal 78.7 1.5 3.2E-05 34.8 2.0 10 3-12 77-86 (131)
218 PRK01381 Trp operon repressor; 78.5 1.9 4.2E-05 32.4 2.5 37 255-291 45-81 (99)
219 PF01978 TrmB: Sugar-specific 78.5 2.6 5.6E-05 29.0 3.1 39 253-292 11-49 (68)
220 COG1656 Uncharacterized conser 78.3 0.96 2.1E-05 37.1 0.9 29 3-33 97-140 (165)
221 PRK11161 fumarate/nitrate redu 78.2 13 0.00029 32.0 8.2 29 264-292 183-211 (235)
222 KOG0794 CDK8 kinase-activating 78.2 18 0.00038 31.6 8.4 78 118-197 162-240 (264)
223 cd06171 Sigma70_r4 Sigma70, re 78.2 5.5 0.00012 25.0 4.5 29 264-292 25-53 (55)
224 TIGR03826 YvyF flagellar opero 78.1 0.68 1.5E-05 37.1 -0.0 30 1-35 1-30 (137)
225 PRK11014 transcriptional repre 78.0 3.6 7.9E-05 32.9 4.2 40 253-292 13-52 (141)
226 cd04761 HTH_MerR-SF Helix-Turn 77.9 2.5 5.3E-05 26.8 2.6 21 267-287 2-22 (49)
227 TIGR02010 IscR iron-sulfur clu 77.5 6.2 0.00014 31.3 5.4 46 147-193 6-51 (135)
228 smart00401 ZnF_GATA zinc finge 77.4 2.1 4.5E-05 28.2 2.1 32 3-34 3-36 (52)
229 cd07377 WHTH_GntR Winged helix 77.3 3.6 7.8E-05 27.6 3.5 26 267-292 27-52 (66)
230 COG1318 Predicted transcriptio 77.2 4.7 0.0001 33.4 4.5 59 221-287 25-83 (182)
231 PF00165 HTH_AraC: Bacterial r 77.2 3.7 8E-05 25.3 3.2 27 263-289 6-32 (42)
232 PF11023 DUF2614: Protein of u 77.0 0.93 2E-05 34.6 0.4 39 4-49 70-108 (114)
233 TIGR02985 Sig70_bacteroi1 RNA 77.0 3.4 7.4E-05 33.1 3.9 32 264-295 128-159 (161)
234 TIGR00721 tfx DNA-binding prot 76.9 4 8.6E-05 32.7 4.0 31 264-294 20-50 (137)
235 PRK14559 putative protein seri 76.7 1.6 3.4E-05 44.1 2.1 7 118-124 160-166 (645)
236 PF05344 DUF746: Domain of Unk 76.6 6.3 0.00014 27.1 4.3 40 259-298 7-46 (65)
237 TIGR01764 excise DNA binding d 76.4 3 6.6E-05 26.1 2.8 22 266-287 2-23 (49)
238 cd06571 Bac_DnaA_C C-terminal 76.4 15 0.00033 26.9 6.9 42 153-197 33-75 (90)
239 cd04476 RPA1_DBD_C RPA1_DBD_C: 76.4 2.1 4.6E-05 35.3 2.5 28 4-34 35-62 (166)
240 PF09862 DUF2089: Protein of u 76.2 3.7 7.9E-05 31.7 3.5 30 266-295 50-79 (113)
241 PF14502 HTH_41: Helix-turn-he 76.2 4.5 9.7E-05 26.1 3.3 28 266-293 7-34 (48)
242 PF13518 HTH_28: Helix-turn-he 76.1 5.8 0.00013 25.3 4.1 32 267-298 14-46 (52)
243 smart00418 HTH_ARSR helix_turn 76.1 6.9 0.00015 25.7 4.7 30 263-292 8-37 (66)
244 smart00420 HTH_DEOR helix_turn 75.9 9.4 0.0002 24.1 5.1 28 265-292 14-41 (53)
245 TIGR02943 Sig70_famx1 RNA poly 75.8 2.3 5.1E-05 35.7 2.7 33 265-297 147-179 (188)
246 cd00730 rubredoxin Rubredoxin; 75.7 2.4 5.2E-05 27.7 2.1 13 24-36 2-14 (50)
247 PF09526 DUF2387: Probable met 75.5 3.2 6.9E-05 29.3 2.7 31 3-33 8-40 (71)
248 PF12840 HTH_20: Helix-turn-he 75.4 5.9 0.00013 26.6 4.1 31 262-292 21-51 (61)
249 PF13453 zf-TFIIB: Transcripti 75.4 2.6 5.6E-05 26.1 2.1 29 5-33 1-29 (41)
250 smart00550 Zalpha Z-DNA-bindin 75.3 8.7 0.00019 26.6 5.0 38 255-292 11-49 (68)
251 PRK13719 conjugal transfer tra 75.2 4.7 0.0001 34.9 4.3 32 264-295 157-188 (217)
252 KOG3134 Predicted membrane pro 75.1 0.88 1.9E-05 39.0 -0.1 33 4-36 1-37 (225)
253 PRK00241 nudC NADH pyrophospha 75.1 2.2 4.7E-05 38.1 2.3 29 3-33 99-127 (256)
254 PF08279 HTH_11: HTH domain; 75.0 7.1 0.00015 25.4 4.4 34 161-195 10-43 (55)
255 PF00440 TetR_N: Bacterial reg 75.0 5.3 0.00011 25.3 3.6 39 253-291 4-42 (47)
256 PRK14890 putative Zn-ribbon RN 74.7 2.6 5.7E-05 28.4 2.1 29 2-32 6-34 (59)
257 KOG1088 Uncharacterized conser 74.7 1.3 2.8E-05 34.1 0.6 17 17-33 92-108 (124)
258 PF12728 HTH_17: Helix-turn-he 74.7 3.5 7.5E-05 26.5 2.7 22 266-287 2-23 (51)
259 TIGR02937 sigma70-ECF RNA poly 74.6 4.3 9.3E-05 31.8 3.8 31 265-295 126-156 (158)
260 PF01325 Fe_dep_repress: Iron 74.6 11 0.00023 25.5 5.1 37 155-193 12-48 (60)
261 PRK09642 RNA polymerase sigma 74.6 3.7 8E-05 33.2 3.5 33 265-297 122-154 (160)
262 PF02082 Rrf2: Transcriptional 74.5 5.1 0.00011 28.9 3.8 44 149-193 8-51 (83)
263 PRK10840 transcriptional regul 74.5 4.6 0.0001 34.4 4.2 32 264-295 164-195 (216)
264 PRK12520 RNA polymerase sigma 74.2 2.9 6.3E-05 35.1 2.8 33 265-297 147-179 (191)
265 PF14952 zf-tcix: Putative tre 74.2 1.9 4.2E-05 27.0 1.2 26 4-35 12-39 (44)
266 PF06827 zf-FPG_IleRS: Zinc fi 73.9 2.5 5.5E-05 24.1 1.7 28 4-31 2-29 (30)
267 PF01418 HTH_6: Helix-turn-hel 73.9 9.9 0.00021 27.0 5.1 25 265-289 34-58 (77)
268 PRK15411 rcsA colanic acid cap 73.7 4.9 0.00011 34.5 4.1 32 264-295 151-182 (207)
269 PRK10857 DNA-binding transcrip 73.6 8.8 0.00019 31.7 5.5 46 147-193 6-51 (164)
270 PRK08351 DNA-directed RNA poly 73.6 1.9 4.2E-05 29.3 1.2 24 1-32 1-24 (61)
271 CHL00174 accD acetyl-CoA carbo 73.3 0.73 1.6E-05 41.8 -1.1 30 4-34 39-68 (296)
272 PRK07500 rpoH2 RNA polymerase 73.3 72 0.0016 28.9 16.8 35 263-297 243-277 (289)
273 PRK08215 sporulation sigma fac 73.2 65 0.0014 28.4 16.6 31 264-294 224-254 (258)
274 PF14446 Prok-RING_1: Prokaryo 73.2 3 6.6E-05 27.6 2.0 27 3-33 5-31 (54)
275 PRK15320 transcriptional activ 73.0 5.3 0.00012 34.1 4.0 32 264-295 178-209 (251)
276 PRK05508 methionine sulfoxide 73.0 3.1 6.8E-05 32.3 2.4 33 17-49 27-61 (119)
277 PRK12529 RNA polymerase sigma 72.8 5.4 0.00012 33.1 4.1 35 264-298 142-176 (178)
278 PRK12531 RNA polymerase sigma 72.8 4.1 9E-05 34.3 3.4 35 264-298 156-190 (194)
279 cd00202 ZnF_GATA Zinc finger D 72.8 1.3 2.7E-05 29.5 0.2 30 5-34 1-32 (54)
280 TIGR00515 accD acetyl-CoA carb 72.8 0.8 1.7E-05 41.5 -1.0 29 4-33 27-55 (285)
281 TIGR02980 SigBFG RNA polymeras 72.8 61 0.0013 27.8 16.3 31 264-294 193-223 (227)
282 KOG0402 60S ribosomal protein 72.6 1.2 2.6E-05 32.0 0.1 31 3-35 36-66 (92)
283 PF03444 HrcA_DNA-bdg: Winged 72.5 6.7 0.00014 28.1 3.8 29 263-291 21-49 (78)
284 COG2888 Predicted Zn-ribbon RN 72.5 2.6 5.6E-05 28.3 1.6 28 4-32 28-59 (61)
285 TIGR02885 spore_sigF RNA polym 72.5 63 0.0014 27.9 16.2 31 264-294 198-228 (231)
286 COG1510 Predicted transcriptio 72.4 6.1 0.00013 32.8 4.1 40 253-292 29-68 (177)
287 PRK15201 fimbriae regulatory p 72.2 6.4 0.00014 33.0 4.2 32 264-295 147-178 (198)
288 PF05732 RepL: Firmicute plasm 71.9 9.3 0.0002 31.7 5.2 27 266-292 76-102 (165)
289 PF04218 CENP-B_N: CENP-B N-te 71.9 3.6 7.9E-05 27.1 2.3 23 266-288 23-45 (53)
290 PF06044 DRP: Dam-replacing fa 71.8 1.8 3.9E-05 37.8 0.9 29 4-33 32-63 (254)
291 PF14353 CpXC: CpXC protein 71.7 3 6.5E-05 32.8 2.2 11 23-33 38-48 (128)
292 PF13545 HTH_Crp_2: Crp-like h 71.6 11 0.00024 26.2 5.0 43 151-194 3-55 (76)
293 cd01104 HTH_MlrA-CarA Helix-Tu 71.5 4.8 0.0001 27.5 2.9 22 267-288 2-23 (68)
294 PRK12532 RNA polymerase sigma 71.5 4.1 8.8E-05 34.3 3.1 33 265-297 152-184 (195)
295 COG2093 DNA-directed RNA polym 71.4 2.3 5.1E-05 28.8 1.2 25 2-32 3-27 (64)
296 COG4530 Uncharacterized protei 71.4 2.2 4.8E-05 32.4 1.2 30 3-35 9-38 (129)
297 TIGR02997 Sig70-cyanoRpoD RNA 71.3 80 0.0017 28.6 19.0 28 264-291 268-295 (298)
298 PF13022 HTH_Tnp_1_2: Helix-tu 70.8 7.9 0.00017 31.0 4.3 54 245-298 11-70 (142)
299 COG1773 Rubredoxin [Energy pro 70.7 3 6.4E-05 27.7 1.6 23 3-29 3-25 (55)
300 PF00356 LacI: Bacterial regul 70.6 6.4 0.00014 25.1 3.1 20 168-188 1-20 (46)
301 PRK00222 methionine sulfoxide 70.6 3.6 7.8E-05 33.1 2.4 35 16-50 36-72 (142)
302 TIGR03829 YokU_near_AblA uncha 70.5 3.4 7.4E-05 30.4 2.0 34 5-38 1-50 (89)
303 TIGR02944 suf_reg_Xantho FeS a 70.4 11 0.00025 29.5 5.3 39 253-292 14-52 (130)
304 COG2197 CitB Response regulato 70.4 6.4 0.00014 33.9 4.1 33 262-294 160-192 (211)
305 PRK12543 RNA polymerase sigma 70.4 3.5 7.6E-05 34.2 2.4 33 265-297 133-165 (179)
306 PF08299 Bac_DnaA_C: Bacterial 70.3 33 0.00072 23.8 8.3 67 209-289 1-70 (70)
307 PRK06288 RNA polymerase sigma 70.3 79 0.0017 28.1 19.5 31 264-294 227-257 (268)
308 COG1654 BirA Biotin operon rep 70.1 11 0.00023 27.2 4.5 30 263-292 17-46 (79)
309 PRK05654 acetyl-CoA carboxylas 69.9 1 2.2E-05 41.0 -1.0 30 4-34 28-57 (292)
310 PF04606 Ogr_Delta: Ogr/Delta- 69.9 3.8 8.3E-05 26.2 2.0 28 5-33 1-37 (47)
311 TIGR02999 Sig-70_X6 RNA polyme 69.8 5.5 0.00012 33.0 3.5 31 264-294 149-179 (183)
312 PRK09652 RNA polymerase sigma 69.8 4.2 9E-05 33.4 2.8 34 264-297 143-176 (182)
313 TIGR02983 SigE-fam_strep RNA p 69.8 5.8 0.00013 32.1 3.6 33 265-297 126-158 (162)
314 COG2771 CsgD DNA-binding HTH d 69.8 9.8 0.00021 25.3 4.2 31 265-295 19-49 (65)
315 KOG3507 DNA-directed RNA polym 69.6 3 6.5E-05 27.9 1.4 25 5-33 22-47 (62)
316 PRK09391 fixK transcriptional 69.4 31 0.00067 29.8 8.3 29 264-292 178-206 (230)
317 PF13413 HTH_25: Helix-turn-he 69.2 3.4 7.4E-05 28.2 1.7 56 160-226 4-60 (62)
318 PRK12544 RNA polymerase sigma 69.2 4.2 9.2E-05 34.8 2.7 39 265-303 164-203 (206)
319 PRK03975 tfx putative transcri 69.1 7 0.00015 31.5 3.7 29 264-292 20-48 (141)
320 cd00729 rubredoxin_SM Rubredox 69.0 4.3 9.3E-05 24.1 1.9 23 5-31 4-26 (34)
321 KOG2593 Transcription initiati 69.0 2.5 5.4E-05 40.0 1.3 33 3-35 128-165 (436)
322 TIGR03697 NtcA_cyano global ni 69.0 25 0.00054 29.1 7.4 29 165-194 142-170 (193)
323 PF05043 Mga: Mga helix-turn-h 69.0 6.8 0.00015 28.3 3.4 34 262-295 27-60 (87)
324 TIGR02844 spore_III_D sporulat 69.0 5.5 0.00012 28.8 2.8 23 264-286 18-40 (80)
325 PF09339 HTH_IclR: IclR helix- 68.9 8.4 0.00018 24.9 3.5 30 263-292 16-45 (52)
326 PRK10188 DNA-binding transcrip 68.8 7.2 0.00016 34.3 4.2 32 264-295 193-224 (240)
327 COG1779 C4-type Zn-finger prot 68.7 3.3 7.1E-05 35.1 1.8 34 4-37 15-57 (201)
328 PF13790 DUF4182: Domain of un 68.7 2.5 5.3E-05 25.8 0.8 14 21-34 1-14 (38)
329 PF01726 LexA_DNA_bind: LexA D 68.4 12 0.00026 25.8 4.4 31 161-192 20-51 (65)
330 PRK09645 RNA polymerase sigma 68.4 6.2 0.00013 32.4 3.5 33 265-297 134-166 (173)
331 cd00092 HTH_CRP helix_turn_hel 68.4 23 0.0005 23.7 5.9 30 164-194 23-52 (67)
332 PRK11920 rirA iron-responsive 68.3 15 0.00032 30.0 5.6 45 148-194 7-51 (153)
333 TIGR03020 EpsA transcriptional 68.3 7.6 0.00016 34.4 4.2 32 264-295 204-235 (247)
334 PRK06759 RNA polymerase factor 68.2 8 0.00017 30.9 4.1 30 264-293 121-150 (154)
335 PF04703 FaeA: FaeA-like prote 68.1 6.8 0.00015 26.8 3.0 30 263-292 13-42 (62)
336 PRK07670 RNA polymerase sigma 68.1 84 0.0018 27.6 19.5 32 264-295 216-247 (251)
337 cd04764 HTH_MlrA-like_sg1 Heli 68.1 6.6 0.00014 26.8 3.1 22 267-288 2-23 (67)
338 PF12116 SpoIIID: Stage III sp 68.1 5.2 0.00011 28.7 2.5 35 257-294 11-45 (82)
339 PRK07122 RNA polymerase sigma 68.0 89 0.0019 27.8 17.9 31 264-294 230-260 (264)
340 PRK07921 RNA polymerase sigma 67.9 1E+02 0.0022 28.5 19.0 31 264-294 281-311 (324)
341 TIGR02859 spore_sigH RNA polym 67.9 7.2 0.00016 32.7 3.9 33 264-296 164-196 (198)
342 TIGR02950 SigM_subfam RNA poly 67.9 6.4 0.00014 31.4 3.4 32 264-295 120-151 (154)
343 smart00354 HTH_LACI helix_turn 67.9 5.2 0.00011 27.8 2.5 20 267-286 2-21 (70)
344 PRK13918 CRP/FNR family transc 67.7 32 0.00068 28.8 7.8 29 264-292 148-176 (202)
345 PRK12528 RNA polymerase sigma 67.6 7.9 0.00017 31.3 4.0 29 265-293 129-157 (161)
346 TIGR03831 YgiT_finger YgiT-typ 67.4 4.1 8.8E-05 25.5 1.7 10 24-33 33-42 (46)
347 PRK09649 RNA polymerase sigma 67.2 8.9 0.00019 32.0 4.3 32 264-295 145-176 (185)
348 COG0777 AccD Acetyl-CoA carbox 67.0 1.6 3.5E-05 38.8 -0.3 29 4-33 29-57 (294)
349 PRK09047 RNA polymerase factor 67.0 7.9 0.00017 31.2 3.8 33 264-296 121-153 (161)
350 PF07638 Sigma70_ECF: ECF sigm 66.9 7.5 0.00016 32.6 3.7 29 265-293 151-179 (185)
351 TIGR02952 Sig70_famx2 RNA poly 66.8 7.9 0.00017 31.5 3.8 30 265-294 138-167 (170)
352 PF01381 HTH_3: Helix-turn-hel 66.6 6 0.00013 25.6 2.5 25 264-288 8-32 (55)
353 cd00090 HTH_ARSR Arsenical Res 66.5 15 0.00032 24.8 4.7 27 266-292 21-47 (78)
354 PF01047 MarR: MarR family; I 66.4 16 0.00034 24.0 4.6 28 265-292 17-44 (59)
355 PRK09644 RNA polymerase sigma 66.4 6.2 0.00013 32.1 3.1 34 264-297 123-156 (165)
356 PRK09639 RNA polymerase sigma 66.3 8.6 0.00019 31.2 3.9 34 264-297 126-159 (166)
357 PRK12527 RNA polymerase sigma 66.3 6.5 0.00014 31.8 3.2 34 264-297 120-153 (159)
358 KOG1010 Rb (Retinoblastoma tum 66.2 11 0.00025 38.7 5.3 77 214-290 684-764 (920)
359 PRK12380 hydrogenase nickel in 66.1 3.7 8E-05 31.7 1.6 16 15-30 62-77 (113)
360 PRK14086 dnaA chromosomal repl 66.0 1E+02 0.0022 31.2 12.0 41 252-294 558-598 (617)
361 COG1321 TroR Mn-dependent tran 65.9 12 0.00026 30.6 4.7 38 254-292 14-51 (154)
362 PF00376 MerR: MerR family reg 65.9 5.7 0.00012 24.2 2.0 18 267-284 1-18 (38)
363 TIGR00155 pqiA_fam integral me 65.7 4.3 9.3E-05 38.7 2.2 30 5-34 15-44 (403)
364 TIGR02947 SigH_actino RNA poly 65.7 6.6 0.00014 32.9 3.2 33 264-296 146-178 (193)
365 PF13613 HTH_Tnp_4: Helix-turn 65.7 16 0.00035 23.8 4.4 39 158-197 11-49 (53)
366 PF10080 DUF2318: Predicted me 65.6 5.2 0.00011 30.3 2.2 29 5-36 37-65 (102)
367 TIGR02531 yecD_yerC TrpR-relat 65.5 9.6 0.00021 28.1 3.6 20 265-284 50-69 (88)
368 TIGR02392 rpoH_proteo alternat 65.2 1E+02 0.0022 27.5 17.7 33 263-295 234-266 (270)
369 TIGR00310 ZPR1_znf ZPR1 zinc f 65.1 4.7 0.0001 34.3 2.1 31 5-35 2-42 (192)
370 PF00126 HTH_1: Bacterial regu 65.0 12 0.00026 25.0 3.8 31 266-296 14-44 (60)
371 smart00550 Zalpha Z-DNA-bindin 65.0 23 0.00049 24.5 5.3 38 156-194 11-49 (68)
372 PF13412 HTH_24: Winged helix- 64.8 27 0.00058 21.9 5.3 29 164-193 15-43 (48)
373 PRK12535 RNA polymerase sigma 64.8 8.7 0.00019 32.5 3.8 39 265-303 149-187 (196)
374 cd04763 HTH_MlrA-like Helix-Tu 64.7 7.8 0.00017 26.6 2.9 22 267-288 2-23 (68)
375 PRK08301 sporulation sigma fac 64.6 7.5 0.00016 33.8 3.4 30 264-293 197-226 (234)
376 PF01599 Ribosomal_S27: Riboso 64.5 8.2 0.00018 24.8 2.6 26 4-31 19-46 (47)
377 PRK12547 RNA polymerase sigma 64.5 8.5 0.00018 31.4 3.6 34 264-297 127-160 (164)
378 PRK13870 transcriptional regul 64.5 9.9 0.00022 33.3 4.2 32 264-295 187-218 (234)
379 PRK12530 RNA polymerase sigma 64.4 6.5 0.00014 33.0 2.9 33 265-297 150-182 (189)
380 PRK00149 dnaA chromosomal repl 64.2 72 0.0016 30.8 10.5 41 252-294 391-432 (450)
381 TIGR02989 Sig-70_gvs1 RNA poly 64.2 11 0.00023 30.3 4.1 30 265-294 127-156 (159)
382 PF13463 HTH_27: Winged helix 64.1 13 0.00027 25.2 3.9 31 262-292 15-45 (68)
383 PF01396 zf-C4_Topoisom: Topoi 64.1 11 0.00025 23.0 3.2 29 4-33 2-34 (39)
384 TIGR00100 hypA hydrogenase nic 63.9 4.4 9.6E-05 31.4 1.6 19 14-32 61-79 (115)
385 PRK13919 putative RNA polymera 63.8 8.9 0.00019 31.8 3.6 31 265-295 151-181 (186)
386 PRK15418 transcriptional regul 63.8 11 0.00023 34.8 4.4 36 256-291 20-55 (318)
387 PRK12542 RNA polymerase sigma 63.6 8.3 0.00018 32.1 3.4 32 265-296 138-169 (185)
388 PF04216 FdhE: Protein involve 63.6 4.6 9.9E-05 36.7 1.9 29 4-32 173-206 (290)
389 COG3809 Uncharacterized protei 63.6 6.1 0.00013 28.1 2.1 29 3-33 1-31 (88)
390 smart00346 HTH_ICLR helix_turn 63.5 27 0.00058 25.1 5.8 29 264-292 19-47 (91)
391 TIGR02366 DHAK_reg probable di 63.5 8.5 0.00018 31.6 3.4 49 248-296 6-54 (176)
392 smart00419 HTH_CRP helix_turn_ 63.5 14 0.00031 22.8 3.8 29 164-193 6-34 (48)
393 TIGR00595 priA primosomal prot 63.4 6.3 0.00014 38.8 3.0 30 3-34 222-251 (505)
394 PRK09415 RNA polymerase factor 63.4 8.5 0.00018 31.9 3.4 33 265-297 143-175 (179)
395 PRK11475 DNA-binding transcrip 63.3 11 0.00024 32.3 4.2 31 265-295 149-179 (207)
396 PRK10434 srlR DNA-bindng trans 63.3 7 0.00015 34.8 3.0 29 264-292 18-46 (256)
397 TIGR02954 Sig70_famx3 RNA poly 63.2 9.4 0.0002 31.2 3.6 40 254-295 126-165 (169)
398 PF07191 zinc-ribbons_6: zinc- 63.1 7.1 0.00015 27.4 2.3 26 4-33 2-27 (70)
399 PRK05580 primosome assembly pr 63.1 6.2 0.00013 40.4 3.0 29 4-34 391-419 (679)
400 TIGR01384 TFS_arch transcripti 63.1 6.2 0.00014 29.8 2.3 28 4-32 63-99 (104)
401 PF06056 Terminase_5: Putative 63.1 11 0.00025 25.3 3.3 24 265-288 13-36 (58)
402 PRK03824 hypA hydrogenase nick 63.0 4.6 0.0001 32.3 1.6 21 14-34 61-81 (135)
403 TIGR00357 methionine-R-sulfoxi 63.0 5.4 0.00012 31.8 2.0 34 17-50 34-69 (134)
404 TIGR01562 FdhE formate dehydro 62.8 6.3 0.00014 36.1 2.6 9 25-33 254-262 (305)
405 PRK11511 DNA-binding transcrip 62.8 31 0.00067 27.0 6.3 44 246-290 7-50 (127)
406 TIGR02010 IscR iron-sulfur clu 62.8 15 0.00032 29.2 4.5 40 253-292 13-52 (135)
407 PRK12518 RNA polymerase sigma 62.8 7.9 0.00017 31.7 3.1 35 264-298 135-169 (175)
408 PRK12533 RNA polymerase sigma 62.7 8.4 0.00018 33.3 3.4 33 264-296 149-181 (216)
409 smart00422 HTH_MERR helix_turn 62.7 7.9 0.00017 26.5 2.6 21 267-287 2-22 (70)
410 PF13411 MerR_1: MerR HTH fami 62.7 6.4 0.00014 26.9 2.1 21 267-287 2-22 (69)
411 PRK03564 formate dehydrogenase 62.6 6.8 0.00015 35.9 2.8 9 4-12 188-196 (309)
412 TIGR02984 Sig-70_plancto1 RNA 62.6 9.9 0.00021 31.5 3.7 32 264-295 155-186 (189)
413 PF12172 DUF35_N: Rubredoxin-l 62.6 4.1 8.9E-05 24.5 1.0 21 4-30 12-32 (37)
414 PRK10219 DNA-binding transcrip 62.5 35 0.00075 25.5 6.4 38 251-289 8-45 (107)
415 COG3355 Predicted transcriptio 62.5 18 0.0004 28.5 4.8 38 255-292 32-69 (126)
416 PF07900 DUF1670: Protein of u 62.4 69 0.0015 27.8 8.6 110 163-285 102-217 (220)
417 PRK10072 putative transcriptio 62.3 8.4 0.00018 28.9 2.8 25 263-287 44-68 (96)
418 COG4643 Uncharacterized protei 62.3 4.2 9.2E-05 37.3 1.4 26 5-30 34-61 (366)
419 PF09889 DUF2116: Uncharacteri 62.3 2.5 5.4E-05 28.6 -0.0 27 2-34 2-29 (59)
420 PF13556 HTH_30: PucR C-termin 62.2 13 0.00028 24.9 3.5 33 265-297 12-44 (59)
421 PF02954 HTH_8: Bacterial regu 62.2 15 0.00032 22.7 3.5 23 266-288 19-41 (42)
422 PRK12519 RNA polymerase sigma 62.2 8.6 0.00019 32.2 3.3 30 265-294 157-186 (194)
423 KOG2907 RNA polymerase I trans 62.1 2.9 6.2E-05 32.0 0.3 31 3-35 7-37 (116)
424 PF13551 HTH_29: Winged helix- 61.9 12 0.00027 27.9 3.8 26 267-292 14-39 (112)
425 PRK12511 RNA polymerase sigma 61.8 8.8 0.00019 32.1 3.2 32 265-296 127-158 (182)
426 PRK09483 response regulator; P 61.8 12 0.00027 31.2 4.2 32 264-295 162-193 (217)
427 PRK12525 RNA polymerase sigma 61.8 11 0.00025 30.7 3.9 30 264-293 133-162 (168)
428 PRK11920 rirA iron-responsive 61.8 16 0.00036 29.7 4.7 39 253-292 13-51 (153)
429 PRK12537 RNA polymerase sigma 61.7 10 0.00022 31.5 3.6 31 264-294 148-178 (182)
430 PRK11753 DNA-binding transcrip 61.5 10 0.00023 32.0 3.7 29 264-292 167-195 (211)
431 PF13744 HTH_37: Helix-turn-he 61.4 18 0.00038 25.9 4.3 30 257-286 23-52 (80)
432 PF13011 LZ_Tnp_IS481: leucine 61.4 20 0.00043 26.2 4.5 37 256-292 16-52 (85)
433 PF04545 Sigma70_r4: Sigma-70, 61.4 22 0.00047 22.6 4.4 31 164-195 18-48 (50)
434 TIGR02939 RpoE_Sigma70 RNA pol 61.3 9.9 0.00021 31.6 3.5 34 264-297 153-186 (190)
435 PRK05572 sporulation sigma fac 61.2 1.1E+02 0.0025 26.7 15.9 33 264-296 217-249 (252)
436 PF00165 HTH_AraC: Bacterial r 61.2 15 0.00033 22.4 3.5 26 164-190 6-31 (42)
437 PRK12536 RNA polymerase sigma 61.1 10 0.00022 31.4 3.5 32 265-296 145-176 (181)
438 PRK13509 transcriptional repre 61.1 10 0.00022 33.6 3.6 29 264-292 18-46 (251)
439 PRK12517 RNA polymerase sigma 61.0 9 0.00019 32.1 3.2 33 265-297 144-176 (188)
440 PF01485 IBR: IBR domain; Int 61.0 5.4 0.00012 26.7 1.5 29 3-33 18-50 (64)
441 PF08063 PADR1: PADR1 (NUC008) 60.9 5.1 0.00011 26.7 1.3 22 4-28 15-36 (55)
442 PRK05658 RNA polymerase sigma 60.9 1.9E+02 0.0042 29.2 16.4 31 264-294 575-605 (619)
443 PRK15103 paraquat-inducible me 60.8 5.9 0.00013 38.0 2.2 32 4-35 11-42 (419)
444 TIGR02850 spore_sigG RNA polym 60.6 1.2E+02 0.0026 26.7 16.3 31 264-294 221-251 (254)
445 PRK01110 rpmF 50S ribosomal pr 60.6 6.3 0.00014 26.7 1.7 28 4-39 28-55 (60)
446 PRK12516 RNA polymerase sigma 60.3 10 0.00022 31.8 3.4 34 264-297 131-164 (187)
447 TIGR02959 SigZ RNA polymerase 60.2 10 0.00022 31.2 3.3 33 264-296 115-147 (170)
448 TIGR02835 spore_sigmaE RNA pol 60.1 11 0.00024 32.8 3.7 30 264-293 197-226 (234)
449 PRK06930 positive control sigm 60.0 9 0.00019 31.9 2.9 33 264-296 129-161 (170)
450 PRK08295 RNA polymerase factor 60.0 10 0.00022 32.1 3.4 33 265-297 170-202 (208)
451 TIGR00738 rrf2_super rrf2 fami 59.9 24 0.00051 27.5 5.3 43 149-193 8-51 (132)
452 PHA00542 putative Cro-like pro 59.8 11 0.00024 27.1 3.1 25 263-287 29-53 (82)
453 PF14471 DUF4428: Domain of un 59.8 2.8 6.1E-05 27.5 -0.1 28 5-33 1-30 (51)
454 PRK12366 replication factor A; 59.8 5.3 0.00012 40.5 1.8 25 4-32 533-557 (637)
455 PF06397 Desulfoferrod_N: Desu 59.7 4.1 8.9E-05 24.6 0.6 22 4-26 7-28 (36)
456 PRK12514 RNA polymerase sigma 59.7 11 0.00024 31.1 3.5 31 265-295 145-175 (179)
457 PRK15482 transcriptional regul 59.7 32 0.0007 30.8 6.8 54 213-288 3-57 (285)
458 PRK12522 RNA polymerase sigma 59.6 9.9 0.00021 31.2 3.1 33 264-296 134-166 (173)
459 PRK12534 RNA polymerase sigma 59.4 11 0.00024 31.4 3.4 32 264-295 152-183 (187)
460 PRK11923 algU RNA polymerase s 59.3 13 0.00028 31.1 3.9 31 265-295 154-184 (193)
461 TIGR03070 couple_hipB transcri 59.2 11 0.00024 24.3 2.8 23 264-286 14-36 (58)
462 PRK05602 RNA polymerase sigma 59.1 11 0.00024 31.3 3.4 34 264-297 143-176 (186)
463 PF07037 DUF1323: Putative tra 59.1 11 0.00024 29.3 3.0 23 266-288 1-23 (122)
464 PRK14873 primosome assembly pr 59.0 7.3 0.00016 39.7 2.6 28 3-32 392-419 (665)
465 PRK12540 RNA polymerase sigma 59.0 13 0.00029 30.9 3.9 33 264-296 126-158 (182)
466 TIGR02960 SigX5 RNA polymerase 59.0 12 0.00026 34.2 3.9 35 264-298 157-191 (324)
467 PRK06260 threonine synthase; V 58.8 4.3 9.2E-05 38.6 0.9 30 1-34 1-30 (397)
468 PF09241 Herp-Cyclin: Herpesvi 58.8 66 0.0014 23.2 8.7 84 211-294 5-99 (106)
469 smart00709 Zpr1 Duplicated dom 58.8 8.3 0.00018 31.8 2.5 31 5-35 2-41 (160)
470 PRK10100 DNA-binding transcrip 58.8 15 0.00032 31.8 4.2 31 265-295 170-200 (216)
471 PF13404 HTH_AsnC-type: AsnC-t 58.8 35 0.00077 21.1 4.8 29 162-191 13-41 (42)
472 PF05269 Phage_CII: Bacterioph 58.7 5.4 0.00012 29.5 1.2 31 266-296 24-54 (91)
473 TIGR02944 suf_reg_Xantho FeS a 58.7 30 0.00064 27.0 5.6 44 148-193 8-51 (130)
474 PRK09648 RNA polymerase sigma 58.5 12 0.00027 31.1 3.6 31 265-295 155-185 (189)
475 PRK14559 putative protein seri 58.3 5.7 0.00012 40.3 1.7 14 21-34 39-52 (645)
476 PRK12545 RNA polymerase sigma 58.3 11 0.00023 32.1 3.2 32 264-295 154-185 (201)
477 PRK09651 RNA polymerase sigma 58.2 14 0.00031 30.3 3.9 30 264-293 134-163 (172)
478 TIGR02702 SufR_cyano iron-sulf 58.2 22 0.00048 30.3 5.1 29 264-292 14-42 (203)
479 COG1476 Predicted transcriptio 58.2 8.5 0.00019 26.8 2.1 24 264-287 13-36 (68)
480 PF13936 HTH_38: Helix-turn-he 58.1 25 0.00054 21.9 4.1 28 162-190 16-43 (44)
481 PRK09643 RNA polymerase sigma 58.1 11 0.00025 31.6 3.3 33 265-297 150-182 (192)
482 COG2816 NPY1 NTP pyrophosphohy 58.0 7 0.00015 35.1 2.0 30 3-34 111-140 (279)
483 PF14206 Cys_rich_CPCC: Cystei 58.0 11 0.00023 27.1 2.6 28 4-32 2-29 (78)
484 PRK11924 RNA polymerase sigma 57.8 11 0.00024 30.7 3.2 34 264-297 140-173 (179)
485 PF01641 SelR: SelR domain; I 57.8 6.8 0.00015 30.8 1.7 34 17-50 31-66 (124)
486 PRK11512 DNA-binding transcrip 57.7 30 0.00066 27.5 5.6 30 263-292 52-81 (144)
487 cd00569 HTH_Hin_like Helix-tur 57.6 15 0.00032 20.5 3.0 21 265-285 21-41 (42)
488 PRK06704 RNA polymerase factor 57.6 10 0.00022 33.2 2.9 33 265-297 132-164 (228)
489 smart00351 PAX Paired Box doma 57.5 17 0.00037 28.5 4.0 27 265-291 33-59 (125)
490 TIGR02948 SigW_bacill RNA poly 57.5 13 0.00027 30.8 3.5 32 264-295 151-182 (187)
491 PRK12541 RNA polymerase sigma 57.3 15 0.00033 29.6 3.9 30 265-294 128-157 (161)
492 COG4861 Uncharacterized protei 57.2 8.8 0.00019 34.2 2.4 52 241-292 135-190 (345)
493 COG1595 RpoE DNA-directed RNA 57.2 13 0.00028 30.9 3.5 33 265-297 143-175 (182)
494 PF09339 HTH_IclR: IclR helix- 57.2 20 0.00044 23.1 3.7 36 157-193 9-44 (52)
495 PF04703 FaeA: FaeA-like prote 57.2 29 0.00063 23.7 4.5 34 161-195 10-43 (62)
496 PRK11302 DNA-binding transcrip 57.2 39 0.00084 30.1 6.8 53 214-288 4-57 (284)
497 TIGR02404 trehalos_R_Bsub treh 57.1 14 0.00031 32.0 3.9 30 263-292 21-51 (233)
498 PRK07037 extracytoplasmic-func 57.0 13 0.00029 29.9 3.5 31 265-295 125-155 (163)
499 PRK09863 putative frv operon r 56.9 1.3E+02 0.0029 30.0 11.2 105 165-294 16-121 (584)
500 PF13824 zf-Mss51: Zinc-finger 56.9 8.4 0.00018 25.6 1.7 24 5-33 1-24 (55)
No 1
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=4.6e-76 Score=507.69 Aligned_cols=301 Identities=58% Similarity=0.902 Sum_probs=281.3
Q ss_pred CCCCCCCCCCc-eeeeCCCCceEcCCCcccccCcccccccccccccCCCCCCCCCccCCCCCCcccCCCcceEEecCCCC
Q 021438 4 SYCADCKRLTE-VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG 82 (312)
Q Consensus 4 ~~Cp~Cg~~~~-ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~ 82 (312)
+.||+|+..+. +++|+.+|++||..||+|+++++||.++|||+|++|+++.||+|||++.||++.++++.|+|+++. +
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~-g 79 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGT-G 79 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCC-C
Confidence 47999998665 999999999999999999999999999999999999989999999999999999999999999987 4
Q ss_pred CCcccccccchhcccc--CCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH
Q 021438 83 GSTELLSGSLGKLQAR--SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIAC 160 (312)
Q Consensus 83 ~~~~~~~~~l~~~~~~--~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~ac 160 (312)
.++.+++ .|.+||++ +++.|+.+..+|..|..||+.++||..+.+.|.++|+++.+.+.++||+.++++|||||+||
T Consensus 80 ~~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 80 TSSSFAS-SLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC 158 (308)
T ss_pred CCHHHHH-HHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence 4444443 38899985 56889999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh
Q 021438 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240 (312)
Q Consensus 161 r~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~ 240 (312)
|+++.|||++||+.++ +++.++|++.++.|.+.|+.. .+....+..+||+|||+.|+|+.+++..|.++++.+.+
T Consensus 159 Rq~~~pRT~kEI~~~a-nv~kKEIgr~~K~i~~~l~~s----~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~ 233 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAVA-NVSKKEIGRCVKLIGEALETS----VDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEE 233 (308)
T ss_pred HhcCCCchHHHHHHHH-cCCHHHHHHHHHHHHHHHhcc----chhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 9999999999999999 699999999999999998862 23335568999999999999999999999999999998
Q ss_pred --ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCCccccccccccccC
Q 021438 241 --LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNLK 311 (312)
Q Consensus 241 --l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~~~~~~~~~~l~ 311 (312)
+..||+|.+||||+|||+++++..+++++||..++||+++|||+.||+||+++..|+|.||.+++++|+||
T Consensus 234 ~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~liP~~~a~~~~lk~Lp 306 (308)
T KOG1597|consen 234 MDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHADKLIPSWYANAVPLKNLP 306 (308)
T ss_pred hccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHhhchhhhChhhhccccchhhcC
Confidence 67899999999999999999999999999999999999999999999999999999999999999999998
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=2.6e-72 Score=511.63 Aligned_cols=287 Identities=35% Similarity=0.628 Sum_probs=266.9
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccCCCCCCCCCccCCCCCCcccCCCcceEEecCCCC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG 82 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~ 82 (312)
...||+||+ +++++|+.+|++||++||+|++|++||+|||||+|++|+. +|++|+|+|.++++||.|++|.|+++..+
T Consensus 11 ~~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~~-~~~~RvG~~~~~~~~~~gl~T~I~~~~~~ 88 (310)
T PRK00423 11 KLVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQR-EKRSRVGAPMTYTIHDKGLSTDIDWRNKD 88 (310)
T ss_pred CCcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCcccc-CCccccCCCCCccccCCCCceEeecCCcc
Confidence 357999998 6899999999999999999999999999999999998764 68999999999999999999999976544
Q ss_pred CCcccccc-------cchhcccc---CCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHH
Q 021438 83 GSTELLSG-------SLGKLQAR---SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIV 152 (312)
Q Consensus 83 ~~~~~~~~-------~l~~~~~~---~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~ia 152 (312)
..|..++. +|++||++ .++.||+|..+++.|+++|+.|+||+.++++|..||+++++.+.++|++.+.++
T Consensus 89 ~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~ 168 (310)
T PRK00423 89 SYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV 168 (310)
T ss_pred cccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHH
Confidence 45544432 37889886 367899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHH
Q 021438 153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQ 232 (312)
Q Consensus 153 aAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~ 232 (312)
|||||+|||++++|+|++||+.++ ++++++|+++|+.|.+.|++ ++++.+|++||+|||+.|++++++.+.|+
T Consensus 169 AAclYiACR~~~~prtl~eI~~~~-~v~~k~i~~~~~~l~k~L~~------~~~~~~p~~~i~r~~~~L~L~~~v~~~A~ 241 (310)
T PRK00423 169 AAALYAACRRCKVPRTLDEIAEVS-RVSRKEIGRCYRFLLRELNL------KLPPTDPIDYVPRFASELGLSGEVQKKAI 241 (310)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHh-CCCHHHHHHHHHHHHHHhCC------CCCCCCHHHHHHHHHHHcCCCHHHHHHHH
Confidence 999999999999999999999999 79999999999999999987 67788999999999999999999999999
Q ss_pred HHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438 233 EAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298 (312)
Q Consensus 233 ~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p 298 (312)
+|++.+.+ +..||+|.+|||||||+|++++|.++|++|||+++||++.||+++||+|.+.++..+|
T Consensus 242 ~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~~~~~ 309 (310)
T PRK00423 242 EILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDIKIP 309 (310)
T ss_pred HHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCcccC
Confidence 99999987 8899999999999999999999999999999999999999999999999999887664
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=4.3e-67 Score=465.49 Aligned_cols=279 Identities=38% Similarity=0.665 Sum_probs=259.8
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccCCCCCCCCCccCCCCCCcccCCCcceEEecCCCC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG 82 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~ 82 (312)
++.||+||+ +++++|++.|++||.+||+|++|+.||.|||||.|+++ ..+ |+|.|.++.+||.|++|+|+++...
T Consensus 1 ~~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~e~---~~~-r~g~P~t~~~~d~~l~t~i~~~~~~ 75 (285)
T COG1405 1 VMSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDER---HER-RVGAPLTPSIHDKGLSTIIGWGDKD 75 (285)
T ss_pred CCCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCccccccc---ccc-cccCCCccccCccchhhhcccchhH
Confidence 368999999 59999999999999999999999999999999999322 334 9999999999999999999987622
Q ss_pred CCcccccccchhcccc---CCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHH
Q 021438 83 GSTELLSGSLGKLQAR---SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIA 159 (312)
Q Consensus 83 ~~~~~~~~~l~~~~~~---~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~a 159 (312)
...+|++||.+ ++.+|+++..++..|+.+++.|+||.++.++|..||+++.+.++++||+.++++|||+|+|
T Consensus 76 -----~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~a 150 (285)
T COG1405 76 -----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAA 150 (285)
T ss_pred -----HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHH
Confidence 12358899975 4578999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh
Q 021438 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE 239 (312)
Q Consensus 160 cr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~ 239 (312)
||+++.|+|+.||+.++ +++.++|+++|+.+.+.|++ .+++.+|.+||+|||+.|+|++++.+.|.+|++.+.
T Consensus 151 cR~~~~prtl~eIa~a~-~V~~kei~rtyr~~~~~L~l------~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~ 223 (285)
T COG1405 151 CRINGVPRTLDEIAKAL-GVSKKEIGRTYRLLVRELKL------KIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAK 223 (285)
T ss_pred HHHcCCCccHHHHHHHH-CCCHHHHHHHHHHHHHhcCC------CCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999 79999999999999999997 677899999999999999999999999999999999
Q ss_pred h--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438 240 D--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298 (312)
Q Consensus 240 ~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p 298 (312)
+ +..||+|.++||||||+|+.++|+++||++||.++|||++|||++||||.++++...+
T Consensus 224 ~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel~~~~~i~~~ 284 (285)
T COG1405 224 RAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELADALDIEVT 284 (285)
T ss_pred HhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHHHHhhccccC
Confidence 8 8899999999999999999999999999999999999999999999999999876553
No 4
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=2.1e-43 Score=328.08 Aligned_cols=253 Identities=22% Similarity=0.387 Sum_probs=224.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccCCCCCCCCCccCCCCCCcccCCCcceEEecCCCCC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG 83 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~~ 83 (312)
+.|++||+ +++..|..+|..+|+.||+|++++.|. +| .+|.+. -.|++|+.++. +
T Consensus 1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~iv--se-v~F~e~--------------------~~G~~v~~~~~-g 55 (521)
T KOG1598|consen 1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIV--AE-VTFVEG--------------------AQGQFVRVGQS-G 55 (521)
T ss_pred CcCCCCCC-CCcccccccCCceeccccceeecccee--EE-eeeecc--------------------cceeEEecccc-C
Confidence 47999999 799999999999999999999999988 44 466632 13677776552 2
Q ss_pred CcccccccchhccccCCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHh
Q 021438 84 STELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163 (312)
Q Consensus 84 ~~~~~~~~l~~~~~~~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~ 163 (312)
.+. + ..++++.++++.+.|..++..|+|++ +++.|..+|+++.+.++.+||+...++|+|+|++||++
T Consensus 56 ~~~--s---------~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e 123 (521)
T KOG1598|consen 56 AGS--S---------LESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLE 123 (521)
T ss_pred Ccc--c---------hHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhh
Confidence 110 0 15678999999999999999999999 99999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCC---HHHHHHHHHHHHHhhh
Q 021438 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMT---NQAVKAAQEAVQKSED 240 (312)
Q Consensus 164 ~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~---~~v~~~A~~i~~~~~~ 240 (312)
++++.+.|++++.+ ++++.||+.|++|.+.|.+.. + .+|.++|..||+||++.|.+. .++...|.+|+++|++
T Consensus 124 ~t~hlliDfS~~Lq-v~Vy~LG~~~l~l~~~L~i~e--n-~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkr 199 (521)
T KOG1598|consen 124 KTDHLLIDFSSYLQ-VSVYDLGSNFLEVTDSLSIGE--N-VSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKR 199 (521)
T ss_pred CCceEEEEeccceE-EehhhhhHHHHHHHHHhcccc--c-cccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHH
Confidence 99999999999995 999999999999999999821 1 278999999999999999753 4589999999999998
Q ss_pred --ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 241 --LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 241 --l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
+.+||+|.+||+||||+||+++|++++..||+.+++|++.||++||+||.+....-+
T Consensus 200 dwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~L 258 (521)
T KOG1598|consen 200 DWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLKEFSDTLSGDL 258 (521)
T ss_pred HHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHHHHhccccccc
Confidence 899999999999999999999999999999999999999999999999999865543
No 5
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.80 E-value=1.7e-18 Score=152.25 Aligned_cols=188 Identities=21% Similarity=0.273 Sum_probs=160.1
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-------
Q 021438 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT------- 179 (312)
Q Consensus 107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v------- 179 (312)
.=+..+|++-|-.|+||+..+.+++.+|++++..+.+.+...+.+++|||.+|++.++.|++++||..+++-+
T Consensus 24 ~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~ 103 (367)
T KOG0835|consen 24 ILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESE 103 (367)
T ss_pred HHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhcc
Confidence 4478999999999999999999999999999999999999999999999999999999999999999987611
Q ss_pred --C-----------HHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHH--HHHHHHHHHHHhhh--cc
Q 021438 180 --T-----------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ--AVKAAQEAVQKSED--LD 242 (312)
Q Consensus 180 --~-----------~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~--v~~~A~~i~~~~~~--l~ 242 (312)
. +..+.++..++.+.||+ ++...+|+.++..|.+.|++++. +.+.+|..++++.+ +.
T Consensus 104 ~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF------~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~ 177 (367)
T KOG0835|consen 104 AAEHLILARLYINLKMQVIRAERRILRELGF------DVHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVF 177 (367)
T ss_pred CcchhhhhhHHhhhhhHHHHHHHHHHHHhCC------eeeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhcccccee
Confidence 0 12344556677888887 77789999999999999999865 58999999999998 88
Q ss_pred CCCChHHHHHHHHHHHHHhcCCCCC-HHHHHHHhCcchhHHHHHHHHHHhhhcccCCcc
Q 021438 243 IRRSPISVAAAVIYIITQLSNDTKP-LKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300 (312)
Q Consensus 243 ~Gr~P~~iaaAaiyla~~~~~~~~~-~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~ 300 (312)
....|.+||+|+||||++..+++++ +...-.+++++...|..+.-.+.+....-+|.|
T Consensus 178 vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~~~p~~ 236 (367)
T KOG0835|consen 178 VRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKRAKPDE 236 (367)
T ss_pred eecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHhcccCH
Confidence 8999999999999999999998876 568888899998888877666655444434433
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=99.77 E-value=2.9e-18 Score=122.60 Aligned_cols=71 Identities=45% Similarity=0.849 Sum_probs=65.9
Q ss_pred HHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHH
Q 021438 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (312)
Q Consensus 113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i 184 (312)
|+++|+.|+||+++.+.|.++|+++.+.+..+||++..++|||||+|||+++.|+|++||++++ ++++++|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~-~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAA-GVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHC-TSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHh-CCCCCcC
Confidence 6899999999999999999999999999999999999999999999999999999999999999 7999886
No 7
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.74 E-value=2.2e-17 Score=149.04 Aligned_cols=187 Identities=19% Similarity=0.252 Sum_probs=151.8
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-CH--HH
Q 021438 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TK--KE 183 (312)
Q Consensus 107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-~~--~~ 183 (312)
.++.++|.++|.+|++|+..+.+|..+|++++-...++...++.+|++|+|+|+|.++.|+.++||..++..+ .+ .+
T Consensus 40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~ 119 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLE 119 (323)
T ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccccc
Confidence 5789999999999999999999999999999999999999999999999999999999999999999987521 11 23
Q ss_pred HHHHHHHHHHHH-hhhh----ccccccCCCCHHHHHHHHHhhcCCCHH----HHHHHHHHHHHhhh--ccCCCChHHHHH
Q 021438 184 IGRAKEFIVKHL-EAEM----GQSVEMGTIHASDYLRRFCSNLGMTNQ----AVKAAQEAVQKSED--LDIRRSPISVAA 252 (312)
Q Consensus 184 i~~~~~~l~~~l-~~~~----~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~~~~--l~~Gr~P~~iaa 252 (312)
....|..+++.+ .+|. +.+|++...+|+.|+.+++..|+.... +.+.||.+++++.. ++....|..||.
T Consensus 120 ~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAv 199 (323)
T KOG0834|consen 120 LEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAV 199 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEe
Confidence 444444433222 1111 234689999999999999999987765 88999999999998 778899999999
Q ss_pred HHHHHHHHhcCCCCCH---HHHHHHhC--cchhHHHHHHHHHHhhh
Q 021438 253 AVIYIITQLSNDTKPL---KEISIVTR--VAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~---~~Ia~~~~--vs~~ti~~~~kel~~~~ 293 (312)
|+||||+++.|...+. +..-+.++ ++..-+....+++....
T Consensus 200 a~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y 245 (323)
T KOG0834|consen 200 ACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLY 245 (323)
T ss_pred ehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHH
Confidence 9999999999876542 12345566 88888888887777654
No 8
>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=1.8e-16 Score=113.25 Aligned_cols=69 Identities=39% Similarity=0.578 Sum_probs=63.9
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHH
Q 021438 214 LRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTI 282 (312)
Q Consensus 214 i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti 282 (312)
|+|||+.|+|++++.+.|.++++.+.+ +..||+|.++|||+||+||+.++.++|++||+++++|++.||
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 689999999999999999999999987 889999999999999999999999999999999999999997
No 9
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.69 E-value=2.6e-15 Score=135.77 Aligned_cols=160 Identities=13% Similarity=0.177 Sum_probs=135.6
Q ss_pred hhhHH-HHHHHHHHHHHhcC--CcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC
Q 021438 103 DRNLI-QAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT 179 (312)
Q Consensus 103 e~~l~-~~~~~I~~~~~~L~--Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v 179 (312)
|..+. .....|.++|..|+ ||+.++.+|..+|++++-.+.+....+..++++|+|+|||.++.|+++.+++....+.
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 44554 46899999999999 9999999999999999998888888999999999999999999999999999866322
Q ss_pred ---CHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcC-------CCHHHHHHHHHHHHHhhh--ccCCCCh
Q 021438 180 ---TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG-------MTNQAVKAAQEAVQKSED--LDIRRSP 247 (312)
Q Consensus 180 ---~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~-------l~~~v~~~A~~i~~~~~~--l~~Gr~P 247 (312)
....|......|.+.|++ ++.+.+|+.++..|...|+ -.+.+.+.|+.+++++.. +..-..|
T Consensus 132 ~~~~~~~Il~~E~~lL~~L~F------~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~P 205 (305)
T TIGR00569 132 PLKALEQVLEYELLLIQQLNF------HLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTP 205 (305)
T ss_pred chhhHHHHHHHHHHHHHHCCC------cEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCH
Confidence 237788888889999987 6778889998888876543 234577889999999886 5566999
Q ss_pred HHHHHHHHHHHHHhcCCCCCH
Q 021438 248 ISVAAAVIYIITQLSNDTKPL 268 (312)
Q Consensus 248 ~~iaaAaiyla~~~~~~~~~~ 268 (312)
..||+||||+|++..+.+++-
T Consensus 206 s~IAlAAI~lA~~~~~~~l~~ 226 (305)
T TIGR00569 206 SQIALAAILHTASRAGLNMES 226 (305)
T ss_pred HHHHHHHHHHHHHHhCCCCcc
Confidence 999999999999999987664
No 10
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=99.62 E-value=2.3e-16 Score=100.99 Aligned_cols=43 Identities=47% Similarity=1.025 Sum_probs=38.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF 47 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f 47 (312)
++||+||+ ..+++|+.+|++||++||.|++|+.++.++|||+|
T Consensus 1 m~Cp~Cg~-~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 1 MKCPNCGS-KEIVFDPERGELVCPNCGLVLEENIIDEGPEWREF 43 (43)
T ss_dssp ESBTTTSS-SEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCHC
T ss_pred CCCcCCcC-CceEEcCCCCeEECCCCCCEeecccccCCcccccC
Confidence 47999999 56999999999999999999999999999999987
No 11
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.54 E-value=8.3e-14 Score=122.96 Aligned_cols=155 Identities=19% Similarity=0.285 Sum_probs=132.4
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhc-------CC
Q 021438 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN-------GT 179 (312)
Q Consensus 107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~-------~v 179 (312)
...+.+|..+|.+|+||..+.++|..+|++++-+....+.+.+.++++|||+|||.++.|+-+.-.+...+ .-
T Consensus 46 i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~ 125 (297)
T COG5333 46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKS 125 (297)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccc
Confidence 45789999999999999999999999999999988899999999999999999999997655543333221 24
Q ss_pred CHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCH--HHHHHHHHHHHHhhh--ccCCCChHHHHHHHH
Q 021438 180 TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN--QAVKAAQEAVQKSED--LDIRRSPISVAAAVI 255 (312)
Q Consensus 180 ~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~--~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAai 255 (312)
+.+.|-.....+.+.|++ ++-+.+|+.++..|...+.+.. +..+.||.+++++.+ +..-..|..||.|++
T Consensus 126 sr~~Il~~E~~lLEaL~f------d~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l 199 (297)
T COG5333 126 SRERILEYEFELLEALDF------DLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAAL 199 (297)
T ss_pred cHHHHHHHHHHHHHHccc------ceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHH
Confidence 577888888888889986 7888999999999998887654 489999999999998 666788999999999
Q ss_pred HHHHHhcCCCCC
Q 021438 256 YIITQLSNDTKP 267 (312)
Q Consensus 256 yla~~~~~~~~~ 267 (312)
++|+...|.+..
T Consensus 200 ~ia~~~~~~~~~ 211 (297)
T COG5333 200 LIACEVLGMPII 211 (297)
T ss_pred HHHHHhcCCccc
Confidence 999999886643
No 12
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.53 E-value=8.6e-14 Score=127.25 Aligned_cols=88 Identities=24% Similarity=0.392 Sum_probs=84.7
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHH
Q 021438 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK 188 (312)
Q Consensus 109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~ 188 (312)
...+|.++|+.|+||..+.+.|..+++++.+.++..||+|.++||||||+||+.+|.|+|++||+.++ +++..+|++.|
T Consensus 219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~-~Vs~~tI~~~y 297 (310)
T PRK00423 219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVA-GVTEVTVRNRY 297 (310)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHc-CCCHHHHHHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999 89999999999
Q ss_pred HHHHHHHhh
Q 021438 189 EFIVKHLEA 197 (312)
Q Consensus 189 ~~l~~~l~~ 197 (312)
+.|.+.|++
T Consensus 298 kel~~~l~~ 306 (310)
T PRK00423 298 KELAEKLDI 306 (310)
T ss_pred HHHHHHhCc
Confidence 999999875
No 13
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.39 E-value=4.2e-12 Score=107.16 Aligned_cols=178 Identities=19% Similarity=0.315 Sum_probs=132.1
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHhc---------
Q 021438 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRT-VKEFCSVAN--------- 177 (312)
Q Consensus 108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~t-l~dia~~~~--------- 177 (312)
...+.|+.+++.|+|-+.++.+|..+|++++-++.+++..+..+|+.|+|+||+.++.|++ .+-+...+.
T Consensus 43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~ 122 (264)
T KOG0794|consen 43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYW 122 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccc
Confidence 3578899999999999999999999999999999999999999999999999999999822 222222211
Q ss_pred ----CCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCC-CHHHHHHHHHHHHHhhh--ccCCCChHHH
Q 021438 178 ----GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM-TNQAVKAAQEAVQKSED--LDIRRSPISV 250 (312)
Q Consensus 178 ----~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l-~~~v~~~A~~i~~~~~~--l~~Gr~P~~i 250 (312)
..+.+.|-...-.+.+.|+. -+-+-+|..-+..+.+.+|+ +.+....+|.|+++..+ ++.-..|.-|
T Consensus 123 ~e~~~~~~~~I~e~Ef~llE~Ld~------~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~I 196 (264)
T KOG0794|consen 123 PEKFPYERKDILEMEFYLLEALDC------YLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQI 196 (264)
T ss_pred hhhcCCCcCcchhhhhhHHhhhce------eEEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHH
Confidence 01123333334445555543 23355677778889999998 55588999999999998 7778999999
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 251 AAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 251 aaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
|-||||+|+...+-..+ +..-....+--.-+.+...+|+..
T Consensus 197 alAcl~Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I~~l 237 (264)
T KOG0794|consen 197 ALACLYIACVIDEKDIP-KAWFAELSVDMEKVKDIVQEILKL 237 (264)
T ss_pred HHHHHHHHHhhcCCChH-HHHHHHHhccHHHHHHHHHHHHHH
Confidence 99999999998865543 333344455555666666666553
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.30 E-value=1.1e-11 Score=110.91 Aligned_cols=89 Identities=27% Similarity=0.372 Sum_probs=85.7
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (312)
Q Consensus 108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~ 187 (312)
+...+|.++|+.|+||+.+...|.+|.+++.+.+.+.||+|..+||||+|+|+++++.++|.+||+.++ ++++.+|++.
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~-~vtevTIrnr 271 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVA-GVTEVTIRNR 271 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHh-CCeeeHHHHH
Confidence 567899999999999999999999999999999999999999999999999999999999999999999 8999999999
Q ss_pred HHHHHHHHhh
Q 021438 188 KEFIVKHLEA 197 (312)
Q Consensus 188 ~~~l~~~l~~ 197 (312)
|+.|.+.+++
T Consensus 272 ykel~~~~~i 281 (285)
T COG1405 272 YKELADALDI 281 (285)
T ss_pred HHHHHHhhcc
Confidence 9999998876
No 15
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.28 E-value=2e-11 Score=106.78 Aligned_cols=89 Identities=24% Similarity=0.343 Sum_probs=84.7
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (312)
Q Consensus 108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~ 187 (312)
..-.+|.++|+.|+||..+++.|.++.+++.+.+...||+|.++|||+||+++++...+++++||..++ ||.+.+|+..
T Consensus 202 ~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vt-gVaE~TIr~s 280 (308)
T KOG1597|consen 202 STGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVT-GVAEVTIRNS 280 (308)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHh-hhhHHHHHHH
Confidence 366889999999999999999999999999999999999999999999999999999999999999999 8999999999
Q ss_pred HHHHHHHHhh
Q 021438 188 KEFIVKHLEA 197 (312)
Q Consensus 188 ~~~l~~~l~~ 197 (312)
|+.|..++..
T Consensus 281 YK~Lyp~~~~ 290 (308)
T KOG1597|consen 281 YKDLYPHADK 290 (308)
T ss_pred HHHHhhchhh
Confidence 9999988763
No 16
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.19 E-value=3e-10 Score=83.36 Aligned_cols=83 Identities=24% Similarity=0.378 Sum_probs=77.7
Q ss_pred HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-CHHHHHH
Q 021438 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGR 186 (312)
Q Consensus 108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-~~~~i~~ 186 (312)
.+..+|.++++.+++|..+...|..+++++...+.+.++++..+++||+|+|||.++.|.+++|+...+ +. +..+|.+
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~-~~~~~~~i~~ 82 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVT-GYATEEEILR 82 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHh-CCCCHHHHHH
Confidence 468899999999999999999999999999998888999999999999999999999999999999999 68 9999988
Q ss_pred HHHHH
Q 021438 187 AKEFI 191 (312)
Q Consensus 187 ~~~~l 191 (312)
.++.+
T Consensus 83 ~e~~i 87 (88)
T cd00043 83 MEKLL 87 (88)
T ss_pred HHHHh
Confidence 87765
No 17
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=99.09 E-value=7.8e-10 Score=80.27 Aligned_cols=80 Identities=23% Similarity=0.303 Sum_probs=72.3
Q ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-CHHHHHHHHHH
Q 021438 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEF 190 (312)
Q Consensus 112 ~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-~~~~i~~~~~~ 190 (312)
+|.++++.+++|+.+...|..+++++.....+.++++..+++||+|+|||.++.+++..++...+ +. +.++|.+.++.
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~ 80 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYT-GYFTEEEILRMEKL 80 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhh-CCCCHHHHHHHHHH
Confidence 68899999999999999999999999885445559999999999999999999999999999999 78 99999998887
Q ss_pred HH
Q 021438 191 IV 192 (312)
Q Consensus 191 l~ 192 (312)
|.
T Consensus 81 il 82 (83)
T smart00385 81 LL 82 (83)
T ss_pred Hh
Confidence 64
No 18
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.08 E-value=1.6e-09 Score=79.47 Aligned_cols=83 Identities=28% Similarity=0.329 Sum_probs=76.9
Q ss_pred CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-chhHHHH
Q 021438 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRV-AEGTIKN 284 (312)
Q Consensus 208 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~v-s~~ti~~ 284 (312)
.++..|+.++++.+++++++...|..++++... ...+++|..+|+||+|+|+++.+...+.+++...++. +..+|.+
T Consensus 3 ~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~ 82 (88)
T cd00043 3 PTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILR 82 (88)
T ss_pred chHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHH
Confidence 457899999999999999999999999999876 5569999999999999999999999999999999999 9999999
Q ss_pred HHHHHH
Q 021438 285 VYKDLF 290 (312)
Q Consensus 285 ~~kel~ 290 (312)
.+++|+
T Consensus 83 ~e~~il 88 (88)
T cd00043 83 MEKLLL 88 (88)
T ss_pred HHHHhC
Confidence 988873
No 19
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=99.07 E-value=1.1e-09 Score=79.39 Aligned_cols=80 Identities=25% Similarity=0.325 Sum_probs=73.2
Q ss_pred HHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-chhHHHHHHHH
Q 021438 212 DYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRV-AEGTIKNVYKD 288 (312)
Q Consensus 212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~v-s~~ti~~~~ke 288 (312)
+|+.++++.+++++++...|..++++... -..+++|..+|+||+|+|++..+...+.++++..+++ ++.+|.+.+++
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 80 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEKL 80 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHHH
Confidence 48899999999999999999999999876 3346999999999999999999988899999999999 99999999999
Q ss_pred HHh
Q 021438 289 LFP 291 (312)
Q Consensus 289 l~~ 291 (312)
|.+
T Consensus 81 il~ 83 (83)
T smart00385 81 LLE 83 (83)
T ss_pred HhC
Confidence 863
No 20
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.98 E-value=3.9e-08 Score=89.32 Aligned_cols=175 Identities=15% Similarity=0.184 Sum_probs=131.1
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCC---HHHHHHHHHHHHHHHhCC--CCCHHHHHHHh-cCCC
Q 021438 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRN---QEAIVAACLYIACRQENK--PRTVKEFCSVA-NGTT 180 (312)
Q Consensus 107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~---~~~iaaAcly~acr~~~~--p~tl~dia~~~-~~v~ 180 (312)
..|+.+|-++|+..+..+.+.=.|..|+.|+..-..+..-+ ...+|+||+.+|+|.+++ |.++.-..... .-..
T Consensus 79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~fe 158 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFE 158 (335)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccccc
Confidence 57999999999999999999999999999997755443333 789999999999999987 55444333321 1367
Q ss_pred HHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCH----HHHHHHHHHHH-Hhhh-ccCCCChHHHHHHH
Q 021438 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN----QAVKAAQEAVQ-KSED-LDIRRSPISVAAAV 254 (312)
Q Consensus 181 ~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~----~v~~~A~~i~~-~~~~-l~~Gr~P~~iaaAa 254 (312)
.++|.++...+...|+= .+..++|.+|+..|+.+++... .+.+.+..++- .+.+ -..+..|+.||||+
T Consensus 159 aktI~rmELLVLstL~W------rl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~ 232 (335)
T KOG0656|consen 159 AKTIQRMELLVLSTLKW------RLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAA 232 (335)
T ss_pred HHHHHHHHHHHHhhccc------cccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHH
Confidence 89999999999999986 6778999999999999998743 34444444433 3344 34689999999998
Q ss_pred HHHHHHhc-CCC--CCHHHHHHHhCcchhHHHHHHH
Q 021438 255 IYIITQLS-NDT--KPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 255 iyla~~~~-~~~--~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
+.+++... +.. ..+..+.....++...++..|.
T Consensus 233 ~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 233 ILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 87776643 322 2235556667788877777766
No 21
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=98.45 E-value=2.8e-06 Score=80.16 Aligned_cols=179 Identities=15% Similarity=0.182 Sum_probs=140.7
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCC-CCHHHHHHHhc-CCCHHHHHH
Q 021438 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP-RTVKEFCSVAN-GTTKKEIGR 186 (312)
Q Consensus 109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p-~tl~dia~~~~-~v~~~~i~~ 186 (312)
..++|.++=.+++|-+.+...|..|..++.......=.+...++++|+||||+.+++. .+++++.-++. ..+.++|.+
T Consensus 216 Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~ 295 (440)
T COG5024 216 LVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIR 295 (440)
T ss_pred HHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHH
Confidence 4778888999999988999999999999998877766788899999999999998764 56788887776 478999999
Q ss_pred HHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh---hccCCCChHHHHHHHHHHHHHhcC
Q 021438 187 AKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE---DLDIRRSPISVAAAVIYIITQLSN 263 (312)
Q Consensus 187 ~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~---~l~~Gr~P~~iaaAaiyla~~~~~ 263 (312)
+++.+...|+. ++....|..|+.|+...-.-+......+..++..+. ++...+ |+.+||||-|++-.+.+
T Consensus 296 aE~~ml~~l~f------~is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~~~ 368 (440)
T COG5024 296 AERYMLEVLDF------NISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKILS 368 (440)
T ss_pred HHHHHhhhccc------ccCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhhhc
Confidence 99999999987 677888999999998888877777777777776644 255566 99999999999999876
Q ss_pred CCCCHHHHHHHhC-cchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTR-VAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~-vs~~ti~~~~kel~~~~~ 294 (312)
..-.-....-..| .+...++....++.+++.
T Consensus 369 ~~~w~~~l~~ySg~y~~~~l~~~~~~~~~~l~ 400 (440)
T COG5024 369 QNQWDRTLIHYSGNYTNPDLKPLNESNKENLQ 400 (440)
T ss_pred cCCCCccccccCCCCCchhHHHHHHHHHHHhc
Confidence 3322222222334 566666666666666654
No 22
>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=98.36 E-value=7.5e-06 Score=72.48 Aligned_cols=146 Identities=16% Similarity=0.252 Sum_probs=96.2
Q ss_pred HHHHHHhc--CCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcC---CCHHHHHHH
Q 021438 113 ISAMSDRL--GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG---TTKKEIGRA 187 (312)
Q Consensus 113 I~~~~~~L--~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~---v~~~~i~~~ 187 (312)
+-++|+++ +||..|+.+|..+|++++-.+....-++..|.++|+|+||+.++..+|+.+|+.-+.| -+...+-+.
T Consensus 63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk~ 142 (325)
T KOG2496|consen 63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLKY 142 (325)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHhc
Confidence 44445554 8899999999999999998888888899999999999999999999999999986521 223333344
Q ss_pred HHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcC--CCHHH-HH--HHHHHHHHhhh--ccCCCChHHHHHHHHHHHHH
Q 021438 188 KEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG--MTNQA-VK--AAQEAVQKSED--LDIRRSPISVAAAVIYIITQ 260 (312)
Q Consensus 188 ~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~--l~~~v-~~--~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~ 260 (312)
...+.+.|++..+ +..|.-..+-|+.-+-..|. .+++. .. .....++.+.. ...-..|+-||-|||..++-
T Consensus 143 E~~llqsL~f~L~--vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~~ 220 (325)
T KOG2496|consen 143 EFLLLQSLKFSLT--VHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAAG 220 (325)
T ss_pred hHHHHHhhhhhhe--ecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHhc
Confidence 4456666765322 12233333556555544432 12222 11 11344444443 44568999999999955543
No 23
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=98.36 E-value=1e-05 Score=76.53 Aligned_cols=165 Identities=15% Similarity=0.192 Sum_probs=130.6
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHH-HHHHHhCCC-CCHHHHHHHhc-CCCHHH
Q 021438 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY-IACRQENKP-RTVKEFCSVAN-GTTKKE 183 (312)
Q Consensus 107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly-~acr~~~~p-~tl~dia~~~~-~v~~~~ 183 (312)
....+++-++-.+++|..++.-.|..|+.++.....+..+....+..+|++ +|||.+... ..+.|+..+.+ ..+..+
T Consensus 159 ~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~ 238 (391)
T KOG0653|consen 159 AILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREE 238 (391)
T ss_pred HHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHH
Confidence 345899999999999999999999999999988866777888888888866 999975544 44777776665 368899
Q ss_pred HHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHh
Q 021438 184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQL 261 (312)
Q Consensus 184 i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~ 261 (312)
|.++.+.+...|+. ++....|..|+.|+.............+..+++...- -.....|..+|||+.+++.++
T Consensus 239 il~mE~~il~~L~f------~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~ 312 (391)
T KOG0653|consen 239 ILRMEKYILNVLEF------DLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRM 312 (391)
T ss_pred HHHHHHHHHhccCe------eecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHH
Confidence 99999999998886 7778899999999999988776777777777776553 235678899999999999998
Q ss_pred cCCC-CCHHHHHHHhCc
Q 021438 262 SNDT-KPLKEISIVTRV 277 (312)
Q Consensus 262 ~~~~-~~~~~Ia~~~~v 277 (312)
.+.+ .....+...+|-
T Consensus 313 ~~~~~~w~~~~~~~sg~ 329 (391)
T KOG0653|consen 313 LSKGDVWSPTLEHYSGY 329 (391)
T ss_pred hccCCccCCCCeeccCC
Confidence 7655 244444444443
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=98.33 E-value=9.5e-06 Score=64.08 Aligned_cols=93 Identities=20% Similarity=0.330 Sum_probs=78.9
Q ss_pred hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHH
Q 021438 105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKK 182 (312)
Q Consensus 105 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~ 182 (312)
......++|..++..++++..+...|..++.++.........+...+++||+++|||.++. +.++.++..... ..+.+
T Consensus 30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~ 109 (127)
T PF00134_consen 30 MRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKK 109 (127)
T ss_dssp HHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHH
T ss_pred HHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHH
Confidence 3456899999999999999999999999999998888778888999999999999999987 788999988763 36789
Q ss_pred HHHHHHHHHHHHHhh
Q 021438 183 EIGRAKEFIVKHLEA 197 (312)
Q Consensus 183 ~i~~~~~~l~~~l~~ 197 (312)
+|..+.+.+...|+.
T Consensus 110 ~i~~~E~~iL~~L~f 124 (127)
T PF00134_consen 110 DILEMEREILSALNF 124 (127)
T ss_dssp HHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHCCC
Confidence 999999999988875
No 25
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.21 E-value=1.6e-06 Score=82.25 Aligned_cols=91 Identities=19% Similarity=0.253 Sum_probs=70.9
Q ss_pred HHHHHHHHHHHHHhcCC-cH--HHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHH
Q 021438 106 LIQAFKSISAMSDRLGL-VT--TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKK 182 (312)
Q Consensus 106 l~~~~~~I~~~~~~L~L-p~--~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~ 182 (312)
+.+..-+|.+++..|-. |+ .++.+|..+..+........||+|..+++||||+|||++|+++|+.||+.+.+ |+..
T Consensus 163 lvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvh-V~e~ 241 (521)
T KOG1598|consen 163 LVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVH-VCES 241 (521)
T ss_pred ccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHH-HhHH
Confidence 33444556666666544 33 36666666666655444558999999999999999999999999999999995 9999
Q ss_pred HHHHHHHHHHHHHhh
Q 021438 183 EIGRAKEFIVKHLEA 197 (312)
Q Consensus 183 ~i~~~~~~l~~~l~~ 197 (312)
+|.+.|+++.+.+..
T Consensus 242 Tl~kRl~Ef~~T~s~ 256 (521)
T KOG1598|consen 242 TLSKRLKEFSDTLSG 256 (521)
T ss_pred HHHHHHHHHhccccc
Confidence 999999998876653
No 26
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=98.10 E-value=2.1e-05 Score=61.14 Aligned_cols=86 Identities=17% Similarity=0.162 Sum_probs=70.9
Q ss_pred CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhCcchhHHHHH
Q 021438 209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVTRVAEGTIKNV 285 (312)
Q Consensus 209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~vs~~ti~~~ 285 (312)
+|..|+.+|....+.+.++...++.+++.+.. -..+.+|+.|||||+++|....+. +.....+...+|+....++..
T Consensus 2 Tp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c 81 (118)
T PF02984_consen 2 TPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC 81 (118)
T ss_dssp -HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred cHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence 58899999966666677899999999998765 457899999999999999999875 455677889999999999999
Q ss_pred HHHHHhhhc
Q 021438 286 YKDLFPHLA 294 (312)
Q Consensus 286 ~kel~~~~~ 294 (312)
++.|.+...
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999998764
No 27
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=98.08 E-value=0.00034 Score=59.05 Aligned_cols=167 Identities=19% Similarity=0.226 Sum_probs=122.9
Q ss_pred HHHHHHHhcCCc--HHHHHHHHHHHHHHHhC--CCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438 112 SISAMSDRLGLV--TTIKDRANEIYKKVEDQ--KPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (312)
Q Consensus 112 ~I~~~~~~L~Lp--~~v~~~A~~i~~~~~~~--~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~ 187 (312)
.|.+++.+|||. +.+.+.|.+|.+...-. +..-|-.-..-|.-|+=+|.-.-+++..-......+ |.+++...+.
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLS-Gl~k~~Y~~~ 80 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLS-GLSKKAYSRS 80 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhc-cccHHHHHHH
Confidence 478999999994 57999999998876432 344555666778888888888889998877777877 9999999999
Q ss_pred HHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-------ccCCCChHHHHHHHHHHHHH
Q 021438 188 KEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-------LDIRRSPISVAAAVIYIITQ 260 (312)
Q Consensus 188 ~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-------l~~Gr~P~~iaaAaiyla~~ 260 (312)
++.+...|+++. . . -|..+|-.+|+.+ +++.|..++..-.. ...-.+-.-.++||+|+||+
T Consensus 81 ~~sfe~llgln~----~---~----~VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack 148 (262)
T KOG4557|consen 81 FNSFENLLGLNI----K---L----NVRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACK 148 (262)
T ss_pred HHHHHHHhcchh----h---c----CHHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHH
Confidence 999999998731 1 1 2334455555544 66778887766443 22333444578899999999
Q ss_pred hcCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
....+++...+-.+.|++++......|-+..
T Consensus 149 ~lKlKVdK~kli~~sg~~~s~F~~l~kqler 179 (262)
T KOG4557|consen 149 KLKLKVDKLKLIEVSGTSESEFSCLSKQLER 179 (262)
T ss_pred HHHHhhhHhhcccccCCCHHHHHHHHHHHHH
Confidence 9988888888888899999877655554443
No 28
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=97.77 E-value=0.00012 Score=58.48 Aligned_cols=83 Identities=11% Similarity=0.250 Sum_probs=63.0
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHH
Q 021438 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (312)
Q Consensus 107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~--~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i 184 (312)
.-|...|+++|++|+|++++.+....+|.-... ..++++|..+.++.+|+|..||.++.++|++||..... --+..-
T Consensus 12 ~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr-~qpq~~ 90 (135)
T PF01857_consen 12 KLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYR-KQPQAS 90 (135)
T ss_dssp HHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHT-TSTT--
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHH-hccccc
Confidence 347889999999999999998998888877754 35679999999999999999999999999999998773 333333
Q ss_pred HHHHHH
Q 021438 185 GRAKEF 190 (312)
Q Consensus 185 ~~~~~~ 190 (312)
..+|+.
T Consensus 91 ~~Vyr~ 96 (135)
T PF01857_consen 91 SHVYRS 96 (135)
T ss_dssp THHHHS
T ss_pred ccceEE
Confidence 344443
No 29
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=97.53 E-value=0.0051 Score=55.49 Aligned_cols=172 Identities=17% Similarity=0.224 Sum_probs=121.4
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCC-CCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhcC-CCHHHHH
Q 021438 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVANG-TTKKEIG 185 (312)
Q Consensus 109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~-~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~~-v~~~~i~ 185 (312)
.++++-++|+-..|-..+.-.|..+|.++.... ....-....+-.+|+|+|++.+++ |-.+.|||.+++| .+..+|.
T Consensus 148 LlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIl 227 (408)
T KOG0655|consen 148 LLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDIL 227 (408)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHH
Confidence 489999999999999999999999999987643 223345678889999999998875 7899999998874 6889999
Q ss_pred HHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCH--------HHHHHHHHHH---HHhh-hcc-CCCChHHHHH
Q 021438 186 RAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN--------QAVKAAQEAV---QKSE-DLD-IRRSPISVAA 252 (312)
Q Consensus 186 ~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~--------~v~~~A~~i~---~~~~-~l~-~Gr~P~~iaa 252 (312)
.+...|.+.|+- ++.+++.-..+.-|.+-+++++ -....-..++ ..+. .+. .-..-..+||
T Consensus 228 tmE~iilkal~W------~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaqlLDlc~ldids~~fsYrilaA 301 (408)
T KOG0655|consen 228 TMELIILKALKW------ELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQLLDLCILDIDSLEFSYRILAA 301 (408)
T ss_pred HHHHHHHHHhcc------cccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHHHHHHHHhccccccchHHHHHH
Confidence 999999999987 5667777777777776554331 1112222222 2222 222 3566778888
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
||||.-.. ..-+-+++|.--..|.+..+-+.+..
T Consensus 302 Aal~h~~s-------~e~v~kaSG~~w~~ie~cv~wm~Pf~ 335 (408)
T KOG0655|consen 302 AALCHFTS-------IEVVKKASGLEWDSIEECVDWMVPFV 335 (408)
T ss_pred HHHHHHhH-------HHHHHHcccccHHHHHHHHHHHHHHH
Confidence 88884332 23344556666667777766666653
No 30
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=97.29 E-value=0.0002 Score=43.47 Aligned_cols=27 Identities=30% Similarity=0.562 Sum_probs=23.3
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
.|+.|++ . .+....|..+|..||.|++
T Consensus 10 ~C~~C~~-~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 10 PCPVCGS-R--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence 4999998 2 6778899999999999974
No 31
>PHA00626 hypothetical protein
Probab=96.77 E-value=0.0013 Score=43.30 Aligned_cols=31 Identities=19% Similarity=0.538 Sum_probs=23.4
Q ss_pred CCCCCCCCCCceeee----CCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFD----HSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D----~~~G~~vC~~CG~Vv~e 35 (312)
+.||.||+ .+++.. ..+..++|.+||+-...
T Consensus 1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCC-ceeeeeceecccCcceEcCCCCCeech
Confidence 47999999 466642 23689999999997643
No 32
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=96.75 E-value=0.0015 Score=38.81 Aligned_cols=31 Identities=16% Similarity=0.404 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
|....|+.||+. .++....+..+|..||.+.
T Consensus 1 ~~~~~C~~C~~~--~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 1 SNLKKCSKCGGN--GIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CCceEcCCCCCC--eEEEecCCeEEcccCCcEe
Confidence 556789999983 4555778999999999874
No 33
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=96.74 E-value=0.011 Score=53.26 Aligned_cols=90 Identities=20% Similarity=0.246 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHHhcCCcHHH--HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHH-HHHHHhcCCCHH
Q 021438 106 LIQAFKSISAMSDRLGLVTTI--KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK-EFCSVANGTTKK 182 (312)
Q Consensus 106 l~~~~~~I~~~~~~L~Lp~~v--~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~-dia~~~~~v~~~ 182 (312)
+......|-.+...|++|++. ...+..+........++.-.+++.||+||+|+|.|..++|.... .--.++ +.++.
T Consensus 138 v~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~F-d~~k~ 216 (367)
T KOG0835|consen 138 VEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAF-DTTKR 216 (367)
T ss_pred eeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHc-CCcHH
Confidence 344567788889999999754 77777777777767777888999999999999999999886543 444556 68888
Q ss_pred HHHHHHHHHHHHHh
Q 021438 183 EIGRAKEFIVKHLE 196 (312)
Q Consensus 183 ~i~~~~~~l~~~l~ 196 (312)
+|......+.....
T Consensus 217 eid~ic~~l~~lY~ 230 (367)
T KOG0835|consen 217 EIDEICYRLIPLYK 230 (367)
T ss_pred HHHHHHHHHHHHHH
Confidence 88776655554443
No 34
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.73 E-value=0.0012 Score=44.39 Aligned_cols=31 Identities=35% Similarity=0.745 Sum_probs=28.6
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
.+||.|+. ..+++++.+-.+.|..||.++.+
T Consensus 12 VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCPDCGN-EQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECCCCCC-eEEEEecCCcEEECcccCCCccc
Confidence 57999998 68999999999999999999975
No 35
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.67 E-value=0.001 Score=45.42 Aligned_cols=31 Identities=35% Similarity=0.764 Sum_probs=28.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
.+||+|+. ..+++++.+-.+.|..||.++.+
T Consensus 20 VkCpdC~N-~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 20 VKCPDCGN-EQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EECCCCCC-EEEEeccCceEEEecccccEEEe
Confidence 47999998 68999999999999999999875
No 36
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=96.64 E-value=0.0015 Score=39.03 Aligned_cols=27 Identities=19% Similarity=0.652 Sum_probs=15.3
Q ss_pred CCCCCCCCCceeeeCC----CCceEcCCCcccc
Q 021438 5 YCADCKRLTEVVFDHS----AGDTICSECGLVL 33 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~----~G~~vC~~CG~Vv 33 (312)
.||.||+. +..... .-..||.+||.|-
T Consensus 2 fC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGP--LERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B---EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccCh--hhhhcCCCCCccceECCCCCCEE
Confidence 69999983 444433 3449999999983
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=96.48 E-value=0.023 Score=43.67 Aligned_cols=87 Identities=14% Similarity=0.141 Sum_probs=64.4
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhcCCCHHHHHHH
Q 021438 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVANGTTKKEIGRA 187 (312)
Q Consensus 109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~~v~~~~i~~~ 187 (312)
.+.+|+.+....+..+.+...|..+.....-...+-+.++..+||||+|+|.+..+. +.--..+...+ |++..+|...
T Consensus 3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t-~~~~~~l~~c 81 (118)
T PF02984_consen 3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLT-GYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhc-CCCHHHHHHH
Confidence 456777775555556677778887777765554467889999999999999999775 43345566667 8999999999
Q ss_pred HHHHHHHHh
Q 021438 188 KEFIVKHLE 196 (312)
Q Consensus 188 ~~~l~~~l~ 196 (312)
++.|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999887775
No 38
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=96.47 E-value=0.0016 Score=43.30 Aligned_cols=31 Identities=32% Similarity=0.687 Sum_probs=23.6
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
.+||.|+. ..+|+++.+-.+.|..||.+|.+
T Consensus 8 VkCp~C~~-~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCPGCYN-IQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-TTT-S-EEEEETT-SS-EE-SSSTSEEEE
T ss_pred EECCCCCC-eeEEEecCCeEEEcccCCCEecC
Confidence 58999998 68999999999999999999964
No 39
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.11 E-value=0.0031 Score=35.33 Aligned_cols=22 Identities=23% Similarity=0.896 Sum_probs=17.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~ 31 (312)
..||+||.. + ..+..+|.+||.
T Consensus 3 ~~Cp~Cg~~--~----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAE--I----DPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCc--C----CcccccChhhCC
Confidence 789999982 2 357899999996
No 40
>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=96.07 E-value=0.0056 Score=37.27 Aligned_cols=29 Identities=31% Similarity=0.715 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCceeeeC--CCCceEcCCCcc
Q 021438 3 DSYCADCKRLTEVVFDH--SAGDTICSECGL 31 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~--~~G~~vC~~CG~ 31 (312)
...||.||+...+-+|. .+|..+|..||.
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 46799999965555554 459999999984
No 41
>PLN00209 ribosomal protein S27; Provisional
Probab=96.03 E-value=0.0045 Score=44.66 Aligned_cols=31 Identities=32% Similarity=0.641 Sum_probs=28.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
.+||.|+. ..+|+++.+-.+.|..||.++.+
T Consensus 37 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQGCFN-ITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence 57999998 68999999999999999999965
No 42
>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=95.99 E-value=0.034 Score=44.53 Aligned_cols=77 Identities=19% Similarity=0.264 Sum_probs=57.9
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh----ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHH
Q 021438 211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED----LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVY 286 (312)
Q Consensus 211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~----l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~ 286 (312)
..-+..+|++|++++++....|.+.+.+.. |..+|+-.-+...|||..|++.+..++.++|=+.-..-+..-...|
T Consensus 15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qpq~~~~Vy 94 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQPQASSHVY 94 (135)
T ss_dssp HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTSTT--THHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcccccccce
Confidence 446677999999999998999999888764 8899999999999999999999988998888766555444444444
Q ss_pred H
Q 021438 287 K 287 (312)
Q Consensus 287 k 287 (312)
+
T Consensus 95 r 95 (135)
T PF01857_consen 95 R 95 (135)
T ss_dssp H
T ss_pred E
Confidence 3
No 43
>PRK00420 hypothetical protein; Validated
Probab=95.98 E-value=0.0053 Score=47.19 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
-...||.||.+ +..+ .+|..+|..||.++.
T Consensus 22 l~~~CP~Cg~p--Lf~l-k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLP--LFEL-KDGEVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCc--ceec-CCCceECCCCCCeee
Confidence 34689999973 4443 789999999999864
No 44
>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=95.92 E-value=0.0061 Score=36.74 Aligned_cols=31 Identities=19% Similarity=0.508 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
|..||+||+- =+......+...|..||++.+
T Consensus 1 m~FCp~C~nl-L~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGNL-LYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp --BETTTTSB-EEEEEETTTTEEESSSS-EEE
T ss_pred CeeCCCCCcc-ceEcCCCccCcCCCCCCCccC
Confidence 4689999983 333334444458999999853
No 45
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=95.92 E-value=0.0057 Score=44.06 Aligned_cols=31 Identities=26% Similarity=0.624 Sum_probs=28.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
.+||.|+. ..+|+++.+-.+.|..||.++.+
T Consensus 36 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence 57999998 68999999999999999999964
No 46
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.87 E-value=0.007 Score=38.92 Aligned_cols=31 Identities=39% Similarity=0.748 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
|-...||+||. .+..|...+.+.|..||.=+
T Consensus 1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence 55689999998 47777777799999999643
No 47
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.80 E-value=0.0051 Score=33.35 Aligned_cols=22 Identities=27% Similarity=0.854 Sum_probs=17.0
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
.||+||.. + . .+...|..||.-
T Consensus 1 ~Cp~CG~~--~-~---~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAE--I-E---DDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCC--C-C---CcCcchhhhCCc
Confidence 59999983 2 2 478889999974
No 48
>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=95.75 E-value=0.11 Score=40.49 Aligned_cols=65 Identities=12% Similarity=0.278 Sum_probs=52.2
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHh
Q 021438 211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVT 275 (312)
Q Consensus 211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~ 275 (312)
.+|+..++..+++++.+...|..++++-.. ......+.-+++||+++|+++... ..+..++....
T Consensus 35 ~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~ 102 (127)
T PF00134_consen 35 IDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRIS 102 (127)
T ss_dssp HHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHT
T ss_pred HHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHH
Confidence 468888999999999999999999998765 446778999999999999999876 45577777766
No 49
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=95.71 E-value=0.0085 Score=34.66 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
..+||.|++. ..-.| ...+||..||.-
T Consensus 2 ~p~Cp~C~se-~~y~D--~~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSE-YTYED--GELLVCPECGHE 28 (30)
T ss_dssp S---TTT------EE---SSSEEETTTTEE
T ss_pred CCCCCCCCCc-ceecc--CCEEeCCccccc
Confidence 4689999994 33344 778999999974
No 50
>PRK10220 hypothetical protein; Provisional
Probab=95.68 E-value=0.026 Score=42.65 Aligned_cols=29 Identities=31% Similarity=0.575 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
|+...||.|++ .-.-+| ...+||..||.=
T Consensus 1 m~lP~CP~C~s-eytY~d--~~~~vCpeC~hE 29 (111)
T PRK10220 1 MSLPHCPKCNS-EYTYED--NGMYICPECAHE 29 (111)
T ss_pred CCCCcCCCCCC-cceEcC--CCeEECCcccCc
Confidence 78899999999 333343 557999999964
No 51
>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=95.49 E-value=0.0095 Score=39.57 Aligned_cols=31 Identities=39% Similarity=0.768 Sum_probs=22.1
Q ss_pred CCCCCCCCCCCceeeeCCCCc-eEcCCCccccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGD-TICSECGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~-~vC~~CG~Vv~ 34 (312)
+..||.||..-. +.|...|+ +.|..||.-++
T Consensus 2 ~~~CP~CG~~ie-v~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIE-LENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEe-cCCCccCCEEeCCCCCCEEE
Confidence 468999998323 33444466 67999999875
No 52
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.36 E-value=0.012 Score=38.60 Aligned_cols=28 Identities=18% Similarity=0.610 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
...||.||+ + +..+ ..+...|..||+..
T Consensus 20 ~~fCP~Cg~-~-~m~~-~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGS-G-FMAE-HLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCc-c-hhec-cCCcEECCCcCCEE
Confidence 357999998 4 5454 44899999999863
No 53
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=95.20 E-value=0.053 Score=49.72 Aligned_cols=83 Identities=16% Similarity=0.282 Sum_probs=67.2
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHh----CcchhHHHH
Q 021438 211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVT----RVAEGTIKN 284 (312)
Q Consensus 211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~----~vs~~ti~~ 284 (312)
..||..++.+|+++......|.-+..+-.- ......|..||++|+|||++..+.++..++|..++ +....+...
T Consensus 43 ~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~~~ 122 (323)
T KOG0834|consen 43 AKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLELEE 122 (323)
T ss_pred HHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccHHH
Confidence 568999999999998888788888777554 44677889999999999999999999999998775 333347788
Q ss_pred HHHHHHhhh
Q 021438 285 VYKDLFPHL 293 (312)
Q Consensus 285 ~~kel~~~~ 293 (312)
.|.++.+.+
T Consensus 123 ~~~~~~~~I 131 (323)
T KOG0834|consen 123 VYWELKERI 131 (323)
T ss_pred HHHHHHHHH
Confidence 888887763
No 54
>PRK11827 hypothetical protein; Provisional
Probab=95.18 E-value=0.013 Score=39.69 Aligned_cols=29 Identities=17% Similarity=0.433 Sum_probs=24.8
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
-..||.|++ .+.+|....+++|..||.+.
T Consensus 8 ILaCP~ckg--~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 8 IIACPVCNG--KLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred heECCCCCC--cCeEcCCCCeEECCccCeec
Confidence 357999997 58888888899999999884
No 55
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=95.01 E-value=0.17 Score=46.28 Aligned_cols=68 Identities=12% Similarity=0.147 Sum_probs=55.7
Q ss_pred HHHHHHHHhhcC--CCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcc
Q 021438 211 SDYLRRFCSNLG--MTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVA 278 (312)
Q Consensus 211 ~~~i~r~~~~L~--l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs 278 (312)
..+|..+|..|+ ++..+.-.|.-+.++=.- -..-..|.-|+++|+||||+.-...+++.+++..+.-.
T Consensus 60 ~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 60 EKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 357788999999 999999999988877432 23457899999999999999999889999888766543
No 56
>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=94.90 E-value=0.016 Score=32.37 Aligned_cols=24 Identities=29% Similarity=0.801 Sum_probs=19.0
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
.||+|+.. | ......|..||++..
T Consensus 2 ~CP~C~~~--V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAE--V----PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCC--c----hhhcCcCCCCCCCCc
Confidence 69999983 3 356889999999863
No 57
>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=94.87 E-value=0.017 Score=44.33 Aligned_cols=31 Identities=19% Similarity=0.602 Sum_probs=26.4
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
++.||+||.. .||-..--+||..||.++.-.
T Consensus 9 KR~Cp~CG~k---FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAK---FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcch---hccCCCCCccCCCCCCccCcc
Confidence 5789999983 799888889999999998654
No 58
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=94.82 E-value=0.73 Score=37.47 Aligned_cols=88 Identities=15% Similarity=0.149 Sum_probs=67.8
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHh---CCC--CCCCCHHHHHHHHHHHHHHH-hCCCCCHHHHHHHhcCCCHH
Q 021438 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVED---QKP--LRGRNQEAIVAACLYIACRQ-ENKPRTVKEFCSVANGTTKK 182 (312)
Q Consensus 109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~---~~~--~~gr~~~~iaaAcly~acr~-~~~p~tl~dia~~~~~v~~~ 182 (312)
..+++.++....+++..+.-.|..|..++.. ... +...+..-+..+|+.+|.|. .....+-+..+.+. |++.+
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~-gis~~ 132 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVG-GISLK 132 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHH-TS-HH
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhc-CCCHH
Confidence 5678999999999999999999999999887 222 24567778888999999996 56778899999999 89999
Q ss_pred HHHHHHHHHHHHHhh
Q 021438 183 EIGRAKEFIVKHLEA 197 (312)
Q Consensus 183 ~i~~~~~~l~~~l~~ 197 (312)
++.+..+.+...++.
T Consensus 133 eln~lE~~fL~~l~~ 147 (149)
T PF08613_consen 133 ELNELEREFLKLLDY 147 (149)
T ss_dssp HHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHCCC
Confidence 999999998888764
No 59
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=94.71 E-value=0.023 Score=38.27 Aligned_cols=31 Identities=29% Similarity=0.680 Sum_probs=26.9
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
|+...||.|++ .+.+|.+.++++|..||...
T Consensus 6 LeiLaCP~~kg--~L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 6 LEILACPVCKG--PLVYDEEKQELICPRCKLAY 36 (60)
T ss_pred heeeeccCcCC--cceEeccCCEEEecccCcee
Confidence 35568999998 39999999999999999874
No 60
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=94.66 E-value=0.35 Score=44.98 Aligned_cols=134 Identities=18% Similarity=0.175 Sum_probs=92.8
Q ss_pred HHHHHHHHHHHHHHhCC-CCCHHHHHHHhcCCCHHHHHHHHHH---HHHHHhhhhccccccCCCCHHHHHHHHHhhcC-C
Q 021438 149 EAIVAACLYIACRQENK-PRTVKEFCSVANGTTKKEIGRAKEF---IVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG-M 223 (312)
Q Consensus 149 ~~iaaAcly~acr~~~~-p~tl~dia~~~~~v~~~~i~~~~~~---l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~-l 223 (312)
..+--+|-+++.+-+.. +..+.|+...++ .-...++..+. ++..+.+ .+.......|+.++...-. .
T Consensus 180 ql~g~s~m~I~sk~ee~~~~~~~ef~~itd--~ty~~~qv~~~~~~il~~l~~------~~~~pt~~~~l~~~~~~~~~~ 251 (359)
T KOG0654|consen 180 QLVGISAMLIASKYEEIKEPRVEEFCYITD--NTYTYWQVLRMEIDILNALTF------ELVRPTSKTFLRRFLRVAQTP 251 (359)
T ss_pred HHhCcccceeeccchhhcchHHHHHHhhhh--hhhHHHHHHHHHHHHHHHhHH------HHhCchHHHHHHHHHHhhcch
Confidence 34455667777786544 566788877663 33344444444 4444444 3445567789888865433 4
Q ss_pred CHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHH
Q 021438 224 TNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLF 290 (312)
Q Consensus 224 ~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~ 290 (312)
.-++...+..+.+...- ...-..|+-|||||+++|-...+..-+-..+..-+|++..+++.....|.
T Consensus 252 ~~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~ 320 (359)
T KOG0654|consen 252 ELQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH 320 (359)
T ss_pred hHHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence 45566677777776543 44567899999999999999888666677788889999999998888887
No 61
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=94.60 E-value=0.069 Score=40.12 Aligned_cols=32 Identities=28% Similarity=0.713 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
|.+..||.|++ +.+++. .+.++|..|+.=-.+
T Consensus 1 ~~lp~cp~c~s--EytYed-~~~~~cpec~~ew~~ 32 (112)
T COG2824 1 MSLPPCPKCNS--EYTYED-GGQLICPECAHEWNE 32 (112)
T ss_pred CCCCCCCccCC--ceEEec-CceEeCchhcccccc
Confidence 67889999998 355543 459999999976554
No 62
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=94.52 E-value=0.035 Score=40.26 Aligned_cols=30 Identities=30% Similarity=0.560 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
...||.||+ . .+....+|-..|..||.+..
T Consensus 35 ~~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGR-T-TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCC-c-ceeeeccCeEEcCCCCCeec
Confidence 457999998 3 67888999999999999865
No 63
>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=94.45 E-value=0.02 Score=35.06 Aligned_cols=31 Identities=32% Similarity=0.629 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeee---CCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVFD---HSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D---~~~G~~vC~~CG~Vv~ 34 (312)
..||+|+..-.+-.| ...+.+.|.+||.++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 579999983222211 1345799999999864
No 64
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=94.43 E-value=0.034 Score=34.47 Aligned_cols=29 Identities=31% Similarity=0.620 Sum_probs=16.3
Q ss_pred CCCCCCCCCCcee-eeC--CCCceEcCCCccc
Q 021438 4 SYCADCKRLTEVV-FDH--SAGDTICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii-~D~--~~G~~vC~~CG~V 32 (312)
..||.||+...+- +|. .+|..+|..|+-+
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~ 35 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGGD 35 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence 4799999954443 543 4699999999433
No 65
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=94.29 E-value=0.026 Score=36.21 Aligned_cols=27 Identities=26% Similarity=0.733 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
..||.||. +.+.-|+.. .+.|..||+.
T Consensus 20 ~~CPrCG~-gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGP-GVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred ccCCCCCC-cchhhhcCc-eeEeccccce
Confidence 57999996 567777665 8999999986
No 66
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=94.29 E-value=0.021 Score=44.95 Aligned_cols=25 Identities=24% Similarity=0.729 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGL 31 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~ 31 (312)
...||.||.+ ++. .+|+++|..||+
T Consensus 28 ~~hCp~Cg~P--LF~--KdG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTP--LFR--KDGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCc--cee--eCCeEECCCCCc
Confidence 3579999983 544 789999999993
No 67
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=94.25 E-value=0.046 Score=38.25 Aligned_cols=17 Identities=35% Similarity=0.806 Sum_probs=15.4
Q ss_pred eeCCCCceEcCCCcccc
Q 021438 17 FDHSAGDTICSECGLVL 33 (312)
Q Consensus 17 ~D~~~G~~vC~~CG~Vv 33 (312)
++..+|.++|.+||.+.
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 68899999999999884
No 68
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.10 E-value=0.042 Score=36.06 Aligned_cols=28 Identities=18% Similarity=0.689 Sum_probs=19.6
Q ss_pred CCCCCCCCCceeeeCCC--CceEcCCCccccc
Q 021438 5 YCADCKRLTEVVFDHSA--GDTICSECGLVLE 34 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~--G~~vC~~CG~Vv~ 34 (312)
.||.||+. +...... -.++|..||++..
T Consensus 2 FCp~Cg~~--l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNM--LIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCc--cccccCCCCCEEECCcCCCeEE
Confidence 69999982 3333222 3799999998854
No 69
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=94.06 E-value=0.061 Score=36.62 Aligned_cols=29 Identities=24% Similarity=0.634 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCCceeeeCCCC-------ceEcCCCcc
Q 021438 2 ADSYCADCKRLTEVVFDHSAG-------DTICSECGL 31 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D~~~G-------~~vC~~CG~ 31 (312)
++..||-||+ ..+..+...+ .+.|.+||.
T Consensus 2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 4568999987 4565555444 266999999
No 70
>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=93.98 E-value=0.035 Score=43.27 Aligned_cols=31 Identities=10% Similarity=0.203 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
++.||.||.. .||-..--+||..||.+....
T Consensus 9 Kr~Cp~cg~k---FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSK---FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCcc---ccccCCCCccCCCcCCccCcc
Confidence 5689999983 799888999999999998654
No 71
>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=93.95 E-value=4 Score=35.75 Aligned_cols=33 Identities=15% Similarity=0.210 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...|++|||+.+|+|..+|+++.+.....+...
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 568999999999999999999988777766554
No 72
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=93.87 E-value=0.049 Score=44.57 Aligned_cols=30 Identities=27% Similarity=0.561 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeeeCC---CCc-----eEcCCCcccc
Q 021438 4 SYCADCKRLTEVVFDHS---AGD-----TICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~---~G~-----~vC~~CG~Vv 33 (312)
++||+||++..-+.|.. .|. .-|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 58999998532455543 454 3488888764
No 73
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=93.58 E-value=0.35 Score=44.89 Aligned_cols=60 Identities=13% Similarity=0.221 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCC
Q 021438 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP 166 (312)
Q Consensus 107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p 166 (312)
.-..+++.+++.--+|...++.+|-.||.++.-++++...++..+|+|||++|.+.+...
T Consensus 383 rSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~K 442 (497)
T KOG4164|consen 383 RSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLK 442 (497)
T ss_pred HHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhh
Confidence 344677788888889988999999999999988888877788999999999999988553
No 74
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=93.46 E-value=0.2 Score=31.42 Aligned_cols=28 Identities=14% Similarity=0.248 Sum_probs=22.7
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHH
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLF 290 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~ 290 (312)
+-..|..+||+.+|+|+.|+.+|++.|.
T Consensus 15 d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 15 DGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp -TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 4578899999999999999999999873
No 75
>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=93.05 E-value=0.078 Score=35.12 Aligned_cols=31 Identities=23% Similarity=0.299 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceee---e--CCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVF---D--HSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~---D--~~~G~~vC~~CG~Vv~ 34 (312)
..||.||+....+. | ...|...|..||....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 57999999533232 3 1334457999999865
No 76
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=93.04 E-value=6.1 Score=35.07 Aligned_cols=34 Identities=15% Similarity=0.138 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...++++||..+|+|..||+++++.....+...+
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4688999999999999999999988777766544
No 77
>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=92.84 E-value=0.095 Score=39.65 Aligned_cols=30 Identities=20% Similarity=0.433 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
...||.|++ .-.-+| ...+||.+||.--..
T Consensus 2 lp~CP~C~s-eytY~d--g~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 2 LPPCPKCNS-EYTYHD--GTQLICPSCLYEWNE 31 (109)
T ss_pred CCcCCcCCC-cceEec--CCeeECccccccccc
Confidence 468999999 334444 457999999986543
No 78
>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=92.79 E-value=0.14 Score=29.99 Aligned_cols=28 Identities=18% Similarity=0.453 Sum_probs=16.2
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
...|+.||++ .......-..+|.+||..
T Consensus 3 ~rfC~~CG~~--t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAP--TKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--B--EEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCcc--ccCCCCcCEeECCCCcCE
Confidence 4689999984 344445667999999975
No 79
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=92.73 E-value=0.091 Score=40.72 Aligned_cols=34 Identities=29% Similarity=0.611 Sum_probs=24.9
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
|..||.||+---.-.|...+.++|..||+..+-.
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 6799999983222234467799999999987644
No 80
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=92.71 E-value=0.11 Score=32.34 Aligned_cols=25 Identities=32% Similarity=0.852 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECG 30 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG 30 (312)
...||.||. .+.. ..+|.++|-.|+
T Consensus 17 ~~~Cp~C~~--PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGT--PLMR-DKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCC--eeEE-ecCCCEECCCCC
Confidence 468999986 3555 468999999996
No 81
>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=92.58 E-value=0.12 Score=41.51 Aligned_cols=30 Identities=30% Similarity=0.633 Sum_probs=22.4
Q ss_pred CCCCCCCCCCceeeeC---CCCceE-----cCCCcccc
Q 021438 4 SYCADCKRLTEVVFDH---SAGDTI-----CSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~---~~G~~v-----C~~CG~Vv 33 (312)
|.||.||...+-|.|+ ..|..| |.+||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 5899999966667775 566655 88998653
No 82
>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=92.49 E-value=0.17 Score=32.41 Aligned_cols=28 Identities=21% Similarity=0.424 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGL 31 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~ 31 (312)
...||.||+ .....-...+..-|.+|+.
T Consensus 18 g~~CP~Cg~-~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGS-TKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence 457999998 4555545569999999984
No 83
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=92.45 E-value=0.066 Score=40.33 Aligned_cols=41 Identities=22% Similarity=0.467 Sum_probs=28.0
Q ss_pred CCCCCCCCCCce--eeeCCCCceEcCCCcccccCc------ccccccccc
Q 021438 4 SYCADCKRLTEV--VFDHSAGDTICSECGLVLEAY------SVDETSEWR 45 (312)
Q Consensus 4 ~~Cp~Cg~~~~i--i~D~~~G~~vC~~CG~Vv~e~------~id~~~ewr 45 (312)
..||+||+ ..+ -.|...+..+|..||+.-+.. .||-.++|.
T Consensus 22 f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wi 70 (99)
T PRK14892 22 FECPRCGK-VSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVYNKFI 70 (99)
T ss_pred eECCCCCC-eEeeeecCCCcceEECCCCCCccCEECCccccchhhHHHHH
Confidence 47999996 333 345567899999999986532 245556663
No 84
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.25 E-value=0.065 Score=32.69 Aligned_cols=30 Identities=27% Similarity=0.587 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeee---CCCCceEcCCCcccc
Q 021438 4 SYCADCKRLTEVVFD---HSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D---~~~G~~vC~~CG~Vv 33 (312)
..||+|+..-.|-.| ...+.+-|..||.+.
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 579999984222222 346779999999885
No 85
>PF13730 HTH_36: Helix-turn-helix domain
Probab=92.16 E-value=0.4 Score=31.61 Aligned_cols=26 Identities=15% Similarity=0.172 Sum_probs=24.2
Q ss_pred CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 267 PLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+++.||+.+|+|+.||++..++|.+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 79999999999999999999999873
No 86
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=92.01 E-value=0.29 Score=32.29 Aligned_cols=38 Identities=8% Similarity=0.311 Sum_probs=32.3
Q ss_pred hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438 261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298 (312)
Q Consensus 261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p 298 (312)
......+..++|..+|||++|+.+.++++.+.+...+|
T Consensus 15 ~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 15 YLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred HHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 33456789999999999999999999999998877654
No 87
>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=91.92 E-value=0.24 Score=29.09 Aligned_cols=28 Identities=14% Similarity=0.167 Sum_probs=22.4
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+++..|||+.+|.|..|+....+.|.+.
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 4678999999999999999999988763
No 88
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=91.85 E-value=0.12 Score=39.81 Aligned_cols=24 Identities=33% Similarity=0.660 Sum_probs=19.6
Q ss_pred CCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 6 CADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 6 Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
||.||+. -.|+ .+-|.+||+.++-
T Consensus 1 CPvCg~~-l~vt-----~l~C~~C~t~i~G 24 (113)
T PF09862_consen 1 CPVCGGE-LVVT-----RLKCPSCGTEIEG 24 (113)
T ss_pred CCCCCCc-eEEE-----EEEcCCCCCEEEe
Confidence 9999983 3444 7999999999974
No 89
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=91.84 E-value=0.43 Score=30.53 Aligned_cols=30 Identities=20% Similarity=0.200 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+-..|+++||+.+|+|..|++.++++|.+.
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 345899999999999999999999999763
No 90
>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=91.70 E-value=3.9 Score=33.13 Aligned_cols=89 Identities=10% Similarity=0.117 Sum_probs=61.0
Q ss_pred cCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-------ccCCCChHHHHHHHHHHHHHhcC-CCCCHHHHHHHhC
Q 021438 205 MGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-------LDIRRSPISVAAAVIYIITQLSN-DTKPLKEISIVTR 276 (312)
Q Consensus 205 ~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-------l~~Gr~P~~iaaAaiyla~~~~~-~~~~~~~Ia~~~~ 276 (312)
.|..+-.+|+.|+....+++..+.-.|.-.+++... ......+.-+-.+|+.+|.+... ...+-+..|++.|
T Consensus 49 ~p~i~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g 128 (149)
T PF08613_consen 49 VPSISIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG 128 (149)
T ss_dssp --SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT
T ss_pred CCCCcHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC
Confidence 466778899999999999999988777777766543 23466778899999999999875 4577899999999
Q ss_pred cchhHHHHHHHHHHhhh
Q 021438 277 VAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 277 vs~~ti~~~~kel~~~~ 293 (312)
++...+..-=.+++..+
T Consensus 129 is~~eln~lE~~fL~~l 145 (149)
T PF08613_consen 129 ISLKELNELEREFLKLL 145 (149)
T ss_dssp S-HHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHC
Confidence 98777765544554443
No 91
>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=91.58 E-value=0.5 Score=30.56 Aligned_cols=31 Identities=19% Similarity=0.300 Sum_probs=26.3
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
....|+.|||+..|+|..||+++.+...+.+
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 5678999999999999999999998776654
No 92
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=91.49 E-value=0.08 Score=37.41 Aligned_cols=30 Identities=27% Similarity=0.683 Sum_probs=26.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
.+||.|-. ...++.+.+..++|.+|++|+=
T Consensus 35 VkC~gc~~-iT~vfSHaqtvVvc~~c~~il~ 64 (84)
T KOG1779|consen 35 VKCPGCFK-ITTVFSHAQTVVVCEGCSTILC 64 (84)
T ss_pred EEcCCceE-EEEEeecCceEEEcCCCceEEE
Confidence 57999998 5789999999999999999973
No 93
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=91.35 E-value=0.13 Score=38.28 Aligned_cols=30 Identities=30% Similarity=0.746 Sum_probs=22.5
Q ss_pred CCCCCCCCCCcee---ee--CCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVV---FD--HSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii---~D--~~~G~~vC~~CG~Vv~ 34 (312)
..||.||.. .++ .| ...|..+|.+||.-.+
T Consensus 23 FtCp~Cghe-~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 23 FTCPRCGHE-KVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred EecCccCCe-eeeEEEEEecCceeEEEcccCcceEE
Confidence 479999984 454 44 3568899999998754
No 94
>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=91.30 E-value=0.5 Score=31.10 Aligned_cols=31 Identities=23% Similarity=0.163 Sum_probs=26.7
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
+..+|.+++|+.++||..||++.+++|.+..
T Consensus 13 ~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 13 KEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 4458999999999999999999999998765
No 95
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=91.13 E-value=1.1 Score=38.26 Aligned_cols=82 Identities=15% Similarity=0.319 Sum_probs=58.5
Q ss_pred HHHHHHhcCCcHHHHHHHHHHHHHHHhC-----CCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQ-----KPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (312)
Q Consensus 113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~-----~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~ 187 (312)
|+++|=.||+- .++..|.+++..+.+. ..--..+.....+|++|.|||..+...+-..+..++ |+++..+...
T Consensus 96 VrdlaVQfgc~-evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~s-g~~~s~F~~l 173 (262)
T KOG4557|consen 96 VRDLAVQFGCV-EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVS-GTSESEFSCL 173 (262)
T ss_pred HHHHHHHHhHH-HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhccccc-CCCHHHHHHH
Confidence 55666666664 3677788888776442 111234566889999999999999887777777777 8999888777
Q ss_pred HHHHHHHHh
Q 021438 188 KEFIVKHLE 196 (312)
Q Consensus 188 ~~~l~~~l~ 196 (312)
.+.+.+...
T Consensus 174 ~kqler~~~ 182 (262)
T KOG4557|consen 174 SKQLERNYK 182 (262)
T ss_pred HHHHHHHHH
Confidence 777666554
No 96
>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=91.07 E-value=0.62 Score=31.65 Aligned_cols=38 Identities=21% Similarity=0.277 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 254 VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 254 aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+||.... .+..++..+||+.++|+.+|+....+.|.+.
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 4565555 5677889999999999999999999998873
No 97
>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=90.90 E-value=0.13 Score=37.75 Aligned_cols=31 Identities=26% Similarity=0.497 Sum_probs=24.9
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
...||.||. .. +.-...|-.-|..||.++..
T Consensus 35 ky~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 35 KYTCPFCGK-TS-VKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp -BEESSSSS-SE-EEEEETTEEEETTTTEEEE-
T ss_pred CCcCCCCCC-ce-eEEeeeEEeecCCCCCEEeC
Confidence 357999998 34 67788999999999999764
No 98
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=90.85 E-value=13 Score=34.29 Aligned_cols=34 Identities=9% Similarity=0.305 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...|+++||+.+|+|..||+++.+.-...+...+
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999887777666544
No 99
>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=90.85 E-value=0.12 Score=31.89 Aligned_cols=31 Identities=32% Similarity=0.513 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCCceeeeCC-CCceEcCCCccc
Q 021438 2 ADSYCADCKRLTEVVFDHS-AGDTICSECGLV 32 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D~~-~G~~vC~~CG~V 32 (312)
...+|++||..-++..... .....|..||.-
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 3468999998333444333 456789999984
No 100
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=90.80 E-value=15 Score=34.65 Aligned_cols=31 Identities=23% Similarity=0.330 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|+++||+.+|+|...||+..+.-...+.
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr 354 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 5699999999999999999998776555443
No 101
>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=90.59 E-value=0.18 Score=35.21 Aligned_cols=29 Identities=21% Similarity=0.509 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
..||.||.. ...+.......|..||...+
T Consensus 29 q~C~~CG~~--~~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHR--NKKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCcccc--cccccccceEEcCCCCCEEC
Confidence 579999983 22245667899999999865
No 102
>PRK12495 hypothetical protein; Provisional
Probab=90.54 E-value=0.18 Score=43.22 Aligned_cols=32 Identities=22% Similarity=0.668 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
|....|+.||.+ | + ...|.++|..|+.++.+.
T Consensus 40 msa~hC~~CG~P--I-p-a~pG~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 40 MTNAHCDECGDP--I-F-RHDGQEFCPTCQQPVTED 71 (226)
T ss_pred cchhhcccccCc--c-c-CCCCeeECCCCCCccccc
Confidence 566789999983 3 3 458999999999998753
No 103
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=90.50 E-value=0.45 Score=30.10 Aligned_cols=29 Identities=17% Similarity=0.189 Sum_probs=19.1
Q ss_pred HHhcCCCCCHHHHHHHhCcchhHHHHHHH
Q 021438 259 TQLSNDTKPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 259 ~~~~~~~~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
..+.....++++||+.+|++.+||.+-+|
T Consensus 14 ~~l~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 14 EALLEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHHCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 34556678999999999999999996554
No 104
>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=90.22 E-value=0.26 Score=30.37 Aligned_cols=28 Identities=25% Similarity=0.591 Sum_probs=15.3
Q ss_pred CCCCCCCCCceeeeC-----CCC---ceEcCCCccc
Q 021438 5 YCADCKRLTEVVFDH-----SAG---DTICSECGLV 32 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~-----~~G---~~vC~~CG~V 32 (312)
.||.||+...+.+.. +++ .++|.+||..
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 699999854333321 222 3789999964
No 105
>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=90.13 E-value=0.2 Score=38.06 Aligned_cols=27 Identities=30% Similarity=0.817 Sum_probs=21.1
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
.||.||+. + .+..+.++|..||.+...
T Consensus 2 fC~~Cg~~--l--~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSL--M--TPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcc--c--ccCCCeEECcCCCCcccc
Confidence 79999983 3 345689999999998653
No 106
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=90.09 E-value=0.61 Score=47.48 Aligned_cols=82 Identities=12% Similarity=0.252 Sum_probs=67.3
Q ss_pred HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHH
Q 021438 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR 186 (312)
Q Consensus 109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~--~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~ 186 (312)
|...|+.+|++|.|.+.+.+....+|.-... ..+++.|..+.+.-+|+|+.+|..+..+++.+|....+ --......
T Consensus 680 AavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR-~QPqa~~~ 758 (920)
T KOG1010|consen 680 AAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYR-RQPQAVSL 758 (920)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHh-cCchhhhh
Confidence 6788999999999999888887777755433 35668899999999999999999999999999998774 55555666
Q ss_pred HHHHH
Q 021438 187 AKEFI 191 (312)
Q Consensus 187 ~~~~l 191 (312)
+|+.+
T Consensus 759 vyRsV 763 (920)
T KOG1010|consen 759 VYRSV 763 (920)
T ss_pred hhhhe
Confidence 67654
No 107
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=89.61 E-value=0.55 Score=30.22 Aligned_cols=27 Identities=19% Similarity=0.108 Sum_probs=18.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
..|.++||+.+|+|..||.+..+...+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 678999999999999999998877654
No 108
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.60 E-value=0.3 Score=30.30 Aligned_cols=27 Identities=26% Similarity=0.643 Sum_probs=18.3
Q ss_pred CCCCCCCCCceee------eCCCC---ceEcCCCccc
Q 021438 5 YCADCKRLTEVVF------DHSAG---DTICSECGLV 32 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~------D~~~G---~~vC~~CG~V 32 (312)
.||.||.. +.++ ..++| .++|.+||..
T Consensus 2 ~Cp~C~~~-~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNR-EATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCC-eEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 69999984 4433 12333 5899999964
No 109
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=89.38 E-value=0.27 Score=36.15 Aligned_cols=31 Identities=19% Similarity=0.477 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
...||.||. .. +.-...|-..|..||.++.-
T Consensus 36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 36 KYFCPFCGK-HA-VKRQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEeC
Confidence 457999998 44 45577899999999999864
No 110
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=89.36 E-value=0.25 Score=33.60 Aligned_cols=28 Identities=21% Similarity=0.545 Sum_probs=17.5
Q ss_pred CCCCCCCCCCceeeeC--------------CCCc---eEcCCCccc
Q 021438 4 SYCADCKRLTEVVFDH--------------SAGD---TICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~--------------~~G~---~vC~~CG~V 32 (312)
.+||.||. ++..+++ +.-. +.|.+||+-
T Consensus 5 ~kCpKCgn-~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 5 FKCPKCGN-TNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred ccCCCcCC-cchhhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 35999997 4554443 2221 569999874
No 111
>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=89.25 E-value=16 Score=32.88 Aligned_cols=34 Identities=15% Similarity=0.376 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...|++|||+.+|+|+.||+++.+.-.+.+...+
T Consensus 241 e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999998876666555444
No 112
>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=89.17 E-value=0.97 Score=30.70 Aligned_cols=38 Identities=39% Similarity=0.362 Sum_probs=28.5
Q ss_pred CChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHH
Q 021438 245 RSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNV 285 (312)
Q Consensus 245 r~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~ 285 (312)
|+|.-=-|=-+|+. ++-.+++++||+.+||++.||++.
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 44544445556643 566789999999999999999965
No 113
>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=89.01 E-value=0.13 Score=37.25 Aligned_cols=33 Identities=24% Similarity=0.459 Sum_probs=17.5
Q ss_pred CCCCCCCCCCce--eeeC--CCCceEcCCCcccccCc
Q 021438 4 SYCADCKRLTEV--VFDH--SAGDTICSECGLVLEAY 36 (312)
Q Consensus 4 ~~Cp~Cg~~~~i--i~D~--~~G~~vC~~CG~Vv~e~ 36 (312)
..||.|+....+ ..|. ..|.+.|..||...+-.
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 579999953444 3443 56789999999887543
No 114
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.84 E-value=0.29 Score=32.84 Aligned_cols=26 Identities=35% Similarity=0.742 Sum_probs=13.7
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
.|..||. .|--++.--...|.+||.+
T Consensus 11 ~CtSCg~--~i~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 11 VCTSCGR--EIAPGETAVKFPCPNCGEV 36 (61)
T ss_pred eeccCCC--EeccCCceeEeeCCCCCce
Confidence 5666665 2323333344667777733
No 115
>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=88.72 E-value=0.53 Score=30.17 Aligned_cols=20 Identities=25% Similarity=0.413 Sum_probs=17.8
Q ss_pred CHHHHHHHhCcchhHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVY 286 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~ 286 (312)
|++|||+.+|||..|+.+.+
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 57899999999999999665
No 116
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.61 E-value=0.38 Score=30.53 Aligned_cols=27 Identities=30% Similarity=0.645 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
..|.+||.. +..+ ..+.+-|.+||.=+
T Consensus 3 Y~C~~Cg~~--~~~~-~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRE--NEIK-SKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCE--eecC-CCCceECCCCCceE
Confidence 579999983 3333 56889999999744
No 117
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=88.49 E-value=5.7 Score=33.66 Aligned_cols=122 Identities=13% Similarity=0.190 Sum_probs=70.4
Q ss_pred HHHHHHHHHHHHHHHhCCC-CCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHH
Q 021438 148 QEAIVAACLYIACRQENKP-RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ 226 (312)
Q Consensus 148 ~~~iaaAcly~acr~~~~p-~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (312)
...++=|+||+ .+-| +++.+++.++ +++..++..++..|...+..... .+.+-.+ ...| +|...++
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----SGEEGLSLEQLAEIL-ELEPTEVQQLLEELQEKYEGDDR-GLKLIEF-NDVY------KLVTKEE 71 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHhhCCC-CEEEEEE-CCEE------EEEEcHH
Confidence 45667788886 5777 9999999999 79999999999998887753210 0011000 0001 1222333
Q ss_pred HHHHHHHHHHHhhhccCCCChHHHHHHHH-HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 227 AVKAAQEAVQKSEDLDIRRSPISVAAAVI-YIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 227 v~~~A~~i~~~~~~l~~Gr~P~~iaaAai-yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.......+.. .+.|..+.-|++ -||.-.++-++|..+|++..|++. ....++|.+.
T Consensus 72 ~~~~v~~~~~-------~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~---~~ii~~L~~~ 128 (188)
T PRK00135 72 NADYLQKLVK-------TPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNS---DGALQTLLAK 128 (188)
T ss_pred HHHHHHHHhc-------ccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHHC
Confidence 3222222221 112222332333 233344567899999999999996 5556666654
No 118
>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=88.43 E-value=1.2 Score=40.12 Aligned_cols=53 Identities=13% Similarity=0.178 Sum_probs=46.7
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcC
Q 021438 211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSN 263 (312)
Q Consensus 211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~ 263 (312)
..+|.++|.+|+++..+...|.-+.++-.- -..+..|..||+++|||||+..+
T Consensus 49 ~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed 103 (297)
T COG5333 49 LKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVED 103 (297)
T ss_pred HHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeeccc
Confidence 468999999999999999999988888554 45789999999999999999877
No 119
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=88.40 E-value=0.36 Score=32.47 Aligned_cols=28 Identities=21% Similarity=0.546 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccCccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSV 38 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~i 38 (312)
..||+||+. . .--.+|.+||+--+..++
T Consensus 28 ~~C~~CG~~-~------~~H~vC~~CG~Y~gr~v~ 55 (57)
T PRK12286 28 VECPNCGEP-K------LPHRVCPSCGYYKGREVV 55 (57)
T ss_pred eECCCCCCc-c------CCeEECCCCCcCCCEEee
Confidence 469999983 2 357899999987654443
No 120
>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=88.35 E-value=0.14 Score=47.84 Aligned_cols=77 Identities=16% Similarity=0.214 Sum_probs=0.0
Q ss_pred CCcHHHHHHHHHHHHHHH-hCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhh
Q 021438 121 GLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (312)
Q Consensus 121 ~Lp~~v~~~A~~i~~~~~-~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 198 (312)
++|+.++..|..||+... ....+++..-.+-+.+|+|+||...+.+..+....... +++++...+.|..+.+.|+..
T Consensus 11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~-pl~pk~y~~l~~~~~~~L~~~ 88 (353)
T PF05460_consen 11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRS-PLPPKVYKKLLNTFENLLGNS 88 (353)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCC-CCCHHHHHHHHHHHHHHHhCC
Confidence 346789999999999887 34555776667889999999999999999888877777 799999888888888888763
No 121
>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=88.25 E-value=0.74 Score=30.78 Aligned_cols=32 Identities=22% Similarity=0.238 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.++||+..++|+.||+.+.+.|.+.++.
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 35679999999999999999999999987653
No 122
>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=88.13 E-value=0.46 Score=27.00 Aligned_cols=22 Identities=23% Similarity=0.533 Sum_probs=11.8
Q ss_pred CCCCCCCCCceeeeCCCCceEcCC
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSE 28 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~ 28 (312)
.||.||+ .++.+..+-.+.|.+
T Consensus 1 ~CP~C~s--~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGS--KLVREEGEVDIRCPN 22 (28)
T ss_dssp B-TTT----BEEE-CCTTCEEE--
T ss_pred CcCCCCC--EeEcCCCCEeEECCC
Confidence 5999998 477766666777764
No 123
>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=88.01 E-value=1.1 Score=31.40 Aligned_cols=29 Identities=21% Similarity=0.168 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++++++||+.+|+|..|+.+.+++|.+.
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 45789999999999999999999999885
No 124
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=87.98 E-value=29 Score=34.20 Aligned_cols=31 Identities=26% Similarity=0.335 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|+++||..+|||..-||+.-+.....+.
T Consensus 466 e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR 496 (509)
T PRK05901 466 QPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496 (509)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5799999999999999999988876666554
No 125
>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=87.95 E-value=1.9 Score=29.22 Aligned_cols=29 Identities=17% Similarity=0.103 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
..+++.+||+.+|++..|+.+.++.|.+.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56889999999999999999999999884
No 126
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=87.94 E-value=0.88 Score=29.55 Aligned_cols=30 Identities=23% Similarity=0.265 Sum_probs=26.6
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
..+.++||+.+|+|..|++++.+.+.+.+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 368999999999999999999998877664
No 127
>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=87.90 E-value=0.36 Score=35.57 Aligned_cols=31 Identities=26% Similarity=0.517 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
...||.||. .. +.-...|-..|..||.++.-
T Consensus 35 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 35 KYVCPFCGK-KT-VKRGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred CccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEeC
Confidence 457999997 44 56678999999999999764
No 128
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.88 E-value=0.25 Score=38.20 Aligned_cols=32 Identities=19% Similarity=0.367 Sum_probs=23.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
-.||+||+ ..+..-+-.=.-.|..||.=...+
T Consensus 22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred CCCCCCCC-chhhhhhcccCchhhhccccccCC
Confidence 47999998 666554555567899999866543
No 129
>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=87.88 E-value=0.31 Score=28.62 Aligned_cols=25 Identities=28% Similarity=0.589 Sum_probs=17.2
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
.|.+||.. +.+.....+-|..||.=
T Consensus 2 ~C~~Cg~~---~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAE---VELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSS---E-BSTSSTSSBSSSS-S
T ss_pred CCCcCCCe---eEcCCCCcEECCcCCCe
Confidence 58899983 23455667899999963
No 130
>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=87.85 E-value=0.94 Score=33.29 Aligned_cols=31 Identities=32% Similarity=0.275 Sum_probs=26.9
Q ss_pred hcCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
++....|+++|++.+|+|..||.+.-+.|..
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 6667799999999999999999987777764
No 131
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=87.80 E-value=2.3 Score=29.76 Aligned_cols=71 Identities=15% Similarity=0.232 Sum_probs=42.5
Q ss_pred HHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-CHHHHHHHHHHH
Q 021438 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEFI 191 (312)
Q Consensus 113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-~~~~i~~~~~~l 191 (312)
|.+++..++++..... .+|+.........-....-+.-|+-|+. ..+.++.|++..+ |. +...+.+.+++.
T Consensus 4 ~~~la~~~~~s~~~l~---~~f~~~~~~s~~~~~~~~r~~~a~~~l~----~~~~~~~~ia~~~-g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 4 LEDLAEALGMSPRHLQ---RLFKKETGTTPKQYLRDRRLERARRLLR----DTDLSVTEIALRV-GFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHhCCCHHHHH---HHHHHHhCcCHHHHHHHHHHHHHHHHHH----cCCCCHHHHHHHh-CCCChHHHHHHHHHH
Confidence 6788899999876433 3444432211100011122333334432 2289999999999 89 999998888664
No 132
>PRK05978 hypothetical protein; Provisional
Probab=87.77 E-value=0.41 Score=38.84 Aligned_cols=31 Identities=16% Similarity=0.390 Sum_probs=23.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
.+||.||. ..+..-+-.=..-|..||.-.+-
T Consensus 34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCC-CcccccccccCCCccccCCcccc
Confidence 58999998 67755455555789999987653
No 133
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=87.70 E-value=0.95 Score=37.40 Aligned_cols=30 Identities=10% Similarity=-0.020 Sum_probs=27.7
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+-+.+..+||+.+|+|+.|+++|++.|.+.
T Consensus 26 d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 26 DGRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 456889999999999999999999999986
No 134
>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=87.59 E-value=0.36 Score=30.68 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=20.1
Q ss_pred HHHhcCCCCCHHHHHHHhCcchhHHHHHH
Q 021438 258 ITQLSNDTKPLKEISIVTRVAEGTIKNVY 286 (312)
Q Consensus 258 a~~~~~~~~~~~~Ia~~~~vs~~ti~~~~ 286 (312)
+.+++....|..+||+.+|||..||.+..
T Consensus 14 i~~l~~~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 14 IKELYAEGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 33455455889999999999999998654
No 135
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=87.51 E-value=26 Score=33.13 Aligned_cols=32 Identities=22% Similarity=0.321 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...|+++||..+|+|..+||+..+.-...+..
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~ 361 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 361 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 46899999999999999999998877766544
No 136
>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=87.39 E-value=0.084 Score=31.97 Aligned_cols=30 Identities=27% Similarity=0.747 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
..||.||..=++.+++..-+-+|..||.-+
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCee
Confidence 368899974466777777788898888743
No 137
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=87.21 E-value=0.96 Score=28.48 Aligned_cols=30 Identities=17% Similarity=0.113 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++.++.+||+.+|++..|+.+.++.|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 356889999999999999999999998874
No 138
>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=87.19 E-value=2.3 Score=28.13 Aligned_cols=27 Identities=11% Similarity=0.140 Sum_probs=23.4
Q ss_pred CCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++.|||+.+|||.+|+..+.+.-...
T Consensus 24 ~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 679999999999999999988765544
No 139
>COG4640 Predicted membrane protein [Function unknown]
Probab=87.19 E-value=0.34 Score=44.99 Aligned_cols=28 Identities=21% Similarity=0.699 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
|..||.||+. . .++++-|+.||.=+..+
T Consensus 1 M~fC~kcG~q-k-----~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 1 MKFCPKCGSQ-K-----AEDDVQCTQCGHKFTSR 28 (465)
T ss_pred CCcccccccc-c-----ccccccccccCCcCCch
Confidence 6789999983 2 25677799999887653
No 140
>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=87.02 E-value=1.3 Score=28.27 Aligned_cols=32 Identities=19% Similarity=0.220 Sum_probs=26.7
Q ss_pred hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+..-+.+..||++.++++.+||+...+.|.+.
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 44466889999999999999999999998874
No 141
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=87.01 E-value=0.7 Score=32.65 Aligned_cols=31 Identities=13% Similarity=0.252 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCceeeeCC-------CCceEcC--CCccccc
Q 021438 3 DSYCADCKRLTEVVFDHS-------AGDTICS--ECGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~-------~G~~vC~--~CG~Vv~ 34 (312)
|+.||.||+. ..|.+.. +-...|+ +||.-.-
T Consensus 1 mm~CP~Cg~~-a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 1 MFHCPLCQHA-AHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred CccCCCCCCc-cEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 6899999984 5666642 2236788 8998764
No 142
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=86.87 E-value=25 Score=32.32 Aligned_cols=31 Identities=10% Similarity=0.266 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
+.+.|++|||..+|+|..+||++.+.-...+
T Consensus 274 ~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kL 304 (317)
T PRK07405 274 GQPLTLAKIGERLNISRERVRQIEREALSKL 304 (317)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3679999999999999999998876554443
No 143
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=86.84 E-value=1.2 Score=29.42 Aligned_cols=30 Identities=17% Similarity=0.224 Sum_probs=26.2
Q ss_pred CCCC-CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTK-PLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~-~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+..+ +.+++|+.+++|..|+++.++.|.+.
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3345 79999999999999999999999874
No 144
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=86.81 E-value=1.2 Score=36.33 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=27.7
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+-..|..+||+.+|+|+.|+++|++.|.+.
T Consensus 21 d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 21 NARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 456889999999999999999999999996
No 145
>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=86.73 E-value=0.53 Score=33.36 Aligned_cols=28 Identities=25% Similarity=0.140 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
...|++|||+.+|+|+.||+++++.+..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 3578999999999999999999886544
No 146
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=86.71 E-value=1 Score=35.51 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=27.0
Q ss_pred CCCCC-HHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKP-LKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~-~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
|.++| .++.|..++|.+.|+++.|++|.+.
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 66765 8999999999999999999999884
No 147
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=86.70 E-value=0.45 Score=35.01 Aligned_cols=32 Identities=25% Similarity=0.481 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
...||.||. .. +.-...|-.-|..||.++.-.
T Consensus 36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 36 KHVCPVCGR-PK-VKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred CccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEeCC
Confidence 457999997 34 456788999999999998653
No 148
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=86.46 E-value=0.16 Score=33.88 Aligned_cols=26 Identities=31% Similarity=0.883 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCC-Cccccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSE-CGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~-CG~Vv~ 34 (312)
+..|+.||.. | ..|+.+|++ ||.+++
T Consensus 8 H~HC~VCg~a--I----p~de~~CSe~C~eil~ 34 (64)
T COG4068 8 HRHCVVCGKA--I----PPDEQVCSEECGEILN 34 (64)
T ss_pred CccccccCCc--C----CCccchHHHHHHHHHH
Confidence 4689999983 3 257889986 998875
No 149
>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=86.37 E-value=0.45 Score=31.86 Aligned_cols=27 Identities=19% Similarity=0.530 Sum_probs=18.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccCcc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~ 37 (312)
..||+||.. ...-.+|.+||+.=.-.+
T Consensus 27 ~~c~~cg~~-------~~~H~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 27 VKCPNCGEP-------KLPHRVCPSCGYYKGRQV 53 (56)
T ss_dssp EESSSSSSE-------ESTTSBCTTTBBSSSSSS
T ss_pred eeeccCCCE-------ecccEeeCCCCeECCEEE
Confidence 479999972 246789999997644333
No 150
>PHA02591 hypothetical protein; Provisional
Probab=86.34 E-value=1.1 Score=31.86 Aligned_cols=32 Identities=9% Similarity=0.195 Sum_probs=25.3
Q ss_pred HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHH
Q 021438 256 YIITQLSNDTKPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 256 yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
-+|-++.....|+.+||+.+|++..++++..+
T Consensus 50 ~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 50 SVTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 34455555678899999999999999997654
No 151
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=86.33 E-value=23 Score=31.39 Aligned_cols=32 Identities=22% Similarity=0.295 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+|++|||..+|+|..||+++.+.....+..
T Consensus 220 e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 220 EELVLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56899999999999999999998776666544
No 152
>PRK08402 replication factor A; Reviewed
Probab=86.18 E-value=0.6 Score=43.65 Aligned_cols=27 Identities=37% Similarity=0.812 Sum_probs=23.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
..||.|+. .++.|...|...|..||.|
T Consensus 213 ~aCp~CnK--kv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRR--KVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCe--EEEEecCCCCEeCCCCCCc
Confidence 47999997 4666888999999999975
No 153
>PF12773 DZR: Double zinc ribbon
Probab=86.09 E-value=0.44 Score=30.88 Aligned_cols=28 Identities=21% Similarity=0.633 Sum_probs=12.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
..||+||.. +. .......+|..||..++
T Consensus 13 ~fC~~CG~~--l~-~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 13 KFCPHCGTP--LP-PPDQSKKICPNCGAENP 40 (50)
T ss_pred cCChhhcCC--hh-hccCCCCCCcCCcCCCc
Confidence 345555542 21 22233455666665543
No 154
>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=86.06 E-value=6.7 Score=28.81 Aligned_cols=71 Identities=15% Similarity=0.236 Sum_probs=48.7
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHhhhccCCCC-hHHHH-HHHHHHHHHhcCCCCCHHHHHHHhC-cchhHHHHHHH
Q 021438 211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRRS-PISVA-AAVIYIITQLSNDTKPLKEISIVTR-VAEGTIKNVYK 287 (312)
Q Consensus 211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~l~~Gr~-P~~ia-aAaiyla~~~~~~~~~~~~Ia~~~~-vs~~ti~~~~k 287 (312)
+..+..+|..+|++.+.. ...+|. +.+.| .-+.|++-+..| .|..+|++.+| .+.+||...++
T Consensus 2 ~~Ii~~Va~~~~v~~~~i------------~~~~R~~~~~~aR~ia~yl~~~~~~--~s~~~Ig~~fg~r~hStV~~a~~ 67 (90)
T cd06571 2 ELIIEAVAEYFGISVEDL------------RSKSRKKEIALARQIAMYLARELTG--LSLPEIGRAFGGRDHSTVLHAVR 67 (90)
T ss_pred HHHHHHHHHHhCCCHHHH------------hcCCCCcCcchHHHHHHHHHHHHhC--CCHHHHHHHhCCCCHhHHHHHHH
Confidence 345666666666665321 112222 33334 567888888875 56899999999 99999999999
Q ss_pred HHHhhhcc
Q 021438 288 DLFPHLAR 295 (312)
Q Consensus 288 el~~~~~~ 295 (312)
.+.+.+..
T Consensus 68 ri~~~~~~ 75 (90)
T cd06571 68 KIEELLEE 75 (90)
T ss_pred HHHHHHHh
Confidence 88886643
No 155
>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=86.01 E-value=1.2 Score=29.12 Aligned_cols=28 Identities=18% Similarity=0.215 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
...|.+|||+..|+|+.|+++++..-.+
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 4577999999999999999999876554
No 156
>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=86.01 E-value=0.52 Score=32.48 Aligned_cols=27 Identities=30% Similarity=0.715 Sum_probs=17.5
Q ss_pred CCCCCCCCCcee--------------eeCCCCc---eEcCCCccc
Q 021438 5 YCADCKRLTEVV--------------FDHSAGD---TICSECGLV 32 (312)
Q Consensus 5 ~Cp~Cg~~~~ii--------------~D~~~G~---~vC~~CG~V 32 (312)
.||.||+. +.. +|-++.. ++|++||+.
T Consensus 2 ~C~KCg~~-~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNE-EYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCc-ceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 69999973 332 3322222 689999987
No 157
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=86.01 E-value=1.6 Score=28.30 Aligned_cols=24 Identities=13% Similarity=0.386 Sum_probs=21.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHH
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
..|+++||+..|+|..||++.+++
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHh
Confidence 379999999999999999988765
No 158
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=85.93 E-value=0.35 Score=29.25 Aligned_cols=29 Identities=28% Similarity=0.603 Sum_probs=19.6
Q ss_pred CCCCCCCCCCceeee----CCCCceEcCCCcccc
Q 021438 4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D----~~~G~~vC~~CG~Vv 33 (312)
..||+|+.. --+.| .....+-|+.||.+.
T Consensus 3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence 579999983 22233 234458899999874
No 159
>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=85.57 E-value=3.2 Score=37.48 Aligned_cols=66 Identities=14% Similarity=0.129 Sum_probs=54.8
Q ss_pred HHHHHHHHhhc--CCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhC
Q 021438 211 SDYLRRFCSNL--GMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTR 276 (312)
Q Consensus 211 ~~~i~r~~~~L--~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~ 276 (312)
+..+..|++++ .++..|+..|....++..- ....-+|-.|.++++||||+...+-+|..++++-..
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 44566677665 5899999999998888764 456789999999999999999999999999988765
No 160
>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=85.49 E-value=1 Score=30.14 Aligned_cols=29 Identities=24% Similarity=0.195 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
-.++.+++|+.++||+.|||+-+.+|.+.
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46889999999999999999888877664
No 161
>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=85.27 E-value=1.6 Score=28.34 Aligned_cols=31 Identities=26% Similarity=0.363 Sum_probs=27.0
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+.++||+.+++|+.||+.+.+.+.+.+..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 4689999999999999999999988776543
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=85.06 E-value=0.64 Score=31.02 Aligned_cols=25 Identities=20% Similarity=0.679 Sum_probs=17.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
..||+||+. ..---||..||+--+.
T Consensus 27 ~~C~~cG~~-------~~~H~vc~~cG~Y~gr 51 (55)
T TIGR01031 27 VVCPNCGEF-------KLPHRVCPSCGYYKGR 51 (55)
T ss_pred eECCCCCCc-------ccCeeECCccCeECCE
Confidence 469999972 2356899999976543
No 163
>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=84.94 E-value=7.6 Score=32.26 Aligned_cols=29 Identities=17% Similarity=0.053 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++|+++||+.+|+|..|+.+..++|.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 56899999999999999999999999885
No 164
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=84.57 E-value=0.68 Score=30.50 Aligned_cols=29 Identities=34% Similarity=0.672 Sum_probs=21.2
Q ss_pred CCCCCCCCCceeeeCCCCc----eEcCCCcccc
Q 021438 5 YCADCKRLTEVVFDHSAGD----TICSECGLVL 33 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~----~vC~~CG~Vv 33 (312)
.||+||....+..|.+.|. -=|.-|..=+
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence 6999999778888988885 2366665544
No 165
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=84.54 E-value=1.2 Score=30.47 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCceeeeCCCCc--eEcCCCccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGD--TICSECGLV 32 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~--~vC~~CG~V 32 (312)
...||.||.....+.+ ..|- .+|..||..
T Consensus 6 lKPCPFCG~~~~~v~~-~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVKA-ISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEEe-cCceEEEEcCCCCcC
Confidence 3579999984333333 3333 689999985
No 166
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=84.49 E-value=0.28 Score=41.28 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=22.6
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
..||.|+.. =-..|.-+....|..||.++.+
T Consensus 118 Y~Cp~C~~r-ytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 118 FFCPNCHIR-FTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred EECCCCCcE-EeHHHHhhcCCcCCCCCCCCee
Confidence 469999973 2233445678999999999875
No 167
>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=84.46 E-value=0.99 Score=30.37 Aligned_cols=30 Identities=20% Similarity=0.491 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCceeeeCCCC--ceEcCCCccc
Q 021438 3 DSYCADCKRLTEVVFDHSAG--DTICSECGLV 32 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G--~~vC~~CG~V 32 (312)
.-.||.|+.-..+..=.++| ..-|-.||+-
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 35799999854443322333 3789999987
No 168
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=84.36 E-value=0.81 Score=33.96 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCceeeeCC-CCceEcCCCccccc
Q 021438 3 DSYCADCKRLTEVVFDHS-AGDTICSECGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~-~G~~vC~~CG~Vv~ 34 (312)
|..||.||. .=+++.-. -....|..|++|..
T Consensus 1 m~FCP~Cgn-~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 1 MLFCPTCGN-MLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred CcccCCCCC-EEEEecCCeEeeEEcCCCCceee
Confidence 468999998 33333222 25678999999963
No 169
>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=84.00 E-value=1.6 Score=25.58 Aligned_cols=27 Identities=19% Similarity=0.356 Sum_probs=21.6
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 166 PRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 166 p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
|.|-.||++.. |.+.+++.|.++++.+
T Consensus 2 ~mtr~diA~~l-G~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYL-GLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHHH-TS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHh-CCcHHHHHHHHHHHHH
Confidence 67889999999 8999999999988764
No 170
>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=83.95 E-value=0.53 Score=30.76 Aligned_cols=30 Identities=27% Similarity=0.506 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCCceeee-CCCCceEcCCCcc
Q 021438 2 ADSYCADCKRLTEVVFD-HSAGDTICSECGL 31 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D-~~~G~~vC~~CG~ 31 (312)
+..+|++||..-++... .+.....|..||.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 34679999973233322 2245678999997
No 171
>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=83.94 E-value=0.55 Score=40.53 Aligned_cols=34 Identities=29% Similarity=0.662 Sum_probs=25.8
Q ss_pred CCCCCCCCC-CceeeeCCCCc---eEcCCCcccccCcc
Q 021438 4 SYCADCKRL-TEVVFDHSAGD---TICSECGLVLEAYS 37 (312)
Q Consensus 4 ~~Cp~Cg~~-~~ii~D~~~G~---~vC~~CG~Vv~e~~ 37 (312)
+.|-+||.+ ..+..+++.|. ..|.+||.|.|..+
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYi 38 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYI 38 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCccccee
Confidence 479999984 34567777664 89999999987543
No 172
>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=83.92 E-value=0.86 Score=36.81 Aligned_cols=28 Identities=25% Similarity=0.699 Sum_probs=20.4
Q ss_pred CCC--CCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 5 YCA--DCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 5 ~Cp--~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
.|| .|++ .+..+ .+|.+.|..||..+++
T Consensus 20 aC~~~~C~k--Kv~~~-~~~~y~C~~C~~~~~~ 49 (146)
T PF08646_consen 20 ACPNEKCNK--KVTEN-GDGSYRCEKCNKTVEN 49 (146)
T ss_dssp E-TSTTTS---B-EEE-TTTEEEETTTTEEESS
T ss_pred CCCCccCCC--EeecC-CCcEEECCCCCCcCCC
Confidence 599 9998 46665 7799999999988753
No 173
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=83.88 E-value=12 Score=25.95 Aligned_cols=26 Identities=19% Similarity=0.404 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhCc-chhHHHHHHHHHH
Q 021438 265 TKPLKEISIVTRV-AEGTIKNVYKDLF 290 (312)
Q Consensus 265 ~~~~~~Ia~~~~v-s~~ti~~~~kel~ 290 (312)
+.++.+||..+|. +...+.+.+|+..
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 6889999999999 9999998887764
No 174
>PRK04217 hypothetical protein; Provisional
Probab=83.71 E-value=1.4 Score=33.90 Aligned_cols=32 Identities=16% Similarity=0.133 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+++++||+.+|+|..||+++++...+.+..
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999998877776654
No 175
>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=83.51 E-value=1.4 Score=32.80 Aligned_cols=31 Identities=26% Similarity=0.203 Sum_probs=25.3
Q ss_pred HhcCCCCCHHHHHHHhCcchhHHHHHHHHHH
Q 021438 260 QLSNDTKPLKEISIVTRVAEGTIKNVYKDLF 290 (312)
Q Consensus 260 ~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~ 290 (312)
.+..-.+||+|||+.+|||..||.+.-+.+.
T Consensus 50 ~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 50 ELLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 3444679999999999999999997766655
No 176
>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=83.32 E-value=0.93 Score=26.73 Aligned_cols=23 Identities=26% Similarity=0.788 Sum_probs=14.5
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGL 31 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~ 31 (312)
.|+.||- ++|.......|..||.
T Consensus 3 ~C~~CGy----~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY----IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC----EECCCcCCCcCcCCCC
Confidence 5777774 4555556667777765
No 177
>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=83.11 E-value=1.6 Score=29.77 Aligned_cols=30 Identities=17% Similarity=0.216 Sum_probs=25.1
Q ss_pred CCCC-CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTK-PLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~-~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
|..+ +..++|+..+||..|+++.++.|.+.
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 5667 79999999999999999999998774
No 178
>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=83.06 E-value=7.6 Score=28.87 Aligned_cols=31 Identities=16% Similarity=0.198 Sum_probs=27.3
Q ss_pred cCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
....+++.|||+.+|++..|+.+..++|.+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3467899999999999999999999998874
No 179
>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=82.98 E-value=0.63 Score=29.14 Aligned_cols=30 Identities=30% Similarity=0.599 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCceeeeCC-CCceEcCCCccc
Q 021438 3 DSYCADCKRLTEVVFDHS-AGDTICSECGLV 32 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~-~G~~vC~~CG~V 32 (312)
...|+.||..-++..... .....|..||..
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGST 35 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence 457899996333333333 367889999873
No 180
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.94 E-value=0.49 Score=30.66 Aligned_cols=27 Identities=37% Similarity=0.714 Sum_probs=21.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
..|-.||. .+..|.....+-|..||.=
T Consensus 7 Y~C~~Cg~--~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGR--EVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCC--eeehhhccCceeCCCCCcE
Confidence 47999998 3545777888999999964
No 181
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=82.88 E-value=2.9 Score=28.94 Aligned_cols=32 Identities=6% Similarity=0.092 Sum_probs=27.2
Q ss_pred hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.+-..+.+++|+.+|+|..||+++.+.|.+.
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~ 40 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLREW 40 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 33445779999999999999999999999764
No 182
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=82.74 E-value=1.8 Score=29.13 Aligned_cols=31 Identities=29% Similarity=0.299 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
-..+.+++|+.+|+|+.||++...+|.+.+.
T Consensus 18 ~~~~~~ela~~l~~S~rti~~~i~~L~~~f~ 48 (59)
T PF08280_consen 18 KWITLKELAKKLNISERTIKNDINELNEFFP 48 (59)
T ss_dssp TSBBHHHHHHHCTS-HHHHHHHHHHHHTT--
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence 4578999999999999999999888877543
No 183
>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=82.73 E-value=0.39 Score=31.21 Aligned_cols=32 Identities=16% Similarity=0.397 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
...+|++|+..-.-..+..+.++-|.-||++-
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 45789999973111135667899999999993
No 184
>PRK02935 hypothetical protein; Provisional
Probab=82.68 E-value=0.93 Score=34.15 Aligned_cols=38 Identities=24% Similarity=0.502 Sum_probs=24.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccCccccccccccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA 48 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~ 48 (312)
..||+|++.+.+.=+ ...|-.|+.-+. +|.+.|-..|+
T Consensus 71 V~CP~C~K~TKmLGr----vD~CM~C~~PLT---Ld~~legkefd 108 (110)
T PRK02935 71 VICPSCEKPTKMLGR----VDACMHCNQPLT---LDRSLEGKEFD 108 (110)
T ss_pred eECCCCCchhhhccc----eeecCcCCCcCC---cCccccccCcC
Confidence 479999986554322 358999998874 35444433343
No 185
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=82.26 E-value=2 Score=31.04 Aligned_cols=39 Identities=13% Similarity=0.250 Sum_probs=29.2
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 254 VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 254 aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.+|+|..-.+.+.+.++||+..++++..+++..+.|.+.
T Consensus 14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 344444333344899999999999999999999999884
No 186
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=82.11 E-value=0.52 Score=39.61 Aligned_cols=29 Identities=38% Similarity=0.690 Sum_probs=20.0
Q ss_pred CCCCCCCCCCce----eeeCCCC---ceEcCCCcccccC
Q 021438 4 SYCADCKRLTEV----VFDHSAG---DTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~i----i~D~~~G---~~vC~~CG~Vv~e 35 (312)
..||.||+ .++ +. ..| .+-|.+||+|-.+
T Consensus 7 ~~Cp~Cg~-eev~hEVik--~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 7 IECPSCGS-EEVSHEVIK--ERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EECCCCCc-chhhHHHHH--hcCCceEEEccCCCcEeec
Confidence 47999995 333 22 123 4789999999854
No 187
>PF14122 YokU: YokU-like protein
Probab=82.08 E-value=0.87 Score=32.98 Aligned_cols=39 Identities=31% Similarity=0.599 Sum_probs=25.6
Q ss_pred CCCCCCCC------CceeeeCCCCc----------eEcCCCcccccCcccccccc
Q 021438 5 YCADCKRL------TEVVFDHSAGD----------TICSECGLVLEAYSVDETSE 43 (312)
Q Consensus 5 ~Cp~Cg~~------~~ii~D~~~G~----------~vC~~CG~Vv~e~~id~~~e 43 (312)
+|--||+. +++-++-..|. ++|++||.|-.+..+...-|
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhHHHHHHh
Confidence 36667752 34555555555 89999999987766554444
No 188
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=82.00 E-value=2.4 Score=34.22 Aligned_cols=30 Identities=13% Similarity=0.060 Sum_probs=27.4
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+-+.|+.+||+.+|+|+.|+++|.+.|.+.
T Consensus 20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 20 DARISNAELAERVGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 445899999999999999999999999985
No 189
>PRK05949 RNA polymerase sigma factor; Validated
Probab=81.93 E-value=43 Score=30.97 Aligned_cols=30 Identities=10% Similarity=0.244 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
...|++|||+.+|+|..+|+++...-.+.+
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~~~rAl~kL 314 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQLEHQALAHL 314 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 579999999999999999998876544444
No 190
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=81.49 E-value=1.2 Score=35.98 Aligned_cols=29 Identities=31% Similarity=0.593 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceeeeC---CCCc-----eEcCCCccc
Q 021438 4 SYCADCKRLTEVVFDH---SAGD-----TICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~---~~G~-----~vC~~CG~V 32 (312)
|.||.|++..+-+.|+ +.|. -.|.+||.=
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~R 37 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGER 37 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccc
Confidence 5899999865556664 3343 358888754
No 191
>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=81.27 E-value=2.1 Score=28.18 Aligned_cols=26 Identities=27% Similarity=0.239 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHH
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDL 289 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel 289 (312)
+.+|++|.|+.+||+..+++++++++
T Consensus 14 fhlp~~eAA~~Lgv~~T~LKr~CR~~ 39 (52)
T PF02042_consen 14 FHLPIKEAAKELGVSVTTLKRRCRRL 39 (52)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 56899999999999999999998754
No 192
>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=81.23 E-value=2.4 Score=29.28 Aligned_cols=31 Identities=16% Similarity=0.140 Sum_probs=24.8
Q ss_pred hcCCCCCHHHHHHHhCcc-hhHHHHHHHHHHh
Q 021438 261 LSNDTKPLKEISIVTRVA-EGTIKNVYKDLFP 291 (312)
Q Consensus 261 ~~~~~~~~~~Ia~~~~vs-~~ti~~~~kel~~ 291 (312)
-+|++-|.+|||+.+|++ .+|+....+.|.+
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 368889999999999986 9999999998876
No 193
>PHA02942 putative transposase; Provisional
Probab=81.07 E-value=1 Score=42.63 Aligned_cols=29 Identities=17% Similarity=0.436 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
..||.||... .+.......|.+||+..+-
T Consensus 326 q~Cs~CG~~~---~~l~~r~f~C~~CG~~~dr 354 (383)
T PHA02942 326 VSCPKCGHKM---VEIAHRYFHCPSCGYENDR 354 (383)
T ss_pred ccCCCCCCcc---CcCCCCEEECCCCCCEeCc
Confidence 5799999732 2344567999999999754
No 194
>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=81.05 E-value=0.88 Score=45.30 Aligned_cols=43 Identities=19% Similarity=0.516 Sum_probs=29.5
Q ss_pred CCCCCCCCCCce-----eee----CCCCceEcCCCcccccCcc---ccccccccc
Q 021438 4 SYCADCKRLTEV-----VFD----HSAGDTICSECGLVLEAYS---VDETSEWRI 46 (312)
Q Consensus 4 ~~Cp~Cg~~~~i-----i~D----~~~G~~vC~~CG~Vv~e~~---id~~~ewr~ 46 (312)
..||+||....+ .+| +.+-.++|..||..++|+. ....-+|+.
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~ 255 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVA 255 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEe
Confidence 579999975333 332 4456799999999999863 223466764
No 195
>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=80.96 E-value=35 Score=29.34 Aligned_cols=31 Identities=23% Similarity=0.318 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|.+|||+.+|+|..||+++++.-.+.+.
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999999999998876666554
No 196
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=80.95 E-value=40 Score=29.92 Aligned_cols=170 Identities=15% Similarity=0.184 Sum_probs=88.2
Q ss_pred hHHHHHHHHHHHHHhc--CCc---HHHHHH-HHHHHHHHHhCCCCCCCCHHHHHHHHHHHH----HHHhC---CCCCHHH
Q 021438 105 NLIQAFKSISAMSDRL--GLV---TTIKDR-ANEIYKKVEDQKPLRGRNQEAIVAACLYIA----CRQEN---KPRTVKE 171 (312)
Q Consensus 105 ~l~~~~~~I~~~~~~L--~Lp---~~v~~~-A~~i~~~~~~~~~~~gr~~~~iaaAcly~a----cr~~~---~p~tl~d 171 (312)
-+.+....+..++.++ ++| ++.+.. ...+.+-+......+|.++.+.|.=||==+ +|.++ .||++++
T Consensus 28 Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~~v~vpR~~~~ 107 (247)
T COG1191 28 LIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKNDSVKVPRSLRE 107 (247)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCCCccCcHHHHH
Confidence 3456677778887777 455 233333 344666666667778888887776654333 45444 5677666
Q ss_pred HHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-------c--c
Q 021438 172 FCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-------L--D 242 (312)
Q Consensus 172 ia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-------l--~ 242 (312)
...- +..+...+...++- +| ....++..||++.+-+..+....+...- . .
T Consensus 108 ~~~~--------i~~~~~~l~~el~r-----------~p--t~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~ 166 (247)
T COG1191 108 LGRR--------IEEAIDELEQELGR-----------EP--TDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDD 166 (247)
T ss_pred HHHH--------HHHHHHHHHHHhCC-----------CC--cHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhcccc
Confidence 6442 22333334433331 01 1123455555554433333322221110 0 0
Q ss_pred CCC------ChH-----HHHHHHHHHHHH------------hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 243 IRR------SPI-----SVAAAVIYIITQ------------LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 243 ~Gr------~P~-----~iaaAaiyla~~------------~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
.|. .|. ..--..++=+.. .+...+|++||++++|||++.|.+..+.....+..
T Consensus 167 d~~~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai~kLr~ 242 (247)
T COG1191 167 DDDVDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAIKKLRK 242 (247)
T ss_pred ccchhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 010 010 001111111111 12346999999999999999999888877776544
No 197
>PF12773 DZR: Double zinc ribbon
Probab=80.93 E-value=1.2 Score=28.73 Aligned_cols=22 Identities=23% Similarity=0.832 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECG 30 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG 30 (312)
...||.||.. ...+..+|..||
T Consensus 29 ~~~C~~Cg~~------~~~~~~fC~~CG 50 (50)
T PF12773_consen 29 KKICPNCGAE------NPPNAKFCPNCG 50 (50)
T ss_pred CCCCcCCcCC------CcCCcCccCccc
Confidence 4579999973 235788899888
No 198
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=80.93 E-value=6.6 Score=35.45 Aligned_cols=63 Identities=14% Similarity=0.051 Sum_probs=48.8
Q ss_pred ccCCCCHHHHHHHHHhhcC-CCHHHHHHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHH
Q 021438 204 EMGTIHASDYLRRFCSNLG-MTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTI 282 (312)
Q Consensus 204 ~~~~~~p~~~i~r~~~~L~-l~~~v~~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti 282 (312)
+.....|..++.++-+.+. |++.-.+.|..|++. |.-++ ..+..+||+.++||+.||
T Consensus 6 ~~~~~~~~~i~~~i~~~~~~Lt~~e~~Ia~yil~~---------~~~v~-------------~~si~~lA~~~~vS~aTi 63 (292)
T PRK11337 6 DSALPNGIGLGPYIRMKQEGLTPLESRVVEWLLKP---------GDLSE-------------ATALKDIAEALAVSEAMI 63 (292)
T ss_pred cccccCchhHHHHHHHHHhhcCHHHHHHHHHHHhC---------HHHHH-------------hcCHHHHHHHhCCChHHH
Confidence 4445678899999998886 999888888888854 44433 356789999999999999
Q ss_pred HHHHHH
Q 021438 283 KNVYKD 288 (312)
Q Consensus 283 ~~~~ke 288 (312)
-+-+|.
T Consensus 64 ~Rf~kk 69 (292)
T PRK11337 64 VKVAKK 69 (292)
T ss_pred HHHHHH
Confidence 876543
No 199
>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=80.56 E-value=12 Score=36.06 Aligned_cols=163 Identities=13% Similarity=0.213 Sum_probs=0.0
Q ss_pred HHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCC------------------CHHHHHH
Q 021438 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR------------------TVKEFCS 174 (312)
Q Consensus 113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~------------------tl~dia~ 174 (312)
+..++..++++...++.|..+.+.+.-.|+...- ..=|+.+=.+..+..- .+..|+.
T Consensus 116 ~~eia~~l~~~~~~ve~~l~~iq~leP~GIgAr~-----L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i~~ 190 (429)
T TIGR02395 116 LEEIADELEVSEEEVEKVLELIQRLDPAGVGARD-----LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRLAK 190 (429)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhcCCCCccCcCC-----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHHHH
Q ss_pred HhcCCCHHHHHHHHHHHHHHHhhhhcccc----ccCCCCHHHHHHHHHh------------hcCCCHHHH----------
Q 021438 175 VANGTTKKEIGRAKEFIVKHLEAEMGQSV----EMGTIHASDYLRRFCS------------NLGMTNQAV---------- 228 (312)
Q Consensus 175 ~~~~v~~~~i~~~~~~l~~~l~~~~~~~~----~~~~~~p~~~i~r~~~------------~L~l~~~v~---------- 228 (312)
.. +++..++..++..|+ .|+-..+..+ ....+.|..+|.+.-. +|.+++...
T Consensus 191 ~l-~is~~~v~~~~~~I~-~L~P~Pg~~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~~~ 268 (429)
T TIGR02395 191 KL-GLSEEELKEALDLIK-SLSPKPGKEFADPEEVEYVIPDVIVTKKNGEWVVELNGRSLPELRINEEYFKLLKDAEKEA 268 (429)
T ss_pred HH-CcCHHHHHHHHHHHh-CCCCCCcccccCCCCCCccCCCEEEEEECCEEEEEEcCCCCceEEECHHHHHHHHhccchH
Q ss_pred ---------HHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCC---------CCCHHHHHHHhCcchhHHHHHHH
Q 021438 229 ---------KAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSND---------TKPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 229 ---------~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~---------~~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
+.|..+++... ++-.++--.+-.++-+-.++ ++++++||+.+|++++||++..+
T Consensus 269 ~~~ylk~k~~~A~~li~~i~-----~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 269 AAQYLKQKLKEARWLIKALE-----QREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
No 200
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=80.37 E-value=3.4 Score=31.22 Aligned_cols=29 Identities=21% Similarity=0.194 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
-..|..+||+.+|+++.|++++++.|.+.
T Consensus 16 ~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 16 ARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46889999999999999999999999885
No 201
>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=80.13 E-value=0.95 Score=30.09 Aligned_cols=30 Identities=17% Similarity=0.408 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCcee--eeCCCCceEcCCCccc
Q 021438 3 DSYCADCKRLTEVV--FDHSAGDTICSECGLV 32 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii--~D~~~G~~vC~~CG~V 32 (312)
...|++|.+.+-+. ++.+.-.++|..||..
T Consensus 22 aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 22 ALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred eEECcccchhhcccccccCCceEEEcCCCCCc
Confidence 35799999754343 6677778999999963
No 202
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=80.09 E-value=0.91 Score=30.36 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
-+..|+.||. -.+ ..+|..||....
T Consensus 4 ~mr~C~~Cgv-YTL-------k~~CP~CG~~t~ 28 (56)
T PRK13130 4 KIRKCPKCGV-YTL-------KEICPVCGGKTK 28 (56)
T ss_pred cceECCCCCC-EEc-------cccCcCCCCCCC
Confidence 4678999997 333 678999998754
No 203
>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=80.02 E-value=6.8 Score=24.81 Aligned_cols=29 Identities=7% Similarity=0.108 Sum_probs=21.3
Q ss_pred cCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
+|. +++++.|+..||...|+..+++...+
T Consensus 14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~~~ 42 (45)
T PF05225_consen 14 NGK-MSIRKAAKKYGVPRSTLRRRLRGKPS 42 (45)
T ss_dssp TTS-S-HHHHHHHHT--HHHHHHHHHHTTT
T ss_pred hCC-CCHHHHHHHHCcCHHHHHHHHcCCCC
Confidence 444 99999999999999999988876443
No 204
>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=79.83 E-value=5.1 Score=26.68 Aligned_cols=28 Identities=14% Similarity=0.165 Sum_probs=24.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.+++.+||+.++++..|+....+.|.+.
T Consensus 21 ~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 21 ELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp GEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3899999999999999999999999874
No 205
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=79.79 E-value=59 Score=31.20 Aligned_cols=179 Identities=11% Similarity=0.177 Sum_probs=88.3
Q ss_pred HHHHHHHHHHHHHhc---CC--cHHHHHHHHHHHHHHHhCCCCCCCCHHHHHH-----HH-HHHH---------------
Q 021438 106 LIQAFKSISAMSDRL---GL--VTTIKDRANEIYKKVEDQKPLRGRNQEAIVA-----AC-LYIA--------------- 159 (312)
Q Consensus 106 l~~~~~~I~~~~~~L---~L--p~~v~~~A~~i~~~~~~~~~~~gr~~~~iaa-----Ac-ly~a--------------- 159 (312)
+..-...+..++.++ ++ .+-+.+....+++.+......+|.++...+- +. -+++
T Consensus 181 I~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~ 260 (415)
T PRK07598 181 IKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK 260 (415)
T ss_pred HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHH
Confidence 344456666666665 22 2445666666888887777777776655553 11 1121
Q ss_pred -------H----HHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHH
Q 021438 160 -------C----RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAV 228 (312)
Q Consensus 160 -------c----r~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~ 228 (312)
- ...|.+.+..||+..+ |++...+..........+-+.. .+.......+..-+... ..+++-.
T Consensus 261 l~~lrk~~r~L~~~lgR~pt~~EiA~~l-~is~~~vr~~l~~~~~~~SLd~----~vg~~~d~~l~d~l~~~-~~~pee~ 334 (415)
T PRK07598 261 LNKIKKAQRKISQEKGRTPTIEDIAQEL-EMTPTQVREVLLRVPRSVSLET----KVGKDKDTELGDLLETD-DISPEEM 334 (415)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHh-CCCHHHHHHHHHHccCCccccc----ccCCCccccHHHhccCC-CCCHHHH
Confidence 0 1235567788999988 8999998887665433332210 01111111111111111 1122111
Q ss_pred HHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhc-CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 229 KAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLS-NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 229 ~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~-~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
-.-..+......+...=.|.-- -+|.+--.+. +...|++|||+.+|+|..+|+++.+.-...
T Consensus 335 ~~~~~l~~~L~~~L~~L~~reR--~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~K 397 (415)
T PRK07598 335 LMRESLQRDLQHLLADLTSRER--DVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQK 397 (415)
T ss_pred HHHHHHHHHHHHHHHhCCHHHH--HHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0111111111111111112111 1111111122 357899999999999999999887654443
No 206
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=79.72 E-value=1.2 Score=38.11 Aligned_cols=30 Identities=23% Similarity=0.455 Sum_probs=22.0
Q ss_pred CCCCCCCCC-CceeeeCCCCceEcCCCcccc
Q 021438 4 SYCADCKRL-TEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~-~~ii~D~~~G~~vC~~CG~Vv 33 (312)
..||.|+++ +.++.|...=.+.|..||..-
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 469999995 466666444457899999873
No 207
>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=79.57 E-value=1.6 Score=23.86 Aligned_cols=24 Identities=29% Similarity=0.742 Sum_probs=13.7
Q ss_pred CCCCCCCCceeeeCCCCceEcCCCcc
Q 021438 6 CADCKRLTEVVFDHSAGDTICSECGL 31 (312)
Q Consensus 6 Cp~Cg~~~~ii~D~~~G~~vC~~CG~ 31 (312)
|..||. .|..-...-...|.+||.
T Consensus 1 C~sC~~--~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGR--PIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCC--cccCcccCceEeCCCCCC
Confidence 667776 232222244578888883
No 208
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=79.53 E-value=1.7 Score=32.86 Aligned_cols=31 Identities=19% Similarity=0.473 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeee------CC--C-Cc-eEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFD------HS--A-GD-TICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D------~~--~-G~-~vC~~CG~Vv~e 35 (312)
..||+||.. ....+ .. . .. ++|+.|+.-|.=
T Consensus 3 ~~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCceeee
Confidence 689999984 33333 12 2 22 799999887753
No 209
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=79.50 E-value=2.4 Score=36.54 Aligned_cols=37 Identities=11% Similarity=0.213 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCCcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~ 300 (312)
--+|+.|+|..+++|..||++..+++.+.-+.++|-+
T Consensus 104 glLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtr 140 (220)
T PF07900_consen 104 GLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTR 140 (220)
T ss_pred CcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccC
Confidence 3478999999999999999999999999888888844
No 210
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=79.47 E-value=26 Score=34.02 Aligned_cols=167 Identities=12% Similarity=0.192 Sum_probs=0.0
Q ss_pred HHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCC--------------------HHHH
Q 021438 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRT--------------------VKEF 172 (312)
Q Consensus 113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~t--------------------l~di 172 (312)
+..++..|+++...++.|..+.+.+.-.|+...- ..=|+.+=.+..+ ... +..|
T Consensus 141 ~~eia~~l~~~~~~v~~~l~~lQ~leP~GigAr~-----L~ECLllQl~~~~-~~~~~~~~~~il~~~le~la~~~~~~i 214 (455)
T PRK05932 141 LEEIAESLGVELDEVEAVLKRIQSFDPAGVGARD-----LQECLLLQLEQLD-DTPRLDEAMEIISDHLDLLARRDFRTL 214 (455)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhcCCCCccCcCC-----HHHHHHHHHhccC-CCchHHHHHHHHHHHHHHHHcCCHHHH
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHHhhhhccccc---cCCCCHHHHH----------------------HHHHhhcCCC--H
Q 021438 173 CSVANGTTKKEIGRAKEFIVKHLEAEMGQSVE---MGTIHASDYL----------------------RRFCSNLGMT--N 225 (312)
Q Consensus 173 a~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~---~~~~~p~~~i----------------------~r~~~~L~l~--~ 225 (312)
+..+ +++..++..+...|+. |+=..+..+. ...+-|..+| ..|.+.+.-+ +
T Consensus 215 a~~l-~is~~~v~~~~~~Ir~-L~P~Pg~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~in~~Y~~~~~~~~~~ 292 (455)
T PRK05932 215 AKKL-GVKEEDLQEALDLIRS-LDPKPGAGFGTEEPEYVVPDVFVRKINGGWLVELNPDSLPRLRINQEYAALVSRSARD 292 (455)
T ss_pred HHHH-CcCHHHHHHHHHHHhC-CCCCCccccCCCCCCccCCCEEEEEeCCEEEEEECCCCCceEEECHHHHHHHHhccch
Q ss_pred HHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC---------CCCHHHHHHHhCcchhHHHHHHH
Q 021438 226 QAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND---------TKPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 226 ~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~---------~~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
+...-..+=++.+.. -...++-.++--.+-.++-+-.++ ++++++||+.+|++++||.+..+
T Consensus 293 e~~~ylk~k~~~A~~li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 293 EDKQFLREKLQEAKWLIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
No 211
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=79.39 E-value=1.1 Score=28.76 Aligned_cols=14 Identities=29% Similarity=0.669 Sum_probs=7.6
Q ss_pred eEcCCCcccccCcc
Q 021438 24 TICSECGLVLEAYS 37 (312)
Q Consensus 24 ~vC~~CG~Vv~e~~ 37 (312)
+.|..||+|-++..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 35666666655443
No 212
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=79.18 E-value=23 Score=34.24 Aligned_cols=51 Identities=12% Similarity=0.124 Sum_probs=40.4
Q ss_pred ccCCCChHHHHHH---HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 241 LDIRRSPISVAAA---VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 241 l~~Gr~P~~iaaA---aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
+..+++-..++-| |.|++-++.+. +..+|++.+|.+.+||...++.+.+.+
T Consensus 362 l~s~~R~~~i~~aR~iamyl~r~~~~~--s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 362 ILSNSRNVKALLARRIGMYVAKNYLGS--SLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HhCCCCCccccHHHHHHHHHHHHHhCC--CHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4444445566666 99999887654 799999999999999999999888853
No 213
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.06 E-value=1.6 Score=32.89 Aligned_cols=26 Identities=27% Similarity=0.650 Sum_probs=21.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
..||.||. .-+++ ++-|.+||+-+..
T Consensus 7 ~~cPvcg~-~~iVT-----eL~c~~~etTVrg 32 (122)
T COG3877 7 NRCPVCGR-KLIVT-----ELKCSNCETTVRG 32 (122)
T ss_pred CCCCcccc-cceeE-----EEecCCCCceEec
Confidence 58999998 45666 7899999998864
No 214
>PRK00118 putative DNA-binding protein; Validated
Probab=79.00 E-value=2.4 Score=32.31 Aligned_cols=32 Identities=22% Similarity=0.125 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...|.++||+.+|+|+.||.++++.....+..
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999998766655443
No 215
>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=79.00 E-value=2.4 Score=26.46 Aligned_cols=22 Identities=23% Similarity=0.268 Sum_probs=19.6
Q ss_pred CHHHHHHHhCcchhHHHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
+..|+|+.+||+..||++..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 6789999999999999988764
No 216
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=78.87 E-value=1.6 Score=29.31 Aligned_cols=27 Identities=22% Similarity=0.568 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
+..||+||.. . ----||.+||+--+..
T Consensus 27 ~~~c~~cG~~-~------l~Hrvc~~cg~Y~g~~ 53 (57)
T COG0333 27 LSVCPNCGEY-K------LPHRVCLKCGYYKGRQ 53 (57)
T ss_pred ceeccCCCCc-c------cCceEcCCCCCccCeE
Confidence 3579999972 2 2467999999765443
No 217
>PF15616 TerY-C: TerY-C metal binding domain
Probab=78.67 E-value=1.5 Score=34.80 Aligned_cols=10 Identities=20% Similarity=0.581 Sum_probs=7.8
Q ss_pred CCCCCCCCCC
Q 021438 3 DSYCADCKRL 12 (312)
Q Consensus 3 ~~~Cp~Cg~~ 12 (312)
..-||+||..
T Consensus 77 ~PgCP~CGn~ 86 (131)
T PF15616_consen 77 APGCPHCGNQ 86 (131)
T ss_pred CCCCCCCcCh
Confidence 3579999984
No 218
>PRK01381 Trp operon repressor; Provisional
Probab=78.55 E-value=1.9 Score=32.37 Aligned_cols=37 Identities=22% Similarity=0.170 Sum_probs=28.9
Q ss_pred HHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 255 IYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 255 iyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
+-++..+..-.+||+||++.+|||..||...-+.|..
T Consensus 45 ~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~ 81 (99)
T PRK01381 45 VRIVEELLRGELSQREIKQELGVGIATITRGSNSLKT 81 (99)
T ss_pred HHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhcc
Confidence 3344445566799999999999999999987776654
No 219
>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=78.53 E-value=2.6 Score=29.05 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=30.8
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.+|.+.. ..-+.+..+||+.+|++..|+.+..+.|.+.
T Consensus 11 ~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 11 AKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34555443 3346889999999999999999999999874
No 220
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=78.30 E-value=0.96 Score=37.14 Aligned_cols=29 Identities=21% Similarity=0.427 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCceee---------------eCCCCceEcCCCcccc
Q 021438 3 DSYCADCKRLTEVVF---------------DHSAGDTICSECGLVL 33 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~---------------D~~~G~~vC~~CG~Vv 33 (312)
...||+|++. ++. -..+-...|..||.+-
T Consensus 97 ~~RCp~CN~~--L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPECNGE--LEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcccCCE--eccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 4689999973 221 1222346799999884
No 221
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=78.20 E-value=13 Score=32.01 Aligned_cols=29 Identities=14% Similarity=0.007 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++|+++||+.+|+|..|+.+..++|.+.
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~ 211 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKS 211 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 56899999999999999999999988875
No 222
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=78.18 E-value=18 Score=31.62 Aligned_cols=78 Identities=21% Similarity=0.213 Sum_probs=50.9
Q ss_pred HhcCC-cHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHh
Q 021438 118 DRLGL-VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (312)
Q Consensus 118 ~~L~L-p~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 196 (312)
.-+|+ ++...+-+..+...-+...+.-=..|..+|-||+|+||-..+.+.+-.=+++ . .+|...+....+++.+...
T Consensus 162 qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~~~w~~e-l-~vD~ekV~~~v~~I~~lYe 239 (264)
T KOG0794|consen 162 QDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIPKAWFAE-L-SVDMEKVKDIVQEILKLYE 239 (264)
T ss_pred HHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChHHHHHHH-H-hccHHHHHHHHHHHHHHHH
Confidence 33444 3345555555555444444444468899999999999998887775444444 3 4788888777777776665
Q ss_pred h
Q 021438 197 A 197 (312)
Q Consensus 197 ~ 197 (312)
.
T Consensus 240 ~ 240 (264)
T KOG0794|consen 240 L 240 (264)
T ss_pred H
Confidence 4
No 223
>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=78.18 E-value=5.5 Score=25.02 Aligned_cols=29 Identities=10% Similarity=0.243 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
...+.++||+.+|++..||.++.+...+.
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45789999999999999999888877654
No 224
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=78.08 E-value=0.68 Score=37.08 Aligned_cols=30 Identities=33% Similarity=0.630 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
|++..||.||.. ++. +|..+|.+|..-.++
T Consensus 1 m~l~nC~~Cgkl--F~~---~~~~iCp~C~~~~e~ 30 (137)
T TIGR03826 1 MELANCPKCGRL--FVK---TGRDVCPSCYEEEER 30 (137)
T ss_pred CCCccccccchh--hhh---cCCccCHHHhHHHHH
Confidence 788999999982 333 488999999988654
No 225
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=78.04 E-value=3.6 Score=32.94 Aligned_cols=40 Identities=18% Similarity=0.290 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.+|++..-.|...+.++||+..|++..++++.++.|...
T Consensus 13 ~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 13 ALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 4455555445666789999999999999999999999884
No 226
>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=77.90 E-value=2.5 Score=26.76 Aligned_cols=21 Identities=19% Similarity=0.325 Sum_probs=18.3
Q ss_pred CHHHHHHHhCcchhHHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~k 287 (312)
+..|+|+.+||++.||+...+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999997643
No 227
>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=77.46 E-value=6.2 Score=31.32 Aligned_cols=46 Identities=20% Similarity=0.179 Sum_probs=37.4
Q ss_pred CHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 147 ~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
+.+.-+.+.+|+|-+..+-|.+..+|++.. +++...+.+.+..|.+
T Consensus 6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~~-~ip~~~l~kil~~L~~ 51 (135)
T TIGR02010 6 KGRYAVTAMLDLALNAETGPVTLADISERQ-GISLSYLEQLFAKLRK 51 (135)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 344556788899876566789999999999 7999999999888775
No 228
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=77.42 E-value=2.1 Score=28.17 Aligned_cols=32 Identities=25% Similarity=0.767 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCceee-eCCCCc-eEcCCCccccc
Q 021438 3 DSYCADCKRLTEVVF-DHSAGD-TICSECGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~-D~~~G~-~vC~~CG~Vv~ 34 (312)
...|.+|+...+..+ +...|. ++|..||+-..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHH
Confidence 467999997434433 345565 89999998743
No 229
>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=77.26 E-value=3.6 Score=27.56 Aligned_cols=26 Identities=15% Similarity=0.261 Sum_probs=24.0
Q ss_pred CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 267 PLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.++||+.+++|.+|+++.++.|.+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 48999999999999999999999874
No 230
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=77.20 E-value=4.7 Score=33.38 Aligned_cols=59 Identities=17% Similarity=0.178 Sum_probs=35.8
Q ss_pred cCCCHHHHHHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHH
Q 021438 221 LGMTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 221 L~l~~~v~~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
..+.+.+.+..........++ .-..+||+++-. .....|..+||.-.|.|+.|||++.+
T Consensus 25 tl~~~evlkli~~~~~~lTWv----dSLavAAga~ar----ekag~Ti~EIAeelG~TeqTir~hlk 83 (182)
T COG1318 25 TLFRPEVLKLIKDPYERLTWV----DSLAVAAGALAR----EKAGMTISEIAEELGRTEQTVRNHLK 83 (182)
T ss_pred HhccHHHHHHHhCcccccchh----hHHHHHHHHHHH----HHccCcHHHHHHHhCCCHHHHHHHHh
Confidence 345555554444333333321 123444444332 34568899999999999999999875
No 231
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=77.19 E-value=3.7 Score=25.30 Aligned_cols=27 Identities=11% Similarity=0.206 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHH
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDL 289 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel 289 (312)
..+.++.+||..+|+|+..+++.+|+.
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 346889999999999999999888865
No 232
>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=77.02 E-value=0.93 Score=34.63 Aligned_cols=39 Identities=23% Similarity=0.450 Sum_probs=24.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN 49 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~ 49 (312)
..||+|+..+...=+ ..-|-.|+.-+. +|.+.|-..|++
T Consensus 70 V~CP~C~K~TKmLGr----~D~CM~C~~pLT---Ld~~legkef~~ 108 (114)
T PF11023_consen 70 VECPNCGKQTKMLGR----VDACMHCKEPLT---LDPSLEGKEFDE 108 (114)
T ss_pred eECCCCCChHhhhch----hhccCcCCCcCc---cCchhhcchhhH
Confidence 479999986443332 248999998874 344444334543
No 233
>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=76.95 E-value=3.4 Score=33.09 Aligned_cols=32 Identities=19% Similarity=0.225 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||+.+|+|+.||++++....+.+..
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35789999999999999999999887776543
No 234
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=76.95 E-value=4 Score=32.74 Aligned_cols=31 Identities=13% Similarity=0.190 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|++|||+.+|+|+.||+++.+...+.+.
T Consensus 20 ~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 20 KGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 4679999999999999999988887777665
No 235
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=76.73 E-value=1.6 Score=44.14 Aligned_cols=7 Identities=29% Similarity=0.695 Sum_probs=3.5
Q ss_pred HhcCCcH
Q 021438 118 DRLGLVT 124 (312)
Q Consensus 118 ~~L~Lp~ 124 (312)
+.+++|.
T Consensus 160 ~~~~~p~ 166 (645)
T PRK14559 160 QQLGIPA 166 (645)
T ss_pred hccCCcH
Confidence 4455554
No 236
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=76.64 E-value=6.3 Score=27.14 Aligned_cols=40 Identities=13% Similarity=0.146 Sum_probs=35.8
Q ss_pred HHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438 259 TQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298 (312)
Q Consensus 259 ~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p 298 (312)
.++++..++..+.|+.+|+.+.+|++..+.+...+..|=|
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDP 46 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDP 46 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCC
Confidence 3567889999999999999999999999999998887766
No 237
>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=76.45 E-value=3 Score=26.07 Aligned_cols=22 Identities=14% Similarity=0.155 Sum_probs=19.4
Q ss_pred CCHHHHHHHhCcchhHHHHHHH
Q 021438 266 KPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
++.+|+|+.+|++..||.+..+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999998764
No 238
>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=76.42 E-value=15 Score=26.87 Aligned_cols=42 Identities=19% Similarity=0.192 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhcC-CCHHHHHHHHHHHHHHHhh
Q 021438 153 AACLYIACRQENKPRTVKEFCSVANG-TTKKEIGRAKEFIVKHLEA 197 (312)
Q Consensus 153 aAcly~acr~~~~p~tl~dia~~~~~-v~~~~i~~~~~~l~~~l~~ 197 (312)
..+.|++-+.. ..|+.+|+..+ | .+..++..+++++.+.+..
T Consensus 33 ~ia~yl~~~~~--~~s~~~Ig~~f-g~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 33 QIAMYLARELT--GLSLPEIGRAF-GGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HHHHHHHHHHh--CCCHHHHHHHh-CCCCHhHHHHHHHHHHHHHHh
Confidence 35678775544 66899999999 7 9999999999999988864
No 239
>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=76.36 E-value=2.1 Score=35.29 Aligned_cols=28 Identities=25% Similarity=0.694 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
..||.|++. +. +...|.+.|..|+..++
T Consensus 35 ~aC~~C~kk--v~-~~~~~~~~C~~C~~~~~ 62 (166)
T cd04476 35 PACPGCNKK--VV-EEGNGTYRCEKCNKSVP 62 (166)
T ss_pred ccccccCcc--cE-eCCCCcEECCCCCCcCC
Confidence 369999983 44 33449999999998874
No 240
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=76.24 E-value=3.7 Score=31.72 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=28.2
Q ss_pred CCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
=+++++++..|||=+|+|+|..+|.+.++.
T Consensus 50 GnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 50 GNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 458999999999999999999999999988
No 241
>PF14502 HTH_41: Helix-turn-helix domain
Probab=76.17 E-value=4.5 Score=26.09 Aligned_cols=28 Identities=32% Similarity=0.221 Sum_probs=25.1
Q ss_pred CCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
.++.|.++.+++|..||.+.++.|.+.-
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~g 34 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENG 34 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCC
Confidence 4589999999999999999999998863
No 242
>PF13518 HTH_28: Helix-turn-helix domain
Probab=76.06 E-value=5.8 Score=25.32 Aligned_cols=32 Identities=16% Similarity=0.205 Sum_probs=26.1
Q ss_pred CHHHHHHHhCcchhHHHHHHHHHHhh-hcccCC
Q 021438 267 PLKEISIVTRVAEGTIKNVYKDLFPH-LARIIP 298 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~kel~~~-~~~~~p 298 (312)
|+.++|..+|+|..||.+..+...+. ...|.|
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l~~ 46 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGGIEGLKP 46 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHhcc
Confidence 89999999999999999988887774 333444
No 243
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=76.05 E-value=6.9 Score=25.67 Aligned_cols=30 Identities=13% Similarity=0.151 Sum_probs=26.9
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.+.+..+|++.++++..|+++..+.|.+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 556889999999999999999999999874
No 244
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=75.89 E-value=9.4 Score=24.07 Aligned_cols=28 Identities=21% Similarity=0.233 Sum_probs=25.6
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
..+..+|++.++++..|+++..+.|.+.
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4789999999999999999999998875
No 245
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=75.83 E-value=2.3 Score=35.72 Aligned_cols=33 Identities=9% Similarity=-0.040 Sum_probs=28.4
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.||+.++......+...+
T Consensus 147 g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 147 GFESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 577999999999999999999887777776655
No 246
>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=75.71 E-value=2.4 Score=27.65 Aligned_cols=13 Identities=23% Similarity=0.667 Sum_probs=7.9
Q ss_pred eEcCCCcccccCc
Q 021438 24 TICSECGLVLEAY 36 (312)
Q Consensus 24 ~vC~~CG~Vv~e~ 36 (312)
.+|..||+|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 4566666666553
No 247
>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=75.45 E-value=3.2 Score=29.27 Aligned_cols=31 Identities=19% Similarity=0.608 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCcee--eeCCCCceEcCCCcccc
Q 021438 3 DSYCADCKRLTEVV--FDHSAGDTICSECGLVL 33 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii--~D~~~G~~vC~~CG~Vv 33 (312)
.-.||.|++-..+. .+...-..-|-.||+.-
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 45799999854443 34444557899999984
No 248
>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=75.42 E-value=5.9 Score=26.63 Aligned_cols=31 Identities=19% Similarity=0.201 Sum_probs=27.1
Q ss_pred cCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.+.+.+..+||+.+|++.+|+..+.+.|.+.
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 4678899999999999999999999999873
No 249
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=75.38 E-value=2.6 Score=26.10 Aligned_cols=29 Identities=24% Similarity=0.454 Sum_probs=16.1
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
.||.|+..-..+.=..---.+|.+||=+-
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 59999973111111111225699998763
No 250
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=75.32 E-value=8.7 Score=26.61 Aligned_cols=38 Identities=16% Similarity=0.121 Sum_probs=29.9
Q ss_pred HHHHHHhcCC-CCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 255 IYIITQLSND-TKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 255 iyla~~~~~~-~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
|+..-...|. .+++.+||+.+|++..++++....|.+.
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3333344455 4999999999999999999998888875
No 251
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=75.19 E-value=4.7 Score=34.88 Aligned_cols=32 Identities=13% Similarity=0.125 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||+.+++|+.|+++..+.|++.++.
T Consensus 157 ~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 157 FGFSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 46789999999999999999999999998764
No 252
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=75.13 E-value=0.88 Score=38.98 Aligned_cols=33 Identities=27% Similarity=0.637 Sum_probs=27.3
Q ss_pred CCCCCCCCC-CceeeeCCCCc---eEcCCCcccccCc
Q 021438 4 SYCADCKRL-TEVVFDHSAGD---TICSECGLVLEAY 36 (312)
Q Consensus 4 ~~Cp~Cg~~-~~ii~D~~~G~---~vC~~CG~Vv~e~ 36 (312)
..|-+||+. .++..+++.|. ..|.+|+.|+|+.
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkY 37 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKY 37 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhH
Confidence 479999984 47888999994 7899999998753
No 253
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=75.06 E-value=2.2 Score=38.11 Aligned_cols=29 Identities=14% Similarity=0.432 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
...||.||+. +......-...|..||.+.
T Consensus 99 ~~fC~~CG~~--~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHP--MHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred CccccccCCC--CeecCCceeEECCCCCCEE
Confidence 4689999984 3333445568999999764
No 254
>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=75.04 E-value=7.1 Score=25.41 Aligned_cols=34 Identities=21% Similarity=0.283 Sum_probs=28.1
Q ss_pred HHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 021438 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (312)
Q Consensus 161 r~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l 195 (312)
..++-|+|..++++.+ ++|..+|.+.++.|.+.+
T Consensus 10 ~~~~~~it~~eLa~~l-~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 10 LESKEPITAKELAEEL-GVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHTTTSBEHHHHHHHC-TS-HHHHHHHHHHHHHTT
T ss_pred HHcCCCcCHHHHHHHh-CCCHHHHHHHHHHHHHCC
Confidence 3466679999999999 899999999999987655
No 255
>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=74.96 E-value=5.3 Score=25.30 Aligned_cols=39 Identities=10% Similarity=0.221 Sum_probs=27.7
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
|++-+..+.-=...|.++||+.+|++..++-.+|....+
T Consensus 4 aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k~~ 42 (47)
T PF00440_consen 4 AALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPSKDD 42 (47)
T ss_dssp HHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSHHH
T ss_pred HHHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCCHHH
Confidence 444444433224688999999999999999988754433
No 256
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=74.75 E-value=2.6 Score=28.36 Aligned_cols=29 Identities=24% Similarity=0.537 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
+...|..||.. |..-...-...|.+||.+
T Consensus 6 ~~~~CtSCg~~--i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 6 EPPKCTSCGIE--IAPREKAVKFLCPNCGEV 34 (59)
T ss_pred cCccccCCCCc--ccCCCccCEeeCCCCCCe
Confidence 44568888862 322122345778888876
No 257
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=74.72 E-value=1.3 Score=34.08 Aligned_cols=17 Identities=35% Similarity=0.741 Sum_probs=14.6
Q ss_pred eeCCCCceEcCCCcccc
Q 021438 17 FDHSAGDTICSECGLVL 33 (312)
Q Consensus 17 ~D~~~G~~vC~~CG~Vv 33 (312)
.|-.+|+++|.+||.|.
T Consensus 92 ~~v~EG~l~CpetG~vf 108 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVF 108 (124)
T ss_pred hhhccceEecCCCCcEe
Confidence 45678999999999996
No 258
>PF12728 HTH_17: Helix-turn-helix domain
Probab=74.68 E-value=3.5 Score=26.54 Aligned_cols=22 Identities=14% Similarity=0.182 Sum_probs=19.1
Q ss_pred CCHHHHHHHhCcchhHHHHHHH
Q 021438 266 KPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
+|.+|+|+.+|+|..|+.+..+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999997664
No 259
>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=74.60 E-value=4.3 Score=31.83 Aligned_cols=31 Identities=26% Similarity=0.276 Sum_probs=27.2
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+..+||+..|+|+.||+++.+...+.+..
T Consensus 126 g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 126 GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5789999999999999999999988876643
No 260
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=74.59 E-value=11 Score=25.52 Aligned_cols=37 Identities=14% Similarity=0.262 Sum_probs=30.2
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 155 CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 155 cly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
+||-... .+.+.+..|||+.+ +++..++..++++|.+
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L-~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERL-GVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHH-TS-HHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCCccHHHHHHHH-CCChHHHHHHHHHHHH
Confidence 3565555 88999999999999 8999999999988764
No 261
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=74.58 E-value=3.7 Score=33.24 Aligned_cols=33 Identities=12% Similarity=0.139 Sum_probs=26.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..|.+|||+.+|+|+.|+++++......+...+
T Consensus 122 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 122 EKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577999999999999999998877666655443
No 262
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=74.52 E-value=5.1 Score=28.87 Aligned_cols=44 Identities=20% Similarity=0.305 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 149 EAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 149 ~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
+.-.-+.+|+|-...+.|.+..||++.. +++...+.+....|.+
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~-~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERL-GISPSYLRKILQKLKK 51 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHH-TS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHH-CcCHHHHHHHHHHHhh
Confidence 3445566777766666789999999999 7999999999988876
No 263
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=74.50 E-value=4.6 Score=34.38 Aligned_cols=32 Identities=19% Similarity=0.063 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...|-++||+.+++|+.||+++.+.|+..++.
T Consensus 164 ~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 164 EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 45789999999999999999999999998764
No 264
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=74.25 E-value=2.9 Score=35.08 Aligned_cols=33 Identities=9% Similarity=-0.032 Sum_probs=28.0
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..|.+|||+.+|+|+.||++++......+...+
T Consensus 147 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 147 ELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999887777766544
No 265
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=74.17 E-value=1.9 Score=27.01 Aligned_cols=26 Identities=23% Similarity=0.658 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCC--CcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSE--CGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~--CG~Vv~e 35 (312)
.+||.||.. + -.+| +.|.+ |+.|...
T Consensus 12 rkCp~CGt~-N----G~R~-~~CKN~~C~~~~~~ 39 (44)
T PF14952_consen 12 RKCPKCGTY-N----GTRG-LSCKNKSCPQVFNV 39 (44)
T ss_pred ccCCcCcCc-c----Cccc-ccccCCccchhhhc
Confidence 589999973 2 2233 67875 9988753
No 266
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=73.93 E-value=2.5 Score=24.12 Aligned_cols=28 Identities=18% Similarity=0.419 Sum_probs=16.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~ 31 (312)
..||.|+....-+.....+..+|..|-.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 5799999843334445677799998854
No 267
>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=73.90 E-value=9.9 Score=26.97 Aligned_cols=25 Identities=24% Similarity=0.258 Sum_probs=19.1
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHH
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDL 289 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel 289 (312)
..+..+||+.++||++||-+-.|.|
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HccHHHHHHHcCCCHHHHHHHHHHh
Confidence 5778999999999999999877654
No 268
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=73.69 E-value=4.9 Score=34.47 Aligned_cols=32 Identities=9% Similarity=0.044 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...|-+|||+.+++|+.|++++.+.|++.++.
T Consensus 151 ~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 151 AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 35678999999999999999999999998764
No 269
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=73.56 E-value=8.8 Score=31.73 Aligned_cols=46 Identities=17% Similarity=0.164 Sum_probs=36.9
Q ss_pred CHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 147 ~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
+.+.-..+.+|+|-...+-|.+..+|++.. +++..-+.+.+..|.+
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~~~-~ip~~~l~kIl~~L~~ 51 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISERQ-GISLSYLEQLFSRLRK 51 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 344556778888855556789999999999 8999999999888775
No 270
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=73.56 E-value=1.9 Score=29.31 Aligned_cols=24 Identities=25% Similarity=0.753 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
|....|.+|+.. + + ...|..||..
T Consensus 1 M~~kAC~~C~~i---~-~----~~~CP~Cgs~ 24 (61)
T PRK08351 1 MTEKACRHCHYI---T-T----EDRCPVCGSR 24 (61)
T ss_pred CchhhhhhCCcc---c-C----CCcCCCCcCC
Confidence 556689999972 2 2 1169999973
No 271
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=73.34 E-value=0.73 Score=41.77 Aligned_cols=30 Identities=23% Similarity=0.476 Sum_probs=22.6
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
.+||.|+. .-...|-.....||..||+-..
T Consensus 39 ~kc~~C~~-~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 39 VQCENCYG-LNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred eECCCccc-hhhHHHHHHcCCCCCCCCCCcC
Confidence 47999998 3344555667799999999764
No 272
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=73.28 E-value=72 Score=28.86 Aligned_cols=35 Identities=11% Similarity=0.262 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+|++|||..+|+|..||+++.+.-.+.+...+
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999988877666655443
No 273
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=73.24 E-value=65 Score=28.40 Aligned_cols=31 Identities=13% Similarity=0.238 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|++|||+.+|+|..||+++.+...+.+.
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~al~kLr 254 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4579999999999999999998877666554
No 274
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=73.17 E-value=3 Score=27.59 Aligned_cols=27 Identities=26% Similarity=0.613 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
..+|+.||.. +.| ..--+||..||.+.
T Consensus 5 ~~~C~~Cg~~---~~~-~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKK---FKD-GDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCc---ccC-CCCEEECCCCCCcc
Confidence 4689999973 222 23458999999985
No 275
>PRK15320 transcriptional activator SprB; Provisional
Probab=73.05 E-value=5.3 Score=34.06 Aligned_cols=32 Identities=16% Similarity=0.141 Sum_probs=29.0
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+++|||+.+++|+.||+++...|.+.++.
T Consensus 178 kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 178 SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 45789999999999999999999999998764
No 276
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=72.98 E-value=3.1 Score=32.33 Aligned_cols=33 Identities=21% Similarity=0.484 Sum_probs=27.5
Q ss_pred eeCCCCceEcCCCcccc--cCcccccccccccccC
Q 021438 17 FDHSAGDTICSECGLVL--EAYSVDETSEWRIFAN 49 (312)
Q Consensus 17 ~D~~~G~~vC~~CG~Vv--~e~~id~~~ewr~f~~ 49 (312)
...+.|.++|..||.-| .+.-+|.|.-|.+|.+
T Consensus 27 ~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~ 61 (119)
T PRK05508 27 DFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDD 61 (119)
T ss_pred CcCCCeEEEecCCCCccccccccccCCCCCcccCc
Confidence 34678999999999988 5557899999999974
No 277
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=72.85 E-value=5.4 Score=33.10 Aligned_cols=35 Identities=20% Similarity=0.285 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p 298 (312)
...+.+|||+.+|+|+.|++.++..-+..+-..+|
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 35789999999999999999998766665544444
No 278
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=72.82 E-value=4.1 Score=34.30 Aligned_cols=35 Identities=14% Similarity=0.255 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p 298 (312)
..++.+|||+.+|+|..|++.+++.....+...++
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 35789999999999999999998877777666554
No 279
>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=72.80 E-value=1.3 Score=29.48 Aligned_cols=30 Identities=33% Similarity=0.834 Sum_probs=18.0
Q ss_pred CCCCCCCCCceeee--CCCCceEcCCCccccc
Q 021438 5 YCADCKRLTEVVFD--HSAGDTICSECGLVLE 34 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D--~~~G~~vC~~CG~Vv~ 34 (312)
.|.+|+...+.... +..+...|..||+-..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 37778764333333 2366778888887643
No 280
>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=72.79 E-value=0.8 Score=41.47 Aligned_cols=29 Identities=14% Similarity=0.458 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
.+||.|+. .-...|-.....||..||+-.
T Consensus 27 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQ-VLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eECCCCcc-hhhHHHHHhhCCCCCCCCCcC
Confidence 47999998 233344556678999999975
No 281
>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=72.76 E-value=61 Score=27.84 Aligned_cols=31 Identities=13% Similarity=0.219 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...++++||+.+|+|..||+++.+.....+.
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4578999999999999999999887776654
No 282
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=72.57 E-value=1.2 Score=31.98 Aligned_cols=31 Identities=23% Similarity=0.439 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
...|+-||.. -+-...-|-..|.+|..|+.-
T Consensus 36 ky~CsfCGK~--~vKR~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 36 KYTCSFCGKK--TVKRKAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhcchh--hhhhhceeEEecCCccceecc
Confidence 4579999983 356678899999999999864
No 283
>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=72.52 E-value=6.7 Score=28.13 Aligned_cols=29 Identities=24% Similarity=0.151 Sum_probs=26.2
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
+.++.-++||+.+++++.||||-+..|.+
T Consensus 21 ~~PVgSk~ia~~l~~s~aTIRN~M~~Le~ 49 (78)
T PF03444_consen 21 GEPVGSKTIAEELGRSPATIRNEMADLEE 49 (78)
T ss_pred CCCcCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 56788899999999999999999999877
No 284
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=72.49 E-value=2.6 Score=28.35 Aligned_cols=28 Identities=21% Similarity=0.505 Sum_probs=15.9
Q ss_pred CCCCCCCCCCceeeeC----CCCceEcCCCccc
Q 021438 4 SYCADCKRLTEVVFDH----SAGDTICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~----~~G~~vC~~CG~V 32 (312)
..||+||. ..|.... ..-.++|.+||..
T Consensus 28 F~CPnCGe-~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 28 FPCPNCGE-VEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eeCCCCCc-eeeehhhhHHHcCCceECCCcCcc
Confidence 45888885 2333331 2345778788754
No 285
>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=72.45 E-value=63 Score=27.87 Aligned_cols=31 Identities=10% Similarity=0.235 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|+++||+.+|+|..+|++..+...+.+.
T Consensus 198 ~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 198 KDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4679999999999999999999887776654
No 286
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=72.39 E-value=6.1 Score=32.79 Aligned_cols=40 Identities=25% Similarity=0.225 Sum_probs=34.1
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.||-+-.++..++++.||+.++|.|.+.++...|+|.+.
T Consensus 29 G~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~ 68 (177)
T COG1510 29 GQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDW 68 (177)
T ss_pred HHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhc
Confidence 4555555567789999999999999999999999999884
No 287
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=72.20 E-value=6.4 Score=32.97 Aligned_cols=32 Identities=16% Similarity=0.227 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||+.+++|+.||++..+.|++.++.
T Consensus 147 qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 147 SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 35778999999999999999999999998764
No 288
>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=71.94 E-value=9.3 Score=31.66 Aligned_cols=27 Identities=22% Similarity=0.231 Sum_probs=25.4
Q ss_pred CCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++++||+.+|+|..|+.+.+|+|.+.
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 679999999999999999999999985
No 289
>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=71.87 E-value=3.6 Score=27.06 Aligned_cols=23 Identities=17% Similarity=0.328 Sum_probs=17.7
Q ss_pred CCHHHHHHHhCcchhHHHHHHHH
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
.++.+||..+||+.+||++.+|.
T Consensus 23 ~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 23 ESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp T-HHHHHHHHT--CCHHHHHHHC
T ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Confidence 38999999999999999988764
No 290
>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=71.80 E-value=1.8 Score=37.83 Aligned_cols=29 Identities=21% Similarity=0.580 Sum_probs=10.1
Q ss_pred CCCCCCCCCCce---eeeCCCCceEcCCCcccc
Q 021438 4 SYCADCKRLTEV---VFDHSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~i---i~D~~~G~~vC~~CG~Vv 33 (312)
..||+||+. .+ --...-.+..|.+|+.-.
T Consensus 32 ~yCP~Cg~~-~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 32 MYCPNCGSK-PLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp ---TTT--S-S-EE--------EEE-TTT--EE
T ss_pred CcCCCCCCh-hHhhccCCCccceeECCCCchHH
Confidence 479999984 23 223455779999998643
No 291
>PF14353 CpXC: CpXC protein
Probab=71.74 E-value=3 Score=32.81 Aligned_cols=11 Identities=27% Similarity=0.797 Sum_probs=9.4
Q ss_pred ceEcCCCcccc
Q 021438 23 DTICSECGLVL 33 (312)
Q Consensus 23 ~~vC~~CG~Vv 33 (312)
..+|.+||...
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 48999999876
No 292
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=71.56 E-value=11 Score=26.17 Aligned_cols=43 Identities=19% Similarity=0.252 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhC----------CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 021438 151 IVAACLYIACRQEN----------KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (312)
Q Consensus 151 iaaAcly~acr~~~----------~p~tl~dia~~~~~v~~~~i~~~~~~l~~~ 194 (312)
+|...++++-+... .|.+..+||+.+ |++..++.+.++.+.+.
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~-g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADML-GVSRETVSRILKRLKDE 55 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHH-TSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHH-CCCHHHHHHHHHHHHHC
Confidence 34445555555432 578999999999 89999999999988754
No 293
>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=71.51 E-value=4.8 Score=27.49 Aligned_cols=22 Identities=14% Similarity=0.241 Sum_probs=19.6
Q ss_pred CHHHHHHHhCcchhHHHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
+..|||+.+||+..|+++..++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999988764
No 294
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=71.48 E-value=4.1 Score=34.32 Aligned_cols=33 Identities=9% Similarity=0.108 Sum_probs=27.3
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.|++.++......+...+
T Consensus 152 g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 152 GFSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577999999999999999999877666665544
No 295
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=71.44 E-value=2.3 Score=28.85 Aligned_cols=25 Identities=36% Similarity=0.854 Sum_probs=15.7
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
....|.+|+.. +. ...-+|..||.=
T Consensus 3 ~~kAC~~Ck~l---~~---~d~e~CP~Cgs~ 27 (64)
T COG2093 3 TEKACKNCKRL---TP---EDTEICPVCGST 27 (64)
T ss_pred hhHHHhhcccc---CC---CCCccCCCCCCc
Confidence 34568888862 22 345678888854
No 296
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.43 E-value=2.2 Score=32.40 Aligned_cols=30 Identities=7% Similarity=0.094 Sum_probs=24.9
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
++.||+||++ .+|-.+--+||..||.-...
T Consensus 9 KridPetg~K---FYDLNrdPiVsPytG~s~P~ 38 (129)
T COG4530 9 KRIDPETGKK---FYDLNRDPIVSPYTGKSYPR 38 (129)
T ss_pred cccCccccch---hhccCCCccccCcccccchH
Confidence 4689999984 68888889999999987643
No 297
>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=71.32 E-value=80 Score=28.61 Aligned_cols=28 Identities=11% Similarity=0.195 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
...|++|||+.+|+|..||++..+.-.+
T Consensus 268 ~~~Tl~EIa~~lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 268 EPLTLAEIGRRLNLSRERVRQIEAKALR 295 (298)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5799999999999999999988765544
No 298
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=70.84 E-value=7.9 Score=31.01 Aligned_cols=54 Identities=11% Similarity=0.092 Sum_probs=35.5
Q ss_pred CChHHHHHHHHHHHHHhcC---CCCCHHHHHHHhCcchhHHHHHHH---HHHhhhcccCC
Q 021438 245 RSPISVAAAVIYIITQLSN---DTKPLKEISIVTRVAEGTIKNVYK---DLFPHLARIIP 298 (312)
Q Consensus 245 r~P~~iaaAaiyla~~~~~---~~~~~~~Ia~~~~vs~~ti~~~~k---el~~~~~~~~p 298 (312)
-+|.-.=||.+.....++. .++|+.+||+.+||++.|+=++-+ ++.++...+..
T Consensus 11 L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~ 70 (142)
T PF13022_consen 11 LTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELAD 70 (142)
T ss_dssp S-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHH
Confidence 3456666777777777664 569999999999999999987763 46666555443
No 299
>COG1773 Rubredoxin [Energy production and conversion]
Probab=70.68 E-value=3 Score=27.74 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSEC 29 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~C 29 (312)
..+|..||= |+|++.|+-.|..|
T Consensus 3 ~~~C~~CG~----vYd~e~Gdp~~gi~ 25 (55)
T COG1773 3 RWRCSVCGY----VYDPEKGDPRCGIA 25 (55)
T ss_pred ceEecCCce----EeccccCCccCCCC
Confidence 344555552 45555555444444
No 300
>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=70.64 E-value=6.4 Score=25.12 Aligned_cols=20 Identities=30% Similarity=0.514 Sum_probs=17.6
Q ss_pred CHHHHHHHhcCCCHHHHHHHH
Q 021438 168 TVKEFCSVANGTTKKEIGRAK 188 (312)
Q Consensus 168 tl~dia~~~~~v~~~~i~~~~ 188 (312)
|++|||..+ |++..++.+++
T Consensus 1 Ti~dIA~~a-gvS~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREA-GVSKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHH-TSSHHHHHHHH
T ss_pred CHHHHHHHH-CcCHHHHHHHH
Confidence 689999999 89999988774
No 301
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=70.57 E-value=3.6 Score=33.06 Aligned_cols=35 Identities=23% Similarity=0.476 Sum_probs=28.2
Q ss_pred eeeCCCCceEcCCCcccc--cCcccccccccccccCC
Q 021438 16 VFDHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (312)
Q Consensus 16 i~D~~~G~~vC~~CG~Vv--~e~~id~~~ewr~f~~~ 50 (312)
......|.++|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 36 ~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 72 (142)
T PRK00222 36 LDNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKP 72 (142)
T ss_pred CCCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcc
Confidence 344678999999999988 45578899999999754
No 302
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=70.52 E-value=3.4 Score=30.39 Aligned_cols=34 Identities=26% Similarity=0.608 Sum_probs=22.8
Q ss_pred CCCCCCC------CCceeeeCCCCc----------eEcCCCcccccCccc
Q 021438 5 YCADCKR------LTEVVFDHSAGD----------TICSECGLVLEAYSV 38 (312)
Q Consensus 5 ~Cp~Cg~------~~~ii~D~~~G~----------~vC~~CG~Vv~e~~i 38 (312)
.|+-|++ .+++.+|...|. ++|.+||.+.-+.-+
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~dev 50 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDDTT 50 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecHHH
Confidence 4899954 135566666663 689999988655433
No 303
>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=70.42 E-value=11 Score=29.48 Aligned_cols=39 Identities=15% Similarity=0.132 Sum_probs=31.4
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.+||+. ..+...+..+||+..+++..++.++.+.|.+.
T Consensus 14 ~l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 14 VLTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HHHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3455553 33456899999999999999999999999884
No 304
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=70.42 E-value=6.4 Score=33.90 Aligned_cols=33 Identities=21% Similarity=0.241 Sum_probs=28.7
Q ss_pred cCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
.....+-+|||+.+++|+.||+.+...|+..++
T Consensus 160 la~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 160 LAEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred HHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 334677899999999999999999999998765
No 305
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=70.42 E-value=3.5 Score=34.21 Aligned_cols=33 Identities=18% Similarity=0.226 Sum_probs=27.5
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.|++.++......+...+
T Consensus 133 ~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 133 DYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467999999999999999999877777665544
No 306
>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=70.35 E-value=33 Score=23.82 Aligned_cols=67 Identities=15% Similarity=0.249 Sum_probs=0.0
Q ss_pred CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhccCCCChHHHH--HHHHHHHHHhcCCCCCHHHHHHHhC-cchhHHHHH
Q 021438 209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRRSPISVA--AAVIYIITQLSNDTKPLKEISIVTR-VAEGTIKNV 285 (312)
Q Consensus 209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~l~~Gr~P~~ia--aAaiyla~~~~~~~~~~~~Ia~~~~-vs~~ti~~~ 285 (312)
+|++.+..+|..+|++.+-. ...+|.+..+- -.+.||+-.+.+.+ +.+|++.+| -..+|+...
T Consensus 1 t~~~Ii~~Va~~~~v~~~~i------------~s~~R~~~i~~aR~va~yL~r~~~~~s--l~~Ig~~fg~rdHstV~~a 66 (70)
T PF08299_consen 1 TIEDIIEAVAEYFGVSVEDI------------RSKSRKRKIVEARQVAMYLARELTGLS--LSEIGRYFGGRDHSTVIHA 66 (70)
T ss_dssp -HHHHHHHHHHHTT--HHHH------------HSS---HHHHHHHHHHHHHHHHHS-----HHHHHHHCTSSTHHHHHHH
T ss_pred CHHHHHHHHHHHHCCCHHHH------------hCCCCChhhcchHHHHHHHHHHHhCCC--HHHHHHHhCCCCHHHHHHH
Q ss_pred HHHH
Q 021438 286 YKDL 289 (312)
Q Consensus 286 ~kel 289 (312)
++.+
T Consensus 67 ~~ki 70 (70)
T PF08299_consen 67 IRKI 70 (70)
T ss_dssp HHHH
T ss_pred HHhC
No 307
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=70.27 E-value=79 Score=28.09 Aligned_cols=31 Identities=29% Similarity=0.312 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...+.++||..+|+|+.||+++++.....+.
T Consensus 227 ~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 257 (268)
T PRK06288 227 EDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257 (268)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4688999999999999999977765554443
No 308
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=70.14 E-value=11 Score=27.23 Aligned_cols=30 Identities=3% Similarity=-0.008 Sum_probs=27.5
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+...+..+|++.+|+|+.+|-+.++.|.+.
T Consensus 17 ~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~ 46 (79)
T COG1654 17 GNFVSGEKLAEELGISRTAVWKHIQQLREE 46 (79)
T ss_pred CCcccHHHHHHHHCccHHHHHHHHHHHHHh
Confidence 457899999999999999999999999975
No 309
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=69.92 E-value=1 Score=40.97 Aligned_cols=30 Identities=20% Similarity=0.537 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
.+||.|+. .-...|-.....||..||+-..
T Consensus 28 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 28 TKCPSCGQ-VLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred eECCCccc-hhhHHHHHhcCCCCCCCCCCee
Confidence 47999998 3344445556689999999763
No 310
>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=69.88 E-value=3.8 Score=26.21 Aligned_cols=28 Identities=18% Similarity=0.458 Sum_probs=17.5
Q ss_pred CCCCCCCCCceeee-------CCCCceEcCC--Ccccc
Q 021438 5 YCADCKRLTEVVFD-------HSAGDTICSE--CGLVL 33 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D-------~~~G~~vC~~--CG~Vv 33 (312)
.||.||+. ..+.- ..+--..|++ ||.-.
T Consensus 1 ~CP~Cg~~-a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSK-ARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCe-eEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 59999984 34332 1223467887 88764
No 311
>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=69.83 E-value=5.5 Score=32.96 Aligned_cols=31 Identities=19% Similarity=0.160 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...+.+|||+.+|+|+.||+.++..-...+.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3578999999999999999999876665544
No 312
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=69.80 E-value=4.2 Score=33.38 Aligned_cols=34 Identities=15% Similarity=0.134 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+.++||..+|+|+.||+++.+.....+...+
T Consensus 143 ~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999999887777766554
No 313
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=69.80 E-value=5.8 Score=32.09 Aligned_cols=33 Identities=12% Similarity=0.240 Sum_probs=28.6
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.||+++.......+...+
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 577999999999999999999988888776654
No 314
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=69.79 E-value=9.8 Score=25.33 Aligned_cols=31 Identities=26% Similarity=0.422 Sum_probs=27.4
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+.++||...++|+.|++...+.++..++.
T Consensus 19 G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~ 49 (65)
T COG2771 19 GKSNKEIARILGISEETVKTHLRNIYRKLGV 49 (65)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 4889999999999999999999999887653
No 315
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=69.60 E-value=3 Score=27.91 Aligned_cols=25 Identities=36% Similarity=0.879 Sum_probs=15.8
Q ss_pred CCCCCCCCCceeeeCCCCc-eEcCCCcccc
Q 021438 5 YCADCKRLTEVVFDHSAGD-TICSECGLVL 33 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~-~vC~~CG~Vv 33 (312)
.|-+||.. +.+- .|+ +-|.+||+=|
T Consensus 22 iCgdC~~e-n~lk---~~D~irCReCG~RI 47 (62)
T KOG3507|consen 22 ICGDCGQE-NTLK---RGDVIRCRECGYRI 47 (62)
T ss_pred Eecccccc-cccc---CCCcEehhhcchHH
Confidence 58888874 3322 344 5688888743
No 316
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=69.37 E-value=31 Score=29.84 Aligned_cols=29 Identities=10% Similarity=0.043 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++++++||+.+|++..|+.+..++|.+.
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56889999999999999999999999874
No 317
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=69.19 E-value=3.4 Score=28.18 Aligned_cols=56 Identities=14% Similarity=0.233 Sum_probs=31.3
Q ss_pred HHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCC-CCHHHHHHHHHhhcCCCHH
Q 021438 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGT-IHASDYLRRFCSNLGMTNQ 226 (312)
Q Consensus 160 cr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~-~~p~~~i~r~~~~L~l~~~ 226 (312)
-..+....|+.|++..+ +++...|...... ++ ..+|. +-...|+..||+.||++++
T Consensus 4 ~~R~~~glsl~~va~~t-~I~~~~l~aiE~~-----~~-----~~lp~~~y~rg~lr~Ya~~Lgld~~ 60 (62)
T PF13413_consen 4 EAREAKGLSLEDVAEET-KISVSYLEAIENG-----DF-----DSLPSPVYARGYLRKYARFLGLDPD 60 (62)
T ss_dssp HHHHCTT--HHHHHHHC-S--HHHHHHHHCT------G-----CCSSSHHHHHHHHHHHHHHTT--HH
T ss_pred HHHHHcCCCHHHHHHHh-CCCHHHHHHHHCc-----Ch-----hhCCcHHHHHHHHHHHHHHhCcCcc
Confidence 34577789999999999 6887765433210 01 01221 1235799999999999875
No 318
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=69.17 E-value=4.2 Score=34.81 Aligned_cols=39 Identities=13% Similarity=0.212 Sum_probs=30.4
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC-Cccccc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII-PDWFAN 303 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~-p~~~~~ 303 (312)
..+.+|||+.+|+|+.|++.++......+...+ ..||++
T Consensus 164 g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~~~~ 203 (206)
T PRK12544 164 ELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKWFLK 203 (206)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 577999999999999999999877777665543 345544
No 319
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=69.11 E-value=7 Score=31.50 Aligned_cols=29 Identities=10% Similarity=0.099 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
...|++|||+.+|+|..||++..+...+.
T Consensus 20 ~GlTq~EIAe~LGiS~~tVs~ie~ra~kk 48 (141)
T PRK03975 20 RGLTQQEIADILGTSRANVSSIEKRAREN 48 (141)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45889999999999999998877655554
No 320
>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=69.04 E-value=4.3 Score=24.09 Aligned_cols=23 Identities=22% Similarity=0.647 Sum_probs=11.0
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGL 31 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~ 31 (312)
+|+.||- +++...-..+|..||.
T Consensus 4 ~C~~CG~----i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 4 VCPVCGY----IHEGEEAPEKCPICGA 26 (34)
T ss_pred ECCCCCC----EeECCcCCCcCcCCCC
Confidence 4666664 2222222346666665
No 321
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=69.01 E-value=2.5 Score=39.99 Aligned_cols=33 Identities=27% Similarity=0.685 Sum_probs=24.5
Q ss_pred CCCCCCCCCC-Cc----eeeeCCCCceEcCCCcccccC
Q 021438 3 DSYCADCKRL-TE----VVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 3 ~~~Cp~Cg~~-~~----ii~D~~~G~~vC~~CG~Vv~e 35 (312)
...||.|++. +. -..|..+|...|..||.=|.+
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 3589999983 11 246788999999999975543
No 322
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=68.99 E-value=25 Score=29.06 Aligned_cols=29 Identities=17% Similarity=0.139 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 021438 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (312)
Q Consensus 165 ~p~tl~dia~~~~~v~~~~i~~~~~~l~~~ 194 (312)
.|.|..|||+.+ |++..++.+.++++.+.
T Consensus 142 ~~~t~~~iA~~l-G~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAI-GSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHh-CCcHHHHHHHHHHHHHC
Confidence 688999999999 89999999999998764
No 323
>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=68.97 E-value=6.8 Score=28.33 Aligned_cols=34 Identities=18% Similarity=0.197 Sum_probs=27.6
Q ss_pred cCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
.+...++.++|+...+|.+|+.+..+++.+.+..
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999999999999998764
No 324
>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=68.96 E-value=5.5 Score=28.75 Aligned_cols=23 Identities=17% Similarity=0.228 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhCcchhHHHHHH
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVY 286 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~ 286 (312)
-..++++||+.+|||..||+...
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHh
Confidence 45789999999999999999754
No 325
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=68.93 E-value=8.4 Score=24.94 Aligned_cols=30 Identities=17% Similarity=0.272 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+...++.|||+.+|++.+|+.+..+.|.+.
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345789999999999999999988888763
No 326
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=68.82 E-value=7.2 Score=34.33 Aligned_cols=32 Identities=19% Similarity=0.311 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+|.+|||..+++|+.|++.+.+.+.+.++.
T Consensus 193 ~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 193 EGKTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 45889999999999999999999999988763
No 327
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=68.74 E-value=3.3 Score=35.10 Aligned_cols=34 Identities=21% Similarity=0.505 Sum_probs=21.4
Q ss_pred CCCCCCCCCC-ce--eee-CCCCc-----eEcCCCcccccCcc
Q 021438 4 SYCADCKRLT-EV--VFD-HSAGD-----TICSECGLVLEAYS 37 (312)
Q Consensus 4 ~~Cp~Cg~~~-~i--i~D-~~~G~-----~vC~~CG~Vv~e~~ 37 (312)
..||.||+.- .. .+| +--|. .+|..||+=..|-.
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~ 57 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVK 57 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccccee
Confidence 5799999831 11 112 33444 78999999876543
No 328
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=68.67 E-value=2.5 Score=25.78 Aligned_cols=14 Identities=21% Similarity=0.835 Sum_probs=12.4
Q ss_pred CCceEcCCCccccc
Q 021438 21 AGDTICSECGLVLE 34 (312)
Q Consensus 21 ~G~~vC~~CG~Vv~ 34 (312)
.|.+||+.|+.+|+
T Consensus 1 MGtIvCq~C~~~Id 14 (38)
T PF13790_consen 1 MGTIVCQHCNETID 14 (38)
T ss_pred CCEEEeccccceee
Confidence 38899999999986
No 329
>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=68.45 E-value=12 Score=25.76 Aligned_cols=31 Identities=19% Similarity=0.324 Sum_probs=22.9
Q ss_pred HHhCCCCCHHHHHHHhcCCC-HHHHHHHHHHHH
Q 021438 161 RQENKPRTVKEFCSVANGTT-KKEIGRAKEFIV 192 (312)
Q Consensus 161 r~~~~p~tl~dia~~~~~v~-~~~i~~~~~~l~ 192 (312)
..+|.|-|++||++.+ |++ ...+.+.++.|.
T Consensus 20 ~~~G~~Pt~rEIa~~~-g~~S~~tv~~~L~~Le 51 (65)
T PF01726_consen 20 EENGYPPTVREIAEAL-GLKSTSTVQRHLKALE 51 (65)
T ss_dssp HHHSS---HHHHHHHH-TSSSHHHHHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHh-CCCChHHHHHHHHHHH
Confidence 4789999999999999 886 787777776665
No 330
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=68.42 E-value=6.2 Score=32.35 Aligned_cols=33 Identities=18% Similarity=0.167 Sum_probs=26.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.|+++++..-...+...+
T Consensus 134 g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 134 GWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 577999999999999999988876666655443
No 331
>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=68.40 E-value=23 Score=23.69 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=25.9
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 021438 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (312)
Q Consensus 164 ~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~ 194 (312)
..+.+..|+++.+ |++..++.+.++.|.+.
T Consensus 23 ~~~~s~~ela~~~-g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYL-GLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHH-CCCHHHHHHHHHHHHHC
Confidence 4679999999999 89999999998887753
No 332
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=68.32 E-value=15 Score=30.01 Aligned_cols=45 Identities=13% Similarity=0.190 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 021438 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (312)
Q Consensus 148 ~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~ 194 (312)
.+.-+-+.+|+|. ..+.+.+.++|++.. +++..-+.+.+..|++.
T Consensus 7 ~~YAlr~L~~LA~-~~~~~~s~~eIA~~~-~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 7 TNYAIRMLMYCAA-NDGKLSRIPEIARAY-GVSELFLFKILQPLVEA 51 (153)
T ss_pred HhHHHHHHHHHHh-CCCCcCcHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence 3455667889984 456688999999999 89999999998888753
No 333
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=68.30 E-value=7.6 Score=34.43 Aligned_cols=32 Identities=28% Similarity=0.395 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..++-+|||+.+++|+.|++.+.+.+++.++.
T Consensus 204 ~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 204 DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 35789999999999999999999999987753
No 334
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=68.18 E-value=8 Score=30.91 Aligned_cols=30 Identities=17% Similarity=0.328 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
...|.+|||+.+|+|+.||+++.......+
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 357899999999999999999987766654
No 335
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=68.09 E-value=6.8 Score=26.80 Aligned_cols=30 Identities=13% Similarity=0.031 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.+++-+|||+++|+|..++|.....|.+.
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 456788999999999999999888777764
No 336
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=68.08 E-value=84 Score=27.57 Aligned_cols=32 Identities=19% Similarity=0.277 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||+.+|+|+.||+++++.....+..
T Consensus 216 ~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 216 EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56889999999999999999998776665543
No 337
>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=68.07 E-value=6.6 Score=26.81 Aligned_cols=22 Identities=27% Similarity=0.359 Sum_probs=19.1
Q ss_pred CHHHHHHHhCcchhHHHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
+..|||+.+||+..|||..-++
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999977654
No 338
>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=68.06 E-value=5.2 Score=28.70 Aligned_cols=35 Identities=20% Similarity=0.311 Sum_probs=21.5
Q ss_pred HHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 257 IITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 257 la~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
++-.+...+-|.++.|+++|||.+|+- |++.+.+.
T Consensus 11 i~~yIi~~~aTVR~~Ak~FGvSKSTVH---kDvteRL~ 45 (82)
T PF12116_consen 11 IANYIIETKATVRQAAKVFGVSKSTVH---KDVTERLP 45 (82)
T ss_dssp HHHHHHHH---HHHHHHHHTS-HHHHH---HHHTTHHH
T ss_pred HHHHHHHcccHHHHHHHHHCCcHHHHH---HHHHHHHH
Confidence 344444557889999999999999997 44444433
No 339
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=68.04 E-value=89 Score=27.82 Aligned_cols=31 Identities=6% Similarity=0.163 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|+++||+.+|+|..||+++.+.....+.
T Consensus 230 ~~~t~~EIA~~lgis~~~V~~~~~ral~kLr 260 (264)
T PRK07122 230 ESMTQTQIAERVGISQMHVSRLLAKTLARLR 260 (264)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4688999999999999999998877666553
No 340
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=67.93 E-value=1e+02 Score=28.47 Aligned_cols=31 Identities=10% Similarity=0.359 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
.+.|+++||+.+|+|...||+.-+.-...+.
T Consensus 281 ~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr 311 (324)
T PRK07921 281 QPRTLDQIGKLFGLSRERVRQIEREVMSKLR 311 (324)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5689999999999999999988765555443
No 341
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=67.89 E-value=7.2 Score=32.68 Aligned_cols=33 Identities=21% Similarity=0.223 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...|.+|||+.+|+++.||+.++....+.+...
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 468899999999999999999998888776543
No 342
>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=67.89 E-value=6.4 Score=31.44 Aligned_cols=32 Identities=16% Similarity=0.120 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||..+|+|+.|+++++......+..
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999998776665543
No 343
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=67.88 E-value=5.2 Score=27.81 Aligned_cols=20 Identities=20% Similarity=0.461 Sum_probs=17.0
Q ss_pred CHHHHHHHhCcchhHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVY 286 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~ 286 (312)
+++|||+.+|||..||...+
T Consensus 2 t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 67899999999999998654
No 344
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=67.66 E-value=32 Score=28.77 Aligned_cols=29 Identities=14% Similarity=0.101 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++|+++||+.+|+|..|+.+..++|.+.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 57899999999999999999999999874
No 345
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=67.62 E-value=7.9 Score=31.34 Aligned_cols=29 Identities=14% Similarity=0.030 Sum_probs=25.2
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
..+.+|||+.+|+|..||+.++..-.+.+
T Consensus 129 g~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 129 GLGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 57799999999999999999988776654
No 346
>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=67.40 E-value=4.1 Score=25.45 Aligned_cols=10 Identities=30% Similarity=0.959 Sum_probs=7.3
Q ss_pred eEcCCCcccc
Q 021438 24 TICSECGLVL 33 (312)
Q Consensus 24 ~vC~~CG~Vv 33 (312)
.+|.+||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3588888764
No 347
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=67.22 E-value=8.9 Score=32.03 Aligned_cols=32 Identities=16% Similarity=0.049 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||+.+|+|+.|+++++..-...+..
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35779999999999999999998877776655
No 348
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=67.04 E-value=1.6 Score=38.83 Aligned_cols=29 Identities=17% Similarity=0.512 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
.+||.||. .-...|-.....||..||+-.
T Consensus 29 ~KCp~c~~-~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 29 TKCPSCGE-MLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eECCCccc-eeeHHHHHhhhhcccccCccc
Confidence 47999997 333445566789999999875
No 349
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=67.02 E-value=7.9 Score=31.17 Aligned_cols=33 Identities=18% Similarity=0.241 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...+.+|||+.+|+|+.|++.++..-...+...
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357799999999999999999887766665443
No 350
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=66.85 E-value=7.5 Score=32.62 Aligned_cols=29 Identities=17% Similarity=0.195 Sum_probs=25.3
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
..|.+|||..+|+|+.|++++++.+...+
T Consensus 151 Gls~~EIA~~lgiS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 151 GLSVEEIAERLGISERTVRRRLRRARAWL 179 (185)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 35899999999999999999998887654
No 351
>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=66.77 E-value=7.9 Score=31.45 Aligned_cols=30 Identities=23% Similarity=0.340 Sum_probs=25.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
..+.+|||+.+|+|+.|+++++....+.+.
T Consensus 138 g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 138 NLPIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 477999999999999999999887776654
No 352
>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=66.61 E-value=6 Score=25.64 Aligned_cols=25 Identities=16% Similarity=0.179 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHH
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
..+|++++|+.+|++..||.+..+.
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhcC
Confidence 4578999999999999999976544
No 353
>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=66.50 E-value=15 Score=24.79 Aligned_cols=27 Identities=15% Similarity=0.149 Sum_probs=24.7
Q ss_pred CCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.+..+|++.++++..|+++.++.|.+.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~ 47 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEA 47 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHC
Confidence 889999999999999999999998663
No 354
>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=66.44 E-value=16 Score=24.02 Aligned_cols=28 Identities=14% Similarity=0.152 Sum_probs=24.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
..++.+||+.++++.+|+.+..+.|.+.
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 3889999999999999999999999874
No 355
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=66.37 E-value=6.2 Score=32.15 Aligned_cols=34 Identities=15% Similarity=0.039 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+.+|||..+|+|+.|++.++....+.+...+
T Consensus 123 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 123 HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3577999999999999999999988888776665
No 356
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=66.33 E-value=8.6 Score=31.19 Aligned_cols=34 Identities=15% Similarity=0.174 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+.++||..+|+|+.|+++++......+...+
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999987777766554
No 357
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=66.32 E-value=6.5 Score=31.75 Aligned_cols=34 Identities=6% Similarity=0.078 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+.+|||+.+|+|+.|++.++..-...+...+
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3577999999999999999999876666655443
No 358
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=66.16 E-value=11 Score=38.72 Aligned_cols=77 Identities=18% Similarity=0.281 Sum_probs=66.1
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHhhh----ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHH
Q 021438 214 LRRFCSNLGMTNQAVKAAQEAVQKSED----LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDL 289 (312)
Q Consensus 214 i~r~~~~L~l~~~v~~~A~~i~~~~~~----l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel 289 (312)
+..+|.+|.++++.....|.+.+.... |..-|+-.-|.-.|+|+.+++....++.++|-..-.-.+......||+.
T Consensus 684 L~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa~~~vyRsV 763 (920)
T KOG1010|consen 684 LNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQAVSLVYRSV 763 (920)
T ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCchhhhhhhhhe
Confidence 456788899999999999999888664 6778999999999999999999999999999888888888888888765
Q ss_pred H
Q 021438 290 F 290 (312)
Q Consensus 290 ~ 290 (312)
+
T Consensus 764 ~ 764 (920)
T KOG1010|consen 764 L 764 (920)
T ss_pred e
Confidence 4
No 359
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=66.06 E-value=3.7 Score=31.73 Aligned_cols=16 Identities=13% Similarity=0.399 Sum_probs=6.7
Q ss_pred eeeeCCCCceEcCCCc
Q 021438 15 VVFDHSAGDTICSECG 30 (312)
Q Consensus 15 ii~D~~~G~~vC~~CG 30 (312)
+..+..-+...|.+||
T Consensus 62 L~I~~vp~~~~C~~Cg 77 (113)
T PRK12380 62 LHIVYKPAQAWCWDCS 77 (113)
T ss_pred EEEEeeCcEEEcccCC
Confidence 3333334444444444
No 360
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=66.05 E-value=1e+02 Score=31.18 Aligned_cols=41 Identities=15% Similarity=0.222 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 252 AAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 252 aAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
-.|+||+-.+.+ .++.+|++.+|-...||...+|.|.+.+.
T Consensus 558 qiAMYL~r~lt~--~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~ 598 (617)
T PRK14086 558 QIAMYLCRELTD--LSLPKIGQQFGRDHTTVMHADRKIRALMA 598 (617)
T ss_pred HHHHHHHHHHcC--CCHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence 567899988764 66899999999999999999998888554
No 361
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=65.89 E-value=12 Score=30.57 Aligned_cols=38 Identities=18% Similarity=0.231 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 254 VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 254 aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+||.... .+.....++||+.++|+++|+.+..+.|.+.
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~ 51 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAERLKVSPPSVTEMLKRLERL 51 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHHhCCCcHHHHHHHHHHHHC
Confidence 4565555 4455778999999999999999999999874
No 362
>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=65.89 E-value=5.7 Score=24.19 Aligned_cols=18 Identities=17% Similarity=0.309 Sum_probs=14.8
Q ss_pred CHHHHHHHhCcchhHHHH
Q 021438 267 PLKEISIVTRVAEGTIKN 284 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~ 284 (312)
+..|+|+.+|||..|||.
T Consensus 1 ti~e~A~~~gvs~~tlR~ 18 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRY 18 (38)
T ss_dssp EHHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 357999999999999994
No 363
>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=65.70 E-value=4.3 Score=38.72 Aligned_cols=30 Identities=27% Similarity=0.625 Sum_probs=18.6
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
.||+|+...++..-...+...|..||.++.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 588888642222223344567888888884
No 364
>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=65.70 E-value=6.6 Score=32.93 Aligned_cols=33 Identities=18% Similarity=0.144 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...+.+|||+.+|+|+.||+.++..-...+...
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999987666655443
No 365
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=65.67 E-value=16 Score=23.81 Aligned_cols=39 Identities=10% Similarity=0.031 Sum_probs=31.6
Q ss_pred HHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhh
Q 021438 158 IACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (312)
Q Consensus 158 ~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~ 197 (312)
++.-.-....+..+++..+ ||+..++.+.+..+...|..
T Consensus 11 l~L~~LR~~~~~~~La~~F-gIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 11 LTLMYLRLNLTFQDLAYRF-GISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred HHHHHHHcCCcHhHHhhhe-eecHHHHHHHHHHHHHHHHH
Confidence 3344445678899999999 89999999999998888764
No 366
>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=65.63 E-value=5.2 Score=30.35 Aligned_cols=29 Identities=17% Similarity=0.502 Sum_probs=21.6
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~ 36 (312)
.|--|+.. ... ...+++||..||+++.-.
T Consensus 37 aCeiC~~~-GY~--q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 37 ACEICGPK-GYY--QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred eccccCCC-ceE--EECCEEEEecCCCEEehh
Confidence 58889873 333 446889999999998643
No 367
>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=65.52 E-value=9.6 Score=28.05 Aligned_cols=20 Identities=25% Similarity=0.277 Sum_probs=18.4
Q ss_pred CCCHHHHHHHhCcchhHHHH
Q 021438 265 TKPLKEISIVTRVAEGTIKN 284 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~ 284 (312)
..|.++||+.+|+|..||.+
T Consensus 50 G~S~~eIA~~LgISrsTIyR 69 (88)
T TIGR02531 50 GKTYSDIEAETGASTATISR 69 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHH
Confidence 46899999999999999987
No 368
>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=65.25 E-value=1e+02 Score=27.46 Aligned_cols=33 Identities=21% Similarity=0.330 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
+..+|+++||..+|||..+|+++.+.....+..
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 347899999999999999999888776665543
No 369
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=65.06 E-value=4.7 Score=34.27 Aligned_cols=31 Identities=29% Similarity=0.608 Sum_probs=18.6
Q ss_pred CCCCCCCCCce---eee--CCCC-----ceEcCCCcccccC
Q 021438 5 YCADCKRLTEV---VFD--HSAG-----DTICSECGLVLEA 35 (312)
Q Consensus 5 ~Cp~Cg~~~~i---i~D--~~~G-----~~vC~~CG~Vv~e 35 (312)
.||+||..... .++ +--| ...|..||+=-.|
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 42 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSND 42 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccce
Confidence 59999964221 122 1133 3679999987543
No 370
>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=65.01 E-value=12 Score=24.96 Aligned_cols=31 Identities=10% Similarity=0.086 Sum_probs=27.5
Q ss_pred CCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
.+....|+.+++|.++|.+.+++|.+.++.-
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS-
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhCCe
Confidence 3688899999999999999999999998863
No 371
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=64.96 E-value=23 Score=24.46 Aligned_cols=38 Identities=18% Similarity=0.183 Sum_probs=29.6
Q ss_pred HHHHHHHhCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 021438 156 LYIACRQENK-PRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (312)
Q Consensus 156 ly~acr~~~~-p~tl~dia~~~~~v~~~~i~~~~~~l~~~ 194 (312)
|+...+..+- +.+..||+..+ |++..++.+.+..|.+.
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~l-gl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNL-GLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHH-CCCHHHHHHHHHHHHHC
Confidence 4445556666 49999999999 89999998887776643
No 372
>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=64.81 E-value=27 Score=21.92 Aligned_cols=29 Identities=21% Similarity=0.250 Sum_probs=23.0
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 164 ~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
+-+.|..|++..+ |++..++.+.++.|.+
T Consensus 15 ~~~~t~~ela~~~-~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKL-GISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHH-TS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 4459999999999 8999999999888764
No 373
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=64.80 E-value=8.7 Score=32.53 Aligned_cols=39 Identities=18% Similarity=0.101 Sum_probs=31.0
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCCccccc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFAN 303 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~~~~ 303 (312)
..+.+|||+.+|+|+.|+++++..-...+...++....+
T Consensus 149 g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~ 187 (196)
T PRK12535 149 GYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQAS 187 (196)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccch
Confidence 467999999999999999999877777776666544443
No 374
>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=64.73 E-value=7.8 Score=26.57 Aligned_cols=22 Identities=9% Similarity=0.332 Sum_probs=18.8
Q ss_pred CHHHHHHHhCcchhHHHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
+..|+|+.+||+..||+...++
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999976554
No 375
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=64.62 E-value=7.5 Score=33.82 Aligned_cols=30 Identities=20% Similarity=0.328 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
...|.+|||+.+|+|+.||+++.......+
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~~L 226 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIKRL 226 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 468899999999999999998875555444
No 376
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=64.52 E-value=8.2 Score=24.79 Aligned_cols=26 Identities=23% Similarity=0.691 Sum_probs=17.8
Q ss_pred CCCC--CCCCCCceeeeCCCCceEcCCCcc
Q 021438 4 SYCA--DCKRLTEVVFDHSAGDTICSECGL 31 (312)
Q Consensus 4 ~~Cp--~Cg~~~~ii~D~~~G~~vC~~CG~ 31 (312)
..|| .||. .-+.-++. ....|..||+
T Consensus 19 k~CP~~~CG~-GvFMA~H~-dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGA-GVFMAEHK-DRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTS-SSEEEE-S-SEEEETTTSS
T ss_pred hcCCCcccCC-ceEeeecC-CCccCCCccc
Confidence 4699 8998 54555544 5899999996
No 377
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=64.51 E-value=8.5 Score=31.35 Aligned_cols=34 Identities=18% Similarity=0.208 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+.+|||..+|+|+.|+++++......+...+
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3577999999999999999999988777766544
No 378
>PRK13870 transcriptional regulator TraR; Provisional
Probab=64.49 E-value=9.9 Score=33.31 Aligned_cols=32 Identities=16% Similarity=0.211 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+|-.|||..+|+|+.|++.+.+.+.+.++.
T Consensus 187 ~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 187 VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 46788999999999999999999998887653
No 379
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=64.42 E-value=6.5 Score=32.98 Aligned_cols=33 Identities=6% Similarity=0.038 Sum_probs=26.6
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||..+|+|+.|++.++..-...+...+
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 150 ELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577999999999999999998876666555433
No 380
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=64.23 E-value=72 Score=30.78 Aligned_cols=41 Identities=17% Similarity=0.241 Sum_probs=34.5
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHh-CcchhHHHHHHHHHHhhhc
Q 021438 252 AAVIYIITQLSNDTKPLKEISIVT-RVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 252 aAaiyla~~~~~~~~~~~~Ia~~~-~vs~~ti~~~~kel~~~~~ 294 (312)
..|.||+-++.+ .|+.+|++.+ |.+.+||...++.+.+.+.
T Consensus 391 ~iamyl~~~~~~--~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~ 432 (450)
T PRK00149 391 QIAMYLAKELTD--LSLPEIGRAFGGRDHTTVLHAVRKIEKLLE 432 (450)
T ss_pred HHHHHHHHHhcC--CCHHHHHHHcCCCCHhHHHHHHHHHHHHHH
Confidence 567899988876 4799999999 5999999999999888553
No 381
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=64.20 E-value=11 Score=30.35 Aligned_cols=30 Identities=10% Similarity=0.019 Sum_probs=25.4
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
..+.+|||+.+|+|+.|++.+.......+.
T Consensus 127 g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 127 GVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 577999999999999999999877666543
No 382
>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=64.13 E-value=13 Score=25.18 Aligned_cols=31 Identities=13% Similarity=0.212 Sum_probs=24.8
Q ss_pred cCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.+.+.++.+|++.++++..|+.+..++|.+.
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4567889999999999999999999999885
No 383
>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=64.06 E-value=11 Score=23.00 Aligned_cols=29 Identities=24% Similarity=0.468 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceeeeCCCCc-eEcCC---Ccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGD-TICSE---CGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~-~vC~~---CG~Vv 33 (312)
..||.||+ .-++.....|. +.|++ |.+..
T Consensus 2 ~~CP~Cg~-~lv~r~~k~g~F~~Cs~yP~C~~~~ 34 (39)
T PF01396_consen 2 EKCPKCGG-PLVLRRGKKGKFLGCSNYPECKYTE 34 (39)
T ss_pred cCCCCCCc-eeEEEECCCCCEEECCCCCCcCCeE
Confidence 57999997 34444444544 57876 76654
No 384
>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=63.93 E-value=4.4 Score=31.40 Aligned_cols=19 Identities=11% Similarity=0.408 Sum_probs=10.0
Q ss_pred ceeeeCCCCceEcCCCccc
Q 021438 14 EVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 14 ~ii~D~~~G~~vC~~CG~V 32 (312)
.+..+..-+...|.+||..
T Consensus 61 ~L~I~~~p~~~~C~~Cg~~ 79 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSEE 79 (115)
T ss_pred EEEEEeeCcEEEcccCCCE
Confidence 3444455555556666533
No 385
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=63.78 E-value=8.9 Score=31.82 Aligned_cols=31 Identities=16% Similarity=0.197 Sum_probs=26.0
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+.+|||+.+|+|+.||+++.....+.+..
T Consensus 151 ~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 151 GYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5779999999999999999888776666544
No 386
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=63.76 E-value=11 Score=34.82 Aligned_cols=36 Identities=11% Similarity=-0.058 Sum_probs=29.0
Q ss_pred HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 256 YIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 256 yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
-+|+..+-..+||.|||+.+|+|..++.+-.++=.+
T Consensus 20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345555677899999999999999999977766555
No 387
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=63.60 E-value=8.3 Score=32.10 Aligned_cols=32 Identities=16% Similarity=0.306 Sum_probs=25.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
..+.+|||..+|+|+.|+++++..-...+...
T Consensus 138 g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 138 NLTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47799999999999999999886655555443
No 388
>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=63.58 E-value=4.6 Score=36.67 Aligned_cols=29 Identities=31% Similarity=0.673 Sum_probs=12.3
Q ss_pred CCCCCCCCCCce-eeeCCC--Cc--eEcCCCccc
Q 021438 4 SYCADCKRLTEV-VFDHSA--GD--TICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~i-i~D~~~--G~--~vC~~CG~V 32 (312)
..||.||+...+ +..... |. +.|+-||+-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~ 206 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTE 206 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--E
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCe
Confidence 589999995322 222222 53 899999864
No 389
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.57 E-value=6.1 Score=28.14 Aligned_cols=29 Identities=28% Similarity=0.520 Sum_probs=19.9
Q ss_pred CCCCCCCCCCCceeeeCCCCc--eEcCCCcccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGD--TICSECGLVL 33 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~--~vC~~CG~Vv 33 (312)
+..||.|+- +++.....|- -.|..|+-|-
T Consensus 1 ~llCP~C~v--~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 1 MLLCPICGV--ELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred CcccCcCCc--eeeeeeecCceeeeCCccccEe
Confidence 468999996 3444433443 5799999884
No 390
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=63.49 E-value=27 Score=25.10 Aligned_cols=29 Identities=14% Similarity=0.115 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.+.+..+||+.+|++..|+.+..+.|.+.
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 46899999999999999999999999763
No 391
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=63.48 E-value=8.5 Score=31.59 Aligned_cols=49 Identities=16% Similarity=0.214 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 248 ISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 248 ~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
..|+.|++=|.....=.++|+++||+.+||+..|.=.+|+..++.+..+
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK~dLl~~~ 54 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDKYELLTWI 54 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCHHHHHHHH
Confidence 4466666665554433579999999999999999999988776665543
No 392
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=63.46 E-value=14 Score=22.81 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 164 ~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
..|.+..|+++.+ +++..++.+.++.|.+
T Consensus 6 ~~~~s~~~la~~l-~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 6 RLPLTRQEIAELL-GLTRETVSRTLKRLEK 34 (48)
T ss_pred EeccCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3578999999999 8999999998888765
No 393
>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=63.44 E-value=6.3 Score=38.81 Aligned_cols=30 Identities=20% Similarity=0.568 Sum_probs=24.2
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
...||+|+. .+.+....+.+.|..||....
T Consensus 222 ~~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 222 ILCCPNCDV--SLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred ccCCCCCCC--ceEEecCCCeEEcCCCcCcCC
Confidence 357999997 477777889999999998854
No 394
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=63.39 E-value=8.5 Score=31.91 Aligned_cols=33 Identities=33% Similarity=0.314 Sum_probs=27.6
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.|+++++..-.+.+...+
T Consensus 143 g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 143 ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577999999999999999999987777665543
No 395
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=63.35 E-value=11 Score=32.34 Aligned_cols=31 Identities=13% Similarity=0.063 Sum_probs=27.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+-++||+.+++|+.|++.+...|++.++.
T Consensus 149 G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 149 GYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 5778999999999999999999999988753
No 396
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=63.31 E-value=7 Score=34.76 Aligned_cols=29 Identities=14% Similarity=0.051 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
-.++.+|+|+.++||+.|||+..++|.+.
T Consensus 18 ~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 18 GKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred CCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 45789999999999999999999998765
No 397
>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=63.17 E-value=9.4 Score=31.16 Aligned_cols=40 Identities=25% Similarity=0.340 Sum_probs=29.6
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 254 VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 254 aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
-|+....+. ..+.+|||+.+|+|+.|++++.......+..
T Consensus 126 ~i~~l~~~~--g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 126 TAIILRYYH--DLTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred HHHHHHHHc--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334333343 4779999999999999999998777666544
No 398
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=63.12 E-value=7.1 Score=27.35 Aligned_cols=26 Identities=23% Similarity=0.698 Sum_probs=16.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
..||.|+. .+..+ .|.+.|..|+.-+
T Consensus 2 ~~CP~C~~--~L~~~--~~~~~C~~C~~~~ 27 (70)
T PF07191_consen 2 NTCPKCQQ--ELEWQ--GGHYHCEACQKDY 27 (70)
T ss_dssp -B-SSS-S--BEEEE--TTEEEETTT--EE
T ss_pred CcCCCCCC--ccEEe--CCEEECccccccc
Confidence 47999998 36555 4899999998754
No 399
>PRK05580 primosome assembly protein PriA; Validated
Probab=63.11 E-value=6.2 Score=40.38 Aligned_cols=29 Identities=17% Similarity=0.507 Sum_probs=24.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
..||+|+. .+.+....+.+.|..||....
T Consensus 391 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 391 AECPHCDA--SLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred cCCCCCCC--ceeEECCCCeEECCCCcCCCC
Confidence 57999997 578878889999999998753
No 400
>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=63.09 E-value=6.2 Score=29.76 Aligned_cols=28 Identities=25% Similarity=0.540 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceeee------CCCC---ceEcCCCccc
Q 021438 4 SYCADCKRLTEVVFD------HSAG---DTICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D------~~~G---~~vC~~CG~V 32 (312)
..||.||+. ..++= .++| .++|.+||..
T Consensus 63 ~~Cp~Cg~~-~a~f~~~Q~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 63 VECPKCGHK-EAYYWLLQTRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred CCCCCCCCC-eeEEEEeccCCCCCCcEEEEEeCCCCCe
Confidence 579999984 43331 1223 4889999974
No 401
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=63.07 E-value=11 Score=25.26 Aligned_cols=24 Identities=21% Similarity=0.113 Sum_probs=20.3
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHH
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
.-++++||+.+|++..||.+..+.
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHh
Confidence 456999999999999999977653
No 402
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.05 E-value=4.6 Score=32.26 Aligned_cols=21 Identities=24% Similarity=0.623 Sum_probs=14.2
Q ss_pred ceeeeCCCCceEcCCCccccc
Q 021438 14 EVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 14 ~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
.+..+...+...|.+||.+..
T Consensus 61 ~L~i~~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 61 EIIFEEEEAVLKCRNCGNEWS 81 (135)
T ss_pred EEEEEecceEEECCCCCCEEe
Confidence 455556667788888886653
No 403
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=62.97 E-value=5.4 Score=31.77 Aligned_cols=34 Identities=21% Similarity=0.317 Sum_probs=27.7
Q ss_pred eeCCCCceEcCCCcccc--cCcccccccccccccCC
Q 021438 17 FDHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (312)
Q Consensus 17 ~D~~~G~~vC~~CG~Vv--~e~~id~~~ewr~f~~~ 50 (312)
.....|.++|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 34 ~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 69 (134)
T TIGR00357 34 DNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKP 69 (134)
T ss_pred CCCCCeEEEccCCCCccccccchhcCCCCCcCcCcc
Confidence 34678999999999988 44578899999999743
No 404
>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=62.85 E-value=6.3 Score=36.06 Aligned_cols=9 Identities=33% Similarity=0.763 Sum_probs=5.8
Q ss_pred EcCCCcccc
Q 021438 25 ICSECGLVL 33 (312)
Q Consensus 25 vC~~CG~Vv 33 (312)
+|.+||.-+
T Consensus 254 ~C~~C~~Yl 262 (305)
T TIGR01562 254 TCDSCQGYL 262 (305)
T ss_pred eccccccch
Confidence 666666655
No 405
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=62.83 E-value=31 Score=26.97 Aligned_cols=44 Identities=14% Similarity=0.233 Sum_probs=33.0
Q ss_pred ChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHH
Q 021438 246 SPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLF 290 (312)
Q Consensus 246 ~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~ 290 (312)
....+..+.-|+-.... .+.++.++|+.+|+|+.++...+|+..
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34445555556665544 469999999999999999998888763
No 406
>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=62.79 E-value=15 Score=29.16 Aligned_cols=40 Identities=13% Similarity=0.179 Sum_probs=33.0
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.+|||..-.+...+.++||+..+++...+++....|.+.
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5667776533456899999999999999999999999884
No 407
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=62.77 E-value=7.9 Score=31.74 Aligned_cols=35 Identities=23% Similarity=0.318 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p 298 (312)
...+.+|||+.+|+|+.||+++.......+...+.
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35679999999999999999999887777766553
No 408
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=62.74 E-value=8.4 Score=33.28 Aligned_cols=33 Identities=21% Similarity=0.309 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...+.+|||+.+|+|+.|+++++......+...
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999987766665543
No 409
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=62.73 E-value=7.9 Score=26.46 Aligned_cols=21 Identities=14% Similarity=0.256 Sum_probs=18.3
Q ss_pred CHHHHHHHhCcchhHHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~k 287 (312)
+.+|+|+.+|+++.||+...+
T Consensus 2 s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999997644
No 410
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=62.65 E-value=6.4 Score=26.92 Aligned_cols=21 Identities=19% Similarity=0.338 Sum_probs=18.1
Q ss_pred CHHHHHHHhCcchhHHHHHHH
Q 021438 267 PLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~k 287 (312)
+..|+|+.+|+|..|||..-+
T Consensus 2 ti~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 468999999999999997644
No 411
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=62.64 E-value=6.8 Score=35.88 Aligned_cols=9 Identities=22% Similarity=1.006 Sum_probs=5.0
Q ss_pred CCCCCCCCC
Q 021438 4 SYCADCKRL 12 (312)
Q Consensus 4 ~~Cp~Cg~~ 12 (312)
..||.||+.
T Consensus 188 ~~CPvCGs~ 196 (309)
T PRK03564 188 QFCPVCGSM 196 (309)
T ss_pred CCCCCCCCc
Confidence 456666653
No 412
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=62.63 E-value=9.9 Score=31.49 Aligned_cols=32 Identities=13% Similarity=0.230 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.++||..+|+|+.||+++.......+..
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999998776666544
No 413
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=62.56 E-value=4.1 Score=24.48 Aligned_cols=21 Identities=43% Similarity=1.102 Sum_probs=10.6
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECG 30 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG 30 (312)
.+|++||. +.+-+ ..+|..||
T Consensus 12 ~rC~~Cg~---~~~pP---r~~Cp~C~ 32 (37)
T PF12172_consen 12 QRCRDCGR---VQFPP---RPVCPHCG 32 (37)
T ss_dssp EE-TTT-----EEES-----SEETTTT
T ss_pred EEcCCCCC---EecCC---CcCCCCcC
Confidence 46888886 34432 26788887
No 414
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=62.55 E-value=35 Score=25.53 Aligned_cols=38 Identities=3% Similarity=0.166 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHH
Q 021438 251 AAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDL 289 (312)
Q Consensus 251 aaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel 289 (312)
..+.-|+... ...++++.+||+.+|+|+.++.+.+++.
T Consensus 8 ~~~~~~i~~~-~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 8 QTLIAWIDEH-IDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHh-cCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3344444444 3456899999999999999999888875
No 415
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=62.51 E-value=18 Score=28.45 Aligned_cols=38 Identities=13% Similarity=0.219 Sum_probs=31.1
Q ss_pred HHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 255 IYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 255 iyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+|++-.-.+-+.+..+||+.++.+.+|+.+..+.|.+.
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 45554435668999999999999999999999988874
No 416
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=62.39 E-value=69 Score=27.78 Aligned_cols=110 Identities=15% Similarity=0.205 Sum_probs=60.2
Q ss_pred hCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhh---ccccccCCC--CHHHHHHHHHhhcCCCHHHHHHHHHHHHH
Q 021438 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM---GQSVEMGTI--HASDYLRRFCSNLGMTNQAVKAAQEAVQK 237 (312)
Q Consensus 163 ~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~---~~~~~~~~~--~p~~~i~r~~~~L~l~~~v~~~A~~i~~~ 237 (312)
.|.-.|..|++..+ ++|..+|++-.+.+.+.-+... +...++++. +-...+..|.... -..++.+...+--+.
T Consensus 102 QgglLT~~Dla~LL-~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~l~g~-~~~eiar~t~HS~~a 179 (220)
T PF07900_consen 102 QGGLLTQEDLAMLL-GISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLYLKGK-PTPEIARRTNHSPEA 179 (220)
T ss_pred cCCcccHHHHHHHH-CCCHHHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHHHcCC-CHHHHHHHhccCHHH
Confidence 34457899999999 8999999999999988855421 111133321 1223333333321 112232222222222
Q ss_pred hhh-ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHH
Q 021438 238 SED-LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNV 285 (312)
Q Consensus 238 ~~~-l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~ 285 (312)
..+ +.... -+.+ +.+...+..+||.++|.|+..|...
T Consensus 180 v~rYi~~F~-------rV~~----l~~~~~~~~eia~~tg~S~~Lv~eY 217 (220)
T PF07900_consen 180 VDRYIKDFK-------RVLM----LYEKGMSPEEIAFITGMSERLVKEY 217 (220)
T ss_pred HHHHHHhhH-------HhHH----HHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 222 11111 1111 2345677899999999999988754
No 417
>PRK10072 putative transcriptional regulator; Provisional
Probab=62.35 E-value=8.4 Score=28.86 Aligned_cols=25 Identities=12% Similarity=0.108 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHH
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
...++|.++|+.+|+|..||+++-+
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 3468899999999999999998753
No 418
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.32 E-value=4.2 Score=37.25 Aligned_cols=26 Identities=31% Similarity=0.707 Sum_probs=21.4
Q ss_pred CCCCCCCCCceeeeC-C-CCceEcCCCc
Q 021438 5 YCADCKRLTEVVFDH-S-AGDTICSECG 30 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~-~-~G~~vC~~CG 30 (312)
.||.||+...+-+|. . .|+.+|..||
T Consensus 34 ~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 34 PCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCccCCccccccCCccCCccEEEEeec
Confidence 799999977776654 3 6999999999
No 419
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=62.29 E-value=2.5 Score=28.63 Aligned_cols=27 Identities=19% Similarity=0.522 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEcC-CCccccc
Q 021438 2 ADSYCADCKRLTEVVFDHSAGDTICS-ECGLVLE 34 (312)
Q Consensus 2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~-~CG~Vv~ 34 (312)
.+..||+||.+ +-. .+..|+ .|+....
T Consensus 2 ~HkHC~~CG~~--Ip~----~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 2 PHKHCPVCGKP--IPP----DESFCSPKCREEYR 29 (59)
T ss_pred CCCcCCcCCCc--CCc----chhhhCHHHHHHHH
Confidence 35789999973 332 488996 7887654
No 420
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=62.19 E-value=13 Score=24.86 Aligned_cols=33 Identities=9% Similarity=0.096 Sum_probs=25.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+..+.|+..++..+|++.|.+.|.+..+.-+
T Consensus 12 ~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl 44 (59)
T PF13556_consen 12 NGNISKTARALHIHRNTLRYRLKKIEELLGLDL 44 (59)
T ss_dssp TT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--T
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCC
Confidence 456889999999999999999999999876543
No 421
>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=62.17 E-value=15 Score=22.71 Aligned_cols=23 Identities=9% Similarity=0.112 Sum_probs=18.2
Q ss_pred CCHHHHHHHhCcchhHHHHHHHH
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
-.+.+.|+.+|++..|+..++++
T Consensus 19 gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 19 GNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp T-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 34789999999999999988765
No 422
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=62.17 E-value=8.6 Score=32.20 Aligned_cols=30 Identities=20% Similarity=0.140 Sum_probs=24.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
..+.+|||+.+|+|+.||+.++..-.+.+.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 578999999999999999988765555544
No 423
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=62.08 E-value=2.9 Score=31.98 Aligned_cols=31 Identities=19% Similarity=0.574 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
...|++||+. +..-...+.++|..|+.+..-
T Consensus 7 ~~FC~~CG~l--l~~~~~~~~~~C~~Ck~~~~v 37 (116)
T KOG2907|consen 7 LDFCSDCGSL--LEEPSAQSTVLCIRCKIEYPV 37 (116)
T ss_pred cchhhhhhhh--cccccccCceEeccccccCCH
Confidence 4579999972 444556777889999988653
No 424
>PF13551 HTH_29: Winged helix-turn helix
Probab=61.91 E-value=12 Score=27.94 Aligned_cols=26 Identities=15% Similarity=0.093 Sum_probs=23.6
Q ss_pred CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 267 PLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 267 ~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+..+||+.+|+|..||.+..+.+.+.
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~ 39 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREG 39 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence 69999999999999999999887764
No 425
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=61.82 E-value=8.8 Score=32.08 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=25.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
..+.+|||+.+|+|+.|+++++......+...
T Consensus 127 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 127 GLSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 57799999999999999999986555555443
No 426
>PRK09483 response regulator; Provisional
Probab=61.80 E-value=12 Score=31.23 Aligned_cols=32 Identities=19% Similarity=0.240 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.++||+.+++|+.|++++.+.|+..++.
T Consensus 162 ~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 162 KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 34678899999999999999999999998753
No 427
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=61.78 E-value=11 Score=30.72 Aligned_cols=30 Identities=17% Similarity=0.093 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
...+.+|||+.+|+|+.|++++++.-...+
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra~~~~ 162 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEAFKCC 162 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 357899999999999999999887666554
No 428
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=61.75 E-value=16 Score=29.69 Aligned_cols=39 Identities=15% Similarity=0.209 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
+.+|||.. .+...+.++||+..++++.-+++.+..|.+.
T Consensus 13 ~L~~LA~~-~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 13 MLMYCAAN-DGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHHHHHhC-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56677743 4556789999999999999999999999884
No 429
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=61.74 E-value=10 Score=31.45 Aligned_cols=31 Identities=26% Similarity=0.170 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...+.+|||+.+|+|+.|+++++....+.+.
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 3577999999999999999999877666543
No 430
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=61.49 E-value=10 Score=31.96 Aligned_cols=29 Identities=17% Similarity=0.093 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
.++|+++||+.+|++..|+.+..++|.+.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 47899999999999999999999998874
No 431
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=61.43 E-value=18 Score=25.86 Aligned_cols=30 Identities=7% Similarity=0.009 Sum_probs=21.0
Q ss_pred HHHHhcCCCCCHHHHHHHhCcchhHHHHHH
Q 021438 257 IITQLSNDTKPLKEISIVTRVAEGTIKNVY 286 (312)
Q Consensus 257 la~~~~~~~~~~~~Ia~~~~vs~~ti~~~~ 286 (312)
+...+....+||+++|+.+|++.++|.+-.
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~ 52 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLE 52 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHH
Confidence 444445567899999999999999998654
No 432
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=61.39 E-value=20 Score=26.20 Aligned_cols=37 Identities=8% Similarity=0.054 Sum_probs=30.0
Q ss_pred HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 256 YIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 256 yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
-|+-++.....++.++|..+|||..|..++.......
T Consensus 16 ~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~ 52 (85)
T PF13011_consen 16 RLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAE 52 (85)
T ss_pred HHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 4555565667889999999999999999988877654
No 433
>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=61.38 E-value=22 Score=22.61 Aligned_cols=31 Identities=19% Similarity=0.247 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 021438 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (312)
Q Consensus 164 ~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l 195 (312)
..+.|+.||+..+ |++..++.+..+...+.|
T Consensus 18 ~~~~t~~eIa~~l-g~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAERL-GISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHHH-TSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHH-CCcHHHHHHHHHHHHHHh
Confidence 6778999999999 899999998877665544
No 434
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=61.32 E-value=9.9 Score=31.55 Aligned_cols=34 Identities=12% Similarity=0.140 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+.+|||+.+|+|+.|+++++....+.+...+
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999999877777665443
No 435
>PRK05572 sporulation sigma factor SigF; Validated
Probab=61.16 E-value=1.1e+02 Score=26.72 Aligned_cols=33 Identities=9% Similarity=0.191 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...|+++||+.+|+|..||+++.+...+.+...
T Consensus 217 ~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 217 KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999888777766543
No 436
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=61.15 E-value=15 Score=22.43 Aligned_cols=26 Identities=15% Similarity=0.161 Sum_probs=18.6
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 021438 164 NKPRTVKEFCSVANGTTKKEIGRAKEF 190 (312)
Q Consensus 164 ~~p~tl~dia~~~~~v~~~~i~~~~~~ 190 (312)
..+.++.|||..+ |++...+.+.+++
T Consensus 6 ~~~~~l~~iA~~~-g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 6 QQKLTLEDIAEQA-GFSPSYFSRLFKK 31 (42)
T ss_dssp -SS--HHHHHHHH-TS-HHHHHHHHHH
T ss_pred cCCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 4568999999999 8999988887765
No 437
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=61.07 E-value=10 Score=31.42 Aligned_cols=32 Identities=19% Similarity=0.126 Sum_probs=26.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
..+.+|||+.+|+|+.||++++..-...+...
T Consensus 145 g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 145 GLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57799999999999999999987776665543
No 438
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=61.06 E-value=10 Score=33.62 Aligned_cols=29 Identities=7% Similarity=0.005 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
-.++++|+|+.+|||+.|||+..++|.+.
T Consensus 18 ~~~~~~ela~~l~vS~~TirRdL~~Le~~ 46 (251)
T PRK13509 18 GFVTVEKVIERLGISPATARRDINKLDES 46 (251)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45889999999999999999999998663
No 439
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=61.05 E-value=9 Score=32.15 Aligned_cols=33 Identities=12% Similarity=0.047 Sum_probs=28.0
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.||+.++......+...+
T Consensus 144 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 144 GFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577999999999999999999887777766554
No 440
>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=60.97 E-value=5.4 Score=26.71 Aligned_cols=29 Identities=21% Similarity=0.638 Sum_probs=16.3
Q ss_pred CCCCCC--CCCCCceeeeCCCCc--eEcCCCcccc
Q 021438 3 DSYCAD--CKRLTEVVFDHSAGD--TICSECGLVL 33 (312)
Q Consensus 3 ~~~Cp~--Cg~~~~ii~D~~~G~--~vC~~CG~Vv 33 (312)
...||. |+. -+..+..... +.|..||...
T Consensus 18 ~~~Cp~~~C~~--~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 18 IRWCPNPDCEY--IIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp CC--TTSST-----ECS-SSTTS--CCTTSCCSEE
T ss_pred ccCCCCCCCcc--cEEecCCCCCCeeECCCCCCcC
Confidence 358988 997 3555555555 8999999764
No 441
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=60.93 E-value=5.1 Score=26.68 Aligned_cols=22 Identities=32% Similarity=0.685 Sum_probs=14.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSE 28 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~ 28 (312)
..||.|++ ..+++|.. .++|+.
T Consensus 15 ~~Cp~C~~-~~l~~~~~--~Y~C~G 36 (55)
T PF08063_consen 15 EPCPKCKG-GQLYFDGS--GYKCTG 36 (55)
T ss_dssp ---SSSSE--EEEEETT--EEEEES
T ss_pred CCCCCCCC-CeEEecCC--ccEeCc
Confidence 57999998 68888855 788873
No 442
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=60.91 E-value=1.9e+02 Score=29.25 Aligned_cols=31 Identities=16% Similarity=0.239 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|+++|+..+|||..-||+..+.-...+.
T Consensus 575 ~~~tl~ei~~~lgvs~eRVrQie~~al~kLr 605 (619)
T PRK05658 575 TDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605 (619)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 5689999999999999999987766555443
No 443
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=60.79 E-value=5.9 Score=37.99 Aligned_cols=32 Identities=22% Similarity=0.533 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e 35 (312)
..||+|+....+..-...+...|..||.++..
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 45999997322222123345779999999853
No 444
>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=60.62 E-value=1.2e+02 Score=26.69 Aligned_cols=31 Identities=13% Similarity=0.258 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|+++||..+|+|..+|++..+...+.+.
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4689999999999999999998887766553
No 445
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=60.57 E-value=6.3 Score=26.75 Aligned_cols=28 Identities=7% Similarity=-0.045 Sum_probs=18.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCcccccCcccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id 39 (312)
..||+||.. . ----+|. ||+--+..+++
T Consensus 28 ~~c~~cg~~-~------~pH~vc~-cG~Y~gr~v~~ 55 (60)
T PRK01110 28 SVDKTTGEY-H------LPHHVSP-KGYYKGRKVLK 55 (60)
T ss_pred eEcCCCCce-e------ccceecC-CcccCCeEeec
Confidence 468999872 1 2456799 99877655544
No 446
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=60.33 E-value=10 Score=31.82 Aligned_cols=34 Identities=24% Similarity=0.222 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+.+|||+.+|+|+.|+++++..-...+...+
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3577999999999999999999876666655443
No 447
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=60.21 E-value=10 Score=31.17 Aligned_cols=33 Identities=12% Similarity=0.021 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...+.+|||+.+|+|+.|+++++......+...
T Consensus 115 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357799999999999999998886666555443
No 448
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=60.07 E-value=11 Score=32.81 Aligned_cols=30 Identities=20% Similarity=0.309 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
...|.+|||+.+|+|+.||+++.......+
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~~~L 226 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRILKRL 226 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 568999999999999999999975544443
No 449
>PRK06930 positive control sigma-like factor; Validated
Probab=59.97 E-value=9 Score=31.88 Aligned_cols=33 Identities=15% Similarity=0.146 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...+.++||+.+|+|+.|++.+++.....+...
T Consensus 129 eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 129 YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999988777766543
No 450
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=59.97 E-value=10 Score=32.06 Aligned_cols=33 Identities=18% Similarity=0.198 Sum_probs=28.1
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.|++++.......+...+
T Consensus 170 ~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 170 GKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999988777765543
No 451
>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=59.87 E-value=24 Score=27.54 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHh-CCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 149 EAIVAACLYIACRQE-NKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 149 ~~iaaAcly~acr~~-~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
+....+.+|++ +.. +.|.+..+|++.+ +++...+.+....|.+
T Consensus 8 ~~al~~l~~la-~~~~~~~~s~~eia~~~-~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 8 EYALRALLDLA-LNPDEGPVSVKEIAERQ-GISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHH-hCCCCCcCcHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 34455666666 433 4589999999999 7999999999888775
No 452
>PHA00542 putative Cro-like protein
Probab=59.82 E-value=11 Score=27.13 Aligned_cols=25 Identities=24% Similarity=0.272 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHH
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
...+++.++|+.+||+..||.+..+
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 3467999999999999999997764
No 453
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=59.77 E-value=2.8 Score=27.46 Aligned_cols=28 Identities=32% Similarity=0.654 Sum_probs=18.6
Q ss_pred CCCCCCCCCcee--eeCCCCceEcCCCcccc
Q 021438 5 YCADCKRLTEVV--FDHSAGDTICSECGLVL 33 (312)
Q Consensus 5 ~Cp~Cg~~~~ii--~D~~~G~~vC~~CG~Vv 33 (312)
.|+-||..-.+. ...+.| +||.+|--=+
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 599999742221 235678 8999998544
No 454
>PRK12366 replication factor A; Reviewed
Probab=59.76 E-value=5.3 Score=40.49 Aligned_cols=25 Identities=36% Similarity=0.848 Sum_probs=20.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
..||.|+. .++. ..|.+.|..||.+
T Consensus 533 ~aCp~Cnk--Kv~~--~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRK--RVEE--VDGEYICEFCGEV 557 (637)
T ss_pred ecccccCe--EeEc--CCCcEECCCCCCC
Confidence 47999987 3543 5799999999988
No 455
>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=59.72 E-value=4.1 Score=24.60 Aligned_cols=22 Identities=23% Similarity=0.637 Sum_probs=8.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTIC 26 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC 26 (312)
.+|..||.. --+.+...|.++|
T Consensus 7 YkC~~CGni-Vev~~~g~g~lvC 28 (36)
T PF06397_consen 7 YKCEHCGNI-VEVVHDGGGPLVC 28 (36)
T ss_dssp EE-TTT--E-EEEEE--SS-EEE
T ss_pred EEccCCCCE-EEEEECCCCCEEe
Confidence 467777762 2234455666776
No 456
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=59.72 E-value=11 Score=31.07 Aligned_cols=31 Identities=16% Similarity=0.151 Sum_probs=25.5
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..|.+|||+.+|+|+.||++++..-...+..
T Consensus 145 g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 145 GLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 4779999999999999999998766655543
No 457
>PRK15482 transcriptional regulator MurR; Provisional
Probab=59.70 E-value=32 Score=30.85 Aligned_cols=54 Identities=11% Similarity=0.145 Sum_probs=36.9
Q ss_pred HHHHHHhhcC-CCHHHHHHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHH
Q 021438 213 YLRRFCSNLG-MTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 213 ~i~r~~~~L~-l~~~v~~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
++.++-.... |++.-.+.|..|++. |.-++ ..+..++|+.+|||++||-+-+|.
T Consensus 3 ~l~~i~~~~~~Lt~~e~~Ia~yIl~n---------~~~v~-------------~~si~elA~~~~vS~aTv~Rf~kk 57 (285)
T PRK15482 3 YLTKIRNAESEFTENEQKIADFLRAN---------VSELK-------------SVSSRKMAKQLGISQSSIVKFAQK 57 (285)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHHHhC---------HHHHH-------------hcCHHHHHHHhCCCHHHHHHHHHH
Confidence 3445554443 777777777777754 43332 467889999999999999876543
No 458
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=59.57 E-value=9.9 Score=31.20 Aligned_cols=33 Identities=18% Similarity=0.195 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...+.+|||+.+|+|+.|++.++......+...
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999987666655443
No 459
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=59.35 E-value=11 Score=31.36 Aligned_cols=32 Identities=19% Similarity=0.233 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||..+|+|+.||+++.......+..
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 45779999999999999999998877766544
No 460
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=59.35 E-value=13 Score=31.09 Aligned_cols=31 Identities=13% Similarity=0.175 Sum_probs=25.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+.+|||+.+|+|+.||++++......+..
T Consensus 154 g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 154 GLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5679999999999999999998766665543
No 461
>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=59.22 E-value=11 Score=24.31 Aligned_cols=23 Identities=13% Similarity=0.040 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHH
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVY 286 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~ 286 (312)
..+++.++|+.+|++..||++.-
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 46789999999999999999764
No 462
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=59.11 E-value=11 Score=31.28 Aligned_cols=34 Identities=9% Similarity=0.022 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+.+|||+.+|+|..||+++...-...+...+
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999999877776665544
No 463
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=59.10 E-value=11 Score=29.25 Aligned_cols=23 Identities=17% Similarity=0.179 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCcchhHHHHHHHH
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
.|.+|+|+.+|++..||.++.++
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 47899999999999999988765
No 464
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.05 E-value=7.3 Score=39.69 Aligned_cols=28 Identities=21% Similarity=0.578 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
...||+|+. .+.+-...+.+.|..||.-
T Consensus 392 ~~~C~~C~~--~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 392 PARCRHCTG--PLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred eeECCCCCC--ceeEecCCCeeECCCCcCC
Confidence 357999997 4677666788999999984
No 465
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=59.04 E-value=13 Score=30.92 Aligned_cols=33 Identities=18% Similarity=0.209 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
...+.+|||+.+|+|+.|++.++..-.+.+...
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~ 158 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457799999999999999999887666665443
No 466
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=59.00 E-value=12 Score=34.17 Aligned_cols=35 Identities=9% Similarity=0.048 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p 298 (312)
...+.+|||+.+|+|+.|+++++..-.+.+...++
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 35679999999999999999998776666655544
No 467
>PRK06260 threonine synthase; Validated
Probab=58.84 E-value=4.3 Score=38.63 Aligned_cols=30 Identities=33% Similarity=0.594 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
|...+|+.||.. ++...-...|..||-.++
T Consensus 1 ~~~~~C~~cg~~----~~~~~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 1 MYWLKCIECGKE----YDPDEIIYTCPECGGLLE 30 (397)
T ss_pred CCEEEECCCCCC----CCCCCccccCCCCCCeEE
Confidence 778899999983 444445678999997764
No 468
>PF09241 Herp-Cyclin: Herpesviridae viral cyclin; InterPro: IPR015322 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 represents a domain found in a family of viral cyclins that specifically activate CDK6 of host cells to a very high degree []. This domain adopts a helical structure consisting of five alpha-helices, with one helix surrounded by the others.; PDB: 1XO2_A 1JOW_A 2F2C_A 2EUF_A 1BU2_A.
Probab=58.84 E-value=66 Score=23.19 Aligned_cols=84 Identities=15% Similarity=0.198 Sum_probs=53.4
Q ss_pred HHHHHHHHhhcCCCHHHH----HH-HHHHHHHhhh-ccCCCChHHHHHHHHHHHHHhcCC--CCC---HHHHHHHhCcch
Q 021438 211 SDYLRRFCSNLGMTNQAV----KA-AQEAVQKSED-LDIRRSPISVAAAVIYIITQLSND--TKP---LKEISIVTRVAE 279 (312)
Q Consensus 211 ~~~i~r~~~~L~l~~~v~----~~-A~~i~~~~~~-l~~Gr~P~~iaaAaiyla~~~~~~--~~~---~~~Ia~~~~vs~ 279 (312)
-+|+--+|+.|.++++.. .. ...|++..-+ -..--.|--|+|+-+.-....-+. .-. +++++.+++.|.
T Consensus 5 tdflip~c~alkipe~~wpql~e~~s~tickaliqpniall~p~licaggllttiet~ntn~~~wt~yledl~~ilnfst 84 (106)
T PF09241_consen 5 TDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNFST 84 (106)
T ss_dssp GGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTCHH
T ss_pred hhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhccc
Confidence 467788999999997643 32 3344444333 112346888888888776665432 222 689999999999
Q ss_pred hHHHHHHHHHHhhhc
Q 021438 280 GTIKNVYKDLFPHLA 294 (312)
Q Consensus 280 ~ti~~~~kel~~~~~ 294 (312)
.|||..-....|.+.
T Consensus 85 ntirt~kdqv~ea~~ 99 (106)
T PF09241_consen 85 NTIRTVKDQVSEAFS 99 (106)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred chhhhHHHHHHHHHH
Confidence 999987666666543
No 469
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=58.81 E-value=8.3 Score=31.77 Aligned_cols=31 Identities=16% Similarity=0.367 Sum_probs=18.5
Q ss_pred CCCCCCCCCc--e-eee-CCCCc-----eEcCCCcccccC
Q 021438 5 YCADCKRLTE--V-VFD-HSAGD-----TICSECGLVLEA 35 (312)
Q Consensus 5 ~Cp~Cg~~~~--i-i~D-~~~G~-----~vC~~CG~Vv~e 35 (312)
.||+||.... + .++ +.-|+ ..|.+||+=-.|
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e 41 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNE 41 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccce
Confidence 6999996422 1 111 22333 679999997543
No 470
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=58.79 E-value=15 Score=31.77 Aligned_cols=31 Identities=26% Similarity=0.295 Sum_probs=27.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+-+|||+.+++|+.|++++...+...++.
T Consensus 170 G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 170 GASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 5778999999999999999999999887653
No 471
>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=58.77 E-value=35 Score=21.13 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=22.6
Q ss_pred HhCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 021438 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (312)
Q Consensus 162 ~~~~p~tl~dia~~~~~v~~~~i~~~~~~l 191 (312)
+.+..+++.+|+..+ |++..++.+.+++|
T Consensus 13 q~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 13 QEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 456779999999999 89999999888776
No 472
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=58.70 E-value=5.4 Score=29.52 Aligned_cols=31 Identities=23% Similarity=0.257 Sum_probs=24.1
Q ss_pred CCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438 266 KPLKEISIVTRVAEGTIKNVYKDLFPHLARI 296 (312)
Q Consensus 266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~ 296 (312)
++|+.||+..|++++||.+.-.++.+....+
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~a~l 54 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKMAML 54 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHHHHH
Confidence 5689999999999999998766655554443
No 473
>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=58.69 E-value=30 Score=27.05 Aligned_cols=44 Identities=9% Similarity=0.155 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 148 ~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
.+....+.+|+|- ..+.+.+..||++.. +++...+.+.++.|.+
T Consensus 8 ~~yal~~l~~la~-~~~~~~s~~eia~~l-~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 8 TDYATLVLTTLAQ-NDSQPYSAAEIAEQT-GLNAPTVSKILKQLSL 51 (130)
T ss_pred HhHHHHHHHHHHh-CCCCCccHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3445666777773 345689999999999 8999999999888775
No 474
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=58.50 E-value=12 Score=31.11 Aligned_cols=31 Identities=10% Similarity=0.118 Sum_probs=25.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+.+|||+.+|+|+.||+.++..-...+..
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 155 GLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5779999999999999999998766665543
No 475
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=58.35 E-value=5.7 Score=40.25 Aligned_cols=14 Identities=21% Similarity=0.643 Sum_probs=9.3
Q ss_pred CCceEcCCCccccc
Q 021438 21 AGDTICSECGLVLE 34 (312)
Q Consensus 21 ~G~~vC~~CG~Vv~ 34 (312)
.|.-.|.+||.-+.
T Consensus 39 ~~~~fC~~CG~~~~ 52 (645)
T PRK14559 39 VDEAHCPNCGAETG 52 (645)
T ss_pred cccccccccCCccc
Confidence 56667777776554
No 476
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=58.34 E-value=11 Score=32.08 Aligned_cols=32 Identities=6% Similarity=-0.034 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||..+|+|+.|++.++..-...+..
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35779999999999999999887655555443
No 477
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=58.25 E-value=14 Score=30.32 Aligned_cols=30 Identities=20% Similarity=0.161 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~ 293 (312)
...+.+|||+.+|+|+.|+++++..-...+
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 457799999999999999999987666654
No 478
>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=58.25 E-value=22 Score=30.29 Aligned_cols=29 Identities=10% Similarity=0.157 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
-..++.+||+.+|++..|+++.+++|.+.
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34899999999999999999999999875
No 479
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=58.24 E-value=8.5 Score=26.82 Aligned_cols=24 Identities=21% Similarity=0.145 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHH
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYK 287 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~k 287 (312)
...||.++|+.+|||..||-..=+
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHc
Confidence 458999999999999999985433
No 480
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=58.10 E-value=25 Score=21.94 Aligned_cols=28 Identities=11% Similarity=0.224 Sum_probs=18.5
Q ss_pred HhCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 021438 162 QENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (312)
Q Consensus 162 ~~~~p~tl~dia~~~~~v~~~~i~~~~~~ 190 (312)
......++++||..+ |++..+|.+.+++
T Consensus 16 l~~~G~s~~~IA~~l-g~s~sTV~relkR 43 (44)
T PF13936_consen 16 LLEQGMSIREIAKRL-GRSRSTVSRELKR 43 (44)
T ss_dssp HHCS---HHHHHHHT-T--HHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHH-CcCcHHHHHHHhc
Confidence 345668999999999 8999999887653
No 481
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=58.08 E-value=11 Score=31.59 Aligned_cols=33 Identities=24% Similarity=0.271 Sum_probs=26.5
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||..+|+|..|+++++..-...+...+
T Consensus 150 g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 150 GYSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999866555554443
No 482
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=58.04 E-value=7 Score=35.13 Aligned_cols=30 Identities=20% Similarity=0.461 Sum_probs=19.9
Q ss_pred CCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (312)
Q Consensus 3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~ 34 (312)
.+.|+.||+++.. . ...=-.+|.+||...=
T Consensus 111 ~RFCg~CG~~~~~-~-~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKTYP-R-EGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcCcc-c-cCceeeeCCCCCCccC
Confidence 4689999985221 1 1122389999999864
No 483
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=58.03 E-value=11 Score=27.14 Aligned_cols=28 Identities=18% Similarity=0.250 Sum_probs=18.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (312)
Q Consensus 4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V 32 (312)
..||-||.. .+..+.....-||.-|+.-
T Consensus 2 ~~CPCCg~~-Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYY-TLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcE-EeccCCCcCceECCCCCcc
Confidence 579999983 3322222227899999986
No 484
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=57.84 E-value=11 Score=30.70 Aligned_cols=34 Identities=21% Similarity=0.265 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
...+..+||..+|+|+.||+++...-.+.+...+
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999999999887777665443
No 485
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=57.82 E-value=6.8 Score=30.80 Aligned_cols=34 Identities=24% Similarity=0.460 Sum_probs=26.3
Q ss_pred eeCCCCceEcCCCcccc--cCcccccccccccccCC
Q 021438 17 FDHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (312)
Q Consensus 17 ~D~~~G~~vC~~CG~Vv--~e~~id~~~ewr~f~~~ 50 (312)
.....|.++|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 31 ~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 66 (124)
T PF01641_consen 31 DHKEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQP 66 (124)
T ss_dssp CTTSSEEEEETTTS-EEEEGGGEETSSSSSSEESSC
T ss_pred CCCCCEEEEcCCCCCccccCcccccCCcCCccccCc
Confidence 34578999999999988 44567889999999853
No 486
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=57.69 E-value=30 Score=27.51 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=27.0
Q ss_pred CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
...+++.+||+.++++.+|+....+.|.+.
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~ 81 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCK 81 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 346899999999999999999999999874
No 487
>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=57.63 E-value=15 Score=20.49 Aligned_cols=21 Identities=19% Similarity=0.186 Sum_probs=18.2
Q ss_pred CCCHHHHHHHhCcchhHHHHH
Q 021438 265 TKPLKEISIVTRVAEGTIKNV 285 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~ 285 (312)
..+..+|++.+|++..||.++
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 358999999999999999864
No 488
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=57.63 E-value=10 Score=33.21 Aligned_cols=33 Identities=21% Similarity=0.253 Sum_probs=26.7
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..+.+|||+.+|+|+.|++++...-.+.+...+
T Consensus 132 g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 132 QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999998766666555444
No 489
>smart00351 PAX Paired Box domain.
Probab=57.52 E-value=17 Score=28.47 Aligned_cols=27 Identities=15% Similarity=0.175 Sum_probs=23.9
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFP 291 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~ 291 (312)
..+.++||+.+|||..|+.+.++...+
T Consensus 33 G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 33 GVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 468899999999999999999888765
No 490
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=57.48 E-value=13 Score=30.83 Aligned_cols=32 Identities=28% Similarity=0.290 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
...+.+|||+.+|+|+.|++++.......+..
T Consensus 151 ~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999998776665543
No 491
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=57.29 E-value=15 Score=29.59 Aligned_cols=30 Identities=17% Similarity=0.018 Sum_probs=25.1
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
..+.++||..+|+|+.|++.++..-...+.
T Consensus 128 ~~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 128 GFSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 567999999999999999998876665543
No 492
>COG4861 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.24 E-value=8.8 Score=34.16 Aligned_cols=52 Identities=23% Similarity=0.282 Sum_probs=35.7
Q ss_pred ccCCCChHHHHHHHHHHHHHhcC----CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 241 LDIRRSPISVAAAVIYIITQLSN----DTKPLKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 241 l~~Gr~P~~iaaAaiyla~~~~~----~~~~~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
..+||..++.-+-..-+.+.++. ...+.+|||.++|||..|....+..|.|.
T Consensus 135 ~~~~RpA~~ftp~raqv~~ALL~aP~lv~~P~REIAasAgVsvGTa~~t~d~LrE~ 190 (345)
T COG4861 135 LHSDRPANPFTPKRAQVVCALLDAPQLVDAPLREIAASAGVSVGTAKETMDTLRET 190 (345)
T ss_pred CCCCCCCCCCChhhhhHhHhhhCCHHHhcchHHHHHHhccceechHHHHHHHHHhc
Confidence 33455433333444444444443 35789999999999999999999998884
No 493
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=57.21 E-value=13 Score=30.90 Aligned_cols=33 Identities=18% Similarity=0.228 Sum_probs=27.6
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLARII 297 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~ 297 (312)
..|..|||+.+|++..|++.++..=.+.+...+
T Consensus 143 gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 143 GLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577999999999999999999877666665544
No 494
>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=57.18 E-value=20 Score=23.07 Aligned_cols=36 Identities=22% Similarity=0.289 Sum_probs=27.1
Q ss_pred HHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438 157 YIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (312)
Q Consensus 157 y~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~ 193 (312)
.-+...++.+.++.||++.+ |++..++.+....|.+
T Consensus 9 L~~l~~~~~~~t~~eia~~~-gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIARAL-GLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHCHHCTBSCEEHHHHHHHH-TS-HHHHHHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 33445567778999999999 8999998888777653
No 495
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=57.17 E-value=29 Score=23.68 Aligned_cols=34 Identities=18% Similarity=0.181 Sum_probs=25.5
Q ss_pred HHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHH
Q 021438 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (312)
Q Consensus 161 r~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l 195 (312)
+..+.|.+-+|||+.+ |++....++.+..|.+.=
T Consensus 10 ~~~~~p~~T~eiA~~~-gls~~~aR~yL~~Le~eG 43 (62)
T PF04703_consen 10 KEQNGPLKTREIADAL-GLSIYQARYYLEKLEKEG 43 (62)
T ss_dssp HHHTS-EEHHHHHHHH-TS-HHHHHHHHHHHHHCT
T ss_pred HHcCCCCCHHHHHHHh-CCCHHHHHHHHHHHHHCC
Confidence 3448899999999999 899999888877766543
No 496
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=57.16 E-value=39 Score=30.15 Aligned_cols=53 Identities=17% Similarity=0.318 Sum_probs=36.4
Q ss_pred HHHHHhhcC-CCHHHHHHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHH
Q 021438 214 LRRFCSNLG-MTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKD 288 (312)
Q Consensus 214 i~r~~~~L~-l~~~v~~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~ke 288 (312)
+.++-..+. |++.-.+.|..|++. |.-++ ..|.+++|+.+|||+.||-+-.|.
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yil~n---------~~~v~-------------~~si~~lA~~~~vS~aTv~Rf~kk 57 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVILAS---------PQTAI-------------HSSIATLAKMANVSEPTVNRFCRS 57 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhC---------HHHHH-------------hcCHHHHHHHhCCCHHHHHHHHHH
Confidence 344544443 777777777777754 43333 367889999999999999876543
No 497
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=57.09 E-value=14 Score=32.00 Aligned_cols=30 Identities=17% Similarity=0.120 Sum_probs=26.4
Q ss_pred CCCCC-HHHHHHHhCcchhHHHHHHHHHHhh
Q 021438 263 NDTKP-LKEISIVTRVAEGTIKNVYKDLFPH 292 (312)
Q Consensus 263 ~~~~~-~~~Ia~~~~vs~~ti~~~~kel~~~ 292 (312)
|.++| -.++|+..|||..|||+++.+|.+.
T Consensus 21 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~e 51 (233)
T TIGR02404 21 GDYLPSEHELMDQYGASRETVRKALNLLTEA 51 (233)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 55665 7899999999999999999999884
No 498
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=56.97 E-value=13 Score=29.94 Aligned_cols=31 Identities=16% Similarity=0.209 Sum_probs=24.6
Q ss_pred CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438 265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295 (312)
Q Consensus 265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~ 295 (312)
..+.+|||+.+|+|+.||+.+...-.+.+-.
T Consensus 125 ~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 125 GETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5679999999999999999886655554433
No 499
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=56.90 E-value=1.3e+02 Score=30.04 Aligned_cols=105 Identities=16% Similarity=0.295 Sum_probs=62.4
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCH-HHHHHHHHhhcCCCHHHHHHHHHHHHHhhhccC
Q 021438 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHA-SDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243 (312)
Q Consensus 165 ~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p-~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~l~~ 243 (312)
.|.|..++|..+ |||.++|.+-++.|.+.|.... +....- .-| .|...+. .....+.+
T Consensus 16 ~~~t~~~LA~~l-~VS~RTIr~dI~~in~~l~~~~-----~~~i~~~~Gy------~l~~~~~--~~~~~~~~------- 74 (584)
T PRK09863 16 QDRSGGELAQQL-GVSRRTIVRDIAYINFTLNGKA-----IGSISGSAKY------HLEILNR--RSLFQLLQ------- 74 (584)
T ss_pred CCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHhcc-----hhheecCCce------EEEeCCH--HHHHHHHh-------
Confidence 589999999999 8999999999999988775410 100000 001 1211110 00011111
Q ss_pred CCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438 244 RRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLA 294 (312)
Q Consensus 244 Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~ 294 (312)
...|.-.. + +...+....++..++|+.+.||++||.+-.+++.+.+.
T Consensus 75 ~~~~e~~~---i-l~~Ll~~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 75 KSDNEDRL---L-LLRLLLNTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred cCCHHHHH---H-HHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 01222221 1 11112245688999999999999999999999988655
No 500
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=56.87 E-value=8.4 Score=25.63 Aligned_cols=24 Identities=25% Similarity=0.690 Sum_probs=18.4
Q ss_pred CCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (312)
Q Consensus 5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv 33 (312)
.||.|++. . ...-.+.|..||...
T Consensus 1 ~Cpv~~~~--~---~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKD--L---PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCccc--c---ccccCCcCCCCCCcC
Confidence 49999983 1 445678899999986
Done!